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)
{
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: 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);
}
}
public itk.simple.Image NalozObrazy(itk.simple.Image original, itk.simple.Image segmented)
{
itk.simple.MinimumMaximumImageFilter maxminFilter = new MinimumMaximumImageFilter();
maxminFilter.Execute(original);
double max = maxminFilter.GetMaximum();
itk.simple.CastImageFilter caster1 = new CastImageFilter();
caster1.SetOutputPixelType(itk.simple.PixelIDValueEnum.sitkInt16);
itk.simple.Image castImg = caster1.Execute(segmented);
itk.simple.MultiplyImageFilter multiplyFilter = new MultiplyImageFilter();
itk.simple.Image multiplyImage = multiplyFilter.Execute(castImg, max);
itk.simple.MaximumImageFilter maximumFilter = new MaximumImageFilter();
itk.simple.Image maximumImage = maximumFilter.Execute(original, multiplyImage);
//itk.simple.IntensityWindowingImageFilter windower = new IntensityWindowingImageFilter();
//windower.SetWindowMinimum(0);
//windower.SetWindowMaximum(255);
//windower.SetOutputMinimum(0);
//windower.SetOutputMaximum(1);
//itk.simple.Image window = windower.Execute(maximumImage);
itk.simple.ImageFileWriter writer = new ImageFileWriter();
writer.SetFileName("Wynik.dcm");
writer.Execute(maximumImage);
return(maximumImage);
}
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 < 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 {
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: {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 = 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: SimpleGaussian <input> <sigma> <output>");
return;
}
ImageFileReader reader = new ImageFileReader();
reader.setFileName(args[0]);
SmartPointerImage image = reader.execute();
Console.WriteLine(image.toString());
Gaussian gaussian = new Gaussian();
gaussian.setSigma(Double.Parse(args[1]));
image = gaussian.execute(image);
Console.WriteLine(image.toString());
ImageFileWriter writer = new ImageFileWriter();
writer.setFileName(args[2]);
writer.execute(image);
} catch (Exception ex) {
Console.WriteLine(ex);
}
}
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 void SetInput(string filePath)
{
string fileName = string.Format("{0}", filePath);
sitk.Image inputImage = ImageFileReader.ReadImage(fileName);
sitk.Image outputImage = BinaryThinningImageFilter.BinaryThinning(inputImage);
string newFileName = string.Format("temporary\\{0}.jpg", Guid.NewGuid().ToString());
ImageFileWriter.WriteImage(outputImage, newFileName);
originalBitmap = new Bitmap(Image.FromFile(newFileName));
}
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);
}
public HttpResponseMessage GetImage(string id)
{
byte[] imageByteArray = _imageProviderService.GetImageAsByteArray(UserId, id);
if (imageByteArray == null)
{
return(null);
}
ImageFileWriter.SaveImageSnapshot(imageByteArray, DateTimeProviderInstance, _snapshotImagePath, Logger, UserId, UserIp);
HttpResponseMessage response = CreateImageResponseMessage(imageByteArray);
return(response);
}
/// <summary>
/// Writes the image asynchronous.
/// </summary>
/// <param name="image">The ITK image.</param>
/// <param name="path">The file system location where the image should be written.</param>
/// <param name="filename">The name of the file.</param>
/// <param name="ct">The cancellation token.</param>
/// <returns>
/// A <see cref="T:System.Threading.Tasks.Task" /> representing the asynchronous operation.
