From c524232f734de875d69e2f190f01a6c976024368 Mon Sep 17 00:00:00 2001 From: Gard Spreemann Date: Thu, 14 Jun 2018 20:39:01 +0200 Subject: GUDHI 2.2.0 as released by upstream in a tarball. --- cython/doc/_templates/layout.html | 122 ++++++++++----------- cython/doc/alpha_complex_ref.rst | 4 + cython/doc/alpha_complex_sum.inc | 22 ++++ cython/doc/alpha_complex_sum.rst | 22 ---- cython/doc/alpha_complex_user.rst | 12 +- cython/doc/bottleneck_distance_sum.inc | 15 +++ cython/doc/bottleneck_distance_sum.rst | 15 --- cython/doc/bottleneck_distance_user.rst | 6 +- cython/doc/citation.rst | 4 + cython/doc/conf.py | 3 +- cython/doc/cubical_complex_ref.rst | 4 + cython/doc/cubical_complex_sum.inc | 15 +++ cython/doc/cubical_complex_sum.rst | 15 --- cython/doc/cubical_complex_user.rst | 7 +- .../doc/euclidean_strong_witness_complex_ref.rst | 4 + cython/doc/euclidean_witness_complex_ref.rst | 4 + cython/doc/examples.rst | 4 + cython/doc/fileformats.rst | 4 + cython/doc/index.rst | 18 +-- cython/doc/installation.rst | 15 ++- cython/doc/periodic_cubical_complex_ref.rst | 4 + cython/doc/persistence_graphical_tools_ref.rst | 5 +- cython/doc/persistence_graphical_tools_sum.inc | 12 ++ cython/doc/persistence_graphical_tools_sum.rst | 12 -- cython/doc/persistence_graphical_tools_user.rst | 71 +++++------- cython/doc/persistent_cohomology_sum.inc | 27 +++++ cython/doc/persistent_cohomology_sum.rst | 27 ----- cython/doc/persistent_cohomology_user.rst | 4 + cython/doc/pyplots/barcode_persistence.py | 7 -- cython/doc/pyplots/diagram_persistence.py | 8 -- cython/doc/pyplots/show_palette_values.py | 3 - cython/doc/reader_utils_ref.rst | 4 + cython/doc/rips_complex_ref.rst | 4 + cython/doc/rips_complex_sum.inc | 17 +++ cython/doc/rips_complex_sum.rst | 17 --- cython/doc/rips_complex_user.rst | 84 +++++++++++++- cython/doc/simplex_tree_ref.rst | 4 + cython/doc/simplex_tree_sum.inc | 14 +++ cython/doc/simplex_tree_sum.rst | 14 --- cython/doc/simplex_tree_user.rst | 6 +- cython/doc/strong_witness_complex_ref.rst | 4 + cython/doc/tangential_complex_ref.rst | 4 + cython/doc/tangential_complex_sum.inc | 15 +++ cython/doc/tangential_complex_sum.rst | 15 --- cython/doc/tangential_complex_user.rst | 13 ++- cython/doc/todos.rst | 4 + cython/doc/witness_complex_ref.rst | 4 + cython/doc/witness_complex_sum.inc | 19 ++++ cython/doc/witness_complex_sum.rst | 19 ---- cython/doc/witness_complex_user.rst | 6 +- 50 files changed, 452 insertions(+), 310 deletions(-) create mode 100644 cython/doc/alpha_complex_sum.inc delete mode 100644 cython/doc/alpha_complex_sum.rst create mode 100644 cython/doc/bottleneck_distance_sum.inc delete mode 100644 cython/doc/bottleneck_distance_sum.rst create mode 100644 cython/doc/cubical_complex_sum.inc delete mode 100644 cython/doc/cubical_complex_sum.rst create mode 100644 cython/doc/persistence_graphical_tools_sum.inc delete mode 100644 cython/doc/persistence_graphical_tools_sum.rst create mode 100644 cython/doc/persistent_cohomology_sum.inc delete mode 100644 cython/doc/persistent_cohomology_sum.rst delete mode 100755 cython/doc/pyplots/barcode_persistence.py delete mode 100755 cython/doc/pyplots/diagram_persistence.py delete mode 100755 cython/doc/pyplots/show_palette_values.py create mode 100644 cython/doc/rips_complex_sum.inc delete mode 100644 cython/doc/rips_complex_sum.rst create mode 100644 cython/doc/simplex_tree_sum.inc delete mode 100644 cython/doc/simplex_tree_sum.rst create mode 100644 cython/doc/tangential_complex_sum.inc delete mode 100644 cython/doc/tangential_complex_sum.rst create mode 100644 cython/doc/witness_complex_sum.inc delete mode 100644 cython/doc/witness_complex_sum.rst (limited to 'cython/doc') diff --git a/cython/doc/_templates/layout.html b/cython/doc/_templates/layout.html index 8e4eba40..1161ed8e 100644 --- a/cython/doc/_templates/layout.html +++ b/cython/doc/_templates/layout.html @@ -56,6 +56,12 @@

{%- endif %} {%- endblock %} +

GUDHI

+

File formats

+

GUDHI installation

+

Acknowledging the GUDHI library

+

Index

+

Examples

{%- if sidebars != None %} {#- new style sidebar: explicitly include/exclude templates #} {%- for sidebartemplate in sidebars %} @@ -64,13 +70,6 @@ {%- else %} {#- old style sidebars: using blocks -- should be deprecated #} {%- block sidebartoc %} -

