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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.

...

  • psana.cfg - set non-default parameters to run psana for ImgAlgos::ImgPeakFinder and ImgAlgos::ImgPeakFilter
    The psana running 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

...

module CSPadPixCoords::CSPadImageProducer

How to write the CSPad image in text file:

Code Block
bgColor#F7F7ED
[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

See Package CSPadPixCoords

 

Example for module CSPadPixCoords::

...

CSPadNDArrProducer

See Module CSPadPixCoords::CSPad2x2ImageProducerCSPadNDArrProducer

Example of the configuration script for psana (cspad2x2-test.cfg):module CSPadNDArrProducer working in sequence with ImgAlgos::NDArrAverage is shown in Example for module ImgAlgos::NDArrAverage 

 

Example for module CSPadPixCoords::CSPad2x2NDArrProducer

No Format
# Run this script:
# psana -c psana-meca1113-r0045-cspad-cspad2x2-dark-hotpix.cfg
Code Block
bgColor#F7F7ED
[psana]
files# Default calibration       directory:
# calib-dir = /reg/d/psdm/<instrument>mec/<experiment>/xtc/<file-name-1>.xtc
events        = 5
modulesmeca1113/calib

files = exp=meca1113:run=45
events = 400
#skip-events = 0

modules = CSPadPixCoords.CSPad2x2NDArrProducer:1 \
       =   CSPadPixCoords.CSPad2x2ImageProducerCSPad2x2NDArrProducer:2 \
          ImgAlgos.NDArrAverage:1 \
          ImgAlgos.ImgSaveInFileNDArrAverage:2


[CSPadPixCoords.CSPad2x2ImageProducerCSPad2x2NDArrProducer:1]
source  = MecTargetChamber.0:Cspad2x2.1
inkey   = 
outkey  = DetInfo(:Cspad2x2)
inkey          = 
outimgkey      = Image
tiltIsApplied  = true
print_bits     = 15

[ImgAlgos.ImgSaveInFilecspad2x2.1_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        = DetInfo(MecTargetChamber.0:Cspad2x2).1
key           = Image
fnamecspad2x2.1_ndarr
avefile         = cspad2x2
saveAll .1-ave
rmsfile      = true
#eventSavecspad2x2.1-rms
maskfile     = 5

Command to run:
psana -c cspad2x2-test.cfg
One of the saved files cspad2x2-<run>-<timestamp>.txt is plotted as an image by the command
./PlotCameraImageFromFile.py cspad2x2-<run>-<timestamp>.txt 0 1200

Image RemovedImage Removed

Configuration file for cspad2x2 with pedestal subtraction

Note

Access to the CSPad2x2 aligned geometry is added on 2013-02-13
and is available for offline release > ana-0.9.1.

Example of <psana-config-file.cfg>:

Code Block
bgColor#F7F7ED
[psana]
files    = /reg/d/psdm/mec/mec73313/xtc/e268-r0180-s02-c00.xtc
#calib-dir = ./calib

modules  = cspad_mod.CsPadCalib CSPadPixCoords.CSPad2x2ImageProducer ImgAlgos.ImgSaveInFile
events   = 5

[cspad_mod.CsPadCalibcspad2x2.1-msk
hotpixfile   = cspad2x2.1-hot
#evts_stage1  = 100
#gate_width1  = 100.
thr_rms_ADU  = 10
thr_min_ADU  = 4
thr_max_ADU  = 10000
print_bits   = 29


[ImgAlgos.NDArrAverage:2]
source        = DetInfo(MecTargetChamber.0:Cspad2x2.3)2
inputKeykey      = 
outputKey     = calibratedcspad2x2.2_arrndarr
doPedestalsavefile   = yes
doPixelStatus = no
doCommonMode  = no


[CSPadPixCoords.CSPad2x2ImageProducer]
calibDir cspad2x2.2-ave
rmsfile      = /reg/d/psdm/mec/mec73313/calib
typeGroupName  = CsPad2x2::CalibV1
#sourcecspad2x2.2-rms
maskfile        = DetInfo(MecTargetChamber.0:Cspad2x2.3)
sourcecspad2x2.2-msk
hotpixfile   = cspad2x2.2-hot
#evts_stage1  = 100
#gate_width1  = :Cspad2x2100.3
inkeythr_rms_ADU  = 10
thr_min_ADU  = 4
thr_max_ADU    = calibrated_arr
outimgkey10000
print_bits   = 29

This script makes ndarrays for two cspad2x2 detectors and use them evaluate average, rms, mask and hot pixel arrays.

See Module CSPadPixCoords::CSPad2x2NDArrProducer

Example for module CSPadPixCoords::CSPad2x2NDArrReshape

Example of configuration file

Code Block
[psana]
#files = = Image
tiltIsApplied exp=meca1113:run=376
#events = true
print_bits     = 15


[ImgAlgos.ImgSaveInFile]
source10
##skip-events = 0

modules = cspad_mod.CsPadCalib \
         = DetInfo(MecTargetChamberCSPadPixCoords.0:Cspad2x2.3)
keyCSPad2x2NDArrProducer:clb \
            = Image
fnameCSPadPixCoords.CSPad2x2NDArrProducer:raw \
          = cspad2x2.3
saveAllCSPadPixCoords.CSPad2x2NDArrReshape \
        = true
print_bits  ImgAlgos.NDArrAverage:clb \
         = 3
#eventSaveImgAlgos.NDArrAverage:raw
#         = 5

Example of psana configuration file to get cspad2x2 images for two detectors and save them in files, one in txt, another in tiff formats:

Code Block
bgColor#F7F7ED
[psana]
filesEventKeys

[cspad_mod.CsPadCalib]
inputKey      = /reg/d/psdm/xpp/xpptut13/xtc/e308-r0008-s02-c00.xtc \
outputKey     = clb_data
doPedestals     /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 \ 
     = yes
doPixelStatus = yes
doCommonMode  = yes

[CSPadPixCoords.CSPad2x2NDArrProducer:clb]
source     = MecTargetChamber.0:Cspad2x2.1
inkey      = clb_data
outkey     = cspad_mod.CsPadCalib:1 \ 
cspad2x2.1_clb:as_data
outtype    = int16
print_bits      = 5

[CSPadPixCoords.CSPad2x2ImageProducer:0 \
CSPad2x2NDArrProducer:raw]
source           CSPadPixCoords.CSPad2x2ImageProducer:1 \ 
= MecTargetChamber.0:Cspad2x2.1
inkey      = 
outkey     = ImgAlgoscspad2x2.ImgSaveInFile:0  \
1_raw:as_data
outtype           ImgAlgos.ImgSaveInFile:1

events   = int16
print_bits = 5

[cspad_mod.CsPadCalib:0CSPadPixCoords.CSPad2x2NDArrReshape]
source        = DetInfo(XppGonMecTargetChamber.0:Cspad2x2.0)
inputKey1
keys_in      = 
outputKey     = calibrated_arr0
doPedestals   = yes
doPixelStatus = no
doCommonMode  = yes

[cspad_mod.CsPadCalib:1cspad2x2.1_raw:as_data cspad2x2.1_clb:as_data
print_bits = 255

[ImgAlgos.NDArrAverage:clb]
source        = DetInfo(XppGonMecTargetChamber.0:Cspad2x2.1)
inputKeykey      = 
outputKey     = calibratedcspad2x2.1_arr1clb
doPedestals  avefile = yes
doPixelStatus = no
doCommonMode  = yes


[CSPadPixCoords.CSPad2x2ImageProducer:0]
calibDir arr-ave-clb
rmsfile        = /reg/d/psdm/xpp/xpptut13/xtc/calib
typeGroupName= arr-rms-clb
print_bits    = CsPad2x2::CalibV1
source   255

[ImgAlgos.NDArrAverage:raw]
source        = DetInfo(XppGonMecTargetChamber.0:Cspad2x2.0)1
inkeykey            = calibratedcspad2x2.1_arr0raw
outimgkeyavefile        = Image
tiltIsAppliedarr-ave-raw
rmsfile    = false
useWidePixCenter = falsearr-rms-raw
print_bits   = 255

This script produces raw and calibrated ndarrays shaped as data (185,388,2), then pass these arrays  as

keys_in    =

...

cspad2x2.1_raw:as_data cspad2x2.1_clb:as_data

to 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
#!/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
serverSLAC National Accelerator Laboratory
keyPSAS-45

 

Example for module CSPadPixCoords::CSPad2x2ImageProducer

See Module CSPadPixCoords::CSPad2x2ImageProducer

Example of the configuration script for psana (cspad2x2-test.cfg):

Code Block
bgColor#F7F7ED
[psana]
files         = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-1>.xtc
events        = 5
modules       = CSPadPixCoords.CSPad2x2ImageProducer ImgAlgos.ImgSaveInFile

[CSPadPixCoords.CSPad2x2ImageProducer

Example for package ImgPixSpectra

See 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
bgColor#F7F7ED
# Command to run this script: 
# psana -c psana-cxib2313-r0114-cspad-pix-spectra.cfg
#
# Other useful commands: 
# psana -n 5 -m  PrintSeparator,PrintEventId,psana_examples.DumpCsPad /reg/d/psdm/cxi/cxib2313/xtc/e336-r0114*
# psana -n 5 -m EventKeys exp=cxib2313:run=114:xtc

[psana]
files      = exp=cxib2313:run=114:xtc
#calib-dir = ./calib
skip-events = 0
events      = 100
modules     = cspad_mod.CsPadCalib ImgPixSpectra.CSPadPixSpectra

[cspad_mod.CsPadCalib]
source         = DetInfo(CxiDs1.0:Cspad.0:Cspad2x2)
inputKeyinkey          = 
outputKeyoutimgkey      = calibratedImage
doPedestalstiltIsApplied   = yes
doPixelStatus = no
doCommonModetrue
print_bits     = yes15

[ImgPixSpectraImgAlgos.CSPadPixSpectraImgSaveInFile]
source        = CxiDs1.0:Cspad.0
inputKeyDetInfo(:Cspad2x2)
key       = calibrated
amin          =   -20.
amaxImage
fname          =    20.
nbinscspad2x2
saveAll         =    10
arr_fnametrue
#eventSave     = cspad_spectral_array.txt

where module cspad_mod.CsPadCalib subtracts pedestals, apply common mode correction, and save CSPAD array in the event store with key "calibrated", which is used in the next module ImgPixSpectra.CSPadPixSpectra.

5

Command to run:To run this script use command
psana -c

...

cspad2x2-test.cfg

which produces two files:

  • cspad_spectral_array.txt – array of 10-bin amplitude spectra for all pixels

  • cspad_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:
Image Removed

Example for module ImgPixSpectra::CSPad2x2PixSpectra

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

Image AddedImage Added

Configuration file for cspad2x2 with pedestal subtraction

Note

Access to the CSPad2x2 aligned geometry is added on 2013-02-13
and is available for offline release > ana-0.9.1.

