# chromatic_tda
`chromatic_tda` is a package for computing six-packs of persistent diagrams of colored point clouds. Currently point clouds in R^2 with 2 or 3 colors are supported (see Future).
# Installation
## Install with `pip`
The package is uploaded to [PyPI](https://pypi.org/project/chromatic-tda/), so it can be installed with `pip`.
Run `pip install chromatic_tda`.
## Install from [github project](https://github.com/OnDraganov/chromatic-tda)
The project uses `poetry` for Python dependecy management, which allows you to easily install all you need to run the package:
- Clone the repository
- Install `poetry`
- Go to the repository folder in terminal
- Run `poetry shell`
- Run `poetry install`
- [optional] Run `poetry run pytest` to check that the code runs
# How to use
The basic use of the package is as follows:
```
import chromatic_tda as chro
points, labels = ... # load points, labels
chro_alpha = chro.ChromaticAlphaComplex(points, labels) simplicial_complex = chro_alpha.get_simplicial_complex(
sub_complex=‘bi-chromatic’
complex=‘all’
relative=‘mono-chromatic’
) # these options of make sense for three colors; for two use, e.g., just sub_complex='mono-chromatic'
six_pack = simplicial_complex.bars_six_pack() chro.plot_six_pack(six_pack)
```
For more details check the docstrings of the methods and the jupyter notebook file `manual` (in [github repo](https://github.com/OnDraganov/chromatic-tda)). For more background on the theory, check the resources listed below.
# Future
The code is under active developement. The future plans include:
- Adding support for points in R^3
- Making persistence computation faster with clearing.
- Add more details and examples about how to use the code.
# Resources
The code is based on research done at Institute of Science and Technology by Ranita Biswas, Sebastiano Cultrera di Montesano, Ondřej Draganov, Herbert Edelsbrunner and Morteza Saghafian. A draft write up can be found on [arxiv](https://arxiv.org/abs/2212.03128). An updated version is currently being written.
A presentation about the main concepts used in this package can be viewed on YouTube: [AATRN Online Seminar: TDA for Chromatic Point Clouds](https://youtu.be/HIqiF00yKaw).
# Contact
If you have any questions to the code, do not hesitate to contat us. We are also eager to hear from you if you try the code out, and happy to chat about how you can use it on your data. Use, e.g., the mail in my [github profile](https://github.com/OnDraganov).
# License
Copyright ©2023. Institute of Science and Technology Austria (IST Austria). All Rights Reserved.
This file is part of chromatic_tda, which is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
You should have received a copy of the GNU Affero General Public License along with this program. If not, see <https://www.gnu.org/licenses/>.
Contact the Technology Transfer Office, ISTA, Am Campus 1, A-3400 Klosterneuburg, Austria, +43-(0)2243 9000, twist@ist.ac.at, for commercial licensing opportunities.
Raw data
{
"_id": null,
"home_page": "https://github.com/OnDraganov/chromatic-tda",
"name": "chromatic-tda",
"maintainer": "",
"docs_url": null,
"requires_python": ">=3.9,<3.13",
"maintainer_email": "",
"keywords": "tda,topological data analysis,chromatic,chromatic alpha,delaunay,persistence,persistent homology",
"author": "Ondrej Draganov",
"author_email": "ondrej.draganov@ist.ac.at",
"download_url": "https://files.pythonhosted.org/packages/3e/28/eab7712dfef7ec9d25f047a65937b7feb5efa943e78ec23324b1622d0dbc/chromatic_tda-1.0.4.tar.gz",
"platform": null,
"description": "# chromatic_tda\n\n`chromatic_tda` is a package for computing six-packs of persistent diagrams of colored point clouds. Currently point clouds in R^2 with 2 or 3 colors are supported (see Future).\n\n# Installation\n\n## Install with `pip`\n\nThe package is uploaded to [PyPI](https://pypi.org/project/chromatic-tda/), so it can be installed with `pip`.\n\nRun `pip install chromatic_tda`.