DEFAULT: appropriate dark_cmask.fits file in ../cal/
OVERRIDE ALLOWED: name of user's calibration file
-e2 Input uncertainty of dark calibration file (FITS) Currently set to zero in the file (FITS)
DEFAULT: appropriate dark_unc.fits file in ../cal/
OVERRIDE ALLOWED: name of user's calibration file
-i2 Input dark calibration file (FITS)
DEFAULT: appropriate dark.fits file in ../cal/
OVERRIDE ALLOWED: name of user's calibration file
-p Input PMASK file (FITS)
DEFAULT: appropriate pmask.fits file in ../cal/
OVERRIDE ALLOWED: name of user's calibration file
Pipeline namelist files:
-n Namelist file
DEFAULT: appropriate cubesub.nl file in ../cdf/
OVERRIDE ALLOWED: name of user's namelist file
Pipeline input datafiles:
-d Input DMASK file (FITS)
[pipeline datafile --- override not allowed]
-e1 Input UNC file (FITS)
[pipeline datafile --- override not allowed]
-i1 Input FLUX file (FITS)
[pipeline datafile --- override not allowed]
Pipeline output datafiles:
-o1 Output FLUX file (FITS)
[pipeline datafile --- override not allowed]
-o2 Output UNC file (FITS)
[pipeline datafile --- override not allowed]
Pipeline datafiles updated:
(none)
4.8 cvti2r4 Module
This module converts from integer to floating point.
The module is used in the following pipelines: BCDACQ; BCD
Constant values:
-a Offset to add to all input samples (in DN)
DEFAULT: 32768
OVERRIDES ALLOWED: an integer
-b Input sample value indicating "missing data
DEFAULT: -1
OVERRIDES ALLOWED: an integer
-f "no" disables forcing ".fits" onto following FITS file names.
DEFAULT: yes
OVERRIDES ALLOWED: no | yes
-g Output Ge BMASK file --- not used for CUPID.
DEFAULT: (none)
OVERRIDES ALLOWED: filename
-k DMASK output bit to set for input saturated samples
DEFAULT: 3
OVERRIDES ALLOWED: an integer mask value
-m Whether input "missing data" are in rows or columns
DEFAULT: row
OVERRIDES ALLOWED: row | col
-n Input namelist file --- not used for CUPID.
DEFAULT: (none)
OVERRIDES ALLOWED: filename
-q "yes" enables MIPS24 0 -- NaN processing -- Not used for CUPID.
DEFAULT: no
OVERRIDES ALLOWED: no | yes
-r Number of planes to remove from bottom of the data cube.
DEFAULT: 0
OVERRIDES ALLOWED: integer
-s Input sample value indicating saturation.
DEFAULT: 32767
OVERRIDES ALLOWED: an integer
-t "no" disables 2's-complement data conversion.
DEFAULT: yes
OVERRIDES ALLOWED: no | yes
-x [pl#,bit#] Set, at plane number specified by pl#, DMASK bit# specified by bit# --- not used for CUPID
DEFAULT: (none)
OVERRIDES ALLOWED: pl#,bit# (no blanks at comma)
Pipeline calibration files:
(none)
Pipeline namelist files:
(none)
Pipeline input datafiles:
-i Input raw file (FITS)
[pipeline datafile --- override not allowed]
Pipeline output datafiles:
-d Output DMASK file (FITS)
[pipeline datafile --- override not allowed]
-o Output FLUX file (FITS)
[pipeline datafile --- override not allowed]
Pipeline datafiles updated:
(none)
4.9 darkbase Module
This module zeros the dark baseline.
The module is used in the following pipelines: BCD
Constant values:
-b Input BMASK file (FITS)
DEFAULT: (none)
OVERRIDES ALLOWED: name of user's file
-c Input CMASK file (FITS)
DEFAULT: (none)
OVERRIDES ALLOWED: name of user's file
-fb BMASK fatal bitmask
DEFAULT: 0
OVERRIDES ALLOWED: integer bitmask
-fc CMASK fatal bitmask
DEFAULT: 0
OVERRIDES ALLOWED: integer bitmask
-fd DMASK fatal bitmask.
DEFAULT: 16392 (bits # 3, 14)
OVERRIDES ALLOWED: integer bitmask
-fp PMASK fatal bitmask
DEFAULT: 18304 (bits # 7,8,9,10,14)
OVERRIDES ALLOWED: integer bitmask
-o2 Output UNC file (FITS)
DEFAULT: (none)
OVERRIDES ALLOWED: name of user's file
-t1 Trim fraction for averaging. For instance 0.8 means that 0.2 of values are discarded to obtain the mean. Half of discarded samples are the largest, and half are the smallest of the set.
The module is used in the following pipelines: BCDACQ; BCD
Constant values:
-a Path for ancillary files. Specified directory contains error code files and some libraries needed for normal execution
DEFAULT: (none)
OVERRIDES ALLOWED: path to anc. files
-c Readout channel to exclude: 0 = None.
DEFAULT: 0
OVERRIDES ALLOWED: N >= 0
-d Flag for printing debug statements: 0 = Do not print; 1 = Print
DEFAULT: 0
OVERRIDES ALLOWED: 0 or 1
-f1 Trim fraction for averaging. (0.0 = compute median)
DEFAULT: 0.0
OVERRIDES ALLOWED: 0.0 >= X >= 1.0
-f2 Trim fraction for standard deviation. (e.g. 0.9 means that 0.1 of values are discarded to obtain the standard deviation. Half of discarded samples are the largest, and half are the smallest of the set.)
DEFAULT: 0.9
OVERRIDES ALLOWED: 0.0 <= X <= 1.0
-g Flag for applying additive or multiplicative correction: 0 = Additive; 1 = Multiplicative.
