adding initial documentation

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docs/components/1__pulsar_querying/pq_overview.md

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+# **Pulsar Querying**
+
+## **Installation** 
+Before using the OpenXNAV Pulsar Querying Tool, you will need to install the necessary python packages. You can do this using your preferred python package manager, but instructions are provided below for using ```Anaconda```
+
+Inside the ```open-xnav/1__pulsar_querying/``` directory, there is an ```environment.yml``` file. This file can be passed to your preferred package manager to create a new environment that can run the tool. 
+
+### **Create New Environment**
+
+The default environment name in ```environment.yml``` is ```openXNAV-gui```. If you wish to change the environment name, simply edit ```environment.yml``` before creating the environment. 
+
+Open your Anaconda Prompt (or activate Anaconda in a terminal window). Navigate to ```open-xnav/`1__pulsar_querying/``` and run the following command: 
+```shell
+conda env create -f environment.yaml
+```
+
+To activate your environment, run the following command: 
+```shell
+conda activate openXNAV-gui
+```
+NOTE: If you altered the environment name, you will need to alter the above command to reflect that new name. 
+
+
+
+### **Install KivyMD**
+
+The tool also depends on [KivyMD](https://kivymd.readthedocs.io/en/latest/), which is a library built off of the popular [Kivy](https://kivy.org/) library. This package is not available through ```conda```, so you must install it using ```pip```. 
+
+First, make sure you have activated the ```openXNAV-gui ``` environment in your terminal. Then, run the following command: 
+
+```shell
+pip install kivymd
+```
+
+If you are getting a ```ReadTimeoutError``` response during installation, you might be using a VPN or have a slower internet connection. If this happens, try running the following instead: 
+
+```shell
+pip install --default-timeout=1000 kivymd
+```
+
+If that still does not work, you can troubleshoot your issues further using the ```pip``` documentation [here](https://pip.pypa.io/en/stable/user_guide/). 
+
+
+
+
+## **Using The Tool**
+
+### **Load/Generate Database**
+
+Once you have successfully installed all the required packages, you are ready to run the tool!
+
+First, ensure you have navigated to ```open-xnav/1__pulsar_querying/``` in your terminal and have your ```openXNAV-gui``` environment activated. 
+
+Then, simply run the following in your terminal: 
+```shell
+python run.py
+```
+
+Upon startup, the tool will need to pull the current ATNF Pulsar Catalogue from the web. This process only need to be done the first time you open the application. 
+
+![loadingDatabase](loading.PNG)
+
+However, if you wish to update the database, simply delete the ```.../pulsar_database/``` directory from your file system. Then, relaunch the application. Once the database has been generated, you can continue begin querying. 
+
+![databaseGenerated](successfulGeneration.PNG)
+
+You should see the OpenXNAV launch window with the blue ```Launch Application``` button active. In the future, when you open the application, the tool will locate the previously-generated database and you can quickly continue to the querying functionality.
+
+![startPage](startPage.PNG)
+
+
+### **Query For Pulsars**
+
+After you click ```Launch Application```, the query tool will display.
+
+![queryPage](queryPage_blank.PNG)
+
+There are three fields that you need to provide to execute a query: 
+
+- **Right Ascension** (HH:MM:SS)
+- **Declination** (DD:MM:SS)
+- **Search Radius** (Degrees)
+
+These values will create a query, searching for all known pulsars that are within a given search radius of the provided coordinates in space. 
