Matrices of pixels for r0=3 and 4 and different dr values

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title	r0=3, dr=0.1 and r0=4 dr=0.2 examples
collapse	true

r0=3  dr=0.1 (4 pixels)   r0=3  dr=0.5 (12 pixels)   r0=3  dr=1 (24 pixels) 
0 0 0 0 0 0 0 0 0         0 0 0 0 0 0 0 0 0          0 0 0 0 1 0 0 0 0       
0 0 0 0 1 0 0 0 0         0 0 0 1 1 1 0 0 0          0 0 1 1 1 1 1 0 0       
0 0 0 0 0 0 0 0 0         0 0 0 0 0 0 0 0 0          0 1 0 0 0 0 0 1 0       
0 0 0 0 0 0 0 0 0         0 1 0 0 0 0 0 1 0          0 1 0 0 0 0 0 1 0       
0 1 0 0 + 0 0 1 0         0 1 0 0 + 0 0 1 0          1 1 0 0 + 0 0 1 1       
0 0 0 0 0 0 0 0 0         0 1 0 0 0 0 0 1 0          0 1 0 0 0 0 0 1 0       
0 0 0 0 0 0 0 0 0         0 0 0 0 0 0 0 0 0          0 1 0 0 0 0 0 1 0       
0 0 0 0 1 0 0 0 0         0 0 0 1 1 1 0 0 0          0 0 1 1 1 1 1 0 0       
0 0 0 0 0 0 0 0 0         0 0 0 0 0 0 0 0 0          0 0 0 0 1 0 0 0 0

r0=4  dr=0.2 (12 pixels)   r0=4  dr=0.3 (16 pixels)    r0=4  dr=0.5 (24 pixels)
0 0 0 0 0 0 0 0 0 0 0      0 0 0 0 0 0 0 0 0 0 0       0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 1 1 1 0 0 0 0      0 0 0 0 1 1 1 0 0 0 0       0 0 0 1 1 1 1 1 0 0 0
0 0 0 0 0 0 0 0 0 0 0      0 0 1 0 0 0 0 0 1 0 0       0 0 1 0 0 0 0 0 1 0 0
0 0 0 0 0 0 0 0 0 0 0      0 0 0 0 0 0 0 0 0 0 0       0 1 0 0 0 0 0 0 0 1 0
0 1 0 0 0 0 0 0 0 1 0      0 1 0 0 0 0 0 0 0 1 0       0 1 0 0 0 0 0 0 0 1 0
0 1 0 0 0 + 0 0 0 1 0      0 1 0 0 0 + 0 0 0 1 0       0 1 0 0 0 + 0 0 0 1 0
0 1 0 0 0 0 0 0 0 1 0      0 1 0 0 0 0 0 0 0 1 0       0 1 0 0 0 0 0 0 0 1 0
0 0 0 0 0 0 0 0 0 0 0      0 0 0 0 0 0 0 0 0 0 0       0 1 0 0 0 0 0 0 0 1 0
0 0 0 0 0 0 0 0 0 0 0      0 0 1 0 0 0 0 0 1 0 0       0 0 1 0 0 0 0 0 1 0 0
0 0 0 0 1 1 1 0 0 0 0      0 0 0 0 1 1 1 0 0 0 0       0 0 0 1 1 1 1 1 0 0 0
0 0 0 0 0 0 0 0 0 0 0      0 0 0 0 0 0 0 0 0 0 0       0 0 0 0 0 0 0 0 0 0 0

