initial import of Terrasaur code

.gitignore

@@ -0,0 +1,9 @@
+/.idea/
+/bin/
+/doc/_build
+/dist/
+/target/
+/3rd-party
+.DS_Store
+doc/tools/shortDescriptions.rst
+doc/tools/index.rst

CHANGELOG.md

@@ -0,0 +1,8 @@
+# SBCLT Changelog
+
+Repository is https://gitlab.jhuapl.edu/sbmt/sbclt/command-line-tools.  Git hash for each merge to main branch (except the most recent) are listed below in reverse chronological order.
+
+## November 26, 2024 
+
+- Initial release
+  

README.md

@@ -1 +1,60 @@
 # Terrasaur
+
+Terrasaur is a suite of programs written in Java and C++. These stand-alone
+command line analysis and shape model manipulation programs that complement the
+[Small Body Mapping Tool](https://sbmt.jhuapl.edu/) and create data products that
+are well-suited to being visualized in the SBMT GUI. Among other functions,
+these programs facilitate the building of digital terrain models (DTMs) of
+small bodies, permit assessing the quality of these DTMs, and construct a
+broad suite of DTM products that characterize the geophysical and surface
+properties of small bodies.
+
+## Quick Start
+
+### Prerequisites
+
+The Terrasaur package requires Java 21 or later.  Some freely available versions are
+
+* [Amazon Corretto](https://aws.amazon.com/corretto/)
+* [Azul Zulu](https://www.azul.com/downloads/?package=jdk)
+* [Eclipse Temurin](https://adoptium.net/)
+* [OpenJDK](https://jdk.java.net/).  Most Linux distributions and HomeBrew have OpenJDK packages.
+
+### Build the package
+
+This is an optional step if you don't want to use the prebuilt
+package.  Check out the code:
+
+    git clone https://github.com/JHUAPL/Terrasaur.git
+
+The 3rd party executables and libraries are assumed to exist in
+`3rd-party/$(uname -s)_$(uname -m)` (e.g. `3rd-party/Darwin_x86_64` on an
+Intel macOS machine).  The script to build the 3rd party products is in the
+`support-libraries` directory.
+
+    cd support-libraries
+    ./buildAll.bash ../3rd-party/$(uname -s)_$(uname -m)
+
+Maven must be installed to build the software.  Once the `3rd-party`
+directory has been built, compile the Terrasaur package using the
+`mkPackage.bash` script:
+
+    ./mkPackage.bash
+
+This will create executable and source packages in the dist directory,
+named SBCLT-YYYY.MM.DD.tar.gz and SBCLT-YYYY.MM.DD-src.tar.gz
+
+[Sphinx](https://www.sphinx-doc.org/en/master/) with the
+[PD](https://sphinx-themes.org/sample-sites/sphinx-theme-pd/)
+theme is used to create the documentation in the `doc/` folder.
+
+### Install the executable package
+
+    cd (your destination directory)
+    tar xfz (path to command-line-tools)/dist/Terrasaur-YYYY.MM.DD.tar.gz
+
+The `scripts/` directory contains all the applications in the
+package.  Running without any arguments will display a usage message.
+
+The `doc/` directory contains documentation including a javadoc
+directory.

doc/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

doc/_static/style.css

@@ -0,0 +1,13 @@
+.wy-nav-content {
+    max-width: 100%;
+}
+
+.figures-row {
+    display: flex;
+    justify-content: space-between;
+}
+.figures-row img {
+    max-width: 90%; /* Adjust percentage as needed */
+    height: auto;   /* Maintains aspect ratio */
+}
+

doc/_templates/layout.html

@@ -0,0 +1,4 @@
+{% extends "!layout.html" %}
+{% block extrahead %}
+    <link href="{{ pathto("_static/style.css", True) }}" rel="stylesheet" type="text/css">
+{% endblock %}

doc/conf.py

@@ -0,0 +1,62 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Themes used -------------------------------------------------------------
+
+import sphinx_theme_pd
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'Terrasaur'
+copyright = '2024, Johns Hopkins University Applied Physics Laboratory'
+author = 'Hari.Nair@jhuapl.edu'
+highlight_language = 'none'
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+# html_theme = 'alabaster'
+html_theme = 'sphinx_theme_pd'
+html_theme_path = [sphinx_theme_pd.get_html_theme_path()]
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+#html_style = 'style.css'
+
+def setup(app):
+    app.add_css_file('style.css')

doc/index.rst

@@ -0,0 +1,54 @@
+Terrasaur documentation
+=============================================
+
+This package contains command line analysis tools contained in Terrasaur.
+
+Prerequisites
+~~~~~~~~~~~~~
+
+The Terrasaur package requires Java 21 or later.  Some freely available versions are
+
+* `Amazon Corretto <https://aws.amazon.com/corretto/>`__
+* `Azul Zulu <https://www.azul.com/downloads/?package=jdk>`__
+* `Eclipse Temurin <https://adoptium.net/>`__
+* `OpenJDK <https://jdk.java.net/>`__.  Most Linux distributions and HomeBrew have OpenJDK packages.
+
+Download
+~~~~~~~~
+
+Packages for use on Mac OS X and Linux are available at ...
+
+Windows users may use the Linux package with the `Windows Subsystem for Linux <https://docs.microsoft.com/en-us/windows/wsl/>`__.
+
+Install
+~~~~~~~
+
+::
+
+   cd (your destination directory)
+   tar xfz Terrasaur-YYYY.MM.DD.tar.gz
+
+The scripts/ directory contains all of the applications in the package. Running without any arguments will display a usage message.
+
+The doc/ directory contains documentation including a javadoc directory.
+
+Documentation and Examples
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+`This <tools/index.html>`__ page shows the usage of each utility.
+
+Examples for use are shown at ...
+
+Build from source
+~~~~~~~~~~~~~~~~~
+
+Source code is available at ...
+
+Third party libraries are available at ...
+
+Contents
+~~~~~~~~
+
+.. toctree::
+
+   tools/index

doc/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

doc/make_doc.bash

@@ -0,0 +1,88 @@
+#!/bin/bash
+
+# This program generates a file containing documentation of all
+# programs in this software system by running all programs with no
+# arguments and piping the usage output to a file.
+
+if [ -z "$1" ]; then
+    echo "usage: $0 scriptDir"
+    echo "e.g.   $0 ../Terrasaur-2024.12.21/scripts"
+    exit 0
+fi
+
+rootDir=$(
+    cd "$(dirname "$0")"
+    pwd -P
+)
+scriptDir=$1
+
+docfile=${rootDir}/tools/shortDescriptions.rst
+indexfile=${rootDir}/tools/index.rst
+rm -f "$docfile" "$indexfile"
+
+cat >>"$indexfile" <<EOF
+===========
+Tools Index
+===========
+
+EOF
+
+cat >>"$docfile" <<EOF
+==================
+Terrasaur Programs
+==================
+
+EOF
+
+programsToSkip=()
+
+for f in $(find "${scriptDir}" -type f -maxdepth 1 | sort -f); do
+    f=$(basename "$f")
+    flink=$(echo "$f" | awk '{print tolower($0)}' | sed -e 's/[^[:alnum:]|-]/\-/g')
+
+    skip=0
+    # Ignore programs that begin with lowercase letter or the string "Immutable"
+    if [[ "$f" =~ ^([a-z].*|Immutable.*) ]]; then
+        skip=1
+    fi
+
+    for program in "${programsToSkip[@]}"; do
+        if [[ "$f" == "$program" ]]; then
+            skip=1
+            break
+        fi
+    done
+
+    if [ $skip -eq 1 ]; then
+        echo "Skipping $f"
+        continue
+    fi
+
+    echo "Generating documentation for $f"
+
+    shortDescription=$("${scriptDir}"/"$f" -shortDescription)
+
+    mkdir -p toolDescriptions
+    "${scriptDir}"/"$f" >toolDescriptions/"${f}".txt
+
+    if [ -e tools/"${f}".rst ]; then
+        cat >>"$indexfile" <<EOF
+:doc:\`$f\`: $shortDescription
+
+EOF
+    else
+        cat >>"$indexfile" <<EOF
+\`$f <shortDescriptions.html#${flink}>\`__: $shortDescription
+
+EOF
+        cat >>"$docfile" <<EOF
+$f
+$(printf '=%.0s' {1..100})
+
+.. include:: ../toolDescriptions/${f}.txt
+    :literal:
+
+
+EOF
+    fi
+done

doc/tools/CompareOBJ.rst

@@ -0,0 +1,133 @@
+.. _CompareOBJ:
+
+##########
+CompareOBJ
+##########
+
+*****
+Usage
+*****
+
+CompareOBJ reports the differences between two OBJ shape files.  It can also find the 
+optimal rotation and/or translation to best fit one model to the other.
+
+.. include:: ../toolDescriptions/CompareOBJ.txt
+    :literal:
+
+********
+Examples
+********
+
+Local Model Comparison
+######################
+
+Download the :download:`reference<./support_files/EVAL20_wtr.obj>` and :download:`comparison<./support_files/EVAL20.obj>` 
+shape models.  You can view them in a tool such as 
+`ParaView<https://www.paraview.org/>`.
+
+.. figure:: images/CompareOBJ_local_1.png
+
+   This image shows the reference (pink) and comparison (grey) shape models.
+
+Run CompareOBJ to find the optimal transform to align the comparison with the reference:
+::
+
+    CompareOBJ -computeOptimalRotationAndTranslation -model F3H-1/EVAL20.obj \ 
+    -reference F3H-1/EVAL20_wtr.obj -computeVerticalError verticalError.txt \
+    -saveOptimalShape optimal.obj -savePlateDiff plateDiff.txt -savePlateIndex plateIndex.txt
+
+The screen output is
+::
+
+    Translation: 4.62205663e-04,7.83045454e-04,-2.29286045e-04
+    Rotation quaternion: 9.99865353e-01,5.09597815e-03,1.50904931e-02,3.94767030e-03
+    Rotation angle (degrees) and axis: 1.88048990e+00,3.10547953e-01,9.19611823e-01,2.40570289e-01
+    Center of rotation: -2.80636488e-02,2.59626158e-01,-3.68889950e-02
+    4x4 Transformation matrix:
+    9.99513386e-01  -7.74047588e-03   3.02171569e-02   4.62205663e-04
+    8.04807917e-03   9.99916894e-01  -1.00714394e-02   7.83045454e-04
+    -3.01366880e-02   1.03097286e-02   9.99492616e-01  -2.29286045e-04
+    0.00000000e+00   0.00000000e+00   0.00000000e+00   1.00000000e+00
+    Using 319740 of 319740 points (excluding 0.0% largest distances)
+    Min Distance:              2.7101076120651766E-11
+    Max Distance:              1.3343678431994644E-5
+    Mean Distance:             3.6381274026976392E-6
+    Mean Square Distance:      1.9828385012474584E-11
+    Root Mean Square Distance: 4.452907478544168E-6
+    Mean Vertical Distance:             3.643513246881461E-6
+    Mean Square Vertical Distance:      1.9878841624828557E-11
+    Root Mean Square Vertical Distance: 4.458569459459901E-6
+    Direction perpendicular to plane: 0.1308102982873679 0.9899926953698763 0.05294458401250757
+    Magnitude of projection perpendicular to plane: 8.235310856890277E-4
+    Projection vector of translation parallel to plane: 3.544793163646046E-4 -3.2244305568425196E-5 -2.728875559193712E-4
+    Magnitude of projection vector of translation parallel to plane: 4.485118718022471E-4
+    319740 plates used in error calculation out of 320000 total in the shape model
+
+
+.. figure:: images/CompareOBJ_local_2.png
+
+   This image shows the reference (pink), comparison (grey), and transformed comparison (blue) shape models.
+
+Global Model Comparison
+#######################
+
+Use the :download:`low resolution Bennu<./support_files/Bennu49k.obj>` shape model for this 
+example.  We will use the ShapeFormatConverter tool to create a transformed 
+model for comparison:
+
+::
+
+    ShapeFormatConverter -input Bennu/Bennu49k.obj -output BennuComparison.obj \
+    -rotate 5,0,0,1 -translate 0.01,-0.01,0.01
+
+This rotates the shape model by 5 degrees about the z axis and then translates 
+by the vector [0.01, -0.01, 0.01].  The units and frame are the same used in 
+the OBJ file, namely km and IAU_BENNU.
+
+.. figure:: images/CompareOBJ_global_1.png
+
+   This image shows the reference (pink) and comparison (grey, 50% opacity) shape models.
+
+Run CompareOBJ to find the optimal transform to align the comparison with the reference:
+
+::
+
+    CompareOBJ -computeOptimalRotationAndTranslation \
+    -model BennuComparison.obj \
+    -reference Bennu/Bennu49k.obj \
+    -computeVerticalError CompareOBJ/terrasaur-verticalError.txt \
+    -saveOptimalShape CompareOBJ/terrasaur-optimal.obj \
+    -savePlateDiff CompareOBJ/terrasaur-plateDiff.txt \
+    -savePlateIndex CompareOBJ/terrasaur-plateIndex.txt
+
+The screen output is
+
+::
+
+    Translation: -9.96162524e-03,7.99729762e-03,-1.00000044e-02
+    Rotation quaternion: 9.99048223e-01,-2.15657319e-08,-3.22625083e-08,4.36193625e-02
+    Rotation angle (degrees) and axis: 4.99999715e+00,-4.94407314e-07,-7.39637317e-07,1.00000000e+00
+    Center of rotation: -1.29539855e-02,-9.43799800e-03,8.39669000e-03
+    4x4 Transformation matrix:
+    9.96194702e-01  -8.71556932e-02  -6.63449701e-08  -9.96162524e-03
+    8.71556932e-02   9.96194702e-01   4.02758721e-08   7.99729762e-03
+    6.25822362e-08  -4.59049522e-08   1.00000000e+00  -1.00000044e-02
+    0.00000000e+00   0.00000000e+00   0.00000000e+00   1.00000000e+00
+    Using 49152 of 49152 points (excluding 0.0% largest distances)
+    Min Distance:              0.0
+    Max Distance:              3.563071622544315E-8
+    Mean Distance:             7.04333531909585E-9
+    Mean Square Distance:      7.536457599802241E-17
+    Root Mean Square Distance: 8.681277325257063E-9
+    Mean Vertical Distance:             7.043335319394247E-9
+    Mean Square Vertical Distance:      7.536457599439208E-17
+    Root Mean Square Vertical Distance: 8.681277325047973E-9
+    Direction perpendicular to plane: 0.6497386220463811 0.7600912355533176 -0.010051699174815498
+    Magnitude of projection perpendicular to plane: -2.9325978832850564E-4
+    Projection vector of translation parallel to plane: -0.00977108302826207 0.00822020181894647 -0.010002952125253225
+    Magnitude of projection vector of translation parallel to plane: 0.016220506549103512
+    49152 plates used in error calculation out of 49152 total in the shape model
+
+.. figure:: images/CompareOBJ_global_2.png
+
+   This image shows the reference (pink), comparison (grey, 50% opacity), and transformed comparison (blue) shape models.

doc/tools/CreateSBMTStructure.rst

@@ -0,0 +1,17 @@
+###################
+CreateSBMTStructure
+###################
+
+*****
+Usage
+*****
+
+CreateSBMTStructure will create an SBMT Ellipse file given a set of points 
+on the surface.  Each set of three points will generate an ellipse where
+the first two points define the long axis, and the third point is the short 
+axis.
+
+
+.. include:: ../toolDescriptions/CreateSBMTStructure.txt
+    :literal:
+

doc/tools/DumpConfig.rst

@@ -0,0 +1,8 @@
+.. _DumpConfig:
+
+==========
+DumpConfig
+==========
+
+.. include:: ../toolDescriptions/DumpConfig.txt
+    :literal:

doc/tools/RenderShapeFromSumFile.rst

@@ -0,0 +1,91 @@
+.. _RenderShapeFromSumFile:
+
+######################
+RenderShapeFromSumFile
+######################
+
+*****
+Usage
+*****
+
+RenderShapeFromSumFile generates a simulated image from a sumfile.
+
+.. include:: ../toolDescriptions/RenderShapeFromSumFile.txt
+    :literal:
+  
+********
+Examples
+********
+
+:download:`This<./support_files/g_12570mm_alt_obj_0000n00000_v014.obj>` 
+is a very low resolution shape model of Bennu from the OSIRIS-REx mission.  You can substitute higher resolution
+models from ???.  You will also need :download:`M605862153F5.SUM<support_files/M605862153F5.SUM>` which contains  
+observation geometry we will use to create a simulated image.
+
+Run RenderShapeFromSumFile:
+
+::
+
+    RenderShapeFromSumFile -model g_12570mm_alt_obj_0000n00000_v014.obj  -sumFile M605862153F5.SUM -output M605862153F5.png
+
+.. container:: figures-row
+
+    .. figure:: images/M605862153F5_12570.png
+        :alt: This simulated image uses the supplied 12 m/pixel shape model.
+
+        This simulated image uses the supplied 12 m/pixel shape model.
+
+    .. figure:: images/M605862153F5_00870.png
+        :alt: This simulated image uses a 87 cm/pixel shape model.
+
+        This simulated image uses a 87 cm/pixel shape model.
+
+    .. figure:: images/ocams20190314t190123s972_map_iofl2pan_77236.png
+        :alt: This is the actual image from MAPCAM.
+
+        This is the actual image from MAPCAM.
+
+Generate a FITS file.  The FITS header contains additional information such as illumination
+angles and range for each pixel in the image:
+
+::
+
+    RenderShapeFromSumFile -model g_12570mm_alt_obj_0000n00000_v014.obj  -sumFile M605862153F5.SUM -output M605862153F5.fits
+
+Here is the header from the FITS file:
+
+::
+
+    SIMPLE  =                    T / Java FITS: Wed Jan 15 14:53:52 EST 2025        
+    BITPIX  =                  -64 / bits per data element                          
+    NAXIS   =                    3 / dimensionality of data                         
+    NAXIS1  =                 2048 / n'th data dimension                            
+    NAXIS2  =                 2048 / n'th data dimension                            
+    NAXIS3  =                   11 / n'th data dimension                            
+    EXTEND  =                    T / allow extensions                               
+    UTC     = '2019 MAR 14 19:01:23.961' / Time from the SUM file                   
+    TITLE   = 'M605862153F5'       / Title of SUM file                              
+    PLANE1  = 'brightness'         / from 0 to 1                                    
+    PLANE2  = 'incidence'          / degrees                                        
+    PLANE3  = 'emission'           / degrees                                        
+    PLANE4  = 'phase   '           / degrees                                        
+    PLANE5  = 'range   '           / kilometers                                     
+    PLANE6  = 'facetX  '           / kilometers                                     
+    PLANE7  = 'facetY  '           / kilometers                                     
+    PLANE8  = 'facetZ  '           / kilometers                                     
+    PLANE9  = 'normalX '           / X component of unit normal                     
+    PLANE10 = 'normalY '           / Y component of unit normal                     
+    PLANE11 = 'normalZ '           / Z component of unit normal                     
+    MMFL    =             125.1963 / From SUM file                                  
+    SCOBJ   = '{1.4378777439; 3.5947718256; 0.1647121385}' / From SUM file          
+    CX      = '{-0.0219390994; -0.0187737183; 0.9995830248}' / From SUM file        
+    CY      = '{0.9129225176; -0.407945255; 0.0123752087}' / From SUM file          
+    CZ      = '{0.4075428232; 0.9128133525; 0.0260889017}' / From SUM file          
+    SZ      = '{-0.4941045298; -0.8687927376; 0.0325559925}' / From SUM file        
+    KMAT1   = '{117.647; 0; 0}'    / From SUM file                                  
+    KMAT2   = '{0; -117.636; 0}'   / From SUM file                                  
+    DIST    = '[0.0, 0.0, 0.0, 0.0]' / From SUM file                                
+    SIGVSO  = '{1; 1; 1}'          / From SUM file                                  
+    SIGPTG  = '{1; 1; 1}'          / From SUM file                                  
+    END                                                                             
+

doc/tools/ShapeFormatConverter.rst

@@ -0,0 +1,46 @@
+.. _ShapeFormatConverter:
+
+####################
+ShapeFormatConverter
+####################
+
+*****
+Usage
+*****
+
+ShapeFormatConverter can transform and convert shape models.  Supported input formats are
+icq, fits, llr, obj, pds, plt, ply, sbmt, stl, sum, or vtk.  Supported output formats are
+obj, plt, sbmt, stl, sum, or vtk.
+
+.. include:: ../toolDescriptions/ShapeFormatConverter.txt
+    :literal:
+  
+********
+Examples
+********
+
+Download :download:`rectangular_cuboid.obj <./support_files/rectangular_cuboid.obj>`.  This is a rectangular 
+cuboid centered on the origin with dimension 2 in the X direction, 4 in the Y direction, 
+and 8 in the Z direction.
+
+Turn it into a cube and save as an STL file:
+
+::
+
+    ShapeFormatConverter -input rectangular_cuboid.obj -output cube.stl -scale 1,0.5,0.25
+
+..  figure:: images/ShapeFormatConverter_cube.png
+
+    This image shows the original shape and the resized cube (pink)
+
+
+Rotate it by 90 degrees around (1, 1, 1):
+
+::
+
+    ShapeFormatConverter -input rectangular_cuboid.obj -output rotated.stl -rotate 90,1,1,1
+
+..  figure:: images/ShapeFormatConverter_rotated.png
+
+    This image shows the original shape and the rotated shape (pink)
+

doc/tools/support_files/M605862153F5.SUM

@@ -0,0 +1,16 @@
+M605862153F5
+2019 MAR 14 19:01:23.961
+  1024  1024  3000 65535                                      NPX, NLN, THRSH   
+    1.2519630000e+02    5.1300000000e+02    5.1300000000e+02  MMFL, CTR         
+    1.4378777439e+00    3.5947718256e+00    1.6471213851e-01  SCOBJ             
+   -2.1939099413e-02   -1.8773718273e-02    9.9958302478e-01  CX                
+    9.1292251760e-01   -4.0794525500e-01    1.2375208737e-02  CY                
+    4.0754282325e-01    9.1281335246e-01    2.6088901655e-02  CZ                
+   -4.9410452981e-01   -8.6879273764e-01    3.2555992468e-02  SZ                
+  117.6470    0.0000    0.0000    0.0000 -117.6360    0.0000  K-MATRIX          
+        0.00000        0.00000        0.00000        0.00000  DISTORTION        
+    1.0000000000e+00    1.0000000000e+00    1.0000000000e+00  SIGMA_VSO                
+    1.0000000000e-03    1.0000000000e-03    1.0000000000e-03  SIGMA_PTG                
+LANDMARKS
+LIMB FITS
+END FILE

doc/tools/support_files/rectangular_cuboid.obj

@@ -0,0 +1,25 @@
+#
+# Rectangle example for Terrasaur
+#
+
+v -1.0 -2.0 -4.0
+v -1.0 -2.0  4.0
+v -1.0  2.0 -4.0
+v -1.0  2.0  4.0
+v  1.0 -2.0 -4.0
+v  1.0 -2.0  4.0
+v  1.0  2.0 -4.0
+v  1.0  2.0  4.0
+
+f 3 2 1
+f 2 3 4
+f 5 6 7
+f 8 7 6
+f 8 4 3
+f 3 7 8
+f 1 2 6
+f 6 5 1
+f 1 5 7
+f 7 3 1
+f 6 2 4
+f 8 4 6

mkPackage.bash

@@ -0,0 +1,257 @@
+#!/bin/bash
+
+# Configure these for the package
+packageName=Terrasaur
+appPackage="terrasaur"
+scriptPath=$(
+    cd "$(dirname "$0")" || exit 1
+    pwd -P
+)
+srcPath="${scriptPath}/src/main/java"
+srcFile="${srcPath}/${appPackage}/utils/AppVersion.java"
+appSrcDir="${appPackage}/apps"
+
+function build_jar() {
+    rev=$1
+
+    cd "${scriptPath}" || exit 1
+
+    # store the version number in pom.xml
+    cp -p pom.xml pom.bak
+    sed "s,<version>0.0.1-SNAPSHOT</version>,<version>$rev</version>,g" pom.bak >pom.xml
+
+    # install dependencies to the local maven repository
+    if [ -d dependency ]; then
+        cd dependency || exit 1
+
+        for pom in *.pom; do
+            base=$(basename "$pom" .pom)
+            jar="${base}.jar"
+
+            # Extract groupId, artifactId, and version from the POM file
+            groupId=$(grep -m1 '<groupId>' "$pom" | sed -E 's|.*<groupId>(.*)</groupId>.*|\1|' | tr '.' '/')
+            artifactId=$(grep -m1 '<artifactId>' "$pom" | sed -E 's|.*<artifactId>(.*)</artifactId>.*|\1|')
+            version=$(grep -m1 '<version>' "$pom" | sed -E 's|.*<version>(.*)</version>.*|\1|')
+
+            if [ -z "$groupId" ] || [ -z "$artifactId" ] || [ -z "$version" ]; then
+                echo "Skipping ${base}: Unable to extract Maven coordinates."
+                continue
+            fi
+
+            # Construct the expected JAR and POM paths in the local Maven repository
+            repo_path="$HOME/.m2/repository/$groupId/$artifactId/$version"
+            jar_path="$repo_path/$artifactId-$version.jar"
+            pom_path="$repo_path/$artifactId-$version.pom"
+
+            if [ -f "$jar_path" ] || [ -f "$pom_path" ]; then
+                echo "${base} is already installed in local repository."
+                continue
+            fi
+
+            # Install the artifact
+            if [ -e "$jar" ]; then
+                mvn -q install:install-file -Dfile="$jar" -DpomFile="$pom"
+            else
+                mvn -q install:install-file -Dfile="$pom" -DpomFile="$pom"
+            fi
+
+            echo "Installed ${base} in local repository"
+        done
+
+        cd ..
+    else
+        # install the third party jar files
+        mvn -q install:install-file -Dfile=3rd-party/"${ARCH}"/spice/spice.jar -DgroupId=gov.nasa.jpl.naif -DartifactId=spice -Dversion=N0067 -Dpackaging=jar
+        mvn -q install:install-file -Dfile=3rd-party/"${ARCH}"/vtk/lib/java/vtk.jar -DgroupId=com.kitware -DartifactId=vtk-apl -Dversion=9.2.6-apl -Dpackaging=jar
+
+        # Deploy to surfshop
+
+#        echo mvn deploy:deploy-file -Dfile=3rd-party/"${ARCH}"/spice/spice.jar -DgroupId=gov.nasa.jpl.naif -DartifactId=spice -Dversion=N0067 -Dpackaging=jar -DrepositoryId=third-party -Durl=http://surfshop:8082/artifactory/libs-3rdparty-local/
+#        echo mvn deploy:deploy-file -Dfile=3rd-party/"${ARCH}"/vtk/lib/java/vtk.jar -DgroupId=com.kitware -DartifactId=vtk-apl -Dversion=9.2.6-apl -Dpackaging=jar -DrepositoryId=third-party -Durl=http://surfshop:8082/artifactory/libs-3rdparty-local/
+
+    fi
+
+    # ARCH needed for maven-surefire-plugin
+    export ARCH
+    mvn clean install
+
+    # restore the old pom file
+    mv pom.bak pom.xml
+
+    # install the maven products
+    rsync -a "${scriptPath}"/target/${packageName}.jar "${libDir}"
+    rsync -a "${scriptPath}"/target/${packageName}_lib "${libDir}"
+
+    # shellcheck disable=SC2086
+    rsync -a "${scriptPath}"/3rd-party/ ${libDir}
+
+}
+
+function make_scripts() {
+
+    classes=$(jar tf "${scriptPath}"/target/${packageName}.jar | grep $appSrcDir | grep -v '\$' | grep -v "package-info" | grep class)
+
+    for class in $classes; do
+        base=$(basename "$class" ".class")
+        tool=${scriptDir}/${base}
+        path=$(dirname "$class" | sed 's,/,.,g').${base}
+        echo "#!/bin/bash" >${tool}
+        echo 'script_dir=$(dirname $(which $0))' >>${tool}
+        echo 'script_dir=$(cd $script_dir; pwd -P)' >>${tool}
+        echo 'root=$(dirname $script_dir)' >>${tool}
+        echo 'MEMSIZE=""' >>${tool}
+        echo 'ARCH=$(uname -s)_$(uname -m)' >>${tool}
+        echo 'export PATH="${root}/lib/${ARCH}/altwg:${root}/lib/${ARCH}/spice/JNISpice/exe:${PATH}"' >>${tool}
+        echo 'JAVA_LIBRARY_PATH=""' >>${tool}
+        echo 'if [ ! -z $JAVA_HOME ]; then' >>${tool}
+        echo '  JAVA_LIBRARY_PATH="${JAVA_HOME}/lib:${JAVA_LIBRARY_PATH}"' >>${tool}
+        echo 'fi' >>${tool}
+        echo 'JAVA_LIBRARY_PATH="${root}/lib/${ARCH}/spice/JNISpice/lib:${JAVA_LIBRARY_PATH}"' >>${tool}
+        echo 'JAVA_LIBRARY_PATH="${root}/lib/${ARCH}/vtk/lib:${JAVA_LIBRARY_PATH}"' >>${tool}
+        echo 'JAVA_LIBRARY_PATH="${root}/lib/${ARCH}/vtk/lib/java/vtk-$(uname -s)-$(uname -m):${JAVA_LIBRARY_PATH}"' >>${tool}
+        echo 'if [ "$(uname -s)" == "Darwin" ]; then' >>${tool}
+        echo '    MEMSIZE=$(sysctl hw.memsize | awk '\''{print int($2/1024)}'\'')' >>${tool}
+        echo '    export DYLD_LIBRARY_PATH=$JAVA_LIBRARY_PATH' >>${tool}
+        echo 'elif [ "$(uname -s)" == "Linux" ]; then' >>${tool}
+        echo '    MEMSIZE=$(grep MemTotal /proc/meminfo | awk '\''{print $2}'\'')' >>${tool}
+        echo '    export LD_LIBRARY_PATH=$JAVA_LIBRARY_PATH' >>${tool}
+        echo 'fi' >>${tool}
+        echo 'java=$(which java)' >>${tool}
+        echo 'if [ -z "$java" ]; then' >>${tool}
+        echo '    echo "Java executable not found in your PATH"' >>${tool}
+        echo '    exit 1' >>${tool}
+        echo 'fi' >>${tool}
+        echo 'fullVersion=$($java -version 2>&1 | head -1 |awk -F\" '\''{print $2}'\'')' >>${tool}
+        echo 'version=$(echo $fullVersion | awk -F\. '\''{print $1}'\'')' >>${tool}
+        echo 'if [ "$version" -lt "'$REQUIRED_JAVA_VERSION'" ];then' >>${tool}
+        echo '    echo "minimum Java version required is '$REQUIRED_JAVA_VERSION'.  Version found is $fullVersion."' >>${tool}
+        echo '    exit 1' >>${tool}
+        echo 'fi' >>${tool}
+        echo '$java' "-Djava.library.path=\${JAVA_LIBRARY_PATH} -Xmx\${MEMSIZE}K -cp \${root}/lib/*:\${root}/lib/${packageName}_lib/* $path \"\$@\"" >>${tool}
+
+        chmod +x ${tool}
+    done
+
+}
+
+function make_doc {
+    cwd=$(pwd)
+
+    # build javadoc
+    javadoc -quiet -Xdoclint:none -cp ${libDir}/*:${libDir}/${packageName}_lib/* -d ${docDir}/javadoc -sourcepath ${srcPath} -subpackages ${appPackage} -overview ${docDir}/src/overview.html
+    /bin/rm -fr "${docDir}"/src
+
+    # sphinx
+    cd ${scriptPath}/doc || exit 1
+
+    python3 -m venv "${scriptPath}"/venv
+    source "${scriptPath}"/venv/bin/activate
+    site_package_path=$(python3 -c 'import sysconfig; print(sysconfig.get_paths()["purelib"])')
+    if [ -z "$PYTHONPATH" ]; then
+        export PYTHONPATH=$site_package_path
+    else
+        export PYTHONPATH=$site_package_path:$PYTHONPATH
+    fi
+
+    python3 -m pip --default-timeout=1000 install -U sphinx
+    python3 -m pip --default-timeout=1000 install sphinx-theme-pd
+
+    ./make_doc.bash ${scriptDir}
+    sphinx-build -b html . _build
+    rsync -a _build/ ${docDir}
+    /bin/rm -fr toolDescriptions tools/shortDescriptions.rst tools/index.rst _build
+
+    cd "$cwd" || exit 1
+}
+
+### Don't need to modify anything below this line
+
+# update maven-compiler-plugin block in pom if this version changes
+REQUIRED_JAVA_VERSION=21
+
+java=$(which java)
+if [ -z $java ]; then
+    echo "Java executable not found in your PATH"
+    exit 0
+fi
+fullVersion=$(java -version 2>&1 | head -1 | awk -F\" '{print $2}')
+version=$(echo $fullVersion | awk -F\. '{print $1}')
+if [ "$version" -lt "$REQUIRED_JAVA_VERSION" ]; then
+    echo "minimum Java version required is $REQUIRED_JAVA_VERSION.  Version found is $fullVersion."
+    exit 0
+fi
+
+if [ -d .git ]; then
+
+    date=$(git log -1 --format=%cd --date=format:%Y.%m.%d)
+    rev=$(git rev-parse --verify --short HEAD)
+
+    if [[ $(git diff --stat) != '' ]]; then
+        echo 'WARNING: the following files have not been checked in:'
+        git status --short
+        echo "waiting for 5 seconds ..."
+        sleep 5
+        rev=${rev}M
+    fi
+
+else
+    date=$(date -u +"%Y.%m.%d")
+    rev="UNVERSIONED"
+fi
+
+ARCH=$(uname -s)_$(uname -m)
+pkgBase=${packageName}-${date}
+
+scriptDir=${pkgBase}/scripts
+scriptDir=$(
+    mkdir -p "${scriptDir}"
+    cd "${scriptDir}" || exit 1
+    pwd -P
+)
+libDir=${pkgBase}/lib
+libDir=$(
+    mkdir -p "${libDir}"
+    cd "${libDir}" || exit 1
+    pwd -P
+)
+docDir=${pkgBase}/doc
+docDir=$(
+    mkdir -p "${docDir}"
+    cd "${docDir}" || exit 1
+    pwd -P
+)
+
+if [ ! -d ${scriptPath}/3rd-party/${ARCH} ]; then
+    echo "third party libraries should be installed in 3rd-party/${ARCH}.  Please install them and run this script again."
+    exit 0
+fi
+
+# Build the jar file
+build_jar ${rev}
+
+# create the executable scripts
+make_scripts
+
+# create documentation
+make_doc
+
+# Create distribution files for each architecture
+mkdir -p dist
+for arch in 3rd-party/*; do
+    this_arch=$(basename "$arch")
+    tarfile=./dist/${pkgBase}-${rev}_${this_arch}.tar
+    tar --exclude='lib' -cf "$tarfile" "${pkgBase}"
+    tar rf "$tarfile" "${pkgBase}"/lib/"${this_arch}" "${pkgBase}"/lib/${packageName}.jar "${pkgBase}"/lib/${packageName}_lib
+    gzip "${tarfile}"
+    echo "Created ${tarfile}.gz"
+done
+
+mvn -q -Dmdep.copyPom=true dependency:copy-dependencies
+rsync -a README.md CHANGELOG.md mkPackage.bash pom.xml doc src target/dependency "${pkgBase}"-src/
+tar cfz ./dist/"${pkgBase}"-${rev}-src.tar.gz ./"${pkgBase}"-src
+echo -e "\nCreated ./dist/${pkgBase}-${rev}-src.tar.gz"
+/bin/rm -fr ./"${pkgBase}" ./"${pkgBase}"-src
+
+if [ -d .git ]; then
+    git restore "$srcFile"
+fi

pom.xml

@@ -0,0 +1,330 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+    <groupId>edu.jhuapl.ses.srn</groupId>
+    <artifactId>Terrasaur</artifactId>
+    <version>0.0.1-SNAPSHOT</version>
+
+    <!-- Specifies organization -->
+    <organization>
+        <name>Johns Hopkins University Applied Physics Lab</name>
+        <url>https://www.jhuapl.edu</url>
+    </organization>
+
+    <!-- publish to surfshop -->
+    <distributionManagement>
+        <repository>
+            <id>central</id>
+            <name>surfshop-snapshots</name>
+            <url>http://surfshop.jhuapl.edu:8081/artifactory/libs-snapshot-local
+            </url>
+        </repository>
+    </distributionManagement>
+
+    <properties>
+        <package>Terrasaur</package>
+
+        <!-- main method in manifest, not that important which one you pick -->
+        <mainClass>terrasaur.apps.CompareOBJ</mainClass>
+
+        <!-- Sets proper encoding -->
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <project.reporting.outputEncoding>UTF-8
+        </project.reporting.outputEncoding>
+
+        <maven.compiler.release>21</maven.compiler.release>
+        <javafx.version>21.0.5</javafx.version>
+
+        <immutables.version>2.10.1</immutables.version>
+        <jackfruit.version>1.1.1</jackfruit.version>
+    </properties>
+
+    <build>
+        <finalName>${package}</finalName>
+        <sourceDirectory>src/main/java</sourceDirectory>
+        <plugins>
+
+            <plugin>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <version>3.13.0</version>
+                <configuration>
+                    <release>${maven.compiler.release}</release>
+                    <annotationProcessorPaths>
+                        <annotationProcessorPath>
+                            <groupId>org.immutables</groupId>
+                            <artifactId>value</artifactId>
+                            <version>${immutables.version}</version>
+                        </annotationProcessorPath>
+                        <annotationProcessorPath>
+                            <groupId>org.immutables</groupId>
+                            <artifactId>builder</artifactId>
+                            <version>${immutables.version}</version>
+                        </annotationProcessorPath>
+                        <annotationProcessorPath>
+                            <groupId>edu.jhuapl.ses</groupId>
+                            <artifactId>jackfruit</artifactId>
+                            <version>${jackfruit.version}</version>
+                        </annotationProcessorPath>
+                    </annotationProcessorPaths>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-dependency-plugin</artifactId>
+                <version>3.8.1</version>
+                <executions>
+                    <execution>
+                        <id>copy-dependencies</id>
+                        <phase>prepare-package</phase>
+                        <goals>
+                            <goal>copy-dependencies</goal>
+                        </goals>
+                        <configuration>
+                            <outputDirectory>${project.build.directory}/${package}_lib
+                            </outputDirectory>
+                            <overWriteReleases>false</overWriteReleases>
+                            <overWriteSnapshots>false</overWriteSnapshots>
+                            <overWriteIfNewer>true</overWriteIfNewer>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-surefire-plugin</artifactId>
+                <version>3.5.2</version>
+                <configuration>
+                    <argLine>
+                        -Djava.library.path=${project.basedir}/3rd-party/${env.ARCH}/spice/JNISpice/lib
+                    </argLine>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-enforcer-plugin</artifactId>
+                <version>3.5.0</version>
+                <executions>
+                    <execution>
+                        <id>enforce-maven</id>
+                        <goals>
+                            <goal>enforce</goal>
+                        </goals>
+                        <configuration>
+                            <rules>
+                                <requireMavenVersion>
+                                    <version>3.6.3</version>
+                                </requireMavenVersion>
+                            </rules>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-source-plugin</artifactId>
+                <version>3.3.1</version>
+                <executions>
+                    <execution>
+                        <id>attach-sources</id>
+                        <goals>
+                            <goal>jar</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <artifactId>maven-resources-plugin</artifactId>
+                <version>3.3.1</version>
+                <executions>
+                    <execution>
+                        <id>copy-resources</id>
+                        <phase>validate</phase>
+                        <goals>
+                            <goal>copy-resources</goal>
+                        </goals>
+                        <configuration>
+                            <outputDirectory>${project.basedir}/target/${package}
+                            </outputDirectory>
+                            <resources>
+                                <resource>
+                                    <directory>resources</directory>
+                                    <filtering>true</filtering>
+                                </resource>
+                            </resources>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-jar-plugin</artifactId>
+                <version>3.4.2</version>
+                <configuration>
+                    <archive>
+                        <manifest>
+                            <addClasspath>true</addClasspath>
+                            <classpathPrefix>lib/</classpathPrefix>
+                            <mainClass>${mainClass}</mainClass>
+                        </manifest>
+                        <manifestEntries>
+                            <Class-Path>.</Class-Path>
+                        </manifestEntries>
+                    </archive>
+                </configuration>
+            </plugin>
+
+            <plugin>
+                <groupId>org.codehaus.mojo</groupId>
+                <artifactId>exec-maven-plugin</artifactId>
+                <version>3.5.0</version>
+                <executions>
+                    <execution>
+                        <phase>generate-sources</phase>
+                        <id>createVersionFile</id>
+                        <goals>
+                            <goal>exec</goal>
+                        </goals>
+                        <configuration>
+                            <executable>${project.basedir}/src/main/bash/createVersionFile.bash
+                            </executable>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
+    </build>
+    <dependencies>
+        <!-- javafx dependencies -->
+        <dependency>
+            <groupId>org.openjfx</groupId>
+            <artifactId>javafx-controls</artifactId>
+            <version>${javafx.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.openjfx</groupId>
+            <artifactId>javafx-fxml</artifactId>
+            <version>${javafx.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.openjfx</groupId>
+            <artifactId>javafx-graphics</artifactId>
+            <version>${javafx.version}</version>
+        </dependency>
+
+        <!-- adding all the platform libs only adds a couple more MB -->
+        <dependency>
+            <groupId>org.openjfx</groupId>
+            <artifactId>javafx-graphics</artifactId>
+            <version>${javafx.version}</version>
+            <classifier>win</classifier>
+        </dependency>
+        <dependency>
+            <groupId>org.openjfx</groupId>
+            <artifactId>javafx-graphics</artifactId>
+            <version>${javafx.version}</version>
+            <classifier>mac</classifier>
+        </dependency>
+        <dependency>
+            <groupId>org.openjfx</groupId>
+            <artifactId>javafx-graphics</artifactId>
+            <version>${javafx.version}</version>
+            <classifier>linux</classifier>
+        </dependency>
+        <dependency>
+            <groupId>commons-beanutils</groupId>
+            <artifactId>commons-beanutils</artifactId>
+            <version>1.10.0</version>
+        </dependency>
+        <dependency>
+            <groupId>commons-cli</groupId>
+            <artifactId>commons-cli</artifactId>
+            <version>1.9.0</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-configuration2</artifactId>
+            <version>2.11.0</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-csv</artifactId>
+            <version>1.13.0</version>
+        </dependency>
+        <dependency>
+            <groupId>commons-io</groupId>
+            <artifactId>commons-io</artifactId>
+            <version>2.18.0</version>
+        </dependency>
+        <dependency>
+            <groupId>com.beust</groupId>
+            <artifactId>jcommander</artifactId>
+            <version>1.72</version>
+        </dependency>
+        <dependency>
+            <groupId>com.google.code.gson</groupId>
+            <artifactId>gson</artifactId>
+            <version>2.12.1</version>
+        </dependency>
+
+        <dependency>
+            <groupId>com.kitware</groupId>
+            <artifactId>vtk-apl</artifactId>
+            <version>9.2.6-apl</version>
+        </dependency>
+        <dependency>
+            <groupId>edu.jhuapl.ses</groupId>
+            <artifactId>picante</artifactId>
+            <version>1.0.0</version>
+        </dependency>
+        <dependency>
+            <groupId>edu.jhuapl.ses</groupId>
+            <artifactId>jackfruit</artifactId>
+            <version>${jackfruit.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>gov.nasa.gsfc.heasarc</groupId>
+            <artifactId>nom-tam-fits</artifactId>
+            <version>1.20.2</version>
+        </dependency>
+        <dependency>
+            <groupId>gov.nasa.jpl.naif</groupId>
+            <artifactId>spice</artifactId>
+            <version>N0067</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-text</artifactId>
+            <version>1.13.0</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.logging.log4j</groupId>
+            <artifactId>log4j-api</artifactId>
+            <version>2.24.3</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.logging.log4j</groupId>
+            <artifactId>log4j-core</artifactId>
+            <version>2.24.3</version>
+        </dependency>
+        <dependency>
+            <groupId>org.immutables</groupId>
+            <artifactId>value</artifactId>
+            <version>${immutables.version}</version>
+            <scope>provided</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.immutables</groupId>
+            <artifactId>builder</artifactId>
+            <version>${immutables.version}</version>
+            <scope>provided</scope>
+        </dependency>
+    </dependencies>
+    <repositories>
+        <repository>
+            <id>maven_central</id>
+            <name>Maven Central</name>
+            <url>https://repo.maven.apache.org/maven2/</url>
+        </repository>
+    </repositories>
+</project>

src/main/bash/createVersionFile.bash

@@ -0,0 +1,60 @@
+#!/bin/bash
+
+# This script is run from maven.  See the exec-maven-plugin block in the pom.xml file.
+
+# these should be consistent with the root-level mkPackage.bash script
+package=Terrasaur
+srcFile="../java/terrasaur/utils/AppVersion.java"
+
+cd $(dirname $0)
+
+date=$(date -u +"%Y-%b-%d %H:%M:%S %Z")
+
+rev=$(git rev-parse --verify --short HEAD)
+if [ $? -gt 0 ]; then
+    lastCommit=$(date -u +"%y.%m.%d")
+    rev="UNVERSIONED"
+else
+    lastCommit=$(git log -1 --format=%cd --date=format:%y.%m.%d)
+    rev=$(git rev-parse --verify --short HEAD)
+
+    if [[ $(git diff --stat) != '' ]]; then
+        if [[ $(git status -s --untracked=no | grep -v pom.xml | grep -v pom.bak | grep -v .m2 | grep -v $srcFile) != '' ]]; then
+            rev=${rev}M
+        fi
+    fi
+fi
+
+mkdir -p $(dirname $srcFile)
+
+touch $srcFile
+
+    cat <<EOF > $srcFile
+
+package terrasaur.utils;
+
+public class AppVersion {
+    public final static String lastCommit = "$lastCommit";
+    // an M at the end of gitRevision means this was built from a "dirty" git repository
+    public final static String gitRevision = "$rev";
+    public final static String applicationName = "$package";
+    public final static String dateString = "$date";
+
+	private AppVersion() {}
+
+    /**
+     * $package version $lastCommit-$rev built $date
+     */
+    public static String getFullString() {
+      return String.format("%s version %s-%s built %s", applicationName, lastCommit, gitRevision, dateString);
+    }
+
+    /**
+     * $package version $lastCommit-$rev
+     */
+    public static String getVersionString() {
+      return String.format("%s version %s-%s", applicationName, lastCommit, gitRevision);
+    }
+}
+
+EOF

src/main/java/terrasaur/altwg/pipeline/ALTWGProductNamer.java

@@ -0,0 +1,325 @@
+package terrasaur.altwg.pipeline;
+
+import terrasaur.enums.AltwgDataType;
+import terrasaur.fits.FitsHdr.FitsHdrBuilder;
+import terrasaur.fits.HeaderTag;
+import terrasaur.utils.StringUtil;
+
+public class ALTWGProductNamer implements ProductNamer {
+
+  public ALTWGProductNamer() {
+    super();
+  }
+
+  /**
+   * Parse the productName and return the portion of the name corresponding to a given field. Fields
+   * are assumed separated by "_" in the filename.
+   *
+   * @param productName
+   * @param fieldNum
+   * @return
+   */
+  @Override
+  public String getNameFrag(String productName, int fieldNum) {
+
+    String[] fields = productName.split("_");
+    String returnField = "ERROR";
+    if (fieldNum > fields.length) {
+      System.out.println(
+          "ERROR, field:" + fieldNum + " requested is beyond the number of fields found.");
+      System.out.println("returning:" + returnField);
+    } else {
+      returnField = fields[fieldNum];
+    }
+    return returnField;
+  }
+
+  @Override
+  public String productbaseName(
+      FitsHdrBuilder hdrBuilder, AltwgDataType altwgProduct, boolean isGlobal) {
+
+    String gsd = "gsd";
+    String dataSrc = "dataSrc";
+    String productType = altwgProduct.getFileFrag();
+    String prodVer = getVersion(hdrBuilder);
+
+    // extract ground sample distance. gsdD is in mm!
+    double gsdD = gsdFromHdr(hdrBuilder);
+
+    int gsdI = (int) Math.round(gsdD);
+    String fileUnits = "mm";
+    gsd = String.format("%05d", gsdI) + fileUnits;
+
+    // System.out.println("gsd:" + gsd);
+    // System.out.println("file units:" + fileUnits);
+
+    HeaderTag key = HeaderTag.DATASRC;
+    if (hdrBuilder.containsKey(key)) {
+      dataSrc = hdrBuilder.getCard(key).getValue().toLowerCase();
+
+      // check whether dataSrc needs to be modified
+      dataSrc = HeaderTag.getSDP(dataSrc);
+      // data source should only be 3 chars long
+      if (dataSrc.length() > 3) {
+        dataSrc = dataSrc.substring(0, 3);
+      }
+    }
+
+    key = HeaderTag.CLON;
+    String cLon = null;
+    if (hdrBuilder.containsKey(key)) {
+      cLon = hdrBuilder.getCard(key).getValue();
+    }
+    if (cLon == null) {
+      if (isGlobal) {
+        // set center longitude to 0.0 if value not parsed and this is a global product
+        cLon = "0.0";
+      } else {
+        String errMesg = "ERROR! Could not parse CLON from fits header!";
+        throw new RuntimeException(errMesg);
+      }
+    }
+    // System.out.println("clon:" + cLon);
+    key = HeaderTag.CLAT;
+    String cLat = null;
+    if (hdrBuilder.containsKey(key)) {
+      cLat = hdrBuilder.getCard(key).getValue();
+    }
+    if (cLat == null) {
+      if (isGlobal) {
+        // set center latitude to 0.0 if value not parsed and this is a global product
+        cLat = "0.0";
+      } else {
+        String errMesg = "ERROR! Could not parse CLAT from fits header!";
+        throw new RuntimeException(errMesg);
+      }
+    }
+    // System.out.println("clat" + cLat);
+
+    String region = "l";
+    if (isGlobal) {
+      region = "g";
+    }
+
+    String clahLon = ALTWGProductNamer.clahLon(cLat, cLon);
+
+    // pds likes having filenames all in the same case, so chose lowercase
+    String outFile =
+        ALTWGProductNamer.altwgBaseName(region, gsd, dataSrc, productType, clahLon, prodVer);
+    return outFile;
+  }
+
+  /**
+   * Retrieve the product version string. Returns initial default value if product version keyword
+   * not found in builder.
+   *
+   * @param hdrBuilder
+   */
+  @Override
+  public String getVersion(FitsHdrBuilder hdrBuilder) {
+    String prodVer = "prodVer";
+
+    // note: this has been changed to MAP_VER in the SIS
+    HeaderTag key = HeaderTag.MAP_VER;
+    // key = HeaderTag.PRODVERS;
+    if (hdrBuilder.containsKey(key)) {
+      prodVer = hdrBuilder.getCard(key).getValue();
+      prodVer = prodVer.replaceAll("\\.", "");
+    }
+
+    return prodVer;
+  }
+
+  // Given the fields return the altwg PDS base name
+  public static String altwgBaseName(
+      String region, String gsd, String dataSource, String desc, String lahLon, String version) {
+
+    StringBuilder sb = new StringBuilder();
+    String delim = "_";
+    sb.append(region);
+    sb.append(delim);
+    sb.append(gsd);
+    sb.append(delim);
+
+    // data source should only be 3 characters long
+    if (dataSource.length() > 3) {
+      System.out.println("WARNING! dataSource:" + dataSource + " longer than 3 chars!");
+      dataSource = dataSource.substring(0, 3);
+      System.out.println(
+          "Will set data source to:"
+              + dataSource
+              + " but"
+              + " this might NOT conform to the ALTWG naming convention!");
+    }
+    sb.append(dataSource);
+    sb.append(delim);
+    sb.append(desc);
+    sb.append(delim);
+    sb.append(lahLon);
+    sb.append(delim);
+    sb.append("v");
+
+    // remove '.' from version string
+    version = version.replaceAll("\\.", "");
+    sb.append(version);
+
+    // pds likes having filenames all in the same case, so chose lowercase
+    String outFile = sb.toString().toLowerCase();
+
+    return outFile;
+  }
+
+  /**
+   * Parse center lat, lon strings and return the formatted clahLon portion of the PDS filename.
+   *
+   * @param clat
+   * @param clon
+   * @return
+   */
+  public static String clahLon(String clat, String clon) {
+
+    // String cLon = "";
+
+    // remove all whitespace that may exist in the strings
+    clat = clat.replaceAll("\\s+", "");
+    clon = clon.replaceAll("\\s+", "");
+
+    double cLonD = StringUtil.parseSafeD(clon);
+    double cLatD = StringUtil.parseSafeD(clat);
+
+    String clahLon = clahLon(cLatD, cLonD);
+    return clahLon;
+  }
+
+  public static String clahLon(double cLatD, double cLonD) {
+
+    String cLon = "";
+
+    if (cLonD == Double.NaN) {
+
+      // unable to parse center longitude using normal method (see V in getProductCards())
+      cLon = "xxxxxx";
+
+    } else {
+
+      if (cLonD < 0) {
+        // transform to 0-360
+        cLonD = cLonD + 360D;
+      }
+      // format double to 2 significant digits
+      cLon = String.format("%06.2f", cLonD);
+    }
+
+    // remove decimal point
+    cLon = cLon.replace(".", "");
+
+    String cLat = "";
+
+    // System.out.println("cLatD:" + Double.toString(cLatD));
+    if (cLatD == Double.NaN) {
+
+      // unable to parse center latitude
+      cLat = "xxxxxx";
+
+    } else {
+
+      double tol = 0.0101D;
+
+      // determine whether latitude is within tolerance of its rounded value.
+      // if so then use rounded value
+      double roundValue = Math.round(cLatD);
+      double diffTol = Math.abs(roundValue - cLatD);
+      if (diffTol < tol) {
+        cLatD = roundValue;
+      }
+      String hemiSphere = (cLatD >= 0) ? "N" : "S";
+
+      if (cLatD < 0) {
+        // remove negative sign if in southern hemisphere
+        cLatD = cLatD * -1.0D;
+      }
+      // format cLat to 2 significant digits
+      cLat = String.format("%05.2f", cLatD);
+      cLat = cLat.replace(".", "");
+
+      // trim to length 4.
+      cLat = cLat.substring(0, Math.min(cLat.length(), 4));
+      cLat = cLat + hemiSphere;
+    }
+
+    String clahLon = cLat + cLon;
+    return clahLon;
+  }
+
+  /**
+   * return GSD parsed from FitsHdrBuilder. Returns 0 if valid GSD could not be parsed. GSD is in
+   * mm.
+   *
+   * @param hdrBuilder
+   * @return
+   */
+  @Override
+  public double gsdFromHdr(FitsHdrBuilder hdrBuilder) {
+
+    String gsd = "gsd";
+    double gsdD = Double.NaN;
+
+    // extract ground sample distance using GSD first
+    HeaderTag key = HeaderTag.GSD;
+    if (hdrBuilder.containsKey(key)) {
+      gsd = hdrBuilder.getCard(key).getValue();
+      gsdD = StringUtil.parseSafeD(gsd);
+      if (gsdD < 0D) {
+        // keyword value not initialized
+        gsdD = Double.NaN;
+        System.out.println("WARNING! keyword GSD not set!");
+      }
+    } else {
+      System.out.println("could not find " + key.toString() + " to parse GSD from.");
+    }
+    if (Double.isNaN(gsdD)) {
+      // could not parse GSD into valid number, try GSDI
+      key = HeaderTag.GSDI;
+      if (hdrBuilder.containsKey(key)) {
+        gsdD = StringUtil.parseSafeD(hdrBuilder.getCard(key).getValue());
+        if (gsdD < 0D) {
+          // keyword value not initialized
+          gsdD = Double.NaN;
+          System.out.println("WARNING! keyword GSDI not set!");
+        }
+      } else {
+        System.out.println("could not find " + key.toString() + " to parse GSD from.");
+      }
+      if (Double.isNaN(gsdD)) {
+        // still cannot parse gsd. Set to -999
+        System.out.println(
+            "WARNING: No valid values of GSD or GSDI could be parsed from fits header!");
+        System.out.println("Setting gsd = -999");
+        gsdD = -999D;
+      }
+    }
+
+    if (hdrBuilder.getCard(key).getComment().contains("[cm]")) {
+
+      // mandated to use mm! change the units
+      gsdD = gsdD * 10.0D;
+    }
+
+    return gsdD;
+  }
+
+  @Override
+  public NameConvention getNameConvention() {
+    return NameConvention.ALTPRODUCT;
+  }
+
+  @Override
+  /** Parse the filename using the ALTWGProduct naming convention and return the GSD value. */
+  public double gsdFromFilename(String filename) {
+    String[] splitStr = filename.split("_");
+    // GSD is second element
+    String gsd = splitStr[1];
+    gsd = gsd.replace("mm", "");
+    return StringUtil.parseSafeD(gsd);
+  }
+}

src/main/java/terrasaur/altwg/pipeline/AltwgMLNNamer.java

@@ -0,0 +1,190 @@
+package terrasaur.altwg.pipeline;
+
+import terrasaur.enums.AltwgDataType;
+import terrasaur.fits.FitsHdr.FitsHdrBuilder;
+import terrasaur.fits.HeaderTag;
+import terrasaur.utils.StringUtil;
+
+public class AltwgMLNNamer implements ProductNamer {
+
+  public AltwgMLNNamer() {
+    super();
+  }
+
+  @Override
+  public String getNameFrag(String productName, int fieldNum) {
+
+    String nameFrag = "";
+
+    return nameFrag;
+  }
+
+  /**
+   * ALTWG MLN naming convention applies only to one productType - the ALTWG NFT-MLN.
+   *
+   * @param hdrBuilder - contains values that are used to create the MLN according to naming
+   *     convention.
+   * @param altwgProduct - N/A. Included here as part of the interface structure.
+   * @param isGlobal - N/A. Included here as part of the interface structure.
+   */
+  @Override
+  public String productbaseName(
+      FitsHdrBuilder hdrBuilder, AltwgDataType altwgProduct, boolean isGlobal) {
+
+    // initialize string fragments for NFT name. This will help identify
+    // which string fragments have not been updated by the method.
+    String gsd = "gsd";
+    String dataSrc = "dataSrc";
+    String dataSrcfile = "dataSrcFile";
+    String productType = "nftdtm";
+    String cLon = "cLon";
+    String cLat = "cLat";
+    String prodVer = "prodVer";
+    String productID = "prodID";
+
+    // find relevant information in the hdrBuilder map.
+    double gsdD = gsdFromHdr(hdrBuilder);
+    int gsdI = (int) Math.round(gsdD);
+    String fileUnits = "mm";
+    gsd = String.format("%05d", gsdI) + fileUnits;
+    // HeaderTag key = HeaderTag.GSD;
+    // if (hdrBuilder.containsKey(key)) {
+    // gsd = hdrBuilder.getCard(key).getValue();
+    //
+    // double gsdD = Double.parseDouble(gsd);
+    // String fileUnits = "";
+    // if (hdrBuilder.getCard(key).getComment().contains("[mm]")) {
+    // fileUnits = "mm";
+    // } else if (hdrBuilder.getCard(key).getComment().contains("[cm]")) {
+    //
+    // // mandated to use mm! change the units
+    // gsdD = gsdD * 10.0D;
+    // gsdI = (int) Math.round(gsdD);
+    // }
+    //
+    // System.out.println("gsd:" + gsd);
+    // System.out.println("file units:" + fileUnits);
+    //
+    // }
+
+    HeaderTag key = HeaderTag.DATASRC;
+    if (hdrBuilder.containsKey(key)) {
+      dataSrc = hdrBuilder.getCard(key).getValue().toLowerCase();
+      // data source should only be 3 chars long
+      if (dataSrc.length() > 3) {
+        dataSrc = dataSrc.substring(0, 3);
+      }
+    }
+
+    key = HeaderTag.CLON;
+    if (hdrBuilder.containsKey(key)) {
+      cLon = hdrBuilder.getCard(key).getValue();
+    }
+
+    key = HeaderTag.CLAT;
+    if (hdrBuilder.containsKey(key)) {
+      cLat = hdrBuilder.getCard(key).getValue();
+    }
+
+    key = HeaderTag.DATASRCF;
+    if (hdrBuilder.containsKey(key)) {
+      dataSrcfile = hdrBuilder.getCard(key).getValue();
+    }
+
+    key = HeaderTag.PRODVERS;
+    if (hdrBuilder.containsKey(key)) {
+      prodVer = hdrBuilder.getCard(key).getValue();
+      prodVer = prodVer.replaceAll("\\.", "");
+    }
+
+    // hardcode region to local
+    String region = "l";
+
+    StringBuilder sb = new StringBuilder();
+    String delim = "_";
+    sb.append(region);
+    sb.append(delim);
+    sb.append(gsd);
+    sb.append(delim);
+    sb.append(dataSrc);
+    sb.append(delim);
+    sb.append(productType);
+    sb.append(delim);
+
+    /*
+     * determine product ID. For OLA it is the center lat,lon For SPC it is the NFT feature id,
+     * which is assumed to be the first 5 chars in DATASRC
+     */
+    if (dataSrc.contains("ola")) {
+
+      // follow ALTWG product naming convention for center lat, lon
+      productID = ALTWGProductNamer.clahLon(cLat, cLon);
+    } else {
+      productID = dataSrcfile.substring(0, 5);
+    }
+    sb.append(productID);
+    sb.append(delim);
+    sb.append("v");
+    sb.append(prodVer);
+
+    return sb.toString().toLowerCase();
+  }
+
+  @Override
+  public String getVersion(FitsHdrBuilder hdrBuilder) {
+
+    String version = "";
+
+    return version;
+  }
+
+  /**
+   * Extract ground sample distance from FitsHdrBuilder. GSD is needed as part of naming convention.
+   * GSD in units of mm.
+   */
+  @Override
+  public double gsdFromHdr(FitsHdrBuilder hdrBuilder) {
+
+    // find relevant information in the hdrBuilder map.
+    double gsdD = Double.NaN;
+    HeaderTag key = HeaderTag.GSD;
+    if (hdrBuilder.containsKey(key)) {
+      String gsd = hdrBuilder.getCard(key).getValue();
+
+      gsdD = Double.parseDouble(gsd);
+      String fileUnits = "";
+      if (hdrBuilder.getCard(key).getComment().contains("[mm]")) {
+        fileUnits = "mm";
+      } else if (hdrBuilder.getCard(key).getComment().contains("[cm]")) {
+
+        // mandated to use mm! change the units
+        gsdD = gsdD * 10.0D;
+        fileUnits = "mm";
+      }
+      System.out.println("gsd:" + gsd);
+      System.out.println("file units:" + fileUnits);
+
+    } else {
+      String errMesg =
+          "ERROR! Could not find keyword:" + HeaderTag.GSD.toString() + " in hdrBuilder";
+      throw new RuntimeException(errMesg);
+    }
+
+    return gsdD;
+  }
+
+  @Override
+  public NameConvention getNameConvention() {
+    return NameConvention.ALTNFTMLN;
+  }
+
+  @Override
+  /** Parse the filename using the ALTWG MLN naming convention and return the GSD value. */
+  public double gsdFromFilename(String filename) {
+    String[] splitStr = filename.split("_");
+    // GSD is second element
+    String gsd = splitStr[1];
+    gsd = gsd.replace("mm", "");
+    return StringUtil.parseSafeD(gsd);
+  }
+}

src/main/java/terrasaur/altwg/pipeline/DartNamer.java

@@ -0,0 +1,304 @@
+package terrasaur.altwg.pipeline;
+
+import java.util.HashMap;
+import java.util.Map;
+import terrasaur.enums.AltwgDataType;
+import terrasaur.fits.FitsHdr.FitsHdrBuilder;
+import terrasaur.fits.HeaderTag;
+import terrasaur.utils.StringUtil;
+
+/**
+ * Determines product names for DART shape models and ancillary products.
+ *
+ * @author espirrc1
+ */
+public class DartNamer implements ProductNamer {
+
+  public static String getBaseName(Map<NameFields, String> nameFragments) {
+
+    // check to see if the map contains all the fragments needed. Throw runtimeexception if it
+    // doesn't
+    validateMap(nameFragments);
+
+    StringBuilder sb = new StringBuilder();
+    String delim = "_";
+    sb.append(nameFragments.get(NameFields.REGION));
+    sb.append(delim);
+    sb.append(nameFragments.get(NameFields.GSD));
+    sb.append(delim);
+
+    // data source should only be 3 characters long
+    String dataSource = nameFragments.get(NameFields.DATASRC);
+    if (dataSource.length() > 3) {
+      System.out.println("WARNING! dataSource:" + dataSource + " longer than 3 chars!");
+      dataSource = dataSource.substring(0, 3);
+      System.out.println(
+          "Will set data source to:"
+              + dataSource
+              + " but"
+              + " this might NOT conform to the ALTWG naming convention!");
+    }
+    sb.append(dataSource);
+    sb.append(delim);
+
+    sb.append(nameFragments.get(NameFields.DATATYPE));
+    sb.append(delim);
+    sb.append(nameFragments.get(NameFields.TBODY));
+    sb.append(delim);
+    sb.append(nameFragments.get(NameFields.CLATLON));
+    sb.append(delim);
+    sb.append("v");
+
+    // remove '.' from version string
+    String version = nameFragments.get(NameFields.VERSION);
+    version = version.replaceAll("\\.", "");
+    sb.append(version);
+
+    // pds likes having filenames all in the same case, so chose lowercase
+    String outFile = sb.toString().toLowerCase();
+
+    return outFile;
+  }
+
+  /**
+   * Parse the productName and return the portion of the name corresponding to a given field. Fields
+   * are assumed separated by "_" in the filename.
+   *
+   * @param productName
+   * @param fieldNum
+   * @return
+   */
+  @Override
+  public String getNameFrag(String productName, int fieldNum) {
+
+    String[] fields = productName.split("_");
+    String returnField = "ERROR";
+    if (fieldNum > fields.length) {
+      System.out.println(
+          "ERROR, field:" + fieldNum + " requested is beyond the number of fields found.");
+      System.out.println("returning:" + returnField);
+    } else {
+      returnField = fields[fieldNum];
+    }
+    return returnField;
+  }
+
+  @Override
+  public String productbaseName(
+      FitsHdrBuilder hdrBuilder, AltwgDataType altwgProduct, boolean isGlobal) {
+
+    String gsd = "gsd";
+    String dataSrc = "dataSrc";
+
+    Map<NameFields, String> nameFragments = new HashMap<NameFields, String>();
+
+    // data type
+    String productType = altwgProduct.getFileFrag();
+    nameFragments.put(NameFields.DATATYPE, productType);
+
+    // product version
+    String prodVer = getVersion(hdrBuilder);
+    nameFragments.put(NameFields.VERSION, prodVer);
+
+    // extract ground sample distance. gsdD is in mm!
+    double gsdD = gsdFromHdr(hdrBuilder);
+
+    int gsdI = (int) Math.round(gsdD);
+    String fileUnits = "mm";
+    gsd = String.format("%05d", gsdI) + fileUnits;
+    nameFragments.put(NameFields.GSD, gsd);
+
+    // data source
+    HeaderTag key = HeaderTag.DATASRC;
+    if (hdrBuilder.containsKey(key)) {
+      dataSrc = hdrBuilder.getCard(key).getValue().toLowerCase();
+      // check whether dataSrc needs to be modified
+      dataSrc = HeaderTag.getSDP(dataSrc);
+      // data source should only be 3 chars long
+      if (dataSrc.length() > 3) {
+        dataSrc = dataSrc.substring(0, 3);
+      }
+    }
+    nameFragments.put(NameFields.DATASRC, dataSrc);
+
+    // center lon
+    key = HeaderTag.CLON;
+    String cLon = null;
+    if (hdrBuilder.containsKey(key)) {
+      cLon = hdrBuilder.getCard(key).getValue();
+    }
+    if (cLon == null) {
+      if (isGlobal) {
+        // set center longitude to 0.0 if value not parsed and this is a global product
+        cLon = "0.0";
+      } else {
+        String errMesg = "ERROR! Could not parse CLON from fits header!";
+        throw new RuntimeException(errMesg);
+      }
+    }
+
+    // center lat
+    key = HeaderTag.CLAT;
+    String cLat = null;
+    if (hdrBuilder.containsKey(key)) {
+      cLat = hdrBuilder.getCard(key).getValue();
+    }
+    if (cLat == null) {
+      if (isGlobal) {
+        // set center latitude to 0.0 if value not parsed and this is a global product
+        cLat = "0.0";
+      } else {
+        String errMesg = "ERROR! Could not parse CLAT from fits header!";
+        throw new RuntimeException(errMesg);
+      }
+    }
+
+    String clahLon = ALTWGProductNamer.clahLon(cLat, cLon);
+    nameFragments.put(NameFields.CLATLON, clahLon);
+
+    // region
+    String region = "l";
+    if (isGlobal) {
+      region = "g";
+    }
+    nameFragments.put(NameFields.REGION, region);
+
+    // target body
+    key = HeaderTag.TARGET;
+    String tBody = "unkn";
+    if (hdrBuilder.containsKey(key)) {
+      tBody = hdrBuilder.getCard(key).getValue();
+      tBody = getBodyStFrag(tBody);
+    }
+    nameFragments.put(NameFields.TBODY, tBody);
+
+    // pds likes having filenames all in the same case, so chose lowercase
+    String outFile = DartNamer.getBaseName(nameFragments);
+    return outFile;
+  }
+
+  @Override
+  public String getVersion(FitsHdrBuilder hdrBuilder) {
+
+    String prodVer = "prodVer";
+
+    // note: this has been changed to MAP_VER in the SIS
+    HeaderTag key = HeaderTag.MAP_VER;
+    // key = HeaderTag.PRODVERS;
+    if (hdrBuilder.containsKey(key)) {
+      prodVer = hdrBuilder.getCard(key).getValue();
+      prodVer = prodVer.replaceAll("\\.", "");
+    }
+
+    return prodVer;
+  }
+
+  @Override
+  public double gsdFromHdr(FitsHdrBuilder hdrBuilder) {
+
+    String gsd = "gsd";
+    double gsdD = Double.NaN;
+
+    // extract ground sample distance using GSD first
+    HeaderTag key = HeaderTag.GSD;
+    if (hdrBuilder.containsKey(key)) {
+      gsd = hdrBuilder.getCard(key).getValue();
+      gsdD = StringUtil.parseSafeD(gsd);
+      if (gsdD < 0D) {
+        // keyword value not initialized
+        gsdD = Double.NaN;
+        System.out.println("WARNING! keyword GSD not set!");
+      }
+    } else {
+      System.out.println("could not find " + key.toString() + " to parse GSD from.");
+    }
+    if (Double.isNaN(gsdD)) {
+      // could not parse GSD into valid number, try GSDI
+      key = HeaderTag.GSDI;
+      if (hdrBuilder.containsKey(key)) {
+        gsdD = StringUtil.parseSafeD(hdrBuilder.getCard(key).getValue());
+        if (gsdD < 0D) {
+          // keyword value not initialized
+          gsdD = Double.NaN;
+          System.out.println("WARNING! keyword GSDI not set!");
+        }
+      } else {
+        System.out.println("could not find " + key.toString() + " to parse GSD from.");
+      }
+      if (Double.isNaN(gsdD)) {
+        // still cannot parse gsd. Set to -999
+        System.out.println(
+            "WARNING: No valid values of GSD or GSDI could be parsed from fits header!");
+        System.out.println("Setting gsd = -999");
+        gsdD = -999D;
+      }
+    }
+
+    if (hdrBuilder.getCard(key).getComment().contains("[cm]")) {
+
+      // mandated to use mm! change the units
+      gsdD = gsdD * 10.0D;
+    }
+
+    return gsdD;
+  }
+
+  @Override
+  public NameConvention getNameConvention() {
+    return NameConvention.DARTPRODUCT;
+  }
+
+  /**
+   * Parse target body string to get the proper string fragment for the target body name.
+   *
+   * @param tBody
+   * @return
+   */
+  private String getBodyStFrag(String tBody) {
+
+    String returnFrag = tBody;
+
+    if (tBody.toLowerCase().contains("didy")) {
+      returnFrag = "didy";
+    } else {
+      if (tBody.toLowerCase().contains("dimo")) {
+        returnFrag = "dimo";
+      } else {
+        System.out.println("Could not parse target string fragment from:" + tBody);
+      }
+    }
+
+    return returnFrag;
+  }
+
+  private static void validateMap(Map<NameFields, String> nameFragments) {
+
+    NameFields[] reqFields = new NameFields[7];
+    reqFields[0] = NameFields.REGION;
+    reqFields[1] = NameFields.GSD;
+    reqFields[2] = NameFields.DATASRC;
+    reqFields[3] = NameFields.DATATYPE;
+    reqFields[4] = NameFields.TBODY;
+    reqFields[5] = NameFields.CLATLON;
+    reqFields[6] = NameFields.VERSION;
+
+    for (NameFields requiredField : reqFields) {
+
+      if (!nameFragments.containsKey(requiredField)) {
+        String errMesg = "ERROR! Missing required field:" + requiredField.toString();
+        throw new RuntimeException(errMesg);
+      }
+    }
+  }
+
+  @Override
+  /** Parse the filename using the DART naming convention and return the GSD value. */
+  public double gsdFromFilename(String filename) {
+
+    String[] splitStr = filename.split("_");
+    // GSD is second element
+    String gsd = splitStr[1];
+    gsd = gsd.replace("mm", "");
+    return StringUtil.parseSafeD(gsd);
+  }
+}

src/main/java/terrasaur/altwg/pipeline/NameConvention.java

@@ -0,0 +1,26 @@
+package terrasaur.altwg.pipeline;
+
+/**
+ * Enum to store the different types of naming conventions.
+ * 
+ * @author espirrc1
+ *
+ */
+public enum NameConvention {
+
+  ALTPRODUCT, ALTNFTMLN, DARTPRODUCT, NOMATCH, NONEUSED;
+
+  public static NameConvention parseNameConvention(String name) {
+    for (NameConvention nameConvention : values()) {
+      if (nameConvention.toString().toLowerCase().equals(name.toLowerCase())) {
+        System.out.println("parsed naming convention:" + nameConvention.toString());
+        return nameConvention;
+      }
+    }
+    NameConvention nameConvention = NameConvention.NOMATCH;
+    System.out
+        .println("NameConvention.parseNameConvention()" + " could not parse naming convention:"
+            + name + ". Returning:" + nameConvention.toString());
+    return nameConvention;
+  }
+}

src/main/java/terrasaur/altwg/pipeline/NameFields.java

@@ -0,0 +1,13 @@
+package terrasaur.altwg.pipeline;
+
+/**
+ * Enum to describe the different parts of the product name. Used by concrete classes implementing
+ * ProductNamer.
+ * 
+ * @author espirrc1
+ *
+ */
+public enum NameFields {
+
+  GSD, DATATYPE, VERSION, DATASRC, CLATLON, REGION, TBODY;
+}

src/main/java/terrasaur/altwg/pipeline/NamingFactory.java

@@ -0,0 +1,111 @@
+package terrasaur.altwg.pipeline;
+
+import java.io.File;
+import java.util.Map;
+import terrasaur.enums.AltwgDataType;
+import terrasaur.fits.AltPipelnEnum;
+import terrasaur.fits.FitsHdr.FitsHdrBuilder;
+
+/**
+ * Factory class for returning concrete classes that implement the ProductNamer interface.
+ *
+ * @author espirrc1
+ */
+public class NamingFactory {
+
+  public static ProductNamer getNamingConvention(NameConvention namingConvention) {
+
+    switch (namingConvention) {
+      case ALTPRODUCT:
+        return new ALTWGProductNamer();
+
+      case ALTNFTMLN:
+        return new AltwgMLNNamer();
+
+      case DARTPRODUCT:
+        return new DartNamer();
+
+      default:
+        System.err.println(
+            "ERROR! Naming convention:" + namingConvention.toString() + " not supported!");
+        throw new RuntimeException();
+    }
+  }
+
+  /**
+   * Parse for keyword in pipeline config file that specifies what naming convention to use.
+   *
+   * @param pipeConfig
+   * @return
+   */
+  public static ProductNamer parseNamingConvention(
+      Map<AltPipelnEnum, String> pipeConfig, boolean verbose) {
+
+    ProductNamer productNamer = null;
+
+    if ((pipeConfig.containsKey(AltPipelnEnum.NAMINGCONVENTION))) {
+      String value = pipeConfig.get(AltPipelnEnum.NAMINGCONVENTION);
+      productNamer = parseNamingConvention(value);
+    } else {
+      String errMesg = "ERROR! Naming convention should have been defined in pipeConfig!";
+      throw new RuntimeException(errMesg);
+    }
+
+    return productNamer;
+  }
+
+  /**
+   * Parse string to determine the naming convention to use. Naming convention supplied by
+   * ProductNamer interface.
+   *
+   * @param value
+   * @return
+   */
+  public static ProductNamer parseNamingConvention(String value) {
+
+    if (value.length() < 1) {
+      String errMesg = "ERROR! Cannot pass empty string to NamingFactory.parseNamingConvention!";
+      throw new RuntimeException(errMesg);
+    }
+    NameConvention nameConvention = NameConvention.parseNameConvention(value);
+    return NamingFactory.getNamingConvention(nameConvention);
+  }
+
+  /**
+   * Given the naming convention, hdrBuilder, productType, and original output file, return the
+   * renamed output file and cross reference file. Output is returned as a File[] array where
+   * array[0] is the output basename, array[1] is the cross-reference file. If no naming convention
+   * is specified (NONEUSED) then array[0] is the same as outfile, array[1] is null.
+   *
+   * @param namingConvention
+   * @param hdrBuilder
+   * @param productType
+   * @param isGlobal
+   * @param outfile - proposed output filename. If Naming convention results in a renamed OBJ then
+   *     this is not used. If no naming convention specified then outputFiles[0] = outfile.
+   * @return
+   */
+  public static File[] getBaseNameAndCrossRef(
+      NameConvention namingConvention,
+      FitsHdrBuilder hdrBuilder,
+      AltwgDataType productType,
+      boolean isGlobal,
+      String outfile) {
+
+    File[] outputFiles = new File[2];
+
+    // default to no renaming.
+    File crossrefFile = null;
+    String basename = outfile;
+
+    if (namingConvention != NameConvention.NONEUSED) {
+      ProductNamer productNamer = NamingFactory.getNamingConvention(namingConvention);
+      basename = productNamer.productbaseName(hdrBuilder, productType, isGlobal);
+      crossrefFile = new File(outfile + ".crf");
+    }
+
+    outputFiles[0] = new File(basename);
+    outputFiles[1] = crossrefFile;
+    return outputFiles;
+  }
+}

