/// <summary>
/// Rotates volume along given axis.
/// </summary>
/// <param name="volume"></param>
/// <param name="angles"></param>
public static void RotateData(ref vtkImageData volume, double[] angles)
{
// Rotation along image center
double[] center = volume.GetExtent().Divide(2);
// Dimensions of rotated image
int[] outExtent = volume.GetExtent().Multiply(1.1).Round().ToInt32();
// Rotation parameters
var rotate = new vtkTransform();
rotate.Translate(center[1], center[3], center[5]);
rotate.RotateX(angles[0]);
rotate.RotateY(angles[1]);
rotate.RotateZ(angles[2]); // z angle should be 0
rotate.Translate(-center[1], -center[3], -center[5]);
// Perform rotation
var slice = new vtkImageReslice();
slice.SetInput(volume);
slice.SetResliceTransform(rotate);
slice.SetInterpolationModeToCubic();
slice.SetOutputSpacing(volume.GetSpacing()[0], volume.GetSpacing()[1], volume.GetSpacing()[2]);
slice.SetOutputOrigin(volume.GetOrigin()[0], volume.GetOrigin()[1], volume.GetOrigin()[2]);
slice.SetOutputExtent(outExtent[0], outExtent[1], outExtent[2], outExtent[3], outExtent[4], outExtent[5]);
}
private static void ResliceVolume(vtkImageData volume)
{
using (var reslicer = new vtkImageReslice())
{
RegisterVtkErrorEvents(reslicer);
reslicer.SetInput(volume);
reslicer.SetInformationInput(volume);
// 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(0);
// This ensures VTK obeys the real spacing, results in all VTK slices being isotropic.
// Effective spacing is the minimum of these three.
reslicer.SetOutputSpacing(1.0, 1.0, 1.0);
using (vtkMatrix4x4 resliceAxesMatrix = ConvertToVtkMatrix(new double[, ] {
{ 1, 0, 0, 0 }, { 0, 1, 0, 0 }, { 0, 0, 1, 0 }, { 0, 0, 0, 1 }
}))
{
reslicer.SetResliceAxes(resliceAxesMatrix);
// Clamp the output based on the slice extent
const int sliceExtentX = 50;
const int sliceExtentY = 50;
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
const float originX = -sliceExtentX * 1f / 2;
const float originY = -sliceExtentY * 1f / 2;
reslicer.SetOutputOrigin(originX, originY, 0);
reslicer.SetInterpolationModeToLinear();
using (vtkExecutive exec = reslicer.GetExecutive())
{
RegisterVtkErrorEvents(exec);
exec.Update();
}
using (var output = reslicer.GetOutput())
{
// just to give it something to do with the output
GC.KeepAlive(output);
}
}
}
}
// 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;
}
}
}
}
/// <summary>
/// Gets the pixel data representing a thick slice (a.k.a. slab) of the volume.
/// </summary>
private static byte[] GetSlabPixelData(IVolumeReference volumeReference, Matrix resliceAxes, Vector3D stackOrientation, int rows, int columns, int subsamples, float rowSpacing, float columnSpacing, float sliceThickness, VolumeInterpolationMode interpolation, VolumeProjectionMode projection)
{
if (subsamples <= 1) return GetSlicePixelData(volumeReference, resliceAxes, rows, columns, rowSpacing, columnSpacing, interpolation);
var subsampleSpacing = sliceThickness/(subsamples - 1);
using (var reslicer = new vtkImageReslice())
using (var resliceAxesMatrix = new vtkMatrix4x4())
using (var executive = reslicer.GetExecutive())
using (var volume = volumeReference.Volume.CreateVtkVolumeHandle())
{
// update the reslice axes matrix with the values from the slicing orientation
resliceAxesMatrix.SetElements(resliceAxes);
// determine offset for start of slab (we centre the slab on the requested slice position, as DICOM defines "image position (patient)" to be centre of the thick slice)
var slabOffset = volumeReference.RotateToVolumeOrientation(-sliceThickness/2f*stackOrientation) + new Vector3D(resliceAxes[0, 3], resliceAxes[1, 3], resliceAxes[2, 3]);
resliceAxesMatrix.SetElement(0, 3, slabOffset.X);
resliceAxesMatrix.SetElement(1, 3, slabOffset.Y);
resliceAxesMatrix.SetElement(2, 3, slabOffset.Z);
// register for errors on the reslicer
reslicer.RegisterVtkErrorEvents();
// set input to the volume
reslicer.SetInput(volume.vtkImageData);
reslicer.SetInformationInput(volume.vtkImageData);
// instruct reslicer to output a 3D slab volume
reslicer.SetOutputDimensionality(3);
// use the volume's padding value for all pixels that are outside the volume
