def __getitem__(self, ref_name):
if ref_name not in self.keys():
if ref_name not in self.references_list:
warnings.warn(f"No reference named {ref_name} "
f"(available: {self.references_list})")
return None
self.data[ref_name] = read_tiff(self.data_path /
f"{ref_name}.tiff")
return self.data[ref_name]
def hemispheres(self):
if self._hemispheres is None:
# If reference is symmetric generate hemispheres block:
if self.metadata["symmetric"]:
# initialize empty stack:
stack = np.full(self.metadata["shape"], 2, dtype=np.uint8)
# Use bgspace description to fill out with hemisphere values:
front_ax_idx = self.space.axes_order.index("frontal")
# Fill out with 2s the right hemisphere:
slices = [slice(None) for _ in range(3)]
slices[front_ax_idx] = slice(
stack.shape[front_ax_idx] // 2 + 1, None)
stack[tuple(slices)] = 1
self._hemispheres = stack
else:
self._hemispheres = read_tiff(self.root_dir /
HEMISPHERES_FILENAME)
return self._hemispheres
def annotation(self):
if self._annotation is None:
self._annotation = read_tiff(self.root_dir / ANNOTATION_FILENAME)
return self._annotation
def reference(self):
if self._reference is None:
self._reference = read_tiff(self.root_dir / REFERENCE_FILENAME)
return self._reference