\n\n## Install from [github project](https://github.com/OnDraganov/chromatic-tda)\n\nThe project uses `poetry` for Python dependecy management, which allows you to easily install all you need to run the package:\n\n- Clone the repository\n- Install `poetry`\n- Go to the repository folder in terminal\n- Run `poetry shell`\n- Run `poetry install`\n- [optional] Run `poetry run pytest` to check that the code runs\n\n# How to use\n\nThe basic use of the package is as follows:\n```\nimport chromatic_tda as chro\npoints, labels = ... # load points, labels\nchro_alpha = chro.ChromaticAlphaComplex(points, labels) simplicial_complex = chro_alpha.get_simplicial_complex(\n sub_complex=\u2018bi-chromatic\u2019\n complex=\u2018all\u2019\n relative=\u2018mono-chromatic\u2019\n) # these options of make sense for three colors; for two use, e.g., just sub_complex='mono-chromatic'\nsix_pack = simplicial_complex.bars_six_pack() chro.plot_six_pack(six_pack)\n```\n\nFor more details check the docstrings of the methods and the jupyter notebook file `manual` (in [github repo](https://github.com/OnDraganov/chromatic-tda)). For more background on the theory, check the resources listed below.\n\n# Future\n\nThe code is under active developement. The future plans include:\n- Adding support for points in R^3\n- Making persistence computation faster with clearing.\n- Add more details and examples about how to use the code.\n\n# Resources\n\nThe code is based on research done at Institute of Science and Technology by Ranita Biswas, Sebastiano Cultrera di Montesano, Ond\u0159ej Draganov, Herbert Edelsbrunner and Morteza Saghafian. A draft write up can be found on [arxiv](https://arxiv.org/abs/2212.03128). An updated version is currently being written.\n\nA presentation about the main concepts used in this package can be viewed on YouTube: [AATRN Online Seminar: TDA for Chromatic Point Clouds](https://youtu.be/HIqiF00yKaw).\n\n# Contact\n\nIf you have any questions to the code, do not hesitate to contat us. We are also eager to hear from you if you try the code out, and happy to chat about how you can use it on your data. Use, e.g., the mail in my [github profile](https://github.com/OnDraganov).\n\n# License\n\nCopyright \u00a92023. Institute of Science and Technology Austria (IST Austria). All Rights Reserved. \n\nThis file is part of chromatic_tda, which is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version.\n \nThis program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.\n \nYou should have received a copy of the GNU Affero General Public License along with this program. If not, see <https://www.gnu.org/licenses/>.\n \nContact the Technology Transfer Office, ISTA, Am Campus 1, A-3400 Klosterneuburg, Austria, +43-(0)2243 9000, twist@ist.ac.at, for commercial licensing opportunities.",
"bugtrack_url": null,
"license": "AGPL-3.0-or-later",
"summary": "Tool to compute six-packs of persistence diagrams for chromatic point clouds",
"version": "1.0.4",
"project_urls": {
"Documentation": "https://github.com/OnDraganov/chromatic-tda",
"Homepage": "https://github.com/OnDraganov/chromatic-tda",
"Repository": "https://github.com/OnDraganov/chromatic-tda"
},
"split_keywords": [
"tda",
"topological data analysis",
"chromatic",
"chromatic alpha",
"delaunay",
"persistence",
"persistent homology"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "09f89fa009d4c6f3699bffad6664ef838661dc4c5973d3672b69ea797d9e90c4",
"md5": "bae03bfcd7503d8a0fc83218a8ad450e",
"sha256": "7f1d4e47a7690d0f4c07b539b9cfbca94069d3b989eed539f45ee2f96b31832a"
},
"downloads": -1,
"filename": "chromatic_tda-1.0.4-py3-none-any.whl",
"has_sig": false,
"md5_digest": "bae03bfcd7503d8a0fc83218a8ad450e",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.9,<3.13",
"size": 38892,
"upload_time": "2023-08-31T16:05:09",
"upload_time_iso_8601": "2023-08-31T16:05:09.457201Z",
"url": "https://files.pythonhosted.org/packages/09/f8/9fa009d4c6f3699bffad6664ef838661dc4c5973d3672b69ea797d9e90c4/chromatic_tda-1.0.4-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "3e28eab7712dfef7ec9d25f047a65937b7feb5efa943e78ec23324b1622d0dbc",
"md5": "07007482724548c2f056ce946ca0fd29",
"sha256": "4101f516eab25c129d4a69eda02d6d260b1ff21ef1a22cc5bc7ef6f26fca6984"
},
"downloads": -1,
"filename": "chromatic_tda-1.0.4.tar.gz",
"has_sig": false,
"md5_digest": "07007482724548c2f056ce946ca0fd29",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.9,<3.13",
"size": 32110,
"upload_time": "2023-08-31T16:05:11",
"upload_time_iso_8601": "2023-08-31T16:05:11.759743Z",
"url": "https://files.pythonhosted.org/packages/3e/28/eab7712dfef7ec9d25f047a65937b7feb5efa943e78ec23324b1622d0dbc/chromatic_tda-1.0.4.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2023-08-31 16:05:11",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "OnDraganov",
"github_project": "chromatic-tda",
"travis_ci": false,
"coveralls": false,
"github_actions": false,
"lcname": "chromatic-tda"
}
JSON
