def edge_distances(labels, atlas_edge=None, path=None, spacing=None):
"""Measure the distance between edge images.
Args:
labels: Labels image as Numpy array.
atlas_edge: Image as a Numpy array of the atlas reduced to its edges.
Defaults to None to load from the corresponding registered
file path based on ``path``.
path: Path from which to load ``atlas_edge`` if it is None.
spacing: Grid spacing sequence of same length as number of image
axis dimensions; defaults to None.
Returns:
An image array of the same shape as ``labels_edge`` with
label edge values replaced by corresponding distance values.
"""
if atlas_edge is None:
atlas_edge = sitk_io.load_registered_img(
path, config.RegNames.IMG_ATLAS_EDGE.value)
# create distance map between edges of original and new segmentations
labels_edge = vols.make_labels_edge(labels)
dist_to_orig, _, _ = cv_nd.borders_distance(
atlas_edge != 0, labels_edge != 0, spacing=spacing)
return dist_to_orig, labels_edge
def make_labels_level_img(img_path, level, prefix=None, show=False):
"""Replace labels in an image with their parents at the given level.
Labels that do not fall within a parent at that level will remain in place.
Args:
img_path: Path to the base image from which the corresponding
registered image will be found.
level: Ontological level at which to group child labels.
prefix: Start of path for output image; defaults to None to
use ``img_path`` instead.
show: True to show the images after generating them; defaults to False.
"""
# load original labels image and setup ontology dictionary
labels_sitk = sitk_io.load_registered_img(img_path,
config.RegNames.IMG_LABELS.value,
get_sitk=True)
labels_np = sitk.GetArrayFromImage(labels_sitk)
ref = ontology.load_labels_ref(config.load_labels)
labels_ref_lookup = ontology.create_aba_reverse_lookup(ref)
ids = list(labels_ref_lookup.keys())
for key in ids:
keys = [key, -1 * key]
for region in keys:
if region == 0: continue
# get ontological label
label = labels_ref_lookup[abs(region)]
label_level = label[ontology.NODE][config.ABAKeys.LEVEL.value]
if label_level == level:
# get children (including parent first) at given level
# and replace them with parent
label_ids = ontology.get_children_from_id(
labels_ref_lookup, region)
labels_region = np.isin(labels_np, label_ids)
print("replacing labels within", region)
labels_np[labels_region] = region
labels_level_sitk = sitk_io.replace_sitk_with_numpy(labels_sitk, labels_np)
# generate an edge image at this level
labels_edge = vols.make_labels_edge(labels_np)
labels_edge_sikt = sitk_io.replace_sitk_with_numpy(labels_sitk,
labels_edge)
# write and optionally display labels level image
imgs_write = {
config.RegNames.IMG_LABELS_LEVEL.value.format(level):
labels_level_sitk,
config.RegNames.IMG_LABELS_EDGE_LEVEL.value.format(level):
labels_edge_sikt,
}
out_path = prefix if prefix else img_path
sitk_io.write_reg_images(imgs_write, out_path)
if show:
for img in imgs_write.values():
if img: sitk.Show(img)
def make_labels_level_img(img_path, level, prefix=None, show=False):
"""Replace labels in an image with their parents at the given level.
Labels that do not fall within a parent at that level will remain in place.
Args:
img_path: Path to the base image from which the corresponding
registered image will be found.
level: Ontological level at which to group child labels.
prefix: Start of path for output image; defaults to None to
use ``img_path`` instead.
show: True to show the images after generating them; defaults to False.
"""
# load original labels image and setup ontology dictionary
labels_sitk = sitk_io.load_registered_img(img_path,
config.RegNames.IMG_LABELS.value,
get_sitk=True)
labels_np = sitk.GetArrayFromImage(labels_sitk)
ref = ontology.LabelsRef(config.load_labels).load()
# remap labels to given level
labels_np = ontology.make_labels_level(labels_np, ref, level)
labels_level_sitk = sitk_io.replace_sitk_with_numpy(labels_sitk, labels_np)
# generate an edge image at this level
labels_edge = vols.make_labels_edge(labels_np)
labels_edge_sikt = sitk_io.replace_sitk_with_numpy(labels_sitk,
labels_edge)
# write and optionally display labels level image
imgs_write = {
config.RegNames.IMG_LABELS_LEVEL.value.format(level):
labels_level_sitk,
config.RegNames.IMG_LABELS_EDGE_LEVEL.value.format(level):
labels_edge_sikt,
}
out_path = prefix if prefix else img_path
sitk_io.write_reg_images(imgs_write, out_path)
if show:
for img in imgs_write.values():
if img: sitk.Show(img)