void SliceNavigationController::Update(SliceNavigationController::ViewDirection viewDirection,
bool top,
bool frontside,
bool rotated)
{
TimeGeometry::ConstPointer worldTimeGeometry = m_InputWorldTimeGeometry;
if (m_BlockUpdate || (m_InputWorldTimeGeometry.IsNull() && m_InputWorldGeometry3D.IsNull()) ||
((worldTimeGeometry.IsNotNull()) && (worldTimeGeometry->CountTimeSteps() == 0)))
{
return;
}
m_BlockUpdate = true;
if (m_InputWorldTimeGeometry.IsNotNull() && m_LastUpdateTime < m_InputWorldTimeGeometry->GetMTime())
{
Modified();
}
if (m_InputWorldGeometry3D.IsNotNull() && m_LastUpdateTime < m_InputWorldGeometry3D->GetMTime())
{
Modified();
}
this->SetViewDirection(viewDirection);
this->SetTop(top);
this->SetFrontSide(frontside);
this->SetRotated(rotated);
if (m_LastUpdateTime < GetMTime())
{
m_LastUpdateTime = GetMTime();
// initialize the viewplane
SlicedGeometry3D::Pointer slicedWorldGeometry = SlicedGeometry3D::Pointer();
BaseGeometry::ConstPointer currentGeometry = BaseGeometry::ConstPointer();
if (m_InputWorldTimeGeometry.IsNotNull())
if (m_InputWorldTimeGeometry->IsValidTimeStep(GetTime()->GetPos()))
currentGeometry = m_InputWorldTimeGeometry->GetGeometryForTimeStep(GetTime()->GetPos());
else
currentGeometry = m_InputWorldTimeGeometry->GetGeometryForTimeStep(0);
else
currentGeometry = m_InputWorldGeometry3D;
m_CreatedWorldGeometry = mitk::TimeGeometry::Pointer();
switch (viewDirection)
{
case Original:
if (worldTimeGeometry.IsNotNull())
{
m_CreatedWorldGeometry = worldTimeGeometry->Clone();
worldTimeGeometry = m_CreatedWorldGeometry.GetPointer();
slicedWorldGeometry = dynamic_cast<SlicedGeometry3D *>(
m_CreatedWorldGeometry->GetGeometryForTimeStep(this->GetTime()->GetPos()).GetPointer());
if (slicedWorldGeometry.IsNotNull())
{
break;
}
}
else
{
const SlicedGeometry3D *worldSlicedGeometry =
dynamic_cast<const SlicedGeometry3D *>(currentGeometry.GetPointer());
if ( worldSlicedGeometry != nullptr )
{
slicedWorldGeometry = static_cast<SlicedGeometry3D *>(currentGeometry->Clone().GetPointer());
break;
}
}
slicedWorldGeometry = SlicedGeometry3D::New();
slicedWorldGeometry->InitializePlanes(currentGeometry, PlaneGeometry::None, top, frontside, rotated);
slicedWorldGeometry->SetSliceNavigationController(this);
break;
case Axial:
slicedWorldGeometry = SlicedGeometry3D::New();
slicedWorldGeometry->InitializePlanes(currentGeometry, PlaneGeometry::Axial, top, frontside, rotated);
slicedWorldGeometry->SetSliceNavigationController(this);
break;
case Frontal:
slicedWorldGeometry = SlicedGeometry3D::New();
slicedWorldGeometry->InitializePlanes(currentGeometry, PlaneGeometry::Frontal, top, frontside, rotated);
slicedWorldGeometry->SetSliceNavigationController(this);
break;
case Sagittal:
slicedWorldGeometry = SlicedGeometry3D::New();
slicedWorldGeometry->InitializePlanes(currentGeometry, PlaneGeometry::Sagittal, top, frontside, rotated);
slicedWorldGeometry->SetSliceNavigationController(this);
break;
default:
itkExceptionMacro("unknown ViewDirection");
}
m_Slice->SetPos(0);
m_Slice->SetSteps((int)slicedWorldGeometry->GetSlices());
if ( worldTimeGeometry.IsNull() )
{
auto createdTimeGeometry = ProportionalTimeGeometry::New();
createdTimeGeometry->Initialize( slicedWorldGeometry, 1 );
m_CreatedWorldGeometry = createdTimeGeometry;
m_Time->SetSteps(0);
m_Time->SetPos(0);
m_Time->InvalidateRange();
}
else
{
m_BlockUpdate = true;
m_Time->SetSteps(worldTimeGeometry->CountTimeSteps());
m_Time->SetPos(0);
const TimeBounds &timeBounds = worldTimeGeometry->GetTimeBounds();
m_Time->SetRange(timeBounds[0], timeBounds[1]);
m_BlockUpdate = false;
const auto currentTemporalPosition = this->GetTime()->GetPos();
assert( worldTimeGeometry->GetGeometryForTimeStep( currentTemporalPosition ).IsNotNull() );
