C++ code is documented!

rahil-makadia · Mar 26, 2024 · 61f91c1 · 61f91c1
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -33,3 +33,25 @@ target_compile_definitions(libgrss PRIVATE VERSION_INFO=${${PROJECT_NAME}_VERSIO
 
 # compile tests
 add_subdirectory(tests/cpp/prop)
+
+# build the documentation
+find_package(Doxygen)
+if (DOXYGEN_FOUND)
+    # set input and output files
+    set(DOXYGEN_IN ${CMAKE_SOURCE_DIR}/docs/doxygen/doxygen.config)
+    set(DOXYGEN_OUT ${CMAKE_SOURCE_DIR}/docs/doxygen/doxyfile.out)
+
+    # configure the file and fill out CMake variables
+    configure_file(${DOXYGEN_IN} ${DOXYGEN_OUT} @ONLY)
+
+    # note: the option ALL allows building the docs with the binaries
+    add_custom_target(
+        doxygen_docs ALL
+        COMMAND ${DOXYGEN_EXECUTABLE} ${DOXYGEN_OUT}
+        WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/docs/doxygen
+        COMMENT "Generating API documentation with Doxygen"
+        VERBATIM
+    )
+else (DOXYGEN_FOUND)
+    message(FATAL_ERROR "Doxygen needs to be installed to generate the doxygen documentation")
+endif (DOXYGEN_FOUND)
diff --git a/README.md b/README.md
@@ -79,4 +79,4 @@ GRSS Development Team:
 * Siegfried Eggl
 * Davide Farnocchia
 
