Page History
Table of Contents |
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Motivation
Development of this application was stimulated by the discussion with Marcin Sikorski (meeting on 2012-08-30), doing xcs experiments.
Users need in real-time algorithm for calculation of image vs time auto-correlation function
Code Block |
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g2(tau) = <I(t)*I(t+tau)> / (<I(t)> * <I(t+tau)>), |
where I(t)
is an image 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 50010^5-10^6 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 timest
with time differencetau
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 delay between images.
Desired time for evaluation of the auto-correlation function should be comparable with run duration ~<1 <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/Nnodesabout T/N_nodes_) 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 file and sub-process management in this job, as discussed described below.
Code location
All modules for this application resides in the package ImgAlgos:
Module | Functionality |
---|---|
ImgVsTimeSplitInFiles | splitter |
CorAna | base class with common methods |
CorAnaData | data processing for split files |
CorAnaInputParameters | provides storage for input parameters |
CorAnaMergeFiles | merging algorithm |
CorAnaProcResults | Example showing how to access results using C++ and produce a table for presentation |
CorAnaPars.py | singleton class for parameter storage in the wrapping file manager |
CorAnaSubmit.py | global methods for the file manager |
app/corana_submit | pythonic script which defines the sequence of procedures in the file manager |
Image splitting
Image splitting is implemented as a regular psana module ImgAlgos::ImgVsTimeSplitInFiles.
Command:
Code Block |
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psana -c <config-file> <xtc-file-list>
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For example:
app/corana.cpp | main module for the part of image vs time correlation processing |
app/corana_merge.cpp | main module for merging |
app/corana_procres.cpp | main module for processing of results from correlator array |
data/psana-corana.cfg | psana configuration file for ImgVsTimeSplitInFiles |
data/PlotCorAnaResults.py | example of the python script which plots the resulting graphics |
Image splitting
Image splitting is implemented as a regular psana module ImgAlgos::ImgVsTimeSplitInFiles.
Command to run interactively on psana####
or submit in batch from pslogin##
node:
Code Block |
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psana -c <config-file> <xtc-file-list>
bsub -q psfehq -o log-file 'psana -c <config-file> <xtc-file-list>'
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For example:
Code Block |
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psana -c ImgAlgos/data/psana-corana.cfg /reg/ |
Code Block |
psana -c ana-misc-exp/psana-xcsi0112-r0015-img-auto-correlation.cfg /reg/d/psdm/XCS/xcsi0112/xtc/e167-r0015-*
|
Produce files:
where ImgAlgos/data/psana-corana.cfg
is an example of the configuration script for psana
and /reg/d/psdm/XCS/xcsi0112/xtc/e167-r0015-*
are the input xtc files for particular run.
Note |
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A couple of limitations due to LCLS policy: |
Produces the files:
Code Block |
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cor-ana-r0015-b0000.bin - file with a part of image vs time
cor-ana-r0015-b0001.bin
cor-ana-r0015-b0002.bin
cor-ana-r0015-b0003.bin
cor-ana-r0015-b0004.bin
cor-ana-r0015-b0005.bin
cor-ana-r0015-b0006.bin
cor-ana-r0015-b0007.bin
cor-ana-r0015-time |
Code Block |
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-time-ind.txt - list of time-recordrecords for all events in processed run with time index. img-xcs. cor-ana-r0015-time-ind.txt - list of time-records for all events in processed run with time index. cor-ana-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. |
...
- The <int16_t> image data array is split for ordered number of equal parts and each part is saved in the output img-xcs-r0015-b000N(by the parameters
nfiles_out
in psana-corana.cfg file) and each part is saved in the outputcor-ana-r0015-b####.bin
file sequentially for all selected events. - The appropriate time record for each selected event is saved in the file
imgcor-xcsana-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
imgcor-xcsana-r0015-time.txt
is re-winded processed and for each record the time index is evaluated as unsigned value ofCode 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
imgcor-xcsana-r0015-time-ind.txt
- The file
img-xcs-r0015-med.txt
contains input parameters, 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.
Time correlation processing
ImgAlgos/test/corana
application
Command:
- , are saved in file
cor-ana-r0015-med.txt
.
Note |
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This approach allows to apply the modest event selection algorithms in |
Time correlation processing
ImgAlgos/app/corana
application
Command to run interactively on psana####
or submit in batch from pslogin##
node:
Code Block |
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|
Code Block |
<path>/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>] [-b <basedir>h]' |
For example the interactive and batch mode commands:
Code Block |
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<path>/corana -f imgcor-xcsana-r0015-b0001.bin -t my-tau.txt bsub -q psnehqpsfehq -o ~/<path-from-home-dir>/log.txtlog-file '<path>/corana -f imgcor-xcsana-r0015-b0000.bin' |
...
