svSlicer is a tool for mapping 3D simulation results from SimVascular software to a centerline. The quantities of interest, namely "pressure" and "velocity" area extracted from the 3D results, sliced at each centerline point, and integrated over the respective area of the slice to derive scaler quantities "pressure" and "flow".
Modified version of slice extractor from https://github.com/lucapegolotti/cardiovascular/tree/master/slice-vtu-results-centerlines/c++
VTK is required for svSlicer. You can either install it with a package
manager (e.g. brew install vtk on macOS, apt install libvtk9-dev on Ubuntu) or build it using:
mkdir -p ./vtk/src
git clone --recursive https://gitlab.kitware.com/vtk/vtk.git ./vtk/src
mkdir -p ./vtk/build
cmake -DBUILD_SHARED_LIBS:BOOL=ON \
-DCMAKE_BUILD_TYPE=Release \
-DCMAKE_CXX_COMPILER=/share/software/user/open/gcc/12.1.0/bin/g++ \
-DCMAKE_C_COMPILER=/share/software/user/open/gcc/12.1.0/bin/gcc \
-S ./vtk/src -B ./vtk/build/
cmake --build ./vtk/build/ -- -j4
You can build svSlicer with the following commands:
mkdir Release
cd Release
cmake -DCMAKE_BUILD_TYPE=Release ..
cmake --build .
cmake --install .For macOS, LLVM is required. It can be installed using
brew install llvm.
OMP_NUM_THREADS=<NUM_THREADS> svslicer <path/to/3d_result.vtu> <path/to/centerline.vtp> <path/to/output_file.vtp>Runtime statistics for a case with 3619 slices of a 3D mesh with 1.6 million cells for 200 timesteps using two 12-core Intel Xeon Gold 5118 CPUs.
| Number of parallel processes | Total runtime [s] | Slices per second [1/s] |
|---|---|---|
| 1 | 1231 | 3.0 |
| 2 | 653 | 5.6 |
| 4 | 373 | 9.9 |
| 8 | 229 | 16.4 |
| 12 | 191 | 19.7 |
| 16 | 179 | 21.1 |
| 20 | 183 | 21.5 |
| 24 | 185 | 20.5 |
clang-format is used to ensure consistent formatting throughout the code. Use
the following code to automatically apply the right format to your code changes:
clang-format -i --style=file:.clang_format src/main.cpp
This format is also enforced for pull requests to be allowed.