User-level Parameters

PypeIt allows you to customize its execution without having to change the code directly.

Although not ubiquitous, most optional arguments of PypeIt’s algorithms are contained within the PypeItPar superset. PypeIt uses the configobj class to parse the user-supplied arguments in the PypeIt Reduction File into an instance of PypeItPar that is passed to all of PypeIt’s main modules. The syntax used to set parameters using the PypeIt Reduction File is important and the nesting of the parameter changes must match the Current PypeItPar Parameter Hierarchy.

Parameter Precedence

The parameter changes also follow a specific precedence. From lowest to highest, the precedence order is as follows:

  • Defaults: The parameter tables below, starting with PypeItPar Keywords, all provide the global defaults for each parameter.

  • Instrument-specific parameters: Each Spectrograph derived class (e.g., ShaneKastSpectrograph) provides its own default values for PypeItPar, as defined by its default_pypeit_par method. This allows the developers to define parameters as a general expectation for what works for each spectrograph. For example, see default_pypeit_par() for Shane/Kast. All of the default changes made for each spectrograph are listed here. Importantly, the parameters tabulated there are not required to be put in your PypeIt Reduction File if you’re trying to reduce data from that instrument. Only those parameters that the user wishes to be different from the default as set by their specified instrument need to be changed via the PypeIt Reduction File.

  • Configuration-specific parameters: Each Spectrograph derived class (e.g., ShaneKastSpectrograph) also defines default parameters to use for specific instrument configurations via its config_specific_par method. This allows the code to automatically define, e.g., the archived arc spectrum used for wavelength calibration given the grating used. For example, see config_specific_par() for Shane/Kast. These configuration-specific parameters are currently not documented here; however, they can be viewed by looking at the source code display in the API documentation.

  • User-specified parameters: Finally, parameters defined by the user in the PypeIt Reduction File take ultimate precedence.

Warning

Default values of parameters that actually point to data files provided by PypeIt (e.g. the spectrum parameter for FlexurePar) in its root directory will point to the relevant location on disk of whoever generated the documentation, which will be different for your installation.

How to change a parameter

To change a parameter, set its value in the Parameter Block of the PypeIt Reduction File. The syntax of the configuration block is important (particularly the number of square brackets used in the parameter hierarchy), but the indentation is not. The indentation will just make the block easier to read. The PypeIt Reduction File Parameter Block always includes the lines that sets the spectrograph:

[rdx]
    spectrograph = keck_deimos

The nesting of the PypeIt parameters is as illustrated in the Current PypeItPar Parameter Hierarchy section below. Here are a few examples of how to change various parameters; for additional examples see the Instrument-Specific Default Configuration section. Errors should be raised if you try to define a parameter that doesn’t exist.

  • To change the threshold used for detecting slit/order edges, add:

    [calibrations]
        [[slitedges]]
            edge_thresh = 100
    
  • To change the exposure time range used to identify an arc and flat-field frames and to increase the LA Cosmic sigma-clipping threshold for arc frames, add:

    [calibrations]
        [[arcframe]]
            exprng = None,10
            [[process]]
                sigclip = 6.
        [[pixelflatframe]]
            exprng = 11,30
    

How to change the image processing parameters for all frame types

To change the base-level image processing parameters that will be applied to all frame types, you can use the baseprocess parameter group. This allows you to set these parameters once instead of having to include lines in your PypeIt file for each frame type. Any frame-type-specific alterations can still be made and will overwrite the base-level processing parameters. For example, to change the sigma-clipping level used by the LA Cosmic routine to default to 3.0 but to use a value of 6.0 for arc frames, you can add the following to your PypeIt file:

[baseprocess]
    sigclip = 3.0
[calibrations]
    [[arcframe]]
        [[[process]]]
            sigclip = 6.0

Warning

Specifically for developers, note that baseprocess is only a “pseudo” parameter group and is not actually associated with any underlying PypeIt parameter class. It is instead a flag for the code that parses the PypeIt Reduction File to distribute the associated image processing parameters to all of the frame-specific parameter sets.

Current PypeItPar Parameter Hierarchy

[calibrations]: CalibrationsPar Keywords
[[biasframe]]: FrameGroupPar Keywords
[[[[scattlight]]]]: ScatteredLightPar Keywords
[[darkframe]]: FrameGroupPar Keywords
[[[[scattlight]]]]: ScatteredLightPar Keywords
[[[[scattlight]]]]: ScatteredLightPar Keywords
[[tiltframe]]: FrameGroupPar Keywords
[[[[scattlight]]]]: ScatteredLightPar Keywords
[[pixelflatframe]]: FrameGroupPar Keywords
[[[[scattlight]]]]: ScatteredLightPar Keywords
[[pinholeframe]]: FrameGroupPar Keywords
[[[[scattlight]]]]: ScatteredLightPar Keywords
[[alignframe]]: FrameGroupPar Keywords
[[[[scattlight]]]]: ScatteredLightPar Keywords
[[alignment]]: AlignPar Keywords
[[traceframe]]: FrameGroupPar Keywords
[[[[scattlight]]]]: ScatteredLightPar Keywords
[[illumflatframe]]: FrameGroupPar Keywords
[[[[scattlight]]]]: ScatteredLightPar Keywords
[[lampoffflatsframe]]: FrameGroupPar Keywords
[[[[scattlight]]]]: ScatteredLightPar Keywords
[[scattlightframe]]: FrameGroupPar Keywords
[[[[scattlight]]]]: ScatteredLightPar Keywords
[[[[scattlight]]]]: ScatteredLightPar Keywords
[[standardframe]]: FrameGroupPar Keywords
[[[[scattlight]]]]: ScatteredLightPar Keywords
[[flatfield]]: FlatFieldPar Keywords
[[slitedges]]: EdgeTracePar Keywords
[scienceframe]: FrameGroupPar Keywords
[[[scattlight]]]: ScatteredLightPar Keywords
[[findobj]]: FindObjPar Keywords
[[skysub]]: SkySubPar Keywords
[[extraction]]: ExtractionPar Keywords
[[slitmask]]: SlitMaskPar Keywords

PypeItPar Keywords

Class Instantiation: PypeItPar

Key

Type

Options

Default

Description

calibrations

CalibrationsPar

CalibrationsPar Keywords

Parameters for the calibration algorithms

coadd1d

Coadd1DPar

Coadd1DPar Keywords

Par set to control 1D coadds. Only used in the after-burner script.

coadd2d

Coadd2DPar

Coadd2DPar Keywords

Par set to control 2D coadds. Only used in the after-burner script.

collate1d

Collate1DPar

Collate1DPar Keywords

Par set to control collating 1d spectra. Only used in the after-burner script.

flexure

FlexurePar

FlexurePar Keywords

Parameters used by the flexure-correction procedure. Flexure corrections are not performed by default. To turn on, either set the parameters in the ‘flexure’ parameter group or set ‘flexure = True’ in the ‘rdx’ parameter group to use the default flexure-correction parameters.

fluxcalib

FluxCalibratePar

FluxCalibratePar Keywords

Parameters used by the flux-calibration procedure. Flux calibration is not performed by default. To turn on, either set the parameters in the ‘fluxcalib’ parameter group or set ‘fluxcalib = True’ in the ‘rdx’ parameter group to use the default flux-calibration parameters.

rdx

ReduxPar

ReduxPar Keywords

PypeIt reduction rules.

reduce

ReducePar

ReducePar Keywords

Parameters determining sky-subtraction, object finding, and extraction

scienceframe

FrameGroupPar

FrameGroupPar Keywords

The frames and combination rules for the science observations

sensfunc

SensFuncPar

SensFuncPar Keywords

Par set to control sensitivity function computation. Only used in the after-burner script.

telluric

TelluricPar

TelluricPar Keywords

Par set to control telluric fitting. Only used in the pypeit_sensfunc and pypeit_telluric after-burner scripts.


CalibrationsPar Keywords

Class Instantiation: CalibrationsPar

Key

Type

Options

Default

Description

alignframe

FrameGroupPar

FrameGroupPar Keywords

The frames and combination rules for the align frames

alignment

AlignPar

AlignPar Keywords

Define the procedure for the alignment of traces

arcframe

FrameGroupPar

FrameGroupPar Keywords

The frames and combination rules for the wavelength calibration

biasframe

FrameGroupPar

FrameGroupPar Keywords

The frames and combination rules for the bias correction

bpm_usebias

bool

False

Make a bad pixel mask from bias frames? Bias frames must be provided.

calib_dir

str

Calibrations

The name of the directory for the processed calibration frames. The host path for the directory is set by the redux_path (see ReduxPar). Beware that success when changing the default value is not well tested!

darkframe

FrameGroupPar

FrameGroupPar Keywords

The frames and combination rules for the dark-current correction

flatfield

FlatFieldPar

FlatFieldPar Keywords

Parameters used to set the flat-field procedure

illumflatframe

FrameGroupPar

FrameGroupPar Keywords

The frames and combination rules for the illumination flat

lampoffflatsframe

FrameGroupPar

FrameGroupPar Keywords

The frames and combination rules for the lamp off flats

pinholeframe

FrameGroupPar

FrameGroupPar Keywords

The frames and combination rules for the pinholes

pixelflatframe

FrameGroupPar

FrameGroupPar Keywords

The frames and combination rules for the pixel flat

raise_chk_error

bool

True

Raise an error if the calibration check fails

scattlight_pad

int

5

Number of unbinned pixels to extend the slit edges by when masking the slits.

scattlightframe

FrameGroupPar

FrameGroupPar Keywords

The frames and combination rules for the scattered light frames

skyframe

FrameGroupPar

FrameGroupPar Keywords

The frames and combination rules for the sky background observations

slitedges

EdgeTracePar

EdgeTracePar Keywords

Slit-edge tracing parameters

standardframe

FrameGroupPar

FrameGroupPar Keywords

The frames and combination rules for the spectrophotometric standard observations

tiltframe

FrameGroupPar

FrameGroupPar Keywords

The frames and combination rules for the wavelength tilts

tilts

WaveTiltsPar

WaveTiltsPar Keywords

Define how to trace the slit tilts using the trace frames

traceframe

FrameGroupPar

FrameGroupPar Keywords

The frames and combination rules for images used for slit tracing

wavelengths

WavelengthSolutionPar

WavelengthSolutionPar Keywords

Parameters used to derive the wavelength solution


AlignPar Keywords

Class Instantiation: AlignPar

Key

Type

Options

Default

Description

locations

list, ndarray

0.0, 1.0

Locations of the bars, in a list, specified as a fraction of the slit width

snr_thresh

int, float

1.0

S/N ratio threshold for finding an alignment trace. This should be a low number to ensure that the algorithm finds all bars. The algorithm will then only use the N most significant detections, where N is the number of elements specified in the “locations” keyword argument

trace_npoly

int

4

Order of the polynomial to use when fitting the trace of a single bar

trim_edge

list

0, 0

Trim the slit by this number of pixels left/right before finding alignment bars


FlatFieldPar Keywords

Class Instantiation: FlatFieldPar

Key

Type

Options

Default

Description

fit_2d_det_response

bool

False

Set this variable to True if you want to compute and account for the detector response in the flatfield image. Note that detector response refers to pixel sensitivity variations that primarily depend on (x,y) detector coordinates. In most cases, the default 2D bspline is sufficient to account for detector response (i.e. set this parameter to False). Note that this correction will _only_ be performed for the spectrographs that have a dedicated response correction implemented. Currently,this correction is only implemented for Keck+KCWI.

illum_iter

int

0

The number of rejection iterations to perform when constructing the slit-illumination profile. No rejection iterations are performed if 0. WARNING: Functionality still being tested.

illum_rej

int, float

5.0

The sigma threshold used in the rejection iterations used to refine the slit-illumination profile. Rejection iterations are only performed if illum_iter > 0.

method

str

bspline, skip

bspline

Method used to flat field the data; use skip to skip flat-fielding. Options are: None, bspline, skip

pixelflat_file

str

Filename of the image to use for pixel-level field flattening

pixelflat_max_wave

int, float

All values of the normalized pixel flat are set to 1 for wavelengths above this value.

pixelflat_min_wave

int, float

All values of the normalized pixel flat are set to 1 for wavelengths below this value.

rej_sticky

bool

False

Propagate the rejected pixels through the stages of the flat-field fitting (i.e, from the spectral fit, to the spatial fit, and finally to the 2D residual fit). If False, pixels rejected in each stage are included in each subsequent stage.

saturated_slits

str

crash, mask, continue

crash

Behavior when a slit is encountered with a large fraction of saturated pixels in the flat-field. The options are: ‘crash’ - Raise an error and halt the data reduction; ‘mask’ - Mask the slit, meaning no science data will be extracted from the slit; ‘continue’ - ignore the flat-field correction, but continue with the reduction.

slit_illum_finecorr

bool

True

If True, a fine correction to the spatial illumination profile will be performed. The fine correction is a low order 2D polynomial fit to account for a gradual change to the spatial illumination profile as a function of wavelength.

slit_illum_pad

int, float

5.0

The number of pixels to pad the slit edges when constructing the slit-illumination profile. Single value applied to both edges.

slit_illum_ref_idx

int

0

The index of a reference slit (0-indexed) used for estimating the relative spectral sensitivity (or the relative blaze). This parameter is only used if slit_illum_relative = True.

slit_illum_relative

bool

False

Generate an image of the relative spectral illumination for a multi-slit setup. If you set use_specillum = True for any of the frames that use the flatfield model, this must be set to True. Currently, this is only used for SlicerIFU reductions.

slit_illum_smooth_npix

int

10

The number of pixels used to determine smoothly varying relative weights is given by nspec/slit_illum_smooth_npix, where nspec is the number of spectral pixels.

slit_trim

int, float, tuple

3.0

The number of pixels to trim each side of the slit when selecting pixels to use for fitting the spectral response function. Single values are used for both slit edges; a two-tuple can be used to trim the left and right sides differently.

spat_samp

int, float

5.0

Spatial sampling for slit illumination function. This is the width of the median filter in pixels used to determine the slit illumination function, and thus sets the minimum scale on which the illumination function will have features.

spec_samp_coarse

int, float

50.0

bspline break point spacing in units of pixels for 2-d bspline-polynomial fit to flat field image residuals. This should be a large number unless you are trying to fit a sky flat with lots of narrow spectral features.

spec_samp_fine

int, float

1.2

bspline break point spacing in units of pixels for spectral fit to flat field blaze function.

tweak_slits

bool

True

Use the illumination flat field to tweak the slit edges. This will work even if illumflatten is set to False

tweak_slits_maxfrac

float

0.1

If tweak_slit is True, this sets the maximum fractional amount (of a slits width) allowed for trimming each (i.e. left and right) slit boundary, i.e. the default is 10% which means slits would shrink or grow by at most 20% (10% on each side)

tweak_slits_thresh

float

0.93

If tweak_slits is True, this sets the illumination function threshold used to tweak the slit boundaries based on the illumination flat. It should be a number less than 1.0

twod_fit_npoly

int

Order of polynomial used in the 2D bspline-polynomial fit to flat-field image residuals. The code determines the order of these polynomials to each slit automatically depending on the slit width, which is why the default is None. Alter this paramter at your own risk!


EdgeTracePar Keywords

Class Instantiation: EdgeTracePar

Key

Type

Options

Default

Description

add_missed_orders

bool

False

For any Echelle spectrograph (fixed-format or otherwise), attempt to add orders that have been missed by the automated edge tracing algorithm. For fixed-format Echelles, this is based on the expected positions on on the detector. Otherwise, the detected orders are modeled and roughly used to predict the locations of missed orders; see additional parameters order_width_poly, order_gap_poly, and order_spat_range.

add_predict

str

nearest

Sets the method used to predict the shape of the left and right traces for a user-defined slit inserted. Options are (1) straight inserts traces with a constant spatial pixels position, (2) nearest inserts traces with a form identical to the automatically identified trace at the nearest spatial position to the inserted slit, or (3) pca uses the PCA decomposition to predict the shape of the traces.

add_slits

str, list

Add one or more user-defined slits. The syntax to define a slit to add is: ‘det:spec:spat_left:spat_right’ where det=detector, spec=spectral pixel, spat_left=spatial pixel of left slit boundary, and spat_righ=spatial pixel of right slit boundary. For example, ‘2:2000:2121:2322,3:2000:1201:1500’ will add a slit to detector 2 passing through spec=2000 extending spatially from 2121 to 2322 and another on detector 3 at spec=2000 extending from 1201 to 1500.

auto_pca

bool

True

During automated tracing, attempt to construct a PCA decomposition of the traces. When True, the edge traces resulting from the initial detection, centroid refinement, and polynomial fitting must meet a set of criteria for performing the pca; see pypeit.edgetrace.EdgeTraceSet.can_pca(). If False, the sync_predict parameter cannot be set to pca; if it is not, the value is set to nearest and a warning is issued when validating the parameter set.

bound_detector

bool

False

When the code is ready to synchronize the left/right trace edges, the traces should have been constructed, vetted, and cleaned. This can sometimes lead to no valid traces. This parameter dictates what to do next. If bound_detector is True, the code will artificially add left and right edges that bound the detector; if False, the code identifies the slit-edge tracing as being unsuccessful, warns the user, and ends gracefully. Note that setting bound_detector to True is needed for some long-slit data where the slit edges are, in fact, beyond the edges of the detector.

clip

bool

True

Remove traces flagged as bad, instead of only masking them. This is currently only used by centroid_refine().

det_buffer

int

5

The minimum separation between the detector edges and a slit edge for any added edge traces. Must be positive.

det_min_spec_length

int, float

0.33

The minimum spectral length (as a fraction of the detector size) of a trace determined by direct measurements of the detector data (as opposed to what should be included in any modeling approach; see fit_min_spec_length).

dlength_range

int, float

Similar to minimum_slit_dlength, but constrains the fractional change in the slit length as a function of wavelength. For example, a value of 0.2 means that slit length should not vary more than 20%as a function of wavelength.

edge_detect_clip

int, float

Sigma clipping level for peaks detected in the collapsed, Sobel-filtered significance image.

edge_thresh

int, float

20.0

Threshold for finding edges in the Sobel-filtered significance image.

exclude_regions

list, str

User-defined regions to exclude from the slit tracing. To set this parameter, the text should be a comma separated list of pixel ranges (in the x direction) to be excluded and the detector number. For example, the following string 1:0:20,1:300:400 would select two regions in det=1 between pixels 0 and 20 and between 300 and 400.

filt_iter

int

0

Number of median-filtering iterations to perform on sqrt(trace) image before applying to Sobel filter to detect slit/order edges.

fit_function

str

polynomial, legendre, chebyshev

legendre

Function fit to edge measurements. Options are: polynomial, legendre, chebyshev

fit_maxdev

int, float

5.0

Maximum deviation between the fitted and measured edge position for rejection in spatial pixels.

fit_maxiter

int

25

Maximum number of rejection iterations during edge fitting.

fit_min_spec_length

float

0.6

Minimum unmasked spectral length of a traced slit edge to use in any modeling procedure (polynomial fitting or PCA decomposition).

fit_niter

int

1

Number of iterations of re-measuring and re-fitting the edge data; see fit_trace().

fit_order

int

5

Order of the function fit to edge measurements.

follow_span

int

20

In the initial connection of spectrally adjacent edge detections, this sets the number of previous spectral rows to consider when following slits forward.

