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About
This page provides examples for selected modules from Psana Module Catalog.
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Configuration file for pedestals calibration of two CSPAD2x2 simultaneously:
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[psana]
files = /reg/d/psdm/xpp/xpptut13/xtc/e308-r0070-s02-c00.xtc \
/reg/d/psdm/xpp/xpptut13/xtc/e308-r0070-s03-c00.xtc
modules = cspad_mod.CsPad2x2Pedestals:0 \
cspad_mod.CsPad2x2Pedestals:1
#skip-events = 100
#events = 1111
[cspad_mod.CsPad2x2Pedestals:0]
source = DetInfo(XppGon.0:Cspad2x2.0)
output = pedestals-ave-xppi0513-r0070-Cspad2x2.0.dat
noise = pedestals-rms-xppi0513-r0070-Cspad2x2.0.dat
[cspad_mod.CsPad2x2Pedestals:1]
source = DetInfo(XppGon.0:Cspad2x2.1)
output = pedestals-ave-xppi0513-r0070-Cspad2x2.1.dat
noise = pedestals-rms-xppi0513-r0070-Cspad2x2.1.dat
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Command to run this script:
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psana -c psana-xppi0513-r0070-cspad2x2-pedestals.cfg
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The xtc file name(s) may be passed as an argument:
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psana -c psana-xppi0513-r0070-cspad2x2-pedestals.cfg /reg/d/psdm/xpp/xpptut13/xtc/e308-r0070-*.xtc
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How to write the CSPad image in text file:
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[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
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Example of the configuration script for psana (cspad2x2-test.cfg):
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[psana]
files = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-1>.xtc
events = 5
modules = CSPadPixCoords.CSPad2x2ImageProducer ImgAlgos.ImgSaveInFile
[CSPadPixCoords.CSPad2x2ImageProducer]
source = DetInfo(:Cspad2x2)
inkey =
outimgkey = Image
tiltIsApplied = true
print_bits = 15
[ImgAlgos.ImgSaveInFile]
source = DetInfo(:Cspad2x2)
key = Image
fname = cspad2x2
saveAll = true
#eventSave = 5
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Example of <psana-config-file.cfg>:
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[psana]
files = /reg/d/psdm/mec/mec73313/xtc/e268-r0180-s02-c00.xtc
#calib-dir = ./calib
modules = cspad_mod.CsPadCalib CSPadPixCoords.CSPad2x2ImageProducer ImgAlgos.ImgSaveInFile
events = 5
[cspad_mod.CsPadCalib]
source = DetInfo(MecTargetChamber.0:Cspad2x2.3)
inputKey =
outputKey = calibrated_arr
doPedestals = yes
doPixelStatus = no
doCommonMode = no
[CSPadPixCoords.CSPad2x2ImageProducer]
calibDir = /reg/d/psdm/mec/mec73313/calib
typeGroupName = CsPad2x2::CalibV1
#source = DetInfo(MecTargetChamber.0:Cspad2x2.3)
source = :Cspad2x2.3
inkey = calibrated_arr
outimgkey = Image
tiltIsApplied = true
print_bits = 15
[ImgAlgos.ImgSaveInFile]
source = DetInfo(MecTargetChamber.0:Cspad2x2.3)
key = Image
fname = cspad2x2.3
saveAll = true
print_bits = 3
#eventSave = 5
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Example of psana configuration file to get cspad2x2 images for two detectors and save them in files, one in txt, another in tiff formats:
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[psana]
files = /reg/d/psdm/xpp/xpptut13/xtc/e308-r0008-s02-c00.xtc \
/reg/d/psdm/xpp/xpptut13/xtc/e308-r0008-s03-c00.xtc
#modules = cspad_mod.CsPad2x2Pedestals
#calib-dir = ./calib
calib-dir = /reg/d/psdm/xpp/xpptut13/xtc/calib
modules = cspad_mod.CsPadCalib:0 \
cspad_mod.CsPadCalib:1 \
CSPadPixCoords.CSPad2x2ImageProducer:0 \
CSPadPixCoords.CSPad2x2ImageProducer:1 \
ImgAlgos.ImgSaveInFile:0 \
ImgAlgos.ImgSaveInFile:1
events = 5
[cspad_mod.CsPadCalib:0]
source = DetInfo(XppGon.0:Cspad2x2.0)
inputKey =
outputKey = calibrated_arr0
doPedestals = yes
doPixelStatus = no
doCommonMode = yes
[cspad_mod.CsPadCalib:1]
source = DetInfo(XppGon.0:Cspad2x2.1)
inputKey =
outputKey = calibrated_arr1
doPedestals = yes
doPixelStatus = no
doCommonMode = yes
[CSPadPixCoords.CSPad2x2ImageProducer:0]
calibDir = /reg/d/psdm/xpp/xpptut13/xtc/calib
typeGroupName = CsPad2x2::CalibV1
source = DetInfo(XppGon.0:Cspad2x2.0)
inkey = calibrated_arr0
outimgkey = Image
tiltIsApplied = false
useWidePixCenter = false
print_bits = 15
[CSPadPixCoords.CSPad2x2ImageProducer:1]
calibDir = /reg/d/psdm/xpp/xpptut13/xtc/calib
typeGroupName = CsPad2x2::CalibV1
source = DetInfo(XppGon.0:Cspad2x2.1)
inkey = calibrated_arr1
outimgkey = Image
tiltIsApplied = false
useWidePixCenter = false
print_bits = 15
[ImgAlgos.ImgSaveInFile:0]
source = DetInfo(:Cspad2x2.0)
key = Image
fname = cspad2x2.0
ftype = txt
#ftype = tiff
saveAll = true
print_bits = 3
#eventSave = 5
[ImgAlgos.ImgSaveInFile:1]
source = DetInfo(:Cspad2x2.1)
key = Image
fname = cspad2x2.1
#ftype = txt
ftype = tiff
saveAll = true
print_bits = 3
#eventSave = 5
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...
See module description in Module ImgPixSpectra::CSPadPixSpectra
Configuration file psana-cxib2313-r0114-cspad-pix-spectra.cfg:
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# Command to run this script:
# psana -c psana-cxib2313-r0114-cspad-pix-spectra.cfg
#
# Other useful commands:
# psana -n 5 -m PrintSeparator,PrintEventId,psana_examples.DumpCsPad /reg/d/psdm/cxi/cxib2313/xtc/e336-r0114*
# psana -n 5 -m EventKeys exp=cxib2313:run=114:xtc
[psana]
files = exp=cxib2313:run=114:xtc
#calib-dir = ./calib
skip-events = 0
events = 100
modules = cspad_mod.CsPadCalib ImgPixSpectra.CSPadPixSpectra
[cspad_mod.CsPadCalib]
source = DetInfo(CxiDs1.0:Cspad.0)
inputKey =
outputKey = calibrated
doPedestals = yes
doPixelStatus = no
doCommonMode = yes
[ImgPixSpectra.CSPadPixSpectra]
source = CxiDs1.0:Cspad.0
inputKey = calibrated
amin = -20.
amax = 20.
nbins = 10
arr_fname = cspad_spectral_array.txt
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...
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See module description in Module ImgPixSpectra::CSPad2x2PixSpectra
Configuration file example for CSPad2x2PixSpectra:
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[psana]
files = /reg/d/psdm/<instrument>/<experiment>/<file-name>.xtc
modules = ImgPixSpectra.CSPad2x2PixSpectra
[ImgPixSpectra.CSPad2x2PixSpectra]
source = CxiSc1.0:Cspad2x2.0
amin = 500.
amax = 1000.
