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meganmansfield / ERS_NIRCam

Demonstration to duplicate the data reduction of a transit of WASP-39b observed with NIRCam/F322W2 as part of the JWST Transiting Exoplanet Early Release Science Program (ERS 1366). This demonstration follows the data reduction with Eureka! presented in Ahrer et al. (2022).
MIT License
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Stage 1: ModuleNotFoundError #4

Open jkrick opened 1 year ago

jkrick commented 1 year ago

Running your demo exactly as the instructions have suggested. I am stuck with an error on Stage 1. The ModuleNotFoundError suggests I need to ' pip install stcal[opencv]', but I did do that in setting up the environment, and did it again at the top of the notebook, at which point python tells me 'Requirement already satisfied'.

Full traceback is: Starting Stage 1 Processing Input directory: /home/jkrick/stagejkrick/JK_workingdir/JWST/ERS_NIRCam/Uncalibrated/ Output directory: /home/jkrick/stagejkrick/JK_workingdir/JWST/ERS_NIRCam/Stage1/S1_2023-03-13_nircam_wasp39b_run2/ Copying S1 control file

Found 4 data file(s) ending in 04103_*nrcalong_uncal.fits Starting file 1 of 4: jw01366002001_04103_00001-seg001_nrcalong_uncal.fits 2023-03-13 21:48:47,731 - stpipe.EurekaS1Pipeline - INFO - EurekaS1Pipeline instance created. 2023-03-13 21:48:47,735 - stpipe.EurekaS1Pipeline.group_scale - INFO - GroupScaleStep instance created. 2023-03-13 21:48:47,738 - stpipe.EurekaS1Pipeline.dq_init - INFO - DQInitStep instance created. 2023-03-13 21:48:47,740 - stpipe.EurekaS1Pipeline.saturation - INFO - SaturationStep instance created. 2023-03-13 21:48:47,743 - stpipe.EurekaS1Pipeline.ipc - INFO - IPCStep instance created. 2023-03-13 21:48:47,745 - stpipe.EurekaS1Pipeline.superbias - INFO - SuperBiasStep instance created. 2023-03-13 21:48:47,748 - stpipe.EurekaS1Pipeline.refpix - INFO - RefPixStep instance created. 2023-03-13 21:48:47,750 - stpipe.EurekaS1Pipeline.rscd - INFO - RscdStep instance created. 2023-03-13 21:48:47,752 - stpipe.EurekaS1Pipeline.firstframe - INFO - FirstFrameStep instance created. 2023-03-13 21:48:47,755 - stpipe.EurekaS1Pipeline.lastframe - INFO - LastFrameStep instance created. 2023-03-13 21:48:47,757 - stpipe.EurekaS1Pipeline.linearity - INFO - LinearityStep instance created. 2023-03-13 21:48:47,760 - stpipe.EurekaS1Pipeline.dark_current - INFO - DarkCurrentStep instance created. 2023-03-13 21:48:47,762 - stpipe.EurekaS1Pipeline.reset - INFO - ResetStep instance created. 2023-03-13 21:48:47,765 - stpipe.EurekaS1Pipeline.persistence - INFO - PersistenceStep instance created. 2023-03-13 21:48:47,767 - stpipe.EurekaS1Pipeline.jump - INFO - JumpStep instance created. 2023-03-13 21:48:47,771 - stpipe.EurekaS1Pipeline.ramp_fit - INFO - RampFitStep instance created. 2023-03-13 21:48:47,773 - stpipe.EurekaS1Pipeline.gain_scale - INFO - GainScaleStep instance created. 2023-03-13 21:48:47,795 - stpipe.Eureka_RampFitStep - INFO - Eureka_RampFitStep instance created. 2023-03-13 21:48:48,556 - stpipe.EurekaS1Pipeline - INFO - Step EurekaS1Pipeline running with args ('/home/jkrick/stagejkrick/JK_workingdir/JWST/ERS_NIRCam/Uncalibrated/jw01366002001_04103_00001-seg001_nrcalong_uncal.fits',). 2023-03-13 21:48:48,577 - stpipe.EurekaS1Pipeline - INFO - Step EurekaS1Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': '/home/jkrick/stagejkrick/JK_workingdir/JWST/ERS_NIRCam/Stage1/S1_2023-03-13_nircam_wasp39b_run2/', 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': True, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_calibrated_ramp': False, 'steps': {'group_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dq_init': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'saturation': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'n_pix_grow_sat': 1}, 'ipc': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'superbias': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'refpix': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}, 'rscd': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'type': 'baseline'}, 'firstframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'lastframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'linearity': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dark_current': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'dark_output': None}, 'reset': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'persistence': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'input_trapsfilled': '', 'flag_pers_cutoff': 40.0, 'save_persistence': False, 'save_trapsfilled': True}, 'jump': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'rejection_threshold': 6.0, 'three_group_rejection_threshold': 6.0, 'four_group_rejection_threshold': 5.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 1000.0, 'min_jump_to_flag_neighbors': 10.0}, 'ramp_fit': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'int_name': '', 'save_opt': False, 'opt_name': '', 'maximum_cores': 'half'}, 'gain_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}}} 2023-03-13 21:49:01,808 - stpipe.EurekaS1Pipeline - INFO - Prefetching reference files for dataset: 'jw01366002001_04103_00001-seg001_nrcalong_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'superbias'] 2023-03-13 21:49:01,826 - stpipe.EurekaS1Pipeline - INFO - Prefetch for DARK reference file is '/home/jkrick/stagejkrick/JK_workingdir/JWST/eureka/crds_cache/references/jwst/nircam/jwst_nircam_dark_0355.fits'. 2023-03-13 21:49:01,829 - stpipe.EurekaS1Pipeline - INFO - Prefetch for GAIN reference file is '/home/jkrick/stagejkrick/JK_workingdir/JWST/eureka/crds_cache/references/jwst/nircam/jwst_nircam_gain_0097.fits'. 2023-03-13 21:49:01,831 - stpipe.EurekaS1Pipeline - INFO - Prefetch for LINEARITY reference file is '/home/jkrick/stagejkrick/JK_workingdir/JWST/eureka/crds_cache/references/jwst/nircam/jwst_nircam_linearity_0052.fits'. 