if ( dynamic_cast<const mitk::ProportionalTimeGeometry*>( worldTimeGeometry.GetPointer() ) != nullptr )
{
const TimePointType minimumTimePoint =
worldTimeGeometry->TimeStepToTimePoint( currentTemporalPosition );
const TimePointType stepDuration =
worldTimeGeometry->TimeStepToTimePoint( currentTemporalPosition + 1 ) - minimumTimePoint;
auto createdTimeGeometry = ProportionalTimeGeometry::New();
createdTimeGeometry->Initialize( slicedWorldGeometry, worldTimeGeometry->CountTimeSteps() );
createdTimeGeometry->SetFirstTimePoint( minimumTimePoint );
createdTimeGeometry->SetStepDuration( stepDuration );
m_CreatedWorldGeometry = createdTimeGeometry;
}
else
{
auto createdTimeGeometry = mitk::ArbitraryTimeGeometry::New();
const TimeStepType numberOfTimeSteps = worldTimeGeometry->CountTimeSteps();
createdTimeGeometry->ReserveSpaceForGeometries( numberOfTimeSteps );
for ( TimeStepType i = 0; i < numberOfTimeSteps; ++i )
{
const BaseGeometry::Pointer clonedGeometry = slicedWorldGeometry->Clone().GetPointer();
const auto bounds = worldTimeGeometry->GetTimeBounds( i );
createdTimeGeometry->AppendNewTimeStep( clonedGeometry,
bounds[0], bounds[1]);
}
createdTimeGeometry->Update();
m_CreatedWorldGeometry = createdTimeGeometry;
}
}
}
// unblock update; we may do this now, because if m_BlockUpdate was already
// true before this method was entered, then we will never come here.
m_BlockUpdate = false;
// Send the geometry. Do this even if nothing was changed, because maybe
// Update() was only called to re-send the old geometry and time/slice data.
this->SendCreatedWorldGeometry();
this->SendSlice();
this->SendTime();
// Adjust the stepper range of slice stepper according to geometry
this->AdjustSliceStepperRange();
}
void mitk::Image::Initialize(const mitk::PixelType& type, int sDim, const mitk::PlaneGeometry& geometry2d, bool flipped, unsigned int channels, int tDim )
{
SlicedGeometry3D::Pointer slicedGeometry = SlicedGeometry3D::New();
slicedGeometry->InitializeEvenlySpaced(static_cast<PlaneGeometry*>(geometry2d.Clone().GetPointer()), sDim, flipped);
Initialize(type, *slicedGeometry, channels, tDim);
}
void
SliceNavigationController::Update(
SliceNavigationController::ViewDirection viewDirection,
bool top, bool frontside, bool rotated )
{
const TimeSlicedGeometry* worldTimeSlicedGeometry =
dynamic_cast< const TimeSlicedGeometry * >(
m_InputWorldGeometry.GetPointer() );
if( m_BlockUpdate ||
m_InputWorldGeometry.IsNull() ||
( (worldTimeSlicedGeometry != NULL) && (worldTimeSlicedGeometry->GetTimeSteps() == 0) )
)
{
return;
}
m_BlockUpdate = true;
if ( m_LastUpdateTime < m_InputWorldGeometry->GetMTime() )
{
Modified();
}
this->SetViewDirection( viewDirection );
this->SetTop( top );
this->SetFrontSide( frontside );
this->SetRotated( rotated );
if ( m_LastUpdateTime < GetMTime() )
{
m_LastUpdateTime = GetMTime();
// initialize the viewplane
SlicedGeometry3D::Pointer slicedWorldGeometry = NULL;
m_CreatedWorldGeometry = NULL;
switch ( viewDirection )
{
case Original:
if ( worldTimeSlicedGeometry != NULL )
{
m_CreatedWorldGeometry = static_cast< TimeSlicedGeometry * >(
m_InputWorldGeometry->Clone().GetPointer() );
worldTimeSlicedGeometry = m_CreatedWorldGeometry.GetPointer();
slicedWorldGeometry = dynamic_cast< SlicedGeometry3D * >(
m_CreatedWorldGeometry->GetGeometry3D( this->GetTime()->GetPos() ) );
if ( slicedWorldGeometry.IsNotNull() )
{
break;
}
}
else
{
const SlicedGeometry3D *worldSlicedGeometry =
dynamic_cast< const SlicedGeometry3D * >(
m_InputWorldGeometry.GetPointer());
if ( worldSlicedGeometry != NULL )
{
slicedWorldGeometry = static_cast< SlicedGeometry3D * >(
m_InputWorldGeometry->Clone().GetPointer());
break;
}
}
//else: use Transversal: no "break" here!!
case Transversal:
slicedWorldGeometry = SlicedGeometry3D::New();
slicedWorldGeometry->InitializePlanes(
m_InputWorldGeometry, PlaneGeometry::Transversal,
top, frontside, rotated );
slicedWorldGeometry->SetSliceNavigationController( this );
break;
case Frontal:
slicedWorldGeometry = SlicedGeometry3D::New();
slicedWorldGeometry->InitializePlanes( m_InputWorldGeometry,
PlaneGeometry::Frontal, top, frontside, rotated );
slicedWorldGeometry->SetSliceNavigationController( this );
break;
case Sagittal:
slicedWorldGeometry = SlicedGeometry3D::New();
slicedWorldGeometry->InitializePlanes( m_InputWorldGeometry,
PlaneGeometry::Sagittal, top, frontside, rotated );
slicedWorldGeometry->SetSliceNavigationController( this );
break;
default:
itkExceptionMacro("unknown ViewDirection");
}
m_Slice->SetPos( 0 );
m_Slice->SetSteps( (int)slicedWorldGeometry->GetSlices() );
if ( m_CreatedWorldGeometry.IsNull() )
{
// initialize TimeSlicedGeometry
m_CreatedWorldGeometry = TimeSlicedGeometry::New();
}
if ( worldTimeSlicedGeometry == NULL )
{
m_CreatedWorldGeometry->InitializeEvenlyTimed( slicedWorldGeometry, 1 );
m_Time->SetSteps( 0 );
m_Time->SetPos( 0 );
m_Time->InvalidateRange();
}
else
{
m_BlockUpdate = true;
m_Time->SetSteps( worldTimeSlicedGeometry->GetTimeSteps() );
m_Time->SetPos( 0 );
const TimeBounds &timeBounds = worldTimeSlicedGeometry->GetTimeBounds();
m_Time->SetRange( timeBounds[0], timeBounds[1] );
m_BlockUpdate = false;
assert( worldTimeSlicedGeometry->GetGeometry3D( this->GetTime()->GetPos() ) != NULL );
slicedWorldGeometry->SetTimeBounds(
worldTimeSlicedGeometry->GetGeometry3D( this->GetTime()->GetPos() )->GetTimeBounds() );
//@todo implement for non-evenly-timed geometry!
m_CreatedWorldGeometry->InitializeEvenlyTimed(
slicedWorldGeometry, worldTimeSlicedGeometry->GetTimeSteps() );
}
}
// unblock update; we may do this now, because if m_BlockUpdate was already
// true before this method was entered, then we will never come here.
m_BlockUpdate = false;
// Send the geometry. Do this even if nothing was changed, because maybe
// Update() was only called to re-send the old geometry and time/slice data.
