神经元数据处理工具（npu）

图像与 SWC 需同名，例如 1.tif / 1.swc。

安装

pip install neuron-process-utils
# 开发：
# pip install -e .

距离类型（--dist-type / -t）

后续新类型：在 npu/distance.py 的 DIST_TYPE_REGISTRY 注册即可。

命令

# 处理 SWC：orphan parent → -1，并从 1 连续编号
npu_swc_process -i ./CWMBS/swc
npu_swc_process -i ./CWMBS/swc -o ./CWMBS/process_swc

# SWC → mask（可用 -r 覆盖全部节点半径）
npu_swc_to_mask -i ./CWMBS/img -s ./CWMBS/process_swc -o ./CWMBS/process_mask
npu_swc_to_mask -i ./CWMBS/img -s ./CWMBS/process_swc -o ./CWMBS/process_mask -r 1

# SWC → dist（默认 soft_centerline，中间 mask 自动 r=1）
npu_swc_to_dist -i ./CWMBS/img -s ./CWMBS/process_swc -o ./CWMBS/process_dist
npu_swc_to_dist -i ./CWMBS/img -s ./CWMBS/process_swc -o ./CWMBS/process_dist -t soft_centerline --lns 10
npu_swc_to_dist -i ./CWMBS/img -s ./CWMBS/process_swc -o ./CWMBS/process_dist -t sironi --lns 10 --sironi-a 6
npu_swc_to_dist -i ./CWMBS/img -s ./CWMBS/process_swc -o ./CWMBS/process_dist -t pointtree --kernel-len 3
npu_swc_to_dist -i ./CWMBS/img -s ./CWMBS/process_swc -o ./CWMBS/process_dist -t pointtree_gaussian --sigma 3
npu_swc_to_dist -i ./CWMBS/img -s ./CWMBS/process_swc -o ./CWMBS/process_dist -t inside_edt
npu_swc_to_dist -i ./CWMBS/img -s ./CWMBS/process_swc -o ./CWMBS/process_dist -t inside_edt --normalize --uint8

# Mask → dist
npu_mask_to_dist -m ./CWMBS/process_mask -o ./CWMBS/process_dist
npu_mask_to_dist -m ./CWMBS/process_mask -o ./CWMBS/process_dist -t soft_centerline --lns 10
npu_mask_to_dist -m ./CWMBS/process_mask -o ./CWMBS/process_dist -t inside_edt --normalize

# nnUNet 概率图 .npz → tif
npu_nnunet_prob_to_tif -i ./preds -o ./preds_tif --uint8 -c 1

--uint8（旧旗标 --s 仍可用）将结果缩放到 [0,255] 存 uint8；默认 float32。