/// <summary>
/// Allows specification of the slice plane, through point, and extent via two points in patient space
/// </summary>
public static VolumeSlicerParams Create(IVolumeHeader volume, Vector3D sourceOrientationColumnPatient, Vector3D sourceOrientationRowPatient,
Vector3D startPointPatient, Vector3D endPointPatient)
{
Vector3D sourceOrientationNormalPatient = sourceOrientationColumnPatient.Cross(sourceOrientationRowPatient);
Vector3D normalLinePatient = (endPointPatient - startPointPatient).Normalize();
Vector3D normalPerpLinePatient = sourceOrientationNormalPatient.Cross(normalLinePatient);
Vector3D slicePlanePatientX = normalLinePatient;
Vector3D slicePlanePatientY = sourceOrientationNormalPatient;
Vector3D slicePlanePatientZ = normalPerpLinePatient;
Matrix slicePlanePatientOrientation = Math3D.OrientationMatrixFromVectors(slicePlanePatientX, slicePlanePatientY, slicePlanePatientZ);
Matrix _resliceAxes = volume.RotateToVolumeOrientation(slicePlanePatientOrientation);
Vector3D lineMiddlePointPatient = new Vector3D(
(startPointPatient.X + endPointPatient.X) / 2,
(startPointPatient.Y + endPointPatient.Y) / 2,
(startPointPatient.Z + endPointPatient.Z) / 2);
VolumeSlicerParams slicerParams = new VolumeSlicerParams(_resliceAxes);
slicerParams.SliceThroughPointPatient = new Vector3D(lineMiddlePointPatient);
slicerParams.SliceExtentXMillimeters = (endPointPatient - startPointPatient).Magnitude;
return(slicerParams);
}
private static float GetIdealSliceSpacing(IVolumeHeader volumeHeader, Vector3D unitSpacingAxis)
{
// the ideal spacing is simply the diagonal of the voxel projected on to the spacing axis
// any larger than this value, and it becomes possible for an entire voxel to fit in between two consecutive output locations (i.e. missed for interpolation)
// any smaller than this value, and some voxels will have two or more output locations within their bounds
return(Math.Abs(unitSpacingAxis.Dot(volumeHeader.RotateToPatientOrientation(volumeHeader.VoxelSpacing))));
}
private static float GetIdealSliceSpacing(IVolumeHeader volumeHeader, Vector3D unitSpacingAxis)
{
// the ideal spacing is simply the diagonal of the voxel projected on to the spacing axis
// any larger than this value, and it becomes possible for an entire voxel to fit in between two consecutive output locations (i.e. missed for interpolation)
// any smaller than this value, and some voxels will have two or more output locations within their bounds
// note: voxel actually has 4 possible diagonals depending on the orientation, so we do this calculation for all diagonals and take the largest one
var p = volumeHeader.RotateToPatientOrientation(volumeHeader.VoxelSpacing);
return(new[] { p, new Vector3D(-p.X, p.Y, p.Z), new Vector3D(p.X, -p.Y, p.Z), new Vector3D(-p.X, -p.Y, p.Z) }
.Select(v => Math.Abs(unitSpacingAxis.Dot(v))).Max());
}
/// <summary>
/// The effective spacing defines output pixel spacing for slices generated by the VolumeSlicer.
/// </summary>
private static float GetEffectiveSpacing(IVolumeHeader volume)
{
// Because we supply the real spacing to the VTK reslicer, the slices are interpolated
// as if the volume were isotropic. This results in an effective spacing that is the
// minimum spacing for the volume.
//
// N.B.: this behaviour is different than if had asked VTK to render it, because we are
// asking directly for pixel data out. If VTK renders it, then we scrape the rendering
// for the pixel data, the spacing would be exactly 1mm because the interpolation would
// happened during rendering.