GUDHI

-

File formats

-

GUDHI installation

-

Acknowledging the GUDHI library

-

Index

-

Examples

- {%- include "localtoc.html" %} {%- endblock %} {%- block sidebarrel %} @@ -166,60 +165,61 @@ diff --git a/cython/doc/alpha_complex_ref.rst b/cython/doc/alpha_complex_ref.rst index 6a122b09..7da79543 100644 --- a/cython/doc/alpha_complex_ref.rst +++ b/cython/doc/alpha_complex_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ============================== Alpha complex reference manual ============================== diff --git a/cython/doc/alpha_complex_sum.inc b/cython/doc/alpha_complex_sum.inc new file mode 100644 index 00000000..1680a712 --- /dev/null +++ b/cython/doc/alpha_complex_sum.inc @@ -0,0 +1,22 @@ +================================================================= =================================== =================================== +:Author: Vincent Rouvreau :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 +:Requires: CGAL :math:`\geq` 4.7.0 Eigen3 +================================================================= =================================== =================================== + ++----------------------------------------------------------------+------------------------------------------------------------------------+ +| .. figure:: | Alpha_complex is a simplicial complex constructed from the finite | +| ../../doc/Alpha_complex/alpha_complex_representation.png | cells of a Delaunay Triangulation. | +| :alt: Alpha complex representation | | +| :figclass: align-center | The filtration value of each simplex is computed as the square of the | +| | circumradius of the simplex if the circumsphere is empty (the simplex | +| Alpha complex representation | is then said to be Gabriel), and as the minimum of the filtration | +| | values of the codimension 1 cofaces that make it not Gabriel | +| | otherwise. All simplices that have a filtration value strictly | +| | greater than a given alpha squared value are not inserted into the | +| | complex. | +| | | +| | This package requires having CGAL version 4.7 or higher (4.8.1 is | +| | advised for better performance). | ++----------------------------------------------------------------+------------------------------------------------------------------------+ +| :doc:`alpha_complex_user` | :doc:`alpha_complex_ref` | ++----------------------------------------------------------------+------------------------------------------------------------------------+ diff --git a/cython/doc/alpha_complex_sum.rst b/cython/doc/alpha_complex_sum.rst deleted file mode 100644 index 1680a712..00000000 --- a/cython/doc/alpha_complex_sum.rst +++ /dev/null @@ -1,22 +0,0 @@ -================================================================= =================================== =================================== -:Author: Vincent Rouvreau :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 -:Requires: CGAL :math:`\geq` 4.7.0 Eigen3 -================================================================= =================================== =================================== - -+----------------------------------------------------------------+------------------------------------------------------------------------+ -| .. figure:: | Alpha_complex is a simplicial complex constructed from the finite | -| ../../doc/Alpha_complex/alpha_complex_representation.png | cells of a Delaunay Triangulation. | -| :alt: Alpha complex representation | | -| :figclass: align-center | The filtration value of each simplex is computed as the square of the | -| | circumradius of the simplex if the circumsphere is empty (the simplex | -| Alpha complex representation | is then said to be Gabriel), and as the minimum of the filtration | -| | values of the codimension 1 cofaces that make it not Gabriel | -| | otherwise. All simplices that have a filtration value strictly | -| | greater than a given alpha squared value are not inserted into the | -| | complex. | -| | | -| | This package requires having CGAL version 4.7 or higher (4.8.1 is | -| | advised for better performance). | -+----------------------------------------------------------------+------------------------------------------------------------------------+ -| :doc:`alpha_complex_user` | :doc:`alpha_complex_ref` | -+----------------------------------------------------------------+------------------------------------------------------------------------+ diff --git a/cython/doc/alpha_complex_user.rst b/cython/doc/alpha_complex_user.rst index db7edd6f..d1e9c7cd 100644 --- a/cython/doc/alpha_complex_user.rst +++ b/cython/doc/alpha_complex_user.rst @@ -1,11 +1,15 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Alpha complex user manual ========================= Definition ---------- -.. include:: alpha_complex_sum.rst +.. include:: alpha_complex_sum.inc -Alpha_complex is constructing a :doc:`Simplex_tree ` using +Alpha_complex is constructing a :doc:`Simplex_tree ` using `Delaunay Triangulation `_ :cite:`cgal:hdj-t-15b` from `CGAL `_ (the Computational Geometry Algorithms Library :cite:`cgal:eb-15b`). @@ -99,9 +103,9 @@ Filtration value computation algorithm **end for** **end for** **end for** - + make_filtration_non_decreasing() - + prune_above_filtration() Dimension 2 diff --git a/cython/doc/bottleneck_distance_sum.inc b/cython/doc/bottleneck_distance_sum.inc new file mode 100644 index 00000000..030fad9e --- /dev/null +++ b/cython/doc/bottleneck_distance_sum.inc @@ -0,0 +1,15 @@ +================================================================= =================================== =================================== +:Author: François Godi :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 +:Requires: CGAL :math:`\geq` 4.8.0 +================================================================= =================================== =================================== + ++-----------------------------------------------------------------+----------------------------------------------------------------------+ +| .. figure:: | Bottleneck distance measures the similarity between two persistence | +| ../../doc/Bottleneck_distance/perturb_pd.png | diagrams. It's the shortest distance b for which there exists a | +| :figclass: align-center | perfect matching between the points of the two diagrams (+ all the | +| | diagonal points) such that any couple of matched points are at | +| Bottleneck distance is the length of | distance at most b. | +| the longest edge | | ++-----------------------------------------------------------------+----------------------------------------------------------------------+ +| :doc:`bottleneck_distance_user` | | ++-----------------------------------------------------------------+----------------------------------------------------------------------+ diff --git a/cython/doc/bottleneck_distance_sum.rst b/cython/doc/bottleneck_distance_sum.rst deleted file mode 100644 index 030fad9e..00000000 --- a/cython/doc/bottleneck_distance_sum.rst +++ /dev/null @@ -1,15 +0,0 @@ -================================================================= =================================== =================================== -:Author: François Godi :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 -:Requires: CGAL :math:`\geq` 4.8.0 -================================================================= =================================== =================================== - -+-----------------------------------------------------------------+----------------------------------------------------------------------+ -| .. figure:: | Bottleneck distance measures the similarity between two persistence | -| ../../doc/Bottleneck_distance/perturb_pd.png | diagrams. It's the shortest distance b for which there exists a | -| :figclass: align-center | perfect matching between the points of the two diagrams (+ all the | -| | diagonal points) such that any couple of matched points are at | -| Bottleneck distance is the length of | distance at most b. | -| the longest edge | | -+-----------------------------------------------------------------+----------------------------------------------------------------------+ -| :doc:`bottleneck_distance_user` | | -+-----------------------------------------------------------------+----------------------------------------------------------------------+ diff --git a/cython/doc/bottleneck_distance_user.rst b/cython/doc/bottleneck_distance_user.rst index 7692dce2..605db022 100644 --- a/cython/doc/bottleneck_distance_user.rst +++ b/cython/doc/bottleneck_distance_user.rst @@ -1,9 +1,13 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Bottleneck distance user manual =============================== Definition ---------- -.. include:: bottleneck_distance_sum.rst +.. include:: bottleneck_distance_sum.inc Function -------- diff --git a/cython/doc/citation.rst b/cython/doc/citation.rst index f4fdf83b..117eb9dd 100644 --- a/cython/doc/citation.rst +++ b/cython/doc/citation.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Acknowledging the GUDHI library ############################### diff --git a/cython/doc/conf.py b/cython/doc/conf.py index a13c9751..4a54d4fd 100755 --- a/cython/doc/conf.py +++ b/cython/doc/conf.py @@ -85,7 +85,7 @@ version = gudhi.__version__ # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. -exclude_patterns = ['_build'] +exclude_patterns = ['_build', '*.inc'] # The reST default role (used for this markup: `text`) to use for all # documents. @@ -125,6 +125,7 @@ html_theme_options = { "sidebarbgcolor": "#A1ADCD", "sidebartextcolor": "black", "sidebarlinkcolor": "#334D5C", + "body_max_width": "1200px", } # Add any paths that contain custom themes here, relative to this directory. diff --git a/cython/doc/cubical_complex_ref.rst b/cython/doc/cubical_complex_ref.rst index 84aa4223..1fe9d5fb 100644 --- a/cython/doc/cubical_complex_ref.rst +++ b/cython/doc/cubical_complex_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Cubical complex reference manual ################################ diff --git a/cython/doc/cubical_complex_sum.inc b/cython/doc/cubical_complex_sum.inc new file mode 100644 index 00000000..280ad0e0 --- /dev/null +++ b/cython/doc/cubical_complex_sum.inc @@ -0,0 +1,15 @@ +================================================================= =================================== =================================== +:Author: Pawel Dlotko :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 +================================================================= =================================== =================================== + ++--------------------------------------------------------------------------+----------------------------------------------------------------------+ +| .. figure:: | The cubical complex is an example of a structured complex useful in | +| ../../doc/Bitmap_cubical_complex/Cubical_complex_representation.png | computational mathematics (specially rigorous numerics) and image | +| :alt: Cubical complex representation | analysis. | +| :figclass: align-center | | +| | | +| Cubical complex representation | | ++--------------------------------------------------------------------------+----------------------------------------------------------------------+ +| :doc:`cubical_complex_user` | * :doc:`cubical_complex_ref` | +| | * :doc:`periodic_cubical_complex_ref` | ++--------------------------------------------------------------------------+----------------------------------------------------------------------+ diff --git a/cython/doc/cubical_complex_sum.rst b/cython/doc/cubical_complex_sum.rst deleted file mode 100644 index 280ad0e0..00000000 --- a/cython/doc/cubical_complex_sum.rst +++ /dev/null @@ -1,15 +0,0 @@ -================================================================= =================================== =================================== -:Author: Pawel Dlotko :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 -================================================================= =================================== =================================== - -+--------------------------------------------------------------------------+----------------------------------------------------------------------+ -| .. figure:: | The cubical complex is an example of a structured complex useful in | -| ../../doc/Bitmap_cubical_complex/Cubical_complex_representation.png | computational mathematics (specially rigorous numerics) and image | -| :alt: Cubical complex representation | analysis. | -| :figclass: align-center | | -| | | -| Cubical complex representation | | -+--------------------------------------------------------------------------+----------------------------------------------------------------------+ -| :doc:`cubical_complex_user` | * :doc:`cubical_complex_ref` | -| | * :doc:`periodic_cubical_complex_ref` | -+--------------------------------------------------------------------------+----------------------------------------------------------------------+ diff --git a/cython/doc/cubical_complex_user.rst b/cython/doc/cubical_complex_user.rst index 34598f02..320bd79b 100644 --- a/cython/doc/cubical_complex_user.rst +++ b/cython/doc/cubical_complex_user.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Cubical complex user manual =========================== Definition @@ -144,6 +148,7 @@ the program output is: .. testoutput:: Periodic cubical complex is of dimension 2 - 42 simplices. + Examples. --------- @@ -152,6 +157,6 @@ End user programs are available in cython/example/ folder. Bibliography ============ -.. bibliography:: ../../bibliography.bib +.. bibliography:: ../../biblio/bibliography.bib :filter: docnames :style: unsrt diff --git a/cython/doc/euclidean_strong_witness_complex_ref.rst b/cython/doc/euclidean_strong_witness_complex_ref.rst index bebf0f9a..1a602cd5 100644 --- a/cython/doc/euclidean_strong_witness_complex_ref.rst +++ b/cython/doc/euclidean_strong_witness_complex_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ================================================= Euclidean strong witness complex reference manual ================================================= diff --git a/cython/doc/euclidean_witness_complex_ref.rst b/cython/doc/euclidean_witness_complex_ref.rst index 29b8806f..28daf965 100644 --- a/cython/doc/euclidean_witness_complex_ref.rst +++ b/cython/doc/euclidean_witness_complex_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ========================================== Euclidean witness complex reference manual ========================================== diff --git a/cython/doc/examples.rst b/cython/doc/examples.rst index 1e596e18..d42f5a92 100644 --- a/cython/doc/examples.rst +++ b/cython/doc/examples.