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@stscieisenhamer stscieisenhamer released this 10 Jan 16:00
1.4.0
7e6d78d
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Learn about vigilant mode.

1.4.0 (2022-01-10)

ami_analyze

  • Call img_median_replace to replace NaN's and pixels flagged with
    DO_NOT_USE in the input image. [#6334]

assign_wcs

  • Open the specwcs reference file for WFSS modes using the with context
    manager. [#6160]

  • Fix bug in NIRspec where bounding_box can be oversized in height for
    some of the slits. [#6257]

  • Updated create_grism_bbox to be more robust against failures caused by
    bad input data. [#6309]

  • Added a function that, when given RA, Dec, lambda, computes which ones project
    into a given NIRSpec IFU slice. [#6316]

  • Changed in_ifu_slice in util.py to return the indices of elements in slice.
    Also the x tolerance on finding slice elements was increased. [#6326]

  • Fix a bug due to which, under certain circumstances, PC-matrix and
    CDELT coefficients may be removed from FITS WCS of data products. [#6453]

  • Fixed bug in NIRSpec MOS slitlet meta data calculations for background slits
    consisting of multiple shutters. [#6454]

  • Enabled spectral order as input to WCS for NIRISS SOSS mode. [#6496]

associations

  • Remove MIR_FLATMRS from Asn_Lv3MIRMRS rule. [#6548]

  • Fix bug causing pytest to encounter an error in test collection when
    running with recent commits to astropy main (5.0.dev). [#6176]

  • Enhanced level-2b ASN rules for NIRSpec internal lamp exposures to
    handle certain opmode/grating/lamp combinations that result in no data
    on one of the detectors. [#6304]

  • Removed Constraint_ExtCal from Asn_Lv2WFSC constraints, as it was
    redundant with Constraint_Image_Science present. [#6384]

  • Added constraint to Asn_Lv2ImageNonScience to prevent creation of asns
    for NRC_TACQ exposures with WFSC_LOS_JITTER in the DMS_NOTE. Also added
    new reduce method, Constraint.notall [#6404]

barshadow

  • Modify computation of correction array to remove dependencies on the
    centering of the source within the slitlet, because for extended/uniform
    sources the centering is irrelevant. This fixes bugs encountered when
    computing the correction for background signal contained within slits with
    an off-center point source. [#6454, #6459]

cube_build

  • Fix bug when creating cubes using output_type=channel. [#6138]

  • Move computationally intensive routines to C extensions and
    removed miri psf weight function. [#6093]

  • Moved cube blotting to a C extension [#6256]

  • Moved variable definitions to top of code in C extension to
    support changes in #6093. [#6255]

  • Added weighting option driz (3D drizzling) [#6297]

  • Using assign_wsc.utils.in_ifu_slice function to determine which NIRSpec
    sky values mapped to each detector slice. [#6326]

  • Fixed error in final exposure times calculated by blend headers. Only the input models
    used in the IFU cube are passed to blend headers. [#6360]

  • Update of documentation to explain 3d drizzling and remove miri psf weighting [#6371]

  • Fix a bug when creating internal_cal type cubes [#6398]

  • Fix incorrect spatial footprint for single band MRS IFU cubes [#6478]

dark_current

  • Refactored the code in preparation for moving the code to STCAL. [#6336]

  • Moved dark current code from JWST to STCAL. [spacetelecope/stcal#63] [#6444]

  • Updated step docs to explain unique form of MIRI dark reference data [#6529]

datamodels

  • Remove astropy.io registration of JwstDataModel. [#6179]

  • Update VELOSYS keyword comment [#6298]

  • Added new keywords FPE_SIDE and ICE_SIDE to core schema [#6314]

  • Fix bug preventing extra arguments when calling datamodels.open
    on an ASDF file. [#6327]

  • Implement memmap argument when calling datamodels.open on an ASDF
    file. [#6327]

  • Fix bug in schema that disallowed valid p_grating values. [#6333]

