diff --git a/Core/Code/DataManagement/mitkImage.cpp b/Core/Code/DataManagement/mitkImage.cpp index b1f2121bce..54344b60ed 100644 --- a/Core/Code/DataManagement/mitkImage.cpp +++ b/Core/Code/DataManagement/mitkImage.cpp @@ -1,1435 +1,1439 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkImage.h" #include "mitkHistogramGenerator.h" #include "mitkPicHelper.h" #include "mitkImageTimeSelector.h" #include "ipFunc/mitkIpFunc.h" #include "mitkIpPicTypeMultiplex.h" #include #include template class MITK_CORE_EXPORT itk::SmartPointerForwardReference; mitk::Image::Image() : m_Dimension(0), m_Dimensions(NULL), m_OffsetTable(NULL), m_CompleteData(NULL), m_PixelType(NULL), m_TimeSelectorForExtremaObject(NULL) { m_CountOfMinValuedVoxels.resize(1, 0); m_CountOfMaxValuedVoxels.resize(1, 0); m_ScalarMin.resize(1, itk::NumericTraits::max()); m_ScalarMax.resize(1, itk::NumericTraits::NonpositiveMin()); m_Scalar2ndMin.resize(1, itk::NumericTraits::max()); m_Scalar2ndMax.resize(1, itk::NumericTraits::NonpositiveMin()); m_Initialized = false; mitk::HistogramGenerator::Pointer generator = mitk::HistogramGenerator::New(); m_HistogramGeneratorObject = generator; } mitk::Image::~Image() { Clear(); m_ReferenceCountLock.Lock(); m_ReferenceCount = 3; m_ReferenceCountLock.Unlock(); m_HistogramGeneratorObject = NULL; m_TimeSelectorForExtremaObject = NULL; m_ReferenceCountLock.Lock(); m_ReferenceCount = 0; m_ReferenceCountLock.Unlock(); delete [] m_OffsetTable; } const mitk::PixelType& mitk::Image::GetPixelType(int /*n*/) const { return m_PixelType; } unsigned int mitk::Image::GetDimension() const { return m_Dimension; } unsigned int mitk::Image::GetDimension(int i) const { if((i>=0) && (i<(int)m_Dimension)) return m_Dimensions[i]; return 1; } void* mitk::Image::GetData() { if(m_Initialized==false) { if(GetSource()==NULL) return NULL; if(GetSource()->Updating()==false) GetSource()->UpdateOutputInformation(); } m_CompleteData=GetChannelData(); return m_CompleteData->GetData(); } template void AccessPixel(mitkIpPicDescriptor* pic, const mitk::Index3D& p, double& value, int timestep) { if ( (p[0]>=0 && p[1] >=0 && p[2]>=0 && timestep>=0) && (unsigned int)p[0] < pic->n[0] && (unsigned int)p[1] < pic->n[1] && (unsigned int)p[2] < pic->n[2] && (unsigned int)timestep < pic->n[3] ) { if(pic->bpe!=24) { value = (double) (((T*) pic->data)[ p[0] + p[1]*pic->n[0] + p[2]*pic->n[0]*pic->n[1] + timestep*pic->n[0]*pic->n[1]*pic->n[2] ]); } else { double returnvalue = (((T*) pic->data)[p[0]*3 + 0 + p[1]*pic->n[0]*3 + p[2]*pic->n[0]*pic->n[1]*3 + timestep*pic->n[0]*pic->n[1]*pic->n[2]*3 ]); returnvalue += (((T*) pic->data)[p[0]*3 + 1 + p[1]*pic->n[0]*3 + p[2]*pic->n[0]*pic->n[1]*3 + timestep*pic->n[0]*pic->n[1]*pic->n[2]*3]); returnvalue += (((T*) pic->data)[p[0]*3 + 2 + p[1]*pic->n[0]*3 + p[2]*pic->n[0]*pic->n[1]*3 + timestep*pic->n[0]*pic->n[1]*pic->n[2]*3]); value = returnvalue; } } else { value = 0; } }; double mitk::Image::GetPixelValueByIndex(const mitk::Index3D &position, unsigned int timestep) { mitkIpPicDescriptor* pic = this->GetPic(); double value = 0; if (this->GetTimeSteps() < timestep) { timestep = this->GetTimeSteps(); } mitkIpPicTypeMultiplex3(AccessPixel, pic, position, value, timestep); return value; } double mitk::Image::GetPixelValueByWorldCoordinate(const mitk::Point3D& position, unsigned int timestep) { mitkIpPicDescriptor* pic = this->GetPic(); double value = 0; if (this->GetTimeSteps() < timestep) { timestep = this->GetTimeSteps(); } Index3D itkIndex; this->GetGeometry()->WorldToIndex(position,itkIndex); mitkIpPicTypeMultiplex3(AccessPixel, pic, itkIndex, value, timestep); return value; } vtkImageData* mitk::Image::GetVtkImageData(int t, int n) { if(m_Initialized==false) { if(GetSource()==NULL) return NULL; if(GetSource()->Updating()==false) GetSource()->UpdateOutputInformation(); } ImageDataItemPointer volume=GetVolumeData(t, n); if(volume.GetPointer()==NULL || volume->GetVtkImageData() == NULL) return NULL; #if ((VTK_MAJOR_VERSION > 4) || ((VTK_MAJOR_VERSION==4) && (VTK_MINOR_VERSION>=4) )) float *fspacing = const_cast(GetSlicedGeometry(t)->GetFloatSpacing()); double dspacing[3] = {fspacing[0],fspacing[1],fspacing[2]}; volume->GetVtkImageData()->SetSpacing( dspacing ); #else volume->GetVtkImageData()->SetSpacing(const_cast(GetSlicedGeometry(t)->GetFloatSpacing())); #endif return volume->GetVtkImageData(); } mitkIpPicDescriptor* mitk::Image::GetPic() { if(m_Initialized==false) { if(GetSource()==NULL) return NULL; if(GetSource()->Updating()==false) GetSource()->UpdateOutputInformation(); } m_CompleteData=GetChannelData(); if(m_CompleteData.GetPointer()==NULL) return NULL; return m_CompleteData->GetPicDescriptor(); } mitk::Image::ImageDataItemPointer mitk::Image::GetSliceData(int s, int t, int n, void *data, ImportMemoryManagementType importMemoryManagement) { if(IsValidSlice(s,t,n)==false) return NULL; // slice directly available? int pos=GetSliceIndex(s,t,n); if(m_Slices[pos].GetPointer()!=NULL) return m_Slices[pos]; // is slice available as part of a volume that is available? ImageDataItemPointer sl, ch, vol; vol=m_Volumes[GetVolumeIndex(t,n)]; if((vol.GetPointer()!=NULL) && (vol->IsComplete())) { sl=new ImageDataItem(*vol, 2, data, importMemoryManagement == ManageMemory, ((size_t) s)*m_OffsetTable[2]*(m_PixelType.GetBpe()/8)); sl->SetComplete(true); return m_Slices[pos]=sl; } // is slice available as part of a channel that is available? ch=m_Channels[n]; if((ch.GetPointer()!=NULL) && (ch->IsComplete())) { sl=new ImageDataItem(*ch, 2, data, importMemoryManagement == ManageMemory, (((size_t) s)*m_OffsetTable[2]+((size_t) t)*m_OffsetTable[3])*(m_PixelType.GetBpe()/8)); sl->SetComplete(true); return m_Slices[pos]=sl; } // slice is unavailable. Can we calculate it? if((GetSource()!=NULL) && (GetSource()->Updating()==false)) { // ... wir mussen rechnen!!! .... m_RequestedRegion.SetIndex(0, 0); m_RequestedRegion.SetIndex(1, 0); m_RequestedRegion.SetIndex(2, s); m_RequestedRegion.SetIndex(3, t); m_RequestedRegion.SetIndex(4, n); m_RequestedRegion.SetSize(0, m_Dimensions[0]); m_RequestedRegion.SetSize(1, m_Dimensions[1]); m_RequestedRegion.SetSize(2, 1); m_RequestedRegion.SetSize(3, 1); m_RequestedRegion.SetSize(4, 1); m_RequestedRegionInitialized=true; GetSource()->Update(); if(IsSliceSet(s,t,n)) //yes: now we can call ourselves without the risk of a endless loop (see "if" above) return GetSliceData(s,t,n,data,importMemoryManagement); else return NULL; } else { ImageDataItemPointer item = AllocateSliceData(s,t,n,data,importMemoryManagement); item->SetComplete(true); return item; } } mitk::Image::ImageDataItemPointer mitk::Image::GetVolumeData(int t, int n, void *data, ImportMemoryManagementType importMemoryManagement) { if(IsValidVolume(t,n)==false) return NULL; ImageDataItemPointer ch, vol; // volume directly available? int pos=GetVolumeIndex(t,n); vol=m_Volumes[pos]; if((vol.GetPointer()!=NULL) && (vol->IsComplete())) return vol; // is volume available as part of a channel that is available? ch=m_Channels[n]; if((ch.GetPointer()!=NULL) && (ch->IsComplete())) { vol=new ImageDataItem(*ch, 3, data, importMemoryManagement == ManageMemory, (((size_t) t)*m_OffsetTable[3])*(m_PixelType.GetBpe()/8)); vol->SetComplete(true); return m_Volumes[pos]=vol; } // let's see if all slices of the volume are set, so that we can (could) combine them to a volume bool complete=true; unsigned int s; for(s=0;sSetComplete(true); } else { vol=m_Volumes[pos]; // ok, let's combine the slices! if(vol.GetPointer()==NULL) vol=new ImageDataItem(m_PixelType, 3, m_Dimensions, NULL, true); vol->SetComplete(true); size_t size=m_OffsetTable[2]*(m_PixelType.GetBpe()/8); for(s=0;sGetParent()!