--- a/bindings/python/CMakeLists.txt Thu Jul 15 10:25:08 2010 -0700
+++ b/bindings/python/CMakeLists.txt Wed Aug 25 14:31:36 2010 -0700
@@ -10,6 +10,7 @@
filtration.cpp
chain.cpp
static-persistence.cpp
+ persistence-diagram.cpp
simplex.cpp
birthid.cpp
zigzag-persistence.cpp
--- a/bindings/python/dionysus.cpp Thu Jul 15 10:25:08 2010 -0700
+++ b/bindings/python/dionysus.cpp Wed Aug 25 14:31:36 2010 -0700
@@ -12,6 +12,8 @@
void export_birthid();
void export_zigzag_persistence();
void export_cohomology_persistence();
+void export_point();
+void export_persistence_diagram();
void export_rips();
void export_pairwise_distances();
@@ -36,6 +38,8 @@
export_filtration();
export_static_persistence();
export_chain();
+ export_point();
+ export_persistence_diagram();
export_birthid();
export_zigzag_persistence();
--- a/bindings/python/dionysus/__init__.py Thu Jul 15 10:25:08 2010 -0700
+++ b/bindings/python/dionysus/__init__.py Wed Aug 25 14:31:36 2010 -0700
@@ -26,3 +26,13 @@
def vertex_dim_cmp(s1, s2):
return cmp(s1.dimension(), s2.dimension()) or vertex_cmp(s1, s2)
+
+# TBD: Port this into C++
+def point_iterator( point ):
+
+ yield point.x
+ yield point.y
+ if not point.data is None:
+ yield point.data
+
+Point.__iter__ = point_iterator
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bindings/python/persistence-diagram.cpp Wed Aug 25 14:31:36 2010 -0700
@@ -0,0 +1,95 @@
+#include<topology/persistence-diagram.h>
+#include<utilities/types.h>
+
+#include<boost/python.hpp>
+#include<boost/python/init.hpp>
+#include<boost/shared_ptr.hpp>
+#include<boost/python/stl_iterator.hpp>
+#include <boost/python/def.hpp>
+
+
+namespace bp = boost::python;
+
+
+namespace dionysus{
+namespace python{
+
+typedef bp::object Data;
+typedef PDPoint<Data> PointD;
+typedef PersistenceDiagram<Data> PersistenceDiagramD;
+
+} } //namespace dionysus::python
+
+namespace dp = dionysus::python;
+
+
+template<class PDPoint>
+RealType get_x_coord( const PDPoint& p ){
+ return p.x( );
+}
+
+template<class PDPoint>
+RealType get_y_coord( const PDPoint& p ){
+ return p.y( );
+}
+
+template<class PDPoint>
+bp::object get_data( const PDPoint& p ){
+ return p.data( );
+}
+
+void export_point( ){
+
+ bp::class_<dp::PointD>("Point")
+ .def( bp::init< RealType, RealType, bp::optional<dp::Data> >( ) )
+ .add_property( "x", &get_x_coord<dp::PointD> )
+ .add_property( "y", &get_y_coord<dp::PointD> )
+ .add_property( "data", &get_data<dp::PointD> )
+ .def( repr(bp::self) )
+ ;
+
+}
+
+
+
+template<class PersistenceDiagram, class Point>
+boost::shared_ptr<PersistenceDiagram> init_from_points_sequence( Dimension dimension, bp::object point_sequence ){
+
+ typedef bp::stl_input_iterator<Point> PointIterator;
+
+ PointIterator beg = PointIterator( point_sequence ), end = PointIterator( );
+ // The following line is commented out until we can figure out the Evaluator class in make_point
+ //boost::shared_ptr<PersistenceDiagram> p( new PersistenceDiagram( beg, end );
+ boost::shared_ptr<PersistenceDiagram> p( new PersistenceDiagram( dimension ) );
+
+ for( PointIterator cur=beg; cur!=end; cur++ )
+ (*p).push_back( *cur );
+ return p;
+
+}
+
+
+template<class PersistenceDiagram>
+Dimension get_dimension( PersistenceDiagram dgm ){
+ return dgm.dimension( );
+}
+
+template<class PersistenceDiagram>
+SizeType get_length( PersistenceDiagram dgm ){
+ return dgm.size( );
+}
+
