def body_edge_table():
"""
Extract rows for a particular body from the merge table.
Useful for debugging, or for warming up the merge graph cache.
"""
global logger
global MERGE_TABLE
data = request.json
user = data.get("user", "unknown")
body_id = data["body-id"]
server = data["server"] + ':' + str(data["port"])
uuid = data["uuid"]
segmentation_instance = data["segmentation-instance"]
find_missing_edges = data.get("find-missing-edges", True)
body_logger = PrefixedLogger(logger, f"User {user}: Body {body_id}: ")
instance_info = DvidInstanceInfo(server, uuid, segmentation_instance)
body_logger.info("Recevied body-edge-table request")
try:
session = default_dvid_session(appname='cleave-server', user=user)
_mutid, _supervoxels, edges, scores = MERGE_GRAPH.extract_edges(*instance_info, body_id, find_missing_edges, session=session, logger=body_logger)
except requests.HTTPError as ex:
status_name = str(HTTPStatus(ex.response.status_code)).split('.')[1]
if ex.response.status_code == HTTPStatus.NOT_FOUND:
msg = f"Body not found: {body_id}"
else:
msg = f"Received error from DVID: {status_name}"
body_logger.error(msg)
return msg, ex.response.status_code
response = StringIO()
table = pd.DataFrame(edges, columns=['id_a', 'id_b'])
table['score'] = scores
table.to_csv(response, index=False, header=True)
return response.getvalue()
def session_id(_):
time.sleep(0.01)
return id(default_dvid_session())
def _run_cleave(data):
"""
Helper function that actually performs the cleave,
and can be run in a separate process.
Must not use any flask functions.
"""
global logger
global MERGE_TABLE
user = data.get("user", "unknown")
method = data.get("method", DEFAULT_METHOD)
body_id = data["body-id"]
seeds = { int(k): v for k,v in data["seeds"].items() }
server = data["server"] + ':' + str(data["port"])
uuid = data["uuid"]
segmentation_instance = data["segmentation-instance"]
find_missing_edges = data.get("find-missing-edges", True)
body_logger = PrefixedLogger(logger, f"User {user}: Body {body_id}: ")
instance_info = DvidInstanceInfo(server, uuid, segmentation_instance)
# Remove empty seed classes (if any)
for label in list(seeds.keys()):
if len(seeds[label]) == 0:
del seeds[label]
cleave_response = copy.copy(data)
cleave_response["seeds"] = dict(sorted((k, sorted(v)) for (k,v) in data["seeds"].items()))
cleave_response["assignments"] = {}
cleave_response["warnings"] = []
cleave_response["info"] = []
if not data["seeds"]:
msg = "Request contained no seeds!"
body_logger.error(msg)
body_logger.info(f"Responding with error PRECONDITION_FAILED.")
cleave_response.setdefault("errors", []).append(msg)
return cleave_response, HTTPStatus.PRECONDITION_FAILED # code 412
# Extract this body's edges from the complete merge graph
with Timer() as timer:
try:
session = default_dvid_session(appname='cleave-server', user=user)
mutid, supervoxels, edges, scores = MERGE_GRAPH.extract_edges(*instance_info, body_id, find_missing_edges, session=session, logger=body_logger)
except requests.HTTPError as ex:
status_name = str(HTTPStatus(ex.response.status_code)).split('.')[1]
if ex.response.status_code == HTTPStatus.NOT_FOUND:
msg = f"Body not found: {body_id}"
else:
msg = f"Received error from DVID: {status_name}"
body_logger.error(msg)
body_logger.info(f"Responding with error {status_name}.")
cleave_response.setdefault("errors", []).append(msg)
return cleave_response, ex.response.status_code
body_logger.info(f"Extracting body graph (mutid={mutid}) took {timer.timedelta}")
unexpected_seeds = set(chain(*seeds.values())) - set(supervoxels)
if unexpected_seeds:
msg = f"Request contained seeds that do not belong to body: {sorted(unexpected_seeds)}"
body_logger.error(msg)
body_logger.info("Responding with error PRECONDITION_FAILED.")
cleave_response.setdefault("errors", []).append(msg)
return cleave_response, HTTPStatus.PRECONDITION_FAILED # code 412
try:
# Perform the cleave computation
with Timer() as timer:
results = cleave(edges, scores, seeds, supervoxels, method=method)
except InvalidCleaveMethodError as ex:
body_logger.error(str(ex))
body_logger.info("Responding with error BAD_REQUEST.")
cleave_response.setdefault("errors", []).append(str(ex))
return cleave_response, HTTPStatus.BAD_REQUEST # code 400
body_logger.info(f"Computing cleave took {timer.timedelta}")
# Convert assignments to JSON
df = pd.DataFrame({'node': supervoxels, 'label': results.output_labels})
df.sort_values('node', inplace=True)
for label, group in df.groupby('label'):
cleave_response["assignments"][str(label)] = group['node'].tolist()
if results.disconnected_components:
msg = (f"Cleave result contains non-contiguous objects for seeds: "
f"{sorted(results.disconnected_components)}")
body_logger.warning(msg)
cleave_response["info"].append(msg)
if results.contains_unlabeled_components:
num_unlabeled = len(cleave_response["assignments"]["0"])
msg = f"Cleave result is not complete. {num_unlabeled} supervoxels remain unassigned."
body_logger.error(msg)
body_logger.warning(msg)
cleave_response["warnings"].append(msg)
body_logger.info("Sending cleave results")
return ( cleave_response, HTTPStatus.OK )