mitk::ScalarType mitk::Cuboid::GetVolume()
{
TimeGeometry* geometry = GetTimeGeometry();
return geometry->GetExtentInWorld(0)
* geometry->GetExtentInWorld(1)
* geometry->GetExtentInWorld(2);
}
void mitk::SlicedData::SetOrigin(const mitk::Point3D& origin)
{
TimeGeometry* timeGeometry = GetTimeGeometry();
assert(timeGeometry!=NULL);
mitk::SlicedGeometry3D* slicedGeometry;
unsigned int steps = timeGeometry->CountTimeSteps();
for(unsigned int timestep = 0; timestep < steps; ++timestep)
{
slicedGeometry = GetSlicedGeometry(timestep);
if(slicedGeometry != NULL)
{
slicedGeometry->SetOrigin(origin);
if(slicedGeometry->GetEvenlySpaced())
{
mitk::PlaneGeometry* geometry2D = slicedGeometry->GetPlaneGeometry(0);
geometry2D->SetOrigin(origin);
slicedGeometry->InitializeEvenlySpaced(geometry2D, slicedGeometry->GetSlices());
}
}
//ProportionalTimeGeometry* timeGeometry = dynamic_cast<ProportionalTimeGeometry *>(GetTimeGeometry());
//if(timeGeometry != NULL)
//{
// timeGeometry->Initialize(slicedGeometry, steps);
// break;
//}
}
}
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;
}
mitk::ScalarType mitk::Cylinder::GetVolume()
{
TimeGeometry* geometry = GetTimeGeometry();
return geometry->GetExtentInWorld(0) * 0.5
* geometry->GetExtentInWorld(2) * 0.5
* vnl_math::pi
* geometry->GetExtentInWorld(1);
}
void mitk::UnstructuredGrid::CalculateBoundingBox()
{
//
// first make sure, that the associated time sliced geometry has
// the same number of geometry 3d's as vtkUnstructuredGrids are present
//
TimeGeometry* timeGeometry = GetTimeGeometry();
if ( timeGeometry->CountTimeSteps() != m_GridSeries.size() )
{
itkExceptionMacro(<<"timeGeometry->CountTimeSteps() != m_GridSeries.size() -- use Initialize(timeSteps) with correct number of timeSteps!");
}
void mitk::PointSet::UpdateOutputInformation()
{
if ( this->GetSource( ) )
{
this->GetSource( )->UpdateOutputInformation( );
}
//
// first make sure, that the associated time sliced geometry has
// the same number of geometry 3d's as PointSets are present
//
TimeGeometry* timeGeometry = GetTimeGeometry();
if ( timeGeometry->CountTimeSteps() != m_PointSetSeries.size() )
{
itkExceptionMacro(<<"timeGeometry->CountTimeSteps() != m_PointSetSeries.size() -- use Initialize(timeSteps) with correct number of timeSteps!");
}
void mitk::SlicedData::SetSpacing(mitk::Vector3D aSpacing)
{
TimeGeometry *timeGeometry = GetTimeGeometry();
assert(timeGeometry != nullptr);
unsigned int steps = timeGeometry->CountTimeSteps();
for (unsigned int timestep = 0; timestep < steps; ++timestep)
{
mitk::SlicedGeometry3D *slicedGeometry = GetSlicedGeometry(timestep);
if (slicedGeometry != nullptr)
{
slicedGeometry->SetSpacing(aSpacing);
}
}
timeGeometry->Update();
}
void SliceNavigationController::SetGeometryTime(const itk::EventObject &geometryTimeEvent)
{
if (m_CreatedWorldGeometry.IsNull())
{
return;
}
const SliceNavigationController::GeometryTimeEvent *timeEvent =
