Python library for science observations from the James Webb Space Telescope

Space Telescope Science Institute

Last update: Dec 30, 2022

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Overview

JWST Calibration Pipeline

JWST requires Python 3.7 or above and a C compiler for dependencies.

Linux and MacOS platforms are tested and supported. Windows is not currently supported.

Installation

The easiest way to install the latest jwst release into a fresh virtualenv or conda environment is

pip install jwst

Detailed Installation

The jwst package can be installed into a virtualenv or conda environment via pip. We recommend that for each installation you start by creating a fresh environment that only has Python installed and then install the jwst package and its dependencies into that bare environment. If using conda environments, first make sure you have a recent version of Anaconda or Miniconda installed. If desired, you can create multiple environments to allow for switching between different versions of the jwst package (e.g. a released version versus the current development version).

In all cases, the installation is generally a 3-step process:

Create a conda environment
Activate that environment
Install the desired version of the jwst package into that environment

Details are given below on how to do this for different types of installations, including tagged releases, DMS builds used in operations, and development versions. Remember that all conda operations must be done from within a bash/zsh shell.

Installing latest releases

You can install the latest released version via pip. From a bash/zsh shell:

conda create -n <env_name> python
conda activate <env_name>
pip install jwst

You can also install a specific version (from jwst 0.17.0 onward):

conda create -n <env_name> python
conda activate <env_name>
pip install jwst==1.3.3

Installing specific versions before jwst 0.17.0 need to be installed from Github:

conda create -n <env_name> python
conda activate <env_name>
pip install git+https://github.com/spacetelescope/[email protected]

Installing the development version from Github

You can install the latest development version (not as well tested) from the Github master branch:

conda create -n <env_name> python
conda activate <env_name>
pip install git+https://github.com/spacetelescope/jwst

Installing a DMS Operational Build

There may be occasions where an exact copy of an operational DMS build is desired (e.g. for validation testing or debugging operational issues). We package releases for DMS builds via environment snapshots that specify the exact versions of all packages to be installed.

To install a particular DMS build, consult the Software vs DMS build version map table shown below to determine the correct jwst tag. For example, to install the version of jwst used in DMS build 7.8.2, use jwst tag 1.3.2. The overall procedure is similar to the 3-step process outlined in the previous section, but the details of each command vary, due to the use of environment snapshot files that specify all of the particular packages to install. Also note that different snapshot files are used for Linux and Mac OS systems.

Linux:

conda create -n jwstdp-1.3.2 --file https://ssb.stsci.edu/releases/jwstdp/1.3.2/conda_python_stable-deps.txt
conda activate jwstdp-1.3.2
pip install -r https://ssb.stsci.edu/releases/jwstdp/1.3.2/reqs_stable-deps.txt

MacOS:

conda create -n jwstdp-1.3.2 --file https://ssb.stsci.edu/releases/jwstdp/1.3.2/conda_python_macos-stable-deps.txt
conda activate jwstdp-1.3.2
pip install -r https://ssb.stsci.edu/releases/jwstdp/1.3.2/reqs_macos-stable-deps.txt

Each DMS delivery has its own installation instructions, which may be found in the corresponding release documentation linked from this page: https://github.com/astroconda/astroconda-releases/tree/master/jwstdp The installation procedures may change from time to time, so consulting the documentation page for the specific version in question is the best way to get that version installed.

Installing for Developers

If you want to be able to work on and test the source code with the jwst package, the high-level procedure to do this is to first create a conda environment using the same procedures outlined above, but then install your personal copy of the code overtop of the original code in that environment. Again, this should be done in a separate conda environment from any existing environments that you may have already installed with released versions of the jwst package.

As usual, the first two steps are to create and activate an environment:

conda create -n <env_name> python
conda activate <env_name>

To install your own copy of the code into that environment, you first need to fork and clone the jwst repo:

cd <where you want to put the repo>
git clone https://github.com/spacetelescope/jwst
cd jwst

Note: python setup.py install and python setup.py develop commands do not work.

Install from your local checked-out copy as an "editable" install:

pip install -e .

If you want to run the unit or regression tests and/or build the docs, you can make sure those dependencies are installed too:

pip install -e ".[test]"
pip install -e ".[docs]"
pip install -e ".[test,docs]"

Need other useful packages in your development environment?

pip install ipython jupyter matplotlib pylint

Calibration References Data System (CRDS) Setup

CRDS is the system that manages the reference files needed to run the pipeline. Inside the STScI network, the pipeline works with default CRDS setup with no modifications. To run the pipeline outside the STScI network, CRDS must be configured by setting two environment variables:

export CRDS_PATH=$HOME/crds_cache
export CRDS_SERVER_URL=https://jwst-crds.stsci.edu

Documentation

Documentation (built daily from the Github master branch) is available at:

https://jwst-pipeline.readthedocs.io/en/latest/

To build the docs yourself, clone this repository and build the documentation with:

pip install -e ".[docs]"
cd docs
make html
make latexpdf

Contributions and Feedback

We welcome contributions and feedback on the project. Please follow the contributing guidelines to submit an issue or a pull request.

We strive to provide a welcoming community to all of our users by abiding with the Code of Conduct.

If you have questions or concerns regarding the software, please open an issue at https://github.com/spacetelescope/jwst/issues or contact the JWST Help Desk.

Software vs DMS build version map

jwst tag	DMS build	CRDS_CONTEXT	Date	Notes
1.3.3	B7.8.2	0764	2021-10-05	Same as 1.3.2, but with installation bug fix
1.3.2	B7.8.2	0764	2021-09-03	Final release candidate for B7.8.2
1.3.1	B7.8.1	0742	2021-08-09	Final release candidate for B7.8.1
1.3.0	B7.8.1rc1	0741	2021-08-02	First release candidate for B7.8.1
1.2.3	B7.8	0732	2021-06-08	Final release candidate for B7.8
1.2.2	B7.8rc3	0732	2021-06-08	Third release candidate for B7.8
1.2.1	B7.8rc2	0732	2021-06-07	Second release candidate for B7.8
1.2.0	B7.8rc1	0723	2021-05-24	First release candidate for B7.8
1.1.0	B7.7.1	0682	2021-02-26	Final release candidate for B7.7.1
1.0.0	B7.7.1rc1	0678	2021-02-22	First release candidate for B7.7.1
0.18.3	B7.7	0670	2021-01-25	Final release candidate for B7.7
0.18.2	B7.7rc3	0668	2021-01-19	Third release candidate for B7.7
0.18.1	B7.7rc2	0664	2021-01-08	Second release candidate for B7.7
0.18.0	B7.7rc1	0645	2020-12-21	First release candidate for B7.7
0.17.1	B7.6	0641	2020-09-15	Final release candidate for B7.6
0.17.0	B7.6rc1	0637	2020-08-28	First release candidate for B7.6
0.16.2	B7.5	0619	2020-06-10	Same as 0.16.1, but with installation bug fix
0.16.1	B7.5	0619	2020-05-19	Final release candidate for B7.5
0.16.0	B7.5rc1	0614	2020-05-04	First release candidate for B7.5
0.15.1	B7.4.2	0586	2020-03-10	Final release candidate for B7.4.2
0.15.0	B7.4.2rc1	0585	2020-02-28	First release candidate for B7.4.2
0.14.2	B7.4	0570	2019-11-18	Final release candidate for B7.4
0.14.1	B7.4rc2	0568	2019-11-11	Second release candidate for B7.4
0.14.0	B7.4rc1	0563	2019-10-25	First release candidate for B7.4
0.13.8	B7.3.1	0541	2019-09-05	Patch for Build 7.3 released as Build 7.3.1
0.13.7	B7.3	0535	2019-06-21	Final release candidate for Build 7.3
0.13.6	B7.3rc4	0534	2019-06-20	Fourth release candidate for Build 7.3
0.13.5	B7.3rc3	0534	2019-06-19	Third release candidate for Build 7.3
0.13.4	B7.3rc2	0534	2019-06-18	Second release candidate for Build 7.3
0.13.3	B7.3rc1	0532	2019-06-04	First release candidate for Build 7.3
0.13.2		0500*	2019-05-14	DMS test, no delivery to I&T
0.13.1		0500*	2019-03-08	DMS test, no delivery to I&T
0.13.0		0500	2019-02-15	DMS test, no delivery to I&T
0.12.3	B7.2.1	0500	2019-01-15	DMS Build 7.2.1 patch release
0.12.2	B7.2	0495	2018-11-07	Final release candidate for Build 7.2
0.12.1	B7.2rc2	0495	2018-11-01	Second release candidate for Build 7.2
0.12.0	B7.2rc1	0493*	2018-10-09	First release candidate for Build 7.2
0.11.0		0482*	2018-09-10	DMS test, no delivery to I&T
0.10.0		0477*	2018-07-31	DMS test, no delivery to I&T
0.9.6	B7.1.3	0468	2018-06-08	Final release candidate for Build 7.1.3
0.9.5	B7.1.3rc3	0468	2018-06-06	Third release candidate for Build 7.1.3
0.9.4	B7.1.3rc2	0463*	2018-05-29	Second release candidate for Build 7.1.3
0.9.3	B7.1.3rc1	0457*	2018-05-11	First release candidate for Build 7.1.3
0.9.2		0441*	2018-03-28	DMS test, no delivery to I&T
0.9.1		0432*	2018-02-16	DMS test, no delivery to I&T
0.9.0	B7.1.2	0422	2017-12-22	DMS patch release to I&T 2018-02-15
0.8.0	B7.1.1	0422	2017-11-06	DMS patch release to I&T 2018-01-17
0.8.0	B7.1	0422	2017-11-06	Final, delivered to I&T 2017-11-17
0.7.7	B7.0	0303	2016-12-13	Final, delivered to I&T

