void mitk::Surface::CalculateBoundingBox()
{
TimeGeometry *timeGeometry = this->GetTimeGeometry();
if (timeGeometry->CountTimeSteps() != m_PolyDatas.size())
mitkThrow() << "Number of geometry time steps is inconsistent with number of poly data pointers.";
for (unsigned int i = 0; i < m_PolyDatas.size(); ++i)
{
vtkPolyData *polyData = m_PolyDatas[i].GetPointer();
double bounds[6] = {0};
if (polyData != nullptr && polyData->GetNumberOfPoints() > 0)
{
// polyData->Update(); //VTK6_TODO vtk pipeline
polyData->ComputeBounds();
polyData->GetBounds(bounds);
}
BaseGeometry::Pointer geometry = timeGeometry->GetGeometryForTimeStep(i);
if (geometry.IsNull())
mitkThrow() << "Time-sliced geometry is invalid (equals nullptr).";
geometry->SetFloatBounds(bounds);
}
timeGeometry->Update();
m_CalculateBoundingBox = false;
}
void mitk::ProportionalTimeGeometry::ReplaceTimeStepGeometries(const BaseGeometry* geometry)
{
for (TimeStepType currentStep = 0; currentStep < this->CountTimeSteps(); ++currentStep)
{
BaseGeometry::Pointer clonedGeometry = geometry->Clone();
this->SetTimeStepGeometry(clonedGeometry.GetPointer(), currentStep);
}
}
void mitk::SurfaceDeformationDataInteractor3D::ColorizeSurface(vtkPolyData* polyData, int timeStep, const Point3D &pickedPoint, int mode, double scalar)
{
if (polyData == NULL)
return;
vtkPoints* points = polyData->GetPoints();
vtkPointData* pointData = polyData->GetPointData();
if ( pointData == NULL )
return;
vtkDataArray* scalars = pointData->GetScalars();
if (scalars == NULL)
return;
if (mode == COLORIZATION_GAUSS)
{
// Get picked point and transform into local coordinates
Point3D localPickedPoint;
BaseGeometry::Pointer geometry = this->GetDataNode()->GetData()->GetGeometry(timeStep);
geometry->WorldToIndex( pickedPoint, localPickedPoint );
Vector3D v1 = localPickedPoint.GetVectorFromOrigin();
vtkDataArray* normal = polyData->GetPointData()->GetVectors("planeNormal");
if (normal != NULL)
{
m_ObjectNormal[0] = normal->GetComponent(0, 0);
m_ObjectNormal[1] = normal->GetComponent(0, 1);
m_ObjectNormal[2] = normal->GetComponent(0, 2);
}
double denom = m_GaussSigma * m_GaussSigma * 2;
for (vtkIdType i = 0; i < points->GetNumberOfPoints(); ++i)
{
// Get original point
double* point = points->GetPoint(i);
Vector3D v0;
v0[0] = point[0];
v0[1] = point[1];
v0[2] = point[2];
// Calculate distance of this point from line through picked point
double d = itk::CrossProduct(m_ObjectNormal, (v1 - v0)).GetNorm();
double t = exp(- d * d / denom);
scalars->SetComponent(i, 0, t);
}
}
else if (mode == COLORIZATION_CONSTANT)
{
for (vtkIdType i = 0; i < pointData->GetNumberOfTuples(); ++i)
{
scalars->SetComponent(i, 0, scalar);
}
}
polyData->Modified();
pointData->Update();
}
void ItkImageIO::Write()
{
const mitk::Image *image = dynamic_cast<const mitk::Image *>(this->GetInput());
if (image == NULL)
{
mitkThrow() << "Cannot write non-image data";
}
// Switch the current locale to "C"
LocaleSwitch localeSwitch("C");
// Clone the image geometry, because we might have to change it
// for writing purposes
BaseGeometry::Pointer geometry = image->GetGeometry()->Clone();
// Check if geometry information will be lost
if (image->GetDimension() == 2 && !geometry->Is2DConvertable())
{
MITK_WARN << "Saving a 2D image with 3D geometry information. Geometry information will be lost! You might "
"consider using Convert2Dto3DImageFilter before saving.";
// set matrix to identity
mitk::AffineTransform3D::Pointer affTrans = mitk::AffineTransform3D::New();
affTrans->SetIdentity();
mitk::Vector3D spacing = geometry->GetSpacing();
mitk::Point3D origin = geometry->GetOrigin();
geometry->SetIndexToWorldTransform(affTrans);
geometry->SetSpacing(spacing);
geometry->SetOrigin(origin);
}
LocalFile localFile(this);
const std::string path = localFile.GetFileName();
MITK_INFO << "Writing image: " << path << std::endl;
try
{
// Implementation of writer using itkImageIO directly. This skips the use
// of templated itkImageFileWriter, which saves the multiplexing on MITK side.