dynamic_cast< const SliceNavigationController::GeometryTimeEvent * >(&geometryTimeEvent);
assert( timeEvent != nullptr );
TimeGeometry *timeGeometry = timeEvent->GetTimeGeometry();
assert( timeGeometry != nullptr );
int timeStep = (int)timeEvent->GetPos();
ScalarType timeInMS;
timeInMS = timeGeometry->TimeStepToTimePoint(timeStep);
timeStep = m_CreatedWorldGeometry->TimePointToTimeStep(timeInMS);
this->GetTime()->SetPos(timeStep);
}
void SlicesRotator::RotateToPoint( SliceNavigationController *rotationPlaneSNC,
SliceNavigationController *rotatedPlaneSNC,
const Point3D &point, bool linked )
{
MITK_WARN << "Deprecated function! Use SliceNavigationController::ReorientSlices() instead";
SliceNavigationController *thirdSNC = NULL;
SNCVector::iterator iter;
for ( iter = m_RotatableSNCs.begin(); iter != m_RotatableSNCs.end(); ++iter )
{
if ( ((*iter) != rotationPlaneSNC)
&& ((*iter) != rotatedPlaneSNC) )
{
thirdSNC = *iter;
break;
}
}
if ( thirdSNC == NULL )
{
return;
}
const PlaneGeometry *rotationPlane = rotationPlaneSNC->GetCurrentPlaneGeometry();
const PlaneGeometry *rotatedPlane = rotatedPlaneSNC->GetCurrentPlaneGeometry();
const PlaneGeometry *thirdPlane = thirdSNC->GetCurrentPlaneGeometry();
if ( (rotationPlane == NULL) || (rotatedPlane == NULL)
|| (thirdPlane == NULL) )
{
return;
}
if ( rotatedPlane->DistanceFromPlane( point ) < 0.001 )
{
// Skip irrelevant rotations
return;
}
Point3D projectedPoint;
Line3D intersection;
Point3D rotationCenter;
if ( !rotationPlane->Project( point, projectedPoint )
|| !rotationPlane->IntersectionLine( rotatedPlane, intersection )
|| !thirdPlane->IntersectionPoint( intersection, rotationCenter ) )
{
return;
}
// All pre-requirements are met; execute the rotation
Point3D referencePoint = intersection.Project( projectedPoint );
Vector3D toProjected = referencePoint - rotationCenter;
Vector3D toCursor = projectedPoint - rotationCenter;
// cross product: | A x B | = |A| * |B| * sin(angle)
Vector3D axisOfRotation;
vnl_vector_fixed< ScalarType, 3 > vnlDirection =
vnl_cross_3d( toCursor.GetVnlVector(), toProjected.GetVnlVector() );
axisOfRotation.SetVnlVector( vnlDirection );
// scalar product: A * B = |A| * |B| * cos(angle)
// tan = sin / cos
ScalarType angle = - atan2(
(double)(axisOfRotation.GetNorm()),
(double)(toCursor * toProjected) );
angle *= 180.0 / vnl_math::pi;
// create RotationOperation and apply to all SNCs that should be rotated
RotationOperation op(OpROTATE, rotationCenter, axisOfRotation, angle);
if ( !linked )
{
BaseRenderer *renderer = rotatedPlaneSNC->GetRenderer();
if ( renderer == NULL )
{
return;
}
DisplayGeometry *displayGeometry = renderer->GetDisplayGeometry();
Point2D point2DWorld, point2DDisplayPre, point2DDisplayPost;
displayGeometry->Map( rotationCenter, point2DWorld );
displayGeometry->WorldToDisplay( point2DWorld, point2DDisplayPre );
TimeGeometry *timeGeometry= rotatedPlaneSNC->GetCreatedWorldGeometry();