Matrices of pixels for r0=5 and 6 and different dr values

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title	r0=5, dr=0.05 and r0=6, dr=0.2 examples
collapse	true

r0=5  dr=0.05 (12 pixels)      r0=5  dr=0.5  (28 pixels)            
0 0 0 0 0 0 0 0 0 0 0 0 0      0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 1 0 0 0 0 0 0      0 0 0 0 1 1 1 1 1 0 0 0 0
0 0 0 1 0 0 0 0 0 1 0 0 0      0 0 0 1 0 0 0 0 0 1 0 0 0
0 0 1 0 0 0 0 0 0 0 1 0 0      0 0 1 0 0 0 0 0 0 0 1 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0      0 1 0 0 0 0 0 0 0 0 0 1 0
0 0 0 0 0 0 0 0 0 0 0 0 0      0 1 0 0 0 0 0 0 0 0 0 1 0
0 1 0 0 0 0 + 0 0 0 0 1 0      0 1 0 0 0 0 + 0 0 0 0 1 0
0 0 0 0 0 0 0 0 0 0 0 0 0      0 1 0 0 0 0 0 0 0 0 0 1 0
0 0 0 0 0 0 0 0 0 0 0 0 0      0 1 0 0 0 0 0 0 0 0 0 1 0
0 0 1 0 0 0 0 0 0 0 1 0 0      0 0 1 0 0 0 0 0 0 0 1 0 0
0 0 0 1 0 0 0 0 0 1 0 0 0      0 0 0 1 0 0 0 0 0 1 0 0 0
0 0 0 0 0 0 1 0 0 0 0 0 0      0 0 0 0 1 1 1 1 1 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0      0 0 0 0 0 0 0 0 0 0 0 0 0

r0=6  dr=0.2 (12 pixels)        r0=6  dr=0.5 (28 pixels)      
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0     0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 1 1 1 0 0 0 0 0 0     0 0 0 0 0 1 1 1 1 1 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0     0 0 0 1 0 0 0 0 0 0 0 1 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0     0 0 1 0 0 0 0 0 0 0 0 0 1 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0     0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0     0 1 0 0 0 0 0 0 0 0 0 0 0 1 0
0 1 0 0 0 0 0 0 0 0 0 0 0 1 0     0 1 0 0 0 0 0 0 0 0 0 0 0 1 0
0 1 0 0 0 0 0 + 0 0 0 0 0 1 0     0 1 0 0 0 0 0 + 0 0 0 0 0 1 0
0 1 0 0 0 0 0 0 0 0 0 0 0 1 0     0 1 0 0 0 0 0 0 0 0 0 0 0 1 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0     0 1 0 0 0 0 0 0 0 0 0 0 0 1 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0     0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0     0 0 1 0 0 0 0 0 0 0 0 0 1 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0     0 0 0 1 0 0 0 0 0 0 0 1 0 0 0
0 0 0 0 0 0 1 1 1 0 0 0 0 0 0     0 0 0 0 0 1 1 1 1 1 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0     0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

Matrix of pixels for r0=7

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title	r0=7, dr=2 example
collapse	true

 r0=7  dr=2 (108 pixels)   
 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 1 1 1 1 1 1 1 1 1 0 0 0 0 0
 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0
 0 0 0 1 1 1 0 0 0 0 0 0 0 1 1 1 0 0 0
 0 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 1 0 0
 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0
 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0
 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0
 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0
 1 1 1 0 0 0 0 0 0 + 0 0 0 0 0 0 1 1 1
 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0
 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0
 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0
 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0
 0 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 1 0 0
 0 0 0 1 1 1 0 0 0 0 0 0 0 1 1 1 0 0 0
 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0
 0 0 0 0 0 1 1 1 1 1 1 1 1 1 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0

...

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# Import
import psana

# Initialize a detector object
det = psana.Detector(detInfo, env'myAreaDetectorName')
# Merges photons split among pixels and returns n-d array with integer number of photons per pixel.
nphotons_nda = det.photons(evt, adu_per_photon, nda_calib=None, mask=None, adu_per_photon=None)

The det.photons() function divides the pixel intensities (ADUs) by adu_per_photon, resulting in a fractional number of photons for each pixel. This function is a wrapper around photons() method in PyAlgos:

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# Import
from ImgAlgos.PyAlgos import photons

# Merges photons split among pixels and returns n-d array with integer number of photons per pixel.
nphotons_nda = photons(fphotons, maskadu_per_photon=30)

