...

Application panel under ROI (Region Of Interest) tab has a minimal number of control fields, which allow to specify the file with image and open/close Mask Editor UI in separate window.

Image Removed

When launched, Mask Editor works as completely independent application. The Mask Editor allows to draw on image any number of a few geometry figure types and finally generate and save positive or negative mask for loaded image.

Image RemovedImage Removed

...

controlls re-implemented algorithms of the command line roicon, described in Make ndarray for ROI mask.

Image Added

The files with ndarray and geometry constants should be selected as input parameters in the first two options of this GUI. The names of other intermediate and output files for "Image", "Mask image", and "Mask ndarray" are optional. Next three buttons

3. reconstruct image from ndarray,
4. Open Mask Editor, and
5. Convert mask image to ndarray

executes associated procedures. "Mask control bits" parameter controls sensor pixels, which will to be masked. For example, for CSPAD

Mask control bits = 0 - do not mask sensor pixels
+1-mask edges,
+2-wide pixels,
+4-non-bounded pixels,
+8-non-bounded pixel neighbours.

When launched, Mask Editor works as completely independent application. The Mask Editor allows to draw on image any number of a few geometry figure types and finally generate and save positive or negative mask for loaded image. When mask is created it needs to be saved in the "Mask image" file. After that mask editor can be closed.

Image AddedImage Added

All files and images of the ROI application can be "Plot"-ted and "View"-ed. For now, mask file is saved in the work directory and is not deployed. In stead, its path could be used in the ImgAlgos.NDArrCalib module.

Anchor

	Single File Manager
	Single File Manager

Single File Manager

Image Added

File manager tool consists of Status panel and control panel:

Image Added

File manager control panel contains a set of control fields with functionality as follows.

Button Browse - launches the file selection window which helps to select any calibration file in any location. Location is hinted in the intermediate pop-up window. Selected file is displayed in the next-left information field.
View button - opens/closes the file viewer in separate window.
Plot buttons - opens/closes the plotter window and plots the file as 2-d image (if applicable).
Delete button - deletes the selected file from disc.
Move/Copy buttons - perform associated actions on selected file. The destination directory and file name is defined by the Instrument/Experiment/Detector selection panel and next-right filelds:
for detector selection button - sets the destination detector name from drop down menu,
calibration type selection button - sets the destination calibration type, and
two editable fields - set the run range for destination calibrationfile.

Anchor

	Group File Manager
	Group File Manager

Group File Manager

Image Added

Anchor

	Geometry
	Geometry

Geometry

Image Added Image Added

Anchor

	Metrology
	Metrology

Metrology

Image Added

Metrology tool processes xlsx files from opitcal measurements, produces calibration constants of types geometry, center and tilt, and deploy them in calibration directory.

xlsx files are human-made, so, one has to be careful and check that the text file, produced in auto-conversion by command #2 has correct format.

Alignment

Image Added

Alignment tool works with geometry files, produced in Metrology tool and allows to tune quad or other sensor positions in the detector, using image with real objects (rings, shadows, etc).

More details about this tool can be found in Detector Alignment Tool.

Anchor

	Configuration
	Configuration

Configuration

Configuration tool has its own tab bar switching between panels with sets of parameters.

Image Added

Two panels are implemented currently:

Anchor

	Configuration Parameters
	Configuration Parameters

Configuration Parameters

Image Added

This panel has a few active fields:

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

...

Single File Manager

Image Removed

File manager tool consists of Status panel and control panel:

Image Removed

File manager control panel contains a set of control fields with functionality as follows.

Button Browse - launches the file selection window which helps to select any calibration file in any location. Location is hinted in the intermediate pop-up window. Selected file is displayed in the next-left information field.
View button - opens/closes the file viewer in separate window.
Plot buttons - opens/closes the plotter window and plots the file as 2-d image (if applicable).
Delete button - deletes the selected file from disc.
Move/Copy buttons - perform associated actions on selected file. The destination directory and file name is defined by the Instrument/Experiment/Detector selection panel and next-right filelds:
for detector selection button - sets the destination detector name from drop down menu,
calibration type selection button - sets the destination calibration type, and
two editable fields - set the run range for destination calibrationfile.