src/main/java/terrasaur/altwg/pipeline/ProductNamer.java

@@ -0,0 +1,21 @@
+package terrasaur.altwg.pipeline;
+
+import terrasaur.enums.AltwgDataType;
+import terrasaur.fits.FitsHdr.FitsHdrBuilder;
+
+public interface ProductNamer {
+
+  public String getNameFrag(String productName, int fieldNum);
+
+  public String productbaseName(FitsHdrBuilder hdrBuilder, AltwgDataType altwgProduct,
+      boolean isGlobal);
+
+  public String getVersion(FitsHdrBuilder hdrBuilder);
+
+  public double gsdFromHdr(FitsHdrBuilder hdrBuilder);
+
+  public NameConvention getNameConvention();
+
+  public double gsdFromFilename(String filename);
+
+}

src/main/java/terrasaur/apps/AdjustShapeModelToOtherShapeModel.java

@@ -0,0 +1,289 @@
+package terrasaur.apps;
+
+import java.io.File;
+import java.nio.charset.Charset;
+import java.util.*;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.Options;
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.math3.geometry.euclidean.threed.Vector3D;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import terrasaur.smallBodyModel.BoundingBox;
+import terrasaur.smallBodyModel.SmallBodyModel;
+import terrasaur.templates.TerrasaurTool;
+import terrasaur.utils.Log4j2Configurator;
+import terrasaur.utils.NativeLibraryLoader;
+import terrasaur.utils.PolyDataUtil;
+import spice.basic.Plane;
+import spice.basic.Vector3;
+import vtk.vtkGenericCell;
+import vtk.vtkPoints;
+import vtk.vtkPolyData;
+import vtk.vtksbCellLocator;
+
+/**
+ * AdjustShapeModelToOtherShapeModel program. See the usage string for more information about this
+ * program.
+ *
+ * @author Eli Kahn
+ * @version 1.0
+ */
+public class AdjustShapeModelToOtherShapeModel implements TerrasaurTool {
+
+  private static final Logger logger = LogManager.getLogger();
+
+  @Override
+  public String shortDescription() {
+    return "Adjust vertices of one shape model to lie on the surface of another.";
+  }
+
+  @Override
+  public String fullDescription(Options options) {
+
+    String header =
+        """
+                \n
+                This program takes 2 shape models in OBJ format and tries to adjust
+                to vertices of the first shape model so they lie on the surface of the
+                second shape model. It does this by shooting a ray starting from the origin
+                in the direction of each point of the first model into the second model and
+                then changes the point of the first model to the intersection point.""";
+    return TerrasaurTool.super.fullDescription(options, header, "");
+  }
+
+    private static Options defineOptions() {
+    Options options = TerrasaurTool.defineOptions();
+    options.addOption(
+        Option.builder("from")
+            .hasArg()
+            .desc(
+                "path to first shape model in OBJ format which will get shifted to the second shape model")
+            .build());
+    options.addOption(
+        Option.builder("to")
+            .hasArg()
+            .desc(
+                "path to second shape model in OBJ format which the first shape model will try to match to")
+            .build());
+    options.addOption(
+        Option.builder("output")
+            .hasArg()
+            .desc(
+                "path to adjusted shape model in OBJ format generated by this program by shifting first to second")
+            .build());
+    options.addOption(
+        Option.builder("filelist")
+            .desc(
+                """
+                  If specified then the second required argument to this program,
+                  "to" is a file containing a list of OBJ files to match to.
+                  In this situation the ray is shot into each of the shape models in this
+                  list and any intersection points are averaged together to produce the
+                  final intersection point. Note that any individual shape model in this
+                  list may be only a piece of the the complete shape model (e.g. a mapola).
+                  However, the global shape model formed when all these pieces are
+                  combined together, may not have any holes or gaps.""")
+            .build());
+    options.addOption(
+        Option.builder("fit-plane-radius")
+            .hasArg()
+            .desc(
+                """
+                  If present, find a local normal at each point in the first shape
+                  model by fitting a plane to all points within the specified radius.
+                  Use this normal to adjust the point to the second shape model rather
+                  than the radial vector.""")
+            .build());
+    options.addOption(
+        Option.builder("local")
+            .desc(
+                """
+                  Use when adjusting a local OBJ file to another.  The best fit plane to the
+                  first shape model is used to adjust the vertices rather than the radial vector
+                  for each point.
+""")
+            .build());
+    return options;
+  }
+
+  static Vector3D computeMeanPoint(List<Vector3D> points) {
+    Vector3D meanPoint = new Vector3D(0., 0., 0.);
+    for (Vector3D point : points) meanPoint = meanPoint.add(point);
+    meanPoint = meanPoint.scalarMultiply(1. / points.size());
+    return meanPoint;
+  }
+
+  public static void adjustShapeModelToOtherShapeModel(
+      vtkPolyData frompolydata,
+      ArrayList<vtkPolyData> topolydata,
+      double planeRadius,
+      boolean localModel)
+      throws Exception {
+    vtkPoints points = frompolydata.GetPoints();
+    long numberPoints = frompolydata.GetNumberOfPoints();
+
+    boolean fitPlane = (planeRadius > 0);
+    SmallBodyModel sbModel = new SmallBodyModel(frompolydata);
+    double diagonalLength = new BoundingBox(frompolydata.GetBounds()).getDiagonalLength();
+
+    ArrayList<vtksbCellLocator> cellLocators = new ArrayList<>();
+    for (vtkPolyData polydata : topolydata) {
+      vtksbCellLocator cellLocator = new vtksbCellLocator();
+      cellLocator.SetDataSet(polydata);
+      cellLocator.CacheCellBoundsOn();
+      cellLocator.AutomaticOn();
+      cellLocator.BuildLocator();
+      cellLocators.add(cellLocator);
+    }
+
+    vtkGenericCell cell = new vtkGenericCell();
+    double tol = 1e-6;
+    double[] t = new double[1];
+    double[] pcoords = new double[3];
+    int[] subId = new int[1];
+    long[] cell_id = new long[1];
+
+    double[] localNormal = null;
+    if (localModel) {
+      // fit a plane to the local model and check that the normal points outward
+      Plane localPlane = PolyDataUtil.fitPlaneToPolyData(frompolydata);
+      Vector3 localNormalVector = localPlane.getNormal();
+      if (localNormalVector.dot(localPlane.getPoint()) < 0)
+        localNormalVector = localNormalVector.negate();
+      localNormal = localNormalVector.toArray();
+    }
+
+    double[] p = new double[3];
+    Vector3D origin = new Vector3D(0., 0., 0.);
+    for (int i = 0; i < numberPoints; ++i) {
+      points.GetPoint(i, p);
+
+      Vector3D lookDir;
+
+      if (fitPlane) {
+        // fit a plane to the local area
+        System.arraycopy(p, 0, origin.toArray(), 0, 3);
+        lookDir = new Vector3D(sbModel.getNormalAtPoint(p, planeRadius)).normalize();
+      } else if (localModel) {
+        System.arraycopy(p, 0, origin.toArray(), 0, 3);
+        lookDir = new Vector3D(localNormal).normalize();
+      } else {
+        // use radial vector
+        lookDir = new Vector3D(p).normalize();
+      }
+
+      Vector3D lookPt = lookDir.scalarMultiply(diagonalLength);
+      lookPt = lookPt.add(origin);
+
+      List<Vector3D> intersections = new ArrayList<>();
+      for (vtksbCellLocator cellLocator : cellLocators) {
+        double[] intersectPoint = new double[3];
+
+        // trace ray from the lookPt to the origin - first intersection is the farthest intersection
+        // from the origin
+        int result =
+            cellLocator.IntersectWithLine(
+                lookPt.toArray(),
+                origin.toArray(),
+                tol,
+                t,
+                intersectPoint,
+                pcoords,
+                subId,
+                cell_id,
+                cell);
+        Vector3D intersectVector = new Vector3D(intersectPoint);
+
+        if (fitPlane || localModel) {
+          // NOTE: result should return 1 in case of intersection but doesn't sometimes.
+          // Use the norm of intersection point to test for intersection instead.
+
+          NavigableMap<Double, Vector3D> pointsMap = new TreeMap<>();
+          if (intersectVector.getNorm() > 0) {
+            pointsMap.put(origin.subtract(intersectVector).getNorm(), intersectVector);
+          }
+
+          lookPt = lookDir.scalarMultiply(-diagonalLength);
+          lookPt = lookPt.add(origin);
+          result =
+              cellLocator.IntersectWithLine(
+                  lookPt.toArray(),
+                  origin.toArray(),
+                  tol,
+                  t,
+                  intersectPoint,
+                  pcoords,
+                  subId,
+                  cell_id,
+                  cell);
+
+          intersectVector = new Vector3D(intersectPoint);
+          if (intersectVector.getNorm() > 0) {
+            pointsMap.put(origin.subtract(intersectVector).getNorm(), intersectVector);
+          }
+
+          if (!pointsMap.isEmpty()) intersections.add(pointsMap.get(pointsMap.firstKey()));
+        } else {
+          if (result > 0) intersections.add(intersectVector);
+        }
+      }
+
+      if (intersections.isEmpty()) throw new Exception("Error: no intersections at all");
+
+      Vector3D meanIntersectionPoint = computeMeanPoint(intersections);
+      points.SetPoint(i, meanIntersectionPoint.toArray());
+    }
+  }
+
+  public static void main(String[] args) throws Exception {
+    TerrasaurTool defaultOBJ = new AdjustShapeModelToOtherShapeModel();
+
+    Options options = defineOptions();
+
+    CommandLine cl = defaultOBJ.parseArgs(args, options);
+
+    Map<MessageLabel, String> startupMessages = defaultOBJ.startupMessages(cl);
+    for (MessageLabel ml : startupMessages.keySet())
+      logger.info(String.format("%s %s", ml.label, startupMessages.get(ml)));
+
+    boolean loadListFromFile = cl.hasOption("filelist");
+    double planeRadius = Double.parseDouble(cl.getOptionValue("fit-plane-radius", "-1"));
+    boolean localModel = cl.hasOption("local");
+
+    NativeLibraryLoader.loadVtkLibraries();
+
+    String fromfile = cl.getOptionValue("from");
+    String tofile = cl.getOptionValue("to");
+    String outfile = cl.getOptionValue("output");
+
+    Log4j2Configurator.getInstance();
+    logger.info("loading <from-obj-file>: {}", fromfile);
+    vtkPolyData frompolydata = PolyDataUtil.loadShapeModelAndComputeNormals(fromfile);
+
+    ArrayList<vtkPolyData> topolydata = new ArrayList<>();
+    if (loadListFromFile) {
+      List<String> lines = FileUtils.readLines(new File(tofile), Charset.defaultCharset());
+      for (String file : lines) {
+
+        // checking length prevents trying to load an empty line, such as the
+        // last line of the file.
+        if (file.length() > 1) {
+          logger.info("loading <to-obj-file>: {}", file);
+          topolydata.add(PolyDataUtil.loadShapeModelAndComputeNormals(file));
+        }
+      }
+    } else {
+      logger.info("loading <to-obj-file>: {}", tofile);
+      topolydata.add(PolyDataUtil.loadShapeModelAndComputeNormals(tofile));
+    }
+
+    adjustShapeModelToOtherShapeModel(frompolydata, topolydata, planeRadius, localModel);
+
+    PolyDataUtil.saveShapeModelAsOBJ(frompolydata, outfile);
+
+    logger.info("wrote {}", outfile);
+  }
+}

src/main/java/terrasaur/apps/AppendOBJ.java

@@ -0,0 +1,142 @@
+package terrasaur.apps;
+
+import java.util.Map;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.Options;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.spi.StandardLevel;
+import terrasaur.templates.TerrasaurTool;
+import terrasaur.utils.NativeLibraryLoader;
+import terrasaur.utils.PolyDataUtil;
+import vtk.vtkAppendPolyData;
+import vtk.vtkObjectBase;
+import vtk.vtkPolyData;
+
+/**
+ * AppendOBJ program. See the usage string for more information about this program.
+ *
+ * @author Eli Kahn
+ * @version 1.0
+ */
+public class AppendOBJ implements TerrasaurTool {
+
+  private static final Logger logger = LogManager.getLogger();
+
+  @Override
+  public String shortDescription() {
+    return "Combine multiple shape files (OBJ or VTK format) into one.";
+  }
+
+  @Override
+  public String fullDescription(Options options) {
+    String header = "This program combines input shape models into a single shape model.";
+    return TerrasaurTool.super.fullDescription(options, header, "");
+  }
+
+  private static Options defineOptions() {
+    Options options = TerrasaurTool.defineOptions();
+    options.addOption(
+        Option.builder("logFile")
+            .hasArg()
+            .desc("If present, save screen output to log file.")
+            .build());
+    StringBuilder sb = new StringBuilder();
+    for (StandardLevel l : StandardLevel.values()) sb.append(String.format("%s ", l.name()));
+    options.addOption(
+        Option.builder("logLevel")
+            .hasArg()
+            .desc(
+                "If present, print messages above selected priority.  Valid values are "
+                    + sb.toString().trim()
+                    + ".  Default is INFO.")
+            .build());
+
+    options.addOption(
+        Option.builder("boundary")
+            .desc("Only save out boundary. This option implies -vtk.")
+            .build());
+    options.addOption(
+        Option.builder("decimate")
+            .hasArg()
+            .desc(
+                "Reduce the number of facets in the output shape model.  The argument should be between 0 and 1.  "
+                    + "For example, if a model has 100 facets and <arg> is 0.90, "
+                    + "there will be approximately 10 facets after the decimation.")
+            .build());
+    options.addOption(
+        Option.builder("input")
+            .required()
+            .hasArgs()
+            .desc(
+                "input file(s) to read.  Format is derived from the allowed extension: "
+                    + "icq, llr, obj, pds, plt, ply, stl, or vtk.  Multiple files can be specified "
+                    + "with a single -input option, separated by whitespace.  Alternatively, you may "
+                    + "specify -input multiple times.")
+            .build());
+    options.addOption(
+        Option.builder("output").required().hasArg().desc("output file to write.").build());
+    options.addOption(
+        Option.builder("vtk").desc("Save output file in VTK format rather than OBJ.").build());
+    return options;
+  }
+
+  public static void main(String[] args) throws Exception {
+
+    TerrasaurTool defaultOBJ = new AppendOBJ();
+
+    Options options = defineOptions();
+
+    CommandLine cl = defaultOBJ.parseArgs(args, options);
+
+    Map<MessageLabel, String> startupMessages = defaultOBJ.startupMessages(cl);
+    for (MessageLabel ml : startupMessages.keySet())
+      logger.info(String.format("%s %s", ml.label, startupMessages.get(ml)));
+
+    boolean boundaryOnly = cl.hasOption("boundary");
+    boolean vtkFormat = boundaryOnly || cl.hasOption("vtk");
+    boolean decimate = cl.hasOption("decimate");
+    double decimationPercentage =
+        decimate ? Double.parseDouble(cl.getOptionValue("decimate")) : 1.0;
+
+    NativeLibraryLoader.loadVtkLibraries();
+
+    String outfile = cl.getOptionValue("output");
+    String[] infiles = cl.getOptionValues("input");
+
+    vtkAppendPolyData append = new vtkAppendPolyData();
+    append.UserManagedInputsOn();
+    append.SetNumberOfInputs(infiles.length);
+
+    for (int i = 0; i < infiles.length; ++i) {
+      logger.info("loading {} {} / {}", infiles[i], i + 1, infiles.length);
+
+      vtkPolyData polydata = PolyDataUtil.loadShapeModel(infiles[i]);
+
+      if (polydata == null) {
+        logger.warn("Cannot load {}", infiles[i]);
+      } else {
+        if (boundaryOnly) {
+          vtkPolyData boundary = PolyDataUtil.getBoundary(polydata);
+          boundary.GetCellData().SetScalars(null);
+          polydata.DeepCopy(boundary);
+        }
+
+        append.SetInputDataByNumber(i, polydata);
+      }
+      System.gc();
+      vtkObjectBase.JAVA_OBJECT_MANAGER.gc(false);
+    }
+
+    append.Update();
+
+    vtkPolyData outputShape = append.GetOutput();
+    if (decimate) PolyDataUtil.decimatePolyData(outputShape, decimationPercentage);
+
+    if (vtkFormat) PolyDataUtil.saveShapeModelAsVTK(outputShape, outfile);
+    else PolyDataUtil.saveShapeModelAsOBJ(append.GetOutput(), outfile);
+
+    logger.info("Wrote " + outfile);
+  }
+}

src/main/java/terrasaur/apps/BatchSubmit.java

@@ -0,0 +1,88 @@
+package terrasaur.apps;
+
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.Options;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import terrasaur.templates.TerrasaurTool;
+import terrasaur.utils.batch.BatchSubmitFactory;
+import terrasaur.utils.batch.BatchSubmitI;
+import terrasaur.utils.batch.BatchType;
+import terrasaur.utils.batch.GridType;
+
+public class BatchSubmit implements TerrasaurTool {
+
+  private static final Logger logger = LogManager.getLogger();
+
+
+  @Override
+  public String shortDescription() {
+    return "Run a command on a cluster.";
+  }
+
+  @Override
+  public String fullDescription(Options options) {
+
+    String footer = "\nRun a command on a cluster.\n";
+
+    return TerrasaurTool.super.fullDescription(options, "", footer);
+
+  }
+
+  private static Options defineOptions() {
+    Options options = TerrasaurTool.defineOptions();
+    options.addOption(
+        Option.builder("command")
+            .required()
+            .hasArgs()
+            .desc("Required.  Command(s) to run.")
+            .build());
+
+    StringBuilder sb = new StringBuilder();
+    for (GridType type : GridType.values()) sb.append(String.format("%s ", type.name()));
+    options.addOption(
+        Option.builder("gridType")
+            .hasArg()
+            .desc("Grid type.  Valid values are " + sb + ". Default is LOCAL.")
+            .build());
+
+    options.addOption(
+        Option.builder("workingDir")
+            .hasArg()
+            .desc("Working directory to run command.  Default is current directory.")
+            .build());
+    return options;
+    }
+
+  public static void main(String[] args) {
+
+    TerrasaurTool defaultOBJ = new BatchSubmit();
+
+    Options options = defineOptions();
+
+    CommandLine cl = defaultOBJ.parseArgs(args, options);
+
+    Map<MessageLabel, String> startupMessages = defaultOBJ.startupMessages(cl);
+    for (MessageLabel ml : startupMessages.keySet())
+      logger.info(String.format("%s %s", ml.label, startupMessages.get(ml)));
+
+    List<String> cmdList = Arrays.asList(cl.getOptionValues("command"));
+    BatchType batchType = BatchType.GRID_ENGINE;
+    GridType gridType =
+        cl.hasOption("gridType") ? GridType.valueOf(cl.getOptionValue("gridType")) : GridType.LOCAL;
+
+    BatchSubmitI submitter = BatchSubmitFactory.getBatchSubmit(cmdList, batchType, gridType);
+    String workingDir = "";
+    try {
+      submitter.runBatchSubmitinDir(workingDir);
+    } catch (InterruptedException | IOException e) {
+      logger.error(e.getLocalizedMessage(), e);
+    }
+  }
+
+}

src/main/java/terrasaur/apps/CKFromSumFile.java

@@ -0,0 +1,295 @@
+package terrasaur.apps;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.nio.charset.Charset;
+import java.time.ZoneId;
+import java.time.ZonedDateTime;
+import java.time.format.DateTimeFormatter;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.NavigableMap;
+import java.util.TreeMap;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.Options;
+import org.apache.commons.configuration2.PropertiesConfiguration;
+import org.apache.commons.configuration2.builder.fluent.Configurations;
+import org.apache.commons.configuration2.ex.ConfigurationException;
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.FilenameUtils;
+import org.apache.commons.text.WordUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.spi.StandardLevel;
+import spice.basic.KernelDatabase;
+import spice.basic.Matrix33;
+import spice.basic.ReferenceFrame;
+import spice.basic.SpiceErrorException;
+import spice.basic.SpiceException;
+import spice.basic.SpiceQuaternion;
+import spice.basic.TDBTime;
+import spice.basic.Vector3;
+import terrasaur.config.CKFromSumFileConfig;
+import terrasaur.config.CKFromSumFileConfigFactory;
+import terrasaur.templates.TerrasaurTool;
+import terrasaur.utils.*;
+import terrasaur.utils.math.MathConversions;
+
+public class CKFromSumFile implements TerrasaurTool {
+
+  private final static Logger logger = LogManager.getLogger();
+
+  @Override
+  public String shortDescription() {
+    return "Create a CK from a list of sumfiles.";
+  }
+
+  @Override
+  public String fullDescription(Options options) {
+    String footer = "Create a CK from a list of sumfiles.";
+    return TerrasaurTool.super.fullDescription(options, "", footer);
+  }
+
+  private static Options defineOptions() {
+    Options options = TerrasaurTool.defineOptions();
+    options.addOption(Option.builder("config").required().hasArg()
+            .desc("Required.  Name of configuration file.").build());
+    options.addOption(Option.builder("dumpConfig").hasArg()
+            .desc("Write out an example configuration to the named file.").build());
+    options.addOption(Option.builder("logFile").hasArg()
+            .desc("If present, save screen output to log file.").build());
+    StringBuilder sb = new StringBuilder();
+    for (StandardLevel l : StandardLevel.values())
+      sb.append(String.format("%s ", l.name()));
+    options.addOption(Option.builder("logLevel").hasArg()
+            .desc("If present, print messages above selected priority.  Valid values are "
+                    + sb.toString().trim() + ".  Default is INFO.")
+            .build());
+    options.addOption(Option.builder("sumFile").hasArg().required().desc("""
+        Required.  File listing sumfiles to read.  This is a text file, one per line.
+        Lines starting with # are ignored.
+
+        Example:
+
+        D717506120G0.SUM
+        D717506126G0.SUM
+        D717506127G0.SUM
+        D717506128G0.SUM
+        D717506129G0.SUM
+        D717506131G0.SUM
+        # This is a comment
+        D717506132G0.SUM
+        """).build());
+    return options;
+  }
+
+  private final CKFromSumFileConfig config;
+  private final NavigableMap<SumFile, String> sumFiles;
+
+  private CKFromSumFile(){config=null;sumFiles=null;}
+
+  public CKFromSumFile(CKFromSumFileConfig config, NavigableMap<SumFile, String> sumFiles) {
+    this.config = config;
+    this.sumFiles = sumFiles;
+  }
+
+  public String writeMSOPCKFiles(String basename, List<String> comments) throws SpiceException {
+
+    ReferenceFrame instrFrame = new ReferenceFrame(config.instrumentFrameName());
+    ReferenceFrame scFrame = new ReferenceFrame(config.spacecraftFrame());
+    ReferenceFrame j2000 = new ReferenceFrame("J2000");
+    ReferenceFrame bodyFixed = new ReferenceFrame(config.bodyFrame());
+
+    ReferenceFrame ref = config.J2000() ? j2000 : bodyFixed;
+
+    logger.debug("Body fixed frame: {}", bodyFixed.getName());
+    logger.debug("Instrument frame: {}", instrFrame.getName());
+    logger.debug("Spacecraft frame: {}", scFrame.getName());
+    logger.debug(" Reference frame: {}", ref.getName());
+
+    File commentFile = new File(basename + "-comments.txt");
+    if (commentFile.exists())
+      if (!commentFile.delete())
+        logger.error("{} exists but cannot be deleted!", commentFile.getPath());
+
+    String setupFile = basename + ".setup";
+    String inputFile = basename + ".inp";
+
+    try (PrintWriter pw = new PrintWriter(commentFile)) {
+      StringBuilder sb = new StringBuilder();
+
+      DateTimeFormatter dtf = DateTimeFormatter.ofPattern("uuuu-MM-dd HH:mm:ss z");
+      ZonedDateTime now = ZonedDateTime.now(ZoneId.of("UTC"));
+
+      sb.append("This CK was created on ").append(dtf.format(now)).append(" from the following sumFiles:\n");
+      for (SumFile sumFile : sumFiles.keySet()) {
+        sb.append(String.format("\t%s %s\n", sumFile.utcString(), sumFiles.get(sumFile)));
+      }
+      sb.append("\n");
+      sb.append("providing the orientation of ").append(scFrame.getName()).append(" with respect to ").append(config.J2000() ? "J2000" : bodyFixed.getName()).append(".  ");
+      double first = new TDBTime(sumFiles.firstKey().utcString()).getTDBSeconds();
+      double last = new TDBTime(sumFiles.lastKey().utcString()).getTDBSeconds() + config.extend();
+      sb.append("The coverage period is ").append(new TDBTime(first).toUTCString("ISOC", 3)).append(" to ").append(new TDBTime(last).toUTCString("ISOC", 3)).append(" UTC.");
+
+      String allComments = sb.toString();
+      for (String comment : allComments.split("\\r?\\n"))
+        pw.println(WordUtils.wrap(comment, 80));
+    } catch (FileNotFoundException e) {
+      logger.error(e.getLocalizedMessage(), e);
+    }
+
+    Map<String, String> map = new TreeMap<>();
+    map.put("LSK_FILE_NAME", "'" + config.lsk() + "'");
+    map.put("SCLK_FILE_NAME", "'" + config.sclk() + "'");
+    map.put("CK_TYPE", "3");
+    map.put("COMMENTS_FILE_NAME", String.format("'%s'", commentFile.getPath()));
+    map.put("INSTRUMENT_ID", String.format("%d", scFrame.getIDCode()));
+    map.put("REFERENCE_FRAME_NAME",
+        String.format("'%s'", config.J2000() ? "J2000" : bodyFixed.getName()));
+    if (!config.fk().isEmpty())
+      map.put("FRAMES_FILE_NAME", "'" + config.fk() + "'");
+    map.put("ANGULAR_RATE_PRESENT", "'MAKE UP/NO AVERAGING'");
+    map.put("INPUT_TIME_TYPE", "'UTC'");
+    map.put("INPUT_DATA_TYPE", "'SPICE QUATERNIONS'");
+    map.put("PRODUCER_ID", "'Hari.Nair@jhuapl.edu'");
+
+    try (PrintWriter pw = new PrintWriter(setupFile)) {
+      pw.println("\\begindata");
+      for (String key : map.keySet()) {
+        pw.printf("%s = %s\n", key, map.get(key));
+      }
+    } catch (FileNotFoundException e) {
+      logger.error(e.getLocalizedMessage(), e);
+    }
+
+    NavigableMap<Double, SpiceQuaternion> attitudeMap = new TreeMap<>();
+    for (SumFile s : sumFiles.keySet()) {
+      TDBTime t = new TDBTime(s.utcString());
+
+      Vector3[] rows = new Vector3[3];
+      rows[0] = MathConversions.toVector3(s.cx());
+      rows[1] = MathConversions.toVector3(s.cy());
+      rows[2] = MathConversions.toVector3(s.cz());
+
+      Vector3 row0 = rows[Math.abs(config.flipX()) - 1];
+      Vector3 row1 = rows[Math.abs(config.flipY()) - 1];
+      Vector3 row2 = rows[Math.abs(config.flipZ()) - 1];
+
+      if (config.flipX() < 0)
+        row0 = row0.negate();
+      if (config.flipY() < 0)
+        row1 = row1.negate();
+      if (config.flipZ() < 0)
+        row2 = row2.negate();
+
+      Matrix33 refToInstr = new Matrix33(row0, row1, row2);
+
+      if (config.J2000()) {
+        Matrix33 j2000ToBodyFixed = j2000.getPositionTransformation(bodyFixed, t);
+        refToInstr = refToInstr.mxm(j2000ToBodyFixed);
+      }
+
+      Matrix33 instrToSc = instrFrame.getPositionTransformation(scFrame, t);
+      Matrix33 refToSc = instrToSc.mxm(refToInstr);
+
+      SpiceQuaternion q = new SpiceQuaternion(refToSc);
+      attitudeMap.put(t.getTDBSeconds(), q);
+    }
+
+    if (config.extend() > 0) {
+      var lastEntry = attitudeMap.lastEntry();
+      attitudeMap.put(lastEntry.getKey() + config.extend(), lastEntry.getValue());
+    }
+
+    try (PrintWriter pw = new PrintWriter(new FileWriter(inputFile))) {
+      for (double t : attitudeMap.keySet()) {
+        SpiceQuaternion q = attitudeMap.get(t);
+        pw.printf("%s %.14e %.14e %.14e %.14e\n", new TDBTime(t).toUTCString("ISOC", 6),
+            q.getElt(0), q.getElt(1), q.getElt(2), q.getElt(3));
+      }
+    } catch (IOException e) {
+      logger.error(e.getLocalizedMessage(), e);
+    }
+
+      return String.format("msopck %s %s %s.bc", setupFile, inputFile, basename);
+  }
+
+  public static void main(String[] args) throws SpiceException, IOException {
+    TerrasaurTool defaultOBJ = new CKFromSumFile();
+    
+    Options options = defineOptions();
+
+    CommandLine cl = defaultOBJ.parseArgs(args, options);
+
+    Map<MessageLabel, String> startupMessages = defaultOBJ.startupMessages(cl);
+    for (MessageLabel ml : startupMessages.keySet())
+      logger.info(String.format("%s %s", ml.label, startupMessages.get(ml)));
+
+    if (cl.hasOption("dumpConfig")){
+      CKFromSumFileConfigFactory factory = new CKFromSumFileConfigFactory();
+      PropertiesConfiguration config = factory.toConfig(factory.getTemplate());
+      try {
+        String filename = cl.getOptionValue("dumpConfig");
+        config.write(new PrintWriter(filename));
+        logger.info("Wrote {}", filename);
+      } catch (ConfigurationException | IOException e) {
+        logger.error(e.getLocalizedMessage(), e);
+      }
+      System.exit(0);
+    }
+
+    NativeLibraryLoader.loadSpiceLibraries();
+
+    PropertiesConfiguration config = null;
+    CKFromSumFileConfigFactory factory = new CKFromSumFileConfigFactory();
+    try {
+      config = new Configurations().properties(new File(cl.getOptionValue("config")));
+    } catch (ConfigurationException e1) {
+      logger.error(e1.getLocalizedMessage(), e1);
+    }
+
+    CKFromSumFileConfig appConfig = factory.fromConfig(config);
+
+    for (String kernel : appConfig.metakernel())
+      KernelDatabase.load(kernel);
+
+    NavigableMap<SumFile, String> sumFiles = new TreeMap<>((o1, o2) -> {
+      try {
+        return Double.compare(new TDBTime(o1.utcString()).getTDBSeconds(),
+            new TDBTime(o2.utcString()).getTDBSeconds());
+      } catch (SpiceErrorException e) {
+        logger.error(e.getLocalizedMessage(), e);
+      }
+      return 0;
+    });
+
+    List<String> lines =
+        FileUtils.readLines(new File(cl.getOptionValue("sumFile")), Charset.defaultCharset());
+    for (String line : lines) {
+      if (line.strip().startsWith("#"))
+        continue;
+      String[] parts = line.strip().split("\\s+");
+      String filename = parts[0].trim();
+      sumFiles.put(SumFile.fromFile(new File(filename)), FilenameUtils.getBaseName(filename));
+    }
+
+    CKFromSumFile app = new CKFromSumFile(appConfig, sumFiles);
+    TDBTime begin = new TDBTime(sumFiles.firstKey().utcString());
+    TDBTime end = new TDBTime(sumFiles.lastKey().utcString());
+    String picture = "YYYY_DOY";
+    String command = app.writeMSOPCKFiles(
+        String.format("ck_%s_%s", begin.toString(picture), end.toString(picture)),
+        new ArrayList<>());
+
+    logger.info("To generate the CK, run:\n\t{}", command);
+
+    logger.info("Finished.");
+
+  }
+
+}

src/main/java/terrasaur/apps/ColorSpots.java

@@ -0,0 +1,567 @@
+package terrasaur.apps;
+
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.io.Reader;
+import java.util.*;
+import java.util.concurrent.TimeUnit;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.Options;
+import org.apache.commons.csv.CSVFormat;
+import org.apache.commons.csv.CSVRecord;
+import org.apache.commons.math3.geometry.euclidean.threed.Vector3D;
+import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics;
+import org.apache.commons.math3.util.Pair;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.spi.StandardLevel;
+import picante.math.vectorspace.VectorIJK;
+import terrasaur.smallBodyModel.SmallBodyModel;
+import terrasaur.templates.TerrasaurTool;
+import terrasaur.utils.*;
+import terrasaur.utils.math.MathConversions;
+import terrasaur.utils.mesh.TriangularFacet;
+import vtk.vtkCell;
+import vtk.vtkIdList;
+import vtk.vtkObject;
+import vtk.vtkPoints;
+import vtk.vtkPolyData;
+
+/**
+ * Read a file containing (x, y, z, value), or (lat, lon, value) along with an OBJ and write out
+ * facet, color
+ *
+ * @author nairah1
+ */
+public class ColorSpots implements TerrasaurTool {
+
+  private static final Logger logger = LogManager.getLogger();
+
+  private ColorSpots() {}
+
+  @Override
+  public String shortDescription() {
+    return "Assign values to facets in a shape model from an input dataset.";
+  }
+
+  @Override
+  public String fullDescription(Options options) {
+
+    String header = "";
+    String footer =
+        """
+
+                This program reads an OBJ file along with a CSV file containing locations and values and writes the \
+                mean value and standard deviation for each facet within a specified distance of an input point to standard \
+                out.  Latitude and longitude are specified in degrees.  Longitude is east longitude.  Units of x, y, z, and \
+                radius are the same as the units in the supplied OBJ file.
+                """;
+    return TerrasaurTool.super.fullDescription(options, header, footer);
+  }
+
+  private enum FORMAT {
+    LL,
+    LLR,
+    XYZ
+  }
+
+  private enum FIELD {
+    MIN,
+    MAX,
+    MEDIAN,
+    N,
+    RMS,
+    SUM,
+    STD,
+    VARIANCE
+  }
+
+  private vtkPolyData polyData;
+  private SmallBodyModel smallBodyModel;
+
+  public ColorSpots(vtkPolyData polyData) {
+    this.polyData = polyData;
+    this.smallBodyModel = new SmallBodyModel(polyData);
+  }
+
+  private long getXYZ(double lat, double lon, double[] pt) {
+    double[] origin = {0., 0., 0.};
+    Vector3D lookDir = new Vector3D(lon, lat);
+
+    return smallBodyModel.computeRayIntersection(origin, lookDir.toArray(), pt);
+  }
+
+  private ArrayList<double[]> readCSV(String filename, FORMAT format) {
+
+    ArrayList<double[]> returnArray = new ArrayList<>();
+
+    try (Reader in = new FileReader(filename)) {
+      Iterable<CSVRecord> records = CSVFormat.DEFAULT.parse(in);
+      for (CSVRecord record : records) {
+        double[] values = new double[4];
+        values[3] = Double.NaN;
+        if (format == FORMAT.LL) {
+          double lon = Math.toRadians(Double.parseDouble(record.get(0).trim()));
+          double lat = Math.toRadians(Double.parseDouble(record.get(1).trim()));
+
+          if (getXYZ(lat, lon, values) < 0) continue;
+          try {
+            values[3] = Double.parseDouble(record.get(2));
+          } catch (NumberFormatException e) {
+            continue;
+          }
+        } else {
+          if (format == FORMAT.LLR) {
+            double lon = Math.toRadians(Double.parseDouble(record.get(0).trim()));
+            double lat = Math.toRadians(Double.parseDouble(record.get(1).trim()));
+            double rad = Double.parseDouble(record.get(2).trim());
+            Vector3D xyz = new Vector3D(lon, lat).scalarMultiply(rad);
+            values[0] = xyz.getX();
+            values[1] = xyz.getY();
+            values[2] = xyz.getZ();
+          } else if (format == FORMAT.XYZ) {
+            values[0] = Double.parseDouble(record.get(0).trim());
+            values[1] = Double.parseDouble(record.get(1).trim());
+            values[2] = Double.parseDouble(record.get(2).trim());
+          }
+          smallBodyModel.findClosestCell(values);
+          try {
+            values[3] = Double.parseDouble(record.get(3).trim());
+          } catch (NumberFormatException e) {
+            continue;
+          }
+        }
+        returnArray.add(values);
+      }
+    } catch (IOException e) {
+      logger.error(e.getLocalizedMessage(), e);
+    }
+
+    return returnArray;
+  }
+
+  public TreeMap<Long, DescriptiveStatistics> getStatsFast(
+      ArrayList<double[]> valuesList, double radius, boolean weight, boolean atVertices) {
+    return atVertices
+        ? getStatsVertex(valuesList, radius, weight)
+        : getStatsFacet(valuesList, radius, weight);
+  }
+
+  private TreeMap<Long, DescriptiveStatistics> getStatsVertex(
+      ArrayList<double[]> valuesList, double radius, boolean weight) {
+
+    TreeMap<Long, DescriptiveStatistics> statMap = new TreeMap<>();
+    for (long i = 0; i < smallBodyModel.getSmallBodyPolyData().GetNumberOfPoints(); i++) {
+      DescriptiveStatistics stats = new DescriptiveStatistics();
+      statMap.put(i, stats);
+    }
+    // double[] xyz = new double[3];
+
+    for (double[] values : valuesList) {
+      Vector3D xyz = new Vector3D(values[0], values[1], values[2]);
+      double value = values[3];
+
+      vtkIdList pointIDs = new vtkIdList();
+      smallBodyModel.getPointLocator().FindPointsWithinRadius(radius, xyz.toArray(), pointIDs);
+      // pointIDs.InsertNextId(smallBodyModel.getPointLocator().FindClosestPoint(xyz));
+
+      for (int i = 0; i < pointIDs.GetNumberOfIds(); i++) {
+        long pointID = pointIDs.GetId(i);
+        DescriptiveStatistics stats = statMap.get(pointID);
+
+        Vector3D p = new Vector3D(smallBodyModel.getSmallBodyPolyData().GetPoint(pointID));
+        double dist = p.distance(xyz);
+
+        // cell center can be farther than radius as long as one point is closer than //
+        // radius
+        if (dist < radius) {
+          double thisValue = value;
+          if (weight) thisValue *= (1 - dist / radius);
+          stats.addValue(thisValue);
+
+          // if (thisValue < 0)
+          // System.out.printf("Cell %d dist %f radius %f xyz %f %f %f value %f thisValue %e\n",
+          // cellID, dist, radius,
+          // xyz[0], xyz[1], xyz[2],
+          // value, thisValue);
+        }
+      } // point loop
+    } // values loop
+
+    return statMap;
+  }
+
+  private TreeMap<Long, DescriptiveStatistics> getStatsFacet(
+      ArrayList<double[]> valuesList, double radius, boolean weight) {
+
+    TreeMap<Long, DescriptiveStatistics> statMap = new TreeMap<>();
+    for (long i = 0; i < smallBodyModel.getSmallBodyPolyData().GetNumberOfCells(); i++) {
+      DescriptiveStatistics stats = new DescriptiveStatistics();
+      statMap.put(i, stats);
+    }
+
+    for (double[] values : valuesList) {
+      Vector3D xyz = new Vector3D(values[0], values[1], values[2]);
+      double value = values[3];
+
+      Set<Long> cellIDs = smallBodyModel.findClosestCellsWithinRadius(xyz.toArray(), radius);
+      // cellIDs.add(smallBodyModel.findClosestCell(xyz));
+
+      for (Long cellID : cellIDs) {
+        DescriptiveStatistics stats = statMap.get(cellID);
+
+        TriangularFacet tf = PolyDataUtil.getFacet(polyData, cellID);
+        Vector3D p = MathConversions.toVector3D(tf.getCenter());
+        double dist = p.distance(xyz);
+
+        // cell center can be farther than radius as long as one point is closer than //
+        // radius
+        if (dist < radius) {
+          double thisValue = value;
+          if (weight) thisValue *= (1 - dist / radius);
+          stats.addValue(thisValue);
+
+          // if (thisValue < 0)
+          // System.out.printf("Cell %d dist %f radius %f xyz %f %f %f value %f thisValue %e\n",
+          // cellID, dist, radius,
+          // xyz[0], xyz[1], xyz[2],
+          // value, thisValue);
+        }
+      } // cell loop
+    } // values loop
+
+    return statMap;
+  }
+
+  public TreeMap<Integer, DescriptiveStatistics> getStats(
+      ArrayList<double[]> valuesList, double radius) {
+
+    // for each value, store indices of closest cells and distances
+    TreeMap<Integer, ArrayList<Pair<Long, Double>>> closestCells = new TreeMap<>();
+    for (int i = 0; i < valuesList.size(); i++) {
+      double[] values = valuesList.get(i);
+      Vector3D xyz = new Vector3D(values);
+
+      TreeSet<Long> sortedCellIDs =
+          new TreeSet<>(smallBodyModel.findClosestCellsWithinRadius(values, radius));
+      sortedCellIDs.add(smallBodyModel.findClosestCell(values));
+
+      ArrayList<Pair<Long, Double>> distances = new ArrayList<>();
+      for (long cellID : sortedCellIDs) {
+        TriangularFacet tf = PolyDataUtil.getFacet(polyData, cellID);
+        Vector3D p = MathConversions.toVector3D(tf.getCenter());
+        double dist = p.distance(xyz);
+        distances.add(Pair.create(cellID, dist));
+      }
+      closestCells.put(i, distances);
+    }
+
+    TreeMap<Integer, DescriptiveStatistics> statMap = new TreeMap<>();
+    for (int cellID = 0; cellID < polyData.GetNumberOfCells(); cellID++) {
+      DescriptiveStatistics stats = statMap.get(cellID);
+      if (stats == null) {
+        stats = new DescriptiveStatistics();
+        statMap.put(cellID, stats);
+      }
+
+      for (int i = 0; i < valuesList.size(); i++) {
+        double[] values = valuesList.get(i);
+
+        ArrayList<Pair<Long, Double>> distances = closestCells.get(i);
+        for (Pair<Long, Double> pair : distances) {
+
+          if (pair.getFirst().intValue() < cellID) continue;
+
+          if (pair.getFirst().intValue() > cellID) break;
+
+          if (pair.getFirst().intValue() == cellID) {
+            double dist = pair.getSecond();
+            if (dist < radius) {
+              double thisValue = (1 - dist / radius) * values[3];
+              stats.addValue(thisValue);
+            }
+          }
+        }
+      }
+    } // cell loop
+
+    return statMap;
+  }
+
+  public static void main(String[] args) {
+    // run the VTK garbage collector every 30 seconds
+    vtkObject.JAVA_OBJECT_MANAGER.getAutoGarbageCollector().SetScheduleTime(30, TimeUnit.SECONDS);
+    vtkObject.JAVA_OBJECT_MANAGER.getAutoGarbageCollector().SetAutoGarbageCollection(true);
+    // vtkObject.JAVA_OBJECT_MANAGER.getAutoGarbageCollector().SetDebug(true);
+
+    try {
+      ColorSpotsMain(args);
+    } catch (Exception e) {
+      logger.error(e.getLocalizedMessage(), e);
+    }
+
+    vtkObject.JAVA_OBJECT_MANAGER.getAutoGarbageCollector().SetAutoGarbageCollection(false);
+  }
+
+  private static Options defineOptions() {
+    Options options = TerrasaurTool.defineOptions();
+    options.addOption(
+        Option.builder("additionalFields")
+            .hasArg()
+            .desc(
+                "Specify additional fields to write out. Allowed values are min, max, median, n, rms, sum, std, variance. "
+                    + "More than one field may be specified in a comma separated list (e.g. "
+                    + "-additionalFields sum,median,rms).  Additional fields will be written out after the mean and std columns.")
+            .build());
+    options.addOption(
+        Option.builder("allFacets")
+            .desc(
+                "Report values for all facets in OBJ shape model, even if facet is not within searchRadius "
+                    + "of any points. Prints NaN if facet not within searchRadius.  Default is to only "
+                    + "print facets which have contributions from input points.")
+            .build());
+    options.addOption(
+        Option.builder("info")
+            .required()
+            .hasArg()
+            .desc(
+                "Required.  Name of CSV file containing value to plot."
+                    + "  Default format is lon, lat, radius, value.  See -xyz and -llOnly options for alternate formats.")
+            .build());
+    options.addOption(
+        Option.builder("llOnly").desc("Format of -info file is lon, lat, value.").build());
+    options.addOption(
+        Option.builder("logFile")
+            .hasArg()
+            .desc("If present, save screen output to log file.")
+            .build());
+    StringBuilder sb = new StringBuilder();
+    for (StandardLevel l : StandardLevel.values()) sb.append(String.format("%s ", l.name()));
+    options.addOption(
+        Option.builder("logLevel")
+            .hasArg()
+            .desc(
+                "If present, print messages above selected priority.  Valid values are "
+                    + sb.toString().trim()
+                    + ".  Default is INFO.")
+            .build());
+    options.addOption(
+        Option.builder("normalize")
+            .desc(
+                "Report values per unit area (divide by total area of facets within search ellipse).")
+            .build());
+    options.addOption(
+        Option.builder("noWeight")
+            .desc("Do not weight points by distance from facet/vertex.")
+            .build());
+    options.addOption(
+        Option.builder("obj")
+            .required()
+            .hasArg()
+            .desc("Required.  Name of shape model to read.")
+            .build());
+    options.addOption(
+        Option.builder("outFile")
+            .hasArg()
+            .desc("Specify output file to store the output.")
+            .build());
+    options.addOption(
+        Option.builder("searchRadius")
+            .hasArg()
+            .desc(
+                "Each facet will be colored using a weighted average of all points within searchRadius of the facet/vertex.  "
+                    + "If not present, set to sqrt(2)/2 * mean facet edge length.")
+            .build());
+    options.addOption(
+        Option.builder("writeVertices")
+            .desc(
+                "Convert output from a per facet to per vertex format. Each line will be of the form"
+                    + " x, y, z, value, sigma where x, y, z are the vector components of vertex V. "
+                    + " Default is to only report facetID, facet_value, facet_sigma.")
+            .build());
+    options.addOption(
+        Option.builder("xyz").desc("Format of -info file is x, y, z, value.").build());
+    return options;
+  }
+
+  public static void ColorSpotsMain(String[] args) throws Exception {
+
+    TerrasaurTool defaultOBJ = new ColorSpots();
+
+    Options options = defineOptions();
+
+    CommandLine cl = defaultOBJ.parseArgs(args, options);
+
+    Map<MessageLabel, String> startupMessages = defaultOBJ.startupMessages(cl);
+    for (MessageLabel ml : startupMessages.keySet())
+      logger.info(String.format("%s %s", ml.label, startupMessages.get(ml)));
+
+    NativeLibraryLoader.loadVtkLibraries();
+
+    final boolean writeVerts = cl.hasOption("writeVertices");
+    final boolean allFacets = cl.hasOption("allFacets");
+    final boolean normalize = cl.hasOption("normalize") && !writeVerts;
+    final boolean weight = !cl.hasOption("noWeight");
+    FORMAT format = FORMAT.LLR;
+    for (Option option : cl.getOptions()) {
+      if (option.getOpt().equals("xyz")) {
+        format = FORMAT.XYZ;
+      }
+      if (option.getOpt().equals("llOnly")) {
+        format = FORMAT.LL;
+      }
+    }
+
+    vtkPolyData polyData = PolyDataUtil.loadShapeModelAndComputeNormals(cl.getOptionValue("obj"));
+
+    double radius;
+    if (cl.hasOption("searchRadius")) {
+      radius = Double.parseDouble(cl.getOptionValue("searchRadius"));
+    } else {
+      PolyDataStatistics stats = new PolyDataStatistics(polyData);
+      radius = stats.getMeanEdgeLength() * Math.sqrt(2) / 2;
+      logger.info("Using search radius of " + radius);
+    }
+
+    ColorSpots cs = new ColorSpots(polyData);
+    ArrayList<double[]> infoValues = cs.readCSV(cl.getOptionValue("info"), format);
+    TreeMap<Long, DescriptiveStatistics> statMap =
+        cs.getStatsFast(infoValues, radius, weight, writeVerts);
+
+    double totalArea = 0;
+    if (normalize) {
+      for (int facet = 0; facet < polyData.GetNumberOfCells(); facet++) {
+        vtkCell cell = polyData.GetCell(facet);
+        vtkPoints points = cell.GetPoints();
+        double[] pt0 = points.GetPoint(0);
+        double[] pt1 = points.GetPoint(1);
+        double[] pt2 = points.GetPoint(2);
+
+        TriangularFacet tf =
+            new TriangularFacet(new VectorIJK(pt0), new VectorIJK(pt1), new VectorIJK(pt2));
+        double area = tf.getArea();
+
+        totalArea += area;
+        points.Delete();
+        cell.Delete();
+      }
+    }
+
+    ArrayList<FIELD> fields = new ArrayList<>();
+    if (cl.hasOption("additionalFields")) {
+      for (String s : cl.getOptionValue("additionalFields").trim().toUpperCase().split(",")) {
+        for (FIELD f : FIELD.values()) {
+          if (f.name().equalsIgnoreCase(s)) fields.add(f);
+        }
+      }
+    }
+
+    TreeMap<Long, ArrayList<Double>> map = new TreeMap<>();
+    long numPoints = (writeVerts ? polyData.GetNumberOfPoints() : polyData.GetNumberOfCells());
+    for (long index = 0; index < numPoints; index++) {
+      DescriptiveStatistics stats = statMap.get(index);
+      ArrayList<Double> values = new ArrayList<>();
+      if (stats != null) {
+        values.add(stats.getMean());
+        values.add(stats.getStandardDeviation());
+        for (FIELD f : fields) {
+          if (f == FIELD.MIN) values.add(stats.getMin());
+          if (f == FIELD.MAX) values.add(stats.getMax());
+          if (f == FIELD.MEDIAN) values.add(stats.getPercentile(50));
+          if (f == FIELD.N) values.add((double) stats.getN());
+          if (f == FIELD.RMS) values.add(Math.sqrt(stats.getSumsq() / stats.getN()));
+          if (f == FIELD.STD) values.add(stats.getStandardDeviation());
+          if (f == FIELD.SUM) values.add(stats.getSum());
+          if (f == FIELD.VARIANCE) values.add(stats.getVariance());
+        }
+      } else {
+        values.add(Double.NaN);
+        values.add(Double.NaN);
+        for (FIELD f : fields) {
+          if (f == FIELD.MIN) values.add(Double.NaN);
+          if (f == FIELD.MAX) values.add(Double.NaN);
+          if (f == FIELD.MEDIAN) values.add(Double.NaN);
+          if (f == FIELD.N) values.add(Double.NaN);
+          if (f == FIELD.RMS) values.add(Double.NaN);
+          if (f == FIELD.STD) values.add(Double.NaN);
+          if (f == FIELD.SUM) values.add(Double.NaN);
+          if (f == FIELD.VARIANCE) values.add(Double.NaN);
+        }
+      }
+      map.put(index, values);
+    }
+
+    ArrayList<String> returnList;
+
+    if (writeVerts) {
+      returnList = writeVertices(map, polyData, allFacets);
+    } else {
+      returnList = writeFacets(map, allFacets, normalize, totalArea);
+    }
+
+    if (cl.hasOption("outFile")) {
+      try (PrintWriter pw = new PrintWriter(cl.getOptionValue("outFile"))) {
+        for (String s : returnList) pw.println(s);
+      }
+    } else {
+      for (String string : returnList) System.out.println(string);
+    }
+  }
+
+  private static ArrayList<String> writeFacets(
+      TreeMap<Long, ArrayList<Double>> map,
+      boolean allFacets,
+      boolean normalize,
+      double totalArea) {
+
+    ArrayList<String> returnList = new ArrayList<>();
+
+    for (Long facet : map.keySet()) {
+      ArrayList<Double> values = map.get(facet);
+      Double value = values.get(0);
+      Double sigma = values.get(1);
+      if (allFacets || !value.isNaN()) {
+        if (normalize) {
+          value /= totalArea;
+          sigma /= totalArea;
+        }
+        StringBuilder sb = new StringBuilder(String.format("%d, %e, %e", facet, value, sigma));
+        for (int i = 2; i < values.size(); i++) {
+          value = values.get(i);
+          if (normalize) value /= totalArea;
+          sb.append(String.format(", %e", value));
+        }
+        returnList.add(sb.toString());
+      }
+    }
+    return returnList;
+  }
+
+  private static ArrayList<String> writeVertices(
+      TreeMap<Long, ArrayList<Double>> map, vtkPolyData polyData, boolean allFacets) {
+
+    ArrayList<String> returnList = new ArrayList<>();
+
+    double[] thisPt = new double[3];
+    for (Long vertex : map.keySet()) {
+      ArrayList<Double> values = map.get(vertex);
+      Double value = values.get(0);
+      Double sigma = values.get(1);
+      if (allFacets || !value.isNaN()) {
+        // get vertex x,y,z values
+        polyData.GetPoint(vertex, thisPt);
+        StringBuilder sb =
+            new StringBuilder(
+                String.format("%e, %e, %e, %e, %e", thisPt[0], thisPt[1], thisPt[2], value, sigma));
+        for (int i = 2; i < values.size(); i++) {
+          value = values.get(i);
+          sb.append(String.format(", %e", value));
+        }
+        returnList.add(sb.toString());
+      }
+    }
+    return returnList;
+  }
+}

src/main/java/terrasaur/apps/CreateSBMTStructure.java

@@ -0,0 +1,217 @@
+package terrasaur.apps;
+
+import java.awt.*;
+import java.io.File;
+import java.io.PrintWriter;
+import java.nio.charset.Charset;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.Options;
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.math3.geometry.euclidean.threed.Rotation;
+import org.apache.commons.math3.geometry.euclidean.threed.Vector3D;
+import org.apache.commons.math3.geometry.euclidean.twod.Vector2D;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import terrasaur.templates.TerrasaurTool;
+import terrasaur.utils.*;
+import terrasaur.utils.math.RotationUtils;
+import vtk.vtkPolyData;
+
+public class CreateSBMTStructure implements TerrasaurTool {
+
+  private static final Logger logger = LogManager.getLogger();
+
+  /**
+   * This doesn't need to be private, or even declared, but you might want to if you have other
+   * constructors.
+   */
+  private CreateSBMTStructure() {}
+
+  @Override
+  public String shortDescription() {
+    return "Construct ellipses from user-defined points on an image.";
+  }
+
+  @Override
+  public String fullDescription(Options options) {
+    String header =
+        "This tool creates an SBMT ellipse file from a set of point on an image.";
+    String footer = "";
+    return TerrasaurTool.super.fullDescription(options, header, footer);
+  }
+
+  /**
+   * Create an Ellipse as an SBMT structure from three points. The first two points define the long
+   * axis and the third point defines the short axis.
+   *
+   * @param p1 First point
+   * @param p2 Second point
+   * @param p3 Third point
+   * @return An SBMT structure describing the ellipse
+   */
+  private static SBMTEllipseRecord createRecord(
+      int id, String name, Vector3D p1, Vector3D p2, Vector3D p3) {
+    // Create a local coordinate system where X axis contains long axis and Y axis contains short
+    // axis
+
+    Vector3D origin = p1.add(p2).scalarMultiply(0.5);
+    Vector3D X = p1.subtract(p2).normalize();
+    Vector3D Y = p3.subtract(origin).normalize();
+
+    // Create a rotation matrix to go from body fixed frame to this local coordinate system
+    Rotation globalToLocal = RotationUtils.IprimaryJsecondary(X, Y);
+
+    // All of these vectors should have a Z coordinate of zero
+    Vector3D p1Local = globalToLocal.applyTo(p1);
+    Vector3D p2Local = globalToLocal.applyTo(p2);
+    Vector3D p3Local = globalToLocal.applyTo(p3);
+
+    // fit an ellipse to the three points on the plane
+    Vector2D a = new Vector2D(p1Local.getX(), p1Local.getY());
+    Vector2D b = new Vector2D(p2Local.getX(), p2Local.getY());
+    Vector2D c = new Vector2D(p3Local.getX(), p3Local.getY());
+
+    Vector2D center = a.add(b).scalarMultiply(0.5);
+    double majorAxis = a.subtract(b).getNorm();
+    double minorAxis = 2 * c.subtract(center).getNorm();
+
+    double rotation = Math.atan2(b.getY() - a.getY(), b.getX() - a.getX());
+    double flattening = (majorAxis - minorAxis) / majorAxis;
+
+    ImmutableSBMTEllipseRecord.Builder record =
+        ImmutableSBMTEllipseRecord.builder()
+            .id(id)
+            .name(name)
+            .x(origin.getX())
+            .y(origin.getY())
+            .z(origin.getZ())
+            .lat(origin.getDelta())
+            .lon(origin.getAlpha())
+            .radius(origin.getNorm())
+            .slope(0)
+            .elevation(0)
+            .acceleration(0)
+            .potential(0)
+            .diameter(majorAxis)
+            .flattening(flattening)
+            .angle(rotation)
+            .color(Color.BLACK)
+            .dummy("")
+            .label("");
+    return record.build();
+  }
+
+  private static Options defineOptions() {
+    Options options = TerrasaurTool.defineOptions();
+    options.addOption(
+        Option.builder("input")
+            .required()
+            .hasArg()
+            .desc(
+                """
+Required.  Name or input file.  This is a text file with a pair of pixel coordinates per line.  The pixel
+coordinates are offsets from the image center. For example:
+
+# My test file
+
+627.51274 876.11775
+630.53612 883.55992
+626.3499 881.46681
+
+Empty lines or lines beginning with # are ignored.
+
+Each set of three points are used to create the SBMT structures.  The first two points are the long
+axis and the third is a location for the semi-minor axis.""")
+            .build());
+    options.addOption(
+        Option.builder("objFile")
+            .required()
+            .hasArg()
+            .desc("Required.  Name of OBJ shape file.")
+            .build());
+    options.addOption(
+        Option.builder("output")
+            .required()
+            .hasArg()
+            .desc("Required.  Name of output file.")
+            .build());
+    options.addOption(
+        Option.builder("sumFile")
+            .required()
+            .hasArg()
+            .desc("Required.  Name of sum file to read.")
+            .build());
+    return options;
+  }
+
+  public static void main(String[] args) {
+    TerrasaurTool defaultOBJ = new CreateSBMTStructure();
+
+    Options options = defineOptions();
+
+    CommandLine cl = defaultOBJ.parseArgs(args, options);
+
+    Map<MessageLabel, String> startupMessages = defaultOBJ.startupMessages(cl);
+    for (MessageLabel ml : startupMessages.keySet())
+      logger.info(String.format("%s %s", ml.label, startupMessages.get(ml)));
+
+    NativeLibraryLoader.loadSpiceLibraries();
+    NativeLibraryLoader.loadVtkLibraries();
+
+    SumFile sumFile = SumFile.fromFile(new File(cl.getOptionValue("sumFile")));
+
+    try {
+      String objFile = cl.getOptionValue("objFile");
+      vtkPolyData polyData = PolyDataUtil.loadShapeModel(objFile);
+      if (polyData == null) {
+        logger.error("Cannot read shape model {}!", objFile);
+        System.exit(0);
+      }
+      RangeFromSumFile rfsf = new RangeFromSumFile(sumFile, polyData);
+
+      List<Vector3D> intercepts = new ArrayList<>();
+      List<String> lines =
+          FileUtils.readLines(new File(cl.getOptionValue("input")), Charset.defaultCharset());
+      for (String line :
+          lines.stream().filter(s -> !(s.isBlank() || s.strip().startsWith("#"))).toList()) {
+        String[] parts = line.split("\\s+");
+        int ix = (int) Math.round(Double.parseDouble(parts[0]));
+        int iy = (int) Math.round(Double.parseDouble(parts[1]));
+
+        Map.Entry<Long, Vector3D> entry = rfsf.findIntercept(ix, iy);
+        long cellID = entry.getKey();
+        if (cellID > -1) intercepts.add(entry.getValue());
+      }
+
+      logger.info("Found {} sets of points", intercepts.size() / 3);
+
+      List<SBMTEllipseRecord> records = new ArrayList<>();
+      for (int i = 0; i < intercepts.size(); i += 3) {
+
+        // p1 and p2 define the long axis of the ellipse
+        Vector3D p1 = intercepts.get(i);
+        Vector3D p2 = intercepts.get(i+1);
+
+        // p3 lies on the short axis
+        Vector3D p3 = intercepts.get(i+2);
+
+        SBMTEllipseRecord record = createRecord(i/3, String.format("Ellipse %d", i/3), p1, p2, p3);
+        records.add(record);
+      }
+
+      try (PrintWriter pw = new PrintWriter(cl.getOptionValue("output"))) {
+        for (SBMTEllipseRecord record : records) pw.println(record.toString());
+      }
+      logger.info("Wrote {}", cl.getOptionValue("output"));
+    } catch (Exception e) {
+      logger.error(e.getLocalizedMessage(), e);
+      throw new RuntimeException(e);
+    }
+
+    logger.info("Finished");
+  }
+}

src/main/java/terrasaur/apps/DSK2OBJ.java

@@ -0,0 +1,196 @@
+package terrasaur.apps;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.PrintWriter;
+import java.util.Map;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.Options;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.spi.StandardLevel;
+import spice.basic.Body;
+import spice.basic.CSPICE;
+import spice.basic.DLADescriptor;
+import spice.basic.DSK;
+import spice.basic.DSKDescriptor;
+import spice.basic.SpiceException;
+import spice.basic.Surface;
+import terrasaur.templates.TerrasaurTool;
+
+public class DSK2OBJ implements TerrasaurTool {
+
+  private static final Logger logger = LogManager.getLogger();
+
+  @Override
+  public String shortDescription() {
+    return "Create an OBJ from a DSK.";
+  }
+
+  @Override
+  public String fullDescription(Options options) {
+    String header = "";
+    String footer = "\nCreate an OBJ from a DSK.\n";
+    return TerrasaurTool.super.fullDescription(options, header, footer);
+  }
+
+  private static Options defineOptions() {
+    Options options = TerrasaurTool.defineOptions();
+    options.addOption(
+        Option.builder("body")
+            .hasArg()
+            .desc(
+                "If present, convert shape for named body.  Default is to use the first body in the DSK.")
+            .build());
+    options.addOption(
+        Option.builder("dsk").hasArg().required().desc("Required.  Name of input DSK.").build());
+    options.addOption(
+        Option.builder("logFile")
+            .hasArg()
+            .desc("If present, save screen output to log file.")
+            .build());
+    StringBuilder sb = new StringBuilder();
+    for (StandardLevel l : StandardLevel.values()) sb.append(String.format("%s ", l.name()));
+    options.addOption(
+        Option.builder("logLevel")
+            .hasArg()
+            .desc(
+                "If present, print messages above selected priority.  Valid values are "
+                    + sb.toString().trim()
+                    + ".  Default is INFO.")
+            .build());
+    options.addOption(Option.builder("obj").hasArg().desc("Name of output OBJ.").build());
+    options.addOption(
+        Option.builder("printBodies")
+            .desc("If present, print bodies and surface ids in DSK.")
+            .build());
+    options.addOption(
+        Option.builder("surface")
+            .hasArg()
+            .desc(
+                "If present, use specified surface id.  Default is to use the first surface id for the body.")
+            .build());
+    return options;
+  }
+
+  public static void main(String[] args) {
+    TerrasaurTool defaultOBJ = new DSK2OBJ();
+
+    Options options = defineOptions();
+
+    CommandLine cl = defaultOBJ.parseArgs(args, options);
+
+    Map<MessageLabel, String> startupMessages = defaultOBJ.startupMessages(cl);
+    for (MessageLabel ml : startupMessages.keySet())
+      logger.info(String.format("%s %s", ml.label, startupMessages.get(ml)));
+
+    System.loadLibrary("JNISpice");
+
+    String dskName = cl.getOptionValue("dsk");
+    File dskFile = new File(dskName);
+    if (!dskFile.exists()) {
+      logger.warn("Input DSK " + dskName + "does not exist!");
+      System.exit(0);
+    }
+
+    try {
+      DSK dsk = DSK.openForRead(dskName);
+      Body[] bodies = dsk.getBodies();
+
+      if (cl.hasOption("printBodies")) {
+        logger.info("found bodies and surface ids:");
+        for (int i = 0; i < bodies.length; i++) {
+          Body b = bodies[i];
+          Surface[] surfaces = dsk.getSurfaces(b);
+          StringBuilder sb = new StringBuilder();
+          sb.append(String.format("%d) %s", i, b.getName()));
+          for (Surface s : surfaces) sb.append(String.format(" %d", s.getIDCode()));
+          logger.info(sb.toString());
+        }
+      }
+
+      Body b = cl.hasOption("body") ? new Body(cl.getOptionValue("body")) : bodies[0];
+      boolean missingBody = true;
+      for (Body body : bodies) {
+        if (b.equals(body)) {
+          missingBody = false;
+          break;
+        }
+      }
+      if (missingBody) {
+        logger.warn(String.format("Body %s not found in DSK!  Valid bodies are:", b.getName()));
+        for (Body body : bodies) logger.warn(body.getName());
+        System.exit(0);
+      }
+
+      Surface[] surfaces = dsk.getSurfaces(b);
+      Surface s =
+          cl.hasOption("surface")
+              ? new Surface(Integer.parseInt(cl.getOptionValue("surface")), b)
+              : surfaces[0];
+      boolean missingSurface = true;
+      for (Surface surface : surfaces) {
+        if (s.equals(surface)) {
+          missingSurface = false;
+          break;
+        }
+      }
+      if (missingSurface) {
+        logger.warn(
+            String.format(
+                "Surface %d for body %s not found in DSK!  Valid surfaces are:",
+                s.getIDCode(), b.getName()));
+        for (Surface surface : surfaces) logger.warn(Integer.toString(surface.getIDCode()));
+        System.exit(0);
+      }
+
+      DLADescriptor dladsc = dsk.beginBackwardSearch();
+      boolean found = true;
+      while (found) {
+
+        DSKDescriptor dskdsc = dsk.getDSKDescriptor(dladsc);
+
+        if (b.getIDCode() == dskdsc.getCenterID() && s.getIDCode() == dskdsc.getSurfaceID()) {
+
+          // number of plates and vertices
+          int[] np = new int[1];
+          int[] nv = new int[1];
+          CSPICE.dskz02(dsk.getHandle(), dladsc.toArray(), nv, np);
+
+          double[][] vertices = CSPICE.dskv02(dsk.getHandle(), dladsc.toArray(), 1, nv[0]);
+          int[][] plates = CSPICE.dskp02(dsk.getHandle(), dladsc.toArray(), 1, np[0]);
+
+          if (cl.hasOption("obj")) {
+            try (PrintWriter pw = new PrintWriter(cl.getOptionValue("obj"))) {
+              for (double[] v : vertices) {
+                pw.printf("v %20.16f %20.16f %20.16f\r\n", v[0], v[1], v[2]);
+              }
+              for (int[] p : plates) {
+                pw.printf("f %d %d %d\r\n", p[0], p[1], p[2]);
+              }
+              logger.info(
+                  String.format(
+                      "Wrote %d vertices and %d plates to %s for body %d surface %d",
+                      nv[0],
+                      np[0],
+                      cl.getOptionValue("obj"),
+                      dskdsc.getCenterID(),
+                      dskdsc.getSurfaceID()));
+            } catch (FileNotFoundException e) {
+              logger.warn(e.getLocalizedMessage());
+            }
+          }
+        }
+
+        found = dsk.hasPrevious(dladsc);
+        if (found) {
+          dladsc = dsk.getPrevious(dladsc);
+        }
+      }
+
+    } catch (SpiceException e) {
+      logger.warn(e.getLocalizedMessage());
+    }
+  }
+}

