From f6749b75490814dc3164f16c2629e2ba99919f19 Mon Sep 17 00:00:00 2001
From: Pietro Incardona <incardon@mpi-cbg.de>
Date: Tue, 9 Dec 2014 19:30:30 +0100
Subject: [PATCH] Added GraphML writer
---
src/GraphMLWriter.hpp | 643 ++++++++++++++++++++++++++++++++++++++++++
src/MatLabWriter.hpp | 4 +-
2 files changed, 645 insertions(+), 2 deletions(-)
create mode 100644 src/GraphMLWriter.hpp
diff --git a/src/GraphMLWriter.hpp b/src/GraphMLWriter.hpp
new file mode 100644
index 00000000..eea1c1c8
--- /dev/null
+++ b/src/GraphMLWriter.hpp
@@ -0,0 +1,643 @@
+#ifndef GRAPHML_WRITER_HPP
+#define GRAPHML_WRITER_HPP
+
+#include "map_graph.hpp"
+#include <iostream>
+#include <boost/fusion/include/mpl.hpp>
+#include <boost/fusion/include/for_each.hpp>
+#include <fstream>
+
+/*! \brief this class is a functor for "for_each" algorithm
+ *
+ * This class is a functor for "for_each" algorithm. For each
+ * element of the boost::vector the operator() is called.
+ * Is mainly used to create a string containing all the vertex
+ * properties
+ *
+ */
+
+template<typename G>
+struct vertex_prop
+{
+ // Properties counter
+ int cnt = 0;
+
+ // vertex properties
+ std::string & v_prop;
+
+ // Attribute names
+ std::string * attributes_names;
+
+ // Number of attributes name defined into the vertex
+ int n_attr = 0;
+
+ /*! \brief Constructor
+ *
+ * Create a vertex properties list
+ *
+ * \param v_prop std::string that is filled with the graph properties in the GraphML format
+ * \param stub SFINAE, it basically check if G has properties names defined, if yes this
+ * constructor is selected over the other one
+ *
+ */
+ vertex_prop(std::string & v_prop, typename G::V_type::attributes & a_name)
+ :v_prop(v_prop),attributes_names(a_name.name)
+ {
+ // Calculate the number of attributes name
+ n_attr = sizeof(a_name.name)/sizeof(std::string);
+ };
+
+ /*! \brief Constructor
+ *
+ * Create a vertex properties list
+ *
+ * \param v_prop std::string that is filled with the graph properties in the GraphML format
+ * \param n_prop number of properties
+ *
+ */
+ vertex_prop(std::string & v_prop)
+ :v_prop(v_prop),attributes_names(NULL)
+ {
+ };
+
+ //! It call the functor for each member
+ template<typename T>
+ void operator()(T& t)
+ {
+ //! Create an entry for the attribute
+ if (cnt < n_attr)
+ {
+ // if it is a yFile extension property name, does not process it
+ if (attributes_names[t] == "x" || attributes_names[t] == "y"
+ || attributes_names[t] == "z" || attributes_names[t] == "shape" )
+ {cnt++; return ;}
+
+ // Create a property string based on the type of the property
+ if (typeid(T) == typeid(float))
+ v_prop += "<key id=\"v" + std::to_string(cnt) + "\" for=\"node\" attr.name=" + attributes_names[t] + " attr.type=\"float\"/>";
+ else if (typeid(T) == typeid(double))
+ v_prop += "<key id=\"v" + std::to_string(cnt) + "\" for=\"node\" attr.name=" + attributes_names[t] + " attr.type=\"double\"/>";
+ else if (typeid(T) == typeid(int))
+ v_prop += "<key id=\"v" + std::to_string(cnt) + "\" for=\"node\" attr.name=" + attributes_names[t] + " attr.type=\"int\"/>";
+ else if (typeid(T) == typeid(long int))
+ v_prop += "<key id=\"v" + std::to_string(cnt) + "\" for=\"node\" attr.name=" + attributes_names[t] + " attr.type=\"long\"/>";
+ else if (typeid(T) == typeid(bool))
+ v_prop += "<key id=\"v" + std::to_string(cnt) + "\" for=\"node\" attr.name=" + attributes_names[t] + " attr.type=\"boolean\"/>";
+ else if (typeid(T) == typeid(std::string))
+ v_prop += "<key id=\"v" + std::to_string(cnt) + "\" for=\"node\" attr.name=" + attributes_names[t] + " attr.type=\"string\"/>";
+ }
+
+ cnt++;
+ }
+};
+
+/*! \brief this class is a functor for "for_each" algorithm
+ *
+ * This class is a functor for "for_each" algorithm. For each
+ * element of the boost::vector the operator() is called.
+ * Is mainly used to create a string containing all the vertex
+ * properties
+ *
+ */
+
+template<typename G>
+struct vertex_node
+{
+ // Vertex object container
+ const typename G::V_container & vo;
+
+ // Properties counter
+ int cnt = 0;
+
+ // vertex counter
+ size_t v_c = 0;
+
+ // vertex node string
+ std::string & v_node;
+
+ // vertex yFile geometry extension
+ std::string yFile_geometry_ext;
+
+ // vertex yFile shape extension
+ std::string yFile_shape_ext;
+
+ // Attribute names
+ std::string * attributes_names;
+
+ // Number of attributes name defined into the vertex
+ int n_attr = 0;
+
+ /*! \brief Constructor
+ *
+ * Create a vertex node
+ *
+ * \param v_node std::string that is filled with the graph node definition in the GraphML format
+ * \param n_obj object container to access its properties for example encapc<...>
+ * \param stub SFINAE, it basically check if G has properties names defined, if yes this
+ * constructor is selected over the other one
+ *
+ */
+ vertex_node(std::string & v_node, const typename G::V_container & n_obj, typename G::V_type::attributes & a_name)
+ :vo(n_obj),v_node(v_node),attributes_names(a_name.name)
+ {
+ // Calculate the number of attributes name
+ n_attr = sizeof(a_name.name)/sizeof(std::string);
+ };
+
+ /*! \brief Constructor
+ *
+ * Create a vertex properties list
+ *
+ * \param v_prop std::string that is filled with the graph properties in the GraphML format
+ * \param n_obj object container to access its properties for example encapc<...>
+ * \param n_prop number of properties
+ *
+ */
+ vertex_node(std::string & v_node, const typename G::V_container & n_obj)
+ :vo(n_obj),v_node(v_node),attributes_names(NULL)
+ {
+ };
+
+ /*! \brief Create a new node
+ *
+ * Create a new node
+ *
+ */
+ void new_node()
+ {
+ // start a new node
+ v_node += "<node id=\"n"+ std::to_string(v_c) + "\">";
+
+ // reset the counter properties
+ cnt = 0;
+
+ // reset the yFile geometry extension node
+ yFile_geometry_ext.clear();
+
+ // reset the yFile shape extension node
+ yFile_shape_ext.clear();
+ }
+
+ /*! \brief Close a node
+ *
+ * Close a node
+ *
+ */
+ void end_node()
+ {
+ // close a node
+ v_node += "</node>";
+ }
+
+ //! It call the functor for each member
+ template<typename T>
+ void operator()(T& t)
+ {
+ //! Create an entry for the attribute
+ if (T::value < n_attr)
+ {
+ // if it is a yFile extension property name process as yFile extension
+ if (attributes_names[T::value] == "x")
+ {yFile_geometry_ext += " x=" + std::to_string(vo.template get<T::value>());}
+ else if (attributes_names[T::value] == "y")
+ {yFile_geometry_ext += " x=" + std::to_string(vo.template get<T::value>());}
+ else if (attributes_names[T::value] == "z")
+ {yFile_geometry_ext += " z=" + std::to_string(vo.template get<T::value>());}
+ else if (attributes_names[T::value] == "shape" )
+ {yFile_shape_ext += " shape=" + std::to_string(vo.template get<T::value>());}
+ else
+ {
+ // Create a property string based on the type of the property
+ if (typeid(decltype(vo.template get<T::value>())) == typeid(float))
+ v_node += "<data key=\"key" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</>";
+ else if (typeid(decltype(vo.template get<T::value>())) == typeid(double))
+ v_node += "<data key=\"key" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</>";
+ else if (typeid(decltype(vo.template get<T::value>())) == typeid(int))
+ v_node += "<data key=\"key" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</>";
+ else if (typeid(decltype(vo.template get<T::value>())) == typeid(long int))
+ v_node += "<data key=\"key" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</>";
+ else if (typeid(decltype(vo.template get<T::value>())) == typeid(bool))
+ v_node += "<data key=\"key" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</>";
+ else if (typeid(decltype(vo.template get<T::value>())) == typeid(std::string))
+ v_node += "<data key=\"key" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</>";
+ }
+ }
+
+ cnt++;
+ }
+};
+
+/*! \brief this class is a functor for "for_each" algorithm
+ *
+ * This class is a functor for "for_each" algorithm. For each
+ * element of the boost::vector the operator() is called.