/// </returns>
/// <exception cref="ArgumentNullException">
/// image
/// or
/// path
/// or
/// filename
/// or
/// ct
/// </exception>
public async Task WriteImageAsync(Image image, string path, string filename, CancellationToken ct)
{
if (image == null)
{
throw new ArgumentNullException(nameof(image));
}
if (string.IsNullOrWhiteSpace(path))
{
throw new ArgumentNullException(nameof(path));
}
if (string.IsNullOrWhiteSpace(filename))
{
throw new ArgumentNullException(nameof(filename));
}
if (ct == null)
{
throw new ArgumentNullException(nameof(ct));
}
await Task.Run(
() =>
{
using (ImageFileWriter writer = new ImageFileWriter())
{
try
{
ct.Register(() =>
{
writer.Abort();
});
ct.ThrowIfCancellationRequested();
writer.SetUseCompression(true);
writer.SetFileName(Path.Combine(path, filename));
writer.Execute(image);
}
catch (OperationCanceledException e)
{
throw new AmiException("The writing of the ITK image has been cancelled.", e);
}
catch (Exception e)
{
throw new AmiException("The ITK image could not be written.", e);
}
}
}, ct);
}
/// <inheritdoc/>
public async Task WriteImageAsync(Image image, string path, string filename, CancellationToken ct)
{
Ensure.ArgumentNotNull(image, nameof(image));
Ensure.ArgumentNotNull(ct, nameof(ct));
if (string.IsNullOrWhiteSpace(path))
{
throw new ArgumentNullException(nameof(path));
}
if (string.IsNullOrWhiteSpace(filename))
{
throw new ArgumentNullException(nameof(filename));
}
var fs = fileSystemStrategy.Create(path);
if (fs == null)
{
throw new UnexpectedNullException("Filesystem could not be created based on the provided path.");
}
using (ImageFileWriter writer = new ImageFileWriter())
{
try
{
ct.Register(() =>
{
writer.Abort();
});
ct.ThrowIfCancellationRequested();
writer.SetUseCompression(true);
writer.SetFileName(fs.Path.Combine(path, filename));
writer.Execute(image);
await Task.CompletedTask;
}
catch (OperationCanceledException e)
{
throw new AmiException("The writing of the ITK image has been cancelled.", e);
}
catch (Exception e)
{
throw new AmiException("The ITK image could not be written.", e);
}
}
}
public void zapiszObraz()
{
try
{
ImageFileWriter writer = new ImageFileWriter();
string sciezka = Directory.GetCurrentDirectory();
string pathString = Path.Combine(sciezka, nazwaObrazu);
if (Directory.Exists(pathString) == false)
{
Directory.CreateDirectory(pathString);
}
pathString = Path.Combine(pathString, nazwaObrazu);
// writer.SetFileName(p);
writer.Execute(obraz, pathString, false);
}
catch (ArgumentNullException e)
{
throw new Exception("Przed zapisem wybierz plik");
}
}
public void zapiszObraz()
{
try
{
ImageFileWriter writer = new ImageFileWriter();
string sciezka = Directory.GetCurrentDirectory();
string pathString = Path.Combine(sciezka, nazwaObrazu);
if (Directory.Exists(pathString) == false)
{
Directory.CreateDirectory(pathString);
}
pathString = Path.Combine(pathString, nazwaObrazu);
// writer.SetFileName(p);
writer.Execute(obraz, pathString, false);
}
catch(ArgumentNullException e)
{
throw new Exception("Przed zapisem wybierz plik");
}
}
public void zapiszObraz(Image obraz1)
{
try {
ImageFileWriter writer = new ImageFileWriter();
string sciezka = Directory.GetCurrentDirectory();
string pathString = Path.Combine(sciezka, "Wyniki");
Random r = new Random();
string e = r.Next(1,100).ToString();
string nazwaPliku1 = "segmentacja" + "_" + e+".dcm";
if (Directory.Exists(pathString) == false)
{
Directory.CreateDirectory(pathString);
}
pathString = Path.Combine(pathString, nazwaPliku1);
// writer.SetFileName(p);
writer.Execute(obraz1, pathString, false);
}
catch
{
throw new Exception("Blad podczas zapisu");
}
}