const unsigned int dimension = image->GetDimension();
const unsigned int *const dimensions = image->GetDimensions();
const mitk::PixelType pixelType = image->GetPixelType();
const mitk::Vector3D mitkSpacing = geometry->GetSpacing();
const mitk::Point3D mitkOrigin = geometry->GetOrigin();
// Due to templating in itk, we are forced to save a 4D spacing and 4D Origin,
// though they are not supported in MITK
itk::Vector<double, 4u> spacing4D;
spacing4D[0] = mitkSpacing[0];
spacing4D[1] = mitkSpacing[1];
spacing4D[2] = mitkSpacing[2];
spacing4D[3] = 1; // There is no support for a 4D spacing. However, we should have a valid value here
itk::Vector<double, 4u> origin4D;
origin4D[0] = mitkOrigin[0];
origin4D[1] = mitkOrigin[1];
origin4D[2] = mitkOrigin[2];
origin4D[3] = 0; // There is no support for a 4D origin. However, we should have a valid value here
// Set the necessary information for imageIO
m_ImageIO->SetNumberOfDimensions(dimension);
m_ImageIO->SetPixelType(pixelType.GetPixelType());
m_ImageIO->SetComponentType(pixelType.GetComponentType() < PixelComponentUserType ?
static_cast<itk::ImageIOBase::IOComponentType>(pixelType.GetComponentType()) :
itk::ImageIOBase::UNKNOWNCOMPONENTTYPE);
m_ImageIO->SetNumberOfComponents(pixelType.GetNumberOfComponents());
itk::ImageIORegion ioRegion(dimension);
for (unsigned int i = 0; i < dimension; i++)
{
m_ImageIO->SetDimensions(i, dimensions[i]);
m_ImageIO->SetSpacing(i, spacing4D[i]);
m_ImageIO->SetOrigin(i, origin4D[i]);
mitk::Vector3D mitkDirection;
mitkDirection.SetVnlVector(geometry->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(i));
itk::Vector<double, 4u> direction4D;
direction4D[0] = mitkDirection[0];
direction4D[1] = mitkDirection[1];
direction4D[2] = mitkDirection[2];
// MITK only supports a 3x3 direction matrix. Due to templating in itk, however, we must
// save a 4x4 matrix for 4D images. in this case, add an homogneous component to the matrix.
if (i == 3)
{
direction4D[3] = 1; // homogenous component
}
else
{
direction4D[3] = 0;
}
vnl_vector<double> axisDirection(dimension);
for (unsigned int j = 0; j < dimension; j++)
{
axisDirection[j] = direction4D[j] / spacing4D[i];
}
m_ImageIO->SetDirection(i, axisDirection);
ioRegion.SetSize(i, image->GetLargestPossibleRegion().GetSize(i));
ioRegion.SetIndex(i, image->GetLargestPossibleRegion().GetIndex(i));
}
// use compression if available
m_ImageIO->UseCompressionOn();
m_ImageIO->SetIORegion(ioRegion);
m_ImageIO->SetFileName(path);
// Handle time geometry
const ArbitraryTimeGeometry *arbitraryTG = dynamic_cast<const ArbitraryTimeGeometry *>(image->GetTimeGeometry());
if (arbitraryTG)
{
itk::EncapsulateMetaData<std::string>(m_ImageIO->GetMetaDataDictionary(),
PROPERTY_KEY_TIMEGEOMETRY_TYPE,
ArbitraryTimeGeometry::GetStaticNameOfClass());
std::stringstream stream;
stream << arbitraryTG->GetTimeBounds(0)[0];
for (TimeStepType pos = 0; pos < arbitraryTG->CountTimeSteps(); ++pos)
{
stream << " " << arbitraryTG->GetTimeBounds(pos)[1];
}
std::string data = stream.str();
itk::EncapsulateMetaData<std::string>(
m_ImageIO->GetMetaDataDictionary(), PROPERTY_KEY_TIMEGEOMETRY_TIMEPOINTS, data);
}
// Handle properties
mitk::PropertyList::Pointer imagePropertyList = image->GetPropertyList();
for (const auto &property : *imagePropertyList->GetMap())
{
IPropertyPersistence::InfoResultType infoList =
mitk::CoreServices::GetPropertyPersistence()->GetInfo(property.first, GetMimeType()->GetName(), true);
if (infoList.empty())
{
continue;
}
std::string value = infoList.front()->GetSerializationFunction()(property.second);
if (value == mitk::BaseProperty::VALUE_CANNOT_BE_CONVERTED_TO_STRING)
{
continue;
}
std::string key = infoList.front()->GetKey();
itk::EncapsulateMetaData<std::string>(m_ImageIO->GetMetaDataDictionary(), key, value);
}
ImageReadAccessor imageAccess(image);
m_ImageIO->Write(imageAccess.GetData());
}
catch (const std::exception &e)
{
mitkThrow() << e.what();
}
}
void LabelSetImageIO::Write()
{
ValidateOutputLocation();
const LabelSetImage* input = static_cast<const LabelSetImage*>(this->GetInput());
const std::string& locale = "C";
const std::string& currLocale = setlocale( LC_ALL, NULL );
if ( locale.compare(currLocale)!=0 )
{
try
{
setlocale(LC_ALL, locale.c_str());
}
catch(...)
