def test_saving_loading_and_copying_process_for_Attribute_dict():
"""
Checks the saving,loading and copying functionality for an attribute dict
Returns An Assertion Error in case an exception is thrown
-------
"""
try:
ad = AttributeDict(test_p, read_only=False)
ad[1]["b"] = 2
assert "b" in ad[1]
for i in range(100):
ad[i] = {"glia_probability": np.ones((10, 2)).astype(np.uint8)}
start = time.time()
ad.push()
logging.debug("Saving AttributeDict took %0.4f." %
(time.time() - start))
logging.debug("AttributeDict file size:\t%0.2f kB" %
(os.path.getsize(test_p) / 1.e3))
del ad
logging.info('PASSED: test_saving_process_for_Attribute_dict')
except Exception as e:
logging.warning('FAILED: test_saving_process_for_Attribute_dict. ' +
str(e))
raise AssertionError
try:
start = time.time()
ad = AttributeDict(test_p, read_only=True)
logging.debug("Loading AttributeDict took %0.4f." %
(time.time() - start))
assert len(list(ad.keys())) == 100
assert np.all(
ad[0]["glia_probability"] == np.ones((10, 2)).astype(np.uint8))
ad.update({100: "b"})
assert 100 in ad
start = time.time()
dc_constr = ad.copy_intern()
logging.debug("Copying dict from AttributeDict took %0.4f." %
(time.time() - start))
assert len(list(dc_constr.keys())) == 101
del ad
os.remove(test_p)
logging.info(
'PASSED: test_loading_and_copying_process_for_Attribute_dict')
except Exception as e:
logging.warning(
'FAILED: test_loading_and_copying_process_for_Attribute_dict. ' +
str(e))
raise AssertionError
except EOFError:
break
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([