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vtuinterface

Python-Interface for reading and writing VTU files and exactracting time series data from PVD/VTU files

https://github.com/joergbuchwald/vtuinterface

Science Score: 77.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: joss.theoj.org, zenodo.org
  • ✓
    Committers with academic emails
    1 of 5 committers (20.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (17.2%) to scientific vocabulary

Keywords

julia pvd pvd-files python series-data timesteps vtk vtu vtu-files
Last synced: 6 months ago · JSON representation ·

Repository

Python-Interface for reading and writing VTU files and exactracting time series data from PVD/VTU files

Basic Info
  • Host: GitHub
  • Owner: joergbuchwald
  • License: bsd-3-clause
  • Language: Jupyter Notebook
  • Default Branch: master
  • Homepage:
  • Size: 12.6 MB
Statistics
  • Stars: 16
  • Watchers: 1
  • Forks: 9
  • Open Issues: 3
  • Releases: 9
Topics
julia pvd pvd-files python series-data timesteps vtk vtu vtu-files
Created over 5 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog Contributing License Citation Authors

README.md

DOI VTUinterface codecov DOI

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:

IMAGE ALT TEXT HERE

0. Installation

Note: VTUinterface requires the vtk wrapper for python. Alternatively, a version based on 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/

2. Quick start

CAUTION: naming style of methods has changed (2021-05-20)

Basic Usage (python)

Although, a python package, VTUinterface is tested to work through PyCall under julia as well:

Basic Usage (julia)

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.

Owner

  • Name: Jörg Buchwald
  • Login: joergbuchwald
  • Kind: user
  • Location: Leipzig
  • Company: UFZ

bio: https://www.researchgate.net/profile/Joerg-Buchwald other gits: - https://gitlab.com/joergbuchwald - https://gitlab.opengeosys.org/joergbuchwald

Citation (CITATION.cff) 

cff-version: 1.1.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Buchwald
    given-names: Jörg
    orcid:  https://orcid.org/0000-0001-5174-3603
title: "VTUinterface"
version: v0.69
date-released: 2017-12-18
doi: 10.21105/joss.03673
license: BSD 3-Clause
repository-code: "https://github.com/joergbuchwald/VTUinterface"

GitHub Events

Total
  • Push event: 1
  • Create event: 1
Last Year
  • Push event: 1
  • Create event: 1

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 205
  • Total Committers: 5
  • Avg Commits per committer: 41.0
  • Development Distribution Score (DDS): 0.117
Past Year
  • Commits: 3
  • Committers: 1
  • Avg Commits per committer: 3.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
joergbuchwald j****d@u****e 181
Dominik Kern d****t@g****m 21
Simon Richter s****r@h****e 1
Christoph Lehmann c****n@u****e 1
Dominik Kern d****1@i****e 1
Committer Domains (Top 20 + Academic)
ufz.de: 2 ifgt.tu-freiberg.de: 1 htwk-leipzig.de: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 11
  • Total pull requests: 17
  • Average time to close issues: 6 days
  • Average time to close pull requests: 4 days
  • Total issue authors: 4
  • Total pull request authors: 4
  • Average comments per issue: 0.64
  • Average comments per pull request: 0.94
  • Merged pull requests: 16
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: less than a minute
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • joergbuchwald (8)
  • bilke (1)
  • rd-conti (1)
  • cpgr (1)
Pull Request Authors
  • joergbuchwald (11)
  • dominik-kern (7)
  • chleh (1)
  • Eqrisi (1)
Top Labels
Issue Labels
enhancement (3)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 146 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 12
  • Total maintainers: 1
pypi.org: vtuinterface
  • Versions: 12
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 146 Last month
Rankings
Dependent packages count: 7.5%
Forks count: 12.1%
Stargazers count: 16.1%
Average: 18.4%
Dependent repos count: 22.5%
Downloads: 34.0%
Maintainers (1)
joergbuchwald
Last synced: 6 months ago

Dependencies

setup.py pypi
  • lxml *
.github/workflows/python-package.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • codecov/codecov-action v1 composite