mitk::Image::Image(const Image &other) : SlicedData(other), m_Dimension(0), m_Dimensions(NULL),
m_ImageDescriptor(NULL), m_OffsetTable(NULL), m_CompleteData(NULL), m_ImageStatistics(NULL)
{
m_Dimensions = new unsigned int[MAX_IMAGE_DIMENSIONS];
FILL_C_ARRAY( m_Dimensions, MAX_IMAGE_DIMENSIONS, 0u);
this->Initialize( other.GetPixelType(), other.GetDimension(), other.GetDimensions());
//Since the above called "Initialize" method doesn't take the geometry into account we need to set it
//here manually
TimeGeometry::Pointer cloned = other.GetTimeGeometry()->Clone();
this->SetTimeGeometry(cloned.GetPointer());
if (this->GetDimension() > 3)
{
const unsigned int time_steps = this->GetDimension(3);
for (unsigned int i = 0u; i < time_steps; ++i)
{
ImageDataItemPointer volume = const_cast<Image&>(other).GetVolumeData(i);
this->SetVolume(volume->GetData(), i);
}
}
else
{
ImageDataItemPointer volume = const_cast<Image&>(other).GetVolumeData(0);
this->SetVolume(volume->GetData(), 0);
}
}
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());
}
else
Superclass::SetGeometry(geometry.GetGeometryForTimeStep(0));
/* //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);
}*/
}
void mitk::SurfaceGLMapper2D::SetDataNode( mitk::DataNode* node )
{
Superclass::SetDataNode( node );
bool useCellData;
if (dynamic_cast<BoolProperty *>(node->GetProperty("deprecated useCellDataForColouring")) == NULL)
useCellData = false;
else
useCellData = dynamic_cast<BoolProperty *>(node->GetProperty("deprecated useCellDataForColouring"))->GetValue();
if (!useCellData)
{
// search min/max point scalars over all time steps
double dataRange[2] = {0,0};
double range[2];
Surface::Pointer input = const_cast< Surface* >(dynamic_cast<const Surface*>( this->GetDataNode()->GetData() ));
if(input.IsNull()) return;
const TimeGeometry::Pointer inputTimeGeometry = input->GetTimeGeometry();
if(( inputTimeGeometry.IsNull() ) || ( inputTimeGeometry->CountTimeSteps() == 0 ) ) return;
for (unsigned int timestep=0; timestep<inputTimeGeometry->CountTimeSteps(); timestep++)
{
vtkPolyData * vtkpolydata = input->GetVtkPolyData( timestep );
if((vtkpolydata==NULL) || (vtkpolydata->GetNumberOfPoints() < 1 )) continue;
vtkDataArray *vpointscalars = vtkpolydata->GetPointData()->GetScalars();
if (vpointscalars) {
vpointscalars->GetRange( range, 0 );
if (dataRange[0]==0 && dataRange[1]==0) {
dataRange[0] = range[0];
dataRange[1] = range[1];
}
else {
if (range[0] < dataRange[0]) dataRange[0] = range[0];
if (range[1] > dataRange[1]) dataRange[1] = range[1];
}
}
}
if (dataRange[1] - dataRange[0] > 0) {
m_LUT->SetTableRange( dataRange );
m_LUT->Build();
}
}
}
std::vector<BaseData::Pointer> ItkImageIO::Read()
{
std::vector<BaseData::Pointer> result;
mitk::LocaleSwitch localeSwitch("C");
Image::Pointer image = Image::New();
const unsigned int MINDIM = 2;
const unsigned int MAXDIM = 4;
const std::string path = this->GetLocalFileName();
MITK_INFO << "loading " << path << " via itk::ImageIOFactory... " << std::endl;
// Check to see if we can read the file given the name or prefix
if (path.empty())
{
mitkThrow() << "Empty filename in mitk::ItkImageIO ";
}
// Got to allocate space for the image. Determine the characteristics of
// the image.