Note: CRDS_CONTEXT values flagged with an asterisk in the above table are estimates (formal CONTEXT deliveries are only provided with final builds).

Unit Tests

Unit tests can be run via pytest. Within the top level of your local jwst repo checkout:

pip install -e ".[test]"
pytest

Need to parallelize your test runs over all available cores?

pip install pytest-xdist
pytest -n auto

Regression Tests

Latest regression test results can be found here (STScI staff only):

https://plwishmaster.stsci.edu:8081/job/RT/job/JWST/

The test builds start at 6pm local Baltimore time Monday through Saturday on jwcalibdev.

To run the regression tests on your local machine, get the test dependencies and set the environment variable TEST_BIGDATA to our Artifactory server (STSci staff members only):

pip install -e ".[test]"
export TEST_BIGDATA=https://bytesalad.stsci.edu/artifactory

To run all the regression tests (except the very slow ones):

pytest --bigdata jwst/regtest

You can control where the test results are written with the --basetemp=<PATH> arg to pytest. NOTE that pytest will wipe this directory clean for each test session, so make sure it is a scratch area.

If you would like to run a specific test, find its name or ID and use the -k option:

pytest --bigdata jwst/regtest -k nirspec

If developers need to update the truth files in our nightly regression tests, there are instructions in the repository wiki.

https://github.com/spacetelescope/jwst/wiki/Maintaining-Regression-Tests

Comments

JP-1258: Remove drizproduct and multiproduct

@hbushouse @jdavies-st @philhodge This PR is just to get show what I have done so far - and where I am stuck. It is not to be merged. The plan is to use this new multiresamp model and delete the multiprod and drizproduct data models.

I combined the drizproduct, multiprod and lev3_prod into a single schema - multiresamp.schema I probably should move the meta type data out and put it in the core schema but first I need some help on how to define multiresamp.py the MultiResampModel. How do I define it to make it be able to handle the 1 product case as we would have for imager resampled data or the multiple products case for multi slit data when both types of data are defined by multiresamp.schema (they just have single products or multiple products) ? It seems circular.

Resolves #4507 / JP-1258 Resolves #4228 / JP-1124
extract_1d resample datamodels

opened by jemorrison 100
Initial versions of spectroscopic aperture correction datamodels

Issue JP-1049 was created by Alicia Canipe:

For spectroscopy the aperture correction file will generally be a FITS table with columns FILTER, PUPIL (NIRISS and NIRCam) or SUBARRAY (MIRI) or one of GRATING (NIRSpec IFU and MOS) or SLIT (NIRSpec fixed slit), ORDER (used only for the NIRISS WFSS mode), NELEM, WAVELENGTH, HEIGHT, APCORR, SKYIN, and SKYOUT. The latter three values are floating point arrays of length given by the integer value NELEM. Wavelengths are in microns, HEIGHT is the slit extraction width in arc-seconds analgous to the RADIUS value for imaging, and the APCORR value is a multiplicative correction factor greater than or equal to 1.0. For spectroscopy the sky background subtraction is generally assumed to be carried out prior to the spectroscopic extractions, such as using a background image or a scaled background template. Nonetheless there is the option for the SKYIN and SKYOUT values to be specified as a function of wavelength. The SKYIN and SKYOUT values are in pixels by assumption, and are measured in cross dispersion direction on both sides of the spectrum. If the two values are identical, no background subtraction needs to be carried out. [The definition of SKYIN and SKYOUT for spectroscopy requires further* *discussion.]

For the case of MIRI/MRS the aperture correction values will be given as a two-dimensional floating point image of dimensions 1032x1024 pixels, analogous to the photometric calibration reference file. As with the other modes the aperture correction values will be multiplicative corrections greater than or equal to 1.0.

The table below provides the formatting details and the CRDS and table row selection criteria for each instrument.

{color:#ff8b00}THIS TABLE IS NOT FINAL.{color}

!image-2019-10-14-10-21-36-088.png!
datamodels reference files jira apcorr

opened by stscijgbot 85
NIRSpec MOS level 3 spectral combination issues
Issue JP-936 was created by James Muzerolle:

I am testing calwebb_spec3 using a set of simulated MOS exposures, which consists of a 3-shutter nod pattern. The level 3 products, with source-based files containing 2D unrectified spectra from all exposures and the combined 2D and 1D products, were generated correctly. However, the combined 2D products appear to have a couple of problems:

Data for the same source on both detectors are not being combined; the NRS2 data are being dropped entirely unless a particular source has no spectrum at all on NRS1.

The combined products tend to appear somewhat jumbled, and the source spectrum from the 3 nods don't seem to overlap (a screen shot of one example is attached). It's possible I have not included fully correct WCS pointing information in the headers since I wasn't clear on exactly what needs to go where (keyword values need to be added by hand in this case); I essentially cut-and-pasted the SCI headers from a "real" example generated from the nOPs test runs. Do I also need to make changes to the primary headers?

The input data, level 2b products, and the level 3 products for one source can be found in /grp/jwst/wit4/nirspec/Muzerolle/Files_spec3.

bug resample jira
opened by stscijgbot 78
MRS alpha-beta cubes for commissioning

Issue JP-1013 was created by David Law:

In order to support commissioning activities to determine the MRS PSF (known to be different in the alpha-beta directions) it will be necessary to construct alpha-beta cubes for dithered observations. These are cubes in which the along-slice and across-slice directions are aligned with the X/Y spaxel axes of the cube.

This has been on the long-term agenda of the MIRI team for a while, but was pending an easy solution of how it might be implemented that is now resolved.

Essentially, what is necessary is a data cube with astronomical RA/DEC coordinates in which the rotation of the cube is set such that the along-slice (alpha) direction is along the X-axis of the cube. This can be achieved simply by applying a rotation angle Theta when computing the Xi-Eta pixel coordinates from the input RA/DEC coordinatates, where Theta is defined as the position angle of the along-slice direction in the first exposure (computed using the embedded wcs). Specification of a keyword when running cube_build would thus determine whether the position angle of the cube is 0 (which it always is at the moment) or allow it to be aligned with the IFU hardware. Both kinds of cubes would be equally astronomically valid.

