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About
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.
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psana.cfg- set non-default parameters to runpsanaforImgAlgos::ImgPeakFinderandImgAlgos::ImgPeakFilter
Thepsanarunning this script saves images and peaks for event 115 in text files.PlotCameraImageFromFile.py- Plots image and spectrum for image saved in file.PlotCameraImageAndPeaks.py- Plots image with found peaks and spectrum.
Examples for package cspad_mod
Example for module cspad_mod::CsPad2x2Pedestals
Configuration file for pedestals calibration of two CSPAD2x2 simultaneously:
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Output files contain results, which can be plotted for average values:
and rms values:
Examples for package CSPadPixCoords
Example for
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module CSPadPixCoords::CSPadImageProducer
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 |
Example for module CSPadPixCoords::
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CSPadNDArrProducer
See Module CSPadPixCoords::CSPad2x2ImageProducerCSPadNDArrProducer
Example of the configuration script for psana (cspad2x2-test.cfg):module CSPadNDArrProducer working in sequence with ImgAlgos::NDArrAverage is shown in Example for module ImgAlgos::NDArrAverage
Example for module CSPadPixCoords::CSPad2x2NDArrProducer
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# Run this script:
# psana -c psana-meca1113-r0045-cspad-cspad2x2-dark-hotpix.cfg
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[psana] files# Default calibration directory: # calib-dir = /reg/d/psdm/<instrument>mec/<experiment>/xtc/<file-name-1>.xtc events = 5 modulesmeca1113/calib files = exp=meca1113:run=45 events = 400 #skip-events = 0 modules = CSPadPixCoords.CSPad2x2NDArrProducer:1 \ = CSPadPixCoords.CSPad2x2ImageProducer ImgAlgos.ImgSaveInFile CSPadPixCoords.CSPad2x2NDArrProducer:2 \ ImgAlgos.NDArrAverage:1 \ ImgAlgos.NDArrAverage:2 [CSPadPixCoords.CSPad2x2ImageProducerCSPad2x2NDArrProducer:1] source = MecTargetChamber.0:Cspad2x2.1 inkey = outkey = DetInfo(:Cspad2x2) inkey = outimgkey = Image tiltIsApplied = truecspad2x2.1_ndarr outtype = int16 print_bits = 3 [CSPadPixCoords.CSPad2x2NDArrProducer:2] source = MecTargetChamber.0:Cspad2x2.2 inkey = outkey = cspad2x2.2_ndarr outtype = int16 print_bits = 153 [ImgAlgos.ImgSaveInFileNDArrAverage:1] source = DetInfo(MecTargetChamber.0:Cspad2x2).1 key = Image fnamecspad2x2.1_ndarr avefile = cspad2x2.1-ave saveAllrmsfile = true #eventSavecspad2x2.1-rms maskfile = 5 |
Command to run:
psana -c cspad2x2-test.cfg
One of the saved files cspad2x2-<run>-<timestamp>.txt is plotted as an image by the command
./PlotCameraImageFromFile.py cspad2x2-<run>-<timestamp>.txt 0 1200
Configuration file for cspad2x2 with pedestal subtraction
| Note |
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Access to the CSPad2x2 aligned geometry is added on 2013-02-13 |
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 cspad2x2.1-msk hotpixfile = cspad2x2.1-hot #evts_stage1 = 100 #gate_width1 = 100. thr_rms_ADU = 10 thr_min_ADU = 4 thr_max_ADU = 10000 print_bits = 29 [ImgAlgos.NDArrAverage:2] source = DetInfo(MecTargetChamber.0:Cspad2x2.3)2 inputKeykey = outputKey = calibratedcspad2x2.2_arrndarr doPedestalsavefile = yes doPixelStatus = no doCommonMode = no [CSPadPixCoords.CSPad2x2ImageProducer] calibDircspad2x2.2-ave rmsfile = /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] sourcecspad2x2.2-rms maskfile = cspad2x2.2-msk hotpixfile = cspad2x2.2-hot #evts_stage1 = 100 #gate_width1 = 100. thr_rms_ADU = 10 thr_min_ADU = 4 thr_max_ADU = 10000 print_bits = 29 |
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::CSPad2x2NDArrReshape
Example of configuration file
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[psana] #files = exp=meca1113:run=376 #events = 10 ##skip-events = 0 modules = cspad_mod.CsPadCalib \ = DetInfo(MecTargetChamberCSPadPixCoords.0:Cspad2x2.3) keyCSPad2x2NDArrProducer:clb \ CSPadPixCoords.CSPad2x2NDArrProducer:raw \ = Image fname CSPadPixCoords.CSPad2x2NDArrReshape \ = cspad2x2.3 saveAll = true print_bitsImgAlgos.NDArrAverage:clb \ = 3 #eventSave ImgAlgos.NDArrAverage:raw # = 5 |
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 \ EventKeys [cspad_mod.CsPadCalib] inputKey = outputKey /reg/d/psdm/xpp/xpptut13/xtc/e308-r0008-s03-c00.xtc #modules = cspadclb_mod.CsPad2x2Pedestals #calib-dirdata doPedestals = ./calib calib-diryes doPixelStatus = /reg/d/psdm/xpp/xpptut13/xtc/calib modulesyes doCommonMode = cspad_mod.CsPadCalib:0 \ yes [CSPadPixCoords.CSPad2x2NDArrProducer:clb] source cspad_mod.CsPadCalib:1 \ = MecTargetChamber.0:Cspad2x2.1 inkey CSPadPixCoords.CSPad2x2ImageProducer:0 \ = clb_data outkey CSPadPixCoords.CSPad2x2ImageProducer:1 \ ImgAlgos.ImgSaveInFile:0 \ = cspad2x2.1_clb:as_data outtype ImgAlgos.ImgSaveInFile:1 events = int16 print_bits = 5 [cspad_modCSPadPixCoords.CsPadCalibCSPad2x2NDArrProducer:0raw] source = DetInfo(XppGonMecTargetChamber.0:Cspad2x2.0)1 inputKeyinkey = outputKeyoutkey = calibrated_arr0 doPedestalscspad2x2.1_raw:as_data outtype = yes doPixelStatus = noint16 doCommonModeprint_bits = yes5 [cspad_mod.CsPadCalib:1CSPadPixCoords.CSPad2x2NDArrReshape] source = DetInfo(XppGonMecTargetChamber.0:Cspad2x2.1) inputKeykeys_in = cspad2x2.1_raw:as_data cspad2x2.1_clb:as_data print_bits = outputKey255 [ImgAlgos.NDArrAverage:clb] source = calibrated_arr1 doPedestalsMecTargetChamber.0:Cspad2x2.1 key = yes doPixelStatus = no doCommonMode = yes [CSPadPixCoords.CSPad2x2ImageProducer:0] calibDir cspad2x2.1_clb avefile = arr-ave-clb rmsfile = /reg/d/psdm/xpp/xpptut13/xtc/calib typeGroupNamearr-rms-clb print_bits = CsPad2x2::CalibV1255 [ImgAlgos.NDArrAverage:raw] source = DetInfo(XppGonMecTargetChamber.0:Cspad2x2.0) inkey 1 key = calibratedcspad2x2.1_arr0raw outimgkey avefile = Image tiltIsAppliedarr-ave-raw rmsfile = false useWidePixCenter = falsearr-rms-raw print_bits = 255 |
This script produces raw and calibrated ndarrays shaped as data (185,388,2), then pass these arrays as
keys_in =
...
cspad2x2.1_raw:as_data cspad2x2.1_clb:as_datato the CSPadPixCoords.CSPad2x2NDArrReshape module, which produces two reshaped (2,185,388) arrays and saves them in the event store with default keys
cspad2x2.1_raw, cspad2x2.1_clb(suffixes are dropped)
then both re-shaped arrays are averaged and saved in files on disk.
Example of associated python script:
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#!/usr/bin/env python
import sys
import numpy as np
import matplotlib.pyplot as plt
import psana
psana.setConfigFile('psana-meca1113-r0376-cspad2x2-CSPad2x2NDArrReshape.cfg')
dsname = 'exp=meca1113:run=376'
print "Data source: %s" % dsname
ds = psana.DataSource(dsname)
#------------------------------
print "Initializing Matplotlib Plotter"
fig = plt.figure(figsize=(10,5), dpi=80, facecolor='w', edgecolor='w', frameon=True)
plt.ion()
plt.show()
evnum = 0
evnum_max = 50
for evt in ds.events() :
evtid = evt.get(psana.EventId)
evnum += 1
if evnum > evnum_max : break
img_as_data = evt.get(psana.ndarray_int16_3, psana.Source('DetInfo(MecTargetChamber.0:Cspad2x2.1)'), 'cspad2x2.1_clb:as_data')
img_reshpd = evt.get(psana.ndarray_int16_3, psana.Source('DetInfo(MecTargetChamber.0:Cspad2x2.1)'), 'cspad2x2.1_clb')
print 'img_as_data.shape = ', img_as_data.shape
print 'img_reshpd.shape = ', img_reshpd.shape
img_as_data.shape = (2*185,388)
img_reshpd.shape = (2*185,388)
ax1 = fig.add_axes([0.05, 0.06, 0.44, 0.87])
ax2 = fig.add_axes([0.55, 0.06, 0.44, 0.87])
fig.canvas.set_window_title('Image from arrays "as-data" and "reshaped"')
imsh1 = ax1.imshow(img_as_data, interpolation='nearest', aspect='auto', origin='upper') # , extent=img_range)
imsh2 = ax2.imshow(img_reshpd, interpolation='nearest', aspect='auto', origin='upper') # , extent=img_range)
plt.title("Event: %d.%d" % evtid.time())
plt.draw()
plt.clf() |
This script retrieves from the event store calibrated ndarrays shaped as data (185,388,2) and re-shaped (2,185,388), then re-shape both to 2-d arrays (2*185,388) and plot them. Re-shaped array looks as recognizable (without spaces between ASICs) cspad2x2 image. Array shapes "as data" looks as an overlap of two images.