2023-03-13 21:49:01,833 - stpipe.EurekaS1Pipeline - INFO - Prefetch for MASK reference file is '/home/jkrick/stagejkrick/JK_workingdir/JWST/eureka/crds_cache/references/jwst/nircam/jwst_nircam_mask_0063.fits'. 2023-03-13 21:49:01,835 - stpipe.EurekaS1Pipeline - INFO - Prefetch for READNOISE reference file is '/home/jkrick/stagejkrick/JK_workingdir/JWST/eureka/crds_cache/references/jwst/nircam/jwst_nircam_readnoise_0157.fits'. 2023-03-13 21:49:01,837 - stpipe.EurekaS1Pipeline - INFO - Prefetch for REFPIX reference file is 'N/A'. 2023-03-13 21:49:01,838 - stpipe.EurekaS1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'. 2023-03-13 21:49:01,839 - stpipe.EurekaS1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'. 2023-03-13 21:49:01,840 - stpipe.EurekaS1Pipeline - INFO - Prefetch for SATURATION reference file is '/home/jkrick/stagejkrick/JK_workingdir/JWST/eureka/crds_cache/references/jwst/nircam/jwst_nircam_saturation_0097.fits'. 2023-03-13 21:49:01,843 - stpipe.EurekaS1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/home/jkrick/stagejkrick/JK_workingdir/JWST/eureka/crds_cache/references/jwst/nircam/jwst_nircam_superbias_0141.fits'. 2023-03-13 21:49:01,846 - stpipe.EurekaS1Pipeline - INFO - Starting calwebb_detector1 ... 2023-03-13 21:49:29,130 - stpipe.EurekaS1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(119, 12, 256, 2048) from jw01366002001_04103_00001-seg001_nrcalong_uncal.fits>,). 2023-03-13 21:49:29,134 - stpipe.EurekaS1Pipeline.group_scale - INFO - Step group_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/home/jkrick/stagejkrick/JK_workingdir/JWST/ERS_NIRCam/Uncalibrated'} 2023-03-13 21:49:54,040 - stpipe.EurekaS1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed 2023-03-13 21:49:54,041 - stpipe.EurekaS1Pipeline.group_scale - INFO - Step will be skipped 2023-03-13 21:49:54,047 - stpipe.EurekaS1Pipeline.group_scale - INFO - Step group_scale done 2023-03-13 21:49:54,369 - stpipe.EurekaS1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(119, 12, 256, 2048) from jw01366002001_04103_00001-seg001_nrcalong_uncal.fits>,). 2023-03-13 21:49:54,374 - stpipe.EurekaS1Pipeline.dq_init - INFO - Step dq_init parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/home/jkrick/stagejkrick/JK_workingdir/JWST/ERS_NIRCam/Uncalibrated'} 2023-03-13 21:49:54,419 - stpipe.EurekaS1Pipeline.dq_init - INFO - Using MASK reference file /home/jkrick/stagejkrick/JK_workingdir/JWST/eureka/crds_cache/references/jwst/nircam/jwst_nircam_mask_0063.fits 2023-03-13 21:49:59,728 - stpipe.EurekaS1Pipeline.dq_init - INFO - Extracting mask subarray to match science data 2023-03-13 21:49:59,764 - stpipe.EurekaS1Pipeline.dq_init - INFO - Step dq_init done 2023-03-13 21:50:00,125 - stpipe.EurekaS1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(119, 12, 256, 2048) from jw01366002001_04103_00001-seg001_nrcalong_uncal.fits>,). 2023-03-13 21:50:00,129 - stpipe.EurekaS1Pipeline.saturation - INFO - Step saturation parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/home/jkrick/stagejkrick/JK_workingdir/JWST/ERS_NIRCam/Uncalibrated', 'n_pix_grow_sat': 1} 2023-03-13 21:50:00,177 - stpipe.EurekaS1Pipeline.saturation - INFO - Using SATURATION reference file /home/jkrick/stagejkrick/JK_workingdir/JWST/eureka/crds_cache/references/jwst/nircam/jwst_nircam_saturation_0097.fits 2023-03-13 21:50:04,855 - stpipe.EurekaS1Pipeline.saturation - INFO - Extracting reference file subarray to match science data 2023-03-13 21:50:39,751 - stpipe.EurekaS1Pipeline.saturation - INFO - Detected 3978 saturated pixels 2023-03-13 21:50:40,271 - stpipe.EurekaS1Pipeline.saturation - INFO - Detected 0 A/D floor pixels 2023-03-13 21:50:40,294 - stpipe.EurekaS1Pipeline.saturation - INFO - Step saturation done 2023-03-13 21:50:40,587 - stpipe.EurekaS1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(119, 12, 256, 2048) from jw01366002001_04103_00001-seg001_nrcalong_uncal.fits>,). 2023-03-13 21:50:40,605 - stpipe.EurekaS1Pipeline.ipc - INFO - Step ipc parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/home/jkrick/stagejkrick/JK_workingdir/JWST/ERS_NIRCam/Uncalibrated'} 2023-03-13 21:50:40,606 - stpipe.EurekaS1Pipeline.ipc - INFO - Step skipped. 2023-03-13 21:50:40,616 - stpipe.EurekaS1Pipeline.ipc - INFO - Step ipc done 2023-03-13 21:50:40,880 - stpipe.EurekaS1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(119, 12, 256, 2048) from jw01366002001_04103_00001-seg001_nrcalong_uncal.fits>,). 2023-03-13 21:50:40,885 - stpipe.EurekaS1Pipeline.superbias - INFO - Step superbias parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/home/jkrick/stagejkrick/JK_workingdir/JWST/ERS_NIRCam/Uncalibrated'} 2023-03-13 21:50:40,959 - stpipe.EurekaS1Pipeline.superbias - INFO - Using SUPERBIAS reference file /home/jkrick/stagejkrick/JK_workingdir/JWST/eureka/crds_cache/references/jwst/nircam/jwst_nircam_superbias_0141.fits 2023-03-13 21:50:46,865 - stpipe.EurekaS1Pipeline.superbias - INFO - Step superbias done 2023-03-13 21:50:47,160 - stpipe.EurekaS1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(119, 12, 256, 2048) from jw01366002001_04103_00001-seg001_nrcalong_uncal.fits>,). 