DEFAULT: 0
OVERRIDES ALLOWED: 0 or 1
-ia Input dark calibration subsequent to input file (FITS)
DEFAULT: (none)
OVERRIDES ALLOWED: users filename
-ib Input dark calibration preceding input file (FITS)
DEFAULT: (none)
OVERRIDES ALLOWED: users filename
-ic Input canonical dark calibration file (FITS) Required if preceding and subsequent darks are specified.
DEFAULT: (none)
OVERRIDES ALLOWED: users filename
-ig Input GMASK file (FITS)
DEFAULT: (none)
OVERRIDES ALLOWED: users GMASK file
-l Name of log file
DEFAULT: STDOUT.
OVERRIDES ALLOWED: user filename
-mg Threshold Gmask level. See -ig above. Pixels exceeding threshold are ignored in darkdrift computations
DEFAULT: (not used)
OVERRIDES ALLOWED: X
-o2 Output file with amount of correction to subtract from input file (FITS)
DEFAULT: (none)
OVERRIDES ALLOWED: users filename
-p Data plane to compute amount of correction: 1 (current default) = All; 2 = First plane; 3 = Last plane
DEFAULT: 1
OVERRIDES ALLOWED: 1, 2, 0r 3
-t Flag for transposing input file: 1 = Do not transpose input; 2 = Transpose input.
DEFAULT: 1
OVERRIDES ALLOWED: 1 or 2
-te Temperature of uisition of input data
DEFAULT: (not used)
OVERRIDES ALLOWED: X
-tea Temperature of uisition of dark subsequent to data
DEFAULT: (not used)
OVERRIDES ALLOWED: X
-teb Temperature of uisition of dark preceding data
DEFAULT: (not used)
OVERRIDES ALLOWED: X
-ti Relative time of uisition of input data. 8-byte decimal scalar
DEFAULT: (not used)
OVERRIDES ALLOWED: X
-tia Relative time of uisition of dark subsequent to data. 8-byte decimal scalar
DEFAULT: (not used)
OVERRIDES ALLOWED: X
-tib Relative time of uisition of dark preceding data. 8-byte decimal scalar
DEFAULT: (not used)
OVERRIDES ALLOWED: X
-v Flag for verbose output: 0 = No; 1 = Yes
DEFAULT: 0
OVERRIDES ALLOWED: 0 or 1
-vv Flag for superverbose output: 0 = No; 1 = Yes
DEFAULT: 0
OVERRIDES ALLOWED: 0 or 1
Pipeline calibration files:
(none)
Pipeline namelist files:
-n Namelist file
DEFAULT: appropriate darkdrift.nl file in ../cdf/
OVERRIDE ALLOWED: name of user's namelist file
Pipeline input datafiles:
-i Input FLUX file (FITS)
[pipeline datafile --- override not allowed]
-iu Input UNC file (FITS)
[pipeline datafile --- override not allowed]
Pipeline output datafiles:
-o1 Output FLUX file (FITS)
[pipeline datafile --- override not allowed]
-o3 Output table: trim mean, standard deviation, amount of correction, and uncertainty of correction at each read-out channel and each plane
[pipeline datafile --- override not allowed]
-ou Output UNC file (FITS)
[pipeline datafile --- override not allowed]
Pipeline datafiles updated:
(none)
4.11 darkest Module
This module combines a number of dark cube images into one.
The module is used in the following pipelines: DARK
Constant values:
-ac Abnormal file indexes in input list; separated by comma (no space) and increasing
DEFAULT: (none)
OVERRIDES ALLOWED: [untested option]
-ap Abnormal plane indexes with abnormal input file; separated by comma (no space) and increasing
-sb DMASK bit indicating saturation. Used for resetting saturation-corrected samples.
DEFAULT: 4
OVERRIDES ALLOWED: 0 < N < 32767
-sv Ouput saturation value. Samples that were corrected for saturation by SATCOR are reset to this value, if option -a is used.
DEFAULT: 300,000
OVERRIDES ALLOWED: N > 0.0
-v Flag for verbose mode.
DEFAULT: (no)
OVERRIDES ALLOWED: - (minus sign) for yes
Pipeline calibration files:
-p Input PMASK file (FITS)
DEFAULT: appropriate pmask.fits file in ../cal/
OVERRIDE ALLOWED: name of user's calibration file
Pipeline namelist files:
-n Namelist file
DEFAULT: appropriate droopop.nl file in ../cdf/
OVERRIDE ALLOWED: name of user's namelist file
Pipeline input datafiles:
-i1 Input FLUX file (FITS)
[pipeline datafile --- override not allowed]
-i2 Input UNC file (FITS)
[pipeline datafile --- override not allowed]
Pipeline output datafiles:
-o1 Output FLUX file (FITS)
[pipeline datafile --- override not allowed]
-o2 Output UNC file (FITS) --- Note that the uncertainty of droop correction is not propagated; it is written as a header keyword.
[pipeline datafile --- override not allowed]
Pipeline datafiles updated:
-d DMASK file to update (FITS)
[pipeline datafile --- override not allowed]
4.14 droopres Module
This module removes residual droop.
The module is used in the following pipelines: BCD
Constant values:
-c Input CMASK file (FITS)
DEFAULT: (none)
OVERRIDES ALLOWED: user CMASK file
-fb BMASK fatal bitmask
DEFAULT: 16384 (bit 14)
OVERRIDES ALLOWED: N >= 0 bitmask value
-fc CMASK fatal bitmask
DEFAULT: 0
OVERRIDES ALLOWED: N >= 0 bitmask value
-fd DMASK fatal bitmask
DEFAULT: 16392 (bits 3,14)
OVERRIDES ALLOWED: N >= 0 bitmask value
-fp PMASK fatal bitmask
DEFAULT: 18304 (bits 7,8,9,10,14)
OVERRIDES ALLOWED: N >= 0 bitmask value
-t1 Trim fraction for averaging. (e.g. 0.8 means that 0.2 of values are discarded to obtain the mean. Half of discarded samples are the largest, and half are the smallest of the set.)
