About

This page provides examples for selected modules from psana - Module Catalog.

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See Module CSPadPixCoords::CSPad2x2NDArrProducer

Example for module CSPadPixCoords::

...

CSPad2x2NDArrReshape

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

[psana]
files#files = exp=meca1113:run=376
#events = 10
##skip-events     = /reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-1>.xtc
events= 0

modules = cspad_mod.CsPadCalib \
          = 5
modulesCSPadPixCoords.CSPad2x2NDArrProducer:clb \
         = CSPadPixCoords.CSPad2x2ImageProducer ImgAlgos.ImgSaveInFile

[CSPadPixCoords.CSPad2x2ImageProducer]
sourceCSPad2x2NDArrProducer:raw \
          = DetInfo(:Cspad2x2)
inkeyCSPadPixCoords.CSPad2x2NDArrReshape \
          =ImgAlgos.NDArrAverage:clb \
outimgkey         = Image
tiltIsAppliedImgAlgos.NDArrAverage:raw
#   = true
print_bits     = 15EventKeys

[ImgAlgoscspad_mod.ImgSaveInFileCsPadCalib]
sourceinputKey        = DetInfo(:Cspad2x2)
keyoutputKey     = clb_data
doPedestals   = yes
doPixelStatus = Imageyes
fnamedoCommonMode  = yes

[CSPadPixCoords.CSPad2x2NDArrProducer:clb]
source      = cspad2x2
saveAllMecTargetChamber.0:Cspad2x2.1
inkey       = trueclb_data
#eventSaveoutkey     = 5

...

cspad2x2

...

.

...

Image RemovedImage Removed

Configuration file for cspad2x2 with pedestal subtraction

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

[psana]
files1_clb:as_data
outtype    = /reg/d/psdm/mec/mec73313/xtc/e268-r0180-s02-c00.xtc
#calib-dir = ./calib

modules  = cspad_mod.CsPadCalib CSPadPixCoords.CSPad2x2ImageProducer ImgAlgos.ImgSaveInFile
events   = int16
print_bits = 5

[cspad_mod.CsPadCalibCSPadPixCoords.CSPad2x2NDArrProducer:raw]
source        = DetInfo(MecTargetChamber.0:Cspad2x2.3)1
inputKeyinkey      = 
outputKeyoutkey     = calibrated_arr
doPedestalscspad2x2.1_raw:as_data
outtype   = yes
doPixelStatus = noint16
doCommonModeprint_bits  = no
5

[CSPadPixCoords.CSPad2x2ImageProducerCSPad2x2NDArrReshape]
calibDirsource     =  = /reg/d/psdm/mec/mec73313/calib
typeGroupNameMecTargetChamber.0:Cspad2x2.1
keys_in    = CsPad2x2::CalibV1
#source cspad2x2.1_raw:as_data cspad2x2.1_clb:as_data
print_bits = 255

[ImgAlgos.NDArrAverage:clb]
source       = DetInfo(MecTargetChamber.0:Cspad2x2.3)1
sourcekey          = :Cspad2x2.3
inkey    cspad2x2.1_clb
avefile      = calibrated_arr-ave-clb
outimgkeyrmsfile      = Image
tiltIsApplied  = truearr-rms-clb
print_bits     = 15255


[ImgAlgos.ImgSaveInFileNDArrAverage:raw]
source         = DetInfo(MecTargetChamber.0:Cspad2x2.3)1
key            = Image
fnamecspad2x2.1_raw
avefile          = cspad2x2.3
saveAllarr-ave-raw
rmsfile        = truearr-rms-raw
print_bits     = 3
#eventSave= 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:

#!/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:

Example for module CSPadPixCoords::CSPad2x2ImageProducer

See Module CSPadPixCoords::CSPad2x2ImageProducer

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

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

[CSPadPixCoords.CSPad2x2ImageProducer]
source

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

[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
true
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

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 AddedImage Added

Configuration file for cspad2x2 with pedestal subtraction

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

[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.CsPadCalib]
source          = txt
ftypeDetInfo(MecTargetChamber.0:Cspad2x2.3)
inputKey      = 
outputKey     = tiffcalibrated_arr
saveAlldoPedestals   = yes
doPixelStatus = no
doCommonMode  = true
print_bitsno


[CSPadPixCoords.CSPad2x2ImageProducer]
calibDir       = 3
#eventSave     = 5

Example for package ImgPixSpectra

See Package ImgPixSpectra

Modules:

• ImgPixSpectra::CSPadPixSpectra
• ImgPixSpectra::CSPad2x2PixSpectra
• ImgPixSpectra::CameraPixSpectra

Example for module ImgPixSpectra::CSPadPixSpectra

See module description in Module ImgPixSpectra::CSPadPixSpectra
Configuration file psana-cxib2313-r0114-cspad-pix-spectra.cfg:

# 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/reg/d/psdm/mec/mec73313/calib
typeGroupName  = CsPad2x2::CalibV1
#source        = DetInfo(MecTargetChamber.0:Cspad2x2.3)
source         = :Cspad2x2.3
inkey          = calibrated_arr
outimgkey      = Image
tiltIsApplied  = true
print_bits     = 15


[ImgAlgos.ImgSaveInFile]
source         = DetInfo(CxiDs1MecTargetChamber.0:CspadCspad2x2.03)
inputKeykey      = 
outputKey     = calibratedImage
doPedestalsfname     = yes
doPixelStatus = no
doCommonMode  = yes

