diff options
Diffstat (limited to 'src/cython')
| -rw-r--r-- | src/cython/cython/periodic_cubical_complex.pyx | 14 | ||||
| -rw-r--r-- | src/cython/doc/cubical_complex_user.rst | 45 | ||||
| -rw-r--r-- | src/cython/doc/fileformats.rst | 55 | ||||
| -rw-r--r-- | src/cython/doc/witness_complex_user.rst | 2 | ||||
| -rw-r--r-- | src/cython/include/Cubical_complex_interface.h | 6 |
5 files changed, 89 insertions, 33 deletions
diff --git a/src/cython/cython/periodic_cubical_complex.pyx b/src/cython/cython/periodic_cubical_complex.pyx index 581c7b69..3025f125 100644 --- a/src/cython/cython/periodic_cubical_complex.pyx +++ b/src/cython/cython/periodic_cubical_complex.pyx @@ -33,7 +33,7 @@ __license__ = "GPL v3" cdef extern from "Cubical_complex_interface.h" namespace "Gudhi": cdef cppclass Periodic_cubical_complex_base_interface "Gudhi::Cubical_complex::Cubical_complex_interface<Gudhi::cubical_complex::Bitmap_cubical_complex_periodic_boundary_conditions_base<double>>": - Periodic_cubical_complex_base_interface(vector[unsigned] dimensions, vector[double] top_dimensional_cells) + Periodic_cubical_complex_base_interface(vector[unsigned] dimensions, vector[double] top_dimensional_cells, vector[bool] periodic_dimensions) Periodic_cubical_complex_base_interface(string perseus_file) int num_simplices() int dimension() @@ -58,7 +58,7 @@ cdef class PeriodicCubicalComplex: # Fake constructor that does nothing but documenting the constructor def __init__(self, dimensions=None, top_dimensional_cells=None, - perseus_file=''): + periodic_dimensions=None, perseus_file=''): """PeriodicCubicalComplex constructor from dimensions and top_dimensional_cells or from a Perseus-style file name. @@ -66,6 +66,8 @@ cdef class PeriodicCubicalComplex: :type dimensions: list of int :param top_dimensional_cells: A list of cells filtration values. :type top_dimensional_cells: list of double + :param periodic_dimensions: A list of top dimensional cells periodicity value. + :type periodic_dimensions: list of boolean Or @@ -75,10 +77,10 @@ cdef class PeriodicCubicalComplex: # The real cython constructor def __cinit__(self, dimensions=None, top_dimensional_cells=None, - perseus_file=''): - if (dimensions is not None) and (top_dimensional_cells is not None) and (perseus_file is ''): - self.thisptr = new Periodic_cubical_complex_base_interface(dimensions, top_dimensional_cells) - elif (dimensions is None) and (top_dimensional_cells is None) and (perseus_file is not ''): + periodic_dimensions=None, perseus_file=''): + if (dimensions is not None) and (top_dimensional_cells is not None) and (periodic_dimensions is not None) and (perseus_file is ''): + self.thisptr = new Periodic_cubical_complex_base_interface(dimensions, top_dimensional_cells, periodic_dimensions) + elif (dimensions is None) and (top_dimensional_cells is None) and (periodic_dimensions is None) and (perseus_file is not ''): if os.path.isfile(perseus_file): self.thisptr = new Periodic_cubical_complex_base_interface(str.encode(perseus_file)) else: diff --git a/src/cython/doc/cubical_complex_user.rst b/src/cython/doc/cubical_complex_user.rst index 2bfac62a..34598f02 100644 --- a/src/cython/doc/cubical_complex_user.rst +++ b/src/cython/doc/cubical_complex_user.rst @@ -81,23 +81,7 @@ filtration to all cubes. There are a number of constructors that can be used to who want to use the code directly. They can be found in the :doc:`cubical_complex_ref`. Currently one input from a text file is used. It uses a format used already in `Perseus software <http://www.sas.upenn.edu/~vnanda/perseus/>`_ by Vidit Nanda. -Below we are providing a description of the format. The first line contains a number d begin the dimension of the -bitmap (2 in the example below). Next d lines are the numbers of top dimensional cubes in each dimensions (3 and 3 -in the example below). Next, in lexicographical order, the filtration of top dimensional cubes is given (1 4 6 8 -20 4 7 6 5 in the example below). - -.. figure:: - ../../doc/Bitmap_cubical_complex/exampleBitmap.png - :alt: Example of a input data. - :figclass: align-center - - Example of a input data. - -The input file for the following complex is: - -.. literalinclude:: ../../data/bitmap/cubicalcomplexdoc.txt - -.. centered:: ../../data/bitmap/cubicalcomplexdoc.txt +The file format is described here: :doc:`Perseus <fileformats>`. .. testcode:: @@ -124,15 +108,9 @@ Imposing periodic boundary conditions in the direction i, means that the left an :math:`\mathcal{K}` are considered the same. In particular, if for a bitmap :math:`\mathcal{K}` periodic boundary conditions are imposed in all directions, then complex :math:`\mathcal{K}` became n-dimensional torus. One can use various constructors from the file Bitmap_cubical_complex_periodic_boundary_conditions_base.h to construct cubical -complex with periodic boundary conditions. One can also use Perseus style input files. To indicate