src/main/java/terrasaur/apps/DifferentialVolumeEstimator.java

@@ -0,0 +1,995 @@
+package terrasaur.apps;
+
+import java.awt.geom.Path2D;
+import java.awt.geom.Point2D;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.PrintWriter;
+import java.nio.charset.Charset;
+import java.util.AbstractMap;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.NavigableMap;
+import java.util.NavigableSet;
+import java.util.Set;
+import java.util.TreeMap;
+import java.util.TreeSet;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.Options;
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.FilenameUtils;
+import org.apache.commons.math3.geometry.euclidean.threed.Rotation;
+import org.apache.commons.math3.geometry.euclidean.threed.Vector3D;
+import org.apache.commons.math3.util.Pair;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import picante.math.vectorspace.RotationMatrixIJK;
+import terrasaur.smallBodyModel.SBMTStructure;
+import terrasaur.smallBodyModel.SmallBodyModel;
+import terrasaur.templates.TerrasaurTool;
+import terrasaur.utils.*;
+import terrasaur.utils.math.MathConversions;
+import vtk.vtkCellArray;
+import vtk.vtkDoubleArray;
+import vtk.vtkIdList;
+import vtk.vtkPoints;
+import vtk.vtkPolyData;
+import vtk.vtkPolyDataWriter;
+
+/**
+ * Given a reference surface (either from a shape model or a set of points), find a best fit
+ * reference plane. Find the height above this plane for the reference surface and an input shape
+ * model. Report the differential height and volume between these two surfaces on a uniform grid.
+ * <p>
+ * This class uses three coordinate systems:
+ * <ul>
+ * <li>The global coordinate system. This is the coordinate system of the input data.</li>
+ * <li>The local coordinate system. This has the X and Y axes in the best fit plane to the reference
+ * data. The origin is optionally set by the user.</li>
+ * <li>The native coordinate system. This is not seen by the user. The XY plane is the same as the
+ * local coordinate system, but the origin may be translated and there may be a rotation applied
+ * about the Z axis.</li>
+ * </ul>
+ * 
+ * @author Hari.Nair@jhuapl.edu
+ *
+ */
+public class DifferentialVolumeEstimator implements TerrasaurTool {
+
+  private static final Logger logger = LogManager.getLogger();
+
+  private DifferentialVolumeEstimator() {}
+
+
+  @Override
+  public String shortDescription() {
+      return "Find volume difference between two shape models.";
+  }
+
+  // degree of polynomial used to fit surface
+  private final int POLYNOMIAL_DEGREE = 2;
+
+  @Override
+  public String fullDescription(Options options) {
+		String header = "";
+		String footer = "\nThis program finds the volume difference between a shape model and a reference surface.  "
+		    +"The reference surface can either be another shape model or a degree "+POLYNOMIAL_DEGREE+" fit to a set of supplied points.  "+
+		    "A local coordinate system is derived from the reference surface.  The heights of the shape and reference at "+
+		    "each grid point are reported. ";
+    return TerrasaurTool.super.fullDescription(options, header, footer);
+
+  }
+
+
+
+  /** input shape model */
+  private vtkPolyData globalPolyData;
+  /** shape model in native coordinates */
+  private SmallBodyModel nativeSBM;
+  /** number of radial profiles */
+  private Integer numProfiles;
+
+  public void setNumProfiles(Integer numProfiles) {
+    this.numProfiles = numProfiles;
+  }
+
+  /** true if local +Z is aligned with the center radial direction */
+  private boolean radialUp;
+
+  public void setRadialUp(boolean radialUp) {
+    this.radialUp = radialUp;
+  }
+
+  /** reference points in global coordinates */
+  private List<Vector3D> referencePoints;
+
+  public void setReferencePoints(List<Vector3D> referencePoints) {
+    this.referencePoints = referencePoints;
+  }
+
+  /** reference model in global coordinates */
+  private vtkPolyData referencePolyData;
+
+  public void setReferencePolyData(vtkPolyData referencePolyData) {
+    this.referencePolyData = referencePolyData;
+  }
+
+  /** Reference shape in native coordinates */
+  private SmallBodyModel referenceSBM;
+  /** reference surface in native coordinates */
+  private FitSurface referenceSurface;
+
+  private double gridSpacing;
+  private double gridHalfExtent;
+
+  /** global coordinates of the highest point of the shape model */
+  private Vector3D highPoint;
+  /** global coordinates of the lowest point of the shape model */
+  private Vector3D lowPoint;
+
+  /** this plane converts coordinates from native to global and back */
+  private FitPlane plane;
+
+  /** Inner edge of the ROI */
+  private Path2D.Double roiInner;
+  /** Outer edge of the ROI */
+  private Path2D.Double roiOuter;
+
+  // local grid is in the same plane as native grid but is translated and rotated
+  private Entry<Rotation, Vector3D> nativeToLocal;
+
+  // the origin of the local coordinate system, in global coordinates
+  private enum ORIGIN {
+    MIN_HEIGHT, MAX_HEIGHT, CUSTOM, DEFAULT
+  }
+
+  public Vector3D nativeToLocal(Vector3D nativeIJK) {
+      return nativeToLocal.getKey().applyTo(nativeIJK.subtract(nativeToLocal.getValue()));
+  }
+
+  public Vector3D localToNative(Vector3D local) {
+      return nativeToLocal.getKey().applyInverseTo(local).add(nativeToLocal.getValue());
+  }
+
+  /**
+   * Set the inner boundary of the ROI
+   * 
+   * @param filename file containing points in global coordinates
+   */
+  public void setInnerROI(String filename) {
+    List<Vector3D> points = readPointsFromFile(filename);
+    roiInner = createOutline(points);
+  }
+
+  /**
+   * Set the outer boundary of the ROI
+   * 
+   * @param filename file containing points in global coordinates
+   */
+  public void setOuterROI(String filename) {
+    List<Vector3D> points = readPointsFromFile(filename);
+    roiOuter = createOutline(points);
+  }
+
+  /**
+   * Construct an outline on the local grid from a list of points in global coordinates.
+   * 
+   * @param points points in global coordinates
+   * @return outline on local grid
+   */
+  private Path2D.Double createOutline(List<Vector3D> points) {
+
+    Path2D.Double outline = new Path2D.Double();
+    for (int i = 0; i < points.size(); i++) {
+      Vector3D nativeIJK = plane.globalToLocal(points.get(i));
+      Vector3D localIJK =
+          nativeToLocal.getKey().applyTo(nativeIJK.subtract(nativeToLocal.getValue()));
+      if (i == 0) {
+        outline.moveTo(localIJK.getX(), localIJK.getY());
+      } else {
+        outline.lineTo(localIJK.getX(), localIJK.getY());
+      }
+    }
+    outline.closePath();
+
+    return outline;
+  }
+
+  public DifferentialVolumeEstimator(vtkPolyData polyData) {
+    this.globalPolyData = polyData;
+    this.referencePolyData = null;
+    this.referencePoints = null;
+    this.numProfiles = 0;
+    this.radialUp = false;
+  }
+
+  /**
+   * Get the height of the shape model above the reference plane
+   * 
+   * @param x in native coordinates
+   * @param y in native coordinates
+   * @return height, or {@link Double#NaN} if no intersection found
+   */
+  public double getHeight(double x, double y) {
+
+    double height = Double.NaN;
+    double[] origin = {x, y, 0};
+    double[] direction = {0, 0, 1};
+    double[] intersect = new double[3];
+
+    long cellID = nativeSBM.computeRayIntersection(origin, direction, intersect);
+    if (cellID < 0) {
+      direction[2] = -1;
+      cellID = nativeSBM.computeRayIntersection(origin, direction, intersect);
+    }
+    if (cellID >= 0)
+      height = direction[2] * new Vector3D(origin).distance(new Vector3D(intersect));
+
+    if (Double.isNaN(height))
+      return Double.NaN;
+
+    return height;
+  }
+
+  /**
+   * Get the height of the reference surface above the reference plane.
+   * 
+   * @param x in native coordinates
+   * @param y in native coordinates
+   * @return height of surface at (x,y) above reference plane
+   */
+  public double getRefHeight(double x, double y) {
+
+    double[] origin = {x, y, 0};
+    double[] direction = {0, 0, 1};
+    double[] intersect;
+
+    double refHeight = Double.NaN;
+    if (referenceSBM != null) {
+      intersect = new double[3];
+
+      long cellID = referenceSBM.computeRayIntersection(origin, direction, intersect);
+      if (cellID < 0) {
+        direction[2] = -1;
+        cellID = referenceSBM.computeRayIntersection(origin, direction, intersect);
+      }
+      if (cellID >= 0) {
+        refHeight = direction[2] * new Vector3D(origin).distance(new Vector3D(intersect));
+      }
+    } else {
+      refHeight = referenceSurface.value(x, y);
+    }
+
+    if (Double.isNaN(refHeight))
+      return Double.NaN;
+
+    return refHeight;
+  }
+
+  /**
+   * Create an array of grid points with heights
+   * 
+   * @param gridHalfExtent half-size of grid
+   * @param gridSpacing spacing between points
+   * @return grid points sorted by x coordinate, then y
+   */
+  private NavigableSet<GridPoint> createGrid(double gridHalfExtent, double gridSpacing) {
+    Set<Vector3D> localGrid = new HashSet<>();
+
+    for (double x = 0; x <= gridHalfExtent; x += gridSpacing) {
+      for (double y = 0; y <= gridHalfExtent; y += gridSpacing) {
+        localGrid.add(new Vector3D(x, y, 0));
+        if (y != 0)
+          localGrid.add(new Vector3D(x, -y, 0));
+        if (x != 0)
+          localGrid.add(new Vector3D(-x, y, 0));
+        if (x != 0 && y != 0)
+          localGrid.add(new Vector3D(-x, -y, 0));
+      }
+    }
+    this.gridSpacing = gridSpacing;
+    this.gridHalfExtent=gridHalfExtent;
+
+    GridPoint highGridPoint = null;
+    GridPoint lowGridPoint = null;
+    NavigableSet<GridPoint> gridPoints = new TreeSet<>();
+    for (Vector3D localPoint : localGrid) {
+      GridPoint gp = new GridPoint(localPoint);
+      gridPoints.add(gp);
+      if (Double.isFinite(gp.height)) {
+        if (highGridPoint == null || highGridPoint.height < gp.height)
+          highGridPoint = gp;
+        if (lowGridPoint == null || lowGridPoint.height > gp.height)
+          lowGridPoint = gp;
+      }
+    }
+
+    if (highGridPoint != null)
+      highPoint = highGridPoint.globalIJK;
+    if (lowGridPoint != null)
+      lowPoint = lowGridPoint.globalIJK;
+
+    return gridPoints;
+  }
+
+  /**
+   * Create the reference surface, either from a fit to a set of points or from an input shape
+   * model.
+   * 
+   * @param localOriginInGlobalCoordinates local origin in global coordinates
+   */
+  public void createReference(Vector3D localOriginInGlobalCoordinates) {
+
+    double[] pt = new double[3];
+
+    if (referencePolyData != null) {
+      if (referencePoints != null) {
+        logger.warn(
+            "Both -referenceList and -referenceShape were specified.  Reference surface will be set to argument of -referenceShape.");
+      }
+      referencePoints = new ArrayList<>();
+      for (int i = 0; i < referencePolyData.GetNumberOfPoints(); i++) {
+        referencePolyData.GetPoint(i, pt);
+        referencePoints.add(new Vector3D(pt));
+      }
+    }
+
+    // this is the best fit plane to the reference points. It can convert points in input
+    // (global) coordinates to native coordinates and vice versa
+    plane = new FitPlane(referencePoints);
+
+    // set the +Z direction for the local plane
+    Vector3D referenceNormal = radialUp ? plane.getTransform().getValue() : Vector3D.PLUS_K;
+
+    // check if the plane normal is pointing in the same direction as the reference normal. If not,
+    // flip the plane
+    Pair<Rotation, Vector3D> transform = plane.getTransform();
+    Vector3D planeNormal = transform.getKey().applyInverseTo(referenceNormal);
+    if (planeNormal.dotProduct(referenceNormal) < 0)
+      plane = plane.reverseNormal();
+
+    // create the SmallBodyModel for the shape to evaluate
+    vtkPolyData nativePolyData = new vtkPolyData();
+    nativePolyData.DeepCopy(globalPolyData);
+    vtkPoints points = nativePolyData.GetPoints();
+    for (int i = 0; i < points.GetNumberOfPoints(); i++) {
+      points.GetPoint(i, pt);
+      Vector3D nativePoint = plane.globalToLocal(new Vector3D(pt));
+      double[] data = nativePoint.toArray();
+      points.SetPoint(i, data);
+    }
+    nativeSBM = new SmallBodyModel(nativePolyData);
+
+    // now define the reference shape/surface
+    if (referencePolyData != null) {
+      // create the SmallBodyModel for the reference shape
+      nativePolyData = new vtkPolyData();
+      nativePolyData.DeepCopy(referencePolyData);
+      points = nativePolyData.GetPoints();
+      for (int i = 0; i < points.GetNumberOfPoints(); i++) {
+        points.GetPoint(i, pt);
+        Vector3D nativePoint = plane.globalToLocal(new Vector3D(pt));
+        double[] data = nativePoint.toArray();
+        points.SetPoint(i, data);
+      }
+
+      referenceSBM = new SmallBodyModel(nativePolyData);
+    } else {
+      // create the reference surface
+      List<Vector3D> nativePoints = new ArrayList<>();
+      for (Vector3D v : referencePoints) {
+        Vector3D nativePoint = plane.globalToLocal(v);
+        nativePoints.add(nativePoint);
+      }
+
+      referenceSurface = new FitSurface(nativePoints, POLYNOMIAL_DEGREE);
+    }
+
+    // create a rotation matrix to go from native to local (where the Z axis is the same for both
+    // and the X axis is aligned in the same direction as the global X axis)
+    Pair<Rotation, Vector3D> globalToLocalTransform = plane.getTransform();
+    Vector3D kRow = Vector3D.PLUS_K;
+    Vector3D iRow = globalToLocalTransform.getKey().applyTo(Vector3D.PLUS_I);
+    Vector3D jRow = Vector3D.crossProduct(kRow, iRow).normalize();
+    kRow = Vector3D.crossProduct(iRow, jRow).normalize();
+    iRow = iRow.normalize();
+
+    Vector3D translateNativeToLocal = Vector3D.ZERO;
+    if (localOriginInGlobalCoordinates.getNorm() > 0) {
+      // translation to go from native to local (where localOriginInGlobalCoordinates defines 0,0 in
+      // the local frame)
+      Vector3D nativeOriginInGlobalCoordinates = plane.localToGlobal(Vector3D.ZERO);
+      Vector3D translateNativeToLocalInGlobalCoordinates =
+          localOriginInGlobalCoordinates.subtract(nativeOriginInGlobalCoordinates);
+      // TODO: check that the Z component is zero (it should be?)
+      translateNativeToLocal =
+          globalToLocalTransform.getKey().applyTo(translateNativeToLocalInGlobalCoordinates);
+    }
+
+    Rotation rotateNativeToLocal =
+        MathConversions.toRotation(new RotationMatrixIJK(iRow.getX(), jRow.getX(), kRow.getX(),
+            iRow.getY(), jRow.getY(), kRow.getY(), iRow.getZ(), jRow.getZ(), kRow.getZ()));
+
+    this.nativeToLocal = new AbstractMap.SimpleEntry<>(rotateNativeToLocal, translateNativeToLocal);
+  }
+
+  /**
+   * The header for grid and profile CSV files. Each line begins with a #
+   * 
+   * @param header string at beginning of header
+   * @return complete header
+   */
+  public static String getHeader(String header) {
+    StringBuffer sb = new StringBuffer();
+    sb.append(header);
+    sb.append("# Local X and Y are grid coordinates in the local reference frame\n");
+    sb.append("# Angle is measured from the local X axis, in degrees\n");
+    sb.append("# ROI flag is 1 if point is in the region of interest, 0 if not\n");
+    sb.append("# Global X, Y, and Z are the local grid points in the global "
+        + " (input) reference system\n");
+    sb.append("# Reference Height is the height of the reference model (or fit surface) above "
+        + "the local grid plane\n");
+    sb.append("# Model Height is the height of the shape model above the local grid plane.  "
+        + "NaN means there is no model intersection at this grid point.\n");
+    sb.append("# Bin volume is the grid cell area times the model - reference height\n");
+    sb.append("#\n");
+    sb.append(String.format("%s, ", "Local X"));
+    sb.append(String.format("%s, ", "Local Y"));
+    sb.append(String.format("%s, ", "Angle"));
+    sb.append(String.format("%s, ", "ROI Flag"));
+    sb.append(String.format("%s, ", "Global X"));
+    sb.append(String.format("%s, ", "Global Y"));
+    sb.append(String.format("%s, ", "Global Z"));
+    sb.append(String.format("%s, ", "Reference Height"));
+    sb.append(String.format("%s, ", "Model Height"));
+    sb.append(String.format("%s, ", "Model - Reference"));
+    sb.append(String.format("%s", "Bin Volume"));
+    return sb.toString();
+  }
+
+
+  /**
+   * The header for the sector CSV file. Each line begins with a #
+   *
+   * @param header string at beginning of header
+   * @return complete header
+   */
+  public static String getSectorHeader(String header) {
+    StringBuilder sb = new StringBuilder();
+    sb.append(header);
+    sb.append("# Angle is measured from the local X axis, in degrees\n");
+    sb.append(
+        "# Sector volume is the grid cell area times the model - reference height summed over all grid cells in the ROI.\n");
+    sb.append("#\n");
+    sb.append(String.format("%s, ", "Index"));
+    sb.append(String.format("%s, ", "Start angle (degrees)"));
+    sb.append(String.format("%s, ", "Stop angle (degrees)"));
+    sb.append(String.format("%s, ", "Sector Volume above reference surface"));
+    sb.append(String.format("%s, ", "Sector Volume below reference surface"));
+    sb.append(String.format("%s", "Total Sector Volume"));
+
+    return sb.toString();
+  }
+
+  private String toCSV(GridPoint gp) {
+    StringBuilder sb = new StringBuilder();
+
+    sb.append(String.format("%f, ", gp.localIJK.getX()));
+    sb.append(String.format("%f, ", gp.localIJK.getY()));
+
+    double angle = Math.toDegrees(Math.atan2(gp.localIJK.getY(), gp.localIJK.getX()));
+    if (angle < 0)
+      angle += 360;
+    sb.append(String.format("%f, ", angle));
+    sb.append(String.format("%d, ", isInsideROI(gp.localIJK) ? 1 : 0));
+
+    sb.append(String.format("%f, ", gp.globalIJK.getX()));
+    sb.append(String.format("%f, ", gp.globalIJK.getY()));
+    sb.append(String.format("%f, ", gp.globalIJK.getZ()));
+
+    sb.append(String.format("%g, ", gp.referenceHeight));
+    sb.append(String.format("%g, ", gp.height));
+    sb.append(String.format("%g, ", gp.differentialHeight));
+    sb.append(String.format("%g", gridSpacing * gridSpacing * gp.differentialHeight));
+
+    return sb.toString();
+  }
+
+  /**
+   *
+   * @param localIJ Point on the local grid.  The Z coordinate is ignored
+   * @return true if the point is inside the outer boundary and outside the inner boundary. If the
+   *     outer boundary is null then all points are considered to be inside the outer boundary. If the
+   *     inner boundary is null all points are considered to be outside the inner boundary.
+   */
+  private boolean isInsideROI(Vector3D localIJ) {
+    Point2D thisPoint = new Point2D.Double(localIJ.getX(), localIJ.getY());
+    boolean insideROI = roiOuter == null || roiOuter.contains(thisPoint);
+    if (roiInner != null) {
+      if (insideROI && roiInner.contains(thisPoint))
+        insideROI = false;
+    }
+    return insideROI;
+  }
+
+  /**
+   * Write out a VTK file with the local grid points. Useful for a sanity check.
+   * 
+   * @param gridPointsList grid points
+   * @param profilesMap grid points along each profile
+   * @param sectorsMap grid points within each sector
+   * @param vtkFile file to write
+   */
+  private void writeReferenceVTK(Collection<GridPoint> gridPointsList,
+      Map<Integer, Collection<GridPoint>> profilesMap,
+      Map<Integer, Collection<GridPoint>> sectorsMap, String vtkFile) {
+
+    Map<Vector3D, Boolean> roiMap = new HashMap<>();
+    Map<Vector3D, Integer> profileMap = new HashMap<>();
+    Map<Vector3D, Integer> sectorMap = new HashMap<>();
+
+    for (GridPoint gp : gridPointsList) {
+      Vector3D localIJK = gp.localIJK;
+      Vector3D nativeIJK =
+          nativeToLocal.getKey().applyInverseTo(localIJK).add(nativeToLocal.getValue());
+      Vector3D globalIJK = plane.localToGlobal(nativeIJK);
+      roiMap.put(globalIJK, isInsideROI(gp.localIJK));
+      profileMap.put(globalIJK, 0);
+      sectorMap.put(globalIJK, 0);
+    }
+
+    for (int i : profilesMap.keySet()) {
+      for (GridPoint gp : profilesMap.get(i)) {
+        Vector3D localIJK = gp.localIJK;
+        Vector3D nativeIJK =
+            nativeToLocal.getKey().applyInverseTo(localIJK).add(nativeToLocal.getValue());
+        Vector3D globalIJK = plane.localToGlobal(nativeIJK);
+        profileMap.put(globalIJK, i + 1);
+      }
+    }
+
+    for (int i : sectorsMap.keySet()) {
+      for (GridPoint gp : sectorsMap.get(i)) {
+        Vector3D localIJK = gp.localIJK;
+        Vector3D nativeIJK =
+            nativeToLocal.getKey().applyInverseTo(localIJK).add(nativeToLocal.getValue());
+        Vector3D globalIJK = plane.localToGlobal(nativeIJK);
+        sectorMap.put(globalIJK, i + 1);
+      }
+    }
+
+    vtkDoubleArray insideROI = new vtkDoubleArray();
+    insideROI.SetName("Inside ROI");
+
+    vtkDoubleArray profiles = new vtkDoubleArray();
+    profiles.SetName("Profiles");
+
+    vtkDoubleArray sectors = new vtkDoubleArray();
+    sectors.SetName("Sectors");
+
+    vtkPoints pointsXYZ = new vtkPoints();
+    for (Vector3D point : roiMap.keySet()) {
+      double[] array = point.toArray();
+      pointsXYZ.InsertNextPoint(array);
+      insideROI.InsertNextValue(roiMap.get(point) ? 1 : 0);
+      profiles.InsertNextValue(profileMap.get(point));
+      sectors.InsertNextValue(sectorMap.get(point));
+    }
+
+    vtkPolyData polyData = new vtkPolyData();
+    polyData.SetPoints(pointsXYZ);
+    polyData.GetPointData().AddArray(insideROI);
+    polyData.GetPointData().AddArray(profiles);
+    polyData.GetPointData().AddArray(sectors);
+
+    vtkCellArray cells = new vtkCellArray();
+    polyData.SetPolys(cells);
+
+    for (int i = 0; i < pointsXYZ.GetNumberOfPoints(); i++) {
+      vtkIdList idList = new vtkIdList();
+      idList.InsertNextId(i);
+      cells.InsertNextCell(idList);
+    }
+
+    vtkPolyDataWriter writer = new vtkPolyDataWriter();
+    writer.SetInputData(polyData);
+    writer.SetFileName(vtkFile);
+    writer.SetFileTypeToBinary();
+    writer.Update();
+  }
+
+  /**
+   * Write the local grid out to a file
+   * 
+   * @param gridPoints grid points
+   * @param header file header
+   * @param outputBasename CSV file to write
+   */
+  private void writeGridCSV(Collection<GridPoint> gridPoints, String header, String outputBasename) {
+    String csvFile = outputBasename + "_grid.csv";
+
+    try (PrintWriter pw = new PrintWriter(csvFile)) {
+      pw.println(getHeader(header));
+      for (GridPoint gp : gridPoints)
+        pw.println(toCSV(gp));
+    } catch (FileNotFoundException e) {
+      logger.warn("Can't write " + csvFile);
+      logger.warn(e.getLocalizedMessage());
+    }
+  }
+
+  /**
+   * Write profiles to file
+   * 
+   * @param gridPoints grid points
+   * @param header file header
+   * @param outputBasename CSV file to write
+   */
+  private Map<Integer, Collection<GridPoint>> writeProfileCSV(Collection<GridPoint> gridPoints,
+      String header, String outputBasename) {
+    Map<Integer, Collection<GridPoint>> profileMap = new HashMap<>();
+
+    if (numProfiles == 0)
+      return profileMap;
+
+    // sort grid points into radial bins
+    NavigableMap<Integer, Set<GridPoint>> radialMap = new TreeMap<>();
+    for (GridPoint gp : gridPoints) {
+      double radius = gp.localIJK.getNorm() / gridSpacing;
+      int key = (int) radius;
+      Set<GridPoint> set = radialMap.computeIfAbsent(key, k -> new HashSet<>());
+        set.add(gp);
+    }
+
+    final double deltaAngle = 2 * Math.PI / numProfiles;
+    for (int i = 0; i < numProfiles; i++) {
+
+      Collection<GridPoint> profileGridPoints = new HashSet<>();
+      profileMap.put(i, profileGridPoints);
+
+      double angle = deltaAngle * i;
+      String csvFile = String.format("%s_profile_%03d.csv", outputBasename,
+          (int) Math.round(Math.toDegrees(angle)));
+
+      try (PrintWriter pw = new PrintWriter(csvFile)) {
+        pw.println(getHeader(header));
+        for (int bin : radialMap.keySet()) {
+
+          // stop profile at grid edge
+          double thisX = Math.abs(Math.cos(angle) * bin) * gridSpacing;
+          if (thisX > gridHalfExtent) continue;
+          double thisY = Math.abs(Math.sin(angle) * bin) * gridSpacing;
+          if (thisY > gridHalfExtent) continue;
+
+          // sort points in this radial bin by angular distance from profile angle
+          NavigableSet<GridPoint> sortedByAngle = new TreeSet<>((o1, o2) -> {
+            double angle1 = Math.atan2(o1.localIJK.getY(), o1.localIJK.getX());
+            if (angle1 < 0)
+              angle1 += 2 * Math.PI;
+            double angle2 = Math.atan2(o2.localIJK.getY(), o2.localIJK.getX());
+            if (angle2 < 0)
+              angle2 += 2 * Math.PI;
+            return Double.compare(Math.abs(angle1 - angle), Math.abs(angle2 - angle));
+          });
+
+            sortedByAngle.addAll(radialMap.get(bin));
+
+          pw.println(toCSV(sortedByAngle.first()));
+          GridPoint thisPoint = sortedByAngle.first();
+          if (Double.isFinite(thisPoint.differentialHeight))
+            profileGridPoints.add(thisPoint);
+        }
+      } catch (FileNotFoundException e) {
+        logger.warn("Can't write {}", csvFile);
+        logger.warn(e.getLocalizedMessage());
+      }
+
+    }
+
+    return profileMap;
+  }
+
+  /**
+   * Write sector volumes to a file
+   *
+   * @param gridPoints grid points
+   * @param header file header
+   * @param outputBasename CSV file to write
+   */
+  private Map<Integer, Collection<GridPoint>> writeSectorCSV(Collection<GridPoint> gridPoints,
+      String header, String outputBasename) {
+
+    // grid points in each sector
+    Map<Integer, Collection<GridPoint>> sectorMap = new HashMap<>();
+
+    if (numProfiles == 0)
+      return sectorMap;
+
+    String csvFile = outputBasename + "_sector.csv";
+
+    NavigableMap<Double, Double> aboveMap = new TreeMap<>();
+    NavigableMap<Double, Double> belowMap = new TreeMap<>();
+    final double deltaAngle = 2 * Math.PI / numProfiles;
+    for (int i = 0; i < numProfiles; i++) {
+      aboveMap.put(i * deltaAngle, 0.);
+      belowMap.put(i * deltaAngle, 0.);
+    }
+
+    // run through all the grid points and put them in the appropriate sector
+    double gridCellArea = gridSpacing * gridSpacing;
+    for (GridPoint gp : gridPoints) {
+      Vector3D localIJK = gp.localIJK;
+      double azimuth = Math.atan2(localIJK.getY(), localIJK.getX());
+      if (azimuth < 0)
+        azimuth += 2 * Math.PI;
+      double key = aboveMap.floorKey(azimuth);
+
+      int sector = (int) (key / deltaAngle);
+      Collection<GridPoint> sectorGridPoints = sectorMap.computeIfAbsent(sector, k -> new HashSet<>());
+
+        if (isInsideROI(gp.localIJK)) {
+        double dv = gridCellArea * gp.differentialHeight;
+        if (Double.isFinite(dv)) {
+          if (dv > 0) {
+              aboveMap.compute(key, (k, value) -> value + dv);
+          } else {
+              belowMap.compute(key, (k, value) -> value + dv);
+          }
+          sectorGridPoints.add(gp);
+        }
+      }
+    }
+
+    try (PrintWriter pw = new PrintWriter(csvFile)) {
+      pw.println(getSectorHeader(header));
+      for (double azimuth : aboveMap.keySet()) {
+        StringBuffer sb = new StringBuffer();
+        sb.append(String.format("%d, ", (int) (azimuth / deltaAngle)));
+        sb.append(String.format("%.2f, ", Math.toDegrees(azimuth)));
+        sb.append(String.format("%.2f, ", Math.toDegrees(azimuth + deltaAngle)));
+        sb.append(String.format("%e, ", aboveMap.get(azimuth)));
+        sb.append(String.format("%e, ", belowMap.get(azimuth)));
+        sb.append(String.format("%e", aboveMap.get(azimuth) + belowMap.get(azimuth)));
+        pw.println(sb);
+      }
+
+    } catch (FileNotFoundException e) {
+      logger.warn("Can't write " + csvFile);
+      logger.warn(e.getLocalizedMessage());
+    }
+
+    return sectorMap;
+
+  }
+
+  private class GridPoint implements Comparable<GridPoint> {
+    Vector3D localIJK;
+    Vector3D globalIJK;
+    double referenceHeight;
+    double height;
+    double differentialHeight;
+
+    /**
+     * Create a grid point from an input location in local coordinates
+     * 
+     * @param xy point in local coordinates.  Z value is ignored.
+     */
+    public GridPoint(Vector3D xy) {
+      this.localIJK = xy;
+      Vector3D nativeIJK =
+          nativeToLocal.getKey().applyInverseTo(localIJK).add(nativeToLocal.getValue());
+      globalIJK = plane.localToGlobal(nativeIJK);
+      referenceHeight = getRefHeight(nativeIJK.getX(), nativeIJK.getY());
+      height = getHeight(nativeIJK.getX(), nativeIJK.getY());
+      differentialHeight = height - referenceHeight;
+    }
+
+    /**
+     * sort by the x coordinate on the local grid, then by the y coordinate.
+     */
+    @Override
+    public int compareTo(GridPoint o) {
+      int compare = Double.compare(localIJK.getX(), o.localIJK.getX());
+      if (compare == 0)
+        compare = Double.compare(localIJK.getY(), o.localIJK.getY());
+      return compare;
+    }
+  }
+
+  private static List<Vector3D> readPointsFromFile(String filename) {
+    List<Vector3D> points = new ArrayList<>();
+
+    try {
+      if (FilenameUtils.getExtension(filename).equalsIgnoreCase("vtk")) {
+
+        vtkPolyData polydata = PolyDataUtil.loadShapeModel(filename);
+        double[] pt = new double[3];
+        for (int i = 0; i < polydata.GetNumberOfPoints(); i++) {
+          polydata.GetPoint(i, pt);
+          points.add(new Vector3D(pt));
+        }
+      } else {
+        List<String> lines = FileUtils.readLines(new File(filename), Charset.defaultCharset());
+        for (String line : lines) {
+          if (line.trim().isEmpty() || line.trim().startsWith("#"))
+            continue;
+          SBMTStructure structure = SBMTStructure.fromString(line);
+          points.add(structure.centerXYZ());
+        }
+      }
+    } catch (Exception e) {
+      logger.warn(e.getLocalizedMessage());
+    }
+    return points;
+  }
+  private static Options defineOptions() {
+    Options options = TerrasaurTool.defineOptions();
+    options.addOption(Option.builder("gridExtent").required().hasArg().desc(
+                    "Required.  Size of local grid, in same units as shape model and reference surface.  Grid is assumed to be square.")
+            .build());
+    options.addOption(Option.builder("gridSpacing").required().hasArg()
+            .desc(
+                    "Required.  Spacing of local grid, in same units as shape model and reference surface.")
+            .build());
+    options.addOption(Option.builder("logFile").hasArg()
+            .desc("If present, save screen output to log file.").build());
+    options.addOption(Option.builder("logLevel").hasArg()
+            .desc("If present, print messages above selected priority.  Valid values are "
+                    + "ALL, OFF, SEVERE, WARNING, INFO, CONFIG, FINE, FINER, or FINEST.  Default is INFO.")
+            .build());
+    options.addOption(Option.builder("numProfiles").hasArg().desc(
+                    "Number of radial profiles to create.  Profiles are evenly spaced in degrees and evaluated "
+                            + "at intervals of gridSpacing in the radial direction.")
+            .build());
+    options.addOption(Option.builder("origin").hasArg()
+            .desc("If present, set origin of local coordinate system.  "
+                    + "Options are MAX_HEIGHT (set to maximum elevation of the shape model), "
+                    + "MIN_HEIGHT (set to minimum elevation of the shape model), "
+                    + "or a three element vector specifying the desired origin, comma separated, no spaces (e.g. 11.45,-45.34,0.932).")
+            .build());
+    options.addOption(Option.builder("output").hasArg().required().desc(
+                    "Basename of output files.  Files will be named ${output}_grid.csv for the grid, ${output}_sector.csv for the sectors, "
+                            + "and ${output}_profile_${degrees}.csv for profiles.")
+            .build());
+    options.addOption(Option.builder("radialUp")
+            .desc("Specify +Z direction of local coordinate system to be in the radial "
+                    + "direction.  Default is to align local +Z along global +Z.")
+            .build());
+    options.addOption(Option.builder("referenceList").hasArg().desc(
+                    "File containing reference points.  If the file extension is .vtk it is read as a VTK file, "
+                            + "otherwise it is assumed to be an SBMT structure file.")
+            .build());
+    options.addOption(Option.builder("referenceShape").hasArg().desc("Reference shape.").build());
+    options.addOption(Option.builder("referenceVTK").hasArg()
+            .desc("If present, write out a VTK file with the reference surface at each grid point.  "
+                    + "If an ROI is defined color points inside/outside the boundaries.")
+            .build());
+    options.addOption(Option.builder("roiInner").hasArg().desc(
+                    "Flag points closer to the origin than this as outside the ROI. Supported formats are the same as referenceList.")
+            .build());
+    options.addOption(Option.builder("roiOuter").hasArg().desc(
+                    "Flag points closer to the origin than this as outside the ROI. Supported formats are the same as referenceList.")
+            .build());
+    options.addOption(Option.builder("shapeModel").hasArg().required()
+            .desc("Shape model for volume computation.").build());    return options;
+  }
+
+
+  public static void main(String[] args)  {
+    TerrasaurTool defaultOBJ = new DifferentialVolumeEstimator();
+
+    Options options = defineOptions();
+
+    CommandLine cl = defaultOBJ.parseArgs(args, options);
+
+    Map<MessageLabel, String> startupMessages = defaultOBJ.startupMessages(cl);
+    for (MessageLabel ml : startupMessages.keySet())
+      logger.info(String.format("%s %s", ml.label, startupMessages.get(ml)));
+
+    StringBuilder header = new StringBuilder();
+    header.append("# ").append(new Date()).append("\n");
+    header.append("# ").append(defaultOBJ.getClass().getSimpleName()).append(" [").append(AppVersion.getVersionString()).append("]\n");
+    header.append("# ").append(startupMessages.get(MessageLabel.ARGUMENTS)).append("\n");
+
+    NativeLibraryLoader.loadVtkLibraries();
+
+    double gridHalfExtent = Double.parseDouble(cl.getOptionValue("gridExtent")) / 2;
+    double gridSpacing = Double.parseDouble(cl.getOptionValue("gridSpacing"));
+
+    String outputBasename = cl.getOptionValue("output");
+    String dirName = FilenameUtils.getFullPath(outputBasename);
+    if (!dirName.trim().isEmpty()) {
+      File dir = new File(dirName);
+      if (!dir.exists())
+        dir.mkdirs();
+    }
+
+      vtkPolyData polyData = null;
+      try {
+          polyData = PolyDataUtil.loadShapeModel(cl.getOptionValue("shapeModel"));
+      } catch (Exception e) {
+          logger.error("Cannot load shape model!");
+          logger.error(e.getLocalizedMessage(), e);
+      }
+
+      ORIGIN originType = ORIGIN.DEFAULT;
+    Vector3D localOrigin = Vector3D.ZERO;
+    if (cl.hasOption("origin")) {
+      String originString = cl.getOptionValue("origin");
+      if (originString.contains(",")) {
+        String[] parts = originString.split(",");
+        if (parts.length == 3) {
+          localOrigin = new Vector3D(Double.parseDouble(parts[0].trim()),
+              Double.parseDouble(parts[1].trim()), Double.parseDouble(parts[2].trim()));
+          originType = ORIGIN.CUSTOM;
+        }
+      } else {
+        originType = ORIGIN.valueOf(originString.toUpperCase());
+      }
+    }
+    DifferentialVolumeEstimator app = new DifferentialVolumeEstimator(polyData);
+
+    if (cl.hasOption("numProfiles"))
+      app.setNumProfiles(Integer.parseInt(cl.getOptionValue("numProfiles")));
+
+    if (cl.hasOption("radialUp"))
+      app.setRadialUp(true);
+
+    if (cl.hasOption("referenceShape")) {
+        try {
+            app.setReferencePolyData(PolyDataUtil.loadShapeModel(cl.getOptionValue("referenceShape")));
+        } catch (Exception e) {
+            logger.error("Cannot load reference shape model!");
+            logger.error(e.getLocalizedMessage(), e);
+        }
+    }
+    if (cl.hasOption("referenceList"))
+      app.setReferencePoints(readPointsFromFile(cl.getOptionValue("referenceList")));
+
+    app.createReference(localOrigin);
+
+    // Shift the origin if needed
+    switch (originType) {
+      case CUSTOM:
+      case DEFAULT:
+        break;
+      case MAX_HEIGHT:
+        app.createGrid(gridHalfExtent, 0.1 * gridSpacing);
+        localOrigin = app.highPoint;
+        app.createReference(localOrigin);
+        break;
+      case MIN_HEIGHT:
+        app.createGrid(gridHalfExtent, 0.1 * gridSpacing);
+        localOrigin = app.lowPoint;
+        app.createReference(localOrigin);
+        break;
+    }
+
+    if (cl.hasOption("roiInner"))
+      app.setInnerROI(cl.getOptionValue("roiInner"));
+
+    if (cl.hasOption("roiOuter"))
+      app.setOuterROI(cl.getOptionValue("roiOuter"));
+
+    NavigableSet<GridPoint> gridPoints = app.createGrid(gridHalfExtent, gridSpacing);
+
+    app.writeGridCSV(gridPoints, header.toString(), outputBasename);
+    Map<Integer, Collection<GridPoint>> profileMap =
+        app.writeProfileCSV(gridPoints, header.toString(), outputBasename);
+    Map<Integer, Collection<GridPoint>> sectorMap =
+        app.writeSectorCSV(gridPoints, header.toString(), outputBasename);
+
+    if (cl.hasOption("referenceVTK")) {
+      app.writeReferenceVTK(gridPoints, profileMap, sectorMap, cl.getOptionValue("referenceVTK"));
+    }
+
+    logger.info("Finished.");
+  }
+}

src/main/java/terrasaur/apps/DumpConfig.java

@@ -0,0 +1,76 @@
+package terrasaur.apps;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.nio.file.Paths;
+import java.time.Instant;
+import java.time.ZoneOffset;
+import java.time.format.DateTimeFormatter;
+import java.util.Locale;
+import org.apache.commons.cli.Options;
+import org.apache.commons.configuration2.PropertiesConfiguration;
+import org.apache.commons.configuration2.PropertiesConfigurationLayout;
+import org.apache.commons.configuration2.ex.ConfigurationException;
+import org.apache.commons.text.WordUtils;
+import terrasaur.config.ConfigBlock;
+import terrasaur.config.ConfigBlockFactory;
+import terrasaur.config.TerrasaurConfig;
+import terrasaur.templates.TerrasaurTool;
+import terrasaur.utils.AppVersion;
+
+public class DumpConfig implements TerrasaurTool {
+
+  @Override
+  public String shortDescription() {
+    return "Write a sample configuration file to use with Terrasaur, using defaults for DART.";
+  }
+
+  @Override
+  public String fullDescription(Options options) {
+    return WordUtils.wrap(
+        "This program writes out sample configuration files to be used with Terrasaur.  "
+            + "It takes a single argument, which is the name of the directory that will contain "
+            + "the configuration files to be written.",
+        80);
+  }
+
+  public static void main(String[] args) {
+    // if no arguments, print the usage and exit
+    if (args.length == 0) {
+      System.out.println(new DumpConfig().fullDescription(null));
+      System.exit(0);
+    }
+
+    // if -shortDescription is specified, print short description and exit.
+    for (String arg : args) {
+      if (arg.equals("-shortDescription")) {
+        System.out.println(new DumpConfig().shortDescription());
+        System.exit(0);
+      }
+    }
+
+    File path = Paths.get(args[0]).toFile();
+
+    ConfigBlock configBlock = TerrasaurConfig.getTemplate();
+    try (PrintWriter pw = new PrintWriter(path)) {
+      PropertiesConfiguration config = new ConfigBlockFactory().toConfig(configBlock);
+      PropertiesConfigurationLayout layout = config.getLayout();
+
+      String now =
+          DateTimeFormatter.ofPattern("yyyy-MM-dd HH:mm:ss")
+              .withLocale(Locale.getDefault())
+              .withZone(ZoneOffset.UTC)
+              .format(Instant.now());
+      layout.setHeaderComment(
+          String.format(
+              "Configuration file for %s\nCreated %s UTC", AppVersion.getVersionString(), now));
+
+      config.write(pw);
+    } catch (ConfigurationException | IOException e) {
+      throw new RuntimeException(e);
+    }
+
+    System.out.println("Wrote config file to " + path.getAbsolutePath());
+  }
+}

src/main/java/terrasaur/apps/GetSpots.java

@@ -0,0 +1,626 @@
+package terrasaur.apps;
+
+import java.io.File;
+import java.io.PrintStream;
+import java.nio.charset.Charset;
+import java.util.*;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.Options;
+import org.apache.commons.io.FileUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import spice.basic.AberrationCorrection;
+import spice.basic.Body;
+import spice.basic.CSPICE;
+import spice.basic.FOV;
+import spice.basic.Instrument;
+import spice.basic.LatitudinalCoordinates;
+import spice.basic.Matrix33;
+import spice.basic.Plane;
+import spice.basic.PositionVector;
+import spice.basic.ReferenceFrame;
+import spice.basic.SCLK;
+import spice.basic.SCLKTime;
+import spice.basic.SpiceException;
+import spice.basic.StateRecord;
+import spice.basic.TDBTime;
+import spice.basic.Vector3;
+import terrasaur.smallBodyModel.SmallBodyModel;
+import terrasaur.templates.TerrasaurTool;
+import terrasaur.utils.CellInfo;
+import terrasaur.utils.NativeLibraryLoader;
+import terrasaur.utils.PolyDataUtil;
+import terrasaur.utils.SPICEUtil;
+import terrasaur.utils.math.MathConversions;
+import vtk.vtkIdList;
+import vtk.vtkPolyData;
+
+/**
+ *
+ *
+ * <h2>NAME</h2>
+ *
+ * GetSpots - find relevant OSIRIS-REx data for assigning values to facets in an OSIRIS-REx map
+ * interchange (OBJ) file
+ *
+ * <h2>SYNOPSIS</h2>
+ *
+ * <code>GetSpots --spice <em>spicemetakernel</em> --obj <em>objfile</em> --instype
+ * <em>instrumenttype</em> --sclk <em>sclkfile</em> --maxdist <em>distance</em></code>
+ *
+ * <h2>DESCRIPTION</h2>
+ *
+ * GetSpots identifies those times, listed in <em>sclkfile</em>, when the boresight of
+ * <em>instrumenttype</em> intersects the surface of Bennu less than <em>distance</em> milliradians
+ * from the center of individual facets in the OBJ file described in <em>objfile</em>. Needed spice
+ * files for this calculation are listed in <em>spicemetakernel</em>.
+ *
+ * <p>At the time a three-dimensional map is made, a designated DSK file will be used to create an
+ * OBJ file that act as a framework on which a map will be made. (This is done with the utility
+ * {@link DSK2OBJ}.) The OBJ file identifies a set of vertices (in body centered Cartesian
+ * coordinates) and groups these vertices to identify facets. Facet numbers correspond to their
+ * ordinal position in the list of facet identifications. An ancillary file locates the center of
+ * each facet in latitude (deg), longitude (deg), and range (km) from center of figure.
+ *
+ * <p>Mapmakers may wish to assign a value to a facet based on an algorithmic combination of one or
+ * more observations that are in the proximity of the facet. In order to do this, they need to
+ * understand which observations are candidates for their analysis. Knowing the distance and
+ * position angle of the observation relative to the center of the facet is the discriminator for
+ * determining which observations are candidates, and GetSpots provides this information.
+ *
+ * <p>For all observations taken by OSIRIS-REx, the unique value of a counter on the spacecraft when
+ * the observation was made is known. This is called the sclk ("sklock") value. SPICE files provide
+ * spacecraft ephemeris and orientation, Bennu position, orientation, and shape, and instrument
+ * boresight and orientations. When combined with the sclk value, the intersection of the boresight
+ * on the surface of Bennu can be calculated.
+ *
+ * <p>A simple text file of sclk values (one per line) acts as input to getspots. GetSpots can
+ * determine which boresight values corresponding to the sclk values do not exceed the maximum
+ * distance criteria for each facet, along with the position angle of the spot, and the fraction of
+ * the facet covered by the spot. The position angle is valued from 0 to 359 degrees North being 0
+ * with east being 90 degrees. Spots that do not completely intersect the surface of Bennu are
+ * flagged. Any additional information on the input line following the sclk value is echoed to the
+ * output unchanged, allowing other data useful in the subsequent analysis to be carried along in
+ * the output.
+ *
+ * <h2>INPUTS</h2>
+ *
+ * <em>spicemetakernel</em> is a spice metakernel listing all required spice files (DSK, SPK, PCK,
+ * etc.) needed to perform the analysis. Only files needed for this analysis are in the metakernel
+ * (e.g. no ambiguity about which file to use.) Required contents of this metakernel is TBD.
+ *
+ * <p><em>instrumenttype</em> is a code that specifies the boresight and field of view of the
+ * instrument to use in the analysis. This must be one of "OLA", "OTES", "OVIRS", "POLYCAM",
+ * "MAPCAM", "SAMCAM", or "NAVCAM".
+ *
+ * <p><em>distance</em> is the maximum distance of the instrument boresight from the center of the
+ * facet expressed in milliradians.
+ *
+ * <p><em>sclkfile</em> is a text file that contains the sclk values for one or more times of
+ * observation by an instrument. Leading whitespace is ignored. One or more whitespace characters
+ * must separate the sclkvalue from the rest of the line. The format is as follows:<br>
+ * <code>
+ * &nbsp;BEGIN<br>
+ * &nbsp;sclkvalue [otherdata]<br>
+ * &nbsp;sclkvalue [otherdata]<br>
+ * &nbsp;.<br>
+ * &nbsp;.<br>
+ * &nbsp;END<br>
+ * </code> Where:<br>
+ * &nbsp;<code>sclkvalue</code> is a string (format TBD)<br>
+ * &nbsp;<code>[otherdata]</code> includes all additional data (including whitespace) in the line up
+ * to, but not including, the linefeed character.
+ *
+ * <h2>OUTPUT</h2>
+ *
+ * All output is written to standard output.
+ *
+ * <p>Output is a text file, with each line terminated by linefeeds.<br>
+ * <code>
+ * &nbsp;F1<br>
+ * &nbsp;sclkvalue dist pos frac flag inc ems phs [otherdata]<br>
+ * &nbsp;sclkvalue dist pos frac flag inc ems phs [otherdata]<br>
+ * &nbsp;..<br>
+ * &nbsp;F2<br>
+ * &nbsp;sclkvalue dist pos frac flag inc ems phs [otherdata]<br>
+ * &nbsp;sclkvalue dist pos frac flag inc ems phs [otherdata]<br>
+ * &nbsp;F3<br>
+ * &nbsp;F4<br>
+ * &nbsp;..<br>
+ * &nbsp;FN<br>
+ * &nbsp;END<br>
+ * </code> Where:<br>
+ * &nbsp;F<em>N</em> is a facet identifier that identifies facet number <em>N</em>. Each sclkvalue
+ * that meets the distance criteria for facet number <em>N</em> is listed sequentially after the
+ * facet identifier. If no sclk values meet the distance criteria, then no values are listed, and
+ * the next facet identifier follows on the next line. &nbsp; <code>sclkvalue</code> is the sclk
+ * exactly as it appeared in the input file.<br>
+ * &nbsp;<code>dist</code> is a real number that describes the distance of the spot from the center
+ * of the facet in units of milliradians.<br>
+ * &nbsp;<code>pos</code> is the position angle of the center of the instrument boresight
+ * intersection on the surface measured in degrees from North, with East being 90 degrees.<br>
+ * &nbsp;<code>frac</code> is a real number greater than or equal to 0.0 and less than or equal to
+ * 100.0 that describes the fraction of the facet covered by the spot. If the value is 0.0, then the
+ * spot does not cover any portion of the facet. If the value is 100.0 then the facet is entirely
+ * covered by the spot.<br>
+ * &nbsp;<code>flag</code> is 1 if any portion of the spot does not intersect the surface of Bennu,
+ * otherwise it is 0. <br>
+ * &nbsp;<code>inc</code> is the incidence angle in degrees<br>
+ * &nbsp;<code>ems</code> is the emission angle in degrees<br>
+ * &nbsp;<code>phs</code> is the phase angle in degrees<br>
+ * &nbsp;<code>[otherdata]</code> is all textual data on the line following the sclk value, up to
+ * the linefeed, unchanged.
+ *
+ * @author nairah1
+ */
+public class GetSpots implements TerrasaurTool {
+
+  private static final Logger logger = LogManager.getLogger();
+
+  private GetSpots() {}
+
+  @Override
+  public String shortDescription() {
+    return "find relevant OSIRIS-REx data for assigning values to facets in an OBJ file.";
+  }
+
+  @Override
+  public String fullDescription(Options options) {
+    String header =
+        """
+                    This program identifies those times when the boresight of instrumenttype intersects the surface
+                    of Bennu less than a specified distance from the center of individual facets in shape model.
+                    """;
+    String footer =
+        """
+                    All output is written to standard output in the following format:
+                     F1
+                     sclkvalue dist pos frac flag inc ems phs [otherdata]
+                     sclkvalue dist pos frac flag inc ems phs [otherdata]
+                     ..
+                     F2
+                     sclkvalue dist pos frac flag inc ems phs [otherdata]
+                     sclkvalue dist pos frac flag inc ems phs [otherdata]
+                     ..
+                     F3
+                     F4
+                     ..
+                     FN
+                     END
+                    Where:
+                     FN is a facet identifier that identifies facet number N. Each sclkvalue that meets the distance criteria for facet number N is listed sequentially\
+                     after the facet identifier. If no sclk values meet the distance criteria, then no values are listed, and the next facet identifier follows on the \
+                    next line.
+                     sclkvalue is the sclk exactly as it appeared in the input file.
+                     dist is a real number that describes the distance of the spot from the center of the facet in units of milliradians.
+                     pos is the position angle of the center of the instrument boresight intersection on the surface measured in degrees from North, with East being 90 degrees.
+                     frac is a real number greater than or equal to 0.0 and less than or equal to 100.0 that describes the fraction of the facet covered by the spot. \
+                    If the value is 0.0, then the spot does not cover any portion of the facet. If the value is 100.0 then the facet is entirely covered by the spot.
+                     flag is 1 if any portion of the spot does not intersect the surface of Bennu, otherwise it is 0.\s
+                     inc is the incidence angle in degrees
+                     ems is the emission angle in degrees
+                     phs is the phase angle in degrees
+                     [otherdata] is all textual data on the line following the sclk value, up to the linefeed, unchanged.
+                    """;
+    return TerrasaurTool.super.fullDescription(options, header, footer);
+  }
+
+  private String spicemetakernel;
+  private String objfile;
+  private String instrument;
+  private String sclkfile;
+  private int debugLevel;
+  private double maxdist;
+  private vtkPolyData polydata;
+  private SmallBodyModel smallBodyModel;
+  private HashMap<Integer, String> coverageMap;
+
+  private int SC_ID;
+  private String SC_ID_String;
+  private ReferenceFrame BodyFixed;
+  private String TARGET;
+  private final Vector3 NORTH = new Vector3(0, 0, 1e6);
+  private int instID;
+
+  private PrintStream outputStream;
+
+  public GetSpots(
+      String spicemetakernel,
+      String objfile,
+      String instrument,
+      String sclkfile,
+      double maxdist,
+      int debugLevel) {
+    this.spicemetakernel = spicemetakernel;
+    this.objfile = objfile;
+    this.instrument = instrument;
+    this.sclkfile = sclkfile;
+    this.maxdist = maxdist;
+    this.debugLevel = debugLevel;
+
+    coverageMap = new HashMap<>();
+
+    outputStream = System.out;
+  }
+
+  /**
+   * Find facets covered by the FOV of the instrument. For each facet, find the distance and
+   * position angle of the instrument boresight and the fraction of the facet covered by the FOV.
+   *
+   * @param line String where the first "word" is an sclk time
+   * @throws SpiceException
+   */
+  private void findCoverage(String line) throws SpiceException {
+    String[] parts = line.split(" ");
+    if (parts.length == 0) return;
+
+    SCLKTime sclkTime = new SCLKTime(new SCLK(SC_ID), parts[0]);
+    TDBTime tdbTime = new TDBTime(sclkTime.getTDBSeconds());
+
+    Instrument instrument = new Instrument(instID);
+    FOV fov = new FOV(instrument);
+    Matrix33 instrToBodyFixed =
+        fov.getReferenceFrame().getPositionTransformation(BodyFixed, tdbTime);
+    Vector3 bsightBodyFixed = instrToBodyFixed.mxv(fov.getBoresight());
+
+    StateRecord sr =
+        new StateRecord(
+            new Body(SC_ID_String),
+            tdbTime,
+            BodyFixed,
+            new AberrationCorrection("LT+S"),
+            new Body(TARGET));
+    Vector3 scposBodyFixed = sr.getPosition();
+
+    PositionVector sunPos =
+        new StateRecord(
+                new Body("SUN"),
+                tdbTime,
+                BodyFixed,
+                new AberrationCorrection("LT+S"),
+                new Body(TARGET))
+            .getPosition();
+
+    double[] double3 = new double[3];
+    long cellID =
+        smallBodyModel.computeRayIntersection(
+            scposBodyFixed.toArray(), bsightBodyFixed.hat().toArray(), double3);
+    if (cellID == -1) return; // no boresight intersection
+
+    Vector3 bsightIntersectVector = new Vector3(double3);
+
+    if (debugLevel > 1) {
+      LatitudinalCoordinates lc = new LatitudinalCoordinates(bsightIntersectVector);
+      System.out.printf(
+          "# %s %f %f %s\n",
+          sclkTime,
+          Math.toDegrees(lc.getLatitude()),
+          Math.toDegrees(lc.getLongitude()),
+          bsightIntersectVector);
+    }
+
+    // flag is 1 if any portion of the spot does not intersect the surface
+    int flag = 0;
+    Vector<Vector3> boundaryBodyFixed = new Vector<>();
+    if (fov.getShape().equals("RECTANGLE") || fov.getShape().equals("POLYGON")) {
+      for (Vector3 boundary : fov.getBoundary()) {
+        boundaryBodyFixed.add(instrToBodyFixed.mxv(boundary));
+      }
+    } else if (fov.getShape().equals("CIRCLE")) {
+      // bounds contains a single vector parallel to a ray that lies in the cone
+      // that makes up the boundary of the FOV
+      Vector3[] bounds = fov.getBoundary();
+
+      for (int i = 0; i < 8; i++) {
+        // not ideal, but check every 45 degrees along the perimeter of the circle for intersection
+        // with the
+        // surface
+        Matrix33 rotateAlongPerimeter = new Matrix33(fov.getBoresight(), i * Math.toRadians(45));
+        Vector3 perimeterVector = rotateAlongPerimeter.mxv(bounds[0]);
+        boundaryBodyFixed.add(instrToBodyFixed.mxv(perimeterVector));
+      }
+    } else {
+      // TODO: add ELLIPSE
+      System.err.printf(
+          "Instrument %s: Unsupported FOV shape %s\n", instrument.getName(), fov.getShape());
+      System.exit(0);
+    }
+
+    // check all of the boundary vectors for surface intersections
+    for (Vector3 vector : boundaryBodyFixed) {
+      cellID =
+          smallBodyModel.computeRayIntersection(
+              scposBodyFixed.toArray(), vector.hat().toArray(), double3);
+      if (cellID == -1) {
+        flag = 1;
+        break;
+      }
+    }
+
+    vtkIdList idList = new vtkIdList();
+    for (int i = 0; i < polydata.GetNumberOfCells(); ++i) {
+
+      polydata.GetCellPoints(i, idList);
+      double[] pt0 = polydata.GetPoint(idList.GetId(0));
+      double[] pt1 = polydata.GetPoint(idList.GetId(1));
+      double[] pt2 = polydata.GetPoint(idList.GetId(2));
+
+      CellInfo ci = CellInfo.getCellInfo(polydata, i, idList);
+      Vector3 facetNormal = MathConversions.toVector3(ci.normal());
+      Vector3 facetCenter = MathConversions.toVector3(ci.center());
+
+      // check that facet faces the observer
+      Vector3 facetToSC = scposBodyFixed.sub(facetCenter);
+      double emission = facetToSC.sep(facetNormal);
+      if (emission > Math.PI / 2) continue;
+
+      double dist =
+          findDist(scposBodyFixed, bsightIntersectVector, facetCenter) * 1e3; // milliradians
+      if (dist < maxdist) {
+
+        Vector3 facetToSun = sunPos.sub(facetCenter);
+        double incidence = facetToSun.sep(facetNormal);
+        double phase = facetToSun.sep(facetToSC);
+
+        Vector3 pt0v = new Vector3(pt0);
+        Vector3 pt1v = new Vector3(pt1);
+        Vector3 pt2v = new Vector3(pt2);
+
+        Vector3 span1 = pt1v.sub(pt0v);
+        Vector3 span2 = pt2v.sub(pt0v);
+
+        Plane facetPlane = new Plane(pt0v, span1, span2);
+        Vector3 localNorth = facetPlane.project(NORTH).sub(facetCenter);
+        Vector3 bsightIntersectProjection =
+            facetPlane.project(bsightIntersectVector).sub(facetCenter);
+
+        // 0 = North, 90 = East
+        double pos =
+            Math.toDegrees(Math.acos(localNorth.hat().dot(bsightIntersectProjection.hat())));
+        if (localNorth.cross(bsightIntersectProjection).dot(facetNormal) > 0) pos = 360 - pos;
+
+        int nCovered = 0;
+        if (SPICEUtil.isInFOV(fov, instrToBodyFixed.mtxv(pt0v.sub(scposBodyFixed)))) nCovered++;
+        if (SPICEUtil.isInFOV(fov, instrToBodyFixed.mtxv(pt1v.sub(scposBodyFixed)))) nCovered++;
+        if (SPICEUtil.isInFOV(fov, instrToBodyFixed.mtxv(pt2v.sub(scposBodyFixed)))) nCovered++;
+        double frac;
+        if (nCovered == 3) {
+          frac = 1;
+        } else {
+          final double sep012 = span1.negate().sep(pt2v.sub(pt1v)); // angle at vertex 1
+          final double sep021 = span2.negate().sep(pt1v.sub(pt2v)); // angle at vertex 2
+
+          // check 0.5*nPts^2 points if they fall in FOV
+          int nPts = 50;
+          Vector<Vector3> pointsInFacet = new Vector<>();
+          for (int ii = 0; ii < nPts; ii++) {
+            Vector3 x = pt0v.add(span1.scale(ii / (nPts - 1.)));
+            for (int jj = 0; jj < nPts; jj++) {
+              Vector3 y = x.add(span2.scale(jj / (nPts - 1.)));
+
+              // if outside the facet, angle 01y will be larger than angle 012
+              if (span1.negate().sep(y.sub(pt1v)) > sep012) continue;
+              // if outside the facet, angle 02y will be larger than angle 021
+              if (span2.negate().sep(y.sub(pt2v)) > sep021) continue;
+              pointsInFacet.add(instrToBodyFixed.mtxv(y.sub(scposBodyFixed)));
+            }
+          }
+
+          if (pointsInFacet.isEmpty()) {
+            frac = 0;
+          } else {
+            List<Boolean> isInFOV = SPICEUtil.isInFOV(fov, pointsInFacet);
+            nCovered = 0;
+            for (boolean b : isInFOV) if (b) nCovered++;
+            frac = ((double) nCovered) / pointsInFacet.size();
+          }
+        }
+
+        StringBuilder output =
+            new StringBuilder(
+                String.format(
+                    "%s %.4f %5.1f %.1f %d %.1f %.1f %.1f",
+                    sclkTime,
+                    dist,
+                    pos,
+                    frac * 100,
+                    flag,
+                    Math.toDegrees(incidence),
+                    Math.toDegrees(emission),
+                    Math.toDegrees(phase)));
+        for (int j = 1; j < parts.length; j++) output.append(String.format(" %s", parts[j]));
+        output.append("\n");
+        String coverage = coverageMap.get(i);
+        if (coverage == null) {
+          coverageMap.put(i, output.toString());
+        } else {
+          coverage += output;
+          coverageMap.put(i, coverage);
+        }
+      }
+    }
+  }
+
+  /**
+   * Find the angular distance between pt1 and pt2 as seen from scPos. All coordinates are in the
+   * body fixed frame.
+   *
+   * @param scPos Spacecraft position
+   * @param pt1 Point 1
+   * @param pt2 Point 2
+   * @return distance between pt1 and pt2 in radians.
+   */
+  private double findDist(Vector3 scPos, Vector3 pt1, Vector3 pt2) {
+    Vector3 scToPt1 = pt1.sub(scPos).hat();
+    Vector3 scToPt2 = pt2.sub(scPos).hat();
+
+    return Math.acos(scToPt1.dot(scToPt2));
+  }
+
+  public void printMap() {
+    if (debugLevel > 0) {
+      for (int i = 0; i < polydata.GetNumberOfCells(); ++i) {
+        outputStream.printf("F%d\n", i + 1);
+        String output = coverageMap.get(i);
+        if (output != null) outputStream.print(coverageMap.get(i));
+      }
+    } else {
+      List<Integer> list = new ArrayList<>(coverageMap.keySet());
+      Collections.sort(list);
+      for (Integer i : list) {
+        outputStream.printf("F%d\n", i + 1);
+        outputStream.print(coverageMap.get(i));
+      }
+    }
+    outputStream.println("END");
+  }
+
+  public void process() throws Exception {
+    boolean useNEAR = false;
+    if (instrument.equalsIgnoreCase("OLA_LOW")) {
+      // instID = -64400; // ORX_OLA_BASE
+      // instID = -64401; // ORX_OLA_ART
+      instID = -64403; // ORX_OLA_LOW
+    }
+    if (instrument.equalsIgnoreCase("OLA_HIGH")) {
+      instID = -64402; // ORX_OLA_HIGH
+    } else if (instrument.equalsIgnoreCase("OTES")) {
+      instID = -64310; // ORX_OTES
+    } else if (instrument.equalsIgnoreCase("OVIRS_SCI")) {
+      // instID = -64320; // ORX_OVIRS <- no instrument kernel for this
+      instID = -64321; // ORX_OVIRS_SCI
+      // instID = -64322; // ORX_OVIRS_SUN
+    } else if (instrument.equalsIgnoreCase("REXIS")) {
+      instID = -64330; // ORX_REXIS
+    } else if (instrument.equalsIgnoreCase("REXIS_SXM")) {
+      instID = -64340; // ORX_REXIS_SXM
+    } else if (instrument.equalsIgnoreCase("POLYCAM")) {
+      instID = -64360; // ORX_OCAMS_POLYCAM
+    } else if (instrument.equalsIgnoreCase("MAPCAM")) {
+      instID = -64361; // ORX_OCAMS_MAPCAM
+    } else if (instrument.equalsIgnoreCase("SAMCAM")) {
+      instID = -64362; // ORX_OCAMS_SAMCAM
+    } else if (instrument.equalsIgnoreCase("NAVCAM")) {
+      // instID = -64070; // ORX_NAVCAM <- no frame kernel for this
+      // instID = -64081; // ORX_NAVCAM1 <- no instrument kernel for this
+      instID = -64082; // ORX_NAVCAM2 <- no instrument kernel for this
+    } else if (instrument.equalsIgnoreCase("NIS_RECT")) {
+      useNEAR = true;
+      //      instID = -93021;
+      instID = -93023; // relative to NEAR_NIS_BASE
+    } else if (instrument.equalsIgnoreCase("NIS_SQUARE")) {
+      useNEAR = true;
+      //      instID = -93022;
+      instID = -93024; // relative to NEAR_NIS_BASE
+    }
+
+    NativeLibraryLoader.loadVtkLibraries();
+    polydata = PolyDataUtil.loadShapeModelAndComputeNormals(objfile);
+    smallBodyModel = new SmallBodyModel(polydata);
+
+    NativeLibraryLoader.loadSpiceLibraries();
+    CSPICE.furnsh(spicemetakernel);
+
+    if (useNEAR) {
+      SC_ID = -93;
+      SC_ID_String = "-93"; // "NEAR";
+      TARGET = "2000433";
+      BodyFixed = new ReferenceFrame("IAU_EROS");
+    } else {
+      SC_ID = -64;
+      SC_ID_String = "-64"; // "ORX_SPACECRAFT";
+      TARGET = "2101955";
+      BodyFixed = new ReferenceFrame("IAU_BENNU");
+    }
+
+    List<String> sclkLines = FileUtils.readLines(new File(sclkfile), Charset.defaultCharset());
+    boolean foundBegin = false;
+    for (String line : sclkLines) {
+      String trimLine = line.trim();
+      if (trimLine.startsWith("#")) continue;
+      if (trimLine.startsWith("BEGIN")) {
+        foundBegin = true;
+        continue;
+      }
+      if (foundBegin && !trimLine.startsWith("END")) {
+        if (trimLine.startsWith("#")) continue;
+
+        findCoverage(trimLine);
+      }
+    }
+  }
+
+  private static Options defineOptions() {
+    Options options = TerrasaurTool.defineOptions();
+    options.addOption(Option.builder("spice").required().hasArg().desc("SPICE metakernel").build());
+    options.addOption(Option.builder("obj").required().hasArg().desc("Shape file").build());
+    options.addOption(
+        Option.builder("instype")
+            .required()
+            .hasArg()
+            .desc(
+                "one of OLA_LOW, OLA_HIGH, OTES, OVIRS_SCI, REXIS, REXIS_SXM, POLYCAM, MAPCAM, SAMCAM, or NAVCAM")
+            .build());
+    options.addOption(
+        Option.builder("sclk")
+            .required()
+            .hasArg()
+            .desc(
+                """
+file containing sclk values for instrument observation times.  All values between the strings BEGIN and END will be processed.
+       For example:
+            BEGIN
+            3/605862045.24157
+            END""")
+            .build());
+    options.addOption(
+        Option.builder("maxdist")
+            .required()
+            .hasArg()
+            .desc("maximum distance of boresight from facet center in milliradians")
+            .build());
+    options.addOption(
+        Option.builder("all-facets")
+            .desc(
+                "Optional.  If present, entries for all facets will be output, even if there is no intersection.")
+            .build());
+    options.addOption(
+        Option.builder("verbose")
+            .hasArg()
+            .desc(
+                "Optional.  A level of 1 is equivalent to -all-facets.  A level of 2 or higher will print out the boresight intersection position at each sclk.")
+            .build());
+    return options;
+  }
+
+  public static void main(String[] args) {
+
+    TerrasaurTool defaultOBJ = new GetSpots();
+
+    Options options = defineOptions();
+
+    CommandLine cl = defaultOBJ.parseArgs(args, options);
+
+    Map<MessageLabel, String> startupMessages = defaultOBJ.startupMessages(cl);
+    for (MessageLabel ml : startupMessages.keySet())
+      logger.info(String.format("%s %s", ml.label, startupMessages.get(ml)));
+
+    String spicemetakernel = cl.getOptionValue("spice");
+    String objfile = cl.getOptionValue("obj");
+    String instrumenttype = cl.getOptionValue("instype");
+    String sclkfile = cl.getOptionValue("sclk");
+    double distance = Double.parseDouble(cl.getOptionValue("maxdist"));
+    int debugLevel = Integer.parseInt(cl.getOptionValue("verbose", "0"));
+    if (cl.hasOption("all-facets")) debugLevel = debugLevel == 0 ? 1 : debugLevel + 1;
+
+    GetSpots gs =
+        new GetSpots(spicemetakernel, objfile, instrumenttype, sclkfile, distance, debugLevel);
+    try {
+      gs.process();
+      gs.printMap();
+    } catch (Exception e) {
+      logger.error(e.getLocalizedMessage(), e);
+    }
+  }
+}

src/main/java/terrasaur/apps/ImpactLocator.java

@@ -0,0 +1,764 @@
+package terrasaur.apps;
+
+import java.io.File;
+import java.io.PrintWriter;
+import java.util.*;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.Options;
+import org.apache.commons.math3.analysis.UnivariateFunction;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.spi.StandardLevel;
+import spice.basic.*;
+import terrasaur.smallBodyModel.SmallBodyModel;
+import terrasaur.templates.TerrasaurTool;
+import terrasaur.utils.*;
+import terrasaur.utils.math.MathConversions;
+import vtk.vtkCellArray;
+import vtk.vtkLine;
+import vtk.vtkPoints;
+import vtk.vtkPolyData;
+import vtk.vtkPolyDataWriter;
+
+/**
+ * Find the impact point and time given an initial position and velocity.
+ *
+ * @author nairah1
+ */
+public class ImpactLocator implements UnivariateFunction, TerrasaurTool {
+
+  private static final Logger logger = LogManager.getLogger();
+
+  @Override
+  public String shortDescription() {
+    return "Calculate impact time and position from a sumFile.";
+  }
+
+  @Override
+  public String fullDescription(Options options) {
+    String header = "";
+    String footer =
+        """
+               Given a sum file, shape model, and spacecraft velocity in the J2000 frame,
+               this program will calculate an impact time and position.
+
+               NOTE: Spacecraft position is assumed to be in kilometers.  If not, use the
+               -distanceScale option to convert to km.
+
+               NOTE:  Do not include a "pinpoint" or impact SPK in the kernels to
+               load.""";
+    return TerrasaurTool.super.fullDescription(options, header, footer);
+  }
+
+  private ReferenceFrame J2000;
+  private ReferenceFrame bodyFixed;
+  private SmallBodyModel sbm;
+  private Double finalHeight;
+  private Double finalStep;
+  private TDBTime t0;
+  private StateVector initialObserverJ2000;
+  private StateVector initialTargetJ2000;
+
+  private Vector3 observerAccelerationJ2000;
+  private Vector3 targetAccelerationJ2000;
+
+  private StateVector lastState;
+
+  private vtkPolyData rayBundlePolyData;
+  private vtkCellArray rayBundleCells;
+  private vtkPoints rayBundlePoints;
+
+  private ImpactLocator() {}
+
+  public ImpactLocator(
+      ReferenceFrame J2000,
+      ReferenceFrame bodyFixed,
+      SmallBodyModel sbm,
+      Double finalHeight,
+      Double finalStep,
+      TDBTime t0,
+      StateVector initialObserverJ2000,
+      StateVector initialTargetJ2000,
+      TDBTime t1,
+      StateVector finalObserverJ2000,
+      StateVector finalTargetJ2000)
+      throws SpiceErrorException {
+    this.J2000 = J2000;
+    this.bodyFixed = bodyFixed;
+    this.sbm = sbm;
+    this.finalHeight = finalHeight;
+    this.finalStep = finalStep;
+    this.t0 = t0;
+    this.initialObserverJ2000 = initialObserverJ2000;
+    this.initialTargetJ2000 = initialTargetJ2000;
+
+    if (t1 == null) {
+      observerAccelerationJ2000 = new Vector3();
+      targetAccelerationJ2000 = new Vector3();
+    } else {
+      double duration = t1.getTDBSeconds() - t0.getTDBSeconds();
+      observerAccelerationJ2000 =
+          finalObserverJ2000
+              .getVelocity()
+              .sub(initialObserverJ2000.getVelocity())
+              .scale(1. / duration);
+      targetAccelerationJ2000 =
+          finalTargetJ2000.getVelocity().sub(initialTargetJ2000.getVelocity()).scale(1. / duration);
+    }
+  }
+
+  /**
+   * find the body state at time t. Assume a constant velocity in the J2000 frame.
+   *
+   * @param et ephemeris time
+   * @return Body state at time et
+   */
+  public StateVector getStateBodyFixed(TDBTime et) {
+
+    try {
+      double delta = et.sub(t0).getMeasure();
+
+      Vector3 observerPosJ2000 =
+          initialObserverJ2000
+              .getPosition()
+              .add(initialObserverJ2000.getVelocity().scale(delta))
+              .add(observerAccelerationJ2000.scale(0.5 * delta * delta));
+
+      Vector3 targetPosJ2000 =
+          initialTargetJ2000
+              .getPosition()
+              .add(initialTargetJ2000.getVelocity().scale(delta))
+              .add(targetAccelerationJ2000.scale(0.5 * delta * delta));
+
+      Vector3 scPosJ2000 = observerPosJ2000.sub(targetPosJ2000);
+      Vector3 observerVelJ2000 =
+          initialObserverJ2000.getVelocity().add(observerAccelerationJ2000.scale(delta));
+      Vector3 targetVelJ2000 =
+          initialTargetJ2000.getVelocity().add(targetAccelerationJ2000.scale(delta));
+      Vector3 scVelJ2000 = observerVelJ2000.sub(targetVelJ2000);
+
+      StateVector scStateJ2000 = new StateVector(scPosJ2000, scVelJ2000);
+      StateVector scStateBodyFixed =
+          new StateVector(J2000.getStateTransformation(bodyFixed, et).mxv(scStateJ2000));
+
+      if (lastState == null) {
+        lastState = scStateBodyFixed;
+        rayBundlePolyData = new vtkPolyData();
+        rayBundleCells = new vtkCellArray();
+        rayBundlePoints = new vtkPoints();
+
+        rayBundlePolyData.SetPoints(rayBundlePoints);
+        rayBundlePolyData.SetLines(rayBundleCells);
+      }
+      long id0 = rayBundlePoints.InsertNextPoint(lastState.getPosition().toArray());
+      long id1 = rayBundlePoints.InsertNextPoint(scStateBodyFixed.getPosition().toArray());
+      lastState = scStateBodyFixed;
+
+      vtkLine line = new vtkLine();
+      line.GetPointIds().SetId(0, id0);
+      line.GetPointIds().SetId(1, id1);
+
+      rayBundleCells.InsertNextCell(line);
+
+      return scStateBodyFixed;
+
+    } catch (SpiceException e) {
+      logger.error(e.getLocalizedMessage(), e);
+    }
+    return null;
+  }
+
+  /** return range from surface at time t */
+  @Override
+  public double value(double t) {
+
+    TDBTime thisTime = new TDBTime(t);
+
+    StateVector scStateBodyFixed = getStateBodyFixed(thisTime);
+
+    Vector3 closestPoint =
+        new Vector3(sbm.findClosestPoint(scStateBodyFixed.getPosition().toArray()));
+
+    Vector3 toSurface = scStateBodyFixed.getPosition().sub(closestPoint);
+    return toSurface.norm();
+  }
+
+  private NavigableSet<ImpactRecord> findTrajectory() {
+    NavigableSet<ImpactRecord> records = new TreeSet<>();
+    try {
+
+      lastState = null;
+
+      TDBTime et = t0;
+
+      StateVector scStateBodyFixed = getStateBodyFixed(et);
+
+      Vector3 closestPoint =
+          new Vector3(sbm.findClosestPoint(scStateBodyFixed.getPosition().toArray()));
+      Vector3 toSurface = scStateBodyFixed.getPosition().sub(closestPoint);
+      double altitude = toSurface.norm();
+
+      // time it takes to get halfway to the surface
+      TDBDuration delta = new TDBDuration(altitude / (2 * scStateBodyFixed.getVelocity().norm()));
+
+      boolean keepGoing = true;
+      while (keepGoing) {
+        LatitudinalCoordinates lc = new LatitudinalCoordinates(scStateBodyFixed.getPosition());
+        records.add(
+            new ImpactRecord(
+                et,
+                scStateBodyFixed,
+                new LatitudinalCoordinates(altitude, lc.getLongitude(), lc.getLatitude())));
+
+        et = et.add(delta);
+
+        scStateBodyFixed = getStateBodyFixed(et);
+
+        closestPoint = new Vector3(sbm.findClosestPoint(scStateBodyFixed.getPosition().toArray()));
+        toSurface = scStateBodyFixed.getPosition().sub(closestPoint);
+        altitude = toSurface.norm();
+
+        // check that we're still moving towards the target
+        if (scStateBodyFixed.getPosition().dot(scStateBodyFixed.getVelocity()) > 0) {
+          logger.warn(
+              "Stopping at {}; passed closest approach to the body center.",
+              et.toUTCString("ISOC", 3));
+          keepGoing = false;
+        }
+
+        if (altitude > finalHeight) {
+          delta = new TDBDuration(toSurface.norm() / (2 * scStateBodyFixed.getVelocity().norm()));
+        } else if (altitude > finalStep) {
+          delta = new TDBDuration(finalStep / scStateBodyFixed.getVelocity().norm());
+        } else {
+          keepGoing = false;
+        }
+      }
+
+      LatitudinalCoordinates lc = new LatitudinalCoordinates(scStateBodyFixed.getPosition());
+      records.add(
+          new ImpactRecord(
+              et,
+              scStateBodyFixed,
+              new LatitudinalCoordinates(altitude, lc.getLongitude(), lc.getLatitude())));
+
+    } catch (SpiceException e) {
+      logger.error(e.getLocalizedMessage(), e);
+    }
+    return records;
+  }
+
+  static class ImpactRecord implements Comparable<ImpactRecord> {
+    TDBTime et;
+    StateVector scStateBodyFixed;
+    LatitudinalCoordinates lc;
+
+    private ImpactRecord(TDBTime et, StateVector scStateBodyFixed, LatitudinalCoordinates lc) {
+      this.et = et;
+      this.scStateBodyFixed = scStateBodyFixed;
+      this.lc = lc;
+    }
+
+    @Override
+    public int compareTo(ImpactRecord o) {
+      try {
+        return Double.compare(et.getTDBSeconds(), o.et.getTDBSeconds());
+      } catch (SpiceErrorException e) {
+        // completely unnecessary exception
+        return 0;
+      }
+    }
+  }
+
+  private static Vector3 correctForAberration(
+      Vector3 targetLTS, Body observer, Body target, TDBTime t) throws SpiceException {
+    RemoveAberration ra = new RemoveAberration(target, observer);
+
+    return ra.getGeometricPosition(t, targetLTS);
+  }
+
+  private static Options defineOptions() {
+    Options options = TerrasaurTool.defineOptions();
+    options.addOption(
+        Option.builder("date")
+            .hasArgs()
+            .desc("Initial UTC date.  Required if -sumFile is not used.")
+            .build());
+    options.addOption(
+        Option.builder("finalHeight")
+            .hasArg()
+            .desc("Height above surface in meters to consider \"impact\".  Default is 1 meter.")
+            .build());
+    options.addOption(
+        Option.builder("finalStep")
+            .hasArg()
+            .desc(
+                "Continue printing output below finalHeight in increments of approximate finalStep "
+                    + "(in meters) until zero.  Default is to stop at finalHeight.")
+            .build());
+    options.addOption(
+        Option.builder("frame")
+            .required()
+            .hasArg()
+            .desc("Required.  Name of body fixed frame.")
+            .build());
+    options.addOption(
+        Option.builder("instrumentFrame")
+            .hasArg()
+            .desc(
+                "SPICE ID for the camera reference frame.  Required if -outputTransform "
+                    + "AND -sumFile are used.")
+            .build());
+    options.addOption(
+        Option.builder("logFile")
+            .hasArg()
+            .desc("If present, save screen output to log file.")
+            .build());
+    StringBuilder sb = new StringBuilder();
+    for (StandardLevel l : StandardLevel.values()) sb.append(String.format("%s ", l.name()));
+    options.addOption(
+        Option.builder("logLevel")
+            .hasArg()
+            .desc(
+                "If present, print messages above selected priority.  Valid values are "
+                    + sb.toString().trim()
+                    + ".  Default is INFO.")
+            .build());
+    options.addOption(
+        Option.builder("objFile")
+            .required()
+            .hasArg()
+            .desc("Required.  Name of OBJ shape file.")
+            .build());
+    options.addOption(
+        Option.builder("observer")
+            .required()
+            .hasArg()
+            .desc("Required.  SPICE ID for the impactor.")
+            .build());
+    options.addOption(
+        Option.builder("observerFrame")
+            .hasArg()
+            .desc(
+                "SPICE ID for the impactor's reference frame.  Required if -outputTransform is used.")
+            .build());
+    options.addOption(
+        Option.builder("outputTransform")
+            .hasArg()
+            .desc(
+                "If present, write out a transform file that can be used by TransformShape to place "
+                    + "coordinates in the spacecraft frame in the body fixed frame.  The rotation "
+                    + " is evaluated at the sumfile time.  The translation is evaluated at the impact time.  "
+                    + "Requires -observerFrame option.")
+            .build());
+    options.addOption(
+        Option.builder("position")
+            .hasArg()
+            .desc(
+                "Spacecraft to body vector in body fixed coordinates.  Units are km.  "
+                    + "Spacecraft is at the origin to be consistent with sumFile convention.")
+            .build());
+    options.addOption(
+        Option.builder("spice")
+            .required()
+            .hasArgs()
+            .desc(
+                "Required.  SPICE metakernel file containing body fixed frame and spacecraft kernels.  "
+                    + "Can specify more than one kernel, separated by whitespace.")
+            .build());
+    options.addOption(
+        Option.builder("sumFile")
+            .hasArg()
+            .desc(
+                "Name of sum file to read.  Coordinate system is assumed to be in the body "
+                    + "fixed frame with the spacecraft at the origin.")
+            .build());
+    options.addOption(
+        Option.builder("target")
+            .required()
+            .hasArg()
+            .desc("Required.  SPICE ID for the target.")
+            .build());
+    options.addOption(
+        Option.builder("trajectory")
+            .hasArg()
+            .desc(
+                "If present, name of output VTK file containing trajectory in body fixed coordinates.")
+            .build());
+    options.addOption(
+        Option.builder("verbosity")
+            .hasArg()
+            .desc("This option does nothing!  Use -logLevel instead.")
+            .build());
+    options.addOption(
+        Option.builder("velocity")
+            .hasArg()
+            .desc(
+                "Spacecraft velocity in J2000 relative to the body.  Units are km/s.  "
+                    + "If not specified, velocity is calculated using SPICE.")
+            .build());
+    return options;
+  }
+
+  public static void main(String[] args) throws Exception {
+    TerrasaurTool defaultOBJ = new ImpactLocator();
+
+    Options options = defineOptions();
+
+    CommandLine cl = defaultOBJ.parseArgs(args, options);
+
+    Map<MessageLabel, String> startupMessages = defaultOBJ.startupMessages(cl);
+    for (MessageLabel ml : startupMessages.keySet())
+      logger.info(String.format("%s %s", ml.label, startupMessages.get(ml)));
+
+    NativeLibraryLoader.loadVtkLibraries();
+    NativeLibraryLoader.loadSpiceLibraries();
+
+    String objFile = cl.getOptionValue("objFile");
+    SmallBodyModel sbm = new SmallBodyModel(PolyDataUtil.loadShapeModel(objFile));
+
+    for (String kernel : cl.getOptionValues("spice")) KernelDatabase.load(kernel);
+    ReferenceFrame J2000 = new ReferenceFrame("J2000");
+    ReferenceFrame bodyFixed = new ReferenceFrame(cl.getOptionValue("frame"));
+    Body observer = new Body(cl.getOptionValue("observer"));
+    Body target = new Body(cl.getOptionValue("target"));
+
+    final double finalHeight =
+        cl.hasOption("finalHeight")
+            ? Double.parseDouble(cl.getOptionValue("finalHeight")) / 1e3
+            : 1e-3;
+    if (finalHeight <= 0) {
+      logger.warn("Argument to -finalHeight must be positive!");
+      System.exit(0);
+    }
+
+    final double finalStep =
+        cl.hasOption("finalStep")
+            ? Double.parseDouble(cl.getOptionValue("finalStep")) / 1e3
+            : Double.MAX_VALUE;
+    if (finalStep <= 0) {
+      logger.warn("Argument to -finalStep must be positive!");
+      System.exit(0);
+    }
+
+    // initial spacecraft position relative to target body
+    Vector3 initialPos = new Vector3();
+    TDBTime et = null;
+    SumFile sumFile = null;
+    if (cl.hasOption("sumFile")) {
+      sumFile = SumFile.fromFile(new File(cl.getOptionValue("sumFile")));
+
+      et = new TDBTime(sumFile.utcString());
+
+      Matrix33 bodyFixedToJ2000 = bodyFixed.getPositionTransformation(J2000, et);
+      Vector3 scObjJ2000 = bodyFixedToJ2000.mxv(MathConversions.toVector3(sumFile.scobj()));
+      initialPos = correctForAberration(scObjJ2000, observer, target, et);
+      initialPos = bodyFixedToJ2000.mtxv(initialPos).negate();
+
+    } else if (cl.hasOption("date")) {
+      String[] parts = cl.getOptionValues("date");
+      StringBuilder sb = new StringBuilder();
+      for (String part : parts) sb.append(part).append(" ");
+      et = new TDBTime(sb.toString());
+    } else {
+      logger.warn("Either -sumFile or -date must be specified.");
+      System.exit(0);
+    }
+    TDBTime et0 = et;
+    AberrationCorrection abCorrNone = new AberrationCorrection("NONE");
+
+    // target's state relative to observer
+    StateRecord sr = new StateRecord(target, et, bodyFixed, abCorrNone, observer);
+
+    /*-
+    // aberration test
+    sr = new StateRecord(target, et, J2000, abCorrNone, observer);
+    StateRecord srLTS =
+        new StateRecord(target, et, J2000, new AberrationCorrection("LT+S"), observer);
+    RemoveAberration ra = new RemoveAberration(target, observer);
+    Vector3 estimatedGeometric = ra.getGeometricPosition(et, srLTS.getPosition());
+
+    System.out.printf("LT+S position:       %s\n", new Vector3(srLTS.getPosition()));
+    System.out.printf("geometric position:  %s\n", new Vector3(sr.getPosition()));
+    Vector3 difference = sr.getPosition().sub(srLTS.getPosition());
+    System.out.printf("difference:          %s %f\n", difference, difference.norm());
+    System.out.printf("aberration angle:    %.3e\n", srLTS.getPosition().sep(sr.getPosition()));
+    System.out.printf("estimated geometric: %s\n", estimatedGeometric);
+    difference = sr.getPosition().sub(estimatedGeometric);
+    System.out.printf("difference:          %s %f\n", difference, difference.norm());
+    System.out.printf("angle:               %.3e\n", estimatedGeometric.sep(sr.getPosition()));
+    System.out.println();
+    System.exit(0);
+    */
+
+    // this is only true with aberration correction NONE!
+    Vector3 scPosBodyFixed = sr.getPosition().negate();
+
+    if (cl.hasOption("position")) {
+      String[] parts = cl.getOptionValue("position").split(",");
+      double[] tmp = new double[3];
+      for (int i = 0; i < 3; i++) tmp[i] = Double.parseDouble(parts[i].trim());
+      initialPos.assign(tmp);
+    } else if (!cl.hasOption("sumFile")) {
+      // use position calculated by SPICE
+      initialPos = scPosBodyFixed;
+    }
+
+    if (Math.abs(scPosBodyFixed.sub(initialPos).norm()) > 0) {
+      logger.warn(
+          String.format(
+              "Warning!  Spacecraft position relative to target from SPICE is %s while input position is %s",
+              new Vector3(scPosBodyFixed), initialPos.toString()));
+      logger.warn(String.format("Difference is %e km", initialPos.sub(scPosBodyFixed).norm()));
+      logger.warn("Continuing with input position");
+    }
+
+    Vector3 initialPosJ2000 = bodyFixed.getPositionTransformation(J2000, et).mxv(initialPos);
+
+    // relative to solar system barycenter in J2000
+    StateVector initialTargetJ2000 =
+        new StateRecord(target, et, J2000, abCorrNone, new Body(0)).getStateVector();
+    StateVector initialObserverJ2000 =
+        new StateVector(
+            initialPosJ2000.add(initialTargetJ2000.getPosition()),
+            new StateRecord(observer, et, J2000, abCorrNone, new Body(0)).getVelocity());
+
+    if (cl.hasOption("velocity")) {
+      String[] parts = cl.getOptionValue("velocity").split(",");
+      double[] tmp = new double[3];
+      for (int i = 0; i < 3; i++) tmp[i] = Double.parseDouble(parts[i].trim());
+      Vector3 scVelJ2000 = new Vector3(tmp);
+
+      initialObserverJ2000 =
+          new StateVector(
+              initialObserverJ2000.getPosition(), scVelJ2000.add(initialTargetJ2000.getVelocity()));
+
+      StateRecord obs = new StateRecord(observer, et, J2000, abCorrNone, new Body(0));
+      logger.info(
+          String.format(
+              "spacecraft velocity relative to target from SPICE at %s is %s",
+              et.toUTCString("ISOC", 3), obs.getVelocity().sub(initialTargetJ2000.getVelocity())));
+      logger.info(String.format("Specified velocity is %s", scVelJ2000));
+    }
+
+    ImpactLocator ifsf =
+        new ImpactLocator(
+            J2000,
+            bodyFixed,
+            sbm,
+            finalHeight,
+            finalStep,
+            et,
+            initialObserverJ2000,
+            initialTargetJ2000,
+            null,
+            null,
+            null);
+
+    NavigableSet<ImpactRecord> records = ifsf.findTrajectory();
+    TDBTime first = records.first().et;
+
+    StateVector scStateBodyFixed = ifsf.getStateBodyFixed(first);
+    StateVector scStateJ2000 =
+        new StateVector(bodyFixed.getStateTransformation(J2000, first).mxv(scStateBodyFixed));
+
+    System.out.printf("T0: %s%n", first.toUTCString("ISOC", 3));
+    System.out.printf("Frame %s: %s%n", bodyFixed.getName(), scStateBodyFixed);
+    System.out.printf("Frame J2000: %s%n", scStateJ2000);
+    System.out.printf(
+        "%s: Observer velocity relative to SSB (J2000): %s%n",
+        first.toUTCString("ISOC", 3), initialObserverJ2000.getVelocity());
+
+    // find coverage of observer and target
+    int numSPK = KernelDatabase.ktotal("SPK");
+    double lastTarget = -Double.MAX_VALUE;
+    double lastObserver = -Double.MAX_VALUE;
+    for (int i = 0; i < numSPK; i++) {
+      String filename = KernelDatabase.getFileName(i, "SPK");
+      SPK thisSPK = SPK.openForRead(filename);
+      SpiceWindow coverage = thisSPK.getCoverage(target.getIDCode());
+      if (coverage.card() > 0) {
+        double[] lastInterval = coverage.getInterval(coverage.card() - 1);
+        lastTarget = Math.max(lastTarget, lastInterval[1]);
+        logger.debug(
+            "SPK {}: body {}, last time is {}",
+            filename,
+            target.getName(),
+            new TDBTime(lastTarget).toUTCString("ISOC", 3));
+      }
+      coverage = thisSPK.getCoverage(observer.getIDCode());
+      if (coverage.card() > 0) {
+        double[] lastInterval = coverage.getInterval(coverage.card() - 1);
+        lastObserver = Math.max(lastObserver, lastInterval[1]);
+        logger.debug(
+            "SPK {}: body {}, last time is {}",
+            filename,
+            observer.getName(),
+            new TDBTime(lastObserver).toUTCString("ISOC", 3));
+      }
+    }
+
+    double lastET = Math.min(records.last().et.getTDBSeconds(), lastTarget);
+    lastET = Math.min(lastET, lastObserver);
+    TDBTime last = new TDBTime(lastET);
+    StateRecord finalObserverJ2000 =
+        new StateRecord(observer, last, J2000, abCorrNone, new Body(0));
+    StateRecord finalTargetJ2000 = new StateRecord(target, last, J2000, abCorrNone, new Body(0));
+    System.out.printf(
+        "%s: Observer velocity relative to SSB (J2000): %s%n",
+        last.toUTCString("ISOC", 3), finalObserverJ2000.getVelocity());
+
+    double duration = last.getTDBSeconds() - first.getTDBSeconds();
+    Vector3 observerAccelerationJ2000 =
+        finalObserverJ2000
+            .getVelocity()
+            .sub(initialObserverJ2000.getVelocity())
+            .scale(1. / duration);
+    Vector3 targetAccelerationJ2000 =
+        finalTargetJ2000.getVelocity().sub(initialTargetJ2000.getVelocity()).scale(1. / duration);
+
+    System.out.printf("Estimated time of impact %s\n", last.toUTCString("ISOC", 6));
+    System.out.printf("Estimated time to impact %.6f seconds\n", duration);
+    System.out.printf("Estimated observer acceleration (J2000): %s\n", observerAccelerationJ2000);
+    System.out.printf("Estimated target acceleration (J2000): %s\n", targetAccelerationJ2000);
+    System.out.printf(
+        "observer acceleration relative to target: %s\n",
+        observerAccelerationJ2000.sub(targetAccelerationJ2000));
+
+    System.out.println();
+
+    // Run again with constant accelerations for target and observer
+    ifsf =
+        new ImpactLocator(
+            J2000,
+            bodyFixed,
+            sbm,
+            finalHeight,
+            finalStep,
+            first,
+            initialObserverJ2000,
+            initialTargetJ2000,
+            last,
+            finalObserverJ2000,
+            finalTargetJ2000);
+    records = ifsf.findTrajectory();
+
+    System.out.printf(
+        "%26s, %13s, %13s, %13s, %13s, %13s, %13s, %12s, %12s, %12s",
+        "UTC",
+        "X (km)",
+        "Y (km)",
+        "Z (km)",
+        "VX (km/s)",
+        "VY (km/s)",
+        "VZ (km/s)",
+        "Lat (deg)",
+        "Lon (deg)",
+        "Alt (m)\n");
+    for (ImpactRecord record : records) {
+      PositionVector p = record.scStateBodyFixed.getPosition();
+      VelocityVector v = record.scStateBodyFixed.getVelocity();
+      System.out.printf(
+          String.format(
+              "%26s, %13.6e, %13.6e, %13.6e, %13.6e, %13.6e, %13.6e, %12.4f, %12.4f, %12.4f\n",
+              record.et.toUTCString("ISOC", 6),
+              p.getElt(0),
+              p.getElt(1),
+              p.getElt(2),
+              v.getElt(0),
+              v.getElt(1),
+              v.getElt(2),
+              Math.toDegrees(record.lc.getLatitude()),
+              Math.toDegrees(record.lc.getLongitude()),
+              record.lc.getRadius() * 1e3));
+    }
+
+    if (cl.hasOption("trajectory")) {
+
+      File trajectoryFile = new File(cl.getOptionValue("trajectory"));
+      File parent = trajectoryFile.getParentFile();
+      if (parent != null && !parent.exists()) parent.mkdirs();
+
+      vtkPolyDataWriter writer = new vtkPolyDataWriter();
+      writer.SetInputData(ifsf.rayBundlePolyData);
+      writer.SetFileName(cl.getOptionValue("trajectory"));
+      writer.SetFileTypeToBinary();
+      writer.Update();
+    }
+
+    if (cl.hasOption("outputTransform")) {
+      if (cl.hasOption("observerFrame")) {
+        // evaluate rotation at -date or -sumFile time
+
+        File transformFile = new File(cl.getOptionValue("outputTransform"));
+        File parent = transformFile.getParentFile();
+        if (!parent.exists()) parent.mkdirs();
+
+        ReferenceFrame scFrame =
+            new ReferenceFrame(cl.getOptionValue("observerFrame").toUpperCase());
+        Matrix33 scToBodyFixed;
+
+        if (sumFile != null) {
+
+          // scToBodyFixed = scFrame.getPositionTransformation(bodyFixed, et0);
+          // logger.info("scToBody (SPICE):\n" + scToBodyFixed);
+
+          ReferenceFrame instrFrame = null;
+          if (cl.hasOption("instrumentFrame"))
+            instrFrame = new ReferenceFrame(cl.getOptionValue("instrumentFrame").toUpperCase());
+          if (instrFrame == null) {
+            logger.error("-instrumentFrame needed for -outputTransform.  Exiting.");
+            System.exit(0);
+          }
+          Matrix33 scToCamera = scFrame.getPositionTransformation(instrFrame, et0);
+
+          // DART SPECIFIC!!!!!! TODO: create a Terrasaur config file with project-specific
+          // defaults,
+          // like spice kernel, camera flips, etc.
+
+          // flip -1, 2, -3
+
+          Vector3 row0 = MathConversions.toVector3(sumFile.cx().negate());
+          Vector3 row1 = MathConversions.toVector3(sumFile.cy());
+          Vector3 row2 = MathConversions.toVector3(sumFile.cz().negate());
+
+          Matrix33 bodyFixedToCamera = new Matrix33(row0, row1, row2);
+
+          scToBodyFixed = bodyFixedToCamera.mtxm(scToCamera);
+
+          // logger.info("scToBody (SUMFILE):\n" + scToBodyFixed);
+        } else {
+          scToBodyFixed = scFrame.getPositionTransformation(bodyFixed, et0);
+        }
+
+        PositionVector p = records.last().scStateBodyFixed.getPosition();
+        try (PrintWriter pw = new PrintWriter(transformFile)) {
+
+          List<String> transform = new ArrayList<>();
+          for (int i = 0; i < 3; i++) {
+            StringBuilder sb = new StringBuilder();
+            for (int j = 0; j < 3; j++) sb.append(String.format("%f ", scToBodyFixed.getElt(i, j)));
+            sb.append(String.format("%f ", p.getElt(i)));
+            transform.add(sb.toString());
+          }
+          transform.add("0 0 0 1");
+          StringBuilder sb = new StringBuilder();
+          for (String s : transform) sb.append(String.format("%s\n", s));
+
+          pw.println(sb);
+        }
+        /*-
+        Pair<Vector3, Matrix33> transform =
+            CommandLineOptionsUtil.getTransformation(cl.getOptionValue("outputTransform"));
+        System.out.printf("translate\n\t%s\n\t%s\n", p.toString(),
+            transform.getFirst().toString());
+        System.out.printf("rotate\n\t%s\n\t%s\n", scToBodyFixed.toString(),
+            transform.getSecond().toString());
+            */
+      } else {
+        logger.warn("-observerFrame needed for -outputTransform");
+      }
+    }
+  }
+}

