multipers 2.2.3__cp312-cp312-win_amd64.whl → 2.3.1__cp312-cp312-win_amd64.whl

multipers/torch/rips_density.py

@@ -1,304 +1,310 @@
-from typing import Callable, Literal, Optional
-
-import numpy as np
-import torch
-from gudhi.rips_complex import RipsComplex
-
-import multipers as mp
-from multipers.ml.convolutions import DTM, KDE
-from multipers.simplex_tree_multi import _available_strategies
-from multipers.torch.diff_grids import get_grid
-
-
-def function_rips_signed_measure_old(
-    x,
-    theta: Optional[float] = None,
-    function: Literal["dtm", "gaussian", "exponential"] | Callable = "dtm",
-    threshold: float = np.inf,
-    grid_strategy: _available_strategies = "regular_closest",
-    resolution: int = 100,
-    return_original: bool = False,
-    return_st: bool = False,
-    safe_conversion: bool = False,
-    num_collapses: int = -1,
-    expand_collapse: bool = False,
-    dtype=torch.float32,
-    **sm_kwargs,
-):
-    """
-    Computes a torch-differentiable function-rips signed measure.
-
-    Input
-    -----
-     - x (num_pts, dim) : The point cloud
-     - theta: For density-like functions : the bandwidth
-     - threshold : rips threshold
-     - function : Either "dtm", "gaussian", or "exponenetial" or Callable.
-       Function to compute the second parameter.
-     - grid_strategy: grid coarsenning strategy.
-     - resolution : when coarsenning, the target resolution,
-     - return_original : Also returns the non-differentiable signed measure.
-     - safe_conversion : Activate this if you encounter crashes.
-     - **kwargs : for the signed measure computation.
-    """
-    assert isinstance(x, torch.Tensor)
-    if function == "dtm":
-        assert theta is not None, "Provide a theta to compute DTM"
-        codensity = DTM(masses=[theta]).fit(x).score_samples_diff(x)[0].type(dtype)
-    elif function in ["gaussian", "exponential"]:
-        assert theta is not None, "Provide a theta to compute density estimation"
-        codensity = (
-            -KDE(
-                bandwidth=theta,
-                kernel=function,
-                return_log=True,
-            )
-            .fit(x)
-            .score_samples(x)
-            .type(dtype)
-        )
-    else:
-        assert callable(function), "Function has to be callable"
-        if theta is None:
-            codensity = function(x).type(dtype)
-        else:
-            codensity = function(x, theta=theta).type(dtype)
-
-    distance_matrix = torch.cdist(x, x).type(dtype)
-    if threshold < np.inf:
-        distance_matrix[distance_matrix > threshold] = np.inf
-
-    st = RipsComplex(
-        distance_matrix=distance_matrix.detach(), max_edge_length=threshold
-    ).create_simplex_tree()
-    # detach makes a new (reference) tensor, without tracking the gradient
-    st = mp.SimplexTreeMulti(st, num_parameters=2, safe_conversion=safe_conversion)
-    st.fill_lowerstar(
-        codensity.detach(), parameter=1
-    )  # fills the codensity in the second parameter of the simplextree
-
-    # simplificates the simplextree for computation, the signed measure will be recovered from the copy afterward
-    st_copy = st.grid_squeeze(
-        grid_strategy=grid_strategy, resolution=resolution, coordinate_values=True
-    )
-    if sm_kwargs.get("degree", None) is None and sm_kwargs.get("degrees", [None]) == [
-        None
-    ]:
-        expansion_degree = st.num_vertices
-    else:
-        expansion_degree = (
-            max(np.max(sm_kwargs.get("degrees", 1)), sm_kwargs.get("degree", 1)) + 1
-        )
-    st.collapse_edges(num=num_collapses)
-    if not expand_collapse:
-        st.expansion(expansion_degree)  # edge collapse
-    sms = mp.signed_measure(st, **sm_kwargs)  # computes the signed measure
-    del st
-
-    simplices_list = tuple(
-        s for s, _ in st_copy.get_simplices()
-    )  # not optimal, we may want to do that in cython to get edges and nodes
-    sms_diff = []
-    for sm, weights in sms:
-        indices, not_found_indices = st_copy.pts_to_indices(
-            sm, simplices_dimensions=[1, 0]
-        )
-        if sm_kwargs.get("verbose", False):
-            print(
-                f"Found {(1-(indices == -1).mean()).round(2)} indices. \
-                Out : {(indices == -1).sum()}, {len(not_found_indices)}"
-            )
-        sm_diff = torch.empty(sm.shape).type(dtype)
-        # sim_dim = sm_diff.shape[1] // 2
-
-        # fills the Rips-filtrations of the signed measure.
