Release notes and known issues in build 9.2 of the JWST Operations Pipeline, released on May 23, 2023, are provided in this article.

On this page

This article provides a list of all relevant changes to the operations pipeline that was released with build 9.2. This build focused mainly on updates to the JWST Science Calibration Pipeline, but includes information relevant to changes in other subsystems that might affect what users see in their data.

Highlights of this build

Build 9.2

Words in bold are GUI menus/
panels or data software packages;
bold italics are buttons in GUI
tools or package parameters.
Memory leaks in the cube_build step for IFU data have been fixed, greatly reducing the amount of memory used by the step and preventing out-of-memory errors.
The dq_init step has been updated to propagate "DO_NOT_USE" data quality flags from the MASK reference file to both the PIXELDQ and GROUPDQ arrays of the science exposure. With this, all bad pixels are set to a value of NaN in the count rate ("rate"/"rateints") products created by the calwebb_detector1 pipeline.
Major enhancements and bug fixes have been applied to the near-IR "snowball" and MIRI "shower" flagging algorithms in the jump detection step, which greatly increase the scientific utility of the results. For more information on the algorithms and new step parameters see the jump step documentation. Note that the snowball and shower flagging is currently skipped by default in standard processing, while testing of the new algorithms continues. Once they have been thoroughly vetted, they will be reactivated through parameter reference file updates in CRDS.
A bug has been fixed in the ramp_fit step to correctly compute the count rate for pixels that only have good (e.g., unsaturated) data in the first group of an integration. Previously, there was an error in the effective integration time that was used to convert the first group value into a count rate. Note that this is distinct from pixels where the "zero frame" value is used to compute a count rate (when all groups are bad). The count rate values from zero frame data were correct.

Data affected by this build

Provided below is a list of products in MAST generated by the JWST Science Calibration Pipeline that may be most significantly affected by the updates in build 9.2. The changes listed in the release notes may affect other modes as well, but many of these will be transparent to the MAST user.

The data and pipeline stage affected for data in MAST are:

Stage 1 pipeline results ("rate", "rateints" products) for most instrument modes can potentially be affected by the updates to:
- the dq_init step to propagate "DO_NOT_USE" data quality flags from the MASK reference files into the science GROUPDQ arrays
- the jump step enhancements and bug fixes for near-IR "snowball" and MIRI "shower" detection and flagging^*.
- the ramp_fit step bug fix for count rate computations of pixels in which only the first group is not saturated and on-board frame averaging was used (e.g., fields with bright stars)
MIRI MRS stage 2 and 3 products (residual_fringe and straylight step bug fixes)
MIRI MRS time-series observations (TSO) stage 2 products (assign_wcs step bug fix)
NIRSpec fixed slit observations stage 2 and 3 products (photom step bug fix)

^*Note that the snowball and shower correction is turned off, by default, in the operations pipeline while further testing is completed. But it is available for offline use. A couple of known issues have already been resolved in the development version of the pipeline.

Release notes

Build 9.2 of the JWST Operations Pipeline was released on May 23, 2023 to the Barbara A. Mikulski Archive for Space Telescopes (MAST). This build includes changes to the JWST Science Calibration Pipeline released in version 1.10.1 of the jwst calibration pipeline package via the PyPI repository.

The following fixes or changes were included in build 9.2. Changes to specific steps in the pipeline are listed below, along with descriptions to more general changes made to specific packages and related subsystems. This release also includes changes to the JWST Science Data Processing subsystem (SDP) version JWSTDP-2023.1.1 which creates raw (uncal) products.

assign_wcs step

The step was fixed to correct a bug in the computation of WCS bounding box for MIRI MRS TSO observations. assign_wcs assumed that the bounding box for all MIRI MRS data was a 2-D image, but this only applies for non-TSO MRS data. The fix now correctly handles the computation of the WCS bounding box for the TSO MRS 3-D data cubes.

cube_build step

Updated the interface to C extension modules to fix memory allocation and leak issues. This update significantly reduces the amount of memory used when building IFU cubes.

dq_init step

The step was updated to propagate "DO_NOT_USE" DQ flags from the MASK reference file to both the PIXELDQ and GROUPDQ arrays of the science exposure. This has the effect of preventing slope computations for bad pixels downstream in the ramp_fit step.

extract_1d step

The step was updated to automatically skip the processing of the NIRSpec fixed slit "rateints" (multi-integration) product because this is not a supported mode.
The logic for handling the use_source_posn parameter, which indicates if an offset to account for the expected location of the source is applied, was fixed. This parameter can be set in 3 different ways, so the fix now honors the appropriate hierarchy of precedence. The highest to lowest order of precedence is (1) command-line override settings, (2) reference file settings, and 3) internal decisions by the step code of whether or not to use the source position.
Updated the syntax of unit strings for surface brightness quantities so that they can be properly parsed by astropy.units.

flat_field step

The step was updated to allow the correct handling of NIRSpec fixed slit for "rateints" products. These type of products are multi-integration, so the update now correctly applies the correction to each integration individually.

jump step

Several updates to the near-IR "snowball" and MIRI "shower" flagging algorithms were implemented, which significantly increases the scientific utility of the results. Significant changes include the use of ellipses instead of circles in fitting snowball shapes and the inclusion of more stringent tests to prevent incorrect identification of snowballs. The shower detection algorithm is completely new and is now able to find extended emission far below the single pixel signal-to-noise ratio. It also allows detected showers to flag groups after the detection event. These algorithms are currently not applied to the MAST data, but can be activated by users via the "pars_jumpstep" reference file that define the jump step runtime parameters. Instrument teams are in the process to finishing testing of these steps and expect to turn on this algorithm for those modes where the data is correctly flagged.

outlier_detection step

Updated the step documentation (in ReadTheDocs) to more completely describe the actions of the various parameters that control the step.

pathloss step

Updated the step to loop over all integrations when given a MIRI LRS fixed slit "rateints" (multi-integration) product as input.

photom step

Fixed a bug in the handling of NIRSpec fixed slit exposures containing multiple slits, so that each slit gets the proper flux calibration applied depending on whether each slit contains a point or extended source.
Corrected the units of the data stored in the "photom_uniform" array to MJy/sr (surface brightness), to allow for correct usage in master_background processing.
Fixed the labeling of NIRISS SOSS flux units to consistently store spectral point source data in units of "MJy".

ramp_fit step

Fixed a bug in the slope computation for pixels that only have good data (e.g., unsaturated) in the first group of any integration, so that it uses the correct effective exposure time for the first group. This because when on-board frame averaging is in use, the effective integration time of the first group is not the same as the elapsed time between all subsequent groups.

resample/resample_spec steps

Added the step argument output_wcs, which allows a user to supply a GWCS definition for the resampled output file in the form of an ASDF file.
Fixed a bug in the use of DQ bits to reject bad pixels when resampling the variance arrays for a given image, so that pixels rejected from the resampled science image are also rejected when constructing the resample variance and error images.

resample_spec step

The step has been updated automatically skip processing when given a NIRSpec fixed slit "rateints" (multi-integration) product as input, because this is not a supported mode.

residual_fringe step

Updated the step to allow proper handling of NaN pixel values in the input images.

straylight step

Updated the step to allow proper handling of NaN pixels values in the input images.

tweakreg step

Added the function adjust_wcs to the tweakreg.utils module, which can be used to apply additional user-provided rotations and scale corrections to an imaging WCS.
Added a trap for failures in source catalog construction for each input image, so that an empty catalog is returned instead of the step crashing.
Added a trap for failures in the alignment of a single image to an absolute reference catalog (e.g., Gaia), due to not enough sources available in the reference catalog.
Changed the validation of the fit to make the step work for a larger set of step parameters. This provides better information about the magnitude of the corrections and prevents the step from aborting the alignment.

