Known Issues with JWST Data Products

Issues that affect (or recently affected) JWST data products available from the MAST Archive are covered in this article.

On this page

See also: JWST Calibration Pipeline Caveats

The tables below are an aggregation of known issues in the pipeline for several instrument modes and features. Each table concisely describes issues that affect data products in the MAST Archive. Some of these tables are also reproduced in their corresponding pipeline caveats articles. For each issue, the table describes:

  • symptoms of the issue from a user perspective,
  • cause(s) of the issue,
  • workaround(s) to fix the issue for a particular dataset, and
  • the long-term plan to fix the issue in data products served by MAST.

Issues shaded in blue have been mitigated; please see the "mitigation plan" column for more information.

Information about planned improvements to the calibration reference data can be found in this table

This page is as complete as possible to provide a single place to search for issues, but this means the page is quite long. 

Words in bold are GUI menus/
panels or data software packages; 
bold italics are buttons in GUI
tools or package parameters.

Some issues can be fixed by reprocessing data on your computer, using the latest JWST Science Calibration Pipeline (aka jwst) software release and/or context (PMAP) in the Calibration Reference Data System (CRDS). It takes a few weeks to integrate a new Science Calibration Pipeline into a full Operations Pipeline software build, which includes testing, fixing subsystem interface issues, and finally installing the software in operations. After that, fixes in the new Operations Pipeline software and/or reference data will be reflected in new (or replaced) products in MAST. Please refer to Table 1 in JWST Operations Pipeline Build Information that indicates when that version of the jwst software was released in operations and which context in CRDS they were tested with. 

Please direct all questions and comments about this page to the JWST Help Desk. Your feedback will influence the priority of needed upgrades or fixes, and help make this page better for everyone. Also, please notify us, via the helpdesk, if you encounter problems that are not covered in this article. 



General issues

See also: JWST General Calibration Pipeline Caveats

SymptomsCauseWorkaroundMitigation Plan
GI02: 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. Also see issue NC-I01. 

Updated issue

Improve accuracy of the guide star catalog. This is a long-term project. (Updated "Workaround" to mention NC-I01)

GI03: 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.

There is no workaround that works for all science cases.

The correction is not recommended for NIRISS SOSS or AMI,  MIRI coronagraphic data, and data with 1–4 groups.

For general science cases, users can re-run the pipeline calwebb_detector1 with the jump step parameters set:
   find_showers = True  (For MIRI)
   expand_large_events = True (for NIR instruments)


Updated issue

See the section titled "Large Events (Snowballs and Showers)" in the JumpStep documentation, and  the Snowballs and Shower Artifacts article, for information on modifying the parameters for your science case and observations.

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.

GI04: NIR instruments only: There is large-scale striping (horizontal for NIRCam, vertical for NIRISS and NIRSpec) across the field and not fully removed in the reference pixel subtraction. Note that IRS2 readout for NIRSpec substantially mitigates this behavior.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. 

Updated issue

A mitigation plan is being developed.


GI05: Stage 3 processing of large imaging mosaics can take a longer than the normal amount of time to process.Unknown.

None.

Created issue

Updates are planned for the methods used in the tweakreg and resample steps to make them more efficient.

GI06: World Coordinate System (WCS) in pure parallel data products is incorrect by amounts that are different for every dither position.In pure parallel data, the values of the WCS-related header keywords are currently derived using a “coarse” algorithm, because the guide star information is currently not being transferred from the headers of prime exposures to those of the associated pure parallel exposures. Typical errors are of order 0.1 arcsec. While these errors can be benign for imaging data (since the spatial offsets can be corrected in the tweakreg step of the calwebb_image3 pipeline), they are problematic for pure parallel WFSS-mode grism exposures, because the placement of spectral extraction boxes by the calwebb_spec2 pipeline relies on the WCS information in the data headers.

The WCS in pure parallel data products can be corrected by running a script in the JWST caveat examples github repository

Created issue

Over the longer term, this issue will be addressed in front-end processing during visit preparation. An implementation date is to be determined.

GI01: 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 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.

Updated Operations Pipeline

Proper motion was applied correctly. STScI reprocessed affected data products with an updated Operations Pipeline installed on August 24, 2023. Reprocessing of affected data typically takes 2-4 weeks after the update.

General issues for time-series observations

See also: JWST Time Series Observations Pipeline Caveats

SymptomsCauseWorkaroundMitigation Plan

GI-TS01: 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".

Updated Operations Pipeline

A change to the JWST Science Data Processing subsystem to correctly compute the barycentric and heliocentric time, and JWST barycentric position keywords was part of the updated Operations Pipeline, installed on August 24, 2023. STScI reprocessed affected data products, which  typically takes 2–4 weeks after the update.



MIRI

MIRI low resolution spectroscopy (LRS)

See also: JWST MIRI LRS Pipeline Caveats

SymptomsCauseWorkaroundMitigation Plan

MR-LRS03: 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.

Updated issue

The jump step algorithm and default parameters are continually being examined and optimized; improvements are expected in future builds (spring 2024 and beyond). The issue likely cannot be entirely eliminated as it differs greatly between observations (and indeed many are not affected).

MR-LRS04: 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.

Created issue

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.

MR-LRS05: The "ERR" extension in "rate" data products (and other error estimates downstream) is incorrect.Error values are estimated incorrectly by the pipeline.

Bootstrap uncertainty from science spectra.

Created issue

The root cause of incorrect error estimates in the pipeline is being investigated.

MR-LRS06: Target acquisition images taken with FASTGRPAVG readout patterns are incorrectly calibrated.The calibration pipeline does not compute the exposure time for these readout modes when fitting a slope to the uncalibrated data.

