def test_skeleton_read_write_with_props(simple_skeleton_with_properties,
tmp_path):
sk = simple_skeleton_with_properties
fname = os.path.join(tmp_path, 'test.swc')
skeleton_io.write_skeleton_h5(sk, fname, overwrite=True)
skback = skeleton_io.read_skeleton_h5(fname)
assert np.all(
skback.vertex_properties['test'] == sk.vertex_properties['test'])
assert np.all(skback.mesh_to_skel_map == sk.mesh_to_skel_map)
def write_to_h5(self, filename, overwrite=True):
"""Write the skeleton to an HDF5 file. Note that this is done in the original dimensons, not the scaled dimensions.
Parameters
----------
filename : str
Filename to save file
overwrite : bool, optional
Flag to specify whether to overwrite existing files, by default True
"""
existing_voxel_scaling = self.voxel_scaling
self.voxel_scaling = None
skeleton_io.write_skeleton_h5(self, filename, overwrite=overwrite)
self.voxel_scaling = existing_voxel_scaling
def test_skeleton_read_write(simple_skeleton, overwrite_flag, file_exist):
sk = simple_skeleton
with tempfile.NamedTemporaryFile(suffix='.h5',
delete=(not file_exist)) as tf:
fname = tf.name
skeleton_io.write_skeleton_h5(sk, fname, overwrite=overwrite_flag)
if file_exist and not overwrite_flag:
with pytest.raises(OSError):
skback = skeleton_io.read_skeleton_h5(fname)
else:
skback = skeleton_io.read_skeleton_h5(fname)
assert np.all(skback.vertices == sk.vertices)
assert np.all(skback.edges == sk.edges)
assert skback.root == sk.root