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• Dir work button - launch directory selection window for work directory. Selected directory shows up in the next right information field.
• Dir results button - launch directory selection window for results directory. Selected directory shows up in the next right information field. This directory is not currently in use.
• File prefix editable field - sets common prefix of all files created in the work directory, excluding the log file.
• Queue combo box - sets the queue name for batch jobs from available list containing psnehq, psfehq, etc. 
• Event start/end editable fields - set the first and last event in current run for calibration processing job.
• Threshold RMS, ADU (editable field) - sets the threshold on RMS in ADU (Analog to Digit Units) for hot pixel mask. If RMS for pixel exceeds this threshold - pixel is marked as hot in the hot pixel mask file. "Zero" is a special value, indicating that no pixels will be flagged as hot pixels because of noise.
• Threshold MIN/MAX (editable fields) - if a pixel's pedestal is outside the MIN/MAX range it will be flagged in the hot pixel mask file.
• Deploy hotpix mask check box - if checked - hotpixel mask file will be deployed along with pedestal file at click on Deploy button in the List of run items.
  
  

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Completely implemented applications under calibman tabs:

• Dark
• ROI - mask conversion will be available since ana-0.13.14 
• File Manager
  • Single File Manager
  • Group File Manager
• Configuration - new list of queues will be available since ana-0.13.14 
• Geometry
  • Metrology - implemented for CSPAD CXI-V1, XPP-V2, CSPAD2x2
  • Alignment - will be available since ana-0.14.01 

calibrun - command-line application is fully functional

Recommended updates

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On 2015-04-0815: wait for ana-0current (a.14.01k.a. ana-0.14.01) does not need in updates.

 

 

How to get and run calibman

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cd <your-favorite-directory>;
sit_setup ana-current;
calibman;

Get latest version, compile, and run

The latest version of this application with recent modifications for packages can be created and executed from the local release directory. Login to psana, then run use commands with appropriate substitutions for <...> fields:

cd <your-favorite-test-directory>;
newrel ana-current test-CalibManager;
cd test-CalibManager;
sit_setup <release-tag>;
addpkg CalibManager HEAD;
addpkg <package2> HEAD;
addpkg <package3> HEAD;
...
scons;
calibman;

First session

No matter what tool tab is opening by default in the first session, it would be better to make sure that configuration parameters are set correctly. To do that click on tab Configuration, which opens Configuration Settings panel,  then click on tab Parameters. Most parameters can be used with default values, but it is important to check, that

First session

No matter what tool tab is opening by default in the first session, it would be better to make sure that configuration parameters are set correctly. To do that click on tab Configuration, which opens Configuration Settings panel,  then click on tab Parameters. Most parameters can be used with default values, but it is important to check, that

• correct queue will be used for batch jobs. If necessary, change Queue in combo box.

• correct

• correct queue will be used for batch jobs. If necessary, change Queue in combo box.

• correct range of events is set for event processing.

• Threshold on rms is good for calibrated detector(s). Evaluation of this threshold requires in simple analysis which can be done after the 1st iteration on event averaging. Files containing averaged intensities and their rms values can be plotted as image and spectra. Spectrum of rms gives a rough idea of how to set this threshold. When threshold is set, second iteration on event averaging will produce correct mask-file for hot pixels, which rms exceeds the threshold.

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Available since release ana-0.10.16  (CalibManager V00-00-40)16.


Command line interface for dark-run calibration of detectors is implemented by P.O.C.s request. It can be started by the command calibrun with parameters.  The list of parameters can be dumped on terminal by the command:

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Usage:   calibrun [options] args
Example: calibrun -e xppi0613 -d CSPAD,OPAL1000 -c ./calib -P -D -r 173

