void CreateVectorField(ref vtkImageData image)
{
// Specify the size of the image data
image.SetDimensions(3, 3, 3);
image.SetNumberOfScalarComponents(3);
image.SetScalarTypeToFloat();
image.AllocateScalars();
image.SetSpacing(10.0, 10.0, 10.0);
int[] dims = image.GetDimensions();
float[] pixel = new float[] { 0.0f, 0.0f, 0.0f };
IntPtr pPixel;
// Zero the vectors
for (int z = 0; z < dims[2]; z++)
{
for (int y = 0; y < dims[1]; y++)
{
for (int x = 0; x < dims[0]; x++)
{
pPixel = image.GetScalarPointer(x, y, 0);
Marshal.Copy(pixel, 0, pPixel, 3);
}
}
}
// Set two of the pixels to non zero values
pixel[0] = 8.0f;
pixel[1] = 8.0f;
pixel[2] = -8.0f;
pPixel = image.GetScalarPointer(0, 2, 0);
Marshal.Copy(pixel, 0, pPixel, 3);
pixel[0] = 8.0f;
pixel[1] = -8.0f;
pixel[2] = 8.0f;
pPixel = image.GetScalarPointer(2, 0, 2);
Marshal.Copy(pixel, 0, pPixel, 3);
}
void CreateVectorField(ref vtkImageData image)
{
// Specify the size of the image data
image.SetDimensions(3, 3, 3);
image.SetNumberOfScalarComponents(3);
image.SetScalarTypeToFloat();
image.AllocateScalars();
image.SetSpacing(10.0, 10.0, 10.0);
int[] dims = image.GetDimensions();
float[] pixel = new float[] {0.0f, 0.0f, 0.0f};
IntPtr pPixel;
// Zero the vectors
for(int z = 0; z < dims[2]; z++) {
for(int y = 0; y < dims[1]; y++) {
for(int x = 0; x < dims[0]; x++) {
pPixel = image.GetScalarPointer(x, y, 0);
Marshal.Copy(pixel, 0, pPixel, 3);
}
}
}
// Set two of the pixels to non zero values
pixel[0] = 8.0f;
pixel[1] = 8.0f;
pixel[2] = -8.0f;
pPixel = image.GetScalarPointer(0, 2, 0);
Marshal.Copy(pixel, 0, pPixel, 3);
pixel[0] = 8.0f;
pixel[1] = -8.0f;
pixel[2] = 8.0f;
pPixel = image.GetScalarPointer(2, 0, 2);
Marshal.Copy(pixel, 0, pPixel, 3);
}
/// <summary>
/// The main entry method called by the CSharp driver
/// </summary>
/// <param name="argv"></param>
public static void AVTestCutMaterial(String [] argv)
{
//Prefix Content is: ""
// Lets create a data set.[]
data = new vtkImageData();
data.SetExtent((int)0,(int)31,(int)0,(int)31,(int)0,(int)31);
data.SetScalarTypeToFloat();
// First the data array:[]
gauss = new vtkImageGaussianSource();
gauss.SetWholeExtent((int)0,(int)30,(int)0,(int)30,(int)0,(int)30);
gauss.SetCenter((double)18,(double)12,(double)20);
gauss.SetMaximum((double)1.0);
gauss.SetStandardDeviation((double)10.0);
gauss.Update();
a = gauss.GetOutput().GetPointData().GetScalars();
a.SetName((string)"Gauss");
data.GetCellData().SetScalars((vtkDataArray)a);
//skipping Delete gauss
// Now the material array:[]
ellipse = new vtkImageEllipsoidSource();
ellipse.SetWholeExtent((int)0,(int)30,(int)0,(int)30,(int)0,(int)30);
ellipse.SetCenter((double)11,(double)12,(double)13);
ellipse.SetRadius((double)5,(double)9,(double)13);
ellipse.SetInValue((double)1);
ellipse.SetOutValue((double)0);
ellipse.SetOutputScalarTypeToInt();
ellipse.Update();
m = ellipse.GetOutput().GetPointData().GetScalars();
m.SetName((string)"Material");
data.GetCellData().AddArray((vtkAbstractArray)m);
//skipping Delete ellipse
cut = new vtkCutMaterial();
cut.SetInput((vtkDataObject)data);
cut.SetMaterialArrayName((string)"Material");
cut.SetMaterial((int)1);
cut.SetArrayName((string)"Gauss");
cut.SetUpVector((double)1,(double)0,(double)0);
cut.Update();
mapper2 = vtkPolyDataMapper.New();
mapper2.SetInputConnection((vtkAlgorithmOutput)cut.GetOutputPort());
mapper2.SetScalarRange((double)0,(double)1);
//apper2 SetScalarModeToUseCellFieldData[]
//apper2 SetColorModeToMapScalars []
