First version of CubicalPersistence

2 files changed, 64 insertions, 0 deletions

diff --git a/src/python/gudhi/sklearn/__init__.py b/src/python/gudhi/sklearn/__init__.py
new file mode 100644
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+++ b/src/python/gudhi/sklearn/__init__.py
diff --git a/src/python/gudhi/sklearn/cubical_persistence.py b/src/python/gudhi/sklearn/cubical_persistence.py
new file mode 100644
index 00000000..a58fa77c
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+++ b/src/python/gudhi/sklearn/cubical_persistence.py
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+from .. import CubicalComplex
+from sklearn.base import TransformerMixin
+
+class CubicalPersistence(TransformerMixin):
+    # Fast way to find primes and should be enough
+    available_primes_ = [2, 3, 5, 7, 11, 13, 17, 19, 23, 29, 31, 37, 41, 43, 47, 53, 59, 61, 67, 71, 73, 79, 83, 89, 97]
+    """
+    This is a class for computing the persistence diagrams from a cubical complex.
+    """
+    def __init__(self, dimensions=None, persistence_dim=0, min_persistence=0):
+        """
+        Constructor for the CubicalPersistence class.
+
+        Parameters:
+            dimensions (list of int): A list of number of top dimensional cells.
+            persistence_dim (int): The returned persistence diagrams dimension. Default value is `0`.
+            min_persistence (float): The minimum persistence value to take into account (strictly greater than
+                `min_persistence`). Default value is `0.0`. Sets `min_persistence` to `-1.0` to see all values.
+        """
+        self.dimensions_ = dimensions
+        self.persistence_dim_ = persistence_dim
+
+        self.homology_coeff_field_ = None
+        for dim in self.available_primes_:
+            if dim > persistence_dim + 1:
+                self.homology_coeff_field_ = dim
+                break
+        if self.homology_coeff_field_ == None:
+            raise ValueError("persistence_dim must be less than 96")
+
+        self.min_persistence_ = min_persistence
+
+    def transform(self, X):
+        """
+        Compute all the cubical complexes and their persistence diagrams.
+
+        Parameters:
+            X (list of double OR numpy.ndarray): Cells filtration values.
+
+        Returns:
+            Persistence diagrams
+        """
+        cubical_complex = CubicalComplex(top_dimensional_cells = X,
+                                         dimensions = self.dimensions_)
+        cubical_complex.compute_persistence(homology_coeff_field = self.homology_coeff_field_,
+                                            min_persistence = self.min_persistence_)
+        self.diagrams_ = cubical_complex.persistence_intervals_in_dimension(self.persistence_dim_)
+        if self.persistence_dim_ == 0:
+            # return all but the last, always [ 0., inf]
+            self.diagrams_ = self.diagrams_[:-1]
+        return self.diagrams_
+
+    def fit_transform(self, X):
+        """
+        Compute all the cubical complexes and their persistence diagrams.
+
+        Parameters:
+            X (list of double OR numpy.ndarray): Cells filtration values.
+
+        Returns:
+            Persistence diagrams
+        """
+        self.transform(X)
+        return self.diagrams_