public VolumeSliceArgs(int rows, int columns,
float rowSpacing, float columnSpacing,
Vector3D rowOrientationPatient,
Vector3D columnOrientationPatient,
float sliceThickness, int subsamples,
VolumeInterpolationMode interpolation,
VolumeProjectionMode projection)
{
Platform.CheckPositive(rows, "rows");
Platform.CheckPositive(columns, "columns");
Platform.CheckPositive(rowSpacing, "rowSpacing");
Platform.CheckPositive(columnSpacing, "columnSpacing");
Platform.CheckPositive(sliceThickness, "sliceThickness");
Platform.CheckForNullReference(rowOrientationPatient, "rowOrientationPatient");
Platform.CheckForNullReference(columnOrientationPatient, "columnOrientationPatient");
_rows = rows;
_columns = columns;
_rowSpacing = rowSpacing;
_columnSpacing = columnSpacing;
_rowOrientationPatient = rowOrientationPatient.Normalize();
_columnOrientationPatient = columnOrientationPatient.Normalize();
_sliceThickness = sliceThickness;
_subsamples = subsamples;
_interpolation = interpolation;
_projection = projection;
}
public VolumeSliceArgs(int rows, int columns,
float rowSpacing, float columnSpacing,
Vector3D rowOrientationPatient,
Vector3D columnOrientationPatient,
float sliceThickness,
VolumeInterpolationMode interpolation)
: this(rows, columns, rowSpacing, columnSpacing, rowOrientationPatient, columnOrientationPatient, sliceThickness, 0, interpolation, VolumeProjectionMode.Average) {}
public VolumeSliceArgs(int rows, int columns,
float rowSpacing, float columnSpacing,
Vector3D rowOrientationPatient,
Vector3D columnOrientationPatient,
float sliceThickness, int subsamples,
VolumeInterpolationMode interpolation,
VolumeProjectionMode projection)
{
try
{
Platform.CheckPositive(rows, "rows");
Platform.CheckPositive(columns, "columns");
}
catch (ExtensionException ex)
{
Platform.Log(LogLevel.Error, rows);
}
Platform.CheckPositive(rowSpacing, "rowSpacing");
Platform.CheckPositive(columnSpacing, "columnSpacing");
Platform.CheckPositive(sliceThickness, "sliceThickness");
Platform.CheckForNullReference(rowOrientationPatient, "rowOrientationPatient");
Platform.CheckForNullReference(columnOrientationPatient, "columnOrientationPatient");
_rows = rows;
_columns = columns;
_rowSpacing = rowSpacing;
_columnSpacing = columnSpacing;
_rowOrientationPatient = rowOrientationPatient.Normalize();
_columnOrientationPatient = columnOrientationPatient.Normalize();
_sliceThickness = sliceThickness;
_subsamples = subsamples;
_interpolation = interpolation;
_projection = projection;
}
public VolumeSliceArgs(int rows, int columns,
float rowSpacing, float columnSpacing,
Vector3D rowOrientationPatient,
Vector3D columnOrientationPatient,
float sliceThickness,
VolumeInterpolationMode interpolation)
: this(rows, columns, rowSpacing, columnSpacing, rowOrientationPatient, columnOrientationPatient, sliceThickness, 0, interpolation, VolumeProjectionMode.Average)
{
}
/// <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 == 0)
{
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);
}
}
}
/// <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;
}
}
}