Merge branch 'main' into jp-4265

Author: tapastro

changes/10384.associations.rst

@@ -0,0 +1 @@
+Bypass unnecessary compare_asns calls to improve generator runtime. Factor-of-3 runtime improvement is realized for one large NRC_WFSS pool tested

docs/jwst/firstframe/api_ref.rst

@@ -0,0 +1,15 @@
+===
+API
+===
+
+Public Step API
+===============
+
+.. automodapi:: jwst.firstframe.firstframe_step
+   :no-inheritance-diagram:
+
+Complete Developer API
+======================
+
+.. automodapi:: jwst.firstframe.firstframe_sub
+   :no-inheritance-diagram:

docs/jwst/firstframe/arguments.rst

@@ -4,11 +4,11 @@ Step Arguments
 The ``firstframe`` step has the following step-specific arguments.
 
 ``--bright_use_group1`` (boolean, default=True)
-    If True, setting the group 1 groupdq to DO_NOT_USE will not be done
+    If True, setting the group 1 ``groupdq`` to DO_NOT_USE will not be done
     for pixels that have the saturation flag set for group 3.
     This will allow a slope to be determined for pixels that saturate in group 3.
     This change in flagging will only impact pixels that saturate in group 3, the behavior
     for all other pixels will be unchanged.
     The ``bright_use_group1`` flag can be set for all data, only data/pixels that saturate
     in group 3 will see a difference in behavior. These pixels will be marked with
-    the FLUX_ESTIMATED DQ flag in the pixeldq image.
+    the FLUX_ESTIMATED DQ flag in the ``pixeldq`` image.

docs/jwst/firstframe/description.rst

@@ -1,11 +1,13 @@
 Description
 ===========
 
-:Class: `jwst.firstframe.FirstFrameStep`
+:Class: `jwst.firstframe.firstframe_step.FirstFrameStep`
 :Alias: firstframe
 
-The ``firstframe`` step has been deprecated and will be removed
-in a future release. Flagging the first group  has been added to the RSCD step.
+.. warning::
+    The ``firstframe`` step has been deprecated and will be removed
+    in a future release. Flagging the first group  has been added to
+    the :ref:`RSCD step <rscd_step>`.
 
 The MIRI first frame correction step flags the first group in every integration
 as bad (the "DO_NOT_USE" data quality flag is added to the GROUPDQ array), but

docs/jwst/firstframe/index.rst

@@ -4,10 +4,14 @@
 First Frame Correction
 ======================
 
+.. warning::
+    The ``firstframe`` step has been deprecated and will be removed
+    in a future release. Flagging the first group  has been added to
+    the :ref:`RSCD step <rscd_step>`.
+
 .. toctree::
    :maxdepth: 2
 
    description.rst
    arguments.rst
-
-.. automodapi:: jwst.firstframe
+   api_ref.rst

docs/jwst/flatfield/api_ref.rst

@@ -0,0 +1,15 @@
+===
+API
+===
+
+Public Step API
+===============
+
+.. automodapi:: jwst.flatfield.flat_field_step
+   :no-inheritance-diagram:
+
+Complete Developer API
+======================
+
+.. automodapi:: jwst.flatfield.flat_field
+   :no-inheritance-diagram:

docs/jwst/flatfield/index.rst

@@ -7,7 +7,6 @@ Flatfield Correction
    :maxdepth: 2
 
    main.rst
-   reference_files.rst
    arguments.rst
-   
-.. automodapi:: jwst.flatfield
+   reference_files.rst
+   api_ref.rst

docs/jwst/flatfield/main.rst

@@ -1,7 +1,7 @@
 Description
 ===========
 
-:Class: `jwst.flatfield.FlatFieldStep`
+:Class: `jwst.flatfield.flat_field_step.FlatFieldStep`
 :Alias: flat_field
 
 At its basic level this step flat-fields an input science dataset by dividing
@@ -17,7 +17,7 @@ to "COMPLETE" in the output science data.
 
 Imaging and Non-NIRSpec Spectroscopic Data
 ------------------------------------------
-Simple imaging data, usually in the form of an ImageModel, and some
+Simple imaging data, usually in the form of an `~stdatamodels.jwst.datamodels.ImageModel`, and some
 spectroscopic modes, use a straight-forward approach that involves applying
 a single flat-field reference file to the science image. The spectroscopic
 modes included in this category are NIRCam WFSS and Time-Series Grism,
@@ -75,7 +75,7 @@ that is divided into the SCI and ERR arrays is constructed on-the-fly
 by extracting the relevant section from the reference files, and then --
 for each pixel -- interpolating to the appropriate wavelength for that
 pixel.  This interpolation requires knowledge of the dispersion direction,
-which is read from keyword "DISPAXIS."  See the Reference File section for
+which is read from keyword "DISPAXIS."  See :ref:`flat_ref_nirspec_spec` for
 further details.
 
 For NIRSpec Fixed Slit (FS) and MOS exposures, an on-the-fly flat-field is
@@ -84,8 +84,8 @@ exposure. For NIRSpec IFU exposures, a single full-frame flat-field is
 constructed, which is applied to the entire science image.
 
 NIRSpec NRS_BRIGHTOBJ data are processed just like NIRSpec fixed slit
-data, except that NRS_BRIGHTOBJ data are stored in a CubeModel,
-rather than a MultiSlitModel.  A 2-D flat-field image is constructed
+data, except that NRS_BRIGHTOBJ data are stored in a `~stdatamodels.jwst.datamodels.CubeModel`,
+rather than a `~stdatamodels.jwst.datamodels.MultiSlitModel`.  A 2-D flat-field image is constructed
 on-the-fly as usual, but this image is then divided into each plane of
 the 3-D science data arrays.
 

docs/jwst/flatfield/reference_files.rst

@@ -7,13 +7,20 @@ spectroscopic exposures use the three reference files :ref:`fflat_reffile` (fore
 
 .. include:: ../references_general/flat_reffile.inc
 
+.. _flat_ref_nirspec_spec:
+
 Reference Files for NIRSpec Spectroscopy
 ========================================
 For NIRSpec spectroscopic data, the flat-field reference files allow for variations in
 the flat field with wavelength, as well as from pixel to pixel.  There is a
 separate flat-field reference file for each of three sections of the
-instrument:  the fore optics (FFLAT), the spectrograph (SFLAT), and the
-detector (DFLAT).  The contents of the reference files differ from one mode
+instrument:
+
+* the fore optics (:ref:`fflat_reffile`)
+* the spectrograph (:ref:`sflat_reffile`)
+* the detector (:ref:`dflat_reffile`)
+
+The contents of the reference files differ from one mode
 to another (see below), but in general they may contain a flat-field image and
 a 1-D array.  The image provides pixel-to-pixel values for the flat field
 that may vary slowly (or not at all) with wavelength, while the 1-D array
@@ -45,8 +52,8 @@ there are different flat fields for fixed-slit data, IFU data, and for
 multi-object spectroscopic data.  Here is a summary of the contents of these
 files.
 
-For the fore optics (FFLAT), the flat field for fixed-slit data contains just a
-FAST_VARIATION table (i.e. there is no image).  This table has five rows,
+For the fore optics (:ref:`fflat_reffile`), the flat field for fixed-slit data contains just a
+FAST_VARIATION table (i.e., there is no image).  This table has five rows,
 one for each of the fixed slits.  The FFLAT for IFU data also contains
 just a FAST_VARIATION table, but it has only one row with the value "ANY"
 in the "slit_name" column.  For multi-object spectroscopic data, the FFLAT
@@ -57,22 +64,18 @@ than to detector pixels.  The array size is 365 columns by 171 rows,
 and there are multiple planes to handle the slow variation
 of flat field with wavelength.
 
-For the spectrograph optics (SFLAT), the flat-field files have nearly the same
+For the spectrograph optics (:ref:`sflat_reffile`), the flat-field files have nearly the same
 format for fixed-slit data, IFU, and multi-object data.  The difference is
 that for fixed-slit and IFU data, the image is just a single plane,
-i.e. the only variation with wavelength is in the FAST_VARIATION table,
+i.e., the only variation with wavelength is in the FAST_VARIATION table,
 while there are multiple planes in the image for multi-object spectroscopic
 data (and therefore there is also a corresponding WAVELENGTH table, with
 one row for each plane of the image).
 
-For the detector section, the DFLAT file contains a 3-D image
-(i.e. the flat field at multiple wavelengths), a corresponding
+For the detector section, the :ref:`dflat_reffile` contains a 3-D image
+(i.e., the flat field at multiple wavelengths), a corresponding
 WAVELENGTH table, and a FAST_VARIATION table with one row.
 
-As just described, there are 3 types of reference files for NIRSpec (FFLAT,
-SFLAT, and DFLAT), and within each of these types, there are several formats,
-which are now described.
-
 .. include:: ../references_general/fflat_reffile.inc
 
 .. include:: ../references_general/sflat_reffile.inc

docs/jwst/fringe/api_ref.rst

@@ -0,0 +1,15 @@
+===
+API
+===
+
+Public Step API
+===============
+
+.. automodapi:: jwst.fringe.fringe_step
+   :no-inheritance-diagram:
+
+Complete Developer API
+======================
+
+.. automodapi:: jwst.fringe.fringe
+   :no-inheritance-diagram: