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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

server	SLAC National Accelerator Laboratory
key	PSAS-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.

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

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

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 with psana does a few things:

module AcqirisArrProducer gets Acqiris data from event store and saves them back in the event store as uniform ndarrays<double,2> for waveforms and times
two instances of the module ImgSaveInFile save arrays of waveforms and times for local event 5.

This script saves 3 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

...

                  
files         = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\
                /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-2>.xtc
#skip-events = 100
events      =  5
modules = ImgAlgos.PnccdImageProducer ImgAlgos.ImgSaveInFile

[ImgAlgos.PnccdImageProducer]
source        = DetInfo(:pnCCD)
inkey         =
outimgkey     = imgpnccd
print_bits    = 1

[ImgAlgos.ImgSaveInFile]
source        = DetInfo(:pnCCD)
key           = imgpnccd
fname         = pnccd-img-ev
saveAll       = true
#eventSave     = 82
print_bits    = 1

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]

...

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        = 
key_wform     = acqiris_wform
key_wtime     = acqiris_wtime
fname_prefix  = acq
print_bits    = 3


[ImgAlgos.AcqirisAverage]
source           
#calib-dir = /reg/d/psdm/SXR/sxrb5914/calib
files = exp= AmoETOF.0:Acqiris.0
key_in     sxrb5914:run=245
events = 10

modules = ImgAlgos.Tahometer \
          = acqiris_wform
key_aveImgAlgos.PnccdNDArrProducer \
          ImgAlgos.NDArrCalib \
    = acqiris_average
fname_ave_prefix     =ImgAlgos.PnccdImageProducer acq\
thresholds           = -0.005 -0.005 -0.005 -0.005 -0.005
is_positive_signal   = no
do_inverse_selection = yes
#skip_events          = 0
#proc_events          = 100
print_bits           = 255

Psana with this script runs over 1000 events apply threshold-based selection algorithm and produces files:

acq-amo01509-r0125-config.txt -- with Acqiris configuration parameters
acq-amo01509-r0125-ave-wfs.txt with averaged array of waveforms, which were below threshold (averaging for bae-line level):

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  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        =  100
below_thre_value =    0
bkgd_ind_min     = 10000
bkgd_ind_max     = 10200
bkgd_ind_inc     =    1
print_bits       =    1

[ImgAlgos.PnccdImageProducer]
source        = DetInfo(Camp.0:pnCCD.1)
inkey         = calibrated
outimgkey     = pnccd-img
gap_rows      = 0
gap_cols      = 16
keygap_wformvalue     = acqiris_wform
key_wtime     = acqiris_wtime
fname_prefix  = acq
0
print_bits    = 1


[ImgAlgos.AcqirisCalibNDArrAverage]
source               = AmoETOF= DetInfo(Camp.0:AcqirispnCCD.01)
key_in          = pnccd-img
avefile      = acqiris_wform
key_outpnccd-ave
rmsfile      = pnccd-rms
#maskfile     = pnccd-msk
#hotpixfile   = wfpnccd-calibratedhot
fnamethr_base_line rms_ADU  = 160
thr_min_ADU  = 2
thr_max_ADU  = acq-amo01509-r0125-ave-wfs.txt
#skip_events   10000
print_bits   = 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]       = 0
#proc_events          = 100
print_bits           = 255


[ImgAlgos.ImgSaveInFile:wf_raw]
source         = AmoETOF.0:Acqiris.0
key                      = acqiris_wform
fnamefiles           = acq-AmoETOF-wform-raw
ftype/reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc
modules         = ImgAlgos.CameraImageProducer ImgAlgos.ImgSaveInFile
events          = txt
#ftype 5

[ImgAlgos.CameraImageProducer] 
source          = tiff
#saveAllDetInfo(:Opal1000)
key_in          = true
print_bitskey_out         = img
subtract_offset = 3true
eventSaveprint_bits      = 515


[ImgAlgos.ImgSaveInFile:wf_calib]
source         = AmoETOF.0:Acqiris.0DetInfo(:Opal1000)
key            = wf-calibratedimg
fname          = acqimg-AmoETOFfrom-wformmy-calibrated
ftype   experiment
saveAll       = txttrue
#ftype  #eventSave        = tiff
#saveAll        = true
print_bits     = 3
eventSave      = 5

In this script the base-line level for all waveforms is loaded from file and is subtracted in module ImgAlgos.AcqirisCalib.

For example, the raw and calibrated waveforms for event 5 were saved in the files:

acq-AmoETOF-wform-raw-r0125-e00000005-20091018-182512.194787218.txt
acq-AmoETOF-wform-calibrated-r0125-e00000005-20091018-182512.194787218.txt

which content is presented on plots:

Image Removed Image Removed

...

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]

...

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
files         = 7


[ImgAlgos.AcqirisAverage:bl]
source/reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\
               = AmoETOF.0:Acqiris.0
key_in /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-2>.xtc
modules       = ImgAlgos.PrincetonImageProducer  \
     = acqiris_wform
#key_ave          ImgAlgos.ImgSaveInFile
events    = 
fname_ave_prefix     = acq-bline
thresholds 3

[ImgAlgos.PrincetonImageProducer] 
source          = -0.005 -0.005 -0.005 -0.005 -0.005 
is_positive_signal   = no
do_inverse_selection = yes
skip_events DetInfo(:Princeton)
key_in          = 
key_out         = 0img
proc_events          = 1000subtract_offset = true
print_bits           = 31


[ImgAlgos.AcqirisCalibImgSaveInFile]
source               = AmoETOF.0:Acqiris.0
key_in   DetInfo(:Princeton)
key            = acqiris_wform
key_outimg
fname              = wfimg-calibrated
fname_base_linexcs
saveAll       = acq-blinetrue
skip_events   print_bits       = 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   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