Technical note: alpha may not increase to the right, and beta may not increase up in these cubes. The alpha/beta coordinate system contains some flips relative to V2/V3 (and by extension RA/DEC) that should not be reproduced so that these cubes are simply rotated with respect to the standard PA=0 cubes. This may mean, for instance, that beta increases downwards.
cube_build jira

opened by stscijgbot 69
Convert IFU extract1d and apcorr reference files from fits to asdf

Issue JP-1749 was created on JIRA by Jane Morrison:

A new extract1d reference file for IFU data has been created. This preliminary file has been supplied by the MIRI INS team (David Law). JP-1736 (closed) created a datamodel for this new reference file. The reference file is a fits file containing two extensions. The first extension contains basic data (single values in a table). The second extension contains a table with integer values and five columns with arrays (size set by integer value in the table). This type of data may not be easily represented by an asdf file and it may be appropriate to leave it as a fits file.
team-coffee

opened by stscijgbot-jp 65
NIRSPEC: MOS Flat field

Issue JP-1691 was created on JIRA by Jane Morrison:

This ticket is the remaining work not finished in JP-1663. PR 5284 was merged in the JWST Pipeline and fixed some of the NIRSPEC MOS issues but there are remaining differences between the NIRSPEC and JWST flat field pipeline steps
team-coffee

opened by stscijgbot-jp 57
NIRSpec calwebb_spec2 flat_field step producing wrong results

Issue JP-335 was created by Maria Pena-Guerrero:

The step is running to completion, however it is producing strange results. The medians for all modes are off (we would like it to be of the order 1e-7), but the mode least affected is IFU. I am attaching a plot for an IFU slice, the slits plots for Fixed Slit (FS), and for MOS. The results for FS and MOS are not correct, i.e. the resulting arrays are not finding the spectrum and their value is NaN. For the FS data, the algorithm is producing correct results for slit S200A1, however the algorithm finds very little pixels with signal for slits S200A2 and S1600A1 and not finding any pixels for slit S400A1.

I have placed files for FS, IFU, and MOS data and results at:

/grp/jwst/wit4/nirspec/penaguerrero/flat_field_problems

There you will find the pdf plots that our code produces. Our code re-creates the flat_field algorithm and then compares with the pipeline's resulting flat, this is why we expect machine precision differences (1e-7) between the two. The files *_calc.fits are the calculated flat by our code, and the *_comp.fits is the comparison between the pipeline's (_intflat.fits) and the calculated one.
flatfield NIRSPEC jira in_progress

opened by stscijgbot 51
Initial versions of updated spectroscopic photom datamodels
Issue JP-1018 was created by Alicia Canipe:

INS is requesting initial versions of mode-separated spectroscopic photom datamodels to use to generate new spectroscopic flux calibration reference files. This will require updates to existing datamodels and some new datamodels (previously imaging and spectroscopic files were combined).

The photom reference files have multiplicative flux calibration factors.

Changes needed:

Add EXP_TYPE to selection criteria ** For reference files that will be used for multiple modes, set EXP_TYPE to one of the two modes and add P_EXP_TY keyword (P_EXP_TY = MIR_LRS-FIXEDSLIT|MIR_LRS-SLITLESS|)

Update datamodels to handle mode-separated reference files (imaging vs. spec)

Include pixel area information (https://jira.stsci.edu/browse/JP-1007)

The tables below summarize the formatting updates by instrument ({color:#de350b}red text){color}:

{color:#ff8b00}* THIS IS NOT FINAL YET *{color} !image-2019-09-24-10-11-13-999.png!
photom jira
opened by stscijgbot 50
Resample step imprinting spacial dependence on stellar surface brightness

Issue JP-950 was created by Misty Cracraft:

I recently ran a test to see what the spread of surface brightness values was across an image when given stars of the same initial values. I used MIRISim 2.1.0 to create an image with 50 stars scattered randomly across the field. The stars were all given the same input flux, but with MIRISim adding noise, the stars were not expected to be exactly the same. When I ran this simulation all the way through the pipeline, the surface brightness levels out of calwebb_image3 had a distinct dependence on y position on the image. I went back and checked photometry on the stars output from detector1 and calwebb_image2, and the spread in y was more random there. I tested the individual steps of calwebb_image3, and even up through outlier detection, the spread looks random. So it has to be resample that is imprinting this dependence. I'll attach plots of the photometry at a few different stages to show the problem.
bug question resample jira

opened by stscijgbot 47
Implement NIRCAM TSO grism extraction from CubeModel in extract 2D

In TSO mode, the data arrays are 3D, where each plane of the cube corresponds to the countrate image for a given integration within the exposure. I think we've already enabled the various calwebb_spec2 steps to handle this form of data (a "CubeModel", as opposed to a more normal 2D "ImageModel"). So the thing to ensure is that extract_2d does an extraction from the input 3D cube, producing an output 3D cube that is simply smaller in the first two (x, y) dimensions, but still has all of the axis 3 planes. The extract_1d step then knows to produce a 1D spectrum from each plane of the 3D cube that it's given.
NIRCAM time series observations (TSO) Requirement

opened by sosey 47
CRDS wait causes hung pipeline

On a fresh conda environment CRDS will not continue and the reduction hangs. 2017-10-12 08:46:26,891 - stpipe.MRSCubePipeline - INFO - MRSCubePipeline instance created. 2017-10-12 08:46:26,893 - stpipe.MRSCubePipeline.cube_build - INFO - CubeBuildStep instance created. ^C--------------------------------------------------------------------------- KeyboardInterrupt Traceback (most recent call last) in () ----> 1 runCubePipe(arglist[0])

in runCubePipe((f, args)) 181 182 def runCubePipe((f, args)): --> 183 MRSCubePipeline(steps={'cube_build': args}).run(f) 184 185

/Users/one/anaconda2/envs/jwst/lib/python2.7/site-packages/jwst-0.7.8rc3.dev10-py2.7-macosx-10.7-x86_64.egg/jwst/stpipe/step.pyc in run(self, *args) 343 if (len(args) and len(self.reference_file_types) and not self.skip 344 and self.prefetch_references): --> 345 self._precache_reference_files(args[0]) 346 347 self.log.info(

/Users/one/anaconda2/envs/jwst/lib/python2.7/site-packages/jwst-0.7.8rc3.dev10-py2.7-macosx-10.7-x86_64.egg/jwst/stpipe/pipeline.pyc in _precache_reference_files(self, input_file) 168 try: 169 with datamodels.open(input_file) as model: --> 170 super(Pipeline, self)._precache_reference_files_opened(model) 171 except (ValueError, TypeError, IOError): 172 self.log.info(

/Users/one/anaconda2/envs/jwst/lib/python2.7/site-packages/jwst-0.7.8rc3.dev10-py2.7-macosx-10.7-x86_64.egg/jwst/stpipe/step.pyc in _precache_reference_files_opened(self, model_or_container) 590 # recurse on each contained model 591 for contained_model in model_or_container: --> 592 self._precache_reference_files_opened(contained_model) 593 else: 594 # precache a single model object

/Users/one/anaconda2/envs/jwst/lib/python2.7/site-packages/jwst-0.7.8rc3.dev10-py2.7-macosx-10.7-x86_64.egg/jwst/stpipe/step.pyc in _precache_reference_files_opened(self, model_or_container) 593 else: 594 # precache a single model object --> 595 self._precache_reference_files_impl(model_or_container) 596 597 def _precache_reference_files_impl(self, model):

/Users/one/anaconda2/envs/jwst/lib/python2.7/site-packages/jwst-0.7.8rc3.dev10-py2.7-macosx-10.7-x86_64.egg/jwst/stpipe/step.pyc in _precache_reference_files_impl(self, model) 611 fetch_types = sorted(set(self.reference_file_types) - set(ovr_refs.keys())) 612 --> 613 crds_refs = crds_client.get_multiple_reference_paths(model, fetch_types) 614 615 ref_path_map = dict(list(crds_refs.items()) + list(ovr_refs.items()))

/Users/one/anaconda2/envs/jwst/lib/python2.7/site-packages/jwst-0.7.8rc3.dev10-py2.7-macosx-10.7-x86_64.egg/jwst/stpipe/crds_client.pyc in get_multiple_reference_paths(input_file, reference_file_types) 99 try: 100 if crds_cache_locking is not None: --> 101 with crds_cache_locking.get_cache_lock(): 102 bestrefs = crds.getreferences(data_dict, reftypes=reference_file_types, observatory="jwst") 103 else:

/Users/one/anaconda2/envs/jwst/lib/python2.7/site-packages/lockfile/init.pyc in enter(self) 195 Context manager support. 196 """ --> 197 self.acquire() 198 return self 199

/Users/one/anaconda2/envs/jwst/lib/python2.7/site-packages/crds/core/crds_cache_locking.pyc in acquire(self, *args, **keys) 66 def acquire(self, *args, **keys): 67 log.verbose("Acquiring lock", repr(self)) ---> 68 result = super(CrdsLockFile, self).acquire(*args, **keys) 69 log.verbose("Lock acquired", repr(self)) 70 return result

/Users/one/anaconda2/envs/jwst/lib/python2.7/site-packages/lockfile/linklockfile.pyc in acquire(self, timeout) 48 raise AlreadyLocked("%s is already locked" % 49 self.path) ---> 50 time.sleep(timeout is not None and timeout / 10 or 0.1) 51 else: 52 # Link creation succeeded. We're good to go.