-The GRSS library was developed by Rahil Makadia as part of his PhD dissertation at the University of Illinois at Urbana-Champaign. This work was supported by a NASA Space Technologies Graduate Research Opportunities (NSTGRO) Fellowship, Grant #80NSSC22K1173. The author would like to thank his advisor, Dr. Siegfried Eggl as well as his collaborators, Dr. Steven R. Chesley, and Dr. Davide Farnocchia for their guidance and support.
+The GRSS library was developed by Rahil Makadia as part of his PhD dissertation at the University of Illinois at Urbana-Champaign. This work was supported by a NASA Space Technologies Graduate Research Opportunities (NSTGRO) Fellowship, Grant #80NSSC22K1173. Rahil would like to thank his advisor, Dr. Siegfried Eggl as well as his collaborators, Dr. Steven R. Chesley, and Dr. Davide Farnocchia for their guidance and support.
diff --git a/docs/doxygen/doxygen.config b/docs/doxygen/doxygen.config
diff --git a/docs/source/_static/grss-doxygen.png b/docs/source/_static/grss-doxygen.png
diff --git a/docs/source/api_cpp.rst b/docs/source/api_cpp.rst
@@ -0,0 +1,58 @@
+C++ API
+=======
+
+.. toctree::
+   :hidden:
+
+   cppsummary/approach
+   cppsummary/elements
+   cppsummary/force
+   cppsummary/gr15
+   cppsummary/interpolate
+   cppsummary/parallel
+   cppsummary/simulation
+   cppsummary/spk
+   cppsummary/stm
+   cppsummary/timeconvert
+   cppsummary/utilities
+
+.. taken from autosummary code for Python API for consistency and symmetry to satisfy the OCD gods (and my psychotic brain)
+.. raw:: html
+
+   <table class="autosummary longtable table autosummary">
+   <tbody>
+   <tr class="row-odd"><td><p><a class="reference internal" href="cppsummary/approach.html" title="approach.h"><code class="xref py py-obj docutils literal notranslate"><span class="pre">approach.h</span></code></a></p></td>
+   <td><p>GRSS C++ close approach submodule</p></td>
+   </tr>
+   <tr class="row-even"><td><p><a class="reference internal" href="cppsummary/elements.html" title="elements.h"><code class="xref py py-obj docutils literal notranslate"><span class="pre">elements.h</span></code></a></p></td>
+   <td><p>GRSS C++ orbital elements submodule</p></td>
+   </tr>
+   <tr class="row-odd"><td><p><a class="reference internal" href="cppsummary/force.html" title="force.h"><code class="xref py py-obj docutils literal notranslate"><span class="pre">force.h</span></code></a></p></td>
+   <td><p>GRSS C++ force function submodule</p></td>
+   </tr>
+   <tr class="row-even"><td><p><a class="reference internal" href="cppsummary/gr15.html" title="gr15.h"><code class="xref py py-obj docutils literal notranslate"><span class="pre">gr15.h</span></code></a></p></td>
+   <td><p>GRSS C++ Gauss-Radau 15<sup>th</sup> order integrator submodule</p></td>
+   </tr>
+   <tr class="row-odd"><td><p><a class="reference internal" href="cppsummary/interpolate.html" title="interpolate.h"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interpolate.h</span></code></a></p></td>
+   <td><p>GRSS C++ integrator state interpolation submodule</p></td>
+   </tr>
+   <tr class="row-even"><td><p><a class="reference internal" href="cppsummary/parallel.html" title="parallel.h"><code class="xref py py-obj docutils literal notranslate"><span class="pre">parallel.h</span></code></a></p></td>
+   <td><p>GRSS C++ parallel propagation submodule</p></td>
+   </tr>
+   <tr class="row-odd"><td><p><a class="reference internal" href="cppsummary/simulation.html" title="simulation.h"><code class="xref py py-obj docutils literal notranslate"><span class="pre">simulation.h</span></code></a></p></td>
+   <td><p>GRSS C++ propagator simulation submodule</p></td>
+   </tr>
+   <tr class="row-even"><td><p><a class="reference internal" href="cppsummary/spk.html" title="spk.h"><code class="xref py py-obj docutils literal notranslate"><span class="pre">spk.h</span></code></a></p></td>
+   <td><p>GRSS C++ SPK file submodule</p></td>
+   </tr>
+   <tr class="row-odd"><td><p><a class="reference internal" href="cppsummary/stm.html" title="stm.h"><code class="xref py py-obj docutils literal notranslate"><span class="pre">stm.h</span></code></a></p></td>
+   <td><p>GRSS C++ state transition matrix submodule</p></td>
+   </tr>
+   <tr class="row-even"><td><p><a class="reference internal" href="cppsummary/timeconvert.html" title="timeconvert.h"><code class="xref py py-obj docutils literal notranslate"><span class="pre">timeconvert.h</span></code></a></p></td>
+   <td><p>GRSS C++ time conversion submodule</p></td>
+   </tr>
+   <tr class="row-odd"><td><p><a class="reference internal" href="cppsummary/utilities.html" title="utilities.h"><code class="xref py py-obj docutils literal notranslate"><span class="pre">utilities.h</span></code></a></p></td>
+   <td><p>GRSS C++ utilities submodule</p></td>
+   </tr>
+   </tbody>
+   </table>
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -66,24 +66,7 @@
         "alt_text": "GRSS - Home",
         "text": f"{project} v{version} documentation",
     },
-    # "icon_links": [
-    #     {
-    #         "name": "GitHub",
-    #         "url": "https://github.com/rahil-makadia/grss",
-    #         "icon": "fa-brands fa-github",
-    #     },
-    #     {
-    #         "name": "PyPI Downloads",
-    #         "url": "https://pypi.org/project/grss/",
-    #         "icon": "https://img.shields.io/pypi/dw/grss",
-    #         "type": "url",
-    #     },
-    #     {
-    #         "name": "PyPI",
-    #         "url": "https://pypi.org/project/grss/",
-    #         "icon": "fa-brands fa-python",
-    #     },
-    # ],
+    "navigation_with_keys": True,
     "extra_footer": ("Created using "
                         "<a href=https://sphinx-book-theme.readthedocs.io/>"
                         "The Sphinx Book Theme</a>."),