2023-03-13 21:50:47,163 - stpipe.EurekaS1Pipeline.refpix - INFO - Step refpix parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/home/jkrick/stagejkrick/JK_workingdir/JWST/ERS_NIRCam/Uncalibrated', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True} 2023-03-13 21:50:51,668 - stpipe.EurekaS1Pipeline.refpix - INFO - NIR subarray data 2023-03-13 21:50:51,674 - stpipe.EurekaS1Pipeline.refpix - INFO - 4 readout amplifiers used 2023-03-13 21:50:51,676 - stpipe.EurekaS1Pipeline.refpix - INFO - The following parameters are valid for this mode: 2023-03-13 21:50:51,677 - stpipe.EurekaS1Pipeline.refpix - INFO - odd_even_columns = True 2023-03-13 21:50:51,678 - stpipe.EurekaS1Pipeline.refpix - INFO - use_side_ref_pixels = True 2023-03-13 21:50:51,679 - stpipe.EurekaS1Pipeline.refpix - INFO - side_smoothing_length = 11 2023-03-13 21:50:51,680 - stpipe.EurekaS1Pipeline.refpix - INFO - side_gain = 1.0 2023-03-13 21:50:51,682 - stpipe.EurekaS1Pipeline.refpix - INFO - The following parameters are not applicable and are ignored 2023-03-13 21:50:51,683 - stpipe.EurekaS1Pipeline.refpix - INFO - odd_even_rows = False 2023-03-13 21:57:15,940 - stpipe.EurekaS1Pipeline.refpix - INFO - Step refpix done 2023-03-13 21:57:16,176 - stpipe.EurekaS1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(119, 12, 256, 2048) from jw01366002001_04103_00001-seg001_nrcalong_uncal.fits>,). 2023-03-13 21:57:16,182 - stpipe.EurekaS1Pipeline.linearity - INFO - Step linearity parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/home/jkrick/stagejkrick/JK_workingdir/JWST/ERS_NIRCam/Uncalibrated'} 2023-03-13 21:57:16,235 - stpipe.EurekaS1Pipeline.linearity - INFO - Using Linearity reference file /home/jkrick/stagejkrick/JK_workingdir/JWST/eureka/crds_cache/references/jwst/nircam/jwst_nircam_linearity_0052.fits 2023-03-13 21:57:16,739 - stpipe.EurekaS1Pipeline.linearity - WARNING - Keyword UAZ_DO_NOT_USE does not correspond to an existing DQ mnemonic, so will be ignored 2023-03-13 21:57:16,742 - stpipe.EurekaS1Pipeline.linearity - WARNING - Keyword UAZ_NO_LIN_SAMP does not correspond to an existing DQ mnemonic, so will be ignored 2023-03-13 21:57:16,744 - stpipe.EurekaS1Pipeline.linearity - WARNING - Keyword UAZ_BAD_LIN_FIT does not correspond to an existing DQ mnemonic, so will be ignored 2023-03-13 21:57:16,746 - stpipe.EurekaS1Pipeline.linearity - WARNING - Keyword UAZ_NO_WELL_SAMP does not correspond to an existing DQ mnemonic, so will be ignored 2023-03-13 21:57:16,748 - stpipe.EurekaS1Pipeline.linearity - WARNING - Keyword UAZ_MODEL_FIT_FAIL does not correspond to an existing DQ mnemonic, so will be ignored 2023-03-13 21:57:16,750 - stpipe.EurekaS1Pipeline.linearity - WARNING - Keyword UAZ_WELL_NOT_DEFINED does not correspond to an existing DQ mnemonic, so will be ignored 2023-03-13 21:57:16,751 - stpipe.EurekaS1Pipeline.linearity - WARNING - Keyword UAZ_MASTER_MASK does not correspond to an existing DQ mnemonic, so will be ignored 2023-03-13 21:57:36,152 - stpipe.EurekaS1Pipeline.linearity - INFO - Step linearity done 2023-03-13 21:57:36,362 - stpipe.EurekaS1Pipeline.persistence - INFO - Step persistence running with args (<RampModel(119, 12, 256, 2048) from jw01366002001_04103_00001-seg001_nrcalong_uncal.fits>,). 2023-03-13 21:57:36,364 - stpipe.EurekaS1Pipeline.persistence - INFO - Step persistence parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/home/jkrick/stagejkrick/JK_workingdir/JWST/ERS_NIRCam/Uncalibrated', 'input_trapsfilled': '', 'flag_pers_cutoff': 40.0, 'save_persistence': False, 'save_trapsfilled': True} 2023-03-13 21:57:36,366 - stpipe.EurekaS1Pipeline.persistence - INFO - Step skipped. 2023-03-13 21:57:36,373 - stpipe.EurekaS1Pipeline.persistence - INFO - Step persistence done 2023-03-13 21:57:36,557 - stpipe.EurekaS1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(119, 12, 256, 2048) from jw01366002001_04103_00001-seg001_nrcalong_uncal.fits>,). 2023-03-13 21:57:36,561 - stpipe.EurekaS1Pipeline.dark_current - INFO - Step dark_current parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': '/home/jkrick/stagejkrick/JK_workingdir/JWST/ERS_NIRCam/Stage1/S1_2023-03-13_nircam_wasp39b_run2/', 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/home/jkrick/stagejkrick/JK_workingdir/JWST/ERS_NIRCam/Uncalibrated', 'dark_output': None} 2023-03-13 21:57:36,609 - stpipe.EurekaS1Pipeline.dark_current - INFO - Using DARK reference file /home/jkrick/stagejkrick/JK_workingdir/JWST/eureka/crds_cache/references/jwst/nircam/jwst_nircam_dark_0355.fits 2023-03-13 21:57:37,327 - stpipe.EurekaS1Pipeline.dark_current - INFO - Science data nints=119, ngroups=12, nframes=4, groupgap=1 2023-03-13 21:57:37,328 - stpipe.EurekaS1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=80, nframes=1, groupgap=0 2023-03-13 21:58:10,809 - stpipe.EurekaS1Pipeline.dark_current - INFO - Step dark_current done 2023-03-13 21:58:11,026 - stpipe.EurekaS1Pipeline.jump - INFO - Step jump running with args (<RampModel(119, 12, 256, 2048) from jw01366002001_04103_00001-seg001_nrcalong_uncal.fits>,). 2023-03-13 21:58:11,029 - stpipe.EurekaS1Pipeline.jump - INFO - Step jump parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/home/jkrick/stagejkrick/JK_workingdir/JWST/ERS_NIRCam/Uncalibrated', 'rejection_threshold': 6.0, 'three_group_rejection_threshold': 6.0, 'four_group_rejection_threshold': 5.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 1000.0, 'min_jump_to_flag_neighbors': 10.0} 2023-03-13 21:58:11,050 - stpipe.EurekaS1Pipeline.jump - INFO - CR rejection threshold = 6 sigma 2023-03-13 21:58:11,078 - stpipe.EurekaS1Pipeline.jump - INFO - Using GAIN reference file: /home/jkrick/stagejkrick/JK_workingdir/JWST/eureka/crds_cache/references/jwst/nircam/jwst_nircam_gain_0097.fits 2023-03-13 21:58:11,174 - stpipe.EurekaS1Pipeline.jump - INFO - Using READNOISE reference file: /home/jkrick/stagejkrick/JK_workingdir/JWST/eureka/crds_cache/references/jwst/nircam/jwst_nircam_readnoise_0157.fits 2023-03-13 21:58:15,742 - stpipe.EurekaS1Pipeline.jump - INFO - Extracting gain subarray to match science data 2023-03-13 21:58:17,705 - stpipe.EurekaS1Pipeline.jump - INFO - Executing two-point difference method 2023-03-13 21:58:30,964 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 1: 2023-03-13 21:58:32,245 - stpipe.EurekaS1Pipeline.jump - WARNING - /home/jovyan/my-conda-envs/ers-nircam/lib/python3.9/site-packages/stcal/jump/twopoint_difference.py:154: RuntimeWarning: All-NaN slice encountered max_ratio = np.nanmax(ratio, axis=0)

