multipers 2.2.3__cp311-cp311-win_amd64.whl → 2.3.0__cp311-cp311-win_amd64.whl

multipers/ml/tools.py

@@ -1,113 +1,113 @@
-from types import FunctionType
-from typing import Iterable
-
-import numpy as np
-from joblib import Parallel, delayed
-from sklearn.base import BaseEstimator, TransformerMixin
-
-import multipers as mp
-from multipers.simplex_tree_multi import SimplexTreeMulti
-
-
-def get_simplex_tree_from_delayed(x) -> mp.SimplexTreeMulti:
-    f, args, kwargs = x
-    return f(*args, **kwargs)
-
-
-def get_simplextree(x) -> mp.SimplexTreeMulti:
-    if isinstance(x, mp.SimplexTreeMulti):
-        return x
-    if len(x) == 3 and isinstance(x[0], FunctionType):
-        return get_simplex_tree_from_delayed(x)
-    else:
-        raise TypeError("Not a valid SimplexTree !")
-
-
-def filtration_grid_to_coordinates(F, return_resolution):
-    # computes the mesh as a coordinate list
-    mesh = np.meshgrid(*F)
-    coordinates = np.concatenate([stuff.flatten()[:, None] for stuff in mesh], axis=1)
-    if return_resolution:
-        return coordinates, tuple(len(f) for f in F)
-    return coordinates
-
-
-def get_filtration_weights_grid(
-    num_parameters: int = 2,
-    resolution: int | Iterable[int] = 3,
-    *,
-    min: float = 0,
-    max: float = 20,
-    dtype=float,
-    remove_homothetie: bool = True,
-    weights=None,
-):
-    """
-    Provides a grid of weights, for filtration rescaling.
-     - num parameter : the dimension of the grid tensor
-     - resolution :  the size of each coordinate
-     - min : minimum weight
-     - max : maximum weight
-     - weights : custom weights (instead of linspace between min and max)
-     - dtype : the type of the grid values (useful for int weights)
-    """
-    from itertools import product
-
-    # if isinstance(resolution, int):
-    try:
-        float(resolution)
-        resolution = [resolution] * num_parameters
-    except:
-        pass
-    if weights is None:
-        weights = [
-            np.linspace(start=min, stop=max, num=r, dtype=dtype) for r in resolution
-        ]
-    try:
-        float(weights[0])  # same weights for each filtrations
-        weights = [weights] * num_parameters
-    except:
-        None
-    out = np.asarray(list(product(*weights)))
-    if remove_homothetie:
-        _, indices = np.unique(
-            [x / x.max() for x in out if x.max() != 0], axis=0, return_index=True
-        )
-        out = out[indices]
-    return list(out)
-
-
-class SimplexTreeEdgeCollapser(BaseEstimator, TransformerMixin):
-    def __init__(
-        self,
-        num_collapses: int = 0,
-        full: bool = False,
-        max_dimension: int | None = None,
-        n_jobs: int = 1,
-    ) -> None:
-        super().__init__()
-        self.full = full
-        self.num_collapses = num_collapses
-        self.max_dimension = max_dimension
-        self.n_jobs = n_jobs
-        return
-
-    def fit(self, X: np.ndarray | list, y=None):
-        return self
-
-    def transform(self, X):
-        edges_list = Parallel(n_jobs=-1, prefer="threads")(
-            delayed(mp.SimplextreeMulti.get_edge_list)(x) for x in X
-        )
-        collapsed_edge_lists = Parallel(n_jobs=self.n_jobs)(
-            delayed(mp._collapse_edge_list)(
-                edges, full=self.full, num=self.num_collapses
-            )
-            for edges in edges_list
-        )
-        collapsed_simplextrees = Parallel(n_jobs=-1, prefer="threads")(
-            delayed(mp.SimplexTreeMulti._reconstruct_from_edge_list)(
-                collapsed_edge_lists, swap=True, expand_dim=self.max_dimension
-            )
-        )
-        return collapsed_simplextrees
+from types import FunctionType
+from typing import Iterable
+
+import numpy as np
+from joblib import Parallel, delayed
+from sklearn.base import BaseEstimator, TransformerMixin
+
+import multipers as mp
+from multipers.simplex_tree_multi import SimplexTreeMulti
+
+
+def get_simplex_tree_from_delayed(x) -> mp.SimplexTreeMulti:
+    f, args, kwargs = x
+    return f(*args, **kwargs)
+
+
+def get_simplextree(x) -> mp.SimplexTreeMulti:
+    if isinstance(x, mp.SimplexTreeMulti):
+        return x
+    if len(x) == 3 and isinstance(x[0], FunctionType):
+        return get_simplex_tree_from_delayed(x)
+    else:
+        raise TypeError("Not a valid SimplexTree !")
