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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::

...

ImgSaveInFile

Code Block

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

[ImgAlgos.ImgSaveInFile:1]
source         = DetInfo(:Opal1000)   # or CxiDs1.0:Cspad.0
key
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  =  img
fname  =  1000
experiment  = cxii0212
calib-dir   = anamy-cxii0212/calib

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

[cspad_mod.CsPadCalib]
inputKey/reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-N>.xtc

events      =  1000
outputKey   experiment  = calibratedcxii0212
doPedestalscalib-dir   = yes
doPixelStatus = no
doCommonMode  = yes

[ImgAlgos.CSPadMaskApply]
sourceana-cxii0212/calib

modules = cspad_mod.CsPadCalib \
            = DetInfo(CxiDs1.0:Cspad.0)
inkeyImgAlgos.CSPadMaskApply \
          CSPadPixCoords.CSPadImageProducer \
   =  calibrated
outkey     ImgAlgos.ImgPeakFinder \
      = masked_arr
mask_fname    ImgAlgos.ImgPeakFilter \
         = <your-local-directory>/<mask-file-name>.dat
masked_amp ImgAlgos.ImgSaveInFile:1

[cspad_mod.CsPadCalib]
inputKey      = 
outputKey =  0
print_bits  = calibrated
doPedestals   = yes
doPixelStatus =  5
mask_control_bitsno
doCommonMode  = 15yes

[CSPadPixCoordsImgAlgos.CSPadImageProducerCSPadMaskApply]
calibDirsource            = /reg/d/psdm/<instrument>/<experiment>/calib
typeGroupName  = CsPad::CalibV1
sourceDetInfo(CxiDs1.0:Cspad.0)
inkey             = CxiDs1.0:Cspad.0
keycalibrated
outkey            = masked_arr
imgkeymask_fname        = <your-local-directory>/<mask-file-name>.dat
masked_amp        =  img0
print_bits        =  0
#tiltIsApplied 5
mask_control_bits = true15

[ImgAlgosCSPadPixCoords.ImgPeakFinderCSPadImageProducer] 
source calibDir        = DetInfo(= /reg/d/psdm/<instrument>/<experiment>/calib
typeGroupName  = CsPad::CalibV1
source         = CxiDs1.0:Cspad.0)
key            = img
peaksKeymasked_arr
imgkey         = peaksimg
threshold_lowprint_bits     = 2
threshold_high 0
#tiltIsApplied  = 5
sigma true

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

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

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

Example for Module ImgAlgos::CSPadArrAverage

See Module ImgAlgos::

...

CSPadArrAverage

Configuration file example for evaluation of pedestals:

Code Block

[psana]
modules = ... ImgAlgos.ImgSaveInFile:1 ...ImgAlgos.CSPadArrAverage
files   = <path-to-the-dark-run-file>.xtc

[ImgAlgos.ImgSaveInFile:1CSPadArrAverage]
source         = DetInfo(:Opal1000)   # or CxiDs1.0:Cspad.0)
key     =
avefile = cspad-pedestals-ave.dat
rmsfile = cspad-pedestals-rms.dat
print_bits   = img15
fnameevts_stage1 = 100
evts_stage2        = my-img
#eventSave     = 5
saveAll        = true

See Module ImgAlgos::ImgSaveInFile

Example for Module ImgAlgos::CSPadArrAverage

...

= 100
gate_width1 = 100
gate_width2 =  10

Configuration file example for evaluation of pedestalsbackground:

Code Block
[psana]
modulesfiles   = ImgAlgos.CSPadArrAverage
files   = <path-to-the-darkbackground-run-file>.xtc

[modules     = cspad_mod.CsPadCalib ImgAlgos.CSPadArrAverage]
source skip-events = DetInfo(CxiDs1.0:Cspad.0)
key500
events      =
avefile = cspad-pedestals-ave.dat
rmsfile = cspad-pedestals-rms.dat
print_bits 1000000

[cspad_mod.CsPadCalib]
inputKey      = 
outputKey     = 15calibrated
evts_stage1doPedestals = 100
evts_stage2 = 100yes
gate_width1doPixelStatus = 100
gate_width2no
doCommonMode  =  10

Configuration file example for evaluation of background:

Code Block

[psana]
files  no

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

[cspad_mod.CsPadCalib]
inputKey    -background-ave.dat
rmsfile = cspad-background-rms.dat
print_bits  = 
outputKey     = calibrated
doPedestals   = 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

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

Code Block

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

...

Selected events

ev-007713:

ev-008944:

Example for

...

Module ImgAlgos::CSPadArrPeakAnalysis

See Module ImgAlgos::CSPadArrPeakAnalysis

Example of the psana configuration file:

Code Block

modules = cspad_mod.CsPadCalib \

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

Code Block

[psana]         ImgAlgos.CSPadMaskApply \
          ImgAlgos.CSPadArrPeakFinder \
          ImgAlgos.CSPadArrPeakAnalysis

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

[ImgAlgos.CSPadArrPeakAnalysis]
source             = DetInfo(CxiDs1.0:Cspad.0)
key             
files   = peaks
print_bits     = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/e158-r0021-s00-c00.xtc \
  = 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 AddedImage Added

Example for TimeStampFilter and XtcOutputModule

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

Code Block

[psana]          /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/e158-r0021-s01-c00.xtc \
                /reg/d/psdm/                                         
files         = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/e158-r0021-s02s00-c00.xtc \
                /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/e158-r0021-s03s01-c00.xtc \
                /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/e158-r0021-s04s02-c00.xtc \
                /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/e158-r0021-s05s03-c00.xtc

skip-events   = 10
events \
        = 100
modules       = ImgAlgos.TimeStampFilter  /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

...

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

Example for Module ImgAlgos::CSPadArrPeakAnalysis

See Module ImgAlgos::CSPadArrPeakAnalysis

Example of the psana configuration file:

Code Block

modules = cspad_mod.CsPadCalib \
          ImgAlgos.CSPadMaskApply \
          ImgAlgos.CSPadArrPeakFinder \
          ImgAlgos.CSPadArrPeakAnalysis

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

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

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

Image RemovedImage Removed