def skeleton_evaluation(job_id, config_path):
fu.log("start processing job %i" % job_id)
fu.log("reading config from %s" % config_path)
with open(config_path, 'r') as f:
config = json.load(f)
# read the input cofig
input_path = config['input_path']
input_key = config['input_key']
skeleton_path = config['skeleton_path']
skeleton_key = config['skeleton_key']
output_path = config['output_path']
skeleton_format = config['skeleton_format']
n_threads = config.get('threads_per_job', 1)
# TODO adapt nskel.SkeletonMetrics to new n5 skeleton format
skeleton_ids = os.listdir(skeleton_file)
skeleton_ids = [int(sk) for sk in skeleton_ids if sk.isdigit()]
skeleton_ids.sort()
metrics = nskel.SkeletonMetrics(os.path.join(input_path, input_key),
os.path.join(skeleton_path, skeleton_key),
skeleton_ids, n_threads)
# TODO expose parameters for different eval options
correct, split, merge, n_merges = metrics.computeGoogleScore(n_threads)
res = {'correct': correct, 'split': split, 'merge': merge, 'n_merges': n_merges}
with open(output_path, 'w') as f:
json.dump(res, f)
# log success
fu.log_job_success(job_id)
def build_skeleton_metrics(label_file, skeleton_file, n_threads=-1):
assert os.path.exists(label_file), label_file
assert os.path.exists(skeleton_file), skeleton_file
skeleton_ids = os.listdir(skeleton_file)
skeleton_ids = [int(sk) for sk in skeleton_ids if sk.isdigit()]
skeleton_ids.sort()
return nskel.SkeletonMetrics(label_file, skeleton_file, skeleton_ids,
n_threads)
def load_skeleton_metrics(label_file, skeleton_file, serialization_file):
assert os.path.exists(label_file), label_file
assert os.path.exists(skeleton_file), skeleton_file
assert os.path.exists(serialization_file), serialization_file
skeleton_ids = os.listdir(skeleton_file)
skeleton_ids = [int(sk) for sk in skeleton_ids if sk.isdigit()]
skeleton_ids.sort()
return nskel.SkeletonMetrics(label_file, skeleton_file, skeleton_ids,
serialization_file)
def test_nodes(self):
import nifty.skeletons as nskel
metrics = nskel.SkeletonMetrics('./tmp/seg.n5/seg', './tmp/skels.n5',
[1, 2], 1)
out = metrics.getNodeAssignments()
self.assertEqual(list(out.keys()), [1, 2])
out1 = [out[1][k] for k in sorted(out[1].keys())]
out2 = [out[2][k] for k in sorted(out[2].keys())]
self.assertEqual(list(out1), 6 * [3])
self.assertEqual(list(out2), [0, 0, 0, 0, 2, 2])