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);
}
/// <summary>
/// Converts 3D byte array to vtkImageData.
/// </summary>
/// <param name="data">Input array.</param>
/// <param name="dims">Input array dimensions. Give the begin and end extent for each dimension.</param>
/// <returns>Converted array.</returns>
public static vtkImageData byteToVTK1D(byte[] data, int[] dims)
{
int h = dims[1] - dims[0] + 1;
int w = dims[3] - dims[2] + 1;
int d = dims[5] - dims[4] + 1;
//Create VTK data for putput
vtkImageData vtkdata = vtkImageData.New();
//Character array for conversion
vtkUnsignedCharArray charArray = vtkUnsignedCharArray.New();
//Pin byte array
GCHandle pinnedArray = GCHandle.Alloc(data, GCHandleType.Pinned);
//Set character array input
charArray.SetArray(pinnedArray.AddrOfPinnedObject(), h * w * d, 1);
//Set vtkdata properties and connect array
//Data from char array
vtkdata.GetPointData().SetScalars(charArray);
//Number of scalars/pixel
vtkdata.SetNumberOfScalarComponents(1);
//Set data extent
vtkdata.SetExtent(dims[0], dims[1], dims[2], dims[3], dims[4], dims[5]);
//Scalar type
vtkdata.SetScalarTypeToUnsignedChar();
vtkdata.Update();
return(vtkdata);
}
private vtkImageData CreateVolumeImageData()
{
vtkImageData imageData = new vtkImageData();
imageData.SetDimensions(this.Width, this.Height, this.Depth);
imageData.SetSpacing(GetFirstFrame().PixelSpacing.Column, GetFirstFrame().PixelSpacing.Row, GetSliceSpacing());
imageData.AllocateScalars();
imageData.SetScalarTypeToUnsignedShort();
imageData.GetPointData().SetScalars(BuildVolumeImageData());
return(imageData);
}
public static void UpdateSectionImage(Rectangle imageRect)
{
if (SectionImageData == null)
{
SectionImageData = vtkImageData.New();
}
SectionImageData.DeepCopy(RectImageData);
for (int i = 0; i < imageRect.Width; i++)
{
SectionImageData.GetPointData().GetScalars().SetTuple1(HSectionNum * imageRect.Width + i, 255);
}
for (int i = 0; i < imageRect.Height; i++)
{
SectionImageData.GetPointData().GetScalars().SetTuple1(i * imageRect.Width + VSectionNum, 255);
}
SectionImageData.Update();
UpdateImageView();
}
private void Window_Activated(object sender, EventArgs e)
{
// 一定要先 vtkformhost.Child = vtkControl;下面三条顺序不能乱 否则报错 切记！
vtkformhost.Child = vtkControl;
vtkRenderWindow renWin = vtkControl.RenderWindow;
vtkRenderer aRenderer = renWin.GetRenderers().GetFirstRenderer();
renWin.AddRenderer(aRenderer);
Marshal.Copy(ys1, 0, temp128, imgLine * imgPixel * imgNum);
temp.SetArray(temp128, imgLine * imgPixel * imgNum, 1);
testimgdata.SetDimensions(imgLine, imgPixel, imgNum);
testimgdata.SetSpacing(1, 1, 4);
testimgdata.SetScalarTypeToUnsignedChar();
testimgdata.SetNumberOfScalarComponents(1);
testimgdata.AllocateScalars();
testimgdata.GetPointData().SetScalars(temp);
testimgdata.Modified();
VtkSetColor();
VtkSetOpacity();
volumeProperty.SetColor(colorTransferFunction);
volumeProperty.SetScalarOpacity(opacityTransferFunction);
volumeProperty.ShadeOn();
volumeProperty.SetInterpolationTypeToLinear();
volumeMapper.SetVolumeRayCastFunction(compositeFunction);
volumeMapper.SetInput(testimgdata);
volume.SetMapper(volumeMapper);
volume.SetProperty(volumeProperty);