[ImgPixSpectra.CSPadPixSpectra]
sourcecspad2x2.3
saveAll        = CxiDs1.0:Cspad.0
inputKeytrue
print_bits      = calibrated3
amin#eventSave       = 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:

[psana]
files    =   -20.
amax/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 =  20./calib
nbinscalib-dir = /reg/d/psdm/xpp/xpptut13/xtc/calib

modules  = cspad_mod.CsPadCalib:0 \  
 =    10
arr_fname     = cspad_spectral_array.txt

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

To run this script use command

psana -c psana-cxib2313-r0114-cspad-pix-spectra.cfg

which produces two files:

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

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

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

[ImgPixSpectra.CSPad2x2PixSpectramod.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        = CxiSc1DetInfo(XppGon.0:Cspad2x2.01)
amininputKey      = 
outputKey   =  = 500.
amaxcalibrated_arr1
doPedestals   = yes
doPixelStatus = no
doCommonMode    =  1000.
nbinsyes


[CSPadPixCoords.CSPad2x2ImageProducer:0]
calibDir         =   100
arr_fname/reg/d/psdm/xpp/xpptut13/xtc/calib
typeGroupName     = cspad2x2-pix-spectra.txt

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

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:

[psana]CsPad2x2::CalibV1
source           = 
filesDetInfo(XppGon.0:Cspad2x2.0)
inkey            = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\
calibrated_arr0
outimgkey        = Image
tiltIsApplied    = false
useWidePixCenter  /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-2>.xtc

modules= false
print_bits       = ImgAlgos.Tahometer15

[ImgAlgosCSPadPixCoords.TahometerCSPad2x2ImageProducer:1]
dncalibDir         = 10
print_bits = 7

Example for module ImgAlgos::PnccdImageProducer

See Module ImgAlgos::PnccdImageProducer

Example of the psana configuration file:

[psana]   /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
filesfname          = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\
cspad2x2.0
ftype          = txt
#ftype      /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-2>.xtc
#skip-events    = 100tiff
eventssaveAll        =  5
modulestrue
print_bits     = 3
#eventSave     = ImgAlgos.PnccdImageProducer ImgAlgos.ImgSaveInFile5

[ImgAlgos.PnccdImageProducerImgSaveInFile:1]
source         = DetInfo(:pnCCDCspad2x2.1)
inkey  key       =
outimgkey     = imgpnccd
print_bits    = 1

[ImgAlgos.ImgSaveInFile]
sourceImage
fname          = DetInfo(:pnCCD)
key cspad2x2.1
#ftype          = imgpnccdtxt
fnameftype          = pnccd-img-evtiff
saveAll        = true
#eventSaveprint_bits     = 82
print_bits3
#eventSave     = 1

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

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:

5

Example for package ImgPixSpectra

See Package ImgPixSpectra

Modules:

• ImgPixSpectra::CSPadPixSpectra
• ImgPixSpectra::CSPad2x2PixSpectra
• ImgPixSpectra::CameraPixSpectra

Example for module ImgPixSpectra::CSPadPixSpectra

See module description in Module ImgPixSpectra::CSPadPixSpectra
Configuration file psana-cxib2313-r0114-cspad-pix-spectra.cfg:

# 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

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

[cspad_mod.CsPadCalib]
source        = 
#calib-dir = /reg/d/psdm/SXR/sxrb5914/calib
files = exp=sxrb5914:run=245
events = 10

modules = ImgAlgos.Tahometer \
DetInfo(CxiDs1.0:Cspad.0)
inputKey      = 
outputKey     = calibrated
doPedestals   = yes
doPixelStatus = no
doCommonMode  = yes

[ImgPixSpectra.CSPadPixSpectra]
source          ImgAlgos.PnccdNDArrProducer \
= CxiDs1.0:Cspad.0
inputKey          ImgAlgos.NDArrCalib \
= calibrated
amin          ImgAlgos.PnccdImageProducer= \
          ImgAlgos.NDArrAverage

[ImgAlgos.Tahometer]
dn-20.
amax         = 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_bits20.
nbins         =    10
arr_fname     = cspad_spectral_array.txt

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

To run this script use command

psana -c psana-cxib2313-r0114-cspad-pix-spectra.cfg

which produces two files:

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

[psana]
files         = /reg/d/psdm/<instrument>/<experiment>/<file-name>.xtc
modules       =    1ImgPixSpectra.CSPad2x2PixSpectra

[ImgAlgosImgPixSpectra.PnccdImageProducerCSPad2x2PixSpectra]
source        = DetInfo(CampCxiSc1.0:pnCCDCspad2x2.1)0
inkeyamin          = calibrated
outimgkey  500.
amax   = pnccd-img
gap_rows      =  0
gap_cols1000.
nbins         = 16  100
gaparr_valuefname     = 0cspad2x2-pix-spectra.txt

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

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:

[psana]   
print_bits    = 1

[ImgAlgos.NDArrAverage]
source       = DetInfo(Camp.0:pnCCD.1)
key
files          = pnccd-img
avefile/reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\
      = pnccd-ave
rmsfile      = pnccd-rms
#maskfile   /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-2>.xtc

modules   = pnccd-msk
#hotpixfile   = pnccd-hot
thr_rms_ADU  = 160
thr_min_ADU  = 2
thr_max_ADUImgAlgos.Tahometer

[ImgAlgos.Tahometer]
dn         = 1000010
print_bits   = 29

Image RemovedImage RemovedImage Removed

7

Example for module ImgAlgos::

...

