diff options
| author | mathieu <mathieu.carriere3@gmail.com> | 2020-03-10 19:49:58 -0400 |
|---|---|---|
| committer | mathieu <mathieu.carriere3@gmail.com> | 2020-03-10 19:49:58 -0400 |
| commit | 700e632ee467fe482dc4dcb363433eed953df86b (patch) | |
| tree | 3330c42b17ee8369600d5a341c7c9478c83e0fb0 | |
| parent | 5b7df6d0f6807b87ad936f7c322355de22bd516f (diff) | |
| parent | 7a5b614aa3bd06897e0135f0cda4e61f16951b20 (diff) | |
Merge branch 'master' of https://github.com/GUDHI/gudhi-devel into extended_persistence
44 files changed, 532 insertions, 197 deletions
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md new file mode 100644 index 00000000..a18ff8bd --- /dev/null +++ b/.github/CONTRIBUTING.md @@ -0,0 +1,48 @@ +# Contributing to GUDHI + +First of all, thank you for the time you may take to contribute to GUDHI ! + +# In case you have a question + +Please, check our [contact web page](https://gudhi.inria.fr/contact/). + +# In case you found an issue + +Please, first check [opened issues on GUDHI](https://github.com/GUDHI/gudhi-devel/issues). + +If the problem you are facing is not referenced, do not hesitate to open a [new issue](https://github.com/GUDHI/gudhi-devel/issues/new). + +This place is also a good place if you have some enhancement you want to propose. +There is a label **enhancement** in the [new issue](https://github.com/GUDHI/gudhi-devel/issues/new) page. + +# In case you want to contribute to GUDHI + +## You are not familiar with GitHub ? + +Please take some time to read our [how to use GitHub to contribute to GUDHI](how_to_use_github_to_contribute_to_gudhi.md). + +## Something you want to improve in the documentation + +For C++ documentation, you can find it in the directories: +* *src/common/doc* for the main page and installation instructions +* *src/NAME_OF_THE_MODULE/doc* for the main page of a module +* *src/NAME_OF_THE_MODULE/include/gudhi* for the documentation generated from the code. +We use Doxygen to generate the code and you will be able to verify the result in CircleCI Doxygen target in the artifacts. + +For Python documentation, you can find it in the directories: +* *src/python/doc* for the main page, installation instructionsand for the main pages of the modules +* *src/python/gudhi/NAME_OF_THE_MODULE.pyx* for the documentation generated from the code. +We use Sphinx to generate the code and you will be able to verify the result in CircleCI Sphinx target in the artifacts. + +## Something you want to improve in the code + +We don't ask for any paperwork but we expect you don't submit anything you are not allowed to: +* check that your work contract and your employer allow you to contribute to this open source project. +* insure you do not violate someone's intellectual property. +* ... + +Please, take some time to read our [code conventions](code_conventions.md) + +As a convention, we set a Pull Request as a **Draft Pull Request** when we work on something we want the other contributors to see. + +We click on **Ready for review** to ask for a peer review of the contribution. diff --git a/.github/build-requirements.txt b/.github/build-requirements.txt new file mode 100644 index 00000000..7de60d23 --- /dev/null +++ b/.github/build-requirements.txt @@ -0,0 +1,5 @@ +setuptools +wheel +numpy +Cython +pybind11
\ No newline at end of file diff --git a/for_dev/code_conventions.md b/.github/code_conventions.md index 5882f78e..9724f722 100644 --- a/for_dev/code_conventions.md +++ b/.github/code_conventions.md @@ -21,6 +21,27 @@ * The name of the "project" should be in this form: `Package_[tests|examples|…]`. E.g. `project(Simplex_tree_examples)`. * The name if each "target" (first parameter of add_executable) should be in this form: `Package_{name of the cpp file without extension}`. E.g `add_executable(Subsampling_test_sparsify_point_set test_sparsify_point_set.cpp)`. +### Code style +We are using [google c++ style guide](https://google.github.io/styleguide/cppguide.html) recommendations with 120 characters per line of code. +[clang-format](https://clang.llvm.org/docs/ClangFormat.html) can be used to format automatically your code: +```bash +cd src # there is a .clang-format file with these specifications +clang-format -style=file -i Simplex_tree/include/gudhi/Simplex_tree.h # -i means in place, your file will be modified +``` + +### Template +Please use the file [following template](copyright_template.h). + ## Python -In progress...
\ No newline at end of file +In progress... + +### Code style +We are using [PEP8 Python style guide](https://www.python.org/dev/peps/pep-0008/) recommendations with 120 characters per line of code. +[black](https://black.readthedocs.io/en/stable/) can be used to format automatically your code: +```bash +black -l 120 src/python/example/bottleneck_basic_example.py +``` + +### Template +Please use the file [following template](copyright_template.py). diff --git a/.github/copyright_template.h b/.github/copyright_template.h new file mode 100644 index 00000000..30034f1b --- /dev/null +++ b/.github/copyright_template.h @@ -0,0 +1,14 @@ +/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + * Author(s): [AUTHOR NAME] + * + * Copyright (C) [YEAR] [COPYRIGHT] + * + * Modification(s): + * - YYYY/MM Author: Description of the modification + */ + +#ifndef [FILE_NAME]_H_ +#define [FILE_NAME]_H_ + +#endif // [FILE_NAME]_H_
\ No newline at end of file diff --git a/.github/copyright_template.py b/.github/copyright_template.py new file mode 100644 index 00000000..667f985d --- /dev/null +++ b/.github/copyright_template.py @@ -0,0 +1,8 @@ +# This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. +# See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. +# Author(s): [AUTHOR NAME] +# +# Copyright (C) [YEAR] [COPYRIGHT] +# +# Modification(s): +# - YYYY/MM Author: Description of the modification diff --git a/for_dev/for_maintainers/new_gudhi_version_creation.md b/.github/for_maintainers/new_gudhi_version_creation.md index 4a40f373..f176d392 100644 --- a/for_dev/for_maintainers/new_gudhi_version_creation.md +++ b/.github/for_maintainers/new_gudhi_version_creation.md @@ -87,9 +87,6 @@ ln -s @GUDHI_VERSION@ latest * Tick the *This is a pre-release* check button if this is a release candidate (untick if this is an official version) * Click the *Publish the release* button -***[Where X, Y and Z corresponds respectively to the major, minor, and patch version number]*** - - ## Mail sending Send version mail to the following lists : * gudhi-devel@lists.gforge.inria.fr diff --git a/for_dev/for_maintainers/next_release_template.md b/.github/for_maintainers/next_release_template.md index a2805a55..a2805a55 100644 --- a/for_dev/for_maintainers/next_release_template.md +++ b/.github/for_maintainers/next_release_template.md diff --git a/.github/how_to_use_github_to_contribute_to_gudhi.md b/.github/how_to_use_github_to_contribute_to_gudhi.md new file mode 100644 index 00000000..6ab05e36 --- /dev/null +++ b/.github/how_to_use_github_to_contribute_to_gudhi.md @@ -0,0 +1,124 @@ +# How to use github to contribute to gudhi + +Similar information is available in many places: +* https://jarv.is/notes/how-to-pull-request-fork-github/ (this one is using `upstream/master` when creating a new branch) +* https://help.github.com/en/github/getting-started-with-github/fork-a-repo +* https://blog.scottlowe.org/2015/01/27/using-fork-branch-git-workflow/ +* https://gist.github.com/Chaser324/ce0505fbed06b947d962 +* etc + +## Get a github account +I assume the account is called **LOGIN**, please replace as appropriate below. Log in to github.com using this account. + +## Fork GUDHI/gudhi-devel project +Go to https://github.com/GUDHI/gudhi-devel and click on **fork** (top right). +Feel free to also click on the star next to it to show you like the project! +You can see your fork at https://github.com/LOGIN/gudhi-devel + +## Create a local clone on your computer +```bash +git clone https://github.com/LOGIN/gudhi-devel.git +``` + +This creates a directory gudhi-devel, which you are free to move around or rename. For the following, change to that directory: +```bash +cd gudhi-devel +``` + +Everytime you clone the repository, you will have to download the *submodules*. + +## Submodules +An