{
mitkThrow() << "Could not set locale " << currLocale;
}
}
mitk::Image::Pointer inputVector = mitk::LabelSetImageConverter::ConvertLabelSetImageToImage(input);
// image write
if ( inputVector.IsNull() )
{
mitkThrow() << "Cannot write non-image data";
}
itk::NrrdImageIO::Pointer nrrdImageIo = itk::NrrdImageIO::New();
// Clone the image geometry, because we might have to change it
// for writing purposes
BaseGeometry::Pointer geometry = inputVector->GetGeometry()->Clone();
// Check if geometry information will be lost
if (inputVector->GetDimension() == 2 &&
!geometry->Is2DConvertable())
{
MITK_WARN << "Saving a 2D image with 3D geometry information. Geometry information will be lost! You might consider using Convert2Dto3DImageFilter before saving.";
// set matrix to identity
mitk::AffineTransform3D::Pointer affTrans = mitk::AffineTransform3D::New();
affTrans->SetIdentity();
mitk::Vector3D spacing = geometry->GetSpacing();
mitk::Point3D origin = geometry->GetOrigin();
geometry->SetIndexToWorldTransform(affTrans);
geometry->SetSpacing(spacing);
geometry->SetOrigin(origin);
}
LocalFile localFile(this);
const std::string path = localFile.GetFileName();
MITK_INFO << "Writing image: " << path << std::endl;
try
{
// Implementation of writer using itkImageIO directly. This skips the use
// of templated itkImageFileWriter, which saves the multiplexing on MITK side.
const unsigned int dimension = inputVector->GetDimension();
const unsigned int* const dimensions = inputVector->GetDimensions();
const mitk::PixelType pixelType = inputVector->GetPixelType();
const mitk::Vector3D mitkSpacing = geometry->GetSpacing();
const mitk::Point3D mitkOrigin = geometry->GetOrigin();
// Due to templating in itk, we are forced to save a 4D spacing and 4D Origin,
// though they are not supported in MITK
itk::Vector<double, 4u> spacing4D;
spacing4D[0] = mitkSpacing[0];
spacing4D[1] = mitkSpacing[1];
spacing4D[2] = mitkSpacing[2];
spacing4D[3] = 1; // There is no support for a 4D spacing. However, we should have a valid value here
itk::Vector<double, 4u> origin4D;
origin4D[0] = mitkOrigin[0];
origin4D[1] = mitkOrigin[1];
origin4D[2] = mitkOrigin[2];
origin4D[3] = 0; // There is no support for a 4D origin. However, we should have a valid value here
// Set the necessary information for imageIO
nrrdImageIo->SetNumberOfDimensions(dimension);
nrrdImageIo->SetPixelType(pixelType.GetPixelType());
nrrdImageIo->SetComponentType(pixelType.GetComponentType() < PixelComponentUserType ?
static_cast<itk::ImageIOBase::IOComponentType>(pixelType.GetComponentType()) :
itk::ImageIOBase::UNKNOWNCOMPONENTTYPE);
nrrdImageIo->SetNumberOfComponents(pixelType.GetNumberOfComponents());
itk::ImageIORegion ioRegion(dimension);
for (unsigned int i = 0; i < dimension; i++)
{
nrrdImageIo->SetDimensions(i, dimensions[i]);
nrrdImageIo->SetSpacing(i, spacing4D[i]);
nrrdImageIo->SetOrigin(i, origin4D[i]);
mitk::Vector3D mitkDirection;
mitkDirection.SetVnlVector(geometry->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(i));
itk::Vector<double, 4u> direction4D;
direction4D[0] = mitkDirection[0];
direction4D[1] = mitkDirection[1];
direction4D[2] = mitkDirection[2];
// MITK only supports a 3x3 direction matrix. Due to templating in itk, however, we must
// save a 4x4 matrix for 4D images. in this case, add an homogneous component to the matrix.
if (i == 3)
{
direction4D[3] = 1; // homogenous component
}
else
{
direction4D[3] = 0;
}
vnl_vector<double> axisDirection(dimension);
for (unsigned int j = 0; j < dimension; j++)
{
axisDirection[j] = direction4D[j] / spacing4D[i];
}
nrrdImageIo->SetDirection(i, axisDirection);
ioRegion.SetSize(i, inputVector->GetLargestPossibleRegion().GetSize(i));
ioRegion.SetIndex(i, inputVector->GetLargestPossibleRegion().GetIndex(i));
}
//use compression if available
nrrdImageIo->UseCompressionOn();
nrrdImageIo->SetIORegion(ioRegion);
nrrdImageIo->SetFileName(path);
// label set specific meta data
char keybuffer[512];
char valbuffer[512];
sprintf(keybuffer, "modality");
sprintf(valbuffer, "org.mitk.image.multilabel");
itk::EncapsulateMetaData<std::string>(nrrdImageIo->GetMetaDataDictionary(), std::string(keybuffer), std::string(valbuffer));
sprintf(keybuffer, "layers");
sprintf(valbuffer, "%1d", input->GetNumberOfLayers());
itk::EncapsulateMetaData<std::string>(nrrdImageIo->GetMetaDataDictionary(), std::string(keybuffer), std::string(valbuffer));
for (unsigned int layerIdx = 0; layerIdx<input->GetNumberOfLayers(); layerIdx++)
{
sprintf(keybuffer, "layer_%03d", layerIdx); // layer idx
sprintf(valbuffer, "%1d", input->GetNumberOfLabels(layerIdx)); // number of labels for the layer
itk::EncapsulateMetaData<std::string>(nrrdImageIo->GetMetaDataDictionary(), std::string(keybuffer), std::string(valbuffer));
mitk::LabelSet::LabelContainerConstIteratorType iter = input->GetLabelSet(layerIdx)->IteratorConstBegin();
unsigned int count(0);
while (iter != input->GetLabelSet(layerIdx)->IteratorConstEnd())
{
std::auto_ptr<TiXmlDocument> document;
document.reset(new TiXmlDocument());
TiXmlDeclaration* decl = new TiXmlDeclaration("1.0", "", ""); // TODO what to write here? encoding? etc....