EpixNDArrProducer

See Module ImgAlgos::CameraImageProducerEpixNDArrProducer

Example of the psana configuration file:

[psana]
files         = exp=xppi0414:run=94
events        = 100
modules       = ImgAlgos.EpixNDArrProducer \
                ImgAlgos.NDArrAverage

[ImgAlgos.EpixNDArrProducer]
source = DetInfo(:Epix10k)
key_in =
key_out = epix-nda
outtype = float
print_bits = 255

[ImgAlgos.NDArrAverage]
source       = DetInfo(:Epix10k)
key   
files       = epix-nda
avefile   = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc
modules      = 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:

[psana] ImgAlgos.CameraImageProducer ImgAlgos.ImgSaveInFile
events          = 5

[ImgAlgos.CameraImageProducer] 
source          = DetInfo(:Opal1000)
key_in          = 
key_out         = img
subtract_offset = true
print_bits      = 15

[ImgAlgos.ImgSaveInFile]
source        = DetInfo(:Opal1000)
key  
files         = img
fname/reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\
         = img-from-my-experiment
saveAll      /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-2>.xtc
#skip-events = true100
#eventSaveevents      = 1

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

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

Example for module ImgAlgos::PrincetonImageProducer

See Module ImgAlgos::PrincetonImageProducer

Example of the psana configuration file:

[psana] 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
files#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:

[psana] = /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         
#calib-dir = DetInfo(:Princeton)
key_in          = 
key_out/reg/d/psdm/SXR/sxrb5914/calib
files = exp=sxrb5914:run=245
events = 10

modules = ImgAlgos.Tahometer \
          ImgAlgos.PnccdNDArrProducer \
  = img
subtract_offset = true
print_bits      = 31

[ImgAlgos.ImgSaveInFile]NDArrCalib \
source        = DetInfo(:Princeton)
key   ImgAlgos.PnccdImageProducer \
         = img
fname ImgAlgos.NDArrAverage

[ImgAlgos.Tahometer]
dn         = img-xcs
saveAll       = true
print_bits    = 31

Image Removed

...

Example for module ImgAlgos::AcqirisArrProducer

See description of parameters in Module ImgAlgos::AcqirisArrProducer

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

# 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.AcqirisArrProducer100
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        = AmoETOFDetInfo(Camp.0:AcqirispnCCD.0
key_in1)
inkey         = calibrated
outimgkey     = pnccd-img
keygap_wformrows      = acqiris_wform0
keygap_wtimecols      = acqiris_wtime16
fname_prefixgap_value     = acq0
print_bits    = 111


[ImgAlgos.ImgSaveInFile:wfNDArrAverage]
source         = AmoETOFDetInfo(Camp.0:AcqirispnCCD.01)
key            = acqiris_wform
fname   pnccd-img
avefile       = acqpnccd-AmoETOF-wform
ftype  ave
rmsfile        = txtpnccd-rms
#ftype#maskfile     = pnccd-msk
#hotpixfile    = tiff
#saveAllpnccd-hot
thr_rms_ADU  = 160
thr_min_ADU  = 2
thr_max_ADU  = true10000
print_bits     = 3
eventSave      = 5


[ImgAlgos.ImgSaveInFile:wt]
source= 29

Image AddedImage AddedImage Added

Example for module ImgAlgos::CameraImageProducer

See Module ImgAlgos::CameraImageProducer

Example of the psana configuration file:

[psana]         = AmoETOF.0:Acqiris.0
key            = acqiris_wtime
fname          = acq-AmoETOF-wtime
ftype          = txt
#ftype          = tiff
#saveAll        = true
print_bitsfiles     = 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 Removed  Image Removed

...

= /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc
modules         = ImgAlgos.CameraImageProducer ImgAlgos.ImgSaveInFile
events          = 5

[ImgAlgos.CameraImageProducer] 
source          = DetInfo(:Opal1000)
key_in          = 
key_out         = img
subtract_offset = true
print_bits      = 15

[ImgAlgos.ImgSaveInFile]
source        = DetInfo(:Opal1000)
key           = img
fname         = img-from-my-experiment
saveAll       = true
#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 of the psana configuration file:

[psana]                                                               
files        

...

Example for module ImgAlgos::AcqirisAverage

See description of parameters in Module ImgAlgos::AcqirisAverage

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

# 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<INSTRUMENT>/amo01509<experiment>/xtc/e8<file-r0125name-s00-c001>.xtc /reg/d\
                /reg/d/psdm/AMO<INSTRUMENT>/amo01509<experiment>/xtc/e8<file-r0125name-s01-c002>.xtc
filesmodules     = exp=amo01509:run=125:xtc

modules = ImgAlgos.AcqirisArrProducerPrincetonImageProducer \
                ImgAlgos.AcqirisAverage
ImgSaveInFile
skip-events =   0
events      = 10003


[ImgAlgos.AcqirisArrProducerPrincetonImageProducer] 
source          = AmoETOF.0:Acqiris.0DetInfo(:Princeton)
key_in          = 
key_wform  out   = acqiris_wform
key_wtime     = acqiris_wtimeimg
fnamesubtract_prefixoffset  = acqtrue
print_bits      = 331


[ImgAlgos.AcqirisAverageImgSaveInFile]
source        = DetInfo(:Princeton)
key      = AmoETOF.0:Acqiris.0
key_in     = img
fname         = acqiris_wform
key_aveimg-xcs
saveAll          = true
print_bits    = acqiris_average
fname_ave31

