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https://github.com/cns-iu/hra-glb-preprocessor
Make meshes manifold and filling holes. Generate OFF file for a single mesh from GLB
https://github.com/cns-iu/hra-glb-preprocessor
Last synced: about 2 months ago
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Make meshes manifold and filling holes. Generate OFF file for a single mesh from GLB
- Host: GitHub
- URL: https://github.com/cns-iu/hra-glb-preprocessor
- Owner: cns-iu
- Created: 2024-04-29T22:09:07.000Z (9 months ago)
- Default Branch: main
- Last Pushed: 2024-08-22T14:53:56.000Z (5 months ago)
- Last Synced: 2024-08-23T15:44:34.493Z (5 months ago)
- Language: Python
- Size: 227 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# hra-glb-preprocessor
**Version:** 1.0.0
**Release date:** 15 June 2024
## Quick Start
### Via Docker
Install Docker and run `./docker-run.sh`.
### Via Ubuntu / local unix machine
First install all system packages in [system-packages.txt](./system-packages.txt):
```bash
sudo apt install `cat system-packages.txt`
```
Then you can run the pipeline with:
```bash
./logged-run.sh
```
### Output
In both cases a `dist` directory will be created that contains the processed off and glb models, plus a `log.txt` with debugging information as needed.
## Overview:
hra-glb-preprocessor project includes:
1. Preprocess (fix non-manifold meshes and filling holes) 3D models using both Blender Python API (Stage 1) and CGAL (Stage 2). There are two options: preprocess one single GLB file or preprocess all the GLB files in one directory;
2. Generate OFF files for all the GLB files in one directory if needed.
## Installation Instructions
For Stage 1:
1. Install Blender (**Please install Blender 4.1 or lower**)
- Ubuntu:
1. Please follow instructions at https://docs.blender.org/manual/en/latest/getting_started/installing/linux.html.
2. Add blender to path: https://docs.blender.org/manual/en/latest/advanced/command_line/launch/linux.html
- MacOS:
1. Please follow instructions at https://docs.blender.org/manual/en/latest/getting_started/installing/macos.html
2. Add blender to path: https://docs.blender.org/manual/en/latest/advanced/command_line/launch/macos.html
- Windows:
1. Please follow instructions at https://docs.blender.org/manual/en/latest/getting_started/installing/windows.html
2. Add blender to path:
1. Find the directory where Blender is installed, e.g., [C:\Program Files\Blender Foundation\Blender\blender.exe]()
2. Add both [C:\Program Files\Blender Foundation\Blender\blender.exe](), [C:\Program Files\Blender Foundation\Blender]() (Please replace the two paths using your blender installation path) to environment variable. Please see https://www.computerhope.com/issues/ch000549.htm if you are not sure how to add environment variables on Windows.
3. Restart the cmd or powershell.
4. Test by entering "blender" in cmd. If Blender is started automatically, the environment variables are successfully added.
2. Install Pandas in Blender Python
- Linux & MacOS & Windows
```bash
blender --background --python install_package.py
```
For Stage 2, install C++ libraries and dependencies as well as Python packages:
3. CMake
```bash
sudo apt-get install build-essential libssl-dev
cd /tmp
wget https://github.com/Kitware/CMake/releases/download/v3.20.0/cmake-3.20.0.tar.gz
tar -zxvf cmake-3.20.0.tar.gz
cd cmake-3.20.0
./bootstrap
make
sudo make install
```
4. Boost
```bash
sudo apt-get update
sudo apt-get install libboost-all-dev
```
5. GMP
```bash
sudo apt-get install libgmp-dev
```
6. MPFR
```bash
sudo apt-get install libmpfr-dev
```
7. CGAL
```bash
sudo apt-get install libcgal-dev
```
8. Eigen3
```bash
sudo apt install libeigen3-dev
```
9. cpprestsdk
```bash
sudo apt-get install libcpprest-dev
```
10. pygltflib
```bash
pip install pygltflib
```
## Compilation
1. Change directory to mesh_processing_cgal
```bash
cd mesh_processing_cgal
```
2. Compile the code using CMake:
```bash
mkdir build
cd build
cmake ..
make
```
## Usage
Stage 1:
1. Change directory to mesh_processing_blender
```bash
cd mesh_processing_blender
```
2. To pre-process a single model, run glb_preprocessor.py by specifying input_glb_path and output_glb_path
```bash
python3 glb_preprocessor.py input_glb_path output_glb_path
```
e.g.,
```bash
python3 glb_preprocessor.py ../model/3d-vh-f-blood-vasculature.glb ../output/3d-vh-f-blood-vasculature.glb
```
3. Download and pre-process all organ models and generate OFF models in Stage 1.
```bash
python3 glb_preprocessor_all_organs.py --url url --downloaded_dir downloaded_dir --output_glb_model_dir preprocessed_glb_model_dir
```
There are three arguments:
- **url** is the endpoint to download all the latest reference organ models; the default value is https://apps.humanatlas.io/api/v1/reference-organs.
- **downloaded_dir** is the directory to cache all the models; the default value is downloaded_organs/.
- **output_glb_model_dir** is the output diretory to store all the preprocessed GLB models; the default value is ../all_preprocessed_glb_models/.
e.g.,
```bash
python3 glb_preprocessor_all_organs.py --url https://apps.humanatlas.io/api/v1/reference-organs --downloaded_dir downloaded_folder/ --output_glb_model_dir all_preprocessed_glb_models/ --output_off_model_dir all_preprocessed_off_models/
```
Stage 2:
4. Change directory to mesh_processing_cgal
```bash
cd mesh_processing_cgal
```
5. Process the preprocessed models from Stage 1 using CGAL and generate OFF models
```bash
python3 all_organ_preprocessor_cgal.py --preproceesed_models_stage_1 dir_models_stage_1 --output_off_model_dir output_off_model_dir
```
There are two arguments:
- **preprocessed_models_stage_1** is the diretory of all the preprocessed GLB models from Stage 1; the default value is ../all_preprocessed_glb_models/.
- **output_off_model_dir** is the output directory to store all the preprocessed OFF models, which are generated based on the GLB models; the default value is all_preprocessed_off_models_cgal/.