def label_categorical_slice():
label_session_id = request.args.get('label_session', type=int, default=None)
element_index = request.args.get('i', type=int, default=None)
if label_session_id is None or element_index is None:
abort(400)
label_session = sessions.get_session_by_id(db.session, label_session_id)
if label_session is None or label_session.session_type != LabelSessionType.CATEGORICAL_SLICE.name:
abort(400)
dataset = backend.get_dataset(label_session.dataset)
if dataset is None:
abort(400)
element = labels.get_element_by_index(db.session, label_session, element_index)
image = backend.get_image(dataset, element.image_1_name)
if image is None:
abort(400)
im_slice = backend.ImageSlice(element.image_1_name, element.slice_1_index, backend.SliceType[element.slice_1_type])
_, max_value = backend.get_image_info(image)
slice_label_value = element.current_label_value()
return render_template('label_categorical_slice.html',
label_session=label_session,
dataset=dataset,
element_id=element.id,
image_slice=im_slice,
slice_label_value=slice_label_value,
image_max=max_value,
previous_index=max(0, element_index - 1),
next_index=min(label_session.element_count - 1, element_index + 1))
def export_slices(session_id: int):
with application.app_context():
label_session = sessions.get_session_by_id(db.session, session_id)
if label_session is None:
print('Session with id {} not found'.format(session_id))
return
session_slices_dir_path = os.path.join(
EXPORTED_SLICES_DIR_PATH, label_session.session_name + ' Slices')
session_slices_dir_path = inc_dir_name(session_slices_dir_path)
os.makedirs(session_slices_dir_path, exist_ok=True)
slices = sampling.get_slices_from_session(label_session)
dataset = backend.get_dataset(label_session.dataset)
for sl in slices:
d_img = backend.get_image(dataset, sl.image_name)
sl_max = backend.get_image_info(d_img)[1]
sl_img = backend.get_slice(d_img, sl.slice_index, sl.slice_type, 0,
sl_max)
save_name = '{}_{}_{}.png'.format(sl.image_name,
sl.slice_type.name,
sl.slice_index)
save_path = os.path.join(session_slices_dir_path, save_name)
sl_img.save(save_path)
print('Saved {}'.format(save_path))
def viewer():
dataset_name = request.args.get('dataset', type=str, default=None)
image_name = request.args.get('image', type=str, default=None)
if dataset_name is None or image_name is None:
abort(400)
dataset = backend.get_dataset(dataset_name)
if dataset is None:
abort(400)
image = backend.get_image(dataset, image_name)
if image is None:
abort(400)
slice_counts, max_value = backend.get_image_info(image)
return render_template('viewer.html',
viewer_mode='viewer',
dataset=dataset,
image=image,
image_count=0,
image_index=0,
slice_counts=slice_counts,
image_max=max_value)
def test_get_image_path(self):
dataset = backend.get_dataset('dataset1')
image = backend.get_image(dataset, 'img1.nii.gz')
self.assertEqual(
image.path,
os.path.join(backend.DATASETS_PATH, 'dataset1', 'img1.nii.gz'))
def label_compare():
label_session_id = request.args.get('label_session', type=int, default=None)
comparison_index = request.args.get('i', type=int, default=None)
if label_session_id is None or comparison_index is None:
abort(400)
assert 0 <= comparison_index
label_session = sessions.get_session_by_id(db.session, label_session_id)
if label_session is None or label_session.session_type != LabelSessionType.COMPARISON_SLICE.name:
abort(400)
dataset = backend.get_dataset(label_session.dataset)
if dataset is None:
abort(400)
element = labels.get_element_by_index(db.session, label_session, comparison_index)
slice_1 = backend.ImageSlice(element.image_1_name, element.slice_1_index, backend.SliceType[element.slice_1_type])
slice_2 = backend.ImageSlice(element.image_2_name, element.slice_2_index, backend.SliceType[element.slice_2_type])
image_1 = backend.get_image(dataset, slice_1.image_name)
image_2 = backend.get_image(dataset, slice_2.image_name)
_, image_1_max = backend.get_image_info(image_1)
_, image_2_max = backend.get_image_info(image_2)
current_label_value = element.current_label_value()
return render_template('label_compare.html',
label_session=label_session,
prompt=label_session.prompt,
dataset=dataset,
element_id=element.id,
slice_1=slice_1,
slice_2=slice_2,
image_1_max=image_1_max,
image_2_max=image_2_max,
current_label_value=current_label_value,
sort_mode=False,
previous_index=max(0, comparison_index - 1),
next_index=min(label_session.element_count - 1, comparison_index + 1))
def label_sort_compare():
label_session_id = request.args.get('label_session')
if label_session_id is None:
abort(404)
