multipers 2.0.0__cp311-cp311-macosx_13_0_x86_64.whl

multipers/torch/rips_density.py

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+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 = "dtm",
+    threshold: float = np.inf,
+    grid_strategy: Literal["regular_closest", "exact", "quantile"] = "exact",
+    resolution: int = 100,
+    safe_conversion: bool = False,
+    num_collapses: int = -1,
+    expand_collapse: bool = False,
+    dtype=torch.float32,
+    plot=False,
+    return_st: bool = False,
+    *,
+    log_density: bool = True,
+    **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=log_density,
+            )
+            .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)
+
+    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
+    distances = distance_matrix.ravel()
+    if threshold < np.inf:
+        distances = distances[distances < threshold]
+    reduced_grid = get_grid(strategy=grid_strategy)((distances, codensity), resolution)
+
+    st = st.grid_squeeze(reduced_grid, 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
+
+    s = mp.Slicer(st)
+    degrees = sm_kwargs.get("degrees", [])
+    if sm_kwargs.get("degree", None) is not None:
+        degrees = [sm_kwargs.get("degree", None)] + degrees
+    s = mp.slicer.minimal_presentation(s, degrees=degrees)
+    sms = tuple(
+        sm 
+        for slicer_of_degree in s
+        for sm in mp.signed_measure(slicer_of_degree, grid_conversion=reduced_grid, **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)
+        )
+    if return_st:
+        sms = (sms, st)
+    return sms

multipers-2.0.0.dist-info/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2023 David Loiseaux
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

multipers-2.0.0.dist-info/METADATA

@@ -0,0 +1,29 @@
+Metadata-Version: 2.1
+Name: multipers
+Version: 2.0.0
+Summary: Scikit-style Multiparameter persistence toolkit
+Home-page: https://github.com/DavidLapous/multipers
+Author: David Loiseaux
+Author-email: david.loiseaux@inria.fr
+License: MIT
+Keywords: TDA Persistence Multiparameter sklearn
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: License :: OSI Approved :: MIT License
+Requires-Python: >=3.10
+License-File: LICENSE
+Requires-Dist: gudhi
+Requires-Dist: numpy
+Requires-Dist: filtration-domination
+Requires-Dist: pykeops
+Requires-Dist: scikit-learn
+Requires-Dist: joblib
+Requires-Dist: pot
+

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+multipers/data/MOL2.py,sha256=Deu94qPDQFMf_qNwwtn5zYSYO2KmVBufQfUjq3NDkrI,12988
+multipers/data/__init__.py,sha256=w7uUe4LOHbdbKU4R8MNs7em65wZJN0v5ukoG1otFanQ,24
+multipers/data/UCR.py,sha256=PuT8l3i26y0goBzIESwdgJAe6YFCyDiWSoxECcP5rhs,798
+multipers/data/immuno_regions.py,sha256=BNN81DOwdu6sJTkaSeziAYyx0jd0kuZZB5Se0Fo95vA,903
+multipers/data/graphs.py,sha256=wef36QXuzi2EMQJi6W_sEB3JnShfSAbfylP6-2rLSUA,16346

multipers-2.0.0.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: bdist_wheel (0.43.0)
+Root-Is-Purelib: false
+Tag: cp311-cp311-macosx_13_0_x86_64
+

multipers-2.0.0.dist-info/top_level.txt

@@ -0,0 +1 @@
+multipers