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Examples ######## diff --git a/cython/doc/fileformats.rst b/cython/doc/fileformats.rst index 4f0b6f6d..ff20f26e 100644 --- a/cython/doc/fileformats.rst +++ b/cython/doc/fileformats.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + File formats ############ diff --git a/cython/doc/index.rst b/cython/doc/index.rst index 3945d72a..4e444fb0 100644 --- a/cython/doc/index.rst +++ b/cython/doc/index.rst @@ -34,32 +34,32 @@ Data structures Alpha complex ============= -.. include:: alpha_complex_sum.rst +.. include:: alpha_complex_sum.inc Cubical complex =============== -.. include:: cubical_complex_sum.rst +.. include:: cubical_complex_sum.inc Rips complex ============ -.. include:: rips_complex_sum.rst +.. include:: rips_complex_sum.inc Simplex tree ============ -.. include:: simplex_tree_sum.rst +.. include:: simplex_tree_sum.inc Tangential complex ================== -.. include:: tangential_complex_sum.rst +.. include:: tangential_complex_sum.inc Witness complex =============== -.. include:: witness_complex_sum.rst +.. include:: witness_complex_sum.inc Toolbox @@ -68,17 +68,17 @@ Toolbox Bottleneck distance =================== -.. include:: bottleneck_distance_sum.rst +.. include:: bottleneck_distance_sum.inc Persistence cohomology ====================== -.. include:: persistent_cohomology_sum.rst +.. include:: persistent_cohomology_sum.inc Persistence graphical tools =========================== -.. include:: persistence_graphical_tools_sum.rst +.. include:: persistence_graphical_tools_sum.inc Bibliography ************ diff --git a/cython/doc/installation.rst b/cython/doc/installation.rst index c182f176..43ff85c5 100644 --- a/cython/doc/installation.rst +++ b/cython/doc/installation.rst @@ -1,12 +1,16 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Installation ############ Compiling ********* - -The library uses c++11 and requires `Boost `_ with -version 1.48.0 or more recent. It is a multi-platform library and compiles on -Linux, Mac OSX and Visual Studio 2015. +The library uses c++11 and requires `Boost `_ ≥ 1.48.0 +and `CMake `_ ≥ 3.1. +It is a multi-platform library and compiles on Linux, Mac OSX and Visual +Studio 2015. It also requires cmake to generate makefiles, and cython to compile the library. @@ -43,6 +47,9 @@ following command in a terminal: export PYTHONPATH='$PYTHONPATH:/path-to-gudhi/build/cython' ctest -R py_test +If tests fail, please try to :code:`import gudhi` and check the errors. +The problem can come from a third-party library bad link or installation. + Documentation ============= diff --git a/cython/doc/periodic_cubical_complex_ref.rst b/cython/doc/periodic_cubical_complex_ref.rst index c6190a1b..4b831647 100644 --- a/cython/doc/periodic_cubical_complex_ref.rst +++ b/cython/doc/periodic_cubical_complex_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Periodic cubical complex reference manual ######################################### diff --git a/cython/doc/persistence_graphical_tools_ref.rst b/cython/doc/persistence_graphical_tools_ref.rst index 27c2f68a..a2c6bcef 100644 --- a/cython/doc/persistence_graphical_tools_ref.rst +++ b/cython/doc/persistence_graphical_tools_ref.rst @@ -1,8 +1,11 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ============================================ Persistence graphical tools reference manual ============================================ .. autofunction:: gudhi.__min_birth_max_death -.. autofunction:: gudhi.show_palette_values .. autofunction:: gudhi.plot_persistence_barcode .. autofunction:: gudhi.plot_persistence_diagram diff --git a/cython/doc/persistence_graphical_tools_sum.inc b/cython/doc/persistence_graphical_tools_sum.inc new file mode 100644 index 00000000..d602daa7 --- /dev/null +++ b/cython/doc/persistence_graphical_tools_sum.inc @@ -0,0 +1,12 @@ +================================================================= =================================== =================================== +:Author: Vincent Rouvreau :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 +:Requires: Matplotlib Numpy +================================================================= =================================== =================================== + ++-----------------------------------------------------------------+-----------------------------------------------------------------------+ +| .. 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. | +| | | ++-----------------------------------------------------------------+-----------------------------------------------------------------------+ +| :doc:`persistence_graphical_tools_user` | :doc:`persistence_graphical_tools_ref` | ++-----------------------------------------------------------------+-----------------------------------------------------------------------+ diff --git a/cython/doc/persistence_graphical_tools_sum.rst b/cython/doc/persistence_graphical_tools_sum.rst deleted file mode 100644 index d602daa7..00000000 --- a/cython/doc/persistence_graphical_tools_sum.rst +++ /dev/null @@ -1,12 +0,0 @@ -================================================================= =================================== =================================== -:Author: Vincent Rouvreau :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 -:Requires: Matplotlib Numpy -================================================================= =================================== =================================== - -+-----------------------------------------------------------------+-----------------------------------------------------------------------+ -| .. 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. | -| | | -+-----------------------------------------------------------------+-----------------------------------------------------------------------+ -| :doc:`persistence_graphical_tools_user` | :doc:`persistence_graphical_tools_ref` | -+-----------------------------------------------------------------+-----------------------------------------------------------------------+ diff --git a/cython/doc/persistence_graphical_tools_user.rst b/cython/doc/persistence_graphical_tools_user.rst index 9033331f..292915eb 100644 --- a/cython/doc/persistence_graphical_tools_user.rst +++ b/cython/doc/persistence_graphical_tools_user.rst @@ -1,49 +1,26 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Persistence graphical tools user manual ======================================= Definition ---------- -.. include:: persistence_graphical_tools_sum.rst - - -Show palette values -------------------- - -This function is useful to show the color palette values of dimension: - +.. include:: persistence_graphical_tools_sum.inc -.. testcode:: - - import gudhi - plt = gudhi.show_palette_values(alpha=1.0) - plt.show() - -.. plot:: - - import gudhi - plt = gudhi.show_palette_values(alpha=1.0) - plt.show() Show persistence as a barcode ----------------------------- This function can display the persistence result as a barcode: -.. testcode:: - - import gudhi - - periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \ - '/data/bitmap/3d_torus.txt') - diag = periodic_cc.persistence() - plt = gudhi.plot_persistence_barcode(diag) - plt.show() - .. plot:: + :include-source: import gudhi - periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \ - '/data/bitmap/3d_torus.txt') + 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) @@ -54,24 +31,32 @@ Show persistence as a diagram This function can display the persistence result as a diagram: -.. testcode:: +.. plot:: + :include-source: import gudhi - - rips_complex = gudhi.RipsComplex(off_file=gudhi.