if ( !timeGeometry )
{
return;
}
timeGeometry->ExecuteOperation( &op );
displayGeometry->Map( rotationCenter, point2DWorld );
displayGeometry->WorldToDisplay( point2DWorld, point2DDisplayPost );
Vector2D vector2DDisplayDiff = point2DDisplayPost - point2DDisplayPre;
//Vector2D origin = displayGeometry->GetOriginInMM();
displayGeometry->MoveBy( vector2DDisplayDiff );
rotatedPlaneSNC->SendCreatedWorldGeometryUpdate();
}
else
{
SNCVector::iterator iter;
for ( iter = m_RotatableSNCs.begin(); iter != m_RotatableSNCs.end(); ++iter )
{
BaseRenderer *renderer = (*iter)->GetRenderer();
if ( renderer == NULL )
{
continue;
}
DisplayGeometry *displayGeometry = renderer->GetDisplayGeometry();
Point2D point2DWorld, point2DDisplayPre, point2DDisplayPost;
displayGeometry->Map( rotationCenter, point2DWorld );
displayGeometry->WorldToDisplay( point2DWorld, point2DDisplayPre );
TimeGeometry* timeGeometry = (*iter)->GetCreatedWorldGeometry();
if ( !timeGeometry )
{
continue;
}
timeGeometry->ExecuteOperation( &op );
displayGeometry->Map( rotationCenter, point2DWorld );
displayGeometry->WorldToDisplay( point2DWorld, point2DDisplayPost );
Vector2D vector2DDisplayDiff = point2DDisplayPost - point2DDisplayPre;
//Vector2D origin = displayGeometry->GetOriginInMM();
displayGeometry->MoveBy( vector2DDisplayDiff );
(*iter)->SendCreatedWorldGeometryUpdate();
}
}
} // end RotateToPoint
bool SlicesRotator::DoRotationStep(Action*, const StateEvent* e)
{
const DisplayPositionEvent* posEvent = dynamic_cast<const DisplayPositionEvent*>(e->GetEvent());
if (!posEvent) return false;
Point3D cursor = posEvent->GetWorldPosition();
Vector3D toProjected = m_LastCursorPosition - m_CenterOfRotation;
Vector3D toCursor = cursor - m_CenterOfRotation;
// cross product: | A x B | = |A| * |B| * sin(angle)
Vector3D axisOfRotation;
vnl_vector_fixed< ScalarType, 3 > vnlDirection = vnl_cross_3d( toCursor.GetVnlVector(), toProjected.GetVnlVector() );
axisOfRotation.SetVnlVector(vnlDirection);
// scalar product: A * B = |A| * |B| * cos(angle)
// tan = sin / cos
ScalarType angle = - atan2( (double)(axisOfRotation.GetNorm()), (double)(toCursor * toProjected) );
angle *= 180.0 / vnl_math::pi;
m_LastCursorPosition = cursor;
// create RotationOperation and apply to all SNCs that should be rotated
RotationOperation rotationOperation(OpROTATE, m_CenterOfRotation, axisOfRotation, angle);
// iterate the OTHER slice navigation controllers: these are filled in DoDecideBetweenRotationAndSliceSelection
for (SNCVector::iterator iter = m_SNCsToBeRotated.begin(); iter != m_SNCsToBeRotated.end(); ++iter)
{
// - remember the center of rotation on the 2D display BEFORE rotation
// - execute rotation
// - calculate new center of rotation on 2D display
// - move display IF the center of rotation has moved slightly before and after rotation
// DM 2012-10: this must probably be due to rounding errors only, right?
