NAME

USAGE

DESCRIPTION

The xapipeline task duplicates most of the XRISM pipeline (in particular, it does not produce trend data). It allows the user to run all or part of the pipeline processing, and to vary the calibration files and filtering (screening) criteria used. A number of other pipeline processing parameters can also be changed.

Pipeline Stages

The pipeline is divided into 3 stages:

1. Calibration
2. Data screening
3. Product creation

Each stage may be run singly or in combination with the preceding stage. This is controlled by the 'entry_stage' and 'exit_stage' parameters.

Xtend Stage 1 consists of the following steps:

For each event file:
1. (optional) Run coordevt on hot pixel file
2. Run coordevt
3. Run xtdphas
4. Run xtdflagpix
5. Run xtdpi
6. Run xtdpi
7. Create flickering pixel file
   1. Filter Xtend events STATUS[1]==b0
   2. Run searchflickpix
   3. Run coordevt on flickering pixel events
8. Run xtdflagpix with flickering pixels

Resolve Stage 1 consists of the following steps:

1. (optional) Calculate GTIFOUNDALL (gtiinvert on GTILOST)
2. (optional) Run rslctsfluct
3. (optional) Run rsladrgti
4. Run rslmxsgti if the MXS is on and 'calc_mxsgti=yes'
5. Run rslanticopi
6. For each event file:
   1. Run coordevt
   2. Run rslflagpix
   3. Run rslplsclip
   4. Run rslsecid
7. Merge GTI
1. Obtain the following GTI if they exist: GTIOBS, GTITEL, GTIADROFF (or CRYOFREEGOOD)
1. If the calpixel is being used ('linetocorrect=MnKa'; 'calmethod=Cal-pix'), the above GTI are merged
2. If MXS is on, the parameter 'linetocorrect' is checked to determine if MXS direct GTI (GTIMXSFNON13)
   or indirect GTI (GTIMXSFNON24) is additionally merged with the above GTI
3. If the Fe55 filter wheel source is being used ('linetocorrect= MnKa'; 'calmethod=Fe55'), the above GTI are merged along with the Fe55 event file GTI, GTIMXSFNOFF13 and GTI GTIMXSFNOFF24 (if the MXS is operating in continuous mode) or GTIMXSCSOFF13 and GTI GTIMXSCSOFF24 (if the MXS is operating in intermittent mode), GTIMKF, and GTI for when the satellite is not in the SAA
2. This merged GTI is used later as an input to rslgain
8. Calculate GHF (gain history file)
   1. Merge pointing and slew event files
   2. Filter the merged event file
   1. If 'calmethod=Cal-pix' the merged event file is filtered by selecting
      (ftselect) on PIXEL==12
   2. If 'calmethod=MXS' the merged event file is filtered by selecting
      (ftselect) on PIXEL!=12
   3. If 'calmethod=Fe55' no pixel filtering is applied to the merged event file
   3. Run ftsort on filtered merged file
   4. Run rslgain on filtered, sorted merged file using the appropriately merged GTI
9. For each event file:
   1. Run rslpha2pi (GHF input)
   2. Run rslflagpix
   3. Run rslsecid
   4. Run rslseccor
   5. Run rslpha2pi (GHF input)

The data screening (Stage 2) is identical to that in the production pipeline when default parameters are used. The xapipeline task uses the individual instrument pipelines (xtdpipeline, rslpipeline) to screen the data. For details on the default screening applied to the events, see:

• xafilter - Create the EHK from attitude and orbital data, and create the MKF from housekeeping data based on the CalDB 'mkfconf' file
• ahgtigen - Create the GTI from the EHK and MKF file parameters based on CalDB selection file
• ahscreen - Screen the data based on GTI and CalDB selection file

The product creation (Stage 3) creates quick look preview products in an identical fashion as the production pipeline. The images, spectra, and lightcurves are created in the individual instrument pipelines.

Xtend Stage 3 consists of the following steps:

1. Run extractor
2. Create ximage plot command file
3. Run ximage
4. Create lcurve plot command file
5. Run lcurve
6. Run xtdrmf
7. Create xspec command file
8. Run xspec

Resolve Stage 3 consists of the following steps:

1. Run extractor
2. Create ximage plot command file
3. Run ximage
4. Create lcurve plot command file
5. Run lcurve
6. Run rslmkrmf
7. Create xspec command file
8. Run xspec

Instruments

The xapipeline task allows for the processing of data on an instrument-by-instrument basis. This is controlled by the 'instrument' parameter. Possible values are:

• ALL - Process all data for all modules of all instruments
• XTEND - Process Xtend data only
• RESOLVE - Process Resolve data only

More than one value may be specified at a time.

INPUT

The input to xapipeline is specified using (at minimum) the 'indir' parameter. This should be specified as the top-level sequence directory, e.g.:

   xapipeline indir=/path/to/100050020 ...

Paths to specific housekeeping and satellite data files can be specified using the 'attitude', 'housekeeping', 'extended_housekeeping', 'makefilter', 'orbit', and 'timfile' parameters, but this should NOT be necessary if 'indir' is specified correctly.

Note that errors can occur if a subdirectory of a sequence directory is used for the 'indir' parameter or if the output is stored within the sequence directory.

OUTPUT

Report

An output report is produced with the default name xapipeline.log. The name of the log can be changed with the 'logfile' parameter. This lists all processing done in any particular run of xapipeline. The level of detail of this report is controlled by the 'chatter' parameter.

Note that setting chatter to 3 can produce very large output reports.

File names, etc.

The number of output files depends on both pipeline processing stage(s) and the instrument(s) selected. All output files are written to the directory specified by the 'outdir' parameter. The archive directory structure is NOT reproduced (i.e. all output files are in a single directory).

The names of files produced are the same as those found in the HEASARC archive. However, the usual xaXXXXXXXXX prefix (where "XXXXXXXXX" is the sequence number) can be replaced by a character string set by the 'stemoutputs' parameter; this defaults to the value set by the 'steminputs' parameter.

PARAMETERS

indir = indir/ [string]

Directory containing the input data. This should be the full, or relative path to the top-level sequence directory, e.g.:

   /path/to/805062010/

Note: Problems can arise if a subdirectory of the top-level sequence directory is used.

outdir = outdir/ [string]

Output directory used for all output data, as well as the report file. If 'clobber' is set to no, and this directory already exists, the task fails. This should NEVER be a subdirectory of the input directory (the top level sequence directory).

