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Example for module NDArrDropletFinder

See description of the module in Module ImgAlgos::NDArrDropletFinder

This module is a more generic implementation of the Module ImgAlgos::ImgPeakFinder in case of data segmented for multiple sensors, like in cspad.

The minimal configuration file for psana may look like psana-xppd7114-r0081-cspad2x2-NDArrDropletFinder.cfg

[psana]
#calib-dir = /reg/d/psdm/XPP/xppd7114/calib - is used by default
files = exp=xppd7114:run=81
events = 10
modules = CSPadPixCoords.CSPad2x2NDArrProducer \
          ImgAlgos.NDArrCalib \
          CSPadPixCoords.CSPad2x2NDArrReshape \
          ImgAlgos.NDArrDropletFinder


[CSPadPixCoords.CSPad2x2NDArrProducer]
source  = XppGon.0:Cspad2x2.0
inkey   = 
outkey  = nda_raw
outtype = int16
print_bits  = 3


[ImgAlgos.NDArrCalib]
source  = XppGon.0:Cspad2x2.0
key_in  = nda_raw
key_out = nda_clb:as_data
do_peds = yes
do_cmod = yes
do_stat = yes
do_mask = no
do_bkgd = no
do_gain = no
do_nrms = no
do_thre = no
fname_mask =
fname_bkgd =
masked_value     =    0
threshold_nrms   =    3
threshold        =  100
below_thre_value =    0
bkgd_ind_min     =    0
bkgd_ind_max     = 1000
bkgd_ind_inc     =   10
print_bits       =  255


[CSPadPixCoords.CSPad2x2NDArrReshape]
source     = XppGon.0:Cspad2x2.0
keys_in    = nda_clb:as_data
print_bits = 0


[ImgAlgos.NDArrDropletFinder]
source         = XppGon.0:Cspad2x2.0
key            = nda_clb
key_droplets   = nda_droplets
key_smeared    = nda_sme
threshold_low  = 1
threshold_high = 3
sigma          = 1.5
smear_radius   = 3
peak_radius    = 3
low_value      = -0.1
windows = 0 10 160 20  350 \
          1 10 160 10  150 \
          1 30 170 220 370
fname_prefix = test
print_bits = 511

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

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

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 one may get images like:

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

  struct Droplet{
    unsigned seg;     // segment index (in 3-d ndarray of data) of the found droplet
    double   row;     // row index of the droplet center
    double   col;     // columnindex of the droplet center 
    double   ampmax;  // amplitude in the droplet maximum
    double   amptot;  // total amplitude in the range of peak_radius
    unsigned npix;    // number of pixels in the range of peak_radius
  };

The shape of the ndarray with table of droplets is [<number-of-droplets>, 6].

File with droplets data is a text table of the same paramaters, for example

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 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)

For each event in the data set this script executes psana-xppd7114-r0081-cspad2x2-NDArrDropletFinder.cfg then gets its results as numpy arrays nda_droplets and nda_smeared and prints them.

This script can be executed by the command

./psana-xppd7114-r0081-cspad2x2-NDArrDropletFinder.py

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)

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 HEAD
scons

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

Packages PSCalib and CSPadPixCoords need to be added because they have been modified on the top of ana-0.13.13 release. They need to be compiled together due to dependency between packages.

 

References

 

 

 

 

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