KeyboardInterrupt:
crds interface

opened by baileyji 46
JP-3043 user option to select wavelength range of IFU cube not working for NIRSpec
Resolves JP-3043

Closes #

This PR addresses a bug for NIRSpec IFU when trying to select the wavelength ranges to make the IFU cube. The code what not using these parameters for NIRSpec data.

Checklist for maintainers

[x] added entry in CHANGES.rst within the relevant release section

[ ] updated or added relevant tests

[ ] updated relevant documentation

[x] added relevant milestone

[x] added relevant label(s)

[ ] ran regression tests, post a link to the Jenkins job below. How to run regression tests on a PR

[ ] Make sure the JIRA ticket is resolved properly

cube_build
opened by jemorrison 3
JP-2013 NIRSpec leakcal and nodded exposures
Resolves JP-2013

Closes #5911

This PR follows changes made in how associates are created for NIRSpec exposures with both leakcal and nodded exposures (#7405). The calspec2 pipeline was changed to subtract leakcal images from science and background data before the background step is run on the science data.

Checklist for maintainers

[x] added entry in CHANGES.rst within the relevant release section

[x] updated or added relevant tests

[x] updated relevant documentation

[x] added relevant milestone

[x] added relevant label(s)

[ ] ran regression tests, post a link to the Jenkins job below. How to run regression tests on a PR

[ ] Make sure the JIRA ticket is resolved properly

imprint pipeline testing spec2 pipeline documentation
opened by jemorrison 1
wfss_contam use datamodel in with context
When the DataModel is cleaned up (del is called) during garbage collection it will close any opened hdulists. This will make any subsequent attempts to load data from the hdulist fail (with ValueError: I/O operation on closed file).

DataModel prior to the below PR contained a self reference which created a reference cycle which made python fail to collect the object during generation 0 passes with the garbage collector. This meant that the hdulist was not immediately closed when the model fell out of scope.

Code in wfss_contam relied on this persistance as the model created in the following line is no longer referenced on subsequent lines.

dimage = datamodels.open(dir_image_name).data

python will attempt to clean up the opened data model and fail, keeping the hdulist (stored at dir_image_name) open. This allowed later lines that reference dimage to load the array data within the hdulist.

Fixing the reference cycle in stdatamodels in this PR: https://github.com/spacetelescope/stdatamodels/pull/109 makes the datamodel more easily garbage collected which causes wfss_contam to fail due to the hdulist closing when the model is collected.

To keep the model in scope, the above line is replaced with a with context to make it explicit that the datamodel is held open which it's contents are read.

This is work towards fixing JP-2798.

Checklist for maintainers

[x] added entry in CHANGES.rst within the relevant release section

[ ] updated or added relevant tests

[ ] updated relevant documentation

[x] added relevant milestone

[x] added relevant label(s)

[x] ran regression tests, post a link to the Jenkins job below. How to run regression tests on a PR

[ ] Make sure the JIRA ticket is resolved properly

Wide Field Slitless Spec (WFSS) wfss_contam
opened by braingram 2
Add scipy and numpy nightly wheels to dev dependencies
This PR adds the scipy and numpy nightly wheels to the dev dependencies, so that we can detect issues like the scipy 1.10.0 release prior to that release.

Checklist for maintainers

[ ] added entry in CHANGES.rst within the relevant release section

[ ] updated or added relevant tests

[ ] updated relevant documentation

[ ] added relevant milestone

[ ] added relevant label(s)

[ ] ran regression tests, post a link to the Jenkins job below. How to run regression tests on a PR

[ ] Make sure the JIRA ticket is resolved properly

testing installation no-changelog-entry-needed automation
opened by WilliamJamieson 4
Output files *_outlier_i2d.fits not saved to the specified output_dir

When running the pipeline with the call method with a specified output directory (using output_dir in call) all the files except those ending with outlier_i2d.fits are correct saved into the specified output directory. The outlier_i2d.fits files are saved in the current direction.

This is a minor bug, but somewhat annoying when running many exposures with specific subdirs for their output.

opened by karllark 4
Opencv dependency in stcal being optional causes uncaught error in jump step

After a clean install of the newest version (1.8.5), running the Detector1 pipeline now crashes if parameter jump.use_ellipses = True. This is because stcal requires opencv-python to work, which is now an optional requirement and not automatically installed. I'm not sure why this packages was made optional, but since it was, I think there should either be a fallback that does not require opencv, or proper error handling that tells JWST pipeline users why the pipeline is failing if functions are used that require opencv. Right now it simply fails throwing a generic NameError on the line the function is called. (Or maybe it should just be added in again as a requirement, but I am not privy to the reasons it was removed in the first place.)

There is a warning that is raised when opencv cannot be imported in stcal, but it doesn't actually cause an Exceptions when an opencv function is called and opencv is not installed.
jump installation

opened by m-samland 2

Releases(1.9.2)

1.9.2(Jan 4, 2023)
What's Changed

pin scipy below 1.10.0 by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/7420

Full Changelog: https://github.com/spacetelescope/jwst/compare/1.9.1...1.9.2
Source code(tar.gz)
Source code(zip)
1.9.1(Jan 4, 2023)
What's Changed

JP-3037 Modify entrypoint functions to not return anything unless failure by @stscieisenhamer in https://github.com/spacetelescope/jwst/pull/7418

Full Changelog: https://github.com/spacetelescope/jwst/compare/1.9.0...1.9.1
Source code(tar.gz)
Source code(zip)
1.9.0(Dec 27, 2022)
What's Changed

JP-2984: Update ASN rules for NIS_WFSS to keep grisms separate by @hbushouse in https://github.com/spacetelescope/jwst/pull/7351

(JP-2991) Require asdf-transform-schemas greater than 0.3.0 by @dmggh in https://github.com/spacetelescope/jwst/pull/7352

JP-3006 Remove defaulting of the is_psf column by @stscieisenhamer in https://github.com/spacetelescope/jwst/pull/7356

use pip instead of conda to install certifi, to solve pip freeze issue by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/7355

Fix recently updated regression test by @hbushouse in https://github.com/spacetelescope/jwst/pull/7357

Update user documentation by @cshanahan1 in https://github.com/spacetelescope/jwst/pull/6919

(JP-3002) Add SUB400X256ALWB subarray to NIRCam allowed values by @dmggh in https://github.com/spacetelescope/jwst/pull/7361

JP-3012: Add note for install issue on Mojave by @tapastro in https://github.com/spacetelescope/jwst/pull/7360

Wrong Python version expected in init.py by @gruselhaus in https://github.com/spacetelescope/jwst/pull/7366

remove CRDS PUB server from test by @nden in https://github.com/spacetelescope/jwst/pull/7368

Cache CRDS_PATH reffile contents in CI workflows by @jdavies-st in https://github.com/spacetelescope/jwst/pull/7333

Add test for duplicate data when resaving model to fits by @braingram in https://github.com/spacetelescope/jwst/pull/7358

Add missing change log entry for stcal update by @hbushouse in https://github.com/spacetelescope/jwst/pull/7364

JP-2802: Fix a bug in the definition of NIRSpec resampled WCS by @mcara in https://github.com/spacetelescope/jwst/pull/7359

use ruff in place of flake8 by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/7054

Replace getch with readchar in okify_regtests by @jdavies-st in https://github.com/spacetelescope/jwst/pull/7371

(JP-3007) Add keywords for source RA and Dec for WFSS extractions. by @dmggh in https://github.com/spacetelescope/jwst/pull/7372

JP-3009: Add cleanups for files left behind while running tests by @WilliamJamieson in https://github.com/spacetelescope/jwst/pull/7375

make tests requiring opencv conditional by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/7377

JP-2988: Update ramp_fit tests for change in saturation flag propagation by @kmacdonald-stsci in https://github.com/spacetelescope/jwst/pull/7363

JP-2998 Extract1D using custom json files by @jemorrison in https://github.com/spacetelescope/jwst/pull/7369

JP-2900 Redux : Sort combine1d wavelength array prior to creation of spectral wcs by @tapastro in https://github.com/spacetelescope/jwst/pull/7374

expand CI matrix to test more Python versions by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/7378

JP-2912: Store offsets for WFSS source contamination correction in subarray metadata by @tapastro in https://github.com/spacetelescope/jwst/pull/7343

JP-2969: Fix MOS handling of source IDs by @hbushouse in https://github.com/spacetelescope/jwst/pull/7379