Sphinx doc

Method photons receives (float) n-d numpy array fphotons representing image intensity in terms of (float) fractional number of photons and an associated mask of bad pixels. Both arrays should have the same shape. Two lowest dimensions represent pixel rows and columns in 2-d pixel matrix arrays. Algorithm works with good pixels defined by the mask array (1/0 = good/bad pixel). Array fphotons is represented with two arrays; An array containing whole number of photons (integer) and the leftover fractional number of photon array (float) of the same shape. Assuming the photons are only split between two adjacent pixels, we round up the adjacent pixels if they sum up to be above 0.9 photons. The algorithm is best explained using an example:

Let's say we measured the following ADUs on our detector. "adu_per_photon" is user-defined, but for this example let's set it to 1:

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ADUs (adu_per_photon=1): 0.0 3.5 0.1 0.2 0.2 0.4 0.0 1.2 0.1 4.7 3.4 0.0 0.5 0.4 0.4 0.1

...

To see how we get from ADUs to Photons, we split the ADUs into whole photons and fractional photons.

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ADUs               =  Whole photons   +    Fractional photons
 
Whole photons0.0 3.5 0.1 0.2     +    Fractional photons
0 3 0 0                0.0 0.5 0.1 0.2   
0.2 0.4 0.0 1.2    =     0 0 0 1    0.2 0.4  +       0.2 0.4 0.0 0.2
0.1 4.7 3.4 0.0          0 4 3 0              0.1 0.7 0.4 0.0
0.5 0.4 0.4 0.1          0 0 0 0              0.5 0.4 0.4 0.1

Assuming the photons are only split by two adjacent pixels, we search for a pixel that has at least 0.5 photons with an adjacent pixel that sum up to above 0.9 photons. In cases where a pixel has multiple adjacent pixels which sum up to above 0.9 photons, we take the largest adjacent pixel. If such an adjacent pair of pixels is found, then the adjacent pixel values are merged into one pixel. It is merged into the pixel with the larger value. (See "After merging adjacent pixels" example below).

...

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Fractional photons
0.0 0.5 0.1 0.2
0.2 0.4 0.0 0.2
0.1 0.7 0.4 0.0
0.5 0.4 0.4 0.1
 
After merging adjacent pixels:
0.0 0.9 0.1 0.02
0.2 0.0 0.0 0.02
0.1 1.1 0.0 0.0
0.9 0.0 0.4 0.1

Rounded whole photons:
0 1 0 0
0 0 0 0
0 1 0 0
1 0 0 0

...

References

ImgAlgos.PyAlgos - code documentation
psalgos - new peak- code example in Sphinx finder and other algorithms code documentation
Peak Finding - short announcement about peak finders
Hit and Peak Finders - examples in Chris' tutorial
Peak Finding Module - (depricated) psana module, it demonstaration examples and results
Psana Module Catalog - (depricated) peak finding psana modules
Psana Module Examples - (depricated) peak finding examples in psana modules
GUI for tuning peak finding - Chun's page in development
Auto-generated documentation - references to code-based documentation for a few other useful packages
pyimgalgos.PeakStore - class helping to save peak parameter records in the text file
pyimgalgos.TDFileContainer - class helping to retrieve peak parameter records from the text file
Test of Peak Finders - example of exploitation of peak finders
Test of Peak Finders - V2 - example of exploitation of peak finders after revision 1 (uniformization)
photons - sphinx doc
Peak Finding Module - (depricated) psana module, it demonstaration examples and results
Psana Module Catalog - (depricated) peak finding psana modules
Psana Module Examples - (depricated) peak finding examples in psana modules

Versions Compared

Old Version 39

New Version Current

Key

Matrices of pixels for r0=3 and 4 and different dr values

Matrices of pixels for r0=5 and 6 and different dr values

Matrix of pixels for r0=7

References

Page History

Versions Compared

Old Version 39

New Version Current

Key

Matrices of pixels for r0=3 and 4 and different dr values

Matrices of pixels for r0=5 and 6 and different dr values

Matrix of pixels for r0=7

References