# 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        = -0AmoETOF.01 -0:Acqiris.01 -0.01 -0.01 -0.01 
is_positive_signal0
key_in      = no
do_inverse_selection = no
skipkey_eventswform     = acqiris_wform
key_wtime     = 1001acqiris_wtime
procfname_eventsprefix     = acq
print_bits    = 11


[ImgAlgos.ImgSaveInFile:wf]
source         = AmoETOF.0:Acqiris.0
key            = acqiris_wform
fname          = acq-AmoETOF-wform
ftype          = 1000txt
#ftype          = tiff
#saveAll        = true
print_bits     = 3
eventSave      = 315


[ImgAlgos.Tahometer]
print_bitsImgSaveInFile:wt]
source         = 7

This script works with psana as follows:

for the 1st 1000 events averages waveforms below threshold and saves results in the file acq-bline-amo01509-r0125-ave-wfs.txt;
for the next 1000 events subtracts baseline level and averages waveforms above thresholds and saves results in the file acq-signal-amo01509-r0125-ave-wfs.txt.

This script produces three files:

acq-amo01509-r0125-config.txt - with Acqris configuration parameters:

Code Block

Acqiris::ConfigV1:
  nbrBanks=1 channelMask=69905 nbrChannels=5 nbrConvertersPerChannel=4
  horiz: sampInterval=2.5e-10 delayTime=0 nbrSegments=1 nbrSamples=10000
  vert(0): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0
  vert(1): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0
  vert(2): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0
  vert(3): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0
  vert(4): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0

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

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
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:

AmoETOF.0:Acqiris.0
key            = acqiris_wtime
fname          = acq-AmoETOF-wtime
ftype          = txt
#ftype          = tiff
#saveAll        = true
print_bits     = 3
eventSave      = 5

This script with psana does a few things:

module AcqirisArrProducer gets Acqiris data objects from event store, adjusts trigger time corrections, and saves them back in the event store as uniform ndarrays<double,2> objects for waveforms and times
two instances of the module ImgSaveInFile save arrays of waveforms and wave-times for locally counted event 5.

This script saves 3 text files:

acq-amo01509-r0125.txt -- with configuration parameters:

Code Block

Acqiris::ConfigV1:
  nbrBanks=1 channelMask=69905 nbrChannels=5 nbrConvertersPerChannel=4
  horiz: sampInterval=2.5e-10 delayTime=0 nbrSegments=1 nbrSamples=10000
  vert(0): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0
  vert(1): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0
  vert(2): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0
  vert(3): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0
  vert(4): fullScale=0.1 slope=1.52588e-06 offset=0 coupling=3 bandwidth=0

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

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

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>.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
printkey_bits wform     = 31acqiris_wform
evtskey_stage1wtime     = 100acqiris_wtime
evts_stage2 fname_prefix  = acq
print_bits    = 100
gate_width13


[ImgAlgos.AcqirisAverage]
source     = 200
gate_width2     = 20

Example for module ImgAlgos::ImgMaskEvaluation
See Module ImgAlgos::ImgMaskEvaluation
Configuration parameters for psana:

Code Block

bgColor	#F7F7ED

[ImgAlgos.ImgMaskEvaluation] 
source          = DetInfo(:Opal1000)AmoETOF.0:Acqiris.0
key_in             = 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= acqiris_wform
key_ave               = 0
dracqiris_average
fname_ave_prefix     = acq
thresholds         = 1
thre_SoN  = -0.005 -0.005 -0.005 -0.005 -0.005
is_positive_signal   = no
do_inverse_selection = yes
#skip_events          = 30
frac_nois#proc_events          = 0.05100
print_bits           = 63255

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

...

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

bgColorbgColors	#F7F7ED	#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[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(CxiDs1AmoETOF.0:CspadAcqiris.0)
inputKeykey_in        = calibrated
outputKeykey_wform     = bkgdacqiris_subtracted_arrwform
bkgdkey_fnamewtime     = <the-file-name-with-background-array>
norm_sector   = 0acqiris_wtime
fname_prefix  = acq
print_bits    = 01


[CSPadPixCoordsImgAlgos.CSPadImageProducerAcqirisCalib]
calibDirsource      = /reg/d/psdm/<instrument>/<experiment>/calib
typeGroupName = CsPad::CalibV1
source        = CxiDs1AmoETOF.0:CspadAcqiris.0
key_in               = calibrated
imgkeyacqiris_wform
key_out              = current_img
#tiltIsApplied = true

[ImgAlgos.ImgRadialCorrection]
sourcewf-calibrated
fname_base_line      = acq-amo01509-r0125-ave-wfs.txt
#skip_events          = DetInfo(CxiDs1.0:Cspad.0)
inkey
#proc_events          = current_img
outkey100
print_bits           = r_cor_img
xcenter255


[ImgAlgos.ImgSaveInFile:wf_raw]
source         = 866
ycenterAmoETOF.0:Acqiris.0
key            = 857acqiris_wform
rminfname          = 100
rmaxacq-AmoETOF-wform-raw
ftype          = 810
n_phi_binstxt
#ftype          = 60tiff
event#saveAll         = 0true
print_bits     = 3
eventSave      = 5


[ImgAlgos.ImgSaveInFile:1wf_calib]
source         = CxiDs1AmoETOF.0:CspadAcqiris.0
key            = r_cor_imgwf-calibrated
fname          = <fileacq-nameAmoETOF-for-image-array>wform-calibrated
ftype          = txt
#ftype          = tiff
#saveAll        = true
print_bits     = 3
eventSave      = 85

...