aCamera.SetViewUp(0, -1, 0);
aCamera.SetPosition(-1, 0, 1);
aCamera.ComputeViewPlaneNormal();
aRenderer.AddVolume(volume);
aRenderer.SetBackground(0, 0, 0.6);
aRenderer.SetActiveCamera(aCamera);
aRenderer.ResetCamera();
renWin.SetSize(800, 800);
renWin.Render();
}
private void Dispose(bool disposing)
{
if (_disposed)
{
return;
}
if (disposing && _vtkVolume != null)
{
_vtkVolume.GetPointData().Dispose();
_vtkVolume.Dispose();
_vtkVolume = null;
}
_volumeArrayPinned.Free();
_disposed = true;
}
private void Dispose(bool disposing)
{
if (_disposed)
{
return;
}
if (disposing && _vtkImageData != null)
{
_vtkImageData.GetPointData().Dispose();
_vtkImageData.Dispose();
_vtkImageData = null;
}
_pinningHandle.Free();
_disposed = true;
}
private static vtkImageData CreateVtkVolume(short[] data, int width, int height, int depth)
{
var vtkVolume = new vtkImageData();
RegisterVtkErrorEvents(vtkVolume);
vtkVolume.SetDimensions(width, height, depth);
vtkVolume.SetOrigin(0, 0, 0);
vtkVolume.SetSpacing(1.0, 1.0, 1.0);
using (var array = ConvertToVtkShortArray(data))
{
vtkVolume.SetScalarTypeToShort();
vtkVolume.GetPointData().SetScalars(array);
// This call is necessary to ensure vtkImageData data's info is correct (e.g. updates WholeExtent values)
vtkVolume.UpdateInformation();
}
return(vtkVolume);
}
/// <summary>
/// Converts 3D byte array to vtkImageData.
/// </summary>
/// <param name="data">Input array.</param>
/// <param name="orientation">Data orientation as a list of axes (0-2)</param>
/// <returns>Converted array.</returns>
public static vtkImageData byteToVTK(byte[,,] data, int[] orientation = null)
{
//Get input dimensions
int[] dims = new int[] { data.GetLength(0), data.GetLength(1), data.GetLength(2) };
//Create VTK data for putput
vtkImageData vtkdata = vtkImageData.New();
//Character array for conversion
vtkUnsignedCharArray charArray = vtkUnsignedCharArray.New();
//Pin byte array
GCHandle pinnedArray = GCHandle.Alloc(data, GCHandleType.Pinned);
//Set character array input
charArray.SetArray(pinnedArray.AddrOfPinnedObject(), dims[0] * dims[1] * dims[2], 1);
//Set vtkdata properties and connect array
//Data from char array
vtkdata.GetPointData().SetScalars(charArray);
//Number of scalars/pixel
vtkdata.SetNumberOfScalarComponents(1);
//Data extent, 1st and last axis are swapped from the char array
//Data is converted back to original orientation
vtkdata.SetExtent(0, dims[2] - 1, 0, dims[1] - 1, 0, dims[0] - 1);
//Scalar type
vtkdata.SetScalarTypeToUnsignedChar();
vtkdata.SetSpacing(1.0, 1.0, 1.0);
vtkdata.Update();
pinnedArray.Free();
//Return vtk data
if (orientation == null)
{
return(vtkdata);
}
else
{
vtkImagePermute permuter = vtkImagePermute.New();
permuter.SetInput(vtkdata);
permuter.SetFilteredAxes(orientation[0], orientation[1], orientation[2]);
permuter.Update();
return(permuter.GetOutput());
}
}
protected void Dispose(bool disposing)
{
if (!_disposed)
{
if (disposing)
{
if (_cachedVtkVolume != null)
{
_cachedVtkVolume.GetPointData().Dispose();
_cachedVtkVolume.Dispose();
_cachedVtkVolume = null;
}
}
// This should have been taken care of by caller of Obtain, release here just to be safe.