CAUTION: If 'clobber' is set to yes, and this directory already exists, this task overwrites files, as needed, in this directory.

steminputs [string]

Base (stem) for FITS input files (e.g., xa100050020). This string is used as the base file name for finding input files. For example, if 'steminputs=xa100050020', then to find the attitude file, xapipeline matches the regular expression /xa100050020\.att(\..+)?$/ against all files found in the 'indir' directory.

When doing this matching, xapipeline prefers files that match the original archive directory structure over files with the same name that do not. For example, if the files:

   /path/to/805062010/xtend/event_uf/xa805062010xtd_0_uf.evt

   /path/to/805062010/xtend/event_uf_2/xa805062010xtd_0_uf.evt

both exist, xapipeline uses the first file, and not the second. If two files of the same name are found and neither one resides in an archive directory structure, xapipeline exits with an error.

Note: The above file finding issues can be avoided if the downloaded archive data set is left "pristine", by specifying an output directory outside of the input directory tree.

stemoutputs = DEFAULT [string]

Base (stem) output name used for creating output files. If set to DEFAULT, 'steminputs' is used.

entry_stage = 1 [integer 1|2]

Entry stage, 1 or 2.

Stage 1: Re-calibrate unfiltered event files.

Stage 2: Start from existing unfiltered event files.

(exit_stage = 2) [integer 1|2|3]

Exit stage, 1, 2, or 3.

Stage 1: Produces calibrated unfiltered event files.

Stage 2: Produces screened event files.

Stage 3: Produces quick look preview products.

instrument = ALL [string ALL|RESOLVE|XTEND]

Comma-delimited list of which instruments to process. More than one value may be specified at one time.

verify_input = no [boolean yes|no]

If 'verify_input=yes', input FITS files are verified with ftverify.

(attitude = DEFAULT) [string]

Attitude file.

(housekeeping = DEFAULT) [string]

General housekeeping file.

(extended_housekeeping = DEFAULT) [string]

Extended housekeeping file.

(makefilter = DEFAULT) [string]

Makefilter file.

(orbit = DEFAULT) [string]

Orbit file.

(timfile = DEFAULT) [string]

Time file.

(obsgti = DEFAULT) [string]

Observation GTI file.

(calc_pointing = yes) [boolean yes|no]

If 'calc_pointing=yes', calculate nominal pointing.

(calc_optaxis = yes) [boolean yes|no]

If 'calc_optaxis=yes', calculate optical axis keywords.

(create_ehkmkf = no) [boolean yes|no]

If 'create_ehkmkf=yes', create the EHK and MKF files.

(makeregion = no) [boolean yes|no]

If 'makeregion=yes', a region file for data product extraction is made. The region file is in SKY coordinates and corresponds to a circle of radius 130 SKY pixels (equivalent to ~3.83 arcmin), whose center is at the SKY position that corresponds the center of the Resolve detector (based on nominal pointing keywords).

(ra = -999.99999) [double]

RA of nominal pointing [degrees]. If 'calc_pointing=yes', the 'ra' value is derived from the calculated nominal pointing. If 'calc_pointing=no', a valid value for 'ra' must be provided in place of the default value.

(dec = -999.99999) [double]

Dec of nominal pointing [degrees]. If 'calc_pointing=yes', the 'dec' value is derived from the calculated nominal pointing. If 'calc_pointing=no', a valid value for 'dec' must be provided in place of the default value.

(roll = 0.0) [double]

Roll angle of nominal pointing [degrees].

(leapsecfile = REFDATA) [filename CALDB|REFDATA|file name]

Name of the leap second file. If set to CALDB or REFDATA, the file in the calibration database or in the REFDATA area, respectively, is used.

(selectfile = CALDB) [filename CALDB|file name]

The file containing selection expressions. If 'selectfile' is set to CALDB, the file is read from the calibration database.

(selectfilemioa = CALDB) [filename CALDB|file name]

The file containing selection expressions for the MIOA failure mode (PSP contingency). If 'selectfilemioa' is set to CALDB, the file is read from the calibration database.

(selectfilemiob = CALDB) [filename CALDB|file name]

The file containing selection expressions for the MIOB failure mode (PSP contingency). If 'selectfilemiob' is set to CALDB, the file is read from the calibration database.

(mkfconf = CALDB) [filename CALDB|file name]

Input makefilter configuration file. If 'mkfconf' is set to CALDB, the file is read from the calibration database.

(cor2file = CALDB) [filename CALDB|file name]

Parameter for xamkehk: Input cutoff rigidity Suzaku file.

(cor3file = CALDB) [filename CALDB|file name]

Parameter for xamkehk: Input cutoff rigidity IGRF 2016 file.

(saafile = CALDB) [filename CALDB|file name]

Parameter for xamkehk: Input SAA vertices for each instrument.

(xtd_teldef = CALDB) [filename CALDB|file name]

Parameter for coordevt: Xtend teldef file.

(xtd_badpixfile = CALDB) [filename CALDB|file name]

Parameter for xtdflagpix: Bad pixel file for Xtend.

(xtd_maskfile = CALDB) [filename CALDB|file name]

Parameter for xtdflagpix: Mask file for Xtend.

(xtd_vtevnodd = CALDB) [filename CALDB|file name]

Parameter for xtdpi: Xtend even-odd file.

(xtd_ctifile = CALDB) [filename CALDB|file name]

Parameter for xtdpi: Xtend CTI file.

(xtd_chtrailfile = CALDB) [filename CALDB|file name]

Parameter for xtdpi: Xtend charge trail ('chtrailfile' in xtdpi) file.

(xtd_spthfile = CALDB) [filename CALDB|file name]

Parameter for xtdpi: Xtend split threshold ('spthfile' in xtdpi) file.

(xtd_gainfile = CALDB) [filename CALDB|file name]

Parameter for xtdpi: Xtend gain file.

(xtd_patternfile = CALDB) [filename CALDB|file name]

Parameter for xtdpi: Xtend grade pattern file.

(xtd_rmfparamfile = CALDB) [filename CALDB|file name]

Parameter for xtdmkrmf: Xtend RMF parameter file

(rsl_teldef = CALDB) [filename CALDB|file name]

Parameter for coordevt: Resolve teldef file.

(rsl_coeftime = CALDB) [string CALDB|file name]

Parameter for rslsamcnt: Input file with arrival time coeffs for Resolve.

(rsl_pulsefile = CALDB) [filename CALDB|file name]

Parameter for rslseccor: Input file with pulse amplitudes.

(rsl_pixdeffile = CALDB) [filename CALDB|file name]

Parameter for rslflagpix: Input Resolve electrical pixel map file.

(rsl_gainfile = CALDB) [filename CALDB|file name]

Parameter for rslgain, rslpha2pi: Input Resolve gain coefficients file.

