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dolfin-warp

https://github.com/mgenet/dolfin_warp

Science Score: 67.0%

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    Low similarity (8.4%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: mgenet
  • License: lgpl-3.0
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 808 KB
Statistics
  • Stars: 6
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 3
Created over 2 years ago · Last pushed 8 months ago
Metadata Files
Readme License Citation

README.md

DOI PyPi Version PyPI Downloads

dolfin_warp

A set of FEniCS- and VTK-based python tools for Finite Element Digital Image Correlation/Image Registration/Motion Tracking, basically implementing the method described in [Genet, Stoeck, von Deuster, Lee & Kozerke (2018). Equilibrated Warping: Finite Element Image Registration with Finite Strain Equilibrium Gap Regularization. Medical Image Analysis.] and [Genet (2023). Finite strain formulation of the discrete equilibrium gap principle: application to mechanically consistent regularization for large motion tracking. Comptes Rendus Mécanique.].

The library has notably been used in: * [Genet, Stoeck, von Deuster, Lee & Kozerke (2018). Equilibrated Warping: Finite Element Image Registration with Finite Strain Equilibrium Gap Regularization. Medical Image Analysis.] * [Zou, Xi, Zhao, Koh, Gao, Su, Tan, Allen, Lee, Genet & Zhong (2018). Quantification of Biventricular Strains in Heart Failure With Preserved Ejection Fraction Patient Using Hyperelastic Warping Method. Frontiers in Physiology.] * [Finsberg, Xi, Tan, Zhong, Genet, Sundnes, Lee & Wall (2018). Efficient estimation of personalized biventricular mechanical function employing gradient-based optimization. International Journal for Numerical Methods in Biomedical Engineering.] * [Berberoğlu, Stoeck, Moireau, Kozerke & Genet (2019). Validation of Finite Element Image Registration‐based Cardiac Strain Estimation from Magnetic Resonance Images. PAMM.] * [Finsberg, Xi, Zhao, Tan, Genet, Sundnes, Lee, Zhong & Wall (2019). Computational quantification of patient-specific changes in ventricular dynamics associated with pulmonary hypertension. American Journal of Physiology-Heart and Circulatory Physiology.] * [Lee & Genet (2019). Validation of Equilibrated Warping—Image Registration with Mechanical Regularization—On 3D Ultrasound Images. Functional Imaging and Modeling of the Heart (FIMH). Cham: Springer International Publishing.] * [Škardová, Rambausek, Chabiniok & Genet (2019). Mechanical and Imaging Models-Based Image Registration. VipIMAGE 2019. Cham: Springer International Publishing.] * [Zou, Leng, Xi, Zhao, Koh, Gao, Tan, Tan, Allen, Lee, Genet & Zhong (2020). Three-dimensional biventricular strains in pulmonary arterial hypertension patients using hyperelastic warping. Computer Methods and Programs in Biomedicine.] * [Gusseva, Hussain, Friesen, Moireau, Tandon, Patte, Genet, Hasbani, Greil, Chapelle & Chabiniok (2021). Biomechanical Modeling to Inform Pulmonary Valve Replacement in Tetralogy of Fallot Patients after Complete Repair. Canadian Journal of Cardiology.] * [Berberoğlu, Stoeck, Moireau, Kozerke & Genet (2021). In-silico study of accuracy and precision of left-ventricular strain quantification from 3D tagged MRI. PLOS ONE.] * [Castellanos, Škardová, Bhattaru, Berberoğlu, Greil, Tandon, Dillenbeck, Burkhardt, Hussain, Genet & Chabiniok (2021). Left Ventricular Torsion Obtained Using Equilibrated Warping in Patients with Repaired Tetralogy of Fallot. Pediatric Cardiology.] * [Berberoğlu, Stoeck, Kozerke & Genet (2022). Quantification of left ventricular strain and torsion by joint analysis of 3D tagging and cine MR images. Medical Image Analysis.] * [Patte, Brillet, Fetita, Gille, Bernaudin, Nunes, Chapelle & Genet (2022). Estimation of regional pulmonary compliance in idiopathic pulmonary fibrosis based on personalized lung poromechanical modeling. Journal of Biomechanical Engineering.] * [Laville, Fetita, Gille, Brillet, Nunes, Bernaudin & Genet (2023). Comparison of optimization parametrizations for regional lung compliance estimation using personalized pulmonary poromechanical modeling. Biomechanics and Modeling in Mechanobiology.] * [Genet (2023). Finite strain formulation of the discrete equilibrium gap principle: application to mechanically consistent regularization for large motion tracking. Comptes Rendus Mécanique.] * [Škardová, Hussain, Genet & Chabiniok (2023). Effect of Spatial and Temporal Resolution on the Accuracy of Motion Tracking Using 2D and 3D Cine Cardiac Magnetic Resonance Imaging Data. Functional Imaging and Modeling of the Heart (FIMH) Cham: Springer Nature Switzerland.] * [Peyraut & Genet (2024). Finite strain formulation of the discrete equilibrium gap principle: application to direct parameter estimation from large full-fields measurements. Comptes Rendus Mécanique.]