ReleasePinnedVtkVolume();
_volumeDataInt16 = null;
_volumeDataUInt16 = null;
_disposed = true;
}
}
public void Generate(CImage3D BinarySubImageSeq, Color Colour, cPoint3D Pos)
{
vtkImageData ImageData1 = new vtkImageData();
ImageData1.SetDimensions(BinarySubImageSeq.Width, BinarySubImageSeq.Height, BinarySubImageSeq.Depth);
ImageData1.SetNumberOfScalarComponents(1);
//ImageData1.SetSpacing(BinarySubImageSeq.XResolution, BinarySubImageSeq.YResolution, BinarySubImageSeq.ZResolution);
ImageData1.SetScalarTypeToFloat();
vtkFloatArray array1 = new vtkFloatArray();
for (int i = 0; i < BinarySubImageSeq.ImageSize; i++)
array1.InsertTuple1(i, BinarySubImageSeq.Data[i]);
ImageData1.GetPointData().SetScalars(array1);
vtkExtractVOI VOI = new vtkExtractVOI();
VOI.SetInput(ImageData1);
VOI.SetSampleRate(1, 1, 1);
vtkMarchingCubes ContourObject = vtkMarchingCubes.New();
vtk_PolyDataMapper = vtkPolyDataMapper.New();
//ContourActor = new vtkActor();
VOI.SetVOI(0, BinarySubImageSeq.Width - 1, 0, BinarySubImageSeq.Height - 1, 0, BinarySubImageSeq.Depth - 1);
ContourObject.SetInput(VOI.GetOutput());
ContourObject.SetValue(0, 0.5);
vtkAlgorithmOutput AlgoOutPut = null;
vtk_PolyData = ContourObject.GetOutput();
AlgoOutPut = ContourObject.GetOutputPort();
vtk_PolyDataMapper.SetInput(vtk_PolyData);
vtk_PolyDataMapper.ScalarVisibilityOn();
vtk_PolyDataMapper.SetScalarModeToUseFieldData();
vtkActor TmpActor = vtkActor.New();
TmpActor.SetMapper(vtk_PolyDataMapper);
TmpActor.SetPosition(Pos.X, Pos.Y, Pos.Z);
//Console.WriteLine("PosX"+Pos.X+" PosY"+Pos.Y+" PosZ"+Pos.Z);
#region deal with the containers
this.Position = new cPoint3D(Pos.X, Pos.Y, Pos.Z);
this.Colour = Colour;
CreateVTK3DObject(1);
// vtk_PolyData = ContourObject.GetOutput();
// compute convex hull
hullFilter = vtkHull.New();
hullFilter.SetInputConnection(AlgoOutPut);
hullFilter.AddRecursiveSpherePlanes(1);
hullFilter.Update();
// this.BackfaceCulling(false);
Information = new cInformation(AlgoOutPut, this, hullFilter);
#endregion
}
private static vtkImageData CreateVtkVolume(short[] data, int width, int height, int depth)
{
var vtkVolume = new vtkImageData();
RegisterVtkErrorEvents(vtkVolume);
vtkVolume.SetDimensions(width, height, depth);
vtkVolume.SetOrigin(0, 0, 0);
vtkVolume.SetSpacing(1.0, 1.0, 1.0);
using (var array = ConvertToVtkShortArray(data))
{
vtkVolume.SetScalarTypeToShort();
vtkVolume.GetPointData().SetScalars(array);
// This call is necessary to ensure vtkImageData data's info is correct (e.g. updates WholeExtent values)
vtkVolume.UpdateInformation();
}
return vtkVolume;
}
private static vtkImageData CreateVtkVolume(Volume volume)
{
var vtkVolume = new vtkImageData();
vtkVolume.RegisterVtkErrorEvents();
vtkVolume.SetDimensions(volume.ArrayDimensions.Width, volume.ArrayDimensions.Height, volume.ArrayDimensions.Depth);
vtkVolume.SetOrigin(0, 0, 0);
vtkVolume.SetSpacing(volume.VoxelSpacing.X, volume.VoxelSpacing.Y, volume.VoxelSpacing.Z);
if (volume.BitsPerVoxel == 16)
{
if (!volume.Signed)
{
using (var array = new vtkUnsignedShortArray())
{
array.SetArray((ushort[]) volume.Array, (VtkIdType) volume.ArrayLength, 1);
