JWST Calibration Pipeline

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Breaking Changes Make wfss_contam expect the direct image to have a WCS object instead of the segmentation map (#9935) Drop support for datamodels without int_times table (#10042) Remove deprecated AmiAverageStep (deprecated since 1.18.1) (#10057) Fix a bug where accessing array-like attributes that did not exist would set them to default values. For example, creating ImageModel((10,10)) and then accessing model.err no longer sets model.err to its default (in this case, a 10x10 array of zeros). model.get_default() must now be used instead. Setting the value must be done explicitly, e.g. model.err = model.get_default("err"). (#10267) Fix a bug where accessing metadata attributes that did not exist would set them to their schema-defined default, if one was defined. For example, creating an empty SlitModel() and then accessing model.source_id no longer sets model.source_id to its default of 0. Instead, it remains empty until specifically set. Use model.source_id = model.get_default("source_id") to set it to the default value if desired. (#10344) stpipe Remove kwargs from the JwstStep.run signature to match the parent method (Step.run). (#9878) Add an option to Step.prepare_output to open the input with a specific datamodel class. (#9903) Add the add_asn_id_to_output_name method to JwstStep to allow an ASN ID to be automatically appended to output filenames. (#10295) Associations Improved association diff error messages. (#9914) Add TA verification images to spec2 associations for MIRI LRS fixed-slit and slitless data (#10011) Added Asn_Lv2WFSSMIR and Asn_Lv3WFSSMIR rule classes for creating MIRI WFSS associations. (#10094) Associations that used to produce asn_type of "wfs-image2" now produces "image2" instead. (#10124) Deprecate YAML as a valid format for reading and writing association files (#10294 ) Bypass unnecessary compare_asns calls to improve generator runtime. Factor-of-3 runtime improvement is realized for one large NRC_WFSS pool tested (#10384 ) set_telescope_pointing Removed deprecated lib.compute_va_effects and lib.compute_va_effects_vector functions; use the functions from stcal.velocity_aberration module instead. (#10106 ) Pipeline Added support of MIRI WFSS mode to calwebb_spec2 (#9689) Use Step.prepare_output in pipeline steps to open input models and make copies only when necessary. (#9903) Use polygon unions to make S_REGION keywords more accurately represent true combined footprint for WFSS spec3 products (#9915) Replaced the spec2 pipeline call to nsclean with a call to clean_flicker_noise. (#9981) Add new step targ_centroid to spec2 pipeline for MIRI LRS fixed-slit and slitless data, off by default (#10011) Fixed datamodel cal_logs not grouping log messages from steps into the pipeline category for some products. (#10292) Added support for NIRISS SOSS superstripe mode to detector1, spec2, and tso3 pipelines. (#10317 ) Added support for NIRCam DHS substripe mode to Spec2Pipeline steps. (#10353) Processing of MIRI WFSS data added to calwebb_spec3 pipeline. (#10357) model_blender Add custom ModelBlender rule for wheelpos tolerance values (#10412) adaptive_trace_model (spec2, spec3) Add a new adaptive_trace_model step to the spec2 and spec3 pipelines to create a model of the spectral trace. Optionally, the trace model can be used to oversample the flux data, prior to resampling or cube building, to address undersampling effects. Only IFU data is supported in the initial implementation. (#10066) Fix a couple minor bugs in intermediate products, edge clipping, and spline knots for the adaptive_trace_model step. (#10299) Fix an out-of-bounds issue with the adaptive_trace_model step when scaling the spline model in some regions. (#10393) ami_analyze / ami_normalize / ami_average (ami3) Remove deprecated AmiAverageStep (deprecated since 1.18.1) (#10057) assign_mtwcs (image3, spec3) Fix indexing bug for associations that have background exposures before science exposures (#10050) assign_wcs (image2, spec2) Added MIRI WFSS pipeline. (#9689) Remove legacy support for the old-style NIRSpec WCS. All processed data should now have a full slit-based WCS implementation. (#9879) Replace grating equation transforms from stdatamodels with their gwcs counterparts (#9995 ) Replace functions in util (compute_scale, wcs_bbox_from_shape) with equivalent functions in stcal.alignment.util. (#10024) Add a non-empty frame for the "coordinates" transform in the NIRSpec IFU WCS. (#10117 ) background (image2, spec2) Add a catch for missing bkg reference file in NIRISS SOSS processing. (#10002 ) Refactor to skip unnecessary data copies and remove the subtract_images and asn_intake modules. (#10131) Add wfss_mask parameter to allow user-supplied background mask for wfss data (#10144 ) Added MIRI WFSS background subtraction of a reference file. (#10280) Bug fix for non-finite values causing the SOSS background subtraction to skip (#10444 ) clean_flicker_noise (detector1) Simplify WCS access for NIRSpec FS and MOS data processed with the mask_science_regions option. (#9879) Add an option to correct 1/f noise in TSO data with reference to a median image (background_method=median_image). Add support for masking expected spectral traces for NIRISS SOSS data when mask_science_regions=True. (#10281) Interpret string values of "none" or "None" as Python None, for the user_mask parameter. (#10389 ) combine_1d (spec3) Add a failsafe that skips processing an input spectrum if its wavelength array is not monotonic (#10352) cube_build (spec2 IFU, spec3) Always create a wavetab extension and added linear_wave as option. (#10345 ) dq_init (detector1) New spec, --user_supplied_dqfile, for user to pass in their own DQ array. See step documentation for more details. (#10100) emicorr (detector1 MIR) Deprecate the 'user_supplied_reffile' step parameter. The auto-generated parameter 'override_emicorr' should be used instead. (#10222) extract_1d (spec2, spec3) Refactor SOSS extraction to compute reference wavelength maps and spectral traces only once, instead of every integration. (#9886) For SOSS ATOCA, reuse regularization factor integration-by-integration for well-separated blue part of order 2 and order 3, similar to what was already done for order 1 & 2 combined extraction. Improve runtime of SOSS ATOCA extraction; with default options, factor-of-5 improvement for first integration and almost factor-of-2 improvement for subsequent integrations. (#9900) Add PA_APER keyword to EXTRACT1D extension headers. (#9925) Enabling sigma_clipping in the background annulus for IFU source_type POINT. (#9953 ) Allow multiprocessing by integration for SOSS. New step-level parameter soss_maximum_cores turns multiprocessing on (off by default). (#9990) A number of changes to the SOSS ATOCA implementation to impute missing data, use the same uncertainty across integrations, and precompute quantities to improve runtime by a typical factor of 15-30. Multiprocessing removed from SOSS. (#10022 ) Fix a bug where file written by soss_wave_grid_out did not ingest properly as soss_wave_grid_in (#10105) Replace hard-coded pastasoss constants with pastasoss reference file metadata attributes (#10240 ) Remove padsize argument from jwst.extract_1d.soss_extract.pastasoss.get_soss_wavemaps (#10322) extract_2d (spec2 MOS) Allow source_ids parameter to select from the input catalog for WFSS data. Add source_ra and source_dec parameters to select objects by sky position for WFSS data. (#9973) Fix a bug where defining source_dec without source_ra did not raise an error. Add source_max_sep parameter to specify maximum distance in arcsec from user-input ra, dec pair that should be considered a match. (#10078) firstframe (detector1 MIR) Deprecate the FirstFrame step. Use the RSCD step instead for first-integration flagging. (#10085) klip (coron3) Modified the jwst.coron.klip.klip function to update the target model in place and make the PSF output model optional. (#10202) msaflagopen (spec2 IFU, spec2 MOS) Simplify WC

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