mergeData_Norm.py

import numpy as np
import sys, os
import nrrd

if (len(sys.argv) < 2):
    print('Error: missing arguments!')
    print('e.g. python createMask.py imageOut.nrrd imageIn1.nrrd [ImageIn#.nrrd...]')
else:
    Iout = str(sys.argv[1])
    for i in range(2,len(sys.argv)):
        try:
            Iin = str(sys.argv[i])
            print('Processing %s...'% (Iin))
            data, header = nrrd.read(Iin)
            sh = np.shape(data)
            if (i == 2):
                dataSum = np.uint64(data)
                shTest = sh
            else:
                if (sh == shTest):
                    dataSum = dataSum + np.uint64(data)
                    with open(Iout.replace('.nrrd','').replace('.NRRD','')+".txt", "a") as myfile:
                        myfile.write(Iin)
                else:
                    print('ERROR: %s not the same size!'% (Iin))
        except:
            print("Unexpected error:", sys.exc_info()[0])
        dataMin = np.min(dataSum)
        dataMax = np.max(dataSum)
        dataSum = np.uint8(np.round(np.multiply(np.divide(np.subtract(dataSum, dataMin),np.float(dataMax)),255.0)))

    dataMin = np.min(dataSum)
    dataMax = np.max(dataSum)

    normData = np.uint8(np.round(np.multiply(np.divide(np.subtract(dataSum, dataMin),np.float(dataMax)),255.0)))

    nrrd.write(Iout, normData, options=header)
    print('saved to ' + Iout)