def test_read_and_write_and_read():
for i in range(0, len(INPUT_FILES)):
input_file = INPUT_FILES[i]
output_file = OUTPUT_FILES[i]
first = wknml.parse_nml(input_file)
with open(output_file, 'wb') as f:
wknml.write_nml(f, first)
second = wknml.parse_nml(output_file)
assert first == second
def save_snapshot_pickle_read_and_write():
for i in range(0, len(INPUT_FILES)):
input_file = INPUT_FILES[i]
output_file = SNAPSHOT_FILES[i]
parsed = wknml.parse_nml(input_file)
with open(output_file + '.pickle', 'wb') as f:
pickle.dump(parsed, f)
def save_snapshot_nml_read_and_write():
for i in range(0, len(INPUT_FILES)):
input_file = INPUT_FILES[i]
output_file = OUTPUT_FILES[i]
parsed = wknml.parse_nml(input_file)
with open(output_file + '.snapshot', 'wb') as f:
wknml.write_nml(f, parsed)
def calc_supervoxel_eftpl(nml_filepath, h5_filepath, dset_vals=None, dset_folder='with_background', dset_suffix='labels',
size=None, dset_start=np.zeros((1,3), dtype=int),
):
with open(nml_filepath, "rb") as f:
nml = wknml.parse_nml(f)
if dset_vals is None:
with h5py.File(h5_filepath, 'r') as h5file:
dset = h5file[dset_folder]
dset_vals = [str(k) for k in dset.keys()]
eftpl = np.zeros(len(dset_vals))
h5_dim_idcs = [HDF5_DIM_ORDER.index(ax) for ax in 'xyz']
selection = None
if size is not None:
selection = tuple(slice(dset_start[ax],dset_start[ax]+size[ax]) for ax in h5_dim_idcs)
for i, dset_val in enumerate(dset_vals):
with h5py.File(h5_filepath, 'r') as h5file:
dset = h5file['/'.join([dset_folder, dset_val, dset_suffix])]
if size is None:
Vlbls = dset[:]
else:
Vlbls = np.zeros(tuple(size[ax] for ax in h5_dim_idcs), dtype=dset.dtype)
dset.read_direct(Vlbls, selection)
eftpl[i] = calc_eftpl(nml, Vlbls, dset_start)
return eftpl, dset_vals
def __init__(self,
nml_path: str = None,
parameters: Parameters = None,
strict=True):
""" The Skeleton constructor expects either a path to a nml file or a Parameters object as input arguments
Args:
nml_path: Path to nml file. If constructed via an nml file, the skeleton object is populated with all the
trees and additional properties specified in the .nml file
parameters (optional): Parameters (wkskel.types.Parameters) specifying the most rudimentary properties
of the skeleton.
strict (optional): Controls assertions ensuring that resulting skeleton objects are compatible with
webKnossos. Default: True
Examples:
Using nml_path:
nml_path = '/path/to/example.nml'
skel = Skeleton(nml_path)
Using parameters:
parameters = Skeleton.define_parameters(name="2017-01-12_FD0156-2", scale=(11.24, 11.24, 32))
skel = Skeleton(parameters=parameters)
"""
assert (nml_path is not None) ^ (parameters is not None), \
'To construct a skeleton object, either a path to a nml file or the skeleton parameters need to passed'
self.nodes = list()
self.edges = list()
self.names = list()
self.colors = list()
self.tree_ids = list()
self.group_ids = list()
self.groups = list()
self.branchpoints = list()
self.parameters = Parameters()
self.nml_path = str()
self.strict = strict
self.defaults = self.DEFAULTS
# Construct from nml file
if nml_path is not None:
assert os.path.exists(nml_path), \
'not a valid path: {}'.format(nml_path)
try:
with open(nml_path, "rb") as f:
nml = wknml.parse_nml(f)
except IOError:
print('not a valid nml file: {}'.format(nml_path))
self._nml_to_skeleton(nml)
# Construct from parameters
else:
assert type(parameters) is Parameters, \
'provided parameters must be of type wkskel.types.Parameters'
self._parameters_to_skeleton(parameters)
def test_snapshot_read_and_compare_nml():
for i in range(0, len(INPUT_FILES)):
input_file = INPUT_FILES[i]
snapshot_file = SNAPSHOT_FILES[i]
output_file = OUTPUT_FILES[i]
parsed = wknml.parse_nml(input_file)
with open(output_file, 'wb') as f:
wknml.write_nml(f, parsed)
assert filecmp.cmp(snapshot_file + '.snapshot', output_file)
def test_snapshot_read_and_compare_pickle():
for i in range(0, len(INPUT_FILES)):
input_file = INPUT_FILES[i]
snapshot_file = SNAPSHOT_FILES[i]
output_file = OUTPUT_FILES[i]
parsed = wknml.parse_nml(input_file)
with open(output_file + '.pickle.cmp', 'wb') as f:
pickle.dump(parsed, f)
assert filecmp.cmp(snapshot_file + '.pickle', output_file + '.pickle.cmp')
def test_generate_nml():
with open("testdata/nml_with_invalid_ids.nml", "r") as file:
test_nml = parse_nml(file)
(graph, parameter_dict) = generate_graph(test_nml)
test_result_nml = generate_nml(tree_dict=graph, parameters=parameter_dict)
with open("testdata/expected_result.nml", "r") as file:
expected_nml = parse_nml(file)
# need to save and load the test_result_nml since reading applies default values
# thus this is needed to be able to compare the nmls
with open("testoutput/temp.nml", "wb") as file:
write_nml(file=file, nml=test_result_nml)
with open("testoutput/temp.nml", "r") as file:
test_result_nml = parse_nml(file)
assert test_result_nml == expected_nml
def test_no_default_values_written():
input_file_name = "testdata/nml_without_default_values.nml"
output_file_name = "testoutput/nml_without_default_values.nml"
# read and write the test file
with open(input_file_name, "r") as file:
test_nml = parse_nml(file)
with open(output_file_name, "wb") as output_file:
write_nml(file=output_file, nml=test_nml)
# read the written testfile and compare the content
with open(input_file_name, "r") as file:
test_nml = parse_nml(file)
with open(output_file_name, "r") as output_file:
test_result_nml = parse_nml(output_file)
assert test_nml == test_result_nml, "The testdata file and the testoutput file do not have the same content."