+
+The OpenXNAV tool leverages the open-source ```psrqpy``` library. More information about this package, and how queries are executed, can be found [here](https://psrqpy.readthedocs.io/en/latest/query.html).
+
+The query results will display to the GUI interface, and will also be stored in a sub-directory within ```.../query_results/```. 
+
+![queryResults](rawQuery.PNG)
+
+For information about how these sub-directories are tagged, see below. 
+
+#### Tagging Results
+
+There is an optional ```Tag``` field that OpenXNAV also provides. This allows you to specify the tag for this query you are about to execute. If a tag is provided, that will be used to name the sub-directory within ```.../query_results/``` where all pulsars returned by the query are stored. 
+
+![tagging](tagging.PNG)
+
+**Sample Queries**
+
+Below are couple sample queries that you can run to get familiar with the OpenXNAV tool. There are additional sample query results contained in the ```.../query_results/``` directory. 
+
+|    Query    | Right Ascension | Declination | Radius |
+| --------------------- | ----------- | ----------- | ----------- |
+| *Parker Solar Probe* | 9.805475733988583 | 12.005839937612905 | 15.0 |
+| *L2* | 18:24:32.00819 | -24:52:10.720 | 30.0 |
+
+
+## **Output Files**
+
+### **STK Integration**
+
+Right now, the OpenXNAV Pulsar Querying Tool only outputs pulsar data into the ```.st``` format. This is the format that is required by STK to perform subsequent mission planning. 
+
+To display the format of this file, here is ```J00012_5431.st``` as an example: 
+
+```
+stk.v.12.0
+WrittenBy    OpenXNAV
+
+BEGIN Star
+
+    Name		 J0012_5431
+
+    BEGIN PathDescription
+
+        Epoch		  58912.0
+        RefFrame		 J2000
+        RightAscension		  3.097083333333333
+        Declination		  +54:31:47
+        ProperMotionRAPerYr		 0
+        ProperMotionDecPerYr		 0
+        Parallax		  0
+        RadialVelocity		  0.0000000000000000e+00
+
+    END PathDescription
+
+    BEGIN PhysicalData
+
+        Magnitude		  None
+
+    END PhysicalData
+
+    BEGIN IdentityData
+
+        Id		 0
+
+    END IdentityData
+
+
+    BEGIN Extensions
+
+        BEGIN ExternData
+        END ExternData
+
+        BEGIN ADFFileData
+        END ADFFileData
+
+        BEGIN AccessConstraints
+            LineOfSight IncludeIntervals
+
+            UsePreferredMaxStep No
+            PreferredMaxStep 360
+        END AccessConstraints
+
+        BEGIN Desc
+        END Desc
+
+        BEGIN Crdn
+        END Crdn
+
+        BEGIN Graphics
+
+            BEGIN Attributes
+
+                MarkerColor		 #00ff00
+                LabelColor		 #00ff00
+                MarkerStyle		 2
+                FontStyle		 0
+
+            END Attributes
+
+            BEGIN Graphics
+
+                Show		 On
+                Inherit		 On
+                ShowLabel		 On
+                ShowMarker		 On
+
+            END Graphics
+        END Graphics
+
+        BEGIN VO
+        END VO
+
+    END Extensions
+
+END Star
+```
+
+You will need to provide these ```.st``` file(s) to STK to successfully execute OpenXNAV's mission planning functionality. 
+
+### **Other File Formats**
+
+However, if you would like pulsar information to be stored/saved in a different format, you can modify the source code. 
+
+Navigate to ```queryPulsar.py``` and locate the following function: 
+```python
+def saveToFile(self, root_directory) ...
+```
+Here, you can alter/update the code to print the pulsar information into your desired format. Once this function has been updated, query results will automatically store in this new format. All query results will still appear in ```.../query_results/```.
+