  • Add NDArrayType to list of valid types for RegionsModel.regions. [#6333]

  • Fix a bug in wcs_ref_models where SpecwcsModel was failing the SimpleModel
    validation as it contains a list of models rather than one simple model.
    Also add some missing allowed BAND values for MIRI MRS distortion
    and regions files. Fix an incorrect comment on
    FilteroffsetModel. [#6362]

  • Changed reference file model name from ResidualFringeModel to
    FringeFreq [#6385]

  • Updated data products documentation to indicate that variance and error arrays
    are now included in resampled products. [#6420]

  • Added SOSS-specific extraction parameters to core schema; add new
    datamodel to store SOSS model traces and aperture weights [#6422]

  • Added the MirLrsPathlossModel for use in the ``pathloss` step. [#6435]

  • Added new column 'reference_order' to 'planned_star_table' in
    guider_raw and guider_cal schemas [#6368]

  • Moved new column 'reference_order' in guider schemas' planned
    star table to second in order, after 'guide_star_order' [#6465]

  • Updated moving_target schema changing mt_detector_x/y to mt_sci_x/y [#6485]

  • Fixed names of NIRISS SOSS extract_1d parameter keywords to be legal FITS [#6499]

  • Update PATTTYPE enum values to match spellings used in keyword dictionary [#6501]

  • Updated documentation to point to stdatamodels.util
    for calls to create_history_entry [#6537]

  • Added keyword EXP_TYPE to PsfMaskModel schema [#6540]

  • Updated FILTEROFFSET reference file docs to add NIRCam information. [#6541]

dark_current

  • Fixed bug during save of optional averaged darks output, bug with
    providing step a file instead of a datamodel, added regression test [#6450]

documentation

  • Update text to point to the JWST CRDS website. [#6549]

extract_1d

  • Updated to propagate SRCTYPE keyword during extraction of MIRI LRS
    fixed-slit inputs that are in SlitModel form. [#6212]

  • Assign 0-indexed integration number to INT_NUM if input
    INT_TIMES table is empty. [#6369]

  • Change INT_NUM assignment to 1-indexed. [#6388]

  • Added NRS_LAMP as an exp_type that has the extract1d ref file in asdf format [#6460]

  • Added the center_xy step argument to allow user-specified x/y
    center of IFU extraction apertures [#6503]

  • Delivery of new algorithm ATOCA for SOSS extraction, along with four new reference
    files: speckernel, specprofile, spectrace and wavemap. [#6467]

  • Added step parameter soss_atoca to turn ATOCA algorithm on, with box extraction
    the default algorithm [#6551]

flatfield

  • Updated flatfield step docs to include complete details on how the
    variance and error arrays are updated. [#6245]

  • Fixed a bug in flatfield for NIRSpec BrightObj mode where the S-flat cutout
    was calculated incorrectly by not accounting for the slit offset [#6332]

  • Added check to NRS_LAMP exposures that routes imaging exposures to the imaging
    half of flatfield, where they will skip the step as expected [#6462]

jump

  • Updated jump detection step to use common code moved to stcal [#6089]

  • In stcal (pr #72), several changes were made to fix existing bugs in the
    twopoint difference routine for jump detection. Some of these issues
    resulted in jumps erroneously being flagged for pixels with only two
    usable groups (i.e one usable difference). This PR on the JWST side
    fixes one of the unit tests to account for this. [#6552]

lib

  • Implement the MAST AUI interface to the Engineering Database. [#6288]

  • Fix ROLL_REF and angle_to_vector calculations [#6452]

  • Fix bad implementation of angle_to_vector in set_telescope_pointing. [#6452]

  • Use TRACK algorithms for moving target exposures. [#6452]

  • Move setting of the default method to calc_transforms. [#6482]

linearity

  • Use the common code in STCAL for linearity correction. [#6386]