(rsl_linefitfile = CALDB) [filename CALDB|file name]

Parameter for rslgain: Input calibration line file for Resolve.

(rsl_gainantfile = CALDB) [filename CALDB|file name]

Parameter for rslanticopi: Input antico gain file for Resolve.

(rsl_delayfile = CALDB) [filename CALDB|file name]

Parameter for rslmxsgti: Input instrument time delay file for Resolve.

(rsl_mxsledfile = CALDB) [filename CALDB|file name]

Parameter for rslmxsgti: MXS time offset and afterglow characteristics file.

(rsl_plsclipfile = CALDB) [filename CALDB|file name]

Parameter for rslpsclip: Input clipped pulse threshold file.

(rsl_rmfparamfile = CALDB) [filename CALDB|file name]

Parameter for rslmkrmf: Resolve RMF parameter file.

(xtd_mkflabel = SXI#SCI) [string]

Label to use for Xtend MKF GTI creation. The hash is replaced by one of the following strings corresponding to the appropriate mode: CCDW1, CCD12WA, or CCD34WF.

(xtd_ehklabel = SXI#SCI) [string]

Label to use for Xtend EHK GTI creation. The hash is replaced by one of the following strings corresponding to the appropriate mode: CCDW1, CCD12WA, or CCD34WF.

(xtd_evtlabel = SXI#SCI) [string]

Label to use for Xtend event screening. The hash is replaced by one of the following strings corresponding to the appropriate mode: CCDW1, CCD12WA, or CCD34WF.

(rsl_mkflabel = PIXELALL) [string]

Label to use for Resolve MKF GTI creation.

(rsl_ehklabel = PIXELALL) [string]

Label to use for Resolve EHK GTI creation.

(rsl_evtlabel = PIXELALL) [string]

Label to use for Resolve event screening.

(coordevt_startsys = LOWEST) [string LOWEST|RAW|ACT|DET|FOC|SKY|HIGHEST]

Parameter for coordevt: Name of the intitial coordinate system for coordinate conversions.

(stopsys = HIGHEST) [string LOWEST|RAW|ACT|DET|FOC|SKY|HIGHEST]

Parameter for coordevt: Name of the final coordinate system for coordinate conversions.

(annaber = no) [string yes|no|invert]

Parameter for coordevt: Apply annual aberration correction.

(followsun = yes) [boolean yes|no]

Parameter for coordevt: Recalculate the Sun position for each event.

(orbaber = no) [string yes|no|invert]

Parameter for coordevt: Apply satellite orbital aberration correction.

(attinterp = LINEAR) [string LINEAR|CONSTANT]

Parameter for coordevt: Sky attitude interpolation method.

(attdt = 32.0) [double]

Parameter for coordevt: Allowed margin for time extrapolation [s] in the input attidue file ('attfile' in coordevt).

(chkattgap = no) [boolean yes|no]

Parameter for coordevt: Limit attitude interpolation if gaps are present.

(attext = ATTITUDE) [string]

Parameter for coordevt: Attitude extension name.

(attcol = QPARAM) [string]

Parameter for coordevt: Attitude column name.

(attform = QUAT) [string QUAT|EULER]

Parameter for coordevt: Attitude format.

(orbext = ORBIT) [string]

Parameter for coordevt: Orbit extension name.

(orbcol = VELOCITY) [string]

Parameter for coordevt: Orbital velocity column name.

(orbform = VECTOR) [string VECTOR|COMPONENTS|KEPLERIAN]

Parameter for coordevt: Orbital velocity format.

(coordevt_randomize = TELDEF) [string yes|no|teldef]

Parameter for coordevt: Randomize coordinates when rebinning.

(randsys = TELDEF) [string TELDEF|LOWEST|RAW|ACT|DET|FOC]

Parameter for coordevt: Starting from coordinate system specified by 'randsys' (default specified in RANCOORD keyword in Xtend teldef file), coordinate conversions are randomized, up to the highest coordinate system.

(randscalesys = TELDEF) [string]

Parameter for coordevt: Name of the coordinate system to determine the scaling factor for the randomization interval, +/- 0.5 of a pixel in that coordinate system. The default is to get the name from the RAN_SCL keyword in the Xtend teldef file.

(infileext = EVENTS) [string]

Parameter for coordevt: Event extension name.

(inclfloatcol = no) [boolean yes|no]

Parameter for coordevt: Write non-rounded coordinate columns.

(inclfloatskycol = no) [boolean yes|no]

Parameter for coordevt: Write non-rounded SKY coordinate columns.

(floatcolsuffix = _FLOAT) [string]

Parameter for coordevt: Suffix for non-rounded coordinate columns.

(startwithfloat = no) [boolean yes|no]

Parameter for coordevt: Start with non-rounded 'startsys' coordinates.

(blankcol = yes) [boolean yes|no]

Parameter for coordevt: Assign null values to columns not calculated.

(btnull = 255) [integer]

Parameter for coordevt: TNULL for byte (B) columns.

(itnull = -999) [integer]

Parameter for coordevt: TNULL for short (I) columns.

(jtnull = -999) [integer]

Parameter for coordevt: TNULL for long (J) columns.

(ktnull = -999) [integer]

Parameter for coordevt: TNULL for long (K) columns.

(sbtnull = 255) [integer]

Parameter for coordevt: TNULL for signed byte columns.

(uitnull = -999) [integer]

Parameter for coordevt: TNULL for unsigned short columns.

(ujtnull = -999) [integer]

Parameter for coordevt: TNULL for unsigned long columns.

(calc_hotpix = no) [boolean yes|no]

Run coordevt on hot pixel file.

(calc_modegti = yes) [boolean yes|no]

Whether to execute xtdmodegti to create the segment and mode GTI for Xtend using the exposure file.

(colbound = -32768,-32767,32767) [string]

Parameter for xtdphas: TNULL, TLMIN, and TLMAX for PHAS.

(chipcol = CCD_ID) [string NONE|CCD identification]

Parameter for searchflickpix: Chip ID, or column (or NONE). If set to NONE, then all events are searched together for flickering pixels. Otherwise, events are searched separately by 'chipcol' grouping.

(xcol = ACTX) [string]

Parameter for searchflickpix: X-coordinate column.

(ycol = ACTY) [string]

Parameter for searchflickpix: Y-coordinate column.

(chancol = PI) [string NONE|PI|column name]

Parameter for searchflickpix: Name of output pulse height column. The column, in the PIXELS extension, contains average pulse height values of the flickering events for each detected pixel. Feature disabled if set to NONE.

