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Diffstat (limited to 'src/python/gudhi/sklearn/cubical_persistence.py')
-rw-r--r-- | src/python/gudhi/sklearn/cubical_persistence.py | 110 |
1 files changed, 110 insertions, 0 deletions
diff --git a/src/python/gudhi/sklearn/cubical_persistence.py b/src/python/gudhi/sklearn/cubical_persistence.py new file mode 100644 index 00000000..672af278 --- /dev/null +++ b/src/python/gudhi/sklearn/cubical_persistence.py @@ -0,0 +1,110 @@ +# 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): Vincent Rouvreau +# +# Copyright (C) 2021 Inria +# +# Modification(s): +# - YYYY/MM Author: Description of the modification + +from .. import CubicalComplex +from sklearn.base import BaseEstimator, TransformerMixin + +import numpy as np +# joblib is required by scikit-learn +from joblib import Parallel, delayed + +# Mermaid sequence diagram - https://mermaid-js.github.io/mermaid-live-editor/ +# sequenceDiagram +# USER->>CubicalPersistence: fit_transform(X) +# CubicalPersistence->>thread1: _tranform(X[0]) +# CubicalPersistence->>thread2: _tranform(X[1]) +# Note right of CubicalPersistence: ... +# thread1->>CubicalPersistence: [array( H0(X[0]) ), array( H1(X[0]) )] +# thread2->>CubicalPersistence: [array( H0(X[1]) ), array( H1(X[1]) )] +# Note right of CubicalPersistence: ... +# CubicalPersistence->>USER: [[array( H0(X[0]) ), array( H1(X[0]) )],<br/> [array( H0(X[1]) ), array( H1(X[1]) )],<br/> ...] + + +class CubicalPersistence(BaseEstimator, TransformerMixin): + """ + This is a class for computing the persistence diagrams from a cubical complex. + """ + + def __init__( + self, + homology_dimensions, + newshape=None, + homology_coeff_field=11, + min_persistence=0.0, + n_jobs=None, + ): + """ + Constructor for the CubicalPersistence class. + + Parameters: + homology_dimensions (int or list of int): The returned persistence diagrams dimension(s). + Short circuit the use of :class:`~gudhi.representations.preprocessing.DimensionSelector` when only one + dimension matters (in other words, when `homology_dimensions` is an int). + newshape (tuple of ints): If cells filtration values require to be reshaped + (cf. :func:`~gudhi.sklearn.cubical_persistence.CubicalPersistence.transform`), set `newshape` + to perform `numpy.reshape(X, newshape, order='C')` in + :func:`~gudhi.sklearn.cubical_persistence.CubicalPersistence.transform` method. + homology_coeff_field (int): The homology coefficient field. Must be a prime number. Default value is 11. + min_persistence (float): The minimum persistence value to take into account (strictly greater than + `min_persistence`). Default value is `0.0`. Set `min_persistence` to `-1.0` to see all values. + n_jobs (int): cf. https://joblib.readthedocs.io/en/latest/generated/joblib.Parallel.html + """ + self.homology_dimensions = homology_dimensions + self.newshape = newshape + self.homology_coeff_field = homology_coeff_field + self.min_persistence = min_persistence + self.n_jobs = n_jobs + + def fit(self, X, Y=None): + """ + Nothing to be done, but useful when included in a scikit-learn Pipeline. + """ + return self + + def __transform(self, cells): + cubical_complex = CubicalComplex(top_dimensional_cells=cells) + cubical_complex.compute_persistence( + homology_coeff_field=self.homology_coeff_field, min_persistence=self.min_persistence + ) + return [ + cubical_complex.persistence_intervals_in_dimension(dim) for dim in self.homology_dimensions + ] + + def __transform_only_this_dim(self, cells): + cubical_complex = CubicalComplex(top_dimensional_cells=cells) + cubical_complex.compute_persistence( + homology_coeff_field=self.homology_coeff_field, min_persistence=self.min_persistence + ) + return cubical_complex.persistence_intervals_in_dimension(self.homology_dimensions) + + def transform(self, X, Y=None): + """Compute all the cubical complexes and their associated persistence diagrams. + + :param X: List of cells filtration values (`numpy.reshape(X, newshape, order='C'` if `newshape` is set with a tuple of ints). + :type X: list of list of float OR list of numpy.ndarray + + :return: Persistence diagrams in the format: + + - If `homology_dimensions` was set to `n`: `[array( Hn(X[0]) ), array( Hn(X[1]) ), ...]` + - If `homology_dimensions` was set to `[i, j]`: `[[array( Hi(X[0]) ), array( Hj(X[0]) )], [array( Hi(X[1]) ), array( Hj(X[1]) )], ...]` + :rtype: list of (,2) array_like or list of list of (,2) array_like + """ + if self.newshape is not None: + X = np.reshape(X, self.newshape, order='C') + + # Depends on homology_dimensions is an integer or a list of integer (else case) + if isinstance(self.homology_dimensions, int): + # threads is preferred as cubical construction and persistence computation releases the GIL + return Parallel(n_jobs=self.n_jobs, prefer="threads")( + delayed(self.__transform_only_this_dim)(cells) for cells in X + ) + else: + # threads is preferred as cubical construction and persistence computation releases the GIL + return Parallel(n_jobs=self.n_jobs, prefer="threads")(delayed(self.__transform)(cells) for cells in X) + |