Pipeline modules

The calwebb_detector1 pipeline module has been updated to add the undersampling_correction step for all non-TSO data. This step is currently skipped for all instruments.
The calwebb_spec2 pipeline module has been updated to move the MIRI MRS straylight correction step, so that it occurs before the flat_field step. This change was necessary because the artifact is due to internal reflections within the detector, and it should not take into account any of the pixel area-on-sky normalizations that will be introduced by the flat field step.
The calwebb_spec2 pipeline module has been updated to make a deep copy of the current data before calling the resample_spec and extract_1d steps, to avoid potential issues with either of those steps modifying the input data in-place.

Product associations

Updated the "image2" association rules for coronagraphic reference PSF exposures that have linked background observations. With this change, the linked background exposures are now subtracted during calwebb_image2 processing.

General changes

jwst.datamodels has been moved out of the jwst package and put into the stdatamodels package as stdatamodels.jwst.datamodels. For now, imports from jwst.datamodels will continue to work and will automatically redirect to stdatamodels.
jwst.transforms was moved out of the jwst package and put into stdatamodels.jwst.transforms.

JWST Science Data Processing subsystem changes

The JSDP subsystem processes data from the telescope and creates raw ("_uncal") products. The following changes have been included in this build:

The set_telescope_pointing function used to set basic WCS pointing information in raw products has been updated to fill the values of the TARG_RA and TARG_DEC keywords in pure parallel exposures by copying values from RA_REF and DEC_REF. These values are computed from the aperture information, because pure parallel exposures do not carry any target information of their own.
Fixed a bug in the set_telescope_pointing function to correctly calculate the CRPIX* keywords for MIRI_TACQ exposures with aperture MIRIM_TAMR.
Fixed a bug in the processing and creation of "uncal" products that was leaving all of the BJD column entries of the "INT_TIMES" table extension set to zero.

Known issues for build 9.2

The following issues were not resolved in the jwst calibration pipeline package (version 1.10.2) that was released with build 9.2 and patch 9.2.1:

MIRI MRS and NIRSpec IFU outlier_detection (in the stage 3 calwebb_spec3 pipeline) can have anomalous results, due to several high-level issues, including undersampling. A completely new approach to outlier detection in IFU data is being developed, which will replace the current algorithm in a future build. The current outlier_detection step is skipped by default in standard pipeline processing, in order to avoid the poor results.

Some step and mode-specific issues will be fixed or included in build 9.3:

The stage 2 and 3 resample step, which uses drizzle, has a bug that can cause regions of the input images to not appear in the resampled image, under certain circumstances.
The pathloss correction step is accidentally applying the correction twice to NIRSpec fixed slit data sets. This has been fixed for build 9.3.
Association generator rules will be updated to properly handle NIRCam coronagraphy observations that obtain data from all 4 short-wavelength channel detectors (module A only). Given that only one of the detectors has the coronagraphic mask and target in the field of view, special handling is required so that only those data receive coronagraphic processing in the calwebb_coron3 pipeline, while data from the other detectors are treated as normal imaging and get processed by the calwebb_image3 pipeline.
A new step, pixel_replace, has been developed for use in the calwebb_spec2 pipeline, which can be used to replace bad pixels in 2-D spectroscopic images with values interpolated from their neighbors. This prevents contamination of extracted 1-D spectra by bad pixels.
The NIRCam wide field slitless spectroscopy (WFSS) spectral trace and dispersion calibration data currently available in CRDS are not a good match to in-flight data. Updated calibrations have been derived by the NIRCam team, using a more complex form of WCS transforms, which require updates to the calibration pipeline code in order to apply them. Those updates, and the use of the latest in-flight calibrations, will be available in build 9.3.
If you are working with reprocessed data, you might find that the VELOSYS keyword in the SCI extension header might be missing and the pipeline will be unable to correct for the JWST spacecraft motion during the wavelength calibration step. This will not be noticeable for most of the science cases but it seems to have a larger impact for MIRI MRS data.
There is a known bug in the calwebb_spec2 background subtraction step for wide field slitless spectroscopy (WFSS) images. Any bad pixels that are set to NaN will cause the output of the step to be an image completely filled with NaNs, as well as all downstream products. This bug has been fixed for build 9.3.

A more in detail version of the issues is provided below

General issues

Symptoms	Cause	Workaround	Mitigation Plan
`TARG_RA` and `TARG_DEC` in the FITS primary header are not at the epoch of the JWST exposure. This is one reason the 1-D spectral extraction aperture can be offset from the target location in the 2-D extracted spectrum image (see relevant instrument modes below).	Initially, science data processing was not applying proper motion to the target coordinates specified by the user (`PROP_RA`, `PROP_DEC`). After a 23 May 2023 update, science data processing began applying a proper motion correction that was too small by a factor of 0.36533.	Download uncalibrated data. Update `TARG_RA` and `TARG_DEC` (see workaround). Rerun calibration pipeline.	Apply proper motion correctly. STScI will reprocess affected data products with an updated operations pipeline, planned for installation on 24 Aug 2023. Reprocessing of affected data typically takes 2-4 weeks after the update.
Embedded world coordinate system (WCS) in JWST data products is incorrect.	Errors in the guide star catalog, misidentified guide stars, and uncertainties in the spacecraft roll angle result in errors in the WCS of pipeline data products even when target acquisition was performed to place science targets in the correct location. Typical errors are a few tenths of an arcsec, with some cases that are greater than 1 arcsec.	The workaround depends on instrument and mode. Currently, workarounds are available for MIRI MRS and NIRCam imaging (see mode-specific issues below).	Improve accuracy of the guide star catalog. This is a long-term project.
Images contain snowballs and shower artifacts.	These are caused by large cosmic ray impacts. The calwebb_detector1 pipeline includes a snowball/shower correction, but it is turned off by default while testing is underway.	Re-run the pipeline calwebb_detector1 with the jump step parameters set: find_showers = True (For MIRI) expand_large_events = True (for NIR instruments)	Snowball/shower correction in the jump detection step of calwebb_detector1 will be implemented via delivery of new parameter reference files for each instrument, as they become available. Reprocess affected data products with updated reference files. The schedule is TBD, depending on testing results for each instrument. Reprocessing of affected data typically takes 2–4 weeks.
NIR instruments only: There is large-scale striping (horizontal for NIRCam, vertical for NIRISS and NIRSpec) across the field.	1/f noise from the SIDECAR ASICs (detector readout electronics) causes this effect.	There are several community tools available that are designed to remove 1/f noise.	A mitigation plan is being developed.

