Spitzer Documentation & Tools
CUPID User's Guide

Chapter 4. The Modules

The following modules are available in CUPID:

 

·         basecal          --- perform baseline calibration

·         coadd2d        --- coadd a number of 2D images into one using trimmed averaging

·         copy_file      --- copy a file

·         cropfits         --- cut out a subimage

·         crosstalk       --- remove crosstalk

·         cubesub        --- subtract the dark

·         cvti2r4          --- convert from integer to floating point

·         darkbase       --- zero the dark baseline

·         darkdrift       --- remove "jail bars"

·         darkest          --- combine a number of dark cube images into one

·         dntoflux        --- convert from DN to electrons

·         droopop        --- correct for global droop

·         droopres       --- remove residual droop

·         extract           --- extract a 1D spectrum table

·         flatap            --- apply FLAT

·         fpgen            --- generate final product

·         hdrupd8        --- update header keywords

·         imagest         --- correct saturated values

·         imsubtract     --- subtract two images

·         irs_tune         --- convert spectrum from e-/sec to Jy and align orders

·         lineariz          --- correct for non-linearity

·         profile           --- generate a wavelength-collapsed average spatial profile table

·         radhit            --- flag radhits

·         remove_file --- delete a file

·         ridge             --- output a table containing the x,y positions of the peak

·         rowdroop      --- correct for droop per row

·         slope_finder    --- compute slope estimates of ramps

·         slremov         --- remove stray light

·         snest_irs        --- compute uncertainty file

·         tbl2fits          --- create a FITS binary table from an ASCII IPAC table

·         velocity         --- add velocity header keywords

4.1            basecal Module

This module performs baseline calibration.

 

The module is used in the following pipelines:  BCD

 

Constant values:

 

-b      Output baseline image

         DEFAULT:  (none)

         OVERRIDES ALLOWED:  user filename

 

-m     maximum pixel value to use

         DEFAULT:  9.9E9

         OVERRIDES ALLOWED:  X > 0.0

 

-p      pmask file

         DEFAULT:  (none)

          OVERRIDES ALLOWED:  user filename

 

-r       RSS baseline and input sigmas

         DEFAULT:  no

         OVERRIDES ALLOWED:  yes | no

 

-u      Input uncertainty data cube

         DEFAULT:  (none)

         OVERRIDES ALLOWED:  user filename

 

-v      Output uncertainty data cube

         DEFAULT:  (none)

          OVERRIDES ALLOWED:  user filename

 

-x      number of samples to skip

         DEFAULT:  0

         OVERRIDES ALLOWED:  N >= 0

 

 

Pipeline calibration files:

 

-z      Input umask file

         DEFAULT: appropriate umask.fits file in ../cal/

         OVERRIDE ALLOWED: name of user's calibration file

 

Pipeline namelist files:

 

-n      NAMELIST file

         DEFAULT: appropriate basecal.nl file in ../cdf/

         OVERRIDE ALLOWED: name of user's namelist file

 

Pipeline input datafiles:

 

-i       Input data cube

         [pipeline datafile --- override not allowed]

 

Pipeline output datafiles:

 

-o      Output data cube

         [pipeline datafile --- override not allowed]

 

Pipeline datafiles updated:

 

-d      Input dmask file

         [pipeline datafile --- override not allowed]

4.2            coadd2d Module

This module coadds a number of 2D images into one using trimmed averaging.

 

The module is used in the following pipelines:  COADD

 

Constant values:

 

-D           Debugging mode: adds debugging data

               DEFAULT:  0

               OVERRIDES ALLOWED:  N >= 0

 

-HELP     Print out an example NAMELIST file

               DEFAULT:  normal run

               OVERRIDES ALLOWED:  [not to override]

 

-V           Verbose mode: more functional info

               DEFAULT:  0

               OVERRIDES ALLOWED:  N >= 0

 

-ag          Pixels with fewer data points than this value are marked in AMASK file.

