Skeletonization

MASCAF supports three ways to obtain a skeleton.

Option 1: Internal CGAL integration

MASCAF includes native CGAL operations:

• repair(mesh → mesh)

• simplify(mesh → mesh)

• skeletonize(mesh → .polylines.txt)

The C++ project lives in cpp/ and the Python interface lives in mascaf.cgal.

Windows setup

1. Install Visual Studio or Build Tools for Visual Studio with C++ support.

2. Install CMake and make sure cmake is on PATH.

3. Install vcpkg and set the VCPKG_ROOT environment variable.

4. Open a terminal where your compiler environment is available (e.g., Visual Studio Developer Command Prompt).

5. Configure the native project from the repo root:

   cmake -S cpp -B cpp/build -DCMAKE_TOOLCHAIN_FILE="%VCPKG_ROOT%/scripts/buildsystems/vcpkg.cmake"
   

6. Build the executables:

   cmake --build cpp/build --config Release
   

7. Confirm that mesh_repair.exe, mesh_simplify.exe, and mesh_skeletonize.exe exist in the build output.

Linux and macOS setup

1. Install a C++17-capable compiler toolchain.

2. Install CMake.

3. Install vcpkg and export VCPKG_ROOT.

4. Configure from the repo root:

   cmake -S cpp -B cpp/build -DCMAKE_TOOLCHAIN_FILE="$VCPKG_ROOT/scripts/buildsystems/vcpkg.cmake"
   

5. Build:

   cmake --build cpp/build --config Release
   

6. Confirm mesh_repair, mesh_simplify, and mesh_skeletonize exist in the build output.

Python build orchestration

MASCAF provides helpers to drive the build from Python:

from mascaf import CGALBuilder, CGALConfig

config = CGALConfig(build_dir="cpp/build")
builder = CGALBuilder(config)

builder.run_configure()
builder.run_build(config="Release")

Running CGAL operations from Python

from mascaf import CGALConfig, CGALOperator

config = CGALConfig(build_dir="cpp/build")
ops = CGALOperator(config=config)

ops.skeletonize(
    "neuron.obj",
    "neuron.polylines.txt",
    quality_speed_tradeoff=0.5,
    medially_centered_speed_tradeoff=5.0,
)

Shell usage

The skeletonization executable accepts:

mesh_skeletonize <input.obj> <output.polylines.txt> [w_H] [w_M]

where w_H is quality_speed_tradeoff and w_M is medially_centered_speed_tradeoff.

Example:

mesh_skeletonize neuron.obj neuron.polylines.txt 0.5 5.0

Option 2: CGAL Lab

The CGAL distribution includes a demo application (CGAL Lab) for interactive skeletonization.

1. Download CGAL Lab 6.1.

2. Open CGAL Lab and load your mesh.

3. Run Operations → Triangulated Surface Mesh Skeletonization → Mean Curvature Skeleton (Advanced).

4. Export the result as a polylines text file.

Option 3: Any compatible tool

Any external tool that produces a MASCAF-compatible polylines file works:

N x1 y1 z1 x2 y2 z2 ... xN yN zN

One line per branch, starting with the number of points on that line.

Troubleshooting

• Executable not found — Build the native cpp/ project first and confirm the configuration (Release/Debug) matches what you built.

• VCPKG_ROOT is not set — Export the environment variable before invoking CMake or CGALBuilder.

• CMake cannot find CGAL or Eigen — Confirm you configured with the vcpkg toolchain file and that cpp/vcpkg.json dependencies were resolved.

• Skeletonization fails on the mesh — The CGAL path expects a closed triangle mesh.

• You already have a skeleton — Skip CGAL entirely and load with from_txt().