.gitignore

 *.pyc
 *.kdev4*
+.spyproject
+.DS_Store
+build
+dist
+*.egg-info
+.vscode

.gitlab-ci.yml

+stages:
+  - test
+  - deploy
+
+tests-on-ubuntu-20.04-with-apt: # MG20230608: This leads to seg fault while manipulating vtk objects inside cpp fenics expressions… # MG20241020: I think the mesh reader fails…
+  stage: test
+  when: manual
+  tags:
+    - ci.inria.fr
+    - large
+  image: ubuntu:20.04
+  script:
+    - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt upgrade -y
+    - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt install -y build-essential git gnuplot python3-matplotlib python3-numpy python3-pandas python3-pip python-is-python3 # MG20220814: environment variables are needed to prevent tzdata installation hanging while waiting timezone info, cf. https://anonoz.github.io/tech/2020/04/24/docker-build-stuck-tzdata.html
+    - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt install -y software-properties-common; add-apt-repository -y ppa:fenics-packages/fenics; apt update; apt install -y fenics; export DISPLAY=0:0
+#     - apt update; apt install -y libopenblas-base; export OMP_NUM_THREADS="1" # MG20221201: This seems to fail in Ubuntu 20.04
+    - apt update; apt install -y libvtk7-dev python3-vtk7; export CPATH="/usr/include/vtk-7.1":$CPATH
+    - apt update; apt install -y libgl1-mesa-dev libglu1-mesa-dev libxcursor-dev libxft-dev libxinerama1 gcc-multilib xvfb gmsh; pip install gmsh
+    - apt update; apt install -y python3-h5py; pip install meshio; pip install numpy==1.23.5 # MG20220814: meshio needs updated numpy apparently # MG20230103: apparently numpy >= 1.24 does not work anymore with the old version of pandas (and probably other stuff) present in Ubuntu 20.04 apt repo, cf. https://stackoverflow.com/a/74975994
+    - pip install git+https://gitlab.inria.fr/mgenet/myPythonLibrary.git git+https://gitlab.inria.fr/mgenet/myVTKPythonLibrary.git git+https://gitlab.inria.fr/mgenet/vtkpython_cbl.git git+https://gitlab.inria.fr/mgenet/dolfin_mech.git
+    - cd Tests; ln -s ../dolfin_warp; make
+
+tests-on-ubuntu-22.04-with-apt: # MG20230608: This leads to seg fault while manipulating vtk objects inside cpp fenics expressions… # MG20241020: I think the image reader fails…
+  stage: test
+  when: manual
+  tags:
+    - ci.inria.fr
+    - large
+  image: ubuntu:22.04
+  script:
+    - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt upgrade -y
+    - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt install -y build-essential git gnuplot python3-matplotlib python3-numpy python3-pandas python3-pip python-is-python3 # MG20220814: environment variables are needed to prevent tzdata installation hanging while waiting timezone info, cf. https://anonoz.github.io/tech/2020/04/24/docker-build-stuck-tzdata.html
+    - apt update; apt install -y software-properties-common; add-apt-repository -y ppa:fenics-packages/fenics; apt update; apt install -y fenics; export DISPLAY=0:0
+    - apt update; apt install -y libopenblas-base; export OMP_NUM_THREADS="1"
+    - apt update; apt install -y libvtk9-dev python3-vtk9; export CPATH="/usr/include/vtk-9.1":$CPATH
+    - apt update; apt install -y libgl1-mesa-dev libglu1-mesa-dev libxcursor-dev libxft-dev libxinerama1 gcc-multilib xvfb gmsh; pip install gmsh
+    - apt update; apt install -y python3-h5py; pip install meshio; pip install numpy==1.24.4 # MG20220814: meshio needs updated numpy apparently # MG20230103: apparently numpy >= 1.25 does not work with FEniCS
+    - pip install git+https://gitlab.inria.fr/mgenet/myPythonLibrary.git git+https://gitlab.inria.fr/mgenet/myVTKPythonLibrary.git git+https://gitlab.inria.fr/mgenet/vtkpython_cbl.git git+https://gitlab.inria.fr/mgenet/dolfin_mech.git
+    - cd Tests; ln -s ../dolfin_warp; make
+
+tests-on-ubuntu-24.04-with-apt: # MG 20241017: apt python version is 3.12, which seems incompatible with numpy 1.24…
+  stage: test
+  when: manual
+  tags:
+    - ci.inria.fr
+    - large
+  image: ubuntu:24.04
+  script:
+    - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt upgrade -y
+    - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt install -y build-essential git gnuplot python3-matplotlib python3-numpy python3-pandas python3-pip python-is-python3 # MG20220814: environment variables are needed to prevent tzdata installation hanging while waiting timezone info, cf. https://anonoz.github.io/tech/2020/04/24/docker-build-stuck-tzdata.html
+    - apt update; apt install -y software-properties-common; add-apt-repository -y ppa:fenics-packages/fenics; apt update; apt install -y fenics; export DISPLAY=0:0
+    # - apt update; apt install -y libopenblas-base; export OMP_NUM_THREADS="1" # MG20241017: Not present in Ubuntu 24.04
+    - apt update; apt install -y libvtk9-dev python3-vtk9; export CPATH="/usr/include/vtk-9.1":$CPATH
+    - apt update; apt install -y libgl1-mesa-dev libglu1-mesa-dev libxcursor-dev libxft-dev libxinerama1 gcc-multilib xvfb gmsh; pip install --break-system-packages gmsh
+    - apt update; apt install -y python3-h5py; pip install --break-system-packages meshio; pip install --break-system-packages numpy==1.24.4 # MG20220814: meshio needs latest numpy apparently # MG20230103: apparently numpy >= 1.25 does not work with FEniCS
+    - pip install --break-system-packages git+https://gitlab.inria.fr/mgenet/myPythonLibrary.git git+https://gitlab.inria.fr/mgenet/myVTKPythonLibrary.git git+https://gitlab.inria.fr/mgenet/vtkpython_cbl.git git+https://gitlab.inria.fr/mgenet/dolfin_mech.git
+    - cd Tests; ln -s ../dolfin_warp; make
+
+tests-on-ubuntu-20.04:
+  stage: test
+  only:
+    - devel
+    - /^devel-.*/
+  tags:
+    - ci.inria.fr
+    - large
+  image: ubuntu:20.04
+  script:
+    - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt upgrade -y
+    - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt install -y build-essential gcc-multilib git gnuplot libgl1-mesa-dev libglu1-mesa-dev libxcursor-dev libxinerama1 libxft-dev wget xvfb
+    # - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt install -y libopenblas-base; export OMP_NUM_THREADS="1" # MG20221201: This seems to fail in Ubuntu 20.04
+    - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh; bash Miniconda3-latest-Linux-x86_64.sh -b -p /root/miniconda; eval "$(/root/miniconda/bin/conda shell.bash hook)"; conda init
+    # - conda install conda-libmamba-solver; conda config --set solver libmamba # MG20241017: This is now the default solver, cf. https://conda.org/blog/2023-11-06-conda-23-10-0-release
+    - conda create -y -c conda-forge -n dolfin_warp expat=2.5 fenics=2019.1.0 matplotlib=3.5 meshio=5.3 mpi4py=3.1.3 numpy=1.23.5 pandas=1.3 pip python=3.10 scipy=1.8 vtk=9.1; conda activate dolfin_warp # MG20230608: need to install meshio via conda because pip install has h5py dependency issues # MG20230608: need to install vtk9 because vtk7 seems to require python2 # MG20241020: expat > 2.5 seems to break vtkXMLDataParser, cf. https://gitlab.kitware.com/vtk/vtk/-/issues/19258
+    - conda activate dolfin_warp; conda env config vars set CPATH=$CONDA_PREFIX/include/vtk-9.1; conda deactivate; conda activate dolfin_warp
+    - pip install git+https://gitlab.inria.fr/mgenet/myPythonLibrary.git git+https://gitlab.inria.fr/mgenet/myVTKPythonLibrary.git git+https://gitlab.inria.fr/mgenet/vtkpython_cbl.git git+https://gitlab.inria.fr/mgenet/dolfin_mech.git
+    - cd Tests; ln -s ../dolfin_warp; make
+
+tests-on-ubuntu-22.04:
+  stage: test
+  only:
+    - devel
+    - /^devel-.*/
+  tags:
+    - ci.inria.fr
+    - large
+  image: ubuntu:22.04
+  script:
+    - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt upgrade -y
+    - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt install -y build-essential gcc-multilib git gnuplot libgl1-mesa-dev libglu1-mesa-dev libxcursor-dev libxinerama1 libxft-dev wget xvfb
+    - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt install -y libopenblas-base; export OMP_NUM_THREADS="1"
+    - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh; bash Miniconda3-latest-Linux-x86_64.sh -b -p /root/miniconda; eval "$(/root/miniconda/bin/conda shell.bash hook)"; conda init
+    # - conda install conda-libmamba-solver; conda config --set solver libmamba # MG20241017: This is now the default solver, cf. https://conda.org/blog/2023-11-06-conda-23-10-0-release
+    - conda create -y -c conda-forge -n dolfin_warp expat=2.5 fenics=2019.1.0 matplotlib=3.5 meshio=5.3 mpi4py=3.1.3 numpy=1.23.5 pandas=1.3 pip python=3.10 scipy=1.8 vtk=9.1; conda activate dolfin_warp # MG20230608: need to install meshio via conda because pip install has h5py dependency issues
+    - conda activate dolfin_warp; conda env config vars set CPATH=$CONDA_PREFIX/include/vtk-9.1; conda deactivate; conda activate dolfin_warp
+    - pip install git+https://gitlab.inria.fr/mgenet/myPythonLibrary.git git+https://gitlab.inria.fr/mgenet/myVTKPythonLibrary.git git+https://gitlab.inria.fr/mgenet/vtkpython_cbl.git git+https://gitlab.inria.fr/mgenet/dolfin_mech.git
+    - cd Tests; ln -s ../dolfin_warp; make
+
+tests-on-ubuntu-24.04:
+  stage: test
+  only:
+    - devel
+    - /^devel-.*/
+  tags:
+    - ci.inria.fr
+    - large
+  image: ubuntu:24.04
+  script:
+    - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt upgrade -y
+    - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt install -y build-essential gcc-multilib git gnuplot libgl1-mesa-dev libglu1-mesa-dev libxcursor-dev libxinerama1 libxft-dev wget xvfb
+    # - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt install -y libopenblas-base; export OMP_NUM_THREADS="1" # MG20241017: Not present in Ubuntu 24.04
+    - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh; bash Miniconda3-latest-Linux-x86_64.sh -b -p /root/miniconda;  eval "$(/root/miniconda/bin/conda shell.bash hook)"; conda init
+    # - conda install conda-libmamba-solver; conda config --set solver libmamba # MG20241017: This is now the default solver, cf. https://conda.org/blog/2023-11-06-conda-23-10-0-release
+    - conda create -y -c conda-forge -n dolfin_warp expat=2.5 fenics=2019.1.0 matplotlib=3.5 meshio=5.3 mpi4py=3.1.3 numpy=1.23.5 pandas=1.3 pip python=3.10 scipy=1.8 vtk=9.1; conda activate dolfin_warp # MG20230608: need to install meshio via conda because pip install has h5py dependency issues
+    - conda activate dolfin_warp; conda env config vars set CPATH=$CONDA_PREFIX/include/vtk-9.1; conda deactivate; conda activate dolfin_warp
+    - pip install git+https://gitlab.inria.fr/mgenet/myPythonLibrary.git git+https://gitlab.inria.fr/mgenet/myVTKPythonLibrary.git git+https://gitlab.inria.fr/mgenet/vtkpython_cbl.git git+https://gitlab.inria.fr/mgenet/dolfin_mech.git
+    - cd Tests; ln -s ../dolfin_warp; make
+
+# docker:
+#   stage: deploy
+#   only:
+#     - master
+#   tags:
+#     - ci.inria.fr
+#     - small
+#   image: docker:19.03.11
+#   services:
+#     - docker:19.03.11-dind
+#   script:
+#     - echo Docker login
+#     - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
+#     - echo Build dolfin_warp-2017.2.0-dev
+#     - docker build -t $CI_REGISTRY/mgenet/dolfin_warp/dolfin_warp-2017.2.0-dev -f Docker/dolfin_warp-2017.2.0-dev/Dockerfile .
+#     - docker push $CI_REGISTRY/mgenet/dolfin_warp/dolfin_warp-2017.2.0-dev
+#     - echo Build dolfin_warp-2017.2.0
+#     - docker build -t $CI_REGISTRY/mgenet/dolfin_warp/dolfin_warp-2017.2.0 -f Docker/dolfin_warp-2017.2.0/Dockerfile .
+#     - docker push $CI_REGISTRY/mgenet/dolfin_warp/dolfin_warp-2017.2.0
+#     - echo Build dolfin_warp-2019.1.0-dev
+#     - docker build -t $CI_REGISTRY/mgenet/dolfin_warp/dolfin_warp-2019.1.0-dev -f Docker/dolfin_warp-2019.1.0-dev/Dockerfile .
+#     - docker push $CI_REGISTRY/mgenet/dolfin_warp/dolfin_warp-2019.1.0-dev
+#     - echo Build dolfin_warp-2019.1.0
+#     - docker build -t $CI_REGISTRY/mgenet/dolfin_warp/dolfin_warp-2019.1.0 -f Docker/dolfin_warp-2019.1.0/Dockerfile .
+#     - docker push $CI_REGISTRY/mgenet/dolfin_warp/dolfin_warp-2019.1.0
+#     - echo Docker logout
+#     - docker logout $CI_REGISTRY
+
+pypi:
+  stage: deploy
+  only:
+    - master
+  tags:
+    - ci.inria.fr
+    - small
+  image: python
+  variables:
+    TWINE_USERNAME: $PYPI_USER
+    TWINE_PASSWORD: $PYPI_PASS
+  script:
+    - pip install -U setuptools twine
+    - python setup.py sdist bdist_wheel
+    - twine upload dist/*
+
+gitlab:
+  stage: deploy
+  only:
+    - master
+  tags:
+    - ci.inria.fr
+    - small
+  image: python
+  script:
+    - pip install -U setuptools twine
+    - python setup.py sdist bdist_wheel
+    - TWINE_USERNAME=gitlab-ci-token TWINE_PASSWORD=${CI_JOB_TOKEN} twine upload --verbose --skip-existing --repository-url https://gitlab.inria.fr/api/v4/projects/${CI_PROJECT_ID}/packages/pypi dist/*