src/main/java/terrasaur/apps/Maplet2FITS.java

@@ -0,0 +1,865 @@
+package terrasaur.apps;
+
+import com.google.common.io.LittleEndianDataInputStream;
+import java.io.BufferedInputStream;
+import java.io.DataInput;
+import java.io.DataInputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.nio.charset.Charset;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import nom.tam.fits.FitsException;
+import nom.tam.fits.HeaderCard;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.Options;
+import org.apache.commons.io.FileUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import picante.math.coords.CoordConverters;
+import picante.math.coords.LatitudinalVector;
+import picante.math.vectorspace.UnwritableVectorIJK;
+import terrasaur.altwg.pipeline.NameConvention;
+import terrasaur.altwg.pipeline.NamingFactory;
+import terrasaur.altwg.pipeline.ProductNamer;
+import terrasaur.enums.AltwgDataType;
+import terrasaur.enums.FitsHeaderType;
+import terrasaur.enums.PlaneInfo;
+import terrasaur.enums.SrcProductType;
+import terrasaur.fits.FitsData;
+import terrasaur.fits.FitsData.FitsDataBuilder;
+import terrasaur.fits.FitsHdr;
+import terrasaur.fits.FitsHdr.FitsHdrBuilder;
+import terrasaur.fits.HeaderTag;
+import terrasaur.fits.ProductFits;
+import terrasaur.fits.UnitDir;
+import terrasaur.templates.TerrasaurTool;
+import terrasaur.utils.Binary16;
+import terrasaur.utils.BinaryUtils;
+import terrasaur.utils.xml.AsciiFile;
+
+/**
+ * Maplet2FITS program. See the usage string for more information about this program.
+ *
+ * @author Eli Kahn
+ * @version 1.0
+ */
+public class Maplet2FITS implements TerrasaurTool {
+  private static final Logger logger = LogManager.getLogger();
+
+  @Override
+  public String shortDescription() {
+    return "Convert a Gaskell maplet to FITS format.";
+  }
+
+  @Override
+  public String fullDescription(Options options) {
+    String header =
+        """
+This program converts a maplet file in Gaskell maplet format to a FITS file.
+The program assumes the Gaskell scale is in units of km.
+By default the generated FITS cube will contain these 10 planes:
+1. latitude
+2. longitude
+3. radius
+4. x position
+5. y position
+6. z position
+7. height
+8. albedo
+9. sigma
+10. quality
+If the --exclude-position option is provided, then only the height, albedo, sigma
+and quality planes are saved out.""";
+    String footer = "";
+    return TerrasaurTool.super.fullDescription(options, header, footer);
+  }
+
+  public static class HazardParams {
+
+    public final boolean noHazard;
+    public final double initialValue;
+
+    private HazardParams(boolean noHazard, double initialValue) {
+      this.noHazard = noHazard;
+      this.initialValue = initialValue;
+    }
+  }
+
+  /**
+   * Generate HazardParams object that contains attributes needed for generating the Hazard plane.
+   *
+   * @param noHazard
+   * @param initialVal
+   * @return
+   */
+  public static HazardParams getHazardParam(boolean noHazard, double initialVal) {
+    return new HazardParams(noHazard, initialVal);
+  }
+
+  /**
+   * Self-contained function call to generate ALTWG FITS files from a given maplet file. Note the
+   * boolean that determines whether to use the outfile string "as-is" or replace the filename with
+   * one using the ALTWG naming convention.
+   *
+   * @param mapletFile
+   * @param outfile
+   * @param productType
+   * @param excludePosition
+   * @param sigmasFile
+   * @param qualityFile
+   * @param namingConvention
+   * @throws IOException
+   * @throws FitsException
+   */
+  public static void run(
+      String mapletFile,
+      String outfile,
+      AltwgDataType productType,
+      boolean excludePosition,
+      String fitsConfigFile,
+      String sigmasFile,
+      String sigsumFile,
+      String qualityFile,
+      String namingConvention,
+      boolean swapBytes,
+      double scalFactor,
+      double sigmaScale,
+      String mapName,
+      HazardParams hazParam)
+      throws IOException, FitsException {
+
+    // sanity check. If no naming convention specified then outfile should be fully qualified path
+    // to an output file, NOT a directory
+    if (namingConvention.isEmpty()) {
+      File outFname = new File(outfile);
+      if (outFname.isDirectory()) {
+        String errMesg =
+            "ERROR! No naming convention specified but output file:"
+                + outfile
+                + " is a directory! Must be a full path to an output file!";
+        throw new RuntimeException(errMesg);
+      }
+    }
+
+    DataInputStream is =
+        new DataInputStream(new BufferedInputStream(new FileInputStream(mapletFile)));
+    DataInput sigmaInput = null;
+    BufferedInputStream sigmabis = null;
+    if (sigmasFile != null) {
+      System.out.println("Parsing " + sigmasFile + " for sigma values.");
+      Path filePath = Paths.get(sigmasFile);
+      if (!Files.exists(filePath)) {
+        System.out.println(
+            "WARNING! sigmas file:"
+                + filePath.toAbsolutePath()
+                + " not found! Sigmas will default to 0!");
+      } else {
+        sigmabis =
+            new BufferedInputStream(new FileInputStream(filePath.toAbsolutePath().toString()));
+        sigmaInput =
+            swapBytes ? new LittleEndianDataInputStream(sigmabis) : new DataInputStream(sigmabis);
+      }
+    }
+    DataInput qualityInput = null;
+    BufferedInputStream qualbis = null;
+    if (qualityFile != null) {
+      System.out.println("Parsing " + qualityFile + " for quality values.");
+      Path filePath = Paths.get(qualityFile);
+      if (!Files.exists(filePath)) {
+        System.out.println(
+            "WARNING! quality file:"
+                + filePath.toAbsolutePath()
+                + " not found! Quality values will default to 0!");
+      } else {
+        qualbis =
+            new BufferedInputStream(new FileInputStream(filePath.toAbsolutePath().toString()));
+        qualityInput =
+            swapBytes ? new LittleEndianDataInputStream(qualbis) : new DataInputStream(qualbis);
+      }
+    }
+
+    double[] V = new double[3];
+    double[] ux = new double[3];
+    double[] uy = new double[3];
+    double[] uz = new double[3];
+
+    /*
+     * Copied from Bob Gaskell READ_MAP.f code:
+     *
+     * bytes 1-2 height/hscale (integer*2 msb) byte 3 relative "albedo" (1-199) (byte)
+     *
+     * If there is missing data at any point, both height and albedo are set to zero.
+     *
+     * The map array is read row by row from the upper left (i,j = -qsz). Rows are increasing in the
+     * Uy direction with spacing = scale Columns are increasing in the Ux direction with spacing =
+     * scale Heights are positive in the Uz direction with units = scale
+     */
+
+    // use the first 4 bytes of the maplet header to store intensity min & dynamic range.
+    float intensityMin = Binary16.toFloat(BinaryUtils.swap(is.readShort()));
+    float intensityRange = Binary16.toFloat(BinaryUtils.swap(is.readShort()));
+
+    // advancing byte pointer past some headers. Unused, per Bob's WRITE_MAP.f
+    is.readByte();
+    is.readByte();
+
+    float scale = is.readFloat();
+    short halfsize = BinaryUtils.swap(is.readShort());
+
+    // x,y,z position uncertainty unit vector * 255.
+    // per Bob's WRITE_MAP.f
+    is.readByte();
+    is.readByte();
+    is.readByte();
+
+    V[0] = is.readFloat();
+    V[1] = is.readFloat();
+    V[2] = is.readFloat();
+    ux[0] = is.readFloat();
+    ux[1] = is.readFloat();
+    ux[2] = is.readFloat();
+    uy[0] = is.readFloat();
+    uy[1] = is.readFloat();
+    uy[2] = is.readFloat();
+    uz[0] = is.readFloat();
+    uz[1] = is.readFloat();
+    uz[2] = is.readFloat();
+    float hscale = is.readFloat();
+
+    // magnitude of position uncertainty
+    is.readFloat();
+
+    // byte 72 of the maplet header is the version number. OLA uses version numbers < 0 and SPC
+    // maplets have
+    // version numbers > 0. A version number of 0 is Bob Gaskell's original maplet format.
+    byte b = is.readByte();
+    logger.info("byte is:" + b);
+    // boolean isOLAMaplet = (is.readByte() < 0);
+    boolean isOLAMaplet = (b < 0);
+    if (isOLAMaplet) {
+      logger.info("byte72 of maplet header indicates this is an OLA maplet.");
+    } else {
+      logger.info("byte72 of maplet header indicates this is an SPC maplet.");
+    }
+
+    logger.info(String.format("V : [%f %f %f]", V[0], V[1], V[2]));
+    logger.info(String.format("ux: [%f %f %f]", ux[0], ux[1], ux[2]));
+    logger.info(String.format("uy: [%f %f %f]", uy[0], uy[1], uy[2]));
+    logger.info(String.format("uz: [%f %f %f]", uz[0], uz[1], uz[2]));
+    logger.info("halfsize: " + halfsize);
+    logger.info("scale: " + scale);
+    logger.info("hscale: " + hscale);
+    logger.info("AltwgProductType:" + productType.toString());
+
+    int totalsize = 2 * halfsize + 1;
+    int numPlanes = 10;
+    if (excludePosition) {
+      numPlanes = 4;
+      if (!hazParam.noHazard) {
+        numPlanes = numPlanes + 1;
+      }
+    }
+    double[][][] data = new double[numPlanes][totalsize][totalsize];
+    double[][][] llrData = new double[numPlanes][totalsize][totalsize];
+
+    for (int i = -halfsize; i <= halfsize; ++i)
+      for (int j = -halfsize; j <= halfsize; ++j) {
+
+        double h = is.readShort() * hscale * scale;
+
+        int n = 0;
+        int llrIndex = 0;
+        double[] p = {
+          V[0] + i * scale * ux[0] + j * scale * uy[0] + h * uz[0],
+          V[1] + i * scale * ux[1] + j * scale * uy[1] + h * uz[1],
+          V[2] + i * scale * ux[2] + j * scale * uy[2] + h * uz[2]
+        };
+        LatitudinalVector lv = CoordConverters.convertToLatitudinal(new UnwritableVectorIJK(p));
+        if (!excludePosition) {
+          data[n++][i + halfsize][j + halfsize] = Math.toDegrees(lv.getLatitude());
+          data[n++][i + halfsize][j + halfsize] = Math.toDegrees(lv.getLongitude());
+          data[n++][i + halfsize][j + halfsize] = lv.getRadius();
+          data[n++][i + halfsize][j + halfsize] = p[0];
+          data[n++][i + halfsize][j + halfsize] = p[1];
+          data[n++][i + halfsize][j + halfsize] = p[2];
+        } else {
+          llrData[llrIndex++][i + halfsize][j + halfsize] = Math.toDegrees(lv.getLatitude());
+          llrData[llrIndex++][i + halfsize][j + halfsize] = Math.toDegrees(lv.getLongitude());
+          llrData[llrIndex++][i + halfsize][j + halfsize] = lv.getRadius();
+        }
+
+        data[n++][i + halfsize][j + halfsize] = h;
+
+        double albedo = is.readUnsignedByte();
+
+        if (isOLAMaplet) {
+          albedo = albedo / 199. * intensityRange + intensityMin;
+        } else {
+          albedo = albedo / 100.0D;
+        }
+        data[n++][i + halfsize][j + halfsize] = albedo;
+
+        // sigmas default to 0 unless a SIGMAS file was specified
+        float sigmaVal = getSigma(sigmaInput, sigmaScale);
+
+        data[n++][i + halfsize][j + halfsize] = sigmaVal;
+
+        // quality defaults to 0 unless a quality file was specified
+        float qualVal = getQuality(qualityInput);
+
+        data[n++][i + halfsize][j + halfsize] = qualVal;
+
+        if ((excludePosition) && (!hazParam.noHazard)) {
+          // NFT MLN; includes Hazard plane, initialized to initial value
+          data[n++][i + halfsize][j + halfsize] = hazParam.initialValue;
+        }
+      }
+
+    is.close();
+    if (sigmabis != null) sigmabis.close();
+    if (qualbis != null) qualbis.close();
+
+    String sigmaSum = null;
+    if (sigsumFile != null) {
+      sigmaSum = parseSigsumFile(sigsumFile);
+    }
+
+    // Map<String, HeaderCard> headerValues = new LinkedHashMap<String, HeaderCard>();
+
+    // create new fits header builder
+    FitsHdrBuilder hdrBuilder = FitsHdr.getBuilder();
+
+    if (fitsConfigFile != null) {
+      // initialize header cards with values from configfile
+      hdrBuilder = FitsHdr.configHdrBuilder(fitsConfigFile, hdrBuilder);
+    }
+
+    if (sigmaSum != null) {
+      // able to parse sigma summary value. Show this in header builder
+      String hdrTag = HeaderTag.SIGMA.toString();
+      // update sigma summary value
+      hdrBuilder.setVCbyHeaderTag(HeaderTag.SIGMA, sigmaSum, HeaderTag.SIGMA.comment());
+
+      // headerValues.put(HeaderTag.SIGMA.toString(),
+      // new HeaderCard(HeaderTag.SIGMA.toString(), sigmaSum, HeaderTag.SIGMA.comment()));
+
+      // define this SIGMA as a measurement of height uncertainty
+
+      hdrBuilder.setVCbyHeaderTag(
+          HeaderTag.SIG_DEF, "height uncertainty", HeaderTag.SIG_DEF.comment());
+
+      // headerValues.put(HeaderTag.SIG_DEF.toString(),
+      // new HeaderCard(HeaderTag.SIG_DEF.toString(), "Uncertainty", HeaderTag.SIG_DEF.comment()));
+      //// "Definition of the SIGMA uncertainty metric"));
+
+    }
+
+    // set the mapletFile as the DATASRC
+    hdrBuilder.setVbyHeaderTag(HeaderTag.DATASRCF, new File(mapletFile).getName());
+
+    // set the MAP_NAME
+    hdrBuilder.setVbyHeaderTag(HeaderTag.MAP_NAME, mapName);
+
+    // create list describing the planes in the datacube
+    List<PlaneInfo> planeList = new ArrayList<>();
+
+    // determine SrcProductType from header builder
+    String dataSource = SrcProductType.UNKNOWN.toString();
+    if (hdrBuilder.containsKey(HeaderTag.DATASRC.toString())) {
+      HeaderCard srcCard = hdrBuilder.getCard(HeaderTag.DATASRC.toString());
+      dataSource = srcCard.getValue();
+    }
+
+    // use scalFactor to determine GSD
+    double gsd = scale * scalFactor;
+
+    // assume all maplets are local, not global.
+    boolean isGlobal = false;
+
+    // create FitsData object. Stores data and relevant information about the data
+    FitsDataBuilder fitsDataB = new FitsDataBuilder(data, isGlobal);
+    FitsData fitsData =
+        fitsDataB
+            .setV(V)
+            .setAltProdType(productType)
+            .setDataSource(dataSource)
+            .setU(ux, UnitDir.UX)
+            .setU(uy, UnitDir.UY)
+            .setU(uz, UnitDir.UZ)
+            .setScale(scale)
+            .setGSD(gsd)
+            .build();
+
+    if (excludePosition) {
+
+      // define SIG_DEF using just "Uncertainty" for NFT
+      hdrBuilder.setVCbyHeaderTag(HeaderTag.SIG_DEF, "Uncertainty", HeaderTag.SIG_DEF.comment());
+
+      // change comment for DQUAL_2
+      hdrBuilder.setCbyHeaderTag(HeaderTag.DQUAL_2, "Data Quality Metric: mean residual [m]");
+
+      planeList.add(PlaneInfo.HEIGHT);
+      // call this plane ALBEDO even if OLA is the source
+      planeList.add(PlaneInfo.ALBEDO);
+      planeList.add(PlaneInfo.SIGMA);
+      planeList.add(PlaneInfo.QUALITY);
+      if (!hazParam.noHazard) {
+        planeList.add(PlaneInfo.HAZARD);
+      }
+
+      // create llrData object. Stores lat,lon,radius information. Needed to fill out fits header
+      FitsDataBuilder llrDataB = new FitsDataBuilder(llrData, isGlobal);
+      FitsData llrFitsData =
+          llrDataB
+              .setV(V)
+              .setAltProdType(productType)
+              .setDataSource(dataSource)
+              .setU(ux, UnitDir.UX)
+              .setU(uy, UnitDir.UY)
+              .setU(uz, UnitDir.UZ)
+              .setScale(scale)
+              .setGSD(gsd)
+              .build();
+
+      // fill out fits header with information in llrFitsData
+      hdrBuilder.setByFitsData(llrFitsData);
+
+      saveNFTFits(hdrBuilder, fitsData, planeList, namingConvention, outfile);
+
+    } else {
+
+      planeList.add(PlaneInfo.LAT);
+      planeList.add(PlaneInfo.LON);
+      planeList.add(PlaneInfo.RAD);
+      planeList.add(PlaneInfo.X);
+      planeList.add(PlaneInfo.Y);
+      planeList.add(PlaneInfo.Z);
+      planeList.add(PlaneInfo.HEIGHT);
+      planeList.add(PlaneInfo.ALBEDO);
+      planeList.add(PlaneInfo.SIGMA);
+      planeList.add(PlaneInfo.QUALITY);
+
+      saveDTMFits(
+          hdrBuilder, fitsData, planeList, namingConvention, productType, isGlobal, outfile);
+    }
+  }
+
+  private static Options defineOptions() {
+    Options options = TerrasaurTool.defineOptions();
+    options.addOption(
+        Option.builder("input-map").required().hasArg().desc("input maplet file").build());
+    options.addOption(
+        Option.builder("output-fits").required().hasArg().desc("output FITS file").build());
+    options.addOption(
+        Option.builder("exclude-position")
+            .desc(
+                "Only save out the height, albedo, sigma, quality, and hazard planes to the output file. Used for creating NFT MLNs.")
+            .build());
+    options.addOption(
+        Option.builder("noHazard")
+            .desc(
+                "Only used in conjunction with -exclude-position. If present then the NFT MLN will NOT include a Hazard plane initially filled with all ones.")
+            .build());
+    options.addOption(
+        Option.builder("hazardVal")
+            .hasArg()
+            .desc(
+                "Only used in conjunction with -exclude-position. If present then will use the specified value.")
+            .build());
+    options.addOption(
+        Option.builder("lsb")
+            .desc(
+                """
+         By default the sigmas and quality binary files are assumed to be in big-endian floating
+          point format. Pass this argument if you know your sigma and quality binary files are
+          in little-endian format. For example, products created by SPC executables are OS
+          dependent and intel Linux OSes use little-endian.""")
+            .build());
+    options.addOption(
+        Option.builder("scalFactor")
+            .hasArg()
+            .desc(
+                "Enter scale factor used to convert scale to ground sample distance in mm i.e. for SPC maplets the scale factor is 1000000 (km to mm).  Set to 1.0e6 by default.")
+            .build());
+    options.addOption(
+        Option.builder("sigmas-file")
+            .hasArg()
+            .desc(
+                "Path to binary sigmas file containing sigma values per pixel, in same order as the maplet file. If this option is omitted, the sigma plane is set to all zeros.")
+            .build());
+    options.addOption(
+        Option.builder("sigsum-file")
+            .hasArg()
+            .desc(
+                "Path to ascii sigma summary file, containing the overall sigma value of the maplet.")
+            .build());
+    options.addOption(
+        Option.builder("sigmaScale")
+            .hasArg()
+            .desc(
+                "Scale sigmas from sigmas-file by <value>. Only applicable if -sigmas-file is used.  Defaults to 1 if not specified.")
+            .build());
+    options.addOption(
+        Option.builder("mapname")
+            .hasArg()
+            .desc("Sets the MAP_NAME fits keyword to <mapname>. Default is 'Non-NFT DTM'")
+            .build());
+    options.addOption(
+        Option.builder("quality-file")
+            .hasArg()
+            .desc(
+                "Path to binary quality file containing quality values. If this option is omitted, the quality plane is set to all zeros.")
+            .build());
+    options.addOption(
+        Option.builder("configFile")
+            .hasArg()
+            .desc(
+                """
+          Path to fits configuration file that contains keywords and values which should be included
+          in the fits header. The fits header will always be fully populated with all keywords
+          that are required by the ALTWG SIS. The values may not be populated or UNK if they cannot
+          be derived from the data itself. This configuration file is a way to populate those values.""")
+            .build());
+    options.addOption(
+        Option.builder("namingConvention")
+            .hasArg()
+            .desc(
+                """
+          Renames the output fits file per the naming convention specified by the string.
+          Currently supports 'altproduct', 'dartproduct', and 'altnftmln' conventions.
+          NOTE that -exclude-position does not automatically choose the 'altnftmln'
+          naming convention! 'ALTWG NFT MLN naming convention (altnftmln) MUST BE EXPLICITLY SPECIFIED
+          The renamed file is placed in the path specified by -output-fits""")
+            .build());
+    return options;
+  }
+
+  public static void main(String[] args) throws FitsException, IOException {
+    TerrasaurTool defaultOBJ = new Maplet2FITS();
+
+    Options options = defineOptions();
+
+    CommandLine cl = defaultOBJ.parseArgs(args, options);
+
+    Map<MessageLabel, String> startupMessages = defaultOBJ.startupMessages(cl);
+    for (MessageLabel ml : startupMessages.keySet())
+      logger.info(String.format("%s %s", ml.label, startupMessages.get(ml)));
+
+    boolean excludePosition = cl.hasOption("exclude-position");
+    boolean noHazard = cl.hasOption("noHazard");
+    String namingConvention = cl.getOptionValue("namingConvention", "noneused");
+    boolean swapBytes = cl.hasOption("lsb");
+    String sigmasFile = cl.hasOption("sigmas-file") ? cl.getOptionValue("sigmas-file") : null;
+    String sigsumFile = cl.hasOption("sigsum-file") ? cl.getOptionValue("sigsum-file") : null;
+    String qualityFile = cl.hasOption("quality-file") ? cl.getOptionValue("quality-file") : null;
+    String fitsConfigFile = cl.hasOption("configFile") ? cl.getOptionValue("configFile") : null;
+    String mapName = cl.getOptionValue("mapname", "Non-NFT DTM");
+
+    double scalFactor =
+        Double.parseDouble(cl.getOptionValue("scalFactor", "1e6").replaceAll("[dD]", "e"));
+    double sigmaScale =
+        Double.parseDouble(cl.getOptionValue("sigmaScale", "1.0").replaceAll("[dD]", "e"));
+    double hazardVal =
+        Double.parseDouble(cl.getOptionValue("hazardVal", "1.0").replaceAll("[dD]", "e"));
+    AltwgDataType altwgProduct = AltwgDataType.NA;
+
+    if (sigsumFile != null) logger.info("using {} to parse for global uncertainty.", sigsumFile);
+
+    if (!namingConvention.isEmpty()) {
+      if (excludePosition) {
+        altwgProduct = AltwgDataType.NFTDTM;
+      } else {
+        altwgProduct = AltwgDataType.DTM;
+      }
+    }
+
+    HazardParams hazParams = getHazardParam(noHazard, hazardVal);
+
+    String mapletFile = cl.getOptionValue("input-map");
+    String outfile = cl.getOptionValue("output-fits");
+    logger.info("altwgProductType:{}", altwgProduct.toString());
+    run(
+        mapletFile,
+        outfile,
+        altwgProduct,
+        excludePosition,
+        fitsConfigFile,
+        sigmasFile,
+        sigsumFile,
+        qualityFile,
+        namingConvention,
+        swapBytes,
+        scalFactor,
+        sigmaScale,
+        mapName,
+        hazParams);
+  }
+
+  public static String parseSigsumFile(String sigsumFile) throws IOException {
+    if (!Files.exists(Paths.get(sigsumFile))) {
+      System.out.println(
+          "Warning! Sigmas summary file:"
+              + sigsumFile
+              + " does not exist! Not "
+              + "able to parse sigma summary.");
+      return null;
+    } else {
+      List<String> content = FileUtils.readLines(new File(sigsumFile), Charset.defaultCharset());
+      String firstLine = content.get(0);
+
+      if (firstLine != null) {
+
+        // first assume format is <mapletfilename> <sigma summary> <blah>
+        // this is the SPC format
+        // try to parse a double from this
+        String[] array = firstLine.split(" +");
+        boolean foundFirst = false;
+        if (array.length > 1) {
+          System.out.println("Assuming sigma summary file of form:");
+          System.out.println("<maplet Filename> <sigma summary> <blah>");
+          for (String s : array) {
+            if (foundFirst) {
+              // second cell after finding the first non-empty cell should be the sigma summary
+              // value!
+              double thisD = Double.parseDouble(s.replaceAll("[dD]", "e"));
+              return Double.isNaN(thisD) ? null : Double.toString(thisD);
+            }
+            if (!s.isEmpty()) {
+              // loop through array until you find first non-empty string.
+              // This should be the maplet filename
+              foundFirst = true;
+            }
+          }
+        } else {
+
+          // assume format is mean on first line, median on second line
+          if (content.size() > 1) {
+            System.out.println("Assuming sigma summary file of form:");
+            System.out.println("<mean value>");
+            System.out.println("<median value>");
+            System.out.println("Will use median value");
+            return content.get(1).replaceAll("\\s+", "");
+          } else {
+            // first line is not null but there is only one line
+            System.out.println("Assuming first value in first line contains sigma summary!");
+            return content.get(0).replaceAll("\\s+", "");
+          }
+        }
+
+        // did not find first non-empty string or did not find sigma
+        System.out.println("WARNING: Could not parse sigma summary file!");
+        return null;
+
+        /*
+         * firstLine = firstLine.replace(" ", ""); double thisD = StringUtil.parseSafeD(firstLine);
+         * if (Double.isNaN(thisD)) { Pattern p = Pattern.compile("^\\s*(\\d+\\.?\\d+)\\s*.*");
+         * Matcher m = p.matcher(firstLine); if (m.matches()) { return m.group(1); } else { return
+         * null; } } else { return Double.toString(thisD); }
+         */
+      } else {
+        return null;
+      }
+    }
+  }
+
+  /**
+   * Given a maplet, return the command call to Maplet2FITS to turn it into a fits file. Allows one
+   * to specify filenames of sigma, sigma summary, and quality files. Set string variables to empty
+   * string if you do not wish to include them in the command call. Method generates the full set of
+   * fits file planes, i.e. NOT an NFT Fits file.
+   *
+   * @param mapletFile - path to maplet
+   * @param configFile - configuration file to use
+   * @param lsb - if True assume sigma and quality files are in little-endian
+   * @param sigmaFile - pointer to sigma file. Leave as empty string if no file exists/needed
+   *     (defaults to 0).
+   * @param sigmaScaleF - sigma scale factor to be used with sigma values read from sigma file.
+   * @param sigsumFile - pointer to simga summary file. Leave as empty string if no file
+   *     exists/needed (defaults to 0)
+   * @param qualityFile - pointer to quality file. Leave as empty string if no file exists/needed
+   *     (defaults to 0).
+   * @return
+   */
+  public static String getCmd(
+      File mapletFile,
+      String outFits,
+      String configFile,
+      boolean altwgNaming,
+      boolean lsb,
+      String sigmaFile,
+      String sigsumFile,
+      String sigmaScaleF,
+      String qualityFile) {
+
+    StringBuilder toolexe = new StringBuilder("Maplet2FITS");
+    if (!configFile.isEmpty()) {
+      toolexe.append(" -configFile ");
+      toolexe.append(configFile);
+    }
+
+    if (altwgNaming) {
+      toolexe.append(" -altwgNaming");
+    }
+
+    if (lsb) {
+      toolexe.append(" -lsb");
+    }
+
+    Path thisFile;
+    if (!sigmaFile.isEmpty()) {
+      thisFile = Paths.get(sigmaFile);
+      if (Files.exists(thisFile)) {
+        toolexe.append(" -sigmas-file ");
+        toolexe.append(thisFile.toAbsolutePath());
+      } else {
+        logger.warn("Could not find sigmas file:{}", sigmaFile);
+      }
+    }
+
+    if (!sigmaScaleF.isEmpty()) {
+      toolexe.append(" -sigmaScale ");
+      toolexe.append(sigmaScaleF);
+    }
+
+    if (!sigsumFile.isEmpty()) {
+      thisFile = Paths.get(sigsumFile);
+      if (Files.exists(thisFile)) {
+        toolexe.append(" -sigsum-file ");
+        toolexe.append(thisFile.toAbsolutePath());
+      } else {
+        logger.warn("Could not find sigma summary file:{}", sigsumFile);
+      }
+    }
+
+    if (!qualityFile.isEmpty()) {
+      thisFile = Paths.get(qualityFile);
+      if (Files.exists(thisFile)) {
+        toolexe.append(" -quality-file ");
+        toolexe.append(thisFile.toAbsolutePath());
+      } else {
+        logger.warn("Could not find quality file:{}", qualityFile);
+      }
+    }
+
+    toolexe.append(" ");
+    toolexe.append(mapletFile.getAbsolutePath());
+    toolexe.append(" ");
+    toolexe.append(outFits);
+
+    return toolexe.toString();
+  }
+
+  private static float getSigma(DataInput dataIn, double sigmaScale) throws IOException {
+    float floatVal = 0f;
+    if (dataIn != null) {
+      floatVal = dataIn.readFloat();
+    }
+    floatVal = floatVal * (float) sigmaScale;
+    return floatVal;
+  }
+
+  private static float getQuality(DataInput dataIn) throws IOException {
+    float floatVal = 0f;
+    if (dataIn != null) {
+      floatVal = dataIn.readFloat();
+    }
+    return floatVal;
+  }
+
+  private static void saveNFTFits(
+      FitsHdrBuilder hdrBuilder,
+      FitsData fitsData,
+      List<PlaneInfo> planeList,
+      String namingConvention,
+      String outfile)
+      throws FitsException, IOException {
+
+    File crossrefFile = null;
+
+    NameConvention nameConvention = NameConvention.parseNameConvention(namingConvention);
+    if (nameConvention != NameConvention.NONEUSED) {
+
+      String outNFTFname = outfile;
+      Path outPath = Paths.get(outNFTFname);
+
+      // save old filename
+      String oldFilename = outPath.getFileName().toString();
+
+      // hardcode for now. NFT is not a nominal Toolkit product.
+      AltwgDataType productType = null;
+      boolean isGlobal = false;
+
+      // generate new NFT output filename based on naming convention
+      ProductNamer productNamer = NamingFactory.parseNamingConvention(namingConvention);
+      String newbaseName = productNamer.productbaseName(hdrBuilder, productType, isGlobal);
+
+      String newFilename = newbaseName + ".fits";
+
+      // replace outfile with new nft filename and write FITS file to it.
+      outNFTFname = outNFTFname.replace(oldFilename, newFilename);
+
+      // save new PDS name in cross-reference file, for future reference
+      crossrefFile = new File(outNFTFname + ".crf");
+      AsciiFile crfFile = new AsciiFile(crossrefFile.getAbsolutePath());
+      crfFile.streamSToFile(newbaseName, 0);
+      crfFile.closeFile();
+
+      outfile = outNFTFname;
+    }
+
+    FitsHeaderType hdrType = FitsHeaderType.NFTMLN;
+    ProductFits.saveNftFits(fitsData, planeList, outfile, hdrBuilder, hdrType, crossrefFile);
+  }
+
+  private static void saveDTMFits(
+      FitsHdrBuilder hdrBuilder,
+      FitsData fitsData,
+      List<PlaneInfo> planeList,
+      String namingConvention,
+      AltwgDataType productType,
+      boolean isGlobal,
+      String outfile)
+      throws FitsException, IOException {
+
+    // Use a different static method to create the ALTWG product. This allows me to differentiate
+    // between different kinds of fits header types.
+    FitsHeaderType hdrType = FitsHeaderType.DTMLOCALALTWG;
+
+    File crossrefFile;
+    String outFitsFname = outfile;
+
+    // possible renaming of output file
+    NameConvention nameConvention = NameConvention.parseNameConvention(namingConvention);
+    File[] outFiles =
+        NamingFactory.getBaseNameAndCrossRef(
+            nameConvention, hdrBuilder, productType, isGlobal, outfile);
+
+    // check if cross-ref file is not null. If so then output file was renamed to naming convention.
+    crossrefFile = outFiles[1];
+    if (crossrefFile != null) {
+
+      // rename fitsFile per naming convention and create a cross-reference file.
+      String baseOutputName = outFiles[0].toString();
+
+      // determine whether original outfile is a directory
+      File outFname = new File(outfile);
+      String outputFolder = outFname.getAbsoluteFile().getParent();
+      if (outFname.isDirectory()) {
+        outputFolder = outfile;
+
+        // cannot create cross-reference file if original outfile was a directory. make it null;
+        crossrefFile = null;
+      }
+      outFitsFname = new File(outputFolder, baseOutputName + ".fits").getAbsolutePath();
+    }
+    ProductFits.saveDataCubeFits(
+        fitsData, planeList, outFitsFname, hdrBuilder, hdrType, crossrefFile);
+  }
+}

src/main/java/terrasaur/apps/OBJ2DSK.java

@@ -0,0 +1,593 @@
+package terrasaur.apps;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.nio.file.FileSystems;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import com.beust.jcommander.JCommander;
+import com.beust.jcommander.Parameter;
+import com.beust.jcommander.ParameterException;
+import org.apache.commons.cli.Options;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import terrasaur.fits.HeaderTag;
+import terrasaur.fits.ProductFits;
+import terrasaur.templates.TerrasaurTool;
+import terrasaur.utils.AppVersion;
+import terrasaur.utils.JCommanderUsage;
+import terrasaur.utils.NativeLibraryLoader;
+import terrasaur.utils.PolyDataUtil;
+import terrasaur.utils.ProcessUtils;
+import vtk.vtkPolyData;
+
+public class OBJ2DSK implements TerrasaurTool {
+
+  private static final Logger logger = LogManager.getLogger();
+
+
+
+  @Override
+  public String shortDescription() {
+      return "Convert an OBJ shape file to SPICE DSK format.";
+  }
+
+  @Override
+  public String fullDescription(Options options) {
+    StringBuilder builder = new StringBuilder();
+    Arguments arguments = new Arguments();
+    JCommander jcommander = new JCommander(arguments);
+    jcommander.setProgramName("OBJ2DSK");
+
+    JCommanderUsage jcUsage = new JCommanderUsage(jcommander);
+    jcUsage.setColumnSize(100);
+    jcUsage.usage(builder, 4, arguments.commandDescription);
+    return builder.toString();
+
+  }
+
+  private enum DSK_KEYS {
+    SURF_NAME, CENTER_NAME, REFFRAME_NAME, NAIF_SURFNAME, NAIF_SURFCODE, NAIF_SURFBODY, METAK, COMMENTFILE
+  }
+
+  private static class Arguments {
+
+    private final String commandDescription = AppVersion.getVersionString()
+        + "\n\nConverts a triangular plate model in OBJ format to a SPICE DSK file.\n"
+        + "The SPICE utility application 'mkdsk' must already be present on your PATH.\n";
+
+    @Parameter(names = "-help", help = true)
+    private boolean help;
+
+    @Parameter(names = "--latMin", description = "<latMin> Minimum latitude of OBJ in degrees.",
+        required = false, order = 0)
+    private double latMin = -90D;
+
+    @Parameter(names = "--latMax", description = "<latMax> Maximum latitude of OBJ in degrees.",
+        required = false, order = 1)
+    private double latMax = 90D;
+
+    @Parameter(names = "--lonMin", description = "<lonMin> Minimum longitude of OBJ in degrees.",
+        required = false, order = 2)
+    private double lonMin = 0;
+
+    @Parameter(names = "--lonMax", description = "<lonMax> Maximum longitude of OBJ in degrees.",
+        required = false, order = 3)
+    private double lonMax = 360D;
+
+    @Parameter(names = "--fitsFile",
+        description = "<filename> path to DTM fits file containing lat,lon"
+            + " information as planes. Assumes PLANE1=latitude, PLANE2=longitude. Use in place of specifying lat/lon min/max values.",
+        required = false, order = 4)
+    private String fitsFile = "";
+
+    @Parameter(names = "--fine-scale",
+        description = "<fine-voxel-scale> Floating point value representing the "
+            + " ratio of the spatial index's fine  voxel edge length to the average plate extent. "
+            + " The 'extent' of a plate in a given coordinate direction is the difference between the maximum and minimum "
+            + " values of that coordinate attained on the plate. Only required if mkdsk version is "
+            + " lower than 66.",
+        required = false, order = 11)
+    double fineVoxScale = Double.NaN;
+
+    @Parameter(names = "--coarse-scale",
+        description = " <coarse-voxel-scale>"
+            + " Integer value representing the ratio of the edge length of coarse voxels to"
+            + " fine voxels. The number must be large enough that the total number of coarse"
+            + " voxels is less than the value of MAXCGR, which is currently 1E5."
+            + " Only required if mkdsk version is lower than 66.",
+        required = false, order = 12)
+    Integer coarseVoxScale = -999;
+
+    @Parameter(names = "--useSetupFile",
+        description = "<inputSetupFile> Use <inputSetupFile>"
+            + " instead of the default setup file created by the tool.",
+        required = false, order = 13)
+    String inputSetup = "";
+
+    @Parameter(names = "--writesetupFile",
+        description = "<outputSetupFile> Write the setup file"
+            + " to the specified path instead of writing it as a temporary file which gets deleted"
+            + " after execution.",
+        required = false, order = 14)
+    String outsetupFname = "";
+
+    @Parameter(names = "--keepTempFiles",
+        description = "enable this to prevent setup files"
+            + " from being deleted. Used for debugging purposes to see what is being sent"
+            + " to mkdsk.",
+        required = false, order = 15)
+    boolean keepTmpFiles = false;
+
+    @Parameter(names = "--mkFile",
+        description = "<spice-meta-kernel-file> path to SPICE meta kernel file."
+            + " Metakernel only needs to point to leap seconds kernel and a frames kernel that contains"
+            + " the digital ID to CENTER_NAME and REF_FRAME_NAME lookup table."
+            + " This argument is REQUIRED if user does NOT supply a setupFile!",
+        required = false, order = 4)
+    String mkFile = "";
+
+    @Parameter(names = "--surfName",
+        description = "<surfaceName> Allows user to modify the "
+            + " SURFACE_NAME (name of the specific shape data set for the central body)"
+            + " used in the default setup file created by the tool. This is a required"
+            + " keyword in the setup file.",
+        required = false, order = 5)
+    String surfaceName = "BENNU";
+
+    @Parameter(names = "--centName", description = "<centerName> Allows user to modify the "
+        + " CENTER_NAME (central body name) used in the default setup file created by the tool. "
+        + " Can also be an ID code.  This is a required keyword in the setup file.",
+        required = false, order = 6)
+    String centerName = "BENNU";
+
+    @Parameter(names = "--refName", description = "<refFrameName> Allows user to modify the "
+        + " REF_FRAME_NAME (reference frame name) used in the default setup file created by the tool. "
+        + " This is a required keyword in the setup file.", required = false, order = 7)
+    String refFrameName = "IAU_BENNU";
+
+    @Parameter(names = "--naif_surfName",
+        description = "<naif surface name> Allows user to add the "
+            + " NAIF_SURFACE_NAME to the default setup file created by the tool. "
+            + " This may be needed under certain conditions. Optional keyword. "
+            + " Default is not to use it.",
+        required = false, order = 8)
+    String naifSurfName = "";
+
+    @Parameter(names = "--naif_surfCode",
+        description = "<integer ID surface code> Allows user to add the "
+            + " NAIF_SURFACE_CODE to the default setup file created by the tool. "
+            + " Allows the tool to associate this ID code to the NAIF_SURFACE_NAME. Optional keyword. "
+            + " Default is not to use it.",
+        required = false, order = 9)
+    String naifSurfCode = "";
+
+    @Parameter(names = "--naif_surfBody",
+        description = "<integer body ID code> Allows user to add the "
+            + " NAIF_SURFACE_BODY to the default setup file created by the tool. "
+            + " This may be needed under certain conditions. Optional keyword."
+            + " Default is not to use it.",
+        required = false, order = 10)
+    String naifSurfBody = "";
+
+    @Parameter(names = "--cmtFile",
+        description = "<commentFile> Specify the comment file"
+            + " that mkdsk will add to the DSK. Comment file is an ASCII file containing"
+            + " additional information about the DSK. Default is single space.",
+        required = false, order = 11)
+    String cmtFile = " ";
+
+    @Parameter(names = "-shortDescription", hidden = true)
+    private boolean shortDescription = false;
+
+    @Parameter(
+        description = " Versions of mkdsk that are V066 and higher will automatically calculate the\n"
+            + "   voxel scales which optimize processing time without exceeding maximum array sizes.\n"
+            + "   However, if you are using a version of mkdsk that is below v066 you can specify the\n"
+            + "   FINE_VOXEL_SCALE and COARSE_VOXEL_SCALE via the '--fine-scale' and '--coarse-scale'\n"
+            + "   optional arguments.\n"
+            + "   Run 'mkdsk' by itself and note the 'Toolkit ver' version number. If it is below\n"
+            + "   066 then you MUST specify the fine and coarse voxel scales.\n"
+            + "   See SPICE documentation notes on recommended values.\n\n"
+            + "Usage: OBJ2DSK [options] <input-obj-file> <output-dsk-file>\nWhere:\n"
+            + "  <input-obj-file>\n" + "          input OBJ file\n" + "  <output-dsk-file>\n"
+            + "          output dsk file\n"
+            + "  NOTE: MUST set --metakFile if not supplying a custom setup file!")
+    private List<String> files = new ArrayList<>();
+
+  }
+
+  private final Double fineVoxScale;
+  private final Integer coarseVoxScale;
+
+  public OBJ2DSK(double fineVoxScale, int coarseVoxScale) {
+    this.fineVoxScale = fineVoxScale;
+    this.coarseVoxScale = coarseVoxScale;
+  }
+
+  public OBJ2DSK() {
+    this(Double.NaN, -1);
+  }
+
+  public static void main(String[] args) throws Exception {
+
+    TerrasaurTool defaultObj = new OBJ2DSK();
+
+    int i = 0;
+    Map<String, Double> latLonMinMax = new HashMap<String, Double>();
+    // String fitsFname = "";
+    // String temp;
+    // String inputSetup = "";
+    // boolean keepTmpFiles = false;
+
+    // check for -shortDescription before looking for required arguments
+    for (String arg : args) {
+      if (arg.equals("-shortDescription")) {
+        System.out.println(defaultObj.shortDescription());
+        System.exit(0);
+      }
+    }
+
+    Arguments arg = new Arguments();
+
+    JCommander command = new JCommander(arg);
+    try {
+      // @Deprecated
+      // command = new JCommander(arg, args);
+      command.parse(args);
+    } catch (ParameterException ex) {
+      System.out.println(defaultObj.fullDescription(null));
+      System.out.println("Error parsing input arguments:");
+      System.out.println(ex.getMessage());
+      command = new JCommander(arg);
+      System.exit(1);
+
+    }
+
+    if ((args.length < 1) || (arg.help)) {
+      System.out.println(defaultObj.fullDescription(null));
+      System.exit(0);
+    }
+
+    // This is to avoid java crashing due to inability to connect to an X display
+    System.setProperty("java.awt.headless", "true");
+
+    String spiceFile = "";
+    String inFile = "";
+    String outFile = "";
+    if (arg.files.size() != 2) {
+      String errMesg = "ERROR! Expecting 2 required inputs: input OBJ, output DSK";
+      throw new RuntimeException(errMesg);
+    } else {
+      spiceFile = arg.mkFile;
+      inFile = arg.files.get(0);
+      outFile = arg.files.get(1);
+    }
+
+    boolean useFitsFile = false;
+    boolean latLonSet = false;
+
+    String fitsFname = arg.fitsFile;
+    if (!fitsFname.isEmpty()) {
+      useFitsFile = true;
+      System.out.println("Will use lat,lons from " + fitsFname + " to set lat,lon bounds.");
+      // load the fits header and parse for min, max lat, lon values
+      latLonMinMax = ProductFits.minMaxLLFromFits(new File(fitsFname));
+
+      if (latLonMinMax.size() < 4) {
+        System.out.println("ERROR! Could not parse all min,max lat/lon corners!");
+        System.out.println("Unable to create DSK for " + inFile + "!");
+        System.exit(1);
+      }
+    } else {
+      // parse lat,lon bounds. Some of these may be set to default values.
+      latLonMinMax.put(HeaderTag.MINLAT.toString(), arg.latMin);
+      latLonMinMax.put(HeaderTag.MAXLAT.toString(), arg.latMax);
+      latLonMinMax.put(HeaderTag.MINLON.toString(), arg.lonMin);
+      latLonMinMax.put(HeaderTag.MAXLON.toString(), arg.lonMax);
+      latLonSet = true;
+    }
+
+    System.out.println("Using these lat, lon bounds:");
+    for (String thisKey : latLonMinMax.keySet()) {
+      System.out.println("key:" + thisKey + ", value:" + latLonMinMax.get(thisKey));
+    }
+
+    NativeLibraryLoader.loadVtkLibraries();
+
+
+    OBJ2DSK obj2dsk;
+    if ((Double.isNaN(arg.fineVoxScale)) || (arg.coarseVoxScale < 0)) {
+      obj2dsk = new OBJ2DSK();
+    } else {
+      obj2dsk = new OBJ2DSK(arg.fineVoxScale, arg.coarseVoxScale);
+    }
+
+    // generate setup file if needed
+    File setupFile = null;
+    Map<DSK_KEYS, String> dskParams = new HashMap<DSK_KEYS, String>();
+    dskParams.put(DSK_KEYS.SURF_NAME, arg.surfaceName);
+    dskParams.put(DSK_KEYS.CENTER_NAME, arg.centerName);
+    dskParams.put(DSK_KEYS.REFFRAME_NAME, arg.refFrameName);
+    dskParams.put(DSK_KEYS.NAIF_SURFNAME, arg.naifSurfName);
+    dskParams.put(DSK_KEYS.NAIF_SURFCODE, arg.naifSurfCode);
+    dskParams.put(DSK_KEYS.NAIF_SURFBODY, arg.naifSurfBody);
+    dskParams.put(DSK_KEYS.COMMENTFILE, arg.cmtFile);
+    dskParams.put(DSK_KEYS.METAK, spiceFile);
+
+    String outsetupFname = arg.outsetupFname;
+    String inputSetup = arg.inputSetup;
+
+    boolean keepTmpFiles = arg.keepTmpFiles;
+    if (inputSetup.isEmpty()) {
+
+      if (spiceFile.isEmpty()) {
+        String errMesg = "ERROR! MUST supply path to SPICE metakernel via --mkFile!";
+        throw new RuntimeException(errMesg);
+      }
+
+      System.out.println("Creating default setup file");
+      setupFile = createSetup(latLonMinMax, obj2dsk.fineVoxScale, obj2dsk.coarseVoxScale, dskParams,
+          outsetupFname);
+      if (keepTmpFiles) {
+        System.out.println("setup file created here:" + outsetupFname);
+      } else {
+        setupFile.deleteOnExit();
+      }
+
+    } else {
+
+      // check that input setup file exists
+      setupFile = new File(inputSetup);
+      if (!setupFile.exists()) {
+        String errMesg = "Custom setup file:" + inputSetup + " not found!";
+        throw new RuntimeException(errMesg);
+      }
+      System.out.println("Using custom setup file:" + inputSetup);
+
+    }
+    obj2dsk.run(inFile, outFile, latLonMinMax, setupFile, outsetupFname, keepTmpFiles);
+
+    /*
+     * for (; i < args.length; ++i) { if (args[i].equals("-shortDescription")) {
+     * System.out.println(defaultObj.shortDescription()); System.exit(0); } else if
+     * (args[i].equals("--latMin")) { latLonMinMax.put(HeaderTag.MINLAT.toString(),
+     * StringUtil.parseSafeD(args[++i])); latLonSet = true; } else if (args[i].equals("--latMax")) {
+     * latLonMinMax.put(HeaderTag.MAXLAT.toString(), StringUtil.parseSafeD(args[++i])); latLonSet =
+     * true; } else if (args[i].equals("--lonMin")) { latLonMinMax.put(HeaderTag.MINLON.toString(),
+     * StringUtil.parseSafeD(args[++i])); latLonSet = true; } else if (args[i].equals("--lonMax")) {
+     * latLonMinMax.put(HeaderTag.MAXLON.toString(), StringUtil.parseSafeD(args[++i])); latLonSet =
+     * true; } else if (args[i].equals("--fits-file")) { fitsFname = args[++i]; useFitsFile = true;
+     * } else if (args[i].equals("--fine-scale")) { temp = args[++i]; fineVoxScale =
+     * StringUtil.parseSafeD(temp); if (fineVoxScale == Double.NaN) {
+     * System.err.println("ERROR! value for fine-scale:" + temp);
+     * System.err.println("Could not be converted into a double!");
+     * System.out.println("Exiting program."); System.exit(1); } userVox = true;
+     * 
+     * } else if (args[i].equals("--coarse-scale")) {
+     * 
+     * temp = args[++i]; double tempD = StringUtil.parseSafeD(temp); if (tempD == Double.NaN) {
+     * System.err.println("ERROR! value for coarse-scale:" + temp);
+     * System.err.println("Could not be converted into a number!");
+     * System.out.println("Exiting program."); System.exit(1); } coarseVoxScale = (int) tempD;
+     * userVox = true;
+     * 
+     * } else if (args[i].equals("--writesetupFile")) { outsetupFname = args[++i]; } else if
+     * (args[i].equals("--useSetupFile")) { inputSetup = args[++i]; keepTmpFiles = true; } else if
+     * (args[i].equals("--keepTempFiles")) { keepTmpFiles = true; } else { break; } }
+     * 
+     * // There must be numRequiredArgs arguments remaining after the options. // Otherwise abort.
+     * int numberRequiredArgs = 3; if (args.length - i != numberRequiredArgs) {
+     * System.out.println(defaultObj.fullDescription()); System.exit(0); }
+     * 
+     * String current = new java.io.File(".").getAbsolutePath();
+     * System.out.println("Running OBJ2DSK. Current dir:" + current);
+     * 
+     * String spicefile = args[i++]; String infile = args[i++]; String outfile = args[i++];
+     */
+
+  }
+
+  public void run(String infile, String outfile, Map<String, Double> latLonMinMax, File setupFile,
+      String outsetupFname, boolean keepTmpFiles) throws Exception {
+
+    System.out.println("Running OBJ2DSK.");
+    System.out.println("FINE_VOXEL_SCALE = " + Double.toString(fineVoxScale));
+    System.out.println("COARSE_VOXEL_SCALE = " + Integer.toString(coarseVoxScale));
+
+    // File setupFile = null;
+    // if (inputSetup.length() < 1) {
+    // System.out.println("Creating default setup file");
+    // setupFile = createSetup(spicefile, latLonMinMax, this.fineVoxScale, this.coarseVoxScale,
+    // outsetupFname);
+    // if (keepTmpFiles) {
+    // System.out.println("setup file created here:" + outsetupFname);
+    // } else {
+    // setupFile.deleteOnExit();
+    // }
+    // } else {
+    // // check that input setup file exists
+    // setupFile = new File(inputSetup);
+    // if (!setupFile.exists()) {
+    // String errMesg = "Custom setup file:" + inputSetup + " not found!";
+    // throw new RuntimeException(errMesg);
+    // }
+    // System.out.println("Using custom setup file:" + inputSetup);
+    // }
+
+    vtkPolyData inpolydata = PolyDataUtil.loadShapeModelAndComputeNormals(infile);
+
+    // We need to save out the OBJ file again in case it contains comment
+    // lines since mkdsk does not support lines beginning with #
+    // The OBJ file is saved to a temporary filename in order to preserve the
+    // original OBJ. The temporary filename is deleted afterwards.
+    File shapeModel = File.createTempFile("shapemodel-", null);
+    shapeModel.deleteOnExit();
+    PolyDataUtil.saveShapeModelAsOBJ(inpolydata, shapeModel.getAbsolutePath());
+
+    // Delete dsk file if already exists since otherwise mkdsk will complain
+    if (new File(outfile).isFile())
+      new File(outfile).delete();
+
+    String command = "mkdsk -setup " + setupFile.getAbsolutePath() + " -input "
+        + shapeModel.getAbsolutePath() + " -output " + outfile;
+    ProcessUtils.runProgramAndWait(command, null, false);
+  }
+
+
+  /**
+   * Create the setup file for mkdsk executable.
+   *
+   * @param latLonCorners
+   * @param fineVoxScale
+   * @param coarseVoxScale
+   * @param dskParams
+   * @param setupFname
+   * @return
+   */
+  private static File createSetup(Map<String, Double> latLonCorners, Double fineVoxScale,
+      Integer coarseVoxScale, Map<DSK_KEYS, String> dskParams, String setupFname) {
+
+    // evaluate latlon corners. Exit program if any are NaN.
+    evaluateCorners(latLonCorners);
+
+    File setupFile;
+
+    if (setupFname.length() < 1) {
+      setupFile = null;
+      try {
+        setupFile = File.createTempFile("setupfile-", null);
+      } catch (IOException e) {
+        String errMesg = "ERROR creating setupfile:" + setupFname;
+        throw new RuntimeException(errMesg);
+      }
+    } else {
+      setupFile = new File(setupFname);
+    }
+    System.out
+        .println("Setup file for mkdsk created here:" + setupFile.getAbsolutePath().toString());
+
+    // relativize the path to the metakernel file. Do this because mkdsk has a limit on the string
+    // length to the metakernel. Get normalized absolute path to mkFile in case the user enters a
+    // relative path string, e.x. ../../SPICE/spice-kernels.mk
+    Path currDir = FileSystems.getDefault().getPath("").toAbsolutePath();
+    Path mkFile = Paths.get(dskParams.get(DSK_KEYS.METAK)).toAbsolutePath().normalize();
+
+    System.out.println("currDir:" + currDir.toString());
+    System.out.println("mkFile:" + mkFile.toString());
+
+    // mkFile path relative to currDir
+    Path relPath = currDir.relativize(mkFile);
+    String spicefile = relPath.toString();
+
+    if (spicefile.length() > 80) {
+      System.out.println("Error: pointer to SPICE metakernel kernel file may not be longer than"
+          + " 80 characters.");
+      System.out.println("The paths inside the metakernel file can be as long as 255 characters.");
+      System.exit(1);
+    }
+
+
+    // create the content of setup file
+    StringBuilder sb = new StringBuilder();
+    sb.append("\\begindata\n");
+    sb.append("COMMENT_FILE        = '" + dskParams.get(DSK_KEYS.COMMENTFILE) + "'\n");
+    sb.append("LEAPSECONDS_FILE    = '" + spicefile + "'\n");
+    sb.append("SURFACE_NAME        = '" + dskParams.get(DSK_KEYS.SURF_NAME) + "'\n");
+    sb.append("CENTER_NAME         = '" + dskParams.get(DSK_KEYS.CENTER_NAME) + "'\n");
+    sb.append("REF_FRAME_NAME      = '" + dskParams.get(DSK_KEYS.REFFRAME_NAME) + "'\n");
+    // sb.append("SURFACE_NAME = 'BENNU'\n");
+    // sb.append("CENTER_NAME = 'BENNU'\n");
+    // sb.append("REF_FRAME_NAME = 'IAU_BENNU'\n");
+    sb.append("START_TIME          = '1950-JAN-1/00:00:00'\n");
+    sb.append("STOP_TIME           = '2050-JAN-1/00:00:00'\n");
+    sb.append("DATA_CLASS          = 2\n");
+    sb.append("INPUT_DATA_UNITS    = ( 'ANGLES    = DEGREES'\n");
+    sb.append("                        'DISTANCES = KILOMETERS' )\n");
+    sb.append("COORDINATE_SYSTEM   = 'LATITUDINAL'\n");
+    String valueString = String.format("MINIMUM_LATITUDE    = %.5f\n",
+        latLonCorners.get(HeaderTag.MINLAT.toString()));
+    sb.append(valueString);
+
+    // out.write("MAXIMUM_LATITUDE = 90\n");
+    valueString = String.format("MAXIMUM_LATITUDE    = %.5f\n",
+        latLonCorners.get(HeaderTag.MAXLAT.toString()));
+    sb.append(valueString);
+
+    // out.write("MINIMUM_LONGITUDE = -180\n");
+    valueString = String.format("MINIMUM_LONGITUDE    = %.5f\n",
+        latLonCorners.get(HeaderTag.MINLON.toString()));
+    sb.append(valueString);
+
+    // out.write("MAXIMUM_LONGITUDE = 180\n");
+    valueString = String.format("MAXIMUM_LONGITUDE    = %.5f\n",
+        latLonCorners.get(HeaderTag.MAXLON.toString()));
+    sb.append(valueString);
+
+    sb.append("DATA_TYPE           = 2\n");
+    sb.append("PLATE_TYPE          = 3\n");
+
+    String val;
+    if (fineVoxScale > 0D) {
+      val = fineVoxScale.toString();
+      val = val.trim();
+      sb.append("FINE_VOXEL_SCALE    = " + val + "\n");
+    }
+    if (coarseVoxScale > 0) {
+      val = coarseVoxScale.toString();
+      val = val.trim();
+      sb.append("COARSE_VOXEL_SCALE  = " + val + "\n");
+    }
+
+    String naifSurf = dskParams.get(DSK_KEYS.NAIF_SURFNAME);
+    String naifCode = dskParams.get(DSK_KEYS.NAIF_SURFCODE);
+    String naifBody = dskParams.get(DSK_KEYS.NAIF_SURFBODY);
+    if ((naifSurf.length() > 0) && (naifCode.length() > 0) && (naifBody.length() > 0)) {
+      sb.append("NAIF_SURFACE_NAME +=" + "'" + dskParams.get(DSK_KEYS.NAIF_SURFNAME) + "'\n");
+      sb.append("NAIF_SURFACE_CODE +=" + dskParams.get(DSK_KEYS.NAIF_SURFCODE) + "\n");
+      sb.append("NAIF_SURFACE_BODY +=" + dskParams.get(DSK_KEYS.NAIF_SURFBODY) + "\n");
+
+    } else {
+      System.out.println("optional NAIF body keywords not set. Will not use them in setup file.");
+    }
+
+    sb.append("\\begintext\n");
+
+    try {
+      FileWriter os = new FileWriter(setupFile);
+      BufferedWriter out = new BufferedWriter(os);
+      out.write(sb.toString());
+      out.close();
+
+    } catch (IOException e) {
+      e.printStackTrace();
+      System.err.println("ERROR creating setupfile for OBJ2DSK! Stopping with error!");
+      System.exit(1);
+    }
+    return setupFile;
+
+  }
+
+  /**
+   * Evaluate results of string parsing. Throw exception if any resolved to NaN
+   * 
+   * @param latLonCorners
+   */
+  private static void evaluateCorners(Map<String, Double> latLonCorners) {
+
+    for (String key : latLonCorners.keySet()) {
+      if (latLonCorners.get(key) == Double.NaN) {
+        System.err.println("ERROR! Value for:" + key + " is NaN! Retry wiht proper string double.");
+        System.err.println("Exiting program!");
+        System.exit(1);
+      }
+    }
+  }
+
+}