(gradecol = GRADE) [string NONE|GRADE]

Parameter for searchflickpix: Name of output event grade column. Only events with specific grades given in the 'grade' parameter for searchflickpix are used in accumulating the chip image for the flickering pixel search. If set to NONE, all grades are used, and the 'grade' parameter is ignored.

(grade = 0,2,3,4,6) [string ALL|grade list]

Parameter for searchflickpix: Event grade(s) for cleaning. This is a list of grade values used in accumulating the chip image for the flickering pixel search. If set to ALL, all grades are used.

(n_division = 1) [integer]

Parameter for searchflickpix: Divide total observation time into the given number.

(cleanimg = no) [boolean yes|no]

Parameter for searchflickpix: Output cleaned image for debugging.

(cellsize = 7) [integer]

Parameter for searchflickpix: Poisson clean cell size (odd integer > 1), in units of pixels. If set to 0 this invokes the simple counts-per-pixel cutoff.

(impfac = 320) [double]

Parameter for searchflickpix: Impact factor for the gamma function used for the Poisson search.

(logprob1 = -5.6) [double]

Parameter for searchflickpix: Log (base 10) Poisson probability threshold for the first step of the flickering pixel search (using the entire chip).

(logprob2 = -5.6) [double]

Parameter for searchflickpix: Log (base 10) of the Poisson probability threshold for the second step of the flickering pixel search (compared to the surrounding pixels).

(iterate = yes) [boolean yes|no]

Parameter for searchflickpix: Iterate the second step of Poisson cleaning.

(flagedge = no) [boolean yes|no]

Parameter for searchflickpix: If set to yes, pixels along the chip edge are flagged as flickering for the entire duration of the observation.

(bthresh = 3) [integer]

Parameter for searchflickpix: Zero background cutoff threshold, applied when the local mean background level is zero.

(duration = no) [boolean yes|no]

Parameter for searchflickpix: Perform detailed search for flickering pixel duration.

(sigma = 3.0) [double]

Parameter for searchflickpix: Significance level for flickering pixel duration.

(firstchip = TLMIN) [string NONE|TLMIN]

Parameter for searchflickpix: Minimum value for chip number in the 'chipcol' column.

(lastchip = TLMAX) [string NONE|TLMAX]

Parameter for searchflickpix: Maximum value for chip number in the 'chipcol' column.

(xmin = TLMIN) [string]

Parameter for searchflickpix: Minimium value for X-coordinate.

(xmax = TLMAX) [string]

Parameter for searchflickpix: Maximum value for X-coordinate.

(ymin = TLMIN) [string]

Parameter for searchflickpix: Minimum value for Y-coordinate.

(ymax = TLMAX) [string]

Parameter for searchflickpix: Maximum value for Y-coordinate.

(chanmin = TLMIN) [string]

Parameter for searchflickpix: Minimum pulse height value (inclusive) for accumulating image to search for flickering pixels.

(chanmax = TLMAX) [string]

Parameter for searchflickpix: Maximum pulse height value (inclusive) for accumulating image to search for flickering pixels.

(outbadpix = no) [boolean yes|no]

Parameter for xtdflagpix: If 'outbadpix=yes', output bad pixel file(s) made by xtdflagpix. It is not possible to specifiy individual names of the bad pixel files. Although an individual run of xtdflagpix allows specifying an output file name, the task xapipeline calls xtdflagpix multiple times and does not allow specifying the bad pixel name.

(outbadimg = yes) [boolean yes|no]

Parameter for xtdflagpix: If 'outbadimg=yes', bad pixel images are output. Note that in xtdflagpix this parameter is a file name, but here there can be multiple files and the user cannot specify the file names, only whether or not the files are output.

(npixnbr = 1) [integer]

Parameter for xtdflagpix: Pixel distance defining a neighbor.

(nboundnbr = 1) [integer]

Parameter for xtdflagpix: Pixel distance defining neighbor from CCD/window/segment boundary.

(citrailnbr = 2) [integer]

Parameter for xtdflagpix: Pixel distance trailing CI row.

(ciprenbr = 1) [integer]

Parameter for xtdflagpix: Pixel distance preceding CI row.

(echoflag = "0,0,0,0,0,0,0,0") [string]

Parameter for xtdflagpix: Flag cosmic ray echo pixels. The order corresponds to CCD_ID-SEGMENT = 0-0, 0-1, 1-0, 1-1, 2-0, 2-1, 3-0, 3-1.

(echonbr = 2) [integer]

Parameter for xtdflagpix: Distance in pixels from a cosmic ray echo pixel to flag a neighbor pixel.

(echomin = 6) [integer]

Parameter for xtdflagpix: Minimum number of events for the cosmic ray echo fraction calculation.

(echospth = 15) [integer]

Parameter for xtdflagpix: Split threshold for cosmic ray echo fraction calculation.

(echofrac = 0.7) [double]

Parameter for xtdflagpix: Minimum fraction of hits defining a cosmic ray echo pixel. For any pixel contained in at least 'echomin' events, if at least a fraction 'echofrac' of those events have a pulse height above 'echospth', that pixel is considered a cosmic ray echo pixel.

(echomap = no) [boolean yes|no]

Parameter for xtdflagpix: Output cosmic ray echo pixel fraction map.

(bad_status = 3:9,11:12,16:19,25:28,30,37) [string]

Parameter for xtdflagpix: List of STATUS flags which are considered bad. If any of these flags are set to 1 for an event, then STATUS flag 1 will also be set to 1 for that event. Colons can be used to specify a range (e.g., "3:5,7" is equivalent to "3,4,5,7").

(copyphas = yes) [boolean yes|no]

Parameter for xtdflagpix: Copy original PHAS before processing.

(xtd_resetflags = yes) [boolean yes|no]

Parameter for xtdflagpix: Reset all xtdflagpix STATUS flags.

(hkext = HK_SXI_USR_USER_HK1) [string]

Parameter for xtdpi: Name of HK extension with video temperatures.

(hkcolstem = SXI_USR_HKTBL_) [string]

Parameter for xtdpi: Column name stem for video temperatures.

(hkvideoid = B,B,B,B) [string]

Parameter for xtdpi: Video card IDs used for the even-odd correction for CCD1, CCD2, CCD3, and CCD4. This parameter must consist of a comma-separated list of 4 characters A or B.

(startcol = PHAS) [string PHAS|PHAS_EVENODD|PHAS_TRAILCORR|PHAS_CTICORR|PHA]

Parameter for xtdpi: Starting point of corrections to calculate PI.