The module is used in the following pipelines: BCDX; COADDX; BKSUBX
Constant values:
-f Fatal bits for BMASK
DEFAULT: 16384
OVERRIDES ALLOWED: N >= 0 bitmask value
-fix This controls if the NaNs should be replaced with approximated values before doing extraction. A value of 0 means "don't replace", while an integer, N, means that for each NaN pixel, the N rows above and N rows below are averaged column by column within the order, and then a line is fit to these column averages to approximate the NaN.
DEFAULT: 2
OVERRIDES ALLOWED: N >= 0
-full Extraction type; 0 = sub_slit and 1 = full_slit.
DEFAULT: 0 if all of the following are true: (a) the "-w" flag is not explicitly set, (b) this is a LO-RES observation, (c) this is not a LO-RES center position observation
OVERRIDES ALLOWED: 0 or 1
-height1 Sets the wavsamp height. Set to 1 to force the wavsamp height to be 1 pixel; set to 0 to use actual height.
DEFAULT: 0
OVERRIDES ALLOWED: 0 or 1
-l Reference wavelength (in microns) of the aperture width specified with the "-w" flag. A value of 0 selects a constant width extraction aperture.
DEFAULT: use value in psf_fov
OVERRIDES ALLOWED: 0.0 <= X <= 50.0
-nanDrop Wavelength bins with NaNs will be removed from the output spectrum. 0 = set flux to -9999; 1 = drop row from output table
DEFAULT: 0
OVERRIDES ALLOWED: 0 or 1
-norm Normalize the fluxes
0 = no normalization
1 = divide by height of wavsamp rectangle
2 = divide by area of wavsamp rectangle
DEFAULT: ch0,ch2,ch3=1 ch1=0
OVERRIDES ALLOWED: 0 1 2
-ord This refers to the spectral order, and is used for low-resolution extractions only. You can set this to:
0 = (as targeted)
1 = 1
2 = (2+bonus)
99 =(1+2+bonus)
DEFAULT: 0
OVERRIDES ALLOWED: 0 <= N <= 3
-over Output overlay file (used by SPICE)
DEFAULT: (none)
OVERRIDES ALLOWED: name of overlay file to write
-p The calibration table that codes the order to be extracted for each FOVID, the default ridge location, and the extraction aperture width at a fiducial wavelength.
DEFAULT: appropriate lincal_satcor.fits file in ../cal/
OVERRIDE ALLOWED: name of user's calibration file
-p Input PMASK file (FITS)
DEFAULT: appropriate pmask.fits file in ../cal/
OVERRIDE ALLOWED: name of user's calibration file
Pipeline namelist files:
-n Namelist file
DEFAULT: appropriate satcor.nl file in ../cdf/
OVERRIDE ALLOWED: name of user's namelist file
Pipeline input datafiles:
-i Input FLUX file (FITS)
[pipeline datafile --- override not allowed]
-u Input UNC file (FITS)
[pipeline datafile --- override not allowed]
Pipeline output datafiles:
-o Output FLUX file (FITS)
[pipeline datafile --- override not allowed]
-s Output UNC file (FITS)
[pipeline datafile --- override not allowed]
Pipeline datafiles updated:
-d Updated DMASK file (FITS). File is updated for samples corrected for saturation.
[pipeline datafile --- override not allowed]
4.20 imsubtract Module
This module subtracts two images.
The module is used in the following pipelines: BKSUB; BCDACQ
Constant values:
-v verbosity of printed messages
DEFAULT: 0
OVERRIDES ALLOWED: N >= 0
Pipeline calibration files:
-i2 Input second image
DEFAULT: appropriate dcsdark.fits file in ../cal/
OVERRIDE ALLOWED: name of user's calibration file
Pipeline namelist files:
(none)
Pipeline input datafiles:
-i1 Input first image
[pipeline datafile --- override not allowed]
-i1_maskfirst Input mask file
[pipeline datafile --- override not allowed]
-i1_unc Input uncertainty
[pipeline datafile --- override not allowed]
-i2_masksecond Input mask file
[pipeline datafile --- override not allowed]
-i2_unc Second Input uncertainty
[pipeline datafile --- override not allowed]
Pipeline output datafiles:
-o Output image
[pipeline datafile --- override not allowed]
-o_mask Output mask file
[pipeline datafile --- override not allowed]
-o_unc Output uncertainty
[pipeline datafile --- override not allowed]
Pipeline datafiles updated:
(none)
4.21 irs_tune Module
This module converts spectrum from e-/sec to Jy and aligns orders.
The module is used in the following pipelines: BCDX; COADDX; BKSUBX
Constant values:
-a Which tuning components to apply. 'Fluxcon' is the conversion factor from electrons per second to Jy, while 'tune' applies the remaining calibration factors. 1 = fluxcon, 2 = tune, 3 = both
DEFAULT: 3
OVERRIDES ALLOWED: 1 or 2 or 3
-m Tuning mode (tune_up OR tune_down). Virtually all users will wish to use the "tune_down" option. The "tune_down" value means to apply the fluxcon table in the normal way, dividing by the factors. The "tune_up" value means to multiply by the factors. If you run irs_tune with tune_down on untuned data, you get tuned data. If you run irs_tune with tune_up on tuned data, you get the untuned data back.