Image Added

Example for module ImgAlgos::AcqirisArrProducer

See description of parameters in Module ImgAlgos::AcqirisArrProducer

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

# 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_prefix     = acq
thresholds           = -0.005 -0.005 -0.005 -0.005 -0.005
is_positive_signal   = no
do_inverse_selection = yes
#skip_events          = 0
#proc_events          = 100
print_bitsAmoETOF.0:Acqiris.0
key_in        =
key_wform     = 255

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

• acq-amo01509-r0125-config.txt -- with Acqiris configuration parameters:

  Code Block

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

• acq-amo01509-r0125-ave-wfs.txt with averaged array of waveforms, which were below threshold (averaging for baseline level):

Image Removed

...

acqiris_wform
key_wtime     = acqiris_wtime
fname_prefix  = acq
print_bits    = 11


[ImgAlgos.ImgSaveInFile:wf]
source         = AmoETOF.0:Acqiris.0
key            = acqiris_wform
fname          = acq-AmoETOF-wform
ftype          = txt
#ftype          = tiff
#saveAll        = true
print_bits     = 3
eventSave      = 5


[ImgAlgos.ImgSaveInFile:wt]
source         = AmoETOF.0:Acqiris.0
key            = acqiris_wtime
fname          = acq-AmoETOF-wtime
ftype          = txt
#ftype          = tiff
#saveAll        = true
print_bits     = 3
eventSave      = 5

This script with psana does a few things:

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

This script saves 3 text files:

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

  Code Block

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

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

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

Image Added  Image Added

Example for module ImgAlgos::AcqirisAverage

See description of parameters in Module ImgAlgos::AcqirisAverage

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

# 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   

...

Example for module ImgAlgos::AcqirisCalib

See description of parameters in Module ImgAlgos::AcqirisCalib

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

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

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

modules = ImgAlgos.AcqirisArrProducer ImgAlgos.AcqirisCalib ImgAlgos.ImgSaveInFile:wf_raw ImgAlgos.ImgSaveInFile:wf_calib

skip-events = 0
events      = 10


[ImgAlgos.AcqirisArrProducer]
source        = AmoETOF.0:Acqiris.0
key_in        = 
key_wform     = acqiris_wform
key_wtime     = acqiris_wtime
fname_prefix  = acq
print_bits    = 1


[ImgAlgos.AcqirisCalib]
source               = AmoETOF.0:Acqiris.0
key_in               = acqiris_wform
key_out              = wf-calibrated
fname_base_line      = acq-amo01509-r0125-ave-wfs.txt
#skip_events          = 0
#proc_events          = 100
print_bits           = 255


[ImgAlgos.ImgSaveInFile:wf_raw]
source         = AmoETOF.0:Acqiris.0
key            = acqiris_wform
fname          = acq-AmoETOF-wform-raw
ftype          = txt
#ftype          = tiff
#saveAll        = true
print_bits     = 3
eventSave      = 5


[ImgAlgos.ImgSaveInFile:wf_calib]
source            = AmoETOF.0:Acqiris.0
key_in               = wf-calibrated
fnameacqiris_wform
key_ave          = acq-AmoETOF-wform-calibrated
ftype   = acqiris_average
fname_ave_prefix      = txtacq
#ftypethresholds           = tiff
#saveAll   -0.005 -0.005 -0.005 -0.005 -0.005
is_positive_signal   = no
do_inverse_selection = true
print_bits yes
#skip_events          = 0
#proc_events          = 3
eventSave100
print_bits           = 5255

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

• acq-

  AmoETOF-wform

  amo01509-

  raw-

  r0125-

  e00000005-20091018-182512.194787218

  config.txt

  acq

  -

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

which content is presented on plots:

Image Removed Image Removed

...

• - 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

Example for module ImgAlgos::AcqirisCalib

See description of parameters in Module ImgAlgos::AcqirisCalib

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

# 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

...

Example for module ImgAlgos::AcqirisCFD

See description of parameters in Module ImgAlgos::AcqirisCFD

Configuration file psana_cfd.cfg:

# Command to run this script: 
# psana -c psana_cfd.cfg;
#
[psana]
modules = ImgAlgos.AcqirisArrProducer ImgAlgos.AcqirisCalib ImgAlgos.AcqirisCFD 
files = /reg/d/psdm/AMO/amo01509/xtc/e8-r0125-s00-c00.xtc
[ImgAlgos.AcqirisArrProducer]
source  = AmoETOF.0:Acqiris.0
key_in  =
key_wform  = acqiris_wform
key_wtime  = acqiris_wtime
fname_prefix  = acq
print_bits  = 0
[ImgAlgos.AcqirisCalib]
source  = AmoETOF.0:Acqiris.0
key_in  = acqiris_wform
key_out  = wf-calibrated
fname_base_line  = acq--r0000-ave-wfs.txt
#skip_events  = 0
#proc_events  = 100
print_bits  = 0
[ImgAlgos.AcqirisCFD]
source  = AmoETOF.0:Acqiris.0
key_wform  = wf-calibrated
baselines =  0.0 0.0 0.0 0.0 0.0
thresholds =  -0.005 -0.005 -0.005 -0.005 -0.005
fractions =  0.5 0.5 0.5 0.5 0.5
deadtimes =  20.0e-9 20.0e-9 20.0e-9 20.0e-9 20.0e-9
leading_edges = 1 1 1 1 1

This script analyzes an AMO run where 5 acqiris channels were in use.  It uses an AcqirisArrProducer to producer the list of waveforms/times for all channels.  It then uses an AcqirisCalib module to do a baseline subtraction using a previously generated file of baselines act--r0000-ave-wfs.txt.  Finally, a constant fraction discriminator algorithm is run on all the waveforms with user specified parameters.  The edges calculated by AcqirisCFD are saved to the event as one ndarray<double,1> per channel, each with a (default) key "acqiris_edges_N" where N is the channel number.  Channels where no edges were found are not saved to the event.

