multipers 2.3.1__cp313-cp313-macosx_13_0_x86_64.whl

multipers/grids.pyx

@@ -0,0 +1,350 @@
+
+from libc.stdint cimport intptr_t, int32_t, int64_t
+from libcpp cimport bool,int,long, float
+
+cimport numpy as cnp
+import numpy as np
+cnp.import_array()
+
+
+from typing import Iterable,Literal,Optional
+from itertools import product
+
+
+available_strategies = ["regular","regular_closest", "regular_left", "partition", "quantile", "precomputed"]
+Lstrategies = Literal["regular","regular_closest", "regular_left", "partition", "quantile", "precomputed"]
+
+ctypedef fused some_int:
+    int32_t
+    int64_t
+    int
+    long
+
+ctypedef fused some_float:
+    float
+    double
+
+
+def compute_grid(
+        x,
+        resolution:Optional[int|Iterable[int]]=None, 
+        strategy:Lstrategies="exact", 
+        bool unique=True, 
+        some_float _q_factor=1., 
+        drop_quantiles=[0,0],
+        bool dense = False,
+        ):
+    """
+    Computes a grid from filtration values, using some strategy.
+
+    Input
+    -----
+    
+    - `filtrations_values`: `Iterable[filtration of parameter for parameter]`
+       where `filtration_of_parameter` is a array[float, ndim=1]
+     - `resolution`:Optional[int|tuple[int]]
+     - `strategy`: either exact, regular, regular_closest, regular_left, partition, quantile, or precomputed.
+     - `unique`: if true, doesn't repeat values in the output grid.
+     - `drop_quantiles` : drop some filtration values according to these quantiles
+    Output
+    ------
+
+    Iterable[array[float, ndim=1]] : the 1d-grid for each parameter.
+    """
+
+    from multipers.slicer import is_slicer
+    from multipers.simplex_tree_multi import is_simplextree_multi
+    from multipers.mma_structures import is_mma
+
+    if resolution is not None and strategy == "exact":
+        raise ValueError("The 'exact' strategy does not support resolution.")
+    if strategy != "exact":
+        assert resolution is not None, "A resolution is required for non-exact strategies"
+
+
+    cdef bool is_numpy_compatible = True
+    if is_slicer(x):
+        initial_grid = x.get_filtrations_values().T
+    elif is_simplextree_multi(x):
+        initial_grid = x.get_filtration_grid()
+    elif is_mma(x):
+        initial_grid = x.get_filtration_values()
+    elif isinstance(x, np.ndarray):
+        initial_grid = x
+    else:
+        x = tuple(x)
+        if len(x) == 0: return []
+        first = x[0]
+        ## is_sm, i.e., iterable tuple(pts,weights)
+        if isinstance(x[0], tuple) and getattr(x[0][0], "shape", None) is not None:
+            initial_grid = tuple(f[0].T for f in x)
+            if isinstance(initial_grid[0], np.ndarray):
+                initial_grid = np.concatenate(initial_grid, axis=1)
+            else:
+                is_numpy_compatbile = False
+                import torch
+                assert isinstance(first[0], torch.Tensor), "Only numpy and torch are supported ftm."
+                initial_grid = torch.cat(initial_grid, axis=1)
+        ## is grid-like (num_params, num_pts)
+        elif isinstance(first,list) or isinstance(first, tuple) or isinstance(first, np.ndarray):
+            initial_grid = tuple(f for f in x)
+        else:
+            is_numpy_compatible = False
+            import torch
+            assert isinstance(first, torch.Tensor), "Only numpy and torch are supported ftm."
+            initial_grid = x
+    if is_numpy_compatible:
+        return _compute_grid_numpy(
+        initial_grid,
+        resolution=resolution, 
+        strategy = strategy, 
+        unique = unique, 
+        _q_factor=_q_factor, 
+        drop_quantiles=drop_quantiles,
+        dense = dense,
+        )
+    from multipers.torch.diff_grids import get_grid
+    return get_grid(strategy)(initial_grid,resolution)
+
+
+
+
+
+
+def _compute_grid_numpy(
+        filtrations_values,
+        resolution=None, 
+        strategy:Lstrategies="exact", 
+        bool unique=True, 
+        some_float _q_factor=1., 
+        drop_quantiles=[0,0],
+        bool dense = False,
+        ):
+    """
+    Computes a grid from filtration values, using some strategy.
+
+    Input
+    -----
+     - `filtrations_values`: `Iterable[filtration of parameter for parameter]`
+       where `filtration_of_parameter` is a array[float, ndim=1]
+     - `resolution`:Optional[int|tuple[int]]
+     - `strategy`: either exact, regular, regular_closest, regular_left, partition, quantile, or precomputed.