See Module CSPadPixCoords::CSPad2x2NDArrReshape
JIRA issue:
| Jira | ||||
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Example for module CSPadPixCoords::CSPad2x2ImageProducer
See Module CSPadPixCoords::CSPad2x2ImageProducer
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 |
Example for package ImgPixSpectra
Modules:
- ImgPixSpectra::CSPadPixSpectra
- ImgPixSpectra::CSPad2x2PixSpectra
- ImgPixSpectra::CameraPixSpectra
Example for module ImgPixSpectra::CSPadPixSpectra
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:Cspad2x2) inputKeyinkey = outputKeyoutimgkey = calibratedImage doPedestals tiltIsApplied = yes doPixelStatus = no doCommonModetrue print_bits = yes15 [ImgPixSpectraImgAlgos.CSPadPixSpectraImgSaveInFile] source = CxiDs1.0:Cspad.0 inputKeyDetInfo(:Cspad2x2) key = calibrated amin = -20. amax Image fname = 20. nbins cspad2x2 saveAll = 10 arr_fnametrue #eventSave = cspad_spectral_array.txt |
where module cspad_mod.CsPadCalib subtracts pedestals, apply common mode correction, and save CSPAD array in the event store with key "calibrated", which is used in the next module ImgPixSpectra.CSPadPixSpectra.
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Command to run:To run this script use commandpsana -c
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cspad2x2-test.cfg
which produces two files:
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One of the saved files cspad2x2-<run>-<timestamp>.txt is plotted as an image by the command
./PlotCameraImageFromFile.py cspad2x2-<run>-<timestamp>.txt 0 1200
Configuration file for cspad2x2 with pedestal subtraction
| Note |
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Access to the CSPad2x2 aligned geometry is added on 2013-02-13 |
Example of <psana-config-file.cfg>
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:
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...
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[psana] files |
...
Plot for content of the file cspad_spectral_array.txt:
Example for module ImgPixSpectra::CSPad2x2PixSpectra
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= /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 = CxiSc1DetInfo(MecTargetChamber.0:Cspad2x2.03) amininputKey = outputKey = = 500. amaxcalibrated_arr doPedestals = yes doPixelStatus = no doCommonMode = 1000. nbinsno [CSPadPixCoords.CSPad2x2ImageProducer] calibDir = /reg/d/psdm/mec/mec73313/calib typeGroupName = 100 arr_fnameCsPad2x2::CalibV1 #source = cspad2x2-pix-spectra.txt |
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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generates image for limited range of pixels for CSPad, CSPad2x2, or Camera, respectively:
Examples for package ImgAlgos
See Package ImgAlgos
Example for module ImgAlgos::Tahometer
See Module ImgAlgos::Tahometer
Example of the psana configuration file:
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[psana]DetInfo(MecTargetChamber.0:Cspad2x2.3) source = files:Cspad2x2.3 inkey = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\ calibrated_arr outimgkey = Image tiltIsApplied /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-2>.xtc modules= true print_bits = ImgAlgos.Tahometer15 [ImgAlgos.TahometerImgSaveInFile] dnsource = 10 print_bits = 7 |
Example for module ImgAlgos::PnccdImageProducer
See Module ImgAlgos::PnccdImageProducer
Example of the psana configuration file:
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[psana]DetInfo(MecTargetChamber.0:Cspad2x2.3) key = Image fname = cspad2x2.3 saveAll = true print_bits = 3 #eventSave = 5 |
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 \ files = /reg/d/psdm/<INSTRUMENT>xpp/<experiment>xpptut13/xtc/<filee308-r0008-names03-1>c00.xtc\ #modules = cspad_mod.CsPad2x2Pedestals #calib-dir = ./calib calib-dir = /reg/d/psdm/<INSTRUMENT>xpp/<experiment>xpptut13/xtc/<file-name-2>.xtc #skip-eventscalib modules = 100 eventscspad_mod.CsPadCalib:0 \ = 5 modules = ImgAlgos.PnccdImageProducer ImgAlgos.ImgSaveInFile [ImgAlgos.PnccdImageProducer] sourcecspad_mod.CsPadCalib:1 \ = DetInfo(:pnCCD) inkeyCSPadPixCoords.CSPad2x2ImageProducer:0 \ CSPadPixCoords.CSPad2x2ImageProducer:1 \ = outimgkey = imgpnccd print_bits = ImgAlgos.ImgSaveInFile:0 \ ImgAlgos.ImgSaveInFile:1 [ImgAlgos.ImgSaveInFileevents = 5 [cspad_mod.CsPadCalib:0] source = DetInfo(:pnCCDXppGon.0:Cspad2x2.0) keyinputKey = outputKey = imgpnccdcalibrated_arr0 fnamedoPedestals = yes doPixelStatus = no doCommonMode = pnccd-img-ev saveAllyes [cspad_mod.CsPadCalib:1] source = true #eventSaveDetInfo(XppGon.0:Cspad2x2.1) inputKey = 82 print_bits outputKey = calibrated_arr1 doPedestals = yes doPixelStatus = 1 |
This script saves text files with images like pnccd-img-ev-<run-date-time.nsec>.txt, which can be presented as:
Example for module ImgAlgos::CameraImageProducer
See Module ImgAlgos::CameraImageProducer
Example of the psana configuration file:
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[psana]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 = files 15 [CSPadPixCoords.CSPad2x2ImageProducer:1] calibDir = /reg/d/psdm/<INSTRUMENT>xpp/<experiment>xpptut13/xtc/<file-name-1>.xtc modulescalib typeGroupName = ImgAlgos.CameraImageProducer ImgAlgos.ImgSaveInFile eventsCsPad2x2::CalibV1 source = 5 [ImgAlgos.CameraImageProducer] sourceDetInfo(XppGon.0:Cspad2x2.1) inkey = DetInfo(:Opal1000) key_incalibrated_arr1 outimgkey = key_out Image tiltIsApplied = imgfalse subtract_offsetuseWidePixCenter = truefalse print_bits = 15 [ImgAlgos.ImgSaveInFile:0] source = DetInfo(:Opal1000Cspad2x2.0) key = imgImage fname = img-from-my-experiment saveAll cspad2x2.0 ftype = true #eventSave = 1 |
This script saves text files with images like img-from-my-experiment-<run-date-time.nsec>.txt, which can be drawn by the python script
./ImgAlgos/data/PlotCameraImageFromFile.py <filename>.txt <Amin> <Amax>
Example for module ImgAlgos::PrincetonImageProducer
See Module ImgAlgos::PrincetonImageProducer
Example of the psana configuration file:
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[psana]txt #ftype = tiff saveAll = true print_bits = 3 #eventSave files= 5 [ImgAlgos.ImgSaveInFile:1] source = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\ DetInfo(:Cspad2x2.1) key = Image fname /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-2>.xtc modules = ImgAlgoscspad2x2.PrincetonImageProducer \1 #ftype ImgAlgos.ImgSaveInFile events= txt ftype = 3 [ImgAlgos.PrincetonImageProducer] sourcetiff saveAll = DetInfo(:Princeton) key_intrue print_bits = 3 key_out#eventSave = img subtract_offset = true print_bits = 31 [ImgAlgos.ImgSaveInFile] source = DetInfo(:Princeton) key = img fname = img-xcs saveAll = true print_bits = 31 |
...
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Example for package ImgPixSpectra
Modules:
- ImgPixSpectra::CSPadPixSpectra
- ImgPixSpectra::CSPad2x2PixSpectra
- ImgPixSpectra::CameraPixSpectra
Example for module ImgPixSpectra::CSPadPixSpectra
See module description in Module ImgPixSpectra::CSPadPixSpectra
Configuration file psana-cxib2313-r0114-cspad-pix-spectra
...
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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# Command to run this script: # psana -c psana-amo01509-r0125-acqiriscxib2313-r0114-cspad-pix-spectra.cfg; # # Other Usefuluseful commands: # psana -n 5 -m EventKeys exp=amo01509:run=125:xtc > test-acqiris-file.txt; PrintSeparator,PrintEventId,psana_examples.DumpCsPad /reg/d/psdm/cxi/cxib2313/xtc/e336-r0114* # psana -n 5 -m psana_examples.DumpAcqirisEventKeys exp=amo01509cxib2313:run=125114:xtc [psana] files > 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= 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 = AmoETOFCxiDs1.0:AcqirisCspad.0 key_ininputKey = calibrated amin = key_wform = acqiris_wform key_wtime -20. amax = acqiris_wtime fname_prefix = acq print_bits = = 11 [ImgAlgos.ImgSaveInFile:wf] source 20. nbins = AmoETOF.0:Acqiris.0 key 10 arr_fname = acqiris_wform fname cspad_spectral_array.txt |
where module cspad_mod.CsPadCalib subtracts pedestals, apply common mode correction, and save CSPAD array in the event store with key "calibrated", which is used in the next module ImgPixSpectra.CSPadPixSpectra.
To run this script use command
psana -c psana-cxib2313-r0114-cspad-pix-spectra.cfg
which produces two files:
cspad_spectral_array.txt– array of 10-bin amplitude spectra for all pixelscspad_spectral_array.txt.sha– file with metadata for array shape:Code Block bgColor #AAFFFF NPIXELS 2296960 NBINS 10 AMIN
...
...
-
...
20
...
AMAX 20 NEVENTS 100 ARRFNAME cspad_spectral_array.txt
Plot for content of the file cspad_spectral_array.txt:
Example for module ImgPixSpectra::CSPad2x2PixSpectra
See module description in Module ImgPixSpectra::CSPad2x2PixSpectra
Configuration file example for CSPad2x2PixSpectra:
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|---|---|---|
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[psana] files = txt #ftype = tiff #saveAll /reg/d/psdm/<instrument>/<experiment>/<file-name>.xtc modules = true print_bits = 3 eventSave = 5 [ImgAlgos.ImgSaveInFile:wtImgPixSpectra.CSPad2x2PixSpectra [ImgPixSpectra.CSPad2x2PixSpectra] source = AmoETOFCxiSc1.0:AcqirisCspad2x2.0 keyamin = = acqiris_wtime fname500. amax = acq-AmoETOF-wtime ftype 1000. nbins = txt #ftype 100 arr_fname = tiff #saveAll cspad2x2-pix-spectra.txt |
To get images from saved file one may execute the auxiliary script:
| Code Block | ||
|---|---|---|
| ||
ImgPixSpectra/data/PlotSpectralArrayFromFile.py cspad2x2-pix-spectra.txt
|
generates image for limited range of pixels for CSPad, CSPad2x2, or Camera, respectively:
Examples for package ImgAlgos
See Package ImgAlgos
Example for module ImgAlgos::Tahometer
See Module ImgAlgos::Tahometer
Example of the psana configuration file:
| Code Block | ||
|---|---|---|
| ||
[psana] = true print_bits files = 3 eventSave/reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\ = 5 |
This script with psana does a few things:
- module AcqirisArrProducer gets Acqiris data objects from event store, adjusts trigger time corrections, and saves them back in the event store as uniform ndarrays<double,2> objects for waveforms and times
- two instances of the module ImgSaveInFile save arrays of waveforms and wave-times for locally counted event 5.