//apper2 ColorByArrayComponent "vtkGhostLevels" 0[]
actor2 = new vtkActor();
actor2.SetMapper((vtkMapper)mapper2);
actor2.SetPosition((double)1.5,(double)0,(double)0);
ren = vtkRenderer.New();
ren.AddActor((vtkProp)actor2);
renWin = vtkRenderWindow.New();
renWin.AddRenderer((vtkRenderer)ren);
p = cut.GetCenterPoint();
n = cut.GetNormal();
cam = ren.GetActiveCamera();
cam.SetFocalPoint(p[0],p[1],p[2]);
cam.SetViewUp(cut.GetUpVector()[0], cut.GetUpVector()[1], cut.GetUpVector()[2]);
cam.SetPosition(
(double)(lindex(n,0))+(double)(lindex(p,0)),
(double)(lindex(n,1))+(double)(lindex(p,1)),
(double)(lindex(n,2))+(double)(lindex(p,2)));
ren.ResetCamera();
iren = vtkRenderWindowInteractor.New();
iren.SetRenderWindow(renWin);
iren.Initialize();
//deleteAllVTKObjects();
}
//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>
/// The main entry method called by the CSharp driver
/// </summary>
/// <param name="argv"></param>
public static void AVTestCutMaterial(String [] argv)
{
//Prefix Content is: ""
// Lets create a data set.[]
data = new vtkImageData();
data.SetExtent((int)0, (int)31, (int)0, (int)31, (int)0, (int)31);
data.SetScalarTypeToFloat();
// First the data array:[]
gauss = new vtkImageGaussianSource();
gauss.SetWholeExtent((int)0, (int)30, (int)0, (int)30, (int)0, (int)30);
gauss.SetCenter((double)18, (double)12, (double)20);
gauss.SetMaximum((double)1.0);
gauss.SetStandardDeviation((double)10.0);
gauss.Update();
a = gauss.GetOutput().GetPointData().GetScalars();
a.SetName((string)"Gauss");
data.GetCellData().SetScalars((vtkDataArray)a);
//skipping Delete gauss
// Now the material array:[]
ellipse = new vtkImageEllipsoidSource();
ellipse.SetWholeExtent((int)0, (int)30, (int)0, (int)30, (int)0, (int)30);
ellipse.SetCenter((double)11, (double)12, (double)13);
ellipse.SetRadius((double)5, (double)9, (double)13);
ellipse.SetInValue((double)1);
ellipse.SetOutValue((double)0);
ellipse.SetOutputScalarTypeToInt();
ellipse.Update();
m = ellipse.GetOutput().GetPointData().GetScalars();
m.SetName((string)"Material");
data.GetCellData().AddArray((vtkAbstractArray)m);
//skipping Delete ellipse
cut = new vtkCutMaterial();
cut.SetInput((vtkDataObject)data);
cut.SetMaterialArrayName((string)"Material");
cut.SetMaterial((int)1);
cut.SetArrayName((string)"Gauss");
cut.SetUpVector((double)1, (double)0, (double)0);
cut.Update();
mapper2 = vtkPolyDataMapper.New();
mapper2.SetInputConnection((vtkAlgorithmOutput)cut.GetOutputPort());
mapper2.SetScalarRange((double)0, (double)1);
//apper2 SetScalarModeToUseCellFieldData[]
//apper2 SetColorModeToMapScalars []
//apper2 ColorByArrayComponent "vtkGhostLevels" 0[]
actor2 = new vtkActor();
actor2.SetMapper((vtkMapper)mapper2);
actor2.SetPosition((double)1.5, (double)0, (double)0);
ren = vtkRenderer.New();
ren.AddActor((vtkProp)actor2);
renWin = vtkRenderWindow.New();
renWin.AddRenderer((vtkRenderer)ren);
p = cut.GetCenterPoint();
n = cut.GetNormal();
cam = ren.GetActiveCamera();
cam.SetFocalPoint(p[0], p[1], p[2]);
cam.SetViewUp(cut.GetUpVector()[0], cut.GetUpVector()[1], cut.GetUpVector()[2]);
cam.SetPosition(
(double)(lindex(n, 0)) + (double)(lindex(p, 0)),
(double)(lindex(n, 1)) + (double)(lindex(p, 1)),
(double)(lindex(n, 2)) + (double)(lindex(p, 2)));
ren.ResetCamera();
iren = vtkRenderWindowInteractor.New();
iren.SetRenderWindow(renWin);
iren.Initialize();
//deleteAllVTKObjects();
}
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
}
