From e64a8b5cfd08759b2e43804539db05f44c2615ad Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 6 Jun 2018 09:16:00 +0000 Subject: Fix sphinx warning and issues due to new version of sphinx Modify the doc for persistence diagram git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/python_2.1.0_fix_vincent@3543 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 3efbc052bce9a11a6b4a758f8229e91eece2a7f4 --- src/cython/doc/_templates/layout.html | 13 +++--- src/cython/doc/alpha_complex_ref.rst | 4 ++ src/cython/doc/alpha_complex_sum.inc | 22 +++++++++ src/cython/doc/alpha_complex_sum.rst | 22 --------- src/cython/doc/alpha_complex_user.rst | 12 +++-- src/cython/doc/bottleneck_distance_sum.inc | 15 ++++++ src/cython/doc/bottleneck_distance_sum.rst | 15 ------ src/cython/doc/bottleneck_distance_user.rst | 6 ++- src/cython/doc/citation.rst | 4 ++ src/cython/doc/conf.py | 3 +- src/cython/doc/cubical_complex_ref.rst | 4 ++ src/cython/doc/cubical_complex_sum.inc | 15 ++++++ src/cython/doc/cubical_complex_sum.rst | 15 ------ src/cython/doc/cubical_complex_user.rst | 5 ++ .../doc/euclidean_strong_witness_complex_ref.rst | 4 ++ src/cython/doc/euclidean_witness_complex_ref.rst | 4 ++ src/cython/doc/examples.rst | 4 ++ src/cython/doc/fileformats.rst | 4 ++ src/cython/doc/index.rst | 18 ++++---- src/cython/doc/installation.rst | 4 ++ src/cython/doc/periodic_cubical_complex_ref.rst | 4 ++ src/cython/doc/persistence_graphical_tools_ref.rst | 4 ++ src/cython/doc/persistence_graphical_tools_sum.inc | 12 +++++ src/cython/doc/persistence_graphical_tools_sum.rst | 12 ----- .../doc/persistence_graphical_tools_user.rst | 53 ++++++++++++---------- src/cython/doc/persistent_cohomology_sum.inc | 27 +++++++++++ src/cython/doc/persistent_cohomology_sum.rst | 27 ----------- src/cython/doc/persistent_cohomology_user.rst | 4 ++ src/cython/doc/pyplots/barcode_persistence.py | 7 --- src/cython/doc/pyplots/diagram_persistence.py | 9 ---- src/cython/doc/reader_utils_ref.rst | 4 ++ src/cython/doc/rips_complex_ref.rst | 4 ++ src/cython/doc/rips_complex_sum.inc | 17 +++++++ src/cython/doc/rips_complex_sum.rst | 17 ------- src/cython/doc/rips_complex_user.rst | 6 ++- src/cython/doc/simplex_tree_ref.rst | 4 ++ src/cython/doc/simplex_tree_sum.inc | 14 ++++++ src/cython/doc/simplex_tree_sum.rst | 14 ------ src/cython/doc/simplex_tree_user.rst | 6 ++- src/cython/doc/strong_witness_complex_ref.rst | 4 ++ src/cython/doc/tangential_complex_ref.rst | 4 ++ src/cython/doc/tangential_complex_sum.inc | 15 ++++++ src/cython/doc/tangential_complex_sum.rst | 15 ------ src/cython/doc/tangential_complex_user.rst | 6 ++- src/cython/doc/todos.rst | 4 ++ src/cython/doc/witness_complex_ref.rst | 4 ++ src/cython/doc/witness_complex_sum.inc | 19 ++++++++ src/cython/doc/witness_complex_sum.rst | 19 -------- src/cython/doc/witness_complex_user.rst | 6 ++- src/cython/setup.py.in | 2 - 50 files changed, 311 insertions(+), 225 deletions(-) create mode 100644 src/cython/doc/alpha_complex_sum.inc delete mode 100644 src/cython/doc/alpha_complex_sum.rst create mode 100644 src/cython/doc/bottleneck_distance_sum.inc delete mode 100644 src/cython/doc/bottleneck_distance_sum.rst create mode 100644 src/cython/doc/cubical_complex_sum.inc delete mode 100644 src/cython/doc/cubical_complex_sum.rst create mode 100644 src/cython/doc/persistence_graphical_tools_sum.inc delete mode 100644 src/cython/doc/persistence_graphical_tools_sum.rst create mode 100644 src/cython/doc/persistent_cohomology_sum.inc delete mode 100644 src/cython/doc/persistent_cohomology_sum.rst delete mode 100755 src/cython/doc/pyplots/barcode_persistence.py delete mode 100755 src/cython/doc/pyplots/diagram_persistence.py create mode 100644 src/cython/doc/rips_complex_sum.inc delete mode 100644 src/cython/doc/rips_complex_sum.rst create mode 100644 src/cython/doc/simplex_tree_sum.inc delete mode 100644 src/cython/doc/simplex_tree_sum.rst create mode 100644 src/cython/doc/tangential_complex_sum.inc delete mode 100644 src/cython/doc/tangential_complex_sum.rst create mode 100644 src/cython/doc/witness_complex_sum.inc delete mode 100644 src/cython/doc/witness_complex_sum.rst (limited to 'src') diff --git a/src/cython/doc/_templates/layout.html b/src/cython/doc/_templates/layout.html