// We don't have documentation on if/why this code is needed
BaseRenderer *renderer = (*iter)->GetRenderer();
if ( !renderer ) continue;
DisplayGeometry *displayGeometry = renderer->GetDisplayGeometry();
Point2D rotationCenter2DWorld, point2DDisplayPreRotation, point2DDisplayPostRotation;
displayGeometry->Map( m_CenterOfRotation, rotationCenter2DWorld );
displayGeometry->WorldToDisplay( rotationCenter2DWorld, point2DDisplayPreRotation );
TimeGeometry* timeGeometry = (*iter)->GetCreatedWorldGeometry();
if (!timeGeometry) continue;
timeGeometry->ExecuteOperation(&rotationOperation);
displayGeometry->Map( m_CenterOfRotation, rotationCenter2DWorld );
displayGeometry->WorldToDisplay( rotationCenter2DWorld, point2DDisplayPostRotation );
Vector2D vector2DDisplayDiff = point2DDisplayPostRotation - point2DDisplayPreRotation;
displayGeometry->MoveBy( vector2DDisplayDiff );
(*iter)->SendCreatedWorldGeometryUpdate();
}
RenderingManager::GetInstance()->RequestUpdateAll();
this->InvokeEvent( SliceRotationEvent() ); // notify listeners
return true;
}
void mitk::Geometry2DDataToSurfaceFilter::GenerateOutputInformation()
{
mitk::Geometry2DData::ConstPointer input = this->GetInput();
mitk::Surface::Pointer output = this->GetOutput();
if ( input.IsNull() || (input->GetGeometry2D() == NULL)
|| (input->GetGeometry2D()->IsValid() == false)
|| (m_UseBoundingBox && (m_BoundingBox.IsNull() || (m_BoundingBox->GetDiagonalLength2() < mitk::eps))) )
{
return;
}
Point3D origin;
Point3D right, bottom;
vtkPolyData *planeSurface = NULL;
// Does the Geometry2DData contain a PlaneGeometry?
if ( dynamic_cast< PlaneGeometry * >( input->GetGeometry2D() ) != NULL )
{
mitk::PlaneGeometry *planeGeometry =
dynamic_cast< PlaneGeometry * >( input->GetGeometry2D() );
if ( m_PlaceByGeometry )
{
// Let the output use the input geometry to appropriately transform the
// coordinate system.
mitk::Geometry3D::TransformType *affineTransform =
planeGeometry->GetIndexToWorldTransform();
TimeGeometry *timeGeometry = output->GetTimeGeometry();
Geometry3D *geometrie3d = timeGeometry->GetGeometryForTimeStep( 0 );
geometrie3d->SetIndexToWorldTransform( affineTransform );
}
if ( !m_UseBoundingBox)
{
// We do not have a bounding box, so no clipping is required.
if ( m_PlaceByGeometry )
{
// Derive coordinate axes and origin from input geometry extent
origin.Fill( 0.0 );
FillVector3D( right, planeGeometry->GetExtent(0), 0.0, 0.0 );
FillVector3D( bottom, 0.0, planeGeometry->GetExtent(1), 0.0 );
}
else
{
// Take the coordinate axes and origin directly from the input geometry.
origin = planeGeometry->GetOrigin();
right = planeGeometry->GetCornerPoint( false, true );
bottom = planeGeometry->GetCornerPoint( true, false );
}
// Since the plane is planar, there is no need to subdivide the grid
// (cf. AbstractTransformGeometry case)
m_PlaneSource->SetXResolution( 1 );
m_PlaneSource->SetYResolution( 1 );
m_PlaneSource->SetOrigin( origin[0], origin[1], origin[2] );
m_PlaneSource->SetPoint1( right[0], right[1], right[2] );
m_PlaneSource->SetPoint2( bottom[0], bottom[1], bottom[2] );
m_PlaneSource->Update();
planeSurface = m_PlaneSource->GetOutput();
}
else
{
// Set up a cube with the extent and origin of the bounding box. This
// cube will be clipped by a plane later on. The intersection of the
// cube and the plane will be the surface we are interested in. Note
// that the bounding box needs to be explicitly specified by the user
// of this class, since it is not necessarily clear from the data
// available herein which bounding box to use. In most cases, this
// would be the bounding box of the input geometry's reference
// geometry, but this is not an inevitable requirement.
mitk::BoundingBox::PointType boundingBoxMin = m_BoundingBox->GetMinimum();
mitk::BoundingBox::PointType boundingBoxMax = m_BoundingBox->GetMaximum();
mitk::BoundingBox::PointType boundingBoxCenter = m_BoundingBox->GetCenter();
m_CubeSource->SetXLength( boundingBoxMax[0] - boundingBoxMin[0] );
m_CubeSource->SetYLength( boundingBoxMax[1] - boundingBoxMin[1] );
m_CubeSource->SetZLength( boundingBoxMax[2] - boundingBoxMin[2] );
m_CubeSource->SetCenter(
boundingBoxCenter[0],
boundingBoxCenter[1],
boundingBoxCenter[2] );
// Now we have to transform the cube, so that it will cut our plane
// appropriately. (As can be seen below, the plane corresponds to the
// z-plane in the coordinate system and is *not* transformed.) Therefore,
// we get the inverse of the plane geometry's transform and concatenate
// it with the transform of the reference geometry, if available.