+ * Is mainly used to create a string containing all the edge
+ * properties
+ *
+ */
+
+template<typename G>
+struct edge_prop
+{
+ // Properties counter
+ int cnt = 0;
+
+ // edge properties
+ std::string & e_prop;
+
+ // Attribute names
+ std::string * attributes_names;
+
+ // Number of attributes name defined into the vertex
+ int n_attr = 0;
+
+ /*! \brief Constructor
+ *
+ * Create an edge properties list
+ *
+ * \param e_prop std::string that is filled with the graph properties in the GraphML format
+ * \param stub SFINAE, it basically check if G::E_type has properties names defined, if yes this
+ * constructor is selected over the other one
+ *
+ */
+ edge_prop(std::string & e_prop, typename G::E_type::attributes & a_name)
+ :e_prop(e_prop),attributes_names(a_name.name)
+ {
+ // Calculate the number of attributes name
+ n_attr = sizeof(a_name.name)/sizeof(std::string);
+ };
+
+ /*! \brief Constructor
+ *
+ * Create an edge properties list
+ *
+ * \param e_prop std::string that is filled with the graph properties in the GraphML format
+ * \param n_prop number of properties
+ *
+ */
+ edge_prop(std::string & v_prop)
+ :e_prop(e_prop),attributes_names(NULL)
+ {
+ };
+
+ //! It call the functor for each member
+ template<typename T>
+ void operator()(T& t)
+ {
+ //! Create an entry for the attribute
+ if (cnt < n_attr)
+ {
+ // if it is a yFile extension property name, does not process it
+ if (attributes_names[t] == "x" || attributes_names[t] == "y"
+ || attributes_names[t] == "z" || attributes_names[t] == "shape" )
+ {cnt++; return ;}
+
+ // Create a property string based on the type of the property
+ if (typeid(T) == typeid(float))
+ e_prop += "<key id=\"v" + std::to_string(cnt) + "\" for=\"node\" attr.name=" + attributes_names[t] + " attr.type=\"float\"/>";
+ else if (typeid(T) == typeid(double))
+ e_prop += "<key id=\"v" + std::to_string(cnt) + "\" for=\"node\" attr.name=" + attributes_names[t] + " attr.type=\"double\"/>";
+ else if (typeid(T) == typeid(int))
+ e_prop += "<key id=\"v" + std::to_string(cnt) + "\" for=\"node\" attr.name=" + attributes_names[t] + " attr.type=\"int\"/>";
+ else if (typeid(T) == typeid(long int))
+ e_prop += "<key id=\"v" + std::to_string(cnt) + "\" for=\"node\" attr.name=" + attributes_names[t] + " attr.type=\"long\"/>";
+ else if (typeid(T) == typeid(bool))
+ e_prop += "<key id=\"v" + std::to_string(cnt) + "\" for=\"node\" attr.name=" + attributes_names[t] + " attr.type=\"boolean\"/>";
+ else if (typeid(T) == typeid(std::string))
+ e_prop += "<key id=\"v" + std::to_string(cnt) + "\" for=\"node\" attr.name=" + attributes_names[t] + " attr.type=\"string\"/>";
+ }
+
+ cnt++;
+ }
+};
+
+/*! \brief this class is a functor for "for_each" algorithm
+ *
+ * This class is a functor for "for_each" algorithm. For each
+ * element of the boost::vector the operator() is called.
