bool mitk::AffineDataInteractor3D::ColorizeSurface(BaseRenderer::Pointer renderer, double scalar)
{
BaseData::Pointer data = this->GetDataNode()->GetData();
if(data.IsNull())
{
MITK_ERROR << "AffineInteractor3D: No data object present!";
return false;
}
// Get the timestep to also support 3D+t
int timeStep = 0;
if (renderer.IsNotNull())
timeStep = renderer->GetTimeStep(data);
// If data is an mitk::Surface, extract it
Surface::Pointer surface = dynamic_cast< Surface* >(data.GetPointer());
vtkPolyData* polyData = NULL;
if (surface.IsNotNull())
polyData = surface->GetVtkPolyData(timeStep);
if (polyData == NULL)
{
MITK_ERROR << "AffineInteractor3D: No poly data present!";
return false;
}
vtkPointData* pointData = polyData->GetPointData();
if (pointData == NULL)
{
MITK_ERROR << "AffineInteractor3D: No point data present!";
return false;
}
vtkDataArray* scalars = pointData->GetScalars();
if (scalars == NULL)
{
MITK_ERROR << "AffineInteractor3D: No scalars for point data present!";
return false;
}
for (unsigned int i = 0; i < pointData->GetNumberOfTuples(); ++i)
{
scalars->SetComponent(i, 0, scalar);
}
polyData->Modified();
pointData->Update();
return true;
}
bool mitk::SceneReaderV1::DecorateBaseDataWithProperties(BaseData::Pointer data, TiXmlElement *baseDataNodeElem, const std::string &workingDir)
{
// check given variables, initialize error variable
assert(baseDataNodeElem);
bool error(false);
// get the file name stored in the <properties ...> tag
const char* baseDataPropertyFile( baseDataNodeElem->Attribute("file") );
// check if the filename was found
if(baseDataPropertyFile)
{
//PropertyList::Pointer dataPropList = data->GetPropertyList();
PropertyListDeserializer::Pointer propertyDeserializer = PropertyListDeserializer::New();
// initialize the property reader
propertyDeserializer->SetFilename(workingDir + Poco::Path::separator() + baseDataPropertyFile);
bool ioSuccess = propertyDeserializer->Deserialize();
error = !ioSuccess;
// get the output
PropertyList::Pointer inProperties = propertyDeserializer->GetOutput();
// store the read-in properties to the given node or throw error otherwise
if( inProperties.IsNotNull() )
{
data->SetPropertyList( inProperties );
}
else
{
MITK_ERROR << "The property deserializer did not return a (valid) property list.";
error = true;
}
}
else
{
MITK_ERROR << "Function DecorateBaseDataWithProperties(...) called with false TiXmlElement. \n \t ->Given element does not contain a 'file' attribute. \n";
error = true;
}
return !error;
}
void mitk::PlanarFigureInteractor::AddPoint(StateMachineAction*, InteractionEvent* interactionEvent)
{
const mitk::InteractionPositionEvent* positionEvent = dynamic_cast<mitk::InteractionPositionEvent*>( interactionEvent );
if ( positionEvent == nullptr )
return;
const DataNode::Pointer node = this->GetDataNode();
const BaseData::Pointer data = node->GetData();
/*
* Added check for "initiallyplaced" due to bug 13097:
*
* There are two possible cases in which a point can be inserted into a PlanarPolygon:
*
* 1. The figure is currently drawn -> the point will be appended at the end of the figure
* 2. A point is inserted at a userdefined position after the initial placement of the figure is finished
*
* In the second case we need to determine the proper insertion index. In the first case the index always has
* to be -1 so that the point is appended to the end.
*
* These changes are necessary because of a mac os x specific issue: If a users draws a PlanarPolygon then the
* next point to be added moves according to the mouse position. If then the user left clicks in order to add
* a point one would assume the last move position is identical to the left click position. This is actually the
* case for windows and linux but somehow NOT for mac. Because of the insertion logic of a new point in the
* PlanarFigure then for mac the wrong current selected point is determined.
*
* With this check here this problem can be avoided. However a redesign of the insertion logic should be considered
*/
bool isFigureFinished = false;
data->GetPropertyList()->GetBoolProperty("initiallyplaced", isFigureFinished);
bool selected = false;
bool isEditable = true;
node->GetBoolProperty("selected", selected);
node->GetBoolProperty("planarfigure.iseditable", isEditable);
if ( !selected || !isEditable )
{
return;
}
mitk::PlanarFigure *planarFigure = dynamic_cast<mitk::PlanarFigure *>(data.GetPointer());
// We can't derive a new control point from a polyline of a Bezier curve
// as all control points contribute to each polyline point.
