so_chunk_paths = args[0]
so_kwargs = args[1]
working_dir = so_kwargs['working_dir']
global_params.wd = working_dir
# TODO: preprocess meshes in case they dont exist and then load mesh dict next to the attribute dict
for p in so_chunk_paths:
# get SV IDs stored in this storage
attr_dc_p = p + "/attr_dict.pkl"
mesh_dc_p = p + "/mesh.pkl"
ad = AttributeDict(attr_dc_p, disable_locking=True)
md = MeshStorage(mesh_dc_p, disable_locking=True)
svixs = list(ad.keys())
# replace SO objects by using rep_coord and IDs stored in the attribute dict
sd = sos_dict_fact(svixs, **so_kwargs)
sos = init_sos(sd)
# compute locations and use already processed meshes
loc_dc_p = p + "/locations.pkl"
loc_dc = CompressedStorage(loc_dc_p, disable_locking=True)
for so in sos:
try:
ix = so.id
if not ix in md.keys():
verts = so.mesh[1].reshape(-1, 3)
else:
verts = md[ix][1].reshape(-1, 3)
if len(verts) == 0:
coords = np.array([
so.rep_coord,
], dtype=np.float32)
try:
args.append(pkl.load(f))
except EOFError:
break
scaling = global_params.config.entries['Dataset']['scaling']
for cc in args:
svixs = list(cc.nodes())
cc_ix = np.min(svixs)
sso = SuperSegmentationObject(cc_ix, version="gliaremoval", nb_cpus=2,
working_dir=global_params.config.working_dir,
create=True, scaling=scaling,
sv_ids=svixs)
so_cc = nx.Graph()
for e in cc.edges():
so_cc.add_edge(sso.get_seg_obj("sv", e[0]),
sso.get_seg_obj("sv", e[1]))
sso._rag = so_cc
sd = sos_dict_fact(svixs)
sos = init_sos(sd)
sso._objects["sv"] = sos
try:
sso.gliasplit(verbose=False)
except Exception as e:
print("\n-------------------------------------\n"
"Splitting of SSV %d failed with %s."
"\n-------------------------------------\n" % (cc_ix, e))
with open(path_out_file, "wb") as f:
pkl.dump("0", f)