def process_body(body_id):
output_path = f'{output_dir}/{body_id}.{options["format"]}'
if skip_existing and os.path.exists(output_path):
return (body_id, 0, 0.0, 0, 'skipped', 0)
with resource_mgr_client.access_context(input_config["server"],
True, 1, 0):
try:
mutid = fetch_mutation_id(server, uuid, seg_instance,
body_id)
except HTTPError:
# FIXME: Better to log the exception strings to a file
return (body_id, 0, 0.0, 0, 'error-mutid', 0)
try:
tar_bytes = fetch_tarfile(server, uuid, tsv_instance,
body_id)
except HTTPError:
# FIXME: Better to log the exception strings to a file
return (body_id, 0, 0.0, 0, 'error-fetch', mutid)
try:
vertex_count, fraction, orig_vertices = \
decimate_existing_mesh( server, uuid, tsv_instance, body_id,
options["decimation"], options["max-vertices"], options["rescale"], options["format"],
output_path,
tar_bytes=tar_bytes )
except:
return (body_id, 0, 0.0, 0, 'error-generate', mutid)
return (body_id, vertex_count, fraction, orig_vertices, 'success',
mutid)
def test_fetch_mutation_id(labelmap_setup):
dvid_server, dvid_repo, _merge_table_path, _mapping_path, _supervoxel_vol = labelmap_setup
instance_info = DvidInstanceInfo(dvid_server, dvid_repo, 'segmentation')
mut_id = fetch_mutation_id(*instance_info, 1)
assert isinstance(mut_id, int)
def _test_extract_edges(labelmap_setup, force_dirty_mapping):
"""
Implementation for testing extract_edges(), starting either with a "clean" mapping
(in which the body column is already correct beforehand),
or a "dirty" mapping (in which the body column is not correct beforehand).
"""
dvid_server, dvid_repo, merge_table_path, mapping_path, _supervoxel_vol = labelmap_setup
instance_info = DvidInstanceInfo(dvid_server, dvid_repo, 'segmentation')
orig_merge_table = load_merge_table(merge_table_path,
mapping_path,
normalize=True)
merge_graph = LabelmapMergeGraph(merge_table_path)
merge_graph.apply_mapping(mapping_path)
if force_dirty_mapping:
# A little white-box manipulation here to ensure that the mapping is dirty
merge_graph.merge_table_df['body'] = np.uint64(0)
merge_graph.mapping[:] = np.uint64(0)
# First test: If nothing has changed in DVID, we get all rows.
# We should be able to repeat this with the same results
# (Make sure the cache is repopulated correctly.)
_mutid, dvid_supervoxels, edges, _scores = merge_graph.extract_edges(
*instance_info, 1)
assert (dvid_supervoxels == [1, 2, 3, 4, 5]).all()
assert (orig_merge_table[['id_a', 'id_b']].values == edges).all().all(), \
f"Original merge table doesn't match fetched:\n{orig_merge_table}\n\n{edges}\n"
# Now change the mapping in DVID and verify it is reflected in the extracted rows.
# For this test, we'll cleave supervoxels [4,5] from the rest of the body.
uuid = post_branch(dvid_server, dvid_repo,
f'extract-rows-test-{force_dirty_mapping}', '')
cleaved_body = post_cleave(dvid_server, uuid, 'segmentation', 1, [4, 5])
cleaved_mutid = fetch_mutation_id(dvid_server, uuid, 'segmentation', 1)
if force_dirty_mapping:
# A little white-box manipulation here to ensure that the mapping is dirty
merge_graph.mapping.loc[2] = 0
merge_graph.merge_table_df['body'].values[0:2] = np.uint64(0)
mutid, dvid_supervoxels, edges, _scores = merge_graph.extract_edges(
dvid_server, uuid, 'segmentation', 1)
assert (dvid_supervoxels == [1, 2, 3]).all()
_cleaved_svs = set([4, 5])
assert (edges == orig_merge_table[[
'id_a', 'id_b'
]].query('id_a not in @_cleaved_svs and id_b not in @_cleaved_svs')
).all().all()
assert mutid == cleaved_mutid, "Expected cached mutation ID to match DVID"
cleaved_mutid = fetch_mutation_id(dvid_server, uuid, 'segmentation',
cleaved_body)
# Check the other body
mutid, dvid_supervoxels, edges, _scores = merge_graph.extract_edges(
dvid_server, uuid, 'segmentation', cleaved_body)
assert (edges == orig_merge_table[[
'id_a', 'id_b'
]].query('id_a in @_cleaved_svs and id_b in @_cleaved_svs')).all().all()
assert mutid == cleaved_mutid, "Expected cached mutation ID to match DVID"