Jwst

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

- Update documentation introduction to include installation and CRDS setup
instructions. [5659]

combine1d
---------

- Fixed code error in combine1d, creating extensions per spectral order
with the same input data [5644]

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

- Fix a bug in estimating the max number of segments that will be needed
to fit any pixel [5653]

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

- Update the check in set_telescope_pointing that determines whether an
exposure is TSO mode to always consider hardwired TSO EXP_TYPEs as TSO,
regardless of TSOVISIT and NINTS settings. [5657]

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

- Fixed error causing multi-segment data to reject int_times
for MJDs [5566]

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

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

- JWSTDMS-410 Asn_Lv2NRSLAMPSpectral: Break out the negative cases [5635]

- Update MIRI LRS-Fixedslit ALONG-SLIT-NOD backgrounds strategies [5620]

cube_build
----------

- Do not allow variables defined in spec (part of the cube_build_step class) to
be changed, to allow calspec2 to loop over a list of files and run the
pipeline. [5603]

datamodels
----------

- Updated schemas for new keywords CROWDFLD, PRIDTYPE, PRIDTPTS, PATTNPTS, SMGRDPAT,
changed name of SUBPXPNS to SUBPXPTS, and new allowed values for PATTTYPE. [5618]

flat_field
----------

- Added DO_NOT_USE to pixels flagged as NON_SCIENCE for non-NIRSpec data [5601]

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

- Account for the background subtracted data in the blot image for determining
the noise image used in flagging outliers [5601]

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

- Updated to populate XREF_SCI, YREF_SCI keywords for all exposures with
TSOVISIT=True, not just NRC_TSGRISM mode. [5616]

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

combine1d
---------

- Output FITS now contains separate combine1d extensions for each spectral
order present in the data [5204]

cube_build
----------

- Tweaked pixel wavelength preselection range to avoid truncation at the ends
of the cubes. [5598]

datamodels
----------

- Fix missing CHANNEL entry in distortion reffile schema. [5553]

extract_1d
----------

- For IFU data (NIRSpec and MIRI) the extraction radius is now a varying size
based on wavelength. The apcorr correction is a function of wavelength and
radius size. Fixes a bug in units conversion for applying the apcorr correction.
The units are now correctly converted from arcseconds to pixels. Added an
new method to apply the apcorr correction for IFU data. [5506]

pipeline
--------

- Removed all unnecessary parameter settings from cfg files for all steps
and pipelines, and removed references to step config files from most
pipeline modules (only kept those that are necessary for intended
functionality). [5574]

skymatch
--------

- Fixed a bug due to which sky matching may fail under certain circumstances
such as using 'mode' statistics on a single pixel (after sigma-clipping). [5567]

stpipe
------

- Removed unused LinearPipeline class. [5590]

wavecorr
--------
- Fixed bugs in wavecorr. [5570]

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

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]

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

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]

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

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]