Page History
...
This page provides examples for selected modules from Psana psana - Module Catalog.
Auxiliary scripts
A few python scripts in ImgPixSpectra/data/
show how to process/plot the spectral array stored in the file.
...
Code Block | ||
---|---|---|
| ||
[psana] files = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-1>.xtc events = 5 modules = cspad_mod.CsPadCalib CSPadPixCoords.CSPadImageProducer ImgAlgos.ImgSaveInFile [cspad_mod.CsPadCalib] inputKey = outputKey = calibrated doPedestals = yes doPixelStatus = no doCommonMode = no #[CSPadPixCoords.CSPadInterpolImageProducer] [CSPadPixCoords.CSPadImageProducer] calibDir = /reg/d/psdm/<instrument>/<experiment>/calib typeGroupName = CsPad::CalibV1 source = CxiDs1.0:Cspad.0 key = calibrated imgkey = Image2D tiltIsApplied = true [ImgAlgos.ImgSaveInFile] source = CxiDs1.0:Cspad.0 #eventSave = 1 saveAll = true |
Example for module CSPadPixCoords::CSPadNDArrProducer
See Module CSPadPixCoords::CSPadNDArrProducer
Example of the module CSPadNDArrProducer working in sequence with ImgAlgos::NDArrAverage is shown in Example for module ImgAlgos::NDArrAverage
...
This script makes ndarrays for two cspad2x2 detectors and use them evaluate average, rms, mask and hot pixel arrays.
See Module CSPadPixCoords::CSPad2x2NDArrProducer
Example for module CSPadPixCoords::CSPad2x2ImageProducer
See Module CSPadPixCoords::CSPad2x2ImageProducer
Example of the configuration script for psana (cspad2x2-test.cfg):
...
Example for package ImgPixSpectra
Modules:
- ImgPixSpectra::CSPadPixSpectra
- ImgPixSpectra::CSPad2x2PixSpectra
- ImgPixSpectra::CameraPixSpectra
...
See module description in Module ImgPixSpectra::CSPadPixSpectra
Configuration file psana-cxib2313-r0114-cspad-pix-spectra.cfg
:
...
See module description in Module ImgPixSpectra::CSPad2x2PixSpectra
Configuration file example for CSPad2x2PixSpectra
:
...
Examples for package ImgAlgos
See Package ImgAlgos
Example for module ImgAlgos::Tahometer
See Module ImgAlgos::Tahometer
Example of the psana configuration file:
...
Example for module ImgAlgos::PnccdImageProducer
See Module ImgAlgos::PnccdImageProducer
Example of the psana configuration file:
...
Example for module ImgAlgos::CameraImageProducer
See Module ImgAlgos::CameraImageProducer
Example of the psana configuration file:
...
Example for module ImgAlgos::PrincetonImageProducer
See Module ImgAlgos::PrincetonImageProducer
Example of the psana configuration file:
...
See description of parameters in Module ImgAlgos::AcqirisArrProducer
Example of the psana configuration file psana-amo01509-r0125-acqiris.cfg
:
...
See description of parameters in Module ImgAlgos::AcqirisAverage
Configuration file psana-amo01509-r0125-acqiris-average.cfg:
...
See description of parameters in Module ImgAlgos::AcqirisCalib
Configuration file psana-amo01509-r0125-acqiris-calib.cfg:
...
See description of parameters in Module ImgAlgos::AcqirisCFD
Configuration file psana_cfd.cfg:
...
See description of parameters in Modules ImgAlgos::AcqirisArrProducer, AcqirisAverage, and AcqirisCalib
Configuration file psana-amo01509-r0125-acqiris-comb.cfg:
...
Example for module ImgAlgos::NDArrAverage
- See Module ImgAlgos::NDArrAverage andModule CSPadPixCoords::CSPadNDArrProducer
The
NDArrAverage
module in combination with CSPadNDArrProducer (or any other device NDArrProducer) can be used for evaluation of averaged pedestals or background using dedicated runs.