src/main/java/terrasaur/apps/PointCloudFormatConverter.java

@@ -0,0 +1,526 @@
+package terrasaur.apps;
+
+import java.io.BufferedInputStream;
+import java.io.BufferedOutputStream;
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.DataInputStream;
+import java.io.DataOutputStream;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.Map;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.Options;
+import org.apache.commons.math3.geometry.euclidean.threed.Vector3D;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.spi.StandardLevel;
+import picante.math.vectorspace.UnwritableVectorIJK;
+import spice.basic.Vector3;
+import terrasaur.enums.FORMATS;
+import terrasaur.smallBodyModel.BoundingBox;
+import terrasaur.templates.TerrasaurTool;
+import terrasaur.utils.*;
+import vtk.vtkCellArray;
+import vtk.vtkFloatArray;
+import vtk.vtkIdList;
+import vtk.vtkPoints;
+import vtk.vtkPolyData;
+import vtk.vtkPolyDataWriter;
+
+public class PointCloudFormatConverter implements TerrasaurTool {
+
+  private static final Logger logger = LogManager.getLogger();
+
+  @Override
+  public String shortDescription() {
+    return "Convert an input point cloud to a new format.";
+  }
+
+  @Override
+  public String fullDescription(Options options) {
+    String header = "";
+    String footer =
+        """
+            This program converts an input point cloud to a new format.
+
+            Supported input formats are ASCII, BIN3 (x,y,z), BIN4 (x, y, z, w), BIN7 (t, x, y, z, s/c x, y, z), FITS, ICQ, OBJ, PLY, and VTK.  Supported output formats are ASCII, BIN3, OBJ, and VTK.
+
+            ASCII format is white spaced delimited x y z coordinates.  BINARY files must contain double precision x y z coordinates.""";
+    return TerrasaurTool.super.fullDescription(options, header, footer);
+  }
+
+  private FORMATS inFormat;
+  private FORMATS outFormat;
+  private vtkPoints pointsXYZ;
+  // private List<Double> receivedIntensity;
+  private vtkPolyData polyData;
+  private Vector3 center;
+  private int halfSize;
+  private double groundSampleDistance;
+  private double clip;
+  private String additionalGMTArgs;
+  private double mapRadius;
+
+  public static vtkPoints readPointCloud(String filename) {
+    PointCloudFormatConverter pcfc = new PointCloudFormatConverter(filename, FORMATS.VTK);
+    pcfc.read(filename, false);
+    return pcfc.getPoints();
+  }
+
+  private PointCloudFormatConverter() {}
+
+  public PointCloudFormatConverter(FORMATS inFormat, String outFilename) {
+    this(inFormat, FORMATS.formatFromExtension(outFilename));
+  }
+
+  public PointCloudFormatConverter(String inFilename, FORMATS outFormat) {
+    this(FORMATS.formatFromExtension(inFilename), outFormat);
+  }
+
+  public PointCloudFormatConverter(String inFilename, String outFilename) {
+    this(FORMATS.formatFromExtension(inFilename), FORMATS.formatFromExtension(outFilename));
+  }
+
+  public PointCloudFormatConverter(FORMATS inFormat, FORMATS outFormat) {
+    this.inFormat = inFormat;
+    this.outFormat = outFormat;
+    this.pointsXYZ = new vtkPoints();
+    this.polyData = null;
+
+    this.center = null;
+    this.mapRadius = Math.sqrt(2);
+    this.halfSize = -1;
+    this.groundSampleDistance = -1;
+    this.clip = 1;
+    this.additionalGMTArgs = "";
+  }
+
+  public PointCloudFormatConverter setPoints(vtkPoints pointsXYZ) {
+    this.pointsXYZ = pointsXYZ;
+    return this;
+  }
+
+  public vtkPoints getPoints() {
+    return pointsXYZ;
+  }
+
+  public void setClip(Double clip) {
+    this.clip = clip;
+  }
+
+  public void setCenter(double[] centerPt) {
+    center = new Vector3(centerPt);
+  }
+
+  public void setMapRadius(double mapRadius) {
+    this.mapRadius = mapRadius;
+  }
+
+  public PointCloudFormatConverter setHalfSize(int halfSize) {
+    this.halfSize = halfSize;
+    return this;
+  }
+
+  public PointCloudFormatConverter setGroundSampleDistance(double groundSampleDistance) {
+    this.groundSampleDistance = groundSampleDistance;
+    return this;
+  }
+
+  public PointCloudFormatConverter setGMTArgs(String args) {
+    this.additionalGMTArgs = args;
+    return this;
+  }
+
+  public void read(String inFile, boolean inLLR) {
+    switch (inFormat) {
+      case ASCII:
+        try (BufferedReader br = new BufferedReader(new FileReader(inFile))) {
+          String line = br.readLine();
+          while (line != null) {
+            line = line.trim();
+            if (!line.isEmpty() && !line.startsWith("#")) {
+              String[] parts = line.split("\\s+");
+              if (inLLR) {
+                double lon = Math.toRadians(Double.parseDouble(parts[0].trim()));
+                double lat = Math.toRadians(Double.parseDouble(parts[1].trim()));
+                double range = Double.parseDouble(parts[2].trim());
+                double[] xyz = new Vector3D(lon, lat).scalarMultiply(range).toArray();
+                pointsXYZ.InsertNextPoint(xyz);
+              } else {
+                double[] xyz = new double[3];
+                xyz[0] = Double.parseDouble(parts[0].trim());
+                xyz[1] = Double.parseDouble(parts[1].trim());
+                xyz[2] = Double.parseDouble(parts[2].trim());
+                pointsXYZ.InsertNextPoint(xyz);
+              }
+            }
+            line = br.readLine();
+          }
+        } catch (IOException e) {
+          logger.error(e.getLocalizedMessage(), e);
+        }
+        break;
+      case BIN3:
+      case BIN4:
+      case BIN7:
+        try (DataInputStream dis =
+            new DataInputStream(new BufferedInputStream(new FileInputStream(inFile)))) {
+          while (dis.available() > 0) {
+            if (inFormat == FORMATS.BIN7) {
+              // skip time field
+              BinaryUtils.readDoubleAndSwap(dis);
+            }
+            if (inLLR) {
+              double lon = Math.toRadians(BinaryUtils.readDoubleAndSwap(dis));
+              double lat = Math.toRadians(BinaryUtils.readDoubleAndSwap(dis));
+              double range = BinaryUtils.readDoubleAndSwap(dis);
+              double[] xyz = new Vector3D(lon, lat).scalarMultiply(range).toArray();
+              pointsXYZ.InsertNextPoint(xyz);
+            } else {
+              double[] xyz = new double[3];
+              xyz[0] = BinaryUtils.readDoubleAndSwap(dis);
+              xyz[1] = BinaryUtils.readDoubleAndSwap(dis);
+              xyz[2] = BinaryUtils.readDoubleAndSwap(dis);
+              pointsXYZ.InsertNextPoint(xyz);
+            }
+          }
+        } catch (IOException e) {
+          logger.error(e.getLocalizedMessage(), e);
+        }
+      case ICQ:
+      case OBJ:
+      case PLT:
+      case PLY:
+      case VTK:
+        try {
+          polyData = PolyDataUtil.loadShapeModel(inFile);
+          pointsXYZ.DeepCopy(polyData.GetPoints());
+        } catch (Exception e) {
+          logger.error(e.getLocalizedMessage(), e);
+        }
+        break;
+      case FITS:
+        try {
+          polyData = PolyDataUtil.loadFITShapeModel(inFile);
+          pointsXYZ.DeepCopy(polyData.GetPoints());
+        } catch (Exception e) {
+          logger.error(e.getLocalizedMessage(), e);
+        }
+        break;
+      default:
+        break;
+    }
+
+    if (clip != 1) {
+      BoundingBox bbox = new BoundingBox();
+      for (int i = 0; i < pointsXYZ.GetNumberOfPoints(); i++) {
+        double[] point = pointsXYZ.GetPoint(i);
+        bbox.update(new UnwritableVectorIJK(point[0], point[1], point[2]));
+      }
+      BoundingBox clipped = bbox.getScaledBoundingBox(clip);
+      vtkPoints clippedPoints = new vtkPoints();
+      for (int i = 0; i < pointsXYZ.GetNumberOfPoints(); i++) {
+        if (clipped.contains(pointsXYZ.GetPoint(i)))
+          clippedPoints.InsertNextPoint(pointsXYZ.GetPoint(i));
+      }
+      pointsXYZ = clippedPoints;
+      polyData = null;
+    }
+  }
+
+  public void write(String outFile, boolean outLLR) {
+    switch (outFormat) {
+      case ASCII:
+        try (PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter(outFile)))) {
+          for (int i = 0; i < pointsXYZ.GetNumberOfPoints(); i++) {
+            double[] thisPoint = pointsXYZ.GetPoint(i);
+            if (outLLR) {
+              Vector3D v = new Vector3D(thisPoint);
+              out.printf(
+                  "%f %f %f\n",
+                  Math.toDegrees(v.getAlpha()), Math.toDegrees(v.getDelta()), v.getNorm());
+            } else {
+              out.printf("%f %f %f\n", thisPoint[0], thisPoint[1], thisPoint[2]);
+            }
+          }
+        } catch (IOException e) {
+          logger.error(e.getLocalizedMessage(), e);
+        }
+        break;
+      case BIN3:
+        try (DataOutputStream os =
+            new DataOutputStream(new BufferedOutputStream(new FileOutputStream(outFile)))) {
+
+          for (int i = 0; i < pointsXYZ.GetNumberOfPoints(); i++) {
+            double[] thisPoint = pointsXYZ.GetPoint(i);
+            if (outLLR) {
+              Vector3D v = new Vector3D(thisPoint);
+
+              BinaryUtils.writeDoubleAndSwap(os, Math.toDegrees(v.getAlpha()));
+              BinaryUtils.writeDoubleAndSwap(os, Math.toDegrees(v.getDelta()));
+              BinaryUtils.writeDoubleAndSwap(os, v.getNorm());
+            } else {
+              for (int ii = 0; ii < 3; ii++) BinaryUtils.writeDoubleAndSwap(os, thisPoint[ii]);
+            }
+          }
+        } catch (IOException e) {
+          logger.error(e.getLocalizedMessage(), e);
+        }
+
+        break;
+      case OBJ:
+        if (polyData != null) {
+          try {
+            PolyDataUtil.saveShapeModelAsOBJ(polyData, outFile);
+          } catch (IOException e) {
+            logger.error(e.getLocalizedMessage(), e);
+          }
+        } else {
+          if (halfSize < 0 || groundSampleDistance < 0) {
+            System.out.printf(
+                "Must supply -halfSize and -groundSampleDistance for %s output\n",
+                    outFormat);
+            return;
+          }
+
+          final double radius = mapRadius * halfSize * groundSampleDistance;
+          vtkPoints vtkPoints = pointsXYZ;
+          if (center != null) {
+            vtkPoints = new vtkPoints();
+            for (int i = 0; i < pointsXYZ.GetNumberOfPoints(); i++) {
+              Vector3 pt = new Vector3(pointsXYZ.GetPoint(i));
+              if (center.sub(new Vector3(pt)).norm() > radius) continue;
+              vtkPoints.InsertNextPoint(pt.toArray());
+            }
+          }
+
+          PointCloudToPlane pctp = new PointCloudToPlane(vtkPoints, halfSize, groundSampleDistance);
+          pctp.getGMU().setFieldToHeight();
+          pctp.getGMU().setGMTArgs(additionalGMTArgs);
+          try {
+            double[][][] regridField = pctp.getGMU().regridField();
+            vtkPolyData griddedXYZ = PolyDataUtil.loadLocalFitsLLRModelN(regridField);
+            PolyDataUtil.saveShapeModelAsOBJ(griddedXYZ, outFile);
+          } catch (Exception e) {
+            logger.error(e.getLocalizedMessage(), e);
+          }
+        }
+        break;
+      case VTK:
+        if (polyData == null) {
+          polyData = new vtkPolyData();
+          polyData.SetPoints(pointsXYZ);
+        }
+
+        vtkCellArray cells = new vtkCellArray();
+        vtkFloatArray albedo = new vtkFloatArray();
+        albedo.SetName("albedo");
+        polyData.SetPolys(cells);
+        polyData.GetPointData().AddArray(albedo);
+
+        for (int i = 0; i < pointsXYZ.GetNumberOfPoints(); i++) {
+          vtkIdList idList = new vtkIdList();
+          idList.InsertNextId(i);
+          cells.InsertNextCell(idList);
+          albedo.InsertNextValue(0.5f);
+        }
+
+        vtkPolyDataWriter writer = new vtkPolyDataWriter();
+        writer.SetInputData(polyData);
+        writer.SetFileName(outFile);
+        writer.SetFileTypeToBinary();
+        writer.Update();
+        break;
+      default:
+        break;
+    }
+  }
+
+  private static Options defineOptions() {
+    Options options = TerrasaurTool.defineOptions();
+    options.addOption(
+        Option.builder("logFile")
+            .hasArg()
+            .desc("If present, save screen output to log file.")
+            .build());
+    StringBuilder sb = new StringBuilder();
+    for (StandardLevel l : StandardLevel.values()) sb.append(String.format("%s ", l.name()));
+    options.addOption(
+        Option.builder("logLevel")
+            .hasArg()
+            .desc(
+                "If present, print messages above selected priority.  Valid values are "
+                    + sb.toString().trim()
+                    + ".  Default is INFO.")
+            .build());
+    options.addOption(
+        Option.builder("inputFormat")
+            .hasArg()
+            .desc(
+                "Format of input file.  If not present format will be inferred from inputFile extension.")
+            .build());
+    options.addOption(
+        Option.builder("inputFile")
+            .required()
+            .hasArg()
+            .desc("Required.  Name of input file.")
+            .build());
+    options.addOption(
+        Option.builder("outputFormat")
+            .hasArg()
+            .desc(
+                "Format of output file.  If not present format will be inferred from outputFile extension.")
+            .build());
+    options.addOption(
+        Option.builder("outputFile")
+            .required()
+            .hasArg()
+            .desc("Required.  Name of output file.")
+            .build());
+    options.addOption(
+        Option.builder("inllr")
+            .desc(
+                "Only used with ASCII or BINARY formats.  If present, input values are assumed to be lon, lat, rad.  Default is x, y, z.")
+            .build());
+    options.addOption(
+        Option.builder("outllr")
+            .desc(
+                "Only used with ASCII or BINARY formats.  If present, output values will be lon, lat, rad.  Default is x, y, z.")
+            .build());
+    options.addOption(
+        Option.builder("centerXYZ")
+            .hasArg()
+            .desc(
+                "Only used to generate OBJ output.  Center output shape on supplied coordinates.  Specify XYZ coordinates as three floating point numbers separated"
+                    + " by commas.")
+            .build());
+    options.addOption(
+        Option.builder("centerLonLat")
+            .hasArg()
+            .desc(
+                "Only used to generate OBJ output.  Center output shape on supplied lon,lat.  Specify lon,lat in degrees as floating point numbers separated"
+                    + " by a comma.  Shape will be centered on the point closest to this lon,lat pair.")
+            .build());
+    options.addOption(
+        Option.builder("halfSize")
+            .hasArg()
+            .desc(
+                "Only used to generate OBJ output.  Used with -groundSampleDistance to resample to a uniform grid.  Grid dimensions are (2*halfSize+1)x(2*halfSize+1).")
+            .build());
+    options.addOption(
+        Option.builder("groundSampleDistance")
+            .hasArg()
+            .desc(
+                "Used with -halfSize to resample to a uniform grid.  Spacing between grid points.  Only used to generate OBJ output.  "
+                    + "Units are the same as the input file, usually km.")
+            .build());
+    options.addOption(
+        Option.builder("mapRadius")
+            .hasArg()
+            .desc(
+                "Only used to generate OBJ output.  Used with -centerXYZ to resample to a uniform grid.  Only include points within "
+                    + "mapRadius*groundSampleDistance*halfSize of centerXYZ.  Default value is sqrt(2).")
+            .build());
+    options.addOption(
+        Option.builder("gmtArgs")
+            .hasArg()
+            .longOpt("gmt-args")
+            .desc(
+                "Only used to generate OBJ output.  Pass additional options to GMTSurface.  May be used multiple times, use once per additional argument.")
+            .build());
+    options.addOption(
+        Option.builder("clip")
+            .hasArg()
+            .desc(
+                "Shrink bounding box to a relative size of <arg> and clip any points outside of it.  Default is 1 (no clipping).")
+            .build());
+    return options;
+  }
+
+  public static void main(String[] args) {
+    TerrasaurTool defaultOBJ = new PointCloudFormatConverter();
+
+    Options options = defineOptions();
+
+    CommandLine cl = defaultOBJ.parseArgs(args, options);
+
+    Map<MessageLabel, String> startupMessages = defaultOBJ.startupMessages(cl);
+    for (MessageLabel ml : startupMessages.keySet())
+      logger.info(String.format("%s %s", ml.label, startupMessages.get(ml)));
+
+    NativeLibraryLoader.loadVtkLibraries();
+    NativeLibraryLoader.loadSpiceLibraries();
+
+    String inFile = cl.getOptionValue("inputFile");
+    String outFile = cl.getOptionValue("outputFile");
+    boolean inLLR = cl.hasOption("inllr");
+    boolean outLLR = cl.hasOption("outllr");
+
+    FORMATS inFormat =
+        cl.hasOption("inputFormat")
+            ? FORMATS.valueOf(cl.getOptionValue("inputFormat").toUpperCase())
+            : FORMATS.formatFromExtension(cl.getOptionValue("inputFile"));
+    FORMATS outFormat =
+        cl.hasOption("outputFormat")
+            ? FORMATS.valueOf(cl.getOptionValue("outputFormat").toUpperCase())
+            : FORMATS.formatFromExtension(cl.getOptionValue("outputFile"));
+
+    PointCloudFormatConverter pcfc = new PointCloudFormatConverter(inFormat, outFormat);
+
+    if (cl.hasOption("centerXYZ")) {
+      String[] params = cl.getOptionValue("centerXYZ").split(",");
+      double[] array = new double[3];
+      for (int i = 0; i < 3; i++) array[i] = Double.parseDouble(params[i].trim());
+      pcfc.setCenter(array);
+    }
+
+    if (cl.hasOption("clip")) {
+      pcfc.setClip(Double.valueOf(cl.getOptionValue("clip")));
+    }
+
+    if (cl.hasOption("gmtArgs")) {
+      StringBuilder gmtArgs = new StringBuilder();
+      for (String arg : cl.getOptionValues("gmtArgs")) gmtArgs.append(String.format("%s ", arg));
+      pcfc.setGMTArgs(gmtArgs.toString());
+    }
+
+    pcfc.read(inFile, inLLR);
+
+    if (cl.hasOption("centerLonLat")) {
+      String[] params = cl.getOptionValue("centerLonLat").split(",");
+      Vector3D lcDir =
+          new Vector3D(
+              Math.toRadians(Double.parseDouble(params[0].trim())),
+              Math.toRadians(Double.parseDouble(params[1].trim())));
+      double[] center = null;
+      double minSep = Double.MAX_VALUE;
+      vtkPoints vtkPoints = pcfc.getPoints();
+      for (int i = 0; i < vtkPoints.GetNumberOfPoints(); i++) {
+        double[] pt = vtkPoints.GetPoint(i);
+        double sep = Vector3D.angle(lcDir, new Vector3D(pt));
+        if (sep < minSep) {
+          minSep = sep;
+          center = pt;
+        }
+      }
+      pcfc.setCenter(center);
+    }
+
+    pcfc.setMapRadius(
+        cl.hasOption("mapRadius") ? Double.parseDouble(cl.getOptionValue("mapRadius")) : Math.sqrt(2));
+
+    if (cl.hasOption("halfSize") && cl.hasOption("groundSampleDistance")) {
+      // resample on a uniform XY grid
+      pcfc.setHalfSize(Integer.parseInt(cl.getOptionValue("halfSize")));
+      pcfc.setGroundSampleDistance(Double.parseDouble(cl.getOptionValue("groundSampleDistance")));
+    }
+
+    pcfc.write(outFile, outLLR);
+  }
+}

src/main/java/terrasaur/apps/PointCloudToPlane.java

@@ -0,0 +1,389 @@
+package terrasaur.apps;
+
+import java.awt.Rectangle;
+import java.awt.image.BufferedImage;
+import java.io.FileNotFoundException;
+import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.Options;
+import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.spi.StandardLevel;
+import picante.math.coords.CoordConverters;
+import picante.math.vectorspace.VectorIJK;
+import spice.basic.LatitudinalCoordinates;
+import spice.basic.Matrix33;
+import spice.basic.SpiceException;
+import spice.basic.Vector3;
+import terrasaur.enums.FORMATS;
+import terrasaur.templates.TerrasaurTool;
+import terrasaur.utils.*;
+import terrasaur.utils.math.MathConversions;
+import terrasaur.utils.saaPlotLib.canvas.DiscreteDataPlot;
+import terrasaur.utils.saaPlotLib.canvas.MapPlot;
+import terrasaur.utils.saaPlotLib.canvas.PlotCanvas;
+import terrasaur.utils.saaPlotLib.canvas.axis.AxisX;
+import terrasaur.utils.saaPlotLib.canvas.axis.AxisY;
+import terrasaur.utils.saaPlotLib.canvas.projection.ProjectionOrthographic;
+import terrasaur.utils.saaPlotLib.canvas.symbol.Circle;
+import terrasaur.utils.saaPlotLib.colorMaps.ColorRamp;
+import terrasaur.utils.saaPlotLib.colorMaps.ColorRamp.TYPE;
+import terrasaur.utils.saaPlotLib.colorMaps.ImmutableColorBar;
+import terrasaur.utils.saaPlotLib.config.ImmutablePlotConfig;
+import terrasaur.utils.saaPlotLib.config.PlotConfig;
+import terrasaur.utils.saaPlotLib.data.DiscreteDataSet;
+import terrasaur.utils.saaPlotLib.util.StringFunctions;
+import vtk.vtkPoints;
+
+public class PointCloudToPlane implements TerrasaurTool {
+
+  private static final Logger logger = LogManager.getLogger();
+
+  @Override
+  public String shortDescription() {
+    return "Find a rotation and translation to transform a point cloud to a height field above the best fit plane.";
+  }
+
+  @Override
+  public String fullDescription(Options options) {
+    String header = "";
+    String footer =
+        "\nThis program finds a rotation and translation to transform a point cloud to a height field above the best fit plane.  "
+            + "Supported input formats are ASCII, BINARY, L2, OBJ, and VTK.\n\n"
+            + "ASCII format is white spaced delimited x y z coordinates.  BINARY files must contain double precision x y z coordinates.  ";
+    return TerrasaurTool.super.fullDescription(options, header, footer);
+  }
+
+  private GMTGridUtil gmu;
+
+  public GMTGridUtil getGMU() {
+    return gmu;
+  }
+
+  public void writeOutput(String outputFile) {
+    if (outputFile != null) {
+      try (PrintStream ps = new PrintStream(outputFile)) {
+        double[][] transformation = gmu.getTransformation();
+        for (int i = 0; i < 4; i++) {
+          for (int j = 0; j < 4; j++) {
+            ps.printf("%24.16e ", transformation[i][j]);
+          }
+          ps.println();
+        }
+      } catch (FileNotFoundException e) {
+        logger.error(e.getLocalizedMessage(), e);
+      }
+    }
+  }
+
+  private PointCloudToPlane() {}
+
+  public PointCloudToPlane(vtkPoints points) {
+    this(points, 0, 0.);
+  }
+
+  public PointCloudToPlane(vtkPoints points, int halfSize, double groundSampleDistance) {
+    double[] x = new double[(int) points.GetNumberOfPoints()];
+    double[] y = new double[(int) points.GetNumberOfPoints()];
+    double[] z = new double[(int) points.GetNumberOfPoints()];
+
+    for (int i = 0; i < points.GetNumberOfPoints(); i++) {
+      double[] thisPoint = points.GetPoint(i);
+      x[i] = thisPoint[0];
+      y[i] = thisPoint[1];
+      z[i] = thisPoint[2];
+    }
+
+    gmu = new GMTGridUtil(halfSize, groundSampleDistance);
+    gmu.setXYZ(x, y, z);
+  }
+
+  public BufferedImage makePlot(List<Vector3> points, String name) throws SpiceException {
+    DescriptiveStatistics stats = new DescriptiveStatistics();
+    VectorStatistics vStats = new VectorStatistics();
+    DiscreteDataSet data = new DiscreteDataSet(name);
+
+    PlotConfig config = ImmutablePlotConfig.builder().title(name).build();
+
+    DiscreteDataPlot canvas;
+    boolean orthographic = false;
+    if (orthographic) {
+      for (Vector3 p : points) {
+        stats.addValue(p.getElt(2));
+        vStats.add(p);
+        LatitudinalCoordinates lc = new LatitudinalCoordinates(p);
+        data.add(lc.getLongitude(), lc.getLatitude(), 0, p.getElt(2));
+      }
+
+      double min = stats.getMin();
+      double max = stats.getMax();
+      ColorRamp ramp = ColorRamp.create(TYPE.CBSPECTRAL, min, max).createReverse();
+      data.setSymbol(new Circle().setSize(1.0));
+      data.setColorRamp(ramp);
+
+      Vector3 center = MathConversions.toVector3(vStats.getMean());
+
+      double halfExtent = 0;
+      for (Vector3 p : points) {
+        double dist = center.sep(p);
+        if (dist > halfExtent) halfExtent = dist;
+      }
+
+      ProjectionOrthographic p =
+          new ProjectionOrthographic(
+              config.width(),
+              config.height(),
+              CoordConverters.convertToLatitudinal(
+                  new VectorIJK(center.getElt(0), center.getElt(1), center.getElt(2))));
+      p.setRadius(Math.max(0.5, .6 / halfExtent));
+
+      canvas = new MapPlot(config, p);
+      canvas.drawAxes();
+      canvas.plot(data);
+      ((MapPlot) canvas).drawLatLonGrid(Math.toRadians(5), Math.toRadians(5), true);
+
+      canvas.drawColorBar(
+          ImmutableColorBar.builder()
+              .rect(new Rectangle(config.leftMargin(), 40, config.width(), 10))
+              .ramp(ramp)
+              .numTicks(5)
+              .tickFunction(StringFunctions.fixedFormat("%.3f"))
+              .build());
+    } else {
+      for (Vector3 p : points) {
+        stats.addValue(p.getElt(2));
+        vStats.add(p);
+        data.add(p.getElt(0), p.getElt(1), 0, p.getElt(2));
+      }
+
+      double min = stats.getMin();
+      double max = stats.getMax();
+      ColorRamp ramp = ColorRamp.create(TYPE.CBSPECTRAL, min, max).createReverse();
+      data.setSymbol(new Circle().setSize(1.0));
+      data.setColorRamp(ramp);
+
+      canvas = new DiscreteDataPlot(config);
+      AxisX xAxis = data.defaultXAxis("X");
+      AxisY yAxis = data.defaultYAxis("Y");
+      canvas.setAxes(xAxis, yAxis);
+      canvas.drawAxes();
+      canvas.plot(data);
+
+      canvas.drawColorBar(
+          ImmutableColorBar.builder()
+              .rect(new Rectangle(config.leftMargin(), 40, config.width(), 10))
+              .ramp(ramp)
+              .numTicks(5)
+              .tickFunction(StringFunctions.fixedFormat("%.3f"))
+              .build());
+    }
+    return canvas.getImage();
+  }
+
+  private static Options defineOptions() {
+    Options options = TerrasaurTool.defineOptions();
+    options.addOption(
+        Option.builder("inputFormat")
+            .hasArg()
+            .desc(
+                "Format of input file.  If not present format is inferred from inputFile extension.")
+            .build());
+    options.addOption(
+        Option.builder("inputFile")
+            .required()
+            .hasArg()
+            .desc("Required.  Name of input file.")
+            .build());
+    options.addOption(
+        Option.builder("inllr")
+            .desc(
+                "If present, input values are assumed to be lon, lat, rad.  Default is x, y, z.  Only used with ASCII or BINARY formats.")
+            .build());
+    options.addOption(
+        Option.builder("logFile")
+            .hasArg()
+            .desc("If present, save screen output to log file.")
+            .build());
+    StringBuilder sb = new StringBuilder();
+    for (StandardLevel l : StandardLevel.values()) sb.append(String.format("%s ", l.name()));
+    options.addOption(
+        Option.builder("logLevel")
+            .hasArg()
+            .desc(
+                "If present, print messages above selected priority.  Valid values are "
+                    + sb.toString().trim()
+                    + ".  Default is INFO.")
+            .build());
+    options.addOption(
+        Option.builder("outputFile")
+            .hasArg()
+            .desc(
+                "Name of output file to contain 4x4 transformation matrix.  The top left 3x3 matrix is the rotation matrix. The top "
+                    + "three entries in the right hand column are the translation vector. The bottom row is always 0 0 0 1.\nTo convert "
+                    + "from global to local:\n  transformed = rotation.mxv(point.sub(translation))")
+            .build());
+    options.addOption(
+        Option.builder("translate")
+            .hasArg()
+            .desc(
+                "Translate surface points and spacecraft position.  "
+                    + "Specify by three floating point numbers separated by commas.  "
+                    + "Default is to use centroid of input point cloud.")
+            .build());
+    options.addOption(
+        Option.builder("plotXYZ")
+            .hasArg()
+            .desc(
+                "Plot X vs Y (in the local frame) colored by Z.  "
+                    + "Argument is the name of PNG file to write.")
+            .build());
+    options.addOption(
+        Option.builder("plotXYR")
+            .hasArg()
+            .desc(
+                "Plot X vs Y (in the local frame) colored by R.  "
+                    + "Argument is the name of PNG file to write.")
+            .build());
+    options.addOption(
+        Option.builder("slope")
+            .desc(
+                "Choose local coordinate frame such that Z points normal to the plane "
+                    + "and X points along the direction of steepest descent.")
+            .build());
+    return options;
+  }
+
+  public static void main(String[] args) throws SpiceException {
+    TerrasaurTool defaultOBJ = new PointCloudToPlane();
+
+    Options options = defineOptions();
+
+    CommandLine cl = defaultOBJ.parseArgs(args, options);
+
+    Map<MessageLabel, String> startupMessages = defaultOBJ.startupMessages(cl);
+    for (MessageLabel ml : startupMessages.keySet())
+      logger.info(String.format("%s %s", ml.label, startupMessages.get(ml)));
+
+    NativeLibraryLoader.loadVtkLibraries();
+    NativeLibraryLoader.loadSpiceLibraries();
+
+    String inFile = cl.getOptionValue("inputFile");
+    boolean inLLR = cl.hasOption("inllr");
+
+    FORMATS inFormat =
+        cl.hasOption("inputFormat")
+            ? FORMATS.valueOf(cl.getOptionValue("inputFormat").toUpperCase())
+            : FORMATS.formatFromExtension(inFile);
+
+    PointCloudFormatConverter pcfc = new PointCloudFormatConverter(inFormat, FORMATS.VTK);
+    pcfc.read(inFile, inLLR);
+    System.out.printf("%d points read from %s\n", pcfc.getPoints().GetNumberOfPoints(), inFile);
+
+    int halfSize = 0;
+    double groundSampleDistance = 0;
+
+    vtkPoints points = pcfc.getPoints();
+    PointCloudToPlane pctp = new PointCloudToPlane(points, halfSize, groundSampleDistance);
+
+    Vector3 translation;
+    if (cl.hasOption("translate")) {
+      translation =
+          MathConversions.toVector3(VectorUtils.stringToVector3D(cl.getOptionValue("translate")));
+      pctp.getGMU().setTranslation(translation.toArray());
+    }
+    pctp.getGMU().calculateTransformation();
+
+    List<Vector3> globalPts = new ArrayList<>();
+    for (int i = 0; i < points.GetNumberOfPoints(); i++)
+      globalPts.add(new Vector3(points.GetPoint(i)));
+
+    double[][] transformation = pctp.getGMU().getTransformation();
+    StringBuilder sb =
+        new StringBuilder(
+            String.format(
+                "translation vector:\n%24.16e%24.16e%24.16e\n",
+                transformation[0][3], transformation[1][3], transformation[2][3]));
+    logger.info(sb.toString());
+    sb = new StringBuilder("rotation matrix:\n");
+    for (int i = 0; i < 3; i++)
+      sb.append(
+          String.format(
+              "%24.16e%24.16e%24.16e\n",
+              transformation[i][0], transformation[i][1], transformation[i][2]));
+    logger.info(sb.toString());
+
+    Matrix33 rotation = new Matrix33(pctp.getGMU().getRotation());
+    translation = new Vector3(pctp.getGMU().getTranslation());
+
+    if (cl.hasOption("slope")) {
+      Vector3 z = rotation.xpose().mxv(new Vector3(0, 0, 1));
+      VectorStatistics vStats = new VectorStatistics();
+      for (Vector3 pt : globalPts) vStats.add(pt);
+
+      Vector3 r = MathConversions.toVector3(vStats.getMean());
+
+      Vector3 y = r.cross(z).hat();
+      Vector3 x = y.cross(z).hat();
+      rotation = new Matrix33(x, y, z);
+    }
+
+    List<Vector3> localPts = new ArrayList<>();
+    for (Vector3 p : globalPts) localPts.add(rotation.mxv(p.sub(translation)));
+
+    VectorStatistics vStats = new VectorStatistics();
+    for (Vector3 localPt : localPts) vStats.add(localPt);
+
+    if (cl.hasOption("plotXYZ")) {
+      BufferedImage image = pctp.makePlot(localPts, "Z (height above plane)");
+      PlotCanvas.writeImage(cl.getOptionValue("plotXYZ"), image);
+    }
+
+    if (cl.hasOption("plotXYR")) {
+
+      // rotate but don't translate
+      List<Vector3> xyr = new ArrayList<>();
+      for (Vector3 p : globalPts) {
+        Vector3 v = rotation.mxv(p);
+        xyr.add(new Vector3(v.getElt(0), v.getElt(1), v.norm()));
+      }
+
+      BufferedImage image = pctp.makePlot(xyr, "R");
+      PlotCanvas.writeImage(cl.getOptionValue("plotXYR"), image);
+    }
+
+    logger.info("statistics on full set");
+    logger.info(vStats);
+
+    Vector3 mean = MathConversions.toVector3(vStats.getMean());
+    Vector3 std = MathConversions.toVector3(vStats.getStandardDeviation());
+    double scale = 5;
+    List<Double> minList = new ArrayList<>();
+    List<Double> maxList = new ArrayList<>();
+    for (int i = 0; i < 3; i++) {
+      minList.add(mean.getElt(i) - scale * std.getElt(i));
+      maxList.add(mean.getElt(i) + scale * std.getElt(i));
+    }
+
+    vStats = new VectorStatistics();
+    for (Vector3 v : localPts) {
+      boolean addThis = true;
+      for (int i = 0; i < 3; i++) {
+        if (v.getElt(i) < minList.get(i) || v.getElt(i) > maxList.get(i)) {
+          addThis = false;
+          break;
+        }
+      }
+      if (addThis) vStats.add(v);
+    }
+
+    logger.info("statistics on set without points more than 5 standard deviations from the mean:");
+    logger.info(vStats);
+
+    if (cl.hasOption("outputFile")) pctp.writeOutput(cl.getOptionValue("outputFile"));
+  }
+}

src/main/java/terrasaur/apps/PrintShapeModelStatistics.java

@@ -0,0 +1,72 @@
+package terrasaur.apps;
+
+import java.util.ArrayList;
+import java.util.Map;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.Options;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import terrasaur.templates.TerrasaurTool;
+import terrasaur.utils.NativeLibraryLoader;
+import terrasaur.utils.PolyDataStatistics;
+import terrasaur.utils.PolyDataUtil;
+import vtk.vtkPolyData;
+
+/**
+ * PrintShapeModelStatistics program. Takes a shape model in OBJ format and prints out various
+ * statistics about it. about this program.
+ *
+ * @author Eli Kahn
+ * @version 1.0
+ */
+public class PrintShapeModelStatistics implements TerrasaurTool {
+
+  private static final Logger logger = LogManager.getLogger();
+
+  private PrintShapeModelStatistics() {}
+
+  @Override
+  public String shortDescription() {
+    return "Print statistics about a shape model.";
+  }
+
+  @Override
+  public String fullDescription(Options options) {
+    String header = "This program prints various statistics about a shape model in OBJ format.";
+    String footer = "";
+    return TerrasaurTool.super.fullDescription(options, header, footer);
+  }
+
+  private static Options defineOptions() {
+    Options options = TerrasaurTool.defineOptions();
+    options.addOption(
+        Option.builder("objFile").required().hasArg().desc("Path to OBJ file.").build());
+    return options;
+  }
+
+  public static void main(String[] args) throws Exception {
+    TerrasaurTool defaultOBJ = new PrintShapeModelStatistics();
+
+    Options options = defineOptions();
+
+    CommandLine cl = defaultOBJ.parseArgs(args, options);
+
+    Map<MessageLabel, String> startupMessages = defaultOBJ.startupMessages(cl);
+    for (MessageLabel ml : startupMessages.keySet())
+      logger.info(String.format("%s %s", ml.label, startupMessages.get(ml)));
+
+    String filename = cl.getOptionValue("objFile");
+
+    NativeLibraryLoader.loadVtkLibraries();
+
+    vtkPolyData polydata = PolyDataUtil.loadShapeModelAndComputeNormals(filename);
+
+    PolyDataStatistics stat = new PolyDataStatistics(polydata);
+    ArrayList<String> stats = stat.getShapeModelStats();
+    for (String line : stats) {
+      logger.info(line);
+    }
+  }
+}

src/main/java/terrasaur/apps/RangeFromSumFile.java

@@ -0,0 +1,407 @@
+package terrasaur.apps;
+
+import java.io.File;
+import java.util.AbstractMap;
+import java.util.Map;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.Options;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.math3.geometry.euclidean.threed.Vector3D;
+import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import picante.math.vectorspace.VectorIJK;
+import spice.basic.Plane;
+import spice.basic.SpiceException;
+import spice.basic.Vector3;
+import terrasaur.smallBodyModel.SmallBodyModel;
+import terrasaur.templates.TerrasaurTool;
+import terrasaur.utils.*;
+import terrasaur.utils.math.MathConversions;
+import terrasaur.utils.mesh.TriangularFacet;
+import vtk.vtkIdList;
+import vtk.vtkPolyData;
+
+public class RangeFromSumFile implements TerrasaurTool {
+  private static final Logger logger = LogManager.getLogger();
+
+  @Override
+  public String shortDescription() {
+    return "Calculate range to surface from a sumfile.";
+  }
+
+  @Override
+  public String fullDescription(Options options) {
+
+    String header = "";
+    String footer =
+            """
+                    This program reads a sumfile along with a shape model and \
+                    calculates the range to the surface.  NOTE: Spacecraft position is \
+                    assumed to be in kilometers.  If not, use the -distanceScale option \
+                    to convert to km.
+                    """;
+    return TerrasaurTool.super.fullDescription(options, header, footer);
+  }
+
+  private SumFile sumFile;
+  private vtkPolyData polyData;
+  private SmallBodyModel smallBodyModel;
+
+  private int xOffset;
+  private int yOffset;
+
+  private long facet;
+
+  private Vector3D scPos;
+  private Vector3D sunXYZ;
+  private Vector3D surfaceIntercept;
+
+  private double tiltDeg;
+  private double tiltDir;
+
+  private double incidence;
+  private double emission;
+  private double phase;
+
+  private double scAzimuth;
+  private double scElevation;
+
+  private double sunAzimuth;
+  private double sunElevation;
+
+  private DescriptiveStatistics stats;
+  private double centerX, centerY;
+
+  public DescriptiveStatistics getStats() {
+    return stats;
+  }
+
+  private RangeFromSumFile() {}
+
+  public RangeFromSumFile(SumFile sumFile, vtkPolyData polyData) {
+
+    this.sumFile = sumFile;
+
+    int nPixelsX = sumFile.imageWidth();
+    int nPixelsY = sumFile.imageHeight();
+    centerX = 0.5 * (nPixelsX - 1);
+    centerY = 0.5 * (nPixelsY - 1);
+
+    this.polyData = polyData;
+
+    smallBodyModel = new SmallBodyModel(polyData);
+
+    scPos = sumFile.scobj().negate();
+    sunXYZ = sumFile.sunDirection();
+
+    stats = new DescriptiveStatistics();
+  }
+
+  public void setDistanceScale(double distanceScale) {
+    this.scPos = sumFile.scobj().scalarMultiply(distanceScale).negate();
+  }
+
+  /**
+   * @param xOffset x offset in pixels
+   * @param yOffset y offset in pixels
+   * @return key is cell index, value is surface intercept for the desired pixel offset from the center of the image.
+   */
+  public Map.Entry<Long, Vector3D> findIntercept(int xOffset, int yOffset) {
+
+    this.xOffset = xOffset;
+    this.yOffset = yOffset;
+
+    Vector3D lookDir = new Vector3D(1.0, sumFile.boresight());
+
+    if (xOffset != 0) {
+      Vector3D offset = new Vector3D(-xOffset, sumFile.xPerPixel());
+      lookDir = lookDir.add(offset);
+    }
+
+    if (yOffset != 0) {
+      Vector3D offset = new Vector3D(-yOffset, sumFile.yPerPixel());
+      lookDir = lookDir.add(offset);
+    }
+
+    double[] tmp = new double[3];
+    facet = smallBodyModel.computeRayIntersection(scPos.toArray(), lookDir.toArray(), tmp);
+
+    if (facet == -1) {
+      surfaceIntercept = null;
+    } else {
+      surfaceIntercept = new Vector3D(tmp);
+
+      vtkIdList idList = new vtkIdList();
+      double[] pt0 = new double[3];
+      double[] pt1 = new double[3];
+      double[] pt2 = new double[3];
+
+      polyData.GetCellPoints(facet, idList);
+
+      // get the ids for each point
+      long id0 = idList.GetId(0);
+      long id1 = idList.GetId(1);
+      long id2 = idList.GetId(2);
+
+      // get points that comprise the cell
+      polyData.GetPoint(id0, pt0);
+      polyData.GetPoint(id1, pt1);
+      polyData.GetPoint(id2, pt2);
+
+      TriangularFacet facet =
+          new TriangularFacet(new VectorIJK(pt0), new VectorIJK(pt1), new VectorIJK(pt2));
+
+      Vector3 center3 = MathConversions.toVector3(facet.getCenter());
+      Vector3D center3D = MathConversions.toVector3D(facet.getCenter());
+      Vector3 normal3 = MathConversions.toVector3(facet.getNormal());
+      Vector3D normal3D = MathConversions.toVector3D(facet.getNormal());
+
+      tiltDeg = Math.toDegrees(center3.sep(normal3));
+      if (tiltDeg > 90) tiltDeg = 180 - tiltDeg;
+
+      tiltDir = Tilts.basicTiltDirDeg(surfaceIntercept.getAlpha(), normal3D);
+
+
+      incidence = Vector3D.angle(sunXYZ, normal3D);
+      emission = Vector3D.angle(scPos, normal3D);
+      phase = Vector3D.angle(sunXYZ, scPos.subtract(center3D));
+
+      try {
+        // scPos is in body fixed coordinates
+        Plane p = new Plane(normal3, center3);
+        Vector3 projectedNorth = p.project(new Vector3(0, 0, 1).add(center3)).sub(center3);
+        Vector3 projected = p.project(MathConversions.toVector3(scPos)).sub(center3);
+
+        scAzimuth = projected.sep(projectedNorth);
+        if (projected.cross(projectedNorth).dot(center3) < 0) scAzimuth = 2 * Math.PI - scAzimuth;
+        scElevation = Math.PI / 2 - emission;
+
+        // sunXYZ is a unit vector pointing to the sun
+        projected = p.project(MathConversions.toVector3(sunXYZ).add(center3)).sub(center3);
+
+        sunAzimuth = projected.sep(projectedNorth);
+        if (projected.cross(projectedNorth).dot(center3) < 0) sunAzimuth = 2 * Math.PI - sunAzimuth;
+        sunElevation = Math.PI / 2 - incidence;
+      } catch (SpiceException e) {
+        logger.error(e.getLocalizedMessage(), e);
+      }
+
+      stats.addValue(scPos.distance(surfaceIntercept));
+    }
+    return new AbstractMap.SimpleEntry<>(facet, surfaceIntercept);
+  }
+
+  public String getHeader(String filename) {
+    StringBuffer sb = new StringBuffer();
+    sb.append("# x increases to the right and y increases down.  Top left corner is 0, 0.\n");
+    sb.append(String.format("# %s\n", filename));
+    sb.append(String.format("%7s", "#   x"));
+    sb.append(String.format("%7s", "y"));
+    sb.append(StringUtils.center("facet", 8));
+    sb.append(StringUtils.center("Tilt", 12));
+    sb.append(StringUtils.center("Tilt Dir", 12));
+    sb.append(StringUtils.center("s/c position XYZ", 36));
+    sb.append(StringUtils.center("surface intercept XYZ", 36));
+    sb.append(StringUtils.center("lon", 12));
+    sb.append(StringUtils.center("lat", 12));
+    sb.append(StringUtils.center("rad", 12));
+    sb.append(StringUtils.center("range", 12));
+    sb.append(StringUtils.center("inc", 12));
+    sb.append(StringUtils.center("ems", 12));
+    sb.append(StringUtils.center("phase", 12));
+    sb.append(StringUtils.center("s/c az", 12));
+    sb.append(StringUtils.center("s/c el", 12));
+    sb.append(StringUtils.center("sun az", 12));
+    sb.append(StringUtils.center("sun el", 12));
+
+    sb.append("\n");
+    sb.append(String.format("%7s", "#    "));
+    sb.append(String.format("%7s", ""));
+    sb.append(String.format("%8s", ""));
+    sb.append(StringUtils.center("(deg)", 12));
+    sb.append(StringUtils.center("(deg)", 12));
+    sb.append(StringUtils.center("(km)", 36));
+    sb.append(StringUtils.center("(km)", 36));
+    sb.append(StringUtils.center("(deg)", 12));
+    sb.append(StringUtils.center("(deg)", 12));
+    sb.append(StringUtils.center("(km)", 12));
+    sb.append(StringUtils.center("(km)", 12));
+    sb.append(StringUtils.center("(deg)", 12));
+    sb.append(StringUtils.center("(deg)", 12));
+    sb.append(StringUtils.center("(deg)", 12));
+    sb.append(StringUtils.center("(deg)", 12));
+    sb.append(StringUtils.center("(deg)", 12));
+    sb.append(StringUtils.center("(deg)", 12));
+    sb.append(StringUtils.center("(deg)", 12));
+    return sb.toString();
+  }
+
+  @Override
+  public String toString() {
+    StringBuilder sb = new StringBuilder();
+    sb.append(String.format("%7.2f", xOffset + centerX));
+    sb.append(String.format("%7.2f", yOffset + centerY));
+    sb.append(String.format("%8d", facet));
+    sb.append(String.format("%12.6f", tiltDeg));
+    sb.append(String.format("%12.6f", tiltDir));
+    sb.append(String.format("%12.6f", scPos.getX()));
+    sb.append(String.format("%12.6f", scPos.getY()));
+    sb.append(String.format("%12.6f", scPos.getZ()));
+    sb.append(String.format("%12.6f", surfaceIntercept.getX()));
+    sb.append(String.format("%12.6f", surfaceIntercept.getY()));
+    sb.append(String.format("%12.6f", surfaceIntercept.getZ()));
+
+    double lon = Math.toDegrees(surfaceIntercept.getAlpha());
+    if (lon < 0) lon += 360;
+    sb.append(String.format("%12.6f", lon));
+    sb.append(String.format("%12.6f", Math.toDegrees(surfaceIntercept.getDelta())));
+    sb.append(String.format("%12.6f", surfaceIntercept.getNorm()));
+
+    sb.append(String.format("%12.6f", scPos.distance(surfaceIntercept)));
+    sb.append(String.format("%12.6f", Math.toDegrees(incidence)));
+    sb.append(String.format("%12.6f", Math.toDegrees(emission)));
+    sb.append(String.format("%12.6f", Math.toDegrees(phase)));
+    sb.append(String.format("%12.6f", Math.toDegrees(scAzimuth)));
+    sb.append(String.format("%12.6f", Math.toDegrees(scElevation)));
+    sb.append(String.format("%12.6f", Math.toDegrees(sunAzimuth)));
+    sb.append(String.format("%12.6f", Math.toDegrees(sunElevation)));
+
+    return sb.toString();
+  }
+
+  private static Options defineOptions() {
+    Options options = TerrasaurTool.defineOptions();
+    options.addOption(
+        Option.builder("sumFile")
+            .required()
+            .hasArg()
+            .desc("Required.  Name of sum file to read.")
+            .build());
+    options.addOption(
+        Option.builder("objFile")
+            .required()
+            .hasArg()
+            .desc("Required.  Name of OBJ shape file.")
+            .build());
+    options.addOption(
+        Option.builder("pixelOffset")
+            .hasArg()
+            .desc(
+                "Pixel offset from center of image, given as a comma separated pair (no spaces).  Default is 0,0.  "
+                    + "x increases to the right and y increases down.")
+            .build());
+    options.addOption(
+        Option.builder("xRange")
+            .hasArg()
+            .desc(
+                "Range of X pixel offsets from center of image, given as a comma separated triplet (xStart, xStop, xSpacing with no spaces).  "
+                    + "For example -50,50,5.")
+            .build());
+    options.addOption(
+        Option.builder("yRange")
+            .hasArg()
+            .desc(
+                "Range of Y pixel offsets from center of image, given as a comma separated triplet (yStart, yStop, ySpacing with no spaces).  "
+                    + "For example -50,50,5.")
+            .build());
+    options.addOption(
+        Option.builder("radius")
+            .hasArg()
+            .desc(
+                "Evaluate all pixels within specified distance (in pixels) of desired pixel.  This value will be rounded to the nearest integer.")
+            .build());
+    options.addOption(
+        Option.builder("distanceScale")
+            .hasArg()
+            .desc(
+                "Spacecraft position is assumed to be in kilometers.  If not, scale by this value (e.g. Use 0.001 if s/c pos is in meters).")
+            .build());
+    options.addOption(
+        Option.builder("stats")
+            .desc("Print out statistics about range to all selected pixels.")
+            .build());
+    return options;
+  }
+
+  public static void main(String[] args) throws Exception {
+    TerrasaurTool defaultOBJ = new RangeFromSumFile();
+
+    Options options = defineOptions();
+
+    CommandLine cl = defaultOBJ.parseArgs(args, options);
+
+    Map<MessageLabel, String> startupMessages = defaultOBJ.startupMessages(cl);
+    for (MessageLabel ml : startupMessages.keySet())
+      logger.info(String.format("%s %s", ml.label, startupMessages.get(ml)));
+    NativeLibraryLoader.loadSpiceLibraries();
+    NativeLibraryLoader.loadVtkLibraries();
+
+    SumFile sumFile = SumFile.fromFile(new File(cl.getOptionValue("sumFile")));
+
+    int xStart = 0;
+    int xStop = 1;
+    int xSpacing = 1;
+    int yStart = 0;
+    int yStop = 1;
+    int ySpacing = 1;
+    if (cl.hasOption("pixelOffset")) {
+      String[] parts = cl.getOptionValue("pixelOffset").split(",");
+
+      int x = Integer.parseInt(parts[0].trim());
+      int y = Integer.parseInt(parts[1].trim());
+
+      xStart = x;
+      xStop = x + 1;
+      yStart = y;
+      yStop = y + 1;
+    }
+
+    if (cl.hasOption("xRange")) {
+      String[] parts = cl.getOptionValue("xRange").split(",");
+      xStart = Integer.parseInt(parts[0].trim());
+      xStop = Integer.parseInt(parts[1].trim());
+      xSpacing = Integer.parseInt(parts[2].trim());
+    }
+
+    if (cl.hasOption("yRange")) {
+      String[] parts = cl.getOptionValue("yRange").split(",");
+      yStart = Integer.parseInt(parts[0].trim());
+      yStop = Integer.parseInt(parts[1].trim());
+      ySpacing = Integer.parseInt(parts[2].trim());
+    }
+
+    int checkRadius = 0;
+    if (cl.hasOption("radius")) {
+      checkRadius = (int) Math.round(Double.parseDouble(cl.getOptionValue("radius")));
+      xStart -= checkRadius;
+      xStop += checkRadius;
+      yStart -= checkRadius;
+      yStop += checkRadius;
+    }
+
+    String objFile = cl.getOptionValue("objFile");
+    vtkPolyData polyData = PolyDataUtil.loadShapeModel(objFile);
+    RangeFromSumFile rfsf = new RangeFromSumFile(sumFile, polyData);
+
+    if (cl.hasOption("distanceScale"))
+      rfsf.setDistanceScale(Double.parseDouble(cl.getOptionValue("distanceScale")));
+
+    System.out.println(rfsf.getHeader(cl.getOptionValue("sumFile")));
+
+    for (int ix = xStart; ix < xStop; ix += xSpacing) {
+      for (int iy = yStart; iy < yStop; iy += ySpacing) {
+        if (checkRadius > 0) {
+          double midx = (xStart + xStop) / 2.;
+          double midy = (yStart + yStop) / 2.;
+          if ((ix - midx) * (ix - midx) + (iy - midy) * (iy - midy) > checkRadius * checkRadius)
+            continue;
+        }
+        long cellID = rfsf.findIntercept(ix, iy).getKey();
+        if (cellID > -1) System.out.println(rfsf);
+      }
+    }
+    if (cl.hasOption("stats")) System.out.println("Range " + rfsf.getStats());
+  }
+}

src/main/java/terrasaur/apps/RenderShapeFromSumFile.java

@@ -0,0 +1,842 @@
+package terrasaur.apps;
+
+import java.awt.AlphaComposite;
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.image.BufferedImage;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.nio.charset.Charset;
+import java.time.Instant;
+import java.util.*;
+import java.util.Map.Entry;
+import java.util.concurrent.Callable;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
+import java.util.stream.IntStream;
+import javax.imageio.ImageIO;
+import net.jafama.FastMath;
+import nom.tam.fits.Fits;
+import nom.tam.fits.Header;
+import nom.tam.fits.ImageHDU;
+import nom.tam.fits.header.DateTime;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.Options;
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.FilenameUtils;
+import org.apache.commons.math3.geometry.euclidean.threed.Rotation;
+import org.apache.commons.math3.geometry.euclidean.threed.Vector3D;
+import org.apache.logging.log4j.Level;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.spi.StandardLevel;
+import terrasaur.smallBodyModel.LocalModelCollection;
+import terrasaur.smallBodyModel.SmallBodyModel;
+import terrasaur.templates.TerrasaurTool;
+import terrasaur.utils.*;
+import terrasaur.utils.math.RotationUtils;
+import terrasaur.utils.saaPlotLib.util.StringFunctions;
+import vtk.vtkIdList;
+import vtk.vtkPoints;
+import vtk.vtkPolyData;
+
+public class RenderShapeFromSumFile implements TerrasaurTool {
+
+  private static final Logger logger = LogManager.getLogger();
+
+  @Override
+  public String shortDescription() {
+    return "Render a simulated camera image given a shape model and sumFile.";
+  }
+
+  @Override
+  public String fullDescription(Options options) {
+    String header = "";
+    String footer = "\nRender a simulated camera image given a shape model and sumFile.\n";
+    return TerrasaurTool.super.fullDescription(options, header, footer);
+  }
+
+  private RenderShapeFromSumFile() {}
+
+  private String globalOBJname;
+  private Double scale;
+  private Rotation rotation;
+
+  /** Sun position in body fixed coordinates */
+  private Vector3D sunXYZ;
+
+  /** Set camera position in body fixed coordinates */
+  private Vector3D cameraXYZ;
+
+  private Rotation cameraToBodyFixed;
+
+  /** set instantaneous field of view in radians/pixel */
+  private double ifov;
+
+  private int nPixelsX, nPixelsY;
+  private double centerX, centerY;
+  private int subPixel;
+
+  private ThreadLocal<SmallBodyModel> sbm;
+  // key is cell index, value is albedo
+  private Map<Long, Double> albedoMap;
+  // key is resolution, value is local shape model
+  private NavigableMap<Double, LocalModelCollection> lmcMap;
+
+  // key is field name, value is pair of comment and metadata value
+  private NavigableMap<String, Map.Entry<String, String>> metadata;
+
+  public RenderShapeFromSumFile(String globalOBJname, Double scale, Rotation rotation) {
+    this.globalOBJname = globalOBJname;
+    this.scale = scale;
+    this.rotation = rotation;
+
+    subPixel = 2;
+
+    sbm = new ThreadLocal<>();
+    albedoMap = new HashMap<>();
+    lmcMap = new TreeMap<>();
+
+    metadata = new TreeMap<>();
+  }
+
+  private void loadAlbedoFile(String albedoFile) {
+    try {
+      List<String> lines = FileUtils.readLines(new File(albedoFile), Charset.defaultCharset());
+      for (String line : lines) {
+        String trimLine = line.strip();
+        if (trimLine.isEmpty() || trimLine.startsWith("#")) continue;
+
+        String[] parts = trimLine.split(",");
+        long index = Long.parseLong(parts[0].trim());
+        albedoMap.put(index, Double.parseDouble(parts[1].trim()));
+      }
+    } catch (IOException e) {
+      logger.error(e.getLocalizedMessage(), e);
+    }
+  }
+
+  private SmallBodyModel getGlobalModel() {
+    if (sbm.get() == null) {
+      try {
+        vtkPolyData model = PolyDataUtil.loadShapeModel(globalOBJname);
+        if (scale != null || rotation != null) {
+          PolyDataStatistics stats = new PolyDataStatistics(model);
+          Vector3D center = new Vector3D(stats.getCentroid());
+
+          vtkPoints points = model.GetPoints();
+          for (int i = 0; i < points.GetNumberOfPoints(); i++) {
+            Vector3D thisPoint = new Vector3D(points.GetPoint(i));
+            if (scale != null)
+              thisPoint = thisPoint.subtract(center).scalarMultiply(scale).add(center);
+            if (rotation != null)
+              thisPoint = rotation.applyTo(thisPoint.subtract(center)).add(center);
+            points.SetPoint(i, thisPoint.toArray());
+          }
+        }
+        sbm.set(new SmallBodyModel(model));
+      } catch (Exception e) {
+        logger.error(e.getLocalizedMessage());
+      }
+    }
+    return sbm.get();
+  }
+
+  public void addMetaData(String key, String comment, String value) {
+    metadata.put(key, new AbstractMap.SimpleEntry<>(comment, value));
+  }
+
+  public void setSubPixel(int subPixel) {
+    this.subPixel = subPixel;
+  }
+
+  /**
+   * Return a unit 3D vector in the body fixed frame given pixel coordinates x and y. (0,0) is the
+   * upper left corner with X increasing to the right and Y increasing down.
+   *
+   * @param ix pixel x value
+   * @param iy pixel y value
+   * @return look direction
+   */
+  public Vector3D pixelToBodyFixed(double ix, double iy) {
+
+    double[] xyz = new double[3];
+    xyz[0] = FastMath.sin(ifov * (ix - centerX));
+    xyz[1] = FastMath.sin(ifov * (iy - centerY));
+    xyz[2] = FastMath.sqrt(1 - xyz[0] * xyz[0] - xyz[1] * xyz[1]);
+
+    return cameraToBodyFixed.applyTo(new Vector3D(xyz));
+  }
+
+  private static class Brightness {
+    private final double incidence;
+    private final double emission;
+    private final double phase;
+    private final double brightness;
+    private final double range;
+    private final double facetX;
+    private final double facetY;
+    private final double facetZ;
+    private final double normalX;
+    private final double normalY;
+    private final double normalZ;
+
+    private Brightness(
+        double incidence,
+        double emission,
+        double phase,
+        double brightness,
+        double range,
+        Vector3D facet,
+        Vector3D normal) {
+      this.incidence = Math.toDegrees(incidence);
+      this.emission = Math.toDegrees(emission);
+      this.phase = Math.toDegrees(phase);
+      this.brightness = brightness;
+      this.range = range;
+      this.facetX = facet.getX();
+      this.facetY = facet.getY();
+      this.facetZ = facet.getZ();
+      this.normalX = normal.getX();
+      this.normalY = normal.getY();
+      this.normalZ = normal.getZ();
+    }
+
+    private double[] values() {
+      return new double[] {
+        this.brightness,
+        this.incidence,
+        this.emission,
+        this.phase,
+        this.range,
+        this.facetX,
+        this.facetY,
+        this.facetZ,
+        this.normalX,
+        this.normalY,
+        this.normalZ
+      };
+    }
+  }
+
+  /**
+   * @param pf Photometric function
+   * @param intersect cell id of intersection point
+   * @param intersectPoint XYZ coordinates of intersection point
+   * @param isDefault true if this is the default model, false if local
+   * @return Brightness structure
+   */
+  private Brightness getBrightness(
+      PhotometricFunction pf,
+      SmallBodyModel sbm,
+      long intersect,
+      Vector3D intersectPoint,
+      boolean isDefault) {
+
+    Vector3D facetToCamera = cameraXYZ.subtract(intersectPoint);
+
+    CellInfo ci = CellInfo.getCellInfo(sbm.getSmallBodyPolyData(), intersect, new vtkIdList());
+    Vector3D normal = ci.normal();
+
+    double emission = Vector3D.angle(facetToCamera, normal);
+    double distFromCamera = facetToCamera.getNorm();
+
+    // speeds up calculation along the limb. Need to combine all pixels in the ifov.
+    double kmPerPixel =
+        ifov * distFromCamera / Math.abs(FastMath.cos(Math.min(Math.toRadians(60), emission)));
+
+    double sum = 0;
+
+    Set<Long> cells = sbm.findClosestCellsWithinRadius(intersectPoint.toArray(), kmPerPixel / 2);
+    cells.add(intersect);
+    double incidence = 0;
+    double phase = 0;
+    for (long cell : cells) {
+
+      ci = CellInfo.getCellInfo(sbm.getSmallBodyPolyData(), cell, new vtkIdList(), true);
+      facetToCamera = cameraXYZ.subtract(ci.center());
+      normal = new Vector3D(sbm.getCellNormals().GetTuple3(cell));
+      emission = Vector3D.angle(facetToCamera, normal);
+      incidence = 0;
+      phase = 0;
+
+      if (sunXYZ != null) {
+        incidence = Vector3D.angle(sunXYZ, normal);
+        phase = Vector3D.angle(facetToCamera, sunXYZ);
+
+        Vector3D sunToFacet = ci.center().subtract(sunXYZ);
+
+        // check for shadowing
+        double[] sunIntersectPoint = new double[3];
+        long sunIntersect =
+            sbm.computeRayIntersection(sunXYZ.toArray(), sunToFacet.toArray(), sunIntersectPoint);
+        if (sunIntersect != cell) {
+          // don't allow points in shadow to have a 0 value
+          sum += .001;
+          continue;
+        }
+      }
+      double albedo = (isDefault && albedoMap.containsKey(cell)) ? albedoMap.get(cell) : 1;
+      sum +=
+          albedo
+              * pf.getValue(
+                  FastMath.cos(incidence), FastMath.cos(emission), FastMath.toDegrees(phase));
+    }
+
+    logger.printf(
+        Level.DEBUG,
+        "Thread %d lat/lon %.2f/%.2f, %s, sum %f, cells %d, %.2f",
+        Thread.currentThread().getId(),
+        Math.toDegrees(intersectPoint.getDelta()),
+        Math.toDegrees(intersectPoint.getAlpha()),
+        intersectPoint.toString(),
+        sum,
+        cells.size(),
+        sum / cells.size());
+
+    return new Brightness(
+        incidence, emission, phase, sum / cells.size(), distFromCamera, facetToCamera, normal);
+  }
+
+  class BrightnessCalculator implements Callable<Map<Integer, Brightness>> {
+
+    Collection<Integer> pixelIndices;
+    PhotometricFunction pf;
+
+    private BrightnessCalculator(Collection<Integer> pixelIndices, PhotometricFunction pf) {
+      this.pixelIndices = pixelIndices;
+      this.pf = pf;
+    }
+
+    @Override
+    public Map<Integer, Brightness> call() throws Exception {
+
+      logger.info("Thread {}: starting", Thread.currentThread().getId());
+
+      int xPixels = subPixel * nPixelsX;
+
+      SmallBodyModel globalModel = getGlobalModel();
+
+      Map<Integer, Brightness> brightness = new HashMap<>();
+      double[] intersectPoint = new double[3];
+      double[] cameraXYZArray = cameraXYZ.toArray();
+      for (Integer index : pixelIndices) {
+        int j = index / xPixels;
+        int i = index % xPixels;
+        Vector3D pixelDir = pixelToBodyFixed(((double) i) / subPixel, ((double) j) / subPixel);
+
+        long intersect =
+            globalModel.computeRayIntersection(cameraXYZArray, pixelDir.toArray(), intersectPoint);
+
+        if (intersect > -1) {
+
+          Vector3D intersectPt3D = new Vector3D(intersectPoint);
+
+          // resolution in m/pixel
+          double resolution = ifov * intersectPt3D.distance(cameraXYZ) * 1e3;
+
+          // if no ceiling entry exists, stick with the global model
+          Entry<Double, LocalModelCollection> lmcEntry = lmcMap.ceilingEntry(resolution);
+          if (lmcEntry != null) {
+
+            LocalModelCollection lmc = lmcEntry.getValue();
+            double[] localIntersectPoint = new double[3];
+
+            SmallBodyModel localModel = lmc.get(intersectPt3D);
+            if (localModel != null) {
+              long localIntersect =
+                  localModel.computeRayIntersection(
+                      cameraXYZArray, pixelDir.toArray(), localIntersectPoint);
+              if (localIntersect != -1) {
+                break;
+              } else {
+                logger.debug(
+                    String.format(
+                        "Thread %d: No intersection with local model for pixel (%d,%d): lat/lon %.2f/%.2f, using global intersection %d %s",
+                        Thread.currentThread().getId(),
+                        i,
+                        j,
+                        Math.toDegrees(intersectPt3D.getDelta()),
+                        Math.toDegrees(intersectPt3D.getAlpha()),
+                        intersect,
+                        intersectPt3D));
+              }
+            }
+          }
+
+          boolean isDefault = lmcEntry == null;
+          Brightness b = getBrightness(pf, globalModel, intersect, intersectPt3D, isDefault);
+          brightness.put(j * xPixels + i, b);
+        }
+      }
+
+      logger.info("Thread {}: finished", Thread.currentThread().getId());
+
+      return brightness;
+    }
+  }
+
+  public double[][][] getFits(PhotometricFunction pf, int numThreads) {
+
+    int xPixels = subPixel * nPixelsX;
+    int yPixels = subPixel * nPixelsY;
+
+    Map<Integer, Brightness> brightness = new HashMap<>();
+    try (ExecutorService executor = Executors.newFixedThreadPool(numThreads)) {
+
+      List<Integer> indices = IntStream.range(0, yPixels * xPixels).boxed().toList();
+
+      int numPixels = indices.size();
+
+      Set<BrightnessCalculator> callables = new HashSet<>();
+      for (int i = 0; i < numThreads; i++) {
+        int fromIndex = i * numPixels / numThreads;
+        int toIndex = Math.min(numPixels, fromIndex + numPixels / numThreads);
+        callables.add(new BrightnessCalculator(indices.subList(fromIndex, toIndex), pf));
+      }
+
+      Set<Future<Map<Integer, Brightness>>> futures = new HashSet<>();
+      for (BrightnessCalculator callable : callables) futures.add(executor.submit(callable));
+
+      for (Future<Map<Integer, Brightness>> future : futures) {
+        try {
+          Map<Integer, Brightness> values = future.get();
+          brightness.putAll(values);
+        } catch (Exception e) {
+          logger.error(e.getLocalizedMessage(), e);
+        }
+      }
+      executor.shutdown();
+    }
+
+    double[][][] img = new double[11][yPixels][xPixels];
+    for (int i = 0; i < xPixels; i++) {
+      for (int j = 0; j < yPixels; j++) {
+        Brightness pixel = brightness.get(j * xPixels + i);
+        if (pixel == null) continue;
+        double[] pixels = pixel.values();
+        for (int k = 0; k < img.length; k++) {
+          img[k][yPixels - j - 1][i] = pixels[k];
+        }
+      }
+    }
+    return img;
+  }
+
+  public BufferedImage getImage(PhotometricFunction pf, int numThreads) {
+
+    int xPixels = subPixel * nPixelsX;
+    int yPixels = subPixel * nPixelsY;
+    BufferedImage image = new BufferedImage(xPixels, yPixels, BufferedImage.TYPE_INT_ARGB);
+    Graphics2D g = image.createGraphics();
+    g.setComposite(AlphaComposite.Clear);
+    g.fillRect(0, 0, image.getWidth(), image.getHeight());
+    g.setComposite(AlphaComposite.Src);
+    g.setColor(Color.BLACK);
+    g.fillRect(0, 0, image.getWidth(), image.getHeight());
+
+    Map<Integer, Brightness> brightness = new HashMap<>();
+    double maxBrightness = -Double.MAX_VALUE;
+
+    try (ExecutorService executor = Executors.newFixedThreadPool(numThreads)) {
+
+      List<Integer> indices = IntStream.range(0, yPixels * xPixels).boxed().toList();
+
+      int numPixels = indices.size();
+
+      Set<BrightnessCalculator> callables = new HashSet<>();
+      for (int i = 0; i < numThreads; i++) {
+        int fromIndex = i * numPixels / numThreads;
+        int toIndex = Math.min(numPixels, fromIndex + numPixels / numThreads);
+        callables.add(new BrightnessCalculator(indices.subList(fromIndex, toIndex), pf));
+      }
+
+      Set<Future<Map<Integer, Brightness>>> futures = new HashSet<>();
+      for (BrightnessCalculator callable : callables) futures.add(executor.submit(callable));
+
+      for (Future<Map<Integer, Brightness>> future : futures) {
+        try {
+          Map<Integer, Brightness> brightnessMap = future.get();
+          for (Brightness b : brightnessMap.values())
+            if (maxBrightness < b.brightness) maxBrightness = b.brightness;
+          brightness.putAll(future.get());
+        } catch (Exception e) {
+          logger.error(e.getLocalizedMessage(), e);
+        }
+      }
+      executor.shutdown();
+    }
+
+    /*-
+    double[] intersectPoint = new double[3];
+
+    Map<Integer, Double> brightness = new HashMap<>();
+
+    double[] cameraXYZArray = cameraXYZ.toArray();
+    for (int i = 0; i < xPixels; i++) {
+      for (int j = 0; j < yPixels; j++) {
+        Vector3D pixelDir = pixelToBodyFixed(((double) i) / scale, ((double) j) / scale);
+
+        int intersect =
+            sbm.computeRayIntersection(cameraXYZArray, pixelDir.toArray(), intersectPoint);
+        if (intersect > 0) {
+          brightness.put(i * xPixels + j,
+              getBrightness(pf, intersect, new Vector3D(intersectPoint)));
+        }
+      }
+    }
+    */
+    if (brightness.isEmpty()) {
+      logger.info("No intersections with shape model found!");
+    } else {
+      for (int j = 0; j < yPixels; j++) {
+        for (int i = 0; i < xPixels; i++) {
+          if (!brightness.containsKey(j * xPixels + i)) continue;
+          double value = brightness.get(j * xPixels + i).brightness;
+
+          int grey = value < 0.01 ? 1 : (int) (255 * value / maxBrightness);
+
+          image.setRGB(i, j, new Color(grey, grey, grey).getRGB());
+        }
+      }
+    }
+
+    BufferedImage img = new BufferedImage(nPixelsX, nPixelsY, BufferedImage.TYPE_INT_RGB);
+    img.createGraphics()
+        .drawImage(image.getScaledInstance(nPixelsX, nPixelsY, Image.SCALE_SMOOTH), 0, 0, null);
+
+    return img;
+  }
+
+  public SumFile loadSumFile(String filename) {
+
+    SumFile sumFile = SumFile.fromFile(new File(filename));
+
+    addMetaData("image.utc", "Imaging date.  Taken from sumfile", sumFile.utcString());
+
+    nPixelsX = sumFile.imageWidth();
+    nPixelsY = sumFile.imageHeight();
+
+    centerX = 0.5 * (nPixelsX - 1);
+    centerY = 0.5 * (nPixelsY - 1);
+
+    // let's assume square pixels
+    ifov = sumFile.horizontalResolution();
+
+    // put the sun far away
+    sunXYZ = sumFile.sunDirection().scalarMultiply(1e8);
+    cameraXYZ = sumFile.scobj().negate();
+
+    cameraToBodyFixed = sumFile.getBodyFixedToCamera().revert();
+
+    double[] intersectPoint = new double[3];
+    Vector3D boresight = sumFile.boresight();
+    long intersect =
+        getGlobalModel()
+            .computeRayIntersection(cameraXYZ.toArray(), boresight.toArray(), intersectPoint);
+    if (intersect > 0) {
+      Vector3D nadirPt = new Vector3D(intersectPoint);
+      double lat = nadirPt.getDelta();
+      double lon = nadirPt.getAlpha();
+      Vector3D normal = new Vector3D(getGlobalModel().getCellNormals().GetTuple3(intersect));
+      double inc = Vector3D.angle(sunXYZ, normal);
+      Vector3D toCamera = cameraXYZ.subtract(nadirPt);
+      double ems = Vector3D.angle(toCamera, normal);
+      double phs = Vector3D.angle(sunXYZ, toCamera);
+      double range = cameraXYZ.subtract(nadirPt).getNorm();
+
+      addMetaData("image.cell", "Index of center pixel cell", Long.toString(intersect));
+      addMetaData("image.lat", "Center latitude", StringFunctions.toDegreesLat("%.2f ").apply(lat));
+      addMetaData(
+          "image.lon", "Center longitude", StringFunctions.toDegreesELon("%.2f ").apply(lon));
+      addMetaData(
+          "image.inc", "Center incidence in degrees", String.format("%.2f", Math.toDegrees(inc)));
+      addMetaData(
+          "image.ems",
+          "Center emission in degrees (may not be zero if facet is tilted)",
+          String.format("%.2f", Math.toDegrees(ems)));
+      addMetaData(
+          "image.phs", "Center phase in degrees", String.format("%.2f", Math.toDegrees(phs)));
+      addMetaData("image.range", "Center point range in m", String.format("%.3f", range * 1e3));
+      addMetaData(
+          "image.resolution",
+          "Center point resolution in m/pixel",
+          String.format("%.3f", ifov * range * 1e3));
+    }
+    return sumFile;
+  }
+
+  /**
+   * load a local model file
+   *
+   * @param lmcName local model filename
+   */
+  public void loadLocalModels(String lmcName) {
+    LocalModelCollection lmc = new LocalModelCollection(128, scale, rotation);
+    try {
+      List<String> lines = FileUtils.readLines(new File(lmcName), Charset.defaultCharset());
+
+      Double localResolution = null;
+
+      for (String line : lines) {
+        String strippedLine = line.strip();
+        if (strippedLine.isEmpty() || strippedLine.startsWith("#")) continue;
+        String[] parts = strippedLine.split(",");
+
+        if (localResolution == null) {
+          localResolution = Double.valueOf(parts[0].strip());
+          logger.debug("Loading {} with a resolution of {} m/pixel", lmcName, localResolution);
+        } else {
+          double lat = Math.toRadians(Double.parseDouble(parts[0]));
+          double lon = Math.toRadians(Double.parseDouble(parts[1]));
+          String filename = parts[2].strip();
+          lmc.addModel(lat, lon, filename);
+        }
+      }
+      this.lmcMap.put(localResolution, lmc);
+    } catch (IOException e) {
+      logger.error(e.getLocalizedMessage());
+    }
+  }
+
+  /**
+   * Write a metadata file containing information about the simulated image.
+   *
+   * @param metadataFile file to write
+   * @param arguments command line arguments
+   */
+  public void writeMetadata(File metadataFile, String arguments) {
+    try (PrintWriter pw = new PrintWriter(metadataFile)) {
+
+      pw.printf("# Created %s by %s\n", Instant.now().toString(), AppVersion.getVersionString());
+      pw.printf("# arguments: %s\n\n", arguments);
+
+      String lastSection = null;
+      for (String key : metadata.keySet()) {
+        String thisSection = key.substring(0, key.indexOf("."));
+        if (lastSection == null) lastSection = thisSection;
+        if (!lastSection.equals(thisSection)) {
+          pw.println();
+          lastSection = thisSection;
+        }
+        Map.Entry<String, String> value = metadata.get(key);
+        String[] comments = value.getKey().split("\\r?\\n");
+        for (String comment : comments) if (!comment.trim().isEmpty()) pw.printf("# %s\n", comment);
+        pw.printf("%s = %s\n", key, value.getValue());
+      }
+
+    } catch (FileNotFoundException e) {
+      logger.log(Level.ERROR, e.getLocalizedMessage(), e);
+    }
+  }
+
+  private static Options defineOptions() {
+    Options options = TerrasaurTool.defineOptions();
+    options.addOption(
+        Option.builder("albedoFile")
+            .hasArg()
+            .desc(
+                """
+                    Name of albedo file.  This is a CSV file with facet
+                    index in the first column and albedo (in the range 0
+                    to 1) in the second.  Additional columns are
+                    ignored.  Albedo for facets not specified will be
+                    set to 1.  Lines starting with # or blank
+                    lines are ignored.  This file applies only to the
+                    default shape model, not any local ones."""
+                    .replaceAll("\\s+", " ")
+                    .strip())
+            .build());
+    options.addOption(
+        Option.builder("localModels")
+            .hasArgs()
+            .desc(
+                """
+                    File containing local shape models, one per line.
+                    The first line of the file should contain the
+                    coarsest resolution in m/pixel where these models
+                    should be used.  Usually this can be about half the
+                    resolution of the next coarser model.  For example,
+                    if the global model has a resolution of 1 m/pixel
+                    the local model file should be used for resolutions
+                    better than 0.5 m/pixel.  Format of each remaining
+                    line is lat, lon, filename as comma separated
+                    values.  Lat and lon are in degrees.  This option
+                    may be specified multiple times to load multiple
+                    sets of models.  Lines starting with # or blank
+                    lines are ignored."""
+                    .replaceAll("\\s+", " ")
+                    .strip())
+            .build());
+    options.addOption(
+        Option.builder("logFile")
+            .hasArg()
+            .desc("If present, save screen output to log file.")
+            .build());
+    StringBuilder sb = new StringBuilder();
+    for (StandardLevel l : StandardLevel.values()) sb.append(String.format("%s ", l.name()));
+    options.addOption(
+        Option.builder("logLevel")
+            .hasArg()
+            .desc(
+                "If present, print messages above selected priority.  Valid values are "
+                    + sb.toString().trim()
+                    + ".  Default is INFO.")
+            .build());
+    options.addOption(
+        Option.builder("model")
+            .required()
+            .hasArg()
+            .desc(
+                "Required.  Default shape model filename.  Supported formats are OBJ, PLT, PLY, STL, or VTK format.")
+            .build());
+    options.addOption(
+        Option.builder("numThreads")
+            .hasArg()
+            .desc("Number of threads to run in parallel when generating the image.  Default is 2.")
+            .build());
+    options.addOption(
+        Option.builder("photo")
+            .hasArg()
+            .desc(PhotometricFunction.getOptionString().trim() + "  Default is OREX.")
+            .build());
+    options.addOption(
+        Option.builder("output")
+            .required()
+            .hasArg()
+            .desc("Required.  Name of image file to write.  Valid extensions are fits or png.")
+            .build());
+    options.addOption(
+        Option.builder("rotateModel")
+            .hasArg()
+            .desc(
+                """
+                    If present, rotate shape model.  Specify by an angle
+                    (degrees) and a 3 element rotation axis vector (XYZ)
+                    separated by commas.
+                    """
+                    .replaceAll("\\s+", " ")
+                    .strip())
+            .build());
+    options.addOption(
+        Option.builder("scaleModel")
+            .hasArg()
+            .desc("If present, factor to scale shape model.  The center is unchanged.")
+            .build());
+    options.addOption(
+        Option.builder("subPixel")
+            .hasArg()
+            .desc(
+                """
+                    Generate the simulated image a factor of subPixel
+                    (must be an integer) larger than the dimensions in
+                    the sum file.  The simulated image is them reduced
+                    in size to the dimensions in the sum file.  The
+                    default is 2.
+                    """
+                    .replaceAll("\\s+", " ")
+                    .strip())
+            .build());
+    options.addOption(
+        Option.builder("sumFile")
+            .required()
+            .hasArg()
+            .desc("Required.  Name of sum file to read.")
+            .build());
+    return options;
+  }
+
+  public static void main(String[] args) throws Exception {
+    TerrasaurTool defaultOBJ = new RenderShapeFromSumFile();
+
+    Options options = defineOptions();
+
+    CommandLine cl = defaultOBJ.parseArgs(args, options);
+
+    Map<MessageLabel, String> startupMessages = defaultOBJ.startupMessages(cl);
+    for (MessageLabel ml : startupMessages.keySet())
+      logger.info(String.format("%s %s", ml.label, startupMessages.get(ml)));
+
+    NativeLibraryLoader.loadVtkLibraries();
+
+    Double scale =
+        cl.hasOption("scaleModel") ? Double.parseDouble(cl.getOptionValue("scaleModel")) : null;
+    Rotation rotation =
+        cl.hasOption("rotateModel")
+            ? RotationUtils.stringToRotation(cl.getOptionValue("rotateModel"))
+            : null;
+
+    RenderShapeFromSumFile app =
+        new RenderShapeFromSumFile(cl.getOptionValue("model"), scale, rotation);
+    SumFile sumFile = app.loadSumFile(cl.getOptionValue("sumFile"));
+
+    if (cl.hasOption("albedoFile")) app.loadAlbedoFile(cl.getOptionValue("albedoFile"));
+
+    if (cl.hasOption("localModels"))
+      for (String localModel : cl.getOptionValues("localModels")) app.loadLocalModels(localModel);
+
+    if (cl.hasOption("subPixel")) app.setSubPixel(Integer.parseInt(cl.getOptionValue("subPixel")));
+
+    PhotometricFunction pf = PhotometricFunction.OREX1;
+    if (cl.hasOption("photo"))
+      pf = PhotometricFunction.getPhotometricFunction(cl.getOptionValue("photo"));
+    int numThreads =
+        cl.hasOption("numThreads") ? Integer.parseInt(cl.getOptionValue("numThreads")) : 2;
+
+    String outputFilename = cl.getOptionValue("output");
+    String dirname = FilenameUtils.getPath(outputFilename);
+    if (dirname.trim().isEmpty()) dirname = ".";
+    String basename = FilenameUtils.getBaseName(outputFilename);
+    String extension = FilenameUtils.getExtension(outputFilename);
+
+    if (extension.equalsIgnoreCase("png")) {
+      BufferedImage image = app.getImage(pf, numThreads);
+      File png = new File(dirname, basename + "." + extension);
+      File metadataFile = new File(dirname, basename + ".txt");
+
+      ImageIO.write(image, "PNG", png);
+      app.writeMetadata(metadataFile, startupMessages.get(MessageLabel.ARGUMENTS));
+      logger.info("Wrote {}", outputFilename);
+    } else if (extension.equalsIgnoreCase("fits")) {
+      Fits fits = new Fits();
+      ImageHDU imageHDU = (ImageHDU) Fits.makeHDU(app.getFits(pf, numThreads));
+      Header header = imageHDU.getHeader();
+      header.addValue(
+          DateTime.TIMESYS_UTC, app.metadata.get("image.utc").getValue(), "Time from the SUM file");
+      header.addValue("TITLE", sumFile.picnm(), "Title of SUM file");
+      header.addValue("PLANE1", "brightness", "from 0 to 1");
+      header.addValue("PLANE2", "incidence", "degrees");
+      header.addValue("PLANE3", "emission", "degrees");
+      header.addValue("PLANE4", "phase", "degrees");
+      header.addValue("PLANE5", "range", "kilometers");
+      header.addValue("PLANE6", "facetX", "kilometers");
+      header.addValue("PLANE7", "facetY", "kilometers");
+      header.addValue("PLANE8", "facetZ", "kilometers");
+      header.addValue("PLANE9", "normalX", "X component of unit normal");
+      header.addValue("PLANE10", "normalY", "Y component of unit normal");
+      header.addValue("PLANE11", "normalZ", "Z component of unit normal");
+      header.addValue("MMFL", sumFile.mmfl(), "From SUM file");
+      header.addValue("SCOBJ", sumFile.scobj().toString(), "From SUM file");
+      header.addValue("CX", sumFile.cx().toString(), "From SUM file");
+      header.addValue("CY", sumFile.cy().toString(), "From SUM file");
+      header.addValue("CZ", sumFile.cz().toString(), "From SUM file");
+      header.addValue("SZ", sumFile.sz().toString(), "From SUM file");
+      header.addValue("KMAT1", sumFile.kmat1().toString(), "From SUM file");
+      header.addValue("KMAT2", sumFile.kmat2().toString(), "From SUM file");
+      header.addValue("DIST", sumFile.distortion().toString(), "From SUM file");
+      header.addValue("SIGVSO", sumFile.sig_vso().toString(), "From SUM file");
+      header.addValue("SIGPTG", sumFile.sig_ptg().toString(), "From SUM file");
+      fits.addHDU(imageHDU);
+      fits.write(outputFilename);
+      fits.close();
+      logger.info("wrote {}", outputFilename);
+    } else {
+      logger.error("Unsupported output file type: {}", outputFilename);
+    }
+  }
+}