vtkVolume.SetScalarTypeToUnsignedShort();
vtkVolume.GetPointData().SetScalars(array);
}
}
else
{
using (var array = new vtkShortArray())
{
array.SetArray((short[]) volume.Array, (VtkIdType) volume.ArrayLength, 1);
vtkVolume.SetScalarTypeToShort();
vtkVolume.GetPointData().SetScalars(array);
}
}
}
else if (volume.BitsPerVoxel == 8)
{
if (!volume.Signed)
{
using (var array = new vtkUnsignedCharArray())
{
array.SetArray((byte[]) volume.Array, (VtkIdType) volume.ArrayLength, 1);
vtkVolume.SetScalarTypeToUnsignedChar();
vtkVolume.GetPointData().SetScalars(array);
}
}
else
{
using (var array = new vtkSignedCharArray())
{
array.SetArray((sbyte[]) volume.Array, (VtkIdType) volume.ArrayLength, 1);
vtkVolume.SetScalarTypeToSignedChar();
vtkVolume.GetPointData().SetScalars(array);
}
}
}
else
{
throw new NotSupportedException("Unsupported volume scalar type.");
}
// This call is necessary to ensure vtkImageData data's info is correct (e.g. updates WholeExtent values)
vtkVolume.UpdateInformation();
return vtkVolume;
}
private void VectorFieldNonZeroExtraction()
{
// Create an image
vtkImageData image = vtkImageData.New();
CreateVectorField(ref image);
// This filter produces a vtkImageData with an array named "Magnitude"
vtkImageMagnitude magnitudeFilter = vtkImageMagnitude.New();
magnitudeFilter.SetInputConnection(image.GetProducerPort());
magnitudeFilter.Update();
image.GetPointData().AddArray(magnitudeFilter.GetOutput().GetPointData().GetScalars());
image.GetPointData().SetActiveScalars("Magnitude");
vtkThresholdPoints thresholdVector = vtkThresholdPoints.New();
thresholdVector.SetInput(image);
thresholdVector.SetInputArrayToProcess(
0,
0,
(int)vtkDataObject.FieldAssociations.FIELD_ASSOCIATION_POINTS,
(int)vtkDataSetAttributes.AttributeTypes.SCALARS,
"Magnitude");
thresholdVector.ThresholdByUpper(0.00001);
thresholdVector.Update();
// in case you want to save imageData
//vtkXMLPolyDataWriter writer = vtkXMLPolyDataWriter.New();
//writer.SetFileName("output.vtp");
//writer.SetInputConnection(thresholdPoints.GetOutputPort());
//writer.Write();
// repesents the pixels
vtkCubeSource cubeSource = vtkCubeSource.New();
cubeSource.SetXLength(2.0);
cubeSource.SetYLength(2.0);
cubeSource.SetZLength(2.0);
vtkGlyph3D glyph = vtkGlyph3D.New();
glyph.SetInput(image);
glyph.SetSourceConnection(cubeSource.GetOutputPort());
// don't scale glyphs according to any scalar data
glyph.SetScaleModeToDataScalingOff();
vtkPolyDataMapper glyphMapper = vtkPolyDataMapper.New();
glyphMapper.SetInputConnection(glyph.GetOutputPort());
// don't color glyphs according to scalar data
glyphMapper.ScalarVisibilityOff();
glyphMapper.SetScalarModeToDefault();
vtkActor actor = vtkActor.New();
actor.SetMapper(glyphMapper);
// represent vector field
vtkGlyph3D vectorGlyph = vtkGlyph3D.New();
vtkArrowSource arrowSource = vtkArrowSource.New();
vtkPolyDataMapper vectorGlyphMapper = vtkPolyDataMapper.New();
int n = image.GetPointData().GetNumberOfArrays();
for (int i = 0; i < n; i++)
{
Debug.WriteLine("name of array[" + i + "]: " + image.GetPointData().GetArrayName(i));
}
vtkPolyData tmp = thresholdVector.GetOutput();
