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  • mgenet/dolfin_warp
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.gitignore
View file @ 16d89f95
...@@ -2,3 +2,7 @@ ...@@ -2,3 +2,7 @@
*.kdev4* *.kdev4*
.spyproject .spyproject
.DS_Store .DS_Store
build
dist
*.egg-info
.vscode
.gitlab-ci.yml 0 → 100644
View file @ 16d89f95
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 0 → 100644
View file @ 16d89f95
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
ImageIterator.py deleted 100644 → 0
View file @ 77e207e9
#coding=utf8
################################################################################
### ###
### Created by Martin Genet, 2016-2019 ###
### ###
### École Polytechnique, Palaiseau, France ###
### ###
################################################################################
from builtins import range
import dolfin
import glob
import numpy
import os
import time
import vtk
import myPythonLibrary as mypy
import myVTKPythonLibrary as myvtk
import dolfin_dic as ddic
################################################################################
class ImageIterator():
def __init__(self,
problem,
solver,
parameters={}):
self.problem = problem
self.printer = self.problem.printer
self.solver = solver
self.working_folder = parameters["working_folder"] if ("working_folder" in parameters) else "."
self.working_basename = parameters["working_basename"] if ("working_basename" in parameters) else "sol"
self.register_ref_frame = parameters["register_ref_frame"] if ("register_ref_frame" in parameters) else False
self.initialize_U_from_file = parameters["initialize_U_from_file"] if ("initialize_U_from_file" in parameters) else False
self.initialize_U_folder = parameters["initialize_U_folder"] if ("initialize_U_folder" in parameters) else "."
self.initialize_U_basename = parameters["initialize_U_basename"] if ("initialize_U_basename" in parameters) else None
self.initialize_U_ext = parameters["initialize_U_ext"] if ("initialize_U_ext" in parameters) else "vtu"
self.initialize_U_array_name = parameters["initialize_U_array_name"] if ("initialize_U_array_name" in parameters) else "displacement"
self.initialize_DU_with_DUold = parameters["initialize_DU_with_DUold"] if ("initialize_DU_with_DUold" in parameters) else False
def iterate(self):
if not os.path.exists(self.working_folder):
os.mkdir(self.working_folder)
pvd_basename = self.working_folder+"/"+self.working_basename
for vtu_filename in glob.glob(pvd_basename+"_[0-9]*.vtu"):
os.remove(vtu_filename)
self.printer.print_str("Initializing QOI file…")
self.printer.inc()
qoi_names = ["k_frame"]+self.problem.get_qoi_names()
qoi_filebasename = self.working_folder+"/"+self.working_basename+"-qoi"
qoi_printer = mypy.DataPrinter(
names=qoi_names,
filename=qoi_filebasename+".dat")
if not (self.register_ref_frame):
self.printer.print_str("Writing initial solution…")
self.printer.inc()
ddic.write_VTU_file(
filebasename=pvd_basename,
function=self.problem.U,
time=self.problem.images_ref_frame)
self.printer.dec()
self.printer.print_str("Writing initial QOI…")
self.printer.inc()
qoi_values = [self.problem.images_ref_frame]+self.problem.get_qoi_values()
qoi_printer.write_line(
values=qoi_values)
self.printer.dec()
self.printer.print_str("Looping over frames…")
if (self.initialize_U_from_file):
mesh_series = ddic.MeshSeries(
problem=self.problem,
folder=self.initialize_U_folder,
basename=self.initialize_U_basename,
ext=self.initialize_U_ext)
dof_to_vertex_map = dolfin.dof_to_vertex_map(self.problem.U_fs)
n_iter_tot = 0
global_success = True
for forward_or_backward in ["forward","backward"]:
self.printer.print_var("forward_or_backward",forward_or_backward)
if (forward_or_backward == "forward"):
if not (self.register_ref_frame):
k_frames = range(self.problem.images_ref_frame+1, self.problem.images_n_frames, +1)
else:
k_frames = range(self.problem.images_ref_frame , self.problem.images_n_frames, +1)
elif (forward_or_backward == "backward"):
if not (self.register_ref_frame):
k_frames = range(self.problem.images_ref_frame-1, -1, -1)
else:
k_frames = range(self.problem.images_ref_frame , -1, -1)
#self.printer.print_var("k_frames",k_frames)
if (forward_or_backward == "backward"):
self.problem.reinit()
self.printer.inc()
success = True
for k_frame in k_frames:
self.printer.print_var("k_frame",k_frame,-1)
if (forward_or_backward == "forward"):
k_frame_old = k_frame-1
elif (forward_or_backward == "backward"):
k_frame_old = k_frame+1
#self.printer.print_var("k_frame_old",k_frame_old,-1)