src/main/java/terrasaur/apps/RotationConversion.java

@@ -0,0 +1,220 @@
+package terrasaur.apps;
+
+import java.io.File;
+import java.nio.charset.Charset;
+import java.util.List;
+import java.util.Map;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.Options;
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.math3.geometry.euclidean.threed.CardanEulerSingularityException;
+import org.apache.commons.math3.geometry.euclidean.threed.Rotation;
+import org.apache.commons.math3.geometry.euclidean.threed.RotationConvention;
+import org.apache.commons.math3.geometry.euclidean.threed.RotationOrder;
+import org.apache.commons.math3.geometry.euclidean.threed.Vector3D;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.spi.StandardLevel;
+import terrasaur.templates.TerrasaurTool;
+
+public class RotationConversion implements TerrasaurTool {
+
+  private static final Logger logger = LogManager.getLogger();
+
+  @Override
+  public String shortDescription() {
+      return "Convert rotations between different types.";
+  }
+
+  @Override
+  public String fullDescription(Options options) {
+
+    String header = "";
+    String footer =
+            """
+                    This program converts rotations between angle and axis, 3x3 matrix, quaternions, \
+                    and ZXZ rotation Euler angles.  Note that the rotation modifies the frame; \
+                    the vector is considered to be fixed.  To find the rotation that modifies the \
+                    vector in a fixed frame, take the transpose of this matrix.
+                    """;
+
+    return TerrasaurTool.super.fullDescription(options, header, footer);
+
+  }
+
+
+  private static Options defineOptions() {
+    Options options = TerrasaurTool.defineOptions();
+    options.addOption(Option.builder("logFile").hasArg()
+            .desc("If present, save screen output to log file.").build());
+    StringBuilder sb = new StringBuilder();
+    for (StandardLevel l : StandardLevel.values())
+      sb.append(String.format("%s ", l.name()));
+    options.addOption(Option.builder("logLevel").hasArg()
+            .desc("If present, print messages above selected priority.  Valid values are "
+                    + sb.toString().trim() + ".  Default is INFO.")
+            .build());
+
+    options.addOption(Option.builder("angle").hasArg().desc("Rotation angle, in radians.").build());
+    options.addOption(
+            Option.builder("axis0").hasArg().desc("First element of rotation axis.").build());
+    options.addOption(
+            Option.builder("axis1").hasArg().desc("Second element of rotation axis.").build());
+    options.addOption(
+            Option.builder("axis2").hasArg().desc("Third element of rotation axis.").build());
+    options.addOption(Option.builder("cardanXYZ1").hasArg()
+            .desc("Cardan angle for the first rotation (about the X axis) in radians.").build());
+    options.addOption(Option.builder("cardanXYZ2").hasArg()
+            .desc("Cardan angle for the second rotation (about the Y axis) in radians.").build());
+    options.addOption(Option.builder("cardanXYZ3").hasArg()
+            .desc("Cardan angle for the third rotation (about the Z axis) in radians.").build());
+    options.addOption(Option.builder("eulerZXZ1").hasArg()
+            .desc("Euler angle for the first rotation (about the Z axis) in radians.").build());
+    options.addOption(Option.builder("eulerZXZ2").hasArg()
+            .desc("Euler angle for the second rotation (about the rotated X axis) in radians.")
+            .build());
+    options.addOption(Option.builder("eulerZXZ3").hasArg()
+            .desc("Euler angle for the third rotation (about the rotated Z axis) in radians.").build());
+    options.addOption(
+            Option.builder("q0").hasArg().desc("Scalar term for quaternion: cos(theta/2)").build());
+    options.addOption(Option.builder("q1").hasArg()
+            .desc("First vector term for quaternion: sin(theta/2) * V[0]").build());
+    options.addOption(Option.builder("q2").hasArg()
+            .desc("Second vector term for quaternion: sin(theta/2) * V[1]").build());
+    options.addOption(Option.builder("q3").hasArg()
+            .desc("Third vector term for quaternion: sin(theta/2) * V[2]").build());
+    options.addOption(Option.builder("matrix").hasArg()
+            .desc("name of file containing rotation matrix to convert to Euler angles.  "
+                    + "Format is 3x3 array in plain text separated by white space.")
+            .build());
+    options.addOption(Option.builder("anglesInDegrees").desc(
+                    "If present, input angles in degrees and print output angles in degrees.  Default is false.")
+            .build());    return options;
+  }
+
+  public static void main(String[] args) throws Exception {
+    RotationConversion defaultOBJ = new RotationConversion();
+    
+    Options options = defineOptions();
+
+    CommandLine cl = defaultOBJ.parseArgs(args, options);
+
+    Map<MessageLabel, String> startupMessages = defaultOBJ.startupMessages(cl);
+    for (MessageLabel ml : startupMessages.keySet())
+      logger.info(String.format("%s %s", ml.label, startupMessages.get(ml)));
+    boolean inDegrees = cl.hasOption("anglesInDegrees");
+
+    boolean axisAndAngle = cl.hasOption("angle") && cl.hasOption("axis0") && cl.hasOption("axis1")
+        && cl.hasOption("axis2");
+    boolean cardanXYZ =
+        cl.hasOption("cardanXYZ1") && cl.hasOption("cardanXYZ2") && cl.hasOption("cardanXYZ3");
+    boolean eulerZXZ =
+        cl.hasOption("eulerZXZ1") && cl.hasOption("eulerZXZ3") && cl.hasOption("eulerZXZ3");
+    boolean quaternion =
+        cl.hasOption("q0") && cl.hasOption("q1") && cl.hasOption("q2") && cl.hasOption("q3");
+    boolean matrix = cl.hasOption("matrix");
+
+    if (!(axisAndAngle || cardanXYZ || eulerZXZ || quaternion || matrix)) {
+      logger.warn(
+          "Must specify input rotation as axis and angle, Cardan or Euler angles, matrix, or quaternion.");
+      System.exit(0);
+    }
+
+    Rotation r = null;
+    if (matrix) {
+      List<String> lines =
+          FileUtils.readLines(new File(cl.getOptionValue("matrix")), Charset.defaultCharset());
+      double[][] m = new double[3][3];
+      for (int i = 0; i < 3; i++) {
+        String[] parts = lines.get(i).trim().split("\\s+");
+        for (int j = 0; j < 3; j++)
+          m[i][j] = Double.parseDouble(parts[j].trim());
+      }
+      r = new Rotation(m, 1e-10);
+    }
+
+    if (axisAndAngle) {
+      double angle = Double.parseDouble(cl.getOptionValue("angle").trim());
+      if (inDegrees)
+        angle = Math.toRadians(angle);
+      r = new Rotation(
+          new Vector3D(Double.parseDouble(cl.getOptionValue("axis0").trim()),
+              Double.parseDouble(cl.getOptionValue("axis1").trim()),
+              Double.parseDouble(cl.getOptionValue("axis2").trim())),
+          angle, RotationConvention.FRAME_TRANSFORM);
+    }
+
+    if (cardanXYZ) {
+      double angle1 = Double.parseDouble(cl.getOptionValue("cardanXYZ1").trim());
+      double angle2 = Double.parseDouble(cl.getOptionValue("cardanXYZ2").trim());
+      double angle3 = Double.parseDouble(cl.getOptionValue("cardanXYZ3").trim());
+      if (inDegrees) {
+        angle1 = Math.toRadians(angle1);
+        angle2 = Math.toRadians(angle2);
+        angle3 = Math.toRadians(angle3);
+      }
+      r = new Rotation(RotationOrder.XYZ, RotationConvention.FRAME_TRANSFORM, angle1, angle2,
+          angle3);
+    }
+
+    if (eulerZXZ) {
+      double angle1 = Double.parseDouble(cl.getOptionValue("eulerZXZ1").trim());
+      double angle2 = Double.parseDouble(cl.getOptionValue("eulerZXZ2").trim());
+      double angle3 = Double.parseDouble(cl.getOptionValue("eulerZXZ3").trim());
+      if (inDegrees) {
+        angle1 = Math.toRadians(angle1);
+        angle2 = Math.toRadians(angle2);
+        angle3 = Math.toRadians(angle3);
+      }
+      r = new Rotation(RotationOrder.ZXZ, RotationConvention.FRAME_TRANSFORM, angle1, angle2,
+          angle3);
+    }
+
+    if (quaternion) {
+      r = new Rotation(Double.parseDouble(cl.getOptionValue("q0").trim()),
+          Double.parseDouble(cl.getOptionValue("q1").trim()),
+          Double.parseDouble(cl.getOptionValue("q2").trim()),
+          Double.parseDouble(cl.getOptionValue("q3").trim()), true);
+    }
+
+    double[][] m = r.getMatrix();
+    String matrixString = String.format(
+        "rotation matrix:\n%24.16e %24.16e %24.16e\n%24.16e %24.16e %24.16e\n%24.16e %24.16e %24.16e",
+        m[0][0], m[0][1], m[0][2], m[1][0], m[1][1], m[1][2], m[2][0], m[2][1], m[2][2]);
+    System.out.println(matrixString);
+
+    String axisAndAngleString = inDegrees
+        ? String.format("angle (degrees), axis:\n%g, %s", Math.toDegrees(r.getAngle()),
+            r.getAxis(RotationConvention.FRAME_TRANSFORM))
+        : String.format("angle (radians), axis:\n%g, %s", r.getAngle(),
+            r.getAxis(RotationConvention.FRAME_TRANSFORM));
+    System.out.println(axisAndAngleString);
+
+    try {
+      double[] angles = r.getAngles(RotationOrder.XYZ, RotationConvention.FRAME_TRANSFORM);
+      String cardanString = inDegrees
+          ? String.format("Cardan XYZ angles (degrees):\n%g, %g, %g", Math.toDegrees(angles[0]),
+              Math.toDegrees(angles[1]), Math.toDegrees(angles[2]))
+          : String.format("Cardan XYZ angles (radians):\n%g, %g, %g", angles[0], angles[1],
+              angles[2]);
+      System.out.println(cardanString);
+    } catch (CardanEulerSingularityException e) {
+      System.out.println("Cardan angles: encountered singularity, cannot solve");
+    }
+
+    try {
+      double[] angles = r.getAngles(RotationOrder.ZXZ, RotationConvention.FRAME_TRANSFORM);
+      String eulerString = inDegrees
+          ? String.format("Euler ZXZ angles (degrees):\n%g, %g, %g", Math.toDegrees(angles[0]),
+              Math.toDegrees(angles[1]), Math.toDegrees(angles[2]))
+          : String.format("Euler ZXZ angles (radians):\n%g, %g, %g", angles[0], angles[1],
+              angles[2]);
+      System.out.println(eulerString);
+    } catch (CardanEulerSingularityException e) {
+      System.out.println("Euler angles: encountered singularity, cannot solve");
+    }
+
+    System.out.printf("Quaternion:\n%g, %g, %g, %g\n", r.getQ0(), r.getQ1(), r.getQ2(), r.getQ3());
+  }
+}

src/main/java/terrasaur/apps/SPKFromSumFile.java

@@ -0,0 +1,450 @@
+package terrasaur.apps;
+
+import java.io.*;
+import java.nio.charset.Charset;
+import java.util.*;
+import org.apache.commons.cli.*;
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.FilenameUtils;
+import org.apache.commons.math3.analysis.polynomials.PolynomialFunction;
+import org.apache.commons.math3.fitting.PolynomialCurveFitter;
+import org.apache.commons.math3.fitting.WeightedObservedPoints;
+import org.apache.commons.math3.geometry.euclidean.threed.Vector3D;
+import org.apache.commons.text.WordUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.spi.StandardLevel;
+import picante.math.intervals.UnwritableInterval;
+import spice.basic.*;
+import terrasaur.templates.TerrasaurTool;
+import terrasaur.utils.*;
+import terrasaur.utils.math.MathConversions;
+
+public class SPKFromSumFile implements TerrasaurTool {
+
+    private final static Logger logger = LogManager.getLogger();
+
+    @Override
+    public String shortDescription() {
+        return "Given three or more sumfiles, create an input file for MKSPK.";
+    }
+
+    @Override
+    public String fullDescription(Options options) {
+        String header = "";
+        String footer = """
+                Given three or more sumfiles, fit a parabola to the spacecraft
+                trajectory in J2000 and create an input file for MKSPK.
+                """;
+        return TerrasaurTool.super.fullDescription(options, header, footer);
+    }
+
+    private Body observer;
+    private Body target;
+    private ReferenceFrame J2000;
+    private ReferenceFrame bodyFixed;
+    private NavigableMap<Double, SumFile> sumFiles;
+    private Map<SumFile, Double> weightMap;
+    private NavigableMap<Double, String> sumFilenames;
+    private UnwritableInterval interval;
+
+    private SPKFromSumFile(){}
+
+    private SPKFromSumFile(Body observer, Body target, ReferenceFrame bodyFixed, Map<String, Double> weightMap,
+                           double extend) throws SpiceException {
+        this.observer = observer;
+        this.target = target;
+        this.bodyFixed = bodyFixed;
+        this.J2000 = new ReferenceFrame("J2000");
+
+        this.sumFiles = new TreeMap<>();
+        this.weightMap = new HashMap<>();
+        this.sumFilenames = new TreeMap<>();
+
+        for (String filename : weightMap.keySet()) {
+            SumFile s = SumFile.fromFile(new File(filename));
+            double tdb = new TDBTime(s.utcString()).getTDBSeconds();
+            this.sumFiles.put(tdb, s);
+            this.weightMap.put(s, weightMap.get(filename));
+            this.sumFilenames.put(tdb, filename);
+        }
+
+        this.interval = new UnwritableInterval(this.sumFiles.firstKey(), this.sumFiles.lastKey() + extend);
+    }
+
+    /**
+     * @param basename        base name for MKSPK input files
+     * @param comments        comments to include in SPK
+     * @param degree          polynomial degree to use for fitting position
+     * @param velocity        User-supplied velocity (if null, use derivative of calculated fit to position)
+     * @param velocityIsJ2000 if true, user-supplied velocity is in J2000 frame
+     * @return command to run MKSPK
+     */
+    public String writeMKSPKFiles(String basename, List<String> comments, int degree, final Vector3 velocity,
+                                  boolean velocityIsJ2000) throws SpiceException {
+
+        String commentFile = basename + "-comments.txt";
+        String setupFile = basename + ".setup";
+        String inputFile = basename + ".inp";
+
+        try (PrintWriter pw = new PrintWriter(commentFile)) {
+            StringBuilder sb = new StringBuilder();
+            if (!comments.isEmpty()) {
+                for (String comment : comments)
+                    sb.append(comment).append("\n");
+                sb.append("\n");
+            }
+            sb.append(String.format("This SPK for %s was generated by fitting a parabola to each component of the " + "SCOBJ vector from " + "the following sumfiles:\n", target));
+            for (String sumFile : sumFilenames.values()) {
+                sb.append(String.format("\t%s\n", sumFile));
+            }
+            sb.append("The SCOBJ vector was transformed to J2000 and an aberration correction ");
+            sb.append(String.format("was applied to find the geometric position relative to %s before the parabola " + "fit.  ", target.getName()));
+            sb.append(String.format("The period covered by this SPK is %s to %s.",
+                    new TDBTime(interval.getBegin()).toUTCString("ISOC", 3),
+                    new TDBTime(interval.getEnd()).toUTCString("ISOC", 3)));
+
+            String allComments = sb.toString();
+            for (String comment : allComments.split("\\r?\\n"))
+                pw.println(WordUtils.wrap(comment, 80));
+        } catch (FileNotFoundException e) {
+            logger.error(e.getLocalizedMessage(), e);
+        }
+
+        int numTXT = KernelDatabase.ktotal("TEXT");
+        File lsk = null;
+        for (int i = 0; i < numTXT; i++) {
+            String filename = KernelDatabase.getFileName(i, "TEXT");
+            if (filename.toLowerCase().endsWith(".tls")) lsk = new File(filename);
+        }
+
+        Map<String, String> map = new TreeMap<>();
+        map.put("INPUT_DATA_TYPE", "'STATES'");
+        map.put("OUTPUT_SPK_TYPE", "13"); // hermite polynomial, unevenly spaced in time
+        map.put("OBJECT_ID", String.format("%d", observer.getIDCode()));
+        map.put("CENTER_ID", String.format("%d", target.getIDCode()));
+        map.put("COMMENT_FILE", String.format("'%s'", commentFile));
+        map.put("REF_FRAME_NAME", "'J2000'");
+        map.put("PRODUCER_ID", "'Hari.Nair@jhuapl.edu'");
+        map.put("DATA_ORDER", "'EPOCH X Y Z VX VY VZ'");
+        map.put("DATA_DELIMITER", "' '");
+        map.put("LEAPSECONDS_FILE", String.format("'%s'", lsk));
+        map.put("TIME_WRAPPER", "'# ETSECONDS'");
+        map.put("POLYNOM_DEGREE", "7");
+        map.put("SEGMENT_ID", "'SPK_STATES_13'");
+        map.put("LINES_PER_RECORD", "1");
+        try (PrintWriter pw = new PrintWriter(setupFile)) {
+            pw.println("\\begindata");
+            for (String key : map.keySet()) {
+                pw.printf("%s = %s\n", key, map.get(key));
+            }
+        } catch (FileNotFoundException e) {
+            logger.error(e.getLocalizedMessage(), e);
+        }
+
+        RemoveAberration ra = new RemoveAberration(target, observer);
+
+        WeightedObservedPoints x = new WeightedObservedPoints();
+        WeightedObservedPoints y = new WeightedObservedPoints();
+        WeightedObservedPoints z = new WeightedObservedPoints();
+        Map<Double, Vector3> geometricMap = new HashMap<>();
+        for (Double t : sumFiles.keySet()) {
+            SumFile sumFile = sumFiles.get(t);
+            double weight = weightMap.get(sumFile);
+            TDBTime tdb = new TDBTime(t);
+            Matrix33 bodyFixedToJ2000 = bodyFixed.getPositionTransformation(J2000, tdb);
+            Vector3 scObjJ2000 = bodyFixedToJ2000.mxv(MathConversions.toVector3(sumFile.scobj()));
+            Vector3 geometricScPos = ra.getGeometricPosition(tdb, scObjJ2000);
+            geometricMap.put(t, geometricScPos);
+            x.add(weight, t, geometricScPos.getElt(0));
+            y.add(weight, t, geometricScPos.getElt(1));
+            z.add(weight, t, geometricScPos.getElt(2));
+        }
+
+        // fit a polynomial to the geometric positions in J2000
+        PolynomialCurveFitter fitter = PolynomialCurveFitter.create(degree);
+        double[] xCoeff = fitter.fit(x.toList());
+        double[] yCoeff = fitter.fit(y.toList());
+        double[] zCoeff = fitter.fit(z.toList());
+
+        PolynomialFunction xPos = new PolynomialFunction(xCoeff);
+        PolynomialFunction xVel = xPos.polynomialDerivative();
+        PolynomialFunction yPos = new PolynomialFunction(yCoeff);
+        PolynomialFunction yVel = yPos.polynomialDerivative();
+        PolynomialFunction zPos = new PolynomialFunction(zCoeff);
+        PolynomialFunction zVel = zPos.polynomialDerivative();
+
+        logger.info("Polynomial fitting coefficients for geometric position of {} relative to {} in J2000:",
+                observer.getName(), target.getName());
+        StringBuilder xMsg = new StringBuilder(String.format("X = %e ", xCoeff[0]));
+        StringBuilder yMsg = new StringBuilder(String.format("Y = %e ", yCoeff[0]));
+        StringBuilder zMsg = new StringBuilder(String.format("Z = %e ", zCoeff[0]));
+        for (int i = 1; i <= degree; i++) {
+            xMsg.append(xCoeff[i] < 0 ? "- " : "+ ").append(String.format("%e ", Math.abs(xCoeff[i]))).append("t").append(i > 1 ? "^" + i : "").append(" ");
+            yMsg.append(yCoeff[i] < 0 ? "- " : "+ ").append(String.format("%e ", Math.abs(yCoeff[i]))).append("t").append(i > 1 ? "^" + i : "").append(" ");
+            zMsg.append(zCoeff[i] < 0 ? "- " : "+ ").append(String.format("%e ", Math.abs(zCoeff[i]))).append("t").append(i > 1 ? "^" + i : "").append(" ");
+        }
+        logger.info(xMsg);
+        logger.info(yMsg);
+        logger.info(zMsg);
+
+        logger.debug("");
+        logger.debug("NOTE: comparing aberration correction=LT+S positions from sumfile with aberration " +
+                "correction=NONE for fit.");
+        for (Double t : sumFiles.keySet()) {
+            TDBTime tdb = new TDBTime(t);
+            SumFile sumFile = sumFiles.get(t);
+            Vector3 j2000Pos = new Vector3(xPos.value(t), yPos.value(t), zPos.value(t));
+            Matrix33 bodyFixedToJ2000 = bodyFixed.getPositionTransformation(J2000, tdb);
+            Vector3D bfPos = MathConversions.toVector3D(bodyFixedToJ2000.mtxv(j2000Pos));
+            // comparing LT+S with NONE here
+            logger.debug("UTC Date:      {}", sumFile.utcString());
+            logger.debug("Sumfile SCOBJ: {}", sumFile.scobj());
+            logger.debug("Fit:           {}", bfPos);
+            logger.debug("residual (m):  {}", sumFile.scobj().subtract(bfPos).scalarMultiply(1000));
+            logger.debug("");
+        }
+
+        try (PrintWriter pw = new PrintWriter(inputFile)) {
+            for (double t = interval.getBegin(); t < interval.getEnd(); t++) {
+
+                if (velocity == null) {
+                    double vx = -xVel.value(t);
+                    double vy = -yVel.value(t);
+                    double vz = -zVel.value(t);
+                    pw.printf("%.16e %.16e %.16e %.16e %.16e %.16e %.16e\n", t, -xPos.value(t), -yPos.value(t),
+                            -zPos.value(t), vx, vy, vz);
+                } else {
+                    Vector3 thisVelocity = new Vector3(velocity);
+                    if (!velocityIsJ2000) {
+                        TDBTime tdb = new TDBTime(t);
+                        thisVelocity = bodyFixed.getPositionTransformation(J2000, tdb).mxv(velocity);
+                    }
+                    double vx = thisVelocity.getElt(0);
+                    double vy = thisVelocity.getElt(1);
+                    double vz = thisVelocity.getElt(2);
+                    pw.printf("%.16e %.16e %.16e %.16e %.16e %.16e %.16e\n", t, -xPos.value(t), -yPos.value(t),
+                            -zPos.value(t), vx, vy, vz);
+                }
+            }
+        } catch (FileNotFoundException e) {
+            logger.error(e.getLocalizedMessage(), e);
+        }
+
+
+        try (PrintWriter pw = new PrintWriter(basename + ".csv")) {
+            pw.println("# Note: fit quantities are without light time or aberration corrections");
+            pw.println("# SCOBJ");
+            pw.println("# UTC, TDB, SumFile, SPICE (body fixed) x, y, z, SCOBJ (body fixed) x, y, z, SCOBJ (J2000) x," +
+                    " y, z, SCOBJ (Geometric J2000) x, y, z, Fit SCOBJ (body fixed) x, y, z, Fit SCOBJ (Geometric " +
+                    "J2000) x, y, z");
+            for (Double t : sumFiles.keySet()) {
+                SumFile sumFile = sumFiles.get(t);
+                pw.printf("%s,", sumFile.utcString());
+                pw.printf("%.3f, ", t);
+                pw.printf("%s, ", FilenameUtils.getBaseName(sumFilenames.get(t)));
+
+                TDBTime tdb = new TDBTime(t);
+                StateRecord sr = new StateRecord(observer, tdb, bodyFixed, new AberrationCorrection("LT+S"), target);
+
+                pw.printf("%s, ", sr.getPosition().getElt(0));
+                pw.printf("%s, ", sr.getPosition().getElt(1));
+                pw.printf("%s, ", sr.getPosition().getElt(2));
+
+                pw.printf("%s, ", sumFile.scobj().getX());
+                pw.printf("%s, ", sumFile.scobj().getY());
+                pw.printf("%s, ", sumFile.scobj().getZ());
+
+                Matrix33 j2000ToBodyFixed = J2000.getPositionTransformation(bodyFixed, tdb);
+                Vector3 scobjJ2000 = j2000ToBodyFixed.mtxv(MathConversions.toVector3(sumFile.scobj()));
+                pw.printf("%s, ", scobjJ2000.getElt(0));
+                pw.printf("%s, ", scobjJ2000.getElt(1));
+                pw.printf("%s, ", scobjJ2000.getElt(2));
+
+                Vector3 geometricScPos = geometricMap.get(t);
+                pw.printf("%s, ", geometricScPos.getElt(0));
+                pw.printf("%s, ", geometricScPos.getElt(1));
+                pw.printf("%s, ", geometricScPos.getElt(2));
+
+                Vector3 fitScOBJJ2000 = new Vector3(xPos.value(t), yPos.value(t), zPos.value(t));
+                Vector3 fitScOBJ = j2000ToBodyFixed.mxv(fitScOBJJ2000);
+                pw.printf("%s, ", fitScOBJ.getElt(0));
+                pw.printf("%s, ", fitScOBJ.getElt(1));
+                pw.printf("%s, ", fitScOBJ.getElt(2));
+
+                pw.printf("%s, ", fitScOBJJ2000.getElt(0));
+                pw.printf("%s, ", fitScOBJJ2000.getElt(1));
+                pw.printf("%s, ", fitScOBJJ2000.getElt(2));
+                pw.println();
+            }
+            pw.println("\n# Velocity");
+            pw.println("# UTC, TDB, SumFile, SPICE (body fixed) x, y, z, SPICE (J2000) x, y, z, Fit (body fixed) x, " +
+                    "y, z, Fit (J2000) x, y, z");
+            for (Double t : sumFiles.keySet()) {
+                SumFile sumFile = sumFiles.get(t);
+                pw.printf("%s,", sumFile.utcString());
+                pw.printf("%.3f, ", t);
+                pw.printf("%s, ", FilenameUtils.getBaseName(sumFilenames.get(t)));
+
+                TDBTime tdb = new TDBTime(t);
+
+                Matrix66 j2000ToBodyFixed = J2000.getStateTransformation(bodyFixed, tdb);
+                StateRecord sr = new StateRecord(observer, tdb, J2000, new AberrationCorrection("NONE"), target);
+                Vector3 velJ2000 = sr.getVelocity();
+                Vector3 velBodyFixed = j2000ToBodyFixed.mxv(sr.getStateVector()).getVector3(1);
+
+                pw.printf("%s, ", velBodyFixed.getElt(0));
+                pw.printf("%s, ", velBodyFixed.getElt(1));
+                pw.printf("%s, ", velBodyFixed.getElt(2));
+
+                pw.printf("%s, ", velJ2000.getElt(0));
+                pw.printf("%s, ", velJ2000.getElt(1));
+                pw.printf("%s, ", velJ2000.getElt(2));
+
+                velJ2000 = new Vector3(xVel.value(t), yVel.value(t), zVel.value(t));
+                if (velocity != null) {
+                    Vector3 thisVelocity = new Vector3(velocity);
+                    if (!velocityIsJ2000) {
+                        thisVelocity = bodyFixed.getPositionTransformation(J2000, tdb).mxv(velocity);
+                    }
+                    double vx = thisVelocity.getElt(0);
+                    double vy = thisVelocity.getElt(1);
+                    double vz = thisVelocity.getElt(2);
+                    velJ2000 = new Vector3(vx, vy, vz);
+                }
+
+                StateVector stateJ2000 = new StateVector(new Vector3(xPos.value(t), yPos.value(t), zPos.value(t)),
+                        velJ2000);
+                velBodyFixed = j2000ToBodyFixed.mxv(stateJ2000).getVector3(1);
+
+                pw.printf("%s, ", velBodyFixed.getElt(0));
+                pw.printf("%s, ", velBodyFixed.getElt(1));
+                pw.printf("%s, ", velBodyFixed.getElt(2));
+
+                pw.printf("%s, ", velJ2000.getElt(0));
+                pw.printf("%s, ", velJ2000.getElt(1));
+                pw.printf("%s, ", velJ2000.getElt(2));
+                pw.println();
+            }
+        } catch (FileNotFoundException e) {
+            logger.error(e.getLocalizedMessage(), e);
+        }
+
+        return String.format("mkspk -setup %s -input %s -output %s.bsp", setupFile, inputFile, basename);
+    }
+
+    private static Options defineOptions() {
+        Options options = TerrasaurTool.defineOptions();
+        options.addOption(Option.builder("degree").hasArg().desc("Degree of polynomial used to fit sumFile locations" + "." + "  Default is 2.").build());
+        options.addOption(Option.builder("extend").hasArg().desc("Extend SPK past the last sumFile by <arg> seconds. "
+                + " Default is zero.").build());
+        options.addOption(Option.builder("frame").hasArg().desc("Name of body fixed frame.  This will default to the "
+                + "target's body fixed frame.").build());
+        options.addOption(Option.builder("logFile").hasArg().desc("If present, save screen output to log file.").build());
+        StringBuilder sb = new StringBuilder();
+        for (StandardLevel l : StandardLevel.values())
+            sb.append(String.format("%s ", l.name()));
+        options.addOption(Option.builder("logLevel").hasArg().desc("If present, print messages above selected " +
+                "priority.  Valid values are " + sb.toString().trim() + ".  Default is INFO.").build());
+        options.addOption(Option.builder("observer").required().hasArg().desc("Required.  SPICE ID for the observer.").build());
+        options.addOption(Option.builder("sumFile").hasArg().required().desc("""
+                File listing sumfiles to read.  This is a text file,
+                one per line.  You can include an optional weight
+                after each filename.  The default weight is 1.0.
+                Lines starting with # are ignored.
+
+                Example:
+
+                D717506120G0.SUM
+                D717506126G0.SUM
+                D717506127G0.SUM
+                D717506128G0.SUM
+                D717506129G0.SUM
+                D717506131G0.SUM
+                # Weight this last image less than the others
+                D717506132G0.SUM 0.25
+                """).build());
+        options.addOption(Option.builder("spice").required().hasArgs().desc("Required.  SPICE metakernel file " +
+                "containing body fixed frame and spacecraft kernels.  Can specify more than one kernel, separated by "
+                + "whitespace.").build());
+        options.addOption(Option.builder("target").required().hasArg().desc("Required.  SPICE ID for the target.").build());
+        options.addOption(Option.builder("velocity").hasArgs().desc("Spacecraft velocity relative to target in the " + "body fixed frame.  If present, use this fixed velocity in the MKSPK input file.  Default is to " + "take the derivative of the fit position.  Specify as three floating point values in km/sec," + "separated by whitespace.").build());
+        options.addOption(Option.builder("velocityJ2000").desc("If present, argument to -velocity is in J2000 frame. "
+                + " Ignored if -velocity is not set.").build());        return options;
+    }
+
+    public static void main(String[] args) throws SpiceException {
+        TerrasaurTool defaultOBJ = new SPKFromSumFile();
+
+        Options options = defineOptions();
+
+        CommandLine cl = defaultOBJ.parseArgs(args, options);
+
+        Map<MessageLabel, String> startupMessages = defaultOBJ.startupMessages(cl);
+        for (MessageLabel ml : startupMessages.keySet())
+            logger.info(String.format("%s %s", ml.label, startupMessages.get(ml)));
+
+        NativeLibraryLoader.loadSpiceLibraries();
+
+
+        final double extend = cl.hasOption("extend") ? Double.parseDouble(cl.getOptionValue("extend")) : 0;
+
+        for (String kernel : cl.getOptionValues("spice"))
+            KernelDatabase.load(kernel);
+
+        Body observer = new Body(cl.getOptionValue("observer"));
+        Body target = new Body(cl.getOptionValue("target"));
+
+        ReferenceFrame bodyFixed = null;
+        if (cl.hasOption("frame")) {
+            bodyFixed = new ReferenceFrame(cl.getOptionValue("frame"));
+        } else {
+            String keyword = String.format("OBJECT_%d_FRAME", target.getIDCode());
+            if (KernelPool.exists(keyword)) {
+                bodyFixed = new ReferenceFrame(KernelPool.getCharacter(keyword)[0]);
+            } else {
+                logger.error("No keyword {} in kernel pool and -frame was not specified!", keyword);
+            }
+        }
+
+        final int degree = cl.hasOption("degree") ? Integer.parseInt(cl.getOptionValue("degree")) : 2;
+        Vector3 velocity = null;
+        if (cl.hasOption("velocity")) {
+            String[] parts = cl.getOptionValues("velocity");
+            if (parts.length == 3) {
+                double x = Double.parseDouble(parts[0]);
+                double y = Double.parseDouble(parts[1]);
+                double z = Double.parseDouble(parts[2]);
+                velocity = new Vector3(x, y, z);
+            }
+        }
+        boolean velocityJ2000 = cl.hasOption("velocityJ2000");
+
+        Map<String, Double> weightMap = new HashMap<>();
+        String first = null;
+        String last = null;
+        try {
+            List<String> lines = FileUtils.readLines(new File(cl.getOptionValue("sumFile")), Charset.defaultCharset());
+            for (String line : lines) {
+                if (line.strip().startsWith("#")) continue;
+                String[] parts = line.strip().split("\\s+");
+                double weight = 1.0;
+                if (parts.length > 1) weight = Double.parseDouble(parts[1]);
+                weightMap.put(parts[0], weight);
+                if (first == null) first = parts[0];
+                last = parts[0];
+            }
+        } catch (IOException e) {
+            logger.error(e.getLocalizedMessage(), e);
+        }
+        SPKFromSumFile app = new SPKFromSumFile(observer, target, bodyFixed, weightMap, extend);
+        String basename = String.format("%s_%s", FilenameUtils.getBaseName(first), FilenameUtils.getBaseName(last));
+        List<String> comments = new ArrayList<>();
+        String command = app.writeMKSPKFiles(basename, comments, degree, velocity, velocityJ2000);
+
+        logger.info("Generate new SPK:\n\t{}", command);
+
+        logger.info("Finished.");
+    }
+
+}

src/main/java/terrasaur/apps/ShapeFormatConverter.java

@@ -0,0 +1,508 @@
+package terrasaur.apps;
+
+import java.io.File;
+import java.io.PrintWriter;
+import java.nio.charset.Charset;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.Options;
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.FilenameUtils;
+import org.apache.commons.math3.geometry.euclidean.threed.Rotation;
+import org.apache.commons.math3.geometry.euclidean.threed.Vector3D;
+import org.apache.commons.math3.linear.Array2DRowRealMatrix;
+import org.apache.commons.math3.linear.LUDecomposition;
+import org.apache.commons.math3.linear.RealMatrix;
+import org.apache.commons.math3.linear.SingularValueDecomposition;
+import org.apache.commons.math3.util.Pair;
+import org.apache.logging.log4j.Level;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import spice.basic.Matrix33;
+import spice.basic.Vector3;
+import terrasaur.templates.TerrasaurTool;
+import terrasaur.utils.*;
+import terrasaur.utils.ImmutableSBMTEllipseRecord.Builder;
+import terrasaur.utils.math.MathConversions;
+import terrasaur.utils.math.RotationUtils;
+import vtk.vtkPoints;
+import vtk.vtkPolyData;
+
+public class ShapeFormatConverter implements TerrasaurTool {
+
+  private static final Logger logger = LogManager.getLogger();
+
+  @Override
+  public String shortDescription() {
+    return "Transform a shape model to a new coordinate system.";
+  }
+
+  @Override
+  public String fullDescription(Options options) {
+
+    String header = "";
+    String footer =
+        "This program will rotate, translate, and/or scale a shape model.  It can additionally transform a "
+            + "single point, a sum file, or an SBMT ellipse file.  For a sum file, the SCOBJ vector is "
+            + "transformed and the cx, cy, cz, and sz vectors are rotated.  For SBMT ellipse files, only "
+            + "center of the ellipse is transformed.  The size, orientation, and all other fields in the "
+            + "file are unchanged.";
+    return TerrasaurTool.super.fullDescription(options, header, footer);
+  }
+
+  private enum COORDTYPE {
+    LATLON,
+    XYZ,
+    POLYDATA
+  }
+
+  private enum FORMATS {
+    ICQ,
+    LLR,
+    OBJ,
+    PDS,
+    PLT,
+    PLY,
+    STL,
+    VTK,
+    FITS,
+    SUM,
+    SBMT
+  }
+
+  private static Options defineOptions() {
+    Options options = TerrasaurTool.defineOptions();
+    options.addOption(
+        Option.builder("centerOfRotation")
+            .hasArg()
+            .desc(
+                "Subtract this point before applying rotation matrix, add back after.  "
+                    + "Specify by three floating point numbers separated by commas.  If not present default is (0,0,0).")
+            .build());
+    options.addOption(
+        Option.builder("decimate")
+            .hasArg()
+            .desc(
+                "Reduce the number of facets in a shape model.  The argument should be between 0 and 1.  "
+                    + "For example, if a model has 100 facets and the argument to -decimate is 0.90, "
+                    + "there will be approximately 10 facets after the decimation.")
+            .build());
+    options.addOption(
+        Option.builder("input")
+            .required()
+            .hasArg()
+            .desc(
+                "Required.  Name of shape model to transform. Extension must be icq, fits, llr, obj, pds, plt, ply, sbmt, stl, sum, or vtk.  "
+                    + "Alternately transform a single point using three floating point numbers separated "
+                    + "by commas to specify XYZ coordinates, or latitude, longitude in degrees separated by commas.  "
+                    + "Transformed point will be written to stdout in the same format as the input string.")
+            .build());
+    options.addOption(
+        Option.builder("inputFormat")
+            .hasArg()
+            .desc(
+                "Format of input file.  If not present format will be inferred from inputFile extension.")
+            .build());
+    options.addOption(
+        Option.builder("output")
+            .hasArg()
+            .desc(
+                "Required for all but single point input.  Name of transformed file.  "
+                    + "Extension must be obj, plt, sbmt, stl, sum, or vtk.")
+            .build());
+    options.addOption(
+        Option.builder("outputFormat")
+            .hasArg()
+            .desc(
+                "Format of output file.  If not present format will be inferred from outputFile extension.")
+            .build());
+    options.addOption(
+        Option.builder("register")
+            .hasArg()
+            .desc("Use SVD to transform input file to best align with register file.")
+            .build());
+    options.addOption(
+        Option.builder("rotate")
+            .hasArg()
+            .desc(
+                "Rotate surface points and spacecraft position.  "
+                    + "Specify by an angle (degrees) and a 3 element rotation axis vector (XYZ)  "
+                    + "separated by commas.")
+            .build());
+    options.addOption(
+        Option.builder("rotateToPrincipalAxes")
+            .desc("Rotate body to align along its principal axes of inertia.")
+            .build());
+    options.addOption(
+        Option.builder("scale")
+            .hasArg()
+            .desc(
+                "Scale the shape model by <arg>.  This can either be one value or three "
+                    + "separated by commas.  One value scales all three axes uniformly, "
+                    + "three values scale the x, y, and z axes respectively.  For example, "
+                    + "-scale 0.5,0.25,1.5 scales the model in the x dimension by 0.5, the "
+                    + "y dimension by 0.25, the z dimension by 1.5.")
+            .build());
+    options.addOption(
+        Option.builder("translate")
+            .hasArg()
+            .desc(
+                "Translate surface points and spacecraft position.  "
+                    + "Specify by three floating point numbers separated by commas.")
+            .build());
+    options.addOption(
+        Option.builder("translateToCenter")
+            .desc("Translate body so that its center of mass is at the origin.")
+            .build());
+    options.addOption(
+        Option.builder("transform")
+            .hasArg()
+            .desc(
+                "Translate and rotate surface points and spacecraft position.  "
+                    + "Specify a file containing a 4x4 combined translation/rotation matrix.  The top left 3x3 matrix "
+                    + "is the rotation matrix.  The top three entries in the right hand column are the translation "
+                    + "vector.  The bottom row is always 0 0 0 1.")
+            .build());
+    return options;
+  }
+
+  public static void main(String[] args) throws Exception {
+
+    TerrasaurTool defaultOBJ = new ShapeFormatConverter();
+
+    Options options = defineOptions();
+
+    CommandLine cl = defaultOBJ.parseArgs(args, options);
+
+    Map<MessageLabel, String> startupMessages = defaultOBJ.startupMessages(cl);
+    for (MessageLabel ml : startupMessages.keySet())
+      logger.info(String.format("%s %s", ml.label, startupMessages.get(ml)));
+
+    NativeLibraryLoader.loadSpiceLibraries();
+    NativeLibraryLoader.loadVtkLibraries();
+
+    String filename = cl.getOptionValue("input");
+    COORDTYPE coordType = COORDTYPE.POLYDATA;
+    vtkPolyData polydata = null;
+    SumFile sumFile = null;
+    List<SBMTEllipseRecord> sbmtEllipse = null;
+
+    String extension = null;
+    if (cl.hasOption("inputFormat")) {
+      try {
+        extension =
+            FORMATS.valueOf(cl.getOptionValue("inputFormat").toUpperCase()).name().toLowerCase();
+      } catch (IllegalArgumentException e) {
+        logger.warn("Unsupported -inputFormat {}", cl.getOptionValue("inputFormat"));
+      }
+    }
+    if (extension == null) extension = FilenameUtils.getExtension(filename).toLowerCase();
+    switch (extension) {
+      case "icq", "llr", "obj", "pds", "plt", "ply", "stl", "vtk" ->
+          polydata = PolyDataUtil.loadShapeModel(filename, extension);
+      case "fits" -> polydata = PolyDataUtil.loadFITShapeModel(filename);
+      case "sum" -> {
+        List<String> lines = FileUtils.readLines(new File(filename), Charset.defaultCharset());
+        sumFile = SumFile.fromLines(lines);
+      }
+      case "sbmt" -> {
+        sbmtEllipse = new ArrayList<>();
+        vtkPoints points = new vtkPoints();
+        polydata = new vtkPolyData();
+        polydata.SetPoints(points);
+        for (String line : FileUtils.readLines(new File(filename), Charset.defaultCharset())) {
+          SBMTEllipseRecord record = SBMTEllipseRecord.fromString(line);
+          sbmtEllipse.add(record);
+          points.InsertNextPoint(record.x(), record.y(), record.z());
+        }
+      }
+      default -> {
+        // Single point
+        String[] params = filename.split(",");
+        vtkPoints points = new vtkPoints();
+        polydata = new vtkPolyData();
+        polydata.SetPoints(points);
+        if (params.length == 2) {
+          double[] array =
+              new Vector3D(
+                      Math.toRadians(Double.parseDouble(params[0].trim())),
+                      Math.toRadians(Double.parseDouble(params[1].trim())))
+                  .toArray();
+          points.InsertNextPoint(array);
+          coordType = COORDTYPE.LATLON;
+        } else if (params.length == 3) {
+          double[] array = new double[3];
+          for (int i = 0; i < 3; i++) array[i] = Double.parseDouble(params[i].trim());
+          points.InsertNextPoint(array);
+          coordType = COORDTYPE.XYZ;
+        } else {
+          logger.error(
+              "Can't read input shape model {} with format {}", filename, extension.toUpperCase());
+          System.exit(0);
+        }
+      }
+    }
+
+    if (cl.hasOption("decimate") && polydata != null) {
+      double reduction = Double.parseDouble(cl.getOptionValue("decimate"));
+      if (reduction < 0) {
+        logger.printf(Level.WARN, "Argument to -decimate is %.f!  Setting to zero.", reduction);
+        reduction = 0;
+      }
+      if (reduction > 1) {
+        logger.printf(Level.WARN, "Argument to -decimate is %.f!  Setting to one.", reduction);
+        reduction = 1;
+      }
+      PolyDataUtil.decimatePolyData(polydata, reduction);
+    }
+
+    if (coordType == COORDTYPE.POLYDATA && !cl.hasOption("output")) {
+      logger.error(String.format("No output file specified for input file %s", filename));
+      System.exit(0);
+    }
+
+    Vector3 centerOfRotation = null;
+    Matrix33 rotation = null;
+    Vector3 translation = null;
+    Vector3 scale = new Vector3(1., 1., 1.);
+    for (Option option : cl.getOptions()) {
+      if (option.getOpt().equals("centerOfRotation"))
+        centerOfRotation =
+            MathConversions.toVector3(
+                VectorUtils.stringToVector3D(cl.getOptionValue("centerOfRotation")));
+
+      if (option.getOpt().equals("rotate"))
+        rotation =
+            MathConversions.toMatrix33(RotationUtils.stringToRotation(cl.getOptionValue("rotate")));
+
+      if (option.getOpt().equals("scale")) {
+        String scaleString = cl.getOptionValue("scale");
+        if (scaleString.contains(",")) {
+          scale = MathConversions.toVector3(VectorUtils.stringToVector3D(scaleString));
+        } else {
+          scale = scale.scale(Double.parseDouble(scaleString));
+        }
+      }
+
+      if (option.getOpt().equals("translate"))
+        translation =
+            MathConversions.toVector3(VectorUtils.stringToVector3D(cl.getOptionValue("translate")));
+
+      if (option.getOpt().equals("transform")) {
+        List<String> lines =
+            FileUtils.readLines(new File(cl.getOptionValue("transform")), Charset.defaultCharset());
+        Pair<Vector3D, Rotation> pair = RotationUtils.stringToTransform(lines);
+        translation = MathConversions.toVector3(pair.getKey());
+        rotation = MathConversions.toMatrix33(pair.getValue());
+      }
+    }
+
+    if (cl.hasOption("rotateToPrincipalAxes")) {
+      if (polydata != null) {
+        PolyDataStatistics stats = new PolyDataStatistics(polydata);
+        if (stats.isClosed()) {
+          ArrayList<double[]> axes = stats.getPrincipalAxes();
+          // make X primary, Y secondary
+          rotation = new Matrix33(new Vector3(axes.get(0)), 1, new Vector3(axes.get(1)), 2);
+        } else {
+          logger.warn("Shape is not closed, cannot determine principal axes.");
+        }
+      }
+    }
+
+    if (cl.hasOption("register")) {
+      String register = cl.getOptionValue("register");
+      vtkPolyData registeredPolydata = null;
+      extension = FilenameUtils.getExtension(register).toLowerCase();
+      if (extension.equals("llr")
+          || extension.equals("obj")
+          || extension.equals("pds")
+          || extension.equals("plt")
+          || extension.equals("ply")
+          || extension.equals("stl")
+          || extension.equals("vtk")) {
+        registeredPolydata = PolyDataUtil.loadShapeModelAndComputeNormals(register);
+      } else {
+        logger.error(String.format("Can't read input shape model for registration: %s", register));
+        System.exit(0);
+      }
+
+      if (registeredPolydata != null) {
+        Vector3D centerA = PolyDataUtil.computePolyDataCentroid(polydata);
+        Vector3D centerB = PolyDataUtil.computePolyDataCentroid(registeredPolydata);
+
+        vtkPoints points = polydata.GetPoints();
+        double[][] pointsA = new double[(int) points.GetNumberOfPoints()][3];
+        for (int i = 0; i < points.GetNumberOfPoints(); i++)
+          pointsA[i] = new Vector3D(points.GetPoint(i)).subtract(centerA).toArray();
+        points = registeredPolydata.GetPoints();
+
+        if (points.GetNumberOfPoints() != polydata.GetPoints().GetNumberOfPoints()) {
+          logger.error("registered polydata does not have the same number of points as input.");
+          System.exit(0);
+        }
+
+        double[][] pointsB = new double[(int) points.GetNumberOfPoints()][3];
+        for (int i = 0; i < points.GetNumberOfPoints(); i++)
+          pointsB[i] = new Vector3D(points.GetPoint(i)).subtract(centerB).toArray();
+
+        double[][] H = new double[3][3];
+        for (int ii = 0; ii < points.GetNumberOfPoints(); ii++) {
+          for (int i = 0; i < 3; i++) {
+            for (int j = 0; j < 3; j++) {
+              H[i][j] += pointsA[ii][i] * pointsB[ii][j];
+            }
+          }
+        }
+
+        RealMatrix pointMatrix = new Array2DRowRealMatrix(H);
+
+        SingularValueDecomposition svd = new SingularValueDecomposition(pointMatrix);
+        RealMatrix uT = svd.getUT();
+        RealMatrix v = svd.getV();
+        RealMatrix R = v.multiply(uT);
+
+        if (new LUDecomposition(R).getDeterminant() < 0) {
+          for (int i = 0; i < 3; i++) {
+            R.multiplyEntry(i, 2, -1);
+          }
+        }
+        rotation = new Matrix33(R.getData());
+        translation = MathConversions.toVector3(centerB);
+        translation = translation.sub(rotation.mxv(MathConversions.toVector3(centerA)));
+      }
+    }
+
+    if (sumFile != null) {
+      if (rotation != null && translation != null)
+        sumFile.transform(
+            MathConversions.toVector3D(translation), MathConversions.toRotation(rotation));
+    } else {
+
+      Vector3 center;
+      if (polydata.GetNumberOfPoints() > 1) {
+        PolyDataStatistics stats = new PolyDataStatistics(polydata);
+        center = new Vector3(stats.getCentroid());
+      } else {
+        center = new Vector3(polydata.GetPoint(0));
+      }
+      if (cl.hasOption("translateToCenter")) translation = center.negate();
+
+      double[] values = new double[3];
+      for (int j = 0; j < 3; j++) values[j] = center.getElt(j) * scale.getElt(j);
+      Vector3 scaledCenter = new Vector3(values);
+
+      vtkPoints points = polydata.GetPoints();
+      for (int i = 0; i < points.GetNumberOfPoints(); i++) {
+        Vector3 thisPoint = new Vector3(points.GetPoint(i));
+        thisPoint = thisPoint.sub(center);
+        for (int j = 0; j < 3; j++) values[j] = thisPoint.getElt(j) * scale.getElt(j);
+        thisPoint = new Vector3(values);
+        thisPoint = thisPoint.add(scaledCenter);
+
+        if (rotation != null) {
+          if (centerOfRotation == null) centerOfRotation = new Vector3();
+          /*-
+          else {
+          	System.out.printf("Center of rotation:\n%s\n", centerOfRotation.toString());
+          	System.out.printf("-centerOfRotation %f,%f,%f\n", centerOfRotation.getElt(0),
+          			centerOfRotation.getElt(1), centerOfRotation.getElt(2));
+          }
+          */
+          thisPoint = rotation.mxv(thisPoint.sub(centerOfRotation)).add(centerOfRotation);
+        }
+        if (translation != null) thisPoint = thisPoint.add(translation);
+        points.SetPoint(i, thisPoint.toArray());
+      }
+    }
+
+    /*-
+    if (rotation != null) {
+    	AxisAndAngle aaa = new AxisAndAngle(rotation);
+    	System.out.printf("Rotation:\n%s\n", rotation.toString());
+    	System.out.printf("-rotate %.5e,%.5e,%.5e,%.5e\n", Math.toDegrees(aaa.getAngle()),
+    			aaa.getAxis().getElt(0), aaa.getAxis().getElt(1), aaa.getAxis().getElt(2));
+    }
+
+    if (translation != null) {
+    	System.out.printf("Translation:\n%s\n", translation.toString());
+    	System.out.printf("-translate %.5e,%.5e,%.5e\n", translation.getElt(0), translation.getElt(1),
+    			translation.getElt(2));
+    }
+    */
+
+    if (coordType == COORDTYPE.LATLON) {
+      double[] pt = new double[3];
+      polydata.GetPoint(0, pt);
+      Vector3D point = new Vector3D(pt);
+      double lon = Math.toDegrees(point.getAlpha());
+      if (lon < 0) lon += 360;
+      System.out.printf("%.16f,%.16f\n", Math.toDegrees(point.getDelta()), lon);
+    } else if (coordType == COORDTYPE.XYZ) {
+      double[] pt = new double[3];
+      polydata.GetPoint(0, pt);
+      System.out.printf("%.16f,%.16f,%.16f\n", pt[0], pt[1], pt[2]);
+    } else {
+      filename = cl.getOptionValue("output");
+      extension = null;
+      if (cl.hasOption("outputFormat")) {
+        try {
+          extension =
+              FORMATS.valueOf(cl.getOptionValue("outputFormat").toUpperCase()).name().toLowerCase();
+        } catch (IllegalArgumentException e) {
+          logger.warn("Unsupported -outputFormat {}", cl.getOptionValue("outputFormat"));
+        }
+      }
+      if (extension == null) extension = FilenameUtils.getExtension(filename).toLowerCase();
+
+      switch (extension) {
+        case "vtk" -> PolyDataUtil.saveShapeModelAsVTK(polydata, filename);
+        case "obj" -> PolyDataUtil.saveShapeModelAsOBJ(polydata, filename);
+        case "plt" -> PolyDataUtil.saveShapeModelAsPLT(polydata, filename);
+        case "stl" -> PolyDataUtil.saveShapeModelAsSTL(polydata, filename);
+        case "sum" -> {
+          try (PrintWriter pw = new PrintWriter(filename)) {
+            pw.print(sumFile.toString());
+          }
+        }
+        case "sbmt" -> {
+          if (sbmtEllipse == null) {
+            logger.error("No input SBMT ellipse specified!");
+            System.exit(0);
+          }
+          double[] pt = new double[3];
+          List<SBMTEllipseRecord> transformedRecords = new ArrayList<>();
+          for (SBMTEllipseRecord record : sbmtEllipse) {
+            polydata.GetPoint(0, pt);
+            Vector3D point = new Vector3D(pt);
+            double lon = Math.toDegrees(point.getAlpha());
+            if (lon < 0) lon += 360;
+            Builder builder = ImmutableSBMTEllipseRecord.builder().from(record);
+            builder.x(point.getX());
+            builder.y(point.getY());
+            builder.z(point.getZ());
+            builder.lat(Math.toDegrees(point.getDelta()));
+            builder.lon(lon);
+            builder.radius(point.getNorm());
+
+            transformedRecords.add(builder.build());
+          }
+          try (PrintWriter pw = new PrintWriter(filename)) {
+            for (SBMTEllipseRecord record : transformedRecords) pw.println(record.toString());
+          }
+        }
+        default -> {
+          logger.error(
+              "Can't write output shape model {} with format {}",
+              filename,
+              extension.toUpperCase());
+          System.exit(0);
+        }
+      }
+      logger.info("Wrote {}", filename);
+    }
+  }
+}

src/main/java/terrasaur/apps/SumFilesFromFlyby.java

@@ -0,0 +1,461 @@
+package terrasaur.apps;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.*;
+import java.util.function.Function;
+import net.jafama.FastMath;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.Options;
+import org.apache.commons.io.FilenameUtils;
+import org.apache.commons.math3.geometry.euclidean.threed.Rotation;
+import org.apache.commons.math3.geometry.euclidean.threed.Vector3D;
+import org.apache.commons.text.WordUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.spi.StandardLevel;
+import picante.math.intervals.IntervalSet;
+import picante.math.intervals.UnwritableInterval;
+import picante.time.TimeConversion;
+import spice.basic.KernelDatabase;
+import spice.basic.SpiceException;
+import spice.basic.SpiceQuaternion;
+import spice.basic.TDBTime;
+import spice.basic.Vector3;
+import terrasaur.templates.TerrasaurTool;
+import terrasaur.utils.*;
+import terrasaur.utils.ImmutableSumFile.Builder;
+import terrasaur.utils.math.MathConversions;
+import terrasaur.utils.math.RotationUtils;
+import terrasaur.utils.spice.SpiceBundle;
+
+public class SumFilesFromFlyby implements TerrasaurTool {
+
+  private static final Logger logger = LogManager.getLogger();
+
+  @Override
+  public String shortDescription() {
+    return "Create sumfiles for a simplified flyby.";
+  }
+
+  @Override
+  public String fullDescription(Options options) {
+
+    String header = "";
+    String footer =
+        """
+
+            This tool creates sumfiles at points along a straight line trajectory past a body to be imaged.
+
+            Assumptions made:
+            1) The flyby is entirely in the equatorial (XY) plane.
+            2) the Sun lies along the body-fixed X axis.
+            3) the flyby happens on the eastern side of the body.
+            4) Rotation and orbital motion of the body are ignored.
+            5) Image (0,0) is at the upper left.  Body north is "up".
+
+            Given these assumptions, the trajectory can be specified using closest approach distance and phase along with speed.
+            """;
+    return TerrasaurTool.super.fullDescription(options, header, footer);
+  }
+
+  private SumFile sumfile;
+  private Function<Double, Vector3D> scPosFunc;
+  private Function<Double, Vector3D> scVelFunc;
+
+  private SumFilesFromFlyby() {}
+
+  public SumFilesFromFlyby(SumFile sumfile, double distance, double phase, double speed) {
+    this.sumfile = sumfile;
+
+    // given phase angle p, closest approach point is (cos p, sin p)
+    Vector3D closestApproach =
+        new Vector3D(FastMath.cos(phase), FastMath.sin(phase), 0.).scalarMultiply(distance);
+    Vector3D velocity =
+        new Vector3D(-FastMath.sin(phase), FastMath.cos(phase), 0.).scalarMultiply(speed);
+
+    /*-
+     * Assumptions:
+     *
+     * Sun lies along the X axis
+     * flyby is in the equatorial (XY) plane
+     *
+     */
+    scPosFunc = t -> closestApproach.add(velocity.scalarMultiply(t));
+
+    scVelFunc = t -> velocity;
+  }
+
+  public SumFile getSumFile(double t) {
+
+    TimeConversion tc = TimeConversion.createUsingInternalConstants();
+
+    Builder builder = ImmutableSumFile.builder().from(sumfile);
+    double imageTime = t + tc.utcStringToTDB(sumfile.utcString());
+    builder.picnm(String.format("%s%d", sumfile.picnm(), (int) Math.round(imageTime)));
+    builder.utcString(tc.format("C").apply(imageTime));
+
+    Vector3D scPos = scPosFunc.apply(t);
+
+    builder.scobj(scPos.negate());
+
+    Rotation bodyFixedToCamera = RotationUtils.KprimaryJsecondary(scPos.negate(), Vector3D.MINUS_K);
+    builder.cx(bodyFixedToCamera.applyInverseTo(Vector3D.PLUS_I));
+    builder.cy(bodyFixedToCamera.applyInverseTo(Vector3D.PLUS_J));
+    builder.cz(bodyFixedToCamera.applyInverseTo(Vector3D.PLUS_K));
+
+    builder.sz(Vector3D.PLUS_I.scalarMultiply(1e8));
+
+    SumFile s = builder.build();
+
+    logger.info(
+        "{}: S/C position {}, phase {}",
+        s.utcString(),
+        s.scobj().negate(),
+        Math.toDegrees(Vector3D.angle(s.scobj().negate(), s.sz())));
+
+    return s;
+  }
+
+  private String writeMSOPCKFiles(
+      String basename, IntervalSet intervals, int frameID, SpiceBundle bundle)
+      throws SpiceException {
+
+    File commentFile = new File(basename + "_msopck-comments.txt");
+    if (commentFile.exists()) commentFile.delete();
+    String setupFile = basename + "_msopck.setup";
+    String inputFile = basename + "_msopck.inp";
+
+    try (PrintWriter pw = new PrintWriter(commentFile)) {
+
+      String allComments = "";
+      for (String comment : allComments.split("\\r?\\n")) pw.println(WordUtils.wrap(comment, 80));
+    } catch (FileNotFoundException e) {
+      logger.error(e.getLocalizedMessage(), e);
+    }
+
+    File fk = bundle.findKernel(String.format(".*%s\\.tf", basename));
+    File lsk = bundle.findKernel(".*naif[0-9]{4}\\.tls");
+
+    Map<String, String> map = new TreeMap<>();
+    map.put("LSK_FILE_NAME", "'" + lsk + "'");
+    map.put("MAKE_FAKE_SCLK", String.format("'%s.tsc'", basename));
+    map.put("CK_TYPE", "3");
+    map.put("COMMENTS_FILE_NAME", String.format("'%s'", commentFile.getPath()));
+    map.put("INSTRUMENT_ID", Integer.toString(frameID));
+    map.put("REFERENCE_FRAME_NAME", "'J2000'");
+    map.put("FRAMES_FILE_NAME", "'" + fk.getPath() + "'");
+    map.put("ANGULAR_RATE_PRESENT", "'MAKE UP/NO AVERAGING'");
+    map.put("INPUT_TIME_TYPE", "'UTC'");
+    map.put("INPUT_DATA_TYPE", "'SPICE QUATERNIONS'");
+    map.put("PRODUCER_ID", "'Hari.Nair@jhuapl.edu'");
+
+    try (PrintWriter pw = new PrintWriter(setupFile)) {
+      pw.println("\\begindata");
+      for (String key : map.keySet()) {
+        pw.printf("%s = %s\n", key, map.get(key));
+      }
+    } catch (FileNotFoundException e) {
+      logger.error(e.getLocalizedMessage(), e);
+    }
+
+    NavigableMap<Double, SpiceQuaternion> attitudeMap = new TreeMap<>();
+
+    double t0 = bundle.getTimeConversion().utcStringToTDB(sumfile.utcString());
+
+    for (UnwritableInterval interval : intervals) {
+      for (double t = interval.getBegin(); t < interval.getEnd(); t += interval.getLength() / 100) {
+
+        double imageTime = t + t0;
+
+        Vector3D scPos = scPosFunc.apply(t);
+        SpiceQuaternion q =
+            new SpiceQuaternion(
+                MathConversions.toMatrix33(
+                    RotationUtils.KprimaryJsecondary(scPos.negate(), Vector3D.MINUS_K)));
+
+        attitudeMap.put(imageTime, q);
+      }
+    }
+
+    try (PrintWriter pw = new PrintWriter(new FileWriter(inputFile))) {
+      for (double t : attitudeMap.keySet()) {
+        SpiceQuaternion q = attitudeMap.get(t);
+        Vector3 v = q.getVector();
+        pw.printf(
+            "%s %.14e %.14e %.14e %.14e\n",
+            new TDBTime(t).toUTCString("ISOC", 6),
+            q.getScalar(),
+            v.getElt(0),
+            v.getElt(1),
+            v.getElt(2));
+      }
+    } catch (IOException e) {
+      logger.error(e.getLocalizedMessage(), e);
+    }
+
+    return String.format("msopck %s %s %s.bc", setupFile, inputFile, basename);
+  }
+
+  /**
+   * @param basename file basename
+   * @param intervals time intervals
+   * @param centerID NAIF id of center body
+   * @param bundle SPICE bundle
+   * @return command to run MKSPK
+   */
+  private String writeMKSPKFiles(
+      String basename, IntervalSet intervals, int centerID, SpiceBundle bundle) {
+
+    String commentFile = basename + "_mkspk-comments.txt";
+    String setupFile = basename + "_mkspk.setup";
+    String inputFile = basename + "_mkspk.inp";
+
+    try (PrintWriter pw = new PrintWriter(commentFile)) {
+
+      String allComments = "";
+      for (String comment : allComments.split("\\r?\\n")) pw.println(WordUtils.wrap(comment, 80));
+    } catch (FileNotFoundException e) {
+      logger.error(e.getLocalizedMessage(), e);
+    }
+
+    File lsk = bundle.findKernel(".*naif[0-9]{4}.tls");
+
+    Map<String, String> map = new TreeMap<>();
+    map.put("INPUT_DATA_TYPE", "'STATES'");
+    map.put("OUTPUT_SPK_TYPE", "13"); // hermite polynomial, unevenly spaced in time
+    map.put("OBJECT_ID", "-999");
+    map.put("CENTER_ID", String.format("%d", centerID));
+    map.put("COMMENT_FILE", String.format("'%s'", commentFile));
+    map.put("REF_FRAME_NAME", "'J2000'");
+    map.put("PRODUCER_ID", "'Hari.Nair@jhuapl.edu'");
+    map.put("DATA_ORDER", "'EPOCH X Y Z VX VY VZ'");
+    map.put("DATA_DELIMITER", "' '");
+    map.put("LEAPSECONDS_FILE", String.format("'%s'", lsk));
+    map.put("TIME_WRAPPER", "'# ETSECONDS'");
+    map.put("POLYNOM_DEGREE", "7");
+    map.put("SEGMENT_ID", "'SPK_STATES_13'");
+    map.put("LINES_PER_RECORD", "1");
+    try (PrintWriter pw = new PrintWriter(setupFile)) {
+      pw.println("\\begindata");
+      for (String key : map.keySet()) {
+        pw.printf("%s = %s\n", key, map.get(key));
+      }
+    } catch (FileNotFoundException e) {
+      logger.error(e.getLocalizedMessage(), e);
+    }
+
+    double t0 = bundle.getTimeConversion().utcStringToTDB(sumfile.utcString());
+
+    try (PrintWriter pw = new PrintWriter(inputFile)) {
+      for (UnwritableInterval interval : intervals) {
+        for (double t = interval.getBegin();
+            t < interval.getEnd();
+            t += interval.getLength() / 100) {
+
+          Vector3D scPos = scPosFunc.apply(t);
+          Vector3D scVel = scVelFunc.apply(t);
+          pw.printf(
+              "%.16e %.16e %.16e %.16e %.16e %.16e %.16e\n",
+              t + t0,
+              scPos.getX(),
+              scPos.getY(),
+              scPos.getZ(),
+              scVel.getX(),
+              scVel.getY(),
+              scVel.getZ());
+        }
+      }
+    } catch (FileNotFoundException e) {
+      logger.error(e.getLocalizedMessage(), e);
+    }
+    return String.format(
+        "mkspk -setup %s -input %s -output %s.bsp", setupFile, inputFile, basename);
+  }
+
+  private static Options defineOptions() {
+    Options options = TerrasaurTool.defineOptions();
+    options.addOption(
+        Option.builder("distance")
+            .hasArg()
+            .required()
+            .desc("Required.  Flyby distance from body center in km.")
+            .build());
+    options.addOption(
+        Option.builder("logFile")
+            .hasArg()
+            .desc("If present, save screen output to log file.")
+            .build());
+    StringBuilder sb = new StringBuilder();
+    for (StandardLevel l : StandardLevel.values()) sb.append(String.format("%s ", l.name()));
+    options.addOption(
+        Option.builder("logLevel")
+            .hasArg()
+            .desc(
+                "If present, print messages above selected priority.  Valid values are "
+                    + sb.toString().trim()
+                    + ".  Default is INFO.")
+            .build());
+    options.addOption(
+        Option.builder("mk")
+            .hasArg()
+            .desc(
+                "Path to NAIF metakernel.  This should contain LSK, FK for the central body, and FK for the spacecraft.  This is used by -mkspk and -msopck.")
+            .build());
+    options.addOption(
+        Option.builder("mkspk")
+            .hasArg()
+            .desc(
+                "If present, create input files for MKSPK.  The argument is the NAIF id for the central body (e.g. 10 for the Sun).  This option requires -lsk.")
+            .build());
+    options.addOption(
+        Option.builder("msopck")
+            .desc("If present, create input files for MSOPCK.  This option requires -lsk.")
+            .build());
+    options.addOption(
+        Option.builder("phase")
+            .hasArg()
+            .required()
+            .desc("Required.  Phase angle at closest approach in degrees.")
+            .build());
+    options.addOption(
+        Option.builder("speed")
+            .hasArg()
+            .required()
+            .desc("Required.  Flyby speed at closest approach in km/s.")
+            .build());
+    options.addOption(
+        Option.builder("template")
+            .hasArg()
+            .required()
+            .desc(
+                "Required.  An existing sumfile to use as a template.  Camera parameters are taken from this "
+                    + "file, while camera position and orientation are calculated.")
+            .build());
+    options.addOption(
+        Option.builder("times")
+            .hasArgs()
+            .desc(
+                "If present, list of times separated by white space.  In seconds, relative to closest approach.")
+            .build());
+    return options;
+  }
+
+  public static void main(String[] args) throws IOException, SpiceException {
+    TerrasaurTool defaultOBJ = new SumFilesFromFlyby();
+
+    Options options = defineOptions();
+
+    CommandLine cl = defaultOBJ.parseArgs(args, options);
+
+    Map<MessageLabel, String> startupMessages = defaultOBJ.startupMessages(cl);
+    for (MessageLabel ml : startupMessages.keySet())
+      logger.info(String.format("%s %s", ml.label, startupMessages.get(ml)));
+
+    double phase = Double.parseDouble(cl.getOptionValue("phase"));
+    if (phase < 0 || phase > 180) {
+      logger.error("Phase angle {} out of range [0, 180]", phase);
+      System.exit(0);
+    }
+
+    String sumFileTemplate = cl.getOptionValue("template");
+
+    String base = FilenameUtils.getBaseName(sumFileTemplate);
+    String ext = FilenameUtils.getExtension(sumFileTemplate);
+    SumFilesFromFlyby app =
+        new SumFilesFromFlyby(
+            SumFile.fromFile(new File(sumFileTemplate)),
+            Double.parseDouble(cl.getOptionValue("distance")),
+            Math.toRadians(phase),
+            Double.parseDouble(cl.getOptionValue("speed")));
+
+    NavigableSet<Double> times = new TreeSet<>();
+    if (cl.hasOption("times")) {
+      for (String s : cl.getOptionValues("times")) times.add(Double.parseDouble(s));
+    } else times.add(0.);
+
+    SpiceBundle bundle = null;
+    if (cl.hasOption("mk")) {
+      NativeLibraryLoader.loadSpiceLibraries();
+      bundle =
+          new SpiceBundle.Builder()
+              .addMetakernels(Collections.singletonList(cl.getOptionValue("mk")))
+              .build();
+      KernelDatabase.load(cl.getOptionValue("mk"));
+    }
+
+    TimeConversion tc =
+        bundle == null ? TimeConversion.createUsingInternalConstants() : bundle.getTimeConversion();
+
+    for (double t : times) {
+      SumFile s = app.getSumFile(t);
+
+      try (PrintWriter pw =
+          new PrintWriter(
+              String.format("%s_%d.%s", base, (int) tc.utcStringToTDB(s.utcString()), ext))) {
+
+        pw.println(s);
+
+      } catch (FileNotFoundException e) {
+        logger.error(e.getLocalizedMessage(), e);
+      }
+    }
+
+    if (cl.hasOption("mkspk")) {
+      if (bundle == null) {
+        logger.error("Need -mk to use -mkspk!");
+      } else {
+        IntervalSet.Builder builder = IntervalSet.builder();
+        for (Double t : times) {
+          Double next = times.higher(t);
+          if (next != null) builder.add(new UnwritableInterval(t, next));
+        }
+        int centerID = Integer.parseInt(cl.getOptionValue("mkspk"));
+
+        String command = app.writeMKSPKFiles(base, builder.build(), centerID, bundle);
+        logger.info("Command to create SPK:\n{}", command);
+      }
+    }
+
+    if (cl.hasOption("msopck")) {
+      if (bundle == null) {
+        logger.error("Need -mk to use -msopck!");
+      } else {
+        IntervalSet.Builder builder = IntervalSet.builder();
+        for (Double t : times) {
+          Double next = times.higher(t);
+          if (next != null) builder.add(new UnwritableInterval(t, next));
+        }
+
+        final int scID = -999;
+        final int frameID = scID * 1000;
+
+        File spacecraftFK = new File(String.format("%s.tf", base));
+        try (PrintWriter pw = new PrintWriter(spacecraftFK)) {
+          pw.println("\\begindata");
+          pw.printf("FRAME_%s_FIXED = %d\n", base, frameID);
+          pw.printf("FRAME_%d_NAME = '%s_FIXED'\n", frameID, base);
+          pw.printf("FRAME_%d_CLASS = 3\n", frameID);
+          pw.printf("FRAME_%d_CENTER = %d\n", frameID, scID);
+          pw.printf("FRAME_%d_CLASS_ID = %d\n", frameID, frameID);
+          pw.println("\\begintext");
+        }
+
+        List<File> kernels = new ArrayList<>(bundle.getKernels());
+        kernels.add(spacecraftFK);
+
+        bundle = new SpiceBundle.Builder().addKernelList(kernels).build();
+
+        File spacecraftSCLK = new File(String.format("%s.tsc", base));
+        if (spacecraftSCLK.exists()) spacecraftSCLK.delete();
+
+        String command = app.writeMSOPCKFiles(base, builder.build(), frameID, bundle);
+        logger.info("Command to create SPK:\n{}", command);
+      }
+    }
+  }
+}

src/main/java/terrasaur/apps/TileLookup.java

@@ -0,0 +1,339 @@
+package terrasaur.apps;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Rectangle;
+import java.awt.RenderingHints;
+import java.awt.image.BufferedImage;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.NavigableMap;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.Options;
+import org.apache.commons.io.FilenameUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import picante.math.coords.LatitudinalVector;
+import terrasaur.templates.TerrasaurTool;
+import terrasaur.utils.saaPlotLib.canvas.MapPlot;
+import terrasaur.utils.saaPlotLib.canvas.PlotCanvas;
+import terrasaur.utils.saaPlotLib.canvas.axis.AxisX;
+import terrasaur.utils.saaPlotLib.canvas.axis.AxisY;
+import terrasaur.utils.saaPlotLib.canvas.projection.Projection;
+import terrasaur.utils.saaPlotLib.canvas.projection.ProjectionOrthographic;
+import terrasaur.utils.saaPlotLib.canvas.projection.ProjectionRectangular;
+import terrasaur.utils.saaPlotLib.colorMaps.ColorRamp;
+import terrasaur.utils.saaPlotLib.colorMaps.ImmutableColorBar;
+import terrasaur.utils.saaPlotLib.colorMaps.ImmutableColorRamp;
+import terrasaur.utils.saaPlotLib.config.ImmutablePlotConfig;
+import terrasaur.utils.saaPlotLib.config.PlotConfig;
+import terrasaur.utils.saaPlotLib.data.DiscreteDataSet;
+import terrasaur.utils.saaPlotLib.data.ImmutableAnnotation;
+import terrasaur.utils.tessellation.FibonacciSphere;
+
+/**
+ * Given a number of tiles on a spherical tesselation, look up a tile index for
+ *
+ * @author nairah1
+ */
+public class TileLookup implements TerrasaurTool {
+
+  private static final Logger logger = LogManager.getLogger();
+
+  @Override
+  public String shortDescription() {
+    return "Locate tiles on the unit sphere.";
+  }
+
+  @Override
+  public String fullDescription(Options options) {
+    String header = "";
+    String footer = "";
+    return TerrasaurTool.super.fullDescription(options, header, footer);
+  }
+
+  /**
+   * Given the base database name and a tile number, return the path to that database file. For
+   * example:
+   *
+   * <pre>
+   * System.out.println(TileLookup.getDBName("/path/to/database/ola.db", 6));
+   * System.out.println(TileLookup.getDBName("./ola.db", 6));
+   * System.out.println(TileLookup.getDBName("ola.db", 6));
+   *
+   * /path/to/database/ola.6.db
+   * ./ola.6.db
+   * ./ola.6.db
+   * </pre>
+   *
+   * @param dbName basename for database (e.g. /path/to/database/ola.db)
+   * @param tile tile index (e.g. 6)
+   * @return path to database file (e.g. /path/to/database/ola.6.db)
+   */
+  public static String getDBName(String dbName, int tile) {
+    String fullPath = FilenameUtils.getFullPath(dbName);
+    if (fullPath.trim().isEmpty()) fullPath = ".";
+    if (!fullPath.endsWith(File.separator)) fullPath += File.separator;
+    return String.format(
+        "%s%s.%d.%s",
+        fullPath, FilenameUtils.getBaseName(dbName), tile, FilenameUtils.getExtension(dbName));
+  }
+
+  private static Options defineOptions() {
+    Options options = TerrasaurTool.defineOptions();
+    options.addOption(
+        Option.builder("nTiles")
+            .hasArg()
+            .required()
+            .desc("Number of points covering the sphere.")
+            .build());
+    options.addOption(
+        Option.builder("printCoords")
+            .desc(
+                "Print a table of points along with their coordinates.  Takes precedence over -printStats, -printDistance, and -png.")
+            .build());
+    options.addOption(
+        Option.builder("printDistance")
+            .hasArg()
+            .desc(
+                "Print a table of points sorted by distance from the input point.  "
+                    + "Format of the input point is longitude,latitude in degrees, comma separated without spaces.  Takes precedence over -png.")
+            .build());
+    options.addOption(
+        Option.builder("printStats")
+            .desc(
+                "Print statistics on the distances (in degrees) between each point and its nearest neighbor.  Takes precedence over -printDistance and -png.")
+            .build());
+    options.addOption(
+        Option.builder("png")
+            .hasArg()
+            .desc(
+                "Plot points and distance to nearest point in degrees.  Argument is the name of the PNG file to write.")
+            .build());
+    return options;
+  }
+
+  public static void main(String[] args) {
+    TerrasaurTool defaultOBJ = new TileLookup();
+
+    Options options = defineOptions();
+
+    CommandLine cl = defaultOBJ.parseArgs(args, options);
+
+    Map<MessageLabel, String> startupMessages = defaultOBJ.startupMessages(cl);
+    for (MessageLabel ml : startupMessages.keySet())
+      logger.info(String.format("%s %s", ml.label, startupMessages.get(ml)));
+
+    final int npts = Integer.parseInt(cl.getOptionValue("nTiles"));
+    FibonacciSphere fs = new FibonacciSphere(npts);
+
+    if (cl.hasOption("printCoords")) {
+      String header = String.format("%7s, %10s, %9s", "# index", "longitude", "latitude");
+      System.out.println(header);
+      // System.out.printf("%7s, %10s, %9s, %6s\n", "# index", "longitude", "latitude", "mapola");
+      for (int i = 0; i < npts; i++) {
+        LatitudinalVector lv = fs.getTileCenter(i);
+        double lon = Math.toDegrees(lv.getLongitude());
+        if (lon < 0) lon += 360;
+        double lat = Math.toDegrees(lv.getLatitude());
+        System.out.printf("%7d, %10.5f, %9.5f\n", i, lon, lat);
+      }
+      System.exit(0);
+    }
+
+    if (cl.hasOption("printStats")) {
+      System.out.println(
+          "Statistics on distances between each point and its nearest neighbor (degrees):");
+      System.out.println(fs.getDistanceStats());
+      System.exit(0);
+    }
+
+    if (cl.hasOption("printDistance")) {
+      String[] parts = cl.getOptionValue("printDistance").split(",");
+      double lon = Math.toRadians(Double.parseDouble(parts[0].trim()));
+      double lat = Math.toRadians(Double.parseDouble(parts[1].trim()));
+      LatitudinalVector lv = new LatitudinalVector(1, lat, lon);
+      NavigableMap<Double, Integer> distanceMap = fs.getDistanceMap(lv);
+      System.out.printf("%11s, %5s, %10s, %9s\n", "#  distance", "index", "longitude", "latitude");
+      System.out.printf("%11s, %5s, %10s, %9s\n", "# (degrees)", "", "(degrees)", "(degrees)");
+      for (Double dist : distanceMap.keySet()) {
+        int index = distanceMap.get(dist);
+        lv = fs.getTileCenter(index);
+        System.out.printf(
+            "%11.5f, %5d, %10.5f, %9.5f\n",
+            Math.toDegrees(dist),
+            index,
+            Math.toDegrees(lv.getLongitude()),
+            Math.toDegrees(lv.getLatitude()));
+      }
+      System.exit(0);
+    }
+
+    if (cl.hasOption("png")) {
+      PlotConfig config = ImmutablePlotConfig.builder().width(1000).height(1000).build();
+
+      String title = String.format("Fibonacci Sphere, n = %d, ", npts);
+
+      Map<String, Projection> projections = new LinkedHashMap<>();
+      projections.put(
+          title + "Rectangular Projection",
+          new ProjectionRectangular(config.width(), config.height() / 2));
+      projections.put(
+          title + "Orthographic Projection (0, 90)",
+          new ProjectionOrthographic(
+              config.width(), config.height(), new LatitudinalVector(1, Math.PI / 2, 0)));
+      projections.put(
+          title + "Orthographic Projection (0, 0)",
+          new ProjectionOrthographic(
+              config.width(), config.height(), new LatitudinalVector(1, 0, 0)));
+      projections.put(
+          title + "Orthographic Projection (90, 0)",
+          new ProjectionOrthographic(
+              config.width(), config.height(), new LatitudinalVector(1, 0, Math.PI / 2)));
+      projections.put(
+          title + "Orthographic Projection (180, 0)",
+          new ProjectionOrthographic(
+              config.width(), config.height(), new LatitudinalVector(1, 0, Math.PI)));
+      projections.put(
+          title + "Orthographic Projection (270, 0)",
+          new ProjectionOrthographic(
+              config.width(), config.height(), new LatitudinalVector(1, 0, 3 * Math.PI / 2)));
+      projections.put(
+          title + "Orthographic Projection (0, -90)",
+          new ProjectionOrthographic(
+              config.width(), config.height(), new LatitudinalVector(1, -Math.PI / 2, 0)));
+
+      final int nColors = 6;
+      ColorRamp ramp = ColorRamp.createLinear(1, nColors - 1);
+      List<Color> colors = new ArrayList<>();
+      colors.add(Color.BLACK);
+      for (int i = 1; i < nColors; i++) colors.add(ramp.getColor(i));
+      colors.add(Color.WHITE);
+      ramp = ImmutableColorRamp.builder().min(0).max(nColors).colors(colors).build();
+
+      double radius = fs.getDistanceStats().getMax();
+      ramp = ColorRamp.createLinear(0, radius).addLimitColors();
+
+      ArrayList<BufferedImage> images = new ArrayList<>();
+      for (String t : projections.keySet()) {
+        config = ImmutablePlotConfig.builder().from(config).title(t).build();
+        Projection p = projections.get(t);
+
+        if (p instanceof ProjectionRectangular)
+          config = ImmutablePlotConfig.builder().from(config).height(500).build();
+        else config = ImmutablePlotConfig.builder().from(config).height(1000).build();
+
+        MapPlot canvas = new MapPlot(config, p);
+        AxisX xLowerAxis = new AxisX(0, 360, "Longitude (degrees)", "%.0fE");
+        AxisY yLeftAxis = new AxisY(-90, 90, "Latitude (degrees)", "%.0f");
+
+        canvas.drawTitle();
+        canvas.setAxes(xLowerAxis, yLeftAxis);
+        // canvas.drawAxes();
+
+        BufferedImage image = canvas.getImage();
+        for (int i = 0; i < config.width(); i++) {
+          for (int j = 0; j < config.height(); j++) {
+            LatitudinalVector lv = p.pixelToSpherical(i, j);
+            if (lv == null) continue;
+            double closestDistance = Math.toDegrees(fs.getNearest(lv).getKey());
+            // int numPoints = fs.getDistanceMap(lv).subMap(0., Math.toRadians(radius)).size();
+            image.setRGB(
+                config.leftMargin() + i,
+                config.topMargin() + j,
+                ramp.getColor(closestDistance).getRGB());
+          }
+        }
+
+        DiscreteDataSet points = new DiscreteDataSet("");
+        for (int i = 0; i < fs.getNumTiles(); i++) {
+          LatitudinalVector lv = fs.getTileCenter(i);
+          points.add(lv.getLongitude(), lv.getLatitude());
+        }
+
+        if (p instanceof ProjectionRectangular) {
+          canvas.drawColorBar(
+              ImmutableColorBar.builder()
+                  .rect(
+                      new Rectangle(
+                          canvas.getPageWidth() - 60, config.topMargin(), 10, config.height()))
+                  .ramp(ramp)
+                  .numTicks(nColors + 1)
+                  .tickFunction(aDouble -> String.format("%.1f", aDouble))
+                  .build());
+
+//          for (int i = 0; i < fs.getNumTiles(); i++) {
+//            LatitudinalVector lv = fs.getTileCenter(i);
+//            canvas.drawCircle(lv, radius, Math.toRadians(1), Color.RED);
+//          }
+        }
+
+        for (int i = 0; i < fs.getNumTiles(); i++) {
+          LatitudinalVector lv = fs.getTileCenter(i);
+          canvas.addAnnotation(
+                  ImmutableAnnotation.builder().text(String.format("%d", i)).build(),
+                  lv.getLongitude(),
+                  lv.getLatitude());
+        }
+
+        images.add(canvas.getImage());
+      }
+
+      int width = 2400;
+      int height = 2400;
+      BufferedImage image = new BufferedImage(width, height, BufferedImage.TYPE_3BYTE_BGR);
+
+      Graphics2D g = image.createGraphics();
+      g.setRenderingHint(
+          RenderingHints.KEY_INTERPOLATION, RenderingHints.VALUE_INTERPOLATION_BILINEAR);
+      int imageWidth = width;
+      int imageHeight = height / 3;
+      g.drawImage(
+          images.getFirst(),
+          width / 6,
+          0,
+          5 * width / 6,
+          imageHeight,
+          0,
+          0,
+          images.getFirst().getWidth(),
+          images.getFirst().getHeight(),
+          null);
+
+      imageWidth = width / 3;
+      for (int i = 1; i < 4; i++) {
+        g.drawImage(
+            images.get(i),
+            (i - 1) * imageWidth,
+            imageHeight,
+            i * imageWidth,
+            2 * imageHeight,
+            0,
+            0,
+            images.get(i).getWidth(),
+            images.get(i).getHeight(),
+            null);
+      }
+      for (int i = 4; i < 7; i++) {
+        g.drawImage(
+            images.get(i),
+            (i - 4) * imageWidth,
+            2 * imageHeight,
+            (i - 3) * imageWidth,
+            3 * imageHeight,
+            0,
+            0,
+            images.get(i).getWidth(),
+            images.get(i).getHeight(),
+            null);
+      }
+      g.dispose();
+
+      PlotCanvas.writeImage(cl.getOptionValue("png"), image);
+    }
+  }
+}