-        # the loop is for the rank invariant
-        for i in range(0, sm_diff.shape[1], 2):
-            idxs = indices[:, i]
-            if (idxs == -1).all():
-                continue
-            useful_idxs = idxs != -1
-            # Retrieves the differentiable values from the distance_matrix
-            if useful_idxs.size > 0:
-                edges_filtrations = torch.cat(
-                    [
-                        distance_matrix[*simplices_list[idx], None]
-                        for idx in idxs[useful_idxs]
-                    ]
-                )
-                # fills theses values into the signed measure
-                sm_diff[:, i][useful_idxs] = edges_filtrations
-        # same for the other axis
-        for i in range(1, sm_diff.shape[1], 2):
-            idxs = indices[:, i]
-            if (idxs == -1).all():
-                continue
-            useful_idxs = idxs != -1
-            if useful_idxs.size > 0:
-                nodes_filtrations = torch.cat(
-                    [codensity[simplices_list[idx]] for idx in idxs[useful_idxs]]
-                )
-                sm_diff[:, i][useful_idxs] = nodes_filtrations
-
-        # fills not-found values as constants
-        if len(not_found_indices) > 0:
-            not_found_indices = indices == -1
-            sm_diff[indices == -1] = torch.from_numpy(sm[indices == -1]).type(dtype)
-
-        sms_diff.append((sm_diff, torch.from_numpy(weights)))
-    flags = [True, return_original, return_st]
-    if np.sum(flags) == 1:
-        return sms_diff
-    return tuple(stuff for stuff, flag in zip([sms_diff, sms, st_copy], flags) if flag)
-
-
-def function_rips_signed_measure(
-    x,
-    theta: Optional[float] = None,
-    function: Literal["dtm", "gaussian", "exponential"] | Callable = "gaussian",
-    threshold: Optional[float] = None,
-    grid_strategy: Literal[
-        "regular_closest", "exact", "quantile", "regular_left"
-    ] = "exact",
-    complex: Literal["rips", "delaunay", "weak_delaunay"] = "rips",
-    resolution: int = 100,
-    safe_conversion: bool = False,
-    num_collapses: Optional[int] = None,
-    expand_collapse: bool = False,
-    dtype=torch.float32,
-    plot=False,
-    # return_st: bool = False,
-    *,
-    log_density: bool = True,
-    vineyard: bool = False,
-    pers_backend=None,
-    **sm_kwargs,
-):
-    """
-    Computes a torch-differentiable function-rips signed measure.
-
-    Input
-    -----
-     - x (num_pts, dim) : The point cloud
-     - theta: For density-like functions : the bandwidth
-     - threshold : rips threshold
-     - function : Either "dtm", "gaussian", or "exponenetial" or Callable.
-       Function to compute the second parameter.
-     - grid_strategy: grid coarsenning strategy.
-     - resolution : when coarsenning, the target resolution,
-     - return_original : Also returns the non-differentiable signed measure.
-     - safe_conversion : Activate this if you encounter crashes.
-     - **kwargs : for the signed measure computation.
