shiftTif

#!/usr/bin/env python
# remove the necessity to have .py extension
import sys
import os.path
import numpy as np
import math
import matplotlib.pyplot as plt  # Just so we can visually confirm we have the same images
import tifffile

option_handle_list = ['--cropByPosition', '--x', '--y']
option_unique_list = ['--info', '--help', '--verbose']
options = {}


for option_handle in option_handle_list:
    if option_handle in sys.argv:
        options[option_handle[2:]] = sys.argv[sys.argv.index(option_handle) + 1]
    else:
        options[option_handle[2:]] = None

for option_handle in option_unique_list:
    if option_handle in sys.argv:
        options[option_handle[2:]] = True
    else:
        options[option_handle[2:]] = None


if options['info'] != None or options['help'] != None:
    print("Function showImage.")
    print("USAGE : shiftTif [imagePath] [options]")
    print("EX : shiftTif image.tif --x -5 --y 10")
    print("")
    print("")
    print("options")
    print(" --x int: shift the image by (int) pixels (can be positive or negative)")
    print(" --y int: shift the image by (int) pixels (can be positive or negative)")
    exit()


if not os.path.exists(sys.argv[1]):
    raise ValueError("Incorrect path, image path must be the first argument")
imagePath = sys.argv[1]

if options['verbose']:
    np.set_printoptions(threshold=sys.maxsize) #writing entire data (not splitting) may consume time

img = tifffile.imread(imagePath)

if options['x'] != None:
    xShift = int(options['x'])
if options['y'] != None:
    yShift = int(options['y'])

for index, elem in enumerate(img):
    if options['y'] != None:
        if yShift > 0:
            img[index] =  np.roll(img[index], yShift, axis=0)
            img[index][:yShift,:] = 0
        elif yShift < 0:
            img[index] =  np.roll(img[index], yShift, axis=0)
            img[index][yShift:,:] = 0
        print(img[index].shape, img[index])

    if options['x'] != None:
        if xShift > 0:
            img[index] =  np.roll(img[index], xShift, axis=1)
            img[index][:,:xShift] = 0
        elif xShift < 0:
            img[index] =  np.roll(img[index], xShift, axis=1)
            img[index][:,xShift:] = 0



img = tifffile.imsave("shifted_" + imagePath, img)