Spec3Pipeline for MRS (MIRI MRS CALSPEC3)¶
Spec3Pipeline combines the calibrated data from multiple exposures (e.g. a dither/nod pattern) into a single combined 3D spectral product and a combined 1D spectrum. Before being combined, the exposures receive additional corrections for the purpose of background matching and subtraction, as well as outlier rejection.
Official documentation for Spec3Pipeline can be found here:
https://jwst-pipeline.readthedocs.io/en/latest/jwst/pipeline/calwebb_spec3.html
The Spec3Pipeline for MRS comprises a linear series of steps. The steps in order are:
Step |
Description |
|---|---|
|
subtract master background spectrum created from input exposures or supplied by user |
|
matches image intensities of input MIRI MRS images |
|
flag any remaining cosmic-rays or other artifacts left over from previous calibrations |
|
produce 3D spectral cubes from the ‘cleaned’ 2D detector image |
|
extract 1D spectrum from 3D cube |
For more information and examples of each of the steps click on the links in the side bar.
Note that the master_background step would normally be run if no background subtraction happened in Spec2Pipeline. However, we will skip the step in this example.
Users of this notebook should be aware that cubes produced will not be perfect and suffer from known issues with MIRISim (oversized MRS PSF, channel 4 flux issues, etc.). Also, the spectral extraction step in the pipeline (extract_1d) does not yet correctly implement the aperture correction factors so the fluxes will be off.
Input data¶
An example of running the file through the Spec3Pipeline is now shown using a simple simulated fullband, 2-point dither observation of a point source (power law plus emission lines spectrum) with the MIRI MRS produced with MIRISim v2.3 and brought to level 2B using the Detector1Pipeline and Spec2Pipeline modules.
Python¶
Start by importing what will be used and set the CRDS_CONTEXT
# imports
import os, glob, shutil
import numpy as np
from matplotlib.colors import LogNorm
from cycler import cycler
import matplotlib.pyplot as plt
from subprocess import call
from jwst import datamodels
from jwst.associations.lib.member import Member
from jwst.associations.asn_from_list import asn_from_list
# set the CRDS_CONTEXT
os.environ["CRDS_CONTEXT"] = "jwst_0641.pmap"
Image3Pipeline requires an association file as input that lists the exposures to be combined. The content of the association file is printed for inspection. It is assumed they are in ‘MRS_science’.
# load the science and background files to lists
my_science_files = glob.glob('MRS_science/*cal.fits')
my_science_files = sorted(my_science_files)
# set the association name
asn_name = 'my_point_source'
# setup an empty level 2 association structure
asn = asn_from_list(my_science_files, product_name=asn_name)
# set some metadata
asn['asn_pool'] = asn_name + '_pool'
asn['asn_type'] = 'spec3'
# print the association and save to file
name, ser = asn.dump()
print(ser)
asn_file = asn_name + '_lvl3_asn.json'
with open(asn_file, 'w') as f:
f.write(ser)
{
"asn_type": "spec3",
"asn_rule": "DMS_Level3_Base",
"version_id": null,
"code_version": "0.17.1",
"degraded_status": "No known degraded exposures in association.",
"program": "noprogram",
"constraints": "No constraints",
"asn_id": "a3001",
"target": "none",
"asn_pool": "my_point_source_pool",
"products": [
{
"name": "my_point_source",
"members": [
{
"expname": "MRS_science/my_point_source_exposure10_cal.fits",
"exptype": "science"
},
{
"expname": "MRS_science/my_point_source_exposure11_cal.fits",
"exptype": "science"
},
{
"expname": "MRS_science/my_point_source_exposure12_cal.fits",
"exptype": "science"
},
{
"expname": "MRS_science/my_point_source_exposure1_cal.fits",
"exptype": "science"
},
{
"expname": "MRS_science/my_point_source_exposure2_cal.fits",
"exptype": "science"
},
{
"expname": "MRS_science/my_point_source_exposure3_cal.fits",
"exptype": "science"
},
{
"expname": "MRS_science/my_point_source_exposure4_cal.fits",
"exptype": "science"
},
{
"expname": "MRS_science/my_point_source_exposure5_cal.fits",
"exptype": "science"
},
{
"expname": "MRS_science/my_point_source_exposure6_cal.fits",
"exptype": "science"
},
{
"expname": "MRS_science/my_point_source_exposure7_cal.fits",
"exptype": "science"
},
{
"expname": "MRS_science/my_point_source_exposure8_cal.fits",
"exptype": "science"
},
{
"expname": "MRS_science/my_point_source_exposure9_cal.fits",
"exptype": "science"
}
]
}
]
}
Import Spec3Pipeline and print the docstring to show some information
from jwst.pipeline import Spec3Pipeline
print(Spec3Pipeline.__doc__)
Spec3Pipeline: Processes JWST spectroscopic exposures from Level 2b to 3.
Included steps are:
assign moving target wcs (assign_mtwcs)
master background subtraction (master_background)
MIRI MRS background matching (mrs_imatch)
outlier detection (outlier_detection)
2-D spectroscopic resampling (resample_spec)
3-D spectroscopic resampling (cube_build)
1-D spectral extraction (extract_1d)
1-D spectral combination (combine_1d)
The association file is passed as input. The output files will be saved in my_output_dir.
Parameters used:
save_results: boolean, optional, default=False
save the results to file
output_dir : boolean, optional, default is the working directory
the location to save the output
steps : dict, optional, default None
pass parameters to steps
The skip parameters is passed to master_background' (becuase there is no background in the simulation), outlier_detection(due to a bug causing the pipeline to crash) andskymatch` (which at the moment appears to be overestimating the background resulting in negative fluxes).
# user specified
my_output_dir = 'demo_output'
# the output directory should be created if it doesn't exist
if not os.path.exists(my_output_dir):
os.mkdir(my_output_dir)
# run the pipeline
Spec3Pipeline.call(asn_file, save_results=True, output_dir=my_output_dir,
steps={'master_background': {'skip': True},
'outlier_detection': {'skip': True},
'mrs_imatch': {'skip': True}})
2020-10-29 12:21:17,528 - CRDS - ERROR - Error determining best reference for 'pars-assignmtwcsstep' = Unknown reference type 'pars-assignmtwcsstep'
2020-10-29 12:21:20,642 - CRDS - ERROR - Error determining best reference for 'pars-masterbackgroundstep' = Unknown reference type 'pars-masterbackgroundstep'
2020-10-29 12:21:23,751 - CRDS - ERROR - Error determining best reference for 'pars-mrsimatchstep' = Unknown reference type 'pars-mrsimatchstep'
2020-10-29 12:21:26,880 - CRDS - ERROR - Error determining best reference for 'pars-outlierdetectionstep' = Unknown reference type 'pars-outlierdetectionstep'
2020-10-29 12:21:29,889 - CRDS - ERROR - Error determining best reference for 'pars-resamplespecstep' = Unknown reference type 'pars-resamplespecstep'
2020-10-29 12:21:33,045 - CRDS - ERROR - Error determining best reference for 'pars-cubebuildstep' = Unknown reference type 'pars-cubebuildstep'
2020-10-29 12:21:36,113 - CRDS - ERROR - Error determining best reference for 'pars-extract1dstep' = Unknown reference type 'pars-extract1dstep'
2020-10-29 12:21:39,272 - CRDS - ERROR - Error determining best reference for 'pars-combine1dstep' = Unknown reference type 'pars-combine1dstep'
2020-10-29 12:21:42,301 - CRDS - ERROR - Error determining best reference for 'pars-spec3pipeline' = Unknown reference type 'pars-spec3pipeline'
2020-10-29 12:21:42,309 - stpipe.Spec3Pipeline - INFO - Spec3Pipeline instance created.
2020-10-29 12:21:42,310 - stpipe.Spec3Pipeline.assign_mtwcs - INFO - AssignMTWcsStep instance created.
2020-10-29 12:21:42,312 - stpipe.Spec3Pipeline.master_background - INFO - MasterBackgroundStep instance created.
2020-10-29 12:21:42,314 - stpipe.Spec3Pipeline.mrs_imatch - INFO - MRSIMatchStep instance created.
2020-10-29 12:21:42,316 - stpipe.Spec3Pipeline.outlier_detection - INFO - OutlierDetectionStep instance created.
2020-10-29 12:21:42,318 - stpipe.Spec3Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2020-10-29 12:21:42,320 - stpipe.Spec3Pipeline.cube_build - INFO - CubeBuildStep instance created.
2020-10-29 12:21:42,322 - stpipe.Spec3Pipeline.extract_1d - INFO - Extract1dStep instance created.
2020-10-29 12:21:42,324 - stpipe.Spec3Pipeline.combine_1d - INFO - Combine1dStep instance created.
