eslavichjgbot
commented
4 years ago Comment by Beth Sargent on JIRA:
Nadia, Howard,
I added 4 rows/columns of zero-valued-pixels to the borders of the SCI, DQ, and ERR planes of the simulations I was working with, so that they are now 2048x2048 instead of 2040x2040. I ran these modified simulations (with the header keyword changes of strings to Boolean values from Phil's suggestions in JP-505) just now, and the pipeline no longer crashed on the msa_flagging step. It made it all the way through to the end of the calwebb_spec2.cfg script (including cube_build) without problems.
Issue JP-506 was created on JIRA by Maria Pena-Guerrero:
We were attempting to test cube_build but the cal web_spec2 pipeline crashes with simulated IFU data at the msa_flagging step. The failure message is copied below.
The file we used for testing can be located at:
████████████████████████████████████
ditherunity_CLEAR_PRISM_M1_m1_noiseless_NRS1_modified_updatedHDR_fixintarget.fits
Traceback:
2019-01-17 23:18:53,668 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2019-01-17 23:18:53,797 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<IFUImageModel(2040, 2040) from ditherunity_CLEAR_PRISM_M1_m1_noiseless_NRS1_modified_updatedHDR_fixintarget.fits>,).
2019-01-17 23:18:54,131 - stpipe.Spec2Pipeline.msa_flagging - INFO - Using reference file ██████████████████████████████████████████████████████████████
2019-01-17 23:18:54,132 - stpipe.Step - INFO - Step instance created.
2019-01-17 23:18:56,103 - stpipe.Spec2Pipeline.msa_flagging - INFO - gwa_ytilt is 0.1346436440944672 deg
2019-01-17 23:18:56,103 - stpipe.Spec2Pipeline.msa_flagging - INFO - gwa_xtilt is 0.3622055649757385 deg
2019-01-17 23:18:56,104 - stpipe.Spec2Pipeline.msa_flagging - INFO - theta_y correction: -0.030260896022953843 deg
2019-01-17 23:18:56,104 - stpipe.Spec2Pipeline.msa_flagging - INFO - theta_x correction: 0.0 deg
2019-01-17 23:18:56,273 - stpipe.Spec2Pipeline.msa_flagging - INFO - SPORDER= 0, wrange=[6e-07, 5.3e-06]
2019-01-17 23:18:59,869 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 5 open slits in quadrant 1
2019-01-17 23:19:00,425 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 3 open slits in quadrant 2
2019-01-17 23:19:00,814 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 9 open slits in quadrant 3
2019-01-17 23:19:02,270 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 3 open slits in quadrant 4
2019-01-17 23:19:02,717 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 0 open slits in quadrant 5
Traceback (most recent call last):
File "/Users/sargent/anaconda/envs/jwst72/lib/python3.6/site-packages/jwst-0.12.2-py3.6-macosx-10.7-x86_64.egg/jwst/pipeline/calwebb_spec2.py", line 91, in process
asn.filename
File "/Users/sargent/anaconda/envs/jwst72/lib/python3.6/site-packages/jwst-0.12.2-py3.6-macosx-10.7-x86_64.egg/jwst/pipeline/calwebb_spec2.py", line 225, in process_exposure_product
input = self.msa_flagging(input)
File "/Users/sargent/anaconda/envs/jwst72/lib/python3.6/site-packages/jwst-0.12.2-py3.6-macosx-10.7-x86_64.egg/jwst/stpipe/step.py", line 400, in run
step_result = self.process(*args)
File "/Users/sargent/anaconda/envs/jwst72/lib/python3.6/site-packages/jwst-0.12.2-py3.6-macosx-10.7-x86_64.egg/jwst/msaflagopen/msaflagopen_step.py", line 42, in process
wcs_reffile_names)
File "/Users/sargent/anaconda/envs/jwst72/lib/python3.6/site-packages/jwst-0.12.2-py3.6-macosx-10.7-x86_64.egg/jwst/msaflagopen/msaflag_open.py", line 51, in do_correction
output_model = flag(input_model, failed_slitlets, wcs_refnames)
File "/Users/sargent/anaconda/envs/jwst72/lib/python3.6/site-packages/jwst-0.12.2-py3.6-macosx-10.7-x86_64.egg/jwst/msaflagopen/msaflag_open.py", line 106, in flag
y_indices, x_indices = np.mgrid[ymin:ymax, xmin:xmax]
File "/Users/sargent/anaconda/envs/jwst72/lib/python3.6/site-packages/numpy/lib/index_tricks.py", line 187, in getitem
nn = _nx.indices(size, typ)
File "/Users/sargent/anaconda/envs/jwst72/lib/python3.6/site-packages/numpy/core/numeric.py", line 1863, in indices
res = empty((N,)+dimensions, dtype=dtype)
ValueError: negative dimensions are not allowed
ERROR RUNNING STEP 'Spec2Pipeline':
One or more products failed to process. Failing calibration.
Traceback (most recent call last):
File "/Users/sargent/anaconda/envs/jwst72/lib/python3.6/site-packages/jwst-0.12.2-py3.6-macosx-10.7-x86_64.egg/jwst/stpipe/cmdline.py", line 297, in step_from_cmdline
step.run(*positional)
File "/Users/sargent/anaconda/envs/jwst72/lib/python3.6/site-packages/jwst-0.12.2-py3.6-macosx-10.7-x86_64.egg/jwst/stpipe/step.py", line 400, in run
step_result = self.process(*args)
File "/Users/sargent/anaconda/envs/jwst72/lib/python3.6/site-packages/jwst-0.12.2-py3.6-macosx-10.7-x86_64.egg/jwst/pipeline/calwebb_spec2.py", line 107, in process
'One or more products failed to process. Failing calibration.'
RuntimeError: One or more products failed to process. Failing calibration.
Traceback (most recent call last):
File "/Users/sargent/anaconda/envs/jwst72/lib/python3.6/site-packages/jwst-0.12.2-py3.6-macosx-10.7-x86_64.egg/EGG-INFO/scripts/strun", line 26, in
step = Step.from_cmdline(sys.argv[1:])
File "/Users/sargent/anaconda/envs/jwst72/lib/python3.6/site-packages/jwst-0.12.2-py3.6-macosx-10.7-x86_64.egg/jwst/stpipe/step.py", line 162, in from_cmdline
return cmdline.step_from_cmdline(args)
File "/Users/sargent/anaconda/envs/jwst72/lib/python3.6/site-packages/jwst-0.12.2-py3.6-macosx-10.7-x86_64.egg/jwst/stpipe/cmdline.py", line 297, in step_from_cmdline
step.run(*positional)
File "/Users/sargent/anaconda/envs/jwst72/lib/python3.6/site-packages/jwst-0.12.2-py3.6-macosx-10.7-x86_64.egg/jwst/stpipe/step.py", line 400, in run
step_result = self.process(*args)
File "/Users/sargent/anaconda/envs/jwst72/lib/python3.6/site-packages/jwst-0.12.2-py3.6-macosx-10.7-x86_64.egg/jwst/pipeline/calwebb_spec2.py", line 107, in process
'One or more products failed to process. Failing calibration.'
RuntimeError: One or more products failed to process. Failing calibration.