The verification images are calibrated correctly; if additional photometry is required, the MIRI team recommends the use these images.
 
For the TA images, count rates can be divided by the FASTGRPAVG frame multiplier to obtain the correct count rate. 

Created issue

The issue will be fixed in the calibration pipeline code in early 2024. 
 
Note: this affects all FASTGRPAVG TA images taken for MIRI.

MR-LRS02: 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.


Updated Operations Pipeline

The new pixel_replace step was implemented in the Operations Pipeline, installed on August 24, 2023. STScI reprocessed affected data products, which typically takes 2–4 weeks after the update.

MR-LRS01: 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

Updated Operations Pipeline 

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)

See also JWST MIRI MRS Pipeline Caveats

SymptomsCauseWorkaroundMitigation Plan
MR-MRS03: 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 notebook is available to to apply a correction for the MRS spectral leak

Updated issue

A correction step will be included in the pipeline in the future for 1-D spectra extracted from point sources. Update: added link to notebook in "Workaround" column.

MR-MRS04: 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.

Created issue

None; additional non-default corrections are science case specific. Calibrations programs will explore possible future mitigations.

MR-MRS05: 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.

Created issue

This is still under investigation; some science cases may permit scene modeling to mitigate impact.

MR-MRS06: 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.

Created issue

The root cause of incorrect error estimates in the pipeline is being investigated.

MR-MRS01: 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.

Updated Operations Pipeline

DAOStarFinder is used to locate point sources in the image constructed from the collapsed 3-D cube. Proper motion is now applied correctly. STScI reprocessed affected data products with an updated Operations Pipeline that was installed on August 24, 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.

MR-MRS02: 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.

For non-TSO data, 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 .

Updated Operations Pipeline

Only for non-TSO data: new time-dependent throughput corrections were applied. STScI reprocessed affected data products with an updated Operations Pipeline that was installed on August 24, 2023. (Reprocessing of affected data typically takes 2–4 weeks after the update.) See this JWST Observer new item for more details.

MR-MRS07: 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.

Resolved

Marked as "resolved" because this is a data analysis issue, not a pipeline issue. STScI will work on documentation to provide some recommendations.

MR-MRS08: Channel 4B field of view is squashed by about 8% relative to the 4A and 4C fields. This is noticeable in observations of sources with fixed limbs comparable in size to the FOV (e.g., giant planets).
Channel 4B distortion solution was incorrect due to limitations in the astrometric calibration.

New 4B distortion solution has been derived that fixes the issue and will be available shortly in CRDS.

Updated Operations Pipeline

New reference files and jwst_1125.pmap context were delivered to Operations Pipeline; reprocessing of affected data typically takes 2–4 weeks after the update.

MIRI imaging

See also: JWST Imaging Pipeline Caveats

SymptomsCauseWorkaroundMitigation Plan

MR-I02: 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.

Created issue

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. 

MR-I03: The photon count rate and derived flux are lower than predicted at wavelengths between 12.8 and 25.5 µm, with the effect increasing with wavelength (see JWST Observer).

The MIRI imager sensitivity at long wavelengths is decreasing with time. The root cause of this issue is still under investigation. Regular monitoring observations are being taken with the MIRI imager to measure the photometric response and to characterize the temporal trend.

New "photom" files were delivered on September 15, 2023 and there are 2 possible workarounds:

  1. Users can divide the values in their data by the current PHOTMJSYR value saved in the image header and then multiply by the calibration factor given by the new "photom" reference file closer in time to the user's observation date; or
  2. Users can reprocess their data with the JWST pipeline using CRDS "jwst_1130.pmap" (or later) with the new "photom" reference files.

Updated issue

In the short term, new "photom" reference files tailored for specific epochs have been provided in CRDS.

STScI will update the pipeline to include a new time-dependent throughput correction, expected to occur in February 2024.

Both mitigation strategies will require a reprocessing of the data.

MR-I01: 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.

Created issue

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. 


MIRI coronagraphic imaging

See also: JWST Coronagraphic Pipeline Caveats 

SymptomsCauseWorkaroundMitigation Plan

MR-CI02: 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.

The public "Coronagraphy_ExampleNB" repository contains a suite of 6 notebooks that will guide the user through reprocessing coronagraphic data through all steps of the pipeline, as well as for customizing parameters at each step. Users will find notebooks suitable for processing "uncal" files retrieved from MAST through stage 2 to yield background-subtracted photometrically-calibrated data products suitable for use in PSF subtraction. Older notebooks are still available in the "old_pipeline_demos" subfolder.

Updated issue

The MIRI team is always considering the scope of what data products the calwebb_coron3 pipeline stage should provide.

MR-CI03: 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.

Created issue

None at this time.

MR-CI04: 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.

Created issue

Mitigation strategies are under investigation.

MR-CI01: 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.

Updated Operations Pipeline

Flux calibration "photom" reference files were updated in October. STScI will reprocess affected data products with updated calibration reference data. Reprocessing of affected data typically takes 2–4 weeks after the update.

MIRI time-series observations

See also: JWST Time Series Observations Pipeline CaveatsMIRI Time Series Observations Pipeline Caveats

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.

SymptomsCauseWorkaroundMitigation Plan
MR-TS01: 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. 

Updated issue

Testing is currently underway on an algorithm that fits and removes the 390 Hz noise signal. This algorithm should be in the Operations Pipeline in early 2024. 

MR-TS02: 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. 

Created issue

As soon as the cause of this problem is understood, the MIRI team will make the required changes to mitigate it. 

MR-TS03: The photon count rate and derived flux for MRS TSO data, 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.

There is no work around at the moment.

