extract_1d step has the following step-specific arguments.
smoothing_lengthis greater than 1 (and is an odd integer), the image data used to perform background extraction will be smoothed in the dispersion direction with a boxcar of this width. If
smoothing_lengthis None (the default), the step will attempt to read the value from the EXTRACT1D reference file. If a value is specified in the reference file, that value will be used. Note that by specifying this parameter in the EXTRACT1D reference file, a different value can be designated for each slit, if desired. If no value is specified either by the user or in the EXTRACT1D reference file, no background smoothing is done.
The type of fit to perform to the background data in each image column (or row, if the dispersion is vertical). There are four allowed values: “poly”, “mean”, and “median”, and None (the default value). If left as None, the step will search the reference file for a value - if none is found,
bkg_fitwill be set to “poly”. If set to “poly”, the background values for each pixel within all background regions in a given column (or row) will be fit with a polynomial of order “bkg_order” (see below). Values of “mean” and “median” compute the simple average and median, respectively, of the background region values in each column (or row). This parameter can also be specified in the EXTRACT1D reference file. If specified in the reference file and given as an argument to the step by the user, the user-supplied value takes precedence.
The order of a polynomial function to be fit to the background regions. The fit is done independently for each column (or row, if the dispersion is vertical) of the input image, and the fitted curve will be subtracted from the target data.
bkg_order= 0 (the minimum allowed value) means to fit a constant. The user-supplied value (if any) overrides the value in the EXTRACT1D reference file. If neither is specified, a value of 0 will be used. If a sufficient number of valid data points is unavailable to construct the polynomial fit, the fit will be forced to 0 for that particular column (or row). If “bkg_fit” is not “poly”, this parameter will be ignored.
The background values will be sigma-clipped to remove outlier values from the determination of the background. The default value is a 3.0 sigma clip.
Most log messages are suppressed while looping over integrations, i.e. when the input is a CubeModel or a 3-D SlitModel. Messages will be logged while processing the first integration, but since they would be the same for every integration, most messages will only be written once. However, since there can be hundreds or thousands of integrations, which can take a long time to process, it would be useful to log a message every now and then to let the user know that the step is still running.
log_incrementis an integer, with default value 50. If it is greater than 0, an INFO message will be printed every
log_incrementintegrations, e.g. “… 150 integrations done”.
This is a boolean flag to specify whether the background should be subtracted. If None, the value in the EXTRACT1D reference file (if any) will be used. If not None, this parameter overrides the value in the reference file.
This is a boolean flag to specify whether the target and background extraction region locations specified in the EXTRACT1D reference file should be shifted to account for the expected position of the source. If None (the default), the step will make the decision of whether to use the source position based on the observing mode and the source type. The source position will only be used for point sources and for modes where the source could be located off-center due to things like nodding or dithering. If turned on, the position of the source is used in conjunction with the World Coordinate System (WCS) to compute the x/y source location. For NIRSpec non-IFU modes, the source position is determined from the
source_xpos/source_yposparameters. For MIRI LRS fixed slit, the dither offset is applied to the sky pointing location to determine source position. All other modes use
targ_ra/targ_dec. If this parameter is specified in the EXTRACT1D reference file, the reference file value will override any automatic settings based on exposure and source type. As always, a value given by the user as an argument to the step overrides all settings in the reference file or within the step code.
A list of two integer values giving the desired x/y location for the center of the circular extraction aperture used for extracting spectra from 3-D IFU cubes. Ignored for non-IFU modes and non-point sources. Must be given in x,y order and in units of pixels along the x,y axes of the 3-D IFU cube, e.g.
--center_xy="27,28". If given, the values override any position derived from the use of the
use_source_posnargument. Default is None.
Switch to select whether or not to apply an APERTURE correction during the Extract1dStep processing. Default is
Switch to select whether or not to enable auto-centroiding of the extraction aperture for IFU point sources. Auto-centroiding works by median collapsing the IFU cube across all wavelengths (shortward of 26 microns where the MRS throughput becomes extremely low) and using DAOStarFinder to locate the brightest source in the field. Default is
Switch to select whether or not to run 1d residual fringe correction on the extracted 1d spectrum (MIRI MRS only). Default is
A string that can be used to override the extraction method for the source_type given by the SRCTYPE keyword. The allowed values are POINT and EXTENDED. The SRCTYPE keyword is not changed, instead the extraction method used is based on this parameter setting. This is only allowed for MIRI MRS IFU data.
A float designating the number of PSF FWHMs to use for the extraction radius. This is a MIRI MRS only paramenter. Values accepted are between 0.5 to 3.0. The default extraction size is set to 2 * FWHM. Values below 2 will result in a smaller radius, a value of 2 results in no change to radius and a value above 2 results in a larger extraction radius.
This is a NIRISS-SOSS algorithm-specific parameter; if True, use the ATOCA algorithm to treat order contamination. Default is
This is a NIRISS-SOSS algorithm-specific parameter; this sets the threshold value for a pixel to be included when modelling the spectral trace. The default value is 0.01.
This is a NIRISS-SOSS algorithm-specific parameter; this is an integer that sets the oversampling factor of the underlying wavelength grid used when modeling the trace. The default value is 2.
This is a NIRISS-SOSS algorithm-specific parameter; filename or SpecModel of the estimate of the target flux. The estimate must be a SpecModel with wavelength and flux values.
This is a NIRISS-SOSS algorithm-specific parameter; filename or SossWaveGridModel containing the wavelength grid used by ATOCA to model each valid pixel of the detector. If not given, the grid is determined based on an estimate of the flux (soss_estimate), the relative tolerance (soss_rtol) required on each pixel model and the maximum grid size (soss_max_grid_size).
This is a NIRISS-SOSS algorithm-specific parameter; filename to hold the wavelength grid calculated by ATOCA, stored in a SossWaveGridModel.
This is a NIRISS-SOSS algorithm-specific parameter; the relative tolerance needed on a pixel model. It is used to determine the sampling of the soss_wave_grid when not directly given. Default value is 1.e-4.
This is a NIRISS-SOSS algorithm-specific parameter; the maximum grid size allowed. It is used when soss_wave_grid is not provided to make sure the computation time or the memory used stays reasonable. Default value is 20000.
This is a NIRISS-SOSS algorithm-specific parameter; this defines a rotation to apply to the reference files to match the observation. It should be specified as a list of three floats, with default values of None.
This is a NIRISS-SOSS algorithm-specific parameter; this is the regularization factor used in the SOSS extraction. If not specified, ATOCA will calculate a best-fit value for the Tikhonov factor.
This is a NIRISS-SOSS algorithm-specific parameter; this specifies the aperture width used to extract the 1D spectrum from the decontaminated trace. The default value is 40.0 pixels.
This is a NIRISS-SOSS algorithm-specific parameter; this parameter sets the method used to handle bad pixels. There are currently two options: “model” will replace the bad pixel values with a modeled value, while “masking” will omit those pixels from the spectrum. The default value is “model”.
This is a NIRISS-SOSS algorithm-specific parameter; if set, this will provide the optional ATOCA model output of traces and pixel weights, with the filename set by this parameter. By default this is set to None and this output is not provided.