__root_source_dir__ + \ - '/data/points/tore3D_1307.off', max_edge_length=0.2) - simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) - diag = simplex_tree.persistence() - plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13) + + # 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' + plt = gudhi.plot_persistence_diagram(persistence_file=persistence_file, + legend=True) plt.show() +If you want more information on a specific dimension, for instance: + .. plot:: + :include-source: import gudhi - rips_complex = gudhi.RipsComplex(off_file=gudhi.__root_source_dir__ + \ - '/data/points/tore3D_1307.off', max_edge_length=0.2) - simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) - diag = simplex_tree.persistence() - plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13) + 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 all points with some transparency + plt = gudhi.plot_persistence_diagram([(dim,interval) for interval in diag[dim]], + max_plots=0, alpha=0.1) plt.show() diff --git a/cython/doc/persistent_cohomology_sum.inc b/cython/doc/persistent_cohomology_sum.inc new file mode 100644 index 00000000..a26df1dc --- /dev/null +++ b/cython/doc/persistent_cohomology_sum.inc @@ -0,0 +1,27 @@ +================================================================= =================================== =================================== +:Author: Clément Maria :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 +================================================================= =================================== =================================== + ++-----------------------------------------------------------------+-----------------------------------------------------------------------+ +| .. figure:: | The theory of homology consists in attaching to a topological space | +| ../../doc/Persistent_cohomology/3DTorus_poch.png | a sequence of (homology) groups, capturing global topological | +| :figclass: align-center | features like connected components, holes, cavities, etc. Persistent | +| | homology studies the evolution -- birth, life and death -- of these | +| Rips Persistent Cohomology on a 3D | features when the topological space is changing. Consequently, the | +| Torus | theory is essentially composed of three elements: topological spaces, | +| | their homology groups and an evolution scheme. | +| | | +| | Computation of persistent cohomology using the algorithm of | +| | :cite:`DBLP:journals/dcg/SilvaMV11` and | +| | :cite:`DBLP:journals/corr/abs-1208-5018` and the Compressed | +| | Annotation Matrix implementation of | +| | :cite:`DBLP:conf/esa/BoissonnatDM13`. | +| | | ++-----------------------------------------------------------------+-----------------------------------------------------------------------+ +| :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` | ++-----------------------------------------------------------------+-----------------------------------------------------------------------+ diff --git a/cython/doc/persistent_cohomology_sum.rst b/cython/doc/persistent_cohomology_sum.rst deleted file mode 100644 index a26df1dc..00000000 --- a/cython/doc/persistent_cohomology_sum.rst +++ /dev/null @@ -1,27 +0,0 @@ -================================================================= =================================== =================================== -:Author: Clément Maria :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 -================================================================= =================================== =================================== - -+-----------------------------------------------------------------+-----------------------------------------------------------------------+ -| .. figure:: | The theory of homology consists in attaching to a topological space | -| ../../doc/Persistent_cohomology/3DTorus_poch.png | a sequence of (homology) groups, capturing global topological | -| :figclass: align-center | features like connected components, holes, cavities, etc. Persistent | -| | homology studies the evolution -- birth, life and death -- of these | -| Rips Persistent Cohomology on a 3D | features when the topological space is changing. Consequently, the | -| Torus | theory is essentially composed of three elements: topological spaces, | -| | their homology groups and an evolution scheme. | -| | | -| | Computation of persistent cohomology using the algorithm of | -| | :cite:`DBLP:journals/dcg/SilvaMV11` and | -| | :cite:`DBLP:journals/corr/abs-1208-5018` and the Compressed | -| | Annotation Matrix implementation of | -| | :cite:`DBLP:conf/esa/BoissonnatDM13`. | -| | | -+-----------------------------------------------------------------+-----------------------------------------------------------------------+ -| :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` | -+-----------------------------------------------------------------+-----------------------------------------------------------------------+ diff --git a/cython/doc/persistent_cohomology_user.rst b/cython/doc/persistent_cohomology_user.rst index bf90c163..ce7fc685 100644 --- a/cython/doc/persistent_cohomology_user.rst +++ b/cython/doc/persistent_cohomology_user.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Persistent cohomology user manual ================================= Definition diff --git a/cython/doc/pyplots/barcode_persistence.py b/cython/doc/pyplots/barcode_persistence.py deleted file mode 100755 index de33d506..00000000 --- a/cython/doc/pyplots/barcode_persistence.py +++ /dev/null @@ -1,7 +0,0 @@ -import gudhi - -periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \ - '/data/bitmap/3d_torus.txt') -diag = periodic_cc.persistence() -plt = gudhi.plot_persistence_barcode(diag) -plt.show() diff --git a/cython/doc/pyplots/diagram_persistence.py b/cython/doc/pyplots/diagram_persistence.py deleted file mode 100755 index c2fbf801..00000000 --- a/cython/doc/pyplots/diagram_persistence.py +++ /dev/null @@ -1,8 +0,0 @@ -import gudhi - -rips_complex = gudhi.RipsComplex(off_file=gudhi.