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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:
...
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:
| Code Block | ||
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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::CSPadNDArrProducer
See Module CSPadPixCoords::CSPadNDArrProducer
Example of the module CSPadNDArrProducer working in sequence with ImgAlgos::NDArrAverage is shown in Example for module ImgAlgos::NDArrAverage
Example for module CSPadPixCoords::CSPad2x2NDArrProducer
| No Format |
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# Run this script:
# psana -c psana-meca1113-r0045-cspad-cspad2x2-dark-hotpix.cfg
[psana]
# Default calibration directory:
# calib-dir = /reg/d/psdm/mec/meca1113/calib
files = exp=meca1113:run=45
events = 400
#skip-events = 0
modules = CSPadPixCoords.CSPad2x2NDArrProducer:1 \
CSPadPixCoords.CSPad2x2NDArrProducer:2 \
ImgAlgos.NDArrAverage:1 \
ImgAlgos.NDArrAverage:2
[CSPadPixCoords.CSPad2x2NDArrProducer:1]
source = MecTargetChamber.0:Cspad2x2.1
inkey =
outkey = cspad2x2.1_ndarr
outtype = int16
print_bits = 3
[CSPadPixCoords.CSPad2x2NDArrProducer:2]
source = MecTargetChamber.0:Cspad2x2.2
inkey =
outkey = cspad2x2.2_ndarr
outtype = int16
print_bits = 3
[ImgAlgos.NDArrAverage:1]
source = MecTargetChamber.0:Cspad2x2.1
key = cspad2x2.1_ndarr
avefile = cspad2x2.1-ave
rmsfile = cspad2x2.1-rms
maskfile = 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 = MecTargetChamber.0:Cspad2x2.2
key = cspad2x2.2_ndarr
avefile = cspad2x2.2-ave
rmsfile = cspad2x2.2-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
See Module CSPadPixCoords::CSPad2x2ImageProducer
Example of the configuration script for psana (cspad2x2-test.cfg):configuration file
| Code Block |
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| Code Block | bgColor | #F7F7ED
[psana] files#files = exp=meca1113:run=376 #events = 10 ##skip-events = 0 modules = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-1>.xtc events= cspad_mod.CsPadCalib \ = 5 modulesCSPadPixCoords.CSPad2x2NDArrProducer:clb \ = CSPadPixCoords.CSPad2x2ImageProducer ImgAlgos.ImgSaveInFile [CSPadPixCoords.CSPad2x2ImageProducer] sourceCSPad2x2NDArrProducer:raw \ = DetInfo(:Cspad2x2) inkeyCSPadPixCoords.CSPad2x2NDArrReshape \ =ImgAlgos.NDArrAverage:clb \ outimgkey = Image tiltIsApplied = true print_bitsImgAlgos.NDArrAverage:raw # = 15 EventKeys [ImgAlgoscspad_mod.ImgSaveInFile] sourceCsPadCalib] inputKey = outputKey = clb_data doPedestals = yes doPixelStatus = yes doCommonMode = DetInfo(:Cspad2x2) keyyes [CSPadPixCoords.CSPad2x2NDArrProducer:clb] source = MecTargetChamber.0:Cspad2x2.1 inkey = Image fnameclb_data outkey = cspad2x2.1_clb:as_data outtype = cspad2x2int16 saveAllprint_bits = 5 [CSPadPixCoords.CSPad2x2NDArrProducer:raw] source = true #eventSaveMecTargetChamber.0:Cspad2x2.1 inkey = 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>:
| Code Block | ||
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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 outkey = cspad2x2.1_raw:as_data outtype = int16 print_bits = 5 [cspad_modCSPadPixCoords.CsPadCalibCSPad2x2NDArrReshape] source = DetInfo(MecTargetChamber.0:Cspad2x2.3) inputKey 1 keys_in = outputKey = calibrated_arr doPedestals = yes doPixelStatus = no doCommonMode = no [CSPadPixCoords.CSPad2x2ImageProducer] calibDir = /reg/d/psdm/mec/mec73313/calib typeGroupName = CsPad2x2::CalibV1 #source cspad2x2.1_raw:as_data cspad2x2.1_clb:as_data print_bits = 255 [ImgAlgos.NDArrAverage:clb] source = DetInfo(MecTargetChamber.0:Cspad2x2.3)1 sourcekey = :Cspad2x2.3 inkey cspad2x2.1_clb avefile = calibrated_arr-ave-clb outimgkeyrmsfile = Image tiltIsApplied = truearr-rms-clb print_bits = 15255 [ImgAlgos.ImgSaveInFileNDArrAverage:raw] source = DetInfo(MecTargetChamber.0:Cspad2x2.3)1 key = cspad2x2.1_raw avefile = Image fname = arr-ave-raw rmsfile = cspad2x2.3 saveAll = true arr-rms-raw print_bits = 3 #eventSave255 |
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:
| Code Block |
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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):
| Code Block | ||
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[psana]
files |
Example of psana configuration file to get cspad2x2 images for two detectors and save them in files, one in txt, another in tiff formats:
| Code Block | ||
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[psana] files = /reg/d/psdm/xpp/xpptut13/xtc/e308-r0008-s02-c00.xtc \ /reg/d/psdm/xpp/xpptut13/xtc/e308-r0008-s03-c00.xtc #modules = cspad_mod.CsPad2x2Pedestals #calib-dir = ./calib calib-dir = /reg/d/psdm/xpp/xpptut13/xtc/calib modules = cspad_mod.CsPadCalib:0 \ cspad_mod.CsPadCalib:1 \ CSPadPixCoords.CSPad2x2ImageProducer:0 \ CSPadPixCoords.CSPad2x2ImageProducer:1 \ ImgAlgos.ImgSaveInFile:0 \ ImgAlgos.ImgSaveInFile:1 events = 5 [cspad_mod.CsPadCalib:0] source = DetInfo(XppGon.0:Cspad2x2.0) inputKey = outputKey = calibrated_arr0 doPedestals = yes doPixelStatus = no doCommonMode = yes [cspad_mod.CsPadCalib:1] source = DetInfo(XppGon.0:Cspad2x2.1) inputKey = outputKey = calibrated_arr1 doPedestals = yes doPixelStatus = no doCommonMode = yes [CSPadPixCoords.CSPad2x2ImageProducer:0] calibDir = /reg/d/psdm/xpp/xpptut13/xtc/calib typeGroupName = CsPad2x2::CalibV1 source = DetInfo(XppGon.0:Cspad2x2.0) inkey = calibrated_arr0 outimgkey = Image tiltIsApplied = false useWidePixCenter = false print_bits = 15 [CSPadPixCoords.CSPad2x2ImageProducer:1] calibDir = /reg/d/psdm/xpp/xpptut13/xtc/calib typeGroupName = CsPad2x2::CalibV1 source = DetInfo(XppGon.0:Cspad2x2.1) inkey/reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-1>.xtc events = calibrated_arr1 outimgkey 5 modules = Image tiltIsApplied = false useWidePixCenter = false print_bits = 15 [ImgAlgos.ImgSaveInFile:0CSPadPixCoords.CSPad2x2ImageProducer ImgAlgos.ImgSaveInFile [CSPadPixCoords.CSPad2x2ImageProducer] source = DetInfo(:Cspad2x2.0) key inkey = Image fnameoutimgkey = cspad2x2.0 ftype = txt #ftype = tiff saveAll Image tiltIsApplied = true print_bits = 3 #eventSave = 515 [ImgAlgos.ImgSaveInFile:1] source = DetInfo(:Cspad2x2.1) key = Image fname = cspad2x2.1 #ftypesaveAll = txttrue ftype#eventSave = tiff saveAll = true print_bits = 3 #eventSave = 5 |
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:
= 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 |
|---|
Access to the CSPad2x2 aligned geometry is added on 2013-02-13 |
