static void Main(string[] args)
{
try {
if (args.Length < 2)
{
Console.WriteLine("Usage: DicomSeriesReader <input_directory> <output_file>");
return;
}
Console.WriteLine("Reading Dicom directory: " + args[0]);
ImageSeriesReader reader = new ImageSeriesReader();
VectorString dicom_names = ImageSeriesReader.GetGDCMSeriesFileNames(args[0]);
reader.SetFileNames(dicom_names);
Image image = reader.Execute();
VectorUInt32 size = image.GetSize();
Console.WriteLine("Image size: " + size[0] + " " + size[1] + " " + size[2]);
Console.WriteLine("Writing image: " + args[1]);
ImageFileWriter writer = new ImageFileWriter();
writer.SetFileName(args[1]);
writer.Execute(image);
if (Environment.GetEnvironmentVariable("SITK_NOSHOW") == null)
{
SimpleITK.Show(image, "Dicom Series");
}
} catch (Exception ex) {
Console.WriteLine("Usage: DicomSeriesReader <input_directory> <output_file>");
Console.WriteLine(ex);
}
}
static void Main(string[] args)
{
try {
// Create an image
PixelIDValueEnum pixelType = PixelIDValueEnum.sitkUInt8;
VectorUInt32 imageSize = new VectorUInt32(new uint[] { 128, 128 });
Image image = new Image(imageSize, pixelType);
// Create a face image
VectorDouble faceSize = new VectorDouble(new double[] { 64, 64 });
VectorDouble faceCenter = new VectorDouble(new double[] { 64, 64 });
Image face = SimpleITK.GaussianSource(pixelType, imageSize, faceSize, faceCenter);
// Create eye images
VectorDouble eyeSize = new VectorDouble(new double[] { 5, 5 });
VectorDouble eye1Center = new VectorDouble(new double[] { 48, 48 });
VectorDouble eye2Center = new VectorDouble(new double[] { 80, 48 });
Image eye1 = SimpleITK.GaussianSource(pixelType, imageSize, eyeSize, eye1Center, 150);
Image eye2 = SimpleITK.GaussianSource(pixelType, imageSize, eyeSize, eye2Center, 150);
// Apply the eyes to the face
face = SimpleITK.Subtract(face, eye1);
face = SimpleITK.Subtract(face, eye2);
face = SimpleITK.BinaryThreshold(face, 200, 255, 255);
// Create the mouth
VectorDouble mouthRadii = new VectorDouble(new double[] { 30, 20 });
VectorDouble mouthCenter = new VectorDouble(new double[] { 64, 76 });
Image mouth = SimpleITK.GaussianSource(pixelType, imageSize, mouthRadii, mouthCenter);
mouth = SimpleITK.BinaryThreshold(mouth, 200, 255, 255);
mouth = SimpleITK.Subtract(255, mouth);
// Paste the mouth onto the face
VectorUInt32 mouthSize = new VectorUInt32(new uint[] { 64, 18 });
VectorInt32 mouthLoc = new VectorInt32(new int[] { 32, 76 });
face = SimpleITK.Paste(face, mouth, mouthSize, mouthLoc, mouthLoc);
// Apply the face to the original image
image = SimpleITK.Add(image, face);
// Display the results
if (Environment.GetEnvironmentVariable("SITK_NOSHOW") == null)
{
SimpleITK.Show(image, "Hello World: CSharp", true);
}
} catch (Exception ex) {
Console.WriteLine(ex);
}
}
static void Main(string[] args)
{
try {
if (args.Length < 2)
{
Console.WriteLine("Usage: N4BiasFieldCorrection inputImage outputImage"
+ " [shrinkFactor] [maskImage] [numberOfIterations]"
+ " [numberOfFittingLevels]\n");
return;
}
// Read input image
Image inputImage = sitk.ReadImage(args[0], PixelIDValueEnum.sitkFloat32);
Image image = inputImage;
Image maskImage;
if (args.Length > 3)
{
maskImage = sitk.ReadImage(args[3], PixelIDValueEnum.sitkUInt8);
}
else
{
maskImage = sitk.OtsuThreshold(image, 0, 1, 200);
}
if (args.Length > 2)
{
uint s = UInt32.Parse(args[2]);
uint[] s_array = new uint[image.GetDimension()];
for (uint i = 0; i < image.GetDimension(); i++)
{
s_array[i] = s;
}
VectorUInt32 shrink = new VectorUInt32(s_array);
image = sitk.Shrink(inputImage, shrink);
maskImage = sitk.Shrink(maskImage, shrink);
}
N4BiasFieldCorrectionImageFilter corrector
= new N4BiasFieldCorrectionImageFilter();
uint numFittingLevels = 4;
if (args.Length > 5)
{
numFittingLevels = UInt32.Parse(args[5]);
}
if (args.Length > 4)
{
uint it = UInt32.Parse(args[4]);
uint[] it_array = new uint[numFittingLevels];
for (uint i = 0; i < numFittingLevels; i++)
{
it_array[i] = it;
}
VectorUInt32 iterations = new VectorUInt32(it_array);
corrector.SetMaximumNumberOfIterations(iterations);
}
Image corrected_image = corrector.Execute(image, maskImage);
Image log_bias_field = corrector.GetLogBiasFieldAsImage(inputImage);
Image bias_field = sitk.Divide(inputImage, sitk.Exp(log_bias_field));
sitk.WriteImage(corrected_image, args[1]);
if (Environment.GetEnvironmentVariable("SITK_NOSHOW") == null)
{
SimpleITK.Show(corrected_image, "N4 Corrected");
}
} catch (Exception ex) {
Console.WriteLine(ex);
}
}