showImage

#!/usr/bin/env python
# remove the necessity to have .py extension

from PIL import Image
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

option_handle_list = ['--showFirstImage', '--showImage', '--stats']
option_unique_list = ['--info', '--showAllImages', '--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:
    print("Function showImage, this function can be used to show npy or tiff images")
    print("USAGE : showImage [imagePath] [options]")
    print("")
    print("options")
    print(" --info: get info about the image file")
    print(" --showImage N: show image number N")
    print(" --showAllImages: show all images")
    print(" --stats N: get stats of image number N, including its histogram")
    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['showImage'] == None and options['showAllImages'] == None and options['stats'] == None:
    options['showAllImages'] = True #default


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

if ".npy" in imagePath:
    images = np.load(imagePath)
else:
    img = Image.open(imagePath)
    print("number of images found : ", img.n_frames)
    images = []
    for i in range(img.n_frames): #number of images
        img.seek(i)
        if options['verbose']:
            print("----------- image " + str(i) + "-----------")
            print("format : " + str(img.format))
            print("size : " + str(img.size))
            print("mode : " + str(img.mode))
        npyImage = np.array(img)
        images.append(npyImage)


if options['stats'] != None:
    imageNumber = int(options['stats'])
    if options['verbose']:
        for i in range(img.n_frames):
            max = np.amax(images[i])
            min = np.amin(images[i])
            val = np.arange(max)
            print("Range (", i, "):", min, max)


    valuesImage = images[imageNumber].flatten()
    max = np.amax(images[imageNumber])
    min = np.amin(images[imageNumber])
    val = np.arange(max)
    print("Range :", min, max)

    print("flat : ", valuesImage)
    histo, bins = np.histogram(valuesImage, bins = max)
    plt.hist(histo, bins='auto')
    #plt.yscale("log")
    plt.show()


if options['showImage'] != None:
    try:
        imageNumber = int(options['showImage'])
        # #images[imageNumber][y][x]
        # print(images[imageNumber][345][138]) #y
        # print(images[imageNumber][150][160]) #y
        # print(images[imageNumber][169][193]) #y
        # getRGB(images[imageNumber][169][193]) #y
        # print("-----")
        # print(images[imageNumber][212][392]) #n
        # print(images[imageNumber][68][49]) #n

        if ".npy" in imagePath:
            plt.imshow(np.squeeze(images[imageNumber])) #removing Z axis
        else:
            plt.imshow(images[imageNumber])
        plt.show()
    except ValueError:
        print('parameter after --showImage must be a number between 0 and ' + str(len(images)))

if options['showAllImages'] != None:
    print("showing ", len(images), " images")
    imageNbToShow = len(images)
    if len(images) > 36:
        imageNbToShow = 36
        print("Too many images (", len(images), "). Showing only the 36 first images")

    sqrt = math.ceil(math.sqrt(imageNbToShow))
    fig = plt.figure(figsize=(sqrt, sqrt))
    for i in range(1, imageNbToShow + 1):
        fig.add_subplot(sqrt, sqrt, i)
        if ".npy" in imagePath:
            plt.imshow(np.squeeze(images[i - 1])) #removing Z axis
        else:
            plt.imshow(images[i - 1])
    plt.show()