document->LinkEndChild(decl);
TiXmlElement * labelElem = GetLabelAsTiXmlElement(iter->second);
document->LinkEndChild(labelElem);
TiXmlPrinter printer;
printer.SetIndent("");
printer.SetLineBreak("");
document->Accept(&printer);
sprintf(keybuffer, "org.mitk.label_%03u_%05u", layerIdx, count);
itk::EncapsulateMetaData<std::string>(nrrdImageIo->GetMetaDataDictionary(), std::string(keybuffer), printer.Str());
++iter;
++count;
}
}
// end label set specific meta data
ImageReadAccessor imageAccess(inputVector);
nrrdImageIo->Write(imageAccess.GetData());
}
catch (const std::exception& e)
{
mitkThrow() << e.what();
}
// end image write
try
{
setlocale(LC_ALL, currLocale.c_str());
}
catch(...)
{
mitkThrow() << "Could not reset locale " << currLocale;
}
}
void mitk::Image::Initialize(const mitk::PixelType& type, const mitk::TimeGeometry& geometry, unsigned int channels, int tDim )
{
unsigned int dimensions[5];
dimensions[0] = (unsigned int)(geometry.GetGeometryForTimeStep(0)->GetExtent(0)+0.5);
dimensions[1] = (unsigned int)(geometry.GetGeometryForTimeStep(0)->GetExtent(1)+0.5);
dimensions[2] = (unsigned int)(geometry.GetGeometryForTimeStep(0)->GetExtent(2)+0.5);
dimensions[3] = (tDim > 0) ? tDim : geometry.CountTimeSteps();
dimensions[4] = 0;
unsigned int dimension = 2;
if ( dimensions[2] > 1 )
dimension = 3;
if ( dimensions[3] > 1 )
dimension = 4;
Initialize( type, dimension, dimensions, channels );
if (geometry.CountTimeSteps() > 1)
{
TimeGeometry::Pointer cloned = geometry.Clone();
SetTimeGeometry(cloned.GetPointer());
// make sure the image geometry flag is properly set for all time steps
for (TimeStepType step = 0; step < cloned->CountTimeSteps(); ++step)
{
if( ! cloned->GetGeometryCloneForTimeStep(step)->GetImageGeometry() )
{
MITK_WARN("Image.3DnT.Initialize") << " Attempt to initialize an image with a non-image geometry. Re-interpretting the initialization geometry for timestep " << step
<< " as image geometry, the original geometry remains unchanged.";
cloned->GetGeometryForTimeStep(step)->ImageGeometryOn();
}
}
}
else
{
// make sure the image geometry coming from outside has proper value of the image geometry flag
BaseGeometry::Pointer cloned = geometry.GetGeometryCloneForTimeStep(0)->Clone();
if( ! cloned->GetImageGeometry() )
{
MITK_WARN("Image.Initialize") << " Attempt to initialize an image with a non-image geometry. Re-interpretting the initialization geometry as image geometry, the original geometry remains unchanged.";
cloned->ImageGeometryOn();
}
Superclass::SetGeometry( cloned );
}
/* //Old //TODO_GOETZ Really necessary?
mitk::BoundingBox::BoundsArrayType bounds = geometry.GetBoundingBoxInWorld()->GetBounds();
if( (bounds[0] != 0.0) || (bounds[2] != 0.0) || (bounds[4] != 0.0) )
{
SlicedGeometry3D* slicedGeometry = GetSlicedGeometry(0);
mitk::Point3D origin; origin.Fill(0.0);
slicedGeometry->IndexToWorld(origin, origin);
bounds[1]-=bounds[0]; bounds[3]-=bounds[2]; bounds[5]-=bounds[4];
bounds[0] = 0.0; bounds[2] = 0.0; bounds[4] = 0.0;
this->m_ImageDescriptor->Initialize( this->m_Dimensions, this->m_Dimension );
slicedGeometry->SetBounds(bounds);
slicedGeometry->GetIndexToWorldTransform()->SetOffset(origin.GetVnlVector().data_block());
ProportionalTimeGeometry::Pointer timeGeometry = ProportionalTimeGeometry::New();
timeGeometry->Initialize(slicedGeometry, m_Dimensions[3]);
SetTimeGeometry(timeGeometry);
}*/
}
bool AffineInteractor3D
::ExecuteAction( Action *action, StateEvent const *stateEvent )
{
bool ok = false;
// Get data object
BaseData *data = m_DataNode->GetData();
if ( data == NULL )
{
MITK_ERROR << "No data object present!";
return ok;
}
// Get Event and extract renderer
const Event *event = stateEvent->GetEvent();
BaseRenderer *renderer = NULL;
vtkRenderWindow *renderWindow = NULL;
vtkRenderWindowInteractor *renderWindowInteractor = NULL;
vtkRenderer *currentVtkRenderer = NULL;
vtkCamera *camera = NULL;
if ( event != NULL )
{
renderer = event->GetSender();
if ( renderer != NULL )
{
renderWindow = renderer->GetRenderWindow();
if ( renderWindow != NULL )
{
renderWindowInteractor = renderWindow->GetInteractor();
