Table of Contents

Setup environment

ssh pslogin
ssh psananeh (or psanafeh for cxi, sxr, and mec)psana
cd <your-directory>
sit_setup

Note
All files in this example are currently available in my local directory: /reg/neh/home/dubrovin/LCLS/PSANA-V01

Pedestals

Examples for xpp50312

Pedestals

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:

Code Block


[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

...

In a few seconds this job produces two text files with averaged pedestals and rms values as one-dimensional (143560) array for CSPad2x2. 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 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 the calibration subdirectories sub-directories somewhere in local user's space, for example:

Code Block
ana-xpp50312/calib/CsPad2x2::CalibV1/XppGon.0:Cspad2x2.0/pixel_gain/ pixel_status/ pedestals/ common_mode/

...

Another file for common mode correction common_mode/0-end.data usually looks like

Code Block
1 50 10

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 ana-xpp50312/psana-xpp50312-r0092.cfg:

Code Block


[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

...

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:

Code Block

bgColor	#DDFFFF

# 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

To produce files with pedestals use command:

Code Block

bgColor	#DDFFFF

psana -c psana-meca6113-r0018-cspad2x2-pedestals.cfg

which produces 6 files with average and rms values for 3 detectors:

Code Block

bgColor	#AAFFFF

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

Example of pedestal-image and spectral plots for 3 detectors, respectively:
Image Added Image Added
Image Added Image Added
Image Added Image Added

Calibration

Default calibration in psana will be done if files are located in right place. So, they were deployed as:

Code Block

bgColor	#AAFFFF

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

Create images in tiff format

Configuration file for psana psana-meca6113-r0028-cspad2x2-tiff.cfg:

Code Block

bgColor	#AAFFFF

# 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

To produce files with images in tiff format use command:

Code Block

bgColor	#DDFFFF

psana -c psana-meca6113-r0028-cspad2x2-tiff.cfg

New files will be produced with names containing time stamp:

Code Block

bgColor	#AAFFFF

 cspad2x2.1-r0028-20131013-155538.754093925.tiff
 cspad2x2.2-r0028-20131013-155538.754093925.tiff
 cspad2x2.3-r0028-20131013-155538.754093925.tiff

Example of image and spectral plots for 3 detectors, respectively:
Image Added Image Added
Image Added Image Added
Image Added Image Added

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:

Code Block
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

or run xtcexplorer:

Code Block
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:

Code Block

# 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:

Image Added Image Added Image Added

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:

Image Added Image Added

Calibration

Default calibration in psana will be done if files are located in right place. So, they were deployed as:

No Format

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

Code Block

# 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

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

% 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:

> On a separate note, the online monitoring software (hummingbird, by Benedikt and Filipe) will need py+psana. However, the default psana calibrations/corrections for the 140k back detector seems wonky. You might recall that there was a teleconference where Veitâ's student (Yi-Tien) discusses how the 0-photon peak had a largish negative ADU, despite turning on common mode correction and dark subtraction (psana's implementation). Would you and your team be able to take a look at these as well? If it's a quick fix, then the online monitoring group will have a much easier time (e.g. they won't have to separately do common mode subtraction).

Standard configuration file

Use psana configuration file psana-cxidg3-cspad2x2-NDArrAverage.cfg (download), which can be executed by command:

Code Block
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:

Image Added Image AddedImage Added

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
psana -c orig.cfg

which produces file with image for event #9, which can be viewed as

Code Block
plims img-cspad2x2-dg3-cxi86415-r0064-e00000009-20150308-162942.145136207.txt

ang brings us an image: Image AddedImage Added - the same image, but spectrum is shown in the range (-100, 100) ADU. This event looks good.

Event #36: Image Addedlooks 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
/reg/d/psdm/CXI/cxi86415/calib/CsPad2x2::CalibV1/CxiDg3.0:Cspad2x2.0/common_mode/9-end.data

The same image looks better now: Image Added

Recommendation: try to play with common mode parameters.

References

NDArrAverage module

Page tree

Versions Compared

Old Version 12

New Version Current

Key

Setup environment

Pedestals

Examples for xpp50312

Pedestals

Calibration

Analysis

Examples for meca6113

Pedestals

Calibration

Create images in tiff format

Examples for meca1113

Get latest version of packages and run psana

Pedestals and bad pixels

Calibration

Create images in tiff format

Examples for mecb3114

Examples for meci0114

Get and run this example in current release

Configuration files

Other option to save image in 16-bit tiff files

Display tiff image

Check tiff file

Convert uint16 tiff to int16 tiff

Examples for cxi86415

Standard configuration file

Loh's configuration file

References

Page tree

Page History

Versions Compared

Old Version 12

New Version Current

Key

Setup environment

Pedestals

Examples for xpp50312

Pedestals

Calibration

Analysis

Examples for meca6113

Pedestals

Calibration

Create images in tiff format

Examples for meca1113

Get latest version of packages and run psana

Pedestals and bad pixels

Calibration

Create images in tiff format

Examples for mecb3114

Examples for meci0114

Get and run this example in current release

Configuration files

Other option to save image in 16-bit tiff files

Display tiff image

Check tiff file

Convert uint16 tiff to int16 tiff

Examples for cxi86415

Standard configuration file

Loh's configuration file

References