2020-10-29 12:21:42,541 - stpipe.Spec3Pipeline - INFO - Step Spec3Pipeline running with args ('my_point_source_lvl3_asn.json',).
2020-10-29 12:21:42,548 - stpipe.Spec3Pipeline - INFO - Step Spec3Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': 'demo_output', 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': True, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'steps': {'assign_mtwcs': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': True, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'assign_mtwcs', 'search_output_file': True, 'input_dir': ''}, 'master_background': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': True, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'user_background': None, 'save_background': False, 'force_subtract': False}, 'mrs_imatch': {'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': '', 'bkg_degree': 1, 'subtract': False}, 'outlier_detection': {'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': False, 'input_dir': '', 'weight_type': 'exptime', 'pixfrac': 1.0, 'kernel': 'square', 'fillval': 'INDEF', 'nlow': 0, 'nhigh': 0, 'maskpt': 0.7, 'grow': 1, 'snr': '4.0 3.0', 'scale': '0.5 0.4', 'backg': 0.0, 'save_intermediate_results': False, 'resample_data': True, 'good_bits': '~DO_NOT_USE', 'scale_detection': False}, 'resample_spec': {'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': '', 'pixfrac': 1.0, 'kernel': 'square', 'fillval': 'INDEF', 'weight_type': 'exptime', 'single': False, 'blendheaders': True}, 'cube_build': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': True, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': False, 'input_dir': '', 'channel': 'all', 'band': 'all', 'grating': 'all', 'filter': 'all', 'output_type': 'band', 'scale1': 0.0, 'scale2': 0.0, 'scalew': 0.0, 'weighting': 'emsm', 'coord_system': 'skyalign', 'rois': 0.0, 'roiw': 0.0, 'weight_power': 0.0, 'wavemin': None, 'wavemax': None, 'single': False, 'xdebug': None, 'ydebug': None, 'zdebug': None, 'skip_dqflagging': False}, 'extract_1d': {'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': '', 'smoothing_length': None, 'bkg_order': None, 'log_increment': 50, 'subtract_background': None, 'use_source_posn': None, 'apply_apcorr': True}, 'combine_1d': {'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': '', 'exptime_key': 'exposure_time'}}}
2020-10-29 12:21:45,523 - stpipe.Spec3Pipeline - INFO - Prefetching reference files for dataset: 'my_point_source_exposure10_cal.fits' reftypes = ['apcorr', 'cubepar', 'drizpars', 'extract1d', 'resol']
2020-10-29 12:21:45,530 - stpipe.Spec3Pipeline - INFO - Prefetch for APCORR reference file is '/Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_apcorr_0006.fits'.
2020-10-29 12:21:45,531 - stpipe.Spec3Pipeline - INFO - Prefetch for CUBEPAR reference file is '/Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_cubepar_0003.fits'.
2020-10-29 12:21:45,531 - stpipe.Spec3Pipeline - INFO - Prefetch for DRIZPARS reference file is '/Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_drizpars_0001.fits'.
2020-10-29 12:21:45,532 - stpipe.Spec3Pipeline - INFO - Prefetch for EXTRACT1D reference file is '/Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_extract1d_0003.json'.
2020-10-29 12:21:45,533 - stpipe.Spec3Pipeline - INFO - Prefetch for RESOL reference file is '/Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_resol_0003.fits'.
2020-10-29 12:21:45,534 - stpipe.Spec3Pipeline - INFO - Starting calwebb_spec3 ...
2020-10-29 12:22:18,719 - stpipe.Spec3Pipeline.mrs_imatch - INFO - Step mrs_imatch running with args (<ModelContainer>,).
2020-10-29 12:22:18,721 - stpipe.Spec3Pipeline.mrs_imatch - INFO - Step mrs_imatch 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': 'mrs_imatch', 'search_output_file': True, 'input_dir': '', 'bkg_degree': 1, 'subtract': False}
2020-10-29 12:22:18,722 - stpipe.Spec3Pipeline.mrs_imatch - INFO - Step skipped.
2020-10-29 12:22:18,726 - stpipe.Spec3Pipeline.mrs_imatch - INFO - Step mrs_imatch done
2020-10-29 12:22:19,050 - stpipe.Spec3Pipeline.outlier_detection - INFO - Step outlier_detection running with args (<ModelContainer>,).
2020-10-29 12:22:19,051 - stpipe.Spec3Pipeline.outlier_detection - INFO - Step outlier_detection 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': True, 'skip': True, 'suffix': 'crf', 'search_output_file': False, 'input_dir': '', 'weight_type': 'exptime', 'pixfrac': 1.0, 'kernel': 'square', 'fillval': 'INDEF', 'nlow': 0, 'nhigh': 0, 'maskpt': 0.7, 'grow': 1, 'snr': '4.0 3.0', 'scale': '0.5 0.4', 'backg': 0.0, 'save_intermediate_results': False, 'resample_data': True, 'good_bits': '~DO_NOT_USE', 'scale_detection': False}
2020-10-29 12:22:19,052 - stpipe.Spec3Pipeline.outlier_detection - INFO - Step skipped.
2020-10-29 12:22:19,056 - stpipe.Spec3Pipeline.outlier_detection - INFO - Step outlier_detection done
2020-10-29 12:22:19,382 - stpipe.Spec3Pipeline.cube_build - INFO - Step cube_build running with args (<ModelContainer>,).
2020-10-29 12:22:19,384 - stpipe.Spec3Pipeline.cube_build - INFO - Step cube_build parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': True, 'output_use_index': True, 'save_results': True, 'skip': False, 'suffix': 's3d', 'search_output_file': False, 'input_dir': '', 'channel': 'all', 'band': 'all', 'grating': 'all', 'filter': 'all', 'output_type': 'band', 'scale1': 0.0, 'scale2': 0.0, 'scalew': 0.0, 'weighting': 'emsm', 'coord_system': 'skyalign', 'rois': 0.0, 'roiw': 0.0, 'weight_power': 0.0, 'wavemin': None, 'wavemax': None, 'single': False, 'xdebug': None, 'ydebug': None, 'zdebug': None, 'skip_dqflagging': False}
2020-10-29 12:22:19,385 - stpipe.Spec3Pipeline.cube_build - INFO - Starting IFU Cube Building Step
2020-10-29 12:22:19,386 - stpipe.Spec3Pipeline.cube_build - INFO - Input interpolation: pointcloud
2020-10-29 12:22:19,386 - stpipe.Spec3Pipeline.cube_build - INFO - Coordinate system to use: skyalign
2020-10-29 12:22:19,387 - stpipe.Spec3Pipeline.cube_build - INFO - Weighting method for point cloud: emsm
2020-10-29 12:22:19,595 - stpipe.Spec3Pipeline.cube_build - INFO - The desired cubes cover the MIRI Channels: ['1', '1', '1', '2', '2', '2', '3', '3', '3', '4', '4', '4']
2020-10-29 12:22:19,596 - stpipe.Spec3Pipeline.cube_build - INFO - The desired cubes cover the MIRI subchannels: ['short', 'medium', 'long', 'short', 'medium', 'long', 'short', 'medium', 'long', 'short', 'medium', 'long']
2020-10-29 12:22:19,596 - stpipe.Spec3Pipeline.cube_build - INFO - Reading cube parameter file /Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_cubepar_0003.fits
2020-10-29 12:22:20,893 - stpipe.Spec3Pipeline.cube_build - INFO - Output Cubes are single channel, single sub-channel IFU Cubes
2020-10-29 12:22:20,894 - stpipe.Spec3Pipeline.cube_build - INFO - Number of IFU cubes produced by this run = 12
2020-10-29 12:22:20,896 - stpipe.Spec3Pipeline.cube_build - INFO - Number of bands in cube: 1
2020-10-29 12:22:21,563 - stpipe.Spec3Pipeline.cube_build - INFO - Cube Geometry:
2020-10-29 12:22:21,564 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2020-10-29 12:22:21,565 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 1 51 26.00 0.00000554 0.13000000 -3.31499988 3.31499988
2020-10-29 12:22:21,565 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 2 41 21.00 0.00000764 0.13000000 -2.66499990 2.66499990
2020-10-29 12:22:21,566 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2020-10-29 12:22:21,567 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 3 850 1.00 4.89049987 0.00100000 4.88999987 5.73999991
2020-10-29 12:22:21,567 - stpipe.Spec3Pipeline.cube_build - INFO - Cube covers channel, subchannel: 1, short
2020-10-29 12:22:21,568 - stpipe.Spec3Pipeline.cube_build - INFO - Output Name: my_point_source_ch1-short_s3d.fits
2020-10-29 12:22:21,989 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 6617 with wavelength below 4.889499866461847
2020-10-29 12:22:21,990 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 11821 with wavelength above 5.740499906882178
2020-10-29 12:22:22,036 - stpipe.Spec3Pipeline.cube_build - INFO - Time to transform pixels to output frame = 0.5 s
