AttenuationCorrection.py

'''
Created on Oct 24, 2014

@author: Admin
'''

import numpy as np


def correctAttenuation(stack, firstIm=0, lastImageAt=0.1):
    '''corrects attenuation of an image stack with first image not attenuated and last attenuated by lastImageAt:= Intensity last/ Intensity first'''
    res = stack[:firstIm + 1].tolist()  # +1 because first image is not modified
    l = len(stack) - firstIm
    for i in range(firstIm + 1, len(stack)):
        im = (stack[i] * (1. + (1. / lastImageAt - 1.) * (i - firstIm) / (l - 1)))
        im[np.where(im > 65535)] = 65535
        res.append(im.astype(np.uint16))
    return res


def correctAttAll(stack, z, firstIm, lastImageAt):
    imOut = []
    for i in range(len(stack) // z):
        imOut += correctAttenuation(stack[i * z:(i + 1) * z], firstIm, lastImageAt)
    return np.array(imOut)


def corrAttMultiCh(ims, z, ch, dicCh, firstIm, lastImageAt):
    ims = np.reshape(ims, (-1, z, ch, ims.shape[-2], ims.shape[-1]))
    imAtt = np.zeros_like(ims)
    for ch in range(ch):
        if ch == dicCh:
            imAtt[:, :, ch] = ims[:, :, ch]
        else:
            imtmp = correctAttAll(np.reshape(ims[:, :, ch], (-1, ims.shape[-2], ims.shape[-1])), z, firstIm,
                                  lastImageAt)
            imAtt[:, :, ch] = np.reshape(imtmp, imAtt[:, :, ch].shape)
    return np.reshape(imAtt, (-1, imAtt.shape[-2], imAtt.shape[-1]))


if __name__ == '__main__':
    pass