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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

#F7F7ED

Code Block
Code Block
bgColor

[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

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cspad2x2

...

Image RemovedImage Removed

Configuration file for cspad2x2 with pedestal subtraction

Note
Access to the CSPad2x2 aligned geometry is added on 2013-02-13 and is available for offline release `> ana-0.9.1`.

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

Code Block

bgColor	#F7F7ED

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

modules  = cspad_mod.CsPadCalib CSPadPixCoords.CSPad2x2ImageProducer ImgAlgos.ImgSaveInFile
events   1_clb:as_data
outtype    = 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:

Code Block

#!/usr/bin/env python

import sys
import numpy as np
import matplotlib.pyplot as plt
import psana

psana.setConfigFile('psana-meca1113-r0376-cspad2x2-CSPad2x2NDArrReshape.cfg')

dsname = 'exp=meca1113:run=376'
print "Data source: %s" % dsname
ds = psana.DataSource(dsname)

#------------------------------
print "Initializing Matplotlib Plotter"
fig = plt.figure(figsize=(10,5), dpi=80, facecolor='w', edgecolor='w', frameon=True)
plt.ion()
plt.show()

evnum = 0
evnum_max = 50

for evt in ds.events() :

    evtid  = evt.get(psana.EventId)

    evnum += 1
    if evnum > evnum_max : break

    img_as_data = evt.get(psana.ndarray_int16_3, psana.Source('DetInfo(MecTargetChamber.0:Cspad2x2.1)'), 'cspad2x2.1_clb:as_data')
    img_reshpd  = evt.get(psana.ndarray_int16_3, psana.Source('DetInfo(MecTargetChamber.0:Cspad2x2.1)'), 'cspad2x2.1_clb')

    print 'img_as_data.shape = ', img_as_data.shape
    print 'img_reshpd.shape  = ', img_reshpd.shape

    img_as_data.shape = (2*185,388)
    img_reshpd.shape = (2*185,388)

    ax1 = fig.add_axes([0.05,  0.06, 0.44, 0.87])
    ax2 = fig.add_axes([0.55,  0.06, 0.44, 0.87])

    fig.canvas.set_window_title('Image from arrays "as-data" and "reshaped"')

    imsh1 = ax1.imshow(img_as_data, interpolation='nearest', aspect='auto', origin='upper') # , extent=img_range)
    imsh2 = ax2.imshow(img_reshpd,  interpolation='nearest', aspect='auto', origin='upper') # , extent=img_range)

    plt.title("Event: %d.%d" % evtid.time())
    plt.draw()
    plt.clf()

This script retrieves from the event store calibrated ndarrays shaped as data (185,388,2) and re-shaped (2,185,388), then re-shape both to 2-d arrays (2*185,388) and plot them. Re-shaped array looks as recognizable (without spaces between ASICs) cspad2x2 image. Array shapes "as data" looks as an overlap of two images.

See Module CSPadPixCoords::CSPad2x2NDArrReshape

JIRA issue:

Jira

server	SLAC National Accelerator Laboratory
key	PSAS-45

Example for module CSPadPixCoords::CSPad2x2ImageProducer

See Module CSPadPixCoords::CSPad2x2ImageProducer

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

Code Block

bgColor	#F7F7ED

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

[CSPadPixCoords.CSPad2x2ImageProducer

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

Code Block

bgColor	#F7F7ED

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

#modules = cspad_mod.CsPad2x2Pedestals

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

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

events   = 5

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

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


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

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



[ImgAlgos.ImgSaveInFile:0]
source         = DetInfo(:Cspad2x2.0)
keyinkey            = Image
fname   outimgkey       = cspad2x2.0
ftype          = txt
#ftype          = tiff
saveAll        = Image
tiltIsApplied  = true
print_bits     = 3
#eventSave     = 5
15

[ImgAlgos.ImgSaveInFile:1]
source         = DetInfo(:Cspad2x2.1)
key            = Image
fname          = cspad2x2.1
#ftypesaveAll       = true
#eventSave   = txt
ftype  = 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 AddedImage Added

Configuration file for cspad2x2 with pedestal subtraction

Note
Access to the CSPad2x2 aligned geometry is added on 2013-02-13 and is available for offline release `> ana-0.9.1`.

