# pygeodesic
Python library to compute geodesic distance over a triangular based surface mesh.
A Cython wrapper of the C++ code by [Kirsanov](https://code.google.com/archive/p/geodesic/), which is an implementation of the exact geodesic algorithm for triangular mesh first described by Mitchell, Mount and Papadimitriou in 1987.
`pygeodesic` is similar to other libraries on PyPi (such as [gdist](https://pypi.org/project/gdist/) and [tvb-gdist](https://pypi.org/project/tvb-gdist/)), but:
* provides a wrapper of the GeodesicAlgorithmExact class
* exposes geodesic path (not just geodesic distance)
* licensed under MIT license similar to the orginal Kirsanov C++ code, rather than GPL
A good alternative to `pygeodesic` is [potpourri3d](https://pypi.org/project/potpourri3d/), which uses the *heat method* and *vector heat method* to compute geodesic distance over surfaces and point clouds. However, this library does not currently output the geodesic path on the surface.
## Requirements
A C++ compiler is required if you are not installing one of the precompiled wheels. Although `pygeodesic` is a Cython wrapper, Cython is not required as the cythonized C++ file is also provided.
[VTK](https://pypi.org/project/vtk/) is used for visualisation in the example notebooks.
## Installation
Install from PyPi:
```
pip install pygeodesic
```
Installation from source (from within folder containing `setup.py`):
```
python setup.py install
```
## Usage
Loading pygeodesic:
```python
import pygeodesic.geodesic as geodesic
```
To read the mesh files provided with the original C++ code:
```python
filename = r'data/flat_triangular_mesh.txt'
result = geodesic.read_mesh_from_file(filename)
if result:
points, faces = result
```
To calculate the geodesic distance and path between two points (the *source* and the *target*) on the mesh:
```python
# Initialise the PyGeodesicAlgorithmExact class instance
geoalg = geodesic.PyGeodesicAlgorithmExact(points, faces)
# Define the source and target point ids with respect to the points array
sourceIndex = 25
targetIndex = 97
# Compute the geodesic distance and the path
distance, path = geoalg.geodesicDistance(sourceIndex, targetIndex)
```
To calculate the geodesic distances from a single point (the source point) to all other points on the mesh:
```python
source_indices = np.array([25])
target_indices = None
distances, best_source = geoalg.geodesicDistances(source_indices, target_indices)
```
To calculate the geodesic distances from two source points to 3 target points:
```python
source_indices = np.array([25,100])
target_indices = np.array([0,10,50])
distances, best_source = geoalg.geodesicDistances(source_indices, target_indices)
```
For more detail, a Jupyter notebook is provided in the examples folder to show how to use `pygeodesic` to compute geodesic distances and paths.
## Example using the Stanford Bunny
A Jupyter notebook is provided showing how to use `pygeodesic` to calculate the geodesic distance and path using the Stanford Bunny as an example.
<img src="https://github.com/mhogg/pygeodesic/blob/main/images/stanford_bunny_geodesic_path.png?raw=true" height="400"/>
Raw data
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"description": "# pygeodesic\n\nPython library to compute geodesic distance over a triangular based surface mesh.\n\nA Cython wrapper of the C++ code by [Kirsanov](https://code.google.com/archive/p/geodesic/), which is an implementation of the exact geodesic algorithm for triangular mesh first described by Mitchell, Mount and Papadimitriou in 1987.\n\n`pygeodesic` is similar to other libraries on PyPi (such as [gdist](https://pypi.org/project/gdist/) and [tvb-gdist](https://pypi.org/project/tvb-gdist/)), but:\n* provides a wrapper of the GeodesicAlgorithmExact class\n* exposes geodesic path (not just geodesic distance)\n* licensed under MIT license similar to the orginal Kirsanov C++ code, rather than GPL\n\nA good alternative to `pygeodesic` is [potpourri3d](https://pypi.org/project/potpourri3d/), which uses the *heat method* and *vector heat method* to compute geodesic distance over surfaces and point clouds. However, this library does not currently output the geodesic path on the surface.\n\n## Requirements\n\nA C++ compiler is required if you are not installing one of the precompiled wheels. Although `pygeodesic` is a Cython wrapper, Cython is not required as the cythonized C++ file is also provided.\n\n[VTK](https://pypi.org/project/vtk/) is used for visualisation in the example notebooks.\n\n\n## Installation\n\nInstall from PyPi:\n```\npip install pygeodesic\n```\n\nInstallation from source (from within folder containing `setup.py`):\n```\npython setup.py install\n```\n\n## Usage\n\nLoading pygeodesic:\n```python\nimport pygeodesic.geodesic as geodesic\n```\n\nTo read the mesh files provided with the original C++ code:\n```python\nfilename = r'data/flat_triangular_mesh.txt'\nresult = geodesic.read_mesh_from_file(filename)\nif result:\n points, faces = result\n```\n\nTo calculate the geodesic distance and path between two points (the *source* and the *target*) on the mesh:\n```python\n# Initialise the PyGeodesicAlgorithmExact class instance\ngeoalg = geodesic.PyGeodesicAlgorithmExact(points, faces)\n\n# Define the source and target point ids with respect to the points array\nsourceIndex = 25\ntargetIndex = 97\n\n# Compute the geodesic distance and the path\ndistance, path = geoalg.geodesicDistance(sourceIndex, targetIndex)\n```\n\nTo calculate the geodesic distances from a single point (the source point) to all other points on the mesh:\n```python\nsource_indices = np.array([25])\ntarget_indices = None\ndistances, best_source = geoalg.geodesicDistances(source_indices, target_indices)\n```\n\nTo calculate the geodesic distances from two source points to 3 target points:\n```python\nsource_indices = np.array([25,100]) \ntarget_indices = np.array([0,10,50])\ndistances, best_source = geoalg.geodesicDistances(source_indices, target_indices)\n```\n\nFor more detail, a Jupyter notebook is provided in the examples folder to show how to use `pygeodesic` to compute geodesic distances and paths.\n\n## Example using the Stanford Bunny\n\nA Jupyter notebook is provided showing how to use `pygeodesic` to calculate the geodesic distance and path using the Stanford Bunny as an example.\n\n<img src=\"https://github.com/mhogg/pygeodesic/blob/main/images/stanford_bunny_geodesic_path.png?raw=true\" height=\"400\"/>\n\n\n\n",
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