TD4-TopologicalPersistence

Emails for project submission:

— steve.oudot@inria.fr
— ringyi.li@polytechnique.edu
— julie.mordacq@inria.fr

Environment

• python 3.11.2 or later
• dependencies
  • pandas
  • jupyter notebook
  • pytest # No need to install if you do not run test code.

Tests

This test code is optional for running code of Q1-Q4. Run following code on the project root directory after installing pytest.

kazetof@inspiron:~/Works/IPParis/TDA/TD4/TD4-TopologicalPersistence$ pwd
/home/kazetof/Works/IPParis/TDA/TD4/TD4-TopologicalPersistence
kazetof@inspiron:~/Works/IPParis/TDA/TD4/TD4-TopologicalPersistence$ ls
LICENSE  README.md  __pycache__  examples  filtrations  persistence  requirements.txt  tests
kazetof@inspiron:~/Works/IPParis/TDA/TD4/TD4-TopologicalPersistence$ PYTHONPATH=./ pytest ./tests -s

Directory structure

kazetof@inspiron:~/Works/IPParis/TDA/TD4/TD4-TopologicalPersistence$ tree
.
├── LICENSE
├── README.md
├── Diagrams.ipynb
├── execution
│   ├── barcode_plot_Q6.py
│   └── main.py # code for timing from reading data to computing barcode
├── filtrations # directoru for data
│   ├── filtration_A.txt
│   ├── filtration_B.txt
│   ├── filtration_C.txt
│   └── filtration_D.txt
├── outputs
│   ├── barcodes
│   │   ├── barcode_filtration_A.txt
│   │   ├── barcode_filtration_B.txt
│   │   └── barcode_filtration_C.txt
│   └── results_of_timing.txt
├── persistence
│   ├── __init__.py
│   ├── boundary_matrix.py
│   ├── compute_barcode.py
│   ├── persistence.py
│   └── reduce_boundary_matrix.py
├── requirements.txt
└── tests # test code is optional for TD, you can run the code without this directory.
    ├── test_boundary_matrix.py
    ├── test_reduce_boundary_matrix.py
    └── testcases
        ├── filtration_1.txt
        └── filtration_2.txt

How to execute

Q4 timing for barcode computation

1. Put filtrations data in filtrations directories with the names of filtration_A.txt, filtration_B.txt, filtration_C.txt, and filtration_D.txt.
2. to run timing code, execute main.py like below on the project root directory.
3. You have generated barcodes in outputs/barcode and timing result in outputs/results_of_timing.txt

kazetof@inspiron:~/Works/IPParis/TDA/TD4/TD4-TopologicalPersistence$ pwd
/home/kazetof/Works/IPParis/TDA/TD4/TD4-TopologicalPersistence
kazetof@inspiron:~/Works/IPParis/TDA/TD4/TD4-TopologicalPersistence$ ls
LICENSE  README.md  drafts  execution  filtrations  outputs  persistence  requirements.txt  tests
kazetof@inspiron:~/Works/IPParis/TDA/TD4/TD4-TopologicalPersistence$ PYTHONPATH=./ python ./execution/main.py

Q5 Diagram

1. Run jupyter notebook "Diagrams.ipyenv" on project directory to see the diagram interactively.

kazetof@inspiron:~/Works/IPParis/TDA/TD4/TD4-TopologicalPersistence$ pwd
/home/kazetof/Works/IPParis/TDA/TD4/TD4-TopologicalPersistence
kazetof@inspiron:~/Works/IPParis/TDA/TD4/TD4-TopologicalPersistence$ ls
Diagrams.ipynb                  LICENSE    drafts     filtrations  persistence       tests
Diagrams.ipynb:Zone.Identifier  README.md  execution  outputs      requirements.txt
kazetof@inspiron:~/Works/IPParis/TDA/TD4/TD4-TopologicalPersistence$ jupyter notebook

Q6 compute barcode

1. Put filtration text files of classical spaces in "./filtrations/filtrations2/"
2. Run "./execution/barcode_plot_Q6.py" in the project root directory like following example.
3. The output barcode will be saved in "./outputs/barcode_Q6".

kazetof@inspiron:~/Works/IPParis/TDA/TD4/TD4-TopologicalPersistence$ pwd
/home/kazetof/Works/IPParis/TDA/TD4/TD4-TopologicalPersistence
kazetof@inspiron:~/Works/IPParis/TDA/TD4/TD4-TopologicalPersistence$ ls
Diagrams.ipynb                  LICENSE    drafts     filtrations  persistence       tests
Diagrams.ipynb:Zone.Identifier  README.md  execution  outputs      requirements.txt
kazetof@inspiron:~/Works/IPParis/TDA/TD4/TD4-TopologicalPersistence$ PYTHONPATH=./ python ./execution/barcode_plot_Q6.py