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

Code Block

bgColor	#F7F7ED

[psana]
files    =      = tiff
saveAll     /reg/d/psdm/mec/mec73313/xtc/e268-r0180-s02-c00.xtc
#calib-dir = ./calib

modules  = cspad_mod.CsPadCalib CSPadPixCoords.CSPad2x2ImageProducer ImgAlgos.ImgSaveInFile
events   = true5
print_bits
[cspad_mod.CsPadCalib]
source        = DetInfo(MecTargetChamber.0:Cspad2x2.3)
#eventSaveinputKey      = 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:

Code Block

bgColor	#F7F7ED

# Command to run this script: 
# psana -c psana-cxib2313-r0114-cspad-pix-spectra.cfg
#
# Other useful commands: 
# psana -n 5 -m  PrintSeparator,PrintEventId,psana_examples.DumpCsPad
outputKey     = calibrated_arr
doPedestals   = yes
doPixelStatus = no
doCommonMode  = no


[CSPadPixCoords.CSPad2x2ImageProducer]
calibDir       = /reg/d/psdm/cximec/cxib2313/xtc/e336-r0114*
# psana -n 5 -m EventKeys exp=cxib2313:run=114:xtc

[psana]
filesmec73313/calib
typeGroupName  = CsPad2x2::CalibV1
#source      = exp=cxib2313:run=114:xtc
#calib-dir = ./calib
skip-events = 0
eventsDetInfo(MecTargetChamber.0:Cspad2x2.3)
source      = 100
modules     = cspad_mod.CsPadCalib ImgPixSpectra.CSPadPixSpectra

[cspad_mod.CsPadCalib]
source:Cspad2x2.3
inkey          = DetInfo(CxiDs1.0:Cspad.0)
inputKeycalibrated_arr
outimgkey      = Image
outputKey   tiltIsApplied  = calibratedtrue
doPedestalsprint_bits   = yes
doPixelStatus = no
doCommonMode  = yes15


[ImgPixSpectraImgAlgos.CSPadPixSpectraImgSaveInFile]
source         = CxiDs1DetInfo(MecTargetChamber.0:CspadCspad2x2.0
inputKey3)
key            = calibratedImage
aminfname          =   -20cspad2x2.3
amaxsaveAll          =    20.
nbins    true
print_bits     =    10
arr_fname3
#eventSave     = cspad_spectral_array.txt

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

To run this script use command

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

which produces two 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

...

:

Code Block

bgColor

...

#F7F7ED

[psana]
files

...

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:

Code Block

bgColor	#F7F7ED

[psana]
files = /reg/d/psdm/xpp/xpptut13/xtc/e308-r0008-s02-c00.xtc \
           = /reg/d/psdm/<instrument>xpp/xpptut13/<experiment>/<file-name>xtc/e308-r0008-s03-c00.xtc
modules       = ImgPixSpectra.CSPad2x2PixSpectra

[ImgPixSpectra.CSPad2x2PixSpectra]
source        = CxiSc1.0:Cspad2x2.0
amin  
#modules = cspad_mod.CsPad2x2Pedestals

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

modules  = cspad_mod.CsPadCalib:0 \ 
        =   500.
amax cspad_mod.CsPadCalib:1 \ 
         =  1000CSPadPixCoords.CSPad2x2ImageProducer:0 \
nbins          = CSPadPixCoords.CSPad2x2ImageProducer:1 \ 100
arr_fname
          = cspad2x2-pix-spectra.txt

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

Code Block

bgColor	#F7F7ED

ImgPixSpectra/data/PlotSpectralArrayFromFile.py cspad2x2-pix-spectra.txt

generates image for limited range of pixels for CSPad, CSPad2x2, or Camera, respectively:
Image RemovedImage Removed Image Removed

Examples for package ImgAlgos

See Package ImgAlgos

Example for module ImgAlgos::Tahometer

See Module ImgAlgos::Tahometer

Example of the psana configuration file:

Code Block

bgColor	#F7F7ED

[psana]ImgAlgos.ImgSaveInFile:0  \
           
filesImgAlgos.ImgSaveInFile:1

events   = 5

[cspad_mod.CsPadCalib:0]
source     = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\
   = DetInfo(XppGon.0:Cspad2x2.0)
inputKey      = 
outputKey     = calibrated_arr0
doPedestals    /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-2>.xtc

modules       = ImgAlgos.Tahometer

[ImgAlgos.Tahometer]
dn= yes
doPixelStatus = no
doCommonMode  = yes

[cspad_mod.CsPadCalib:1]
source         = 10
print_bits = 7

Example for module ImgAlgos::PnccdImageProducer

See Module ImgAlgos::PnccdImageProducer

Example of the psana configuration file:

Code Block

bgColor	#F7F7ED

[psana]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            = 
filescalibrated_arr0
outimgkey        = Image
tiltIsApplied    = /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\
  false
useWidePixCenter = false
print_bits       = 15