fwhm_gaussian

int, float

3.0

The fwhm parameter to use when using Gaussian weighting in fit_trace() when refining the PCA predictions of edges. See description peak_trace().

fwhm_uniform

int, float

3.0

The fwhm parameter to use when using uniform weighting in fit_trace() when refining the PCA predictions of edges. See description of peak_trace().

gap_offset

int, float

5.0

Offset (pixels) used for the slit edge gap width when inserting slit edges (see sync_center) or when nudging predicted slit edges to avoid slit overlaps. This should be larger than minimum_slit_gap when converted to arcseconds.

left_right_pca

bool

False

Construct a PCA decomposition for the left and right traces separately. This can be important for cross-dispersed echelle spectrographs (e.g., Keck-NIRES)

length_range

int, float

Allowed range in slit length compared to the median slit length. For example, a value of 0.3 means that slit lengths should not vary more than 30%. Relatively shorter or longer slits are masked or clipped. Most useful for echelle or multi-slit data where the slits should have similar or identical lengths.

maskdesign_filename

str, list

Mask design info contained in this file or files (comma separated)

maskdesign_maxsep

int, float

50

Maximum allowed offset in pixels between the slit edges defined by the slit-mask design and the traced edges.

maskdesign_sigrej

int, float

3

Number of sigma for sigma-clipping rejection during slit-mask design matching.

maskdesign_step

int, float

1

Step in pixels used to generate a list of possible offsets (within +/- maskdesign_maxsep) between the slit edges defined by the mask design and the traced edges.

match_tol

int, float

3.0

Same-side slit edges below this separation in pixels are considered part of the same edge.

max_nudge

int, float

If parts of any (predicted) trace fall off the detector edge, allow them to be nudged away from the detector edge up to and including this maximum number of pixels. If None, no limit is set; otherwise should be 0 or larger.

max_shift_abs

int, float

0.5

Maximum spatial shift in pixels between an input edge location and the recentroided value.

max_shift_adj

int, float

0.15

Maximum spatial shift in pixels between the edges in adjacent spectral positions.

max_spat_error

int, float

Maximum error in the spatial position of edges in pixels.

minimum_slit_dlength

int, float

Minimum change in the slit length (arcsec) as a function of wavelength in arcsec. This is mostly meant to catch cases when the polynomial fit to the detected edges becomes ill-conditioned (e.g., when the slits run off the edge of the detector) and leads to wild traces. If reducing the order of the polynomial (fit_order) does not help, try using this to remove poorly constrained slits.

minimum_slit_gap

int, float

Minimum slit gap in arcsec. Gaps between slits are determined by the median difference between the right and left edge locations of adjacent slits. Slits with small gaps are merged by removing the intervening traces.If None, no minimum slit gap is applied. This should be smaller than gap_offset when converted to pixels.

minimum_slit_length

int, float

Minimum slit length in arcsec. Slit lengths are determined by the median difference between the left and right edge locations for the unmasked trace locations. This is used to identify traces that are erroneously matched together to form slits. Short slits are expected to be ignored or removed (see clip). If None, no minimum slit length applied.

minimum_slit_length_sci

int, float

Minimum slit length in arcsec for a science slit. Slit lengths are determined by the median difference between the left and right edge locations for the unmasked trace locations. Used in combination with minimum_slit_length, this parameter is used to identify box or alignment slits; i.e., those slits that are shorter than minimum_slit_length_sci but larger than minimum_slit_length are box/alignment slits. Box slits are never removed (see clip), but no spectra are extracted from them. If None, no minimum science slit length is applied.

niter_gaussian

int

6

The number of iterations of fit_trace() to use when using Gaussian weighting.

niter_uniform

int

9

The number of iterations of fit_trace() to use when using uniform weighting.

order_gap_poly

int

3

Order of the Legendre polynomial used to model the spatial gap between orders as a function of the order spatial position. See add_missed_orders.

order_match

int, float

Orders for fixed-format echelle spectrographs are always matched to a predefined expectation for the number of orders found and their relative placement in the detector. This sets the tolerance allowed for matching identified “slits” to echelle orders. Must be relative to the fraction of the detector spatial scale (i.e., a value of 0.05 means that the order locations must be within 5% of the expected value). If None, no limit is used.

order_offset

int, float

Orders for fixed-format echelle spectrographs are always matched to a predefined expectation for the number of orders found and their relative placement in the detector. This sets the offset to introduce to the expected order positions to improve the match for this specific data. This is an additive offset to the measured slit positions; i.e., this should minimize the difference between the expected order positions and self.slit_spatial_center() + offset. Must be in the fraction of the detector spatial scale. If None, no offset is applied.

order_spat_range

list

The spatial range of the detector/mosaic over which to predict order locations. If None, the full detector/mosaic range is used. See add_missed_orders.

order_width_poly

int

2

Order of the Legendre polynomial used to model the spatial width of each order as a function of spatial pixel position. See add_missed_orders.

overlap

bool

False

Assume slits identified as abnormally short are actually due to overlaps between adjacent slits/orders. If set to True, you must have also used length_range to identify left-right edge pairs that have an abnormally short separation. For those short slits, the code attempts to convert the short slits into slit gaps. This is particularly useful for blue orders in Keck-HIRES data.

pad

int

0

Integer number of pixels to consider beyond the slit edges when selecting pixels that are ‘on’ the slit.

pca_function

str

polynomial, legendre, chebyshev

polynomial

Type of function fit to the PCA coefficients for each component. Options are: polynomial, legendre, chebyshev

pca_maxiter

int

25

Maximum number of rejection iterations when fitting the PCA coefficients.

pca_maxrej

int

1

Maximum number of PCA coefficients rejected during a given fit iteration.

pca_min_edges

int

4

Minimum number of edge traces required to perform a PCA decomposition of the trace form. If left_right_pca is True, this minimum applies to the number of left and right traces separately.

pca_n

int

The number of PCA components to keep, which must be less than the number of detected traces. If not provided, determined by calculating the minimum number of components required to explain a given percentage of variance in the edge data; see pca_var_percent.

pca_order

int

2

Order of the function fit to the PCA coefficients.

pca_sigrej

int, float, list

2.0, 2.0

Sigma rejection threshold for fitting PCA components. Individual numbers are used for both lower and upper rejection. A list of two numbers sets these explicitly (e.g., [2., 3.]).

pca_var_percent

int, float

99.8

The percentage (i.e., not the fraction) of the variance in the edge data accounted for by the PCA used to truncate the number of PCA coefficients to keep (see pca_n). Ignored if pca_n is provided directly.

rm_slits

str, list

Remove one or more user-specified slits. The syntax used to define a slit to remove is: ‘det:spec:spat’ where det=detector, spec=spectral pixel, spat=spatial pixel. For example, ‘2:2000:2121,3:2000:1500’ will remove the slit on detector 2 that contains pixel (spat,spec)=(2000,2121) and on detector 3 that contains pixel (2000,2121).

smash_range

list

0.0, 1.0

Range of the slit in the spectral direction (in fractional units) to smash when searching for slit edges. If the spectrum covers only a portion of the image, use that range.

sobel_enhance

int

0

Enhance the sobel filtering? A value of 0 will not enhance the sobel filtering. Any other value > 0 will sum the sobel values. For example, a value of 3 will combine the sobel values for the 3 nearest pixels. This is useful when a slit edge is poorly defined (e.g. vignetted).

sobel_mode

str

nearest, constant

nearest

Mode for Sobel filtering. Default is ‘nearest’; note we find’constant’ works best for DEIMOS.

sync_center

str

median, nearest, gap

median

Mode to use for determining the location of traces to insert. Use median to use the median of the matched left and right edge pairs, nearest to use the length of the nearest slit, or gap to offset by a fixed gap width from the next slit edge.

sync_predict

str

pca, nearest, auto

pca

Mode to use when predicting the form of the trace to insert. Use pca to use the PCA decomposition, nearest to reproduce the shape of the nearest trace, or auto to let PypeIt decide which mode to use between pca and nearest. In general, it will first try pca, and if that is not possible, it will use nearest.

sync_to_edge

bool

True

If adding a first left edge or a last right edge, ignore center_mode for these edges and place them at the edge of the detector (with the relevant shape).

trace_median_frac

int, float

After detection of peaks in the rectified Sobel-filtered image and before refitting the edge traces, the rectified image is median filtered with a kernel width of trace_median_frac*nspec along the spectral dimension.

trace_rms_tol

int, float

After retracing edges using peaks detected in the rectified and collapsed image, the RMS difference (in pixels) between the original and refit traces are calculated. This sets the upper limit of the RMS for traces that will be removed. If None, no limit is set and all new traces are kept.

trace_thresh

int, float

After rectification and median filtering of the Sobel-filtered image (see trace_median_frac), values in the median-filtered image below this threshold are masked in the refitting of the edge trace data. If None, no masking applied.

use_maskdesign

bool

False

Use slit-mask designs to identify slits.


WaveTiltsPar Keywords

Class Instantiation: WaveTiltsPar

Key

Type

Options

Default

Description

cont_rej

int, float, list, ndarray

3, 1.5

The sigma threshold for rejection. Can be a single number or two numbers that give the low and high sigma rejection, respectively.

func2d

str

legendre2d

Type of function for 2D fit

idsonly

bool

False

Only use the arc lines that have an identified wavelength to trace tilts (CURRENTLY NOT USED!)

maxdev2d

int, float

0.25

Maximum absolute deviation (in units of fwhm) rejection threshold used to determines which pixels in global 2d fits to arc line tilts are rejected because they deviate from the model by more than this value

maxdev_tracefit

int, float

0.2

Maximum absolute deviation (in units of fwhm) for the legendre polynomial fits to individual arc line tilt fits during iterative trace fitting (flux weighted, then gaussian weighted)

minmax_extrap

list, ndarray

150.0, 1000.0

Sets how far below the last measured tilt line is extrapolated in tracewave.fit_tilts()

nfwhm_neigh

int, float

3.0

Required separation between neighboring arc lines for them to be considered for tilt tracing in units of the the spectral fwhm (see wavelength parset where fwhm is defined)

rm_continuum

bool

False

Before tracing the line center at each spatial position, remove any low-order continuum in the 2D spectra.

sig_neigh

int, float

10.0

Significance threshold for arcs to be used in line identification for the purpose of identifying neighboring lines. The tracethresh parameter above determines the significance threshold of lines that will be traced, but these lines must be at least nfwhm_neigh fwhm away from neighboring lines. This parameter determines the significance above which a line must be to be considered a possible colliding neighbor. A low value of sig_neigh will result in an overall larger number of lines, which will result in more lines above tracethresh getting rejected

sigrej2d

int, float

3.0

Outlier rejection significance determining which pixels on a fit to an arc line tilt are rejected by the global 2D fit

sigrej_trace

int, float

3.0

Outlier rejection significance to determine which traced arc lines should be included in the global fit

spat_order

int, float, list, ndarray

3

Order of the legendre polynomial to be fit to the tilt of an arc line. This parameter determines both the order of the individual arc line tilts, as well as the order of the spatial direction of the 2d legendre polynomial (spatial, spectral) that is fit to obtain a global solution for the tilts across the slit/order. This can be a single number or a list/array providing the value for each slit

spec_order

int, float, list, ndarray

4

Order of the spectral direction of the 2d legendre polynomial (spatial, spectral) that is fit to obtain a global solution for the tilts across the slit/order. This can be a single number or a list/array providing the value for each slit

tracethresh

int, float, list, ndarray

20.0

Significance threshold for arcs to be used in tracing wavelength tilts. This can be a single number or a list/array providing the value for each slit/order.


WavelengthSolutionPar Keywords

Class Instantiation: WavelengthSolutionPar

Key

Type

Options

Default

Description

bad_orders_maxfrac

float

0.25

For echelle spectrographs (i.e., echelle=True), this is the maximum fraction of orders (per detector) with failed 1D fit, for PypeIt to attempt a refit.

cc_local_thresh

float

0.7

Threshold for the local cross-correlation coefficient, evaluated at each reidentified line, between an input spectrum and the shifted and stretched archive spectrum above which a line must be to be considered a good line for reidentification. The local cross-correlation is evaluated at each candidate reidentified line (using a window of nlocal_cc), and is then used to score the the reidentified lines to arrive at the final set of good reidentifications.

cc_shift_range

tuple

Range of pixel shifts allowed when cross-correlating the input arc spectrum with the archive spectrum. If None, the range will be automatically determined.

cc_thresh

float, list, ndarray

0.7

Threshold for the global cross-correlation coefficient between an input spectrum and member of the archive required to attempt reidentification. Spectra from the archive with a lower cross-correlation are not used for reidentification. This can be a single number or a list/array providing the value for each slit.

ech_norder_coeff

int

4

For echelle spectrographs, this is the order of the final 2d fit to the order dimension.

ech_nspec_coeff

int

4

For echelle spectrographs, this is the order of the final 2d fit to the spectral dimension. You should choose this to be the n_final of the fits to the individual orders.

ech_separate_2d

bool

False

For echelle spectrographs, fit the 2D solutions on separate detectors separately

ech_sigrej

int, float

2.0

For echelle spectrographs, this is the sigma-clipping rejection threshold in the 2d fit to spectral and order dimensions

echelle

bool

False

Is this an echelle spectrograph? If yes an additional 2-d fit wavelength fit will be performed as a function of spectral pixel and order number to improve the wavelength solution

frac_rms_thresh

float

1.5

For echelle spectrographs (i.e., echelle=True), this is the fractional change in the RMS threshold used when a 1D fit is re-attempted for failed orders.

func

str

legendre

Function used for wavelength solution fits

fwhm

int, float

4.0

Spectral sampling of the arc lines. This is the FWHM of an arcline in binned pixels of the input arc image

fwhm_fromlines

bool

True

Estimate spectral resolution in each slit using the arc lines. If True, the estimated FWHM will override fwhm only in the determination of the wavelength solution (including the calculation of the threshold for the solution RMS, see rms_thresh_frac_fwhm), but not for the wave tilts calibration.

fwhm_spat_order

int

0

This parameter determines the spatial polynomial order to use in the 2D polynomial fit to the FWHM of the arc lines. See also, fwhm_spec_order.

fwhm_spec_order

int

1

This parameter determines the spectral polynomial order to use in the 2D polynomial fit to the FWHM of the arc lines. See also, fwhm_spat_order.

lamps

list

Name of one or more ions used for the wavelength calibration. Use None for no calibration. Choose use_header to use the list of lamps recorded in the header of the arc frames (this is currently available only for Keck DEIMOS, Keck LRIS, MMT Blue Channel, and LDT DeVeny).

match_toler

float

2.0

Matching tolerance in pixels when searching for new lines. This is the difference in pixels between the wavlength assigned to an arc line by an iteration of the wavelength solution to the wavelength in the line list. This parameter is also used as the matching tolerance in pixels for a line reidentification. A good line match must match within this tolerance to the shifted and stretched archive spectrum, and the archive wavelength solution at this match must be within match_toler dispersion elements from the line in line list.

method

str

holy-grail, identify, reidentify, echelle, full_template

holy-grail

Method to use to fit the individual arc lines. Note that some of the available methods should not be used; they are unstable and require significant parameter tweaking to succeed. You should use one of ‘holy-grail’, ‘reidentify’, or ‘full_template’. ‘holy-grail’ attempts to get a first guess at line IDs by looking for patterns in the line locations. It is fully automated. When it works, it works well; however, it can fail catastrophically. Instead, ‘reidentify’ and ‘full_template’ are the preferred methods. They require an archived wavelength solution for your specific instrument/grating combination as a reference. This is used to anchor the wavelength solution for the data being reduced. All options are: holy-grail, identify, reidentify, echelle, full_template.

n_final

int, float, list, ndarray

4

Order of final fit to the wavelength solution (there are n_final+1 parameters in the fit). This can be a single number or a list/array providing the value for each slit

n_first

int

2

Order of first guess fit to the wavelength solution.

nfitpix

int

5

Number of pixels to fit when deriving the centroid of the arc lines (an odd number is best)

nlocal_cc

int

11

Size of pixel window used for local cross-correlation computation for each arc line. If not an odd number one will be added to it to make it odd.

nreid_min

int

1

Minimum number of times that a given candidate reidentified line must be properly matched with a line in the arxiv to be considered a good reidentification. If there is a lot of duplication in the arxiv of the spectra in question (i.e. multislit) set this to a number like 1-4. For echelle this depends on the number of solutions in the arxiv. Set this to 1 for fixed format echelle spectrographs. For an echelle with a tiltable grating, this will depend on the number of solutions in the arxiv.

nsnippet

int

2

Number of spectra to chop the arc spectrum into when method is ‘full_template’

numsearch

int

20

Number of brightest arc lines to search for in preliminary identification

qa_log

bool

True

Governs whether the wavelength solution arc line QA plots will have log or linear scalingIf True, the scaling will be log, if False linear

redo_slits

int, list

Redo the input slit(s) [multislit] or order(s) [echelle]

reference

str

arc, sky, pixel

arc

Perform wavelength calibration with an arc, sky frame. Use ‘pixel’ for no wavelength solution.

refframe

str

observed, heliocentric, barycentric

heliocentric

Frame of reference for the wavelength calibration. Options are: observed, heliocentric, barycentric

reid_arxiv

str

Name of the archival wavelength solution file that will be used for the wavelength reidentification. Only used if method is ‘reidentify’ or ‘full_template’.

reid_cont_sub

bool

True

If True, continuum subtract the arc and arxiv spectrum before the wavelength reidentification.

rms_thresh_frac_fwhm

float

0.15

Maximum RMS (expressed as fraction of the FWHM) for keeping a slit/order solution. If fwhm_fromlines is True, FWHM will be computed from the arc lines in each slits, otherwise fwhm will be used. This parameter is used for the ‘holy-grail’, ‘reidentify’, and ‘echelle’ methods and when re-analyzing a slit using the redo_slits parameter.

sigdetect

int, float, list, ndarray

5.0

Sigma threshold above fluctuations for arc-line detection. Arcs are continuum subtracted and the fluctuations are computed after continuum subtraction. This can be a single number or a vector (list or numpy array) that provides the detection threshold for each slit.

sigrej_final

float

3.0

Number of sigma for rejection for the final guess to the wavelength solution.

sigrej_first

float

2.0

Number of sigma for rejection for the first guess to the wavelength solution.

use_instr_flag

bool

False

If True, restrict to lines matching the instrument. WARNING: This is only implemented for shane_kast_red + HolyGrail. Do not use it unless you really know what you are doing.

wvrng_arxiv

list

Cut the arxiv template down to this specified wavelength range [min,max]


Coadd1DPar Keywords

Class Instantiation: Coadd1DPar

Key

Type

Options

Default

Description

coaddfile

str

Output filename

dloglam

int, float

Dispersion in units of log10(wave) in case you want to specify it in the get_wave_grid (for the ‘velocity’ or ‘log10’ options), otherwise a median value is computed from the data.

dv

int, float

Dispersion in units of km/s in case you want to specify it in the get_wave_grid (for the ‘velocity’ option), otherwise a median value is computed from the data.

dwave

int, float

Dispersion in Angstroms in case you want to specify it in the get_wave_grid (for the ‘linear’ option), otherwise a median value is computed from the data.