=vol) { // copy data of slices in volume size_t offset = ((size_t) s)*size; std::memcpy(static_cast(vol->GetData())+offset, sl->GetData(), size); mitkIpPicDescriptor * pic = sl->GetPicDescriptor(); // replace old slice with reference to volume sl=new ImageDataItem(*vol, 2, data, importMemoryManagement == ManageMemory, ((size_t) s)*size); sl->SetComplete(true); mitkIpFuncCopyTags(sl->GetPicDescriptor(), pic); m_Slices[posSl]=sl; } } if(vol->GetPicDescriptor()->info->tags_head==NULL) mitkIpFuncCopyTags(vol->GetPicDescriptor(), m_Slices[GetSliceIndex(0,t,n)]->GetPicDescriptor()); } return m_Volumes[pos]=vol; } // volume is unavailable. Can we calculate it? if((GetSource()!=NULL) && (GetSource()->Updating()==false)) { // ... wir muessen rechnen!!! .... m_RequestedRegion.SetIndex(0, 0); m_RequestedRegion.SetIndex(1, 0); m_RequestedRegion.SetIndex(2, 0); m_RequestedRegion.SetIndex(3, t); m_RequestedRegion.SetIndex(4, n); m_RequestedRegion.SetSize(0, m_Dimensions[0]); m_RequestedRegion.SetSize(1, m_Dimensions[1]); m_RequestedRegion.SetSize(2, m_Dimensions[2]); m_RequestedRegion.SetSize(3, 1); m_RequestedRegion.SetSize(4, 1); m_RequestedRegionInitialized=true; GetSource()->Update(); if(IsVolumeSet(t,n)) //yes: now we can call ourselves without the risk of a endless loop (see "if" above) return GetVolumeData(t,n,data,importMemoryManagement); else return NULL; } else { ImageDataItemPointer item = AllocateVolumeData(t,n,data,importMemoryManagement); item->SetComplete(true); return item; } } mitk::Image::ImageDataItemPointer mitk::Image::GetChannelData(int n, void *data, ImportMemoryManagementType importMemoryManagement) { if(IsValidChannel(n)==false) return NULL; ImageDataItemPointer ch, vol; ch=m_Channels[n]; if((ch.GetPointer()!=NULL) && (ch->IsComplete())) return ch; // let's see if all volumes are set, so that we can (could) combine them to a channel if(IsChannelSet(n)) { // if there is only one time frame we do not need to combine anything if(m_Dimensions[3]<=1) { vol=GetVolumeData(0,n,data,importMemoryManagement); ch=new ImageDataItem(*vol, 3, data, importMemoryManagement == ManageMemory); ch->SetComplete(true); } else { ch=m_Channels[n]; // ok, let's combine the volumes! if(ch.GetPointer()==NULL) ch=new ImageDataItem(m_PixelType, m_Dimension, m_Dimensions, NULL, true); ch->SetComplete(true); size_t size=m_OffsetTable[m_Dimension-1]*(m_PixelType.GetBpe()/8); unsigned int t; ImageDataItemPointerArray::iterator slicesIt = m_Slices.begin()+n*m_Dimensions[2]*m_Dimensions[3]; for(t=0;tGetParent()!=ch) { // copy data of volume in channel size_t offset = ((size_t) t)*m_OffsetTable[3]*(m_PixelType.GetBpe()/8); std::memcpy(static_cast(ch->GetData())+offset, vol->GetData(), size); mitkIpPicDescriptor * pic = vol->GetPicDescriptor(); // replace old volume with reference to channel vol=new ImageDataItem(*ch, 3, data, importMemoryManagement == ManageMemory, offset); vol->SetComplete(true); mitkIpFuncCopyTags(vol->GetPicDescriptor(), pic); m_Volumes[posVol]=vol; // get rid of slices - they may point to old volume ImageDataItemPointer dnull=NULL; for(unsigned int i = 0; i < m_Dimensions[2]; ++i, ++slicesIt) { assert(slicesIt != m_Slices.end()); *slicesIt = dnull; } } } if(ch->GetPicDescriptor()->info->tags_head==NULL) mitkIpFuncCopyTags(ch->GetPicDescriptor(), m_Volumes[GetVolumeIndex(0,n)]->GetPicDescriptor()); } return m_Channels[n]=ch; } // channel is unavailable. Can we calculate it? if((GetSource()!=NULL) && (GetSource()->Updating()==false)) { // ... wir muessen rechnen!!! .... m_RequestedRegion.SetIndex(0, 0); m_RequestedRegion.SetIndex(1, 0); m_RequestedRegion.SetIndex(2, 0); m_RequestedRegion.SetIndex(3, 0); m_RequestedRegion.SetIndex(4, n); m_RequestedRegion.SetSize(0, m_Dimensions[0]); m_RequestedRegion.SetSize(1, m_Dimensions[1]); m_RequestedRegion.SetSize(2, m_Dimensions[2]); m_RequestedRegion.SetSize(3, m_Dimensions[3]); m_RequestedRegion.SetSize(4, 1); m_RequestedRegionInitialized=true; GetSource()->Update(); // did it work? if(IsChannelSet(n)) //yes: now we can call ourselves without the risk of a endless loop (see "if" above) return GetChannelData(n,data,importMemoryManagement); else return NULL; } else { ImageDataItemPointer item = AllocateChannelData(n,data,importMemoryManagement); item->SetComplete(true); return item; } } bool mitk::Image::IsSliceSet(int s, int t, int n) const { if(IsValidSlice(s,t,n)==false) return false; if(m_Slices[GetSliceIndex(s,t,n)].GetPointer()!=NULL) return true; ImageDataItemPointer ch, vol; vol=m_Volumes[GetVolumeIndex(t,n)]; if((vol.GetPointer()!=NULL) && (vol->IsComplete())) return true; ch=m_Channels[n]; if((ch.GetPointer()!=NULL) && (ch->IsComplete())) return true; return false; } bool mitk::Image::IsVolumeSet(int t, int n) const { if(IsValidVolume(t,n)==false) return false; ImageDataItemPointer ch, vol; // volume directly available? vol=m_Volumes[GetVolumeIndex(t,n)]; if((vol.GetPointer()!=NULL) && (vol->IsComplete())) return true; // is volume available as part of a channel that is available? ch=m_Channels[n]; if((ch.GetPointer()!=NULL) && (ch->IsComplete())) return true; // let's see if all slices of the volume are set, so that we can (could) combine them to a volume unsigned int s; for(s=0;sIsComplete())) return true; // let's see if all volumes are set, so that we can (could) combine them to a channel unsigned int t; for(t=0;t(data), s, t, n, CopyMemory); } bool mitk::Image::SetVolume(const void *data, int t, int n) { // const_cast is no risk for ImportMemoryManagementType == CopyMemory return SetImportVolume(const_cast(data), t, n, CopyMemory); } bool mitk::Image::SetChannel(const void *data, int n) { // const_cast is no risk for ImportMemoryManagementType == CopyMemory return SetImportChannel(const_cast(data), n, CopyMemory); } bool mitk::Image::SetImportSlice(void *data, int s, int t, int n, ImportMemoryManagementType importMemoryManagement) { if(IsValidSlice(s,t,n)==false) return false; ImageDataItemPointer sl; if(IsSliceSet(s,t,n)) { sl=GetSliceData(s,t,n,data,importMemoryManagement); if(sl->GetManageMemory()==false) { sl=AllocateSliceData(s,t,n,data,importMemoryManagement); if(sl.GetPointer()==NULL) return false; } if ( sl->GetData() != data ) std::memcpy(sl->GetData(), data, m_OffsetTable[2]*(m_PixelType.GetBpe()/8)); sl->Modified(); //we have changed the data: call Modified()! Modified(); } else { sl=AllocateSliceData(s,t,n,data,importMemoryManagement); if(sl.GetPointer()==NULL) return false; if ( sl->GetData() != data ) std::memcpy(sl->GetData(), data, m_OffsetTable[2]*(m_PixelType.GetBpe()/8)); //we just added a missing slice, which is not regarded as modification. //Therefore, we do not call Modified()! } return true; } bool mitk::Image::SetImportVolume(void *data, int t, int n, ImportMemoryManagementType importMemoryManagement) { if(IsValidVolume(t,n)==false) return false; ImageDataItemPointer vol; if(IsVolumeSet(t,n)) { vol=GetVolumeData(t,n,data,importMemoryManagement); if(vol->GetManageMemory()==false) { vol=AllocateVolumeData(t,n,data,importMemoryManagement); if(vol.GetPointer()==NULL) return false; } if ( vol->GetData() != data ) std::memcpy(vol->GetData(), data, m_OffsetTable[3]*(m_PixelType.GetBpe()/8)); vol->Modified(); vol->SetComplete(true); //we have changed the data: call Modified()! Modified(); } else { vol=AllocateVolumeData(t,n,data,importMemoryManagement); if(vol.GetPointer()==NULL) return false; if ( vol->GetData() != data ) { std::memcpy(vol->GetData(), data, m_OffsetTable[3]*(m_PixelType.GetBpe()/8)); } vol->SetComplete(true); //we just added a missing Volume, which is not regarded as modification. //Therefore, we do not call Modified()! } return true; } bool mitk::Image::SetImportChannel(void *data, int n, ImportMemoryManagementType importMemoryManagement) { if(IsValidChannel(n)==false) return false; ImageDataItemPointer ch; if(IsChannelSet(n)) { ch=GetChannelData(n,data,importMemoryManagement); if(ch->GetManageMemory()==false) { ch=AllocateChannelData(n,data,importMemoryManagement); if(ch.GetPointer()==NULL) return false; } if ( ch->GetData() != data ) std::memcpy(ch->GetData(), data, m_OffsetTable[4]*(m_PixelType.GetBpe()/8)); ch->Modified(); ch->SetComplete(true); //we have changed the data: call Modified()! Modified(); } else { ch=AllocateChannelData(n,data,importMemoryManagement); if(ch.GetPointer()==NULL) return false; if ( ch->GetData() != data ) std::memcpy(ch->GetData(), data, m_OffsetTable[4]*(m_PixelType.GetBpe()/8)); ch->SetComplete(true); //we just added a missing Channel, which is not regarded as modification. //Therefore, we do not call Modified()! } return true; } bool mitk::Image::SetPicSlice(const mitkIpPicDescriptor *pic, int s, int t, int n, ImportMemoryManagementType /*importMemoryManagement*/) { if(pic==NULL) return false; if(pic->dim!