[CSPadPixCoords.CSPad2x2ImageProducer:1]
calibDir         = /reg/d/psdm/<INSTRUMENT>xpp/<experiment>xpptut13/xtc/<file-name-2>.xtc
#skip-eventscalib
typeGroupName    = 100
eventsCsPad2x2::CalibV1
source        =  5
modules = ImgAlgos.PnccdImageProducer ImgAlgos.ImgSaveInFile

[ImgAlgos.PnccdImageProducer]
sourceDetInfo(XppGon.0:Cspad2x2.1)
inkey            = DetInfo(:pnCCD)
inkeycalibrated_arr1
outimgkey        = =Image
outimgkeytiltIsApplied    = false
useWidePixCenter = imgpnccdfalse
print_bits    = 1   = 15



[ImgAlgos.ImgSaveInFile:0]
source         = DetInfo(:pnCCDCspad2x2.0)
key            = imgpnccdImage
fname          = pnccd-img-ev
saveAllcspad2x2.0
ftype          = truetxt
#eventSave#ftype     = 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:

Code Block

[psana]tiff
saveAll        = true
print_bits     = 3
#eventSave     = 5

[ImgAlgos.ImgSaveInFile:1]
source         = DetInfo(:Cspad2x2.1)
key            = Image
fname          = cspad2x2.1
#ftype         
#calib-dir = /reg/d/psdm/SXR/sxrb5914/calib
files = exp=sxrb5914:run=245
events = 10

modules = ImgAlgos.Tahometer \
  txt
ftype          = tiff
saveAll        ImgAlgos.PnccdNDArrProducer= \true
print_bits     = 3
#eventSave     ImgAlgos.NDArrCalib= \
          ImgAlgos.PnccdImageProducer \
          ImgAlgos.NDArrAverage

[ImgAlgos.Tahometer]
dn         = 100
print_bits = 7

[ImgAlgos.PnccdNDArrProducer]
source  = DetInfo(Camp.0:pnCCD.1)
key_in  =
key_out = pnccd-ndarr
outtype = asdata
print_bits = 0

[ImgAlgos.NDArrCalib] 
source = DetInfo(Camp.0:pnCCD.1) 
key_in = pnccd-ndarr 
key_out = calibrated 
do_peds = yes
do_cmod = yes
do_stat = yes
do_mask = no
do_bkgd = no
do_gain = no 
do_nrms = no
do_thre = no
#fname_mask = pnccd-test-mask.txt
#fname_bkgd = pnccd-test-bkgd.txt
masked_value     =    0
threshold_nrms   =  4.0
threshold5

Example for package ImgPixSpectra

See Package ImgPixSpectra

Modules:

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

Example for module ImgPixSpectra::CSPadPixSpectra

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

Code Block

bgColor	#F7F7ED

# Command to run this script: 
# psana -c psana-cxib2313-r0114-cspad-pix-spectra.cfg
#
# Other useful commands: 
# psana -n 5 -m  PrintSeparator,PrintEventId,psana_examples.DumpCsPad /reg/d/psdm/cxi/cxib2313/xtc/e336-r0114*
# psana -n 5 -m EventKeys exp=cxib2313:run=114:xtc

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

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

[ImgPixSpectra.CSPadPixSpectra]
source        = CxiDs1.0:Cspad.0
inputKey      = calibrated
amin          =   -20.
amax          =    20.
nbins        =  100
below_thre_value =    010
bkgdarr_ind_minfname     = 10000
bkgdcspad_ind_max     = 10200
bkgd_ind_inc     =    1
print_bits       =    1

[ImgAlgos.PnccdImageProducer]
source        = DetInfo(Camp.0:pnCCD.1)
inkey         = calibrated
outimgkey     = pnccd-img
gap_rowsspectral_array.txt

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

To run this script use command

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

which produces two files:

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

cspad_spectral_array.txt.sha– file with metadata for array shape:

Code Block

bgColor	#AAFFFF

NPIXELS  2296960
NBINS    10
AMIN     -20
AMAX     20
NEVENTS  100
ARRFNAME cspad_spectral_array.txt

Plot for content of the file cspad_spectral_array.txt:
Image Added

Example for module ImgPixSpectra::CSPad2x2PixSpectra

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

Code Block

bgColor	#F7F7ED

[psana]
files         = 0
gap_cols/reg/d/psdm/<instrument>/<experiment>/<file-name>.xtc
modules      = 16
gap_value     = 0
print_bits    = 1= ImgPixSpectra.CSPad2x2PixSpectra