reslicer.SetBackgroundLevel(volumeReference.PaddingValue);
// ensure the slicer outputs at our desired spacing
reslicer.SetOutputSpacing(columnSpacing, rowSpacing, subsampleSpacing);
// set the reslice axes
reslicer.SetResliceAxes(resliceAxesMatrix);
// clamp the output based on the slice extent
reslicer.SetOutputExtent(0, columns - 1, 0, rows - 1, 0, subsamples - 1);
// set the output origin to the slice through-point (output image will be centered on this location)
// VTK output origin is derived from the center image being 0,0
reslicer.SetOutputOrigin(-columns*columnSpacing/2, -rows*rowSpacing/2, 0);
// select the requested interpolation mode
switch (interpolation)
{
case VolumeInterpolationMode.NearestNeighbor:
reslicer.SetInterpolationModeToNearestNeighbor();
break;
case VolumeInterpolationMode.Linear:
reslicer.SetInterpolationModeToLinear();
break;
case VolumeInterpolationMode.Cubic:
reslicer.SetInterpolationModeToCubic();
break;
}
// select the requested slab projection mode
Action<IntPtr, byte[], int, int, int, bool> slabAggregator;
switch (projection)
{
case VolumeProjectionMode.Maximum:
slabAggregator = SlabProjection.AggregateSlabMaximumIntensity;
break;
case VolumeProjectionMode.Minimum:
slabAggregator = SlabProjection.AggregateSlabMinimumIntensity;
break;
case VolumeProjectionMode.Average:
default:
slabAggregator = SlabProjection.AggregateSlabAverageIntensity;
break;
}
// register for errors on the reslicer executive
executive.RegisterVtkErrorEvents();
executive.Update();
// get the slice output
using (var imageData = reslicer.GetOutput())
{
var pixelData = SlabVtkImageData(imageData, slabAggregator, volumeReference.BitsPerVoxel, volumeReference.Signed);
imageData.ReleaseData();
return pixelData;
}
}
}
/// <summary>
/// Gets the pixel data representing a thin slice of the volume.
/// </summary>
private static byte[] GetSlicePixelData(IVolumeReference volumeReference, Matrix resliceAxes, int rows, int columns, float rowSpacing, float columnSpacing, VolumeInterpolationMode interpolation)
{
using (var reslicer = new vtkImageReslice())
using (var resliceAxesMatrix = new vtkMatrix4x4())
using (var executive = reslicer.GetExecutive())
using (var volume = volumeReference.Volume.CreateVtkVolumeHandle())
{
// update the reslice axes matrix with the values from the slicing orientation
resliceAxesMatrix.SetElements(resliceAxes);
// register for errors on the reslicer
reslicer.RegisterVtkErrorEvents();
// set input to the volume
reslicer.SetInput(volume.vtkImageData);
reslicer.SetInformationInput(volume.vtkImageData);
// 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(volumeReference.PaddingValue);
// ensure the slicer outputs at our desired spacing
reslicer.SetOutputSpacing(columnSpacing, rowSpacing, Math.Min(columnSpacing, rowSpacing));
// set the reslice axes
reslicer.SetResliceAxes(resliceAxesMatrix);
// clamp the output based on the slice extent
reslicer.SetOutputExtent(0, columns - 1, 0, rows - 1, 0, 0);
// set the output origin to the slice through-point (output image will be centered on this location)
// VTK output origin is derived from the center image being 0,0
reslicer.SetOutputOrigin(-columns*columnSpacing/2, -rows*rowSpacing/2, 0);
// select the requested interpolation mode
switch (interpolation)
{
case VolumeInterpolationMode.NearestNeighbor:
reslicer.SetInterpolationModeToNearestNeighbor();
break;
case VolumeInterpolationMode.Linear:
reslicer.SetInterpolationModeToLinear();
break;
case VolumeInterpolationMode.Cubic:
reslicer.SetInterpolationModeToCubic();
break;
}
// register for errors on the reslicer executive
executive.RegisterVtkErrorEvents();
executive.Update();
// get the slice output
using (var imageData = reslicer.GetOutput())
{
var pixelData = ReadVtkImageData(imageData);
imageData.ReleaseData();
return pixelData;
}
}
}
private static void ResliceVolume(vtkImageData volume)
{
using (var reslicer = new vtkImageReslice())
{
RegisterVtkErrorEvents(reslicer);
reslicer.SetInput(volume);
reslicer.SetInformationInput(volume);
// 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(0);
// This ensures VTK obeys the real spacing, results in all VTK slices being isotropic.