periodic boundary -conditions in a given direction, then number of top dimensional cells in this direction have to be multiplied by -1. -For instance: - -.. literalinclude:: ../../data/bitmap/periodiccubicalcomplexdoc.txt - -.. centered:: ../../data/bitmap/periodiccubicalcomplexdoc.txt +complex with periodic boundary conditions. -Indicate that we have imposed periodic boundary conditions in the direction x, but not in the direction y. +One can also use Perseus style input files (see :doc:`Perseus <fileformats>`) for the specific periodic case: .. testcode:: @@ -149,6 +127,23 @@ the program output is: Periodic cubical complex is of dimension 2 - 42 simplices. +Or it can be defined as follows: + +.. testcode:: + + from gudhi import PeriodicCubicalComplex as pcc + periodic_cc = pcc(dimensions=[3,3], + top_dimensional_cells= [0, 0, 0, 0, 1, 0, 0, 0, 0], + periodic_dimensions=[True, False]) + result_str = 'Periodic cubical complex is of dimension ' + repr(periodic_cc.dimension()) + ' - ' + \ + repr(periodic_cc.num_simplices()) + ' simplices.' + print(result_str) + +the program output is: + +.. testoutput:: + + Periodic cubical complex is of dimension 2 - 42 simplices. Examples. --------- diff --git a/src/cython/doc/fileformats.rst b/src/cython/doc/fileformats.rst index 156ef4e4..4f0b6f6d 100644 --- a/src/cython/doc/fileformats.rst +++ b/src/cython/doc/fileformats.rst @@ -23,7 +23,7 @@ Here is a simple sample file:: 3 34.2 34.974 4 3. inf -Other sample files can be found in the data/persistence_diagram folder. +Other sample files can be found in the `data/persistence_diagram` folder. Such files can be generated with :meth:`gudhi.SimplexTree.write_persistence_diagram`, read with @@ -31,3 +31,56 @@ Such files can be generated with :meth:`gudhi.read_persistence_intervals_in_dimension` and displayed with :meth:`gudhi.plot_persistence_barcode` or :meth:`gudhi.plot_persistence_diagram`. + +Iso-cuboid +********** + +Such a file describes an iso-oriented cuboid with diagonal opposite vertices +(min_x, min_y, min_z,...) and (max_x, max_y, max_z, ...). The format is:: + + min_x min_y [min_z ...] + max_x max_y [max_z ...] + +Here is a simple sample file in the 3D case:: + + -1. -1. -1. + 1. 1. 1. + + +Perseus +******* + +This file format is the format used by the +`Perseus software <http://www.sas.upenn.edu/~vnanda/perseus/>`_ by Vidit Nanda. +The first line contains a number d begin the dimension of the bitmap (2 in the +example below). Next d lines are the numbers of top dimensional cubes in each +dimensions (3 and 3 in the example below). Next, in lexicographical order, the +filtration of top dimensional cubes is given (1 4 6 8 20 4 7 6 5 in the example +below). + +.. figure:: + ../../doc/Bitmap_cubical_complex/exampleBitmap.png + :alt: Example of a input data. + :figclass: align-center + + Example of a input data. + +The input file for the following complex is: + +.. literalinclude:: ../../data/bitmap/cubicalcomplexdoc.txt + +.. centered:: ../../data/bitmap/cubicalcomplexdoc.txt + +To indicate periodic boundary conditions in a given direction, then number of +top dimensional cells in this direction have to be multiplied by -1. For +instance: + +.. literalinclude:: ../../data/bitmap/periodiccubicalcomplexdoc.txt + +.. centered:: ../../data/bitmap/periodiccubicalcomplexdoc.txt + + +Indicate that we have imposed periodic boundary conditions in the direction x, +but not in the direction y. + +Other sample files can be found in the `data/bitmap` folder. diff --git a/src/cython/doc/witness_complex_user.rst b/src/cython/doc/witness_complex_user.rst index 29413269..99be5185 100644 --- a/src/cython/doc/witness_complex_user.rst +++ b/src/cython/doc/witness_complex_user.rst @@ -121,7 +121,7 @@ Example2: Computing persistence using strong relaxed witness complex Here is an example of constructing a strong witness complex filtration and computing persistence on it: -* :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py>` +* :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>` Bibliography ============ diff --git a/src/cython/include/Cubical_complex_interface.h b/src/cython/include/Cubical_complex_interface.h index 7c0148f1..fad92c2c 100644 --- a/src/cython/include/Cubical_complex_interface.h +++ b/src/cython/include/Cubical_complex_interface.h @@ -43,6 +43,12 @@ class Cubical_complex_interface : public Bitmap_cubical_complex<CubicalComplexOp : Bitmap_cubical_complex<CubicalComplexOptions>(dimensions, top_dimensional_cells) { } + Cubical_complex_interface(const std::vector<unsigned>& dimensions, + const std::vector<double>& top_dimensional_cells, + const std::vector<bool>& periodic_dimensions) + : Bitmap_cubical_complex<CubicalComplexOptions>(dimensions, top_dimensional_cells, periodic_dimensions) { + } + Cubical_complex_interface(const std::string& perseus_file) : Bitmap_cubical_complex<CubicalComplexOptions>(perseus_file.c_str()) { } |