src/main/java/terrasaur/apps/TransformFrame.java

@@ -0,0 +1,154 @@
+package terrasaur.apps;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.nio.charset.Charset;
+import java.util.List;
+import java.util.Map;
+import java.util.NavigableMap;
+import java.util.TreeMap;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.Options;
+import org.apache.commons.io.FileUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.spi.StandardLevel;
+import spice.basic.KernelDatabase;
+import spice.basic.Matrix33;
+import spice.basic.ReferenceFrame;
+import spice.basic.SpiceErrorException;
+import spice.basic.SpiceException;
+import spice.basic.TDBTime;
+import spice.basic.Vector3;
+import terrasaur.templates.TerrasaurTool;
+import terrasaur.utils.NativeLibraryLoader;
+import terrasaur.utils.SPICEUtil;
+
+public class TransformFrame implements TerrasaurTool {
+  private static final Logger logger = LogManager.getLogger();
+
+
+  @Override
+  public String shortDescription() {
+      return "Transform coordinates between reference frames.";
+  }
+
+  @Override
+  public String fullDescription(Options options) {
+    String header = "";
+    String footer = "\nThis program transforms coordinates between reference frames.\n";
+    return TerrasaurTool.super.fullDescription(options, header, footer);
+  }
+
+  private NavigableMap<TDBTime, Vector3> pointsIn;
+  private NavigableMap<TDBTime, Vector3> pointsOut;
+
+  public TransformFrame() {}
+
+  public void setPoints(NavigableMap<TDBTime, Vector3> pointsIn) {
+    this.pointsIn = pointsIn;
+  }
+
+  public void transformCoordinates(String inFrame, String outFrame) {
+    try {
+      ReferenceFrame from = new ReferenceFrame(inFrame);
+      ReferenceFrame to = new ReferenceFrame(outFrame);
+      pointsOut = new TreeMap<>(SPICEUtil.tdbComparator);
+      for (TDBTime t : pointsIn.keySet()) {
+        Matrix33 transform = from.getPositionTransformation(to, t);
+        pointsOut.put(t, transform.mxv(pointsIn.get(t)));
+      }
+    } catch (SpiceException e) {
+      logger.error(e.getLocalizedMessage());
+    }
+  }
+
+  public void write(String outFile) {
+
+    try (PrintWriter pw = new PrintWriter(outFile)) {
+      for (TDBTime t : pointsOut.keySet()) {
+        Vector3 v = pointsOut.get(t);
+        pw.printf("%.6f,%.6e,%.6e,%.6e\n", t.getTDBSeconds(), v.getElt(0), v.getElt(1),
+            v.getElt(2));
+      }
+    } catch (FileNotFoundException | SpiceException e) {
+      logger.error(e.getLocalizedMessage());
+    }
+
+  }
+
+  private static Options defineOptions() {
+    Options options = TerrasaurTool.defineOptions();
+    options.addOption(Option.builder("inFile").required().hasArg()
+            .desc("Required.  Text file containing comma separated t, x, y, z values.  Time is ET.")
+            .build());
+    options.addOption(Option.builder("inFrame").required().hasArg()
+            .desc("Required.  Name of inFile reference frame.").build());
+    options.addOption(Option.builder("outFile").required().hasArg()
+            .desc("Required.  Name of output file.  It will be in the same format as inFile.").build());
+    options.addOption(Option.builder("outFrame").required().hasArg()
+            .desc("Required.  Name of outFile reference frame.").build());
+    options.addOption(Option.builder("spice").required().hasArg().desc(
+                    "Required.  Name of SPICE metakernel containing kernels needed to make the frame transformation.")
+            .build());
+    options.addOption(Option.builder("logFile").hasArg()
+            .desc("If present, save screen output to log file.").build());
+    StringBuilder sb = new StringBuilder();
+    for (StandardLevel l : StandardLevel.values())
+      sb.append(String.format("%s ", l.name()));
+    options.addOption(Option.builder("logLevel").hasArg()
+            .desc("If present, print messages above selected priority.  Valid values are "
+                    + sb.toString().trim() + ".  Default is INFO.")
+            .build());    return options;
+  }
+
+  public static void main(String[] args) {
+    TerrasaurTool defaultOBJ = new TransformFrame();
+
+    Options options = defineOptions();
+
+    CommandLine cl = defaultOBJ.parseArgs(args, options);
+
+    Map<MessageLabel, String> startupMessages = defaultOBJ.startupMessages(cl);
+    for (MessageLabel ml : startupMessages.keySet())
+      logger.info(String.format("%s %s", ml.label, startupMessages.get(ml)));
+
+    TransformFrame tf = new TransformFrame();
+    NavigableMap<TDBTime, Vector3> map = new TreeMap<>(SPICEUtil.tdbComparator);
+    try {
+      File f = new File(cl.getOptionValue("inFile"));
+      List<String> lines = FileUtils.readLines(f, Charset.defaultCharset());
+      for (String line : lines) {
+        String trim = line.trim();
+        if (trim.isEmpty() || trim.startsWith("#"))
+          continue;
+        String[] parts = trim.split(",");
+        double et = Double.parseDouble(parts[0].trim());
+        if (et > 0) {
+          TDBTime t = new TDBTime(et);
+          Vector3 v = new Vector3(Double.parseDouble(parts[1].trim()),
+              Double.parseDouble(parts[2].trim()), Double.parseDouble(parts[3].trim()));
+          map.put(t, v);
+        }
+      }
+    } catch (IOException e) {
+      logger.error(e.getLocalizedMessage());
+    }
+
+    tf.setPoints(map);
+
+    NativeLibraryLoader.loadSpiceLibraries();
+    try {
+      KernelDatabase.load(cl.getOptionValue("spice"));
+    } catch (SpiceErrorException e) {
+      logger.error(e.getLocalizedMessage());
+    }
+
+    tf.transformCoordinates(cl.getOptionValue("inFrame"), cl.getOptionValue("outFrame"));
+    tf.write(cl.getOptionValue("outFile"));
+  }
+
+}

src/main/java/terrasaur/apps/TranslateTime.java

@@ -0,0 +1,240 @@
+package terrasaur.apps;
+
+import java.util.LinkedHashMap;
+import java.util.Map;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.Options;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.spi.StandardLevel;
+import spice.basic.KernelDatabase;
+import spice.basic.KernelPool;
+import spice.basic.SCLK;
+import spice.basic.SCLKTime;
+import spice.basic.SpiceErrorException;
+import spice.basic.SpiceException;
+import spice.basic.TDBTime;
+import terrasaur.gui.TranslateTimeFX;
+import terrasaur.templates.TerrasaurTool;
+import terrasaur.utils.NativeLibraryLoader;
+
+/**
+ * Translate time between formats.
+ * 
+ * @author nairah1
+ *
+ */
+public class TranslateTime implements TerrasaurTool {
+
+  private static final Logger logger = LogManager.getLogger();
+
+  @Override
+  public String shortDescription() {
+    return "Convert between different time systems.";
+  }
+
+  @Override
+  public String fullDescription(Options options) {
+    String header = "";
+    String footer = "\nConvert between different time systems.\n";
+    return TerrasaurTool.super.fullDescription(options, header, footer);
+
+  }
+
+  private enum Types {
+    JULIAN, SCLK, TDB, TDBCALENDAR, UTC
+  }
+
+  private Map<Integer, SCLK> sclkMap;
+
+  private TranslateTime(){}
+
+  public TranslateTime(Map<Integer, SCLK> sclkMap) {
+    this.sclkMap = sclkMap;
+  }
+
+  private TDBTime tdb;
+
+  public String toJulian() throws SpiceErrorException {
+    return tdb.toString("JULIAND.######");
+  }
+
+  private SCLK sclkKernel;
+
+  public SCLK getSCLKKernel() {
+    return sclkKernel;
+  }
+
+  public void setSCLKKernel(int sclkID) {
+    sclkKernel = sclkMap.get(sclkID);
+    if (sclkKernel == null) {
+      logger.error("SCLK {} is not loaded!", sclkID);
+    }
+  }
+
+  public SCLKTime toSCLK() throws SpiceException {
+    return new SCLKTime(sclkKernel, tdb);
+  }
+
+  public TDBTime toTDB() {
+    return tdb;
+  }
+
+  public String toUTC() throws SpiceErrorException {
+    return tdb.toUTCString("ISOC", 3);
+  }
+
+  public void setJulianDate(double julianDate) throws SpiceErrorException {
+    tdb = new TDBTime(String.format("%.6f JDUTC", julianDate));
+  }
+
+  public void setSCLK(String sclkString) throws SpiceException {
+    tdb = new TDBTime(new SCLKTime(sclkKernel, sclkString));
+  }
+
+  public void setTDB(double tdb) {
+    this.tdb = new TDBTime(tdb);
+  }
+
+  public void setTDBCalendarString(String tdbString) throws SpiceErrorException {
+    tdb = new TDBTime(String.format("%s TDB", tdbString));
+  }
+
+  public void setUTC(String utcStr) throws SpiceErrorException {
+    tdb = new TDBTime(utcStr);
+  }
+
+  private static Options defineOptions() {
+    Options options = TerrasaurTool.defineOptions();
+    options.addOption(Option.builder("logFile").hasArg()
+            .desc("If present, save screen output to log file.").build());
+    StringBuilder sb = new StringBuilder();
+    for (StandardLevel l : StandardLevel.values())
+      sb.append(String.format("%s ", l.name()));
+    options.addOption(Option.builder("logLevel").hasArg()
+            .desc("If present, print messages above selected priority.  Valid values are "
+                    + sb.toString().trim() + ".  Default is INFO.")
+            .build());
+    options.addOption(Option.builder("sclk").hasArg().desc(
+                    "SPICE id of the sclk to use.  Default is to use the first one found in the kernel pool.")
+            .build());
+    options.addOption(Option.builder("spice").required().hasArg()
+            .desc("Required.  SPICE metakernel containing leap second and SCLK.").build());
+    options.addOption(Option.builder("gui").desc("Launch a GUI.").build());
+    options.addOption(Option.builder("inputDate").hasArgs().desc("Date to translate.").build());
+    sb = new StringBuilder();
+    for (Types system : Types.values()) {
+      sb.append(String.format("%s ", system.name()));
+    }
+    options.addOption(Option.builder("inputSystem").hasArg().desc(
+                    "Timesystem of inputDate.  Valid values are " + sb.toString().trim() + ".  Default is UTC.")
+            .build());    return options;
+  }
+
+  public static void main(String[] args) throws SpiceException {
+    TerrasaurTool defaultOBJ = new TranslateTime();
+
+    Options options = defineOptions();
+
+    CommandLine cl = defaultOBJ.parseArgs(args, options);
+
+    Map<MessageLabel, String> startupMessages = defaultOBJ.startupMessages(cl);
+    for (MessageLabel ml : startupMessages.keySet())
+      logger.info(String.format("%s %s", ml.label, startupMessages.get(ml)));
+
+    // This is to avoid java crashing due to inability to connect to an X display
+    if (!cl.hasOption("gui"))
+      System.setProperty("java.awt.headless", "true");
+
+    NativeLibraryLoader.loadSpiceLibraries();
+
+    for (String kernel : cl.getOptionValues("spice"))
+      KernelDatabase.load(kernel);
+
+    LinkedHashMap<Integer, SCLK> sclkMap = new LinkedHashMap<>();
+    String[] sclk_data_type = KernelPool.getNames("SCLK_DATA_*");
+    for (String s : sclk_data_type) {
+      String[] parts = s.split("_");
+      int sclkID = -Integer.parseInt(parts[parts.length - 1]);
+      sclkMap.put(sclkID, new SCLK(sclkID));
+    }
+
+    SCLK sclk = null;
+    if (cl.hasOption("sclk")) {
+      int sclkID = Integer.parseInt(cl.getOptionValue("sclk"));
+      if (sclkMap.containsKey(sclkID))
+        sclk = sclkMap.get(sclkID);
+      else {
+        logger.error("Cannot find SCLK {} in kernel pool!", sclkID);
+        StringBuilder    sb = new StringBuilder();
+        for (Integer id : sclkMap.keySet())
+          sb.append(String.format("%d ", id));
+        logger.error("Loaded IDs are {}", sb.toString());
+      }
+    } else {
+      if (!sclkMap.values().isEmpty())
+        // set the SCLK to the first one found
+        sclk = sclkMap.values().stream().toList().get(0);
+    }
+
+    if (sclk == null) {
+      logger.fatal("Cannot load SCLK");
+      System.exit(0);
+    }
+
+    TranslateTime tt = new TranslateTime(sclkMap);
+
+    if (cl.hasOption("gui")) {
+      TranslateTimeFX.setTranslateTime(tt);
+      TranslateTimeFX.setSCLKIDs(sclkMap.keySet());
+      TranslateTimeFX.main(args);
+      System.exit(0);
+    } else {
+      if (!cl.hasOption("inputDate")) {
+        logger.fatal("Missing required option -inputDate!");
+        System.exit(1);
+      }
+      tt.setSCLKKernel(sclk.getIDCode());
+    }
+
+    StringBuilder sb = new StringBuilder();
+    for (String s : cl.getOptionValues("inputDate"))
+      sb.append(String.format("%s ", s));
+    String inputDate = sb.toString().trim();
+
+    Types type =
+        cl.hasOption("inputSystem") ? Types.valueOf(cl.getOptionValue("inputSystem").toUpperCase())
+            : Types.UTC;
+
+    switch (type) {
+      case JULIAN:
+        tt.setJulianDate(Double.parseDouble(inputDate));
+        break;
+      case SCLK:
+        tt.setSCLK(inputDate);
+        break;
+      case TDB:
+        tt.setTDB(Double.parseDouble(inputDate));
+        break;
+      case TDBCALENDAR:
+        tt.setTDBCalendarString(inputDate);
+        break;
+      case UTC:
+        tt.setUTC(inputDate);
+        break;
+    }
+
+    System.out.printf("# input date %s (%s)\n", inputDate, type.name());
+    System.out.printf("# UTC, TDB (Calendar), DOY, TDB, Julian Date, SCLK (%d)\n",
+        sclk.getIDCode());
+
+    String utcString = tt.toTDB().toUTCString("ISOC", 3);
+    String tdbString = tt.toTDB().toString("YYYY-MM-DDTHR:MN:SC.### ::TDB");
+    String doyString = tt.toTDB().toString("DOY");
+
+    System.out.printf("%s, %s, %s, %.6f, %s, %s\n", utcString, tdbString, doyString,
+        tt.toTDB().getTDBSeconds(), tt.toJulian(), tt.toSCLK().toString());
+
+  }
+}

src/main/java/terrasaur/apps/ValidateNormals.java

@@ -0,0 +1,261 @@
+package terrasaur.apps;
+
+import java.time.Instant;
+import java.time.ZoneId;
+import java.time.format.DateTimeFormatter;
+import java.util.*;
+import java.util.concurrent.Callable;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.Options;
+import org.apache.commons.text.WordUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import terrasaur.templates.TerrasaurTool;
+import terrasaur.utils.*;
+import vtk.vtkCellArray;
+import vtk.vtkIdList;
+import vtk.vtkOBBTree;
+import vtk.vtkOBJReader;
+import vtk.vtkPolyData;
+
+public class ValidateNormals implements TerrasaurTool {
+  private static final Logger logger = LogManager.getLogger();
+
+  private ValidateNormals() {}
+
+  @Override
+  public String shortDescription() {
+    return "Check facet normal directions for an OBJ shape file.";
+  }
+
+  @Override
+  public String fullDescription(Options options) {
+
+    String footer =
+        "\nThis program checks that the normals of the shape model are not pointing inward.\n";
+    return TerrasaurTool.super.fullDescription(options, "", footer);
+  }
+
+  static Options defineOptions() {
+    Options options = TerrasaurTool.defineOptions();
+    options.addOption(
+        Option.builder("origin")
+            .hasArg()
+            .desc(
+                "If present, center of body in xyz coordinates.  "
+                    + "Specify as three floating point values separated by commas.  Default is to use the centroid of "
+                    + "the input shape model.")
+            .build());
+    options.addOption(
+        Option.builder("obj").required().hasArg().desc("Shape model to validate.").build());
+    options.addOption(
+        Option.builder("output")
+            .hasArg()
+            .desc("Write out new OBJ file with corrected vertex orders for facets.")
+            .build());
+    options.addOption(
+        Option.builder("numThreads")
+            .hasArg()
+            .desc("Number of threads to run.  Default is 1.")
+            .build());
+    return options;
+  }
+
+  private vtkPolyData polyData;
+  private ThreadLocal<vtkOBBTree> threadLocalsearchTree;
+  private double[] origin;
+
+  public ValidateNormals(vtkPolyData polyData) {
+    this.polyData = polyData;
+
+    PolyDataStatistics stats = new PolyDataStatistics(polyData);
+    origin = stats.getCentroid();
+
+    threadLocalsearchTree = new ThreadLocal<>();
+  }
+
+  public vtkOBBTree getOBBTree() {
+    vtkOBBTree searchTree = threadLocalsearchTree.get();
+    if (searchTree == null) {
+      searchTree = new vtkOBBTree();
+      searchTree.SetDataSet(polyData);
+      searchTree.SetTolerance(1e-12);
+      searchTree.BuildLocator();
+      threadLocalsearchTree.set(searchTree);
+    }
+    return searchTree;
+  }
+
+  public void setOrigin(double[] origin) {
+    this.origin = origin;
+  }
+
+  private class FlippedNormalFinder implements Callable<List<Long>> {
+
+    private static final DateTimeFormatter defaultFormatter =
+        DateTimeFormatter.ofPattern("yyyy-MM-dd HH:mm:ss z")
+            .withLocale(Locale.getDefault())
+            .withZone(ZoneId.systemDefault());
+
+    private final long index0;
+    private final long index1;
+
+    public FlippedNormalFinder(long index0, long index1) {
+      this.index0 = index0;
+      this.index1 = index1;
+    }
+
+    @Override
+    public List<Long> call() {
+
+      logger.info("Thread {}: indices {} to {}", Thread.currentThread().threadId(), index0, index1);
+      vtkIdList idList = new vtkIdList();
+      vtkIdList cellIds = new vtkIdList();
+      List<Long> flippedNormals = new ArrayList<>();
+
+      final long startTime = Instant.now().getEpochSecond();
+      final long numFacets = index1 - index0;
+      for (int i = 0; i < numFacets; ++i) {
+
+        if (i > 0 && i % (numFacets / 10) == 0) {
+          double pctDone = i / (numFacets * .01);
+          long elapsed = Instant.now().getEpochSecond() - startTime;
+          long estimatedFinish = (long) (elapsed / (pctDone / 100) + startTime);
+          String finish = defaultFormatter.format(Instant.ofEpochSecond(estimatedFinish));
+          logger.info(
+              String.format(
+                  "Thread %d: read %d of %d facets. %.0f%% complete, projected finish %s",
+                  Thread.currentThread().threadId(), index0 + i, index1, pctDone, finish));
+        }
+
+        long index = index0 + i;
+
+        CellInfo ci = CellInfo.getCellInfo(polyData, index, idList);
+        getOBBTree().IntersectWithLine(origin, ci.center().toArray(), null, cellIds);
+
+        // count up all crossings of the surface between the origin and the facet.
+        int numCrossings = 0;
+        for (int j = 0; j < cellIds.GetNumberOfIds(); j++) {
+          if (cellIds.GetId(j) == index) break;
+          numCrossings++;
+        }
+
+        // if numCrossings is even, the radial and normal should point in the same direction. If it
+        // is odd, the
+        // radial and normal should point in opposite directions.
+        boolean shouldBeOpposite = (numCrossings % 2 == 1);
+        boolean isOpposite = (ci.center().dotProduct(ci.normal()) < 0);
+
+        // XOR operator - true if both conditions are different
+        if (isOpposite ^ shouldBeOpposite) flippedNormals.add(index);
+      }
+
+      return flippedNormals;
+    }
+  }
+
+  public void flipNormals(Collection<Long> facets) {
+    vtkCellArray cells = new vtkCellArray();
+    for (long i = 0; i < polyData.GetNumberOfCells(); ++i) {
+      vtkIdList idList = new vtkIdList();
+      polyData.GetCellPoints(i, idList);
+      if (facets.contains(i)) {
+        long id0 = idList.GetId(0);
+        long id1 = idList.GetId(1);
+        long id2 = idList.GetId(2);
+        idList.SetId(0, id0);
+        idList.SetId(1, id2);
+        idList.SetId(2, id1);
+      }
+      cells.InsertNextCell(idList);
+    }
+    polyData.SetPolys(cells);
+  }
+
+  public static void main(String[] args) throws Exception {
+    TerrasaurTool defaultOBJ = new ValidateNormals();
+
+    Options options = defineOptions();
+
+    CommandLine cl = defaultOBJ.parseArgs(args, options);
+
+    Map<MessageLabel, String> startupMessages = defaultOBJ.startupMessages(cl);
+    for (MessageLabel ml : startupMessages.keySet())
+      logger.info(String.format("%s %s", ml.label, startupMessages.get(ml)));
+
+    NativeLibraryLoader.loadVtkLibraries();
+
+    // PolyDataUtil's OBJ reader messes with the normals - not reliable for a local obj
+    vtkOBJReader smallBodyReader = new vtkOBJReader();
+    smallBodyReader.SetFileName(cl.getOptionValue("obj"));
+    smallBodyReader.Update();
+    vtkPolyData polyData = new vtkPolyData();
+    polyData.ShallowCopy(smallBodyReader.GetOutput());
+
+    smallBodyReader.Delete();
+
+    ValidateNormals app = new ValidateNormals(polyData);
+
+    logger.info("Read {} facets from {}", polyData.GetNumberOfCells(), cl.getOptionValue("obj"));
+
+    if (cl.hasOption("origin")) {
+      String[] parts = cl.getOptionValue("origin").split(",");
+      double[] origin = new double[3];
+      for (int i = 0; i < 3; i++) origin[i] = Double.parseDouble(parts[i]);
+      app.setOrigin(origin);
+    }
+
+    Set<Long> flippedNormals = new HashSet<>();
+
+    int numThreads =
+        cl.hasOption("numThreads") ? Integer.parseInt(cl.getOptionValue("numThreads")) : 1;
+    try (ExecutorService executor = Executors.newFixedThreadPool(numThreads)) {
+      List<Future<List<Long>>> futures = new ArrayList<>();
+
+      long numFacets = polyData.GetNumberOfCells() / numThreads;
+      for (int i = 0; i < numThreads; i++) {
+        long fromIndex = i * numFacets;
+        long toIndex = Math.min(polyData.GetNumberOfCells(), fromIndex + numFacets);
+
+        FlippedNormalFinder fnf = app.new FlippedNormalFinder(fromIndex, toIndex);
+        futures.add(executor.submit(fnf));
+      }
+
+      for (Future<List<Long>> future : futures) flippedNormals.addAll(future.get());
+
+      executor.shutdown();
+    }
+
+    logger.info(
+        "Found {} flipped normals out of {} facets",
+        flippedNormals.size(),
+        polyData.GetNumberOfCells());
+
+    if (cl.hasOption("output")) {
+      NavigableSet<Long> sorted = new TreeSet<>(flippedNormals);
+      String header = "";
+      if (!flippedNormals.isEmpty()) {
+        header = "# The following indices were flipped from " + cl.getOptionValue("obj") + ":\n";
+        StringBuilder sb = new StringBuilder("# ");
+        for (Long index : sorted) {
+          sb.append(String.format("%d", index));
+          if (index < sorted.last()) sb.append(", ");
+        }
+        sb.append("\n");
+        header += WordUtils.wrap(sb.toString(), 80, "\n# ", false);
+        logger.info(header);
+      }
+
+      app.flipNormals(flippedNormals);
+      PolyDataUtil.saveShapeModelAsOBJ(app.polyData, cl.getOptionValue("output"), header);
+      logger.info("wrote OBJ file {}", cl.getOptionValue("output"));
+    }
+
+    logger.info("ValidateNormals done");
+  }
+}

src/main/java/terrasaur/apps/ValidateOBJ.java

@@ -0,0 +1,402 @@
+package terrasaur.apps;
+
+import java.util.*;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.Options;
+import org.apache.commons.math3.geometry.euclidean.threed.Vector3D;
+import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics;
+import org.apache.logging.log4j.Level;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.spi.StandardLevel;
+import picante.math.vectorspace.VectorIJK;
+import terrasaur.smallBodyModel.SmallBodyModel;
+import terrasaur.templates.TerrasaurTool;
+import terrasaur.utils.*;
+import terrasaur.utils.mesh.TriangularFacet;
+import vtk.vtkIdList;
+import vtk.vtkPolyData;
+
+/**
+ * Check an OBJ file for the correct number of facets and vertices. Test for duplicate vertices,
+ * unreferenced vertices, and zero area facets.
+ *
+ * <p>Even though this is named "ValidateOBJ" it will work with any format that can be read by
+ * {@link PolyDataUtil#loadShapeModel(String)}.
+ *
+ * @author Hari.Nair@jhuapl.edu
+ */
+public class ValidateOBJ implements TerrasaurTool {
+
+  private static final Logger logger = LogManager.getLogger();
+
+  @Override
+  public String shortDescription() {
+    return "Check a closed shape file in OBJ format for errors.";
+  }
+
+  @Override
+  public String fullDescription(Options options) {
+    String header = "";
+    String footer =
+        """
+                    This program checks that a shape model has the correct number of facets and vertices.  \
+                    It will also check for duplicate vertices, vertices that are not referenced by any facet, and zero area facets.
+                    """;
+    return TerrasaurTool.super.fullDescription(options, header, footer);
+  }
+
+  private vtkPolyData polyData;
+  private String validationMsg;
+
+  private ValidateOBJ() {}
+
+  public ValidateOBJ(vtkPolyData polyData) {
+    this.polyData = polyData;
+  }
+
+  /**
+   * @return {@link vtkPolyData#GetNumberOfCells()}
+   */
+  public long facetCount() {
+    return polyData.GetNumberOfCells();
+  }
+
+  /**
+   * @return {@link vtkPolyData#GetNumberOfPoints()}
+   */
+  public long vertexCount() {
+    return polyData.GetNumberOfPoints();
+  }
+
+  /**
+   * @return description of test result
+   */
+  public String getMessage() {
+    return validationMsg;
+  }
+
+  /**
+   * @return true if number of facets in the shape model satisfies 3*4^n where n is an integer
+   */
+  public boolean testFacets() {
+    boolean meetsCondition = facetCount() % 3 == 0;
+
+    if (meetsCondition) {
+      long facet3 = facetCount() / 3;
+      double logFacet3 = Math.log(facet3) / Math.log(4);
+      if (Math.ceil(logFacet3) != Math.floor(logFacet3)) meetsCondition = false;
+    }
+
+    int n = (int) (Math.log(facetCount() / 3.) / Math.log(4.0) + 0.5);
+    if (meetsCondition) {
+      validationMsg =
+          String.format(
+              "Model has %d facets.  This satisfies f = 3*4^n with n = %d.", facetCount(), n);
+    } else {
+      validationMsg =
+          String.format(
+              "Model has %d facets.  This does not satisfy f = 3*4^n.  A shape model with %.0f facets has n = %d.",
+              facetCount(), 3 * Math.pow(4, n), n);
+    }
+
+    return meetsCondition;
+  }
+
+  /**
+   * @return true if number of vertices in the shape model satisfies v=f/2+2
+   */
+  public boolean testVertices() {
+    boolean meetsCondition = (facetCount() + 4) / 2 == vertexCount();
+    if (meetsCondition)
+      validationMsg =
+          String.format(
+              "Model has %d vertices and %d facets.  This satisfies v = f/2+2.",
+              vertexCount(), facetCount());
+    else
+      validationMsg =
+          String.format(
+              "Model has %d vertices and %d facets.  This does not satisfy v = f/2+2.  Number of vertices should be %d.",
+              vertexCount(), facetCount(), facetCount() / 2 + 2);
+
+    return meetsCondition;
+  }
+
+  /**
+   * @return key is vertex id, value is a list of vertices within a hard coded distance of 1e-10.
+   */
+  public NavigableMap<Long, List<Long>> findDuplicateVertices() {
+
+    SmallBodyModel sbm = new SmallBodyModel(polyData);
+
+    double[] iPt = new double[3];
+
+    NavigableMap<Long, List<Long>> map = new TreeMap<>();
+    double tol = 1e-10;
+    for (long i = 0; i < vertexCount(); i++) {
+      polyData.GetPoint(i, iPt);
+
+      List<Long> closestVertices = new ArrayList<>();
+      for (Long id : sbm.findClosestVerticesWithinRadius(iPt, tol))
+        if (id > i) closestVertices.add(id);
+      if (!closestVertices.isEmpty()) map.put(i, closestVertices);
+
+      if (map.containsKey(i) && !map.get(i).isEmpty()) {
+        StringBuilder sb = new StringBuilder();
+        sb.append(String.format("Duplicates for vertex %d: ", i + 1));
+        for (Long dupId : map.get(i)) sb.append(String.format("%d ", dupId + 1));
+        logger.debug(sb.toString());
+      }
+    }
+
+    validationMsg = String.format("%d vertices have duplicates", map.size());
+
+    return map;
+  }
+
+  /**
+   * @return a list of vertex indices where one or more of the coordinates fail {@link
+   *     Double#isFinite(double)}.
+   */
+  public List<Integer> findMalformedVertices() {
+    double[] iPt = new double[3];
+    NavigableSet<Integer> vertexIndices = new TreeSet<>();
+    for (int i = 0; i < vertexCount(); i++) {
+      polyData.GetPoint(i, iPt);
+      for (int j = 0; j < 3; j++) {
+        if (!Double.isFinite(iPt[j])) {
+          logger.debug("Vertex {}: {} {} {}", i, iPt[0], iPt[1], iPt[2]);
+          vertexIndices.add(i);
+          break;
+        }
+      }
+    }
+    validationMsg = String.format("%d malformed vertices ", vertexIndices.size());
+    return new ArrayList<>(vertexIndices);
+  }
+
+  /**
+   * @return a list of vertex indices that are not referenced by any facet
+   */
+  public List<Long> findUnreferencedVertices() {
+    NavigableSet<Long> vertexIndices = new TreeSet<>();
+    for (long i = 0; i < polyData.GetNumberOfPoints(); i++) {
+      vertexIndices.add(i);
+    }
+
+    vtkIdList idList = new vtkIdList();
+    for (int i = 0; i < facetCount(); ++i) {
+      polyData.GetCellPoints(i, idList);
+      long id0 = idList.GetId(0);
+      long id1 = idList.GetId(1);
+      long id2 = idList.GetId(2);
+
+      vertexIndices.remove(id0);
+      vertexIndices.remove(id1);
+      vertexIndices.remove(id2);
+    }
+
+    if (!vertexIndices.isEmpty()) {
+      double[] pt = new double[3];
+      for (long id : vertexIndices) {
+        polyData.GetPoint(id, pt);
+        logger.debug("Unreferenced vertex {} [{}, {}, {}]", id + 1, pt[0], pt[1], pt[2]);
+        // note OBJ vertices are numbered from 1 but VTK uses 0
+      }
+    }
+
+    validationMsg = String.format("%d unreferenced vertices found", vertexIndices.size());
+
+    return new ArrayList<>(vertexIndices);
+  }
+
+  /**
+   * @return a list of facet indices where the facet has zero area
+   */
+  public List<Integer> findZeroAreaFacets() {
+    List<Integer> zeroAreaFacets = new ArrayList<>();
+    vtkIdList idList = new vtkIdList();
+    double[] pt0 = new double[3];
+    double[] pt1 = new double[3];
+    double[] pt2 = new double[3];
+
+    for (int i = 0; i < facetCount(); ++i) {
+      polyData.GetCellPoints(i, idList);
+      long id0 = idList.GetId(0);
+      long id1 = idList.GetId(1);
+      long id2 = idList.GetId(2);
+      polyData.GetPoint(id0, pt0);
+      polyData.GetPoint(id1, pt1);
+      polyData.GetPoint(id2, pt2);
+
+      // would be faster to check if id0==id1||id0==id2||id1==id2 but there may be
+      // duplicate vertices
+      TriangularFacet facet =
+          new TriangularFacet(new VectorIJK(pt0), new VectorIJK(pt1), new VectorIJK(pt2));
+      double area = facet.getArea();
+      if (area == 0) {
+        zeroAreaFacets.add(i);
+        logger.debug(
+            "Facet {} has zero area.  Vertices are {} [{}, {}, {}], {} [{}, {}, {}],  and {} [{}, {}, {}]",
+            i + 1,
+            id0 + 1,
+            pt0[0],
+            pt0[1],
+            pt0[2],
+            id1 + 1,
+            pt1[0],
+            pt1[1],
+            pt1[2],
+            id2 + 1,
+            pt2[0],
+            pt2[1],
+            pt2[2]);
+      }
+    }
+
+    validationMsg = String.format("%d zero area facets found", zeroAreaFacets.size());
+    return zeroAreaFacets;
+  }
+
+  /**
+   * @return statistics on the angle between the facet radial and normal vectors
+   */
+  public DescriptiveStatistics normalStats() {
+    DescriptiveStatistics stats = new DescriptiveStatistics();
+
+    VectorStatistics cStats = new VectorStatistics();
+    VectorStatistics nStats = new VectorStatistics();
+
+    vtkIdList idList = new vtkIdList();
+    double[] pt0 = new double[3];
+    double[] pt1 = new double[3];
+    double[] pt2 = new double[3];
+    for (int i = 0; i < facetCount(); ++i) {
+      polyData.GetCellPoints(i, idList);
+      long id0 = idList.GetId(0);
+      long id1 = idList.GetId(1);
+      long id2 = idList.GetId(2);
+      polyData.GetPoint(id0, pt0);
+      polyData.GetPoint(id1, pt1);
+      polyData.GetPoint(id2, pt2);
+
+      // would be faster to check if id0==id1||id0==id2||id1==id2 but there may be
+      // duplicate vertices
+      TriangularFacet facet =
+          new TriangularFacet(new VectorIJK(pt0), new VectorIJK(pt1), new VectorIJK(pt2));
+      if (facet.getArea() > 0) {
+        stats.addValue(facet.getCenter().getDot(facet.getNormal()));
+        cStats.add(facet.getCenter());
+        nStats.add(facet.getNormal());
+      }
+    }
+
+    validationMsg =
+        String.format(
+            "Using %d non-zero area facets: Mean angle between radial and normal is %f degrees, "
+                + "angle between mean radial and mean normal is %f degrees",
+            stats.getN(),
+            Math.toDegrees(Math.acos(stats.getMean())),
+            Math.toDegrees(Vector3D.angle(cStats.getMean(), nStats.getMean())));
+
+    return stats;
+  }
+
+  private static Options defineOptions() {
+    Options options = TerrasaurTool.defineOptions();
+    options.addOption(
+        Option.builder("obj").required().hasArg().desc("Shape model to validate.").build());
+    options.addOption(
+        Option.builder("logFile")
+            .hasArg()
+            .desc("If present, save screen output to log file.")
+            .build());
+    StringBuilder sb = new StringBuilder();
+    for (StandardLevel l : StandardLevel.values()) sb.append(String.format("%s ", l.name()));
+    options.addOption(
+        Option.builder("logLevel")
+            .hasArg()
+            .desc(
+                "If present, print messages above selected priority.  Valid values are "
+                    + sb.toString().trim()
+                    + ".  Default is INFO.")
+            .build());
+    options.addOption(Option.builder("output").hasArg().desc("Filename for output OBJ.").build());
+    options.addOption(
+        Option.builder("removeDuplicateVertices")
+            .desc("Remove duplicate vertices.  Use with -output to save OBJ.")
+            .build());
+    options.addOption(
+        Option.builder("removeUnreferencedVertices")
+            .desc("Remove unreferenced vertices.  Use with -output to save OBJ.")
+            .build());
+    options.addOption(
+        Option.builder("removeZeroAreaFacets")
+            .desc("Remove facets with zero area.  Use with -output to save OBJ.")
+            .build());
+    options.addOption(
+        Option.builder("cleanup")
+            .desc(
+                "Combines -removeDuplicateVertices, -removeUnreferencedVertices, and -removeZeroAreaFacets.")
+            .build());
+    return options;
+  }
+
+  public static void main(String[] args) throws Exception {
+    TerrasaurTool defaultOBJ = new ValidateOBJ();
+
+    Options options = defineOptions();
+
+    CommandLine cl = defaultOBJ.parseArgs(args, options);
+
+    Map<MessageLabel, String> startupMessages = defaultOBJ.startupMessages(cl);
+    for (MessageLabel ml : startupMessages.keySet())
+      logger.info(String.format("%s %s", ml.label, startupMessages.get(ml)));
+
+    NativeLibraryLoader.loadVtkLibraries();
+    vtkPolyData polyData = PolyDataUtil.loadShapeModel(cl.getOptionValue("obj"));
+
+    if (polyData == null) {
+      logger.error("Cannot read {}, exiting.", cl.getOptionValue("obj"));
+      System.exit(0);
+    }
+
+    ValidateOBJ vo = new ValidateOBJ(polyData);
+
+    logger.log(vo.testFacets() ? Level.INFO : Level.WARN, vo.getMessage());
+    logger.log(vo.testVertices() ? Level.INFO : Level.WARN, vo.getMessage());
+
+    DescriptiveStatistics stats = vo.normalStats();
+    logger.log(stats.getMean() > 0 ? Level.INFO : Level.WARN, vo.getMessage());
+
+    List<Integer> mfv = vo.findMalformedVertices();
+    logger.log(!mfv.isEmpty() ? Level.WARN : Level.INFO, vo.getMessage());
+
+    NavigableMap<Long, List<Long>> dv = vo.findDuplicateVertices();
+    logger.log(!dv.isEmpty() ? Level.WARN : Level.INFO, vo.getMessage());
+
+    List<Long> urv = vo.findUnreferencedVertices();
+    logger.log(!urv.isEmpty() ? Level.WARN : Level.INFO, vo.getMessage());
+
+    List<Integer> zaf = vo.findZeroAreaFacets();
+    logger.log(!zaf.isEmpty() ? Level.WARN : Level.INFO, vo.getMessage());
+
+    final boolean cleanup = cl.hasOption("cleanup");
+    final boolean removeDuplicateVertices = cleanup || cl.hasOption("removeDuplicateVertices");
+    final boolean removeUnreferencedVertices =
+        cleanup || cl.hasOption("removeUnreferencedVertices");
+    final boolean removeZeroAreaFacets = cleanup || cl.hasOption("removeZeroAreaFacets");
+
+    if (removeDuplicateVertices) polyData = PolyDataUtil.removeDuplicatePoints(polyData);
+
+    if (removeUnreferencedVertices) polyData = PolyDataUtil.removeUnreferencedPoints(polyData);
+
+    if (removeZeroAreaFacets) polyData = PolyDataUtil.removeZeroAreaFacets(polyData);
+
+    if (cl.hasOption("output")) {
+      PolyDataUtil.saveShapeModelAsOBJ(polyData, cl.getOptionValue("output"));
+      logger.info(String.format("Wrote OBJ file %s", cl.getOptionValue("output")));
+    }
+  }
+}

src/main/java/terrasaur/apps/package-info.java

@@ -0,0 +1,5 @@
+/**
+ * Applications that can be run on the command line. Running each without arguments gives a usage
+ * summary.
+ */
+package terrasaur.apps;

src/main/java/terrasaur/config/CKFromSumFileConfig.java

@@ -0,0 +1,99 @@
+package terrasaur.config;
+
+import java.util.List;
+import jackfruit.annotations.Comment;
+import jackfruit.annotations.DefaultValue;
+import jackfruit.annotations.Jackfruit;
+
+@Jackfruit
+public interface CKFromSumFileConfig {
+
+  @Comment("""
+      Body fixed frame for the target body.  If blank, use SPICE-defined
+      body fixed frame.  This will be the reference frame unless the J2000
+      parameter is set to true.""")
+  @DefaultValue("IAU_DIMORPHOS")
+  String bodyFrame();
+
+  @Comment("Target body name.")
+  @DefaultValue("DIMORPHOS")
+  String bodyName();
+
+  @Comment("""
+      Extend CK past the last sumFile by this number of seconds.  Default
+      is zero.  Attitude is assumed to be fixed to the value given by the
+      last sumfile.""")
+  @DefaultValue("0")
+  double extend();
+
+  @Comment("""
+      SPC defines the camera X axis to be increasing to the right, Y to
+      be increasing down, and Z to point into the page:
+
+                      Z
+                    /
+                   /
+                  o---> X
+                  |
+                Y |
+                  v
+
+      SPICE may use a different convention.  Use the flip parameters to
+      map the camera axes to SPICE axes.  flipI = J sets camera axis I
+      to SPICE axis J, where I is an axis name (X, Y, or Z), and J is a
+      signed integer number for an axis. The values of J can be (-1, 1,
+      -2, 2, -3, or 3), indicating the (-X, X, -Y, Y, -Z, Z) axis,
+      respectively.  The user must take care to correctly enter the
+      flipI values so that the resulting flipped axes form a
+      well-defined, right-handed coordinate system.
+
+      Examples:
+         (flipX, flipY, flipZ) = ( 1, 2, 3) SPICE and camera frames coincide.
+         (flipX, flipY, flipZ) = ( 2,-1, 3) SPICE frame is camera frame rotated 90 degrees about Z.
+         (flipX, flipY, flipZ) = (-2, 1, 3) SPICE frame is camera frame rotated -90 degrees about Z.
+         (flipX, flipY, flipZ) = ( 1,-2,-3) rotates the image 180 degrees about X.""")
+  @DefaultValue("-1")
+  int flipX();
+
+  @Comment("Map the camera Y axis to a SPICE axis.  See flipX for details.")
+  @DefaultValue("2")
+  int flipY();
+
+  @Comment("Map the camera Z axis to a SPICE axis.  See flipX for details.")
+  @DefaultValue("-3")
+  int flipZ();
+
+  @Comment("""
+      Supply this frame kernel to MSOPCK.  Only needed if the reference frame
+      (set by bodyFrame or J2000) is not built into SPICE""")
+  @DefaultValue("/project/dart/data/SPICE/flight/fk/didymos_system_001.tf")
+  String fk();
+
+  @Comment("Instrument frame name")
+  @DefaultValue("DART_DRACO")
+  String instrumentFrameName();
+
+  @Comment("If set to true, use J2000 as the reference frame")
+  @DefaultValue("true")
+  boolean J2000();
+
+  @Comment("Path to leapseconds kernel.")
+  @DefaultValue("/project/dart/data/SPICE/flight/lsk/naif0012.tls")
+  String lsk();
+
+  @Comment("Path to spacecraft SCLK file.")
+  @DefaultValue("/project/dart/data/SPICE/flight/sclk/dart_sclk_0204.tsc")
+  String sclk();
+
+  @Comment("Name of spacecraft frame.")
+  @DefaultValue("DART_SPACECRAFT")
+  String spacecraftFrame();
+
+  @Comment("""
+      SPICE metakernel to read.  This may be specified more than once
+      for multiple metakernels.""")
+  @DefaultValue("/project/dart/data/SPICE/flight/mk/current.tm")
+  List<String> metakernel();
+
+
+}

src/main/java/terrasaur/config/CommandLineOptions.java

@@ -0,0 +1,236 @@
+package terrasaur.config;
+
+import java.io.File;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Option;
+import org.apache.logging.log4j.Level;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.spi.StandardLevel;
+import terrasaur.utils.saaPlotLib.colorMaps.ColorRamp;
+import terrasaur.utils.Log4j2Configurator;
+
+public class CommandLineOptions {
+
+  private static final Logger logger = LogManager.getLogger();
+
+  /**
+   * Configuration file to load
+   *
+   * @return
+   */
+  public static Option addConfig() {
+    return Option.builder("config").hasArg().required().desc("Configuration file to load").build();
+  }
+
+  /**
+   * Color ramp style. See {@link ColorRamp.TYPE} for valid values.
+   *
+   * @param defaultCRType
+   * @return
+   */
+  public static Option addColorRamp(ColorRamp.TYPE defaultCRType) {
+    StringBuilder sb = new StringBuilder();
+    for (ColorRamp.TYPE t : ColorRamp.TYPE.values()) sb.append(String.format("%s ", t.name()));
+    return Option.builder("colorRamp")
+        .hasArg()
+        .desc(
+            "Color ramp style.  Valid values are "
+                + sb.toString().trim()
+                + ".  Default is "
+                + defaultCRType.name()
+                + ".  Run the ColorMaps application to see all supported color ramps.")
+        .build();
+  }
+
+  /**
+   * Return a color ramp type or the default value.
+   *
+   * @param cl
+   * @param defaultCRType
+   * @return
+   */
+  public static ColorRamp.TYPE getColorRamp(CommandLine cl, ColorRamp.TYPE defaultCRType) {
+    ColorRamp.TYPE crType =
+        cl.hasOption("colorRamp")
+            ? ColorRamp.TYPE.valueOf(cl.getOptionValue("colorRamp").toUpperCase().strip())
+            : defaultCRType;
+    return crType;
+  }
+
+  /**
+   * Hard lower limit for color bar. If the color bar minimum is set dynamically it will not be
+   * lower than hardMin.
+   *
+   * @return
+   */
+  public static Option addHardMin() {
+    return Option.builder("hardMin")
+        .hasArg()
+        .desc(
+            "Hard lower limit for color bar. If the color bar minimum is set dynamically it will not be lower than hardMin.")
+        .build();
+  }
+
+  /**
+   * Hard upper limit for color bar. If the color bar maximum is set dynamically it will not be
+   * higher than hardMax.
+   *
+   * @return
+   */
+  public static Option addHardMax() {
+    return Option.builder("hardMax")
+        .hasArg()
+        .desc(
+            "Hard upper limit for color bar. If the color bar maximum is set dynamically it will not be higher than hardMax.")
+        .build();
+  }
+
+  /**
+   * Get the hard minimum for the colorbar.
+   *
+   * @param cl
+   * @return
+   */
+  public static double getHardMin(CommandLine cl) {
+    return cl.hasOption("hardMin") ? Double.parseDouble(cl.getOptionValue("hardMin")) : Double.NaN;
+  }
+
+  /**
+   * Get the hard maximum for the colorbar.
+   *
+   * @param cl
+   * @return
+   */
+  public static double getHardMax(CommandLine cl) {
+    return cl.hasOption("hardMax") ? Double.parseDouble(cl.getOptionValue("hardMax")) : Double.NaN;
+  }
+
+  /**
+   * If present, save screen output to log file.
+   *
+   * @return
+   */
+  public static Option addLogFile() {
+    return Option.builder("logFile")
+        .hasArg()
+        .desc("If present, save screen output to log file.")
+        .build();
+  }
+
+  /**
+   * If present, print messages above selected priority. See {@link StandardLevel} for valid values.
+   *
+   * @return
+   */
+  public static Option addLogLevel() {
+    StringBuilder sb = new StringBuilder();
+    for (StandardLevel l : StandardLevel.values()) sb.append(String.format("%s ", l.name()));
+    return Option.builder("logLevel")
+        .hasArg()
+        .desc(
+            "If present, print messages above selected priority.  Valid values are "
+                + sb.toString().trim()
+                + ".  Default is INFO.")
+        .build();
+  }
+
+  /**
+   * Set the logging level from the command line option.
+   *
+   * @param cl
+   */
+  public static void setLogLevel(CommandLine cl) {
+    Log4j2Configurator lc = Log4j2Configurator.getInstance();
+    if (cl.hasOption("logLevel"))
+      lc.setLevel(Level.valueOf(cl.getOptionValue("logLevel").toUpperCase().trim()));
+  }
+
+  /**
+   * Log to file named on the command line as well as others
+   *
+   * @param cl
+   * @param others
+   */
+  public static void setLogFile(CommandLine cl, String... others) {
+    Log4j2Configurator lc = Log4j2Configurator.getInstance();
+    if (cl.hasOption("logFile")) lc.addFile(cl.getOptionValue("logFile"));
+    for (String other : others) lc.addFile(other);
+  }
+
+  /**
+   * Maximum number of simultaneous threads to execute.
+   *
+   * @return
+   */
+  public static Option addNumCPU() {
+    return Option.builder("numCPU")
+        .hasArg()
+        .desc(
+            "Maximum number of simultaneous threads to execute.  Default is numCPU value in configuration file.")
+        .build();
+  }
+
+  /**
+   * Directory to place output files. Default is the working directory.
+   *
+   * @return
+   */
+  public static Option addOutputDir() {
+    return Option.builder("outputDir")
+        .hasArg()
+        .desc("Directory to place output files.  Default is the working directory.")
+        .build();
+  }
+
+  /**
+   * Set the output dir from the command line argument.
+   *
+   * @param cl
+   * @return
+   */
+  public static String setOutputDir(CommandLine cl) {
+    String path = cl.hasOption("outputDir") ? cl.getOptionValue("outputDir") : ".";
+    File parent = new File(path);
+    if (!parent.exists()) parent.mkdirs();
+    return path;
+  }
+
+  /**
+   * Minimum value to plot.
+   *
+   * @return
+   */
+  public static Option addPlotMin() {
+    return Option.builder("plotMin").hasArg().desc("Min value to plot.").build();
+  }
+
+  /**
+   * Get plot min from command line argument
+   *
+   * @param cl
+   * @return
+   */
+  public static double getPlotMin(CommandLine cl) {
+    return cl.hasOption("plotMin") ? Double.parseDouble(cl.getOptionValue("plotMin")) : Double.NaN;
+  }
+
+  /**
+   * Maximum value to plot.
+   *
+   * @return
+   */
+  public static Option addPlotMax() {
+    return Option.builder("plotMax").hasArg().desc("Max value to plot.").build();
+  }
+
+  /**
+   * Get plot max from command line argument
+   *
+   * @param cl
+   * @return
+   */
+  public static double getPlotMax(CommandLine cl) {
+    return cl.hasOption("plotMax") ? Double.parseDouble(cl.getOptionValue("plotMax")) : Double.NaN;
+  }
+}

src/main/java/terrasaur/config/ConfigBlock.java

@@ -0,0 +1,55 @@
+package terrasaur.config;
+
+import jackfruit.annotations.Comment;
+import jackfruit.annotations.DefaultValue;
+import jackfruit.annotations.Include;
+import jackfruit.annotations.Jackfruit;
+
+@Jackfruit
+public interface ConfigBlock {
+
+  String introLines =
+      """
+    ###############################################################################
+    # GENERAL PARAMETERS
+    ###############################################################################
+    """;
+
+  @Comment(
+      introLines
+          + """
+      Set the logging level.  Valid values in order of increasing detail:
+            OFF
+            FATAL
+            ERROR
+            WARN
+            INFO
+            DEBUG
+            TRACE
+            ALL
+       See org.apache.logging.log4j.Level.""")
+  @DefaultValue("INFO")
+  String logLevel();
+
+  @Comment(
+      "Format for log messages.  See https://logging.apache.org/log4j/2.x/manual/layouts.html#PatternLayout for more details.")
+  @DefaultValue("%highlight{%d{yyyy-MM-dd HH:mm:ss.SSS} %-5level [%c{1}:%L] %msg%n%throwable}")
+  String logFormat();
+
+  @Comment(
+      """
+      Format for time strings.  Allowed values are:
+      C     (e.g. 1986 APR 12 16:31:09.814)
+      D     (e.g. 1986-102 // 16:31:12.814)
+      J     (e.g. 2446533.18834276)
+      ISOC  (e.g. 1986-04-12T16:31:12.814)
+      ISOD  (e.g. 1986-102T16:31:12.814)""")
+  @DefaultValue("ISOC")
+  String timeFormat();
+
+  @Include
+  MissionBlock missionBlock();
+
+  @Include
+  SPCBlock spcBlock();
+}

src/main/java/terrasaur/config/MissionBlock.java

@@ -0,0 +1,37 @@
+package terrasaur.config;
+
+import jackfruit.annotations.Comment;
+import jackfruit.annotations.DefaultValue;
+import jackfruit.annotations.Jackfruit;
+
+import java.util.List;
+
+@Jackfruit(prefix = "mission")
+public interface MissionBlock {
+
+  String introLines =
+      """
+      ###############################################################################
+      # MISSION PARAMETERS
+      ###############################################################################
+      """;
+
+  @Comment(introLines + "Mission name (e.g. DART)")
+  @DefaultValue("mission")
+  String missionName();
+
+  @Comment(
+      """
+      SPICE metakernel to read.  This may be specified more than once
+      for multiple metakernels (e.g. /project/dart/data/SPICE/flight/mk/current.tm)""")
+  @DefaultValue("metakernel.tm")
+  List<String> metakernel();
+
+  @Comment("Name of spacecraft frame (e.g. DART_SPACECRAFT)")
+  @DefaultValue("SPACECRAFT_FRAME")
+  String spacecraftFrame();
+
+  @Comment("Instrument frame name (e.g. DART_DRACO)")
+  @DefaultValue("INSTRUMENT_FRAME")
+  String instrumentFrameName();
+}

src/main/java/terrasaur/config/SPCBlock.java

@@ -0,0 +1,54 @@
+package terrasaur.config;
+
+import jackfruit.annotations.Comment;
+import jackfruit.annotations.DefaultValue;
+import jackfruit.annotations.Jackfruit;
+
+@Jackfruit(prefix = "spc")
+public interface SPCBlock {
+
+      String introLines =
+            """
+      ###############################################################################
+      # SPC PARAMETERS
+      ###############################################################################
+      """;
+
+    @Comment(introLines + """
+      SPC defines the camera X axis to be increasing to the right, Y to
+      be increasing down, and Z to point into the page:
+
+                      Z
+                    /
+                   /
+                  o---> X
+                  |
+                Y |
+                  v
+
+      SPICE may use a different convention.  Use the flip parameters to
+      map the camera axes to SPICE axes.  flipI = J sets camera axis I
+      to SPICE axis J, where I is an axis name (X, Y, or Z), and J is a
+      signed integer number for an axis. The values of J can be (-1, 1,
+      -2, 2, -3, or 3), indicating the (-X, X, -Y, Y, -Z, Z) axis,
+      respectively.  The user must take care to correctly enter the
+      flipI values so that the resulting flipped axes form a
+      well-defined, right-handed coordinate system.
+
+      Examples:
+         (flipX, flipY, flipZ) = ( 1, 2, 3) SPICE and camera frames coincide.
+         (flipX, flipY, flipZ) = ( 2,-1, 3) SPICE frame is camera frame rotated 90 degrees about Z.
+         (flipX, flipY, flipZ) = (-2, 1, 3) SPICE frame is camera frame rotated -90 degrees about Z.
+         (flipX, flipY, flipZ) = ( 1,-2,-3) rotates the image 180 degrees about X.""")
+    @DefaultValue("-1")
+    int flipX();
+
+    @Comment("Map the camera Y axis to a SPICE axis.  See flipX for details.")
+    @DefaultValue("2")
+    int flipY();
+
+    @Comment("Map the camera Z axis to a SPICE axis.  See flipX for details.")
+    @DefaultValue("-3")
+    int flipZ();
+
+}

src/main/java/terrasaur/config/TerrasaurConfig.java

@@ -0,0 +1,89 @@
+package terrasaur.config;
+
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.io.StringWriter;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.time.Instant;
+import java.time.ZoneOffset;
+import java.time.format.DateTimeFormatter;
+import java.util.Locale;
+import org.apache.commons.configuration2.PropertiesConfiguration;
+import org.apache.commons.configuration2.PropertiesConfigurationLayout;
+import org.apache.commons.configuration2.builder.fluent.Configurations;
+import org.apache.commons.configuration2.ex.ConfigurationException;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import terrasaur.utils.AppVersion;
+
+public class TerrasaurConfig {
+
+  private static final Logger logger = LogManager.getLogger();
+
+  private static TerrasaurConfig instance = null;
+
+  private TerrasaurConfig() {}
+
+  private ConfigBlock configBlock;
+
+  public static ConfigBlock getConfig() {
+    if (instance == null) {
+      logger.error("Configuration has not been loaded!  Returning null.");
+      return null;
+    }
+    return instance.configBlock;
+  }
+
+  public static ConfigBlock getTemplate() {
+    if (instance == null) {
+      instance = new TerrasaurConfig();
+      ConfigBlockFactory factory = new ConfigBlockFactory();
+      instance.configBlock = factory.getTemplate();
+    }
+    return instance.configBlock;
+  }
+
+  public static ConfigBlock load(Path filename) {
+    if (!Files.exists(filename)) {
+      System.err.println("Cannot load configuration file " + filename);
+      Thread.dumpStack();
+      System.exit(1);
+    }
+    if (instance == null) {
+      instance = new TerrasaurConfig();
+
+      try {
+        PropertiesConfiguration config = new Configurations().properties(filename.toFile());
+        instance.configBlock = new ConfigBlockFactory().fromConfig(config);
+      } catch (ConfigurationException e) {
+        e.printStackTrace();
+      }
+    }
+    return instance.configBlock;
+  }
+
+  @Override
+  public String toString() {
+    StringWriter string = new StringWriter();
+    try (PrintWriter pw = new PrintWriter(string)) {
+      PropertiesConfiguration config = new ConfigBlockFactory().toConfig(instance.configBlock);
+      PropertiesConfigurationLayout layout = config.getLayout();
+
+      String now =
+          DateTimeFormatter.ofPattern("yyyy-MM-dd HH:mm:ss")
+              .withLocale(Locale.getDefault())
+              .withZone(ZoneOffset.UTC)
+              .format(Instant.now());
+      layout.setHeaderComment(
+          String.format(
+              "Configuration file for %s\nCreated %s UTC", AppVersion.getVersionString(), now));
+
+      config.write(pw);
+    } catch (ConfigurationException | IOException e) {
+      e.printStackTrace();
+    }
+    return string.toString();
+  }
+
+}

src/main/java/terrasaur/enums/FORMATS.java

@@ -0,0 +1,60 @@
+package terrasaur.enums;
+
+import org.apache.commons.io.FilenameUtils;
+
+public enum FORMATS {
+
+  ASCII(true), BIN3(true), BIN4(true), BIN7(true), FITS(false), ICQ(false), OBJ(false), PLT(
+      false), PLY(false), VTK(false);
+
+  /** True if this format contains no facet information */
+  public boolean pointsOnly;
+
+  private FORMATS(boolean pointsOnly) {
+    this.pointsOnly = pointsOnly;
+  }
+
+  /**
+   * Guess the format from the (case-insensitive) filename extension.
+   * <p>
+   * ASCII: ascii, txt, xyz
+   * <p>
+   * BINARY: binary, bin
+   * <p>
+   * FITS: fits, fit
+   * <p>
+   * L2: l2, dat
+   * <p>
+   * OBJ: obj
+   * <p>
+   * PLT: plt
+   * <p>
+   * PLY: ply
+   * <p>
+   * VTK: vtk
+   * 
+   * @param filename
+   * @return matched format type, or null if a match is not found
+   */
+  public static FORMATS formatFromExtension(String filename) {
+    String extension = FilenameUtils.getExtension(filename);
+    for (FORMATS f : FORMATS.values()) {
+      if (f.name().equalsIgnoreCase(extension)) {
+        return f;
+      }
+    }
+
+    switch (extension.toUpperCase()) {
+      case "TXT":
+      case "XYZ":
+        return FORMATS.ASCII;
+      case "BIN":
+        return FORMATS.BIN3;
+      case "FIT":
+        return FORMATS.FITS;
+    }
+
+    return null;
+  }
+
+}

src/main/java/terrasaur/enums/FitsHeaderType.java

@@ -0,0 +1,33 @@
+package terrasaur.enums;
+
+/**
+ * Enums for a given fits header format. This is used to keep fits headers for the different types
+ * separately configurable.
+ * 
+ * @author espirrc1
+ *
+ */
+public enum FitsHeaderType {
+
+  ANCIGLOBALGENERIC, ANCILOCALGENERIC, ANCIGLOBALALTWG, ANCIG_FACETRELATION_ALTWG, ANCILOCALALTWG, DTMGLOBALALTWG, DTMLOCALALTWG, DTMGLOBALGENERIC, DTMLOCALGENERIC, NFTMLN;
+
+  public static boolean isGLobal(FitsHeaderType hdrType) {
+
+    boolean globalProduct;
+
+    switch (hdrType) {
+
+      case ANCIGLOBALALTWG:
+      case ANCIGLOBALGENERIC:
+      case DTMGLOBALALTWG:
+      case DTMGLOBALGENERIC:
+        globalProduct = true;
+        break;
+
+      default:
+        globalProduct = false;
+    }
+
+    return globalProduct;
+  }
+}

src/main/java/terrasaur/enums/PlaneInfo.java

@@ -0,0 +1,156 @@
+package terrasaur.enums;
+
+import java.util.ArrayList;
+import java.util.EnumSet;
+import java.util.List;
+import nom.tam.fits.HeaderCard;
+import nom.tam.fits.HeaderCardException;
+
+/**
+ * Enumeration containing the values and comments to use for FITS tags describing data stored in
+ * FITS data cubes. The enumeration name references the type of data stored in a given plane. This
+ * way the user can choose their own value for the FITS keyword (i.e. "PLANE1" or "PLANE10").
+ * 
+ * @author espirrc1
+ * 
+ */
+public enum PlaneInfo {
+
+  //@formatter:off
+  LAT("Latitude of vertices", "[deg]", "deg"),
+  LON("Longitude of vertices", "[deg]", "deg"),
+  RAD("Radius of vertices", "[km]", "km"),
+  X("X coordinate of vertices", "[km]", "km"),
+  Y("Y coordinate of vertices", "[km]", "km"),
+  Z("Z coordinate of vertices", "[km]", "km"),
+  NORM_VECTOR_X("Normal vector X", null, null),
+  NORM_VECTOR_Y("Normal vector Y", null, null),
+  NORM_VECTOR_Z("Normal vector Z", null, null),
+  GRAV_VECTOR_X("Gravity vector X", "[m/s^2]", "m/s**2"),
+  GRAV_VECTOR_Y("Gravity vector Y", "[m/s^2]", "m/s**2"),
+  GRAV_VECTOR_Z("Gravity vector Z", "[m/s^2]", "m/s**2"),
+  GRAV_MAG("Gravitational magnitude", "[m/s^2]", "m/s**2"),
+  GRAV_POT("Gravitational potential", "[J/kg]", "J/kg"),
+  ELEV("Elevation", "[m]", "m"),
+  AREA("Area", "[km^2]", "km**2"),
+
+  // no longer needed! same as HEIGHT!
+  // ELEV_NORM("Elevation relative to normal plane", "[m]", "m"),
+  SLOPE("Slope", "[deg]", "deg"),
+  SHADE("Shaded relief", null, null),
+  TILT("Facet tilt", "[deg]", "deg"),
+  TILT_DIRECTION("Facet tilt direction", "[deg]", "deg"),
+  TILT_AVERAGE("Mean tilt", "[deg]", "deg"),
+  TILT_VARIATION("Tilt variation", "[deg]", "deg"),
+  TILT_AVERAGE_DIRECTION("Mean tilt direction", "[deg]", "deg"),
+  TILT_DIRECTION_VARIATION("Tilt direction variation", "[deg]", "deg"),
+  TILT_RELATIVE("Relative tilt", "[deg]", "deg"),
+  TILT_RELATIVE_DIRECTION("Relative tilt direction", "[deg]", "deg"),
+  TILT_UNCERTAINTY("Tilt Uncertainty", "[deg]", "deg"),
+  FACETRAD("Facet radius", "[m]", "m"),
+  HEIGHT("Height relative to normal plane", "[km]", "km"),
+  RELATIVE_HEIGHT("Max relative height", "[km]", "km"),
+  ALBEDO("Relative albedo", null, null),
+  INTENSITY("Return Intensity", null, null),
+  SIGMA("Sigma", null, null),
+  QUALITY("Quality", null, null),
+  SHADED("Shaded relief", null, null),
+  NUMPOINTS("Number of OLA points used", null, null),
+  HEIGHT_RESIDUAL("Mean of residual between points and fitted height", "[km]", "km"),
+  HEIGHT_STDDEV("Std deviation of residual between points and fitted height", "[km]", "km"),
+  HAZARD("Hazard", "1 indicates a hazard to the spacecraft", null);
+  //@formatter:on
+
+  private String keyValue; // value associated with FITS keyword
+  private String comment; // comment associated with FITS keyword
+  private String units; // units associated with the plane. Usually in PDS4 nomenclature
+
+  PlaneInfo(String keyVal, String comment, String units) {
+    this.keyValue = keyVal;
+    this.comment = comment;
+    this.units = units;
+  }
+
+  public String value() {
+    return keyValue;
+  }
+
+  public String comment() {
+    return comment;
+  }
+
+  public String units() {
+    return units;
+  }
+
+  /**
+   * Try to parse the enum from the given Keyval string. Needs to match exactly (but case
+   * insensitive)!
+   * 
+   * @param keyVal
+   * @return
+   */
+  public static PlaneInfo keyVal2Plane(String keyVal) {
+    for (PlaneInfo planeName : values()) {
+      if ((planeName.value() != null) && (planeName.value().equalsIgnoreCase(keyVal))) {
+        return planeName;
+      }
+    }
+    return null;
+  }
+
+  public static PlaneInfo planeFromString(String plane) {
+    for (PlaneInfo planeName : values()) {
+      if (planeName.toString().equals(plane)) {
+        return planeName;
+      }
+    }
+    return null;
+  }
+
+  /*
+   * Create enumeration set for the first 6 planes. These are the initial planes created from the
+   * Osiris Rex netCDF file.
+   */
+  public static final EnumSet<PlaneInfo> first6HTags = EnumSet.range(PlaneInfo.LAT, PlaneInfo.Z);
+
+  public static List<PlaneInfo> coreTiltPlanes() {
+
+    List<PlaneInfo> coreTilts = new ArrayList<PlaneInfo>();
+    coreTilts.add(PlaneInfo.TILT_AVERAGE);
+    coreTilts.add(PlaneInfo.TILT_VARIATION);
+    coreTilts.add(PlaneInfo.TILT_AVERAGE_DIRECTION);
+    coreTilts.add(PlaneInfo.TILT_DIRECTION_VARIATION);
+    coreTilts.add(PlaneInfo.TILT_RELATIVE);
+    coreTilts.add(PlaneInfo.TILT_RELATIVE_DIRECTION);
+    coreTilts.add(PlaneInfo.RELATIVE_HEIGHT);
+
+    return coreTilts;
+
+  }
+
+  /**
+   * Convert List<PlaneInfo> to List<HeaderCard> where each HeaderCard in List follows the
+   * convention: for each "thisPlane" in List<PlaneInfo> HeaderCard = new HeaderCard("PLANE" + cc,
+   * thisPlane.value(), thisPlane.comment()) The order in List<HeaderCard> follows the order in
+   * List<PlaneInfo>
+   * 
+   * @param planeList
+   * @return
+   * @throws HeaderCardException
+   */
+  public static List<HeaderCard> planesToHeaderCard(List<PlaneInfo> planeList)
+      throws HeaderCardException {
+    List<HeaderCard> planeHeaders = new ArrayList<HeaderCard>();
+    String plane = "PLANE";
+    int cc = 1;
+    for (PlaneInfo thisPlane : planeList) {
+
+      planeHeaders.add(new HeaderCard(plane + cc, thisPlane.value(), thisPlane.comment()));
+      cc++;
+    }
+    return planeHeaders;
+
+  }
+
+}

src/main/java/terrasaur/enums/SigmaFileType.java

@@ -0,0 +1,116 @@
+package terrasaur.enums;
+
+import com.google.common.base.Strings;
+
+/**
+ * Enum for defining the types of sigma files that can be loaded and utilized by the Pipeline. This
+ * allows the pipeline to load and parse different formats of sigma files.
+ * 
+ * @author espirrc1
+ *
+ */
+public enum SigmaFileType {
+
+  SPCSIGMA {
+
+    @Override
+    public String commentSymbol() {
+      return "";
+    }
+
+    @Override
+    public String stringArg() {
+      return "spc";
+    }
+
+    @Override
+    public int sigmaCol() {
+      return 3;
+    }
+  },
+
+  ERRORFROMSQLSIGMA {
+
+    @Override
+    public String commentSymbol() {
+      return "#";
+    }
+
+    @Override
+    public String stringArg() {
+      return "errorfromsql";
+    }
+
+    // should be the Standard Deviation column in ErrorFromSQL file.
+    public int sigmaCol() {
+      return 8;
+    }
+  },
+
+  NOMATCH {
+
+    @Override
+    public String commentSymbol() {
+      return "NAN";
+    }
+
+    @Override
+    public String stringArg() {
+      return "NAN";
+    }
+
+    public int sigmaCol() {
+      return -1;
+    }
+  };
+
+  // returns the symbol that is used to denote comment lines
+  public abstract String commentSymbol();
+
+  // input argument to match
+  public abstract String stringArg();
+
+  // column number where sigma values are stored
+  public abstract int sigmaCol();
+
+  public static SigmaFileType getFileType(String sigmaFileType) {
+
+    if (!Strings.isNullOrEmpty(sigmaFileType)) {
+      for (SigmaFileType thisType : values()) {
+
+        if (sigmaFileType.toLowerCase().equals(thisType.stringArg())) {
+
+          return thisType;
+        }
+      }
+    }
+    return NOMATCH;
+  }
+
+  /**
+   * Return the SigmaFileType associated with the SrcProductType.
+   * 
+   * @param srcType
+   * @return
+   */
+  public static SigmaFileType sigmaTypeFromSrcType(SrcProductType srcType) {
+    SigmaFileType sigmaType = SigmaFileType.NOMATCH;
+    switch (srcType) {
+
+      case SPC:
+        sigmaType = SigmaFileType.SPCSIGMA;
+        break;
+
+      case OLA:
+        sigmaType = SigmaFileType.ERRORFROMSQLSIGMA;
+        break;
+
+      default:
+        sigmaType = SigmaFileType.NOMATCH;
+        break;
+
+    }
+
+    return sigmaType;
+  }
+}

src/main/java/terrasaur/enums/SrcProductType.java

@@ -0,0 +1,93 @@
+package terrasaur.enums;
+
+/**
+ * Enumeration storing the source product type: the product type of the source data used in creation
+ * of an ALTWG product.
+ * 
+ * @author espirrc1
+ *
+ */
+public enum SrcProductType {
+
+  SFM {
+
+    @Override
+    public String getAltwgFrag() {
+      return "sfm";
+    }
+
+  },
+
+  SPC {
+    @Override
+    public String getAltwgFrag() {
+      return "spc";
+    }
+  },
+
+  // OLA Altimetry
+  OLA {
+    @Override
+    public String getAltwgFrag() {
+      return "alt";
+    }
+  },
+
+  // SPC-OLA
+  SPO {
+    @Override
+    public String getAltwgFrag() {
+      return "spo";
+    }
+  },
+
+  TRUTH {
+    @Override
+    public String getAltwgFrag() {
+      return "tru";
+    }
+
+  },
+
+  UNKNOWN {
+    @Override
+    public String getAltwgFrag() {
+      return "unk";
+    }
+  };
+
+  public static SrcProductType getType(String value) {
+    value = value.toUpperCase();
+    for (SrcProductType srcType : values()) {
+      if (srcType.toString().equals(value)) {
+        return srcType;
+      }
+    }
+    return UNKNOWN;
+  }
+
+  /**
+   * Returns the string fragment associated with the source product type. Follows the ALTWG naming
+   * convention.
+   * 
+   * @return
+   */
+  public abstract String getAltwgFrag();
+
+  /**
+   * Return the SrcProductType whose getAltwgFrag() string matches the stringFrag. Return UNKNOWN if
+   * a match is not found.
+   * 
+   * @param stringFrag
+   * @return
+   */
+  public static SrcProductType fromAltwgFrag(String stringFrag) {
+
+    for (SrcProductType prodType : SrcProductType.values()) {
+      if (prodType.getAltwgFrag().equals(stringFrag))
+        return prodType;
+    }
+    return UNKNOWN;
+  }
+
+}