...

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:

# 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    = 71


[ImgAlgos.AcqirisAverage:blAcqirisCalib]
source               = AmoETOF.0:Acqiris.0
key_in               = acqiris_wform
#keykey_aveout              = wf-calibrated
fname_avebase_prefixline      = acq-bline
thresholds-amo01509-r0125-ave-wfs.txt
#skip_events           = -0.005 -0.005 -0.005 -0.005 -0.005 
is_positive_signal   = no
do_inverse_selection = yes
skip_events 0
#proc_events             = 0
proc_events          = 1000
100
print_bits           = 31255


[ImgAlgos.AcqirisCalibImgSaveInFile:wf_raw]
source               = AmoETOF.0:Acqiris.0
key_in               = acqiris_wform
key_outfname          = acq-AmoETOF-wform-raw
ftype   = wf-calibrated
fname_base_line      = acq-bline
skip_eventstxt
#ftype          = 1001tiff
proc_events#saveAll          = 1000true
print_bits     = 3
eventSave      = 475


[ImgAlgos.AcqirisAverageImgSaveInFile:signalwf_calib]
source               = AmoETOF.0:Acqiris.0
key_in               = wf-calibrated
#key_avefname          = acq-AmoETOF-wform-calibrated
ftype   = 
fname_ave_prefix       = acq-signaltxt
thresholds#ftype           = -0.01 -0.01 -0.01 -0.01 -0.01 
is_positive_signaltiff
#saveAll   = no
do_inverse_selection = no
skip_events          = 1001true
procprint_eventsbits          = 10003
print_bitseventSave           = 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 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::NDArrAverage

...

5

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

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

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

which content is presented on plots:

Image Added Image Added

Example for module ImgAlgos::AcqirisCFD

See description of parameters in Module ImgAlgos::AcqirisCFD

Configuration file psana_cfd.cfg:

# Command to run this script: 
# psana -c psana_cfd.cfg;
#
[psana]
modules = ImgAlgos.AcqirisArrProducer ImgAlgos.AcqirisCalib ImgAlgos.AcqirisCFD 
files = /reg/d/psdm/AMO/amo01509/xtc/e8-r0125-s00-c00.xtc
[ImgAlgos.AcqirisArrProducer]
source  = AmoETOF.0:Acqiris.0
key_in  =
key_wform  = acqiris_wform
key_wtime  = acqiris_wtime
fname_prefix  = acq
print_bits  = 0
[ImgAlgos.AcqirisCalib]
source  = AmoETOF.0:Acqiris.0
key_in  = acqiris_wform
key_out  = wf-calibrated
fname_base_line  = acq--r0000-ave-wfs.txt
#skip_events  = 0
#proc_events  = 100
print_bits  = 0
[ImgAlgos.AcqirisCFD]
source  = AmoETOF.0:Acqiris.0
key_wform  = wf-calibrated
baselines =  0.0 0.0 0.0 0.0 0.0
thresholds =  -0.005 -0.005 -0.005 -0.005 -0.005
fractions =  0.5 0.5 0.5 0.5 0.5
deadtimes =  20.0e-9 20.0e-9 20.0e-9 20.0e-9 20.0e-9
leading_edges = 1 1 1 1 1

This script analyzes an AMO run where 5 acqiris channels were in use.  It uses an AcqirisArrProducer to producer the list of waveforms/times for all channels.  It then uses an AcqirisCalib module to do a baseline subtraction using a previously generated file of baselines act--r0000-ave-wfs.txt.  Finally, a constant fraction discriminator algorithm is run on all the waveforms with user specified parameters.  The edges calculated by AcqirisCFD are saved to the event as one ndarray<double,1> per channel, each with a (default) key "acqiris_edges_N" where N is the channel number.  Channels where no edges were found are not saved to the event.

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:

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

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

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

#skip-events = 0
events      = 2010


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


[ImgAlgos.AcqirisAverage:bl]
source               = AmoETOF.0:Acqiris.0
key_in               = acqiris_wform
#key_ave              = 
fname_ave_prefix     = acq-bline
thresholds           = -0.005 -0.005 -0.005 -0.005 -0.005 
is_positive_signal   = no
do_inverse_selection = yes
skip_events          = 0
proc_events          = 1000
print_bits           = 31


[ImgAlgos.AcqirisCalib]
source               = AmoETOF.0:Acqiris.0
key_in               = acqiris_wform
key_out              = wf-calibrated
fname_base_line      = acq-bline
skip_events          = 1001
proc_events          = 1000
print_bits           = 47


[ImgAlgos.AcqirisAverage:signal]
source               = AmoETOF.0:Acqiris.0
key_in               = wf-calibrated
#key_ave              = 
fname_ave_prefix     = acq-signal
thresholds           = -0.01 -0.01 -0.01 -0.01 -0.01 
is_positive_signal   = no
do_inverse_selection = no
skip_events          = 1001
proc_events          = 1000
print_bits           = 31


[ImgAlgos.Tahometer]
print_bits  = 7

This script works with psana as follows:

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

This script produces three files:

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

  Code Block

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

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

Image Added Image Added

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

Image Added Image Added

Example for module ImgAlgos::NDArrImageProducer

See Module ImgAlgos::NDArrImageProducer

Module ImgAlgos.NDArrImageProducer produces image from any detector-associated ndarray

Possible chain of modules:

•           <Package>.<Detector>NDArrProducer
•           ImgAlgos.NDArrCalib
•           ImgAlgos.NDArrImageProducer
•           ImgAlgos.NDArrAverage

Example of the configuration file for cspad

[psana]
files = exp=cxii0114:run=227
events = 100

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

[CSPadPixCoords.CSPadNDArrProducer]
source       = DetInfo(CxiDs1.0:Cspad.0) 
inkey        = 
outkey       = cspad_ndarr
outtype      = float
is_fullsize  = yes
print_bits   = 3

[ImgAlgos.NDArrCalib] 
source  = DetInfo(CxiDs1.0:Cspad.0) 
key_in  = cspad_ndarr
key_out = calibrated
do_peds = yes
do_cmod = yes
do_stat = yes
do_mask = no
do_bkgd = no
do_gain = no 
do_nrms = no
do_thre = no
fname_mask = 
fname_bkgd = 
masked_value     =  -10
threshold_nrms   =    4 
threshold        =    7
below_thre_value =    0
print_bits       =    3 

[ImgAlgos.NDArrImageProducer]
source       = CxiDs1.0:Cspad.0
key_in       = calibrated
key_out      = cspad_img
#type_out     = asinp
#type_out     = float
#x0_off_pix   = 50
#y0_off_pix   = 50
print_bits   = 255
#calibdir     = /reg/neh/home/dubrovin/LCLS/CSPadAlignment-v01/calib-cxi-ds1-2014-03-19/calib

[ImgAlgos.NDArrAverage]
source       = DetInfo(CxiDs1.0:Cspad.0) 
key          = cspad_img
avefile      = cspad-img-ave
rmsfile      = cspad-img-rms
#maskfile    = cspad-img-msk
#hotpixfile  = cspad-img-hot
thr_rms_ADU  = 0
thr_min_ADU  = 4
thr_max_ADU  = 65000
print_bits   = 29

Example of the configuration file for cspad2x2

[psana]
# calib-dir = /reg/d/psdm/mec/meca1113/calib
#calib-dir = /reg/neh/home/dubrovin/LCLS/CSPad2x2Alignment/calib-cspad2x2-01-2013-02-13/calib

files = exp=meca1113:run=376
events = 10
#skip-events = 0

modules = CSPadPixCoords.CSPad2x2NDArrProducer \
          ImgAlgos.NDArrImageProducer \
          ImgAlgos.NDArrAverage

[CSPadPixCoords.CSPad2x2NDArrProducer]
source     = MecTargetChamber.0:Cspad2x2.1
inkey      = 
outkey     = cspad2x2_ndarr
outtype    = int16
print_bits = 5

[ImgAlgos.NDArrImageProducer]
source       = MecTargetChamber.0:Cspad2x2.1
key_in       = cspad2x2_ndarr
key_out      = cspad2x2_img
#type_out     = asinp
#type_out     = float
#x0_off_pix   = 50
#y0_off_pix   = 50
print_bits   = 255
#oname        = CSPAD2X2:V1
#oindex       = 0
#pix_scale_size_um = 218.
#calibdir     = /reg/neh/home/dubrovin/LCLS/CSPad2x2Alignment/calib-cspad2x2-01-2013-02-13/calib
#calibgroup   = CsPad2x2::CalibV1


[ImgAlgos.NDArrAverage]
source       = MecTargetChamber.0:Cspad2x2.1
#key          = cspad2x2_ndarr
key          = cspad2x2_img
avefile      = arr-ave
rmsfile      = arr-rms
maskfile     = arr-msk
hotpixfile   = arr-hot
thr_rms_ADU  = 10
#thr_min_ADU = 2
#thr_max_ADU = 20000
print_bits   = 255

Example for module ImgAlgos::NDArrAverage

• See Module ImgAlgos::NDArrAverage andModule CSPadPixCoords::CSPadNDArrProducer

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

  No Format

  # Run this script: # psana -c psana-meca1113-r0045-cspad-cspad-dark-hotpix.cfg [psana] files = exp=meca1113:run=45 events = 400 #skip-events = 0 modules = CSPadPixCoords.CSPadNDArrProducer \ ImgAlgos.NDArrAverage \ ImgAlgos.Tahometer [CSPadPixCoords.CSPadNDArrProducer] source = MecTargetChamber.0:Cspad.0 inkey = outkey = cspad_ndarr outtype = int16 is_fullsize = yes print_bits = 3 [ImgAlgos.NDArrAverage] source = MecTargetChamber.0:Cspad.0 key = cspad_ndarr avefile = cspad.0-ave rmsfile = cspad.0-rms maskfile = cspad.0-msk hotpixfile = cspad.0-hot thr_rms_ADU = 10 thr_min_ADU = 4 thr_max_ADU = 10000 print_bits = 29 #evts_stage1 = 100 #gate_width1 = 500. #evts_stage2 = 200 #gate_width2 = 100. [ImgAlgos.Tahometer] dn = 100 print_bits = 7

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

Image AddedImage Added

Then, one has to decide how to set parameters for NDArrAverage algorithms, for example, it is quite safe to use

• thr_rms_ADU = 10  – to discard very noisy pixels,
• thr_min_ADU = 4  – to discard presumably dead pixels with 0-intensity,
• thr_max_ADU = 10000 – to discard pixels with intensity significantly exceeding average value. To be on safe side for int16 data this parameter can be set to 2¹⁶-4, where 4 in both cases is just a small arbitrary number for spare safety gap.