               DEFAULT:  1

               OVERRIDES ALLOWED:  N >= 0

 

-bf          BMASK fatal bits

               DEFAULT:  28928 

               OVERRIDES ALLOWED:  N >= 0 bitmask value

 

-cf           Clip at most this fraction of the data (0.0 == no trimming)

               DEFAULT:  0.2

               OVERRIDES ALLOWED:  0.0 < X < 100.0

 

-cm         Clip above Multiple of MedAbsDev

               DEFAULT:  5.0

               OVERRIDES ALLOWED:  X > 0.0

 

-h1          Propagate *all* the headers from the first file in input FLUX files

               DEFAULT:  yes

               OVERRIDES ALLOWED:  [cannot override]

 

-ls           Input files lists 0 = in separate files; 1 = in namelist

               DEFAULT:  0

               OVERRIDES ALLOWED:  0 or 1

 

-pf          PMASK fatal bits

               DEFAULT:  18176 

               OVERRIDES ALLOWED:  N >= 0 bitmask value

 

-pm         List of input (FITS) PMASK files

               DEFAULT:  (none)

               OVERRIDES ALLOWED:  user list of PMASK files

 

-wt          Calculate weighted statistics? (0=no 1=yes)

               DEFAULT:  0 if no FMASK file, else 1

               OVERRIDES ALLOWED:  0 or 1

 

 

Pipeline calibration files:

 

-fm         FMASK (FOV Mask) calibration file (FITS)

               DEFAULT: appropriate fovmask.fits file in ../cal/

               OVERRIDE ALLOWED: name of user's calibration file

 

Pipeline namelist files:

 

-n            Namelist File

               DEFAULT: appropriate coadd2d.nl file in ../cdf/

               OVERRIDE ALLOWED: name of user's namelist file

 

Pipeline input datafiles:

 

-bm         List of (FITS) BMASK files

               [pipeline datafile --- override not allowed]

 

-di           List of input (FITS) FLUX files

               [pipeline datafile --- override not allowed]

 

-si           List of input (FITS) UNC files

               [pipeline datafile --- override not allowed]

 

Pipeline output datafiles:

 

-am         Output AMASK file (FITS)

               [pipeline datafile --- override not allowed]

 

-do          Output FLUX file (FITS)

               [pipeline datafile --- override not allowed]

 

-so          Output UNC file (FITS)

               [pipeline datafile --- override not allowed]

 

-wo         Output ASCII file of weights and filenames

               [pipeline datafile --- override not allowed]

 

Pipeline datafiles updated:

 

(none)

4.3            copy_file Module

This module copies a file.

 

The module is used in the following pipelines:  BCD

 

Constant values:

 

(none)

 

Pipeline calibration files:

 

(none)

 

Pipeline namelist files:

 

(none)

 

Pipeline input datafiles:

 

-i             Input file (any type)

               [pipeline datafile --- override not allowed]

 

Pipeline output datafiles:

 

-o            Output file (any type)

               [pipeline datafile --- override not allowed]

 

Pipeline datafiles updated:

 

(none)

4.4            cropfits Module

This module cuts out a subimage.

 

The module is used in the following pipelines:  BCDACQ; CUTOUT

 

Constant values:

 

-a         Ancillary file path

            DEFAULT:  current directory

            OVERRIDES ALLOWED:  (not used)

 

-b         Print debug statements

            DEFAULT:  0

            OVERRIDES ALLOWED:  0 or 1

 

-h         height

            DEFAULT:  56

            OVERRIDES ALLOWED:  1 <= N <= image size

 

-i1        start i (from 1)

            DEFAULT:  blue=87 red=86

            OVERRIDES ALLOWED:  1 <= N <= image size

 

-j1        start j (from 1)

            DEFAULT:  blue=4 red=66 

            OVERRIDES ALLOWED:  1 <= N <= image size

 

-l          Log filename

            DEFAULT:  stdout 

            OVERRIDES ALLOWED:  name of user's log file

 

-m        Pixel orientation map

            DEFAULT:  (none)

            OVERRIDES ALLOWED:  user output filename

 

-t          IPAC table filename

            DEFAULT:  (none)

            OVERRIDES ALLOWED:  user output filename

 

-v         Verbose output

            DEFAULT:  1

            OVERRIDES ALLOWED:  0 or 1

 

-vv       SuperVerbose output

            DEFAULT:  0

            OVERRIDES ALLOWED:  0 or 1

 

-w        width

            DEFAULT:  41

            OVERRIDES ALLOWED:  1 <= N <= image size

 

-z         Data plane to process (1=all, 2=first, 3=last; Default is all)

            DEFAULT:  1 

            OVERRIDES ALLOWED:  1, 2 or 3

 

Pipeline calibration files:

 

(none)

 

Pipeline namelist files:

 

-n         Namelist file

            DEFAULT: appropriate cropfits_r.nl file in ../cdf/

            OVERRIDE ALLOWED: name of user's namelist file

 

Pipeline input datafiles:

 

-i          Input image (FITS)

            [pipeline datafile --- override not allowed]

 

Pipeline output datafiles:

 

-o         Output image (FITS)

            [pipeline datafile --- override not allowed]

 

Pipeline datafiles updated:

 

(none)

4.5            cropfits2 Module

This module will cut out a subimage, and update WCS info.