[ImgAlgosImgPixSpectra.NDArrAverageCSPad2x2PixSpectra]
source        = DetInfo(CampCxiSc1.0:pnCCDCspad2x2.1)0
keyamin          = pnccd-img
avefile  500.
amax    = pnccd-ave
rmsfile     = = pnccd-rms
#maskfile1000.
nbins     = pnccd-msk
#hotpixfile   =   pnccd-hot100
thr_rms_ADUarr_fname     = 160
thr_min_ADU  = 2
thr_max_ADU  = 10000
print_bits   = 29cspad2x2-pix-spectra.txt

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

Code Block

bgColor	#F7F7ED

ImgPixSpectra/data/PlotSpectralArrayFromFile.py cspad2x2-pix-spectra.txt

generates image for limited range of pixels for CSPad, CSPad2x2, or Camera, respectively:
Image AddedImage Added Image Added

Examples for package ImgAlgos

See Package ImgAlgosImage RemovedImage RemovedImage Removed

Example for module ImgAlgos::

...

Tahometer

See Module ImgAlgos::CameraImageProducerTahometer

Example of the psana configuration file:

Code Block

bgColor	#F7F7ED

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

modules       =  = ImgAlgos.CameraImageProducer Tahometer

[ImgAlgos.ImgSaveInFileTahometer]
eventsdn         = 10
print_bits = 7

Example for module ImgAlgos::EpixNDArrProducer

See Module ImgAlgos::EpixNDArrProducer

Example of the psana configuration file:

Code Block

[psana]
files5

[ImgAlgos.CameraImageProducer] 
source         = exp= DetInfo(:Opal1000)
key_in   xppi0414:run=94
events        = 100
modules       = 
key_outImgAlgos.EpixNDArrProducer \
                ImgAlgos.NDArrAverage

[ImgAlgos.EpixNDArrProducer]
source = img
subtract_offsetDetInfo(:Epix10k)
key_in = true
printkey_bitsout = epix-nda
outtype = float
print_bits  = 15255

[ImgAlgos.ImgSaveInFileNDArrAverage]
source        = DetInfo(:Opal1000Epix10k)
key           = imgepix-nda
fnameavefile         = img-from-my-experiment
saveAll   epix-ave
print_bits    = 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>

= 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::PrincetonImageProducerPnccdImageProducer

Example of the psana configuration file:

Code Block

bgColor	#F7F7ED

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

[ImgAlgos.PnccdImageProducer]
source        = DetInfo(:pnCCD)
inkey       ImgAlgos.ImgSaveInFile
events  =
outimgkey     = imgpnccd
print_bits    = 31

[ImgAlgos.PrincetonImageProducerImgSaveInFile] 
source          = DetInfo(:PrincetonpnCCD)
key_in           = imgpnccd
key_outfname         = pnccd-img
subtract_offset = true-ev
saveAll       = true
#eventSave     = 82
print_bits      = 31

[ImgAlgos.ImgSaveInFile]
source1

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

Advanced example for PnccdImageProducer;

get pnccd ndarray from data,
calibrate ndarray (subtract pedestals, common mode, remove pixels with bad status),
produce image with two gaps from calibrated ndarray,
average image for 10 events:

Code Block
[psana] = DetInfo(:Princeton) key = img fname = img-xcs saveAll = true print_bits #calib-dir = 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 :

Code Block

bgColor	#F7F7ED

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

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

modules = ImgAlgos.AcqirisArrProducer ImgAlgos.ImgSaveInFile:wf ImgAlgos.ImgSaveInFile:wt

skip-events = 0
events      = 100


[ImgAlgos.AcqirisArrProducer]
source        = 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]
source /reg/d/psdm/SXR/sxrb5914/calib
files = exp=sxrb5914:run=245
events = 10

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

[ImgAlgos.Tahometer]
dn         = 100
print_bits = 7

[ImgAlgos.PnccdNDArrProducer]
source  = DetInfo(Camp.0:pnCCD.1)
key_in  =
key_out = pnccd-ndarr
outtype = asdata
print_bits = 0

[ImgAlgos.NDArrCalib] 
source = DetInfo(Camp.0:pnCCD.1) 
key_in = pnccd-ndarr 
key_out = calibrated 
do_peds = yes
do_cmod = yes
do_stat = yes
do_mask = no
do_bkgd = no
do_gain = no 
do_nrms = no
do_thre = no
#fname_mask = pnccd-test-mask.txt
#fname_bkgd = pnccd-test-bkgd.txt
masked_value     =    0
threshold_nrms   =  4.0
threshold        =  100
below_thre_value =    0
bkgd_ind_min     = 10000
bkgd_ind_max     = 10200
bkgd_ind_inc     =    1
print_bits       =    1

