void mitk::BaseGeometry::_SetSpacing(const mitk::Vector3D& aSpacing, bool enforceSetSpacing){
if(mitk::Equal(m_Spacing, aSpacing) == false || enforceSetSpacing)
{
assert(aSpacing[0]>0 && aSpacing[1]>0 && aSpacing[2]>0);
m_Spacing = aSpacing;
AffineTransform3D::MatrixType::InternalMatrixType vnlmatrix;
vnlmatrix = m_IndexToWorldTransform->GetMatrix().GetVnlMatrix();
mitk::VnlVector col;
col = vnlmatrix.get_column(0); col.normalize(); col*=aSpacing[0]; vnlmatrix.set_column(0, col);
col = vnlmatrix.get_column(1); col.normalize(); col*=aSpacing[1]; vnlmatrix.set_column(1, col);
col = vnlmatrix.get_column(2); col.normalize(); col*=aSpacing[2]; vnlmatrix.set_column(2, col);
Matrix3D matrix;
matrix = vnlmatrix;
AffineTransform3D::Pointer transform = AffineTransform3D::New();
transform->SetMatrix(matrix);
transform->SetOffset(m_IndexToWorldTransform->GetOffset());
SetIndexToWorldTransform(transform.GetPointer());
}
}
void
PlaneGeometry::SetMatrixByVectors( const VnlVector &rightVector,
const VnlVector &downVector, ScalarType thickness )
{
VnlVector normal = vnl_cross_3d(rightVector, downVector);
normal.normalize();
normal *= thickness;
AffineTransform3D::Pointer transform = AffineTransform3D::New();
Matrix3D matrix;
matrix.GetVnlMatrix().set_column(0, rightVector);
matrix.GetVnlMatrix().set_column(1, downVector);
matrix.GetVnlMatrix().set_column(2, normal);
transform->SetMatrix(matrix);
transform->SetOffset(m_IndexToWorldTransform->GetOffset());
SetIndexToWorldTransform(transform);
}
void
PlaneGeometry::SetMatrixByVectors( const VnlVector &rightVector,
const VnlVector &downVector, ScalarType thickness /* = 1.0 */ )
{
VnlVector normal = vnl_cross_3d(rightVector, downVector);
normal.normalize();
normal *= thickness;
// Crossproduct vnl_cross_3d is always righthanded, but that is okay here
// because in this method we create a new IndexToWorldTransform and
// a negative thickness could still make it lefthanded.
AffineTransform3D::Pointer transform = AffineTransform3D::New();
Matrix3D matrix;
matrix.GetVnlMatrix().set_column(0, rightVector);
matrix.GetVnlMatrix().set_column(1, downVector);
matrix.GetVnlMatrix().set_column(2, normal);
transform->SetMatrix(matrix);
transform->SetOffset(this->GetIndexToWorldTransform()->GetOffset());
SetIndexToWorldTransform(transform);
}
void mitk::TimeSlicedGeometry::InitializeEvenlyTimed(mitk::Geometry3D* geometry3D, unsigned int timeSteps)
{
assert(geometry3D!=NULL);
geometry3D->Register();
InitializeEmpty(timeSteps);
AffineTransform3D::Pointer transform = AffineTransform3D::New();
transform->SetMatrix(geometry3D->GetIndexToWorldTransform()->GetMatrix());
transform->SetOffset(geometry3D->GetIndexToWorldTransform()->GetOffset());
SetIndexToWorldTransform(transform);
SetBounds(geometry3D->GetBounds());
SetGeometry3D(geometry3D, 0);
SetEvenlyTimed();
UpdateInformation();
SetFrameOfReferenceID(geometry3D->GetFrameOfReferenceID());
SetImageGeometry(geometry3D->GetImageGeometry());
geometry3D->UnRegister();
}
void mitk::TimeSlicedGeometry::UpdateInformation()
{
if(m_TimeSteps==0) return;
unsigned long maxModifiedTime = 0, curModifiedTime;
mitk::ScalarType stmin, stmax;
stmin= ScalarTypeNumericTraits::NonpositiveMin();
stmax= ScalarTypeNumericTraits::max();
TimeBounds timeBounds;
timeBounds[0]=stmax; timeBounds[1]=stmin;
mitk::BoundingBox::Pointer boundingBox=mitk::BoundingBox::New();
mitk::BoundingBox::PointsContainer::Pointer pointscontainer=mitk::BoundingBox::PointsContainer::New();
unsigned int t;
mitk::Geometry3D* geometry3d;
mitk::BoundingBox::ConstPointer nextBoundingBox;
mitk::BoundingBox::PointIdentifier pointid=0;
// Need to check for zero bounding boxes
mitk::ScalarType zeropoint[]={0,0,0,0,0,0};
BoundingBox::BoundsArrayType itkBoundsZero(zeropoint);
for(t=0; t < m_TimeSteps; ++t)
{
geometry3d = GetGeometry3D(t);
assert(geometry3d!=NULL);
curModifiedTime = geometry3d->GetMTime();
if(maxModifiedTime < curModifiedTime)
maxModifiedTime = curModifiedTime;
const TimeBounds & curTimeBounds = geometry3d->GetTimeBounds();
if((curTimeBounds[0] > stmin) && (curTimeBounds[0] < timeBounds[0]))
timeBounds[0] = curTimeBounds[0];
if((curTimeBounds[1] < stmax) && (curTimeBounds[1] > timeBounds[1]))
timeBounds[1] = curTimeBounds[1];
nextBoundingBox = geometry3d->GetBoundingBox();
assert(nextBoundingBox.IsNotNull());
// Only respect non-zero BBes
if (nextBoundingBox->GetBounds() == itkBoundsZero)
{
continue;
}
const mitk::BoundingBox::PointsContainer * nextPoints = nextBoundingBox->GetPoints();
if(nextPoints!=NULL)
{
mitk::BoundingBox::PointsContainer::ConstIterator pointsIt = nextPoints->Begin();
while (pointsIt != nextPoints->End() )
{
pointscontainer->InsertElement( pointid++, pointsIt->Value());
++pointsIt;
}
}
}
if(!(timeBounds[0] < stmax))
{
timeBounds[0] = stmin;
timeBounds[1] = stmax;
}
m_TimeBounds = timeBounds;
assert(timeBounds[0]<=timeBounds[1]);
boundingBox->SetPoints(pointscontainer);
boundingBox->ComputeBoundingBox();
m_BoundingBox = boundingBox;
SetIndexToWorldTransform(GetGeometry3D(0)->GetIndexToWorldTransform());
if(this->GetMTime() < maxModifiedTime)
Modified();
}