 

Updated Operations Pipeline

The science calibration pipeline was modified, on December 5, 2023, to apply the time-dependent throughput correction for TSO data. STScI will reprocess affected data products with the updated Operations Pipeline; reprocessing of affected data typically takes 2–4 weeks after the update. 



NIRCam

NIRCam general issues

SymptomsCauseWorkaroundMitigation Plan
NC-G01: 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 groupBright objects may saturate by the end of a groupbut 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 frame0 is currently only used as an extra data point for saturated ramps.

Updated issue

The NIRCam team will evaluate whether the frame0 correction should be turned on as the default for ramps affected by saturation; however, the investigation is still in progress due to higher priority issues.

NIRCam time series (grism and imaging)

See also: NIRCam Time Series Observations Pipeline Caveats

SymptomsCauseWorkaroundMitigation Plan
NC-TS02: 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.

Updated issue

Default parameters are continually being examined and optimized. Investigation of the optimal extraction height is underway. 

NC-TS03: 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).

Updated issue

The jump step algorithm and default parameters are continually being examined and optimized; improvements are expected in future builds (winter 2023 and beyond).

NC-TS01: 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.

Updated Operations Pipeline

New wavelength reference data was delivered and reprocessing with the latest Science Calibration Pipeline completed in September 2023. 

NIRCam imaging

See also: JWST Imaging Pipeline Caveats

SymptomsCauseWorkaroundMitigation Plan
NC-I01: Misalignment of mosaic tiles in some of the stage 3 data productsThis 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.

Updated issue

Reprocess data with an enhanced calibration reference file (distortion) in CRDS, which may improve alignment in some cases. An update is planned for early 2024. Reprocessing of old data typically takes 24 weeks after the update.


NC-I02: 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.

Created issue

Mitigation is not yet scheduled due to higher priority issues.

NC-I03: 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

Created issue

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.

NC-I04: 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).

Updated issue

The jump step algorithm and default parameters are continually being examined and optimized; improvements are expected in future builds (winter 2023 and beyond).

NC-I05: Running tweakreg on exposures with multiple detectors or modules results in misaligned mosaic tiles and offset WCSs.

Tweakreg groups together data for all detectors for a given exposure using information in the Science Instrument Aperture File (SIAF) to determine positions of the detectors relative to one another. It then finds and matches sources working one exposure (but multiple detectors) at a time.

In some cases, tweakreg does not do a good job of aligning exposures for all detectors with the sources in the field due to uncertainties in the locations of the detectors within the focal plane at the level of a few pixels. The uncertainty is largest between the A and B modules, and smaller between the detectors within a given module.

Use JHAT (which does not do the detector grouping) rather than tweakreg, or call tweakreg separately for each module and align to GAIA, so that the two modules are both shifted to the appropriate WCS.

Another option is to change the metadata in the files such that each detector or module has its own “exposure number”, since that is what tweakreg uses to find and group detectors.

Created issue

Updates to the NIRCam detector positions in SIAF coming this winter should reduce the uncertainties down to a small fraction of a pixel.

More optimal tweakreg step parameters for the Operations Pipeline are still under investigation.

NIRCam coronagraphic imaging

See also: JWST Coronagraphic Pipeline Caveats

SymptomsCauseWorkaroundMitigation Plan
NC-CI01: 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.

Created issue

Mitigation is not yet scheduled because the data are satisfactory without dark subtraction. 

NC-CI02: 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. 

Updated issue

Implement something similar to spaceKLIP for calwebb_coron3. Timeline TBD.

NC-CI03: Absolute flux calibration is incorrect.

The wavelength dependent throughput of the bar occulters are currently a copy of throughputs of the round occulters, despite a slight difference of about 2% due to the different Lyot stops. In addition, flux calibration for all masks is still from pre-flight expectations.

Note: previous text here mistakenly said that the COM (coronagraph optical mount) substrate throughput was not taken into account. That is not the case. 

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.

Updated issue

Data was reprocessed with an enhanced calibration reference file (photom) in CRDS. An update made on October 31, 2023 takes the full coronagraphic throughput into account using in-flight data. Reprocessing of old data typically takes 2–4 weeks after the update.

NIRCam wide field slitless spectroscopy (WFSS)

See also: JWST Wide Field Slitless Spectroscopy Pipeline Caveats

SymptomsCauseWorkaroundMitigation Plan
NC-WFSS01: 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.

Updated issue

Implement the wfss_contam step in calwebb_spec2. Work on this is ongoing and is planned for completion in 2024. 

NC-WFSS02: 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.

Created issue

A mitigation plan is under development.

NC-WFSS03: 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.

Updated Operations Pipeline

Several efficiency improvements have been made at various stages of processing. STScI will continue monitoring issues that get reported.



NIRISS

NIRISS aperture masking interferometry (AMI)

See also: JWST Aperture Masking Interferometry Pipeline Caveats

SymptomsCauseWorkaroundMitigation Plan

NR-AMI01: 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.

Updated issue

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 the Operations Pipeline build planned for installation in early 2024. Reprocessing of affected data typically takes 2–4 weeks

NR-AMI02: 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. 

Updated issue

Apply a new Science Calibration Pipeline step called charge_migration within the calwebb_detector1 stage. STScI will reprocess affected data products with an updated Operations Pipeline in 2024 (date TBD). Reprocessing of affected data typically takes 2–4 weeks after the update.

NIRISS single object slitless spectroscopy (SOSS)

See also: JWST Time Series Observations Pipeline CaveatsNIRISS Time Series Observations Pipeline Caveats

SymptomsCauseWorkaroundMitigation Plan

NR-SOSS02: 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.

Updated issue

Implementation in the Science Calibration Pipeline is under development.

NR-SOSS03: 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.