Example of <psana-config-file.cfg>:
| Code Block | ||
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[psana]
files = | ||
| Code Block | ||
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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/cximec/cxib2313mec73313/xtc/e336-r0114* # psana -n 5 -m EventKeys exp=cxib2313:run=114:xtc [psana] files = exp=cxib2313:run=114:e268-r0180-s02-c00.xtc #calib-dir = ./calib skip-events = 0 events = 100 modules = cspad_mod.CsPadCalib CSPadPixCoords.CSPad2x2ImageProducer ImgPixSpectraImgAlgos.CSPadPixSpectra ImgSaveInFile events = 5 [cspad_mod.CsPadCalib] source = DetInfo(CxiDs1MecTargetChamber.0:CspadCspad2x2.03) inputKey = outputKey = calibrated_arr doPedestals = yes doPixelStatus = no doCommonMode = yesno [ImgPixSpectraCSPadPixCoords.CSPadPixSpectra] sourceCSPad2x2ImageProducer] calibDir = /reg/d/psdm/mec/mec73313/calib typeGroupName = CsPad2x2::CalibV1 #source = CxiDs1DetInfo(MecTargetChamber.0:CspadCspad2x2.0 inputKey3) source = calibrated amin:Cspad2x2.3 inkey = calibrated_arr outimgkey = Image tiltIsApplied -20. amax= true print_bits = 15 [ImgAlgos.ImgSaveInFile] source = 20. nbins= DetInfo(MecTargetChamber.0:Cspad2x2.3) key = = 10Image arr_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:
cspad2x2.3
saveAll = true
print_bits = 3
#eventSave = 5
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Example of psana configuration file to get cspad2x2 images for two detectors and save them in files, one in txt, another in tiff formats:
| Code Block | ||
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[psana] files = /reg/d/psdm/xpp/<instrument>xpptut13/<experiment>/<file-name>xtc/e308-r0008-s02-c00.xtc \ modules = ImgPixSpectra.CSPad2x2PixSpectra [ImgPixSpectra.CSPad2x2PixSpectra] source = CxiSc1.0:Cspad2x2.0 amin /reg/d/psdm/xpp/xpptut13/xtc/e308-r0008-s03-c00.xtc #modules = cspad_mod.CsPad2x2Pedestals #calib-dir = ./calib calib-dir = /reg/d/psdm/xpp/xpptut13/xtc/calib modules = cspad_mod.CsPadCalib:0 \ = cspad_mod.CsPadCalib:1 \ 500. amax = 1000. nbinsCSPadPixCoords.CSPad2x2ImageProducer:0 \ = 100 arr_fnameCSPadPixCoords.CSPad2x2ImageProducer:1 \ = cspad2x2-pix-spectra.txt |
To get images from saved file one may execute the auxiliary script:
| Code Block | ||
|---|---|---|
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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 | ||
|---|---|---|
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[psana] ImgAlgos.ImgSaveInFile:0 \ files ImgAlgos.ImgSaveInFile:1 events = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\ 5 [cspad_mod.CsPadCalib:0] source = DetInfo(XppGon.0:Cspad2x2.0) inputKey /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-2>.xtc modules = outputKey = ImgAlgos.Tahometer [ImgAlgos.Tahometer] dncalibrated_arr0 doPedestals = yes doPixelStatus = no doCommonMode = 10yes print_bits = 7 |
Example for module ImgAlgos::PnccdImageProducer
See Module ImgAlgos::PnccdImageProducer
Example of the psana configuration file:
| Code Block | ||
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[psana][cspad_mod.CsPadCalib:1] source = DetInfo(XppGon.0:Cspad2x2.1) inputKey = outputKey = calibrated_arr1 doPedestals = yes doPixelStatus = no doCommonMode = yes [CSPadPixCoords.CSPad2x2ImageProducer:0] calibDir = /reg/d/psdm/xpp/xpptut13/xtc/calib typeGroupName = CsPad2x2::CalibV1 source = DetInfo(XppGon.0:Cspad2x2.0) inkey = filescalibrated_arr0 outimgkey = Image tiltIsApplied = false useWidePixCenter = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\ false print_bits = 15 [CSPadPixCoords.CSPad2x2ImageProducer:1] calibDir = /reg/d/psdm/<INSTRUMENT>xpp/<experiment>xpptut13/xtc/<file-name-2>.xtc #skip-events = 100 events calib typeGroupName = 5 modules = ImgAlgos.PnccdImageProducer ImgAlgos.ImgSaveInFile [ImgAlgos.PnccdImageProducer] sourceCsPad2x2::CalibV1 source = DetInfo(:pnCCDXppGon.0:Cspad2x2.1) inkey = calibrated_arr1 outimgkey = imgpnccd = Image tiltIsApplied = false useWidePixCenter = false print_bits = 115 [ImgAlgos.ImgSaveInFile:0] source = DetInfo(:pnCCDCspad2x2.0) key = imgpnccdImage fname = pnccd-img-ev saveAllcspad2x2.0 ftype = truetxt #eventSave#ftype = 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:
Example for module ImgAlgos::CameraImageProducer
See Module ImgAlgos::CameraImageProducer
Example of the psana configuration file:
| Code Block | ||
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[psana]tiff saveAll = true print_bits = 3 #eventSave = 5 [ImgAlgos.ImgSaveInFile:1] source = DetInfo(:Cspad2x2.1) key = Image fname files= cspad2x2.1 #ftype = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc modulestxt ftype = ImgAlgos.CameraImageProducer ImgAlgos.ImgSaveInFile eventstiff saveAll = 5 [ImgAlgos.CameraImageProducer] sourcetrue print_bits = 3 #eventSave = DetInfo(:Opal1000) key_in = key_out = img subtract_offset = true print_bits = 15 [ImgAlgos.ImgSaveInFile] source = DetInfo(:Opal1000) key = img fname5 |
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:
| Code Block | ||
|---|---|---|
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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 = img-from-my-experiment saveAll= DetInfo(CxiDs1.0:Cspad.0) inputKey = true #eventSaveoutputKey = 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 | ||
|---|---|---|
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[psana] calibrated doPedestals = yes doPixelStatus = no doCommonMode = yes [ImgPixSpectra.CSPadPixSpectra] source = CxiDs1.0:Cspad.0 inputKey = calibrated amin = -20. amax = 20. nbins = files 10 arr_fname = /reg/d/psdm/<INSTRUMENT>/<experiment>= 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:
| Code Block | ||
|---|---|---|
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[psana] files/xtc/<file-name-1>.xtc\ /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-2>.xtc modules = ImgAlgos.PrincetonImageProducer \ ImgAlgos.ImgSaveInFile events= /reg/d/psdm/<instrument>/<experiment>/<file-name>.xtc modules = 3ImgPixSpectra.CSPad2x2PixSpectra [ImgAlgosImgPixSpectra.PrincetonImageProducerCSPad2x2PixSpectra] source = DetInfo(:Princeton) key_inCxiSc1.0:Cspad2x2.0 amin = key_out 500. amax = img subtract_offset = true print_bits = 31 [ImgAlgos.ImgSaveInFile] source1000. nbins = DetInfo(:Princeton) key 100 arr_fname = img fname = img-xcs saveAll = true print_bits = 31 |
= 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 ImgAlgosAnchor
Example for module ImgAlgos::
...