2020-10-29 12:23:11,755 - stpipe.Spec3Pipeline.cube_build - INFO - Time to set initial dq values = 49.7 s
2020-10-29 12:24:25,120 - stpipe.Spec3Pipeline.cube_build - INFO - Time to match file to ifucube = 73.4 s
2020-10-29 12:24:25,511 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 6617 with wavelength below 4.889499866461847
2020-10-29 12:24:25,512 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 11821 with wavelength above 5.740499906882178
2020-10-29 12:24:25,570 - stpipe.Spec3Pipeline.cube_build - INFO - Time to transform pixels to output frame = 0.4 s
2020-10-29 12:25:17,294 - stpipe.Spec3Pipeline.cube_build - INFO - Time to set initial dq values = 51.7 s
2020-10-29 12:26:29,800 - stpipe.Spec3Pipeline.cube_build - INFO - Time to match file to ifucube = 72.5 s
2020-10-29 12:26:29,861 - stpipe.Spec3Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2020-10-29 12:26:29,862 - stpipe.Spec3Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2020-10-29 12:26:29,863 - stpipe.Spec3Pipeline.cube_build - INFO - Time to find Cube Flux = 0.1 s
2020-10-29 12:26:31,864 - stpipe.Spec3Pipeline.cube_build - INFO - IFUChannel 1
2020-10-29 12:26:31,902 - stpipe.Spec3Pipeline.cube_build - INFO - Number of bands in cube: 1
2020-10-29 12:26:32,603 - stpipe.Spec3Pipeline.cube_build - INFO - Cube Geometry:
2020-10-29 12:26:32,604 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2020-10-29 12:26:32,605 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 1 49 25.00 0.00001065 0.13000000 -3.18499988 3.18499988
2020-10-29 12:26:32,605 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 2 39 20.00 -0.00003592 0.13000000 -2.53499991 2.53499991
2020-10-29 12:26:32,606 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2020-10-29 12:26:32,606 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 3 980 1.00 5.64049987 0.00100000 5.63999987 6.61999991
2020-10-29 12:26:32,607 - stpipe.Spec3Pipeline.cube_build - INFO - Cube covers channel, subchannel: 1, medium
2020-10-29 12:26:32,608 - stpipe.Spec3Pipeline.cube_build - INFO - Output Name: my_point_source_ch1-medium_s3d.fits
2020-10-29 12:26:33,053 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 6386 with wavelength below 5.639499866461847
2020-10-29 12:26:33,054 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 11340 with wavelength above 6.620499913056847
2020-10-29 12:26:33,105 - stpipe.Spec3Pipeline.cube_build - INFO - Time to transform pixels to output frame = 0.5 s
2020-10-29 12:27:26,823 - stpipe.Spec3Pipeline.cube_build - INFO - Time to set initial dq values = 53.7 s
2020-10-29 12:28:40,217 - stpipe.Spec3Pipeline.cube_build - INFO - Time to match file to ifucube = 73.4 s
2020-10-29 12:28:40,637 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 6386 with wavelength below 5.639499866461847
2020-10-29 12:28:40,637 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 11340 with wavelength above 6.620499913056847
2020-10-29 12:28:40,692 - stpipe.Spec3Pipeline.cube_build - INFO - Time to transform pixels to output frame = 0.5 s
2020-10-29 12:29:36,770 - stpipe.Spec3Pipeline.cube_build - INFO - Time to set initial dq values = 56.1 s
2020-10-29 12:30:50,942 - stpipe.Spec3Pipeline.cube_build - INFO - Time to match file to ifucube = 74.2 s
2020-10-29 12:30:51,011 - stpipe.Spec3Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2020-10-29 12:30:51,012 - stpipe.Spec3Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2020-10-29 12:30:51,013 - stpipe.Spec3Pipeline.cube_build - INFO - Time to find Cube Flux = 0.1 s
2020-10-29 12:30:53,367 - stpipe.Spec3Pipeline.cube_build - INFO - IFUChannel 1
2020-10-29 12:30:53,405 - stpipe.Spec3Pipeline.cube_build - INFO - Number of bands in cube: 1
2020-10-29 12:30:54,038 - stpipe.Spec3Pipeline.cube_build - INFO - Cube Geometry:
2020-10-29 12:30:54,039 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2020-10-29 12:30:54,039 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 1 49 25.00 0.00002678 0.13000000 -3.18499988 3.18499988
2020-10-29 12:30:54,040 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 2 39 20.00 0.00004545 0.13000000 -2.53499991 2.53499991
2020-10-29 12:30:54,040 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2020-10-29 12:30:54,041 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 3 1091 1.00 6.42050008 0.00100000 6.42000008 7.51100013
2020-10-29 12:30:54,042 - stpipe.Spec3Pipeline.cube_build - INFO - Cube covers channel, subchannel: 1, long
2020-10-29 12:30:54,043 - stpipe.Spec3Pipeline.cube_build - INFO - Output Name: my_point_source_ch1-long_s3d.fits
2020-10-29 12:30:54,444 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 7703 with wavelength below 6.419500076270197
2020-10-29 12:30:54,444 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 11127 with wavelength above 7.511500128137413
2020-10-29 12:30:54,496 - stpipe.Spec3Pipeline.cube_build - INFO - Time to transform pixels to output frame = 0.5 s
2020-10-29 12:31:53,663 - stpipe.Spec3Pipeline.cube_build - INFO - Time to set initial dq values = 59.2 s
2020-10-29 12:33:05,231 - stpipe.Spec3Pipeline.cube_build - INFO - Time to match file to ifucube = 71.6 s
2020-10-29 12:33:05,619 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 7703 with wavelength below 6.419500076270197
2020-10-29 12:33:05,620 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 11127 with wavelength above 7.511500128137413
2020-10-29 12:33:05,672 - stpipe.Spec3Pipeline.cube_build - INFO - Time to transform pixels to output frame = 0.4 s
2020-10-29 12:34:07,364 - stpipe.Spec3Pipeline.cube_build - INFO - Time to set initial dq values = 61.7 s
2020-10-29 12:35:18,416 - stpipe.Spec3Pipeline.cube_build - INFO - Time to match file to ifucube = 71.1 s
2020-10-29 12:35:18,499 - stpipe.Spec3Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2020-10-29 12:35:18,500 - stpipe.Spec3Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2020-10-29 12:35:18,501 - stpipe.Spec3Pipeline.cube_build - INFO - Time to find Cube Flux = 0.1 s
2020-10-29 12:35:20,435 - stpipe.Spec3Pipeline.cube_build - INFO - IFUChannel 1
2020-10-29 12:35:20,473 - stpipe.Spec3Pipeline.cube_build - INFO - Number of bands in cube: 1
2020-10-29 12:35:21,097 - stpipe.Spec3Pipeline.cube_build - INFO - Cube Geometry:
2020-10-29 12:35:21,098 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2020-10-29 12:35:21,099 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 1 45 23.00 0.00000544 0.17000000 -3.82500004 3.82500004
2020-10-29 12:35:21,099 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 2 37 19.00 -0.00008178 0.17000000 -3.14500003 3.14500003
2020-10-29 12:35:21,100 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2020-10-29 12:35:21,101 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 3 631 1.00 7.49099977 0.00200000 7.48999977 8.75199983
2020-10-29 12:35:21,101 - stpipe.Spec3Pipeline.cube_build - INFO - Cube covers channel, subchannel: 2, short
2020-10-29 12:35:21,102 - stpipe.Spec3Pipeline.cube_build - INFO - Output Name: my_point_source_ch2-short_s3d.fits
2020-10-29 12:35:21,475 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 9353 with wavelength below 7.488999771070667
2020-10-29 12:35:21,476 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 13669 with wavelength above 8.752999831107445
2020-10-29 12:35:21,526 - stpipe.Spec3Pipeline.cube_build - INFO - Time to transform pixels to output frame = 0.4 s
2020-10-29 12:35:52,450 - stpipe.Spec3Pipeline.cube_build - INFO - Time to set initial dq values = 30.9 s
2020-10-29 12:36:47,124 - stpipe.Spec3Pipeline.cube_build - INFO - Time to match file to ifucube = 54.7 s
2020-10-29 12:36:47,486 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 9353 with wavelength below 7.488999771070667
2020-10-29 12:36:47,487 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 13669 with wavelength above 8.752999831107445
2020-10-29 12:36:47,543 - stpipe.Spec3Pipeline.cube_build - INFO - Time to transform pixels to output frame = 0.4 s
2020-10-29 12:37:19,913 - stpipe.Spec3Pipeline.cube_build - INFO - Time to set initial dq values = 32.4 s