Use the PASTASOSS package to predict the wavelength solution for the visit.

Updated issue

Implementation in the Science Calibration Pipeline is under development.

NR-SOSS05: 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).

Created issue

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.

NR-SOSS06: 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. 

Created issue

A mitigation plan is under development.

NR-SOSS07: 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).

Created issue

A mitigation plan is under development.

NR-SOSS08: The pipeline throws an error when trying to extract a SOSS spectrum with the GR700XD/F277W combination.

The pipeline currently does not support this grism/filter combination.

There is currently not a workaround.

Created issue

Updates to the pipeline code to support the GR700XD/F277W combination are under development.

NR-SOSS01: 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".  - deprecated

Updated Operations Pipeline

New reference files were delivered to CRDS which no longer erroneously flag good pixels as "DO_NOT_USE". The new linearity and saturation reference files are available in CRDS contexts "jwst_1152.pmap" and later. The new subarray superbias reference files are available in CRDS contexts "jwst_1170.pmap" and later.

Affected data products will be reprocessed; reprocessing of affected data typically takes 2–4 weeks.

NR-SOSS04: 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.

Updated Operations Pipeline

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. This was implemented in the NIRISS SOSS template in APT 2023.5 (release date: August 24, 2023). 

NIRISS wide field slitless spectroscopy (WFSS)

See also: JWST Wide Field Slitless Spectroscopy Pipeline Caveats

SymptomsCauseWorkaroundMitigation Plan

NR-WFSS01: 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.

Updated issue

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.

NR-WFSS02: 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.

Created issue

Apply new Science Calibration Pipeline step charge_migration within the calwebb_detector1 stage. STScI will reprocess affected data products with an updated Operations Pipeline, planned for installation in December 2023. Reprocessing of affected data typically takes 2–4 weeks after the update. 

NIRISS Imaging

See also: JWST Imaging Pipeline Caveats

SymptomsCauseWorkaroundMitigation Plan

NR-I01: 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.

Updated Operations Pipeline

Applied the new Science Calibration Pipeline step undersampling_correction in the calwebb_detector1 stage. STScI is reprocessing affected data products with an updated Operations pipeline, installed on December 5, 2023. Reprocessing of affected data typically takes 2–4 weeks after the update. 



NIRSpec

NIRSpec general issues

SymptomsCauseWorkaroundMitigation Plan
NS-G03: 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.

Workaround: 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 by running the pixel_replace step. This is disabled by default. Testing has shown improvements in many cases, but degradation in data quality has also been seen in certain circumstances; users should exercise caution if they choose to run the step. Instructions will be added soon.

Updated issue

The team is evaluating options for the pixel_replace step, as the current algorithm produces inconsistent results. 

NS-G05: 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.

Updated issue

Investigation of a fix is underway, possibly for implementation in February 2024.

NS-G06: A pattern of alternating brighter/darker pixel rows over part or all of a detector image.An effect sometimes referred to as alternating column noise (ACN; note that pixel rows in the science data actually represent columns in the detector frame of reference, as the data are rotated to put the dispersion direction horizontally). This is due to the two amplifiers (one for odd and one for even columns) in an output sometimes having slightly different offsets because of drift or a cosmic ray event.

None.

Created issue

The team will investigate why the calwebb_detector1  refpix.odd_even_columns correction does not seem to yield any improvement when this effect is seen.

NS-G01: 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.

Updated Operations Pipeline

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 . Reprocessing of affected data typically takes 2–4 weeks after the update.

NS-G02: 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 , 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.

Updated Operations Pipeline

Updates to spacecraft pointing keywords, which should improve the spectral trace WCS, have been available in the Operations Pipeline since on 24 August 2023. Reprocessing of affected data typically takes 2–4 weeks after the update.

An alternate method of extraction aperture centering for MOS and FS modes was implemented, based on the planned slit position of each source, therefore avoiding sky coordinates altogether. This new algorithm was installed in the Operations Pipeline on December 5, 2023.

NS-G04: 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.

Updated Operations Pipeline

A bug fix was implemented and made available in the Operations Pipeline installed on December 5, 2023. Reprocessing of affected data typically takes 2–4 weeks after the update.

NIRSpec fixed slit (FS) spectroscopy

SymptomsCauseWorkaroundMitigation Plan
NS-FS05: 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, is available.

For outlier improvement, rerun the outlier_detection step in calwebb_spec3 with different values of the snr parameter.

Updated issue

Reference files were updated in October 2023. Reprocessing of affected data typically takes 2–4 weeks after the update.

In the longer term, updated algorithms are under investigation, possibly for inclusion in the Operations Pipeline update planned for February 2024.

NS-FS06: 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.

Updated issue, new due date for reference file

Reprocess data with an enhanced calibration reference file (flat) in CRDS. An update is planned for early 2024. Reprocessing of old data typically takes 2–4 weeks after the update.

NS-FS07: Lower than expected S/N and/or larger than expected discrepancies between dither positions.

Use of the default “inverse variance weighting” using read noise variance in the resample_spec step (resample_spec.weight_type = ivm) does not appear to be appropriate for high signal-to-noise data

When running calwebb_spec2, set resample_spec.weight_type = exptime, and when running calwebb_spec3, set spec3.weight_type = exptime.

Created issue

Investigate whether to change the default weighting to exptime using a modified parameter reference file, and/or investigate other algorithms that handle the high S/N limit more gracefully. Also consider extraction and image combination algorithms that don’t require resampling the 2-D data.

NS-FS08: Lower than expected flux and/or flux inconsistencies between closely spaced dither positions that may result in issues with outlier rejection. In extreme cases this may result in an ~20% error in the absolute flux calibration, although more commonly, the effect is at the ~5% level.

