[WIP] Extended persistence and lower star filtrations

doc/modules/homology.rst

@@ -18,6 +18,7 @@ Undirected simplicial homology
    homology.SparseRipsPersistence
    homology.WeakAlphaPersistence
    homology.EuclideanCechPersistence
+   homology.LowerStarFlagPersistence
 
 Directed simplicial homology
 ----------------------------

doc/modules/plotting.rst

@@ -14,5 +14,6 @@
    plotting.plot_point_cloud
    plotting.plot_heatmap
    plotting.plot_diagram
+   plotting.plot_extended_diagram
    plotting.plot_betti_curves
    plotting.plot_betti_surfaces

gtda/homology/__init__.py

@@ -4,7 +4,7 @@
 
 from .simplicial import VietorisRipsPersistence, WeightedRipsPersistence, \
     SparseRipsPersistence, WeakAlphaPersistence, EuclideanCechPersistence, \
-    FlagserPersistence
+    FlagserPersistence, LowerStarFlagPersistence
 from .cubical import CubicalPersistence
 
 __all__ = [
@@ -14,5 +14,6 @@
     'WeakAlphaPersistence',
     'EuclideanCechPersistence',
     'FlagserPersistence',
+    'LowerStarFlagPersistence',
     'CubicalPersistence',
     ]

gtda/homology/_utils.py

@@ -4,9 +4,8 @@
 import numpy as np
 
 
-def _postprocess_diagrams(
-        Xt, format, homology_dimensions, infinity_values, reduced
-        ):
+def _postprocess_diagrams(Xt, format, homology_dimensions, infinity_values,
+                          reduced):
     # NOTE: `homology_dimensions` must be sorted in ascending order
     def replace_infinity_values(subdiagram):
         np.nan_to_num(subdiagram, posinf=infinity_values, copy=False)
@@ -21,6 +20,7 @@ def replace_infinity_values(subdiagram):
                   for dim in homology_dimensions}
         Xt = [{dim: replace_infinity_values(diagram[dim][slices[dim]])
                for dim in homology_dimensions} for diagram in Xt]
+        n_diagram_cols = 3
     elif format == "gudhi":  # Input is list of list of [dim, (birth, death)]
         # In H0, remove one infinite bar placed at the beginning by GUDHI only
         # if `reduce` is True
@@ -31,23 +31,28 @@ def replace_infinity_values(subdiagram):
                       if pers_info[0] == dim]).reshape(-1, 2)[slices[dim]]
             )
             for dim in homology_dimensions} for diagram in Xt]
+        n_diagram_cols = 3
+    elif format == "extended":  # Input is list of list of subdiagrams
+        Xt = [{dim: diagram[dim]
+               for dim in homology_dimensions} for diagram in Xt]
+        n_diagram_cols = 4
     else:
-        raise ValueError(
-            f"Unknown input format {format} for collection of diagrams."
-            )
+        raise ValueError(f"Unknown input format {format} for collection of "
+                         f"diagrams.")
 
-    # Conversion to array of triples with padding triples
+    # Conversion to array of triples/quadruples with padding
     start_idx_per_dim = np.cumsum(
-            [0] + [np.max([len(diagram[dim]) for diagram in Xt] + [1])
-                   for dim in homology_dimensions]
-            )
+        [0] + [np.max([len(diagram[dim]) for diagram in Xt] + [1])
+               for dim in homology_dimensions]
+        )
     min_values = [min([np.min(diagram[dim][:, 0]) if diagram[dim].size
                        else np.inf for diagram in Xt])
                   for dim in homology_dimensions]
     min_values = [min_value if min_value != np.inf else 0
                   for min_value in min_values]
     n_features = start_idx_per_dim[-1]
-    Xt_padded = np.empty((len(Xt), n_features, 3), dtype=float)
+    Xt_padded = np.empty((len(Xt), n_features, n_diagram_cols), dtype=float)
+    Xt_padded[:, :, 3:] = 1.  # Only applies to extended persistence
 