(vtcor = yes) [boolean yes|no]

If set to yes, the video board temperature correction is enabled.

(evnoddcor = yes) [boolean yes|no]

Parameter for xtdpi: Enable even-odd correction for Xtend PI calculation.

(chtrailcor = yes) [boolean yes|no]

Parameter for xtdpi: Enable charge trail correction for Xtend PI calculaton.

(cticor = yes) [boolean yes|no]

Parameter for xtdpi: Enable CTI correction for Xtend PI calculation.

(gaincor = yes) [boolean yes|no]

Parameter for xtdpi: Enable gain correction for Xtend PI calculation.

(ctigrade = yes) [boolean yes|no]

Parameter for xtdpi: Use grade information in Xtend CTI correction.

(usegoffset = yes) [boolean yes|no]

If set to yes, use of grade-based central-pixel offset (goffset) correction is enabled. This setting is independent of both 'cticor' and 'ctigrade'.

(copygrade = no) [boolean yes|no]

Parameter for xtdpi: Copy existing GRADE and PHA columns to GRADE_COPY and PHA_COPY columns respectively.

(phcut = CALDB) [string]

Parameter for xtdpi: Pulse height cut for CTI correction. If set to CALDB, the value from the header of the CTI CalDB file ('xtd_ctifile') is used.

(badpixopt = 2) [integer 1|2|3]

Parameter for xtdpi: Options for events with bad pixels: ignore bad pixels (1), null bad pixels (2), or null whole event (3).

(spthiter = yes) [boolean yes|no]

Parameter for xtdpi: Enable split threshold iteration.

(spthcaldb = yes) [boolean yes|no]

Parameter for xtdpi: Use split thresholds from 'xtd_spthfile'.

(spthoffset = 15.) [double]

Parameter for xtdpi: Split threshold offset value (if 'spthcaldb=no').

(spthslope = 0.) [double]

Parameter for xtdpi: Split threshold slope value (if 'spthcaldb=no').

(evtthre = DEFAULT) [string]

Parameter for xtdpi: Event threshold. If set to DEFAULT, the task uses the values in the input event file ('infile' in xtdpi) header keyword EVENTTHR, which contains a comma-separated list of values for each CCD_ID and SEGMENT combination.

(negthre = -5000) [integer]

Parameter for xtdpi: Minimum PHAS value for normal event.

(deltatime = 8) [integer]

Parameter for xtdpi: Maximum allowed time gap [s] in HK video temperature search.

(debugcol = no) [boolean yes|no]

Parameter for xtdpi: Write out the debugging columns.

(timecol = TIME) [string]

Parameter for coordevt, searchflickpix, rslctsfluct: Name of TIME column.

(calc_gtilost = no) [boolean yes|no]

Perform calculations on Resolve lost GTI: (1) If no lost GTI file is found as part of the observation sequence, create one. (2) Compute the inverse of the lost GTI.

(calc_fluct = yes) [boolean yes|no]

Run rslctsfluct to calculate the CTS Control and Monitor thermometer temperature fluctuations.

(calc_adrgti = no) [boolean yes|no]

Run rsladrgti to calculate ADR GTI based on ADR recycling intervals.

(calc_mxsgti = no) [boolean yes|no]

Run rslmxsgti to calculate the MXS GTI.

(screenlost = no) [boolean yes|no]

Screen events using the inverse of the lost GTI.

(stimecol = S_TIME) [string]

Parameter for rslmxsgti: Name of S_TIME column.

(tioncol = FWE_TI_LED#_ON) [string]

Parameter for rslmxsgti: Input TI columns with LED on (#=1-4).

(tioffcol = FWE_TI_LED#_OFF) [string]

Parameter for rslmxsgti: Input TI columns with LED off (#=1-4).

(plslencol = FWE_LED#_PLS_LEN) [string]

Parameter for rslmxsgti: Input pulse length columns (#=1-4).

(plsspccol = FWE_LED#_PLS_SPC) [string]

Parameter for rslmxsgti: Input pulse spacing columns (#=1-4).

(iledcol = FWE_I_LED#_CAL) [string]

Parameter for rslmxsgti: Input current columns (#=1-4).

(iledsetcol = FWE_I_LED#_SET_CAL) [string]

Parameter for rslmxsgti: Input LED SET current columns ("#" takes values 1 to 4, inclusive).

(timeoncol = TIME_LED#_ON) [string]

Parameter for rslmxsgti: Output LED-on time columns (#=1-4).

(timeoffcol = TIME_LED#_OFF) [string]

Parameter for rslmxsgti: Output LED-off time columns (#=1-4).

(decaythresh = 0.001) [double]

Parameter for rslmxsgti: Threshold fraction of maximum amplitude defining afterglow.

(calctime = yes) [boolean yes|no]

Parameter for rslmxsgti: Perform time assignment.

(calcgti = yes) [boolean yes|no]

Parameter for rslmxsgti: Produce MXS GTI files.

(afterglow = yes) [boolean yes|no]

Parameter for rslmxsgti: Add afterglow to fine GTI STOP times.

(dtafterglow = FILE) [string]

Parameter for rslmxsgti: Afterglow or offset [ms] applied to GTI stop times (or use file).

(agmethod = table) [string [TABLE]|CALC]

Parameter for rslmxsgti: Lookup table in 'mxsledfile' used to estimate afterglow, or coefficients in 'mxsledfile' used for direct calculation of afterglow.

(itmax = 1000) [integer]

Parameter for rslmxsgti: Maximum number of iterations allowed to reach convergence in determining the afterglow decay time using the functional form of the afterglow.

(reltol = 1.0e-6) [double]

Parameter for rslmxsgti: Tolerance relative to the threshold defining convergence in determining the afterglow decay time using the functional form of the afterglow.

(mxsoffset = FILE) [string]

Parameter for rslmxsgti: Shift [ms] applied to MXS GTI start times (or use file).

(interp = TWOPOINT) [string TWOPOINT|NEAREST]

Parameter for rslmxsgti: Interpolation method.

(margingti = yes) [boolean yes|no]

Parameter for rslmxsgti: Create GTI between 'tstart' and the first input GTI and between 'tstop' and the last input GTI.

(tstart = DEFAULT) [string]

Parameter for rslmxsgti: Value to use for 'tstart' [s], or if 'tstart=DEFAULT', take from the input HK file ('infilehk' in rslmxsgti).

(tstop = DEFAULT) [string]

Parameter for rslmxsgti: Value to use for 'tstop' in seconds, or if 'tstop=DEFAULT', take from the input HK file ('infilehk' in rslmxsgti).