interface to Hera for Wasserstein distance is available on an external git repository. To download it: +```bash +git submodule update --init +``` + +## Configuring a remote for a fork +```bash +git remote add upstream https://github.com/GUDHI/gudhi-devel.git +``` + +because you want to see the real gudhi, not just your clone. +(It is perfectly possible to do things in the reverse order, clone from GUDHI and add the one in LOGIN as extra remote, but the names of the remotes may not match the rest of this document. You can change the name of a remote with `git remote rename oldname newname`) + +## Optional remotes +Optional, if you are interested in one of the old branches +```bash +git remote add oldies https://github.com/GUDHI/branches.git +``` + +Or if you want to spy on someone's work. I assume the someone's account is called **SOMEONE** +```bash +git remote add someone https://github.com/SOMEONE/gudhi-devel.git +``` + +## Stay up-to-date +```bash +git fetch -p --all +``` +This is a command you can run quite regularly. +It tells git to check all that happened on github. +It is safe, it will not mess with your files. + +**Reminder:** Everytime you checkout master or merge from master, afterwards, if the version of one the submodule has changed, or if a submodule was added, you will have to: +```bash +git submodule update --init +``` + +## Create a branch, based on the current master +```bash +git checkout -b some-fancy-name --no-track upstream/master +``` +Your local branch `master` and the one on your github clone are useless and often outdated, but for technical reasons there has to exist at least one branch at all times, it might as well be that one. upstream/master is the real deal, that's what you want to base your new branch on. + +## The real coding is here! +Edit files, test, etc. + +## Commit your changes (locally) +The basic command is just `git commit`, but it will do nothing by default. +You need `git add my_new_file` for every new file you want to commit. +And usually you'll want to use `git commit -a` so that all files that git already knows about and that have been modified get committed. + +## Push your changes (remotely) +```bash +git push -u origin some-fancy-name +``` +This puts a copy of your branch on your online clone of gudhi-devel. +Because of `-u`, it will remember where you like to push this branch, and next time you can just use `git push`. + +## Play again! +Possibly iterate a few times, add more commits and push them. + +## Your pull request is ready +Do not forget to update `.github/next_release.md` to announce your development in the next release note. + +Get your web browser to https://github.com/LOGIN/gudhi-devel, click on the button that says **Branch: some-name** (below the number of commits, above the list of files) and select the branch you are so proud of. +Click on **New pull request** next to it. + +## Follow the instructions ;-) +Note that if your branch is not quite ready, you can make a **draft pull request** (see the arrow next to the confirmation button), and later you will have access to a button to say that the branch is ready for reviews now. +Draft pull requests can be a way to advertise that you are working on something, and possibly ask others for comments or help. + +## Code review +Make sure you follow the discussion on your pull request, answer questions, take comments into account. +You can keep pushing new commits on your branch to your fork of gudhi-devel, the pull request will automatically notice the new commits there. +There is no need to create a new pull request. +Once the branch is under review, fixing issues is good, but please refrain from adding extra features, that just makes the reviewers' job harder and thus slower. +You may want to look at https://github.com/settings/notifications (and other settings nearby) if you don't receive emails when people comment on your pull request. +Some bold reviewer might make changes to your branch. You will then need `git pull` for your local branch to reflect those. + +## Your work is merged! +Once your pull request has been closed (your branch merged), you can remove your branch, both locally and also the branch on your github fork: +```bash +git checkout master # or any other branch, but you cannot remove the branch you are currently in +git branch -d some-fancy-name # local branch delete +git push origin --delete some-fancy-name # remote branch delete +``` +If you add @VincentRouvreau or @mglisse as collaborator (https://github.com/LOGIN/gudhi-devel/settings/collaboration), they may remove the branch on your clone at the same time as they merge the branch, so you only have the local one to remove (or keep if you are nostalgic). + +## Keep in touch +Create a new branch and keep contributing! + +Do not try to reuse an old branch that has already been merged. +Make sure you run the fetch command just before creating any new branch, so you don't base it on some outdated version of master. +You can also work on several branches at the same time, using `git checkout some-fancy-name` and `git checkout name-of-other-branch` to switch between them (commit before switching or things may get complicated). diff --git a/for_dev/next_release.md b/.github/next_release.md index a2805a55..3166b0a8 100644 --- a/for_dev/next_release.md +++ b/.github/next_release.md @@ -1,19 +1,20 @@ We are pleased to announce the release 3.X.X of the GUDHI library. -As a major new feature, the GUDHI library now offers ... +As a major new feature, the GUDHI library now offers a Python interface to [Hera](https://bitbucket.org/grey_narn/hera/src/master/) to compute the Wasserstein distance. +[PyBind11](https://github.com/pybind/pybind11) is now required to build the Python module. We are now using GitHub to develop the GUDHI library, do not hesitate to [fork the GUDHI project on GitHub](https://github.com/GUDHI/gudhi-devel). From a user point of view, we recommend to download GUDHI user version (gudhi.3.X.X.tar.gz). -Below is a list of changes made since GUDHI 3.X-1.X-1: +Below is a list of changes made since GUDHI 3.1.1: -- [Module](link) - - ... +- [Wassertein distance](https://gudhi.inria.fr/python/latest/wasserstein_distance_user.html) + - An another implementation comes from Hera (BSD-3-Clause) which is based on [Geometry Helps to Compare Persistence Diagrams](http://doi.acm.org/10.1145/3064175) by Michael Kerber, Dmitriy Morozov, and Arnur Nigmetov. - [Module](link) - ... - Miscellaneous - - The [list of bugs that were solved since GUDHI-3.X-1.X-1](https://github.com/GUDHI/gudhi-devel/issues?q=label%3A3.1.1+is%3Aclosed) is available on GitHub. + - The [list of bugs that were solved since GUDHI-3.1.1](https://github.com/GUDHI/gudhi-devel/issues?q=label%3A3.2.0+is%3Aclosed) is available on GitHub. All modules are distributed under the terms of the MIT license. However, there are still GPL dependencies for many modules. We invite you to check our [license dedicated web page](https://gudhi.inria.fr/licensing/) for further details. diff --git a/.github/test-requirements.txt b/.github/test-requirements.txt new file mode 100644 index 00000000..bd03f98e --- /dev/null +++ b/.github/test-requirements.txt @@ -0,0 +1,8 @@ +pytest +sphinx +sphinxcontrib-bibtex +sphinx-paramlinks +matplotlib +scipy +scikit-learn +POT