This script saves 3 text files:
acq-amo01509-r0125.txt-- with configuration parameters:Code Block Acqiris::ConfigV1: nbrBanks=1 channelMask=69905 nbrChannels=5 nbrConvertersPerChannel=4 horiz: sampInterval=2.5e-10 delayTime=0 nbrSegments=1 nbrSamples=10000 vert(0): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0 vert(1): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0 vert(2): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0 vert(3): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0 vert(4): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0- 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
Arrays from these files can be plotted for all channels, shown by different colors:
...
/reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-2>.xtc
modules = ImgAlgos.Tahometer
[ImgAlgos.Tahometer]
dn = 10
print_bits = 7
|
Example for module ImgAlgos::EpixNDArrProducer
See Module ImgAlgos::EpixNDArrProducer
Example of the psana configuration file:
| Code Block |
|---|
[psana]
files = exp=xppi0414:run=94
events = 100
modules = ImgAlgos.EpixNDArrProducer \
ImgAlgos.NDArrAverage
[ImgAlgos.EpixNDArrProducer]
source = DetInfo(:Epix10k)
key_in =
key_out = epix-nda
outtype = float
print_bits = 255
[ImgAlgos.NDArrAverage]
source = DetInfo(:Epix10k)
key = epix-nda
avefile = epix-ave
print_bits = 29 |
EpixNDArrProducer gets Epix10k ndarray from data and saves it in the events store with possible type conversion. Then NDArrAverage averages this ndarray over requested number of events (100) and saves it in file.
Example for module ImgAlgos::PnccdImageProducer
See Module ImgAlgos::PnccdImageProducer
Example of the psana configuration file:
| Code Block | ||
|---|---|---|
| ||
[psana] |
...
Example for module ImgAlgos::AcqirisAverage
See description of parameters in Module ImgAlgos::AcqirisAverage
Configuration file psana-amo01509-r0125-acqiris-average.cfg:
| Code Block | ||
|---|---|---|
| ||
# Command to run this script: # psana -c psana-amo01509-r0125-acqiris-average.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.AcqirisAverage skip-events = 0 events = 1000 [ImgAlgos.AcqirisArrProducer] source = AmoETOF.0:Acqiris.0 key_in = key_wform = acqiris_wform key_wtime = acqiris_wtime fname_prefix = acq print_bits = 3 [ImgAlgos.AcqirisAverage] source files = AmoETOF.0:Acqiris.0 key_in/reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\ /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-2>.xtc #skip-events = acqiris_wform key_ave100 events = 5 modules = ImgAlgos.PnccdImageProducer ImgAlgos.ImgSaveInFile [ImgAlgos.PnccdImageProducer] source = acqiris_average fname_ave_prefix = acq thresholdsDetInfo(:pnCCD) inkey = outimgkey = -0.005 -0.005 -0.005 -0.005 -0.005 is_positive_signal = imgpnccd print_bits = no do_inverse_selection = yes #skip_events 1 [ImgAlgos.ImgSaveInFile] source = 0 #proc_eventsDetInfo(:pnCCD) key = 100imgpnccd print_bitsfname = 255 |
Psana with this script runs over 1000 events apply threshold-based selection algorithm and produces files:
acq-amo01509-r0125-config.txt -- with Acqiris configuration parameters:
Code Block Acqiris::ConfigV1: nbrBanks=1 channelMask=69905 nbrChannels=5 nbrConvertersPerChannel=4 horiz: sampInterval=2.5e-10 delayTime=0 nbrSegments=1 nbrSamples=10000 vert(0): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0 vert(1): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0 vert(2): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0 vert(3): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0 vert(4): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0- acq-amo01509-r0125-ave-wfs.txt with averaged array of waveforms, which were below threshold (averaging for baseline level):
...
pnccd-img-ev
saveAll = true
#eventSave = 82
print_bits = 1
|
This script saves text files with images like pnccd-img-ev-<run-date-time.nsec>.txt, which can be presented as:
Advanced example for PnccdImageProducer;
- get pnccd ndarray from data,
- calibrate ndarray (subtract pedestals, common mode, remove pixels with bad status),
- produce image with two gaps from calibrated ndarray,
- average image for 10 events:
| Code Block |
|---|
[psana]
#calib-dir = /reg/d/psdm/SXR/sxrb5914/calib
files = exp=sxrb5914:run=245
events = 10 |
...
Example for module ImgAlgos::AcqirisCalib
See description of parameters in Module ImgAlgos::AcqirisCalib
Configuration file psana-amo01509-r0125-acqiris-calib.cfg:
| Code Block | ||
|---|---|---|
| ||
# Command to run this script: # psana -c psana-amo01509-r0125-acqiris-calib.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.AcqirisCalib ImgAlgos.ImgSaveInFile:wf_raw ImgAlgos.ImgSaveInFile:wf_calib skip-events = 0 eventsTahometer \ =ImgAlgos.PnccdNDArrProducer 10 [ImgAlgos.AcqirisArrProducer] source\ = AmoETOF.0:Acqiris.0 key_inImgAlgos.NDArrCalib \ =ImgAlgos.PnccdImageProducer key_wform\ = acqiris_wform key_wtime ImgAlgos.NDArrAverage [ImgAlgos.Tahometer] dn = acqiris_wtime fname_prefix = acq100 print_bits = 17 [ImgAlgos.AcqirisCalibPnccdNDArrProducer] source = AmoETOFDetInfo(Camp.0:AcqirispnCCD.01) key_in = key_out = pnccd-ndarr outtype = asdata print_bits = 0 [ImgAlgos.NDArrCalib] source = DetInfo(Camp.0:pnCCD.1) key_in = = acqiris_wformpnccd-ndarr key_out = calibrated do_peds = yes do_cmod = yes do_stat = yes do_mask = no do_bkgd = no do_gain = wf-calibrated fname_base_line = acq-amo01509-r0125-ave-wfs.txt #skip_events no do_nrms = no do_thre = no #fname_mask = pnccd-test-mask.txt #fname_bkgd = pnccd-test-bkgd.txt masked_value = 0 threshold_nrms = 4.0 #proc_events threshold = 100 below_thre_value = 0 bkgd_ind_min = 10010000 printbkgd_ind_bitsmax = 10200 bkgd_ind_inc = 255 1 print_bits = 1 [ImgAlgos.ImgSaveInFile:wf_rawPnccdImageProducer] source = AmoETOFDetInfo(Camp.0:AcqirispnCCD.01) keyinkey = calibrated outimgkey = acqiris_wform fname = acq-AmoETOF-wform-raw ftypepnccd-img gap_rows = txt #ftype 0 gap_cols = tiff16 #saveAllgap_value = true0 print_bits = 3 eventSave = 5 1 [ImgAlgos.ImgSaveInFile:wf_calibNDArrAverage] source = AmoETOFDetInfo(Camp.0:AcqirispnCCD.01) key = wfpnccd-calibratedimg fnameavefile = acq-AmoETOF-wform-calibrated ftype pnccd-ave rmsfile = txtpnccd-rms #ftype#maskfile = pnccd-msk #hotpixfile = tiff #saveAllpnccd-hot thr_rms_ADU = 160 thr_min_ADU = 2 thr_max_ADU = true10000 print_bits = 3 eventSave = 5 |
In this script the base-line level for all waveforms is loaded from file and is subtracted in module ImgAlgos.AcqirisCalib.
For example, the raw and calibrated waveforms for event 5 were saved in the files:
acq-AmoETOF-wform-raw-r0125-e00000005-20091018-182512.194787218.txtacq-AmoETOF-wform-calibrated-r0125-e00000005-20091018-182512.194787218.txt
which content is presented on plots:
...
29 |
...
Example for module ImgAlgos::
...
CameraImageProducer
See description of parameters in Module ImgAlgos::AcqirisCFDCameraImageProducer
Example of the psana configuration fileConfiguration file psana_cfd.cfg:
| Code Block | ||
|---|---|---|
| ||
#[psana] Command to run this script: # psana -c psana_cfd.cfg; # [psana] modules = ImgAlgos.AcqirisArrProducer ImgAlgos.AcqirisCalib ImgAlgos.AcqirisCFD files files = /reg/d/psdm/AMO<INSTRUMENT>/amo01509<experiment>/xtc/e8<file-r0125name-s00-c001>.xtc [ImgAlgos.AcqirisArrProducer] sourcemodules = AmoETOF.0:Acqiris.0 key_in = key_wform = acqiris_wform key_wtime = acqiris_wtime fname_prefixImgAlgos.CameraImageProducer ImgAlgos.ImgSaveInFile events = acq print_bits = 05 [ImgAlgos.AcqirisCalibCameraImageProducer] source = AmoETOF.0:Acqiris.0DetInfo(:Opal1000) key_in = acqiris_wform key_out = wf-calibrated fname_base_line = acq--r0000-ave-wfs.txt #skip_events = 0img #procsubtract_eventsoffset = 100true print_bits = 015 [ImgAlgos.AcqirisCFDImgSaveInFile] source = AmoETOF.0:Acqiris.0 key_wform = wf-calibrated baselines = 0.0 0.0 0.0 0.0 0.0 thresholds = -0.005 -0.005 -0.005 -0.005 -0.005 fractions = 0.5 0.5 0.5 0.5 0.5 deadtimes = 20.0e-9 20.0e-9 20.0e-9 20.0e-9 20.0e-9 leading_edges = 1 1 1 1 1 |
This script analyzes an AMO run where 5 acqiris channels were in use. It uses an AcqirisArrProducer to producer the list of waveforms/times for all channels. It then uses an AcqirisCalib module to do a baseline subtraction using a previously generated file of baselines act--r0000-ave-wfs.txt. Finally, a constant fraction discriminator algorithm is run on all the waveforms with user specified parameters. The edges calculated by AcqirisCFD are saved to the event as one ndarray<double,1> per channel, each with a (default) key "acqiris_edges_N" where N is the channel number. Channels where no edges were found are not saved to the event.
...
DetInfo(:Opal1000)
key = img
fname = img-from-my-experiment
saveAll = true
#eventSave = 1
|
This script saves text files with images like img-from-my-experiment-<run-date-time.nsec>.txt, which can be drawn by the python script
./ImgAlgos/data/PlotCameraImageFromFile.py <filename>.txt <Amin> <Amax>
Example for module ImgAlgos::PrincetonImageProducer
See Module ImgAlgos::PrincetonImageProducer
Example of the psana configuration file:
| Code Block | ||
|---|---|---|
| ||
[psana] |
...
