- Added
recombine_lyot
option tolevel_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 usesspacepylot
- Add control over reproject functions, can be
reproject_interp
(default),reproject_exact
, orreproject_adaptive
. For MIRI,reproject_exact
may work better. This applies toanchoring_step
,astrometric_align_step
,level_match_step
,multi_tile_destripe_step
,psf_matching_step
, andrelease_step
- 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
- 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 seemto 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
inlv3_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
- 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
toanchor_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
- Fix packaging to minimise file size
- Error in
pyproject.toml
- 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
andapply_wcs_adjust_step
- Diagnostic plots are compressed by default in
release_step
- 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 inmulti_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
andlv3_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 inrelease step
, to maintain datamodels compatibilityremove_bloat
also applies to PSF matched files inrelease_step
- 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 tosingle_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 inmulti_tile_destripe_step
, instead attempting to clean up the average image- Added support for different
do_large_scale
methods inmulti_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
- 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 filterslv1_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 inmulti_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)
- 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 dictionariesrelease_step
will now also move any individual field mosaics
- Modular refactor
- Include subtracted backgrounds in release