Debug.WriteLine("number of thresholded points: " + tmp.GetNumberOfPoints());
vectorGlyph.SetInputConnection(thresholdVector.GetOutputPort());
// in case you want the point glyphs to be oriented according to
// scalar values in array "ImageScalars" uncomment the following line
image.GetPointData().SetActiveVectors("ImageScalars");
vectorGlyph.SetSourceConnection(arrowSource.GetOutputPort());
vectorGlyph.SetScaleModeToScaleByVector();
vectorGlyph.SetVectorModeToUseVector();
vectorGlyph.ScalingOn();
vectorGlyph.OrientOn();
vectorGlyph.SetInputArrayToProcess(
1,
0,
(int)vtkDataObject.FieldAssociations.FIELD_ASSOCIATION_POINTS,
(int)vtkDataSetAttributes.AttributeTypes.SCALARS,
"ImageScalars");
vectorGlyph.Update();
vectorGlyphMapper.SetInputConnection(vectorGlyph.GetOutputPort());
vectorGlyphMapper.Update();
vtkActor vectorActor = vtkActor.New();
vectorActor.SetMapper(vectorGlyphMapper);
// get a reference to the renderwindow of our renderWindowControl1
vtkRenderWindow renderWindow = renderWindowControl1.RenderWindow;
// renderer
vtkRenderer renderer = renderWindow.GetRenderers().GetFirstRenderer();
// set background color
renderer.SetBackground(.2, .6, .3);
//Add the actors to the renderer, set the background and size
renderer.AddActor(actor);
renderer.AddActor(vectorActor);
}
public FastImageDataFetcherShort(vtkImageData imageData)
{
_vtkDataArray1 = imageData.GetPointData().GetScalars();
this._imageData = imageData;
}
//private void CommonInit(Sequence BinarySubImageSeq)
//{
// vtkImageData ImageData1 = new vtkImageData();
// ImageData1.SetDimensions(BinarySubImageSeq.Width, BinarySubImageSeq.Height, BinarySubImageSeq.Depth);
// ImageData1.SetNumberOfScalarComponents(1);
// ImageData1.SetSpacing(BinarySubImageSeq.XResolution, BinarySubImageSeq.YResolution, BinarySubImageSeq.ZResolution);
// ImageData1.SetScalarTypeToFloat();
// vtkFloatArray array1 = new vtkFloatArray();
// for (int i = 0; i < BinarySubImageSeq.ImageSize; i++)
// array1.InsertTuple1(i, BinarySubImageSeq[0].Data[0][i]);
// ImageData1.GetPointData().SetScalars(array1);
// vtkExtractVOI VOI = new vtkExtractVOI();
// VOI.SetInput(ImageData1);
// VOI.SetSampleRate(1, 1, 1);
// vtkMarchingCubes ContourObject = vtkMarchingCubes.New();
// vtk_PolyDataMapper = vtkPolyDataMapper.New();
// //ContourActor = new vtkActor();
// VOI.SetVOI(0, BinarySubImageSeq.Width - 1, 0, BinarySubImageSeq.Height - 1, 0, BinarySubImageSeq.Depth - 1);
// ContourObject.SetInput(VOI.GetOutput());
// ContourObject.SetValue(0, 0.5);
// vtk_PolyDataMapper.SetInput(ContourObject.GetOutput());
// vtk_PolyDataMapper.ScalarVisibilityOn();
// vtk_PolyDataMapper.SetScalarModeToUseFieldData();
//}
///// <summary>
///// Generate a 3D mesh using marching-cubes algorithm. If voxel value is lower than 1 it is consider as background, else as object
///// </summary>
///// <param name="BinarySubImageSeq">The binary image</param>
///// <param name="Colour">Mesh color</param>
///// <param name="Pos">Postion of the object in the world</param>
//public void Generate(Sequence BinarySubImageSeq, Color Colour, cPoint3D Pos)
//{
// vtkImageData ImageData1 = new vtkImageData();
