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Table of Contents |
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Setup environment
ssh pslogin
ssh psananeh
# or psanafeh for cxi, sxr, and mecpsana
cd <your-directory>
sit_setup
Examples for xpp50312
Pedestals
Configuration file for psana with name for this example In this section we show how to get CSPad2x2 pedestals using psana for "dark" run.
For this example we create the configuration file ana-xpp50312/psana-xpp50312-r0082-pedestals.cfg
:
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[psana]
files = /reg/d/ana01/xpp/xpp50312/xtc/e178-r0082-s04-c00.xtc
modules = cspad_mod.CsPad2x2Pedestals
[cspad_mod.CsPad2x2Pedestals]
#source = DetInfo(:Cspad2x2)
source = DetInfo(XppGon.0:Cspad2x2.0)
output = cspad-pedestals-ave-xpp50312-r0082.dat
noise = cspad-pedestals-rms-xpp50312-r0082.dat
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...
psana -c ana-xpp50312/psana-xpp50312-r0082-pedestals.cfg
In a few seconds this command produce job produces two text files with averaged pedestals and rms values as one-dimensional (143560) array for CSPad2x2, which assumes physical shape . Actual shape of these arrays is assumed to be (185,388,2).
Using, for example, a simple python script this these files may be plotted
./PlotCSPad2x2ArrayFromFile.py cspad-pedestals-ave-xpp50312-r0082.dat 700 1400
./PlotCSPad2x2ArrayFromFile.py cspad-pedestals-rms-xpp50312-r0082.dat 0 20
Averaged pedestals:
RMS of pedestals:
Calibration
By default psana assumes that all calibration files are located in the pre-defined directory/reg/d/psdm/<INSTRUMENT>/<experiment>/calib/
as explained in CsPad Locating calibration in translator#Locating calibration files. However, for analysis it may be convenient to re-define the calibration directory can be re-defined through the psana parameters. In order to fulfill the naming conventions we have to create a tree of calibration subdirectoriesthe calibration sub-directories somewhere in local user's space, for example:
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ana-xpp50312/calib/CsPad2x2::CalibV1/XppGon.0:Cspad2x2.0/pixel_gain/
pixel_status/
pedestals/
common_mode/
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and populate them with all necessary for analysis files. In particular, for pedestals we can use:
cp cspad-pedestals-ave-xpp50312-r0082.dat ana-xpp50312/calib/CsPad2x2::CalibV1/XppGon.0:Cspad2x2.0/pedestals/82-end.data
Another file for common mode correction common_mode/0-end.data
usually looks like
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1 50 10
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Analysis
The files for pixel_status
and pixel_gain
have the same structure like for pedestals
and can be supplied, if necessary, depending and based on analysis.
Analysis
For this example we create the configuration file Configuration script for analysis with psana with name for this example: ana-xpp50312/psana-xpp50312-r0092.cfg
:
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[psana]
files = /reg/d/ana01/xpp/xpp50312/xtc/e178-r0092-s04-c00.xtc
experiment = xpp50312
calib-dir = ana-xpp50312/calib
events = 10
modules = cspad_mod.CsPadCalib CSPadPixCoords.CSPad2x2ImageProducer CSPadPixCoords.SaveImageInFile
[cspad_mod.CsPadCalib]
inputKey =
outputKey = calibrated
doPedestals = yes
doPixelStatus = no
doCommonMode = yes
doPixelGain = no
[CSPadPixCoords.CSPad2x2ImageProducer]
source = DetInfo(:Cspad2x2)
inkey = calibrated
outimgkey = Image
tiltIsApplied = true
print_bits = 15
[CSPadPixCoords.SaveImageInFile]
source = DetInfo(:Cspad2x2)
key = Image
fname = cspad2x2
eventSave = 5
#saveAll = true
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This configuration file provides parameters for psana and three modules.
Currently So far we setup calibration files for cspad_mod.CsPadCalib
module for pedestal subtraction and common mode correction.
Module CSPadPixCoords.CSPad2x2ImageProducer
produces the CSPad2x2 image and saves it in the event.
