class ScanFolderFlatReader(AbstractParallelRoutine):
def __init__(self, config, in_folder, ref_img):
super().__init__(config, in_folder)
self._ref_img = ScanWrapper(ref_img)
self._data_matrix = []
def read_data(self):
print(f'Reading scan from folder {self._in_data_folder.get_folder()}')
tic = time.perf_counter()
self._data_matrix = self._init_data_matrix()
self.run_non_parallel()
# self.run_parallel()
toc = time.perf_counter()
print(f'Done. {toc - tic:0.4f} (s)')
def get_data_matrix(self):
return self._data_matrix
def _run_single_scan(self, idx):
in_file_path = self._in_data_folder.get_file_path(idx)
in_data = ScanWrapper(in_file_path)
in_img = in_data.get_data()
# self._data_matrix[idx, :] = in_img.reshape(in_data.get_number_voxel())
self._data_matrix[idx, :] = convert_3d_2_flat(in_img)
def _init_data_matrix(self):
num_features = self._ref_img.get_number_voxel()
num_sample = self.num_files()
data_matrix = np.zeros((num_sample, num_features))
return data_matrix
class ScanFolderConcatBatchReader(AbstractParallelRoutine):
def __init__(self,
config,
in_ori_folder,
in_jac_folder,
batch_size,
file_list_txt=None):
super().__init__(config, in_ori_folder, file_list_txt)
self._in_jac_folder = DataFolder(in_jac_folder, file_list_txt)
self._ref_ori = ScanWrapper(self._in_data_folder.get_file_path(0))
self._ref_jac = ScanWrapper(self._in_jac_folder.get_file_path(0))
self._chunk_list = self._in_data_folder.get_chunks_list_batch_size(
batch_size)
self._data_matrix = []
self._cur_idx = 0
def read_data(self, idx_batch):
self._reset_cur_idx()
print(f'Reading scans from folder {self._in_data_folder.get_folder()}',
flush=True)
tic = time.perf_counter()
cur_batch = self._chunk_list[idx_batch]
self._init_data_matrix(len(cur_batch))
self.run_non_parallel(cur_batch)
toc = time.perf_counter()
print(f'Done. {toc - tic:0.4f} (s)', flush=True)
def num_batch(self):
return len(self._chunk_list)
def get_data_matrix(self):
return self._data_matrix
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._ref_ori.get_number_voxel()]
jac_data_flat = data_array[self._ref_ori.get_number_voxel():]
self._ref_ori.save_scan_flat_img(ori_data_flat, out_path_ori)
self._ref_jac.save_scan_flat_img(jac_data_flat, out_path_jac)
def get_ref(self):
return self._ref_ori
def _run_single_scan(self, idx):
in_ori_data = ScanWrapper(
self._in_data_folder.get_file_path(idx)).get_data()
in_jac_data = ScanWrapper(
self._in_jac_folder.get_file_path(idx)).get_data()
self._data_matrix[self._cur_idx, :self._ref_ori.get_number_voxel(
)] = convert_3d_2_flat(in_ori_data)
self._data_matrix[
self._cur_idx,
self._ref_ori.get_number_voxel():] = convert_3d_2_flat(in_jac_data)
self._cur_idx += 1
def _init_data_matrix(self, num_sample):
num_features = self._get_number_of_voxel()
del self._data_matrix
self._data_matrix = np.zeros((num_sample, num_features))
def _get_number_of_voxel(self):
return self._get_number_of_voxel_ori() + self._get_number_of_voxel_jac(
)
def _get_number_of_voxel_ori(self):
return self._ref_ori.get_number_voxel()
def _get_number_of_voxel_jac(self):
return self._ref_jac.get_number_voxel()
def _reset_cur_idx(self):
self._cur_idx = 0
class ScanFolderBatchReader(AbstractParallelRoutine):
def __init__(self, config, in_folder, ref_img, batch_size, file_list=None):
super().__init__(config, in_folder, file_list)
self._ref_img = ScanWrapper(self._in_data_folder.get_file_path(0))
self._chunk_list = self._in_data_folder.get_chunks_list_batch_size(
batch_size)
self._data_matrix = []
self._cur_idx = 0
def read_data(self, idx_batch):
self._reset_cur_idx()
print(f'Reading scans from folder {self._in_data_folder.get_folder()}',
flush=True)
tic = time.perf_counter()
cur_batch = self._chunk_list[idx_batch]
self._init_data_matrix(len(cur_batch))
self.run_non_parallel(cur_batch)
toc = time.perf_counter()
print(f'Done. {toc - tic:0.4f} (s)', flush=True)
def num_batch(self):
return len(self._chunk_list)
def get_data_matrix(self):
return self._data_matrix
def get_batch_idx_list(self, idx_batch):
return self._chunk_list[idx_batch]
def save_flat_data(self, data_array, idx, out_folder):
out_path_ori = os.path.join(out_folder, f'pc_{idx}.nii.gz')
self._ref_img.save_scan_flat_img(data_array, out_path_ori)
def get_ref(self):
return self._ref_img
def get_batch_file_name_list(self, idx_batch):
batch_idx_list = self._chunk_list[idx_batch]
file_name_list = [
self._in_data_folder.get_file_name(file_idx)
for file_idx in batch_idx_list
]
return file_name_list
def _run_single_scan(self, idx):
in_file_path = self._in_data_folder.get_file_path(idx)
in_data = ScanWrapper(in_file_path)
in_img = in_data.get_data()
# self._data_matrix[idx, :] = in_img.reshape(in_data.get_number_voxel())
# self._data_matrix[idx, :] = convert_3d_2_flat(in_img)
self._data_matrix[self._cur_idx, :] = convert_3d_2_flat(in_img)
self._cur_idx += 1
def _init_data_matrix(self, num_sample):
num_features = self._get_number_of_voxel()
del self._data_matrix
self._data_matrix = np.zeros((num_sample, num_features))
def _reset_cur_idx(self):
self._cur_idx = 0
def _get_number_of_voxel(self):
return self._ref_img.get_number_voxel()