2023-03-13 21:58:32,269 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4908 pixels with at least one CR from five or more groups. 2023-03-13 21:58:35,945 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 2: 2023-03-13 21:58:37,100 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4286 pixels with at least one CR from five or more groups. 2023-03-13 21:58:40,193 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 3: 2023-03-13 21:58:40,976 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4154 pixels with at least one CR from five or more groups. 2023-03-13 21:58:43,929 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 4: 2023-03-13 21:58:44,709 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4069 pixels with at least one CR from five or more groups. 2023-03-13 21:58:47,565 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 5: 2023-03-13 21:58:48,244 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4394 pixels with at least one CR from five or more groups. 2023-03-13 21:58:51,359 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 6: 2023-03-13 21:58:52,075 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4453 pixels with at least one CR from five or more groups. 2023-03-13 21:58:55,180 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 7: 2023-03-13 21:58:55,843 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4303 pixels with at least one CR from five or more groups. 2023-03-13 21:58:58,949 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 8: 2023-03-13 21:58:59,628 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4901 pixels with at least one CR from five or more groups. 2023-03-13 21:59:02,934 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 9: 2023-03-13 21:59:03,614 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4333 pixels with at least one CR from five or more groups. 2023-03-13 21:59:06,696 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 10: 2023-03-13 21:59:07,390 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4381 pixels with at least one CR from five or more groups. 2023-03-13 21:59:10,473 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 11: 2023-03-13 21:59:11,145 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4243 pixels with at least one CR from five or more groups. 2023-03-13 21:59:14,104 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 12: 2023-03-13 21:59:14,796 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4368 pixels with at least one CR from five or more groups. 2023-03-13 21:59:17,817 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 13: 2023-03-13 21:59:18,596 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4526 pixels with at least one CR from five or more groups. 2023-03-13 21:59:21,716 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 14: 2023-03-13 21:59:22,404 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4206 pixels with at least one CR from five or more groups. 2023-03-13 21:59:25,404 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 15: 2023-03-13 21:59:26,109 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4258 pixels with at least one CR from five or more groups. 2023-03-13 21:59:29,063 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 16: 2023-03-13 21:59:29,747 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4349 pixels with at least one CR from five or more groups. 2023-03-13 21:59:32,871 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 17: 2023-03-13 21:59:33,563 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 3907 pixels with at least one CR from five or more groups. 2023-03-13 21:59:36,378 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 18: 2023-03-13 21:59:37,058 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4316 pixels with at least one CR from five or more groups. 2023-03-13 21:59:40,163 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 19: 2023-03-13 21:59:40,889 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4029 pixels with at least one CR from five or more groups. 2023-03-13 21:59:43,788 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 20: 2023-03-13 21:59:44,456 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4411 pixels with at least one CR from five or more groups. 2023-03-13 21:59:47,624 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 21: 2023-03-13 21:59:48,328 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4271 pixels with at least one CR from five or more groups. 2023-03-13 21:59:51,360 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 22: 2023-03-13 21:59:52,057 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4359 pixels with at least one CR from five or more groups. 2023-03-13 21:59:55,064 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 23: 2023-03-13 21:59:55,780 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4026 pixels with at least one CR from five or more groups. 2023-03-13 21:59:58,682 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 24: 2023-03-13 21:59:59,372 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4554 pixels with at least one CR from five or more groups. 2023-03-13 22:00:02,585 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 25: 2023-03-13 22:00:03,276 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4334 pixels with at least one CR from five or more groups. 2023-03-13 22:00:06,358 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 26: 2023-03-13 22:00:07,055 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4273 pixels with at least one CR from five or more groups. 2023-03-13 22:00:09,994 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 27: 2023-03-13 22:00:10,681 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4014 pixels with at least one CR from five or more groups. 2023-03-13 22:00:13,510 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 28: 2023-03-13 22:00:14,198 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4056 pixels with at least one CR from five or more groups. 2023-03-13 22:00:17,084 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 29: 2023-03-13 22:00:17,753 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 3928 pixels with at least one CR from five or more groups. 2023-03-13 22:00:20,514 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 30: 2023-03-13 22:00:21,188 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4658 pixels with at least one CR from five or more groups. 2023-03-13 22:00:24,503 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 31: 2023-03-13 22:00:25,203 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4404 pixels with at least one CR from five or more groups. 2023-03-13 22:00:28,275 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 32: 2023-03-13 22:00:28,955 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4494 pixels with at least one CR from five or more groups. 2023-03-13 22:00:32,201 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 33: 2023-03-13 22:00:32,888 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 3919 pixels with at least one CR from five or more groups. 2023-03-13 22:00:35,619 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 34: 2023-03-13 22:00:36,310 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4439 pixels with at least one CR from five or more groups. 2023-03-13 22:00:39,427 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 35: 2023-03-13 22:00:40,103 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4228 pixels with at least one CR from five or more groups. 2023-03-13 22:00:43,129 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 36: 2023-03-13 22:00:43,815 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4184 pixels with at least one CR from five or more groups. 2023-03-13 22:00:46,739 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 37: 2023-03-13 22:00:47,426 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4326 pixels with at least one CR from five or more groups. 2023-03-13 22:00:50,430 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 38: 2023-03-13 22:00:51,119 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4269 pixels with at least one CR from five or more groups. 2023-03-13 22:00:54,135 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 39: 2023-03-13 22:00:54,816 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4283 pixels with at least one CR from five or more groups. 2023-03-13 22:00:57,858 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 40: 2023-03-13 22:00:58,549 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4430 pixels with at least one CR from five or more groups. 