...

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 through the psana parameters. In order to fulfill the naming conventions we have to create a tree of the calibration sub-directories somewhere in local user's space, for example:

...

• 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.#-r0376-e0000000#-20131110-101546.244253562.tiff

...

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

1. left mouse click on image
2. click on "Enhance" button
3. 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,

% 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

References

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;

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

1. left mouse click on image
2. click on "Enhance" button
3. 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,

% 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

Standard configuration file

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

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

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:

[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:

psana -c orig.cfg

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

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

/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

• CSPAD2x2 Alignment
• psana -
• CSPad2x2 Alignment
• Psana Module Examples
  • Example for module cspad_mod::CsPad2x2Pedestals
  • Example for module CSPadPixCoords::CSPad2x2ImageProducer
  • Example for module ImgAlgos::ImgSaveInFile
• Psana psana - Module Catalog

NDArrAverage module