Added CSV and VTK writer

src/CSVWriter.hpp

+/*
+ * CSVWriter.hpp
+ *
+ *  Created on: Dec 15, 2014
+ *      Author: Pietro Incardona
+ */
+
+#ifndef CSVWRITER_HPP_
+#define CSVWRITER_HPP_
+
+#include <iostream>
+#include <boost/fusion/include/mpl.hpp>
+#include <boost/fusion/include/for_each.hpp>
+#include <fstream>
+#include "common.hpp"
+#include <boost/mpl/range_c.hpp>
+#include <boost/mpl/for_each.hpp>
+#include "Point_test.hpp"
+#include "csv_multiarray.hpp"
+#include "util.hpp"
+
+/*! \brief 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 properties of the object
+ *
+ * \tparam Tobj object
+ *
+ */
+
+template<typename Tobj>
+struct csv_prp
+{
+	// String
+	std::stringstream & str;
+
+	// Object to write
+	Tobj & obj;
+
+	/*! \brief Constructor
+	 *
+	 * Create a vertex properties list
+	 *
+	 * \param str streamstring
+	 * \param obj object to write
+	 *
+	 */
+	csv_prp(std::stringstream & str, Tobj & obj)
+	:str(str),obj(obj)
+	{
+	};
+
+	//! It call the functor for each member
+    template<typename T>
+    void operator()(T& t)
+    {
+		// This is the type of the csv column
+		typedef typename boost::fusion::result_of::at_c<typename Tobj::type,T::value>::type col_type;
+
+		// Remove the reference from the column type
+		typedef typename boost::remove_reference<col_type>::type col_rtype;
+
+    	csv_value_str<col_rtype>(obj.template get<T::value>(),str);
+    }
+};
+
+/*! \brief 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 properties of the object
+ *
+ * \tparam T object
+ *
+ */
+
+template<typename Tobj, bool attr>
+struct csv_col
+{
+	std::stringstream & str;
+
+	csv_col(std::stringstream & str)
+	:str(str)
+	{
+	};
+
+	//! It call the functor for each member
+    template<typename T>
+    void operator()(T& t)
+    {
+		// This is the type of the csv column
+		typedef typename boost::fusion::result_of::at_c<typename Tobj::type,T::value>::type col_type;
+
+		// Remove the reference from the column type
+		typedef typename boost::remove_reference<col_type>::type col_rtype;
+
+    	csv_col_str<col_rtype>(std::string(Tobj::attributes::name[T::value]),str);
+    }
+};
+
+/*! \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
+ *
+ * Specialization when we do not have vertex attributes
+ *
+ * \tparam G graph type
+ *
+ */
+
+template<typename Tobj>
+struct csv_col<Tobj,false>
+{
+	std::stringstream & str;
+
+	csv_col(std::stringstream & str)
+	:str(str)
+	{
+	};
+
+	//! It call the functor for each member
+    template<typename T>
+    void operator()(T& t)
+    {
+		// This is the type of the csv column
+		typedef typename boost::fusion::result_of::at_c<typename Tobj::type,T::value>::type col_type;
+
+		// Remove the reference from the column type
+		typedef typename boost::remove_reference<col_type>::type col_rtype;
+
+		std::stringstream str2;
+		str2 << "column_" << T::value;
+
+		csv_col_str<col_rtype>(str2.str(),str);
+    }
+};
+
+#define VECTOR 1
+
+/*! \brief CSV Writer
+ *
+ * It write in CSV format vector of objects living into an N-dimensional space
+ *
+ * \tparam v_pos Positional vector
+ * \tparam v_prp Property vector
+ *
+ */
+template <typename v_pos, typename v_prp, unsigned int impl = VECTOR>
+class CSVWriter
+{
+	/*! \brief Get the colums name (also the positional name)
+	 *
+	 */
+	std::string get_csv_colums()
+	{
+		std::stringstream str;
+
+		// write positional columns
+		for (int i = 0 ; i < v_pos::value_type::dims ; i++)
+		{
+			if (i == 0)
+				str << "x[" << i << "]";
+			else
+				str << "," << "x[" << i << "]";
+		}
+
+		// write positional information
+
+		csv_col<typename v_prp::value_type,has_attributes<typename v_prp::value_type>::value> col(str);
+
+		// Iterate through all the vertex and create the vertex list
+		boost::mpl::for_each< boost::mpl::range_c<int,0,v_prp::value_type::max_prop> >(col);
+
+		str << "\n";
+
+		return str.str();
+	}
+
+	/*! \brief Get the csv data section
+	 *
+	 * \param v_pos vector that contain the positional information
+	 * \param v_prp vector that contain the property information
+	 *
+	 */
+	std::string get_csv_data(v_pos & vp, v_prp & vpr)
+	{
+		std::stringstream str;
+
+		// The position and property vector size must match
+		if (vp.size() != vpr.size())
+		{
+			std::cerr << "Error: " << __FILE__ << ":" << __LINE__ << " position vector and property vector must have the same size \n";
+			return std::string("");
+		}
+
+		// Write the data
+		for (size_t i = 0 ; i < vp.size() ; i++)
+		{
+			for (size_t j = 0 ; j < v_pos::value_type::dims ; j++)
+			{
+				if (j == 0)
+					str << vp.template get<0>(i)[j];
+				else
+					str << "," << vp.template get<0>(i)[j];
+			}
+
+			// Object to write
+			typename v_prp::value_type obj = vpr.get(i);
+
+			csv_prp<typename v_prp::value_type> c_prp(str,obj);
+
+			// write the properties to the stream string
+			boost::mpl::for_each< boost::mpl::range_c<int,0,v_prp::value_type::max_prop> >(c_prp);
+
+			str << "\n";
+		}
+
+		return str.str();
+	}
+
+public:
+
+	/*! \brief It write a CSV file
+	 *
+	 * \tparam prp which properties to output [default = -1 (all)]
+	 *
+	 * \param file path where to write
+	 * \param v_pos positional vector
+	 * \param v_prp properties vector
+	 *
+	 */
+
+	bool write(std::string file, v_pos & v , v_prp & prp)
+	{
+		// Header for csv (colums name)
+		std::string csv_header;
+		// Data point
+		std::string point_data;
+
+		// Get csv columns
+		csv_header = get_csv_colums();
+
+		// For each property in the vertex type produce a point data
+		point_data = get_csv_data(v,prp);
+
+		// write the file
+		std::ofstream ofs(file);
+
+		// Check if the file is open
+		if (ofs.is_open() == false)
+		{std::cerr << "Error cannot create the CSV file: " + file;}
+
+		ofs << csv_header << point_data;
+
+		// Close the file
+
+		ofs.close();
+
+		// Completed succefully
+		return true;
+	}
+};
+
+
+#endif /* CSVWRITER_HPP_ */
+

