Description

Overview

The extract_1d step extracts a 1D signal from a 2D or 3D dataset and writes spectral data to an “x1d” product. This works on all JWST spectroscopic modes, including MIRI LRS (slit and slitless) and MRS, NIRCam WFSS and TSGRISM, NIRISS WFSS and SOSS, and NIRSpec fixed-slit, IFU, and MOS.

An EXTRACT1D reference file is used for most modes to specify the location and size of the target and background extraction apertures. The EXTRACT1D reference file is not used for Wide-Field Slitless Spectroscopy data (NIS_WFSS or NRC_WFSS). For these modes the extraction region is instead taken to be the full size of the input 2D subarray or cutout for each source, or restricted to the region within which the world coordinate system (WCS) is defined in each cutout.

For slit-like 2D input data, source and background extractions are done using a rectangular aperture that covers one pixel in the dispersion direction and uses a height in the cross-dispersion direction that is defined by parameters in the EXTRACT1D reference file. For 3D IFU data, on the other hand, the extraction options differ depending on whether the target is a point or extended source. For a point source, the spectrum is extracted using circular aperture photometry, optionally including background subtraction using a circular annulus. For an extended source, rectangular aperture photometry is used, with the entire image being extracted, and no background subtraction, regardless of what was specified in the reference file or step arguments. For either point or extended sources, the photometry makes use of the Astropy affiliated package photutils to define an aperture object and perform extraction.

For most spectral modes an aperture correction will be applied to the extracted 1D spectral data (unless otherwise selected by the user), in order to put the results onto an infinite aperture scale. This is done by creating interpolation functions based on the APCORR reference file data and applying the interpolated aperture correction (a multiplicative factor between 0 and 1) to the extracted, 1D spectral data (corrected data include the “flux”, “surf_bright”, “flux_error”, “sb_error”, and all flux and surface brightness variance columns in the output table).

Input

Calibrated and potentially resampled 2D images or 3D cubes. The format should be a CubeModel, SlitModel, IFUCubeModel, ImageModel, MultiSlitModel, or a ModelContainer. For some JWST modes this is usually a resampled product, such as the “i2d” products for MIRI LRS fixed-slit, NIRSpec fixed-slit, and NIRSpec MOS, or the “s3d” products for MIRI MRS and NIRSpec IFU. For other modes that are not resampled (e.g. MIRI LRS slitless, NIRISS SOSS, NIRSpec BrightObj, and NIRCam and NIRISS WFSS), this will be a “cal” product. For modes that have multiple slit instances (NIRSpec fixed-slit and MOS, WFSS), The SCI extensions should have keyword SLTNAME to specify which slit was extracted, though if there is only one slit (e.g. MIRI LRS and NIRISS SOSS), the slit name can be taken from the EXTRACT1D reference file instead.

Normally the photom step should have been run before running extract_1d. If photom has not been run, a warning will be logged and the output of extract_1d will be in units of count rate. The photom step converts data to units of either surface brightness (MegaJanskys per steradian) or, for point sources observed with NIRSpec and NIRISS SOSS, units of flux density (MegaJanskys).

Output

The output will be in MultiSpecModel format. For each input slit there will be an output table extension with the name EXTRACT1D. This extension will have columns WAVELENGTH, FLUX, FLUX_ERROR, FLUX_VAR_POISSON, FLUX_VAR_RNOISE, FLUX_VAR_FLAT, SURF_BRIGHT, SB_ERROR, SB_VAR_POISSON, SB_VAR_RNOISE, SB_VAR_FLAT, DQ, BACKGROUND, BKGD_ERROR, BKGD_VAR_POISSON, BKGD_VAR_RNOISE, BKGD_VAR_FLAT and NPIXELS. Some metadata will be written to the table header, mostly copied from the input header.