Tahometer
See description of parameters in Module ImgAlgos::AcqirisArrProducerTahometer
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[psana] files = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\ /reg/d/psdm/AMO<INSTRUMENT>/amo01509<experiment>/xtc/e8<file-r0125name-s01-c002>.xtc files modules = exp=amo01509:run=125:xtc modules = ImgAlgos.AcqirisArrProducer ImgAlgos.ImgSaveInFile:wf ImgAlgos.ImgSaveInFile:wt skip-events = 0 eventsImgAlgos.Tahometer [ImgAlgos.Tahometer] dn = 10 print_bits = 100 [ImgAlgos.AcqirisArrProducer] source7 |
Example for module ImgAlgos::EpixNDArrProducer
See Module ImgAlgos::EpixNDArrProducer
Example of the psana configuration file:
| Code Block |
|---|
[psana] files = AmoETOF.0:Acqiris.0 key_inexp=xppi0414:run=94 events = key_wform 100 modules = acqiris_wform key_wtimeImgAlgos.EpixNDArrProducer \ = acqiris_wtime fname_prefix = acq print_bits = 11 ImgAlgos.NDArrAverage [ImgAlgos.ImgSaveInFile:wfEpixNDArrProducer] source = AmoETOF.0:Acqiris.0DetInfo(:Epix10k) key_in = key_out = epix-nda outtype = float print_bits = 255 [ImgAlgos.NDArrAverage] source = acqiris_wform fnameDetInfo(:Epix10k) key = acqepix-AmoETOF-wformnda ftypeavefile = 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]txt #ftype = tiff #saveAll = true print_bits = 3 eventSave = 5 [ImgAlgos.ImgSaveInFile:wt] source = AmoETOF.0:Acqiris.0 key = acqiris_wtime fname files = acq-AmoETOF-wtime ftype /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\ /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-2>.xtc #skip-events = 100 events = txt5 #ftype modules = ImgAlgos.PnccdImageProducer ImgAlgos.ImgSaveInFile [ImgAlgos.PnccdImageProducer] source = tiff #saveAllDetInfo(:pnCCD) inkey = true outimgkey = imgpnccd print_bits = 1 [ImgAlgos.ImgSaveInFile] source = 3 eventSaveDetInfo(:pnCCD) key = 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:
...
imgpnccd
fname = 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 |
...
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/AMOSXR/amo01509/xtc/e8-r0125-s00-c00.xtc /reg/d/psdm/AMO/amo01509/xtc/e8-r0125-s01-c00.xtcsxrb5914/calib files = exp=amo01509sxrb5914:run=125:xtc245 events = 10 modules = ImgAlgos.AcqirisArrProducerTahometer ImgAlgos.AcqirisAverage skip-events = 0 events\ = 1000 [ImgAlgos.AcqirisArrProducer] sourcePnccdNDArrProducer \ = 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 = 3 7 [ImgAlgos.AcqirisAveragePnccdNDArrProducer] source = DetInfo(Camp.0:pnCCD.1) key_in = key_out = pnccd-ndarr outtype = asdata print_bits = 0 [ImgAlgos.NDArrCalib] source = AmoETOFDetInfo(Camp.0:AcqirispnCCD.01) key_in = pnccd-ndarr key_out = calibrated do_peds = yes do_cmod = yes do_stat = yes do_mask = acqiris_wformno keydo_avebkgd = no do_gain = no do_nrms = no do_thre = no #fname_mask = = acqiris_average fname_ave_prefixpnccd-test-mask.txt #fname_bkgd = pnccd-test-bkgd.txt masked_value = acq thresholds 0 threshold_nrms = 4.0 threshold = -0.005 -0.005 -0.005 -0.005 -0.005 is_positive_signal = no do_inverse_selection = yes #skip_events = 100 below_thre_value = 0 bkgd_ind_min = 10000 bkgd_ind_max = 010200 #procbkgd_ind_eventsinc = = 1001 print_bits = = 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):
...
1
[ImgAlgos.PnccdImageProducer]
source = DetInfo(Camp.0:pnCCD.1)
inkey = calibrated
outimgkey = pnccd-img
gap_rows = 0
gap_cols = 16
gap_value = 0
print_bits = 1
[ImgAlgos.NDArrAverage]
source = DetInfo(Camp.0:pnCCD.1)
key = pnccd-img
avefile = pnccd-ave
rmsfile = pnccd-rms
#maskfile = pnccd-msk
#hotpixfile = pnccd-hot
thr_rms_ADU = 160
thr_min_ADU = 2
thr_max_ADU = 10000
print_bits = 29 |
Example for module ImgAlgos::CameraImageProducer
See Module ImgAlgos::CameraImageProducer
Example of the psana configuration file:
| Code Block | ||
|---|---|---|
| ||
[psana]
files |
...
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<INSTRUMENT>/amo01509<experiment>/xtc/e8<file-r0125name-s00-c001>.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 modules = ImgAlgos.CameraImageProducer ImgAlgos.ImgSaveInFile events = 10 5 [ImgAlgos.AcqirisArrProducerCameraImageProducer] source = AmoETOF.0:Acqiris.0DetInfo(:Opal1000) key_in = key_wformout = acqiris_wform key_wtime = acqiris_wtimeimg fnamesubtract_prefixoffset = acqtrue print_bits = 115 [ImgAlgos.AcqirisCalibImgSaveInFile] source = AmoETOF.0:Acqiris.0DetInfo(:Opal1000) key_in = acqiris_wform key_out img fname = wf-calibrated fname_base_line = acq-amo01509-r0125-ave-wfs.txt #skip_events img-from-my-experiment saveAll = 0 #proc_events true #eventSave = 100 print_bits = 255 [ImgAlgos.ImgSaveInFile:wf_raw] source1 |
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] = AmoETOF.0:Acqiris.0 key = acqiris_wform fname = acq-AmoETOF-wform-raw ftype = txt #ftype = tiff #saveAll files = true print_bits = 3 eventSave/reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\ = 5 [ImgAlgos.ImgSaveInFile:wf_calib] source = AmoETOF.0:Acqiris.0 key /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-2>.xtc modules = ImgAlgos.PrincetonImageProducer \ = wf-calibrated fname ImgAlgos.ImgSaveInFile events = acq-AmoETOF-wform-calibrated ftype3 [ImgAlgos.PrincetonImageProducer] source = txt #ftypeDetInfo(:Princeton) key_in = tiff #saveAll key_out = img subtract_offset = true print_bits = 31 [ImgAlgos.ImgSaveInFile] source = DetInfo(:Princeton) key = 3 eventSaveimg fname = img-xcs saveAll = 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:
...
true
print_bits = 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
...
Example for module ImgAlgos::AcqirisCFD
See description of parameters in Module ImgAlgos::AcqirisCFD
Configuration file psana_cfd.cfg :
| Code Block | ||
|---|---|---|
| ||
# Command to run this script: # psana -c psana_cfd-amo01509-r0125-acqiris.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 # Useful commands: # psana -n 5 -m EventKeys exp=amo01509:run=125:xtc > test-acqiris-file.txt; # psana -n 5 -m psana_examples.DumpAcqiris exp=amo01509:run=125:xtc > test-acqiris-file.txt; (C++ version) # psana -n 1 -m psana_examples.dump_acqiris exp=amo01509:run=125:xtc > test-acqiris-file.txt; (python version) [psana] #files = /reg/d/psdm/AMO/amo01509/xtc/e8-r0125-s00-c00.xtc /reg/d/psdm/AMO/amo01509/xtc/e8-r0125-s01-c00.xtc files = exp=amo01509:run=125:xtc modules = ImgAlgos.AcqirisArrProducer ImgAlgos.ImgSaveInFile:wf ImgAlgos.ImgSaveInFile:wt skip-events = 0 events = 100 [ImgAlgos.AcqirisArrProducer] source = AmoETOF.0:Acqiris.0 key_wformin = wf-calibrated baselines = key_wform 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.
...