// ImageData1.SetDimensions(BinarySubImageSeq.Width, BinarySubImageSeq.Height, BinarySubImageSeq.Depth);
// ImageData1.SetNumberOfScalarComponents(1);
// ImageData1.SetSpacing(BinarySubImageSeq.XResolution, BinarySubImageSeq.YResolution, BinarySubImageSeq.ZResolution);
// ImageData1.SetScalarTypeToFloat();
// vtkFloatArray array1 = new vtkFloatArray();
// for (int i = 0; i < BinarySubImageSeq.ImageSize; i++)
// array1.InsertTuple1(i, BinarySubImageSeq[0].Data[0][i]);
// ImageData1.GetPointData().SetScalars(array1);
// vtkExtractVOI VOI = new vtkExtractVOI();
// VOI.SetInput(ImageData1);
// VOI.SetSampleRate(1, 1, 1);
// vtkMarchingCubes ContourObject = vtkMarchingCubes.New();
// vtk_PolyDataMapper = vtkPolyDataMapper.New();
// //ContourActor = new vtkActor();
// VOI.SetVOI(0, BinarySubImageSeq.Width - 1, 0, BinarySubImageSeq.Height - 1, 0, BinarySubImageSeq.Depth - 1);
// // perform the amrching cubes
// ContourObject.SetInput(VOI.GetOutput());
// ContourObject.SetValue(0, 0.5);
// //vtkDecimatePro deci
// //deci SetInputConnection [fran GetOutputPort]
// //deci SetTargetReduction 0.9
// //deci PreserveTopologyOn
// if (MeshSmoother!=null)
// {
// vtkSmoothPolyDataFilter smoother = new vtkSmoothPolyDataFilter();
// smoother.SetInputConnection(ContourObject.GetOutputPort());// [deci GetOutputPort]
// smoother.SetNumberOfIterations(50);
// vtk_PolyData = smoother.GetOutput();
// }
// else
// {
// vtk_PolyData = ContourObject.GetOutput();
// }
// vtk_PolyDataMapper.SetInput(vtk_PolyData);
// vtk_PolyDataMapper.ScalarVisibilityOn();
// vtk_PolyDataMapper.SetScalarModeToUseFieldData();
// this.Position = new cPoint3D(Pos.X, Pos.Y, Pos.Z);
// this.Colour = Colour;
// CreateVTK3DObject(1);
// vtk_PolyData = ContourObject.GetOutput();
// // compute convex hull
// hullFilter = vtkHull.New();
// hullFilter.SetInputConnection(ContourObject.GetOutputPort());
// hullFilter.AddRecursiveSpherePlanes(1);
// hullFilter.Update();
// // this.BackfaceCulling(false);
// Information = new cInformation(ContourObject, this, hullFilter);
//}
public void Generate(cImage BinarySubImageSeq, Color Colour, cPoint3D Pos/*, List<cBiological3DObject> Containers, int ContainerMode*/)
{
vtkImageData ImageData1 = new vtkImageData();
ImageData1.SetDimensions(BinarySubImageSeq.Width, BinarySubImageSeq.Height, BinarySubImageSeq.Depth);
ImageData1.SetNumberOfScalarComponents(1);
ImageData1.SetSpacing(BinarySubImageSeq.Resolution.X, BinarySubImageSeq.Resolution.Y, BinarySubImageSeq.Resolution.Z);
ImageData1.SetScalarTypeToFloat();
vtkFloatArray array1 = new vtkFloatArray();
for (int i = 0; i < BinarySubImageSeq.ImageSize; i++)
array1.InsertTuple1(i, BinarySubImageSeq.SingleChannelImage[0].Data[i]);
ImageData1.GetPointData().SetScalars(array1);
vtkExtractVOI VOI = new vtkExtractVOI();
VOI.SetInput(ImageData1);
VOI.SetSampleRate(1, 1, 1);
vtkMarchingCubes ContourObject = vtkMarchingCubes.New();
vtk_PolyDataMapper = vtkPolyDataMapper.New();
//ContourActor = new vtkActor();
VOI.SetVOI(0, BinarySubImageSeq.Width - 1, 0, BinarySubImageSeq.Height - 1, 0, BinarySubImageSeq.Depth - 1);
