static void Main(string[] args)
{
try {
if (args.Length < 4)
{
Console.WriteLine("Usage: SimpleElastix <fixedImage> <movingImage> <parameterFile> <output>");
return;
}
// Instantiate SimpleElastix
ElastixImageFilter silx;
// Read input
ImageFileReader reader = new ImageFileReader();
reader.SetFileName(args[0]);
silx.SetFixedImage(reader.Execute());
reader.SetFileName(args[1]);
silx.SetMovingImage(reader.Execute());
silx.SetParameterMap(ReadParameterFile(args[2]));
// Perform Registration
silx.LogToConsoleOn();
silx.Execute();
// Write output image
ImageFileWriter writer = new ImageFileWriter();
writer.SetFileName(args[3]);
writer.Execute(silx.GetResultImage());
} catch (Exception e) {
Console.WriteLine(e);
}
}
static void Main(string[] args)
{
if (args.Length < 3)
{
Console.WriteLine("Usage: %s <fixedImageFilter> <movingImageFile> <outputTransformFile>\n", "ImageRegistrationMethod2");
return;
}
ImageFileReader reader = new ImageFileReader();
reader.SetOutputPixelType(PixelIDValueEnum.sitkFloat32);
reader.SetFileName(args[0]);
Image fixedImage = reader.Execute();
fixedImage = SimpleITK.Normalize(fixedImage);
SimpleITK.DiscreteGaussian(fixedImage, 2.0);
reader.SetFileName(args[1]);
Image movingImage = reader.Execute();
movingImage = SimpleITK.Normalize(movingImage);
movingImage = SimpleITK.DiscreteGaussian(movingImage, 2.0);
ImageRegistrationMethod R = new ImageRegistrationMethod();
R.SetMetricAsJointHistogramMutualInformation();
double learningRate = 1;
uint numberOfIterations = 200;
double convergenceMinimumValue = 1e-4;
uint convergenceWindowSize = 5;
R.SetOptimizerAsGradientDescentLineSearch(learningRate,
numberOfIterations,
convergenceMinimumValue,
convergenceWindowSize);
R.SetInitialTransform(new TranslationTransform(fixedImage.GetDimension()));
R.SetInterpolator(InterpolatorEnum.sitkLinear);
IterationUpdate cmd = new IterationUpdate(R);
R.AddCommand(EventEnum.sitkIterationEvent, cmd);
Transform outTx = R.Execute(fixedImage, movingImage);
outTx.WriteTransform(args[2]);
}
static void Main(string[] args)
{
try {
if (args.Length < 3)
{
Console.WriteLine("Usage: SimpleGaussian <input> <sigma> <output>");
return;
}
// Read input image
ImageFileReader reader = new ImageFileReader();
reader.SetFileName(args[0]);
Image image = reader.Execute();
// Execute Gaussian smoothing filter
SmoothingRecursiveGaussianImageFilter gaussian = new SmoothingRecursiveGaussianImageFilter();
gaussian.SetSigma(Double.Parse(args[1]));
Image blurredImage = gaussian.Execute(image);
// Covert the real output image back to the original pixel type , to
// make writing easier , as many file formats don 't support real
// pixels .
CastImageFilter castFilter = new CastImageFilter();
castFilter.SetOutputPixelType(image.GetPixelID());
Image destImage = castFilter.Execute(blurredImage);
// Write output image
ImageFileWriter writer = new ImageFileWriter();
writer.SetFileName(args[2]);
writer.Execute(destImage);
} catch (Exception ex) {
Console.WriteLine(ex);
}
}
static void Main(string[] args)
{
try {
if (args.Length < 3)
{
Console.WriteLine("Usage: {0} <input> <variance> <output>", args[0]);
return;
}
// Read input image
ImageFileReader reader = new ImageFileReader();
reader.SetFileName(args[0]);
Image image = reader.Execute();
// Execute Gaussian smoothing filter
DiscreteGaussianImageFilter filter = new DiscreteGaussianImageFilter();
filter.SetVariance(Double.Parse(args[1]));
MyCommand cmd = new MyCommand(filter);
filter.AddCommand(EventEnum.sitkProgressEvent, cmd);
image = filter.Execute(image);
// Write output image
ImageFileWriter writer = new ImageFileWriter();
writer.SetFileName(args[2]);
writer.Execute(image);
} catch (Exception ex) {
Console.WriteLine(ex);
}
}
static void Main(string[] args)
{
try {
if (args.Length < 1)
{
Console.WriteLine("Usage: ImageIOSelection image_input_file");
return;
}
// Find out which image IOs are supported
ImageFileReader reader = new ImageFileReader();
itk.simple.VectorString image_ios = reader.GetRegisteredImageIOs();
Console.Write("The supported image IOs are: ");
for (int i = 0; i < image_ios.Count; i++)
{
Console.Write(image_ios[i] + " ");
}
Console.WriteLine("\n--------------------");
// Another option is to just print the reader and see which
// IOs are supported
Console.WriteLine(reader.ToString());
Console.WriteLine("--------------------");
// Force the use of a specific IO. If the IO doesn't support
// reading the image type it will throw an exception.