2020-10-29 12:38:16,046 - stpipe.Spec3Pipeline.cube_build - INFO - Time to match file to ifucube = 56.1 s
2020-10-29 12:38:16,083 - stpipe.Spec3Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2020-10-29 12:38:16,083 - stpipe.Spec3Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2020-10-29 12:38:16,084 - stpipe.Spec3Pipeline.cube_build - INFO - Time to find Cube Flux = 0.0 s
2020-10-29 12:38:18,413 - stpipe.Spec3Pipeline.cube_build - INFO - IFUChannel 2
2020-10-29 12:38:18,447 - stpipe.Spec3Pipeline.cube_build - INFO - Number of bands in cube: 1
2020-10-29 12:38:19,047 - stpipe.Spec3Pipeline.cube_build - INFO - Cube Geometry:
2020-10-29 12:38:19,048 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2020-10-29 12:38:19,049 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 1 45 23.00 -0.00003404 0.17000000 -3.82500004 3.82500004
2020-10-29 12:38:19,049 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 2 37 19.00 -0.00014826 0.17000000 -3.14500003 3.14500003
2020-10-29 12:38:19,050 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2020-10-29 12:38:19,051 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 3 750 1.00 8.72100027 0.00200000 8.72000027 10.22000034
2020-10-29 12:38:19,051 - stpipe.Spec3Pipeline.cube_build - INFO - Cube covers channel, subchannel: 2, medium
2020-10-29 12:38:19,052 - stpipe.Spec3Pipeline.cube_build - INFO - Output Name: my_point_source_ch2-medium_s3d.fits
2020-10-29 12:38:19,421 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 7942 with wavelength below 8.719000266981311
2020-10-29 12:38:19,422 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 11827 with wavelength above 10.221000338322483
2020-10-29 12:38:19,469 - stpipe.Spec3Pipeline.cube_build - INFO - Time to transform pixels to output frame = 0.4 s
2020-10-29 12:38:56,399 - stpipe.Spec3Pipeline.cube_build - INFO - Time to set initial dq values = 36.9 s
2020-10-29 12:39:58,984 - stpipe.Spec3Pipeline.cube_build - INFO - Time to match file to ifucube = 62.6 s
2020-10-29 12:39:59,346 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 7942 with wavelength below 8.719000266981311
2020-10-29 12:39:59,346 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 11827 with wavelength above 10.221000338322483
2020-10-29 12:39:59,408 - stpipe.Spec3Pipeline.cube_build - INFO - Time to transform pixels to output frame = 0.4 s
2020-10-29 12:40:37,236 - stpipe.Spec3Pipeline.cube_build - INFO - Time to set initial dq values = 37.8 s
2020-10-29 12:41:39,944 - stpipe.Spec3Pipeline.cube_build - INFO - Time to match file to ifucube = 62.7 s
2020-10-29 12:41:39,988 - stpipe.Spec3Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2020-10-29 12:41:39,989 - stpipe.Spec3Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2020-10-29 12:41:39,990 - stpipe.Spec3Pipeline.cube_build - INFO - Time to find Cube Flux = 0.0 s
2020-10-29 12:41:41,850 - stpipe.Spec3Pipeline.cube_build - INFO - IFUChannel 2
2020-10-29 12:41:41,887 - stpipe.Spec3Pipeline.cube_build - INFO - Number of bands in cube: 1
2020-10-29 12:41:42,493 - stpipe.Spec3Pipeline.cube_build - INFO - Cube Geometry:
2020-10-29 12:41:42,494 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2020-10-29 12:41:42,494 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 1 45 23.00 0.00002886 0.17000000 -3.82500004 3.82500004
2020-10-29 12:41:42,495 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 2 37 19.00 -0.00013414 0.17000000 -3.14500003 3.14500003
2020-10-29 12:41:42,496 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2020-10-29 12:41:42,496 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 3 855 1.00 10.03099973 0.00200000 10.02999973 11.73999981
2020-10-29 12:41:42,497 - stpipe.Spec3Pipeline.cube_build - INFO - Cube covers channel, subchannel: 2, long
2020-10-29 12:41:42,498 - stpipe.Spec3Pipeline.cube_build - INFO - Output Name: my_point_source_ch2-long_s3d.fits
2020-10-29 12:41:42,854 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 8411 with wavelength below 10.028999732923694
2020-10-29 12:41:42,855 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 12388 with wavelength above 11.74099981423933
2020-10-29 12:41:42,902 - stpipe.Spec3Pipeline.cube_build - INFO - Time to transform pixels to output frame = 0.4 s
2020-10-29 12:42:24,100 - stpipe.Spec3Pipeline.cube_build - INFO - Time to set initial dq values = 41.2 s
2020-10-29 12:43:34,921 - stpipe.Spec3Pipeline.cube_build - INFO - Time to match file to ifucube = 70.8 s
2020-10-29 12:43:35,786 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 8411 with wavelength below 10.028999732923694
2020-10-29 12:43:35,787 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 12388 with wavelength above 11.74099981423933
2020-10-29 12:43:35,840 - stpipe.Spec3Pipeline.cube_build - INFO - Time to transform pixels to output frame = 0.9 s
2020-10-29 12:44:19,652 - stpipe.Spec3Pipeline.cube_build - INFO - Time to set initial dq values = 43.8 s
2020-10-29 12:45:33,591 - stpipe.Spec3Pipeline.cube_build - INFO - Time to match file to ifucube = 73.9 s
2020-10-29 12:45:33,649 - stpipe.Spec3Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2020-10-29 12:45:33,650 - stpipe.Spec3Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2020-10-29 12:45:33,651 - stpipe.Spec3Pipeline.cube_build - INFO - Time to find Cube Flux = 0.1 s
2020-10-29 12:45:35,692 - stpipe.Spec3Pipeline.cube_build - INFO - IFUChannel 2
2020-10-29 12:45:35,729 - stpipe.Spec3Pipeline.cube_build - INFO - Number of bands in cube: 1
2020-10-29 12:45:36,387 - stpipe.Spec3Pipeline.cube_build - INFO - Cube Geometry:
2020-10-29 12:45:36,388 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2020-10-29 12:45:36,389 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 1 49 25.00 -0.00013853 0.20000000 -4.90000007 4.90000007
2020-10-29 12:45:36,390 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 2 41 21.00 -0.00001006 0.20000000 -4.10000006 4.10000006
2020-10-29 12:45:36,391 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2020-10-29 12:45:36,392 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 3 650 1.00 11.53149973 0.00300000 11.52999973 13.47999975
2020-10-29 12:45:36,393 - stpipe.Spec3Pipeline.cube_build - INFO - Cube covers channel, subchannel: 3, short
2020-10-29 12:45:36,394 - stpipe.Spec3Pipeline.cube_build - INFO - Output Name: my_point_source_ch3-short_s3d.fits
2020-10-29 12:45:36,785 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 7784 with wavelength below 11.528499732958153
2020-10-29 12:45:36,786 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 11841 with wavelength above 13.4814997499343
2020-10-29 12:45:36,837 - stpipe.Spec3Pipeline.cube_build - INFO - Time to transform pixels to output frame = 0.4 s
2020-10-29 12:46:18,607 - stpipe.Spec3Pipeline.cube_build - INFO - Time to set initial dq values = 41.8 s
2020-10-29 12:47:29,949 - stpipe.Spec3Pipeline.cube_build - INFO - Time to match file to ifucube = 71.3 s
2020-10-29 12:47:30,315 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 7784 with wavelength below 11.528499732958153
2020-10-29 12:47:30,316 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 11841 with wavelength above 13.4814997499343
2020-10-29 12:47:30,372 - stpipe.Spec3Pipeline.cube_build - INFO - Time to transform pixels to output frame = 0.4 s
2020-10-29 12:48:11,381 - stpipe.Spec3Pipeline.cube_build - INFO - Time to set initial dq values = 41.0 s
2020-10-29 12:49:26,256 - stpipe.Spec3Pipeline.cube_build - INFO - Time to match file to ifucube = 74.9 s
2020-10-29 12:49:26,303 - stpipe.Spec3Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2020-10-29 12:49:26,303 - stpipe.Spec3Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2020-10-29 12:49:26,305 - stpipe.Spec3Pipeline.cube_build - INFO - Time to find Cube Flux = 0.0 s
2020-10-29 12:49:28,692 - stpipe.Spec3Pipeline.cube_build - INFO - IFUChannel 3
2020-10-29 12:49:28,731 - stpipe.Spec3Pipeline.cube_build - INFO - Number of bands in cube: 1
2020-10-29 12:49:29,364 - stpipe.Spec3Pipeline.cube_build - INFO - Cube Geometry:
2020-10-29 12:49:29,365 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2020-10-29 12:49:29,365 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 1 47 24.00 -0.00011257 0.20000000 -4.70000007 4.70000007
