Content

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 an 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 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.