+     - `unique`: if true, doesn't repeat values in the output grid.
+     - `drop_quantiles` : drop some filtration values according to these quantiles
+    Output
+    ------
+    Iterable[array[float, ndim=1]] : the 1d-grid for each parameter.
+    """
+    num_parameters = len(filtrations_values)
+    if resolution is None and strategy not in ["exact", "precomputed"]:
+        raise ValueError("Resolution must be provided for this strategy.")
+    elif resolution is not None:
+        try:
+            int(resolution)
+            resolution = [resolution]*num_parameters
+        except:
+            pass
+    try:
+        a,b=drop_quantiles
+    except:
+        a,b=drop_quantiles,drop_quantiles
+
+    if a != 0 or b != 0:
+        boxes = np.asarray([np.quantile(filtration, [a, b], axis=1, method='closest_observation') for filtration in filtrations_values])
+        min_filtration, max_filtration = np.min(boxes, axis=(0,1)), np.max(boxes, axis=(0,1)) # box, birth/death, filtration
+        filtrations_values = [
+                filtration[(m<filtration) * (filtration <M)] 
+                for filtration, m,M in zip(filtrations_values, min_filtration, max_filtration)
+                ]
+
+    to_unique = lambda f : np.unique(f) if isinstance(f,np.ndarray) else f.unique()
+    ## match doesn't work with cython BUG
+    if strategy == "exact":
+        F=tuple(to_unique(f) for f in filtrations_values)
+    elif strategy == "quantile":
+        F = tuple(to_unique(f) for f in filtrations_values)
+        max_resolution = [min(len(f),r) for f,r in zip(F,resolution)]
+        F = tuple( np.quantile(f, q=np.linspace(0,1,num=int(r*_q_factor)), axis=0, method='closest_observation') for f,r in zip(F, resolution) )
+        if unique:
+            F = tuple(to_unique(f) for f in F)
+            if np.all(np.asarray(max_resolution) > np.asarray([len(f) for f in F])):
+                return _compute_grid_numpy(filtrations_values=filtrations_values, resolution=resolution, strategy="quantile",_q_factor=1.5*_q_factor)
+    elif strategy == "regular":
+        F = tuple(np.linspace(np.min(f),np.max(f),num=r, dtype=np.asarray(f).dtype) for f,r in zip(filtrations_values, resolution))
+    elif strategy == "regular_closest":
+        F = tuple(_todo_regular_closest(f,r, unique) for f,r in zip(filtrations_values, resolution))
+    elif strategy == "regular_left":
+        F = tuple(_todo_regular_left(f,r, unique) for f,r in zip(filtrations_values, resolution))
+    elif strategy == "torch_regular_closest":
+        F = tuple(_torch_regular_closest(f,r, unique) for f,r in zip(filtrations_values, resolution))
+    elif strategy == "partition":
+        F = tuple(_todo_partition(f,r, unique) for f,r in zip(filtrations_values, resolution))
+    elif strategy == "precomputed":
+        F=filtrations_values
+    else:
+        raise ValueError(f"Invalid strategy {strategy}. Pick something in {available_strategies}.")
+    if dense:
+        return todense(F)
+    return F
+
+def todense(grid, bool product_order=False):
+    if len(grid) == 0:
+        return np.empty(0)
+    if not isinstance(grid[0], np.ndarray):
+        import torch
+        assert isinstance(grid[0], torch.Tensor)
+        from multipers.torch.diff_grids import todense
+        return todense(grid)
+    dtype = grid[0].dtype
+    if product_order:
+        return np.fromiter(product(*grid), dtype=np.dtype((dtype, len(grid))), count=np.prod([len(f) for f in grid]))
+    mesh = np.meshgrid(*grid)
+    coordinates = np.concatenate(tuple(stuff.ravel()[:,None] for stuff in mesh), axis=1, dtype=dtype)
+    return coordinates
+
+
+
+## TODO : optimize. Pykeops ?