The output WAVELENGTH data is copied from the wavelength array of the input 2D data, if that attribute exists and was populated, otherwise it is calculated from the WCS. FLUX is the flux density in Janskys; see keyword TUNIT2 if the data are in a FITS BINTABLE. FLUX_ERROR is the error estimate for FLUX, and it has the same units as FLUX. The error is calculated as the square root of the sum of the three variance arrays: Poisson, read noise (RNOISE), and flat field (FLAT). SURF_BRIGHT is the surface brightness in MJy / sr, except that for point sources observed with NIRSpec and NIRISS SOSS, SURF_BRIGHT will be set to zero, because there’s no way to express the extracted results from those modes as a surface brightness. SB_ERROR is the error estimate for SURF_BRIGHT, calculated in the same fashion as FLUX_ERROR but using the SB_VAR arrays. While it’s expected that a user will make use of the FLUX column for point-source data and the SURF_BRIGHT column for an extended source, both columns are populated (except for NIRSpec and NIRISS SOSS point sources, as mentioned above). The extract_1d step collapses the input data from 2-D to 1-D by summing one or more rows (or columns, depending on the dispersion direction). A background may optionally be subtracted, but there are also other options for background subtraction prior to extract_1d. For the case of input data in units of MJy / sr, the SURF_BRIGHT and BACKGROUND columns are populated by dividing the sum by the number of pixels (see the NPIXELS column, described below) that were added together. The FLUX column is populated by multiplying the sum by the solid angle of a pixel, and also multiplying by 10^6 to convert from MJy to Jy. For the case of input data in units of MJy (i.e. point sources, NIRSpec or NIRISS SOSS), the SURF_BRIGHT column is set to zero, the FLUX column is just multiplied by 10^6, and the BACKGROUND column is divided by NPIXELS and by the solid angle of a pixel to convert to surface brightness (MJy / sr).

NPIXELS is the number of pixels that were added together for the source extraction region. Note that this is not necessarily a constant, and the value is not necessarily an integer (the data type is float). BACKGROUND is the measured background, scaled to the extraction width used for FLUX and SURF_BRIGHT. BACKGROUND will be zero if background subtraction is not requested. BKGD_ERROR is calculated as the square root of the sum of the BKGD_VAR arrays. DQ is not populated with useful values yet.

Extraction for 2D Slit Data

The operational details of the 1D extraction depend heavily on the parameter values given in the EXTRACT1D reference file. Here we describe their use within the extract_1d step.

Source Extraction Region

As described in the documentation for the EXTRACT1D reference file, the characteristics of the source extraction region can be specified in one of two different ways. The simplest approach is to use the xstart, xstop, ystart, ystop, and extract_width parameters. Note that all of these values are zero-indexed integers, the start and stop limits are inclusive, and the values are in the frame of the image being operated on (which could be a cutout of a larger original image). If dispaxis=1, the limits in the dispersion direction are xstart and xstop and the limits in the cross-dispersion direction are ystart and ystop. If dispaxis=2, the rolls are reversed.

If extract_width is also given, that takes priority over ystart and ystop (for dispaxis=1) for the extraction width, but ystart and ystop will still be used to define the centering of the extraction region in the cross-dispersion direction. For point source data, then the xstart and xstop values (dispaxis = 2) are shifted to account for the expected location of the source. If dispaxis=1, then the ystart and ystop values are modified. The offset amount is internally calculated. If it is not desired to apply this offset, then set use_source_posn = False. If the use_source_posn parameter is None (default), the values of xstart/xstop or ystart/ystop in the extract_1d reference file will be used to determine the center position of the extraction aperture. If these values are not set in the reference file the use_source_posn will be internally set to True for point source data according to the table given in srctype. Any of the extraction location parameters will be modified internally by the step code if the extraction region would extend outside the limits of the input image or outside the domain specified by the WCS.

A more flexible way to specify the source extraction region is via the src_coeff parameter. src_coeff is specified as a list of lists of floating-point polynomial coefficients that define the lower and upper limits of the source extraction region as a function of dispersion. This allows, for example, following a tilted or curved spectral trace or simply following the variation in cross-dispersion FWHM as a function of wavelength. If both src_coeff and ystart/ystop values are given, src_coeff takes precedence. The xstart and xstop values can still be used to limit the range of the extraction in the dispersion direction. More details on the specification and use of polynomial coefficients is given below.

Background Extraction Regions

One or more background extraction regions for a given aperture instance can be specified using the bkg_coeff parameter in the EXTRACT1D reference file. This is directly analogous to the use of src_coeff for specifiying source extraction regions and functions in exactly the same way. More details on the use of polynomial coefficients is given in the next section. Background subtraction will be done if and only if bkg_coeff is given in the EXTRACT1D reference file. The background is determined independently for each column (or row, if dispersion is vertical), using pixel values from all background regions within each column (or row).

Parameters related to background subtraction are smoothing_length, bkg_fit, and bkg_order.

  • If smoothing_length is specified, the 2D image data used to perform background extraction will be smoothed along the dispersion direction using a boxcar of width smoothing_length (in pixels). If not specified, no smoothing of the input 2D image data is performed.

