private vtkImageData CreateVtkVolume()
{
vtkImageData vtkVolume = new vtkImageData();
VtkHelper.RegisterVtkErrorEvents(vtkVolume);
vtkVolume.SetDimensions(ArrayDimensions.Width, ArrayDimensions.Height, ArrayDimensions.Depth);
vtkVolume.SetOrigin(Origin.X, Origin.Y, Origin.Z);
vtkVolume.SetSpacing(VoxelSpacing.X, VoxelSpacing.Y, VoxelSpacing.Z);
if (!this.Signed)
{
vtkVolume.SetScalarTypeToUnsignedShort();
vtkVolume.GetPointData().SetScalars(
VtkHelper.ConvertToVtkUnsignedShortArray(_volumeDataUInt16));
}
else
{
vtkVolume.SetScalarTypeToShort();
vtkVolume.GetPointData().SetScalars(
VtkHelper.ConvertToVtkShortArray(_volumeDataInt16));
}
// This call is necessary to ensure vtkImageData data's info is correct (e.g. updates WholeExtent values)
vtkVolume.UpdateInformation();
return(vtkVolume);
}
private static byte[] MipPixelDataFromVtkSlab(vtkImageData slabImageData)
{
#if true // Do our own MIP, albeit slowly
int[] sliceDimensions = slabImageData.GetDimensions();
int sliceDataSize = sliceDimensions[0] * sliceDimensions[1];
IntPtr slabDataPtr = slabImageData.GetScalarPointer();
byte[] pixelData = MemoryManager.Allocate <byte>(sliceDataSize * sizeof(short));
// Init with first slice
Marshal.Copy(slabDataPtr, pixelData, 0, sliceDataSize * sizeof(short));
// Walk through other slices, finding maximum
unsafe
{
short *psSlab = (short *)slabDataPtr;
fixed(byte *pbFrame = pixelData)
{
short *psFrame = (short *)pbFrame;
for (int sliceIndex = 1; sliceIndex < sliceDimensions[2]; sliceIndex++)
{
for (int i = 0; i < sliceDataSize - 1; ++i)
{
int slabIndex = sliceIndex * sliceDataSize + i;
if (psSlab[slabIndex] > psFrame[i])
{
psFrame[i] = psSlab[slabIndex];
}
}
}
}
}
return(pixelData);
#else // Ideally we'd use VTK to do the MIP (MinIP, Average...)
vtkVolumeRayCastMIPFunction mip = new vtkVolumeRayCastMIPFunction();
vtkVolumeRayCastMapper mapper = new vtkVolumeRayCastMapper();
mapper.SetVolumeRayCastFunction(mip);
mapper.SetInput(slabImageData);
//TODO: Need to figure out how to use mapper to output vtkImageData
vtkImageAlgorithm algo = new vtkImageAlgorithm();
algo.SetInput(mapper.GetOutputDataObject(0));
using (vtkExecutive exec = mapper.GetExecutive())
{
VtkHelper.RegisterVtkErrorEvents(exec);
exec.Update();
// Note: These report no output port, must have to do something else to get mapper to give us data
//return exec.GetOutputData(0);
return(mapper.GetOutputDataObject(0));
}
#endif
}
// Extract slab in specified orientation, if slabThickness is 1, this is identical
// to GenerateVtkSlice above, so they should be collapsed at some point.
// TODO: Tie into Dicom for slice, will need to adjust thickness at least
private vtkImageData GenerateVtkSlab(Matrix resliceAxes, int slabThicknessInVoxels)
{
VtkHelper.StaticInitializationHack();
// Thickness should be at least 1
if (slabThicknessInVoxels < 1)
{
slabThicknessInVoxels = 1;
}
using (vtkImageReslice reslicer = new vtkImageReslice())
{
VtkHelper.RegisterVtkErrorEvents(reslicer);
// Obtain a pinned VTK volume for the reslicer. We'll release this when
// VTK is done reslicing.
vtkImageData volumeVtkWrapper = _volume.ObtainPinnedVtkVolume();
reslicer.SetInput(volumeVtkWrapper);
reslicer.SetInformationInput(volumeVtkWrapper);
if (slabThicknessInVoxels > 1)
{
reslicer.SetOutputDimensionality(3);
}
else
{
reslicer.SetOutputDimensionality(3);
}
// Use the volume's padding value for all pixels that are outside the volume
reslicer.SetBackgroundLevel(_volume.PadValue);
// This ensures VTK obeys the real spacing, results in all VTK slices being isotropic.
