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refactor: upd whole brain routines #53

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Feb 9, 2024
Merged

refactor: upd whole brain routines #53

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17 changes: 0 additions & 17 deletions src/deep_neurographs/intake.py
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Original file line number Diff line number Diff line change
Expand Up @@ -81,7 +81,6 @@ def build_neurograph_from_gcs_zips(
img_path=None,
min_size=MIN_SIZE,
n_proposals_per_leaf=N_PROPOSALS_PER_LEAF,
search_radius=SEARCH_RADIUS,
prune=PRUNE,
prune_depth=PRUNE_DEPTH,
optimize_proposals=OPTIMIZE_PROPOSALS,
Expand All @@ -106,9 +105,6 @@ def build_neurograph_from_gcs_zips(
n_proposals_per_leaf : int, optional
Number of edge proposals generated from each leaf node in an swc file.
The default is the global variable "N_PROPOSALS_PER_LEAF".
search_radius : float, optional
Maximum Euclidean length of an edge proposal. The default is the
global variable "SEARCH_RADIUS".
prune : bool, optional
Indication of whether to prune short branches. The default is the
global variable "PRUNE".
Expand Down Expand Up @@ -152,19 +148,6 @@ def build_neurograph_from_gcs_zips(
t, unit = utils.time_writer(time() - t0)
print(f"Module Runtime(): {round(t, 4)} {unit} \n")

# Generate proposals
if search_radius > 0:
print("Generate Edge Proposals...")
t0 = time()
neurograph.generate_proposals(
search_radius, n_proposals_per_leaf=n_proposals_per_leaf
)
t, unit = utils.time_writer(time() - t0)
print(
"# proposals:",
utils.reformat_number(len(neurograph.mutable_edges)),
)

t, unit = utils.time_writer(time() - total_runtime)
print(f"Total Runtime: {round(t, 4)} {unit}")
print(f"Memory Consumption: {round(utils.get_memory_usage(), 4)} GBs")
Expand Down
8 changes: 6 additions & 2 deletions src/deep_neurographs/neurograph.py
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Original file line number Diff line number Diff line change
Expand Up @@ -116,9 +116,10 @@ def __add_nodes(self, nodes, key, node_ids, cur_id, swc_id):
node_ids[i] = cur_id
self.add_node(
node_ids[i],
xyz=nodes[key][i]["xyz"],
proposals=set(),
radius=nodes[key][i]["radius"],
swc_id=swc_id,
xyz=nodes[key][i]["xyz"],
)
if key == "leafs":
self.leafs.add(cur_id)
Expand Down Expand Up @@ -173,6 +174,8 @@ def generate_proposals(
# Add edge
edge = frozenset((leaf, node))
self.proposals[edge] = {"xyz": np.array([xyz_leaf, xyz])}
self.nodes[node]["proposals"].add(leaf)
self.nodes[leaf]["proposals"].add(node)

# Check whether to optimization proposals
if optimize:
Expand Down Expand Up @@ -264,9 +267,10 @@ def split_edge(self, edge, attrs, idx):
new_node = len(self.nodes) + 1
self.add_node(
new_node,
xyz=tuple(attrs["xyz"][idx]),
proposals=set(),
radius=attrs["radius"][idx],
swc_id=attrs["swc_id"],
xyz=tuple(attrs["xyz"][idx]),
)
self.__add_edge((i, new_node), attrs, np.arange(0, idx + 1))
self.__add_edge(
Expand Down
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