 

The module is used in the following pipelines:    CUTOUT    BCDACQ

 

Constant values:

 

-color   which peakup array
            DEFAULT: blue='b' or red='r'     

            OVERRIDE ALLOWED:

 

-v         verbosity - level of printed messages
            DEFAULT: 1     

            OVERRIDE ALLOWED:

 

-x0       starting X coordinate
            DEFAULT: blue=87 red=86     

            OVERRIDE ALLOWED:

 

-xn       number of pixels in X direction
            DEFAULT: blue=4 red=66     

            OVERRIDE ALLOWED:

 

-y0       starting Y coordinate
            DEFAULT: blue=41 red=41     

            OVERRIDE ALLOWED:

 

-yn       number of pixels in Y direction
            DEFAULT: blue=56 red=56     

            OVERRIDE ALLOWED:

 

Pipeline calibration files:

 

                  (none)

 

Pipeline namelist files:

 

-n       Namelist file
          DEFAULT: appropriate cropfits2_r.nl file in ../cdf/     

          OVERRIDE ALLOWED: name of user's namelist file

 

Pipeline input datafiles:

 

-i       Input image (FITS)
         [pipeline datafile --- override not allowed]

 

Pipeline output datafiles:

 

-o       Output image (FITS)
          [pipeline datafile --- override not allowed]

 

Pipeline datafiles updated:

 

                (none)

4.6            crosstalk Module

This module removes crosstalk.

 

The module is used in the following pipelines:  BCD

 

Constant values:

 

-a0       Value of initial guess for Lorentzian-like slope alpha

            DEFAULT:  4.3

            OVERRIDES ALLOWED:  floating point value

 

-fb       BMASK fatal bitmask

            DEFAULT:  24576 (bits 13,14)

            OVERRIDES ALLOWED:  N >= 0 bitmask value

 

-o1       Output file (FITS) not corrected for cross-talk

            DEFAULT:  (none)

            OVERRIDES ALLOWED:  user filename

 

-t          Threshold signal, in units of standard deviation, to apply correction

            DEFAULT:  2.0

            OVERRIDES ALLOWED:  floating point value

 

-v         Level of verbose output (higher for more output)

            DEFAULT:  0

            OVERRIDES ALLOWED:  N >= 0

 

-w0      Value of initial guess for order shape width (HWHM)

            DEFAULT:  1.5

            OVERRIDES ALLOWED:  floating point value

 

Pipeline calibration files:

 

-i3        Input Omask (spectral order regions) file (FITS)

            DEFAULT: appropriate omask.fits file in ../cal/

            OVERRIDE ALLOWED: name of user's calibration file

 

Pipeline namelist files:

 

-n         Namelist file

            DEFAULT: appropriate crosstalk.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:

 

-o2       Output FLUX file (FITS)

            [pipeline datafile --- override not allowed]

 

-o3       Output residual file (FITS) for amount of cross-talk correction that is subtracted.

            [pipeline datafile --- override not allowed]

 

-o4       Output UNC file (FITS)

            [pipeline datafile --- override not allowed]

 

Pipeline datafiles updated:

 

-b         Input BMASK file (FITS)

            [pipeline datafile --- override not allowed]

4.7            cubesub Module

This module subtracts the dark.

 

The module is used in the following pipelines:  BCD

 

Constant values:

 

-b         Input BMASK file (FITS)

            DEFAULT:  (none)

            OVERRIDES ALLOWED:  name of user file

 

-fb       BMASK fatal bitmask

            DEFAULT:  0

            OVERRIDES ALLOWED:  integer bitmask value

 

-fc        CMASK fatal bitmask

            DEFAULT:  8192 (bit # 13)

            OVERRIDES ALLOWED:  integer bitmask value

 

-fd       DMASK fatal bitmask

            DEFAULT:  16392 (bits # 3,14)

            OVERRIDES ALLOWED:  integer bitmask value

 

-fp       PMASK fatal bitmask

            DEFAULT:  18176 (bits # 8,9,10,14)

            OVERRIDES ALLOWED:  integer bitmask value

 

-q         Flag for outputting Quality Assessment header keywords.  Include in the command line, without argument, to output the keywords.

