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spacetelescope / jwst

Python library for science observations from the James Webb Space Telescope
https://jwst-pipeline.readthedocs.io/en/latest/
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Review b7.8.1 (1.3.0) DMS test runs for issues in Cal #6280

Closed stscijgbot-jp closed 3 years ago

stscijgbot-jp commented 3 years ago

Issue JP-2233 was created on JIRA by Tyler Pauly:

Review DMS test suite results for 7.8.1 (Cal 1.3.0) to look for calibration-related issues.

stscijgbot-jp commented 3 years ago

Comment by Howard Bushouse on JIRA:

Data Processing Runs page is here

stscijgbot-jp commented 3 years ago

Comment by Howard Bushouse on JIRA:

run2370: GSEG4DR-EMTB 2-Aug-2021 CAL 1.3.0

No Level 2a, 2b, or 3 errors (only level 1)

stscijgbot-jp commented 3 years ago

Comment by Howard Bushouse on JIRA:

run2372: QnGV6 2-Aug-2021 CAL 1.3.0

No Level 2a, 2b, or 3 errors (only level 1)

stscijgbot-jp commented 3 years ago

Comment by Howard Bushouse on JIRA:

run2373: GSEG4DR1 2-Aug-2021 CAL 1.3.0

No Level 2a, 2b, or 3 errors (only level 1)

stscijgbot-jp commented 3 years ago

Comment by Howard Bushouse on JIRA:

run2374: QnGV6 2-Aug-2021 CAL 1.3.0

No Level 2a, 2b, or 3 errors (only level 1)

stscijgbot-jp commented 3 years ago

Comment by Howard Bushouse on JIRA:

run2375: GSEG3RR 2-Aug-2021 CAL 1.3.0

No Level 2a, 2b, or 3 errors (only level 1)

stscijgbot-jp commented 3 years ago

Comment by Howard Bushouse on JIRA:

run2377: GSEG4DR-EMTB 2-Aug-2021 CAL 1.3.0

No Level 2a, 2b, or 3 errors (only level 1)

stscijgbot-jp commented 3 years ago

Comment by Howard Bushouse on JIRA:

run2378: SOR7-nOPS10-OTB 2-Aug-2021 CAL 1.3.0

Level 2b:

Error running calwebb_spec2 on jw00624-o028_date_tag_spec2_001_asn.json, with "memory_error_exit=88". Input is jw00624028002_02101_00001_nrcalong_rate.fits, NRC_WFSS with GRISMR, full-frame. Processing log claims to have successfully finished extract_1d step and creating x1d and cal products, each containing data for 1137 slits/sources. Products are not in the level2b results directory.

Level 3:

Error running calwebb_image3 on jw00660-o023_20210802t233327_image3_003.json containing ~100 NIRCam images. Error in skymatch step "spherical_geometry.polygon.MalformedPolygonError: intersection: find all intersections".

stscijgbot-jp commented 3 years ago

Comment by Howard Bushouse on JIRA:

run2380: SIR3_OTB 3-Aug-2021 CAL 1.3.0

No analysis (yet)

stscijgbot-jp commented 3 years ago

Comment by Howard Bushouse on JIRA:

run2382: GSEG4DR-EMTB 3-Aug-2021 CAL 1.3.0

No Level 2a, 2b, or 3 errors (only level 1)

stscijgbot-jp commented 3 years ago

Comment by Howard Bushouse on JIRA:

run2385: SIR3_OTB 3-Aug-2021 CAL 1.3.0

Level 2a:

Error determining dark and superbias ref files for Detector=NRS1, Readpatt=NRSRAPIDD6, Subarray=SUB2048, SUBSTRT1=1, SUBSIZE1=2048, SUBSTRT2=975, SUBSIZE2=32. Darks and superbias for NRSRAPIDD6 only exist in full-frame form. This is a CRDS coverage issue. Ticket already exists (https://jira.stsci.edu/browse/CRDS-426)

Level 3:

Error running calwebb_spec3 on NRS_IFU data. Cube_build fails to create a product, because "ERROR - All the wavelength planes have zero data, check input data", thus no s3d or x1d products created, resulting in DMS error.

