multipers 1.1.3__cp310-cp310-macosx_11_0_universal2.whl

multipers/slicer.pxd

@@ -0,0 +1,94 @@
+from libcpp.utility cimport pair 
+from libcpp cimport bool, int, float
+from libcpp.vector cimport vector
+from libcpp cimport tuple
+
+ctypedef float value_type
+ctypedef vector[vector[pair[value_type, value_type]]] Barcode 
+ctypedef vector[value_type] point_type
+ctypedef vector[value_type] one_filtration_type
+from libc.stdint cimport intptr_t, uint16_t, uint32_t, int32_t
+from cython cimport uint
+
+import numpy as np
+python_value_type=np.float32
+
+from libcpp.string cimport string
+
+cdef extern from "Simplex_tree_multi_interface.h" namespace "Gudhi::multiparameter":
+	cdef cppclass Simplex_tree_multi_interface "Gudhi::multiparameter::Simplex_tree_multi_interface<Gudhi::multiparameter::Simplex_tree_options_multidimensional_filtration>":
+		pass
+
+cdef extern from "gudhi/Simplex_tree/multi_filtrations/Line.h" namespace "Gudhi::multiparameter::multi_filtrations":
+	cdef cppclass Line "Gudhi::multiparameter::multi_filtrations::Line<float>":
+		Line()   except + nogil
+		Line(point_type&)   except + nogil
+		Line(point_type&, point_type&)   except + nogil
+
+from multipers.mma_structures cimport Finitely_critical_multi_filtration
+
+cdef extern from "Persistence_slices_interface.h":
+	cdef cppclass SimplicialNoVineMatrixTruc "SimplicialNoVineMatrixTruc":
+		SimplicialNoVineMatrixTruc()
+		SimplicialNoVineMatrixTruc(Simplex_tree_multi_interface*)
+		SimplicialNoVineMatrixTruc& operator=(const SimplicialNoVineMatrixTruc&)
+		Barcode get_barcode()
+		void push_to[Line](const Line&) 
+		void set_one_filtration(const one_filtration_type&)
+		one_filtration_type get_one_filtration() const 
+		void compute_persistence() 
+		uint32_t num_generators()
+		string to_str()
+
+	cdef cppclass SimplicialVineMatrixTruc "SimplicialVineMatrixTruc<>":
+		SimplicialVineMatrixTruc()
+		SimplicialVineMatrixTruc(Simplex_tree_multi_interface*)
+		SimplicialVineMatrixTruc& operator=(const SimplicialVineMatrixTruc&)
+		void vineyard_update()
+		Barcode get_barcode()
+		void push_to[Line](const Line&) 
+		void set_one_filtration(const one_filtration_type&)
+		one_filtration_type get_one_filtration()
+		void compute_persistence() 
+		uint32_t num_generators()
+		string to_str()
+
+	cdef cppclass GeneralVineTruc "GeneralVineTruc<>":
+		GeneralVineTruc()
+		GeneralVineTruc(const vector[vector[unsigned int]]&, const vector[int]&, const vector[Finitely_critical_multi_filtration]&)
+		GeneralVineTruc& operator=(const GeneralVineTruc&)
+		void vineyard_update()
+		Barcode get_barcode()
+		void push_to[Line](const Line&) 
+		void set_one_filtration(const one_filtration_type&)
+		one_filtration_type get_one_filtration()
+		void compute_persistence() 
+		uint32_t num_generators()
+		string to_str()
+
+	cdef cppclass GeneralVineClementTruc "GeneralVineClementTruc<>":
+		GeneralVineClementTruc()
+		GeneralVineClementTruc(const vector[vector[unsigned int]]&, const vector[int]&, const vector[Finitely_critical_multi_filtration]&)
+		GeneralVineClementTruc& operator=(const GeneralVineClementTruc&)
+		void vineyard_update()
+		Barcode get_barcode()
+		void push_to[Line](const Line&) 
+		void set_one_filtration(const one_filtration_type&)
+		one_filtration_type get_one_filtration()
+		void compute_persistence() 
+		uint32_t num_generators()
+		string to_str()
+
+	cdef cppclass SimplicialVineGraphTruc "SimplicialVineGraphTruc":
+		SimplicialVineGraphTruc()
+		SimplicialVineGraphTruc(Simplex_tree_multi_interface*)
+		SimplicialVineGraphTruc& operator=(const SimplicialVineGraphTruc&)
+		void vineyard_update()
+		Barcode get_barcode()
+		void push_to[Line](const Line&) 
+		void set_one_filtration(const one_filtration_type&)
+		one_filtration_type get_one_filtration()
+		void compute_persistence() 
+		uint32_t num_generators()
+		string to_str()
+