+
+
+def filtration_grid_to_coordinates(F, return_resolution):
+    # computes the mesh as a coordinate list
+    mesh = np.meshgrid(*F)
+    coordinates = np.concatenate([stuff.flatten()[:, None] for stuff in mesh], axis=1)
+    if return_resolution:
+        return coordinates, tuple(len(f) for f in F)
+    return coordinates
+
+
+def get_filtration_weights_grid(
+    num_parameters: int = 2,
+    resolution: int | Iterable[int] = 3,
+    *,
+    min: float = 0,
+    max: float = 20,
+    dtype=float,
+    remove_homothetie: bool = True,
+    weights=None,
+):
+    """
+    Provides a grid of weights, for filtration rescaling.
+     - num parameter : the dimension of the grid tensor
+     - resolution :  the size of each coordinate
+     - min : minimum weight
+     - max : maximum weight
+     - weights : custom weights (instead of linspace between min and max)
+     - dtype : the type of the grid values (useful for int weights)
+    """
+    from itertools import product
+
+    # if isinstance(resolution, int):
+    try:
+        float(resolution)
+        resolution = [resolution] * num_parameters
+    except:
+        pass
+    if weights is None:
+        weights = [
+            np.linspace(start=min, stop=max, num=r, dtype=dtype) for r in resolution
+        ]
+    try:
+        float(weights[0])  # same weights for each filtrations
+        weights = [weights] * num_parameters
+    except:
+        None
+    out = np.asarray(list(product(*weights)))
+    if remove_homothetie:
+        _, indices = np.unique(
+            [x / x.max() for x in out if x.max() != 0], axis=0, return_index=True
+        )
+        out = out[indices]
+    return list(out)
+
+
+class SimplexTreeEdgeCollapser(BaseEstimator, TransformerMixin):
+    def __init__(
+        self,
+        num_collapses: int = 0,
+        full: bool = False,
+        max_dimension: int | None = None,
+        n_jobs: int = 1,
+    ) -> None:
+        super().__init__()
+        self.full = full
+        self.num_collapses = num_collapses
+        self.max_dimension = max_dimension
+        self.n_jobs = n_jobs
+        return
+
+    def fit(self, X: np.ndarray | list, y=None):
+        return self
+
+    def transform(self, X):
+        edges_list = Parallel(n_jobs=-1, prefer="threads")(
+            delayed(mp.SimplextreeMulti.get_edge_list)(x) for x in X
+        )
+        collapsed_edge_lists = Parallel(n_jobs=self.n_jobs)(
+            delayed(mp._collapse_edge_list)(
+                edges, full=self.full, num=self.num_collapses
+            )
+            for edges in edges_list
+        )
+        collapsed_simplextrees = Parallel(n_jobs=-1, prefer="threads")(
+            delayed(mp.SimplexTreeMulti._reconstruct_from_edge_list)(
+                collapsed_edge_lists, swap=True, expand_dim=self.max_dimension
+            )
+        )
+        return collapsed_simplextrees

multipers/mma_structures.pxd

@@ -1,127 +1,127 @@
-from libcpp.utility cimport pair
-from libcpp cimport bool
-from libcpp.vector cimport vector
-from libc.stdint cimport uintptr_t,intptr_t
-
-
-
-from multipers.filtrations cimport *
-ctypedef vector[unsigned int] boundary_type
-ctypedef vector[boundary_type] boundary_matrix
-ctypedef vector[int] simplex_type
-
-cdef extern from "multiparameter_module_approximation/approximation.h" namespace "Gudhi::multiparameter::mma":
-    cdef cppclass Summand[T=*]:
-        ctypedef vector[T] corner_type
-        ctypedef T value_type
-
-        ctypedef pair[vector[T],vector[T]] interval
-        Summand() except +