if (dynamic_cast<PlanarBezierCurve*>(planarFigure) != nullptr && isFigureFinished)
return;
const mitk::PlaneGeometry *planarFigureGeometry = planarFigure->GetPlaneGeometry();
const mitk::AbstractTransformGeometry *abstractTransformGeometry =
dynamic_cast< AbstractTransformGeometry * >( planarFigure->GetGeometry( 0 ) );
if ( abstractTransformGeometry != nullptr)
return;
// If the planarFigure already has reached the maximum number
if ( planarFigure->GetNumberOfControlPoints() >= planarFigure->GetMaximumNumberOfControlPoints() )
{
return;
}
// Extract point in 2D world coordinates (relative to PlaneGeometry of
// PlanarFigure)
Point2D point2D, projectedPoint;
if ( !this->TransformPositionEventToPoint2D( positionEvent, planarFigureGeometry, point2D ) )
{
return;
}
// TODO: check segment of polyline we clicked in
int nextIndex = -1;
// We only need to check which position to insert the control point
// when interacting with a PlanarPolygon. For all other types
// new control points will always be appended
const mitk::BaseRenderer *renderer = interactionEvent->GetSender();
const PlaneGeometry *projectionPlane = renderer->GetCurrentWorldPlaneGeometry();
if (dynamic_cast<mitk::PlanarPolygon*>(planarFigure) && isFigureFinished)
{
nextIndex = this->IsPositionOverFigure(
positionEvent,
planarFigure,
planarFigureGeometry,
projectionPlane,
projectedPoint
);
}
// Add point as new control point
if ( planarFigure->IsPreviewControlPointVisible() )
{
point2D = planarFigure->GetPreviewControlPoint();
}
planarFigure->AddControlPoint( point2D, planarFigure->GetControlPointForPolylinePoint( nextIndex, 0 ) );
if ( planarFigure->IsPreviewControlPointVisible() )
{
planarFigure->SelectControlPoint( nextIndex );
planarFigure->ResetPreviewContolPoint();
}
// Re-evaluate features
planarFigure->EvaluateFeatures();
//this->LogPrintPlanarFigureQuantities( planarFigure );
// Update rendered scene
renderer->GetRenderingManager()->RequestUpdateAll();
}
std::vector<itk::SmartPointer<BaseData> > BaseDICOMReaderService::Read()
{
std::vector<BaseData::Pointer> result;
//special handling of Philips 3D US DICOM.
//Copied from DICOMSeriesReaderService
std::string fileName = this->GetLocalFileName();
if (DicomSeriesReader::IsPhilips3DDicom(fileName))
{
MITK_INFO << "it is a Philips3D US Dicom file" << std::endl;
mitk::LocaleSwitch localeSwitch("C");
std::locale previousCppLocale(std::cin.getloc());
std::locale l("C");
std::cin.imbue(l);
DataNode::Pointer node = DataNode::New();
mitk::DicomSeriesReader::StringContainer stringvec;
stringvec.push_back(fileName);
if (DicomSeriesReader::LoadDicomSeries(stringvec, *node))
{
BaseData::Pointer data = node->GetData();
StringProperty::Pointer nameProp = StringProperty::New(itksys::SystemTools::GetFilenameName(fileName));
data->GetPropertyList()->SetProperty("name", nameProp);
result.push_back(data);
}
std::cin.imbue(previousCppLocale);
return result;
}
//Normal DICOM handling (It wasn't a Philips 3D US)
mitk::StringList relevantFiles = this->GetRelevantFiles();
mitk::DICOMFileReader::Pointer reader = this->GetReader(relevantFiles);
reader->SetAdditionalTagsOfInterest(mitk::GetCurrentDICOMTagsOfInterest());
reader->SetTagLookupTableToPropertyFunctor(mitk::GetDICOMPropertyForDICOMValuesFunctor);
reader->SetInputFiles(relevantFiles);
reader->AnalyzeInputFiles();
reader->LoadImages();
for (unsigned int i = 0; i < reader->GetNumberOfOutputs(); ++i)
{
const mitk::DICOMImageBlockDescriptor& desc = reader->GetOutput(i);
mitk::BaseData::Pointer data = desc.GetMitkImage().GetPointer();
std::string nodeName = "Unnamed_DICOM";
std::string studyDescription = desc.GetPropertyAsString("studyDescription");
std::string seriesDescription = desc.GetPropertyAsString("seriesDescription");
if (!studyDescription.empty())
{
nodeName = studyDescription;
}
if (!seriesDescription.empty())
{
if (!studyDescription.empty())
{
nodeName += "/";
}
nodeName += seriesDescription;
}
StringProperty::Pointer nameProp = StringProperty::New(nodeName);
data->SetProperty("name", nameProp);
result.push_back(data);
}
return result;
}