ex_value

str

OPT

The extraction to coadd, i.e. optimal or boxcar. Must be either ‘OPT’ or ‘BOX’

filter

str

none

Filter for scaling. See flux_calib.load_fitler_file() for naming. Ignore if none

filter_mag

float

Magnitude of the source in the given filter

filter_mask

str, list

List of wavelength regions to mask when doing the scaling (i.e., occasional junk pixels). Colon and comma separateed, e.g. 5552:5559,6010:6030

flux_value

bool

True

If True (default), the code will coadd the fluxed spectra (i.e. the FLAM) in the spec1d files. If False, it will coadd the counts.

lower

int, float

3.0

Lower rejection threshold used for rejecting pixels when combining spectra in units of sigma.

mag_type

str

AB

Magnitude type. AB is the only option currently allowed

maxiter_reject

int

5

Maximum number of iterations for stacking and rejection. The code stops iterating either when the output mask does not change betweeen successive iterations or when maxiter_reject is reached.

maxiter_scale

int

5

Maximum number of iterations performed for rescaling spectra.

maxrej

int

Coadding performs iterative rejection by comparing each exposure to a preliminary stack of all the exposures. If this parameter is set then it will not reject more than maxrej pixels per iteration of this rejection. The default is None, which means no maximum on rejected pixels.

nbests

list, int

Number of orders to use for estimating the per exposure weights. Default is None, which will just use one fourth of the total number of orders. This is only used for Echelle

nmaskedge

int

2

Number of edge pixels to mask. This should be removed/fixed.

ref_percentile

int, float

70.0

Percentile used for selecting the minimum SNR cut from a reference spectrum used to robustly determine the median ratio between spectra. This parameter is used by coadd1d.robust_median_ratio as part of the automatic rescaling procedure. Pixels above this percentile cut are deemed the “good” pixels and are used to compute the ratio of two spectra. This must be a number between 0 and 100.

scale_method

str

auto

Method used to rescale the spectra prior to coadding. The options are: ‘auto’ – Determine the scaling method automatically based on the S/N ratio which works well. ‘poly’ – Polynomial rescaling. ‘median’ – Median rescaling ‘none’ – Do not rescale. ‘hand’ – Pass in hand scaling factors. This option is not well tested.

sigrej_exp

int, float

Rejection threshold used for rejecting exposures with S/N more than sigrej_exp*sigma above the median S/N. If None (the default), no rejection is performed. Currently, only available for multi-slit observations.

sigrej_scale

int, float

3.0

Rejection threshold used for rejecting pixels when rescaling spectra with scale_spec.

sn_clip

int, float

30.0

Errors are capped during rejection so that the S/N is never greater than sn_clip. This prevents overly aggressive rejection in high S/N ratio spectrum which neverthless differ at a level greater than the formal S/N due to systematics.

sn_min_medscale

int, float

0.5

For scale method set to auto, this sets the minimum SNR for which median scaling is attempted.

sn_min_polyscale

int, float

2.0

For scale method set to auto, this sets the minimum SNR for which polynomial scaling is attempted.

sn_smooth_npix

int, float

Number of pixels to median filter by when computing S/N used to decide how to scale and weight spectra. If set to None (default), the code will determine the effective number of good pixels per spectrum in the stack that is being co-added and use 10% of this neff.

spec_samp_fact

float

1.0

Make the wavelength grid sampling finer (spec_samp_fact < 1.0) or coarser (spec_samp_fact > 1.0) by this sampling factor. This basically multiples the ‘native’ spectral pixels by spec_samp_fact, i.e. units spec_samp_fact are pixels.

upper

int, float

3.0

Upper rejection threshold used for rejecting pixels when combining spectra in units of sigma.

wave_grid_max

int, float

Used in case you want to specify the maximum wavelength in your wavelength grid, default=None computes from data

wave_grid_min

int, float

Used in case you want to specify the minimum wavelength in your wavelength grid, default=None computes from data

wave_method

str

linear

Method used to construct wavelength grid for coadding spectra. The routine that creates the wavelength is get_wave_grid(). The options are: ‘iref’ – Use the first wavelength array. ‘velocity’ – Grid is uniform in velocity. ‘log10’ – Grid is uniform in log10(wave). This is the same as velocity. ‘linear’ – Grid is uniform in lambda. ‘concatenate’ – Meld the input wavelength arrays

weight_method

str

auto

Method used to weight the spectra for coadding. The options are: ‘auto’ – Use constant weights if rms_sn < 3.0, otherwise use wavelength dependent.’constant’ – Constant weights based on rms_sn**2’uniform’ – Uniform weighting’wave_dependent’ – Wavelength dependent weights will be used irrespective of the rms_sn ratio. This option will not work well at low S/N ratio although it is useful for objects where only a small fraction of the spectral coverage has high S/N ratio (like high-z quasars).’relative’ – Apply relative weights implying one reference exposure will receive unit weight at all wavelengths and all others receive relatively wavelength dependent weights . Note, relative weighting will only work well when there is at least one spectrum with a reasonable S/N, and a continuum. This option may only be better when the object being used has a strong continuum + emission lines. This is particularly useful if you are dealing with highly variable spectra (e.g. emission lines) andrequire a precision better than ~1 per cent.’ivar’ – Use inverse variance weighting. This is not well tested and should probably be deprecated.


Coadd2DPar Keywords

Class Instantiation: Coadd2DPar

Key

Type

Options

Default

Description

exclude_slits

str, list

Exclude one or more slits from the coaddition. Example syntax – DET01:175,DET02:205 or MSC02:2234. This and only_slits are mutually exclusive. If both are provided, only_slits takes precedence.

manual

str

Manual extraction parameters. det:spat:spec:fwhm:boxcar_radius. Multiple manual extractions are semi-colon separated, and spat,spec are in the pseudo-image generated by COADD2D.boxcar_radius is optional and in pixels (not arcsec!).

offsets

str, list

auto

Offsets for the images being combined (spat pixels). Options are: maskdef_offsets, header, auto, and a list of offsets. Use maskdef_offsets to use the offsets computed during the slitmask design matching (currently available for these Slit-mask design Spectrographs only). If equal to header, the dither offsets recorded in the header, when available, will be used. If auto is chosen, PypeIt will try to compute the offsets using a reference object with the highest S/N, or an object selected by the user (see user_obj). If a list of offsets is provided, PypeIt will use it.

only_slits

str, list

Restrict coaddition to one or more of slits. Example syntax – DET01:175,DET02:205 or MSC02:2234. This and exclude_slits are mutually exclusive. If both are provided, only_slits takes precedence.

spat_toler

int

5

This parameter provides the desired tolerance in spatial pixel used to identify slits in different exposures

use_slits4wvgrid

bool

False

If True, use the slits to set the trace down the center

user_obj

int, list

Object that the user wants to use to compute the weights and/or the offsets for coadding images. For longslit/multislit spectroscopy, provide the SLITID and the OBJID, separated by comma, of the selected object. For echelle spectroscopy, provide the ECH_OBJID of the selected object. See Spec1D Output for more info about SLITID, OBJID and ECH_OBJID. If this parameter is not None, it will be used to compute the offsets only if offsets = auto, and it will used to compute the weights only if weights = auto.

wave_method

str

Argument to get_wave_grid() method, which determines how the 2d coadd wavelength grid is constructed. The default is None, which will use a linear gridfor longslit/multislit coadds and a log10 grid for echelle coadds. Currently supported options with 2d coadding are:* ‘iref’ – Use one of the exposures (the first) as the reference for the wavelength grid * ‘velocity’ – Grid is uniform in velocity* ‘log10’ – Grid is uniform in log10(wave). This is the same as velocity.* ‘linear’ – Grid is uniform in wavelength

weights

str, list

auto

Mode for the weights used to coadd images. Options are: auto, uniform, or a list of weights. If auto is used, PypeIt will try to compute the weights using a reference object with the highest S/N, or an object selected by the user (see user_obj), if uniform is used, uniform weights will be applied. If a list of weights is provided, PypeIt will use it.


Collate1DPar Keywords

Class Instantiation: Collate1DPar

Key

Type

Options

Default

Description

dry_run

bool

False

If set, the script will display the matching File and Object Ids but will not flux, coadd or archive.

exclude_serendip

bool

False

Whether to exclude SERENDIP objects from collating.

exclude_slit_trace_bm

list, str

[]

A list of slit trace bitmask bits that should be excluded.

flux

bool

False

If set, the script will flux calibrate using archived sensfuncs before coadding.

ignore_flux

bool

False

If set, the script will only coadd non-fluxed spectra even if flux data is present. Otherwise fluxed spectra are coadded if all spec1ds have been fluxed calibrated.

match_using

str

ra/dec

Determines how 1D spectra are matched as being the same object. Must be either ‘pixel’ or ‘ra/dec’.

outdir

str

/Users/westfall/Work/packages/pypeit/doc

The path where all coadded output files and report files will be placed.

refframe

str

Perform reference frame correction prior to coadding. Options are: observed, heliocentric, barycentric

spec1d_outdir

str

The path where all modified spec1d files are placed. These are only created if flux calibration or refframe correction are asked for.

tolerance

str, float

1.0

The tolerance used when comparing the coordinates of objects. If two objects are within this distance from each other, they are considered the same object. If match_using is ‘ra/dec’ (the default) this is an angular distance. The defaults units are arcseconds but other units supported by astropy.coordinates.Angle can be used (e.g., ‘0.003d’ or ‘0h1m30s’). If match_using is ‘pixel’ this is a float.

wv_rms_thresh

float

If set, any objects with a wavelength RMS > this value are skipped, else all wavelength RMS values are accepted.


FlexurePar Keywords

Class Instantiation: FlexurePar

Key

Type

Options

Default

Description

excessive_shift

str

crash, set_to_zero, continue, use_median

use_median

Behavior when the measured spectral flexure shift is larger than spec_maxshift. The options are: ‘crash’ - Raise an error and halt the data reduction; ‘set_to_zero’ - Set the flexure shift to zero and continue with the reduction; ‘continue’ - Use the large flexure value whilst issuing a warning; and ‘use_median’ - Use the median flexure shift among all the objects in the same slit (if more than one object is detected) or among all the other slits; if not available, the flexure correction will not be applied.

maxwave

int, float

Maximum wavelength to use for the correlation. If None or greater than the maximum wavelength of either the object or archive sky spectrum, this this parameter has no effect.

minwave

int, float

Minimum wavelength to use for the correlation. If None or less than the minimum wavelength of either the object or archive sky spectrum, this this parameter has no effect.

multi_min_SN

int, float

1

Minimum S/N for analyzing sky spectrum for flexure

spec_maxshift

int

20

Maximum allowed spectral flexure shift in pixels.

spec_method

str

boxcar, slitcen, skip

skip

Method used to correct for flexure. Use skip for no correction. If slitcen is used, the flexure correction is performed before the extraction of objects (not recommended). Options are: None, boxcar, slitcen, skip

spectrum

str

paranal_sky.fits

Archive sky spectrum to be used for the flexure correction.


FluxCalibratePar Keywords

Class Instantiation: FluxCalibratePar

Key

Type

Options

Default

Description

extinct_correct

bool

The default behavior for atmospheric extinction corrections is that if UVIS algorithm is used (which does not correct for telluric absorption) than an atmospheric extinction model is used to correct for extinction below 10,000A, whereas if the IR algorithm is used, then no extinction correction is applied since the atmosphere is modeled directly. To follow these defaults based on the algorithm this parameter should be set to extinct_correct=None. If instead this parameter is set, this overide this default behavior. In other words, it will force an extinction correction if extinct_correct=True, and will not perform an extinction correction if extinct_correct=False.

extinct_file

str

closest

If extinct_file='closest' the code will select the PypeIt-included extinction file for the closest observatory (within 5 deg, geographic coordinates) to the telescope identified in std_file (see Extinction Correction for the list of currently included files). If constructing a sesitivity function for a telescope not within 5 deg of a listed observatory, this parameter may be set to the name of one of the listed extinction files. Alternatively, a custom extinction file may be installed in the PypeIt cache using the pypeit_install_extinctfile script; this parameter may then be set to the name of the custom extinction file.

extrap_sens

bool

False

If False (default), the code will crash if one tries to use sensfunc at wavelengths outside its defined domain. By changing the par[‘sensfunc’][‘extrap_blu’] and par[‘sensfunc’][‘extrap_red’] this domain can be extended. If True the code will blindly extrapolate.

use_archived_sens

bool

False

Use an archived sensfunc to flux calibration


ReduxPar Keywords

Class Instantiation: ReduxPar

Key

Type

Options

Default

Description

calwin

int, float

0

The window of time in hours to search for calibration frames for a science frame

chk_version

bool

True

If True enforce strict PypeIt version checking to ensure that all files were created with the current version of PypeIt. If set to False, the code will attempt to read out-of-date files and keep going. Beware (!!) that this can lead to unforeseen bugs that either cause the code to crash or lead to erroneous results. I.e., you really need to know what you are doing if you set this to False!

detnum

int, list

Restrict reduction to a list of detector indices. In case of mosaic reduction (currently only available for Gemini/GMOS and Keck/DEIMOS) detnum should be a list of tuples of the detector indices that are mosaiced together. E.g., for Gemini/GMOS detnum would be [(1,2,3)] and for Keck/DEIMOS it would be [(1, 5), (2, 6), (3, 7), (4, 8)]

ignore_bad_headers

bool

False

Ignore bad headers (NOT recommended unless you know it is safe).

maskIDs

str, int, list

Restrict reduction to a set of slitmask IDs Example syntax – maskIDs = 818006,818015 This must be used with detnum (for now).

qadir

str

QA

Directory relative to calling directory to write quality assessment files.

quicklook

bool

False

Run a quick look reduction? This is usually good if you want to quickly reduce the data (usually at the telescope in real time) to get an initial estimate of the data quality.

redux_path

str

/Users/westfall/Work/packages/pypeit/doc

Path to folder for performing reductions. Default is the current working directory.

scidir

str

Science

Directory relative to calling directory to write science files.

slitspatnum

str, list

Restrict reduction to a set of slit DET:SPAT values (closest slit is used). Example syntax – slitspatnum = DET01:175,DET01:205 or MSC02:2234 If you are re-running the code, (i.e. modifying one slit) you must have the precise SPAT_ID index.

sortroot

str

A filename given to output the details of the sorted files. If None, the default is the root name of the pypeit file. If off, no output is produced.

spectrograph

str

Spectrograph that provided the data to be reduced. See Spectrographs for valid options.


ReducePar Keywords

Class Instantiation: ReducePar

Key

Type

Options

Default

Description

cube

CubePar

CubePar Keywords

Parameters for cube generation algorithms

extraction

ExtractionPar

ExtractionPar Keywords

Parameters for extraction algorithms

findobj

FindObjPar

FindObjPar Keywords

Parameters for the find object and tracing algorithms

skysub

SkySubPar

SkySubPar Keywords

Parameters for sky subtraction algorithms

slitmask

SlitMaskPar

SlitMaskPar Keywords

Parameters for slitmask

trim_edge

list

3, 3

Trim the slit by this number of pixels left/right when performing sky subtraction


CubePar Keywords

Class Instantiation: CubePar

Key

Type

Options

Default

Description

align

bool

False

If set to True, the input frames will be spatially aligned by cross-correlating the whitelight images with either a reference image (see reference_image) or the whitelight image that is generated using the first spec2d listed in the coadd3d file. Alternatively, the user can specify the offsets (i.e. Delta RA x cos(dec) and Delta Dec, both in arcsec) in the spec2d block of the coadd3d file. See the documentation for examples of this usage.

astrometric

bool

True

If true, an astrometric correction will be applied using the alignment frames.

combine

bool

False

If set to True, the input frames will be combined. Otherwise, a separate datacube will be generated for each input spec2d file, and will be saved as a spec3d file.

dec_max

float

Maximum DEC to use when generating the WCS. If None, the default is maximum DEC based on the WCS of all spaxels. Units should be degrees.

dec_min

float

Minimum DEC to use when generating the WCS. If None, the default is minimum DEC based on the WCS of all spaxels. Units should be degrees.

grating_corr

bool

True

This option performs a small correction for the relative blaze function of all input frames that have (even slightly) different grating angles, or if you are flux calibrating your science data with a standard star that was observed with a slightly different setup.

method

str

subpixel, ngp

subpixel

What method should be used to generate the datacube. There are currently two options: (1) “subpixel” (default) - this algorithm divides each pixel in the spec2d frames into subpixels, and assigns each subpixel to a voxel of the datacube. Flux is conserved, but voxels are correlated, and the error spectrum does not account for covariance between adjacent voxels. See also, spec_subpixel and spat_subpixel. (2) “ngp” (nearest grid point) - this algorithm is effectively a 3D histogram. Flux is conserved, voxels are not correlated, however this option suffers the same downsides as any histogram; the choice of bin sizes can change how the datacube appears. This algorithm takes each pixel on the spec2d frame and puts the flux of this pixel into one voxel in the datacube. Depending on the binning used, some voxels may be empty (zero flux) while a neighboring voxel might contain the flux from two spec2d pixels. Note that all spec2d pixels that contribute to the same voxel are inverse variance weighted (e.g. if two pixels have the same variance, the voxel would be assigned the average flux of the two pixels).

output_filename

str

If combining multiple frames, this string sets the output filename of the combined datacube. If combine=False, the output filenames will be prefixed with spec3d_*

ra_max

float

Maximum RA to use when generating the WCS. If None, the default is maximum RA based on the WCS of all spaxels. Units should be degrees.

ra_min

float

Minimum RA to use when generating the WCS. If None, the default is minimum RA based on the WCS of all spaxels. Units should be degrees.

reference_image

str

White light image of a previously combined datacube. The white light image will be used as a reference when calculating the offsets of the input spec2d files. Ideally, the reference image should have the same shape as the data to be combined (i.e. set the ra_min, ra_max etc. params so they are identical to the reference image).

save_whitelight

bool

False

Save a white light image of the combined datacube. The output filename will be given by the “output_filename” variable with a suffix “_whitelight”. Note that the white light image collapses the flux along the wavelength axis, so some spaxels in the 2D white light image may have different wavelength ranges. To set the wavelength range, use the “whitelight_range” parameter. If combine=False, the individual spec3d files will have a suffix “_whitelight”.

scale_corr

str

This option performs a small correction for the relative spectral illumination scale of different spec2D files. Specify the relative path+file to the spec2D file that you would like to use for the relative scaling. If you want to perform this correction, it is best to use the spec2d file with the highest S/N sky spectrum. You should choose the same frame for both the standards and science frames.

skysub_frame

str

image

Set the sky subtraction to be implemented. The default behaviour is to subtract the sky using the model that is derived from each individual image (i.e. set this parameter to “image”). To turn off sky subtraction completely, set this parameter to “none” (all lowercase). Finally, if you want to use a different frame for the sky subtraction, specify the relative path+file to the spec2D file that you would like to use for the sky subtraction. The model fit to the sky of the specified frame will be used. Note, the sky and science frames do not need to have the same exposure time; the sky model will be scaled to the science frame based on the relative exposure time.

slice_subpixel

int

5

When method=subpixel, slice_subpixel sets the subpixellation scale of each IFU slice. The default option is to divide each slice into 5 sub-slices during datacube creation. See also, spec_subpixel and spat_subpixel.

slit_spec

bool

True

If the data use slits in one spatial direction, set this to True. If the data uses fibres for all spaxels, set this to False.

spat_subpixel

int

5

When method=subpixel, spat_subpixel sets the subpixellation scale of each detector pixel in the spatial direction. The total number of subpixels in each pixel is given by spec_subpixel x spat_subpixel. The default option is to divide each spec2d pixel into 25 subpixels during datacube creation. See also, spec_subpixel and slice_subpixel.

spatial_delta

float

The spatial size of each spaxel to use when generating the WCS (in arcsec). If None, the default is set by the spectrograph file.

spec_subpixel

int

5

When method=subpixel, spec_subpixel sets the subpixellation scale of each detector pixel in the spectral direction. The total number of subpixels in each pixel is given by spec_subpixel x spat_subpixel. The default option is to divide each spec2d pixel into 25 subpixels during datacube creation. See also, spat_subpixel and slice_subpixel.

standard_cube

str

Filename of a standard star datacube. This cube will be used to correct the relative scales of the slits, and to flux calibrate the science datacube.

wave_delta

float

The wavelength step to use when generating the WCS (in Angstroms). If None, the default is set by the wavelength solution.

wave_max

float

Maximum wavelength to use when generating the WCS. If None, the default is maximum wavelength based on the WCS of all spaxels. Units should be Angstroms.

wave_min

float

Minimum wavelength to use when generating the WCS. If None, the default is minimum wavelength based on the WCS of all spaxels. Units should be Angstroms.

weight_method

str

auto, constant, uniform, wave_dependent, relative, ivar

auto

Method used to weight the spectra for coadding. The options are: ‘auto’ – Use constant weights if rms_sn < 3.0, otherwise use wavelength dependent.’constant’ – Constant weights based on rms_sn**2’uniform’ – Uniform weighting’wave_dependent’ – Wavelength dependent weights will be used irrespective of the rms_sn ratio. This option will not work well at low S/N ratio although it is useful for objects where only a small fraction of the spectral coverage has high S/N ratio (like high-z quasars).’relative’ – Apply relative weights implying one reference exposure will receive unit weight at all wavelengths and all others receive relatively wavelength dependent weights . Note, relative weighting will only work well when there is at least one spectrum with a reasonable S/N, and a continuum. This option may only be better when the object being used has a strong continuum + emission lines. This is particularly useful if you are dealing with highly variable spectra (e.g. emission lines) andrequire a precision better than ~1 per cent.’ivar’ – Use inverse variance weighting. This is not well tested and should probably be deprecated.

whitelight_range

list

None, None

A two element list specifying the wavelength range over which to generate the white light image. The first (second) element is the minimum (maximum) wavelength to use. If either of these elements are None, PypeIt will automatically use a wavelength range that ensures all spaxels have the same wavelength coverage. Note, if you are using a reference_image to align all frames, it is preferable to use the same white light wavelength range for all white light images. For example, you may wish to use an emission line map to register two frames.