-    """
-    if num_collapses is None:
-        num_collapses = -1 if complex == "rips" else None
-    assert isinstance(x, torch.Tensor)
-    if function == "dtm":
-        assert theta is not None, "Provide a theta to compute DTM"
-        codensity = DTM(masses=[theta]).fit(x).score_samples_diff(x)[0].type(dtype)
-    elif function in ["gaussian", "exponential"]:
-        assert theta is not None, "Provide a theta to compute density estimation"
-        codensity = (
-            -KDE(
-                bandwidth=theta,
-                kernel=function,
-                return_log=log_density,
-            )
-            .fit(x)
-            .score_samples(x)
-            .type(dtype)
-        )
-    elif isinstance(function, torch.Tensor):
-        assert (
-            function.ndim == 1 and codensity.shape[0] == x.shape[0]
-        ), """
-        When function is a tensor, it is interpreted as the value of some function over x. 
-        """
-        codensity = function
-    else:
-        assert callable(function), "Function has to be callable"
-        if theta is None:
-            codensity = function(x).type(dtype)
-        else:
-            codensity = function(x, theta=theta).type(dtype)
-
-    distance_matrix = torch.cdist(x, x).type(dtype)
-    distances = distance_matrix.ravel()
-    if complex == "rips":
-        threshold = (
-            distance_matrix.max(axis=1).values.min() if threshold is None else threshold
-        )
-        distances = distances[distances <= threshold]
-    elif complex in ["delaunay", "weak_delaunay"]:
-        complex = "delaunay"
-        distances /= 2
-    else:
-        raise ValueError(
-            f"Unimplemented with complex {complex}. You can use rips or delaunay ftm."
-        )
-
-    # simplificates the simplextree for computation, the signed measure will be recovered from the copy afterward
-    reduced_grid = get_grid(strategy=grid_strategy)((distances, codensity), resolution)
-
-    degrees = sm_kwargs.pop("degrees", [])
-    if sm_kwargs.get("degree", None) is not None:
-        degrees = [sm_kwargs.pop("degree", None)] + degrees
-    if complex == "rips":
-        st = RipsComplex(
-            distance_matrix=distance_matrix.detach(), max_edge_length=threshold
-        ).create_simplex_tree()
-        # detach makes a new (reference) tensor, without tracking the gradient
-        st = mp.SimplexTreeMulti(st, num_parameters=2, safe_conversion=safe_conversion)
-        st.fill_lowerstar(
-            codensity.detach(), parameter=1
-        )  # fills the codensity in the second parameter of the simplextree
-        st = st.grid_squeeze(reduced_grid)
-        st.filtration_grid = []
-        if None in degrees:
-            expansion_degree = st.num_vertices
-        else:
-            expansion_degree = max(degrees) + 1
-        st.collapse_edges(num=num_collapses)
-        if not expand_collapse:
-            st.expansion(expansion_degree)  # edge collapse
-
-        s = mp.Slicer(st, vineyard=vineyard, backend=pers_backend)
-    elif complex == "delaunay":
-        s = mp.slicer.from_function_delaunay(
-            x.detach().numpy(), codensity.detach().numpy()
-        )
-        st = mp.slicer.to_simplextree(s)
-        st.flagify(2)
-        s = mp.Slicer(st, vineyard=vineyard, backend=pers_backend).grid_squeeze(
-            reduced_grid
-        )
-
-    s.filtration_grid = []  ## To enforce minpres to be reasonable
-    if None not in degrees:
-        s = s.minpres(degrees=degrees)
-    else:
-        from joblib import Parallel, delayed
-
-        s = tuple(
-            Parallel(n_jobs=-1, backend="threading")(
-                delayed(lambda d: s if d is None else s.minpres(degree=d))(d)
-                for d in degrees
-            )
-        )
-    ## fix previous hack
-    for stuff in s:
-        # stuff.filtration_grid = reduced_grid ## not necessary
-        stuff.filtration_grid = [[1]] * stuff.num_parameters
-
-    sms = tuple(
-        sm
-        for slicer_of_degree, degree in zip(s, degrees)
-        for sm in mp.signed_measure(
-            slicer_of_degree, grid=reduced_grid, degree=degree, **sm_kwargs
-        )
-    )  # computes the signed measure
-    if plot:
-        mp.plots.plot_signed_measures(
-            tuple((sm.detach().numpy(), w.detach().numpy()) for sm, w in sms)
-        )
-    return sms
+from typing import Callable, Literal, Optional
+
+import numpy as np
+import torch
+import gudhi as gd
+
+import multipers as mp
+from multipers.filtrations.density import DTM, KDE
+from multipers.simplex_tree_multi import _available_strategies
+from multipers.torch.diff_grids import get_grid
+
+
+def function_rips_signed_measure_old(
+    x,
+    theta: Optional[float] = None,
+    function: Literal["dtm", "gaussian", "exponential"] | Callable = "dtm",
+    threshold: float = np.inf,
+    grid_strategy: _available_strategies = "regular_closest",
+    resolution: int = 100,
+    return_original: bool = False,
+    return_st: bool = False,
+    safe_conversion: bool = False,
+    num_collapses: int = -1,
+    expand_collapse: bool = False,
+    dtype=torch.float32,
+    **sm_kwargs,
+):
+    """
+    Computes a torch-differentiable function-rips signed measure.