__root_source_dir__ + \ - '/data/points/tore3D_1307.off', max_edge_length=0.2) -simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) -diag = simplex_tree.persistence() -plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13) -plt.show() diff --git a/cython/doc/pyplots/show_palette_values.py b/cython/doc/pyplots/show_palette_values.py deleted file mode 100755 index fdf9645f..00000000 --- a/cython/doc/pyplots/show_palette_values.py +++ /dev/null @@ -1,3 +0,0 @@ -import gudhi -plt = gudhi.show_palette_values(alpha=1.0) -plt.show() diff --git a/cython/doc/reader_utils_ref.rst b/cython/doc/reader_utils_ref.rst index 9c1ea6fc..f3ecebad 100644 --- a/cython/doc/reader_utils_ref.rst +++ b/cython/doc/reader_utils_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ============================= Reader utils reference manual ============================= diff --git a/cython/doc/rips_complex_ref.rst b/cython/doc/rips_complex_ref.rst index b17dc4e0..22b5616c 100644 --- a/cython/doc/rips_complex_ref.rst +++ b/cython/doc/rips_complex_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ============================= Rips complex reference manual ============================= diff --git a/cython/doc/rips_complex_sum.inc b/cython/doc/rips_complex_sum.inc new file mode 100644 index 00000000..5616bfa9 --- /dev/null +++ b/cython/doc/rips_complex_sum.inc @@ -0,0 +1,17 @@ +================================================================= =================================== =================================== +:Author: Clément Maria, Pawel Dlotko, Vincent Rouvreau :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 +================================================================= =================================== =================================== + ++----------------------------------------------------------------+------------------------------------------------------------------------+ +| .. figure:: | Rips complex is a simplicial complex constructed from a one skeleton | +| ../../doc/Rips_complex/rips_complex_representation.png | graph. | +| :figclass: align-center | | +| | The filtration value of each edge is computed from a user-given | +| Rips complex representation | distance function and is inserted until a user-given threshold | +| | value. | +| | | +| | This complex can be built from a point cloud and a distance function, | +| | or from a distance matrix. | ++----------------------------------------------------------------+------------------------------------------------------------------------+ +| :doc:`rips_complex_user` | :doc:`rips_complex_ref` | ++----------------------------------------------------------------+------------------------------------------------------------------------+ diff --git a/cython/doc/rips_complex_sum.rst b/cython/doc/rips_complex_sum.rst deleted file mode 100644 index 5616bfa9..00000000 --- a/cython/doc/rips_complex_sum.rst +++ /dev/null @@ -1,17 +0,0 @@ -================================================================= =================================== =================================== -:Author: Clément Maria, Pawel Dlotko, Vincent Rouvreau :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 -================================================================= =================================== =================================== - -+----------------------------------------------------------------+------------------------------------------------------------------------+ -| .. figure:: | Rips complex is a simplicial complex constructed from a one skeleton | -| ../../doc/Rips_complex/rips_complex_representation.png | graph. | -| :figclass: align-center | | -| | The filtration value of each edge is computed from a user-given | -| Rips complex representation | distance function and is inserted until a user-given threshold | -| | value. | -| | | -| | This complex can be built from a point cloud and a distance function, | -| | or from a distance matrix. | -+----------------------------------------------------------------+------------------------------------------------------------------------+ -| :doc:`rips_complex_user` | :doc:`rips_complex_ref` | -+----------------------------------------------------------------+------------------------------------------------------------------------+ diff --git a/cython/doc/rips_complex_user.rst b/cython/doc/rips_complex_user.rst index 96ba9944..a8c06cf9 100644 --- a/cython/doc/rips_complex_user.rst +++ b/cython/doc/rips_complex_user.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Rips complex user manual ========================= Definition @@ -101,8 +105,8 @@ Finally, it is asked to display information about the Rips complex. .. testcode:: import gudhi - rips_complex = gudhi.RipsComplex(off_file=gudhi.__root_source_dir__ + \ - '/data/points/alphacomplexdoc.off', max_edge_length=12.0) + point_cloud = gudhi.read_off(off_file=gudhi.__root_source_dir__ + '/data/points/alphacomplexdoc.off') + rips_complex = gudhi.RipsComplex(points=point_cloud, 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()) + ' - ' + \ repr(simplex_tree.num_simplices()) + ' simplices - ' + \ @@ -197,7 +201,7 @@ Example from csv file ^^^^^^^^^^^^^^^^^^^^^ This example builds the :doc:`Rips_complex ` from the given -points in an OFF file, and max_edge_length value. +distance matrix in a csv file, and max_edge_length value. Then it creates a :doc:`Simplex_tree ` with it. Finally, it is asked to display information about the Rips complex. @@ -206,8 +210,9 @@ Finally, it is asked to display information about the Rips complex. .. testcode:: import gudhi - rips_complex = gudhi.RipsComplex(csv_file=gudhi.__root_source_dir__ + \ - '/data/distance_matrix/full_square_distance_matrix.csv', max_edge_length=12.0) + distance_matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file=gudhi.__root_source_dir__ + \ + '/data/distance_matrix/full_square_distance_matrix.csv') + rips_complex = gudhi.RipsComplex(distance_matrix=distance_matrix, 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()) + ' - ' + \ repr(simplex_tree.num_simplices()) + ' simplices - ' + \ @@ -240,3 +245,72 @@ the program output is: [0, 3] -> 9.43 [4, 6] -> 9.49 [3, 6] -> 11.00 + +Correlation matrix +------------------ + +Example from a correlation matrix +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Analogously to the case of distance matrix, Rips complexes can be also constructed based on correlation matrix. +Given a correlation matrix M, comportment-wise 1-M is a distance matrix. +This example builds the one skeleton graph from the given corelation matrix and threshold value. +Then it creates a :doc:`Simplex_tree ` with it. + +Finally, it is asked to display information about the simplicial complex. + +.. testcode:: + + import gudhi + import numpy as np + + # User defined correlation matrix is: + # |1 0.06 0.23 0.01 0.89| + # |0.06 1 0.74 0.01 0.61| + # |0.23 0.74 1 0.72 0.03| + # |0.01 0.01 0.72 1 0.7 | + # |0.89 0.61 0.03 0.7 1 | + correlation_matrix=np.array([[1., 0.06, 0.23, 0.01, 0.89], + [0.06, 1., 0.74, 0.01, 0.61], + [0.23, 0.74, 1., 0.72, 0.03], + [0.01, 0.01, 0.72, 1., 0.7], + [0.89, 0.61, 0.03, 0.7, 1.]], float) + + distance_matrix = np.ones((correlation_matrix.shape),float) - correlation_matrix + rips_complex = gudhi.RipsComplex(distance_matrix=distance_matrix, max_edge_length=1.0) + + simplex_tree = rips_complex.create_simplex_tree(max_dimension=1) + result_str = 'Rips complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \ + repr(simplex_tree.num_simplices()) + ' simplices - ' + \ + repr(simplex_tree.num_vertices()) + ' vertices.' + print(result_str) + fmt = '%s -> %.2f' + for filtered_value in simplex_tree.get_filtration(): + print(fmt % tuple(filtered_value)) + +When launching (Rips maximal distance between 2 points is 12.0, is expanded +until dimension 1 - one skeleton graph in other words), the output is: + +.. testoutput:: + + Rips complex is of dimension 1 - 15 simplices - 5 vertices. + [0] -> 0.00 + [1] -> 0.00 + [2] -> 0.00 + [3] -> 0.00 + [4] -> 0.00 + [0, 4] -> 0.11 + [1, 2] -> 0.26 + [2, 3] -> 0.28 + [3, 4] -> 0.30 + [1, 4] -> 0.39 + [0, 2] -> 0.77 + [0, 1] -> 0.94 + [2, 4] -> 0.97 + [0, 3] -> 0.99 + [1, 3] -> 0.99 + +.. note:: + As persistence diagrams points will be under the diagonal, + bottleneck distance and persistence graphical tool will not work properly, + this is a known issue. diff --git a/cython/doc/simplex_tree_ref.rst b/cython/doc/simplex_tree_ref.rst index 6d196843..9eb8c199 100644 --- a/cython/doc/simplex_tree_ref.rst +++ b/cython/doc/simplex_tree_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ============================= Simplex tree reference manual ============================= diff --git a/cython/doc/simplex_tree_sum.inc b/cython/doc/simplex_tree_sum.inc new file mode 100644 index 00000000..fb0e54c1 --- /dev/null +++ b/cython/doc/simplex_tree_sum.inc @@ -0,0 +1,14 @@ +================================================================= =================================== =================================== +:Author: Clément Maria :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 +================================================================= =================================== =================================== + ++----------------------------------------------------------------+------------------------------------------------------------------------+ +| .. figure:: | The simplex tree is an efficient and flexible data structure for | +| ../../doc/Simplex_tree/Simplex_tree_representation.png | representing general (filtered) simplicial complexes. | +| :alt: Simplex tree representation | | +| :figclass: align-center | The data structure is described in | +| | :cite:`boissonnatmariasimplextreealgorithmica` | +| Simplex tree representation | | ++----------------------------------------------------------------+------------------------------------------------------------------------+ +| :doc:`simplex_tree_user` | :doc:`simplex_tree_ref` | ++----------------------------------------------------------------+------------------------------------------------------------------------+ diff --git a/cython/doc/simplex_tree_sum.rst b/cython/doc/simplex_tree_sum.rst deleted file mode 100644 index fb0e54c1..00000000 --- a/cython/doc/simplex_tree_sum.rst +++ /dev/null @@ -1,14 +0,0 @@ -================================================================= =================================== =================================== -:Author: Clément Maria :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 -================================================================= =================================== =================================== - -+----------------------------------------------------------------+------------------------------------------------------------------------+ -| .. figure:: | The simplex tree is an efficient and flexible data structure for | -| ../../doc/Simplex_tree/Simplex_tree_representation.png | representing general (filtered) simplicial complexes. | -| :alt: Simplex tree representation | | -| :figclass: align-center | The data structure is described in | -| | :cite:`boissonnatmariasimplextreealgorithmica` | -| Simplex tree representation | | -+----------------------------------------------------------------+------------------------------------------------------------------------+ -| :doc:`simplex_tree_user` | :doc:`simplex_tree_ref` | -+----------------------------------------------------------------+------------------------------------------------------------------------+ diff --git a/cython/doc/simplex_tree_user.rst b/cython/doc/simplex_tree_user.rst index 4b1dde19..aebeb29f 100644 --- a/cython/doc/simplex_tree_user.rst +++ b/cython/doc/simplex_tree_user.rst @@ -1,9 +1,13 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Simplex tree user manual ======================== Definition ---------- -.. include:: simplex_tree_sum.rst +.. include:: simplex_tree_sum.inc A simplicial complex :math:`\mathbf{K}` on a set of vertices :math:`V = \{1, \cdots ,|V|\}` is a collection of simplices :math:`\{\sigma\}`, :math:`\sigma \subseteq V` such that diff --git a/cython/doc/strong_witness_complex_ref.rst b/cython/doc/strong_witness_complex_ref.rst index 4ed4fe46..d624d711 100644 --- a/cython/doc/strong_witness_complex_ref.rst +++ b/cython/doc/strong_witness_complex_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ======================================= Strong witness complex reference manual ======================================= diff --git a/cython/doc/tangential_complex_ref.rst b/cython/doc/tangential_complex_ref.rst index 35589475..cdfda082 100644 --- a/cython/doc/tangential_complex_ref.rst +++ b/cython/doc/tangential_complex_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + =================================== Tangential complex reference manual =================================== diff --git a/cython/doc/tangential_complex_sum.inc b/cython/doc/tangential_complex_sum.inc new file mode 100644 index 00000000..72b4d7ba --- /dev/null +++ b/cython/doc/tangential_complex_sum.inc @@ -0,0 +1,15 @@ +================================================================= =================================== =================================== +:Author: Clément Jamin :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 +:Requires: CGAL :math:`\geq` 4.8.0 Eigen3 +================================================================= =================================== =================================== + ++----------------------------------------------------------------+------------------------------------------------------------------------+ +| .. figure:: | A Tangential Delaunay complex is a simplicial complex designed to | +| ../../doc/Tangential_complex/tc_examples.png | reconstruct a :math:`k`-dimensional manifold embedded in :math:`d`- | +| :figclass: align-center | dimensional Euclidean space. The input is a point sample coming from | +| | an unknown manifold. The running time depends only linearly on the | +| Tangential complex representation | extrinsic dimension :math:`d` and exponentially on the intrinsic | +| | dimension :math:`k`. | ++----------------------------------------------------------------+------------------------------------------------------------------------+ +| :doc:`tangential_complex_user` | :doc:`tangential_complex_ref` | ++----------------------------------------------------------------+------------------------------------------------------------------------+ diff --git a/cython/doc/tangential_complex_sum.rst b/cython/doc/tangential_complex_sum.rst deleted file mode 100644 