Module SaveImageInFile
saves indicated image(s) in the file(s). Playing with doPedestals
and doCommonMode
parameters, we could get different images:
Raw data without any correction:
Run psana with this configuration file:
psana -c ana-xpp50312/psana-xpp50312-r0092.cfg
Plot obtained text file with an image:
./PlotCameraImageFromFile.py cspad2x2-r0092-2012-07-20-154000.855680176.txt -20 120
Playing with doPedestals
and doCommonMode
parameters, we could get different images.
Raw data without any correction:
Pedestals subtracted:
Pedestals subtracted and common mode corrected:
Examples for meca6113
Pedestals
Configuration file for dark run processing (assuming that meca6113-r0018 is a dark run...) psana-meca6113-r0018-cspad2x2-pedestals.cfg:
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# File: psana-meca6113-r0018-cspad2x2-pedestals.cfg
[psana]
files = /reg/d/psdm/mec/meca6113/xtc/e332-r0018-s03-c00.xtc
modules = cspad_mod.CsPad2x2Pedestals:1 \
cspad_mod.CsPad2x2Pedestals:2 \
cspad_mod.CsPad2x2Pedestals:3
[cspad_mod.CsPad2x2Pedestals:1]
source = DetInfo(MecTargetChamber.0:Cspad2x2.1)
output = pedestals-ave-meca6113-r0018-Cspad2x2.1.dat
noise = pedestals-rms-meca6113-r0018-Cspad2x2.1.dat
[cspad_mod.CsPad2x2Pedestals:2]
source = DetInfo(MecTargetChamber.0:Cspad2x2.2)
output = pedestals-ave-meca6113-r0018-Cspad2x2.2.dat
noise = pedestals-rms-meca6113-r0018-Cspad2x2.2.dat
[cspad_mod.CsPad2x2Pedestals:3]
source = DetInfo(MecTargetChamber.0:Cspad2x2.3)
output = pedestals-ave-meca6113-r0018-Cspad2x2.3.dat
noise = pedestals-rms-meca6113-r0018-Cspad2x2.3.dat
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To produce files with pedestals use command:
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psana -c psana-meca6113-r0018-cspad2x2-pedestals.cfg
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which produces 6 files with average and rms values for 3 detectors:
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pedestals-ave-meca6113-r0018-Cspad2x2.1.dat
pedestals-ave-meca6113-r0018-Cspad2x2.2.dat
pedestals-ave-meca6113-r0018-Cspad2x2.3.dat
pedestals-rms-meca6113-r0018-Cspad2x2.1.dat
pedestals-rms-meca6113-r0018-Cspad2x2.2.dat
pedestals-rms-meca6113-r0018-Cspad2x2.3.dat
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Example of pedestal-image and spectral plots for 3 detectors, respectively:
Calibration
Default calibration in psana will be done if files are located in right place. So, they were deployed as:
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cp pedestals-ave-meca6113-r0018-Cspad2x2.1.dat /reg/d/psdm/mec/meca6113/calib/CsPad2x2::CalibV1/MecTargetChamber.0:Cspad2x2.1/pedestals/18-end.data
cp pedestals-ave-meca6113-r0018-Cspad2x2.2.dat /reg/d/psdm/mec/meca6113/calib/CsPad2x2::CalibV1/MecTargetChamber.0:Cspad2x2.2/pedestals/18-end.data
cp pedestals-ave-meca6113-r0018-Cspad2x2.3.dat /reg/d/psdm/mec/meca6113/calib/CsPad2x2::CalibV1/MecTargetChamber.0:Cspad2x2.3/pedestals/18-end.data
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Create images in tiff format
Configuration file for psana psana-meca6113-r0028-cspad2x2-tiff.cfg:
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# File: psana-meca6113-r0028-cspad2x2-tiff.cfg
#
# To run this script use command:
# % psana -c psana-meca6113-r0028-cspad2x2-tiff.cfg
#
# Also useful command:
# % psana -m EventKeys -n 10 /reg/d/psdm/mec/meca6113/xtc/e332-r0028-s03-c00.xtc
#
[psana]
files = /reg/d/psdm/mec/meca6113/xtc/e332-r0028-s03-c00.xtc
#calib-dir = ./calib
# Default calibration directory:
# calib-dir = /reg/d/psdm/mec/meca6113/calib
modules = cspad_mod.CsPadCalib:1 \
cspad_mod.CsPadCalib:2 \
cspad_mod.CsPadCalib:3 \
CSPadPixCoords.CSPad2x2ImageProducer:1 \
CSPadPixCoords.CSPad2x2ImageProducer:2 \
CSPadPixCoords.CSPad2x2ImageProducer:3 \
ImgAlgos.ImgSaveInFile:1 \
ImgAlgos.ImgSaveInFile:2 \
ImgAlgos.ImgSaveInFile:3
# events = 5
[cspad_mod.CsPadCalib:1]
source = DetInfo(MecTargetChamber.0:Cspad2x2.1)
inputKey =
outputKey = calibrated_arr1
doPedestals = yes
doPixelStatus = no
doCommonMode = no
[cspad_mod.CsPadCalib:2]
source = DetInfo(MecTargetChamber.0:Cspad2x2.2)
inputKey =
outputKey = calibrated_arr2
doPedestals = yes
doPixelStatus = no
doCommonMode = no
[cspad_mod.CsPadCalib:3]
source = DetInfo(MecTargetChamber.0:Cspad2x2.3)
inputKey =
outputKey = calibrated_arr3
doPedestals = yes
doPixelStatus = no
doCommonMode = no
[CSPadPixCoords.CSPad2x2ImageProducer:1]
calibDir = /reg/d/psdm/mec/meca6113/calib
typeGroupName = CsPad2x2::CalibV1
source = DetInfo(MecTargetChamber.0:Cspad2x2.1)
inkey = calibrated_arr1
outimgkey = Image
tiltIsApplied = true
useWidePixCenter = false
print_bits = 15
[CSPadPixCoords.CSPad2x2ImageProducer:2]
calibDir = /reg/d/psdm/mec/meca6113/calib
typeGroupName = CsPad2x2::CalibV1
source = DetInfo(MecTargetChamber.0:Cspad2x2.2)
inkey = calibrated_arr2
outimgkey = Image
tiltIsApplied = true
useWidePixCenter = false
print_bits = 15
[CSPadPixCoords.CSPad2x2ImageProducer:3]
calibDir = /reg/d/psdm/mec/meca6113/calib
typeGroupName = CsPad2x2::CalibV1
source = DetInfo(MecTargetChamber.0:Cspad2x2.3)
inkey = calibrated_arr3
outimgkey = Image
tiltIsApplied = true
useWidePixCenter = false
print_bits = 15
[ImgAlgos.ImgSaveInFile:1]
source = DetInfo(MecTargetChamber.0:Cspad2x2.1)
key = Image
fname = cspad2x2.1
#ftype = txt
ftype = tiff
saveAll = true
print_bits = 3
#eventSave = 5
[ImgAlgos.ImgSaveInFile:2]
source = DetInfo(MecTargetChamber.0:Cspad2x2.2)
key = Image
fname = cspad2x2.2
#ftype = txt
ftype = tiff
saveAll = true
print_bits = 3
#eventSave = 5
[ImgAlgos.ImgSaveInFile:3]
source = DetInfo(MecTargetChamber.0:Cspad2x2.3)
key = Image
fname = cspad2x2.3
#ftype = txt
ftype = tiff
saveAll = true
print_bits = 3
#eventSave = 5
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To produce files with images in tiff format use command:
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psana -c psana-meca6113-r0028-cspad2x2-tiff.cfg
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New files will be produced with names containing time stamp:
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cspad2x2.1-r0028-20131013-155538.754093925.tiff
cspad2x2.2-r0028-20131013-155538.754093925.tiff
cspad2x2.3-r0028-20131013-155538.754093925.tiff
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Example of image and spectral plots for 3 detectors, respectively:
Examples for meca1113
Get latest version of packages and run psana
On 6 p.m. 2013-11-13 all recent code changes are included in release ana-0.10.5 (seen in directory $SIT_RELDIR).
To run psana use commands:
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ssh -Y psana
cd <your-favorite-directory>
sit_setup
cp <path-to-where-it-is-located>/psana-meca1113-r0376-cspad-cspad2x2-tiff.cfg .
psana -c psana-meca1113-r0376-cspad-cspad2x2-tiff.cfg
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or run xtcexplorer:
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xtcexplorer /reg/d/psdm/mec/meca1113/xtc/e356-r0376-s03-c00.xtc |
Pedestals and bad pixels
The configuration file for psana psana-meca1113-r0045-cspad-cspad2x2-dark-hotpix.cfg can be used to produce calibration files with pedestals (dark rate) and mask of bad pixels:
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# Run this script:
# psana -c psana-meca1113-r0045-cspad-cspad2x2-dark-hotpix.cfg
[psana]
# Default calibration directory:
# calib-dir = /reg/d/psdm/mec/meca1113/calib
files = exp=meca1113:run=45
events = 400
#skip-events = 0
modules = CSPadPixCoords.CSPadNDArrProducer \
CSPadPixCoords.CSPad2x2NDArrProducer:1 \
CSPadPixCoords.CSPad2x2NDArrProducer:2 \
CSPadPixCoords.CSPad2x2NDArrProducer:3 \
CSPadPixCoords.CSPad2x2NDArrProducer:4 \
ImgAlgos.NDArrAverage \
ImgAlgos.NDArrAverage:1 \
ImgAlgos.NDArrAverage:2 \
ImgAlgos.NDArrAverage:3 \
ImgAlgos.NDArrAverage:4 \
ImgAlgos.Tahometer
[CSPadPixCoords.CSPadNDArrProducer]
source = MecTargetChamber.0:Cspad.0
inkey =
outkey = cspad_ndarr
outtype = int16
is_fullsize = yes
print_bits = 3
[CSPadPixCoords.CSPad2x2NDArrProducer:1]
source = MecTargetChamber.0:Cspad2x2.1
inkey =
outkey = cspad2x2.1_ndarr
outtype = int16
print_bits = 3
[CSPadPixCoords.CSPad2x2NDArrProducer:2]
source = MecTargetChamber.0:Cspad2x2.2
inkey =
outkey = cspad2x2.2_ndarr
outtype = int16
print_bits = 3
[CSPadPixCoords.CSPad2x2NDArrProducer:3]
source = MecTargetChamber.0:Cspad2x2.3
inkey =
outkey = cspad2x2.3_ndarr
outtype = int16
print_bits = 3
[CSPadPixCoords.CSPad2x2NDArrProducer:4]
source = MecTargetChamber.0:Cspad2x2.4
inkey =
outkey = cspad2x2.4_ndarr
outtype = int16
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 = 2
thr_max_ADU = 65000
print_bits = 93
[ImgAlgos.NDArrAverage:1]
source = MecTargetChamber.0:Cspad2x2.1
key = cspad2x2.1_ndarr
avefile = cspad2x2.1-ave
rmsfile = cspad2x2.1-rms
maskfile = cspad2x2.1-msk
hotpixfile = cspad2x2.1-hot
#evts_stage1 = 100
#gate_width1 = 100.
thr_rms_ADU = 10
thr_min_ADU = 2
thr_max_ADU = 65000
print_bits = 93
[ImgAlgos.NDArrAverage:2]
source = MecTargetChamber.0:Cspad2x2.2
key = cspad2x2.2_ndarr
avefile = cspad2x2.2-ave
rmsfile = cspad2x2.2-rms
maskfile = cspad2x2.2-msk
hotpixfile = cspad2x2.2-hot
#evts_stage1 = 100
#gate_width1 = 100.
thr_rms_ADU = 10
thr_min_ADU = 2
thr_max_ADU = 65000
print_bits = 93
[ImgAlgos.NDArrAverage:3]
source = MecTargetChamber.0:Cspad2x2.3
key = cspad2x2.3_ndarr
avefile = cspad2x2.3-ave
rmsfile = cspad2x2.3-rms
maskfile = cspad2x2.3-msk
hotpixfile = cspad2x2.3-hot
#evts_stage1 = 100
#gate_width1 = 100.
thr_rms_ADU = 10
thr_min_ADU = 2
thr_max_ADU = 65000
print_bits = 93
[ImgAlgos.NDArrAverage:4]
source = MecTargetChamber.0:Cspad2x2.4
key = cspad2x2.4_ndarr
avefile = cspad2x2.4-ave
rmsfile = cspad2x2.4-rms
maskfile = cspad2x2.4-msk
hotpixfile = cspad2x2.4-hot
#evts_stage1 = 100
#gate_width1 = 100.
thr_rms_ADU = 10
thr_min_ADU = 2
thr_max_ADU = 65000
print_bits = 93
[ImgAlgos.Tahometer]
dn = 100
print_bits = 7 |
This script
- runs through 400 events of the xtc file
exp=meca1113:run=45
, uses CSPadNDArrProducer and CSPad2x2NDArrProducer modules to get cspad and four cspad2x2 data and put them as universal
ndarray<T,3>
objects in psana event store,uses NDArrAverage module to evaluate and save in file average, rms, mask, and hot pixel map for all array elements:
No Format cspad.0-ave-meca1113-r0045.dat cspad.0-hot-meca1113-r0045.dat cspad.0-msk-meca1113-r0045.dat cspad.0-rms-meca1113-r0045.dat cspad2x2.1-ave-meca1113-r0045.dat cspad2x2.1-hot-meca1113-r0045.dat cspad2x2.1-msk-meca1113-r0045.dat cspad2x2.1-rms-meca1113-r0045.dat cspad2x2.2-ave-meca1113-r0045.dat cspad2x2.2-hot-meca1113-r0045.dat cspad2x2.2-msk-meca1113-r0045.dat cspad2x2.2-rms-meca1113-r0045.dat cspad2x2.3-ave-meca1113-r0045.dat cspad2x2.3-hot-meca1113-r0045.dat cspad2x2.3-msk-meca1113-r0045.dat cspad2x2.3-rms-meca1113-r0045.dat cspad2x2.4-ave-meca1113-r0045.dat cspad2x2.4-hot-meca1113-r0045.dat cspad2x2.4-msk-meca1113-r0045.dat cspad2x2.4-rms-meca1113-r0045.dat
NDArrAverage module has a bunch of parameters which depend on particular detector/experiments and need to be adjusted looking at spectra of average and rms values from these files. For example averaged image and spectrum and rms spectrum of pixel intensities for
cspad2x2.1-ave-meca1113-r0045.dat and cspad2x2.1-rms-meca1113-r0045.dat
are shown in plots:
These spectra allow to use confidently parameters like
thr_rms_ADU = 10
thr_min_ADU = 2
thr_max_ADU = 65000
Files with mask and hot pixel map contain opposite meaning of 0/1 for bad/good pixels:
Calibration
Default calibration in psana will be done if files are located in right place. So, they were deployed as:
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cp cspad.0-ave-meca1113-r0045.dat /reg/d/psdm/mec/meca1113/calib/CsPad::CalibV1/MecTargetChamber.0:Cspad.0/pedestals/45-end.data
cp cspad2x2.1-ave-meca1113-r0045.dat /reg/d/psdm/mec/meca1113/calib/CsPad2x2::CalibV1/MecTargetChamber.0:Cspad2x2.1/pedestals/45-end.data
cp cspad2x2.2-ave-meca1113-r0045.dat /reg/d/psdm/mec/meca1113/calib/CsPad2x2::CalibV1/MecTargetChamber.0:Cspad2x2.2/pedestals/45-end.data
...
cp cspad.0-hot-meca1113-r0045.dat /reg/d/psdm/mec/meca1113/calib/CsPad::CalibV1/MecTargetChamber.0:Cspad.0/pixel_status/45-end.data
cp cspad2x2.1-hot-meca1113-r0045.dat /reg/d/psdm/mec/meca1113/calib/CsPad2x2::CalibV1/MecTargetChamber.0:Cspad2x2.1/pixel_status/45-end.data
... |
Create images in tiff format
Configuration file for psana psana-meca1113-r0376-cspad-cspad2x2-conv-tiff.cfg
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# Run this script:
# psana -c psana-meca1113-r0376-cspad-cspad2x2-conv-tiff.cfg
#
# Useful commands:
# psana -m EventKeys -n 5 exp=meca1113:run=376
# or
# psana -m EventKeys -n 5 /reg/d/psdm/mec/meca1113/xtc/e356-r0376-s03-c00.xtc
[psana]
# Default calibration directory:
# calib-dir = /reg/d/psdm/mec/meca1113/calib
files = exp=meca1113:run=376
events = 5
#skip-events = 0
modules = cspad_mod.CsPadCalib \
CSPadPixCoords.CSPadImageProducer:0 \
CSPadPixCoords.CSPad2x2ImageProducer:1 \
CSPadPixCoords.CSPad2x2ImageProducer:2 \
CSPadPixCoords.CSPad2x2ImageProducer:3 \
CSPadPixCoords.CSPad2x2ImageProducer:4 \
pyimgalgos.image_crop:0 \
pyimgalgos.image_save_in_file:0 \
pyimgalgos.image_save_in_file:1 \
pyimgalgos.image_save_in_file:2 \
pyimgalgos.image_save_in_file:3 \
pyimgalgos.image_save_in_file:4 \
ImgAlgos.Tahometer
# Calibrate all CSPAD and CSPAD2x2
[cspad_mod.CsPadCalib]
inputKey =
outputKey = calibrated_arr
doPedestals = yes
doPixelStatus = yes
doCommonMode = yes
[CSPadPixCoords.CSPadImageProducer:0]
#calibDir = /reg/d/psdm/mec/meca1113/calib
#typeGroupName = CsPad::CalibV1
source = DetInfo(MecTargetChamber.0:Cspad.0)
key = calibrated_arr
imgkey = image0
tiltIsApplied = false
print_bits = 3
[CSPadPixCoords.CSPad2x2ImageProducer:1]
#calibDir = /reg/d/psdm/mec/meca1113/calib
#typeGroupName = CsPad2x2::CalibV1
source = DetInfo(MecTargetChamber.0:Cspad2x2.1)
inkey = calibrated_arr
outimgkey = image1
tiltIsApplied = true
useWidePixCenter = false
print_bits = 3
[CSPadPixCoords.CSPad2x2ImageProducer:2]
#calibDir = /reg/d/psdm/mec/meca1113/calib
#typeGroupName = CsPad2x2::CalibV1
source = DetInfo(MecTargetChamber.0:Cspad2x2.2)
inkey = calibrated_arr
outimgkey = image2
tiltIsApplied = true
useWidePixCenter = false
print_bits = 3
[CSPadPixCoords.CSPad2x2ImageProducer:3]
#calibDir = /reg/d/psdm/mec/meca1113/calib
#typeGroupName = CsPad2x2::CalibV1
source = DetInfo(MecTargetChamber.0:Cspad2x2.3)
inkey = calibrated_arr
outimgkey = image3
tiltIsApplied = false
useWidePixCenter = false
print_bits = 3
[CSPadPixCoords.CSPad2x2ImageProducer:4]
#calibDir = /reg/d/psdm/mec/meca1113/calib
#typeGroupName = CsPad2x2::CalibV1
source = DetInfo(MecTargetChamber.0:Cspad2x2.4)
inkey = calibrated_arr
outimgkey = image4
tiltIsApplied = true
useWidePixCenter = false
print_bits = 3
[pyimgalgos.image_crop:0]
source = DetInfo(MecTargetChamber.0:Cspad.0)
key_in = image0
key_out = image0_cropped
rowmin = 70
rowmax = 900
colmin = 0
colmax = 825
print_bits = 255
[pyimgalgos.image_save_in_file:0]
source = DetInfo(MecTargetChamber.0:Cspad.0)
key_in = image0_cropped
ofname = cspad.0.tiff
print_bits = 5
[pyimgalgos.image_save_in_file:1]
source = DetInfo(MecTargetChamber.0:Cspad2x2.1)
key_in = image1
ofname = cspad2x2.1.tiff
print_bits = 5
[pyimgalgos.image_save_in_file:2]
source = DetInfo(MecTargetChamber.0:Cspad2x2.2)
key_in = image2
ofname = cspad2x2.2.tiff
print_bits = 5
[pyimgalgos.image_save_in_file:3]
source = DetInfo(MecTargetChamber.0:Cspad2x2.3)
key_in = image3
ofname = cspad2x2.3.tiff
print_bits = 5
[pyimgalgos.image_save_in_file:4]
source = DetInfo(MecTargetChamber.0:Cspad2x2.4)
key_in = image4
ofname = cspad2x2.4.tiff
print_bits = 5
[ImgAlgos.Tahometer]
dn = 100
print_bits = 7
|
Command:
% psana -c psana-meca1113-r0376-cspad-cspad2x2-tiff.cfg
or for other runs:
% psana -c psana-meca1113-r0376-cspad-cspad2x2-tiff.cfg exp=meca1113:run=378
will run over 5 events from xtc files, applys intensity correction for all CSPAD detectors (if calibration files are provided), produces images and save images for one CSPAD and four CSPAD2x2 detectors in 16-bit tiff files, with names like
cspad.0-r0376-e0000000#-20131110-101607.736131763.tiff
cspad2x2.#-r0376-e0000000#-20131110-101546.244253562.tiff
...
Examples for mecb3114
Experiment mecb3114 use different detectors in different runs. Not all of them collected data in each run. Then it make sense to produce tiff files for separate detectors.
Configuration file for MecTargetChamber.0:Cspad2x2: psana-mecb3114-r0008-cspad2x2-tiff.cfg
Configuration file for MecTargetChamber.0:Cspad.0: psana-mecb3114-r0323-cspad-tiff.cfg
Command to run:
% psana -m <file-name>.cfg exp=mecb3114:run=376
Examples for meci0114
Andreas Schropp needs to access cspad image in his custom psana module.
On 2014-03-21 Module ImgAlgos::ExampleDumpImg is add as an example.
Get and run this example in current release
For releases ≤ ana-0.10.14 the updated version of code can be compiled and run from local release directory;
Code Block |
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ssh -Y psana
cd <your-favorite-directory>
kinit
<next 6 lines can be copied and pasted>
newrel ana-0.10.14 my-release-dir;
cd my-release-dir;
sit_setup;
addpkg ImgAlgos HEAD;
addpkg CSPadPixCoords HEAD;
scons -j 8;
<wait a few minutes until it is compiled>
<pick-up *.cfg files and run them>
psana -c psana-meci0114-r0050-exampleimgdump-cspadcalib.cfg
psana -c psana-meci0114-r0050-exampleimgdump-ndarrcalib.cfg
|
These example print too much, but this is an intentional example. Level of verbosity can be controlled by the print_bits
parameter for each module.
Configuration files
- psana-meci0114-r0050-exampleimgdump-cspadcalib.cfg - use sequence of CsPadCalib, CSPadImageProducer, and ExampleDumpImg modules
works with int16_t data on all stages until ExampleDumpImg
- psana-meci0114-r0050-exampleimgdump-ndarrcalib.cfg - use sequence of CSPadNDArrProducer, NDArrCalib, CSPadImageProducer, and ExampleDumpImg modules
CSPadNDArrProducer - creates ndarray<const T,3> for a few generic data types,
NDArrCalib - may apply more corrections than CsPadCalib.
ExampleDumpImg - also may process a few data types such as int16_t, int, float, and double.
Other option to save image in 16-bit tiff files
Psana can use python modules. A few modules in package pyimgalgos were recently developed to process CSPAD data.