label_session = sessions.get_session_by_id(db.session, label_session_id)
if label_session is None:
abort(404)
if label_session.session_type != LabelSessionType.SORT_SLICE.name:
abort(400)
dataset = backend.get_dataset(label_session.dataset)
if dataset is None:
abort(404)
complete, comparison_el, _ = comparesort.add_next_comparison(db.session, label_session)
if complete:
return redirect(url_for('session_overview', session_id=label_session.id))
comparison = sampling.get_comparison_from_element(comparison_el)
slice_1, slice_2 = comparison
image_1 = backend.get_image(dataset, slice_1.image_name)
image_2 = backend.get_image(dataset, slice_2.image_name)
_, image_1_max = backend.get_image_info(image_1)
_, image_2_max = backend.get_image_info(image_2)
current_label_value = None
return render_template('label_compare.html',
label_session=label_session,
prompt=label_session.prompt,
dataset=dataset,
element_id=comparison_el.id,
slice_1=slice_1,
slice_2=slice_2,
image_1_max=image_1_max,
image_2_max=image_2_max,
current_label_value=current_label_value,
sort_mode=True)
def create_thumbnails(label_session: LabelSession):
dataset = backend.get_dataset(label_session.dataset)
slices = sampling.get_slices_from_session(label_session)
session_thumbs_dir_path = get_session_thumbnails_dir_path(label_session)
os.makedirs(session_thumbs_dir_path, exist_ok=True)
for sl in slices:
d_img = backend.get_image(dataset, sl.image_name)
slice_thumb_path = os.path.join(session_thumbs_dir_path,
backend.slice_name(sl) + '.jpg')
backend.get_slice(d_img, sl.slice_index, sl.slice_type, 0,
None).save(slice_thumb_path)
print('Created {} thumbnails for session {}'.format(
len(slices), label_session.session_name))
def thumbnail(dataset_name: str, image_name: str):
dataset = backend.get_dataset(dataset_name)
d_img = backend.get_image(dataset, image_name)
slice_index = request.args.get('slice_index', default=0, type=int)
slice_type_name = request.args.get('slice_type', default='AXIAL', type=str)
intensity_min = request.args.get('min', default=0, type=int)
intensity_max = request.args.get('max', default=0, type=int)
slice_type = backend.SliceType[slice_type_name]
slice_image = backend.get_slice(d_img, slice_index, slice_type, intensity_min, intensity_max)
img_io = BytesIO()
slice_image.save(img_io, 'PNG')
img_io.seek(0)
return send_file(img_io, mimetype='image/png')
def create_thumbnails(label_session: LabelSession):
dataset = backend.get_dataset(label_session.dataset)
slices = sampling.get_slices_from_session(label_session)
dataset_thumbs_path = get_dataset_thumbnails_path(dataset)
os.makedirs(dataset_thumbs_path, exist_ok=True)
created = 0
for sl in slices:
d_img = backend.get_image(dataset, sl.image_name)
slice_thumb_path = os.path.join(dataset_thumbs_path,
get_thumbnail_name(sl))
if not os.path.exists(slice_thumb_path):
img = backend.get_slice(d_img, sl.slice_index, sl.slice_type, 0,
None, THUMB_MAX_PERCENTILE)
img.save(slice_thumb_path)
created += 1
print('Created {} thumbnails for session {} (skipped {}, total {})'.format(
created, label_session.session_name,
len(slices) - created, len(slices)))
def label():
label_session_id = request.args.get('label_session', type=int, default=None)
element_index = request.args.get('i', type=int, default=None)
if label_session_id is None or element_index is None:
abort(400)
label_session = sessions.get_session_by_id(db.session, label_session_id)
if label_session is None or label_session.session_type != LabelSessionType.CATEGORICAL_IMAGE.name:
abort(400)
dataset = backend.get_dataset(label_session.dataset)
if dataset is None:
abort(400)
element = labels.get_element_by_index(db.session, label_session, element_index)
image = backend.get_image(dataset, element.image_1_name)
if image is None:
abort(400)
slice_counts, max_value = backend.get_image_info(image)
image_label_value = element.current_label_value()
return render_template('viewer.html',
viewer_mode='label',
label_session=label_session,
prompt=label_session.prompt,
dataset=dataset,
image=image,
element_id=element.id,
slice_counts=slice_counts,
image_max=max_value,
image_label_value=image_label_value,
previous_index=max(0, element_index - 1),
next_index=min(label_session.element_count - 1, element_index + 1))
def test_get_image_non_existent(self):
dataset = backend.get_dataset('dataset1')
with self.assertRaises(AssertionError):
backend.get_image(dataset, 'non_existent_image.nii.gz')
def test_get_image_name(self):
dataset = backend.get_dataset('dataset1')
image = backend.get_image(dataset, 'img1.nii.gz')
self.assertEqual(image.name, 'img1.nii.gz')
