void mitk::AffineImageCropperInteractor::RotateObject (StateMachineAction*, InteractionEvent* interactionEvent)
{
InteractionPositionEvent* positionEvent = dynamic_cast<InteractionPositionEvent*>(interactionEvent);
if(positionEvent == NULL)
return;
Point2D currentPickedDisplayPoint = positionEvent->GetPointerPositionOnScreen();
if(currentPickedDisplayPoint.EuclideanDistanceTo(m_InitialPickedDisplayPoint) < 1)
return;
vtkRenderer* currentVtkRenderer = interactionEvent->GetSender()->GetVtkRenderer();
if ( currentVtkRenderer && currentVtkRenderer->GetActiveCamera())
{
double vpn[3];
currentVtkRenderer->GetActiveCamera()->GetViewPlaneNormal( vpn );
Vector3D rotationAxis;
rotationAxis[0] = vpn[0];
rotationAxis[1] = vpn[1];
rotationAxis[2] = vpn[2];
rotationAxis.Normalize();
Vector2D move = currentPickedDisplayPoint - m_InitialPickedDisplayPoint;
double rotationAngle = -57.3 * atan(move[0]/move[1]);
if(move[1]<0) rotationAngle +=180;
// Use center of data bounding box as center of rotation
Point3D rotationCenter = m_OriginalGeometry->GetCenter();
if(positionEvent->GetSender()->GetMapperID() == BaseRenderer::Standard2D)
rotationCenter = m_InitialPickedPoint;
// Reset current Geometry3D to original state (pre-interaction) and
// apply rotation
RotationOperation op( OpROTATE, rotationCenter, rotationAxis, rotationAngle );
Geometry3D::Pointer newGeometry = static_cast<Geometry3D*>(m_OriginalGeometry->Clone().GetPointer());
newGeometry->ExecuteOperation( &op );
m_SelectedNode->GetData()->SetGeometry(newGeometry);
interactionEvent->GetSender()->GetRenderingManager()->RequestUpdateAll();
}
}
bool ShowSegmentationAsSmoothedSurface::ThreadedUpdateFunction()
{
Image::Pointer image;
GetPointerParameter("Input", image);
float smoothing;
GetParameter("Smoothing", smoothing);
float decimation;
GetParameter("Decimation", decimation);
float closing;
GetParameter("Closing", closing);
int timeNr = 0;
GetParameter("TimeNr", timeNr);
if (image->GetDimension() == 4)
MITK_INFO << "CREATING SMOOTHED POLYGON MODEL (t = " << timeNr << ')';
else
MITK_INFO << "CREATING SMOOTHED POLYGON MODEL";
MITK_INFO << " Smoothing = " << smoothing;
MITK_INFO << " Decimation = " << decimation;
MITK_INFO << " Closing = " << closing;
Geometry3D::Pointer geometry = dynamic_cast<Geometry3D *>(image->GetGeometry()->Clone().GetPointer());
// Make ITK image out of MITK image
typedef itk::Image<unsigned char, 3> CharImageType;
typedef itk::Image<unsigned short, 3> ShortImageType;
typedef itk::Image<float, 3> FloatImageType;
if (image->GetDimension() == 4)
{
ImageTimeSelector::Pointer imageTimeSelector = ImageTimeSelector::New();
imageTimeSelector->SetInput(image);
imageTimeSelector->SetTimeNr(timeNr);
imageTimeSelector->UpdateLargestPossibleRegion();
image = imageTimeSelector->GetOutput(0);
}
ImageToItk<CharImageType>::Pointer imageToItkFilter = ImageToItk<CharImageType>::New();
try
{
imageToItkFilter->SetInput(image);
}
catch (const itk::ExceptionObject &e)
{
// Most probably the input image type is wrong. Binary images are expected to be
// >unsigned< char images.
MITK_ERROR << e.GetDescription() << endl;
return false;
}
imageToItkFilter->Update();
CharImageType::Pointer itkImage = imageToItkFilter->GetOutput();
// Get bounding box and relabel
MITK_INFO << "Extracting VOI...";
int imageLabel = 1;
bool roiFound = false;
CharImageType::IndexType minIndex;
minIndex.Fill(numeric_limits<CharImageType::IndexValueType>::max());
CharImageType::IndexType maxIndex;
maxIndex.Fill(numeric_limits<CharImageType::IndexValueType>::min());
itk::ImageRegionIteratorWithIndex<CharImageType> iter(itkImage, itkImage->GetLargestPossibleRegion());
for (iter.GoToBegin(); !iter.IsAtEnd(); ++iter)
{
if (iter.Get() == imageLabel)
{
roiFound = true;
iter.Set(1);
CharImageType::IndexType currentIndex = iter.GetIndex();
for (unsigned int dim = 0; dim < 3; ++dim)
{
minIndex[dim] = min(currentIndex[dim], minIndex[dim]);
maxIndex[dim] = max(currentIndex[dim], maxIndex[dim]);
}
}
else
{
iter.Set(0);
}
}
if (!roiFound)
{
ProgressBar::GetInstance()->Progress(8);
MITK_ERROR << "Didn't found segmentation labeled with " << imageLabel << "!" << endl;
return false;
}
ProgressBar::GetInstance()->Progress(1);
// Extract and pad bounding box
typedef itk::RegionOfInterestImageFilter<CharImageType, CharImageType> ROIFilterType;
ROIFilterType::Pointer roiFilter = ROIFilterType::New();
CharImageType::RegionType region;
CharImageType::SizeType size;
for (unsigned int dim = 0; dim < 3; ++dim)
{
size[dim] = maxIndex[dim] - minIndex[dim] + 1;