-        Summand(vector[One_critical_filtration[T]]&, vector[One_critical_filtration[T]]&, int)  except + nogil
-        T get_interleaving() nogil
-        T get_local_weight(const vector[T]&, const T)  nogil
-        void add_bar(T, T, const vector[T]&, vector[T]&, vector[T]&, const bool, const interval&) nogil
-        vector[One_critical_filtration[T]] get_birth_list() nogil
-        vector[One_critical_filtration[T]] get_death_list() nogil
-        void complete_birth(const T)  nogil
-        void complete_death(const T)  nogil
-        int get_dimension()  nogil const 
-        void set_dimension(int) nogil
-        bool contains(const vector[T]&)  nogil const
-        Box[T] get_bounds() nogil const
-        void rescale(const vector[T]&) nogil
-
-
-
-
-
-cdef extern from "multiparameter_module_approximation/utilities.h" namespace "Gudhi::multiparameter::mma":
-    cdef cppclass MultiDiagram_point[T=*]:
-        ctypedef T value_type
-        ctypedef One_critical_filtration[double] filtration_type
-        MultiDiagram_point()   except + nogil
-        MultiDiagram_point(int , T , T )   except + nogil
-        const T& get_birth()    nogil const
-        const T& get_death()  nogil const 
-        int get_dimension() nogil  const 
-
-cdef extern from "multiparameter_module_approximation/utilities.h" namespace "Gudhi::multiparameter::mma":
-    cdef cppclass MultiDiagram[T=*, value_type=*]:
-        MultiDiagram()   except + nogil
-        ctypedef pair[vector[T], vector[T]] bar
-        ctypedef vector[bar] barcode
-        ctypedef vector[float] multipers_bar
-        ctypedef vector[multipers_bar] multipers_barcode
-
-        vector[pair[vector[value_type],vector[value_type]]] get_points(const int) const  
-        vector[vector[double]] to_multipers(const int) nogil const   
-        vector[MultiDiagram_point[T]].const_iterator begin()  
-        vector[MultiDiagram_point[T]].const_iterator end()  
-        unsigned int size() const  
-        MultiDiagram_point[T]& at(unsigned int)  nogil
-
-cdef extern from "multiparameter_module_approximation/utilities.h" namespace "Gudhi::multiparameter::mma":
-    cdef cppclass MultiDiagrams[T=*, value_type=*]:
-        MultiDiagrams()  except + nogil
-        ctypedef pair[vector[pair[double, double]], vector[unsigned int]] plot_interface_type
-        ctypedef vector[T] corner_type
-        ctypedef pair[corner_type, corner_type] bar
-        ctypedef vector[bar] barcode
-        ctypedef vector[T] multipers_bar
-        ctypedef vector[multipers_bar] multipers_barcode
-        ctypedef vector[barcode] barcodes
-        vector[vector[vector[double]]] to_multipers() nogil const    
-        MultiDiagram[T, value_type]& at(const unsigned int)  nogil
-        unsigned int size() nogil const  
-        vector[MultiDiagram[T, value_type]].const_iterator begin()
-        vector[MultiDiagram[T, value_type]].const_iterator end()
-        plot_interface_type _for_python_plot(int, double)  nogil
-        vector[vector[pair[vector[value_type], vector[value_type]]]] get_points()  nogil
-
-cdef extern from "multiparameter_module_approximation/approximation.h" namespace "Gudhi::multiparameter::mma":
-    cdef cppclass Module[T=*]:
-        ctypedef vector[vector[T]] image_type
-        Module()  except + nogil
-        void resize(unsigned int)  nogil
-        Summand[T]& at(unsigned int)  nogil
-        vector[Summand[T]].iterator begin()
-        vector[Summand[T]].iterator end() 
-        void clean(const bool)  nogil
-        void fill(const T)  nogil
-        # vector[image_type] get_vectorization(const T,const T, unsigned int,unsigned int,const Box&)