[ImgAlgos.PnccdImageProducer]
source        = AmoETOFDetInfo(Camp.0:AcqirispnCCD.0
key1)
inkey         = calibrated
outimgkey     = acqiris_wtime
fnamepnccd-img
gap_rows      = 0
gap_cols      = 16
gap_value     = acq-AmoETOF-wtime
ftype0
print_bits    = 1

[ImgAlgos.NDArrAverage]
source       = txt
#ftypeDetInfo(Camp.0:pnCCD.1)
key          = tiff
#saveAll  pnccd-img
avefile      = true
print_bitspnccd-ave
rmsfile      = 3pnccd-rms
eventSave#maskfile     = pnccd-msk
#hotpixfile   = 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

...

pnccd-hot
thr_rms_ADU  = 160
thr_min_ADU  = 2
thr_max_ADU  = 10000
print_bits   = 29

Image AddedImage AddedImage Added

Example for module ImgAlgos::CameraImageProducer

See Module ImgAlgos::CameraImageProducer

Example of the psana configuration file:

Code Block

bgColor	#F7F7ED

[psana]                                                               
files           = /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

...

Example for module ImgAlgos::AcqirisAverage

See description of parameters in Module ImgAlgos::AcqirisAverage

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

Code Block

bgColors	#AAFFFF

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

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

modules = ImgAlgos.AcqirisArrProducer ImgAlgos.AcqirisAverage

skip-events = 0
events      = 1000


[ImgAlgos.AcqirisArrProducer]
sourceimg
fname        = AmoETOF.0:Acqiris.0
key_in        = 
key_wform  = img-from-my-experiment
saveAll   = acqiris_wform
key_wtime     = acqiris_wtime
fname_prefixtrue
#eventSave  = acq
print_bits    = 3


[ImgAlgos.AcqirisAverage]
source 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:

Code Block

bgColor	#F7F7ED

[psana]              = 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
is_positive_signal
files   = no
do_inverse_selection = yes
#skip_events          = 0
#proc_events= /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-1>.xtc\
          = 100
print_bits      /reg/d/psdm/<INSTRUMENT>/<experiment>/xtc/<file-name-2>.xtc
modules       = 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

ImgAlgos.PrincetonImageProducer \
                ImgAlgos.ImgSaveInFile
events          = 3

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

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

Image Added

Anchor

	AcqirisArrProducer
	AcqirisArrProducer

Anchor

AcqirisCalib

Example for module ImgAlgos::

...

AcqirisArrProducer

See description of parameters in Module ImgAlgos::AcqirisCalib AcqirisArrProducer

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

Code Block

bgColorsbgColor	#AAFFFF#F7F7ED

# 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_calibwt

skip-events = 0
events      = 10100


[ImgAlgos.AcqirisArrProducer]
source        = AmoETOF.0:Acqiris.0
key_in        = 
key_wform     = acqiris_wform
key_wtime     = acqiris_wtime
fname_prefix  = acq
print_bits    = 111


[ImgAlgos.AcqirisCalibImgSaveInFile:wf]
source               = AmoETOF.0:Acqiris.0
key_in               = acqiris_wform
key_outfname          = acq-AmoETOF-wform
ftype   = wf-calibrated
fname_base_line      = acq-amo01509-r0125-ave-wfs.txt
#skip_events#ftype          = 0tiff
#proc_events#saveAll          = 100true
print_bits     = 3
eventSave      = 2555


[ImgAlgos.ImgSaveInFile:wf_rawwt]
source         = AmoETOF.0:Acqiris.0
key            = acqiris_wformwtime
fname          = acq-AmoETOF-wform-rawwtime
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:

...

This script with psana does a few things:

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

This script saves 3 text files:

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

Code Block

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

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

...

-20091018-182512.194787218.txt

...

– with wave-times for 5th event

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

Image Added Image Added

Anchor

	AcqirisAverage
	AcqirisAverage

which content is presented on plots:

Image Removed Image Removed

Anchor

AcqirisCFD

Example for module ImgAlgos::

...

AcqirisAverage

See description of parameters in in Module ImgAlgos::AcqirisCFDAcqirisAverage

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

Code Block

bgColors	#AAFFFF

# 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 =  -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.

...