Example for combination of Acqiris modules
See description of parameters in Modules ImgAlgos::AcqirisArrProducer, AcqirisAverage, and AcqirisCalib
Configuration file psana-amo01509-r0125-acqiris-comb.cfg:
| Code Block |
|---|
# Command to run this script: # psana -c psana-amo01509-r0125-acqiris-comb.cfg; [psana] files = exp=amo01509:run=125:xtc modules = ImgAlgos.AcqirisArrProducer ImgAlgos.AcqirisAverage:bl ImgAlgos.AcqirisCalib ImgAlgos.AcqirisAverage:signal ImgAlgos.Tahometer #skip-events = 0 events = 2010 [ImgAlgos.AcqirisArrProducer] source = AmoETOF.0:Acqiris.0 key_in = key_wform = acqiris_wform key_wtime = acqiris_wtime fname_prefix files = acq print_bits = 7 [ImgAlgos.AcqirisAverage:bl] source/reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\ /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-2>.xtc modules = AmoETOF.0:Acqiris.0 key_inImgAlgos.PrincetonImageProducer \ = acqiris_wform #key_ave ImgAlgos.ImgSaveInFile events = 3 [ImgAlgos.PrincetonImageProducer] source = DetInfo(:Princeton) fname_ave_prefixkey_in = acq-bline thresholds key_out = img subtract_offset = -0.005 -0.005 -0.005 -0.005 -0.005 is_positive_signal = no do_inverse_selection = yes skip_events = 0 proc_events = 1000 print_bits true print_bits = 31 [ImgAlgos.AcqirisCalibImgSaveInFile] source = AmoETOF.0:Acqiris.0DetInfo(:Princeton) key_in = acqiris_wform key_outimg fname = wfimg-calibrated fname_base_linexcs saveAll = acq-blinetrue skipprint_eventsbits = 1001 proc_events = 1000 print_bits = 47 [ImgAlgos.AcqirisAverage:signal] source = AmoETOF.0:Acqiris.0 key_in = wf-calibrated #key_ave 31 |
| Anchor | ||||
|---|---|---|---|---|
|
Example for module ImgAlgos::AcqirisArrProducer
See description of parameters in Module ImgAlgos::AcqirisArrProducer
Example of the psana configuration file psana-amo01509-r0125-acqiris.cfg :
| Code Block | ||
|---|---|---|
| ||
# 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 = fname_ave_prefixAmoETOF.0:Acqiris.0 key_in = acq-signal thresholds = key_wform = acqiris_wform key_wtime = acqiris_wtime fname_prefix = acq print_bits = -0.01 -0.01 -0.01 -0.01 -0.01 is_positive_signal11 [ImgAlgos.ImgSaveInFile:wf] source = AmoETOF.0:Acqiris.0 key = no do_inverse_selectionacqiris_wform fname = no skip_eventsacq-AmoETOF-wform ftype = 1001 proc_events txt #ftype = tiff #saveAll = 1000true print_bits = 3 eventSave = 315 [ImgAlgos.Tahometer] print_bitsImgSaveInFile:wt] source = 7 |
This script works with psana as follows:
- for the 1st 1000 events averages waveforms below threshold and saves results in the file acq-bline-amo01509-r0125-ave-wfs.txt;
- for the next 1000 events subtracts baseline level and averages waveforms above thresholds and saves results in the file acq-signal-amo01509-r0125-ave-wfs.txt.
This script produces three files:
acq-amo01509-r0125-config.txt - with Acqris configuration parameters:
Code Block Acqiris::ConfigV1: nbrBanks=1 channelMask=69905 nbrChannels=5 nbrConvertersPerChannel=4 horiz: sampInterval=2.5e-10 delayTime=0 nbrSegments=1 nbrSamples=10000 vert(0): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0 vert(1): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0 vert(2): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0 vert(3): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0 vert(4): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0
- acq-bline-amo01509-r0125-ave-wfs.txt - contains baseline averaged arrays, which can be presented by full scale and zoomed plots:
- acq-signal-amo01509-r0125-ave-wfs.txt- contains signal averaged arrays, which can be presented by full scale and zoomed plots:
Example for module ImgAlgos::NDArrAverage
- See Module ImgAlgos::NDArrAverage
The
NDArrAveragemodule 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 [ImgAlgos.Tahometer] dn = 100 print_bits = 7
Example for module ImgAlgos::ImgAverage
- See Module ImgAlgos::ImgAverage
- The
ImgAveragemodule can be used for evaluation of averaged pedestals or background using dedicated runs. Typical configuration file may looks like this:
AmoETOF.0:Acqiris.0
key = acqiris_wtime
fname = acq-AmoETOF-wtime
ftype = txt
#ftype = tiff
#saveAll = true
print_bits = 3
eventSave = 5
|
This script with psana does a few things:
- module AcqirisArrProducer gets Acqiris data objects from event store, adjusts trigger time corrections, and saves them back in the event store as uniform ndarrays<double,2> objects for waveforms and times
- two instances of the module ImgSaveInFile save arrays of waveforms and wave-times for locally counted event 5.
This script saves 3 text files:
acq-amo01509-r0125.txt-- with configuration parameters:Code Block Acqiris::ConfigV1: nbrBanks=1 channelMask=69905 nbrChannels=5 nbrConvertersPerChannel=4 horiz: sampInterval=2.5e-10 delayTime=0 nbrSegments=1 nbrSamples=10000 vert(0): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0 vert(1): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0 vert(2): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0 vert(3): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0 vert(4): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0- 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
Arrays from these files can be plotted for all channels, shown by different colors:
| Anchor | ||||
|---|---|---|---|---|
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Example for module ImgAlgos::AcqirisAverage
See description of parameters in Module ImgAlgos::AcqirisAverage
Configuration file psana-amo01509-r0125-acqiris-average.cfg:
| Code Block | ||
|---|---|---|
| ||
# Command to run this script:
# psana -c psana-amo01509-r0125-acqiris-average.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.AcqirisAverage
skip-events = 0
events = 1000
[ImgAlgos.AcqirisArrProducer]
source | ||
| Code Block | ||
| ||
[psana] files = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name>.xtc modules = ImgAlgos.CameraImageProducer \ ImgAlgos.ImgAverage events = 1000 [ImgAlgos.CameraImageProducer] source = DetInfo(:Opal1000)AmoETOF.0:Acqiris.0 key_in = key_outwform = acqiris_wform key_wtime = imgacqiris_wtime subtractfname_offsetprefix = trueacq print_bits = 13 [ImgAlgos.ImgAverageAcqirisAverage] source = DetInfo(:Opal1000)AmoETOF.0:Acqiris.0 key_in = img avefileacqiris_wform key_ave = img-ave.dat rmsfile = acqiris_average fname_ave_prefix = img-rms.dat print_bitsacq thresholds = 31 evts_stage1 = -0.005 -0.005 = 100 evts_stage2-0.005 -0.005 -0.005 is_positive_signal = no do_inverse_selection = 100yes gate#skip_width1events = 200 gate_width2 = 20 |
Example for module ImgAlgos::ImgMaskEvaluation
- See Module ImgAlgos::ImgMaskEvaluation
- Configuration parameters for psana:
| Code Block | ||
|---|---|---|
| ||
[ImgAlgos.ImgMaskEvaluation] source0 #proc_events = DetInfo(:Opal1000) key 100 print_bits = 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 |
| Note |
|---|
In this example parameters were chosen in order to get a small number of "noisy" pixel just due to statistics. |
...
255
|
Psana with this script runs over 1000 events apply threshold-based selection algorithm and produces files:
acq-amo01509-r0125-config.txt -- with Acqiris configuration parameters:
Code Block Acqiris::ConfigV1: nbrBanks=1 channelMask=69905 nbrChannels=5 nbrConvertersPerChannel=4 horiz: sampInterval=2.5e-10 delayTime=0 nbrSegments=1 nbrSamples=10000 vert(0): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0 vert(1): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0 vert(2): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0 vert(3): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0 vert(4): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0- acq-amo01509-r0125-ave-wfs.txt with averaged array of waveforms, which were below threshold (averaging for baseline level):
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...
Example for module ImgAlgos::
...
AcqirisCalib
See description of parameters in Module ImgAlgos::
...
Configuration file psana-amo01509-r0125-acqiris-calib.cfg:
| Code Block | |||
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# Command to run this script: # psana -c psana-amo01509-r0125-acqiris-calib.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.AcqirisCalib ImgAlgos.ImgSaveInFile:wf_raw ImgAlgos.ImgSaveInFile:wf_calib skip-events = 0 events = 10 [ImgAlgos.AcqirisArrProducer] source[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_pedsAmoETOF.0:Acqiris.0 key_in = <pedestal-file-name> fnamekey_mask wform = <mask-file-name> fname_bkgdacqiris_wform key_wtime = acqiris_wtime fname_gain prefix = acq print_bits = 31 |
- Example of the mask file and resulting image:
Example for module ImgAlgos::ImgRadialCorrection
- See Module ImgAlgos::ImgRadialCorrection
| Code Block | ||
|---|---|---|
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[psana] files = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-1>.xtc \ 1 [ImgAlgos.AcqirisCalib] source /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-2>.xtc \ = AmoETOF.0:Acqiris.0 key_in ... /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-N>.xtc skip-events = 500 events= acqiris_wform key_out = 10 modules = cspad_mod.CsPadCalib \ # = wf-calibrated fname_base_line ImgAlgos.CSPadBkgdSubtract \ = acq-amo01509-r0125-ave-wfs.txt #skip_events CSPadPixCoords.CSPadImageProducer= \0 #proc_events ImgAlgos.ImgRadialCorrection= \100 print_bits = 255 [ImgAlgos.ImgSaveInFile:1 [cspad_mod.CsPadCalib] inputKeywf_raw] source = outputKeyAmoETOF.0:Acqiris.0 key = calibrated doPedestals = yes doPixelStatus = noacqiris_wform doCommonModefname = no [ImgAlgos.CSPadBkgdSubtract] source = DetInfo(CxiDs1.0:Cspad.0) inputKey= acq-AmoETOF-wform-raw ftype = calibrated outputKeytxt #ftype = bkgd_subtracted_arr bkgd_fnametiff #saveAll = <the-file-name-with-background-array> norm_sector = 0true print_bits = 0 [CSPadPixCoords.CSPadImageProducer] calibDir3 eventSave = /reg/d/psdm/<instrument>/<experiment>/calib typeGroupName = CsPad::CalibV15 [ImgAlgos.ImgSaveInFile:wf_calib] source = CxiDs1AmoETOF.0:CspadAcqiris.0 key = wf-calibrated imgkeyfname = current_img #tiltIsApplied = true [ImgAlgos.ImgRadialCorrection] sourceacq-AmoETOF-wform-calibrated ftype = DetInfo(CxiDs1.0:Cspad.0) inkeytxt #ftype = current_imgtiff outkey#saveAll = r_cor_img xcenter = 866 ycenter = 857 rmin = 100 rmax = 810 n_phi_bins = 60 event = 0true print_bits = 3 [ImgAlgos.ImgSaveInFile:1] source eventSave = CxiDs1.0:Cspad.0 key = r_cor_img fname = <file-name-for-image-array> #saveAll = true eventSave = 8 |
- Note: the option of the background subtraction (
ImgAlgos.CSPadBkgdSubtract) is commented out in this configuration file . In order to evoke this option, the comment sign (#) should be removed from the list ofmodulesand thekey=bkgd_subtracted_arrshould be used inCSPadPixCoords.CSPadImageProducer. - Calibrated image and spectrum:
- Calibrated and radial-corrected image, spectrum, and subtracted r-phi65 distribution for
n_phi_bins=65: 
- Calibrated and radial-corrected image, spectrum, and subtracted r-phi12 distribution for
n_phi_bins=12: 
Example for module ImgAlgos::ImgPeakFinder
- See Module ImgAlgos::ImgPeakFinder
- Configuration file example:
5
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In this script the base-line level for all waveforms is loaded from file and is subtracted in module ImgAlgos.AcqirisCalib.
