/// <summary>
/// Calculates mean and standard deviation images from volume-of-interest
/// along third axis (z).
/// </summary>
/// <param name="input">Input volume as vtkImageData.</param>
/// <param name="meanImage">Mean 2D image.</param>
/// <param name="stdImage">Standard deviation 2D image.</param>
public static void MeanAndStd(vtkImageData input, out double[,] meanImage, out double[,] stdImage)
{
//Get data extent
int[] ext = input.GetExtent();
int[] dims = new int[] { ext[3] - ext[2] + 1, ext[1] - ext[0] + 1, ext[5] - ext[4] + 1 };
Console.WriteLine("Input shape: {0}, {1}, {2}".Format(dims[0], dims[1], dims[2]));
// Convert to byte volume
byte[] bytedata = DataTypes.vtkToByte(input);
byte[,,] bytevolume = DataTypes.VectorToVolume(bytedata, dims);
//int[] dims = new int[] { bytedata.GetLength(0), bytedata.GetLength(1), bytedata.GetLength(2) };
double[,] mean = new double[dims[0], dims[1]];
double[,] std = new double[dims[0], dims[1]];
Parallel.For(0, dims[0], i =>
{
Parallel.For(0, dims[1], j =>
{
//double[] temp = new double[dims[2]]; // has to be initialized in the loop
double[] temp = new double[0]; // has to be initialized in the loop
for (int k = 0; k < dims[2]; k++)
{
//temp[k] = bytevolume[i, j, k];
if (bytevolume[i, j, k] > 0)
{
temp.Concatenate(bytevolume[i, j, k]);
}
}
if (temp.Length > 0)
{
mean[i, j] = temp.Average();
std[i, j] =
Math.Sqrt(temp
.Subtract(temp.Average())
.Pow(2)
.Sum()
/ (temp.Length - 1));
}
else
{
mean[i, j] = 0;
std[i, j] = 0;
}
});
});
meanImage = mean;
stdImage = std;
}
/// <summary>
/// Calculates size[0] x size[0] x size[1] cubic volume of surface from the center of the sample.
/// Currently performs the calculation from upper third of the sample to save memory.
/// Creates a copy from the full data array, then crops the copy to 1/3 size.
/// </summary>
/// <param name="volume">Input sample data that contains vtkImageData.</param>
/// <param name="threshold">Grayscale threshold for sample surface and centering.</param>
/// <param name="size">Size of the calculated surface volume.</param>
/// <param name="surfacecoordinates">Array of z-coordinates of sample surface. These can be used with size parameter to visualize the surface volume.</param>
/// <param name="surfacevoi">Calculated surface volume.</param>
public static void SurfaceExtraction(ref Rendering.renderPipeLine volume, int threshold, int[] size,
out int[,] surfacecoordinates, out byte[,,] surfacevoi)
{
// Convert vtkImageData to byte[,,]
int[] dims = volume.getDims();
dims = new int[] { dims[1] + 1, dims[3] + 1, dims[5] + 1 };
byte[,,] byteVolume =
DataTypes.VectorToVolume(
DataTypes.vtkToByte(volume.idata), dims);
// Crop to upper third of the sample
int[] crop = { 0, byteVolume.GetLength(0) - 1, 0, byteVolume.GetLength(1) - 1, 0, (int)Math.Floor((double)byteVolume.GetLength(2) / 3) };
byteVolume = Functions.Crop3D(byteVolume, crop);
// Get sample center coordinates
int[] center = GetCenter(byteVolume, threshold);
// Get surface
GetSurface(byteVolume, center, size, threshold, out surfacecoordinates, out surfacevoi);
// Free memory
byteVolume = null;
}
/// <summary>
/// Calculates size[0] x size[0] x size[1] cubic volume of surface from the center of the sample.
/// Currently performs the calculation from upper third of the sample to save memory.
/// Creates a copy from the full data array, then crops the copy to 1/3 size.
/// </summary>
/// <param name="volume">Input sample data that contains vtkImageData.</param>
/// <param name="threshold">Grayscale threshold for sample surface and centering.</param>
/// <param name="size">Size of the calculated surface volume.</param>
/// <param name="mode">Cartilage area selected fro VOI extraction. Possible ones: "surface", "deep", "calcified".</param>
/// <param name="surfacecoordinates">Array of z-coordinates of sample surface. These can be used with size parameter to visualize the surface volume.</param>
/// <param name="surfacevoi">Calculated surface volume.</param>
public static void VOIExtraction(ref Rendering.renderPipeLine volume, int threshold, int[] size, string mode,
out int[,] surfacecoordinates, out byte[,,] surfacevoi)
{
// Get cropping dimensions
int[] crop = volume.idata.GetExtent();
crop[4] = (int)Math.Round(crop[5] / 2.0);
// Crop and flip the volume
var cropped = volume.getVOI(crop);
var flipper = vtkImageFlip.New();
flipper.SetInput(cropped);
flipper.SetFilteredAxes(2);
flipper.Update();
// Render cropped volume
//Rendering.RenderToNewWindow(flipper.GetOutput());
// Convert vtkImageData to byte[,,]
int[] dims = new int[] { (crop[1] - crop[0]) + 1, (crop[3] - crop[2]) + 1, (crop[5] - crop[4]) + 1 };
byte[,,] byteVolume =
DataTypes.VectorToVolume(
DataTypes.vtkToByte(flipper.GetOutput()), dims);
// Get sample center coordinates
//int[] center = GetCenter(byteVolume, threshold);
int[] center = new int[] { dims[0] / 2, dims[1] / 2 };
// Get surface
GetSurface(byteVolume, center, size, threshold, out surfacecoordinates, out surfacevoi);
// Free memory
byteVolume = null;
cropped = null;
flipper = null;
}