Add TSI score code #1166
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Add TSI score code #1166
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What do you think, @michalk8? |
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #1166 +/- ##
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+ Coverage 80.55% 80.69% +0.13%
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Files 51 51
Lines 8496 8566 +70
Branches 2221 2234 +13
==========================================
+ Hits 6844 6912 +68
+ Misses 1107 1102 -5
- Partials 545 552 +7
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Merged
michalk8
requested changes
Feb 23, 2024
Adds function for computing terminal state identification.
Add class method to compute TSI score.
Add class method to plot terminal state identification.
* Iterate through macrostates in decreasing order to compute Schur decomposition only once. * Access macrostates via attribute `macrostates`. * Allow passing keyword arguments to `compute_macrostates`. * Simplify value assignment for an optimal identification. * Update docstrings
* Update default values of `x_offset` and `y_offset` and update type hints. * Rename argument `fname` to `save`. * Add arguments `figsize` and `dpi`. * Update docstrings. * Update figure setup. * Fix x-axis labels caused by latest changes to `get_tsi`. * Use `save_fig` function. * Return matplotlib `Figure` and `Axis` instances.
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@michalk8, can you have another look, please? Once the code is fine, I'll add unit tests. |
michalk8
requested changes
Feb 29, 2024
Rename columns from "Number of macrostates" to "number_of_macrostates", "Identified terminal states" to "identified_terminal_states", "Optimal identification" to "optimal identification".
Update column names in plotting DataFrame from "Method" to "method".
Rename attribute to `_tsi` and define it in `__init__`.
* Rename method to `tsi`. * Refactor `tsi` to return TSI score. * TSI is only computed if it has not been computed before, the number of macrostates is larger than previously considered, a new set of terminal states or cluster key is used.
* Add argument `n_macrostates`. * Remove argument `tsi_df` and use class attribute directly instead.
WeilerP
commented
Mar 1, 2024
michalk8
requested changes
Mar 1, 2024
* Update docs.
* Update docstrings. * Update `RuntimeError` message * Update return statement; only `ax` is removed.
Save `terminal_states` in `uns` slot of `tsi` attribute as list.
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@michalk8, do you happen to know why some plotting tests fail after I've added the unit tests? |
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New
GPCCA::get_tsito compute terminal state identification (TSI).GPPCA::get_tsi_scoreto compute TSI score.GPCCA::plot_tsito visualize TSI.Closes
Closes #1165.