When closely spaced nod positions are used as background members for each other, some source flux is subtracted from the extraction region along with the background, but the fraction of source flux subtracted varies with the dither separation of each background member. Currently the pipeline does not account for this in the flux calibration.

For sufficiently bright sources, consider omitting background members in the level 2 association, and/or find separate background exposures from other observations.  Otherwise, when using 5 primary dither points, especially in the S1600A1, edit level 2 association to remove background members separated by less than about 0.375” from the science member in that association. Note that the pipeline already knows not to use sub-pixel spatial or dispersion direction dithers as background members for other exposures at the same primary dither position.

Created issue

Modify default pipeline rules to enforce a minimum separation for background members used in calwebb_spec2. In the longer run, investigate adding a step to calwebb_spec2 to estimate the flux loss due to subtraction of other dithers and correct the flux in the "cal" files to account for this. Once fixes are in place to minimize these effects, reconsider all F-flat reference files for FS, (and possibly also MOS), to allow improved absolute and relative flux accuracy.

NS-FS09: Artificial ~10% deep absorption feature between about 0.97 and 1.02 µm in NIRSpec G140M/F070LP spectra when observed through the S1600A1 aperture.

The lamp flat field images, which are used to create the "sflat" reference files, for the S1600A1 slit are contaminated by the zero-order image, which causes a large positive feature in the "sflat" correction image in the lower part of the aperture.

Use only the spectra extracted from the upper dither positions in the affected wavelength range.

Created issue

Investigate feasibility of editing the "sflat" reference file to remove the contamination, and/or flagging affected pixels as DO_NOT_USE.

NS-FS01: 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.

Updated Operations Pipeline

The reference pixel correction was modified to use unilluminated pixels in the columns at the left and right edges of these subarrays. STScI reprocessed the affected data products with an updated Operations Pipeline that was installed on August 24, 2023. (Reprocessing of affected data typically takes 2–4 weeks after the update.)

NS-FS02: 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.

Updated Operations Pipeline

The pathloss correction was applied only once. STScI reprocessed affected data products with an updated Operations Pipeline that was installed on August 24, 2023. (Reprocessing of affected data typically takes 2–4 weeks after the update.)

NS-FS03: 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.

updated Operations Pipeline

Enhanced the association logic and  changed the SOURCEID numbering scheme. STScI is reprocessing affected data products in the Operations Pipeline that was updated in December 2023. Reprocessing of affected data typically takes 2–4 weeks after the update.

NS-FS04: 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.

Issue resolved

Spectrophotometric observations with this configuration were obtained in August, and updated F-flat reference file were delivered on August 24, 2023.

NIRSpec integral field unit (IFU) spectroscopy

See also: JWST NIRSpec IFU Pipeline Caveats

SymptomsCauseWorkaroundMitigation Plan
NS-IFU03: 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. (Rauscher, B. 2023, arXiv:2306.03250)

notebook demonstrating the use of the NSClean algorithm is now available. 

Updated issue

A workaround notebook is available.

There will be an eventual inclusion of a cleaning algorithm in the Science Calibration Pipeline, pending further testing, possibly in February 2024).

NS-IFU04: 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.

Created issue

An IFU astrometric solution was updated in July 2023, but small pointing offsets may remain. Reprocessing of affected data typically takes 24 weeks after the update.

NS-IFU05: 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.

Created issue

A mitigation plan is under investigation.

NS-IFU06: 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.

Updated issue

None at this time. Any action regarding pipeline or post-processing mitigation await an investigation on the root cause, which has just begun.

NS-IFU01: 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 .

Updated Operations Pipeline

The outlier detection algorithm was updated. STScI reprocessed affected data products with an updated Operations Pipeline that was installed on August 24, 20203. (Reprocessing of affected data typically takes 2–4 weeks after the update.)


NS-IFU02: 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:

  1. change the header keyword SRCTYAPT in the primary extension of each "rate.fits" file to EXTENDED
  2. re-run the calwebb_spec2 pipeline to apply the surface brightness calibration
  3. change the header keyword SRCTYPE in the "SCI" extension header of the new "s3d" products to POINT
  4. 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.

Updated Operations Pipeline

Point source calibration for IFU data was changed to surface brightness units, and 1-D spectra converted back to flux density. STScI reprocessed affected data products with an updated Operations Pipeline that was installed on August 24, 2023. (Reprocessing of affected data typically takes 2–4 weeks after the update.)

NIRSpec multi-object spectroscopy (MOS) 

See also: JWST NIRSpec MOS Pipeline Caveats

SymptomsCauseWorkaroundMitigation Plan
NS-MOS01: 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.

Updated issue 

Updated algorithms are under investigation, possibly for inclusion in the Science Calibration Pipeline in February 2024.

NS-MOS02: 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.

Updated issue, new due date for reference file

Reprocess data with an enhanced calibration reference file (flat) in CRDS. An update is planned for early 2024. Reprocessing of old data typically takes 2–4 weeks after the update.

NS-MOS03: 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 .

Updated issue

An update to the science calibration pipeline code to enable application of the current set of reference files to any slitlet length is expected to be installed in the Operations Pipeline in February 2024.

NS-MOS04: 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.

A notebook demonstrating the use of the NSClean algorithm is now available.

Updated issue

A workaround notebook is available.

Eventual inclusion of the cleaning algorithm in the pipeline is planned, pending further testing, possibly in February 2024.

NS-MOS05: 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.

Created issue

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.

NS-MOS06: Discontinuities in the extracted level 2 spectra and "s2d" images at the upper and/or lower nod positions. These may be as large as ~40%. The effects in level 3 products appear to be much smaller and/or absent.

