Reference File

The reference file is a text file that uses JSON to hold the information needed.

CRDS Selection Criteria

The file is selected based on the values of DETECTOR and FILTER (and GRATING for NIRSpec).

Extract_1D Reference File Format

All the information is specified in a list with key apertures. Each element of this list is a dictionary, one for each aperture (e.g. a slit) that is supported by the given reference file. The particular dictionary to use is found by matching the slit name in the science data with the value of key id.

The following keys are supported (but for IFU data, see below). Key id is required for any element of the apertures list that may be used; the value of id is compared with the slit name (except for a full-frame input image) to select the appropriate aperture. Key dispaxis is similarly required. Key region_type can be omitted, but if it is specified, its value must be “target”. The source extraction region can be specified with ystart, ystop, etc., but a more flexible alternative is to use src_coeff. If background is to be subtracted, this should be specified by giving bkg_coeff. These are described in more detail below.

  • id: the slit name, e.g. “S200A1” (string)
  • dispaxis: dispersion direction, 1 for X, 2 for Y (int)
  • xstart: first pixel in the horizontal direction, X (int)
  • xstop: last pixel in the horizontal direction, X (int)
  • ystart: first pixel in the vertical direction, Y (int)
  • ystop: last pixel in the vertical direction, Y (int)
  • src_coeff: this takes priority for specifying the source extraction region (list of lists of float)
  • bkg_coeff: for specifying background subraction regions (list of lists of float)
  • independent_var: “wavelength” or “pixel” (string)
  • smoothing_length: width of boxcar for smoothing background regions along the dispersion direction (odd int)
  • bkg_order: order of polynomial fit to background regions (int)
  • extract_width: number of pixels in cross-dispersion direction (int)

If src_coeff is given, those coefficients take priority for specifying the source extraction region in the cross-dispersion direction. xstart and xstop (or ystart and ystop if dispaxis is 2) will still be used for the limits in the dispersion direction. Background subtraction will be done if and only if bkg_coeff is given. See below for further details.

For IFU cube data, these keys are used instead of the above:

  • id: the slit name, but this can be “ANY” (string)
  • x_center: X pixel coordinate of the target (pixels, float, the default is the center of the image along the X axis)
  • y_center: Y pixel coordinate of the target (pixels, float, the default is the center of the image along the Y axis)
  • radius: (only used for a point source) the radius of the circular extraction aperture (pixels, float, default is one quarter of the smaller of the image axis lengths)
  • subtract_background: (only used for a point source) if true, subtract a background determined from an annulus with inner and outer radii given by inner_bkg and outer_bkg (boolean)
  • inner_bkg: (only for a point source) radius of the inner edge of the background annulus (pixels, float, default = radius)
  • outer_bkg: (only for a point source) radius of the outer edge of the background annulus (pixels, float, default = inner_bkg * sqrt(2))
  • width: (only for an extended source) the width of the rectangular extraction region; if theta = 0, the width side is along the X axis (pixels, float, default is half of the smaller image axis length)
  • height: (only for an extended source) the height of the rectangular extraction region; if theta = 0, the height side is along the Y axis (pixels, float, default is half of the smaller image axis length)
  • angle: (only for an extended source) the counterclockwise rotation angle of the width side from the positive X axis (degrees)
  • method: one of “exact”, “subpixel”, or “center”, the method used by photutils for computing the overlap between apertures and pixels (string, default is “exact”)
  • subpixels: if method is “subpixel”, pixels will be resampled by this factor in each dimension (int, the default is 5)

The rest of this description pertains to the parameters for non-IFU data.

If src_coeff is not given, the extraction limits can be specified by xstart, xstop, ystart, ystop, and extract_width. Note that all of these values are integers, and that the start and stop limits are inclusive. If dispaxis is 1, the zero-indexed limits in the dispersion direction are xstart and xstop; if dispaxis is 2, the dispersion limits are ystart and ystop. (The dispersion limits can be given even if src_coeff has been used for defining the cross-dispersion limits.) The limits in the cross-dispersion direction can be given by ystart and ystop (or xstart and xstop if dispaxis is 2). If extract_width is also given, that takes priority over ystart to ystop (for dispaxis = 1) for the extraction width, but ystart and ystop (for dispaxis = 1) will still be used to define the middle in the cross-dispersion direction. Any of these parameters can be modified by the step code if the extraction region would extend outside the input image, or outside the domain specified by the WCS.

The source extraction region can be specified more precisely by giving src_coeff, coefficients for polynomial functions for the lower and upper limits of the source extraction region. As described in the previous paragraph, using this key will override the values of ystart and ystop (if dispaxis is 1) or xstart and xstop (if dispaxis is 2), and extract_width. These polynomials are functions of either wavelength (in microns) or pixel number (pixels in the dispersion direction, with respect to the input 2-D slit image), specified by the key independent_var. The default is “pixel”. The values of these polynomial functions are pixel numbers in the direction perpendicular to dispersion. More than one source extraction region may be specified, though this is not expected to be a typical case.

Background regions are specified by giving bkg_coeff, coefficients for polynomial functions for the lower and upper limits of one or more regions. Background subtraction will be done only if bkg_coeff is given in the reference file. See below for an example. See also bkg_order below.

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

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

Note 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 (this should not be confused with bkg_order, described below). The number of coefficients must be at least one, and there is no predefined upper limit. 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 image (identified by key id).

The background is determined independently for each column (or row, if dispaxis is 2) of the spectrum. The smoothing_length parameter is the width of a boxcar for smoothing the background in the dispersion direction. If this is not specified, either in the reference file, the config file, or on the command line, no smoothing will be done along the dispersion direction. Following background smoothing (if any), for each column (row), a polynomial of order bkg_order will be fit to the pixel values in that column (row) in all the background regions. If not specified, a value of 0 will be used, i.e. a constant function, the mean value. The polynomial will then be 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.