+ * Is mainly used to create a string containing all the edge
+ * properties
+ *
+ */
+
+template<typename G>
+struct edge_node
+{
+ // Vertex object container
+ const typename G::E_container & vo;
+
+ // Properties counter
+ int cnt = 0;
+
+ // vertex counter
+ size_t v_c = 0;
+
+ // edge node string
+ std::string & e_node;
+
+ // edge yFile geometry extension
+ std::string yFile_geometry_ext;
+
+ // edge yFile shape extension
+ std::string yFile_shape_ext;
+
+ // Attribute names
+ std::string * attributes_names;
+
+ // Number of attributes name defined into the vertex
+ int n_attr = 0;
+
+ /*! \brief Constructor
+ *
+ * Create an edge node
+ *
+ * \param e_node std::string that is filled with the graph node definition in the GraphML format
+ * \param n_obj object container to access the object properties for example encapc<...>
+ * \param stub SFINAE, it basically check if G has properties names defined, if yes this
+ * constructor is selected over the other one
+ *
+ */
+ edge_node(std::string & e_node, const typename G::E_container & n_obj, typename G::E_type::attributes & a_name)
+ :vo(n_obj),e_node(e_node),attributes_names(a_name.name)
+ {
+ // Calculate the number of attributes name
+ n_attr = sizeof(a_name.name)/sizeof(std::string);
+ };
+
+ /*! \brief Constructor
+ *
+ * Create an edge node
+ *
+ * \param e_node std::string that is filled with the graph properties in the GraphML format
+ * \param n_obj object container to access the object properties for example encapc<...>
+ * \param n_prop number of properties
+ *
+ */
+ edge_node(std::string & v_node, const typename G::V_container & n_obj)
+ :vo(n_obj),e_node(e_node),attributes_names(NULL)
+ {
+ };
+
+ /*! \brief Create a new node
+ *
+ * Create a new node
+ *
+ */
+ void new_node()
+ {
+ // start a new node
+ e_node += "<node id=\"n"+ std::to_string(v_c) + "\">";
+
+ // reset the counter properties
+ cnt = 0;
+
+ // reset the yFile geometry extension node
+ yFile_geometry_ext.clear();
+
+ // reset the yFile shape extension node
+ yFile_shape_ext.clear();
+ }
+
+ /*! \brief Close a node
+ *
+ * Close a node
+ *
+ */
+ void end_node()
+ {
+ // close a node
+ v_node += "</node>";
+ }
+
+ //! It call the functor for each member
+ template<typename T>
+ void operator()(T& t)
+ {
+ //! Create an entry for the attribute
+ if (T::value < n_attr)
+ {
+ // if it is a yFile extension property name process as yFile extension
+ if (attributes_names[T::value] == "x")
+ {yFile_geometry_ext += " x=" + std::to_string(vo.template get<T::value>());}
+ else if (attributes_names[T::value] == "y")
+ {yFile_geometry_ext += " x=" + std::to_string(vo.template get<T::value>());}
+ else if (attributes_names[T::value] == "z")
+ {yFile_geometry_ext += " z=" + std::to_string(vo.template get<T::value>());}
+ else if (attributes_names[T::value] == "shape" )
+ {yFile_shape_ext += " shape=" + std::to_string(vo.template get<T::value>());}
+ else
+ {
+ // Create a property string based on the type of the property
+ if (typeid(decltype(vo.template get<T::value>())) == typeid(float))
+ v_node += "<data key=\"key" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</>";
+ else if (typeid(decltype(vo.template get<T::value>())) == typeid(double))
+ v_node += "<data key=\"key" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</>";
+ else if (typeid(decltype(vo.template get<T::value>())) == typeid(int))
+ v_node += "<data key=\"key" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</>";
+ else if (typeid(decltype(vo.template get<T::value>())) == typeid(long int))
+ v_node += "<data key=\"key" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</>";
+ else if (typeid(decltype(vo.template get<T::value>())) == typeid(bool))
+ v_node += "<data key=\"key" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</>";
+ else if (typeid(decltype(vo.template get<T::value>())) == typeid(std::string))
+ v_node += "<data key=\"key" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</>";
+ }
+ }
+
+ cnt++;
+ }
+};
+
+/*!
