CHANGES.rst

1.3.0 (2025-10-02)

• Fixed crash for astrometric_catalog for background observations
• Fixed crash when filtering out guide stars
• Fixed issue with background files in move_raw_obs_step
• Fixed logging, will now properly output to a log file
• Fix crash for background observations in get_short_band_name
• For background association, strip whitespace and lowercase for more robust matching
• Imports update - now supports numpy>2.0!
• Keep track of expected stripe direction in multi_tile_destripe_step
• Trim off reference pixels for median filter in single_tile_destripe_step
• Keep track of expected stripe direction in single_tile_destripe_step
• Add support for NIRISS
• Fix crash in the persistence correction in lv1_step if some earlier observation is missing
• Fix crash in multi_tile_destripe_step for heavily masked data when doing smoothing
• Fix crash in astrometric_align_step with new gwcs updates
• Fix crash in lv3 step when degrouping NIRCam modules
• Allow for degrouping of NIRCam modules in get_wcs_adjust_step and apply_wcs_adjust_step
• Fix for crash if trying to anchor without first aligning
• Fix for crash if trying to PSF match without some combination of anchoring, aligning
• Change how the level 3 step handles models for newer JWST versions

1.2.0 (2024-09-03)

• Removed raised warning in multi_tile_destripe_step when input images have a variety of rotations
• Added combine_nircam_short option in level_match_step, which will match levels between the four NIRCam short imaging chips before doing matching between mosaic tiles
• lv2_step will now propagate through individual exposure offset times from backgrounds, which is necessary for selecting a reference image in level_match_step
• Added fit_type option to level_match_step for every option, which allows for plane fitting in the level matching in a modular way
• level_match_step fitting method has been changed to resemble the iterative Montage method, which is necessary for plane fitting
• reproject_image in utils can now also reproject error arrays
• make_stacked_image in utils can now also reproject the error and readnoise maps
• Exposed auto_rotate in make_stacked_image in utils
• Added prefilter option to get_wcs_adjust, which uses constrained diffusion to remove large-scale structure
• Added recombine_lyot option to level_match_step, which allows for recombining the lyot coronagraph into the main MIRI science chip before matching between mosaic tiles
• Tidied up level_match_step to make more modular and functional
• Fix bug in astrometric_align_step if first pass of alignment succeeds but second fails
• Add cross-correlation option to get_wcs_adjust_step, which uses spacepylot
• Add control over reproject functions, can be reproject_interp (default), reproject_exact, or reproject_adaptive. For MIRI, reproject_exact may work better. This applies to anchoring_step, astrometric_align_step, level_match_step, multi_tile_destripe_step, psf_matching_step, and release_step
• Fix bug for lv1 hanging on newer Macbooks
• Fix bug for parameters with 'pix' in getting picked up like numbers of pixels
• Updated PHANGS Cy3 config
• Include links to Francesco Belfiore's kernel generation repository in the docs
• Updated various package requirements
• Updated indexing to align with new reproject updates

1.1.0 (2024-03-04)

• If science lv1 data already exists, just copy it over for background data to save processing time
• Include BMAJ in psf_matching_step
• Auto rotate the WCS in level_match_step
• Fix SIP approximation issues in apply_wcs_adjust_step

• astrometric_catalog_step can now use either DAOStarFinder or IRAFStarFinder. Observatory recommendations seem

  to be IRAFStarFinder in general

• Removed factor of 2 for FWHM in lv3 tweakreg-related steps to more closely match observatory recommendations
• Add lower version pins to project requirements to avoid incompatibilities
• Fixed bug in astrometric_align_step where file might already be closed before saving
• Updated PHANGS Cycle 1 config to v1p1 (last couple of observations, and a few small changes to the config)
• Fix bug with process_bgr_like_science in lv3_step
• Added 'filename' option for background association
• Fix in parse_fits_to_table when there is not a defined observation label
• Point Zenodo DOI to "concept" DOI, rather than latest
• Cleaner labels in anchoring_step
• Add acknowledgment for PCA (thanks Liz!)
• Added CITATION.cff

1.0.4 (2024-01-04)

• Fix del in get_wcs_adjust if we skip alignment
• Made plots more consistent and "publication ready" across the board
• Fix bug in anchoring step
• Rename anchor_to_external_step.py to anchor_step.py for consistency
• Fix "too many plots open" warning in anchoring_step
• Include useful pjpipe version info in files
• Save anchoring background in metadata properly in anchoring_step
• Add Zenodo badge

1.0.2 (2023-12-01)

• Fix packaging to minimise file size
• Error in pyproject.toml

1.0.0 (2023-12-01)

• Added documentation
• Ensure multi_tile_destripe_step is properly imported in the pipeline
• Remove an error in multi_tile_destripe_step stripes in stacked image don't align with any particular axis of the array
• Fix crash where quadrants are turned off in median filtering in single_tile_destripe_step
• Fix potential memory leaks in get_wcs_adjust_step and apply_wcs_adjust_step
• Diagnostic plots are compressed by default in release_step