reader.SetImageIO("PNGImageIO");
reader.SetFileName(args[0]);
Image image = reader.Execute();
Console.WriteLine("Read image: " + args[0]);
} catch (Exception ex) {
Console.WriteLine("Read failed: " + ex);
}
}
static void Main(string[] args)
{
try {
if (args.Length < 3) {
Console.WriteLine("Usage: SimpleGaussian <input> <sigma> <output>");
return;
}
// Read input image
ImageFileReader reader = new ImageFileReader();
reader.SetFileName(args[0]);
Image image = reader.Execute();
// Execute Gaussian smoothing filter
SmoothingRecursiveGaussianImageFilter gaussian = new SmoothingRecursiveGaussianImageFilter();
gaussian.SetSigma(Double.Parse(args[1]));
image = gaussian.Execute(image);
// Write output image
ImageFileWriter writer = new ImageFileWriter();
writer.SetFileName(args[2]);
writer.Execute(image);
} catch (Exception ex) {
Console.WriteLine(ex);
}
}
static void Main(string[] args)
{
try {
if (args.Length < 3) {
Console.WriteLine("Usage: {0} <input> <variance> <output>", args[0]);
return;
}
// Read input image
ImageFileReader reader = new ImageFileReader();
reader.SetFileName(args[0]);
Image image = reader.Execute();
// Execute Gaussian smoothing filter
DiscreteGaussianImageFilter filter = new DiscreteGaussianImageFilter();
filter.SetVariance(Double.Parse(args[1]));
MyCommand cmd = new MyCommand(filter);
filter.AddCommand(EventEnum.sitkProgressEvent, cmd);
image = filter.Execute(image);
// Write output image
ImageFileWriter writer = new ImageFileWriter();
writer.SetFileName(args[2]);
writer.Execute(image);
} catch (Exception ex) {
Console.WriteLine(ex);
}
}
static void Main(string[] args)
{
try {
if (args.Length < 3) {
Console.WriteLine("Usage: SimpleGaussian <input> <sigma> <output>");
return;
}
// Read input image
ImageFileReader reader = new ImageFileReader();
reader.SetFileName(args[0]);
Image image = reader.Execute();
// Execute Gaussian smoothing filter
SmoothingRecursiveGaussianImageFilter gaussian = new SmoothingRecursiveGaussianImageFilter();
gaussian.SetSigma(Double.Parse(args[1]));
Image blurredImage = gaussian.Execute(image);
// Covert the real output image back to the original pixel type , to
// make writing easier , as many file formats don 't support real
// pixels .
CastImageFilter castFilter = new CastImageFilter();
castFilter.SetOutputPixelType(image.GetPixelIDValue());
Image destImage = castFilter.Execute(blurredImage);
// Write output image
ImageFileWriter writer = new ImageFileWriter();
writer.SetFileName(args[2]);
writer.Execute(destImage);
} catch (Exception ex) {
Console.WriteLine(ex);
}
}
static void Main(string[] args)
{
try {
if (args.Length < 3)
{
Console.WriteLine("Usage: SimpleGaussian <input> <sigma> <output>");
return;
}
// Read input image
ImageFileReader reader = new ImageFileReader();
reader.SetFileName(args[0]);
Image image = reader.Execute();
// Execute Gaussian smoothing filter
SmoothingRecursiveGaussianImageFilter gaussian = new SmoothingRecursiveGaussianImageFilter();
gaussian.SetSigma(Double.Parse(args[1]));
image = gaussian.Execute(image);
// Write output image
ImageFileWriter writer = new ImageFileWriter();
writer.SetFileName(args[2]);
writer.Execute(image);
} catch (Exception ex) {
Console.WriteLine(ex);
}
}
static void Main(string[] args)
{
if (args.Length < 3)
{
Console.WriteLine("Usage: %s <fixedImageFilter> <movingImageFile> <outputTransformFile>\n", "ImageRegistrationMethod1");
return;
}
ImageFileReader reader = new ImageFileReader();
reader.SetOutputPixelType(PixelIDValueEnum.sitkFloat32);
reader.SetFileName(args[0]);