if ( renderWindowInteractor != NULL )
{
currentVtkRenderer = renderWindowInteractor
->GetInteractorStyle()->GetCurrentRenderer();
if ( currentVtkRenderer != NULL )
{
camera = currentVtkRenderer->GetActiveCamera();
}
}
}
}
}
// Check if we have a DisplayPositionEvent
const DisplayPositionEvent *dpe =
dynamic_cast< const DisplayPositionEvent * >( stateEvent->GetEvent() );
if ( dpe != NULL )
{
m_CurrentPickedPoint = dpe->GetWorldPosition();
m_CurrentPickedDisplayPoint = dpe->GetDisplayPosition();
}
// Get the timestep to also support 3D+t
int timeStep = 0;
ScalarType timeInMS = 0.0;
if ( renderer != NULL )
{
timeStep = renderer->GetTimeStep( data );
timeInMS = renderer->GetTime();
}
// If data is an mitk::Surface, extract it
Surface *surface = dynamic_cast< Surface * >( data );
vtkPolyData *polyData = NULL;
if ( surface != NULL )
{
polyData = surface->GetVtkPolyData( timeStep );
// Extract surface normal from surface (if existent, otherwise use default)
vtkPointData *pointData = polyData->GetPointData();
if ( pointData != NULL )
{
vtkDataArray *normal = polyData->GetPointData()->GetVectors( "planeNormal" );
if ( normal != NULL )
{
m_ObjectNormal[0] = normal->GetComponent( 0, 0 );
m_ObjectNormal[1] = normal->GetComponent( 0, 1 );
m_ObjectNormal[2] = normal->GetComponent( 0, 2 );
}
}
}
// Get geometry object
m_Geometry = data->GetGeometry( timeStep );
// Make sure that the data (if time-resolved) has enough entries;
// if not, create the required extra ones (empty)
data->Expand( timeStep+1 );
switch (action->GetActionId())
{
case AcDONOTHING:
ok = true;
break;
case AcCHECKOBJECT:
{
// Re-enable VTK interactor (may have been disabled previously)
if ( renderWindowInteractor != NULL )
{
renderWindowInteractor->Enable();
}
// Check if we have a DisplayPositionEvent
const DisplayPositionEvent *dpe =
dynamic_cast< const DisplayPositionEvent * >( stateEvent->GetEvent() );
if ( dpe == NULL )
{
ok = true;
break;
}
// Check if an object is present at the current mouse position
DataNode *pickedNode = dpe->GetPickedObjectNode();
StateEvent *newStateEvent;
if ( pickedNode == m_DataNode )
{
// Yes: object will be selected
newStateEvent = new StateEvent( EIDYES );
}
else
{
// No: back to start state
newStateEvent = new StateEvent( EIDNO );
}
this->HandleEvent( newStateEvent );
ok = true;
break;
}
case AcDESELECTOBJECT:
{
// Color object white
m_DataNode->SetColor( 1.0, 1.0, 1.0 );
RenderingManager::GetInstance()->RequestUpdateAll();
// Colorize surface / wireframe as inactive
this->ColorizeSurface( polyData,
m_CurrentPickedPoint, -1.0 );
ok = true;
break;
}
case AcSELECTPICKEDOBJECT:
{
// Color object red
m_DataNode->SetColor( 1.0, 0.0, 0.0 );
RenderingManager::GetInstance()->RequestUpdateAll();
// Colorize surface / wireframe dependend on distance from picked point
this->ColorizeSurface( polyData,
m_CurrentPickedPoint, 0.0 );
ok = true;
break;
}
case AcINITMOVE:
{
// Disable VTK interactor until MITK interaction has been completed
if ( renderWindowInteractor != NULL )
{
renderWindowInteractor->Disable();
}
// Check if we have a DisplayPositionEvent
const DisplayPositionEvent *dpe =
dynamic_cast< const DisplayPositionEvent * >( stateEvent->GetEvent() );
if ( dpe == NULL )
{
ok = true;
break;
}
//DataNode *pickedNode = dpe->GetPickedObjectNode();
m_InitialPickedPoint = m_CurrentPickedPoint;
m_InitialPickedDisplayPoint = m_CurrentPickedDisplayPoint;
if ( currentVtkRenderer != NULL )
{
vtkInteractorObserver::ComputeDisplayToWorld(
currentVtkRenderer,
m_InitialPickedDisplayPoint[0],
m_InitialPickedDisplayPoint[1],
0.0, //m_InitialInteractionPickedPoint[2],
m_InitialPickedPointWorld );
}
// Make deep copy of current Geometry3D of the plane
data->UpdateOutputInformation(); // make sure that the Geometry is up-to-date
m_OriginalGeometry = static_cast< BaseGeometry * >(
data->GetGeometry( timeStep )->Clone().GetPointer() );
ok = true;
break;
}
case AcMOVE:
{
// Check if we have a DisplayPositionEvent
const DisplayPositionEvent *dpe =
dynamic_cast< const DisplayPositionEvent * >( stateEvent->GetEvent() );
if ( dpe == NULL )
{
ok = true;
break;
}
if ( currentVtkRenderer != NULL )