DEFAULT: tune_down
OVERRIDES ALLOWED: tune_up | tune_down
-noise0 Only for generating 'untuned' spectra for testing purposes. Sigma of offset noise to add.
DEFAULT: 0.0
OVERRIDES ALLOWED: X >= 0.0
-noise1 Only for generating 'untuned' spectra for testing purposes. Sigma of gain noise to add.
DEFAULT: 0.0
OVERRIDES ALLOWED: X >= 0.0
-recom Calls the IRS_RETUNE module, which allows tuning for extended sources. Do not use this if you are tuning for point sources. The value of this option must be the full path to the irs_retune executable.
DEFAULT: (no retune command)
OVERRIDES ALLOWED: (no override)
-reout Retune Output file. Only used when -recom is turned on.
DEFAULT: (no retune output file)
OVERRIDES ALLOWED: (no override)
-reout2 Second retune Output file. Only used when -recom is turned on.
DEFAULT: (no retune file)
OVERRIDES ALLOWED: (no override)
-retab Input retuning table. Only used when -recom is turned on
DEFAULT: (no retune table)
OVERRIDES ALLOWED: (no override)
-retab2 Second input retune table. Only used when -recom is turned on.
DEFAULT: (no retune input table)
OVERRIDES ALLOWED: (no override)
-v Verbosity level of printed messages
DEFAULT: 1
OVERRIDES ALLOWED: N >= 0
Pipeline calibration files:
-t Input tuning calibration table.
DEFAULT: appropriate fluxcon.tbl file in ../cal/
OVERRIDE ALLOWED: name of user's calibration file
Pipeline namelist files:
-n Namelist file
DEFAULT: appropriate irs_tune.nl file in ../cdf/
OVERRIDE ALLOWED: name of user's namelist file
Pipeline input datafiles:
-i Input spectrum (IPAC table file)
[pipeline datafile --- override not allowed]
Pipeline output datafiles:
-o Output spectrum (IPAC table file) flux-calibrated, units of Jy.
[pipeline datafile --- override not allowed]
Pipeline datafiles updated:
(none)
4.22 lineariz Module
This module corrects for non-linearity.
The module is used in the following pipelines: BCD
Constant values:
-q Flag for outputing Quality Assessment header keywords
0 = No QA output (default).
1 = QA output written to header of output file (FITS)
2 = QA output written to header of output file (FITS) and to separate QA multi-plane file (FITS) The latter has, for each linearized ramp: Plane 1: Reduced chi-square of the linear fit. Plane 2: Linear correlation coefficient. Plane 3: Root-mean-square dispersion about the linear fit.
3 = QA output same as 1 with the addition of linear coefficients.
4 (current) = QA output same as 2 with the addition of linear coefficients. The coefficients are written in 3 additional planes: Plane 4: Linear fit slopes. Plane 5: Linear fit intercepts. Plane 6: Number of chi-square degrees of freedom in linear fit.
DEFAULT: 0
OVERRIDES ALLOWED: 0 <= N <= 4
-x Number of lower planes to skip in QA computations.
DEFAULT: appropriate lincal_cmask.fits file in ../cal/
OVERRIDE ALLOWED: name of user's calibration file
-l Input non-linearity calibration file (FITS)
DEFAULT: appropriate lincal.fits file in ../cal/
OVERRIDE ALLOWED: name of user's calibration file
-p Input PMASK file (FITS)
DEFAULT: appropriate pmask.fits file in ../cal/
OVERRIDE ALLOWED: name of user's calibration file
Pipeline namelist files:
-n Namelist file
DEFAULT: appropriate lineariz.nl file in ../cdf/
OVERRIDE ALLOWED: name of user's namelist file
Pipeline input datafiles:
-i Input FLUX file (FITS)
[pipeline datafile --- override not allowed]
-u Input UNC file (FITS)
[pipeline datafile --- override not allowed]
Pipeline output datafiles:
-o Output FLUX file (FITS)
[pipeline datafile --- override not allowed]
-s Output UNC file (FITS)
[pipeline datafile --- override not allowed]
Pipeline datafiles updated:
-m Input DMASK file (FITS)
[pipeline datafile --- override not allowed]
4.23 profile Module
This module generates a wavelength-collapsed average spatial profile table.
The module is used in the following pipelines: BCDX; COADDX; BKSUBX
Constant values:
-c Number of "cuts". The profile module divides each pseudorectangle into this number of cuts and integrates the signal within each cut.
DEFAULT: ch0 =1000, ch2 = 2000; ch1, ch3 = 200
OVERRIDES ALLOWED: 2 <= N <= 2000
-fb BMASK fatal bitmask
DEFAULT: 18432
OVERRIDES ALLOWED: N >= 0 bitmask value
-m Size of sliding median
DEFAULT: 7
OVERRIDES ALLOWED: 1 >= N >= 21 (must be ODD integer)
-ord This selects which orders are included
DEFAULT: all targeted orders
OVERRIDES ALLOWED: up to 14 comma-separated integers, no spaces
-t The calibration table that codes the order to be extracted for each FOVID, the default ridge location, and the extraction aperture width at a fiducial wavelength.
-w The wavsamp file. This file specifies the location of the spectral orders on the array in x-y coordinates. It consists of psuedorectangles, which describe the fractional pixels that comprise each wavelength in the spectrum.