# test if both files have the same content
assert filecmp.cmp(
input_file_name, output_file_name
), "The testdata and the testoutput file do not have the same content."
def load_and_save_merged_nml_trees(source: str, destination: str, scale):
assert os.path.isfile(source), "No file was provided as source."
assert os.path.exists(os.path.dirname(os.path.realpath(destination))), "The destination directory does not exists."
logger.info("Reading data")
with open(source, "rb") as f:
nml = parse_nml(f)
logger.info("Starting to merge tree groups")
merged_nml = create_merged_nml(nml, scale)
logger.info("Writing data")
with open(destination, "wb") as f:
write_nml(f, merged_nml)
logger.info("Done")
def test_ensure_max_edge_length():
with open("testdata/nml_with_too_long_edges.nml", "r") as file:
test_nml = parse_nml(file)
max_length = 2.0
scale = np.array(test_nml.parameters.scale)
test_nml_graph = generate_graph(test_nml)
# test if the loaded graph violates the max_length
assert not is_max_length_violated(test_nml_graph[0], max_length, scale)
# test the graph version
test_result_nml_graph, _ = ensure_max_edge_length(test_nml_graph,
max_length)
assert is_max_length_violated(test_result_nml_graph, max_length, scale)
# test the nml version
test_result_nml = ensure_max_edge_length(test_nml, max_length)
test_result_nml, _ = generate_graph(test_result_nml)
assert is_max_length_violated(test_result_nml, max_length, scale)
def test_approximate_minimal_edge_length():
with open("testdata/nml_with_small_distance_nodes.nml", "r") as file:
test_nml = parse_nml(file)
max_length = 2.0
max_angle = 0.2
scale = np.array(test_nml.parameters.scale)
test_nml_graph = generate_graph(test_nml)
# test if the loaded graph violates the max_length
assert not is_minimal_edge_length_violated(test_nml_graph[0], max_length,
max_angle, scale)
# test the graph interface
test_result_nml_graph, _ = approximate_minimal_edge_length(
test_nml_graph, max_length, max_angle)
assert is_minimal_edge_length_violated(test_result_nml_graph, max_length,
max_angle, scale)
# test the graph interface
test_result_nml = approximate_minimal_edge_length(test_nml, max_length,
max_angle)
test_result_nml, _ = generate_graph(test_result_nml)
assert is_minimal_edge_length_violated(test_result_nml, max_length,
max_angle, scale)
parser.add_argument(
"--set_zero",
action="store_true",
help="Set non-marked segments to zero.",
)
parser.add_argument("input", help="Path to input WKW dataset")
parser.add_argument("--layer_name", "-l", help="Segmentation layer name", default="segmentation")
parser.add_argument("nml", help="Path to NML file")
parser.add_argument("output", help="Path to output tiff files")
args = parser.parse_args()
print("Merging merger mode annotations from {} and {}".format(args.input, args.nml))
# Collect equivalence classes from NML
with open(args.nml, "rb") as f:
nml = wknml.parse_nml(f)
ds_in = wkw.Dataset.open(path.join(args.input, args.layer_name, "1"))
cube_size = ds_in.header.block_len * ds_in.header.file_len
equiv_classes = [
set(ds_in.read(node.position, (1,1,1))[0,0,0,0] for node in tree.nodes)
for tree in nml.trees
]
equiv_map = {}
for klass in equiv_classes:
base = next(iter(klass))
for id in klass:
equiv_map[id] = base
def flatten(l):
return [x for y in l for x in y]
def find(pred, l):
return next(x for x in l if pred(x))
parser = ArgumentParser(
description="Splits trees in order to fix unlinked nodes.")
parser.add_argument("source", help="Source NML file")
parser.add_argument("target", help="Target NML file")
args = parser.parse_args()
file = wknml.parse_nml(ET.parse(args.source).getroot())
all_nodes = flatten([t.nodes for t in file.trees])
all_edges = flatten([t.edges for t in file.trees])
all_node_ids = [n.id for n in all_nodes]
max_node_id = max(all_node_ids) + 1
print("trees={} nodes={} edges={} max_node={}".format(len(file.trees),
len(all_nodes),
len(all_edges),
max_node_id))
mat = scipy.sparse.lil_matrix((max_node_id, max_node_id))
for edge in all_edges:
mat[edge.source, edge.target] = 1