Psana Module Catalog - Package pyimgalgos
Psana Module Examples - Examples for Package pyimgalgos
In particular, module pyimgalgos.image_save_in_file
may save image in 16-bit tiff files.
Display tiff image
To display image from tiff file use display
command:
display <file-name>.tiff
then
- left mouse click on image
- click on "Enhance" button
- click on "Equalize" button
Other option - use ImageJ
command:
/reg/common/package/imagej/ImageJ <file-name>.tiff
Check tiff file
To check tiff file format one may use command:
% identify -verbose <file-name>.tiff
which prints information about tiff file structure. For example,
Code Block |
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% identify -verbose cspad.0-r0376-e00000001-20131110-101546.244253562.tiff
Image: cspad.0-r0376-e00000001-20131110-101546.244253562.tiff
Format: TIFF (Tagged Image File Format)
Class: PseudoClass
Geometry: 1750x1750
Type: Grayscale
Endianess: MSB
Colorspace: Gray
Channel depth:
Gray: 16-bits
Channel statistics:
Gray:
Min: 0 (0)
Max: 16383 (0.249989)
Mean: 1023.37 (0.0156156)
Standard deviation: 2132.77 (0.0325439)
Colors: 65536
...
|
Convert uint16 tiff to int16 tiff
Eric Galtier found the way to change file format record for tiff file using convert command:
convert input_file.tiff -define quantum:format=signed output_file.tiff
Other option for floating point conversion: -define quantum:format=floating-point
Examples for cxi86415
This test is done by request
Note |
---|
Loh, Ne-Te writes: |
Standard configuration file
Use psana configuration file psana-cxidg3-cspad2x2-NDArrAverage.cfg (download), which can be executed by command:
Code Block |
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sit_setup
psana -c psana-cxidg3-cspad2x2-NDArrAverage.cfg exp=cxi86415:run=7 |
This job produces 3 files with cspad2x2 shaped arrays for averaged, rms, and maximal intensities.
These arrays can be plotted by the command
Code Block |
---|
plims cspad2x2-ndarr-ave-cxi86415-r0007.dat |
Results for runs 7, 62, and 83 are shown on plots:
These plots show that the dark level is consistent with zero and does not indicate on any offset.
Loh's configuration file
Use configuration file from Loh's e-mail orig.cfg (download)
with minor modifications
- add psana parameters in the header, add list of modules
- remove
typeGroupname = CsPad:CalibV1 from
[CSPadPixCoords.CSPad2x2ImageProducer:2]
- add module
ImgAlgos.ImgSaveInFile:2
just in order to save image:
Code Block |
---|
[psana]
files = exp=cxi86415:run=64
events = 10
modules = CSPadPixCoords.CSPad2x2NDArrProducer:2 \
ImgAlgos.NDArrCalib:2 \
CSPadPixCoords.CSPad2x2ImageProducer:2 \
ImgAlgos.ImgSaveInFile:2
<code from e-mail is here>
[ImgAlgos.ImgSaveInFile:2]
source = DetInfo(CxiDg3.0:Cspad2x2.0)
key = reconstructed
fname = img-cspad2x2-dg3
ftype = txt
#saveAll = true
print_bits = 3
eventSave = 9 |
Run it with command:
Code Block |
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psana -c orig.cfg |
which produces file with image for event #9, which can be viewed as
Code Block |
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plims img-cspad2x2-dg3-cxi86415-r0064-e00000009-20150308-162942.145136207.txt |
ang brings us an image: - the same image, but spectrum is shown in the range (-100, 100) ADU. This event looks good.
Event #36: looks like left-side sensor is not corrected for common mode fluctuation...
In stead of default common_mode parameters (1,25,25,100) let us try (1,50,10,100) in the file
Code Block |
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/reg/d/psdm/CXI/cxi86415/calib/CsPad2x2::CalibV1/CxiDg3.0:Cspad2x2.0/common_mode/9-end.data |
The same image looks better now:
Recommendation: try to play with common mode parameters.
References
NDArrAverage module