diff --git a/Core/Code/DataManagement/mitkImage.cpp b/Core/Code/DataManagement/mitkImage.cpp index 6c052b74df..f07b909904 100644 --- a/Core/Code/DataManagement/mitkImage.cpp +++ b/Core/Code/DataManagement/mitkImage.cpp @@ -1,1275 +1,1276 @@ /*========================================================================= 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 "mitkImageStatisticsHolder.h" #include "mitkPixelTypeMultiplex.h" #include #define FILL_C_ARRAY( _arr, _size, _value) for(unsigned int i=0u; i<_size; i++) \ { _arr[i] = _value; } mitk::Image::Image() : 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); - - m_Initialized = false; + // Initialize the image with minimal values + const unsigned int dim[3] = {1,1,1}; + this->Initialize(mitk::MakeScalarPixelType() , 3, dim, 1); + const unsigned char data = 0; + this->SetVolume( &data ); } 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()); 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(other).GetVolumeData(i); this->SetVolume(volume->GetData(), i); } } else { ImageDataItemPointer volume = const_cast(other).GetVolumeData(0); this->SetVolume(volume->GetData(), 0); } } mitk::Image::~Image() { Clear(); m_ReferenceCountLock.Lock(); m_ReferenceCount = 3; m_ReferenceCountLock.Unlock(); m_ReferenceCountLock.Lock(); m_ReferenceCount = 0; m_ReferenceCountLock.Unlock(); if(m_OffsetTable != NULL) delete [] m_OffsetTable; if(m_ImageStatistics != NULL) delete m_ImageStatistics; } const mitk::PixelType mitk::Image::GetPixelType(int n) const { return this->m_ImageDescriptor->GetChannelTypeById(n); } 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().IsNull()) return NULL; if(GetSource()->Updating()==false) GetSource()->UpdateOutputInformation(); } m_CompleteData=GetChannelData(); // update channel's data // if data was not available at creation point, the m_Data of channel descriptor is NULL // if data present, it won't be overwritten m_ImageDescriptor->GetChannelDescriptor(0).SetData(m_CompleteData->GetData()); return m_CompleteData->GetData(); } template void AccessPixel( const mitk::PixelType ptype, void* data, const unsigned int offset, double& value ) { value = 0.0; if( data == NULL ) return; if(ptype.GetBpe() != 24) { value = (double) (((T*) data)[ offset ]); } else { const unsigned int rgboffset = 3 * offset; double returnvalue = (((T*) data)[rgboffset ]); returnvalue += (((T*) data)[rgboffset + 1]); returnvalue += (((T*) data)[rgboffset + 2]); value = returnvalue; } } double mitk::Image::GetPixelValueByIndex(const mitk::Index3D &position, unsigned int timestep) { double value = 0; if (this->GetTimeSteps() < timestep) { timestep = this->GetTimeSteps(); } value = 0.0; const unsigned int* imageDims = this->m_ImageDescriptor->GetDimensions(); const mitk::PixelType ptype = this->m_ImageDescriptor->GetChannelTypeById(0); // Comparison ?>=0 not needed since all position[i] and timestep are unsigned int // (position[0]>=0 && position[1] >=0 && position[2]>=0 && timestep>=0) // && if ( (unsigned int)position[0] < imageDims[0] && (unsigned int)position[1] < imageDims[1] && ( (imageDims[2] == 0) || (unsigned int)position[2] < imageDims[2]) // in case a 2D Image passed in, the third dimension could be set to 0 causing the if() to fail /*&& (unsigned int)timestep < imageDims[3]*/ ) { const unsigned int offset = position[0] + position[1]*imageDims[0] + position[2]*imageDims[0]*imageDims[1] + timestep*imageDims[0]*imageDims[1]*imageDims[2]; mitkPixelTypeMultiplex3( AccessPixel, ptype, this->GetData(), offset, value ); } return value; } double mitk::Image::GetPixelValueByWorldCoordinate(const mitk::Point3D& position, unsigned int timestep) { double value = 0.0; if (this->GetTimeSteps() < timestep) { timestep = this->GetTimeSteps(); } Index3D itkIndex; this->GetGeometry()->WorldToIndex(position, itkIndex); const unsigned int* imageDims = this->m_ImageDescriptor->GetDimensions(); const mitk::PixelType ptype = this->m_ImageDescriptor->GetChannelTypeById(0); //if ( (itkIndex[0]>=0 && itkIndex[1] >=0 && itkIndex[2]>=0 && timestep>=0) // && // lines above taken from comparison since always true due to unsigned type if((unsigned int)itkIndex[0] < imageDims[0] && (unsigned int)itkIndex[1] < imageDims[1] && (imageDims[2] == 0) || ((unsigned int)itkIndex[2] < imageDims[2])) // in case a 2D Image passed in, the third dimension could be set to 0 causing the if() to fail { const unsigned int offset = itkIndex[0] + itkIndex[1]*imageDims[0] + itkIndex[2]*imageDims[0]*imageDims[1] + timestep*imageDims[0]*imageDims[1]*imageDims[2]; mitkPixelTypeMultiplex3( AccessPixel, ptype, this->GetData(), offset, value ); } return value; } vtkImageData* mitk::Image::GetVtkImageData(int t, int n) { if(m_Initialized==false) { if(GetSource().IsNull()) return NULL; if(GetSource()->Updating()==false) GetSource()->UpdateOutputInformation(); } ImageDataItemPointer volume=GetVolumeData(t, n); if(volume.GetPointer()==NULL || volume->GetVtkImageData() == NULL) return NULL; float *fspacing = const_cast(GetSlicedGeometry(t)->GetFloatSpacing()); double dspacing[3] = {fspacing[0],fspacing[1],fspacing[2]}; volume->GetVtkImageData()->SetSpacing( dspacing ); return volume->GetVtkImageData(); } mitk::Image::ImageDataItemPointer mitk::Image::GetSliceData(int s, int t, int n, void *data, ImportMemoryManagementType importMemoryManagement) { if(IsValidSlice(s,t,n)==false) return NULL; const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize(); // 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, m_ImageDescriptor, 2, data, importMemoryManagement == ManageMemory, ((size_t) s)*m_OffsetTable[2]*(ptypeSize)); 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, m_ImageDescriptor, 2, data, importMemoryManagement == ManageMemory, (((size_t) s)*m_OffsetTable[2]+((size_t) t)*m_OffsetTable[3])*(ptypeSize)); sl->SetComplete(true); return m_Slices[pos]=sl; } // slice is unavailable. Can we calculate it? if((GetSource().IsNotNull()) && (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; const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize(); // 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, m_ImageDescriptor, 3, data, importMemoryManagement == ManageMemory, (((size_t) t)*m_OffsetTable[3])*(ptypeSize)); 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 { mitk::PixelType chPixelType = this->m_ImageDescriptor->GetChannelTypeById(n); vol=m_Volumes[pos]; // ok, let's combine the slices! if(vol.GetPointer()==NULL) vol=new ImageDataItem( chPixelType, 3, m_Dimensions, NULL, true); vol->SetComplete(true); size_t size=m_OffsetTable[2]*(ptypeSize); 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); // FIXME mitkIpPicDescriptor * pic = sl->GetPicDescriptor(); // replace old slice with reference to volume sl=new ImageDataItem(*vol, m_ImageDescriptor, 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().IsNotNull()) && (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, m_ImageDescriptor, m_ImageDescriptor->GetNumberOfDimensions(), data, importMemoryManagement == ManageMemory); ch->SetComplete(true); } else { const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize(); ch=m_Channels[n]; // ok, let's combine the volumes! if(ch.GetPointer()==NULL) ch=new ImageDataItem(this->m_ImageDescriptor, NULL, true); ch->SetComplete(true); size_t size=m_OffsetTable[m_Dimension-1]*(ptypeSize); 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]*(ptypeSize); std::memcpy(static_cast(ch->GetData())+offset, vol->GetData(), size); // REVEIW FIX mitkIpPicDescriptor * pic = vol->GetPicDescriptor(); // replace old volume with reference to channel vol=new ImageDataItem(*ch, m_ImageDescriptor, 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; } } } // REVIEW FIX // 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().IsNotNull()) && (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; const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize(); 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]*(ptypeSize)); 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]*(ptypeSize)); //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; const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize(); 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]*(ptypeSize)); 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]*(ptypeSize)); } vol->SetComplete(true); this->m_ImageDescriptor->GetChannelDescriptor(n).SetData( vol->GetData() ); //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; // channel descriptor const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize(); 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]*(ptypeSize)); 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]*(ptypeSize)); ch->SetComplete(true); this->m_ImageDescriptor->GetChannelDescriptor(n).SetData( ch->GetData() ); //we just added a missing Channel, which is not regarded as modification. //Therefore, we do not call Modified()! } return true; } 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; if( m_ImageStatistics == NULL) { m_ImageStatistics = new mitk::ImageStatisticsHolder( this ); } SetRequestedRegionToLargestPossibleRegion(); } void mitk::Image::Initialize(const mitk::ImageDescriptor::Pointer inDesc) { // store the descriptor this->m_ImageDescriptor = inDesc; // initialize image this->Initialize( inDesc->GetChannelDescriptor(0).GetPixelType(), inDesc->GetNumberOfDimensions(), inDesc->GetDimensions(), 1 ); } 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;im_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 = NULL; return; } for( unsigned int i=0u; im_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]); 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; this->m_ImageDescriptor->Initialize( this->m_Dimensions, this->m_Dimension ); 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(), *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; } switch ( vtkimagedata->GetScalarType() ) { case VTK_BIT: case VTK_CHAR: //pixelType.Initialize(typeid(char), vtkimagedata->GetNumberOfScalarComponents()); Initialize(mitk::MakeScalarPixelType(), m_Dimension, tmpDimensions, channels); break; case VTK_UNSIGNED_CHAR: //pixelType.Initialize(typeid(unsigned char), vtkimagedata->GetNumberOfScalarComponents()); Initialize(mitk::MakeScalarPixelType(), m_Dimension, tmpDimensions, channels); break; case VTK_SHORT: //pixelType.Initialize(typeid(short), vtkimagedata->GetNumberOfScalarComponents()); Initialize(mitk::MakeScalarPixelType(), m_Dimension, tmpDimensions, channels); break; case VTK_UNSIGNED_SHORT: //pixelType.Initialize(typeid(unsigned short), vtkimagedata->GetNumberOfScalarComponents()); Initialize(mitk::MakeScalarPixelType(), m_Dimension, tmpDimensions, channels); break; case VTK_INT: //pixelType.Initialize(typeid(int), vtkimagedata->GetNumberOfScalarComponents()); Initialize(mitk::MakeScalarPixelType(), m_Dimension, tmpDimensions, channels); break; case VTK_UNSIGNED_INT: //pixelType.Initialize(typeid(unsigned int), vtkimagedata->GetNumberOfScalarComponents()); Initialize(mitk::MakeScalarPixelType(), m_Dimension, tmpDimensions, channels); break; case VTK_LONG: //pixelType.Initialize(typeid(long), vtkimagedata->GetNumberOfScalarComponents()); Initialize(mitk::MakeScalarPixelType(), m_Dimension, tmpDimensions, channels); break; case VTK_UNSIGNED_LONG: //pixelType.Initialize(typeid(unsigned long), vtkimagedata->GetNumberOfScalarComponents()); Initialize(mitk::MakeScalarPixelType(), m_Dimension, tmpDimensions, channels); break; case VTK_FLOAT: //pixelType.Initialize(typeid(float), vtkimagedata->GetNumberOfScalarComponents()); Initialize(mitk::MakeScalarPixelType(), m_Dimension, tmpDimensions, channels); break; case VTK_DOUBLE: //pixelType.Initialize(typeid(double), vtkimagedata->GetNumberOfScalarComponents()); Initialize(mitk::MakeScalarPixelType(), m_Dimension, tmpDimensions, channels); break; default: break; } /* Initialize(pixelType, m_Dimension, tmpDimensions, channels); */ const double *spacinglist = vtkimagedata->GetSpacing(); 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; } 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; } bool mitk::Image::IsValidTimeStep(int t) const { return ( ( m_Dimension >= 4 && t <= (int)m_Dimensions[3] && t > 0 ) || (t == 0) ); } void mitk::Image::Expand(unsigned int timeSteps) { if(timeSteps < 1) itkExceptionMacro(<< "Invalid timestep in Image!"); Superclass::Expand(timeSteps); } 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); const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize(); // 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, m_ImageDescriptor, 2, data, importMemoryManagement == ManageMemory, ((size_t) s)*m_OffsetTable[2]*(ptypeSize)); 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, m_ImageDescriptor, 2, data, importMemoryManagement == ManageMemory, (((size_t) s)*m_OffsetTable[2]+((size_t) t)*m_OffsetTable[3])*(ptypeSize)); 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, m_ImageDescriptor, 2, data, importMemoryManagement == ManageMemory, ((size_t) s)*m_OffsetTable[2]*(ptypeSize)); 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); const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize(); // 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, m_ImageDescriptor, 3, data,importMemoryManagement == ManageMemory, (((size_t) t)*m_OffsetTable[3])*(ptypeSize)); return m_Volumes[pos]=vol; } mitk::PixelType chPixelType = this->m_ImageDescriptor->GetChannelTypeById(n); // allocate new volume if(importMemoryManagement == CopyMemory) { vol=new ImageDataItem( chPixelType, 3, m_Dimensions, NULL, true); if(data != NULL) std::memcpy(vol->GetData(), data, m_OffsetTable[3]*(ptypeSize)); } else { vol=new ImageDataItem( chPixelType, 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) { const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize(); ch=new ImageDataItem(this->m_ImageDescriptor, NULL, true); if(data != NULL) std::memcpy(ch->GetData(), data, m_OffsetTable[4]*(ptypeSize)); } else { ch=new ImageDataItem(this->m_ImageDescriptor, 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(); } void mitk::Image::PrintSelf(std::ostream& os, itk::Indent indent) const { unsigned char i; if(m_Initialized) { os << indent << " Dimension: " << m_Dimension << std::endl; os << indent << " Dimensions: "; for(i=0; i < m_Dimension; ++i) os << GetDimension(i) << " "; os << std::endl; for(unsigned int ch=0; ch < this->m_ImageDescriptor->GetNumberOfChannels(); ch++) { mitk::PixelType chPixelType = this->m_ImageDescriptor->GetChannelTypeById(ch); os << indent << " Channel: " << this->m_ImageDescriptor->GetChannelName(ch) << std::endl; os << indent << " PixelType: " << chPixelType.GetTypeId().name() << std::endl; os << indent << " BitsPerElement: " << chPixelType.GetSize() << std::endl; os << indent << " NumberOfComponents: " << chPixelType.GetNumberOfComponents() << std::endl; os << indent << " BitsPerComponent: " << chPixelType.GetBitsPerComponent() << 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; } #include "mitkImageStatisticsHolder.h" //##Documentation mitk::ScalarType mitk::Image::GetScalarValueMin(int t) const { return m_ImageStatistics->GetScalarValueMin(t); } //##Documentation //## \brief Get the maximum for scalar images mitk::ScalarType mitk::Image::GetScalarValueMax(int t) const { return m_ImageStatistics->GetScalarValueMax(t); } //##Documentation //## \brief Get the second smallest value for scalar images mitk::ScalarType mitk::Image::GetScalarValue2ndMin(int t) const { return m_ImageStatistics->GetScalarValue2ndMin(t); } mitk::ScalarType mitk::Image::GetScalarValueMinNoRecompute( unsigned int t ) const { return m_ImageStatistics->GetScalarValueMinNoRecompute(t); } mitk::ScalarType mitk::Image::GetScalarValue2ndMinNoRecompute( unsigned int t ) const { return m_ImageStatistics->GetScalarValue2ndMinNoRecompute(t); } mitk::ScalarType mitk::Image::GetScalarValue2ndMax(int t) const { return m_ImageStatistics->GetScalarValue2ndMax(t); } mitk::ScalarType mitk::Image::GetScalarValueMaxNoRecompute( unsigned int t) const { return m_ImageStatistics->GetScalarValueMaxNoRecompute(t); } mitk::ScalarType mitk::Image::GetScalarValue2ndMaxNoRecompute( unsigned int t ) const { return m_ImageStatistics->GetScalarValue2ndMaxNoRecompute(t); } mitk::ScalarType mitk::Image::GetCountOfMinValuedVoxels(int t ) const { return m_ImageStatistics->GetCountOfMinValuedVoxels(t); } mitk::ScalarType mitk::Image::GetCountOfMaxValuedVoxels(int t) const { return m_ImageStatistics->GetCountOfMaxValuedVoxels(t); } unsigned int mitk::Image::GetCountOfMaxValuedVoxelsNoRecompute( unsigned int t ) const { return m_ImageStatistics->GetCountOfMaxValuedVoxelsNoRecompute(t); } unsigned int mitk::Image::GetCountOfMinValuedVoxelsNoRecompute( unsigned int t ) const { return m_ImageStatistics->GetCountOfMinValuedVoxelsNoRecompute(t); } diff --git a/Core/Code/Testing/mitkImageTest.cpp b/Core/Code/Testing/mitkImageTest.cpp index 6be4c0b921..58b22396ba 100644 --- a/Core/Code/Testing/mitkImageTest.cpp +++ b/Core/Code/Testing/mitkImageTest.cpp @@ -1,336 +1,354 @@ /*========================================================================= 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. =========================================================================*/ // mitk includes #include #include #include #include "mitkItkImageFileReader.h" #include #include // itk includes #include #include // stl includes #include // vtk includes #include int mitkImageTest(int argc, char* argv[]) { MITK_TEST_BEGIN(mitkImageTest); //Create Image out of nowhere mitk::Image::Pointer imgMem = mitk::Image::New(); mitk::PixelType pt = mitk::MakeScalarPixelType(); unsigned int dim[]={100,100,20}; MITK_TEST_CONDITION_REQUIRED( imgMem.IsNotNull(), "An image was created. "); // Initialize image imgMem->Initialize( pt, 3, dim); MITK_TEST_CONDITION_REQUIRED( imgMem->IsInitialized(), "Image::IsInitialized() ?"); MITK_TEST_CONDITION_REQUIRED( imgMem->GetPixelType() == pt, "PixelType was set correctly."); int *p = (int*)imgMem->GetData(); MITK_TEST_CONDITION( p != NULL, "GetData() returned not-NULL pointer."); // FIXME: this is directly changing the image data // filling