About

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

...

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      = 
outputKey     = DetInfo(:Cspad2x2)
keyclb_data
doPedestals   = yes
doPixelStatus = yes
doCommonMode  = yes

[CSPadPixCoords.CSPad2x2NDArrProducer:clb]
source     = MecTargetChamber.0:Cspad2x2.1
inkey      = clb_data
outkey     = Image
fnamecspad2x2.1_clb:as_data
outtype    = int16
print_bits = 5

[CSPadPixCoords.CSPad2x2NDArrProducer:raw]
source     = cspad2x2
saveAllMecTargetChamber.0:Cspad2x2.1
inkey      = 
outkey     = true
#eventSavecspad2x2.1_raw:as_data
outtype    = int16
print_bits = 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

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

[CSPadPixCoords.CSPad2x2NDArrReshape]
source     = MecTargetChamber.0:Cspad2x2.1
keys_in    = cspad2x2.1_raw:as_data cspad2x2.1_clb:as_data
print_bits = 255

[ImgAlgos.NDArrAverage:clb]
source       = MecTargetChamber.0:Cspad2x2.1
key          = cspad2x2.1_clb
avefile        = DetInfo(MecTargetChamber.0:Cspad2x2.3)
inputKey= arr-ave-clb
rmsfile      = 
outputKey     = calibrated_arr
doPedestalsarr-rms-clb
print_bits   = yes255
doPixelStatus = no
doCommonMode  = no


[CSPadPixCoords.CSPad2x2ImageProducer]
calibDir [ImgAlgos.NDArrAverage:raw]
source      = /reg/d/psdm/mec/mec73313/calib
typeGroupName  = CsPad2x2::CalibV1
#source        = DetInfo(MecTargetChamber.0:Cspad2x2.3)1
sourcekey          = :Cspad2x2.3
inkey    cspad2x2.1_raw
avefile      = calibrated_arr-ave-raw
outimgkeyrmsfile      = Image
tiltIsApplied  = true
arr-rms-raw
print_bits     = 15


[ImgAlgos.ImgSaveInFile]
source255

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 

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/reg/d/psdm/<instrument>/<experiment>/xtc/<file-name-1>.xtc
events    =   false
useWidePixCenter = false5
print_bitsmodules       = 15 CSPadPixCoords.CSPad2x2ImageProducer ImgAlgos.ImgSaveInFile

[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 = falsetrue
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  

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        = cspad2x2.1
#ftypeDetInfo(MecTargetChamber.0:Cspad2x2.3)
inputKey      = 
outputKey     = txtcalibrated_arr
ftypedoPedestals   = yes
doPixelStatus = no
doCommonMode    = tiff
saveAllno


[CSPadPixCoords.CSPad2x2ImageProducer]
calibDir       = = true
print_bits/reg/d/psdm/mec/mec73313/calib
typeGroupName  = CsPad2x2::CalibV1
#source        = DetInfo(MecTargetChamber.0:Cspad2x2.3)
#eventSavesource         = 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:Cspad2x2.3
inkey          = calibrated_arr
outimgkey      = Image
tiltIsApplied  = true
print_bits     = 15


[ImgAlgos.ImgSaveInFile]
source       = exp=cxib2313:run=114:xtc
#calib-dir = ./calib
skip-events = 0
eventsDetInfo(MecTargetChamber.0:Cspad2x2.3)
key      = 100
modules     = cspad_mod.CsPadCalib ImgPixSpectra.CSPadPixSpectra

[cspad_mod.CsPadCalib]
sourceImage
fname          = DetInfo(CxiDs1.0:Cspad.0)
inputKeycspad2x2.3
saveAll        = true
outputKeyprint_bits     = calibrated3
doPedestals#eventSave     = yes
doPixelStatus = no
doCommonMode  = yes

[ImgPixSpectra.CSPadPixSpectra]
source5

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 \
           = CxiDs1.0:Cspad.0
inputKey      = calibrated
amin  /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 \ 
        =   -20.
amax  cspad_mod.CsPadCalib:1 \ 
        =    20.
nbinsCSPadPixCoords.CSPad2x2ImageProducer:0 \
         =  CSPadPixCoords.CSPad2x2ImageProducer:1 \ 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.sha– file with metadata for array shape:

...

...

...

  ImgAlgos.ImgSaveInFile:0  

...

\

...

...

...

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    ImgAlgos.ImgSaveInFile:1

events   = 5

[cspad_mod.CsPadCalib:0]
source        = DetInfo(XppGon.0:Cspad2x2.0)
inputKey      = 
outputKey     = /reg/d/psdm/<instrument>/<experiment>/<file-name>.xtc
modules     calibrated_arr0
doPedestals   = yes
doPixelStatus = no
doCommonMode  = ImgPixSpectra.CSPad2x2PixSpectrayes

[ImgPixSpectra.CSPad2x2PixSpectracspad_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         = /reg/d/psdm/xpp/xpptut13/xtc/calib
typeGroupName    = 100
arr_fnameCsPad2x2::CalibV1
source           = 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]DetInfo(XppGon.0:Cspad2x2.0)
inkey            = calibrated_arr0
filesoutimgkey         = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\
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   
files         = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\
Image
fname          = cspad2x2.0
ftype     /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-2>.xtc
#skip-events = 100
events      =  5txt
modules#ftype = ImgAlgos.PnccdImageProducer ImgAlgos.ImgSaveInFile

[ImgAlgos.PnccdImageProducer]
source        = DetInfo(:pnCCD)
inkeytiff
saveAll        = =true
outimgkeyprint_bits     = imgpnccd
print_bits3
#eventSave     = 15

[ImgAlgos.ImgSaveInFile:1]
source         = DetInfo(:pnCCDCspad2x2.1)
key            = imgpnccdImage
fname          = pnccd-img-ev
saveAllcspad2x2.1
#ftype          = truetxt
#eventSaveftype     = 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 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:

[psana]tiff
saveAll        = true
print_bits     = 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 = /reg/d/psdm/SXR/sxrb5914/calib
files = exp=sxrb5914:run=245./calib
skip-events = 0
events = 10

modules = ImgAlgos.Tahometer \
 = 100
modules     =   ImgAlgos.PnccdNDArrProducer \
cspad_mod.CsPadCalib ImgPixSpectra.CSPadPixSpectra

[cspad_mod.CsPadCalib]
source          ImgAlgos.NDArrCalib \
= DetInfo(CxiDs1.0:Cspad.0)
inputKey      = 
outputKey     ImgAlgos.PnccdImageProducer= \calibrated
doPedestals   = yes
doPixelStatus = no
doCommonMode  =  ImgAlgos.NDArrAverageyes

[ImgAlgosImgPixSpectra.TahometerCSPadPixSpectra]
dnsource         = 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_bitsCxiDs1.0:Cspad.0
inputKey      = calibrated
amin          =   -20.
amax          =    20.
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 1000.
nbins      = 0
gap_cols    =  = 16100
gaparr_valuefname     = 0
print_bits    = 1

[ImgAlgos.NDArrAveragecspad2x2-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]]
source       = DetInfo(Camp.0:pnCCD.1)
key   
files       = pnccd-img
avefile      = pnccd-ave
rmsfile/reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\
         = pnccd-rms
#maskfile     = pnccd-msk
#hotpixfile /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-2>.xtc

modules       = 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       = 
files DetInfo(:Epix10k)
key          = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc
modulesepix-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:

[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          
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(:Opal1000pnCCD)
keyinkey         =
outimgkey     = img
fname imgpnccd
print_bits    = 1

[ImgAlgos.ImgSaveInFile]
source        = img-from-my-experiment
saveAllDetInfo(:pnCCD)
key           = true
#eventSaveimgpnccd
fname         = 1pnccd-img-ev
saveAll       = true
#eventSave     = 82
print_bits    = 1

This script saves text files with images like pnccd-img-fromev-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:

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]                                                               
files        #calib-dir = /reg/d/psdm/<INSTRUMENT>SXR/<experiment>/xtc/<file-name-1>.xtc\
      sxrb5914/calib
files = exp=sxrb5914:run=245
events = 10

modules = ImgAlgos.Tahometer \
          /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-2>.xtc
modulesImgAlgos.PnccdNDArrProducer \
         = ImgAlgos.PrincetonImageProducerNDArrCalib \
          ImgAlgos.PnccdImageProducer \
          ImgAlgos.NDArrAverage

[ImgAlgos.ImgSaveInFileTahometer]
eventsdn         = 100
print_bits = 37

[ImgAlgos.PrincetonImageProducerPnccdNDArrProducer] 
source          = DetInfo(:PrincetonCamp.0:pnCCD.1)
key_in          = 
key_out         = img
subtract_offsetpnccd-ndarr
outtype = trueasdata
print_bits      = 310

[ImgAlgos.ImgSaveInFileNDArrCalib] 
source        = DetInfo(:Princeton)Camp.0:pnCCD.1) 
key_in = pnccd-ndarr 
key_out = calibrated 
do_peds = yes
do_cmod = yes
do_stat = img
fname         = 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.AcqirisArrProducer]
source        = AmoETOF.0:Acqiris.0
key_in        =
key_wform     = acqiris_wform
key_wtime     = acqiris_wtime
fname_prefix  = acq
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
gap_value     = 0
print_bits    = 111


[ImgAlgos.ImgSaveInFile:wfNDArrAverage]
source         = AmoETOFDetInfo(Camp.0:AcqirispnCCD.01)
key            = acqiris_wform
fnamepnccd-img
avefile          = acqpnccd-AmoETOF-wformave
ftypermsfile          = 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
eventSave29

Image AddedImage AddedImage Added

Example for module ImgAlgos::CameraImageProducer

See Module ImgAlgos::CameraImageProducer

Example of the psana configuration file:

[psana]         = 5


[ImgAlgos.ImgSaveInFile:wt]
source         = AmoETOF.0:Acqiris.0
key            = acqiris_wtime
fname          = acq-AmoETOF-wtime
ftype          = txt
#ftype        
files  = tiff
#saveAll        = true
print_bits/reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc
modules         = 3
eventSave ImgAlgos.CameraImageProducer ImgAlgos.ImgSaveInFile
events          = 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

...

[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/psdm/AMO<INSTRUMENT>/amo01509<experiment>/xtc/e8<file-r0125name-s01-c002>.xtc
filesmodules     = exp=amo01509:run=125:xtc

modules = ImgAlgos.AcqirisArrProducer ImgAlgos.AcqirisAverage

skip-events = 0
eventsPrincetonImageProducer \
                ImgAlgos.ImgSaveInFile
events          = 10003


[ImgAlgos.AcqirisArrProducerPrincetonImageProducer] 
source          = AmoETOF.0:Acqiris.0DetInfo(:Princeton)
key_in          = 
key_wformout     = acqiris_wform
key_wtime     = acqiris_wtimeimg
fnamesubtract_prefix offset = acqtrue
print_bits      = 331


[ImgAlgos.AcqirisAverageImgSaveInFile]
source               = AmoETOF.0:Acqiris.0
key_in    DetInfo(:Princeton)
key           = acqiris_wform
key_ave   img
fname           = acqiris_average
fname_ave_prefix     = acq
thresholds    img-xcs
saveAll       = -0.005 -0.005 -0.005 -0.005 -0.005
is_positive_signaltrue
print_bits    = 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:

  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

...

31

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        = AmoETOF.0:Acqiris.0
key_in        =
key_wform     = 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

...

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_wformwtime
key_outfname          = acq-AmoETOF-wtime
ftype   = wf-calibrated
fname_base_line      = acq-amo01509-r0125-ave-wfs.txt
#skip_events#ftype          = 0
#proc_events  tiff
#saveAll        = 100true
print_bits           = 255


[ImgAlgos.ImgSaveInFile:wf_raw]
source 3
eventSave        = 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            = wf-calibrated
fname          = acq-AmoETOF-wform-calibrated
ftype          = txt
#ftype          = 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:

...

= 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

which content is presented on plots:

Image Removed Image Removed

Example for module ImgAlgos::

...

AcqirisAverage

See description of parameters in in Module ImgAlgos::AcqirisCFDAcqirisAverage

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

# Command to run this script: 
# psana -c psana_cfd-amo01509-r0125-acqiris-average.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 = # 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               = AmoETOF.0:Acqiris.0
key_in               = acqiris_wform
key_ave              = acqiris_average
fname_ave_prefix     = acq
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.

...

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:

  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


[ImgAlgos.AcqirisArrProducer]
source        = AmoETOF.0:Acqiris.0
key_in

...

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        = 
key_wform     = 1000acqiris_wform
printkey_bitswtime     = acqiris_wtime
fname_prefix  = acq
print_bits    = 311


[ImgAlgos.AcqirisCalib]
source               = AmoETOF.0:Acqiris.0
key_in               = acqiris_wform
key_out              = wf-calibrated
fname_base_line      = acq-bline
skip-amo01509-r0125-ave-wfs.txt
#skip_events          = 10010
proc#proc_events          = 1000100
print_bits           = 47255


[ImgAlgos.AcqirisAverageImgSaveInFile:signalwf_raw]
source               = AmoETOF.0:Acqiris.0
key_in               = wf-calibrated
#key_ave    = acqiris_wform
fname          = acq-AmoETOF-wform-raw
ftype          = txt
#ftype          = 
fname_ave_prefixtiff
#saveAll        = acq-signal
thresholdstrue
print_bits     = 3
eventSave      = -0.01 -0.01 -0.01 -0.01 -0.01 
is_positive_signal5


[ImgAlgos.ImgSaveInFile:wf_calib]
source         = no
do_inverse_selection = no
skip_eventsAmoETOF.0:Acqiris.0
key            = 1001
proc_eventswf-calibrated
fname          = 1000
print_bitsacq-AmoETOF-wform-calibrated
ftype           = 31


[ImgAlgos.Tahometer]
print_bitstxt
#ftype          = 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

...

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 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: 

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:

...

# 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 \
          ImgAlgos.PnccdImageProducer \
          ImgAlgos.ImgSaveInFile
#         ImgAlgos.NDArrAverage \


[ImgAlgos.PnccdNDArrProducer]
source        = DetInfo(Camp.0:pnCCD.0)
key_in  =
key_out = pnccd-ndarr
outtype = asdata
print_bits = 13


[ImgAlgos.NDArrCalib] 
source = DetInfo(Camp.0:pnCCD.0) 
key_in = pnccd-ndarr 
key_out = calibrated
outtype = float
do_peds = yes
do_cmod = yes
do_stat = no
do_mask = no
do_bkgd = no
do_gain = no 
do_nrms = no
do_thre = no
fname_mask = 
fname_bkgd = 
masked_value     =    0
threshold_nrms   =    3 
threshold        =  100
below_thre_value =    0
bkgd_ind_min     =    0
bkgd_ind_max     = 1000
bkgd_ind_inc     =   10
print_bits       =  255 


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


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


 
[ImgAlgos.Tahometer]
dn         = 100
print_bits = 7

Example of ImgAlgos::NDArrCalib for CSPAD

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

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

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

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

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

[ImgAlgos.Tahometer]
dn         = 10
print_bits = 7

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

Case 1: raw, non-calibrated images

do_peds = no; 50-60 ms/event

plots for average and rms value distribution for all pixels
Image AddedImage Added

Case 2: images with subtracted pedestals and applied status mask

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

Image AddedImage Added

Case 3: The same as 2 with common mode subtracted

do_cmod = yes; 107-117 ms/event

Andy's algorithm for CSPAD common mode correction with minor adaptive modifications is applied with parameters:

/reg/d/psdm/cxi/cxi83714/calib/CsPad::CalibV1/CxiDs1.0:Cspad.0/common_mode/135-136.data 

1 10 10 100 - algorithm mode, allowed peak mean, allowed peak rms, threshold on number of pixels in ADU bin.