            DEFAULT:  no

            OVERRIDES ALLOWED:  "-" (minus) for yes

 

-s         Operation mode: 1 = no scaling, 2 = scale dark by 1/GAIN, 3 = scale dark by T_INT*plane_number/GAIN

            DEFAULT:  1

            OVERRIDES ALLOWED:  1 <= N <= 3

 

-v         Flag for verbose mode.  Include in the command line, without argument.

            DEFAULT:  no

            OVERRIDES ALLOWED:  "-" (minus) for yes

 

Pipeline calibration files:

 

-c         Input CMASK (dark calibration status) file (FITS)

            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.

            DEFAULT:  0.80 

            OVERRIDES ALLOWED:  0.00 < X <= 1.00

 

-t2        Trim fraction for standard deviation

            DEFAULT:  0.80 

            OVERRIDES ALLOWED:  0.00 < X <= 1.00

 

-v         Flag for verbose mode.

            DEFAULT:  non-verbose

            OVERRIDES ALLOWED:  "-" (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

 

-u         Input Umask file (FITS) Defines unilluminated region(s)

            DEFAULT: appropriate umask.fits file in ../cal/

            OVERRIDE ALLOWED: name of user's calibration file

 

Pipeline namelist files:

 

-n         Namelist file

            DEFAULT: appropriate darkbase.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]

 

Pipeline datafiles updated:

 

-d         Input DMASK file (FITS)

            [pipeline datafile --- override not allowed]

4.10       darkdrift Module

This module removes "jail bars".

 

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

            DEFAULT:  (none)

            OVERRIDES ALLOWED:  [untested option]

 

-c         Input CMASK filename (Calibration image status)

            DEFAULT:  (none)

            OVERRIDES ALLOWED:  user's CMASK file

 

-e         Factor of median distance for unsymmetrical trim

            DEFAULT:  5.0 

            OVERRIDES ALLOWED:  X > 0.0

 

-fc        CMASK fatal bit templates; separated by comma (no space)

            DEFAULT:  (none)

            OVERRIDES ALLOWED:  [untested option]

 

-fd       DMASK fatal bit templates; separated by comma (no space)

            DEFAULT:  (none)

            OVERRIDES ALLOWED:  [untested option]

 

-fp       PMASK fatal bit templates; separated by comma (no space)

            DEFAULT:  (none)

            OVERRIDES ALLOWED:  [untested option]

 

-p         Input PMASK filename (hardware status)

            DEFAULT:  (none)

            OVERRIDES ALLOWED:  user's PMASK file

 

-q         QA FITS header writer 0=off 1=on

            DEFAULT:  0  

            OVERRIDES ALLOWED:  0 or 1

 

-r          Read noise per pixel

            DEFAULT:  30.0  

            OVERRIDES ALLOWED:  X >= 0.0

 

-t1        Fraction for symmetrical trim-average

            DEFAULT:  1.0

            OVERRIDES ALLOWED:  0.0 <= X <= 1.0

 

-t2        Symmetrical trim fraction for standard deviation

            DEFAULT:  1.0 

            OVERRIDES ALLOWED:  0.0 <= X <= 1.0

 

-u         Fraction for unsymmetrical trim; default

            DEFAULT:  0.0 

            OVERRIDES ALLOWED:  0.0 <= X <= 1.0

 

-v         Flag for verbose mode.

            DEFAULT:  (no)

            OVERRIDES ALLOWED:  - (minus sign) for yes

 

Pipeline calibration files:

 

                  (none)

 

Pipeline namelist files:

 

-n               Namelist file

                  DEFAULT: appropriate darkest_offline.nl file in ../cdf/

                  OVERRIDE ALLOWED: name of user's namelist file

 

Pipeline input datafiles:

 

-d               File with list of input DMASK files (DMASK = 'DCE pixel status')

                  [pipeline datafile --- override not allowed]

 

-i1              File with list of input FLUX images

                  [pipeline datafile --- override not allowed]

 

-i2              File with list of input UNC images

                  [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]

 

-o3             Output CMASK file (FITS)

                  [pipeline datafile --- override not allowed]

 

Pipeline datafiles updated:

 

                  (none)

4.12       dntoflux Module

This module converts from DN to electrons.

 

The module is used in the following pipelines:  BCDACQ; BCD; CUTOUT

 

Constant values:

 

-a         Path for ancillary files.  Specified directory contains error code files and some libraries needed for normal execution.

            DEFAULT:  (none)

            OVERRIDES ALLOWED:  user's path

 

-bd       Threshold for DMASK fatal masking.  --- not used for CUPID.

            DEFAULT:  (not used)

            OVERRIDES ALLOWED:  N >= 0

 

-bp       Threshold for PMASK fatal masking.  --- not used for CUPID.