+
+    Input
+    -----
+     - x (num_pts, dim) : The point cloud
+     - theta: For density-like functions : the bandwidth
+     - threshold : rips threshold
+     - function : Either "dtm", "gaussian", or "exponenetial" or Callable.
+       Function to compute the second parameter.
+     - grid_strategy: grid coarsenning strategy.
+     - resolution : when coarsenning, the target resolution,
+     - return_original : Also returns the non-differentiable signed measure.
+     - safe_conversion : Activate this if you encounter crashes.
+     - **kwargs : for the signed measure computation.
+    """
+    assert isinstance(x, torch.Tensor)
+    if function == "dtm":
+        assert theta is not None, "Provide a theta to compute DTM"
+        codensity = DTM(masses=[theta]).fit(x).score_samples_diff(x)[0].type(dtype)
+    elif function in ["gaussian", "exponential"]:
+        assert theta is not None, "Provide a theta to compute density estimation"
+        codensity = (
+            -KDE(
+                bandwidth=theta,
+                kernel=function,
+                return_log=True,
+            )
+            .fit(x)
+            .score_samples(x)
+            .type(dtype)
+        )
+    else:
+        assert callable(function), "Function has to be callable"
+        if theta is None:
+            codensity = function(x).type(dtype)
+        else:
+            codensity = function(x, theta=theta).type(dtype)
+
+    distance_matrix = torch.cdist(x, x).type(dtype)
+    if threshold < np.inf:
+        distance_matrix[distance_matrix > threshold] = np.inf
+
+    # st = RipsComplex(
+    #     distance_matrix=distance_matrix.detach(), max_edge_length=threshold
+    # ).create_simplex_tree()
+    st = gd.SimplexTree.create_from_array(
+        distance_matrix.detach(), max_filtration=threshold
+    )
+    # detach makes a new (reference) tensor, without tracking the gradient
+    st = mp.SimplexTreeMulti(st, num_parameters=2, safe_conversion=safe_conversion)
+    st.fill_lowerstar(
+        codensity.detach(), parameter=1
+    )  # fills the codensity in the second parameter of the simplextree
+
+    # simplificates the simplextree for computation, the signed measure will be recovered from the copy afterward
+    st_copy = st.grid_squeeze(
+        grid_strategy=grid_strategy, resolution=resolution, coordinate_values=True
+    )
+    if sm_kwargs.get("degree", None) is None and sm_kwargs.get("degrees", [None]) == [
+        None
+    ]:
+        expansion_degree = st.num_vertices
+    else:
+        expansion_degree = (
+            max(np.max(sm_kwargs.get("degrees", 1)), sm_kwargs.get("degree", 1)) + 1
+        )
+    st.collapse_edges(num=num_collapses)
+    if not expand_collapse:
+        st.expansion(expansion_degree)  # edge collapse
+    sms = mp.signed_measure(st, **sm_kwargs)  # computes the signed measure
+    del st
+
+    simplices_list = tuple(
+        s for s, _ in st_copy.get_simplices()
+    )  # not optimal, we may want to do that in cython to get edges and nodes
+    sms_diff = []
+    for sm, weights in sms:
+        indices, not_found_indices = st_copy.pts_to_indices(
+            sm, simplices_dimensions=[1, 0]
+        )
+        if sm_kwargs.get("verbose", False):
+            print(
+                f"Found {(1-(indices == -1).mean()).round(2)} indices. \
+                Out : {(indices == -1).sum()}, {len(not_found_indices)}"
+            )
+        sm_diff = torch.empty(sm.shape).type(dtype)
+        # sim_dim = sm_diff.shape[1] // 2
+
+        # fills the Rips-filtrations of the signed measure.
