From ef8a5bca22be47df00f61d660e84948f1f45f9ba Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 7 Sep 2017 16:07:41 +0000 Subject: Fix doc for user_version git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2650 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 18aebd67968fd48ccfcfcfbff75c614496f4424e --- src/cython/doc/alpha_complex_sum.rst | 2 +- src/cython/doc/alpha_complex_user.rst | 6 +++--- src/cython/doc/bottleneck_distance_sum.rst | 2 +- src/cython/doc/cubical_complex_sum.rst | 22 +++++++++++----------- src/cython/doc/cubical_complex_user.rst | 2 +- src/cython/doc/index.rst | 8 +++++--- src/cython/doc/persistent_cohomology_sum.rst | 2 +- src/cython/doc/persistent_cohomology_user.rst | 2 +- src/cython/doc/rips_complex_sum.rst | 2 +- src/cython/doc/rips_complex_user.rst | 2 +- src/cython/doc/simplex_tree_sum.rst | 2 +- src/cython/doc/tangential_complex_sum.rst | 4 ++-- src/cython/doc/tangential_complex_user.rst | 14 +++++++------- src/cython/doc/witness_complex_sum.rst | 26 ++++++++++++++------------ src/cython/doc/witness_complex_user.rst | 4 ++-- 15 files changed, 52 insertions(+), 48 deletions(-) diff --git a/src/cython/doc/alpha_complex_sum.rst b/src/cython/doc/alpha_complex_sum.rst index a5f6420a..1680a712 100644 --- a/src/cython/doc/alpha_complex_sum.rst +++ b/src/cython/doc/alpha_complex_sum.rst @@ -5,7 +5,7 @@ +----------------------------------------------------------------+------------------------------------------------------------------------+ | .. figure:: | Alpha_complex is a simplicial complex constructed from the finite | -| img/alpha_complex_representation.png | cells of a Delaunay Triangulation. | +| ../../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 | diff --git a/src/cython/doc/alpha_complex_user.rst b/src/cython/doc/alpha_complex_user.rst index e541e6d3..c3a13bef 100644 --- a/src/cython/doc/alpha_complex_user.rst +++ b/src/cython/doc/alpha_complex_user.rst @@ -75,7 +75,7 @@ In order to build the alpha complex, first, a Simplex tree is built from the cel (The filtration value is set to NaN, which stands for unknown value): .. figure:: - img/alpha_complex_doc.png + ../../doc/Alpha_complex/alpha_complex_doc.png :figclass: align-center :alt: Simplex tree structure construction example @@ -112,7 +112,7 @@ computes the filtration value of the triangle, and then propagates the filtratio here: .. figure:: - img/alpha_complex_doc_420.png + ../../doc/Alpha_complex/alpha_complex_doc_420.png :figclass: align-center :alt: Filtration value propagation example @@ -201,6 +201,6 @@ the program output is: CGAL citations ============== -.. bibliography:: how_to_cite_cgal.bib +.. bibliography:: ../../biblio/how_to_cite_cgal.bib :filter: docnames :style: unsrt diff --git a/src/cython/doc/bottleneck_distance_sum.rst b/src/cython/doc/bottleneck_distance_sum.rst index 5c475d0d..030fad9e 100644 --- a/src/cython/doc/bottleneck_distance_sum.rst +++ b/src/cython/doc/bottleneck_distance_sum.rst @@ -5,7 +5,7 @@ +-----------------------------------------------------------------+----------------------------------------------------------------------+ | .. figure:: | Bottleneck distance measures the similarity between two persistence | -| img/perturb_pd.png | diagrams. It's the shortest distance b for which there exists a | +| ../../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. | diff --git a/src/cython/doc/cubical_complex_sum.rst b/src/cython/doc/cubical_complex_sum.rst index 3ddf6375..280ad0e0 100644 --- a/src/cython/doc/cubical_complex_sum.rst +++ b/src/cython/doc/cubical_complex_sum.rst @@ -2,14 +2,14 @@ :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 | -| img/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` | -+-----------------------------------------------------------------+----------------------------------------------------------------------+ ++--------------------------------------------------------------------------+----------------------------------------------------------------------+ +| .. 