ExtractionPar Keywords

Class Instantiation: ExtractionPar

Key

Type

Options

Default

Description

boxcar_radius

int, float

1.5

Boxcar radius in arcseconds used for boxcar extraction

model_full_slit

bool

False

If True local sky subtraction will be performed on the entire slit. If False, local sky subtraction will be applied to only a restricted region around each object. This should be set to True for either multislit observations using narrow slits or echelle observations with narrow slits

return_negative

bool

False

If True the negative traces will be extracted and saved to disk

skip_extraction

bool

False

Do not perform an object extraction

skip_optimal

bool

False

Perform boxcar extraction only (i.e. skip Optimal and local skysub)

sn_gauss

int, float

4.0

S/N threshold for performing the more sophisticated optimal extraction which performs a b-spline fit to the object profile. For S/N < sn_gauss the code will simply optimal extractwith a Gaussian with FWHM determined from the object finding.

std_prof_nsigma

float

30.0

prof_nsigma parameter for Standard star extraction. Prevents undesired rejection. NOTE: Not consumed by the code at present.

use_2dmodel_mask

bool

True

Mask pixels rejected during profile fitting when extracting.Turning this off may help with bright emission lines.

use_user_fwhm

bool

False

Boolean indicating if PypeIt should use the FWHM provided by the user (find_fwhm in FindObjPar) for the optimal extraction. If this parameter is False (default), PypeIt estimates the FWHM for each detected object, and uses find_fwhm as initial guess.


FindObjPar Keywords

Class Instantiation: FindObjPar

Key

Type

Options

Default

Description

ech_find_max_snr

int, float

1.0

Criteria for keeping echelle objects. They must either have a maximum S/N across all the orders greater than this value or satisfy the min_snr criteria described by the min_snr parameters. If maxnumber is set (see above) then these criteria will be applied but only the maxnumber highest (median) S/N ratio objects will be kept.

ech_find_min_snr

int, float

0.3

Criteria for keeping echelle objects. They must either have a maximum S/N across all the orders greater than ech_find_max_snr, value or they must have S/N > ech_find_min_snr on >= ech_find_nabove_min_snr orders. If maxnumber is set (see above) then these criteria will be applied but only the maxnumber highest (median) S/N ratio objects will be kept.

ech_find_nabove_min_snr

int

2

Criteria for keeping echelle objects. They must either have a maximum S/N across all the orders greater than ech_find_max_snr, value or they must have S/N > ech_find_min_snr on >= ech_find_nabove_min_snr orders. If maxnumber is set (see above) then these criteria will be applied but only the maxnumber highest (median) S/N ratio objects will be kept.

find_extrap_npoly

int

3

Polynomial order used for trace extrapolation

find_fwhm

int, float

5.0

Indicates roughly the fwhm of objects in pixels for object finding

find_maxdev

int, float

2.0

Maximum deviation of pixels from polynomial fit to trace used to reject bad pixels in trace fitting.

find_min_max

list

It defines the minimum and maximum of your object in pixels in the spectral direction on the detector. It only used for object finding. This parameter is helpful if your object only has emission lines or at high redshift and the trace only shows in part of the detector.

find_negative

bool

Identify negative objects in object finding for spectra that are differenced. This is used to manually override the default behavior in PypeIt for object finding by setting this parameter to something other than None The default behavior is that PypeIt will search for negative object traces if background frames are present in the PypeIt file that are classified as “science” (i.e. via pypeit_setup -b, and setting bkg_id in the PypeIt file). If background frames are present that are classified as “sky”, then PypeIt will NOT search for negative object traces. If one wishes to explicitly override this default behavior, set this parameter to True to find negative objects or False to ignore them.

find_trim_edge

list

5, 5

Trim the slit by this number of pixels left/right before finding objects

maxnumber_sci

int

10

Maximum number of objects to extract in a science frame. Use None for no limit. This parameter can be useful in situations where systematics lead to spurious extra objects. Setting this parameter means they will be trimmed. For mulitslit maxnumber applies per slit, for echelle observations this applies per order. Note that objects on a slit/order impact the sky-modeling and so maxnumber should never be lower than the true number of detectable objects on your slit. For image differenced observations with positive and negative object traces, maxnumber applies to the number of positive (or negative) traces individually. In other words, if you had two positive objects and one negative object, then you would set maxnumber to be equal to two (not three). Note that if manually extracted apertures are explicitly requested, they do not count against this maxnumber. If more than maxnumber objects are detected, then highest S/N ratio objects will be the ones that are kept. For multislit observations the choice here depends on the slit length. For echelle observations with short slits we set the default to be 1

maxnumber_std

int

5

Maximum number of objects to extract in a standard star frame. Same functionality as maxnumber_sci documented above. For multislit observations the default here is 5, for echelle observations the default is 1

skip_final_global

bool

False

If True, do not update initial sky to get global sky using updated noise model. This should be True for quicklook to save time. This should also be True for near-IR reductions which perform difference imaging, since there we fit sky-residuals rather than the sky itself, so there is no noise model to update.

skip_second_find

bool

False

Only perform one round of object finding (mainly for quick_look)

skip_skysub

bool

False

If True, do not sky subtract when performing object finding. This should be set to True for example when running on data that is already sky-subtracted. Note that for near-IR difference imaging one still wants to remove sky-residuals via sky-subtraction, and so this is typically set to False

snr_thresh

int, float

10.0

S/N threshold for object finding in wavelength direction smashed image.

std_spec1d

str

A PypeIt spec1d file of a previously reduced standard star. The trace of the standard star spectrum is used as a crutch for tracing the object spectra, when a direct trace is not possible (i.e., faint sources). If provided, this overrides use of any standards included in your pypeit file; the standard exposures will still be reduced.

trace_npoly

int

5

Order of legendre polynomial fits to object traces.


SkySubPar Keywords

Class Instantiation: SkySubPar

Key

Type

Options

Default

Description

bspline_spacing

int, float

0.6

Break-point spacing for the bspline sky subtraction fits.

global_sky_std

bool

True

Global sky subtraction will be performed on standard stars. This should be turned off for example for near-IR reductions with narrow slits, since bright standards can fill the slit causing global sky-subtraction to fail. In these situations we go straight to local sky-subtraction since it is designed to deal with such situations

joint_fit

bool

False

Perform a simultaneous joint fit to sky regions using all available slits. Currently, this parameter is only used for IFU data reduction. Note that the current implementation does not account for variations in the instrument FWHM in different slits. This will be addressed by Issue #1660.

local_maskwidth

float

4.0

Initial width of the region in units of FWHM that will be used for local sky subtraction

mask_by_boxcar

bool

False

In global sky evaluation, mask the sky region around the object by the boxcar radius (set in ExtractionPar).

max_mask_frac

float

0.8

Maximum fraction of total pixels on a slit that can be masked by the input masks. If more than this threshold is masked the code will return zeros and throw a warning.

no_local_sky

bool

False

If True, turn off local sky model evaluation, but do fit object profile and perform optimal extraction

no_poly

bool

False

Turn off polynomial basis (Legendre) in global sky subtraction

sky_sigrej

float

3.0

Rejection parameter for local sky subtraction

user_regions

str, list

Provides a user-defined mask defining sky regions. By default, the sky regions are identified automatically. To specify sky regions for all slits, provide a comma separated list of percentages. For example, setting user_regions = :10,35:65,80: selects the first 10%, the inner 30%, and the final 20% of all slits as containing sky. Setting user_regions = user will attempt to load any SkyRegions files generated by the user via the pypeit_skysub_regions tool.


SlitMaskPar Keywords

Class Instantiation: SlitMaskPar

Key

Type

Options

Default

Description

assign_obj

bool

False

If SlitMask object was generated, assign RA,DEC,name to detected objects

bright_maskdef_id

int

maskdef_id (corresponding e.g., to dSlitId and Slit_Number in the DEIMOS/LRIS and MOSFIRE slitmask design, respectively) of a slit containing a bright object that will be used to compute the slitmask offset. This parameter is optional and is ignored if slitmask_offset is provided.

extract_missing_objs

bool

False

Force extraction of undetected objects at the location expected from the slitmask design.

missing_objs_boxcar_rad

int, float

1.0

Indicates the boxcar radius in arcsec for the force extraction of undetected objects.

missing_objs_fwhm

int, float

Indicates the FWHM in arcsec for the force extraction of undetected objects. PypeIt will try to determine the FWHM from the flux profile (by using missing_objs_fwhm as initial guess). If the FWHM cannot be determined, missing_objs_fwhm will be assumed. If you do not want PypeIt to try to determine the FWHM set the parameter use_user_fwhm in ExtractionPar to True. If missing_objs_fwhm is None (which is the default) PypeIt will use the median FWHM of all the detected objects.

obj_toler

int, float

1.0

If slitmask design information is provided, and slit matching is performed (use_maskdesign = True in EdgeTracePar), this parameter provides the desired tolerance (arcsec) to match sources to targeted objects

slitmask_offset

int, float

User-provided slitmask offset (pixels) from the position expected by the slitmask design. This is optional, and if set PypeIt will NOT compute the offset using snr_thrshd or bright_maskdef_id.

snr_thrshd

int, float

50.0

Objects detected above this S/N threshold will be used to compute the slitmask offset. This is the default behaviour for DEIMOS unless slitmask_offset, bright_maskdef_id or use_alignbox is set.

use_alignbox

bool

False

Use stars in alignment boxes to compute the slitmask offset. If this is set to True PypeIt will NOT compute the offset using snr_thrshd or bright_maskdef_id

use_dither_offset

bool

False

Use the dither offset recorded in the header of science frames as the value of the slitmask offset. This is currently only available for Keck MOSFIRE reduction and it is set as the default for this instrument. If set PypeIt will NOT compute the offset using snr_thrshd or bright_maskdef_id. However, it is ignored if slitmask_offset is provided.


FrameGroupPar Keywords

Class Instantiation: FrameGroupPar

Key

Type

Options

Default

Description

exprng

list

None, None

Used in identifying frames of this type. This sets the minimum and maximum allowed exposure times. There must be two items in the list. Use None to indicate no limit; i.e., to select exposures with any time greater than 30 sec, use exprng = [30, None].

frametype

str

align, arc, bias, dark, pinhole, pixelflat, illumflat, lampoffflats, scattlight, science, standard, trace, tilt, sky

science

Frame type. Options are: align, arc, bias, dark, pinhole, pixelflat, illumflat, lampoffflats, scattlight, science, standard, trace, tilt, sky

process

ProcessImagesPar

ProcessImagesPar Keywords

Low level parameters used for basic image processing

useframe

str

A calibrations file to use if it exists.


ProcessImagesPar Keywords

Class Instantiation: ProcessImagesPar

Key

Type

Options

Default

Description

apply_gain

bool

True

Convert the ADUs to electrons using the detector gain

clip

bool

True

Perform sigma clipping when combining. Only used with combine=mean

comb_sigrej

float

Sigma-clipping level for when clip=True; Use None for automatic limit (recommended).

combine

str

median, mean

mean

Method used to combine multiple frames. Options are: median, mean

dark_expscale

bool

False

If designated dark frames are used and have a different exposure time than the science frames, scale the counts by the by the ratio in the exposure times to adjust the dark counts for the difference in exposure time. WARNING: You should always take dark frames that have the same exposure time as your science frames, so use this option with care!

empirical_rn

bool

False

If True, use the standard deviation in the overscan region to measure an empirical readnoise to use in the noise model.

grow

int, float

1.5

Factor by which to expand regions with cosmic rays detected by the LA cosmics routine.

lamaxiter

int

1

Maximum number of iterations for LA cosmics routine.

mask_cr

bool

False

Identify CRs and mask them

n_lohi

list

0, 0

Number of pixels to reject at the lowest and highest ends of the distribution; i.e., n_lohi = low, high. Use None for no limit.

noise_floor

float

0.0

Impose a noise floor by adding the provided fraction of the bias- and dark-subtracted electron counts to the error budget. E.g., a value of 0.01 means that the S/N of the counts in the image will never be greater than 100.

objlim

int, float

3.0

Object detection limit in LA cosmics routine

orient

bool

True

Orient the raw image into the PypeIt frame

overscan_method

str

chebyshev, polynomial, savgol, median, odd_even

savgol

Method used to fit the overscan. Options are: chebyshev, polynomial, savgol, median, odd_even Note: Method “polynomial” is identical to “chebyshev”; the former is deprecated and will be removed.

overscan_par

int, list

5, 65

Parameters for the overscan subtraction. For ‘chebyshev’ or ‘polynomial’, set overcan_par = order; for ‘savgol’, set overscan_par = order, window size ; for ‘median’, set overscan_par = None or omit the keyword.

rmcompact

bool

True

Remove compact detections in LA cosmics routine

satpix

str

reject, force, nothing

reject

Handling of saturated pixels. Options are: reject, force, nothing

scattlight

ScatteredLightPar

ScatteredLightPar Keywords

Scattered light subtraction parameters.

shot_noise

bool

True

Use the bias- and dark-subtracted image to calculate and include electron count shot noise in the image processing error budget

sigclip

int, float

4.5

Sigma level for rejection in LA cosmics routine

sigfrac

int, float

0.3

Fraction for the lower clipping threshold in LA cosmics routine.

spat_flexure_correct

bool

False

Correct slits, illumination flat, etc. for flexure

subtract_continuum

bool

False

Subtract off the continuum level from an image. This parameter should only be set to True to combine arcs with multiple different lamps. For all other cases, this parameter should probably be False.

subtract_scattlight

bool

False

Subtract off the scattered light from an image. This parameter should only be set to True for spectrographs that have dedicated methods to subtract scattered light. For all other cases, this parameter should be False.

trim

bool

True

Trim the image to the detector supplied region

use_biasimage

bool

True

Use a bias image. If True, one or more must be supplied in the PypeIt file.

use_darkimage

bool

False

Subtract off a dark image. If True, one or more darks must be provided.

use_illumflat

bool

True

Use the illumination flat to correct for the illumination profile of each slit.

use_overscan

bool

True

Subtract off the overscan. Detector must have one or code will crash.

use_pattern

bool

False

Subtract off a detector pattern. This pattern is assumed to be sinusoidal along one direction, with a frequency that is constant across the detector.

use_pixelflat

bool

True

Use the pixel flat to make pixel-level corrections. A pixelflat image must be provied.

use_specillum

bool

False

Use the relative spectral illumination profiles to correct the spectral illumination profile of each slit. This is primarily used for slicer IFUs. To use this, you must set slit_illum_relative=True in the flatfield parameter set!


ScatteredLightPar Keywords

Class Instantiation: ScatteredLightPar

Key

Type

Options

Default

Description

finecorr_mask

int, list

A list containing the inter-slit regions that the user wishes to mask during the fine correction to the scattered light. Each integer corresponds to an inter-slit region. For example, “0” corresponds to all pixels left of the leftmost slit, while a value of “1” corresponds to all pixels between the first and second slit (counting from the left). It should be either a single integer value, or a list of integer values. The default (None) means that no inter-slit regions will be masked.

finecorr_method

str

median, poly

If None, a fine correction to the scattered light will not be performed. Otherwise, the allowed methods include: median, poly. ‘median’ will subtract a constant value from an entire CCD row, based on a median of the pixels that are not on slits (see also, ‘finecorr_pad’). ‘poly’ will fit a polynomial to the scattered light in each row, based on the pixels that are not on slits (see also, ‘finecorr_pad’).

finecorr_order

int

2

Polynomial order to use for the fine correction to the scattered light subtraction. It should be a low value.

finecorr_pad

int

4

Number of unbinned pixels to extend the slit edges by when masking the slits for the fine correction to the scattered light.

method

str

model, frame, archive

model

Method used to fit the overscan. Options are: model, frame, archive. ‘model’ will the scattered light model parameters derived from a user-specified frame during their reduction (note, you will need to make sure that you set appropriate scattlight frames in your .pypeit file for this option). ‘frame’ will use each individual frame to determine the scattered light that affects this frame. ‘archive’ will use an archival model parameter solution for the scattered light (note that this option is not currently available for all spectrographs).