  • Update of linearity test to support STCAL PR65 [#6509]

outlier_detection

  • Revert back to using 'linear' interpolation method as default for blot.
    The bug in the implementation of the bilinear interpolator in the drizzle
    package is now fixed. [#6146]

  • Log number of flagged outliers in outlier_detection [#6260]

pathloss

  • Updated the pathloss step and documentation to include processing of
    MIRI LRS fixed-slit exposures. [#6435]

persistence

  • Changed logger from root to __name__ [#6389]

pipeline

  • Added wfss_contam step to calwebb_spec2 pipeline flow for WFSS modes [#6207]

  • Changed logger from root to __name__ for Ami3, Detector1, Dark, and Guider
    Pipelines [#6389]

  • Updated the calwebb_spec2 pipeline to apply the pathloss step to
    MIRI LRS fixed-slit exposures. [#6435]

ramp_fitting

  • Fix special handling for 2 group ramp. [spacetelescope/stcal#70]

  • Fix issue with inappropriately including a flagged group at the beginning
    of a ramp segment. [spacetelescope/stcal#68]

  • Pixels with negative median rates will have VAR_POISSON set to zero.
    [spacetelescope/stcal#59]

  • Update RampFitStep to pass DQ flags as a parameter to the ramp_fit
    algorithm code in stcal. Bump version requirement for stcal. [#6072]

refpix

  • Refactored the subtract_reference routine for NRS IRS2 data to reduce
    memory usage. [#6356]

  • Updated bad link to JDox in the step documentation. [#6372]

regtest

  • Update okifying to handle full folder updates for associations [#6218]

  • Remove default cfg usage from all relevant regtests; replaced with
    either pipeline alias or Step instance [#6391]

resample

  • Refactor resample_spec to use a separate function for computing the output
    rectified WCS for lamp data. [#6296]

  • Fix a crash in resample_spec due to undefined variance arrays. [#6305]

  • Fix handling of weight_type parameter to allow for user override. [#6406]

  • Add support for specifying custom output WCS parameters to the resample
    step. [#6364]

  • Make output_shape to be in the "normal" (nx, ny) order. [#6417]

  • Updated drizzle version to 1.13.4 which contains a fix for the
    bug due to which some 0-weight input pixels may contribute to the output
    image. [#6517]

  • Updated step docs to indicate that the default weighting type is
    now "ivm" [#6529]

  • Fixed a bug in the ResampleSpecData.build_interpolated_output_wcs()
    due to which, under cerain circumstances, computed output image shape
    could be very large resulting in (very) large memory usage and/or
    incorrect output WCS. [#6533]

residual_fringe

  • Added documentation on step [#6387]
  • Fixed incorrect data model name [#6487]
  • Added user option to give wavelength range that no correction will be applied [#6545]

skymatch

  • Improved reliability when matching sky in images with very close sky
    footprints. [#6421]

  • Updated code in skymatch.region.py with latest improvements and bug fixes
    from stsci.skypac.regions.py. [#6451]

  • Updated documentation to clarify details of flat-fielding versus distortion
    corrections [#6546]

source_catalog

  • Fixed issue with non-finite positions for aperture photometry. [#6206]

  • Fixed the documentation for bkg_boxsize to reflect that its data
    type should be integer. [#6300]

  • Renamed filter_kernel to kernel in the call to detect_sources
    to match the new name of the argument in photutils. [#6527]

wavecorr

  • Location of source in NIRSpec fixed slit updated
    (keywords SCRCXPOS, SRCYPOS). [#6243, #6261]

  • Fixed the computation of model.slits[i].source_xpos
    for Nirspec fixed slit data. [#6457]

wfs_combine

  • Changed method of loading input association from datamodels.load() to
    Step.load_as_level3_asn() to prevent error when target acq exposure
    not present [#6464]

wfss_contam

  • Updated to process all defined spectral orders for the grism mode [#6175]

  • Added step documentation [#6210]

  • Fixed handling of filter/pupil names for NIRISS WFSS mode [#6233]

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