\ No newline at end of file diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 8980be10..00000000 --- a/.travis.yml +++ /dev/null @@ -1,78 +0,0 @@ -language: cpp - -sudo: required - -git: - depth: 3 - -os: osx -osx_image: xcode10.2 -compiler: clang - -matrix: - include: - - env: - # 1. Only examples and associated tests - - CMAKE_EXAMPLE='ON' CMAKE_TEST='OFF' CMAKE_UTILITIES='OFF' CMAKE_PYTHON='OFF' MAKE_TARGET='all' CTEST_COMMAND='ctest --output-on-failure' - - env: - # 2. Only unitary tests - - CMAKE_EXAMPLE='OFF' CMAKE_TEST='ON' CMAKE_UTILITIES='OFF' CMAKE_PYTHON='OFF' MAKE_TARGET='all' CTEST_COMMAND='ctest --output-on-failure' - - env: - # 3. Only utilities and associated tests - - CMAKE_EXAMPLE='OFF' CMAKE_TEST='OFF' CMAKE_UTILITIES='ON' CMAKE_PYTHON='OFF' MAKE_TARGET='all' CTEST_COMMAND='ctest --output-on-failure' - - env: - # 4. Only doxygen documentation - - CMAKE_EXAMPLE='OFF' CMAKE_TEST='OFF' CMAKE_UTILITIES='OFF' CMAKE_PYTHON='OFF' MAKE_TARGET='doxygen' CTEST_COMMAND='echo No tests for doxygen target' - - env: - # 5. Only Python, associated tests and sphinx documentation - # $ which python3 => /usr/local/bin/python3 - # cmake => -- Found PythonInterp: /usr/local/bin/python3 (found version "3.7.5") - # In python3-sphinx-build.py, print(sys.executable) => /usr/local/opt/python/bin/python3.7 ??? - # should be : MAKE_TARGET='all sphinx' CTEST_COMMAND='ctest --output-on-failure' - - CMAKE_EXAMPLE='OFF' CMAKE_TEST='OFF' CMAKE_UTILITIES='OFF' CMAKE_PYTHON='ON' MAKE_TARGET='all' CTEST_COMMAND='ctest --output-on-failure -E sphinx' - -cache: - directories: - - $HOME/.cache/pip - - $HOME/Library/Caches/Homebrew - -before_install: - - brew update && brew unlink python@2 && brew upgrade python - -addons: - homebrew: - packages: - - python3 - - cmake - - graphviz - - doxygen - - boost - - eigen - - gmp - - mpfr - - tbb - - cgal - -before_cache: - - rm -f $HOME/.cache/pip/log/debug.log - - brew cleanup - -# When installing through libcgal-dev apt, CMake Error at CGAL Exports.cmake The imported target "CGAL::CGAL Qt5" references the file -install: - - python3 -m pip install --upgrade pip setuptools wheel - - python3 -m pip install --user pytest Cython sphinx sphinxcontrib-bibtex sphinx-paramlinks matplotlib numpy scipy scikit-learn - - python3 -m pip install --user POT pybind11 - -script: - - rm -rf build - - mkdir -p build - - cd build - - cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=${CMAKE_EXAMPLE} -DWITH_GUDHI_TEST=${CMAKE_TEST} -DWITH_GUDHI_UTILITIES=${CMAKE_UTILITIES} -DWITH_GUDHI_PYTHON=${CMAKE_PYTHON} -DUSER_VERSION_DIR=version -DPython_ADDITIONAL_VERSIONS=3 .. - - make ${MAKE_TARGET} - - ${CTEST_COMMAND} - - cd .. - -notifications: - email: - on_success: change # default: always - on_failure: always # default: always diff --git a/CMakeLists.txt b/CMakeLists.txt index d9244dc0..0b5f5144 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -65,7 +65,7 @@ include(GUDHI_user_version_target) # For "make doxygen" - Requires GUDHI_USER_VERSION_DIR to be set - Done in GUDHI_user_version_target for dev version include(GUDHI_doxygen_target) -configure_file(${CMAKE_SOURCE_DIR}/for_dev/for_maintainers/new_gudhi_version_creation.md "${CMAKE_CURRENT_BINARY_DIR}/" @ONLY) +configure_file(${CMAKE_SOURCE_DIR}/.github/for_maintainers/new_gudhi_version_creation.md "${CMAKE_CURRENT_BINARY_DIR}/" @ONLY) message("++ GUDHI_MODULES list is:\"${GUDHI_MODULES}\"") message("++ GUDHI_MISSING_MODULES list is:\"${GUDHI_MISSING_MODULES}\"") diff --git a/Dockerfile_for_circleci_image b/Dockerfile_for_circleci_image index ebd2f366..1eededb5 100644 --- a/Dockerfile_for_circleci_image +++ b/Dockerfile_for_circleci_image @@ -30,7 +30,7 @@ RUN apt-get install -y make \ cmake \ graphviz \ perl \ - texlive-bibtex-extra \ + texlive-full \ biber \ doxygen \ libboost-all-dev \ @@ -42,24 +42,16 @@ RUN apt-get install -y make \ locales \ python3 \ python3-pip \ - python3-pytest \ python3-tk \ - python3-pybind11 \ libfreetype6-dev \ - pkg-config + pkg-config \ + curl -RUN pip3 install \ - setuptools \ - numpy \ - matplotlib \ - scipy \ - Cython \ - POT \ - scikit-learn \ - sphinx \ - sphinx-paramlinks \ - sphinxcontrib-bibtex \ - tensorflow +ADD .github/build-requirements.txt / +ADD .github/test-requirements.txt / + +RUN pip3 install -r build-requirements.txt +RUN pip3 install -r test-requirements.txt # apt clean up RUN apt autoremove && rm -rf /var/lib/apt/lists/* @@ -1,7 +1,7 @@ -[](https://travis-ci.org/GUDHI/gudhi-devel) -[](https://circleci.com/gh/GUDHI/gudhi-devel/tree/master) -[](https://ci.appveyor.com/project/GUDHI/gudhi-devel/branch/master) +[](https://dev.azure.com/GUDHI/gudhi-devel/_build/latest?definitionId=1&branchName=master) +[](https://circleci.com/gh/GUDHI/gudhi-devel/tree/master) +[](https://ci.appveyor.com/project/GUDHI/gudhi-devel/branch/master) [](https://anaconda.org/conda-forge/gudhi) [](https://anaconda.org/conda-forge/gudhi) diff --git a/azure-pipelines.yml b/azure-pipelines.yml new file mode 100644 index 00000000..95b15db2 --- /dev/null +++ b/azure-pipelines.yml @@ -0,0 +1,38 @@ +jobs: + + - job: 'Test' + displayName: "Build and test" + timeoutInMinutes: 0 + cancelTimeoutInMinutes: 60 + + strategy: + matrix: + macOSrelease: + imageName: 'macos-10.14' + CMakeBuildType: Release + customInstallation: 'brew update && brew install graphviz doxygen boost eigen gmp mpfr tbb cgal' + + pool: + vmImage: $(imageName) + + steps: + - task: UsePythonVersion@0 + inputs: + versionSpec: '3.7' + architecture: 'x64' + + - script: | + $(customInstallation) + git submodule update --init + python -m pip install --upgrade pip + python -m pip install --user -r .github/build-requirements.txt + python -m pip install --user -r .github/test-requirements.txt + displayName: 'Install build dependencies' + - script: | + mkdir build + cd build + cmake -DCMAKE_BUILD_TYPE:STRING=$(CMakeBuildType) -DWITH_GUDHI_TEST=ON -DWITH_GUDHI_UTILITIES=ON -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 .. + make + make doxygen + ctest -j 8 --output-on-failure -E sphinx # remove sphinx build as it fails + displayName: 'Build, test and documentation generation' diff --git a/ext/hera b/ext/hera -Subproject 9a89971855acefe39dce0e2adadf53b88ca8f68 +Subproject cb1838e682ec07f80720241cf9098400caeb83c diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt index b0337934..2eecd50c 100644 --- a/src/Alpha_complex/example/CMakeLists.txt +++ b/src/Alpha_complex/example/CMakeLists.txt @@ -32,14 +32,18 @@ if (DIFF_PATH) add_test(Alpha_complex_example_from_off_60_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_60.txt) + set_tests_properties(Alpha_complex_example_from_off_60_diff_files PROPERTIES DEPENDS Alpha_complex_example_from_off_60) add_test(Alpha_complex_example_from_off_32_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt) + set_tests_properties(Alpha_complex_example_from_off_32_diff_files PROPERTIES DEPENDS Alpha_complex_example_from_off_32) add_test(Alpha_complex_example_fast_from_off_60_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/fastalphaoffreader_result_60.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_60.txt) + set_tests_properties(Alpha_complex_example_fast_from_off_60_diff_files PROPERTIES DEPENDS Alpha_complex_example_fast_from_off_60) add_test(Alpha_complex_example_fast_from_off_32_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/fastalphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt) - endif() + set_tests_properties(Alpha_complex_example_fast_from_off_32_diff_files PROPERTIES DEPENDS Alpha_complex_example_fast_from_off_32) +endif() add_executable ( Alpha_complex_example_weighted_3d_from_points Weighted_alpha_complex_3d_from_points.cpp ) target_link_libraries(Alpha_complex_example_weighted_3d_from_points ${CGAL_LIBRARY}) diff --git a/src/Alpha_complex/utilities/CMakeLists.txt b/src/Alpha_complex/utilities/CMakeLists.txt index 57b92942..2ffbdde0 100644 --- a/src/Alpha_complex/utilities/CMakeLists.txt +++ b/src/Alpha_complex/utilities/CMakeLists.txt @@ -2,7 +2,7 @@ project(Alpha_complex_utilities) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) add_executable (alpha_complex_persistence alpha_complex_persistence.cpp) - target_link_libraries(alpha_complex_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) + target_link_libraries(alpha_complex_persistence ${CGAL_LIBRARY} Boost::program_options) if (TBB_FOUND) target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES}) @@ -16,14 +16,20 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) if (DIFF_PATH) add_test(Alpha_complex_utilities_diff_exact_alpha_complex ${DIFF_PATH} "exact.pers" "safe.pers") + set_tests_properties(Alpha_complex_utilities_diff_exact_alpha_complex PROPERTIES DEPENDS + "Alpha_complex_utilities_exact_alpha_complex_persistence;Alpha_complex_utilities_safe_alpha_complex_persistence") + add_test(Alpha_complex_utilities_diff_fast_alpha_complex ${DIFF_PATH} "fast.pers" "safe.pers") + set_tests_properties(Alpha_complex_utilities_diff_fast_alpha_complex PROPERTIES DEPENDS + "Alpha_complex_utilities_fast_alpha_complex_persistence;Alpha_complex_utilities_safe_alpha_complex_persistence") + endif() install(TARGETS alpha_complex_persistence DESTINATION