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://gitlab.inria.fr/mgenet/dolfin_warp
+doi: 10.5281/zenodo.8010275

LEGACY/Docker/dolfin_warp-2017.2.0-dev/Dockerfile

+# FEniCS base
+
+# FROM ubuntu:latest
+# FROM quay.io/fenicsproject/stable:2016.1.0
+# FROM quay.io/fenicsproject/stable:2016.2.0
+# FROM quay.io/fenicsproject/stable:2017.1.0
+FROM quay.io/fenicsproject/stable:2017.2.0
+# FROM quay.io/fenicsproject/stable:current
+# FROM quay.io/fenicsproject/stable:latest
+
+# USER root
+
+# RUN apt-get update; apt-get -y upgrade; apt-get clean; rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+# RUN apt-get update; apt-get install -y software-properties-common; apt-get clean; rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+# RUN add-apt-repository -y ppa:fenics-packages/fenics-2016.1.0
+# RUN add-apt-repository -y ppa:fenics-packages/fenics-2016.2.0
+# RUN add-apt-repository -y ppa:fenics-packages/fenics-2017.1.0
+# RUN add-apt-repository -y ppa:fenics-packages/fenics-2017.2.0
+# RUN add-apt-repository -y ppa:fenics-packages/fenics
+# RUN apt-get update; apt-get install -y fenics; apt-get clean; rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+# basic stuff
+RUN apt-get update; apt-get -y install rename; apt-get clean; rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+# python stuff
+RUN apt-get update; apt-get -y install python-future python-numpy python-scipy python-tk; apt-get clean; rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+# vtk stuff
+RUN apt-get update; apt-get -y install libvtk6-dev python-vtk6; apt-get clean; rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+ENV CPATH="/usr/include/vtk-6.2":$CPATH
+
+# gnuplot stuff
+RUN apt-get update; apt-get -y install gnuplot git; apt-get clean; rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+WORKDIR /home/fenics
+RUN git clone https://github.com/aschn/gnuplot-colorbrewer.git
+RUN echo "set loadpath \"/home/fenics/gnuplot-colorbrewer/diverging:/home/fenics/gnuplot-colorbrewer/qualitative:/home/fenics/gnuplot-colorbrewer/sequential\"" > .gnuplot
+
+# environment setup
+WORKDIR /home/fenics
+RUN mkdir code
+ENV PYTHONPATH=/home/fenics/code:$PYTHONPATH
+ENV PYTHONPATH=/home/fenics/code/myPythonLibrary:$PYTHONPATH
+ENV PYTHONPATH=/home/fenics/code/myVTKPythonLibrary:$PYTHONPATH
+ENV PATH=/home/fenics/code/myPythonLibrary/myPythonLibrary:$PATH
+ENV PATH=/home/fenics/code/myVTKPythonLibrary/myVTKPythonLibrary:$PATH
+ENV PATH=/home/fenics/code/vtkpython_cbl:$PATH
+
+#USER root

