From f5c97bc9fd1c247045d35ddf261f9afe4d024406 Mon Sep 17 00:00:00 2001 From: glisse Date: Fri, 20 Jul 2018 15:03:46 +0000 Subject: First try at interfacing the sparse rips in python. Needs at least documentation and tests. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/sparserips-python@3697 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 75bef59e90355853ee24807ca7453c4bb0a38f43 --- src/cython/cython/rips_complex.pyx | 50 +++++++++++++++++------------ src/cython/include/Rips_complex_interface.h | 39 ++++++++++++++-------- src/cython/test/test_rips_complex.py | 1 - 3 files changed, 55 insertions(+), 35 deletions(-) (limited to 'src/cython') diff --git a/src/cython/cython/rips_complex.pyx b/src/cython/cython/rips_complex.pyx index 59c16bff..620130ca 100644 --- a/src/cython/cython/rips_complex.pyx +++ b/src/cython/cython/rips_complex.pyx @@ -33,7 +33,11 @@ __license__ = "GPL v3" cdef extern from "Rips_complex_interface.h" namespace "Gudhi": cdef cppclass Rips_complex_interface "Gudhi::rips_complex::Rips_complex_interface": - Rips_complex_interface(vector[vector[double]] values, double threshold, bool euclidean) + Rips_complex_interface() + void init_points(vector[vector[double]] values, double threshold) + void init_matrix(vector[vector[double]] values, double threshold) + void init_points_sparse(vector[vector[double]] values, double threshold, double sparse) + void init_matrix_sparse(vector[vector[double]] values, double threshold, double sparse) void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, int dim_max) # RipsComplex python interface @@ -44,14 +48,14 @@ cdef class RipsComplex: function, or a distance matrix. """ - cdef Rips_complex_interface * thisptr + cdef Rips_complex_interface thisref # Fake constructor that does nothing but documenting the constructor - def __init__(self, points=None, distance_matrix=None, max_edge_length=float('inf')): + def __init__(self, points=None, distance_matrix=None, max_edge_length=float('inf'), sparse=None): """RipsComplex constructor. :param max_edge_length: Rips value. - :type max_edge_length: int + :type max_edge_length: float :param points: A list of points in d-Dimension. :type points: list of list of double @@ -61,27 +65,31 @@ cdef class RipsComplex: :param distance_matrix: A distance matrix (full square or lower triangular). :type points: list of list of double + + And in both cases + :param sparse: If this is not None, it switches to building a sparse Rips and represents the approximation parameter epsilon. + :type sparse: float """ # The real cython constructor - def __cinit__(self, points=None, distance_matrix=None, max_edge_length=float('inf')): - if distance_matrix is not None: - self.thisptr = new Rips_complex_interface(distance_matrix, max_edge_length, False) + def __cinit__(self, points=None, distance_matrix=None, max_edge_length=float('inf'), sparse=None): + if sparse is not None: + if distance_matrix is not None: + self.thisref.init_matrix_sparse(distance_matrix, max_edge_length, sparse) + else: + if points is None: + # Empty Rips construction + points=[] + self.thisref.init_points_sparse(points, max_edge_length, sparse) else: - if points is None: - # Empty Rips construction - points=[] - self.thisptr = new Rips_complex_interface(points, max_edge_length, True) - - - def __dealloc__(self): - if self.thisptr != NULL: - del self.thisptr + if distance_matrix is not None: + self.thisref.init_matrix(distance_matrix, max_edge_length) + else: + if points is None: + # Empty Rips construction + points=[] + self.thisref.init_points(points, max_edge_length) - def __is_defined(self): - """Returns true if RipsComplex pointer is not NULL. - """ - return self.thisptr != NULL def create_simplex_tree(self, max_dimension=1): """ @@ -92,5 +100,5 @@ cdef class RipsComplex: :rtype: SimplexTree """ simplex_tree = SimplexTree() - self.thisptr.create_simplex_tree(simplex_tree.thisptr, max_dimension) + self.thisref.create_simplex_tree(simplex_tree.thisptr, max_dimension) return simplex_tree diff --git a/src/cython/include/Rips_complex_interface.h b/src/cython/include/Rips_complex_interface.h index 8b6c9c35..f6fc79a1 100644 --- a/src/cython/include/Rips_complex_interface.h +++ b/src/cython/include/Rips_complex_interface.h @@ -25,8 +25,11 @@ #include #include +#include #include +#include + #include "Simplex_tree_interface.h" #include @@ -43,28 +46,38 @@ class Rips_complex_interface { using Distance_matrix = std::vector::Filtration_value>>; public: - Rips_complex_interface(const std::vector>& values, double threshold, bool euclidean) { - if (euclidean) { - // Rips construction where values is a vector of points - rips_complex_ = new Rips_complex::Filtration_value>(values, threshold, - Gudhi::Euclidean_distance()); - } else { - // Rips construction where values is a distance matrix - rips_complex_ = new Rips_complex::Filtration_value>(values, threshold); - } + void init_points(const std::vector>& points, double threshold) { + rips_complex_.emplace(points, threshold, Gudhi::Euclidean_distance()); + } + void init_matrix(const std::vector>& matrix, double threshold) { + rips_complex_.emplace(matrix, threshold); } - ~Rips_complex_interface() { - delete rips_complex_; + void init_points_sparse(const std::vector>& points, double threshold, double epsilon) { + sparse_rips_complex_.emplace(points, Gudhi::Euclidean_distance(), epsilon); + threshold_ = threshold; + } + void init_matrix_sparse(const std::vector>& matrix, double threshold, double epsilon) { + sparse_rips_complex_.emplace(matrix, epsilon); + threshold_ = threshold; } void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, int dim_max) { - rips_complex_->create_complex(*simplex_tree, dim_max); + if (rips_complex_) + rips_complex_->create_complex(*simplex_tree, dim_max); + else { + sparse_rips_complex_->create_complex(*simplex_tree, dim_max); + // This pruning should be done much earlier! It isn't that useful for sparse Rips, but it would be inconsistent not to do it. + simplex_tree->prune_above_filtration(threshold_); + } simplex_tree->initialize_filtration(); } private: - Rips_complex::Filtration_value>* rips_complex_; + // std::variant would work, but we don't require C++17 yet, and boost::variant is not super convenient. Anyway, storing a graph would make more sense. Or changing the interface completely so there is no such storage. + boost::optional::Filtration_value>> rips_complex_; + boost::optional::Filtration_value>> sparse_rips_complex_; + double threshold_; }; } // namespace rips_complex diff --git a/src/cython/test/test_rips_complex.py b/src/cython/test/test_rips_complex.py index c37b5400..2eb1c61c 100755 --- a/src/cython/test/test_rips_complex.py +++ b/src/cython/test/test_rips_complex.py @@ -30,7 +30,6 @@ __license__ = "GPL v3" def test_empty_rips(): rips_complex = RipsComplex() - assert rips_complex.__is_defined() == True def test_rips_from_points(): point_list = [[0, 0], [1, 0], [0, 1], [1, 1]] -- cgit v1.2.3 From d52036da23f887d56d13dd4f93c1049eb44301b1 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 3 Aug 2018 09:41:38 +0000 Subject: plot persistence density functionnality with its documentation Fix some documentation issue in other graphiacl tools Add scipy as a dependency git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3736 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 6481f1d6aa176bcf587f8875298a91cd22ac0319 --- src/cython/cython/persistence_graphical_tools.py | 74 +++++++++++++++++++++- src/cython/doc/persistence_graphical_tools_ref.rst | 1 + .../doc/persistence_graphical_tools_user.rst | 9 ++- src/cython/setup.py.in | 1 + 4 files changed, 80 insertions(+), 5 deletions(-) (limited to 'src/cython') diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py index 216ab8d6..7f604368 100755 --- a/src/cython/cython/persistence_graphical_tools.py +++ b/src/cython/cython/persistence_graphical_tools.py @@ -1,7 +1,9 @@ import matplotlib.pyplot as plt import matplotlib.patches as mpatches import numpy as np +from scipy.stats import kde import os +import math """This file is part of the Gudhi Library. The Gudhi library (Geometric Understanding in Higher Dimensions) is a generic C++ @@ -79,6 +81,8 @@ def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, :param inf_delta: Infinity is placed at ((max_death - min_birth) x inf_delta). A reasonable value is between 0.05 and 0.5 - default is 0.1. :type inf_delta: float. + :param legend: Display the dimension color legend (default is False). + :type legend: boolean. :returns: A matplotlib object containing horizontal bar plot of persistence (launch `show()` method on it to display it). """ @@ -154,6 +158,8 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, :param inf_delta: Infinity is placed at ((max_death - min_birth) x inf_delta). A reasonable value is between 0.05 and 0.5 - default is 0.1. :type inf_delta: float. + :param legend: Display the dimension color legend (default is False). + :type legend: boolean. :returns: A matplotlib object containing diagram plot of persistence (launch `show()` method on it to display it). """ @@ -174,7 +180,6 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_plots] (min_birth, max_death) = __min_birth_max_death(persistence, band) - ind = 0 delta = ((max_death - min_birth) * inf_delta) # Replace infinity values with max_death + delta for diagram to be more # readable @@ -201,7 +206,6 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, # Infinite death case for diagram to be nicer plt.scatter(interval[1][0], infinity, alpha=alpha, color = palette[interval[0]]) - ind = ind + 1 if legend: dimensions = list(set(item[0] for item in persistence)) @@ -213,3 +217,69 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, # Ends plot on infinity value and starts a little bit before min_birth plt.axis([axis_start, infinity, axis_start, infinity + delta]) return plt + +def plot_persistence_density(persistence=[], persistence_file='', nbins=300, + max_plots=1000, cmap=plt.cm.hot_r, legend=False): + """This function plots the persistence density from persistence values list + or from a :doc:`persistence file `. Be aware that this + function does not distinguish the dimension, it is up to you to select the + required one. + + :param persistence: Persistence values list. + :type persistence: list of tuples(dimension, tuple(birth, death)). + :param persistence_file: A :doc:`persistence file ` style name + (reset persistence if both are set). + :type persistence_file: string + :param nbins: Evaluate a gaussian kde on a regular grid of nbins x nbins + over data extents (default is 300) + :type nbins: int. + :param max_plots: number of maximal plots to be displayed + Set it to 0 to see all, Default value is 1000. + (persistence will be sorted by life time if max_plots is set) + :type max_plots: int. + :param cmap: A matplotlib colormap (default is matplotlib.pyplot.cm.hot_r). + :type cmap: cf. matplotlib colormap. + :param legend: Display the color bar values (default is False). + :type legend: boolean. + :returns: A matplotlib object containing diagram plot of persistence + (launch `show()` method on it to display it). + """ + if persistence_file is not '': + if os.path.isfile(persistence_file): + # Reset persistence + persistence = [] + diag = read_persistence_intervals_grouped_by_dimension(persistence_file=persistence_file) + for key in diag.keys(): + for persistence_interval in diag[key]: + persistence.append((key, persistence_interval)) + else: + print("file " + persistence_file + " not found.") + return None + + if max_plots > 0 and max_plots < len(persistence): + # Sort by life time, then takes only the max_plots elements + persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_plots] + + # Set as numpy array birth and death (remove undefined values - inf and NaN) + birth = np.asarray([(interval[1][0]) for interval in persistence if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))]) + death = np.asarray([(interval[1][1]) for interval in persistence if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))]) + + # line display of equation : birth = death + x = np.linspace(death.min(), birth.max(), 1000) + plt.plot(x, x, color='k', linewidth=1.0) + + # Evaluate a gaussian kde on a regular grid of nbins x nbins over data extents + k = kde.gaussian_kde([birth,death]) + xi, yi = np.mgrid[birth.min():birth.max():nbins*1j, death.min():death.max():nbins*1j] + zi = k(np.vstack([xi.flatten(), yi.flatten()])) + + # Make the plot + plt.pcolormesh(xi, yi, zi.reshape(xi.shape), cmap=cmap) + + if legend: + plt.colorbar() + + plt.title('Persistence density') + plt.xlabel('Birth') + plt.ylabel('Death') + return plt diff --git a/src/cython/doc/persistence_graphical_tools_ref.rst b/src/cython/doc/persistence_graphical_tools_ref.rst index a2c6bcef..54aff4bc 100644 --- a/src/cython/doc/persistence_graphical_tools_ref.rst +++ b/src/cython/doc/persistence_graphical_tools_ref.rst @@ -9,3 +9,4 @@ Persistence graphical tools reference manual .. autofunction:: gudhi.__min_birth_max_death .. autofunction:: gudhi.plot_persistence_barcode .. autofunction:: gudhi.plot_persistence_diagram +.. autofunction:: gudhi.plot_persistence_density diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst index 292915eb..b21de06a 100644 --- a/src/cython/doc/persistence_graphical_tools_user.rst +++ b/src/cython/doc/persistence_graphical_tools_user.rst @@ -43,6 +43,9 @@ This function can display the persistence result as a diagram: legend=True) plt.show() +Persistence density +------------------- + If you want more information on a specific dimension, for instance: .. plot:: @@ -56,7 +59,7 @@ If you want more information on a specific dimension, for instance: gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file=\ persistence_file) dim = 1 - # Display all points with some transparency - plt = gudhi.plot_persistence_diagram([(dim,interval) for interval in diag[dim]], - max_plots=0, alpha=0.1) + # Display persistence density + plt = gudhi.plot_persistence_density([(dim,interval) for interval in diag[dim]], + max_plots=0, legend=True) plt.show() diff --git a/src/cython/setup.py.in b/src/cython/setup.py.in index ee381a1b..22b2954e 100644 --- a/src/cython/setup.py.in +++ b/src/cython/setup.py.in @@ -49,6 +49,7 @@ setup( install_requires = [ "matplotlib", "numpy", + "scipy", "cython", ], ) -- cgit v1.2.3 From feb6244de8f602e36fe101eb553ad5a6265665ee Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 3 Aug 2018 09:55:26 +0000 Subject: Add SciPy as a dependency in the installation process documentation git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3737 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 2d9d2c3f32ba3af5e9565f89e986ac437370b68e --- src/cython/doc/installation.rst | 9 ++++++++- src/cython/doc/persistence_graphical_tools_sum.inc | 4 ++-- 2 files changed, 10 insertions(+), 3 deletions(-) (limited to 'src/cython') diff --git a/src/cython/doc/installation.rst b/src/cython/doc/installation.rst index 43ff85c5..ff6c7273 100644 --- a/src/cython/doc/installation.rst +++ b/src/cython/doc/installation.rst @@ -143,7 +143,7 @@ The following examples require the `Matplotlib `_: * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>` * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>` -Numpy +NumPy ===== The :doc:`persistence graphical tools ` @@ -164,6 +164,13 @@ The following examples require the `NumPy `_: * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>` * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>` +SciPy +===== + +The :doc:`persistence graphical tools ` +module requires `SciPy `_, a Python-based ecosystem of +open-source software for mathematics, science, and engineering. + Threading Building Blocks ========================= diff --git a/src/cython/doc/persistence_graphical_tools_sum.inc b/src/cython/doc/persistence_graphical_tools_sum.inc index d602daa7..c793a352 100644 --- a/src/cython/doc/persistence_graphical_tools_sum.inc +++ b/src/cython/doc/persistence_graphical_tools_sum.inc @@ -1,11 +1,11 @@ ================================================================= =================================== =================================== :Author: Vincent Rouvreau :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 -:Requires: Matplotlib Numpy +:Requires: Matplotlib Numpy Scipy ================================================================= =================================== =================================== +-----------------------------------------------------------------+-----------------------------------------------------------------------+ | .. figure:: | These graphical tools comes on top of persistence results and allows | -| img/graphical_tools_representation.png | the user to build easily barcode and persistence diagram. | +| img/graphical_tools_representation.png | the user to build easily persistence barcode, diagram or density. | | | | +-----------------------------------------------------------------+-----------------------------------------------------------------------+ | :doc:`persistence_graphical_tools_user` | :doc:`persistence_graphical_tools_ref` | -- cgit v1.2.3 From 2f10f837b791a1b002a18f1ba2b22de918eb54fe Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 16 Aug 2018 13:40:06 +0000 Subject: Code review : Try to import module. Functions are unavailable if not available. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3785 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 53c89a30f7992aa8d20e8330628c03291cea6473 --- .../modules/GUDHI_third_party_libraries.cmake | 1 + src/cython/CMakeLists.txt | 8 +- src/cython/cython/persistence_graphical_tools.py | 202 +++++++++++---------- 3 files changed, 108 insertions(+), 103 deletions(-) (limited to 'src/cython') diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake index f03c2177..1ad0c1fd 100644 --- a/src/cmake/modules/GUDHI_third_party_libraries.cmake +++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake @@ -143,6 +143,7 @@ if( PYTHONINTERP_FOUND ) find_python_module("pytest") find_python_module("matplotlib") find_python_module("numpy") + find_python_module("scipy") endif() if(NOT GUDHI_CYTHON_PATH) diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index 1849a6ec..542be9b0 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -54,10 +54,8 @@ if(CYTHON_FOUND) if(NUMPY_FOUND) add_gudhi_debug_info("Numpy version ${NUMPY_VERSION}") endif() - if(MATPLOTLIB_FOUND AND NUMPY_FOUND) - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}persistence_graphical_tools;") - else() - set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MODULES}persistence_graphical_tools;") + if(SCIPY_FOUND) + add_gudhi_debug_info("Scipy version ${SCIPY_VERSION}") endif() message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_VERSION} - Sphinx is ${SPHINX_PATH}") @@ -368,7 +366,7 @@ if(CYTHON_FOUND) add_gudhi_py_test(test_reader_utils) # Documentation generation is available through sphinx - requires all modules - if(SPHINX_PATH AND MATPLOTLIB_FOUND AND NUMPY_FOUND AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + if(SPHINX_PATH AND MATPLOTLIB_FOUND AND NUMPY_FOUND AND SCIPY_FOUND AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) set (GUDHI_SPHINX_MESSAGE "Generating API documentation with Sphinx in ${CMAKE_CURRENT_BINARY_DIR}/sphinx/") # User warning - Sphinx is a static pages generator, and configured to work fine with user_version # Images and biblio warnings because not found on developper version diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py index e172c65b..e154c0b2 100755 --- a/src/cython/cython/persistence_graphical_tools.py +++ b/src/cython/cython/persistence_graphical_tools.py @@ -24,44 +24,42 @@ __author__ = "Vincent Rouvreau, Bertrand Michel" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" +def __min_birth_max_death(persistence, band=0.): + """This function returns (min_birth, max_death) from the persistence. + + :param persistence: The persistence to plot. + :type persistence: list of tuples(dimension, tuple(birth, death)). + :param band: band + :type band: float. + :returns: (float, float) -- (min_birth, max_death). + """ + # Look for minimum birth date and maximum death date for plot optimisation + max_death = 0 + min_birth = persistence[0][1][0] + for interval in reversed(persistence): + if float(interval[1][1]) != float('inf'): + if float(interval[1][1]) > max_death: + max_death = float(interval[1][1]) + if float(interval[1][0]) > max_death: + max_death = float(interval[1][0]) + if float(interval[1][0]) < min_birth: + min_birth = float(interval[1][0]) + if band > 0.: + max_death += band + return (min_birth, max_death) + +""" +Only 13 colors for the palette +""" +palette = ['#ff0000', '#00ff00', '#0000ff', '#00ffff', '#ff00ff', '#ffff00', + '#000000', '#880000', '#008800', '#000088', '#888800', '#880088', + '#008888'] + try: import matplotlib.pyplot as plt import matplotlib.patches as mpatches import numpy as np - from scipy.stats import kde import os - import math - - def __min_birth_max_death(persistence, band=0.): - """This function returns (min_birth, max_death) from the persistence. - - :param persistence: The persistence to plot. - :type persistence: list of tuples(dimension, tuple(birth, death)). - :param band: band - :type band: float. - :returns: (float, float) -- (min_birth, max_death). - """ - # Look for minimum birth date and maximum death date for plot optimisation - max_death = 0 - min_birth = persistence[0][1][0] - for interval in reversed(persistence): - if float(interval[1][1]) != float('inf'): - if float(interval[1][1]) > max_death: - max_death = float(interval[1][1]) - if float(interval[1][0]) > max_death: - max_death = float(interval[1][0]) - if float(interval[1][0]) < min_birth: - min_birth = float(interval[1][0]) - if band > 0.: - max_death += band - return (min_birth, max_death) - - """ - Only 13 colors for the palette - """ - palette = ['#ff0000', '#00ff00', '#0000ff', '#00ffff', '#ff00ff', '#ffff00', - '#000000', '#880000', '#008800', '#000088', '#888800', '#880088', - '#008888'] def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max_barcodes=1000, inf_delta=0.1, legend=False): @@ -220,71 +218,79 @@ try: plt.axis([axis_start, infinity, axis_start, infinity + delta]) return plt - def plot_persistence_density(persistence=[], persistence_file='', nbins=300, - max_plots=1000, cmap=plt.cm.hot_r, legend=False): - """This function plots the persistence density from persistence values list - or from a :doc:`persistence file `. Be aware that this - function does not distinguish the dimension, it is up to you to select the - required one. - - :param persistence: Persistence values list. - :type persistence: list of tuples(dimension, tuple(birth, death)). - :param persistence_file: A :doc:`persistence file ` style name - (reset persistence if both are set). - :type persistence_file: string - :param nbins: Evaluate a gaussian kde on a regular grid of nbins x nbins - over data extents (default is 300) - :type nbins: int. - :param max_plots: number of maximal plots to be displayed - Set it to 0 to see all, Default value is 1000. - (persistence will be sorted by life time if max_plots is set) - :type max_plots: int. - :param cmap: A matplotlib colormap (default is matplotlib.pyplot.cm.hot_r). - :type cmap: cf. matplotlib colormap. - :param legend: Display the color bar values (default is False). - :type legend: boolean. - :returns: A matplotlib object containing diagram plot of persistence - (launch `show()` method on it to display it). - """ - if persistence_file is not '': - if os.path.isfile(persistence_file): - # Reset persistence - persistence = [] - diag = read_persistence_intervals_grouped_by_dimension(persistence_file=persistence_file) - for key in diag.keys(): - for persistence_interval in diag[key]: - persistence.append((key, persistence_interval)) - else: - print("file " + persistence_file + " not found.") - return None - - if max_plots > 0 and max_plots < len(persistence): - # Sort by life time, then takes only the max_plots elements - persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_plots] - - # Set as numpy array birth and death (remove undefined values - inf and NaN) - birth = np.asarray([(interval[1][0]) for interval in persistence if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))]) - death = np.asarray([(interval[1][1]) for interval in persistence if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))]) - - # line display of equation : birth = death - x = np.linspace(death.min(), birth.max(), 1000) - plt.plot(x, x, color='k', linewidth=1.0) - - # Evaluate a gaussian kde on a regular grid of nbins x nbins over data extents - k = kde.gaussian_kde([birth,death]) - xi, yi = np.mgrid[birth.min():birth.max():nbins*1j, death.min():death.max():nbins*1j] - zi = k(np.vstack([xi.flatten(), yi.flatten()])) - - # Make the plot - plt.pcolormesh(xi, yi, zi.reshape(xi.shape), cmap=cmap) - - if legend: - plt.colorbar() - - plt.title('Persistence density') - plt.xlabel('Birth') - plt.ylabel('Death') - return plt + try: + from scipy.stats import kde + import math + + def plot_persistence_density(persistence=[], persistence_file='', nbins=300, + max_plots=1000, cmap=plt.cm.hot_r, legend=False): + """This function plots the persistence density from persistence values list + or from a :doc:`persistence file `. Be aware that this + function does not distinguish the dimension, it is up to you to select the + required one. + + :param persistence: Persistence values list. + :type persistence: list of tuples(dimension, tuple(birth, death)). + :param persistence_file: A :doc:`persistence file ` style name + (reset persistence if both are set). + :type persistence_file: string + :param nbins: Evaluate a gaussian kde on a regular grid of nbins x nbins + over data extents (default is 300) + :type nbins: int. + :param max_plots: number of maximal plots to be displayed + Set it to 0 to see all, Default value is 1000. + (persistence will be sorted by life time if max_plots is set) + :type max_plots: int. + :param cmap: A matplotlib colormap (default is matplotlib.pyplot.cm.hot_r). + :type cmap: cf. matplotlib colormap. + :param legend: Display the color bar values (default is False). + :type legend: boolean. + :returns: A matplotlib object containing diagram plot of persistence + (launch `show()` method on it to display it). + """ + if persistence_file is not '': + if os.path.isfile(persistence_file): + # Reset persistence + persistence = [] + diag = read_persistence_intervals_grouped_by_dimension(persistence_file=persistence_file) + for key in diag.keys(): + for persistence_interval in diag[key]: + persistence.append((key, persistence_interval)) + else: + print("file " + persistence_file + " not found.") + return None + + if max_plots > 0 and max_plots < len(persistence): + # Sort by life time, then takes only the max_plots elements + persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_plots] + + # Set as numpy array birth and death (remove undefined values - inf and NaN) + birth = np.asarray([(interval[1][0]) for interval in persistence if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))]) + death = np.asarray([(interval[1][1]) for interval in persistence if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))]) + + # line display of equation : birth = death + x = np.linspace(death.min(), birth.max(), 1000) + plt.plot(x, x, color='k', linewidth=1.0) + + # Evaluate a gaussian kde on a regular grid of nbins x nbins over data extents + k = kde.gaussian_kde([birth,death]) + xi, yi = np.mgrid[birth.min():birth.max():nbins*1j, death.min():death.max():nbins*1j] + zi = k(np.vstack([xi.flatten(), yi.flatten()])) + + # Make the plot + plt.pcolormesh(xi, yi, zi.reshape(xi.shape), cmap=cmap) + + if legend: + plt.colorbar() + + plt.title('Persistence density') + plt.xlabel('Birth') + plt.ylabel('Death') + return plt + + except ImportError: + # Continue in case of import error, functions won't be available + pass except ImportError: # Continue in case of import error, functions won't be available -- cgit v1.2.3 From efab7ccf5850ccc58018b7f856d209c4094e67c5 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 16 Aug 2018 14:35:08 +0000 Subject: Bug fix git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3788 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: d8b898ca963d8d956307bb1dfd8abea1acbe6c96 --- src/cython/cython/persistence_graphical_tools.py | 1 - 1 file changed, 1 deletion(-) (limited to 'src/cython') diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py index e154c0b2..14c4cf3f 100755 --- a/src/cython/cython/persistence_graphical_tools.py +++ b/src/cython/cython/persistence_graphical_tools.py @@ -205,7 +205,6 @@ try: # Infinite death case for diagram to be nicer plt.scatter(interval[1][0], infinity, alpha=alpha, color = palette[interval[0]]) - ind = ind + 1 if legend: dimensions = list(set(item[0] for item in persistence)) -- cgit v1.2.3 From b7354cd2ab0b265787348866da5d08cce15aee66 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 17 Aug 2018 09:38:55 +0000 Subject: Code review : add a parameter to select dimension for plot_persistence_density. Default is None and mix all dimensions git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3794 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 493f5ecfad2bcf0ee4a40ec7b315863c471d088f --- src/cython/cython/persistence_graphical_tools.py | 43 +++++++++++++++--------- 1 file changed, 28 insertions(+), 15 deletions(-) (limited to 'src/cython') diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py index 14c4cf3f..949f5c37 100755 --- a/src/cython/cython/persistence_graphical_tools.py +++ b/src/cython/cython/persistence_graphical_tools.py @@ -221,26 +221,31 @@ try: from scipy.stats import kde import math - def plot_persistence_density(persistence=[], persistence_file='', nbins=300, - max_plots=1000, cmap=plt.cm.hot_r, legend=False): - """This function plots the persistence density from persistence values list - or from a :doc:`persistence file `. Be aware that this - function does not distinguish the dimension, it is up to you to select the - required one. + def plot_persistence_density(persistence=[], persistence_file='', + nbins=300, max_plots=1000, dimension=None, + cmap=plt.cm.hot_r, legend=False): + """This function plots the persistence density from persistence + values list or from a :doc:`persistence file `. Be + aware that this function does not distinguish the dimension, it is + up to you to select the required one. :param persistence: Persistence values list. :type persistence: list of tuples(dimension, tuple(birth, death)). - :param persistence_file: A :doc:`persistence file ` style name - (reset persistence if both are set). + :param persistence_file: A :doc:`persistence file ` + style name (reset persistence if both are set). :type persistence_file: string - :param nbins: Evaluate a gaussian kde on a regular grid of nbins x nbins - over data extents (default is 300) + :param nbins: Evaluate a gaussian kde on a regular grid of nbins x + nbins over data extents (default is 300) :type nbins: int. :param max_plots: number of maximal plots to be displayed Set it to 0 to see all, Default value is 1000. (persistence will be sorted by life time if max_plots is set) :type max_plots: int. - :param cmap: A matplotlib colormap (default is matplotlib.pyplot.cm.hot_r). + :param dimension: the dimension to be selected in the intervals + (default is None to mix all dimensions). + :type dimension: int. + :param cmap: A matplotlib colormap (default is + matplotlib.pyplot.cm.hot_r). :type cmap: cf. matplotlib colormap. :param legend: Display the color bar values (default is False). :type legend: boolean. @@ -259,13 +264,21 @@ try: print("file " + persistence_file + " not found.") return None - if max_plots > 0 and max_plots < len(persistence): + persistence_dim = [] + if dimension is not None: + persistence_dim = [(dim_interval) for dim_interval in persistence if (dim_interval[0] == dimension)] + else: + persistence_dim = persistence + + if max_plots > 0 and max_plots < len(persistence_dim): # Sort by life time, then takes only the max_plots elements - persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_plots] + persistence_dim = sorted(persistence_dim, + key=lambda life_time: life_time[1][1]-life_time[1][0], + reverse=True)[:max_plots] # Set as numpy array birth and death (remove undefined values - inf and NaN) - birth = np.asarray([(interval[1][0]) for interval in persistence if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))]) - death = np.asarray([(interval[1][1]) for interval in persistence if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))]) + birth = np.asarray([(interval[1][0]) for interval in persistence_dim if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))]) + death = np.asarray([(interval[1][1]) for interval in persistence_dim if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))]) # line display of equation : birth = death x = np.linspace(death.min(), birth.max(), 1000) -- cgit v1.2.3 From 1865751c055ad01ba159a13d22e42204195c2ccb Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 17 Aug 2018 09:50:15 +0000 Subject: Doc review : rephrase max_plots explanation git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3795 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: f6059d3a242eed53dfdddb76ffed33f99892f4bc --- src/cython/cython/persistence_graphical_tools.py | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) (limited to 'src/cython') diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py index 949f5c37..0b3357f8 100755 --- a/src/cython/cython/persistence_graphical_tools.py +++ b/src/cython/cython/persistence_graphical_tools.py @@ -138,21 +138,22 @@ try: def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, band=0., max_plots=1000, inf_delta=0.1, legend=False): - """This function plots the persistence diagram from persistence values list - or from a :doc:`persistence file `. + """This function plots the persistence diagram from persistence values + list or from a :doc:`persistence file `. :param persistence: Persistence values list. :type persistence: list of tuples(dimension, tuple(birth, death)). :param persistence_file: A :doc:`persistence file ` style name (reset persistence if both are set). :type persistence_file: string - :param alpha: plot transparency value (0.0 transparent through 1.0 opaque - default is 0.6). + :param alpha: plot transparency value (0.0 transparent through 1.0 + opaque - default is 0.6). :type alpha: float. :param band: band (not displayed if :math:`\leq` 0. - default is 0.) :type band: float. - :param max_plots: number of maximal plots to be displayed - Set it to 0 to see all, Default value is 1000. - (persistence will be sorted by life time if max_plots is set) + :param max_plots: maximal number of points to display. Selected points + are those with the longest life time. Set it to 0 to see all, + default value is 1000. :type max_plots: int. :param inf_delta: Infinity is placed at ((max_death - min_birth) x inf_delta). A reasonable value is between 0.05 and 0.5 - default is 0.1. @@ -237,9 +238,9 @@ try: :param nbins: Evaluate a gaussian kde on a regular grid of nbins x nbins over data extents (default is 300) :type nbins: int. - :param max_plots: number of maximal plots to be displayed - Set it to 0 to see all, Default value is 1000. - (persistence will be sorted by life time if max_plots is set) + :param max_plots: maximal number of points to display. Selected points + are those with the longest life time. Set it to 0 to see all, + default value is 1000. :type max_plots: int. :param dimension: the dimension to be selected in the intervals (default is None to mix all dimensions). -- cgit v1.2.3 From 67ae5aa70e70097f72f868ebba1fa8e7ff96297d Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 17 Aug 2018 12:41:10 +0000 Subject: doc review : modification of persistence barcode example to make it more relevant git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3796 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 17acc09cdf7d09b13c177334efb1e309c4fd8d9c --- .../doc/persistence_graphical_tools_user.rst | 25 +++++++++++----------- 1 file changed, 12 insertions(+), 13 deletions(-) (limited to 'src/cython') diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst index b21de06a..0047f9c8 100644 --- a/src/cython/doc/persistence_graphical_tools_user.rst +++ b/src/cython/doc/persistence_graphical_tools_user.rst @@ -19,12 +19,15 @@ This function can display the persistence result as a barcode: import gudhi - perseus_file = gudhi.__root_source_dir__ + '/data/bitmap/3d_torus.txt' - periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=perseus_file) - diag = periodic_cc.persistence() - print("diag = ", diag) - plt = gudhi.plot_persistence_barcode(diag) - plt.show() + off_file = gudhi.__root_source_dir__ + '/data/points/tore3D_300.off' + point_cloud = gudhi.read_off(off_file=off_file) + + rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.7) + simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) + diag = simplex_tree.persistence(min_persistence=0.4) + + plot = gudhi.plot_persistence_barcode(diag) + plot.show() Show persistence as a diagram ----------------------------- @@ -53,13 +56,9 @@ If you want more information on a specific dimension, for instance: import gudhi + # rips_on_tore3D_1307.pers obtained from write_persistence_diagram method persistence_file=gudhi.