class ScanFolderConcatBatchReaderWithMask(ScanFolderConcatBatchReader):
def __init__(self,
mask_img_path,
config,
in_ori_folder,
in_jac_folder,
batch_size,
file_list_txt=None):
super().__init__(config, in_ori_folder, in_jac_folder, batch_size,
file_list_txt)
self._mask_img = ScanWrapper(mask_img_path)
self._masked_ref_ori = ScanWrapperWithMask(
self._in_data_folder.get_file_path(0), self._mask_img.get_path())
self._masked_ref_jac = ScanWrapperWithMask(
self._in_jac_folder.get_file_path(0), self._mask_img.get_path())
def save_flat_data(self, data_array, idx, out_folder):
out_path_ori = os.path.join(out_folder, f'pc_ori_{idx}.nii.gz')
out_path_jac = os.path.join(out_folder, f'pc_jac_{idx}.nii.gz')
ori_data_flat = data_array[:self._get_number_of_voxel_ori()]
jac_data_flat = data_array[self._get_number_of_voxel_ori():]
self._masked_ref_ori.save_scan_flat_img(ori_data_flat, out_path_ori)
self._masked_ref_jac.save_scan_flat_img(jac_data_flat, out_path_jac)
def _run_single_scan(self, idx):
in_ori_data_obj = ScanWrapperWithMask(
self._in_data_folder.get_file_path(idx), self._mask_img.get_path())
in_jac_data_obj = ScanWrapperWithMask(
self._in_jac_folder.get_file_path(idx), self._mask_img.get_path())
self._data_matrix[self._cur_idx, :self._get_number_of_voxel_ori(
)] = in_ori_data_obj.get_data_flat()
self._data_matrix[self._cur_idx,
self._get_number_of_voxel_ori(
):] = in_jac_data_obj.get_data_flat()
self._cur_idx += 1
def _get_number_of_voxel_ori(self):
return self._masked_ref_ori.get_data_flat().shape[0]
def _get_number_of_voxel_jac(self):
return self._masked_ref_jac.get_data_flat().shape[0]
class ScanFolderBatchWithMaskReader(ScanFolderBatchReader):
def __init__(self, config, in_folder, mask_img, batch_size, file_list_txt):
super().__init__(config, in_folder, None, batch_size, file_list_txt)
self._mask_img = ScanWrapper(mask_img)
self._masked_ref = ScanWrapperWithMask(
self._in_data_folder.get_file_path(0), self._mask_img.get_path())
def save_flat_data(self, data_array, idx, out_folder):
out_path = os.path.join(out_folder, f'pc_{idx}.nii.gz')
self._masked_ref.save_scan_flat_img(data_array, out_path)
def _run_single_scan(self, idx):
in_data = ScanWrapperWithMask(self._in_data_folder.get_file_path(idx),
self._mask_img.get_path())
self._data_matrix[self._cur_idx, :] = in_data.get_data_flat()
self._cur_idx += 1
def _get_number_of_voxel(self):
return self._masked_ref.get_data_flat().shape[0]
class CalcJacobian(AbstractParallelRoutine):
def __init__(self, config, in_dat_folder, out_folder, ref_img,
file_list_txt):
super().__init__(config, in_dat_folder, file_list_txt)
self._ref_img = ScanWrapper(ref_img)
self._out_data_folder = DataFolder.get_data_folder_obj(
config, out_folder, data_list_txt=file_list_txt)
self._jacobian_tool = config['deedsBCV_jacobian']
def _run_single_scan(self, idx):
in_dat_prefix = self._in_data_folder.get_file_path(idx)
out_file_path = self._out_data_folder.get_file_path(idx)
ref_img_path = self._ref_img.get_path()
jacobian_cmd_str = f'{self._jacobian_tool} -M {ref_img_path} -O {in_dat_prefix} -J {out_file_path}'
logger.info(jacobian_cmd_str)
os.system(jacobian_cmd_str)