CODE EXAMPLE FOR PYTHON

custom 3d image generator for segmentation

import glob
import os

import keras
import numpy as np
import skimage
from imgaug import augmenters as iaa


class DataGenerator(keras.utils.Sequence):
    """Generates data for Keras"""
    """This structure guarantees that the network will only train once on each sample per epoch"""

    def __init__(self, list_IDs, im_path, label_path, batch_size=4, dim=(128, 128, 128),
                 n_classes=4, shuffle=True, augment=False):
        'Initialization'
        self.dim = dim
        self.batch_size = batch_size
        self.list_IDs = list_IDs
        self.im_path = im_path
        self.label_path = label_path
        self.n_classes = n_classes
        self.shuffle = shuffle
        self.augment = augment
        self.on_epoch_end()

    def __len__(self):
        'Denotes the number of batches per epoch'
        return int(np.floor(len(self.list_IDs) / self.batch_size))

    def __getitem__(self, index):
        'Generate one batch of data'
        # Generate indexes of the batch
        indexes = self.indexes[index * self.batch_size:(index + 1) * self.batch_size]

        # Find list of IDs
        list_IDs_temp = [self.list_IDs[k] for k in indexes]

        # Generate data
        X, y = self.__data_generation(list_IDs_temp)

        return X, y

    def on_epoch_end(self):
        'Updates indexes after each epoch'
        self.indexes = np.arange(len(self.list_IDs))
        if self.shuffle == True:
            np.random.shuffle(self.indexes)

    def __data_generation(self, list_IDs_temp):

        if self.augment:
            pass

        if not self.augment:

            X = np.empty([self.batch_size, *self.dim])
            Y = np.empty([self.batch_size, *self.dim, self.n_classes])

            # Generate data
            for i, ID in enumerate(list_IDs_temp):
                img_X = skimage.io.imread(os.path.join(im_path, ID))
                X[i,] = img_X

                img_Y = skimage.io.imread(os.path.join(label_path, ID))
                Y[i,] = keras.utils.to_categorical(img_Y, num_classes=self.n_classes)

            X = X.reshape(self.batch_size, *self.dim, 1)
            return X, Y

params = {'dim': (128, 128, 128),
          'batch_size': 4,
          'im_path': "some/path/for/the/images/",
          'label_path': "some/path/for/the/label_images",
          'n_classes': 4,
          'shuffle': True,
          'augment': True}



partition = {}
im_path = "some/path/for/the/images/"
label_path = "some/path/for/the/label_images/"

images = glob.glob(os.path.join(im_path, "*.tif"))
images_IDs = [name.split("/")[-1] for name in images]

partition['train'] = images_IDs

training_generator = DataGenerator(partition['train'], **params)