Keras Dicom Images Data Generator and Augmenter from Dataframes (Benefits from ImageDataGenerator).

DCMDataFrameIterator.py

import numpy as np
import pandas as pd
import pydicom
import cv2
from sklearn.model_selection import train_test_split
from tensorflow.keras.preprocessing.image import ImageDataGenerator
from keras_preprocessing.image.dataframe_iterator import DataFrameIterator

# tested on tf 2.1 

class DCMDataFrameIterator(DataFrameIterator):
    def __init__(self, *arg, **kwargs):
        self.white_list_formats = ('dcm')
        super(DCMDataFrameIterator, self).__init__(*arg, **kwargs)
        self.dataframe = kwargs['dataframe']
        self.x = self.dataframe[kwargs['x_col']]
        self.y = self.dataframe[kwargs['y_col']]
        self.color_mode = kwargs['color_mode']
        self.target_size = kwargs['target_size']

    def _get_batches_of_transformed_samples(self, indices_array):
        # get batch of images
        batch_x = np.array([self.read_dcm_as_array(dcm_path, self.target_size, color_mode=self.color_mode)
                            for dcm_path in self.x.iloc[indices_array]])

        batch_y = np.array(self.y.iloc[indices_array].astype(np.uint8))  # astype because y was passed as str

        # transform images
        if self.image_data_generator is not None:
            for i, (x, y) in enumerate(zip(batch_x, batch_y)):
                transform_params = self.image_data_generator.get_random_transform(x.shape)
                batch_x[i] = self.image_data_generator.apply_transform(x, transform_params)
                # you can change y here as well, eg: in semantic segmentation you want to transform masks as well 
                # using the same image_data_generator transformations.

        return batch_x, batch_y

    @staticmethod
    def read_dcm_as_array(dcm_path, target_size=(256, 256), color_mode='rgb'):
        image_array = pydicom.dcmread(dcm_path).pixel_array
        image_array = cv2.resize(image_array, target_size, interpolation=cv2.INTER_NEAREST)  #this returns a 2d array
        image_array = np.expand_dims(image_array, -1)
        if color_mode == 'rgb':
            image_array = cv2.cvtColor(image_array, cv2.COLOR_GRAY2RGB)
        return image_array

      
# read data
# Assuming it has two cols:
# image_path: path to each image with its extension
# target: labels (here it is 0s and 1s) -> binary classification
df = pd.read_csv("yourDfPath.csv", dtype=str)

# split for testing
train_df, test_df = train_test_split(df, test_size=0.2)

# augmentation parameters
# you can use preprocessing_function instead of rescale in all generators
# if you are using a pretrained network
train_augmentation_parameters = dict(
    rescale=1.0/255.0,
    rotation_range=10,
    zoom_range=0.2,
    horizontal_flip=True,
    fill_mode='nearest',
    brightness_range = [0.8, 1.2],
    validation_split = 0.2
)

valid_augmentation_parameters = dict(
    rescale=1.0/255.0,
    validation_split = 0.2
)

test_augmentation_parameters = dict(
    rescale=1.0/255.0
)

# training parameters
BATCH_SIZE = 32
CLASS_MODE = 'binary'
COLOR_MODE = 'grayscale'
TARGET_SIZE = (300, 300)
EPOCHS = 10
SEED = 1337

train_consts = {
    'seed': SEED,
    'batch_size': BATCH_SIZE,
    'class_mode': CLASS_MODE,
    'color_mode': COLOR_MODE,
    'target_size': TARGET_SIZE,  
    'subset': 'training'
}

valid_consts = {
    'seed': SEED,
    'batch_size': BATCH_SIZE,
    'class_mode': CLASS_MODE,
    'color_mode': COLOR_MODE,
    'target_size': TARGET_SIZE, 
    'subset': 'validation'
}

test_consts = {
    'batch_size': 1,  # should be 1 in testing
    'class_mode': CLASS_MODE,
    'color_mode': COLOR_MODE,
    'target_size': TARGET_SIZE,  # resize input images
    'shuffle': False
}

# Using the training phase generators 
train_augmenter = ImageDataGenerator(**train_augmentation_parameters)
valid_augmenter = ImageDataGenerator(**valid_augmentation_parameters)


train_generator = DCMDataFrameIterator(dataframe=train_df,
                             x_col='image_path',
                             y_col='target',
                             image_data_generator=train_augmenter,
                             **train_consts)

valid_generator = DCMDataFrameIterator(dataframe=train_df,
                             x_col='image_path',
                             y_col='target',
                             image_data_generator=valid_augmenter,
                             **valid_consts)

# define model architecture like how you normally do
model = ... 

# training
history = model.fit_generator(
	generator=train_generator,
	steps_per_epoch=len(train_generator),
	epochs=EPOCHS,
	validation_data=valid_generator,
	validation_steps=len(valid_generator)
)



# Using the testing generator to evaluate the model after training
test_augmenter = ImageDataGenerator(**test_augmentation_parameters)
test_generator = DCMDataFrameIterator(dataframe=test_df,
                             x_col='image_path',
                             y_col='target',
                             image_data_generator=test_augmenter,
                             **test_consts)
test_loss, test_accuracy = model.evaluate(test_generator, steps=len(test_generator))

Hi! I try to use DICOM with uint16 bit with your DICOM Dataloader. Thanks for sharing it!
the rescaling don't work properly. the value output in the batch doesn't change if I change the rescale value from 0 to 1/255 or 1/(2**16-1).

The problem is in _get_batches_of_transformed_samples. there is no link to the "image_data_generator.standardize" method.
after the for loop I add:

batch_x = self.image_data_generator.standardize(batch_x.astype('float64'))

now it works for me

Hi! I try to use DICOM with uint16 bit with your DICOM Dataloader. Thanks for sharing it! the rescaling don't work properly. the value output in the batch doesn't change if I change the rescale value from 0 to 1/255 or 1/(2**16-1).

The problem is in _get_batches_of_transformed_samples. there is no link to the "image_data_generator.standardize" method. after the for loop I add:

batch_x = self.image_data_generator.standardize(batch_x.astype('float64'))

now it works for me

You are welcome! and thanks for the note.

both keras_preprocessing and tensorflow.keras.preprocessing deprecated.

both keras_preprocessing and tensorflow.keras.preprocessing deprecated.

Thanks for the note, this may be a reference for future contributors.