diff --git a/Applications/CLI/CMakeLists.txt b/Applications/CLI/CMakeLists.txt
index edb87aa77c7ff8a7b3c1afdfeda1f8c8193aeccc..40cd7e7fc084cb3824065427865db2e3866871ed 100644
--- a/Applications/CLI/CMakeLists.txt
+++ b/Applications/CLI/CMakeLists.txt
@@ -8,6 +8,8 @@ TARGET_LINK_LIBRARIES(ogs
BaseLib
FileIO
MeshLib
+ InSituLib
+ ${CATALYST_LIBRARIES}
${Boost_LIBRARIES}
)
diff --git a/Applications/DataExplorer/DataExplorer.cmake b/Applications/DataExplorer/DataExplorer.cmake
index 815b4acc2b0af1b0bfc723ef470a350123316c70..a3b1bfbdebec6af6cae82a4dc669fc47473c592b 100644
--- a/Applications/DataExplorer/DataExplorer.cmake
+++ b/Applications/DataExplorer/DataExplorer.cmake
@@ -80,6 +80,7 @@ TARGET_LINK_LIBRARIES( DataExplorer
BaseLib
GeoLib
FileIO
+ InSituLib
MeshLib
#MSHGEOTOOLS
QtBase
diff --git a/Applications/DataExplorer/DataView/MshView.cpp b/Applications/DataExplorer/DataView/MshView.cpp
index 232f5a99b165910094ddf9e0b300bf76be6ed877..4597811071da2bfae9478f901c840b8cd1d11314 100644
--- a/Applications/DataExplorer/DataView/MshView.cpp
+++ b/Applications/DataExplorer/DataView/MshView.cpp
@@ -37,7 +37,7 @@
#include "Legacy/MeshIO.h"
//#include "RapidXmlIO/RapidVtuInterface.h"
-#include "XmlIO/Boost/BoostVtuInterface.h"
+#include "FileIO/VtkIO/VtuInterface.h"
#include "Writer.h" // necessary to avoid Linker Error in Windows
#include "SHPInterface.h"
#include "TetGenInterface.h"
@@ -269,7 +269,7 @@ int MshView::writeToFile() const
QFileInfo fi(fileName);
if (fi.suffix().toLower() == "vtu")
{
- FileIO::BoostVtuInterface vtkIO;
+ FileIO::VtuInterface vtkIO;
vtkIO.setMesh(mesh);
vtkIO.writeToFile(fileName.toStdString().c_str());
}
diff --git a/Applications/Utils/FileConverter/CMakeLists.txt b/Applications/Utils/FileConverter/CMakeLists.txt
index 3f9894899d2452c5352d41c5fcd12e37b2fe47ad..9dd4c33035ec247b28ea4ec656e15ff0eb4e9d33 100644
--- a/Applications/Utils/FileConverter/CMakeLists.txt
+++ b/Applications/Utils/FileConverter/CMakeLists.txt
@@ -48,6 +48,8 @@ IF (QT4_FOUND)
GeoLib
MeshLib
FileIO
+ InSituLib
+ ${CATALYST_LIBRARIES}
${QT_LIBRARIES}
)
ENDIF () # QT4_FOUND
@@ -58,7 +60,8 @@ IF (Boost_FOUND)
FileIO
MeshLib
logog
- ${Boost_LIBRARIES}
+ InSituLib
+ ${CATALYST_LIBRARIES}
)
SET_TARGET_PROPERTIES(generateMatPropsFromMatID
PROPERTIES FOLDER Utilities)
@@ -69,6 +72,8 @@ SET_TARGET_PROPERTIES(GMSH2OGS PROPERTIES FOLDER Utilities)
TARGET_LINK_LIBRARIES (GMSH2OGS
MeshLib
FileIO
+ InSituLib
+ ${CATALYST_LIBRARIES}
)
IF(MSVC)
TARGET_LINK_LIBRARIES (GMSH2OGS winmm)
@@ -80,6 +85,8 @@ TARGET_LINK_LIBRARIES (OGS2VTK
MeshLib
FileIO
zlib
+ InSituLib
+ ${CATALYST_LIBRARIES}
)
ADD_EXECUTABLE (VTK2OGS VTK2OGS.cpp)
@@ -88,6 +95,8 @@ TARGET_LINK_LIBRARIES (VTK2OGS
MeshLib
FileIO
zlib
+ InSituLib
+ ${CATALYST_LIBRARIES}
)
ADD_EXECUTABLE (VTK2TIN VTK2TIN.cpp)
diff --git a/Applications/Utils/FileConverter/FEFLOW2OGS.cpp b/Applications/Utils/FileConverter/FEFLOW2OGS.cpp
index 9e795298e48a1371b1c800992eef0633af85e516..67f47efc52bb412098e83be81e98870037ea1701 100644
--- a/Applications/Utils/FileConverter/FEFLOW2OGS.cpp
+++ b/Applications/Utils/FileConverter/FEFLOW2OGS.cpp
@@ -27,7 +27,7 @@
// FileIO
#include "Legacy/MeshIO.h"
#include "FEFLOWInterface.h"
-#include "XmlIO/Boost/BoostVtuInterface.h"
+#include "FileIO/VtkIO/VtuInterface.h"
// MeshLib
#include "Mesh.h"
@@ -97,7 +97,7 @@ int main (int argc, char* argv[])
ogs_mesh_fname += ".vtu";
}
INFO("Writing %s.", ogs_mesh_fname.c_str());
- FileIO::BoostVtuInterface mesh_io;
+ FileIO::VtuInterface mesh_io;
mesh_io.setMesh(mesh);
mesh_io.writeToFile(ogs_mesh_fname);
}
diff --git a/Applications/Utils/FileConverter/GMSH2OGS.cpp b/Applications/Utils/FileConverter/GMSH2OGS.cpp
index 5c8d280aa45c8228b7a2016a2fce9cd31cb1ced9..7db6b3c853a8b3856aa846aa6e716931a9d964f3 100644
--- a/Applications/Utils/FileConverter/GMSH2OGS.cpp
+++ b/Applications/Utils/FileConverter/GMSH2OGS.cpp
@@ -32,7 +32,7 @@
// FileIO
#include "Legacy/MeshIO.h"
#include "GMSHInterface.h"
-#include "XmlIO/Boost/BoostVtuInterface.h"
+#include "FileIO/VtkIO/VtuInterface.h"
// MeshLib
#include "Mesh.h"
@@ -101,7 +101,7 @@ int main (int argc, char* argv[])
ogs_mesh_fname += ".vtu";
}
INFO("Writing %s.", ogs_mesh_fname.c_str());
- FileIO::BoostVtuInterface mesh_io;
+ FileIO::VtuInterface mesh_io;
mesh_io.setMesh(mesh);
mesh_io.writeToFile(ogs_mesh_fname);
}
diff --git a/Applications/Utils/FileConverter/OGS2VTK.cpp b/Applications/Utils/FileConverter/OGS2VTK.cpp
index c3a3fd0de521561a0e0390bf3bad81d6fa2c7a57..b994ea62b6fd6694fcf753d613d7aba1ca5d6566 100644
--- a/Applications/Utils/FileConverter/OGS2VTK.cpp
+++ b/Applications/Utils/FileConverter/OGS2VTK.cpp
@@ -24,7 +24,7 @@
#include "LogogSimpleFormatter.h"
// FileIO
-#include "XmlIO/Boost/BoostVtuInterface.h"
+#include "FileIO/VtkIO/VtuInterface.h"
#include "readMeshFromFile.h"
// MeshLib
@@ -51,7 +51,7 @@ int main (int argc, char* argv[])
MeshLib::Mesh* mesh (FileIO::readMeshFromFile(mesh_in.getValue()));
INFO("Mesh read: %d nodes, %d elements.", mesh->getNNodes(), mesh->getNElements());
- FileIO::BoostVtuInterface vtu;
+ FileIO::VtuInterface vtu;
vtu.setMesh(mesh);
vtu.writeToFile(mesh_out.getValue());
diff --git a/Applications/Utils/FileConverter/VTK2OGS.cpp b/Applications/Utils/FileConverter/VTK2OGS.cpp
index a53e96f6fa7d816f78b65a0199994a92a2c556e5..d1b414478443f0dc3fe5df7a291f3c6e48a20943 100644
--- a/Applications/Utils/FileConverter/VTK2OGS.cpp
+++ b/Applications/Utils/FileConverter/VTK2OGS.cpp
@@ -24,7 +24,7 @@
#include "LogogSimpleFormatter.h"
// FileIO
-#include "XmlIO/Boost/BoostVtuInterface.h"
+#include "FileIO/VtkIO/VtuInterface.h"
#include "Legacy/MeshIO.h"
// MeshLib
@@ -48,7 +48,7 @@ int main (int argc, char* argv[])
cmd.add(mesh_out);
cmd.parse(argc, argv);
- MeshLib::Mesh* mesh (FileIO::BoostVtuInterface::readVTUFile(mesh_in.getValue()));
+ MeshLib::Mesh* mesh (FileIO::VtuInterface::readVTUFile(mesh_in.getValue()));
INFO("Mesh read: %d nodes, %d elements.", mesh->getNNodes(), mesh->getNElements());
FileIO::Legacy::MeshIO meshIO;
diff --git a/Applications/Utils/FileConverter/generateMatPropsFromMatID.cpp b/Applications/Utils/FileConverter/generateMatPropsFromMatID.cpp
index c5ec2c4f590e414d5c469cf75722fe8ed46e22ad..5b1f6a9f8cf0c31e1a968af87ab6444d2fa02568 100644
--- a/Applications/Utils/FileConverter/generateMatPropsFromMatID.cpp
+++ b/Applications/Utils/FileConverter/generateMatPropsFromMatID.cpp
@@ -22,7 +22,7 @@
// FileIO
#include "readMeshFromFile.h"
-#include "XmlIO/Boost/BoostVtuInterface.h"
+#include "FileIO/VtkIO/VtuInterface.h"
// MeshLib
#include "Mesh.h"
@@ -78,7 +78,7 @@ int main (int argc, char* argv[])
std::string new_mshname(name + "_new.vtu");
INFO("Writing mesh to file \"%s\".", new_mshname.c_str());
- FileIO::BoostVtuInterface mesh_io;
+ FileIO::VtuInterface mesh_io;
mesh_io.setMesh(mesh);
mesh_io.writeToFile (new_mshname);
diff --git a/Applications/Utils/MeshEdit/CMakeLists.txt b/Applications/Utils/MeshEdit/CMakeLists.txt
index dec1139cc270d30ef2f90cbd541eb0a0de069d00..671e3f55f3329d43a1fc7bdce4013d28463a8b30 100644
--- a/Applications/Utils/MeshEdit/CMakeLists.txt
+++ b/Applications/Utils/MeshEdit/CMakeLists.txt
@@ -18,6 +18,8 @@ IF(QT4_FOUND)
FileIO
MathLib
MeshLib
+ InSituLib
+ ${CATALYST_LIBRARIES}
${QT_LIBRARIES}
)
@@ -32,6 +34,8 @@ TARGET_LINK_LIBRARIES( removeMeshElements
FileIO
MathLib
MeshLib
+ InSituLib
+ ${CATALYST_LIBRARIES}
)
SET_TARGET_PROPERTIES(removeMeshElements PROPERTIES FOLDER Utilities)
@@ -39,6 +43,8 @@ ADD_EXECUTABLE( DataExplorer5NodeReordering DataExplorer5NodeReordering.cpp )
TARGET_LINK_LIBRARIES( DataExplorer5NodeReordering
FileIO
MeshLib
+ InSituLib
+ ${CATALYST_LIBRARIES}
)
SET_TARGET_PROPERTIES(DataExplorer5NodeReordering PROPERTIES FOLDER Utilities)
@@ -46,6 +52,8 @@ ADD_EXECUTABLE( MoveMesh MoveMesh.cpp )
TARGET_LINK_LIBRARIES( MoveMesh
FileIO
MeshLib
+ InSituLib
+ ${CATALYST_LIBRARIES}
)
SET_TARGET_PROPERTIES(MoveMesh PROPERTIES FOLDER Utilities)
@@ -56,6 +64,8 @@ TARGET_LINK_LIBRARIES( appendLinesAlongPolyline
MathLib
MeshLib
MeshGeoToolsLib
+ InSituLib
+ ${CATALYST_LIBRARIES}
)
SET_TARGET_PROPERTIES(appendLinesAlongPolyline
@@ -67,6 +77,8 @@ TARGET_LINK_LIBRARIES( editMaterialID
FileIO
MathLib
MeshLib
+ InSituLib
+ ${CATALYST_LIBRARIES}
)
SET_TARGET_PROPERTIES(editMaterialID
diff --git a/Applications/Utils/MeshEdit/DataExplorer5NodeReordering.cpp b/Applications/Utils/MeshEdit/DataExplorer5NodeReordering.cpp
index 0d135670ac279ecb6070393cb8100c01285e3eba..4a4bcc0a37ac2d65f2d56ef631b16f19f4098bf3 100644
--- a/Applications/Utils/MeshEdit/DataExplorer5NodeReordering.cpp
+++ b/Applications/Utils/MeshEdit/DataExplorer5NodeReordering.cpp
@@ -21,7 +21,7 @@
// FileIO
#include "readMeshFromFile.h"
-#include "XmlIO/Boost/BoostVtuInterface.h"
+#include "FileIO/VtkIO/VtuInterface.h"
// MeshLib
#include "Mesh.h"
@@ -30,7 +30,7 @@
void reorderNodes(std::vector<MeshLib::Element*> &elements)
{
std::size_t nElements (elements.size());
- for (std::size_t i=0; i<nElements; ++i)
+ for (std::size_t i=0; i<nElements; ++i)
{
const unsigned nElemNodes (elements[i]->getNBaseNodes());
std::vector<MeshLib::Node*> nodes(elements[i]->getNodes(), elements[i]->getNodes() + nElemNodes);
@@ -93,12 +93,12 @@ int main (int argc, char* argv[])
INFO("Reordering nodes... ");
reorderNodes(const_cast<std::vector<MeshLib::Element*>&>(mesh->getElements()));
-
- FileIO::BoostVtuInterface writer;
+
+ FileIO::VtuInterface writer;
writer.setMesh(mesh);
writer.writeToFile(output_mesh_arg.getValue().c_str());
- INFO("VTU file written.");
+ INFO("VTU file written.");
delete formatter;
delete logogCout;
diff --git a/Applications/Utils/MeshEdit/MoveMesh.cpp b/Applications/Utils/MeshEdit/MoveMesh.cpp
index cda6fa193eb75f225327f64d7e322f0f8d17fa10..011c84888cd6bdd4babc5f400b4fb17162babeb3 100644
--- a/Applications/Utils/MeshEdit/MoveMesh.cpp
+++ b/Applications/Utils/MeshEdit/MoveMesh.cpp
@@ -23,7 +23,7 @@
// FileIO
#include "readMeshFromFile.h"
-#include "XmlIO/Boost/BoostVtuInterface.h"
+#include "FileIO/VtkIO/VtuInterface.h"
// GeoLib
#include "AABB.h"
@@ -93,7 +93,7 @@ int main(int argc, char *argv[])
out_fname += "_displaced.vtu";
}
- FileIO::BoostVtuInterface mesh_io;
+ FileIO::VtuInterface mesh_io;
mesh_io.setMesh(mesh);
mesh_io.writeToFile(out_fname);
diff --git a/Applications/Utils/OGSFileConverter/OGSFileConverter.cpp b/Applications/Utils/OGSFileConverter/OGSFileConverter.cpp
index 5cc53bd35fa2b84fee368621befe2ec1e2b3dbcf..f33e8c1c94f160e6f6ac297808ae251aed1f7c66 100644
--- a/Applications/Utils/OGSFileConverter/OGSFileConverter.cpp
+++ b/Applications/Utils/OGSFileConverter/OGSFileConverter.cpp
@@ -32,7 +32,7 @@
// mesh
#include "Legacy/MeshIO.h"
-#include "XmlIO/Boost/BoostVtuInterface.h"
+#include "FileIO/VtkIO/VtuInterface.h"
OGSFileConverter::OGSFileConverter(QWidget* parent)
: QDialog(parent)
@@ -124,7 +124,7 @@ void OGSFileConverter::convertVTU2MSH(const QStringList &input, const QString &o
if (fileExists(output_str))
continue;
- FileIO::BoostVtuInterface vtu;
+ FileIO::VtuInterface vtu;
MeshLib::Mesh const*const mesh (vtu.readVTUFile(it->toStdString().c_str()));
if (mesh == nullptr)
{
@@ -159,11 +159,11 @@ void OGSFileConverter::convertMSH2VTU(const QStringList &input, const QString &o
OGSError::box("Error reading mesh " + fi.fileName());
continue;
}
- FileIO::BoostVtuInterface vtu;
+ FileIO::VtuInterface vtu;
vtu.setMesh(mesh);
vtu.writeToFile(output_str);
delete mesh;
- }
+ }
OGSError::box("File conversion finished");
}
diff --git a/FileIO/VtkIO/VtuInterface.cpp b/FileIO/VtkIO/VtuInterface.cpp
index 964e19867e4cb8d2cd989098980f74568fe782fa..8f9f8c2047b3a64b25a2987ae8be5105de96cb24 100644
--- a/FileIO/VtkIO/VtuInterface.cpp
+++ b/FileIO/VtkIO/VtuInterface.cpp
@@ -2,7 +2,7 @@
* \file
* \author Lars Bilke
* \date 2014-09-25
- * \brief Implementation of the BoostVtuInterface class.
+ * \brief Implementation of the VtuInterface class.
*
* \copyright
* Copyright (c) 2012-2014, OpenGeoSys Community (http://www.opengeosys.org)
diff --git a/FileIO/VtkIO/VtuInterface.h b/FileIO/VtkIO/VtuInterface.h
index c93d4fea454379fcc369daf68cacc97c063d0fff..4be1b61e762bd9d24e327d682766a7ceadb9deab 100644
--- a/FileIO/VtkIO/VtuInterface.h
+++ b/FileIO/VtkIO/VtuInterface.h
@@ -46,7 +46,7 @@ public:
/// Sets the mesh to write.
void setMesh(const MeshLib::Mesh* mesh);
- int writeToFile(std::string const &filen_name);
+ int writeToFile(std::string const &file_name);
private:
diff --git a/FileIO/XmlIO/Boost/BoostVtuInterface.cpp b/FileIO/XmlIO/Boost/BoostVtuInterface.cpp
deleted file mode 100644
index ba2c27de1321a80727b6ac775ee351fd5ef6abca..0000000000000000000000000000000000000000
--- a/FileIO/XmlIO/Boost/BoostVtuInterface.cpp
+++ /dev/null
@@ -1,604 +0,0 @@
-/**
- * \file
- * \author Karsten Rink
- * \date 2012-12-05
- * \brief Implementation of the BoostVtuInterface class.
- *
- * \copyright
- * Copyright (c) 2012-2014, OpenGeoSys Community (http://www.opengeosys.org)
- * Distributed under a Modified BSD License.
- * See accompanying file LICENSE.txt or
- * http://www.opengeosys.org/project/license
- *
- * \file BoostVtuInterface.cpp
- * @date 2012-12-05
- * @author Karsten Rink
- * @brief Read VTU files employing boost.
- */
-
-#include "BoostVtuInterface.h"
-#include "zLibDataCompressor.h"
-#include <fstream>
-
-#include <boost/version.hpp>
-#include <boost/foreach.hpp>
-#include <boost/property_tree/xml_parser.hpp>
-
-// ThirdParty/logog
-#include "logog/include/logog.hpp"
-
-#include "FileTools.h"
-
-// MSH
-#include "Elements/Line.h"
-#include "Elements/Hex.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 "MeshLib/Node.h"
-
-namespace FileIO
-{
-using namespace boost;
-
-BoostVtuInterface::BoostVtuInterface() :
- _mesh(nullptr), _use_compressor(false), _doc()
-{
-}
-
-BoostVtuInterface::~BoostVtuInterface()
-{}
-
-MeshLib::Mesh* BoostVtuInterface::readVTUFile(const std::string &file_name)
-{
- std::ifstream in(file_name.c_str());
- if (in.fail())
- {
- ERR("BoostVtuInterface::readVTUFile(): Can't open xml-file %s.", file_name.c_str());
- return nullptr;
- }
-
- // build DOM tree
- using boost::property_tree::ptree;
- ptree doc;
- read_xml(in, doc);
-
- if (isVTKUnstructuredGrid(doc))
- {
- ptree const& root_node = doc.get_child("VTKFile");
- optional<std::string> const& compressor (getXmlAttribute("compressor", root_node));
- bool is_compressed = static_cast<bool>(compressor);
- if (is_compressed)
- {
- if (*compressor != "vtkZLibDataCompressor")
- {
- ERR("BoostVtuInterface::readVTUFile(): Unknown compression method.");
- return nullptr;
- }
-
- // TODO: remove this once compressed data can be handled!!
- 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");
- 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));
-
- if ((nNodes == 0) || (nElems == 0))
- {
- ERR("BoostVtuInterface::readVTUFile() - Number of nodes is %d, number of elements is %d.",
- nNodes, nElems);
- return nullptr;
- }
-
- std::vector<MeshLib::Node*> nodes(nNodes);
- std::vector<MeshLib::Element*> elements(nElems);
- std::vector<unsigned> mat_ids(nElems, 0);
- std::vector<unsigned> cell_types(nElems);
-
- 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);
- 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)
- {
- if (*format == "ascii")
- for(unsigned i = 0; i < nElems; i++)
- iss >> mat_ids[i];
- else if (*format == "appended")
- {
- //uncompress
- }
- }
- }
- else
- 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);
-
- if (format)
- {
- if (*format == "ascii")
- {
- std::stringstream iss (data_array_node.data());
- double x,y,z;
- for(unsigned i = 0; i < nNodes; i++)
- {
- iss >> x >> y >> z;
- nodes[i] = new MeshLib::Node(x, y, z, i);
- }
- }
- else if (*format == "appended")
- {
- //uncompress
- }
- }
- }
-
- if (grid_piece.first == "Cells")
- {
- ptree const& cells = grid_piece.second;
-
- // cell types
- OptionalPtree const& types = findDataArray("types", cells);
- if (!types)
- ERR("BoostVtuInterface::readVTUFile(): Cannot find \"types\" data array.");
-
- std::stringstream iss (types->data());
- optional<std::string> const& format = getXmlAttribute("format", *types);
- if (*format == "ascii")
- {
- for(unsigned i = 0; i < nElems; i++)
- iss >> cell_types[i];
- }
- else if (*format == "appended")
- {
- //uncompress
- }
-
- // connectivity / element nodes
- OptionalPtree const& connectivity = findDataArray("connectivity", cells);
- if (!connectivity)
- 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);
- 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]);
- }
- }
- }
-
- INFO("Reading VTU mesh finished.");
- INFO("Name: %s", BaseLib::extractBaseNameWithoutExtension(file_name).c_str());
- INFO("Nr. Nodes: %d", nodes.size());
- INFO("Nr. Elements: %d", elements.size());
- return new MeshLib::Mesh(BaseLib::extractBaseNameWithoutExtension(file_name), nodes,
- elements);
-
- } // piece
- } // unstructured grid
-
- return nullptr;
-}
-
-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];
- MeshLib::Node** edge_nodes = new MeshLib::Node*[2];
- edge_nodes[0] = nodes[node_ids[0]];
- edge_nodes[1] = nodes[node_ids[1]];
- return new MeshLib::Line(edge_nodes, material);
- break;
- }
- case 5: { //triangle
- 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]];
- tri_nodes[2] = nodes[node_ids[2]];
- return new MeshLib::Tri(tri_nodes, material);
- break;
- }
- case 9: { //quad
- 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++)
- 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];
- MeshLib::Node** quad_nodes = new MeshLib::Node*[4];
- quad_nodes[0] = nodes[node_ids[0]];
- quad_nodes[1] = nodes[node_ids[1]];
- quad_nodes[2] = nodes[node_ids[3]];
- quad_nodes[3] = nodes[node_ids[2]];
- return new MeshLib::Quad(quad_nodes, material);
- break;
- }
- case 10: {
- 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++)
- 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];
- MeshLib::Node** hex_nodes = new MeshLib::Node*[8];
- 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];
- MeshLib::Node** voxel_nodes = new MeshLib::Node*[8];
- voxel_nodes[0] = nodes[node_ids[0]];
- voxel_nodes[1] = nodes[node_ids[1]];
- voxel_nodes[2] = nodes[node_ids[3]];
- voxel_nodes[3] = nodes[node_ids[2]];
- voxel_nodes[4] = nodes[node_ids[4]];
- voxel_nodes[5] = nodes[node_ids[5]];
- voxel_nodes[6] = nodes[node_ids[7]];
- voxel_nodes[7] = nodes[node_ids[6]];
- return new MeshLib::Hex(voxel_nodes, material);
- break;
- }
- case 14: { //pyramid
- 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++)
- 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];
- MeshLib::Node** prism_nodes = new MeshLib::Node*[6];
- for (unsigned k(0); k < 6; k++)
- prism_nodes[k] = nodes[node_ids[k]];
- return new MeshLib::Prism(prism_nodes, material);
- break;
- }
- default:
- 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"))
- {
- 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")
- {
- 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")
- {
- ERR("BoostVtuInterface::isVTKFile(): Only little endian files are supported.");
- return false;
- }
- return true;
-}
-
-bool BoostVtuInterface::isVTKUnstructuredGrid(const property_tree::ptree &vtk_root)
-{
- if (isVTKFile(vtk_root))
- {
- const OptionalPtree &u_grid_node = vtk_root.get_child_optional(
- "VTKFile.UnstructuredGrid");
- if (u_grid_node)
- return true;
- ERR("Error in BoostVtuInterface::isVTKUnstructuredGrid(): Not an unstructured grid.");
- }
- return false;
-}
-
-unsigned char* BoostVtuInterface::uncompressData(property_tree::ptree const& compressed_data_node)
-{
- const unsigned char* compressed_data = reinterpret_cast<const unsigned char*>(compressed_data_node.data().c_str());
- unsigned long compressed_size = strlen(compressed_data_node.data().c_str());
- unsigned char* uncompressed_data = NULL;
- unsigned long uncompressed_size = 0;
- // unsigned long result =
- zLibDataCompressor::UncompressBuffer(compressed_data, compressed_size, uncompressed_data, uncompressed_size);
- return uncompressed_data;
-}
-
-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>")
- continue;
- if (it->second.get_child_optional(key))
- return it->second.get_child(key).data();
- }
-
- return optional<std::string>();
-}
-
-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;
- }
-
- return OptionalPtree();
-}
-
-void BoostVtuInterface::setMesh(const MeshLib::Mesh* mesh)
-{
- if (!mesh)
- {
- ERR("BoostVtuInterface::write(): No mesh specified.");
- return;
- }
- this->_mesh = const_cast<MeshLib::Mesh*>(mesh);
- buildPropertyTree();
-};
-
-void BoostVtuInterface::addScalarPointProperty(std::string const& name,
- std::vector<double> const& prop_vals)
-{
- if (_doc.empty()) {
- WARN("BoostVtuInterface::addPointProperty(): propertry tree empty (no mesh set)");
- return;
- }
-
- if (_mesh->getNNodes() != prop_vals.size()) {
- WARN("BoostVtuInterface::addPointProperty(): number of values for propertry %s (%d) does not match the number of nodes (%d)", name.c_str(), prop_vals.size(), _mesh->getNNodes());
- return;
- }
-
-#if BOOST_VERSION <= 105500
- const std::string data_array_close("\t\t\t\t");
- const std::string data_array_indent("\t\t\t\t ");
-#endif
-
- // go to the node where data should be inserted
- using boost::property_tree::ptree;
- ptree &root_node = _doc.get_child("VTKFile");
- ptree &piece_node = root_node.get_child("UnstructuredGrid.Piece");
- ptree &pointdata_node = piece_node.get_child("PointData");
-
- // prepare the data
- std::stringstream oss(std::stringstream::out);
- oss.precision(_out.precision());
-#if BOOST_VERSION <= 105500
- oss << "\n" << data_array_indent;
- std::copy(prop_vals.cbegin(), prop_vals.cend(), std::ostream_iterator<double>(oss, " "));
- oss << "\n" << data_array_close;
-#else
- std::copy(prop_vals.cbegin(), prop_vals.cend(), std::ostream_iterator<double>(oss, " "));
-#endif
- this->addDataArray(pointdata_node, name, "Float64", oss.str());
- oss.str(std::string());
-}
-
-void BoostVtuInterface::buildPropertyTree()
-{
- _doc.clear();
- 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());
-
-#if BOOST_VERSION <= 105500
- const std::string data_array_close("\t\t\t\t");
- const std::string data_array_indent("\t\t\t\t ");
-#endif
-
- using boost::property_tree::ptree;
-
- ptree &root_node = _doc.put("VTKFile", "");
- root_node.put("<xmlattr>.type", "UnstructuredGrid");
- root_node.put("<xmlattr>.version", "0.1");
- root_node.put("<xmlattr>.byte_order", "LittleEndian");
-
- if (_use_compressor)
- root_node.put("<xmlattr>.compressor", "vtkZLibDataCompressor");
-
- ptree &piece_node = root_node.put("UnstructuredGrid.Piece", "");
- const std::string str_nNodes (std::to_string(nNodes));
- const std::string str_nElems (std::to_string(nElems));
- piece_node.put("<xmlattr>.NumberOfPoints", str_nNodes.c_str());
- piece_node.put("<xmlattr>.NumberOfCells", str_nElems.c_str());
-
- // scalar arrays for point- and cell-data
- piece_node.add("PointData", "");
- // add node_area array here if necessary!
- ptree &celldata_node = piece_node.add("CellData", "");
- celldata_node.put("<xmlattr>.Scalars", "MaterialIDs");
-
- std::stringstream oss(std::stringstream::out);
- oss.precision(_out.precision());
-#if BOOST_VERSION <= 105500
- oss << std::endl << data_array_indent;
- for (unsigned i = 0; i < nElems; i++)
- oss << elements[i]->getValue() << " ";
- oss << std::endl << data_array_close;
-#else
- for (unsigned i = 0; i < nElems; i++)
- oss << elements[i]->getValue() << " ";
-#endif
- this->addDataArray(celldata_node, "MaterialIDs", "Int32", oss.str());
- oss.str(std::string());
- oss.clear();
-
- // point coordinates
- ptree &points_node = piece_node.add("Points", "");
-#if BOOST_VERSION <= 105500
- 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;
- oss << data_array_close;
-#else
- for (unsigned i = 0; i < nNodes; i++)
- oss << (*nodes[i])[0] << " " << (*nodes[i])[1] << " " << (*nodes[i])[2] << " ";
-#endif
- this->addDataArray(points_node, "Points", "Float64", oss.str(), 3);
- oss.str(std::string());
- oss.clear();
-
- // cells with node ids
- ptree &cells_node = piece_node.add("Cells", "");
- std::stringstream offstream(std::stringstream::out);
- std::stringstream typestream(std::stringstream::out);
-#if BOOST_VERSION <= 105500
- oss << std::endl;
- offstream << std::endl << data_array_indent;
- typestream << std::endl << data_array_indent;
-#endif
- unsigned offset_count(0);
- for (unsigned i = 0; i < nElems; i++)
- {
- MeshLib::Element* element (elements[i]);
- const unsigned nElemNodes (element->getNBaseNodes());
-#if BOOST_VERSION <= 105500
- oss << data_array_indent;
-#endif
- for (unsigned j = 0; j < nElemNodes; j++)
- oss << element->getNode(j)->getID() << " ";
-#if BOOST_VERSION <= 105500
- oss << std::endl;
-#endif
- offset_count += nElemNodes;
- offstream << offset_count << " ";
- typestream << this->getVTKElementID(element->getGeomType()) << " ";
- }
-#if BOOST_VERSION <= 105500
- oss << data_array_close;
- offstream << std::endl << data_array_close;
- typestream << std::endl << data_array_close;
-#endif
-
- // connectivity attributes
- this->addDataArray(cells_node, "connectivity", "Int32", oss.str());
- this->addDataArray(cells_node, "offsets", "Int32", offstream.str());
- this->addDataArray(cells_node, "types", "UInt8", typestream.str());
-}
-
-bool BoostVtuInterface::write()
-{
- if (_doc.empty()) {
- ERR("BoostVtuInterface::write(): No mesh specified.");
- return false;
- }
-#if BOOST_VERSION <= 105500
- property_tree::xml_writer_settings<char> settings('\t', 1);
-#else
- property_tree::xml_writer_settings<std::string> settings('\t', 1);
-#endif // BOOST_VERSION
- write_xml(_out, _doc, settings);
- return true;
-}
-
-unsigned BoostVtuInterface::getVTKElementID(MeshElemType type) const
-{
- switch (type)
- {
- case MeshElemType::LINE:
- return 3;
- case MeshElemType::TRIANGLE:
- return 5;
- case MeshElemType::QUAD:
- return 9;
- case MeshElemType::TETRAHEDRON:
- return 10;
- case MeshElemType::HEXAHEDRON:
- return 12;
- case MeshElemType::PYRAMID:
- return 14;
- case MeshElemType::PRISM:
- return 13;
- default:
- return std::numeric_limits<unsigned>::max();
- }
-}
-
-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());
- dataarray_node.put("<xmlattr>.Name", name.c_str());
- if (nComponents > 1)
- dataarray_node.put("<xmlattr>.NumberOfComponents", std::to_string(nComponents).c_str());
- std::string comp_type = (_use_compressor) ? "appended" : "ascii";
- dataarray_node.put("<xmlattr>.format", comp_type.c_str());
- // ---- offset attribute for compressed data! ----
-}
-} // end namespace FileIO
diff --git a/FileIO/XmlIO/Boost/BoostVtuInterface.h b/FileIO/XmlIO/Boost/BoostVtuInterface.h
deleted file mode 100644
index 57d28ddad450de1b02971eda3add233656dd8c23..0000000000000000000000000000000000000000
--- a/FileIO/XmlIO/Boost/BoostVtuInterface.h
+++ /dev/null
@@ -1,99 +0,0 @@
-/**
- * \file
- * \author Karsten Rink
- * \date 2012-12-05
- * \brief Implementation of the BoostVtuInterface class.
