...

• source (default: "DetInfo(SxrBeamline.0:Opal1000.1)" ) – source of data for Opal camera
  or
• source (default: "DetInfo(:Princeton)" ) – source of data for Princeton camera

Auxiliary scripts

A few python scripts in ImgPixSpectra/data/ show how to process/plot the spectral array stored in the file.

• PlotSpectralArrayFromFile.py - allows to plot content of the spectral array as a 2-d plot. For example, the command

  Code Block
  ImgPixSpectra/data/PlotSpectralArrayFromFile.py mini-cspad-pix-spectra.txt

  generates image for limited range of pixels for CSPad, MiniCSPad, or Camera, respectively:
  Image RemovedImage Removed Image Removed

• SpectralArray.py - provides access to the spectral array stored in the file. The class SpectralArray defined in this script is used in the PlotSpectralArrayFromFile.py.

• MergeArrays.py - sums the arrays from different files defined in the list and saves resulting array in a single file with the same shape. In this script the list of files is hardwired in the get_list_of_input_file_names() method. The output file name, out_fname, is also hardwired in the call to spectra_merging(out_fname).

Package ImgAlgos

This packages contains a few psana modules for image processing

Module ImgAlgos::CSPadCommonModeCorrection

See also Example for Package ImgPixSpectra.

Package ImgAlgos

This packages contains a few psana modules for image processing

Module ImgAlgos::CSPadCommonModeCorrection

Alternative to the cspad_mod.CsPadCalib algorithm for the common mode correction.
Takes the CSPad data array with subtracted pedestals, evaluate the average amplitude for each 2x1 section for amplitudes below the threshold, and subtract it from all pixel amplitudes. This algorithm consumes about 30 ms/event on psana0205.

Module configuration parameters:

• source (default: "DetInfo(:Cspad)" ) – source of data for CSPad
• inputKey (default: "calibrated" ) – key for input data, by default expects data from cspad_mod.CsPadCalib
• outputKey (default: "cm_subtracted" ) – output key for the next data processing stage
• ampthr (default: 30 ) – threshold to exclude the large pixel amplitudes in average

Module ImgAlgos::ImgPixAmpFilter

The ImgAlgos::ImgPixAmpFilter is a filter for event selection.
This filter counts the number of image pixels in the specified window with amplitude exceeding the threshold. If the number of high-amplitude pixels exceed the numPixMin, the event is passed for further analysis.

The algorithm performance was tested for CSPad images. This algorithm consumes up to 15 ms/event on psana0205 for full CSPad (1650x1650) window size. For smaller window consumed time is negligible, comparing to the image reconstruction time, which is ~70 ms/event (for cspad_mod.CsPadCalib and CSPadPixCoords::CSPadImageProducer) Alternative to the cspad_mod.CsPadCalib algorithm for the common mode correction.
Takes the CSPad data array with subtracted pedestals, evaluate the average amplitude for each 2x1 section for amplitudes below the threshold, and subtract it from all pixel amplitudes. This algorithm consumes about 30 ms/event on psana0205.

Module configuration parameters:

• source (default: "DetInfo(:Cspad)") – source of data for CSPad
• inputKey key (default: "calibratedImage2D") – key for input image data, by default expects data from cspad_mod.CsPadCalib
• outputKey (default: "cm_subtracted" ) – output key for the next data processing stage
• ampthr (default: 30 ) – threshold to exclude the large pixel amplitudes in average

Module ImgAlgos::ImgPixAmpFilter

The ImgAlgos::ImgPixAmpFilter is a filter for event selection.
This filter counts the number of image pixels in the specified window with amplitude exceeding the threshold. If the number of high-amplitude pixels exceed the numPixMin, the event is passed for further analysis.

The algorithm performance was tested for CSPad images. This algorithm consumes up to 15 ms/event on psana0205 for full CSPad (1650x1650) window size. For smaller window consumed time is negligible, comparing to the image reconstruction time, which is ~70 ms/event (for cspad_mod.CsPadCalib and CSPadPixCoords::CSPadImageProducer) on psana0205.

Module configuration parameters:

• source (default: "DetInfo(:Cspad)") – source of data
• key (default: "Image2D") – key for input image data
• threshold (default: 10) – minimal threshold on pixel amplitude
• numPixMin (default: 100) – minimal number of pixels with amplitude above the threshold
• filterIsOn (default: true) – On/Off the filter
• xmin (default: 0) – minimal column number
• xmax (default: 100000) – maximal column number
• ymin (default: 0) – minimal row number
• ymax (default: 100000) – maximal row number
• print_bits (default: 0) – verbosity:
  • =0 - print nothing,
  • +1 - input pars,
  • +2 - summary,
  • +4 - per event number of pixels above the threshold
  • +8 - event ID.

Remarks:

• The default key ("Image2D") stands for the CSPadPixCoords::Image2D<double> image object. Other key names work for the ndarray<double,2> image object.
• The xmin, xmax, ymin, ymax (in pixels) defines the window in the image for pixel counting. Default values means the entire image range.
• The threshold, numPixMin, and the window extents have to be adjusted for particular experiment.

