def _run_interface(self, runtime):
src_paths = self._get_filelist(self.inputs.dicom_files)
stacks = dcmstack.parse_and_stack(src_paths)
self.out_list = []
for key, stack in stacks.iteritems():
nw = NiftiWrapper(stack.to_nifti(embed_meta=True))
const_meta = nw.meta_ext.get_class_dict(('global', 'const'))
out_path = self._get_out_path(const_meta)
if not self.inputs.embed_meta:
nw.remove_extension()
nb.save(nw.nii_img, out_path)
self.out_list.append(out_path)
return runtime
def _run_interface(self, runtime):
src_paths = self._get_filelist(self.inputs.dicom_files)
stacks = dcmstack.parse_and_stack(src_paths)
self.out_list = []
for key, stack in list(stacks.items()):
nw = NiftiWrapper(stack.to_nifti(embed_meta=True))
const_meta = nw.meta_ext.get_class_dict(("global", "const"))
out_path = self._get_out_path(const_meta)
if not self.inputs.embed_meta:
nw.remove_extension()
nb.save(nw.nii_img, out_path)
self.out_list.append(out_path)
return runtime
def _run_interface(self, runtime):
src_paths = self._get_filelist(self.inputs.dicom_files)
include_regexes = dcmstack.default_key_incl_res
if isdefined(self.inputs.include_regexes):
include_regexes += self.inputs.include_regexes
exclude_regexes = dcmstack.default_key_excl_res
if isdefined(self.inputs.exclude_regexes):
exclude_regexes += self.inputs.exclude_regexes
meta_filter = dcmstack.make_key_regex_filter(exclude_regexes, include_regexes)
stack = dcmstack.DicomStack(meta_filter=meta_filter)
for src_path in src_paths:
src_dcm = dicom.read_file(src_path, force=True)
stack.add_dcm(src_dcm)
nii = stack.to_nifti(embed_meta=True)
nw = NiftiWrapper(nii)
self.out_path = self._get_out_path(nw.meta_ext.get_class_dict(("global", "const")))
if not self.inputs.embed_meta:
nw.remove_extension()
nb.save(nii, self.out_path)
return runtime
def _run_interface(self, runtime):
src_paths = self._get_filelist(self.inputs.dicom_files)
include_regexes = dcmstack.default_key_incl_res
if isdefined(self.inputs.include_regexes):
include_regexes += self.inputs.include_regexes
exclude_regexes = dcmstack.default_key_excl_res
if isdefined(self.inputs.exclude_regexes):
exclude_regexes += self.inputs.exclude_regexes
meta_filter = dcmstack.make_key_regex_filter(exclude_regexes,
include_regexes)
stack = dcmstack.DicomStack(meta_filter=meta_filter)
for src_path in src_paths:
src_dcm = dicom.read_file(src_path, force=True)
stack.add_dcm(src_dcm)
nii = stack.to_nifti(embed_meta=True)
nw = NiftiWrapper(nii)
self.out_path = \
self._get_out_path(nw.meta_ext.get_class_dict(('global', 'const')))
if not self.inputs.embed_meta:
nw.remove_extension()
nb.save(nii, self.out_path)
return runtime