}
region.SetIndex(minIndex);
region.SetSize(size);
roiFilter->SetInput(itkImage);
roiFilter->SetRegionOfInterest(region);
roiFilter->ReleaseDataFlagOn();
roiFilter->ReleaseDataBeforeUpdateFlagOn();
typedef itk::ConstantPadImageFilter<CharImageType, CharImageType> PadFilterType;
PadFilterType::Pointer padFilter = PadFilterType::New();
const PadFilterType::SizeValueType pad[3] = { 10, 10, 10 };
padFilter->SetInput(roiFilter->GetOutput());
padFilter->SetConstant(0);
padFilter->SetPadLowerBound(pad);
padFilter->SetPadUpperBound(pad);
padFilter->ReleaseDataFlagOn();
padFilter->ReleaseDataBeforeUpdateFlagOn();
padFilter->Update();
CharImageType::Pointer roiImage = padFilter->GetOutput();
roiImage->DisconnectPipeline();
roiFilter = nullptr;
padFilter = nullptr;
// Correct origin of real geometry (changed by cropping and padding)
typedef Geometry3D::TransformType TransformType;
TransformType::Pointer transform = TransformType::New();
TransformType::OutputVectorType translation;
for (unsigned int dim = 0; dim < 3; ++dim)
translation[dim] = (int)minIndex[dim] - (int)pad[dim];
transform->SetIdentity();
transform->Translate(translation);
geometry->Compose(transform, true);
ProgressBar::GetInstance()->Progress(1);
// Median
MITK_INFO << "Median...";
typedef itk::BinaryMedianImageFilter<CharImageType, CharImageType> MedianFilterType;
MedianFilterType::Pointer medianFilter = MedianFilterType::New();
CharImageType::SizeType radius = { 0 };
medianFilter->SetRadius(radius);
medianFilter->SetBackgroundValue(0);
medianFilter->SetForegroundValue(1);
medianFilter->SetInput(roiImage);
medianFilter->ReleaseDataFlagOn();
medianFilter->ReleaseDataBeforeUpdateFlagOn();
medianFilter->Update();
ProgressBar::GetInstance()->Progress(1);
// Intelligent closing
MITK_INFO << "Intelligent closing...";
unsigned int surfaceRatio = (unsigned int)((1.0f - closing) * 100.0f);
typedef itk::IntelligentBinaryClosingFilter<CharImageType, ShortImageType> ClosingFilterType;
ClosingFilterType::Pointer closingFilter = ClosingFilterType::New();
closingFilter->SetInput(medianFilter->GetOutput());
closingFilter->ReleaseDataFlagOn();
closingFilter->ReleaseDataBeforeUpdateFlagOn();
closingFilter->SetSurfaceRatio(surfaceRatio);
closingFilter->Update();
ShortImageType::Pointer closedImage = closingFilter->GetOutput();
closedImage->DisconnectPipeline();
roiImage = nullptr;
medianFilter = nullptr;
closingFilter = nullptr;
ProgressBar::GetInstance()->Progress(1);
// Gaussian blur
MITK_INFO << "Gauss...";
typedef itk::BinaryThresholdImageFilter<ShortImageType, FloatImageType> BinaryThresholdToFloatFilterType;
BinaryThresholdToFloatFilterType::Pointer binThresToFloatFilter = BinaryThresholdToFloatFilterType::New();
binThresToFloatFilter->SetInput(closedImage);
binThresToFloatFilter->SetLowerThreshold(1);
binThresToFloatFilter->SetUpperThreshold(1);
binThresToFloatFilter->SetInsideValue(100);
binThresToFloatFilter->SetOutsideValue(0);
binThresToFloatFilter->ReleaseDataFlagOn();
binThresToFloatFilter->ReleaseDataBeforeUpdateFlagOn();
typedef itk::DiscreteGaussianImageFilter<FloatImageType, FloatImageType> GaussianFilterType;
// From the following line on, IntelliSense (VS 2008) is broken. Any idea how to fix it?
GaussianFilterType::Pointer gaussFilter = GaussianFilterType::New();
gaussFilter->SetInput(binThresToFloatFilter->GetOutput());
gaussFilter->SetUseImageSpacing(true);
gaussFilter->SetVariance(smoothing);
gaussFilter->ReleaseDataFlagOn();
gaussFilter->ReleaseDataBeforeUpdateFlagOn();
typedef itk::BinaryThresholdImageFilter<FloatImageType, CharImageType> BinaryThresholdFromFloatFilterType;
BinaryThresholdFromFloatFilterType::Pointer binThresFromFloatFilter = BinaryThresholdFromFloatFilterType::New();
binThresFromFloatFilter->SetInput(gaussFilter->GetOutput());
binThresFromFloatFilter->SetLowerThreshold(50);
binThresFromFloatFilter->SetUpperThreshold(255);
binThresFromFloatFilter->SetInsideValue(1);
binThresFromFloatFilter->SetOutsideValue(0);
binThresFromFloatFilter->ReleaseDataFlagOn();
binThresFromFloatFilter->ReleaseDataBeforeUpdateFlagOn();
binThresFromFloatFilter->Update();
CharImageType::Pointer blurredImage = binThresFromFloatFilter->GetOutput();
blurredImage->DisconnectPipeline();
closedImage = nullptr;
binThresToFloatFilter = nullptr;
gaussFilter = nullptr;
ProgressBar::GetInstance()->Progress(1);
// Fill holes
MITK_INFO << "Filling cavities...";
typedef itk::ConnectedThresholdImageFilter<CharImageType, CharImageType> ConnectedThresholdFilterType;