Image AddedImage Added

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

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

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

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

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

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

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

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

modules = ImgAlgos.Tahometer \
          ImgAlgos.PnccdNDArrProducer \
= cspad_ndarr
avefile      = cspad-calib-ave
rmsfile      ImgAlgos.NDArrCalib \
= cspad-calib-rms
#maskfile     = cspad-msk
#hotpixfile    ImgAlgos.PnccdImageProducer \
          ImgAlgos.ImgSaveInFile
#= cspad-hot
thr_rms_ADU  = 10
thr_min_ADU  = 4
thr_max_ADU  = 10000
print_bits   = 29

[ImgAlgos.Tahometer]
dn         ImgAlgos.NDArrAverage= \


[ImgAlgos.PnccdNDArrProducer]
source        = DetInfo(Camp.0:pnCCD.0)
key_in  =
key_out = pnccd-ndarr10
print_bits = 7

doPedestals = yes

doCommonMode = no; 100-110ms
Image AddedImage Added

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

Image AddedImage Added

Conclusion:

• Results of ImgAlgos.NDArrCalib well reproduce cspad_mod.CsPadCalib

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

Example of ImgAlgos::NDArrCalib for Fccd960

• Calibration

To calibrate fccd960 for dark runs use command

calibman

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

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


[ImgAlgos.NDArrCalib] 
source = DetInfo(Camp.0:pnCCD.0) 
key_in = pnccd-ndarr 
key_out = calibrated 
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    12-13.data     = calibrated
outimgkeyfile is not used
  = pnccd-img
gap_size      = 20
gap_value     = 0
print_bits 78-81.data    = 1


[ImgAlgos.ImgSaveInFile]
source      run range 0078 - 0081
   = DetInfo(Camp.0:pnCCD.0)
key        pixel_status   = pnccd-img
fname
               = pnccd-img-from-arr
ftype12-13.data      file is not used
  = txt
saveAll       = true
print_bits    = 31


 
[ImgAlgos.Tahometer]
dn 78-81.data      run range 0078 = 100
print_bits = 7- 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:Example of ImgAlgos::NDArrCalib for CSPAD

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

modules	 = ImgAlgos.TahometerPixCoordsProducer \
          CSPadPixCoords.CSPadNDArrProducer cspad_mod.CsPadCalib \
          ImgAlgos.NDArrCalib \
          ImgAlgos.NDArrAverage CSPadPixCoords.CSPadNDArrProducer

[CSPadPixCoordsImgAlgos.CSPadNDArrProducerPixCoordsProducer]
source       = DetInfo(CxiDs1.0:Cspad.0) 
inkey        print_bits = 
outkey       = cspad_ndarr
outtype0

[cspad_mod.CsPadCalib]
source      = float
is_fullsize  = yes
print_bits   = 3

[ImgAlgos.NDArrCalib] 
source  = DetInfo(CxiDs1.0:Cspad.0) 
key_in
inputKey    = cspad_ndarr
key_out = calibrated
do_peds = yes
do_cmodoutputKey = yes
do_stat = yes
do_mask = no
do_bkgd = no
do_gain = no 
do_nrmscalibrated
doPedestals     = no
do_threyes
doPixelStatus   = no
fname_maskdoCommonMode  = 
fname_bkgd = 
masked_valueno

