multipers 2.4.0b1__cp312-cp312-macosx_11_0_arm64.whl

multipers/ml/point_clouds.py

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+from collections.abc import Iterable
+from typing import Literal, Optional
+
+import gudhi as gd
+import numpy as np
+from joblib import Parallel, delayed
+from sklearn.base import BaseEstimator, TransformerMixin
+from scipy.spatial.distance import cdist
+from tqdm import tqdm
+
+import multipers as mp
+import multipers.slicer as mps
+from multipers.filtrations.density import DTM, KDE, available_kernels
+
+
+class PointCloud2FilteredComplex(BaseEstimator, TransformerMixin):
+    def __init__(
+        self,
+        bandwidths=[],
+        masses=[],
+        threshold: float = -np.inf,
+        complex: Literal["alpha", "rips", "delaunay"] = "rips",
+        sparse: Optional[float] = None,
+        num_collapses: int = -2,
+        kernel: available_kernels = "gaussian",
+        log_density: bool = True,
+        expand_dim: int = 1,
+        progress: bool = False,
+        n_jobs: Optional[int] = None,
+        fit_fraction: float = 1,
+        verbose: bool = False,
+        safe_conversion: bool = False,
+        output_type: Optional[
+            Literal["slicer", "simplextree", "slicer_vine", "slicer_novine"]
+        ] = None,
+        reduce_degrees: Optional[Iterable[int]] = None,
+    ) -> None:
+        """
+        (Rips or Alpha or Delaunay) + (Density Estimation or DTM) 1-critical 2-filtration.
+
+        Parameters
+        ----------
+         - bandwidth : real : The kernel density estimation bandwidth, or the DTM mass. If negative, it replaced by abs(bandwidth)*(radius of the dataset)
+         - threshold : real,  max edge lenfth of the rips or max alpha square of the alpha
+         - sparse : real, sparse rips (c.f. rips doc) WARNING : ONLY FOR RIPS
+         - num_collapse : int, Number of edge collapses applied to the simplextrees, WARNING : ONLY FOR RIPS
+         - expand_dim : int, expand the rips complex to this dimension. WARNING : ONLY FOR RIPS
+         - kernel : the kernel used for density estimation. Available ones are, e.g., "dtm", "gaussian", "exponential".
+         - progress : bool, shows the calculus status
+         - n_jobs : number of processes
+         - fit_fraction : real, the fraction of data on which to fit
+         - verbose : bool, Shows more information if true.
+
+        Output
+        ------
+        A list of SimplexTreeMulti whose first parameter is a rips and the second is the codensity.
+        """
+        super().__init__()
+        self.bandwidths = bandwidths
+        self.masses = masses
+        self.num_collapses = num_collapses
+        self.kernel = kernel
+        self.log_density = log_density
+        self.progress = progress
+        self._bandwidths = np.empty((0,))
+        self._threshold = np.inf
+        self.n_jobs = n_jobs
+        self._scale = np.empty((0,))
+        self.fit_fraction = fit_fraction
+        self.expand_dim = expand_dim
+        self.verbose = verbose
+        self.complex = complex
+        self.threshold = threshold
+        self.sparse = sparse
+        self._get_sts = lambda: Exception("Fit first")
+        self.safe_conversion = safe_conversion
+        self.output_type = output_type
+        self._output_type = None
+        self.reduce_degrees = reduce_degrees
+        self._vineyard = None
+
+        assert (
+            output_type != "simplextree" or reduce_degrees is None
+        ), "Reduced complex are not simplicial. Cannot return a simplextree."