2020-10-29 12:49:29,366 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 2 41 21.00 -0.00007863 0.20000000 -4.10000006 4.10000006
2020-10-29 12:49:29,366 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2020-10-29 12:49:29,367 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 3 757 1.00 13.37149989 0.00300000 13.36999989 15.64099991
2020-10-29 12:49:29,368 - stpipe.Spec3Pipeline.cube_build - INFO - Cube covers channel, subchannel: 3, medium
2020-10-29 12:49:29,369 - stpipe.Spec3Pipeline.cube_build - INFO - Output Name: my_point_source_ch3-medium_s3d.fits
2020-10-29 12:49:29,742 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 6977 with wavelength below 13.368499885546044
2020-10-29 12:49:29,743 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 11286 with wavelength above 15.642499905312434
2020-10-29 12:49:29,792 - stpipe.Spec3Pipeline.cube_build - INFO - Time to transform pixels to output frame = 0.4 s
2020-10-29 12:50:16,165 - stpipe.Spec3Pipeline.cube_build - INFO - Time to set initial dq values = 46.4 s
2020-10-29 12:51:39,985 - stpipe.Spec3Pipeline.cube_build - INFO - Time to match file to ifucube = 83.8 s
2020-10-29 12:51:40,354 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 6977 with wavelength below 13.368499885546044
2020-10-29 12:51:40,355 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 11286 with wavelength above 15.642499905312434
2020-10-29 12:51:40,419 - stpipe.Spec3Pipeline.cube_build - INFO - Time to transform pixels to output frame = 0.4 s
2020-10-29 12:52:27,345 - stpipe.Spec3Pipeline.cube_build - INFO - Time to set initial dq values = 46.9 s
2020-10-29 12:53:53,784 - stpipe.Spec3Pipeline.cube_build - INFO - Time to match file to ifucube = 86.4 s
2020-10-29 12:53:53,844 - stpipe.Spec3Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2020-10-29 12:53:53,845 - stpipe.Spec3Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2020-10-29 12:53:53,846 - stpipe.Spec3Pipeline.cube_build - INFO - Time to find Cube Flux = 0.1 s
2020-10-29 12:53:55,867 - stpipe.Spec3Pipeline.cube_build - INFO - IFUChannel 3
2020-10-29 12:53:55,905 - stpipe.Spec3Pipeline.cube_build - INFO - Number of bands in cube: 1
2020-10-29 12:53:56,597 - stpipe.Spec3Pipeline.cube_build - INFO - Cube Geometry:
2020-10-29 12:53:56,598 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2020-10-29 12:53:56,599 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 1 47 24.00 -0.00013548 0.20000000 -4.70000007 4.70000007
2020-10-29 12:53:56,599 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 2 41 21.00 -0.00007256 0.20000000 -4.10000006 4.10000006
2020-10-29 12:53:56,600 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2020-10-29 12:53:56,601 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 3 877 1.00 15.44149958 0.00300000 15.43999958 18.07099960
2020-10-29 12:53:56,601 - stpipe.Spec3Pipeline.cube_build - INFO - Cube covers channel, subchannel: 3, long
2020-10-29 12:53:56,602 - stpipe.Spec3Pipeline.cube_build - INFO - Output Name: my_point_source_ch3-long_s3d.fits
2020-10-29 12:53:56,995 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 7034 with wavelength below 15.438499580370262
2020-10-29 12:53:56,996 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 9855 with wavelength above 18.072499603265896
2020-10-29 12:53:57,054 - stpipe.Spec3Pipeline.cube_build - INFO - Time to transform pixels to output frame = 0.5 s
2020-10-29 12:54:49,711 - stpipe.Spec3Pipeline.cube_build - INFO - Time to set initial dq values = 52.7 s
2020-10-29 12:56:30,798 - stpipe.Spec3Pipeline.cube_build - INFO - Time to match file to ifucube = 101.1 s
2020-10-29 12:56:31,177 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 7034 with wavelength below 15.438499580370262
2020-10-29 12:56:31,178 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 9855 with wavelength above 18.072499603265896
2020-10-29 12:56:31,234 - stpipe.Spec3Pipeline.cube_build - INFO - Time to transform pixels to output frame = 0.4 s
2020-10-29 12:57:25,236 - stpipe.Spec3Pipeline.cube_build - INFO - Time to set initial dq values = 54.0 s
2020-10-29 12:59:03,345 - stpipe.Spec3Pipeline.cube_build - INFO - Time to match file to ifucube = 98.1 s
2020-10-29 12:59:03,410 - stpipe.Spec3Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2020-10-29 12:59:03,411 - stpipe.Spec3Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2020-10-29 12:59:03,412 - stpipe.Spec3Pipeline.cube_build - INFO - Time to find Cube Flux = 0.1 s
2020-10-29 12:59:05,812 - stpipe.Spec3Pipeline.cube_build - INFO - IFUChannel 3
2020-10-29 12:59:05,850 - stpipe.Spec3Pipeline.cube_build - INFO - Number of bands in cube: 1
2020-10-29 12:59:06,410 - stpipe.Spec3Pipeline.cube_build - INFO - Cube Geometry:
2020-10-29 12:59:06,411 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2020-10-29 12:59:06,411 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 1 35 18.00 0.00006316 0.34999999 -6.12499990 6.12499990
2020-10-29 12:59:06,412 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 2 29 15.00 -0.00016948 0.34999999 -5.07499991 5.07499991
2020-10-29 12:59:06,413 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2020-10-29 12:59:06,413 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 3 546 1.00 17.66299985 0.00600000 17.65999985 20.93599988
2020-10-29 12:59:06,414 - stpipe.Spec3Pipeline.cube_build - INFO - Cube covers channel, subchannel: 4, short
2020-10-29 12:59:06,415 - stpipe.Spec3Pipeline.cube_build - INFO - Output Name: my_point_source_ch4-short_s3d.fits
2020-10-29 12:59:06,736 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 5749 with wavelength below 17.656999847386032
2020-10-29 12:59:06,736 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 5741 with wavelength above 20.938999875914305
2020-10-29 12:59:06,782 - stpipe.Spec3Pipeline.cube_build - INFO - Time to transform pixels to output frame = 0.4 s
2020-10-29 12:59:24,517 - stpipe.Spec3Pipeline.cube_build - INFO - Time to set initial dq values = 17.7 s
2020-10-29 13:00:16,453 - stpipe.Spec3Pipeline.cube_build - INFO - Time to match file to ifucube = 51.9 s
2020-10-29 13:00:16,777 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 5749 with wavelength below 17.656999847386032
2020-10-29 13:00:16,778 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 5741 with wavelength above 20.938999875914305
2020-10-29 13:00:16,824 - stpipe.Spec3Pipeline.cube_build - INFO - Time to transform pixels to output frame = 0.4 s
2020-10-29 13:00:34,268 - stpipe.Spec3Pipeline.cube_build - INFO - Time to set initial dq values = 17.4 s
2020-10-29 13:01:26,524 - stpipe.Spec3Pipeline.cube_build - INFO - Time to match file to ifucube = 52.3 s
2020-10-29 13:01:26,541 - stpipe.Spec3Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2020-10-29 13:01:26,541 - stpipe.Spec3Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2020-10-29 13:01:26,542 - stpipe.Spec3Pipeline.cube_build - INFO - Time to find Cube Flux = 0.0 s
2020-10-29 13:01:28,385 - stpipe.Spec3Pipeline.cube_build - INFO - IFUChannel 4
2020-10-29 13:01:28,416 - stpipe.Spec3Pipeline.cube_build - INFO - Number of bands in cube: 1
2020-10-29 13:01:28,961 - stpipe.Spec3Pipeline.cube_build - INFO - Cube Geometry:
2020-10-29 13:01:28,961 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2020-10-29 13:01:28,962 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 1 35 18.00 0.00006653 0.34999999 -6.12499990 6.12499990
2020-10-29 13:01:28,962 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 2 29 15.00 -0.00015177 0.34999999 -5.07499991 5.07499991
2020-10-29 13:01:28,963 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2020-10-29 13:01:28,964 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 3 632 1.00 20.42300008 0.00600000 20.42000008 24.21200011
2020-10-29 13:01:28,964 - stpipe.Spec3Pipeline.cube_build - INFO - Cube covers channel, subchannel: 4, medium
2020-10-29 13:01:28,965 - stpipe.Spec3Pipeline.cube_build - INFO - Output Name: my_point_source_ch4-medium_s3d.fits
2020-10-29 13:01:29,294 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 4506 with wavelength below 20.41700007626787
