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bug4931patch1.patch
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• yung
Aug 31 2010, 3:43 PM
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bug4931patch1.patch
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Index: DataManagement/mitkImage.cpp
===================================================================
--- DataManagement/mitkImage.cpp (revision 25468)
+++ DataManagement/mitkImage.cpp (working copy)
@@ -181,8 +181,17 @@
return NULL;
if(GetSource()->Updating()==false)
GetSource()->UpdateOutputInformation();
+
}
- m_CompleteData=GetChannelData();
+ //m_CompleteData=GetChannelData();
+ m_CompleteData = GetImageData();
+//TODO
+/*
+for(int i=this->GetNumberOfChannels()-1; i>=0; i--)
+{
+ m_CompleteData=GetChannelData(i);
+}
+*/
if(m_CompleteData.GetPointer()==NULL)
return NULL;
return m_CompleteData->GetPicDescriptor();
@@ -377,9 +386,13 @@
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=new ImageDataItem(m_PixelType, m_Dimension, m_Dimensions, NULL, true);
+//TODO
+ch=new ImageDataItem(m_PixelType, 4, m_Dimensions, NULL, true);
ch->SetComplete(true);
- size_t size=m_OffsetTable[m_Dimension-1]*(m_PixelType.GetBpe()/8);
+ //size_t size=m_OffsetTable[m_Dimension-1]*(m_PixelType.GetBpe()/8);
+//TODO
+size_t size=m_OffsetTable[3]*(m_PixelType.GetBpe()/8);
unsigned int t;
ImageDataItemPointerArray::iterator slicesIt = m_Slices.begin()+n*m_Dimensions[2]*m_Dimensions[3];
for(t=0;t<m_Dimensions[3];++t)
@@ -451,6 +464,108 @@
}
}
+mitk::Image::ImageDataItemPointer mitk::Image::GetImageData(void *data, ImportMemoryManagementType importMemoryManagement)
+{
+ ImageDataItemPointer img, ch, vol;
+
+ int numOfChannels = GetNumberOfChannels();
+ if (numOfChannels==1)
+ {
+ return GetChannelData(0, data, importMemoryManagement);
+ }
+
+ // add channel as 5. dimension
+ if(m_CompleteData.GetPointer()==NULL)
+ {
+ unsigned int dimensions[5];
+ for(int i=0; i<5; i++)
+ {
+ dimensions[i] = 1;
+ }
+ for(int i=0; i<m_Dimension; i++)
+ {
+ dimensions[i] = m_Dimensions[i];
+ }
+ dimensions[4] = numOfChannels; // channel
+
+ m_CompleteData = new ImageDataItem(m_PixelType, 5, dimensions, NULL, true);
+ }
+ m_CompleteData->SetComplete(true);
+ size_t size = m_OffsetTable[4]*(m_PixelType.GetBpe()/8); // size of a channel in byte
+
+ // merge every channel
+ for(int n=0; n<numOfChannels; n++)
+ {
+ ch = GetChannelData(n, data, importMemoryManagement);
+
+ // copy data of channel to image (m_CompleteData)
+ size_t offset = ((size_t) n)*m_OffsetTable[4]*(m_PixelType.GetBpe()/8);
+ std::memcpy(static_cast<char*>(m_CompleteData->GetData())+offset, ch->GetData(), size);
+
+ mitkIpPicDescriptor * pic = ch->GetPicDescriptor();
+
+ // replace old channel with reference to image
+ ch = new ImageDataItem(*m_CompleteData, 3, data, importMemoryManagement == ManageMemory, offset);
+ ch->SetComplete(true);
+ mitkIpFuncCopyTags(ch->GetPicDescriptor(), pic);
+
+ m_Channels[n] = ch;
+
+ }
+
+ ImageDataItemPointerArray::iterator it, end;
+ // get rid of volumes - they may point to old channel
+ for( it=m_Volumes.begin(), end=m_Volumes.end(); it!=end; ++it )
+ {
+ (*it)=NULL;
+ }
+ // get rid of slices - they may point to old volume
+ for( it=m_Slices.begin(), end=m_Slices.end(); it!=end; ++it )
+ {
+ (*it)=NULL;
+ }
+
+ if(m_CompleteData->GetPicDescriptor()->info->tags_head==NULL)
