From 9899ae167f281d10b1684dfcd02c6838c5bf28df Mon Sep 17 00:00:00 2001 From: Gard Spreemann Date: Fri, 2 Feb 2018 13:51:45 +0100 Subject: GUDHI 2.1.0 as released by upstream in a tarball. --- cython/cython/periodic_cubical_complex.pyx | 14 +-- cython/cython/simplex_tree.pyx | 141 +++++++++++++++++++++----- cython/doc/_templates/layout.html | 6 +- cython/doc/conf.py | 4 +- cython/doc/cubical_complex_user.rst | 45 ++++---- cython/doc/fileformats.rst | 55 +++++++++- cython/doc/python3-sphinx-build.py | 2 +- cython/doc/witness_complex_user.rst | 2 +- cython/example/simplex_tree_example.py | 2 - cython/include/Cubical_complex_interface.h | 6 ++ cython/include/Simplex_tree_interface.h | 4 + cython/include/Tangential_complex_interface.h | 4 +- cython/setup.py.in | 4 +- cython/test/test_cubical_complex.py | 10 +- cython/test/test_simplex_tree.py | 38 ++++++- 15 files changed, 262 insertions(+), 75 deletions(-) (limited to 'cython') diff --git a/cython/cython/periodic_cubical_complex.pyx b/cython/cython/periodic_cubical_complex.pyx index 581c7b69..3025f125 100644 --- a/cython/cython/periodic_cubical_complex.pyx +++ b/cython/cython/periodic_cubical_complex.pyx @@ -33,7 +33,7 @@ __license__ = "GPL v3" cdef extern from "Cubical_complex_interface.h" namespace "Gudhi": cdef cppclass Periodic_cubical_complex_base_interface "Gudhi::Cubical_complex::Cubical_complex_interface>": - Periodic_cubical_complex_base_interface(vector[unsigned] dimensions, vector[double] top_dimensional_cells) + Periodic_cubical_complex_base_interface(vector[unsigned] dimensions, vector[double] top_dimensional_cells, vector[bool] periodic_dimensions) Periodic_cubical_complex_base_interface(string perseus_file) int num_simplices() int dimension() @@ -58,7 +58,7 @@ cdef class PeriodicCubicalComplex: # Fake constructor that does nothing but documenting the constructor def __init__(self, dimensions=None, top_dimensional_cells=None, - perseus_file=''): + periodic_dimensions=None, perseus_file=''): """PeriodicCubicalComplex constructor from dimensions and top_dimensional_cells or from a Perseus-style file name. @@ -66,6 +66,8 @@ cdef class PeriodicCubicalComplex: :type dimensions: list of int :param top_dimensional_cells: A list of cells filtration values. :type top_dimensional_cells: list of double + :param periodic_dimensions: A list of top dimensional cells periodicity value. + :type periodic_dimensions: list of boolean Or @@ -75,10 +77,10 @@ cdef class PeriodicCubicalComplex: # The real cython constructor def __cinit__(self, dimensions=None, top_dimensional_cells=None, - perseus_file=''): - if (dimensions is not None) and (top_dimensional_cells is not None) and (perseus_file is ''): - self.thisptr = new Periodic_cubical_complex_base_interface(dimensions, top_dimensional_cells) - elif (dimensions is None) and (top_dimensional_cells is None) and (perseus_file is not ''): + periodic_dimensions=None, perseus_file=''): + if (dimensions is not None) and (top_dimensional_cells is not None) and (periodic_dimensions is not None) and (perseus_file is ''): + self.thisptr = new Periodic_cubical_complex_base_interface(dimensions, top_dimensional_cells, periodic_dimensions) + elif (dimensions is None) and (top_dimensional_cells is None) and (periodic_dimensions is None) and (perseus_file is not ''): if os.path.isfile(perseus_file): self.thisptr = new Periodic_cubical_complex_base_interface(str.encode(perseus_file)) else: diff --git a/cython/cython/simplex_tree.pyx b/cython/cython/simplex_tree.pyx index 45487158..0cb575d2 100644 --- a/cython/cython/simplex_tree.pyx +++ b/cython/cython/simplex_tree.pyx @@ -37,11 +37,13 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": cdef