2020-10-29 13:01:29,295 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 6252 with wavelength above 24.21500010928139
2020-10-29 13:01:29,345 - stpipe.Spec3Pipeline.cube_build - INFO - Time to transform pixels to output frame = 0.4 s
2020-10-29 13:01:49,518 - stpipe.Spec3Pipeline.cube_build - INFO - Time to set initial dq values = 20.2 s
2020-10-29 13:02:50,696 - stpipe.Spec3Pipeline.cube_build - INFO - Time to match file to ifucube = 61.2 s
2020-10-29 13:02:51,019 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 4506 with wavelength below 20.41700007626787
2020-10-29 13:02:51,020 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 6252 with wavelength above 24.21500010928139
2020-10-29 13:02:51,068 - stpipe.Spec3Pipeline.cube_build - INFO - Time to transform pixels to output frame = 0.4 s
2020-10-29 13:03:11,595 - stpipe.Spec3Pipeline.cube_build - INFO - Time to set initial dq values = 20.5 s
2020-10-29 13:04:15,642 - stpipe.Spec3Pipeline.cube_build - INFO - Time to match file to ifucube = 64.0 s
2020-10-29 13:04:15,663 - stpipe.Spec3Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2020-10-29 13:04:15,664 - stpipe.Spec3Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2020-10-29 13:04:15,665 - stpipe.Spec3Pipeline.cube_build - INFO - Time to find Cube Flux = 0.0 s
2020-10-29 13:04:18,255 - stpipe.Spec3Pipeline.cube_build - INFO - IFUChannel 4
2020-10-29 13:04:18,288 - stpipe.Spec3Pipeline.cube_build - INFO - Number of bands in cube: 1
2020-10-29 13:04:18,855 - stpipe.Spec3Pipeline.cube_build - INFO - Cube Geometry:
2020-10-29 13:04:18,856 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(arcsec) Min & Max (xi, eta arcsec)
2020-10-29 13:04:18,856 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 1 35 18.00 0.00006629 0.34999999 -6.12499990 6.12499990
2020-10-29 13:04:18,857 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 2 29 15.00 -0.00013666 0.34999999 -5.07499991 5.07499991
2020-10-29 13:04:18,857 - stpipe.Spec3Pipeline.cube_build - INFO - axis# Naxis CRPIX CRVAL CDELT(microns) Min & Max (microns)
2020-10-29 13:04:18,858 - stpipe.Spec3Pipeline.cube_build - INFO - Axis 3 741 1.00 23.89299939 0.00600000 23.88999939 28.33599943
2020-10-29 13:04:18,859 - stpipe.Spec3Pipeline.cube_build - INFO - Cube covers channel, subchannel: 4, long
2020-10-29 13:04:18,859 - stpipe.Spec3Pipeline.cube_build - INFO - Output Name: my_point_source_ch4-long_s3d.fits
2020-10-29 13:04:19,187 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 5021 with wavelength below 23.88699938962236
2020-10-29 13:04:19,188 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 5310 with wavelength above 28.338999428320676
2020-10-29 13:04:19,231 - stpipe.Spec3Pipeline.cube_build - INFO - Time to transform pixels to output frame = 0.4 s
2020-10-29 13:04:44,024 - stpipe.Spec3Pipeline.cube_build - INFO - Time to set initial dq values = 24.8 s
2020-10-29 13:05:57,410 - stpipe.Spec3Pipeline.cube_build - INFO - Time to match file to ifucube = 73.4 s
2020-10-29 13:05:57,747 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 5021 with wavelength below 23.88699938962236
2020-10-29 13:05:57,748 - stpipe.Spec3Pipeline.cube_build - INFO - # of detector pixels not mapped to output plane: 5310 with wavelength above 28.338999428320676
2020-10-29 13:05:57,798 - stpipe.Spec3Pipeline.cube_build - INFO - Time to transform pixels to output frame = 0.4 s
2020-10-29 13:06:22,226 - stpipe.Spec3Pipeline.cube_build - INFO - Time to set initial dq values = 24.4 s
2020-10-29 13:07:36,511 - stpipe.Spec3Pipeline.cube_build - INFO - Time to match file to ifucube = 74.3 s
2020-10-29 13:07:36,539 - stpipe.Spec3Pipeline.cube_build - INFO - Average # of holes/wavelength plane is < 1
2020-10-29 13:07:36,540 - stpipe.Spec3Pipeline.cube_build - INFO - Total # of holes for IFU cube is : 0
2020-10-29 13:07:36,541 - stpipe.Spec3Pipeline.cube_build - INFO - Time to find Cube Flux = 0.0 s
2020-10-29 13:07:38,399 - stpipe.Spec3Pipeline.cube_build - INFO - IFUChannel 4
2020-10-29 13:07:38,430 - stpipe.Spec3Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 0.000908318 -0.000714579 0.000908318 0.000729865 359.999102763 0.000729865 359.999102763 -0.000714579
2020-10-29 13:07:38,433 - stpipe.Spec3Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 0.000877317 -0.000722028 0.000877317 0.000650194 359.999143984 0.000650194 359.999143984 -0.000722028
2020-10-29 13:07:38,436 - stpipe.Spec3Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 0.000893443 -0.000640661 0.000893443 0.000731561 359.999160110 0.000731561 359.999160110 -0.000640661
2020-10-29 13:07:38,439 - stpipe.Spec3Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 0.001044329 -0.000931785 0.001044329 0.000768215 359.998966552 0.000768215 359.998966552 -0.000931785
2020-10-29 13:07:38,442 - stpipe.Spec3Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 0.001004848 -0.000998258 0.001004848 0.000701742 359.998927070 0.000701742 359.998927070 -0.000998258
2020-10-29 13:07:38,445 - stpipe.Spec3Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 0.001067750 -0.000984137 0.001067750 0.000715863 359.998989972 0.000715863 359.998989972 -0.000984137
2020-10-29 13:07:38,447 - stpipe.Spec3Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 0.001194806 -0.001121170 0.001194806 0.001101052 359.998528139 0.001101052 359.998528139 -0.001121170
2020-10-29 13:07:38,450 - stpipe.Spec3Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 0.001165213 -0.001189740 0.001165213 0.001032482 359.998609657 0.001032482 359.998609657 -0.001189740
2020-10-29 13:07:38,452 - stpipe.Spec3Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 0.001142293 -0.001183670 0.001142293 0.001038553 359.998586738 0.001038553 359.998586738 -0.001183670
2020-10-29 13:07:38,455 - stpipe.Spec3Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 0.001715941 -0.001530586 0.001715941 0.001191636 359.998410385 0.001191636 359.998410385 -0.001530586
2020-10-29 13:07:38,458 - stpipe.Spec3Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 0.001719308 -0.001512886 0.001719308 0.001209336 359.998413752 0.001209336 359.998413752 -0.001512886
2020-10-29 13:07:38,461 - stpipe.Spec3Pipeline.cube_build - INFO - Update S_REGION to POLYGON ICRS 0.001719066 -0.001497769 0.001719066 0.001224454 359.998413510 0.001224454 359.998413510 -0.001497769
2020-10-29 13:07:39,200 - stpipe.Spec3Pipeline.cube_build - INFO - Saved model in demo_output/my_point_source_ch1-short_s3d.fits
2020-10-29 13:07:39,893 - stpipe.Spec3Pipeline.cube_build - INFO - Saved model in demo_output/my_point_source_ch1-medium_s3d.fits
2020-10-29 13:07:41,088 - stpipe.Spec3Pipeline.cube_build - INFO - Saved model in demo_output/my_point_source_ch1-long_s3d.fits
2020-10-29 13:07:41,721 - stpipe.Spec3Pipeline.cube_build - INFO - Saved model in demo_output/my_point_source_ch2-short_s3d.fits
2020-10-29 13:07:42,367 - stpipe.Spec3Pipeline.cube_build - INFO - Saved model in demo_output/my_point_source_ch2-medium_s3d.fits
2020-10-29 13:07:43,024 - stpipe.Spec3Pipeline.cube_build - INFO - Saved model in demo_output/my_point_source_ch2-long_s3d.fits
2020-10-29 13:07:43,673 - stpipe.Spec3Pipeline.cube_build - INFO - Saved model in demo_output/my_point_source_ch3-short_s3d.fits
2020-10-29 13:07:44,337 - stpipe.Spec3Pipeline.cube_build - INFO - Saved model in demo_output/my_point_source_ch3-medium_s3d.fits
2020-10-29 13:07:45,008 - stpipe.Spec3Pipeline.cube_build - INFO - Saved model in demo_output/my_point_source_ch3-long_s3d.fits
2020-10-29 13:07:45,626 - stpipe.Spec3Pipeline.cube_build - INFO - Saved model in demo_output/my_point_source_ch4-short_s3d.fits
2020-10-29 13:07:46,238 - stpipe.Spec3Pipeline.cube_build - INFO - Saved model in demo_output/my_point_source_ch4-medium_s3d.fits
2020-10-29 13:07:46,851 - stpipe.Spec3Pipeline.cube_build - INFO - Saved model in demo_output/my_point_source_ch4-long_s3d.fits
2020-10-29 13:07:46,852 - stpipe.Spec3Pipeline.cube_build - INFO - Step cube_build done
2020-10-29 13:07:47,248 - stpipe.Spec3Pipeline.extract_1d - INFO - Step extract_1d running with args (<ModelContainer>,).
