/// <summary>
/// Function for removing sample edges.
/// </summary>
/// <param name="stack"></param>
/// <param name="side"></param>
/// <param name="get_center"></param>
/// <returns></returns>
public static vtkImageData center_crop(vtkImageData stack, int side = 400, bool get_center = true)
{
//Get input dimensions
int[] dims = stack.GetExtent();
//Find the center of the sample
int x1; int x2; int y1; int y2;
int[] center = find_center(stack, 70, new int[] { 0, (dims[5] - dims[4] + 1) / 3 });//GetCenter(bytedata,80);
//Compute new volume sides
y2 = Math.Min(center[0] + (side / 2), dims[1]);
y1 = Math.Max(y2 - side + 1, dims[0]);
x2 = Math.Min(center[1] + (side / 2), dims[3]);
x1 = Math.Max(x2 - side + 1, dims[2]);
//Create VOI extractor
vtkExtractVOI cropper = vtkExtractVOI.New();
cropper.SetVOI(y1, y2, x1, x2, dims[4], dims[5]);
cropper.SetInput(stack);
cropper.Update();
return(cropper.GetOutput());
}
/// <summary>
/// Gets a 2D slice from the 3D data.
/// </summary>
/// <param name="volume">Full 3D data.</param>
/// <param name="sliceN">Number of slice to be selected.</param>
/// <param name="axis">Axis on which selection will be made.</param>
/// <returns></returns>
public static vtkImageData volumeSlicer(vtkImageData volume, int[] sliceN, int axis)
{
//Initialize VOI extractor and permuter.
//Permuter will correct the orientation of the output image
vtkExtractVOI slicer = vtkExtractVOI.New();
vtkImagePermute permuter = vtkImagePermute.New();
//Connect data to slicer
slicer.SetInput(volume);
slicer.Update();
//Get data dimensions
int[] dims = slicer.GetOutput().GetExtent();
//Get slice
//Coronal plane
if (axis == 0)
{
//Set VOI
slicer.SetVOI(sliceN[0] - 1, sliceN[0], dims[2], dims[3], dims[4], dims[5]);
slicer.Update();
//Permute image (not necessary here)
permuter.SetInputConnection(slicer.GetOutputPort());
permuter.SetFilteredAxes(1, 2, 0);
permuter.Update();
}
//Transverse plane YZ
if (axis == 1)
{
//Set VOI
slicer.SetVOI(dims[0], dims[1], sliceN[1] - 1, sliceN[1], dims[4], dims[5]);
slicer.Update();
//Permute image
permuter.SetInputConnection(slicer.GetOutputPort());
permuter.SetFilteredAxes(0, 2, 1);
permuter.Update();
}
//Transverse plane, XZ
if (axis == 2)
{
//Set VOI
slicer.SetVOI(dims[0], dims[1], dims[2], dims[3], sliceN[2] - 1, sliceN[2]);
slicer.Update();
//Permute image
permuter.SetInputConnection(slicer.GetOutputPort());
permuter.SetFilteredAxes(0, 1, 2);
permuter.Update();
}
//slicer.Update();
//Return copy of the slice
return(permuter.GetOutput());
}
/// <summary>
/// Scans the input mask slice by slice and selects the largest binary component of each slice.
/// Return cleaned mask as vtkImageData
/// </summary>
/// <param name="input"></param>
/// <param name="extent"></param>
/// <param name="threshold"></param>
/// <param name="axes"></param>
/// <returns></returns>
public static vtkImageData FalsePositiveSuppresion(vtkImageData input, int[] extent, double threshold, int axis, double scale = 1.0)
{
//Slice extractor
vtkExtractVOI slicer = vtkExtractVOI.New();
//Permuter
vtkImagePermute permuter = vtkImagePermute.New();
//List of outputs
List <byte[, , ]> outputs = new List <byte[, , ]>();
//List of output orientations
List <int[]> orientations = new List <int[]>();
//vtkImageData size
int[] full_extent = input.GetExtent();
//Set range for slices
int start = 0, stop = 0;
int[] size = new int[2];
int[] outextent = new int[4];
if (axis == 0)
{
start = extent[0];
stop = extent[1];
size = new int[] { extent[3] - extent[2] + 1, extent[5] - extent[4] + 1 };
outextent = new int[] { extent[2], extent[3] + 1, extent[4], extent[5] + 1 };
}
if (axis == 1)
{
start = extent[2];
stop = extent[3];
size = new int[] { extent[1] - extent[0] + 1, extent[5] - extent[4] + 1 };
outextent = new int[] { extent[0], extent[1] + 1, extent[4], extent[5] + 1 };
}
if (axis == 2)
{
start = extent[4];
stop = extent[5];
size = new int[] { extent[1] - extent[0] + 1, extent[3] - extent[2] + 1 };
outextent = new int[] { extent[0], extent[1] + 1, extent[2], extent[3] + 1 };
}
//Temporary array for output
byte[,,] output = new byte[full_extent[1] + 1, full_extent[3] + 1, full_extent[5] + 1];
int[] outsize = new int[] { size[0], size[1], stop - start + 1 };
//Loop over current axis
for (int k = start; k < stop; k++)
{
byte[] bytedata = new byte[size[0] * size[1]];
//Select slice
if (axis == 0)
{
slicer.Dispose();
slicer = vtkExtractVOI.New();
slicer.SetInput(input);
slicer.SetVOI(k, k, extent[2], extent[3], extent[4], extent[5]);
slicer.Update();
permuter.Dispose();
permuter = vtkImagePermute.New();
permuter.SetInput(slicer.GetOutput());
permuter.SetFilteredAxes(1, 2, 0);
permuter.Update();
}
if (axis == 1)
{
slicer.Dispose();
slicer = vtkExtractVOI.New();
slicer.SetInput(input);
slicer.SetVOI(extent[0], extent[1], k, k, extent[4], extent[5]);
slicer.Update();
permuter.Dispose();
permuter = vtkImagePermute.New();
permuter.SetInput(slicer.GetOutput());
permuter.SetFilteredAxes(0, 2, 1);
permuter.Update();
}
if (axis == 2)
{
slicer.Dispose();
slicer = vtkExtractVOI.New();
slicer.SetInput(input);
slicer.SetVOI(extent[0], extent[1], extent[2], extent[3], k, k);
slicer.Update();
permuter.Dispose();
permuter = vtkImagePermute.New();
permuter.SetInput(slicer.GetOutput());
permuter.SetFilteredAxes(0, 1, 2);
permuter.Update();
}
//Convert data to byte
bytedata = DataTypes.vtkToByte(permuter.GetOutput());
slicer.Dispose();
permuter.Dispose();
//convert data to Mat
Mat image = new Mat(size[1], size[0], MatType.CV_8UC1, bytedata);
//Get largest binary object
Mat bw = Processing.LargestBWObject(image, 0.7 * 255.0);
//Set slice to byte array
if (bw.Sum().Val0 > 0)
{
output = DataTypes.setByteSlice(output, bw, outextent, axis, k);
}
}
return(DataTypes.byteToVTK(output));
}
//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
}
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
}