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

bgColorbgColors	#F7F7ED#AAFFFF

[psana]# Command to run this script: 
# psana -c psana_cfd.cfg;
#
[psana]
modules = ImgAlgos.AcqirisArrProducer                                                    
files         ImgAlgos.AcqirisCalib ImgAlgos.AcqirisCFD 
files = /reg/d/psdm/<instrument>AMO/<experiment>amo01509/xtc/<filee8-r0125-names00-1>c00.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 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         = 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:


[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

Code Block

bgColor	#F7F7ED

[psana]               = AmoETOF.0:Acqiris.0
key_in               = acqiris_wform
#key_ave              = 
fname_ave_prefix        = acq-bline
thresholds        
files   = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name>.xtc
modules = ImgAlgos.CameraImageProducer \
          ImgAlgos.ImgPeakFinderAB
events  = 10

[ImgAlgos.CameraImageProducer] 
source-0.005 -0.005 -0.005 -0.005 -0.005 
is_positive_signal   = no
do_inverse_selection = yes
skip_events          = DetInfo(:Opal1000)
key_in0
proc_events          = 1000
keyprint_outbits         = img
subtract_offset = true
print_bits      = 131


[ImgAlgos.ImgPeakFinderABAcqirisCalib]
source                 = DetInfo(:Opal1000)AmoETOF.0:Acqiris.0
key_in                    = imgacqiris_wform
key_peaks_out          = peaks
#key_signal_out        = signalwf-arrcalibrated
#hotfname_pix_mask_inp_file = ana-misc-exp/mask.dat
#hot_pix_mask_out_file = noise-mask-out.dat
#frac_noisy_evts_filebase_line      = noise-frac-out.dat
evt_file_out acq-bline
skip_events          = tmp/img-

rmin      1001
proc_events          = 1000
print_bits   10
dr        = 47


[ImgAlgos.AcqirisAverage:signal]
source         =       1
SoNThr_noise= AmoETOF.0:Acqiris.0
key_in        =     3
SoNThr_signal  = wf-calibrated
#key_ave    =     3
frac_noisy_imgs     =   0.9
peakfname_npixave_minprefix     = acq-signal
thresholds  =     3
peak_npix_max    = -0.01  =   100
peak_amp_tot_thr -0.01 -0.01 -0.01 -0.01 
is_positive_signal   =     0.
peak_SoN_thr  no
do_inverse_selection = no
skip_events      =    = 4.1001
event_npeak_minproc_events      =    = 51000
event_npeak_maxprint_bits      =  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:

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

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
eventsNDArrImageProducer \
         = 1000ImgAlgos.NDArrAverage

[ImgAlgosCSPadPixCoords.CameraImageProducerCSPadNDArrProducer] 
source          = DetInfo(:Opal1000)
key_inCxiDs1.0:Cspad.0) 
inkey          = 
key_outoutkey       = cspad_ndarr
outtype      = imgfloat
subtractis_offsetfullsize  = trueyes
print_bits      = 13

[ImgAlgos.ImgAverageNDArrCalib] 
source          = DetInfo(:Opal1000)CxiDs1.0:Cspad.0) 
key_in  = cspad_ndarr
key_out = calibrated
do_peds = yes
do_cmod = yes
do_stat = yes
do_mask  = imgno
avefiledo_bkgd = no
do_gain = no 
do_nrms = no
do_thre  = img-ave-for-peds
rmsfile    no
fname_mask = 
fname_bkgd = 
masked_value     =  img-rms-for-thre
evts_stage1 10
threshold_nrms   =    =4 100
evts_stage2threshold     = 100
gate_width1  =   = 507
gatebelow_thre_width2value =    = 100
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 Removed Image Removed
img-rms-for-thre-r0093.dat - may be used multiplied by number of rms as a threshold:
Image Removed Image Removed
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 \
   3 

[ImgAlgos.NDArrImageProducer]
source       = CxiDs1.0:Cspad.0
key_in          ImgAlgos.ImgHitFinder \
    = calibrated
key_out      ImgAlgos.ImgAverage
skip-events = 0
events cspad_img
#type_out     = 1000

[ImgAlgos.CameraImageProducer] 
sourceasinp
#type_out          = DetInfo(:Opal1000)
key_in       float
#x0_off_pix   = 50
key#y0_off_outpix         = img50
subtractprint_offsetbits   = true255
print_bits#calibdir      = 1/reg/neh/home/dubrovin/LCLS/CSPadAlignment-v01/calib-cxi-ds1-2014-03-19/calib

[ImgAlgos.ImgHitFinderNDArrAverage] 
source           = DetInfo(:Opal1000)CxiDs1.0:Cspad.0) 
key_in           = cspad_img
key_outavefile          = img_hits
fname_peds = cspad-img-ave
rmsfile      = cspad-img-ave-for-peds-r0093.dat
fname_maskrms
#maskfile       = 
fname_gain       = 
fname_thre       = img-rms-for-thre-r0093.dat
masked_value   cspad-img-msk
#hotpixfile  = cspad-img-hot
thr_rms_ADU  = 0
threthr_min_modeADU        = 34
#threthr_max_modeADU        = 265000
threprint_parambits   =    = 5
thre_below_value = 0
thre_above_value = 1
win_row_min      = 10
win_row_max      = 1000
win_col_min29

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 \
      = 10
win_col_max    ImgAlgos.NDArrImageProducer \
 = 1000
print_bits       = 39ImgAlgos.NDArrAverage