Typical configuration file may looks like this:No Format # Run this script: # psana -c psana-meca1113-r0045-cspad-cspad-dark-hotpix.cfg [psana] files = exp=meca1113:run=45 events = 400 #skip-events = 0 modules = CSPadPixCoords.CSPadNDArrProducer \ ImgAlgos.NDArrAverage \ ImgAlgos.Tahometer [CSPadPixCoords.CSPadNDArrProducer] source = MecTargetChamber.0:Cspad.0 inkey = outkey = cspad_ndarr outtype = int16 is_fullsize = yes print_bits = 3 [ImgAlgos.NDArrAverage] source = MecTargetChamber.0:Cspad.0 key = cspad_ndarr avefile = cspad.0-ave rmsfile = cspad.0-rms maskfile = cspad.0-msk hotpixfile = cspad.0-hot thr_rms_ADU = 10 thr_min_ADU = 4 thr_max_ADU = 10000 print_bits = 29 #evts_stage1 = 100 #gate_width1 = 500. #evts_stage2 = 200 #gate_width2 = 100. [ImgAlgos.Tahometer] dn = 100 print_bits = 7
- Module
ImgAlgos.Tahometer
is not required in this configuration file and is added for convenience to print timing statistics for this job. - Evaluation of average intensity in 2 or 3 stages using gate-based algorithms excludes out-layers in intensity spectra and makes average more stable and reliable. However, the gate width is not an universal parameter. In order to set this parameter one has to look at spectrum of averaged intensities for particular device. The same is valid for evaluation of hot/bad pixel masks. One has to plot spectra of averaged intensity and rms values. Averaged intensity and rms spectra for exp=meca1113:run=45 are shown on plots, respectively:
...
Example for module ImgAlgos::NDArrCalib
- See Module ImgAlgos::NDArrCalib, Module ImgAlgos::NDArrAverage
The
NDArrCalib
module in combination with PnccdNDArrProducer (or any other device NDArrProducer) can be used for evaluation of averaged pedestals or background using dedicated runs.
Typical configuration file may looks like this:
Code Block |
---|
[psana] files = exp=amoa1214:run=7 #skip-events = 100 events = 5 modules = ImgAlgos.Tahometer \ ImgAlgos.PnccdNDArrProducer \ ImgAlgos.NDArrCalib \ ImgAlgos.PnccdImageProducer \ ImgAlgos.ImgSaveInFile # ImgAlgos.NDArrAverage \ [ImgAlgos.PnccdNDArrProducer] source = DetInfo(Camp.0:pnCCD.0) key_in = key_out = pnccd-ndarr outtype = asdata print_bits = 13 [ImgAlgos.NDArrCalib] source = DetInfo(Camp.0:pnCCD.0) key_in = pnccd-ndarr key_out = calibrated do_peds = yes do_cmod = yes do_stat = no do_mask = no do_bkgd = no do_gain = no do_nrms = no do_thre = no fname_mask = fname_bkgd = fname_rms = masked_value = 0 threshold_nrms = 03 threshold = 100 below_thre_value = 50 0 bkgd_ind_min = 0 bkgd_ind_max = 1000 bkgd_ind_inc = 10 print_bits = 255 [ImgAlgos.PnccdImageProducer] source = DetInfo(Camp.0:pnCCD.0) #inkey = pnccd-ndarr inkey = calibrated outimgkey = pnccd-img gap_size = 20 gap_value = 0 print_bits = 1 [ImgAlgos.ImgSaveInFile] source = DetInfo(Camp.0:pnCCD.0) key = pnccd-img fname = pnccd-img-from-arr ftype = txt saveAll = true print_bits = 31 [ImgAlgos.Tahometer] dn = 100 print_bits = 7 |
...
Example for module ImgAlgos::ImgAverage
- See Module ImgAlgos::ImgAverage
- The
ImgAverage
module can be used for evaluation of averaged pedestals or background using dedicated runs. Typical configuration file may looks like this:
...
Example for module ImgAlgos::ImgMaskEvaluation
- See Module ImgAlgos::ImgMaskEvaluation
- Configuration parameters for psana:
...
Example for module ImgAlgos::ImgCalib
Code Block | ||
---|---|---|
| ||
[ImgAlgos.CameraImageProducer] source = DetInfo(:Opal1000) key_in = key_out = img subtract_offset = true print_bits = 1 [ImgAlgos.ImgCalib] source = DetInfo(:Opal1000) key_in = img key_out = calibrated fname_peds = <pedestal-file-name> fname_mask = <mask-file-name> fname_bkgd = fname_gain = print_bits = 31 |
...