cppclass Simplex_tree_interface_full_featured "Gudhi::Simplex_tree_interface": Simplex_tree() double simplex_filtration(vector[int] simplex) + void assign_simplex_filtration(vector[int] simplex, double filtration) void initialize_filtration() int num_vertices() int num_simplices() void set_dimension(int dimension) int dimension() + int upper_bound_dimension() bint find_simplex(vector[int] simplex) bint insert_simplex_and_subfaces(vector[int] simplex, double filtration) @@ -50,8 +52,9 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": vector[pair[vector[int], double]] get_star(vector[int] simplex) vector[pair[vector[int], double]] get_cofaces(vector[int] simplex, int dimension) - void remove_maximal_simplex(vector[int] simplex) void expansion(int max_dim) + void remove_maximal_simplex(vector[int] simplex) + bool prune_above_filtration(double filtration) cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi": cdef cppclass Simplex_tree_persistence_interface "Gudhi::Persistent_cohomology_interface>": @@ -103,8 +106,8 @@ cdef class SimplexTree: return self.pcohptr != NULL def filtration(self, simplex): - """This function returns the simplicial complex filtration value for a - given N-simplex. + """This function returns the filtration value for a given N-simplex in + this simplicial complex, or +infinity if it is not in the complex. :param simplex: The N-simplex, represented by a list of vertex. :type simplex: list of int. @@ -113,15 +116,31 @@ cdef class SimplexTree: """ return self.thisptr.simplex_filtration(simplex) + def assign_filtration(self, simplex, filtration): + """This function assigns the simplicial complex filtration value for a + given N-simplex. + + :param simplex: The N-simplex, represented by a list of vertex. + :type simplex: list of int. + :param filtration: The simplicial complex filtration value. + :type filtration: float + """ + self.thisptr.assign_simplex_filtration(simplex, filtration) + def initialize_filtration(self): """This function initializes and sorts the simplicial complex filtration vector. .. note:: - This function must be launched before persistence, betti_numbers, - persistent_betti_numbers or get_filtration after inserting or - removing simplices. + This function must be launched before + :func:`persistence()`, + :func:`betti_numbers()`, + :func:`persistent_betti_numbers()`, + or :func:`get_filtration()` + after :func:`inserting` or + :func:`removing` + simplices. """ self.thisptr.initialize_filtration() @@ -148,21 +167,42 @@ cdef class SimplexTree: :returns: the simplicial complex dimension. :rtype: int + + .. note:: + + This function is not constant time because it can recompute + dimension if required (can be triggered by + :func:`remove_maximal_simplex()` + or + :func:`prune_above_filtration()` + methods). """ return self.thisptr.dimension() - def set_dimension(self, dimension): - """This function sets the dimension of the simplicial complex. + def upper_bound_dimension(self): + """This function returns a valid dimension upper bound of the + simplicial complex. - insert and remove_maximal_simplex functions do not update dimension - value of the `SimplexTree`. + :returns: an upper bound on the dimension of the simplicial complex. + :rtype: int + """ + return self.thisptr.upper_bound_dimension() - `AlphaComplex`, `RipsComplex`, `TangentialComplex` and `WitnessComplex` - automatically sets the correct dimension in their `create_simplex_tree` - functions. + def set_dimension(self, dimension): + """This function sets the dimension of the simplicial complex. :param dimension: The new dimension value. :type dimension: int. + + .. note:: + + This function must be used with caution because it disables + dimension recomputation when required + (this recomputation can be triggered by + :func:`remove_maximal_simplex()` + or + :func:`prune_above_filtration()` + ). """ self.thisptr.set_dimension(dimension) @@ -182,14 +222,17 @@ cdef class SimplexTree: def insert(self, simplex, filtration=0.0): """This function inserts the given N-simplex and its subfaces with the - given filtration value (default value is '0.0'). + given filtration value (default value is '0.0'). If some of those + simplices are already present with a higher filtration value, their + filtration value is lowered. :param simplex: The N-simplex to insert, represented by a list of vertex. :type simplex: list of int. :param filtration: The filtration value of the simplex. :type filtration: float. - :returns: true if the simplex was found, false otherwise. + :returns: true if the simplex was not yet in the complex, false + otherwise (whatever its original filtration value). :rtype: bool """ cdef vector[int] csimplex @@ -286,9 +329,57 @@ cdef class SimplexTree: :param simplex: The N-simplex, represented by a list of vertex. :type simplex: list of int. + + .. note:: + + Be aware that removing is shifting data in a flat_map + (:func:`initialize_filtration()` to be done). + + .. note:: + + The dimension of the simplicial complex may be lower after calling + remove_maximal_simplex than it was before. However, + :func:`upper_bound_dimension()` + method will return the old value, which + remains a valid upper bound. If you care, you can call + :func:`dimension()` + to recompute the exact dimension. """ self.thisptr.remove_maximal_simplex(simplex) + def prune_above_filtration(self, filtration): + """Prune above filtration value given as parameter. + + :param filtration: Maximum threshold value. + :type filtration: float. + :returns: The filtration modification information. + :rtype: bint + + + .. note:: + + Some simplex tree functions require the filtration to be valid. + prune_above_filtration function is not launching + :func:`initialize_filtration()` + but returns the filtration modification + information. If the complex has changed , please call + :func:`initialize_filtration()` + to recompute it. + + .. note:: + + Note that the dimension of the simplicial complex may be lower + after calling + :func:`prune_above_filtration()` + than it was before. However, + :func:`upper_bound_dimension()` + will return the old value, which remains a + valid upper bound. If you care, you can call + :func:`dimension()` + method to recompute the exact dimension. + """ + return self.thisptr.prune_above_filtration(filtration) + def expansion(self, max_dim): """Expands the Simplex_tree containing only its one skeleton until dimension max_dim. @@ -312,7 +403,7 @@ cdef class SimplexTree: """This function returns the persistence of the simplicial complex. :param homology_coeff_field: The homology coefficient field. Must be a - prime number + prime number. Default value is 11. :type homology_coeff_field: int. :param min_persistence: The minimum persistence value to take into account (strictly greater than min_persistence). Default value is @@ -336,8 +427,9 @@ cdef class SimplexTree: :returns: The Betti numbers ([B0, B1, ..., Bn]). :rtype: list of int - :note: betti_numbers function requires persistence function to be - launched first. + :note: betti_numbers function requires + :func:`persistence()` + function to be launched first. """ cdef vector[int] bn_result if self.pcohptr != NULL: @@ -361,7 +453,8 @@ cdef class SimplexTree: :returns: The persistent Betti numbers ([B0, B1, ..., Bn]). :rtype: list of int - :note: persistent_betti_numbers function requires persistence + :note: persistent_betti_numbers function requires + :func:`persistence()` function to be launched first. """ cdef vector[int] pbn_result @@ -381,8 +474,9 @@ cdef class SimplexTree: :returns: The persistence intervals. :rtype: list of pair of float - :note: intervals_in_dim function requires persistence function to be - launched first. + :note: intervals_in_dim function requires + :func:`persistence()` + function to be launched first. """ cdef vector[pair[double,double]] intervals_result if self.pcohptr != NULL: @@ -399,8 +493,9 @@ cdef class SimplexTree: :param persistence_file: The specific dimension. :type persistence_file: string. - :note: intervals_in_dim function requires persistence function to be - launched first. + :note: intervals_in_dim function requires + :func:`persistence()` + function to be launched first. """ if self.pcohptr != NULL: if persistence_file != '': diff --git a/cython/doc/_templates/layout.html b/cython/doc/_templates/layout.html index 243f33c6..8e4eba40 100644 --- a/cython/doc/_templates/layout.html +++ b/cython/doc/_templates/layout.html @@ -198,6 +198,8 @@
  • @@ -208,6 +210,8 @@
  • C++ installation manual
  • Python documentation
  • Python installation manual
    • +
  • Utilities
    • +
  • Tutorial
  • @@ -255,7 +259,7 @@ {%- if hasdoc('copyright') %} {% trans path=pathto('copyright'), copyright=copyright|e %}© Copyright {{ copyright }}.{% endtrans %} {%- else %} - {% trans copyright=copyright|e %}© Copyright {{ copyright }}.{% endtrans %} + {% trans copyright=copyright|e %} {{ copyright }}.{% endtrans %} {%- endif %} {%- endif %} {%- if last_updated %} diff --git a/cython/doc/conf.py b/cython/doc/conf.py index 19a880d4..a13c9751 100755 --- a/cython/doc/conf.py +++ b/cython/doc/conf.py @@ -62,7 +62,7 @@ import gudhi # General information about the project. project = gudhi.__name__ -copyright = gudhi.__copyright__ +copyright = gudhi.__copyright__ + ' - ' + gudhi.__license__ # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the @@ -158,7 +158,7 @@ html_static_path = ['_static'] # If not '', a 'Last updated on:' timestamp is inserted at every page bottom, # using the given strftime format. -#html_last_updated_fmt = '%b %d, %Y' +html_last_updated_fmt = '%b %d, %Y' # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. diff --git a/cython/doc/cubical_complex_user.rst b/cython/doc/cubical_complex_user.rst index 2bfac62a..34598f02 100644 --- a/cython/doc/cubical_complex_user.rst +++ b/cython/doc/cubical_complex_user.rst @@ -81,23 +81,7 @@ filtration to all cubes. There are a number of constructors that can be used to who want to use the code directly. They can be found in the :doc:`cubical_complex_ref`. Currently one input from a text file is used. It uses a format used already in `Perseus software `_ by Vidit Nanda. -Below we are providing a description of the format. The first line contains a number d begin the dimension of the -bitmap (2 in the example below). Next d lines are the numbers of top dimensional cubes in each dimensions (3 and 3 -in the example below). Next, in lexicographical order, the filtration of top dimensional cubes is given (1 4 6 8 -20 4 7 6 5 in the example below). - -.. figure:: - ../../doc/Bitmap_cubical_complex/exampleBitmap.png - :alt: Example of a input data. - :figclass: align-center - - Example of a input data. - -The input file for the following complex is: - -.. literalinclude:: ../../data/bitmap/cubicalcomplexdoc.txt - -.. centered:: ../../data/bitmap/cubicalcomplexdoc.txt +The file format is described here: :doc:`Perseus `. .. testcode:: @@ -124,15 +108,9 @@ Imposing periodic boundary conditions in the direction i, means that the left an :math:`\mathcal{K}` are considered the same. In particular, if for a bitmap :math:`\mathcal{K}` periodic boundary conditions are imposed in all directions, then complex :math:`\mathcal{K}` became n-dimensional torus. One can use various constructors from the file Bitmap_cubical_complex_periodic_boundary_conditions_base.h to construct cubical -complex with periodic boundary conditions. One can also use Perseus style input files. To indicate periodic boundary -conditions in a given direction, then number of top dimensional cells in this direction have to be multiplied by -1. -For instance: - -.. literalinclude:: ../../data/bitmap/periodiccubicalcomplexdoc.txt - -.. centered:: ../../data/bitmap/periodiccubicalcomplexdoc.txt +complex with periodic boundary conditions. -Indicate that we have imposed periodic boundary conditions in the direction x, but not in the direction y. +One can also use Perseus style input files (see :doc:`Perseus `) for the specific periodic case: .. testcode:: @@ -149,6 +127,23 @@ the program output is: Periodic cubical complex is of dimension 2 - 42 simplices. +Or it can be defined as follows: + +.. testcode:: + + from gudhi import PeriodicCubicalComplex as pcc + periodic_cc = pcc(dimensions=[3,3], + top_dimensional_cells= [0, 0, 0, 0, 1, 0, 0, 0, 0], + periodic_dimensions=[True, False]) + result_str = 'Periodic cubical complex is of dimension ' + repr(periodic_cc.dimension()) + ' - ' + \ + repr(periodic_cc.num_simplices()) + ' simplices.' + print(result_str) + +the program output is: + +.. testoutput:: + + Periodic cubical complex is of dimension 2 - 42 simplices. Examples. --------- diff --git a/cython/doc/fileformats.rst b/cython/doc/fileformats.rst index 156ef4e4..4f0b6f6d 100644 --- a/cython/doc/fileformats.rst +++ b/cython/doc/fileformats.rst @@ -23,7 +23,7 @@ Here is a simple sample file:: 3 34.2 34.974 4 3. inf -Other sample files can be found in the data/persistence_diagram folder. +Other sample files can be found in the `data/persistence_diagram` folder. Such files can be generated with :meth:`gudhi.SimplexTree.write_persistence_diagram`, read with @@ -31,3 +31,56 @@ Such files can be generated with :meth:`gudhi.read_persistence_intervals_in_dimension` and displayed with :meth:`gudhi.plot_persistence_barcode` or :meth:`gudhi.plot_persistence_diagram`. + +Iso-cuboid +********** + +Such a file describes an iso-oriented cuboid with diagonal opposite vertices +(min_x, min_y, min_z,...) and (max_x, max_y, max_z, ...). The format is:: + + min_x min_y [min_z ...] + max_x max_y [max_z ...] + +Here is a simple sample file in the 3D case:: + + -1. -1. -1. + 1. 1. 1. + + +Perseus +******* + +This file format is the format used by the +`Perseus software `_ by Vidit Nanda. +The first line contains a number d begin the dimension of the bitmap (2 in the +example below). Next d lines are the numbers of top dimensional cubes in each +dimensions (3 and 3 in the example below). Next, in lexicographical order, the +filtration of top dimensional cubes is given (1 4 6 8 20 4 7 6 5 in the example +below). + +.. figure:: + ../../doc/Bitmap_cubical_complex/exampleBitmap.png + :alt: Example of a input data. + :figclass: align-center + + Example of a input data. + +The input file for the following complex is: + +.. literalinclude:: ../../data/bitmap/cubicalcomplexdoc.txt + +.. centered:: ../../data/bitmap/cubicalcomplexdoc.txt + +To indicate periodic boundary conditions in a given direction, then number of +top dimensional cells in this direction have to be multiplied by -1. For +instance: + +.. literalinclude:: ../../data/bitmap/periodiccubicalcomplexdoc.txt + +.. centered:: ../../data/bitmap/periodiccubicalcomplexdoc.txt + + +Indicate that we have imposed periodic boundary conditions in the direction x, +but not in the direction y. + +Other sample files can be found in the `data/bitmap` folder. diff --git a/cython/doc/python3-sphinx-build.py b/cython/doc/python3-sphinx-build.py index 44b94169..84d158cf 100755 --- a/cython/doc/python3-sphinx-build.py +++ b/cython/doc/python3-sphinx-build.py @@ -1,4 +1,4 @@ -#!