multipers/slicer.pyx

@@ -0,0 +1,276 @@
+from multipers.simplex_tree_multi import SimplexTreeMulti
+
+from multipers.slicer cimport *
+import numpy as np
+cimport cython
+
+cdef class SlicerNoVineSimplcial:
+    cdef SimplicialNoVineMatrixTruc truc
+
+    def get_ptr(self):
+        return <intptr_t>(&self.truc)
+    def __cinit__(self, st, bool vine=False):
+        cdef intptr_t ptr = st.thisptr
+        cdef Simplex_tree_multi_interface* st_ptr = <Simplex_tree_multi_interface*>(ptr)
+        self.truc = SimplicialNoVineMatrixTruc(st_ptr)
+    def get_barcode(self):
+        return self.truc.get_barcode()
+    def persistence_on_line(self,basepoint,direction=None):
+        basepoint = np.asarray(basepoint)
+        cdef Line line
+        if direction is None:
+            line = Line(basepoint)
+        else:
+            line = Line(basepoint,direction)
+        self.truc.push_to[Line](line)
+        self.truc.compute_persistence()
+        return self.truc.get_barcode()
+    def compute_persistence(self,one_filtration=None):
+        if one_filtration is not None:
+            self.truc.set_one_filtration(one_filtration)
+        self.truc.compute_persistence()
+        # return self.truc.get_barcode()
+    def get_barcode(self):
+        return self.truc.get_barcode()
+    def sliced_filtration(self,basepoint, direction=None):
+        basepoint = np.asarray(basepoint)
+        cdef Line line
+        if direction is None:
+            line = Line(basepoint)
+        else:
+            line = Line(basepoint,direction)
+        self.truc.push_to[Line](line)
+        return np.asarray(self.truc.get_one_filtration())
+    def __len__(self):
+        return self.truc.num_generators()
+    def __repr__(self):
+        return self.truc.to_str().decode()
+
+cdef class SlicerVineSimplcial:
+    cdef SimplicialVineMatrixTruc truc
+
+    def get_ptr(self):
+        return <intptr_t>(&self.truc)
+    def __cinit__(self, st, bool vine=False):
+        cdef intptr_t ptr = st.thisptr
+        cdef Simplex_tree_multi_interface* st_ptr = <Simplex_tree_multi_interface*>(ptr)
+        self.truc = SimplicialVineMatrixTruc(st_ptr)
+    def vine_update(self,basepoint,direction=None):
+        basepoint = np.asarray(basepoint)
+        cdef Line line
+        if direction is None:
+            line = Line(basepoint)
+        else:
+            line = Line(basepoint,direction)
+        self.truc.push_to[Line](line)        
+        self.truc.vineyard_update()
+    def get_barcode(self):
+        return self.truc.get_barcode()
+    def persistence_on_line(self,basepoint,direction=None):
+        basepoint = np.asarray(basepoint)
+        cdef Line line
+        if direction is None:
+            line = Line(basepoint)
+        else:
+            line = Line(basepoint,direction)
+        self.truc.push_to[Line](line)
+        self.truc.compute_persistence()
+        return self.truc.get_barcode()
+    def compute_persistence(self,one_filtration=None):
+        if one_filtration is not None:
+            self.truc.set_one_filtration(one_filtration)
+        self.truc.compute_persistence()
+        # return self.truc.get_barcode()
+    def get_barcode(self):
+        return self.truc.get_barcode()
+    def sliced_filtration(self,basepoint, direction=None):
+        basepoint = np.asarray(basepoint)
+        cdef Line line
+        if direction is None:
+            line = Line(basepoint)
+        else:
+            line = Line(basepoint,direction)
+        self.truc.push_to[Line](line)
+        return np.asarray(self.truc.get_one_filtration())
+    def __len__(self):
+        return self.truc.num_generators()
+    def __repr__(self):
+        return self.truc.to_str().decode()
+
+cdef class SlicerClement:
+    cdef GeneralVineClementTruc truc
+    def __cinit__(self, generator_maps, generator_dimensions, filtration_values):
+        cdef uint32_t num_generators = len(generator_maps)
+        cdef vector[vector[uint32_t]] c_generator_maps
+        cdef vector[Finitely_critical_multi_filtration] c_filtration_values
+        for stuff in generator_maps:
+            c_generator_maps.push_back(<vector[uint32_t]>(stuff))
+        cdef Finitely_critical_multi_filtration cf
+        for f in filtration_values:
+            cf.clear()
+            for truc in f:
+                cf.push_back(truc)
+            c_filtration_values.push_back(cf)
+        cdef vector[int] c_generator_dimensions = generator_dimensions
+        assert num_generators == c_generator_maps.size() == c_filtration_values.size(), "Invalid input, shape do not coincide."
+        self.truc = GeneralVineClementTruc(c_generator_maps,c_generator_dimensions, c_filtration_values)
+
+
+    def get_ptr(self):
+        return <intptr_t>(&self.truc)
+    def vine_update(self,basepoint,direction=None):
+        basepoint = np.asarray(basepoint)
+        cdef Line line
+        if direction is None:
+            line = Line(basepoint)
+        else:
+            line = Line(basepoint,direction)
+        self.truc.push_to[Line](line)        
+        self.truc.vineyard_update()
+    def get_barcode(self):
+        return self.truc.get_barcode()
+    def persistence_on_line(self,basepoint,direction=None):
+        basepoint = np.asarray(basepoint)
+        cdef Line line
+        if direction is None:
+            line = Line(basepoint)
+        else:
+            line = Line(basepoint,direction)