nbins = 100
arr_fname = cspad2x2-pix-spectra.txt
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To get images from saved file one may execute the auxiliary script:
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ImgPixSpectra/data/PlotSpectralArrayFromFile.py cspad2x2-pix-spectra.txt
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Example of the psana configuration file:
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[psana]
files = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\
/reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-2>.xtc
modules = ImgAlgos.Tahometer
[ImgAlgos.Tahometer]
dn = 10
print_bits = 7
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Example of the psana configuration file:
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[psana]
files = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\
/reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-2>.xtc
#skip-events = 100
events = 5
modules = ImgAlgos.PnccdImageProducer ImgAlgos.ImgSaveInFile
[ImgAlgos.PnccdImageProducer]
source = DetInfo(:pnCCD)
inkey =
outimgkey = imgpnccd
print_bits = 1
[ImgAlgos.ImgSaveInFile]
source = DetInfo(:pnCCD)
key = imgpnccd
fname = pnccd-img-ev
saveAll = true
#eventSave = 82
print_bits = 1
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Example of the psana configuration file:
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[psana]
files = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc
modules = ImgAlgos.CameraImageProducer ImgAlgos.ImgSaveInFile
events = 5
[ImgAlgos.CameraImageProducer]
source = DetInfo(:Opal1000)
key_in =
key_out = img
subtract_offset = true
print_bits = 15
[ImgAlgos.ImgSaveInFile]
source = DetInfo(:Opal1000)
key = img
fname = img-from-my-experiment
saveAll = true
#eventSave = 1
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Example of the psana configuration file:
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[psana]
files = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\
/reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-2>.xtc
modules = ImgAlgos.PrincetonImageProducer \
ImgAlgos.ImgSaveInFile
events = 3
[ImgAlgos.PrincetonImageProducer]
source = DetInfo(:Princeton)
key_in =
key_out = img
subtract_offset = true
print_bits = 31
[ImgAlgos.ImgSaveInFile]
source
source = DetInfo(:Princeton)
key = img
fname = img-xcs
saveAll = true
print_bits = 31
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Image Added
Example for module ImgAlgos::AcqirisArrProducer
See description of parameters in Module ImgAlgos::AcqirisArrProducer
Example of the psana configuration file psana-amo01509-r0125-acqiris.cfg :
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[psana]
# Command to run this script:
# psana -c psana-amo01509-r0125-acqiris.cfg;
#
# Useful commands:
# psana -n 5 -m EventKeys exp=amo01509:run=125:xtc > test-acqiris-file.txt;
# psana -n 5 -m psana_examples.DumpAcqiris exp=amo01509:run=125:xtc > test-acqiris-file.txt; (C++ version)
# psana -n 1 -m psana_examples.dump_acqiris exp=amo01509:run=125:xtc > test-acqiris-file.txt; (python version)
[psana]
#files = /reg/d/psdm/AMO/amo01509/xtc/e8-r0125-s00-c00.xtc /reg/d/psdm/AMO/amo01509/xtc/e8-r0125-s01-c00.xtc
files = exp=amo01509:run=125:xtc
modules = ImgAlgos.AcqirisArrProducer ImgAlgos.ImgSaveInFile:wf ImgAlgos.ImgSaveInFile:wt
skip-events = 0
events = 100
[ImgAlgos.AcqirisArrProducer]
source = AmoETOF.0:Acqiris.0
key_in =
key_wform = acqiris_wform
key_wtime = acqiris_wtime
fname_prefix = acq
print_bits = 11
[ImgAlgos.ImgSaveInFile:wf]
source = AmoETOF.0:Acqiris.0
key = acqiris_wform
fname = acq-AmoETOF-wform
ftype = txt
#ftype = tiff
#saveAll = true
print_bits = 3
eventSave = 5
[ImgAlgos.ImgSaveInFile:wt]
source = AmoETOF.0:Acqiris.0
key = acqiris_wtime
fname = DetInfo(:Princeton)
key acq-AmoETOF-wtime
ftype = imgtxt
fname#ftype = img-xcs
saveAlltiff
#saveAll = true
print_bits = 3
eventSave = 31
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...