LEGACY/Docker/dolfin_warp-2017.2.0/Dockerfile

+FROM registry.gitlab.inria.fr/mgenet/dolfin_warp/dolfin_warp-2017.2.0-dev
+
+# RUN pip install myPythonLibrary
+# RUN pip install myVTKPythonLibrary
+
+RUN apt-get update; apt-get -y install git; apt-get clean; rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+WORKDIR /home/fenics/code
+RUN git clone https://gitlab.inria.fr/mgenet/myPythonLibrary.git
+RUN git clone https://gitlab.inria.fr/mgenet/myVTKPythonLibrary.git
+RUN git clone https://gitlab.inria.fr/mgenet/vtkpython_cbl.git
+RUN git clone https://gitlab.inria.fr/mgenet/dolfin_mech.git
+RUN git clone https://gitlab.inria.fr/mgenet/dolfin_warp.git

LEGACY/Docker/dolfin_warp-2019.1.0-dev/Dockerfile

+# FEniCS base
+FROM quay.io/fenicsproject/stable:2019.1.0.r3
+
+# basic stuff
+RUN apt-get update; apt-get -y install rename; apt-get clean; rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+# python3 stuff
+RUN apt-get update; apt-get -y install python3-future python3-numpy python3-scipy python3-tk; apt-get clean; rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+RUN pip install numpy==1.15
+
+# vtk stuff
+RUN apt-get update; apt-get -y install libvtk7-dev python3-vtk7; apt-get clean; rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+ENV CPATH="/usr/include/vtk-7.1":$CPATH
+
+# gnuplot stuff
+RUN apt-get update; apt-get -y install gnuplot git; apt-get clean; rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+WORKDIR /home/fenics
+RUN git clone https://github.com/aschn/gnuplot-colorbrewer.git
+RUN echo "set loadpath \"/home/fenics/gnuplot-colorbrewer/diverging:/home/fenics/gnuplot-colorbrewer/qualitative:/home/fenics/gnuplot-colorbrewer/sequential\"" > .gnuplot
+
+# optimization stuff
+RUN pip install git+https://github.com/dolfin-adjoint/pyadjoint.git@2019.1.0 cma nlopt sklearn
+
+# environment setup
+WORKDIR /home/fenics
+RUN mkdir code
+ENV PYTHONPATH=/home/fenics/code:$PYTHONPATH
+ENV PYTHONPATH=/home/fenics/code/myPythonLibrary:$PYTHONPATH
+ENV PYTHONPATH=/home/fenics/code/myVTKPythonLibrary:$PYTHONPATH
+ENV PATH=/home/fenics/code/myPythonLibrary/myPythonLibrary:$PATH
+ENV PATH=/home/fenics/code/myVTKPythonLibrary/myVTKPythonLibrary:$PATH
+ENV PATH=/home/fenics/code/vtkpython_cbl:$PATH

LEGACY/Docker/dolfin_warp-2019.1.0/Dockerfile

+FROM registry.gitlab.inria.fr/mgenet/dolfin_warp/dolfin_warp-2019.1.0-dev
+
+# RUN pip install myPythonLibrary
+# RUN pip install myVTKPythonLibrary
+
+RUN apt-get update; apt-get -y install git; apt-get clean; rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+WORKDIR /home/fenics/code
+RUN git clone https://gitlab.inria.fr/mgenet/myPythonLibrary.git
+RUN git clone https://gitlab.inria.fr/mgenet/myVTKPythonLibrary.git
+RUN git clone https://gitlab.inria.fr/mgenet/vtkpython_cbl.git
+RUN git clone https://gitlab.inria.fr/mgenet/dolfin_mech.git
+RUN git clone https://gitlab.inria.fr/mgenet/dolfin_warp.git

LICENSE

+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+  A "Combined Work" is a work produced by combining or linking an
+Application with the Library.  The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+  The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+  The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
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+Library.

README.md

+# 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, 50, 1–22.](https://doi.org/10.1016/j.media.2018.07.007)] and [[Genet (2023). Finite strain formulation of the discrete equilibrium gap principle: application to mechanically consistent regularization for large motion tracking. Comptes Rendus Mécanique, 351, 429-458.](https://doi.org/10.5802/crmeca.228)].
+
+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, 50, 1–22.](https://doi.org/10.1016/j.media.2018.07.007)]
+* [[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.](https://doi.org/10.3389/fphys.2018.01295)]
+* [[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.](https://doi.org/10.1002/cnm.2982)]
+* [[Berberoğlu, Stoeck, Moireau, Kozerke & Genet (2019). Validation of Finite Element Image Registration‐based Cardiac Strain Estimation from Magnetic Resonance Images. PAMM.](https://doi.org/10.1002/pamm.201900418)]
+* [[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.](https://doi.org/10.1152/ajpheart.00094.2019)]
+* [[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.](https://doi.org/10.1007/978-3-030-21949-9_36)]
+* [[Škardová, Rambausek, Chabiniok & Genet (2019). Mechanical and Imaging Models-Based Image Registration. VipIMAGE 2019. Cham: Springer International Publishing.](https://doi.org/10.1007/978-3-030-32040-9_9)]
+* [[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.](https://doi.org/10.1016/j.cmpb.2020.105345)]
+* [[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.](https://doi.org/10.1016/j.cjca.2021.06.018)]
+* [[Berberoğlu, Stoeck, Moireau, Kozerke & Genet (2021). In-silico study of accuracy and precision of left-ventricular strain quantification from 3D tagged MRI. PLOS ONE.](https://doi.org/10.1371/journal.pone.0258965)]
+* [[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.](https://doi.org/10.1007/s00246-021-02608-y)]
+* [[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.](https://doi.org/10.1016/j.media.2022.102598)]
+* [[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.](https://doi.org/10.1115/1.4054106)]
+* [[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.](https://doi.org/10.1007/s10237-023-01691-9)]
+* [[Genet (2023). Finite strain formulation of the discrete equilibrium gap principle: application to mechanically consistent regularization for large motion tracking. Comptes Rendus Mécanique, 351, 429-458.](https://doi.org/10.5802/crmeca.228)]
+
+(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](https://mgenet.gitlabpages.inria.fr/dolfin_warp-tutorials).
+
+### Installation
+
+A working installation of [FEniCS](https://fenicsproject.org) (version 2019.1.0; including the dolfin python interface) & [VTK](https://vtk.org) (also including python interface) is required to run `dolfin_warp`.
+To setup a system, the simplest is to use [conda](https://conda.io): first install [miniconda](https://docs.conda.io/projects/miniconda/en/latest) (note that for Microsoft Windows machines you first need to install WSL, the [Windows Subsystem for Linux](https://learn.microsoft.com/en-us/windows/wsl/install), 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 x86_64 version of miniconda), and then install the necessary packages:
+```
+conda create -y -c conda-forge -n dolfin_warp 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 dolfin_warp
+conda env config vars set CPATH=$CONDA_PREFIX/include/vtk-9.2
+conda activate dolfin_warp
+pip install dolfin_warp
+```

