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update: memory efficient to_npz #30

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Merged
huangziwei merged 2 commits into from
Jan 26, 2026
Merged

update: memory efficient to_npz #30

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update: memory efficient to_npz
jonathanoesterle Jan 26, 2026
453f84c
update: memory efficient to_npz
jonathanoesterle Jan 26, 2026
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43 changes: 35 additions & 8 deletions skeliner/io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -355,8 +355,6 @@ def to_npz(
if not path.suffix:
path = path.with_suffix(".npz")

c = {} if not compress else {"compress": True}

if cache_kdtree:
skeleton._ensure_nodes_kdtree()
skeleton._ensure_node_neighbors()
Expand All @@ -367,11 +365,39 @@ def to_npz(
# ragged node2verts → index + offset
if skeleton.node2verts is not None:
n2v_idx = np.concatenate(skeleton.node2verts)
n2v_off = np.cumsum([0, *map(len, skeleton.node2verts)]).astype(np.int64)
n2v_off = np.cumsum([0, *map(len, skeleton.node2verts)])

# Determine smallest dtype for n2v_idx
if len(n2v_idx) > 0:
idx_min, idx_max = n2v_idx.min(), n2v_idx.max()
if idx_min >= 0 and idx_max <= np.iinfo(np.uint16).max:
n2v_idx = n2v_idx.astype(np.uint16)
elif idx_min < 0 and idx_min >= np.iinfo(np.int16).min and idx_max <= np.iinfo(np.int16).max:
n2v_idx = n2v_idx.astype(np.int16)
elif idx_min >= 0 and idx_max <= np.iinfo(np.uint32).max:
n2v_idx = n2v_idx.astype(np.uint32)
elif idx_min < 0 and idx_min >= np.iinfo(np.int32).min and idx_max <= np.iinfo(np.int32).max:
n2v_idx = n2v_idx.astype(np.int32)
else:
n2v_idx = n2v_idx.astype(np.int64)
else:
n2v_idx = n2v_idx.astype(np.uint16)

# Determine smallest dtype for n2v_off
off_min, off_max = n2v_off.min(), n2v_off.max()
if off_min >= 0 and off_max <= np.iinfo(np.uint16).max:
n2v_off = n2v_off.astype(np.uint16)
elif off_min < 0 and off_min >= np.iinfo(np.int16).min and off_max <= np.iinfo(np.int16).max:
n2v_off = n2v_off.astype(np.int16)
elif off_min >= 0 and off_max <= np.iinfo(np.uint32).max:
n2v_off = n2v_off.astype(np.uint32)
elif off_min < 0 and off_min >= np.iinfo(np.int32).min and off_max <= np.iinfo(np.int32).max:
n2v_off = n2v_off.astype(np.int32)
else:
n2v_off = n2v_off.astype(np.int64)
else:
n2v_idx = np.array([], dtype=np.int64)
n2v_off = np.array([0], dtype=np.int64)

n2v_idx = np.array([], dtype=np.uint16)
n2v_off = np.array([0], dtype=np.uint16)
# ----------- NEW: persist the metadata dict -------------------------
# We wrap it in a 0-D object array because np.savez can only store
# ndarrays — this keeps the archive a single *.npz* with no sidecars.
Expand All @@ -397,7 +423,9 @@ def to_npz(
tree_payload["neighbors_idx"] = data.astype(np.int64, copy=False)
tree_payload["neighbors_off"] = offsets.astype(np.int64, copy=False)

np.savez(
save_fun = np.savez_compressed if compress else np.savez

save_fun(
path,
nodes=skeleton.nodes,
edges=skeleton.edges,
Expand All @@ -416,7 +444,6 @@ def to_npz(
**extra,
**meta,
**tree_payload,
**c,
)


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