Example for module ImgAlgos::NDArrCalib

• 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

[psana]                                                               
files = exp=amoa1214:run=7
#skip-events = 100
events      = 5

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

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:

...

 \
          ImgAlgos.

...

PnccdImageProducer \
          ImgAlgos.ImgSaveInFile
#         ImgAlgos.

...

NDArrAverage \


[

...

ImgAlgos.

...

PnccdNDArrProducer]
source        = 

...

DetInfo(Camp.0:

...

pnCCD.0

...

)
key_in  =
key_out = pnccd-ndarr
outtype = asdata
print_bits = 13


[ImgAlgos.NDArrCalib] 
source = DetInfo(Camp.0:pnCCD.0) 
key_in = pnccd-ndarr 
key_out = calibrated
outtype = float
do_peds = yes
do_cmod = yes
do_stat = no
do_mask = no
do_bkgd = no
do_gain = no 
do_nrms = no
do_thre = no
fname_mask = 
fname_bkgd = 
masked_value     =    0
threshold_nrms   =    3 
threshold        =  100
below_thre_value =    0
bkgd_ind_min     = 

...

...

0

...

...

bkgd_

...

ind_max     = 

...

1000

...

bkgd_

...

ind_

...

inc  

...

...

  =   

...

10
print_bits       = 

...

 255 


[ImgAlgos.PnccdImageProducer]
source        = 

...

DetInfo(Camp.0:pnCCD.0)
#inkey         = pnccd-ndarr
inkey         = 

...

Image RemovedImage Removed

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

[psana]calibrated
outimgkey     = pnccd-img
gap_size      = 20
gap_value     = 0
print_bits    = 1


[ImgAlgos.ImgSaveInFile]
source        = DetInfo(Camp.0:pnCCD.0)
key           = pnccd-img
fname         = pnccd-img-from-arr
ftype         = txt
saveAll       = true
print_bits    = 31


 
[ImgAlgos.Tahometer]
dn         = 100
print_bits = 7

Example of ImgAlgos::NDArrCalib for CSPAD

[psana]
files = exp=amoa1214cxi83714:run=7136
#skip-events = 100
events      = 5

modules = ImgAlgos.Tahometer \
          ImgAlgosCSPadPixCoords.PnccdNDArrProducerCSPadNDArrProducer \
          ImgAlgos.NDArrCalib \
          ImgAlgos.PnccdImageProducer \
          ImgAlgos.ImgSaveInFile
#         ImgAlgos.NDArrAverage \


[ImgAlgosCSPadPixCoords.PnccdNDArrProducerCSPadNDArrProducer]
source        = DetInfo(CampCxiDs1.0:pnCCDCspad.0)
key_in 
inkey        = 
outkey       =
key_out cspad_ndarr
outtype      = pnccd-ndarr
outtypefloat
is_fullsize  = asdatayes
print_bits   = 133


[ImgAlgos.NDArrCalib] 
source  = DetInfo(CampCxiDs1.0:pnCCDCspad.0) 
key_in  = pnccd-cspad_ndarr 
key_out = calibrated
outtype = double
do_peds = yes
do_cmod = yes
do_stat = noyes
do_mask = no
do_bkgd = no
do_gain = no 
do_nrms = no
do_thre = no
fname_mask = 
fname_bkgd = 
masked_value     =    0-10
threshold_nrms   =    34 
threshold        =    1007
below_thre_value =    0
bkgd_ind_min     =    0
bkgd_ind_max     = 1000
bkgd_ind_inc     =   10
print_bits       =  255  3 


[ImgAlgos.PnccdImageProducerNDArrAverage]
source        = DetInfo(CampCxiDs1.0:pnCCDCspad.0) 
#inkey         = pnccd-ndarr
inkeykey          = calibrated
outimgkey     = pnccd-img
gap_size      = 20
gap_value     = 0
print_bits    = 1


[ImgAlgos.ImgSaveInFile]
source        = DetInfo(Camp.0:pnCCD.0)
key     avefile      = pnccdcspad-imgave
fnamermsfile         = pnccd-img-from-arr
ftypecspad-rms
#maskfile     = cspad-msk
#hotpixfile   = txt
saveAllcspad-hot
thr_rms_ADU  = 10
thr_min_ADU  = 4
thr_max_ADU  = true10000
print_bits    = 31
29

 
[ImgAlgos.Tahometer]
dn         = 100
print_bits = 7

Example of ImgAlgos::NDArrCalib for CSPAD

   = 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

[psana]
# Default calibration directory:
# calib-dir = /reg/d/psdm/mec/cxi83714/calib
# calib-dir = /reg/neh/home1/dubrovin/LCLS/CSPadAlignment-v01/calib-mec-2013-12-10/

files = exp=cxi83714:run=136
events = 100
#skip-events = 4000

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

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

[CSPadPixCoords.CSPadNDArrProducer]
source       = DetInfo(CxiDs1.0:Cspad.0) 
inkey        = calibrated_data
outkey       = cspad_ndarr
outtype      = float
is_fullsize  = yes
print_bits   = 3

[psana]
files = exp=cxi83714:run=136
events = 100

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

[CSPadPixCoords.CSPadNDArrProducer]
source       = DetInfo(CxiDs1.0:Cspad.0) 
inkey        = 
outkey       = cspad_ndarr
outtype      = float
is_fullsize  = yes
print_bits   = 3