// Effective spacing is the minimum of these three.
reslicer.SetOutputSpacing(_volume.Spacing.X, _volume.Spacing.Y, _volume.Spacing.Z);
reslicer.SetResliceAxes(VtkHelper.ConvertToVtkMatrix(resliceAxes));
// Clamp the output based on the slice extent
int sliceExtentX = GetSliceExtentX();
int sliceExtentY = GetSliceExtentY();
reslicer.SetOutputExtent(0, sliceExtentX - 1, 0, sliceExtentY - 1, 0, slabThicknessInVoxels - 1);
// Set the output origin to reflect the slice through point. The slice extent is
// centered on the slice through point.
// VTK output origin is derived from the center image being 0,0
float originX = -sliceExtentX * EffectiveSpacing / 2;
float originY = -sliceExtentY * EffectiveSpacing / 2;
reslicer.SetOutputOrigin(originX, originY, 0);
switch (_slicing.InterpolationMode)
{
case InterpolationModes.NearestNeighbor:
reslicer.SetInterpolationModeToNearestNeighbor();
break;
case InterpolationModes.Linear:
reslicer.SetInterpolationModeToLinear();
break;
case InterpolationModes.Cubic:
reslicer.SetInterpolationModeToCubic();
break;
}
using (vtkExecutive exec = reslicer.GetExecutive())
{
VtkHelper.RegisterVtkErrorEvents(exec);
exec.Update();
_volume.ReleasePinnedVtkVolume();
return(reslicer.GetOutput());
}
}
}
// Extract slice in specified orientation
private vtkImageData GenerateVtkSlice(Matrix resliceAxes)
{
using (vtkImageReslice reslicer = new vtkImageReslice())
{
VtkHelper.RegisterVtkErrorEvents(reslicer);
// Obtain a pinned VTK volume for the reslicer. We'll release this when
// VTK is done reslicing.
using (var volume = _volume.Volume.CreateVtkVolumeHandle())
{
reslicer.SetInput(volume.vtkImageData);
reslicer.SetInformationInput(volume.vtkImageData);
// Must instruct reslicer to output 2D images
reslicer.SetOutputDimensionality(2);
// Use the volume's padding value for all pixels that are outside the volume
reslicer.SetBackgroundLevel(_volume.Volume.PaddingValue);
// This ensures VTK obeys the real spacing, results in all VTK slices being isotropic.
// Effective spacing is the minimum of these three.
reslicer.SetOutputSpacing(_volume.Volume.VoxelSpacing.X, _volume.Volume.VoxelSpacing.Y, _volume.Volume.VoxelSpacing.Z);
using (vtkMatrix4x4 resliceAxesMatrix = VtkHelper.ConvertToVtkMatrix(resliceAxes))
{
reslicer.SetResliceAxes(resliceAxesMatrix);
// Clamp the output based on the slice extent
int sliceExtentX = GetSliceExtentX();
int sliceExtentY = GetSliceExtentY();
reslicer.SetOutputExtent(0, sliceExtentX - 1, 0, sliceExtentY - 1, 0, 0);
// Set the output origin to reflect the slice through point. The slice extent is
// centered on the slice through point.
// VTK output origin is derived from the center image being 0,0
float originX = -sliceExtentX * EffectiveSpacing / 2;
float originY = -sliceExtentY * EffectiveSpacing / 2;
reslicer.SetOutputOrigin(originX, originY, 0);
switch (_slicerParams.InterpolationMode)
{
case VolumeSlicerInterpolationMode.NearestNeighbor:
reslicer.SetInterpolationModeToNearestNeighbor();
break;
case VolumeSlicerInterpolationMode.Linear:
reslicer.SetInterpolationModeToLinear();
break;
case VolumeSlicerInterpolationMode.Cubic:
reslicer.SetInterpolationModeToCubic();
break;
}
using (vtkExecutive exec = reslicer.GetExecutive())
{
VtkHelper.RegisterVtkErrorEvents(exec);
exec.Update();
}
var output = reslicer.GetOutput();
//Just in case VTK uses the matrix internally.
return(output);
}
}
}
}
static Volume()
{
// Volume is the root of all VTK use through the API, so this is the place to initialize it
VtkHelper.StaticInitializationHack();
}