2023-03-13 22:01:01,763 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 41: 2023-03-13 22:01:02,455 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4731 pixels with at least one CR from five or more groups. 2023-03-13 22:01:05,804 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 42: 2023-03-13 22:01:06,494 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 3987 pixels with at least one CR from five or more groups. 2023-03-13 22:01:09,337 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 43: 2023-03-13 22:01:10,010 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4880 pixels with at least one CR from five or more groups. 2023-03-13 22:01:13,337 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 44: 2023-03-13 22:01:14,016 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4223 pixels with at least one CR from five or more groups. 2023-03-13 22:01:16,939 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 45: 2023-03-13 22:01:17,611 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4347 pixels with at least one CR from five or more groups. 2023-03-13 22:01:20,744 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 46: 2023-03-13 22:01:21,416 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4334 pixels with at least one CR from five or more groups. 2023-03-13 22:01:24,480 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 47: 2023-03-13 22:01:25,166 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4347 pixels with at least one CR from five or more groups. 2023-03-13 22:01:28,262 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 48: 2023-03-13 22:01:28,968 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4190 pixels with at least one CR from five or more groups. 2023-03-13 22:01:31,909 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 49: 2023-03-13 22:01:32,605 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4214 pixels with at least one CR from five or more groups. 2023-03-13 22:01:35,628 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 50: 2023-03-13 22:01:36,310 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4631 pixels with at least one CR from five or more groups. 2023-03-13 22:01:39,724 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 51: 2023-03-13 22:01:40,403 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4886 pixels with at least one CR from five or more groups. 2023-03-13 22:01:43,932 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 52: 2023-03-13 22:01:44,635 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4332 pixels with at least one CR from five or more groups. 2023-03-13 22:01:47,742 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 53: 2023-03-13 22:01:48,414 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4116 pixels with at least one CR from five or more groups. 2023-03-13 22:01:51,345 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 54: 2023-03-13 22:01:52,032 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4182 pixels with at least one CR from five or more groups. 2023-03-13 22:01:55,053 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 55: 2023-03-13 22:01:55,739 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4033 pixels with at least one CR from five or more groups. 2023-03-13 22:01:58,599 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 56: 2023-03-13 22:01:59,278 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 3953 pixels with at least one CR from five or more groups. 2023-03-13 22:02:02,004 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 57: 2023-03-13 22:02:02,699 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 3995 pixels with at least one CR from five or more groups. 2023-03-13 22:02:05,561 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 58: 2023-03-13 22:02:06,237 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4213 pixels with at least one CR from five or more groups. 2023-03-13 22:02:09,273 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 59: 2023-03-13 22:02:09,963 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4317 pixels with at least one CR from five or more groups. 2023-03-13 22:02:13,036 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 60: 2023-03-13 22:02:13,736 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4910 pixels with at least one CR from five or more groups. 2023-03-13 22:02:17,251 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 61: 2023-03-13 22:02:17,922 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4415 pixels with at least one CR from five or more groups. 2023-03-13 22:02:21,071 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 62: 2023-03-13 22:02:21,774 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4558 pixels with at least one CR from five or more groups. 2023-03-13 22:02:25,014 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 63: 2023-03-13 22:02:25,691 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4480 pixels with at least one CR from five or more groups. 2023-03-13 22:02:28,926 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 64: 2023-03-13 22:02:29,616 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4121 pixels with at least one CR from five or more groups. 2023-03-13 22:02:32,526 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 65: 2023-03-13 22:02:33,193 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 3841 pixels with at least one CR from five or more groups. 2023-03-13 22:02:35,875 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 66: 2023-03-13 22:02:36,560 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4004 pixels with at least one CR from five or more groups. 2023-03-13 22:02:39,364 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 67: 2023-03-13 22:02:40,049 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4131 pixels with at least one CR from five or more groups. 2023-03-13 22:02:42,993 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 68: 2023-03-13 22:02:43,674 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 3958 pixels with at least one CR from five or more groups. 2023-03-13 22:02:46,515 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 69: 2023-03-13 22:02:47,209 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4204 pixels with at least one CR from five or more groups. 2023-03-13 22:02:50,140 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 70: 2023-03-13 22:02:50,815 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4017 pixels with at least one CR from five or more groups. 2023-03-13 22:02:53,656 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 71: 2023-03-13 22:02:54,332 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4232 pixels with at least one CR from five or more groups. 2023-03-13 22:02:57,351 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 72: 2023-03-13 22:02:58,053 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4039 pixels with at least one CR from five or more groups. 2023-03-13 22:03:00,945 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 73: 2023-03-13 22:03:01,620 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4266 pixels with at least one CR from five or more groups. 2023-03-13 22:03:04,698 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 74: 2023-03-13 22:03:05,354 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4159 pixels with at least one CR from five or more groups. 2023-03-13 22:03:08,305 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 75: 2023-03-13 22:03:08,983 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4246 pixels with at least one CR from five or more groups. 2023-03-13 22:03:12,045 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 76: 2023-03-13 22:03:12,725 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4055 pixels with at least one CR from five or more groups. 2023-03-13 22:03:15,628 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 77: 2023-03-13 22:03:16,330 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4652 pixels with at least one CR from five or more groups. 2023-03-13 22:03:19,679 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 78: 2023-03-13 22:03:20,351 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4339 pixels with at least one CR from five or more groups. 2023-03-13 22:03:23,438 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 79: 2023-03-13 22:03:24,126 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4322 pixels with at least one CR from five or more groups. 2023-03-13 22:03:27,074 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 80: 2023-03-13 22:03:27,766 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4131 pixels with at least one CR from five or more groups. 