index c9356116..797afb27 100644 --- a/src/cython/doc/_templates/layout.html +++ b/src/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 %} diff --git a/src/cython/doc/alpha_complex_ref.rst b/src/cython/doc/alpha_complex_ref.rst index 6a122b09..7da79543 100644 --- a/src/cython/doc/alpha_complex_ref.rst +++ b/src/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/src/cython/doc/alpha_complex_sum.inc b/src/cython/doc/alpha_complex_sum.inc new file mode 100644 index 00000000..1680a712 --- /dev/null +++ b/src/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/src/cython/doc/alpha_complex_sum.rst b/src/cython/doc/alpha_complex_sum.rst deleted file mode 100644 index 1680a712..00000000 --- a/src/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/src/cython/doc/alpha_complex_user.rst b/src/cython/doc/alpha_complex_user.rst index db7edd6f..d1e9c7cd 100644 --- a/src/cython/doc/alpha_complex_user.rst +++ b/src/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/src/cython/doc/bottleneck_distance_sum.inc b/src/cython/doc/bottleneck_distance_sum.inc new file mode 100644 index 00000000..030fad9e --- /dev/null +++ b/src/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/src/cython/doc/bottleneck_distance_sum.rst b/src/cython/doc/bottleneck_distance_sum.rst deleted file mode 100644 index 030fad9e..00000000 --- a/src/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/src/cython/doc/bottleneck_distance_user.rst b/src/cython/doc/bottleneck_distance_user.rst index 7692dce2..605db022 100644 --- a/src/cython/doc/bottleneck_distance_user.rst +++ b/src/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/src/cython/doc/citation.rst b/src/cython/doc/citation.rst index f4fdf83b..117eb9dd 100644 --- a/src/cython/doc/citation.rst +++ b/src/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/src/cython/doc/conf.py b/src/cython/doc/conf.py index a13c9751..4a54d4fd 100755 --- a/src/cython/doc/conf.py +++ b/src/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/src/cython/doc/cubical_complex_ref.rst b/src/cython/doc/cubical_complex_ref.rst index 84aa4223..1fe9d5fb 100644 --- a/src/cython/doc/cubical_complex_ref.rst +++ b/src/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/src/cython/doc/cubical_complex_sum.inc b/src/cython/doc/cubical_complex_sum.inc new file mode 100644 index 00000000..280ad0e0 --- /dev/null +++ b/src/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/src/cython/doc/cubical_complex_sum.rst b/src/cython/doc/cubical_complex_sum.rst deleted file mode 100644 index 280ad0e0..00000000 --- a/src/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/src/cython/doc/cubical_complex_user.rst b/src/cython/doc/cubical_complex_user.rst index dd82ad93..320bd79b 100644 --- a/src/cython/doc/cubical_complex_user.rst +++ b/src/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. --------- diff --git a/src/cython/doc/euclidean_strong_witness_complex_ref.rst b/src/cython/doc/euclidean_strong_witness_complex_ref.rst index bebf0f9a..1a602cd5 100644 --- a/src/cython/doc/euclidean_strong_witness_complex_ref.rst +++ b/src/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/src/cython/doc/euclidean_witness_complex_ref.rst b/src/cython/doc/euclidean_witness_complex_ref.rst index 29b8806f..28daf965 100644 --- a/src/cython/doc/euclidean_witness_complex_ref.rst +++ b/src/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/src/cython/doc/examples.rst b/src/cython/doc/examples.rst index 1e596e18..d42f5a92 100644 --- a/src/cython/doc/examples.rst +++ b/src/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/src/cython/doc/fileformats.rst b/src/cython/doc/fileformats.rst index 4f0b6f6d..ff20f26e 100644 --- a/src/cython/doc/fileformats.rst +++ b/src/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/src/cython/doc/index.rst b/src/cython/doc/index.rst index 3945d72a..4e444fb0 100644 --- a/src/cython/doc/index.rst +++ b/src/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/src/cython/doc/installation.rst b/src/cython/doc/installation.rst index b0bc5f38..43ff85c5 100644 --- a/src/cython/doc/installation.rst +++ b/src/cython/doc/installation.