diff --git a/docs/source/cppsummary/approach.rst b/docs/source/cppsummary/approach.rst
@@ -0,0 +1,6 @@
+approach.h
+==========
+
+.. doxygenfile:: approach.h
+   :project: GRSS
+
diff --git a/docs/source/cppsummary/elements.rst b/docs/source/cppsummary/elements.rst
@@ -0,0 +1,6 @@
+elements.h
+==========
+
+.. doxygenfile:: elements.h
+   :project: GRSS
+
diff --git a/docs/source/cppsummary/force.rst b/docs/source/cppsummary/force.rst
@@ -0,0 +1,6 @@
+force.h
+=======
+
+.. doxygenfile:: force.h
+   :project: GRSS
+
diff --git a/docs/source/cppsummary/gr15.rst b/docs/source/cppsummary/gr15.rst
@@ -0,0 +1,6 @@
+gr15.h
+======
+
+.. doxygenfile:: gr15.h
+   :project: GRSS
+
diff --git a/docs/source/cppsummary/interpolate.rst b/docs/source/cppsummary/interpolate.rst
@@ -0,0 +1,6 @@
+interpolate.h
+=============
+
+.. doxygenfile:: interpolate.h
+   :project: GRSS
+
diff --git a/docs/source/cppsummary/parallel.rst b/docs/source/cppsummary/parallel.rst
@@ -0,0 +1,6 @@
+parallel.h
+==========
+
+.. doxygenfile:: parallel.h
+   :project: GRSS
+
diff --git a/docs/source/cppsummary/simulation.rst b/docs/source/cppsummary/simulation.rst
@@ -0,0 +1,6 @@
+simulation.h
+============
+
+.. doxygenfile:: simulation.h
+   :project: GRSS
+
diff --git a/docs/source/cppsummary/spk.rst b/docs/source/cppsummary/spk.rst
@@ -0,0 +1,6 @@
+spk.h
+=====
+
+.. doxygenfile:: spk.h
+   :project: GRSS
+
diff --git a/docs/source/cppsummary/stm.rst b/docs/source/cppsummary/stm.rst
@@ -0,0 +1,6 @@
+stm.h
+=====
+
+.. doxygenfile:: stm.h
+   :project: GRSS
+
diff --git a/docs/source/cppsummary/timeconvert.rst b/docs/source/cppsummary/timeconvert.rst
@@ -0,0 +1,6 @@
+timeconvert.h
+=============
+
+.. doxygenfile:: timeconvert.h
+   :project: GRSS
+
diff --git a/docs/source/cppsummary/utilities.rst b/docs/source/cppsummary/utilities.rst
@@ -0,0 +1,6 @@
+utilities.h
+===========
+
+.. doxygenfile:: utilities.h
+   :project: GRSS
+
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -23,6 +23,7 @@ Continue reading on the following pages to learn more about the library:
    fit
    examples
    api_py
+   api_cpp
    genindex
 
 ----------------
@@ -35,4 +36,4 @@ GRSS Development Team:
 * Siegfried Eggl
 * Davide Farnocchia
 
-The GRSS library was developed by Rahil Makadia as part of his PhD dissertation at the University of Illinois at Urbana-Champaign. This work was supported by a NASA Space Technologies Graduate Research Opportunities (NSTGRO) Fellowship, Grant #80NSSC22K1173. The author would like to thank his advisor, Dr. Siegfried Eggl as well as his collaborators, Dr. Steven R. Chesley, and Dr. Davide Farnocchia for their guidance and support.
+The GRSS library was developed by Rahil Makadia as part of his PhD dissertation at the University of Illinois at Urbana-Champaign. This work was supported by a NASA Space Technologies Graduate Research Opportunities (NSTGRO) Fellowship, Grant #80NSSC22K1173. Rahil would like to thank his advisor, Dr. Siegfried Eggl as well as his collaborators, Dr. Steven R. Chesley, and Dr. Davide Farnocchia for their guidance and support.
diff --git a/grss/fit/__init__.py b/grss/fit/__init__.py
@@ -1,4 +1,4 @@
-"""GRSS orbit determination subpackage"""
+"""GRSS Python orbit determination subpackage"""
 import warnings
 from .fit_optical import *
 from .fit_radar import *

