Class: | jwst.pipeline.Spec3Pipeline |
---|---|
Alias: | calwebb_spec3 |
Stage 3 processing for spectroscopic observations is intended for combining the
calibrated data from multiple exposures (e.g. a dither/nod pattern) into a single
combined 2D or 3D spectral product and a combined 1D spectrum.
Before being combined, the exposures may receive additional corrections for the
purpose of background matching and subtraction, as well as outlier rejection.
The steps applied by the calwebb_spec3
pipeline are shown below.
This pipeline is intended for non-TSO spectra only. TSO spectral data should be
processed using the :ref:`calwebb_tso3 <calwebb_tso3>` pipeline.
Instrument/Mode | NIRSpec | MIRI | NIRISS | NIRCam | ||||
---|---|---|---|---|---|---|---|---|
Step | FS | MOS | IFU | FS | MRS | SOSS | WFSS | WFSS |
:ref:`assign_mtwcs <assign_mtwcs_step>`1 | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
:ref:`master_background <master_background_step>`2 | ✓ | ✓ | ✓ | ✓ | ||||
:ref:`exp_to_source <exp_to_source>` | ✓ | ✓ | ✓ | ✓ | ||||
:ref:`mrs_imatch <mrs_imatch_step>` | ✓ | |||||||
:ref:`outlier_detection <outlier_detection_step>` | ✓ | ✓ | ✓ | ✓ | ✓ | |||
:ref:`pixel_replace <pixel_replace_step>` | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | |
:ref:`resample_spec <resample_step>` | ✓ | ✓ | ✓ | |||||
:ref:`cube_build <cube_build_step>` | ✓ | ✓ | ||||||
:ref:`extract_1d <extract_1d_step>` | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
:ref:`spectral_leak <spectral_leak_step>` | ✓ | |||||||
:ref:`combine_1d <combine_1d_step>` | ✓ | ✓ | ✓ |
1The :ref:`assign_mtwcs <assign_mtwcs_step>` step is only applied to observations of a moving target (TARGTYPE='moving').
2The master background subtraction step is applied to NIRSpec MOS exposures in the :ref:`calwebb_spec2 <calwebb_spec2>` pipeline.
Notice that NIRCam and NIRISS WFSS, as well as NIRISS SOSS data, receive only minimal
processing by calwebb_spec3
.
WFSS 2D input data are reorganized into source-based products by the
:ref:`exp_to_source <exp_to_source>` step (see below), have 1D
extracted spectra produced for each source, and then the 1D spectra for each source
are combined into a final 1D spectrum.
NIRISS SOSS inputs do not go through the :ref:`exp_to_source <exp_to_source>` step,
because they contain data for a single source.
Hence the only processing that they receive is to extract a 1D spectrum from each
input and then combine those spectra into a final 1D spectrum.
This type of processing is intended only for NIRISS SOSS exposures that are not
obtained in TSO mode.
TSO mode NIRISS SOSS exposures should be processed with the
:ref:`calwebb_tso3 <calwebb_tso3>` pipeline.
The calwebb_spec3
pipeline does not have any optional arguments.
Data model: | ~jwst.datamodels.ImageModel, ~jwst.datamodels.IFUImageModel, ~jwst.datamodels.SlitModel, or ~jwst.datamodels.MultiSlitModel |
---|---|
File suffix: | _cal |
The inputs to calwebb_spec3
should be in the form of an ASN file that
lists the multiple exposures to be processed into combined output products.
The individual exposures should be calibrated the ("_cal") products from
:ref:`calwebb_spec2 <calwebb_spec2>` processing.
The member list for each product in the ASN file can also contain exposures of dedicated background targets, which are intended for use in the :ref:`master_background <master_background_step>` step. These input exposures must be the "x1d" products (extracted 1-D spectra) of the background target(s) and are usually the "x1d" files produced by the :ref:`calwebb_spec2 <calwebb_spec2>` pipeline. They must be listed in the ASN file with "exptype" values of "background" in order to be correctly identified as background exposures. See the :ref:`master_background <master_background_step>` for more details.
Data model: | ~jwst.datamodels.MultiExposureModel |
---|---|
File suffix: | _cal |
For NIRSpec fixed-slit, NIRSpec MOS, and NIRCam and NIRISS WFSS, which have a defined set of slits or sources, the data from the input calibrated exposures is reorganized by the :ref:`exp_to_source <exp_to_source>` step so that all of the instances of data for a particular source/slit are contained in a single product. These are referred to as "source-based" products, as opposed to the input exposure-based products. The source-based collections of data are saved in intermediate files, one per source/slit. The root names of the source-based files contain the source ID as an identifier and use the same "_cal" suffix as the input calibrated exposure files. An example source-based file name is "jw00042-o001_s00000002_niriss_gr150r_f150w_cal.fits", where "s00000002" is the source id.
The reorganized sets of data are sent to subsequent steps to process and combine all the data for one source at a time.
Data model: | ~jwst.datamodels.ImageModel |
---|---|
File suffix: | _crf |
If the :ref:`outlier_detection <outlier_detection_step>` step is applied, a new version of each input calibrated exposure is created, in which the DQ array has been updated to flag pixels detected as outliers. These files use the "_crf" (CR-Flagged) product type suffix and also includes the association candidate ID as a new field in the original product root name, e.g. "jw96090001001_03101_00001_nrs2_o001_crf.fits."
Data model: | ~jwst.datamodels.SlitModel |
---|---|
File suffix: | _s2d |
When processing non-IFU modes, a resampled/rectified 2D product of type "_s2d" is created containing the rectified and combined data for a given slit/source, which is the output of the :ref:`resample_spec <resample_step>` step.
Data model: | ~jwst.datamodels.IFUCubeModel |
---|---|
File suffix: | _s3d |
When processing IFU exposures, a resampled and combined 3D IFU cube product created by the :ref:`cube_build <cube_build_step>` step is saved as an "_s3d" file.
Data model: | ~jwst.datamodels.MultiSpecModel |
---|---|
File suffix: | _x1d |
All types of inputs result in a 1D extracted spectral data product, which is saved as a "_x1d" file, and is normally the result of performing the :ref:`extract_1d <extract_1d_step>` step on the combined "_s2d" or "_s3d" product.
For NIRCam and NIRISS WFSS, as well as NIRISS SOSS data, the :ref:`extract_1d <extract_1d_step>` is performed on the individual unresampled 2D cutout images, resulting in multiple 1-D spectra per source in a "_x1d" product. Those spectra are combined using the subsequent :ref:`combine_1d <combine_1d_step>` step (see below).
Data model: | ~jwst.datamodels.CombinedSpecModel |
---|---|
File suffix: | _c1d |
For NIRCam and NIRISS WFSS, as well as NIRISS SOSS data, the :ref:`combine_1d <combine_1d_step>` combines the multiple 1-D spectra for a given source into a final spectrum, which is saved as a "_c1d" product.