General issues for time-series observations

Symptoms	Cause	Workaround	Mitigation Plan
For time-series data (for all instruments), FITS primary header keywords are different from the "INT_TIMES" extension. Particularly, this concerns the start/end times (`BSTRTIME` and `BENDTIME`) and the barycentric correction (`BARTDELT`) keyword.	"INT_TIMES" are based on the group times directly read into the engineering data. This is not the case with the header keywords, which do not account for electronic shifts on the reading of the data.	Use "INT_TIMES".	A mitigation plan is under development.

MIRI

MIRI low resolution spectroscopy (LRS)

Symptoms	Cause	Workaround	Mitigation Plan
Extracted 1-D spectra ("x1d" files) often show salt-and-pepper noise (i.e., spikes and divots one pixel across).	Pixels flagged as "DO_NOT_USE" appear as "NaN" in the spectral images, and the signal in those pixels is missing from the summed signal at that wavelength in the extracted spectra.	Users can apply the new pixel_replace step in the developmental pipeline, which replaces the pixels flagged "DO_NOT_USE" with pixels in the same column by normalizing nearby spatial profiles in the 2-D spectral images. The best solution is to download the developmental program and just run it. The default for pixel_replace is to use 3 rows above and below the problematic row. This value can be changed by setting the n_adjacent_rows argument. (JP-3005)	The new pixel_replace step will be part of the updated operations pipeline, planned for installation on 24 Aug 2023. STScI will reprocess affected data products, and that typically takes 2–4 weeks after the update.
Spectra of bright sources can experience data dropouts at wavelengths where they are brightest (in the "x1d" files). The problem can also be seen in 2-D spectral images, with the peak column flagged as "DO_NOT_USE" in several adjacent rows where the spectrum is brightest.	The jump detection step in calwebb_detector1 can flag pixels with strong signals as "DO_NOT_USE" in the spectral images even though the data are viable. These pixels are "NaN" in the spectral images and their signal is missing from the affected wavelengths in the extracted spectra.	Users can run calwebb_detector1 themselves and adjust the rejection_threshold parameter in the jump step to eliminate (or reduce) improper flagging. A generic workaround is challenging to produce as the occurrence and severity of the issue depends on several factors, e.g., target brightness and number of groups per integration.	The jump step algorithm and default parameters are continually being examined and optimized; improvements are expected in future builds (autumn 2023 and beyond). The issue likely cannot be entirely eliminated as it differs greatly between observations (and indeed many are not affected).
Spectra extracted from the LRS slit ("x1d" files) can show major disparities between the nods or with expected values.	The pathloss correction is generating incorrect results due to a poor understanding of the location of the source in the slit.	The "pathloss" reference file has already been modified to apply a correction as though the source were in the center of the slit, no matter where it actually is (or where it is believed to be). Exception: If the source position and telescope pointing indicate that the target is outside of the slit, then no pathloss correction is applied.	The Science Calibration Pipeline will be modified to allow the user to rerun the pathloss correction with a default position of the center of the slit. The operations pipeline will be modified to determine the source position based on the TA verification image. Neither of these solutions are ready for implementation.
Mitigated issues
Spectra extracted from LRS slit and slitless data ("x1d" files) can have little or no signal, or even negative signal, even though the 2-D spectral images look fine.	The pipeline is extracting the spectrum from the wrong location in the 2-D spectral images because the positions it is using to determine the location of the source are inaccurate.	Users can set the location and the width of the extraction apertures themselves when running calwebb_spec2 or calwebb_spec3 manually. A notebook demonstrating the spectral extraction capabilities of the JWST calibration pipeline for MIRI LRS is available in this repository.	The pipeline was updated in May 2023 to default to apertures centered on the nominal position of the level 3 spectrum in the aperture. This change is fully in operations, data have been reprocessed.

MIRI medium resolution spectroscopy (MRS)

Symptoms	Cause	Workaround	Mitigation Plan
The photon count rate and derived flux is lower than predicted at long wavelengths, with maximum deficit roughly a factor of 2 at 28 µm.	MRS sensitivity at long wavelengths is decreasing with time.	Use the new Science Calibration Pipeline software (jwst 1.11.0 onwards) to apply the time-dependent throughput correction, using new reference data (jwst_1094.pmap onwards). This is available as of 21 Jun 2023. (JP-3224)	Apply the new time-dependent throughput correction. STScI will reprocess affected data products with an updated operations pipeline, planned for installation on 24 Aug 2023. Reprocessing of affected data typically takes 2–4 weeks after the update. See JWST Observer.
World coordinate system (WCS) of data cubes is incorrect. Extracted flux from a point source is much fainter than expected or negative.	WCS is typically off by 0.3" and in some cases more than 1". Spectral extraction aperture is centered on target coordinates assuming WCS is correct.	Install the latest release of the jwst package and then run the Science Calibration Pipeline on the affected dataset. Starting in jwst 1.11.0, the extract_1d step supports setting ifu_autocen = True. (JP-3011)	Use DAOStarFinder to locate point sources in the image constructed from collapsed 3-D cube. Apply proper motion correctly. STScI will reprocess affected data products with an updated operations pipeline, planned for installation on 24 Aug 2023. Reprocessing of affected data typically takes 2–4 weeks after the update. STScI plans to provide software that updates the MIRI MRS WCS based on simultaneous imaging data. An availability date is to be determined.
Spectra show unexpected features around 12.2 µm.	There is a spectral leak in the MRS where a small amount of light from 6 µm is received by the 12 µm channel.	None at present—a correction notebook is in progress.	A correction step will be included in the pipeline in the future for 1-D spectra extracted from point sources.
Spectra show residual regular periodic amplitude modulations.	MRS experiences significant spectral fringing, which varies with the astronomical scene and cannot be automatically corrected in its entirety for all science targets.	Run the 2-D or 1-D (preferred) residual_fringe correction steps available in the pipeline (jwst 1.11.0 onwards). This is discussed in greater detail on JWST MIRI MRS Pipeline Caveats.	None; additional non-default corrections are science case specific. Calibrations programs will explore possible future mitigations.
Spectra extracted from small spatial regions show amplitude modulations of variable frequency (distinct from ordinary spectral fringes).	The MRS is not Nyquist sampled, and resampling the raw data to a rectified data cube introduces artifacts if extracting spectra on scales smaller than the PSF. See detailed discussion by Law et al. 2023.	Extract spectra from apertures comparable to PSF in width.	This is still under investigation; some science cases may permit scene modeling to mitigate impact.
The "ERR" extension in "rate" data products (and other error estimates downstream) is incorrect, sometimes by factors of 10–50.	Error values are estimated incorrectly by the pipeline.	Bootstrap uncertainty from science spectra, being careful to eliminate residual fringing first.	The root cause of incorrect error estimates in the pipeline is being investigated.
Custom user-derived backgrounds provided to the master_background step do not work as expected.	Backgrounds must be provided in surface brightness units.	No workaround is available at present; user custom backgrounds are beyond default scope of the pipeline.	Develop a JDox article discussing how to create custom backgrounds from science data and the limitations thereof.

MIRI imaging

Symptoms

Cause

Workaround

Mitigation Plan

Image has residual background.

The backgrounds for longer wavelength images can be quite high, and difficult to work with if dedicated background images are not taken and subtracted off in the pipeline.

Users can create a median sky (background image) and subtract it off for themselves if there is no extended source such as a galaxy or nebula in the image. This is most useful for long wavelength imaging, but can also be used for shorter wavelength images.