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + Installation ############ diff --git a/src/cython/doc/periodic_cubical_complex_ref.rst b/src/cython/doc/periodic_cubical_complex_ref.rst index c6190a1b..4b831647 100644 --- a/src/cython/doc/periodic_cubical_complex_ref.rst +++ b/src/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/src/cython/doc/persistence_graphical_tools_ref.rst b/src/cython/doc/persistence_graphical_tools_ref.rst index a69c8ba2..a2c6bcef 100644 --- a/src/cython/doc/persistence_graphical_tools_ref.rst +++ b/src/cython/doc/persistence_graphical_tools_ref.rst @@ -1,3 +1,7 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + ============================================ Persistence graphical tools reference manual ============================================ diff --git a/src/cython/doc/persistence_graphical_tools_sum.inc b/src/cython/doc/persistence_graphical_tools_sum.inc new file mode 100644 index 00000000..d602daa7 --- /dev/null +++ b/src/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/src/cython/doc/persistence_graphical_tools_sum.rst b/src/cython/doc/persistence_graphical_tools_sum.rst deleted file mode 100644 index d602daa7..00000000 --- a/src/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/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst index 46f871c7..292915eb 100644 --- a/src/cython/doc/persistence_graphical_tools_user.rst +++ b/src/cython/doc/persistence_graphical_tools_user.rst @@ -1,8 +1,12 @@ +: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 +.. include:: persistence_graphical_tools_sum.inc Show persistence as a barcode @@ -10,22 +14,13 @@ 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) @@ -36,24 +31,32 @@ Show persistence as a diagram This function can display the persistence result as a diagram: -.. testcode:: +.. plot:: + :include-source: import gudhi - - point_cloud = gudhi.read_off(off_file=gudhi.__root_source_dir__ + '/data/points/tore3D_1307.off') - rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.3) - simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) - diag = simplex_tree.persistence() - plt = gudhi.plot_persistence_diagram(diag) + + # 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 - point_cloud = gudhi.read_off(off_file=gudhi.__root_source_dir__ + '/data/points/tore3D_1307.off') - rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.3) - simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) - diag = simplex_tree.persistence() - plt = gudhi.plot_persistence_diagram(diag) + 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/src/cython/doc/persistent_cohomology_sum.inc b/src/cython/doc/persistent_cohomology_sum.inc new file mode 100644 index 00000000..a26df1dc --- /dev/null +++ b/src/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/src/cython/doc/persistent_cohomology_sum.rst b/src/cython/doc/persistent_cohomology_sum.rst deleted file mode 100644 index a26df1dc..00000000 --- a/src/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/src/cython/doc/persistent_cohomology_user.rst b/src/cython/doc/persistent_cohomology_user.rst index bf90c163..ce7fc685 100644 --- a/src/cython/doc/persistent_cohomology_user.rst +++ b/src/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/src/cython/doc/pyplots/barcode_persistence.py b/src/cython/doc/pyplots/barcode_persistence.py deleted file mode 100755 index de33d506..00000000 --- a/src/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/src/cython/doc/pyplots/diagram_persistence.py b/src/cython/doc/pyplots/diagram_persistence.py deleted file mode 100755 index 3bab0ca1..00000000 --- a/src/cython/doc/pyplots/diagram_persistence.py +++ /dev/null @@ -1,9 +0,0 @@ -import gudhi - -point_cloud = gudhi.read_off(off_file=gudhi.