this->SendCreatedWorldGeometry();
this->SendSlice();
this->SendTime();
// Adjust the stepper range of slice stepper according to geometry
this->AdjustSliceStepperRange();
}
void mitk::Image::Initialize(const mitk::PixelType& type, unsigned int dimension, const unsigned int *dimensions, unsigned int channels)
{
Clear();
m_Dimension=dimension;
if(!dimensions)
itkExceptionMacro(<< "invalid zero dimension image");
unsigned int i;
for(i=0;i<dimension;++i)
{
if(dimensions[i]<1)
itkExceptionMacro(<< "invalid dimension[" << i << "]: " << dimensions[i]);
}
// create new array since the old was deleted
m_Dimensions = new unsigned int[MAX_IMAGE_DIMENSIONS];
// initialize the first four dimensions to 1, the remaining 4 to 0
FILL_C_ARRAY(m_Dimensions, 4, 1u);
FILL_C_ARRAY((m_Dimensions+4), 4, 0u);
// copy in the passed dimension information
std::memcpy(m_Dimensions, dimensions, sizeof(unsigned int)*m_Dimension);
this->m_ImageDescriptor = mitk::ImageDescriptor::New();
this->m_ImageDescriptor->Initialize( this->m_Dimensions, this->m_Dimension );
for(i=0;i<4;++i)
{
m_LargestPossibleRegion.SetIndex(i, 0);
m_LargestPossibleRegion.SetSize (i, m_Dimensions[i]);
}
m_LargestPossibleRegion.SetIndex(i, 0);
m_LargestPossibleRegion.SetSize(i, channels);
if(m_LargestPossibleRegion.GetNumberOfPixels()==0)
{
delete [] m_Dimensions;
m_Dimensions = nullptr;
return;
}
for( unsigned int i=0u; i<channels; i++)
{
this->m_ImageDescriptor->AddNewChannel( type );
}
PlaneGeometry::Pointer planegeometry = PlaneGeometry::New();
planegeometry->InitializeStandardPlane(m_Dimensions[0], m_Dimensions[1]);
SlicedGeometry3D::Pointer slicedGeometry = SlicedGeometry3D::New();
slicedGeometry->InitializeEvenlySpaced(planegeometry, m_Dimensions[2]);
ProportionalTimeGeometry::Pointer timeGeometry = ProportionalTimeGeometry::New();
timeGeometry->Initialize(slicedGeometry, m_Dimensions[3]);
for (TimeStepType step = 0; step < timeGeometry->CountTimeSteps(); ++step)
{
timeGeometry->GetGeometryForTimeStep(step)->ImageGeometryOn();
}
SetTimeGeometry(timeGeometry);
ImageDataItemPointer dnull=nullptr;
m_Channels.assign(GetNumberOfChannels(), dnull);
m_Volumes.assign(GetNumberOfChannels()*m_Dimensions[3], dnull);
m_Slices.assign(GetNumberOfChannels()*m_Dimensions[3]*m_Dimensions[2], dnull);
ComputeOffsetTable();
Initialize();
m_Initialized = true;
}
mitk::Image::Pointer mitk::PicFileReader::CreateImage()
{
Image::Pointer output = Image::New();
std::string fileName = this->GetLocalFileName();
mitkIpPicDescriptor *header = mitkIpPicGetHeader(const_cast<char *>(fileName.c_str()), NULL);
if (!header)
{
mitkThrow() << "File could not be read.";
}
header = mitkIpPicGetTags(const_cast<char *>(fileName.c_str()), header);
int channels = 1;
mitkIpPicTSV_t *tsv;
if ((tsv = mitkIpPicQueryTag(header, "SOURCE HEADER")) != NULL)
{
if (tsv->n[0] > 1e+06)
{
mitkIpPicTSV_t *tsvSH;
tsvSH = mitkIpPicDelTag(header, "SOURCE HEADER");
mitkIpPicFreeTag(tsvSH);
}
}
if ((tsv = mitkIpPicQueryTag(header, "ICON80x80")) != NULL)
{
mitkIpPicTSV_t *tsvSH;
tsvSH = mitkIpPicDelTag(header, "ICON80x80");
mitkIpPicFreeTag(tsvSH);
}
if ((tsv = mitkIpPicQueryTag(header, "VELOCITY")) != NULL)
{
++channels;
mitkIpPicDelTag(header, "VELOCITY");
}
if (header == NULL || header->bpe == 0)
{
mitkThrow() << " Could not read file " << fileName;
}
// if pic image only 2D, the n[2] value is not initialized
unsigned int slices = 1;
if (header->dim == 2)
{
header->n[2] = slices;
}
// First initialize the geometry of the output image by the pic-header
SlicedGeometry3D::Pointer slicedGeometry = mitk::SlicedGeometry3D::New();
PicHelper::InitializeEvenlySpaced(header, header->n[2], slicedGeometry);
// if pic image only 3D, the n[3] value is not initialized
unsigned int timesteps = 1;
if (header->dim > 3)
{
timesteps = header->n[3];
}
slicedGeometry->ImageGeometryOn();
ProportionalTimeGeometry::Pointer timeGeometry = ProportionalTimeGeometry::New();
timeGeometry->Initialize(slicedGeometry, timesteps);
// Cast the pic descriptor to ImageDescriptor and initialize the output
output->Initialize(CastToImageDescriptor(header));
output->SetTimeGeometry(timeGeometry);
mitkIpPicFree(header);
return output;
}