2023-03-13 22:03:30,662 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 81: 2023-03-13 22:03:31,338 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4159 pixels with at least one CR from five or more groups. 2023-03-13 22:03:34,303 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 82: 2023-03-13 22:03:34,998 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4228 pixels with at least one CR from five or more groups. 2023-03-13 22:03:37,996 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 83: 2023-03-13 22:03:38,675 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4384 pixels with at least one CR from five or more groups. 2023-03-13 22:03:41,719 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 84: 2023-03-13 22:03:42,416 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4501 pixels with at least one CR from five or more groups. 2023-03-13 22:03:45,629 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 85: 2023-03-13 22:03:46,316 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4015 pixels with at least one CR from five or more groups. 2023-03-13 22:03:49,178 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 86: 2023-03-13 22:03:49,865 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4255 pixels with at least one CR from five or more groups. 2023-03-13 22:03:52,864 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 87: 2023-03-13 22:03:53,566 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4108 pixels with at least one CR from five or more groups. 2023-03-13 22:03:56,466 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 88: 2023-03-13 22:03:57,188 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4155 pixels with at least one CR from five or more groups. 2023-03-13 22:04:00,177 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 89: 2023-03-13 22:04:00,864 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4189 pixels with at least one CR from five or more groups. 2023-03-13 22:04:03,912 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 90: 2023-03-13 22:04:04,594 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4211 pixels with at least one CR from five or more groups. 2023-03-13 22:04:07,507 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 91: 2023-03-13 22:04:08,180 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4189 pixels with at least one CR from five or more groups. 2023-03-13 22:04:11,113 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 92: 2023-03-13 22:04:11,808 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4459 pixels with at least one CR from five or more groups. 2023-03-13 22:04:14,981 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 93: 2023-03-13 22:04:15,666 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4786 pixels with at least one CR from five or more groups. 2023-03-13 22:04:18,984 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 94: 2023-03-13 22:04:19,677 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4856 pixels with at least one CR from five or more groups. 2023-03-13 22:04:23,221 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 95: 2023-03-13 22:04:23,897 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4264 pixels with at least one CR from five or more groups. 2023-03-13 22:04:26,922 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 96: 2023-03-13 22:04:27,639 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4099 pixels with at least one CR from five or more groups. 2023-03-13 22:04:30,632 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 97: 2023-03-13 22:04:31,321 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4217 pixels with at least one CR from five or more groups. 2023-03-13 22:04:34,340 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 98: 2023-03-13 22:04:35,033 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4197 pixels with at least one CR from five or more groups. 2023-03-13 22:04:37,996 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 99: 2023-03-13 22:04:38,680 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4540 pixels with at least one CR from five or more groups. 2023-03-13 22:04:41,884 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 100: 2023-03-13 22:04:42,570 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4650 pixels with at least one CR from five or more groups. 2023-03-13 22:04:45,877 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 101: 2023-03-13 22:04:46,537 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4095 pixels with at least one CR from five or more groups. 2023-03-13 22:04:49,397 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 102: 2023-03-13 22:04:50,080 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4175 pixels with at least one CR from five or more groups. 2023-03-13 22:04:53,018 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 103: 2023-03-13 22:04:53,705 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4368 pixels with at least one CR from five or more groups. 2023-03-13 22:04:56,820 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 104: 2023-03-13 22:04:57,502 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4297 pixels with at least one CR from five or more groups. 2023-03-13 22:05:00,548 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 105: 2023-03-13 22:05:01,255 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4138 pixels with at least one CR from five or more groups. 2023-03-13 22:05:04,129 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 106: 2023-03-13 22:05:04,815 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4007 pixels with at least one CR from five or more groups. 2023-03-13 22:05:07,698 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 107: 2023-03-13 22:05:08,368 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4190 pixels with at least one CR from five or more groups. 2023-03-13 22:05:11,355 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 108: 2023-03-13 22:05:12,048 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4184 pixels with at least one CR from five or more groups. 2023-03-13 22:05:15,108 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 109: 2023-03-13 22:05:15,784 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4690 pixels with at least one CR from five or more groups. 2023-03-13 22:05:19,149 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 110: 2023-03-13 22:05:19,852 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4423 pixels with at least one CR from five or more groups. 2023-03-13 22:05:23,002 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 111: 2023-03-13 22:05:23,684 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4032 pixels with at least one CR from five or more groups. 2023-03-13 22:05:26,490 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 112: 2023-03-13 22:05:27,169 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4389 pixels with at least one CR from five or more groups. 2023-03-13 22:05:30,276 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 113: 2023-03-13 22:05:30,984 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4319 pixels with at least one CR from five or more groups. 2023-03-13 22:05:33,965 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 114: 2023-03-13 22:05:34,657 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4427 pixels with at least one CR from five or more groups. 2023-03-13 22:05:37,889 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 115: 2023-03-13 22:05:38,566 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4401 pixels with at least one CR from five or more groups. 2023-03-13 22:05:41,625 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 116: 2023-03-13 22:05:42,319 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4307 pixels with at least one CR from five or more groups. 2023-03-13 22:05:45,435 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 117: 2023-03-13 22:05:46,133 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4079 pixels with at least one CR from five or more groups. 2023-03-13 22:05:49,054 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 118: 2023-03-13 22:05:49,740 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4555 pixels with at least one CR from five or more groups. 2023-03-13 22:05:52,942 - stpipe.EurekaS1Pipeline.jump - INFO - Working on integration 119: 2023-03-13 22:05:53,640 - stpipe.EurekaS1Pipeline.jump - INFO - From highest outlier, two-point found 4306 pixels with at least one CR from five or more groups. 2023-03-13 22:05:56,807 - stpipe.EurekaS1Pipeline.jump - INFO - Flagging large events (snowballs, showers).