+        return
+
+    def _get_distance_quantiles_and_threshold(self, X, qs):
+        ## if we dont need to compute a distance matrix
+        if len(qs) == 0 and self.threshold >= 0:
+            self._scale = []
+            return []
+        if self.progress:
+            print("Estimating scale...", flush=True, end="")
+        ## subsampling
+        indices = np.random.choice(
+            len(X), min(len(X), int(self.fit_fraction * len(X)) + 1), replace=False
+        )
+
+        def compute_max_scale(x):
+            from pykeops.numpy import LazyTensor
+
+            a = LazyTensor(x[None, :, :])
+            b = LazyTensor(x[:, None, :])
+            return np.sqrt(((a - b) ** 2).sum(2).max(1).min(0)[0])
+
+        diameter = np.max([compute_max_scale(x) for x in (X[i] for i in indices)])
+        self._scale = diameter * np.array(qs)
+
+        if self.threshold == -np.inf:
+            self._threshold = diameter
+        elif self.threshold > 0:
+            self._threshold = self.threshold
+        else:
+            self._threshold = -diameter * self.threshold
+
+        if self.threshold > 0:
+            self._scale[self._scale > self.threshold] = self.threshold
+
+        if self.progress:
+            print(f"Done. Chosen scales {qs} are {self._scale}", flush=True)
+        return self._scale
+
+    def _get_sts_rips(self, x):
+        assert self._output_type is not None and self._vineyard is not None
+        if self.sparse is None:
+            st_init = gd.SimplexTree.create_from_array(
+                cdist(x,x), max_filtration=self._threshold
+            )
+        else:
+            st_init = gd.RipsComplex(
+                points=x, max_edge_length=self._threshold, sparse=self.sparse
+            ).create_simplex_tree(max_dimension=1)
+        st_init = mp.simplex_tree_multi.SimplexTreeMulti(
+            st_init, num_parameters=2, safe_conversion=self.safe_conversion
+        )
+        codensities = self._get_codensities(x_fit=x, x_sample=x)
+        num_axes = codensities.shape[0]
+        sts = [st_init] + [st_init.copy() for _ in range(num_axes - 1)]
+        # no need to multithread here, most operations are memory
+        for codensity, st_copy in zip(codensities, sts):
+            # RIPS has contigus vertices, so vertices are ordered.
+            st_copy.fill_lowerstar(codensity, parameter=1)
+
+        def reduce(st):
+            if self.verbose:
+                print("Num simplices :", st.num_simplices)
+            if isinstance(self.num_collapses, int):
+                st.collapse_edges(num=self.num_collapses)
+                if self.verbose:
+                    print(", after collapse :", st.num_simplices, end="")
+            elif self.num_collapses == "full":
+                st.collapse_edges(full=True)
+                if self.verbose:
+                    print(", after collapse :", st.num_simplices, end="")
+            if self.expand_dim > 1:
+                st.expansion(self.expand_dim)
+                if self.verbose:
+                    print(", after expansion :", st.num_simplices, end="")
+            if self.verbose:
+                print("")
+            if self._output_type == "slicer":
+                st = mp.Slicer(st, vineyard=self._vineyard)
+                if self.reduce_degrees is not None:
+                    st = mp.slicer.minimal_presentation(
+                        st, degrees=self.reduce_degrees, vineyard=self._vineyard
+                    )
+            return st
+
+        return Parallel(backend="threading", n_jobs=self.n_jobs)(
+            delayed(reduce)(st) for st in sts
+        )
+
+    def _get_sts_alpha(self, x: np.ndarray, return_alpha=False):
+        assert self._output_type is not None and self._vineyard is not None
+        alpha_complex = gd.AlphaComplex(points=x)
+        st = alpha_complex.create_simplex_tree(max_alpha_square=self._threshold**2)
+        vertices = np.array([i for (i,), _ in st.get_skeleton(0)])
+        new_points = np.asarray(
+            [alpha_complex.get_point(int(i)) for i in vertices]
+        )  # Seems to be unsafe for some reason
+        # new_points = x
+        st = mp.simplex_tree_multi.SimplexTreeMulti(
+            st, num_parameters=2, safe_conversion=self.safe_conversion
+        )
+        codensities = self._get_codensities(x_fit=x, x_sample=new_points)
+        num_axes = codensities.shape[0]
+        sts = [st] + [st.copy() for _ in range(num_axes - 1)]
+        # no need to multithread here, most operations are memory
+        max_vertices = vertices.max() + 2  # +1 to be safe
+        for codensity, st_copy in zip(codensities, sts):
+            alligned_codensity = np.array([np.nan] * max_vertices)
+            alligned_codensity[vertices] = codensity
+            # alligned_codensity = np.array([codensity[i] if i in vertices else np.nan for i in range(max_vertices)])
+            st_copy.fill_lowerstar(alligned_codensity, parameter=1)
+        if "slicer" in self._output_type:
+            sts2 = (mp.Slicer(st, vineyard=self._vineyard) for st in sts)
+            if self.reduce_degrees is not None:
+                sts = tuple(
+                    mp.slicer.minimal_presentation(
+                        s, degrees=self.reduce_degrees, vineyard=self._vineyard
+                    )