src/CSVWriter_unit_tests.hpp

+#ifndef CSVWRITER_UNIT_TESTS_HPP_
+#define CSVWRITER_UNIT_TESTS_HPP_
+
+#include "CSVWriter.hpp"
+#include "Vector/vector_test_util.hpp"
+
+BOOST_AUTO_TEST_SUITE( csv_writer_test )
+
+
+BOOST_AUTO_TEST_CASE( csv_writer_particles )
+{
+	// Allocate a property vector
+	auto v_prp = allocate_openfpm(16);
+	// Vector of position
+	openfpm::vector<Point<3,float>> v_pos;
+
+	// create a positional vector
+	for (size_t i = 0 ; i < v_prp.size() ; i++)
+	{
+		Point<3,float> p({1.0,2.0,3.0});
+
+		v_pos.add(p);
+	}
+
+	// CSVWriter test
+	CSVWriter<openfpm::vector<Point<3,float>>, openfpm::vector<Point_test<float>> > csv_writer;
+
+	// Write the CSV
+	csv_writer.write("csv_out.csv",v_pos,v_prp);
+
+	bool test = compare("csv_out.csv","csv_out_test.csv");
+	BOOST_REQUIRE_EQUAL(true,test);
+
+
+}
+
+BOOST_AUTO_TEST_SUITE_END()
+
+#endif

src/GraphMLWriter.hpp

 #ifndef GRAPHML_WRITER_HPP
 #define GRAPHML_WRITER_HPP
 
-#include "map_graph.hpp"
+#include "Graph/map_graph.hpp"
 #include <iostream>
-#include <boost/fusion/include/mpl.hpp>
-#include <boost/fusion/include/for_each.hpp>
 #include <fstream>
 #include "common.hpp"
 
@@ -425,7 +423,7 @@ struct edge_node
 	void end_node()
 	{
 		// close a node
-		e_node += "</node>\n";
+		e_node += "</edge>\n";
 	}
 