For example, the raw and calibrated waveforms for event 5 were saved in the files:
acq-AmoETOF-wform-raw-r0125-e00000005-20091018-182512.194787218.txtacq-AmoETOF-wform-calibrated-r0125-e00000005-20091018-182512.194787218.txt
which content is presented on plots:
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Example for module ImgAlgos::AcqirisCFD
See description of parameters in Module ImgAlgos::AcqirisCFD
Configuration file psana_cfd.cfg:
| Code Block | ||
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# Command to run this script:
# psana -c psana_cfd.cfg;
#
[psana]
modules = ImgAlgos.AcqirisArrProducer ImgAlgos.AcqirisCalib ImgAlgos.AcqirisCFD
files = /reg/d/psdm/AMO/amo01509/xtc/e8-r0125-s00-c00.xtc
[ImgAlgos.AcqirisArrProducer]
source = AmoETOF.0:Acqiris.0
key_in =
key_wform = acqiris_wform
key_wtime = acqiris_wtime
fname_prefix = acq
print_bits = 0
[ImgAlgos.AcqirisCalib]
source = AmoETOF.0:Acqiris.0
key_in = acqiris_wform
key_out = wf-calibrated
fname_base_line = acq--r0000-ave-wfs.txt
#skip_events = 0
#proc_events = 100
print_bits = 0
[ImgAlgos.AcqirisCFD]
source = AmoETOF.0:Acqiris.0
key_wform = wf-calibrated
baselines = 0.0 0.0 0.0 0.0 0.0
thresholds = -0.005 -0.005 -0.005 -0.005 -0.005
fractions = 0.5 0.5 0.5 0.5 0.5
deadtimes = 20.0e-9 20.0e-9 20.0e-9 20.0e-9 20.0e-9
leading_edges = 1 1 1 1 1 |
This script analyzes an AMO run where 5 acqiris channels were in use. It uses an AcqirisArrProducer to producer the list of waveforms/times for all channels. It then uses an AcqirisCalib module to do a baseline subtraction using a previously generated file of baselines act--r0000-ave-wfs.txt. Finally, a constant fraction discriminator algorithm is run on all the waveforms with user specified parameters. The edges calculated by AcqirisCFD are saved to the event as one ndarray<double,1> per channel, each with a (default) key "acqiris_edges_N" where N is the channel number. Channels where no edges were found are not saved to the event.
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Example for combination of Acqiris modules
See description of parameters in Modules ImgAlgos::AcqirisArrProducer, AcqirisAverage, and AcqirisCalib
Configuration file psana-amo01509-r0125-acqiris-comb.cfg:
| Code Block | ||
|---|---|---|
# Command to run this script:
# psana -c psana-amo01509-r0125-acqiris-comb.cfg;
[psana]
files = exp=amo01509:run=125:xtc
modules = ImgAlgos.AcqirisArrProducer ImgAlgos.AcqirisAverage:bl ImgAlgos.AcqirisCalib ImgAlgos.AcqirisAverage:signal ImgAlgos.Tahometer
#skip-events = 0
events = 2010
[ImgAlgos.AcqirisArrProducer]
source | ||
| Code Block | ||
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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_radiusAmoETOF.0:Acqiris.0 key_in = 2 peakkey_radiuswform = 3 xminacqiris_wform key_wtime = acqiris_wtime fname_prefix = acq print_bits = 200 xmax7 [ImgAlgos.AcqirisAverage:bl] source = 800 ymin = AmoETOF.0:Acqiris.0 key_in = 100 ymax = acqiris_wform #key_ave = 900 testEvent = 115 printfname_ave_bitsprefix = 0 finderIsOnacq-bline thresholds = true |
- This algorithm consumes ~15 ms/event on psana0101 for full Opal1000 (1024x1024) camera image.
- Smearing algorithm use a "safety margin" which is currently set to 10 pixels (offset from each boarder of the full image size).
- Image on different stages of this algorithm:
- raw image,
- image in the window with amplitudes above the
threshold_low- few peaks at the edges were discarded by the window limits,
- image still contains many 1-photon pixels, which need to be eliminated,
- smeared image,
- raw image with found peaks (marked by the red circles)
- zoom of the previous plot.
Example for module ImgAlgos::ImgPeakFilter
| Code Block | ||
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[ImgAlgos.ImgPeakFilter] source = DetInfo(:Opal1000) key -0.005 -0.005 -0.005 -0.005 -0.005 is_positive_signal = no do_inverse_selection = yes skip_events = 0 proc_events = peaks threshold_peak = 51000 thresholdprint_total= 0 n_peaks_minbits = 10 print_bits = 11 fname31 [ImgAlgos.AcqirisCalib] source = img selection_mode = SELECTION_ON |
Example for module ImgAlgos::ImgPeakFinderAB
- See Module ImgAlgos::ImgPeakFinderAB
- Configuration file example:
| Code Block | ||
|---|---|---|
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[psana]AmoETOF.0:Acqiris.0 key_in = acqiris_wform key_out = wf-calibrated fname_base_line = acq-bline skip_events = 1001 proc_events = 1000 print_bits files = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name>.xtc modules = ImgAlgos.CameraImageProducer \ 47 [ImgAlgos.AcqirisAverage:signal] source ImgAlgos.ImgPeakFinderAB events = 10 [ImgAlgos.CameraImageProducer] sourceAmoETOF.0:Acqiris.0 key_in = DetInfo(:Opal1000) key_in = wf-calibrated #key_ave = key_out = img subtract_offset = true print_bitsfname_ave_prefix = 1 [ImgAlgos.ImgPeakFinderAB] sourceacq-signal thresholds = -0.01 -0.01 -0.01 = DetInfo(:Opal1000) key-0.01 -0.01 is_positive_signal = no do_inverse_selection = no skip_events = img1001 keyproc_peaks_outevents = peaks1000 #keyprint_signal_outbits = 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_mode31 [ImgAlgos.Tahometer] print_bits = 7 |
This script works with psana as follows:
- for the 1st 1000 events averages waveforms below threshold and saves results in the file acq-bline-amo01509-r0125-ave-wfs.txt;
- for the next 1000 events subtracts baseline level and averages waveforms above thresholds and saves results in the file acq-signal-amo01509-r0125-ave-wfs.txt.
This script produces three files:
acq-amo01509-r0125-config.txt - with Acqris configuration parameters:
Code Block Acqiris::ConfigV1: nbrBanks=1 channelMask=69905 nbrChannels=5 nbrConvertersPerChannel=4 horiz: sampInterval=2.5e-10 delayTime=0 nbrSegments=1 nbrSamples=10000 vert(0): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0 vert(1): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0 vert(2): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0 vert(3): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0 vert(4): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0
- acq-bline-amo01509-r0125-ave-wfs.txt - contains baseline averaged arrays, which can be presented by full scale and zoomed plots:
- acq-signal-amo01509-r0125-ave-wfs.txt- contains signal averaged arrays, which can be presented by full scale and zoomed plots:
Example for module ImgAlgos::NDArrImageProducer
See Module ImgAlgos::NDArrImageProducer
Module ImgAlgos.NDArrImageProducer produces image from any detector-associated ndarray
Possible chain of modules:
- <Package>.<Detector>NDArrProducer
- ImgAlgos.NDArrCalib
- ImgAlgos.NDArrImageProducer
- ImgAlgos.NDArrAverage
Example of the configuration file for cspad
| Code Block |
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[psana] files = exp=cxii0114:run=227 events = 100 modules = ImgAlgos.Tahometer \ CSPadPixCoords.CSPadNDArrProducer \ ImgAlgos.NDArrCalib \ ImgAlgos.NDArrImageProducer \ ImgAlgos.NDArrAverage [CSPadPixCoords.CSPadNDArrProducer] source = DetInfo(CxiDs1.0:Cspad.0) inkey = outkey = SELECTIONcspad_ON out_file_bitsndarr outtype = float is_fullsize = 15yes print_bits = 3 [ImgAlgos.NDArrCalib] source = DetInfo(CxiDs1.0:Cspad.0) key_in = cspad_ndarr key_out 513 |
- Results:
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.