SensFuncPar Keywords

Class Instantiation: SensFuncPar

Key

Type

Options

Default

Description

IR

TelluricPar

TelluricPar Keywords

Parameters for the IR sensfunc algorithm

UVIS

SensfuncUVISPar

SensfuncUVISPar Keywords

Parameters for the UVIS sensfunc algorithm

algorithm

str

UVIS, IR

UVIS

Specify the algorithm for computing the sensitivity function. The options are: (1) UVIS = Should be used for data with \(\lambda < 7000\) A. No detailed model of telluric absorption but corrects for atmospheric extinction. (2) IR = Should be used for data with \(\lambda > 7000\) A. Peforms joint fit for sensitivity function and telluric absorption using HITRAN models.

extrap_blu

float

0.1

Fraction of minimum wavelength coverage to grow the wavelength coverage of the sensitivitity function in the blue direction (i.e., if the standard star spectrum cuts off at wave_min) the sensfunc will be extrapolated to cover down to (1.0 - extrap_blu) * wave_min

extrap_red

float

0.1

Fraction of maximum wavelength coverage to grow the wavelength coverage of the sensitivitity function in the red direction (i.e., if the standard star spectrumcuts off at wave_max) the sensfunc will be extrapolated to cover up to (1.0 + extrap_red) * wave_max

flatfile

str

Flat field file to be used if the sensitivity function model will utilize the blaze function computed from a flat field file in the Calibrations directory, e.g.Calibrations/Flat_A_0_DET01.fits

hydrogen_mask_wid

float

10.0

Mask width from line center for hydrogen recombination lines in Angstroms (total mask width is 2x this value).

mask_helium_lines

bool

False

Mask certain HeII recombination lines prominent in O-type stars in the sensitivity function fit A region equal to 0.5 * hydrogen_mask_wid on either side of the line center is masked.

mask_hydrogen_lines

bool

True

Mask hydrogen Balmer, Paschen, Brackett, and Pfund recombination lines in the sensitivity function fit. A region equal to hydrogen_mask_wid on either side of the line center is masked.

multi_spec_det

list

List of detectors (identified by their string name, like DET01) to splice together for multi-detector instruments (e.g. DEIMOS). It is assumed that there is no overlap in wavelength across detectors (might be ok if there is). If entered as a list of integers, they should be converted to the detector name. Cannot be used with detector mosaics.

polyorder

int, list

5

Polynomial order for sensitivity function fitting

samp_fact

float

1.5

Sampling factor to make the wavelength grid for sensitivity function finer or coarser. samp_fact > 1.0 oversamples (finer), samp_fact < 1.0 undersamples (coarser).

star_dec

float

DEC of the standard star. This will override values in the header (i.e., if they are wrong or absent)

star_mag

float

Magnitude of the standard star (for near-IR mainly)

star_ra

float

RA of the standard star. This will override values in the header (i.e., if they are wrong or absent)

star_type

str

Spectral type of the standard star (for near-IR mainly)


SensfuncUVISPar Keywords

Class Instantiation: SensfuncUVISPar

Key

Type

Options

Default

Description

extinct_correct

bool

True

If extinct_correct=True the code will use an atmospheric extinction model to extinction correct the data below 10000A. Note that this correction makes no sense if one is telluric correcting and this shold be set to False

extinct_file

str

closest

If extinct_file='closest' the code will select the PypeIt-included extinction file for the closest observatory (within 5 deg, geographic coordinates) to the telescope identified in std_file (see Extinction Correction for the list of currently included files). If constructing a sesitivity function for a telescope not within 5 deg of a listed observatory, this parameter may be set to the name of one of the listed extinction files. Alternatively, a custom extinction file may be installed in the PypeIt cache using the pypeit_install_extinctfile script; this parameter may then be set to the name of the custom extinction file.

nresln

int, float

20

Parameter governing the spacing of the bspline breakpoints in terms of number of resolution elements.

polycorrect

bool

True

Whether you want to correct the sensfunc with polynomial in the telluric and recombination line regions

polyfunc

bool

False

Whether you want to use the polynomial fit as your final SENSFUNC

resolution

int, float

3000.0

Expected resolution of the standard star spectrum. This should be measured from the data.

sensfunc

str

FITS file that contains or will contain the sensitivity function.

std_file

str

Standard star file to generate sensfunc

std_obj_id

str, int

Specifies object in spec1d file to use as standard. The brightest object found is used otherwise.

telluric

bool

False

If telluric=True the code creates a synthetic standard star spectrum using the Kurucz models, the sens func is created setting nresln=1.5 it contains the correction for telluric lines.

telluric_correct

bool

False

If telluric_correct=True the code will grab the sens_dict[‘telluric’] tag from the sensfunc dictionary and apply it to the data.

trans_thresh

float

0.9

Parameter for selecting telluric regions which are masked. Locations below this transmission value are masked. If you have significant telluric absorption you should be using telluric.sensnfunc_telluric


TelluricPar Keywords

Class Instantiation: TelluricPar

Key

Type

Options

Default

Description

bal_wv_min_max

list, ndarray

Min/max wavelength of broad absorption features. If there are several BAL features, the format for this mask is [wave_min_bal1, wave_max_bal1,wave_min_bal2, wave_max_bal2,…]. These masked pixels will be ignored during the fitting.

bounds_norm

tuple

(0.1, 3.0)

Normalization bounds for scaling the initial object model.

delta_coeff_bounds

tuple

(-20.0, 20.0)

Parameters setting the polynomial coefficient bounds for sensfunc optimization.

delta_redshift

float

0.1

Range within the redshift can be varied for telluric fitting, i.e. the code performs a bounded optimization within the redshift +- delta_redshift

disp

bool

False

Argument for scipy.optimize.differential_evolution which will display status messages to the screen indicating the status of the optimization. See documentation for telluric.Telluric for a description of the output and how to know if things are working well.

fit_wv_min_max

list

Pixels within this mask will be used during the fitting. The format is the same with bal_wv_min_max, but this mask is good pixel masks.

func

str

legendre

Polynomial model function

lower

int, float

3.0

Lower rejection threshold in units of sigma_corr*sigma, where sigma is the formal noise of the spectrum, and sigma_corr is an empirically determined correction to the formal error. The distribution of input chi (defined by chi = (data - model)/sigma) values is analyzed, and a correction factor to the formal error sigma_corr is returned which is multiplied into the formal errors. In this way, a rejection threshold of i.e. 3-sigma, will always correspond to roughly the same percentile. This renormalization is performed with coadd1d.renormalize_errors function, and guarantees that rejection is not too agressive in cases where the empirical errors determined from the chi-distribution differ significantly from the formal noise which is used to determine chi.

mask_lyman_a

bool

True

Mask the blueward of Lyman-alpha line during the fitting?

maxiter

int

2

Maximum number of iterations for the telluric + object model fitting. The code performs multiple iterations rejecting outliers at each step. The fit is then performed anew to the remaining good pixels. For this reason if you run with the disp=True option, you will see that the f(x) loss function gets progressively better during the iterations.

minmax_coeff_bounds

tuple

(-5.0, 5.0)

Parameters setting the polynomial coefficient bounds for sensfunc optimization. Bounds are currently determined as follows. We compute an initial fit to the sensfunc in the init_sensfunc_model() function. That deterines a set of coefficients. The bounds are then determined according to: [(np.fmin(np.abs(this_coeff)*obj_params[‘delta_coeff_bounds’][0], obj_params[‘minmax_coeff_bounds’][0]), np.fmax(np.abs(this_coeff)*obj_params[‘delta_coeff_bounds’][1], obj_params[‘minmax_coeff_bounds’][1]))]

model

str

exp

Types of polynomial model. Options are poly, square, exp corresponding to normal polynomial, squared polynomial, or exponentiated polynomial

npca

int

8

Number of pca for the objmodel=qso qso PCA fit

objmodel

str

The object model to be used for telluric fitting. Currently the options are: qso, star, and poly

only_orders

int, list, ndarray

Order number, or list of order numbers if you only want to fit specific orders

pca_file

str

qso_pca_1200_3100.fits

Fits file containing quasar PCA model. Needed for objmodel=qso. NOTE: This parameter no longer includes the full pathname to the Telluric Model file, but is just the filename of the model itself.

pca_lower

int, float

1220.0

Minimum wavelength for the qso pca model

pca_upper

int, float

3100.0

Maximum wavelength for the qso pca model

pix_shift_bounds

tuple

(-5.0, 5.0)

Bounds for the pixel shift optimization in telluric model fit in units of pixels. The atmosphere will be allowed to shift within this range during the fit.

polish

bool

True

If True then differential evolution will perform an additional optimizatino at the end to polish the best fit at the end, which can improve the optimization slightly. See scipy.optimize.differential_evolution for details.

polyorder

int

3

Order of the polynomial model fit

popsize

int

30

A multiplier for setting the total population size for the differential evolution optimization. See scipy.optimize.differential_evolution for details.

recombination

int, float

0.7

The recombination constant for the differential evolution optimization. This should be in the range [0, 1]. See scipy.optimize.differential_evolution for details.

redshift

int, float

0.0

The redshift for the object model. This is currently only used by objmodel=qso

resln_frac_bounds

tuple

(0.6, 1.4)

Bounds for the resolution fit optimization which is part of the telluric model. This range is in units of the resln_guess, so the (0.6, 1.4) would bound the spectral resolution fit to be within the range bounds_resln = (0.6*resln_guess, 1.4*resln_guess)

resln_guess

int, float

A guess for the resolution of your spectrum expressed as lambda/dlambda. The resolution is fit explicitly as part of the telluric model fitting, but this guess helps determine the bounds for the optimization (see next). If not provided, the wavelength sampling of your spectrum will be used and the resolution calculated using a typical sampling of 3 spectral pixels per resolution element.

seed

int

777

An initial seed for the differential evolution optimization, which is a random process. The default is a seed = 777 which will be used to generate a unique seed for every order. A specific seed is used because otherwise the random number generator will use the time for the seed, and the results will not be reproducible.

sn_clip

int, float

30.0

This adds an error floor to the ivar, preventing too much rejection at high-S/N (i.e., standard stars, bright objects) using the function utils.clip_ivar. A small erorr is added to the input ivar so that the output ivar_out will never give S/N greater than sn_clip. This prevents overly aggressive rejection in high S/N ratio spectra which neverthless differ at a level greater than the formal S/N due to the fact that our telluric models are only good to about 3%.

star_dec

float

Object declination in decimal deg

star_mag

float, int

AB magnitude in V band

star_ra

float

Object right-ascension in decimal deg

star_type

str

stellar type

sticky

bool

True

Sticky parameter for the utils.djs_reject algorithm for iterative model fit rejection. If set to True then points rejected from a previous iteration are kept rejected, in other words the bad pixel mask is the OR of all previous iterations and rejected pixels accumulate. If set to False, the bad pixel mask is the mask from the previous iteration, and if the model fit changes between iterations, points can alternate from being rejected to not rejected. At present this code only performs optimizations with differential evolution and experience shows that sticky needs to be True in order for these to converge. This is because the outliers can be so large that they dominate the loss function, and one never iteratively converges to a good model fit. In other words, the deformations in the model between iterations with sticky=False are too small to approach a reasonable fit.

telgridfile

str

File containing the telluric grid for the observatory in question. These grids are generated from HITRAN models for each observatory using nominal site parameters. They must be downloaded from the GoogleDrive and installed in your PypeIt installation via the pypeit_install_telluric script. NOTE: This parameter no longer includes the full pathname to the Telluric Grid file, but is just the filename of the grid itself.

tell_norm_thresh

int, float

0.9

Threshold of telluric absorption region

tell_npca

int

5

Number of telluric PCA components used. Can be set to any number from 1 to 10.

teltype

str

pca

Method used to evaluate telluric models, either pca or grid. The grid option uses a fixed grid of pre-computed HITRAN+LBLRTM atmospheric transmission models for each observatory, whereas the pca option uses principal components of a larger model grid to compute an accurate pseudo-telluric model with a much lighter telgridfile.

tol

float

0.001

Relative tolerance for converage of the differential evolution optimization. See scipy.optimize.differential_evolution for details.

upper

int, float

3.0

Upper rejection threshold in units of sigma_corr*sigma, where sigma is the formal noise of the spectrum, and sigma_corr is an empirically determined correction to the formal error. See above for description.

Instrument-Specific Default Configuration

The following provides the changes to the global default parameters provided above for each instrument. That is, if one were to include these in the PypeIt file, you would be reproducing the effect of the default_pypeit_par method specific to each derived Spectrograph class.

BOK BC (bok_bc)

Alterations to the default parameters are:

[rdx]
    spectrograph = bok_bc
[calibrations]
    [[biasframe]]
        exprng = None, 0.001,
        [[[process]]]
            combine = median
            use_biasimage = False
            use_overscan = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 999999, None,
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        exprng = None, 120,
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            combine = median
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        exprng = 999999, None,
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_illumflat = False
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            noise_floor = 0.01
            use_illumflat = False
    [[standardframe]]
        exprng = None, 120,
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            noise_floor = 0.01
            use_illumflat = False
    [[wavelengths]]
        lamps = NeI, ArI, ArII, HeI,
        fwhm = 2.6
        rms_thresh_frac_fwhm = 0.19
    [[slitedges]]
        edge_thresh = 50.0
        sync_predict = nearest
[scienceframe]
    exprng = 90, None,
    [[process]]
        mask_cr = True
        sigclip = 5.0
        objlim = 2.0
        use_biasimage = False
        use_overscan = False
        noise_floor = 0.01
        use_illumflat = False
[reduce]
    [[findobj]]
        snr_thresh = 5.0
    [[skysub]]
        sky_sigrej = 5.0
        global_sky_std = False
        no_poly = True
[sensfunc]
    polyorder = 7

GEMINI-S FLAMINGOS (gemini_flamingos1)

Alterations to the default parameters are:

[rdx]
    spectrograph = gemini_flamingos1
[calibrations]
    [[biasframe]]
        [[[process]]]
            combine = median
            use_biasimage = False
            use_overscan = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 20, None,
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        exprng = 1, 50,
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_illumflat = False
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            noise_floor = 0.01
            use_illumflat = False
    [[standardframe]]
        exprng = None, 60,
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            noise_floor = 0.01
            use_illumflat = False
    [[wavelengths]]
        method = full_template
        lamps = ArI, ArII, ThAr, NeI,
        sigdetect = 3
        fwhm = 20
        reid_arxiv = magellan_fire_long.fits
        rms_thresh_frac_fwhm = 0.05
        match_toler = 5.0
    [[slitedges]]
        trace_thresh = 5.0
        sync_predict = nearest
    [[tilts]]
        tracethresh = 5
[scienceframe]
    exprng = 20, None,
    [[process]]
        mask_cr = True
        use_biasimage = False
        use_overscan = False
        noise_floor = 0.01
        use_illumflat = False
[reduce]
    [[findobj]]
        snr_thresh = 5.0
        find_trim_edge = 50, 50,

GEMINI-S FLAMINGOS (gemini_flamingos2)

Alterations to the default parameters are:

[rdx]
    spectrograph = gemini_flamingos2
[calibrations]
    [[biasframe]]
        [[[process]]]
            combine = median
            use_biasimage = False
            use_overscan = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 20, None,
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        exprng = 50, None,
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        exprng = 50, None,
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_illumflat = False
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            noise_floor = 0.01
            use_illumflat = False
    [[standardframe]]
        exprng = None, 30,
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            noise_floor = 0.01
            use_illumflat = False
    [[wavelengths]]
        lamps = OH_NIRES,
        fwhm = 5.0
        rms_thresh_frac_fwhm = 0.1
        match_toler = 5.0
    [[slitedges]]
        edge_thresh = 200.0
        fit_min_spec_length = 0.4
        trace_thresh = 10.0
        sync_predict = nearest
    [[tilts]]
        tracethresh = 5
        spat_order = 4
[scienceframe]
    exprng = 20, None,
    [[process]]
        mask_cr = True
        use_biasimage = False
        use_overscan = False
        noise_floor = 0.01
        use_illumflat = False
[reduce]
    [[findobj]]
        snr_thresh = 5.0
        find_trim_edge = 10, 10,
    [[skysub]]
        sky_sigrej = 5.0
[sensfunc]
    algorithm = IR
    polyorder = 8
    [[IR]]
        telgridfile = TellPCA_3000_26000_R10000.fits

GEMINI-N GMOS-N (gemini_gmos_north_e2v)

Alterations to the default parameters are:

[rdx]
    spectrograph = gemini_gmos_north_e2v
    detnum = (1, 2, 3),
[calibrations]
    [[biasframe]]
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        [[[process]]]
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            combine = median
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[standardframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[wavelengths]]
        method = full_template
        lamps = CuI, ArI, ArII,
        fwhm = 5.0
        rms_thresh_frac_fwhm = 0.08
        nsnippet = 1
    [[slitedges]]
        edge_thresh = 100.0
        follow_span = 80
        fit_order = 3
    [[tilts]]
        tracethresh = 10.0
[scienceframe]
    [[process]]
        mask_cr = True
        noise_floor = 0.01
[flexure]
    spec_method = boxcar

GEMINI-N GMOS-N (gemini_gmos_north_ham)

Alterations to the default parameters are:

[rdx]
    spectrograph = gemini_gmos_north_ham
    detnum = (1, 2, 3),
[calibrations]
    [[biasframe]]
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        [[[process]]]
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            combine = median
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[standardframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[wavelengths]]
        method = full_template
        lamps = CuI, ArI, ArII,
        fwhm = 5.0
        rms_thresh_frac_fwhm = 0.08
        nsnippet = 1
    [[slitedges]]
        edge_thresh = 100.0
        follow_span = 80
        fit_order = 3
    [[tilts]]
        tracethresh = 10.0
[scienceframe]
    [[process]]
        mask_cr = True
        noise_floor = 0.01
[flexure]
    spec_method = boxcar

GEMINI-N GMOS-N (gemini_gmos_north_ham_ns)

Alterations to the default parameters are:

[rdx]
    spectrograph = gemini_gmos_north_ham_ns
    detnum = (1, 2, 3),
[calibrations]
    [[biasframe]]
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        [[[process]]]
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            combine = median
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[standardframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[wavelengths]]
        method = full_template
        lamps = CuI, ArI, ArII,
        fwhm = 5.0
        rms_thresh_frac_fwhm = 0.08
        nsnippet = 1
    [[slitedges]]
        edge_thresh = 100.0
        follow_span = 80
        fit_order = 3
    [[tilts]]
        tracethresh = 10.0
[scienceframe]
    [[process]]
        mask_cr = True
        noise_floor = 0.01
[flexure]
    spec_method = boxcar

GEMINI-S GMOS-S (gemini_gmos_south_ham)

Alterations to the default parameters are:

[rdx]
    spectrograph = gemini_gmos_south_ham
    detnum = (1, 2, 3),
[calibrations]
    [[biasframe]]
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        [[[process]]]
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            combine = median
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[standardframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[wavelengths]]
        method = full_template
        lamps = CuI, ArI, ArII,
        fwhm = 5.0
        rms_thresh_frac_fwhm = 0.08
        nsnippet = 1
    [[slitedges]]
        edge_thresh = 100.0
        follow_span = 80
        fit_order = 3
        bound_detector = True
    [[tilts]]
        tracethresh = 10.0
[scienceframe]
    [[process]]
        mask_cr = True
        noise_floor = 0.01
[flexure]
    spec_method = boxcar
[sensfunc]
    algorithm = IR
    [[IR]]
        telgridfile = TellPCA_3000_26000_R10000.fits

GEMINI-N GNIRS (gemini_gnirs_echelle)

Alterations to the default parameters are:

[rdx]
    spectrograph = gemini_gnirs_echelle
[calibrations]
    [[biasframe]]
        [[[process]]]
            combine = median
            use_biasimage = False
            use_overscan = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        exprng = None, 30,
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_illumflat = False
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        exprng = None, 30,
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            noise_floor = 0.01
            use_illumflat = False
    [[standardframe]]
        exprng = None, 30,
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            noise_floor = 0.01
            use_illumflat = False
    [[flatfield]]
        tweak_slits_thresh = 0.9
    [[tilts]]
        spat_order = 1
[scienceframe]
    exprng = 30, None,
    [[process]]
        mask_cr = True
        use_biasimage = False
        use_overscan = False
        noise_floor = 0.01
        use_illumflat = False
[reduce]
    [[findobj]]
        find_trim_edge = 2, 2,
        maxnumber_sci = 2
        maxnumber_std = 1
    [[skysub]]
        bspline_spacing = 0.8
        global_sky_std = False
        no_poly = True
    [[extraction]]
        model_full_slit = True
[sensfunc]
    algorithm = IR
    polyorder = 6
    [[IR]]
        telgridfile = TellPCA_3000_26000_R10000.fits

GEMINI-N GNIRS (gemini_gnirs_ifu)

Alterations to the default parameters are:

[rdx]
    spectrograph = gemini_gnirs_ifu
[calibrations]
    [[biasframe]]
        [[[process]]]
            combine = median
            use_biasimage = False
            use_overscan = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        exprng = None, 30,
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_illumflat = False
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        exprng = None, 30,
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            noise_floor = 0.01
            use_illumflat = False
    [[standardframe]]
        exprng = None, 30,
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            noise_floor = 0.01
            use_illumflat = False
    [[flatfield]]
        tweak_slits_thresh = 0.0
        tweak_slits_maxfrac = 0.0
        slit_trim = 2
        slit_illum_finecorr = False
    [[slitedges]]
        pad = 2
    [[tilts]]
        spat_order = 1
        spec_order = 1
[scienceframe]
    exprng = 30, None,
    [[process]]
        mask_cr = True
        sigclip = 4.0
        objlim = 1.5
        use_biasimage = False
        use_overscan = False
        noise_floor = 0.01
        use_illumflat = False
[reduce]
    [[findobj]]
        find_trim_edge = 2, 2,
        maxnumber_sci = 2
        maxnumber_std = 1
    [[skysub]]
        global_sky_std = False
        no_poly = True
    [[extraction]]
        model_full_slit = True
        skip_extraction = True
    [[cube]]
        grating_corr = False
[flexure]
    spec_maxshift = 0
[sensfunc]
    algorithm = IR
    polyorder = 6
    [[UVIS]]
        extinct_correct = False
    [[IR]]
        telgridfile = TellPCA_3000_26000_R10000.fits

GTC OSIRIS (gtc_maat)

Alterations to the default parameters are:

[rdx]
    spectrograph = gtc_maat
[calibrations]
    [[biasframe]]
        exprng = None, 0.001,
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 999999, None,
        [[[process]]]
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            clip = False
            use_pixelflat = False
            use_illumflat = False
            subtract_continuum = True
    [[tiltframe]]
        [[[process]]]
            clip = False
            use_pixelflat = False
            use_illumflat = False
            subtract_continuum = True
    [[pixelflatframe]]
        [[[process]]]
            combine = median
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        exprng = 999999, None,
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[standardframe]]
        exprng = None, 300,
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[flatfield]]
        slit_illum_finecorr = False
    [[wavelengths]]
        method = full_template
        lamps = XeI, HgI, NeI, ArI,
        reid_cont_sub = False
    [[slitedges]]
        sync_predict = nearest
        bound_detector = True
    [[tilts]]
        spat_order = 1
        spec_order = 1
[scienceframe]
    exprng = 90, None,
    [[process]]
        mask_cr = True
        sigclip = 4.0
        objlim = 1.5
        use_biasimage = False
        noise_floor = 0.01
        use_illumflat = False
[reduce]
    [[findobj]]
        maxnumber_std = 1
        skip_final_global = True
        skip_skysub = True
    [[skysub]]
        no_poly = True
    [[extraction]]
        skip_extraction = True
[flexure]
    spec_maxshift = 3
[sensfunc]
    [[UVIS]]
        extinct_correct = False

GTC OSIRIS (gtc_osiris)

Alterations to the default parameters are:

[rdx]
    spectrograph = gtc_osiris
[calibrations]
    [[biasframe]]
        exprng = None, 0.001,
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 999999, None,
        [[[process]]]
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            clip = False
            use_pixelflat = False
            use_illumflat = False
            subtract_continuum = True
    [[tiltframe]]
        [[[process]]]
            clip = False
            use_pixelflat = False
            use_illumflat = False
            subtract_continuum = True
    [[pixelflatframe]]
        [[[process]]]
            combine = median
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        exprng = 999999, None,
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[standardframe]]
        exprng = None, 180,
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[wavelengths]]
        method = full_template
        lamps = XeI, HgI, NeI, ArI,
        reid_cont_sub = False
    [[slitedges]]
        sync_predict = nearest
        bound_detector = True
    [[tilts]]
        spat_order = 5
        spec_order = 5
[scienceframe]
    exprng = 90, None,
    [[process]]
        mask_cr = True
        noise_floor = 0.01
[reduce]
    [[findobj]]
        maxnumber_std = 1
    [[skysub]]
        no_poly = True

GTC OSIRIS (gtc_osiris_plus)

Alterations to the default parameters are:

[rdx]
    spectrograph = gtc_osiris_plus
[calibrations]
    [[biasframe]]
        exprng = None, 0.001,
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 999999, None,
        [[[process]]]
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            clip = False
            use_pixelflat = False
            use_illumflat = False
            subtract_continuum = True
    [[tiltframe]]
        [[[process]]]
            clip = False
            use_pixelflat = False
            use_illumflat = False
            subtract_continuum = True
    [[pixelflatframe]]
        [[[process]]]
            combine = median
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        exprng = 999999, None,
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[standardframe]]
        exprng = None, 300,
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[wavelengths]]
        method = full_template
        lamps = XeI, HgI, NeI, ArI,
        reid_cont_sub = False
    [[slitedges]]
        sync_predict = nearest
        bound_detector = True
    [[tilts]]
        spat_order = 5
        spec_order = 5
[scienceframe]
    exprng = 90, None,
    [[process]]
        mask_cr = True
        noise_floor = 0.01
[reduce]
    [[findobj]]
        maxnumber_std = 1
    [[skysub]]
        no_poly = True

JWST NIRCAM (jwst_nircam)

Alterations to the default parameters are:

[rdx]
    spectrograph = jwst_nircam
[calibrations]
    [[biasframe]]
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        [[[process]]]
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[standardframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[wavelengths]]
        refframe = observed
[scienceframe]
    [[process]]
        sigclip = 5.0
        objlim = 2.0
        noise_floor = 0.01
[reduce]
    trim_edge = 0, 0,
    [[findobj]]
        find_trim_edge = 0, 0,
        maxnumber_sci = 2
        find_fwhm = 2.0
    [[skysub]]
        bspline_spacing = 1.2
        sky_sigrej = 4.0
        max_mask_frac = 0.95
    [[extraction]]
        boxcar_radius = 0.25
        sn_gauss = 6.0
        model_full_slit = True
        use_2dmodel_mask = False

JWST NIRSPEC (jwst_nirspec)

Alterations to the default parameters are:

[rdx]
    spectrograph = jwst_nirspec
[calibrations]
    [[biasframe]]
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        [[[process]]]
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[standardframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[wavelengths]]
        refframe = observed
[scienceframe]
    [[process]]
        sigclip = 5.0
        objlim = 2.0
        noise_floor = 0.01
[reduce]
    trim_edge = 0, 0,
    [[findobj]]
        find_trim_edge = 0, 0,
        maxnumber_sci = 2
        find_fwhm = 2.0
    [[skysub]]
        bspline_spacing = 5.0
        sky_sigrej = 4.0
        mask_by_boxcar = True
        max_mask_frac = 0.95
    [[extraction]]
        boxcar_radius = 0.2
        sn_gauss = 5.0
        model_full_slit = True
        use_2dmodel_mask = False

KECK DEIMOS (keck_deimos)

Alterations to the default parameters are:

[rdx]
    spectrograph = keck_deimos
    detnum = (1, 5), (2, 6), (3, 7), (4, 8),
[calibrations]
    [[biasframe]]
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            clip = False
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            clip = False
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            combine = median
            satpix = nothing
            comb_sigrej = 10.0
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        [[[process]]]
            use_biasimage = False
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            noise_floor = 0.01
    [[standardframe]]
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            noise_floor = 0.01
    [[wavelengths]]
        lamps = ArI, NeI, KrI, XeI,
        match_toler = 2.5
        n_first = 3
    [[slitedges]]
        edge_thresh = 50.0
        follow_span = 1000
        fit_order = 3
        minimum_slit_length_sci = 4.0
        minimum_slit_gap = 0.25
    [[tilts]]
        tracethresh = 10
[scienceframe]
    [[process]]
        mask_cr = True
        sigclip = 4.0
        objlim = 1.5
        use_biasimage = False
        noise_floor = 0.01
[flexure]
    spec_method = boxcar
[sensfunc]
    [[IR]]
        telgridfile = TellPCA_3000_26000_R15000.fits

KECK ESI (keck_esi)

Alterations to the default parameters are:

[rdx]
    spectrograph = keck_esi
[calibrations]
    [[biasframe]]
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 1, None,
        [[[process]]]
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        exprng = 300, None,
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
            subtract_scattlight = True
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
            subtract_scattlight = True
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[standardframe]]
        exprng = None, 60,
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[wavelengths]]
        method = reidentify
        echelle = True
        ech_sigrej = 3.0
        lamps = CuI, ArI, NeI, HgI, XeI, ArII,
        fwhm = 2.9
        reid_arxiv = keck_esi_ECH.fits
        cc_thresh = 0.5
        cc_local_thresh = 0.5
        rms_thresh_frac_fwhm = 0.103
    [[slitedges]]
        edge_thresh = 5.0
        det_min_spec_length = 0.2
        max_shift_adj = 3.0
        fit_min_spec_length = 0.4
        left_right_pca = True
        pca_order = 3
        pca_sigrej = 1.5
        add_missed_orders = True
    [[tilts]]
        tracethresh = 10.0
[scienceframe]
    exprng = 60, None,
    [[process]]
        satpix = nothing
        mask_cr = True
        sigclip = 20.0
        noise_floor = 0.01
        subtract_scattlight = True
[reduce]
    [[findobj]]
        find_trim_edge = 4, 4,
        maxnumber_sci = 2
        maxnumber_std = 1
    [[extraction]]
        model_full_slit = True

KECK HIRES (keck_hires)

Alterations to the default parameters are:

[rdx]
    spectrograph = keck_hires
    detnum = (1, 2, 3),
[calibrations]
    [[biasframe]]
        [[[process]]]
            overscan_method = median
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        [[[process]]]
            overscan_method = median
            mask_cr = True
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            overscan_method = median
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            overscan_method = median
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            overscan_method = median
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        [[[process]]]
            overscan_method = median
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[alignframe]]
        [[[process]]]
            overscan_method = median
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            overscan_method = median
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            overscan_method = median
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            overscan_method = median
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            overscan_method = median
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            overscan_method = median
            mask_cr = True
            use_biasimage = False
            noise_floor = 0.01
            use_pixelflat = False
            use_illumflat = False
    [[standardframe]]
        [[[process]]]
            overscan_method = median
            mask_cr = True
            use_biasimage = False
            noise_floor = 0.01
            use_pixelflat = False
            use_illumflat = False
    [[flatfield]]
        tweak_slits_thresh = 0.9
    [[wavelengths]]
        method = echelle
        echelle = True
        ech_nspec_coeff = 5
        ech_norder_coeff = 3
        lamps = ThAr,
        bad_orders_maxfrac = 0.5
        reid_cont_sub = False
        cc_shift_range = (-80.0, 80.0)
        cc_thresh = 0.6
        cc_local_thresh = 0.25
        rms_thresh_frac_fwhm = 0.1
        match_toler = 1.5
        n_first = 3
        ech_separate_2d = True
    [[slitedges]]
        edge_thresh = 8.0
        max_shift_adj = 0.5
        fit_order = 8
        left_right_pca = True
        trace_thresh = 10.0
        max_nudge = 0.0
        dlength_range = 0.25
        length_range = 0.3
        add_missed_orders = True
        overlap = True
    [[tilts]]
        tracethresh = 15
        spec_order = 5
[scienceframe]
    [[process]]
        overscan_method = median
        mask_cr = True
        use_biasimage = False
        noise_floor = 0.01
        use_pixelflat = False
        use_illumflat = False
[reduce]
    [[findobj]]
        find_trim_edge = 3, 3,
    [[skysub]]
        global_sky_std = False
    [[extraction]]
        model_full_slit = True
[coadd1d]
    wave_method = log10
[sensfunc]
    algorithm = IR
    [[IR]]
        telgridfile = TellPCA_3000_10500_R120000.fits
        pix_shift_bounds = (-40.0, 40.0)
[telluric]
    resln_frac_bounds = (0.25, 1.25)
    pix_shift_bounds = (-40.0, 40.0)

KECK KCRM (keck_kcrm)

Alterations to the default parameters are:

[rdx]
    spectrograph = keck_kcrm
[calibrations]
    [[biasframe]]
        exprng = None, 0.001,
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 0.01, None,
        [[[process]]]
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            combine = median
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[alignment]]
        locations = 0.1, 0.3, 0.5, 0.7, 0.9,
    [[traceframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[standardframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[flatfield]]
        spec_samp_coarse = 20.0
        tweak_slits_thresh = 0.0
        tweak_slits_maxfrac = 0.0
        slit_illum_relative = True
        slit_illum_ref_idx = 14
        slit_illum_smooth_npix = 5
        fit_2d_det_response = True
    [[wavelengths]]
        fwhm_spat_order = 2
    [[slitedges]]
        edge_thresh = 5
        fit_order = 4
        pad = 2
[scienceframe]
    [[process]]
        mask_cr = True
        sigclip = 4.0
        objlim = 1.5
        noise_floor = 0.01
        use_specillum = True
[reduce]
    [[skysub]]
        bspline_spacing = 0.4
    [[extraction]]
        skip_extraction = True
[flexure]
    spec_maxshift = 3
[sensfunc]
    [[UVIS]]
        extinct_correct = False
    [[IR]]
        telgridfile = TellPCA_3000_26000_R15000.fits

KECK KCWI (keck_kcwi)

Alterations to the default parameters are:

[rdx]
    spectrograph = keck_kcwi
[calibrations]
    scattlight_pad = 6
    [[biasframe]]
        exprng = None, 0.001,
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
            use_pattern = True
    [[darkframe]]
        exprng = 0.01, None,
        [[[process]]]
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
            use_pattern = True
    [[arcframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            combine = median
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
            subtract_scattlight = True
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[alignment]]
        locations = 0.1, 0.3, 0.5, 0.7, 0.9,
    [[traceframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_illumflat = False
            use_pattern = True
            subtract_scattlight = True
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[standardframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
            use_pattern = True
    [[flatfield]]
        spec_samp_coarse = 20.0
        spat_samp = 1.0
        tweak_slits_thresh = 0.0
        tweak_slits_maxfrac = 0.0
        slit_illum_relative = True
        slit_illum_ref_idx = 14
        slit_illum_smooth_npix = 5
        fit_2d_det_response = True
    [[wavelengths]]
        fwhm_spat_order = 2
    [[slitedges]]
        edge_thresh = 5
        fit_order = 4
        pad = 2
[scienceframe]
    [[process]]
        mask_cr = True
        sigclip = 4.0
        objlim = 1.5
        noise_floor = 0.01
        use_specillum = True
        use_pattern = True
        subtract_scattlight = True
        [[[scattlight]]]
            finecorr_method = median
[reduce]
    [[extraction]]
        skip_extraction = True
[flexure]
    spec_maxshift = 3
[sensfunc]
    [[UVIS]]
        extinct_correct = False
    [[IR]]
        telgridfile = TellPCA_3000_26000_R15000.fits

KECK LRISb (keck_lris_blue)

Alterations to the default parameters are:

[rdx]
    spectrograph = keck_lris_blue
[calibrations]
    [[biasframe]]
        exprng = None, 0.001,
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 999999, None,
        [[[process]]]
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        exprng = None, 300,
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        exprng = 999999, None,
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        exprng = None, 300,
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        exprng = None, 300,
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[standardframe]]
        exprng = 1, 61,
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
            spat_flexure_correct = True
    [[wavelengths]]
        sigdetect = 10.0
        rms_thresh_frac_fwhm = 0.06
        n_first = 3
        n_final = 5
    [[slitedges]]
        edge_thresh = 15.0
        det_min_spec_length = 0.1
        fit_order = 3
        fit_min_spec_length = 0.2
        sync_center = gap
        minimum_slit_length = 3.0
        minimum_slit_length_sci = 5.0
[scienceframe]
    exprng = 61, None,
    [[process]]
        mask_cr = True
        noise_floor = 0.01
        spat_flexure_correct = True
[flexure]
    spec_method = boxcar
[sensfunc]
    [[IR]]
        telgridfile = TellPCA_3000_26000_R10000.fits

KECK LRISb (keck_lris_blue_orig)

Alterations to the default parameters are:

[rdx]
    spectrograph = keck_lris_blue_orig
[calibrations]
    [[biasframe]]
        exprng = None, 0.001,
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 999999, None,
        [[[process]]]
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        exprng = None, 300,
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        exprng = 999999, None,
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        exprng = None, 300,
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        exprng = None, 300,
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[standardframe]]
        exprng = 1, 61,
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
            spat_flexure_correct = True
    [[wavelengths]]
        sigdetect = 10.0
        rms_thresh_frac_fwhm = 0.06
        n_first = 3
        n_final = 5
    [[slitedges]]
        edge_thresh = 15.0
        det_min_spec_length = 0.1
        fit_order = 3
        fit_min_spec_length = 0.2
        sync_center = gap
        minimum_slit_length = 3.0
        minimum_slit_length_sci = 5.0
[scienceframe]
    exprng = 61, None,
    [[process]]
        mask_cr = True
        noise_floor = 0.01
        spat_flexure_correct = True
[flexure]
    spec_method = boxcar
[sensfunc]
    [[IR]]
        telgridfile = TellPCA_3000_26000_R10000.fits

KECK LRISr (keck_lris_red)

Alterations to the default parameters are:

[rdx]
    spectrograph = keck_lris_red
[calibrations]
    [[biasframe]]
        exprng = None, 0.001,
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 999999, None,
        [[[process]]]
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        exprng = None, 60,
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        exprng = 999999, None,
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        exprng = None, 60,
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        exprng = None, 60,
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[standardframe]]
        exprng = 1, 61,
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
            spat_flexure_correct = True
    [[wavelengths]]
        sigdetect = 10.0
        rms_thresh_frac_fwhm = 0.05
        n_first = 3
        n_final = 5
    [[slitedges]]
        fit_order = 3
        sync_center = gap
        minimum_slit_length = 3.0
        minimum_slit_length_sci = 5.0
    [[tilts]]
        tracethresh = 25
        maxdev_tracefit = 1.0
        spat_order = 4
        spec_order = 7
        maxdev2d = 1.0
        sigrej2d = 5.0
[scienceframe]
    exprng = 61, None,
    [[process]]
        mask_cr = True
        sigclip = 5.0
        objlim = 5.0
        noise_floor = 0.01
        spat_flexure_correct = True
[reduce]
    [[skysub]]
        bspline_spacing = 0.8
[flexure]
    spec_method = boxcar
[sensfunc]
    algorithm = IR
    polyorder = 9
    [[IR]]
        telgridfile = TellPCA_3000_26000_R10000.fits