ModuleNotFoundError Traceback (most recent call last) Input In [7], in <cell line: 1>() ----> 1 s1_meta = s1.rampfitJWST(eventlabel, ecf_path=ecf_path, input_meta=input_meta_S1)

File /stage/irsa-staff-jkrick/JK_workingdir/JWST/Eureka/src/eureka/S1_detector_processing/s1_process.py:108, in rampfitJWST(eventlabel, ecf_path, input_meta) 105 hdulist[0].header['NDITHPTS'] = 1 106 hdulist[0].header['NRIMDTPT'] = 1 --> 108 EurekaS1Pipeline().run_eurekaS1(filename, meta, log) 110 # Calculate total run time 111 total = (time_pkg.time() - t0) / 60.

File /stage/irsa-staff-jkrick/JK_workingdir/JWST/Eureka/src/eureka/S1_detector_processing/s1_process.py:221, in EurekaS1Pipeline.run_eurekaS1(self, filename, meta, log) 217 self.ramp_fit.custom_exponents = \ 218 meta.default_ramp_fit_custom_exponents 220 # Run Stage 1 --> 221 self(filename) 223 return

File /home/jovyan/my-conda-envs/ers-nircam/lib/python3.9/site-packages/stpipe/step.py:454, in Step.run(self, args) 452 self.prefetch(args) 453 try: --> 454 step_result = self.process(*args) 455 except TypeError as e: 456 if "process() takes exactly" in str(e):

File /home/jovyan/my-conda-envs/ers-nircam/lib/python3.9/site-packages/jwst/pipeline/calwebb_detector1.py:119, in Detector1Pipeline.process(self, input) 116 input = self.dark_current(input) 118 # apply the jump step --> 119 input = self.jump(input) 121 # save the corrected ramp data, if requested 122 if self.save_calibrated_ramp:

File /home/jovyan/my-conda-envs/ers-nircam/lib/python3.9/site-packages/stpipe/step.py:454, in Step.run(self, args) 452 self.prefetch(args) 453 try: --> 454 step_result = self.process(*args) 455 except TypeError as e: 456 if "process() takes exactly" in str(e):

File /home/jovyan/my-conda-envs/ers-nircam/lib/python3.9/site-packages/jwst/jump/jump_step.py:70, in JumpStep.process(self, input) 67 readnoise_model = datamodels.ReadnoiseModel(readnoise_filename) 69 # Call the jump detection routine ---> 70 result = run_detect_jumps(input_model, gain_model, readnoise_model, 71 rej_thresh, three_grp_rej_thresh, four_grp_rej_thresh, max_cores, 72 max_jump_to_flag_neighbors, min_jump_to_flag_neighbors, 73 flag_4_neighbors) 74 gain_model.close() 75 readnoise_model.close()

