void FiberBundleReader::GenerateOutputInformation()
{
m_OutputCache = OutputType::New();
std::string ext = itksys::SystemTools::GetFilenameLastExtension(m_FileName);
ext = itksys::SystemTools::LowerCase(ext);
if ( m_FileName == "")
{
}
else if (ext == ".fib")
{
try
{
TiXmlDocument doc( m_FileName );
doc.LoadFile();
TiXmlHandle hDoc(&doc);
TiXmlElement* pElem;
TiXmlHandle hRoot(0);
pElem = hDoc.FirstChildElement().Element();
// save this for later
hRoot = TiXmlHandle(pElem);
pElem = hRoot.FirstChildElement(FiberBundleReader::XML_GEOMETRY).Element();
// read geometry
mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New();
// read origin
mitk::Point3D origin;
double temp = 0;
pElem->Attribute(FiberBundleReader::XML_ORIGIN_X, &temp);
origin[0] = temp;
pElem->Attribute(FiberBundleReader::XML_ORIGIN_Y, &temp);
origin[1] = temp;
pElem->Attribute(FiberBundleReader::XML_ORIGIN_Z, &temp);
origin[2] = temp;
geometry->SetOrigin(origin);
// read spacing
float spacing[3];
pElem->Attribute(FiberBundleReader::XML_SPACING_X, &temp);
spacing[0] = temp;
pElem->Attribute(FiberBundleReader::XML_SPACING_Y, &temp);
spacing[1] = temp;
pElem->Attribute(FiberBundleReader::XML_SPACING_Z, &temp);
spacing[2] = temp;
geometry->SetSpacing(spacing);
// read transform
vtkMatrix4x4* m = vtkMatrix4x4::New();
pElem->Attribute(FiberBundleReader::XML_MATRIX_XX, &temp);
m->SetElement(0,0,temp);
pElem->Attribute(FiberBundleReader::XML_MATRIX_XY, &temp);
m->SetElement(1,0,temp);
pElem->Attribute(FiberBundleReader::XML_MATRIX_XZ, &temp);
m->SetElement(2,0,temp);
pElem->Attribute(FiberBundleReader::XML_MATRIX_YX, &temp);
m->SetElement(0,1,temp);
pElem->Attribute(FiberBundleReader::XML_MATRIX_YY, &temp);
m->SetElement(1,1,temp);
pElem->Attribute(FiberBundleReader::XML_MATRIX_YZ, &temp);
m->SetElement(2,1,temp);
pElem->Attribute(FiberBundleReader::XML_MATRIX_ZX, &temp);
m->SetElement(0,2,temp);
pElem->Attribute(FiberBundleReader::XML_MATRIX_ZY, &temp);
m->SetElement(1,2,temp);
pElem->Attribute(FiberBundleReader::XML_MATRIX_ZZ, &temp);
m->SetElement(2,2,temp);
m->SetElement(0,3,origin[0]);
m->SetElement(1,3,origin[1]);
m->SetElement(2,3,origin[2]);
m->SetElement(3,3,1);
geometry->SetIndexToWorldTransformByVtkMatrix(m);
// read bounds
float bounds[] = {0, 0, 0, 0, 0, 0};
pElem->Attribute(FiberBundleReader::XML_SIZE_X, &temp);
bounds[1] = temp;
pElem->Attribute(FiberBundleReader::XML_SIZE_Y, &temp);
bounds[3] = temp;
pElem->Attribute(FiberBundleReader::XML_SIZE_Z, &temp);
bounds[5] = temp;
geometry->SetFloatBounds(bounds);
// read bounds
float bounds2[] = {0, 0, 0};
bounds2[0] = bounds[1];
bounds2[1] = bounds[3];
bounds2[2] = bounds[5];
m_OutputCache->SetBounds(bounds2);
geometry->SetImageGeometry(true);
m_OutputCache->SetGeometry(geometry);
// generate tract container
ContainerType::Pointer tractContainer = ContainerType::New();
int fiberID = 0;
pElem = hRoot.FirstChildElement(FiberBundleReader::XML_FIBER_BUNDLE).FirstChild().Element();
for( pElem; pElem; pElem=pElem->NextSiblingElement())
{
TiXmlElement* pElem2 = pElem->FirstChildElement();
ContainerTractType::Pointer tract = ContainerTractType::New();
for( pElem2; pElem2; pElem2=pElem2->NextSiblingElement())
{
ContainerPointType point;
pElem2->Attribute(FiberBundleReader::XML_POS_X, &temp);
point[0] = temp;
pElem2->Attribute(FiberBundleReader::XML_POS_Y, &temp);
point[1] = temp;
pElem2->Attribute(FiberBundleReader::XML_POS_Z, &temp);
point[2] = temp;
tract->InsertElement(tract->Size(), point);
}
pElem->Attribute(FiberBundleReader::XML_ID, &fiberID);
tractContainer->CreateIndex(fiberID);
tractContainer->SetElement(fiberID, tract);
}
m_OutputCache->addTractContainer(tractContainer);
m_OutputCache->initFiberGroup();
MITK_INFO << "Fiber bundle read";
}
catch(...)
{
MITK_INFO << "Could not read file ";
}
}
else if (ext == ".vfib")
{
// generate tract container
ContainerType::Pointer tractContainer = ContainerType::New();
mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New();
///We create a Generic Reader to test de .vtk/
vtkDataReader *chooser=vtkDataReader::New();
chooser->SetFileName(m_FileName.c_str() );
if( chooser->IsFilePolyData())
{
vtkPolyDataReader *reader = vtkPolyDataReader::New();
reader->SetFileName( m_FileName.c_str() );
reader->Update();
if ( reader->GetOutput() != NULL )
{
vtkPolyData* output = reader->GetOutput();
output->ComputeBounds();
double bounds[3];
output->GetBounds(bounds);
double center[3];
output->GetCenter(center);
Point3D origin;
origin.SetElement(0, -center[0]);
origin.SetElement(1, -center[1]);
origin.SetElement(2, -center[2]);
MITK_INFO << origin;
mitk::Surface::Pointer surf = mitk::Surface::New();
surf->SetVtkPolyData(output);
mitk::Geometry3D* geom = surf->GetGeometry();
//geom->SetOrigin(origin);
geom->SetImageGeometry(true);
m_OutputCache->SetBounds(bounds);
m_OutputCache->SetGeometry(geom);
vtkCellArray* cells = output->GetLines();
cells->InitTraversal();
for (int i=0; i<output->GetNumberOfCells(); i++)
{
ContainerTractType::Pointer tract = ContainerTractType::New();
vtkCell* cell = output->GetCell(i);
int p = cell->GetNumberOfPoints();
vtkPoints* points = cell->GetPoints();
for (int j=0; j<p; j++)
{
double p[3];
points->GetPoint(j, p);
ContainerPointType point;
point[0] = p[0];
point[1] = p[1];
point[2] = p[2];
tract->InsertElement(tract->Size(), point);
}
tractContainer->InsertElement(i, tract);
}
}
reader->Delete();
}
chooser->Delete();
m_OutputCache->addTractContainer(tractContainer);
m_OutputCache->initFiberGroup();
MITK_INFO << "Fiber bundle read";
}
}