src/main/java/terrasaur/fits/AltPipelnEnum.java

@@ -0,0 +1,302 @@
+package terrasaur.fits;
+
+import java.util.EnumSet;
+import java.util.Map;
+
+public enum AltPipelnEnum {
+
+  // settings enums. Used to determine type of product to create.
+  ANCIGLOBAL,
+
+  // optional: tells code to skip generation of products for highest res shape model
+  SKIPORIGINALSHP,
+
+  // controls whether or not certain global products get created.
+  // REQUIRED TO BE IN CONFIGFILE:
+  DOGLOBALSHAPE, OBJTOFITS, ADDOBJCOMMENTS, GLOBALRES0, DUMBERVALUES, DOGRAVGLOBAL, DOGLOBALGRAV_ANCI, DOGLOBALTILT_ANCI, DOGLOBALMISC_ANCI, DOGLOBALTILT,
+
+  // controls number of slots per job to use when running global distributed gravity
+  // in grid engine mode. Does not apply if running in local parallel mode
+  GLOBALGRAVSLOTS,
+
+  // controls number of slots per job to use when running local distributed gravity
+  // in grid engine mode. Does not apply if running in local parallel mode
+  LOCALGRAVSLOTS,
+
+  // full path to SPICE metakernel to use when generating DSK products
+  DSKERNEL,
+
+  // enable/disable the creation of global and local DSK files
+  DOGLOBALDSK, DOLOCALDSK,
+
+  // global tilt semi-major axis in km. Now a required variable
+  GTILTMAJAXIS,
+
+  // settings for every local product generated by the pipeline
+  USEOLDMAPLETS, DODTMFITSOBJ, DOGRAVLOCAL, GENLOCALGRAV, DOLOCALTILT, DOLOCAL_GRAVANCI, DOLOCAL_TILTANCI, DOLOCAL_MISCANCI,
+
+  // controls whether to use average gravitational potential for global and local gravity
+  // calculations. =0 use minimum reference potential, =1 use average reference potential
+  AVGGRAVPOTGLOBAL, AVGGRAVPOTLOCAL,
+
+  // controls RunBigMap.
+  // integrate slope to height required. Defaults to "n" if this enum does not exist in config file.
+  // otherwise will evaluate value. 0="n", 1="y"
+  INTSLOPE,
+
+  // use grotesque model in RunBigMap. Defaults to not using it if this enum does not exist in
+  // config file
+  // otherwise will evaluate value. 0="do not use grotesque model", 1="do use grotesque model"
+  USEGROTESQUE,
+
+  // controls the source data, product destination, naming convention,
+  // and process flow.
+  DATASOURCE, REPORTTYPE, INDATADIR, OUTPUTDIR, PDSNAMING, RENAMEGLOBALOBJ, USEBIGMAPS, DOREPORT,
+
+  // shape model density and rotation rate are now required variables. This way we can easily spot
+  // what we are using
+  // as defaults.
+  SMDENSITY, SMRRATE,
+
+  // stores type of naming convention. Ex. AltProduct, AltNFTMLN, DartProduct.
+  NAMINGCONVENTION,
+
+  // set values that cannot be derived from data.
+  REPORTBASENAME, VERSION,
+
+  // everything after this is not a required keyword
+
+  // (Optional) controls whether there is an external body that needs to be accounted for when
+  // running gravity code
+  // the values should be a csv string with no spaces. THe values are: mass(kg),x,y,z where x,y,z
+  // are the body
+  // fixed coordinates in km.
+  // e.g. 521951167,1.19,0,0
+  EXTERNALBODY,
+
+  // (Optional). If the keyword exists and value is 1 then no GLOBAL DTMs are assumed to be created.
+  // for example, in the DART Derived Product set we are not creating g_*dtm*.fits files
+  NOGLOBALDTM,
+  
+  // (Optional). If the keyword exists then evaluate the shapes to process by parsing the 
+  // comma-separated values. Ex.values are 0,1,2 then pipeline will assume it has to 
+  // process shape0, shape1, shape2. The pipeline will also disregard the values in 
+  // DUMBERVALUES that otherwise determine how many shape files to process.
+  SHAPE2PROC,
+  
+  // (optional) controls whether or not STL files get generated. If these do not exist in the
+  // pipeConfig file then they will NOT
+  // get generated!
+  GLOBALSTL, LOCALSTL,
+
+  // keywords for local products
+  //
+  // MAPSmallerSZ: resize local DTMs to a different half size. For pipeline we may want to generate
+  // DTMs at halfsize + tilt radius then resize the DTMs to halfsize in order to have tilts
+  // evaluated with the full range of points at the edges.
+  //
+  // MAPFILE: contains pointer to map centers file (optional). Used by TileShapeModelWithBigmaps.
+  // defaults to auto-generated tiles if this is not specified.
+  // allow for pointers to different files for 30cm and 10cm map products.
+  DOLOCALMAP, MAPDIR, MAPSCALE, MAPHALFSZ, REPORT, MAPSmallerSZ, MAPFILE, ISTAGSITE, LTILTMAJAXIS, LTILTMINAXIS, LTILTPA, MAXSCALE,
+
+  // settings for local tag sites. Note TAGSFILE is not optional.
+  // it contains the tagsite name and lat,lon of tag site tile center
+  TAGDIR, TAGSCALE, TAGHALFSZ, TAGSFILE, REPORTTAG,
+
+  // pointer to OLA database. only required if DATASOURCE is OLA
+  OLADBPATH,
+
+  // force sigma files to all be NaN
+  FORCESIGMA_NAN,
+
+  // global sigma scale factor
+  SIGMA_SCALEFACTOR,
+
+  // local sigma scale factor
+  LOCAL_SIGMA_SCALEFACTOR,
+
+  // SIGMA file type. No longer tied to DataSource!
+  SIGMAFILE_TYPE,
+
+  // force the Report page to be HTML. Default is created at PHP
+  REPORTASHTML,
+
+  /*
+   * The following are used to change default values used by the pipeline these are the shape model
+   * density, rotation rate, gravitational algorithm, gravitational constant, global average
+   * reference potential, local average reference potential. Added values defining the tilt ellipse
+   * to use when evaluating tilts. Note the different enums for global versus local tilt ellipse
+   * parameters. The pipeline will use default values for these enums if they are not defined in the
+   * pipeline configuration file.
+   */
+  GALGORITHM, GRAVCONST, GTILTMINAXIS, GTILTPA, MASSUNCERT, VSEARCHRAD_PCTGSD, FSEARCHRAD_PCTGSD, PXPERDEG,
+
+  // The following are options to subvert normal pipeline operations or to configure pipeline for
+  // other missions
+
+
+  // global objs are supplied at all resolutions as the starting point.
+  // This means we can skip ICQ2PLT, ICQDUMBER, and PLT2OBJ calls
+  OBJASINPUT,
+
+  // gzip the obj files to save space
+  DOGZIP,
+
+  // specify the queue to use in the GRID ENGINE
+  GRIDQUEUE,
+
+  // default mode for local product creation is to parallelize DistributedGravity
+  // for each tile. Then processing for each job is done in local mode.
+  // set this flag to 1 to submit DistributedGravity for each tile sequentially,
+  // and have each job spawn to the grid engine
+  DISTGRAVITY_USEGRID,
+
+  // override grid engine mode and use local parallel mode with the specified number of cores
+  LOCALPARALLEL,
+
+  // when creating local gravity products skip creation of gravity files that already exist
+  USEOLDGRAV,
+
+  // override ancillary fits table default setting (binary). Set to ASCII instead
+  ANCITXTTABLE,
+
+  // contains pointer to fits header config file (optional)
+  FITSCONFIGFILE,
+
+  // contains pointer to OBJ comments header file (optional). Will only
+  // add commentes if ADDOBJCOMMENTS flag is set.
+  OBJCOMHEADER,
+
+  // identifies whether there are poisson reconstruct data products to include in the webpage report
+  LOCALPOISSON, GLOBALPOISSON;
+
+  /*
+   * The following enumerations are required to exist in the altwg pipeline config file.
+   */
+  public static final EnumSet<AltPipelnEnum> reqTags = EnumSet.range(DOGLOBALSHAPE, VERSION);
+
+  /*
+   * The following enumerations do not have to be present in the config file. But, if they are not
+   * then the pipeline should use the default values associated with the enums.
+   */
+  public static final EnumSet<AltPipelnEnum> overrideTags = EnumSet.range(SMDENSITY, GTILTPA);
+
+  public static String mapToString(Map<AltPipelnEnum, String> pipeConfig) {
+    StringBuilder sb = new StringBuilder();
+    for (Map.Entry<AltPipelnEnum, String> entry : pipeConfig.entrySet()) {
+      sb.append(String.format("%s:%s\n", entry.getKey().toString(), entry.getValue()));
+    }
+
+    return sb.toString();
+  }
+
+  public static AltPipelnEnum fromString(String textString) {
+    for (AltPipelnEnum anciType : AltPipelnEnum.values()) {
+      if (anciType.toString().equals(textString))
+        return anciType;
+    }
+    return null;
+  }
+
+  /**
+   * Convenience method for evaluating configuration parameter where the value indicates whether or
+   * not the parameter is true or false via an integer value. Assumes 0 or less = false, 1 or more =
+   * true. If the key does not exist then return false.
+   * 
+   * @param pipeConfig
+   * @param key
+   * @return
+   */
+  public static boolean isTrue(Map<AltPipelnEnum, String> pipeConfig, AltPipelnEnum key) {
+    boolean returnFlag = false;
+    int parsedVal = 0;
+    if (pipeConfig.containsKey(key)) {
+      try {
+        parsedVal = Integer.valueOf(pipeConfig.get(key));
+      } catch (NumberFormatException e) {
+        System.err.println("ERROR! Could not parse integer value for pipeConfig line:");
+        System.err.println(key.toString() + "," + pipeConfig.get(key));
+        System.err.println("Stopping with error!");
+        System.exit(1);
+      }
+
+      if (parsedVal > 0) {
+        returnFlag = true;
+      }
+
+    }
+    return returnFlag;
+  }
+
+  /**
+   * Checks to see whether key exists. If so then return value mapped to key. Otherwise return empty
+   * string.
+   * 
+   * @param pipeConfig
+   * @param key
+   * @return
+   */
+  public static String checkAndGet(Map<AltPipelnEnum, String> pipeConfig, AltPipelnEnum key) {
+    String value = "";
+    if (pipeConfig.containsKey(key)) {
+      value = pipeConfig.get(key);
+    }
+    return value;
+  }
+
+  /*
+   * Some enums will have a default value, e.g. the ones in the overrideTags EnumSet. It is easier
+   * to keep them as string values then convert them to other primitives as needed. Sometimes other
+   * executables will be called w/ the default values, so it is better to keep them as strings to
+   * avoid double conversion.
+   */
+  public static String getDefault(AltPipelnEnum thisEnum) {
+
+    if (overrideTags.contains(thisEnum)) {
+
+      switch (thisEnum) {
+
+        // shape model density and rotation rate must now be explicitly defined in the configuration
+        // file!
+        // case SMDENSITY:
+        // return "1.186";
+        //
+        // case SMRRATE:
+        // return "0.00040626";
+
+        case GALGORITHM:
+          return "werner";
+
+        case GRAVCONST:
+          return "6.67408e-11";
+
+        case LTILTMAJAXIS:
+          return "0.0125";
+
+        case GTILTMINAXIS:
+          return "0.0125";
+
+        case GTILTPA:
+        case LTILTPA:
+          return "0.0";
+
+        case MASSUNCERT:
+          return "0.01";
+
+        case VSEARCHRAD_PCTGSD:
+          return "0.25";
+
+        case FSEARCHRAD_PCTGSD:
+          return "0.5";
+
+        default:
+          return "NA";
+
+      }
+    }
+    return "NA";
+
+  };
+
+}

src/main/java/terrasaur/fits/AltwgAnciGlobal.java

@@ -0,0 +1,60 @@
+package terrasaur.fits;
+
+import java.util.ArrayList;
+import java.util.List;
+import nom.tam.fits.HeaderCard;
+import nom.tam.fits.HeaderCardException;
+import terrasaur.enums.FitsHeaderType;
+
+public class AltwgAnciGlobal extends AnciTableFits implements AnciFitsHeader {
+
+  public AltwgAnciGlobal(FitsHdr fitsHeader) {
+    super(fitsHeader, FitsHeaderType.ANCIGLOBALALTWG);
+  }
+
+  // methods below override the concrete methods in AnciTableFits abstract class or
+  // are specific to this class
+
+  /**
+   * Create fits header as a list of HeaderCard. List contains the keywords in the order of
+   * appearance in the ALTWG fits header. Overrides default implementation in AnciTableFits.
+   */
+  @Override
+  public List<HeaderCard> createFitsHeader() throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+
+    headers.addAll(getHeaderInfo("header information"));
+    headers.addAll(getMissionInfo("mission information"));
+    headers.addAll(getIDInfo("identification info"));
+    headers.addAll(getMapDataSrc("shape data source"));
+    headers.addAll(getProcInfo("processing information"));
+    headers.addAll(getMapInfo("map specific information"));
+    headers.addAll(getSpatialInfo("summary spatial information"));
+    headers.addAll(getSpecificInfo("product specific"));
+
+    return headers;
+
+  }
+
+  /**
+   * Contains OREX-SPOC specific keywords.
+   */
+  @Override
+  public List<HeaderCard> getIDInfo(String comment) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    if (comment.length() > 0) {
+      headers.add(new HeaderCard(COMMENT, comment, false));
+    }
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.SPOC_ID));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.SDPAREA));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.SDPDESC));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.MPHASE));
+
+    return headers;
+
+  }
+
+
+}

src/main/java/terrasaur/fits/AltwgAnciGlobalFacetRelation.java

@@ -0,0 +1,74 @@
+package terrasaur.fits;
+
+import java.util.ArrayList;
+import java.util.List;
+import nom.tam.fits.HeaderCard;
+import nom.tam.fits.HeaderCardException;
+import terrasaur.enums.FitsHeaderType;
+
+public class AltwgAnciGlobalFacetRelation extends AnciTableFits implements AnciFitsHeader {
+
+  public AltwgAnciGlobalFacetRelation(FitsHdr fitsHeader) {
+
+    super(fitsHeader, FitsHeaderType.ANCIG_FACETRELATION_ALTWG);
+  }
+
+  // methods below override the concrete methods in AnciTableFits abstract class or
+  // are specific to this class
+
+  /**
+   * Create fits header as a list of HeaderCard. List contains the keywords in the order of
+   * appearance in the ALTWG fits header. Overrides default implementation in AnciTableFits.
+   */
+  @Override
+  public List<HeaderCard> createFitsHeader() throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+
+    headers.addAll(getHeaderInfo("header information"));
+    headers.addAll(getMissionInfo("mission information"));
+    headers.addAll(getIDInfo("identification info"));
+    headers.addAll(getMapDataSrc("shape data source"));
+    headers.addAll(getProcInfo("processing information"));
+    headers.addAll(getMapInfo("map specific information"));
+    headers.addAll(getSpatialInfo("summary spatial information"));
+    headers.addAll(getSpecificInfo("product specific"));
+
+    return headers;
+
+  }
+
+  /**
+   * Return the HeaderCards associated with a specific product. By default we use the ALTWG specific
+   * product keywords
+   * 
+   * @param comment
+   * @return
+   * @throws HeaderCardException
+   */
+  @Override
+  public List<HeaderCard> getSpecificInfo(String comment) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    if (comment.length() > 0) {
+      headers.add(new HeaderCard(COMMENT, comment, false));
+    }
+
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.OBJINDX));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.GSDINDX));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.GSDINDXI));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.SIGMA));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.SIG_DEF));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.DQUAL_1));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.DQUAL_2));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.DSIG_DEF));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.DENSITY));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.ROT_RATE));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.REF_POT));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.TILT_MAJ));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.TILT_MIN));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.TILT_PA));
+
+    return headers;
+  }
+}

src/main/java/terrasaur/fits/AltwgAnciLocal.java

@@ -0,0 +1,60 @@
+package terrasaur.fits;
+
+import java.util.ArrayList;
+import java.util.List;
+import nom.tam.fits.HeaderCard;
+import nom.tam.fits.HeaderCardException;
+import terrasaur.enums.FitsHeaderType;
+
+public class AltwgAnciLocal extends AnciTableFits implements AnciFitsHeader {
+
+  public AltwgAnciLocal(FitsHdr fitsHeader) {
+    super(fitsHeader, FitsHeaderType.ANCILOCALALTWG);
+  }
+
+  // methods below override the concrete methods in AnciTableFits abstract class or
+  // are specific to this class
+
+  /**
+   * Create fits header as a list of HeaderCard. List contains the keywords in the order of
+   * appearance in the ALTWG fits header. Overrides default implementation in AnciTableFits.
+   */
+  @Override
+  public List<HeaderCard> createFitsHeader() throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+
+    headers.addAll(getHeaderInfo("header information"));
+    headers.addAll(getMissionInfo("mission information"));
+    headers.addAll(getIDInfo("identification info"));
+    headers.addAll(getMapDataSrc("shape data source"));
+    headers.addAll(getProcInfo("processing information"));
+    headers.addAll(getMapInfo("map specific information"));
+    headers.addAll(getSpatialInfo("summary spatial information"));
+    headers.addAll(getSpecificInfo("product specific"));
+
+    return headers;
+
+  }
+
+  /**
+   * Contains OREX-SPOC specific keywords.
+   */
+  @Override
+  public List<HeaderCard> getIDInfo(String comment) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    if (comment.length() > 0) {
+      headers.add(new HeaderCard(COMMENT, comment, false));
+    }
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.SPOC_ID));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.SDPAREA));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.SDPDESC));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.MPHASE));
+
+    return headers;
+
+  }
+
+
+}

src/main/java/terrasaur/fits/AltwgGlobalDTM.java

@@ -0,0 +1,87 @@
+package terrasaur.fits;
+
+import java.util.ArrayList;
+import java.util.List;
+import nom.tam.fits.HeaderCard;
+import nom.tam.fits.HeaderCardException;
+import terrasaur.enums.FitsHeaderType;
+import terrasaur.utils.DTMHeader;
+
+/**
+ * Contains methods for building fits header corresponding to ALTWG Global DTM. Methods that are
+ * specific to the ALTWG Global DTM fits header are contained here. Default methods contained in
+ * DTMFits class.
+ * 
+ * @author espirrc1
+ *
+ */
+public class AltwgGlobalDTM extends DTMFits implements DTMHeader {
+
+  public AltwgGlobalDTM(FitsHdr fitsHeader) {
+    super(fitsHeader, FitsHeaderType.DTMGLOBALALTWG);
+  }
+
+  /**
+   * Fits header block containing observation or ID related information. Includes keywords specific
+   * to OREX-SPOC
+   * 
+   * @return
+   * @throws HeaderCardException
+   */
+  @Override
+  public List<HeaderCard> getIDInfo(String comment) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    if (comment.length() > 0) {
+      headers.add(new HeaderCard(COMMENT, comment, false));
+    }
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.SPOC_ID));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.SDPAREA));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.SDPDESC));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.MPHASE));
+
+    return headers;
+
+  }
+
+  /**
+   * return Fits header block that contains information about the fits header itself. Custom to
+   * OREX-SPOC
+   * 
+   * @return
+   * @throws HeaderCardException
+   */
+  @Override
+  public List<HeaderCard> getHeaderInfo(String comment) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    if (comment.length() > 0) {
+      headers.add(new HeaderCard(COMMENT, comment, false));
+    }
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.HDRVERS));
+
+    return headers;
+
+  }
+
+
+  /**
+   * Added GSDI - specific to OREX-SPOC.
+   */
+  @Override
+  public List<HeaderCard> getMapInfo(String comment) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    if (comment.length() > 0) {
+      headers.add(new HeaderCard(COMMENT, comment, false));
+    }
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.MAP_NAME));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.MAP_VER));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.MAP_TYPE));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.GSD));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.GSDI));
+
+    return headers;
+  }
+
+}

src/main/java/terrasaur/fits/AltwgLocalDTM.java

@@ -0,0 +1,132 @@
+package terrasaur.fits;
+
+import java.util.ArrayList;
+import java.util.List;
+import nom.tam.fits.HeaderCard;
+import nom.tam.fits.HeaderCardException;
+import terrasaur.enums.FitsHeaderType;
+import terrasaur.utils.DTMHeader;
+
+/**
+ * Contains methods for building fits header corresponding to ALTWG local DTM. Methods that are
+ * specific to the ALTWG Local DTM fits header are contained here. Default methods are contained in
+ * DTMFits class.
+ * 
+ * @author espirrc1
+ *
+ */
+public class AltwgLocalDTM extends DTMFits implements DTMHeader {
+
+  public AltwgLocalDTM(FitsHdr fitsHeader) {
+    super(fitsHeader, FitsHeaderType.DTMLOCALALTWG);
+  }
+
+  /**
+   * Fits header block containing observation or ID related information. Includes keywords specific
+   * to OREX-SPOC
+   * 
+   * @return
+   * @throws HeaderCardException
+   */
+  @Override
+  public List<HeaderCard> getIDInfo(String comment) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    if (comment.length() > 0) {
+      headers.add(new HeaderCard(COMMENT, comment, false));
+    }
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.SPOC_ID));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.SDPAREA));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.SDPDESC));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.MPHASE));
+
+    return headers;
+
+  }
+
+  @Override
+  public List<HeaderCard> getSpecificInfo(String comment) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    if (comment.length() > 0) {
+      headers.add(new HeaderCard(COMMENT, comment, false));
+    }
+
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.SIGMA));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.SIG_DEF));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.DQUAL_1));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.DQUAL_2));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.PXPERDEG));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.DENSITY));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.ROT_RATE));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.REF_POT));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.TILT_MAJ));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.TILT_MIN));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.TILT_PA));
+
+    return headers;
+  }
+
+  /**
+   * Include corner points, center vector and ux,uy,uz describing local plane
+   */
+  @Override
+  public List<HeaderCard> getSpatialInfo(String comment) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    if (comment.length() > 0) {
+      headers.add(new HeaderCard(COMMENT, comment, false));
+    }
+
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.CLON));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.CLAT));
+
+    headers.addAll(getCornerCards());
+    headers.addAll(getCenterVec());
+    headers.addAll(getUX());
+    headers.addAll(getUY());
+    headers.addAll(getUZ());
+
+    return headers;
+  }
+
+  /**
+   * return Fits header block that contains information about the fits header itself. Custom to
+   * OREX-SPOC
+   * 
+   * @return
+   * @throws HeaderCardException
+   */
+  @Override
+  public List<HeaderCard> getHeaderInfo(String comment) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    if (comment.length() > 0) {
+      headers.add(new HeaderCard(COMMENT, comment, false));
+    }
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.HDRVERS));
+
+    return headers;
+
+  }
+
+  /**
+   * Added GSDI - specific to OREX-SPOC.
+   */
+  @Override
+  public List<HeaderCard> getMapInfo(String comment) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    if (comment.length() > 0) {
+      headers.add(new HeaderCard(COMMENT, comment, false));
+    }
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.MAP_NAME));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.MAP_VER));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.MAP_TYPE));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.GSD));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.GSDI));
+
+    return headers;
+  }
+
+}

src/main/java/terrasaur/fits/AnciFitsHeader.java

@@ -0,0 +1,12 @@
+package terrasaur.fits;
+
+import java.util.List;
+
+import nom.tam.fits.HeaderCard;
+import nom.tam.fits.HeaderCardException;
+
+public interface AnciFitsHeader {
+
+  public List<HeaderCard> createFitsHeader() throws HeaderCardException;
+
+}

src/main/java/terrasaur/fits/AnciTableFits.java

@@ -0,0 +1,291 @@
+package terrasaur.fits;
+
+import java.util.ArrayList;
+import java.util.List;
+import nom.tam.fits.HeaderCard;
+import nom.tam.fits.HeaderCardException;
+import terrasaur.enums.FitsHeaderType;
+
+/**
+ * Abstract generic class with concrete methods and attributes for creating a FITS table with
+ * generalized fits header. Specific implementations can be written to create custom fits headers as
+ * needed.
+ * 
+ * @author espirrc1
+ *
+ */
+public abstract class AnciTableFits {
+
+  public final String COMMENT = "COMMENT";
+  FitsHdr fitsHdr;
+  public final FitsHeaderType fitsHeaderType;
+
+  public AnciTableFits(FitsHdr fitsHdr, FitsHeaderType fitsHeaderType) {
+    this.fitsHdr = fitsHdr;
+    this.fitsHeaderType = fitsHeaderType;
+  }
+
+  public List<HeaderCard> createFitsHeader() throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+
+    headers.addAll(getHeaderInfo("header information"));
+    headers.addAll(getMissionInfo("mission information"));
+    headers.addAll(getIDInfo("identification info"));
+    headers.addAll(getMapDataSrc("shape data source"));
+    headers.addAll(getProcInfo("processing information"));
+    headers.addAll(getMapInfo("map specific information"));
+    headers.addAll(getSpatialInfo("summary spatial information"));
+
+    return headers;
+
+  }
+
+  /**
+   * return Fits header block that contains information about the fits header itself.
+   * 
+   * @return
+   * @throws HeaderCardException
+   */
+  public List<HeaderCard> getHeaderInfo(String comment) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    if (comment.length() > 0) {
+      headers.add(new HeaderCard(COMMENT, comment, false));
+    }
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.HDRVERS));
+
+    return headers;
+
+  }
+
+  /**
+   * Fits header block containing information about the mission.
+   * 
+   * @return
+   * @throws HeaderCardException
+   */
+  public List<HeaderCard> getMissionInfo(String comment) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    if (comment.length() > 0) {
+      headers.add(new HeaderCard(COMMENT, comment, false));
+    }
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.MISSION));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.HOSTNAME));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.TARGET));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.ORIGIN));
+
+    return headers;
+
+  }
+
+  /**
+   * Fits header block containing observation or ID related information.
+   * 
+   * @return
+   * @throws HeaderCardException
+   */
+  public List<HeaderCard> getIDInfo(String comment) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    if (comment.length() > 0) {
+      headers.add(new HeaderCard(COMMENT, comment, false));
+    }
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.MPHASE));
+
+    return headers;
+
+  }
+
+  /**
+   * Fits header block containing information about the source data used to create the map.
+   * 
+   * @param comment
+   * @return
+   * @throws HeaderCardException
+   */
+  public List<HeaderCard> getMapDataSrc(String comment) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    if (comment.length() > 0) {
+      headers.add(new HeaderCard(COMMENT, comment, false));
+    }
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.DATASRC));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.DATASRCF));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.DATASRCV));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.DATASRCS));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.DATASRCD));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.CREATOR));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.OBJ_FILE));
+    return headers;
+
+  }
+
+  public List<HeaderCard> getMapInfo(String comment) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    if (comment.length() > 0) {
+      headers.add(new HeaderCard(COMMENT, comment, false));
+    }
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.MAP_NAME));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.MAP_VER));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.MAP_TYPE));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.GSD));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.GSDI));
+
+    return headers;
+  }
+
+  /**
+   * Fits header block containing information about the software processing done to generate the
+   * product.
+   * 
+   * @param comment
+   * @return
+   * @throws HeaderCardException
+   */
+  public List<HeaderCard> getProcInfo(String comment) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    if (comment.length() > 0) {
+      headers.add(new HeaderCard(COMMENT, comment, false));
+    }
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.PRODNAME));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.DATEPRD));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.SOFTWARE));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.SOFT_VER));
+
+    return headers;
+
+  }
+
+  public List<HeaderCard> getSpatialInfo(String comment) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    if (comment.length() > 0) {
+      headers.add(new HeaderCard(COMMENT, comment, false));
+    }
+
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.CLON));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.CLAT));
+
+    headers.addAll(getCornerCards());
+
+    // add CNTR_V_X,Y,Z
+    headers.addAll(getCenterVec());
+
+    // add UX_X,Y,Z
+    headers.addAll(getUX());
+
+    // add UY_X,Y,Z
+    headers.addAll(getUY());
+
+    // add UZ_X,Y,Z
+    headers.addAll(getUZ());
+
+    return headers;
+  }
+
+  /**
+   * Return the HeaderCards associated with a specific product. By default we use the ALTWG specific
+   * product keywords
+   * 
+   * @param comment
+   * @return
+   * @throws HeaderCardException
+   */
+  public List<HeaderCard> getSpecificInfo(String comment) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    if (comment.length() > 0) {
+      headers.add(new HeaderCard(COMMENT, comment, false));
+    }
+
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.SIGMA));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.SIG_DEF));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.DQUAL_1));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.DQUAL_2));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.DSIG_DEF));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.DENSITY));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.ROT_RATE));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.REF_POT));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.TILT_MAJ));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.TILT_MIN));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.TILT_PA));
+
+    return headers;
+  }
+
+  /**
+   * Return headercards associated with the upper/lower left/right corners of the image.
+   * 
+   * @return
+   * @throws HeaderCardException
+   */
+  public List<HeaderCard> getCornerCards() throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    String fmtS = "%18.13f";
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.LLCLNG, fmtS));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.LLCLAT, fmtS));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.URCLNG, fmtS));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.URCLAT, fmtS));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.LRCLNG, fmtS));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.LRCLAT, fmtS));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.ULCLNG, fmtS));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.ULCLAT, fmtS));
+
+    return headers;
+  }
+
+  /**
+   * Return headercards for vector to center of image.
+   * 
+   * @return
+   * @throws HeaderCardException
+   */
+  public List<HeaderCard> getCenterVec() throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.CNTR_V_X));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.CNTR_V_Y));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.CNTR_V_Z));
+
+    return headers;
+  }
+
+  public List<HeaderCard> getUX() throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.UX_X));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.UX_Y));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.UX_Z));
+
+    return headers;
+
+  }
+
+  public List<HeaderCard> getUY() throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.UY_X));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.UY_Y));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.UY_Z));
+
+    return headers;
+
+  }
+
+  public List<HeaderCard> getUZ() throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.UZ_X));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.UZ_Y));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.UZ_Z));
+
+    return headers;
+
+  }
+
+}

src/main/java/terrasaur/fits/DTMFits.java

@@ -0,0 +1,351 @@
+package terrasaur.fits;
+
+import java.util.ArrayList;
+import java.util.List;
+import nom.tam.fits.HeaderCard;
+import nom.tam.fits.HeaderCardException;
+import terrasaur.enums.FitsHeaderType;
+
+/**
+ * Abstract generic class with concrete methods and attributes for creating a FITS DTM cube with a
+ * generalized fits header. Specific implementations can be written to create custom fits headers as
+ * needed.
+ * 
+ * @author espirrc1
+ *
+ */
+public abstract class DTMFits {
+
+  public final String COMMENT = "COMMENT";
+  final FitsHdr fitsHdr;
+  private FitsData fitsData;
+  private boolean dataContained = false;
+  public final FitsHeaderType fitsHeaderType;
+
+  public DTMFits(FitsHdr fitsHdr, FitsHeaderType fitsHeaderType) {
+    this.fitsHdr = fitsHdr;
+    this.fitsHeaderType = fitsHeaderType;
+  }
+
+  public void setData(FitsData fitsData) {
+    this.fitsData = fitsData;
+    dataContained = true;
+  }
+
+  public List<HeaderCard> createFitsHeader(List<HeaderCard> planeList) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+
+    headers.addAll(getHeaderInfo("header information"));
+    headers.addAll(getMissionInfo("mission information"));
+    headers.addAll(getIDInfo("identification info"));
+    headers.addAll(getMapDataSrc("data source"));
+    headers.addAll(getProcInfo("processing information"));
+    headers.addAll(getMapInfo("map specific information"));
+    headers.addAll(getSpatialInfo("summary spatial information"));
+    headers.addAll(getPlaneInfo("plane information", planeList));
+    headers.addAll(getSpecificInfo("product specific"));
+
+    // end keyword
+    headers.add(getEnd());
+
+    return headers;
+  }
+
+  /**
+   * return Fits header block that contains information about the fits header itself. No string
+   * passed, so no comment in header.
+   * 
+   * @return
+   * @throws HeaderCardException
+   */
+  public List<HeaderCard> getHeaderInfo() throws HeaderCardException {
+    return getHeaderInfo("");
+  }
+
+  /**
+   * return Fits header block that contains information about the fits header itself. This is a
+   * custom section and so is left empty here. It can be defined in the concrete classes that extend
+   * this class.
+   * 
+   * @return
+   * @throws HeaderCardException
+   */
+  public List<HeaderCard> getHeaderInfo(String comment) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    return headers;
+
+  }
+
+  /**
+   * Fits header block containing information about the mission.
+   * 
+   * @return
+   * @throws HeaderCardException
+   */
+  public List<HeaderCard> getMissionInfo(String comment) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    if (comment.length() > 0) {
+      headers.add(new HeaderCard(COMMENT, comment, false));
+    }
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.MISSION));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.HOSTNAME));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.TARGET));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.ORIGIN));
+
+    return headers;
+
+  }
+
+  /**
+   * Fits header block containing observation or ID related information.
+   * 
+   * @return
+   * @throws HeaderCardException
+   */
+  public List<HeaderCard> getIDInfo(String comment) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    if (comment.length() > 0) {
+      headers.add(new HeaderCard(COMMENT, comment, false));
+    }
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.MPHASE));
+
+    return headers;
+
+  }
+
+  /**
+   * Fits header block containing information about the source data used to create the map.
+   * 
+   * @param comment
+   * @return
+   * @throws HeaderCardException
+   */
+  public List<HeaderCard> getMapDataSrc(String comment) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    if (comment.length() > 0) {
+      headers.add(new HeaderCard(COMMENT, comment, false));
+    }
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.DATASRC));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.DATASRCF));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.DATASRCV));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.DATASRCS));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.DATASRCD));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.OBJ_FILE));
+
+    return headers;
+
+  }
+
+  public List<HeaderCard> getMapInfo(String comment) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    if (comment.length() > 0) {
+      headers.add(new HeaderCard(COMMENT, comment, false));
+    }
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.MAP_NAME));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.MAP_VER));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.MAP_TYPE));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.GSD));
+
+    return headers;
+  }
+
+  /**
+   * Fits header block containing information about the software processing done to generate the
+   * product.
+   * 
+   * @param comment
+   * @return
+   * @throws HeaderCardException
+   */
+  public List<HeaderCard> getProcInfo(String comment) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    if (comment.length() > 0) {
+      headers.add(new HeaderCard(COMMENT, comment, false));
+    }
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.PRODNAME));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.DATEPRD));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.SOFTWARE));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.SOFT_VER));
+
+    return headers;
+
+  }
+
+  /**
+   * Creates header block containing spatial information for the DTM, e.g. corner locations, vector
+   * to center, Ux, Uy, Uz.
+   * 
+   * @param comment
+   * @return
+   * @throws HeaderCardException
+   */
+  public List<HeaderCard> getSpatialInfo(String comment) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    if (comment.length() > 0) {
+      headers.add(new HeaderCard(COMMENT, comment, false));
+    }
+
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.CLON));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.CLAT));
+    headers.addAll(getCornerCards());
+
+    // remove these keywords. They are specific to local and MLNs
+    // headers.addAll(getCenterVec());
+    // headers.addAll(getUX());
+    // headers.addAll(getUY());
+    // headers.addAll(getUZ());
+
+    return headers;
+  }
+
+  /**
+   * Return the HeaderCards describing each DTM plane. Used to build the portion of the fits header
+   * that contains information about the planes in the DTM cube. Checks to see that all data planes
+   * are described by comparing size of planeList against length of fits data.
+   * 
+   * @param comment
+   * @param planeList
+   * @return
+   * @throws HeaderCardException
+   */
+  public List<HeaderCard> getPlaneInfo(String comment, List<HeaderCard> planeList)
+      throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    if (comment.length() > 0) {
+      headers.add(new HeaderCard(COMMENT, comment, false));
+    }
+    headers.addAll(planeList);
+
+    if (!dataContained) {
+      String errMesg = "ERROR! Cannot return keywords describing the DTM cube without "
+          + "having the actual data!";
+      throw new RuntimeException(errMesg);
+    }
+
+    // check if planeList describes all the planes in data, throw runtime exception if not.
+    if (planeList.size() != fitsData.getData().length) {
+      System.out.println("Error: plane List has " + planeList.size() + " planes but datacube has "
+          + fitsData.getData().length + " planes");
+      for (HeaderCard thisPlane : planeList) {
+        System.out.println(thisPlane.getKey() + ":" + thisPlane.getValue());
+      }
+      String errMesg = "Error: plane List has " + planeList.size() + " planes but datacube "
+          + " has " + fitsData.getData().length + " planes";
+      throw new RuntimeException(errMesg);
+    }
+
+    return headers;
+  }
+
+  /**
+   * Return the HeaderCards associated with a specific product.
+   * 
+   * @param comment
+   * @return
+   * @throws HeaderCardException
+   */
+  public List<HeaderCard> getSpecificInfo(String comment) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    if (comment.length() > 0) {
+      headers.add(new HeaderCard(COMMENT, comment, false));
+    }
+
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.SIGMA));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.SIG_DEF));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.PXPERDEG));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.DENSITY));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.ROT_RATE));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.REF_POT));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.TILT_MAJ));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.TILT_MIN));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.TILT_PA));
+
+    return headers;
+  }
+
+  /**
+   * Return headercards associated with the upper/lower left/right corners of the image.
+   * 
+   * @return
+   * @throws HeaderCardException
+   */
+  public List<HeaderCard> getCornerCards() throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    String fmtS = "%18.13f";
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.LLCLNG, fmtS));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.LLCLAT, fmtS));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.URCLNG, fmtS));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.URCLAT, fmtS));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.LRCLNG, fmtS));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.LRCLAT, fmtS));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.ULCLNG, fmtS));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.ULCLAT, fmtS));
+
+    return headers;
+  }
+
+  /**
+   * Return headercards for vector to center of image.
+   * 
+   * @return
+   * @throws HeaderCardException
+   */
+  public List<HeaderCard> getCenterVec() throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.CNTR_V_X));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.CNTR_V_Y));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.CNTR_V_Z));
+
+    return headers;
+  }
+
+  public List<HeaderCard> getUX() throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.UX_X));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.UX_Y));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.UX_Z));
+
+    return headers;
+
+  }
+
+  public List<HeaderCard> getUY() throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.UY_X));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.UY_Y));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.UY_Z));
+
+    return headers;
+
+  }
+
+  public List<HeaderCard> getUZ() throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.UZ_X));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.UZ_Y));
+    headers.add(fitsHdr.getHeaderCardD(HeaderTag.UZ_Z));
+
+    return headers;
+
+  }
+
+  public HeaderCard getEnd() throws HeaderCardException {
+    return new HeaderCard(HeaderTag.END.toString(), HeaderTag.END.value(), HeaderTag.END.comment());
+  }
+
+}

src/main/java/terrasaur/fits/FitsData.java

@@ -0,0 +1,190 @@
+package terrasaur.fits;
+
+import terrasaur.enums.AltwgDataType;
+import terrasaur.enums.SrcProductType;
+
+public class FitsData {
+
+  private final double[][][] data;
+  private final double[] V;
+  private final double[] ux;
+  private final double[] uy;
+  private final double[] uz;
+  private final double scale;
+  private final double gsd;
+  private final boolean hasV;
+  private final boolean hasUnitv;
+  private final boolean hasGsd;
+  private final boolean isGlobal;
+  private final boolean hasAltType;
+  private final AltwgDataType altProd;
+  private final String dataSource;
+
+  private FitsData(FitsDataBuilder b) {
+    this.data = b.data;
+    this.V = b.V;
+    this.ux = b.ux;
+    this.uy = b.uy;
+    this.uz = b.uz;
+    this.scale = b.scale;
+    this.gsd = b.gsd;
+    this.hasV = b.hasV;
+    this.hasUnitv = b.hasUnitv;
+    this.hasGsd = b.hasGsd;
+    this.hasAltType = b.hasAltType;
+    this.isGlobal = b.isGlobal;
+    this.altProd = b.altProd;
+    this.dataSource = b.dataSource;
+  }
+
+  public AltwgDataType getAltProdType() {
+    return this.altProd;
+  }
+
+  public String getSrcProdType() {
+    return this.dataSource;
+  }
+
+  public double[][][] getData() {
+    return this.data;
+  }
+
+  public boolean hasV() {
+    return this.hasV;
+  }
+
+  public double[] getV() {
+    return this.V;
+  }
+
+  public boolean hasUnitv() {
+    return this.hasUnitv;
+  }
+
+  public double[] getUnit(UnitDir udir) {
+    switch (udir) {
+      case UX:
+        return this.ux;
+
+      case UY:
+        return this.uy;
+
+      case UZ:
+        return this.uz;
+
+      default:
+        throw new RuntimeException();
+    }
+  }
+
+  public double getScale() {
+    return this.scale;
+  }
+
+  public boolean hasGsd() {
+    return this.hasGsd;
+  }
+
+  public boolean hasAltType() {
+    return this.hasAltType;
+  }
+
+  public boolean isGlobal() {
+    return this.isGlobal;
+  }
+
+  public double getGSD() {
+    if (this.hasGsd) {
+      return this.gsd;
+    } else {
+      String errMesg = "ERROR! fitsData does not have gsd!";
+      throw new RuntimeException(errMesg);
+    }
+  }
+
+
+  public static class FitsDataBuilder {
+    private final double[][][] data;
+    private double[] V = null;
+    private double[] ux = null;
+    private double[] uy = null;
+    private double[] uz = null;
+    private boolean hasV = false;
+    private boolean hasUnitv = false;
+    private boolean hasGsd = false;
+    private boolean isGlobal = false;
+    private boolean hasAltType = false;
+    private double scale = Double.NaN;
+    private double gsd = Double.NaN;
+    private AltwgDataType altProd = null;
+    private String dataSource = SrcProductType.UNKNOWN.toString();
+
+    /**
+     * Constructor. isGlobal used to fill out fits keyword describing whether data is local or
+     * global. May also be used for fits naming convention.
+     * 
+     * @param data
+     * @param isGlobal
+     */
+    public FitsDataBuilder(double[][][] data, boolean isGlobal) {
+      this.data = data;
+      this.isGlobal = isGlobal;
+    }
+
+    public FitsDataBuilder setAltProdType(AltwgDataType altProd) {
+      this.altProd = altProd;
+      this.hasAltType = true;
+      return this;
+    }
+
+    public FitsDataBuilder setDataSource(String dataSource) {
+      this.dataSource = dataSource;
+      return this;
+    }
+
+    public FitsDataBuilder setV(double[] V) {
+      this.V = V;
+      this.hasV = true;
+      return this;
+    }
+
+    public FitsDataBuilder setU(double[] uvec, UnitDir udir) {
+      switch (udir) {
+        case UX:
+          this.ux = uvec;
+          this.hasUnitv = true;
+          break;
+
+        case UY:
+          this.uy = uvec;
+          this.hasUnitv = true;
+          break;
+
+        case UZ:
+          this.uz = uvec;
+          this.hasUnitv = true;
+          break;
+
+        default:
+          throw new RuntimeException();
+
+      }
+      return this;
+    }
+
+    public FitsDataBuilder setScale(double scale) {
+      this.scale = scale;
+      return this;
+    }
+
+    public FitsDataBuilder setGSD(double gsd) {
+      this.gsd = gsd;
+      this.hasGsd = true;
+      return this;
+    }
+
+    public FitsData build() {
+      return new FitsData(this);
+    }
+  }
+}

src/main/java/terrasaur/fits/FitsHeader.java

@@ -0,0 +1,684 @@
+package terrasaur.fits;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.charset.Charset;
+import java.util.EnumMap;
+import java.util.List;
+import java.util.Map;
+import org.apache.commons.io.FileUtils;
+import nom.tam.fits.FitsException;
+import nom.tam.fits.HeaderCard;
+import nom.tam.fits.HeaderCardException;
+import terrasaur.utils.StringUtil;
+
+/**
+ * @deprecated this class has been replaced by the FitsHdr class and the FitsHeaderFactory
+ *             implementation of the FitsHdr class. USE THIS CLASS AT YOUR PERIL. THE KEYWORDS HAVE
+ *             NOT BEEN UPDATED SINCE THIS CLASS WAS DEPRECATED.
+ * @author espirrc1
+ *
+ */
+@Deprecated
+public class FitsHeader {
+
+  public final FitsValCom bitPix;
+  public final FitsValCom nAxis1;
+  public final FitsValCom nAxis2;
+  public final FitsValCom nAxis3;
+
+  // fits keywords common to all ALTWG products
+  public final FitsValCom hdrVers;
+  public final FitsValCom mission;
+  public final FitsValCom hostName;
+  public final FitsValCom target;
+  public final FitsValCom origin;
+  public final FitsValCom spocid;
+  public final FitsValCom sdparea;
+  public final FitsValCom sdpdesc;
+  public final FitsValCom missionPhase;
+  public final FitsValCom dataSource;
+  public final FitsValCom dataSourceV;
+  public final FitsValCom dataSourceS;
+  public final FitsValCom dataSourceFile;
+  public final FitsValCom datasrcd;
+  public final FitsValCom productName;
+  public final FitsValCom dateprd;
+  public final FitsValCom productType;
+  public final FitsValCom productVer;
+  public final FitsValCom author;
+
+  // for ancillary fits products
+  // map Name(description): tilt, gravity, slope, etc
+  // map Type: global or local
+  public final FitsValCom objFile;
+  public final FitsValCom mapName;
+  public final FitsValCom mapType;
+
+  // center lon, lat. common to both local and global anci fits
+  public final FitsValCom clon;
+  public final FitsValCom clat;
+
+  // global anci fits geometry
+  public final FitsValCom minlon;
+  public final FitsValCom maxlon;
+  public final FitsValCom minlat;
+  public final FitsValCom maxlat;
+
+  // local anci fits geometry
+  public final FitsValCom ulcLon;
+  public final FitsValCom ulcLat;
+  public final FitsValCom llcLon;
+  public final FitsValCom llcLat;
+  public final FitsValCom lrcLon;
+  public final FitsValCom lrcLat;
+  public final FitsValCom urcLon;
+  public final FitsValCom urcLat;
+  public final FitsValCom cntr_v_x;
+  public final FitsValCom cntr_v_y;
+  public final FitsValCom cntr_v_z;
+  public final FitsValCom ux_x;
+  public final FitsValCom ux_y;
+  public final FitsValCom ux_z;
+  public final FitsValCom uy_x;
+  public final FitsValCom uy_y;
+  public final FitsValCom uy_z;
+  public final FitsValCom uz_x;
+  public final FitsValCom uz_y;
+  public final FitsValCom uz_z;
+  public final FitsValCom gsd;
+  public final FitsValCom gsdi;
+
+  // common to both local and global anci fits
+  public final FitsValCom sigma;
+  public final FitsValCom sigDef;
+  public final FitsValCom dqual1;
+  public final FitsValCom dqual2;
+  public final FitsValCom dsigDef;
+  public final FitsValCom density;
+  public final FitsValCom rotRate;
+  public final FitsValCom refPot;
+  public final FitsValCom tiltRad;
+  public final FitsValCom tiltMaj;
+  public final FitsValCom tiltMin;
+  public final FitsValCom tiltPa;
+  public final FitsValCom mapVer;
+
+  public final EnumMap<HeaderTag, FitsValCom> tag2valcom;
+
+  private FitsHeader(FitsHeaderBuilder b) {
+    this.bitPix = b.bitPix;
+    this.nAxis1 = b.nAxis1;
+    this.nAxis2 = b.nAxis2;
+    this.nAxis3 = b.nAxis3;
+    this.hdrVers = b.hdrVers;
+    this.mission = b.mission;
+    this.hostName = b.hostName;
+    this.target = b.target;
+    this.origin = b.origin;
+    this.spocid = b.spocid;
+    this.sdparea = b.sdparea;
+    this.sdpdesc = b.sdpdesc;
+    this.missionPhase = b.missionPhase;
+    this.dataSource = b.dataSource;
+    this.dataSourceFile = b.dataSourceFile;
+    this.dataSourceV = b.dataSourceV;
+    this.datasrcd = b.datasrcd;
+    this.dataSourceS = b.dataSourceS;
+    this.productName = b.productName;
+    this.dateprd = b.dateprd;
+    this.productType = b.productType;
+    this.productVer = b.productVer;
+    this.objFile = b.objFile;
+    this.author = b.author;
+    this.mapName = b.mapName;
+    this.mapType = b.mapType;
+    this.clon = b.clon;
+    this.clat = b.clat;
+    this.minlon = b.minlon;
+    this.maxlon = b.maxlon;
+    this.minlat = b.minlat;
+    this.maxlat = b.maxlat;
+    this.ulcLon = b.ulcLon;
+    this.ulcLat = b.ulcLat;
+    this.llcLon = b.llcLon;
+    this.llcLat = b.llcLat;
+    this.lrcLon = b.lrcLon;
+    this.lrcLat = b.lrcLat;
+    this.urcLon = b.urcLon;
+    this.urcLat = b.urcLat;
+    this.cntr_v_x = b.cntr_v_x;
+    this.cntr_v_y = b.cntr_v_y;
+    this.cntr_v_z = b.cntr_v_z;
+    this.ux_x = b.ux_x;
+    this.ux_y = b.ux_y;
+    this.ux_z = b.ux_z;
+    this.uy_x = b.uy_x;
+    this.uy_y = b.uy_y;
+    this.uy_z = b.uy_z;
+    this.uz_x = b.uz_x;
+    this.uz_y = b.uz_y;
+    this.uz_z = b.uz_z;
+    this.gsd = b.gsd;
+    this.gsdi = b.gsdi;
+    this.sigma = b.sigma;
+    this.sigDef = b.sigDef;
+    this.dqual1 = b.dqual1;
+    this.dqual2 = b.dqual2;
+    this.dsigDef = b.dsigDef;
+    this.mapVer = b.mapVer;
+    this.density = b.density;
+    this.rotRate = b.rotRate;
+    this.refPot = b.refPot;
+    this.tiltRad = b.tiltRad;
+
+    // hardcode semi-major and semi-minor axis = radius
+    // since we only deal with circles for now
+    this.tiltMaj = b.tiltRad;
+    this.tiltMin = b.tiltRad;
+    this.tiltPa = b.tiltPa;
+    this.tag2valcom = b.tag2valcom;
+  }
+
+  public static class FitsHeaderBuilder {
+
+    // initialize the FITS keywords. Some of them may not change during the mission, but
+    // the option to change them is given via the public methods.
+    private FitsValCom bitPix = new FitsValCom("32", null);
+    private FitsValCom nAxis1 = new FitsValCom("1024", null);
+    private FitsValCom nAxis2 = new FitsValCom("1024", null);
+    private FitsValCom nAxis3 = new FitsValCom("numberPlanesNotSet", null);
+
+    private FitsValCom hdrVers =
+        new FitsValCom(HeaderTag.HDRVERS.value(), HeaderTag.HDRVERS.comment());
+    private FitsValCom mission =
+        new FitsValCom(HeaderTag.MISSION.value(), HeaderTag.MISSION.comment());
+    private FitsValCom hostName = new FitsValCom(HeaderTag.HOSTNAME.value(), null);
+    private FitsValCom target = new FitsValCom(HeaderTag.TARGET.value(), null);
+    private FitsValCom origin =
+        new FitsValCom(HeaderTag.ORIGIN.value(), HeaderTag.ORIGIN.comment());
+    private FitsValCom spocid =
+        new FitsValCom(HeaderTag.SPOC_ID.value(), HeaderTag.SPOC_ID.comment());
+    private FitsValCom sdparea =
+        new FitsValCom(HeaderTag.SDPAREA.value(), HeaderTag.SDPAREA.comment());
+    private FitsValCom sdpdesc =
+        new FitsValCom(HeaderTag.SDPDESC.value(), HeaderTag.SDPDESC.comment());
+    private FitsValCom missionPhase =
+        new FitsValCom(HeaderTag.MPHASE.value(), HeaderTag.MPHASE.comment());
+    private FitsValCom dataSource =
+        new FitsValCom(HeaderTag.DATASRC.value(), HeaderTag.DATASRC.comment());
+    private FitsValCom dataSourceFile =
+        new FitsValCom(HeaderTag.DATASRCF.value(), HeaderTag.DATASRCF.comment());
+    private FitsValCom dataSourceS =
+        new FitsValCom(HeaderTag.DATASRCS.value(), HeaderTag.DATASRCS.comment());
+    private FitsValCom dataSourceV =
+        new FitsValCom(HeaderTag.DATASRCV.value(), HeaderTag.DATASRCV.comment());
+    private FitsValCom software =
+        new FitsValCom(HeaderTag.SOFTWARE.value(), HeaderTag.SOFTWARE.comment());
+    private FitsValCom softver =
+        new FitsValCom(HeaderTag.SOFT_VER.value(), HeaderTag.SOFT_VER.comment());
+    private FitsValCom datasrcd =
+        new FitsValCom(HeaderTag.DATASRCD.value(), HeaderTag.DATASRCD.comment());
+    private FitsValCom productName =
+        new FitsValCom(HeaderTag.PRODNAME.value(), HeaderTag.PRODNAME.comment());
+    private FitsValCom dateprd =
+        new FitsValCom(HeaderTag.DATEPRD.value(), HeaderTag.DATEPRD.comment());
+    private FitsValCom productType = new FitsValCom("productTypeNotSet", null);
+    private FitsValCom productVer =
+        new FitsValCom(HeaderTag.PRODVERS.value(), HeaderTag.PRODVERS.comment());
+    private FitsValCom mapVer =
+        new FitsValCom(HeaderTag.MAP_VER.value(), HeaderTag.MAP_VER.comment());
+
+    private FitsValCom objFile =
+        new FitsValCom(HeaderTag.OBJ_FILE.value(), HeaderTag.OBJ_FILE.comment());
+    private FitsValCom author =
+        new FitsValCom(HeaderTag.CREATOR.value(), HeaderTag.CREATOR.comment());
+
+    private FitsValCom mapName =
+        new FitsValCom(HeaderTag.MAP_NAME.value(), HeaderTag.MAP_NAME.comment());
+    private FitsValCom mapType =
+        new FitsValCom(HeaderTag.MAP_TYPE.value(), HeaderTag.MAP_TYPE.comment());
+    private FitsValCom clon = new FitsValCom("-999", HeaderTag.CLON.comment());
+    private FitsValCom clat = new FitsValCom("-999", HeaderTag.CLAT.comment());
+    private FitsValCom minlon = new FitsValCom("-999", HeaderTag.MINLON.comment());
+    private FitsValCom maxlon = new FitsValCom("-999", HeaderTag.MAXLON.comment());
+    private FitsValCom minlat = new FitsValCom("-999", HeaderTag.MINLAT.comment());
+    private FitsValCom maxlat = new FitsValCom("-999", HeaderTag.MAXLAT.comment());
+    private FitsValCom pxperdeg = new FitsValCom("-999", HeaderTag.PXPERDEG.comment());
+    private FitsValCom ulcLon = new FitsValCom("-999", HeaderTag.ULCLNG.comment());
+    private FitsValCom ulcLat = new FitsValCom("-999", HeaderTag.ULCLAT.comment());
+    private FitsValCom llcLon = new FitsValCom("-999", HeaderTag.LLCLNG.comment());
+    private FitsValCom llcLat = new FitsValCom("-999", HeaderTag.LLCLAT.comment());
+    private FitsValCom lrcLon = new FitsValCom("-999", HeaderTag.LRCLNG.comment());
+    private FitsValCom lrcLat = new FitsValCom("-999", HeaderTag.LRCLAT.comment());
+    private FitsValCom urcLon = new FitsValCom("-999", HeaderTag.URCLNG.comment());
+    private FitsValCom urcLat = new FitsValCom("-999", HeaderTag.URCLAT.comment());
+    private FitsValCom cntr_v_x = new FitsValCom("-999", HeaderTag.CNTR_V_X.comment());
+    private FitsValCom cntr_v_y = new FitsValCom("-999", HeaderTag.CNTR_V_Y.comment());
+    private FitsValCom cntr_v_z = new FitsValCom("-999", HeaderTag.CNTR_V_Z.comment());
+    private FitsValCom ux_x = new FitsValCom("-999", HeaderTag.UX_X.comment());
+    private FitsValCom ux_y = new FitsValCom("-999", HeaderTag.UX_Y.comment());
+    private FitsValCom ux_z = new FitsValCom("-999", HeaderTag.UX_Z.comment());
+    private FitsValCom uy_x = new FitsValCom("-999", HeaderTag.UY_X.comment());
+    private FitsValCom uy_y = new FitsValCom("-999", HeaderTag.UY_Y.comment());
+    private FitsValCom uy_z = new FitsValCom("-999", HeaderTag.UY_Z.comment());
+    private FitsValCom uz_x = new FitsValCom("-999", HeaderTag.UZ_X.comment());
+    private FitsValCom uz_y = new FitsValCom("-999", HeaderTag.UZ_Y.comment());
+    private FitsValCom uz_z = new FitsValCom("-999", HeaderTag.UZ_Z.comment());
+    private FitsValCom gsd = new FitsValCom("-999", HeaderTag.GSD.comment());
+    private FitsValCom gsdi = new FitsValCom("-999", HeaderTag.GSDI.comment());
+    private FitsValCom sigma = new FitsValCom("-999", "N/A");
+    private FitsValCom sigDef = new FitsValCom(HeaderTag.SIGMA.value(), HeaderTag.SIGMA.comment());
+    private FitsValCom dqual1 = new FitsValCom("-999", HeaderTag.DQUAL_1.comment());
+    private FitsValCom dqual2 = new FitsValCom("-999", HeaderTag.DQUAL_2.comment());
+    private FitsValCom dsigDef =
+        new FitsValCom(HeaderTag.DSIG_DEF.value(), HeaderTag.DSIG_DEF.comment());
+    private FitsValCom density = new FitsValCom("-999", HeaderTag.DENSITY.comment());
+    private FitsValCom rotRate = new FitsValCom("-999", HeaderTag.ROT_RATE.comment());
+    private FitsValCom refPot = new FitsValCom("-999", HeaderTag.REF_POT.comment());
+    private FitsValCom tiltRad = new FitsValCom("-999", HeaderTag.TILT_RAD.comment());
+    private FitsValCom tiltMaj = new FitsValCom("-999", HeaderTag.TILT_MAJ.comment());
+    private FitsValCom tiltMin = new FitsValCom("-999", HeaderTag.TILT_MIN.comment());
+    private FitsValCom tiltPa = new FitsValCom("0", HeaderTag.TILT_PA.comment());
+
+    private EnumMap<HeaderTag, FitsValCom> tag2valcom =
+        new EnumMap<HeaderTag, FitsValCom>(HeaderTag.class);
+
+    public FitsHeaderBuilder() {
+
+      /*
+       * initialize the map between header tags and the fits val com variables. This allows us to
+       * use enumeration to select which of the fitsvalcom variables we want to update, eliminating
+       * the need for specific 'set' statements for each variable.
+       */
+      tag2valcom.put(HeaderTag.HDRVERS, hdrVers);
+      tag2valcom.put(HeaderTag.MISSION, mission);
+      tag2valcom.put(HeaderTag.HOSTNAME, hostName);
+      tag2valcom.put(HeaderTag.TARGET, target);
+      tag2valcom.put(HeaderTag.ORIGIN, origin);
+      tag2valcom.put(HeaderTag.SPOC_ID, spocid);
+      tag2valcom.put(HeaderTag.SDPAREA, sdparea);
+      tag2valcom.put(HeaderTag.SDPDESC, sdpdesc);
+      tag2valcom.put(HeaderTag.MPHASE, missionPhase);
+      tag2valcom.put(HeaderTag.DATASRC, dataSource);
+      tag2valcom.put(HeaderTag.DATASRCV, dataSourceV);
+      tag2valcom.put(HeaderTag.DATASRCF, dataSourceFile);
+      tag2valcom.put(HeaderTag.DATASRCS, dataSourceS);
+      // removed from ALTWG keywords per Map Format SIS draft v2
+      tag2valcom.put(HeaderTag.DATASRCD, datasrcd);
+      tag2valcom.put(HeaderTag.SOFTWARE, software);
+      tag2valcom.put(HeaderTag.SOFT_VER, softver);
+      tag2valcom.put(HeaderTag.PRODNAME, productName);
+      tag2valcom.put(HeaderTag.DATEPRD, dateprd);
+      tag2valcom.put(HeaderTag.PRODVERS, productVer);
+      tag2valcom.put(HeaderTag.MAP_VER, mapVer);
+      tag2valcom.put(HeaderTag.CREATOR, author);
+      tag2valcom.put(HeaderTag.OBJ_FILE, objFile);
+      tag2valcom.put(HeaderTag.CLON, clon);
+      tag2valcom.put(HeaderTag.CLAT, clat);
+      tag2valcom.put(HeaderTag.MINLON, minlon);
+      tag2valcom.put(HeaderTag.MAXLON, maxlon);
+      tag2valcom.put(HeaderTag.MINLAT, minlat);
+      tag2valcom.put(HeaderTag.MAXLAT, maxlat);
+      tag2valcom.put(HeaderTag.PXPERDEG, pxperdeg);
+      tag2valcom.put(HeaderTag.LLCLNG, llcLon);
+      tag2valcom.put(HeaderTag.LLCLAT, llcLat);
+      tag2valcom.put(HeaderTag.LRCLNG, lrcLon);
+      tag2valcom.put(HeaderTag.LRCLAT, lrcLat);
+      tag2valcom.put(HeaderTag.URCLNG, urcLon);
+      tag2valcom.put(HeaderTag.URCLAT, urcLat);
+      tag2valcom.put(HeaderTag.ULCLNG, ulcLon);
+      tag2valcom.put(HeaderTag.ULCLAT, ulcLat);
+      tag2valcom.put(HeaderTag.CNTR_V_X, cntr_v_x);
+      tag2valcom.put(HeaderTag.CNTR_V_Y, cntr_v_y);
+      tag2valcom.put(HeaderTag.CNTR_V_Z, cntr_v_z);
+      tag2valcom.put(HeaderTag.UX_X, ux_x);
+      tag2valcom.put(HeaderTag.UX_Y, ux_y);
+      tag2valcom.put(HeaderTag.UX_Z, ux_z);
+      tag2valcom.put(HeaderTag.UY_X, uy_x);
+      tag2valcom.put(HeaderTag.UY_Y, uy_y);
+      tag2valcom.put(HeaderTag.UY_Z, uy_z);
+      tag2valcom.put(HeaderTag.UZ_X, ux_x);
+      tag2valcom.put(HeaderTag.UZ_Y, ux_y);
+      tag2valcom.put(HeaderTag.UZ_Z, ux_z);
+      tag2valcom.put(HeaderTag.GSD, gsd);
+      tag2valcom.put(HeaderTag.GSDI, gsdi);
+      tag2valcom.put(HeaderTag.SIGMA, sigma);
+      tag2valcom.put(HeaderTag.SIG_DEF, sigDef);
+      tag2valcom.put(HeaderTag.DQUAL_1, dqual1);
+      tag2valcom.put(HeaderTag.DQUAL_2, dqual2);
+      tag2valcom.put(HeaderTag.DSIG_DEF, dsigDef);
+      tag2valcom.put(HeaderTag.DENSITY, density);
+      tag2valcom.put(HeaderTag.ROT_RATE, rotRate);
+      tag2valcom.put(HeaderTag.REF_POT, refPot);
+      tag2valcom.put(HeaderTag.TILT_RAD, tiltRad);
+      tag2valcom.put(HeaderTag.TILT_MAJ, tiltMaj);
+      tag2valcom.put(HeaderTag.TILT_MIN, tiltMin);
+      tag2valcom.put(HeaderTag.TILT_PA, tiltPa);
+      tag2valcom.put(HeaderTag.MAP_NAME, mapName);
+      tag2valcom.put(HeaderTag.MAP_TYPE, mapType);
+      tag2valcom.put(HeaderTag.MAP_VER, mapVer);
+
+    }
+
+    public FitsHeaderBuilder setTarget(String val, String comment) {
+      this.target.setV(val);
+      this.target.setC(comment);
+      return this;
+    }
+
+    public FitsHeaderBuilder setBitPix(String val, String comment) {
+      this.bitPix.setV(val);
+      this.bitPix.setC(comment);
+      return this;
+    }
+
+    public FitsHeaderBuilder setNAx1(String val, String comment) {
+      this.nAxis1.setV(val);
+      this.nAxis1.setC(comment);
+      return this;
+    }
+
+    public FitsHeaderBuilder setNAx2(String val, String comment) {
+      this.nAxis2.setV(val);
+      this.nAxis2.setC(comment);
+      return this;
+    }
+
+    public FitsHeaderBuilder setNAx3(String val, String comment) {
+      this.nAxis3.setV(val);
+      this.nAxis3.setC(comment);
+      return this;
+    }
+
+    public FitsHeaderBuilder setVCbyHeaderTag(HeaderTag hdrTag, String value, String comment) {
+
+      if (tag2valcom.containsKey(hdrTag)) {
+        tag2valcom.get(hdrTag).setVC(value, comment);
+      }
+      return this;
+    }
+
+    public FitsHeaderBuilder setVbyHeaderTag(HeaderTag hdrTag, String value) {
+      if (tag2valcom.containsKey(hdrTag)) {
+        tag2valcom.get(hdrTag).setV(value);
+      }
+      return this;
+    }
+
+    public FitsHeaderBuilder setCbyHeaderTag(HeaderTag hdrTag, String comment) {
+      if (tag2valcom.containsKey(hdrTag)) {
+        tag2valcom.get(hdrTag).setC(comment);
+      }
+      return this;
+    }
+
+    /**
+     * Set values in the ancillary header builder class by parsing the headerCard. Parse appropriate
+     * values as determined by the value of the headercard key.
+     * 
+     * @param headerCard
+     * @return
+     */
+    public FitsHeaderBuilder setbyHeaderCard(HeaderCard headerCard) {
+      HeaderTag hdrTag = HeaderTag.END;
+      try {
+        hdrTag = HeaderTag.valueOf(headerCard.getKey());
+        setVCbyHeaderTag(hdrTag, headerCard.getValue(), headerCard.getComment());
+      } catch (IllegalArgumentException e) {
+        if ((headerCard.getKey().contains("COMMENT")) || (headerCard.getKey().contains("PLANE"))) {
+        } else {
+          System.out.println(headerCard.getKey() + " not a HeaderTag");
+        }
+      } catch (NullPointerException ne) {
+        System.out.println("null pointer exception for:" + headerCard.getKey());
+      }
+
+      return this;
+
+    }
+
+    public FitsHeader build() {
+
+      return new FitsHeader(this);
+    }
+
+  }
+
+  /**
+   * Loops through map of fits header cards and tries to parse values relevant to the ALTWG Fits
+   * file.
+   * 
+   * @param map
+   */
+  public static FitsHeaderBuilder copyFitsHeader(Map<String, HeaderCard> map) {
+
+    FitsHeaderBuilder hdrBuilder = new FitsHeaderBuilder();
+
+    // loop through each of the HeaderCards in the map and see if any will help build the altwg
+    // header
+    for (Map.Entry<String, HeaderCard> entry : map.entrySet()) {
+      HeaderCard thisCard = entry.getValue();
+      hdrBuilder.setbyHeaderCard(thisCard);
+    }
+    return hdrBuilder;
+  }
+
+  /**
+   * Copy the fits header from fits file and use it to populate and return FitsHeaderBuilder.
+   * 
+   * @param fitsFile
+   * @return
+   */
+  public static FitsHeaderBuilder copyFitsHeader(File fitsFile) {
+
+    FitsHeaderBuilder hdrBuilder = new FitsHeaderBuilder();
+    try {
+      Map<String, HeaderCard> map = FitsUtil.getFitsHeaderAsMap(fitsFile.getCanonicalPath());
+      hdrBuilder = copyFitsHeader(map);
+      return hdrBuilder;
+    } catch (FitsException | IOException e) {
+      // TODO Auto-generated catch block
+      e.printStackTrace();
+      String errmesg = "ERROR in FitsHeader.copyFitsHeader()! " + " Unable to parse fits file:"
+          + fitsFile.toString() + " for fits header!";
+      System.err.println(errmesg);
+      System.exit(1);
+
+    }
+    return hdrBuilder;
+  }
+
+  /**
+   * Parse a fits configuration file and update a FitsHeaderBuilder. The builder is used to generate
+   * a fits header.
+   * 
+   * @param configFile
+   * @param hdrBuilder - can either be an existing builder or null. If null then will create and
+   *        return a new builder.
+   * @return
+   * @throws IOException
+   */
+  public static FitsHeaderBuilder configHdrBuilder(String configFile, FitsHeaderBuilder hdrBuilder)
+      throws IOException {
+
+    File checkF = new File(configFile);
+    if (!checkF.exists()) {
+      // System.out.println("ERROR:FITS header configuration file:" + configFile + " does not
+      // exist!");
+      String errMesg = "ERROR:FITS header configuration file:" + configFile + " does not exist!";
+      throw new RuntimeException(errMesg);
+    }
+
+    if (hdrBuilder == null) {
+      System.out.println("builder passed to FitsHeader.configHdrBuilder() is null. Generating"
+          + " new FitsHeaderBuilder");
+      hdrBuilder = new FitsHeaderBuilder();
+    }
+    List<String> content = FileUtils.readLines(new File(configFile), Charset.defaultCharset());
+    boolean separatorFound = false;
+    for (String line : content) {
+
+      String[] keyval = line.split("#");
+      if (keyval.length > 1) {
+
+        separatorFound = true;
+        // check if there is a match w/ HeaderTags
+        HeaderTag thisTag = HeaderTag.tagFromString(keyval[0]);
+
+        if (thisTag != HeaderTag.NOMATCH) {
+          // pass to fits header builder and see if it matches on a fits keyword
+
+          if (keyval.length == 2) {
+            // assume user only wants to overwrite the value portion. Leave the comments alone.
+            System.out.println("setting " + thisTag.toString() + " to " + keyval[1]);
+            hdrBuilder.setVbyHeaderTag(thisTag, keyval[1]);
+          } else if (keyval.length == 3) {
+            if (keyval[2].contains("null")) {
+              // user explicitly wants to override any comment in this header with null
+              hdrBuilder.setVCbyHeaderTag(thisTag, keyval[1], null);
+            } else {
+              System.out.println("setting " + thisTag.toString() + " to " + keyval[1]
+                  + ", comment to " + keyval[2]);
+              hdrBuilder.setVCbyHeaderTag(thisTag, keyval[1], keyval[2]);
+            }
+          } else {
+            System.out.println(
+                "Warning: the following line in the config file line has more than 2 colons:");
+            System.out.println(line);
+            System.out.println("Cannot parse. skipping this line");
+          }
+
+        }
+      }
+    }
+    if (!separatorFound) {
+      System.out.println("WARNING! The fits config file:" + configFile
+          + " does not appear to be a valid config file! There is no # separator!");
+    }
+    return hdrBuilder;
+  }
+
+  /**
+   * Given a fits keyword return the object containing the keyword value and comment.
+   * 
+   * @param tag - fits keyword as enumeration.
+   * @return HeaderCard
+   * @throws HeaderCardException
+   */
+  public HeaderCard getHeaderCard(HeaderTag tag) throws HeaderCardException {
+
+    // format for double values
+    String fmtS = "%18.13f";
+    if (tag2valcom.containsKey(tag)) {
+      FitsValCom valcom = tag2valcom.get(tag);
+
+      /*
+       * FitsValCom stores the values as String because extracting the value from the source fits
+       * file returns it as a string. Need to convert geometry values to double and store it in the
+       * HeaderCard as a double. Then when written to the fits file it will not have quotes around
+       * the value.
+       */
+
+      /*
+       * type of value to store in headercard. =0 string (single quotes around value) =1 formatted
+       * double =2 free-form double
+       */
+      int returnType = 0;
+
+      switch (tag) {
+
+        case PXPERDEG:
+        case CLON:
+        case CLAT:
+        case MINLON:
+        case MAXLON:
+        case MINLAT:
+        case MAXLAT:
+        case URCLNG:
+        case URCLAT:
+        case LRCLNG:
+        case LRCLAT:
+        case LLCLNG:
+        case LLCLAT:
+        case ULCLNG:
+        case ULCLAT:
+        case GSDI:
+          returnType = 1;
+          break;
+
+        case CNTR_V_X:
+        case CNTR_V_Y:
+        case CNTR_V_Z:
+        case UX_X:
+        case UX_Y:
+        case UX_Z:
+        case UY_X:
+        case UY_Y:
+        case UY_Z:
+        case UZ_X:
+        case UZ_Y:
+        case UZ_Z:
+        case DENSITY:
+        case ROT_RATE:
+        case REF_POT:
+        case TILT_RAD:
+        case TILT_MAJ:
+        case TILT_MIN:
+        case TILT_PA:
+        case GSD:
+        case SIGMA:
+        case DQUAL_1:
+        case DQUAL_2:
+          returnType = 2;
+          break;
+
+        default:
+          returnType = 0;
+          break;
+      }
+
+      switch (returnType) {
+        case 0:
+          return new HeaderCard(tag.toString(), valcom.getV(), valcom.getC());
+
+        case 1:
+          return new HeaderCard(tag.toString(), StringUtil.str2fmtD(fmtS, valcom.getV()),
+              valcom.getC());
+
+        case 2:
+          return new HeaderCard(tag.toString(), StringUtil.parseSafeD(valcom.getV()),
+              valcom.getC());
+
+      }
+
+    }
+
+    String errMesg = "ERROR!, cannot find fits keyword:" + tag.toString();
+    throw new RuntimeException(errMesg);
+  }
+
+  /**
+   * Initialize fits header builder for using keyword/values from a fits config file. Can be used to
+   * initialize headerBuilder for any fits file.
+   * 
+   * @param configFile
+   * @return
+   */
+  public static FitsHeaderBuilder initHdrBuilder(String configFile) {
+    FitsHeaderBuilder hdrBuilder = new FitsHeaderBuilder();
+
+    if (configFile != null) {
+      // try to load config file if it exists and modify fits header builder with it.
+      try {
+        configHdrBuilder(configFile, hdrBuilder);
+      } catch (IOException e) {
+        // TODO Auto-generated catch block
+        e.printStackTrace();
+        System.out.println("Error trying to read config file:" + configFile);
+      }
+    }
+    return hdrBuilder;
+  }
+
+}

src/main/java/terrasaur/fits/FitsHeaderFactory.java

@@ -0,0 +1,213 @@
+package terrasaur.fits;
+
+import java.util.ArrayList;
+import java.util.List;
+import nom.tam.fits.HeaderCard;
+import nom.tam.fits.HeaderCardException;
+import terrasaur.enums.FitsHeaderType;
+import terrasaur.utils.DTMHeader;
+
+/**
+ * Factory class that returns List<HeaderCard> where the HeaderCard objects are in the correct order
+ * for writing to a fits header. Also contains methods for creating List<HeaderCard> for different
+ * sections of a fits header
+ * 
+ * @author espirrc1
+ *
+ */
+public class FitsHeaderFactory {
+
+  private static final String PLANE = "PLANE";
+  private static final String COMMENT = "COMMENT";
+
+
+  public static DTMHeader getDTMHeader(FitsHdr fitsHdr, FitsHeaderType headerType) {
+
+    switch (headerType) {
+
+      case NFTMLN:
+        return new NFTmln(fitsHdr);
+
+      case DTMLOCALALTWG:
+        return new AltwgLocalDTM(fitsHdr);
+
+      case DTMGLOBALALTWG:
+        return new AltwgGlobalDTM(fitsHdr);
+
+      case DTMGLOBALGENERIC:
+        return new GenericGlobalDTM(fitsHdr);
+
+      case DTMLOCALGENERIC:
+        return new GenericLocalDTM(fitsHdr);
+
+      default:
+        return null;
+    }
+
+  }
+
+  public static AnciFitsHeader getAnciHeader(FitsHdr fitsHdr, FitsHeaderType headerType) {
+
+    switch (headerType) {
+      case ANCIGLOBALGENERIC:
+        return new GenericAnciGlobal(fitsHdr);
+
+      case ANCILOCALGENERIC:
+        return new GenericAnciLocal(fitsHdr);
+
+      case ANCIGLOBALALTWG:
+        return new AltwgAnciGlobal(fitsHdr);
+
+      case ANCIG_FACETRELATION_ALTWG:
+        return new AltwgAnciGlobalFacetRelation(fitsHdr);
+
+      case ANCILOCALALTWG:
+        return new AltwgAnciLocal(fitsHdr);
+
+      default:
+        return null;
+    }
+
+  }
+
+
+  /**
+   * Fits Header block that contains information about the fits header itself. Ex. Header version
+   * number.
+   * 
+   * @param fitsHdr
+   * @return
+   * @throws HeaderCardException
+   */
+  public static List<HeaderCard> getHeaderInfo(FitsHeader fitsHdr) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    headers.add(new HeaderCard(COMMENT, "header information", false));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.HDRVERS));
+
+    return headers;
+
+  }
+
+  /**
+   * Fits header block that contains information about the mission Ex. MISSION name, HOST name,
+   * Target name.
+   * 
+   * @param fitsHdr
+   * @return
+   * @throws HeaderCardException
+   */
+  public static List<HeaderCard> getMissionInfo(FitsHeader fitsHdr) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    headers.add(new HeaderCard(COMMENT, "mission information", false));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.MISSION));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.HOSTNAME));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.TARGET));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.ORIGIN));
+
+    return headers;
+
+  }
+
+  /**
+   * Fits header block that contains ID information, i.e. information that would uniquely identify
+   * the data product.
+   * 
+   * @param fitsHdr
+   * @return
+   * @throws HeaderCardException
+   */
+  public static List<HeaderCard> getIdInfo(FitsHeader fitsHdr) throws HeaderCardException {
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    headers.add(new HeaderCard(COMMENT, "identification info", false));
+
+    // check latest Map Format SIS revision to see if SPOC handles these keywords
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.SPOC_ID));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.SDPAREA));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.SDPDESC));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.MPHASE));
+
+    return headers;
+
+  }
+
+  /**
+   * Fits header block that contains information about the source shape model used to create the
+   * fits file.
+   * 
+   * @param fitsHdr
+   * @return
+   * @throws HeaderCardException
+   */
+  public static List<HeaderCard> getShapeSourceInfo(FitsHeader fitsHdr) throws HeaderCardException {
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    headers.add(new HeaderCard(COMMENT, "shape data source", false));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.DATASRC));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.DATASRCF));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.DATASRCV));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.DATASRCS));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.DATASRCD));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.OBJ_FILE));
+
+    return headers;
+  }
+
+  public static List<HeaderCard> getProcInfo(FitsHeader fitsHdr) throws HeaderCardException {
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    headers.add(new HeaderCard(COMMENT, "processing information", false));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.PRODNAME));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.DATEPRD));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.SOFTWARE));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.SOFT_VER));
+
+    return headers;
+
+  }
+
+  public static List<HeaderCard> getMapSpecificInfo(FitsHeader fitsHdr) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+    headers.add(new HeaderCard(COMMENT, "map specific information", false));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.MAP_NAME));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.MAP_VER));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.MAP_TYPE));
+
+    return headers;
+
+    // check latest Map Format SIS revision to see if SPOC handles these keywords
+    // MAP_PROJ*
+    // GSD*
+    // GSDI*
+  }
+
+  public static List<HeaderCard> getSummarySpatialInfo(FitsHeader fitsHdr,
+      FitsHeaderType fitsHeaderType) throws HeaderCardException {
+
+    List<HeaderCard> headers = new ArrayList<HeaderCard>();
+
+    // this section common to all fitsHeaderTypes
+    headers.add(new HeaderCard(COMMENT, "summary spatial information", false));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.CLON));
+    headers.add(fitsHdr.getHeaderCard(HeaderTag.CLAT));
+
+    switch (fitsHeaderType) {
+      case ANCILOCALGENERIC:
+        headers.add(fitsHdr.getHeaderCard(HeaderTag.LLCLNG));
+        headers.add(fitsHdr.getHeaderCard(HeaderTag.LLCLAT));
+        headers.add(fitsHdr.getHeaderCard(HeaderTag.URCLNG));
+        headers.add(fitsHdr.getHeaderCard(HeaderTag.URCLAT));
+        headers.add(fitsHdr.getHeaderCard(HeaderTag.LRCLNG));
+        headers.add(fitsHdr.getHeaderCard(HeaderTag.LRCLAT));
+        headers.add(fitsHdr.getHeaderCard(HeaderTag.ULCLNG));
+        headers.add(fitsHdr.getHeaderCard(HeaderTag.ULCLAT));
+        break;
+
+      default:
+        // default does nothing because switch only handles specific cases.
+        break;
+    }
+    return headers;
+
+  }
+}