ContourObject.SetInput(VOI.GetOutput());
ContourObject.SetValue(0, 0.5);
vtkAlgorithmOutput AlgoOutPut = null;
if (MeshSmoother != null)
{
//vtkSmoothPolyDataFilter smoother = new vtkSmoothPolyDataFilter();
vtkWindowedSincPolyDataFilter smoother = new vtkWindowedSincPolyDataFilter();
smoother.SetInputConnection(ContourObject.GetOutputPort());// [deci GetOutputPort]
smoother.SetNumberOfIterations(MeshSmoother.NumberOfIterations);
vtk_PolyData = smoother.GetOutput();
//smoother.GetOutputPort();
AlgoOutPut = smoother.GetOutputPort();
}
else
{
vtk_PolyData = ContourObject.GetOutput();
AlgoOutPut = ContourObject.GetOutputPort();
}
vtk_PolyDataMapper.SetInput(vtk_PolyData);
vtk_PolyDataMapper.ScalarVisibilityOn();
vtk_PolyDataMapper.SetScalarModeToUseFieldData();
vtkActor TmpActor = vtkActor.New();
TmpActor.SetMapper(vtk_PolyDataMapper);
TmpActor.SetPosition(Pos.X, Pos.Y, Pos.Z);
//Console.WriteLine("PosX"+Pos.X+" PosY"+Pos.Y+" PosZ"+Pos.Z);
#region deal with the containers
if (this.Containers != null)
{
if (this.Containers.ContainerMode == 0)
{
cPoint3D Centroid = new cPoint3D((float)TmpActor.GetCenter()[0], (float)TmpActor.GetCenter()[1], (float)TmpActor.GetCenter()[2]);
bool IsInside = false;
for (int Idx = 0; Idx < Containers.Containers.Count; Idx++)
{
cBiological3DVolume CurrentContainer = (cBiological3DVolume)(Containers.Containers[Idx]);
if (CurrentContainer.IsPointInside(Centroid))
{
IsInside = true;
ContainerIdx = Idx;
break;
}
}
if (IsInside)
{
this.SetPosition(new cPoint3D(Pos.X, Pos.Y, Pos.Z));
this.Colour = Colour;
CreateVTK3DObject(1);
// vtk_PolyData = ContourObject.GetOutput();
// compute convex hull
hullFilter = vtkHull.New();
hullFilter.SetInputConnection(AlgoOutPut);
hullFilter.AddRecursiveSpherePlanes(0);
hullFilter.Update();
Information = new cInformation(AlgoOutPut, this, hullFilter);
this.Detected = true;
}
else
{
this.Detected = false;
}
}
else if (Containers.ContainerMode == 1)
{
this.Detected = true;
//bool IsInside = false;
for (int Idx = 0; Idx < Containers.Containers.Count; Idx++)
{
cBiological3DVolume CurrentContainer = (cBiological3DVolume)(Containers.Containers[Idx]);
if (CurrentContainer.IsPointInside(Pos))
{
//IsInside = false;
this.Detected = false;
return;
}
}
this.SetPosition(new cPoint3D(Pos.X, Pos.Y, Pos.Z));
this.Colour = Colour;
CreateVTK3DObject(1);
// vtk_PolyData = ContourObject.GetOutput();
// compute convex hull
hullFilter = vtkHull.New();
hullFilter.SetInputConnection(AlgoOutPut);
hullFilter.AddRecursiveSpherePlanes(0);
hullFilter.Update();
Information = new cInformation(AlgoOutPut, this, hullFilter);
this.Detected = true;
}
}
else
{
this.SetPosition(new cPoint3D(Pos.X, Pos.Y, Pos.Z));
this.Colour = Colour;
CreateVTK3DObject(1);
// vtk_PolyData = ContourObject.GetOutput();
// compute convex hull
hullFilter = vtkHull.New();
hullFilter.SetInputConnection(AlgoOutPut);
hullFilter.AddRecursiveSpherePlanes(1);
hullFilter.Update();
// this.BackfaceCulling(false);
Information = new cInformation(AlgoOutPut, this, hullFilter);
}
#endregion
}
/// <summary>
/// Calculates mean and standard deviation images from volume-of-interest. Obsolete.