+void export_persistence_diagram( ){
+
+ bp::class_<dp::PersistenceDiagramD>("PersistenceDiagram")
+ .def( "__init__", bp::make_constructor( &init_from_points_sequence< dp::PersistenceDiagramD, dp::PointD > ) )
+ .def( bp::init< Dimension >( ) )
+ .def( "append", &dp::PersistenceDiagramD::push_back )
+ .add_property( "dimension", &get_dimension<dp::PersistenceDiagramD> )
+ .def( repr(bp::self) )
+ .def( "__iter__", bp::range( &dp::PersistenceDiagramD::begin, &dp::PersistenceDiagramD::end ) )
+ .def( "__len__", &get_length<dp::PersistenceDiagramD> )
+ ;
+
+ bp::def( "bottleneck_distance", bottleneck_distance<dp::PersistenceDiagramD,dp::PersistenceDiagramD> );
+}
--- a/doc/python/overview.rst Thu Jul 15 10:25:08 2010 -0700
+++ b/doc/python/overview.rst Wed Aug 25 14:31:36 2010 -0700
@@ -21,3 +21,4 @@
alphashapes.rst
rips.rst
zigzag-persistence.rst
+ persistence-diagram.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/python/persistence-diagram.rst Wed Aug 25 14:31:36 2010 -0700
@@ -0,0 +1,84 @@
+:class:`PersistenceDiagram` class
+==================================
+
+.. class:: PersistenceDiagram
+
+ .. method:: __init__( dimension )
+
+ Initializes : an empty( no points ) :class:`PersistenceDiagram` object and sets
+ the :attr:`~PersistenceDiagram.dimension` attribute( must be integer ) e.g.::
+
+ dia = PersistenceDiagram( 1 )
+
+ .. method:: __init__( dimension, point_seq )
+
+ Initializes :class:`PersistenceDiagram` of specified dimension from the given sequence `seq` of :class:`Point` objects, e.g.::
+
+ dia = PersistenceDiagram( 1, [Point(1,2)] )
+
+ .. method:: append( p )
+
+ Adds point `p` to the persistence diagram.
+
+ .. attribute:: dimension
+
+ Dimension of the persistence diagram. Must be an integer. Must be set at initialization.
+
+ .. method:: __iter__( )
+
+ Iterator over the points in the persistence diagram,
+ e.g.::
+
+ for p in dia: print p
+
+ .. method:: __len__( )
+
+ :returns: The number of points in the diagram.
+
+
+
+Utility functions for persistence diagrams
+--------------------------------------------
+
+
+.. function:: bottleneck_distance(dia1, dia2)
+
+ Calculates the bottleneck distance between the two persistence diagrams.
+
+
+
+:class:`Point` class
+======================
+
+.. class:: Point
+
+ .. method:: __init__( x, y [, data])
+
+ Initializes :class:`Point` with the given real-valued coordinates and
+ optionally real value `data`, e.g.::
+
+ s = Point( 1, 1.1, 1.11 )
+
+ .. attribute:: x
+
+ x coordinate of the point
+
+ .. attribute:: y
+
+ y coordinate of the point
+
+ .. attribute:: data
+
+ Real value stored in the simplex.
+
+ .. method:: __iter__( )
+
+ Point objects are iterable, returning two or three elements depending on presence of data, e.g.::
+
+ p = Point( 1, 1.1, 1.11 )
+ for i in p: print p
+
+ 1
+ 1.1
+ 1.11
+
--- a/include/topology/persistence-diagram.h Thu Jul 15 10:25:08 2010 -0700
+++ b/include/topology/persistence-diagram.h Wed Aug 25 14:31:36 2010 -0700
@@ -85,6 +85,9 @@
PersistenceDiagram() {}
+ PersistenceDiagram( Dimension dimension ):
+ dimension_( dimension ) {}
+
template<class OtherData>
PersistenceDiagram(const PersistenceDiagram<OtherData>& other);
@@ -110,8 +113,11 @@
std::ostream& operator<<(std::ostream& out) const;
+ const Dimension& dimension( ) const { return dimension_; }
+
private:
PointVector points_;
+ Dimension dimension_;
private:
/* Serialization */