DEFAULT: appropriate wavsamp.tbl file in ../cal/
OVERRIDE ALLOWED: name of user's calibration file
Pipeline namelist files:
-n Namelist file
DEFAULT: appropriate profile.nl file in ../cdf/
OVERRIDE ALLOWED: name of user's namelist file
Pipeline input datafiles:
-b Input BMASK file (FITS)
[pipeline datafile --- override not allowed]
-i Input FLUX file (FITS)
[pipeline datafile --- override not allowed]
Pipeline output datafiles:
-o Output spectrum file (IPAC table file)
[pipeline datafile --- override not allowed]
-q The Output qa file which tells you six things about the profile:
profMaxFlux - max value of dn for all cuts
profLocMaxFlux - location (%) of max dn cut
profMaxStdev - max value of stdev for all cuts
profLocMaxStdev - location (%) of max stdev cut
profMaxRStdev - max value of stdev/dn for all cuts
profLocMaxRStdev - location of max stdev/dn cut
[pipeline datafile --- override not allowed]
Pipeline datafiles updated:
(none)
4.24 radhit Module
This module flags radhits.
The module is used in the following pipelines: BCD
Constant values:
-S Radhit magnitude threshhold for declaring post-radhit samples as bad. Should be capitalized in command line.
DEFAULT: (none)
OVERRIDES ALLOWED: X > 0.0
-d Flag for printing debug statements: 0 = Do not print; 1 = Print.
DEFAULT: 0
OVERRIDES ALLOWED: 0 or 1
-f Bitmask reset integer. Perform logical AND of DMASK samples and this value, to reset selected bits.
DEFAULT: 65019 in second instance of RADHIT (bits 4,9 reset to detect radhits anew)
OVERRIDES ALLOWED: N >= 0 bitmask value
-g Gain (e-/DN).
DEFAULT: 1.0 (already in e-)
OVERRIDES ALLOWED: X > 0.0
-h Maximum number of radhits detectable in a ramp.
DEFAULT: 16
OVERRIDES ALLOWED: N >= 0
-i4 Input readnoise (specified for each pixel) file (FITS) See parameter -r below as alternative.
DEFAULT: (none)
OVERRIDES ALLOWED: users file
-k Maximum segment length to store pseudoinverse.
DEFAULT: (none)
OVERRIDES ALLOWED: N >= 0
-m NominalRHMag or threshold for ratio of signal jump to sample uncertainty to declare a radhit.
DEFAULT: 80.0
OVERRIDES ALLOWED: X >= 0.0
-p RHPriorProb or threshold for probability that a signal jump is a radhit.
DEFAULT: 0.01
OVERRIDES ALLOWED: X >= 0.0
-r Input readnoise, in electrons. One value specified for whole array.
DEFAULT: ch0, ch1 = 26.0; ch2, ch3 = 46.0
OVERRIDES ALLOWED: X >= 0.0
-t Probability threshold at which to declare that a radhit occurred.
DEFAULT: 0.99
OVERRIDES ALLOWED: X >= 0.0
-v Flag for verbose output: 0 = No; 1 = Yes
DEFAULT: 0
OVERRIDES ALLOWED: 0 or 1
-vv Flag for superverbose output: 0 = No; 1 = Yes.
DEFAULT: 0
OVERRIDES ALLOWED: 0 or 1
-w Maximum segment length after decimation.
DEFAULT: (none)
OVERRIDES ALLOWED: N >=1
-x Number of samples to skip at start of ramp for radhit detection.
DEFAULT: ch2=1 others=0
OVERRIDES ALLOWED: N >= 0
-xp Minimum number of ramp samples required for skipping.
DEFAULT: 5 (no samples are skipped for 4-sample ramps)
OVERRIDES ALLOWED: N >= 0
Pipeline calibration files:
-i3 Input PMASK file (FITS)
DEFAULT: appropriate pmask.fits file in ../cal/
OVERRIDE ALLOWED: name of user's calibration file
Pipeline namelist files:
-n Number of post-radhit samples to declare bad.
DEFAULT: appropriate radhit.nl file in ../cdf/
OVERRIDE ALLOWED: name of user's namelist file
Pipeline input datafiles:
-i1 Input FLUX file (FITS)
[pipeline datafile --- override not allowed]
-i2 Input DMASK file (FITS)
[pipeline datafile --- override not allowed]
Pipeline output datafiles:
-l Log file, listing input parameters.
[pipeline datafile --- override not allowed]
-o1 Output radhit probability per sample file (FITS) 3-D cube.
[pipeline datafile --- override not allowed]
-o2 Output sample number per pixel with declared radhits file (FITS) 2-D plane.
[pipeline datafile --- override not allowed]
-o3 Output radhit magnitude per pixel file (FITS) 2-D plane.
[pipeline datafile --- override not allowed]
-o4 Output slope per pixel file (FITS) Peculiarly written in two adjacent planes (where ramp was segmented) of a 3-D cube.
[pipeline datafile --- override not allowed]
-o5 Output DMASK file (FITS) (same file as input DMASK)
[pipeline datafile --- override not allowed]
Pipeline datafiles updated:
(none)
4.25 remove_file Module
This module deletes a file.
The module is used in the following pipelines: BCDACQ; BCD
Constant values:
(none)
Pipeline calibration files:
(none)
Pipeline namelist files:
(none)
Pipeline input datafiles:
- File to be deleted (any type)
[pipeline datafile --- override not allowed]
Pipeline output datafiles:
(none)
Pipeline datafiles updated:
(none)
4.26 ridge Module
This module outputs a table containing the x,y positions of the peak.
The module is used in the following pipelines: BCDX; COADDX; BKSUBX
Constant values:
-c Explicitly select the ridge position (position percent).
DEFAULT: search for peak
OVERRIDES ALLOWED: 0.0 <= X <= 100.0
-f The calibration table that codes the order to be extracted for each FOVID, the default ridge location, and the extraction aperture width at a fiducial wavelength.