= acqiris_wform
key_wtime = acqiris_wtime
fname_prefix = acq
print_bits = 11
[ImgAlgos.ImgSaveInFile:wf]
source = AmoETOF.0:Acqiris.0
key = acqiris_wform
fname = acq-AmoETOF-wform
ftype = txt
#ftype = tiff
#saveAll = true
print_bits = 3
eventSave = 5
[ImgAlgos.ImgSaveInFile:wt]
source = AmoETOF.0:Acqiris.0
key = acqiris_wtime
fname = 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 | ||||
|---|---|---|---|---|
|
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 = AmoETOF.0:Acqiris.0
key_in = acqiris_wform
key_ave = acqiris_average
fname_ave_prefix = acq
thresholds = -0.005 -0.005 -0.005 -0.005 -0.005
is_positive_signal = no
do_inverse_selection = yes
#skip_events = 0
#proc_events = 100
print_bits = 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):
| Anchor | ||||
|---|---|---|---|---|
|
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
events = 10
[ImgAlgos.AcqirisArrProducer]
source = AmoETOF.0:Acqiris.0
key_in =
key_wform = acqiris_wform
key_wtime = acqiris_wtime
fname_prefix = acq
print_bits = 1
[ImgAlgos.AcqirisCalib]
source = AmoETOF.0:Acqiris.0
key_in = acqiris_wform
key_out = wf-calibrated
fname_base_line = acq-amo01509-r0125-ave-wfs.txt
#skip_events = 0
#proc_events = 100
print_bits = 255
[ImgAlgos.ImgSaveInFile:wf_raw]
source = AmoETOF.0:Acqiris.0
key = acqiris_wform
fname = acq-AmoETOF-wform-raw
ftype = txt
#ftype = tiff
#saveAll = true
print_bits = 3
eventSave = 5
[ImgAlgos.ImgSaveInFile:wf_calib]
source = AmoETOF.0:Acqiris.0
key = wf-calibrated
fname = acq-AmoETOF-wform-calibrated
ftype = txt
#ftype = tiff
#saveAll = true
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:
| Anchor | ||||
|---|---|---|---|---|
|
Example for module ImgAlgos::AcqirisCFD
See description of parameters in Module ImgAlgos::AcqirisCFD
Configuration file psana_cfd.cfg:
| Code Block | ||
|---|---|---|
| ||
# 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.
| Anchor | ||||
|---|---|---|---|---|
|
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 = acq
print_bits = 7
[ImgAlgos.AcqirisAverage:bl]
source = AmoETOF.0:Acqiris.0
key_in = acqiris_wform
#key_ave =
fname_ave_prefix = acq-bline
thresholds = -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 = 31
[ImgAlgos.AcqirisCalib]
source = 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 = 47
[ImgAlgos.AcqirisAverage:signal]
source = AmoETOF.0:Acqiris.0
key_in = wf-calibrated
#key_ave =
fname_ave_prefix = acq-signal
thresholds = -0.01 -0.01 -0.01 -0.01 -0.01
is_positive_signal = no
do_inverse_selection = no
skip_events = 1001
proc_events = 1000
print_bits = 31
[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 |
|---|
[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 = cspad_ndarr
outtype = float
is_fullsize = yes
print_bits = 3
[ImgAlgos.NDArrCalib]
source = DetInfo(CxiDs1.0:Cspad.0)
key_in = cspad_ndarr
key_out = 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 = 7
below_thre_value = 0
print_bits = 3
[ImgAlgos.NDArrImageProducer]
source = CxiDs1.0:Cspad.0
key_in = calibrated
key_out = cspad_img
#type_out = asinp
#type_out = float
#x0_off_pix = 50
#y0_off_pix = 50
print_bits = 255
#calibdir = /reg/neh/home/dubrovin/LCLS/CSPadAlignment-v01/calib-cxi-ds1-2014-03-19/calib
[ImgAlgos.NDArrAverage]
source = DetInfo(CxiDs1.0:Cspad.0)
key = cspad_img
avefile = 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 = /reg/d/psdm/mec/meca1113/calib
#calib-dir = /reg/neh/home/dubrovin/LCLS/CSPad2x2Alignment/calib-cspad2x2-01-2013-02-13/calib
files = exp=meca1113:run=376
events = 10
#skip-events = 0
modules = CSPadPixCoords.CSPad2x2NDArrProducer \
ImgAlgos.NDArrImageProducer \
ImgAlgos.NDArrAverage
[CSPadPixCoords.CSPad2x2NDArrProducer]
source = MecTargetChamber.0:Cspad2x2.1
inkey =
outkey = cspad2x2_ndarr
outtype = int16
print_bits = 5
[ImgAlgos.NDArrImageProducer]
source = MecTargetChamber.0:Cspad2x2.1
key_in = cspad2x2_ndarr
key_out = cspad2x2_img
#type_out = asinp
#type_out = float
#x0_off_pix = 50
#y0_off_pix = 50
print_bits = 255
#oname = CSPAD2X2:V1
#oindex = 0
#pix_scale_size_um = 218.
#calibdir = /reg/neh/home/dubrovin/LCLS/CSPad2x2Alignment/calib-cspad2x2-01-2013-02-13/calib
#calibgroup = CsPad2x2::CalibV1
[ImgAlgos.NDArrAverage]
source = MecTargetChamber.0:Cspad2x2.1
#key = cspad2x2_ndarr
key = cspad2x2_img
avefile = arr-ave
rmsfile = arr-rms
maskfile = arr-msk
hotpixfile = arr-hot
thr_rms_ADU = 10
#thr_min_ADU = 2
#thr_max_ADU = 20000
print_bits = 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 [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 |
|---|
[psana]
files = exp=amoa1214:run=7
#skip-events = 100
events = 5
modules = ImgAlgos.Tahometer \
ImgAlgos.PnccdNDArrProducer \
ImgAlgos.NDArrCalib \
ImgAlgos.PnccdImageProducer \
ImgAlgos.ImgSaveInFile
# ImgAlgos.NDArrAverage \
[ImgAlgos.PnccdNDArrProducer]
source = DetInfo(Camp.0:pnCCD.0)
key_in =
key_out = pnccd-ndarr
outtype = asdata
print_bits = 13
[ImgAlgos.NDArrCalib]
source = DetInfo(Camp.0:pnCCD.0)
key_in = pnccd-ndarr
key_out = calibrated
outtype = float
do_peds = yes
do_cmod = yes
do_stat = no
do_mask = no
do_bkgd = no
do_gain = no
do_nrms = no
do_thre = no
fname_mask =
fname_bkgd =
masked_value = 0
threshold_nrms = 3
threshold = 100
below_thre_value = 0
bkgd_ind_min = 0
bkgd_ind_max = 1000
bkgd_ind_inc = 10
print_bits = 255
[ImgAlgos.PnccdImageProducer]
source = DetInfo(Camp.0:pnCCD.0)
#inkey = pnccd-ndarr
inkey = calibrated
outimgkey = pnccd-img
gap_size = 20
gap_value = 0
print_bits = 1
[ImgAlgos.ImgSaveInFile]
source = DetInfo(Camp.0:pnCCD.0)
key = pnccd-img
fname = pnccd-img-from-arr
ftype = txt
saveAll = true
print_bits = 31
[ImgAlgos.Tahometer]
dn = 100
print_bits = 7 |
Example of ImgAlgos::NDArrCalib for CSPAD
| Code Block |
|---|
[psana]
files = exp=cxi83714:run=136
events = 100
modules = ImgAlgos.Tahometer \
CSPadPixCoords.CSPadNDArrProducer \
ImgAlgos.NDArrCalib \
ImgAlgos.NDArrAverage
[CSPadPixCoords.CSPadNDArrProducer]
source = DetInfo(CxiDs1.0:Cspad.0)
inkey =
outkey = cspad_ndarr
outtype = float
is_fullsize = yes
print_bits = 3
[ImgAlgos.NDArrCalib]
source = DetInfo(CxiDs1.0:Cspad.0)
key_in = cspad_ndarr
key_out = calibrated
outtype = double
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 = 7
below_thre_value = 0
bkgd_ind_min = 0
bkgd_ind_max = 1000
bkgd_ind_inc = 10
print_bits = 3
[ImgAlgos.NDArrAverage]
source = DetInfo(CxiDs1.0:Cspad.0)
key = calibrated
avefile = cspad-ave
rmsfile = cspad-rms
#maskfile = cspad-msk
#hotpixfile = cspad-hot
thr_rms_ADU = 10
thr_min_ADU = 4
thr_max_ADU = 10000
print_bits = 29
[ImgAlgos.Tahometer]
dn = 10
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 \
CSPadPixCoords.CSPadNDArrProducer \
ImgAlgos.NDArrAverage \
ImgAlgos.Tahometer
[cspad_mod.CsPadCalib]
inputKey =
outputKey = calibrated_data
doPedestals = yes
doPixelStatus = yes
doCommonMode = yes
[CSPadPixCoords.CSPadNDArrProducer]
source = DetInfo(CxiDs1.0:Cspad.0)
inkey = calibrated_data
outkey = cspad_ndarr
outtype = float
is_fullsize = yes
print_bits = 3
[ImgAlgos.NDArrAverage]
source = DetInfo(CxiDs1.0:Cspad.0)
key = cspad_ndarr
avefile = cspad-calib-ave
rmsfile = cspad-calib-rms
#maskfile = cspad-msk
#hotpixfile = 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
|
...