=2) return false; if((pic->n[0]!=m_Dimensions[0]) || (pic->n[1]!=m_Dimensions[1])) return false; if(SetSlice(pic->data,s,t,n)) //@todo: add geometry! { ImageDataItemPointer sl; sl=GetSliceData(s,t,n,NULL,CopyMemory); mitkIpFuncCopyTags(sl->GetPicDescriptor(), const_cast(pic)); return true; } else return false; } bool mitk::Image::SetPicVolume(const mitkIpPicDescriptor *pic, int t, int n, ImportMemoryManagementType /*importMemoryManagement*/) { if(pic==NULL) return false; if((pic->dim==2) && ((m_Dimension==2) || ((m_Dimension>2) && (m_Dimensions[2]==1)))) return SetPicSlice(pic, 0, t, n); if(pic->dim!=3) return false; if((pic->n[0]!=m_Dimensions[0]) || (pic->n[1]!=m_Dimensions[1]) || (pic->n[2]!=m_Dimensions[2])) return false; if(SetVolume(pic->data,t,n)) //@todo: add geometry! { ImageDataItemPointer vol; vol=GetVolumeData(t,n,NULL,CopyMemory); mitkIpFuncCopyTags(vol->GetPicDescriptor(), const_cast(pic)); return true; } else return false; } bool mitk::Image::SetPicChannel(const mitkIpPicDescriptor *pic, int n, ImportMemoryManagementType /*importMemoryManagement*/) { if(pic==NULL) return false; if(pic->dim<=3) return SetPicVolume(pic, 0, n); if(pic->dim!=m_Dimension) return false; unsigned int i; for(i=0;in[i]!=m_Dimensions[i]) return false; } if(SetChannel(pic->data,n)) //@todo: add geometry! { ImageDataItemPointer ch; ch=GetChannelData(n,NULL,CopyMemory); // commented the next line, because // it crashes when called from mitkDICOMFileReader for the Live3D data // mitkIpFuncCopyTags(ch->GetPicDescriptor(), pic); return true; } else return false; } void mitk::Image::Initialize() { ImageDataItemPointerArray::iterator it, end; for( it=m_Slices.begin(), end=m_Slices.end(); it!=end; ++it ) { (*it)=NULL; } for( it=m_Volumes.begin(), end=m_Volumes.end(); it!=end; ++it ) { (*it)=NULL; } for( it=m_Channels.begin(), end=m_Channels.end(); it!=end; ++it ) { (*it)=NULL; } m_CompleteData = NULL; this->GetTimeSelector(); // just to create m_TimeSelectorForExtremaObject SetRequestedRegionToLargestPossibleRegion(); } mitk::ImageTimeSelector* mitk::Image::GetTimeSelector() const { if(m_TimeSelectorForExtremaObject.IsNull()) { m_TimeSelectorForExtremaObject = ImageTimeSelector::New(); ImageTimeSelector* timeSelector = static_cast( m_TimeSelectorForExtremaObject.GetPointer() ); timeSelector->SetInput(this); this->UnRegister(); } return static_cast( m_TimeSelectorForExtremaObject.GetPointer() ); } void mitk::Image::Initialize(const mitk::PixelType& type, unsigned int dimension, unsigned int *dimensions, unsigned int channels) { Clear(); m_Dimension=dimension; if(!dimensions) itkExceptionMacro(<< "invalid zero dimension image"); unsigned int i; for(i=0;i4?m_Dimension:4]; std::memcpy(m_Dimensions, dimensions, sizeof(unsigned int)*m_Dimension); if(m_Dimension<4) { unsigned int *p; for(i=0,p=m_Dimensions+m_Dimension;i<4-m_Dimension;++i, ++p) *p=1; } 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 = NULL; return; } m_PixelType=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]); if(dimension>=4) { TimeBounds timebounds; timebounds[0] = 0.0; timebounds[1] = 1.0; slicedGeometry->SetTimeBounds(timebounds); } TimeSlicedGeometry::Pointer timeSliceGeometry = TimeSlicedGeometry::New(); timeSliceGeometry->InitializeEvenlyTimed(slicedGeometry, m_Dimensions[3]); timeSliceGeometry->ImageGeometryOn(); SetGeometry(timeSliceGeometry); ImageDataItemPointer dnull=NULL; 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; } void mitk::Image::Initialize(const mitk::PixelType& type, const mitk::Geometry3D& geometry, unsigned int channels, int tDim ) { unsigned int dimensions[5]; dimensions[0] = (unsigned int)(geometry.GetExtent(0)+0.5); dimensions[1] = (unsigned int)(geometry.GetExtent(1)+0.5); dimensions[2] = (unsigned int)(geometry.GetExtent(2)+0.5); dimensions[3] = 0; dimensions[4] = 0; unsigned int dimension = 2; if ( dimensions[2] > 1 ) dimension = 3; if ( tDim > 0) { dimensions[3] = tDim; } else { const mitk::TimeSlicedGeometry* timeGeometry = dynamic_cast(&geometry); if ( timeGeometry != NULL ) { dimensions[3] = timeGeometry->GetTimeSteps(); } } if ( dimensions[3] > 1 ) dimension = 4; Initialize( type, dimension, dimensions, channels ); SetGeometry(static_cast(geometry.Clone().GetPointer())); mitk::BoundingBox::BoundsArrayType bounds = geometry.GetBoundingBox()->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; slicedGeometry->SetBounds(bounds); slicedGeometry->GetIndexToWorldTransform()->SetOffset(origin.Get_vnl_vector().data_block()); GetTimeSlicedGeometry()->InitializeEvenlyTimed(slicedGeometry, m_Dimensions[3]); } } void mitk::Image::Initialize(const mitk::PixelType& type, int sDim, const mitk::Geometry2D& geometry2d, bool flipped, unsigned int channels, int tDim ) { SlicedGeometry3D::Pointer slicedGeometry = SlicedGeometry3D::New(); slicedGeometry->InitializeEvenlySpaced(static_cast(geometry2d.Clone().GetPointer()), sDim, flipped); Initialize(type, *slicedGeometry, channels, tDim); } void mitk::Image::Initialize(const mitk::Image* image) { Initialize(*image->GetPixelType().GetTypeId(), *image->GetTimeSlicedGeometry()); } void mitk::Image::Initialize(vtkImageData* vtkimagedata, int channels, int tDim, int sDim) { if(vtkimagedata==NULL) return; m_Dimension=vtkimagedata->GetDataDimension(); unsigned int i, *tmpDimensions=new unsigned int[m_Dimension>4?m_Dimension:4]; for(i=0;iGetDimensions()[i]; if(m_Dimension<4) { unsigned int *p; for(i=0,p=tmpDimensions+m_Dimension;i<4-m_Dimension;++i, ++p) *p=1; } if(sDim>=0) { tmpDimensions[2]=sDim; if(m_Dimension < 3) m_Dimension = 3; } if(tDim>=0) { tmpDimensions[3]=tDim; if(m_Dimension < 4) m_Dimension = 4; } mitk::PixelType pixelType; switch ( vtkimagedata->GetScalarType() ) { case VTK_BIT: case VTK_CHAR: pixelType.Initialize(typeid(char), vtkimagedata->GetNumberOfScalarComponents()); break; case VTK_UNSIGNED_CHAR: pixelType.Initialize(typeid(unsigned char), vtkimagedata->GetNumberOfScalarComponents()); break; case VTK_SHORT: pixelType.Initialize(typeid(short), vtkimagedata->GetNumberOfScalarComponents()); break; case VTK_UNSIGNED_SHORT: pixelType.Initialize(typeid(unsigned short), vtkimagedata->GetNumberOfScalarComponents()); break; case VTK_INT: pixelType.Initialize(typeid(int), vtkimagedata->GetNumberOfScalarComponents()); break; case VTK_UNSIGNED_INT: pixelType.Initialize(typeid(unsigned int), vtkimagedata->GetNumberOfScalarComponents()); break; case VTK_LONG: pixelType.Initialize(typeid(long), vtkimagedata->GetNumberOfScalarComponents()); break; case VTK_UNSIGNED_LONG: pixelType.Initialize(typeid(unsigned long), vtkimagedata->GetNumberOfScalarComponents()); break; case VTK_FLOAT: pixelType.Initialize(typeid(float), vtkimagedata->GetNumberOfScalarComponents()); break; case VTK_DOUBLE: pixelType.Initialize(typeid(double), vtkimagedata->GetNumberOfScalarComponents()); break; default: break; } Initialize(pixelType, m_Dimension, tmpDimensions, channels); #if ((VTK_MAJOR_VERSION > 4) || ((VTK_MAJOR_VERSION==4) && (VTK_MINOR_VERSION>=4) )) const double *spacinglist = vtkimagedata->GetSpacing(); #else const float *spacinglist = vtkimagedata->GetSpacing(); #endif Vector3D spacing; FillVector3D(spacing, spacinglist[0], 1.0, 1.0); if(m_Dimension>=2) spacing[1]=spacinglist[1]; if(m_Dimension>=3) spacing[2]=spacinglist[2]; // access origin of vtkImage Point3D origin; vtkFloatingPointType vtkorigin[3]; vtkimagedata->GetOrigin(vtkorigin); FillVector3D(origin, vtkorigin[0], 0.0, 0.0); if(m_Dimension>=2) origin[1]=vtkorigin[1]; if(m_Dimension>=3) origin[2]=vtkorigin[2]; SlicedGeometry3D* slicedGeometry = GetSlicedGeometry(0); // re-initialize PlaneGeometry with origin and direction PlaneGeometry* planeGeometry = static_cast(slicedGeometry->GetGeometry2D(0)); planeGeometry->SetOrigin(origin); // re-initialize SlicedGeometry3D slicedGeometry->SetOrigin(origin); slicedGeometry->SetSpacing(spacing); GetTimeSlicedGeometry()->InitializeEvenlyTimed(slicedGeometry, m_Dimensions[3]); delete [] tmpDimensions; } void mitk::Image::Initialize(const mitkIpPicDescriptor* pic, int channels, int tDim, int sDim) { if(pic==NULL) return; Clear(); m_Dimension=pic->dim; m_Dimensions=new unsigned int[m_Dimension>4?m_Dimension:4]; std::memcpy(m_Dimensions, pic->n, sizeof(unsigned int)*m_Dimension); if(m_Dimension<4) { unsigned int i, *p; for(i=0,p=m_Dimensions+m_Dimension;i<4-m_Dimension;++i, ++p) *p=1; } if(sDim>=0) { m_Dimensions[2]=sDim; if(m_Dimension < 3) m_Dimension = 3; } if(tDim>=0) { m_Dimensions[3]=tDim; if(m_Dimension < 4) m_Dimension = 4; } unsigned int i; 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); m_PixelType=PixelType(pic); SlicedGeometry3D::Pointer slicedGeometry = SlicedGeometry3D::New(); PicHelper::InitializeEvenlySpaced(pic, m_Dimensions[2], slicedGeometry); TimeSlicedGeometry::Pointer timeSliceGeometry = TimeSlicedGeometry::New(); timeSliceGeometry->InitializeEvenlyTimed(slicedGeometry, m_Dimensions[3]); timeSliceGeometry->ImageGeometryOn(); SetGeometry(timeSliceGeometry); ImageDataItemPointer dnull=NULL; 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; } bool mitk::Image::IsValidSlice(int s, int t, int n) const { if(m_Initialized) return ((s>=0) && (s<(int)m_Dimensions[2]) && (t>=0) && (t< (int) m_Dimensions[3]) && (n>=0) && (n< (int)GetNumberOfChannels())); else return false; } bool mitk::Image::IsValidVolume(int t, int n) const { if(m_Initialized) return IsValidSlice(0, t, n); else return false; } bool mitk::Image::IsValidChannel(int n) const { if(m_Initialized) return IsValidSlice(0, 0, n); else return false; } void mitk::Image::ComputeOffsetTable() { if(m_OffsetTable!=NULL) delete [] m_OffsetTable; m_OffsetTable=new size_t[m_Dimension>4 ? m_Dimension+1 : 4+1]; unsigned int i; size_t num=1; m_OffsetTable[0] = 1; for (i=0; i < m_Dimension; ++i) { num *= m_Dimensions[i]; m_OffsetTable[i+1] = num; } for (;i < 4; ++i) m_OffsetTable[i+1] = num; } int mitk::Image::GetSliceIndex(int s, int t, int n) const { if(IsValidSlice(s,t,n)==false) return false; return ((size_t)s)+((size_t) t)*m_Dimensions[2]+((size_t) n)*m_Dimensions[3]*m_Dimensions[2]; //?? } int mitk::Image::GetVolumeIndex(int t, int n) const { if(IsValidVolume(t,n)==false) return false; return ((size_t)t)+((size_t) n)*m_Dimensions[3]; //?? } mitk::Image::ImageDataItemPointer mitk::Image::AllocateSliceData(int s, int t, int n, void *data, ImportMemoryManagementType importMemoryManagement) { int pos; pos=GetSliceIndex(s,t,n); // is slice available as part of a volume that is available? ImageDataItemPointer sl, ch, vol; vol=m_Volumes[GetVolumeIndex(t,n)]; if(vol.GetPointer()!=NULL) { sl=new ImageDataItem(*vol, 2, data, importMemoryManagement == ManageMemory, ((size_t) s)*m_OffsetTable[2]*(m_PixelType.GetBpe()/8)); sl->SetComplete(true); return m_Slices[pos]=sl; } // is slice available as part of a channel that is available? ch=m_Channels[n]; if(ch.GetPointer()!=NULL) { sl=new ImageDataItem(*ch, 2, data, importMemoryManagement == ManageMemory, (((size_t) s)*m_OffsetTable[2]+((size_t) t)*m_OffsetTable[3])*(m_PixelType.GetBpe()/8)); sl->SetComplete(true); return m_Slices[pos]=sl; } // allocate new volume (instead of a single slice to keep data together!) m_Volumes[GetVolumeIndex(t,n)]=vol=AllocateVolumeData(t,n,NULL,importMemoryManagement); sl=new ImageDataItem(*vol, 2, data, importMemoryManagement == ManageMemory, ((size_t) s)*m_OffsetTable[2]*(m_PixelType.GetBpe()/8)); sl->SetComplete(true); return m_Slices[pos]=sl; ////ALTERNATIVE: //// allocate new slice //sl=new ImageDataItem(m_PixelType, 2, m_Dimensions); //m_Slices[pos]=sl; //return vol; } mitk::Image::ImageDataItemPointer mitk::Image::AllocateVolumeData(int t, int n, void *data, ImportMemoryManagementType importMemoryManagement) { int pos; pos=GetVolumeIndex(t,n); // is volume available as part of a channel that is available? ImageDataItemPointer ch, vol; ch=m_Channels[n]; if(ch.GetPointer()!=NULL) { vol=new ImageDataItem(*ch, 3, data, importMemoryManagement == ManageMemory, (((size_t) t)*m_OffsetTable[3])*(m_PixelType.GetBpe()/8)); return m_Volumes[pos]=vol; } // allocate new volume if(importMemoryManagement == CopyMemory) { vol=new ImageDataItem(m_PixelType, 3, m_Dimensions, NULL, true); if(data != NULL) std::memcpy(vol->GetData(), data, m_OffsetTable[3]*(m_PixelType.GetBpe()/8)); } else { vol=new ImageDataItem(m_PixelType, 3, m_Dimensions, data, importMemoryManagement == ManageMemory); } m_Volumes[pos]=vol; return vol; } mitk::Image::ImageDataItemPointer mitk::Image::AllocateChannelData(int n, void *data, ImportMemoryManagementType importMemoryManagement) { ImageDataItemPointer ch; // allocate new channel if(importMemoryManagement == CopyMemory) { ch=new ImageDataItem(m_PixelType, m_Dimension, m_Dimensions, NULL, true); if(data != NULL) std::memcpy(ch->GetData(), data, m_OffsetTable[4]*(m_PixelType.GetBpe()/8)); } else { ch=new ImageDataItem(m_PixelType, m_Dimension, m_Dimensions, data, importMemoryManagement == ManageMemory); } m_Channels[n]=ch; return ch; } unsigned int* mitk::Image::GetDimensions() const { return m_Dimensions; } void mitk::Image::Clear() { Superclass::Clear(); delete [] m_Dimensions; m_Dimensions = NULL; } void mitk::Image::SetGeometry(Geometry3D* aGeometry3D) { // Please be aware of the 0.5 offset/pixel-center issue! See Geometry documentation for further information if(aGeometry3D->GetImageGeometry()==false) { MITK_INFO << "WARNING: Applied a non-image geometry onto an image. Please be SURE that this geometry is pixel-center-based! If it is not, you need to call Geometry3D->ChangeImageGeometryConsideringOriginOffset(true) before calling image->setGeometry(..)\n"; } Superclass::SetGeometry(aGeometry3D); GetTimeSlicedGeometry()->ImageGeometryOn(); } const mitk::Image::HistogramType* mitk::Image::GetScalarHistogram(int t) const { mitk::ImageTimeSelector* timeSelector = this->GetTimeSelector(); if(timeSelector!