            DEFAULT:  (not used)

            OVERRIDES ALLOWED:  N >= 0

 

-c         Factor for scaling whole array, if operation code = 0

            DEFAULT:  (not used)

            OVERRIDES ALLOWED:  X > 0.0

 

-c1       Factor for scaling read-out channel 1, if operation code = 1;

            DEFAULT:  4.6 (from FITS keyword)

            OVERRIDES ALLOWED:  X > 0.0

 

-c2       Factor for scaling read-out channel 2, if operation code = 1;

            DEFAULT:  4.6 (from FITS keyword)

            OVERRIDES ALLOWED:  X > 0.0

 

-c3       Factor for scaling read-out channel 3, if operation code = 1;

            DEFAULT:  4.6 (from FITS keyword)

            OVERRIDES ALLOWED:  X > 0.0

 

-c4       Factor for scaling read-out channel 4, if operation code = 1;

            DEFAULT:  4.6 (from FITS keyword)

            OVERRIDES ALLOWED:  X > 0.0

 

-co       Operation code: 0 = Scale array by a single factor; 1 = Scale each read-out channel by a unique factor.

            DEFAULT:  1

            OVERRIDES ALLOWED:  0 <= N <= 1

 

-d         Flag for printing debug statements: 0 = Do not print; 1 = Print.

            DEFAULT:  0 

            OVERRIDES ALLOWED:  0 or 1

 

-ip        Input PMASK file (FITS)

            DEFAULT:  (none)

            OVERRIDES ALLOWED:  user's PMASK file

 

-l    l     Log file;

            DEFAULT:  STDOUT 

            OVERRIDES ALLOWED:  output log file

 

-o2       Output file (FITS) where fatally masked pixels or samples in the PMASK or DMASK are set to NaN.

            DEFAULT:  (none)

            OVERRIDES ALLOWED:  user's output file

 

-p         Code for data plane to process: 1 = All; 2 = First; 3 = Last.

            DEFAULT:  1 

            OVERRIDES ALLOWED:  1 <= N <= 3

 

-s         Specification of output units.  REQUIRED.  Output is written in the BUNIT header keyword as a character string.

            DEFAULT:  e- 

            OVERRIDES ALLOWED:  a character string

 

-t          Code for normalization by the value of header keyword EXPTIME: 0 = Do not normalize; 1 = Normalize.

            DEFAULT:  0  

            OVERRIDES ALLOWED:  0 or 1

 

-u         Input uncertainty of scaling factor.  Required if operation = 0 and -ou option is specified.

            DEFAULT:  (not used)

            OVERRIDES ALLOWED:  X > 0.0

 

-u1       Input uncertainty of scaling factor for read-out channel 1.  Required if operation = 1 and -ou option is specified.

            DEFAULT:  (not used) 

            OVERRIDES ALLOWED:  X > 0.0

 

-u2       Input uncertainty of scaling factor for read-out channel 2.  Required  if operation = 1 and -ou option is specified.

            DEFAULT:  (not used)

            OVERRIDES ALLOWED:  X > 0.0

 

-u3       Input uncertainty of scaling factor for read-out channel 3.  Required if operation = 1 and -ou option is specified.

            DEFAULT:  (not used) 

            OVERRIDES ALLOWED:  X > 0.0

 

-u4       Input uncertainty of scaling factor for read-out channel 4.  Required if operation = 1 and -ou option is specified.

            DEFAULT:  (not used) 

            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

 

Pipeline calibration files:

 

                  (none)

 

Pipeline namelist files:

 

-n               Input namelist file

                  DEFAULT: appropriate dntoflux_r.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              Name DMASK 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]

 

-ou             Output UNC file (FITS)

                  [pipeline datafile --- override not allowed]

 

Pipeline datafiles updated:

 

                  (none)

4.13       droopop Module

This module corrects for global droop.

 

The module is used in the following pipelines:  BCD

 

Constant values:

 

-a         Flag for resetting saturation-corrected samples: 0 = Do not reset; 1 = Reset to the value specified in -sv.

            DEFAULT:  1 

            OVERRIDES ALLOWED:  0 or 1

 

-b         Input BMASK file (FITS)

            DEFAULT:  (none) 

            OVERRIDES ALLOWED:  user's file

 

-c         Input CMASK file (FITS)

            DEFAULT:  (none)

            OVERRIDES ALLOWED:  user's file

 

-e         Uncertainty of droop coupling constant for entire array.

