Single photon counting

singlephotons.py

def findsinglephotons(image, thresupper, threslower, maxsize=2):
    '''
    identifies single photons in the image and returns the for each photon the integrated counts on the image
    
    * a photon need to be above the thresupper in order to be found
    * surrounding regions of a photon will be added as long as they are above the threslower value
    * maxsize=2 controlls over how many pixels a photon may spread
    
    Stephan Kuschel, 2019
    https://gist.github.com/skuschel/4823d53067263507a04c07ff7f84255f
    '''
    import skimage.measure as skm
    import numpy as np
    up = skm.label(image > thresupper, connectivity=1)
    N = np.max(up)
    print('{} possible events found'.format(N))
    upNs = np.bincount(up.flatten())
    low = skm.label(image > threslower, connectivity=1)
    lowNs = np.bincount(low.flatten())
    photons = []
    #finalmask = np.zeros_like(image)
    for iup, upN in enumerate(upNs):
        if upN > maxsize:
            continue
        # find index of value iup in up
        upmask = up==iup
        ilow = np.max(low[upmask])
        if lowNs[ilow] > maxsize:
            continue
        mask = low==ilow
        photons.append(np.sum(image[mask]))
        #finalmask[mask] += 1
    return np.asarray(photons)#, finalmask