return(volume.GetMinimumSpacing());
}
private SizeF GetPixelSpacing(IVolumeHeader volumeHeader)
{
var columnHasValue = ColumnSpacing.HasValue;
var rowHasValue = RowSpacing.HasValue;
if (!columnHasValue && !rowHasValue)
{
var spacing = GetMinimumComponent(volumeHeader.VoxelSpacing);
return(new SizeF(spacing, spacing));
}
else if (columnHasValue && rowHasValue)
{
return(new SizeF(ColumnSpacing.Value, RowSpacing.Value));
}
else
{
var spacing = columnHasValue ? ColumnSpacing.Value : RowSpacing.Value;
return(new SizeF(spacing, spacing));
}
}
// Derived from either a specified extent in millimeters or from the volume dimensions (default)
private static Size GetSliceExtent(IVolumeHeader volume, IVolumeSlicerParams slicerParams)
{
var effectiveSpacing = GetEffectiveSpacing(volume);
var longOutputDimension = volume.GetLongAxisMagnitude() / effectiveSpacing;
var shortOutputDimenstion = volume.GetShortAxisMagnitude() / effectiveSpacing;
var diagonalDimension = (int)Math.Sqrt(longOutputDimension * longOutputDimension + shortOutputDimenstion * shortOutputDimenstion);
var columns = diagonalDimension;
if (!FloatComparer.AreEqual(slicerParams.SliceExtentXMillimeters, 0f))
{
columns = (int)(slicerParams.SliceExtentXMillimeters / effectiveSpacing + 0.5f);
}
var rows = diagonalDimension;
if (!FloatComparer.AreEqual(slicerParams.SliceExtentYMillimeters, 0f))
{
rows = (int)(slicerParams.SliceExtentYMillimeters / effectiveSpacing + 0.5f);
}
return(new Size(columns, rows));
}
// VTK treats the reslice point as the center of the output image. Given the plane orientation
// and size of the output image, we can derive the top left of the output image in patient space
private static Vector3D GetTopLeftOfSlicePatient(Size frameSize, Vector3D throughPoint, IVolumeHeader volume, IVolumeSlicerParams slicerParams)
{
// This is the center of the output image
var centerImageCoord = new PointF(frameSize.Width / 2f, frameSize.Height / 2f);
// These offsets define the x and y vector magnitudes to arrive at our point
var effectiveSpacing = GetEffectiveSpacing(volume);
var offsetX = centerImageCoord.X * effectiveSpacing;
var offsetY = centerImageCoord.Y * effectiveSpacing;
// To determine top left of slice in volume, subtract offset vectors along x and y
//
// Our reslice plane x and y vectors
var resliceAxes = slicerParams.SlicingPlaneRotation;
var xVec = new Vector3D(resliceAxes[0, 0], resliceAxes[0, 1], resliceAxes[0, 2]);
var yVec = new Vector3D(resliceAxes[1, 0], resliceAxes[1, 1], resliceAxes[1, 2]);
// Offset along x and y from reslicePoint
var topLeftOfSliceVolume = throughPoint - (offsetX * xVec + offsetY * yVec);
// Convert volume point to patient space
return(volume.ConvertToPatient(topLeftOfSliceVolume));
}
private static float GetIdealSliceSpacing(IVolumeHeader volumeHeader, Vector3D unitSpacingAxis)
{
// the ideal spacing is simply the diagonal of the voxel projected on to the spacing axis
// any larger than this value, and it becomes possible for an entire voxel to fit in between two consecutive output locations (i.e. missed for interpolation)
// any smaller than this value, and some voxels will have two or more output locations within their bounds
// note: voxel actually has 4 possible diagonals depending on the orientation, so we do this calculation for all diagonals and take the largest one
var p = volumeHeader.RotateToPatientOrientation(volumeHeader.VoxelSpacing);
return new[] {p, new Vector3D(-p.X, p.Y, p.Z), new Vector3D(p.X, -p.Y, p.Z), new Vector3D(-p.X, -p.Y, p.Z)}
.Select(v => Math.Abs(unitSpacingAxis.Dot(v))).Max();
}
public static float GetLongAxisMagnitude(this IVolumeHeader volume)
{
return(volume.VolumeSize.Max());
}
private static float GetIdealSliceSpacing(IVolumeHeader volumeHeader, Vector3D unitSpacingAxis)
{
// the ideal spacing is simply the diagonal of the voxel projected on to the spacing axis
// any larger than this value, and it becomes possible for an entire voxel to fit in between two consecutive output locations (i.e. missed for interpolation)
// any smaller than this value, and some voxels will have two or more output locations within their bounds
return Math.Abs(unitSpacingAxis.Dot(volumeHeader.RotateToPatientOrientation(volumeHeader.VoxelSpacing)));
}
/// <summary>
/// The effective spacing defines output pixel spacing for slices generated by the VolumeSlicer.
/// </summary>
private static float GetEffectiveSpacing(IVolumeHeader volume)
{
// Because we supply the real spacing to the VTK reslicer, the slices are interpolated
// as if the volume were isotropic. This results in an effective spacing that is the
// minimum spacing for the volume.
//
// N.B.: this behaviour is different than if had asked VTK to render it, because we are
// asking directly for pixel data out. If VTK renders it, then we scrape the rendering
// for the pixel data, the spacing would be exactly 1mm because the interpolation would
// happened during rendering.
return volume.GetMinimumSpacing();
}
// Derived from either a specified extent in millimeters or from the volume dimensions (default)
private static Size GetSliceExtent(IVolumeHeader volume, IVolumeSlicerParams slicerParams)
{
var effectiveSpacing = GetEffectiveSpacing(volume);
var longOutputDimension = volume.GetLongAxisMagnitude()/effectiveSpacing;
var shortOutputDimenstion = volume.GetShortAxisMagnitude()/effectiveSpacing;
var diagonalDimension = (int) Math.Sqrt(longOutputDimension*longOutputDimension + shortOutputDimenstion*shortOutputDimenstion);
var columns = diagonalDimension;
if (!FloatComparer.AreEqual(slicerParams.SliceExtentXMillimeters, 0f))
columns = (int) (slicerParams.SliceExtentXMillimeters/effectiveSpacing + 0.5f);
var rows = diagonalDimension;
if (!FloatComparer.AreEqual(slicerParams.SliceExtentYMillimeters, 0f))
rows = (int) (slicerParams.SliceExtentYMillimeters/effectiveSpacing + 0.5f);
return new Size(columns, rows);
}
// VTK treats the reslice point as the center of the output image. Given the plane orientation
// and size of the output image, we can derive the top left of the output image in patient space
private static Vector3D GetTopLeftOfSlicePatient(Size frameSize, Vector3D throughPoint, IVolumeHeader volume, IVolumeSlicerParams slicerParams)
{
// This is the center of the output image
var centerImageCoord = new PointF(frameSize.Width/2f, frameSize.Height/2f);
// These offsets define the x and y vector magnitudes to arrive at our point
var effectiveSpacing = GetEffectiveSpacing(volume);
var offsetX = centerImageCoord.X*effectiveSpacing;
var offsetY = centerImageCoord.Y*effectiveSpacing;
// To determine top left of slice in volume, subtract offset vectors along x and y
//
// Our reslice plane x and y vectors
var resliceAxes = slicerParams.SlicingPlaneRotation;
var xVec = new Vector3D(resliceAxes[0, 0], resliceAxes[0, 1], resliceAxes[0, 2]);
var yVec = new Vector3D(resliceAxes[1, 0], resliceAxes[1, 1], resliceAxes[1, 2]);
// Offset along x and y from reslicePoint
var topLeftOfSliceVolume = throughPoint - (offsetX*xVec + offsetY*yVec);
// Convert volume point to patient space
return volume.ConvertToPatient(topLeftOfSliceVolume);
}
public static float GetShortAxisMagnitude(this IVolumeHeader volume)
{
return(volume.VolumeSize.Min());
}
private float GetSliceSpacing(IVolumeHeader volumeHeader, Vector3D slicerAxisZ)
{
return(SliceSpacing ?? (SliceThickness.HasValue ? SliceThickness.Value : GetIdealSliceSpacing(volumeHeader, slicerAxisZ)));
}
private float GetSliceSpacing(IVolumeHeader volumeHeader, Vector3D slicerAxisZ)
{
return SliceSpacing ?? (SliceThickness.HasValue ? SliceThickness.Value : GetIdealSliceSpacing(volumeHeader, slicerAxisZ));
}
private SizeF GetPixelSpacing(IVolumeHeader volumeHeader)
{
var columnHasValue = ColumnSpacing.HasValue;
var rowHasValue = RowSpacing.HasValue;
if (!columnHasValue && !rowHasValue)
{
var spacing = GetMinimumComponent(volumeHeader.VoxelSpacing);
return new SizeF(spacing, spacing);
}
else if (columnHasValue && rowHasValue)
{
return new SizeF(ColumnSpacing.Value, RowSpacing.Value);
}
else
{
var spacing = columnHasValue ? ColumnSpacing.Value : RowSpacing.Value;
return new SizeF(spacing, spacing);
}
}
/// <summary>
/// Allows specification of the slice plane, through point, and extent via two points in patient space
/// </summary>
public static VolumeSlicerParams Create(IVolumeHeader volume, Vector3D sourceOrientationColumnPatient, Vector3D sourceOrientationRowPatient,
Vector3D startPointPatient, Vector3D endPointPatient)
{
Vector3D sourceOrientationNormalPatient = sourceOrientationColumnPatient.Cross(sourceOrientationRowPatient);
Vector3D normalLinePatient = (endPointPatient - startPointPatient).Normalize();
Vector3D normalPerpLinePatient = sourceOrientationNormalPatient.Cross(normalLinePatient);
Vector3D slicePlanePatientX = normalLinePatient;
Vector3D slicePlanePatientY = sourceOrientationNormalPatient;
Vector3D slicePlanePatientZ = normalPerpLinePatient;
Matrix slicePlanePatientOrientation = Math3D.OrientationMatrixFromVectors(slicePlanePatientX, slicePlanePatientY, slicePlanePatientZ);
Matrix _resliceAxes = volume.RotateToVolumeOrientation(slicePlanePatientOrientation);
Vector3D lineMiddlePointPatient = new Vector3D(
(startPointPatient.X + endPointPatient.X)/2,
(startPointPatient.Y + endPointPatient.Y)/2,
(startPointPatient.Z + endPointPatient.Z)/2);
VolumeSlicerParams slicerParams = new VolumeSlicerParams(_resliceAxes);
slicerParams.SliceThroughPointPatient = new Vector3D(lineMiddlePointPatient);
slicerParams.SliceExtentXMillimeters = (endPointPatient - startPointPatient).Magnitude;
return slicerParams;
}
public static float GetMaximumSpacing(this IVolumeHeader volume)
{
return(volume.VoxelSpacing.Max());
}