m_ImageIO->SetFileName(path);
m_ImageIO->ReadImageInformation();
unsigned int ndim = m_ImageIO->GetNumberOfDimensions();
if (ndim < MINDIM || ndim > MAXDIM)
{
MITK_WARN << "Sorry, only dimensions 2, 3 and 4 are supported. The given file has " << ndim
<< " dimensions! Reading as 4D.";
ndim = MAXDIM;
}
itk::ImageIORegion ioRegion(ndim);
itk::ImageIORegion::SizeType ioSize = ioRegion.GetSize();
itk::ImageIORegion::IndexType ioStart = ioRegion.GetIndex();
unsigned int dimensions[MAXDIM];
dimensions[0] = 0;
dimensions[1] = 0;
dimensions[2] = 0;
dimensions[3] = 0;
ScalarType spacing[MAXDIM];
spacing[0] = 1.0f;
spacing[1] = 1.0f;
spacing[2] = 1.0f;
spacing[3] = 1.0f;
Point3D origin;
origin.Fill(0);
unsigned int i;
for (i = 0; i < ndim; ++i)
{
ioStart[i] = 0;
ioSize[i] = m_ImageIO->GetDimensions(i);
if (i < MAXDIM)
{
dimensions[i] = m_ImageIO->GetDimensions(i);
spacing[i] = m_ImageIO->GetSpacing(i);
if (spacing[i] <= 0)
spacing[i] = 1.0f;
}
if (i < 3)
{
origin[i] = m_ImageIO->GetOrigin(i);
}
}
ioRegion.SetSize(ioSize);
ioRegion.SetIndex(ioStart);
MITK_INFO << "ioRegion: " << ioRegion << std::endl;
m_ImageIO->SetIORegion(ioRegion);
void *buffer = new unsigned char[m_ImageIO->GetImageSizeInBytes()];
m_ImageIO->Read(buffer);
image->Initialize(MakePixelType(m_ImageIO), ndim, dimensions);
image->SetImportChannel(buffer, 0, Image::ManageMemory);
const itk::MetaDataDictionary &dictionary = m_ImageIO->GetMetaDataDictionary();
// access direction of itk::Image and include spacing
mitk::Matrix3D matrix;
matrix.SetIdentity();
unsigned int j, itkDimMax3 = (ndim >= 3 ? 3 : ndim);
for (i = 0; i < itkDimMax3; ++i)
for (j = 0; j < itkDimMax3; ++j)
matrix[i][j] = m_ImageIO->GetDirection(j)[i];
// re-initialize PlaneGeometry with origin and direction
PlaneGeometry *planeGeometry = image->GetSlicedGeometry(0)->GetPlaneGeometry(0);
planeGeometry->SetOrigin(origin);
planeGeometry->GetIndexToWorldTransform()->SetMatrix(matrix);
// re-initialize SlicedGeometry3D
SlicedGeometry3D *slicedGeometry = image->GetSlicedGeometry(0);
slicedGeometry->InitializeEvenlySpaced(planeGeometry, image->GetDimension(2));
slicedGeometry->SetSpacing(spacing);
MITK_INFO << slicedGeometry->GetCornerPoint(false, false, false);
MITK_INFO << slicedGeometry->GetCornerPoint(true, true, true);
// re-initialize TimeGeometry
TimeGeometry::Pointer timeGeometry;
if (dictionary.HasKey(PROPERTY_NAME_TIMEGEOMETRY_TYPE) || dictionary.HasKey(PROPERTY_KEY_TIMEGEOMETRY_TYPE))
{ // also check for the name because of backwards compatibility. Past code version stored with the name and not with
// the key
itk::MetaDataObject<std::string>::ConstPointer timeGeometryTypeData = nullptr;