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 8c9a3ed6..36fa3ba9 100644 --- a/src/cython/doc/cubical_complex_user.rst +++ b/src/cython/doc/cubical_complex_user.rst @@ -157,6 +157,6 @@ End user programs are available in cython/example/ folder. Bibliography ============ -.. bibliography:: bibliography.bib +.. bibliography:: ../../bibliography.bib :filter: docnames :style: unsrt diff --git a/src/cython/doc/index.rst b/src/cython/doc/index.rst index f6d10567..3945d72a 100644 --- a/src/cython/doc/index.rst +++ b/src/cython/doc/index.rst @@ -1,8 +1,10 @@ GUDHI Python module documentation ################################# -.. image:: img/Gudhi_banner.png - :align: center +.. figure:: + ../../doc/common/Gudhi_banner.png + :alt: Gudhi banner + :figclass: align-center Introduction ************ @@ -81,6 +83,6 @@ Persistence graphical tools Bibliography ************ -.. bibliography:: bibliography.bib +.. bibliography:: ../../biblio/bibliography.bib :filter: docnames :style: unsrt diff --git a/src/cython/doc/persistent_cohomology_sum.rst b/src/cython/doc/persistent_cohomology_sum.rst index d1f79cb4..a26df1dc 100644 --- a/src/cython/doc/persistent_cohomology_sum.rst +++ b/src/cython/doc/persistent_cohomology_sum.rst @@ -4,7 +4,7 @@ +-----------------------------------------------------------------+-----------------------------------------------------------------------+ | .. figure:: | The theory of homology consists in attaching to a topological space | -| img/3DTorus_poch.png | a sequence of (homology) groups, capturing global topological | +| ../../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 | diff --git a/src/cython/doc/persistent_cohomology_user.rst b/src/cython/doc/persistent_cohomology_user.rst index 72f1a7f7..bf90c163 100644 --- a/src/cython/doc/persistent_cohomology_user.rst +++ b/src/cython/doc/persistent_cohomology_user.rst @@ -109,6 +109,6 @@ We provide several example files: run these examples with -h for details on thei Bibliography ============ -.. bibliography:: bibliography.bib +.. bibliography:: ../../biblio/bibliography.bib :filter: docnames :style: unsrt diff --git a/src/cython/doc/rips_complex_sum.rst b/src/cython/doc/rips_complex_sum.rst index 2b65fc19..5616bfa9 100644 --- a/src/cython/doc/rips_complex_sum.rst +++ b/src/cython/doc/rips_complex_sum.rst @@ -4,7 +4,7 @@ +----------------------------------------------------------------+------------------------------------------------------------------------+ | .. figure:: | Rips complex is a simplicial complex constructed from a one skeleton | -| img/rips_complex_representation.png | graph. | +| ../../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 | diff --git a/src/cython/doc/rips_complex_user.rst b/src/cython/doc/rips_complex_user.rst index 6b48422b..96ba9944 100644 --- a/src/cython/doc/rips_complex_user.rst +++ b/src/cython/doc/rips_complex_user.rst @@ -26,7 +26,7 @@ structure, and then expands the simplicial complex when required. Vertex name correspond to the index of the point in the given range (aka. the point cloud). .. figure:: - img/rips_complex_representation.png + ../../doc/Rips_complex/rips_complex_representation.png :align: center Rips-complex one skeleton graph representation diff --git a/src/cython/doc/simplex_tree_sum.rst b/src/cython/doc/simplex_tree_sum.rst index 3174fb62..fb0e54c1 100644 --- a/src/cython/doc/simplex_tree_sum.rst +++ b/src/cython/doc/simplex_tree_sum.rst @@ -4,7 +4,7 @@ +----------------------------------------------------------------+------------------------------------------------------------------------+ | .. figure:: | The simplex tree is an efficient and flexible data structure for | -| img/Simplex_tree_representation.png | representing general (filtered) simplicial complexes. | +| ../../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` | diff --git a/src/cython/doc/tangential_complex_sum.rst b/src/cython/doc/tangential_complex_sum.rst index 2b05bc10..72b4d7ba 100644 --- a/src/cython/doc/tangential_complex_sum.rst +++ b/src/cython/doc/tangential_complex_sum.rst @@ -5,10 +5,10 @@ +----------------------------------------------------------------+------------------------------------------------------------------------+ | .. figure:: | A Tangential Delaunay complex is a simplicial complex designed to | -| img/tc_examples.png | reconstruct a :math:`k`-dimensional manifold embedded in :math:`d`- | +| ../../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 | +| 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 d670cfdb..efa6d7ce 100644 --- a/src/cython/doc/tangential_complex_user.rst +++ b/src/cython/doc/tangential_complex_user.rst @@ -22,7 +22,7 @@ Let us start with the description of the Tangential complex of a simple example, with :math:`k = 1` and :math:`d = 2`. The input data is 4 points :math:`P` located on a curve embedded in 2D. -.. figure:: img/tc_example_01.png +.. figure:: ../../doc/Tangential_complex/tc_example_01.png :alt: The input :figclass: align-center @@ -31,7 +31,7 @@ example, with :math:`k = 1` and :math:`d = 2`. The input data is 4 points For each point :math:`p`, estimate its tangent subspace :math:`T_p` (e.g. using PCA). -.. figure:: img/tc_example_02.png +.. figure:: ../../doc/Tangential_complex/tc_example_02.png :alt: The estimated normals :figclass: align-center @@ -42,7 +42,7 @@ Let us add the Voronoi diagram of the points in orange. For each point :math:`p`, construct its star in the Delaunay triangulation of :math:`P` restricted to :math:`T_p`. -.. figure:: img/tc_example_03.png +.. figure:: ../../doc/Tangential_complex/tc_example_03.png :alt: The Voronoi diagram :figclass: align-center @@ -62,7 +62,7 @@ simplex is not in the star of all its vertices. Let us take the same example. -.. figure:: img/tc_example_07_before.png +.. figure:: ../../doc/Tangential_complex/tc_example_07_before.png :alt: Before :figclass: align-center @@ -70,7 +70,7 @@ Let us take the same example. Let us slightly move the tangent subspace :math:`T_q` -.. figure:: img/tc_example_07_after.png +.. figure:: ../../doc/Tangential_complex/tc_example_07_after.png :alt: After :figclass: align-center @@ -79,7 +79,7 @@ Let us slightly move the tangent subspace :math:`T_q` Now, the star of :math:`Q` contains :math:`QP`, but the star of :math:`P` does not contain :math:`QP`. We have an inconsistency. -.. figure:: img/tc_example_08.png +.. figure:: ../../doc/Tangential_complex/tc_example_08.png :alt: After :figclass: align-center @@ -191,6 +191,6 @@ The output is: Bibliography ============ -.. bibliography:: bibliography.bib +.. bibliography:: ../../biblio/bibliography.bib :filter: docnames :style: unsrt diff --git a/src/cython/doc/witness_complex_sum.rst b/src/cython/doc/witness_complex_sum.rst index b65522ba..a8a126a0 100644 --- a/src/cython/doc/witness_complex_sum.rst +++ b/src/cython/doc/witness_complex_sum.rst @@ -3,15 +3,17 @@ :Euclidean version requires: CGAL :math:`\geq` 4.6.0 Eigen3 ================================================================= =================================== =================================== -+-----------------------------------------------------------------+----------------------------------------------------------------------+ -| .. image:: | Witness complex :math:`Wit(W,L)` is a simplicial complex defined on | -| img/Witness_complex_representation.png | two sets of points in :math:`\mathbb{R}^D`. | -| | | -| | The data structure is described in | -| | :cite:`boissonnatmariasimplextreealgorithmica`. | -+-----------------------------------------------------------------+----------------------------------------------------------------------+ -| :doc:`witness_complex_user` | * :doc:`witness_complex_ref` | -| | * :doc:`strong_witness_complex_ref` | -| | * :doc:`euclidean_witness_complex_ref` | -| | * :doc:`euclidean_strong_witness_complex_ref` | -+-----------------------------------------------------------------+----------------------------------------------------------------------+ ++-------------------------------------------------------------------+----------------------------------------------------------------------+ +| .. 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 aa9cbb2c..29413269 100644 --- a/src/cython/doc/witness_complex_user.rst +++ b/src/cython/doc/witness_complex_user.rst @@ -33,7 +33,7 @@ Both definitions can be relaxed by a real value :math:`\alpha`: which leads to definitions of **weak relaxed witness complex** (or just relaxed witness complex for short) and **strong relaxed witness complex** respectively. -.. figure:: img/swit.svg +.. figure:: ../../doc/Witness_complex/swit.svg :alt: Strongly witnessed simplex :figclass: align-center @@ -126,6 +126,6 @@ Here is an example of constructing a strong witness complex filtration and compu Bibliography ============ -.. bibliography:: bibliography.bib +.. bibliography:: ../../biblio/bibliography.bib :filter: docnames :style: unsrt -- cgit v1.2.3