0.10.1 (2023-11-20)

• Can specify CRDS context at the pipeline level
• median_filter is now the default in single_tile_destripe_step
• Added fallback for median_filter in single_tile_destripe_step when too much data is masked
• Remove mask option in median_filter in single_tile_destripe_step, since it's always used anyway
• Changed up how do_large_scale works in multi_tile_destripe_step, which seems significantly improved and simplified
• Added fallback for in multi_tile_destripe_step when too much data is masked in quadrants
• Changed how tweakreg grouping is done in get_wcs_adjust_step and lv3_step to account for code changes in the pipeline
• Added option to decouple the short NIRCam chips for tweakreg in lv3_step
• Added option to move the various diagnostic plots in release_step
• remove_bloat is now False by default in release step, to maintain datamodels compatibility
• remove_bloat also applies to PSF matched files in release_step

0.10.0 (2023-11-14)

• Added PSF modelling routines. These are currently very preliminary, but at least exist
• Allow for external, absolute catalog in get_wcs_adjust_step
• Add PSF matching routines (psf_matching)
• Add anchoring routines (anchoring)
• Include useful outputs from these in the release_step
• If not grouping dithers in get_wcs_adjust_step, respect that in how the transforms are written out
• single_tile_destripe_step can now run on rate files (pre-flat fielding)
• Bugfixing in single_tile_destripe_step
• Decoupled horizontal/vertical destriping methods in single_tile_destripe_step, since the noise properties are distinct in these two axes
• Add smooth option to single_tile_destripe_step, based on Dan Coe's smooth1overf algorithm
• Added control over how values are extended beyond array edge for filtering in single_tile_destripe_step
• Lots of bugfixing in multi_tile_destripe_step
• multi_tile_destripe_step can un-flat before correcting
• Level between amplifiers in multi_tile_destripe_step
• Make vertical stripe subtraction optional in multi_tile_destripe_step
• Added median option to multi_tile_destripe_step to do a median rather than mean image
• Added iterative option to multi_tile_destripe_step that will keep things going until sigma-based convergence
• Added sigma-clip median option for creating stacked images
• do_large_scale now works completely differently in multi_tile_destripe_step, instead attempting to clean up the average image
• Added support for different do_large_scale methods in multi_tile_destripe_step, which may work better in certain situations
• Added a median filter do_large_scale method, which may be more robust than the boxcar. THIS IS NOW THE DEFAULT
• Added a sigma-clipped do_large_scale method, as should be optimal in observations that aren't full of emission
• Added a smooth convolution do_large_scale method, based on Dan Coe's smooth1overf algorithm
• Added control over how values are extended beyond array edge for do_large_scale
• Added option in lv3_step to degroup dithers for tweakreg
• Added option in lv3_step to degroup NIRCam modules, since the WCS is currently inconsistent between the two
• Fixed crash in lv3_step if one of the group/degroup parameters is not defined
• Be smarter about keeping track of exposure numbers in lv3_step
• regress_against_previous will now search for files in priority order, for fallback between versions
• Make sure backgrounds are included in label for regress_against_previous
• f-string fixes

0.9.2 (2023-09-18)

• Allow multiple options for e.g. proposal ID in download_step
• Fix potential error with file validation in download_step
• move_raw_obs_step is smarter about missing filters
• lv1_step is smarter about grouping dithers
• Fix plotting error if quadrants=False and using median filter in single_tile_destripe_step
• Fix potential subarray issues with lyot_separate_step/lyot_mask_step
• do_large_scale defaults to False in multi_tile_destripe_step
• Much improved diagnostic plots in multi_tile_destripe_step
• Catch errors in level_match_step where all data might be NaN
• Rename do_vertical_subtraction in config files
• Caught some typos from lazy copy/pasting docstrings
• Additions and updates for #2130 (Local Group) and #3707 (Cy2 Treasury)

0.9.1 (2023-09-04)

• If not supplied, will default to running on all CPUs, not 1
• Include option for producing background images
• Include Gaia query for astrometric catalogs (gaia_query_step)
• Include option to produce mosaics for each individual field (mosaic_individual_fields_step)
• Parallelise up the download integrity verification in download_step
• Catch warnings as errors in integrity verification in download_step
• Include array information when creating asn files to ensure we don't associate backgrounds incorrectly
• Change naming system for lyot separate to ensure compatibility with later steps
• get_wcs_step now sorts shifts to be more human-readable
• Add local background subtraction to level_match_step, which may help for mosaics without overlaps
• release_step now takes the lv3 directory as an argument, rather than parsing any progress dictionaries
• release_step will now also move any individual field mosaics

0.9 (2023-07-25)

• Modular refactor
• Include subtracted backgrounds in release