Tests/Makefile

+test:
+	set -e; for i in test_*.py; do echo $$i; set -e; python $$i; done

Tests/[Genet,2023]/generate_images_and_meshes_from_HeartSlice.py

+#coding=utf8
+
+################################################################################
+
+import math
+import os
+
+import myVTKPythonLibrary as myvtk
+import dolfin_mech        as dmech
+import dolfin_warp        as dwarp
+
+################################################################################
+
+def generate_images_and_meshes_from_HeartSlice(
+        n_voxels         : int         ,
+        deformation_type : str         ,
+        texture_type     : str         ,
+        noise_level      : float       ,
+        k_run            : int   = None,
+        run_model        : bool  = True,
+        generate_images  : bool  = True,
+        mesh_size        : float = None):
+
+    images_folder = "generate_images"
+    if not os.path.exists(images_folder):
+        os.mkdir(images_folder)
+
+    working_basename  = "heart"
+    working_basename += "-"+deformation_type
+    if (mesh_size is not None):
+        working_basename += "-h="+str(mesh_size)
+
+    if (mesh_size is None):
+        mesh_size = 1./n_voxels
+    mesh_params = {"X0":0.5, "Y0":0.5, "Ri":0.2, "Re":0.4, "l":mesh_size, "mesh_filebasename":images_folder+"/"+working_basename+"-mesh"}
+    if   ("-coarse"    in deformation_type):
+        mesh_params["l"] = 0.05
+        mesh_params["mesh_filebasename"] = images_folder+"/"+working_basename+"-mesh-coarse"
+    elif ("-fine"      in deformation_type):
+        mesh_params["l"] = 0.01
+        mesh_params["mesh_filebasename"] = images_folder+"/"+working_basename+"-mesh-fine"
+    elif ("-ultrafine" in deformation_type):
+        mesh_params["l"] = 0.005
+        mesh_params["mesh_filebasename"] = images_folder+"/"+working_basename+"-mesh-ultrafine"
+
+    load_params = {"type":"disp", "dRi":-0.10, "dRe":-0.05, "dTi":-math.pi/4, "dTe":-math.pi/8}
+    if ("nocontract" in deformation_type):
+        load_params["dRi"] = 0.
+        load_params["dRe"] = 0.
+    if ("notwist" in deformation_type):
+        load_params["dTi"] = 0.
+        load_params["dTe"] = 0.
+
+    # print (run_model)
+    if (run_model):
+        dmech.run_HeartSlice_Hyperelasticity(
+            incomp                                 = 0,
+            mesh_params                            = mesh_params,
+            mat_params                             = {"model":"CGNH", "parameters":{"E":1., "nu":0.3}},
+            step_params                            = {"dt_ini":1/20},
+            load_params                            = load_params,
+            res_basename                           = images_folder+"/"+working_basename,
+            write_vtus_with_preserved_connectivity = True,
+            verbose                                = 1)
+
+    if (generate_images):
+        ref_image = myvtk.createImageFromSizeAndRes(
+            dim  = 2       ,
+            size = 1.      ,
+            res  = n_voxels,
+            up   = 1       )
+
+        s = [0.1]*2
+        ref_image_model = lambda X:math.sqrt(abs(math.sin(math.pi*X[0]/s[0]))
+                                           * abs(math.sin(math.pi*X[1]/s[1])))
+
+        if (noise_level == 0):
+            noise_params = {"type":"no"}
+        else:
+            noise_params = {"type":"normal", "stdev":noise_level}
+
+        dwarp.compute_warped_images(
+            working_folder                  = images_folder,
+            working_basename                = "heart-"+deformation_type,
+            working_ext                     = "vtu",
+            working_displacement_field_name = "U",
+            ref_image                       = ref_image,
+            ref_frame                       = 0,
+            ref_image_model                 = ref_image_model,
+            noise_params                    = noise_params,
+            suffix                          = texture_type+"-noise="+str(noise_level)+(k_run is not None)*("-run="+str(k_run).zfill(2)),
+            print_warped_mesh               = 0,
+            verbose                         = 0)
+
+########################################################################
+
+if (__name__ == "__main__"):
+    import fire
+    fire.Fire(generate_images_and_meshes_from_HeartSlice)
+
+    # import argparse
+    # from distutils.util import strtobool
+    # parser = argparse.ArgumentParser()
+    # parser.add_argument("--n_dim"                , type=int  , choices=[2]        )
+    # parser.add_argument("--n_voxels"             , type=int                       )
+    # parser.add_argument("--deformation_type"     , type=str                       )
+    # parser.add_argument("--texture_type"         , type=str  , choices=["tagging"])
+    # parser.add_argument("--noise_level"          , type=float                     )
+    # parser.add_argument("--k_run"                , type=int                         , default=None)
+    # parser.add_argument("--run_model"            , type=lambda x: bool(strtobool(x)), default=True) # MG20220901: Watch out! All non empty strings evaluate to True!
+    # parser.add_argument("--generate_images"      , type=lambda x: bool(strtobool(x)), default=True) # MG20220901: Watch out! All non empty strings evaluate to True!
+
+    # args = parser.parse_args()
+    # # print (args.run_model)
+
+    # generate_images_and_meshes_from_HeartSlice(
+    #     n_dim            = args.n_dim,
+    #     n_voxels         = args.n_voxels,
+    #     deformation_type = args.deformation_type,
+    #     texture_type     = args.texture_type,
+    #     noise_level      = args.noise_level,
+    #     k_run            = args.k_run,
+    #     run_model        = args.run_model,
+    #     generate_images  = args.generate_images)

Tests/[Genet,2023]/generate_images_and_meshes_from_Struct.py

+#coding=utf8
+
+################################################################################
+
+import dolfin
+import math
+import typing
+
+import dolfin_mech as dmech
+import dolfin_warp as dwarp
+
+################################################################################
+
+def generate_images_and_meshes_from_Struct(
+        n_dim            : int                        ,
+        n_voxels         : int                        ,
+        structure_type   : str                        ,
+        deformation_type : str                        ,
+        texture_type     : str                        ,
+        noise_level      : float                      ,
+        k_run            : typing.Optional[int] = None, # MG20220815: This can be written "int | None" starting with python 3.10
+        mesh_size        : float                = 0.1 ,
+        generate_images  : bool                 = True,
+        compute_meshes   : bool                 = True):
+
+    images = {
+        "n_dim":n_dim,
+        "L":[1.]*n_dim,
+        "n_voxels":[n_voxels]*n_dim,
+        "upsampling_factors":[1]*n_dim,
+        "T":1.,
+        "n_frames":21,
+        "data_type":"float"}
+
+    images["folder"] = "generate_images"
+
+    images["basename"]  = structure_type
+    images["basename"] += "-"+deformation_type
+    images["basename"] += "-"+texture_type
+    images["basename"] += "-noise="+str(noise_level)
+    if (k_run is not None):
+        images["basename"] += "-run="+str(k_run).zfill(2)
+    images["ext"] = "vti"
+
+    if (structure_type == "square"):
+        if (deformation_type == "translation"):
+            Xmin = [0.1,0.2]
+            Xmax = [0.7,0.8]
+        elif (deformation_type in ("no", "rotation", "compression", "shear")):
+            Xmin = [0.2,0.2]
+            Xmax = [0.8,0.8]
+        else: assert (0)
+        structure = {"type":"box", "Xmin":Xmin, "Xmax":Xmax}
+    elif (structure_type == "disc"):
+        if (deformation_type == "translation"):
+            X0 = [0.4,0.5]
+        elif (deformation_type in ("no", "rotation", "compression", "shear")):
+            X0 = [0.5,0.5]
+        else: assert (0)
+        R = 0.35
+        structure = {"type":"disc", "X0":X0, "R":R}
+    elif (structure_type == "ring"):
+        if (deformation_type == "translation"):
+            X0 = [0.4,0.5]
+        elif (deformation_type in ("no", "rotation", "compression", "shear", "inflate", "twist")):
+            X0 = [0.5,0.5]
+        else: assert (0)
+        Ri = 0.15
+        Re = 0.35
+        structure = {"type":"heart", "X0":X0, "Ri":Ri, "Re":Re}
+
+    if (texture_type == "tagging"):
+        texture = {"type":"tagging", "s":0.1}
+
+    if (noise_level == 0):
+        noise = {"type":"no"}
+    else:
+        noise = {"type":"normal", "stdev":noise_level}
+
+    if (deformation_type == "no"):
+        deformation = {"type":"no"}
+    elif (deformation_type == "translation"):
+        deformation = {"type":"translation", "Dx":0.2, "Dy":0.}
+    elif (deformation_type == "rotation"):
+        deformation = {"type":"rotation", "Cx":0.5, "Cy":0.5, "Rz":45.} # 90 be require more time steps?
+    elif (deformation_type == "compression"):
+        deformation = {"type":"homogeneous", "X0":0.5, "Y0":0.5, "Exx":-0.20}
+    elif (deformation_type == "shear"):
+        deformation = {"type":"homogeneous", "X0":0.5, "Y0":0.5, "Fxy":+0.20}
+    elif (deformation_type == "inflate"):
+        deformation = {"type":"heart", "dRi":-0.10, "dRe":0., "dTi":0., "dTe":0.}
+    elif (deformation_type == "twist"):
+        deformation = {"type":"heart", "dRi":0., "dRe":0., "dTi":-math.pi/4, "dTe":0.}
+
+    evolution = {"type":"linear"}
+
+    if (generate_images):
+        dwarp.generate_images(
+            images           = images,
+            structure        = structure,
+            texture          = texture,
+            noise            = noise,
+            deformation      = deformation,
+            evolution        = evolution,
+            keep_temp_images = 0,
+            verbose          = 1)
+
+    if (compute_meshes):
+        if (structure_type == "square"):
+            n_cells = int((0.8-0.2)/mesh_size)
+            if (n_dim == 2):
+                mesh = dolfin.RectangleMesh(
+                    dolfin.Point(Xmin),
+                    dolfin.Point(Xmax),
+                    n_cells, n_cells,
+                    "crossed")
+            elif (n_dim == 3):
+                mesh = dolfin.BoxMesh(
+                    dolfin.Point(Xmin),
+                    dolfin.Point(Xmax),
+                    n_cells, n_cells, n_cells)
+        elif (structure_type == "disc"):
+            # import mshr
+            # geometry = mshr.Circle(dolfin.Point(X0[0], X0[1]), R)
+            # mesh = mshr.generate_mesh(geometry, r/mesh_size)
+            mesh, _, _, _, _, _, _, _ = dmech.run_Disc_Mesh(params={"X0":X0[0], "Y0":X0[1], "R":R, "l":mesh_size})
+        elif (structure_type == "ring"):
+            # import mshr
+            # geometry = mshr.Circle(dolfin.Point(X0[0], X0[1]), Re)\
+            #          - mshr.Circle(dolfin.Point(X0[0], X0[1]), Ri)
+            # mesh = mshr.generate_mesh(geometry, (Re-Ri)/mesh_size)
+            mesh, _, _, _, _, _, _, _, _ = dmech.run_HeartSlice_Mesh(params={"X0":X0[0], "Y0":X0[1], "Ri":Ri, "Re":Re, "l":mesh_size})
+
+        working_folder = images["folder"]
+        
+        working_basename  = structure_type
+        working_basename += "-"+deformation_type
+        working_basename += "-h="+str(mesh_size)
+
+        dolfin.File(working_folder+"/"+working_basename+".xml") << mesh
+
+        dwarp.compute_warped_mesh(
+            working_folder   = working_folder,
+            working_basename = working_basename,
+            images           = images,
+            structure        = structure,
+            deformation      = deformation,
+            evolution        = evolution,
+            mesh             = mesh,
+            mesh_ext         = "vtu",
+            verbose          = 1)
+
+########################################################################
+
+if (__name__ == "__main__"):
+    import fire
+    fire.Fire(generate_images_and_meshes_from_Struct)
+
+    # import argparse
+    # from distutils.util import strtobool
+    # parser = argparse.ArgumentParser()
+    # parser.add_argument("--n_dim"           , type=int  , choices=[2,3]                                              )
+    # parser.add_argument("--n_voxels"        , type=int                                                               )
+    # parser.add_argument("--deformation_type", type=str  , choices=["translation", "rotation", "compression", "shear"])
+    # parser.add_argument("--texture_type"    , type=str  , choices=["no", "tagging"]                                  )
+    # parser.add_argument("--noise_level"     , type=float                                                             )
+    # parser.add_argument("--k_run"           , type=int                                                 , default=None)
+    # parser.add_argument("--generate_images" , type=lambda x: bool(strtobool(x))                        , default=True) # MG20220901: Watch out! All non empty strings evaluate to True!
+    # parser.add_argument("--compute_meshes"  , type=lambda x: bool(strtobool(x))                        , default=True) # MG20220901: Watch out! All non empty strings evaluate to True!
+    # args = parser.parse_args()
+
+    # generate_images_and_meshes_from_Struct(
+    #     n_dim            = args.n_dim,
+    #     n_voxels         = args.n_voxels,
+    #     deformation_type = args.deformation_type,
+    #     texture_type     = args.texture_type,
+    #     noise_level      = args.noise_level,
+    #     k_run            = args.k_run,
+    #     generate_images  = args.generate_images,
+    #     compute_meshes   = args.compute_meshes)