ConnectedThresholdFilterType::Pointer connectedThresFilter = ConnectedThresholdFilterType::New();
CharImageType::IndexType corner;
corner[0] = 0;
corner[1] = 0;
corner[2] = 0;
connectedThresFilter->SetInput(blurredImage);
connectedThresFilter->SetSeed(corner);
connectedThresFilter->SetLower(0);
connectedThresFilter->SetUpper(0);
connectedThresFilter->SetReplaceValue(2);
connectedThresFilter->ReleaseDataFlagOn();
connectedThresFilter->ReleaseDataBeforeUpdateFlagOn();
typedef itk::BinaryThresholdImageFilter<CharImageType, CharImageType> BinaryThresholdFilterType;
BinaryThresholdFilterType::Pointer binThresFilter = BinaryThresholdFilterType::New();
binThresFilter->SetInput(connectedThresFilter->GetOutput());
binThresFilter->SetLowerThreshold(0);
binThresFilter->SetUpperThreshold(0);
binThresFilter->SetInsideValue(50);
binThresFilter->SetOutsideValue(0);
binThresFilter->ReleaseDataFlagOn();
binThresFilter->ReleaseDataBeforeUpdateFlagOn();
typedef itk::AddImageFilter<CharImageType, CharImageType, CharImageType> AddFilterType;
AddFilterType::Pointer addFilter = AddFilterType::New();
addFilter->SetInput1(blurredImage);
addFilter->SetInput2(binThresFilter->GetOutput());
addFilter->ReleaseDataFlagOn();
addFilter->ReleaseDataBeforeUpdateFlagOn();
addFilter->Update();
ProgressBar::GetInstance()->Progress(1);
// Surface extraction
MITK_INFO << "Surface extraction...";
Image::Pointer filteredImage = Image::New();
CastToMitkImage(addFilter->GetOutput(), filteredImage);
filteredImage->SetGeometry(geometry);
ImageToSurfaceFilter::Pointer imageToSurfaceFilter = ImageToSurfaceFilter::New();
imageToSurfaceFilter->SetInput(filteredImage);
imageToSurfaceFilter->SetThreshold(50);
imageToSurfaceFilter->SmoothOn();
imageToSurfaceFilter->SetDecimate(ImageToSurfaceFilter::NoDecimation);
m_Surface = imageToSurfaceFilter->GetOutput(0);
ProgressBar::GetInstance()->Progress(1);
// Mesh decimation
if (decimation > 0.0f && decimation < 1.0f)
{
MITK_INFO << "Quadric mesh decimation...";
vtkQuadricDecimation *quadricDecimation = vtkQuadricDecimation::New();
quadricDecimation->SetInputData(m_Surface->GetVtkPolyData());
quadricDecimation->SetTargetReduction(decimation);
quadricDecimation->AttributeErrorMetricOn();
quadricDecimation->GlobalWarningDisplayOff();
quadricDecimation->Update();
vtkCleanPolyData* cleaner = vtkCleanPolyData::New();
cleaner->SetInputConnection(quadricDecimation->GetOutputPort());
cleaner->PieceInvariantOn();
cleaner->ConvertLinesToPointsOn();
cleaner->ConvertStripsToPolysOn();
cleaner->PointMergingOn();
cleaner->Update();
m_Surface->SetVtkPolyData(cleaner->GetOutput());
}
ProgressBar::GetInstance()->Progress(1);
// Compute Normals
vtkPolyDataNormals* computeNormals = vtkPolyDataNormals::New();
computeNormals->SetInputData(m_Surface->GetVtkPolyData());
computeNormals->SetFeatureAngle(360.0f);
computeNormals->FlipNormalsOff();
computeNormals->Update();
m_Surface->SetVtkPolyData(computeNormals->GetOutput());
return true;
}
mitk::ProportionalTimeGeometry::Pointer mitk::ProportionalTimeGeometryToXML::FromXML(TiXmlElement *timeGeometryElement)
{
if (!timeGeometryElement)
{
MITK_ERROR << "Cannot deserialize ProportionalTimeGeometry from nullptr.";
return nullptr;
}
int numberOfTimeSteps = 0;
if (TIXML_SUCCESS != timeGeometryElement->QueryIntAttribute("NumberOfTimeSteps", &numberOfTimeSteps))
{
MITK_WARN << "<ProportionalTimeGeometry> found without NumberOfTimeSteps attribute. Counting...";
}
// might be missing!
TimePointType firstTimePoint;
std::string firstTimePoint_s;
TimePointType stepDuration;
std::string stepDuration_s;
try
{
if (TIXML_SUCCESS == timeGeometryElement->QueryStringAttribute("FirstTimePoint", &firstTimePoint_s))
{
firstTimePoint = boost::lexical_cast<double>(firstTimePoint_s);
}
else
{
firstTimePoint = -std::numeric_limits<TimePointType>::max();
}
if (TIXML_SUCCESS == timeGeometryElement->QueryStringAttribute("StepDuration", &stepDuration_s))
{
stepDuration = boost::lexical_cast<double>(stepDuration_s);
}
else
{
stepDuration = std::numeric_limits<TimePointType>::infinity();
}
}
catch (boost::bad_lexical_cast &e)
{
MITK_ERROR << "Could not parse string as number: " << e.what();
return nullptr;
}
// list of all geometries with their time steps
std::multimap<TimeStepType, BaseGeometry::Pointer> allReadGeometries;
int indexForUnlabeledTimeStep(-1);
for (TiXmlElement *currentElement = timeGeometryElement->FirstChildElement(); currentElement != nullptr;
currentElement = currentElement->NextSiblingElement())
{
// different geometries could have been inside a ProportionalTimeGeometry.