 	//! It call the functor for each member
@@ -478,7 +476,7 @@ class GraphMLWriter
 	std::string get_vertex_properties_list()
 	{
 		//! vertex property output string
-		std::string v_out("<key id=\"d0\" for=\"node\" yfiles.type=\"nodegraphics\"/>\n");
+		std::string v_out("");
 
 		// create a vertex property functor
 		vertex_prop<Graph> vp(v_out);
@@ -633,7 +631,7 @@ public:
 		     http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd\">\n";
 
 		// Graph header to define an header
-		graph_header = "<graph id=\"" + graph_name + "\" edgedefault=\"directed\">\n";
+		graph_header = "<graph id=\"" + graph_name + "\" edgedefault=\"undirected\">\n";
 		// Graph header end
 		graph_header_end =  "</graph>\n";
 

src/GraphMLWriter_unit_tests.hpp

@@ -13,6 +13,7 @@
 #include "GraphMLWriter.hpp"
 #include "VTKWriter.hpp"
 #include "Graph/CartesianGraphFactory.hpp"
+#include "util.hpp"
 
 BOOST_AUTO_TEST_SUITE( graphml_writer_test )
 
@@ -81,34 +82,35 @@ BOOST_AUTO_TEST_CASE( graphml_writer_use)
 	g_csr2.addEdge(2,0);
 	g_csr2.addEdge(3,2);
 
-	VTKWriter<Graph_CSR<ne_cp,ne_cp>> gv2(g_csr2);
+	// Create a graph ML
+	GraphMLWriter<Graph_CSR<ne_cp,ne_cp>> gv2(g_csr2);
+	gv2.write("test_graph2.graphml");
 
-	gv2.write("test_graph2.vtk");
+	// check that match
+
+	bool test = compare("test_graph2.graphml","test_graph2_test.graphml");
+	BOOST_REQUIRE_EQUAL(true,test);
 
 	//! Create a graph
 
 	CartesianGraphFactory<3,Graph_CSR<ne_cp,ne_cp>> g_factory;
 
 	// Cartesian grid
-	std::vector<size_t> sz;
-	sz.push_back(GS_SIZE);
-	sz.push_back(GS_SIZE);
-	sz.push_back(GS_SIZE);
+	size_t sz[] = {GS_SIZE,GS_SIZE,GS_SIZE};
 
 	// Box
 	Box<3,float> box({0.0,0.0,0.0},{1.0,1.0,1.0});
 
 	Graph_CSR<ne_cp,ne_cp> g_csr = g_factory.construct<5,float,2,ne_cp::x,ne_cp::y,ne_cp::z>(sz,box);
 
+	// Create a graph ML
 	GraphMLWriter<Graph_CSR<ne_cp,ne_cp>> gw(g_csr);
+	gw.write("test_graph.graphml");
 
-//	std::cout << std::is_class<ne_cp::attributes>;
-
-	gw.write("test_graph.gml");
-
-	VTKWriter<Graph_CSR<ne_cp,ne_cp>> gv(g_csr);
 
-	gv.write("test_graph.vtk");
+	// check that match
+	test = compare("test_graph.graphml","test_graph_test.graphml");
+	BOOST_REQUIRE_EQUAL(true,test);
 }
 
 BOOST_AUTO_TEST_SUITE_END()

