def label_patches(self, patches, max_patches=None):
if max_patches is not None:
patches = itertools.islice(patches, max_patches)
for patch in patches:
assert isinstance(patch, Patch)
os.makedirs(root_dir(FOLDER_TEMP_DATA), exist_ok=True)
path_patch = root_dir(FOLDER_TEMP_DATA, 'patch.png')
path_outln = root_dir(FOLDER_TEMP_DATA, 'outln.png')
images = {
path_patch: patch.cropped_image(),
path_outln: outline_regions(image=patch.cropped_image(),
region_labels=patch.cropped_mask())
}
[imsave(fname=rel_path, arr=resize(img, output_shape=(600, 600))) for rel_path, img in images.items()]
labels = LABELS_Ki67 + ['Not well defined']
while patch.expert_label not in labels:
# noinspection PyTypeChecker
gui = buttonbox("Ki67 - Manual labelling", choices=labels,
images=list(images.keys()), run=False)
gui.ui.set_pos("+0+0")
patch.expert_label = gui.run()
print(patch.expert_label)
self.labelled_patches.append(patch)
from src.data_loader import sample_names, images, root_dir, FOLDER_EXPERIMENTS, get_expert_Ki67
MAX_PATIENTS = 1000
MAX_IMAGES_PER_PATIENT = 5
MAX_PATCHES_PER_IMAGE = 2
SCALE = None # None to deactivate
GAUSSIAN_FILTER_SD = 2
CLUSTERING_NUM_CENTROIDS = 4
RADIUS_FILL_HOLES = 5
WIDTH_REMOVE_THIN_STRUCTURES = 12
if __name__ == "__main__":
execution_id = datetime.datetime.now().strftime('%Y-%m-%d-%H-%M-%S')
results_dir = root_dir(FOLDER_EXPERIMENTS(version=6), execution_id)
os.makedirs(results_dir, exist_ok=True)
logging.basicConfig(level=logging.INFO,
handlers=[
logging.FileHandler(
os.path.join(results_dir, 'log.txt')),
logging.StreamHandler()
])
p_names = sample_names()
for idx_p, p_name in enumerate(p_names[0:MAX_PATIENTS]):
for idx_img, (path_image, original_image) in enumerate(
images(patient_name=p_name,
max_images=MAX_IMAGES_PER_PATIENT)):
def load_labelled_patches(self, training_label):
data_dir = root_dir(FOLDER_LABELLED_DATA, training_label)
self.labelled_patches = Patch.load_all(folder=data_dir)
def save_labelled_patches(self, training_label):
data_dir = root_dir(FOLDER_LABELLED_DATA, training_label)
os.makedirs(data_dir, exist_ok=False)
for patch in self.labelled_patches:
patch.save(folder=data_dir)