# 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
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

Anchor

	AcqirisCalib
	AcqirisCalib

Example for module ImgAlgos::AcqirisCalib

See description of parameters in Module ImgAlgos::AcqirisCalib

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

Code Block

bgColors	#AAFFFF

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

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

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

skip-events = 0
events      = 10


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

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

which content is presented on plots:

Image Added Image Added

Anchor

	AcqirisCFD
	AcqirisCFD

Example for module ImgAlgos::AcqirisCFD

See description of parameters in Module ImgAlgos::AcqirisCFD

Configuration file psana_cfd.cfg:

Code Block

bgColors	#AAFFFF

# 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.

Anchor

	ImgAlgos::AcqirisCombinedExample
	ImgAlgos::AcqirisCombinedExample

Example for combination of Acqiris modules

See description of parameters in Modules ImgAlgos::AcqirisArrProducer, AcqirisAverage, and AcqirisCalib

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

Code Block

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

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

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

#skip-events = 0
events      = 2010


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


[ImgAlgos.AcqirisAverage:bl]
source               = 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

Code Block

[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

Code Block

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

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

modules = CSPadPixCoords.CSPad2x2NDArrProducer \
          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

...

Example for combination of Acqiris modules

See description of parameters in Modules ImgAlgos::AcqirisArrProducer, AcqirisAverage, and AcqirisCalib

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

Code Block

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

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

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

#skip-events = 0
events      = 2010


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


[ImgAlgos.AcqirisAverage:bl]
source               = AmoETOF.0:Acqiris.0
key_in       = cspad2x2_ndarr
key_out       = acqiriscspad2x2_wformimg
#key#type_aveout        = asinp
#type_out      = float
fname#x0_aveoff_prefix  pix   = acq-bline
thresholds50
#y0_off_pix        = 50
print_bits   = -0.005 -0.005 -0.005 -0.005 -0.005 
is_positive_signal255
#oname        = no
do_inverse_selection = yes
skip_eventsCSPAD2X2:V1
#oindex          = 0
proc_events     #pix_scale_size_um = 218.
#calibdir     = 1000
print_bits           = 31/reg/neh/home/dubrovin/LCLS/CSPad2x2Alignment/calib-cspad2x2-01-2013-02-13/calib
#calibgroup   = CsPad2x2::CalibV1


[ImgAlgos.AcqirisCalibNDArrAverage]
source       = MecTargetChamber.0:Cspad2x2.1
#key          = AmoETOF.0:Acqiris.0
key_in     cspad2x2_ndarr
key          = acqiriscspad2x2_wformimg
key_outavefile      = arr-ave
rmsfile       = wfarr-calibrated
fname_base_linerms
maskfile      = acqarr-blinemsk
skip_eventshotpixfile   = arr-hot
thr_rms_ADU  = 10
#thr_min_ADU = 2
#thr_max_ADU = 100120000
proc_events          = 1000
print_bits           = 47


[ImgAlgos.AcqirisAverage:signal]
source               = AmoETOF.0:Acqiris.0
key_in   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 =

...

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

...

MecTargetChamber.0:Cspad.0
key          = cspad_ndarr
avefile      = cspad.0-ave
rmsfile      = cspad.0-rms
maskfile     = cspad.0-msk
hotpixfile   = cspad.0-hot
thr_rms_ADU  = 10
thr_min_ADU  = 4
thr_max_ADU  = 10000
print_bits   = 29
#evts_stage1  = 100
#gate_width1  = 500.
#evts_stage2  = 200
#gate_width2  = 100.


[ImgAlgos.Tahometer]
dn         = 100
print_bits = 7

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

Image AddedImage Added

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

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

Example for module ImgAlgos::NDArrCalib

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

Example of ImgAlgos::NDArrCalib for pnCCD

Code Block
[psana] files = exp=amoa1214:run=7 #skip-events = 100 events = 5 modules = ImgAlgos.Tahometer

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.

...

PnccdNDArrProducer \
          ImgAlgos.

...

NDArrCalib \

...

   ImgAlgos.PnccdImageProducer \

...

ImgAlgos.ImgSaveInFile
#

...

ImgAlgos.NDArrAverage \


[ImgAlgos.

...

PnccdNDArrProducer]
source        =

...

DetInfo(Camp.0:

...

pnCCD.0)
key_in

...

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

Code Block

[psana]        =
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           = 
files = exp=amoa1214:run=7
#skip-events = 100
eventspnccd-img
fname         = pnccd-img-from-arr
ftype         = txt
saveAll       = 5

modulestrue
print_bits    = 31


 
[ImgAlgos.Tahometer \]
dn         = ImgAlgos.PnccdNDArrProducer \
          ImgAlgos.NDArrCalib100
print_bits = 7

Example of ImgAlgos::NDArrCalib for CSPAD

Code Block

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

modules = ImgAlgos.Tahometer \
          ImgAlgosCSPadPixCoords.PnccdImageProducerCSPadNDArrProducer \
          ImgAlgos.ImgSaveInFileNDArrCalib \
#          ImgAlgos.NDArrAverage \


[ImgAlgosCSPadPixCoords.PnccdNDArrProducerCSPadNDArrProducer]
source        = DetInfo(CampCxiDs1.0:pnCCDCspad.0)
key_in 
inkey        =
key_out 
outkey       = pnccd-cspad_ndarr
outtype      = float
is_fullsize  = asdatayes
print_bits   = 13
3

[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        =  100  7
below_thre_value =    0
bkgd_ind_min     =    0
bkgd_ind_max     = 1000
bkgd_ind_inc     =   10
print_bits       =    2553 


[ImgAlgos.PnccdImageProducerNDArrAverage]
source        = DetInfo(CampCxiDs1.0:pnCCDCspad.0)
#inkey 
key          = calibrated
avefile      = cspad-ave
rmsfile      = cspad-rms
#maskfile     = pnccdcspad-ndarrmsk
inkey#hotpixfile   =    cspad-hot
thr_rms_ADU  = 10
thr_min_ADU  = calibrated
outimgkey   4
thr_max_ADU  = pnccd-img10000
gapprint_sizebits   = 29

[ImgAlgos.Tahometer]
dn   = 20
gap_value     = 010
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

= 7

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

Case 1: raw, non-calibrated images

do_peds = no; 50-60 ms/event

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

Case 2: images with subtracted pedestals and applied status mask

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

Image AddedImage Added

Case 3: The same as 2 with common mode subtracted

do_cmod = yes; 107-117 ms/event

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

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

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

Image AddedImage Added

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

Code Block

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

Code Block

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

modules#skip-events = ImgAlgos.Tahometer \
          CSPadPixCoords.CSPadNDArrProducer \
          ImgAlgos.NDArrCalib \
          ImgAlgos.NDArrAverage

[CSPadPixCoords.CSPadNDArrProducer]
source       = DetInfo(CxiDs1.0:Cspad.0) 
inkey4000

modules = cspad_mod.CsPadCalib \
          =CSPadPixCoords.CSPadNDArrProducer \
outkey       = cspad_ndarr
outtype  ImgAlgos.NDArrAverage \
   = float
is_fullsize  = yes
print_bits   = 3ImgAlgos.Tahometer

[ImgAlgoscspad_mod.NDArrCalibCsPadCalib] 
sourceinputKey  = DetInfo(CxiDs1.0:Cspad.0) 
key_in  = cspad_ndarr
key_out = calibrated
do_peds = yes
do_cmod
outputKey     = yes
do_stat = yes
do_mask = no
do_bkgdcalibrated_data
doPedestals   = noyes
do_gaindoPixelStatus = no 
do_nrms = no
do_threyes
doCommonMode  = no
fname_mask = 
fname_bkgd = 
masked_value     =  -10
threshold_nrms   =    4 
thresholdyes

[CSPadPixCoords.CSPadNDArrProducer]
source       =  =DetInfo(CxiDs1.0:Cspad.0) 
inkey    7
below_thre_value =   = 0
bkgd_ind_mincalibrated_data
outkey     =  =  0
bkgd_ind_maxcspad_ndarr
outtype      = 1000float
bkgd_ind_inc   is_fullsize  =   10yes
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
Image RemovedImage Removed

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

Image AddedImage Added

Conclusion:

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

Example of ImgAlgos::NDArrCalib for Fccd960

Calibration

To calibrate fccd960 for dark runs use command

calibman

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

Code Block
Content of:

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 RemovedImage Removed

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

Code Block

[psana]
# Default calibration directory:
# calib-dir = /reg/d/psdm/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 \
  12-13.data      file is not used
                ImgAlgos.NDArrAverage \
78-81.data      run range 0078 - 0081
   ImgAlgos.Tahometer

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

[CSPadPixCoords.CSPadNDArrProducer]
source       = DetInfo(CxiDs1.0:Cspad.0) 
inkey 12-13.data      file is not = calibrated_dataused
outkey       = cspad_ndarr
outtype      = float
is_fullsize  = yes
print_bits 78-81.data     = 3

[ImgAlgos.NDArrAverage]
source     run range 0078 - 0081
   = DetInfo(CxiDs1.0:Cspad.0) 
key       pixel_status   = cspad_ndarr
avefile        = cspad-calib-ave
rmsfile      = cspad-calib-rms
#maskfile12-13.data     = cspad-msk
#hotpixfile file is =not cspad-hot
thr_rms_ADUused
  = 10
thr_min_ADU  = 4
thr_max_ADU  = 10000
print_bits   = 29

[ImgAlgos.Tahometer]
dn   78-81.data      = 10
print_bits = 7

...