This notebook demonstrates how it can be done.

This is not something that can (or should) be changed in the pipeline, and will need to be done as an offline step as shown in the notebook.

The "cal" data product has "tree ring" like pattern.

The "tree ring" pattern of curves in MIRI images is a residual detector effect that is not removed in all cases by the reference files.

Creating and subtracting a median background can remove residual detector patterns in the background like the 'tree rings'.

This notebook demonstrates how it can be done.

Reference file and pipeline updates may be available at a future date to remove residual patterns such as the "tree rings" from all data, but there is no timeline on when this might be accomplished.

MIRI coronagraphic imaging

Symptoms	Cause	Workaround	Mitigation Plan
Absolute flux calibration is incorrect.	An error was made when computing the aperture correction for coronagraphic PSFs.	Multiply fluxes by a factor that will be available by the end of August, 2023.	Update flux calibration "photom" reference files. STScI will reprocess affected data products with updated calibration reference data, expected to be available in CRDS by the end of August 2023. Reprocessing of affected data typically takes 2–4 weeks after the update.
Users will want to perform their own PSF subtraction with the data products.	PSF subtraction has too many free parameters to capture them in a one-size-fits-all automated processing pipeline.	See this notebook for a guide to the different stage 2 "cal"/"calints" output files and how to organize them for PSF subtraction. It also demonstrates how to retrieve these files from MAST, how use them as input to stage 3 of the pipeline, and explains the different stage 3 data products.	The MIRI team is always considering the scope of what data products the calwebb_coron3 pipeline stage should provide.
Tweak stage 1 and 2 parameters to optimize data calibration.	Default parameters may not be optimal for all datasets.	spaceKLIP, provided by the ERS team, can run pipeline steps as well as perform highly tunable PSF subtraction on the data products. There are examples of different pipeline parameter values they have found helpful, which can be found in the MIRI config file under the "tests" folder. Pipeline stages 1 and 2 are shared with the MIRI imager, so users may look there for more examples.	None at this time.
Current Lyot flat-fielding causes a sharp discontinuity underneath the coronagraphic mask.	A sharp edge in the Lyot coronagraph's flat-fielding reference file creates a sharp discontinuity underneath the coronagraphic mask, in stage 2 pipeline products. This can result in artifacts during certain image processing steps that are sensitive to abrupt changes.	For now, users should be aware that this sharp discontinuity is an artifact of the calibration pipeline and does not represent astrophysical information. They should take this into account during post-processing.	Mitigation strategies are under investigation.

MIRI time-series observations

Users should assume that all pipeline issues mentioned in this article for imaging, LRS, and MRS modes also apply to TSOs with those modes. Listed here are additional issues that are TSO-specific.

Symptoms	Cause	Workaround	Mitigation Plan
Spatially and temporally varying noise in subarray TSOs ("390 Hz noise")	This noise originates in the detector electronics. This affects subarrays SLITLESSPRISM, SUB64, and SUB128 subarrays.	The noise can be subtracted to a large extent by measuring and subtracting a background for each individual integration. Some residual noise will remain.	Testing is currently underway on an algorithm that fits and removes the 390 Hz noise signal. This is expected to be integrated into the pipeline in autumn of 2023. In the future, the MIRI team will likely make changes to the detector readout pattern that will remove the pattern entirely.
Discontinuities in persistence behavior are seen in the SLITLESSPRISM subarray at the start of the exposure.	This is currently under investigation.	Users should consider increasing the detector settling time from 30 mins to 1 hour. This is particularly important for phase curves.	As soon as the cause of this problem is understood, the MIRI team will make the required changes to mitigate it.

NIRCam

NIRCam general issues

Symptoms	Cause	Workaround	Mitigation Plan
Bright objects in the field are saturated even though the ETC predicted that they would not saturate "fully."	For most NIRCam readout patterns, there are many frames included in a group. Bright objects may saturate by the end of a group, but remain unsaturated in the first frame (frame0).	The calwebb_detector1 pipeline includes an option to correct an image using the unsaturated frame0 exposure, but this is turned off by default. To turn it on, rerun calwebb_detector1 with ramp_fit parameter suppress_one_group set to False. Note that the operations pipeline has a bug in the frame0 correction. An update is planned for 24 Aug 2023 (jwst Science Calibration Pipeline version 1.11.3.)	The NIRCam team is evaluating whether the frame0 correction should be turned on as the default.

NIRCam time series (grism and imaging)

Symptoms	Cause	Workaround	Mitigation Plan
Wavelengths in extracted spectra ("x2d," "x1d") have incorrect dispersion relative to stellar model spectra.	Operations pipeline is using pre-launch wavelength reference data. Science Calibration Pipeline had a bug.	This workaround notebook shows how to run the calwebb_image2 and calwebb_tso3 pipelines on grism time-series data. This notebook assumes that the updated reference files (specwcs) are present in CRDS. These reference files will contain the wavelength solution derived from commissioning data.	Use new wavelength reference data with updated Science Calibration Pipeline. STScI will reprocess affected data products with an updated calibration reference data and updated operations pipeline, planned for installation on 24 Aug 2023. Reprocessing of affected data typically takes 2–4 weeks after the update.
For grism time-series observations, extract_2d always produces a cutout that is 64 pixels in height (cross-dispersion direction), regardless of whether the original image is full frame or subarray. This may not include enough background pixels for background subtraction.	The pipeline default cutout height has been set to be equal to the height of the smallest available NIRCam grism subarray (2048 × 64 pixels)	Rerun the 2-D spectral extraction step (extract_2d) in calwebb_spec2 to produce cutouts with larger height and more background pixels using the *tsgrism_extract_height* parameter.	A mitigation plan is under development.
An excessive number of pixels are flagged as outliers in the subarray data, leading to a lower signal-to-noise ratio of the "rate" products (slope images) per integration.	Some subarrays do not have reference pixels on all sides. Without a reference pixel correction, the data becomes noisier and the jump step in calwebb_detector1 sometimes identifies too many pixels as outliers.	Rerun the jump detection step in calwebb_detector1 with an increased rejection_threshold (default is 4.0).	Mitigation is not yet scheduled, due to higher priority issues.