- 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:
| Code Block | ||
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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= calibrated do_peds = yes do_cmod = yes do_stat = yes do_mask = no do_bkgd = no do_gain = no do_nrms = no do_thre = no fname_mask = fname_bkgd = masked_value = -10 threshold_nrms = 4 threshold = = DetInfo(:Opal1000) key_in 7 below_thre_value = = key_out0 print_bits = img subtract_offset = true print_bits 3 = 1 [ImgAlgos.ImgAverageNDArrImageProducer] source = DetInfo(:Opal1000)CxiDs1.0:Cspad.0 key_in = calibrated key_out = cspad_img avefile#type_out = asinp #type_out = img-ave-for-peds rmsfilefloat #x0_off_pix = 50 #y0_off_pix = img-rms-for-thre evts_stage150 print_bits = 100255 evts_stage2#calibdir = 100 gate_width1/reg/neh/home/dubrovin/LCLS/CSPadAlignment-v01/calib-cxi-ds1-2014-03-19/calib [ImgAlgos.NDArrAverage] source = 50 gate_width2DetInfo(CxiDs1.0:Cspad.0) key = 10 print_bitscspad_img avefile = 31 |
- Run psana using command:
| Code Block | ||
|---|---|---|
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psana -c psana-amo74213-r0093-opal-img-average.cfg
|
- At the end of this procedure two files will be created:
- img-ave-for-peds-r0093.dat - may be used for pedestal subtraction:
- img-rms-for-thre-r0093.dat - may be used multiplied by number of rms as a threshold:
- The file with accumulated pixel hits can be obtained using configuration file:
cspad-img-ave
rmsfile = cspad-img-rms
#maskfile = cspad-img-msk
#hotpixfile = cspad-img-hot
thr_rms_ADU = 0
thr_min_ADU = 4
thr_max_ADU = 65000
print_bits = 29 |
Example of the configuration file for cspad2x2
| Code Block | ||
|---|---|---|
[psana]
# calib-dir | ||
| 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.xtcmec/meca1113/calib #calib-dir = /reg/neh/home/dubrovin/LCLS/CSPad2x2Alignment/calib-cspad2x2-01-2013-02-13/calib files = exp=amo74213meca1113:run=93:xtc modules = ImgAlgos.CameraImageProducer376 events = 10 #skip-events = 0 modules = CSPadPixCoords.CSPad2x2NDArrProducer \ ImgAlgos.ImgHitFinderNDArrImageProducer \ ImgAlgos.ImgAverage skip-events = 0 events = 1000 [ImgAlgos.CameraImageProducer] source NDArrAverage [CSPadPixCoords.CSPad2x2NDArrProducer] source = DetInfo(:Opal1000) key_in MecTargetChamber.0:Cspad2x2.1 inkey = key_outoutkey = cspad2x2_ndarr outtype = img subtract_offset = trueint16 print_bits = 15 [ImgAlgos.ImgHitFinderNDArrImageProducer] source = DetInfo(:Opal1000)MecTargetChamber.0:Cspad2x2.1 key_in = imgcspad2x2_ndarr key_out = cspad2x2_img_hits fname#type_pedsout = img-ave-for-peds-r0093.dat fname_mask asinp #type_out = float fname#x0_off_gainpix = 50 #y0_off_pix = 50 fnameprint_threbits = 255 #oname = img-rms-for-thre-r0093.dat masked_value = 0 thre_modeCSPAD2X2:V1 #oindex = 3 #thre_mode 0 #pix_scale_size_um = 218. #calibdir = 2 thre_param/reg/neh/home/dubrovin/LCLS/CSPad2x2Alignment/calib-cspad2x2-01-2013-02-13/calib #calibgroup = CsPad2x2::CalibV1 [ImgAlgos.NDArrAverage] source = 5 thre_below_value = 0 thre_above_value = MecTargetChamber.0:Cspad2x2.1 win_row_min#key = 10 win_row_max = cspad2x2_ndarr key = 1000 win_col_min = 10 win_col_maxcspad2x2_img avefile = 1000 print_bitsarr-ave rmsfile = 39 [ImgAlgos.ImgAverage] sourcearr-rms maskfile = arr-msk hotpixfile = DetInfo(:Opal1000) keyarr-hot thr_rms_ADU = img_hits sumfile = img-sum-result= 10 #thr_min_ADU = 2 #thr_max_ADU = 20000 print_bits = 25 |
- and run it by the command:
...
| bgColor | #F7F7ED |
|---|
255 |
Example for module ImgAlgos::NDArrAverage
- See Module ImgAlgos::NDArrAverage andModule CSPadPixCoords::CSPadNDArrProducer
The
NDArrAveragemodule 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
...
- Which creates the file: img-sum-result-r0093.dat for
thre_mode = 2andthre_mode = 3, respectively: 
Example for module ImgAlgos::ImgSpectra
- See Module ImgAlgos::ImgSpectra
- Configuration file for psana:
...
| bgColor | #F7F7ED |
|---|
[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.Tahometeris 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:
Then, one has to decide how to set parameters for NDArrAverage algorithms, for example, it is quite safe to use
- thr_rms_ADU = 10 – to discard very noisy pixels,
- thr_min_ADU = 4 – to discard presumably dead pixels with 0-intensity,
- thr_max_ADU = 10000 – to discard pixels with intensity significantly exceeding average value. To be on safe side for int16 data this parameter can be set to 216-4, where 4 in both cases is just a small arbitrary number for spare safety gap.
Example for module ImgAlgos::NDArrCalib
See Module ImgAlgos::NDArrCalib, Module ImgAlgos::NDArrAverageThe
NDArrCalibmodule in combination with any device NDArrProducer (for example PnccdNDArrProducer) can be used to apply intensity corrections to ndarray.
Typical configuration files are shown below.
Example of ImgAlgos::NDArrCalib for pnCCD
| Code Block |
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[psana] 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 files = DetInfo(:Opal1000) key exp=amoa1214:run=7 #skip-events = 100 events = 5 modules = =ImgAlgos.Tahometer spectra\ fname = spec-xppi0412 saveAllImgAlgos.PnccdNDArrProducer \ = true [ImgAlgos.ImgSaveInFile]NDArrCalib \ source = DetInfo(:Opal1000) key ImgAlgos.PnccdImageProducer \ = imgImgAlgos.ImgSaveInFile fname# = img-xppi0412 saveAllImgAlgos.NDArrAverage \ [ImgAlgos.PnccdNDArrProducer] source = true |
- This script can be used in order to produce text files with image and spectral array:
- or graphics for several images:
Example for module ImgAlgos::ImgSpectraProc
- See Module ImgAlgos::ImgSpectraProc
- Configuration file for psana:
| Code Block | ||
|---|---|---|
| ||
[ImgAlgos.ImgSpectraProc] source = DetInfo(:Opal1000)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 outtype = float do_peds = yes do_cmod = spectrayes printdo_bitsstat = no do_mask = no do_bkgd = 15 |
- For each event it prints something similar to:
| Code Block | ||
|---|---|---|
| ||
[info:ImgAlgos.ImgSpectraProc] Spectral array shape =3, 1024 [info:ImgAlgos.ImgSpectraProc] Image spectra for run=0060 Evt=000100 Column:no do_gain = no do_nrms = no do_thre = no fname_mask = fname_bkgd = masked_value = 0 0 threshold_nrms 100= 3 200 threshold 300 = 400 100 below_thre_value = 5000 bkgd_ind_min 600= 0 bkgd_ind_max 700 800= 1000 bkgd_ind_inc 900= 1000 Signal:10 print_bits 1211 = 4062 255 11150 [ImgAlgos.PnccdImageProducer] source 17070 16406 = 12949DetInfo(Camp.0:pnCCD.0) #inkey 7991 5168= pnccd-ndarr inkey 3968 3542 = 3811 Refer.:calibrated outimgkey 933 = pnccd-img gap_size 3485 10425= 20 gap_value 17128 17791= 0 print_bits 13522 = 83151 [ImgAlgos.ImgSaveInFile] source 5000 3390= DetInfo(Camp.0:pnCCD.0) key 2967 3193 Diff. : 0.259= pnccd-img fname 0.153 0.067 -0.003 = -0.081 -0.043 -0.040pnccd-img-from-arr ftype 0.033 0.157 = txt saveAll 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 ... true print_bits = 31 [ImgAlgos.ImgSaveInFile:1Tahometer] sourcedn = DetInfo(:Opal1000) # or CxiDs1.0:Cspad.0 key 100 print_bits = 7 |
Example of ImgAlgos::NDArrCalib for CSPAD
| Code Block |
|---|
[psana] files = exp=cxi83714:run=136 events = 100 modules = ImgAlgos.Tahometer \ = img fname CSPadPixCoords.CSPadNDArrProducer \ = my-img #ftypeImgAlgos.NDArrCalib \ = txt #ftypeImgAlgos.NDArrAverage [CSPadPixCoords.CSPadNDArrProducer] source = DetInfo(CxiDs1.0:Cspad.0) inkey = bin #ftype = outkey = pngcspad_ndarr ftypeouttype = float is_fullsize = tiffyes #eventSaveprint_bits = 3 [ImgAlgos.NDArrCalib] source = 5 saveAllDetInfo(CxiDs1.0:Cspad.0) key_in = cspad_ndarr key_out = calibrated outtype = double do_peds = true |
- See Module ImgAlgos::ImgSaveInFile
Example for module ImgPeakFinder and ImgPeakFilter for CSPad
- Module
ImgAlgos::ImgPeakFinderworks on image. In order to apply this algorithm to CSPad the image should be produced. In next example the image is produced using consequtive modulescspad_mod.CsPadCalib,ImgAlgos.CSPadMaskApply, andCSPadPixCoords.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 \ yes do_cmod = yes do_stat = yes do_mask = no do_bkgd = no do_gain = no do_nrms = no do_thre = no fname_mask = fname_bkgd = masked_value = -10 threshold_nrms = 4 threshold = 7 below_thre_value = 0 bkgd_ind_min = 0 bkgd_ind_max = 1000 bkgd_ind_inc = 10 print_bits = 3 [ImgAlgos.ImgPeakFinder \NDArrAverage] source ImgAlgos.ImgPeakFilter \ = DetInfo(CxiDs1.0:Cspad.0) key ImgAlgos.ImgSaveInFile:1 [cspad_mod.CsPadCalib] inputKey= calibrated avefile = cspad-ave outputKeyrmsfile = calibratedcspad-rms doPedestals#maskfile = yes doPixelStatus = no doCommonModecspad-msk #hotpixfile = yes [ImgAlgos.CSPadMaskApply] source cspad-hot thr_rms_ADU = DetInfo(CxiDs1.0:Cspad.0) inkey = calibrated outkey = masked_arr mask_fname = <your-local-directory>/<mask-file-name>.dat masked_amp = 010 thr_min_ADU = 4 thr_max_ADU = 10000 print_bits = 5 mask_control_bits = 15 [CSPadPixCoords.CSPadImageProducer] calibDir29 [ImgAlgos.Tahometer] dn = /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 xmin10 print_bits = 7 |
For test purpose we use exp=cxi83714:run=136 and loop over 100 exents.
Case 1: raw, non-calibrated images
do_peds = no; 50-60 ms/event
plots for average and rms value distribution for all pixels
Case 2: images with subtracted pedestals and applied status mask
do_peds = yes; 60-70 ms/event
do_stat = yes
Case 3: The same as 2 with common mode subtracted
do_cmod = yes; 107-117 ms/event
Andy's algorithm for CSPAD common mode correction with minor adaptive modifications is applied with parameters:
/reg/d/psdm/cxi/cxi83714/calib/CsPad::CalibV1/CxiDs1.0:Cspad.0/common_mode/135-136.data
1 10 10 100 - algorithm mode, allowed peak mean, allowed peak rms, threshold on number of pixels in ADU bin.