Tests/[Genet,2023]/plot_disp_error_vs_mesh_size-ref/heart-contractandtwist-tagging-discrete-equilibrated-tractions-normal-tangential-with_refine.dat

+#      noise_level             regul_level              mesh_size              disp_err_avg            disp_err_std            disp_err_min            disp_err_max     
+           0.0                     0.0                     0.1             0.015962164014165964            0.0             0.015962164014165964    0.015962164014165964 
+           0.0                     0.0                     0.05            0.042734835029093976            0.0             0.042734835029093976    0.042734835029093976 
+           0.0                     0.0                    0.025             0.1028629303673039             0.0              0.1028629303673039      0.1028629303673039  
+           0.0                     0.0                    0.0125            0.1667576966947951             0.0              0.1667576966947951      0.1667576966947951  
+           0.0                     0.0                   0.00625            0.211275858626953              0.0              0.211275858626953       0.211275858626953   
+ 
+ 
+           0.0                     0.1                     0.1             0.014836859253818181            0.0             0.014836859253818181    0.014836859253818181 
+           0.0                     0.1                     0.05            0.01402212672105198             0.0             0.01402212672105198     0.01402212672105198  
+           0.0                     0.1                    0.025            0.019056550311953465            0.0             0.019056550311953465    0.019056550311953465 
+           0.0                     0.1                    0.0125            0.0193049708800561             0.0              0.0193049708800561      0.0193049708800561  
+           0.0                     0.1                   0.00625           0.01983827666253226             0.0             0.01983827666253226     0.01983827666253226  
+ 
+ 
+           0.1                     0.0                     0.1             0.03655036903642049    0.0006651313560001717    0.035317286778453305    0.037475925851265156 
+           0.1                     0.0                     0.05            0.09149609522146633    0.0016940786152186704    0.08939129653320196     0.09472372495016612  
+           0.1                     0.0                    0.025             0.1499321421902205    0.0023791258316908574     0.1469107367349529     0.15511113845791144  
+           0.1                     0.0                    0.0125           0.18085919729808114     0.00220587689392177     0.17830436619716208     0.18620392137368155  
+           0.1                     0.0                   0.00625            0.1983644210935879     0.007554064630692438    0.19381635948011608     0.22023635676331854  
+ 
+ 
+           0.1                     0.1                     0.1             0.022274065397688468   0.0007105992957698582    0.021390867388747528    0.023763231828068734 
+           0.1                     0.1                     0.05            0.028343001489011043   0.0002776335895695596    0.027958012795979686    0.028810336890601775 
+           0.1                     0.1                    0.025            0.030821775392859057   0.0005336460825933512    0.029780833182624505    0.031631739673439054 
+           0.1                     0.1                    0.0125           0.030854798067260332   0.0004183420112449717    0.030038878845465116    0.03144793566698627  
+           0.1                     0.1                   0.00625           0.10029266911440327     0.11094975435011085     0.030188280471457718    0.40479315245531644  
+ 
+ 

Tests/[Genet,2023]/plot_disp_error_vs_mesh_size-ref/heart-contractandtwist-tagging-discrete-equilibrated-tractions-normal-tangential.dat

+#      noise_level             regul_level              mesh_size              disp_err_avg            disp_err_std            disp_err_min            disp_err_max     
+           0.0                     0.0                     0.1             0.015962164014165964            0.0             0.015962164014165964    0.015962164014165964 
+           0.0                     0.0                     0.05            0.055067415210899924            0.0             0.055067415210899924    0.055067415210899924 
+           0.0                     0.0                    0.025             0.3896090323996506             0.0              0.3896090323996506      0.3896090323996506  
+           0.0                     0.0                    0.0125            0.9301481213112067             0.0              0.9301481213112067      0.9301481213112067  
+           0.0                     0.0                   0.00625            0.9820837244733407             0.0              0.9820837244733407      0.9820837244733407  
+ 
+ 
+           0.0                     0.1                     0.1             0.014836859253818181            0.0             0.014836859253818181    0.014836859253818181 
+           0.0                     0.1                     0.05            0.01428394299809057             0.0             0.01428394299809057     0.01428394299809057  
+           0.0                     0.1                    0.025             0.9176460987052593             0.0              0.9176460987052593      0.9176460987052593  
+           0.0                     0.1                    0.0125            0.966242962683782              0.0              0.966242962683782       0.966242962683782   
+           0.0                     0.1                   0.00625            0.9857602375986628             0.0              0.9857602375986628      0.9857602375986628  
+ 
+ 
+           0.1                     0.0                     0.1             0.03655036903642049    0.0006651313560001717    0.035317286778453305    0.037475925851265156 
+           0.1                     0.0                     0.05            0.12524783161739536     0.005525325821283487    0.11413330547434246     0.13238173827965505  
+           0.1                     0.0                    0.025             0.5921728364473541     0.13418284098136607      0.4653752849260762      0.8942222565567713  
+           0.1                     0.0                    0.0125            0.6968344531057828     0.15720902669803632      0.5216937272222719      0.9381104154427546  
+           0.1                     0.0                   0.00625            0.9475388011653388      0.3277005205271885      0.6733323444742123      1.8513643559295057  
+ 
+ 
+           0.1                     0.1                     0.1             0.022274065397688468   0.0007105992957698582    0.021390867388747528    0.023763231828068734 
+           0.1                     0.1                     0.05            0.31420585990807676     0.24513130582077655     0.030219799218450853     0.622625403307605   
+           0.1                     0.1                    0.025             0.9379244797263316     0.011586789881604616     0.918279231114799       0.9540782994533524  
+           0.1                     0.1                    0.0125            0.9746665532882666    0.0041583220091513245     0.9685277522579792      0.9807985968197472  
+           0.1                     0.1                   0.00625            0.9908080349416327    0.0017877466144524989     0.9880099959877723      0.9940434445109201  
+ 
+ 

