diff --git a/FileIO/RapidXmlIO/BoostVtuInterface.cpp b/FileIO/RapidXmlIO/BoostVtuInterface.cpp
index 182140490934b4eb54748d070bbe94f6acb232e3..e3d69f2681d7701d5060123c5d3f8804d16e87f4 100644
--- a/FileIO/RapidXmlIO/BoostVtuInterface.cpp
+++ b/FileIO/RapidXmlIO/BoostVtuInterface.cpp
@@ -1,56 +1,58 @@
/**
- * Copyright (c) 2012, OpenGeoSys Community (http://www.opengeosys.net)
+ * @copyright
+ * Copyright (c) 2013, OpenGeoSys Community (http://www.opengeosys.net)
* Distributed under a Modified BSD License.
* See accompanying file LICENSE.txt or
* http://www.opengeosys.org/LICENSE.txt
*
* \file BoostVtuInterface.cpp
- *
- * Created on 2012-12-05 by Karsten Rink
+ * @date 2012-12-05
+ * @author Karsten Rink
+ * @brief Read VTU files employing boost.
*/
#include "BoostVtuInterface.h"
-#include <iostream>
#include <fstream>
#include <boost/foreach.hpp>
-#include "StringTools.h"
+// ThirdParty/logog
+#include "logog/include/logog.hpp"
+
#include "FileTools.h"
#include "ProjectData.h"
+#include "StringTools.h"
// MSH
-#include "Mesh.h"
-#include "Node.h"
#include "Elements/Edge.h"
-#include "Elements/Tri.h"
-#include "Elements/Quad.h"
-#include "Elements/Tet.h"
#include "Elements/Hex.h"
-#include "Elements/Pyramid.h"
#include "Elements/Prism.h"
+#include "Elements/Pyramid.h"
+#include "Elements/Quad.h"
+#include "Elements/Tet.h"
+#include "Elements/Tri.h"
+#include "Mesh.h"
+#include "Node.h"
-namespace FileIO {
-
+namespace FileIO
+{
using namespace boost;
-BoostVtuInterface::BoostVtuInterface()
-: _export_name(""), _mesh(nullptr), /*_doc(),*/ _use_compressor(false)
+BoostVtuInterface::BoostVtuInterface() :
+ _export_name(""), _mesh(nullptr), _use_compressor(false)
{
}
BoostVtuInterface::~BoostVtuInterface()
-{
-// delete _doc;
-}
+{}
MeshLib::Mesh* BoostVtuInterface::readVTUFile(const std::string &file_name)
{
- std::cout << "Reading OGS mesh ... " << std::endl;
+ INFO("BoostVtuInterface::readVTUFile(): Reading OGS mesh.");
std::ifstream in(file_name.c_str());
if (in.fail())
{
- std::cout << "\nRapidVtuInterface::readVTUFile() - Can't open xml-file." << std::endl;
+ ERR("BoostVtuInterface::readVTUFile(): Can't open xml-file %s.", file_name.c_str());
return nullptr;
}
@@ -58,7 +60,7 @@ MeshLib::Mesh* BoostVtuInterface::readVTUFile(const std::string &file_name)
using boost::property_tree::ptree;
ptree doc;
read_xml(in, doc);
-
+
if (isVTKUnstructuredGrid(doc))
{
ptree const& root_node = doc.get_child("VTKFile");
@@ -68,27 +70,29 @@ MeshLib::Mesh* BoostVtuInterface::readVTUFile(const std::string &file_name)
{
if (*compressor != "vtkZLibDataCompressor")
{
- std::cout << "BoostVtuInterface::readVTUFile() - Unknown compression method." << std::endl;
+ ERR("BoostVtuInterface::readVTUFile(): Unknown compression method.");
return nullptr;
}
// TODO: remove this once compressed data can be handled!!
- std::cout << "Handling of compressed meshes not yet implemented." << std::endl;
+ INFO("Handling of compressed meshes not yet implemented.");
return nullptr;
}
//skip to <Piece>-tag and start parsing content
- OptionalPtree const& piece_node = root_node.get_child_optional("UnstructuredGrid.Piece");
+ OptionalPtree const& piece_node = root_node.get_child_optional(
+ "UnstructuredGrid.Piece");
if (piece_node)
{
-
- const unsigned nNodes = static_cast<unsigned>(piece_node->get("<xmlattr>.NumberOfPoints", 0));
- const unsigned nElems = static_cast<unsigned>(piece_node->get("<xmlattr>.NumberOfCells", 0));
+ const unsigned nNodes =
+ static_cast<unsigned>(piece_node->get("<xmlattr>.NumberOfPoints", 0));
+ const unsigned nElems =
+ static_cast<unsigned>(piece_node->get("<xmlattr>.NumberOfCells", 0));
if ((nNodes == 0) || (nElems == 0))
{
- std::cout << "BoostVtuInterface::readVTUFile() - Number of nodes is " << nNodes
- << ", number of elements is " << nElems << "." << std::endl;
+ ERR("BoostVtuInterface::readVTUFile() - Number of nodes is %d, number of elements is %d.",
+ nNodes, nElems);
return nullptr;
}
@@ -97,36 +101,42 @@ MeshLib::Mesh* BoostVtuInterface::readVTUFile(const std::string &file_name)
std::vector<unsigned> mat_ids(nElems, 0);
std::vector<unsigned> cell_types(nElems);
- BOOST_FOREACH( ptree::value_type const& grid_piece, *piece_node )
+ BOOST_FOREACH( ptree::value_type const & grid_piece, *piece_node )
{
if (grid_piece.first == "CellData")
{
- const OptionalPtree& cell_data_node = findDataArray("MaterialIDs", grid_piece.second);
+ const OptionalPtree& cell_data_node = findDataArray(
+ "MaterialIDs",
+ grid_piece.second);
if (cell_data_node)
{
- optional<std::string> const& format = getXmlAttribute("format", *cell_data_node);
- std::stringstream iss (cell_data_node->data());//v.second.get<std::string>("DataArray"));
- if (format)
+ optional<std::string> const& format =
+ getXmlAttribute("format", *cell_data_node);
+ std::stringstream iss (cell_data_node->data()); //v.second.get<std::string>("DataArray"));
+ if (format)
{
if (*format == "ascii")
- for(unsigned i=0; i<nElems; i++)
+ for(unsigned i = 0; i < nElems; i++)
iss >> mat_ids[i];
- else if (*format == "appended")
- {
- //uncompress
- }
+ else if (*format == "appended")
+ {
+ //uncompress
+ }
}
}
else
- std::cerr << "MaterialIDs not found, setting every cell to 0." << std::endl;
+ WARN("BoostVtuInterface::readVTUFile(): MaterialIDs not found, setting every cell to 0.");
}
-
+
if (grid_piece.first == "Points")
{
// This node may or may not have an attribute "Name" with the value "Points".
// However, there shouldn't be any other DataArray nodes so most likely not checking the name isn't a problem.
- ptree const& data_array_node = grid_piece.second.get_child("DataArray");
- optional<std::string> const& format = getXmlAttribute("format", data_array_node);
+ ptree const& data_array_node = grid_piece.second.get_child(
+ "DataArray");
+ optional<std::string> const& format = getXmlAttribute(
+ "format",
+ data_array_node);
if (format)
{
@@ -134,10 +144,13 @@ MeshLib::Mesh* BoostVtuInterface::readVTUFile(const std::string &file_name)
{
std::stringstream iss (data_array_node.data());
double x,y,z;
- for(unsigned i=0; i<nNodes; i++)
+ for(unsigned i = 0; i < nNodes; i++)
{
iss >> x >> y >> z;
- nodes[i] = new MeshLib::Node(x,y,z,i);
+ nodes[i] = new MeshLib::Node(x,
+ y,
+ z,
+ i);
}
}
else if (*format == "appended")
@@ -154,7 +167,7 @@ MeshLib::Mesh* BoostVtuInterface::readVTUFile(const std::string &file_name)
// cell types
OptionalPtree const& types = findDataArray("types", cells);
if (!types)
- std::cerr << "Cannot find \"types\" data array.\n";
+ ERR("BoostVtuInterface::readVTUFile(): Cannot find \"types\" data array.");
std::stringstream iss (types->data());
optional<std::string> const& format = getXmlAttribute("format", *types);
@@ -168,35 +181,37 @@ MeshLib::Mesh* BoostVtuInterface::readVTUFile(const std::string &file_name)
//uncompress
}
-
// connectivity / element nodes
OptionalPtree const& connectivity = findDataArray("connectivity", cells);
if (!connectivity)
- std::cerr << "Cannot find \"connectivity\" data array.\n";
+ ERR("BoostVtuInterface::readVTUFile(): Cannot find \"connectivity\" data array.");
std::string conn_string = connectivity->data();
if (!conn_string.empty())
{
- optional<std::string> const& format = getXmlAttribute("format", *connectivity);
+ optional<std::string> const& format =
+ getXmlAttribute("format", *connectivity);
if (*format == "appended")
{
//uncompress
}
std::stringstream iss (conn_string);
- for(unsigned i=0; i<nElems; i++)
- elements[i] = readElement(iss, nodes, mat_ids[i], cell_types[i]);
+ for(unsigned i = 0; i < nElems; i++)
+ elements[i] = readElement(iss,
+ nodes,
+ mat_ids[i],
+ cell_types[i]);
}
}
-
-
}
- std::cout << "finished." << std::endl;
- std::cout << "Nr. Nodes: " << nodes.size() << std::endl;
- std::cout << "Nr. Elements: " << elements.size() << std::endl;
- return new MeshLib::Mesh(BaseLib::extractBaseNameWithoutExtension(file_name), nodes, elements);
+ INFO("BoostVtuInterface::readVTUFile(): \tfinished.");
+ INFO("BoostVtuInterface::readVTUFile(): Nr. Nodes: %d", nodes.size());
+ INFO("BoostVtuInterface::readVTUFile(): Nr. Elements: ", elements.size());
+ return new MeshLib::Mesh(BaseLib::extractBaseNameWithoutExtension(file_name), nodes,
+ elements);
} // piece
} // unstructured grid
@@ -204,13 +219,16 @@ MeshLib::Mesh* BoostVtuInterface::readVTUFile(const std::string &file_name)
return nullptr;
}
-MeshLib::Element* BoostVtuInterface::readElement(std::stringstream &iss, const std::vector<MeshLib::Node*> &nodes, unsigned material, unsigned type)
+MeshLib::Element* BoostVtuInterface::readElement(std::stringstream &iss,
+ const std::vector<MeshLib::Node*> &nodes,
+ unsigned material, unsigned type)
{
unsigned node_ids[8];
switch (type)
{
case 3: { //line
- for (unsigned i(0); i<2; i++) iss >> node_ids[i];
+ for (unsigned i(0); i < 2; i++)
+ iss >> node_ids[i];
MeshLib::Node** edge_nodes = new MeshLib::Node*[2];
edge_nodes[0] = nodes[node_ids[0]];
edge_nodes[1] = nodes[node_ids[1]];
@@ -218,7 +236,8 @@ MeshLib::Element* BoostVtuInterface::readElement(std::stringstream &iss, const s
break;
}
case 5: { //triangle
- for (unsigned i(0); i<3; i++) iss >> node_ids[i];
+ for (unsigned i(0); i < 3; i++)
+ iss >> node_ids[i];
MeshLib::Node** tri_nodes = new MeshLib::Node*[3];
tri_nodes[0] = nodes[node_ids[0]];
tri_nodes[1] = nodes[node_ids[1]];
@@ -227,15 +246,17 @@ MeshLib::Element* BoostVtuInterface::readElement(std::stringstream &iss, const s
break;
}
case 9: { //quad
- for (unsigned i(0); i<4; i++) iss >> node_ids[i];
+ for (unsigned i(0); i < 4; i++)
+ iss >> node_ids[i];
MeshLib::Node** quad_nodes = new MeshLib::Node*[4];
- for (unsigned k(0); k<4; k++)
+ for (unsigned k(0); k < 4; k++)
quad_nodes[k] = nodes[node_ids[k]];
return new MeshLib::Quad(quad_nodes, material);
break;
}
case 8: { //pixel
- for (unsigned i(0); i<4; i++) iss >> node_ids[i];
+ for (unsigned i(0); i < 4; i++)
+ iss >> node_ids[i];
MeshLib::Node** quad_nodes = new MeshLib::Node*[4];
quad_nodes[0] = nodes[node_ids[0]];
quad_nodes[1] = nodes[node_ids[1]];
@@ -245,23 +266,26 @@ MeshLib::Element* BoostVtuInterface::readElement(std::stringstream &iss, const s
break;
}
case 10: {
- for (unsigned i(0); i<4; i++) iss >> node_ids[i];
+ for (unsigned i(0); i < 4; i++)
+ iss >> node_ids[i];
MeshLib::Node** tet_nodes = new MeshLib::Node*[4];
- for (unsigned k(0); k<4; k++)
+ for (unsigned k(0); k < 4; k++)
tet_nodes[k] = nodes[node_ids[k]];
return new MeshLib::Tet(tet_nodes, material);
break;
}
case 12: { //hexahedron
- for (unsigned i(0); i<8; i++) iss >> node_ids[i];
+ for (unsigned i(0); i < 8; i++)
+ iss >> node_ids[i];
MeshLib::Node** hex_nodes = new MeshLib::Node*[8];
- for (unsigned k(0); k<8; k++)
+ for (unsigned k(0); k < 8; k++)
hex_nodes[k] = nodes[node_ids[k]];
return new MeshLib::Hex(hex_nodes, material);
break;
}
case 11: { //voxel
- for (unsigned i(0); i<8; i++) iss >> node_ids[i];
+ for (unsigned i(0); i < 8; i++)
+ iss >> node_ids[i];
MeshLib::Node** voxel_nodes = new MeshLib::Node*[8];
voxel_nodes[0] = nodes[node_ids[0]];
voxel_nodes[1] = nodes[node_ids[1]];
@@ -275,45 +299,46 @@ MeshLib::Element* BoostVtuInterface::readElement(std::stringstream &iss, const s
break;
}
case 14: { //pyramid
- for (unsigned i(0); i<5; i++) iss >> node_ids[i];
+ for (unsigned i(0); i < 5; i++)
+ iss >> node_ids[i];
MeshLib::Node** pyramid_nodes = new MeshLib::Node*[5];
- for (unsigned k(0); k<5; k++)
+ for (unsigned k(0); k < 5; k++)
pyramid_nodes[k] = nodes[node_ids[k]];
return new MeshLib::Pyramid(pyramid_nodes, material);
break;
}
case 13: { //wedge
- for (unsigned i(0); i<6; i++) iss >> node_ids[i];
+ for (unsigned i(0); i < 6; i++)
+ iss >> node_ids[i];
MeshLib::Node** prism_nodes = new MeshLib::Node*[6];
- for (unsigned k(0); k<6; k++)
+ for (unsigned k(0); k < 6; k++)
prism_nodes[k] = nodes[node_ids[k]];
return new MeshLib::Prism(prism_nodes, material);
break;
}
default:
- std::cout << "Error in RapidVtuInterface::readElement() - Unknown mesh element type \"" << type << "\" ..." << std::endl;
+ ERR("BoostVtuInterface::readElement(): Unknown mesh element type \"%d\".", type);
return nullptr;
}
-
}
bool BoostVtuInterface::isVTKFile(const property_tree::ptree &vtk_root)
{
if (!vtk_root.get_child_optional("VTKFile"))
{
- std::cout << "Error in BoostVtuInterface::readVTUFile() - Not a VTK File." << std::endl;
+ ERR("BoostVtuInterface::isVTKFile(): Not a VTK file.");
return false;
}
optional<std::string> const& att_version (getXmlAttribute("version", vtk_root));
if (att_version && *att_version == "0.1")
{
- std::cout << "Error in BoostVtuInterface::readVTUFile() - Unsupported file format version." << std::endl;
+ ERR("BoostVtuInterface::isVTKFile(): Unsupported file format version.");
return false;
}
optional<std::string> const& att_order (getXmlAttribute("byte_order", vtk_root));
if (att_order && *att_order == "LittleEndian")
{
- std::cout << "Error in BoostVtuInterface::readVTUFile() - Only little endian files are supported." << std::endl;
+ ERR("BoostVtuInterface::isVTKFile(): Only little endian files are supported.");
return false;
}
return true;
@@ -323,27 +348,27 @@ bool BoostVtuInterface::isVTKUnstructuredGrid(const property_tree::ptree &vtk_ro
{
if (isVTKFile(vtk_root))
{
- const OptionalPtree &u_grid_node = vtk_root.get_child_optional("VTKFile.UnstructuredGrid");
+ const OptionalPtree &u_grid_node = vtk_root.get_child_optional(
+ "VTKFile.UnstructuredGrid");
if (u_grid_node)
return true;
- std::cout << "Error in BoostVtuInterface::readVTUFile() - Not an unstructured grid." << std::endl;
+ ERR("Error in BoostVtuInterface::isVTKUnstructuredGrid(): Not an unstructured grid.");
}
return false;
}
unsigned char* BoostVtuInterface::uncompressData(property_tree::ptree const& compressed_data_node)
{
- //rapidxml::xml_node<>* data_node = node->first_node("AppendedData");
const char* compressed_data = compressed_data_node.data().c_str();
-
- return NULL;
+ return nullptr;
}
-const optional<std::string> BoostVtuInterface::getXmlAttribute(std::string const& key, property_tree::ptree const& tree)
+const optional<std::string> BoostVtuInterface::getXmlAttribute(std::string const& key,
+ property_tree::ptree const& tree)
{
- for (property_tree::ptree::const_iterator it = tree.begin(); it != tree.end(); ++it)
- {
- if (it->first != "<xmlattr>")
+ for (property_tree::ptree::const_iterator it = tree.begin(); it != tree.end(); ++it)
+ {
+ if (it->first != "<xmlattr>")
continue;
if (it->second.get_child_optional(key))
return it->second.get_child(key).data();
@@ -352,41 +377,39 @@ const optional<std::string> BoostVtuInterface::getXmlAttribute(std::string const
return optional<std::string>();
}
-const OptionalPtree BoostVtuInterface::findDataArray(std::string const& array_name, property_tree::ptree const& tree)
+const OptionalPtree BoostVtuInterface::findDataArray(std::string const& array_name,
+ property_tree::ptree const& tree)
{
- // Loop over all "DataArray" children.
- for (property_tree::ptree::const_iterator it = tree.begin(); it != tree.end(); ++it)
- {
- if (it->first == "DataArray")
- {
- optional<std::string> const& value = getXmlAttribute("Name", it->second);
- if (value && *value == array_name)
- return it->second;
+ // Loop over all "DataArray" children.