(dt = 0.) [double]

Parameter for rslmxsgti: Time gap [s] between input GTI times and corresponding output GTI times. Output start times are later than the input stop times by 'dt', and output stop times are earlier than the input start times by 'dt'.

(antpsp = A) [string A|B]

Parameter for rslflagpix: Antico PSP to use for coincidence (A = PSP-A, B = PSP-B).

(checkpsp = yes) [boolean yes|no]

Parameter for rslflagpix: If 'checkpsp=yes', the contingency mode PSPCTGCY keyword is queried. The PSP side checked for antico coincidence is switched from A to B if 'antpsp=A' and PSPCTGCY=MIOAFAIL, and from B to A if 'antpsp=B' and PSPCTGCY=MIOBFAIL.

(antshift = CALDB) [string CALDB|time offset value]

Parameter for rslflagpix: Time offset [s] between event time and central time for defining the window used for antico flagging.

(calcant = yes) [boolean yes|no]

Parameter for rslflagpix: Flag antico events.

(antdtpre = CALDB) [string CALDB|time interval value]

Parameter for rslflagpix: Delta time [s] preceding an antico event.

(antdtfol = CALDB) [string CALDB|time interval value]

Parameter for rslflagpix: Delta time [s] following an antico event.

(antphathr = 71) [integer]

Parameter for rslflagpix: PHA threshold for antico events.

(antdurthr = 2) [integer]

Parameter for rslflagpix: Duration threshold for antico events in units of 80 microseconds.

(calcctrec = yes) [boolean yes|no]

Parameter for rslflagpix: If 'calcctrec=yes', events are checked for recoil crosstalk flagging; if 'calcctrec=no', this is skipped.

(ctrecdt = CALDB) [string CALDB|time interval value]

Parameter for rslflagpix: Delta time [s] for flagging recoil crosstalk.

(calcprox = yes) [boolean yes|no]

Parameter for rslflagpix: If 'calcprox=yes', events are checked for basic temporal proximity with any other event.

(proxdt = CALDB) [string CALDB|time interval value]

Parameter for rslflagpix: Time interval [s] between events required for proximity crosstalk to be flagged.

(calcctel = yes) [boolean yes|no]

Parameter for rslflagpix: If 'calcctel=yes', events are checked for electrical crosstalk flagging using the 'cteldt' time interval.

(cteldt = CALDB) [string CALDB|time interval value]

Parameter for rslflagpix: Delta time [s] for flagging electrical crosstalk.

(ctelnear = 1) [integer]

Parameter for rslflagpix: Number of nearby pixels to be checked for electrical crosstalk, where proximity is defined by 'rsl_pixdeffile' and restricted to quadrants of the Resolve detector.

(calcctel2 = yes) [boolean yes|no]

Parameter for rslflagpix: If 'calcctel2=yes', events are checked for electrical crosstalk 2 flagging using the 'cteldt2' time interval.

(cteldt2 = CALDB) [string CALDB|time interval value]

Parameter for rslflagpix: Delta time [s] for flagging electrical crosstalk 2.

(ctelnear2 = 1) [integer]

Parameter for rslflagpix: Number of nearby pixels to be checked for electrical crosstalk 2, where proximity is defined by 'rsl_pixdeffile' and restricted to quadrants of the Resolve detector.

(pxpithr = "600 600 600 600") [string]

Parameter for rslflagpix: Events with PI values below one of the appropriate thresholds in the list 'pxpithr' are excluded from the flagging types that are specified by the 'usepxpithr' parameter. The four threshold values correspond to the four different pixel event-to-event flagging types, in the following order: proximity, electrical crosstalk 1, electrical crosstalk 2, and recoil crosstalk. Note that if only a single value is specified for 'pxpithr', rslflagpix assumes that the single value applies to all four flagging types.

(usepxpithr = ALL) [string ALL|NONE|PROX|CTEL|CTEL2|CTREC]

Parameter for rslflagpix: A comma-delimited list specifying the types of flagging for which events with PI values below a threshold set in the list 'pxpithr' are excluded from consideration for flagging. The options for 'usepxpithr' include ALL, NONE, PROX (proximity), CTEL (electrical crosstalk 1), CTEL2 (electrical crosstalk 2), and CTREC (recoil crosstalk).

(calcmxs = yes) [boolean yes|no]

Parameter for rslflagpix: If 'calcmxs=yes', events are checked for coincidence with MXS events.

(kalow = 5860.) [double]

Parameter for rslflagpix: Lower energy limit [eV] of Mn K-alpha for recoil PHA test.

(kahigh = 5930.) [double]

Parameter for rslflagpix: Upper energy limit [eV] of Mn K-alpha for recoil PHA test.

(kblow = 6450.) [double]

Parameter for rslflagpix: Lower energy limit [eV] of Mn K-beta for recoil PHA test.

(kbhigh = 6520.) [double]

Parameter for rslflagpix: Upper energy limit [eV] of Mn K-beta for recoil PHA test.

(dtflag = no) [boolean yes|no]

Parameter for rslflagpix: Add additional columns to the output containing actual delta time values for crosstalk and antico.

(rsl_resetflags = ALL) [string ALL|NONE|PROX|CTEL|CTEL2|CTREC|ANT|GTI|MXS]

Parameter for rslflagpix: Reset selected Resolve event STATUS flags before processing. Multiple values may be specified as a comma-separated list.

(dtprimary = CALDB) [string CALDB|time interval value]

Parameter for rslsecid: Time interval [ms] that distinguishes between primary and secondary events, used if 'regrade=yes'.

(dtlowmid = CALDB) [string CALDB|time interval value]

Parameter for rslsecid: Time interval [ms] that distinguishes between low- and mid-resolution events, used if 'regrade=yes'.

(dtmidhigh = CALDB) [string CALDB|time interval value]

Parameter for rslsecid: Time interval [ms] that distinguishes high- and mid-resolution events, used if 'regrade=yes'.

(tol = 2.0) [double]

Parameter for rslsecid: Allowed tolerance [ns] for associating secondaries and primaries.

(grpxpithr = 600) [integer]

Parameter for rslsecid: If 'usegrpxpithr=ALL', events with PI below this value are labeled as orphans, and skipped during regrading if 'regrade=yes'.

(usegrpxpithr = ALL) [string ALL|NONE]

Parameter for rslsecid: If 'usegrpxpithr=ALL', events with PI < 'grpxpithr' are defined as orphans, and skipped during regrading if 'regrade=yes'. If 'usegrpxpithr=NONE', PI is not considered in associating and regrading events.