{
vtkInteractorObserver::ComputeDisplayToWorld(
currentVtkRenderer,
m_CurrentPickedDisplayPoint[0],
m_CurrentPickedDisplayPoint[1],
0.0, //m_InitialInteractionPickedPoint[2],
m_CurrentPickedPointWorld );
}
Vector3D interactionMove;
interactionMove[0] = m_CurrentPickedPointWorld[0] - m_InitialPickedPointWorld[0];
interactionMove[1] = m_CurrentPickedPointWorld[1] - m_InitialPickedPointWorld[1];
interactionMove[2] = m_CurrentPickedPointWorld[2] - m_InitialPickedPointWorld[2];
if ( m_InteractionMode == INTERACTION_MODE_TRANSLATION )
{
Point3D origin = m_OriginalGeometry->GetOrigin();
Vector3D transformedObjectNormal;
data->GetGeometry( timeStep )->IndexToWorld(
m_ObjectNormal, transformedObjectNormal );
data->GetGeometry( timeStep )->SetOrigin(
origin + transformedObjectNormal * (interactionMove * transformedObjectNormal) );
}
else if ( m_InteractionMode == INTERACTION_MODE_ROTATION )
{
if ( camera )
{
double vpn[3];
camera->GetViewPlaneNormal( vpn );
Vector3D viewPlaneNormal;
viewPlaneNormal[0] = vpn[0];
viewPlaneNormal[1] = vpn[1];
viewPlaneNormal[2] = vpn[2];
Vector3D rotationAxis =
itk::CrossProduct( viewPlaneNormal, interactionMove );
rotationAxis.Normalize();
int *size = currentVtkRenderer->GetSize();
double l2 =
(m_CurrentPickedDisplayPoint[0] - m_InitialPickedDisplayPoint[0]) *
(m_CurrentPickedDisplayPoint[0] - m_InitialPickedDisplayPoint[0]) +
(m_CurrentPickedDisplayPoint[1] - m_InitialPickedDisplayPoint[1]) *
(m_CurrentPickedDisplayPoint[1] - m_InitialPickedDisplayPoint[1]);
double rotationAngle = 360.0 * sqrt(l2/(size[0]*size[0]+size[1]*size[1]));
// Use center of data bounding box as center of rotation
Point3D rotationCenter = m_OriginalGeometry->GetCenter();;
// Reset current Geometry3D to original state (pre-interaction) and
// apply rotation
RotationOperation op( OpROTATE, rotationCenter, rotationAxis, rotationAngle );
BaseGeometry::Pointer newGeometry = static_cast< BaseGeometry * >(
m_OriginalGeometry->Clone().GetPointer() );
newGeometry->ExecuteOperation( &op );
data->SetClonedGeometry(newGeometry, timeStep);
}
}
RenderingManager::GetInstance()->RequestUpdateAll();
ok = true;
break;
}
default:
return Superclass::ExecuteAction( action, stateEvent );
}
return ok;
}
void ItkImageIO::Write()
{
const mitk::Image* image = dynamic_cast<const mitk::Image*>(this->GetInput());
if (image == NULL)
{
mitkThrow() << "Cannot write non-image data";
}
struct LocaleSwitch
{
LocaleSwitch(const std::string& newLocale)
: m_OldLocale(std::setlocale(LC_ALL, NULL))
, m_NewLocale(newLocale)
{
if (m_OldLocale == NULL)
{
m_OldLocale = "";
}
else if (m_NewLocale != m_OldLocale)
{
// set the locale
if (std::setlocale(LC_ALL, m_NewLocale.c_str()) == NULL)
{
MITK_INFO << "Could not set locale " << m_NewLocale;
m_OldLocale = NULL;
}
}
}
~LocaleSwitch()
{
if (m_OldLocale != NULL && std::setlocale(LC_ALL, m_OldLocale) == NULL)
{
MITK_INFO << "Could not reset locale " << m_OldLocale;
}
}
private:
const char* m_OldLocale;
const std::string m_NewLocale;
};
// Switch the current locale to "C"
LocaleSwitch localeSwitch("C");
// Clone the image geometry, because we might have to change it
// for writing purposes
BaseGeometry::Pointer geometry = image->GetGeometry()->Clone();
// Check if geometry information will be lost
if (image->GetDimension() == 2 &&
!geometry->Is2DConvertable())
{
MITK_WARN << "Saving a 2D image with 3D geometry information. Geometry information will be lost! You might consider using Convert2Dto3DImageFilter before saving.";
// set matrix to identity
mitk::AffineTransform3D::Pointer affTrans = mitk::AffineTransform3D::New();
affTrans->SetIdentity();
mitk::Vector3D spacing = geometry->GetSpacing();
mitk::Point3D origin = geometry->GetOrigin();
geometry->SetIndexToWorldTransform(affTrans);
geometry->SetSpacing(spacing);
geometry->SetOrigin(origin);
}
LocalFile localFile(this);
const std::string path = localFile.GetFileName();
MITK_INFO << "Writing image: " << path << std::endl;
try
{
// Implementation of writer using itkImageIO directly. This skips the use
// of templated itkImageFileWriter, which saves the multiplexing on MITK side.