+def _todo_regular_closest(some_float[:] f, int r, bool unique):
+    f_array = np.asarray(f)
+    f_regular = np.linspace(np.min(f), np.max(f),num=r, dtype=f_array.dtype)
+    f_regular_closest = np.asarray([f[<long>np.argmin(np.abs(f_array-f_regular[i]))] for i in range(r)])
+    if unique: f_regular_closest = np.unique(f_regular_closest)
+    return f_regular_closest
+
+def _todo_regular_left(some_float[:] f, int r, bool unique):
+    sorted_f = np.sort(f)
+    f_regular = np.linspace(sorted_f[0],sorted_f[-1],num=r, dtype=sorted_f.dtype)
+    f_regular_closest = sorted_f[np.searchsorted(sorted_f,f_regular)]
+    if unique: f_regular_closest = np.unique(f_regular_closest)
+    return f_regular_closest
+
+def _torch_regular_closest(f, int r, bool unique=True):
+    import torch
+    f_regular = torch.linspace(f.min(),f.max(), r, dtype=f.dtype)
+    f_regular_closest =torch.tensor([f[(f-x).abs().argmin()] for x in f_regular]) 
+    if unique: f_regular_closest = f_regular_closest.unique()
+    return f_regular_closest
+
+def _todo_partition(some_float[:] data,int resolution, bool unique):
+    if data.shape[0] < resolution: resolution=data.shape[0]
+    k = data.shape[0] // resolution
+    partitions = np.partition(data, k)
+    f = partitions[[i*k for i in range(resolution)]]
+    if unique: f= np.unique(f)
+    return f
+
+
+def compute_bounding_box(stuff, inflate = 0.):
+    r"""
+    Returns a array of shape (2, num_parameters)
+    such that for any filtration value $y$ of something in stuff,
+    then if (x,z) is the output of this function, we have
+    $x\le y \le z$.
+    """
+    box = np.array(compute_grid(stuff,strategy="regular",resolution=2)).T
+    if inflate:
+        box[0] -= inflate
+        box[1] += inflate
+    return box
+
+def push_to_grid(some_float[:,:] points, grid, bool return_coordinate=False):
+    """
+    Given points and a grid (list of one parameter grids),
+    pushes the points onto the grid.
+    """
+    num_points, num_parameters = points.shape[0], points.shape[1]
+    cdef cnp.ndarray[long,ndim=2] coordinates = np.empty((num_points, num_parameters),dtype=np.int64)
+    for parameter in range(num_parameters):
+        coordinates[:,parameter] = np.searchsorted(grid[parameter],points[:,parameter])
+    if return_coordinate:
+        return coordinates
+    out = np.empty((num_points,num_parameters), grid[0].dtype)
+    for parameter in range(num_parameters):
+        out[:,parameter] = grid[parameter][coordinates[:,parameter]]
+    return out
+
+
+def coarsen_points(some_float[:,:] points, strategy="exact", int resolution=-1, bool coordinate=False):
+    grid = _compute_grid_numpy(points.T, strategy=strategy, resolution=resolution)
+    if coordinate:
+        return push_to_grid(points, grid, coordinate), grid
+    return push_to_grid(points, grid, coordinate)
+
+
+
+def evaluate_in_grid(pts, grid, mass_default=None):
+    """    
+    Input
+    -----
+     - pts: of the form array[int, ndim=2]
+     - grid of the form Iterable[array[float, ndim=1]]
+    """
+    first_filtration = grid[0]
+    dtype = first_filtration.dtype
+    if isinstance(first_filtration, np.ndarray):
+        if mass_default is not None:
+            grid = tuple(np.concatenate([g, [m]]) for g,m in zip(grid, mass_default))
+        def empty_like(x):
+            return np.empty_like(x, dtype=dtype)
+    else: 
+        import torch
+        # assert isinstance(first_filtration, torch.Tensor), f"Invalid grid type. Got {type(grid[0])}, expected numpy or torch array."
+        if mass_default is not None:
+            grid = tuple(torch.cat([g, torch.tensor(m)[None]]) for g,m in zip(grid, mass_default))
+        def empty_like(x):
+            return torch.empty(x.shape,dtype=dtype)
+
+    coords= empty_like(pts)
+    for i in range(coords.shape[1]):
+        coords[:,i] = grid[i][pts[:,i]]
+    return coords
+
+def sm_in_grid(pts, weights, grid, int num_parameters=-1, mass_default=None):
+    """Given a measure whose points are coordinates,
+    pushes this measure in this grid.
+    Input
+    -----
+     - pts: of the form array[int, ndim=2]
+     - weights: array[int, ndim=1]
+     - grid of the form Iterable[array[float, ndim=1]]
+     - num_parameters: number of parameters
+    """
+    first_filtration = grid[0]
+    dtype = first_filtration.dtype
+    def to_int(x):
+        return np.asarray(x,dtype=np.int64)
+    if isinstance(first_filtration, np.ndarray):
+        if mass_default is not None:
+            grid = tuple(np.concatenate([g, [m]]) for g,m in zip(grid, mass_default))
+        def empty_like(x, weights):
+            return np.empty_like(x, dtype=dtype), np.asarray(weights)
+    else: 
+        import torch
+        # assert isinstance(first_filtration, torch.Tensor), f"Invalid grid type. Got {type(grid[0])}, expected numpy or torch array."
