NonmanifoldLevel::NonmanifoldLevel(subdivision::Mesh& subdivision)
{
VertexPositionMapType averagedCenters;
VertexPositionMapType averagedMidpoints;
VertexEdgeCountMapType valencies;
VertexAdjacencyMapType cornerAdjacentMaps;
VertexAdjacencyMapType midpointAdjacentMaps;
VertexVectorType corners;
VertexVertexMapType vertexMap;
for (int i = 0; i < subdivision.getNumberVertices(); i++) {
subdivision::Vertex& vertex = subdivision.getVertex(i);
subdivision::Vertex& created = createVertex(vertex);
corners.push_back(&created);
vertexMap[&vertex] = &created;
valencies[&created] = 0;
float* averagedCenter = new float[3];
averagedCenters[&created] = averagedCenter;
averagedCenter[0] = 0;
averagedCenter[1] = 0;
averagedCenter[2] = 0;
float* averagedEnd = new float[3];
averagedMidpoints[&created] = averagedEnd;
averagedEnd[0] = 0;
averagedEnd[1] = 0;
averagedEnd[2] = 0;
}
VertexVectorType midpoints;
for (int i = 0; i < subdivision.getNumberEdges(); i++) {
subdivision::Edge& edge = subdivision.getEdge(i);
subdivision::HalfEdge& firstHalfEdge = edge.getFirstHalf();
subdivision::HalfEdge& secondHalfEdge = edge.getSecondHalf();
subdivision::Vertex& fromVertex = firstHalfEdge.getFromVertex();
subdivision::Vertex& toVertex = firstHalfEdge.getToVertex();
subdivision::Vertex* midpoint = new subdivision::Vertex();
midpoints.push_back(midpoint);
_subdivision.add(*midpoint);
float* averagedCenter = new float[3];
averagedCenters[midpoint] = averagedCenter;
averagedCenter[0] = 0;
averagedCenter[1] = 0;
averagedCenter[2] = 0;
_midpointMappings[&firstHalfEdge] = midpoint;
_midpointMappings[&secondHalfEdge] = midpoint;
subdivision::Vertex* mappedFromVertex = vertexMap[&fromVertex];
subdivision::Vertex* mappedToVertex = vertexMap[&toVertex];
valencies[mappedFromVertex]++;
valencies[mappedToVertex]++;
_subdivision.createEdge(*mappedFromVertex, *midpoint);
_subdivision.createEdge(*midpoint, *mappedToVertex);
midpoint->_coordinates[0] = fromVertex._coordinates[0] + toVertex._coordinates[0];
midpoint->_coordinates[1] = fromVertex._coordinates[1] + toVertex._coordinates[1];
midpoint->_coordinates[2] = fromVertex._coordinates[2] + toVertex._coordinates[2];
midpoint->_coordinates[3] = 1;
averagedMidpoints[mappedFromVertex][0] += midpoint->_coordinates[0];
averagedMidpoints[mappedFromVertex][1] += midpoint->_coordinates[1];
averagedMidpoints[mappedFromVertex][2] += midpoint->_coordinates[2];
averagedMidpoints[mappedToVertex][0] += midpoint->_coordinates[0];
averagedMidpoints[mappedToVertex][1] += midpoint->_coordinates[1];
averagedMidpoints[mappedToVertex][2] += midpoint->_coordinates[2];
}
VertexVectorType centers;
for (int i = 0; i < subdivision.getNumberFaces(); i++) {
subdivision::Face& face = subdivision.getFace(i);
subdivision::Vertex* center = new subdivision::Vertex();
centers.push_back(center);
_centerMappings[&face] = center;
_subdivision.add(*center);
for (int j = 0; j < face.getNumberHalfEdges(); j++) {
subdivision::HalfEdge& halfEdge = face.getHalfEdge(j);
subdivision::Vertex* midpoint = _midpointMappings[&halfEdge];
subdivision::Edge* edge = _subdivision.createEdge(*midpoint, *center);
}
center->_coordinates[0] = 0;
center->_coordinates[1] = 0;
center->_coordinates[2] = 0;
center->_coordinates[3] = 1;
for (int j = 0; j < face.getNumberVertices(); j++) {
subdivision::Vertex& vertex = face.getVertex(j);
center->_coordinates[0] += vertex._coordinates[0];
center->_coordinates[1] += vertex._coordinates[1];
center->_coordinates[2] += vertex._coordinates[2];
}
center->_coordinates[0] /= face.getNumberVertices();
center->_coordinates[1] /= face.getNumberVertices();
center->_coordinates[2] /= face.getNumberVertices();
}
for (int i = 0; i < subdivision.getNumberFaces(); i++) {
subdivision::Face& face = subdivision.getFace(i);
subdivision::Vertex* center = _centerMappings[&face];
int numberEdges = face.getNumberHalfEdges();
subdivision::HalfEdge& lastHalfEdge = face.getHalfEdge(numberEdges - 1);
subdivision::Vertex* last = _midpointMappings[&lastHalfEdge];
for (int j = 0; j < face.getNumberHalfEdges(); j++) {
subdivision::HalfEdge& halfEdge = face.getHalfEdge(j);
subdivision::Vertex& oldCorner = halfEdge.getFromVertex();
subdivision::Vertex* corner = vertexMap[&oldCorner];
subdivision::Vertex* next = _midpointMappings[&halfEdge];
_subdivision.createFace(*corner, *next, *center, *last);
averagedCenters[next][0] += center->_coordinates[0];
averagedCenters[next][1] += center->_coordinates[1];
averagedCenters[next][2] += center->_coordinates[2];
averagedCenters[corner][0] += center->_coordinates[0];
averagedCenters[corner][1] += center->_coordinates[1];
averagedCenters[corner][2] += center->_coordinates[2];
last = next;
}
}
for (int i = 0; i < corners.size(); i++) {
subdivision::Vertex* corner = corners[i];
int valence = valencies[corner];
corner->_coordinates[0] *= (valence - 3) / 3;
corner->_coordinates[1] *= (valence - 3) / 3;
corner->_coordinates[2] *= (valence - 3) / 3;
corner->_coordinates[0] += averagedMidpoints[corner][0] / (valence * 3);
corner->_coordinates[1] += averagedMidpoints[corner][1] / (valence * 3);
corner->_coordinates[2] += averagedMidpoints[corner][2] / (valence * 3);
corner->_coordinates[0] += averagedCenters[corner][0] / (valence * 3);
corner->_coordinates[1] += averagedCenters[corner][1] / (valence * 3);
corner->_coordinates[2] += averagedCenters[corner][2] / (valence * 3);
}
for (int i = 0; i < midpoints.size(); i++) {
subdivision::Vertex* midpoint = midpoints[i];
midpoint->_coordinates[0] += averagedCenters[midpoint][0];
midpoint->_coordinates[1] += averagedCenters[midpoint][1];
midpoint->_coordinates[2] += averagedCenters[midpoint][2];
midpoint->_coordinates[0] /= 4;
midpoint->_coordinates[1] /= 4;
midpoint->_coordinates[2] /= 4;
}
}
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";
}
}