// Effective spacing is the minimum of these three.
reslicer.SetOutputSpacing(1.0, 1.0, 1.0);
using (vtkMatrix4x4 resliceAxesMatrix = ConvertToVtkMatrix(new double[,] {{1, 0, 0, 0}, {0, 1, 0, 0}, {0, 0, 1, 0}, {0, 0, 0, 1}}))
{
reslicer.SetResliceAxes(resliceAxesMatrix);
// Clamp the output based on the slice extent
const int sliceExtentX = 50;
const int sliceExtentY = 50;
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
const float originX = -sliceExtentX*1f/2;
const float originY = -sliceExtentY*1f/2;
reslicer.SetOutputOrigin(originX, originY, 0);
reslicer.SetInterpolationModeToLinear();
using (vtkExecutive exec = reslicer.GetExecutive())
{
RegisterVtkErrorEvents(exec);
exec.Update();
}
using (var output = reslicer.GetOutput())
{
// just to give it something to do with the output
GC.KeepAlive(output);
}
}
}
}
/// <summary>
/// Rotates 3D vtk volume around x and y axes.
/// </summary>
/// <param name="input"></param>
/// <param name="angle"></param>
/// <param name="axis"></param>
/// <param name="out_extent"></param>
/// <returns></returns>
public static vtkImageData rotate_sample(vtkImageData input, double angle, int axis, int out_extent = 0)
{
//get input data dimensions
int[] dims = input.GetExtent();
//Compute centers
int[] centers = new int[] { (dims[1] + dims[0]) / 2, (dims[3] + dims[2]) / 2, (dims[5] + dims[4]) / 2 };
//Set rotation axis
int[] axes = new int[3];
axes[axis] = 1;
int[] new_dims = new int[] { dims[0], dims[1], dims[2], dims[3], dims[4], dims[5] };
int[] new_centers = new int[] { centers[0], centers[1], centers[2] };
//Compute new sample dimensions
if (axis == 0)
{
new_dims[3] = (int)(Math.Cos(Math.Abs(angle / 180) * Math.PI) * new_dims[3] + Math.Sin(Math.Abs(angle / 180) * Math.PI) * new_dims[5]);
new_dims[5] = (int)(Math.Sin(Math.Abs(angle / 180) * Math.PI) * new_dims[3] + Math.Cos(Math.Abs(angle / 180) * Math.PI) * new_dims[5]);
new_centers[1] = (Math.Abs(new_dims[3]) + Math.Abs(new_dims[2])) / 2;
new_centers[2] = (Math.Abs(new_dims[5]) + Math.Abs(new_dims[4])) / 2;
}
if (axis == 1)
{
new_dims[1] = (int)(Math.Cos(Math.Abs(angle / 180) * Math.PI) * new_dims[1] + Math.Sin(Math.Abs(angle / 180) * Math.PI) * new_dims[5]);
new_dims[5] = (int)(Math.Sin(Math.Abs(angle / 180) * Math.PI) * new_dims[1] + Math.Cos(Math.Abs(angle / 180) * Math.PI) * new_dims[5]);
new_centers[0] = (Math.Abs(new_dims[0]) + Math.Abs(new_dims[1])) / 2;
new_centers[2] = (Math.Abs(new_dims[5]) + Math.Abs(new_dims[4])) / 2;
}
//Image transformation
vtkTransform transform = vtkTransform.New();
transform.Translate(centers[0], centers[1], centers[2]);
transform.RotateWXYZ(angle, axes[0], axes[1], axes[2]);
if (out_extent == 0)
{
transform.Translate(-centers[0], -centers[1], -centers[2]);
}
else
{
transform.Translate(-new_centers[0], -new_centers[1], -new_centers[2]);
}
//Console.ReadKey();
transform.Update();
//Compute new data extent
int[] diff = new int[] { new_dims[1] - dims[1], new_dims[3] - dims[3], new_dims[5] - dims[5] };
new_dims[0] += diff[0] / 2; new_dims[1] -= diff[0] / 2;
new_dims[2] += diff[1] / 2; new_dims[3] -= diff[1] / 2;
new_dims[4] += diff[2] / 2; new_dims[5] -= diff[2] / 2;
//Image reslicing
vtkImageReslice rotater = vtkImageReslice.New();
rotater.SetInput(input);
rotater.SetInformationInput(input);
rotater.SetResliceTransform(transform);
rotater.SetInterpolationModeToCubic();
//rotater.SetInterpolationModeToLinear();
if (out_extent == 1)
{
rotater.SetOutputSpacing(input.GetSpacing()[0], input.GetSpacing()[1], input.GetSpacing()[2]);
rotater.SetOutputOrigin(input.GetOrigin()[0], input.GetOrigin()[1], input.GetOrigin()[2]);
rotater.SetOutputExtent(new_dims[0], new_dims[1], new_dims[2], new_dims[3], new_dims[4], new_dims[5]);
}
rotater.Update();
vtkImageData output = vtkImageData.New();
output.DeepCopy(rotater.GetOutput());
rotater.Dispose();
transform.Dispose();
return(output);
}