(regrade = no) [boolean yes|no]

Parameter for rslsecid: If 'regrade=yes', the events are regraded based on their assigned times and the 'dtprimary', 'dtlowmid', and 'dtmidhigh' parameters. A newly calculated grade is written into the column specified by the 'itypecol' parameter.

(phaout = PHA2) [string]

Parameter for rslseccor: Name of output PHA column.

(skipthre = yes) [boolean yes|no]

Parameter for rslseccor: If set to yes, ignore trigger threshold in CALDB query.

(gaincoeff = H) [string H|M|L]

Parameter for rslgain: Type of gain coefficients to use.

(linetocorrect = Mnka) [string MnKa|MnKb|CuKa|CuKb|CrKa|CrKb|AlKa|AlKb|MgKa|MgKb]

Parameter for rslgain: Line to fit (HDU name in 'rsl_linefitfile').

(calmethod = Fe55) [string Cal-pix|MXS|Fe55]

Parameter for rslgain: If 'calmethod' is set to Cal-pix, the energy correction is calculated for the calibration pixel (pixel 12) only. If 'calmethod' is set to MXS, the energy correction is calculated for all pixels, but using only events detected during MXS operation as specified by the 'gtifile' parameter. If 'calmethod' is set to Fe55, all pixels and all relevant events are used.

(numevent = 1000) [integer]

Parameter for rslgain: Maximum number of events collected for each spectrum used to calculate a single gain correction.

(minevent = 200) [integer]

Parameter for rslgain: Minimum number of events collected for each spectrum used to calculate a single gain correction.

(grpoverlap = 50.) [double]

Parameter for rslgain: Percentage of overlap between adjacent groups.

(startenergy = -1.) [double]

Parameter for rslgain: Lower limit of energy range [eV] over which the spectra are collected (-1 = automatic).

(stopenergy = -1.) [double]

Parameter for rslgain: Upper limit of energy range [eV] over which the spectra are collected (-1 = automatic).

(extraspread = 40.) [double]

Parameter for rslgain: Energy [eV] by which the energy range is extended on either side, beyond the lowest and highest energies in 'rsl_linefitfile', for the selected calibration feature.

(broadening = 1.0) [double]

Parameter for rslgain: FWHM [eV] initial Gaussian broadening of calibration line profile. If 'fitwidth' is set to no, the profile width is fixed at this value.

(gridprofile = no) [boolean yes|no]

Parameter for rslgain: If 'gridprofile' is set to yes, only output the theoretical profile, including any convolution due to the broadening parameter; no fitting is conducted.

(fitwidth = yes) [boolean yes|no]

Parameter for rslgain: Fit spectral line width.

(background = CONST) [string NONE|CONST|SLOPE]

Parameter for rslgain: Fitted background type.

(spangti = no) [boolean yes|no]

Parameter for rslgain: If 'spangti' is set to yes, events in different time intervals in the input GTI file ('gtifile' in rslgain) may be collected in the same spectrum to be fitted.

(usemp = no) [boolean yes|no]

Parameter for rslgain: If 'usemp=no', only high-resolution primaries are included in the fitted spectra. If 'usemp=yes', mid-resolution primaries are also included.

(ckclip = yes) [boolean yes|no]

If 'ckclip' is set to yes, events with FLAG_CLIPPING set to true are not used in fitting.

(calcerr = yes) [boolean yes|no]

Parameter for rslgain: Compute uncertainties on line shift and width.

(writeerrfunc = yes) [boolean yes|no]

Parameter for rslgain: Output uncertainty functions.

(avgwinrad = 30) [double]

Parameter for rslgain: Radius of interval (in units of 'binwidth') used only to update the initial shift estimate prior to fitting, not used in calculating the average results.

(minwidth0 = 8.0) [double]

Parameter for rslgain: Smallest width (in units of 'binwidth') allowed as the initial value in width fitting.

(maxitcycle = 5) [integer]

Parameter for rslgain: Maximum number of fitting iterations.

(r2tol = 0.001) [double]

Parameter for rslgain: Convergence criterion for R-squared fitting coefficient.

(searchstepshift = 2.) [double]

Parameter for rslgain: Step size ['binwidth'] when fitting shift.

(maxdshift = 10.) [double]

Parameter for rslgain: Largest allowed deviation ['binwidth'] from initial guess of shift.

(bisectolshift = 0.001) [double]

Parameter for rslgain: When the bisection method determines the energy shift to within this amount (in units of 'binwidth'), the fitting procedure is completed.

(searchstepwidth = 5.) [double]

Parameter for rslgain: Step size ['binwidth'] when fitting line width.

(maxdwidth = 10.) [double]

Parameter for rslgain: Largest allowed deviation ['binwidth'] during fitting, from initial guess of line width.

(bisectolwidth = 0.001) [double]

Parameter for rslgain: When the bisection method determines the convolution width to within this amount (in units of 'binwidth'), the fitting procedure is completed.

(minwidth = 0.5) [double]

Parameter for rslgain: Smallest width ['binwidth'] to allow in width fitting.

(nerrshift = 100) [integer]

Parameter for rslgain: Number of shift values in uncertainty calculations.

(nerrwidth = 100) [integer]

Parameter for rslgain: Number of width values in uncertainty calculations.

(shifterrfac = 3.0) [double]

Parameter for rslgain: Factor for determining the range of shift uncertainty arrays.

(widtherrfac = 4.0) [double]

Parameter for rslgain: Factor for determining the range of width uncertainty arrays.

(calcupi = yes) [boolean yes|no]

Parameter for rslpha2pi: If 'calcupi=yes', the UPI column is calculated.

(calcpi = yes) [boolean yes|no]

Parameter for rslpha2pi: Calculate PI column.

(secphacol = PHA2) [string]

Parameter for rslpha2pi: Input PHA column to use for secondary correction.

(addepicol = EPI2) [string]

Parameter for rslpha2pi: Output energy column with secondary correction.

(method = FIT) [string FIT|AVERAGE]

Parameter for rslpha2pi: Correction method: If 'method=FIT', the TEMP_FIT column in the input drift correction file ('driftfile' in rslpha2pi) file made by rslgain is used. If 'method=AVERAGE', the TEMP_AVG column is used.

(binwidth = 0.5) [double]

Parameter for rslpha2pi: PI bin width [eV].

(offset = 0.5) [double]

Parameter for rslpha2pi: Offset for first PI [eV].

(tlmax = 59999) [integer]

Parameter for rslpha2pi: Maximum PI channel.

(writetemp = no) [boolean yes|no]

Parameter for rslpha2pi: Output the temperature that was used in the gain determination for each event.