-g The width, given in plus-or-minus percent of the array in the cross-dispersion direction, to be searched for the peak, centered on expected position (for LO-RES only). e.g. if you wish to include 25% of the array to either side of the targeted position, giving you a total extraction width of 50% of the array, you would set a value of 25.0.
DEFAULT: 25.0
OVERRIDES ALLOWED: 0.0 < X <= 100.0
-ghi Explicitly specify the high-end cutoff of peak search area
DEFAULT: ch1, ch3 = 75.0; ch0, ch2 use -g
OVERRIDES ALLOWED: glo < X <= 100.0
-glo Explicitly specify the low-end cutoff of peak search area
DEFAULT: ch1, ch3 = 25.0; ch0, ch2 use -g
OVERRIDES ALLOWED: 0.0 <= X < ghi
-m Number of points to use for median filtering (LO-RES only)
DEFAULT: 5
OVERRIDES ALLOWED: N > 0 (must be ODD integer)
-s The number of sigma to require the peak to be above the mean (LO-RES only)
DEFAULT: 3.0
OVERRIDES ALLOWED: X >= 0.0
-v Level of verbosity
DEFAULT: 1
OVERRIDES ALLOWED: N >= 0
Pipeline calibration files:
-i Wavsamp file
DEFAULT: appropriate wavsamp.tbl file in ../cal/
OVERRIDE ALLOWED: name of user's calibration file
Pipeline namelist files:
-n Namelist file
DEFAULT: appropriate ridge.nl file in ../cdf/
OVERRIDE ALLOWED: name of user's namelist file
Pipeline input datafiles:
-p Input profile file (IPAC ASCII table file)
[pipeline datafile --- override not allowed]
Pipeline output datafiles:
-o Output ridge file (IPAC table file) (contains x,y position of the peak for each order and wavelength)
[pipeline datafile --- override not allowed]
Pipeline datafiles updated:
(none)
4.27 rowdroop Module
This module corrects for droop per row.
The module is used in the following pipelines: BCD
Constant values:
-b Input BMASK file (FITS)
DEFAULT: (none)
OVERRIDES ALLOWED: user's BMASK file
-c Input CMASK file (FITS).
DEFAULT: (none)
OVERRIDES ALLOWED: user's CMASK file
-fb BMASK fatal bitmask
DEFAULT: 0
OVERRIDES ALLOWED: integer bit mask
-fc CMASK fatal bitmask
DEFAULT: 0
OVERRIDES ALLOWED: integer bit mask
-fd DMASK fatal bitmask
DEFAULT: 0
OVERRIDES ALLOWED: integer bit mask
-fp PMASK fatal bitmask
DEFAULT: 0
OVERRIDES ALLOWED: integer bit mask
-r1 Row droop coupling constant for read-out channel 1
DEFAULT: ch0 = 4.5E-5; others = 0.0
OVERRIDES ALLOWED: X >= 0.0
-r2 Row droop coupling constant for read-out channel 2
DEFAULT: ch0 = 4.5E-5; others = 0.0
OVERRIDES ALLOWED: X >= 0.0
-r3 Row droop coupling constant for read-out channel 3
DEFAULT: ch0 = 4.5E-5; others = 0.0
OVERRIDES ALLOWED: X >= 0.0
-r4 Row droop coupling constant for read-out channel 4
DEFAULT: ch0 = 4.5E-5; others = 0.0
OVERRIDES ALLOWED: X >= 0.0
-ru Output uncertainty in the amount of row droop. File (FITS)
DEFAULT: (none)
OVERRIDES ALLOWED: name for output file
-u1 Row droop coupling constant uncertainty for read-out channel 1
DEFAULT: ch0 = 6.8E-6; others = 0.0
OVERRIDES ALLOWED: X >= 0.0
-u2 Row droop coupling constant uncertainty for read-out channel 2
DEFAULT: ch0 = 6.8E-6; others = 0.0
OVERRIDES ALLOWED: X >= 0.0
-u3 Row droop coupling constant uncertainty for read-out channel 3
DEFAULT: ch0 = 6.8E-6; others = 0.0
OVERRIDES ALLOWED: X >= 0.0
-u4 Row droop coupling constant uncertainty for read-out channel 4
DEFAULT: ch0 = 6.8E-6; others = 0.0
OVERRIDES ALLOWED: X >= 0.0
-v Flag for verbose mode. Include in the command line, without argument
DEFAULT: no
OVERRIDES ALLOWED: use minus (-) for verbose
Pipeline calibration files:
-p Input PMASK file (FITS)
DEFAULT: appropriate pmask.fits file in ../cal/
OVERRIDE ALLOWED: name of user's calibration file
Pipeline namelist files:
-n Namelist file
DEFAULT: appropriate rowdroop.nl file in ../cdf/
OVERRIDE ALLOWED: name of user's namelist file
Pipeline input datafiles:
-id Input FLUX file (FITS)
[pipeline datafile --- override not allowed]
-iu Input UNC file (FITS)
[pipeline datafile --- override not allowed]
-md Input saturation-corrected file (FITS) Amount of row droop is computed from this file, and is then subtracted from main input file.
[pipeline datafile --- override not allowed]
-mu Input uncertainty for saturation-corrected file (FITS)
[pipeline datafile --- override not allowed]
Pipeline output datafiles:
-od Output FLUX file (FITS)
[pipeline datafile --- override not allowed]
-ou Output UNC file (FITS)
[pipeline datafile --- override not allowed]
Pipeline datafiles updated:
-d Input DMASK file (FITS)
[pipeline datafile --- override not allowed]
4.28 slope_finder Module
This module computes slope estimates of ramps.