[ImgAlgos.NDArrCalib] 
source  = DetInfo(CxiDs1.0:Cspad.0) 
key_in  = cspad_ndarr
key_out = calibrated
do_peds = yes
do_cmod = yes
do_stat = yes
do_mask = no
do_bkgd = no
do_gain = no 
do_nrms = no
do_thre = no
fname_mask = 
fname_bkgd = 
masked_value     =  -10
threshold_nrms   =    4 
threshold        =    7
below_thre_value =    0
bkgd_ind_min     =    0
bkgd_ind_max     = 1000
bkgd_ind_inc     =   10
print_bits       =    3 

[ImgAlgos.NDArrAverage]
source       = DetInfo(CxiDs1.0:Cspad.0) 
key          = calibratedcspad_ndarr
avefile      = cspad-calib-ave
rmsfile      = cspad-calib-rms
#maskfile     = cspad-msk
#hotpixfile   = cspad-hot
thr_rms_ADU  = 10
thr_min_ADU  = 4
thr_max_ADU  = 10000
print_bits   = 29

[ImgAlgos.Tahometer]
dn         = 10
print_bits = 7

For test purpose we use exp=cxi83714:run=136 and loop over 100 exents.

Case 1: raw, non-calibrated images

doPedestals = yes

doCommonMode do_peds = no; 50-60 ms/event

plots for average and rms value distribution for all pixels
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Case 2: images with subtracted pedestals and applied status mask

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

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Case 3: The same as 2 with common mode subtracted

...

100-110ms
Image AddedImage Added

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

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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:

Content of:

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.

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Comparison with Andy's module cspad_mod.CsPadCalib for common mode correction of int16_t data

[psana]
# Default calibration directory:
# calib-dir = /reg/d/psdm/mecXCS/cxi83714xcsd7814/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 \
for detector: Fccd960
    Camera::CalibV1    
        XcsEndstation.0:Fccd960.0    
            pixel_rms   CSPadPixCoords.CSPadNDArrProducer \
          ImgAlgos.NDArrAverage \      12-13.data      file is not used
          ImgAlgos.Tahometer

[cspad_mod.CsPadCalib]
inputKey      78-81.data      run =range 
outputKey0078 - 0081
   = calibrated_data
doPedestals   = yes
doPixelStatus = yes
doCommonMode  pedestals = yes

[CSPadPixCoords.CSPadNDArrProducer]
source  
     = DetInfo(CxiDs1.0:Cspad.0) 
inkey        = calibrated_data
outkey 12-13.data      file is =not cspad_ndarr
outtypeused
        = float
is_fullsize  = yes
print_bits   = 3

[ImgAlgos.NDArrAverage]
source 78-81.data      run range = DetInfo(CxiDs1.0:Cspad.0) 
key0078 - 0081
           = cspad_ndarr
avefile  pixel_status    = cspad-calib-ave
rmsfile      = cspad-calib-rms
#maskfile     = cspad-msk
#hotpixfile   = cspad-hot
thr_rms_ADU12-13.data  = 10
thr_min_ADU  = 4
thr_max_ADU  = 10000
print_bits   = 29

[ImgAlgos.Tahometer]
dn file is not used
             = 10
print_bits = 7

...

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Conclusion:

...

Results of ImgAlgos.NDArrCalib well reproduce cspad_mod.CsPadCalib

...

 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.

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Example for module ImgAlgos::NDArrDropletFinder

See description in psana - Module Catalog and examples in Peak Finding Module

Example for module ImgAlgos::PixCoordsProducer

...

[ImgAlgos.PixCoordsProducer]
source       = CxiDs1.0:Cspad.0
key_out_area = pix_area
key_out_mask = pix_mask
key_out_ix   = pix_ix
key_out_iy   = pix_iy
x0_off_pix   = 1000
y0_off_pix   = 1000
mask_bits    = 15
print_bits   = 255

...

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

    env = ds.env()
    cls = env.calibStore()
    src = psana.Source('DetInfo(CxiDs1.0:Cspad.0)')
    ...
    A = evt.get(psana.

...

ndarray_int16_3,   src, 'cspad_ndarr').flatten()

    X    = evtcls.get(psana.ndarray_float64_1, psana.Source('DetInfo(CxiDs1.0:Cspad.0)')src, 'x-pix-coords')
    Y    = evtcls.get(psana.ndarray_float64_1, psana.Source('DetInfo(CxiDs1.0:Cspad.0)')src, 'y-pix-coords')
    AArea = evtcls.get(psana.ndarray_int16_3,float64_1, src, 'pix_area')
   psana.Source('DetInfo(CxiDs1.0:Cspad.0)'), 'cspad_ndarr').flatten()

    Area = evt 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_float64uint32_1, psana.Source('DetInfo(CxiDs1.0:Cspad.0)') src, 'pix_areaiy')
    iX   fname= evtcls.get(psana.ndarray_uint32_1,  psana.Source('DetInfo(CxiDs1.0:Cspad.0)'), 'pix_ix')
    iY   = evtstr,                     src, 'geometry-fname')

    // depricated method since ana-0.13.3:
    path_nda = cls.get(psana.ndarray_uint32uint8_1,  psana.Source('DetInfo(CxiDs1.0:Cspad.0)'), 'pix_iy') src, 'geometry-calib')
    path = ''.join(map(chr, path_nda)) if path_nda is not None else 'N/A'

Their shape=(32*185*388,) = (2296960,)

...