if (self.initialize_U_from_file):
mesh = mesh_series.get_mesh(k_frame)
array_U = mesh.GetPointData().GetArray(self.initialize_U_array_name)
array_U = vtk.util.numpy_support.vtk_to_numpy(array_U)[:,:self.problem.mesh_dimension]
# print(array_U)
# array_U = array_U.astype(float)
# print(array_U)
array_U = numpy.reshape(array_U, array_U.size)
# print(array_U)
self.problem.U.vector()[:] = array_U[dof_to_vertex_map]
elif (self.initialize_DU_with_DUold):
self.problem.U.vector().axpy(1., self.problem.DUold.vector())
self.problem.call_before_solve(
k_frame=k_frame,
k_frame_old=k_frame_old)
self.printer.print_str("Running registration…")
success, n_iter = self.solver.solve(
k_frame=k_frame)
n_iter_tot += n_iter
if not (success):
global_success = False
break
self.problem.call_after_solve()
self.printer.print_str("Writing solution…")
self.printer.inc()
ddic.write_VTU_file(
filebasename=pvd_basename,
function=self.problem.U,
time=k_frame)
self.printer.dec()
self.printer.print_str("Writing QOI…")
self.printer.inc()
qoi_printer.write_line(
[k_frame]+self.problem.get_qoi_values())
self.printer.dec()
self.printer.dec()
if not (global_success):
break
self.printer.print_str("Image iterator finished…")
self.printer.inc()
self.printer.print_var("n_iter_tot",n_iter_tot)
self.printer.dec()
self.printer.print_str("Plotting QOI…")
qoi_printer.close()
commandline = "gnuplot -e \"set terminal pdf;"
commandline += " set output '"+qoi_filebasename+".pdf';"
commandline += " set grid;"
for k_qoi in range(1,len(qoi_names)):
commandline += " plot '"+qoi_filebasename+".dat' u 1:"+str(1+k_qoi)+" lw 3 title '"+qoi_names[k_qoi]+"';"
commandline += "\""
os.system(commandline)
return global_success
Docker/dolfin_dic-dev-2017.2.0/Dockerfile → LEGACY/Docker/dolfin_warp-2017.2.0-dev/Dockerfile
View file @ 16d89f95
#FROM ubuntu:latest # FEniCS base
#FROM quay.io/fenicsproject/stable:2016.1.0
#FROM quay.io/fenicsproject/stable:2016.2.0 # FROM ubuntu:latest
#FROM quay.io/fenicsproject/stable:2017.1.0 # 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:2017.2.0
#FROM quay.io/fenicsproject/stable:current # FROM quay.io/fenicsproject/stable:current
#FROM quay.io/fenicsproject/stable:latest # FROM quay.io/fenicsproject/stable:latest
#USER root # 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 -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/*
#RUN apt-get update; apt-get install -y software-properties-common # basic stuff
#RUN add-apt-repository -y ppa:fenics-packages/fenics-2016.1.0 RUN apt-get update; apt-get -y install rename; apt-get clean; rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
#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/*
RUN apt-get update; apt-get -y install python-future python-numpy; 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/* 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 ENV CPATH="/usr/include/vtk-6.2":$CPATH
# gnuplot stuff
RUN apt-get update; apt-get -y install gnuplot git; apt-get clean; rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* RUN apt-get update; apt-get -y install gnuplot git; apt-get clean; rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
WORKDIR /home/fenics WORKDIR /home/fenics
RUN git clone https://github.com/aschn/gnuplot-colorbrewer.git RUN git clone https://github.com/aschn/gnuplot-colorbrewer.git
RUN echo "set loadpath \"/home/fenics/gnuplot-colorbrewer/diverging:/home/fenics/gnuplot-colorbrewer/qualitative:/home/fenics/gnuplot-colorbrewer/sequential\"" > .gnuplot RUN echo "set loadpath \"/home/fenics/gnuplot-colorbrewer/diverging:/home/fenics/gnuplot-colorbrewer/qualitative:/home/fenics/gnuplot-colorbrewer/sequential\"" > .gnuplot
# environment setup
WORKDIR /home/fenics WORKDIR /home/fenics
RUN mkdir code RUN mkdir code
ENV PYTHONPATH=/home/fenics/code:$PYTHONPATH ENV PYTHONPATH=/home/fenics/code:$PYTHONPATH
ENV PATH=/home/fenics/code/myPythonLibrary:/home/fenics/code/myVTKPythonLibrary:/home/fenics/code/vtkpython_cbl:$PATH 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 #USER root
Docker/dolfin_dic/Dockerfile → LEGACY/Docker/dolfin_warp-2017.2.0/Dockerfile
View file @ 16d89f95
FROM dolfin_dic-dev 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/* 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 WORKDIR /home/fenics/code
RUN git clone https://gitlab.inria.fr/mgenet/myPythonLibrary.git 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/myVTKPythonLibrary.git