-        # image_type get_vectorization_in_dimension(const int,const T,unsigned int,unsigned int,const Box&)
-        void add_summand(Summand[T])  nogil
-        void add_summand(Summand[T], int)  nogil
-        unsigned int size() const  
-        Box[T] get_box() const  
-        Box[T] get_bounds() nogil const
-        void set_box(Box[T])  nogil
-        int get_dimension() const 
-        vector[pair[vector[vector[T]], vector[vector[T]]]] get_corners_of_dimension(unsigned int)  nogil
-        image_type get_vectorization_in_dimension(const int, const T, const T, const bool, Box[T]&, unsigned int, unsigned int)  nogil
-        vector[image_type] get_vectorization(const T, const T, const bool, Box[T], unsigned int, unsigned int)  nogil
-        MultiDiagram[One_critical_filtration[T], T] get_barcode(Line[T]&, const int, const bool)  nogil
-        vector[vector[pair[T,T]]] get_barcode2(Line[T]&, const int)  nogil
-        MultiDiagrams[One_critical_filtration[T],T] get_barcodes(const vector[One_critical_filtration[T]]& , const int, const bool )  nogil
-        vector[vector[vector[pair[T,T]]]] get_barcodes2(const vector[Line[T]]& , const int, )  nogil
-        image_type get_landscape(const int,const unsigned int,Box[T],const vector[unsigned int]&)  nogil
-        vector[image_type] get_landscapes(const int,const vector[unsigned int],Box[T],const vector[unsigned int]&)  nogil
-        vector[int] euler_curve(const vector[One_critical_filtration[T]]&) nogil
-        void rescale(vector[T]&, int) nogil
-        void translate(vector[T]&, int) nogil
-        vector[vector[T]] compute_pixels(vector[vector[T]], vector[int], Box[T], T, T, bool,int) nogil
-        vector[vector[pair[vector[vector[int]],vector[vector[int]]]]] to_idx(vector[vector[T]]) nogil
-        vector[vector[vector[int]]] to_flat_idx(vector[vector[T]]) nogil
-        vector[vector[vector[int]]] compute_distances_idx_to(vector[vector[T]],bool, int) nogil
-        vector[vector[T]] compute_distances_to(vector[vector[T]],bool, int) nogil
-        vector[T] get_interleavings(Box[T]) nogil
-        vector[int] get_degree_splits() nogil
-        void compute_distances_to(T*,vector[vector[T]],bool, int) nogil
-        
-
-
-
-
-
-cdef inline list[tuple[list[double],list[double]]] _bc2py(vector[pair[vector[double],vector[double]]] bc):
-    return bc
+from libcpp.utility cimport pair
+from libcpp cimport bool
+from libcpp.vector cimport vector
+from libc.stdint cimport uintptr_t,intptr_t
+
+
+
+from multipers.filtrations cimport *
+ctypedef vector[unsigned int] boundary_type
+ctypedef vector[boundary_type] boundary_matrix
+ctypedef vector[int] simplex_type
+
+cdef extern from "multiparameter_module_approximation/approximation.h" namespace "Gudhi::multiparameter::mma":
+    cdef cppclass Summand[T=*]:
+        ctypedef vector[T] corner_type
+        ctypedef T value_type
+
+        ctypedef pair[vector[T],vector[T]] interval
+        Summand() except +
+        Summand(vector[One_critical_filtration[T]]&, vector[One_critical_filtration[T]]&, int)  except + nogil
+        T get_interleaving() nogil
+        T get_local_weight(const vector[T]&, const T)  nogil
+        void add_bar(T, T, const vector[T]&, vector[T]&, vector[T]&, const bool, const interval&) nogil
+        vector[One_critical_filtration[T]] get_birth_list() nogil
+        vector[One_critical_filtration[T]] get_death_list() nogil
+        void complete_birth(const T)  nogil
+        void complete_death(const T)  nogil
+        int get_dimension()  nogil const 
+        void set_dimension(int) nogil