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 = acq print_bits = 7 [ImgAlgos.AcqirisAverage:bl] source = AmoETOF.0:Acqiris.0 key_in = acqiris_wform #key_ave pedestals = fname_ave_prefix = acq-bline thresholds 12-13.data = -0.005 -0.005 -0.005 -0.005 -0.005 is_positive_signal = no do_inverse_selection = yes skip_events file is not used = 0 proc_events 78-81.data run range 0078 =- 1000 print_bits0081 pixel_status = 31 [ImgAlgos.AcqirisCalib] source = AmoETOF.0:Acqiris.0 key_in12-13.data file is not used = acqiris_wform key_out 78-81.data = wf-calibrated fname_base_line = acq-bline skip_events 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 \ = 1001 proc_events = 1000 print_bitscspad_mod.CsPadCalib \ = 47CSPadPixCoords.CSPadNDArrProducer [ImgAlgos.AcqirisAverage:signalPixCoordsProducer] source = AmoETOFCxiDs1.0:AcqirisCspad.0 key_in print_bits = wf-calibrated #key_ave = fname_ave_prefix = acq-signal thresholds = -0.01 -0.01 -0.01 -0.01 -0.01 is_positive_signal = no do_inverse_selection = no skip_events 0 [cspad_mod.CsPadCalib] source = CxiDs1.0:Cspad.0 inputKey = 1001 proc_eventsoutputKey = calibrated doPedestals = 1000 print_bits = yes doPixelStatus = no doCommonMode = 31no [ImgAlgosCSPadPixCoords.TahometerCSPadNDArrProducer] 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::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 [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
source = CxiDs1.0:Cspad.0
inkey = calibrated
outkey = cspad_ndarr
outtype = int16
is_fullsize = yes
print_bits = 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.PixCoordsProducer]
source = CxiDs1.0:Cspad.0
key_out_area = pix_area
key_out_mask = pix_mask
key_out_ix = pix_ix
key_out_iy = pix_iy
x0_off_pix = 1000
y0_off_pix = 1000
mask_bits = 15
print_bits = 255 |
In python code these arrays can be obtained with env.calibStore().get(...) method:
| Code Block |
|---|
env = ds.env()
cls = env.calibStore()
src = psana.Source('DetInfo(CxiDs1.0:Cspad.0)')
...
A = 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 - See Module ImgAlgos::NDArrCalib, Module ImgAlgos::NDArrAverage
- The
NDArrCalibmodule in combination with PnccdNDArrProducer (or any other device NDArrProducer) can be used for evaluation of averaged pedestals or background using dedicated runs.
Typical configuration file may looks like this:
| Code Block | ||
|---|---|---|
| ||
[psana] files = exp=amoa1214:run=7 #skip-events = 100 events = 5 /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name>.xtc modules = ImgAlgos.Tahometer \ ImgAlgos.PnccdNDArrProducer \ ImgAlgos.NDArrCalib \ ImgAlgos.PnccdImageProducer \ ImgAlgos.ImgSaveInFile #CameraImageProducer \ ImgAlgos.NDArrAverage \ImgAverage events = 1000 [ImgAlgos.PnccdNDArrProducerCameraImageProducer] source = DetInfo(Camp.0:pnCCD.0:Opal1000) key_in = key_out = pnccd-ndarr outtypeimg subtract_offset = asdatatrue print_bits = 13 1 [ImgAlgos.NDArrCalibImgAverage] source = DetInfo(Camp.0:pnCCD.0) key_in = pnccd-ndarr key_out = calibrated do_peds = yes do_cmod = yes do_stat = no do_mask = no do_bkgd = no do_gain = no do_nrms = no do_thre = no fname_mask = fname_bkgd = fname_rms = masked_value:Opal1000) key = img avefile = img-ave.dat rmsfile = img-rms.dat print_bits = 31 evts_stage1 = 100 evts_stage2 = 100 gate_width1 = 0200 thresholdgate_nrmswidth2 = 20 |
Example for module ImgAlgos::ImgMaskEvaluation
- See Module ImgAlgos::ImgMaskEvaluation
- Configuration parameters for psana:
| Code Block | ||
|---|---|---|
| ||
[ImgAlgos.ImgMaskEvaluation] source 0 threshold = 100 below_thre_value =DetInfo(:Opal1000) key 50 bkgd_ind_min = = 0img bkgdfile_indmask_max = 1000 bkgd_ind_inc = 10 print_bits = 255 [ImgAlgos.PnccdImageProducer] sourcesatu = 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 = DetInfo(Camp.0:pnCCD.0) #inkeydr = pnccd-ndarr inkey = 1 thre_SoN = calibrated outimgkey = pnccd-img3 gapfrac_sizenois = 200.05 gapprint_valuebits = 0 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] print_bits = 1 [ImgAlgos.ImgSaveInFile] source = DetInfo(Camp.0:pnCCD.0:Opal1000) key_in = pnccd-img fname key_out = pnccd-img-from-arr ftype subtract_offset = true print_bits = txt saveAll 1 [ImgAlgos.ImgCalib] source = true print_bits = 31 [ImgAlgos.Tahometer] dnDetInfo(:Opal1000) key_in = 100img 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:
| Code Block | ||
|---|---|---|
| ||
[psana] 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 \ ... files = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name>name-N>.xtc modulesskip-events = ImgAlgos.CameraImageProducer \500 events ImgAlgos.ImgAverage events = 1000 [ImgAlgos.CameraImageProducer] source= 10 modules = cspad_mod.CsPadCalib \ # = DetInfo(:Opal1000) key_inImgAlgos.CSPadBkgdSubtract \ =CSPadPixCoords.CSPadImageProducer \ key_out =ImgAlgos.ImgRadialCorrection img\ subtract_offset = true print_bits = ImgAlgos.ImgSaveInFile:1 [ImgAlgoscspad_mod.ImgAverageCsPadCalib] source inputKey = DetInfo(:Opal1000) keyoutputKey = calibrated doPedestals = yes doPixelStatus = no doCommonMode = img avefileno [ImgAlgos.CSPadBkgdSubtract] source = img-ave.dat rmsfile DetInfo(CxiDs1.0:Cspad.0) inputKey = img-rms.dat print_bits calibrated outputKey = 31 evts_stage1bkgd_subtracted_arr bkgd_fname = 100 evts_stage2 <the-file-name-with-background-array> norm_sector = 1000 gateprint_width1bits = 200 gate_width20 [CSPadPixCoords.CSPadImageProducer] calibDir = 20 |
Example for module ImgAlgos::ImgMaskEvaluation
- See Module ImgAlgos::ImgMaskEvaluation
- Configuration parameters for psana:
| Code Block | ||
|---|---|---|
| ||
[ImgAlgos.ImgMaskEvaluation] /reg/d/psdm/<instrument>/<experiment>/calib typeGroupName = CsPad::CalibV1 source = DetInfo(:Opal1000)CxiDs1.0:Cspad.0 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_satucalibrated imgkey = current_img #tiltIsApplied = true [ImgAlgos.ImgRadialCorrection] source = DetInfo(CxiDs1.0 dr :Cspad.0) inkey = 1 thre_SoNcurrent_img outkey = 3 frac_noisr_cor_img xcenter = 0.05 print_bits866 ycenter = 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] source857 rmin = DetInfo(:Opal1000) key_in100 rmax = 810 key_out n_phi_bins = 60 event = img subtract_offset = true0 print_bits = 13 [ImgAlgos.ImgCalibImgSaveInFile:1] source = DetInfo(:Opal1000)CxiDs1.0:Cspad.0 key_in = r_cor_img key_outfname = calibrated fname_peds<file-name-for-image-array> #saveAll = <pedestal-file-name> fname_masktrue eventSave = = <mask-file-name> fname_bkgd = fname_gain = print_bits = 31 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 of the mask file and resulting image:
Example for module ImgAlgos::
...