RUN git clone https://gitlab.inria.fr/mgenet/vtkpython_cbl.git RUN git clone https://gitlab.inria.fr/mgenet/vtkpython_cbl.git
RUN git clone https://gitlab.inria.fr/mgenet/dolfin_cm.git RUN git clone https://gitlab.inria.fr/mgenet/dolfin_mech.git
RUN git clone https://gitlab.inria.fr/mgenet/dolfin_dic.git RUN git clone https://gitlab.inria.fr/mgenet/dolfin_warp.git
Docker/dolfin_dic-dev/Dockerfile → LEGACY/Docker/dolfin_warp-2019.1.0-dev/Dockerfile
View file @ 16d89f95
# FEniCS base
FROM quay.io/fenicsproject/stable:2019.1.0.r3 FROM quay.io/fenicsproject/stable:2019.1.0.r3
RUN apt-get update; apt-get -y install python3-future python3-numpy; 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/*
# 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/* 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 ENV CPATH="/usr/include/vtk-7.1":$CPATH
# gnuplot stuff
RUN apt-get update; apt-get -y install gnuplot git; apt-get clean; rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* RUN apt-get update; apt-get -y install gnuplot git; apt-get clean; rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
WORKDIR /home/fenics WORKDIR /home/fenics
RUN git clone https://github.com/aschn/gnuplot-colorbrewer.git RUN git clone https://github.com/aschn/gnuplot-colorbrewer.git
RUN echo "set loadpath \"/home/fenics/gnuplot-colorbrewer/diverging:/home/fenics/gnuplot-colorbrewer/qualitative:/home/fenics/gnuplot-colorbrewer/sequential\"" > .gnuplot RUN echo "set loadpath \"/home/fenics/gnuplot-colorbrewer/diverging:/home/fenics/gnuplot-colorbrewer/qualitative:/home/fenics/gnuplot-colorbrewer/sequential\"" > .gnuplot
# optimization stuff
RUN pip install git+https://github.com/dolfin-adjoint/pyadjoint.git@2019.1.0 cma nlopt sklearn
# environment setup
WORKDIR /home/fenics WORKDIR /home/fenics
RUN mkdir code RUN mkdir code
ENV PYTHONPATH=/home/fenics/code:$PYTHONPATH ENV PYTHONPATH=/home/fenics/code:$PYTHONPATH
ENV PATH=/home/fenics/code/myPythonLibrary:/home/fenics/code/myVTKPythonLibrary:/home/fenics/code/vtkpython_cbl:$PATH 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 0 → 100644
View file @ 16d89f95
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
README.md
View file @ 16d89f95
# dolfin_dic # dolfin_warp
A set of FEniCS- and VTK-based python tools for Finite Element Digital Image Correlation, basically implementing the method described in [[Genet et al., 2018, Medical Image Analysis]](https://www.medicalimageanalysisjournal.com/article/S1361-8415(18)30534-6/fulltext).
### Requirements 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)].
First you need to install [myPythonLibrary](https://gitlab.inria.fr/mgenet/myPythonLibrary), [myVTKPythonLibrary](https://gitlab.inria.fr/mgenet/myVTKPythonLibrary) as well as [dolfin_cm](https://gitlab.inria.fr/mgenet/dolfin_cm). You also need a working installation of FEniCS (including DOLFIN python interface) & VTK (also including python interface).
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 ### Installation
Get the code:
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:
``` ```
git clone https://gitlab.inria.fr/mgenet/dolfin_dic.git 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
``` ```
To be able to load the library within python, the simplest is to add the folder containing `dolfin_dic` to the `PYTHONPATH` environment variable:
```
export PYTHONPATH=$PYTHONPATH:/path/to/folder
```
(To make this permanent, add the line to `~/.bashrc`.)
Then you should be able to load the library within python:
```
import dolfin_dic as ddic
```
\ No newline at end of file
Tests/Makefile 0 → 100644
View file @ 16d89f95
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 0 → 100644
View file @ 16d89f95
#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 0 → 100644
View file @ 16d89f95
#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 0 → 100644
View file @ 16d89f95
# 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 0 → 100644
View file @ 16d89f95
# 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 0 → 100644
View file @ 16d89f95
#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 0 → 100644
View file @ 16d89f95
# 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 0 → 100644
View file @ 16d89f95
# 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 0 → 100644
View file @ 16d89f95
# 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 0 → 100644
View file @ 16d89f95
# 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 0 → 100644
View file @ 16d89f95
# 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