+        self.truc.push_to[Line](line)
+        self.truc.compute_persistence()
+        return self.truc.get_barcode()
+    def compute_persistence(self,one_filtration=None):
+        if one_filtration is not None:
+            self.truc.set_one_filtration(one_filtration)
+        self.truc.compute_persistence()
+        # return self.truc.get_barcode()
+    def get_barcode(self):
+        return self.truc.get_barcode()
+    def sliced_filtration(self,basepoint, direction=None):
+        basepoint = np.asarray(basepoint)
+        cdef Line line
+        if direction is None:
+            line = Line(basepoint)
+        else:
+            line = Line(basepoint,direction)
+        self.truc.push_to[Line](line)
+        return np.asarray(self.truc.get_one_filtration())
+    def __len__(self):
+        return self.truc.num_generators()
+    def __repr__(self):
+        return self.truc.to_str().decode()
+
+cdef class Slicer:
+    cdef GeneralVineTruc truc
+    def __cinit__(self, generator_maps, generator_dimensions, filtration_values):
+        cdef uint32_t num_generators = len(generator_maps)
+        cdef vector[vector[uint32_t]] c_generator_maps
+        cdef vector[Finitely_critical_multi_filtration] c_filtration_values
+        for stuff in generator_maps:
+            c_generator_maps.push_back(<vector[uint32_t]>(stuff))
+        cdef Finitely_critical_multi_filtration cf
+        for f in filtration_values:
+            cf.clear()
+            for truc in f:
+                cf.push_back(truc)
+            c_filtration_values.push_back(cf)
+        cdef vector[int] c_generator_dimensions = generator_dimensions
+        assert num_generators == c_generator_maps.size() == c_filtration_values.size(), "Invalid input, shape do not coincide."
+        self.truc = GeneralVineTruc(c_generator_maps,c_generator_dimensions, c_filtration_values)
+
+    def get_ptr(self):
+        return <intptr_t>(&self.truc)
+    def vine_update(self,basepoint,direction=None):
+        basepoint = np.asarray(basepoint)
+        cdef Line line
+        if direction is None:
+            line = Line(basepoint)
+        else:
+            line = Line(basepoint,direction)
+        self.truc.push_to[Line](line)        
+        self.truc.vineyard_update()
+    def get_barcode(self):
+        return self.truc.get_barcode()
+    def persistence_on_line(self,basepoint,direction=None):
+        basepoint = np.asarray(basepoint)
+        cdef Line line
+        if direction is None:
+            line = Line(basepoint)
+        else:
+            line = Line(basepoint,direction)
+        self.truc.push_to[Line](line)
+        self.truc.compute_persistence()
+        return self.truc.get_barcode()
+    def compute_persistence(self,one_filtration=None):
+        if one_filtration is not None:
+            self.truc.set_one_filtration(one_filtration)
+        self.truc.compute_persistence()
+        # return self.truc.get_barcode()
+    def get_barcode(self):
+        return self.truc.get_barcode()
+    def sliced_filtration(self,basepoint, direction=None):
+        basepoint = np.asarray(basepoint)
+        cdef Line line
+        if direction is None:
+            line = Line(basepoint)
+        else:
+            line = Line(basepoint,direction)
+        self.truc.push_to[Line](line)
+        return np.asarray(self.truc.get_one_filtration())
+    def __len__(self):
+        return self.truc.num_generators()
+    def __repr__(self):
+        return self.truc.to_str().decode()
+
+cdef class SlicerVineGraph:
+    cdef SimplicialVineGraphTruc truc
+    def __cinit__(self, st, bool vine=False):
+        cdef intptr_t ptr = st.thisptr
+        cdef Simplex_tree_multi_interface* st_ptr = <Simplex_tree_multi_interface*>(ptr)
+        self.truc = SimplicialVineGraphTruc(st_ptr)
+    def vine_update(self,basepoint,direction=None):
+        basepoint = np.asarray(basepoint)
+        cdef Line line
+        if direction is None:
+            line = Line(basepoint)
+        else:
+            line = Line(basepoint,direction)
+        self.truc.push_to[Line](line)        
+        self.truc.vineyard_update()
+    def get_barcode(self):
+        return self.truc.get_barcode()
+
+    def get_ptr(self):
+        return <intptr_t>(&self.truc)
+    def persistence_on_line(self,basepoint,direction=None):
+        basepoint = np.asarray(basepoint)
+        cdef Line line
+        if direction is None:
+            line = Line(basepoint)
+        else:
+            line = Line(basepoint,direction)
+        self.truc.push_to[Line](line)
+        self.truc.compute_persistence()
+        return self.truc.get_barcode()
+    def compute_persistence(self,one_filtration=None):
+        if one_filtration is not None:
+            self.truc.set_one_filtration(one_filtration)
+        self.truc.compute_persistence()
+        # return self.truc.get_barcode()
+    def get_barcode(self):
+        return self.truc.get_barcode()
+    def sliced_filtration(self,basepoint, direction=None):
+        basepoint = np.asarray(basepoint)
+        cdef Line line
+        if direction is None:
+            line = Line(basepoint)
+        else:
+            line = Line(basepoint,direction)
+        self.truc.push_to[Line](line)
+        return np.asarray(self.truc.get_one_filtration())
+    def __len__(self):
+        return self.truc.num_generators()
+    def __repr__(self):
+        return self.truc.to_str().decode()
+
+