if (dictionary.HasKey(PROPERTY_NAME_TIMEGEOMETRY_TYPE))
{
timeGeometryTypeData =
dynamic_cast<const itk::MetaDataObject<std::string> *>(dictionary.Get(PROPERTY_NAME_TIMEGEOMETRY_TYPE));
}
else
{
timeGeometryTypeData =
dynamic_cast<const itk::MetaDataObject<std::string> *>(dictionary.Get(PROPERTY_KEY_TIMEGEOMETRY_TYPE));
}
if (timeGeometryTypeData->GetMetaDataObjectValue() == ArbitraryTimeGeometry::GetStaticNameOfClass())
{
MITK_INFO << "used time geometry: " << ArbitraryTimeGeometry::GetStaticNameOfClass() << std::endl;
typedef std::vector<TimePointType> TimePointVector;
TimePointVector timePoints;
if (dictionary.HasKey(PROPERTY_NAME_TIMEGEOMETRY_TIMEPOINTS))
{
timePoints = ConvertMetaDataObjectToTimePointList(dictionary.Get(PROPERTY_NAME_TIMEGEOMETRY_TIMEPOINTS));
}
else if (dictionary.HasKey(PROPERTY_KEY_TIMEGEOMETRY_TIMEPOINTS))
{
timePoints = ConvertMetaDataObjectToTimePointList(dictionary.Get(PROPERTY_KEY_TIMEGEOMETRY_TIMEPOINTS));
}
if (timePoints.size() - 1 != image->GetDimension(3))
{
MITK_ERROR << "Stored timepoints (" << timePoints.size() - 1 << ") and size of image time dimension ("
<< image->GetDimension(3) << ") do not match. Switch to ProportionalTimeGeometry fallback"
<< std::endl;
}
else
{
ArbitraryTimeGeometry::Pointer arbitraryTimeGeometry = ArbitraryTimeGeometry::New();
TimePointVector::const_iterator pos = timePoints.begin();
TimePointVector::const_iterator prePos = pos++;
for (; pos != timePoints.end(); ++prePos, ++pos)
{
arbitraryTimeGeometry->AppendTimeStepClone(slicedGeometry, *pos, *prePos);
}
timeGeometry = arbitraryTimeGeometry;
}
}
}
if (timeGeometry.IsNull())
{ // Fallback. If no other valid time geometry has been created, create a ProportionalTimeGeometry
MITK_INFO << "used time geometry: " << ProportionalTimeGeometry::GetStaticNameOfClass() << std::endl;
ProportionalTimeGeometry::Pointer propTimeGeometry = ProportionalTimeGeometry::New();
propTimeGeometry->Initialize(slicedGeometry, image->GetDimension(3));
timeGeometry = propTimeGeometry;
}
image->SetTimeGeometry(timeGeometry);
buffer = NULL;
MITK_INFO << "number of image components: " << image->GetPixelType().GetNumberOfComponents() << std::endl;
for (itk::MetaDataDictionary::ConstIterator iter = dictionary.Begin(), iterEnd = dictionary.End(); iter != iterEnd;
++iter)
{
if (iter->second->GetMetaDataObjectTypeInfo() == typeid(std::string))
{
const std::string &key = iter->first;
std::string assumedPropertyName = key;
std::replace(assumedPropertyName.begin(), assumedPropertyName.end(), '_', '.');
std::string mimeTypeName = GetMimeType()->GetName();
// Check if there is already a info for the key and our mime type.