ImgPeakFinder
See Module ImgAlgos::ImgRadialCorrectionImgPeakFinder
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 skip-events = 500 events = 10 modules = cspad_mod.CsPadCalib \ # ImgAlgos.CSPadBkgdSubtract \ CSPadPixCoords.CSPadImageProducer \ ImgAlgos.ImgRadialCorrection \ files ImgAlgos.ImgSaveInFile:1 [cspad_mod.CsPadCalib] inputKey= /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-1>.xtc \ = outputKey = calibrated doPedestals = yes doPixelStatus = no doCommonMode = no [ImgAlgos.CSPadBkgdSubtract] source/reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-2>.xtc \ = DetInfo(CxiDs1.0:Cspad.0) inputKey ... = calibrated outputKey = bkgd_subtracted_arr bkgd_fname = <the-file-name-with-background-array> norm_sector = 0 print_bits /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-N>.xtc modules = 0 [CSPadPixCoords.CSPadImageProducer] calibDirImgAlgos.ImgPeakFinder PrintSeparator #skip-events = 500 events = /reg/d/psdm/<instrument>/<experiment>/calib typeGroupName = CsPad::CalibV1120 [ImgAlgos.ImgPeakFinder] source = CxiDs1.0:Cspad.0DetInfo(:Opal1000) key = calibrated imgkeypeaksKey = peaks threshold_low = current_img #tiltIsApplied20 threshold_high = true [ImgAlgos.ImgRadialCorrection] source 50 sigma = DetInfo(CxiDs1.0:Cspad.0) inkey 1.5 smear_radius = 2 peak_radius = current_img outkey 3 xmin = r_cor_img xcenter = 200 xmax = 866 ycenter = 857800 rminymin = 100 rmaxymax = 810 n_phi_bins = 60900 eventtestEvent = 115 print_bits = 0 print_bitsfinderIsOn = 3 [ImgAlgos.ImgSaveInFile:1]= 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 = CxiDs1.0:Cspad.0DetInfo(:Opal1000) key = r_cor_img fname peaks threshold_peak = 5 threshold_total= 0 n_peaks_min = <file-name-for-image-array> #saveAll 10 print_bits = true11 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:
fname = img
selection_mode = SELECTION_ON
|
Example for module ImgAlgos::
...
ImgPeakFinderAB
See Module ImgAlgos::ImgPeakFinderImgPeakFinderAB
Configuration file example:
| Code Block | ||
|---|---|---|
| ||
[psana] files = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-1>name>.xtc \ modules = ImgAlgos.CameraImageProducer \ ImgAlgos.ImgPeakFinderAB events /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-2>.xtc \ = 10 [ImgAlgos.CameraImageProducer] source ... = DetInfo(:Opal1000) key_in = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-N>.xtc modules key_out = ImgAlgos.ImgPeakFinder PrintSeparator #skip-events img subtract_offset = 500true eventsprint_bits = 1201 [ImgAlgos.ImgPeakFinderImgPeakFinderAB] source = DetInfo(:Opal1000) key = peaksKey = peaksimg threshold_low = 20 threshold_high = 50 sigmakey_peaks_out = 1.5 smear_radius peaks #key_signal_out = 2 peak_radius = 3 xmin = 200 xmax = 800 yminsignal-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 = 100 ymax tmp/img- rmin = 900 testEvent = 115 print_bits 10 dr = 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) key1 SoNThr_noise = = peaks3 threshold_peakSoNThr_signal = 5 threshold_total= 0 n_peaks 3 frac_noisy_imgs = 0.9 peak_npix_min = 10 print_bits 3 peak_npix_max = 11 fname 100 peak_amp_tot_thr = 0. peak_SoN_thr = img selection_mode = SELECTION_ON |
Example for module ImgAlgos::ImgPeakFinderAB
See Module ImgAlgos::ImgPeakFinderAB
Configuration file example:
| Code Block | ||
|---|---|---|
| ||
[psana] 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/<instrument>amo74213/<experiment>/xtc/<file-name>.xtc xtc/e269-r0093-s05-c00.xtc files = exp=amo74213:run=93:xtc modules = ImgAlgos.CameraImageProducer \ ImgAlgos.ImgPeakFinderABImgAverage skip-events = 0 events = 101000 [ImgAlgos.CameraImageProducer] source = DetInfo(:Opal1000) key_in = key_out = img subtract_offset = true print_bits = 1 [ImgAlgos.ImgPeakFinderABImgAverage] 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- rminavefile = img-ave-for-peds rmsfile = 10 dr= img-rms-for-thre evts_stage1 = 100 evts_stage2 = 100 gate_width1 = 50 gate_width2 = = 110 SoNThr_noiseprint_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 | ||
|---|---|---|
| ||
# = 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 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 \ = 4ImgAlgos. event_npeak_min ImgAverage skip-events = 0 events 5 event_npeak_max = 1000 event_amp_tot_thr = [ImgAlgos.CameraImageProducer] source 0. nevents_mask_update = 0 nevents_mask_accum = 50 selection_mode= DetInfo(:Opal1000) key_in = SELECTION key_ON out_file_bitsout = img subtract_offset = 15true print_bits = 1 [ImgAlgos.ImgHitFinder] source = 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 = 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 = 1000 [ImgAlgos.CameraImageProducer] source 0 thre_mode = DetInfo(:Opal1000) key_in3 #thre_mode = 2 keythre_outparam = 5 thre_below_value = img0 subtractthre_above_offsetvalue = true1 printwin_row_bitsmin = 1 [ImgAlgos.ImgAverage] source10 win_row_max = DetInfo(:Opal1000) key1000 win_col_min = 10 win_col_max = img1000 avefileprint_bits = = img-ave-for-peds rmsfile39 [ImgAlgos.ImgAverage] source = img-rms-for-thre evts_stage1DetInfo(:Opal1000) key = 100 evts_stage2 = 100 gate_width1img_hits sumfile = 50 gate_width2 = 10img-sum-result print_bits = 3125 |
Run psana using and run it by the command:
| Code Block | ||
|---|---|---|
| ||
psana -c psana-amo74213-r0093-opal-img-averagehit-finder.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:
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] | ||
