Update docs

CHANGELOG.rst

@@ -13,7 +13,7 @@ API Changes
   if the angle arrays have not been either set or explicitly allocated.  One should be sure
   to either set them (e.g. using ``photon_array.dxdz = [...]``) or explicitly allocate
   them (using ``photon_array.allocateAngles()``).  (#1191)
-- Changed the ``.SED`` attribute name of `ChromaticObject`s to lowercase ``.sed``. (#1245)
+- Changed the ``.SED`` attribute name of `ChromaticObject` to lowercase ``.sed``. (#1245)
 
 
 Config Updates
@@ -35,14 +35,14 @@ New Features
 
 - Updated Roman telescope data to Phase C (aka Cycle 9) specifications (#1017)
 - Added `ShapeData.applyWCS` method to convert HSM shapes to sky coordinates.  Also added
-  the option ``use_sky_coords=True`` to `FindAdaptiveMom` to apply this automatically. (#1219)
+  the option ``use_sky_coords=True`` to `hsm.FindAdaptiveMom` to apply this automatically. (#1219)
 - Added `DoubleZernike` class and related functionality. (#1221)
 - Added some utility functions that we have found useful in our test suite, and which other
   people might want to use to the installed galsim.utilities. (#1240)
-- Added `galsim.utilities.merge_sorted` which merges two or more sorted numpy arrays faster than
+- Added `utilities.merge_sorted` which merges two or more sorted numpy arrays faster than
   the available numpy options. (#1243)
-- Added `galsim.EmissionLine` class to represent emission line SEDs. (#1247, #1249)
-- Updated data in galsim.roman module to Phase C (Cycle 9) information. (#1017, #1251)
+- Added `EmissionLine` class to represent emission line SEDs. (#1247, #1249)
+- Updated data in `roman` module to Phase C (Cycle 9) information. (#1017, #1251)
 
 
 Performance Improvements
@@ -55,12 +55,12 @@ Performance Improvements
   Now it only adds it if there is not already one given by the user. (#1229, #1236)
 - Work around an OMP bug that disables multiprocessing on some systems when omp_get_max_threads
   is called. (#1241)
-- Sped up the `combine_wave_lists` function, using the new `merge_sorted` function. (#1243)
-- No longer keep a separate ``wave_list`` array in `ChromaticObject`s.  These are always
+- Sped up the `combine_wave_list` function, using the new `merge_sorted` function.  (#1243)
+- No longer keep a separate ``wave_list`` array in `ChromaticObject`.  These are always
   equal to the ``wave_list`` in the ``sed`` attribute, so there is no need to duplicate the
   work of computing the ``wave_list``. (#1245)
-- Delayed the calculation of the `sed` attributes of `ChromaticObject`s until they are actually
-  needed.  Since sometimes they aren't needed, this is a performance improvement in those cases.
+- Delayed the calculation of the ``sed`` attributes of `ChromaticObject` until they are actually
+  needed.  Since sometimes they are not needed, this is a performance improvement in those cases.
   (#1245)
 - Reduce long-term memory usage of Silicon class after drawing onto a very large stamp and
   then moving on to smaller stamps. (#1246)

docs/config_input.rst

@@ -114,6 +114,12 @@ The ``input`` fields defined by GalSim are:
     * ``index`` = *str_value* (optional) If set, the power spectrum will only be computed when this index changed.  E.g. if ``index`` is 'file_num', then it will only update with each new file, not with each image.
     * ``variance`` = *float_value* (optional) If set, rescale the overall variance of the generated shears to this value.
 
+* ``initial_image`` specifies an initial image (read from an FITS file) to draw onto, rather than create a new blank image.
+
+    * ``file_name`` = *str_value* (required) The name fo the file with the desired initial image.
+    * ``dir`` = *str_value* (default = '.')  The directory the file is in.
+    * ``read_header`` = *bool_value* (default = False)  Whether to read the header as well.
+
 Another feature of the ``input`` field is that it may optionally be a list.  So you can have multiple input catalogs for instance; one for object parameters and one for overall image parameters perhaps.  When using values with the type 'InputCatalog', you would specify which catalog to use with ``num``.  If you only have a single item for one of the inputs, you can omit the ``num`` parameter when you are using it.
 
 Custom Input Types

docs/config_objects.rst

@@ -237,6 +237,9 @@ Generic Types
     * ``items`` = *list* (required)  A list of profiles.
     * ``index`` = *int_value* (default = 'Sequence' from 0 to len(items)-1)  Which item in the list to select each time.
 
+* 'Eval'  Use Python's ``eval`` function to evaluate a given string as a GSObject.
+
+    * ``str`` = *str_value* (required)  The string to evaluate.
 