+                    for s in sts2
+                )
+            else:
+                sts = tuple(sts2)
+        if return_alpha:
+            return alpha_complex, sts
+        return sts
+
+    def _get_sts_delaunay(self, x: np.ndarray):
+        codensities = self._get_codensities(x_fit=x, x_sample=x)
+
+        def get_st(c):
+            slicer = mps.from_function_delaunay(
+                x,
+                c,
+                verbose=self.verbose,
+                clear=not self.verbose,
+                vineyard=self._vineyard,
+            )
+            if self._output_type == "simplextree":
+                slicer = mps.to_simplextree(slicer)
+            elif self.reduce_degrees is not None:
+                slicer = mp.slicer.minimal_presentation(
+                    slicer,
+                    degrees=self.reduce_degrees,
+                    vineyard=self._vineyard,
+                )
+            else:
+                slicer = slicer
+            return slicer
+
+        sts = Parallel(backend="threading", n_jobs=self.n_jobs)(
+            delayed(get_st)(c) for c in codensities
+        )
+        return sts
+
+    def _get_codensities(self, x_fit, x_sample):
+        x_fit = np.asarray(x_fit, dtype=np.float64)
+        x_sample = np.asarray(x_sample, dtype=np.float64)
+        codensities_kde = np.asarray(
+            [
+                -KDE(
+                    bandwidth=bandwidth, kernel=self.kernel, return_log=self.log_density
+                )
+                .fit(x_fit)
+                .score_samples(x_sample)
+                for bandwidth in self._bandwidths
+            ],
+        ).reshape(len(self._bandwidths), len(x_sample))
+        codensities_dtm = (
+            DTM(masses=self.masses)
+            .fit(x_fit)
+            .score_samples(x_sample)
+            .reshape(len(self.masses), len(x_sample))
+        )
+        return np.concatenate([codensities_kde, codensities_dtm])
+
+    def _define_sts(self):
+        match self.complex:
+            case "rips":
+                self._get_sts = self._get_sts_rips
+                _pref_output = "simplextree"
+            case "alpha":
+                self._get_sts = self._get_sts_alpha
+                _pref_output = "simplextree"
+            case "delaunay":
+                self._get_sts = self._get_sts_delaunay
+                _pref_output = "slicer"
+            case _:
+                raise ValueError(
+                    f"Invalid complex \
+                {self.complex}. Possible choises are rips, delaunay, or alpha."
+                )
+        self._vineyard = (
+            False if self.output_type is None else "novine" not in self.output_type
+        )
+        self._output_type = (
+            _pref_output
+            if self.output_type is None
+            else (
+                "simplextree"
+                if (
+                    self.output_type == "simplextree" or self.reduce_degrees is not None
+                )
+                else "slicer"
+            )
+        )
+
+    def _define_bandwidths(self, X):
+        qs = [q for q in [*-np.asarray(self.bandwidths)] if 0 <= q <= 1]
+        self._get_distance_quantiles_and_threshold(X, qs=qs)
+        self._bandwidths = np.array(self.bandwidths)
+        count = 0
+        for i in range(len(self._bandwidths)):
+            if self.bandwidths[i] < 0:
+                self._bandwidths[i] = self._scale[count]
+                count += 1
+
+    def fit(self, X: np.ndarray | list, y=None):
+        # self.bandwidth = "silverman" ## not good, as is can make bandwidth not constant
+        self._define_sts()
+        self._define_bandwidths(X)
+        # PRECOMPILE FIRST
+        self._get_codensities(X[0][:2], X[0][:2])
+        return self
+
+    def transform(self, X):
+        # precompile first
+        # self._get_sts(X[0][:5])
+        self._get_codensities(X[0][:2], X[0][:2])
+        with tqdm(
+            X, desc="Filling simplextrees", disable=not self.progress, total=len(X)
+        ) as data:
+            stss = Parallel(backend="threading", n_jobs=self.n_jobs)(
+                delayed(self._get_sts)(x) for x in data
+            )
+        return stss
+
+
+class PointCloud2SimplexTree(PointCloud2FilteredComplex):
+    def __init__(
+        self,
+        bandwidths=[],
+        masses=[],
+        threshold: float = np.inf,
+        complex: Literal["alpha", "rips", "delaunay"] = "rips",
+        sparse: float | None = None,
+        num_collapses: int = -2,
+        kernel: available_kernels = "gaussian",
+        log_density: bool = True,
+        expand_dim: int = 1,
+        progress: bool = False,
+        n_jobs: Optional[int] = None,
+        fit_fraction: float = 1,
+        verbose: bool = False,
+        safe_conversion: bool = False,
+        output_type: Optional[
+            Literal["slicer", "simplextree", "slicer_vine", "slicer_novine"]
+        ] = None,
+        reduce_degrees: Optional[Iterable[int]] = None,
+    ) -> None:
+        stuff = locals()
+        stuff.pop("self")
+        keys = list(stuff.keys())
+        for key in keys:
+            if key.startswith("__"):
+                stuff.pop(key)
+        super().__init__(**stuff)
+        from warnings import warn
+
+        warn("This class is deprecated, use PointCloud2FilteredComplex instead.")