+ *
+ * From a Graphbasic structure it write a GraphML format file
+ *
+ */
+
+template <typename Graph>
+class GraphMLWriter
+{
+ Graph & g;
+
+
+
+ /*! \brief It get the vertex properties list
+ *
+ * It get the vertex properties list of the vertex defined as a GraphML header
+ * x y z and shape are reserved properties name for yFile extension, and
+ * define position and shape of the node
+ *
+ * \return a string that define the vertex properties in graphML format
+ *
+ */
+
+ std::string get_vertex_properties_list()
+ {
+ //! vertex property output string
+ std::string v_out("<key id=\"d0\" for=\"node\" yfiles.type=\"nodegraphics\"/>");
+
+ // create a vertex property functor
+ vertex_prop<Graph> vp(v_out);
+
+ // Iterate through all the vertex and create the vertex list
+ boost::mpl::for_each< typename Graph::V_type::type >(vp);
+
+ // return the vertex properties string
+ return v_out;
+ }
+
+ /*! \brief It get the edge properties list
+ *
+ * It get the edge properties list of the edge defined as a GraphML header
+ *
+ * \return a string that define the edge properties in graphML format
+ *
+ */
+
+ std::string get_edge_properties_list()
+ {
+ //! edge property output string
+ std::string v_out;
+
+ // create a vertex property functor
+ edge_prop<Graph> vp(v_out);
+
+ // Iterate through all the vertex and create the vertex list
+ boost::mpl::for_each< typename Graph::E_type::type >(vp);
+
+ // return the edge properties string
+ return v_out;
+ }
+
+ std::string get_vertex_list()
+ {
+ //! vertex node output string
+ std::string v_out;
+
+ //! Get a vertex iterator
+ auto it = g.getVertexIterator();
+
+ // if there is the next element
+ while (it.isNext())
+ {
+ // create a vertex list functor
+ vertex_node<Graph> vn(v_out,g.vertex(it.get()));
+
+ // Iterate through all the vertex and create the vertex list
+ boost::mpl::for_each< typename Graph::V_type::type >(vn);
+
+ // increment the operator
+ ++it;
+ }
+
+ // return the vertex list
+ return v_out;
+ }
+
+ std::string get_edge_list()
+ {
+ //! edge node output string
+ std::string v_out;
+
+ //! Get an edge iterator
+ auto it = g.getEdgeIterator();
+
+ // if there is the next element
+ while (it.isNext())
+ {
+ // create an edge list functor
+ edge_node<Graph> en(v_out,g.edge(it));
+
+ // Iterate through all the vertex and create the vertex list
+ boost::mpl::for_each< typename Graph::E_type::type >(en);
+
+ // increment the operator
+ ++it;
+ }
+
+ // return the edge list
+ return v_out;
+ }
+
+public:
+
+ /*!
+ *
+ * GraphMLWriter constructor, it take a graph and write a GraphML format
+ *
+ * \param g Graph to write
+ *
+ */
+ GraphMLWriter(Graph & g)
+ :g(g)
+ {}
+
+ /*! \brief It write a GraphML file from a graph
+ *
+ * \param file path where to write
+ * \param name of the graph
+ *
+ */
+
+ bool write(std::string file, std::string graph_name="Graph")
+ {
+ // Header for the GraphML
+ std::string gml_header;
+ // Vertex list of the GraphML
+ std::string vertex_list;
+ // End for the GraphML
+ std::string gml_header_end;
+ // Graph header
+ std::string graph_header;
+ // Graph header end
+ std::string graph_header_end;
+ // Edge list of the GraphML
+ std::string edge_list;
+ // vertex properties header
+ std::string vertex_prop_header;
+ // edge properties header
+ std::string edge_prop_header;
+
+ // GraphML header
+ gml_header = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\
+ <graphml xmlns=\"http://graphml.graphdrawing.org/xmlns\"\
+ xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"\
+ xsi:schemaLocation=\"http://graphml.graphdrawing.org/xmlns\
+ http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd\">";
+
+ // Graph header to define an header
+ graph_header = "<graph id=" + graph_name + " edgedefault=\"directed\">";
+ // Graph header end
+ graph_header_end = "</graph>";
+
+ // Vertex properties header
+ vertex_prop_header = get_vertex_properties_list();
+
+ // Edge properties header
+ edge_prop_header = get_edge_properties_list();
+
+ // Get the node graph list
+ vertex_list = get_vertex_list();
+
+ // Get the edge graph list
+ edge_list = get_edge_list();
+
+ // Header end
+ gml_header_end = "</graphml>";
+
+ // write the file
+
+ std::ofstream ofs(file);
+
+ // Check if the file is open
+ if (ofs.is_open())
+ {std::cerr << "Error cannot creare the graphML file: " + file;}
+
+ ofs << gml_header << graph_header << vertex_prop_header << edge_prop_header <<
+ vertex_list << edge_list << graph_header_end << gml_header_end;
+
+ // Completed succefully
+ return true;
+ }
+};
+
+#endif
diff --git a/src/MatLabWriter.hpp b/src/MatLabWriter.hpp
index 5db834a6..a50d3a1e 100644
--- a/src/MatLabWriter.hpp
+++ b/src/MatLabWriter.hpp
@@ -13,7 +13,7 @@
*/
template<unsigned int dim, typename T>
-class TiffWriter
+class MatLabWriter
{
/*! \brief Save grid into tiff files
*
@@ -21,7 +21,7 @@ class TiffWriter
*
*/
- template<typename grid, typename Mem> int write(grid data, std::string file)
+ template<typename grid, typename Mem> int operator<<(grid data, std::string file)
{
// Grid can have several properties we can save only scalar fields
// for each properties save one scalar fields
--
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