NIRCam imaging

Symptoms	Cause	Workaround	Mitigation Plan
Misalignment of mosaic tiles in some of the stage 3 data products	This is usually due to an insufficient number of stars for alignment using the default calwebb_image3 pipeline parameters.	Users can adjust the parameters to the tweakreg step in calwebb_image3 to find more stars across the field for alignment. This notebook shows how to adjust the tweakreg parameters and rerun the stage 3 pipeline. Users can also choose to align to Gaia DR3 or input a custom reference catalog to tweakreg. The community tool JWST/HST Alignment Tool (JHAT) also produces improved alignment.	Reprocess data with an enhanced calibration reference file (distortion) in CRDS, which may improve alignment in some cases. An update is planned for September 2023. Reprocessing of old data typically takes 2–4 weeks after the update.
Some of the mosaic tiles in the stage 3 products are well aligned, but a subset of the tiles are offset.	Guiding on different stars between mosaic tiles can sometimes cause a misalignment.	In calwebb_image3, try adjusting the tweakreg fit_geometry parameter to rscale or general, which provides more flexibility in how the images are adjusted/oriented. Also try adjusting the *separation* and tolerance parameters to provide more stellar matches between images. Alternatively, run JHAT separately on the well-aligned and poorly-aligned data. Then, feed all data into calwebb_image3. Be sure to turn off the tweakreg step since the data have already been aligned.	Mitigation is not yet scheduled due to higher priority issues.
There are large scattered light features on the images of some NIRCam detectors.	There are several NIRCam scattered light artifacts. The most common are claws and wisps, which are caused by light entering directly through the aft optic system (AOS) mask, located in front of the JWST tertiary mirror, without first bouncing off the primary and secondary mirror.	For claws: Avoid position angles that place bright stars in the susceptibility zone. For wisps: Wisps can be subtracted using templates, available to download here: NIRCam Claws and Wisps	For claws: The mitigation plan for removing claws from data is not yet scheduled. However, the NIRCam team is screening all programs to minimize the risk of claws before programs are observed. For wisps: A GO calibration program (PID 3905) aims to improve the wisp templates.
An excessive number of pixels are flagged as outliers in some subarray data.	Some imaging subarrays do not have reference pixels on all sides, especially the extended source subarrays in the long wavelength channel. Without a reference pixel correction, the data become noisier and the jump step in calwebb_detector1 sometimes identifies too many pixels as outliers.	Rerun the jump detection step in calwebb_detector1 with an increased rejection_threshold (default is 4.0).	Mitigation is not yet scheduled due to higher priority issues.

NIRCam coronagraphic imaging

Symptoms	Cause	Workaround	Mitigation Plan
Dark correction leads to worse outcome than not applying any.	On-sky darks are not high enough in SNR and lead to residuals and erroneous jumps in the "rateints" images.	Skip dark correction during calwebb_detector1.	Mitigation is not yet scheduled because the data are satisfactory without dark subtraction.
An excessive number of pixels are flagged as outliers in some subarray data.	The coronagraph subarrays do not have reference pixels on all sides. Without a reference pixel correction, the data become noisier and the jump step in calwebb_detector1 sometimes identifies too many pixels as outliers.	The spaceKLIP open-source package (provided by the community) implements a pseudo-reference pixel correction using a few not-illuminated pixels around (at the edge of) the subarray and forces them to be reference pixels. This way, global DC offsets frame to frame are taken care of.	Implement something similar to spaceKLIP for calwebb_coron3. Timeline TBD.
Absolute flux calibration is incorrect.	The wavelength dependent throughput of the COM (coronagraph optical mount) substrate is not taken into account.	spaceKLIP uses the spectral energy distribution (SED) from published photometry (VO table from VizieR) to assess the expected flux from the star and calibrate the contrast curves, then determines the flux and position of any point source using MCMC and a forward model of the off-axis PSF.	Reprocess data with an enhanced calibration reference file (photom) in CRDS. An update is planned for September 2023 that takes the full coronagraphic throughput into account. Reprocessing of old data typically takes 2–4 weeks after the update.

NIRCam wide field slitless spectroscopy (WFSS)

Symptoms	Cause	Workaround	Mitigation Plan
Adjacent sources are included in extracted spectra.	This occurs in crowded fields with overlapping spectral traces.	No workaround is available yet. The calwebb_spec2 pipeline includes an option to provide a first-order correction for source contamination with the wfss_contam step, but some discrepancies and issues are still being investigated.	Implement the wfss_contam step in calwebb_spec2. STScI will reprocess affected data products with an updated operations pipeline, planned for installation in November 2023. Reprocessing of affected data typically takes 2–4 weeks after the update.
The fluxes of some spectra in the field appear to be too low or even negative.	This is caused by over-subtraction of the background. The background subtraction step in calwebb_spec2 assumes the background is constant and does not vary in time, which can be a limiting factor for low signal-to-noise observations.	Users can manually perform a local background subtraction on extracted 2-D spectra before the 1-D extraction in calwebb_spec2.	A mitigation plan is under development.
The WFSS pipeline has excessive run times when run locally.	Processing WFSS exposures can be prohibitively resource intensive on individual machines due to the number of sources in these files.	Adjust the *wfss_nbright* parameter in the extract_2d step in calwebb_spec2 to limit the number of extracted sources.	A mitigation plan is under development.

NIRISS

NIRISS aperture masking interferometry (AMI)

Symptoms	Cause	Workaround	Mitigation Plan
Interferometric properties returned by the calwebb_ami3 stage of the pipeline require further evaluation. Data are served in FITS files rather than the interferometric convention to use OIFITS formatted files.	The Science Calibration Pipeline is using an older version of the image plane reconstruction software.	The JWST Aperture Masking Interferometry Pipeline Caveats article provides descriptions of how to analyze data products off-line after the calwebb_image2 stage of the Science Calibration Pipeline, with links to analysis tools.	The calwebb_ami3 stage of the Science Calibration Pipeline is currently being updated to use state-of-the-art code and to serve OIFITS formatted files. The fix is planned to become public with or after the operations pipeline build planned for installation in November 2023. Reprocessing of affected data typically takes 2–4 weeks
When the peak pixel of a PSF in AMI mode reaches beyond ~25,000 ADU in an integration, it starts "spilling" charge to its neighboring pixels, thus causing an effective "widening" of the PSF.	This is due to the so-called "brighter-fatter effect" (BFE) that affects near-IR H2RG detectors.	No generic workaround is available until an operations pipeline build planned for installation in November 2023. For advice on specific datasets for which the peak intensity reaches beyond ~25,000 ADU per integration, a help desk ticket can be submitted. The NIRISS AMI Recommended Strategies article in JDox describes how to avoid this problem at the proposal planning stage.	Apply a new Science Calibration Pipeline step called undersampling_correction within the calwebb_detector1 stage. STScI will reprocess affected data products with an updated operations pipeline, planned for installation in November 2023. Reprocessing of affected data typically takes 2–4 weeks after the update.

NIRISS single object slitless spectroscopy (SOSS)