/// </summary>
/// <param name="output"></param>
/// <param name="mu"></param>
/// <param name="std"></param>
/// <param name="input"></param>
/// <param name="depth"></param>
/// <param name="threshold"></param>
public static void get_voi_mu_std(out vtkImageData output, out double[,] mu, out double[,] std, vtkImageData input, int depth, double threshold = 70.0)
{
//Get data extent
int[] dims = input.GetExtent();
int h = dims[1] - dims[0] + 1;
int w = dims[3] - dims[2] + 1;
int d = dims[5] - dims[4] + 1;
//Compute strides
int stridew = 1;
int strideh = w;
int strided = h * w;
byte[] bytedata = DataTypes.vtkToByte(input);
byte[] voidata = new byte[bytedata.Length];
double[,] _mu = new double[h, w];
double[,] _std = new double[h, w];
//Get voi indices
Parallel.For(24, h - 24, (int y) =>
{
Parallel.For(24, w - 24, (int x) =>
{
int start = d - 1;
int stop = 0;
//Compute mean
for (int z = d - 1; z > 0; z -= 1)
{
int pos = z * strided + y * strideh + x * stridew;
double val = (double)bytedata[pos];
if (val >= threshold)
{
start = z;
stop = Math.Max(z - depth, 0);
//Compute mean and std
for (int zz = start; zz > stop; zz -= 1)
{
int newpos = zz * strided + y * strideh + x * stridew;
double newval = (double)bytedata[newpos];
voidata[newpos] = (byte)newval;
_mu[y, x] = newval / (double)depth;
}
for (int zz = start; zz > stop; zz -= 1)
{
int newpos = zz * strided + y * strideh + x * stridew;
double newval = (double)bytedata[newpos];
_std[y, x] += ((double)newval - _mu[y, x]) * ((double)newval - _mu[y, x]);
}
_std[y, x] = Math.Pow(_std[y, x] / (depth - 1), 0.5);
break;
}
}
});
});
mu = _mu;
std = _std;
output = vtkImageData.New();
//Copy voi data to input array
vtkUnsignedCharArray charArray = vtkUnsignedCharArray.New();
//Pin byte array
GCHandle pinnedArray = GCHandle.Alloc(voidata, GCHandleType.Pinned);
//Set character array input
charArray.SetArray(pinnedArray.AddrOfPinnedObject(), h * w * d, 1);
//Set vtkdata properties and connect array
//Data from char array
output.GetPointData().SetScalars(charArray);
//Number of scalars/pixel
output.SetNumberOfScalarComponents(1);
//Data extent, 1st and last axis are swapped from the char array
//Data is converted back to original orientation
output.SetExtent(dims[0], dims[1], dims[2], dims[3], dims[4], dims[5]);
//Scalar type
output.SetScalarTypeToUnsignedChar();
output.Update();
}
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 vtkImageData CreateVolumeImageData()
{
vtkImageData imageData = new vtkImageData();
imageData.SetDimensions(this.Width, this.Height, this.Depth);
imageData.SetSpacing(GetFirstFrame().PixelSpacing.Column, GetFirstFrame().PixelSpacing.Row, GetSliceSpacing());
imageData.AllocateScalars();
imageData.SetScalarTypeToUnsignedShort();
imageData.GetPointData().SetScalars(BuildVolumeImageData());
return imageData;
}
private static vtkImageData CreateVtkVolume(Volume volume)
{
var vtkVolume = new vtkImageData();
vtkVolume.RegisterVtkErrorEvents();
vtkVolume.SetDimensions(volume.ArrayDimensions.Width, volume.ArrayDimensions.Height, volume.ArrayDimensions.Depth);
vtkVolume.SetOrigin(0, 0, 0);
vtkVolume.SetSpacing(volume.VoxelSpacing.X, volume.VoxelSpacing.Y, volume.VoxelSpacing.Z);
if (volume.BitsPerVoxel == 16)
{
if (!volume.Signed)
{
using (var array = new vtkUnsignedShortArray())
{
array.SetArray((ushort[])volume.Array, (VtkIdType)volume.ArrayLength, 1);
vtkVolume.SetScalarTypeToUnsignedShort();
vtkVolume.GetPointData().SetScalars(array);
}
}
else
{
using (var array = new vtkShortArray())
{
array.SetArray((short[])volume.Array, (VtkIdType)volume.ArrayLength, 1);
vtkVolume.SetScalarTypeToShort();
vtkVolume.GetPointData().SetScalars(array);
}
}
}
else if (volume.BitsPerVoxel == 8)
{
if (!volume.Signed)
{
using (var array = new vtkUnsignedCharArray())
{
array.SetArray((byte[])volume.Array, (VtkIdType)volume.ArrayLength, 1);
vtkVolume.SetScalarTypeToUnsignedChar();
vtkVolume.GetPointData().SetScalars(array);
}
}
else
{
using (var array = new vtkSignedCharArray())
{
array.SetArray((sbyte[])volume.Array, (VtkIdType)volume.ArrayLength, 1);
vtkVolume.SetScalarTypeToSignedChar();
vtkVolume.GetPointData().SetScalars(array);
}
}
}
else
{
throw new NotSupportedException("Unsupported volume scalar type.");
}
// This call is necessary to ensure vtkImageData data's info is correct (e.g. updates WholeExtent values)
vtkVolume.UpdateInformation();
return(vtkVolume);
}