Comparison with Andy's module cspad_mod.CsPadCalib for common mode correction of int16_t data
| Code Block |
|---|
[psana] # Default calibration directory: # calib-dir = /reg/d/psdm/mec/cxi83714/calib # calib-dir = /reg/neh/home1/dubrovin/LCLS/CSPadAlignment-v01/calib-mec-2013-12-10/ files = exp=cxi83714:run=136 events = 100 #skip-events = 4000 modules = cspad_mod.CsPadCalib \ = 20 xmaxCSPadPixCoords.CSPadNDArrProducer \ = 1700 yminImgAlgos.NDArrAverage \ = 20 ymaxImgAlgos.Tahometer [cspad_mod.CsPadCalib] inputKey = 1700 #testEventoutputKey = 5 print_bitscalibrated_data doPedestals = yes doPixelStatus = 3 #finderIsOn yes doCommonMode = trueyes [ImgAlgosCSPadPixCoords.ImgPeakFilterCSPadNDArrProducer] source = DetInfo(CxiDs1.0:Cspad.0) keyinkey = peaks threshold_peak = 5 threshold_total= 0 n_peaks_min= calibrated_data outkey = 10 print_bitscspad_ndarr outtype = 11float fnameis_fullsize = cspad-imgyes selectionprint_modebits = SELECTION_ON3 [ImgAlgos.ImgSaveInFile:1NDArrAverage] source = DetInfo(CxiDs1.0:Cspad.0) key = img fname cspad_ndarr avefile = cspad-calib-imgave #eventSavermsfile = 1 saveAllcspad-calib-rms #maskfile = cspad-msk #hotpixfile = true |
Example for module ImgAlgos::CSPadArrAverage
- See Module ImgAlgos::CSPadArrAverage
- 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
|
- Images of the CSPad arrays for averaged and rms values, respectively, in one of the CXI runs:
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 fornorm_sector=0. - Event image and pixel amplitude spectrum before and after the background subtraction are shown in plots:
- Other event with better subtracted background:
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.
- For example, it can be generated by the command
| Code Block | ||
|---|---|---|
| ||
./MakePixelMask.py <input-background-cspad-arr-file-name> <threshold> <output-file-name>
|
- for the averaged background amplitude array
<input-background-cspad-arr-file-name>abtained as a result ofImgAlgos::CSPadArrAveragemodule. - Plots show the averaged background, and the mask arrays generated from this background for three thresholds 10, 20, and 30 EDU:
- The best results in filtering can be achieved in combination of modiles:
cspad-hot
thr_rms_ADU = 10
thr_min_ADU = 4
thr_max_ADU = 10000
print_bits = 29
[ImgAlgos.Tahometer]
dn = 10
print_bits = 7 |
doPedestals = yes
doCommonMode = no; 100-110ms
doPedestals = yes
doPixelStatus = yes
doCommonMode = yes; 150-160ms
Conclusion:
Results of
ImgAlgos.NDArrCalibwell reproducecspad_mod.CsPadCalib- Common mode correction shrinks the width of averaged intensities from 0.60 to 0.54, and rms from 3.78 to 3.27.
- Algorithm is quite time expensive, it takes 30-40ms/event.
Example of ImgAlgos::NDArrCalib for Fccd960
- Calibration
To calibrate fccd960 for dark runs use command
calibman
For test purpose a couple of dark runs were processed and constants were deployed:
| Code Block |
|---|
Content of: /reg/d/psdm/XCS/xcsd7814/calib for detector: Fccd960
Camera::CalibV1
XcsEndstation.0:Fccd960.0
pixel_rms
12-13.data file is not used
78-81.data run range 0078 - 0081
pedestals
12-13.data file is not used
78-81.data run range 0078 - 0081
pixel_status
12-13.data file is not used
78-81.data run range 0078 - 0081 |
- Access data in psana
Example of the configuration file for psana psana-xcsd7814-r0079-fccd960-aver.cfg can be processed by the command
psana -c psana-xcsd7814-r0079-fccd960-aver.cfg
Two averaged images are saved in the text files for exp=xcsd7814:run=79 for raw and calibrated (subtracted dark level) data.
Gain bit coded gain factor 8 is applied automatically.
Example for module ImgAlgos::NDArrDropletFinder
See description in psana - Module Catalog and examples in Peak Finding Module
Example for module ImgAlgos::PixCoordsProducer
See Module ImgAlgos::PixCoordsProducer
Psana configuration file which produces enough data to get CSPAD calibrated intensity and coordinate arrays:
| Code Block | ||
|---|---|---|
[psana]
modules = ImgAlgos.PixCoordsProducer | ||
| Code Block | ||
| ||
modules = cspad_mod.CsPadCalib \ ImgAlgos.CSPadBkgdSubtract cspad_mod.CsPadCalib \ CSPadPixCoords.CSPadNDArrProducer [ImgAlgos.CSPadMaskApply \PixCoordsProducer] source = CxiDs1.0:Cspad.0 print_bits ...= 0 [cspad_mod.CsPadCalib] source = CxiDs1.0:Cspad.0 inputKey = outputKey = calibrated_arr doPedestals = yes doPixelStatus = no doCommonMode = no [ImgAlgosCSPadPixCoords.CSPadBkgdSubtractCSPadNDArrProducer] source = DetInfo(CxiDs1.0:Cspad.0) inputKey inkey = calibrated_arr outputKey outkey = bkgdcspad_subtracted_arr bkgd_fnamendarr outtype = ana-cxi49012/cspad-cxi49012-r0025-background-ave.dat norm_sectorint16 is_fullsize = 0yes print_bits = 0 = 3 |
Additional keywors need to be added to the list of module parameters in order to evaluate pixel area and coordinate indexes (for image) arrays. For example:
| Code Block |
|---|
[ImgAlgos.CSPadMaskApplyPixCoordsProducer] source = DetInfo(CxiDs1.0:Cspad.0) inkeykey_out_area = pix_area key_out_mask = pix_mask key_out_ix = pix_ix key_out_iy = bkgd_subtracted_arr outkeypix_iy x0_off_pix = 1000 y0_off_pix = 1000 mask_bits = masked_arr15 maskprint_fnamebits = 255 |
In python code these arrays can be obtained with env.calibStore().get(...) method:
| Code Block |
|---|
env = ana-cxi49012/cspad-cxi49012-r0025-mask-40.dat masked_amp ds.env() cls = env.calibStore() src = 0 print_bitspsana.Source('DetInfo(CxiDs1.0:Cspad.0)') ... A = 3 mask_control_bits = 1 |
- where
cspad_mod.CsPadCalib- subtracts the pedestals from raw CSPad data,ImgAlgos.CSPadBkgdSubtract- subtracts the background,ImgAlgos.CSPadMaskApply- apply the mask.- In the test with images for background represented by the water and solvent rings this filter provides the background suppression factor about 100.
- The background images that still pass this filter have significantly larger intensity with respect to averaged background:
- Input parameter
mask_control_bitsallows to control masking regions of 2x1. For example, if all edges need to be masked, then usemask_control_bits = 15, which gives image array like: 
- where red regions/lines of pixels of amplitude=8 are masked.
Example for module ImgAlgos::CSPadArrNoise
- See Module ImgAlgos::CSPadArrNoise
evt.get(psana.ndarray_int16_3, src, 'cspad_ndarr').flatten()
X = cls.get(psana.ndarray_float64_1, src, 'x-pix-coords')
Y = cls.get(psana.ndarray_float64_1, src, 'y-pix-coords')
Area = cls.get(psana.ndarray_float64_1, src, 'pix_area')
Mask = cls.get(psana.ndarray_int32_1, src, 'pix_mask')
iX = cls.get(psana.ndarray_uint32_1, src, 'pix_ix')
iY = cls.get(psana.ndarray_uint32_1, src, 'pix_iy')
fname= cls.get(str, src, 'geometry-fname')
// depricated method since ana-0.13.3:
path_nda = cls.get(psana.ndarray_uint8_1, src, 'geometry-calib')
path = ''.join(map(chr, path_nda)) if path_nda is not None else 'N/A' |
Their shape=(32*185*388,) = (2296960,)
These arrays can be processed by users' code directly. In particular, it is easy to conver them in 2-d image numpy array and plot it:
| Code Block |
|---|
import numpy as np
import matplotlib.pyplot as plt
from PSCalib.GeometryAccess import img_from_pixel_arrays
pix_size = 109.92
xmin, ymin = X.min()-pix_size/2, Y.min()-pix_size/2
iX, iY = np.array((X-xmin)/pix_size, dtype=np.uint), np.array((Y-ymin)/pix_size, dtype=np.uint)
img = img_from_pixel_arrays(iX,iY,W=A)
plt.imshow(img)
plt.draw() |
Example for module ImgAlgos::ImgAverage
- See Module ImgAlgos::ImgAverage
- The
ImgAveragemodule can be used for evaluation of averaged pedestals or background using dedicated runs. Typical configuration file may looks like this:
| Code Block | ||
|---|---|---|
| ||
[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
|
Example for module ImgAlgos::ImgMaskEvaluation
- See Module ImgAlgos::ImgMaskEvaluation
- Configuration parameters for psana:
| Code Block | ||
|---|---|---|
| ||
[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
|
| Note |
|---|
In this example parameters were chosen in order to get a small number of "noisy" pixel just due to statistics. |
Typical image:
Plots for fraction of noisy pixels:
Plots for fraction of saturated pixels:
Masks: noisy, saturated, and combined:
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 of the mask file and resulting image:
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
|
Note: the option of the background subtraction (ImgAlgos.CSPadBkgdSubtract) is commented out in this configuration file . In order to evoke this option, the comment sign (#) should be removed from the list of modules and the key=bkgd_subtracted_arr should be used in CSPadPixCoords.CSPadImageProducer.
Calibrated image and spectrum:
Calibrated and radial-corrected image, spectrum, and subtracted r-phi65 distribution for n_phi_bins=65:
Calibrated and radial-corrected image, spectrum, and subtracted r-phi12 distribution for n_phi_bins=12:
Example for module ImgAlgos::ImgPeakFinder
See Module ImgAlgos::ImgPeakFinder
Configuration file example:
| 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
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
|
This algorithm consumes ~15 ms/event on psana0101 for full Opal1000 (1024x1024) camera image.
