def get_chosen_indices(lbl, patch_shape, repetitions, proportion_background):
'''Return the corner indices for each of the selected patches for each image'''
full_indices = compute_patch_indices(lbl.shape, patch_shape)
index_distribution = {'background': [], 'target': []}
index_num = 0
for index in full_indices:
patch_lbl = get_patch_from_3d_data(lbl, patch_shape, index)
if has_labels(patch_lbl):
index_distribution['target'].append(index_num)
else:
index_distribution['background'].append(index_num)
index_num += 1
background_indices = list(
np.random.choice(list(index_distribution['background']),
size=repetitions * int(
np.round(proportion_background *
len(index_distribution['target']))),
replace=True))
indices = background_indices
for _ in range(repetitions):
indices = indices + index_distribution['target']
np.random.shuffle(indices)
return indices, full_indices
def image_to_patches(img, patch_size):
'''
img: image as numpy array
patch_shape: tuple of patch shape (for example: (126,126,45))
returns: list of images (patches) created of the chosen size
'''
indices = compute_patch_indices(img.shape, patch_size)
images = []
for index in indices:
images.append(get_patch_from_3d_data(img, patch_size, index))
return images
def next_patch(img, lbl, patch_shape, indices, index, expand):
'''
Given an image, return the following patch that has not been processed yet.
Params:
img: image in numpy array
patch_shape: desired shape of the patch
indices: localizations of the different patches we are going to get. These
are calculated with function compute_patch_indices.
index: which index on indices are we using in this iteration.
expand: whether to expand dimension of image True/False
Returns:
img: actual patch of the image, numpy array
indices: vector of indices
index: next index to be processed
finished: True/False whether if we have finished with the current image patches or not
'''
if not indices is None:
img = get_patch_from_3d_data(data=img,
patch_shape=patch_shape,
patch_index=indices[index])
lbl = get_patch_from_3d_data(data=lbl,
patch_shape=patch_shape,
patch_index=indices[index])
index += 1
else:
indices = compute_patch_indices(image_shape=img.shape,
patch_size=patch_shape)
img = get_patch_from_3d_data(data=img,
patch_shape=patch_shape,
patch_index=indices[0])
lbl = get_patch_from_3d_data(data=lbl,
patch_shape=patch_shape,
patch_index=indices[0])
index = 1
if index == len(indices):
finished = True
else:
finished = False
if expand:
img = np.expand_dims(img, axis=0)
return img, lbl, indices, index, finished
def patch_wise_prediction(output, data, patch_shape,
overlap=0, batch_size=1):
"""
:param batch_size:
:param model:
:param data:
:param overlap:
:return:
"""
predictions = []
indices = compute_patch_indices(data.shape[-3:],
patch_size=patch_shape,
overlap=overlap,
start=0)
batch = []
i = 0
pbar = tqdm(enumerate(indices),
unit='patches',
total=len(indices),
desc='scan_patches')
sess = tf.get_default_session()
for j, _ in pbar:
while len(batch) < batch_size:
patch = get_patch_from_3d_data(data[0],
patch_shape=patch_shape,
patch_index=indices[i])
batch.append(patch)
i += 1
prediction = sess.run(output,
feed_dict={'img:0': np.asarray(batch)})
batch = []
for predicted_patch in prediction:
predictions.append(predicted_patch)
output_shape = [int(output.shape[1])] + list(data.shape[-3:])
return reconstruct_from_patches(predictions,
patch_indices=indices,
data_shape=output_shape)