diff options
Diffstat (limited to 'src/cython/doc')
| -rw-r--r-- | src/cython/doc/installation.rst | 63 | ||||
| -rw-r--r-- | src/cython/doc/nerve_gic_complex_sum.rst | 2 | ||||
| -rw-r--r-- | src/cython/doc/persistence_graphical_tools_ref.rst | 1 | ||||
| -rw-r--r-- | src/cython/doc/persistence_graphical_tools_sum.inc | 4 | ||||
| -rw-r--r-- | src/cython/doc/persistence_graphical_tools_user.rst | 37 |
5 files changed, 89 insertions, 18 deletions
diff --git a/src/cython/doc/installation.rst b/src/cython/doc/installation.rst index 43ff85c5..ef2f7af2 100644 --- a/src/cython/doc/installation.rst +++ b/src/cython/doc/installation.rst @@ -47,9 +47,61 @@ 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. +Debugging issues +================ + +If tests fail, please check your PYTHONPATH and try to :code:`import gudhi` +and check the errors. The problem can come from a third-party library bad link or installation. +If :code:`import gudhi` succeeds, please have a look to debug informations: + +.. code-block:: python + + import gudhi + print(gudhi.__debug_info__) + +You shall have something like: + +.. code-block:: none + + Python version 2.7.15 + Cython version 0.26.1 + Eigen3 version 3.1.1 + Installed modules are: off_reader;simplex_tree;rips_complex;cubical_complex;periodic_cubical_complex; + persistence_graphical_tools;reader_utils;witness_complex;strong_witness_complex;alpha_complex; + euclidean_witness_complex;euclidean_strong_witness_complex; + Missing modules are: bottleneck_distance;nerve_gic;subsampling;tangential_complex;persistence_graphical_tools; + CGAL version 4.7.1000 + GMP_LIBRARIES = /usr/lib/x86_64-linux-gnu/libgmp.so + GMPXX_LIBRARIES = /usr/lib/x86_64-linux-gnu/libgmpxx.so + TBB version 9107 found and used + +Here, you can see that bottleneck_distance, nerve_gic, subsampling and +tangential_complex are missing because of the CGAL version. +persistence_graphical_tools is not available as numpy and matplotlib are not +available. +Unitary tests cannot be run as pytest is missing. + +A complete configuration would be : + +.. code-block:: none + + Python version 3.6.5 + Cython version 0.28.2 + Pytest version 3.3.2 + Matplotlib version 2.2.2 + Numpy version 1.14.5 + Eigen3 version 3.3.4 + Installed modules are: off_reader;simplex_tree;rips_complex;cubical_complex;periodic_cubical_complex; + persistence_graphical_tools;reader_utils;witness_complex;strong_witness_complex;persistence_graphical_tools; + bottleneck_distance;nerve_gic;subsampling;tangential_complex;alpha_complex;euclidean_witness_complex; + euclidean_strong_witness_complex; + CGAL header only version 4.11.0 + GMP_LIBRARIES = /usr/lib/x86_64-linux-gnu/libgmp.so + GMPXX_LIBRARIES = /usr/lib/x86_64-linux-gnu/libgmpxx.so + TBB version 9107 found and used + Documentation ============= @@ -143,7 +195,7 @@ The following examples require the `Matplotlib <http://matplotlib.org>`_: * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>` * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>` -Numpy +NumPy ===== The :doc:`persistence graphical tools </persistence_graphical_tools_user>` @@ -164,6 +216,13 @@ The following examples require the `NumPy <http://numpy.org>`_: * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>` * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>` +SciPy +===== + +The :doc:`persistence graphical tools </persistence_graphical_tools_user>` +module requires `SciPy <http://scipy.org>`_, a Python-based ecosystem of +open-source software for mathematics, science, and engineering. + Threading Building Blocks ========================= diff --git a/src/cython/doc/nerve_gic_complex_sum.rst b/src/cython/doc/nerve_gic_complex_sum.rst index 72782c7a..523c119f 100644 --- a/src/cython/doc/nerve_gic_complex_sum.rst +++ b/src/cython/doc/nerve_gic_complex_sum.rst @@ -1,5 +1,5 @@ ================================================================= =================================== =================================== -:Author: Mathieu Carrière :Introduced in: GUDHI 2.1.0 :Copyright: GPL v3 +:Author: Mathieu Carrière :Introduced in: GUDHI 2.3.0 :Copyright: GPL v3 :Requires: CGAL :math:`\geq` 4.8.1 ================================================================= =================================== =================================== diff --git a/src/cython/doc/persistence_graphical_tools_ref.rst b/src/cython/doc/persistence_graphical_tools_ref.rst index a2c6bcef..54aff4bc 100644 --- a/src/cython/doc/persistence_graphical_tools_ref.rst +++ b/src/cython/doc/persistence_graphical_tools_ref.rst @@ -9,3 +9,4 @@ Persistence graphical tools reference manual .. autofunction:: gudhi.