https://github.com/joergbuchwald/vtuinterface
Python-Interface for reading and writing VTU files and exactracting time series data from PVD/VTU files
https://github.com/joergbuchwald/vtuinterface
julia pvd pvd-files python series-data timesteps vtk vtu vtu-files
Last synced: 4 months ago
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Python-Interface for reading and writing VTU files and exactracting time series data from PVD/VTU files
- Host: GitHub
- URL: https://github.com/joergbuchwald/vtuinterface
- Owner: joergbuchwald
- License: bsd-3-clause
- Created: 2020-07-26T20:32:02.000Z (almost 5 years ago)
- Default Branch: master
- Last Pushed: 2024-11-13T12:31:03.000Z (6 months ago)
- Last Synced: 2024-12-14T02:48:23.350Z (5 months ago)
- Topics: julia, pvd, pvd-files, python, series-data, timesteps, vtk, vtu, vtu-files
- Language: Jupyter Notebook
- Homepage:
- Size: 12.6 MB
- Stars: 16
- Watchers: 3
- Forks: 9
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Citation: CITATION.cff
- Authors: AUTHORS.md
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README
[](https://zenodo.org/badge/latestdoi/282728412) [](https://github.com/joergbuchwald/VTUinterface/actions/workflows/python-package.yml) [](https://codecov.io/gh/joergbuchwald/VTUinterface) [](https://doi.org/10.21105/joss.03673)
# VTUinterface
VTUinterface is a python package for easy accessing VTU/PVD files as outputed by Finite Element software like OpenGeoSys. It uses the VTK python wrapper and linear interpolation between time steps and grid points to access any points in space and time within the simulation domain.
VTUinterface together with ogs6py can be viewed in action here:
[](https://www.youtube.com/watch?v=eihNKjK-I-s)
## 0. Installation
Note: VTUinterface requires the vtk wrapper for python. Alternatively, [a version](https://github.com/joergbuchwald/VTUinterface/tree/meshio) based on [MESHIO](https://github.com/nschloe/meshio) is also under development.
clone the repository and use pip to install the package
```shell
# pip install [--user] https://github.com/joergbuchwald/VTUinterface/archive/refs/heads/master.zip
```
## 1. Documentation for VTUinterface
You can find the documentation under [https://joergbuchwald.github.io/VTUinterface-doc/](https://joergbuchwald.github.io/VTUinterface-doc/)
## 2. Quick start
## CAUTION: naming style of methods has changed (2021-05-20)
[Basic Usage (python)](https://github.com/joergbuchwald/VTUinterface/blob/master/README_python.md)
Although, a python package, VTUinterface is tested to work through PyCall under julia as well:
[Basic Usage (julia)](https://github.com/joergbuchwald/VTUinterface/blob/master/README_julia.md)
Unittests can be run via
```shell
# python tests/test_vtuinterface.py
```
from the project root directory.
## 3. FAQ/Troubleshooting
Installation:
- If the vtk whell can't be found on PyPI you can checkout https://github.com/pyvista/pyvista/discussions/2064 for unofficial wheels.
As the input data is triangulated with QHull for the linear interpolation it might fail at boundaries or if a wrong input dimension is given.
Possible solutions:
- In order for interpolation to work correctly providing the correct dimension (set via `dim` keyword) of the problem is crucial.
- As the `dim` keyword specifies also the coordinates to use, VTUinterface assumes that `dim=1` refers to the x coordinate and `dim=2` implies that the problem lies in the xy-plane by default. This can be changed by specifying `one_d_axis` for one dimension or `two_d_planenormal` for two dimensions.
- For some meshes it might help to adjust the number of points taken into account by the triangulation, which can be done using the `nneighbors` keyword. Default value is 20.
- Especially along boundaries, linear interpolation with the QHULL method often fails, this can be resolved by using nearest neighbor interpolation.
- Alternatively, you can change now the `interpolation_backend` from scipy to vtk and try out different interpolation kernels.