  • bkg_fit specifies the type of background computation to be performed within each column (or row). The default is “poly”, in which case a polynomial of order bkg_order is fit to the background values within the column (or row). Alternatively, values of “mean” or “median” can be specified in order to compute the simple mean or median of the background values in each column (or row). Note that using “bkg_fit=mean” is mathematically equivalent to “bkg_fit=poly” with “bkg_order=0”.

  • If bkg_fit=poly is specified, bkg_order is used to indicate the polynomial order to be used. The default value is zero, i.e. a constant.

During source extraction, the background fit is evaluated at each pixel within the source extraction region for that column (row), and the fitted values will be subtracted (pixel by pixel) from the source count rate.

Source and Background Coefficient Lists

The interpretation and use of polynomial coefficients to specify source and background extraction regions via src_coeff and bkg_coeff is the same. The coefficients are specified as a list of an even number of lists (an even number because both the lower and upper limits of each extraction region must be specified). The source extraction coefficients will normally be a list of just two lists, the coefficients for the lower limit function and the coefficients for the upper limit function of one extraction region. The limits could just be constant values, e.g. [[324.5], [335.5]]. Straight but tilted lines are linear functions:

[[324.5, 0.0137], [335.5, 0.0137]]

Multiple regions may be specified for either the source or background, or both. It will be common to specify more than one background region. Here is an example for specifying two background regions:

[[315.2, 0.0135], [320.7, 0.0135], [341.1, 0.0139], [346.8, 0.0139]]

This is interpreted as follows:

  • [315.2, 0.0135]: lower limit for first background region

  • [320.7, 0.0135]: upper limit for first background region

  • [341.1, 0.0139]: lower limit for second background region

  • [346.8, 0.0139]: upper limit for second background region

Note: If the dispersion direction is vertical, replace “lower” with “left” and “upper” with “right” in the above description.

Notice especially that src_coeff and bkg_coeff contain floating-point values. For interpreting fractions of a pixel, the convention used here is that the pixel number at the center of a pixel is a whole number. Thus, if a lower or upper limit is a whole number, that limit splits the pixel in two, so the weight for that pixel will be 0.5. To include all the pixels between 325 and 335 inclusive, for example, the lower and upper limits would be given as 324.5 and 335.5 respectively.

The order of a polynomial is specified implicitly to be one less than the number of coefficients. The number of coefficients for a lower or upper extraction region limit must be at least one (i.e. zeroth-order polynomial). There is no predefined upper limit on the number of coefficients (and hence polynomial order). The various polynomials (lower limits, upper limits, possibly multiple regions) do not need to have the same number of coefficients; each of the inner lists specifies a separate polynomial. However, the independent variable (wavelength or pixel) does need to be the same for all polynomials for a given slit.

Polynomials specified via src_coeff and bkg_coeff are functions of either wavelength (in microns) or pixel number (pixels in the dispersion direction, with respect to the input 2D slit image), which is specified by the parameter independent_var. The default is “pixel”. The values of these polynomial functions are pixel numbers in the direction perpendicular to dispersion.

Extraction for 3D IFU Data

For IFU cube data, 1D extraction is controlled by a different set of EXTRACT1D reference file parameters. The use_source_posn parameter is not used when extracting spectra from an IFU cube. Instead, for point source data, the extraction aperture is centered at the RA/DEC target location indicated by the header. If the target location is undefined in the header, then the extraction region is the center of the IFU cube. For extended source data, anything specified in the reference file or step arguments will be ignored; the entire image will be extracted, and no background subtraction will be done.

For point sources a circular extraction aperture is used, along with an optional circular annulus for background extraction and subtraction. The size of the extraction region and the background annulus size varies with wavelength. The extraction related vectors are found in the asdf extract1d reference file. For each element in the wavelength vector there are three size components: radius, inner_bkg, and outer_bkg. The radius vector sets the extraction size; while inner_bkg and outer_bkg specify the limits of an annular background aperture. There are two additional vectors in the reference file, axis_ratio and axis_pa, which are placeholders for possible future functionality. The extraction size parameters are given in units of arcseconds and converted to units of pixels in the extraction process.

The region of overlap between an aperture and a pixel can be calculated by one of three different methods, specified by the method parameter: “exact” (default), limited only by finite precision arithmetic; “center”, the full value in a pixel will be included if its center is within the aperture; or “subsample”, which means pixels will be subsampled N x N and the “center” option will be used for each sub-pixel. When method is “subsample”, the parameter subpixels is used to set the resampling value. The default value is 10.