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0.13.3

===================

ami
---

- Fixed indentation bug in ami_analyze, so now all results are sufficiently
close to the results of the stand-alone prototype. Other modifications include
minor tweaks to more closely match those in the prototype code: changed some of
initial values of the estimation parameters, and the filtering routine
arguments. [3487]

- Updated ami_analyze.cfg to use default value of zero for rotation. [3520]

- ``ami_analyze`` now emits a RuntimeError if the input is _calints or if a
throughput reference file cannot be found. [3567]

- Remove change to filtering routine arguments of 3487. [3612]

assign_wcs
----------

- Fix a one pixel off problem with the NIRSpec NRS2 WCS transforms. [3473]

- Raise a ``ValueError`` if the FWCPOS keyword isn't found in input NIRISS
WFSS images. [3574]

associations
------------

- Added the fxd_slit keyword as the third optical component [3607]

- Orders the elements in Level3 naming in alphabetical order [3614]

- Ensured that higher-order candidates only exist for Level2 associations [3629]

- Improve member checking and removed duplicate product names [3647]

combine_1d
----------

- Unit tests were added to combine_1d. [3490]

datamodels
----------

- Datamodels schemas should now be referenced with
``http://stsci.edu/schemas/jwst_datamodel/image.schema`` instead of
``http://jwst.stsci.edu/schemas/image.schema.yaml``. The datamodels
``BaseExtension`` is renamed internally to ``DataModelExtension``. [3437]

- Added the new column "relresperror" to the "MiriImgPhotomModel" data
model schema. [3512]

- Added all ``SlitModel`` data arrays to ``MultiExposureModel``, so that all input
arrays appear in the output of ``exp_to_source``. [3572]

extract_1d
----------

- An indexing bug was fixed. [3497]

- Pixels with wavelength = NaN are no longer used. [3539]

flatfield
---------

- Remove flatfield step parameter `flat_suffix`. Add boolean step parameter
`save_interpolated_flat`. Refactor flatfield internals. [3493]

- Propagate uncertainty from FFLAT, SFLAT and DFLAT flat fields into science
ERR array and VAR_FLAT array for NIRSpec spectroscopic modes. [3538]

jump
----

- Add multiprocessing capability to JumpStep [3440]

extract_2d
----------

- Replaced a white space in the names of grism objects with an underscore. [3517]

- Update WFSS slit names to use simple integer value, and add accompanying unit
test for NIRCAM grism extract_2d [3632].

master_background
-----------------

- Fix bug in master_background where the flux from the input x1d files
was being combined instead of the background columns. [3468]

- Use the surf_bright column instead of flux in master_background. [3476]

model_blender
-------------

- Allow blendmodels to ignore attributes in asdf tree not in schema [3480]
- Add new rules for dates and times [3554]

photom
------

- Updated to zero-out pixels outside the wavelength range of flux calibration
and set DQ=DO_NOT_USE. [3475, 3489]

pipeline
--------

- ``calwebb_spec3`` was changed to allow processing of WFSS modes. [3517]

- ``calwebb_image2`` was changed to prevent 3D data from being sent to
``resample``. [3544]

- ``calwebb_spec2`` was changed to check for an error in ``assign_wcs`` processing
before executing the ``background`` step. [3574]

refpix
------

- Fixed a bug where pixeldq arrays were being transformed from DMS to detector
coordinates for every group instead of just once

skymatch
--------

- Improved reliability when matching sky in images with very close sky
footprints. [3557]

stpipe
------

- Capability to define reference overrides using a ``DataModel`` instead of
a file path was added. [3514]

tweakreg
--------

- Mask and do not use NON-SCIENCE regions in tweakreg source detection. [3461]

0.13.2

===================

assign_wcs
----------

- The MIRI LRS WCS was updated to include an nverse transform. [3106, 3360]

- The MIRI LRS spectral distortion is implemented now using a spline model. [3106]

- Both ``dither_point_index`` and ``metadata_id`` are used now to match rows
into the MSA meta file. [3448]

- ``MissingMSAFileError`` was renamed to ``MSAFileError`` [3448]

- Added two parameters to ``assign_wcs``, ``slit_y_low`` and ``slit_y_high``,
to allow changing the lower and upper limit of a Nirspec slit in the instrument
model. [2819]

background
----------

- Verify the exposures to be used as background have the same NIRSpec GWA
tilt values as the science exposures. If the background and science
exposures do not have matching GWA tilt values, then skip the background
subtraction step in calspec2. [3252]

barshadow
---------

- Updated to apply the correction to the science data arrays, in addition
to attaching as an extension. [3319]

- Updated to apply the square of the correction to VAR_FLAT [3427]

calwebb_spec3
-------------

- Add the ``master_background`` subtraction step to the pipeline. [3296]

combine_1d
----------

- Fix call to wcs.invert, and don't weight flux by sensitivity if the net
column is all zeros. [3274]

- Modified to use the same columns as now written by extract_1d.
The background parameter has been removed, since dividing by npixels
is now done in extract_1d. [3412]

datamodels
----------

- Fix ``url_mapper`` for fits-schema to allow URLs with of the format
http://stsci.edu/schemas/fits-schema/ to map to the correct location
in the ``jwst`` package. [3239]

- Change ``ModelContainer`` to load and instantiate datamodels from an
association on init. This reverts 1027. [3264]

- Keyword updates to data model schemas, including OBSFOLDR, MIRNGRPS,
MIRNFRMS, and new PATTTYPE values. [3266]

- Keyword updates to remove GS_STATE and change GUIDESTA to string
type. [3314]

- Added BUNIT keyword to gain and readnoise reference file schemas.
[3322]

- Update ``dq_def.schema``, ``group.schema`` and ``int_times.schema`` to comply
with ASDF standard. Remove unused ``extract1d.schema``. [3386]

- Update schemas to add new READPATT and BAND allowed values. [3463]

extract_1d
----------

- This step can now use a reference image for IFU data. The reference
image (for IFU) may be either 2-D or 3-D. When using a reference image
for non-IFU data, background smoothing is now done after scaling the
background count rate. [3258]

- Unit tests were added for IFU data. [3285]

- The target coordinates are used (for some modes) to determine the
extraction location, i.e. correcting for nod/dither offset. For IFU,
the areas of the source aperture and background annulus are computed
differently. [3362

- For IFU data for an extended source, the extraction parameters are
assigned values so that the entire image will be extracted, with no
background subtraction. For non-IFU data, a try/except block was added
to check for a WCS that does not have an inverse. Some code (but not
all) for the now-obsolete RELSENS extension has been deleted. [3390]

- This now writes columns SURF_BRIGHT and SB_ERROR instead of NET and
NERROR. The BACKGROUND column is divided by NPIXELS, so the units will
be surface brightness. This step no longer looks for a RELSENS
extension. [3412]

- The keywords that describe the units for the FLUX and ERROR columns
have been corrected; the units are now specified as "Jy". [3447]

extract_2d
----------

- An attribute ``dither_point`` was added to each slit in a ``MultiSlitModel``
for MOS observations. [3448]

flatfield
---------

- Propagate uncertainty from flat field into science ERR array and new
VAR_FLAT array which holds the variance due to the flat field. [3384]

master_background
-----------------

- Modified the unit tests for ``expand_to_2d``. [3242]

- Modified ``MasterBackgroundStep`` to be skipped if ``BackgroundStep``
was already run on the data. A new ``force_subtract`` parameter is
added to override this logic. [3263]

- ``MasterBackgroundStep`` now can handle BACKGROUND association members
that come from nodded exposures of the source. [3311]

- Updated the DQFlags of the background subtracted data to be DO_NOT_USE
for the pixels that have wavelengths outside the master background [3326]

- Modified ``expand_to_2d`` to loop over pixels for WFSS data. [3408]

outlier_detection
-----------------

- Fixed a bug that was causing the step to crash when calling the
``cube_build`` step for MIRI MRS data. [3296]

pathloss
--------

- Updated to apply the correction to the science data and err arrays. [3323]

- Updated to apply the square of the correction to VAR_FLAT [3427]

photom
------

- Updated to apply the flux calibration to the science data and err arrays.
[3359]

- Updated to compute a wavelength array for NIRISS SOSS exposures using
spectral order 1. [3387]

- Updated to apply the square of the correction to VAR_FLAT [3427]

reffile_utils
-------------

- Improved error messages when problems are encountered in extracting
subarrays from reference files. [3268]

resample_spec
-------------

- Fixed an issue with the spatial component of the WCS where the inverse
transform gave different results for negative ``RA`` and ``360 + RA``. [3404]


set_telescope_pointing
----------------------

- Fix ``populate_model_from_siaf`` to convert SIAF pixel scale from
arcsec to degrees for CDELTn keywords. [3248]

- Updates to prevent crashes when SIAF values needed for crpix or
cdelt keywords are missing. [3316]

- Convert FSM correction values from arcsec to radians. [3367]

srctype
-------

- Updated logic for background targets and nodded exposures. [3310]


transforms
----------

- A field ``dither_point`` was added to the ``Slit`` structure. [3448]


tweakreg
--------

- Bug fix: Improved 2D Histogram (pre-match shift) algorithm in Python. [3281]

- Fixed a bug in handling situations when no useable sources are
detected in any of the input images. [3286]

- Enhanced source catalog extraction algorithm to filter out sources outside
the WCS domain of definition (when available). [3292]

- Changed the type of exception raised when input has incorrect type. [3297]

0.13.1

===================

combine_1d
----------

- Added parameter ``background``; for background data, scale the flux,
error, and net by 1 / NPIXELS, and include NPIXELS in the weight;
changed the default for ``exptime_key`` to "exposure_time". [3180]

- There is now a direct interface for calling the step. This function,
``combine_1d_spectra``, may be passed either a ModelContainer or a
MultiSpecModel object. Previously this function expected the name of
an association file. [3220]

datamodels
----------

- Add back BaseExtension class so url-to-schema mapping works again [3227]

extract_1d
----------

- If flux conversion is done, the FLUX is now set to zero (instead of
copying the NET) if the wavelength of a pixel is outside the range of
the RELSENS array. [3190]

- Added a parameter ``subtract_background`` to ``extract_1d`` indicating
whether the local background should be subtracted. If None, the value
in the extract_1d reference file is used. [3157, 3186]

- ``extract_1d`` can be run by calling ``extract.do_extract1d`` and
passing a dictionary of reference file information. [3202]

- ``ref_dict`` was None in ``run_extract1d``, and a check for that was
missing. [3233]

master_background
-----------------

- Added unit tests for expand_to_2d. Support CombinedSpecModel data
for the 1-D user-supplied background spectrum. [3188]

set_bary_helio_times
--------------------

- Raise an exception when unable to compute converted times. [3197]

set_telescope_pointing
----------------------

- Added population of CDELTn keywords based on SIAF values and fixed bug in calculation
of S_REGION corners. [3184]

0.13.0

===================

ami
---

assign_wcs
----------

- Removed ``transform_bbox_from_datamodels`` in favor of
``transform_bbox_from_shape`` which now works by using last two dimensions
in the ``shape``. [3040]

- Added velocity correction model to the WFSS and TSGRISM wcs pipelines. [2801]

- Refactored how the pipeline handles subarrays in the WCS. Fixed a bug
where the bounding box was overwritten in full frame mode. [2980]

- Rename several functions dealing with calculating bounding boxes for clarity. [3014]

- The bounding box of the MIRI LRS WCS is now in "image" coordinates, not full frame. [3063]

- FITS WCS keywords are written out only if the observation is one of the IMAGING_MODES. [3066]

associations
------------

- Updated docstrings and written documentation. [2856, 2862]

- Fixed NIRISS WFSS catalog naming and implement NIRCam WFSS [3515]

- Fixed treating non-science as TSO [3601]

background
----------

barshadow
---------

combine_1d
----------

coron
-----

- Updated the `stack_refs` routine to update the output data model with metadata
from the first input model. [3111]

csv_tools
---------

cube_build
----------

- Added dq flagging [3804]

cube_skymatch
-------------

dark_current
------------

datamodels
----------

dq_init
-------

emission
--------

engdblog
--------

exp_to_source
-------------

- Updated SourceContainer to wrap each exposure of a MultiExposure in a
SlitModel, allowing pipeline code to simply treat each as DataModel.
[3438]

extract_1d
----------
- Updated to recognize NRC_TSGRISM as WFSS data. SlitDataModel schema now
specifies that the wavelength attribute should be 2-D, with a default
value of 0. [2911]

- Reverse order of RELSENS wavelength and response if the wavelengths are
not increasing. [3005]

- Add a test for constant wavelengths (or constant slope). [3032]

- Fix issue regarding mixing of the syntax for Boolean arrays and for
integer index arrays. [3045]

- Changed the names of time-related keywords for extracted spectra. [3058]

- A new NPIXELS column has been added to the output table. [3108]

extract_2d
----------
- Moved the update of meta information to the MultiSlitModel instead of the
SlitModels that compose it. [2988]

firstframe
----------

fits_generator
--------------

flatfield
---------
- Updated to not extrapolate for wavelengths that are out of bounds,
either due to the WCS, or the wavelengths for a flat-field image cube,
or the wavelengths for the fast-variation component. [2775]

fringe
------

gain_scale
----------

group_scale
-----------

guider_cds
----------

imprint
-------

ipc
---

- Updated the docstrings [2822]

jump
----

- Updated twopoint_difference.py to not use groups with groupdq set to DO_NOT_USE [3495]

jwpsf
-----

lastframe
---------

lib
---

- ``set_telescope_pointing`` now populates WCS keywords from the SIAF file. [3066]

linearity
---------

master_background
-----------------

- Implement the basic step scaffolding for `MasterBackgroundStep`. [3090]

- Record user-supplied master background in MSTRBKGD keyword [3101]

- Add step documentation for master background subtraction [3102]

- Make master background step actually work [3110]

model_blender
-------------

msaflagopen
-----------

outlier_detection
-----------------

pathloss
--------

persistence
-----------

photom
------

pipeline
--------

ramp_fitting
------------
- Ramp-fitting returning zero for all background pixels; Issue 2848, JP-453.

- MIRI ramps with jumps flagged at group 2 result in slopes of 0 in the rate
image; Issue 2233,

- Processing pixels in ramp fitting in which all groups are saturated; Issue
2885.

- Ramp Fit fails when only two groups are in a segment after cosmic ray hits.;
Issue 2832, JP-450.

- Fixed a bug in which the keywords from the input were not included in the OPT
output header.

- Simplified and clarified classification of segment types based on DQ flags.

- Added handling of ramps ending in 2 saturated groups.

- Fix units for Read Noise Variance in ramp_fit (PR 2767). This may needed to
revised based on Mike Regan's comment when he closed this PR.

- Added check to handle integration-specific variances for too short segments.

- More robust handling of ramps flagged as DO_NOT_USE (PR 3016)

refpix
------

- Added a description of processing for IRS2 readout mode data. [2889]
- Fixed a mistake in the time to read one pixel. [2923]

resample
--------

reset
-----

rscd
----

saturation
----------

skymatch
--------

source_catalog
--------------

srctype
-------

scripts
-------

stpipe
------

- Add `Step.record_step_status()` method for use by this step (and any other
pipeline or pipeline step) [3110]

straylight
----------

superbias
---------

timeconversion
--------------
- Updated the docstrings [3020]

transforms
----------

- The `LRSWavelength` model was removed as obsolete.
Instead a spline is used for the wavelength solution. [3106]

tso_photometry
--------------

tweakreg
--------

- Use a more numerically stable ``numpy.linalg.inv`` instead of own matrix
inversion. [3033]

- Bug fix: Use integer division in Python 3. [3072]


wfs_combine
-----------

white_light
-----------

wiimatch
--------

0.12.3

===================

scripts
-------

- ``set_telescope_pointing.py``: Update method of choosing pointing parameters. [2900, 3008, 3022]

- ``set_telescope_pointing.py``: Allow undefined SIAF. [3002, 3006]

0.12.2

===================

associations
------------

- Updated rules based on actual OTB phasing data. [2831]

wfs_combine
-----------

- Renamed the configuration from `wfs_combine` to `calwebb_wfs-image3`. [2831]

Page 15 of 16

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