// By now, we only support Geometry3D
std::string tagName = currentElement->Value();
if (tagName == "Geometry3D")
{
Geometry3D::Pointer restoredGeometry = Geometry3DToXML::FromXML(currentElement);
if (restoredGeometry.IsNotNull())
{
int timeStep(-1);
if (TIXML_SUCCESS != currentElement->QueryIntAttribute("TimeStep", &timeStep))
{
timeStep = indexForUnlabeledTimeStep--; // decrement index for next one
MITK_WARN << "Found <Geometry3D> without 'TimeStep' attribute in <ProportionalTimeGeometry>. No guarantees "
"on order anymore.";
}
if (allReadGeometries.count(static_cast<TimeStepType>(timeStep)) > 0)
{
MITK_WARN << "Found <Geometry3D> tags with identical 'TimeStep' attribute in <ProportionalTimeGeometry>. No "
"guarantees on order anymore.";
}
allReadGeometries.insert(std::make_pair(static_cast<TimeStepType>(timeStep), restoredGeometry.GetPointer()));
}
}
else
{
MITK_WARN << "Found unsupported tag <" << tagName << "> inside <ProportionalTimeGeometry>. Ignoring.";
}
}
// now add all BaseGeometries that were read to a new instance
// of ProportionalTimeGeometry
ProportionalTimeGeometry::Pointer newTimeGeometry = ProportionalTimeGeometry::New();
newTimeGeometry->SetFirstTimePoint(firstTimePoint);
newTimeGeometry->SetStepDuration(stepDuration);
newTimeGeometry->ReserveSpaceForGeometries(allReadGeometries.size());
TimeStepType t(0);
for (auto entry : allReadGeometries)
{
// We add items with newly assigned time steps.
// This avoids great confusion when a file contains
// bogus numbers.
newTimeGeometry->SetTimeStepGeometry(entry.second, t++);
}
// Need to re-calculate global bounding box.
// This is neither stored in a file, nor done by SetTimeStepGeometry
newTimeGeometry->UpdateBoundingBox();
return newTimeGeometry;
}
std::vector<itk::SmartPointer<mitk::BaseData>> mitk::GeometryDataReaderService::Read()
{
// Switch the current locale to "C"
LocaleSwitch localeSwitch("C");
std::vector<itk::SmartPointer<BaseData>> result;
InputStream stream(this);
TiXmlDocument doc;
stream >> doc;
if (!doc.Error())
{
TiXmlHandle docHandle(&doc);
for (TiXmlElement *geomDataElement = docHandle.FirstChildElement("GeometryData").ToElement();
geomDataElement != nullptr;
geomDataElement = geomDataElement->NextSiblingElement())
{
for (TiXmlElement *currentElement = geomDataElement->FirstChildElement(); currentElement != nullptr;
currentElement = currentElement->NextSiblingElement())
{
// different geometries could have been serialized from a GeometryData
// object:
std::string tagName = currentElement->Value();
if (tagName == "Geometry3D")
{
Geometry3D::Pointer restoredGeometry = Geometry3DToXML::FromXML(currentElement);
if (restoredGeometry.IsNotNull())
{
GeometryData::Pointer newGeometryData = GeometryData::New();
newGeometryData->SetGeometry(restoredGeometry);
result.push_back(newGeometryData.GetPointer());
}
else
{
MITK_ERROR << "Invalid <Geometry3D> tag encountered. Skipping.";
}
}
else if (tagName == "ProportionalTimeGeometry")
{
ProportionalTimeGeometry::Pointer restoredTimeGeometry =
ProportionalTimeGeometryToXML::FromXML(currentElement);
if (restoredTimeGeometry.IsNotNull())
{
GeometryData::Pointer newGeometryData = GeometryData::New();
newGeometryData->SetTimeGeometry(restoredTimeGeometry);
result.push_back(newGeometryData.GetPointer());
}
else
{
MITK_ERROR << "Invalid <ProportionalTimeGeometry> tag encountered. Skipping.";
}
}
} // for child of <GeometryData>
} // for <GeometryData>
}
else
{
mitkThrow() << "Parsing error at line " << doc.ErrorRow() << ", col " << doc.ErrorCol() << ": " << doc.ErrorDesc();
}
if (result.empty())
{
mitkThrow() << "Did not read a single GeometryData object from input.";
}
return result;
}
bool
RenderingManager
::InitializeViews( const Geometry3D * dataGeometry, RequestType type, bool preserveRoughOrientationInWorldSpace )
{
MITK_DEBUG << "initializing views";
bool boundingBoxInitialized = false;
Geometry3D::ConstPointer geometry = dataGeometry;
if (dataGeometry && preserveRoughOrientationInWorldSpace)
{
// clone the input geometry
Geometry3D::Pointer modifiedGeometry = dynamic_cast<Geometry3D*>( dataGeometry->Clone().GetPointer() );
assert(modifiedGeometry.IsNotNull());
// construct an affine transform from it
AffineGeometryFrame3D::TransformType::Pointer transform = AffineGeometryFrame3D::TransformType::New();
assert( modifiedGeometry->GetIndexToWorldTransform() );
transform->SetMatrix( modifiedGeometry->GetIndexToWorldTransform()->GetMatrix() );
transform->SetOffset( modifiedGeometry->GetIndexToWorldTransform()->GetOffset() );
// get transform matrix
AffineGeometryFrame3D::TransformType::MatrixType::InternalMatrixType& oldMatrix =
const_cast< AffineGeometryFrame3D::TransformType::MatrixType::InternalMatrixType& > ( transform->GetMatrix().GetVnlMatrix() );