+        if mass_default is not None:
+            grid = tuple(torch.cat([g, torch.tensor(m)[None]]) for g,m in zip(grid, mass_default))
+        def empty_like(x, weights):
+            return torch.empty(x.shape,dtype=dtype), torch.from_numpy(weights)
+
+    pts = to_int(pts)
+    coords,weights = empty_like(pts,weights)
+    for i in range(coords.shape[1]):
+        if num_parameters > 0:
+            coords[:,i] = grid[i%num_parameters][pts[:,i]]
+        else:
+            coords[:,i] = grid[i][pts[:,i]]
+    return (coords, weights)
+
+# TODO : optimize with memoryviews / typing
+def sms_in_grid(sms, grid, int num_parameters=-1, mass_default=None):
+    """Given a measure whose points are coordinates,
+    pushes this measure in this grid.
+    Input
+    -----
+     - sms: of the form (signed_measure_like for num_measures)
+       where signed_measure_like = tuple(array[int, ndim=2], array[int])
+     - grid of the form Iterable[array[float, ndim=1]]
+    """
+    sms = tuple(sm_in_grid(pts,weights,grid=grid,num_parameters=num_parameters, mass_default=mass_default) for pts,weights in sms)
+    return sms

multipers/gudhi/Persistence_slices_interface.h

@@ -0,0 +1,132 @@
+#pragma once
+
+#include "mma_interface_h0.h"
+#include "mma_interface_matrix.h"
+#include "mma_interface_coh.h"
+#include <type_traits>  // For static_assert
+#include "truc.h"
+#include <gudhi/Simplex_tree_multi.h>
+#include <gudhi/One_critical_filtration.h>
+#include <gudhi/Multi_critical_filtration.h>
+
+template <typename Filtration>
+using SimplexTreeMultiOptions = Gudhi::multi_persistence::Simplex_tree_options_multidimensional_filtration<Filtration>;
+
+enum Column_types_strs { LIST, SET, HEAP, VECTOR, NAIVE_VECTOR, UNORDERED_SET, INTRUSIVE_LIST, INTRUSIVE_SET };
+
+using Available_columns = Gudhi::persistence_matrix::Column_types;
+
+template <Available_columns col>
+using BackendOptionsWithVine = Gudhi::multiparameter::truc_interface::Multi_persistence_options<col>;
+template <Available_columns col>
+using BackendOptionsWithoutVine = Gudhi::multiparameter::truc_interface::No_vine_multi_persistence_options<col>;
+
+template <Available_columns col>
+using ClementBackendOptionsWithVine = Gudhi::multiparameter::truc_interface::Multi_persistence_Clement_options<col>;
+
+using SimplicialStructure = Gudhi::multiparameter::truc_interface::SimplicialStructure;
+using PresentationStructure = Gudhi::multiparameter::truc_interface::PresentationStructure;
+
+template <Available_columns col, class Structure = SimplicialStructure>
+using MatrixBackendNoVine =
+    Gudhi::multiparameter::truc_interface::Persistence_backend_matrix<BackendOptionsWithoutVine<col>, Structure>;
+
+template <Available_columns col, class Structure = SimplicialStructure>
+using MatrixBackendVine =
+    Gudhi::multiparameter::truc_interface::Persistence_backend_matrix<BackendOptionsWithVine<col>, Structure>;
+
+template <Available_columns col, class Structure = SimplicialStructure>
+using ClementMatrixBackendVine =
+    Gudhi::multiparameter::truc_interface::Persistence_backend_matrix<ClementBackendOptionsWithVine<col>, Structure>;
+using GraphBackendVine = Gudhi::multiparameter::truc_interface::Persistence_backend_h0<SimplicialStructure>;
+
+using Filtration_value = Gudhi::multi_filtration::One_critical_filtration<float>;
+
+template <Available_columns col = Available_columns::INTRUSIVE_SET>
+using SimplicialNoVineMatrixTruc =
+    Gudhi::multiparameter::truc_interface::Truc<MatrixBackendNoVine<col>, SimplicialStructure, Filtration_value>;
+
+template <Available_columns col = Available_columns::INTRUSIVE_SET>
+using GeneralVineTruc = Gudhi::multiparameter::truc_interface::
+    Truc<MatrixBackendVine<col, PresentationStructure>, PresentationStructure, Filtration_value>;
+
+template <Available_columns col = Available_columns::INTRUSIVE_SET>
+using GeneralNoVineTruc = Gudhi::multiparameter::truc_interface::