(st1ctl1col = ST1_CTL1) [string]

Parameter for rslctsfluct: Name of Stage1 Control #1 column.

(st1ctl2col = ST1_CTL2) [string]

Parameter for rslctsfluct: Name of Stage1 Control #2 column.

(st1ctl3col = ST1_CTL3) [string]

Parameter for rslctsfluct: Name of Stage1 Control #3 column.

(st1ctl4col = ST1_CTL4) [string]

Parameter for rslctsfluct: Name of Stage1 Control #4 column.

(pidctlcol = ADRC_CAMC_PID_CTRL) [string]

Parameter for rslctsfluct: Name of PID control column.

(ctlfluctcol = ADRC_CT_CTL_FLUC) [string]

Parameter for rslctsfluct: Name of column used to store CTL fluctuations.

(monfluctcol = ADRC_CT_MON_FLUC) [string]

Parameter for rslctsfluct: Name of column used to store MON fluctuations.

(winsize = 120.0) [double]

Parameter for rslctsfluct: Window size [s] used to calculate fluctuations.

(filfacmin = 0.5) [double]

Parameter for rslctsfluct: Minimum filling factor used to calculate fluctuations.

(nullstatic = 120.0) [double]

Parameter for rslctsfluct: Null value [microKrms] used if HK temperature readings not updating.

(nullfilfac = 110.0) [double]

Parameter for rslctsfluct: Null value [microKrms] used if window smaller than filfacmin.

(nullnoctrl = 100.0) [double]

Parameter for rslctsfluct: Null value [microKrms] used if PID control not operating.

(fluctcol = S_TIME) [string]

Parameter for rsladrgti: Input file temperature fluctuation column or columns

(fluctthr = 1.1) [double]

Parameter for rsladrgti: Fluctuation threshold or thresholds [microKms]

(adrgtimin = 4300.0) [double]

Parameter for rsladrgti: Minimum length of output ADRON interval [s].

(tempext = HK_SXS_TEMP) [string]

Parameter for rslctsfluct and rsladrgti: Name of HK temperature extension.

(coolext = HK_SXS_COOLERS) [string]

Parameter for rslctsfluct and rsladrgti: Name of HK coolers extension.

(pidselcol = ADRC_CAMC_PID_ SENSOR_SEL) [string]

Parameter for rslctsfluct and rsladrgti: Name of PID sensor selection column.

(pxphaoffset = 0.0) [double]

Parameter for rslgain, rslpha2pi: Average offset added to PHA values before applying the gain. A random offset is added to each PHA between -0.5+pxphaoffset and +0.5+pxphaoffset. Therefore, when 'pxphaoffset=0.5', the random offset is between 0 and 1.

(acphaoffset = 0.0) [double]

Parameter for rslanticopi: Average offset added to PHA values before applying the gain. A random offset is added to each PHA between -0.5+acphaoffset and +0.5+acphaoffset. Therefore, when 'acphaoffset=0.5', the random offset is between 0 and 1.

(itypecol = ITYPE) [string]

Parameter for rslgain, rslpha2pi, rslsecid, rslseccor: Name of ITYPE column.

(ckctrec = yes) [boolean yes|no]

Parameter for rslgain, rslsecid: Exclude events with recoil crosstalk. Applies only to rslgain (set to no for rslsecid).

(ckctel = yes) [boolean yes|no]

Parameter for rslgain, rslsecid: Exclude events with electrical crosstalk 1. Applies only to rslgain (set to no for rslsecid).

(ckctel2 = no) [boolean yes|no]

Parameter for rslgain, rslsecid: Exclude events with electrical crosstalk 2. Applies only to rslgain (set to no for rslsecid).

(ckant = yes) [boolean yes|no]

Parameter for rslgain, rslsecid: Exclude events with antico coincidence. Applies only to rslgain (set to no for rslsecid).

(ckrisetime = yes) [boolean yes|no]

Parameter for rslgain, rslsecid, rslflagpix: Do not use events with RISE_TIME > 127.

(tempidx = NOM) [string]

Parameter for rslgain, rslpha2pi: Input temperature index for selecting gain function to convert energy to PHA profiles during fitting. If set to NOM, the gain function corresponding to the middle (nominal) temperature will be selected.

(ntemp = 3) [integer]

Parameter for rslgain, rslpha2pi: Number of temperatures from gain file to use in interpolation.

(gapdt = -1.0) [double]

Parameter for gain-fitting tasks (e.g. ahgainfit), rslpha2pi: Time [s] between events to define a gap (or < 0).

(extrap = no) [boolean yes|no]

Parameter for gain-fitting tasks (e.g. ahgainfit), rslpha2pi: Allow extrapolation when determining drift temperature.

(randomize = yes) [boolean yes|no]

Parameter for multiple tasks: Allow randomization.

(seed = 2) [integer]

Parameter for multiple tasks: Random number generator seed. If 'seed=0' the system time is used.

(startdate) [string]

Start date/time of xapipeline (output).

(numerrs = 0) [string]

Number of errors from xapipeline (output).

(cleanup = yes) [boolean yes|no]

Delete temporary files if 'cleanup=yes'.

(clobber = no) [boolean yes|no]

Overwrites the existing output file if set to yes.

(chatter = 2) [integer 0|1|2|3]

Chatter level for output. Set to 0 to suppress output, or to 1, 2, or 3 for increasing the chatter of the output.

(logfile = !DEFAULT) [string DEFAULT|NONE|file name]

Log file name. If set to DEFAULT, uses the name of the task and, if preceded by "!", overwrites the file if it exists. If set to NONE, no log file is created.

(debug = no) [boolean yes|no]

Diagnostic output is printed to the screen if set to yes.

(history = yes) [boolean yes|no]

Records tool parameters in HISTORY.

EXAMPLES

1. The following command recalibrates (Stage 1) and re-screens (Stage 2) all Resolve and Xtend data for sequence 100050020 that currently resides in the directory /data/100050020/. The output is stored in a directory called /data/100050020_reproc/.

   xapipeline indir=/data/100050020 outdir=/data/100050020_reproc entry_stage=1 exit_stage=2 \ 
       steminputs=xa100050020 stemoutputs=DEFAULT instrument=ALL verify_input=no

2. The following example re-screens (Stage 2 only) Resolve data for the same data set as in the previous example.

   xapipeline indir=/data/100050020 outdir=/data/100050020_reproc entry_stage=2 \ 
       exit_stage=2 steminputs=xa100050020 stemoutputs=DEFAULT instrument=Resolve verify_input=no

SEE ALSO

LAST MODIFIED