AffineGeometryFrame3D::TransformType::MatrixType::InternalMatrixType newMatrix(oldMatrix);
// get offset and bound
Vector3D offset = modifiedGeometry->GetIndexToWorldTransform()->GetOffset();
Geometry3D::BoundsArrayType oldBounds = modifiedGeometry->GetBounds();
Geometry3D::BoundsArrayType newBounds = modifiedGeometry->GetBounds();
// get rid of rotation other than pi/2 degree
for ( unsigned int i = 0; i < 3; ++i )
{
// i-th column of the direction matrix
Vector3D currentVector;
currentVector[0] = oldMatrix(0,i);
currentVector[1] = oldMatrix(1,i);
currentVector[2] = oldMatrix(2,i);
// matchingRow will store the row that holds the biggest
// value in the column
unsigned int matchingRow = 0;
// maximum value in the column
float max = std::numeric_limits<float>::min();
// sign of the maximum value (-1 or 1)
int sign = 1;
// iterate through the column vector
for (unsigned int dim = 0; dim < 3; ++dim)
{
if ( fabs(currentVector[dim]) > max )
{
matchingRow = dim;
max = fabs(currentVector[dim]);
if(currentVector[dim]<0)
sign = -1;
else
sign = 1;
}
}
// in case we found a negative maximum,
// we negate the column and adjust the offset
// (in order to run through the dimension in the opposite direction)
if(sign == -1)
{
currentVector *= sign;
offset += modifiedGeometry->GetAxisVector(i);
}
// matchingRow is now used as column index to place currentVector
// correctly in the new matrix
vnl_vector<ScalarType> newMatrixColumn(3);
newMatrixColumn[0] = currentVector[0];
newMatrixColumn[1] = currentVector[1];
newMatrixColumn[2] = currentVector[2];
newMatrix.set_column( matchingRow, newMatrixColumn );
// if a column is moved, we also have to adjust the bounding
// box accordingly, this is done here
newBounds[2*matchingRow ] = oldBounds[2*i ];
newBounds[2*matchingRow+1] = oldBounds[2*i+1];
}
// set the newly calculated bounds array
modifiedGeometry->SetBounds(newBounds);
// set new offset and direction matrix
AffineGeometryFrame3D::TransformType::MatrixType newMatrixITK( newMatrix );
transform->SetMatrix( newMatrixITK );
transform->SetOffset( offset );
modifiedGeometry->SetIndexToWorldTransform( transform );
geometry = modifiedGeometry;
}
int warningLevel = vtkObject::GetGlobalWarningDisplay();
vtkObject::GlobalWarningDisplayOff();
if ( (geometry.IsNotNull() ) && (const_cast< mitk::BoundingBox * >(
geometry->GetBoundingBox())->GetDiagonalLength2() > mitk::eps) )
{
boundingBoxInitialized = true;
}
if (geometry.IsNotNull() )
{ // make sure bounding box has an extent bigger than zero in any direction
// clone the input geometry
Geometry3D::Pointer modifiedGeometry = dynamic_cast<Geometry3D*>( dataGeometry->Clone().GetPointer() );
assert(modifiedGeometry.IsNotNull());
Geometry3D::BoundsArrayType newBounds = modifiedGeometry->GetBounds();
for( unsigned int dimension = 0; ( 2 * dimension ) < newBounds.Size() ; dimension++ )
{
//check for equality but for an epsilon
if( Equal( newBounds[ 2 * dimension ], newBounds[ 2 * dimension + 1 ] ) )
{
newBounds[ 2 * dimension + 1 ] += 1;
}
}
// set the newly calculated bounds array
modifiedGeometry->SetBounds(newBounds);
geometry = modifiedGeometry;
}
RenderWindowList::iterator it;
for ( it = m_RenderWindowList.begin(); it != m_RenderWindowList.end(); ++it )
{
mitk::BaseRenderer *baseRenderer =
mitk::BaseRenderer::GetInstance( it->first );
baseRenderer->GetDisplayGeometry()->SetConstrainZoomingAndPanning(m_ConstrainedPaddingZooming);
int id = baseRenderer->GetMapperID();
if ( ((type == REQUEST_UPDATE_ALL)
|| ((type == REQUEST_UPDATE_2DWINDOWS) && (id == 1))
|| ((type == REQUEST_UPDATE_3DWINDOWS) && (id == 2)))
)
{
this->InternalViewInitialization( baseRenderer, geometry,
boundingBoxInitialized, id );
}
}
if ( m_TimeNavigationController != NULL )
{
if ( boundingBoxInitialized )
{
m_TimeNavigationController->SetInputWorldGeometry( geometry );
}
m_TimeNavigationController->Update();
}
this->RequestUpdateAll( type );
vtkObject::SetGlobalWarningDisplay( warningLevel );
// Inform listeners that views have been initialized
this->InvokeEvent( mitk::RenderingManagerViewsInitializedEvent() );
return boundingBoxInitialized;
}
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< Geometry3D * >(
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 );
Geometry3D::Pointer newGeometry = static_cast< Geometry3D * >(
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;
}
std::vector<itk::SmartPointer<mitk::BaseData>> mitk::PointSetReaderService::Read()
{
// Switch the current locale to "C"
LocaleSwitch localeSwitch("C");
std::vector<itk::SmartPointer<mitk::BaseData>> result;
InputStream stream(this);
TiXmlDocument doc;
stream >> doc;
if (!doc.Error())
{
TiXmlHandle docHandle(&doc);
// unsigned int pointSetCounter(0);