/usr/bin/python3 +#!/usr/bin/env python3 """ Emulate sphinx-build for python3 diff --git a/cython/doc/witness_complex_user.rst b/cython/doc/witness_complex_user.rst index 29413269..99be5185 100644 --- a/cython/doc/witness_complex_user.rst +++ b/cython/doc/witness_complex_user.rst @@ -121,7 +121,7 @@ Example2: Computing persistence using strong relaxed witness complex Here is an example of constructing a strong witness complex filtration and computing persistence on it: -* :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py>` +* :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>` Bibliography ============ diff --git a/cython/example/simplex_tree_example.py b/cython/example/simplex_tree_example.py index 831d9da8..51a60e73 100755 --- a/cython/example/simplex_tree_example.py +++ b/cython/example/simplex_tree_example.py @@ -48,8 +48,6 @@ if st.insert([0, 1, 2], filtration=4.0): else: print("Not inserted...") -# FIXME: Remove this line -st.set_dimension(3) print("dimension=", st.dimension()) st.initialize_filtration() diff --git a/cython/include/Cubical_complex_interface.h b/cython/include/Cubical_complex_interface.h index 7c0148f1..fad92c2c 100644 --- a/cython/include/Cubical_complex_interface.h +++ b/cython/include/Cubical_complex_interface.h @@ -43,6 +43,12 @@ class Cubical_complex_interface : public Bitmap_cubical_complex(dimensions, top_dimensional_cells) { } + Cubical_complex_interface(const std::vector& dimensions, + const std::vector& top_dimensional_cells, + const std::vector& periodic_dimensions) + : Bitmap_cubical_complex(dimensions, top_dimensional_cells, periodic_dimensions) { + } + Cubical_complex_interface(const std::string& perseus_file) : Bitmap_cubical_complex(perseus_file.c_str()) { } diff --git a/cython/include/Simplex_tree_interface.h b/cython/include/Simplex_tree_interface.h index 09e7e992..54a4f824 100644 --- a/cython/include/Simplex_tree_interface.h +++ b/cython/include/Simplex_tree_interface.h @@ -52,6 +52,10 @@ class Simplex_tree_interface : public Simplex_tree { return (Base::find(vh) != Base::null_simplex()); } + void assign_simplex_filtration(const Simplex& vh, Filtration_value filtration) { + Base::assign_filtration(Base::find(vh), filtration); + } + bool insert(const Simplex& simplex, Filtration_value filtration = 0) { Insertion_result result = Base::insert_simplex_and_subfaces(simplex, filtration); return (result.second); diff --git a/cython/include/Tangential_complex_interface.h b/cython/include/Tangential_complex_interface.h index 5e9dc0e4..0c3a510e 100644 --- a/cython/include/Tangential_complex_interface.h +++ b/cython/include/Tangential_complex_interface.h @@ -105,9 +105,7 @@ class Tangential_complex_interface { } void create_simplex_tree(Simplex_tree<>* simplex_tree) { - int max_dim = tangential_complex_->create_complex>(*simplex_tree); - // FIXME - simplex_tree->set_dimension(max_dim); + tangential_complex_->create_complex>(*simplex_tree); simplex_tree->initialize_filtration(); } diff --git a/cython/setup.py.in b/cython/setup.py.in index fefa36bb..c767e93d 100644 --- a/cython/setup.py.in +++ b/cython/setup.py.in @@ -23,7 +23,7 @@ from Cython.Build import cythonize along with this program. If not, see . """ -__author__ = "Vincent Rouvreau" +__author__ = "GUDHI Editorial Board" __copyright__ = "Copyright (C) 2016 INRIA" __license__ = "GPL v3" @@ -41,7 +41,7 @@ gudhi = Extension( setup( name = 'gudhi', - author='Vincent Rouvreau', + author='GUDHI Editorial Board', author_email='gudhi-contact@lists.gforge.inria.fr', version='@GUDHI_VERSION@', url='http://gudhi.gforge.inria.fr/', diff --git a/cython/test/test_cubical_complex.py b/cython/test/test_cubical_complex.py index 9a365823..0e81554d 100755 --- a/cython/test/test_cubical_complex.py +++ b/cython/test/test_cubical_complex.py @@ -62,17 +62,17 @@ def test_dimension_or_perseus_file_constructor(): assert cub.__is_defined() == False assert cub.__is_persistence_defined() == False -def test_dimension_constructor(): +def test_dimension_simple_constructor(): cub = CubicalComplex(dimensions=[3, 3], top_dimensional_cells = [1,2,3,4,5,6,7,8,9]) assert cub.__is_defined() == True assert cub.__is_persistence_defined() == False - assert cub.persistence() == [(1, (0.0, 100.0)), (0, (0.0, float('inf')))] + assert cub.persistence() == [(0, (1.0, float('inf')))] assert cub.__is_persistence_defined() == True - assert cub.betti_numbers() == [1, 0] - assert cub.persistent_betti_numbers(0, 1000) == [0, 0] + assert cub.betti_numbers() == [1, 0, 0] + assert cub.persistent_betti_numbers(0, 1000) == [0, 0, 0] -def test_dimension_constructor(): +def test_dimension_file_constructor(): # Create test file test_file = open('CubicalOneSphere.txt', 'w') test_file.write('2\n3\n3\n0\n0\n0\n0\n100\n0\n0\n0\n0\n') diff --git a/cython/test/test_simplex_tree.py b/cython/test/test_simplex_tree.py index 4d452d7d..6dec5d94 100755 --- a/cython/test/test_simplex_tree.py +++ b/cython/test/test_simplex_tree.py @@ -34,9 +34,13 @@ def test_insertion(): # insert test assert st.insert([0, 1]) == True + + assert st.dimension() == 1 + assert st.insert([0, 1, 2], filtration=4.0) == True - # FIXME: Remove this line - st.set_dimension(2) + + assert st.dimension() == 2 + assert st.num_simplices() == 7 assert st.num_vertices() == 3 @@ -86,8 +90,9 @@ def test_insertion(): assert st.find([2]) == True st.initialize_filtration() - assert st.persistence() == [(1, (4.0, float('inf'))), (0, (0.0, float('inf')))] + assert st.persistence(persistence_dim_max = True) == [(1, (4.0, float('inf'))), (0, (0.0, float('inf')))] assert st.__is_persistence_defined() == True + assert st.betti_numbers() == [1, 1] assert st.persistent_betti_numbers(-0.1, 10000.0) == [0, 0] assert st.persistent_betti_numbers(0.0, 10000.0) == [1, 0] @@ -129,3 +134,30 @@ def test_expansion(): ([1, 2], 0.5), ([0, 1, 2], 0.5), ([1, 2, 3], 0.5), ([5], 0.6), ([6], 0.6), ([5, 6], 0.6), ([4], 0.7), ([2, 4], 0.7), ([0, 3], 0.8), ([0, 1, 3], 0.8), ([0, 2, 3], 0.8), ([0, 1, 2, 3], 0.8), ([4, 6], 0.9), ([3, 6], 1.0)] + +def test_automatic_dimension(): + st = SimplexTree() + assert st.__is_defined() == True + assert st.__is_persistence_defined() == False + + # insert test + assert st.insert([0,1,3], filtration=0.5) == True + assert st.insert([0,1,2], filtration=1.) == True + + assert st.num_vertices() == 4 + assert st.num_simplices() == 11 + + assert st.dimension() == 2 + assert st.upper_bound_dimension() == 2 + + assert st.prune_above_filtration(0.6) == True + assert st.dimension() == 2 + assert st.upper_bound_dimension() == 2 + + st.assign_filtration([0, 1, 3], 0.7) + assert st.filtration([0, 1, 3]) == 0.7 + + st.remove_maximal_simplex([0, 1, 3]) + assert st.upper_bound_dimension() == 2 + assert st.dimension() == 1 + assert st.upper_bound_dimension() == 1 -- cgit v1.2.3