Symptoms	Cause	Workaround	Mitigation Plan
Too many pixels are flagged as "DO_NOT_USE" which are then set to "NaN" values in the science array. Some of these pixels are fine for SOSS data analysis.	Several detector-level reference files (mask, linearity, saturation, super bias) need to be updated to not cause certain pixels to be flagged as "DO_NOT_USE".	Use the attached Jupyter notebook to turn off setting pixels to "DO_NOT_USE".	Regenerate and redeliver the mask, linearity, saturation, and superbias reference files. Reprocess affected data products with updated calibration reference data, planned to be available in CRDS in the fall of 2023. Reprocessing of affected data typically takes 2–4 weeks.
The shape of the spectral trace varies from visit to visit for all the NIRISS/SOSS orders. Distortion is higher at longer wavelengths. This might lead to lower SNR in the extracted spectra.	The actual pupil wheel position (PWCPOS) that sets the GR700XD grism in the optical path on each visit does not land exactly at the commanded position; this causes a distortion in the shape of the spectral trace.	Use the PASTASOSS package to predict spectral traces given the PWCPOS, or use the package as a starting point to perform spectral tracing and thus extraction.	A mitigation plan is under development.
The wavelength solution varies from visit to visit, appearing to be shifted by a handful of pixels.	The actual pupil wheel position (PWCPOS) that sets the GR700XD grism in the optical path on each visit does not land exactly at the commanded position; this causes a distortion in the wavelength solution.	Identify stellar spectral lines to correct wavelength solution on each visit.	A workaround considering wavelength-dependent distortions is being implemented in the PASTASOSS package. Expected delivery is before fall 2023. Implementation in the Science Calibration Pipeline is still under development.
The shape of the spectral trace and wavelength solution sometimes varies from exposure to exposure on a given visit, including between subsequent CLEAR and F277W exposures.	The actual pupil wheel position (PWCPOS) that sets the GR700XD grism in the optical path on each visit does not land exactly at the commanded position. When the position lands above a certain threshold from the commanded position, the onboard mechanism tries to re-adjust the position between exposures until it meets the threshold.	If trying to match CLEAR and F227W exposures, perform a translation and/or rotation of the F227W exposure to match the CLEAR exposure. Use stellar lines to match the wavelength solution on the F277W exposure.	The NIRISS team has implemented the addition of a "Short First Exposure" consisting of a single group, single integration at the beginning of every exposure that requires an F277W exposure. This will give the on-board mechanism the opportunity to re-adjust the pupil wheel position if needed before the science exposures. Implementation will be available in APT 2023.5 (release date: 24 Aug 2023).
Observations show a background that abruptly increases in flux at around column ~700.	This is due to the background (typically dominated by zodiacal light background at NIRISS/SOSS wavelengths) being dispersed by the GR700XD grism into the detector (see Albert et al., 2023; Section 8.5).	Scale the background taken during commissioning for SUBSTRIP256 and for SUBSTRIP96 to observations using non-illuminated regions of the detector (see NIRISS Time Series Observations Pipeline Caveats on the efficiency of this procedure).	Calibration program 4479 is studying background templates at different positions in the sky, as well as the variation of the background due to the pupil wheel position (PWCPOS) varying from visit to visit. Implementation on the JWST pipeline is still under development.
There is evident banding in the cross-dispersion direction, which varies from group-to-group and integration-to-integration.	This is due to residual, uncorrected 1/f noise left over from the reference pixel correction step.	There are several community tools available designed to remove 1/f noise.	A mitigation plan is under development.
Large number of outliers identified in the jump detection step, which cause lower SNR in the "_rateints" (count rate per integration) products.	The default parameters of the jump step in the JWST pipeline are too aggressive and flag too many pixels as cosmic rays.	Re-run the jump detection step in calwebb_detector1 with a rejection_threshold value > 10 (default is 4.0).	A mitigation plan is under development.

NIRISS wide field slitless spectroscopy (WFSS)

Symptoms	Cause	Workaround	Mitigation Plan
Spectral traces are offset from where they should be, causing offsets in wavelength zero point.	The current "specwcs" reference file (as of CRDS version jwst_1105.pmap) incorparates the field dependence in the wavelength dispersion silution. However, the shape of the spectral traces also vary as a function of detector position. There may also be a dependence on filter wheel position angle at the time of observation.	None.	In-depth investigation is underway to calibrate the change in shape of the spectral traces as a function of detector position and quantify whether there is a dependence on the filter wheel position angle at the time of observation on the spectral traces.
For direct imaging: when the peak pixel of a star (or other compact object) reaches beyond ~25,000 e^- in an integration (after bias and dark subtraction and linearity correction), it starts "spilling" charge to its neighboring pixels. This causes an effective "widening" of the PSF or charge distribution, as well as flux loss for those objects in the combined, resampled products of the calwebb_image3 stage of the Science Calibration Pipeline. This effect is strongest for the most undersampled modes (i.e., filters with pivot wavelength <= 2 μm).	This is due to the so-called "brighter-fatter effect" (BFE) that affects near-IR H2RG detectors, in combination with the current way "jumps" are detected and dealt with in the calwebb_detector1 pipeline stage, and how the latter affects image combination in the calwebb_image3 pipeline stage.	No efficient workaround is available at present.	Apply new Science Calibration Pipeline step undersampling_correction within the calwebb_detector1 stage. STScI will reprocess affected data products with an updated operations pipeline, planned for installation in November 2023. Reprocessing of affected data typically takes 2–4 weeks after the update.

NIRISS Imaging

Symptoms	Cause	Workaround	Mitigation Plan
When the peak pixel of a star (or other compact object) reaches beyond ~25,000 e^- in an integration (after bias and dark subtraction and linearity correction), it starts "spilling" charge to its neighboring pixels. This causes an effective "widening" of the PSF or charge distribution, as well as flux loss for those objects in the combined, resampled products of the calwebb_image3 stage of the Science Calibration Pipeline. This effect is strongest for the most undersampled modes (i.e., filters with pivot wavelength <= 2 μm).	This is due to the so-called "brighter-fatter effect" (BFE) that affects near-IR H2RG detectors, in combination with the current way "jumps" are detected and dealt with in the calwebb_detector1 pipeline stage, and how the latter affects image combination in the calwebb_image3 pipeline stage.	No efficient workaround is available at present.	Apply new Science Calibration Pipeline step undersampling_correction within the calwebb_detector1 stage. STScI will reprocess affected data products with an updated operations pipeline, planned for installation in November 2023. Reprocessing of affected data typically takes 2–4 weeks after the update.

NIRSpec

NIRSpec general issues

Symptoms	Cause	Workaround	Mitigation Plan
No flux or negative flux in FS or MOS extracted 1-D spectrum ("x1d" product), despite obvious flux in 2-D spectrum ("s2d" product).	Extraction aperture is offset along the spatial axis, for example, due to an error in target coordinates or the world coordinate system. For targets with large proper motion, see `TARG_RA` and `TARG_DEC` issue in the General issues section above.	For high proper motion targets, if the processing date (`DATE` keyword in FITS header) is before 23 May 2023, download new data products from MAST. Rerun the extract_1d step with a modified "extract1d" reference file containing the desired extraction aperture location (using either ystart and ystop or src_coef) and the parameter use_source_posn set to False. See this workaround notebook for an example of how to do this using FS data.	Fix the `TARG_RA` and `TARG_DEC` issue (see General issues table). Investigation is underway on whether errors in world coordinates system (e.g., due to large errors in the guide star catalog coordinates) can cause 1-D spectral extraction to fail. The timescale for a fix is uncertain, possibly in the next operations pipeline planned for installation in November 2023.
Extracted 1-D spectrum ("x1d" product) has spurious positive and negative features, typically one pixel wide.	Pixels marked as "DO_NOT_USE" in reference data are not included in the 1-D extracted spectrum.	Use the new Science Calibration Pipeline software (jwst 1.11.0 onwards) to estimate the value for each "DO_NOT_USE" pixel from neighboring 2-D profiles before extracting the 1-D spectrum. This is disabled by default. Instructions on enabling the pixel_replace step will be added soon. (JP-3005)	Test that the pixel_replace algorithm works well for NIRSpec fixed slit data. If it does, enable the pixel_replace step by default in the parameter reference file update (estimated for September 2023).
Unexpected flux levels in spectra of sources not centered in a slit.	A bug was found in the code used to interpolate the pathloss correction from the pathloss reference data. Affects FS and MOS point source data.	None.	A bug fix has been implemented and will be available in the next operations pipeline planned for installation in November 2023. Reprocessing of affected data typically takes 2–4 weeks after the update.
Wavelengths of spectral features does not match expectation in spectra of sources not centered in a slit.	The calwebb_spec2 pipeline performs a wavelength correction for offset point sources based on their expected position within the slit. However, the correction values are not being propagated to the resample_spec step, so the "s2d" products always have the wavelength scale appropriate for centered sources only. Affects FS and MOS point source data.	None.	Investigation of a fix is underway, possibly for implementation in the next operations pipeline planned for installation in November 2023. Reprocessing of affected data typically takes 2–4 weeks after the update.
A few pixel rows exhibit anomalous count rates in "rate" images for IRS2 data.	Some reference pixels are "bad" (e.g., excessive noise or "telegraph" behavior) and are flagged as such. However, those flags are not considered in the refpix step of the calwebb_detector1 pipeline, resulting in anomalous corrections for the associated science pixels.	None.	A flag check has been implemented, along with an improved algorithm to filter out noisy reference pixels. STScI will reprocess affected data products with an updated operations pipeline, planned for installation on 24 Aug 2023. Reprocessing of affected data typically takes 2–4 weeks after the update.