__root_source_dir__ + \ - '/data/points/tore3D_1307.off') -rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.3) -simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) -diag = simplex_tree.persistence() -plt = gudhi.plot_persistence_diagram(diag) -plt.show() diff --git a/src/cython/doc/reader_utils_ref.rst b/src/cython/doc/reader_utils_ref.rst index 9c1ea6fc..f3ecebad 100644 --- a/src/cython/doc/reader_utils_ref.rst +++ b/src/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/src/cython/doc/rips_complex_ref.rst b/src/cython/doc/rips_complex_ref.rst index b17dc4e0..22b5616c 100644 --- a/src/cython/doc/rips_complex_ref.rst +++ b/src/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/src/cython/doc/rips_complex_sum.inc b/src/cython/doc/rips_complex_sum.inc new file mode 100644 index 00000000..5616bfa9 --- /dev/null +++ b/src/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/src/cython/doc/rips_complex_sum.rst b/src/cython/doc/rips_complex_sum.rst deleted file mode 100644 index 5616bfa9..00000000 --- a/src/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/src/cython/doc/rips_complex_user.rst b/src/cython/doc/rips_complex_user.rst index 7738aef0..a8c06cf9 100644 --- a/src/cython/doc/rips_complex_user.rst +++ b/src/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 @@ -243,7 +247,7 @@ the program output is: [3, 6] -> 11.00 Correlation matrix ---------------- +------------------ Example from a correlation matrix ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ diff --git a/src/cython/doc/simplex_tree_ref.rst b/src/cython/doc/simplex_tree_ref.rst index 6d196843..9eb8c199 100644 --- a/src/cython/doc/simplex_tree_ref.rst +++ b/src/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/src/cython/doc/simplex_tree_sum.inc b/src/cython/doc/simplex_tree_sum.inc new file mode 100644 index 00000000..fb0e54c1 --- /dev/null +++ b/src/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/src/cython/doc/simplex_tree_sum.rst b/src/cython/doc/simplex_tree_sum.rst deleted file mode 100644 index fb0e54c1..00000000 --- a/src/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/src/cython/doc/simplex_tree_user.rst b/src/cython/doc/simplex_tree_user.rst index 4b1dde19..aebeb29f 100644 --- a/src/cython/doc/simplex_tree_user.rst +++ b/src/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/src/cython/doc/strong_witness_complex_ref.rst b/src/cython/doc/strong_witness_complex_ref.rst index 4ed4fe46..d624d711 100644 --- a/src/cython/doc/strong_witness_complex_ref.rst +++ b/src/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/src/cython/doc/tangential_complex_ref.rst b/src/cython/doc/tangential_complex_ref.rst index 35589475..cdfda082 100644 --- a/src/cython/doc/tangential_complex_ref.rst +++ b/src/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/src/cython/doc/tangential_complex_sum.inc b/src/cython/doc/tangential_complex_sum.inc new file mode 100644 index 00000000..72b4d7ba --- /dev/null +++ b/src/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/src/cython/doc/tangential_complex_sum.rst b/src/cython/doc/tangential_complex_sum.rst deleted file mode 100644 index 72b4d7ba..00000000 --- a/src/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/src/cython/doc/tangential_complex_user.rst b/src/cython/doc/tangential_complex_user.rst index fafb3193..5ce69e86 100644 --- a/src/cython/doc/tangential_complex_user.rst +++ b/src/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 ---------- diff --git a/src/cython/doc/todos.rst b/src/cython/doc/todos.rst index 78972a4c..ca274ced 100644 --- a/src/cython/doc/todos.rst +++ b/src/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/src/cython/doc/witness_complex_ref.rst b/src/cython/doc/witness_complex_ref.rst index c78760cb..9987d3fd 100644 --- a/src/cython/doc/witness_complex_ref.rst +++ b/src/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/src/cython/doc/witness_complex_sum.inc b/src/cython/doc/witness_complex_sum.inc new file mode 100644 index 00000000..a8a126a0 --- /dev/null +++ b/src/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/src/cython/doc/witness_complex_sum.rst b/src/cython/doc/witness_complex_sum.rst deleted file mode 100644 index a8a126a0..00000000 --- a/src/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/src/cython/doc/witness_complex_user.rst b/src/cython/doc/witness_complex_user.rst index 99be5185..40e94134 100644 --- a/src/cython/doc/witness_complex_user.rst +++ b/src/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 ----------- diff --git a/src/cython/setup.py.in b/src/cython/setup.py.in index a798717d..ee381a1b 100644 --- a/src/cython/setup.py.in +++ b/src/cython/setup.py.in @@ -46,8 +46,6 @@ setup( version='@GUDHI_VERSION@', url='http://gudhi.gforge.inria.fr/', ext_modules = cythonize(gudhi), - - #install_requires = required, install_requires = [ "matplotlib", "numpy", -- cgit v1.2.3