updates for v1.1.0

doc/index.rst

@@ -16,7 +16,7 @@ The Terrasaur package requires Java 21 or later.  Some freely available versions
 Download
 ~~~~~~~~
 
-Binary packages for use on Mac OS X and Linux are available at ...
+Binary packages for use on Mac OS X and Linux are available at `GitHub <https://github.com/JHUAPL/Terrasaur/releases>`__.
 
 We have not tried using the softare on Microsoft Windows, but users may try the Linux package with the `Windows Subsystem for Linux <https://docs.microsoft.com/en-us/windows/wsl/>`__.
 

doc/make.bat

@@ -1,35 +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
+@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/tools/ColorSpots.rst

@@ -0,0 +1,70 @@
+.. _ColorSpots:
+
+##########
+ColorSpots
+##########
+
+ColorSpots takes as input a shape model and a file containing (x, y, z, value), 
+or (lat, lon, value).  It writes out the mean and standard deviation of values 
+within a specified range for each facet.
+
+.. include:: ../toolDescriptions/ColorSpots.txt
+    :literal:
+
+********
+Examples
+********
+
+Download the :download:`Apophis<./support_files/apophis_g_15618mm_rdr_obj_0000n00000_v001.obj>` 
+shape model and the :download:`info<./support_files/xyzrandom.txt>` file containing 
+cartesian coordinates and a random value.
+
+Run ColorSpots:
+
+::
+
+    ColorSpots -obj apophis_g_15618mm_rdr_obj_0000n00000_v001.obj -xyz \ 
+    -info xyzrandom.txt -outFile apophis_value_at_vertex.csv -noWeight \ 
+    -allFacets -additionalFields n -searchRadius 0.015 -writeVertices 
+
+The first few lines of apophis_value_at_vertex.csv look like:
+
+::
+
+    % head apophis_value_at_vertex.csv
+    0.000000e+00, 0.000000e+00, 1.664960e-01, -3.805764e-02, 5.342315e-01, 4.000000e+01
+    1.589500e-02, 0.000000e+00, 1.591030e-01, 6.122849e-02, 6.017192e-01, 5.000000e+01
+    7.837000e-03, 1.486800e-02, 1.591670e-01, -6.072964e-03, 5.220682e-01, 5.700000e+01
+    -7.747000e-03, 1.506300e-02, 1.621040e-01, 9.146163e-02, 5.488631e-01, 4.900000e+01
+    -1.554900e-02, 0.000000e+00, 1.657970e-01, -8.172811e-03, 5.270302e-01, 3.400000e+01
+    -7.982000e-03, -1.571100e-02, 1.694510e-01, -2.840524e-02, 5.045911e-01, 3.900000e+01
+    8.060000e-03, -1.543300e-02, 1.655150e-01, 3.531959e-02, 5.464390e-01, 4.900000e+01
+    3.179500e-02, 0.000000e+00, 1.515820e-01, -1.472434e-02, 5.967265e-01, 5.400000e+01
+    2.719700e-02, 1.658200e-02, 1.508930e-01, -9.050683e-03, 5.186966e-01, 4.700000e+01
+    1.554100e-02, 2.901300e-02, 1.530770e-01, -7.053547e-02, 4.980369e-01, 7.000000e+01
+
+The columns are:
+
+.. list-table:: ColorSpots Vertex output
+   :header-rows: 1
+
+   * - Column
+     - Value
+   * - 1
+     - X
+   * - 2
+     - Y
+   * - 3
+     - Z
+   * - 4
+     - mean value in region
+   * - 5
+     - standard deviation in region
+   * - 6
+     - number of points in region
+
+.. figure:: images/ColorSpots-n.png
+    :alt: Number of points in region at each vertex
+
+    This image shows the number of points in the region at each vertex.
+

doc/tools/CompareOBJ.rst

@@ -23,7 +23,7 @@ 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/>`.
+`ParaView <https://www.paraview.org/>`__.
 
 .. figure:: images/CompareOBJ_local_1.png
 
@@ -32,8 +32,8 @@ shape models.  You can view them in a tool such as
 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 \
+    CompareOBJ -computeOptimalRotationAndTranslation -model EVAL20.obj \ 
+    -reference EVAL20_wtr.obj -computeVerticalError verticalError.txt \
     -saveOptimalShape optimal.obj -savePlateDiff plateDiff.txt -savePlateIndex plateIndex.txt
 
 The screen output is
@@ -77,7 +77,7 @@ model for comparison:
 
 ::
 
-    ShapeFormatConverter -input Bennu/Bennu49k.obj -output BennuComparison.obj \
+    ShapeFormatConverter -input 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 
@@ -94,11 +94,11 @@ Run CompareOBJ to find the optimal transform to align the comparison with the re
 
     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
+    -reference Bennu49k.obj \
+    -computeVerticalError terrasaur-verticalError.txt \
+    -saveOptimalShape terrasaur-optimal.obj \
+    -savePlateDiff terrasaur-plateDiff.txt \
+    -savePlateIndex terrasaur-plateIndex.txt
 
 The screen output is
 

doc/tools/PointCloudOverlap.rst

@@ -0,0 +1,38 @@
+.. _PointCloudOverlap:
+
+#################
+PointCloudOverlap
+#################
+
+*****
+Usage
+*****
+
+.. include:: ../toolDescriptions/PointCloudOverlap.txt
+    :literal:
+
+********
+Examples
+********
+ 
+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/PointCloudOverlap_1.png
+
+   This image shows the reference (pink) and input (blue) shape models.
+
+Run PointCloudOverlap:
+
+::
+
+    PointCloudOverlap -inputFile EVAL20.obj -referenceFile EVAL20_wtr.obj -outputFile overlap.vtk 
+
+Note that OBJ is supported as an input format but not as an output format.
+
+
+.. figure:: images/PointCloudOverlap_2.png
+
+   The points in white are those in the input model that overlap the reference.
+

doc/tools/TriAx.rst

@@ -0,0 +1,43 @@
+.. _TriAx:
+
+=====
+TriAx
+=====
+
+TriAx is an implementation of the SPC tool TRIAX, which generates a triaxial ellipsoid in ICQ format.
+
+*****
+Usage
+*****
+
+.. include:: ../toolDescriptions/TriAx.txt
+    :literal:
+
+*******
+Example
+*******
+
+Generate an ellipsoid with dimensions 10, 8, 6, with q = 8.
+
+::
+
+    TriAx -A 10 -B 8 -C 6 -Q 8 -output triax.icq -saveOBJ 
+
+The following ellipsoid is generated:
+
+.. container:: figures-row
+
+    .. figure:: images/TriAx_X.png
+        :alt: looking down from the +X direction
+
+        looking down from the +X direction
+
+    .. figure:: images/TriAx_Y.png
+        :alt: looking down from the +Y direction
+
+        looking down from the +Y direction
+
+    .. figure:: images/TriAx_Z.png
+        :alt: looking down from the +Z direction
+
+        looking down from the +Z direction