index 72b4d7ba..00000000 --- a/cython/doc/tangential_complex_sum.rst +++ /dev/null @@ -1,15 +0,0 @@ -================================================================= =================================== =================================== -:Author: Clément Jamin :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 -:Requires: CGAL :math:`\geq` 4.8.0 Eigen3 -================================================================= =================================== =================================== - -+----------------------------------------------------------------+------------------------------------------------------------------------+ -| .. figure:: | A Tangential Delaunay complex is a simplicial complex designed to | -| ../../doc/Tangential_complex/tc_examples.png | reconstruct a :math:`k`-dimensional manifold embedded in :math:`d`- | -| :figclass: align-center | dimensional Euclidean space. The input is a point sample coming from | -| | an unknown manifold. The running time depends only linearly on the | -| Tangential complex representation | extrinsic dimension :math:`d` and exponentially on the intrinsic | -| | dimension :math:`k`. | -+----------------------------------------------------------------+------------------------------------------------------------------------+ -| :doc:`tangential_complex_user` | :doc:`tangential_complex_ref` | -+----------------------------------------------------------------+------------------------------------------------------------------------+ diff --git a/cython/doc/tangential_complex_user.rst b/cython/doc/tangential_complex_user.rst index efa6d7ce..5ce69e86 100644 --- a/cython/doc/tangential_complex_user.rst +++ b/cython/doc/tangential_complex_user.rst @@ -1,6 +1,10 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Tangential complex user manual ============================== -.. include:: tangential_complex_sum.rst +.. include:: tangential_complex_sum.inc Definition ---------- @@ -122,8 +126,8 @@ This example builds the Tangential complex of point set read in an OFF file. .. testcode:: import gudhi - tc = gudhi.TangentialComplex(off_file=gudhi.__root_source_dir__ + \ - '/data/points/alphacomplexdoc.off') + tc = gudhi.TangentialComplex(intrisic_dim = 1, + off_file=gudhi.__root_source_dir__ + '/data/points/alphacomplexdoc.off') result_str = 'Tangential contains ' + repr(tc.num_simplices()) + \ ' simplices - ' + repr(tc.num_vertices()) + ' vertices.' print(result_str) @@ -169,7 +173,8 @@ simplices. .. testcode:: import gudhi - tc = gudhi.TangentialComplex(points=[[0.0, 0.0], [1.0, 0.0], [0.0, 1.0], [1.0, 1.0]]) + tc = gudhi.TangentialComplex(intrisic_dim = 1, + points=[[0.0, 0.0], [1.0, 0.0], [0.0, 1.0], [1.0, 1.0]]) result_str = 'Tangential contains ' + repr(tc.num_vertices()) + ' vertices.' print(result_str) diff --git a/cython/doc/todos.rst b/cython/doc/todos.rst index 78972a4c..ca274ced 100644 --- a/cython/doc/todos.rst +++ b/cython/doc/todos.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ========== To be done ========== diff --git a/cython/doc/witness_complex_ref.rst b/cython/doc/witness_complex_ref.rst index c78760cb..9987d3fd 100644 --- a/cython/doc/witness_complex_ref.rst +++ b/cython/doc/witness_complex_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ================================ Witness complex reference manual ================================ diff --git a/cython/doc/witness_complex_sum.inc b/cython/doc/witness_complex_sum.inc new file mode 100644 index 00000000..a8a126a0 --- /dev/null +++ b/cython/doc/witness_complex_sum.inc @@ -0,0 +1,19 @@ +================================================================= =================================== =================================== +:Author: Siargey Kachanovich :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 +:Euclidean version requires: CGAL :math:`\geq` 4.6.0 Eigen3 +================================================================= =================================== =================================== + ++-------------------------------------------------------------------+----------------------------------------------------------------------+ +| .. figure:: | Witness complex :math:`Wit(W,L)` is a simplicial complex defined on | +| ../../doc/Witness_complex/Witness_complex_representation.png | two sets of points in :math:`\mathbb{R}^D`. | +| :alt: Witness complex representation | | +| :figclass: align-center | The data structure is described in | +| | :cite:`boissonnatmariasimplextreealgorithmica`. | +| | | +| Witness complex representation | | ++-------------------------------------------------------------------+----------------------------------------------------------------------+ +| :doc:`witness_complex_user` | * :doc:`witness_complex_ref` | +| | * :doc:`strong_witness_complex_ref` | +| | * :doc:`euclidean_witness_complex_ref` | +| | * :doc:`euclidean_strong_witness_complex_ref` | ++-------------------------------------------------------------------+----------------------------------------------------------------------+ diff --git a/cython/doc/witness_complex_sum.rst b/cython/doc/witness_complex_sum.rst deleted file mode 100644 index a8a126a0..00000000 --- a/cython/doc/witness_complex_sum.rst +++ /dev/null @@ -1,19 +0,0 @@ -================================================================= =================================== =================================== -:Author: Siargey Kachanovich :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 -:Euclidean version requires: CGAL :math:`\geq` 4.6.0 Eigen3 -================================================================= =================================== =================================== - -+-------------------------------------------------------------------+----------------------------------------------------------------------+ -| .. figure:: | Witness complex :math:`Wit(W,L)` is a simplicial complex defined on | -| ../../doc/Witness_complex/Witness_complex_representation.png | two sets of points in :math:`\mathbb{R}^D`. | -| :alt: Witness complex representation | | -| :figclass: align-center | The data structure is described in | -| | :cite:`boissonnatmariasimplextreealgorithmica`. | -| | | -| Witness complex representation | | -+-------------------------------------------------------------------+----------------------------------------------------------------------+ -| :doc:`witness_complex_user` | * :doc:`witness_complex_ref` | -| | * :doc:`strong_witness_complex_ref` | -| | * :doc:`euclidean_witness_complex_ref` | -| | * :doc:`euclidean_strong_witness_complex_ref` | -+-------------------------------------------------------------------+----------------------------------------------------------------------+ diff --git a/cython/doc/witness_complex_user.rst b/cython/doc/witness_complex_user.rst index 99be5185..40e94134 100644 --- a/cython/doc/witness_complex_user.rst +++ b/cython/doc/witness_complex_user.rst @@ -1,7 +1,11 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Witness complex user manual =========================== -.. include:: witness_complex_sum.rst +.. include:: witness_complex_sum.inc Definitions ----------- -- cgit v1.2.3