[CSPadPixCoords.CSPadNDArrProducer]
source     =  -10
threshold_nrms   =  CxiDs1.0:Cspad.0
inkey  4 
threshold        =    7
below_thre_value =calibrated
outkey     0
bkgd_ind_min     = cspad_ndarr
outtype    0
bkgd_ind_max     = 1000int16
bkgdis_ind_incfullsize     =   10yes
print_bits       =    3 

[ImgAlgos.NDArrAverage= 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:

[ImgAlgos.PixCoordsProducer]
source       = DetInfo(CxiDs1.0:Cspad.0) 
key          = calibrated
avefile      = cspad-ave
rmsfile      = cspad-rms
#maskfile  _out_area = pix_area
key_out_mask = pix_mask
key_out_ix   = pix_ix
key_out_iy   = cspad-msk
#hotpixfilepix_iy
x0_off_pix   = cspad-hot1000
thry0_rmsoff_ADUpix   = 101000
thr_min_ADUmask_bits    = 415
thr_max_ADUprint_bits   = 10000
 255

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

    env = ds.env()
print_bits   = 29

[ImgAlgos.Tahometer]
dn    cls = env.calibStore()
   = 10
print_bitssrc = 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 RemovedImage Removed

Case 2: images with subtracted pedestals and applied status mask

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

Image RemovedImage Removed

Case 3: The same as 2 with common mode subtracted

...

Andy's algorithm for CSPAD common mode correction with minor adaptive modifications is applied with parameters:

...

psana.Source('DetInfo(CxiDs1.0:Cspad.0

...

1 10 10 100 - algorithm mode, allowed peak mean, allowed peak rms, threshold on number of pixels in ADU bin.

Image RemovedImage Removed

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)')
    ...
    A = evt.get(psana.ndarray_int16_3,   src, 'cspad_ndarr').flatten()

    X    = cls.get(psana.ndarray_float64_1, src, 'x-pix-coords')
    Y    = cls.get(psana.ndarray_float64_1, src, 'y-pix-coords')
    Area = cls.get(psana.ndarray_float64_1, src, 'pix_area')
    Mask = cls.get(psana.ndarray_int32_1,   src, 'pix_mask')
    iX   = cls.get(psana.ndarray_uint32_1,  src, 'pix_ix')
    iY   = cls.get(psana.ndarray_uint32_1,  src, 'pix_iy')
    fname= cls.get(str,            = DetInfo(CxiDs1.0:Cspad.0) 
inkey        = calibrated_data
outkeysrc, 'geometry-fname')

    // depricated method = cspad_ndarr
outtypesince ana-0.13.3:
    path_nda  = float
is_fullsize  = yes
print_bits   = 3

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

[ImgAlgos.Tahometer]
dn         = 10
print_bits = 7

...

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:

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()

Image RemovedImage Removed

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 for module ImgAlgos::ImgAverage

...

[psana]
#skip-events = 50
events      =  10
files = exp=cxi83714:run=136

modules = cspad_mod.CsPadCalib \
          ImgAlgos.CSPadArrPeakFinder \
          ImgAlgos.CSPadArrSaveInFile \
          pyimgalgos.ex_peaks_nda
#         EventKeys


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


[ImgAlgos.CSPadArrPeakFinder]
source            = DetInfo(CxiDs1.0:Cspad.0)
key               = calibrated
key_peaks_out     = 
key_peaks_nda     = peaks_nda
hot_pix_mask_inp_file = ana-cxi83714/cspad-cxi83714-r0136-noise-mask-ini.dat
hot_pix_mask_out_file = ana-cxi83714/cspad-cxi83714-r0136-noise-mask-out.dat
frac_noisy_evts_file  = ana-cxi83714/cspad-cxi83714-r0136-noise-frac.dat
evt_file_out        = cxi83714/cspad-ev-
rmin                =     8
dr                  =     1
SoNThr_noise        =     3
SoNThr_signal       =     4
frac_noisy_imgs     =   0.9
peak_npix_min       =     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

...