+ for (property_tree::ptree::const_iterator it = tree.begin(); it != tree.end(); ++it)
+ if (it->first == "DataArray")
+ {
+ optional<std::string> const& value = getXmlAttribute("Name", it->second);
+ if (value && *value == array_name)
+ return it->second;
}
- }
- return OptionalPtree();
+ return OptionalPtree();
}
-
int BoostVtuInterface::write(std::ostream& stream)
{
//if (this->_export_name.empty())
if (!_mesh)
{
- std::cout << "Error in XmlStnInterface::write() - No station list specified..." << std::endl;
+ ERR("BoostVtuInterface::write(): No mesh specified.");
return 0;
}
- const size_t nNodes (_mesh->getNNodes());
- const size_t nElems (_mesh->getNElements());
+ const std::size_t nNodes (_mesh->getNNodes());
+ const std::size_t nElems (_mesh->getNElements());
const std::vector<MeshLib::Node*> &nodes (_mesh->getNodes());
const std::vector<MeshLib::Element*> &elements (_mesh->getElements());
const std::string data_array_close("\t\t\t\t");
const std::string data_array_indent("\t\t\t\t ");
- using boost::property_tree::ptree;
+ using boost::property_tree::ptree;
ptree doc;
ptree &root_node = doc.put("VTKFile", "");
@@ -411,7 +434,7 @@ int BoostVtuInterface::write(std::ostream& stream)
std::stringstream oss(std::stringstream::out);
oss << std::endl << data_array_indent;
- for (unsigned i=0; i<nElems; i++)
+ for (unsigned i = 0; i < nElems; i++)
oss << elements[i]->getValue() << " ";
oss << std::endl << data_array_close;
this->addDataArray(celldata_node, "MaterialIDs", "Int32", oss.str());
@@ -421,8 +444,9 @@ int BoostVtuInterface::write(std::ostream& stream)
// point coordinates
ptree &points_node = piece_node.add("Points", "");
oss << std::endl;
- for (unsigned i=0; i<nNodes; i++)
- oss << data_array_indent << (*nodes[i])[0] << " " << (*nodes[i])[1] << " " << (*nodes[i])[2] << std::endl;
+ for (unsigned i = 0; i < nNodes; i++)
+ oss << data_array_indent << (*nodes[i])[0] << " " << (*nodes[i])[1] << " " <<
+ (*nodes[i])[2] << std::endl;
oss << data_array_close;
this->addDataArray(points_node, "Points", "Float32", oss.str(), 3);
oss.str(std::string());
@@ -437,12 +461,12 @@ int BoostVtuInterface::write(std::ostream& stream)
typestream << std::endl << data_array_indent;
unsigned offset_count(0);
- for (unsigned i=0; i<nElems; i++)
+ for (unsigned i = 0; i < nElems; i++)
{
MeshLib::Element* element (elements[i]);
const unsigned nElemNodes (element->getNNodes());
oss << data_array_indent;
- for (unsigned j=0; j<nElemNodes; j++)
+ for (unsigned j = 0; j < nElemNodes; j++)
oss << element->getNode(j)->getID() << " ";
oss << std::endl;
offset_count += nElemNodes;
@@ -459,7 +483,7 @@ int BoostVtuInterface::write(std::ostream& stream)
this->addDataArray(cells_node, "types", "UInt8", typestream.str());
property_tree::xml_writer_settings<char> settings('\t', 1);
- write_xml(stream, doc, settings);
+ write_xml(stream, doc, settings);
return 1;
}
@@ -486,7 +510,9 @@ unsigned BoostVtuInterface::getVTKElementID(MshElemType::type type) const
}
}
-void BoostVtuInterface::addDataArray(property_tree::ptree &parent_node, const std::string &name, const std::string &data_type, const std::string &data, unsigned nComponents)
+void BoostVtuInterface::addDataArray(property_tree::ptree &parent_node, const std::string &name,
+ const std::string &data_type, const std::string &data,
+ unsigned nComponents)
{
property_tree::ptree &dataarray_node = parent_node.add("DataArray", data.c_str());
dataarray_node.put("<xmlattr>.type", data_type.c_str());
@@ -497,7 +523,4 @@ void BoostVtuInterface::addDataArray(property_tree::ptree &parent_node, const st
dataarray_node.put("<xmlattr>.format", comp_type.c_str());
// ---- offset attribute for compressed data! ----
}
-
-
} // end namespace FileIO
-