- *
- * \copyright
- * Copyright (c) 2012-2014, OpenGeoSys Community (http://www.opengeosys.org)
- * Distributed under a Modified BSD License.
- * See accompanying file LICENSE.txt or
- * http://www.opengeosys.org/project/license
- *
- */
-
-#ifndef BOOSTVTUINTERFACE_H_
-#define BOOSTVTUINTERFACE_H_
-
-#include "FileIO/Writer.h"
-
-#include <string>
-#include <vector>
-
-#include <boost/property_tree/ptree.hpp>
-#include <boost/optional.hpp>
-
-#include "MeshLib/MeshEnums.h"
-
-typedef boost::optional<const boost::property_tree::ptree&> OptionalPtree;
-
-namespace MeshLib {
- class Mesh;
- class Node;
- class Element;
-}
-
-namespace FileIO
-{
-
-/**
- * \brief Reads and writes VtkXMLUnstructuredGrid-files (vtu) to and from OGS data structures.
- *
- * XML parsing is performed using boost::property_tree::ptree.
- */
-class BoostVtuInterface : public Writer
-{
-public:
- BoostVtuInterface();
- ~BoostVtuInterface();
-
- /// Read an unstructured grid from a VTU file
- static MeshLib::Mesh* readVTUFile(const std::string &file_name);
-
- /// Decide if the mesh data should be written compressed (default is false).
- void setCompressData(bool flag=true) { _use_compressor = flag; };
-
- /// Set mesh for writing.
- void setMesh(const MeshLib::Mesh* mesh);
-
- void addScalarPointProperty(std::string const& name, std::vector<double> const& prop_vals);
-
-private:
- /** Method builds a tree structure storing the mesh data. This method is called from
- * setMesh().
- */
- void buildPropertyTree();
-
- /// Adds a VTK-DataArray of the given name and datatype to the DOM tree and inserts the data-string at that node
- void addDataArray(boost::property_tree::ptree &parent_node, const std::string &name, const std::string &data_type, const std::string &data, unsigned nComponents = 1);
-
- bool write();
-
- /// Returns the ID used by VTK for a given cell type (e.g. "5" for a triangle, etc.)
- unsigned getVTKElementID(MeshElemType type) const;
-
- /// Check if the root node really specifies an XML file
- static bool isVTKFile(const boost::property_tree::ptree &vtk_root);
-
- /// Check if the file really specifies a VTK Unstructured Grid
- static bool isVTKUnstructuredGrid(const boost::property_tree::ptree &vtk_root);
-
- /// Construct an Element-object from the data given to the method and the data at the current stream position.
- static MeshLib::Element* readElement(std::stringstream &iss, const std::vector<MeshLib::Node*> &nodes, unsigned material, unsigned type);
-
- static unsigned char* uncompressData(boost::property_tree::ptree const& compressed_data_node);
-
- /// Get an XML attribute value corresponding to given string from a property tree.
- static const boost::optional<std::string> getXmlAttribute(std::string const& key, boost::property_tree::ptree const& tree);
-
- /// Find first child of a tree, which is a DataArray and has requested name.
- static const OptionalPtree findDataArray(std::string const& array_name, boost::property_tree::ptree const& tree);
-
- MeshLib::Mesh* _mesh;
- bool _use_compressor;
- boost::property_tree::ptree _doc;
-};
-
-}
-
-#endif /* BOOSTVTUINTERFACE_H_ */
diff --git a/FileIO/readMeshFromFile.cpp b/FileIO/readMeshFromFile.cpp
index d26add422201cdbe44b269a8be14146f72471555..b83bf396cad7e8513bb0776f8da8911259581ce2 100644
--- a/FileIO/readMeshFromFile.cpp
+++ b/FileIO/readMeshFromFile.cpp
@@ -27,7 +27,7 @@
// FileIO
#include "Legacy/MeshIO.h"
-#include "XmlIO/Boost/BoostVtuInterface.h"
+#include "FileIO/VtkIO/VtuInterface.h"
#include "readMeshFromFile.h"
namespace FileIO
@@ -41,7 +41,7 @@ MeshLib::Mesh* readMeshFromFile(const std::string &file_name)
}
if (BaseLib::hasFileExtension("vtu", file_name))
- return BoostVtuInterface::readVTUFile(file_name);
+ return VtuInterface::readVTUFile(file_name);
ERR("readMeshFromFile(): Unknown mesh file format in file %s.", file_name.c_str());
return nullptr;