NIRSpec fixed slit (FS) spectroscopy

Symptoms	Cause	Workaround	Mitigation Plan
Spectra obtained with the SLIT = S200A1 and S200A2 option in APT are not combined to create a single spectrum with continuous wavelength coverage.	Association logic does not realize that `SOURCEID` = 1 observed with S200A1 is the same target as `SOURCEID` = 2 observed with S200A2.	Update `SOURCEID` in the "SCI" extension headers, so that a single unique value is used for all exposures of the science target. Manually create an association file that includes all exposures of the science target as members. Use calwebb_spec3 to reprocess the association. See the workaround notebook for an example.	Enhance the association logic and perhaps change the `SOURCEID` numbering scheme. STScI will reprocess affected data products with an updated operations pipeline, planned for installation in November 2023. Reprocessing of affected data typically takes 2–4 weeks after the update. (JP-3233)
Background spectra taken from one fixed slit does not match the point source spectrum extracted from a different slit.	The pathloss step as applied to FS data had a bug that led to the correction being applied twice. This affects all FS exposures; the impact on point sources is minor (a few percent at most), but higher for extended sources.	None.	Apply pathloss correction only once. STScI will reprocess affected data products with an updated operations pipeline, planned for installation on 24 Aug 2023. Reprocessing of affected data typically takes 2–4 weeks after the update.
The shape of spectra taken with the SUB512, SUB512S, or SUB32 subarrays exhibits unexpected features and wavelength-dependent flux discrepancies of 10% or more.	Some subarrays have no reference pixels, which means bias drifts are not corrected.	Rerun calwebb_detector 1 starting from the "_uncal" files. Before the linearity step, identify non-iluminated pixels in the detector and estimate their median value; this will provide an estimate of the detector pedestal level on each group. Remove this value from each group, and then run the remaining calwebb_detector1 steps.	Modify the reference pixel correction to use unilluminated pixels in the columns at the left and right edges of these subarrays. STScI will reprocess affected data products with an updated operations pipeline, planned for installation on 24 Aug 2023. Reprocessing of affected data typically takes 2–4 weeks after the update.
FS spectra obtained with the G140M grating exhibit flux discrepancies of up to 20%.	No spectrophotometric observations for this grating were obtained during commissioning, so the F-flat reference file (flux calibration) for this specific case is the model-based pre-flight version.	None.	Spectrophotometric observations with this configuration will be obtained in August, and updated F-flat reference file will be delivered as soon as possible after that.
Many significant outliers and "NaN" appear in the 2-D and 1-D extracted spectra.	The outlier_detection step generally has a hard time finding many outliers. Step parameters need to be tuned to the noise characteristics of each data set, although in many cases outliers are still missed. Also, the initial bad pixel flags set in the mask and dark reference files for subarrays contain too many "DO_NOT_USE" designations, which result in "NaN" pixel values.	"NaN" values can be resolved by removing "DO_NOT_USE" DQ flags and re-running the ramp_fit step in calwebb_detector1. A worked example on how to do that, using NIRISS SOSS data, can be found at https://github.com/spacetelescope/jwst-caveat-examples/blob/main/NIRISS_SOSS/do_not_use_workaround.ipynb. For outlier improvement, rerun the outlier_detection step in calwebb_spec3 with different values of the snr parameter.	Fix problems with subarray bad pixel masks—reference files will be updated in early August 2023. Reprocessing of affected data typically takes 2–4 weeks after the update. In the longer term, investigate algorithmic changes such as the equivalent of the new IFU outlier rejection methodology, possibly for inclusion in the next operations pipeline planned for installation in November 2023.
Level 3 extracted spectra have errors that are all "NaN."	The flat field reference file uncertainties are currently zero. The resultant flat error component calculated from these is "NaN", which propagates to the combined error as "NaN".	Recalculate the combined error using only the read noise and photon noise components; instructions will soon be available. See this worked example for more on how to do this.	Reprocess data with an enhanced calibration reference file (flat) in CRDS. An update is planned for the end of Aug 2023. Reprocessing of old data typically takes 2–4 weeks after the update.

NIRSpec integral field unit (IFU) spectroscopy

Symptoms	Cause	Workaround	Mitigation Plan
There is a hole at the peak of the PSF or an otherwise distorted PSF in IFU "s3d" cube.	This is due to overly aggressive outlier detection.	Option 1: Turn off outlier rejection in the cube_build step of calwebb_spec3. However, this may allow other outliers to remain in the cube. Option 2: Reprocess data using the Science Calibration Pipeline, jwst 1.11.3 and onward. This version will be installed in the operations pipeline with build 9.3), planned for installation on 24 Aug 2023.	Update outlier detection algorithm. STScI will reprocess affected data products with an updated operations pipeline, planned for installation on 24 Aug 2023. Reprocessing of affected data typically takes 2–4 weeks after the update.
Negative and/or surplus flux in the extracted 1-D spectra is seen, typically with an irregular wavelength-dependent undulation.	Correlated noise from low-level detector thermal instabilities, seen as vertical banding in 2-D count rate images, particularly in exposures of the NRS2 detector. While the IRS2 readout modes reduces this effect, it is not completely eliminated.	Run the NSClean script developed by B. Rauscher on count rate images, using an appropriate mask.	There will be an eventual inclusion of a cleaning algorithm in the Science Calibration Pipeline, pending further testing (timeline uncertain, but possibly in the updated operations pipeline planned for installation in November 2023).
There is missing flux in the "x1d" spectrum of point sources.	Astrometric or pointing uncertainty may cause the default extraction aperture to miss the intended target or be off-center.	Option 1: Rerun the extract_1d pipeline step in calwebb_spec3 at specified coordinates. Option 2: Install the latest release of the jwst package and then run the Science Calibration Pipeline on the affected dataset. Starting in jwst 1.11.0, the extract_1d step supports setting ifu_autocen = True.	An IFU astrometric solution was updated in July 2023, but small pointing offsets may remain. Reprocessing of affected data typically takes 2–4 weeks after the update.
Flux is not conserved in 1-D-extracted spectra of point sources when using a different output spaxel sampling.	The cube_build algorithm was designed to conserve flux assuming input units of surface brightness. However, the NIRSpec point source calibration produces units of flux density, which is not compatible.	If using data processed with the current operations pipeline build, do the following: change the header keyword `SRCTYAPT` in the primary extension of each "rate.fits" file to `EXTENDED` re-run the calwebb_spec2 pipeline to apply the surface brightness calibration change the header keyword `SRCTYPE` in the SCI extension header of the new "s3d" products to `POINT` re-run the extract_1d step Otherwise, install the release candidate for the coming operations pipeline (jwst 1.11.3 and onward) and re-run calwebb_spec2.	The point source calibration for IFU data will be changed to surface brightness units, and 1-D spectra converted back to flux density. STSCI will reprocess affected data products with an updated operations pipeline, planned for installation on 24 Aug 2023. Reprocessing of affected data typically takes 2–4 weeks after the update.
Spectra extracted from single spaxels on/near point sources show a sinusoidal modulation.	NIRSpec is undersampled, and distortion causes spectral traces (particularly for the gratings) to be curved on the detector. Resampling the raw data to a rectified data cube introduces artifacts if extracting spectra on scales smaller than the PSF. See detailed discussion by Law et al. 2023.	Extract spectra from larger apertures comparable in width to the PSF. Combining dithers/nods also reduces, but does not eliminate, the effect.	A mitigation plan is under investigation.
The centroid of point sources appears to drift slightly as a function of wavelength.	The cause is unclear, but likely related to the filter transmission. The drift is typically of order 20 milliarcsec over the wavelength range of a given disperser.	None.	None at this time. Any action regarding pipeline or post-processing mitigation await an investigation on the root cause, which has just begun.

