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0.18.0

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

ami
---
- Update code to use two new input parameters: psf_offset,rotation_search [5548]

- Update code and unit tests to use new ami_analyze algorithms [5390]

- Update ami_analyze to extract a SUB80 subarray from full-frame images [5437]

assign_wcs
----------

- Add nrs_verify to the NIRSpec exposure list [5403]

- Enable resample_spec for NIRSpec line lamp exposures [5484]

- Added SIP approximation to WCS for imaging modes. FITS WCS keywords added to meta.wcsinfo. [5507]

- Fix bug where subarray bounding boxes were 1 pixel too small. [5543]

- Mark Nirspec slits which project on less than one pixel as invalid. [5554]

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

- Asn_Lv2WFSS: Add segmentation map exposure to Level2 WFSS associations [5532]

- Add new dither keyword subpxpts to constraints [5525]

- Add further constraints to rule Asn_Lv2NRSLAMPSpectral such that associations
are created only when LAMP is on and OPMODE indicates a valid optical path. [5496]

- Restrict association creation based on optical path for NIRSpec Fixed-slit and IFU [5504]

- Asn_Lv3SpecAux: Add optical element constraint [5479]

- Add utility asn_gather [5468]

- Do not allow target acqs to be considered TSO [5385]

- Add NRS_VERIFY to the list of target acq/confirmation images [5395]

cube_build
----------

- When making SINGLE type cubes for outlier detection or mrs_imatch data not in the
appropriate channel/grating is skipped [5347]

- If outlier detection has flagged all the data on a input file as DO_NOT_USE, then
skip the file in creating an ifucube [5347]

- Refactor DataTypes handling of ModelContainer. [5409]

datamodels
----------

- Skip serializing `None` in datamodels to be compatible with `asdf>=2.8` [5371]

- Implement full class deprecator decorator and use for MIRIRampModel [5382]

- Add NRS_VERIFY to the core schema as an allowed EXP_TYPE [5395]

- Remove logging from DataModel.close [5413]

- Updated keyword schemas for EXP_TYPE and MODULE, to keep in sync with the
JWST Keyword Dictionary [5452]

- Added flatfield and photom correction arrays to slit data models [5460]

- Move core ``jwst.datamodels`` code to ``stdatamodels`` package and add it as
an install dependency [5433]

- Update schemas to include new allowed SUBARRAY values for FGS ASIC tuning
modes [5531]

- Add meta.visit.pointing_engdb_quality entry to correspond to ENGQLPTG keyword [5556]

- Update Moving Target CHEBY table extension schema for changes to column
definitions in the JWSTKD and SDP [5558]

- Update distortion reference file schema to have ``meta.instrument.channel``
keyword [5553]

extract_1d
----------

- Fixed bug involving the determination of source RA/Dec for resampled Slit
data. [5353]

- Updated to use an EXTRACT1D reference file for NIRCam TSGRISM exposures;
added step param "bkg_fit" to allow for mean and median options in background
computation, in addition to the existing polynomial fit; fixed bug in
background computation that was preventing background subtraction from
ever happening. [5414]

- Fixed bug involving the processing of WFSS observations when there's only
one spectrum instance for a given source. [5439]

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

- Addressed deprecated get_children method of XML parser. Changed type of PATTSIZE from
float to string in templates. [5536]

flatfield
---------

- Fixed bug in sending NIRSpec AUTOWAVE exposures to the spectroscopic
processing branch. [5356]

- Updated branch logic to handle NRS_LAMP exposures as spectroscopic. [5370]

- Updated NIRSpec fixed-slit processing to compute and save correction
values for both point and uniform sources in the primary slit when it
contains a point source, in order to support master background corrections.
[5462]

jump
----

- Fixed bug in the minimum number of groups per integration for the jump
detection step by changing it from 3 to 5. [5376]

- Various rework to reduce memory usage and increase readability. [5404]

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

- Update the NIRSpec MOS master background logic to only proceed with processing
after verifying that there are both background and source slits available in
the input dataset. [5370]

