Content

Example for module NDArrDropletFinder

See description of the module in Module ImgAlgos::NDArrDropletFinder

...

which defines parameters of a few modules with functionality as follows.

Script functionality

• CSPadPixCoords.CSPad2x2NDArrProducer - get raw data for XppGon.0:Cspad2x2.0 and put them in the event store as ndarray with key nda_raw
• ImgAlgos.NDArrCalib - get ndarray with key nda_raw, applies a bunch of intensity corrections, and saves in the event store the ndarray with key nda_clb:as_data
• CSPadPixCoords.CSPad2x2NDArrReshape - re-shuffle cspad2x2 pixels shaped as data [185,388,2] to "natural" ndarray format [2,185,388]
• ImgAlgos.NDArrDropletFinder - gets calibrated and shaped as two 2-d segments ndarray  nda_clb, applies smearing (if sigma>0), find droplets (wide peaks), and saves them in the event store and in the file (if fname_prefix is not empty).

Remarks about parameters

• For each new set of smearing parameters (if applied, sigma>0) the droplet-finder parameters need to be re-tuned.
• Number of windows per sensor is unlimited but the should not overlap each other in order to get rid of duplication of found peaks in the overlapping regions. 
• Parameter low_value = −0.1 is set for demonstration purpose - in order to distinguish on plot sensors' pixels from image bins.
• Parameter fname_prefix = test is set in demonstration purpose in order to save image and peak data files for browser

Running script with psana

This file can be executed by the command

...

This job generates a bunch of files for all events with names like test-xppd7114-r0081-e000006-<suffix>.txt, where <suffix> stands for raw (data), smeared (if requested), and peaks. Using browser ImgAlgos/data/PlotNDArrayAndPeaks.py launched by the command (from release directory):

ImgAlgos/data/PlotNDArrayAndPeaks.py -i test-xppd7114-r0081-e000009-smeared.txt
### or ###
ImgAlgos/data/PlotNDArrayAndPeaks.py -i test-xppd7114-r0081-e000009-raw.txt

one may get images like:

Image Modified

Fig.1: Image of cspad2x2, containing two 2x1 segments. Droplet-finder is applied to the calibrated and smeared data in three windows.

Format of the ndarray of droplets

Content of the record for each droplet is defined by the structure of six components

...

0         127       137       5.01175   60.1614   20      
0         129       166       4.55816   52.7998   20      
0         155       131       4.09197   48.5101   20      
1         105       17        3.65102   17.5217   6       
1         145       49        3.87695   30.5501   15      
1         116       249       3.07719   20.5181   11      
1         139       325       3.60641   60.2324   27    
...

Access droplet data in python

Example of the python script psana-xppd7114-r0081-cspad2x2-NDArrDropletFinder.py:

#!/usr/bin/env python

import sys
import numpy as np
import psana

psana.setConfigFile('psana-xppd7114-r0081-cspad2x2-NDArrDropletFinder.cfg')

dsname = 'exp=xppd7114:run=81'
print """Data source: %s""" % dsname
ds = psana.DataSource(dsname)

evnum_max = 50

#------------------------------

for evnum, evt in enumerate(ds.events()) :
    evtid  = evt.get(psana.EventId)
    if evnum > evnum_max : break

    nda_droplets   = evt.get(psana.ndarray_float32_2, psana.Source('DetInfo(XppGon.0:Cspad2x2.0)'), 'nda_droplets')
    nda_smeared    = evt.get(psana.ndarray_float64_3, psana.Source('DetInfo(XppGon.0:Cspad2x2.0)'), 'nda_sme')
    nda_calibrated = evt.get(psana.ndarray_float64_3, psana.Source('DetInfo(XppGon.0:Cspad2x2.0)'), 'nda_clb')

    print print 50*'=', '\nEvent: %d' % evnum
    if (nda_smeared is not None) : print 'nda_smeared.shape = ', nda_smeared.shape

    if (nda_calibrated is not None) : print 'nda_calibrated.shape = ', nda_calibrated.shape

    if (nda_droplets is not None) :
        print 'nda_droplets.shape  = ', nda_droplets.shape
        for droplet in nda_droplets :
            seg, row, col, amax, atot, npix = droplet
            print '    seg:%2d  row:%3d  col:%3d  amax:%8.1f  atot:%8.1f  npix:%2d' % \
                   (seg, row, col, amax, atot, npix)    

...