m_Transform->Identity();
m_Transform->Concatenate(
planeGeometry->GetVtkTransform()->GetLinearInverse()
);
Geometry3D *referenceGeometry = planeGeometry->GetReferenceGeometry();
if ( referenceGeometry )
{
m_Transform->Concatenate(
referenceGeometry->GetVtkTransform()
);
}
// Transform the cube accordingly (s.a.)
m_PolyDataTransformer->SetInputConnection( m_CubeSource->GetOutputPort() );
m_PolyDataTransformer->SetTransform( m_Transform );
// Initialize the plane to clip the cube with, as lying on the z-plane
m_Plane->SetOrigin( 0.0, 0.0, 0.0 );
m_Plane->SetNormal( 0.0, 0.0, 1.0 );
// Cut the plane with the cube.
m_PlaneCutter->SetInputConnection( m_PolyDataTransformer->GetOutputPort() );
m_PlaneCutter->SetCutFunction( m_Plane );
// The output of the cutter must be converted into appropriate poly data.
m_PlaneStripper->SetInputConnection( m_PlaneCutter->GetOutputPort() );
m_PlaneStripper->Update();
if ( m_PlaneStripper->GetOutput()->GetNumberOfPoints() < 3 )
{
return;
}
m_PlanePolyData->SetPoints( m_PlaneStripper->GetOutput()->GetPoints() );
m_PlanePolyData->SetPolys( m_PlaneStripper->GetOutput()->GetLines() );
m_PlaneTriangler->SetInputData( m_PlanePolyData );
// Get bounds of the resulting surface and use it to generate the texture
// mapping information
m_PlaneTriangler->Update();
m_PlaneTriangler->GetOutput()->ComputeBounds();
double *surfaceBounds =
m_PlaneTriangler->GetOutput()->GetBounds();
origin[0] = surfaceBounds[0];
origin[1] = surfaceBounds[2];
origin[2] = surfaceBounds[4];
right[0] = surfaceBounds[1];
right[1] = surfaceBounds[2];
right[2] = surfaceBounds[4];
bottom[0] = surfaceBounds[0];
bottom[1] = surfaceBounds[3];
bottom[2] = surfaceBounds[4];
// Now we tell the data how it shall be textured afterwards;
// description see above.
m_TextureMapToPlane->SetInputConnection( m_PlaneTriangler->GetOutputPort() );
m_TextureMapToPlane->AutomaticPlaneGenerationOn();
m_TextureMapToPlane->SetOrigin( origin[0], origin[1], origin[2] );
m_TextureMapToPlane->SetPoint1( right[0], right[1], right[2] );
m_TextureMapToPlane->SetPoint2( bottom[0], bottom[1], bottom[2] );
// Need to call update so that output data and bounds are immediately
// available
m_TextureMapToPlane->Update();
// Return the output of this generation process
planeSurface = dynamic_cast< vtkPolyData * >(
m_TextureMapToPlane->GetOutput()
);
}
}
// Does the Geometry2DData contain an AbstractTransformGeometry?
else if ( mitk::AbstractTransformGeometry *abstractGeometry =
dynamic_cast< AbstractTransformGeometry * >( input->GetGeometry2D() ) )
{
// In the case of an AbstractTransformGeometry (which holds a possibly
// non-rigid transform), we proceed slightly differently: since the
// plane can be arbitrarily deformed, we need to transform it by the
// abstract transform before clipping it. The setup for this is partially
// done in the constructor.