This script saves text files
acq-amo01509-r0125.txt -- with configuration parameters- acq-AmoETOF-wform-r0125-20091018-182512.194787218.txt – with waveforms for 5th event
- acq-AmoETOF-wtime-r0125-20091018-182512.194787218.txt – with wave-times for 5th event
Example for module ImgAlgos::ImgAverage
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The ImgAverage module can be used for evaluation of averaged pedestals or background using dedicated runs. Typical configuration file may looks like this:
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[psana]
files = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name>.xtc
modules = ImgAlgos.CameraImageProducer \
ImgAlgos.ImgAverage
events = 1000
[ImgAlgos.CameraImageProducer]
source = DetInfo(:Opal1000)
key_in =
key_out = img
subtract_offset = true
print_bits = 1
[ImgAlgos.ImgAverage]
source = DetInfo(:Opal1000)
key = img
avefile = img-ave.dat
rmsfile = img-rms.dat
print_bits = 31
evts_stage1 = 100
evts_stage2 = 100
gate_width1 = 200
gate_width2 = 20
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Configuration parameters for psana:
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[ImgAlgos.ImgMaskEvaluation]
source = DetInfo(:Opal1000)
key = img
file_mask_satu = img-mask-satu.dat
file_mask_nois = img-mask-nois.dat
file_mask_comb = img-mask-comb.dat
file_frac_satu = img-frac-satu.dat
file_frac_nois = img-frac-nois.dat
thre_satu = 400
frac_satu = 0
dr = 1
thre_SoN = 3
frac_nois = 0.05
print_bits = 63
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...
See Module ImgAlgos::ImgCalib
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[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
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...
See Module ImgAlgos::ImgRadialCorrection
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[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
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...
Configuration file example:
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[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
modules = ImgAlgos.ImgPeakFinder PrintSeparator
#skip-events = 500
events = 120
[ImgAlgos.ImgPeakFinder]
source = DetInfo(:Opal1000)
key =
peaksKey = peaks
threshold_low = 20
threshold_high = 50
sigma = 1.5
smear_radius = 2
peak_radius = 3
xmin = 200
xmax = 800
ymin = 100
ymax = 900
testEvent = 115
print_bits = 0
finderIsOn = true
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...
Example for module ImgAlgos::ImgPeakFilter
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[ImgAlgos.ImgPeakFilter]
source = DetInfo(:Opal1000)
key = peaks
threshold_peak = 5
threshold_total= 0
n_peaks_min = 10
print_bits = 11
fname = img
selection_mode = SELECTION_ON
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...
Configuration file example:
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[psana]
files = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name>.xtc
modules = ImgAlgos.CameraImageProducer \
ImgAlgos.ImgPeakFinderAB
events = 10
[ImgAlgos.CameraImageProducer]
source = DetInfo(:Opal1000)
key_in =
key_out = img
subtract_offset = true
print_bits = 1
[ImgAlgos.ImgPeakFinderAB]
source = DetInfo(:Opal1000)
key = img
key_peaks_out = peaks
#key_signal_out = signal-arr
#hot_pix_mask_inp_file = ana-misc-exp/mask.dat
#hot_pix_mask_out_file = noise-mask-out.dat
#frac_noisy_evts_file = noise-frac-out.dat
evt_file_out = tmp/img-
rmin = 10
dr = 1
SoNThr_noise = 3
SoNThr_signal = 3
frac_noisy_imgs = 0.9
peak_npix_min = 3
peak_npix_max = 100
peak_amp_tot_thr = 0.
peak_SoN_thr = 4.
event_npeak_min = 5
event_npeak_max = 1000
event_amp_tot_thr = 0.
nevents_mask_update = 0
nevents_mask_accum = 50
selection_mode = SELECTION_ON
out_file_bits = 15
print_bits = 513
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...
ImgHitFinder in regular mode needs in file with pedestals (offset) to correct the image and file with threshold.
In amo74213 run 93 these files can be obtained directly from data, discarding signal hits as outliers using
ImgAlgos.ImgAverage module as follows with configuration file:
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# File: psana-amo74213-r0093-opal-img-average.cfg
[psana]
#files = /reg/d/psdm/AMO/amo74213/xtc/e269-r0093-s05-c00.xtc
files = exp=amo74213:run=93:xtc
modules = ImgAlgos.CameraImageProducer \
ImgAlgos.ImgAverage
skip-events = 0
events = 1000
[ImgAlgos.CameraImageProducer]
source = DetInfo(:Opal1000)
key_in =
key_out = img
subtract_offset = true
print_bits = 1
[ImgAlgos.ImgAverage]
source = DetInfo(:Opal1000)
key = img
avefile = img-ave-for-peds
rmsfile = img-rms-for-thre
evts_stage1 = 100
evts_stage2 = 100
gate_width1 = 50
gate_width2 = 10
print_bits = 31
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Run psana using command:
| Code Block |
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psana -c psana-amo74213-r0093-opal-img-average.cfg
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...