__root_source_dir__ + \ '/data/persistence_diagram/rips_on_tore3D_1307.pers' - diag = \ - gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file=\ - persistence_file) - dim = 1 - # Display persistence density - plt = gudhi.plot_persistence_density([(dim,interval) for interval in diag[dim]], - max_plots=0, legend=True) + plt = gudhi.plot_persistence_density(persistence_file=persistence_file, + max_plots=0, dimension=1, legend=True) plt.show() -- cgit v1.2.3 From a5464d68d2848d21fc777809ab686b1bbf4e0139 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 17 Aug 2018 13:32:41 +0000 Subject: Code review : Add a bw_method parameter to plot_persistence_density for the standard deviation of the Gaussian git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3799 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 3bbc988434951bb429acd44b1f31f8310bb9ba9c --- src/cython/cython/persistence_graphical_tools.py | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) (limited to 'src/cython') diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py index 0b3357f8..026e365d 100755 --- a/src/cython/cython/persistence_graphical_tools.py +++ b/src/cython/cython/persistence_graphical_tools.py @@ -223,7 +223,8 @@ try: import math def plot_persistence_density(persistence=[], persistence_file='', - nbins=300, max_plots=1000, dimension=None, + nbins=300, bw_method=None, + max_plots=1000, dimension=None, cmap=plt.cm.hot_r, legend=False): """This function plots the persistence density from persistence values list or from a :doc:`persistence file `. Be @@ -238,6 +239,14 @@ try: :param nbins: Evaluate a gaussian kde on a regular grid of nbins x nbins over data extents (default is 300) :type nbins: int. + :param bw_method: The method used to calculate the estimator + bandwidth. This can be 'scott', 'silverman', a scalar constant + or a callable. If a scalar, this will be used directly as + kde.factor. If a callable, it should take a gaussian_kde + instance as only parameter and return a scalar. If None + (default), 'scott' is used. See scipy.stats.gaussian_kde + documentation for more details. + :type bw_method: str, scalar or callable, optional. :param max_plots: maximal number of points to display. Selected points are those with the longest life time. Set it to 0 to see all, default value is 1000. @@ -286,7 +295,7 @@ try: plt.plot(x, x, color='k', linewidth=1.0) # Evaluate a gaussian kde on a regular grid of nbins x nbins over data extents - k = kde.gaussian_kde([birth,death]) + k = kde.gaussian_kde([birth,death], bw_method=bw_method) xi, yi = np.mgrid[birth.min():birth.max():nbins*1j, death.min():death.max():nbins*1j] zi = k(np.vstack([xi.flatten(), yi.flatten()])) -- cgit v1.2.3 From 24c661e98b8f8e0f2c492fcf63e68615dbd9ae84 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 17 Aug 2018 13:45:08 +0000 Subject: Doc review : inf_delta explanation improvement git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3800 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 01fff74d79228431d77a46b713ac656ab7e84dc0 --- src/cython/cython/persistence_graphical_tools.py | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) (limited to 'src/cython') diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py index 026e365d..4c8467bd 100755 --- a/src/cython/cython/persistence_graphical_tools.py +++ b/src/cython/cython/persistence_graphical_tools.py @@ -71,14 +71,16 @@ try: :param persistence_file: A :doc:`persistence file ` style name (reset persistence if both are set). :type persistence_file: string - :param alpha: barcode transparency value (0.0 transparent through 1.0 opaque - default is 0.6). + :param alpha: barcode transparency value (0.0 transparent through 1.0 + opaque - default is 0.6). :type alpha: float. :param max_barcodes: number of maximal barcodes to be displayed. Set it to 0 to see all, Default value is 1000. (persistence will be sorted by life time if max_barcodes is set) :type max_barcodes: int. - :param inf_delta: Infinity is placed at ((max_death - min_birth) x inf_delta). - A reasonable value is between 0.05 and 0.5 - default is 0.1. + :param inf_delta: Infinity is placed at ((max_death - min_birth) x + inf_delta) above the highest point. A reasonable value is between + 0.05 and 0.5 - default is 0.1. :type inf_delta: float. :param legend: Display the dimension color legend (default is False). :type legend: boolean. @@ -155,8 +157,9 @@ try: are those with the longest life time. Set it to 0 to see all, default value is 1000. :type max_plots: int. - :param inf_delta: Infinity is placed at ((max_death - min_birth) x inf_delta). - A reasonable value is between 0.05 and 0.5 - default is 0.1. + :param inf_delta: Infinity is placed at ((max_death - min_birth) x + inf_delta) above the highest point. A reasonable value is between + 0.05 and 0.5 - default is 0.1. :type inf_delta: float. :param legend: Display the dimension color legend (default is False). :type legend: boolean. -- cgit v1.2.3 From 7e1d78ec22e0e53bbf4a36aaea1b77fa48f5d40d Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 17 Aug 2018 13:58:46 +0000 Subject: Code review : Rename max_plots with max_intervals for persistence density git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3801 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 8d20ee2f721b856bba69bc5bc10db26032649129 --- src/cython/cython/persistence_graphical_tools.py | 14 +++++++------- src/cython/doc/persistence_graphical_tools_user.rst | 2 +- 2 files changed, 8 insertions(+), 8 deletions(-) (limited to 'src/cython') diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py index 4c8467bd..96b579bd 100755 --- a/src/cython/cython/persistence_graphical_tools.py +++ b/src/cython/cython/persistence_graphical_tools.py @@ -250,10 +250,10 @@ try: (default), 'scott' is used. See scipy.stats.gaussian_kde documentation for more details. :type bw_method: str, scalar or callable, optional. - :param max_plots: maximal number of points to display. Selected points - are those with the longest life time. Set it to 0 to see all, - default value is 1000. - :type max_plots: int. + :param max_intervals: maximal number of intervals to display. + Selected points are those with the longest life time. Set it + to 0 to see all. Default value is 1000. + :type max_intervals: int. :param dimension: the dimension to be selected in the intervals (default is None to mix all dimensions). :type dimension: int. @@ -283,11 +283,11 @@ try: else: persistence_dim = persistence - if max_plots > 0 and max_plots < len(persistence_dim): - # Sort by life time, then takes only the max_plots elements + if max_intervals > 0 and max_intervals < len(persistence_dim): + # Sort by life time, then takes only the max_intervals elements persistence_dim = sorted(persistence_dim, key=lambda life_time: life_time[1][1]-life_time[1][0], - reverse=True)[:max_plots] + reverse=True)[:max_intervals] # Set as numpy array birth and death (remove undefined values - inf and NaN) birth = np.asarray([(interval[1][0]) for interval in persistence_dim if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))]) diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst index 0047f9c8..fda086c3 100644 --- a/src/cython/doc/persistence_graphical_tools_user.rst +++ b/src/cython/doc/persistence_graphical_tools_user.rst @@ -60,5 +60,5 @@ If you want more information on a specific dimension, for instance: persistence_file=gudhi.__root_source_dir__ + \ '/data/persistence_diagram/rips_on_tore3D_1307.pers' plt = gudhi.plot_persistence_density(persistence_file=persistence_file, - max_plots=0, dimension=1, legend=True) + max_intervals=0, dimension=1, legend=True) plt.show() -- cgit v1.2.3 From 6ebc098c9bbf233b5a4325faec04236feedab191 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 17 Aug 2018 14:48:08 +0000 Subject: Code review : rename max_plots and max_barcodes as max_intervals for peristence_graphical_tools git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3803 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: ad73f7e6cc6d72c3ba24b5ac947265c78a29f387 --- src/cython/cython/persistence_graphical_tools.py | 43 ++++++++++++++---------- 1 file changed, 26 insertions(+), 17 deletions(-) (limited to 'src/cython') diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py index 96b579bd..85d2a5ad 100755 --- a/src/cython/cython/persistence_graphical_tools.py +++ b/src/cython/cython/persistence_graphical_tools.py @@ -62,7 +62,8 @@ try: import os def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, - max_barcodes=1000, inf_delta=0.1, legend=False): + max_intervals=1000, max_barcodes=1000, + inf_delta=0.1, legend=False): """This function plots the persistence bar code from persistence values list or from a :doc:`persistence file `. @@ -74,10 +75,10 @@ try: :param alpha: barcode transparency value (0.0 transparent through 1.0 opaque - default is 0.6). :type alpha: float. - :param max_barcodes: number of maximal barcodes to be displayed. - Set it to 0 to see all, Default value is 1000. - (persistence will be sorted by life time if max_barcodes is set) - :type max_barcodes: int. + :param max_intervals: maximal number of intervals to display. + Selected points are those with the longest life time. Set it + to 0 to see all. Default value is 1000. + :type max_intervals: int. :param inf_delta: Infinity is placed at ((max_death - min_birth) x inf_delta) above the highest point. A reasonable value is between 0.05 and 0.5 - default is 0.1. @@ -99,9 +100,13 @@ try: print("file " + persistence_file + " not found.") return None - if max_barcodes > 0 and max_barcodes < len(persistence): - # Sort by life time, then takes only the max_plots elements - persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_barcodes] + if max_barcodes is not 1000: + print('Deprecated parameter. It has been replaced by max_intervals') + max_intervals = max_barcodes + + if max_intervals > 0 and max_intervals < len(persistence): + # Sort by life time, then takes only the max_intervals elements + persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_intervals] persistence = sorted(persistence, key=lambda birth: birth[1][0]) @@ -139,7 +144,7 @@ try: return plt def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, - band=0., max_plots=1000, inf_delta=0.1, legend=False): + band=0., max_intervals=1000, max_plots=1000, inf_delta=0.1, legend=False): """This function plots the persistence diagram from persistence values list or from a :doc:`persistence file `. @@ -153,10 +158,10 @@ try: :type alpha: float. :param band: band (not displayed if :math:`\leq` 0. - default is 0.) :type band: float. - :param max_plots: maximal number of points to display. Selected points - are those with the longest life time. Set it to 0 to see all, - default value is 1000. - :type max_plots: int. + :param max_intervals: maximal number of intervals to display. + Selected points are those with the longest life time. Set it + to 0 to see all. Default value is 1000. + :type max_intervals: int. :param inf_delta: Infinity is placed at ((max_death - min_birth) x inf_delta) above the highest point. A reasonable value is between 0.05 and 0.5 - default is 0.1. @@ -178,9 +183,13 @@ try: print("file " + persistence_file + " not found.") return None - if max_plots > 0 and max_plots < len(persistence): - # Sort by life time, then takes only the max_plots elements - persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_plots] + if max_plots is not 1000: + print('Deprecated parameter. It has been replaced by max_intervals') + max_intervals = max_plots + + if max_intervals > 0 and max_intervals < len(persistence): + # Sort by life time, then takes only the max_intervals elements + persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_intervals] (min_birth, max_death) = __min_birth_max_death(persistence, band) delta = ((max_death - min_birth) * inf_delta) @@ -227,7 +236,7 @@ try: def plot_persistence_density(persistence=[], persistence_file='', nbins=300, bw_method=None, - max_plots=1000, dimension=None, + max_intervals=1000, dimension=None, cmap=plt.cm.hot_r, legend=False): """This function plots the persistence density from persistence values list or from a :doc:`persistence file `. Be -- cgit v1.2.3 From b301bf80daaac521f16d43120a8a30a2af9eb515 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 17 Aug 2018 15:29:19 +0000 Subject: Makes clearer dependencies for each function of persistence graphical tools git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3804 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 7572f54368ff235f5e78df74121bf6b1ee107177 --- src/cython/doc/persistence_graphical_tools_sum.inc | 2 +- src/cython/doc/persistence_graphical_tools_user.rst | 9 +++++++++ 2 files changed, 10 insertions(+), 1 deletion(-) (limited to 'src/cython') diff --git a/src/cython/doc/persistence_graphical_tools_sum.inc b/src/cython/doc/persistence_graphical_tools_sum.inc index c793a352..5577cf99 100644 --- a/src/cython/doc/persistence_graphical_tools_sum.inc +++ b/src/cython/doc/persistence_graphical_tools_sum.inc @@ -1,6 +1,6 @@ ================================================================= =================================== =================================== :Author: Vincent Rouvreau :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 -:Requires: Matplotlib Numpy Scipy +:Requires: matplotlib numpy scipy ================================================================= =================================== =================================== +-----------------------------------------------------------------+-----------------------------------------------------------------------+ diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst index fda086c3..b2124fdd 100644 --- a/src/cython/doc/persistence_graphical_tools_user.rst +++ b/src/cython/doc/persistence_graphical_tools_user.rst @@ -12,6 +12,9 @@ Definition Show persistence as a barcode ----------------------------- +.. note:: + this function requires matplotlib and numpy to be available + This function can display the persistence result as a barcode: .. plot:: @@ -32,6 +35,9 @@ This function can display the persistence result as a barcode: Show persistence as a diagram ----------------------------- +.. note:: + this function requires matplotlib and numpy to be available + This function can display the persistence result as a diagram: .. plot:: @@ -49,6 +55,9 @@ This function can display the persistence result as a diagram: Persistence density ------------------- +.. note:: + this function requires matplotlib, numpy and scipy to be available + If you want more information on a specific dimension, for instance: .. plot:: -- cgit v1.2.3 From 44aaa06e1da4a2e4557886c9c7096edbe9d00f53 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Mon, 10 Sep 2018 08:37:45 +0000 Subject: Doc review : Add a link to scipy.stats.gaussian_kde official documentation git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3878 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: dd6e1a4131be1ed0306a48f9b095e0d09ddee848 --- src/cython/cython/persistence_graphical_tools.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'src/cython') diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py index 85d2a5ad..f5550e3a 100755 --- a/src/cython/cython/persistence_graphical_tools.py +++ b/src/cython/cython/persistence_graphical_tools.py @@ -256,8 +256,10 @@ try: or a callable. If a scalar, this will be used directly as kde.factor. If a callable, it should take a gaussian_kde instance as only parameter and return a scalar. If None - (default), 'scott' is used. See scipy.stats.gaussian_kde - documentation for more details. + (default), 'scott' is used. See + `scipy.stats.gaussian_kde documentation + `_ + for more details. :type bw_method: str, scalar or callable, optional. :param max_intervals: maximal number of intervals to display. Selected points are those with the longest life time. Set it -- cgit v1.2.3 From 629a456684e9bbf4c2ef5dbfefebe85e9c04a39d Mon Sep 17 00:00:00 2001 From: glisse Date: Mon, 10 Sep 2018 09:23:07 +0000 Subject: Add minimal testing for sparse rips in python git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/sparserips-python@3879 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 14cde17f1ef634539937b215e82bcfe3c8c784f0 --- src/cython/test/test_rips_complex.py | 12 ++++++++++++ 1 file changed, 12 insertions(+) (limited to 'src/cython') diff --git a/src/cython/test/test_rips_complex.py b/src/cython/test/test_rips_complex.py index 2eb1c61c..73cdac17 100755 --- a/src/cython/test/test_rips_complex.py +++ b/src/cython/test/test_rips_complex.py @@ -67,6 +67,18 @@ def test_filtered_rips_from_points(): assert simplex_tree.num_simplices() == 8 assert simplex_tree.num_vertices() == 4 +def test_sparse_filtered_rips_from_points(): + point_list = [[0, 0], [1, 0], [0, 1], [1, 1]] + filtered_rips = RipsComplex(points=point_list, max_edge_length=1.0, sparse=.001) + + simplex_tree = filtered_rips.create_simplex_tree(max_dimension=1) + + assert simplex_tree.__is_defined() == True + assert simplex_tree.__is_persistence_defined() == False + + assert simplex_tree.num_simplices() == 8 + assert simplex_tree.num_vertices() == 4 + def test_rips_from_distance_matrix(): distance_matrix = [[0], [1, 0], -- cgit v1.2.3 From 4bf56301ea1aa0c43855bea88344c80db237adbb Mon Sep 17 00:00:00 2001 From: glisse Date: Mon, 10 Sep 2018 09:29:57 +0000 Subject: sparse rips example git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/sparserips-python@3880 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 8dfc1b3218d3ac3e97a04bf25e59e2d48fc8db1d --- .../example/sparse_rips_persistence_diagram.py | 43 ++++++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100755 src/cython/example/sparse_rips_persistence_diagram.py (limited to 'src/cython') diff --git a/src/cython/example/sparse_rips_persistence_diagram.py b/src/cython/example/sparse_rips_persistence_diagram.py new file mode 100755 index 00000000..3bed87c1 --- /dev/null +++ b/src/cython/example/sparse_rips_persistence_diagram.py @@ -0,0 +1,43 @@ +#!/usr/bin/env python + +import gudhi + +"""This file is part of the Gudhi Library. The Gudhi library + (Geometric Understanding in Higher Dimensions) is a generic C++ + library for computational topology. + + Author(s): Marc Glisse + + Copyright (C) 2016 Inria + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . +""" + +__author__ = "Marc Glisse" +__copyright__ = "Copyright (C) 2016 Inria" +__license__ = "GPL v3" + +print("#####################################################################") +print("RipsComplex creation from points") +rips = gudhi.RipsComplex(points=[[0, 0], [0, 0.1], [1, 0], [0, 1], [1, 1]], + max_edge_length=42, sparse=.5) + +simplex_tree = rips.create_simplex_tree(max_dimension=2) + + +diag = simplex_tree.persistence(homology_coeff_field=2, min_persistence=0) +print("diag=", diag) + +pplot = gudhi.plot_persistence_diagram(diag) +pplot.show() -- cgit v1.2.3 From bdbbbc71e7d82526b24f76cc3b9916ad53919d41 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Mon, 10 Sep 2018 09:32:00 +0000 Subject: Code review : More explicit message when import fails in plot persistence graphical tools git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3881 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 96f9e3da3bd68d6cba65242b9890c4beb463c863 --- src/cython/cython/persistence_graphical_tools.py | 309 ++++++++++++----------- 1 file changed, 161 insertions(+), 148 deletions(-) (limited to 'src/cython') diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py index f5550e3a..e66643d2 100755 --- a/src/cython/cython/persistence_graphical_tools.py +++ b/src/cython/cython/persistence_graphical_tools.py @@ -55,39 +55,39 @@ palette = ['#ff0000', '#00ff00', '#0000ff', '#00ffff', '#ff00ff', '#ffff00', '#000000', '#880000', '#008800', '#000088', '#888800', '#880088', '#008888'] -try: - import matplotlib.pyplot as plt - import matplotlib.patches as mpatches - import numpy as np - import os - - def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, - max_intervals=1000, max_barcodes=1000, - inf_delta=0.1, legend=False): - """This function plots the persistence bar code from persistence values list - or from a :doc:`persistence file `. - - :param persistence: Persistence values list. - :type persistence: list of tuples(dimension, tuple(birth, death)). - :param persistence_file: A :doc:`persistence file ` style name - (reset persistence if both are set). - :type persistence_file: string - :param alpha: barcode transparency value (0.0 transparent through 1.0 - opaque - default is 0.6). - :type alpha: float. - :param max_intervals: maximal number of intervals to display. - Selected points are those with the longest life time. Set it - to 0 to see all. Default value is 1000. - :type max_intervals: int. - :param inf_delta: Infinity is placed at ((max_death - min_birth) x - inf_delta) above the highest point. A reasonable value is between - 0.05 and 0.5 - default is 0.1. - :type inf_delta: float. - :param legend: Display the dimension color legend (default is False). - :type legend: boolean. - :returns: A matplotlib object containing horizontal bar plot of persistence - (launch `show()` method on it to display it). - """ +def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, + max_intervals=1000, max_barcodes=1000, + inf_delta=0.1, legend=False): + """This function plots the persistence bar code from persistence values list + or from a :doc:`persistence file `. + + :param persistence: Persistence values list. + :type persistence: list of tuples(dimension, tuple(birth, death)). + :param persistence_file: A :doc:`persistence file ` style name + (reset persistence if both are set). + :type persistence_file: string + :param alpha: barcode transparency value (0.0 transparent through 1.0 + opaque - default is 0.6). + :type alpha: float. + :param max_intervals: maximal number of intervals to display. + Selected points are those with the longest life time. Set it + to 0 to see all. Default value is 1000. + :type max_intervals: int. + :param inf_delta: Infinity is placed at ((max_death - min_birth) x + inf_delta) above the highest point. A reasonable value is between + 0.05 and 0.5 - default is 0.1. + :type inf_delta: float. + :param legend: Display the dimension color legend (default is False). + :type legend: boolean. + :returns: A matplotlib object containing horizontal bar plot of persistence + (launch `show()` method on it to display it). + """ + try: + import matplotlib.pyplot as plt + import matplotlib.patches as mpatches + import numpy as np + import os + if persistence_file is not '': if os.path.isfile(persistence_file): # Reset persistence @@ -143,34 +143,43 @@ try: plt.axis([axis_start, infinity, 0, ind]) return plt - def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, - band=0., max_intervals=1000, max_plots=1000, inf_delta=0.1, legend=False): - """This function plots the persistence diagram from persistence values - list or from a :doc:`persistence file `. - - :param persistence: Persistence values list. - :type persistence: list of tuples(dimension, tuple(birth, death)). - :param persistence_file: A :doc:`persistence file ` style name - (reset persistence if both are set). - :type persistence_file: string - :param alpha: plot transparency value (0.0 transparent through 1.0 - opaque - default is 0.6). - :type alpha: float. - :param band: band (not displayed if :math:`\leq` 0. - default is 0.) - :type band: float. - :param max_intervals: maximal number of intervals to display. - Selected points are those with the longest life time. Set it - to 0 to see all. Default value is 1000. - :type max_intervals: int. - :param inf_delta: Infinity is placed at ((max_death - min_birth) x - inf_delta) above the highest point. A reasonable value is between - 0.05 and 0.5 - default is 0.1. - :type inf_delta: float. - :param legend: Display the dimension color legend (default is False). - :type legend: boolean. - :returns: A matplotlib object containing diagram plot of persistence - (launch `show()` method on it to display it). - """ + except ImportError: + print("This function is not available, you may be missing numpy and/or matplotlib.") + +def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, + band=0., max_intervals=1000, max_plots=1000, inf_delta=0.1, legend=False): + """This function plots the persistence diagram from persistence values + list or from a :doc:`persistence file `. + + :param persistence: Persistence values list. + :type persistence: list of tuples(dimension, tuple(birth, death)). + :param persistence_file: A :doc:`persistence file ` style name + (reset persistence if both are set). + :type persistence_file: string + :param alpha: plot transparency value (0.0 transparent through 1.0 + opaque - default is 0.6). + :type alpha: float. + :param band: band (not displayed if :math:`\leq` 0. - default is 0.) + :type band: float. + :param max_intervals: maximal number of intervals to display. + Selected points are those with the longest life time. Set it + to 0 to see all. Default value is 1000. + :type max_intervals: int. + :param inf_delta: Infinity is placed at ((max_death - min_birth) x + inf_delta) above the highest point. A reasonable value is between + 0.05 and 0.5 - default is 0.1. + :type inf_delta: float. + :param legend: Display the dimension color legend (default is False). + :type legend: boolean. + :returns: A matplotlib object containing diagram plot of persistence + (launch `show()` method on it to display it). + """ + try: + import matplotlib.pyplot as plt + import matplotlib.patches as mpatches + import numpy as np + import os + if persistence_file is not '': if os.path.isfile(persistence_file): # Reset persistence @@ -230,104 +239,108 @@ try: plt.axis([axis_start, infinity, axis_start, infinity + delta]) return plt + except ImportError: + print("This function is not available, you may be missing numpy and/or matplotlib.") + +def plot_persistence_density(persistence=[], persistence_file='', + nbins=300, bw_method=None, + max_intervals=1000, dimension=None, + cmap=None, legend=False): + """This function plots the persistence density from persistence + values list or from a :doc:`persistence file `. Be + aware that this function does not distinguish the dimension, it is + up to you to select the required one. + + :param persistence: Persistence values list. + :type persistence: list of tuples(dimension, tuple(birth, death)). + :param persistence_file: A :doc:`persistence file ` + style name (reset persistence if both are set). + :type persistence_file: string + :param nbins: Evaluate a gaussian kde on a regular grid of nbins x + nbins over data extents (default is 300) + :type nbins: int. + :param bw_method: The method used to calculate the estimator + bandwidth. This can be 'scott', 'silverman', a scalar constant + or a callable. If a scalar, this will be used directly as + kde.factor. If a callable, it should take a gaussian_kde + instance as only parameter and return a scalar. If None + (default), 'scott' is used. See + `scipy.stats.gaussian_kde documentation + `_ + for more details. + :type bw_method: str, scalar or callable, optional. + :param max_intervals: maximal number of intervals to display. + Selected points are those with the longest life time. Set it + to 0 to see all. Default value is 1000. + :type max_intervals: int. + :param dimension: the dimension to be selected in the intervals + (default is None to mix all dimensions). + :type dimension: int. + :param cmap: A matplotlib colormap (default is + matplotlib.pyplot.cm.hot_r). + :type cmap: cf. matplotlib colormap. + :param legend: Display the color bar values (default is False). + :type legend: boolean. + :returns: A matplotlib object containing diagram plot of persistence + (launch `show()` method on it to display it). + """ try: + import matplotlib.pyplot as plt + import numpy as np from scipy.stats import kde + import os import math - def plot_persistence_density(persistence=[], persistence_file='', - nbins=300, bw_method=None, - max_intervals=1000, dimension=None, - cmap=plt.cm.hot_r, legend=False): - """This function plots the persistence density from persistence - values list or from a :doc:`persistence file `. Be - aware that this function does not distinguish the dimension, it is - up to you to select the required one. - - :param persistence: Persistence values list. - :type persistence: list of tuples(dimension, tuple(birth, death)). - :param persistence_file: A :doc:`persistence file ` - style name (reset persistence if both are set). - :type persistence_file: string - :param nbins: Evaluate a gaussian kde on a regular grid of nbins x - nbins over data extents (default is 300) - :type nbins: int. - :param bw_method: The method used to calculate the estimator - bandwidth. This can be 'scott', 'silverman', a scalar constant - or a callable. If a scalar, this will be used directly as - kde.factor. If a callable, it should take a gaussian_kde - instance as only parameter and return a scalar. If None - (default), 'scott' is used. See - `scipy.stats.gaussian_kde documentation - `_ - for more details. - :type bw_method: str, scalar or callable, optional. - :param max_intervals: maximal number of intervals to display. - Selected points are those with the longest life time. Set it - to 0 to see all. Default value is 1000. - :type max_intervals: int. - :param dimension: the dimension to be selected in the intervals - (default is None to mix all dimensions). - :type dimension: int. - :param cmap: A matplotlib colormap (default is - matplotlib.pyplot.cm.hot_r). - :type cmap: cf. matplotlib colormap. - :param legend: Display the color bar values (default is False). - :type legend: boolean. - :returns: A matplotlib object containing diagram plot of persistence - (launch `show()` method on it to display it). - """ - if persistence_file is not '': - if os.path.isfile(persistence_file): - # Reset persistence - persistence = [] - diag = read_persistence_intervals_grouped_by_dimension(persistence_file=persistence_file) - for key in diag.keys(): - for persistence_interval in diag[key]: - persistence.append((key, persistence_interval)) - else: - print("file " + persistence_file + " not found.") - return None - - persistence_dim = [] - if dimension is not None: - persistence_dim = [(dim_interval) for dim_interval in persistence if (dim_interval[0] == dimension)] + if persistence_file is not '': + if os.path.isfile(persistence_file): + # Reset persistence + persistence = [] + diag = read_persistence_intervals_grouped_by_dimension(persistence_file=persistence_file) + for key in diag.keys(): + for persistence_interval in diag[key]: + persistence.append((key, persistence_interval)) else: - persistence_dim = persistence + print("file " + persistence_file + " not found.") + return None - if max_intervals > 0 and max_intervals < len(persistence_dim): - # Sort by life time, then takes only the max_intervals elements - persistence_dim = sorted(persistence_dim, - key=lambda life_time: life_time[1][1]-life_time[1][0], - reverse=True)[:max_intervals] + persistence_dim = [] + if dimension is not None: + persistence_dim = [(dim_interval) for dim_interval in persistence if (dim_interval[0] == dimension)] + else: + persistence_dim = persistence - # Set as numpy array birth and death (remove undefined values - inf and NaN) - birth = np.asarray([(interval[1][0]) for interval in persistence_dim if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))]) - death = np.asarray([(interval[1][1]) for interval in persistence_dim if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))]) + if max_intervals > 0 and max_intervals < len(persistence_dim): + # Sort by life time, then takes only the max_intervals elements + persistence_dim = sorted(persistence_dim, + key=lambda life_time: life_time[1][1]-life_time[1][0], + reverse=True)[:max_intervals] - # line display of equation : birth = death - x = np.linspace(death.min(), birth.max(), 1000) - plt.plot(x, x, color='k', linewidth=1.0) + # Set as numpy array birth and death (remove undefined values - inf and NaN) + birth = np.asarray([(interval[1][0]) for interval in persistence_dim if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))]) + death = np.asarray([(interval[1][1]) for interval in persistence_dim if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))]) - # Evaluate a gaussian kde on a regular grid of nbins x nbins over data extents - k = kde.gaussian_kde([birth,death], bw_method=bw_method) - xi, yi = np.mgrid[birth.min():birth.max():nbins*1j, death.min():death.max():nbins*1j] - zi = k(np.vstack([xi.flatten(), yi.flatten()])) + # line display of equation : birth = death + x = np.linspace(death.min(), birth.max(), 1000) + plt.plot(x, x, color='k', linewidth=1.0) - # Make the plot - plt.pcolormesh(xi, yi, zi.reshape(xi.shape), cmap=cmap) + # Evaluate a gaussian kde on a regular grid of nbins x nbins over data extents + k = kde.gaussian_kde([birth,death], bw_method=bw_method) + xi, yi = np.mgrid[birth.min():birth.max():nbins*1j, death.min():death.max():nbins*1j] + zi = k(np.vstack([xi.flatten(), yi.flatten()])) - if legend: - plt.colorbar() + # default cmap value cannot be done at argument definition level as matplotlib is not yet defined. + if cmap is None: + cmap = plt.cm.hot_r + # Make the plot + plt.pcolormesh(xi, yi, zi.reshape(xi.shape), cmap=cmap) - plt.title('Persistence density') - plt.xlabel('Birth') - plt.ylabel('Death') - return plt + if legend: + plt.colorbar() - except ImportError: - # Continue in case of import error, functions won't be available - pass + plt.title('Persistence density') + plt.xlabel('Birth') + plt.ylabel('Death') + return plt -except ImportError: - # Continue in case of import error, functions won't be available - pass + except ImportError: + print("This function is not available, you may be missing numpy, matplotlib and/or scipy.") -- cgit v1.2.3 From 24683e8d0134e7ede7033f05b83c44dd72ff7e3a Mon Sep 17 00:00:00 2001 From: mcarrier Date: Tue, 18 Sep 2018 22:01:20 +0000 Subject: git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Nerve_GIC@3897 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: f5fe42a6f42443ca7217c69f8a18780cdb85669e --- src/Nerve_GIC/include/gudhi/GIC.h | 18 ++++++++++++++++++ src/cython/cython/nerve_gic.pyx | 9 +++++++++ 2 files changed, 27 insertions(+) (limited to 'src/cython') diff --git a/src/Nerve_GIC/include/gudhi/GIC.h b/src/Nerve_GIC/include/gudhi/GIC.h index 2c37dfae..242ecf7d 100644 --- a/src/Nerve_GIC/include/gudhi/GIC.h +++ b/src/Nerve_GIC/include/gudhi/GIC.h @@ -389,6 +389,24 @@ class Cover_complex { distances[index[boost::source(*ei, one_skeleton)]][index[boost::target(*ei, one_skeleton)]]); } + public: + /** \brief Reads and stores the distance matrices from vector stored in memory. + * + * @param[in] distance_matrix input vector representing the distance matrix. + * + */ + template + void set_distances_from_range(InputRange const & distance_matrix) { + n = distance_matrix.size(); data_dimension = 0; point_cloud_name = "matrix"; + for(int i = 0; i < n; i++){ + point_cloud.emplace_back(); + boost::add_vertex(one_skeleton_OFF); + vertices.push_back(boost::add_vertex(one_skeleton)); + cover.emplace_back(); + } + distances = distance_matrix; + } + public: // Pairwise distances. /** \private \brief Computes all pairwise distances. */ diff --git a/src/cython/cython/nerve_gic.pyx b/src/cython/cython/nerve_gic.pyx index 01dd0a4b..5f01b379 100644 --- a/src/cython/cython/nerve_gic.pyx +++ b/src/cython/cython/nerve_gic.pyx @@ -68,6 +68,7 @@ cdef extern from "Nerve_gic_interface.h" namespace "Gudhi": void plot_DOT() void plot_OFF() void set_point_cloud_from_range(vector[vector[double]] cloud) + void set_distances_from_range(vector[vector[double]] distance_matrix) # CoverComplex python interface cdef class CoverComplex: @@ -111,6 +112,14 @@ cdef class CoverComplex: """ return self.thisptr.set_point_cloud_from_range(cloud) + def set_distances_from_range(self, distance_matrix): + """ Reads and stores the input distance matrix from a vector stored in memory. + + :param distance_matrix: Input vector containing the distance matrix. + :type distance_matrix: vector[vector[double]] + """ + return self.thisptr.set_distances_from_range(distance_matrix) + def compute_confidence_level_from_distance(self, distance): """Computes the confidence level of a specific bottleneck distance threshold. -- cgit v1.2.3 From d95c0d8f3d28067527116a2c1eac06f5bf083995 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 28 Sep 2018 09:00:25 +0000 Subject: https://gitlab.inria.fr/GUDHI/gudhi-devel/issues/32 - [Cmake - Qt5] CMake outputs an error when Qt5 is not installed Modify/add cmake messages for missing modules git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cmake_missing_modules_clarification_vincent@3912 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 37e1035f7c27ce994e05386801d72959696de7d4 --- CMakeLists.txt | 12 +- src/CMakeLists.txt | 12 +- src/GudhUI/CMakeLists.txt | 81 ++- src/cmake/modules/GUDHI_doxygen_target.cmake | 8 +- src/cmake/modules/GUDHI_modules.cmake | 5 +- .../modules/GUDHI_third_party_libraries.cmake | 4 +- src/cython/CMakeLists.txt | 681 +++++++++++---------- 7 files changed, 434 insertions(+), 369 deletions(-) (limited to 'src/cython') diff --git a/CMakeLists.txt b/CMakeLists.txt index afacede9..d61df992 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -6,6 +6,10 @@ include(CMakeGUDHIVersion.txt) list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/src/cmake/modules/") +# Reset cache +set(GUDHI_MODULES "" CACHE INTERNAL "GUDHI_MODULES") +set(GUDHI_MISSING_MODULES "" CACHE INTERNAL "GUDHI_MISSING_MODULES") + # This variable is used by Cython CMakeLists.txt and by GUDHI_third_party_libraries to know its path set(GUDHI_CYTHON_PATH "src/cython") @@ -37,8 +41,6 @@ add_gudhi_module(Tangential_complex) add_gudhi_module(Witness_complex) add_gudhi_module(Nerve_GIC) -message("++ GUDHI_MODULES list is:\"${GUDHI_MODULES}\"") - # Include module CMake subdirectories # GUDHI_SUB_DIRECTORIES is managed in CMAKE_MODULE_PATH/GUDHI_modules.cmake foreach(GUDHI_MODULE ${GUDHI_MODULES}) @@ -54,9 +56,15 @@ add_subdirectory(src/GudhUI) if (WITH_GUDHI_PYTHON) # specific for cython module add_subdirectory(${GUDHI_CYTHON_PATH}) +else() + message("++ Python module will not be compiled because WITH_GUDHI_PYTHON is set to OFF") + set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python") endif() # For "make user_version" - Requires GUDHI_modules to be performed include(GUDHI_user_version_target) # For "make doxygen" - Requires GUDHI_USER_VERSION_DIR to be set - Done in GUDHI_user_version_target for dev version include(GUDHI_doxygen_target) + +message("++ GUDHI_MODULES list is:\"${GUDHI_MODULES}\"") +message("++ GUDHI_MISSING_MODULES list is:\"${GUDHI_MISSING_MODULES}\"") diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 6c446104..b40d506a 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -6,6 +6,9 @@ include(CMakeGUDHIVersion.txt) list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/modules/") +set(GUDHI_MODULES "" CACHE INTERNAL "GUDHI_MODULES") +set(GUDHI_MISSING_MODULES "" CACHE INTERNAL "GUDHI_MISSING_MODULES") + # This variable is used by Cython CMakeLists.txt and by GUDHI_third_party_libraries to know its path set(GUDHI_CYTHON_PATH "cython") @@ -35,8 +38,6 @@ add_gudhi_module(Tangential_complex) add_gudhi_module(Witness_complex) add_gudhi_module(Nerve_GIC) -message("++ GUDHI_MODULES list is:\"${GUDHI_MODULES}\"") - # For "make doxygen" - Requires GUDHI_USER_VERSION_DIR to be set set(GUDHI_USER_VERSION_DIR ${CMAKE_SOURCE_DIR}) include(GUDHI_doxygen_target) @@ -60,7 +61,14 @@ add_subdirectory(GudhUI) if (WITH_GUDHI_PYTHON) # specific for cython module add_subdirectory(${GUDHI_CYTHON_PATH}) +else() + message("++ Python module will not be compiled because WITH_GUDHI_PYTHON is set to OFF") + set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python") endif() + +message("++ GUDHI_MODULES list is:\"${GUDHI_MODULES}\"") +message("++ GUDHI_MISSING_MODULES list is:\"${GUDHI_MISSING_MODULES}\"") + #--------------------------------------------------------------------------------------- #--------------------------------------------------------------------------------------- diff --git a/src/GudhUI/CMakeLists.txt b/src/GudhUI/CMakeLists.txt index b357b8f7..0945e758 100644 --- a/src/GudhUI/CMakeLists.txt +++ b/src/GudhUI/CMakeLists.txt @@ -1,40 +1,55 @@ project(GudhUI) # Need to find OpenGL first as find_package(Qt5) tries to #include"GL/gl.h" on some platforms -find_package(OpenGL) +find_package(OpenGL QUIET) if (OPENGL_FOUND) - find_package(Qt5 COMPONENTS Widgets Xml OpenGL) - find_package(QGLViewer) - - if ( CGAL_FOUND AND Qt5_FOUND AND QGLVIEWER_FOUND AND NOT CGAL_VERSION VERSION_EQUAL 4.8.0) - - set(CMAKE_AUTOMOC ON) - set(CMAKE_AUTOUIC ON) - set(CMAKE_INCLUDE_CURRENT_DIR ON) - - SET(Boost_USE_STATIC_LIBS ON) - SET(Boost_USE_MULTITHREAD OFF) - include_directories (${QGLVIEWER_INCLUDE_DIR}) - - add_executable ( GudhUI - gui/gudhui.cpp - gui/MainWindow.cpp - gui/Menu_k_nearest_neighbors.cpp - gui/Menu_uniform_neighbors.cpp - gui/Menu_edge_contraction.cpp - gui/Menu_persistence.cpp - view/Viewer_instructor.cpp - view/Viewer.cpp - ) - target_link_libraries( GudhUI Qt5::Widgets Qt5::Xml Qt5::OpenGL ) - target_link_libraries( GudhUI ${QGLVIEWER_LIBRARIES} ) - target_link_libraries( GudhUI ${OPENGL_gl_LIBRARY} ${OPENGL_glu_LIBRARY} ) - if (TBB_FOUND) - target_link_libraries( GudhUI ${TBB_LIBRARIES}) + find_package(Qt5 COMPONENTS Widgets Xml OpenGL QUIET) + if (Qt5_FOUND) + find_package(QGLViewer QUIET) + if ( QGLVIEWER_FOUND) + + if ( CGAL_FOUND AND NOT CGAL_VERSION VERSION_EQUAL 4.8.0) + set(CMAKE_AUTOMOC ON) + set(CMAKE_AUTOUIC ON) + set(CMAKE_INCLUDE_CURRENT_DIR ON) + + SET(Boost_USE_STATIC_LIBS ON) + SET(Boost_USE_MULTITHREAD OFF) + include_directories (${QGLVIEWER_INCLUDE_DIR}) + + add_executable ( GudhUI + gui/gudhui.cpp + gui/MainWindow.cpp + gui/Menu_k_nearest_neighbors.cpp + gui/Menu_uniform_neighbors.cpp + gui/Menu_edge_contraction.cpp + gui/Menu_persistence.cpp + view/Viewer_instructor.cpp + view/Viewer.cpp + ) + target_link_libraries( GudhUI Qt5::Widgets Qt5::Xml Qt5::OpenGL ) + target_link_libraries( GudhUI ${QGLVIEWER_LIBRARIES} ) + target_link_libraries( GudhUI ${OPENGL_gl_LIBRARY} ${OPENGL_glu_LIBRARY} ) + if (TBB_FOUND) + target_link_libraries( GudhUI ${TBB_LIBRARIES}) + endif() + + install(TARGETS GudhUI DESTINATION bin) + set(GUDHI_MODULES ${GUDHI_MODULES} "GudhUI" CACHE INTERNAL "GUDHI_MODULES") + else() + message("++ GudhUI will not be compiled because CGAL < 4.8.0 or not found") + set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "GudhUI" CACHE INTERNAL "GUDHI_MISSING_MODULES") + endif() + else() + message("++ GudhUI will not be compiled because QGLViewer is not found") + set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "GudhUI" CACHE INTERNAL "GUDHI_MISSING_MODULES") endif() - - install(TARGETS GudhUI DESTINATION bin) - + else() + message("++ GudhUI will not be compiled because Qt5 COMPONENTS Widgets Xml OpenGL are not found") + set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "GudhUI" CACHE INTERNAL "GUDHI_MISSING_MODULES") endif() -endif(OPENGL_FOUND) +else() + message("++ GudhUI will not be compiled because OpenGL is not