Example of <psana-config-file.cfg>See module description in Module ImgPixSpectra::CSPad2x2PixSpectra
Configuration file example for CSPad2x2PixSpectra:

Code Block
bgColor#F7F7ED
[psana]
files         = /reg/d/psdm/mec/<instrument>mec73313/<experiment>/<file-name>xtc/e268-r0180-s02-c00.xtc
modules#calib-dir = ./calib

modules  = cspad_mod.CsPadCalib CSPadPixCoords.CSPad2x2ImageProducer ImgAlgos.ImgSaveInFile
events   = ImgPixSpectra.CSPad2x2PixSpectra5

[ImgPixSpectracspad_mod.CSPad2x2PixSpectraCsPadCalib]
source        = CxiSc1DetInfo(MecTargetChamber.0:Cspad2x2.0
amin3)
inputKey      = 
outputKey     = calibrated_arr
doPedestals   = yes
doPixelStatus = no
doCommonMode   500.
amax  = no


[CSPadPixCoords.CSPad2x2ImageProducer]
calibDir       = /reg/d/psdm/mec/mec73313/calib
typeGroupName  = CsPad2x2::CalibV1
#source        = DetInfo(MecTargetChamber.0:Cspad2x2.3)
source         = 1000:Cspad2x2.3
nbinsinkey          =   100
arr_fnamecalibrated_arr
outimgkey      = Image
tiltIsApplied  = true
print_bits     = cspad2x2-pix-spectra.txt

To get images from saved file one may execute the auxiliary script:

Code Block
bgColor#F7F7ED
ImgPixSpectra/data/PlotSpectralArrayFromFile.py cspad2x2-pix-spectra.txt

generates image for limited range of pixels for CSPad, CSPad2x2, or Camera, respectively:
Image RemovedImage Removed Image Removed

Examples for package ImgAlgos

See Package ImgAlgos

Example for module ImgAlgos::Tahometer

See Module ImgAlgos::Tahometer

Example of the psana configuration file:

Code Block
bgColor#F7F7ED
[psana]15


[ImgAlgos.ImgSaveInFile]
source         = DetInfo(MecTargetChamber.0:Cspad2x2.3)
key            = Image
filesfname          = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\
cspad2x2.3
saveAll        = true
print_bits     =  /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-2>.xtc

modules   3
#eventSave     = ImgAlgos.Tahometer

[ImgAlgos.Tahometer]
dn         = 10
print_bits = 7

Example for module ImgAlgos::PnccdImageProducer

See Module ImgAlgos::PnccdImageProducer

5

Example of psana configuration file to get cspad2x2 images for two detectors and save them in files, one in txt, another in tiff formatsExample of the psana configuration file:

Code Block
bgColor#F7F7ED
[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 \
           
files  CSPadPixCoords.CSPad2x2ImageProducer:1 \ 
       = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\
   ImgAlgos.ImgSaveInFile:0  \
           /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-2>.xtc
#skip-events = 100
events   ImgAlgos.ImgSaveInFile:1

events   =  5
modules = ImgAlgos.PnccdImageProducer ImgAlgos.ImgSaveInFile

[ImgAlgos.PnccdImageProducercspad_mod.CsPadCalib:0]
source        = DetInfo(:pnCCDXppGon.0:Cspad2x2.0)
inkeyinputKey      =   =
outimgkeyoutputKey     = imgpnccd
print_bits  calibrated_arr0
doPedestals   = yes
doPixelStatus = no
doCommonMode  = 1yes

[ImgAlgos.ImgSaveInFilecspad_mod.CsPadCalib:1]
source        = DetInfo(:pnCCD)
keyXppGon.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    = imgpnccd
fnameCsPad2x2::CalibV1
source           = pnccd-img-ev
saveAllDetInfo(XppGon.0:Cspad2x2.0)
inkey            = true
#eventSavecalibrated_arr0
outimgkey        = 82Image
print_bitstiltIsApplied    = 1

This script saves text files with images like pnccd-img-ev-<run-date-time.nsec>.txt, which can be presented as:
Image Removed

Example for module ImgAlgos::CameraImageProducer

See Module ImgAlgos::CameraImageProducer

Example of the psana configuration file:

Code Block
bgColor#F7F7ED
[psana]false
useWidePixCenter = false
print_bits       = 15

[CSPadPixCoords.CSPad2x2ImageProducer:1]
calibDir         = /reg/d/psdm/xpp/xpptut13/xtc/calib
typeGroupName    = CsPad2x2::CalibV1
source           = DetInfo(XppGon.0:Cspad2x2.1)
inkey            = calibrated_arr1
outimgkey        = Image
tiltIsApplied    = false
useWidePixCenter = false
print_bits       = 
files15



[ImgAlgos.ImgSaveInFile:0]
source           = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc
modules= DetInfo(:Cspad2x2.0)
key            = ImgAlgos.CameraImageProducer ImgAlgos.ImgSaveInFile
eventsImage
fname          = 5

[ImgAlgos.CameraImageProducer] 
sourcecspad2x2.0
ftype          = DetInfo(:Opal1000)
key_intxt
#ftype          = tiff
key_outsaveAll         = imgtrue
subtract_offsetprint_bits     = true
print_bits 3
#eventSave     = 155

[ImgAlgos.ImgSaveInFile:1]
source         = DetInfo(:Opal1000Cspad2x2.1)
key            = img
fnameImage
fname          = cspad2x2.1
#ftype          = txt
ftype          = img-from-my-experimenttiff
saveAll        = true
print_bits     = 3
#eventSave     = 1

This script saves text files with images like img-from-my-experiment-<run-date-time.nsec>.txt, which can be drawn by the python script

./ImgAlgos/data/PlotCameraImageFromFile.py <filename>.txt <Amin> <Amax>

Example for module ImgAlgos::PrincetonImageProducer

See Module ImgAlgos::PrincetonImageProducer

5

Example for package ImgPixSpectra

See 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.cfgExample of the psana configuration file:

Code Block
bgColor#F7F7ED
[psana]# Command to run this script: 
# psana -c psana-cxib2313-r0114-cspad-pix-spectra.cfg
#
# Other useful commands: 
# psana -n 5 -m  PrintSeparator,PrintEventId,psana_examples.DumpCsPad /reg/d/psdm/cxi/cxib2313/xtc/e336-r0114*
# psana -n 5 -m EventKeys exp=cxib2313:run=114:xtc

[psana]
files      = exp=cxib2313:run=114:xtc
#calib-dir = ./calib
skip-events = 0
events      = 100
modules     = cspad_mod.CsPadCalib ImgPixSpectra.CSPadPixSpectra

[cspad_mod.CsPadCalib]
source        = DetInfo(CxiDs1.0:Cspad.0)
inputKey   
files   = 
outputKey     = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\
       calibrated
doPedestals   = yes
doPixelStatus = no
doCommonMode  = yes

[ImgPixSpectra.CSPadPixSpectra]
source         /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-2>.xtc
modules= CxiDs1.0:Cspad.0
inputKey       = ImgAlgos.PrincetonImageProducer \calibrated
amin          =      ImgAlgos.ImgSaveInFile
events-20.
amax          = 3

[ImgAlgos.PrincetonImageProducer] 
source          = DetInfo(:Princeton)
key_in 20.
nbins         = 
key_out         = img
subtract_offset = true
print_bits      = 31

[ImgAlgos.ImgSaveInFile]
source        = DetInfo(:Princeton)
key           = img
fname  10
arr_fname       = img-xcs
saveAll       = true
print_bits    = 31

Image Removed

 

...

Example for module ImgAlgos::AcqirisArrProducer

See description of parameters in Module ImgAlgos::AcqirisArrProducer

...

= 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 pixels

  • cspad_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:
Image Added

Example for module ImgPixSpectra::CSPad2x2PixSpectra

See module description in Module ImgPixSpectra::CSPad2x2PixSpectra
Configuration file example for CSPad2x2PixSpectra:

Code Block
bgColor#F7F7ED
[psana]
files         = /reg/d/psdm/<instrument>/<experiment>/<file-name>.xtc
modules       = ImgPixSpectra.CSPad2x2PixSpectra

[ImgPixSpectra.CSPad2x2PixSpectra]
source        = CxiSc1.0:Cspad2x2.0
amin          =   500.
amax    # Command to run this script:
# psana -c psana-amo01509-r0125-acqiris.cfg;
#
# Useful commands:
# psana -n 5 -m EventKeys exp=amo01509:run=125:xtc > test-acqiris-file.txt;
# psana -n 5 -m psana_examples.DumpAcqiris exp=amo01509:run=125:xtc > test-acqiris-file.txt;    (C++ version)
# psana -n 1 -m psana_examples.dump_acqiris exp=amo01509:run=125:xtc > test-acqiris-file.txt;   (python version)

[psana]
#files = /reg/d/psdm/AMO/amo01509/xtc/e8-r0125-s00-c00.xtc /reg/d/psdm/AMO/amo01509/xtc/e8-r0125-s01-c00.xtc
files = exp=amo01509:run=125:xtc

modules = ImgAlgos.AcqirisArrProducer ImgAlgos.ImgSaveInFile:wf ImgAlgos.ImgSaveInFile:wt

skip-events = 0
events      = 100


[ImgAlgos.AcqirisArrProducer]
source 1000.
nbins         = AmoETOF.0:Acqiris.0
key_in  100
arr_fname     = cspad2x2-pix-spectra.txt

To get images from saved file one may execute the auxiliary script:

Code Block
bgColor#F7F7ED
ImgPixSpectra/data/PlotSpectralArrayFromFile.py cspad2x2-pix-spectra.txt

generates image for limited range of pixels for CSPad, CSPad2x2, or Camera, respectively:
Image AddedImage Added Image Added

Examples for package ImgAlgos

See Package ImgAlgos

Example for module ImgAlgos::Tahometer

See Module ImgAlgos::Tahometer

Example of the psana configuration file:

Code Block
bgColor#F7F7ED
[psana]   =
key_wform     = acqiris_wform
key_wtime     = acqiris_wtime
fname_prefix
files    = acq
print_bits    = 11


[ImgAlgos.ImgSaveInFile:wf]
source/reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\
         = AmoETOF.0:Acqiris.0
key      /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-2>.xtc

modules       = acqiris_wform
fnameImgAlgos.Tahometer

[ImgAlgos.Tahometer]
dn         = 10
print_bits = 7

Example for module ImgAlgos::EpixNDArrProducer

See Module ImgAlgos::EpixNDArrProducer

Example of the psana configuration file:

Code Block
[psana]
files= acq-AmoETOF-wform
ftype         = = txt
#ftypeexp=xppi0414:run=94
events          = tiff100
#saveAllmodules       = =ImgAlgos.EpixNDArrProducer true
print_bits\
        = 3
eventSave      = 5ImgAlgos.NDArrAverage


[ImgAlgos.ImgSaveInFile:wtEpixNDArrProducer]
source         = AmoETOF.0:Acqiris.0DetInfo(:Epix10k)
key_in =
key_out = epix-nda
outtype = float
print_bits = 255

[ImgAlgos.NDArrAverage]
source       = acqiris_wtime
fnameDetInfo(:Epix10k)
key          = epix-nda
avefile      = epix-ave
print_bits   = 29

EpixNDArrProducer gets Epix10k ndarray from data and saves it in the events store with possible type conversion. Then NDArrAverage averages this ndarray over requested number of events (100) and saves it in file.

Example for module ImgAlgos::PnccdImageProducer

See Module ImgAlgos::PnccdImageProducer

Example of the psana configuration file:

Code Block
bgColor#F7F7ED
[psana]  acq-AmoETOF-wtime
ftype          = txt
#ftype          = tiff
#saveAll        = true
print_bits     = 3
eventSave      = 5

This script saves text files

  • acq-amo01509-r0125.txt -- with configuration parameters
  • acq-AmoETOF-wform-r0125-20091018-182512.194787218.txt – with waveforms for 5th event
  • acq-AmoETOF-wtime-r0125-20091018-182512.194787218.txt – with wave-times for 5th event

Arrays from these files can be plotted for all channels, shown by different colors:

Image Removed  Image Removed

 

 

...