2020-10-29 13:07:47,250 - stpipe.Spec3Pipeline.extract_1d - INFO - Step extract_1d 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': True, 'skip': False, 'suffix': 'x1d', 'search_output_file': False, 'input_dir': '', 'smoothing_length': None, 'bkg_order': None, 'log_increment': 50, 'subtract_background': None, 'use_source_posn': None, 'apply_apcorr': True}
2020-10-29 13:07:47,255 - stpipe.Spec3Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_extract1d_0003.json
2020-10-29 13:07:47,258 - stpipe.Spec3Pipeline.extract_1d - INFO - Using APCORR file /Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_apcorr_0006.fits
2020-10-29 13:07:47,351 - stpipe.Spec3Pipeline.extract_1d - INFO - Turning on source position correction for exp_type = MIR_MRS
2020-10-29 13:07:47,351 - stpipe.Spec3Pipeline.extract_1d - INFO - Setting use_source_posn to False for source type EXTENDED
2020-10-29 13:07:47,352 - stpipe.Spec3Pipeline.extract_1d - INFO - Source type = EXTENDED
2020-10-29 13:07:49,292 - stpipe.Spec3Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_extract1d_0003.json
2020-10-29 13:07:49,294 - stpipe.Spec3Pipeline.extract_1d - INFO - Using APCORR file /Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_apcorr_0006.fits
2020-10-29 13:07:49,334 - stpipe.Spec3Pipeline.extract_1d - INFO - Turning on source position correction for exp_type = MIR_MRS
2020-10-29 13:07:49,334 - stpipe.Spec3Pipeline.extract_1d - INFO - Setting use_source_posn to False for source type EXTENDED
2020-10-29 13:07:49,335 - stpipe.Spec3Pipeline.extract_1d - INFO - Source type = EXTENDED
False 3.9721757086029103e-13
2020-10-29 13:07:51,536 - stpipe.Spec3Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_extract1d_0003.json
2020-10-29 13:07:51,539 - stpipe.Spec3Pipeline.extract_1d - INFO - Using APCORR file /Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_apcorr_0006.fits
2020-10-29 13:07:51,578 - stpipe.Spec3Pipeline.extract_1d - INFO - Turning on source position correction for exp_type = MIR_MRS
2020-10-29 13:07:51,579 - stpipe.Spec3Pipeline.extract_1d - INFO - Setting use_source_posn to False for source type EXTENDED
2020-10-29 13:07:51,579 - stpipe.Spec3Pipeline.extract_1d - INFO - Source type = EXTENDED
False 3.9721757086029103e-13
2020-10-29 13:07:54,060 - stpipe.Spec3Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_extract1d_0003.json
2020-10-29 13:07:54,062 - stpipe.Spec3Pipeline.extract_1d - INFO - Using APCORR file /Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_apcorr_0006.fits
2020-10-29 13:07:54,104 - stpipe.Spec3Pipeline.extract_1d - INFO - Turning on source position correction for exp_type = MIR_MRS
2020-10-29 13:07:54,105 - stpipe.Spec3Pipeline.extract_1d - INFO - Setting use_source_posn to False for source type EXTENDED
2020-10-29 13:07:54,105 - stpipe.Spec3Pipeline.extract_1d - INFO - Source type = EXTENDED
False 3.9721757086029103e-13
2020-10-29 13:07:55,559 - stpipe.Spec3Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_extract1d_0003.json
2020-10-29 13:07:55,562 - stpipe.Spec3Pipeline.extract_1d - INFO - Using APCORR file /Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_apcorr_0006.fits
2020-10-29 13:07:55,602 - stpipe.Spec3Pipeline.extract_1d - INFO - Turning on source position correction for exp_type = MIR_MRS
2020-10-29 13:07:55,602 - stpipe.Spec3Pipeline.extract_1d - INFO - Setting use_source_posn to False for source type EXTENDED
2020-10-29 13:07:55,603 - stpipe.Spec3Pipeline.extract_1d - INFO - Source type = EXTENDED
False 6.792656142896652e-13
2020-10-29 13:07:57,266 - stpipe.Spec3Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_extract1d_0003.json
2020-10-29 13:07:57,268 - stpipe.Spec3Pipeline.extract_1d - INFO - Using APCORR file /Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_apcorr_0006.fits
2020-10-29 13:07:57,307 - stpipe.Spec3Pipeline.extract_1d - INFO - Turning on source position correction for exp_type = MIR_MRS
2020-10-29 13:07:57,308 - stpipe.Spec3Pipeline.extract_1d - INFO - Setting use_source_posn to False for source type EXTENDED
2020-10-29 13:07:57,309 - stpipe.Spec3Pipeline.extract_1d - INFO - Source type = EXTENDED
False 6.792656142896652e-13
2020-10-29 13:07:59,244 - stpipe.Spec3Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_extract1d_0003.json
2020-10-29 13:07:59,247 - stpipe.Spec3Pipeline.extract_1d - INFO - Using APCORR file /Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_apcorr_0006.fits
2020-10-29 13:07:59,285 - stpipe.Spec3Pipeline.extract_1d - INFO - Turning on source position correction for exp_type = MIR_MRS
2020-10-29 13:07:59,286 - stpipe.Spec3Pipeline.extract_1d - INFO - Setting use_source_posn to False for source type EXTENDED
2020-10-29 13:07:59,286 - stpipe.Spec3Pipeline.extract_1d - INFO - Source type = EXTENDED
False 6.792656142896652e-13
2020-10-29 13:08:00,766 - stpipe.Spec3Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_extract1d_0003.json
2020-10-29 13:08:00,768 - stpipe.Spec3Pipeline.extract_1d - INFO - Using APCORR file /Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_apcorr_0006.fits
2020-10-29 13:08:00,804 - stpipe.Spec3Pipeline.extract_1d - INFO - Turning on source position correction for exp_type = MIR_MRS
2020-10-29 13:08:00,805 - stpipe.Spec3Pipeline.extract_1d - INFO - Setting use_source_posn to False for source type EXTENDED
2020-10-29 13:08:00,806 - stpipe.Spec3Pipeline.extract_1d - INFO - Source type = EXTENDED
False 9.401600280189515e-13
2020-10-29 13:08:02,489 - stpipe.Spec3Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_extract1d_0003.json
2020-10-29 13:08:02,491 - stpipe.Spec3Pipeline.extract_1d - INFO - Using APCORR file /Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_apcorr_0006.fits
2020-10-29 13:08:02,528 - stpipe.Spec3Pipeline.extract_1d - INFO - Turning on source position correction for exp_type = MIR_MRS
2020-10-29 13:08:02,529 - stpipe.Spec3Pipeline.extract_1d - INFO - Setting use_source_posn to False for source type EXTENDED
2020-10-29 13:08:02,530 - stpipe.Spec3Pipeline.extract_1d - INFO - Source type = EXTENDED
False 9.401600280189515e-13
2020-10-29 13:08:04,481 - stpipe.Spec3Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_extract1d_0003.json
2020-10-29 13:08:04,484 - stpipe.Spec3Pipeline.extract_1d - INFO - Using APCORR file /Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_apcorr_0006.fits
2020-10-29 13:08:04,520 - stpipe.Spec3Pipeline.extract_1d - INFO - Turning on source position correction for exp_type = MIR_MRS
2020-10-29 13:08:04,521 - stpipe.Spec3Pipeline.extract_1d - INFO - Setting use_source_posn to False for source type EXTENDED
2020-10-29 13:08:04,521 - stpipe.Spec3Pipeline.extract_1d - INFO - Source type = EXTENDED
False 9.401600280189515e-13
2020-10-29 13:08:05,545 - stpipe.Spec3Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_extract1d_0003.json
2020-10-29 13:08:05,548 - stpipe.Spec3Pipeline.extract_1d - INFO - Using APCORR file /Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_apcorr_0006.fits
2020-10-29 13:08:05,587 - stpipe.Spec3Pipeline.extract_1d - INFO - Turning on source position correction for exp_type = MIR_MRS