[ImgAlgosCSPadPixCoords.ImgAverageCSPad2x2NDArrProducer] 
source          = DetInfo(:Opal1000)
keyMecTargetChamber.0:Cspad2x2.1
inkey      = 
outkey      = imgcspad2x2_hits
sumfile     ndarr
outtype    = img-sum-resultint16
print_bits = 5

[ImgAlgos.NDArrImageProducer]
source       = 25

and run it by the command:

Code Block

bgColor	#F7F7ED

psana -c psana-amo74213-r0093-opal-img-hit-finder.cfg

Which creates the file: img-sum-result-r0093.dat for thre_mode = 2 and thre_mode = 3, respectively:
Image Removed Image Removed
Example for module ImgAlgos::ImgSpectra
See Module ImgAlgos::ImgSpectra
Configuration file for psana:

Code Block

bgColor	#F7F7ED

[psana]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               
files= 0
#pix_scale_size_um = 218.
#calibdir     = /reg/dneh/psdmhome/<instrument>dubrovin/<experiment>LCLS/xtc/<file-name>.xtc

modulesCSPad2x2Alignment/calib-cspad2x2-01-2013-02-13/calib
#calibgroup       =  CsPad2x2::CalibV1


[ImgAlgos.CameraImageProducer \
NDArrAverage]
source       = MecTargetChamber.0:Cspad2x2.1
#key          ImgAlgos.ImgSpectra \
= cspad2x2_ndarr
key          = cspad2x2_img
avefile      ImgAlgos.ImgSaveInFile:2
#= arr-ave
rmsfile      = arr-rms
maskfile         ImgAlgos.ImgSaveInFile
#= arr-msk
hotpixfile   = arr-hot
thr_rms_ADU  = 10
#thr_min_ADU = 2
#thr_max_ADU = 20000
print_bits     psana_examples.DumpOpal1k \

events          = 100

[ImgAlgos.CameraImageProducer] 
source= 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

See Module ImgAlgos::NDArrCalib, Module ImgAlgos::NDArrAverageThe NDArrCalib module in combination with any device NDArrProducer (for example PnccdNDArrProducer) can be used to apply intensity corrections to ndarray.
Typical configuration files are shown below.

Example of ImgAlgos::NDArrCalib for pnCCD

Code Block
[psana]

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          = 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  
files =  400 exp=amoa1214:run=7
#skip-events = 100
events    500  = 5

modules = 600ImgAlgos.Tahometer \
    700     800 ImgAlgos.PnccdNDArrProducer \
   900    1000
Signal:   ImgAlgos.NDArrCalib 1211\
    4062   11150   17070ImgAlgos.PnccdImageProducer \
  16406   12949    7991 ImgAlgos.ImgSaveInFile
#   5168    3968  ImgAlgos.NDArrAverage  3542\


[ImgAlgos.PnccdNDArrProducer]
source        3811
Refer.:     933    3485   10425   17128   17791   13522    8315    5000    3390    2967    3193
Diff. :   0.259   0.153   0.067  -0.003  -0.081  -0.043  -0.040   0.033   0.157   0.177   0.176
[info:ImgAlgos.ImgSpectraProc] Run=0060 Evt=000100 Time=20120507-125420.982421325 done...

Example for module ImgAlgos::ImgSaveInFile

Code Block

bgColor	#F7F7ED

modules = ... ImgAlgos.ImgSaveInFile:1 ...

[ImgAlgos.ImgSaveInFile:1]
source         = DetInfo(:Opal1000)   # or CxiDs1.0:Cspad.0
key= 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       =     = img
fname255 


[ImgAlgos.PnccdImageProducer]
source        = DetInfo(Camp.0:pnCCD.0)
#inkey         = pnccd-ndarr
inkey         = calibrated
outimgkey     = mypnccd-img
#ftypegap_size      = 20
gap_value     = txt
#ftype  0
print_bits    = 1


[ImgAlgos.ImgSaveInFile]
source        = bin
#ftypeDetInfo(Camp.0:pnCCD.0)
key           = png
ftype pnccd-img
fname         = tiff
#eventSavepnccd-img-from-arr
ftype         = 5txt
saveAll       = true
print_bits    = true