Example for module ImgAlgos::AcqirisAverage

See description of parameters in Module ImgAlgos::AcqirisAverage

Configuration file psana-amo01509-r0125-acqiris-average.cfg:

Code Block
bgColors#AAFFFF
# 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 =
files         = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\
                /reg/d/psdm/AMO<INSTRUMENT>/amo01509<experiment>/xtc/e8<file-r0125name-s00-c002>.xtc /reg/d/psdm/AMO/amo01509/xtc/e8-r0125-s01-c00.xtc
files = exp=amo01509:run=125:xtc


#skip-events = 100
events      =  5
modules = ImgAlgos.AcqirisArrProducerPnccdImageProducer ImgAlgos.AcqirisAverage

skip-events = 0
events      = 1000


ImgSaveInFile

[ImgAlgos.AcqirisArrProducerPnccdImageProducer]
source        = AmoETOF.0:Acqiris.0
key_in    DetInfo(:pnCCD)
inkey    = 
key_wform     = acqiris_wform
key_wtime
outimgkey     = acqiris_wtime
fname_prefix  = acq
imgpnccd
print_bits    = 31


[ImgAlgos.AcqirisAverageImgSaveInFile]
source               = AmoETOF.0:Acqiris.0DetInfo(:pnCCD)
key_in           = imgpnccd
fname   = acqiris_wform
key_ave     = pnccd-img-ev
saveAll        = acqiris_average
fname_ave_prefixtrue
#eventSave     = acq82
thresholdsprint_bits      = 1

This script saves text files with images like pnccd-img-ev-<run-date-time.nsec>.txt, which can be presented as:
Image Added

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]     = 
is_positive_signal                     = true
do_inverse_selection = false
#skip_events          = 0
#proc_events          = 100
print_bits           = 255

Psana with this script runs over 1000 events and produces file acq-amo01509-r0125-ave-wfs.txt with averaged array of waveforms:

Image Removed

...

Example for module ImgAlgos::AcqirisCalib

See description of parameters in Module ImgAlgos::AcqirisCalib

Configuration file psana-amo01509-r0125-acqiris-calib.cfg:

Code Block
bgColors#AAFFFF
# 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
#calib-dir = /reg/d/psdm/SXR/sxrb5914/calib
files = exp=sxrb5914:run=245
events = 10

modules = ImgAlgos.Tahometer \
          ImgAlgos.PnccdNDArrProducer \
          ImgAlgos.NDArrCalib \
          ImgAlgos.PnccdImageProducer \
          ImgAlgos.NDArrAverage

[ImgAlgos.Tahometer]
dn         = 100
print_bits = 7

[ImgAlgos.PnccdNDArrProducer]
source  = DetInfo(Camp.0:pnCCD.1)
key_in  =
key_out = pnccd-ndarr
outtype = asdata
print_bits = 0

[ImgAlgos.NDArrCalib] 
source = DetInfo(Camp.0:pnCCD.1) 
key_in = pnccd-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 = pnccd-test-mask.txt
#fname_bkgd = pnccd-test-bkgd.txt
masked_value     =    0
threshold_nrms   =  4.0
threshold        =       = acqiris_wform
key_out 100
below_thre_value =             = wf-calibrated
fname_base_line 0
bkgd_ind_min     = acq-amo01509-r0125-ave-wfs.txt
#skip_events    10000
bkgd_ind_max      = 010200
#procbkgd_ind_eventsinc     =     = 1001
print_bits       =    = 2551


[ImgAlgos.ImgSaveInFile:wf_rawPnccdImageProducer]
source         = AmoETOFDetInfo(Camp.0:AcqirispnCCD.0
key1)
inkey         = calibrated
outimgkey     = acqiris_wform
fnamepnccd-img
gap_rows      = 0
gap_cols      = acq-AmoETOF-wform-raw
ftype     16
gap_value     = txt
#ftype          = tiff
#saveAll        = true0
print_bits     = 3
eventSave      = 5


1

[ImgAlgos.ImgSaveInFile:wf_calibNDArrAverage]
source         = AmoETOFDetInfo(Camp.0:AcqirispnCCD.01)
key            = wfpnccd-calibratedimg
fnameavefile          = acq-AmoETOF-wform-calibrated
ftypepnccd-ave
rmsfile          = txtpnccd-rms
#ftype#maskfile     =  pnccd-msk
#hotpixfile   = tiff
#saveAllpnccd-hot
thr_rms_ADU  = 160
thr_min_ADU  = 2
thr_max_ADU  = true10000
print_bits     = 3
eventSave      = 5

In this script the base-line level for all waveforms is 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.txt
  • acq-AmoETOF-wform-calibrated-r0125-e00000005-20091018-182512.194787218.txt

Image Removed Image Removed

 

...

29

Image AddedImage AddedImage Added

Example for module ImgAlgos::CameraImageProducer

See Module ImgAlgos::CameraImageProducer

Example of the psana configuration file:

Code Block
bgColor#F7F7ED
[psana]

...

Example for combination of Acqiris modules

See description of parameters in Modules ImgAlgos::AcqirisArrProducer, AcqirisAverage, and AcqirisCalib

Configuration file psana-amo01509-r0125-acqiris-comb.cfg:

Code Block
# Command to run this script: 
# psana -c psana-amo01509-r0125-acqiris-comb.cfg;

[psana]
files = exp=amo01509:run=125:xtc

modules = ImgAlgos.AcqirisArrProducer ImgAlgos.AcqirisAverage:bl  ImgAlgos.AcqirisCalib ImgAlgos.AcqirisAverage:signal ImgAlgos.Tahometer

#skip-events = 0
events      = 2010


[ImgAlgos.AcqirisArrProducer]
source        = AmoETOF.0:Acqiris.0
key_in        = 
key_wform     = acqiris_wform
key_wtime  
files   = acqiris_wtime
fname_prefix  = acq
print_bits    = 7


[ImgAlgos.AcqirisAverage:bl]
source  /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc
modules             = AmoETOF.0:Acqiris.0
key_in  ImgAlgos.CameraImageProducer ImgAlgos.ImgSaveInFile
events             = acqiris_wform
#key_ave    5

[ImgAlgos.CameraImageProducer] 
source          = DetInfo(:Opal1000)
fname_ave_prefix     = acq-bline
thresholds key_in          = -0.005 -0.005 -0.005 -0.005 -0.005 
is_positive_signal   = no
do_inverse_selection = yes
skip_events
key_out            = 0img
procsubtract_events          offset = 1000true
print_bits           = 31
15

[ImgAlgos.AcqirisCalibImgSaveInFile]
source        = DetInfo(:Opal1000)
key      = AmoETOF.0:Acqiris.0
key_in    = img
fname          = acqiris_wform
key_outimg-from-my-experiment
saveAll       = true
#eventSave      = wf-calibrated
fname_base_line      = acq-bline
skip_events   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
bgColor#F7F7ED
[psana]       = 1001
proc_events          = 1000
print_bits           = 47


[ImgAlgos.AcqirisAverage:signal]
source               = AmoETOF.0:Acqiris.0
key_in               = wf-calibrated
#key_ave     
files         = 
fname_ave_prefix/reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\
                /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-2>.xtc
modules       = acq-signal
thresholds ImgAlgos.PrincetonImageProducer \
               = -0.01 -0.01 -0.01 -0.01 -0.01 
is_positive_signalImgAlgos.ImgSaveInFile
events          = no
do_inverse_selection = no
skip_events3

[ImgAlgos.PrincetonImageProducer] 
source          = 1001
proc_eventsDetInfo(:Princeton)
key_in          = 1000
printkey_bitsout         = img
subtract_offset = 31


[ImgAlgos.Tahometer]true
print_bits      = 7

This scriptworks with psana as follows:

  • for the 1st 1000 events averages waveforms below thresholds 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:

Image Removed Image Removed

  • acq-signal-amo01509-r0125-ave-wfs.txt- contains signal averaged arrays, which can be presented by full scale and zoomed plots:

Image Removed Image Removed

 

 

 

...

Example for module ImgAlgos::ImgAverage

...

31

[ImgAlgos.ImgSaveInFile]
source        = DetInfo(:Princeton)
key           = img
fname         = img-xcs
saveAll       = true
print_bits    = 31

Image Added

 

Anchor
AcqirisArrProducer
AcqirisArrProducer

Example for module ImgAlgos::AcqirisArrProducer

See description of parameters in Module ImgAlgos::AcqirisArrProducer

Example of the psana configuration file psana-amo01509-r0125-acqiris.cfg :

Code Block
bgColor#F7F7ED
[psana]# Command to run this script:
# psana -c psana-amo01509-r0125-acqiris.cfg;
#
# Useful commands:
# psana -n 5 -m EventKeys exp=amo01509:run=125:xtc           > test-acqiris-file.txt;
# psana -n 5 -m psana_examples.DumpAcqiris exp=amo01509:run=125:xtc > test-acqiris-file.txt;    (C++ version)
# psana -n 1 -m psana_examples.dump_acqiris exp=amo01509:run=125:xtc > test-acqiris-file.txt;                       
files   = (python version)

[psana]
#files = /reg/d/psdm/AMO/amo01509/xtc/e8-r0125-s00-c00.xtc /reg/d/psdm/<instrument>AMO/<experiment>amo01509/xtc/<file-name>e8-r0125-s01-c00.xtc
files = exp=amo01509:run=125:xtc

modules = ImgAlgos.CameraImageProducer \
   AcqirisArrProducer ImgAlgos.ImgSaveInFile:wf ImgAlgos.ImgSaveInFile:wt

skip-events = 0
events      = ImgAlgos.ImgAverage
events  = 1000100


[ImgAlgos.CameraImageProducerAcqirisArrProducer] 
source          = DetInfo(:Opal1000)AmoETOF.0:Acqiris.0
key_in          = 
key_outwform     = acqiris_wform
key_wtime     = imgacqiris_wtime
subtractfname_offsetprefix  = trueacq
print_bits      = 111


[ImgAlgos.ImgAverageImgSaveInFile:wf] 
source          = DetInfo(:Opal1000)AmoETOF.0:Acqiris.0
key             = img
avefileacqiris_wform
fname          = img-ave.dat
rmsfileacq-AmoETOF-wform
ftype          = img-rms.dat
print_bitstxt
#ftype       = 31
evts_stage1  = tiff
#saveAll  = 100
evts_stage2     = 100true
gateprint_width1bits     = 200
gate_width23
eventSave      = 20
Code Block
bgColor#F7F7ED
[ImgAlgos.ImgMaskEvaluation] 
source 5


[ImgAlgos.ImgSaveInFile:wt]
source         = DetInfo(:Opal1000)AmoETOF.0:Acqiris.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_satuacqiris_wtime
fname          = acq-AmoETOF-wtime
ftype       = 0
dr  = txt
#ftype           = 1tiff
thre_SoN#saveAll        = 3true
fracprint_noisbits     = 3
eventSave  = 0.05
print_bits      = 63
Note

In this example parameters were chosen in order to get a small number of "noisy" pixel just due to statistics.

