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About

This page provides examples for selected modules from Psana Module Catalog.

Auxiliary scripts

A few python scripts in ImgPixSpectra/data/ show how to process/plot the spectral array stored in the file.

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  • psana.cfg - set non-default parameters to 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:

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Output files contain results, which can be plotted for average values:

and rms values:

Example for package CSPadPixCoords

How to write the CSPad image in text file:

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See Package CSPadPixCoords

Example for module CSPadPixCoords::CSPad2x2ImageProducer

See Module CSPadPixCoords::CSPad2x2ImageProducer

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Code Block
[psana]
files    = /reg/d/psdm/xpp/xpptut13/xtc/e308-r0008-s02-c00.xtc \
           /reg/d/psdm/xpp/xpptut13/xtc/e308-r0008-s03-c00.xtc

#modules = cspad_mod.CsPad2x2Pedestals

#calib-dir = ./calib
calib-dir = /reg/d/psdm/xpp/xpptut13/xtc/calib

modules  = cspad_mod.CsPadCalib:0 \ 
           cspad_mod.CsPadCalib:1 \ 
           CSPadPixCoords.CSPad2x2ImageProducer:0 \
           CSPadPixCoords.CSPad2x2ImageProducer:1 \ 
           ImgAlgos.ImgSaveInFile:0  \
           ImgAlgos.ImgSaveInFile:1

events   = 5

[cspad_mod.CsPadCalib:0]
source        = DetInfo(XppGon.0:Cspad2x2.0)
inputKey      = 
outputKey     = calibrated_arr0
doPedestals   = yes
doPixelStatus = no
doCommonMode  = yes

[cspad_mod.CsPadCalib:1]
source        = DetInfo(XppGon.0:Cspad2x2.1)
inputKey      = 
outputKey     = calibrated_arr1
doPedestals   = yes
doPixelStatus = no
doCommonMode  = yes


[CSPadPixCoords.CSPad2x2ImageProducer:0]
calibDir         = /reg/d/psdm/xpp/xpptut13/xtc/calib
typeGroupName    = CsPad2x2::CalibV1
source           = DetInfo(XppGon.0:Cspad2x2.0)
inkey            = calibrated_arr0
outimgkey        = Image
tiltIsApplied    = false
useWidePixCenter = false
print_bits       = 15

[CSPadPixCoords.CSPad2x2ImageProducer:1]
calibDir         = /reg/d/psdm/xpp/xpptut13/xtc/calib
typeGroupName    = CsPad2x2::CalibV1
source           = DetInfo(XppGon.0:Cspad2x2.1)
inkey            = calibrated_arr1
outimgkey        = Image
tiltIsApplied    = false
useWidePixCenter = false
print_bits       = 15



[ImgAlgos.ImgSaveInFile:0]
source         = DetInfo(:Cspad2x2.0)
key            = Image
fname          = cspad2x2.0
ftype          = txt
#ftype          = tiff
saveAll        = true
print_bits     = 3
#eventSave     = 5

[ImgAlgos.ImgSaveInFile:1]
source         = DetInfo(:Cspad2x2.1)
key            = Image
fname          = cspad2x2.1
#ftype          = txt
ftype          = tiff
saveAll        = true
print_bits     = 3
#eventSave     = 5

Example for package ImgPixSpectra

See Package ImgPixSpectra

Modules:

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generates image for limited range of pixels for CSPad, MiniCSPad, or Camera, respectively:

Examples for package ImgAlgos

See Package ImgAlgos

Example for module ImgAlgos::Tahometer

See Module ImgAlgos::Tahometer

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Code Block
[psana]           
files         = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\
                /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-2>.xtc

modules       = ImgAlgos.Tahometer

[ImgAlgos.Tahometer]
dn         = 10
print_bits = 7

Example for module ImgAlgos::PnccdImageProducer

See Module ImgAlgos::PnccdImageProducer

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

Example for module ImgAlgos::CameraImageProducer

See Module ImgAlgos::CameraImageProducer

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

Example for module ImgAlgos::PrincetonImageProducer

See Module ImgAlgos::PrincetonImageProducer

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Code Block
[psana]                                                               
files         = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\
                /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-2>.xtc
modules       = ImgAlgos.PrincetonImageProducer \
                ImgAlgos.ImgSaveInFile
events          = 3