In order to eliminate too excessive printout from psana modules, set parameters print_bits = 0 or 1 in the configuration file.

Get latest version (if needed)

.

Examples for exp=cxif5315:run=165

Example 1

Shows how to get ndarray with CSPAD  data in psana, calibrate it, find peaks (droplets) in imaging data and plot them offline.

Configuration file: psana-cxif5315-r0165-cspad-ds2-NDArrDropletFinder.cfg

ROI Mask: roi_mask_nda.txt

Command to run job:

psana -c psana-cxif5315-r0165-cspad-ds2-NDArrDropletFinder.cfg

Command to see results:

ImgAlgos/data/PlotNDArrayAndPeaks.py -g /reg/d/psdm/CXI/cxif5315/calib/CsPad::CalibV1/CxiDs2.0:Cspad.0/geometry/1-end.data -i test-cxif5315-r0165-e000001-raw.txt

Image Added

Example 2

Shows how to get ndarray with CSPAD  data in psana, calibrate it, prepare and apply mask, find peaks (droplets) in imaging data and plot them offline.

Configuration file: psana-cxif5315-r0165-cspad-ds2-NDArrDropletFinder-v2.cfg

ROI Mask: roi_mask_nda-v2.txt is produced in calibman (tab ROI):

image without mask for event 10:Image Added(dark is subtracted).

mask production stages in the mask editor: Image Added Image Added Image Added

Use this mask-ndarray roi_mask_nda-v2.txt in the NDArrDropletFinder with additional list of segment windows:

windows =  0 0 185 0 388 \
           1 0 185 0 388 \ 
           8 0 185 0 388 \
           9 0 185 0 388 \
          16 0 185 0 388 \
          17 0 185 0 388 \
          24 0 185 0 388 \
          25 0 185 0 388 

which contains 8 closest to the beam 2x1 sensors.

Command:

psana -c psana-cxif5315-r0165-cspad-ds2-NDArrDropletFinder-v2.cfg

produces files with image and list of peaks for all requested events, which can be viewed by the command

ImgAlgos/data/PlotNDArrayAndPeaks.py -g /reg/d/psdm/CXI/cxif5315/calib/CsPad::CalibV1/CxiDs2.0:Cspad.0/geometry/1-end.data -i test-cxif5315-r0165-e000001-raw.txt

This viewer shows images like: Image Added

Example 3

Example 3 has the same functionality as Example 2. Also this example shows how to

• gets raw ndarray with CSPAD data, subtract pedestals and background, apply common mode correction, apply mask, find peaks,
• access psana data structures from the python script,
• reconstruct CSPAD image,
• apply selection to the list of droplets and make the list of "bold" beaks,
• skip events without "bold" peaks,
• and interactively plot images with overlayed peaks.

file with mask: roi_mask_nda_v3.txt

file with background: bkgd-cxif5315-r0165.dat  obtained by averaging calibrated ndarray with module ImgAlgos.NDArrAverage over 1000 events: Image Added

psana configuration file:  psana-cxif5315-r0165-cspad-ds2-NDArrDropletFinder-v3.cfg - download

python script for interactive psana: psana-cxif5315-r0165-cspad-ds2-NDArrDropletFinder-v3.py.txt - download

Interactive job can be launched by the command:

python psana-cxif5315-r0165-cspad-ds2-NDArrDropletFinder-v3.py

• which does all work and plots images with peaks like Image Added - background is not subtracted, or Image Added- background is subtracted

Get latest version

Release ana-current (ana-0.13.18 or later) has the latest version of all necessary packages.

In case of any packages updates relative to the current release, the new version of the code can be tested from local release directory (test_release_directory)Until the psana release > ana-0.13.13 is created, one has to work from local release directory:

ssh psana
kinit
cd <one-of-your-directories>
newrel ana-current test_release_directory
cd test_release_directory
sit_setup
addpkg ImgAlgos HEAD
addpkg pdscalibdata HEAD
addpkg PSCalib HEAD
addpkg CSPadPixCoords<other-package-name> HEAD
scons

...
psana -c psana-xppd7114-r0081-cspad2x2-NDArrDropletFinder.cfg

References

• psana - Module Catalog
• psana - Module Examples
• CSPAD2x2 Alignment