Example for module ImgAlgos::ImgRadialCorrection
See Module ImgAlgos::ImgRadialCorrection
Code Block | ||
---|---|---|
| ||
[psana] files = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-1>.xtc \ /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-2>.xtc \ ... /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-N>.xtc skip-events = 500 events = 10 modules = cspad_mod.CsPadCalib \ # ImgAlgos.CSPadBkgdSubtract \ CSPadPixCoords.CSPadImageProducer \ ImgAlgos.ImgRadialCorrection \ ImgAlgos.ImgSaveInFile:1 [cspad_mod.CsPadCalib] inputKey = outputKey = calibrated doPedestals = yes doPixelStatus = no doCommonMode = no [ImgAlgos.CSPadBkgdSubtract] source = DetInfo(CxiDs1.0:Cspad.0) inputKey = calibrated outputKey = bkgd_subtracted_arr bkgd_fname = <the-file-name-with-background-array> norm_sector = 0 print_bits = 0 [CSPadPixCoords.CSPadImageProducer] calibDir = /reg/d/psdm/<instrument>/<experiment>/calib typeGroupName = CsPad::CalibV1 source = CxiDs1.0:Cspad.0 key = calibrated imgkey = current_img #tiltIsApplied = true [ImgAlgos.ImgRadialCorrection] source = DetInfo(CxiDs1.0:Cspad.0) inkey = current_img outkey = r_cor_img xcenter = 866 ycenter = 857 rmin = 100 rmax = 810 n_phi_bins = 60 event = 0 print_bits = 3 [ImgAlgos.ImgSaveInFile:1] source = CxiDs1.0:Cspad.0 key = r_cor_img fname = <file-name-for-image-array> #saveAll = true eventSave = 8 |
...
Example for module ImgAlgos::ImgPeakFinder
See Module ImgAlgos::ImgPeakFinder
Configuration file example:
...
Example for module ImgAlgos::ImgPeakFinderAB
See Module ImgAlgos::ImgPeakFinderAB
Configuration file example:
...
Example for module ImgAlgos::ImgHitFinder
See Module ImgAlgos::ImgHitFinder
ImgHitFinder in regular mode needs in file with pedestals (offset) to correct the image and file with threshold.
...
Example for module ImgAlgos::ImgSpectra
See Module ImgAlgos::ImgSpectra
Configuration file for psana:
...
Example for module ImgAlgos::ImgSpectraProc
See Module ImgAlgos::ImgSpectraProc
Configuration file for psana:
...
Code Block | ||
---|---|---|
| ||
modules = ... ImgAlgos.ImgSaveInFile:1 ... [ImgAlgos.ImgSaveInFile:1] source = DetInfo(:Opal1000) # or CxiDs1.0:Cspad.0 key = img fname = my-img #ftype = txt #ftype = bin #ftype = png ftype = tiff #eventSave = 5 saveAll = true |
See Module ImgAlgos::ImgSaveInFile
Example for module ImgPeakFinder and ImgPeakFilter for CSPad
...
Example for module ImgAlgos::CSPadArrAverage
See Module ImgAlgos::CSPadArrAverage
Configuration file example for evaluation of pedestals:
...
Example for module ImgAlgos::CSPadBkgdSubtract
See Module ImgAlgos::CSPadBkgdSubtract
Code Block | ||
---|---|---|
| ||
[psana] files = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-1>.xtc \ /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-2>.xtc \ ... /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-N>.xtc skip-events = 500 events = 10 modules = cspad_mod.CsPadCalib ImgAlgos.CSPadBkgdSubtract [cspad_mod.CsPadCalib] inputKey = outputKey = calibrated doPedestals = yes doPixelStatus = no doCommonMode = no [ImgAlgos.CSPadBkgdSubtract] source = DetInfo(CxiDs1.0:Cspad.0) inputKey = calibrated outputKey = bkgd_subtracted bkgd_fname = <the-file-name-with-background-array> norm_sector = 0 print_bits = 3 |
The file with the background array, bkgd_fname
, was obtained by averaging 1000 events using module CSPadArrAverage. Subtraction is done with normalization for norm_sector=0
.
...
Example for Module ImgAlgos::CSPadMaskApply
See Module ImgAlgos::CSPadMaskApply
The array for mask contains zeros and ones for masked and passed pixels, respectively, and has a shape of full-size CSPad array 4*8*185388.
...