            DEFAULT:  ch0=0.45, ch1=0.49, ch2=0.20, ch3=0.19

            OVERRIDES ALLOWED:  N > 0.00

 

-fb       BMASK fatal bitmask.

            DEFAULT:  0 

            OVERRIDES ALLOWED:  0 < N < 32767

 

-fc        CMASK fatal bitmask.

            DEFAULT:  0 

            OVERRIDES ALLOWED:  0 < N < 32767

 

-fd       DMASK fatal bitmask.

            DEFAULT:  0 

            OVERRIDES ALLOWED:  0 < N < 32767

 

-fp       PMASK fatal bitmask.

            DEFAULT:  0  

            OVERRIDES ALLOWED:  0 < N < 32767

 

-g         Flag for computing amount of droop from the first plane of data cube (or first plane of reference cube, if present).

            DEFAULT:  (no) 

            OVERRIDES ALLOWED:  - (minus sign) for yes

 

-j1        Input reference FLUX file (FITS) Amount of droop is computed from this file, and is then subtracted from main input file.

            DEFAULT:  (none) 

            OVERRIDES ALLOWED:  user's FLUX file

 

-j2        Input reference UNC file (FITS)

            DEFAULT:  (none)

            OVERRIDES ALLOWED:  user's UNC file

 

-q         Flag for outputting Quality Assessment header keywords.  Include in the command line, without argument, to output the keywords.

            DEFAULT:  (yes) 

            OVERRIDES ALLOWED:  (cannot override)

 

-r          Droop coupling constant for entire array (not per pixel)

            DEFAULT:  ch0=0.068, ch1=0.074, ch2=0.030, ch3=0.028

            OVERRIDES ALLOWED:  N > 0.0

 

-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.)

            DEFAULT:  0.8 

            OVERRIDES ALLOWED:  0.0 < X <= 1.0

 

-t2        Trim fraction for standard deviation

            DEFAULT:  0.8 

            OVERRIDES ALLOWED:  0.0 < X <= 1.0

 

-v         Flag for verbose mode

            DEFAULT:  (not verbose)

            OVERRIDES ALLOWED:  "-" (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

 

-u         Input UMASK file (FITS) (defines unilluminated region)

            DEFAULT: appropriate umask.fits file in ../cal/

            OVERRIDE ALLOWED: name of user's calibration file

 

Pipeline namelist files:

 

-n         Namelist file

            DEFAULT: appropriate droopres.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]

 

-d         Input DMASK file (FITS)

            [pipeline datafile --- override not allowed]

 

-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)

            [pipeline datafile --- override not allowed]

 

Pipeline datafiles updated:

 

(none)

4.15       extract Module

This module extracts a 1D spectrum table.

 

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:  ch0, ch2 = ../cal/psf_fov.tbl; ch1, ch3 = (none)

                  OVERRIDES ALLOWED:  user’s psf_fov.tbl file

 

-v               Level of verbosity

                  DEFAULT:  1 

                  OVERRIDES ALLOWED:  N >= 0

 

-w              Width (pixels) of the extraction aperture at the reference wavelength

                  DEFAULT:  ch0, ch2 = use the value given in the psf_fov; ch1, ch3 = use full width of order  

                  OVERRIDES ALLOWED:  X > 0.0

 

Pipeline calibration files:

 

(none)

 

Pipeline namelist files:

 

-n         Namelist file

            DEFAULT: appropriate extract.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]

 

-e         Input UNC file (FITS)

            [pipeline datafile --- override not allowed]

 

-i          Input FLUX file (FITS)

            [pipeline datafile --- override not allowed]

 

-r          Output table from running the RIDGE module in the previous step.

            [pipeline datafile --- override not allowed]

 

Pipeline output datafiles:

 

-o         Output spectrum table (IPAC table file)

            [pipeline datafile --- override not allowed]

 

Pipeline datafiles updated:

 

(none)

4.16       flatap Module

This module applies FLAT.

 

The module is used in the following pipelines:  BCDACQ; BCD

 

Constant values:

 

-cm      CMASK fatal bitmask

            DEFAULT:  444 (bits 2,3,4,5,7,8) 

            OVERRIDES ALLOWED:  N >= 0 bitmask value

 

-ct        Input CMASK for Transmission calibrator flatfield file (FITS)

            DEFAULT:  (none) 

            OVERRIDES ALLOWED:  user filename

 

-dm      BMASK or DMASK fatal bitmask

            DEFAULT:  28672 (bits 12,13,14) 

            OVERRIDES ALLOWED:  N >= 0 bitmask value

 

-l          Output log file

            DEFAULT:  (none) 

            OVERRIDES ALLOWED:  user logfile name

 

-n         Namelist file

            DEFAULT:  (none)  

            OVERRIDES ALLOWED:  user namelist

 

-pm      PMASK fatal bitmask

            DEFAULT:  18176 (bits 8,9,10,14)

            OVERRIDES ALLOWED:  N >= 0 bitmask value

 

-t          Input Transmission calibrator flatfield file (FITS). Flatfield is multiplied pixel-by-pixel by this file before applied.