=NULL) { timeSelector->SetTimeNr(t); timeSelector->UpdateLargestPossibleRegion(); mitk::HistogramGenerator* generator = static_cast(m_HistogramGeneratorObject.GetPointer()); generator->SetImage(timeSelector->GetOutput()); generator->ComputeHistogram(); return static_cast(generator->GetHistogram()); } return NULL; } #include "mitkImageAccessByItk.h" //#define BOUNDINGOBJECT_IGNORE template < typename ItkImageType > void mitk::_ComputeExtremaInItkImage(ItkImageType* itkImage, mitk::Image* mitkImage, int t) { typename ItkImageType::RegionType region; region = itkImage->GetBufferedRegion(); if(region.Crop(itkImage->GetRequestedRegion()) == false) return; if(region != itkImage->GetRequestedRegion()) return; itk::ImageRegionConstIterator it(itkImage, region); typedef typename ItkImageType::PixelType TPixel; TPixel value = 0; if ( !mitkImage || !mitkImage->IsValidTimeStep( t ) ) return; mitkImage->Expand(t+1); // make sure we have initialized all arrays mitkImage->m_CountOfMinValuedVoxels[t] = 0; mitkImage->m_CountOfMaxValuedVoxels[t] = 0; mitkImage->m_Scalar2ndMin[t]= mitkImage->m_ScalarMin[t] = itk::NumericTraits::max(); mitkImage->m_Scalar2ndMax[t]= mitkImage->m_ScalarMax[t] = itk::NumericTraits::NonpositiveMin(); while( !it.IsAtEnd() ) { value = it.Get(); // if ( (value > mitkImage->m_ScalarMin) && (value < mitkImage->m_Scalar2ndMin) ) mitkImage->m_Scalar2ndMin = value; // else if ( (value < mitkImage->m_ScalarMax) && (value > mitkImage->m_Scalar2ndMax) ) mitkImage->m_Scalar2ndMax = value; // else if (value > mitkImage->m_ScalarMax) mitkImage->m_ScalarMax = value; // else if (value < mitkImage->m_ScalarMin) mitkImage->m_ScalarMin = value; // if numbers start with 2ndMin or 2ndMax and never have that value again, the previous above logic failed #ifdef BOUNDINGOBJECT_IGNORE if( value > -32765) { #endif // update min if ( value < mitkImage->m_ScalarMin[t] ) { mitkImage->m_Scalar2ndMin[t] = mitkImage->m_ScalarMin[t]; mitkImage->m_ScalarMin[t] = value; mitkImage->m_CountOfMinValuedVoxels[t] = 1; } else if ( value == mitkImage->m_ScalarMin[t] ) { ++mitkImage->m_CountOfMinValuedVoxels[t]; } else if ( value < mitkImage->m_Scalar2ndMin[t] ) { mitkImage->m_Scalar2ndMin[t] = value; } // update max if ( value > mitkImage->m_ScalarMax[t] ) { mitkImage->m_Scalar2ndMax[t] = mitkImage->m_ScalarMax[t]; mitkImage->m_ScalarMax[t] = value; mitkImage->m_CountOfMaxValuedVoxels[t] = 1; } else if ( value == mitkImage->m_ScalarMax[t] ) { ++mitkImage->m_CountOfMaxValuedVoxels[t]; } else if ( value > mitkImage->m_Scalar2ndMax[t] ) { mitkImage->m_Scalar2ndMax[t] = value; } #ifdef BOUNDINGOBJECT_IGNORE } #endif ++it; } //// guard for wrong 2dMin/Max on single constant value images if (mitkImage->m_ScalarMax[t] == mitkImage->m_ScalarMin[t]) { mitkImage->m_Scalar2ndMax[t] = mitkImage->m_Scalar2ndMin[t] = mitkImage->m_ScalarMax[t]; } mitkImage->m_LastRecomputeTimeStamp.Modified(); //MITK_DEBUG <<"extrema "<::NonpositiveMin()<<" "<m_ScalarMin<<" "<m_Scalar2ndMin<<" "<m_Scalar2ndMax<<" "<m_ScalarMax<<" "<::max(); } bool mitk::Image::IsValidTimeStep(int t) const { return ( ( m_Dimension >= 4 && t <= (int)m_Dimensions[3] && t > 0 ) || (t == 0) ); } -void mitk::Image::Expand( int timeSteps ) const +void mitk::Image::Expand( unsigned int timeSteps ) { if(timeSteps < 1) itkExceptionMacro(<< "Invalid timestep in Image!"); if(! IsValidTimeStep( timeSteps-1 ) ) return; - if(timeSteps > (int)m_ScalarMin.size() ) + Superclass::Expand(timeSteps); + if(timeSteps > m_ScalarMin.size() ) { m_ScalarMin.resize(timeSteps, itk::NumericTraits::max()); m_ScalarMax.resize(timeSteps, itk::NumericTraits::NonpositiveMin()); m_Scalar2ndMin.resize(timeSteps, itk::NumericTraits::max()); m_Scalar2ndMax.resize(timeSteps, itk::NumericTraits::NonpositiveMin()); m_CountOfMinValuedVoxels.resize(timeSteps, 0); m_CountOfMaxValuedVoxels.resize(timeSteps, 0); } } void mitk::Image::ResetImageStatistics() const { m_ScalarMin.assign(1, itk::NumericTraits::max()); m_ScalarMax.assign(1, itk::NumericTraits::NonpositiveMin()); m_Scalar2ndMin.assign(1, itk::NumericTraits::max()); m_Scalar2ndMax.assign(1, itk::NumericTraits::NonpositiveMin()); m_CountOfMinValuedVoxels.assign(1, 0); m_CountOfMaxValuedVoxels.assign(1, 0); } void mitk::Image::ComputeImageStatistics(int t) const { // timestep valid? if (!IsValidTimeStep(t)) return; // image modified? if (this->GetMTime() > m_LastRecomputeTimeStamp.GetMTime()) this->ResetImageStatistics(); // adapt vector length - this->Expand(t+1); + // the const_cast is necessary since the whole statistics are provided + // with const-methods but are actually stored inside the object with mutable + // members. This should be resolved in a redesign of the image class. + const_cast(this)->Expand(t+1); // do we have valid information already? if( m_ScalarMin[t] != itk::NumericTraits::max() || m_Scalar2ndMin[t] != itk::NumericTraits::max() ) return; // Values already calculated before... if(this->m_PixelType.GetNumberOfComponents() == 1) { // recompute mitk::ImageTimeSelector* timeSelector = this->GetTimeSelector(); if(timeSelector!=NULL) { timeSelector->SetTimeNr(t); timeSelector->UpdateLargestPossibleRegion(); mitk::Image* image = timeSelector->GetOutput(); mitk::Image* thisImage = const_cast(this); AccessByItk_2( image, _ComputeExtremaInItkImage, thisImage, t ); } } else if(this->m_PixelType.GetNumberOfComponents() > 1) { m_ScalarMin[t] = 0; m_ScalarMax[t] = 255; } } mitk::ScalarType mitk::Image::GetScalarValueMin(int t) const { ComputeImageStatistics(t); return m_ScalarMin[t]; } mitk::ScalarType mitk::Image::GetScalarValueMax(int t) const { ComputeImageStatistics(t); return m_ScalarMax[t]; } mitk::ScalarType mitk::Image::GetScalarValue2ndMin(int t) const { ComputeImageStatistics(t); return m_Scalar2ndMin[t]; } mitk::ScalarType mitk::Image::GetScalarValue2ndMax(int t) const { ComputeImageStatistics(t); return m_Scalar2ndMax[t]; } mitk::ScalarType mitk::Image::GetCountOfMinValuedVoxels(int t) const { ComputeImageStatistics(t); return m_CountOfMinValuedVoxels[t]; } mitk::ScalarType mitk::Image::GetCountOfMaxValuedVoxels(int t) const { ComputeImageStatistics(t); return m_CountOfMaxValuedVoxels[t]; } void mitk::Image::PrintSelf(std::ostream& os, itk::Indent indent) const { unsigned char i; if(m_Initialized) { os << indent << " PixelType: " << m_PixelType.GetTypeId()->name() << std::endl; os << indent << " BitsPerElement: " << m_PixelType.GetBpe() << std::endl; os << indent << " NumberOfComponents: " << m_PixelType.GetNumberOfComponents() << std::endl; os << indent << " BitsPerComponent: " << m_PixelType.GetBitsPerComponent() << std::endl; os << indent << " Dimension: " << m_Dimension << std::endl; os << indent << " Dimensions: "; for(i=0; i < m_Dimension; ++i) os << GetDimension(i) << " "; os << std::endl; } else { os << indent << " Image not initialized: m_Initialized: false" << std::endl; } Superclass::PrintSelf(os,indent); } bool mitk::Image::IsRotated() const { const mitk::Geometry3D* geo = this->GetGeometry(); bool ret = false; if(geo) { const vnl_matrix_fixed & mx = geo->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix(); float ref = 0; for(short k = 0; k < 3; ++k) ref += mx[k][k]; ref/=1000; // Arbitrary value; if a non-diagonal (nd) element is bigger then this, matrix is considered nd. for(short i = 0; i < 3; ++i) { for(short j = 0; j < 3; ++j) { if(i != j) { if(abs(mx[i][j]) > ref) // matrix is nd ret = true; } } } } return ret; } diff --git a/Core/Code/DataManagement/mitkImage.h b/Core/Code/DataManagement/mitkImage.h index 74f9337cdb..3c2dc23d4d 100644 --- a/Core/Code/DataManagement/mitkImage.h +++ b/Core/Code/DataManagement/mitkImage.h @@ -1,658 +1,658 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef MITKIMAGE_H_HEADER_INCLUDED_C1C2FCD2 #define MITKIMAGE_H_HEADER_INCLUDED_C1C2FCD2 #include "mitkCommon.h" #include "mitkSlicedData.h" #include "mitkPixelType.h" #include "mitkBaseData.h" #include "mitkLevelWindow.h" #include "mitkPlaneGeometry.h" #ifndef __itkHistogram_h #include #endif class vtkImageData; namespace mitk { class SubImageSelector; class ImageDataItem; class ImageTimeSelector; //##Documentation //## @brief Image class for storing images //## //## Can be asked for header information, the data vector, //## the mitkIpPicDescriptor struct or vtkImageData objects. If not the complete //## data is required, the appropriate SubImageSelector class should be used //## for access. //## Image organizes sets of slices (s x 2D), volumes (t x 3D) and channels (n //## x ND). Channels are for different kind of data, e.g., morphology in //## channel 0, velocities in channel 1. All channels must have the same Geometry! In //## particular, the dimensions of all channels are the same, only the pixel-type //## may differ between channels. //## //## For importing ITK images use of mitk::ITKImageImport is recommended, see //## \ref Adaptor. //## //## For ITK v3.8 and older: Converting coordinates from the ITK physical //## coordinate system (which does not support rotated images) to the MITK world //## coordinate system should be performed via the Geometry3D of the Image, see //## Geometry3D::WorldToItkPhysicalPoint. //## @ingroup Data class MITK_CORE_EXPORT Image : public SlicedData { friend class SubImageSelector; public: mitkClassMacro(Image, SlicedData); itkNewMacro(Self); /** Smart Pointer type to a ImageDataItem. */ typedef itk::SmartPointerForwardReference ImageDataItemPointer; //## @param ImportMemoryManagementType This parameter is evaluated when setting new data to an image. //## The different options are: //## CopyMemory: Data to be set is copied and assigned to a new memory block. Data memory block will be freed on deletion of mitk::Image. //## MamageMemory: Data to be set will be referenced, and Data memory block will be freed on deletion of mitk::Image. //## Reference Memory: Data to be set will be referenced, but Data memory block will not be freed on deletion of mitk::Image. //## DontManageMemory = ReferenceMemory. enum ImportMemoryManagementType { CopyMemory, ManageMemory, ReferenceMemory, DontManageMemory = ReferenceMemory }; //##Documentation //## @brief Vector container of SmartPointers to ImageDataItems; //## Class is only for internal usage to allow convenient access to all slices over iterators; //## See documentation of ImageDataItem for details. typedef std::vector ImageDataItemPointerArray; typedef itk::Statistics::Histogram HistogramType; public: //##Documentation //## @brief Returns the PixelType of channel @a n. const mitk::PixelType& GetPixelType(int n = 0) const; //##Documentation //## @brief Get dimension of the image //## unsigned int GetDimension() const; //##Documentation //## @brief Get the size of dimension @a i (e.g., i=0 results in the number of pixels in x-direction). //## //## @sa GetDimensions() unsigned int GetDimension(int i) const; //## @brief Get the data vector of the complete image, i.e., of all channels linked together. //## //## If you only want to access a slice, volume at a specific time or single channel //## use one of the SubImageSelector classes. virtual void* GetData(); //## @brief Get the pixel value at one specific index position. //## @brief Get the pixel value at one specific position. //## //## The pixel type is always being converted to double. double GetPixelValueByIndex(const mitk::Index3D& position, unsigned int timestep = 0); //## @brief Get the pixel value at one specific world position. //## //## The pixel type is always being converted to double. double GetPixelValueByWorldCoordinate(const mitk::Point3D& position, unsigned int timestep = 0); //##Documentation //## @brief Get a volume at a specific time @a t of channel @a n as a vtkImageData. virtual vtkImageData* GetVtkImageData(int t = 0, int n = 0); //##Documentation //## @brief Get the complete image, i.e., all channels linked together, as a @a mitkIpPicDescriptor. //## //## If you only want to access a slice, volume at a specific time or single channel //## use one of the SubImageSelector classes. virtual mitkIpPicDescriptor* GetPic(); //##Documentation //## @brief Check whether slice @a s at time @a t in channel @a n is set virtual bool IsSliceSet(int s = 0, int t = 0, int n = 0) const; //##Documentation //## @brief Check whether volume at time @a t in channel @a n is set virtual bool IsVolumeSet(int t = 0, int n = 0) const; //##Documentation //## @brief Check whether the channel @a n is set virtual bool IsChannelSet(int n = 0) const; //##Documentation //## @brief Set @a data as slice @a s at time @a t in channel @a n. It is in //## the responsibility of the caller to ensure that the data vector @a data //## is really a slice (at least is not smaller than a slice), since there is //## no chance to check this. //## //## The data is copied to an array managed by the image. If the image shall //## reference the data, use SetImportSlice with ImportMemoryManagementType //## set to ReferenceMemory. For importing ITK images use of mitk:: //## ITKImageImport is recommended. //## @sa SetPicSlice, SetImportSlice, SetImportVolume virtual bool SetSlice(const void *data, int s = 0, int t = 0, int n = 0); //##Documentation //## @brief Set @a data as volume at time @a t in channel @a n. It is in //## the responsibility of the caller to ensure that the data vector @a data //## is really a volume (at least is not smaller than a volume), since there is //## no chance to check this. //## //## The data is copied to an array managed by the image. If the image shall //## reference the data, use SetImportVolume with ImportMemoryManagementType //## set to ReferenceMemory. For importing ITK images use of mitk:: //## ITKImageImport is recommended. //## @sa SetPicVolume, SetImportVolume virtual bool SetVolume(const void *data, int t = 0, int n = 0); //##Documentation //## @brief Set @a data in channel @a n. It is in //## the responsibility of the caller to ensure that the data vector @a data //## is really a channel (at least is not smaller than a channel), since there is //## no chance to check this. //## //## The data is copied to an array managed by the image. If the image shall //## reference the data, use SetImportChannel with ImportMemoryManagementType //## set to ReferenceMemory. For importing ITK images use of mitk:: //## ITKImageImport is recommended. //## @sa SetPicChannel, SetImportChannel virtual bool SetChannel(const void *data, int n = 0); //##Documentation //## @brief Set @a data as slice @a s at time @a t in channel @a n. It is in //## the responsibility of the caller to ensure that the data vector @a data //## is really a slice (at least is not smaller than a slice), since there is //## no chance to check this. //## //## The data is managed according to the parameter \a importMemoryManagement. //## @sa SetPicSlice virtual bool SetImportSlice(void *data, int s = 0, int t = 0, int n = 0, ImportMemoryManagementType importMemoryManagement = CopyMemory ); //##Documentation //## @brief Set @a data as volume at time @a t in channel @a n. It is in //## the responsibility of the caller to ensure that the data vector @a data //## is really a volume (at least is not smaller than a volume), since there is //## no chance to check this. //## //## The data is managed according to the parameter \a importMemoryManagement. //## @sa SetPicVolume virtual bool SetImportVolume(void *data, int t = 0, int n = 0, ImportMemoryManagementType importMemoryManagement = CopyMemory ); //##Documentation //## @brief Set @a data in channel @a n. It is in //## the responsibility of the caller to ensure that the data vector @a data //## is really a channel (at least is not smaller than a channel), since there is //## no chance to check this. //## //## The data is managed according to the parameter \a importMemoryManagement. //## @sa SetPicChannel virtual bool SetImportChannel(void *data, int n = 0, ImportMemoryManagementType importMemoryManagement = CopyMemory ); //##Documentation //## @brief Set @a pic as slice @a s at time @a t in channel @a n. //## //## The data is copied to an array managed by the image. //## @todo The corresponding @a Geomety3D and depending @a Geometry2D entries //## are updated according to the information provided in the tags of @a pic. //## @return @a false : dimensions and/or data-type of @a pic does not //## comply with image //## @a true success virtual bool SetPicSlice(const mitkIpPicDescriptor *pic, int s = 0, int t = 0, int n = 0, ImportMemoryManagementType importMemoryManagement = CopyMemory ); //##Documentation //## @brief Set @a pic as volume at time @a t in channel @a n. //## //## The data is copied to an array managed by the image. //## @todo The corresponding @a Geomety3D and depending @a Geometry2D entries //## are updated according to the information provided in the tags of @a pic. //## @return @a false : dimensions and/or data-type of @a pic does not //## comply with image //## @a true success virtual bool SetPicVolume(const mitkIpPicDescriptor *pic, int t = 0, int n = 0, ImportMemoryManagementType importMemoryManagement = CopyMemory ); //##Documentation //## @brief Set @a pic in channel @a n. //## //## The data is copied to an array managed by the image. //## @todo The corresponding @a Geomety3D and depending @a Geometry2D entries //## are updated according to the information provided in the tags of @a pic. //## @return @a false : dimensions and/or data-type of @a pic does not //## comply with image //## @a true success virtual bool SetPicChannel(const mitkIpPicDescriptor *pic, int n = 0, ImportMemoryManagementType importMemoryManagement = CopyMemory ); //##Documentation //## initialize new (or re-initialize) image information //## @warning Initialize() by pic assumes a plane, evenly spaced geometry starting at (0,0,0). virtual void Initialize(const mitk::PixelType& type, unsigned int dimension, unsigned int *dimensions, unsigned int channels = 1); //##Documentation //## initialize new (or re-initialize) image information by a Geometry3D //## //## @param tDim override time dimension (@a n[3]) if @a geometry is a TimeSlicedGeometry (if >0) virtual void Initialize(const mitk::PixelType& type, const mitk::Geometry3D& geometry, unsigned int channels = 1, int tDim=-1); //##Documentation //## initialize new (or re-initialize) image information by a Geometry2D and number of slices //## //## Initializes the bounding box according to the width/height of the //## Geometry2D and @a sDim via SlicedGeometry3D::InitializeEvenlySpaced. //## The spacing is calculated from the Geometry2D. //## @param tDim override time dimension (@a n[3]) if @a geometry is a TimeSlicedGeometry (if >0) //## \sa SlicedGeometry3D::InitializeEvenlySpaced virtual void Initialize(const mitk::PixelType& type, int sDim, const mitk::Geometry2D& geometry2d, bool flipped = false, unsigned int channels = 1, int tDim=-1); //##Documentation //## initialize new (or re-initialize) image information by another //## mitk-image. //## Only the header is used, not the data vector! //## virtual void Initialize(const mitk::Image* image); //##Documentation //## initialize new (or re-initialize) image information by @a pic. //## Dimensions and @a Geometry3D /@a Geometry2D are set according //## to the tags in @a pic. //## Only the header is used, not the data vector! Use SetPicVolume(pic) //## to set the data vector. //## //## @param tDim override time dimension (@a n[3]) in @a pic (if >0) //## @param sDim override z-space dimension (@a n[2]) in @a pic (if >0) //## @warning Initialize() by pic assumes a plane, evenly spaced geometry starting at (0,0,0). virtual void Initialize(const mitkIpPicDescriptor* pic, int channels = 1, int tDim = -1, int sDim = -1); //##Documentation //## initialize new (or re-initialize) image information by @a vtkimagedata, //## a vtk-image. //## Only the header is used, not the data vector! Use //## SetVolume(vtkimage->GetScalarPointer()) to set the data vector. //## //## @param tDim override time dimension in @a vtkimagedata (if >0 and <) //## @param sDim override z-space dimension in @a vtkimagedata (if >0 and <) virtual void Initialize(vtkImageData* vtkimagedata, int channels = 1, int tDim = -1, int sDim = -1); //##Documentation //## initialize new (or re-initialize) image information by @a itkimage, //## a templated itk-image. //## Only the header is used, not the data vector! Use //## SetVolume(itkimage->GetBufferPointer()) to set the data vector. //## //## @param tDim override time dimension in @a itkimage (if >0 and <) //## @param sDim override z-space dimension in @a itkimage (if >0 and <) template void InitializeByItk(const itkImageType* itkimage, int channels = 1, int tDim = -1, int sDim=-1) { if(itkimage==NULL) return; MITK_DEBUG << "Initializing MITK image from ITK image."; // build array with dimensions in each direction with at least 4 entries m_Dimension=itkimage->GetImageDimension(); unsigned int i, *tmpDimensions=new unsigned int[m_Dimension>4?m_Dimension:4]; for(i=0;iGetLargestPossibleRegion().GetSize().GetSize()[i]; if(m_Dimension<4) { unsigned int *p; for(i=0,p=tmpDimensions+m_Dimension;i<4-m_Dimension;++i, ++p) *p=1; } // overwrite number of slices if sDim is set if((m_Dimension>2) && (sDim>=0)) tmpDimensions[2]=sDim; // overwrite number of time points if tDim is set if((m_Dimension>3) && (tDim>=0)) tmpDimensions[3]=tDim; // rough initialization of Image Initialize(mitk::PixelType(typeid(typename itkImageType::PixelType)), m_Dimension, tmpDimensions, channels); const typename itkImageType::SpacingType & itkspacing = itkimage->GetSpacing(); MITK_DEBUG << "ITK spacing " << itkspacing; // access spacing of itk::Image Vector3D spacing; FillVector3D(spacing, itkspacing[0], 1.0, 1.0); if(m_Dimension >= 2) spacing[1]=itkspacing[1]; if(m_Dimension >= 3) spacing[2]=itkspacing[2]; // access origin of itk::Image Point3D origin; const typename itkImageType::PointType & itkorigin = itkimage->GetOrigin(); MITK_DEBUG << "ITK origin " << itkorigin; FillVector3D(origin, itkorigin[0], 0.0, 0.0); if(m_Dimension>=2) origin[1]=itkorigin[1]; if(m_Dimension>=3) origin[2]=itkorigin[2]; // access direction of itk::Image and include spacing const typename itkImageType::DirectionType & itkdirection = itkimage->GetDirection(); MITK_DEBUG << "ITK direction " << itkdirection; mitk::Matrix3D matrix; matrix.SetIdentity(); unsigned int j, itkDimMax3 = (m_Dimension >= 3? 3 : m_Dimension); // check if spacing has no zero entry and itkdirection has no zero columns bool itkdirectionOk = true; mitk::ScalarType columnSum; for( j=0; j < itkDimMax3; ++j ) { columnSum = 0.0; for ( i=0; i < itkDimMax3; ++i) { columnSum += fabs(itkdirection[i][j]); } if(columnSum < mitk::eps) { itkdirectionOk = false; } if ( (spacing[j] < - mitk::eps) // (normally sized) negative value && (j==2) && (m_Dimensions[2] == 1) ) { // Negative spacings can occur when reading single DICOM slices with ITK via GDCMIO // In these cases spacing is not determind by ITK correctly (because it distinguishes correctly // between slice thickness and inter slice distance -- slice distance is meaningless for // single slices). // I experienced that ITK produced something meaningful nonetheless because is is // evaluating the tag "(0018,0088) Spacing between slices" as a fallback. This tag is not // reliable (http://www.itk.org/pipermail/insight-users/2005-September/014711.html) // but gives at least a hint. // In real world cases I experienced that this tag contained the correct inter slice distance // with a negative sign, so we just invert such negative spacings. MITK_WARN << "Illegal value of itk::Image::GetSpacing()[" << j <<"]=" << spacing[j] << ". Using inverted value " << -spacing[j]; spacing[j] = -spacing[j]; } else if (spacing[j] < mitk::eps) // value near zero { MITK_ERROR << "Illegal value of itk::Image::GetSpacing()[" << j <<"]=" << spacing[j] << ". Using 1.0 instead."; spacing[j] = 1.0; } } if(itkdirectionOk == false) { MITK_ERROR << "Illegal matrix returned by itk::Image::GetDirection():" << itkdirection << " Using identity instead."; for ( i=0; i < itkDimMax3; ++i) for( j=0; j < itkDimMax3; ++j ) if ( i == j ) matrix[i][j] = spacing[j]; else matrix[i][j] = 0.0; } else { for ( i=0; i < itkDimMax3; ++i) for( j=0; j < itkDimMax3; ++j ) matrix[i][j] = itkdirection[i][j]*spacing[j]; } // re-initialize PlaneGeometry with origin and direction PlaneGeometry* planeGeometry = static_cast(GetSlicedGeometry(0)->GetGeometry2D(0)); planeGeometry->SetOrigin(origin); planeGeometry->GetIndexToWorldTransform()->SetMatrix(matrix); // re-initialize