multipers/tensor.pxd

@@ -0,0 +1,13 @@
+from libc.stdint cimport uint16_t
+from libcpp.vector cimport vector
+from libcpp cimport bool, float
+
+
+ctypedef float dtype
+ctypedef uint16_t index_type
+
+cdef extern from "tensor/tensor.h" namespace "tensor":
+	cdef cppclass static_tensor_view[float, uint16_t]:
+		static_tensor_view()   except + nogil
+		static_tensor_view(dtype*,const  vector[index_type]&) except + nogil
+		const vector[index_type]& get_resolution() 

multipers/test.pyx

@@ -0,0 +1,44 @@
+# cimport multipers.tensor as mt
+from libc.stdint cimport intptr_t, uint16_t
+from libcpp.vector cimport vector
+from libcpp cimport bool, int, float
+from libcpp.utility cimport pair
+from typing import Optional,Iterable,Callable
+
+
+ctypedef float value_type 
+# ctypedef uint16_t index_type 
+
+import numpy as np
+# cimport numpy as cnp
+# cnp.import_array()
+
+# cdef extern from "multi_parameter_rank_invariant/rank_invariant.h" namespace "Gudhi::rank_invariant":
+#     void get_hilbert_surface(const intptr_t, mt.static_tensor_view, const vector[index_type], const vector[index_type], index_type, index_type, const vector[index_type], bool, bool) except + nogil
+
+
+from multipers.simplex_tree_multi import SimplexTreeMulti
+
+
+def numpy_to_tensor(array:np.ndarray):
+    cdef vector[index_type] shape = array.shape
+    cdef dtype[::1] contigus_array_view = np.ascontiguousarray(array)
+    cdef dtype* dtype_ptr = &contigus_array_view[0]
+    cdef mt.static_tensor_view tensor
+    with nogil:
+        tensor = mt.static_tensor_view(dtype_ptr, shape)
+    return tensor.get_resolution()
+
+# def hilbert2d(simplextree:SimplexTreeMulti, grid_shape:np.ndarray|list, vector[index_type] degrees, bool mobius_inversion):
+# 	# assert simplextree.num_parameters == 2
+# 	cdef intptr_t ptr = simplextree.thisptr
+# 	cdef vector[index_type] c_grid_shape = grid_shape
+# 	cdef dtype[::1] container = np.zeros(grid_shape, dtype=np.float32).flatten()
+# 	cdef dtype* container_ptr = &container[0]
+# 	cdef mt.static_tensor_view c_container = mt.static_tensor_view(container_ptr, c_grid_shape)
+# 	cdef index_type i = 0
+# 	cdef index_type j = 1
+# 	cdef vector[index_type] fixed_values = [[],[]]
+# 	# get_hilbert_surface(ptr, c_container, c_grid_shape, degrees,i,j,fixed_values, False, False)
+# 	return container.reshape(grid_shape)
+

multipers-1.1.3.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-1.1.3.dist-info/METADATA

@@ -0,0 +1,22 @@
+Metadata-Version: 2.1
+Name: multipers
+Version: 1.1.3
+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
+

multipers-1.1.3.dist-info/RECORD

@@ -0,0 +1,63 @@
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multipers-1.1.3.dist-info/WHEEL

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+Tag: cp310-cp310-macosx_11_0_universal2
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multipers-1.1.3.dist-info/top_level.txt

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