NIRSpec multiobject spectroscopy (MOS)

Symptoms	Cause	Workaround	Mitigation Plan
Significant outliers appear in the 2-D and 1-D extracted spectra.	The outlier_detection step generally has a hard time finding many outliers. Step parameters need to be tuned to the noise characteristics of each data set, although in many cases outliers are still missed.	For outlier improvement, rerun the outlier_detection step in calwebb_spec3 with different values of the snr parameter.	Investigate the algorithmic changes such as the equivalent of the new IFU outlier rejection methodology, possibly for inclusion into the next operations pipeline build scheduled for installation in operations in November 2023.
Level 3 extracted spectra have errors that are all "NaN".	The flat field reference file uncertainties are currently zero. The resultant flat error component calculated from these is "NaN", which propagates to the combined error as "NaN".	Recalculate the combined error using only the read noise and photon noise components. See this worked example for more on how to do this.	Reprocess data with an enhanced calibration reference file (flat) in CRDS. An update is planned for the end of August 2023. Reprocessing of old data typically takes 2–4 weeks after the update.
Spectra extracted from slitlets consisting of more than 3 shutters exhibit unexpected wavelength-dependent flux discrepancies.	A bug in the pathloss step prevents the application of the correction in longer slitlets, for either point or extended sources.	Edit the MSA metafile to break up slitlets longer than 3 shutters into smaller slitlets. A link to a description of how to do this will be added here by 31 Aug 2023 .	The science calibration pipeline code must be modified to enable application of the current set of reference files to any slitlet length. The timeline for this change is uncertain, possibly for operations pipeline build 10 (scheduled for installation in operations in November 2023).
Negative and/or surplus flux seen in extracted 1-D spectra, typically with an irregular wavelength-dependent undulation.	Correlated noise from low level detector thermal instabilities, seen as vertical banding in 2-D count rate images, particularly in exposures of the NRS2 detector. While the "IRS2" readout modes reduce this effect, it is not completely eliminated.	No workaround is available yet. It may be possible to improve the noise levels using the NSClean script developed by B. Rauscher on count rate images, using an appropriate mask. However, this has not yet been tested/verified by the team.	Eventual inclusion of the cleaning algorithm in the pipeline is planned, pending further testing. The timeline is uncertain, possibly for operations pipeline build 10 (scheduled for installation in operations in November 2023).
Unexpected variations are seen in continuum or line fluxes as a function of field position.	The flux calibration for MOS is currently based on spectrophotometric observations at a single point in the MOS field of view. The flat field calibration accounts for spatial variations from the MSA aperture plane, through the grating wheel, and at the detector, but not in the OTE or filter wheel. Large variations (>~ 5%) are not expected, but this needs to be confirmed.	None.	Spectrophotometric observations at multiple field points have been obtained and are being analyzed. Updates to the flux calibration, if needed, are planned in fall 2023.

NIRSpec bright object time series (BOTS)

Symptoms	Cause	Workaround	Mitigation Plan
Large number of outlier pixels are identified in the jump step, which leads to lower SNR of the "rateints" products (slope images) per integration.	The jump step default threshold, in combination with the current reference file uncertainties, results in too many pixels being flagged as cosmic rays.	Rerun the jump step with the a rejection_threshold value > 10 (default is 4.0).	A mitigation plan is under development.
There is vertical striping across the NIRSpec BOTS rate images (2-D spectra), which appears as negative and/or surplus flux in extracted 1-D spectra (typically with an irregular wavelength-dependent undulation).	Correlated noise from low level detector thermal instabilities (1/f noise) is seen as vertical banding in 2-D count rate images, particularly in exposures of the NRS2 detector.	Run NSClean script developed by B. Rauscher on count rate images, using an appropriate mask. Several additional community tools that mitigate 1/f noise are also available.	Eventual inclusion of a cleaning algorithm in the pipeline is planned, pending further testing. The timeline is uncertain, possibly for operations pipeline build 10 (scheduled for installation in operations in November 2023).
The extracted 1-D spectrum ("x1d" product) has spurious absorption features, typically one pixel wide.	Pixels marked as "DO_NOT_USE" in the reference data are not included in 1-D extracted spectrum.	Use new science calibration pipeline software (jwst 1.11.0 onwards) to estimate the value for each "DO_NOT_USE" pixel from neighboring 2-D profiles before extracting 1-D spectrum. This is disabled by default, and has not yet been tested; systematic errors may be introduced in TSO data. Another workaround would be to remove "DO_NOT_USE" DQ flags on affected pixels. See this demo on how to do it, based on NIRISS SOSS data. (JP-3005)	Test that the pixel_replace algorithm works well for NIRSpec fixed slit data. If it does, enable the pixel_replace step by default in the parameter reference file update (estimated for September 2023). Users can enable this step by following commands in this file.
The shape of spectra taken with the SUB512, SUB512S, or SUB32 subarrays exhibits unexpected features and wavelength-dependent flux discrepancies of 10% or more. This causes time-series observations (TSO) light curve scatter to increase by orders of magnitude larger than expected.	Some subarrays have no reference pixels, which means bias drifts are not corrected.	Rerun calwebb_detector 1 starting from the "_uncal" files. Before the linearity step, identify non-iluminated pixels in the detector and estimate their median value; this will provide an estimate of the detector pedestal level on each group. Remove this value from each group, and then run the remaining calwebb_detector1 steps.	Modify the reference pixel correction to use unilluminated pixels in the columns at the left and right edges of these subarrays. This will be implemented in the operations pipeline planned for 24 Aug 2023.

Notable updates	19 Aug 2023 Updated to record all the known issues affecting this build.
Originally published	24 May 2023

JWST Operations Pipeline Build 9.2 Release Notes