JP-3020 Pin PRD versions for tests that are not testing changes in PRD by @stscieisenhamer in https://github.com/spacetelescope/jwst/pull/7380

JP-2807: Update ATOCA algorithm by @tapastro in https://github.com/spacetelescope/jwst/pull/6945

consolidate duplicated job blocks into include: in initial test matrix by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/7382

Fix associations ListCategory enum bug by @jdavies-st in https://github.com/spacetelescope/jwst/pull/7370

Update deprecation notice to name the CRDS_PATH variable appropriately by @stscieisenhamer in https://github.com/spacetelescope/jwst/pull/7392

rebase on top of documentation commits pushed to release branches by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/7394

JP-3019: Remove code trimming zero-valued cube planes by @drlaw1558 in https://github.com/spacetelescope/jwst/pull/7391

JP-3014: Updating CI tests for new NaN values for invalid data in STCAL ramp fitting. by @kmacdonald-stsci in https://github.com/spacetelescope/jwst/pull/7389

Rollback stpipe version in setup by @hbushouse in https://github.com/spacetelescope/jwst/pull/7399

JP-3030: Update slit model to include var_flat by @jemorrison in https://github.com/spacetelescope/jwst/pull/7397

Rollforward stpipe version in setup by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/7400

Use log instead of print in tweakreg by @mcara in https://github.com/spacetelescope/jwst/pull/7402

JP-3034: Change import for photutils CircularAnnulus by @hbushouse in https://github.com/spacetelescope/jwst/pull/7407

Fix incorrect deallocation attempts of unallocated memory in cube builder by @mcara in https://github.com/spacetelescope/jwst/pull/7408

fix deprecation warnings introduced by Pytest 7.2 by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/7325

JP-2013 Fix NIRSpec IFU NOD background subtract and include leakcal in the Level2 associations by @stscieisenhamer in https://github.com/spacetelescope/jwst/pull/7405

JP-2921: Add FITS WCS keywords to WFSS mode by @nden in https://github.com/spacetelescope/jwst/pull/7373

JP-3028 Do not clobber reprocessing lists when Level 2 rules are operating on 'c' type candidates by @stscieisenhamer in https://github.com/spacetelescope/jwst/pull/7410

run coverage in parallel by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/7411

test opencv functionality separately by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/7414

replace usages of np.int() with int() by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/7403

Update NIRSpec MOS regtests with flight data by @hbushouse in https://github.com/spacetelescope/jwst/pull/7413

update reference values for approximation test after GWCS SIP fit change by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/7415

Merge the two update_wcsinfo functions into one by @mcara in https://github.com/spacetelescope/jwst/pull/7412

Pin tweakwcs version to 0.8.1 and update tweakreg unit test by @mcara in https://github.com/spacetelescope/jwst/pull/7417

move scripts into subpackage so that they can be packaged with entry_points.console_scripts by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/7406

release procedures for JWST 1.9.0 / DMS build B9.1rc1 by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/7416

New Contributors

@gruselhaus made their first contribution in https://github.com/spacetelescope/jwst/pull/7366

Full Changelog: https://github.com/spacetelescope/jwst/compare/1.8.5...1.9.0
Source code(tar.gz)
Source code(zip)
1.8.5(Dec 12, 2022)
What's Changed

Update deprecation notice to name the CRDS_PATH variable appropriately by @stscieisenhamer in https://github.com/spacetelescope/jwst/pull/7392

Full Changelog: https://github.com/spacetelescope/jwst/compare/1.8.4...1.8.5
Source code(tar.gz)
Source code(zip)
1.8.4(Nov 16, 2022)
Update CRDS documentation.

Clarify how to manage a local CRDS cache.

Source code(tar.gz)
Source code(zip)
1.8.3(Nov 11, 2022)

Publish a note about the CRDS PUB server freeze and deprecation.
Source code(tar.gz)
Source code(zip)
1.8.2(Oct 20, 2022)
What's Changed

Add note about source catalog pixel indexing by @larrybradley in https://github.com/spacetelescope/jwst/pull/7300

Revert "JP-2940 Return non-zero status from the set_telescope_pointin… by @stscieisenhamer in https://github.com/spacetelescope/jwst/pull/7301

update metadata for 1.8.2 release by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/7302

Full Changelog: https://github.com/spacetelescope/jwst/compare/1.8.1...1.8.2
Source code(tar.gz)
Source code(zip)
1.8.1(Oct 17, 2022)
What's Changed

JP-2946: Update NOUTPUTS allowed values by @hbushouse in https://github.com/spacetelescope/jwst/pull/7062

JP-2970 Allow XML_DATA usage to override PRD specification by @stscieisenhamer in https://github.com/spacetelescope/jwst/pull/7063

JP-2932: Adjust rotation convention of IFUalign for MIRI by @drlaw1558 in https://github.com/spacetelescope/jwst/pull/7058

JP-2812 : Allow user-provided custom image catalogs for tweakreg by @mcara in https://github.com/spacetelescope/jwst/pull/7022

Change to new asdf resource entry point by @WilliamJamieson in https://github.com/spacetelescope/jwst/pull/7057

JP-2909: Expanding Sequence Number Field by @kmacdonald-stsci in https://github.com/spacetelescope/jwst/pull/7061

Fix handling of ASN directory path by the ModelContainer by @mcara in https://github.com/spacetelescope/jwst/pull/7071

JP-2971 Make the GWCSDrizzle.outcon attribute a property with setter by @stscieisenhamer in https://github.com/spacetelescope/jwst/pull/7295

metadata updates for release 1.8.1 (DMS build B9.0rc2) by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/7064

Full Changelog: https://github.com/spacetelescope/jwst/compare/1.8.0...1.8.1
Source code(tar.gz)
Source code(zip)
1.8.0(Oct 10, 2022)
What's Changed

starting 1.7.3 development by @nden in https://github.com/spacetelescope/jwst/pull/7041

JP-2913: Fix the coron median replace algorithm by @hbushouse in https://github.com/spacetelescope/jwst/pull/7044

Modify default parameters for FITS SIP fitting in the assign_wcs by @mcara in https://github.com/spacetelescope/jwst/pull/7037

Relax SIP fitting parameters in the tweakreg step by @mcara in https://github.com/spacetelescope/jwst/pull/7038

check whether requirements-sdp.txt is empty before publishing to PyPI by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/7045

JP-2694: reset input model after Source Catalog Step by @cshanahan1 in https://github.com/spacetelescope/jwst/pull/6942

JP-2627: Fixes to pixel scale in resample and photometry keywords by @cshanahan1 in https://github.com/spacetelescope/jwst/pull/7033

JP-2038: Enforcing no path data in association files and expanding documentation by @kmacdonald-stsci in https://github.com/spacetelescope/jwst/pull/7008

fix definition of pixel ratio by @cshanahan1 in https://github.com/spacetelescope/jwst/pull/7048

JP-2917: Master_background reopens files from asn_table, potentially ignoring input datamodels by @tapastro in https://github.com/spacetelescope/jwst/pull/7046

JP-2918: Fix bad resampled frames for NRS MOS by @hbushouse in https://github.com/spacetelescope/jwst/pull/7047

JP-2679: Update bkg_subtract to handle 3D coronagraphic data by @dmggh in https://github.com/spacetelescope/jwst/pull/7049

JP-2927: Fix short spectrum bug in combine1d by @hbushouse in https://github.com/spacetelescope/jwst/pull/7053

Migrate set_telescope_pointing to pysiaf-based exclusively by @stscieisenhamer in https://github.com/spacetelescope/jwst/pull/6993

Update WCS (or slit metadata) after image (or spectrum) resampling. by @mairanteodoro in https://github.com/spacetelescope/jwst/pull/7042

JP-2681 add residual_fringe to calwebb_spec2 pipeline by @jemorrison in https://github.com/spacetelescope/jwst/pull/7051

use canonical filename for RTD configuration by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/7050

JP-2940 Return non-zero status from the set_telescope_pointing command-line when an error occurs by @stscieisenhamer in https://github.com/spacetelescope/jwst/pull/7056

JP-2679: Update docs to reflect background subtraction update to acc… by @dmggh in https://github.com/spacetelescope/jwst/pull/7055