IPropertyPersistence::InfoResultType infoList = mitk::CoreServices::GetPropertyPersistence()->GetInfoByKey(key);
auto predicate = [mimeTypeName](const PropertyPersistenceInfo::ConstPointer &x) {
return x.IsNotNull() && x->GetMimeTypeName() == mimeTypeName;
};
auto finding = std::find_if(infoList.begin(), infoList.end(), predicate);
if (finding == infoList.end())
{
auto predicateWild = [](const PropertyPersistenceInfo::ConstPointer &x) {
return x.IsNotNull() && x->GetMimeTypeName() == PropertyPersistenceInfo::ANY_MIMETYPE_NAME();
};
finding = std::find_if(infoList.begin(), infoList.end(), predicateWild);
}
PropertyPersistenceInfo::ConstPointer info;
if (finding != infoList.end())
{
assumedPropertyName = (*finding)->GetName();
info = *finding;
}
else
{ // we have not found anything suitable so we generate our own info
PropertyPersistenceInfo::Pointer newInfo = PropertyPersistenceInfo::New();
newInfo->SetNameAndKey(assumedPropertyName, key);
newInfo->SetMimeTypeName(PropertyPersistenceInfo::ANY_MIMETYPE_NAME());
info = newInfo;
}
std::string value =
dynamic_cast<itk::MetaDataObject<std::string> *>(iter->second.GetPointer())->GetMetaDataObjectValue();
mitk::BaseProperty::Pointer loadedProp = info->GetDeserializationFunction()(value);
image->SetProperty(assumedPropertyName.c_str(), loadedProp);
// Read properties should be persisted unless they are default properties
// which are written anyway
bool isDefaultKey(false);
for (const auto &defaultKey : m_DefaultMetaDataKeys)
{
if (defaultKey.length() <= assumedPropertyName.length())
{
// does the start match the default key
if (assumedPropertyName.substr(0, defaultKey.length()).find(defaultKey) != std::string::npos)
{
isDefaultKey = true;
break;
}
}
}
if (!isDefaultKey)
{
mitk::CoreServices::GetPropertyPersistence()->AddInfo(info);
}
}
}
MITK_INFO << "...finished!" << std::endl;
result.push_back(image.GetPointer());
return result;
}
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
RenderingManager
::InitializeViews(const TimeGeometry * dataGeometry, RequestType type, bool /*preserveRoughOrientationInWorldSpace*/)
{
MITK_DEBUG << "initializing views";
bool boundingBoxInitialized = false;
TimeGeometry::ConstPointer timeGeometry = dataGeometry;
TimeGeometry::Pointer modifiedGeometry = NULL;
if (dataGeometry != NULL)
{
modifiedGeometry = dataGeometry->Clone();
}
int warningLevel = vtkObject::GetGlobalWarningDisplay();
vtkObject::GlobalWarningDisplayOff();
if ((timeGeometry.IsNotNull()) && (const_cast<mitk::BoundingBox *>(
timeGeometry->GetBoundingBoxInWorld())->GetDiagonalLength2() > mitk::eps))
{
boundingBoxInitialized = true;
}
if (timeGeometry.IsNotNull())
{// make sure bounding box has an extent bigger than zero in any direction
// clone the input geometry
//Old Geometry3D::Pointer modifiedGeometry = dynamic_cast<Geometry3D*>( dataGeometry->Clone().GetPointer() );
assert(modifiedGeometry.IsNotNull());
for (TimeStepType step = 0; step < modifiedGeometry->CountTimeSteps(); ++step)
{
BaseGeometry::BoundsArrayType newBounds = modifiedGeometry->GetGeometryForTimeStep(step)->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;
if( Equal( newBounds[ 2 * dimension ], newBounds[ 2 * dimension + 1 ] ) ) // newBounds will still be equal if values are beyond double precision
{
mitkThrow()<< "One dimension of object data has zero length, please make sure you're not using numbers beyond double precision as coordinates.";
}
}
}
modifiedGeometry->GetGeometryForTimeStep(step)->SetBounds(newBounds);
}
}
timeGeometry = modifiedGeometry;
RenderWindowList::const_iterator it;
for (it = m_RenderWindowList.cbegin(); it != m_RenderWindowList.cend(); ++it)
{
mitk::BaseRenderer *baseRenderer =
mitk::BaseRenderer::GetInstance(it->first);
baseRenderer->SetConstrainZoomingAndPanning(m_ConstrainedPanningZooming);
int id = baseRenderer->GetMapperID();
if (((type == REQUEST_UPDATE_ALL)
|| ((type == REQUEST_UPDATE_2DWINDOWS) && (id == 1))
|| ((type == REQUEST_UPDATE_3DWINDOWS) && (id == 2)))
)
{
this->InternalViewInitialization(baseRenderer, timeGeometry,
boundingBoxInitialized, id);
}
}
if (boundingBoxInitialized)
{
m_TimeNavigationController->SetInputWorldTimeGeometry(timeGeometry);
}
m_TimeNavigationController->Update();
this->RequestUpdateAll(type);
vtkObject::SetGlobalWarningDisplay(warningLevel);
// Inform listeners that views have been initialized
this->InvokeEvent(mitk::RenderingManagerViewsInitializedEvent());
return boundingBoxInitialized;
}