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

- Implement memory check in resample to prevent huge arrays [5354]

photom
------

- Updated NIRSpec fixed-slit processing to compute and save correction
values for both point and uniform sources in the primary slit when it
contains a point source, in order to support master background corrections.
[5463]

pipeline
--------

- Update ``Image3Pipeline`` to allow sky subtraction when input contains
only one image (group). [5423]
- Enable resample_spec for NIRSpec line lamp exposures in Spec2Pipeline [5484]

ramp_fitting
------------

- Update to store output as an `IFUImageModel` for NIRSpec AUTOWAVE exposures
using the IFU mode. [5356]

- Update to add 'DO_NOT_USE' DQ flag to pixels with all groups flagged as
saturated. [5367]

resample
--------

- Implement memory check in resample to prevent huge arrays [5354]

- Add ``pixel_scale_ratio`` parameter to allow finer output grid. [5389]
- Enable resample_spec for NIRSpec line lamp exposures [5484]

reset
-----
- Turn the step back on for the calwebb_detector1 pipeline [5485]

saturation
----------

- Set saturation threshold to A-to-D limit of 65535 for pixels flagged with
NO_SAT_CHECK in the saturation reference file, instead of skipping any
test of those pixels. [5394]
- Flag groups values below A/D floor (0 DN) (5422)

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

- Add logging of the found quaternion information [5495]
- Handle cases where engineering database's pointing mnemonics are all zero over the requested time range [5540]
- Set value of keyword ENGQLPTG to CALCULATED or PLANNED depending on whether pointing telemetry was used to
update the WCS [5556]

skymatch
--------

- Fix a bug in ``skymatch`` that would result in a crash when ``skymethod``
contains ``'global'`` and the *single image group*'s sky cannot be computed
(e.g., because all pixels are flagged as "bad"). [5440]

stpipe
------

- Implement utility function all_steps and fix crds reference file retrieval for non-datamodels [5492]

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

- Place aperture using header keywords XREF_SCI and YREF_SCI instead of
CRPIX1 and CRPIX2 [5533]

- Fixed the flux units in the output photometry catalog. [5529]

tweakreg
--------

- Add support for the new ``fitgeom`` mode: ``'rshift'`` that can fit only
for shifts and a rotation. [5475]

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

- Add checking for bad pixels by using DO_NOT_USE rather than DQ>0. [5500, 5519]

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

- Add support for step parameters ``min_wavelength`` and ``max_wavelength`` to modify
the wavelength region over which the flux integration is calculated. [5501]

0.17.1

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

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

- Add product name override to the `IFUGratingBkg` class, to prevent the default
"clear" suffix showing up in NIRSpec IFU product names. [5326]

barshadow
---------

- Implement using a user-supplied correction which overrides all references. [5302]

- Implement applying the inverse operation. [5302]

blendmeta
---------

- Do not close files that were not opened by blendmodels [5299]

cube_build
----------

- If every wavelength plane of the IFU cube contains 0 data, cube_build is skipped [5294]

- Remove "clear" suffix from MIRI MRS product name templates [5326]

flat_field
----------

- Update how the flat field reference dq mask is used for NIRSpec MOS data [5284]

- Implement providing a user-supplied flat field which overrides all references. [5302]

- Implement applying the inverse operation. [5302]

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

- Create new step `MasterBackgroundNrsSlits` step to handle NIRSpec MOS data in `Spec2Pipeline` [5317]

- Implement option to save the 2d version of the calculated master background [5317]

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

- Fix bug where background was being subtracted on the input data [4858]

pathloss
--------

- Implement using a user-supplied correction which overrides all references. [5302]

- Implement applying the inverse operation. [5302]

photom
------

- Implement using a user-supplied correction which overrides all references. [5302]

- Implement applying the inverse operation. [5302]

pipeline
--------

- Spec3Pipeline check whether master background subtraction has already occurred. [5308]

- Implement master background subtraction in Spec2Pipeline for NIRSpec MOS data. [5302]

