Fix documentation

docs/source/api_reference/analysis/create_stamps.rst

@@ -0,0 +1,5 @@
+Module: create_stamps
+=====================
+
+.. automodule:: kbmod.analysis.create_stamps
+   :members:

docs/source/api_reference/analysis/plotting.rst

@@ -0,0 +1,5 @@
+Module: plotting
+================
+
+.. automodule:: kbmod.analysis.plotting
+   :members:

docs/source/api_reference/analysis/visualizer.rst

@@ -0,0 +1,5 @@
+Module: visualizer
+==================
+
+.. automodule:: kbmod.analysis.visualizer
+   :members:

docs/source/api_reference/filters/basic_filter.rst

@@ -0,0 +1,5 @@
+Module: basic_filters
+=====================
+
+.. automodule:: kbmod.filters.basic_filters
+   :members:

docs/source/api_reference/filters/clustering_filters.rst

@@ -0,0 +1,5 @@
+Module: clustering_filters
+==========================
+
+.. automodule:: kbmod.filters.clustering_filters
+   :members:

docs/source/api_reference/filters/known_object_filters.rst

@@ -0,0 +1,5 @@
+Module: known_object_filters
+============================
+
+.. automodule:: kbmod.filters.known_object_filters
+   :members:

docs/source/api_reference/filters/sigma_g_filter.rst

@@ -0,0 +1,5 @@
+Module: sigma_g_filter
+======================
+
+.. automodule:: kbmod.filters.sigma_g_filter
+   :members:

docs/source/api_reference/index.rst

@@ -10,7 +10,9 @@ Object Search
    configuration
    run_search_referenceapi
    search_referenceapi
+   results
    trajectory_explorer
+   trajectory_generator
    work_unit
 
 Preprocessing
@@ -20,7 +22,13 @@ Preprocessing
    :maxdepth: 1
 
    image_collection
-   masking
+   standardizers/butler_standardizer
+   standardizers/fits_standardizer
+   standardizers/kbmodv1
+   standardizers/kbmodv05
+   standardizers/multi_extension_fits
+   standardizers/single_extension_fits
+   standardizers/standardizer
    reprojection
 
 Filtering Results
@@ -29,19 +37,22 @@ Filtering Results
 .. toctree::
    :maxdepth: 1
 
-   filters/base_filter
+   filters/basic_filter
+   filters/clustering_filters
+   filters/known_object_filters
+   filters/sigma_g_filter
    filters/stamp_filters
-   filters/stats_filters
 
 Analyzing Results
 -----------------
 
 .. toctree::
    :maxdepth: 1
 
-   analysis_utils
+   analysis/create_stamps
+   analysis/plotting
+   analysis/visualizer
    jointfit_functions
-   result_list
 
 Miscelaneous utilities
 ----------------------
@@ -53,4 +64,5 @@ Miscelaneous utilities
    fake_data/insert_fake_orbit
    file_utils
    trajectory_utils
+   util_functions
    wcs_utils

docs/source/api_reference/results.rst

@@ -0,0 +1,5 @@
+Module: results
+===============
+
+.. automodule:: kbmod.results
+   :members:

docs/source/api_reference/standardizers/butler_standardizer.rst

@@ -0,0 +1,5 @@
+Module: butler_standardizer
+===========================
+
+.. automodule:: kbmod.standardizers.butler_standardizer
+   :members:

docs/source/api_reference/standardizers/fits_standardizer.rst

@@ -0,0 +1,5 @@
+Module: fits_standardizer
+=========================
+
+.. automodule:: kbmod.standardizers.fits_standardizers.fits_standardizer
+   :members:

docs/source/api_reference/standardizers/kbmodv05.rst

@@ -0,0 +1,5 @@
+Module: kbmodv05
+================
+
+.. automodule:: kbmod.standardizers.fits_standardizers.kbmodv05
+   :members:

docs/source/api_reference/standardizers/kbmodv1.rst

@@ -0,0 +1,5 @@
+Module: kbmodv1
+===============
+
+.. automodule:: kbmod.standardizers.fits_standardizers.kbmodv1
+   :members:

docs/source/api_reference/standardizers/multi_extension_fits.rst

@@ -0,0 +1,5 @@
+Module: multi_extension_fits
+============================
+
+.. automodule:: kbmod.standardizers.fits_standardizers.multi_extension_fits
+   :members:

docs/source/api_reference/standardizers/single_extension_fits.rst

@@ -0,0 +1,5 @@
+Module: single_extension_fits
+=============================
+
+.. automodule:: kbmod.standardizers.fits_standardizers.single_extension_fits
+   :members:

docs/source/api_reference/standardizers/standardizer.rst

@@ -0,0 +1,5 @@
+Module: standardizer
+=====================
+
+.. automodule:: kbmod.standardizers.standardizer
+   :members:

docs/source/api_reference/trajectory_generator.rst

@@ -0,0 +1,5 @@
+Module: trajectory_generator
+============================
+
+.. automodule:: kbmod.trajectory_generator
+   :members:

notebooks/reprojection/heliocentric_reproject_algo_comparison.ipynb

@@ -191,7 +191,6 @@
     "    per_distance_earth_dist_diff_geom = []\n",
     "\n",
     "    for ra in range(min_ra, max_ra, ra_step):\n",
-    "\n",
     "        icrs_ra1 = ra  # range of 0-360\n",
     "        icrs_dec1 = 10.0  # perhaps set this to 10.\n",
     "        icrs_time1 = Time(\"2023-03-20T16:00:00\", format=\"isot\", scale=\"utc\")\n",

src/kbmod/analysis/plotting.py

@@ -39,12 +39,12 @@ def iter_over_obj(objects):
     iterates over them sorted by date-time stamp.
 
