def _get_voxel_time_series_region(self, ts_h5, x, y, z, var=0, mode=0):
region_mapping_volume_gid = ts_h5.region_mapping_volume.load()
if region_mapping_volume_gid is None:
raise Exception("Invalid method called for TS without Volume Mapping!")
volume_rm_h5_class, volume_rm_h5_path = self._load_h5_of_gid(region_mapping_volume_gid.hex)
volume_rm_h5 = volume_rm_h5_class(volume_rm_h5_path)
volume_rm_shape = volume_rm_h5.array_data.shape
x, y, z = preprocess_space_parameters(x, y, z, volume_rm_shape[0], volume_rm_shape[1], volume_rm_shape[2])
idx_slices = slice(x, x + 1), slice(y, y + 1), slice(z, z + 1)
idx = int(volume_rm_h5.array_data[idx_slices])
time_length = ts_h5.data.shape[0]
var, mode = int(var), int(mode)
voxel_slices = prepare_time_slice(time_length), slice(var, var + 1), slice(idx, idx + 1), slice(mode, mode + 1)
connectivity_gid = volume_rm_h5.connectivity.load()
connectivity_h5_class, connectivity_h5_path = self._load_h5_of_gid(connectivity_gid.hex)
connectivity_h5 = connectivity_h5_class(connectivity_h5_path)
label = connectivity_h5.region_labels.load()[idx]
background, back_min, back_max = None, None, None
if idx < 0:
back_min, back_max = ts_h5.get_min_max_values()
background = numpy.ones((time_length, 1)) * ts_h5.out_of_range(back_min)
label = 'background'
volume_rm_h5.close()
connectivity_h5.close()
result = postprocess_voxel_ts(ts_h5, voxel_slices, background, back_min, back_max, label)
return result
def get_volume_view(self, x_plane, y_plane, z_plane, **kwargs):
shape = self.array_data.shape
length_1d = shape[0]
length_2d = shape[1]
length_3d = shape[2]
# Work with space inside Volume:
x_plane, y_plane, z_plane = preprocess_space_parameters(x_plane, y_plane, z_plane, length_1d,
length_2d, length_3d)
slice_x, slice_y, slice_z = self.get_volume_slice(x_plane, y_plane, z_plane)
return [[slice_x.tolist()], [slice_y.tolist()], [slice_z.tolist()]]
def get_voxel_region(self, x_plane, y_plane, z_plane):
data_shape = self.array_data.shape
x_plane, y_plane, z_plane = preprocess_space_parameters(x_plane, y_plane, z_plane, data_shape[0],
data_shape[1], data_shape[2])
slices = slice(x_plane, x_plane + 1), slice(y_plane, y_plane + 1), slice(z_plane, z_plane + 1)
voxel = self.array_data[slices][0, 0, 0]
if voxel != -1:
conn_index = load_entity_by_gid(self.connectivity.load().hex)
return conn_index.region_labels[int(voxel)]
else:
return 'background'