+        bool contains(const vector[T]&)  nogil const
+        Box[T] get_bounds() nogil const
+        void rescale(const vector[T]&) nogil
+
+
+
+
+
+cdef extern from "multiparameter_module_approximation/utilities.h" namespace "Gudhi::multiparameter::mma":
+    cdef cppclass MultiDiagram_point[T=*]:
+        ctypedef T value_type
+        ctypedef One_critical_filtration[double] filtration_type
+        MultiDiagram_point()   except + nogil
+        MultiDiagram_point(int , T , T )   except + nogil
+        const T& get_birth()    nogil const
+        const T& get_death()  nogil const 
+        int get_dimension() nogil  const 
+
+cdef extern from "multiparameter_module_approximation/utilities.h" namespace "Gudhi::multiparameter::mma":
+    cdef cppclass MultiDiagram[T=*, value_type=*]:
+        MultiDiagram()   except + nogil
+        ctypedef pair[vector[T], vector[T]] bar
+        ctypedef vector[bar] barcode
+        ctypedef vector[float] multipers_bar
+        ctypedef vector[multipers_bar] multipers_barcode
+
+        vector[pair[vector[value_type],vector[value_type]]] get_points(const int) const  
+        vector[vector[double]] to_multipers(const int) nogil const   
+        vector[MultiDiagram_point[T]].const_iterator begin()  
+        vector[MultiDiagram_point[T]].const_iterator end()  
+        unsigned int size() const  
+        MultiDiagram_point[T]& at(unsigned int)  nogil
+
+cdef extern from "multiparameter_module_approximation/utilities.h" namespace "Gudhi::multiparameter::mma":
+    cdef cppclass MultiDiagrams[T=*, value_type=*]:
+        MultiDiagrams()  except + nogil
+        ctypedef pair[vector[pair[double, double]], vector[unsigned int]] plot_interface_type
+        ctypedef vector[T] corner_type
+        ctypedef pair[corner_type, corner_type] bar
+        ctypedef vector[bar] barcode
+        ctypedef vector[T] multipers_bar
+        ctypedef vector[multipers_bar] multipers_barcode
+        ctypedef vector[barcode] barcodes
+        vector[vector[vector[double]]] to_multipers() nogil const    
+        MultiDiagram[T, value_type]& at(const unsigned int)  nogil
+        unsigned int size() nogil const  
+        vector[MultiDiagram[T, value_type]].const_iterator begin()
+        vector[MultiDiagram[T, value_type]].const_iterator end()
+        plot_interface_type _for_python_plot(int, double)  nogil
+        vector[vector[pair[vector[value_type], vector[value_type]]]] get_points()  nogil
+
+cdef extern from "multiparameter_module_approximation/approximation.h" namespace "Gudhi::multiparameter::mma":
+    cdef cppclass Module[T=*]:
+        ctypedef vector[vector[T]] image_type
+        Module()  except + nogil
+        void resize(unsigned int)  nogil
+        Summand[T]& at(unsigned int)  nogil
+        vector[Summand[T]].iterator begin()
+        vector[Summand[T]].iterator end() 
+        void clean(const bool)  nogil
+        void fill(const T)  nogil
+        # vector[image_type] get_vectorization(const T,const T, unsigned int,unsigned int,const Box&)
+        # image_type get_vectorization_in_dimension(const int,const T,unsigned int,unsigned int,const Box&)
+        void add_summand(Summand[T])  nogil
+        void add_summand(Summand[T], int)  nogil
+        unsigned int size() const  
+        Box[T] get_box() const  
+        Box[T] get_bounds() nogil const
+        void set_box(Box[T])  nogil
+        int get_dimension() const 
+        vector[pair[vector[vector[T]], vector[vector[T]]]] get_corners_of_dimension(unsigned int)  nogil