stscijgbot-jp commented 3 years ago

Comment by Howard Bushouse on JIRA:

run2386: LRE3-OTB 4-Aug-2021 CAL 1.3.0

Level 3:

calwebb_image3 error for jw00759-o148_20210804t105828_image3_003.json, containing FGS Guider2 images, in source_catalog step with "ValueError: positions must not contain any non-finite (e.g., NaN or inf) positions." Fixed in B7.9 by JP-2172.

calwebb_tso3 error for jw00809-o024_20210804t125219_tso3_002.json, containing NRC_TSIMAGE data with TSOVISIT=False and Subarray=SUBGRISM256. tso_photometry step fails due to CRDS rmap returning N/A for TSOPHOT ref file, hence step is skipped, no photometry data to store in output phot product. Known problem with non-TSO exposures getting EXP_TYPE set to TSIMAGE, because it uses the grism subarray. Being worked in JP-2170.

stscijgbot-jp commented 3 years ago

Comment by Howard Bushouse on JIRA:

run2387: LRE4RR-OTB 4-Aug-2021 CAL 1.3.0

No Level 2a, 2b, or 3 errors (only level 1)

stscijgbot-jp commented 3 years ago

Comment by Howard Bushouse on JIRA:

run2392: nOPS11 4-Aug-2021 CAL 1.3.0

No error reports.

run2393: nOPS11 4-Aug-2021 CAL 1.3.0

No error reports.

run2394: nOPS11 5-Aug-2021 CAL 1.3.0

No Level 2a, 2b, or 3 errors (only Level 1)

stscijgbot-jp commented 3 years ago

Comment by Howard Bushouse on JIRA:

run2395: LRE4RR-OTB 5-Aug-2021 CAL 1.3.0

Level 2b:

Error running calwebb_spec2 for NRS lamp exposure with EXP_TYPE=NRS_LAMP, Detector=NRS2, Filter=Opaque, Grating=G140H, Opmode=IFU, Lamp=FLAT4 in flat-field step: 

  File "/dms/local/jwst/pipeline/pkgs/miniconda3/envs/jwstdp-1.3.0.20210802-py38/lib/python3.8/site-packages/jwst/flatfield/flat_field.py", line 297, in do_nirspec_flat_field
    return nirspec_ifu(output_model, f_flat_model, s_flat_model, d_flat_model, dispaxis,
  File "/dms/local/jwst/pipeline/pkgs/miniconda3/envs/jwstdp-1.3.0.20210802-py38/lib/python3.8/site-packages/jwst/flatfield/flat_field.py", line 549, in nirspec_ifu
    flat, flat_dq, flat_err, any_updated = flat_for_nirspec_ifu(
  File "/dms/local/jwst/pipeline/pkgs/miniconda3/envs/jwstdp-1.3.0.20210802-py38/lib/python3.8/site-packages/jwst/flatfield/flat_field.py", line 1703, in flat_for_nirspec_ifu
    ind = np.indices((dy, dx))
  File "/dms/local/jwst/pipeline/pkgs/miniconda3/envs/jwstdp-1.3.0.20210802-py38/lib/python3.8/site-packages/numpy/core/numeric.py", line 1777, in indices
    res = empty((N,)+dimensions, dtype=dtype)
ValueError: negative dimensions are not allowed

Known problem documented in JP-2209. This combination of detector and grating will not have data projected onto the detector and hence should not go through level-2b processing.

stscijgbot-jp commented 3 years ago

Comment by Howard Bushouse on JIRA:

run2400: nOPS11 5-Aug-2021 CAL 1.3.0

Level 2b:

Error running calwebb_spec2 on jw00686-o008_date_tag_spec2_044.json, with "memory_error_exit=88", for NRS_MSASPEC exposure, despite the fact that processing log shows the pipeline completed successfully, with cal, s2d, and x1d products created for ~100 slits/sources. Output products are in the level2b directory. Problem due to odd naming of ASN?

Level 3:

Error running calwebb_spec3 on jw00686-o013_20210805t204653_spec3_001.json, with "memory_error_exit=88", for 24 NRS_IFU exposures. Dies in the middle of the cube_build step after having completed outlier_detection. Might be fixed in B7.9 via application of C extensions for cube building/blotting.