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

31


 
[ImgAlgos.Tahometer]
dn         = 100
print_bits = 7

Example of ImgAlgos::NDArrCalib for CSPAD

#F7F7ED

Code Block
Code Block
bgColor

[psana] files = exp=cxi83714:run=136 events = 100 modules = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-1>.xtcImgAlgos.Tahometer \ CSPadPixCoords...CSPadNDArrProducer \ /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-N>.xtc eventsImgAlgos.NDArrCalib \ = 1000 experimentImgAlgos.NDArrAverage [CSPadPixCoords.CSPadNDArrProducer] source = cxii0212 calib-dir = ana-cxii0212/calib modules = cspad_mod.CsPadCalib \ DetInfo(CxiDs1.0:Cspad.0) inkey ImgAlgos.CSPadMaskApply= \ outkey CSPadPixCoords.CSPadImageProducer \ = cspad_ndarr outtype = float is_fullsize = ImgAlgos.ImgPeakFinder \ yes print_bits ImgAlgos.ImgPeakFilter \ ImgAlgos.ImgSaveInFile:1 [cspad_mod.CsPadCalib] inputKey = outputKey = calibrated doPedestals = yes doPixelStatus = no doCommonMode = yes [ImgAlgos.CSPadMaskApply] source = DetInfo(CxiDs1.0:Cspad.0) inkey = 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 = calibrated outkey 7 below_thre_value = 0 bkgd_ind_min = masked_arr mask_fname 0 bkgd_ind_max = <your-local-directory>/<mask-file-name>.dat masked_amp1000 bkgd_ind_inc = = 010 print_bits = = 5 mask_control_bits = 15 3 [CSPadPixCoordsImgAlgos.CSPadImageProducer] calibDir = /reg/d/psdm/<instrument>/<experiment>/calib typeGroupName = CsPad::CalibV1 source NDArrAverage] source = DetInfo(CxiDs1.0:Cspad.0) key = masked_arrcalibrated imgkeyavefile = img print_bitscspad-ave rmsfile = 0 #tiltIsApplied = true [ImgAlgos.ImgPeakFinder] source cspad-rms #maskfile = DetInfo(CxiDs1.0:Cspad.0) keycspad-msk #hotpixfile = img peaksKey cspad-hot thr_rms_ADU = peaks10 thresholdthr_min_lowADU = 24 thresholdthr_max_highADU = 5 sigma = 1.510000 smearprint_radiusbits = 5 peak_radius = 7 xmin29 [ImgAlgos.Tahometer] dn = 20 xmax = 1700 ymin = 20 ymax = 1700 #testEvent = 5 print_bits = 3 #finderIsOn = true [ImgAlgos.ImgPeakFilter] source = DetInfo(CxiDs1.0:Cspad.0) key = peaks threshold_peak = 5 threshold_total= 0 n_peaks_min = 10 print_bits = 11 fname 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 \
       = cspad-img
selection_mode = SELECTION_ON

[ImgAlgos.ImgSaveInFile:1]
sourceNDArrAverage \
         = CxiDs1.0:Cspad.0
keyImgAlgos.Tahometer

[cspad_mod.CsPadCalib]
inputKey      = 
outputKey     = imgcalibrated_data
fnamedoPedestals   =       yes
doPixelStatus = cspad-imgyes
#eventSavedoCommonMode     = 1
saveAll yes

[CSPadPixCoords.CSPadNDArrProducer]
source       = true

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>.xtcDetInfo(CxiDs1.0:Cspad.0) 
inkey        = calibrated_data
outkey       = cspad_ndarr
outtype      = float
is_fullsize  = yes
print_bits   = 3

[ImgAlgos.CSPadArrAverageNDArrAverage]
source       = DetInfo(CxiDs1.0:Cspad.0) 
key          = cspad_ndarr
avefile      = cspad-pedestalscalib-ave.dat
rmsfile      = cspad-pedestalscalib-rms.dat
print_bits
#maskfile     = 15
evts_stage1 = 100
evts_stage2cspad-msk
#hotpixfile   = 100
gate_width1 = 100
gate_width2 =  10

Configuration file example for evaluation of background:

Code Block

bgColor	#F7F7ED

[psana]
files       = <path-to-the-background-run-file>.xtc
modules     = cspad_mod.CsPadCalib ImgAlgos.CSPadArrAverage
skip-events = 500
events      = 1000000

[cspad_mod.CsPadCalib]
inputKeycspad-hot
thr_rms_ADU  = 10
thr_min_ADU  = 4
thr_max_ADU  = 10000
print_bits   = 29

[ImgAlgos.Tahometer]
dn      = 
outputKey  = 10
print_bits = = calibrated
doPedestals   = yes
doPixelStatus = no
doCommonMode  = no

[ImgAlgos.CSPadArrAverage]
source  = DetInfo(CxiDs1.0:Cspad.0)
key     = calibrated
avefile = cspad-background-ave.dat
rmsfile = cspad-background-rms.dat
print_bits  = 15

Images of the CSPad arrays for averaged and rms values, respectively, in one of the CXI runs:
Image RemovedImage Removed
Example for module ImgAlgos::CSPadBkgdSubtract
See Module ImgAlgos::CSPadBkgdSubtract

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:

Code Block

bgColor	#F7F7ED

[psana]
files = /reg/d/psdm/<instrument>XCS/<experiment>/xtc/<file-name-1>.xtc \xcsd7814/calib for detector: Fccd960
    Camera::CalibV1    /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-2>.xtc \
        XcsEndstation...0:Fccd960.0    
        /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-N>.xtc
skip-events = 500
events   pixel_rms   = 10
modules      = cspad_mod.CsPadCalib ImgAlgos.CSPadBkgdSubtract

[cspad_mod.CsPadCalib]
inputKey      = 
outputKey 12-13.data    = calibrated
doPedestals file is =not yesused
doPixelStatus = no
doCommonMode  = no


[ImgAlgos.CSPadBkgdSubtract]
source        = DetInfo(CxiDs1.0:Cspad.0)
inputKey      = calibrated
outputKey   78-81.data      run range 0078 - 0081
            pedestals    
          = bkgd_subtracted
bkgd_fname    = <the-file-name-with-background-array>
norm_sector   = 0
print_bits    = 3

The file with the background array, bkgd_fname, was obtained by averaging 1000 events using module CSPadArrAverage. Subtraction is done with normalization for norm_sector=0.
Event image and pixel amplitude spectrum before and after the background subtraction are shown in plots:
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*185 388.
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:

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

Code Block

bgColor	#F7F7ED

modules = cspad_mod.CsPadCalib \
          ImgAlgos.CSPadBkgdSubtract cspad_mod.CsPadCalib \
           CSPadPixCoords.CSPadNDArrProducer

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

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

[ImgAlgosCSPadPixCoords.CSPadBkgdSubtractCSPadNDArrProducer]
source          = DetInfo(CxiDs1.0:Cspad.0)
inputKey
inkey           = calibrated_arr
outputKey
outkey          = bkgdcspad_subtracted_arr
bkgd_fnamendarr
outtype    = ana-cxi49012/cspad-cxi49012-r0025-background-ave.dat
norm_sector     = int16
is_fullsize     = 0yes
print_bits      = 0