+        # the loop is for the rank invariant
+        for i in range(0, sm_diff.shape[1], 2):
+            idxs = indices[:, i]
+            if (idxs == -1).all():
+                continue
+            useful_idxs = idxs != -1
+            # Retrieves the differentiable values from the distance_matrix
+            if useful_idxs.size > 0:
+                edges_filtrations = torch.cat(
+                    [
+                        distance_matrix[*simplices_list[idx], None]
+                        for idx in idxs[useful_idxs]
+                    ]
+                )
+                # fills theses values into the signed measure
+                sm_diff[:, i][useful_idxs] = edges_filtrations
+        # same for the other axis
+        for i in range(1, sm_diff.shape[1], 2):
+            idxs = indices[:, i]
+            if (idxs == -1).all():
+                continue
+            useful_idxs = idxs != -1
+            if useful_idxs.size > 0:
+                nodes_filtrations = torch.cat(
+                    [codensity[simplices_list[idx]] for idx in idxs[useful_idxs]]
+                )
+                sm_diff[:, i][useful_idxs] = nodes_filtrations
+
+        # fills not-found values as constants
+        if len(not_found_indices) > 0:
+            not_found_indices = indices == -1
+            sm_diff[indices == -1] = torch.from_numpy(sm[indices == -1]).type(dtype)
+
+        sms_diff.append((sm_diff, torch.from_numpy(weights)))
+    flags = [True, return_original, return_st]
+    if np.sum(flags) == 1:
+        return sms_diff
+    return tuple(stuff for stuff, flag in zip([sms_diff, sms, st_copy], flags) if flag)
+
+
+def function_rips_signed_measure(
+    x,
+    theta: Optional[float] = None,
+    function: Literal["dtm", "gaussian", "exponential"] | Callable = "gaussian",
+    threshold: Optional[float] = None,
+    grid_strategy: Literal[
+        "regular_closest", "exact", "quantile", "regular_left"
+    ] = "exact",
+    complex: Literal["rips", "delaunay", "weak_delaunay"] = "rips",
+    resolution: int = 100,
+    safe_conversion: bool = False,
+    num_collapses: Optional[int] = None,
+    expand_collapse: bool = False,
+    dtype=torch.float32,
+    plot=False,
+    # return_st: bool = False,
+    *,
+    log_density: bool = True,
+    vineyard: bool = False,
+    pers_backend=None,
+    **sm_kwargs,
+):
+    """
+    Computes a torch-differentiable function-rips signed measure.
+
+    Input
+    -----
+     - x (num_pts, dim) : The point cloud
+     - theta: For density-like functions : the bandwidth
+     - threshold : rips threshold
+     - function : Either "dtm", "gaussian", or "exponenetial" or Callable.
+       Function to compute the second parameter.
+     - grid_strategy: grid coarsenning strategy.
+     - resolution : when coarsenning, the target resolution,
+     - return_original : Also returns the non-differentiable signed measure.
+     - safe_conversion : Activate this if you encounter crashes.
+     - **kwargs : for the signed measure computation.
+    """
+    if num_collapses is None:
+        num_collapses = -1 if complex == "rips" else None
+    assert isinstance(x, torch.Tensor)
+    if function == "dtm":
+        assert theta is not None, "Provide a theta to compute DTM"
+        codensity = DTM(masses=[theta]).fit(x).score_samples_diff(x)[0].type(dtype)
+    elif function in ["gaussian", "exponential"]:
+        assert theta is not None, "Provide a theta to compute density estimation"
+        codensity = (
+            -KDE(
+                bandwidth=theta,
+                kernel=function,
+                return_log=log_density,
+            )
+            .fit(x)
+            .score_samples(x)
+            .type(dtype)
+        )
+    elif isinstance(function, torch.Tensor):
+        assert (
+            function.ndim == 1 and codensity.shape[0] == x.shape[0]
+        ), """
+        When function is a tensor, it is interpreted as the value of some function over x. 