JP-2645 - Snowball and Shower flagging in Jump by @mwregan2 in https://github.com/spacetelescope/jwst/pull/7039

release 1.8.0 by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/7059

Full Changelog: https://github.com/spacetelescope/jwst/compare/1.7.2...1.8.0
Source code(tar.gz)
Source code(zip)
1.7.2(Sep 12, 2022)
What's Changed

start post 1.7.1 development by @nden in #7032

Touch weekly cron test setup by @hbushouse in #7035

Fix crashes in assign WCS due to uncaught SIP convergence exceptions by @mcara in #7036

prepare for release 1.7.2 by @nden in #7040

Full Changelog: https://github.com/spacetelescope/jwst/compare/1.7.1...1.7.2
Source code(tar.gz)
Source code(zip)
1.7.1(Sep 8, 2022)
What's Changed

Update NIRISS WFSS regtest with in-flight data by @hbushouse in https://github.com/spacetelescope/jwst/pull/7012

Add ORCID for Thomas Williams by @thomaswilliamsastro in https://github.com/spacetelescope/jwst/pull/7014

Update changelog for 1.7.1 by @nden in https://github.com/spacetelescope/jwst/pull/7016

JP-2866: Fix photom bug for NIRSpec FS data by @hbushouse in https://github.com/spacetelescope/jwst/pull/7019

JP-2861: Refactor Asn_Lv2WFSS to better descriminate what direct images should be used by @stscieisenhamer in https://github.com/spacetelescope/jwst/pull/7010

JP-2865 Add retries and timeout parameters to engineering access calls by @stscieisenhamer in https://github.com/spacetelescope/jwst/pull/7025

JP-2865 Update HTTP status list to include 4xx issues by @stscieisenhamer in https://github.com/spacetelescope/jwst/pull/7026

Fix failing assign_wcs test due to gwcs changes by @mcara in https://github.com/spacetelescope/jwst/pull/7027

JP-2899: Fix pedestal residual in MRS straylight by @drlaw1558 in https://github.com/spacetelescope/jwst/pull/7013

JP-2906: Fix wcs attribute names in wfss_contam step by @hbushouse in https://github.com/spacetelescope/jwst/pull/7028

Remove min_gaia and rename gaia->abs parameters by @mcara in https://github.com/spacetelescope/jwst/pull/7023

Fix failing regression test due to gaia->abs name changes by @mcara in https://github.com/spacetelescope/jwst/pull/7029

Fix test_sip_approx test for gwcs>=0.18.2 by @mcara in https://github.com/spacetelescope/jwst/pull/7030

prepare for 1.7.1 release by @nden in https://github.com/spacetelescope/jwst/pull/7031

Full Changelog: https://github.com/spacetelescope/jwst/compare/1.7.0...1.7.1
Source code(tar.gz)
Source code(zip)
1.7.0(Sep 1, 2022)
What's Changed

JP-2688: Skymatch - Update datamodel data when subtract is True by @mcara in https://github.com/spacetelescope/jwst/pull/6934

JP-2527: Improve memory usage in outlier_detection and resample by @stsci-hack in https://github.com/spacetelescope/jwst/pull/6904

JP-2690: Convenience function for updating FITS WCS info by @mcara in https://github.com/spacetelescope/jwst/pull/6935

JP-2691: Update FITS WCS wcsinfo field at the end of tweakreg by @mcara in https://github.com/spacetelescope/jwst/pull/6936

automatically add labels to pull requests based on changed files by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/6933

(JP-1754) Match FITS keywords to KWD by @dmggh in https://github.com/spacetelescope/jwst/pull/6941

Add P_SUBARR to the DarkModel schema (JP-2656) by @dmggh in https://github.com/spacetelescope/jwst/pull/6951

tweakreg should proceed on errors when updating FITS WCS by @mcara in https://github.com/spacetelescope/jwst/pull/6947

JP-2707: Fix excessive zeroes in resampled variance by @mcara in https://github.com/spacetelescope/jwst/pull/6954

Add details on when crds environmentals be defined by @stscieisenhamer in https://github.com/spacetelescope/jwst/pull/6953

JP-2797: MRS sigma-clipped master background fix by @drlaw1558 in https://github.com/spacetelescope/jwst/pull/6960

JP-2672: Remove trailing dash from end of full subchannel listing by @tapastro in https://github.com/spacetelescope/jwst/pull/6959

JP-2796: Reformatting According to flake8 5.0.3 by @kmacdonald-stsci in https://github.com/spacetelescope/jwst/pull/6958

JP-2804: Mask NON_SCIENCE pixels when calculating the detection threshold by @larrybradley in https://github.com/spacetelescope/jwst/pull/6940

Refactor code for updating FITS WCS and increase SIP accuracy by @mcara in https://github.com/spacetelescope/jwst/pull/6955

Require drizzle>=1.13.6 by @mcara in https://github.com/spacetelescope/jwst/pull/6966

JP-2677: Copy int_times keywords to output spectrum extensions for SOSS ATOCA by @tapastro in https://github.com/spacetelescope/jwst/pull/6930

Revert Fourier Transform code to avoid Poppy's recently updated sign convention (JP-2618) by @dmggh in https://github.com/spacetelescope/jwst/pull/6967

JP-2687: Allow alignment of a single image/group to Gaia bypassing first alignment stage by @mcara in https://github.com/spacetelescope/jwst/pull/6938

JP-2654 JP-2662: Fix bug in NIRSpec IFU DQ flagging and handling of moving target exposures by @jemorrison in https://github.com/spacetelescope/jwst/pull/6971

Update template by @nden in https://github.com/spacetelescope/jwst/pull/6969

Revert "JP-2654 JP-2662: Fix bug in NIRSpec IFU DQ flagging and handling of moving target exposures" by @hbushouse in https://github.com/spacetelescope/jwst/pull/6972

JP-2578: Add P_READPA to ReadnoiseModel schema by @hbushouse in https://github.com/spacetelescope/jwst/pull/6973

JP-2814: Exclude pixels flagged with DO_NOT_USE from source finding by @mcara in https://github.com/spacetelescope/jwst/pull/6974

JP-2811 Update wcs naxis3 when removing wavelength planes from cube by @jemorrison in https://github.com/spacetelescope/jwst/pull/6976

JP-2654 JP-2662 Fix bug in NIRSpec IFU DQ flagging and handling of moving target exposures (new try) by @jemorrison in https://github.com/spacetelescope/jwst/pull/6981

JP-2686: Support user-supplied reference files for stage 2 of WCS alignment by @mcara in https://github.com/spacetelescope/jwst/pull/6946

Fix some errors and typos in the change log by @hbushouse in https://github.com/spacetelescope/jwst/pull/6979

add citation and zenodo badge by @nden in https://github.com/spacetelescope/jwst/pull/6978

JP-2808: Fix handling of SRCTYPE in master background by @hbushouse in https://github.com/spacetelescope/jwst/pull/6980

pin jsonschema below 4.10.0 to fix issues with unit and regression tests by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/6986

update citation with Citation File Format by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/6988

Fix equality of floats comparisons in telescope pointing test by @jdavies-st in https://github.com/spacetelescope/jwst/pull/6990

JP-2669: Updating tests due to new STCAL behavior for NaNs in rateints product. by @kmacdonald-stsci in https://github.com/spacetelescope/jwst/pull/6949

JP-2693: Flag groups do_not_use after detected ramp jumps by @karllark in https://github.com/spacetelescope/jwst/pull/6943

JP-2803: Propagate asn keywords to resample output products for level 2 processing by @tapastro in https://github.com/spacetelescope/jwst/pull/6989

pin asdf to newest patch version to fix dependency for newest jsonschema release by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/6991

JP-2595: Update error propagation docs by @hbushouse in https://github.com/spacetelescope/jwst/pull/6994

JP-2816: Update outlier docs by @stsci-hack in https://github.com/spacetelescope/jwst/pull/6983

JP-2799: Updating how the names of files are computed for index association. by @kmacdonald-stsci in https://github.com/spacetelescope/jwst/pull/6985

JP-2055: remove timeconversion and related scripts by @hbushouse in https://github.com/spacetelescope/jwst/pull/6996

JP-2704 MIRI MRS Failures in Cube when there is no valid data on rate/cal image by @jemorrison in https://github.com/spacetelescope/jwst/pull/6998

JP-2857: Update readpatt pattern keyword name to follow other pattern keyword names by @tapastro in https://github.com/spacetelescope/jwst/pull/7001

Add an ORCID to CITATION.cff by @jdavies-st in https://github.com/spacetelescope/jwst/pull/7000