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

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

Example for module ImgAlgos::ImgAverage

See Module ImgAlgos::ImgAverage

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Code Block
[psana]                                                               
files   = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name>.xtc
modules = ImgAlgos.CameraImageProducer \
          ImgAlgos.ImgAverage
events  = 1000

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

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

Example for module ImgAlgos::ImgMaskEvaluation

See Module ImgAlgos::ImgMaskEvaluation

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Masks: noisy, saturated, and combined:

Example for module ImgAlgos::ImgCalib

See Module ImgAlgos::ImgCalib

...

Example of the mask file and resulting image:

Example for module ImgAlgos::ImgRadialCorrection

See Module ImgAlgos::ImgRadialCorrection

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

Example for module ImgAlgos::ImgPeakFinder

See Module ImgAlgos::ImgPeakFinder

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  1. raw image,
  2. 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,
  3. smeared image,
  4. raw image with found peaks (marked by the red circles)
  5. zoom of the previous plot.

Example for module ImgAlgos::ImgPeakFilter

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

Example for module ImgAlgos::ImgPeakFinderAB

See Module ImgAlgos::ImgPeakFinderAB

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

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

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

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

Results:

Example for module ImgAlgos::ImgSpectra

See Module ImgAlgos::ImgSpectra
Configuration file for psana:

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

or graphics for several images:

Example for module ImgAlgos::ImgSpectraProc

See Module ImgAlgos::ImgSpectraProc
Configuration file for psana:

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Code Block
[info:ImgAlgos.ImgSpectraProc] Spectral array shape =3, 1024
[info:ImgAlgos.ImgSpectraProc] Image spectra for run=0060 Evt=000100
Column:       0     100     200     300     400     500     600     700     800     900    1000
Signal:    1211    4062   11150   17070   16406   12949    7991    5168    3968    3542    3811
Refer.:     933    3485   10425   17128   17791   13522    8315    5000    3390    2967    3193
Diff. :   0.259   0.153   0.067  -0.003  -0.081  -0.043  -0.040   0.033   0.157   0.177   0.176
[info:ImgAlgos.ImgSpectraProc] Run=0060 Evt=000100 Time=20120507-125420.982421325 done...

Example for module ImgAlgos::ImgSaveInFile

Code Block
modules = ... ImgAlgos.ImgSaveInFile:1 ...

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

See Module ImgAlgos::ImgSaveInFile

Example for module ImgPeakFinder and ImgPeakFilter for CSPad

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

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

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

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

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

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

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

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

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

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

Example for module ImgAlgos::CSPadArrAverage

See Module ImgAlgos::CSPadArrAverage

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Images of the CSPad arrays for averaged and rms values, respectively, in one of the CXI runs:

Example for module ImgAlgos::CSPadBkgdSubtract

See Module ImgAlgos::CSPadBkgdSubtract

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Other event with better subtracted background:

Example for Module ImgAlgos::CSPadMaskApply

See Module ImgAlgos::CSPadMaskApply

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Input parameter mask_control_bits allows to control masking regions of 2x1. For example, if all edges need to be masked, then use mask_control_bits = 15, which gives image array like:

where red regions/lines of pixels of amplitude=8 are masked.

Example for module ImgAlgos::CSPadArrNoise

See Module ImgAlgos::CSPadArrNoise

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Pixel mask for noisy pixels with |S/N| > SoNThr:

Example for Module ImgAlgos::CSPadArrPeakFinder

See Module ImgAlgos::CSPadArrPeakFinder

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Selected events

ev-007713:

ev-008944:

Example for module ImgAlgos::CSPadArrPeakAnalysis

See Module ImgAlgos::CSPadArrPeakAnalysis

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After execution in psana the file.root containing histogram(s) and ntuple(s) will be produced. Then, auxiliary script in root, running by the commend
root -q -f proc.C
produces the plots with histograms:

Example for TimeStampFilter and XtcOutputModule

This example demonstrates how to run psana with the time stamp filter and event writer in xtc file.
Both modules are available in psana library and they need only to be described in the configuration file. For example, the configuration file tstamp-filter-and-event-writer.cfg may looks like:

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