3

Additional keywors need to be added to the list of module parameters in order to evaluate pixel area and coordinate indexes (for image) arrays. For example:

Code Block

[ImgAlgos.CSPadMaskApplyPixCoordsProducer]
source            = DetInfo(CxiDs1.0:Cspad.0)
inkeykey_out_area = pix_area
key_out_mask = pix_mask
key_out_ix      = pix_ix
key_out_iy   = bkgd_subtracted_arr
outkeypix_iy
x0_off_pix      = 1000
y0_off_pix      = masked_arr1000
mask_fnamebits    = 15
print_bits   = 255

In python code these arrays can be obtained with env.calibStore().get(...) method:

Code Block
env = ds.env() ana-cxi49012/cspad-cxi49012-r0025-mask-40.dat masked_amp cls = env.calibStore() src = 0 print_bitspsana.Source('DetInfo(CxiDs1.0:Cspad.0)') ... A = 3 mask_control_bits = 1

where
cspad_mod.CsPadCalib - subtracts the pedestals from raw CSPad data,
ImgAlgos.CSPadBkgdSubtract - subtracts the background,
ImgAlgos.CSPadMaskApply - apply the mask.
In the test with images for background represented by the water and solvent rings this filter provides the background suppression factor about 100.
The background images that still pass this filter have significantly larger intensity with respect to averaged background:
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 \
          /reg/d/psdm/cxi/cxi49012/xtc/e158-r0020-s01-c00.xtc \
          /reg/d/psdm/cxi/cxi49012/xtc/e158-r0020-s02-c00.xtc \
          /reg/d/psdm/cxi/cxi49012/xtc/e158-r0020-s03-c00.xtc \
          /reg/d/psdm/cxi/cxi49012/xtc/e158-r0020-s04-c00.xtc \
          /reg/d/psdm/cxi/cxi49012/xtc/e158-r0020-s05-c00.xtc

#skip-events = 1000
events      = 10

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

[ImgAlgos.CSPadArrNoise]
source          = DetInfo(CxiDs1.0:Cspad.0)
key             = calibrated
statusfile      = ana-cxi49012/cspad-cxi49012-r0020-noise-status.dat
maskfile        = ana-cxi49012/cspad-cxi49012-r0200-noise-mask.dat
print_bits      = 255
rmin            = 3
dr              = 1
SoNThr          = 3
frac_noisy_imgs = 0.15

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

Code Block

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

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

See Module ImgAlgos::ImgMaskEvaluation
Configuration parameters for psana:

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
print_bits      = 25

and run it by the command:

Code Block

bgColor	#F7F7ED

psana -c psana-amo74213-r0093-opal-img-hit-finder.cfg

Which creates the file: img-sum-result-r0093.dat for thre_mode = 2 and thre_mode = 3, respectively:
Image Added Image Added

Example for module ImgAlgos::ImgSpectra

See Module ImgAlgos::ImgSpectra

Configuration file for psana:

Code Block

bgColor	#F7F7ED

[psana]                                                               
files = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name>.xtc

modules       =  ImgAlgos.CameraImageProducer \
                 ImgAlgos.ImgSpectra \
                 ImgAlgos.ImgSaveInFile:2
#                ImgAlgos.ImgSaveInFile
#                psana_examples.DumpOpal1k \

events          = 100

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

[ImgAlgos.ImgSpectra] 
source          = DetInfo(:Opal1000)
key_in          = img
key_out         = spectra
sig_band_rowc   = 512.
ref_band_rowc   = 552.
sig_band_tilt   =   0.
ref_band_tilt   =   0.
sig_band_width  =  10 
ref_band_width  =  10 
print_bits      =  3

[ImgAlgos.ImgSpectraProc] 
source          = DetInfo(:Opal1000)
key_in          = spectra
print_bits      =  15

[ImgAlgos.ImgSaveInFile:2]
source        = DetInfo(:Opal1000)
key           = spectra
fname         = spec-xppi0412
saveAll       = true

[ImgAlgos.ImgSaveInFile]
source        = DetInfo(:Opal1000)
key           = img
fname         = img-xppi0412
saveAll       = true

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

[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     800     900    1000
Signal:    1211    4062   11150   17070   16406   12949    7991    5168    3968    3542    3811
Refer.:     933    3485   10425   17128   17791   13522    8315    5000    3390    2967    3193
Diff. :   0.259   0.153   0.067  -0.003  -0.081  -0.043  -0.040   0.033   0.157   0.177   0.176
[info:ImgAlgos.ImgSpectraProc] Run=0060 Evt=000100 Time=20120507-125420.982421325 done...

Example for module ImgAlgos::ImgSaveInFile

Code Block

bgColor	#F7F7ED

modules = ... ImgAlgos.ImgSaveInFile:1 ...