| 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 files = img subtract_offset = true print_bits/reg/d/psdm/<instrument>/<experiment>/xtc/<file-name>.xtc modules = 1 [ ImgAlgos.ImgHitFinder]CameraImageProducer \ source = DetInfo(:Opal1000) key_in ImgAlgos.ImgSpectra \ = img key_out = img_hits fname_peds ImgAlgos.ImgSaveInFile:2 # = img-ave-for-peds-r0093.dat fname_mask = fname_gainImgAlgos.ImgSaveInFile # = fname_thre = img-rms-for-thre-r0093.dat masked_value psana_examples.DumpOpal1k \ events = 0 thre_mode 100 [ImgAlgos.CameraImageProducer] source = 3 #thre_modeDetInfo(:Opal1000) key_in = 2 threkey_paramout = 5 thre_below_value = 0img thresubtract_above_valueoffset = 1true winprint_row_minbits = 10 win_row_max 1 [ImgAlgos.ImgSpectra] source = 1000 win_col_min = 10 win_col_maxDetInfo(:Opal1000) key_in = 1000 print_bits = img key_out = 39 [ImgAlgos.ImgAverage] source = spectra sig_band_rowc = DetInfo(:Opal1000) key512. ref_band_rowc = 552. sig_band_tilt = 0. ref_band_tilt = img_hits sumfile 0. sig_band_width = 10 ref_band_width = =10 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] 3 [ImgAlgos.ImgSpectraProc] source = DetInfo(:Opal1000) key_in = spectra print_bits = 15 [ImgAlgos.ImgSaveInFile:2] source = DetInfo(:Opal1000) key = spectra fname files = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name>.xtc modulesspec-xppi0412 saveAll = true [ImgAlgos.CameraImageProducer \ImgSaveInFile] source = DetInfo(:Opal1000) key ImgAlgos.ImgSpectra \ = img fname ImgAlgos.ImgSaveInFile:2 #= img-xppi0412 saveAll ImgAlgos.ImgSaveInFile # psana_examples.DumpOpal1k \ events = 100 [ImgAlgos.CameraImageProducer= 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 keyprint_out 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:img subtract_offset = true print_bits = 1 [ImgAlgos.ImgSpectra] source = DetInfo(:Opal1000) key_in 0 100 = img key_out200 300 = 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:
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 | ||
| Code Block | ||
| ||
[ImgAlgos.ImgSpectraProc] source = DetInfo(:Opal1000) key_inimg fname = spectra print_bitsmy-img #ftype = 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:txt #ftype = bin #ftype 0 100 = 200png ftype 300 400= tiff #eventSave 500 = 5 saveAll 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
= 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 | ||
| 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 = bincalibrated #ftypeoutkey = png ftypemasked_arr mask_fname = <your-local-directory>/<mask-file-name>.dat masked_amp = tiff #eventSave = 50 saveAllprint_bits = 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 \ ... 5 mask_control_bits = 15 [CSPadPixCoords.CSPadImageProducer] calibDir = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-N>.xtc eventscalib typeGroupName = CsPad::CalibV1 source = CxiDs1.0:Cspad.0 key 1000 experiment = cxii0212 calib-dir = ana-cxii0212/calib modules = cspad_mod.CsPadCalib \ masked_arr imgkey = ImgAlgos.CSPadMaskApply \ img print_bits = 0 #tiltIsApplied = CSPadPixCoords.CSPadImageProducer \ true [ImgAlgos.ImgPeakFinder] source ImgAlgos.ImgPeakFinder \ = DetInfo(CxiDs1.0:Cspad.0) key ImgAlgos.ImgPeakFilter= \img peaksKey = peaks threshold_low = ImgAlgos.ImgSaveInFile:1 [cspad_mod.CsPadCalib] inputKey 2 threshold_high = 5 sigma = outputKey = calibrated doPedestals1.5 smear_radius = yes5 doPixelStatuspeak_radius = no doCommonMode = yes [ImgAlgos.CSPadMaskApply] source 7 xmin = DetInfo(CxiDs1.0:Cspad.0) inkey20 xmax = calibrated1700 outkeyymin = masked_arr mask_fname20 ymax = <your-local-directory>/<mask-file-name>.dat masked_amp 1700 #testEvent = 05 print_bits = 3 #finderIsOn = 5 mask_control_bits = 15true [CSPadPixCoordsImgAlgos.CSPadImageProducer] calibDir = /reg/d/psdm/<instrument>/<experiment>/calib typeGroupName = CsPad::CalibV1ImgPeakFilter] source = DetInfo(CxiDs1.0:Cspad.0) key = masked_arr imgkey peaks threshold_peak = 5 threshold_total= 0 n_peaks_min = img10 print_bits = 11 fname 0 #tiltIsApplied = cspad-img selection_mode = trueSELECTION_ON [ImgAlgos.ImgPeakFinderImgSaveInFile:1] source = DetInfo(CxiDs1.0:Cspad.0) key = img peaksKeyfname = peaks threshold_low = 2 threshold_high = 5 sigma cspad-img #eventSave = 1.5 smear_radiussaveAll = 5 peak_radius = 7 xmin = 20 xmax = 1700 ymin = 20 ymax = 1700 #testEvent = 5true |
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 = 3100 #finderIsOnevts_stage2 = 100 gate_width1 = 100 gate_width2 = 10 |
Configuration file example for evaluation of background:
| Code Block | ||
|---|---|---|
| ||
[psana] filestrue [ImgAlgos.ImgPeakFilter] source = DetInfo(CxiDs1.0:Cspad.0) key<path-to-the-background-run-file>.xtc modules = cspad_mod.CsPadCalib ImgAlgos.CSPadArrAverage skip-events = 500 events = peaks threshold_peak = 51000000 threshold_total= 0 n_peaks_min[cspad_mod.CsPadCalib] inputKey = 10 print_bitsoutputKey = 11calibrated fnamedoPedestals = yes doPixelStatus = cspad-img selection_modeno doCommonMode = SELECTION_ONno [ImgAlgos.ImgSaveInFile:1CSPadArrAverage] source = DetInfo(CxiDs1.0:Cspad.0) key = img fname calibrated avefile = cspad-img #eventSave background-ave.dat rmsfile = 1 saveAll = true 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::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 files = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-1>.xtc \ /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-2>.xtc \ ... = 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 /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 = 1000000 [cspad_mod.CsPadCalib]DetInfo(CxiDs1.0:Cspad.0) inputKey = calibrated outputKey = bkgd_subtracted bkgd_fname = calibrated doPedestals<the-file-name-with-background-array> norm_sector = yes doPixelStatus0 print_bits = 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
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 | ||
| Code Block | ||
| ||
[psana] files = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-1>.xtc \ /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-2>.xtc ImgAlgos.CSPadBkgdSubtract \ ... /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-N>.xtc skip-events = 500 events ImgAlgos.CSPadMaskApply \ = 10 modules = cspad_mod.CsPadCalib ImgAlgos.CSPadBkgdSubtract ... [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 = <theana-filecxi49012/cspad-namecxi49012-withr0025-background-array> norm_sectorave.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 = 0 print 3 mask_control_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.