Errors in rectification when producing the"s2d" image is due to missing WCS information at the edges of CAL image extensions.

Edit the MSA metafile to pretend that an extra shutter at the top and bottom of the slitlet was open. Note that this conflicts with the workaround suggested for NS-MOS03.

Created issue

Modify the pipeline code to expand the size of the "cal" file cutout and the region with a valid WCS to be large enough to avoid resampling artifacts near the edges. A fix is tentatively planned for installation in operations in early 2024.

NS-MOS07: Lower than expected S/N and/or larger than expected discrepancies between dither positions.

Use of the default “inverse variance weighting” using read noise variance in the resample_spec step (resample_spec.weight_type = ivm) does not appear to be appropriate for high signal-to-noise data

When running calwebb_spec2, set resample_spec.weight_type = exptime, and when running calwebb_spec3, set spec3.weight_type = exptime.

Created issue

Investigate whether to change the default weighting to exptime using a modified parameter reference file, and/or investigate other algorithms that handle the high S/N limit more gracefully. Also consider extraction and image combination algorithms that don’t require resampling the 2-D data.

NIRSpec bright object time series  (BOTS) 

See also: JWST Time Series Observations Pipeline CaveatsNIRSpec Time Series Observations Pipeline Caveats

SymptomsCauseWorkaroundMitigation Plan
NS-BOTS02: 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).

Updated issue

A mitigation plan is under development.

NS-BOTS03: 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.

Updated issue

Eventual inclusion of a cleaning algorithm in the pipeline is planned, pending further testing, possibly in February 2024.

NS-BOTS04: 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. 

Updated issue

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.

NS-BOTS05: Artificial ~10% deep absorption feature between about 0.97 and 1.02 µm in NIRSpec G140M/F070LP spectra when observed through the S1600A1 aperture.

The lamp flat field images, which are used to create the "sflat" reference files, for the S1600A1 slit are contaminated by the zero-order image, which causes a large positive feature in the "sflat" correction image in the lower part of the aperture.

Use only the spectra extracted from the upper dither positions in the affected wavelength range.

Created issue

Investigate feasibility of editing the "sflat" reference file to remove the contamination, and/or flagging affected pixels as DO_NOT_USE.

NS-BOTS01: 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. 

Updated Operations Pipeline

The reference pixel correction was modified to use unilluminated pixels in the columns at the left and right edges of these subarrays. This was implemented in the Operations Pipeline on August 24, 2023.




Latest updates
  •  
    • General issues
      • New issue: "World Coordinate System (WCS) in pure parallel data products is incorrect by amounts that are different for every dither position." (GI06)


  •   
    • NIRISS single object slitless spectroscopy (SOSS)

      • Updated: "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." (NR-SOSS01) - updated Operations Pipeline


  •  
    • Miri coronagraphic imaging
      • Updated: "Users will want to perform their own PSF subtraction with the data products." (MR-CI02) - updated workaround


  •  
    • General issues
      • Updated: "NIR instruments only: There is large-scale striping (horizontal for NIRCam, vertical for NIRISS and NIRSpec) across the field and not fully removed in the reference pixel subtraction. Note that IRS2 readout for NIRSpec substantially mitigates this behavior." (GI04) - updated symptoms and workaround columns
      • New issue: "Stage 3 processing of large imaging mosaics can take a longer than the normal amount of time to process." (GI05)
    • MIRI low resolution spectroscopy (LRS)

      • Updated: "Spectra of bright sources can experience data dropouts at wavelengths where they are brightest (in the "x1d" files)...." (MR-LRS03) - updated mitigation plan
    • MIRI time-series observations

      • Updated: "The photon count rate and derived flux for MRS TSO data, is lower than predicted at long wavelengths, with maximum deficit roughly a factor of 2 at 28 µm." (MR-TS03) - updated Operations Pipeline
    • Miri imaging
      • Updated: "The photon count rate and derived flux are lower than predicted at wavelengths between 12.8 and 25.5 µm, with the effect increasing with wavelength." (MR-I03) - updated mitigation plan
    • NIRISS aperture masking interferometry (AMI)

      • Updated: "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." (NR-AMI02)  - updated mitigation plan
    • NIRSpec fixed slit (FS) spectroscopy

      • Updated: "Spectra obtained with the SLIT = S200A1 and S200A2 option in APT are not combined to create a single spectrum with continuous wavelength coverage." (NS-FS03) - updated Operations Pipeline
      • Updated: "FS spectra obtained with the G140M grating exhibit flux discrepancies of up to 20%." (NS-FS04) - reference files delivered
    • NIRISS Imaging

      • Updated: "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...." (NR-I01) - updated Operations Pipeline
    • NIRSpec general issues

      • Updated: "No flux or negative flux in FS or MOS extracted 1-D spectrum ('x1d' product), despite obvious flux in 2-D spectrum ('s2d' product)." (NS-G02) - updated Operations Pipeline
      • Updated: "Unexpected flux levels in spectra of sources not centered in a slit." (NS-G04) - updated Operations Pipeline


    • NIRSpec multi-object spectroscopy (MOS) 

      • Updated: "Spectra extracted from slitlets consisting of more than 3 shutters exhibit unexpected wavelength-dependent flux discrepancies." (NS-MOS03) - updated mitigation plan


  •  
    • NIRCam coronagraphic imagingi

      • Updated: "Absolute flux calibration is incorrect." (NC-CI03) - updated mitigation plan
    • NIRISS single object slitless spectroscopy (SOSS)

      • Updated: "The shape of the spectral trace varies from visit to visit for all the NIRISS/SOSS orders...." (NR-SOSS02) - updated mitigation plan
      • Updated: "The wavelength solution varies from visit to visit, appearing to be shifted by a handful of pixels." (NR-SOSS03) - updated workaround and mitigation plan


