/// <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);
}
/// <summary>
/// Load image files into vtkImageData.
/// </summary>
/// <param name="path">Path to images.</param>
/// <param name="extension">Image extension.</param>
/// <returns></returns>
public static vtkImageData VTKLoader(string path, string extension)
{
/*DEPRECATED!!*/
//Output
vtkImageData data = vtkImageData.New();
//Get files from path
DirectoryInfo d = new DirectoryInfo(@path);
FileInfo[] files = d.GetFiles();
vtkStringArray allfiles = vtkStringArray.New();
//Iterate over files and read image data
foreach (FileInfo file in files)
{
//Fullfile
string fullfile = Path.Combine(path, file.Name);
allfiles.InsertNextValue(fullfile);
}
if (extension == ".png")
{
vtkPNGReader reader = vtkPNGReader.New();
reader.SetFileNames(allfiles);
reader.Update();
data = reader.GetOutput();
reader.Dispose();
}
if (extension == ".jpg")
{
vtkJPEGReader reader = vtkJPEGReader.New();
reader.SetFileNames(allfiles);
reader.Update();
data = reader.GetOutput();
reader.Dispose();
}
if (extension == ".bmp")
{
vtkBMPReader reader = vtkBMPReader.New();
reader.SetFileNames(allfiles);
reader.Update();
data = reader.GetOutput();
reader.Dispose();
}
data.SetScalarTypeToUnsignedChar();
data.Update();
return(data);
}
/// <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());
}
}
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();
}
/// <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();
}