[ImgAlgos.ImgSaveInFile:1]
source         = DetInfo(:Opal1000)   # or CxiDs1.0:Cspad.0
key            = img
fname          = my-img
#ftype          = txt
#ftype          = bin
#ftype          = png
ftype          = tiff
#eventSave     = 5
saveAll        = true

See Module ImgAlgos::ImgSaveInFile

Example for module ImgPeakFinder and ImgPeakFilter for CSPad

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

Code Block

bgColor	#F7F7ED

[psana]
files   = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-1>.xtc \
          ...
          /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-N>.xtc

events      =  1000
experiment  = cxii0212
calib-dir   = ana-cxii0212/calib

modules = cspad_mod.CsPadCalib \
          ImgAlgos.CSPadMaskApply \
          CSPadPixCoords.CSPadImageProducer \
          ImgAlgos.ImgPeakFinder \
          ImgAlgos.ImgPeakFilter \
          ImgAlgos.ImgSaveInFile:1

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

[ImgAlgos.CSPadMaskApply]
source            = DetInfo(CxiDs1.0:Cspad.0)
inkey             = calibrated
outkey            = masked_arr
mask_fname        = <your-local-directory>/<mask-file-name>.dat
masked_amp        =  0
print_bits        =  5
mask_control_bits = 15

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

[ImgAlgos.ImgPeakFinder] 
source         = DetInfo(CxiDs1.0:Cspad.0)
key            = img
peaksKey       = peaks
threshold_low  = 2
threshold_high = 5
sigma          = 1.5
smear_radius   = 5
peak_radius    = 7
xmin           = 20
xmax           = 1700
ymin           = 20
ymax           = 1700
#testEvent      = 5
print_bits     = 3
#finderIsOn     = true

[ImgAlgos.ImgPeakFilter] 
source         = DetInfo(CxiDs1.0:Cspad.0)
key            = peaks
threshold_peak = 5
threshold_total= 0
n_peaks_min    = 10
print_bits     = 11
fname          = cspad-img
selection_mode = SELECTION_ON

[ImgAlgos.ImgSaveInFile:1]
source         = CxiDs1.0:Cspad.0
key            = img
fname          = cspad-img
#eventSave     = 1
saveAll        = true

Example for module ImgAlgos::CSPadArrAverage

See Module ImgAlgos::CSPadArrAverage

Configuration file example for evaluation of pedestals:

Code Block

bgColor	#F7F7ED

[psana]
modules = ImgAlgos.CSPadArrAverage
files   = <path-to-the-dark-run-file>.xtc

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

Configuration file example for evaluation of background:

Code Block

bgColor	#F7F7ED

[psana]
files       = <path-to-the-background-run-file>.xtc
modules     = cspad_mod.CsPadCalib ImgAlgos.CSPadArrAverage
skip-events = 500
events      = 1000000

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

[ImgAlgos.CSPadArrAverage]
source  = DetInfo(CxiDs1.0:Cspad.0)
key     = calibrated
avefile = cspad-background-ave.dat
rmsfile = cspad-background-rms.dat
print_bits  = 15

Images of the CSPad arrays for averaged and rms values, respectively, in one of the CXI runs:
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 \
        /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-2>.xtc \
        ...
        /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-N>.xtc
skip-events = 500
events      = 10
modules     = cspad_mod.CsPadCalib ImgAlgos.CSPadBkgdSubtract

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


[ImgAlgos.CSPadBkgdSubtract]
source        = DetInfo(CxiDs1.0:Cspad.0)
inputKey      = calibrated
outputKey     = bkgd_subtracted
bkgd_fname    = <the-file-name-with-background-array>
norm_sector   = 0
print_bits    = 3

The file with the background array, bkgd_fname, was obtained by averaging 1000 events using module CSPadArrAverage. Subtraction is done with normalization for norm_sector=0.

Event image and pixel amplitude spectrum before and after the background subtraction are shown in plots:
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*185 388.

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 \
          ImgAlgos.CSPadBkgdSubtract \
          ImgAlgos.CSPadMaskApply \
          ...
[cspad_mod.CsPadCalib]
inputKey      = 
outputKey     = calibrated_arr
doPedestals   = yes
doPixelStatus = no
doCommonMode  = no

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

[ImgAlgos.CSPadMaskApply]
source            = DetInfo(CxiDs1.0:Cspad.0)
inkey             = bkgd_subtracted_arr
outkey            = masked_arr
mask_fname        = ana-cxi49012/cspad-cxi49012-r0025-mask-40.dat
masked_amp        =  0
print_bits        =  3
mask_control_bits =  1

where

cspad_mod.CsPadCalib - subtracts the pedestals from raw CSPad data,

ImgAlgos.CSPadBkgdSubtract - subtracts the background,

ImgAlgos.CSPadMaskApply - apply the mask.

In the test with images for background represented by the water and solvent rings this filter provides the background suppression factor about 100.

The background images that still pass this filter have significantly larger intensity with respect to averaged background:
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/cxi/cxi49012/xtc/e158-r0020-s03-c00.xtc \
          /reg/d/psdm/cxi/cxi49012/xtc/e158-r0020-s04-c00.xtc \
          /reg/d/psdm/cxi/cxi49012/xtc/e158-r0020-s05-c00.xtc

#skip-events = 1000
events      = 10

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

[ImgAlgos.CSPadArrNoise]
source          = DetInfo(CxiDs1.0:Cspad.0)
key             = calibrated
statusfile      = ana-cxi49012/cspad-cxi49012-r0020-noise-status.dat
maskfile        = ana-cxi49012/cspad-cxi49012-r0200-noise-mask.dat
print_bits      = 255
rmin            = 3
dr              = 1
SoNThr          = 3
frac_noisy_imgs = 0.15

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

Code Block

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 \
          ImgAlgos.CSPadMaskApply \
          ImgAlgos.CSPadArrPeakFinder

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

[ImgAlgos.CSPadMaskApply]
source            = DetInfo(CxiDs1.0:Cspad.0)
inkey             = calibrated
outkey            = masked_arr
mask_fname        = ana-cxi49012/cspad-cxi49012-r0150-mask-badregs.dat
#mask_fname        = ana-cxi49012/cspad-cxi49012-r0150-mask-bkgd.dat
#mask_fname        = ana-cxi49012/cspad-cxi49012-r0150-mask-rects.dat
masked_amp        =  8
print_bits        =  1
mask_control_bits = 15