+ {
+ mitkIpFuncCopyTags(m_CompleteData->GetPicDescriptor(), m_Channels[0]->GetPicDescriptor());
+ }
+
+ return m_CompleteData;
+
+/*
+ // 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;
@@ -729,6 +844,8 @@
itkExceptionMacro(<< "invalid dimension[" << i << "]: " << dimensions[i]);
}
+//TODO
+/*
m_Dimensions=new unsigned int[m_Dimension>4?m_Dimension:4];
std::memcpy(m_Dimensions, dimensions, sizeof(unsigned int)*m_Dimension);
if(m_Dimension<4)
@@ -737,7 +854,23 @@
for(i=0,p=m_Dimensions+m_Dimension;i<4-m_Dimension;++i, ++p)
*p=1;
}
+*/
+ m_Dimensions=new unsigned int[5];
+ for(unsigned int i=0; i<5; i++)
+ {
+ if (i<dimension)
+ {
+ m_Dimensions[i] = dimensions[i];
+ }
+ else
+ {
+ m_Dimensions[i] = 1;
+ }
+ }
+ m_Dimensions[4] = channels;
+//TODO
+/*
for(i=0;i<4;++i)
{
m_LargestPossibleRegion.SetIndex(i, 0);
@@ -745,7 +878,14 @@
}
m_LargestPossibleRegion.SetIndex(i, 0);
m_LargestPossibleRegion.SetSize(i, channels);
+*/
+ for(unsigned int i=0; i<5; i++)
+ {
+ m_LargestPossibleRegion.SetIndex(i, 0);
+ m_LargestPossibleRegion.SetSize (i, m_Dimensions[i]);
+ }
+
if(m_LargestPossibleRegion.GetNumberOfPixels()==0)
{
delete [] m_Dimensions;
@@ -790,13 +930,14 @@
}
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;
+ dimensions[3] = 1;
+ dimensions[4] = 1;
unsigned int dimension = 2;
if ( dimensions[2] > 1 )
@@ -819,7 +960,41 @@
dimension = 4;
Initialize( type, dimension, dimensions, channels );
+*/
+ 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);
+//TODO
+ dimensions[3] = 1;
+ dimensions[4] = channels;
+ unsigned int dimension = 2;
+ if ( dimensions[2] > 1 )
+ dimension = 3;
+
+ if ( tDim > 0)
+ {
+ dimensions[3] = tDim;
+ }
+ else
+ {
+ const mitk::TimeSlicedGeometry* timeGeometry = dynamic_cast<const mitk::TimeSlicedGeometry*>(&geometry);
+ if ( timeGeometry != NULL )
+ {
+ dimensions[3] = timeGeometry->GetTimeSteps();
+ }
+ }
+
+ if ( dimensions[3] > 1 )
+ dimension = 4;
+
+//TODO
+ if ( dimensions[4] > 1 )
+ dimension = 5;
+
+ Initialize( type, dimension, dimensions, channels );
+
SetGeometry(static_cast<Geometry3D*>(geometry.Clone().GetPointer()));
mitk::BoundingBox::BoundsArrayType bounds = geometry.GetBoundingBox()->GetBounds();
@@ -849,7 +1024,9 @@
void mitk::Image::Initialize(const mitk::Image* image)
{
- Initialize(*image->GetPixelType().GetTypeId(), *image->GetTimeSlicedGeometry());
+//TODO
+ //Initialize(*image->GetPixelType().GetTypeId(), *image->GetTimeSlicedGeometry());
+ Initialize(*image->GetPixelType().GetTypeId(), *image->GetTimeSlicedGeometry(), image->GetNumberOfChannels());
}
void mitk::Image::Initialize(vtkImageData* vtkimagedata, int channels, int tDim, int sDim)
@@ -857,7 +1034,9 @@
if(vtkimagedata==NULL) return;
m_Dimension=vtkimagedata->GetDataDimension();
- unsigned int i, *tmpDimensions=new unsigned int[m_Dimension>4?m_Dimension:4];
+
+/*
+ unsigned int i, *tmpDimensions=new unsigned int[m_Dimension>5?m_Dimension:5];
for(i=0;i<m_Dimension;++i) tmpDimensions[i]=vtkimagedata->GetDimensions()[i];
if(m_Dimension<4)
{
@@ -865,7 +1044,21 @@
for(i=0,p=tmpDimensions+m_Dimension;i<4-m_Dimension;++i, ++p)
*p=1;
}
+*/
+ unsigned int* tmpDimensions = new unsigned int[5];
+ for(unsigned int i=0; i<5; i++)
+ {
+ if (i<m_Dimension)
+ {
+ tmpDimensions[i] = vtkimagedata->GetDimensions()[i];
+ }
+ else
+ {
+ tmpDimensions[i] = 1;