docs/components/3__custom_event_generation/ceg_overview.md

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+# **Timing & Event Generation**
+
+
+In this Python notebook, the ``event_generation`` module from the PLANTS library is demonstrated.
+
+We start by importing the necessary libraries:
+
+```python
+%load_ext autoreload
+%autoreload 2
+from pint_backend import *
+import pulsar_definitions
+pint.logging.setup(level="INFO")
+
+```
+
+
+**Loads the ephemerides kernel**
+
+
+```python
+pint.solar_system_ephemerides.load_kernel("de440")
+```
+
+    INFO     (pint.solar_system_ephemerides ): Set solar system ephemeris to de440 through astropy
+
+
+Creates the time vector that the user hopes to observe at and adds additional error if desired. Specifies what pulsar model to use
+
+
+```python
+time_interval = astrotime.Time( ['2022-07-11T16:00:01.000', '2022-07-11T16:21:01.000'], format='isot', scale='utc')
+obs_fs = 100e6
+n_toa = 10
+error = 5 * u.us
+apply_error = False
+model_name = "j0218" 
+
+```
+
+Loads in the navigation data provided by STK and generates a spacecraft object off of that navigation data. Note that spacecraft is a custom class created in the PINT backend
+
+
+```python
+time, pos, vel = load_nav_data("XNAVSAT_TEMEofDate_Position_Velocity_JD.txt")
+my_spacecraft = SpaceCraft("my_spacecraft", time, pos, vel, overwrite = True)
+
+```
+
+Generates the times of arrival at the barycenter compared to the spacecraft. Note that printing the time of arrival generated is slightly different at the two locations
+
+
+```python
+if(model_name == "j0218"):  
+    pulsar_of_interest = PulsarObj(pulsar_definitions.J0218)
+elif(model_name == "b1821"):
+    pulsar_of_interest = PulsarObj(pulsar_definitions.B1821)
+toas_barycenter = pint.simulation.make_fake_toas_uniform(
+    time_interval[0].mjd, time_interval[1].mjd, n_toa, model=pulsar_of_interest.model, freq = 1e15*u.Hz, obs='barycenter',  error=error)
+toas_spacecraft = pint.simulation.make_fake_toas_uniform(
+    time_interval[0].mjd, time_interval[1].mjd, n_toa, model=pulsar_of_interest.model, freq = 1e15*u.Hz, obs = "my_spacecraft",  error=error)
+
+
+
+print("Barycenter first TOA: " + str(toas_barycenter.get_mjds("True")[0].utc.iso))
+print("Spacecraft first TOA: " + str(toas_spacecraft.get_mjds("True")[0].utc.iso))
+```
+
+    WARNING  (pint.logging                  ): /opt/anaconda/lib/python3.10/site-packages/pint/models/timing_model.py:373 UserWarning: PINT only supports 'T2CMETHOD IAU2000B'
+    WARNING  (pint.logging                  ): /opt/anaconda/lib/python3.10/site-packages/pint/models/model_builder.py:139 UserWarning: Unrecognized parfile line 'EPHVER 2'
+    INFO     (pint.simulation               ): Using CLOCK = TT(TAI), so setting include_bipm = False
+    INFO     (pint.models.absolute_phase    ): The TZRSITE is set at the solar system barycenter.
+    INFO     (pint.models.absolute_phase    ): TZRFRQ was 0.0 or None. Setting to infinite frequency.
+    INFO     (pint.simulation               ): Using CLOCK = TT(TAI), so setting include_bipm = False
+
+
+    Barycenter first TOA: 2022-07-11 15:58:51.816031354
+    Spacecraft first TOA: 2022-07-11 15:58:51.815489874
+
+
+
+```python
+%matplotlib inline
+resolution_factor = 1
+pulsar_of_interest.lightcurve.plot_lightcurve()
+time_vec, photon_vec, probability_arr = pulsar_of_interest.lightcurve.create_toa_vec(0, 10, k=4,resolution_factor= resolution_factor)
+```
+
+
+    
+![png](output_9_0.png)
+    
+
+
+
+```python
+%matplotlib inline
+plt.plot(time_vec[0:10000], photon_vec[0:10000])
+plt.xlabel("Time (s)")
+plt.ylabel("Number of photons received")
+plt.title("Photon vector over 25 ms")
+```
+
+
+
+
+    Text(0.5, 1.0, 'Photon vector over 25 ms')
+
+
+
+
+    
+![png](output_10_1.png)
+    
+
+
+
+```python
+snip = time_vec
+indices = np.argwhere(photon_vec != 0).flatten()
+plt.hist(snip[indices], bins = 500)
+plt.title("Histogram of photons received with bin resolution = 60 ms")
+plt.xlabel("Time (s)")
+plt.ylabel("Number of photons received")
+```
+
+
+
+
+    Text(0, 0.5, 'Number of photons received')
+
+
+
+
+    
+![png](output_11_1.png)
+    
+
+
+
+```python
+%matplotlib inline
+barycenter_toas =  create_obs_time_vec(toas_barycenter.first_MJD, time_vec)
+pulse_fold_barycenter = LightProfile.pulse_folding(barycenter_toas, photon_vec, pulsar_of_interest.lightcurve, mjd = True, start_offset = toas_barycenter.first_MJD, resolution_factor = resolution_factor)
+
+plt.plot(pulsar_of_interest.lightcurve.phase_list, pulse_fold_barycenter)
+plt.xlabel("Phase")
+plt.ylabel("Count")
+spacecraft_toas = create_obs_time_vec(toas_spacecraft.first_MJD, time_vec)
+pulse_fold_spacecraft = LightProfile.pulse_folding(spacecraft_toas, photon_vec, pulsar_of_interest.lightcurve, mjd = True, start_offset = toas_barycenter.first_MJD, resolution_factor = resolution_factor)
+plt.plot(pulsar_of_interest.lightcurve.phase_list, pulse_fold_spacecraft)
+plt.legend(['Barycenter', 'Spacecraft'])
+# plt.plot(pulse_fold_spacecraft.phase_list, pulse_fold_barycenter)
+# plt.show()
+```
+
+
+
+
+    <matplotlib.legend.Legend at 0x7f9a6dc79120>
+
+
+
+
+    
+![png](output_12_1.png)
+    
+
+
+An example of what happens if you fold the pulse with the wrong pulsar of interest
+
+
+```python
+pulse_fold_barycenter = LightProfile.pulse_folding(barycenter_toas, photon_vec, pulsar_of_interest.lightcurve, mjd = True, start_offset = toas_barycenter.first_MJD, resolution_factor = resolution_factor)
+plt.plot(pulsar_of_interest.lightcurve.phase_list, pulse_fold_barycenter)
+plt.xlabel("Phase")
+plt.ylabel("Count")
+```
+
+
+
+
+    Text(0, 0.5, 'Count')
+
+
+
+
+    
+![png](output_14_1.png)
+    
+
+
+
+```python
+np.save("pulsar_vec.npy", np.asarray(photon_vec))
+```