The module is used in the following pipelines: BCD
Constant values:
-df0 DMASK fatal bitmask, for samples that are good, but where delta from previous sample is bad
DEFAULT: = 512 (bit 9)
OVERRIDES ALLOWED: N > 0 bitmask value
-df1 DMASK fatal bitmask
DEFAULT: = 30728 (bits 3,11,12,13,14)
OVERRIDES ALLOWED: N > 0 bitmask value
-dfX DMASK fatal bitmask for radhit samples
DEFAULT: = 512 (bit 9)
OVERRIDES ALLOWED: N > 0 bitmask value
-gain Gain (e-/DN)
DEFAULT: 4.6
OVERRIDES ALLOWED: X >= 0.0
-m Mapping of bits from input DMASK to output BMASK. (e.g. 3:2+9:3+12:4+6:6+13:10+14:11 means DMASK bit 3 set yields BMASK bit 2 set; DMASK bit 9 yields BMASK bit 3, etc)
DEFAULT: 3:2+9:3+12:4+6:6+13:10+14:11
OVERRIDES ALLOWED: similar character string
-mr Minimum number of samples in a ramp or sub-ramp
DEFAULT: 2
OVERRIDES ALLOWED: N >= 0
-o2_dual_flux Output 2-plane file (FITS) with mean pair-wise slopes before and after outlier rejection. Use for debug purposes.
DEFAULT: (none)
OVERRIDES ALLOWED: name of user file
-o2_dual_unc Output 2-plane file (FITS) with mean pair-wise slope uncertainties before and after outlier rejection. Use for debug purposes.
DEFAULT: (none)
OVERRIDES ALLOWED: name of user file
-o2_flux Output file (FITS) with mean pair-wise slopes after outlier rejection. Use for debug purposes.
DEFAULT: (none)
OVERRIDES ALLOWED: name of user file
-o2_pre_flux Output file (FITS) with mean pair-wise slopes before outlier rejection. Use for debug purposes.
DEFAULT: (none)
OVERRIDES ALLOWED: name of user file
-o2_pre_unc Output file (FITS) with mean pair-wise slope uncertainties before outlier rejection. Use for debug purposes.
DEFAULT: (none)
OVERRIDES ALLOWED: name of user file
-o2_unc Output file (FITS) with mean pair-wise slope uncertainties after outlier rejection. Use for debug purposes.
DEFAULT: (none)
OVERRIDES ALLOWED: name of user file
-o_dual_flux Output 2-plane file (FITS) with linear fit slopes before and after outlier rejection. Use for debug purposes.
DEFAULT: (none)
OVERRIDES ALLOWED: name of user file
-o_dual_unc Output 2-plane file (FITS) with linear fit slope uncertainties before and after outlier rejection. Use for debug purposes.
DEFAULT: (none)
OVERRIDES ALLOWED: name of user file
-o_info_outlier Output file (FITS) with number of sample pairs or deltas: Plane 1 is before outlier rejection; Plane 2 is after 1 Outlier-rejection iteration; Plane 3 is after 2 iterations; etc. Value set to -1 when no outliers found. Use for debug purposes.
DEFAULT: (none)
OVERRIDES ALLOWED: name of user file
-o_info_radhit Output file (FITS) with radhit and slope information: Plane 1 is size of delta at the radhit; Plane 2 is slope before radhit; Plane 3 is slope after radhit; Plane 4 is number of radhits in ramp. Use for debug purposes.
DEFAULT: (none)
OVERRIDES ALLOWED: name of user file
-o_pre_flux Output file (FITS) with linear fit slopes before outlier rejection. Use for debug purposes.
DEFAULT: (none)
OVERRIDES ALLOWED: name of user file
-o_pre_unc Output file (FITS) with linear fit slope uncertainties before outlier rejection. Use for debug purposes.
DEFAULT: (none)
OVERRIDES ALLOWED: name of user file
-pf PMASK fatal bitmask
DEFAULT: 32640 (bits 7,8,9,10,11,12,13,14)
OVERRIDES ALLOWED: N > 0 bitmask value
-radhit_maxdel Maximum number of samples to delete after a radhit
DEFAULT: 16 (meaning all samples after radhit deleted)
OVERRIDES ALLOWED: N >= 0
-radhit_thresh Maximum slope (e-/sec) for deleting samples after a radhit
DEFAULT: 500.0 (samples after radhit are deleted only for faint pixels)
OVERRIDES ALLOWED: X > 0.0
-rej_iter Maximum number of outlier rejection iterations. Pair-wise slopes are averaged, and those differring from the mean by more than a factor of the standard deviation (see below) are rejected in one iteration.
DEFAULT: 1
OVERRIDES ALLOWED: N >= 0
-rej_min Minimum number of deltas or pair-wise sample differences, to perform outlier rejection iteration.
DEFAULT: 2
OVERRIDES ALLOWED: N >= 0
-rej_nsig Factor, in units of standard deviation of slope, for rejecting a pair-wise slope during slope-averaging and outlier rejection iteration.
DEFAULT: 2.0
OVERRIDES ALLOWED: X > 0.0
-sat_pct Percent threshold of saturated pixels in either peakup array to reject entire plane (ch0 only)
DEFAULT: 105.0 (entire planes are never rejected for this reason)
OVERRIDES ALLOWED: X > 0.0
-skip_minramp Minimum ramp size to skip samples at the start of a ramp
DEFAULT: 9 (samples skipped at start only for 16 sample ramps)
OVERRIDES ALLOWED: N >= 0
-skip_n Number of samples to skip at the start of a ramp
DEFAULT: 1
OVERRIDES ALLOWED: N >= 0
-t Output slope renormalization divisor (integration time in sec.)
