import numpy as np
# from config.paths import train_images_folder, train_labels_folder
def dice_coeff(gt, pred, eps=1e-5):
dice = np.sum(pred[gt == 1]) * 2.0 / (np.sum(pred) + np.sum(gt))
return dice
def multi_dice_coeff(gt, pred, num_classes):
labels = one_hot_encode_np(gt, num_classes)
outputs = one_hot_encode_np(pred, num_classes)
dices = list()
for cls in range(1, num_classes):
outputs_ = outputs[:, cls]
labels_ = labels[:, cls]
dice_ = dice_coeff(outputs_, labels_)
dices.append(dice_)
return sum(dices) / (num_classes-1)
def one_hot_encode_np(label, num_classes):
""" Numpy One Hot Encode
:param label: Numpy Array of shape BxHxW or BxDxHxW
:param num_classes: K classes
:return: label_ohe, Numpy Array of shape BxKxHxW or BxKxDxHxW
"""
assert len(label.shape) == 3 or len(label.shape) == 4, 'Invalid Label Shape {}'.format(label.shape)
label_ohe = None
if len(label.shape) == 3:
label_ohe = np.zeros((label.shape[0], num_classes, label.shape[1], label.shape[2]))
elif len(label.shape) == 4:
label_ohe = np.zeros((label.shape[0], num_classes, label.shape[1], label.shape[2], label.shape[3]))
for batch_idx, batch_el_label in enumerate(label):
for cls in range(num_classes):
label_ohe[batch_idx, cls] = (batch_el_label == cls)
return label_ohe
def min_max_normalization(input):
return (input - input.min()) / (input.max() - input.min())
def z_score_normalization(input):
input_mean = np.mean(input)
input_std = np.std(input)
# print("Mean = {:.2f} - Std = {:.2f}".format(input_mean,input_std))
return (input - input_mean)/input_std
def zero_pad_3d_image(image, pad_ref=(64,64,64), value_to_pad = 0):
if value_to_pad == 0:
image_padded = np.zeros(pad_ref)
else:
image_padded = value_to_pad * np.ones(pad_ref)
image_padded[:image.shape[0],:image.shape[1],:image.shape[2]] = image
return image_padded