Image fixedImage = reader.Execute();
reader.SetFileName(args[1]);
Image movingImage = reader.Execute();
ImageRegistrationMethod R = new ImageRegistrationMethod();
R.SetMetricAsMeanSquares();
double maxStep = 4.0;
double minStep = 0.01;
uint numberOfIterations = 200;
double relaxationFactor = 0.5;
R.SetOptimizerAsRegularStepGradientDescent(maxStep,
minStep,
numberOfIterations,
relaxationFactor);
R.SetInitialTransform(new TranslationTransform(fixedImage.GetDimension()));
R.SetInterpolator(InterpolatorEnum.sitkLinear);
IterationUpdate cmd = new IterationUpdate(R);
R.AddCommand(EventEnum.sitkIterationEvent, cmd);
Transform outTx = R.Execute(fixedImage, movingImage);
// System.out.println("-------");
// System.out.println(outTx.toString());
// System.out.format("Optimizer stop condition: %s\n", R.getOptimizerStopConditionDescription());
// System.out.format(" Iteration: %d\n", R.getOptimizerIteration());
// System.out.format(" Metric value: %f\n", R.getMetricValue());
outTx.WriteTransform(args[2]);
}
static void Main(string[] args)
{
if ( args.Length < 3 )
{
Console.WriteLine("Usage: %s <fixedImageFilter> <movingImageFile> <outputTransformFile>\n", "ImageRegistrationMethod1");
return;
}
ImageFileReader reader = new ImageFileReader();
reader.SetOutputPixelType( PixelIDValueEnum.sitkFloat32 );
reader.SetFileName(args[0]);
Image fixedImage = reader.Execute();
reader.SetFileName(args[1]);
Image movingImage = reader.Execute();
ImageRegistrationMethod R = new ImageRegistrationMethod();
R.SetMetricAsMeanSquares();
double maxStep = 4.0;
double minStep = 0.01;
uint numberOfIterations = 200;
double relaxationFactor = 0.5;
R.SetOptimizerAsRegularStepGradientDescent( maxStep,
minStep,
numberOfIterations,
relaxationFactor );
R.SetInitialTransform( new TranslationTransform( fixedImage.GetDimension() ) );
R.SetInterpolator( InterpolatorEnum.sitkLinear );
IterationUpdate cmd = new IterationUpdate(R);
R.AddCommand(EventEnum.sitkIterationEvent, cmd);
Transform outTx = R.Execute( fixedImage, movingImage );
// System.out.println("-------");
// System.out.println(outTx.toString());
// System.out.format("Optimizer stop condition: %s\n", R.getOptimizerStopConditionDescription());
// System.out.format(" Iteration: %d\n", R.getOptimizerIteration());
// System.out.format(" Metric value: %f\n", R.getMetricValue());
outTx.WriteTransform(args[2]);
}
public Image wczytajObraz(string sciezka)
{
ImageFileReader r = new ImageFileReader();
r.SetFileName(sciezka);
r.SetOutputPixelType(itk.simple.PixelIDValueEnum.sitkInt16);
var image = r.Execute();
nazwaObrazu = Path.GetFileName(r.GetFileName());
obraz = image;
return obraz;
}
public MainWindow()
{
InitializeComponent();
string[] args = new string[3];
string s = System.AppDomain.CurrentDomain.BaseDirectory;
args[0] = s + "Obrazy\\abc.png";
args[1] = "1";
args[2] = s + "Obrazy\\cba.png";
try
{
if (args.Length < 3)
{
//Console.WriteLine("Usage: SimpleGausian <imput> <sigma> <output>");
lTest.Content = "Usage: SimpleGausian <imput> <sigma> <output>";
return;
}
//Read imput image
ImageFileReader reader = new ImageFileReader();
reader.SetFileName(args[0]);
itk.simple.Image image = reader.Execute();
//Remember format
//itk.simple.Image image2 = new itk.simple.Image(image);
//PixelIDValueEnum id = PixelIDValueEnum.sitkVectorUInt8;
//PixelIDValueEnum id = image2.GetPixelID();
//Execute Gausian smoothing filter
//SmoothingRecursiveGaussianImageFilter gausian = new SmoothingRecursiveGaussianImageFilter();
//gausian.SetSigma(Double.Parse(args[1]));
//image = gausian.Execute(image);
//Convert?