- Include the per-slit failure traceback in any RuntimeError raised in Spec2Pipeline. [5315]

scripts
-------

- Add pointing analysis commands v1_calculate and pointing_summary. [5311]

stpipe
------

- Do not attempt prefetch on pipelines that are set to not allow prefetch. [5363]

ramp_fitting
------------

- Reinstate copying of INT_TIMES table to output rateints product for TSO exposures. [5321]

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

- Fix a bug in the computation of integration time stamps when the INT_TIMES
table is not available. [5318]

0.17.0

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

align_refs
----------

- Add bad pixel replacement for target and psf images [4973]

assign_mtwcs
------------

- Skip the step if any input MT_RA/DEC keyword values are missing. [5015]

assign_wcs
----------

- Enabled ``filteroffset`` correction for NIRISS and NIRCAM imaging modes. [5018, 5027]

- Pass an optional ``input_frame`` parameter in ``assign_wcs.util.wcs_from_footprints``. [5120]

- Improved calculation of bounding boxes in grism images. [5122]

- Added two new optional parameters to ``utils.cerate_grism_bbox`` - ``wfss_extract_half_height``
and ``wavelength_range``. [5140]

- Shifted the bounding box of a resampled WCS by - 0.5 px to account for the
center of the pixel. [5241]

- Enable NIRSpec lamp processing in calspec2 pipeline. [5267]

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

- Update diagrams in documentation to change sloper to detector1. [4986]

- Update level-3 rules to exclude IFU exposures from ``calwebb_tso3`` associations. [5202]

- Fix formatting error in Asn_IFUGrating product name construction. [5231]

barshadow
---------

- Correct bar shadow parity bug for yslit. [5095]

combine_1d
----------

- Skip spectra that are degenerate when combining [5037]

cube_build
----------

- Changed default weighting to 'emsm'. [5277]

- Fixed formatting of NIRSpec s3d output product names. [5231]

- Modified NIRSpec blotting to the find min and max ra and dec for each slice and only
invert those values on slice that fall in range [5144]

- Changed default weighting back to 'msm' until NIRSPEC cube pars ref file contains emsm info [5134]

- Added checks read from cube pars reference file that parameters have valid data [5134]

- Change the name of default cube type from ``world`` to ``skyalign`` [4974]

- Add ``ifualign`` cubes to be cubes rotated on sky to align with ifu instrument plane [4974]

- Change the name of MIRI ``alpha-beta`` cube type to ``internal_cal`` [4974]

- Add ability to make NIRSpec ``internal_cal`` ifu cubes aligned with slicer plane [4974]

- Change default weighting from ``msm`` to ``emsm`` [4974]

- NIRSpec IFU cubes built from all wavelengths rather than those defined in cube par ref file [4974]

- Removed wavelength planes that contained only 0 data. These planes are edge cases [4974]

datamodels
----------

- Add iscopy to ModelContainer init [5256]

- Re-enable FITS-hash by default. [5191]

- Add blend rule for keywords DETECTOR and MODULE. [4998]

- Add methods ``Model.info`` and ``Model.search``. [4660]

- Trim MT_RA, MT_DEC keyword comments to fit within FITS record. [4994]

- Add enum list and default value of 'NONE' for ``meta.instrument.lamp_mode`` [5022]

- Add TIMEUNIT keyword to schemas. [5109]

- Split ``pathloss`` object into ``pathloss_ps`` and ``pathloss_un`` in schemas. [5112]

- Add "PERSISTENCE" DQ flag definition. [5137]

- Fix nonsensical premature closing of FITS file of a ``DataModel``. [4930]

- Add a hash set/check to DataModel I/O to check whether schema traversal is necessary. [5110]

- Update underlying MultiExposureModel from the SourceModelContainer models. [5154]

- Add new MIRI LRS dither patterns to PATTTYPE enum list. [5254]

extract_1d
----------

- Implement aperture corrections in the Extract1dStep. [4902]

- Fix bug in creating a polynomial fit used in background extraction. [4970]

- Recheck the input model container in run_extract1d to select the correct processing [5076]

- Rework/refactor many functions for style and readability. [5079]

- Checks subwcs and new_slit variables exist before trying to delete them. [5093]

- Parameter ``mmag_extract`` is now propagated to the extraction routine. [5122]