            DEFAULT:  (none)  

            OVERRIDES ALLOWED:  user filename

 

-v         Flag for verbose mode

            DEFAULT:  (not verbose)  

            OVERRIDES ALLOWED:  "-" (minus) for verbose

 

Pipeline calibration files:

 

-c         Input CMASK (flatfield calibration status) file (FITS)

            DEFAULT: appropriate flatfield_cmask.fits file in ../cal/

            OVERRIDE ALLOWED: name of user's calibration file

 

-f         Input flatfield calibration file (FITS)

            DEFAULT: appropriate flatfield.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:

 

                  (none)

 

Pipeline input datafiles:

 

-i                Input FLUX file (FITS)

                  [pipeline datafile --- override not allowed]

 

-ui              Input UNC file (FITS)

                  [pipeline datafile --- override not allowed]

 

Pipeline output datafiles:

 

-o               Output FLUX file (FITS)

                  [pipeline datafile --- override not allowed]

 

-uo             Output UNC file (FITS)

                  [pipeline datafile --- override not allowed]

 

Pipeline datafiles updated:

 

-d               Input BMASK or DMASK file (FITS)

                  [pipeline datafile --- override not allowed]

4.17       fpgen Module

This module generates the final product.

 

The module is used in the following pipelines:  BCDACQ; BCD

 

Constant values:

 

-b         Remove blocks of blanks (0=no 1=yes)

            DEFAULT:  1 

            OVERRIDES ALLOWED:  0 or 1

 

-h         Copy HISTORY lines too (0=no 1=yes)

            DEFAULT:  1  

            OVERRIDES ALLOWED:  0 or 1

 

-q         'Quiet' mode (0=normal 1=quiet)

            DEFAULT:  1 

            OVERRIDES ALLOWED:  0 or 1

 

Pipeline calibration files:

 

(none)

 

Pipeline namelist files:

 

-t          Reformatting 'template' file

            DEFAULT: appropriate fpg.tpl file in ../cdf/

            OVERRIDE ALLOWED: name of user's namelist file

 

Pipeline input datafiles:

 

-i          Input datafile

            [pipeline datafile --- override not allowed]

 

Pipeline output datafiles:

 

-o         Output datafile

            [pipeline datafile --- override not allowed]

 

Pipeline datafiles updated:

 

(none)

4.18       hdrupd8 Module

This module updates header keywords.

 

The module is used in the following pipelines:  BCDACQ; BCD

 

Constant values:

 

-d         File containing keywords to add or delete

            DEFAULT:  updates from CUPID 

            OVERRIDES ALLOWED:  file with user updates instead

 

-n         Do not add a comment keyword to file

            DEFAULT:  not add  

            OVERRIDES ALLOWED:  (cannot override)

 

Pipeline calibration files:

 

(none)

 

Pipeline namelist files:

 

(none)

 

Pipeline input datafiles:

 

(none)

 

Pipeline output datafiles:

 

(none)

 

Pipeline datafiles updated:

 

-           File to be updated (FITS)

                  [pipeline datafile --- override not allowed]

4.19       imagest Module

This module corrects saturated values.

 

The module is used in the following pipelines:  BCD

 

Constant values:

 

-h         Threshold to tag A/D saturation (equivalent function to cvti2r4) (practically never used in IRS)

            DEFAULT:  9.9e25  

            OVERRIDES ALLOWED:  X >= 0.0

 

-m        Mode of operation: 1 = slope estimation; 2 = saturation correction

            DEFAULT:  2 

            OVERRIDES ALLOWED:  1 or 2

 

-w        Maximum saturation-corrected value for mode 2.

            DEFAULT:  9.9e25  

            OVERRIDES ALLOWED:  X >= 0.0

 

-x         Number of lower planes to skip.

            DEFAULT:  0  

            OVERRIDES ALLOWED:  X >= 0

 

-z         Number of samples after a radhit to skip

            DEFAULT:  0 

            OVERRIDES ALLOWED:  X >= 0

 

Pipeline calibration files:

 

-l          Non-linearity calibration file (FITS)

            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:  0   

            OVERRIDES ALLOWED:  N >= 0

 

Pipeline calibration files:

 

-c         Input CMASK (non-linearity calibration status) file (FITS)

            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.