KECK LRISr (keck_lris_red_mark4)

Alterations to the default parameters are:

[rdx]
    spectrograph = keck_lris_red_mark4
[calibrations]
    [[biasframe]]
        exprng = None, 0.001,
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 999999, None,
        [[[process]]]
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        exprng = None, 60,
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        exprng = 999999, None,
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        exprng = None, 60,
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        exprng = None, 60,
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[standardframe]]
        exprng = 1, 61,
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
            spat_flexure_correct = True
    [[wavelengths]]
        sigdetect = 10.0
        rms_thresh_frac_fwhm = 0.05
        n_first = 3
        n_final = 5
    [[slitedges]]
        fit_order = 3
        sync_center = gap
        minimum_slit_length = 3.0
        minimum_slit_length_sci = 5.0
    [[tilts]]
        tracethresh = 25
        maxdev_tracefit = 1.0
        spat_order = 4
        spec_order = 7
        maxdev2d = 1.0
        sigrej2d = 5.0
[scienceframe]
    exprng = 61, None,
    [[process]]
        mask_cr = True
        sigclip = 5.0
        objlim = 5.0
        noise_floor = 0.01
        spat_flexure_correct = True
[reduce]
    [[skysub]]
        bspline_spacing = 0.8
[flexure]
    spec_method = boxcar
[sensfunc]
    algorithm = IR
    polyorder = 9
    [[IR]]
        telgridfile = TellPCA_3000_26000_R10000.fits

KECK LRISr (keck_lris_red_orig)

Alterations to the default parameters are:

[rdx]
    spectrograph = keck_lris_red_orig
[calibrations]
    [[biasframe]]
        exprng = None, 0.001,
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 999999, None,
        [[[process]]]
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        exprng = None, 60,
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        exprng = 999999, None,
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        exprng = None, 60,
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        exprng = None, 60,
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[standardframe]]
        exprng = 1, 61,
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
            spat_flexure_correct = True
    [[wavelengths]]
        sigdetect = 10.0
        rms_thresh_frac_fwhm = 0.05
        n_first = 3
        n_final = 5
    [[slitedges]]
        fit_order = 3
        sync_center = gap
        minimum_slit_length = 3.0
        minimum_slit_length_sci = 5.0
    [[tilts]]
        tracethresh = 25
        maxdev_tracefit = 1.0
        spat_order = 4
        spec_order = 7
        maxdev2d = 1.0
        sigrej2d = 5.0
[scienceframe]
    exprng = 61, None,
    [[process]]
        mask_cr = True
        sigclip = 5.0
        objlim = 5.0
        noise_floor = 0.01
        spat_flexure_correct = True
[reduce]
    [[skysub]]
        bspline_spacing = 0.8
[flexure]
    spec_method = boxcar
[sensfunc]
    algorithm = IR
    polyorder = 9
    [[IR]]
        telgridfile = TellPCA_3000_26000_R10000.fits

KECK MOSFIRE (keck_mosfire)

Alterations to the default parameters are:

[rdx]
    spectrograph = keck_mosfire
[calibrations]
    [[biasframe]]
        [[[process]]]
            combine = median
            use_biasimage = False
            use_overscan = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 1, None,
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        exprng = 1, None,
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            noise_floor = 0.01
    [[standardframe]]
        exprng = None, 20,
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            noise_floor = 0.01
    [[wavelengths]]
        lamps = OH_NIRES,
        fwhm = 5.0
        rms_thresh_frac_fwhm = 0.11
    [[slitedges]]
        edge_thresh = 50.0
        sync_predict = nearest
[scienceframe]
    exprng = 20, None,
    [[process]]
        satpix = nothing
        mask_cr = True
        sigclip = 20.0
        use_biasimage = False
        use_overscan = False
        noise_floor = 0.01
[reduce]
    [[skysub]]
        bspline_spacing = 0.8
[fluxcalib]
    extrap_sens = True
[sensfunc]
    extrap_blu = 0.0
    extrap_red = 0.0
    algorithm = IR
    polyorder = 13
    [[IR]]
        telgridfile = TellPCA_3000_26000_R10000.fits

KECK NIRES (keck_nires)

Alterations to the default parameters are:

[rdx]
    spectrograph = keck_nires
[calibrations]
    [[biasframe]]
        [[[process]]]
            combine = median
            use_biasimage = False
            use_overscan = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        exprng = 61, None,
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        exprng = 61, None,
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_illumflat = False
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            noise_floor = 0.01
            use_illumflat = False
    [[standardframe]]
        exprng = None, 60,
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            noise_floor = 0.01
            use_illumflat = False
    [[wavelengths]]
        method = reidentify
        echelle = True
        ech_norder_coeff = 6
        ech_sigrej = 3.0
        lamps = OH_NIRES,
        fwhm = 2.2
        reid_arxiv = keck_nires.fits
        rms_thresh_frac_fwhm = 0.136
        n_final = 3, 4, 4, 4, 4,
    [[slitedges]]
        fit_min_spec_length = 0.4
        left_right_pca = True
        trace_thresh = 10.0
        fwhm_gaussian = 4.0
    [[tilts]]
        tracethresh = 10.0
[scienceframe]
    exprng = 61, None,
    [[process]]
        satpix = nothing
        mask_cr = True
        sigclip = 20.0
        use_biasimage = False
        use_overscan = False
        noise_floor = 0.01
        use_illumflat = False
[reduce]
    [[skysub]]
        bspline_spacing = 0.8
    [[extraction]]
        boxcar_radius = 0.75
[coadd1d]
    wave_method = log10
[coadd2d]
    offsets = header
[sensfunc]
    algorithm = IR
    polyorder = 8
    [[IR]]
        telgridfile = TellPCA_3000_26000_R10000.fits

KECK NIRSPEC (keck_nirspec_low)

Alterations to the default parameters are:

[rdx]
    spectrograph = keck_nirspec_low
[calibrations]
    [[biasframe]]
        [[[process]]]
            combine = median
            use_biasimage = False
            use_overscan = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 20, None,
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        exprng = 20, None,
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_illumflat = False
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            noise_floor = 0.01
            use_illumflat = False
    [[standardframe]]
        exprng = None, 20,
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            noise_floor = 0.01
            use_illumflat = False
    [[flatfield]]
        tweak_slits_thresh = 0.8
    [[wavelengths]]
        lamps = OH_NIRES,
        fwhm = 3.5
        rms_thresh_frac_fwhm = 0.06
    [[slitedges]]
        edge_thresh = 200.0
        sync_predict = nearest
[scienceframe]
    exprng = 20, None,
    [[process]]
        satpix = nothing
        mask_cr = True
        sigclip = 20.0
        use_biasimage = False
        use_overscan = False
        noise_floor = 0.01
        use_illumflat = False
[reduce]
    [[skysub]]
        bspline_spacing = 0.8
[sensfunc]
    algorithm = IR
    polyorder = 8
    [[IR]]
        telgridfile = TellPCA_3000_26000_R25000.fits
        pix_shift_bounds = (-8.0, 8.0)
[telluric]
    pix_shift_bounds = (-8.0, 8.0)

LBT LUCI1 (lbt_luci1)

Alterations to the default parameters are:

[rdx]
    spectrograph = lbt_luci1
[calibrations]
    [[biasframe]]
        [[[process]]]
            combine = median
            use_biasimage = False
            use_overscan = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_illumflat = False
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            noise_floor = 0.01
            use_illumflat = False
    [[standardframe]]
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            noise_floor = 0.01
            use_illumflat = False
    [[wavelengths]]
        lamps = OH_NIRES,
        fwhm = 4.5
        rms_thresh_frac_fwhm = 0.05
    [[slitedges]]
        edge_thresh = 300.0
        sync_predict = nearest
[scienceframe]
    [[process]]
        satpix = nothing
        mask_cr = True
        sigclip = 20.0
        use_biasimage = False
        use_overscan = False
        noise_floor = 0.01
        use_illumflat = False
[reduce]
    [[skysub]]
        bspline_spacing = 0.8
    [[extraction]]
        std_prof_nsigma = 100.0

LBT LUCI2 (lbt_luci2)

Alterations to the default parameters are:

[rdx]
    spectrograph = lbt_luci2
[calibrations]
    [[biasframe]]
        [[[process]]]
            combine = median
            use_biasimage = False
            use_overscan = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_illumflat = False
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            noise_floor = 0.01
            use_illumflat = False
    [[standardframe]]
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            noise_floor = 0.01
            use_illumflat = False
    [[wavelengths]]
        lamps = OH_NIRES,
        fwhm = 5.0
        rms_thresh_frac_fwhm = 0.04
    [[slitedges]]
        edge_thresh = 300
        fit_order = 8
        sync_predict = nearest
[scienceframe]
    [[process]]
        satpix = nothing
        mask_cr = True
        sigclip = 20.0
        use_biasimage = False
        use_overscan = False
        noise_floor = 0.01
        use_illumflat = False
[reduce]
    [[skysub]]
        bspline_spacing = 0.8
        global_sky_std = False
    [[extraction]]
        std_prof_nsigma = 100.0
        model_full_slit = True

LBT MODS1B (lbt_mods1b)

Alterations to the default parameters are:

[rdx]
    spectrograph = lbt_mods1b
[calibrations]
    [[biasframe]]
        exprng = None, 0.001,
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 999999, None,
        [[[process]]]
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            clip = False
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            clip = False
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        exprng = 0, None,
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        exprng = 999999, None,
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        exprng = 0, None,
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[standardframe]]
        exprng = 1, 200,
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[wavelengths]]
        lamps = XeI, KrI, ArI, HgI,
        sigdetect = 10.0
        rms_thresh_frac_fwhm = 0.09
    [[slitedges]]
        edge_thresh = 100.0
        sync_predict = nearest
    [[tilts]]
        maxdev_tracefit = 0.02
        spat_order = 5
        spec_order = 5
        maxdev2d = 0.02
[scienceframe]
    exprng = 200, None,
    [[process]]
        mask_cr = True
        noise_floor = 0.01
[flexure]
    spec_method = boxcar

LBT MODS1R (lbt_mods1r)

Alterations to the default parameters are:

[rdx]
    spectrograph = lbt_mods1r
[calibrations]
    [[biasframe]]
        exprng = None, 0.001,
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 999999, None,
        [[[process]]]
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            clip = False
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            clip = False
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        exprng = 0, None,
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        exprng = 999999, None,
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        exprng = 0, None,
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[standardframe]]
        exprng = 1, 200,
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[wavelengths]]
        lamps = ArI, NeI, KrI, XeI,
        fwhm = 10.0
        rms_thresh_frac_fwhm = 0.09
        match_toler = 2.5
        n_first = 3
    [[slitedges]]
        edge_thresh = 100.0
        sync_predict = nearest
    [[tilts]]
        maxdev_tracefit = 0.02
        spat_order = 5
        spec_order = 5
        maxdev2d = 0.02
[scienceframe]
    exprng = 200, None,
    [[process]]
        mask_cr = True
        noise_floor = 0.01
[flexure]
    spec_method = boxcar

LBT MODS2B (lbt_mods2b)

Alterations to the default parameters are:

[rdx]
    spectrograph = lbt_mods2b
[calibrations]
    [[biasframe]]
        exprng = None, 0.001,
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 999999, None,
        [[[process]]]
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            clip = False
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            clip = False
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        exprng = 0, None,
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        exprng = 999999, None,
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        exprng = 0, None,
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[standardframe]]
        exprng = 1, 200,
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[wavelengths]]
        lamps = XeI, KrI, ArI, HgI,
        sigdetect = 10.0
        rms_thresh_frac_fwhm = 0.09
    [[slitedges]]
        edge_thresh = 100.0
        sync_predict = nearest
    [[tilts]]
        maxdev_tracefit = 0.02
        spat_order = 5
        spec_order = 5
        maxdev2d = 0.02
[scienceframe]
    exprng = 200, None,
    [[process]]
        mask_cr = True
        noise_floor = 0.01
[flexure]
    spec_method = boxcar

LBT MODS2R (lbt_mods2r)

Alterations to the default parameters are:

[rdx]
    spectrograph = lbt_mods2r
[calibrations]
    [[biasframe]]
        exprng = None, 0.001,
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 999999, None,
        [[[process]]]
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            clip = False
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            clip = False
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        exprng = 0, None,
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        exprng = 999999, None,
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        exprng = 0, None,
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[standardframe]]
        exprng = 1, 200,
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[wavelengths]]
        lamps = ArI, NeI, KrI, XeI,
        fwhm = 10.0
        rms_thresh_frac_fwhm = 0.22
        match_toler = 2.5
        n_first = 3
    [[slitedges]]
        edge_thresh = 300.0
        sync_predict = nearest
    [[tilts]]
        maxdev_tracefit = 0.02
        spat_order = 5
        spec_order = 5
        maxdev2d = 0.02
[scienceframe]
    exprng = 200, None,
    [[process]]
        mask_cr = True
        noise_floor = 0.01
[flexure]
    spec_method = boxcar

LDT DeVeny (ldt_deveny)

Alterations to the default parameters are:

[rdx]
    spectrograph = ldt_deveny
[calibrations]
    bpm_usebias = True
    [[biasframe]]
        [[[process]]]
            overscan_method = chebyshev
            overscan_par = 1
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        [[[process]]]
            overscan_method = chebyshev
            overscan_par = 1
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            overscan_method = chebyshev
            overscan_par = 1
            clip = False
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            overscan_method = chebyshev
            overscan_par = 1
            clip = False
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            overscan_method = chebyshev
            overscan_par = 1
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        [[[process]]]
            overscan_method = chebyshev
            overscan_par = 1
            use_illumflat = False
    [[alignframe]]
        [[[process]]]
            overscan_method = chebyshev
            overscan_par = 1
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            overscan_method = chebyshev
            overscan_par = 1
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            overscan_method = chebyshev
            overscan_par = 1
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            overscan_method = chebyshev
            overscan_par = 1
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            overscan_method = chebyshev
            overscan_par = 1
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            overscan_method = chebyshev
            overscan_par = 1
            mask_cr = True
            noise_floor = 0.01
            use_illumflat = False
    [[standardframe]]
        [[[process]]]
            overscan_method = chebyshev
            overscan_par = 1
            mask_cr = True
            noise_floor = 0.01
            use_illumflat = False
    [[flatfield]]
        spec_samp_fine = 30
        tweak_slits = False
        pixelflat_min_wave = 3000.0
        slit_illum_finecorr = False
    [[wavelengths]]
        method = full_template
        lamps = use_header,
        fwhm = 3.0
        nsnippet = 1
    [[slitedges]]
        max_nudge = 5
        sync_predict = nearest
        bound_detector = True
        minimum_slit_length = 170.0
    [[tilts]]
        spat_order = 4
        spec_order = 5
[scienceframe]
    [[process]]
        overscan_method = chebyshev
        overscan_par = 1
        mask_cr = True
        sigclip = 5.0
        objlim = 2.0
        noise_floor = 0.01
        use_illumflat = False
[reduce]
    [[findobj]]
        trace_npoly = 3
        snr_thresh = 50.0
        find_trim_edge = 0, 0,
        maxnumber_sci = 5
        maxnumber_std = 1
        find_fwhm = 4.4
    [[skysub]]
        sky_sigrej = 4.0
    [[extraction]]
        boxcar_radius = 1.9
        use_2dmodel_mask = False
[flexure]
    spec_method = boxcar
    spec_maxshift = 30
[sensfunc]
    [[UVIS]]
        polycorrect = False
        nresln = 15

MAGELLAN FIRE (magellan_fire)

Alterations to the default parameters are:

[rdx]
    spectrograph = magellan_fire
[calibrations]
    [[biasframe]]
        [[[process]]]
            combine = median
            use_biasimage = False
            use_overscan = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 20, None,
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        exprng = 20, None,
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_illumflat = False
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            noise_floor = 0.01
            use_illumflat = False
    [[standardframe]]
        exprng = None, 60,
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            noise_floor = 0.01
            use_illumflat = False
    [[wavelengths]]
        method = reidentify
        echelle = True
        ech_norder_coeff = 6
        ech_sigrej = 3.0
        lamps = OH_FIRE_Echelle,
        sigdetect = 5, 5, 10, 10, 10, 20, 30, 30, 30, 30, 30, 10, 30, 30, 60, 30, 30, 10, 20, 30, 10,
        reid_arxiv = magellan_fire_echelle.fits
        cc_thresh = 0.35
        rms_thresh_frac_fwhm = 0.25
        n_final = 3, 2, 3, 2, 4, 4, 4, 3, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 6, 6, 4,
    [[slitedges]]
        edge_thresh = 3.0
        max_shift_adj = 0.5
        fit_min_spec_length = 0.5
        left_right_pca = True
        pca_order = 3
        trace_thresh = 10.0
    [[tilts]]
        tracethresh = 5
[scienceframe]
    exprng = 20, None,
    [[process]]
        satpix = nothing
        mask_cr = True
        sigclip = 20.0
        use_biasimage = False
        use_overscan = False
        noise_floor = 0.01
        use_illumflat = False
[reduce]
    [[findobj]]
        maxnumber_sci = 2
        maxnumber_std = 1
    [[extraction]]
        model_full_slit = True
[coadd1d]
    wave_method = log10
[sensfunc]
    algorithm = IR
    [[IR]]
        telgridfile = TellPCA_3000_26000_R15000.fits

MAGELLAN FIRE (magellan_fire_long)

Alterations to the default parameters are:

[rdx]
    spectrograph = magellan_fire_long
[calibrations]
    [[biasframe]]
        [[[process]]]
            combine = median
            use_biasimage = False
            use_overscan = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 20, None,
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        exprng = 1, 50,
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_illumflat = False
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            noise_floor = 0.01
            use_illumflat = False
    [[standardframe]]
        exprng = None, 60,
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            noise_floor = 0.01
            use_illumflat = False
    [[wavelengths]]
        method = full_template
        lamps = ArI, ArII, ThAr, NeI,
        sigdetect = 3
        fwhm = 10
        reid_arxiv = magellan_fire_long.fits
        rms_thresh_frac_fwhm = 0.05
        match_toler = 5.0
    [[slitedges]]
        trace_thresh = 10.0
        sync_predict = nearest
    [[tilts]]
        tracethresh = 5
[scienceframe]
    exprng = 20, None,
    [[process]]
        mask_cr = True
        use_biasimage = False
        use_overscan = False
        noise_floor = 0.01
        use_illumflat = False
[reduce]
    [[findobj]]
        snr_thresh = 5
        find_trim_edge = 50, 50,
[sensfunc]
    [[IR]]
        telgridfile = TellPCA_3000_26000_R10000.fits

MAGELLAN MagE (magellan_mage)

Alterations to the default parameters are:

[rdx]
    spectrograph = magellan_mage
[calibrations]
    [[biasframe]]
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 20, None,
        [[[process]]]
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        exprng = 20, None,
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[standardframe]]
        exprng = None, 20,
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[wavelengths]]
        method = reidentify
        echelle = True
        ech_sigrej = 3.0
        lamps = ThAr_MagE,
        fwhm = 3.0
        reid_arxiv = magellan_mage.fits
        cc_thresh = 0.5
        cc_local_thresh = 0.5
        rms_thresh_frac_fwhm = 0.133
    [[slitedges]]
        edge_thresh = 10.0
        max_shift_adj = 3.0
        fit_min_spec_length = 0.3
        left_right_pca = True
    [[tilts]]
        tracethresh = 10.0
[scienceframe]
    exprng = 20, None,
    [[process]]
        satpix = nothing
        mask_cr = True
        sigclip = 20.0
        noise_floor = 0.01
[reduce]
    [[findobj]]
        find_trim_edge = 4, 4,
        maxnumber_sci = 2
        maxnumber_std = 1
    [[extraction]]
        model_full_slit = True
[coadd1d]
    wave_method = log10

HILTNER Echelle (mdm_modspec)

Alterations to the default parameters are:

[rdx]
    spectrograph = mdm_modspec
[calibrations]
    [[biasframe]]
        exprng = None, 0.001,
        [[[process]]]
            overscan_method = median
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 999999, None,
        [[[process]]]
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            clip = False
            use_pixelflat = False
            use_illumflat = False
            subtract_continuum = True
    [[tiltframe]]
        [[[process]]]
            clip = False
            use_pixelflat = False
            use_illumflat = False
            subtract_continuum = True
    [[pixelflatframe]]
        [[[process]]]
            satpix = nothing
            n_lohi = 1, 1,
            comb_sigrej = 3.0
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        exprng = 999999, None,
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[standardframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[flatfield]]
        slit_illum_finecorr = False
    [[wavelengths]]
        method = full_template
        lamps = ArI, XeI, NeI,
        reid_arxiv = mdm_modspec_1200_5100.fits
        n_final = 9
    [[slitedges]]
        sync_predict = nearest
        bound_detector = True
[scienceframe]
    exprng = 10, 600,
    [[process]]
        mask_cr = True
        noise_floor = 0.01

HILTNER MDM4K (mdm_osmos_mdm4k)

Alterations to the default parameters are:

[rdx]
    spectrograph = mdm_osmos_mdm4k
[calibrations]
    [[biasframe]]
        exprng = None, 0.001,
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 999999, None,
        [[[process]]]
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            combine = median
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        exprng = 999999, None,
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[standardframe]]
        exprng = None, 120,
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[wavelengths]]
        method = full_template
        lamps = ArI, XeI,
        sigdetect = 10.0
        reid_arxiv = mdm_osmos_mdm4k.fits
    [[slitedges]]
        sync_predict = nearest
[scienceframe]
    exprng = 90, None,
    [[process]]
        mask_cr = True
        noise_floor = 0.01

HILTNER R4K (mdm_osmos_r4k)

Alterations to the default parameters are:

[rdx]
    spectrograph = mdm_osmos_r4k
[calibrations]
    [[biasframe]]
        exprng = None, 1,
        [[[process]]]
            overscan_method = odd_even
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 999999, None,
        [[[process]]]
            overscan_method = odd_even
            mask_cr = True
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            overscan_method = odd_even
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            overscan_method = odd_even
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            overscan_method = odd_even
            combine = median
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        exprng = 999999, None,
        [[[process]]]
            overscan_method = odd_even
            use_biasimage = False
    [[alignframe]]
        [[[process]]]
            overscan_method = odd_even
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            overscan_method = odd_even
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            overscan_method = odd_even
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            overscan_method = odd_even
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            overscan_method = odd_even
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            overscan_method = odd_even
            mask_cr = True
            use_biasimage = False
            noise_floor = 0.01
    [[standardframe]]
        exprng = None, 120,
        [[[process]]]
            overscan_method = odd_even
            mask_cr = True
            use_biasimage = False
            noise_floor = 0.01
    [[wavelengths]]
        method = full_template
        lamps = HgI, NeI,
        reid_arxiv = mdm_osmos_r4k.fits
        nsnippet = 1
    [[slitedges]]
        sync_predict = nearest
        bound_detector = True
[scienceframe]
    exprng = 90, None,
    [[process]]
        overscan_method = odd_even
        mask_cr = True
        use_biasimage = False
        noise_floor = 0.01

MMT BINOSPEC (mmt_binospec)

Alterations to the default parameters are:

[rdx]
    spectrograph = mmt_binospec
[calibrations]
    [[biasframe]]
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 20, None,
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        exprng = 20, None,
        [[[process]]]
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        [[[process]]]
            use_biasimage = False
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            noise_floor = 0.01
    [[standardframe]]
        exprng = None, 100,
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            noise_floor = 0.01
    [[wavelengths]]
        method = full_template
        lamps = HeI, NeI, ArI, ArII,
        rms_thresh_frac_fwhm = 0.125
    [[slitedges]]
        sync_predict = nearest
    [[tilts]]
        tracethresh = 10.0
        spat_order = 6
        spec_order = 6
[scienceframe]
    exprng = 20, None,
    [[process]]
        mask_cr = True
        sigclip = 5.0
        objlim = 2.0
        use_biasimage = False
        noise_floor = 0.01
[reduce]
    [[skysub]]
        bspline_spacing = 0.8
        global_sky_std = False
[flexure]
    spec_method = boxcar
[sensfunc]
    polyorder = 7
    [[IR]]
        telgridfile = TellPCA_3000_26000_R10000.fits

MMT Blue_Channel (mmt_bluechannel)

Alterations to the default parameters are:

[rdx]
    spectrograph = mmt_bluechannel
[calibrations]
    [[biasframe]]
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 300, None,
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        exprng = 1, None,
        [[[process]]]
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        exprng = None, 600,
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        [[[process]]]
            use_biasimage = False
            use_illumflat = False
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        exprng = None, 600,
        [[[process]]]
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        exprng = 1, None,
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            noise_floor = 0.01
            use_illumflat = False
    [[standardframe]]
        exprng = None, 600,
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            noise_floor = 0.01
            use_illumflat = False
    [[wavelengths]]
        lamps = use_header,
        fwhm = 3.1
    [[slitedges]]
        sync_predict = nearest
        bound_detector = True
[scienceframe]
    [[process]]
        mask_cr = True
        sigclip = 5.0
        objlim = 2.0
        use_biasimage = False
        noise_floor = 0.01
        use_illumflat = False
[reduce]
    [[skysub]]
        bspline_spacing = 0.8
        global_sky_std = False
[sensfunc]
    polyorder = 7

MMT MMIRS (mmt_mmirs)

Alterations to the default parameters are:

[rdx]
    spectrograph = mmt_mmirs
[calibrations]
    [[biasframe]]
        [[[process]]]
            combine = median
            use_biasimage = False
            use_overscan = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 30, None,
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        exprng = 60, None,
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        exprng = 60, None,
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_illumflat = False
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            noise_floor = 0.01
            use_illumflat = False
    [[standardframe]]
        exprng = None, 60,
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            noise_floor = 0.01
            use_illumflat = False
    [[wavelengths]]
        lamps = OH_NIRES,
        rms_thresh_frac_fwhm = 0.125
        match_toler = 5.0
    [[slitedges]]
        edge_thresh = 100.0
        fit_min_spec_length = 0.4
        trace_thresh = 10.0
        sync_predict = nearest
        bound_detector = True
    [[tilts]]
        tracethresh = 5
        spat_order = 7
        spec_order = 5
[scienceframe]
    exprng = 30, None,
    [[process]]
        mask_cr = True
        grow = 0.5
        sigclip = 5.0
        objlim = 2.0
        use_biasimage = False
        use_overscan = False
        noise_floor = 0.01
[reduce]
    [[findobj]]
        snr_thresh = 5.0
    [[skysub]]
        sky_sigrej = 5.0
[sensfunc]
    algorithm = IR
    polyorder = 8
    [[IR]]
        telgridfile = TellPCA_3000_26000_R10000.fits

NOT ALFOSC (not_alfosc)

Alterations to the default parameters are:

[rdx]
    spectrograph = not_alfosc
[calibrations]
    [[biasframe]]
        exprng = None, 1,
        [[[process]]]
            combine = median
            use_biasimage = False
            use_overscan = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 999999, None,
        [[[process]]]
            mask_cr = True
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            clip = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
            subtract_continuum = True
    [[tiltframe]]
        [[[process]]]
            clip = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
            subtract_continuum = True
    [[pixelflatframe]]
        [[[process]]]
            combine = median
            satpix = nothing
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        exprng = 999999, None,
        [[[process]]]
            use_overscan = False
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            use_overscan = False
            noise_floor = 0.01
    [[standardframe]]
        exprng = None, 120,
        [[[process]]]
            mask_cr = True
            use_overscan = False
            noise_floor = 0.01
    [[wavelengths]]
        method = full_template
        lamps = HeI, NeI, ArI,
        sigdetect = 10.0
    [[slitedges]]
        edge_thresh = 30
        sync_predict = nearest
        bound_detector = True
        minimum_slit_gap = 15
[scienceframe]
    exprng = 10, None,
    [[process]]
        mask_cr = True
        use_overscan = False
        noise_floor = 0.01

NOT ALFOSC (not_alfosc_vert)

Alterations to the default parameters are:

[rdx]
    spectrograph = not_alfosc_vert
[calibrations]
    [[biasframe]]
        exprng = None, 1,
        [[[process]]]
            combine = median
            use_biasimage = False
            use_overscan = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 999999, None,
        [[[process]]]
            mask_cr = True
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            clip = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
            subtract_continuum = True
    [[tiltframe]]
        [[[process]]]
            clip = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
            subtract_continuum = True
    [[pixelflatframe]]
        [[[process]]]
            combine = median
            satpix = nothing
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        exprng = 999999, None,
        [[[process]]]
            use_overscan = False
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            use_overscan = False
            noise_floor = 0.01
    [[standardframe]]
        exprng = None, 120,
        [[[process]]]
            mask_cr = True
            use_overscan = False
            noise_floor = 0.01
    [[wavelengths]]
        method = full_template
        lamps = HeI, NeI, ArI,
        sigdetect = 10.0
    [[slitedges]]
        edge_thresh = 30
        sync_predict = nearest
        bound_detector = True
        minimum_slit_gap = 15
[scienceframe]
    exprng = 10, None,
    [[process]]
        mask_cr = True
        use_overscan = False
        noise_floor = 0.01

NTT EFOSC2 (ntt_efosc2)

Alterations to the default parameters are:

[rdx]
    spectrograph = ntt_efosc2
[calibrations]
    [[biasframe]]
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        [[[process]]]
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[standardframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[flatfield]]
        tweak_slits_thresh = 0.9
    [[wavelengths]]
        method = full_template
        lamps = HeI, ArI,
        sigdetect = 10.0
        rms_thresh_frac_fwhm = 0.07
    [[slitedges]]
        edge_thresh = 75.0
        sync_predict = nearest
    [[tilts]]
        tracethresh = 25.0
[scienceframe]
    [[process]]
        mask_cr = True
        noise_floor = 0.01
[reduce]
    [[skysub]]
        sky_sigrej = 5.0
        global_sky_std = False
        no_poly = True
[flexure]
    spec_method = boxcar

P200 DBSPb (p200_dbsp_blue)

Alterations to the default parameters are:

[rdx]
    spectrograph = p200_dbsp_blue
[calibrations]
    bpm_usebias = True
    [[biasframe]]
        exprng = None, 0.001,
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 999999, None,
        [[[process]]]
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        exprng = None, 120,
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            combine = median
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        exprng = 999999, None,
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[standardframe]]
        exprng = None, 120,
        [[[process]]]
            combine = median
            mask_cr = True
            noise_floor = 0.01
    [[wavelengths]]
        method = full_template
        lamps = FeI, ArI, ArII,
    [[slitedges]]
        fit_min_spec_length = 0.55
        sync_predict = nearest
[scienceframe]
    exprng = 90, None,
    [[process]]
        combine = median
        mask_cr = True
        noise_floor = 0.01
[sensfunc]
    [[UVIS]]
        nresln = 5

P200 DBSPr (p200_dbsp_red)

Alterations to the default parameters are:

[rdx]
    spectrograph = p200_dbsp_red
[calibrations]
    bpm_usebias = True
    [[biasframe]]
        exprng = None, 0.001,
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 999999, None,
        [[[process]]]
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        exprng = None, 120,
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            combine = median
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        exprng = 999999, None,
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[standardframe]]
        exprng = None, 120,
        [[[process]]]
            combine = median
            mask_cr = True
            noise_floor = 0.01
    [[wavelengths]]
        method = full_template
        lamps = ArI, ArII, NeI, HeI,
    [[slitedges]]
        sync_predict = nearest
[scienceframe]
    exprng = 90, None,
    [[process]]
        combine = median
        mask_cr = True
        sigclip = 4.0
        objlim = 1.5
        noise_floor = 0.01
[sensfunc]
    [[UVIS]]
        polycorrect = False
    [[IR]]
        telgridfile = TellPCA_3000_26000_R10000.fits

P200 TSPEC (p200_tspec)

Alterations to the default parameters are:

[rdx]
    spectrograph = p200_tspec
[calibrations]
    [[biasframe]]
        [[[process]]]
            combine = median
            use_biasimage = False
            use_overscan = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 0, None,
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        exprng = 100, None,
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        exprng = 100, None,
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_illumflat = False
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_overscan = False
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            noise_floor = 0.01
            use_illumflat = False
    [[standardframe]]
        exprng = None, 60,
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_overscan = False
            noise_floor = 0.01
            use_illumflat = False
    [[wavelengths]]
        method = reidentify
        echelle = True
        ech_norder_coeff = 6
        ech_sigrej = 3.0
        lamps = OH_NIRES,
        fwhm = 2.9
        reid_arxiv = p200_triplespec.fits
        rms_thresh_frac_fwhm = 0.103
        n_final = 3, 4, 4, 4, 4,
    [[slitedges]]
        fit_min_spec_length = 0.3
        left_right_pca = True
        trace_thresh = 5.0
        fwhm_gaussian = 4.0
    [[tilts]]
        tracethresh = 10.0
[scienceframe]
    exprng = 60, None,
    [[process]]
        satpix = nothing
        mask_cr = True
        sigclip = 20.0
        use_biasimage = False
        use_overscan = False
        noise_floor = 0.01
        use_illumflat = False
[reduce]
    [[findobj]]
        maxnumber_sci = 2
        maxnumber_std = 1
    [[skysub]]
        bspline_spacing = 0.8
    [[extraction]]
        boxcar_radius = 0.75
        model_full_slit = True
[coadd1d]
    wave_method = log10
[sensfunc]
    algorithm = IR
    polyorder = 8
    [[IR]]
        telgridfile = TellPCA_3000_26000_R10000.fits

SHANE KASTb (shane_kast_blue)

Alterations to the default parameters are:

[rdx]
    spectrograph = shane_kast_blue
[calibrations]
    [[biasframe]]
        exprng = None, 0.001,
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 999999, None,
        [[[process]]]
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        exprng = None, 61,
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        exprng = 0, None,
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        exprng = 999999, None,
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        exprng = 0, None,
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[standardframe]]
        exprng = 1, 61,
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[wavelengths]]
        method = full_template
        lamps = CdI, HgI, HeI,
        rms_thresh_frac_fwhm = 0.07
        match_toler = 2.5
        n_first = 3
    [[slitedges]]
        sync_predict = nearest
        bound_detector = True
    [[tilts]]
        maxdev_tracefit = 0.02
        spec_order = 5
        maxdev2d = 0.02
[scienceframe]
    exprng = 61, None,
    [[process]]
        mask_cr = True
        noise_floor = 0.01
[flexure]
    spec_method = boxcar
    spectrum = sky_kastb_600.fits
[sensfunc]
    [[IR]]
        telgridfile = TellPCA_3000_26000_R10000.fits

SHANE KASTr (shane_kast_red)

Alterations to the default parameters are:

[rdx]
    spectrograph = shane_kast_red
[calibrations]
    [[biasframe]]
        exprng = None, 0.001,
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 999999, None,
        [[[process]]]
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        exprng = None, 61,
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        exprng = 0, None,
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        exprng = 999999, None,
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        exprng = 0, None,
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[standardframe]]
        exprng = 1, 61,
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[wavelengths]]
        lamps = NeI, HgI, HeI, ArI,
    [[slitedges]]
        sync_predict = nearest
        bound_detector = True
[scienceframe]
    exprng = 61, None,
    [[process]]
        mask_cr = True
        noise_floor = 0.01
[flexure]
    spec_method = boxcar
[sensfunc]
    [[IR]]
        telgridfile = TellPCA_3000_26000_R10000.fits

SHANE KASTr (shane_kast_red_ret)

Alterations to the default parameters are:

[rdx]
    spectrograph = shane_kast_red_ret
[calibrations]
    [[biasframe]]
        exprng = None, 0.001,
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        exprng = 999999, None,
        [[[process]]]
            mask_cr = True
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        exprng = None, 61,
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        exprng = 0, None,
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        exprng = 999999, None,
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        exprng = 0, None,
        [[[process]]]
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[standardframe]]
        exprng = 1, 61,
        [[[process]]]
            mask_cr = True
            noise_floor = 0.01
    [[wavelengths]]
        lamps = NeI, HgI, HeI, ArI,
        rms_thresh_frac_fwhm = 0.09
        use_instr_flag = True
    [[slitedges]]
        sync_predict = nearest
        bound_detector = True
[scienceframe]
    exprng = 61, None,
    [[process]]
        mask_cr = True
        noise_floor = 0.01
[flexure]
    spec_method = boxcar
[sensfunc]
    [[IR]]
        telgridfile = TellPCA_3000_26000_R10000.fits

SOAR blue (soar_goodman_blue)

Alterations to the default parameters are:

[rdx]
    spectrograph = soar_goodman_blue
[calibrations]
    [[biasframe]]
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        exprng = None, 30,
        [[[process]]]
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        [[[process]]]
            use_biasimage = False
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[lampoffflatsframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[scattlightframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[skyframe]]
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            noise_floor = 0.01
    [[standardframe]]
        exprng = None, 120,
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            noise_floor = 0.01
    [[wavelengths]]
        lamps = NeI, ArI, HgI,
        fwhm = 5.0
        rms_thresh_frac_fwhm = 0.17
    [[slitedges]]
        sync_predict = nearest
        bound_detector = True
[scienceframe]
    exprng = 90, None,
    [[process]]
        mask_cr = True
        use_biasimage = False
        noise_floor = 0.01
[flexure]
    spec_method = boxcar
[sensfunc]
    [[IR]]
        telgridfile = TellPCA_3000_26000_R15000.fits

SOAR red (soar_goodman_red)

Alterations to the default parameters are:

[rdx]
    spectrograph = soar_goodman_red
[calibrations]
    [[biasframe]]
        [[[process]]]
            combine = median
            use_biasimage = False
            shot_noise = False
            use_pixelflat = False
            use_illumflat = False
    [[darkframe]]
        [[[process]]]
            mask_cr = True
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[arcframe]]
        exprng = None, 30,
        [[[process]]]
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[tiltframe]]
        [[[process]]]
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[pixelflatframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[pinholeframe]]
        [[[process]]]
            use_biasimage = False
    [[alignframe]]
        [[[process]]]
            satpix = nothing
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[traceframe]]
        [[[process]]]
            use_biasimage = False
            use_pixelflat = False
            use_illumflat = False
    [[illumflatframe]]