  •  
    • MIRI low resolution spectroscopy (LRS)

      • New issue: "The "ERR" extension in "rate" data products (and other error estimates downstream) is incorrect." (MR-LRS05)
      • New issue: "Target acquisition images taken with FASTGRPAVG readout patterns are incorrectly calibrated." (MR-LRS06)


  •   
    • NIRCam general issues

      • Updated: "Bright objects in the field are saturated even though the ETC predicted that they would not saturate 'fully.'" (NC-G01) - updated workaround and mitigation plan.
    • NIRCam time series (grism and imaging)

      • Updated: "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...." (NC-TS02) - updated mitigation plan 
      • Updated: "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." (NC-TS03) - updated mitigation plan
    • NIRCam imaging

      • Updated: "An excessive number of pixels are flagged as outliers in some subarray data." (NC-I04) - updated mitigation plan
      • New issue: "Running tweakreg on exposures with multiple detectors or modules results in misaligned mosaic tiles and offset WCSs." (NC-I05) 
    • NIRCam coronagraphic imaging

      • Updated: "Absolute flux calibration is incorrect." (NC-CI03) - updated due date
    • NIRCam wide field slitless spectroscopy (WFSS)

      • Updated: "Adjacent sources are included in extracted spectra." (NC-WFSS01) - updated mitigation plan
      • Updated: "The WFSS pipeline has excessive run times when run locally." (NC-WFSS03) - updated Operations Pipeline


  •  
    • NIRCam wide field slitless spectroscopy (WFSS)

      • Updated: "Adjacent sources are included in extracted spectra." (NC-WFSS01) - still under investigation
    • NIRSpec general issues

      • Updated: "Wavelengths of spectral features does not match expectation in spectra of sources not centered in a slit." (NS-G05) - updated due date
    • NIRSpec fixed slit (FS) spectroscopy

      • Updated: "Many significant outliers and 'NaN' appear in the 2-D and 1-D extracted spectra." (NS-FS05) - updated mitigation plan
    • NIRSpec integral field unit (IFU) spectroscopy

      • Updated: "Negative and/or surplus flux in the extracted 1-D spectra is seen, typically with an irregular wavelength-dependent undulation." (NS-IFU03) - updated due date
    • NIRSpec multi-object spectroscopy (MOS) 

      • Updated: "Significant outliers appear in the 2-D and 1-D extracted spectra." (NS-MOS01) - updated due date
      • Updated: "Spectra extracted from slitlets consisting of more than 3 shutters exhibit unexpected wavelength-dependent flux discrepancies." (NS-MOS03) - updated mitigation plan and workaround
      • Updated: "Negative and/or surplus flux seen in extracted 1-D spectra, typically with an irregular wavelength-dependent undulation." (NS-MOS04) - updated due date
    • NIRSpec bright object time series  (BOTS) 

      • Updated: "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)." (NS-BOTS03) - updated due date
    • MIRI coronagraphic imaging

      • Updated: "Absolute flux calibration is incorrect." (MR-CI01) - Updated in Operations Pipeline


  •  
    • NIRCam general issues
      • Updated: "Bright objects in the field are saturated even though the ETC predicted that they would not saturate 'fully.'" (NC-G01) - removed pipeline due date from "Workaround" column.

 

  •   
    • NIRSpec general issues

      • New issue: "A pattern of alternating brighter/darker pixel rows over part or all of a detector image." (NS-G06)
      • Updated: "Extracted 1-D spectrum ("x1d" product) has spurious positive and negative features, typically one pixel wide." (NS-G03) - updated workaround and mitigation plan


  •   
    • General issues
    • MIRI time-series observations
      • Updated: "The photon count rate and derived flux for MRS TSO data, is lower than predicted at long wavelengths, with maximum deficit roughly a factor of 2 at 28 µm." (MR-TS03) - updated pipeline due date
    • General issues for time-series observations

      • Updated: "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." (GI-TS01) - updated Operations Pipeline
    • NIRISS wide field slitless spectroscopy (WFSS)

      • Updated: "For direct imaging: when the peak pixel of a star (or other compact object) reaches beyond ~25,000 e- ..." (NR-WFSS02) - updated pipeline due date
    • NIRISS imaging
      • Updated: "When the peak pixel of a star (or other compact object) reaches beyond ~25,000 e- ..." (NR-I01) - updated pipeline due date
    • NIRSpec fixed slit (FS) spectroscopy

      • Updated: "Many significant outliers and "NaN" appear in the 2-D and 1-D extracted spectra." (NS-FS05) - updated reference file due date


    • NIRSpec integral field unit (IFU) spectroscopy

      • Updated: "Negative and/or surplus flux in the extracted 1-D spectra is seen, typically with an irregular wavelength-dependent undulation." (NS-IFU03) - workaround notebook is available.

    • NIRSpec multi-object spectroscopy (MOS)
      • Updated: "Negative and/or surplus flux seen in extracted 1-D spectra, typically with an irregular wavelength-dependent undulation." (NS-MOS04) - workaround notebook is available.

  •   
    • MIRI imaging
      • New issue: The photon count rate and derived flux are lower than predicted at wavelengths between 12.8 and 25.5 µm, with the effect increasing with wavelength (see JWST Observer). (MR-I03)

  •  
    • NIRCam coronagraphic imaging

      • Updated: "Absolute flux calibration is incorrect." (NC-CI03) - updated reference file due date

  •   
    • General issues
      • Updated: "Embedded world coordinate system (WCS) in JWST data products is incorrect." (GI02) - mentioned issue NC-I01 to workaround column.