bin) add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp) - target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) + target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY} Boost::program_options) if (TBB_FOUND) target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES}) endif(TBB_FOUND) @@ -36,15 +42,19 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45" "-o" "exact_3d.pers" "-e") - add_test(NAME Alpha_complex_utilities_safe_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence> + add_test(NAME Alpha_complex_utilities_fast_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence> "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45" "-o" "fast_3d.pers" "-f") if (DIFF_PATH) add_test(Alpha_complex_utilities_diff_exact_alpha_complex_3d ${DIFF_PATH} "exact_3d.pers" "safe_3d.pers") + set_tests_properties(Alpha_complex_utilities_diff_exact_alpha_complex_3d PROPERTIES DEPENDS + "Alpha_complex_utilities_exact_alpha_complex_3d;Alpha_complex_utilities_alpha_complex_3d") add_test(Alpha_complex_utilities_diff_fast_alpha_complex_3d ${DIFF_PATH} "fast_3d.pers" "safe_3d.pers") + set_tests_properties(Alpha_complex_utilities_diff_fast_alpha_complex_3d PROPERTIES DEPENDS + "Alpha_complex_utilities_fast_alpha_complex_3d;Alpha_complex_utilities_alpha_complex_3d") endif() add_test(NAME Alpha_complex_utilities_periodic_alpha_complex_3d_persistence COMMAND $<TARGET_FILE:alpha_complex_3d_persistence> diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt index 3d65963a..9839c59d 100644 --- a/src/Bottleneck_distance/example/CMakeLists.txt +++ b/src/Bottleneck_distance/example/CMakeLists.txt @@ -13,7 +13,7 @@ endif (NOT CGAL_VERSION VERSION_LESS 4.11.0) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp) - target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_PROGRAM_OPTIONS_LIBRARY}) + target_link_libraries(alpha_rips_persistence_bottleneck_distance Boost::program_options) if (TBB_FOUND) target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES}) diff --git a/src/Cech_complex/benchmark/CMakeLists.txt b/src/Cech_complex/benchmark/CMakeLists.txt index b7697764..c04bca53 100644 --- a/src/Cech_complex/benchmark/CMakeLists.txt +++ b/src/Cech_complex/benchmark/CMakeLists.txt @@ -5,7 +5,7 @@ project(Cech_complex_benchmark) file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) add_executable(cech_complex_benchmark cech_complex_benchmark.cpp) -target_link_libraries(cech_complex_benchmark ${Boost_SYSTEM_LIBRARY} ${Boost_FILESYSTEM_LIBRARY}) +target_link_libraries(cech_complex_benchmark Boost::filesystem) if (TBB_FOUND) target_link_libraries(cech_complex_benchmark ${TBB_LIBRARIES}) diff --git a/src/Cech_complex/example/CMakeLists.txt b/src/Cech_complex/example/CMakeLists.txt index ab391215..98757988 100644 --- a/src/Cech_complex/example/CMakeLists.txt +++ b/src/Cech_complex/example/CMakeLists.txt @@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 2.6) project(Cech_complex_examples) add_executable ( Cech_complex_example_step_by_step cech_complex_step_by_step.cpp ) -target_link_libraries(Cech_complex_example_step_by_step ${Boost_PROGRAM_OPTIONS_LIBRARY}) +target_link_libraries(Cech_complex_example_step_by_step Boost::program_options) if (TBB_FOUND) target_link_libraries(Cech_complex_example_step_by_step ${TBB_LIBRARIES}) endif() diff --git a/src/Cech_complex/utilities/CMakeLists.txt b/src/Cech_complex/utilities/CMakeLists.txt index 30b99729..253d7304 100644 --- a/src/Cech_complex/utilities/CMakeLists.txt +++ b/src/Cech_complex/utilities/CMakeLists.txt @@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 2.6) project(Cech_complex_utilities) add_executable(cech_persistence cech_persistence.cpp) -target_link_libraries(cech_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) +target_link_libraries(cech_persistence Boost::program_options) if (TBB_FOUND) target_link_libraries(cech_persistence ${TBB_LIBRARIES}) diff --git a/src/Contraction/example/CMakeLists.txt b/src/Contraction/example/CMakeLists.txt index f0dc885d..c5d31aca 100644 --- a/src/Contraction/example/CMakeLists.txt +++ b/src/Contraction/example/CMakeLists.txt @@ -4,7 +4,6 @@ if (NOT CGAL_VERSION VERSION_LESS 4.11.0) add_executable(RipsContraction Rips_contraction.cpp) add_executable(GarlandHeckbert Garland_heckbert.cpp) - target_link_libraries(GarlandHeckbert ${Boost_TIMER_LIBRARY}) add_test(NAME Contraction_example_tore3D_0.2 COMMAND $<TARGET_FILE:RipsContraction> "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "0.2") diff --git a/src/Doxyfile.in b/src/Doxyfile.in index ec551882..49e781bd 100644 --- a/src/Doxyfile.in +++ b/src/Doxyfile.in @@ -785,6 +785,7 @@ EXCLUDE = data/ \ GudhUI/ \ cmake/ \ python/ \ + ext/ \ README.md # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or diff --git a/src/Persistence_representations/utilities/CMakeLists.txt b/src/Persistence_representations/utilities/CMakeLists.txt index fc51b1d6..85633b7b 100644 --- a/src/Persistence_representations/utilities/CMakeLists.txt +++ b/src/Persistence_representations/utilities/CMakeLists.txt @@ -14,7 +14,7 @@ function(add_persistence_representation_creation_utility creation_utility) install(TARGETS ${creation_utility} DESTINATION bin) endfunction(add_persistence_representation_creation_utility) -function(add_persistence_representation_plot_utility plot_utility tool_extension) +function(add_persistence_representation_plot_utility creation_utility plot_utility tool_extension) add_executable ( ${plot_utility} ${plot_utility}.cpp ) # as the function is called in a subdirectory level, need to '../' to find persistence heat maps files @@ -22,17 +22,21 @@ function(add_persistence_representation_plot_utility plot_utility tool_extension "${CMAKE_CURRENT_BINARY_DIR}/../first.pers${tool_extension}") #add_test(NAME Persistence_representation_utilities_${plot_utility}_second COMMAND $<TARGET_FILE:${plot_utility}> # "${CMAKE_CURRENT_BINARY_DIR}/../second.pers${tool_extension}") + set_tests_properties(Persistence_representation_utilities_${plot_utility}_first PROPERTIES DEPENDS + Persistence_representation_utilities_${creation_utility}) if(GNUPLOT_PATH) add_test(NAME Persistence_representation_utilities_${plot_utility}_first_gnuplot COMMAND ${GNUPLOT_PATH} "-e" "load '${CMAKE_CURRENT_BINARY_DIR}/../first.pers${tool_extension}_GnuplotScript'") #add_test(NAME Persistence_representation_utilities_${plot_utility}_second_gnuplot COMMAND ${GNUPLOT_PATH} # "-e" "load '${CMAKE_CURRENT_BINARY_DIR}/../second.pers${tool_extension}_GnuplotScript'") + set_tests_properties(Persistence_representation_utilities_${plot_utility}_first_gnuplot PROPERTIES DEPENDS + Persistence_representation_utilities_${plot_utility}_first) endif() install(TARGETS ${plot_utility} DESTINATION bin) endfunction(add_persistence_representation_plot_utility) -function(add_persistence_representation_function_utility function_utility tool_extension) +function(add_persistence_representation_function_utility creation_utility function_utility tool_extension) add_executable ( ${function_utility} ${function_utility}.cpp ) # ARGV2 is an optional argument @@ -48,6 +52,8 @@ function(add_persistence_representation_function_utility function_utility tool_e "${CMAKE_CURRENT_BINARY_DIR}/../first.pers${tool_extension}" "${CMAKE_CURRENT_BINARY_DIR}/../second.pers${tool_extension}") endif() + set_tests_properties(Persistence_representation_utilities_${function_utility} PROPERTIES DEPENDS + Persistence_representation_utilities_${creation_utility}) install(TARGETS ${function_utility} DESTINATION bin) endfunction(add_persistence_representation_function_utility) diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt index 89ef232f..e4c471c2 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt +++ b/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt @@ -2,13 +2,24 @@ project(Persistence_representations_heat_maps_utilities) add_persistence_representation_creation_utility(create_pssk "10" "-1" "-1" "4" "-1") add_persistence_representation_creation_utility(create_p_h_m_weighted_by_arctan_of_their_persistence "10" "-1" "-1" "4" "-1") + add_persistence_representation_creation_utility(create_p_h_m_weighted_by_distance_from_diagonal "10" "-1" "-1" "4" "-1") +# Tests output the same file +set_tests_properties(Persistence_representation_utilities_create_p_h_m_weighted_by_distance_from_diagonal PROPERTIES DEPENDS + Persistence_representation_utilities_create_p_h_m_weighted_by_arctan_of_their_persistence) + add_persistence_representation_creation_utility(create_p_h_m_weighted_by_squared_diag_distance "10" "-1" "-1" "4" "-1") +# Tests output the same file +set_tests_properties(Persistence_representation_utilities_create_p_h_m_weighted_by_squared_diag_distance PROPERTIES DEPENDS + Persistence_representation_utilities_create_p_h_m_weighted_by_distance_from_diagonal) + # Need to set grid min and max for further average, distance and scalar_product add_persistence_representation_creation_utility(create_persistence_heat_maps "10" "0" "35" "10" "-1") +set_tests_properties(Persistence_representation_utilities_create_persistence_heat_maps PROPERTIES DEPENDS + Persistence_representation_utilities_create_p_h_m_weighted_by_squared_diag_distance) -add_persistence_representation_plot_utility(plot_persistence_heat_map ".mps") +add_persistence_representation_plot_utility(create_persistence_heat_maps plot_persistence_heat_map ".mps") -add_persistence_representation_function_utility(average_persistence_heat_maps ".mps") -add_persistence_representation_function_utility(compute_distance_of_persistence_heat_maps ".mps" "1") -add_persistence_representation_function_utility(compute_scalar_product_of_persistence_heat_maps ".mps") +add_persistence_representation_function_utility(create_persistence_heat_maps average_persistence_heat_maps ".mps") +add_persistence_representation_function_utility(create_persistence_heat_maps compute_distance_of_persistence_heat_maps ".mps" "1") +add_persistence_representation_function_utility(create_persistence_heat_maps compute_scalar_product_of_persistence_heat_maps ".mps") diff --git a/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt index a025183e..118c1e9b 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt +++ b/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt @@ -3,17 +3,16 @@ project(Persistence_representations_intervals_utilities) add_executable ( plot_histogram_of_intervals_lengths plot_histogram_of_intervals_lengths.cpp ) -add_test(NAME plot_histogram_of_intervals_lengths COMMAND $<TARGET_FILE:plot_histogram_of_intervals_lengths> +add_test(NAME Persistence_representation_utilities_plot_histogram_of_intervals_lengths COMMAND $<TARGET_FILE:plot_histogram_of_intervals_lengths> "${CMAKE_CURRENT_BINARY_DIR}/../first.pers" "-1") install(TARGETS plot_histogram_of_intervals_lengths DESTINATION bin) -add_persistence_representation_plot_utility(plot_persistence_intervals "") -add_persistence_representation_plot_utility(plot_persistence_Betti_numbers "") +add_persistence_representation_plot_utility(plot_histogram_of_intervals_lengths plot_persistence_intervals "") +add_persistence_representation_plot_utility(plot_histogram_of_intervals_lengths plot_persistence_Betti_numbers "") add_persistence_representation_creation_utility(compute_birth_death_range_in_persistence_diagram "-1") - add_executable ( compute_number_of_dominant_intervals compute_number_of_dominant_intervals.cpp ) add_test(NAME Persistence_representation_utilities_compute_number_of_dominant_intervals COMMAND $<TARGET_FILE:compute_number_of_dominant_intervals> diff --git a/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt index 6b24d032..4df84d36 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt +++ b/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt @@ -2,8 +2,8 @@ project(Persistence_representations_landscapes_utilities) add_persistence_representation_creation_utility(create_landscapes "-1") -add_persistence_representation_plot_utility(plot_landscapes ".land") +add_persistence_representation_plot_utility(create_landscapes plot_landscapes ".land") -add_persistence_representation_function_utility(average_landscapes ".land") -add_persistence_representation_function_utility(compute_distance_of_landscapes ".land" "1") -add_persistence_representation_function_utility(compute_scalar_product_of_landscapes ".land") +add_persistence_representation_function_utility(create_landscapes average_landscapes ".land") +add_persistence_representation_function_utility(create_landscapes compute_distance_of_landscapes ".land" "1") +add_persistence_representation_function_utility(create_landscapes compute_scalar_product_of_landscapes ".land") diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt index 36f3196b..8cd965f1 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt @@ -3,8 +3,8 @@ project(Persistence_representations_lanscapes_on_grid_utilities) # Need to set grid min and max for further average, distance and scalar_product add_persistence_representation_creation_utility(create_landscapes_on_grid "100" "0" "35" "-1") -add_persistence_representation_plot_utility(plot_landscapes_on_grid ".g_land") +add_persistence_representation_plot_utility(create_landscapes_on_grid plot_landscapes_on_grid ".g_land") -add_persistence_representation_function_utility(average_landscapes_on_grid ".g_land") -add_persistence_representation_function_utility(compute_distance_of_landscapes_on_grid ".g_land" "1") -add_persistence_representation_function_utility(compute_scalar_product_of_landscapes_on_grid ".g_land") +add_persistence_representation_function_utility(create_landscapes_on_grid average_landscapes_on_grid ".g_land") +add_persistence_representation_function_utility(create_landscapes_on_grid compute_distance_of_landscapes_on_grid ".g_land" "1") +add_persistence_representation_function_utility(create_landscapes_on_grid compute_scalar_product_of_landscapes_on_grid ".g_land") diff --git a/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt index bc982094..5b22ca84 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt +++ b/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt @@ -2,8 +2,8 @@ project(Persistence_vectors_utilities) add_persistence_representation_creation_utility(create_persistence_vectors "-1") -add_persistence_representation_plot_utility(plot_persistence_vectors ".vect") +add_persistence_representation_plot_utility(create_persistence_vectors plot_persistence_vectors ".vect") -add_persistence_representation_function_utility(average_persistence_vectors ".vect") -add_persistence_representation_function_utility(compute_distance_of_persistence_vectors ".vect" "1") -add_persistence_representation_function_utility(compute_scalar_product_of_persistence_vectors ".vect") +add_persistence_representation_function_utility(create_persistence_vectors average_persistence_vectors ".vect") +add_persistence_representation_function_utility(create_persistence_vectors compute_distance_of_persistence_vectors ".vect" "1") +add_persistence_representation_function_utility(create_persistence_vectors compute_scalar_product_of_persistence_vectors ".vect") diff --git a/src/Persistent_cohomology/benchmark/CMakeLists.txt b/src/Persistent_cohomology/benchmark/CMakeLists.txt index 2bb3b0c7..f38cc543 100644 --- a/src/Persistent_cohomology/benchmark/CMakeLists.txt +++ b/src/Persistent_cohomology/benchmark/CMakeLists.txt @@ -3,7 +3,7 @@ project(Persistent_cohomology_benchmark) if(GMP_FOUND) if(GMPXX_FOUND) add_executable ( performance_rips_persistence EXCLUDE_FROM_ALL performance_rips_persistence.cpp ) - target_link_libraries(performance_rips_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) + target_link_libraries(performance_rips_persistence Boost::program_options ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) if (TBB_FOUND) target_link_libraries(performance_rips_persistence ${TBB_LIBRARIES}) endif(TBB_FOUND) diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index 94ec13c5..4c08cd68 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -5,13 +5,13 @@ add_executable(plain_homology plain_homology.cpp) add_executable(persistence_from_simple_simplex_tree persistence_from_simple_simplex_tree.cpp) add_executable(rips_persistence_step_by_step rips_persistence_step_by_step.cpp) -target_link_libraries(rips_persistence_step_by_step ${Boost_PROGRAM_OPTIONS_LIBRARY}) +target_link_libraries(rips_persistence_step_by_step Boost::program_options) add_executable(rips_persistence_via_boundary_matrix rips_persistence_via_boundary_matrix.cpp) -target_link_libraries(rips_persistence_via_boundary_matrix ${Boost_PROGRAM_OPTIONS_LIBRARY}) +target_link_libraries(rips_persistence_via_boundary_matrix Boost::program_options) add_executable(persistence_from_file persistence_from_file.cpp) -target_link_libraries(persistence_from_file ${Boost_PROGRAM_OPTIONS_LIBRARY}) +target_link_libraries(persistence_from_file Boost::program_options) if (TBB_FOUND) target_link_libraries(plain_homology ${TBB_LIBRARIES}) @@ -43,7 +43,7 @@ if(GMP_FOUND) if(GMPXX_FOUND) add_executable(rips_multifield_persistence rips_multifield_persistence.cpp ) target_link_libraries(rips_multifield_persistence - ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) + Boost::program_options ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) if (TBB_FOUND) target_link_libraries(rips_multifield_persistence ${TBB_LIBRARIES}) endif(TBB_FOUND) diff --git a/src/Rips_complex/example/CMakeLists.txt b/src/Rips_complex/example/CMakeLists.txt index e7772bdb..244a93ec 100644 --- a/src/Rips_complex/example/CMakeLists.txt +++ b/src/Rips_complex/example/CMakeLists.txt @@ -53,15 +53,23 @@ if (DIFF_PATH) add_test(Rips_complex_example_from_off_doc_12_1_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_1.txt ${CMAKE_CURRENT_BINARY_DIR}/one_skeleton_rips_for_doc.txt) + set_tests_properties(Rips_complex_example_from_off_doc_12_1_diff_files PROPERTIES DEPENDS Rips_complex_example_from_off_doc_12_1) + add_test(Rips_complex_example_from_off_doc_12_3_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_3.txt ${CMAKE_CURRENT_BINARY_DIR}/full_skeleton_rips_for_doc.txt) + set_tests_properties(Rips_complex_example_from_off_doc_12_3_diff_files PROPERTIES DEPENDS Rips_complex_example_from_off_doc_12_3) + add_test(Rips_complex_example_from_csv_distance_matrix_doc_12_1_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_12_1.txt ${CMAKE_CURRENT_BINARY_DIR}/one_skeleton_rips_for_doc.txt) + set_tests_properties(Rips_complex_example_from_csv_distance_matrix_doc_12_1_diff_files PROPERTIES DEPENDS Rips_complex_example_from_csv_distance_matrix_doc_12_1) + add_test(Rips_complex_example_from_csv_distance_matrix_doc_12_3_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_12_3.txt ${CMAKE_CURRENT_BINARY_DIR}/full_skeleton_rips_for_doc.txt) + set_tests_properties(Rips_complex_example_from_csv_distance_matrix_doc_12_3_diff_files PROPERTIES DEPENDS Rips_complex_example_from_csv_distance_matrix_doc_12_3) + endif() install(TARGETS Rips_complex_example_from_off DESTINATION bin) diff --git a/src/Rips_complex/utilities/CMakeLists.txt b/src/Rips_complex/utilities/CMakeLists.txt index 4b565628..d2448d7b 100644 --- a/src/Rips_complex/utilities/CMakeLists.txt +++ b/src/Rips_complex/utilities/CMakeLists.txt @@ -1,16 +1,16 @@ project(Rips_complex_utilities) add_executable(rips_distance_matrix_persistence rips_distance_matrix_persistence.cpp) -target_link_libraries(rips_distance_matrix_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) +target_link_libraries(rips_distance_matrix_persistence Boost::program_options) add_executable(rips_persistence rips_persistence.cpp) -target_link_libraries(rips_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) +target_link_libraries(rips_persistence Boost::program_options) add_executable(rips_correlation_matrix_persistence rips_correlation_matrix_persistence.cpp) -target_link_libraries(rips_correlation_matrix_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) +target_link_libraries(rips_correlation_matrix_persistence Boost::system Boost::program_options) add_executable(sparse_rips_persistence sparse_rips_persistence.cpp) -target_link_libraries(sparse_rips_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) +target_link_libraries(sparse_rips_persistence Boost::program_options) if (TBB_FOUND) target_link_libraries(rips_distance_matrix_persistence ${TBB_LIBRARIES}) diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt index 8a8cac58..a0aabee2 100644 --- a/src/Simplex_tree/example/CMakeLists.txt +++ b/src/Simplex_tree/example/CMakeLists.txt @@ -35,7 +35,7 @@ endif() if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) add_executable ( Simplex_tree_example_cech_complex_cgal_mini_sphere_3d cech_complex_cgal_mini_sphere_3d.cpp ) - target_link_libraries(Simplex_tree_example_cech_complex_cgal_mini_sphere_3d ${Boost_PROGRAM_OPTIONS_LIBRARY} ${CGAL_LIBRARY}) + target_link_libraries(Simplex_tree_example_cech_complex_cgal_mini_sphere_3d Boost::program_options ${CGAL_LIBRARY}) if (TBB_FOUND) target_link_libraries(Simplex_tree_example_cech_complex_cgal_mini_sphere_3d ${TBB_LIBRARIES}) endif() diff --git a/src/Witness_complex/utilities/CMakeLists.txt b/src/Witness_complex/utilities/CMakeLists.txt index 3ee0c2f6..d986d2d1 100644 --- a/src/Witness_complex/utilities/CMakeLists.txt +++ b/src/Witness_complex/utilities/CMakeLists.txt @@ -4,10 +4,10 @@ project(Witness_complex_utilities) if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) add_executable ( Witness_complex_strong_witness_persistence strong_witness_persistence.cpp ) - target_link_libraries(Witness_complex_strong_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) + target_link_libraries(Witness_complex_strong_witness_persistence Boost::program_options) add_executable ( Witness_complex_weak_witness_persistence weak_witness_persistence.cpp ) - target_link_libraries(Witness_complex_weak_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) + target_link_libraries(Witness_complex_weak_witness_persistence Boost::program_options) if (TBB_FOUND) target_link_libraries(Witness_complex_strong_witness_persistence ${TBB_LIBRARIES}) diff --git a/src/cmake/modules/GUDHI_boost_test.cmake b/src/cmake/modules/GUDHI_boost_test.cmake index c3b29883..4a13404b 100644 --- a/src/cmake/modules/GUDHI_boost_test.cmake +++ b/src/cmake/modules/GUDHI_boost_test.cmake @@ -9,7 +9,6 @@ if (WITH_GUDHI_BOOST_TEST_COVERAGE) set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg") endif() set(GUDHI_UT_LOG_FORMAT "--log_format=XML") - set(GUDHI_UT_LOG_SINK "--log_sink=${CMAKE_BINARY_DIR}/${unitary_test}_UT.xml") set(GUDHI_UT_LOG_LEVEL "--log_level=test_suite") set(GUDHI_UT_REPORT_LEVEL "--report_level=no") else (WITH_GUDHI_BOOST_TEST_COVERAGE) @@ -19,7 +18,11 @@ else (WITH_GUDHI_BOOST_TEST_COVERAGE) endif(WITH_GUDHI_BOOST_TEST_COVERAGE) function(gudhi_add_boost_test unitary_test) - target_link_libraries(${unitary_test} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) + if (WITH_GUDHI_BOOST_TEST_COVERAGE) + set(GUDHI_UT_LOG_SINK "--log_sink=${CMAKE_BINARY_DIR}/${unitary_test}_UT.xml") + endif(WITH_GUDHI_BOOST_TEST_COVERAGE) + + target_link_libraries(${unitary_test} Boost::unit_test_framework) add_test(NAME ${unitary_test} COMMAND $<TARGET_FILE:${unitary_test}> ${GUDHI_UT_LOG_FORMAT} ${GUDHI_UT_LOG_SINK} ${GUDHI_UT_LOG_LEVEL} ${GUDHI_UT_REPORT_LEVEL}) diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake index 359d1c12..6db2c76b 100644 --- a/src/cmake/modules/GUDHI_third_party_libraries.cmake +++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake @@ -6,6 +6,38 @@ if(NOT Boost_FOUND) message(FATAL_ERROR "NOTICE: This program requires Boost and will not be compiled.") endif(NOT Boost_FOUND) +# cf. https://cliutils.gitlab.io/modern-cmake/chapters/packages/Boost.html +# This is needed if your Boost version is newer than your CMake version +# or if you have an old version of CMake (<3.5) +if(NOT TARGET Boost::program_options) + add_library(Boost::program_options IMPORTED INTERFACE) + set_property(TARGET Boost::program_options PROPERTY + INTERFACE_INCLUDE_DIRECTORIES ${Boost_INCLUDE_DIR}) + set_property(TARGET Boost::program_options PROPERTY + INTERFACE_LINK_LIBRARIES ${Boost_LIBRARIES}) +endif() +if(NOT TARGET Boost::filesystem) + add_library(Boost::filesystem IMPORTED INTERFACE) + set_property(TARGET Boost::filesystem PROPERTY + INTERFACE_INCLUDE_DIRECTORIES ${Boost_INCLUDE_DIR}) + set_property(TARGET Boost::filesystem PROPERTY + INTERFACE_LINK_LIBRARIES ${Boost_LIBRARIES}) +endif() +if(NOT TARGET Boost::unit_test_framework) + add_library(Boost::unit_test_framework IMPORTED INTERFACE) + set_property(TARGET Boost::unit_test_framework PROPERTY + INTERFACE_INCLUDE_DIRECTORIES ${Boost_INCLUDE_DIR}) + set_property(TARGET Boost::unit_test_framework PROPERTY + INTERFACE_LINK_LIBRARIES ${Boost_LIBRARIES}) +endif() +if(NOT TARGET Boost::system) + add_library(Boost::system IMPORTED INTERFACE) + set_property(TARGET Boost::system PROPERTY + INTERFACE_INCLUDE_DIRECTORIES ${Boost_INCLUDE_DIR}) + set_property(TARGET Boost::system PROPERTY + INTERFACE_LINK_LIBRARIES ${Boost_LIBRARIES}) +endif() + find_package(GMP) if(GMP_FOUND) INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR}) @@ -85,9 +117,6 @@ add_definitions( -DBOOST_ALL_DYN_LINK ) # problem on Mac with boost_system and boost_thread add_definitions( -DBOOST_SYSTEM_NO_DEPRECATED ) -INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS}) -LINK_DIRECTORIES(${Boost_LIBRARY_DIRS}) - message(STATUS "boost include dirs:" ${Boost_INCLUDE_DIRS}) message(STATUS "boost library dirs:" ${Boost_LIBRARY_DIRS}) diff --git a/src/common/example/CMakeLists.txt b/src/common/example/CMakeLists.txt index 583a0027..fa8eb98c 100644 --- a/src/common/example/CMakeLists.txt +++ b/src/common/example/CMakeLists.txt @@ -12,6 +12,7 @@ if (DIFF_PATH) add_test(Common_example_vector_double_off_reader_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/vectordoubleoffreader_result.txt ${CMAKE_CURRENT_BINARY_DIR}/alphacomplexdoc.off.txt) + set_tests_properties(Common_example_vector_double_off_reader_diff_files PROPERTIES DEPENDS Common_example_vector_double_off_reader) endif() if(NOT CGAL_VERSION VERSION_LESS 4.11.0) diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt index 090a7446..20e72a5f 100644 --- a/src/python/CMakeLists.txt +++ b/src/python/CMakeLists.txt @@ -181,7 +181,7 @@ if(PYTHONINTERP_FOUND) set(GUDHI_PYTHON_LIBRARY_DIRS "${GUDHI_PYTHON_LIBRARY_DIRS}'${MPFR_LIBRARIES_DIR}', ") message("** Add mpfr ${MPFR_LIBRARIES}") endif(MPFR_FOUND) -endif(CGAL_FOUND) + endif(CGAL_FOUND) # Specific for Mac if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin") diff --git a/src/python/doc/persistence_graphical_tools_sum.inc b/src/python/doc/persistence_graphical_tools_sum.inc index 0cdf8072..ef376802 100644 --- a/src/python/doc/persistence_graphical_tools_sum.inc +++ b/src/python/doc/persistence_graphical_tools_sum.inc @@ -2,11 +2,11 @@ :widths: 30 50 20 +-----------------------------------------------------------------+-----------------------------------------------------------------------+-----------------------------------------------+ - | .. figure:: | These graphical tools comes on top of persistence results and allows | :Author: Vincent Rouvreau | - | img/graphical_tools_representation.png | the user to build easily persistence barcode, diagram or density. | | + | .. figure:: | These graphical tools comes on top of persistence results and allows | :Author: Vincent Rouvreau, Theo Lacombe | + | img/graphical_tools_representation.png | the user to display easily persistence barcode, diagram or density. | | | | | :Introduced in: GUDHI 2.0.0 | - | | | | - | | | :Copyright: MIT | + | | Note that these functions return the matplotlib axis, allowing | | + | | for further modifications (title, aspect, etc.) | :Copyright: MIT | | | | | | | | :Requires: matplotlib, numpy and scipy | +-----------------------------------------------------------------+-----------------------------------------------------------------------+-----------------------------------------------+ diff --git a/src/python/doc/persistence_graphical_tools_user.rst b/src/python/doc/persistence_graphical_tools_user.rst index 80002db6..91e52703 100644 --- a/src/python/doc/persistence_graphical_tools_user.rst +++ b/src/python/doc/persistence_graphical_tools_user.rst @@ -20,7 +20,7 @@ This function can display the persistence result as a barcode: .. plot:: :include-source: - import matplotlib.pyplot as plot + import matplotlib.pyplot as plt import gudhi off_file = gudhi.__root_source_dir__ + '/data/points/tore3D_300.off' @@ -31,7 +31,7 @@ This function can display the persistence result as a barcode: diag = simplex_tree.persistence(min_persistence=0.4) gudhi.plot_persistence_barcode(diag) - plot.show() + plt.show() Show persistence as a diagram ----------------------------- @@ -44,15 +44,31 @@ This function can display the persistence result as a diagram: .. plot:: :include-source: - import matplotlib.pyplot as plot + import matplotlib.pyplot as plt import gudhi # rips_on_tore3D_1307.pers obtained from write_persistence_diagram method persistence_file=gudhi.__root_source_dir__ + \ '/data/persistence_diagram/rips_on_tore3D_1307.pers' - gudhi.plot_persistence_diagram(persistence_file=persistence_file, + ax = gudhi.plot_persistence_diagram(persistence_file=persistence_file, legend=True) - plot.show() + # We can modify the title, aspect, etc. + ax.set_title("Persistence diagram of a torus") + ax.set_aspect("equal") # forces to be square shaped + plt.show() + +Note that (as barcode and density) it can also take a simple `np.array` +of shape (N x 2) encoding a persistence diagram (in a given dimension). + +.. plot:: + :include-source: + + import matplotlib.pyplot as plt + import gudhi + import numpy as np + d = np.array([[0, 1], [1, 2], [1, np.inf]]) + gudhi.plot_persistence_diagram(d) + plt.show() Persistence density ------------------- @@ -65,7 +81,7 @@ If you want more information on a specific dimension, for instance: .. plot:: :include-source: - import matplotlib.pyplot as plot + import matplotlib.pyplot as plt import gudhi # rips_on_tore3D_1307.pers obtained from write_persistence_diagram method persistence_file=gudhi.__root_source_dir__ + \ @@ -75,9 +91,9 @@ If you want more information on a specific dimension, for instance: only_this_dim=1) pers_diag = [(1, elt) for elt in birth_death] # Use subplots to display diagram and density side by side - fig, axes = plot.subplots(nrows=1, ncols=2, figsize=(12, 5)) + fig, axes = plt.subplots(nrows=1, ncols=2, figsize=(12, 5)) gudhi.plot_persistence_diagram(persistence=pers_diag, axes=axes[0]) gudhi.plot_persistence_density(persistence=pers_diag, dimension=1, legend=True, axes=axes[1]) - plot.show() + plt.show() diff --git a/src/python/gudhi/nerve_gic.pyx b/src/python/gudhi/nerve_gic.pyx index 382e71c5..45cc8eba 100644 --- a/src/python/gudhi/nerve_gic.pyx +++ b/src/python/gudhi/nerve_gic.pyx @@ -187,7 +187,7 @@ cdef class CoverComplex: def set_automatic_resolution(self): """Computes the optimal length of intervals (i.e. the smallest interval - length avoiding discretization artifacts—see :cite:`Carriere17c`) for a + length avoiding discretization artifacts - see :cite:`Carriere17c`) for a functional cover. :rtype: double @@ -288,7 +288,7 @@ cdef class CoverComplex: def set_graph_from_automatic_rips(self, N=100): """Creates a graph G from a Rips complex whose threshold value is - automatically tuned with subsampling—see. + automatically tuned with subsampling - see :cite:`Carriere17c`. :param N: Number of subsampling iteration (the default reasonable value is 100, but there is no guarantee on how to choose it). diff --git a/src/python/gudhi/persistence_graphical_tools.py b/src/python/gudhi/persistence_graphical_tools.py index 246280de..cc3db467 100644 --- a/src/python/gudhi/persistence_graphical_tools.py +++ b/src/python/gudhi/persistence_graphical_tools.py @@ -5,6 +5,7 @@ # Copyright (C) 2016 Inria # # Modification(s): +# - 2020/02 Theo Lacombe: Added more options for improved rendering and more flexibility. # - YYYY/MM Author: Description of the modification from os import path @@ -14,7 +15,7 @@ import numpy as np from gudhi.reader_utils import read_persistence_intervals_in_dimension from gudhi.reader_utils import read_persistence_intervals_grouped_by_dimension -__author__ = "Vincent Rouvreau, Bertrand Michel" +__author__ = "Vincent Rouvreau, Bertrand Michel, Theo Lacombe" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "MIT" @@ -43,6 +44,19 @@ def __min_birth_max_death(persistence, band=0.0): max_death += band return (min_birth, max_death) + +def _array_handler(a): + ''' + :param a: if array, assumes it is a (n x 2) np.array and return a + persistence-compatible list (padding with 0), so that the + plot can be performed seamlessly. + ''' + if isinstance(a[0][1], np.float64) or isinstance(a[0][1], float): + return [[0, x] for x in a] + else: + return a + + def plot_persistence_barcode( persistence=[], persistence_file="", @@ -52,13 +66,16 @@ def