diff --git a/grss/fit/fit_optical.py b/grss/fit/fit_optical.py
@@ -568,7 +568,7 @@ def apply_weights(obs_array_optical, star_catalog_codes, observer_codes_optical,
             obs_array_optical[i, 3:5] = 2.0
         elif obs_type in ['S']: # satellite
             if obs_code in ['275']: # non-geocentric occultation
-                obs_array_optical[i, 3:5] = 3e-3
+                obs_array_optical[i, 3:5] = 0.05
             elif obs_code in ['250']: # HST
                 obs_array_optical[i, 3:5] = 1.3
             elif obs_code in ['249', 'C49', 'C50']: # SOHO, STEREO-A, STEREO-B
@@ -643,11 +643,11 @@ def apply_weights(obs_array_optical, star_catalog_codes, observer_codes_optical,
                     obs_array_optical[i, 3:5] = 0.5
                     if obs_program == '0':
                         obs_array_optical[i, 3:5] = 0.1
-                    elif obs_program == '1':
+                    elif obs_program in ['1', '4']:
                         obs_array_optical[i, 3:5] = 1.0
-                    elif obs_program in {'2', '3'}:
+                    elif obs_program in ['2', '3']:
                         obs_array_optical[i, 3:5] = 0.5
-                    if obs_date_mjd < 60223.0: # until 2023-10-06
+                    if obs_date_mjd < 59858.0: # until 2022-10-06
                         obs_array_optical[i, 3:5] = 0.1
                 elif obs_code in ['T10', 'T11', 'T13', 'T16', 'T17']:
                     obs_array_optical[i, 3:5] = 0.5
@@ -657,15 +657,15 @@ def apply_weights(obs_array_optical, star_catalog_codes, observer_codes_optical,
                         obs_array_optical[i, 3:5] = 0.1
                     elif obs_program == '1':
                         obs_array_optical[i, 3:5] = 0.2
-                    elif obs_program in {'2', '3'}:
+                    elif obs_program in ['2', '3']:
                         obs_array_optical[i, 3:5] = 0.5
                     if obs_date_mjd < 59858.0: # until 2022-10-06
                         obs_array_optical[i, 3:5] = 0.1
                 elif obs_code in ['T14']:
                     obs_array_optical[i, 3:5] = 0.5
-                    if obs_program in {'0', '7'}:
+                    if obs_program in ['0', '7']:
                         obs_array_optical[i, 3:5] = 0.1
-                    elif obs_program in {'1', '2', '4', '6'}:
+                    elif obs_program in ['1', '2', '4', '6', '8']:
                         obs_array_optical[i, 3:5] = 0.5
                     elif obs_program == '3':
                         obs_array_optical[i, 3:5] = 0.2
@@ -691,12 +691,13 @@ def apply_weights(obs_array_optical, star_catalog_codes, observer_codes_optical,
                     if star_catalog in ['U', 'V', 'W', 'X', 't', 'L', 'q', 'r', 'u', 'e']:
                         obs_array_optical[i, 3:5] = 0.5
                     if obs_code in ['J04']:
-                        if obs_program == '2' and star_catalog in ['t', 'q', 'U', 'V', 'W', 'X']:
+                        if (obs_program in ['2', '$'] and
+                            star_catalog in ['t', 'q', 'U', 'V', 'W', 'X']):
                             obs_array_optical[i, 3:5] = 0.3
                         elif obs_program == '#':
                             obs_array_optical[i, 3:5] = 1.0
                     elif obs_code in ['Z84']:
-                        if obs_program == '1' and star_catalog in ['U', 'V', 'W', 'X']:
+                        if obs_program in ['1', '7'] and star_catalog in ['U', 'V', 'W', 'X']:
                             obs_array_optical[i, 3:5] = 0.3
                 elif obs_code in ['608']:
                     obs_array_optical[i, 3:5] = 0.6
@@ -711,18 +712,22 @@ def apply_weights(obs_array_optical, star_catalog_codes, observer_codes_optical,
                         obs_array_optical[i, 3:5] = 1.0
                 elif obs_code in ['E10']:
                     obs_array_optical[i, 3:5] = 0.4
-                    if obs_program == '(' and star_catalog in ['U', 'V', 'W', 'X']:
+                    if obs_program in ['(', '.'] and star_catalog in ['U', 'V', 'W', 'X']:
                         obs_array_optical[i, 3:5] = 0.2
                 elif obs_code in ['F65']:
                     obs_array_optical[i, 3:5] = 0.4
                     if obs_program == '8' and star_catalog in ['U', 'V', 'W', 'X']:
                         obs_array_optical[i, 3:5] = 0.2
                     elif obs_program == '9' and star_catalog in ['U', 'V', 'W', 'X']:
                         obs_array_optical[i, 3:5] = 0.2
-                elif obs_code in ['K91', 'K92', 'K93', 'Q63', 'Q64', 'V37', 'V39',
+                elif obs_code in ['K91', 'K92', 'K93', 'Q63', 'Q64', 'V39',
                                     'W85', 'W86', 'W87', 'Z24', 'Z31']:
                     obs_array_optical[i, 3:5] = 0.4
-                    if obs_program == '0':
+                    if obs_program in ['0', '3']:
+                        obs_array_optical[i, 3:5] = 0.3
+                elif obs_code in ['V37']:
+                    obs_array_optical[i, 3:5] = 0.4
+                    if obs_program in ['0', '6']:
                         obs_array_optical[i, 3:5] = 0.3
                 elif obs_code in ['Y28']:
                     if star_catalog in ['t', 'U', 'V', 'W', 'X']:
@@ -752,9 +757,12 @@ def apply_weights(obs_array_optical, star_catalog_codes, observer_codes_optical,
                 elif obs_code in ['Z18']:
                     if obs_program == '1' and star_catalog in ['U', 'V', 'W', 'X']:
                         obs_array_optical[i, 3:5] = 0.1
-                elif obs_code in ['181', 'D20']:
+                elif obs_code in ['181']:
                     if obs_program == '1' and star_catalog in ['U', 'V', 'W', 'X']:
                         obs_array_optical[i, 3:5] = 0.5
+                elif obs_code in ['D20']:
+                    if obs_program in ['1', '4'] and star_catalog in ['U', 'V', 'W', 'X']:
+                        obs_array_optical[i, 3:5] = 0.5
                 elif obs_code in ['G37']:
                     if obs_program == '5' and star_catalog in ['U', 'V', 'W', 'X']:
                         obs_array_optical[i, 3:5] = 0.2
@@ -764,6 +772,11 @@ def apply_weights(obs_array_optical, star_catalog_codes, observer_codes_optical,
                 elif obs_code in ['I41']:
                     if obs_program == 'Z':
                         obs_array_optical[i, 3:5] = 1.0
+                elif obs_code in ['W57']:
+                    if obs_program in ['0', '1']:
+                        obs_array_optical[i, 3:5] = 0.4
+                elif obs_code in ['M28']:
+                    obs_array_optical[i, 3:5] = 3.0
                 else:
                     default_weight_counter += 1
                     obs_array_optical[i, 3:5] = 1.0