[ImgAlgos.CSPadArrPeakFinder]
source            = DetInfo(CxiDs1.0:Cspad.0)
key               = masked_arr
key_peaks_out     = peaks

hot_pix_mask_inp_file = ana-cxi49012/cspad-cxi49012-r0150-noise-mask.dat
hot_pix_mask_out_file = ana-cxi49012/cspad-cxi49012-r0150-noise-mask-out.dat
frac_noisy_evts_file  = ana-cxi49012/cspad-cxi49012-r0150-noise-frac.dat

evt_file_out      = tmp/cspad-ev-

rmin              =     3
dr                =     1
SoNThr            =     3
frac_noisy_imgs   =   0.1

peak_npix_min     =     4
peak_npix_max     =    25
peak_amp_tot_thr  =   100.

event_npeak_min   =    10
event_amp_tot_thr =  1000.

nevents_mask_update = 100
nevents_mask_accum  =  50

selection_mode    = SELECTION_ON
out_file_bits     =    15
print_bits        =    512

Results:

Code Block

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 \
          ImgAlgos.CSPadArrPeakFinder \
          pyimgalgos.ex_peaks_nda
#         EventKeys

[cspad_mod.CsPadCalib]
inputKey      = 
outputKey     = calibrated
doPedestals   = yes
doPixelStatus = yes
doCommonMode  = yes

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             = calibrated
outkey            = masked_arr
mask_fname        = ana-cxi49012/cspad-cxi49012-r0150-mask-badregs.dat
#mask_fname        = ana-cxi49012/cspad-cxi49012-r0150-mask-bkgd.dat
#mask_fname        = ana-cxi49012/cspad-cxi49012-r0150-mask-rects.dat
masked_amp        =  8
print_bits        =  1
mask_control_bits = 15

[ImgAlgos.CSPadArrPeakFinder]
source            = DetInfo(CxiDs1.0:Cspad.0)
key               = masked_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.

...

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

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

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Auxiliary scripts

Examples for package cspad_mod

Example for module cspad_mod::CsPad2x2Pedestals

Examples for package CSPadPixCoords

Example for

module CSPadPixCoords::CSPadImageProducer

Example for module CSPadPixCoords::

CSPadNDArrProducer

Example for module CSPadPixCoords::CSPad2x2NDArrProducer

Example for module CSPadPixCoords::CSPad2x2NDArrReshape

Example for module CSPadPixCoords::CSPad2x2ImageProducer

Example for package ImgPixSpectra

Example for module ImgPixSpectra::CSPadPixSpectra

Example for module ImgPixSpectra::CSPad2x2PixSpectra

Examples for package ImgAlgos

Example for module ImgAlgos::Tahometer

Example for module ImgAlgos::PnccdImageProducer

Example for module ImgAlgos::CameraImageProducer

Example for module ImgAlgos::PrincetonImageProducer

Example for package ImgPixSpectra

Example for module ImgPixSpectra::CSPadPixSpectra

Example for module ImgAlgos::AcqirisArrProducer

Example for module ImgPixSpectra::CSPad2x2PixSpectra

Examples for package ImgAlgos

Example for module ImgAlgos::Tahometer

Example for module ImgAlgos::EpixNDArrProducer

Example for module ImgAlgos::PnccdImageProducer

Example for module ImgAlgos::AcqirisAverage

Example for module ImgAlgos::AcqirisCalib

Example for module ImgAlgos::CameraImageProducer

Example for module ImgAlgos::PrincetonImageProducer

Example for combination of Acqiris modules

Example for module ImgAlgos::AcqirisArrProducer

Example for module ImgAlgos::ImgAverage

Example for module ImgAlgos::AcqirisAverage

Example for module ImgAlgos::ImgMaskEvaluation

Example for module ImgAlgos::ImgCalib

Example for module ImgAlgos::

AcqirisCalib

Example for module ImgAlgos::

AcqirisCFD

Example for module ImgAlgos::ImgPeakFilter

Example for module ImgAlgos::ImgPeakFinderAB

Example for combination of Acqiris modules

Example for module ImgAlgos::ImgHitFinder

Example for module ImgAlgos::NDArrImageProducer

Example for module ImgAlgos::ImgSpectra

Example for module ImgAlgos::NDArrAverage

Example for module ImgAlgos::NDArrCalib

Example for module ImgAlgos::ImgSpectraProc

Example for module ImgAlgos::ImgSaveInFile

Example for module ImgPeakFinder and ImgPeakFilter for CSPad

Example for module ImgAlgos::CSPadArrAverage

Example for module ImgAlgos::CSPadBkgdSubtract

Example for Module ImgAlgos::CSPadMaskApply

Example for module ImgAlgos::NDArrDropletFinder

Example for module ImgAlgos::PixCoordsProducer

Example for module ImgAlgos::CSPadArrNoise

Example for Module ImgAlgos::CSPadArrPeakFinder

Example for module ImgAlgos::ImgAverage

Example for module ImgAlgos::ImgMaskEvaluation

Masks: noisy, saturated, and combined:

Example for module ImgAlgos::ImgCalib

Example for module ImgAlgos::ImgRadialCorrection

Example for module ImgAlgos::ImgPeakFinder

Example for module ImgAlgos::ImgPeakFilter

Example for module ImgAlgos::ImgPeakFinderAB

Example for module ImgAlgos::ImgHitFinder

Example for module ImgAlgos::ImgSpectra

Example for module ImgAlgos::ImgSpectraProc

Example for module ImgAlgos::ImgSaveInFile

Example for module ImgPeakFinder and ImgPeakFilter for CSPad

Example for module ImgAlgos::CSPadArrAverage