  • Typical image:
  • Image Removed
  • Plots for fraction of noisy pixels:
  • Image RemovedImage Removed
  • Plots for fraction of saturated pixels:
  • Image RemovedImage Removed
  • Masks: noisy, saturated, and combined:
  • Image RemovedImage RemovedImage Removed

  • Example for module ImgAlgos::ImgCalib

  • See Module ImgAlgos::ImgCalib
Code Block
bgColor#F7F7ED
[ImgAlgos.CameraImageProducer] 
source          = DetInfo(:Opal1000)
key_in          = 
key_out         = img
subtract_offset = true
print_bits      = 1

[ImgAlgos.ImgCalib] 
source          = DetInfo(:Opal1000)
key_in          = img
key_out         = calibrated
fname_peds      = <pedestal-file-name>
fname_mask      = <mask-file-name>
fname_bkgd      = 
fname_gain      = 
print_bits      = 31

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:

Image Added  Image Added

 

 

Anchor
AcqirisAverage
AcqirisAverage

Example for module ImgAlgos::AcqirisAverage

See description of parameters in Module ImgAlgos::AcqirisAverage

Configuration file psana-amo01509-r0125-acqiris-average.cfg:

Code Block
bgColors#AAFFFF
# 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
Code Block
bgColor#F7F7ED
[psana]
files = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-1>.xtc \
        /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-2>.xtc \
        ...
        /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-N>.xtc
skip-events = 500
events      = 10
modules = cspad_mod.CsPadCalib \
#         ImgAlgos.CSPadBkgdSubtract \
          CSPadPixCoords.CSPadImageProducer \
          ImgAlgos.ImgRadialCorrection \
          ImgAlgos.ImgSaveInFile:1
 

[cspad_mod.CsPadCalib]
inputKey      = 
outputKeykey_wform     = calibrated
doPedestalsacqiris_wform
key_wtime     = yes
doPixelStatusacqiris_wtime
fname_prefix  = no
doCommonModeacq
print_bits    = no3


[ImgAlgos.CSPadBkgdSubtractAcqirisAverage]
source               = DetInfo(CxiDs1AmoETOF.0:CspadAcqiris.0)
inputKeykey_in      = calibrated
outputKey         = bkgdacqiris_subtracted_arrwform
bkgdkey_fnameave     = <the-file-name-with-background-array>
norm_sector   = 0
print_bits    = 0

[CSPadPixCoords.CSPadImageProducer]
calibDir acqiris_average
fname_ave_prefix     = /reg/d/psdm/<instrument>/<experiment>/calib
typeGroupName = CsPad::CalibV1
sourceacq
thresholds           = CxiDs1-0.005 -0:Cspad.0
key  005 -0.005 -0.005 -0.005
is_positive_signal   = no
do_inverse_selection = yes
#skip_events   = calibrated
imgkey        = current_img
#tiltIsApplied = true

[ImgAlgos.ImgRadialCorrection]
source0
#proc_events          = DetInfo(CxiDs1.0:Cspad.0)
inkey100
print_bits         = current_img
outkey        = r_cor_img
xcenter       = 866
ycenter       = 857
rmin          = 100
rmax          = 810
n_phi_bins    = 60
event         = 0
print_bits    = 3

[ImgAlgos.ImgSaveInFile:1]
source        = CxiDs1.0:Cspad.0
key           = r_cor_img
fname         = <file-name-for-image-array>
#saveAll       = true
eventSave     = 8
  • Note: the option of the background subtraction (ImgAlgos.CSPadBkgdSubtract) is commented out in this configuration file . In order to evoke this option, the comment sign (#) should be removed from the list of modules and the key=bkgd_subtracted_arr should be used in CSPadPixCoords.CSPadImageProducer.
  • Calibrated image and spectrum:
  • Image RemovedImage Removed
  • Calibrated and radial-corrected image, spectrum, and subtracted r-phi65 distribution for n_phi_bins=65:
  • Image RemovedImage RemovedImage Removed
  • Calibrated and radial-corrected image, spectrum, and subtracted r-phi12 distribution for n_phi_bins=12:
  • Image RemovedImage RemovedImage Removed

  • Example for module ImgAlgos::ImgPeakFinder

  • See Module ImgAlgos::ImgPeakFinder
  • Configuration file example:
  = 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):

Image Added

Anchor
AcqirisCalib
AcqirisCalib

Example for module ImgAlgos::AcqirisCalib

See description of parameters in Module ImgAlgos::AcqirisCalib

Configuration file psana-amo01509-r0125-acqiris-calib.cfg:

Code Block
bgColors#AAFFFF
# 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
Code Block
bgColor#F7F7ED
[psana]                                                               
files         = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-1>.xtc \
                /reg/d/psdm/<instrument>AMO/<experiment>amo01509/xtc/<filee8-r0125-names01-2>c00.xtc \
files                ...
                /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-N>.= exp=amo01509:run=125:xtc

modules = ImgAlgos.AcqirisArrProducer ImgAlgos.AcqirisCalib    = ImgAlgos.ImgPeakFinder PrintSeparator

#skipImgAlgos.ImgSaveInFile:wf_raw ImgAlgos.ImgSaveInFile:wf_calib

skip-events  = 5000
events        = 12010


[ImgAlgos.ImgPeakFinderAcqirisArrProducer] 
source         = DetInfo(:Opal1000)AmoETOF.0:Acqiris.0
key_in        = 
key_wform     = 
peaksKeyacqiris_wform
key_wtime       =  peaks
threshold_lowacqiris_wtime
fname_prefix  =  20acq
threshold_highprint_bits    =  50
sigma1


[ImgAlgos.AcqirisCalib]
source          =  1.5
smear_radius   =  2
peak_radiusAmoETOF.0:Acqiris.0
key_in    =  3
xmin         = acqiris_wform
key_out =  200
xmax           =  800
yminwf-calibrated
fname_base_line      = acq-amo01509-r0125-ave-wfs.txt
#skip_events     =  100
ymax   = 0
#proc_events       =  900
testEvent = 100
print_bits    =  115
print_bits     =  0
finderIsOn255


[ImgAlgos.ImgSaveInFile:wf_raw]
source      =  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:
  • Image RemovedImage RemovedImage RemovedImage RemovedImage Removed
  • 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
bgColor#F7F7ED
[ImgAlgos.ImgPeakFilter] 
source   = AmoETOF.0:Acqiris.0
key            = DetInfo(:Opal1000)
keyacqiris_wform
fname          = acq-AmoETOF-wform-raw
ftype          = peaks
threshold_peaktxt
#ftype          = 5
threshold_total= 0
n_peaks_mintiff
#saveAll        = 10true
print_bits     = 113
fname  eventSave        = img
selection_mode = SELECTION_ON
Code Block
bgColor#F7F7ED
[psana]5


[ImgAlgos.ImgSaveInFile:wf_calib]
source         = AmoETOF.0:Acqiris.0
key            = wf-calibrated
fname          = acq-AmoETOF-wform-calibrated
ftype          = txt
#ftype          = tiff
#saveAll        = true
filesprint_bits     = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name>.xtc
modules = ImgAlgos.CameraImageProducer \
          ImgAlgos.ImgPeakFinderAB
events3
eventSave      = 10

[ImgAlgos.CameraImageProducer] 
source          = DetInfo(:Opal1000)
key_in          = 
key_out         = img
subtract_offset = true
print_bits      = 1

[ImgAlgos.ImgPeakFinderAB]
source                 = DetInfo(:Opal1000)
key                    = img
key_peaks_out          = peaks
#key_signal_out        = signal-arr
#hot_pix_mask_inp_file = ana-misc-exp/mask.dat
#hot_pix_mask_out_file = noise-mask-out.dat
#frac_noisy_evts_file  = noise-frac-out.dat
evt_file_out           = tmp/img-

rmin                =    10
dr                  =     1
SoNThr_noise        =     3
SoNThr_signal       =     3
frac_noisy_imgs     =   0.9
peak_npix_min       =     3
peak_npix_max       =   100
peak_amp_tot_thr    =     0.
peak_SoN_thr        =     4.
event_npeak_min     =     5
event_npeak_max     =  1000
event_amp_tot_thr   =     0.
nevents_mask_update =     0
nevents_mask_accum  =    50
selection_mode      = SELECTION_ON
out_file_bits       =    15
print_bits          =   513
  • Results:
  • Image RemovedImage RemovedImage Removed

  • 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:
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.txt
  • acq-AmoETOF-wform-calibrated-r0125-e00000005-20091018-182512.194787218.txt

which content is presented on plots:

Image Added Image Added

Anchor
AcqirisCFD
AcqirisCFD

Example for module ImgAlgos::AcqirisCFD

See description of parameters in Module ImgAlgos::AcqirisCFD

Configuration file psana_cfd.cfg:

Code Block
bgColors#AAFFFF
# 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
ImgAlgos::AcqirisCombinedExample
ImgAlgos::AcqirisCombinedExample

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:

Image Added Image Added

  • acq-signal-amo01509-r0125-ave-wfs.txt- contains signal averaged arrays, which can be presented by full scale and zoomed plots:

Image Added Image Added

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 NDArrAverage module in combination with CSPadNDArrProducer (or any other device NDArrProducer) can be used for evaluation of averaged pedestals or background using dedicated runs.
    Typical configuration file may looks like this:

    No Format
    # Run this script:
# psana -c psana-meca1113-r0045-cspad-cspad-dark-hotpix.cfg

[psana]
files = exp=meca1113:run=45
events = 400
#skip-events = 0

modules = CSPadPixCoords.CSPadNDArrProducer \
          ImgAlgos.NDArrAverage \
          ImgAlgos.Tahometer


[CSPadPixCoords.CSPadNDArrProducer]
source       = MecTargetChamber.0:Cspad.0
inkey        = 
outkey       = cspad_ndarr
outtype      = int16
is_fullsize  = yes
print_bits   = 3


[ImgAlgos.NDArrAverage]
source       = MecTargetChamber.0:Cspad.0
key          = cspad_ndarr
avefile      = cspad.0-ave
rmsfile      = cspad.0-rms
maskfile     = cspad.0-msk
hotpixfile   = cspad.0-hot
thr_rms_ADU  = 10
thr_min_ADU  = 4
thr_max_ADU  = 10000
print_bits   = 29
#evts_stage1  = 100
#gate_width1  = 500.
#evts_stage2  = 200
#gate_width2  = 100.


[ImgAlgos.Tahometer]
dn         = 100
print_bits = 7
  • Module ImgAlgos.Tahometer is not required in this configuration file and is added for convenience to print timing statistics for this job.
  • Evaluation of average intensity in 2 or 3 stages using gate-based algorithms excludes out-layers in intensity spectra and makes average more stable and reliable. However, the gate width is not an universal parameter. In order to set this parameter one has to look at spectrum of averaged intensities for particular device.  The same is valid for evaluation of hot/bad pixel masks. One has to plot spectra of averaged intensity and rms values. Averaged intensity and rms spectra for exp=meca1113:run=45 are shown on plots, respectively:

Image AddedImage Added

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

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
Image AddedImage Added

Case 2: images with subtracted pedestals and applied status mask

do_peds = yes; 60-70 ms/event
do_stat = yes

Image AddedImage Added

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.

Image AddedImage Added

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
Image AddedImage Added

doPedestals = yes
doPixelStatus = yes
doCommonMode = yes; 150-160ms

Image AddedImage Added

Conclusion:

  • Results of ImgAlgos.NDArrCalib well reproduce cspad_mod.CsPadCalib

  • Common mode correction shrinks the width of averaged intensities from 0.60 to 0.54, and rms from 3.78 to 3.27.
  • Algorithm is quite time expensive, it takes 30-40ms/event.