diff --git a/grss/fit/fit_simulation.py b/grss/fit/fit_simulation.py
@@ -270,8 +270,10 @@ def _plot_residuals(self, t_arr, ra_residuals, dec_residuals, ra_cosdec_residual
         plt.suptitle(iter_string, y=0.95)
         grid_spec = fig.add_gridspec(1, 3, width_ratios=(1,1,1))
         ax1 = fig.add_subplot(grid_spec[0, 0])
-        ax1.plot(t_arr, ra_residuals, '.', label='RA', markersize=markersize)
-        ax1.plot(t_arr, dec_residuals, '.', label='Dec', markersize=markersize)
+        ax1.plot(t_arr, ra_residuals, '.', label='RA', markersize=markersize,
+                    color='C1', alpha=0.5)
+        ax1.plot(t_arr, dec_residuals, '.', label='Dec', markersize=markersize,
+                    color='C0', alpha=0.5)
         ax1.plot(t_arr[is_rejected], ra_residuals[is_rejected], 'ro',
                     markersize=2*markersize, markerfacecolor='none')
         ax1.plot(t_arr[is_rejected], dec_residuals[is_rejected], 'ro',
@@ -398,10 +400,10 @@ def _plot_chi(self, t_arr, ra_chi, dec_chi, delay_chi, doppler_chi,
         if plot_chi_squared:
             plt.subplot(1,2,1)
         if not np.all(np.isnan(ra_chi)) and not np.all(np.isnan(dec_chi)):
-            plt.plot(t_arr, ra_chi, '.', markersize=markersize, label='RA')
-            plt.plot(t_arr, dec_chi, '.', markersize=markersize, label='Dec')
+            plt.plot(t_arr, ra_chi, '.', markersize=markersize, label='RA', color='C1', alpha=0.5)
+            plt.plot(t_arr, dec_chi, '.', markersize=markersize, label='Dec', color='C0', alpha=0.5)
             plt.plot(t_arr[is_rejected], ra_chi[is_rejected], 'ro',
-                        markersize=2*markersize, markerfacecolor='none')#, label='Rejected Obs.')
+                        markersize=2*markersize, markerfacecolor='none', label='Rejected')
             plt.plot(t_arr[is_rejected], dec_chi[is_rejected], 'ro',
                         markersize=2*markersize, markerfacecolor='none')
         if not np.all(np.isnan(doppler_chi)):
@@ -425,8 +427,10 @@ def _plot_chi(self, t_arr, ra_chi, dec_chi, delay_chi, doppler_chi,
         plt.gcf().autofmt_xdate()
         if plot_chi_squared:
             plt.subplot(1,2,2)
-            plt.plot(t_arr, ra_chi_squared, '.', markersize=markersize, label='RA')
-            plt.plot(t_arr, dec_chi_squared, '.', markersize=markersize, label='Dec')
+            plt.plot(t_arr, ra_chi_squared, '.', markersize=markersize,
+                        label='RA', color='C1', alpha=0.5)
+            plt.plot(t_arr, dec_chi_squared, '.', markersize=markersize,
+                        label='Dec', color='C0', alpha=0.5)
             plt.plot(t_arr[is_rejected], ra_chi_squared[is_rejected], 'ro',
                         markersize=2*markersize, markerfacecolor='none')
             plt.plot(t_arr[is_rejected], dec_chi_squared[is_rejected], 'ro',

diff --git a/grss/prop/__init__.py b/grss/prop/__init__.py
@@ -1,4 +1,4 @@
-"""GRSS orbit propagation subpackage"""
+"""GRSS Python orbit propagation subpackage"""
 from ..libgrss import *
 from .prop_parallel import *
 from .prop_unscented import *

diff --git a/grss/utils.py b/grss/utils.py
@@ -1,4 +1,4 @@
-"""GRSS utilities subpackage"""
+"""GRSS Python utilities subpackage"""
 import os
 import sys
 import datetime

diff --git a/grss/version.txt b/grss/version.txt
@@ -1 +1 @@
-3.7.2
+3.8.0