found") + set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "GudhUI" CACHE INTERNAL "GUDHI_MISSING_MODULES") +endif() diff --git a/src/cmake/modules/GUDHI_doxygen_target.cmake b/src/cmake/modules/GUDHI_doxygen_target.cmake index 9e10e566..7a84c4e0 100644 --- a/src/cmake/modules/GUDHI_doxygen_target.cmake +++ b/src/cmake/modules/GUDHI_doxygen_target.cmake @@ -1,7 +1,7 @@ # add a target to generate API documentation with Doxygen -find_package(Doxygen) +find_package(Doxygen QUIET) if(DOXYGEN_FOUND) - # configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile @ONLY) + set(GUDHI_MODULES ${GUDHI_MODULES} "cpp-documentation" CACHE INTERNAL "GUDHI_MODULES") # starting from cmake 3.9 the usage of DOXYGEN_EXECUTABLE is deprecated if(TARGET Doxygen::doxygen) @@ -16,4 +16,6 @@ if(DOXYGEN_FOUND) # In dev version, doxygen target depends on user_version target. Not existing in user version add_dependencies(doxygen user_version) endif() -endif(DOXYGEN_FOUND) +else() + set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "cpp-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES") +endif() diff --git a/src/cmake/modules/GUDHI_modules.cmake b/src/cmake/modules/GUDHI_modules.cmake index f95d0c34..aab1dd08 100644 --- a/src/cmake/modules/GUDHI_modules.cmake +++ b/src/cmake/modules/GUDHI_modules.cmake @@ -1,11 +1,12 @@ # A function to add a new module in GUDHI -set(GUDHI_MODULES "") set(GUDHI_MODULES_FULL_LIST "") function(add_gudhi_module file_path) option("WITH_MODULE_GUDHI_${file_path}" "Activate/desactivate ${file_path} compilation and installation" ON) if (WITH_MODULE_GUDHI_${file_path}) - set(GUDHI_MODULES ${GUDHI_MODULES} ${file_path} PARENT_SCOPE) + set(GUDHI_MODULES ${GUDHI_MODULES} ${file_path} CACHE INTERNAL "GUDHI_MODULES") + else() + set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} ${file_path} CACHE INTERNAL "GUDHI_MISSING_MODULES") endif() # Required by user_version set(GUDHI_MODULES_FULL_LIST ${GUDHI_MODULES_FULL_LIST} ${file_path} PARENT_SCOPE) diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake index f03c2177..122754d5 100644 --- a/src/cmake/modules/GUDHI_third_party_libraries.cmake +++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake @@ -21,11 +21,11 @@ endif() # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html # but it implies to use cmake version 3.1 at least. -find_package(CGAL) +find_package(CGAL QUIET) # Only CGAL versions > 4.4 supports what Gudhi uses from CGAL if (CGAL_VERSION VERSION_LESS 4.4.0) - message("CGAL version ${CGAL_VERSION} is considered too old to be used by Gudhi.") + message("++ CGAL version ${CGAL_VERSION} is considered too old to be used by Gudhi.") unset(CGAL_FOUND) endif() if(CGAL_FOUND) diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index 09ea28f1..8fcd6cbf 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -31,375 +31,406 @@ function( add_gudhi_debug_info DEBUG_INFO ) set(GUDHI_CYTHON_DEBUG_INFO "${GUDHI_CYTHON_DEBUG_INFO} \"${DEBUG_INFO}\\n\" \\\n" PARENT_SCOPE) endfunction( add_gudhi_debug_info ) - -if(CYTHON_FOUND) - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}off_reader;") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}simplex_tree;") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}rips_complex;") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}cubical_complex;") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}periodic_cubical_complex;") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}persistence_graphical_tools;") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}reader_utils;") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}witness_complex;") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}strong_witness_complex;") - - add_gudhi_debug_info("Python version ${PYTHON_VERSION_STRING}") - add_gudhi_debug_info("Cython version ${CYTHON_VERSION}") - if(PYTEST_FOUND) - add_gudhi_debug_info("Pytest version ${PYTEST_VERSION}") - endif() - if(MATPLOTLIB_FOUND) - add_gudhi_debug_info("Matplotlib version ${MATPLOTLIB_VERSION}") - endif() - if(NUMPY_FOUND) - add_gudhi_debug_info("Numpy version ${NUMPY_VERSION}") - endif() - if(MATPLOTLIB_FOUND AND NUMPY_FOUND) +if(PYTHONINTERP_FOUND) + if(CYTHON_FOUND) + set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}off_reader;") + set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}simplex_tree;") + set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}rips_complex;") + set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}cubical_complex;") + set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}periodic_cubical_complex;") set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}persistence_graphical_tools;") - else() - set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MODULES}persistence_graphical_tools;") - endif() + set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}reader_utils;") + set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}witness_complex;") + set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}strong_witness_complex;") + + add_gudhi_debug_info("Python version ${PYTHON_VERSION_STRING}") + add_gudhi_debug_info("Cython version ${CYTHON_VERSION}") + if(PYTEST_FOUND) + add_gudhi_debug_info("Pytest version ${PYTEST_VERSION}") + endif() + if(MATPLOTLIB_FOUND) + add_gudhi_debug_info("Matplotlib version ${MATPLOTLIB_VERSION}") + endif() + if(NUMPY_FOUND) + add_gudhi_debug_info("Numpy version ${NUMPY_VERSION}") + endif() + if(MATPLOTLIB_FOUND AND NUMPY_FOUND) + set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}persistence_graphical_tools;") + else() + set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MODULES}persistence_graphical_tools;") + endif() - message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_VERSION} - Sphinx is ${SPHINX_PATH}") - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_RESULT_OF_USE_DECLTYPE', ") - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ") - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_SYSTEM_NO_DEPRECATED', ") - - # Gudhi and CGAL compilation option - if(MSVC) - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'/fp:strict', ") - else(MSVC) - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-std=c++11', ") - endif(MSVC) - if(CMAKE_COMPILER_IS_GNUCXX) - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-frounding-math', ") - endif(CMAKE_COMPILER_IS_GNUCXX) - if (CMAKE_CXX_COMPILER_ID MATCHES Intel) - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-fp-model strict', ") - endif(CMAKE_CXX_COMPILER_ID MATCHES Intel) - if (DEBUG_TRACES) - # For programs to be more verbose - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DDEBUG_TRACES', ") - endif() + message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_VERSION} - Sphinx is ${SPHINX_PATH}") + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_RESULT_OF_USE_DECLTYPE', ") + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ") + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_SYSTEM_NO_DEPRECATED', ") + + # Gudhi and CGAL compilation option + if(MSVC) + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'/fp:strict', ") + else(MSVC) + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-std=c++11', ") + endif(MSVC) + if(CMAKE_COMPILER_IS_GNUCXX) + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-frounding-math', ") + endif(CMAKE_COMPILER_IS_GNUCXX) + if (CMAKE_CXX_COMPILER_ID MATCHES Intel) + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-fp-model strict', ") + endif(CMAKE_CXX_COMPILER_ID MATCHES Intel) + if (DEBUG_TRACES) + # For programs to be more verbose + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DDEBUG_TRACES', ") + endif() - if (EIGEN3_FOUND) - add_gudhi_debug_info("Eigen3 version ${EIGEN3_VERSION}") - # No problem, even if no CGAL found - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ") - endif (EIGEN3_FOUND) - - if (NOT CGAL_VERSION VERSION_LESS 4.8.1) - set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}bottleneck_distance;") - set(GUDHI_CYTHON_NERVE_GIC "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/nerve_gic.pyx'") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}nerve_gic;") - else() - set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}bottleneck_distance;") - set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}nerve_gic;") - endif () - if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) - set(GUDHI_CYTHON_SUBSAMPLING "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/subsampling.pyx'") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}subsampling;") - set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/tangential_complex.pyx'") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}tangential_complex;") - else() - set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}subsampling;") - set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}tangential_complex;") - endif () - if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) - set(GUDHI_CYTHON_ALPHA_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/alpha_complex.pyx'") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}alpha_complex;") - else() - set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}alpha_complex;") - endif () - if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) - set(GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX - "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_witness_complex.pyx'\ninclude '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_strong_witness_complex.pyx'\n") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}euclidean_witness_complex;") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}euclidean_strong_witness_complex;") - else() - set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}euclidean_witness_complex;") - set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}euclidean_strong_witness_complex;") - endif () - - add_gudhi_debug_info("Installed modules are: ${GUDHI_CYTHON_MODULES}") - if(GUDHI_CYTHON_MISSING_MODULES) - add_gudhi_debug_info("Missing modules are: ${GUDHI_CYTHON_MISSING_MODULES}") - endif() + if (EIGEN3_FOUND) + add_gudhi_debug_info("Eigen3 version ${EIGEN3_VERSION}") + # No problem, even if no CGAL found + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ") + endif (EIGEN3_FOUND) + + if (NOT CGAL_VERSION VERSION_LESS 4.8.1) + set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'") + set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}bottleneck_distance;") + set(GUDHI_CYTHON_NERVE_GIC "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/nerve_gic.pyx'") + set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}nerve_gic;") + else() + set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}bottleneck_distance;") + set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}nerve_gic;") + endif () + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + set(GUDHI_CYTHON_SUBSAMPLING "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/subsampling.pyx'") + set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}subsampling;") + set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/tangential_complex.pyx'") + set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}tangential_complex;") + else() + set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}subsampling;") + set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}tangential_complex;") + endif () + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) + set(GUDHI_CYTHON_ALPHA_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/alpha_complex.pyx'") + set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}alpha_complex;") + else() + set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}alpha_complex;") + endif () + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) + set(GUDHI_CYTHON_EUCLIDEAN_WITNESS_COMPLEX + "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_witness_complex.pyx'\ninclude '${CMAKE_CURRENT_SOURCE_DIR}/cython/euclidean_strong_witness_complex.pyx'\n") + set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}euclidean_witness_complex;") + set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}euclidean_strong_witness_complex;") + else() + set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}euclidean_witness_complex;") + set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MISSING_MODULES}euclidean_strong_witness_complex;") + endif () - if(CGAL_FOUND) - can_cgal_use_cxx11_thread_local() - if (NOT CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT) - if(CMAKE_BUILD_TYPE MATCHES Debug) - add_gudhi_cython_lib("${Boost_THREAD_LIBRARY_DEBUG}") - else() - add_gudhi_cython_lib("${Boost_THREAD_LIBRARY_RELEASE}") - endif() - set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ") + add_gudhi_debug_info("Installed modules are: ${GUDHI_CYTHON_MODULES}") + if(GUDHI_CYTHON_MISSING_MODULES) + add_gudhi_debug_info("Missing modules are: ${GUDHI_CYTHON_MISSING_MODULES}") endif() - # Add CGAL compilation args - if(CGAL_HEADER_ONLY) - add_gudhi_debug_info("CGAL header only version ${CGAL_VERSION}") - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ") - else(CGAL_HEADER_ONLY) - add_gudhi_debug_info("CGAL version ${CGAL_VERSION}") - add_gudhi_cython_lib("${CGAL_LIBRARY}") - set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ") - # If CGAL is not header only, CGAL library may link with boost system, + + if(CGAL_FOUND) + can_cgal_use_cxx11_thread_local() + if (NOT CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT) + if(CMAKE_BUILD_TYPE MATCHES Debug) + add_gudhi_cython_lib("${Boost_THREAD_LIBRARY_DEBUG}") + else() + add_gudhi_cython_lib("${Boost_THREAD_LIBRARY_RELEASE}") + endif() + set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ") + endif() + # Add CGAL compilation args + if(CGAL_HEADER_ONLY) + add_gudhi_debug_info("CGAL header only version ${CGAL_VERSION}") + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ") + else(CGAL_HEADER_ONLY) + add_gudhi_debug_info("CGAL version ${CGAL_VERSION}") + add_gudhi_cython_lib("${CGAL_LIBRARY}") + set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ") + # If CGAL is not header only, CGAL library may link with boost system, + if(CMAKE_BUILD_TYPE MATCHES Debug) + add_gudhi_cython_lib("${Boost_SYSTEM_LIBRARY_DEBUG}") + else() + add_gudhi_cython_lib("${Boost_SYSTEM_LIBRARY_RELEASE}") + endif() + set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ") + endif(CGAL_HEADER_ONLY) + # GMP and GMPXX are not required, but if present, CGAL will link with them. + if(GMP_FOUND) + add_gudhi_debug_info("GMP_LIBRARIES = ${GMP_LIBRARIES}") + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMP', ") + add_gudhi_cython_lib("${GMP_LIBRARIES}") + set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMP_LIBRARIES_DIR}', ") + if(GMPXX_FOUND) + add_gudhi_debug_info("GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}") + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMPXX', ") + add_gudhi_cython_lib("${GMPXX_LIBRARIES}") + set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMPXX_LIBRARIES_DIR}', ") + endif(GMPXX_FOUND) + endif(GMP_FOUND) + endif(CGAL_FOUND) + + # Specific for Mac + if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin") + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-mmacosx-version-min=10.12', ") + set(GUDHI_CYTHON_EXTRA_LINK_ARGS "${GUDHI_CYTHON_EXTRA_LINK_ARGS}'-mmacosx-version-min=10.12', ") + endif(${CMAKE_SYSTEM_NAME} MATCHES "Darwin") + + # Loop on INCLUDE_DIRECTORIES PROPERTY + get_property(GUDHI_INCLUDE_DIRECTORIES DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY INCLUDE_DIRECTORIES) + foreach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES}) + set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${GUDHI_INCLUDE_DIRECTORY}', ") + endforeach() + set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/include', ") + + if (TBB_FOUND AND WITH_GUDHI_USE_TBB) + add_gudhi_debug_info("TBB version ${TBB_INTERFACE_VERSION} found and used") + set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_TBB', ") if(CMAKE_BUILD_TYPE MATCHES Debug) - add_gudhi_cython_lib("${Boost_SYSTEM_LIBRARY_DEBUG}") + add_gudhi_cython_lib("${TBB_DEBUG_LIBRARY}") + add_gudhi_cython_lib("${TBB_MALLOC_DEBUG_LIBRARY}") else() - add_gudhi_cython_lib("${Boost_SYSTEM_LIBRARY_RELEASE}") + add_gudhi_cython_lib("${TBB_RELEASE_LIBRARY}") + add_gudhi_cython_lib("${TBB_MALLOC_RELEASE_LIBRARY}") endif() - set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ") - endif(CGAL_HEADER_ONLY) - # GMP and GMPXX are not required, but if present, CGAL will link with them. - if(GMP_FOUND) - add_gudhi_debug_info("GMP_LIBRARIES = ${GMP_LIBRARIES}") - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMP', ") - add_gudhi_cython_lib("${GMP_LIBRARIES}") - set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMP_LIBRARIES_DIR}', ") - if(GMPXX_FOUND) - add_gudhi_debug_info("GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}") - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMPXX', ") - add_gudhi_cython_lib("${GMPXX_LIBRARIES}") - set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMPXX_LIBRARIES_DIR}', ") - endif(GMPXX_FOUND) - endif(GMP_FOUND) - endif(CGAL_FOUND) - - # Specific for Mac - if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin") - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-mmacosx-version-min=10.12', ") - set(GUDHI_CYTHON_EXTRA_LINK_ARGS "${GUDHI_CYTHON_EXTRA_LINK_ARGS}'-mmacosx-version-min=10.12', ") - endif(${CMAKE_SYSTEM_NAME} MATCHES "Darwin") - - # Loop on INCLUDE_DIRECTORIES PROPERTY - get_property(GUDHI_INCLUDE_DIRECTORIES DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY INCLUDE_DIRECTORIES) - foreach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES}) - set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${GUDHI_INCLUDE_DIRECTORY}', ") - endforeach() - set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/include', ") - - if (TBB_FOUND AND WITH_GUDHI_USE_TBB) - add_gudhi_debug_info("TBB version ${TBB_INTERFACE_VERSION} found and used") - set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_TBB', ") - if(CMAKE_BUILD_TYPE MATCHES Debug) - add_gudhi_cython_lib("${TBB_DEBUG_LIBRARY}") - add_gudhi_cython_lib("${TBB_MALLOC_DEBUG_LIBRARY}") - else() - add_gudhi_cython_lib("${TBB_RELEASE_LIBRARY}") - add_gudhi_cython_lib("${TBB_MALLOC_RELEASE_LIBRARY}") + set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${TBB_LIBRARY_DIRS}', ") + set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${TBB_INCLUDE_DIRS}', ") endif() - set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${TBB_LIBRARY_DIRS}', ") - set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${TBB_INCLUDE_DIRS}', ") - endif() - if(UNIX) - set( GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}") - endif(UNIX) - - # Generate setup.py file to cythonize Gudhi - This file must be named setup.py by convention - configure_file(setup.py.in "${CMAKE_CURRENT_BINARY_DIR}/setup.py" @ONLY) - # Generate gudhi.pyx - Gudhi cython file - configure_file(gudhi.pyx.in "${CMAKE_CURRENT_BINARY_DIR}/gudhi.pyx" @ONLY) - - add_custom_command( - OUTPUT gudhi.so - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/setup.py" "build_ext" "--inplace") - - add_custom_target(cython ALL DEPENDS gudhi.so - COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests") - - # For installation purpose - # TODO(VR) : files matching pattern mechanism is copying all cython directory - install(DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}" DESTINATION "${PYTHON_SITE_PACKAGES}/" FILES_MATCHING - PATTERN "*.so" - PATTERN "*.dylib" - PATTERN "*.pyd") - - # Test examples - if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) - # Bottleneck and Alpha - add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py" - -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3) + if(UNIX) + set( GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}") + endif(UNIX) + + # Generate setup.py file to cythonize Gudhi - This file must be named setup.py by convention + configure_file(setup.py.in "${CMAKE_CURRENT_BINARY_DIR}/setup.py" @ONLY) + # Generate gudhi.pyx - Gudhi cython file + configure_file(gudhi.pyx.in "${CMAKE_CURRENT_BINARY_DIR}/gudhi.pyx" @ONLY) + + add_custom_command( + OUTPUT gudhi.so + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/setup.py" "build_ext" "--inplace") + + add_custom_target(cython ALL DEPENDS gudhi.so + COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests") + + # For installation purpose + # TODO(VR) : files matching pattern mechanism is copying all cython directory + install(DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}" DESTINATION "${PYTHON_SITE_PACKAGES}/" FILES_MATCHING + PATTERN "*.so" + PATTERN "*.dylib" + PATTERN "*.pyd") + + # Test examples + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + # Bottleneck and Alpha + add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py" + -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3) + + if(MATPLOTLIB_FOUND AND NUMPY_FOUND) + # Tangential + add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py" + --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off) + + add_gudhi_py_test(test_tangential_complex) + + # Witness complex AND Subsampling + add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) + + add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) + endif() - if(MATPLOTLIB_FOUND AND NUMPY_FOUND) - # Tangential - add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test + # Subsampling + add_gudhi_py_test(test_subsampling) + + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + if (NOT CGAL_VERSION VERSION_LESS 4.8.1) + # Bottleneck + add_test(NAME bottleneck_basic_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py" - --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off) + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py") - add_gudhi_py_test(test_tangential_complex) + add_gudhi_py_test(test_bottleneck_distance) - # Witness complex AND Subsampling - add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test + # Cover complex + file(COPY ${CMAKE_SOURCE_DIR}/data/points/human.off DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + file(COPY ${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat.off DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + file(COPY ${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1 DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + add_test(NAME cover_complex_nerve_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/nerve_of_a_covering.py" + -f human.off -c 2 -r 10 -g 0.3) - add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test + add_test(NAME cover_complex_coordinate_gic_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2) - endif() + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/coordinate_graph_induced_complex.py" + -f human.off -c 0 -v) - # Subsampling - add_gudhi_py_test(test_subsampling) + add_test(NAME cover_complex_functional_gic_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/functional_graph_induced_complex.py" + -o lucky_cat.off + -f lucky_cat_PCA1 -v) - endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) - if (NOT CGAL_VERSION VERSION_LESS 4.8.1) - # Bottleneck - add_test(NAME bottleneck_basic_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py") + add_test(NAME cover_complex_voronoi_gic_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/voronoi_graph_induced_complex.py" + -f human.off -n 700 -v) - add_gudhi_py_test(test_bottleneck_distance) + add_gudhi_py_test(test_cover_complex) + endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) - # Cover complex - file(COPY ${CMAKE_SOURCE_DIR}/data/points/human.off DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - file(COPY ${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat.off DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - file(COPY ${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1 DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - add_test(NAME cover_complex_nerve_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/nerve_of_a_covering.py" - -f human.off -c 2 -r 10 -g 0.3) + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) + # Alpha + add_test(NAME alpha_complex_from_points_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py") - add_test(NAME cover_complex_coordinate_gic_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/coordinate_graph_induced_complex.py" - -f human.off -c 0 -v) + if(MATPLOTLIB_FOUND AND NUMPY_FOUND) + add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6) + endif() - add_test(NAME cover_complex_functional_gic_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/functional_graph_induced_complex.py" - -o lucky_cat.off - -f lucky_cat_PCA1 -v) + add_gudhi_py_test(test_alpha_complex) - add_test(NAME cover_complex_voronoi_gic_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/voronoi_graph_induced_complex.py" - -f human.off -n 700 -v) + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) - add_gudhi_py_test(test_cover_complex) - endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) + # Euclidean witness + add_gudhi_py_test(test_euclidean_witness_complex) - if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) - # Alpha - add_test(NAME alpha_complex_from_points_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py") + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) - if(MATPLOTLIB_FOUND AND NUMPY_FOUND) - add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test + # Cubical + add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6) - endif() - - add_gudhi_py_test(test_alpha_complex) + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py" + --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt) - endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) + if(NUMPY_FOUND) + add_test(NAME random_cubical_complex_persistence_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py" + 10 10 10) + endif() - if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) - # Euclidean witness - add_gudhi_py_test(test_euclidean_witness_complex) + add_gudhi_py_test(test_cubical_complex) - endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) + # Rips + if(MATPLOTLIB_FOUND AND NUMPY_FOUND) + add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py" + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3) - # Cubical - add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py" - --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt) + add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py + --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -e 0.25 -d 3) + endif() - if(NUMPY_FOUND) - add_test(NAME random_cubical_complex_persistence_example_py_test + add_test(NAME rips_complex_from_points_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py" - 10 10 10) - endif() + ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py) - add_gudhi_py_test(test_cubical_complex) + add_gudhi_py_test(test_rips_complex) - # Rips - if(MATPLOTLIB_FOUND AND NUMPY_FOUND) - add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py" - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3) - - add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test + # Simplex tree + add_test(NAME simplex_tree_example_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py - --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -e 0.25 -d 3) - endif() - - add_test(NAME rips_complex_from_points_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py) - - add_gudhi_py_test(test_rips_complex) - - # Simplex tree - add_test(NAME simplex_tree_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py) - - add_gudhi_py_test(test_simplex_tree) + ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py) - # Witness - add_test(NAME witness_complex_from_nearest_landmark_table_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py) + add_gudhi_py_test(test_simplex_tree) - add_gudhi_py_test(test_witness_complex) - - # Reader utils - add_gudhi_py_test(test_reader_utils) - - # Documentation generation is available through sphinx - requires all modules - if(SPHINX_PATH AND MATPLOTLIB_FOUND AND NUMPY_FOUND AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) - set (GUDHI_SPHINX_MESSAGE "Generating API documentation with Sphinx in ${CMAKE_CURRENT_BINARY_DIR}/sphinx/") - # User warning - Sphinx is a static pages generator, and configured to work fine with user_version - # Images and biblio warnings because not found on developper version - if (GUDHI_CYTHON_PATH STREQUAL "src/cython") - set (GUDHI_SPHINX_MESSAGE "${GUDHI_SPHINX_MESSAGE} \n WARNING : Sphinx is configured for user version, you run it on developper version. Images and biblio will miss") - endif() - # sphinx target requires gudhi.so, because conf.py reads gudhi version from it - add_custom_target(sphinx - WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc - COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/sphinx - DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so" - COMMENT "${GUDHI_SPHINX_MESSAGE}" VERBATIM) - - add_test(NAME sphinx_py_test + # Witness + add_test(NAME witness_complex_from_nearest_landmark_table_py_test WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" - ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/doctest) - - endif() -endif(CYTHON_FOUND) + ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py) + + add_gudhi_py_test(test_witness_complex) + + # Reader utils + add_gudhi_py_test(test_reader_utils) + + # Documentation generation is available through sphinx - requires all modules + if(SPHINX_PATH) + if(MATPLOTLIB_FOUND) + if(NUMPY_FOUND) + if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + set (GUDHI_SPHINX_MESSAGE "Generating API documentation with Sphinx in ${CMAKE_CURRENT_BINARY_DIR}/sphinx/") + # User warning - Sphinx is a static pages generator, and configured to work fine with user_version + # Images and biblio warnings because not found on developper version + if (GUDHI_CYTHON_PATH STREQUAL "src/cython") + set (GUDHI_SPHINX_MESSAGE "${GUDHI_SPHINX_MESSAGE} \n WARNING : Sphinx is configured for user version, you run it on developper version. Images and biblio will miss") + endif() + # sphinx target requires gudhi.so, because conf.py reads gudhi version from it + add_custom_target(sphinx + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/sphinx + DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so" + COMMENT "${GUDHI_SPHINX_MESSAGE}" VERBATIM) + + add_test(NAME sphinx_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}" + ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/doctest) + + # Set missing or not modules + set(GUDHI_MODULES ${GUDHI_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MODULES") + else(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + message("++ Python documentation module will not be compiled because it requires a CGAL with Eigen3 version greater or equal than 4.8.1") + set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES") + endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + else(NUMPY_FOUND) + message("++ Python module will not be compiled because numpy was not found") + set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES") + endif(NUMPY_FOUND) + else(MATPLOTLIB_FOUND) + message("++ Python module will not be compiled because matplotlib was not found") + set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES") + endif(MATPLOTLIB_FOUND) + else(SPHINX_PATH) + message("++ Python module will not be compiled because sphinx and sphinxcontrib-bibtex were not found") + set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES") + endif(SPHINX_PATH) + + + # Set missing or not modules + set(GUDHI_MODULES ${GUDHI_MODULES} "python" CACHE INTERNAL "GUDHI_MODULES") + else(CYTHON_FOUND) + message("++ Python module will not be compiled because cython was not found") + set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python" CACHE INTERNAL "GUDHI_MISSING_MODULES") + endif(CYTHON_FOUND) +else(PYTHONINTERP_FOUND) + message("++ Python module will not be compiled because no Python interpreter was found") + set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python" CACHE INTERNAL "GUDHI_MISSING_MODULES") +endif(PYTHONINTERP_FOUND) -- cgit v1.2.3 From 2ca563e4e1a12443773cd58ab65ef65286bc31dd Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 28 Sep 2018 09:14:37 +0000 Subject: Python Nerve and Graph Induced Complex was introduced in GUDHI 2.3.0 (not 2.1.0) git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3914 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 8e34cf876daf73288caed371c7ce9c51f07fbf7f --- src/cython/doc/nerve_gic_complex_sum.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'src/cython') diff --git a/src/cython/doc/nerve_gic_complex_sum.rst b/src/cython/doc/nerve_gic_complex_sum.rst index 72782c7a..523c119f 100644 --- a/src/cython/doc/nerve_gic_complex_sum.rst +++ b/src/cython/doc/nerve_gic_complex_sum.rst @@ -1,5 +1,5 @@ ================================================================= =================================== =================================== -:Author: Mathieu Carrière :Introduced in: GUDHI 2.1.0 :Copyright: GPL v3 +:Author: Mathieu Carrière :Introduced in: GUDHI 2.3.0 :Copyright: GPL v3 :Requires: CGAL :math:`\geq` 4.8.1 ================================================================= =================================== =================================== -- cgit v1.2.3 From 338b2f41bd14f04193a0b2f6fb0a2321443be45b Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 2 Oct 2018 07:45:51 +0000 Subject: Doc review: max_intervals documentation in plot_persistence_density git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3917 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 90cfd77ad4aad4cdb0937f43dd4f802688f98295 --- src/cython/cython/persistence_graphical_tools.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'src/cython') diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py index e66643d2..139a2332 100755 --- a/src/cython/cython/persistence_graphical_tools.py +++ b/src/cython/cython/persistence_graphical_tools.py @@ -269,7 +269,8 @@ def plot_persistence_density(persistence=[], persistence_file='', `_ for more details. :type bw_method: str, scalar or callable, optional. - :param max_intervals: maximal number of intervals to display. + :param max_intervals: maximal number of points used in the density + estimation. Selected points are those with the longest life time. Set it to 0 to see all. Default value is 1000. :type max_intervals: int. -- cgit v1.2.3 From 5469c3637df2efd1a70a165484b992727782d15c Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 2 Oct 2018 07:51:22 +0000 Subject: Doc review : "Selected points are" -> "Selected intervals are" git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3918 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 79857a4609428fc623f8f4656762261ea664cf12 --- src/cython/cython/persistence_graphical_tools.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'src/cython') diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py index 139a2332..abc205bb 100755 --- a/src/cython/cython/persistence_graphical_tools.py +++ b/src/cython/cython/persistence_graphical_tools.py @@ -70,7 +70,7 @@ def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, opaque - default is 0.6). :type alpha: float. :param max_intervals: maximal number of intervals to display. - Selected points are those with the longest life time. Set it + Selected intervals are those with the longest life time. Set it to 0 to see all. Default value is 1000. :type max_intervals: int. :param inf_delta: Infinity is placed at ((max_death - min_birth) x @@ -162,7 +162,7 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, :param band: band (not displayed if :math:`\leq` 0. - default is 0.) :type band: float. :param max_intervals: maximal number of intervals to display. - Selected points are those with the longest life time. Set it + Selected intervals are those with the longest life time. Set it to 0 to see all. Default value is 1000. :type max_intervals: int. :param inf_delta: Infinity is placed at ((max_death - min_birth) x @@ -271,7 +271,7 @@ def plot_persistence_density(persistence=[], persistence_file='', :type bw_method: str, scalar or callable, optional. :param max_intervals: maximal number of points used in the density estimation. - Selected points are those with the longest life time. Set it + Selected intervals are those with the longest life time. Set it to 0 to see all. Default value is 1000. :type max_intervals: int. :param dimension: the dimension to be selected in the intervals -- cgit v1.2.3 From b4c51b3d92564e2e93e8fa4fe55f98cd06bba57a Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 2 Oct 2018 08:13:28 +0000 Subject: Code review : remove executable property Doc review : Rephrase inf_delta explanation git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3919 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: b45697b675a20cdca7bb42fa7a555df6c35fe0fd --- src/cython/cython/persistence_graphical_tools.py | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) mode change 100755 => 100644 src/cython/cython/persistence_graphical_tools.py (limited to 'src/cython') diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py old mode 100755 new mode 100644 index abc205bb..e63b350b --- a/src/cython/cython/persistence_graphical_tools.py +++ b/src/cython/cython/persistence_graphical_tools.py @@ -61,7 +61,7 @@ def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, """This function plots the persistence bar code from persistence values list or from a :doc:`persistence file `. - :param persistence: Persistence values list. + :param persistence: Persistence intervals values list grouped by dimension. :type persistence: list of tuples(dimension, tuple(birth, death)). :param persistence_file: A :doc:`persistence file ` style name (reset persistence if both are set). @@ -73,9 +73,9 @@ def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, Selected intervals are those with the longest life time. Set it to 0 to see all. Default value is 1000. :type max_intervals: int. - :param inf_delta: Infinity is placed at ((max_death - min_birth) x - inf_delta) above the highest point. A reasonable value is between - 0.05 and 0.5 - default is 0.1. + :param inf_delta: Infinity is placed at :code:`((max_death - min_birth) x + inf_delta)` above :code:`max_death` value. A reasonable value is + between 0.05 and 0.5 - default is 0.1. :type inf_delta: float. :param legend: Display the dimension color legend (default is False). :type legend: boolean. @@ -151,7 +151,7 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, """This function plots the persistence diagram from persistence values list or from a :doc:`persistence file `. - :param persistence: Persistence values list. + :param persistence: Persistence intervals values list grouped by dimension. :type persistence: list of tuples(dimension, tuple(birth, death)). :param persistence_file: A :doc:`persistence file ` style name (reset persistence if both are set). @@ -165,9 +165,9 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, Selected intervals are those with the longest life time. Set it to 0 to see all. Default value is 1000. :type max_intervals: int. - :param inf_delta: Infinity is placed at ((max_death - min_birth) x - inf_delta) above the highest point. A reasonable value is between - 0.05 and 0.5 - default is 0.1. + :param inf_delta: Infinity is placed at :code:`((max_death - min_birth) x + inf_delta)` above :code:`max_death` value. A reasonable value is + between 0.05 and 0.5 - default is 0.1. :type inf_delta: float. :param legend: Display the dimension color legend (default is False). :type legend: boolean. @@ -251,7 +251,7 @@ def plot_persistence_density(persistence=[], persistence_file='', aware that this function does not distinguish the dimension, it is up to you to select the required one. - :param persistence: Persistence values list. + :param persistence: Persistence intervals values list grouped by dimension. :type persistence: list of tuples(dimension, tuple(birth, death)). :param persistence_file: A :doc:`persistence file ` style name (reset persistence if both are set). -- cgit v1.2.3 From 2dde0fc4ea8f24173789a1ce9a9442cb02b96e86 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 2 Oct 2018 08:23:51 +0000 Subject: Doc review : Explain that plot persistence density function doesn't handle degenerate data git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3920 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 7794f7959b98b0245e26077d2f2639f33655d5c9 --- src/cython/cython/persistence_graphical_tools.