Several instances of memory errors in calwebb_image3 outlier_detection step for NIRCam image mosaics, as reported in JWSTDMS-574.

stscijgbot-jp commented 3 years ago

Comment by Howard Bushouse on JIRA:

run2403: GSEG4DR-EMTB 6-Aug-2021 CAL 1.3.0

Level 2b:

Error running calwebb_image2 on NRS_LAMP exposures with GRATING=MIRROR, OPMODE=IMAGE, and LAMP=TEST. Flat-field step aborts with "No flat field algorithm exists for handling data". This is due to having FLAT, SFLAT, and FFLAT all set to N/A in CRDS rmap, but DFLAT still returns a reference file, causing the step to try to apply a spectroscopic flat to an imaging mode exposure (see JP-1942). NIRSpec team is aware and needs to update rmap to return N/A for all flats, thus causing the flat-field step to be skipped.

stscijgbot-jp commented 3 years ago

Comment by Howard Bushouse on JIRA:

run2404: GSEG3RR 6-Aug-2021 CAL 1.3.0

Level 2b:

Same calwebb_image2 error as reported above when processing NRS_LAMP exposures taken in imaging mode. Needs CRDS updates.

Level 3:

Error running calwebb_image3 on FGS image association in source_catalog step: "ValueError: positions must not contain any non-finite (e.g., NaN or inf) positions." Already fixed for B7.9 (JP-2172).

stscijgbot-jp commented 3 years ago

Comment by Howard Bushouse on JIRA:

run2405: LRE3RR-OTB 6-Aug-2021 CAL 1.3.0

No analysis results (yet)

run2407: SIR3 6-Aug-2021

No analysis results (yet)

run2408: SIR3_OTB 6-Aug-2021

No analysis results (yet)

run2409: SIR3_OTB 6-Aug-2021

No analysis results (yet)

stscijgbot-jp commented 3 years ago

Comment by Howard Bushouse on JIRA:

run2410: SOR7-nOPS10-OTB 6-Aug-2021 CAL 1.3.0

Level 2b:

Error in calwebb_spec2 for NRS_MSASPEC exposure, in assign_wcs step with "jwst.assign_wcs.util.MSAFileError: MSA configuration file has more than 1 shutter with primary source". Problem with data in MSA meta data file.

Level 3:

Error in calwebb_spec3 for NRS_IFU exposures at end of cube_build step "All the wavelength planes have zero data". Garbage input data.

Error in calwebb_spec3 for NRC_WFSS exposures in combine_1d step "Spectrum is degenerate with length 1. Problem with input wavelengths". Garbage input data.

Error in calwebb_image3 for NRC_IMAGE exposures in skymatch step with "MalformedPolygonError". Garbage input data.

Error in calwebb_coron3 for MIR_4QPM exposures in klip step with "numpy.linalg.LinAlgError: Eigenvalues did not converge". Garbage input data.

stscijgbot-jp commented 3 years ago

Comment by Howard Bushouse on JIRA:

run2413: LRE3-OTB 7-Aug-2021 CAL 1.3.0

Level 3:

Error running calwebb_image3 on FGS image association in source_catalog step: "ValueError: positions must not contain any non-finite (e.g., NaN or inf) positions." Already fixed for B7.9 (JP-2172).

Error in calwebb_tso3 for NRC_TSIMAGE exposure(s) with TSOVISIT=False. Already fixed for B7.9 in JP-2170.

stscijgbot-jp commented 3 years ago

Comment by Howard Bushouse on JIRA:

run 2414: LRE4RR-OTB 7-Aug-2021 CAL 1.3.0

Error running calwebb_spec2 for NRS lamp exposure with EXP_TYPE=NRS_LAMP, Detector=NRS2, Filter=Opaque, Grating=G140H, Opmode=IFU, Lamp=FLAT4 in flat-field step: "negative dimensions are not allowed". No data on detector NRS2. See JP-2209.

stscijgbot-jp commented 3 years ago

Comment by Howard Bushouse on JIRA:

run2415: SOR7-nOPS10-OTB 7-Aug-2021 CAL 1.3.0

Level 2a:

calwebb_detector1 error for MIR_LRS-SLITLESS with TSOVISIT=True. Pipeline seems to end successfully, after creating rate and rateints products. Some other problem during process shutdown or cleanup.

Level 2b:

Error in calwebb_spec2 for NRS_MSASPEC exposure, in assign_wcs step with "jwst.assign_wcs.util.MSAFileError: MSA configuration file has more than 1 shutter with primary source". Problem with data in MSA meta data file.