calibrun - command line calibration utility

Options:
  -h, --help            show this help message and exit
  -e EXP, --exp=EXP     experiment name, ex.: cxi12345
  -r RUNNUM, --run=RUNNUM
                        run number
  -n NUM_EVENTS, --num_events=NUM_EVENTS
                        number of events to process
  -s SKIP_EVENTS, --skip_events=SKIP_EVENTS
                        number of events to skip before processing
  -m SCAN_EVENTS, --scan_events=SCAN_EVENTS
                        number of events to scan data and search for selected
                        detector(s)
  -f EVENT_CODE, --event_code=EVENT_CODE
                        event code for dark event selection
  -t THR_RMS, --thr_rms=THR_RMS
                        threshold on rms for hot pixel mask evaluation
  -v RUNRANGE, --runrange=RUNRANGE
                        validity run range, ex.: 123-567 or 123-end
  -q QUEUE, --queue=QUEUE
                        queue name, ex: psnehq, psfehq, psanacsq. If specified
                        - run in batch
  -w WORKDIR, --workdir=WORKDIR
                        work directory, ex: ./work
  -c CALIBDIR, --calibdir=CALIBDIR
                        non-standard calibration directory, ex: ./calib
  -x XTCDIR, --xtcdir=XTCDIR
                        non-standard path to xtc directory(<INS>/<EXP>/xtc areto xtc directory(<INS>/<EXP>/xtc are
                        required), ex: .mydir/xpp/xppi0613/xtc, or
                        required), ex: .mydir/xpp/xppi0613/reg/d/ffb/cxi/cxi12345/xtc
  -d DETECTOR, --detector=DETECTOR
                        detector names separated by comma,
                        ex:CSPAD,CSPAD2x2,PNCCD
  -p PRINT_BITS, --print_bits=PRINT_BITS
                        0-print nothing, +1-debug, +2-info, +4-warning,
                        +8-error, +16-critical; default=036, minimal
                        recommended=020
  -P, --process         process xtc files and produce calib files under the
                        "work" directory
  -D, --deploy          deploy calibrated files under the "calib" directory
  -L, --loadcfg         load and use configuration parameters from file after
                        "calibman"

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otherwise, desired parameters need to be defined in the command line.  If parameters are not defined either in the command line or in the configuration file, then application will dump to terminal hint-warnings about missing option(s) which needs to be added to the command line in order to complete job. An example of the command with minimal set of self-sufficient parameters should looks like

calibrun -e xppi0613 -d CSPAD,OPAL1000 -P -D -r 173

This command will process (-P) xtc files for experiment (-e) xppi0613, run (-r) 173, detectors (-d) CSPAD and (,) OPAL1000, and deploy (-D) them for default run range 173-end under the default calib directory /reg/d/psdm/xpp/xppi0613/calib/

By default the image-averaging psana job is processed interactively. If queue (-q <queue-name>) option is provided, it is submitted in batch.

By default the calibrun command produces quite extensive output on terminal which in most cases is sufficient to figure out what is going on.  If the print-control option (-p  0) is provided, the major output will be suppressed and only begin, end of job comments, and warning messages will be printed. Most complete output can be found in the session  log file auto-saved in the work directory with relevant time stamp in the name, for example: ./work/2014-04-16-16:43:52-log.txt

GUI-based calibration manager calibman has the same file name conventions and can always be used to inspect all output files and problems generated by the command line application  calibrun.

References

calibrun -e xppi0613 -d CSPAD,OPAL1000 -P -D -r 173

This command will process (-P) xtc files for experiment (-e) xppi0613, run (-r) 173, detectors (-d) CSPAD and (,) OPAL1000, and deploy (-D) them for default run range 173-end under the default calib directory /reg/d/psdm/xpp/xppi0613/calib/

By default the image-averaging psana job is processed interactively. If queue (-q <queue-name>) option is provided, it is submitted in batch.

By default the calibrun command produces quite extensive output on terminal which in most cases is sufficient to figure out what is going on.  If the print-control option (-p  0) is provided, the major output will be suppressed and only begin, end of job comments, and warning messages will be printed. Most complete output can be found in the session  log file auto-saved in the work directory with relevant time stamp in the name, for example: ./work/2014-04-16-16:43:52-log.txt

GUI-based calibration manager calibman has the same file name conventions and can always be used to inspect all output files and problems generated by the command line application  calibrun.

How to run on ffb data

Command calibrun can work on ffb data using option -x <path-to-xtc>. This option sets non-standard path to xtc files. For example:

calibrun <options> -x /reg/d/ffb/cxi/cxi12345/xtc <more-options> 

The "live" mode is turning on automatically if the directory path has "ffb" sub-folder.

References

• Calibration Store
•  Calibration Management Tool
• Description of Calibration database
• Mask Editor 
• Make ndarray for ROI mask
• Detector Alignment Tool
• Detector Geometry