File /home/jovyan/my-conda-envs/ers-nircam/lib/python3.9/site-packages/jwst/jump/jump.py:40, in run_detect_jumps(input_model, gain_model, readnoise_model, rejection_thresh, three_grp_thresh, four_grp_thresh, max_cores, max_jump_to_flag_neighbors, min_jump_to_flag_neighbors, flag_4_neighbors) 36 log.info('Extracting readnoise subarray to match science data') 37 readnoise_2d = reffile_utils.get_subarray_data(input_model, 38 readnoise_model) ---> 40 new_gdq, new_pdq = detect_jumps(frames_per_group, data, gdq, pdq, err, 41 gain_2d, readnoise_2d, 42 rejection_thresh, three_grp_thresh, 43 four_grp_thresh, max_cores, 44 max_jump_to_flag_neighbors, 45 min_jump_to_flag_neighbors, 46 flag_4_neighbors, dqflags.pixel) 48 # Update the DQ arrays of the output model with the jump detection results 49 output_model.groupdq = new_gdq

File /home/jovyan/my-conda-envs/ers-nircam/lib/python3.9/site-packages/stcal/jump/jump.py:221, in detect_jumps(frames_per_group, data, gdq, pdq, err, gain_2d, readnoise_2d, rejection_thresh, three_grp_thresh, four_grp_thresh, max_cores, max_jump_to_flag_neighbors, min_jump_to_flag_neighbors, flag_4_neighbors, dqflags, after_jump_flag_dn1, after_jump_flag_n1, after_jump_flag_dn2, after_jump_flag_n2, min_sat_area, min_jump_area, expand_factor, use_ellipses, sat_required_snowball, expand_large_events) 219 # This is the flag that controls the flagging of either snowballs or showers. 220 if expand_large_events: --> 221 flag_large_events(gdq, jump_flag, sat_flag, min_sat_area=min_sat_area, 222 min_jump_area=min_jump_area, 223 expand_factor=expand_factor, use_ellipses=use_ellipses, 224 sat_required_snowball=sat_required_snowball) 226 else: 227 yinc = int(n_rows / n_slices)

File /home/jovyan/my-conda-envs/ers-nircam/lib/python3.9/site-packages/stcal/jump/jump.py:359, in flag_large_events(gdq, jump_flag, sat_flag, min_sat_area, min_jump_area, expand_factor, use_ellipses, sat_required_snowball) 355 else: 356 # this line needs to be changed later to just look at saturation flags. 357 new_flagged_pixels = gdq[integration, group, :, :] - gdq[integration, group - 1, :, :] --> 359 sat_circles = find_circles(new_flagged_pixels, sat_flag, min_sat_area) 360 sat_pixels = np.bitwise_and(new_flagged_pixels, sat_flag) 361 saty, satx = np.where(sat_pixels == sat_flag)

File /home/jovyan/my-conda-envs/ers-nircam/lib/python3.9/site-packages/stcal/jump/jump.py:458, in find_circles(dqplane, bitmask, min_area) 456 circles = [cv.minEnclosingCircle(con) for con in bigcontours] 457 else: --> 458 raise ModuleNotFoundError(ELLIPSE_PACKAGE_WARNING) 459 return circles

ModuleNotFoundError: opencv-python must be installed (pip install stcal[opencv]) in order to use ellipses

jkrick commented 1 year ago

And here are those 'requirement already satisfied' statements from the pip install stcal[opencv] so you can see that it does appear to have installed it.

Requirement already satisfied: stcal[opencv] in /home/jovyan/my-conda-envs/ers-nircam/lib/python3.9/site-packages (1.3.4) Requirement already satisfied: scipy>=1.6.0 in /home/jovyan/my-conda-envs/ers-nircam/lib/python3.9/site-packages (from stcal[opencv]) (1.9.1) Requirement already satisfied: numpy>=1.17 in /home/jovyan/my-conda-envs/ers-nircam/lib/python3.9/site-packages (from stcal[opencv]) (1.22.0) Requirement already satisfied: astropy>=5.0.4 in /home/jovyan/my-conda-envs/ers-nircam/lib/python3.9/site-packages (from stcal[opencv]) (5.2.1) Requirement already satisfied: opencv-python>=4.6.0.66 in /home/jovyan/my-conda-envs/ers-nircam/lib/python3.9/site-packages (from stcal[opencv]) (4.7.0.72) Requirement already satisfied: pyerfa>=2.0 in /home/jovyan/my-conda-envs/ers-nircam/lib/python3.9/site-packages (from astropy>=5.0.4->stcal[opencv]) (2.0.0.1) Requirement already satisfied: packaging>=19.0 in /home/jovyan/my-conda-envs/ers-nircam/lib/python3.9/site-packages (from astropy>=5.0.4->stcal[opencv]) (23.0) Requirement already satisfied: PyYAML>=3.13 in /home/jovyan/my-conda-envs/ers-nircam/lib/python3.9/site-packages (from astropy>=5.0.4->stcal[opencv]) (6.0)

meganmansfield commented 1 year ago

Hi, sorry for the delay in following up on this! We ran into a similar issue when setting up this demo, which is why we added the line "pip install stcal[opencv]" to the install instructions. Can you let me know what version of opencv-python you have? Perhaps there's an issue with the version.

jkrick commented 1 year ago

Name: opencv-python Version: 4.7.0.72 Summary: Wrapper package for OpenCV python bindings. Home-page: https://github.com/opencv/opencv-python Author: Author-email: License: Apache 2.0 Location: /home/jovyan/my-conda-envs/ers-nircam/lib/python3.9/site-packages Requires: numpy, numpy, numpy Required-by: