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Motivation

Development of this application was stimulated by the discussion with Marcin Sikorski, doing xcs experiments.
Users need in real-time algorithm for calculation of image vs time auto-correlation function 

g2(tau) = <I(t)*I(t+tau)> / (<I(t)> * <I(t+tau)>),

where I(t) is an intensity at time t, and tau is a delay between two measurements.
Typical experimental condition can be described as follows:

  • Run duration is about one hour at frequency up to 120 Hz that gives up to 500-10^6 images.
  • Currently typical imaging devise is a Princeton camera with 1300x1340 pixels.
  • Need to calculate g2(tau) for each pixel, averaged over all possible image times t with time difference tau between images.
  • A set of tau should have about 30-100 points in log scale uniformly covering the run duration.
  • Use for example xcsi0112-r0015: 500 images with 8 sec between images.
    Desired time for evaluation of the auto-correlation function should be comparable with run duration ~<1 hour. Currently this algorithm takes a few hours that can not be used for fast feedback in real time experiment.

Algorithm

Basic idea is (1) to split image vs time for small parts in image, (2) to process each part on separate computer node, (3) to merge results at the end of processing. It is clear that significant speedup (~T/Nnodes) is achieved at the 2nd stage. These three stages are performed in separate C++ applications. Wrapping python script allows to submit job by a single command. It takes care about numerous files and sub-process management in this job, as discussed below.

Code location

All modules for this application resides in the package ImgAlgos.

Image splitting

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

Command:

psana -c <config-file> <xtc-file-list>

For example:

psana -c ana-misc-exp/psana-xcsi0112-r0015-img-auto-correlation.cfg  /reg/d/psdm/XCS/xcsi0112/xtc/e167-r0015-*

Produce files:

img-xcs-r0015-b0000.bin - file with a part of image vs time
img-xcs-r0015-b0001.bin
img-xcs-r0015-b0002.bin
img-xcs-r0015-b0003.bin
img-xcs-r0015-b0004.bin
img-xcs-r0015-b0005.bin
img-xcs-r0015-b0006.bin
img-xcs-r0015-b0007.bin
img-xcs-r0015-time.txt - list of time-record for all events in processed run.
img-xcs-r0015-med.txt - file with metadata. In particular it has the original image size, number of image parts for splitting, number of images in run, etc.

Time correlation processing

ImgAlgos/test/corana application

Command:

<path>/corana -f <fname-data> [-t <fname-tau>] -h [-l <logfile>] [-b <basedir>]

For example the interactive and batch mode commands:

<path>/corana -f img-xcs-r0015-b0001.bin -t my-tau.txt 
bsub -q psnehq -o ~/<path-from-home-dir>/log.txt '<path>/corana -f img-xcs-r0015-b0000.bin'

Where ~/<path-from-home-dir>/ or <path> is arbitrary choice and is a matter of taste.

Produce files:

img-xcs-r0015-tau.txt          - string of tau values for which the auto-correlation function is evaluated
img-xcs-r0015-b0000-result.bin - auto-correlators for the part of the image for all tau values 
img-xcs-r0015-b0001-result.bin
img-xcs-r0015-b0002-result.bin
img-xcs-r0015-b0003-result.bin
img-xcs-r0015-b0004-result.bin
img-xcs-r0015-b0005-result.bin
img-xcs-r0015-b0006-result.bin
img-xcs-r0015-b0007-result.bin

Merging results

ImgAlgos/test/corana_merge application

Command:

<path>/corana_merge -f <fname-data> [-t <fname-tau>] -h [-l <logfile>] [-b <basedir>]

For example:

<path>/corana_merge -f img-xcs-r0015-b0001-result.bin -t my-tau.txt

Produce file:

img-xcs-r0015-image-result.bin

Wrapping script

./CorAnaSubmit.py

./CorAnaSubmit.py -c <config-file> -t <fname-tau> [-x] <xtc-file-list>

For example:

./CorAnaSubmit.py -c ana-misc-exp/psana-xcsi0112-r0015-img-auto-correlation.cfg -t my-tau.txt /reg/d/psdm/XCS/xcsi0112/xtc/e167-r0015-s00-c00.xtc

File formats

  • img-xcs-r0015-b000N.bin:
    Currently it saves uint16_t amplitude for each pixel in binary format for: 
    <data-for-img-partN-of-img1> <data-for-img-partN-of-img2> ... <data-for-img-partN-of-imgLast>
  • img-xcs-r0015-med.txt: 
    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
  • img-xcs-r0015-time.txt: 
         1  1339858956.672  0.000  20120616-080236.671607864  005366  00000
     2  1339858964.698  8.026  20120616-080244.698036743  008255  00001
     3  1339858972.816  8.118  20120616-080252.816395836  011177  00002
     4  1339858980.826  8.010  20120616-080300.826443448  014060  00003
    ...
    where each record has: 
    <image-in-file#> <dt(sec)> <time-stamp> <fiducials> <event#-since-configure>
    *img-xcs-r0015-b000N-result.bin:
    Currently it saves float correlator for each pixel in binary format for: 
    <corr-for-img-partN-of-tau1> <corr-for-img-partN-of-tau2> ... <corr-for-img-partN-of-tauLast>
    *my-tau.txt: 
     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.
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