const unsigned int dimension = image->GetDimension();
const unsigned int* const dimensions = image->GetDimensions();
const mitk::PixelType pixelType = image->GetPixelType();
const mitk::Vector3D mitkSpacing = geometry->GetSpacing();
const mitk::Point3D mitkOrigin = geometry->GetOrigin();
// Due to templating in itk, we are forced to save a 4D spacing and 4D Origin,
// though they are not supported in MITK
itk::Vector<double, 4u> spacing4D;
spacing4D[0] = mitkSpacing[0];
spacing4D[1] = mitkSpacing[1];
spacing4D[2] = mitkSpacing[2];
spacing4D[3] = 1; // There is no support for a 4D spacing. However, we should have a valid value here
itk::Vector<double, 4u> origin4D;
origin4D[0] = mitkOrigin[0];
origin4D[1] = mitkOrigin[1];
origin4D[2] = mitkOrigin[2];
origin4D[3] = 0; // There is no support for a 4D origin. However, we should have a valid value here
// Set the necessary information for imageIO
m_ImageIO->SetNumberOfDimensions(dimension);
m_ImageIO->SetPixelType(pixelType.GetPixelType());
m_ImageIO->SetComponentType(pixelType.GetComponentType() < PixelComponentUserType ?
static_cast<itk::ImageIOBase::IOComponentType>(pixelType.GetComponentType()) :
itk::ImageIOBase::UNKNOWNCOMPONENTTYPE);
m_ImageIO->SetNumberOfComponents( pixelType.GetNumberOfComponents() );
itk::ImageIORegion ioRegion( dimension );
for(unsigned int i = 0; i < dimension; i++)
{
m_ImageIO->SetDimensions(i, dimensions[i]);
m_ImageIO->SetSpacing(i, spacing4D[i]);
m_ImageIO->SetOrigin(i, origin4D[i]);
mitk::Vector3D mitkDirection;
mitkDirection.SetVnlVector(geometry->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(i));
itk::Vector<double, 4u> direction4D;
direction4D[0] = mitkDirection[0];
direction4D[1] = mitkDirection[1];
direction4D[2] = mitkDirection[2];
// MITK only supports a 3x3 direction matrix. Due to templating in itk, however, we must
// save a 4x4 matrix for 4D images. in this case, add an homogneous component to the matrix.
if (i == 3)
{
direction4D[3] = 1; // homogenous component
}
else
{
direction4D[3] = 0;
}
vnl_vector<double> axisDirection(dimension);
for(unsigned int j = 0; j < dimension; j++)
{
axisDirection[j] = direction4D[j] / spacing4D[i];
}
m_ImageIO->SetDirection(i, axisDirection);
ioRegion.SetSize(i, image->GetLargestPossibleRegion().GetSize(i));
ioRegion.SetIndex(i, image->GetLargestPossibleRegion().GetIndex(i));
}
//use compression if available
m_ImageIO->UseCompressionOn();
m_ImageIO->SetIORegion(ioRegion);
m_ImageIO->SetFileName(path);
// ***** Remove const_cast after bug 17952 is fixed ****
ImageReadAccessor imageAccess(const_cast<mitk::Image*>(image));
m_ImageIO->Write(imageAccess.GetData());
}
catch (const std::exception& e)
{
mitkThrow() << e.what();
}
}
void mitk::SurfaceStampImageFilter::SurfaceStamp(int time)
{
mitk::Image::Pointer inputImage = this->GetInput();
const mitk::TimeGeometry *surfaceTimeGeometry = GetInput()->GetTimeGeometry();
const mitk::TimeGeometry *imageTimeGeometry = inputImage->GetTimeGeometry();
// Convert time step from image time-frame to surface time-frame
mitk::TimePointType matchingTimePoint = imageTimeGeometry->TimeStepToTimePoint(time);
mitk::TimeStepType surfaceTimeStep = surfaceTimeGeometry->TimePointToTimeStep(matchingTimePoint);
vtkPolyData *polydata = m_Surface->GetVtkPolyData(surfaceTimeStep);
if (!polydata)
mitkThrow() << "Polydata is null.";
vtkSmartPointer<vtkTransformPolyDataFilter> transformFilter = vtkSmartPointer<vtkTransformPolyDataFilter>::New();
transformFilter->SetInputData(polydata);
// transformFilter->ReleaseDataFlagOn();
vtkSmartPointer<vtkTransform> transform = vtkSmartPointer<vtkTransform>::New();
BaseGeometry::Pointer geometry = surfaceTimeGeometry->GetGeometryForTimeStep(surfaceTimeStep);
transform->PostMultiply();
transform->Concatenate(geometry->GetVtkTransform()->GetMatrix());
// take image geometry into account. vtk-Image information will be changed to unit spacing and zero origin below.