Module ImgAlgos::ImgPeakFinder

This algorithm was motivated by users of amo42112:
1. Select the pixels in the window xmin, xmax, ymin, ymax
with amplitudes above the threshold_low.
2. Smear image for selected pixels, using 2-d matrix of weights over pixels
from -smear_radius to +smear_radius around each smeared pixel amplitude.
The matrix of weights is defined by the 2-d Gaussian function of width sigma.
3. Find peaks as pixels with absolute-maximal amplitude above the threshold_high in the center of the matrix -peak_radius to +peak_radius.
4. Put the vector of found peaks in the event with key peaksKey. Each entry of this vector has an object of the struct Peak, containing x, y positions, peak pixel amplitude, the total amplitude in the matrix, defined by the peak_radius, and the number of pixels in the matrix above threshold_low:

• threshold (default: 10) – minimal threshold on pixel amplitude
• numPixMin (default: 100) – minimal number of pixels with amplitude above the threshold
• filterIsOn (default: true) – On/Off the filter
• xmin (default: 0) – minimal column number
• xmax (default: 100000) – maximal column number
• ymin (default: 0) – minimal row number
• ymax (default: 100000) – maximal row number
• print_bits (default: 0) – verbosity:
  • =0 - print nothing,
  • +1 - input pars,
  • +2 - summary,
  • +4 - per event number of pixels above the threshold
  • +8 - event ID.

Remarks:

• The default key ("Image2D") stands for the CSPadPixCoords::Image2D<double> image object. Other key names work for the ndarray<double,2> image object.
• The xmin, xmax, ymin, ymax (in pixels) defines the window in the image for pixel counting. Default values means the entire image range.
• The threshold, numPixMin, and the window extents have to be adjusted for particular experiment.

Module ImgAlgos::ImgPeakFinder

This algorithm was motivated by users of amo42112:
1. Select the pixels in the window xmin, xmax, ymin, ymax
with amplitudes above the threshold_low.
2. Smear image for selected pixels, using 2-d matrix of weights over pixels
from -smear_radius to +smear_radius around each smeared pixel amplitude.
The matrix of weights is defined by the 2-d Gaussian function of width sigma.
3. Find peaks as pixels with absolute-maximal amplitude above the threshold_high in the center of the matrix -peak_radius to +peak_radius.
4. Put the vector of found peaks in the event with key peaksKey. Each entry of this vector has an object of the struct Peak, containing x, y positions, peak pixel amplitude, the total amplitude in the matrix, defined by the peak_radius, and the number of pixels in the matrix above threshold_low:

struct Peak{
   double x;
   double y; 
   double ampmax;  // amplitude in the peak masimum   
   double amptot;  // total amplitude in the range of {{peak_radius}}
   unsigned npix;  // number of pixels in the range

struct Peak{
   double x;
   double y; 
   double ampmax;  // amplitude in the peak masimum   
   double amptot;  // total amplitude in the range of {{peak_radius}}
   unsigned npix;  // number of pixels in the range of {{peak_radius}}
} ;

Module configuration parameters:

...

• This algorithm consumes ~15 ms/event on psana0101 for full Opal1000 (1024x1024) camera image.
• Smearing algorithm use a "safety margin" which is currently set to 10 pixels (offset from each boarder of the full image size).

Image on different stages of this algorithm:
Image RemovedImage RemovedImage RemovedImage RemovedImage Removed

1. raw image,
2. image in the window with amplitudes above the threshold_low
   • few peaks at the edges were discarded by the window limits,
   • image still contains many 1-photon pixels, which need to be eliminated,
3. smeared image,
4. raw image with found peaks (marked by the red circles)
5. zoom of the previous plot.

See also Example for Module ImgAlgos::ImgPeakFinder.

Module Module ImgAlgos::ImgPeakFilter

This module use results and should work after the ImgAlgos::ImgPeakFinder.
It gets the vector of peaks for the source and key, loops over all founded peaks and counts the number of peaks above the thresholds threshold_peak and threshold_total. If the filterIsOn is "on" ("true" or "yes" state) and the number of found peaks exceeds the n_peaks_min the event is passed for further analysis/processing.

...

1. If the first and/or last event numbers are defined, then the filter will select events in this range only.
2. If the evtstring is defined, only listed events of event ranges will be selected. For example, the evtstring parameter can be defined as

   Code Block
   2,5,11-15,20-25,29,30

   that means the list of events:

   Code Block
   2 5 11 12 13 14 15 20 21 22 23 24 25 29 30

   In the evtstring parameter the comma "," and sign minus "-" as a dash are the only allowed separators. Blank spaces are also allowed. Other characters may abort the program. The evtstring mode has higher priority than the 1st mode.
   The filterIsOn allows easy turn on/off this filter in *.cfg file.