JP-2819: Populate wavelength extension for MIRI LRS slitless by @tapastro in https://github.com/spacetelescope/jwst/pull/6964

Update code to use tweakwcs 0.8.0 by @mcara in https://github.com/spacetelescope/jwst/pull/7006

JP-2678: Expose additional parameters in TweakRegStep. by @mairanteodoro in https://github.com/spacetelescope/jwst/pull/6987

JP-2859 Bug fix for cube_build when user changes input spatial scale to use for IFU cube by @jemorrison in https://github.com/spacetelescope/jwst/pull/7002

JP-2863: Add BACKGROUND to MIRI PATTTYPE list by @hbushouse in https://github.com/spacetelescope/jwst/pull/7009

Expose tweakreg_catalog params in tweakreg by @thomaswilliamsastro in https://github.com/spacetelescope/jwst/pull/7003

JP-2375: NIRISS V3 of CONF files by @nden in https://github.com/spacetelescope/jwst/pull/6803

JP-2819: Bugfix - ensure wavelength array is of equivalent shape to data array by @tapastro in https://github.com/spacetelescope/jwst/pull/7005

prepare for 1.7.0 release by @nden in https://github.com/spacetelescope/jwst/pull/7011

New Contributors

@mairanteodoro made their first contribution in https://github.com/spacetelescope/jwst/pull/6987

Full Changelog: https://github.com/spacetelescope/jwst/compare/1.6.2...1.7.0
Source code(tar.gz)
Source code(zip)
1.6.2(Aug 11, 2022)
What's Changed

pin certifi to 2022.5.18.1 by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/6927

Update NIS_SOSS regtest with in-flight data by @hbushouse in https://github.com/spacetelescope/jwst/pull/6926

JP-2676: Fix units of source catalog error array by @larrybradley in https://github.com/spacetelescope/jwst/pull/6928

JP-2580 update loading of drizpars table by @jemorrison in https://github.com/spacetelescope/jwst/pull/6921

Fix: skymatch not saving subtracted values for input ASN by @mcara in https://github.com/spacetelescope/jwst/pull/6922

Document calculation of readnoise variance (JP-2670) by @dmggh in https://github.com/spacetelescope/jwst/pull/6924

Fix inability of residual fringe code to run on MRS LONG detector by @drlaw1558 in https://github.com/spacetelescope/jwst/pull/6929

Full Changelog: https://github.com/spacetelescope/jwst/compare/1.6.1...1.6.2
Source code(tar.gz)
Source code(zip)
1.6.1(Jul 15, 2022)
What's Changed

Update some regtests with real data by @hbushouse in https://github.com/spacetelescope/jwst/pull/6837

update pull request template to be more explicit by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/6897

update stpipe requirement to >=0.4.1 by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/6925

Full Changelog: https://github.com/spacetelescope/jwst/compare/1.6.0...1.6.1
Source code(tar.gz)
Source code(zip)
1.6.0(Jul 11, 2022)
What's Changed

JP-2387: A couple tweaks to the skymatch docs by @hbushouse in https://github.com/spacetelescope/jwst/pull/6891

JP-2562: Skip tweakreg step when multiple matches to a single reference source are detected by @mcara in https://github.com/spacetelescope/jwst/pull/6896

JP-2653: Fix IFU variance propagation in extract_1d by @drlaw1558 in https://github.com/spacetelescope/jwst/pull/6892

copy changelog workflow from asdf by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/6890

JP-2562: Fix code for processing exceptions in tweakreg by @mcara in https://github.com/spacetelescope/jwst/pull/6898

JP-2661: Variance propagation error by @tapastro in https://github.com/spacetelescope/jwst/pull/6899

JP-2611: Update saturation handling of NO_SAT_CHECK by @hbushouse in https://github.com/spacetelescope/jwst/pull/6901

JP-2657: Add unit test for better coverage of recent jump detection code updat… by @dmggh in https://github.com/spacetelescope/jwst/pull/6900

update setup to use latest stcal release by @hbushouse in https://github.com/spacetelescope/jwst/pull/6902

JP-2623: Multiprocessing failure in ramp fitting. by @kmacdonald-stsci in https://github.com/spacetelescope/jwst/pull/6880

Reset requirements-sdp to post-release (empty) state by @hbushouse in https://github.com/spacetelescope/jwst/pull/6903

JP-2651: Fully Saturated Exposures To Return NoneType by @kmacdonald-stsci in https://github.com/spacetelescope/jwst/pull/6895

JP-2626: Add check to all lv3_asns to prevent single-obs group candidates by @tapastro in https://github.com/spacetelescope/jwst/pull/6886

JP-2665: Add MIRI dither pattern SCAN-CALIBRATION by @hbushouse in https://github.com/spacetelescope/jwst/pull/6908

Update default parameters for source catalog step by @larrybradley in https://github.com/spacetelescope/jwst/pull/6911

JP-2667: Fix calwebb_tso3 failure when checking for null results by @hbushouse in https://github.com/spacetelescope/jwst/pull/6912

XFail NRS unit tests for new ref files by @hbushouse in https://github.com/spacetelescope/jwst/pull/6913

Update NIRCam TSGrism regtest by @hbushouse in https://github.com/spacetelescope/jwst/pull/6914

JP 2652 Set DQ flags in extract 1d for IFU data by @jemorrison in https://github.com/spacetelescope/jwst/pull/6909

JP-2633: Add unit to time keyword comment strings by @tapastro in https://github.com/spacetelescope/jwst/pull/6910

Use datamodels.open in calwebb_coron3 (JP-2116) by @dmggh in https://github.com/spacetelescope/jwst/pull/6855

Switch to using external wiimatch package by @mcara in https://github.com/spacetelescope/jwst/pull/6916

JP-2664: Fix NRS-MOS source ids to be 5 digits and positive by @tapastro in https://github.com/spacetelescope/jwst/pull/6915

JP-2664: Bugfix for source_id reassignment by @tapastro in https://github.com/spacetelescope/jwst/pull/6917

JP-2663: Update datamodels schemas to match KWD by @hbushouse in https://github.com/spacetelescope/jwst/pull/6918

Full Changelog: https://github.com/spacetelescope/jwst/compare/1.5.3...1.6.0
Source code(tar.gz)
Source code(zip)
1.5.3(Jun 20, 2022)
What's Changed

JP-2587 Check spec2 data is IFUImageModel for straylight step by @jemorrison in https://github.com/spacetelescope/jwst/pull/6861

JP-2612: Speed up algorithm for computing sampling wavelengths by @mcara in https://github.com/spacetelescope/jwst/pull/6860

Update README and change log by @hbushouse in https://github.com/spacetelescope/jwst/pull/6865

JP-2603: Catch None return from SOSS F277W in Level3 by @tapastro in https://github.com/spacetelescope/jwst/pull/6863

Update all docs for zeroframe processing by @hbushouse in https://github.com/spacetelescope/jwst/pull/6868

JP-2624: Update ami_average for different size inputs by @hbushouse in https://github.com/spacetelescope/jwst/pull/6870

xfail NIRCam grism tests until ref files are fixed by @hbushouse in https://github.com/spacetelescope/jwst/pull/6871

JP-1297: Update contribution guide by @cshanahan1 in https://github.com/spacetelescope/jwst/pull/6864

JP-2637: Only load science members in calwebb_image3 by @hbushouse in https://github.com/spacetelescope/jwst/pull/6875

JP-2610: Refpix documentation update (with rebase) by @stscirij in https://github.com/spacetelescope/jwst/pull/6872

Add asdf-standard to dev requirements by @WilliamJamieson in https://github.com/spacetelescope/jwst/pull/6876

JP-2606: Catch two more SOSS errors raised. by @tapastro in https://github.com/spacetelescope/jwst/pull/6877

Add a MIRI coron3 regression test by @hbushouse in https://github.com/spacetelescope/jwst/pull/6879

JP-2604: Update ref file schemas with current CRDS selectors by @tapastro in https://github.com/spacetelescope/jwst/pull/6866

Fix SIAF default handling for missing SIAF values using pysiaf by @stscieisenhamer in https://github.com/spacetelescope/jwst/pull/6869

Reduce memory usage in skymatch by @mcara in https://github.com/spacetelescope/jwst/pull/6874

Update pointing tests for new SIAF content by @hbushouse in https://github.com/spacetelescope/jwst/pull/6881

JP-2630: Implement MRS cross-artifact algorithm in MRS straylight correction by @drlaw1558 in https://github.com/spacetelescope/jwst/pull/6873

