void mitk::ConnectomicsNetworkWriter::Write()
{
MITK_INFO << "Writing connectomics network";
InputType::ConstPointer input = dynamic_cast<const InputType*>(this->GetInput());
if (input.IsNull() )
{
MITK_ERROR <<"Sorry, input to ConnectomicsNetworkWriter is NULL!";
return;
}
if ( this->GetOutputLocation().empty() )
{
MITK_ERROR << "Sorry, filename has not been set!" ;
return ;
}
std::string ext = itksys::SystemTools::GetFilenameLastExtension(this->GetOutputLocation());
ext = itksys::SystemTools::LowerCase(ext);
// default extension is .cnf
if(ext == "")
{
ext = ".cnf";
this->SetOutputLocation(this->GetOutputLocation() + ext);
}
if (ext == ".cnf")
{
// Get geometry of the network
mitk::BaseGeometry* geometry = input->GetGeometry();
// Create XML document
TiXmlDocument documentXML;
{ // begin document
TiXmlDeclaration* declXML = new TiXmlDeclaration( "1.0", "", "" ); // TODO what to write here? encoding? etc....
documentXML.LinkEndChild( declXML );
TiXmlElement* mainXML = new TiXmlElement(mitk::ConnectomicsNetworkDefinitions::XML_CONNECTOMICS_FILE);
mainXML->SetAttribute(mitk::ConnectomicsNetworkDefinitions::XML_FILE_VERSION, mitk::ConnectomicsNetworkDefinitions::VERSION_STRING);
documentXML.LinkEndChild(mainXML);
TiXmlElement* geometryXML = new TiXmlElement(mitk::ConnectomicsNetworkDefinitions::XML_GEOMETRY);
{ // begin geometry
geometryXML->SetDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_XX, geometry->GetMatrixColumn(0)[0]);
geometryXML->SetDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_XY, geometry->GetMatrixColumn(0)[1]);
geometryXML->SetDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_XZ, geometry->GetMatrixColumn(0)[2]);
geometryXML->SetDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_YX, geometry->GetMatrixColumn(1)[0]);
geometryXML->SetDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_YY, geometry->GetMatrixColumn(1)[1]);
geometryXML->SetDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_YZ, geometry->GetMatrixColumn(1)[2]);
geometryXML->SetDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_ZX, geometry->GetMatrixColumn(2)[0]);
geometryXML->SetDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_ZY, geometry->GetMatrixColumn(2)[1]);
geometryXML->SetDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_ZZ, geometry->GetMatrixColumn(2)[2]);
geometryXML->SetDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_ORIGIN_X, geometry->GetOrigin()[0]);
geometryXML->SetDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_ORIGIN_Y, geometry->GetOrigin()[1]);
geometryXML->SetDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_ORIGIN_Z, geometry->GetOrigin()[2]);
geometryXML->SetDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_SPACING_X, geometry->GetSpacing()[0]);
geometryXML->SetDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_SPACING_Y, geometry->GetSpacing()[1]);
geometryXML->SetDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_SPACING_Z, geometry->GetSpacing()[2]);
} // end geometry
mainXML->LinkEndChild(geometryXML);
TiXmlElement* verticesXML = new TiXmlElement(mitk::ConnectomicsNetworkDefinitions::XML_VERTICES);
{ // begin vertices section
VertexVectorType vertexVector = dynamic_cast<const InputType*>(this->GetInput())->GetVectorOfAllNodes();
for( unsigned int index = 0; index < vertexVector.size(); index++ )
{
// not localized as of yet TODO
TiXmlElement* vertexXML = new TiXmlElement(mitk::ConnectomicsNetworkDefinitions::XML_VERTEX );
vertexXML->SetAttribute( mitk::ConnectomicsNetworkDefinitions::XML_VERTEX_ID , vertexVector[ index ].id );
vertexXML->SetAttribute( mitk::ConnectomicsNetworkDefinitions::XML_VERTEX_LABEL , vertexVector[ index ].label );
vertexXML->SetDoubleAttribute( mitk::ConnectomicsNetworkDefinitions::XML_VERTEX_X , vertexVector[ index ].coordinates[0] );
vertexXML->SetDoubleAttribute( mitk::ConnectomicsNetworkDefinitions::XML_VERTEX_Y , vertexVector[ index ].coordinates[1] );
vertexXML->SetDoubleAttribute( mitk::ConnectomicsNetworkDefinitions::XML_VERTEX_Z , vertexVector[ index ].coordinates[2] );
verticesXML->LinkEndChild(vertexXML);
}
} // end vertices section
mainXML->LinkEndChild(verticesXML);
TiXmlElement* edgesXML = new TiXmlElement(mitk::ConnectomicsNetworkDefinitions::XML_EDGES);
{ // begin edges section
EdgeVectorType edgeVector = dynamic_cast<const InputType*>(this->GetInput())->GetVectorOfAllEdges();
for(unsigned int index = 0; index < edgeVector.size(); index++ )
{
TiXmlElement* edgeXML = new TiXmlElement(mitk::ConnectomicsNetworkDefinitions::XML_EDGE );
edgeXML->SetAttribute( mitk::ConnectomicsNetworkDefinitions::XML_EDGE_ID , index );
edgeXML->SetAttribute( mitk::ConnectomicsNetworkDefinitions::XML_EDGE_SOURCE_ID , edgeVector[ index ].second.sourceId );
edgeXML->SetAttribute( mitk::ConnectomicsNetworkDefinitions::XML_EDGE_TARGET_ID , edgeVector[ index ].second.targetId );
edgeXML->SetAttribute( mitk::ConnectomicsNetworkDefinitions::XML_EDGE_WEIGHT_ID , edgeVector[ index ].second.weight );
edgeXML->SetDoubleAttribute( mitk::ConnectomicsNetworkDefinitions::XML_EDGE_DOUBLE_WEIGHT_ID , edgeVector[ index ].second.edge_weight );
edgesXML->LinkEndChild(edgeXML);
}
} // end edges section
mainXML->LinkEndChild(edgesXML);
} // end document
documentXML.SaveFile( this->GetOutputLocation().c_str() );
MITK_INFO << "Connectomics network written";
}
}