     Parameters
-    -----------
+    ----------
     objects : `astropy.table.Table`
         Table of objects.
 
     Returns
-    --------
+    -------
     obj : `iterator`
         Iterator over individual object observations.
     """
@@ -316,7 +316,7 @@ def plot_cutouts(axes, cutouts, remove_extra_axes=True):
          left empty are removed from the plot.
 
     Raises
-    -------
+    ------
     ValueError - When number of given axes is less than
     the number of given cutouts.
     """
@@ -560,6 +560,26 @@ def plot_result_row(row, times=None, figure=None):
 
 
 def compute_lightcurve_histogram(row, min_val=0.0, max_val=1000.0, bins=20):
+    """Compute a historgram from a light curve.
+
+    Parameters
+    ----------
+    row : astropy Table row
+        The row for this results.
+    min_val : `float`
+        The minimum bin edge for the historgram.
+        Default: 0.0
+    max_val : `float`
+        The maximum bin edge for the historgram.
+        Default: 1000.0
+    bins : `int`
+        The number of bins.
+
+    Returns
+    -------
+    numpy histogram object
+        The histogram.
+    """
     psi = row["psi_curve"]
     phi = row["phi_curve"]
     valid = (phi != 0) & np.isfinite(psi) & np.isfinite(phi)

src/kbmod/analysis/visualizer.py

@@ -59,8 +59,7 @@ def count_num_days(self):
         self.results.table["num_days"] = num_days
 
     def plot_daily_coadds(self, result_idx, filename=None):
-        """Plots a coadded stamp for each day of valid observations for a
-        given result.
+        """Plots a coadded stamp for each day of valid observations for a given result.
 
         Parameters
         ----------
@@ -71,7 +70,7 @@ def plot_daily_coadds(self, result_idx, filename=None):
             image file.
 
         Raises
-        ----------
+        ------
         `RuntimeError` if `num_days` or `all_stamps` are not in the
         results table (i.e. not been generated with `count_num_days` or
         `generate_all_stamps`).

src/kbmod/results.py

@@ -481,8 +481,8 @@ def is_empty_value(self, colname):
         is an 'empty' value (None or anything of length 0). Used to mark or
         filter missing values.
 
-        Parameter
-        ---------
+        Parameters
+        ----------
         colname : str
             The name of the column to check.
 
@@ -590,8 +590,8 @@ def get_filtered(self, label=None):
     def revert_filter(self, label=None, add_column=None):
         """Revert the filtering by re-adding filtered ResultRows.
 
-        Note
-        ----
+        Notes
+        -----
         Filtered rows are appended to the end of the list. Does not return
         the results to the original ordering.
 
@@ -647,8 +647,8 @@ def revert_filter(self, label=None, add_column=None):
     def write_table(self, filename, overwrite=True, cols_to_drop=(), extra_meta=None):
         """Write the unfiltered results to a single (ecsv) file.
 
-        Parameter
-        ---------
+        Parameters
+        ----------
         filename : `str`
             The name of the result file.
         overwrite : `bool`

src/kbmod/standardizers/fits_standardizers/fits_standardizer.py

@@ -99,7 +99,7 @@ def resolveFromPath(cls, tgt):
             `"hdulist"`` key contains the constructed `~fits.HDUList` object.
 
         Raises
-        -----
+        ------
         FileNotFoundError - when file doesn't exist
         """
         resources = {}
@@ -146,7 +146,7 @@ def resolveTarget(cls, tgt):
             containing `~fits.HDUList` when ``canStandardize`` is `True`.
 
         Raises
-        -----
+        ------
         FileNotFoundError - when target is path to file that doesn't exist
         TypeError - when target is not HDUList or a filepath.
         """

src/kbmod/trajectory_utils.py

@@ -355,8 +355,8 @@ def match_trajectory_sets(traj_query, traj_base, threshold, times=[0.0]):
     query trajectories and base trajectories such that each trajectory is used in
     at most one pair.
 
-    Note
-    ----
+    Notes
+    -----
     This function is designed to evaluate the performance of searches by determining
     which true trajectories (traj_query) were found in the result set (traj_base).
 

src/kbmod/util_functions.py

@@ -57,7 +57,7 @@ def mjd_to_day(mjd):
         mjd format date.
 
     Returns
-    ----------
+    -------
     A `str` with a calendar date, in the format YYYY-MM-DD.
     e.g., mjd=60000 -> '2023-02-25'
     """