Example for module ImgAlgos::CSPadArrNoise
See Module ImgAlgos::CSPadArrNoise
Code Block | ||
---|---|---|
| ||
[psana] modules = cspad_mod.CsPadCalib ImgAlgos.CSPadArrNoise files = /reg/d/psdm/cxi/cxi49012/xtc/e158-r0020-s00-c00.xtc \ /reg/d/psdm/cxi/cxi49012/xtc/e158-r0020-s01-c00.xtc \ /reg/d/psdm/cxi/cxi49012/xtc/e158-r0020-s02-c00.xtc \ /reg/d/psdm/cxi/cxi49012/xtc/e158-r0020-s03-c00.xtc \ /reg/d/psdm/cxi/cxi49012/xtc/e158-r0020-s04-c00.xtc \ /reg/d/psdm/cxi/cxi49012/xtc/e158-r0020-s05-c00.xtc #skip-events = 1000 events = 10 [cspad_mod.CsPadCalib] inputKey = outputKey = calibrated doPedestals = yes doPixelStatus = no doCommonMode = no [ImgAlgos.CSPadArrNoise] source = DetInfo(CxiDs1.0:Cspad.0) key = calibrated statusfile = ana-cxi49012/cspad-cxi49012-r0020-noise-status.dat maskfile = ana-cxi49012/cspad-cxi49012-r0200-noise-mask.dat print_bits = 255 rmin = 3 dr = 1 SoNThr = 3 frac_noisy_imgs = 0.15 |
...
Example for Module ImgAlgos::CSPadArrPeakFinder
See Module ImgAlgos::CSPadArrPeakFinder
Code Block | ||
---|---|---|
| ||
[psana] files = \ /reg/d/psdm/cxi/cxi49012/xtc/e158-r0150-s00-c00.xtc \ /reg/d/psdm/cxi/cxi49012/xtc/e158-r0150-s01-c00.xtc \ /reg/d/psdm/cxi/cxi49012/xtc/e158-r0150-s02-c00.xtc \ /reg/d/psdm/cxi/cxi49012/xtc/e158-r0150-s03-c00.xtc \ # /reg/d/psdm/cxi/cxi49012/xtc/e158-r0150-s04-c00.xtc \ suddenly it became unavailable... /reg/d/psdm/cxi/cxi49012/xtc/e158-r0150-s05-c00.xtc #skip-events = 1000 #events = 200 modules = cspad_mod.CsPadCalib \ ImgAlgos.CSPadMaskApply \ ImgAlgos.CSPadArrPeakFinder [cspad_mod.CsPadCalib] inputKey = outputKey = calibrated doPedestals = yes doPixelStatus = no doCommonMode = no [ImgAlgos.CSPadMaskApply] source = DetInfo(CxiDs1.0:Cspad.0) inkey = calibrated outkey = masked_arr mask_fname = ana-cxi49012/cspad-cxi49012-r0150-mask-badregs.dat #mask_fname = ana-cxi49012/cspad-cxi49012-r0150-mask-bkgd.dat #mask_fname = ana-cxi49012/cspad-cxi49012-r0150-mask-rects.dat masked_amp = 8 print_bits = 1 mask_control_bits = 15 [ImgAlgos.CSPadArrPeakFinder] source = DetInfo(CxiDs1.0:Cspad.0) key = masked_arr key_peaks_out = peaks hot_pix_mask_inp_file = ana-cxi49012/cspad-cxi49012-r0150-noise-mask.dat hot_pix_mask_out_file = ana-cxi49012/cspad-cxi49012-r0150-noise-mask-out.dat frac_noisy_evts_file = ana-cxi49012/cspad-cxi49012-r0150-noise-frac.dat evt_file_out = tmp/cspad-ev- rmin = 3 dr = 1 SoNThr = 3 frac_noisy_imgs = 0.1 peak_npix_min = 4 peak_npix_max = 25 peak_amp_tot_thr = 100. event_npeak_min = 10 event_amp_tot_thr = 1000. nevents_mask_update = 100 nevents_mask_accum = 50 selection_mode = SELECTION_ON out_file_bits = 15 print_bits = 512 |
...
Example for module ImgAlgos::CSPadArrPeakAnalysis
See Module ImgAlgos::CSPadArrPeakAnalysis
Example of the psana configuration file:
...
For this configuration file psana will skip 10 events and loop over the next 100 events from the /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/e158-r0021-s0*-c00.xtc
files and run consecutively modules = ImgAlgos.TimeStampFilter PSXtcOutput.XtcOutputModule
. Parameters of these modules are described in the bottom part of the configuration file. Module TimeStampFilter
passes events from the specified time interval and prints some useful information. Module XtcOutputModule
will write passed events in the file with auto-generated name ./test_out/e158-r0021.xtcf
.
See also: Module ImgAlgos::TimeStampFilter and PSXtcOutput::PSXtcOutput
Examples for Package pyimgalgos
...
See description of modules in Package pyimgalgos.
Example of configuration file for CSPAD
...
pyana -c py-meca6113-r0028-cspad2x2.cfg
References
Psana psana - Module Catalog