     for i, dim in enumerate(homology_dimensions):
         start_idx, end_idx = start_idx_per_dim[i:i + 2]
@@ -58,8 +63,10 @@ def replace_infinity_values(subdiagram):
             subdiagram = diagram[dim]
             end_idx_nontrivial = start_idx + len(subdiagram)
             # Populate nontrivial part of the subdiagram
-            Xt_padded[j, start_idx:end_idx_nontrivial, :2] = subdiagram
-            # Insert padding triples
+            Xt_padded[j, start_idx:end_idx_nontrivial, :2] = subdiagram[:, :2]
+            Xt_padded[j, start_idx:end_idx_nontrivial, 3:] = \
+                subdiagram[:, 2:]  # Only applies to extended persistence
+            # Insert padding triples/quadruples
             Xt_padded[j, end_idx_nontrivial:end_idx, :2] = [padding_value] * 2
 
     return Xt_padded

gtda/homology/simplicial.py

@@ -16,7 +16,7 @@
 from ._utils import _postprocess_diagrams
 from ..base import PlotterMixin
 from ..externals.python import ripser, SparseRipsComplex, CechComplex
-from ..plotting import plot_diagram
+from ..plotting import plot_diagram, plot_extended_diagram
 from ..utils._docs import adapt_fit_transform_docs
 from ..utils.intervals import Interval
 from ..utils.validation import validate_params, check_point_clouds
@@ -302,8 +302,8 @@ def transform(self, X, y=None):
         X = check_point_clouds(X, accept_sparse=True,
                                distance_matrices=self._is_precomputed)
 
-        Xt = Parallel(n_jobs=self.n_jobs)(
-            delayed(self._ripser_diagram)(x) for x in X)
+        Xt = Parallel(n_jobs=self.n_jobs)(delayed(self._ripser_diagram)(x)
+                                          for x in X)
 
         Xt = _postprocess_diagrams(
             Xt, "ripser", self._homology_dimensions, self.infinity_values_,
@@ -691,8 +691,8 @@ def transform(self, X, y=None):
         X = check_point_clouds(X, accept_sparse=True, force_all_finite=True,
                                distance_matrices=self._is_precomputed)
 
-        Xt = Parallel(n_jobs=self.n_jobs)(
-            delayed(self._ripser_diagram)(x) for x in X)
+        Xt = Parallel(n_jobs=self.n_jobs)(delayed(self._ripser_diagram)(x)
+                                          for x in X)
 
         Xt = _postprocess_diagrams(
             Xt, "ripser", self._homology_dimensions, self.infinity_values_,
@@ -962,8 +962,8 @@ def transform(self, X, y=None):
         X = check_point_clouds(X, accept_sparse=True,
                                distance_matrices=self._is_precomputed)
 
-        Xt = Parallel(n_jobs=self.n_jobs)(
-            delayed(self._gudhi_diagram)(x) for x in X)
+        Xt = Parallel(n_jobs=self.n_jobs)(delayed(self._gudhi_diagram)(x)
+                                          for x in X)
 
         Xt = _postprocess_diagrams(
             Xt, "gudhi", self._homology_dimensions, self.infinity_values_,
@@ -1213,8 +1213,8 @@ def transform(self, X, y=None):
         check_is_fitted(self)
         X = check_point_clouds(X)
 
-        Xt = Parallel(n_jobs=self.n_jobs)(
-            delayed(self._weak_alpha_diagram)(x) for x in X)
+        Xt = Parallel(n_jobs=self.n_jobs)(delayed(self._weak_alpha_diagram)(x)
+                                          for x in X)
 
         Xt = _postprocess_diagrams(
             Xt, "ripser", self._homology_dimensions, self.infinity_values_,
@@ -1728,8 +1728,8 @@ def transform(self, X, y=None):
         check_is_fitted(self)
         X = check_point_clouds(X, accept_sparse=True, distance_matrices=True)
 