origin = abstractGeometry->GetPlane()->GetOrigin();
right = origin + abstractGeometry->GetPlane()->GetAxisVector( 0 );
bottom = origin + abstractGeometry->GetPlane()->GetAxisVector( 1 );
// Define the plane
m_PlaneSource->SetOrigin( origin[0], origin[1], origin[2] );
m_PlaneSource->SetPoint1( right[0], right[1], right[2] );
m_PlaneSource->SetPoint2( bottom[0], bottom[1], bottom[2] );
// Set the plane's resolution (unlike for non-deformable planes, the plane
// grid needs to have a certain resolution so that the deformation has the
// desired effect).
if ( m_UseGeometryParametricBounds )
{
m_PlaneSource->SetXResolution(
(int)abstractGeometry->GetParametricExtent(0)
);
m_PlaneSource->SetYResolution(
(int)abstractGeometry->GetParametricExtent(1)
);
}
else
{
m_PlaneSource->SetXResolution( m_XResolution );
m_PlaneSource->SetYResolution( m_YResolution );
}
if ( m_PlaceByGeometry )
{
// Let the output use the input geometry to appropriately transform the
// coordinate system.
mitk::Geometry3D::TransformType *affineTransform =
abstractGeometry->GetIndexToWorldTransform();
TimeGeometry *timeGeometry = output->GetTimeGeometry();
Geometry3D *g3d = timeGeometry->GetGeometryForTimeStep( 0 );
g3d->SetIndexToWorldTransform( affineTransform );
vtkGeneralTransform *composedResliceTransform = vtkGeneralTransform::New();
composedResliceTransform->Identity();
composedResliceTransform->Concatenate(
abstractGeometry->GetVtkTransform()->GetLinearInverse() );
composedResliceTransform->Concatenate(
abstractGeometry->GetVtkAbstractTransform()
);
// Use the non-rigid transform for transforming the plane.
m_VtkTransformPlaneFilter->SetTransform(
composedResliceTransform
);
}
else
{
// Use the non-rigid transform for transforming the plane.
m_VtkTransformPlaneFilter->SetTransform(
abstractGeometry->GetVtkAbstractTransform()
);
}
if ( m_UseBoundingBox )
{
mitk::BoundingBox::PointType boundingBoxMin = m_BoundingBox->GetMinimum();
mitk::BoundingBox::PointType boundingBoxMax = m_BoundingBox->GetMaximum();
//mitk::BoundingBox::PointType boundingBoxCenter = m_BoundingBox->GetCenter();
m_Box->SetXMin( boundingBoxMin[0], boundingBoxMin[1], boundingBoxMin[2] );
m_Box->SetXMax( boundingBoxMax[0], boundingBoxMax[1], boundingBoxMax[2] );
}
else
{
// Plane will not be clipped
m_Box->SetXMin( -10000.0, -10000.0, -10000.0 );
m_Box->SetXMax( 10000.0, 10000.0, 10000.0 );
}
m_Transform->Identity();
m_Transform->Concatenate( input->GetGeometry2D()->GetVtkTransform() );
m_Transform->PreMultiply();
m_Box->SetTransform( m_Transform );
m_PlaneClipper->SetInputConnection(m_VtkTransformPlaneFilter->GetOutputPort() );
m_PlaneClipper->SetClipFunction( m_Box );
m_PlaneClipper->GenerateClippedOutputOff(); // important to NOT generate normals data for clipped part
m_PlaneClipper->InsideOutOn();
m_PlaneClipper->SetValue( 0.0 );
m_PlaneClipper->Update();
planeSurface = m_PlaneClipper->GetOutput();
}
m_NormalsUpdater->SetInputData( planeSurface );
m_NormalsUpdater->AutoOrientNormalsOn(); // that's the trick! Brings consistency between
// normals direction and front/back faces direction (see bug 1440)
m_NormalsUpdater->ComputePointNormalsOn();
m_NormalsUpdater->Update();
output->SetVtkPolyData( m_NormalsUpdater->GetOutput() );
output->CalculateBoundingBox();
}