def write_preprocessed_data(self, dir_output):
if all(x is None for x in self._stacks):
raise exceptions.ObjectNotCreated("run")
# Write all slices
for i in range(0, self._N_stacks):
slices = self._stacks[i].write(directory=dir_output,
write_mask=True,
write_slices=False)
def get_data(self):
if type(self._stacks) is not list:
raise exceptions.ObjectNotCreated("read_data")
return [st.Stack.from_stack(s) for s in self._stacks]
def evaluate_slice_similarities(self):
if self._slice_projections is None:
raise exceptions.ObjectNotCreated("compute_slice_projections")
self._slice_similarities = {
stack.get_filename(): {}
for stack in self._stacks
}
similarity_measures = {
m: SimilarityMeasures.similarity_measures[m]
for m in self._measures
}
for i_stack, stack in enumerate(self._stacks):
slices = stack.get_slices()
N_slices = self._get_original_number_of_slices(stack)
stack_name = stack.get_filename()
self._slice_similarities[stack_name] = {
m: np.ones(N_slices) * self._init_value
for m in self._measures
}
if self._verbose:
ph.print_info("Stack %d/%d: Compute similarity measures ... " %
(i_stack + 1, len(self._stacks)),
newline=False)
for slice in slices:
i_slice = slice.get_slice_number()
slice_nda = np.squeeze(sitk.GetArrayFromImage(slice.sitk))
slice_proj_nda = np.squeeze(
sitk.GetArrayFromImage(
self._slice_projections[i_stack][i_slice].sitk))
mask_nda = np.ones_like(slice_nda)
if self._use_slice_masks:
mask_nda *= np.squeeze(
sitk.GetArrayFromImage(slice.sitk_mask))
if self._use_reference_mask:
mask_nda *= np.squeeze(
sitk.GetArrayFromImage(self._slice_projections[i_stack]
[i_slice].sitk_mask))
indices = np.where(mask_nda > 0)
if len(indices[0]) > 0:
for m in self._measures:
try:
self._slice_similarities[stack_name][m][i_slice] = \
similarity_measures[m](
slice_nda[indices], slice_proj_nda[indices])
except ValueError as e:
# Error in case only a few/to less non-zero entries
# exist
if m == "SSIM":
self._slice_similarities[
stack_name][m][i_slice] = \
SimilarityMeasures.UNDEF[m]
else:
raise ValueError(e.message)
else:
for m in self._measures:
self._slice_similarities[
stack_name][m][i_slice] = \
SimilarityMeasures.UNDEF[m]
if self._verbose:
print("done")
def get_data(self):
if type(self._stacks) is not list:
raise exceptions.ObjectNotCreated("read_data")
return self._stacks