-        Xt = Parallel(n_jobs=self.n_jobs)(
-            delayed(self._flagser_diagram)(x) for x in X)
+        Xt = Parallel(n_jobs=self.n_jobs)(delayed(self._flagser_diagram)(x)
+                                          for x in X)
 
         Xt = _postprocess_diagrams(
             Xt, "flagser", self._homology_dimensions, self.infinity_values_,
@@ -1772,3 +1772,181 @@ def plot(Xt, sample=0, homology_dimensions=None, plotly_params=None):
             Xt[sample], homology_dimensions=homology_dimensions,
             plotly_params=plotly_params
             )
+
+
+# @adapt_fit_transform_docs
+class LowerStarFlagPersistence(BaseEstimator, TransformerMixin, PlotterMixin):
+    """TODO"""
+    _hyperparameters = {
+        "homology_dimensions": {
+            "type": (list, tuple),
+            "of": {"type": int, "in": Interval(0, np.inf, closed="left")}
+            },
+        "coeff": {"type": int, "in": Interval(2, np.inf, closed="left")},
+        "extended": {"type": bool},
+        "infinity_values": {"type": (Real, type(None))},
+        "reduced_homology": {"type": bool},
+        "collapse_edges": {"type": bool}
+        }
+
+    def __init__(self, homology_dimensions=(0, 1), coeff=2, extended=True,
+                 infinity_values=np.inf, reduced_homology=False,
+                 collapse_edges=False, n_jobs=None):
+        self.homology_dimensions = homology_dimensions
+        self.coeff = coeff
+        self.extended = extended
+        self.infinity_values = infinity_values
+        self.reduced_homology = reduced_homology
+        self.collapse_edges = collapse_edges
+        self.n_jobs = n_jobs
+
+    def _lower_star_extended_diagram(self, X):
+        n_points = max(X.shape)
+        n_points_cone = n_points + 1
+        n_diag = min(X.shape)
+        X = X.tocoo().astype(np.float32)  # ripser needs single precision
+
+        data_diag = np.zeros(n_points_cone, dtype=X.dtype)
+        data_diag[:n_diag] = X.diagonal()
+        max_value = data_diag[:n_points].max()
+        min_value = data_diag[:n_points].min()
+        data_diag[-1] = min_value - 1
+
+        off_diag = X.row != X.col
+        row_off_diag, col_off_diag = X.row[off_diag], X.col[off_diag]
+
+        row = np.concatenate([row_off_diag, np.arange(n_points)])
+        col = np.concatenate([col_off_diag, np.full(n_points, n_points)])
+        data = np.concatenate([
+            np.maximum(data_diag[row_off_diag], data_diag[col_off_diag]),
+            min_value + 2 * (max_value - min_value) + 1
+            - (data_diag[:n_points]-min_value)
+            ])
+
+        X = coo_matrix((data, (row, col)),
+                       shape=(n_points_cone, n_points_cone))
+        X.setdiag(data_diag)
+
+        Xdgms = ripser(
+            X, metric="precomputed", maxdim=self._max_homology_dimension,
+            coeff=self.coeff, collapse_edges=self.collapse_edges
+            )["dgms"]
+
+        for i in range(len(Xdgms)):
+            mask_down_sweep = Xdgms[i] > max_value
+            sgn = 2 * np.logical_not(
+                np.logical_xor.reduce(mask_down_sweep, axis=1,
+                                      keepdims=True)).astype(int) - 1
+            Xdgms[i][mask_down_sweep] = \
+                min_value + 2 * (max_value - min_value) + 1\
+                - (Xdgms[i][mask_down_sweep]-min_value)
+            if not i:
+                Xdgms[i] = np.hstack([Xdgms[i][:-1, :], sgn[:-1, :]])
+            else:
+                Xdgms[i] = np.hstack([Xdgms[i], sgn])
+
+        return Xdgms
+
+    def _lower_star_diagram(self, X):
+        n_points = max(X.shape)
+        n_diag = min(X.shape)
+        X = X.tocoo()