Auxiliary scripts for ImgAlgos package

A few auxiliary scripts for example are located in the directory ImgAlgos/data:

• psana.cfg - set non-default parameters to run psana for ImgAlgos::ImgPeakFinder and ImgAlgos::ImgPeakFilter
  The psana running this script saves images and peaks for event 115 in text files.
• PlotCameraImageFromFile.py - Plots image and spectrum for image saved in file.
• PlotCameraImageAndPeaks.py - Plots image with found peaks and spectrum.

Module ImgAlgos::CSPadArrAverage

Module ImgAlgos::CSPadArrAverage

This module averages the CSPad data array and saves two files for averaged and rms values in CSPad format \[5920=4*8*185\]\[388\]. In contrast to the [cspad_mod.CsPadPedestals|PCDS:Psana Module Catalog#Modulecspadmod.CsPadPedestals], the input data can be specified with a {{key}}, that allows to average CSPad array for already pre-processed data, for example {{"calibrated"}}. This feature can be used to evaluate the averaged signal or background event. Implemented algorithm of averaging allows to eliminate large statistical fluctuations in the pixel amplitude spectrum. In advanced case averaging may have up to three stages, depending on configuration parameters:

...

Default version of the configuration parameters works the same way as cspad_mod.CsPadPedestals. In this case module gets raw events and stage 0 continues for entire input data sample.

Example of the configuration file for evaluation of pedestals:

[psana]
modules = ImgAlgos.CSPadArrAverage
files   = <path-to-the-dark-run-file>.xtc

[ImgAlgos.CSPadArrAverage]
source  = DetInfo(CxiDs1.0:Cspad.0)
key     =
avefile = cspad-pedestals-ave.dat
rmsfile = cspad-pedestals-rms.dat
print_bits  = 15
evts_stage1 = 100
evts_stage2 = 100
gate_width1 = 100
gate_width2 =  10

Example of the configuration file for evaluation of background:

[psana]
modules = cspad_mod.CsPadCalib ImgAlgos.CSPadArrAverage
files   = <path-to-the-background-run-file>.xtc
skip-events = 500
events      = 1000000

[cspad_mod.CsPadCalib]
inputKey      = 
outputKey     = calibrated
doPedestals   = yes
doPixelStatus = no
doCommonMode  = no

[ImgAlgos.CSPadArrAverage]
source  = DetInfo(CxiDs1.0:Cspad.0)
key     = calibrated
avefile = cspad-background-ave.dat
rmsfile = cspad-background-rms.dat
print_bits  = 15

See also Example for Module ImgAlgos::CSPadArrAverage.Images of the CSPad arrays for averaged and rms values, respectively, in one of the CXI runs:
Image RemovedImage Removed

Module ImgAlgos::CSPadBkgdSubtract

...

• source (default: "DetInfo(:Cspad)") – input source of data
• inputKey (default: " " ) – key for input data, by default use raw data
• outputKey (default: "bkgd_subtracted" ) – output key for the next data processing stage

• Wiki Markup
  {{bkgd_fname}} (default: "cspad_background.dat" ) -- file with CSPad array \[4*8*185\]\[388\] of averaged background

• norm_sector (default: 0) – CSPad sector in quad from 0 to 7
• print_bits (default: 0) – module verbosity:
  • =0 - print nothing,
  • +1 - input pars,
  • +2 - event ID,
  • +4 - normalization factor for each event,
  • +8 - part of the background array.

...

• • of

...

• • the background array.

See also Example for Module ImgAlgos::CSPadBkgdSubtract.

...

The file with the background array, bkgd_fname, was obtained by averaging 1000 events using module CSPadArrAverage. Subtraction is done with normalization for norm_sector=0.
Event image and pixel amplitude spectrum before and after the background subtraction are shown in plots:
Image RemovedImage Removed
Image RemovedImage Removed

Other event with better subtracted background:
Image RemovedImage Removed

Module ImgAlgos::ImgRadialCorrection

...

• source (default: "DetInfo()") – input source of data
• inkey (default: " " ) – key for input data, by default use raw data
• outkey (default: "rad_corrected" ) – output key for further image processing
• xcenter (default: 850) – x coordinate of the image center
• ycenter (default: 850) – y coordinate of the image center
• rmin (default: 10) – radius minimal image is not processed for r<rmin
• rmax (default:1000) – radius maximal image is not processed for r>rmax
• n_phi_bins (default: 12) – number of angular sectors for the background averaging.
• event (default: 0) – test event for print/save
• print_bits (default: 0) – module verbosity:
  • =0 - print nothing,
  • +1 - input pars,
  • +2 - summary,
  • +4 - event ID,
  • +8 - info about input image type (ndarray<double,2> or Image2D<double>).

Example of the module application

Calibrated image and spectrum:
Image RemovedImage Removed

Calibrated and radial-corrected image, spectrum, and subtracted r-phi65 distribution for n_phi_bins=65:
Image RemovedImage RemovedImage Removed

Calibrated and radial-corrected image, spectrum, and subtracted r-phi12 distribution for n_phi_bins=12:
Image RemovedImage RemovedImage Removed See also Example for Module ImgAlgos::ImgRadialCorrection.