+ }
+ }
+
if(sDim>=0)
{
tmpDimensions[2]=sDim;
@@ -878,6 +1071,13 @@
if(m_Dimension < 4)
m_Dimension = 4;
}
+//TODO
+ if(channels>1)
+ {
+ tmpDimensions[4]=channels;
+ if(m_Dimension < 5)
+ m_Dimension = 5;
+ }
mitk::PixelType pixelType;
@@ -966,15 +1166,31 @@
m_Dimension=pic->dim;
+//TODO
+/*
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)
+ if(m_Dimension<5)
{
unsigned int i, *p;
for(i=0,p=m_Dimensions+m_Dimension;i<4-m_Dimension;++i, ++p)
*p=1;
}
+*/
+ m_Dimensions = new unsigned int[5];
+ for(unsigned int i=0; i<5; i++)
+ {
+ if (i<m_Dimension)
+ {
+ m_Dimensions[i] = pic->n[i];
+ }
+ else
+ {
+ m_Dimensions[i] = 1;
+ }
+ }
+
if(sDim>=0)
{
m_Dimensions[2]=sDim;
@@ -987,7 +1203,14 @@
if(m_Dimension < 4)
m_Dimension = 4;
}
-
+//TODO
+ if(channels>1)
+ {
+ m_Dimensions[4]=channels;
+ if(m_Dimension < 5)
+ m_Dimension = 5;
+ }
+/*
unsigned int i;
for(i=0;i<4;++i)
{
@@ -996,6 +1219,12 @@
}
m_LargestPossibleRegion.SetIndex(i, 0);
m_LargestPossibleRegion.SetSize(i, channels);
+*/
+ for(unsigned int i=0; i<5; i++)
+ {
+ m_LargestPossibleRegion.SetIndex(i, 0);
+ m_LargestPossibleRegion.SetSize (i, m_Dimensions[i]);
+ }
m_PixelType=PixelType(pic);
SlicedGeometry3D::Pointer slicedGeometry = SlicedGeometry3D::New();
Index: DataManagement/mitkImage.h
===================================================================
--- DataManagement/mitkImage.h (revision 25468)
+++ DataManagement/mitkImage.h (working copy)
@@ -536,6 +536,10 @@
//## @warning for internal use only
virtual ImageDataItemPointer GetChannelData(int n = 0, void *data = NULL, ImportMemoryManagementType importMemoryManagement = CopyMemory);
+ //##Documentation
+ //## @warning for internal use only
+ virtual ImageDataItemPointer GetImageData(void *data = NULL, ImportMemoryManagementType importMemoryManagement = CopyMemory);
+
template < typename ItkImageType >
friend void _ComputeExtremaInItkImage(ItkImageType* itkImage, mitk::Image * mitkImage, int t);
Index: IO/mitkPicFileReader.cpp
===================================================================
--- IO/mitkPicFileReader.cpp (revision 25468)
+++ IO/mitkPicFileReader.cpp (working copy)
@@ -49,6 +49,14 @@
int channels = 1;
+//TODO
+if (header->dim == 5)
+{
+ channels = header->n[4];
+ header->dim = 4;
+}
+
+
mitkIpPicTSV_t *tsv;
if ( (tsv = mitkIpPicQueryTag( header, "SOURCE HEADER" )) != NULL)
{
@@ -193,7 +201,10 @@
if( m_FileName != "")
{
+//TODO
mitkIpPicDescriptor* pic=MITKipPicGet(const_cast<char *>(m_FileName.c_str()), output->GetPic());
+ //mitkIpPicDescriptor* pic=MITKipPicGet(const_cast<char *>(m_FileName.c_str()), NULL);
+
// comes upside-down (in MITK coordinates) from PIC file
ConvertHandedness(pic);
@@ -224,6 +235,32 @@
mitkIpPicDelTag( pic, "VELOCITY" );
}
+
+//TODO
+/*
+if (pic->dim <= 4)
+{
+ output->SetChannel(pic->data, 0);
+}
+else
+{
+ int bytesPerPixel = pic->bpe / 8;
+ int bytesPerChannel = 1;
+
+ for(int i=0; i<4; i++)
+ {
+ bytesPerChannel *= pic->n[i];
+ }
+ bytesPerChannel *= bytesPerPixel;
+
+ for(int n=0; n<pic->n[4]; n++)
+ {
+ output->SetChannel((void*)((char*)pic->data + (n * bytesPerChannel)), n);
+ }
+}
+*/
+
+
//slice-wise reading
//currently much too slow.
//else

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Event Timeline

• yung added a comment.Aug 31 2010, 3:43 PM

First patch to fix channel problem

MITK · MIC · IMSY · DKFZ