2020-10-29 13:08:05,588 - stpipe.Spec3Pipeline.extract_1d - INFO - Setting use_source_posn to False for source type EXTENDED
2020-10-29 13:08:05,589 - stpipe.Spec3Pipeline.extract_1d - INFO - Source type = EXTENDED
False 2.8792399019336705e-12
2020-10-29 13:08:06,776 - stpipe.Spec3Pipeline.extract_1d - INFO - Using EXTRACT1D reference file /Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_extract1d_0003.json
2020-10-29 13:08:06,779 - stpipe.Spec3Pipeline.extract_1d - INFO - Using APCORR file /Users/patrickkavanagh/crds_mirror/references/jwst/miri/jwst_miri_apcorr_0006.fits
2020-10-29 13:08:06,817 - stpipe.Spec3Pipeline.extract_1d - INFO - Turning on source position correction for exp_type = MIR_MRS
2020-10-29 13:08:06,818 - stpipe.Spec3Pipeline.extract_1d - INFO - Setting use_source_posn to False for source type EXTENDED
2020-10-29 13:08:06,819 - stpipe.Spec3Pipeline.extract_1d - INFO - Source type = EXTENDED
False 2.8792399019336705e-12
2020-10-29 13:08:08,318 - stpipe.Spec3Pipeline.extract_1d - INFO - Saved model in demo_output/my_point_source_ch1-short_x1d.fits
False 2.8792399019336705e-12
2020-10-29 13:08:08,412 - stpipe.Spec3Pipeline.extract_1d - INFO - Saved model in demo_output/my_point_source_ch1-medium_x1d.fits
2020-10-29 13:08:08,501 - stpipe.Spec3Pipeline.extract_1d - INFO - Saved model in demo_output/my_point_source_ch1-long_x1d.fits
2020-10-29 13:08:08,592 - stpipe.Spec3Pipeline.extract_1d - INFO - Saved model in demo_output/my_point_source_ch2-short_x1d.fits
2020-10-29 13:08:08,681 - stpipe.Spec3Pipeline.extract_1d - INFO - Saved model in demo_output/my_point_source_ch2-medium_x1d.fits
2020-10-29 13:08:08,771 - stpipe.Spec3Pipeline.extract_1d - INFO - Saved model in demo_output/my_point_source_ch2-long_x1d.fits
2020-10-29 13:08:08,860 - stpipe.Spec3Pipeline.extract_1d - INFO - Saved model in demo_output/my_point_source_ch3-short_x1d.fits
2020-10-29 13:08:08,953 - stpipe.Spec3Pipeline.extract_1d - INFO - Saved model in demo_output/my_point_source_ch3-medium_x1d.fits
2020-10-29 13:08:09,045 - stpipe.Spec3Pipeline.extract_1d - INFO - Saved model in demo_output/my_point_source_ch3-long_x1d.fits
2020-10-29 13:08:09,133 - stpipe.Spec3Pipeline.extract_1d - INFO - Saved model in demo_output/my_point_source_ch4-short_x1d.fits
2020-10-29 13:08:09,221 - stpipe.Spec3Pipeline.extract_1d - INFO - Saved model in demo_output/my_point_source_ch4-medium_x1d.fits
2020-10-29 13:08:09,313 - stpipe.Spec3Pipeline.extract_1d - INFO - Saved model in demo_output/my_point_source_ch4-long_x1d.fits
2020-10-29 13:08:09,313 - stpipe.Spec3Pipeline.extract_1d - INFO - Step extract_1d done
2020-10-29 13:08:09,323 - stpipe.Spec3Pipeline - INFO - Ending calwebb_spec3
2020-10-29 13:08:09,324 - stpipe.Spec3Pipeline - INFO - Step Spec3Pipeline done
We can plot the combined cubes in each MRS sub-band
cube_files = glob.glob(os.path.join(my_output_dir, '*s3d.fits'))
cube_files = sorted(cube_files)
fig, axs = plt.subplots(4, 3, figsize=(12, 12))
axs = axs.ravel()
for n, c in enumerate(cube_files):
cdm = datamodels.open(c)
axs[n].imshow(np.sum(cdm.data[200:-200], axis=0), cmap='jet', interpolation='nearest',
origin='lower', norm=LogNorm())
axs[n].set_facecolor('black')
plt.tight_layout()
plt.show()
Since we have set the source type to ‘POINT’ above, the extract_1d step will use an aperture extraction and subtract a background with default values. The aperture centre is at pixel x/2, y/2, the radius is y/4, and the background annulus is from the radius to the radius*sqrt(2). In the future, more advanced extraction methods are planned. One can set also the aperture properties using a custom aperture reference file. Please contact pkavanagh@cp.dias.ie if you want to do this.
We can also plot the spectra. Note that an additional aperture correction factor for the encircled energy in the aperture should also be applied but we forego this here since the CDPs are currently not available.
spec_files = glob.glob(os.path.join(my_output_dir, '*1d.fits'))
spec_files = sorted(spec_files)
fig, axs = plt.subplots(1, 1, figsize=(12, 7))
plt.rc('axes', prop_cycle=(cycler('color', ['r', 'g', 'b', 'm', 'c', 'y'])))
for n, s in enumerate(spec_files):
sdm = datamodels.open(s)
axs.plot(sdm.spec[0].spec_table['WAVELENGTH'][20:-20],
sdm.spec[0].spec_table['FLUX'][20:-20], marker='.', markersize=0,
linestyle='-', linewidth=1)
axs.set_ylabel(r'Flux (Jy)', fontsize=22)
axs.set_ylim(0, 2)
axs.set_xlim(5, 25)
axs.set_xlabel('micron', fontsize=22)
axs.grid()
plt.tight_layout()
plt.show()
Command line¶
To achieve the same result from the command line there are a couple of options. However, one must still generate the association file. In this case, it is best to copy the template above into a text file and save it to my_point_source_lvl3_asn.json. The content is printed here for convenience.
{
"asn_type": "spec3",
"asn_rule": "DMS_Level3_Base",
"version_id": null,
"code_version": "0.13.7",
"degraded_status": "No known degraded exposures in association.",
"program": "noprogram",
"constraints": "No constraints",
"asn_id": "a3001",
"target": "none",
"asn_pool": "my_point_source_pool",
"products": [
{
"name": "my_point_source",
"members": [
{
"expname": "MRS_science/my_point_source_exposure10_photom.fits",
"exptype": "science"
},
{
"expname": "MRS_science/my_point_source_exposure11_photom.fits",
"exptype": "science"
},
{
"expname": "MRS_science/my_point_source_exposure12_photom.fits",
"exptype": "science"
},
{
"expname": "MRS_science/my_point_source_exposure1_photom.fits",
"exptype": "science"
},
{
"expname": "MRS_science/my_point_source_exposure2_photom.fits",
"exptype": "science"
},
{
"expname": "MRS_science/my_point_source_exposure3_photom.fits",
"exptype": "science"
},
{
"expname": "MRS_science/my_point_source_exposure4_photom.fits",
"exptype": "science"
},
{
"expname": "MRS_science/my_point_source_exposure5_photom.fits",
"exptype": "science"
},
{
"expname": "MRS_science/my_point_source_exposure6_photom.fits",
"exptype": "science"
},
{
"expname": "MRS_science/my_point_source_exposure7_photom.fits",
"exptype": "science"
},
{
"expname": "MRS_science/my_point_source_exposure8_photom.fits",
"exptype": "science"
},
{
"expname": "MRS_science/my_point_source_exposure9_photom.fits",
"exptype": "science"
}
]
}
]
}
Option 1:
Run the Spec3Pipeline class using the strun command:
mkdir demo_output
strun jwst.pipeline.Spec3Pipeline my_point_source_lvl3_asn.json --output_dir demo_output --steps.master_background.skip True --steps.outlier_detection.skip True --steps.mrs_imatch.skip True
This will produce the same output file in the user-defined --output_dir
Option 2:
Collect the pipeline configuration files in your working directory (if they are not already there) using collect_pipeline_configs and then run the Spec3Pipeline using the strun command with the associated calwebb_spec3.cfg file. This option is a little more flexible as one can create edit the cfg files, use them again, etc.
mkdir demo_output
collect_pipeline_cfgs cfgs/
strun cfgs/calwebb_spec3.cfg my_point_source_lvl3_asn.json --output_dir demo_output --steps.master_background.skip True --steps.outlier_detection.skip True --steps.mrs_imatch.skip True
This will produce the same output file in the user-defined --output_dir