- Updated the logic for when and how to use the source position to offset the
location of the extraction regions specified in the EXTRACT1D reference file. [5157]

- Fixed the conversion of flux to surface brightness for IFU extended source case [5201]

- Fixed bugs in aperture correction for NIRSpec multi-slit modes. [5260]

extract_2d
----------

- Check that ``subwcs`` and ``new_slit`` variables exist before trying to delete them [5093]

- Move NIRSpec wavecorr routines to the ``wavecorr`` step. [5133]

- Added a new optional integer parameter to extract_2d (``wfss_extract_half_height``)
which allows a user to specify the extraction height in the
cross-dispersion direction for WFSS mode. [5140]

flat_field
----------
- For NIRSpec BOTS and ALLSLITS add the slit start corner to the subarray start corner
when determining what region of the flat_field reference files to extract. [5269]

- Enable NIRSpec lamp processing in calspec2 pipeline. [5267]

fringe
------

- Update the fringe step to handle 3D inputs for MIRI MRS TSO mode. [5202]


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

- Fix open files bug [4995]

- Update to include pathloss corrections to NIRSpec IFU background [5125]

mrs_imatch
----------

- MRSIMatchStep to create its ModelContainers with `iscopy=True` [5256]

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

- Update median filter to use numpy's nanmedian. [5114]

- Fix outlier_detection bug when saving intermediate results. [5108]

- Update logic to correctly handle input ``CubeModel`` that have only
1 integration. [5211]

pathloss
--------

- Fix bug in NIRSpec IFU data that causes valid pixel dq flags to set to
NON-SCIENCE in the region of an overlapping bounding box slice [5047]

- Update to save both point source and uniform source 2D pathloss correction
arrays to output. [5112]

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

- Flag pixels with high persistence using "PERSISTENCE" DQ flag instead
of "DO_NOT_USE". [5137]

pipeline
--------

- Refactor the ``Image3Pipeline`` to use ``stpipe`` infrastructure. [4990]

- Fix ``Coron3Pipeline`` to blend headers just from each input science model,
not every integration. [5007]

- Fix open files bug in ``get_config_from_reference`` class method, and in
``Spec2Pipeline``, ``Spec3Pipeline`` and ``tso3``. [4995]

- Update ``calwebb_tso3`` to do more robust checking of input data type.
[5107]

- Update the ``Spec2Pipeline`` to include the new ``wavecorr`` step and put
``srctype`` before ``wavecorr``. [5133]

- Update the ``Spec2Pipeline`` to skip ``extract_1d`` for IFU data that
have not had a cube built (e.g. MIRI MRS TSO), and update the
``calwebb_tso-spec2.cfg`` configuration to turn on the ``fringe`` step
and turn off ``cube_build`` for MIRI MRS TSO. [5202]

- Update the ``Coron3Pipeline`` logic to correctly handle inputs that have
only 1 integration. [5211]

- Refactor Spec2Pipeline for execution logic and step flow isolation [5214]

- Update ``Ami3Pipeline`` to only process psf and science members from the
input ASN. [5243]

- Enable NIRSpec lamp processing in calspec2 pipeline. [5267]

photom
------

- Fix bug in NIRSpec IFU data that causes valid pixel dq flags to set to
NON-SCIENCE in the region of an overlapping bounding box slice [5047]

ramp_fitting
------------

- Add multi-processing capability. [4815]

- Fix crash when DRPFRMS1 is not set [5096]

- Update to always create the rateints product, even when NINTS=1. [5211]

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

- Fix artifacts in resampled NIRSpec slit data caused by NaNs in the WCS [5217]

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

- Use ``gwcs.WCS`` instead of FITS WCS. [5120]

- Changed the type of column ``is_star`` from float to bool. [5140]

- Implemented algorithm for determining whether a source is a star.
[5234]

stpipe
------

- Limit reference file prefetch to the first "science" exptype
when a pipeline has an association as input. [5031]

- Remove further sloper references. [4989]

- Enable prefetch of pars reference files for associations. [5249]

transforms
----------

- Wrap first spherical angle ("RA") at 360 degrees in the forward ``V23ToSky``
transformation and to 180 degrees for the inverse transformation ("V2").
This is now done using models defined in ``astropy`` and ``gwcs`` packages
replacing ``V23ToSky`` model in JWST's WCS pipeline. [5206]

wavecorr
--------

- Implemented the ``wavecorr`` step by pulling routines from the
``extract_2d`` step. [5133]

0.16.2

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

- Fixed ``packaging`` dependency installation issue. [4977]

0.16.1

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

assign_wcs
----------

- Update keyword and attribute usage around SkyObject to reflect updated keywords. [4943]

- Refactor PPS origin of NIRSpec MOS shutters from top left to bottom left. [4959]

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

- Modify NIRSpec IFU level-3 ASN rules to include only one grating per association [4926]

calwebb_coron3
--------------

- Update coron3 for new outlier detection application [4968]

datamodels
----------

- Add ``to_container`` to ``CubeModel`` to convert a cube to a list of images [4968]

- Add ``getarray_noinit`` to ``DataModel`` to access arrays without causing initialization [4968]

- Limit looping over HDU's while resolving arrays in schema [4951]

- Relax asdf requirement and use validator flag when asdf 2.6.x is installed [4905]

- Updated core schema to include recent Keyword Dictionary changes
(remove TIME-END; add TDB-BEG, TDB-MID, TDB-END, XPOSURE, TELAPSE)
[4925]

- Populate meta.asn.table_name when an association is loaded into a
``ModelContainer``. [4873]

extract_1d
----------

- Add aperture correction in extract_1d processing. [4902]

lib
---

- Update SkyObject keys. [4943]

mrs_imatch
----------

- Fix ``mrs_imatch`` to avoid calls to ``sigma_clipped_stats`` with all-zero
arrays. [4944]

photom
------

- Fix flux units in photom for MultiSlit cases. [4958]

pipeline
--------

- Updated calwebb_image3 pipeline to only load science and background member
types from an input ASN. [4937]

- Updated the calwebb_spec2 pipeline to only use the basename of the source
catalog file when updating the source_catalogue keyword for WFSS inputs.
[4940]

rscd
----

- Fixed bug when the READPATT/SUBARRAY data is not found in RSCD reference file [4934]

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

- Add more concentration indices and update step docs. [4906, 4908]

- Added fallback background estimation method to make background
estimation moare robust. [4929]

- Fixed the nearest-neighbor code to handle the case of exactly one
detected source. [4929]

- Update abmag error calculation. [4945]

- Exit gracefully if APCORR ref file is missing. [4948]

tweakreg
--------

- Added align_to_gaia processing as an option [4599]

0.16.0

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

ami
---

- Reorganized step documentation [4697]

assign_wcs
----------

- Updated MIRI imaging distortion to use new filteroffset file format [4776]

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

- Update asn_from_list to have default values in the asn header [4720]

- Update rules so exclude dark files from associations [4668]

- Update association rules so that nodded observations produce level 3 asn's [4675]

cmdline
-------

- Re-enable exception tracebacks from strun for issues outside step processing [4761]

coron
-----

- Reorganized step documentation [4697]

datamodels
----------

- Update schemas to add moving_target_position and cheby tables to the level1b
schema [4760]

- Deprecate ``DrizProductModel`` and ``MultiProductModel`` and replace with
updated versions of ``ImageModel`` and ``SlitModel`` that include "CON" and
"WHT" arrays for resampled data. [4552]

- Remove lev3_prod schema and move resample-related keywords to
core schema. [4552]

- Add data models for spectroscopic mode APCORR reference files. [4770]

- Added ``pupil`` to the ``FilteroffsetModel`` to support NIRCAM and NIRISS WCS. [4750]

- Removed old MIRI-specific filteroffset schema. [4776]

- Added FASTGRPAVG[8,16,32,64] to the READPATT keyword allowed values. [4818]

- Added the SRCTYAPT keyword and moved SRCTYPE to the SCI extension header of
all applicable data model schemas. [4885]