 

Example of ImgAlgos::NDArrCalib for Fccd960

  • Calibration

To calibrate fccd960 for dark runs use command

calibman

For test purpose a couple of dark runs were processed and constants were deployed:

Code Block
Content of: /reg/d/psdm/XCS/xcsd7814/calib for detector: Fccd960
    Camera::CalibV1    
        XcsEndstation.0:Fccd960.0    
            pixel_rms    
                12-13.data      file is not used
                78-81.data      run range 0078 - 0081
            pedestals    
                12-13.data      file is not used
                78-81.data      run range 0078 - 0081
            pixel_status    
                12-13.data      file is not used
                78-81.data      run range 0078 - 0081

 

  • Access data in psana

Example of the configuration file for psana psana-xcsd7814-r0079-fccd960-aver.cfg can be processed by the command

psana -c psana-xcsd7814-r0079-fccd960-aver.cfg

Two averaged images are saved in the text files for exp=xcsd7814:run=79 for raw and calibrated (subtracted dark level) data.

Gain bit coded gain factor 8 is applied automatically.

Image AddedImage Added

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 \
           cspad_mod.CsPadCalib \
           CSPadPixCoords.CSPadNDArrProducer

[ImgAlgos.PixCoordsProducer]
source     = CxiDs1.0:Cspad.0
print_bits = 0

[cspad_mod.CsPadCalib]
source          = CxiDs1.0:Cspad.0
inputKey        = 
outputKey       = calibrated
doPedestals     = yes
doPixelStatus   = no
doCommonMode    = no

[CSPadPixCoords.CSPadNDArrProducer]
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 ImgAverage module can be used for evaluation of averaged pedestals or background using dedicated runs. Typical configuration file may looks like this:
Code Block
bgColor#F7F7ED
[psana]                                                               
files   = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name>.xtc
modules = ImgAlgos.CameraImageProducer \
          ImgAlgos.ImgAverage
events  = 1000

[ImgAlgos.CameraImageProducer] 
source          = DetInfo(:Opal1000)
key_in          = 
key_out         = img
subtract_offset = true
print_bits      = 1

[ImgAlgos.ImgAverage] 
source          = DetInfo(:Opal1000)
key             = img
avefile         = img-ave.dat
rmsfile         = img-rms.dat
print_bits      = 31
evts_stage1     = 100
evts_stage2     = 100
gate_width1     = 200
gate_width2     = 20

Example for module ImgAlgos::ImgMaskEvaluation

Code Block
bgColor#F7F7ED
[ImgAlgos.ImgMaskEvaluation] 
source          = DetInfo(:Opal1000)
key             = img
file_mask_satu	= img-mask-satu.dat
file_mask_nois	= img-mask-nois.dat
file_mask_comb	= img-mask-comb.dat
file_frac_satu	= img-frac-satu.dat
file_frac_nois	= img-frac-nois.dat
thre_satu   	= 400   
frac_satu       = 0
dr              = 1
thre_SoN        = 3
frac_nois       = 0.05
print_bits      = 63
Note

In this example parameters were chosen in order to get a small number of "noisy" pixel just due to statistics.

Typical image:

Image Added

Plots for fraction of noisy pixels:

Image AddedImage Added

Plots for fraction of saturated pixels:

Image AddedImage Added

Masks: noisy, saturated, and combined:

  Image Added Image Added Image Added

Example for module ImgAlgos::ImgCalib

See Module ImgAlgos::ImgCalib

Code Block
bgColor#F7F7ED
[ImgAlgos.CameraImageProducer] 
source          = DetInfo(:Opal1000)
key_in          = 
key_out         = img
subtract_offset = true
print_bits      = 1

[ImgAlgos.ImgCalib] 
source          = DetInfo(:Opal1000)
key_in          = img
key_out         = calibrated
fname_peds      = <pedestal-file-name>
fname_mask      = <mask-file-name>
fname_bkgd      = 
fname_gain      = 
print_bits      = 31

Example of the mask file and resulting image:
Image AddedImage Added

Example for module ImgAlgos::ImgRadialCorrection

See Module ImgAlgos::ImgRadialCorrection

Code Block
bgColor#F7F7ED
[psana]
files = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-1>.xtc \
        /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-2>.xtc \
        ...
        /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-N>.xtc
skip-events = 500
events      = 10
modules = cspad_mod.CsPadCalib \
#         ImgAlgos.CSPadBkgdSubtract \
          CSPadPixCoords.CSPadImageProducer \
          ImgAlgos.ImgRadialCorrection \
          ImgAlgos.ImgSaveInFile:1
 

[cspad_mod.CsPadCalib]
inputKey      = 
outputKey     = calibrated
doPedestals   = yes
doPixelStatus = no
doCommonMode  = no

[ImgAlgos.CSPadBkgdSubtract]
source        = DetInfo(CxiDs1.0:Cspad.0)
inputKey      = calibrated
outputKey     = bkgd_subtracted_arr
bkgd_fname    = <the-file-name-with-background-array>
norm_sector   = 0
print_bits    = 0

[CSPadPixCoords.CSPadImageProducer]
calibDir      = /reg/d/psdm/<instrument>/<experiment>/calib
typeGroupName = CsPad::CalibV1
source        = CxiDs1.0:Cspad.0
key           = calibrated
imgkey        = current_img
#tiltIsApplied = true

[ImgAlgos.ImgRadialCorrection]
source        = DetInfo(CxiDs1.0:Cspad.0)
inkey         = current_img
outkey        = r_cor_img
xcenter       = 866
ycenter       = 857
rmin          = 100
rmax          = 810
n_phi_bins    = 60
event         = 0
print_bits    = 3

[ImgAlgos.ImgSaveInFile:1]
source        = CxiDs1.0:Cspad.0
key           = r_cor_img
fname         = <file-name-for-image-array>
#saveAll       = true
eventSave     = 8

Note: the option of the background subtraction (ImgAlgos.CSPadBkgdSubtract) is commented out in this configuration file . In order to evoke this option, the comment sign (#) should be removed from the list of modules and the key=bkgd_subtracted_arr should be used in CSPadPixCoords.CSPadImageProducer.

Calibrated image and spectrum:
Image AddedImage Added

Calibrated and radial-corrected image, spectrum, and subtracted r-phi65 distribution for n_phi_bins=65:

Image AddedImage AddedImage Added

Calibrated and radial-corrected image, spectrum, and subtracted r-phi12 distribution for n_phi_bins=12:
Image AddedImage AddedImage Added

Example for module ImgAlgos::ImgPeakFinder

See Module ImgAlgos::ImgPeakFinder

Configuration file example:

Code Block
bgColor#F7F7ED
[psana]                                                               
files         = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-1>.xtc \
                /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-2>.xtc \
                ...
                /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-N>.xtc

modules       = ImgAlgos.ImgPeakFinder PrintSeparator

#skip-events  = 500
events        = 120

[ImgAlgos.ImgPeakFinder] 
source         = DetInfo(:Opal1000)
key            = 
peaksKey       =  peaks
threshold_low  =  20
threshold_high =  50
sigma          =  1.5
smear_radius   =  2
peak_radius    =  3
xmin           =  200
xmax           =  800
ymin           =  100
ymax           =  900
testEvent      =  115
print_bits     =  0
finderIsOn     =  true

This algorithm consumes ~15 ms/event on psana0101 for full Opal1000 (1024x1024) camera image.

Smearing algorithm use a "safety margin" which is currently set to 10 pixels (offset from each boarder of the full image size).

Image on different stages of this algorithm:

Image AddedImage AddedImage AddedImage AddedImage Added

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
bgColor#F7F7ED
[ImgAlgos.ImgPeakFilter] 
source         = DetInfo(:Opal1000)
key            = peaks
threshold_peak = 5
threshold_total= 0
n_peaks_min    = 10
print_bits     = 11
fname          = img
selection_mode = SELECTION_ON

Example for module ImgAlgos::ImgPeakFinderAB

See Module ImgAlgos::ImgPeakFinderAB

Configuration file example:

Code Block
bgColor#F7F7ED
[psana]                                                               
files   = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name>.xtc
modules = ImgAlgos.CameraImageProducer \
          ImgAlgos.ImgPeakFinderAB
events  = 10

[ImgAlgos.CameraImageProducer] 
source          = DetInfo(:Opal1000)
key_in          = 
key_out         = img
subtract_offset = true
print_bits      = 1

[ImgAlgos.ImgPeakFinderAB]
source                 = DetInfo(:Opal1000)
key                    = img
key_peaks_out          = peaks
#key_signal_out        = signal-arr
#hot_pix_mask_inp_file = ana-misc-exp/mask.dat
#hot_pix_mask_out_file = noise-mask-out.dat
#frac_noisy_evts_file  = noise-frac-out.dat
evt_file_out           = tmp/img-

rmin                =    10
dr                  =     1
SoNThr_noise        =     3
SoNThr_signal       =     3
frac_noisy_imgs     =   0.9
peak_npix_min       =     3
peak_npix_max       =   100
peak_amp_tot_thr    =     0.
peak_SoN_thr        =     4.
event_npeak_min     =     5
event_npeak_max     =  1000
event_amp_tot_thr   =     0.
nevents_mask_update =     0
nevents_mask_accum  =    50
selection_mode      = SELECTION_ON
out_file_bits       =    15
print_bits          =   513

Results:
Image AddedImage AddedImage Added

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
bgColor#F7F7ED
# File: psana-amo74213-r0093-opal-img-average.cfg

[psana]
#files = /reg/d/psdm/AMO/amo74213/xtc/e269-r0093-s05-c00.xtc
files = exp=amo74213:run=93:xtc

modules = ImgAlgos.CameraImageProducer \
          ImgAlgos.ImgAverage
skip-events = 0
events      = 1000

[ImgAlgos.CameraImageProducer] 
source          = DetInfo(:Opal1000)
key_in          = 
key_out         = img
subtract_offset = true
print_bits      = 1

[ImgAlgos.ImgAverage] 
source          = DetInfo(:Opal1000)
key             = img
avefile         = img-ave-for-peds
rmsfile         = img-rms-for-thre
evts_stage1     = 100
evts_stage2     = 100
gate_width1     = 50
gate_width2     = 10
print_bits      = 31

Run psana using command:

Code Block
bgColor#F7F7ED
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:
Image AddedImage Added

img-rms-for-thre-r0093.dat - may be used multiplied by number of rms as a threshold:
Image AddedImage Added

The file with accumulated pixel hits can be obtained using configuration file:

Code Block
bgColor#F7F7ED
# File: psana-amo74213-r0093-opal-img-hit-finder.cfg

[psana]
#files = /reg/d/psdm/AMO/amo74213/xtc/e269-r0093-s05-c00.xtc
files = exp=amo74213:run=93:xtc

modules = ImgAlgos.CameraImageProducer \
          ImgAlgos.ImgHitFinder \
          ImgAlgos.ImgAverage
skip-events = 0
events      = 1000

[ImgAlgos.CameraImageProducer] 
source          = DetInfo(:Opal1000)
key_in          = 
key_out         = img
subtract_offset = true
print_bits      = 1

[ImgAlgos.ImgHitFinder] 
source           = DetInfo(:Opal1000)
key_in           = img
key_out          = img_hits
fname_peds       = img-ave-for-peds-r0093.dat
fname_mask       = 
fname_gain       = 
fname_thre       = img-rms-for-thre-r0093.dat
masked_value     = 0
thre_mode        = 3
#thre_mode        = 2
thre_param       = 5
thre_below_value = 0
thre_above_value = 1
win_row_min      = 10
win_row_max      = 1000
win_col_min      = 10
win_col_max      = 1000
print_bits       = 39

[ImgAlgos.ImgAverage] 
source          = DetInfo(:Opal1000)
key             = img_hits
sumfile         = img-sum-result
Code Block
bgColor#F7F7ED
# File: psana-amo74213-r0093-opal-img-average.cfg

[psana]
#files = /reg/d/psdm/AMO/amo74213/xtc/e269-r0093-s05-c00.xtc
files = exp=amo74213:run=93:xtc

modules = ImgAlgos.CameraImageProducer \
          ImgAlgos.ImgAverage
skip-events = 0
events      = 1000

[ImgAlgos.CameraImageProducer] 
source          = DetInfo(:Opal1000)
key_in          = 
key_out         = img
subtract_offset = true
print_bits      = 1

[ImgAlgos.ImgAverage] 
source          = DetInfo(:Opal1000)
key             = img
avefile         = img-ave-for-peds
rmsfile         = img-rms-for-thre
evts_stage1     = 100
evts_stage2     = 100
gate_width1     = 50
gate_width2     = 10
print_bits      = 3125

...

and run it by the command:

Code Block
bgColor#F7F7ED
psana -c psana-amo74213-r0093-opal-img-averagehit-finder.cfg

...