...

Group File Manager

Image Removed

...

Geometry

Image Removed

...

Metrology

Image Removed

...

Configuration

Configuration tool has its own tab bar switching between panels with sets of parameters.

Image Removed

Two panels are implemented currently:

...

Configuration Parameters

Image Removed

This panel has a few active fields:

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 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.

...

Note
Modal dialog assumes that one of the buttons in this type of dialog window need to be clicked, otherwise UI will be frozen.

Project status

Current 2015-04-08 status corresponds to:

Code Block
relinfo Pkg/Rel TEST BASE(ana-0.1113.018) CalibManager HEAD V00-00-4183 ImgAlgos HEAD V00-03-80 PSCalib HEAD V00-02-33 PSQt HEAD -

Completely implemented applications under calibman tabs:

Dark
ROI
File Manager
- Single File Manager
- Group File Manager
Configuration

Partly implemented calibman tab(s):

Geometry
- Metrology

...

- - implemented for CSPAD CXI-V1, XPP-V2, CSPAD2x2
- Alignment

calibrun - command-line application is fully functional

Recommended updates

...

On 20142015-04-29

Use default version of all involved packages.

Until 15: ana-current is not pointing to (a.k.a. ana-0.11.0 use command

sit_setup ana-0.11.0

.14.01) does not need in updates.

How How to get and run calibman

Run application in current release

...

Code Block
cd <your-favorite-directory>; sit_setup ana-0.11.0; 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:

Code Block

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

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.

How to calibrate / deploy files for dark correction

Click on tab Dark.
Set Instrument, Experiment, from combo boxes and click on Select button to select Detector(s) from pop-up window.
Set filter for runs using combo boxes to the right from labels Show runs and for detectors.
For runs in the table, which you want to calibrate, click on button Go, relax and wait until button Deploy show-up to the right from button. A few buttons Go can be clicked sequentially for different runs in order to run appropriate jobs in batch simultaneously.
Change validity range if necessary, click on Deploy button. If everything is ok, it is done!

Known problems and ways around

World is not perfect. Anything may happen during this long workflow. Expert mode sheds light on most of the problems. Here is a list of most frequent problems;

AFS token is expired for your terminal session. Batch system will complain. Before launching calibman application, first execute kinit and aklog commands.
job on data from NEH/FEH are submitted to the wrong butch queue psfehq/psnehq. Set appropriate queue.
DB has a list of sources (detectors) which does not coincide with what is written in xtc file. After job is submitted, check the list of detectors found in xtc scan and check only available detectors in the Detector selection menu.

Command line interface

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

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:

Code Block
calibrun -h

which prints

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 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.

How to calibrate / deploy files for dark correction

Click on tab Dark.
Set Instrument, Experiment, from combo boxes and click on Select button to select Detector(s) from pop-up window.
Set filter for runs using combo boxes to the right from labels Show runs and for detectors.
For runs in the table, which you want to calibrate, click on button Go, relax and wait until button Deploy show-up to the right from button. A few buttons Go can be clicked sequentially for different runs in order to run appropriate jobs in batch simultaneously.
Change validity range if necessary, click on Deploy button. If everything is ok, it is done!

Known problems and ways around

World is not perfect. Anything may happen during this long workflow. Expert mode sheds light on most of the problems. Here is a list of most frequent problems;

AFS token is expired for your terminal session. Batch system will complain. Before launching calibman application, first execute kinit and aklog commands.
job on data from NEH/FEH are submitted to the wrong butch queue psfehq/psnehq. Set appropriate queue.
DB has a list of sources (detectors) which does not coincide with what is written in xtc file. After job is submitted, check the list of detectors found in xtc scan and check only available detectors in the Detector selection menu.

