Go through a diffraction map and produce a sum image, average image, stdev image, and a real space residual image.

MakeDiffMapImages.py

# Created 2015, Zack Gainsforth
import matplotlib
matplotlib.use('Qt4Agg')
import matplotlib.pyplot as plt
from matplotlib.image import imsave
import numpy as np
import sys
import math
import os
from numba import jit
from tifffile import imread

def ComputeFileScalar(FileName):
    Arr = imread(FileName)
    return np.std(Arr)

### EDIT ME FOR EACH DIFFRACTION MAP!!!! ###
x_pixels = 114
y_pixels = 19
FileFormatStr = '/DanteACI2_05 10 keV/DanteACI2_05 10 keV/DanteACI2_05_%05d.tif'
### DONE EDITING! ###


print 'First pass: compute the average and sum images.'

# Get the first image, and therefore the size of the image.
FileName = os.getcwd() + FileFormatStr % (1)
Arr = imread(FileName).astype('float')

# Get a sum image.
SumImg = np.zeros(Arr.shape).astype('float')
SkippedFiles = 0
for i in range(y_pixels*x_pixels):
	FileName = os.getcwd() + FileFormatStr % (i+1)
	if not os.path.isfile(FileName):
		print "File %s doesn't exist." % FileName
		SkippedFiles += 1
		continue
	print 'Pass 1: ' + FileName
	Arr = imread(FileName).astype('float')
	SumImg += Arr

np.savetxt('SumImage.txt', SumImg)
AvgImg = np.copy(SumImg) / (y_pixels*x_pixels-SkippedFiles)
np.savetxt('AvgImage.txt', AvgImg)

print 'Second pass: compute the stdev and residual images.'

StDevImage = np.zeros(AvgImg.shape).astype('float')

R = np.zeros((x_pixels,y_pixels), dtype=(float))
S = np.zeros((x_pixels,y_pixels), dtype=(float))

for y in range(y_pixels):
    for x in range(x_pixels):
        FileName = FileFormatStr % (x + y*x_pixels + 1)
        FileName = os.getcwd() + FileName
        if not os.path.isfile(FileName):
            R[x,y] = 0
            S[x,y] = 0
            print "File %s doesn't exist.  R=0" % FileName
            continue
        print 'Pass 2: ' + FileName
        Arr = imread(FileName)
        StDevArr = (Arr - AvgImg)
        R[x,y] = np.sum(np.sum(StDevArr))
        S[x,y] = np.std(Arr)
        StDevImage += StDevArr**2

# Save the residual image.
np.savetxt('ResidualImage.txt', R)
np.savetxt('SpikeImage.txt', S)

# Save the stdev image
np.savetxt('StDevImage.txt', StDevImage/(x_pixels*y_pixels-SkippedFiles))

print 'Done'