//PixelIDValueEnum id = image.GetPixelID();
//SimpleITK.Cast(image, id);
//id = image.GetPixelID();
//Write output image
ImageFileWriter writer = new ImageFileWriter();
writer.SetFileName(args[2]);
writer.Execute(image);
lTest.Content = "Chyba się udało, sprwadź :P";
}
catch (Exception ex)
{
//Console.WriteLine(ex);
lTest.Content = ex;
}
}
public Image wczytajObraz(string sciezka)
{
ImageFileReader r = new ImageFileReader();
r.SetFileName(sciezka);
r.SetOutputPixelType(itk.simple.PixelIDValueEnum.sitkInt16);
var image = r.Execute();
nazwaObrazu = Path.GetFileName(r.GetFileName());
obraz = image;
return(obraz);
}
static void example1(string inputImageFileName, string outputImageFileName)
{
ImageFileReader reader = new ImageFileReader();
reader.SetImageIO("PNGImageIO");
reader.SetFileName(inputImageFileName);
Image image = reader.Execute();
ImageFileWriter writer = new ImageFileWriter();
writer.SetFileName(outputImageFileName);
writer.Execute(image);
}
/// <summary>
/// Reads the image asynchronous.
/// </summary>
/// <param name="path">The location of the image on the file system.</param>
/// <param name="ct">The cancellation token.</param>
/// <returns>
/// The ITK image.
/// </returns>
/// <exception cref="ArgumentNullException">
/// path
/// or
/// ct
/// </exception>
public async Task <Image> ReadImageAsync(string path, CancellationToken ct)
{
if (string.IsNullOrWhiteSpace(path))
{
throw new ArgumentNullException(nameof(path));
}
if (ct == null)
{
throw new ArgumentNullException(nameof(ct));
}
return(await Task.Run(
() =>
{
// TODO:
// - check if path is a directory
// - check if path contains multiple files
// - determine file format
// read DICOM image series
// https://simpleitk.readthedocs.io/en/master/Examples/DicomSeriesReader/Documentation.html
using (ImageFileReader reader = new ImageFileReader())
{
try
{
ct.Register(() =>
{
reader.Abort();
});
ct.ThrowIfCancellationRequested();
reader.SetFileName(path);
Image image = reader.Execute();
image = ApplyRescaleIntensityImageFilter(image);
image = ApplyCastImageFilter(image);
return image;
}
catch (OperationCanceledException e)
{
throw new AmiException("The reading of the ITK image has been cancelled.", e);
}
catch (Exception e)
{
throw new AmiException("The ITK image could not be read.", e);
}
}
}, ct));
}
static void Main(string[] args)
{
try {
if (args.Length < 4)
{
Console.WriteLine("Usage: SimpleElastix <fixedImage> <movingImage> <inputImage> <parameterFile> <output>");
return;
}
// Make transform
SimpleElastix elastix;
ImageFileReader reader = new ImageFileReader();
reader.SetFileName(args[0]);
elastix.SetFixedImage(reader.Execute());
reader.SetFileName(args[1]);
elastix.SetMovingImage(reader.Execute());
elastix.SetParameterMap(ReadParameterFile(args[3]));
elastix.Execute();
// Instantiate transformix
SimpleTransformix transformix;
// Read input
reader.SetFileName(args[4]);
transformix.SetInputImage(reader.execute());
transformix.SetTransformParameterMapList(elastix.GetTransformParameterMapList());
// Perform warp
transformix.LogToConsoleOn();
transformix.Execute();
// Write result image
sitk.WriteImage(transformix.GetResultImage(), args[5]);
} catch (Exception ex) {
Console.WriteLine(ex);
}
}
/// <inheritdoc/>
public ImageReaderBase CreateImageReader(string path)
{
if (string.IsNullOrWhiteSpace(path))
{
throw new ArgumentNullException(nameof(path));
}
var fs = fileSystemStrategy.Create(path);
if (fs == null)
{
throw new UnexpectedNullException("Filesystem could not be created based on the provided path.");
}
if (fs.IsDirectory(path))
{
var entryPath = DiscoverEntryPath(fs.Directory.GetFiles(path));
if (string.IsNullOrWhiteSpace(entryPath))
{
// By default try to read DICOM image series
// https://simpleitk.readthedocs.io/en/master/Examples/DicomSeriesReader/Documentation.html
ImageSeriesReader seriesReader = new ImageSeriesReader();
seriesReader.SetFileNames(ImageSeriesReader.GetGDCMSeriesFileNames(path));
return(seriesReader);
}
else
{
// Try to read the image based on the entry path
ImageFileReader reader = new ImageFileReader();
reader.SetFileName(entryPath);
return(reader);
}
}
else
{
ImageFileReader reader = new ImageFileReader();
reader.SetFileName(path);
return(reader);
}
}