__min_birth_max_death .. autofunction:: gudhi.plot_persistence_barcode .. autofunction:: gudhi.plot_persistence_diagram +.. autofunction:: gudhi.plot_persistence_density diff --git a/src/cython/doc/persistence_graphical_tools_sum.inc b/src/cython/doc/persistence_graphical_tools_sum.inc index d602daa7..5577cf99 100644 --- a/src/cython/doc/persistence_graphical_tools_sum.inc +++ b/src/cython/doc/persistence_graphical_tools_sum.inc @@ -1,11 +1,11 @@ ================================================================= =================================== =================================== :Author: Vincent Rouvreau :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3 -:Requires: Matplotlib Numpy +:Requires: matplotlib numpy scipy ================================================================= =================================== =================================== +-----------------------------------------------------------------+-----------------------------------------------------------------------+ | .. figure:: | These graphical tools comes on top of persistence results and allows | -| img/graphical_tools_representation.png | the user to build easily barcode and persistence diagram. | +| img/graphical_tools_representation.png | the user to build easily persistence barcode, diagram or density. | | | | +-----------------------------------------------------------------+-----------------------------------------------------------------------+ | :doc:`persistence_graphical_tools_user` | :doc:`persistence_graphical_tools_ref` | diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst index 292915eb..b2124fdd 100644 --- a/src/cython/doc/persistence_graphical_tools_user.rst +++ b/src/cython/doc/persistence_graphical_tools_user.rst @@ -12,6 +12,9 @@ Definition Show persistence as a barcode ----------------------------- +.. note:: + this function requires matplotlib and numpy to be available + This function can display the persistence result as a barcode: .. plot:: @@ -19,16 +22,22 @@ This function can display the persistence result as a barcode: import gudhi - perseus_file = gudhi.__root_source_dir__ + '/data/bitmap/3d_torus.txt' - periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=perseus_file) - diag = periodic_cc.persistence() - print("diag = ", diag) - plt = gudhi.plot_persistence_barcode(diag) - plt.show() + off_file = gudhi.__root_source_dir__ + '/data/points/tore3D_300.off' + point_cloud = gudhi.read_off(off_file=off_file) + + rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.7) + simplex_tree = rips_complex.create_simplex_tree(max_dimension=3) + diag = simplex_tree.persistence(min_persistence=0.4) + + plot = gudhi.plot_persistence_barcode(diag) + plot.show() Show persistence as a diagram ----------------------------- +.. note:: + this function requires matplotlib and numpy to be available + This function can display the persistence result as a diagram: .. plot:: @@ -43,6 +52,12 @@ This function can display the persistence result as a diagram: legend=True) plt.show() +Persistence density +------------------- + +.. note:: + this function requires matplotlib, numpy and scipy to be available + If you want more information on a specific dimension, for instance: .. plot:: @@ -50,13 +65,9 @@ If you want more information on a specific dimension, for instance: import gudhi + # rips_on_tore3D_1307.pers obtained from write_persistence_diagram method persistence_file=gudhi.__root_source_dir__ + \ '/data/persistence_diagram/rips_on_tore3D_1307.pers' - diag = \ - gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file=\ - persistence_file) - dim = 1 - # Display all points with some transparency - plt = gudhi.plot_persistence_diagram([(dim,interval) for interval in diag[dim]], - max_plots=0, alpha=0.1) + plt = gudhi.plot_persistence_density(persistence_file=persistence_file, + max_intervals=0, dimension=1, legend=True) plt.show() |