for (TiXmlElement *currentPointSetElement =
docHandle.FirstChildElement("point_set_file").FirstChildElement("point_set").ToElement();
currentPointSetElement != NULL;
currentPointSetElement = currentPointSetElement->NextSiblingElement())
{
mitk::PointSet::Pointer newPointSet = mitk::PointSet::New();
// time geometry assembled for addition after all points
// else the SetPoint method would already transform the points that we provide it
mitk::ProportionalTimeGeometry::Pointer timeGeometry = mitk::ProportionalTimeGeometry::New();
if (currentPointSetElement->FirstChildElement("time_series") != NULL)
{
for (TiXmlElement *currentTimeSeries = currentPointSetElement->FirstChildElement("time_series")->ToElement();
currentTimeSeries != NULL;
currentTimeSeries = currentTimeSeries->NextSiblingElement())
{
unsigned int currentTimeStep(0);
TiXmlElement *currentTimeSeriesID = currentTimeSeries->FirstChildElement("time_series_id");
currentTimeStep = atoi(currentTimeSeriesID->GetText());
timeGeometry->Expand(currentTimeStep + 1); // expand (default to identity) in any case
TiXmlElement *geometryElem = currentTimeSeries->FirstChildElement("Geometry3D");
if (geometryElem)
{
Geometry3D::Pointer geometry = Geometry3DToXML::FromXML(geometryElem);
if (geometry.IsNotNull())
{
timeGeometry->SetTimeStepGeometry(geometry, currentTimeStep);
}
else
{
MITK_ERROR << "Could not deserialize Geometry3D element.";
}
}
else
{
MITK_WARN << "Fallback to legacy behavior: defining PointSet geometry as identity";
}
newPointSet = this->ReadPoints(newPointSet, currentTimeSeries, currentTimeStep);
}
}
else
{
newPointSet = this->ReadPoints(newPointSet, currentPointSetElement, 0);
}
newPointSet->SetTimeGeometry(timeGeometry);
result.push_back(newPointSet.GetPointer());
}
}
else
{
mitkThrow() << "Parsing error at line " << doc.ErrorRow() << ", col " << doc.ErrorCol() << ": " << doc.ErrorDesc();
}
return result;
}
mitk::BaseGeometry::Pointer mitk::PointSetReaderService::ReadGeometry(TiXmlElement *parentElement)
{
TiXmlElement *geometryElem = parentElement->FirstChildElement("geometry3d");
if (!geometryElem)
return nullptr;
// data to generate
AffineTransform3D::MatrixType matrix;
AffineTransform3D::OffsetType offset;
bool isImageGeometry(false);
unsigned int frameOfReferenceID(0);
BaseGeometry::BoundsArrayType bounds;
bool somethingMissing(false);
// find data in xml structure
TiXmlElement *imageGeometryElem = geometryElem->FirstChildElement("image_geometry");
if (imageGeometryElem)
{
std::string igs = imageGeometryElem->GetText();
isImageGeometry = igs == "true" || igs == "TRUE" || igs == "1";
}
else
somethingMissing = true;
TiXmlElement *frameOfReferenceElem = geometryElem->FirstChildElement("frame_of_reference_id");
if (frameOfReferenceElem)
{
frameOfReferenceID = atoi(frameOfReferenceElem->GetText());
}
else
somethingMissing = true;
TiXmlElement *indexToWorldElem = geometryElem->FirstChildElement("index_to_world");
if (indexToWorldElem)
{
TiXmlElement *matrixElem = indexToWorldElem->FirstChildElement("matrix3x3");
TiXmlElement *offsetElem = indexToWorldElem->FirstChildElement("offset");
if (indexToWorldElem && offsetElem)
{
TiXmlElement *col0 = matrixElem->FirstChildElement("column_0");
TiXmlElement *col1 = matrixElem->FirstChildElement("column_1");
TiXmlElement *col2 = matrixElem->FirstChildElement("column_2");
if (col0 && col1 && col2)
{
somethingMissing |= TIXML_SUCCESS != col0->QueryDoubleAttribute("x", &matrix[0][0]);
somethingMissing |= TIXML_SUCCESS != col0->QueryDoubleAttribute("y", &matrix[1][0]);
somethingMissing |= TIXML_SUCCESS != col0->QueryDoubleAttribute("z", &matrix[2][0]);
somethingMissing |= TIXML_SUCCESS != col1->QueryDoubleAttribute("x", &matrix[0][1]);
somethingMissing |= TIXML_SUCCESS != col1->QueryDoubleAttribute("y", &matrix[1][1]);
somethingMissing |= TIXML_SUCCESS != col1->QueryDoubleAttribute("z", &matrix[2][1]);
somethingMissing |= TIXML_SUCCESS != col2->QueryDoubleAttribute("x", &matrix[0][2]);
somethingMissing |= TIXML_SUCCESS != col2->QueryDoubleAttribute("y", &matrix[1][2]);
somethingMissing |= TIXML_SUCCESS != col2->QueryDoubleAttribute("z", &matrix[2][2]);
}
else
somethingMissing = true;
somethingMissing |= TIXML_SUCCESS != offsetElem->QueryDoubleAttribute("x", &offset[0]);
somethingMissing |= TIXML_SUCCESS != offsetElem->QueryDoubleAttribute("y", &offset[1]);
somethingMissing |= TIXML_SUCCESS != offsetElem->QueryDoubleAttribute("z", &offset[2]);
}
else
somethingMissing = true;
TiXmlElement *boundsElem = geometryElem->FirstChildElement("bounds");
if (boundsElem)
{
TiXmlElement *minBoundsElem = boundsElem->FirstChildElement("min");
TiXmlElement *maxBoundsElem = boundsElem->FirstChildElement("max");
if (minBoundsElem && maxBoundsElem)
{
somethingMissing |= TIXML_SUCCESS != minBoundsElem->QueryDoubleAttribute("x", &bounds[0]);
somethingMissing |= TIXML_SUCCESS != minBoundsElem->QueryDoubleAttribute("y", &bounds[2]);
somethingMissing |= TIXML_SUCCESS != minBoundsElem->QueryDoubleAttribute("z", &bounds[4]);
somethingMissing |= TIXML_SUCCESS != maxBoundsElem->QueryDoubleAttribute("x", &bounds[1]);
somethingMissing |= TIXML_SUCCESS != maxBoundsElem->QueryDoubleAttribute("y", &bounds[3]);
somethingMissing |= TIXML_SUCCESS != maxBoundsElem->QueryDoubleAttribute("z", &bounds[5]);
}
else
somethingMissing = true;
}
else
somethingMissing = true;
}
else
somethingMissing = true;
if (somethingMissing)
{
MITK_ERROR << "XML structure of geometry inside a PointSet file broken. Refusing to build Geometry3D";
return nullptr;
}
else
{
Geometry3D::Pointer g = Geometry3D::New();
g->SetImageGeometry(isImageGeometry);
g->SetFrameOfReferenceID(frameOfReferenceID);
g->SetBounds(bounds);
AffineTransform3D::Pointer transform = AffineTransform3D::New();
transform->SetMatrix(matrix);
transform->SetOffset(offset);
g->SetIndexToWorldTransform(transform);
return g.GetPointer();
}
}
void mitk::AffineBaseDataInteractor3D::RotateObject (StateMachineAction*, InteractionEvent* interactionEvent)
{
InteractionPositionEvent* positionEvent = dynamic_cast<InteractionPositionEvent*>(interactionEvent);
if(positionEvent == NULL)
return;
Point2D currentPickedDisplayPoint = positionEvent->GetPointerPositionOnScreen();
Point3D currentWorldPoint = positionEvent->GetPositionInWorld();
vtkCamera* camera = NULL;
vtkRenderer* currentVtkRenderer = NULL;
if ((interactionEvent->GetSender()) != NULL)
{
camera = interactionEvent->GetSender()->GetVtkRenderer()->GetActiveCamera();
currentVtkRenderer = interactionEvent->GetSender()->GetVtkRenderer();
}
if ( camera && currentVtkRenderer)
{
double vpn[3];
camera->GetViewPlaneNormal( vpn );
Vector3D viewPlaneNormal;
viewPlaneNormal[0] = vpn[0];
viewPlaneNormal[1] = vpn[1];
viewPlaneNormal[2] = vpn[2];
Vector3D interactionMove;
interactionMove[0] = currentWorldPoint[0] - m_InitialPickedWorldPoint[0];
interactionMove[1] = currentWorldPoint[1] - m_InitialPickedWorldPoint[1];
interactionMove[2] = currentWorldPoint[2] - m_InitialPickedWorldPoint[2];
if (interactionMove[0] == 0 && interactionMove[1] == 0 && interactionMove[2] == 0)
return;
Vector3D rotationAxis = itk::CrossProduct(viewPlaneNormal, interactionMove);
rotationAxis.Normalize();
int* size = currentVtkRenderer->GetSize();
double l2 =
(currentPickedDisplayPoint[0] - m_InitialPickedDisplayPoint[0]) *
(currentPickedDisplayPoint[0] - m_InitialPickedDisplayPoint[0]) +
(currentPickedDisplayPoint[1] - m_InitialPickedDisplayPoint[1]) *
(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();
int timeStep = 0;
if ((interactionEvent->GetSender()) != NULL)
timeStep = interactionEvent->GetSender()->GetTimeStep(this->GetDataNode()->GetData());
// Reset current Geometry3D to original state (pre-interaction) and
// apply rotation
RotationOperation op( OpROTATE, rotationCenter, rotationAxis, rotationAngle );
Geometry3D::Pointer newGeometry = static_cast<Geometry3D*>(m_OriginalGeometry->Clone().GetPointer());
newGeometry->ExecuteOperation( &op );
mitk::TimeGeometry::Pointer timeGeometry = this->GetDataNode()->GetData()->GetTimeGeometry();
if (timeGeometry.IsNotNull())
timeGeometry->SetTimeStepGeometry(newGeometry, timeStep);
interactionEvent->GetSender()->GetRenderingManager()->RequestUpdateAll();
}
}
bool mitk::SurfaceDeformationDataInteractor3D::ColorizeSurface(vtkPolyData* polyData, int timeStep, const Point3D &pickedPoint, int mode, double scalar)
{
if (polyData == NULL)
return false;
vtkPoints* points = polyData->GetPoints();
vtkPointData* pointData = polyData->GetPointData();
if ( pointData == NULL )
return false;
vtkDataArray* scalars = pointData->GetScalars();
if (scalars == NULL)
return false;
if (mode == COLORIZATION_GAUSS)
{
// Get picked point and transform into local coordinates
Point3D localPickedPoint;
Geometry3D::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 (unsigned int 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 (unsigned int i = 0; i < pointData->GetNumberOfTuples(); ++i)
{
scalars->SetComponent(i, 0, scalar);
}
}
polyData->Modified();
pointData->Update();
return true;
}
bool mitk::SurfaceDeformationDataInteractor3D::DeformObject (StateMachineAction*, InteractionEvent* interactionEvent)
{
const InteractionPositionEvent* positionEvent = dynamic_cast<const InteractionPositionEvent*>(interactionEvent);
if(positionEvent == NULL)
return false;
int timeStep = interactionEvent->GetSender()->GetTimeStep(this->GetDataNode()->GetData());
vtkPolyData* polyData = m_Surface->GetVtkPolyData(timeStep);