DEFAULT: FITS keywords GRPTIME + RAMPTIME
OVERRIDES ALLOWED: X > 0.0
-v Level of verbose output: 0 = No output; 1 = minimal; 2 = nominal; 3 = Print outlier info.; 4 = Print slopes before and after radhits; 5 = Print coordinates of radhit samples
DEFAULT: 2
OVERRIDES ALLOWED: 0 <= N <= 5
Pipeline calibration files:
-ip Input PMASK file (FITS)
DEFAULT: appropriate pmask.fits file in ../cal/
OVERRIDE ALLOWED: name of user's calibration file
Pipeline namelist files:
-n Namelist file
DEFAULT: appropriate slope_finder.nl file in ../cdf/
OVERRIDE ALLOWED: name of user's namelist file
Pipeline input datafiles:
-i Input FLUX file (FITS)
[pipeline datafile --- override not allowed]
-id Input DMASK file (FITS)
[pipeline datafile --- override not allowed]
-iu Input UNC file (FITS)
[pipeline datafile --- override not allowed]
Pipeline output datafiles:
-o_flux Output FLUX file (FITS)
[pipeline datafile --- override not allowed]
-o_unc Output UNC file (FITS)
[pipeline datafile --- override not allowed]
-ob Output BMASK file (FITS)
[pipeline datafile --- override not allowed]
Pipeline datafiles updated:
(none)
4.29 slremov Module
This module removes stray light.
The module is used in the following pipelines: BCD
Constant values:
-c Input CMASK file (FITS)
DEFAULT: (none)
OVERRIDES ALLOWED: user filename
-d Input DMASK file (FITS)
DEFAULT: (none)
OVERRIDES ALLOWED: user filename
-e1 Output UNC file (FITS)
DEFAULT: (none)
OVERRIDES ALLOWED: user filename
-e2 Output UNC file (FITS) not corrected for stray-light.
DEFAULT: (none)
OVERRIDES ALLOWED: user filename
-fb BMASK fatal bitmask
DEFAULT: 28672 (bits 12,13,14)
OVERRIDES ALLOWED: N >= 0 bitmask value
-fc CMASK fatal bitmask
DEFAULT: 0
OVERRIDES ALLOWED: N >= 0 bitmask value
-fd DMASK fatal bitmask
DEFAULT: 0
OVERRIDES ALLOWED: N >= 0 bitmask value
-fp PMASK fatal bitmask
DEFAULT: 18304 (bits 7,8,9,10,14)
OVERRIDES ALLOWED: N >= 0 bitmask value
-i2 Input UNC file (FITS)
DEFAULT: (none)
OVERRIDES ALLOWED: user filename
-o2 Output file (FITS) not corrected for stray-light
DEFAULT: (none)
OVERRIDES ALLOWED: user filename
-s Critical signal-to-noise ratio to qualify a model fit
DEFAULT: 0.0 (not used)
OVERRIDES ALLOWED: X
-t Flag indicating no-pedestal-subtraction mode if = 1
DEFAULT: 1
OVERRIDES ALLOWED: 0 or 1
-u Column number separating peak-up arrays and spectral orders
DEFAULT: 84
OVERRIDES ALLOWED: N
-v Flag for verbose mode
DEFAULT: (not verbose)
OVERRIDES ALLOWED: "-" (minus) for verbose
-x Column number of the geometric center of Lmask regions
DEFAULT: 60
OVERRIDES ALLOWED: N
Pipeline calibration files:
-a Input table file containing stray light decay constants.
DEFAULT: appropriate slt_coeffs.tbl file in ../cal/
OVERRIDE ALLOWED: name of user's calibration file
-l Input Lmask file (FITS) Defines SL regions between orders where stray light correction is measured.
DEFAULT: appropriate lmask.fits file in ../cal/
OVERRIDE ALLOWED: name of user's calibration file
-p Input PMASK file (FITS)
DEFAULT: appropriate pmask.fits file in ../cal/
OVERRIDE ALLOWED: name of user's calibration file
Pipeline namelist files:
-n Namelist file
DEFAULT: appropriate slremov.nl file in ../cdf/
OVERRIDE ALLOWED: name of user's namelist file
Pipeline input datafiles:
-i1 Input FLUX file (FITS)
[pipeline datafile --- override not allowed]
Pipeline output datafiles:
-o1 Output FLUX file (FITS)
[pipeline datafile --- override not allowed]
Pipeline datafiles updated:
-b Input BMASK file (FITS)
[pipeline datafile --- override not allowed]
4.30 snest_irs Module
This module will compute uncertainty file.
The module is used in the following pipelines: BCD
Constant values:
-a Output file (FITS) adjusted by adding ramp offsets, unique to each ramp. This calculation is internal and not propagated. Currently not output for CUPID.
DEFAULT: (none)
OVERRIDES ALLOWED: filename
-confusion Confusion noise, for use in this module only.
DEFAULT: 0
OVERRIDES ALLOWED: C >= 0.0
-d Input DMASK file (FITS) --- Not used for CUPID.
DEFAULT: (none)
OVERRIDES ALLOWED: filename
-dmask_fatal Fatal integer bitmask for DMASK --- not used for CUPID
DEFAULT: 30728 (bits #3, 11, 12, 13, 14)
OVERRIDES ALLOWED: integer bitmask
-gain Gain factor, for noise calculation in this module only (electron/DN)
DEFAULT: 4.6
OVERRIDES ALLOWED: X >= 0.0
-nd Multiple of "delta" (mean pairwise sample difference) for outlier rejection in a ramp. Internal calculation only, not propagated.
DEFAULT: 3.0
OVERRIDES ALLOWED: floating point number
-readnoise Read noise, for use in this module only (electron)