src/VTKWriter.hpp

+/*
+ * VTKWriter.hpp
+ *
+ *  Created on: Dec 15, 2014
+ *      Author: Pietro Incardona
+ */
+
+#ifndef VTKWRITER_HPP_
+#define VTKWRITER_HPP_
+
+#include "Graph/map_graph.hpp"
+#include <iostream>
+#include <boost/fusion/include/mpl.hpp>
+#include <boost/fusion/include/for_each.hpp>
+#include <fstream>
+#include "common.hpp"
+
+/*! \brief Get the type
+ *
+ * It convert T to a string identify the corrispondent type in VTK format
+ *
+ */
+
+template <typename T> std::string getType()
+{
+	// Create a property string based on the type of the property
+	if (typeid(T) == typeid(float))
+		return "float";
+	else if (typeid(T) == typeid(double))
+		return "double";
+	else if (typeid(T) == typeid(char))
+		return "char";
+	else if (typeid(T) == typeid(unsigned char))
+		return "unsigned_char";
+	else if (typeid(T) == typeid(short))
+		return "short";
+	else if (typeid(T) == typeid(unsigned short))
+		return "unsigned_short";
+	else if (typeid(T) == typeid(int))
+		return "int";
+	else if (typeid(T) == typeid(unsigned int))
+		return "unsigned_int";
+	else if (typeid(T) == typeid(long int))
+		return "long";
+	else if (typeid(T) == typeid(unsigned long int))
+		return "unsigned_long";
+	else if (typeid(T) == typeid(bool))
+		return "bit";
+	return "";
+}
+
+/*! \brief Set a conversion map between A and B
+ *
+ * Convert A to B
+ *
+ * \tparam B destination type
+ * \tparam A source type
+ *
+ */
+
+template<typename A>
+class convert
+{
+public:
+	template<typename B> static B to(const A & data)
+	{
+		return static_cast<B>(data);
+	}
+};
+
+/*! \brief Partial specialization when A is a string
+ *
+ *
+ */
+
+template<>
+class convert<std::string>
+{
+public:
+	template<typename B> static B to(const std::string & data)
+	{
+		return atof(data.c_str());
+	}
+};
+
+/*! \brief It specify the VTK output file type
+ *
+ */
+
+enum file_type
+{
+	BINARY,
+	ASCII
+};
+
+/*! \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
+ *
+ * \tparam G graph type
+ * \tparam attr has the vertex attributes
+ *
+ */
+
+template<typename G, bool attr>
+struct vtk_vertex_node
+{
+	// Vertex spatial type information
+	typedef typename G::V_type::s_type s_type;
+
+	s_type (& x)[3];
+
+	// Vertex object container
+	typename G::V_container & vo;
+
+	// vertex node string
+	std::string & v_node;
+
+	/*! \brief Constructor
+	 *
+	 * Create a vertex properties list
+	 *
+	 * \param v_node 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<...>
+	 *
+	 */
+	vtk_vertex_node(std::string & v_node, typename G::V_container & n_obj, s_type (&x)[3])
+	:x(x),vo(n_obj),v_node(v_node)
+	{
+	};
+
+	//! \brief Write collected information
+	void write()
+	{
+		v_node += std::to_string(x[0]) + " " + std::to_string(x[1]) + " " + std::to_string(x[2]) + "\n";
+	}
+
+	//! It call the functor for each member
+    template<typename T>
+    void operator()(T& t)
+    {
+    	// if the attribute name is x y or z, create a string with the value of the properties and store it
+		if (G::V_type::attributes::name[T::value] == "x"){x[0] = convert<typename boost::remove_reference<decltype(vo.template get<T::value>())>::type>::template to<s_type>(vo.template get<T::value>());}
+		else if (G::V_type::attributes::name[T::value] == "y"){x[1] = convert<typename boost::remove_reference<decltype(vo.template get<T::value>())>::type>::template to<s_type>(vo.template get<T::value>());}
+		else if (G::V_type::attributes::name[T::value] == "z"){x[2] = convert<typename boost::remove_reference<decltype(vo.template get<T::value>())>::type>::template to<s_type>(vo.template get<T::value>());}
+    }
+};
+
+/*! \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
+ *
+ * Specialization when we do not have vertex attributes
+ *
+ * \tparam G graph type
+ *
+ */
+
+template<typename G>
+struct vtk_vertex_node<G,false>
+{
+	// Vertex object container
+	typename G::V_container & vo;
+
+	// vertex node string
+	std::string & v_node;
+
+	/*! \brief Constructor
+	 *
+	 * Create a vertex properties list
+	 *
+	 * \param v_node 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<...>
+	 *
+	 */
+	vtk_vertex_node(std::string & v_node, typename G::V_container & n_obj)
+	:vo(n_obj),v_node(v_node)
+	{
+	};
+
+	//! It call the functor for each member
+    template<typename T>
+    void operator()(T& t)
+    {
+    	v_node += "0 0 0\n";
+    }
+};
+
+
+/*! \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 vtk_edge_node
+{
+	// Vertex object container
+	typename G::E_container & vo;
+
+	// edge node string
+	std::string & e_node;
+
+	/*! \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
+	 *
+	 */
+	vtk_edge_node(std::string & e_node, typename G::E_container & n_obj)
+	:vo(n_obj),e_node(e_node)
+	{
+	};
+
+	/*! \brief Create a new node