    • MIRI medium resolution spectroscopy (MRS)

      • Updated: "Custom user-derived backgrounds provided to the master_background step do not work as expected." (MR-MRS07) - resolved
      • Updated: "Channel 4B field of view is squashed by about 8% relative to the 4A and 4C fields. This is noticeable in observations of sources with fixed limbs comparable in size to the FOV (e.g., giant planets)." (MR-MRS08) - updated in Operations Pipeline
      • Updated: "Spectra show unexpected features around 12.2 µm." (MR-MRS03) - added notebook for workaround.

    • NIRSpec general issues

      • Updated: "No flux or negative flux in FS or MOS extracted 1-D spectrum ("x1d" product), despite obvious flux in 2-D spectrum ("s2d" product)." (NS-G02) - updated mitigation plan

    • NIRSpec fixed slit (FS) spectroscopy

      • Updated: "Level 3 extracted spectra have errors that are all 'NaN.'" (NS-FS06) - updated reference file due date

    • NIRSpec multi-object spectroscopy (MOS) 

      • Updated: "Level 3 extracted spectra have errors that are all 'NaN'." (NS-MOS02) - updated reference file due date


  •   
    • NIRSpec multi-object spectroscopy (MOS) 

      • New issue: "Discontinuities in the extracted level 2 spectra and "s2d" images at the upper and/or lower nod positions. These may be as large as ~40%. The effects in level 3 products appear to be much smaller and/or absent." (NS-MOS06)
      • New issue: "Lower than expected S/N and/or larger than expected discrepancies between dither positions." (NS-MOS07)

    • NIRSpec fixed slit (FS) spectroscopy

      • New issue: "Lower than expected S/N and/or larger than expected discrepancies between dither positions." (NS-FS07)
      • New issue: "Lower than expected flux and/or flux inconsistencies between closely spaced dither positions that may result in issues with outlier rejection. In extreme cases this may result in an ~20% error in the absolute flux calibration, although more commonly, the effect is at the ~5% level." (NS-FS08)
      • New issue: "Artificial ~10% deep absorption feature between about 0.97 and 1.02 µm in NIRSpec G140M/F070LP spectra when observed through the S1600A1 aperture." (NS-FS09)

    • NIRSpec bright object time series  (BOTS) 

      • New issue: "Artificial ~10% deep absorption feature between about 0.97 and 1.02 µm in NIRSpec G140M/F070LP spectra when observed through the S1600A1 aperture." (NS-BOTS05)

    • MIRI time-series observations

      • Updated: "Spatially and temporally varying noise in subarray TSOs ('390 Hz noise')" (MR-TS01) - updated availability date in Operations Pipeline

    • NIRISS aperture masking interferometry (AMI)

      • Updated: "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." (NR-AMI01) - updated availability date in Operations Pipeline

    • NIRCam imaging
      • Updated: "Misalignment of mosaic tiles in some of the stage 3 data products" (NC-I01) - updated availability date in Operations Pipeline


  •  
    • General issues
    • MIRI medium resolution spectroscopy (MRS)
      • New issue: "Channel 4B field of view is squashed by about 8% relative to the 4A and 4C fields. This is noticeable in observations of sources with fixed limbs comparable in size to the FOV (e.g., giant planets)." (MR-MRS08)
    • MIRI time-series observations
      • New issue: "The photon count rate and derived flux for MRS TSO data, is lower than predicted at long wavelengths, with maximum deficit roughly a factor of 2 at 28 µm." (MR-TS03)


  •   
    • NIRISS single object slitless spectroscopy
      • New issue: The pipeline currently cannot extract a 1-D spectrum from science observations using the GR700XD grism in combination with the F277W filter. (NR-SOSS08)

  •  
    • NIRISS wide field slitless spectroscopy
      • Updated: "specwcs" reference files from jwst_1105.pmap account for the change in the wavelength dispersion solution as a function of detector position. (NR-WFSS01)

  •  
    • NIRSpec general issues
      • Updated: "A few pixel rows exhibit anomalous count rates in "rate" images for IRS2 data." (NS-G01)
    • NIRSpec IFU
      • Updated: "The centroid of point sources appears to drift slightly as a function of wavelength." (NS-IFU06)

  •  
    • NIRSpec general issues
      • New issue: "Unexpected flux levels in spectra of sources not centered in a slit." (NS-G04)
      • New issue: "Wavelengths of spectral features does not match expectation in spectra of sources not centered in a slit." (NS-G05)

  •  
    • NIRSpec general issues
      • Updated: a workaround notebook was added for issue "No flux or negative flux in FS or MOS extracted 1-D spectrum ("x1d" product), despite obvious flux in 2-D spectrum ("s2d" product)." (NS-G02)
         
    • NIRSpec FS spectroscopy

      • Updated: “Many significant outliers and "NaN" appear in the 2-D and 1-D extracted spectra.” (NS-FS05)

      • Updated: Example workaround added to issue "Level 3 extracted spectra have errors that are all "NaN."" (NS-FS06)

    • NIRSpec BOTS

      • Updated: "Large number of outlier pixels are identified in the jump step, which leads to lower SNR of the "rateints" products (slope images) per integration." (NS-BOTS02)

      • Updated: "The extracted 1-D spectrum ("x1d" product) has spurious absorption features, typically one pixel wide." (NS-BOTS04)

      • Updated: "The shape of spectra taken with the SUB512, SUB512S, or SUB32 subarrays exhibits unexpected features and wavelength-dependent flux discrepancies of 10% or more." (NS-FS01)

    • NIRSpec IFU
      • New issue: "Spectra extracted from single spaxels on/near point sources show a sinusoidal modulation." (NS-IFU05)
Originally published