Command line interface

Available since release ana-0.10.16.

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:

Code Block
calibrun -h

which prints

Code Block

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

Code Block

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   event code experimentfor name, ex.: cxi12345dark event selection
  -rt RUNNUMTHR_RMS, --run=RUNNUMthr_rms=THR_RMS
                        run numberthreshold on rms for hot pixel mask evaluation
  -nv NUM_EVENTSRUNRANGE, --num_events=NUM_EVENTSrunrange=RUNRANGE
                        number of events to processvalidity run range, ex.: 123-567 or 123-end
  -sq SKIP_EVENTSQUEUE, --skip_events=SKIP_EVENTSqueue=QUEUE
                        numberqueue ofname, eventsex: topsnehq, skippsfehq, beforepsanacsq. processing
  -t THR_RMS, --thr_rms=THR_RMSIf specified
                        threshold- onrun rms for hot pixel mask evaluationin batch
  -vw RUNRANGEWORKDIR, --runrangeworkdir=RUNRANGEWORKDIR
                        validitywork run rangedirectory, ex.: 123-567 or 123-end./work
  -qc QUEUECALIBDIR, --queuecalibdir=QUEUECALIBDIR
                        non-standard queuecalibration namedirectory, ex: psnehq, psfehq, psanacsq. If specified./calib
  -x XTCDIR, --xtcdir=XTCDIR
                        non- run in batch
  -w WORKDIR, --workdir=WORKDIRstandard path to xtc directory(<INS>/<EXP>/xtc are
                        work directoryrequired), ex: ./work
  -c CALIBDIR, --calibdir=CALIBDIRmydir/xpp/xppi0613/xtc, or
                        non-standard calibration directory, ex: ./calib/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
                   deploy calibrated files under the "calibcalibman" directory

The calibrun application reuses code and approach developed for calibman. At start calibrun loads parameters from configuration file confpars-calibman.txt. By default this file is the same configuration file as for calibman. If parameters were already set in confpars-calibman.txt, then calibrun can be started with a single parameter - run number (-r <run-number>) and options for processing (-P) and deployment (-D), for example:

...

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

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:

Code Block
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.

Versions Compared

Old Version 30

New Version Current

Key

Single File Manager

Group File Manager

Geometry

Metrology

Alignment

Configuration

Configuration Parameters

Single File Manager

Group File Manager

Geometry

Metrology

Configuration

Configuration Parameters

Project status

Recommended updates

On 20142015-04-29
Use default version of all involved packages.
Until 15: ana-current is not pointing to (a.k.a. ana-0.11.0 use command

sit_setup ana-0.11.0

.14.01) does not need in updates.

How How to get and run calibman

Run application in current release

Get latest version, compile, and run

First session

How to calibrate / deploy files for dark correction

Known problems and ways around

Command line interface

First session

How to calibrate / deploy files for dark correction

Known problems and ways around

Command line interface

References

How to run on ffb data

References

Page History

Versions Compared

Old Version 30

New Version Current

Key

Single File Manager

Group File Manager

Geometry

Metrology

Alignment

Configuration

Configuration Parameters

Single File Manager

Group File Manager

Geometry

Metrology

Configuration

Configuration Parameters

Project status

Recommended updates

On 20142015-04-29Use default version of all involved packages.Until 15: ana-current is not pointing to (a.k.a. ana-0.11.0 use command sit_setup ana-0.11.0 .14.01) does not need in updates.

How How to get and run calibman

Run application in current release

Get latest version, compile, and run

First session

How to calibrate / deploy files for dark correction

Known problems and ways around

Command line interface

First session

How to calibrate / deploy files for dark correction

Known problems and ways around

Command line interface

References

How to run on ffb data

References

On 20142015-04-29
Use default version of all involved packages.
Until 15: ana-current is not pointing to (a.k.a. ana-0.11.0 use command

sit_setup ana-0.11.0

.14.01) does not need in updates.