+        """
+        codensity = function
+    else:
+        assert callable(function), "Function has to be callable"
+        if theta is None:
+            codensity = function(x).type(dtype)
+        else:
+            codensity = function(x, theta=theta).type(dtype)
+
+    distance_matrix = torch.cdist(x, x).type(dtype)
+    distances = distance_matrix.ravel()
+    if complex == "rips":
+        threshold = (
+            distance_matrix.max(axis=1).values.min() if threshold is None else threshold
+        )
+        distances = distances[distances <= threshold]
+    elif complex in ["delaunay", "weak_delaunay"]:
+        complex = "delaunay"
+        distances /= 2
+    else:
+        raise ValueError(
+            f"Unimplemented with complex {complex}. You can use rips or delaunay ftm."
+        )
+
+    # simplificates the simplextree for computation, the signed measure will be recovered from the copy afterward
+    reduced_grid = get_grid(strategy=grid_strategy)((distances, codensity), resolution)
+
+    degrees = sm_kwargs.pop("degrees", [])
+    if sm_kwargs.get("degree", None) is not None:
+        degrees = [sm_kwargs.pop("degree", None)] + degrees
+    if complex == "rips":
+        # st = RipsComplex(
+        #     distance_matrix=distance_matrix.detach(), max_edge_length=threshold
+        # ).create_simplex_tree()
+        st = gd.SimplexTree.create_from_array(
+            distance_matrix.detach(), max_filtration=threshold
+        )
+        # detach makes a new (reference) tensor, without tracking the gradient
+        st = mp.SimplexTreeMulti(st, num_parameters=2, safe_conversion=safe_conversion)
+        st.fill_lowerstar(
+            codensity.detach(), parameter=1
+        )  # fills the codensity in the second parameter of the simplextree
+        st = st.grid_squeeze(reduced_grid)
+        st.filtration_grid = []
+        if None in degrees:
+            expansion_degree = st.num_vertices
+        else:
+            expansion_degree = max(degrees) + 1
+        st.collapse_edges(num=num_collapses)
+        if not expand_collapse:
+            st.expansion(expansion_degree)  # edge collapse
+
+        s = mp.Slicer(st, vineyard=vineyard, backend=pers_backend)
+    elif complex == "delaunay":
+        s = mp.slicer.from_function_delaunay(
+            x.detach().numpy(), codensity.detach().numpy()
+        )
+        st = mp.slicer.to_simplextree(s)
+        st.flagify(2)
+        s = mp.Slicer(st, vineyard=vineyard, backend=pers_backend).grid_squeeze(
+            reduced_grid
+        )
+
+    s.filtration_grid = []  ## To enforce minpres to be reasonable
+    if None not in degrees:
+        s = s.minpres(degrees=degrees)
+    else:
+        from joblib import Parallel, delayed
+
+        s = tuple(
+            Parallel(n_jobs=-1, backend="threading")(
+                delayed(lambda d: s if d is None else s.minpres(degree=d))(d)
+                for d in degrees
+            )
+        )
+    ## fix previous hack
+    for stuff in s:
+        # stuff.filtration_grid = reduced_grid ## not necessary
+        stuff.filtration_grid = [[1]] * stuff.num_parameters
+
+    sms = tuple(
+        sm
+        for slicer_of_degree, degree in zip(s, degrees)
+        for sm in mp.signed_measure(
+            slicer_of_degree, grid=reduced_grid, degree=degree, **sm_kwargs
+        )
+    )  # computes the signed measure
+    if plot:
+        mp.plots.plot_signed_measures(
+            tuple((sm.detach().numpy(), w.detach().numpy()) for sm, w in sms)
+        )
+    return sms