# calwebb_spec2: Stage 2 Spectroscopic Processing¶

Config

calwebb_spec2.cfg, calwebb_tso-spec2.cfg

Class

Spec2Pipeline

The Spec2Pipeline applies additional instrumental corrections and calibrations to countrate products that result in a fully calibrated individual exposure. There are two unique configuration files to be used to control this pipeline, depending on whether the data are to be treated as Time Series Observation (TSO). Non-TSO exposures use the calwebb_spec2 configuration, which applies all applicable steps to the data. The calwebb_tso-spec2 configuration, on the other hand, should be used for TSO exposures, for which some steps are set to be skipped by default (see the list of steps in the table below). Both configurations call the Spec2Pipeline module; the only difference is which steps are applied.

The Spec2Pipeline is the “Swiss army knife” of pipeline modules, containing many steps that are only applied to certain instruments or instrument modes. The logic for determining which steps are appropriate is built into the pipeline module itself and is mostly based on either the instrument name or the exposure type (EXP_TYPE keyword) of the data. The list of steps is shown in the table below and indicates which steps are applied to various spectroscopic modes, as well as which ones are used by the calwebb_tso-spec2.cfg configuration for TSO data. The instrument mode abbreviations used in the table are as follows:

• NIRSpec FS = Fixed Slit

• NIRSpec MOS = Multi-Object Spectroscopy

• NIRSpec IFU = Integral Field Unit

• MIRI FS = LRS Fixed Slit

• MIRI SL = LRS Slitless

• MIRI MRS = Medium Resolution Spectroscopy (IFU)

• NIRISS SOSS = Single Object Slitless Spectroscopy

• NIRISS and NIRCam WFSS = Wide-Field Slitless Spectroscopy

Instrument/Mode

NIRSpec

MIRI

NIRISS

NIRCam

All

Step

FS

MOS

IFU

FS

SL

MRS

SOSS

WFSS

WFSS

TSO

assign_wcs

background

imprint

msaflagopen

wavecorr

straylight

fringe

pathloss

photom

resample_spec

cube_build

extract_1d

1The exact order of the extract_2d, srctype, and flat_field steps depends on the observing mode. For NIRISS and NIRCam WFSS, as well as NIRCam TSO grism exposures, the order is flat_field followed by extract_2d (no wavecorr or srctype). For all other modes the order is extract_2d, srctype, wavecorr, and flat_field.

The resample_spec step produces a resampled/rectified product for non-IFU modes of some spectroscopic exposures. If the resample_spec step is not applied to a given exposure, the extract_1d operation will be performed on the original (unresampled) data. The cube_build step produces a resampled/rectified cube for IFU exposures, which is then used as input to the extract_1d step.

## Arguments¶

The calwebb_spec2 pipeline has one optional argument:

--save_bsub  boolean  default=False


If set to True, the results of the background subtraction step will be saved to an intermediate file, using a product type of “_bsub” or “_bsubints”, depending on whether the data are 2D (averaged over integrations) or 3D (per-integration results).

## Inputs¶

### 2D or 3D countrate data¶

Data model
File suffix

_rate or _rateints

The input to the Spec2Pipeline pipeline is a countrate exposure, in the form of either “_rate” or “_rateints” data. A single input file can be processed or an ASN file listing multiple inputs can be used, in which case the processing steps will be applied to each input exposure, one at a time. If “_rateints” products are used as input, each step applies its algorithm to each integration in the exposure, where appropriate.

Note that the steps background and imprint can only be executed when the pipeline is given an ASN file as input, because they rely on multiple, associated exposures to perform their tasks. The ASN file must list not only the input science exposure(s), but must also list the exposures to be used as background or imprint.

Background subtraction for Wide-Field Slitless Spectroscopy (WFSS) exposures, on the other hand, is accomplished by scaling and subtracting a master background image contained in a CRDS reference file and hence does not require an ASN as input.

The input data model type IFUImageModel is only used for MIRI MRS and NIRSpec IFU exposures.

## Outputs¶

### 2D or 3D background-subtracted data¶

Data model
File suffix

_bsub or _bsubints

This is an intermediate product that is only created if “–save_bsub” is set to True and will contain the data as output from the background step. If the input is a “_rate” product, this will be a “_bsub” product, while “_rateints” inputs will be saved as “_bsubints.”

### 2D or 3D calibrated data¶

Data model
File suffix

_cal or _calints

The output is a fully calibrated, but unrectified, exposure, using the product type suffix “_cal” or “_calints”, dependening on the type of input, e.g. “jw80600012001_02101_00003_mirimage_cal.fits.” This is the output of the photom step, or whichever step is performed last before applying either resample_spec, cube_build, or extract_1d.

The output data model type can be any of the 4 listed above and is completely dependent on the type of input data and the observing mode. For data sets that do not go through extract_2d processing, the output will be either a ImageModel, IFUImageModel, or CubeModel, matching the corresponding input data type.

Of the data types that do go through extract_2d processing, the output type will consist of either a single slit model or a mutli-slit model:

The multi-slit model is simply an array of multiple slit models, each one containing the data and relevant meta data for a particular extracted slit or source. A MultiSlitModel product will contain multiple tuples of SCI, ERR, DQ, WAVELENGTH, etc. arrays; one for each of the extracted slits/sources.

### 2D resampled data¶

Data model
File suffix

_s2d

If the input is a 2D exposure type that gets resampled/rectified by the resample_spec step, the rectified 2D spectral product is saved as a “_s2d” file. This image is intended for use as a quick-look product only and is not used in subsequent processing. The 2D unresampled, calibrated (“_cal”) products are passed along as input to subsequent Stage 3 processing.

If the input to the resample_spec step is a MultiSlitModel, then the resampled output will be in the form of a MultiProductModel, which contains an array of individual models, one per slit. Otherwise the output will be a DrizProductModel.

### 3D resampled (IFU cube) data¶

Data model

IFUCubeModel

File suffix

_s3d

If the data are NIRSpec IFU or MIRI MRS, the result of the cube_build step will be 3D IFU spectroscopic cube saved to a “_s3d” file. The IFU cube is built from the data contained in a single exposure and is intended for use as a quick-look product only. The 2D unresampled, calibrated (“_cal”) products are passed along as input to subsequent Stage 3 processing.

### 1D extracted spectral data¶

Data model

MultiSpecModel

File suffix

_x1d or _x1dints

All types of inputs result in a 1D extracted spectral data product, which is saved as a “_x1d” or “_x1dints” file, depending on the input type. Observing modes such as MIRI LRS fixed slit and MRS, NIRCam and NIRISS WFSS, and NIRSpec fixed slit, MOS, and IFU result in an “_x1d” product containing extracted spectral data for one or more slits/sources. TSO modes, such as MIRI LRS slitless, NIRCam TSO grism, NIRISS SOSS, and NIRSpec Bright Object, for which the data are 3D stacks of integrations, result in “_x1dints” products containing extracted spectral data for each integration with the exposure.