void mitk::ExampleDataStructureWriterService::Write()
{
MITK_INFO << "Writing ExampleDataStructure";
InputType::ConstPointer input = dynamic_cast<const InputType *>(this->GetInput());
if (input.IsNull())
{
MITK_ERROR << "Sorry, input to ExampleDataStructureWriterService is nullptr!";
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 .txt
if (ext == "")
{
ext = ".txt";
this->SetOutputLocation(this->GetOutputLocation() + ext);
}
try
{
std::ofstream file(this->GetOutputLocation());
if (file.is_open())
{
file << input->GetData();
}
else
{
mitkThrow() << "Could not open file " << this->GetOutputLocation() << " for writing.";
}
MITK_INFO << "Example Data Structure has been written";
}
catch (mitk::Exception e)
{
MITK_ERROR << e.GetDescription();
}
catch (...)
{
MITK_ERROR << "Unknown error occurred while trying to write file.";
}
}
void mitk::ConnectomicsNetworkCSVWriter::Write()
{
MITK_INFO << "Writing connectomics network";
InputType::ConstPointer input = dynamic_cast<const InputType*>(this->GetInput());
if (input.IsNull() )
{
MITK_ERROR <<"Sorry, input to ConnectomicsNetworkMatrixWriter is nullptr!";
return;
}
this->ValidateOutputLocation();
std::ostream* out;
std::ofstream outStream;
if( this->GetOutputStream() )
{
out = this->GetOutputStream();
}
else
{
outStream.open( this->GetOutputLocation().c_str() );
out = &outStream;
}
if ( !out->good() )
{
mitkThrow() << "Could not open stream.";
}
try
{
const std::string& locale = "C";
const std::string& currLocale = setlocale( LC_ALL, nullptr );
setlocale(LC_ALL, locale.c_str());
std::locale previousLocale(out->getloc());
std::locale I("C");
out->imbue(I);
// construct header
std::stringstream header;
mitk::StringProperty::Pointer addHeaderInfoProperty = dynamic_cast<mitk::StringProperty*>(input->GetProperty(connectomicsDataAdditionalHeaderInformation.c_str()).GetPointer());
if(addHeaderInfoProperty.IsNotNull())
{
std::string additionalHeaderInfo = addHeaderInfoProperty->GetValue();
// if the additional header info contains newlines we need to add #
// in front of the new lines
std::vector<std::string> strings;
boost::split(strings, additionalHeaderInfo, boost::is_any_of("\n"));
for( unsigned int index(0); index < strings.size(); ++index)
{
header << "#" << strings[index] << "\n";
}
}
// construct body
std::stringstream body;
std::vector< InputType::VertexDescriptorType > nodes = input->GetVectorOfAllVertexDescriptors();
for(unsigned int i(0); i < nodes.size(); ++i)
{
for(unsigned int j(0); j < i; ++j)
{
double weight(0);
if( input->EdgeExists(nodes[i], nodes[j]) )
{
weight = (input->GetEdge(nodes[i], nodes[j])).edge_weight;
}
body << (input->GetNode(nodes[i])).label << " "
<< (input->GetNode(nodes[j])).label << " "
<< weight << "\n";
}
}
(*out)<< header.str() << body.str();
setlocale(LC_ALL, currLocale.c_str());
MITK_INFO << "Connectomics network connection list written";
}
catch(...)
{
mitkThrow() << "Error while writing to stream.";
}
}
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";
}
}