JP-2594 Explain about CRDS PUB by @stscieisenhamer in https://github.com/spacetelescope/jwst/pull/6862

JP-2016: Flat_field step should ignore flatfield pixels with NO_FLAT_FIELD DQ bit set by @stscirij in https://github.com/spacetelescope/jwst/pull/6882

JP-2123: Update ami_analyze arguments docs by @hbushouse in https://github.com/spacetelescope/jwst/pull/6884

JP-2647 Fixed bug in selecting values from cubepars reference file by @jemorrison in https://github.com/spacetelescope/jwst/pull/6885

JP-2650: Fix SourceCatalogStep bug with input filename by @tapastro in https://github.com/spacetelescope/jwst/pull/6889

JP-2632: Change suffix for Lv3_Image members with imaging exp_types and background member_exptype by @tapastro in https://github.com/spacetelescope/jwst/pull/6878

JP-2655 release 1.5.3 by @zacharyburnett in https://github.com/spacetelescope/jwst/pull/6894

Full Changelog: https://github.com/spacetelescope/jwst/compare/1.5.2...1.5.3
Source code(tar.gz)
Source code(zip)
1.5.2(May 21, 2022)
JWST Build 8.0

Release notes

Association generator software and rules have been updated to:

fix unnecessarily large memory footprint for large pools

prevent level 2 and 3 associations for NIRCam TSGRISM exposures on the NRCBLONG (NRCB5) detector

add valid optical paths for NRS_LAMP exposures, in order to generate or exclude associations for specific lamp, disperser, and detector combinations

Updates to the Level-1b set_telescope_pointing script to:

add the "fgsid" option

Updates to Level-2a processing for all exposure modes include:

enable the use of NIRCam "frame zero" data to estimate slopes for pixels that are saturated in all groups

reduce memory usage in the dark_current step and improved memory performance of the entire pipeline

bug fix in "ramp_fitting" for handling CR hits that occur in the first good group after flagged first frames

fixed the handling of segmented data products in the MIRI "reset" step

updated the "saturation" step to flag neighbors of saturated pixels, to account for charge spilling

*Updates to Level-2b imaging (calwebb_image2) processing include:

corrections to the computation of the CRPIXn keyword values

fixes to the parsing of the FILTEROFFSET reference file used in the "assign_wcs" step

Updates to Level-2b spectroscopic (calwebb_spec2) processing include:

a fix for spectral tearing in MIRI MRS IFU cubes

the implementation of the IDT-supplied algorithm for NIRISS SOSS 1-D spectral extraction

addition of the "background" step parameter "wfss_mmag_extract", which is used to limit the list of sources used in the computations

updated the IFU "cube_build" step to use "drizzle" weighting by default, rather than "EMSM"

Updates to the Level-3 imaging (calwebb_image3) processing include:

changes to some of the default parameter values for the "tweakreg" step, to eliminate errors encountered for some commissioning observations

Updates to the Level-3 spectroscopic (calwebb_spec3) processing include:

the implementation of the IDT-supplied algorithm for NIRISS SOSS 1-D spectral extraction

Source code(tar.gz)
Source code(zip)
1.5.1(May 17, 2022)

JWST Build 8.0 rc2
Source code(tar.gz)
Source code(zip)
1.5.0(May 6, 2022)

JWST Build 8.0 rc1
Source code(tar.gz)
Source code(zip)
1.4.6(Mar 25, 2022)

Add option --force-level1bmodel.to set_telescope_pointing.
Source code(tar.gz)
Source code(zip)
1.4.5(Mar 24, 2022)

Source code(tar.gz)
Source code(zip)
1.4.4(Mar 16, 2022)

This patch release includes fixes for set_telescope_pointing.
Source code(tar.gz)
Source code(zip)
1.4.3(Feb 4, 2022)

The default COARSE tracking algorithm, COARSE_TR_202111, was updated to use FGS1 exclusively.
Source code(tar.gz)
Source code(zip)
1.4.2(Jan 20, 2022)
What's Changed

Open changelog for development by @stscieisenhamer in https://github.com/spacetelescope/jwst/pull/6555

Update CRDS dependency by @stscieisenhamer in https://github.com/spacetelescope/jwst/pull/6567

SPB-778 Bugfix: JWST dependency uploads occuring with failed regressions by @shahm0 in https://github.com/spacetelescope/jwst/pull/6568

JP-2277: Add a blurb to step docs with external calls to stcal by @tapastro in https://github.com/spacetelescope/jwst/pull/6566

update version of stcal to 0.6.0 by @cshanahan1 in https://github.com/spacetelescope/jwst/pull/6570

JP-2384: Update names of MIRI coronagraphic dither patterns by @tapastro in https://github.com/spacetelescope/jwst/pull/6573

Prepare changelog for release by @nden in https://github.com/spacetelescope/jwst/pull/6574

open change log for post 1.4.1 development by @nden in https://github.com/spacetelescope/jwst/pull/6575

JP-2386: Added MIRI-MRS cross band options to outlier detection by @jemorrison in https://github.com/spacetelescope/jwst/pull/6666

JP-2024: Update default value of skymatch's 'skymethod' step parameter by @tapastro in https://github.com/spacetelescope/jwst/pull/6580

JP-2495: Change restriction on Level-2b association creation to nrc_image instead of nrc_tacq by @tapastro in https://github.com/spacetelescope/jwst/pull/6681

JP-2385: Changed logic in validation of grism bounding boxes by @tapastro in https://github.com/spacetelescope/jwst/pull/6579

Prepare for 1.4.2 by @stscieisenhamer in https://github.com/spacetelescope/jwst/pull/6682

New Contributors

@shahm0 made their first contribution in https://github.com/spacetelescope/jwst/pull/6568

Full Changelog: https://github.com/spacetelescope/jwst/compare/1.4.0...1.4.2
Source code(tar.gz)
Source code(zip)
1.4.1(Jan 15, 2022)
1.4.1 (2022-01-15)

dark_current

Added docs mention of external algorithm in stcal [#6566]

datamodels

Update names of MIRI coronagraphic flats dither patterns [#6573]

jump

Added docs mention of external algorithm in stcal [#6566]

Fix issue in jump detection that occurred when there were only 2 usable differences with no other groups flagged. This PR also added tests and fixed some of the logging statements in two-point difference. [spacetelescope/stcal#74]

linearity

Added docs mention of external algorithm in stcal [#6566]

ramp_fitting

Added docs mention of external algorithm in stcal [#6566]

saturation

Added docs mention of external algorithm in stcal [#6566]

Source code(tar.gz)
Source code(zip)
1.4.0(Jan 10, 2022)
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]

Source code(tar.gz)
Source code(zip)
1.3.3(Oct 6, 2021)
What's Changed

Avoid photutils 1.2.0 [#6378]

Source code(tar.gz)
Source code(zip)
1.3.2(Sep 3, 2021)
Changes in jwst 1.3.2

associations

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]

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

Moved cube blotting to a c extension [#6256]

pipeline

Updated calwebb_tso3 to be more robust in handling null results from the tso_photometry step. [#6265]

Source code(tar.gz)
Source code(zip)
1.3.1(Aug 9, 2021)
Changes in jwst v1.3.1

lib

Fixed a bug in set_telescope_pointing that was setting wrong meta for the pointing quality [#6264]

Source code(tar.gz)
Source code(zip)
1.3.0(Aug 1, 2021)
Changes in jwst v1.3.0

associations

Ensure no Lv3_WFSC associations created on group candidates [#6131]

datamodels

Add new PATTTYPE values for MIRI Coronagraphic flats: 4QPM_LFLAT, 4QPM_PFLAT, LYOT_LFLAT, LYOT_PFLAT. [#6232]

Update DarkModel to use uint32 for DQ array. [#6228]

Add NOUTPUTS keyword to the DarkModel schema. [#6213]

lib

Add overriding of the matrix calculations to set_telescope_pointing.py [#5843]

Add guide star-based pointing algorithm to set_telescope_pointing.py [#5843]

resample

Fix the extreme memory consumption seen in resampling of variance arrays. [#6251]

tweakreg

Add an upper tweak threshold of 10 arcsec to tweakreg [#6252]

wfs_combine

-- Add option to flip the dither locations so that images with different filters will have the same pixel locations [#6101]

-- Fixed the refine option to correctly use the cross correlation to align the images if the WCS is off [#6101]
Source code(tar.gz)
Source code(zip)