BaseGeometry::Pointer imageGeometry = imageTimeGeometry->GetGeometryForTimeStep(time);
transform->Concatenate(imageGeometry->GetVtkTransform()->GetLinearInverse());
transformFilter->SetTransform(transform);
transformFilter->Update();
polydata = transformFilter->GetOutput();
if (!polydata || !polydata->GetNumberOfPoints())
mitkThrow() << "Polydata retrieved from transformation is null or has no points.";
MeshType::Pointer mesh = MeshType::New();
mesh->SetCellsAllocationMethod(MeshType::CellsAllocatedDynamicallyCellByCell);
unsigned int numberOfPoints = polydata->GetNumberOfPoints();
mesh->GetPoints()->Reserve(numberOfPoints);
vtkPoints *points = polydata->GetPoints();
MeshType::PointType point;
for (unsigned int i = 0; i < numberOfPoints; i++)
{
double *aux = points->GetPoint(i);
point[0] = aux[0];
point[1] = aux[1];
point[2] = aux[2];
mesh->SetPoint(i, point);
}
// Load the polygons into the itk::Mesh
typedef MeshType::CellAutoPointer CellAutoPointerType;
typedef MeshType::CellType CellType;
typedef itk::TriangleCell<CellType> TriangleCellType;
typedef MeshType::PointIdentifier PointIdentifierType;
typedef MeshType::CellIdentifier CellIdentifierType;
// Read the number of polygons
CellIdentifierType numberOfPolygons = 0;
numberOfPolygons = polydata->GetNumberOfPolys();
PointIdentifierType numberOfCellPoints = 3;
CellIdentifierType i = 0;
for (i = 0; i < numberOfPolygons; i++)
{
vtkIdList *cellIds;
vtkCell *vcell = polydata->GetCell(i);
cellIds = vcell->GetPointIds();
CellAutoPointerType cell;
auto *triangleCell = new TriangleCellType;
PointIdentifierType k;
for (k = 0; k < numberOfCellPoints; k++)
{
triangleCell->SetPointId(k, cellIds->GetId(k));
}
cell.TakeOwnership(triangleCell);
mesh->SetCell(i, cell);
}
if (!mesh->GetNumberOfPoints())
mitkThrow() << "Generated itk mesh is empty.";
if (m_MakeOutputBinary)
{
this->SurfaceStampBinaryOutputProcessing(mesh);
}
else
{
AccessFixedDimensionByItk_1(inputImage, SurfaceStampProcessing, 3, mesh);
}
}
void mitk::SurfaceDeformationDataInteractor3D::DeformObject (StateMachineAction*, InteractionEvent* interactionEvent)
{
const InteractionPositionEvent* positionEvent = dynamic_cast<const InteractionPositionEvent*>(interactionEvent);
if(positionEvent == NULL)
return;
int timeStep = interactionEvent->GetSender()->GetTimeStep(this->GetDataNode()->GetData());
vtkPolyData* polyData = m_Surface->GetVtkPolyData(timeStep);
BaseGeometry::Pointer geometry = this->GetDataNode()->GetData()->GetGeometry(timeStep);
double currentWorldPoint[4];
mitk::Point2D currentDisplayPoint = positionEvent->GetPointerPositionOnScreen();
vtkInteractorObserver::ComputeDisplayToWorld(
interactionEvent->GetSender()->GetVtkRenderer(),
currentDisplayPoint[0],
currentDisplayPoint[1],
0.0, //m_InitialInteractionPickedPoint[2],
currentWorldPoint);
// Calculate mouse move in 3D space
Vector3D interactionMove;
interactionMove[0] = currentWorldPoint[0] - m_InitialPickedWorldPoint[0];
interactionMove[1] = currentWorldPoint[1] - m_InitialPickedWorldPoint[1];
interactionMove[2] = currentWorldPoint[2] - m_InitialPickedWorldPoint[2];
// Transform mouse move into geometry space
this->GetDataNode()->GetData()->UpdateOutputInformation();// make sure that the Geometry is up-to-date
Vector3D interactionMoveIndex;
geometry->WorldToIndex(interactionMove, interactionMoveIndex);
// Get picked point and transform into local coordinates
Point3D pickedPoint;
geometry->WorldToIndex(m_InitialPickedPoint, pickedPoint);
Vector3D v1 = pickedPoint.GetVectorFromOrigin();
vtkDataArray* normal = polyData->GetPointData()->GetVectors("planeNormal");
if (normal != NULL)
{
m_ObjectNormal[0] = normal->GetComponent(0, 0);
m_ObjectNormal[1] = normal->GetComponent(0, 1);
m_ObjectNormal[2] = normal->GetComponent(0, 2);
}
Vector3D v2 = m_ObjectNormal * (interactionMoveIndex * m_ObjectNormal);
vtkPoints* originalPoints = m_OriginalPolyData->GetPoints();
vtkPoints* deformedPoints = polyData->GetPoints();
double denom = m_GaussSigma * m_GaussSigma * 2;
double point[3];
for (vtkIdType i = 0; i < deformedPoints->GetNumberOfPoints(); ++i)
{
// Get original point
double* originalPoint = originalPoints->GetPoint( i );
Vector3D v0;
v0[0] = originalPoint[0];
v0[1] = originalPoint[1];
v0[2] = originalPoint[2];
// Calculate distance of this point from line through picked point
double d = itk::CrossProduct(m_ObjectNormal, (v1 - v0)).GetNorm();
Vector3D t = v2 * exp(- d * d / denom);
point[0] = originalPoint[0] + t[0];
point[1] = originalPoint[1] + t[1];
point[2] = originalPoint[2] + t[2];
deformedPoints->SetPoint(i, point);
}
// Make sure that surface is colorized at initial picked position as long as we are in deformation state
m_SurfaceColorizationCenter = m_InitialPickedPoint;
polyData->Modified();
m_Surface->Modified();
interactionEvent->GetSender()->GetRenderingManager()->RequestUpdateAll();
}