The file with accumulated pixel hits can be obtained using configuration file:
| Code Block |
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# File: psana-amo74213-r0093-opal-img-hit-finder.cfg
[psana]
#files = /reg/d/psdm/AMO/amo74213/xtc/e269-r0093-s05-c00.xtc
files = exp=amo74213:run=93:xtc
modules = ImgAlgos.CameraImageProducer \
ImgAlgos.ImgHitFinder \
ImgAlgos.ImgAverage
skip-events = 0
events = 1000
[ImgAlgos.CameraImageProducer]
source = DetInfo(:Opal1000)
key_in =
key_out = img
subtract_offset = true
print_bits = 1
[ImgAlgos.ImgHitFinder]
source = DetInfo(:Opal1000)
key_in = img
key_out = img_hits
fname_peds = img-ave-for-peds-r0093.dat
fname_mask =
fname_gain =
fname_thre = img-rms-for-thre-r0093.dat
masked_value = 0
thre_mode = 3
#thre_mode = 2
thre_param = 5
thre_below_value = 0
thre_above_value = 1
win_row_min = 10
win_row_max = 1000
win_col_min = 10
win_col_max = 1000
print_bits = 39
[ImgAlgos.ImgAverage]
source = DetInfo(:Opal1000)
key = img_hits
sumfile = img-sum-result
print_bits = 25
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and run it by the command:
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psana -c psana-amo74213-r0093-opal-img-hit-finder.cfg
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...
See Module ImgAlgos::ImgSpectra
Configuration file for psana:
| Code Block |
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[psana]
files = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name>.xtc
modules = ImgAlgos.CameraImageProducer \
ImgAlgos.ImgSpectra \
ImgAlgos.ImgSaveInFile:2
# ImgAlgos.ImgSaveInFile
# psana_examples.DumpOpal1k \
events = 100
[ImgAlgos.CameraImageProducer]
source = DetInfo(:Opal1000)
key_in =
key_out = img
subtract_offset = true
print_bits = 1
[ImgAlgos.ImgSpectra]
source = DetInfo(:Opal1000)
key_in = img
key_out = spectra
sig_band_rowc = 512.
ref_band_rowc = 552.
sig_band_tilt = 0.
ref_band_tilt = 0.
sig_band_width = 10
ref_band_width = 10
print_bits = 3
[ImgAlgos.ImgSpectraProc]
source = DetInfo(:Opal1000)
key_in = spectra
print_bits = 15
[ImgAlgos.ImgSaveInFile:2]
source = DetInfo(:Opal1000)
key = spectra
fname = spec-xppi0412
saveAll = true
[ImgAlgos.ImgSaveInFile]
source = DetInfo(:Opal1000)
key = img
fname = img-xppi0412
saveAll = true
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...
See Module ImgAlgos::ImgSpectraProc
Configuration file for psana:
| Code Block |
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[ImgAlgos.ImgSpectraProc]
source = DetInfo(:Opal1000)
key_in = spectra
print_bits = 15
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For each event it prints something similar to:
| Code Block |
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[info:ImgAlgos.ImgSpectraProc] Spectral array shape =3, 1024
[info:ImgAlgos.ImgSpectraProc] Image spectra for run=0060 Evt=000100
Column: 0 100 200 300 400 500 600 700 800 900 1000
Signal: 1211 4062 11150 17070 16406 12949 7991 5168 3968 3542 3811
Refer.: 933 3485 10425 17128 17791 13522 8315 5000 3390 2967 3193
Diff. : 0.259 0.153 0.067 -0.003 -0.081 -0.043 -0.040 0.033 0.157 0.177 0.176
[info:ImgAlgos.ImgSpectraProc] Run=0060 Evt=000100 Time=20120507-125420.982421325 done...
|
Example for module ImgAlgos::ImgSaveInFile
| 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
|
...
Module ImgAlgos::ImgPeakFinder works on image. In order to apply this algorithm to CSPad the image should be produced. In next example the image is produced using consequtive modules cspad_mod.CsPadCalib, ImgAlgos.CSPadMaskApply, and CSPadPixCoords.CSPadImageProducer:
| Code Block |
|---|
|
[psana]
files = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-1>.xtc \
...
/reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-N>.xtc
events = 1000
experiment = cxii0212
calib-dir = ana-cxii0212/calib
modules = cspad_mod.CsPadCalib \
ImgAlgos.CSPadMaskApply \
CSPadPixCoords.CSPadImageProducer \
ImgAlgos.ImgPeakFinder \
ImgAlgos.ImgPeakFilter \
ImgAlgos.ImgSaveInFile:1
[cspad_mod.CsPadCalib]
inputKey =
outputKey = calibrated
doPedestals = yes
doPixelStatus = no
doCommonMode = yes
[ImgAlgos.CSPadMaskApply]
source = DetInfo(CxiDs1.0:Cspad.0)
inkey = calibrated
outkey = masked_arr
mask_fname = <your-local-directory>/<mask-file-name>.dat
masked_amp = 0
print_bits = 5
mask_control_bits = 15
[CSPadPixCoords.CSPadImageProducer]
calibDir = /reg/d/psdm/<instrument>/<experiment>/calib
typeGroupName = CsPad::CalibV1
source = CxiDs1.0:Cspad.0
key = masked_arr
imgkey = img
print_bits = 0
#tiltIsApplied = true
[ImgAlgos.ImgPeakFinder]
source = DetInfo(CxiDs1.0:Cspad.0)
key = img
peaksKey = peaks
threshold_low = 2
threshold_high = 5
sigma = 1.5
smear_radius = 5
peak_radius = 7
xmin = 20
xmax = 1700
ymin = 20
ymax = 1700
#testEvent = 5
print_bits = 3
#finderIsOn = true
[ImgAlgos.ImgPeakFilter]
source = DetInfo(CxiDs1.0:Cspad.0)
key = peaks
threshold_peak = 5
threshold_total= 0
n_peaks_min = 10
print_bits = 11
fname = cspad-img
selection_mode = SELECTION_ON
[ImgAlgos.ImgSaveInFile:1]
source = CxiDs1.0:Cspad.0
key = img
fname = cspad-img
#eventSave = 1
saveAll = true
|
...
Configuration file example for evaluation of pedestals:
| Code Block |
|---|
|
[psana]
modules = ImgAlgos.CSPadArrAverage
files = <path-to-the-dark-run-file>.xtc
[ImgAlgos.CSPadArrAverage]
source = DetInfo(CxiDs1.0:Cspad.0)
key =
avefile = cspad-pedestals-ave.dat
rmsfile = cspad-pedestals-rms.dat
print_bits = 15
evts_stage1 = 100
evts_stage2 = 100
gate_width1 = 100
gate_width2 = 10
|
Configuration file example for evaluation of background:
| Code Block |
|---|
|
[psana]
files = <path-to-the-background-run-file>.xtc
modules = cspad_mod.CsPadCalib ImgAlgos.CSPadArrAverage
skip-events = 500
events = 1000000
[cspad_mod.CsPadCalib]
inputKey =
outputKey = calibrated
doPedestals = yes
doPixelStatus = no
doCommonMode = no
[ImgAlgos.CSPadArrAverage]
source = DetInfo(CxiDs1.0:Cspad.0)
key = calibrated
avefile = cspad-background-ave.dat
rmsfile = cspad-background-rms.dat
print_bits = 15
|
...
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 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.
For example, it can be generated by the command
| Code Block |
|---|
|
./MakePixelMask.py <input-background-cspad-arr-file-name> <threshold> <output-file-name>
|
...
The best results in filtering can be achieved in combination of modiles:
| Code Block |
|---|
|
modules = cspad_mod.CsPadCalib \
ImgAlgos.CSPadBkgdSubtract \
ImgAlgos.CSPadMaskApply \
...
[cspad_mod.CsPadCalib]
inputKey =
outputKey = calibrated_arr
doPedestals = yes
doPixelStatus = no
doCommonMode = no
[ImgAlgos.CSPadBkgdSubtract]
source = DetInfo(CxiDs1.0:Cspad.0)
inputKey = calibrated_arr
outputKey = bkgd_subtracted_arr
bkgd_fname = ana-cxi49012/cspad-cxi49012-r0025-background-ave.dat
norm_sector = 0
print_bits = 0
[ImgAlgos.CSPadMaskApply]
source = DetInfo(CxiDs1.0:Cspad.0)
inkey = bkgd_subtracted_arr
outkey = masked_arr
mask_fname = ana-cxi49012/cspad-cxi49012-r0025-mask-40.dat
masked_amp = 0
print_bits = 3
mask_control_bits = 1
|
...