(If you use it for your own work please let me know!)

Tutorials

Interactive tutorials can be found at https://mgenet.gitlabpages.inria.fr/dolfin_warp-tutorials.

Installation

A working installation of FEniCS (version 2019.1.0; including the dolfin python interface) & VTK (also including python interface) is required to run dolfin_warp. To setup a system, the simplest is to use conda: first install miniconda (note that for Microsoft Windows machines you first need to install WSL, the Windows Subsystem for Linux, and then install miniconda for linux inside the WSL; for Apple MacOS machines with Apple Silicon CPUs, you still need to install the MacOS Intel x8664 version of miniconda), and then install the necessary packages: ``` conda create -y -c conda-forge -n dolfinwarp expat=2.5 fenics=2019.1.0 gnuplot=5.4 matplotlib=3.5 meshio=5.3 mpi4py=3.1.3 numpy=1.23.5 pandas=1.3 pip python=3.10 scipy=1.9 vtk=9.2 conda activate dolfinwarp conda env config vars set CPATH=$CONDAPREFIX/include/vtk-9.2 conda activate dolfinwarp pip install dolfinwarp ```

Owner

  • Name: Martin Genet
  • Login: mgenet
  • Kind: user
  • Location: Paris
  • Company: École Polytechnique

Citation (CITATION.cff) 

cff-version: 1.2.0
authors:
  - family-names: Genet
    given-names: Martin
    orcid: 0000-0003-2204-201X
  - family-names: Patte
    given-names: Cécile
    orcid: 0000-0001-8553-886X
  - family-names: Berberoğlu
    given-names: Ezgi
    orcid: 0000-0002-4607-8845
  - family-names: Álvarez-Barrientos
    given-names: Felipe
    orcid: 0000-0003-4468-7951
  - family-names: Laville
    given-names: Colin
  - family-names: Peyraut
    given-names: Alice
    orcid: 0009-0000-9445-8060
  - family-names: Daby-Seesaram
    given-names: Alexandre
    orcid: 0000-0002-2374-0971
title: "dolfin_warp"
url: https://github.com/mgenet/dolfin_warp
doi: 10.5281/zenodo.8010275

GitHub Events

Total
  • Release event: 1
  • Watch event: 5
  • Delete event: 14
  • Member event: 2
  • Push event: 101
  • Pull request event: 5
  • Create event: 10
Last Year
  • Release event: 1
  • Watch event: 5
  • Delete event: 14
  • Member event: 2
  • Push event: 101
  • Pull request event: 5
  • Create event: 10

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 0
  • Total pull requests: 4
  • Average time to close issues: N/A
  • Average time to close pull requests: 7 minutes
  • Total issue authors: 0
  • Total pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 4
  • Average time to close issues: N/A
  • Average time to close pull requests: 7 minutes
  • Issue authors: 0
  • Pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
Pull Request Authors
  • mgenet (3)
  • fgalvarez1 (1)
Top Labels
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Packages

  • Total packages: 1
  • Total downloads:
    • pypi 103 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 33
  • Total maintainers: 1
pypi.org: dolfin-warp

[![PyPi Version](https://img.shields.io/pypi/v/dolfin-warp.svg?style=flat-square)](https://pypi.org/project/dolfin-warp)

  • Versions: 33
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 103 Last month
Rankings
Dependent packages count: 10.1%
Average: 18.3%
Dependent repos count: 21.6%
Downloads: 23.1%
Maintainers (1)
martin.genet
Last synced: 6 months ago

Dependencies

LEGACY/Docker/dolfin_warp-2017.2.0/Dockerfile docker
  • registry.gitlab.inria.fr/mgenet/dolfin_warp/dolfin_warp-2017.2.0-dev latest build
LEGACY/Docker/dolfin_warp-2017.2.0-dev/Dockerfile docker
  • quay.io/fenicsproject/stable 2017.2.0 build
LEGACY/Docker/dolfin_warp-2019.1.0/Dockerfile docker
  • registry.gitlab.inria.fr/mgenet/dolfin_warp/dolfin_warp-2019.1.0-dev latest build
LEGACY/Docker/dolfin_warp-2019.1.0-dev/Dockerfile docker
  • quay.io/fenicsproject/stable 2019.1.0.r3 build
setup.py pypi
  • dolfin_mech *