docs/getting_started.md

@@ -0,0 +1,20 @@
+---
+hide:
+  - navigation
+---
+
+# **Getting Started**
+
+Each component of OpenXNAV can be used individually, or strung together as an end-to-end pipeline. To get started with OpenXNAV, select the module you are interested in leveraging and access the documentation. 
+
+## [**Pulsar Querying**](components/1__pulsar_querying/pq_overview.md)
+Query for all known pulsars catalogued in the ATNF database by providing a coordinate in space, and a search radius. 
+
+## [**Mission Planning**](components/2__mission_planning/mp_overview.md)
+Model the desired flight path, taking into account spacecraft orientation, viewing angle and line of sight. 
+
+## [**Timing & Event Generation**](components/3__custom_event_generation/ceg_overview.md)
+Generate representative photon arrival events at the location of interest along the user-defined trajectory. 
+
+
+

docs/index.md

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+---
+hide:
+  - navigation
+---
+
+# 
+
+![OpenXNAV Logo](/assets/images/logo/png/23-03611_OpenXNav_Color-full.png#only-light){ width=50% }
+![OpenXNAV Logo](/assets/images/logo/png/23-03611_OpenXNav_White-lightblue-full.png#only-dark){ width=50% }
+
+*Open-source modular toolkit for simulating high-fidelity pulsar X-ray events.* 
+
+
+## **Introduction to OpenXNAV**
+
+OpenXNAV is designed to aid development and testing of Pulsar-based Autonomous Navigation (XNAV) Positioning, Navigation, and Timing (PNT) solutions.
+
+You can read our IEEE paper to learn more: [IEEE.org](https://ieeexplore.ieee.org/document/10139942).
+
+
+
+## **Components**
+
+* [Pulsar Querying](components/1__pulsar_querying/pq_overview.md)
+* [Mission Planning](components/2__mission_planning/mp_overview.md)
+* [Timing & Event Generation](components/3__custom_event_generation/ceg_overview.md)

docs/stylesheets/extra.css

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