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'src/cython') diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py index e63b350b..d7be936f 100644 --- a/src/cython/cython/persistence_graphical_tools.py +++ b/src/cython/cython/persistence_graphical_tools.py @@ -249,7 +249,8 @@ def plot_persistence_density(persistence=[], persistence_file='', """This function plots the persistence density from persistence values list or from a :doc:`persistence file `. Be aware that this function does not distinguish the dimension, it is - up to you to select the required one. + up to you to select the required one. This function also does not handle + degenerate data set (scipy correlation matrix inversion can fail). :param persistence: Persistence intervals values list grouped by dimension. :type persistence: list of tuples(dimension, tuple(birth, death)). -- cgit v1.2.3 From 42e599ebd89231c276a3c6e1b9121ea13f25d118 Mon Sep 17 00:00:00 2001 From: glisse Date: Tue, 2 Oct 2018 09:21:13 +0000 Subject: More doc changes for python sparse rips git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/sparserips-python@3921 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: f9a33e3c4a6fc6d68a81b753a88ff9d39bdcfb9f --- biblio/bibliography.bib | 3 +- src/Rips_complex/doc/Intro_rips_complex.h | 2 +- src/cython/cython/rips_complex.pyx | 3 +- src/cython/doc/rips_complex_user.rst | 52 ++++++++++++++++++++----------- 4 files changed, 38 insertions(+), 22 deletions(-) (limited to 'src/cython') diff --git a/biblio/bibliography.bib b/biblio/bibliography.bib index 16f43d6f..e85876d3 100644 --- a/biblio/bibliography.bib +++ b/biblio/bibliography.bib @@ -1073,9 +1073,10 @@ language={English} @article{buchet16efficient, title = {Efficient and Robust Persistent Homology for Measures}, author = {Micka\"{e}l Buchet and Fr\'{e}d\'{e}ric Chazal and Steve Y. Oudot and Donald Sheehy}, - booktitle = {Computational Geometry: Theory and Applications}, + journal = {Computational Geometry: Theory and Applications}, volume = {58}, pages = {70--96}, + doi = "https://doi.org/10.1016/j.comgeo.2016.07.001", year = {2016} } diff --git a/src/Rips_complex/doc/Intro_rips_complex.h b/src/Rips_complex/doc/Intro_rips_complex.h index 3db5287e..e54ae57c 100644 --- a/src/Rips_complex/doc/Intro_rips_complex.h +++ b/src/Rips_complex/doc/Intro_rips_complex.h @@ -39,7 +39,7 @@ namespace rips_complex { * (Wikipedia) * is an abstract simplicial complex * defined on a finite metric space, where each simplex corresponds to a subset - * of point whose diameter is smaller that some given threshold. + * of points whose diameter is smaller that some given threshold. * Varying the threshold, we can also see the Rips complex as a filtration of * the \f$(n-1)-\f$dimensional simplex, where the filtration value of each * simplex is the diameter of the corresponding subset of points. diff --git a/src/cython/cython/rips_complex.pyx b/src/cython/cython/rips_complex.pyx index 620130ca..ecf039b6 100644 --- a/src/cython/cython/rips_complex.pyx +++ b/src/cython/cython/rips_complex.pyx @@ -62,8 +62,7 @@ cdef class RipsComplex: Or - :param distance_matrix: A distance matrix (full square or lower - triangular). + :param distance_matrix: A distance matrix (full square or lower triangular). :type points: list of list of double And in both cases diff --git a/src/cython/doc/rips_complex_user.rst b/src/cython/doc/rips_complex_user.rst index a8c06cf9..9fa3a677 100644 --- a/src/cython/doc/rips_complex_user.rst +++ b/src/cython/doc/rips_complex_user.rst @@ -7,27 +7,22 @@ Rips complex user manual Definition ---------- -======================================================= ===================================== ===================================== -:Authors: Clément Maria, Pawel Dlotko, Vincent Rouvreau :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 -======================================================= ===================================== ===================================== +==================================================================== ================================ ====================== +:Authors: Clément Maria, Pawel Dlotko, Vincent Rouvreau, Marc Glisse :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 +==================================================================== ================================ ====================== +-------------------------------------------+----------------------------------------------------------------------+ | :doc:`rips_complex_user` | :doc:`rips_complex_ref` | +-------------------------------------------+----------------------------------------------------------------------+ -`Rips complex `_ is a one skeleton graph that allows to -construct a simplicial complex from it. The input can be a point cloud with a given distance function, or a distance -matrix. +The `Rips complex `_ is a simplicial complex defined as the clique complex of a graph. The graph is defined on a set of points with one vertex for each point and an edge between any 2 points, of weight (aka filtration value) the distance between the 2 points. This graph (and thus the complex) can be restricted to edges shorter than some threshold, to reduce its size. -The filtration value of each edge is computed from a user-given distance function, or directly from the distance -matrix. +The input discrete metric space can be provided as a point cloud plus a distance function, or as a distance matrix. -All edges that have a filtration value strictly greater than a given threshold value are not inserted into the complex. +When creating a simplicial complex from the graph, `RipsComplex` inserts the graph into the data +structure, and then expands the simplicial complex (adds the simplices corresponding to cliques) when required. The expansion can be stopped at dimension `max_dimension`, by default 1. -When creating a simplicial complex from this one skeleton graph, Rips inserts the one skeleton graph into the data -structure, and then expands the simplicial complex when required. - -Vertex name correspond to the index of the point in the given range (aka. the point cloud). +A vertex name corresponds to the index of the point in the given range (aka. the point cloud). .. figure:: ../../doc/Rips_complex/rips_complex_representation.png @@ -38,8 +33,27 @@ Vertex name correspond to the index of the point in the given range (aka. the po On this example, as edges (4,5), (4,6) and (5,6) are in the complex, simplex (4,5,6) is added with the filtration value set with :math:`max(filtration(4,5), filtration(4,6), filtration(5,6))`. And so on for simplex (0,1,2,3). -If the Rips_complex interfaces are not detailed enough for your need, please refer to rips_persistence_step_by_step.cpp -example, where the graph construction over the Simplex_tree is more detailed. +If the `RipsComplex` interfaces are not detailed enough for your need, please refer to rips_persistence_step_by_step.cpp +C++ example, where the graph construction over the Simplex_tree is more detailed. + +A Rips complex can easily become huge, even if we limit the length of the edges +and the dimension of the simplices. One easy trick, before building a Rips +complex on a point cloud, is to call `sparsify_point_set` which removes points +that are too close to each other. This does not change its persistence diagram +by more than the length used to define "too close". + +A more general technique is to use a sparse approximation of the Rips +introduced by Don Sheehy :cite:`sheehy13linear`. We are using the version +described in :cite:`buchet16efficient` (except that we multiply all filtration +values by 2, to match the usual Rips complex), which proves a +:math:`\frac{1+\epsilon}{1-\epsilon}`-interleaving, although in practice the +error is usually smaller. A more intuitive presentation of the idea is +available in :cite:`cavanna15geometric`, and in a video +:cite:`cavanna15visualizing`. Passing an extra argument `sparse=0.3` at the +construction of a `RipsComplex` object asks it to build a sparse Rips with +parameter `ε=0.3`, while the default `sparse=None` builds the +regular Rips complex. + Point cloud ----------- @@ -47,7 +61,7 @@ Point cloud Example from a point cloud ^^^^^^^^^^^^^^^^^^^^^^^^^^ -This example builds the one skeleton graph from the given points, and max_edge_length value. +This example builds the neighborhood graph from the given points, up to max_edge_length. Then it creates a :doc:`Simplex_tree ` with it. Finally, it is asked to display information about the simplicial complex. @@ -92,10 +106,12 @@ until dimension 1 - one skeleton graph in other words), the output is: [4, 6] -> 9.49 [3, 6] -> 11.00 +Notice that if we use `rips_complex = gudhi.RipsComplex(points=[[1, 1], [7, 0], [4, 6], [9, 6], [0, 14], [2, 19], [9, 17]], max_edge_length=12.0, sparse=2)`, asking for very sparse version (theory only gives some guarantee on the meaning of the output if `sparse<1`), 2 to 5 edges disappear, depending on the random vertex used to start the sparsification. + Example from OFF file ^^^^^^^^^^^^^^^^^^^^^ -This example builds the :doc:`Rips_complex ` from the given +This example builds the :doc:`RipsComplex ` from the given points in an OFF file, and max_edge_length value. Then it creates a :doc:`Simplex_tree ` with it. @@ -200,7 +216,7 @@ until dimension 1 - one skeleton graph in other words), the output is: Example from csv file ^^^^^^^^^^^^^^^^^^^^^ -This example builds the :doc:`Rips_complex ` from the given +This example builds the :doc:`RipsComplex ` from the given distance matrix in a csv file, and max_edge_length value. Then it creates a :doc:`Simplex_tree ` with it. -- cgit v1.2.3 From cae07e49a1700613bf709f7d0bbf3d1c640d4a2c Mon Sep 17 00:00:00 2001 From: glisse Date: Tue, 2 Oct 2018 11:09:47 +0000 Subject: Catch exception by const& git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3922 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 1b0cea99516d6b42e5ab3b0fdb21468b321e6d6c --- src/cython/include/Alpha_complex_interface.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'src/cython') diff --git a/src/cython/include/Alpha_complex_interface.h b/src/cython/include/Alpha_complex_interface.h index 8cf527fc..faa059d1 100644 --- a/src/cython/include/Alpha_complex_interface.h +++ b/src/cython/include/Alpha_complex_interface.h @@ -60,7 +60,7 @@ class Alpha_complex_interface { Point_d ph = alpha_complex_->get_point(vh); for (auto coord = ph.cartesian_begin(); coord < ph.cartesian_end(); coord++) vd.push_back(*coord); - } catch (std::out_of_range outofrange) { + } catch (std::out_of_range const&) { // std::out_of_range is thrown in case not found. Other exceptions must be re-thrown } return vd; -- cgit v1.2.3 From 9e7c5464fd0f3e12e0b309e7b8ebbad1f830e4a7 Mon Sep 17 00:00:00 2001 From: glisse Date: Fri, 5 Oct 2018 13:43:21 +0000 Subject: pasto git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3933 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 3fc8b696f0c457256e0c8bf74ffffa580dbb69d4 --- src/cython/cython/simplex_tree.pyx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'src/cython') diff --git a/src/cython/cython/simplex_tree.pyx b/src/cython/cython/simplex_tree.pyx index e302486b..8397d9d9 100644 --- a/src/cython/cython/simplex_tree.pyx +++ b/src/cython/cython/simplex_tree.pyx @@ -515,7 +515,7 @@ cdef class SimplexTree: :returns: The persistence intervals. :rtype: list of pair of list of int - :note: intervals_in_dim function requires + :note: persistence_pairs function requires :func:`persistence()` function to be launched first. """ -- cgit v1.2.3 From 0567f550258966a12911cd3ffe490852c022c358 Mon Sep 17 00:00:00 2001 From: glisse Date: Sat, 6 Oct 2018 14:01:16 +0000 Subject: Doc tweaks. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/sparserips-python@3936 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 3c75c674876bcb38d0a87de41d406832baf61b55 --- biblio/bibliography.bib | 2 ++ src/cython/cython/rips_complex.pyx | 1 + src/cython/doc/rips_complex_user.rst | 5 ++--- 3 files changed, 5 insertions(+), 3 deletions(-) (limited to 'src/cython') diff --git a/biblio/bibliography.bib b/biblio/bibliography.bib index e85876d3..a8c040ed 100644 --- a/biblio/bibliography.bib +++ b/biblio/bibliography.bib @@ -1084,6 +1084,7 @@ language={English} author = {Nicholas J. Cavanna and Mahmoodreza Jahanseir and Donald R. Sheehy}, booktitle = {Proceedings of the Canadian Conference on Computational Geometry}, title = {A Geometric Perspective on Sparse Filtrations}, + url = {http://research.cs.queensu.ca/cccg2015/CCCG15-papers/01.pdf}, year = {2015} } @@ -1102,5 +1103,6 @@ language={English} volume = {49}, number = {4}, pages = {778--796}, + doi = "10.1007/s00454-013-9513-1", year = {2013} } diff --git a/src/cython/cython/rips_complex.pyx b/src/cython/cython/rips_complex.pyx index ecf039b6..cb9aad2e 100644 --- a/src/cython/cython/rips_complex.pyx +++ b/src/cython/cython/rips_complex.pyx @@ -66,6 +66,7 @@ cdef class RipsComplex: :type points: list of list of double And in both cases + :param sparse: If this is not None, it switches to building a sparse Rips and represents the approximation parameter epsilon. :type sparse: float """ diff --git a/src/cython/doc/rips_complex_user.rst b/src/cython/doc/rips_complex_user.rst index 9fa3a677..95bb40b6 100644 --- a/src/cython/doc/rips_complex_user.rst +++ b/src/cython/doc/rips_complex_user.rst @@ -15,12 +15,11 @@ Definition | :doc:`rips_complex_user` | :doc:`rips_complex_ref` | +-------------------------------------------+----------------------------------------------------------------------+ -The `Rips complex `_ is a simplicial complex defined as the clique complex of a graph. The graph is defined on a set of points with one vertex for each point and an edge between any 2 points, of weight (aka filtration value) the distance between the 2 points. This graph (and thus the complex) can be restricted to edges shorter than some threshold, to reduce its size. +The `Rips complex `_ is a simplicial complex that generalizes proximity (ε-ball) graphs to higher dimensions. The vertices correspond to the input points, and a simplex is present if and only if its diameter is smaller than some parameter α. Considering all parameters α defines a filtered simplicial complex, where the filtration value of a simplex is its diameter. The filtration can be restricted to values α smaller than some threshold, to reduce its size. The input discrete metric space can be provided as a point cloud plus a distance function, or as a distance matrix. -When creating a simplicial complex from the graph, `RipsComplex` inserts the graph into the data -structure, and then expands the simplicial complex (adds the simplices corresponding to cliques) when required. The expansion can be stopped at dimension `max_dimension`, by default 1. +When creating a simplicial complex from the graph, `RipsComplex` first builds the graph and inserts it into the data structure. It then expands the simplicial complex (adds the simplices corresponding to cliques) when required. The expansion can be stopped at dimension `max_dimension`, by default 1. A vertex name corresponds to the index of the point in the given range (aka. the point cloud). -- cgit v1.2.3 From c537a466ffdd812d92098bcea04cdf6f0bfc64ec Mon Sep 17 00:00:00 2001 From: glisse Date: Wed, 10 Oct 2018 21:17:19 +0000 Subject: Example text and copyright year git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/sparserips-python@3937 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 6d5bf6a2c55f7c4fd4f3f5159651b3ffa057ffdd --- src/cython/example/sparse_rips_persistence_diagram.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'src/cython') diff --git a/src/cython/example/sparse_rips_persistence_diagram.py b/src/cython/example/sparse_rips_persistence_diagram.py index 3bed87c1..d58c244c 100755 --- a/src/cython/example/sparse_rips_persistence_diagram.py +++ b/src/cython/example/sparse_rips_persistence_diagram.py @@ -8,7 +8,7 @@ import gudhi Author(s): Marc Glisse - Copyright (C) 2016 Inria + Copyright (C) 2018 Inria This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -25,11 +25,11 @@ import gudhi """ __author__ = "Marc Glisse" -__copyright__ = "Copyright (C) 2016 Inria" +__copyright__ = "Copyright (C) 2018 Inria" __license__ = "GPL v3" print("#####################################################################") -print("RipsComplex creation from points") +print("Sparse RipsComplex creation from points") rips = gudhi.RipsComplex(points=[[0, 0], [0, 0.1], [1, 0], [0, 1], [1, 1]], max_edge_length=42, sparse=.5) -- cgit v1.2.3 From d16910a5c74552b3b1feffc3e793ec5b6d52f952 Mon Sep 17 00:00:00 2001 From: glisse Date: Wed, 10 Oct 2018 21:43:35 +0000 Subject: Use math instead of unicode for epsilon git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/sparserips-python@3938 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 8cccce774b7406d90a55d0e2827fad6dc3855b39 --- src/cython/doc/rips_complex_user.