image const unsigned int size = dim[0]*dim[1]*dim[2]; for(unsigned int i=0; iGetData(); MITK_TEST_CONDITION( p2 != NULL, "GetData() returned not-NULL pointer."); bool isEqual = true; for(unsigned int i=0; iGetSliceData(dim[2]/2)->GetData(); MITK_TEST_CONDITION_REQUIRED( p2 != NULL, "Valid slice data returned"); unsigned int xy_size = dim[0]*dim[1]; unsigned int start_mid_slice = (dim[2]/2)*xy_size; isEqual = true; for(unsigned int i=0; i(); imgMem->Initialize( pType , 3, dim); MITK_TEST_CONDITION_REQUIRED(imgMem->GetDimension()== 3, "Testing initialization parameter dimension!"); MITK_TEST_CONDITION_REQUIRED(imgMem->GetPixelType() == pType, "Testing initialization parameter pixeltype!"); MITK_TEST_CONDITION_REQUIRED(imgMem->GetDimension(0) == dim[0] && imgMem->GetDimension(1)== dim[1] && imgMem->GetDimension(2)== dim[2], "Testing initialization of dimensions!"); MITK_TEST_CONDITION( imgMem->IsInitialized(), "Image is initialized."); // Setting volume again: imgMem->SetVolume(imgMem->GetData()); //----------------- // geometry information for image mitk::Point3D origin; mitk::Vector3D right, bottom; mitk::Vector3D spacing; mitk::FillVector3D(origin, 17.0, 19.92, 7.83); mitk::FillVector3D(right, 1.0, 2.0, 3.0); mitk::FillVector3D(bottom, 0.0, -3.0, 2.0); mitk::FillVector3D(spacing, 0.78, 0.91, 2.23); //InitializeStandardPlane(rightVector, downVector, spacing) mitk::PlaneGeometry::Pointer planegeometry = mitk::PlaneGeometry::New(); planegeometry->InitializeStandardPlane(100, 100, right, bottom, &spacing); planegeometry->SetOrigin(origin); // Testing Initialize(const mitk::PixelType& type, const mitk::Geometry3D& geometry, unsigned int slices) with PlaneGeometry and GetData(): "; imgMem->Initialize( mitk::MakePixelType(), *planegeometry); MITK_TEST_CONDITION_REQUIRED( imgMem->GetGeometry()->GetOrigin() == static_cast(planegeometry)->GetOrigin(), "Testing correct setting of geometry via initialize!"); p = (int*)imgMem->GetData(); MITK_TEST_CONDITION_REQUIRED( p!=NULL, "GetData() returned valid pointer."); // Testing Initialize(const mitk::PixelType& type, int sDim, const mitk::PlaneGeometry& geometry) and GetData(): "; imgMem->Initialize( mitk::MakePixelType() , 40, *planegeometry); p = (int*)imgMem->GetData(); MITK_TEST_CONDITION_REQUIRED( p!=NULL, "GetData() returned valid pointer."); //----------------- // testing origin information and methods MITK_TEST_CONDITION_REQUIRED( mitk::Equal(imgMem->GetGeometry()->GetOrigin(), origin), "Testing correctness of origin via GetGeometry()->GetOrigin(): "); MITK_TEST_CONDITION_REQUIRED( mitk::Equal(imgMem->GetTimeSlicedGeometry()->GetOrigin(), origin), "Testing correctness of origin via GetTimeSlicedGeometry()->GetOrigin(): "); // Setting origin via SetOrigin(origin): "; mitk::FillVector3D(origin, 37.0, 17.92, 27.83); imgMem->SetOrigin(origin); // Test origin MITK_TEST_CONDITION_REQUIRED( mitk::Equal(imgMem->GetGeometry()->GetOrigin(), origin), "Testing correctness of changed origin via GetGeometry()->GetOrigin(): "); MITK_TEST_CONDITION_REQUIRED( mitk::Equal(imgMem->GetTimeSlicedGeometry()->GetOrigin(), origin), "Testing correctness of changed origin via GetTimeSlicedGeometry()->GetOrigin(): "); MITK_TEST_CONDITION_REQUIRED( mitk::Equal(imgMem->GetSlicedGeometry()->GetGeometry2D(0)->GetOrigin(), origin), "Testing correctness of changed origin via GetSlicedGeometry()->GetGeometry2D(0)->GetOrigin(): "); //----------------- // testing spacing information and methods MITK_TEST_CONDITION_REQUIRED(mitk::Equal(imgMem->GetGeometry()->GetSpacing(), spacing), "Testing correct spacing from Geometry3D!"); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(imgMem->GetTimeSlicedGeometry()->GetSpacing(), spacing), "Testing correctspacing from TimeSlicedGeometry!"); mitk::FillVector3D(spacing, 7.0, 0.92, 1.83); imgMem->SetSpacing(spacing); MITK_TEST_CONDITION_REQUIRED( mitk::Equal(imgMem->GetGeometry()->GetSpacing(), spacing), "Testing correctness of changed spacing via GetGeometry()->GetSpacing(): "); MITK_TEST_CONDITION_REQUIRED( mitk::Equal(imgMem->GetTimeSlicedGeometry()->GetSpacing(), spacing), "Testing correctness of changed spacing via GetTimeSlicedGeometry()->GetSpacing(): "); MITK_TEST_CONDITION_REQUIRED( mitk::Equal(imgMem->GetSlicedGeometry()->GetGeometry2D(0)->GetSpacing(), spacing), "Testing correctness of changed spacing via GetSlicedGeometry()->GetGeometry2D(0)->GetSpacing(): "); mitk::Image::Pointer vecImg = mitk::Image::New(); vecImg->Initialize( imgMem->GetPixelType(), *imgMem->GetGeometry(), 2 /* #channels */, 