 Other Attributes
 ----------------

docs/sed.rst

@@ -9,3 +9,6 @@ Spectral Energy Distributions
     .. automethod:: galsim.SED._mul_sed
     .. automethod:: galsim.SED._mul_bandpass
     .. automethod:: galsim.SED._mul_scalar
+
+.. autoclass:: galsim.EmissionLine
+    :members:

docs/zernike.rst

@@ -11,7 +11,11 @@ Zernike Functions
     .. automethod:: galsim.zernike.Zernike.__rmul__
     .. automethod:: galsim.zernike.Zernike.__call__
 
+.. autoclass:: galsim.zernike.DoubleZernike
+
 .. autofunction:: galsim.zernike.noll_to_zern
 .. autofunction:: galsim.zernike.zernikeRotMatrix
 .. autofunction:: galsim.zernike.zernikeBasis
+.. autofunction:: galsim.zernike.zernikeGradBases
+.. autofunction:: galsim.zernike.doubleZernikeBasis
 .. autofunction:: galsim.zernike.describe_zernike

galsim/chromatic.py

@@ -89,7 +89,7 @@ class ChromaticObject:
         >>> gal = bulge + disk
 
     The ``sed`` instances above describe the flux density in photons/nm/cm^2/s of an object, possibly
-    normalized with either the `sed.withFlux` or `sed.withMagnitude` methods (see their docstrings
+    normalized with either the `SED.withFlux` or `SED.withMagnitude` methods (see their docstrings
     for details about these and other normalization options).  Note that for dimensional
     consistency, in this case, the ``flux`` attribute of the multiplied `GSObject` is interpreted
     as being dimensionless instead of in its normal units of [photons/s/cm^2].  The photons/s/cm^2

galsim/hsm.py

@@ -233,9 +233,9 @@ def applyWCS(self, wcs, image_pos):
 
         The values that are different from the original are:
 
-        moments_sigma is changed to be in units of arcsec.
-        observed_shape is changed to be in (u,v) coordinates.
-        moments_centroid is changed to be in (u,v) coordinates relative to image_pos.
+        * ``moments_sigma`` is changed to be in units of arcsec.
+        * ``observed_shape`` is changed to be in (u,v) coordinates.
+        * ``moments_centroid`` is changed to be in (u,v) coordinates relative to image_pos.
 
         .. note::
 
@@ -704,7 +704,7 @@ def FindAdaptiveMom(object_image, weight=None, badpix=None, guess_sig=5.0, preci
     for the coordinate variables. These coordinates are measured in arcsec and are oriented
     such that +v is towards North and +u is towards West. In this case, the returned values are
     all in arcsec, and are based instead on Iuu, Ivv, and Iuv.  To enable this feature, use
-    ``use_sky_coords=True`.  See also the method `ShapeData.applyWCS` for more details.
+    ``use_sky_coords=True``.  See also the method `ShapeData.applyWCS` for more details.
 
     .. note::
 

galsim/utilities.py

@@ -1702,7 +1702,7 @@ class CaptureLog:
     """A context manager that saves logging output into a string that is accessible for
     checking in unit tests.
 
-    After exiting the context, the attribute `output` will have the logging output.
+    After exiting the context, the attribute ``output`` will have the logging output.
 
     Sample usage:
 

galsim/zernike.py

@@ -961,19 +961,19 @@ class DoubleZernike:
     separate annuli:
 
     .. math::
-        DZ_{k, j}(u, v, x, y) = Z_k(u, v) Z_j(x, y)
+        DZ_{k,j}(u, v, x, y) = Z_k(u, v) Z_j(x, y)
 
     The double Zernike's therefore satisfy the orthonormality condition:
 
     .. math::
-        \int_{annuli} DZ_(k, j) DZ_(k', j') = A1 A2 \delta_{k, k'} \delta_{j, j'}
+        \int_{annuli} DZ_{k,j} DZ_{k',j'} = A_1 A_2 \delta_{k, k'} \delta_{j, j'}
 
-    where A1 and A2 are the areas of the two annuli.
+    where :math:`A_1` and :math:`A_2` are the areas of the two annuli.
 
     Double Zernikes series are useful for representing the field and pupil
     dependent wavefronts of a telescope.  We adopt the typical convention that
-    the first index (the `k` index) corresponds to the field-dependence, while
-    the second index (the `j` index) corresponds to the pupil-dependence.
+    the first index (the ``k`` index) corresponds to the field-dependence, while
+    the second index (the ``j`` index) corresponds to the pupil-dependence.
 
     Parameters:
         coef:       [kmax, jmax] array of double Zernike coefficients.  Like the
@@ -1131,8 +1131,8 @@ def coef(self):
         """DoubleZernike coefficients.
 
         The coefficients are stored in a 2D array, where the first index
-        corresponds to the `uv` dependence and the second index corresponds to
-        the `xy` dependence.  The indices are Noll indices.  As an example, when
+        corresponds to the ``uv`` dependence and the second index corresponds to
+        the ``xy`` dependence.  The indices are Noll indices.  As an example, when
         describing a telescope wavefront the (1, 4) tuple corresponds to a
         constant (over the field) pupil defocus.  The (2, 5) term is a linear
         (over the field) astigmatism, etc.