Smearing algorithm use a "safety margin" which is currently set to 10 pixels (offset from each boarder of the full image size).
Image on different stages of this algorithm:
raw image,
image in the window with amplitudes above the threshold_low
- few peaks at the edges were discarded by the window limits,
- image still contains many 1-photon pixels, which need to be eliminated,
smeared image,
raw image with found peaks (marked by the red circles)
zoom of the previous plot.
Example for module ImgAlgos::ImgPeakFilter
| Code Block | ||
|---|---|---|
| ||
[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
|
Example for module ImgAlgos::ImgPeakFinderAB
See Module ImgAlgos::ImgPeakFinderAB
Configuration file example:
| Code Block | ||
|---|---|---|
| ||
[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
|
Results:
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.
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:
| Code Block | ||
|---|---|---|
| ||
# 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
|
Run psana using command:
| Code Block | ||
|---|---|---|
| ||
psana -c psana-amo74213-r0093-opal-img-average.cfg
|
At the end of this procedure two files will be created:
img-ave-for-peds-r0093.dat - may be used for pedestal subtraction:
img-rms-for-thre-r0093.dat - may be used multiplied by number of rms as a threshold:
The file with accumulated pixel hits can be obtained using configuration file:
| Code Block | ||
|---|---|---|
| ||
# 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
|
and run it by the command:
| Code Block | ||
|---|---|---|
| ||
psana -c psana-amo74213-r0093-opal-img-hit-finder.cfg
|
Which creates the file: img-sum-result-r0093.dat for thre_mode = 2 and thre_mode = 3, respectively:
Example for module ImgAlgos::ImgSpectra
See Module ImgAlgos::ImgSpectra
Configuration file for psana:
| Code Block | ||
|---|---|---|
| ||
[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
|
This script can be used in order to produce text files with image and spectral array:
or graphics for several images:
Example for module ImgAlgos::ImgSpectraProc
See Module ImgAlgos::ImgSpectraProc
Configuration file for psana:
| Code Block | ||
|---|---|---|
| ||
[ImgAlgos.ImgSpectraProc]
source = DetInfo(:Opal1000)
key_in = spectra
print_bits = 15
|
For each event it prints something similar to:
| Code Block | ||
|---|---|---|
| ||
[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
|
See Module ImgAlgos::ImgSaveInFile
Example for module ImgPeakFinder and ImgPeakFilter for CSPad
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
|
Example for module ImgAlgos::CSPadArrAverage
See Module ImgAlgos::CSPadArrAverage
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
|
Images of the CSPad arrays for averaged and rms values, respectively, in one of the CXI runs:
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.
Event image and pixel amplitude spectrum before and after the background subtraction are shown in plots:
Other event with better subtracted background:
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.
For example, it can be generated by the command
| Code Block | ||
|---|---|---|
| ||
./MakePixelMask.py <input-background-cspad-arr-file-name> <threshold> <output-file-name>
|
for the averaged background amplitude array <input-background-cspad-arr-file-name> abtained as a result of ImgAlgos::CSPadArrAverage module.
Plots show the averaged background, and the mask arrays generated from this background for three thresholds 10, 20, and 30 EDU:
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
|
where
cspad_mod.CsPadCalib - subtracts the pedestals from raw CSPad data,
ImgAlgos.CSPadBkgdSubtract - subtracts the background,
ImgAlgos.CSPadMaskApply - apply the mask.
In the test with images for background represented by the water and solvent rings this filter provides the background suppression factor about 100.
The background images that still pass this filter have significantly larger intensity with respect to averaged background:
Input parameter mask_control_bits allows to control masking regions of 2x1. For example, if all edges need to be masked, then use mask_control_bits = 15, which gives image array like:
where red regions/lines of pixels of amplitude=8 are masked.
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
|
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
|
Pixel status (fraction of events where S/N > SoNThr):
For cspad-cxi49012-r0020 with parameters from confguration file (frac_noisy_imgs=0.15) we get, depending on number of events:
Nnoisy, Ntotal, Nnoisy/Ntotal pixels =94585 2296960 0.041 for 10 events
Nnoisy, Ntotal, Nnoisy/Ntotal pixels =2112 2296960 0.00092 for 100 events
Pixel mask for noisy pixels with |S/N| > SoNThr:
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 | ||
| 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 statusfilemasked_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-r0020r0150-noise-mask-statusout.dat maskfile frac_noisy_evts_file = ana-cxi49012/cspad-cxi49012-r0200r0150-noise-maskfrac.dat printevt_file_bitsout = 255tmp/cspad-ev- rmin = 3 dr = 1 SoNThr = 3 frac_noisy_imgs = 0.15 |
...
dr |
...
| 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 SoNThr 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 |
- Pixel status (fraction of events where
S/N > SoNThr): -
- For cspad-cxi49012-r0020 with parameters from confguration file (
frac_noisy_imgs=0.15) we get, depending on number of events: Nnoisy, Ntotal, Nnoisy/Ntotal pixels =94585 2296960 0.041for 10 eventsNnoisy, Ntotal, Nnoisy/Ntotal pixels =2112 2296960 0.00092for 100 events- Pixel mask for noisy pixels with
|S/N| > SoNThr: -
Example for Module ImgAlgos::CSPadArrPeakFinder
- See Module ImgAlgos::CSPadArrPeakFinder
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
|
Selected events
ev-007713:
ev-008944:
Next example shows how to use ImgAlgos::CSPadArrPeakFinder in combination with python module pyimgalgos.ex_peaks_nda:
| Code Block | ||
|---|---|---|
[psana]
#skip-events = 50
events | ||
| 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_bits10 files = 15exp=cxi83714:run=136 [ImgAlgos.CSPadArrPeakFinder] source = DetInfo(CxiDs1.0:Cspad.0) keymodules = cspad_mod.CsPadCalib \ = masked_arr key_peaks_outImgAlgos.CSPadArrPeakFinder \ = 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 pyimgalgos.ex_peaks_nda # = tmp/cspad-ev- rmin EventKeys [cspad_mod.CsPadCalib] inputKey = outputKey = calibrated doPedestals = yes doPixelStatus = yes doCommonMode 3 dr= yes [ImgAlgos.CSPadArrPeakFinder] source = DetInfo(CxiDs1.0:Cspad.0) key = 1 SoNThr = calibrated key_peaks_out = key_peaks_nda = 3 frac_noisy_imgs = 0.1 peak_npix_min = 4 peak_npix_maxpeaks_nda hot_pix_mask_inp_file = ana-cxi83714/cspad-cxi83714-r0136-noise-mask-ini.dat hot_pix_mask_out_file = ana-cxi83714/cspad-cxi83714-r0136-noise-mask-out.dat frac_noisy_evts_file = ana-cxi83714/cspad-cxi83714-r0136-noise-frac.dat evt_file_out = 25 peak_amp_tot_thr = 100. event_npeak_min= cxi83714/cspad-ev- rmin = 10 event_amp_tot_thr = 1000. nevents_mask_update = 100 nevents_mask_accum = 50 selection_mode 8 dr = 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
|
...
1
SoNThr_noise = 3
SoNThr_signal = 4
frac_noisy_imgs = 0.9
peak_npix_min = 3
peak_npix_max = 500
peak_amp_tot_thr = 0.
peak_SoN_thr = 5.
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 = 3681
[pyimgalgos.ex_peaks_nda]
source = DetInfo(CxiDs1.0:Cspad.0)
key_in = peaks_nda
print_bits = 255 |
Example for module ImgAlgos::CSPadArrPeakAnalysis
See Module ImgAlgos::CSPadArrPeakAnalysis
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
|
After execution in psana the file.root containing histogram(s) and ntuple(s) will be produced. Then, auxiliary script in root, running by the commend
root -q -f proc.C
produces the plots with histograms:
Example for TimeStampFilter and XtcOutputModule
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
|
Command to run psana is:
psana -c ./tstamp-filter-and-event-writer.cfg
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
Example for module ImgAlgos::UsdUsbEncoderFilter
Example of configuration file:
| Code Block |
|---|
[psana]
files = exp=amo75113:run=156
events = 10
modules = ImgAlgos.UsdUsbEncoderFilter
[ImgAlgos.UsdUsbEncoderFilter]
source = DetInfo(:USDUSB)
mode = 1
ifname = tstamp-code-in.txt
ofname = tstamp-code-out.txt
print_bits = 31 |
See also: Module ImgAlgos::UsdUsbEncoderFilter
Examples for Package pyimgalgos
Package pyimgalgos contains python modules which work with both frameworks pyana and psana.
Configuration file for pyana and/or psana should have relevant sections with parameters for [pyana] and/or [psana]. Alean section is ignored in each framework at run time. This is the only difference between two frameworks in the configuration file. All module descriptions are the same for two frameworks, as shown in examples below.
See description of modules in Package pyimgalgos.
Example of configuration file for CSPAD
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 = pyimgalgos.tahometer pyimgalgos.cspad_arr_producer pyimgalgos.cspad_image_producer pyimgalgos.image_save_in_file [psana] files = exp=xcs72913:run=49 events = 5 #skip-events = 0 modules = pyimgalgos.tahometer pyimgalgos.cspad_arr_producer pyimgalgos.cspad_image_producer pyimgalgos.image_save_in_file verbose = 1 [pyimgalgos.tahometer] dn = 10 print_bits = 255 [pyimgalgos.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 [pyimgalgos.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 [pyimgalgos.image_save_in_file] key_in = cspad_image ofname = img-for-cspad.txt print_bits = 255 |
To run this script use command
psana -c py-xcs72913-r0049-cspad.cfg
or
pyana -c py-xcs72913-r0049-cspad.cfg
Example of configuration file for CSPAD2x2
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 = pyimgalgos.tahometer pyimgalgos.cspad_arr_producer pyimgalgos.cspad_image_producer pyimgalgos.image_save_in_file [psana] files = exp=meca6113:run=28 events = 5 #skip-events = 0 modules = pyimgalgos.tahometer pyimgalgos.cspad_arr_producer pyimgalgos.cspad_image_producer pyimgalgos.image_save_in_file [pyimgalgos.tahometer] dn = 10 print_bits = 255 [pyimgalgos.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 [pyimgalgos.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 [pyimgalgos.image_save_in_file] key_in = cspad2x2_image ofname = img-for-cspad2x2.tiff print_bits = 255 |
To run this script use command
psana -c py-meca6113-r0028-cspad2x2.cfg
or
pyana -c py-meca6113-r0028-cspad2x2.cfg
References
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