+        image_type get_vectorization_in_dimension(const int, const T, const T, const bool, Box[T]&, unsigned int, unsigned int)  nogil
+        vector[image_type] get_vectorization(const T, const T, const bool, Box[T], unsigned int, unsigned int)  nogil
+        MultiDiagram[One_critical_filtration[T], T] get_barcode(Line[T]&, const int, const bool)  nogil
+        vector[vector[pair[T,T]]] get_barcode2(Line[T]&, const int)  nogil
+        MultiDiagrams[One_critical_filtration[T],T] get_barcodes(const vector[One_critical_filtration[T]]& , const int, const bool )  nogil
+        vector[vector[vector[pair[T,T]]]] get_barcodes2(const vector[Line[T]]& , const int, )  nogil
+        image_type get_landscape(const int,const unsigned int,Box[T],const vector[unsigned int]&)  nogil
+        vector[image_type] get_landscapes(const int,const vector[unsigned int],Box[T],const vector[unsigned int]&)  nogil
+        vector[int] euler_curve(const vector[One_critical_filtration[T]]&) nogil
+        void rescale(vector[T]&, int) nogil
+        void translate(vector[T]&, int) nogil
+        vector[vector[T]] compute_pixels(vector[vector[T]], vector[int], Box[T], T, T, bool,int) nogil
+        vector[vector[pair[vector[vector[int]],vector[vector[int]]]]] to_idx(vector[vector[T]]) nogil
+        vector[vector[vector[int]]] to_flat_idx(vector[vector[T]]) nogil
+        vector[vector[vector[int]]] compute_distances_idx_to(vector[vector[T]],bool, int) nogil
+        vector[vector[T]] compute_distances_to(vector[vector[T]],bool, int) nogil
+        vector[T] get_interleavings(Box[T]) nogil
+        vector[int] get_degree_splits() nogil
+        void compute_distances_to(T*,vector[vector[T]],bool, int) nogil
+        
+
+
+
+
+
+cdef inline list[tuple[list[double],list[double]]] _bc2py(vector[pair[vector[double],vector[double]]] bc):
+    return bc

multipers/mma_structures.pyx

@@ -363,7 +363,7 @@ cdef class PyModule_f64:
               axes = [plt.gca()]
             for dim_idx in range(ndim):
                 if not separated:
-                    plt.sca(axes[dim_idx]) if ndim > 1 else  plt.sca(axes)
+                    plt.sca(axes[dim_idx])
                 self.plot(dims[dim_idx],box=box, separated = separated, **kwargs)
             return
         corners = self.cmod.get_corners_of_dimension(degree)
@@ -1315,7 +1315,7 @@ cdef class PyModule_f32:
               axes = [plt.gca()]
             for dim_idx in range(ndim):
                 if not separated:
-                    plt.sca(axes[dim_idx]) if ndim > 1 else  plt.sca(axes)
+                    plt.sca(axes[dim_idx])
                 self.plot(dims[dim_idx],box=box, separated = separated, **kwargs)
             return
         corners = self.cmod.get_corners_of_dimension(degree)
@@ -2267,7 +2267,7 @@ cdef class PyModule_i32:
               axes = [plt.gca()]
             for dim_idx in range(ndim):
                 if not separated:
-                    plt.sca(axes[dim_idx]) if ndim > 1 else  plt.sca(axes)
+                    plt.sca(axes[dim_idx])
                 self.plot(dims[dim_idx],box=box, separated = separated, **kwargs)
             return
         corners = self.cmod.get_corners_of_dimension(degree)
@@ -2635,7 +2635,7 @@ cdef class PyModule_i64:
               axes = [plt.gca()]
             for dim_idx in range(ndim):
                 if not separated:
-                    plt.sca(axes[dim_idx]) if ndim > 1 else  plt.sca(axes)
+                    plt.sca(axes[dim_idx])
                 self.plot(dims[dim_idx],box=box, separated = separated, **kwargs)
             return
         corners = self.cmod.get_corners_of_dimension(degree)