Geometry3D::Pointer geometry = this->GetDataNode()->GetData()->GetGeometry(timeStep);
Point3D currentPickedPoint = positionEvent->GetPositionInWorld();
// Calculate mouse move in 3D space
Vector3D interactionMove;
interactionMove[0] = currentPickedPoint[0] - m_InitialPickedPoint[0];
interactionMove[1] = currentPickedPoint[1] - m_InitialPickedPoint[1];
interactionMove[2] = currentPickedPoint[2] - m_InitialPickedPoint[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 (unsigned int 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();
return true;
}
mitk::Geometry3D::Pointer mitk::Geometry3DToXML::FromXML( TiXmlElement* geometryElement )
{
if (!geometryElement)
{
MITK_ERROR << "Cannot deserialize Geometry3D from nullptr.";
return nullptr;
}
AffineTransform3D::MatrixType matrix;
AffineTransform3D::OffsetType offset;
bool isImageGeometry(false);
unsigned int frameOfReferenceID(0);
BaseGeometry::BoundsArrayType bounds;
if ( TIXML_SUCCESS != geometryElement->QueryUnsignedAttribute("FrameOfReferenceID", &frameOfReferenceID) )
{
MITK_WARN << "Missing FrameOfReference for Geometry3D.";
}
if ( TIXML_SUCCESS != geometryElement->QueryBoolAttribute("ImageGeometry", &isImageGeometry) )
{
MITK_WARN << "Missing bool ImageGeometry for Geometry3D.";
}
// matrix
if ( TiXmlElement* matrixElem = geometryElement->FirstChildElement("IndexToWorld")->ToElement() )
{
bool matrixComplete = true;
for ( unsigned int r = 0; r < 3; ++r )
{
for ( unsigned int c = 0; c < 3; ++c )
{
std::stringstream element_namer;
element_namer << "m_" << r << "_" << c;
std::string string_value;
if (TIXML_SUCCESS == matrixElem->QueryStringAttribute(element_namer.str().c_str(),
&string_value))
{
try
{
matrix[r][c] = boost::lexical_cast<double>(string_value);
}
catch (boost::bad_lexical_cast& e)
{
MITK_ERROR << "Could not parse '" << string_value << "' as number: " << e.what();
return nullptr;
}
}
else
{
matrixComplete = false;
}
}
}
if ( !matrixComplete )
{
MITK_ERROR << "Could not parse all Geometry3D matrix coefficients!";
return nullptr;
}
} else
{
MITK_ERROR << "Parse error: expected Matrix3x3 child below Geometry3D node";
return nullptr;
}
// offset
if ( TiXmlElement* offsetElem = geometryElement->FirstChildElement("Offset")->ToElement() )
{
bool vectorComplete = true;
std::string offset_string[3];
vectorComplete &= TIXML_SUCCESS == offsetElem->QueryStringAttribute("x", &offset_string[0]);
vectorComplete &= TIXML_SUCCESS == offsetElem->QueryStringAttribute("y", &offset_string[1]);
vectorComplete &= TIXML_SUCCESS == offsetElem->QueryStringAttribute("z", &offset_string[2]);
if ( !vectorComplete )
{
MITK_ERROR << "Could not parse complete Geometry3D offset!";
return nullptr;
}
for ( unsigned int d = 0; d < 3; ++d )
try
{
offset[d] = boost::lexical_cast<double>(offset_string[d]);
}
catch ( boost::bad_lexical_cast& e )
{
MITK_ERROR << "Could not parse '" << offset_string[d] << "' as number: " << e.what();
return nullptr;
}
}
else
{
MITK_ERROR << "Parse error: expected Offset3D child below Geometry3D node";
return nullptr;
}
// bounds
if ( TiXmlElement* boundsElem = geometryElement->FirstChildElement("Bounds")->ToElement() )
{
bool vectorsComplete(true);
std::string bounds_string[6];
if ( TiXmlElement* minElem = boundsElem->FirstChildElement("Min")->ToElement() )
{
vectorsComplete &= TIXML_SUCCESS == minElem->QueryStringAttribute("x", &bounds_string[0]);
vectorsComplete &= TIXML_SUCCESS == minElem->QueryStringAttribute("y", &bounds_string[2]);
vectorsComplete &= TIXML_SUCCESS == minElem->QueryStringAttribute("z", &bounds_string[4]);
} else
{
vectorsComplete = false;
}
if ( TiXmlElement* maxElem = boundsElem->FirstChildElement("Max")->ToElement() )
{
vectorsComplete &= TIXML_SUCCESS == maxElem->QueryStringAttribute("x", &bounds_string[1]);
vectorsComplete &= TIXML_SUCCESS == maxElem->QueryStringAttribute("y", &bounds_string[3]);
vectorsComplete &= TIXML_SUCCESS == maxElem->QueryStringAttribute("z", &bounds_string[5]);
} else
{
vectorsComplete = false;
}
if ( !vectorsComplete )
{
MITK_ERROR << "Could not parse complete Geometry3D bounds!";
return nullptr;
}
for (unsigned int d = 0; d < 6; ++d)
try
{
bounds[d] = boost::lexical_cast<double>(bounds_string[d]);
}
catch (boost::bad_lexical_cast& e)
{
MITK_ERROR << "Could not parse '" << bounds_string[d] << "' as number: " << e.what();
return nullptr;
}
}
// build GeometryData from matrix/offset
AffineTransform3D::Pointer newTransform = AffineTransform3D::New();
newTransform->SetMatrix(matrix);
newTransform->SetOffset(offset);
Geometry3D::Pointer newGeometry = Geometry3D::New();
newGeometry->SetFrameOfReferenceID(frameOfReferenceID);
newGeometry->SetImageGeometry(isImageGeometry);
newGeometry->SetIndexToWorldTransform(newTransform);
newGeometry->SetBounds(bounds);
return newGeometry;
}