Level 3:

calwebb_spec3 error for NRC_WFSS exposure(s), with apparent memory error at end of extract_1d step. No clue.

Error in calwebb_image3 for NRC_IMAGE exposures in skymatch step with "MalformedPolygonError". Garbage input data.

Error in calwebb_coron3 for MIR_4QPM exposures in klip step with "numpy.linalg.LinAlgError: Eigenvalues did not converge". Garbage input data.

Error in calwebb_image3 for NIRCam imaging exposures after successfully creating i2d, cat, and segm products. No clue.

Error in calwebb_spec3 for NIS_WFSS exposure(s) after pipeline completes successfully with x1d and c1d products saved. No clue.

stscijgbot-jp commented 3 years ago

Comment by Howard Bushouse on JIRA:

run2417: nOPS11 8-Aug-2021 CAL 1.3.0

Level 3:

Errors in calwebb_spec3 with "memory_error_exit=88" for NRS_MSASPEC exposures in midst of outlier_detection and resample_spec steps.

Error in calwebb_spec3 with "memory_error_exit=88" for NRS_IFU in midst of cube_build step.

Error in calwebb_image3 for NRC_IMAGE exposures in midst of outlier_detection step, with memory error.

stscijgbot-jp commented 3 years ago

Comment by Howard Bushouse on JIRA:

run2423: nOPS8.1 10-Aug-2021 CAL 1.3.0

Level 3:

Error in calwebb_image3 for NRC_IMAGE exposures in skymatch step: "cannot convert float NaN to integer". Likely garbage data.

Error in calwebb_image3 for NRC_IMAGE exposures in source_catalog step: "positions must not contain any non-finite positions". Fixed for B7.9 by JP-2172.

stscijgbot-jp commented 3 years ago

Comment by Howard Bushouse on JIRA:

run2444: nOPS11 15-Aug-2021 CAL 1.3.1

Level 3:

Error in calwebb_image3 for NRC_IMAGE exposures in midst of outlier_detection step, with memory error.

stscijgbot-jp commented 3 years ago

Comment by Howard Bushouse on JIRA:

run2446: LRE3-OTB 16-Aug-2021 CAL 1.3.1

Level 3:

Error running calwebb_image3 on FGS image association in source_catalog step: "ValueError: positions must not contain any non-finite (e.g., NaN or inf) positions." Already fixed for B7.9 (JP-2172).

Error in calwebb_tso3 for NRC_TSIMAGE exposure(s) with TSOVISIT=False. Already fixed for B7.9 in JP-2170.

stscijgbot-jp commented 3 years ago

Comment by Howard Bushouse on JIRA:

run2447: LRE4RR-OTB 16-Aug-2021 CAL 1.3.1

Level 2:

Error running calwebb_spec2 for NRS lamp exposure with EXP_TYPE=NRS_LAMP, Detector=NRS2, Filter=Opaque, Grating=G140H, Opmode=IFU, Lamp=FLAT4 in flat-field step. Known problem documented in JP-2209. This combination of detector and grating will not have data projected onto the detector and hence should not go through level-2b processing.

stscijgbot-jp commented 3 years ago

Comment by Howard Bushouse on JIRA:

run2455: remoteOTB1_trimmed_01a 22-Aug-2021 CAL 1.3.1

Level 2:

Several MIR_CORONCAL exposures fail in photom step of calwebb_image2, due to attempted use of ref file jwst_miri_photom_0042.fits. This is an old ref file that has an incorrect DATAMODL keyword value - MiriImgPhotomModel - which causes it to get loaded as a generic ReferenceFileModel. This leads to errors when trying to access the phot_table attribute of the model. Need to either fix the DATAMODL keyword value in the ref file (and redeliver) or perhaps even need a separate rmap entry for MIR_CORONCAL exposures. Checking with CRDS and MIRI folks.

Fixed in CRDS context 757 by adding MIR_CORONCAL to the list of EXP_TYPE's for jwst_miri_photom_0073.fits.

stscijgbot-jp commented 3 years ago

Comment by Howard Bushouse on JIRA:

run2454: EvaluationSuite06 20-Aug-2021 CAL 1.3.1

Level 2:

Several NIRCam WFSS exposures crash during the background step of the calwebb_spec2 pipeline, due to garbage source list info from the garbage input images. JP-2264 filed to fix for B7.9.