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'src/cython') diff --git a/src/cython/doc/rips_complex_user.rst b/src/cython/doc/rips_complex_user.rst index 95bb40b6..cddf4f16 100644 --- a/src/cython/doc/rips_complex_user.rst +++ b/src/cython/doc/rips_complex_user.rst @@ -45,7 +45,7 @@ A more general technique is to use a sparse approximation of the Rips introduced by Don Sheehy :cite:`sheehy13linear`. We are using the version described in :cite:`buchet16efficient` (except that we multiply all filtration values by 2, to match the usual Rips complex), which proves a -:math:`\frac{1+\epsilon}{1-\epsilon}`-interleaving, although in practice the +:math:`\frac{1+\varepsilon}{1-\varepsilon}`-interleaving, although in practice the error is usually smaller. A more intuitive presentation of the idea is available in :cite:`cavanna15geometric`, and in a video :cite:`cavanna15visualizing`. Passing an extra argument `sparse=0.3` at the -- cgit v1.2.3 From b6f3903f0ce07fe243ea7a3c18098043114f7f6a Mon Sep 17 00:00:00 2001 From: glisse Date: Wed, 10 Oct 2018 21:52:27 +0000 Subject: epsilon + code block git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/sparserips-python@3939 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 6a88d96a67d9d02f95e63fd627c295abebb49ce8 --- src/cython/doc/rips_complex_user.rst | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) (limited to 'src/cython') diff --git a/src/cython/doc/rips_complex_user.rst b/src/cython/doc/rips_complex_user.rst index cddf4f16..933643e2 100644 --- a/src/cython/doc/rips_complex_user.rst +++ b/src/cython/doc/rips_complex_user.rst @@ -15,7 +15,7 @@ Definition | :doc:`rips_complex_user` | :doc:`rips_complex_ref` | +-------------------------------------------+----------------------------------------------------------------------+ -The `Rips complex `_ is a simplicial complex that generalizes proximity (ε-ball) graphs to higher dimensions. The vertices correspond to the input points, and a simplex is present if and only if its diameter is smaller than some parameter α. Considering all parameters α defines a filtered simplicial complex, where the filtration value of a simplex is its diameter. The filtration can be restricted to values α smaller than some threshold, to reduce its size. +The `Rips complex `_ is a simplicial complex that generalizes proximity (:math:`\varepsilon`-ball) graphs to higher dimensions. The vertices correspond to the input points, and a simplex is present if and only if its diameter is smaller than some parameter α. Considering all parameters α defines a filtered simplicial complex, where the filtration value of a simplex is its diameter. The filtration can be restricted to values α smaller than some threshold, to reduce its size. The input discrete metric space can be provided as a point cloud plus a distance function, or as a distance matrix. @@ -50,7 +50,7 @@ error is usually smaller. A more intuitive presentation of the idea is available in :cite:`cavanna15geometric`, and in a video :cite:`cavanna15visualizing`. Passing an extra argument `sparse=0.3` at the construction of a `RipsComplex` object asks it to build a sparse Rips with -parameter `ε=0.3`, while the default `sparse=None` builds the +parameter :math:`\varepsilon=0.3`, while the default `sparse=None` builds the regular Rips complex. @@ -105,7 +105,13 @@ until dimension 1 - one skeleton graph in other words), the output is: [4, 6] -> 9.49 [3, 6] -> 11.00 -Notice that if we use `rips_complex = gudhi.RipsComplex(points=[[1, 1], [7, 0], [4, 6], [9, 6], [0, 14], [2, 19], [9, 17]], max_edge_length=12.0, sparse=2)`, asking for very sparse version (theory only gives some guarantee on the meaning of the output if `sparse<1`), 2 to 5 edges disappear, depending on the random vertex used to start the sparsification. +Notice that if we use + +.. code-block:: python + + rips_complex = gudhi.RipsComplex(points=[[1, 1], [7, 0], [4, 6], [9, 6], [0, 14], [2, 19], [9, 17]], max_edge_length=12.0, sparse=2) + +asking for a very sparse version (theory only gives some guarantee on the meaning of the output if `sparse<1`), 2 to 5 edges disappear, depending on the random vertex used to start the sparsification. Example from OFF file ^^^^^^^^^^^^^^^^^^^^^ -- cgit v1.2.3 From e9d843d0a5c48315c45e8639e8bf9b79ccf904af Mon Sep 17 00:00:00 2001 From: glisse Date: Wed, 10 Oct 2018 21:55:26 +0000 Subject: add example to the list of examples git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/sparserips-python@3940 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: fe3c41785e3bb72766f7a817851583f82b9f7d15 --- src/cython/doc/examples.rst | 1 + 1 file changed, 1 insertion(+) (limited to 'src/cython') diff --git a/src/cython/doc/examples.rst b/src/cython/doc/examples.rst index 1f02f8a2..edbc2f72 100644 --- a/src/cython/doc/examples.rst +++ b/src/cython/doc/examples.rst @@ -22,6 +22,7 @@ Examples * :download:`rips_complex_diagram_persistence_from_off_file_example.py <../example/rips_complex_diagram_persistence_from_off_file_example.py>` * :download:`rips_complex_diagram_persistence_from_distance_matrix_file_example.py <../example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py>` * :download:`rips_persistence_diagram.py <../example/rips_persistence_diagram.py>` + * :download:`sparse_rips_persistence_diagram.py <../example/sparse_rips_persistence_diagram.py>` * :download:`random_cubical_complex_persistence_example.py <../example/random_cubical_complex_persistence_example.py>` * :download:`coordinate_graph_induced_complex.py <../example/coordinate_graph_induced_complex.py>` * :download:`functional_graph_induced_complex.py <../example/functional_graph_induced_complex.py>` -- cgit v1.2.3 From 665ba1dfe82b663ed755267b74c62706ec6eb88a Mon Sep 17 00:00:00 2001 From: glisse Date: Wed, 10 Oct 2018 22:04:13 +0000 Subject: add myself as coauthor git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/sparserips-python@3941 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 61cf8acdce3bc5cb0c8261166e195eccc3f8bb54 --- src/cython/doc/rips_complex_sum.inc | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'src/cython') diff --git a/src/cython/doc/rips_complex_sum.inc b/src/cython/doc/rips_complex_sum.inc index 5616bfa9..ea26769a 100644 --- a/src/cython/doc/rips_complex_sum.inc +++ b/src/cython/doc/rips_complex_sum.inc @@ -1,6 +1,6 @@ -================================================================= =================================== =================================== -:Author: Clément Maria, Pawel Dlotko, Vincent Rouvreau :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 -================================================================= =================================== =================================== +===================================================================== =========================== =================================== +:Author: Clément Maria, Pawel Dlotko, Vincent Rouvreau, Marc Glisse :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 +===================================================================== =========================== =================================== +----------------------------------------------------------------+------------------------------------------------------------------------+ | .. figure:: | Rips complex is a simplicial complex constructed from a one skeleton | -- cgit v1.2.3 From 354da3ae06ffa2479d56e9ea45cefbe218da2c76 Mon Sep 17 00:00:00 2001 From: glisse Date: Wed, 10 Oct 2018 22:11:23 +0000 Subject: Make RipsComplex a clickable link git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/sparserips-python@3942 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 642ae449f85cf8516fc632716ea14b22f74ec517 --- src/cython/doc/rips_complex_user.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'src/cython') diff --git a/src/cython/doc/rips_complex_user.rst b/src/cython/doc/rips_complex_user.rst index 933643e2..e0c71cd1 100644 --- a/src/cython/doc/rips_complex_user.rst +++ b/src/cython/doc/rips_complex_user.rst @@ -19,7 +19,7 @@ The `Rips complex ` The input discrete metric space can be provided as a point cloud plus a distance function, or as a distance matrix. -When creating a simplicial complex from the graph, `RipsComplex` first builds the graph and inserts it into the data structure. It then expands the simplicial complex (adds the simplices corresponding to cliques) when required. The expansion can be stopped at dimension `max_dimension`, by default 1. +When creating a simplicial complex from the graph, :doc:`RipsComplex ` first builds the graph and inserts it into the data structure. It then expands the simplicial complex (adds the simplices corresponding to cliques) when required. The expansion can be stopped at dimension `max_dimension`, by default 1. A vertex name corresponds to the index of the point in the given range (aka. the point cloud). -- cgit v1.2.3 From 07c214f675595b75a2a9d1f8dc2888487aa6086a Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 17 Oct 2018 08:11:14 +0000 Subject: Some indentation fix git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/sparserips-python@3960 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 6dce53b98bc0b299a3621602f385b3b44e16d489 --- src/cython/doc/rips_complex_user.rst | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) (limited to 'src/cython') diff --git a/src/cython/doc/rips_complex_user.rst b/src/cython/doc/rips_complex_user.rst index e0c71cd1..0aeffe55 100644 --- a/src/cython/doc/rips_complex_user.rst +++ b/src/cython/doc/rips_complex_user.rst @@ -69,7 +69,7 @@ Finally, it is asked to display information about the simplicial complex. import gudhi rips_complex = gudhi.RipsComplex(points=[[1, 1], [7, 0], [4, 6], [9, 6], [0, 14], [2, 19], [9, 17]], - max_edge_length=12.0) + max_edge_length=12.0) simplex_tree = rips_complex.create_simplex_tree(max_dimension=1) result_str = 'Rips complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \ @@ -109,9 +109,11 @@ Notice that if we use .. code-block:: python - rips_complex = gudhi.RipsComplex(points=[[1, 1], [7, 0], [4, 6], [9, 6], [0, 14], [2, 19], [9, 17]], max_edge_length=12.0, sparse=2) + rips_complex = gudhi.RipsComplex(points=[[1, 1], [7, 0], [4, 6], [9, 6], [0, 14], [2, 19], [9, 17]], + max_edge_length=12.0, sparse=2) -asking for a very sparse version (theory only gives some guarantee on the meaning of the output if `sparse<1`), 2 to 5 edges disappear, depending on the random vertex used to start the sparsification. +asking for a very sparse version (theory only gives some guarantee on the meaning of the output if `sparse<1`), +2 to 5 edges disappear, depending on the random vertex used to start the sparsification. Example from OFF file ^^^^^^^^^^^^^^^^^^^^^ -- cgit v1.2.3 From 4f07edab3e86ffe9f0bcd8c055592dff22fab2ce Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 18 Oct 2018 19:30:14 +0000 Subject: Add persistence_dim_max argument in simplex tree persistence documentation git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3963 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: ef8f3b0c2b0e3cdbda73687f1e65877213918830 --- src/cython/cython/simplex_tree.pyx | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) (limited to 'src/cython') diff --git a/src/cython/cython/simplex_tree.pyx b/src/cython/cython/simplex_tree.pyx index 8397d9d9..0ab97f80 100644 --- a/src/cython/cython/simplex_tree.pyx +++ b/src/cython/cython/simplex_tree.pyx @@ -44,8 +44,8 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": 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, + bool find_simplex(vector[int] simplex) + bool insert_simplex_and_subfaces(vector[int] simplex, double filtration) vector[pair[vector[int], double]] get_filtration() vector[pair[vector[int], double]] get_skeleton(int dimension) @@ -355,7 +355,7 @@ cdef class SimplexTree: :param filtration: Maximum threshold value. :type filtration: float. :returns: The filtration modification information. - :rtype: bint + :rtype: bool .. note:: @@ -406,7 +406,7 @@ cdef class SimplexTree: value than its faces by increasing the filtration values. :returns: The filtration modification information. - :rtype: bint + :rtype: bool .. note:: @@ -432,6 +432,10 @@ cdef class SimplexTree: 0.0. Sets min_persistence to -1.0 to see all values. :type min_persistence: float. + :param persistence_dim_max: If true, the persistent homology for the + maximal dimension in the complex is computed. If false, it is + ignored. Default is false. + :type persistence_dim_max: bool :returns: The persistence of the simplicial complex. :rtype: list of pairs(dimension, pair(birth, death)) """ -- cgit v1.2.3 From e8401b6fd2f9ff533824a6773f592b448d0863ed Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 31 Oct 2018 11:48:04 +0000 Subject: Make dependency with boost 1.56 instead of 1.48 git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_1.56_vincent@3967 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a5941b8c4f65ec8e6f62117aceb5f22e0142f255 --- src/cmake/modules/GUDHI_third_party_libraries.cmake | 2 +- src/common/doc/installation.h | 2 +- src/cython/doc/installation.rst | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) (limited to 'src/cython') diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake index b020ebfc..cde3725c 100644 --- a/src/cmake/modules/GUDHI_third_party_libraries.cmake +++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake @@ -1,6 +1,6 @@ # This files manage third party libraries required by GUDHI -find_package(Boost 1.48.0 REQUIRED COMPONENTS system filesystem unit_test_framework program_options thread) +find_package(Boost 1.56.0 REQUIRED COMPONENTS system filesystem unit_test_framework program_options thread) if(NOT Boost_FOUND) message(FATAL_ERROR "NOTICE: This program requires Boost and will not be compiled.") diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index df7eed37..bf2d0a87 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -5,7 +5,7 @@ * Examples of GUDHI headers inclusion can be found in \ref utilities. * * \section compiling Compiling - * The library uses c++11 and requires Boost ≥ 1.48.0 + * The library uses c++11 and requires Boost ≥ 1.56.0 * and CMake ≥ 3.1. * It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015. * diff --git a/src/cython/doc/installation.rst b/src/cython/doc/installation.rst index ef2f7af2..040f6b4a 100644 --- a/src/cython/doc/installation.rst +++ b/src/cython/doc/installation.rst @@ -7,7 +7,7 @@ Installation Compiling ********* -The library uses c++11 and requires `Boost `_ ≥ 1.48.0 +The library uses c++11 and requires `Boost `_ ≥ 1.56.0 and `CMake `_ ≥ 3.1. It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015. -- cgit v1.2.3 From e105da964b96218459c8822816de36273f6cdf17 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Mon, 17 Dec 2018 20:57:42 +0000 Subject: Merge tangential-miro branch Add reference to cubical in persistence module git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@4038 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 832343cd6e2357c9e229d5b34f6de03e50d2da67 --- .../include/gudhi/Tangential_complex.h | 57 ++++++++++++++-------- src/cython/doc/persistent_cohomology_user.rst | 14 +++--- 2 files changed, 46 insertions(+), 25 deletions(-) (limited to 'src/cython') diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex.h b/src/Tangential_complex/include/gudhi/Tangential_complex.h index d1c846cf..37cdf1b4 100644 --- a/src/Tangential_complex/include/gudhi/Tangential_complex.h +++ b/src/Tangential_complex/include/gudhi/Tangential_complex.h @@ -30,6 +30,7 @@ #include #include #include +#include #include #include @@ -356,7 +357,7 @@ class Tangential_complex { tbb::parallel_for(tbb::blocked_range(0, m_points.size()), Compute_tangent_triangulation(*this)); } else { #endif // GUDHI_USE_TBB - // Sequential + // Sequential for (std::size_t i = 0; i < m_points.size(); ++i) compute_tangent_triangulation(i); #ifdef GUDHI_USE_TBB } @@ -629,12 +630,12 @@ class Tangential_complex { // Don't export infinite cells if (!export_infinite_simplices && is_infinite(c)) continue; - if (!export_inconsistent_simplices && !is_simplex_consistent(c)) continue; - if (static_cast(c.size()) > max_dim) max_dim = static_cast(c.size()); // Add the missing center vertex c.insert(idx); + if (!export_inconsistent_simplices && !is_simplex_consistent(c)) continue; + // Try to insert the simplex bool inserted = tree.insert_simplex_and_subfaces(c).second; @@ -689,6 +690,10 @@ class Tangential_complex { // Don't export infinite cells if (!export_infinite_simplices && is_infinite(c)) continue; + if (static_cast(c.size()) > max_dim) max_dim = static_cast(c.size()); + // Add the missing center vertex + c.insert(idx); + if (!export_inconsistent_simplices && !is_simplex_consistent(c)) continue; // Unusual simplex dim? @@ -701,10 +706,6 @@ class Tangential_complex { check_lower_and_higher_dim_simplices = 1; } - if (static_cast(c.size()) > max_dim) max_dim = static_cast(c.size()); - // Add the missing center vertex - c.insert(idx); - // Try to insert the simplex bool added = complex.add_simplex(c, check_lower_and_higher_dim_simplices == 1); @@ -800,7 +801,7 @@ class Tangential_complex { tbb::parallel_for(tbb::blocked_range(0, m_points.size()), Compute_tangent_triangulation(*this)); } else { #endif // GUDHI_USE_TBB - // Sequential + // Sequential for (std::size_t i = 0; i < m_points.size(); ++i) compute_tangent_triangulation(i); #ifdef GUDHI_USE_TBB } @@ -835,7 +836,7 @@ class Tangential_complex { Refresh_tangent_triangulation(*this, updated_pts_ds)); } else { #endif // GUDHI_USE_TBB - // Sequential + // Sequential for (std::size_t i = 0; i < m_points.size(); ++i) refresh_tangent_triangulation(i, updated_pts_ds); #ifdef GUDHI_USE_TBB } @@ -983,10 +984,9 @@ class Tangential_complex { // of the sphere "star sphere" centered at "center_vertex" // and which contains all the // circumspheres of the star of "center_vertex" - boost::optional squared_star_sphere_radius_plus_margin = boost::make_optional(false, FT()); - // This is the strange way boost is recommending to get rid of "may be used uninitialized in this function". - // Former code was : - // boost::optional squared_star_sphere_radius_plus_margin; + // If th the m_max_squared_edge_length is set the maximal radius of the "star sphere" + // is at most square root of m_max_squared_edge_length + boost::optional squared_star_sphere_radius_plus_margin = m_max_squared_edge_length; // Insert points until we find a point which is outside "star sphere" for (auto nn_it = ins_range.begin(); nn_it != ins_range.end(); ++nn_it) { @@ -999,10 +999,16 @@ class Tangential_complex { Point neighbor_pt; FT neighbor_weight; compute_perturbed_weighted_point(neighbor_point_idx, neighbor_pt, neighbor_weight); - + GUDHI_CHECK(!m_max_squared_edge_length || + squared_star_sphere_radius_plus_margin.value() <= m_max_squared_edge_length.value(), + std::invalid_argument("Tangential_complex::compute_star - set a bigger value with set_max_squared_edge_length.")); if (squared_star_sphere_radius_plus_margin && - k_sqdist(center_pt, neighbor_pt) > *squared_star_sphere_radius_plus_margin) + k_sqdist(center_pt, neighbor_pt) > squared_star_sphere_radius_plus_margin.value()) { + GUDHI_CHECK(triangulation.current_dimension() >= tangent_space_dim, + std::invalid_argument("Tangential_complex::compute_star - Dimension of the star is only " + \ + std::to_string(triangulation.current_dimension()))); break; + } Tr_point proj_pt = project_point_and_compute_weight(neighbor_pt, neighbor_weight, tsb, local_tr_traits); @@ -1044,7 +1050,7 @@ class Tangential_complex { FT sq_power_sphere_diam = 4 * point_weight(c); if (!squared_star_sphere_radius_plus_margin || - sq_power_sphere_diam > *squared_star_sphere_radius_plus_margin) { + sq_power_sphere_diam > squared_star_sphere_radius_plus_margin.value()) { squared_star_sphere_radius_plus_margin = sq_power_sphere_diam; } } @@ -1055,12 +1061,22 @@ class Tangential_complex { if (squared_star_sphere_radius_plus_margin) { // "2*m_last_max_perturb" because both points can be perturbed squared_star_sphere_radius_plus_margin = - CGAL::square(std::sqrt(*squared_star_sphere_radius_plus_margin) + 2 * m_last_max_perturb); + CGAL::square(std::sqrt(squared_star_sphere_radius_plus_margin.value()) + 2 * m_last_max_perturb); + + // Reduce the square radius to m_max_squared_edge_length if necessary + if (m_max_squared_edge_length && squared_star_sphere_radius_plus_margin.value() > m_max_squared_edge_length.value()) { + squared_star_sphere_radius_plus_margin = m_max_squared_edge_length.value(); + } // Save it in `m_squared_star_spheres_radii_incl_margin` - m_squared_star_spheres_radii_incl_margin[i] = *squared_star_sphere_radius_plus_margin; + m_squared_star_spheres_radii_incl_margin[i] = squared_star_sphere_radius_plus_margin.value(); } else { - m_squared_star_spheres_radii_incl_margin[i] = FT(-1); + if (m_max_squared_edge_length) { + squared_star_sphere_radius_plus_margin = m_max_squared_edge_length.value(); + m_squared_star_spheres_radii_incl_margin[i] = m_max_squared_edge_length.value(); + } else { + m_squared_star_spheres_radii_incl_margin[i] = FT(-1); + } } } } @@ -1968,6 +1984,8 @@ class Tangential_complex { return os; } + void set_max_squared_edge_length(FT max_squared_edge_length) { m_max_squared_edge_length = max_squared_edge_length; } + private: const K m_k; const int m_intrinsic_dim; @@ -1993,6 +2011,7 @@ class Tangential_complex { // and their center vertex Stars_container m_stars; std::vector m_squared_star_spheres_radii_incl_margin; + boost::optional m_max_squared_edge_length; #ifdef GUDHI_TC_USE_ANOTHER_POINT_SET_FOR_TANGENT_SPACE_ESTIM Points m_points_for_tse; diff --git a/src/cython/doc/persistent_cohomology_user.rst b/src/cython/doc/persistent_cohomology_user.rst index ce7fc685..de83cda1 100644 --- a/src/cython/doc/persistent_cohomology_user.rst +++ b/src/cython/doc/persistent_cohomology_user.rst @@ -10,12 +10,14 @@ Definition :Author: Clément Maria :Introduced in: GUDHI PYTHON 2.0.0 :Copyright: GPL v3 ===================================== ===================================== ===================================== -+---------------------------------------------+----------------------------------------------------------------------+ -| :doc:`persistent_cohomology_user` | Please refer to each data structure that contains persistence | -| | feature for reference: | -| | | -| | * :doc:`simplex_tree_ref` | -+---------------------------------------------+----------------------------------------------------------------------+ ++-----------------------------------------------------------------+-----------------------------------------------------------------------+ +| :doc:`persistent_cohomology_user` | Please refer to each data structure that contains persistence | +| | feature for reference: | +| | | +| | * :doc:`simplex_tree_ref` | +| | * :doc:`cubical_complex_ref` | +| | * :doc:`periodic_cubical_complex_ref` | ++-----------------------------------------------------------------+-----------------------------------------------------------------------+ Computation of persistent cohomology using the algorithm of :cite:`DBLP:journals/dcg/SilvaMV11` and -- cgit v1.2.3