SlicedGeometry3D SlicedGeometry3D* slicedGeometry = GetSlicedGeometry(0); slicedGeometry->InitializeEvenlySpaced(planeGeometry, m_Dimensions[2]); slicedGeometry->SetSpacing(spacing); // re-initialize TimeSlicedGeometry GetTimeSlicedGeometry()->InitializeEvenlyTimed(slicedGeometry, m_Dimensions[3]); // clean-up delete [] tmpDimensions; this->Initialize(); }; //##Documentation //## @brief Check whether slice @a s at time @a t in channel @a n is valid, i.e., //## is (or can be) inside of the image virtual bool IsValidSlice(int s = 0, int t = 0, int n = 0) const; //##Documentation //## @brief Check whether volume at time @a t in channel @a n is valid, i.e., //## is (or can be) inside of the image virtual bool IsValidVolume(int t = 0, int n = 0) const; //##Documentation //## @brief Check whether the channel @a n is valid, i.e., //## is (or can be) inside of the image virtual bool IsValidChannel(int n = 0) const; //##Documentation //## @brief Returns true if an image is rotated, i.e. its geometry's //## transformation matrix has nonzero elements besides the diagonal. //## Non-diagonal elements are checked if larger then 1/1000 of the matrix' trace. bool IsRotated() const; //##Documentation //## @brief Get the sizes of all dimensions as an integer-array. //## //## @sa GetDimension(int i); unsigned int* GetDimensions() const; //##Documentation //## @brief Sets a geometry to an image. virtual void SetGeometry(Geometry3D* aGeometry3D); virtual const HistogramType* GetScalarHistogram(int t=0) const; //##Documentation //## \brief Get the minimum for scalar images virtual ScalarType GetScalarValueMin(int t=0) const; //##Documentation //## \brief Get the maximum for scalar images virtual ScalarType GetScalarValueMax(int t=0) const; //##Documentation //## \brief Get the second smallest value for scalar images virtual ScalarType GetScalarValue2ndMin(int t=0) const; //##Documentation //## \brief Get the smallest value for scalar images, but do not recompute it first virtual mitk::ScalarType GetScalarValueMinNoRecompute( unsigned int t = 0 ) const { if ( t < m_ScalarMin.size() ) return m_ScalarMin[t]; else return itk::NumericTraits::max(); } //##Documentation //## \brief Get the second smallest value for scalar images, but do not recompute it first virtual mitk::ScalarType GetScalarValue2ndMinNoRecompute( unsigned int t = 0 ) const { if ( t < m_Scalar2ndMin.size() ) return m_Scalar2ndMin[t]; else return itk::NumericTraits::max(); } //##Documentation //## \brief Get the second largest value for scalar images virtual ScalarType GetScalarValue2ndMax(int t=0) const; //##Documentation //## \brief Get the largest value for scalar images, but do not recompute it first virtual mitk::ScalarType GetScalarValueMaxNoRecompute( unsigned int t = 0 ) const { if ( t < m_ScalarMax.size() ) return m_ScalarMax[t]; else return itk::NumericTraits::NonpositiveMin(); } //##Documentation //## \brief Get the second largest value for scalar images, but do not recompute it first virtual mitk::ScalarType GetScalarValue2ndMaxNoRecompute( unsigned int t = 0 ) const { if ( t < m_Scalar2ndMax.size() ) return m_Scalar2ndMax[t]; else return itk::NumericTraits::NonpositiveMin(); } //##Documentation //## \brief Get the count of voxels with the smallest scalar value in the dataset mitk::ScalarType GetCountOfMinValuedVoxels(int t = 0) const; //##Documentation //## \brief Get the count of voxels with the largest scalar value in the dataset mitk::ScalarType GetCountOfMaxValuedVoxels(int t = 0) const; //##Documentation //## \brief Get the count of voxels with the largest scalar value in the dataset virtual unsigned int GetCountOfMaxValuedVoxelsNoRecompute( unsigned int t = 0 ) const { if ( t < m_CountOfMaxValuedVoxels.size() ) return m_CountOfMaxValuedVoxels[t]; else return 0; } //##Documentation //## \brief Get the count of voxels with the smallest scalar value in the dataset virtual unsigned int GetCountOfMinValuedVoxelsNoRecompute( unsigned int t = 0 ) const { if ( t < m_CountOfMinValuedVoxels.size() ) return m_CountOfMinValuedVoxels[t]; else return 0; } //##Documentation //## @warning for internal use only virtual ImageDataItemPointer GetSliceData(int s = 0, int t = 0, int n = 0, void *data = NULL, ImportMemoryManagementType importMemoryManagement = CopyMemory); //##Documentation //## @warning for internal use only virtual ImageDataItemPointer GetVolumeData(int t = 0, int n = 0, void *data = NULL, ImportMemoryManagementType importMemoryManagement = CopyMemory); //##Documentation //## @warning for internal use only virtual ImageDataItemPointer GetChannelData(int n = 0, void *data = NULL, ImportMemoryManagementType importMemoryManagement = CopyMemory); template < typename ItkImageType > friend void _ComputeExtremaInItkImage(ItkImageType* itkImage, mitk::Image * mitkImage, int t); protected: int GetSliceIndex(int s = 0, int t = 0, int n = 0) const; int GetVolumeIndex(int t = 0, int n = 0) const; void ComputeOffsetTable(); - virtual void Expand( int timeSteps ) const; + virtual void Expand( unsigned int timeSteps ); virtual bool IsValidTimeStep(int t) const; virtual void ResetImageStatistics() const; virtual void ComputeImageStatistics(int t=0) const; virtual ImageDataItemPointer AllocateSliceData(int s = 0, int t = 0, int n = 0, void *data = NULL, ImportMemoryManagementType importMemoryManagement = CopyMemory); virtual ImageDataItemPointer AllocateVolumeData(int t = 0, int n = 0, void *data = NULL, ImportMemoryManagementType importMemoryManagement = CopyMemory); virtual ImageDataItemPointer AllocateChannelData(int n = 0, void *data = NULL, ImportMemoryManagementType importMemoryManagement = CopyMemory); Image(); virtual ~Image(); virtual void Clear(); //## @warning Has to be called by every Initialize method! virtual void Initialize(); ImageTimeSelector* GetTimeSelector() const; virtual void PrintSelf(std::ostream& os, itk::Indent indent) const; mutable ImageDataItemPointerArray m_Channels; mutable ImageDataItemPointerArray m_Volumes; mutable ImageDataItemPointerArray m_Slices; unsigned int m_Dimension; unsigned int *m_Dimensions; size_t *m_OffsetTable; ImageDataItemPointer m_CompleteData; PixelType m_PixelType; mutable itk::Object::Pointer m_HistogramGeneratorObject; mutable itk::Object::Pointer m_TimeSelectorForExtremaObject; mutable std::vector m_CountOfMinValuedVoxels; mutable std::vector m_CountOfMaxValuedVoxels; mutable std::vector m_ScalarMin; mutable std::vector m_ScalarMax; mutable std::vector m_Scalar2ndMin; mutable std::vector m_Scalar2ndMax; itk::TimeStamp m_LastRecomputeTimeStamp; }; //##Documentation //## @brief Cast an itk::Image (with a specific type) to an mitk::Image. //## //## CastToMitkImage does not cast pixel types etc., just image data //## Needs "mitkImage.h" header included. //## If you get a compile error, try image.GetPointer(); //## @ingroup Adaptor //## \sa mitkITKImageImport template void CastToMitkImage(const itk::SmartPointer& itkimage, itk::SmartPointer& mitkoutputimage) { if(mitkoutputimage.IsNull()) { mitkoutputimage = mitk::Image::New(); } mitkoutputimage->InitializeByItk(itkimage.GetPointer()); mitkoutputimage->SetChannel(itkimage->GetBufferPointer()); } //##Documentation //## @brief Cast an itk::Image (with a specific type) to an mitk::Image. //## //## CastToMitkImage does not cast pixel types etc., just image data //## Needs "mitkImage.h" header included. //## If you get a compile error, try image.GetPointer(); //## @ingroup Adaptor //## \sa mitkITKImageImport template void CastToMitkImage(const ItkOutputImageType* itkimage, itk::SmartPointer& mitkoutputimage) { if(mitkoutputimage.IsNull()) { mitkoutputimage = mitk::Image::New(); } mitkoutputimage->InitializeByItk(itkimage); mitkoutputimage->SetChannel(itkimage->GetBufferPointer()); } } // namespace mitk #endif /* MITKIMAGE_H_HEADER_INCLUDED_C1C2FCD2 */