+    Truc<MatrixBackendNoVine<col, PresentationStructure>, PresentationStructure, Filtration_value>;
+
+template <Available_columns col = Available_columns::INTRUSIVE_SET>
+using GeneralVineClementTruc = Gudhi::multiparameter::truc_interface::
+    Truc<ClementMatrixBackendVine<col, PresentationStructure>, PresentationStructure, Filtration_value>;
+
+template <Available_columns col = Available_columns::INTRUSIVE_SET>
+using SimplicialVineMatrixTruc =
+    Gudhi::multiparameter::truc_interface::Truc<MatrixBackendVine<col>, SimplicialStructure, Filtration_value>;
+using SimplicialVineGraphTruc =
+    Gudhi::multiparameter::truc_interface::Truc<GraphBackendVine, SimplicialStructure, Filtration_value>;
+
+// multicrititcal
+using Multi_critical_filtrationValue = Gudhi::multi_filtration::Multi_critical_filtration<float>;
+template <Available_columns col = Available_columns::INTRUSIVE_SET>
+using KCriticalVineTruc = Gudhi::multiparameter::truc_interface::
+    Truc<MatrixBackendVine<col, PresentationStructure>, PresentationStructure, Multi_critical_filtrationValue>;
+
+template <bool is_vine, Available_columns col = Available_columns::INTRUSIVE_SET>
+using Matrix_interface = std::conditional_t<is_vine,
+                                            MatrixBackendVine<col, PresentationStructure>,
+                                            MatrixBackendNoVine<col, PresentationStructure>>;
+
+template <bool is_kcritical, typename value_type>
+using filtration_options = std::conditional_t<is_kcritical,
+                                              Gudhi::multi_filtration::Multi_critical_filtration<value_type>,
+                                              Gudhi::multi_filtration::One_critical_filtration<value_type>>;
+
+template <bool is_vine,
+          bool is_kcritical,
+          typename value_type,
+          Available_columns col = Available_columns::INTRUSIVE_SET>
+using MatrixTrucPythonInterface = Gudhi::multiparameter::truc_interface::
+    Truc<Matrix_interface<is_vine, col>, PresentationStructure, filtration_options<is_kcritical, value_type>>;
+
+enum class BackendsEnum { Matrix, Graph, Clement, GudhiCohomology };
+
+// Create a template metafunction to simplify the type selection
+template <BackendsEnum backend, bool is_vine, Available_columns col>
+struct PersBackendOptsImpl;
+
+template <bool is_vine, Available_columns col>
+struct PersBackendOptsImpl<BackendsEnum::Matrix, is_vine, col> {
+  using type = Matrix_interface<is_vine, col>;
+};
+
+template <bool is_vine, Available_columns col>
+struct PersBackendOptsImpl<BackendsEnum::Clement, is_vine, col> {
+  static_assert(is_vine, "Clement is vine");
+  using type = ClementMatrixBackendVine<col, PresentationStructure>;
+};
+
+template <bool is_vine, Available_columns col>
+struct PersBackendOptsImpl<BackendsEnum::GudhiCohomology, is_vine, col> {
+  static_assert(!is_vine, "Gudhi is not vine");
+  using type = Gudhi::multiparameter::truc_interface::Persistence_backend_cohomology<PresentationStructure>;
+};
+
+template <bool is_vine, Available_columns col>
+struct PersBackendOptsImpl<BackendsEnum::Graph, is_vine, col> {
+  static_assert(is_vine, "Graph backend requires is_vine to be true");
+  using type = GraphBackendVine;
+};
+
+// Helper alias to extract the type
+template <BackendsEnum backend, bool is_vine, Available_columns col>
+using PersBackendOpts = typename PersBackendOptsImpl<backend, is_vine, col>::type;
+
+template <BackendsEnum backend>
+using StructureStuff = std::conditional_t<backend == BackendsEnum::Graph, SimplicialStructure, PresentationStructure>;
+
+template <BackendsEnum backend,
+          bool is_vine,
+          bool is_kcritical,
+          typename value_type,
+          Available_columns col = Available_columns::INTRUSIVE_SET>
+using TrucPythonInterface = Gudhi::multiparameter::truc_interface::
+    Truc<PersBackendOpts<backend, is_vine, col>, StructureStuff<backend>, filtration_options<is_kcritical, value_type>>;