Tests/[Genet,2023]/plot_disp_error_vs_mesh_size.py

+#coding=utf8
+
+########################################################################
+
+import numpy
+import os
+
+import myPythonLibrary as mypy
+import dolfin_warp     as dwarp
+
+########################################################################
+
+def plot_disp_error_vs_mesh_size(
+        images_folder                            : str          ,
+        sol_folder                               : str          ,
+        structure_type                           : str          ,
+        deformation_type                         : str          ,
+        texture_type                             : str          ,
+        regul_type                               : str          ,
+        noise_level_lst                          : list         ,
+        n_runs_for_noisy_images                  : int          ,
+        regul_level_lst                          : list         ,
+        mesh_size_lst                            : list         ,
+        with_refine                              : bool  = False,
+        error_for_nan                            : float = None ,
+        generate_datafile                        : bool  = True ,
+        generate_datafile_with_limited_precision : bool  = False,
+        generate_plotfile                        : bool  = True ,
+        generate_plot                            : bool  = True ):
+
+    print ("structure_type:"  , structure_type  )
+    print ("deformation_type:", deformation_type)
+    print ("texture_type:"    , texture_type    )
+    print ("regul_type:"      , regul_type      )
+
+    script_basename = "plot_disp_error_vs_mesh_size"
+
+    if not os.path.exists(script_basename):
+        os.mkdir(script_basename)
+    
+    datafile_basename  = script_basename
+    datafile_basename += "/"+structure_type
+    datafile_basename += "-"+deformation_type
+    datafile_basename += "-"+texture_type
+    datafile_basename += "-"+regul_type
+    if (with_refine):
+        datafile_basename += "-with_refine"
+
+########################################################################
+
+    if (generate_datafile) or (generate_datafile_with_limited_precision):
+
+        if (generate_datafile): data_printer = mypy.DataPrinter(
+            names=["noise_level", "regul_level", "mesh_size", "disp_err_avg", "disp_err_std", "disp_err_min", "disp_err_max"],
+            filename=datafile_basename+".dat",
+            limited_precision=False)
+
+        if (generate_datafile_with_limited_precision): data_printer2 = mypy.DataPrinter(
+            names=["noise_level", "regul_level", "mesh_size", "disp_err_avg", "disp_err_std", "disp_err_min", "disp_err_max"],
+            filename=datafile_basename+"-limited_precision.dat",
+            limited_precision=True)
+
+        if (generate_datafile): data_printer3 = mypy.DataPrinter(
+            names=["noise_level", "regul_level", "mesh_size", "disp_err"],
+            filename=datafile_basename+"-all_points.dat",
+            limited_precision=False)
+
+        if (structure_type in ("square", "disc", "ring")):
+            ref_disp_array_name = "displacement"
+        elif (structure_type in ("heart")):
+            ref_disp_array_name = "U"
+        else: assert (0)
+
+        for noise_level in noise_level_lst:
+         for regul_level in regul_level_lst:
+          for k_mesh_size, mesh_size in enumerate(mesh_size_lst):
+
+            print ("noise_level:", noise_level)
+            print ("regul_level:", regul_level)
+            print ("mesh_size:"  , mesh_size  )
+
+            n_runs = n_runs_for_noisy_images if (noise_level > 0) else 1
+            disp_err_lst = []
+
+            for k_run in range(1, n_runs+1):
+
+                print ("k_run:", k_run)
+
+                images_basename  = structure_type
+                images_basename += "-"+deformation_type
+                images_basename += "-"+texture_type
+                images_basename += "-noise="+str(noise_level)
+                if (n_runs > 1):
+                    images_basename += "-run="+str(k_run).zfill(2)
+
+                sol_basename  = images_basename
+                if not (with_refine):
+                    sol_basename += "-h="+str(mesh_size)
+                sol_basename += "-"+regul_type
+                sol_basename += "-regul="+str(regul_level)
+                if (with_refine):
+                    sol_basename += "-refine="+str(k_mesh_size)
+
+                # import time
+                # t = time.time()
+                # disp_err_vtk = dwarp.compute_displacement_error_with_vtk(
+                #     working_folder=sol_folder,
+                #     working_basename=sol_basename,
+                #     working_disp_array_name="displacement",
+                #     ref_folder=images_folder,
+                #     ref_basename=structure_type+"-"+deformation_type+"-h="+str(mesh_size),
+                #     ref_disp_array_name=ref_disp_array_name,
+                #     verbose=0)
+                # print ("t (vtk)", time.time() - t)
+                # print ("disp_err_vtk:", disp_err_vtk)
+                # t = time.time()
+                # disp_err_np = dwarp.compute_displacement_error_with_numpy(
+                #     working_folder=sol_folder,
+                #     working_basename=sol_basename,
+                #     working_disp_array_name="displacement",
+                #     ref_folder=images_folder,
+                #     ref_basename=structure_type+"-"+deformation_type+"-h="+str(mesh_size),
+                #     ref_disp_array_name=ref_disp_array_name,
+                #     verbose=0)
+                # print ("t (np)", time.time() - t)
+                # print ("disp_err_np:", disp_err_np)
+                # assert (disp_err_np == disp_err_vtk)
+                # t = time.time()
+                # disp_err_fenics = dwarp.compute_displacement_error_with_fenics(
+                #     working_folder=sol_folder,
+                #     working_basename=sol_basename,
+                #     working_disp_array_name="displacement",
+                #     ref_folder=images_folder,
+                #     ref_basename=structure_type+"-"+deformation_type,
+                #     ref_disp_array_name=ref_disp_array_name,
+                #     verbose=0)
+                # print ("t (fenics)", time.time() - t)
+                # print ("disp_err_fenics:", disp_err_fenics)
+                # disp_err = disp_err_fenics
+
+                try:
+                    disp_err = dwarp.compute_displacement_error_with_fenics(
+                        working_folder=sol_folder,
+                        working_basename=sol_basename,
+                        working_disp_array_name="displacement",
+                        ref_folder=images_folder,
+                        ref_basename=structure_type+"-"+deformation_type,
+                        ref_disp_array_name=ref_disp_array_name,
+                        verbose=0)
+                    # disp_err = dwarp.compute_displacement_error(
+                    #     working_folder=sol_folder,
+                    #     working_basename=sol_basename,
+                    #     working_disp_array_name="displacement",
+                    #     ref_folder=images_folder,
+                    #     ref_basename=structure_type+"-"+deformation_type+"-h="+str(mesh_size),
+                    #     ref_disp_array_name=ref_disp_array_name,
+                    #     verbose=0)
+                except:
+                    disp_err = error_for_nan
+                print ("disp_err:", disp_err)
+
+                disp_err_lst.append(disp_err)
+
+                if (error_for_nan is not None):
+                    if numpy.isnan(disp_err) or (disp_err > error_for_nan):
+                        disp_err = error_for_nan
+                if (generate_datafile): data_printer3.write_line([noise_level, regul_level, mesh_size, disp_err])
+
+            disp_err_avg = numpy.mean(disp_err_lst)
+            disp_err_std = numpy.std(disp_err_lst)
+            disp_err_min = numpy.min(disp_err_lst)
+            disp_err_max = numpy.max(disp_err_lst)
+            print ("disp_err_avg:", disp_err_avg)
+            print ("disp_err_std:", disp_err_std)
+            print ("disp_err_min:", disp_err_min)
+            print ("disp_err_max:", disp_err_max)
+
+            if (error_for_nan is not None):
+                if numpy.isnan(disp_err_avg) or (disp_err_avg > error_for_nan):
+                    disp_err_avg = error_for_nan
+                    disp_err_std = 0.
+                    if (disp_err_min > error_for_nan):
+                        disp_err_min = error_for_nan
+                    disp_err_max = error_for_nan
+
+            if (generate_datafile                       ): data_printer.write_line([noise_level, regul_level, mesh_size, disp_err_avg, disp_err_std, disp_err_min, disp_err_max])
+            if (generate_datafile_with_limited_precision): data_printer2.write_line([noise_level, regul_level, mesh_size, disp_err_avg, disp_err_std, disp_err_min, disp_err_max])
+
+          if (generate_datafile                       ): data_printer.write_line(); data_printer.write_line()
+          if (generate_datafile_with_limited_precision): data_printer2.write_line(); data_printer2.write_line()
+          if (generate_datafile                       ): data_printer3.write_line(); data_printer3.write_line()
+
+        if (generate_datafile                       ): data_printer.close()
+        if (generate_datafile_with_limited_precision): data_printer2.close()
+        if (generate_datafile                       ): data_printer3.close()
+
+########################################################################
+
+    if (generate_plotfile):
+
+        plotfile = open(datafile_basename+".plt", "w")
+        plotfile.write('''\
+set terminal pdf enhanced size 5,3; outputfile_ext = "pdf"
+
+load "Set1.plt"
+
+set linestyle  1 pointtype 0
+set linestyle  2 pointtype 0
+set linestyle  3 pointtype 0
+set linestyle  4 pointtype 0
+set linestyle  5 pointtype 0
+set linestyle  6 pointtype 0
+set linestyle  7 pointtype 0
+set linestyle  8 pointtype 0
+set linestyle  9 pointtype 0
+set linestyle 10 pointtype 0
+set linestyle 11 pointtype 0
+set linestyle 12 pointtype 0
+
+set style fill transparent solid 0.1 noborder
+
+datafile_basename = "'''+datafile_basename+'''"
+datafile_name = datafile_basename.".dat"
+poinfile_name = datafile_basename."-all_points.dat"
+
+set output datafile_basename.".".outputfile_ext
+
+set title "'''+structure_type+'''-'''+deformation_type+'''-'''+regul_type+'''"
+
+set key outside right center box textcolor variable width -3
+
+set grid
+
+set xlabel "mesh size"
+set xrange [0.1/2**4:0.1]
+# set format x "%g"
+set logscale x
+
+set ylabel "normalized displacement error (%)"
+set yrange [1e-1:1e+3]
+set logscale y
+
+plot ''')
+        for k_noise_level,noise_level in enumerate(noise_level_lst):
+         for k_regul_level,regul_level in enumerate(regul_level_lst):
+            if   (noise_level == 0.0): lc = 1
+            elif (noise_level == 0.1): lc = 2
+            elif (noise_level == 0.2): lc = 3
+            elif (noise_level == 0.3): lc = 4
+            else: assert (0)
+            if   (regul_level == 0.0 ): dt = 1
+            elif (regul_level == 0.1 ): dt = 2
+            elif (regul_level == 0.99): dt = 3
+            else: assert (0)
+            # index_for_plot = k_regul_level*len(noise_level_lst)+k_noise_level+1
+            index_for_data = k_noise_level*len(regul_level_lst)+k_regul_level
+            plotfile.write((('''     ''')*((k_noise_level>0)or(k_regul_level>0)))+'''datafile_name index '''+str(index_for_data)+''' using ($3):(100*$4)                        with lines        linestyle '''+str(lc)+''' dashtype '''+str(dt)+''' linewidth 3   title "noise = '''+"{:1.1f}".format(noise_level)+''', regul = '''+"{:1.2f}".format(regul_level)+'''"'''+''',\\\n''')
+            if (noise_level == 0): continue
+            # plotfile.write(  '''     '''                                         +'''datafile_name index '''+str(index_for_data)+''' using ($3):(100*$4):(100*$5)               with errorbars    linestyle '''+str(lc)+'''             notitle'''                                   +''',\\\n''')
+            # plotfile.write(  '''     '''                                         +'''datafile_name index '''+str(index_for_data)+''' using ($3):(100*$4-100*$5):(100*$4+100*$5) with filledcurves linestyle '''+str(lc)+'''             notitle'''                                   +((''',\\
+            plotfile.write(  '''     '''                    +'''poinfile_name index '''+str(index_for_data)+''' using ($3):(100*$4) with points linestyle '''+str(lc)+'''             notitle'''                                   +((''',\\
+''')*((k_noise_level<len(noise_level_lst)-1)or(k_regul_level<len(regul_level_lst)-1))))
+
+        plotfile.close()
+
+########################################################################
+
+    if (generate_plot):
+
+        os.system("gnuplot "+datafile_basename+".plt")
+        os.system("convert -density 300 "+datafile_basename+".pdf"+" "+datafile_basename+".png")
+
+########################################################################
+
+if (__name__ == "__main__"):
+    import fire
+    fire.Fire(plot_disp_error_vs_mesh_size)