+
+        data_diag = np.zeros(n_points, dtype=X.dtype)
+        data_diag[:n_diag] = X.diagonal()
+
+        off_diag = X.row != X.col
+        row_off_diag, col_off_diag = X.row[off_diag], X.col[off_diag]
+
+        row = np.concatenate([row_off_diag, np.arange(n_points)])
+        col = np.concatenate([col_off_diag, np.arange(n_points)])
+        data = np.concatenate([
+            np.maximum(data_diag[row_off_diag], data_diag[col_off_diag]),
+            data_diag]
+            )
+
+        X = coo_matrix((data, (row, col)))
+
+        Xdgms = ripser(
+            X, metric="precomputed", maxdim=self._max_homology_dimension,
+            coeff=self.coeff, collapse_edges=self.collapse_edges
+            )["dgms"]
+
+        return Xdgms
+
+    def fit(self, X, y=None):
+        """TODO"""
+        check_point_clouds(X, accept_sparse=True, distance_matrices=True)
+        validate_params(
+            self.get_params(), self._hyperparameters, exclude=["n_jobs"])
+
+        self._homology_dimensions = sorted(self.homology_dimensions)
+        self._max_homology_dimension = self._homology_dimensions[-1]
+
+        if self.extended:
+            self._diagram_computer = self._lower_star_extended_diagram
+            self._format = "extended"
+        else:
+            self._diagram_computer = self._lower_star_diagram
+            self._format = "ripser"
+
+        self._is_fitted = True
+
+        return self
+
+    def transform(self, X, y=None):
+        """TODO"""
+        check_is_fitted(self, "_is_fitted")
+        X = check_point_clouds(X, accept_sparse=True, distance_matrices=True)
+
+        Xt = Parallel(n_jobs=self.n_jobs)(delayed(self._diagram_computer)(x)
+                                          for x in X)
+
+        Xt = _postprocess_diagrams(
+            Xt, self._format, self._homology_dimensions, self.infinity_values,
+            self.reduced_homology
+            )
+        return Xt
+
+    @staticmethod
+    def plot(Xt, sample=0, homology_dimensions=None, plotly_params=None):
+        """Plot a sample from a collection of persistence diagrams, with
+        homology in multiple dimensions.
+
+        Parameters
+        ----------
+        Xt : ndarray of shape (n_samples, n_features, 3)
+            Collection of persistence diagrams, such as returned by
+            :meth:`transform`.
+
+        sample : int, optional, default: ``0``
+            Index of the sample in `Xt` to be plotted.
+
+        homology_dimensions : list, tuple or None, optional, default: ``None``
+            Which homology dimensions to include in the plot. ``None`` means
+            plotting all dimensions present in ``Xt[sample]``.
+
+        plotly_params : dict or None, optional, default: ``None``
+            Custom parameters to configure the plotly figure. Allowed keys are
+            ``"traces"`` and ``"layout"``, and the corresponding values should
+            be dictionaries containing keyword arguments as would be fed to the
+            :meth:`update_traces` and :meth:`update_layout` methods of
+            :class:`plotly.graph_objects.Figure`.
+
+        Returns
+        -------
+        fig : :class:`plotly.graph_objects.Figure` object
+            Plotly figure.
+
+        """
+        Xt_sample = Xt[sample]
+        if Xt_sample.shape[1] == 4:
+            return plot_extended_diagram(
+                Xt_sample, homology_dimensions=homology_dimensions,
+                plotly_params=plotly_params
+                )
+
+        return plot_diagram(
+            Xt_sample, homology_dimensions=homology_dimensions,
+            plotly_params=plotly_params
+            )