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
|
Index map in median algorithm for rmin=3, dr=1:
| Code Block |
|---|
|
CSPadArrNoise::printMatrixOfIndexesForMedian():
0 0 0 0 1 0 0 0 0
0 0 1 1 1 1 1 0 0
0 1 0 0 0 0 0 1 0
0 1 0 0 0 0 0 1 0
1 1 0 0 + 0 0 1 1
0 1 0 0 0 0 0 1 0
0 1 0 0 0 0 0 1 0
0 0 1 1 1 1 1 0 0
0 0 0 0 1 0 0 0 0
|
...
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
|
Results:
| Code Block |
|---|
|
[info:TimeInterval::startTime] Start time: 2012-06-12 15:32:02
[info:ImgAlgos.CSPadArrPeakFinder] N processed events = 1000 N selected = 55 Fraction of selected = 0.055
[info:ImgAlgos.CSPadArrPeakFinder] N processed events = 2000 N selected = 62 Fraction of selected = 0.031
[info:ImgAlgos.CSPadArrPeakFinder] N processed events = 3000 N selected = 81 Fraction of selected = 0.027
[info:ImgAlgos.CSPadArrPeakFinder] N processed events = 4000 N selected = 95 Fraction of selected = 0.02375
[info:ImgAlgos.CSPadArrPeakFinder] N processed events = 5000 N selected = 150 Fraction of selected = 0.03
[info:ImgAlgos.CSPadArrPeakFinder] N processed events = 6000 N selected = 265 Fraction of selected = 0.0441667
[info:ImgAlgos.CSPadArrPeakFinder] N processed events = 7000 N selected = 404 Fraction of selected = 0.0577143
[info:ImgAlgos.CSPadArrPeakFinder] ===== JOB SUMMARY =====
[info:TimeInterval::stopTime] Time to process 7945 events is 3747.48 sec, or 0.471678 sec/event
|
...
Example of the psana configuration file:
| Code Block |
|---|
|
modules = cspad_mod.CsPadCalib \
ImgAlgos.CSPadMaskApply \
ImgAlgos.CSPadArrPeakFinder \
ImgAlgos.CSPadArrPeakAnalysis
# ...configuration parameters of other modules...
[ImgAlgos.CSPadArrPeakAnalysis]
source = DetInfo(CxiDs1.0:Cspad.0)
key = peaks
print_bits = 7
fname_root = file.root
|
...
This example demonstrates how to run psana with the time stamp filter and event writer in xtc file.
Both modules are available in psana library and they need only to be described in the configuration file. For example, the configuration file tstamp-filter-and-event-writer.cfg may looks like:
| Code Block |
|---|
|
[psana]
files = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/e158-r0021-s00-c00.xtc \
/reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/e158-r0021-s01-c00.xtc \
/reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/e158-r0021-s02-c00.xtc \
/reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/e158-r0021-s03-c00.xtc \
/reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/e158-r0021-s04-c00.xtc \
/reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/e158-r0021-s05-c00.xtc
skip-events = 10
events = 100
modules = ImgAlgos.TimeStampFilter PSXtcOutput.XtcOutputModule
[PSXtcOutput.XtcOutputModule]
dirName = ./test_out
[ImgAlgos.TimeStampFilter]
tsinterval = 2012-02-02 18:17:00.409143728 / 2012-02-02 18:17:00.525853474
filterIsOn = true
print_bits = 11
|
...
