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