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

- Resulting MultiExposureModels are now updated with header information from the inputs. [4771]

extract_1d
----------

- Updates for handling resampled input data as ``ImageModel``, ``SlitModel``,
and ``MultiSlitModel``, instead of ``DrizProductModel`` and ``MultiProductModel``,
which are deprecated. [4552]

- Remove pixel-by-pixel calls to wcs; copy input keywords to output for
more types of input data. [4685]

- Updated to create a single ``x1d`` product per source for WFSS data, containing
all extracted spectra for a given source, instead of multiple ``x1d`` files per
source. [4846]

extract_2d
----------

- Change the source type for NIRSpec MOS sources with stellarity = -1 from
UNKNOWN to POINT. [4686]

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

- Updated step arguments in the documentation. [4723]

- Fix issue with files left open at end of step [4775]

mrs_imatch
----------

- Updated step to use EMSM cube weighting, and to perform iterative sigma
rejection of sources prior to running the background solver. [4732]

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

- Updated step arguments in the documentation. [4723]

- Change outlier and resample DQ bit usage. [4726]
Default value of ``good_bits`` now includes all DQ flags except ``DO_NOT_USE``.
Also, newly flagged outliers are flagged with ``DO_NOT_USE + OUTLIER``.

- Added a hardcoded declaration of a reasonable scale parameter for MIRI MRS as a stopgap
measure until a parameter reference file can pass one more cleanly. [4778]

pipeline
--------

- Update ``calwebb_detector1`` to reduce the memory used in processing. [4643]

- Update ``calwebb_coron3`` to return ``ImageModel`` instead of ``DrizProductModel``,
when necessary. [4552]

- Fix issue with files left open at end of ``calwebb_spec2`` [4775]

- Update ``calwebb_spec3`` to use suffix ``c1d`` for ``combine_1d`` products.
[4846]

- Update ``calwebb_spec3`` to update the ASNTABLE keyword in all output
products, to reflect the name of the spec3 ASN used as input. [4865]

resample
--------

- Update to return resampled data in an ``ImageModel``, instead of
``DrizProductModel``. [4552]

- Updated documentation to include step arguments and reference file
description. [4723]

- Change outlier and resample DQ bit usage. [4726]
The parameter ``good_bits`` has been removed in favor of allowing all
DQ flags except for ``DO_NOT_USE``

- Updated to reject pixels with DQ flag NON_SCIENCE, in addition to
DO_NOT_USE. [4851]

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

- Update to return resampled data in a ``SlitModel`` or ``MultiSlitModel``,
instead of ``DrizProductModel`` or ``MultiProductModel``. [4552]

- Fix bug that was causing resampled MIRI LRS fixed-slit data to be all zero.
[4552]

- Enable model metadata blending [4765]

rscd
----

- Added baseline algorithm that flags groups [4669]

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

- Update to add moving target coords to the header [4760]

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

- Update to use ``ImageModel`` for resampled input data, instead of
``DrizProductModel``. [4552]

- Updated step arguments in the documentation. [4723]

- Updated to include aperture photometry and aperture corrections. [4819]

- Rename AB-to-Vega reference file type to ABVEGAOFFSET. [4872]

srctype
-------

- Change default source type for NRS_IFU from POINT to EXTENDED. Change the source
type for NIRSpec MOS sources with stellarity = -1 from UNKNOWN to POINT. [4686]

- Modified the step to use the SRCTYAPT keyword to get the user input value from
the APT and store the derived source type in the SRCTYPE keyword. [4885]

stpipe
------

- Unhide exceptions during CRDS steppars retrieval [4691]

- Add command line and environmental options to not retrieve steppars references [4676]

- Use only a single member of an association for CRDS STEPPARS checking [4684]

- Fix handling of the boolean-like environmental variables PASS_INVALID_VALUES and STRICT_VALIDATION [4842]

strun
-----

- Re-enable exception tracebacks from strun for issues outside step processing [4761]

tweakreg
--------

- Updated step arguments in the documentation. [4723]


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

- Update the value of the ASNTABLE keyword in the output ``wfscmb`` product. [4849]

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