plot_persistence_barcode( inf_delta=0.1, legend=False, colormap=None, - axes=None + axes=None, + fontsize=16, ): """This function plots the persistence bar code from persistence values list + , a np.array of shape (N x 2) (representing a diagram + in a single homology dimension), or from a :doc:`persistence file <fileformats>`. - :param persistence: Persistence intervals values list grouped by dimension. - :type persistence: list of tuples(dimension, tuple(birth, death)). + :param persistence: Persistence intervals values list. Can be grouped by dimension or not. + :type persistence: an array of (dimension, array of (birth, death)) or an array of (birth, death). :param persistence_file: A :doc:`persistence file <fileformats>` style name (reset persistence if both are set). :type persistence_file: string @@ -81,11 +98,19 @@ def plot_persistence_barcode( :param axes: A matplotlib-like subplot axes. If None, the plot is drawn on a new set of axes. :type axes: `matplotlib.axes.Axes` + :param fontsize: Fontsize to use in axis. + :type fontsize: int :returns: (`matplotlib.axes.Axes`): The axes on which the plot was drawn. """ try: import matplotlib.pyplot as plt import matplotlib.patches as mpatches + from matplotlib import rc + plt.rc('text', usetex=True) + plt.rc('font', family='serif') + + + persistence = _array_handler(persistence) if persistence_file != "": if path.isfile(persistence_file): @@ -163,7 +188,7 @@ def plot_persistence_barcode( loc="lower right", ) - axes.set_title("Persistence barcode") + axes.set_title("Persistence barcode", fontsize=fontsize) # Ends plot on infinity value and starts a little bit before min_birth axes.axis([axis_start, infinity, 0, ind]) @@ -183,13 +208,16 @@ def plot_persistence_diagram( inf_delta=0.1, legend=False, colormap=None, - axes=None + axes=None, + fontsize=16, + greyblock=True ): """This function plots the persistence diagram from persistence values - list or from a :doc:`persistence file <fileformats>`. + list, a np.array of shape (N x 2) representing a diagram in a single + homology dimension, or from a :doc:`persistence file <fileformats>`. - :param persistence: Persistence intervals values list grouped by dimension. - :type persistence: list of tuples(dimension, tuple(birth, death)). + :param persistence: Persistence intervals values list. Can be grouped by dimension or not. + :type persistence: an array of (dimension, array of (birth, death)) or an array of (birth, death). :param persistence_file: A :doc:`persistence file <fileformats>` style name (reset persistence if both are set). :type persistence_file: string @@ -214,11 +242,20 @@ def plot_persistence_diagram( :param axes: A matplotlib-like subplot axes. If None, the plot is drawn on a new set of axes. :type axes: `matplotlib.axes.Axes` + :param fontsize: Fontsize to use in axis. + :type fontsize: int + :param greyblock: if we want to plot a grey patch on the lower half plane for nicer rendering. Default True. + :type greyblock: boolean :returns: (`matplotlib.axes.Axes`): The axes on which the plot was drawn. """ try: import matplotlib.pyplot as plt import matplotlib.patches as mpatches + from matplotlib import rc + plt.rc('text', usetex=True) + plt.rc('font', family='serif') + + persistence = _array_handler(persistence) if persistence_file != "": if path.isfile(persistence_file): @@ -256,19 +293,18 @@ def plot_persistence_diagram( # Replace infinity values with max_death + delta for diagram to be more # readable infinity = max_death + delta + axis_end = max_death + delta / 2 axis_start = min_birth - delta - # line display of equation : birth = death - x = np.linspace(axis_start, infinity, 1000) - # infinity line and text - axes.plot(x, x, color="k", linewidth=1.0) - axes.plot(x, [infinity] * len(x), linewidth=1.0, color="k", alpha=alpha) - axes.text(axis_start, infinity, r"$\infty$", color="k", alpha=alpha) # bootstrap band if band > 0.0: + x = np.linspace(axis_start, infinity, 1000) axes.fill_between(x, x, x + band, alpha=alpha, facecolor="red") - + # lower diag patch + if greyblock: + axes.add_patch(mpatches.Polygon([[axis_start, axis_start], [axis_end, axis_start], [axis_end, axis_end]], fill=True, color='lightgrey')) # Draw points in loop + pts_at_infty = False # Records presence of pts at infty for interval in reversed(persistence): if float(interval[1][1]) != float("inf"): # Finite death case @@ -279,10 +315,23 @@ def plot_persistence_diagram( color=colormap[interval[0]], ) else: + pts_at_infty = True # Infinite death case for diagram to be nicer axes.scatter( interval[1][0], infinity, alpha=alpha, color=colormap[interval[0]] ) + if pts_at_infty: + # infinity line and text + axes.plot([axis_start, axis_end], [axis_start, axis_end], linewidth=1.0, color="k") + axes.plot([axis_start, axis_end], [infinity, infinity], linewidth=1.0, color="k", alpha=alpha) + # Infinity label + yt = axes.get_yticks() + yt = yt[np.where(yt < axis_end)] # to avoid ploting ticklabel higher than infinity + yt = np.append(yt, infinity) + ytl = ["%.3f" % e for e in yt] # to avoid float precision error + ytl[-1] = r'$+\infty$' + axes.set_yticks(yt) + axes.set_yticklabels(ytl) if legend: dimensions = list(set(item[0] for item in persistence)) @@ -293,11 +342,11 @@ def plot_persistence_diagram( ] ) - axes.set_xlabel("Birth") - axes.set_ylabel("Death") + axes.set_xlabel("Birth", fontsize=fontsize) + axes.set_ylabel("Death", fontsize=fontsize) + axes.set_title("Persistence diagram", fontsize=fontsize) # Ends plot on infinity value and starts a little bit before min_birth - axes.axis([axis_start, infinity, axis_start, infinity + delta]) - axes.set_title("Persistence diagram") + axes.axis([axis_start, axis_end, axis_start, infinity + delta/2]) return axes except ImportError: @@ -313,16 +362,22 @@ def plot_persistence_density( dimension=None, cmap=None, legend=False, - axes=None + axes=None, + fontsize=16, + greyblock=False ): """This function plots the persistence density from persistence - values list or from a :doc:`persistence file <fileformats>`. Be + values list, np.array of shape (N x 2) representing a diagram + in a single homology dimension, + or from a :doc:`persistence file <fileformats>`. Be aware that this function does not distinguish the dimension, it is up to you to select the required one. This function also does not handle degenerate data set (scipy correlation matrix inversion can fail). - :param persistence: Persistence intervals values list grouped by dimension. - :type persistence: list of tuples(dimension, tuple(birth, death)). + :param persistence: Persistence intervals values list. + Can be grouped by dimension or not. + :type persistence: an array of (dimension, array of (birth, death)) + or an array of (birth, death). :param persistence_file: A :doc:`persistence file <fileformats>` style name (reset persistence if both are set). :type persistence_file: string @@ -355,11 +410,22 @@ def plot_persistence_density( :param axes: A matplotlib-like subplot axes. If None, the plot is drawn on a new set of axes. :type axes: `matplotlib.axes.Axes` + :param fontsize: Fontsize to use in axis. + :type fontsize: int + :param greyblock: if we want to plot a grey patch on the lower half plane + for nicer rendering. Default False. + :type greyblock: boolean :returns: (`matplotlib.axes.Axes`): The axes on which the plot was drawn. """ try: import matplotlib.pyplot as plt + import matplotlib.patches as mpatches from scipy.stats import kde + from matplotlib import rc + plt.rc('text', usetex=True) + plt.rc('font', family='serif') + + persistence = _array_handler(persistence) if persistence_file != "": if dimension is None: @@ -418,12 +484,16 @@ def plot_persistence_density( # Make the plot img = axes.pcolormesh(xi, yi, zi.reshape(xi.shape), cmap=cmap) + if greyblock: + axes.add_patch(mpatches.Polygon([[birth.min(), birth.min()], [death.max(), birth.min()], [death.max(), death.max()]], fill=True, color='lightgrey')) + if legend: plt.colorbar(img, ax=axes) - axes.set_xlabel("Birth") - axes.set_ylabel("Death") - axes.set_title("Persistence density") + axes.set_xlabel("Birth", fontsize=fontsize) + axes.set_ylabel("Death", fontsize=fontsize) + axes.set_title("Persistence density", fontsize=fontsize) + return axes except ImportError: |