            DEFAULT:  ch0, ch2 = ../cal/psf_fov.tbl; ch1, ch3 = (none)

            OVERRIDES ALLOWED:  user’s psf_fov.tbl file

 

-v         Level of verbosity

            DEFAULT:  1  

            OVERRIDES ALLOWED:  N >= 0

 

Pipeline calibration files:

 

-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.

            DEFAULT:  ch0, ch2 = ../cal/psf_fov.tbl; ch1, ch3 = (none) 

            OVERRIDES ALLOWED:  users psf_fov.tbl file

 

-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)

                       DEFAULT: ch0 = 40.0, ch1 = 33.0, ch2 = 67.0, ch3 = 55.0 

                       OVERRIDES ALLOWED:  X > 0.0

 

-v                   Verbose mode.  Higher number means more detailed STDOUT.

                       DEFAULT:  1  

                       OVERRIDES ALLOWED:  integer

 

Pipeline calibration files:

 

(none)

 

Pipeline namelist files:

 

-n         Namelist file

            DEFAULT: appropriate snest_irs.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]

 

Pipeline output datafiles:

 

-o         Output UNC file (FITS)

            [pipeline datafile --- override not allowed]

 

Pipeline datafiles updated:

 

(none)

4.31       snest_irs2 Module

This module will compute uncertainty file (updated outlier rejection logic).

 

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)     

                                 OVERRIDE ALLOWED: filename

 

-confusion         Confusion noise, for use in this module only.
                          DEFAULT: 0     

                          OVERRIDE ALLOWED: C >= 0.0

 

-dmask_fatal     Fatal integer bitmask for DMASK --- not used for CUPID
                          DEFAULT: 30728 (bits #3, 11, 12, 13, 14)     

                          OVERRIDE ALLOWED: integer bitmask

 

-dmask_radhit   Bit used to flag radhit bit in DMASK
                          DEFAULT: 512 (bit #9)     

                          OVERRIDE ALLOWED: integer bitmask

 

-gain                  Gain factor, for noise calculation in this module only (electron/DN)
                          DEFAULT: 4.6     

                          OVERRIDE ALLOWED: X >= 0.0

 

-readnoise          Read noise, for use in this module only (electron)
                           DEFAULT: ch0=40.0, ch1=33.0, ch2=67.0, ch3=55.0     

                           OVERRIDE ALLOWED: X > 0.0

 

-v                         Verbose mode. Higher number means more detailed STDOUT.
                            DEFAULT: 1     

                            OVERRIDE ALLOWED: integer

 

Pipeline calibration files:

 

      (none)

 

Pipeline namelist files:

 

-n                         Namelist file
                            DEFAULT: appropriate snest_irs2.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]

 

Pipeline output datafiles:

 

-o                         Output UNC file (FITS)
                             [pipeline datafile --- override not allowed]

 

Pipeline datafiles updated:

 

-d                          Input DMASK file (FITS) --- Not used for CUPID.
                             [pipeline datafile --- override not allowed]

4.32       tbl2fits Module

This module creates a FITS binary table from an ASCII IPAC table.

 

The module is used in the following pipelines:  BCDX; COADDX; BKSUBX

 

Constant values:

 

-v         Level of printed messages

            DEFAULT:  1

            OVERRIDES ALLOWED:  N >= 0

 

Pipeline calibration files:

 

(none)

 

Pipeline namelist files:

 

(none)

 

Pipeline input datafiles:

 

-i          Input ASCII table

            [pipeline datafile --- override not allowed]

 

Pipeline output datafiles:

 

-o         Output FITS table

            [pipeline datafile --- override not allowed]

 

Pipeline datafiles updated:

 

(none)

4.33       velocity Module

This module adds velocity header keywords.

 

The module is used in the following pipelines:  BCDACQ; BCD

 

Constant values:

 

(none)

 

Pipeline calibration files:

 

(none)

 

Pipeline namelist files:

 

-t          velocity table

            DEFAULT: appropriate velocity.tbl file in ../cdf/

            OVERRIDE ALLOWED: name of user's namelist file

 

Pipeline input datafiles:

 

-i          Input datafile

            [pipeline datafile --- override not allowed]

 

Pipeline output datafiles:

 

-o         Output datafile

            [pipeline datafile --- override not allowed]

 

Pipeline datafiles updated:

 

(none)