Tests/[Genet,2023]/plot_disp_error_vs_regul_strength-ref/heart-contractandtwist-tagging-continuous-elastic.dat

+#      noise_level             regul_level             disp_err_avg            disp_err_std     
+           0.0                     0.99             0.5816852389172984             0.0          
+           0.0                     0.8             0.19368023004774895             0.0          
+           0.0                     0.4             0.09145007253920429             0.0          
+           0.0                     0.2             0.05665768439651671             0.0          
+           0.0                     0.1             0.033945826072207176            0.0          
+           0.0                     0.05            0.02492552630823139             0.0          
+           0.0                    0.025            0.022309037733112866            0.0          
+           0.0                    0.0125           0.022298499424028593            0.0          
+           0.0                    0.001            0.023769174394975282            0.0          
+ 
+ 
+           0.1                     0.99             0.697464532051001      0.02185600436962613  
+           0.1                     0.8              0.1994415254313896    0.0011354080298153068 
+           0.1                     0.4             0.09762662605531053    0.0016378049258639095 
+           0.1                     0.2             0.06462602712232121    0.0017966491004197647 
+           0.1                     0.1             0.04759551156664602     0.001323131822203368 
+           0.1                     0.05            0.04630896601464008    0.0013500020318863804 
+           0.1                    0.025            0.04908141796337479    0.0013137626001367654 
+           0.1                    0.0125           0.05235282142634371    0.0013139148250238917 
+           0.1                    0.001             0.0587169249628267    0.0013645664091331115 
+ 
+ 
+           0.2                     0.99             0.6665357317447584     0.03114323063824824  
+           0.2                     0.8             0.21491632018018417    0.0027358772490789717 
+           0.2                     0.4             0.11304358729454123    0.0018577242902248243 
+           0.2                     0.2             0.08515073788249392    0.0026164119262251967 
+           0.2                     0.1             0.07916806062949974     0.003129854967537309 
+           0.2                     0.05            0.08622217610024792    0.0026927473833285166 
+           0.2                    0.025            0.09755895684795715    0.0028209462553182023 
+           0.2                    0.0125           0.10875841456324378    0.0037901107560656365 
+           0.2                    0.001            0.13118952356750835     0.008054871316094782 
+ 
+ 
+           0.3                     0.99             0.6718630985485015     0.02429877283957384  
+           0.3                     0.8             0.23783953645516176     0.002341794380396059 
+           0.3                     0.4             0.13487858075738235      0.0047761195829776  
+           0.3                     0.2             0.11582118308871751     0.002875721300744551 
+           0.3                     0.1              0.1181812568404764     0.003441515252626044 
+           0.3                     0.05            0.13498732765945082    0.0032368417872816347 
+           0.3                    0.025            0.15744393942137425     0.00450417006869567  
+           0.3                    0.0125            0.1797674138614367     0.004590900713791106 
+           0.3                    0.001             0.2817265903366749     0.04295230986904851  
+ 
+ 

Tests/[Genet,2023]/plot_disp_error_vs_regul_strength-ref/heart-contractandtwist-tagging-continuous-equilibrated.dat

+#      noise_level             regul_level             disp_err_avg            disp_err_std     
+           0.0                     0.99            0.26153064798170134             0.0          
+           0.0                     0.8              0.2533805247613701             0.0          
+           0.0                     0.4             0.23004080628673707             0.0          
+           0.0                     0.2             0.19642142258356401             0.0          
+           0.0                     0.1             0.15140511212657487             0.0          
+           0.0                     0.05            0.11278152210054591             0.0          
+           0.0                    0.025            0.08770617747870728             0.0          
+           0.0                    0.0125           0.07012265766540846             0.0          
+           0.0                    0.001            0.023769174394975282            0.0          
+ 
+ 
+           0.1                     0.99            0.26175085030890904    8.392223477230087e-05 
+           0.1                     0.8             0.25418261204546155    0.0002694680486175075 
+           0.1                     0.4             0.23203660186990738    0.0005894278021557493 
+           0.1                     0.2             0.20030585529666028    0.0008688353316659991 
+           0.1                     0.1             0.15714112905528754    0.0014175372215870464 
+           0.1                     0.05            0.11829852493283641    0.0010614184241990472 
+           0.1                    0.025            0.09344896473869002    0.0011857756532892341 
+           0.1                    0.0125           0.07592479660991878     0.001053351874213409 
+           0.1                    0.001             0.0587169249628267    0.0013645664091331115 
+ 
+ 
+           0.2                     0.99            0.26280330171357746    0.00033313081767704023
+           0.2                     0.8              0.2565668116738946     0.000490734150600739 
+           0.2                     0.4             0.23732846835764496    0.0012561674158990384 
+           0.2                     0.2             0.20997900765613844    0.0021498065105989696 
+           0.2                     0.1             0.17182820664687853    0.0025341966582828083 
+           0.2                     0.05             0.1338227932916132     0.001547922691162716 
+           0.2                    0.025            0.10784527159036258     0.001436205648938557 
+           0.2                    0.0125            0.0932597859241224     0.00177477408030495  
+           0.2                    0.001            0.13118952356750835     0.008054871316094782 
+ 
+ 
+           0.3                     0.99             0.2642032154019099    0.0005154854858673839 
+           0.3                     0.8             0.25985065267751883    0.0008379347794531446 
+           0.3                     0.4             0.24478881106718312    0.0013328936814169725 
+           0.3                     0.2             0.22374439485980235     0.001587655807206933 
+           0.3                     0.1             0.19210275344694655     0.002242225851465886 
+           0.3                     0.05            0.15627975959934196     0.003676743574428354 
+           0.3                    0.025            0.13065951293126338     0.004462778546757685 
+           0.3                    0.0125           0.11756169938692887     0.003526680736307381 
+           0.3                    0.001             0.2817265903366749     0.04295230986904851  
+ 
+ 