0 /*tDim*/ ); vecImg->SetImportChannel(imgMem->GetData(), 0, mitk::Image::CopyMemory ); vecImg->SetImportChannel(imgMem->GetData(), 1, mitk::Image::CopyMemory ); MITK_TEST_CONDITION_REQUIRED(vecImg->GetChannelData(0)->GetData() != NULL && vecImg->GetChannelData(1)->GetData() != NULL, "Testing set and return of channel data!"); MITK_TEST_CONDITION_REQUIRED( vecImg->IsValidSlice(0,0,1) , ""); MITK_TEST_OUTPUT(<< " Testing whether CopyMemory worked"); MITK_TEST_CONDITION_REQUIRED(imgMem->GetData() != vecImg->GetData(), ""); MITK_TEST_OUTPUT(<< " Testing destruction after SetImportChannel"); vecImg = NULL; MITK_TEST_CONDITION_REQUIRED(vecImg.IsNull() , "testing destruction!"); //----------------- MITK_TEST_OUTPUT(<< "Testing initialization via vtkImageData"); MITK_TEST_OUTPUT(<< " Setting up vtkImageData"); vtkImageData* vtkimage = vtkImageData::New(); vtkimage->Initialize(); vtkimage->SetDimensions( 2, 3, 4); double vtkorigin[] = {-350,-358.203, -1363.5}; vtkimage->SetOrigin(vtkorigin); mitk::Point3D vtkoriginAsMitkPoint; mitk::vtk2itk(vtkorigin, vtkoriginAsMitkPoint); double vtkspacing[] = {1.367, 1.367, 2}; vtkimage->SetSpacing(vtkspacing); vtkimage->SetScalarType( VTK_SHORT ); vtkimage->AllocateScalars(); std::cout<<"[PASSED]"<Initialize(vtkimage); MITK_TEST_CONDITION_REQUIRED(mitkByVtkImage->IsInitialized(), ""); vtkimage->Delete(); MITK_TEST_OUTPUT(<< " Testing whether spacing has been correctly initialized from vtkImageData"); mitk::Vector3D spacing2 = mitkByVtkImage->GetGeometry()->GetSpacing(); mitk::Vector3D vtkspacingAsMitkVector; mitk::vtk2itk(vtkspacing, vtkspacingAsMitkVector); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(spacing2,vtkspacingAsMitkVector), ""); MITK_TEST_OUTPUT(<< " Testing whether GetSlicedGeometry(0)->GetOrigin() has been correctly initialized from vtkImageData"); mitk::Point3D origin2 = mitkByVtkImage->GetSlicedGeometry(0)->GetOrigin(); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(origin2,vtkoriginAsMitkPoint), ""); MITK_TEST_OUTPUT(<< " Testing whether GetGeometry()->GetOrigin() has been correctly initialized from vtkImageData"); origin2 = mitkByVtkImage->GetGeometry()->GetOrigin(); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(origin2,vtkoriginAsMitkPoint), ""); MITK_TEST_OUTPUT(<< " Testing whether GetTimeSlicedGeometry()->GetOrigin() has been correctly initialized from vtkImageData"); origin2 = mitkByVtkImage->GetTimeSlicedGeometry()->GetOrigin(); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(origin2,vtkoriginAsMitkPoint), ""); // TODO test the following initializers on channel-incorporation // void mitk::Image::Initialize(const mitk::PixelType& type, unsigned int dimension, unsigned int *dimensions, unsigned int channels) // void mitk::Image::Initialize(const mitk::PixelType& type, int sDim, const mitk::Geometry2D& geometry2d, bool flipped, unsigned int channels, int tDim ) // void mitk::Image::Initialize(const mitk::Image* image) // void mitk::Image::Initialize(const mitkIpPicDescriptor* pic, int channels, int tDim, int sDim) //mitk::Image::Pointer vecImg = mitk::Image::New(); //vecImg->Initialize(PixelType(typeid(float), 6, itk::ImageIOBase::SYMMETRICSECONDRANKTENSOR), *imgMem->GetGeometry(), 2 /* #channels */, 0 /*tDim*/, false /*shiftBoundingBoxMinimumToZero*/ ); //vecImg->Initialize(PixelType(typeid(itk::Vector)), *imgMem->GetGeometry(), 2 /* #channels */, 0 /*tDim*/, false /*shiftBoundingBoxMinimumToZero*/ ); // testing access by index coordinates and by world coordinates - MITK_TEST_CONDITION_REQUIRED(argc == 2, "Check if test image is accessible!"); - const std::string filename = std::string(argv[1]); - mitk::ItkImageFileReader::Pointer imageReader = mitk::ItkImageFileReader::New(); - try - { - imageReader->SetFileName(filename); - imageReader->Update(); - } - catch(...) { - MITK_TEST_FAILED_MSG(<< "Could not read file for testing: " << filename); - return 0; - } - - mitk::Image::Pointer image = imageReader->GetOutput(); - - // generate a random point in world coordinates - mitk::Point3D xMax, yMax, zMax, xMaxIndex, yMaxIndex, zMaxIndex; - xMaxIndex.Fill(0.0f); - yMaxIndex.Fill(0.0f); - zMaxIndex.Fill(0.0f); - xMaxIndex[0] = image->GetLargestPossibleRegion().GetSize()[0]; - yMaxIndex[1] = image->GetLargestPossibleRegion().GetSize()[1]; - zMaxIndex[2] = image->GetLargestPossibleRegion().GetSize()[2]; - image->GetGeometry()->IndexToWorld(xMaxIndex, xMax); - image->GetGeometry()->IndexToWorld(yMaxIndex, yMax); - image->GetGeometry()->IndexToWorld(zMaxIndex, zMax); - MITK_INFO << "Origin " << image->GetGeometry()->GetOrigin()[0] << " "<< image->GetGeometry()->GetOrigin()[1] << " "<< image->GetGeometry()->GetOrigin()[2] << ""; - MITK_INFO << "MaxExtend " << xMax[0] << " "<< yMax[1] << " "<< zMax[2] << ""; - mitk::Point3D point; - - itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer randomGenerator = itk::Statistics::MersenneTwisterRandomVariateGenerator::New(); - randomGenerator->Initialize( std::rand() ); // initialize with random value, to get sensible random points for the image - point[0] = randomGenerator->GetUniformVariate( image->GetGeometry()->GetOrigin()[0], xMax[0]); - point[1] = randomGenerator->GetUniformVariate( image->GetGeometry()->GetOrigin()[1], yMax[1]); - point[2] = randomGenerator->GetUniformVariate( image->GetGeometry()->GetOrigin()[2], zMax[2]); - MITK_INFO << "RandomPoint " << point[0] << " "<< point[1] << " "<< point[2] << ""; - - // test values and max/min - mitk::ScalarType imageMin = image->GetStatistics()->GetScalarValueMin(); - mitk::ScalarType imageMax = image->GetStatistics()->GetScalarValueMax(); - mitk::ScalarType value = image->GetPixelValueByWorldCoordinate(point); - MITK_INFO << imageMin << " "<< imageMax << " "<< value << ""; - MITK_TEST_CONDITION( (value >= imageMin && value <= imageMax), "Value returned is between max/min"); - - mitk::Image::Pointer cloneImage = image->Clone(); - MITK_TEST_CONDITION_REQUIRED(cloneImage->GetDimension() == image->GetDimension(), "Clone (testing dimension)"); - MITK_TEST_CONDITION_REQUIRED(cloneImage->GetPixelType() == image->GetPixelType(), "Clone (testing pixel type)"); - - for (unsigned int i = 0u; i < cloneImage->GetDimension(); ++i) - { - MITK_TEST_CONDITION_REQUIRED(cloneImage->GetDimension(i) == image->GetDimension(i), "Clone (testing dimension " << i << ")"); - } - //access via itk - if(image->GetDimension()> 3) // CastToItk only works with 3d images so we need to check for 4d images - { - mitk::ImageTimeSelector::Pointer selector = mitk::ImageTimeSelector::New(); - selector->SetTimeNr(0); - selector->SetInput(image); - selector->Update(); - image = selector->GetOutput(); - } - if(image->GetDimension()==3) + // PERFORM TESTS ON IMAGE FROM HDD, IF FILENAME WAS PROVIDED + if (argc > 1) { - typedef itk::Image ItkFloatImage3D; - ItkFloatImage3D::Pointer itkimage; - mitk::CastToItkImage(image, itkimage); - MITK_TEST_CONDITION_REQUIRED(itkimage.IsNotNull(), "Test conversion to itk::Image!"); - - mitk::Point3D itkPhysicalPoint; - image->GetGeometry()->WorldToItkPhysicalPoint(point, itkPhysicalPoint); - MITK_INFO << "ITKPoint " << itkPhysicalPoint[0] << " "<< itkPhysicalPoint[1] << " "<< itkPhysicalPoint[2] << ""; - - mitk::Point3D backTransformedPoint; - image->GetGeometry()->ItkPhysicalPointToWorld(itkPhysicalPoint, backTransformedPoint); - - MITK_TEST_CONDITION_REQUIRED( mitk::Equal(point,backTransformedPoint), "Testing world->itk-physical->world consistency"); - - itk::Index<3> idx; - bool status = itkimage->TransformPhysicalPointToIndex(itkPhysicalPoint, idx); - - MITK_INFO << "ITK Index " << idx[0] << " "<< idx[1] << " "<< idx[2] << ""; - - if(status) - { - float valByItk = itkimage->GetPixel(idx); - MITK_TEST_CONDITION_REQUIRED( mitk::Equal(valByItk, value), "Compare value of pixel returned by mitk in comparison to itk"); - } - else - { - MITK_WARN<< "Index is out buffered region!"; - } + MITK_TEST_CONDITION_REQUIRED(argc == 2, "Check if test image is accessible!"); + const std::string filename = std::string(argv[1]); + mitk::ItkImageFileReader::Pointer imageReader = mitk::ItkImageFileReader::New(); + try + { + imageReader->SetFileName(filename); + imageReader->Update(); + } + catch(...) { + MITK_TEST_FAILED_MSG(<< "Could not read file for testing: " << filename); + return 0; + } + + mitk::Image::Pointer image = imageReader->GetOutput(); + + // generate a random point in world coordinates + mitk::Point3D xMax, yMax, zMax, xMaxIndex, yMaxIndex, zMaxIndex; + xMaxIndex.Fill(0.0f); + yMaxIndex.Fill(0.0f); + zMaxIndex.Fill(0.0f); + xMaxIndex[0] = image->GetLargestPossibleRegion().GetSize()[0]; + yMaxIndex[1] = image->GetLargestPossibleRegion().GetSize()[1]; + zMaxIndex[2] = image->GetLargestPossibleRegion().GetSize()[2]; + image->GetGeometry()->IndexToWorld(xMaxIndex, xMax); + image->GetGeometry()->IndexToWorld(yMaxIndex, yMax); + image->GetGeometry()->IndexToWorld(zMaxIndex, zMax); + MITK_INFO << "Origin " << image->GetGeometry()->GetOrigin()[0] << " "<< image->GetGeometry()->GetOrigin()[1] << " "<< image->GetGeometry()->GetOrigin()[2] << ""; + MITK_INFO << "MaxExtend " << xMax[0] << " "<< yMax[1] << " "<< zMax[2] << ""; + mitk::Point3D point; + + itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer randomGenerator = itk::Statistics::MersenneTwisterRandomVariateGenerator::New(); + randomGenerator->Initialize( std::rand() ); // initialize with random value, to get sensible random points for the image + point[0] = randomGenerator->GetUniformVariate( image->GetGeometry()->GetOrigin()[0], xMax[0]); + point[1] = randomGenerator->GetUniformVariate( image->GetGeometry()->GetOrigin()[1], yMax[1]); + point[2] = randomGenerator->GetUniformVariate( image->GetGeometry()->GetOrigin()[2], zMax[2]); + MITK_INFO << "RandomPoint " << point[0] << " "<< point[1] << " "<< point[2] << ""; + + // test values and max/min + mitk::ScalarType imageMin = image->GetStatistics()->GetScalarValueMin(); + mitk::ScalarType imageMax = image->GetStatistics()->GetScalarValueMax(); + mitk::ScalarType value = image->GetPixelValueByWorldCoordinate(point); + MITK_INFO << imageMin << " "<< imageMax << " "<< value << ""; + MITK_TEST_CONDITION( (value >= imageMin && value <= imageMax), "Value returned is between max/min"); + + mitk::Image::Pointer cloneImage = image->Clone(); + MITK_TEST_CONDITION_REQUIRED(cloneImage->GetDimension() == image->GetDimension(), "Clone (testing dimension)"); + MITK_TEST_CONDITION_REQUIRED(cloneImage->GetPixelType() == image->GetPixelType(), "Clone (testing pixel type)"); + + for (unsigned int i = 0u; i < cloneImage->GetDimension(); ++i) + { + MITK_TEST_CONDITION_REQUIRED(cloneImage->GetDimension(i) == image->GetDimension(i), "Clone (testing dimension " << i << ")"); + } + + //access via itk + if(image->GetDimension()> 3) // CastToItk only works with 3d images so we need to check for 4d images + { + mitk::ImageTimeSelector::Pointer selector = mitk::ImageTimeSelector::New(); + selector->SetTimeNr(0); + selector->SetInput(image); + selector->Update(); + image = selector->GetOutput(); + } + + if(image->GetDimension()==3) + { + typedef itk::Image ItkFloatImage3D; + ItkFloatImage3D::Pointer itkimage; + mitk::CastToItkImage(image, itkimage); + MITK_TEST_CONDITION_REQUIRED(itkimage.IsNotNull(), "Test conversion to itk::Image!"); + + mitk::Point3D itkPhysicalPoint; + image->GetGeometry()->WorldToItkPhysicalPoint(point, itkPhysicalPoint); + MITK_INFO << "ITKPoint " << itkPhysicalPoint[0] << " "<< itkPhysicalPoint[1] << " "<< itkPhysicalPoint[2] << ""; + + mitk::Point3D backTransformedPoint; + image->GetGeometry()->ItkPhysicalPointToWorld(itkPhysicalPoint, backTransformedPoint); + + MITK_TEST_CONDITION_REQUIRED( mitk::Equal(point,backTransformedPoint), "Testing world->itk-physical->world consistency"); + + itk::Index<3> idx; + bool status = itkimage->TransformPhysicalPointToIndex(itkPhysicalPoint, idx); + + MITK_INFO << "ITK Index " << idx[0] << " "<< idx[1] << " "<< idx[2] << ""; + + if(status) + { + float valByItk = itkimage->GetPixel(idx); + MITK_TEST_CONDITION_REQUIRED( mitk::Equal(valByItk, value), "Compare value of pixel returned by mitk in comparison to itk"); + } + else + { + MITK_WARN<< "Index is out buffered region!"; + } + } + else + { + MITK_INFO << "Image does not contain three dimensions, some test cases are skipped!"; + } } - else - { - MITK_INFO << "Image does not contain three dimensions, some test cases are skipped!"; - } + // clone generated 3D image with one slice in z direction (cf. bug 11058) unsigned int* threeDdim = new unsigned int[3]; threeDdim[0] = 100; threeDdim[1] = 200; threeDdim[2] = 1; mitk::Image::Pointer threeDImage = mitk::Image::New(); threeDImage->Initialize(mitk::MakeScalarPixelType(), 3, threeDdim); mitk::Image::Pointer cloneThreeDImage = threeDImage->Clone(); // check that the clone image has the same dimensionality as the source image MITK_TEST_CONDITION_REQUIRED( cloneThreeDImage->GetDimension() == 3, "Testing if the clone image initializes with 3D!"); + + // Testing for Bug-11600 + // Create a new image, store into datamanger, press reinit/global reinit.. should not crash + mitk::Image::Pointer newImageEmpty = mitk::Image::New(); + MITK_TEST_CONDITION_REQUIRED( newImageEmpty.IsNotNull(), "An image was created. "); + MITK_TEST_CONDITION_REQUIRED( newImageEmpty->IsInitialized(), "Image::IsInitialized() ?"); + MITK_TEST_CONDITION_REQUIRED( imgMem->GetDimension(0) > 0, "x-Dimension > 0"); + MITK_TEST_CONDITION_REQUIRED( imgMem->GetDimension(1) > 0, "y-Dimension > 0"); + MITK_TEST_CONDITION_REQUIRED( imgMem->GetDimension(2) > 0, "z-Dimension > 0"); + + MITK_TEST_END(); } \ No newline at end of file