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::CSPadArrNoisePlots 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 | ||
|---|---|---|
| ||
[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 \ ImgAlgos.CSPadBkgdSubtract /reg/d/psdm/cxi/cxi49012/xtc/e158-r0020-s04-c00.xtc \ ImgAlgos.CSPadMaskApply \ /reg/d/psdm/cxi/cxi49012/xtc/e158-r0020-s05-c00.xtc #skip-events = 1000 events ...= 10 [cspad_mod.CsPadCalib] inputKey = outputKey = calibrated_arr doPedestals = yes doPixelStatus = no doCommonMode = no [ImgAlgos.CSPadBkgdSubtractCSPadArrNoise] source = DetInfo(CxiDs1.0:Cspad.0) inputKeykey = calibrated_arr outputKey statusfile = ana-cxi49012/cspad-cxi49012-r0020-noise-status.dat maskfile = ana-cxi49012/cspad-cxi49012-r0200-noise-mask.dat print_bits = 255 rmin = 3 dr = bkgd_subtracted_arr bkgd_fname1 SoNThr = 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
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::CSPadArrPeakFinderSee Module ImgAlgos::CSPadArrNoise
| Code Block | ||
|---|---|---|
| ||
[psana] modulesfiles = cspad_mod.CsPadCalib ImgAlgos.CSPadArrNoise files\ = /reg/d/psdm/cxi/cxi49012/xtc/e158-r0020r0150-s00-c00.xtc \ /reg/d/psdm/cxi/cxi49012/xtc/e158-r0020r0150-s01-c00.xtc \ /reg/d/psdm/cxi/cxi49012/xtc/e158-r0020r0150-s02-c00.xtc \ /reg/d/psdm/cxi/cxi49012/xtc/e158-r0020r0150-s03-c00.xtc \ # /reg/d/psdm/cxi/cxi49012/xtc/e158-r0020r0150-s04-c00.xtc \ suddenly it became unavailable... /reg/d/psdm/cxi/cxi49012/xtc/e158-r0020r0150-s05-c00.xtc #skip-events = 1000 events#events = 10200 [modules = 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 \ ImgAlgos.CSPadMaskApply \ = 3 dr ImgAlgos.CSPadArrPeakFinder [cspad_mod.CsPadCalib] inputKey = 1 SoNThroutputKey = calibrated doPedestals = yes doPixelStatus = 3 frac_noisy_imgsno doCommonMode = 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
no
[ImgAlgos.CSPadMaskApply]
source = DetInfo(CxiDs1.0:Cspad.0)
inkey = calibrated
outkey = masked_arr
mask_fname = ana-cxi49012/cspad-cxi49012-r0150-mask-badregs.dat
#mask_fname = ana-cxi49012/cspad-cxi49012-r0150-mask-bkgd.dat
#mask_fname = ana-cxi49012/cspad-cxi49012-r0150-mask-rects.dat
masked_amp = 8
print_bits = 1
mask_control_bits = 15
[ImgAlgos.CSPadArrPeakFinder]
source = DetInfo(CxiDs1.0:Cspad.0)
key = masked_arr
key_peaks_out = peaks
hot_pix_mask_inp_file = ana-cxi49012/cspad-cxi49012-r0150-noise-mask.dat
hot_pix_mask_out_file = ana-cxi49012/cspad-cxi49012-r0150-noise-mask-out.dat
frac_noisy_evts_file = ana-cxi49012/cspad-cxi49012-r0150-noise-frac.dat
evt_file_out = tmp/cspad-ev-
rmin = 3
dr = 1
SoNThr = 3
frac_noisy_imgs = 0.1
peak_npix_min = 4
peak_npix_max = 25
peak_amp_tot_thr = 100.
event_npeak_min = 10
event_amp_tot_thr = 1000.
nevents_mask_update = 100
nevents_mask_accum = 50
selection_mode = SELECTION_ON
out_file_bits = 15
print_bits = 512
|
Results:
| Code Block | ||
|---|---|---|
| ||
[info:TimeInterval::startTime] Start time: 2012-06-12 15:32:02
[info:ImgAlgos.CSPadArrPeakFinder] N processed events = 1000 N selected = 55 Fraction of selected = 0.055
[info:ImgAlgos.CSPadArrPeakFinder] N processed events = 2000 N selected = 62 Fraction of selected = 0.031
[info:ImgAlgos.CSPadArrPeakFinder] N processed events = 3000 N selected = 81 Fraction of selected = 0.027
[info:ImgAlgos.CSPadArrPeakFinder] N processed events = 4000 N selected = 95 Fraction of selected = 0.02375
[info:ImgAlgos.CSPadArrPeakFinder] N processed events = 5000 N selected = 150 Fraction of selected = 0.03
[info:ImgAlgos.CSPadArrPeakFinder] N processed events = 6000 N selected = 265 Fraction of selected = 0.0441667
[info:ImgAlgos.CSPadArrPeakFinder] N processed events = 7000 N selected = 404 Fraction of selected = 0.0577143
[info:ImgAlgos.CSPadArrPeakFinder] ===== JOB SUMMARY =====
[info:TimeInterval::stopTime] Time to process 7945 events is 3747.48 sec, or 0.471678 sec/event
|
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 = 10
files = exp=cxi83714:run=136
modules = cspad_mod.CsPadCalib \
| ||
| Code Block | ||
| ||
[psana] files = \ /reg/d/psdm/cxi/cxi49012/xtc/e158-r0150-s00-c00.xtc \ /reg/d/psdm/cxi/cxi49012/xtc/e158-r0150-s01-c00.xtc \ /reg/d/psdm/cxi/cxi49012/xtc/e158-r0150-s02-c00.xtc \ /reg/d/psdm/cxi/cxi49012/xtc/e158-r0150-s03-c00.xtc \ # /reg/d/psdm/cxi/cxi49012/xtc/e158-r0150-s04-c00.xtc \ suddenly it became unavailable... /reg/d/psdm/cxi/cxi49012/xtc/e158-r0150-s05-c00.xtc #skip-events = 1000 #events = 200 modules = cspad_mod.CsPadCalib \ ImgAlgos.CSPadMaskApply \ ImgAlgos.CSPadArrPeakFinder [cspad_mod.CsPadCalib] inputKey = outputKey = calibrated doPedestals = yes doPixelStatus = no doCommonMode = no [ImgAlgos.CSPadMaskApply] source = DetInfo(CxiDs1.0:Cspad.0) inkey = calibrated outkey = masked_arr mask_fname = ana-cxi49012/cspad-cxi49012-r0150-mask-badregs.dat #mask_fname = ana-cxi49012/cspad-cxi49012-r0150-mask-bkgd.dat #mask_fname = ana-cxi49012/cspad-cxi49012-r0150-mask-rects.dat masked_amp = 8 print_bits = 1 mask_control_bits = 15 [ImgAlgos.CSPadArrPeakFinder] source = DetInfo(CxiDs1.0:Cspad.0) key = masked_arr key_peaks_out = peaks hot_pix_mask_inp_file = ana-cxi49012/cspad-cxi49012-r0150-noise-mask.dat hot_pix_mask_out_file = ana-cxi49012/cspad-cxi49012-r0150-noise-mask-out.dat frac_noisy_evts_file = ana-cxi49012/cspad-cxi49012-r0150-noise-frac.dat evt_file_out = tmp/cspad-ev- rmin ImgAlgos.CSPadArrPeakFinder =\ 3 dr pyimgalgos.ex_peaks_nda # EventKeys [cspad_mod.CsPadCalib] inputKey = = 1 SoNThroutputKey = calibrated doPedestals = yes doPixelStatus = yes doCommonMode = yes [ImgAlgos.CSPadArrPeakFinder] source 3 frac_noisy_imgs = = DetInfo(CxiDs1.0:Cspad.1 peak_npix_min0) key = 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_bitscalibrated key_peaks_out = key_peaks_nda = peaks_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 = cxi83714/cspad-ev- rmin = 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:
8
dr = 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:
...
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.
...
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.
...
See description of modules in Package pyimgalgos.
Example of configuration file for CSPAD
File py-xcs72913-r0049-cspad.cfg:
...
pyana -c py-xcs72913-r0049-cspad.cfg
Example of configuration file for CSPAD2x2
File py-meca6113-r0028-cspad2x2.cfg
...
pyana -c py-meca6113-r0028-cspad2x2.cfg
References
Psana psana - Module Catalog
Overview
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