Which creates the file: img-sum-result-r0093.dat

...

for thre_mode = 2 and thre_mode = 3, respectively:
Image Added  Image Added

Example for module ImgAlgos::ImgSpectra

See Module ImgAlgos::ImgSpectra

Configuration file for psana

...

:

Code Block
bgColor#F7F7ED#F7F7ED
[psana]                                                               
files# File: psana-amo74213-r0093-opal-img-hit-finder.cfg

[psana]
#files = /reg/d/psdm/AMO<instrument>/amo74213<experiment>/xtc/e269-r0093-s05-c00<file-name>.xtc
files = exp=amo74213:run=93:xtc

modules = ImgAlgos.CameraImageProducer \


modules       =  ImgAlgos.CameraImageProducer \
                 ImgAlgos.ImgSpectra \
            ImgAlgos.ImgHitFinder \
     ImgAlgos.ImgSaveInFile:2
#                ImgAlgos.ImgSaveInFile
#                ImgAlgos.ImgAverage
skip-events = 0
eventspsana_examples.DumpOpal1k \

events          = 1000100

[ImgAlgos.CameraImageProducer] 
source          = DetInfo(:Opal1000)
key_in          = 
key_out         = img
subtract_offset = true
print_bits      = 1

[ImgAlgos.ImgHitFinderImgSpectra] 
source           = DetInfo(:Opal1000)
key_in           = img
key_out          = img_hits
fname_pedsspectra
sig_band_rowc   = 512.
ref_band_rowc   = img-ave-for-peds-r0093.dat
fname_mask552.
sig_band_tilt   =    = 
fname_gain0.
ref_band_tilt   =    = 
fname_thre0.
sig_band_width  =     = img-rms-for-thre-r0093.dat
masked_value     = 0
thre_mode10 
ref_band_width  =  10 
print_bits      =  = 3
#thre_mode3

[ImgAlgos.ImgSpectraProc] 
source          = 2
thre_paramDetInfo(:Opal1000)
key_in       = 5
thre_below_value = 0
thre_above_value = 1spectra
winprint_row_minbits      = 10
win_row_max 15

[ImgAlgos.ImgSaveInFile:2]
source        = 1000
win_col_minDetInfo(:Opal1000)
key           = 10
win_col_maxspectra
fname         = 1000
print_bitsspec-xppi0412
saveAll       = 39true

[ImgAlgos.ImgAverageImgSaveInFile] 
source          = DetInfo(:Opal1000)
key             = img_hits
sumfilefname         = img-sum-result
print_bitsxppi0412
saveAll       = 25true
  • and run it by the command:
Code Block
bgColor#F7F7ED
psana -c psana-amo74213-r0093-opal-img-hit-finder.cfg

...

This script can be used in order to produce text files with image and spectral array:
Image AddedImage AddedImage Added

or graphics for several images:
Image AddedImage AddedImage Added

...

Example for module ImgAlgos::

...

ImgSpectraProc

See Module ImgAlgos::

...

ImgSpectraProc

Configuration file for psana:

Code Block
bgColor#F7F7ED
[psana]ImgAlgos.ImgSpectraProc] 
source          = DetInfo(:Opal1000)
key_in          = spectra
print_bits      =  15

For each event it prints something similar to:

Code Block
bgColor#F7F7ED
[info:ImgAlgos.ImgSpectraProc] Spectral array shape =3, 1024
[info:ImgAlgos.ImgSpectraProc] Image spectra for run=0060 Evt=000100
Column:       0     100     200     300     400     500     600     700  
files = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name>.xtc

modules  800     900 =  ImgAlgos.CameraImageProducer \1000
Signal:    1211    4062   11150   17070   16406  ImgAlgos.ImgSpectra \
12949    7991    5168    3968    3542 ImgAlgos.ImgSaveInFile:2
#   3811
Refer.:     933    3485   10425 ImgAlgos.ImgSaveInFile
#  17128   17791   13522    8315    psana_examples.DumpOpal1k \

events5000    3390    2967   = 1003193

[ImgAlgosDiff.CameraImageProducer] 
source:   0.259   0.153   0.067 = DetInfo(:Opal1000)
key_in          = 
key_out         = img
subtract_offset = true
print_bits      = 1

[ImgAlgos.ImgSpectra]  -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
bgColor#F7F7ED
modules = ... ImgAlgos.ImgSaveInFile:1 ...

[ImgAlgos.ImgSaveInFile:1]
source          = DetInfo(:Opal1000)
key_in   #       = img
key_out         = spectra
sig_band_rowc   = 512.
ref_band_rowc   = 552.
sig_band_tilt   =   0.
ref_band_tilt   =   0.
sig_band_width  =  10 
ref_band_width  =  10 
print_bitsor CxiDs1.0:Cspad.0
key            = img
fname          =  3

[ImgAlgos.ImgSpectraProc] 
sourcemy-img
#ftype           = DetInfo(:Opal1000)
key_intxt
#ftype          = spectra
print_bits      =  15

[ImgAlgos.ImgSaveInFile:2]
sourcebin
#ftype          = DetInfo(:Opal1000)
keypng
ftype           = spectratiff
fname #eventSave        = spec-xppi04125
saveAll        = true

See Module ImgAlgos::ImgSaveInFile

Example for module ImgPeakFinder and ImgPeakFilter for CSPad

Module ImgAlgos::ImgPeakFinder works on image. In order to apply this algorithm to CSPad the image should be produced. In next example the image is produced using consequtive modules cspad_mod.CsPadCalib, ImgAlgos.CSPadMaskApply, and CSPadPixCoords.CSPadImageProducer:

Code Block
bgColor#F7F7ED
[psana]
files   = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-1>.xtc \

[ImgAlgos.ImgSaveInFile]
source        = DetInfo(:Opal1000)
key           = img
fname...
         = img-xppi0412
saveAll /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-N>.xtc

events       = true
  • This script can be used in order to produce text files with image and spectral array:
  • Image Removed Image Removed Image Removed
  • or graphics for several images:
  • Image RemovedImage RemovedImage Removed

  • Example for module ImgAlgos::ImgSpectraProc

  • See Module ImgAlgos::ImgSpectraProc
  • Configuration file for psana:
Code Block
bgColor#F7F7ED
[ImgAlgos.ImgSpectraProc] 
source          = DetInfo(:Opal1000)
key_in 1000
experiment  = cxii0212
calib-dir   = ana-cxii0212/calib

modules = cspad_mod.CsPadCalib \
          =ImgAlgos.CSPadMaskApply spectra
print_bits\
         = CSPadPixCoords.CSPadImageProducer 15
  • For each event it prints something similar to:
Code Block
bgColor#F7F7ED
[info:ImgAlgos.ImgSpectraProc] Spectral array shape =3, 1024
[info:ImgAlgos.ImgSpectraProc] Image spectra for run=0060 Evt=000100
Column:\
          ImgAlgos.ImgPeakFinder \
       0   ImgAlgos.ImgPeakFilter \
 100     200     300ImgAlgos.ImgSaveInFile:1

[cspad_mod.CsPadCalib]
inputKey      400= 
outputKey    500 = calibrated
doPedestals   600= yes
doPixelStatus = no
doCommonMode  700 = yes

[ImgAlgos.CSPadMaskApply]
source    800     900    1000
Signal:= DetInfo(CxiDs1.0:Cspad.0)
inkey    1211    4062   11150  = 17070calibrated
outkey   16406   12949    7991  = masked_arr
mask_fname 5168    3968    3542= <your-local-directory>/<mask-file-name>.dat
masked_amp    3811
Refer.:    = 933 0
print_bits   3485   10425  = 17128 5
mask_control_bits  17791 = 15

[CSPadPixCoords.CSPadImageProducer]
calibDir  13522    8315 = /reg/d/psdm/<instrument>/<experiment>/calib
typeGroupName  5000 = CsPad::CalibV1
source   3390    2967  =  3193
Diff. :   0.259CxiDs1.0:Cspad.0
key   0.153   0.067  -0.003  -0.081  -0.043  -0.040= masked_arr
imgkey    0.033   0.157   0.177= img
print_bits   0.176
[info:ImgAlgos.ImgSpectraProc] Run=0060 Evt=000100 Time=20120507-125420.982421325 done...

  • Example for module ImgAlgos::ImgSaveInFile

Code Block
bgColor#F7F7ED
modules = ... ImgAlgos.ImgSaveInFile:1 ... 0
#tiltIsApplied  = true

[ImgAlgos.ImgSaveInFile:1ImgPeakFinder] 
source         = DetInfo(:Opal1000)   # or= DetInfo(CxiDs1.0:Cspad.0)
key            = img
fnamepeaksKey       = peaks
threshold_low  = my-img
#ftype 2
threshold_high = 5
sigma          = txt
#ftype1.5
smear_radius      = 5
peak_radius    = bin7
#ftypexmin           = png20
ftypexmax           = tiff1700
#eventSaveymin     = 5
saveAll        = true
  • See Module ImgAlgos::ImgSaveInFile

  • Example for module ImgPeakFinder and ImgPeakFilter for CSPad

  • Module ImgAlgos::ImgPeakFinder works on image. In order to apply this algorithm to CSPad the image should be produced. In next example the image is produced using consequtive modules cspad_mod.CsPadCalib, ImgAlgos.CSPadMaskApply, and CSPadPixCoords.CSPadImageProducer:
Code Block
bgColor#F7F7ED
[psana]
files   = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-1>.xtc \
    20
ymax           = 1700
#testEvent      ...
= 5
print_bits     = 3
#finderIsOn      /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-N>.xtc

events = true

[ImgAlgos.ImgPeakFilter] 
source     =  1000
experiment  = cxii0212
calib-dirDetInfo(CxiDs1.0:Cspad.0)
key            = ana-cxii0212/calib

modulespeaks
threshold_peak = cspad_mod.CsPadCalib \
5
threshold_total= 0
n_peaks_min    = 10
print_bits     ImgAlgos.CSPadMaskApply= \11
fname          CSPadPixCoords.CSPadImageProducer \
 = cspad-img
selection_mode = SELECTION_ON

[ImgAlgos.ImgSaveInFile:1]
source         = ImgAlgos.ImgPeakFinder \
CxiDs1.0:Cspad.0
key            ImgAlgos.ImgPeakFilter= \img
fname          ImgAlgos.ImgSaveInFile:1

[cspad_mod.CsPadCalib]
inputKey= cspad-img
#eventSave      = 1
outputKeysaveAll     = calibrated
doPedestals   = yes
doPixelStatus = no
doCommonMode  = yestrue

Example for module ImgAlgos::CSPadArrAverage

See Module ImgAlgos::CSPadArrAverage

Configuration file example for evaluation of pedestals:

Code Block
bgColor#F7F7ED
[psana]
modules = ImgAlgos.CSPadArrAverage
files   = <path-to-the-dark-run-file>.xtc

[ImgAlgos.CSPadMaskApplyCSPadArrAverage]
source            = DetInfo(CxiDs1.0:Cspad.0)
inkey        key     =
avefile = cspad-pedestals-ave.dat
rmsfile = cspad-pedestals-rms.dat
print_bits  = 15
evts_stage1 = 100
evts_stage2 = 100
gate_width1 = 100
gate_width2 =  10

Configuration file example for evaluation of background:

Code Block
bgColor#F7F7ED
[psana]
files calibrated
outkey            = masked_arr
mask_fname        = <your-local-directory>/<mask-file-name>.dat
masked_amp        =  0
print_bits        =  5
mask_control_bits = 15

[CSPadPixCoords.CSPadImageProducer]
calibDir       = /reg/d/psdm/<instrument>/<experiment>/calib
typeGroupName  = CsPad::CalibV1
source  <path-to-the-background-run-file>.xtc
modules     = cspad_mod.CsPadCalib ImgAlgos.CSPadArrAverage
skip-events = 500
events       = CxiDs1.0:Cspad.0
key1000000

[cspad_mod.CsPadCalib]
inputKey      = 
outputKey     = masked_arr
imgkey      calibrated
doPedestals   = img
print_bits    yes
doPixelStatus =  0no
#tiltIsApplieddoCommonMode  = trueno

[ImgAlgos.ImgPeakFinderCSPadArrAverage] 
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:
Image AddedImage Added

Example for module ImgAlgos::CSPadBkgdSubtract

See Module ImgAlgos::CSPadBkgdSubtract

Code Block
bgColor#F7F7ED
[psana]
files = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-1>.xtc \
img
peaksKey       = peaks
threshold_low  = 2
threshold_high = 5
sigma          = 1.5
smear_radius   = 5
peak_radius    = 7
xmin         /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-2>.xtc \
 = 20
xmax      ...
     = 1700
ymin      /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-N>.xtc
skip-events = 500
events       = 2010
ymaxmodules     = cspad_mod.CsPadCalib ImgAlgos.CSPadBkgdSubtract

[cspad_mod.CsPadCalib]
inputKey      = 1700
#testEventoutputKey      = 5calibrated
print_bitsdoPedestals   = yes
doPixelStatus = 3
#finderIsOn   no
doCommonMode  = trueno


[ImgAlgos.ImgPeakFilterCSPadBkgdSubtract] 
source         = DetInfo(CxiDs1.0:Cspad.0)
key)
inputKey      = calibrated
outputKey     = bkgd_subtracted
bkgd_fname    = <the-file-name-with-background-array>
norm_sector        = 0
print_bits    = peaks
threshold_peak = 5
threshold_total= 0
n_peaks_min    = 10
print_bits     = 11
fname          = cspad-img
selection_mode = SELECTION_ON

[ImgAlgos.ImgSaveInFile: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:
Image AddedImage Added
Image AddedImage Added

Other event with better subtracted background:
Image AddedImage Added

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
bgColor#F7F7ED
./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:
Image AddedImage AddedImage AddedImage Added
The best results in filtering can be achieved in combination of modiles:

Code Block
bgColor#F7F7ED
modules = cspad_mod.CsPadCalib \
1]
source         = CxiDs1.0:Cspad.0
key   ImgAlgos.CSPadBkgdSubtract \
          =ImgAlgos.CSPadMaskApply img\
fname          = cspad-img
#eventSave...
[cspad_mod.CsPadCalib]
inputKey      = 1
saveAlloutputKey     = calibrated_arr
doPedestals   = true
Code Block
bgColor#F7F7ED
[psana]
modules = ImgAlgos.CSPadArrAverage
files   = <path-to-the-dark-run-file>.xtcyes
doPixelStatus = no
doCommonMode  = no

[ImgAlgos.CSPadArrAverageCSPadBkgdSubtract]
source        = DetInfo(CxiDs1.0:Cspad.0)
keyinputKey      =
avefile calibrated_arr
outputKey     = cspad-pedestals-ave.dat
rmsfilebkgd_subtracted_arr
bkgd_fname    = ana-cxi49012/cspad-pedestals-rmscxi49012-r0025-background-ave.dat
print_bits  = 15
evts_stage1 = 100
evts_stage2norm_sector   = 1000
gateprint_width1bits  = 100
gate_width2 =  10
  • Configuration file example for evaluation of background:
Code Block
bgColor#F7F7ED
[psana]
files0

[ImgAlgos.CSPadMaskApply]
source       = <path-to-the-background-run-file>.xtc
modules     = cspad_mod.CsPadCalib ImgAlgos.CSPadArrAverage
skip-events = 500
eventsDetInfo(CxiDs1.0:Cspad.0)
inkey             = 1000000

[cspad_mod.CsPadCalib]
inputKeybkgd_subtracted_arr
outkey      = 
outputKey     = calibrated
doPedestalsmasked_arr
mask_fname   = yes
doPixelStatus = no
doCommonMode  = no

[ImgAlgos.CSPadArrAverage]
sourceana-cxi49012/cspad-cxi49012-r0025-mask-40.dat
masked_amp        = DetInfo(CxiDs1.0:Cspad.0)
key 0
print_bits        = calibrated
avefile 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:
Image AddedImage AddedImage Added
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:
Image Added
where red regions/lines of pixels of amplitude=8 are masked.

...

Example for module ImgAlgos::

...

CSPadArrNoise

See Module ImgAlgos::

...

CSPadArrNoise

Code Block
bgColor#F7F7ED
[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/<instrument>cxi/<experiment>cxi49012/xtc/<filee158-r0020-names03-1>c00.xtc \
          /reg/d/psdm/<instrument>cxi/<experiment>cxi49012/xtc/<filee158-r0020-names04-2>c00.xtc \
        ...
        /reg/d/psdm/<instrument>cxi/<experiment>cxi49012/xtc/<filee158-r0020-names05-N>c00.xtc
skip
#skip-events = 5001000
events      = 10
modules     = cspad_mod.CsPadCalib ImgAlgos.CSPadBkgdSubtract

[cspad_mod.CsPadCalib]
inputKey      = 
outputKey     = calibrated
doPedestals   = yes
doPixelStatus = no
doCommonMode  = no


[ImgAlgos.CSPadBkgdSubtractCSPadArrNoise]
source          = DetInfo(CxiDs1.0:Cspad.0)
inputKeykey             = calibrated
outputKeystatusfile      = bkgd_subtracted
bkgd_fnameana-cxi49012/cspad-cxi49012-r0020-noise-status.dat
maskfile        = <theana-filecxi49012/cspad-namecxi49012-withr0200-background-array>
norm_sector   = 0
print_bitsnoise-mask.dat
print_bits      = 255
rmin            = 3
dr              = 1
SoNThr          = 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:
  • Image RemovedImage Removed
  • Image RemovedImage Removed
  • Other event with better subtracted background:
  • Image RemovedImage Removed

  • 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
bgColor#F7F7ED
./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:
  • Image RemovedImage RemovedImage RemovedImage Removed
  • The best results in filtering can be achieved in combination of modiles:
frac_noisy_imgs = 0.15

Index map in median algorithm for rmin=3, dr=1:

Code Block
bgColor#F7F7ED
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):

Image AddedImage AddedImage Added

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:

Image AddedImage Added

Example for Module ImgAlgos::CSPadArrPeakFinder

See Module ImgAlgos::CSPadArrPeakFinder

Code Block
bgColor#F7F7ED
[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 \
Code Block
bgColor#F7F7ED
modules = cspad_mod.CsPadCalib \
          ImgAlgos.CSPadBkgdSubtract \
          ImgAlgos.CSPadMaskApply \
          ...
[cspad_mod.CsPadCalib]
inputKey      = 
outputKey     = calibrated_arr
doPedestals   = yes
doPixelStatus = no
doCommonMode  = no

[ImgAlgos.CSPadBkgdSubtract]
source        = DetInfo(CxiDs1.0:Cspad.0)
inputKey      = calibrated_arr
outputKey     = bkgd_subtracted_arr
bkgd_fname    = ana-cxi49012/cspad-cxi49012-r0025-background-ave.dat
norm_sector   = 0
print_bits    = 0

[ImgAlgos.CSPadMaskApply]
source            = DetInfo(CxiDs1.0:Cspad.0)
inkey             = bkgd_subtracted_arr
outkey            = masked_arr
mask_fname        = ana-cxi49012/cspad-cxi49012-r0025-mask-40.dat
masked_amp        = ImgAlgos.CSPadMaskApply 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:
  • Image RemovedImage RemovedImage Removed
  • 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:
  • Image Removed
  • where red regions/lines of pixels of amplitude=8 are masked.

  • Example for module ImgAlgos::CSPadArrNoise

  • See Module ImgAlgos::CSPadArrNoise
Code Block
bgColor#F7F7ED
[psana]
modules = cspad_mod.CsPadCalib ImgAlgos.CSPadArrNoise

files   = /reg/d/psdm/cxi/cxi49012/xtc/e158-r0020-s00-c00.xtc \
  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        =  /reg/d/psdm/cxi/cxi49012/xtc/e158-r0020-s01-c00.xtc \
ana-cxi49012/cspad-cxi49012-r0150-mask-rects.dat
masked_amp        =  8
print_bits          /reg/d/psdm/cxi/cxi49012/xtc/e158-r0020-s02-c00.xtc \
=  1
mask_control_bits = 15

[ImgAlgos.CSPadArrPeakFinder]
source             /reg/d/psdm/cxi/cxi49012/xtc/e158-r0020-s03-c00.xtc \
= DetInfo(CxiDs1.0:Cspad.0)
key             /reg/d/psdm/cxi/cxi49012/xtc/e158-r0020-s04-c00.xtc \
 = masked_arr
key_peaks_out     = peaks

hot_pix_mask_inp_file = /reg/d/psdm/cxi/cxi49012/xtc/e158-r0020-s05-c00.xtc

#skip-events = 1000
events      = 10

[cspad_mod.CsPadCalib]
inputKeyana-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      = 
outputKeytmp/cspad-ev-

rmin     = calibrated
doPedestals   = yes
doPixelStatus = no
doCommonMode  = no

[ImgAlgos.CSPadArrNoise]
source    3
dr      = DetInfo(CxiDs1.0:Cspad.0)
key         =    = calibrated1
statusfileSoNThr       = ana-cxi49012/cspad-cxi49012-r0020-noise-status.dat
maskfile    =    = ana-cxi49012/cspad-cxi49012-r0200-noise-mask.dat
print_bits 3
frac_noisy_imgs   =   = 255
rmin0.1

peak_npix_min     =       = 3
dr      4
peak_npix_max     =   = 1
SoNThr25
peak_amp_tot_thr  =   100.

event_npeak_min   =  =  310
fracevent_amp_noisytot_imgsthr =  01000.15
  • Index map in median algorithm for rmin=3, dr=1:
Code Block
bgColor#F7F7ED
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):
  • Image Removed Image Removed Image Removed
  • 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:
  • Image Removed Image Removed

  • Example for Module ImgAlgos::CSPadArrPeakFinder

  • See Module ImgAlgos::CSPadArrPeakFinder


nevents_mask_update = 100
nevents_mask_accum  =  50

selection_mode    = SELECTION_ON
out_file_bits     =    15
print_bits        =    512

Results:

Code Block
bgColor#F7F7ED
[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:

Image AddedImage AddedImage Added

ev-008944:

Image AddedImage AddedImage Added

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
bgColor#F7F7ED
[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             =ImgAlgos.CSPadArrPeakFinder calibrated\
outkey            = masked_arr
mask_fnamepyimgalgos.ex_peaks_nda
#        = ana-cxi49012/cspad-cxi49012-r0150-mask-badregs.dat
#mask_fname EventKeys

[cspad_mod.CsPadCalib]
inputKey        = ana-cxi49012/cspad-cxi49012-r0150-mask-bkgd.dat
#mask_fname   
outputKey     = ana-cxi49012/cspad-cxi49012-r0150-mask-rects.dat
masked_amp   calibrated
doPedestals     =  8
print_bits        =  1
mask_control_bitsyes
doPixelStatus = yes
doCommonMode  = 15yes

[ImgAlgos.CSPadArrPeakFinder]
source            = DetInfo(CxiDs1.0:Cspad.0)
key               = masked_arrcalibrated
key_peaks_out     = 
key_peaks_outnda     = peaks_nda

hot_pix_mask_inp_file = ana-cxi49012cxi83714/cspad-cxi49012cxi83714-r0150r0136-noise-mask-ini.dat
hot_pix_mask_out_file = ana-cxi49012cxi83714/cspad-cxi49012cxi83714-r0150r0136-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  = ana-cxi83714/cspad-cxi83714-r0136-noise-frac.dat
evt_file_out     =     4
peak_npix_max= cxi83714/cspad-ev-
rmin     =    25
peak_amp_tot_thr  =   100.

event_npeak_min  = =    10
event_amp_tot_thr =  1000.

nevents_mask_update = 100
nevents_mask_accum  =  50

selection_mode8
dr            = SELECTION_ON
out_file_bits     =    15 1
printSoNThr_bitsnoise        =    512
  • Results:
Code Block
bgColor#F7F7ED
[info:TimeInterval::startTime] Start time: 2012-06-12 15:32:02
[info:ImgAlgos.CSPadArrPeakFinder]    N processed3
SoNThr_signal events = 1000  N selected = 55     4
frac_noisy_imgs  Fraction of selected =   0.055
[info:ImgAlgos.CSPadArrPeakFinder]9
peak_npix_min    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

...

 3
peak_npix_max       =   500
peak_amp_tot_thr    =     0.
peak_SoN_thr        =     5.
event_npeak_min     =     5
event_npeak_max     =  1000
event_amp_tot_thr   =     0.
nevents_mask_update =     0
nevents_mask_accum  =    50
selection_mode      = SELECTION_ON
out_file_bits       =    15
print_bits          =  3681

[pyimgalgos.ex_peaks_nda]
source        = DetInfo(CxiDs1.0:Cspad.0)
key_in        = peaks_nda
print_bits    = 255

 

 

 

...

Example for module ImgAlgos::CSPadArrPeakAnalysis

See Module ImgAlgos::CSPadArrPeakAnalysis

Example of the psana configuration file:

Code Block
bgColor#F7F7ED
modules = cspad_mod.CsPadCalib \
          ImgAlgos.CSPadMaskApply \
          ImgAlgos.CSPadArrPeakFinder \
          ImgAlgos.CSPadArrPeakAnalysis

# ...configuration parameters of other modules...

[ImgAlgos.CSPadArrPeakAnalysis]
source             = DetInfo(CxiDs1.0:Cspad.0)
key                = peaks
print_bits         = 7
fname_root         = file.root

After execution in psana the file.root containing histogram(s) and ntuple(s) will be produced. Then, auxiliary script in root, running by the commend

root -q -f proc.C

produces the plots with histograms:

Image ModifiedImage Modified

Example for TimeStampFilter and XtcOutputModule

This example demonstrates how to run psana with the time stamp filter and event writer in xtc file.

Both modules are available in psana library and they need only to be described in the configuration file. For example, the configuration file tstamp-filter-and-event-writer.cfg may looks like:

Code Block
bgColor#F7F7ED
[psana]                                                               
files         = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/e158-r0021-s00-c00.xtc \
                /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/e158-r0021-s01-c00.xtc \
                /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/e158-r0021-s02-c00.xtc \
                /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/e158-r0021-s03-c00.xtc \
                /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/e158-r0021-s04-c00.xtc \
                /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/e158-r0021-s05-c00.xtc

skip-events   = 10
events        = 100
modules       = ImgAlgos.TimeStampFilter  PSXtcOutput.XtcOutputModule 

[PSXtcOutput.XtcOutputModule]
dirName       = ./test_out

[ImgAlgos.TimeStampFilter]
tsinterval    = 2012-02-02 18:17:00.409143728 / 2012-02-02 18:17:00.525853474
filterIsOn    = true
print_bits    = 11

Command to run psana is:

psana -c ./tstamp-filter-and-event-writer.cfg

For this configuration file psana will skip 10 events and loop over the next 100 events from the /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/e158-r0021-s0*-c00.xtc files and run consecutively modules = ImgAlgos.TimeStampFilter PSXtcOutput.XtcOutputModule. Parameters of these modules are described in the bottom part of the configuration file. Module TimeStampFilter passes events from the specified time interval and prints some useful information. Module XtcOutputModule will write passed events in the file with auto-generated name ./test_out/e158-r0021.xtcf.

See also: Module ImgAlgos::TimeStampFilter and PSXtcOutput::PSXtcOutput

...

Examples for Package py_img_algos

Example for module ImgAlgos::UsdUsbEncoderFilter

Example of configuration file:

Code Block
[psana]
files = exp=amo75113:run=156
events = 10

modules = ImgAlgos.UsdUsbEncoderFilter

[ImgAlgos.UsdUsbEncoderFilter]
source  = DetInfo(:USDUSB)
mode    = 1
ifname  = tstamp-code-in.txt 
ofname  = tstamp-code-out.txt
print_bits = 31

See also: Module ImgAlgos::UsdUsbEncoderFilter

 

Examples for Package pyimgalgos

Package pyimgalgos

...

contains python modules which work with both frameworks pyana and psana.

Configuration file for pyana and/or psana should have relevant sections with parameters for [pyana] and/or [psana]. Alean section is ignored in each framework at run time. This is the only difference between two frameworks in the configuration file. All module descriptions are the same for two frameworks, as shown in examples below.

See description of modules in Package

...

pyimgalgos.

Example of configuration file for CSPAD

File py-xcs72913-r0049-cspad.cfg:

Code Block
bgColor#AAFFFF
# Run this script:
# psana -c py-xcs72913-r0049-cspad.cfg
# pyana -c py-xcs72913-r0049-cspad.cfg
#
# Useful commands:
# psana -m EventKeys -n 5 /reg/d/psdm/xcs/xcs72913/xtc/e265-r0049-*
# psana -m psana_examples.dump_cspad -n 5 exp=xcs72913:run=49
# pyana -m pyana_examples.dump_cspad -n 5 /reg/d/psdm/xcs/xcs72913/xtc/e265-r0049-*

[pyana]
files  = /reg/d/psdm/xcs/xcs72913/xtc/e265-r0049-s00-c00.xtc /reg/d/psdm/xcs/xcs72913/xtc/e265-r0049-s04-c00.xtc /reg/d/psdm/xcs/xcs72913/xtc/e265-r0049-s05-c00.xtc
num-events = 5
#skip-events = 0
#num-cpu = 1
verbose = 1 ; logging output: 0-nothing?, 1+INFO, 2+DEBUG, ...
modules = py_img_algospyimgalgos.tahometer py_img_algospyimgalgos.cspad_arr_producer py_img_algospyimgalgos.cspad_image_producer py_img_algospyimgalgos.image_save_in_file


[psana]
files = exp=xcs72913:run=49
events = 5                 
#skip-events = 0
modules = py_img_algospyimgalgos.tahometer py_img_algospyimgalgos.cspad_arr_producer py_img_algospyimgalgos.cspad_image_producer py_img_algospyimgalgos.image_save_in_file
verbose = 1 


[py_img_algospyimgalgos.tahometer]
dn         = 10
print_bits = 255


[py_img_algospyimgalgos.cspad_arr_producer]
#source    = -|Cspad-*
source     = XcsEndstation-0|Cspad-0 
data_type  = double
#data_type  = float
#data_type  = unsigned
#data_type  = uint16
val_miss   = 0
key_out    = cspad_array
print_bits = 1


[py_img_algospyimgalgos.cspad_image_producer]
calib_dir  = /reg/d/psdm/xcs/xcs72913/calib/CsPad::CalibV1/XcsEndstation.0:Cspad.0/
key_in     = cspad_array
key_out    = cspad_image
print_bits = 1

# Supported output file formats tiff, gif, png, eps, jpg, jpeg, txt, npy(default), npz
[py_img_algospyimgalgos.image_save_in_file]
key_in     = cspad_image
ofname     = img-for-cspad.txt
print_bits = 255

To run this script use command

psana -c py-xcs72913-r0049-cspad.cfg

or

pyana -c py-xcs72913-r0049-cspad.cfg

Example of configuration file for CSPAD2x2

File py-meca6113-r0028-cspad2x2.cfg

Code Block
bgColor#AAFFFF
# Run this script:
# psana -c py-meca6113-r0028-cspad2x2.cfg
# pyana -c py-meca6113-r0028-cspad2x2.cfg
#
# Useful commands:
# psana -m EventKeys -n 5 /reg/d/psdm/mec/meca6113/xtc/e332-r0028-s03-c00.xtc
# psana -m psana_examples.dump_cspad -n 5 exp=meca6113:run=28
# pyana -m pyana_examples.dump_cspad -n 5 /reg/d/psdm/mec/meca6113/xtc/e332-r0028-s03-c00.xtc

[pyana]
files  = /reg/d/psdm/mec/meca6113/xtc/e332-r0028-s03-c00.xtc
num-events = 5
#skip-events = 0
#num-cpu = 1
verbose = 0 ; logging output: 0-nothing?, 1+INFO, 2+DEBUG, ...
modules = py_img_algospyimgalgos.tahometer py_img_algospyimgalgos.cspad_arr_producer py_img_algospyimgalgos.cspad_image_producer py_img_algospyimgalgos.image_save_in_file


[psana]
files = exp=meca6113:run=28
events = 5 
#skip-events = 0
modules = py_img_algospyimgalgos.tahometer py_img_algospyimgalgos.cspad_arr_producer py_img_algospyimgalgos.cspad_image_producer py_img_algospyimgalgos.image_save_in_file


[py_img_algospyimgalgos.tahometer]
dn         = 10
print_bits = 255


[py_img_algospyimgalgos.cspad_arr_producer]
#source    = -|Cspad-*
source     = MecTargetChamber-0|Cspad2x2-3
#data_type  = double
data_type  = float
#data_type  = unsigned
#data_type  = uint16
#data_type  = uint32
val_miss   = 0
key_out    = cspad2x2_array
print_bits = 255


[py_img_algospyimgalgos.cspad_image_producer]
calib_dir  = /reg/d/psdm/mec/meca6113/calib/CsPad2x2::CalibV1/MecTargetChamber.0:Cspad2x2.3/
key_in     = cspad2x2_array
key_out    = cspad2x2_image
print_bits = 1

# Supported output file formats tiff, gif, png, eps, jpg, jpeg, txt, npy(default), npz
[py_img_algospyimgalgos.image_save_in_file]
key_in     = cspad2x2_image
ofname     = img-for-cspad2x2.tiff 
print_bits = 255

To run this script use command

psana -c py-meca6113-r0028-cspad2x2.cfg

or

pyana -c py-meca6113-r0028-cspad2x2.cfg

References

...

psana - Module Catalog