Image RemovedImage Removed

Conclusion:

...

Results of ImgAlgos.NDArrCalib well reproduce cspad_mod.CsPadCalib

...

run range 0078 - 0081

Access data in psana

Example of the configuration file for psana psana-xcsd7814-r0079-fccd960-aver.cfg can be processed by the command

psana -c psana-xcsd7814-r0079-fccd960-aver.cfg

Two averaged images are saved in the text files for exp=xcsd7814:run=79 for raw and calibrated (subtracted dark level) data.

Gain bit coded gain factor 8 is applied automatically.

Image AddedImage Added

Example for module ImgAlgos::NDArrDropletFinder

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

Example for module ImgAlgos::PixCoordsProducer

...

Code Block

[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 env.calibStore().get(...) method:

Code Block

    env = ds.env()
    cls = env.calibStore()
    src = psana.Source('DetInfo(CxiDs1.0:Cspad.0)')
    ...
    A = evt.get(psana.ndarray_int16_3,   psana.Source('DetInfo(CxiDs1.0:Cspad.0)')src, 'cspad_ndarr').flatten()

    X    = cls.get(psana.ndarray_float64_1, psana.Source('DetInfo(CxiDs1.0:Cspad.0)')1, src, 'x-pix-coords')
    Y    = cls.get(psana.ndarray_float64_1, psana.Source('DetInfo(CxiDs1.0:Cspad.0)')src, 'y-pix-coords')
    Area = cls.get(psana.ndarray_float64_1, psana.Source('DetInfo(CxiDs1.0:Cspad.0)') src, 'pix_area')
    Mask = cls.get(psana.ndarray_int32_1,   src, 'pix_areamask')
    iX   = cls.get(psana.ndarray_uint32_1,  psana.Source('DetInfo(CxiDs1.0:Cspad.0)')src, 'pix_ix')
    iY   = cls.get(psana.ndarray_uint32_1,  psana.Source('DetInfo(CxiDs1.0:Cspad.0)')src, 'pix_iy')

    fname= cls.get(str,                // if needed, the path tosrc, "geometry" calibration file can be also extracted as'geometry-fname')

    // depricated method since ana-0.13.3:
    path_nda = cls.get(psana.ndarray_uint8_1, src, 'geometry-calib')
    path = ''.join(map(chr, path_nda)) if path_nda is not None else 'N/A'

...

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Example for module CSPadPixCoords::

CSPad2x2NDArrReshape

Example for module CSPadPixCoords::CSPad2x2ImageProducer

Example for package ImgPixSpectra

Example for module ImgPixSpectra::CSPadPixSpectra

Example for module ImgPixSpectra::CSPad2x2PixSpectra

Examples for package ImgAlgos

Example for module ImgAlgos::Tahometer

Example for module ImgAlgos::PnccdImageProducer

Example for package ImgPixSpectra

Example for module ImgPixSpectra::CSPadPixSpectra

Example for module ImgPixSpectra::CSPad2x2PixSpectra

Examples for package ImgAlgos

Example for module ImgAlgos::

Tahometer

Example for module ImgAlgos::EpixNDArrProducer

Example for module ImgAlgos::

PnccdImageProducer

Example for module ImgAlgos::AcqirisArrProducer

Example for module ImgAlgos::CameraImageProducer

Example for module ImgAlgos::AcqirisAverage

Example for module ImgAlgos::PrincetonImageProducer

Example for module ImgAlgos::

AcqirisArrProducer

Example for module ImgAlgos::

AcqirisAverage

Example for module ImgAlgos::AcqirisCalib

Example for module ImgAlgos::AcqirisCFD

Example for combination of Acqiris modules

Example for module ImgAlgos::NDArrImageProducer

Example for combination of Acqiris modules

Example for module ImgAlgos::NDArrAverage

Example for module ImgAlgos::NDArrAverage

Example for module ImgAlgos::NDArrCalib

Example for module ImgAlgos::NDArrCalib

Example for module ImgAlgos::NDArrDropletFinder

Example for module ImgAlgos::PixCoordsProducer