Produce files:
Code Block |
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imgcor-xcsana-r0015-tau.txt - string of {{tau}} values for which the auto-correlation function is evaluated imgcor-xcsana-r0015-b0000-result.bin - auto-correlators for the part of the image for all {{tau}} values imgcor-xcsana-r0015-b0001-result.bin imgcor-xcsana-r0015-b0002-result.bin imgcor-xcsana-r0015-b0003-result.bin imgcor-xcsana-r0015-b0004-result.bin imgcor-xcsana-r0015-b0005-result.bin imgcor-xcsana-r0015-b0006-result.bin imgcor-xcsana-r0015-b0007-result.bin |
Merging results
ImgAlgos/testapp/corana_merge
application
Command to run interactively on psana####
or submit in batch from pslogin##
node:
Code Block |
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<path>/corana_merge -f <fname-data> [-t <fname-tau>] -h [-l <logfile>] [-b <basedir>] h] bsub -q psfehq -o log-file 'corana_merge -f <fname-data> [-t <fname-tau>] [-l <logfile>] [-h]' |
For For example:
Code Block |
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<path>/corana_merge -f imgcor-xcsana-r0015-b0001-result.bin -t my-tau.txt |
Produce This procedure produces file:
Code Block |
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imgcor-xcsana-r0015-image-result.bin |
Wrapping script
Example of how to get and process results
ImgAlgos/app/corana_procres
Command to run interactively on psana####
or submit in batch from pslogin##
node:./CorAnaSubmit.py
Code Block |
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./CorAnaSubmit.pycorana_procres -cf <config<fname-file>data> [-t <fname-tau>] [-xl <logfile>] <xtc-file-list> |
For example:
Code Block |
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./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
[-h]
bsub -q psfehq -o log-file 'corana_procres -f <fname-data> [-t <fname-tau>] [-l <logfile>] [-h]'
|
Basically it reads files with results and produces the histogram-like table *-hist.txt
.
Automatic processing
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 management. Command to start:
Code Block |
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corana_submit [-c <config-file>] [-t <fname-tau>] [-x] <xtc-file-list>
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For example:
Code Block |
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corana_submit -c ImgAlgos/data/psana-corana.cfg -t my-tau.txt /reg/d/psdm/XCS/xcsi0112/xtc/e167-r0015-s00-c00.xtc
|
This script sequentially performs operations for single run as follows:
- Initialize all parameters
- Run psana to split image for files
- Check that all split files are produced
- Submit job for time-correlation processing
- Check that all processed files are produced
- Submit job for merging
- Check that merged file is produced
- Submit job for test processing of the file with results
- List all created files
- Clean-up files in the work directory
- 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####
Code Block |
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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_procres -f <fname-data> [-t <fname-tau>] [-l <logfile>] [-h]
|
or submit in batch from pslogin##
node:
Code Block |
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bsub -q psfehq -o log-file 'psana -c <config-file> <xtc-file-list>'
bsub -q psfehq -o log-file 'corana -f <fname-data> [-t <fname-tau>] [-l <logfile>] [-h]'
bsub -q psfehq -o log-file 'corana_merge -f <fname-data> [-t <fname-tau>] [-l <logfile>] [-h]'
bsub -q psfehq -o log-file 'corana_procres -f <fname-data> [-t <fname-tau>] [-l <logfile>] [-h]'
|
The corana
batch jobs can be submitted and run on separate butch nodes in parallel. All other procedures can be submitted when previous is successfully finished and all necessary files are produced.
The corana_procres
command is optional and is currently used for test purpose only. But, it may be replaced by real analysis code.
File formats
- File with split-image data for selected events
cor-ana-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
cor-ana-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
cor-ana-r0015-time.txt
:
where each record has: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 ...
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
cor-ana-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
img-xcs-r0015-b000N.bin
:
Currently it saves 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>
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
img-xcs-r0015-time.txt
:
where each record has: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 ...
Code Block <image-in-file#> <t(sec)-from-the-1st-event> <dt(sec)> <time-stamp> <fiducials> <event#-since-configure>
img-xcs-r0015-time.txt
:
where each record has: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 ...
Code Block <image-in-file#> <dt(sec)> <time-stamp> <fiducials> <event#-since-configure> <time-index-starting-from-0>
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>
-since-configure> <time-index-starting-from-0>
- File with split-image correlators for each value of
tau
cor-ana-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
:
contains theCode 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
tau
values presented in terms of number of ordered images in the file.
my-tau.txt
: Code Block |
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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
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Quick start guide
We assume that everything is set up to work on LCLS analysis farm, otherwise see Computing (including Analysis) and Account Setup.
How to run this procedure
If the version of the package ImgAlgos is available as a current software release, then you may run the script command(s) directly, for example:
Code Block |
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cd <your-favorite-directory>
mkdir work_corana
sit_setup
corana_submit [-c <config-file>] [-t <fname-tau>] [-x] <xtc-file-list>
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Note |
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If the code in the package ImgAlgos has been recently changed and the updated release is not yet available, then one need to create the local release directory, get the latest/HEAD version of the package, and compile the code as shown below: |
Code Block |
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cd <your-favorite-directory>
newrel ana-current myReleaseDirectory
cd myReleaseDirectory
sit_setup
addpkg ImgAlgos HEAD
scons
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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:
File name tail | Format | Content |
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*-image-result.bin | binary for <float> | correlators for all image pixels for all tau values |
*-time-ind.txt | text | time records for all selected events/images |
*-tau.txt | text | the list of tau intervals |
*-med.txt | text | meta data parameters |
*-hist.txt | text | Histogram array with correlators averaged for ring regions of the image for all |
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:
Code Block |
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./ImgAlgos/data/PlotCorAnaResults.py work_corana/cor-ana-r0015-hist.txt
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Note |
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Another option is to use python script for direct processing of the resulting files. |