File py-xcs72913-r0049-cspad.cfg:
| Code Block |
|---|
|
# Run this script:
# psana -c py-xcs72913-r0049-cspad.cfg
# pyana -c py-xcs72913-r0049-cspad.cfg
#
# Useful commands:
# psana -m EventKeys -n 5 /reg/d/psdm/xcs/xcs72913/xtc/e265-r0049-*
# psana -m psana_examples.dump_cspad -n 5 exp=xcs72913:run=49
# pyana -m pyana_examples.dump_cspad -n 5 /reg/d/psdm/xcs/xcs72913/xtc/e265-r0049-*
[pyana]
files = /reg/d/psdm/xcs/xcs72913/xtc/e265-r0049-s00-c00.xtc /reg/d/psdm/xcs/xcs72913/xtc/e265-r0049-s04-c00.xtc /reg/d/psdm/xcs/xcs72913/xtc/e265-r0049-s05-c00.xtc
num-events = 5
#skip-events = 0
#num-cpu = 1
verbose = 1 ; logging output: 0-nothing?, 1+INFO, 2+DEBUG, ...
modules = py_img_algos.tahometer py_img_algos.cspad_arr_producer py_img_algos.cspad_image_producer py_img_algos.image_save_in_file
[psana]
files = exp=xcs72913:run=49
events = 5
#skip-events = 0
modules = py_img_algos.tahometer py_img_algos.cspad_arr_producer py_img_algos.cspad_image_producer py_img_algos.image_save_in_file
verbose = 1
[py_img_algos.tahometer]
dn = 10
print_bits = 255
[py_img_algos.cspad_arr_producer]
#source = -|Cspad-*
source = XcsEndstation-0|Cspad-0
data_type = double
#data_type = float
#data_type = unsigned
#data_type = uint16
val_miss = 0
key_out = cspad_array
print_bits = 1
[py_img_algos.cspad_image_producer]
calib_dir = /reg/d/psdm/xcs/xcs72913/calib/CsPad::CalibV1/XcsEndstation.0:Cspad.0/
key_in = cspad_array
key_out = cspad_image
print_bits = 1
# Supported output file formats tiff, gif, png, eps, jpg, jpeg, txt, npy(default), npz
[py_img_algos.image_save_in_file]
key_in = cspad_image
ofname = img-for-cspad.txt
print_bits = 255
|
...
File py-meca6113-r0028-cspad2x2.cfg
| Code Block |
|---|
|
# Run this script:
# psana -c py-meca6113-r0028-cspad2x2.cfg
# pyana -c py-meca6113-r0028-cspad2x2.cfg
#
# Useful commands:
# psana -m EventKeys -n 5 /reg/d/psdm/mec/meca6113/xtc/e332-r0028-s03-c00.xtc
# psana -m psana_examples.dump_cspad -n 5 exp=meca6113:run=28
# pyana -m pyana_examples.dump_cspad -n 5 /reg/d/psdm/mec/meca6113/xtc/e332-r0028-s03-c00.xtc
[pyana]
files = /reg/d/psdm/mec/meca6113/xtc/e332-r0028-s03-c00.xtc
num-events = 5
#skip-events = 0
#num-cpu = 1
verbose = 0 ; logging output: 0-nothing?, 1+INFO, 2+DEBUG, ...
modules = py_img_algos.tahometer py_img_algos.cspad_arr_producer py_img_algos.cspad_image_producer py_img_algos.image_save_in_file
[psana]
files = exp=meca6113:run=28
events = 5
#skip-events = 0
modules = py_img_algos.tahometer py_img_algos.cspad_arr_producer py_img_algos.cspad_image_producer py_img_algos.image_save_in_file
[py_img_algos.tahometer]
dn = 10
print_bits = 255
[py_img_algos.cspad_arr_producer]
#source = -|Cspad-*
source = MecTargetChamber-0|Cspad2x2-3
#data_type = double
data_type = float
#data_type = unsigned
#data_type = uint16
#data_type = uint32
val_miss = 0
key_out = cspad2x2_array
print_bits = 255
[py_img_algos.cspad_image_producer]
calib_dir = /reg/d/psdm/mec/meca6113/calib/CsPad2x2::CalibV1/MecTargetChamber.0:Cspad2x2.3/
key_in = cspad2x2_array
key_out = cspad2x2_image
print_bits = 1
# Supported output file formats tiff, gif, png, eps, jpg, jpeg, txt, npy(default), npz
[py_img_algos.image_save_in_file]
key_in = cspad2x2_image
ofname = img-for-cspad2x2.tiff
print_bits = 255
|
...
