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Image splitting

Image splitting is implemented as a regular psana module ImgAlgos::ImgVsTimeSplitInFiles.

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• The <int16_t> image data array is split for ordered (in psana *.cfg file) number of equal parts and each part is saved in the output img-xcs-r0015-b####.bin file sequentially for all selected events.
• The appropriate time record for selected event is saved in the file img-xcs-r0015-time.txt.
• At the end of the splitting procedure:
  • the average time difference and its rms between sequential events is evaluated for all recorded time records.
  • The file img-xcs-r0015-time.txt is re-processed and for each record the time index is evaluated as unsigned value of

    Code Block
    <time-index> = (<event-time> + 0.5 <average-time-between-events>) / <average-time-between-events>

  • Event record with time index is saved in the file img-xcs-r0015-time-ind.txt
• All metadata parameters which are required for further processing, such as input parameters, image size, <average-time-between-events, maximal value of the time index etc., are saved in file img-xcs-r0015-med.txt.

Time correlation processing

ImgAlgos/app/corana application

Command to run interactively on psana#### or submit in batch from pslogin## node:

Time correlation processing

ImgAlgos/app/corana application

Command to run interactively on psana#### or submit in batch from pslogin## node:

corana -f <fname-data> [-t <fname-tau>] [-l <logfile>] [-h] 
bsub -q psfehq -o log-file 'corana -f <fname-data> [-t <fname-tau>] [-l <logfile>] [-h]'

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ImgAlgos/app/corana_submit - is a wrapping script which allows to run all of above procedures by a single command from pslogin## node and it keeps eye on processing of jobs in batch and doing the file managmentmanagement. Command to start:

corana_submit [-c <config-file>] [-t <fname-tau>] [-x] <xtc-file-list>

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corana_submit -c ImgAlgos/data/psana-xcsi0112-r0015-img-auto-correlation.cfg -t my-tau.txt /reg/d/psdm/XCS/xcsi0112/xtc/e167-r0015-s00-c00.xtc 

Manual sequential processing

In case of manual processing of all scripts, commands need to be issued in a right order. Commands corana, corana_merge, and corana_procres should have the same list of parameters. This is important, because all file names for these procedures are generated by the same base class ImgAlgos/src/CorAna.cpp

Right sequence of commands to run interactively on psana####

This script sequentially performs operations for single run as follows:

1. Initialize all parameters
2. Run psana to split image for files
3. Check that all split files are produced
4. Submit job for time-correlation processing
5. Check that all processed files are produced
6. Submit job for merging
7. Check that merged file is produced
8. Submit job for test processing of the file with results
9. List all created files
10. Clean-up files in the work directory
11. List of preserved files

    Note
    The next to last procedure deletes all intermediate split- and log- files. In debugging mode this procedure may be turned off.

Manual sequential processing

In case of manual processing of all scripts, commands need to be issued in a right order. Commands corana, corana_merge, and corana_procres should have the same list of parameters. This is important, because all file names for these procedures are generated by the same base class ImgAlgos/src/CorAna.cpp

Right sequence of commands to run interactively on psana####

psana -c <config-file> <xtc-file-list>
corana         -f <fname-data> [-t

psana -c <config-file> <xtc-file-list>
corana         -f <fname-data> [-t <fname-tau>] [-l <logfile>] [-h] 
corana_merge   -f <fname-data> [-t <fname-tau>] [-l <logfile>] [-h] 
corana_merge   -f <fname-data> [-t <fname-tau>] [-l <logfile>] [-h]
corana_procres -f <fname-data> [-t <fname-tau>] [-l <logfile>] [-h]

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• File with split-image data for selected events img-xcs-r0015-b000N.bin:
  Currently this file contains <uint16_t> amplitude for each pixel in binary format for:

  Code Block
  <data-for-img-partN-of-img1> <data-for-img-partN-of-img2> ... <data-for-img-partN-of-imgLast>

• File with metadata parameters img-xcs-r0015-med.txt:

  Code Block
  IMAGE_ROWS 1300 IMAGE_COLS 1340 IMAGE_SIZE 1742000 NUMBER_OF_FILES 8 BLOCK_SIZE 217750 REST_SIZE 0 NUMBER_OF_IMGS 500 FILE_TYPE bin DATA_TYPE uint16_t TIME_SEC_AVE 8.088413 TIME_SEC_RMS 0.063639 TIME_INDEX_MAX 499

• File with image time records img-xcs-r0015-time.txt:

  Code Block
  1 0.000000 0.000000 20120616-080236.671607864 5366 0 2 8.026429 8.026429 20120616-080244.698036743 8255 1 3 16.144788 8.118359 20120616-080252.816395836 11177 2 4 24.154835 8.010048 20120616-080300.826443448 14060 3 ...

  where each record has:

  Code Block
  <image-in-file#> <t(sec)-from-the-1st-event> <dt(sec)> <time-stamp> <fiducials> <event#-since-configure>

• File with image time records and evaluated time index img-xcs-r0015-time-ind.txt:

  Code Block
  1 0.000000 0.000000 20120616-080236.671607864 5366 0 0 2 8.026429 8.026429 20120616-080244.698036743 8255 1 1 3 16.144788 8.118359 20120616-080252.816395836 11177 2 2 4 24.154835 8.010048 20120616-080300.826443448 14060 3 3 5 32.281937 8.127102 20120616-080308.953545010 16985 4 4 ...

  where each record has:

  Code Block
  <image-in-file#> <t(sec)-from-the-1st-event> <dt(sec)> <time-stamp> <fiducials> <event#-since-configure> <time-index-starting-from-0>

• File with split-image correlators for each value of tau img-xcs-r0015-b000N-result.bin:
  Currently it saves <float> correlator for each pixel in binary format for:

  Code Block
  <corr-for-img-partN-of-tau1> <corr-for-img-partN-of-tau2> ... <corr-for-img-partN-of-tauLast>

• my-tau.txt:

  Code Block
  1 3 5 7 9 10 12 14 16 18 20 24 28 30 32 36 40 ... 160 180 200 240 280 300 320 360 400

  contains the tau values presented in terms of number of ordered images in the file.

Quick start guide

We assume that everything is set up to work on LCLS analysis farm, otherwise see Computing and Account Setup.

How to run this procedure

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• 28 30 32 36 40 ... 160 180 200 240 280 300 320 360 400

  contains the tau values presented in terms of number of ordered images in the file.

Quick start guide

We assume that everything is set up to work on LCLS analysis farm, otherwise see Computing and Account Setup.

How to run this procedure

If the version of the package ImgAlgos is already current software release, then you may run the script command(s) directly, for example:

cd <your-favorite-directory>
mkdir work_corana
sit_setup
corana_submit [-c <config-file>] [-t <fname-tau>] [-x] <xtc-file-list>

cd <your-favorite-directory>
mkdir work_coranadirectory>
newrel ana-current myReleaseDirectory
cd myReleaseDirectory
sit_setup
corana_submit [-c <config-file>] [-t <fname-tau>] [-x] <xtc-file-list>

cd <your-favorite-directory>
newrel ana-current myReleaseDirectory
cd myReleaseDirectory
sit_setup
addpkg ImgAlgos HEAD
scons

Where to find results

The procedure will produce a bunch of files in the work_corana directory. The most important files are

How to look at results

It is assumed that all files listed in previous section may be used for further analysis, depending on particular goals.

...

addpkg ImgAlgos HEAD
scons

Where to find results

The procedure will produce a bunch of files in the work_corana directory. If everything is OK, then all spit - and log- files will be removed at the end of automatic corana_submit procedure. The most important files are preserved for further analysis:

How to look at results

It is assumed that all files listed in previous section may be used for further analysis, depending on particular goals. The optional script corana_procres is designed as an example of how to access data from C++ code. Class CorAnaProcResults produces the file *-hist.txt
A simple python script shows how to plot this file:

./ImgAlgos/data/PlotCorAnaResults.py work_corana/img-xcs-r0015-hist.txt

Image Added