Tests/[Genet,2023]/plot_disp_error_vs_regul_strength-ref/heart-contractandtwist-tagging-continuous-linear-elastic.dat

+#      noise_level             regul_level             disp_err_avg            disp_err_std     
+           0.0                     0.99             0.8514218516003781             0.0          
+           0.0                     0.8             0.17423536065711664             0.0          
+           0.0                     0.4             0.07153400447260017             0.0          
+           0.0                     0.2              0.0426625799816099             0.0          
+           0.0                     0.1             0.026950823291853433            0.0          
+           0.0                     0.05            0.023212595676364408            0.0          
+           0.0                    0.025            0.021771433080173215            0.0          
+           0.0                    0.0125           0.021943585297099614            0.0          
+           0.0                    0.001            0.023769174394975282            0.0          
+ 
+ 
+           0.1                     0.99             0.852485265763319      0.007861422196648293 
+           0.1                     0.8             0.18413822901450452    0.0019054004423010981 
+           0.1                     0.4             0.07709267173488878    0.0016768645238988756 
+           0.1                     0.2             0.050478241000622946    0.00172830768671845  
+           0.1                     0.1             0.04144551871694992     0.001049322342383999 
+           0.1                     0.05            0.04384573454629243    0.0011743842500646024 
+           0.1                    0.025            0.04794209876751785     0.001211384278680234 
+           0.1                    0.0125           0.051789860547709024   0.0012477276821368105 
+           0.1                    0.001             0.0587169249628267    0.0013645664091331115 
+ 
+ 
+           0.2                     0.99             0.8408314548323632     0.016136150476958766 
+           0.2                     0.8             0.21422285036517802    0.0050808243953227306 
+           0.2                     0.4             0.09197337164247792     0.001424401055186962 
+           0.2                     0.2             0.07181460118358135    0.0030235613605553366 
+           0.2                     0.1             0.07188141414267642     0.002862960472454493 
+           0.2                     0.05            0.08294067563189514     0.002559112549758695 
+           0.2                    0.025            0.09567138029528952     0.00212874166789014  
+           0.2                    0.0125           0.10802283103273554    0.0036108736998476496 
+           0.2                    0.001            0.13118952356750835     0.008054871316094782 
+ 
+ 
+           0.3                     0.99             0.8359775881049206     0.022574940551918974 
+           0.3                     0.8              0.2893190699445056     0.015393679571473681 
+           0.3                     0.4             0.11301912986154447    0.0029631920299840304 
+           0.3                     0.2             0.10178421989288382    0.0025732499710975853 
+           0.3                     0.1             0.11056021791055948     0.002758204305122169 
+           0.3                     0.05            0.13012609849438583     0.002521647874051257 
+           0.3                    0.025             0.154245857961794     0.0029241472368820385 
+           0.3                    0.0125            0.1824500500650738     0.005011402666181719 
+           0.3                    0.001             0.2817265903366749     0.04295230986904851  
+ 
+ 

Tests/[Genet,2023]/plot_disp_error_vs_regul_strength-ref/heart-contractandtwist-tagging-continuous-linear-equilibrated.dat

+#      noise_level             regul_level             disp_err_avg            disp_err_std     
+           0.0                     0.99            0.26176907357634355             0.0          
+           0.0                     0.8             0.25737648801831986             0.0          
+           0.0                     0.4              0.2380717652601589             0.0          
+           0.0                     0.2             0.20497132376547259             0.0          
+           0.0                     0.1             0.15292320728449685             0.0          
+           0.0                     0.05            0.10429484147604344             0.0          
+           0.0                    0.025            0.07651058678104866             0.0          
+           0.0                    0.0125           0.05658306418776406             0.0          
+           0.0                    0.001            0.023769174394975282            0.0          
+ 
+ 
+           0.1                     0.99             0.2619727075130125    7.804786102445839e-05 
+           0.1                     0.8             0.25796531657384836    0.00012057688275377603
+           0.1                     0.4             0.23999774766666593    0.00041577545775570775
+           0.1                     0.2             0.20890663103471535    0.0008720071988507903 
+           0.1                     0.1              0.1596788768384036     0.001682947128399755 
+           0.1                     0.05            0.11059935677478269    0.0013292033173343185 
+           0.1                    0.025            0.08240256274899171    0.0014064305516321982 
+           0.1                    0.0125           0.06282692063242155    0.0015077643013726824 
+           0.1                    0.001             0.0587169249628267    0.0013645664091331115 
+ 
+ 
+           0.2                     0.99            0.26298912717885303    0.00033016357357358003
+           0.2                     0.8              0.2598005198493086    0.00031581685927636367
+           0.2                     0.4             0.24489504533875506    0.0008032987374102602 
+           0.2                     0.2             0.21876514143041192    0.0018789885764728424 
+           0.2                     0.1              0.176658900809636     0.0031151363980191984 
+           0.2                     0.05            0.12829543861760245    0.0021753474986908067 
+           0.2                    0.025            0.09809755793527879     0.001408776581681979 
+           0.2                    0.0125           0.08129149891559301     0.002525005942575945 
+           0.2                    0.001            0.13118952356750835     0.008054871316094782 
+ 
+ 
+           0.3                     0.99             0.2643279130469586    0.0005078960688163275 
+           0.3                     0.8             0.26238225580702135    0.0006390601762918886 
+           0.3                     0.4              0.2515361747181659    0.0009679284590499659 
+           0.3                     0.2             0.23189323389102462    0.0013150124382134468 
+           0.3                     0.1             0.19818032826331716    0.0023123736432799366 
+           0.3                     0.05            0.15244726949571172     0.005038949572545782 
+           0.3                    0.025            0.12132980879108539     0.005329033241025868 
+           0.3                    0.0125           0.10755846695843137     0.003975549129724922 
+           0.3                    0.001             0.2817265903366749     0.04295230986904851  
+ 
+ 

Tests/[Genet,2023]/plot_disp_error_vs_regul_strength-ref/heart-contractandtwist-tagging-discrete-equilibrated-tractions-normal-tangential.dat

+#      noise_level             regul_level             disp_err_avg            disp_err_std     
+           0.0                     0.99            0.01502388509498367             0.0          
+           0.0                     0.8             0.014797104337154313            0.0          
+           0.0                     0.4             0.01440795240847769             0.0          
+           0.0                     0.2             0.01455592370546379             0.0          
+           0.0                     0.1             0.014814075659159301            0.0          
+           0.0                     0.05            0.015373063216052573            0.0          
+           0.0                    0.025            0.016167334612908014            0.0          
+           0.0                    0.0125           0.017193048075291727            0.0          
+           0.0                    0.001            0.023769174394975282            0.0          
+ 
+ 
+           0.1                     0.99            0.024473749826257284   0.0009227437827716936 
+           0.1                     0.8             0.02483992707101328    0.0008752490098760181 
+           0.1                     0.4             0.02569871413934796    0.0008697965398781323 
+           0.1                     0.2             0.026766482413945282   0.0008572185859865812 
+           0.1                     0.1             0.028244824883774815   0.0008513354791712042 
+           0.1                     0.05            0.03035645504174131    0.0009327933349009069 
+           0.1                    0.025            0.03284022280077821    0.0009574758336122536 
+           0.1                    0.0125           0.035676858183218925   0.0010074682424075518 
+           0.1                    0.001            0.05661630186659864    0.0006583046470288724 
+ 
+ 
+           0.2                     0.99            0.045927081376641324   0.0014637549037967547 
+           0.2                     0.8             0.046626140591942214   0.0014023691101281797 
+           0.2                     0.4             0.04927486180021969    0.0010921139581210385 
+           0.2                     0.2             0.051992719060593315   0.0010540789214171515 
+           0.2                     0.1             0.05558228091662622    0.0011247656216955184 
+           0.2                     0.05            0.05998619581549295    0.0013223958859000622 
+           0.2                    0.025            0.06565954248216936    0.0014421631006750852 
+           0.2                    0.0125           0.07193385981883141    0.0013681544551986183 
+           0.2                    0.001            0.13118952356750835     0.008054871316094782 
+ 
+ 
+           0.3                     0.99            0.07595244237323535     0.002880403777644044 
+           0.3                     0.8             0.07720326559343532     0.002925209040129758 
+           0.3                     0.4             0.08227397522084508      0.0039370962523901  
+           0.3                     0.2             0.08698054936470609     0.003993353564990639 
+           0.3                     0.1             0.09318003959242836     0.004521563104319278 
+           0.3                     0.05             0.0998098270450993     0.005441394334415846 
+           0.3                    0.025            0.10950220791986061     0.006088195419470233 
+           0.3                    0.0125           0.12162359604677295     0.010469936156434744 
+           0.3                    0.001             0.2817265903366749     0.04295230986904851  
+ 
+