public void zapiszObraz(Image obraz1)
{
try {
ImageFileWriter writer = new ImageFileWriter();
string sciezka = Directory.GetCurrentDirectory();
string pathString = Path.Combine(sciezka, "Wyniki");
Random r = new Random();
string e = r.Next(1, 100).ToString();
string nazwaPliku1 = "segmentacja" + "_" + e + ".dcm";
if (Directory.Exists(pathString) == false)
{
Directory.CreateDirectory(pathString);
}
pathString = Path.Combine(pathString, nazwaPliku1);
// writer.SetFileName(p);
writer.Execute(obraz1, pathString, false);
}
catch
{
throw new Exception("Blad podczas zapisu");
}
}
static void Main(string[] args)
{
try {
if (args.Length < 3) {
Console.WriteLine("Usage: SimpleGaussian <input> <sigma> <output>");
public async Task <IActionResult> ClassifyImage(IFormFile imageFile)
{
if (imageFile.Length == 0)
{
return(BadRequest());
}
//Save the temp image file into the temp-folder
IImageFileWriter imageWriter = new ImageFileWriter();
string fileName = await imageWriter.UploadImageAsync(imageFile, _tempImagesFolderPath);
string imageFilePath = Path.Combine(_tempImagesFolderPath, fileName);
//Convert image stream to byte[]
//
//byte[] imageData = null;
//MemoryStream image = new MemoryStream();
//await imageFile.CopyToAsync(image);
//imageData = image.ToArray();
//if (!imageData.IsValidImage())
// return StatusCode(StatusCodes.Status415UnsupportedMediaType);
_logger.LogInformation($"Start processing image...");
//Measure execution time
var watch = System.Diagnostics.Stopwatch.StartNew();
//Set the specific image data
var imageInputData = new ImageInputData {
ImagePath = imageFilePath
};
//Predict code for provided image
ImageLabelPredictions imageLabelPredictions = _predictionEnginePool.Predict(imageInputData);
//Stop measuring time
watch.Stop();
var elapsedMs = watch.ElapsedMilliseconds;
_logger.LogInformation($"Image processed in {elapsedMs} miliseconds");
//try
//{
// // DELETE FILE WHEN CLOSED
// using (FileStream fs = new FileStream(imageFilePath, FileMode.Open, FileAccess.Read, FileShare.Read, 4096, FileOptions.DeleteOnClose))
// {
// // temp file exists
// fs.Close();
// }
//}
//catch (Exception e)
//{
// throw e;
//}
//Predict the image's label (The one with highest probability)
ImagePredictedLabelWithProbability imageBestLabelPrediction
= FindBestLabelWithProbability(imageLabelPredictions, imageInputData);
//return new ObjectResult(result);
return(Ok(imageBestLabelPrediction));
}
public itk.simple.Image SegmetacjaSledziony(itk.simple.Image image)
{
itk.simple.MorphologicalGradientImageFilter gradientFilter = new MorphologicalGradientImageFilter();
gradientFilter.SetKernelType(KernelEnum.sitkCross);
gradientFilter.SetKernelRadius(1);
itk.simple.Image gradientImage = gradientFilter.Execute(image);
itk.simple.SigmoidImageFilter sigmoidFilter = new SigmoidImageFilter();
sigmoidFilter.SetOutputMinimum(0);
sigmoidFilter.SetOutputMaximum(1);
sigmoidFilter.SetAlpha(1.5);
sigmoidFilter.SetBeta(100);
itk.simple.Image sigmoidImage = sigmoidFilter.Execute(gradientImage);
itk.simple.BinaryThresholdImageFilter threshFilter = new BinaryThresholdImageFilter();
threshFilter.SetLowerThreshold(100);
threshFilter.SetUpperThreshold(180);
threshFilter.SetOutsideValue(0);
threshFilter.SetInsideValue(1);
itk.simple.Image threshImage = threshFilter.Execute(image);
itk.simple.CastImageFilter castThresh = new CastImageFilter();
castThresh.SetOutputPixelType(itk.simple.PixelIDValueEnum.sitkInt16);
itk.simple.Image castThreshImage = castThresh.Execute(threshImage);
itk.simple.SubtractImageFilter substractFilter = new SubtractImageFilter();
itk.simple.Image substractImage = substractFilter.Execute(castThreshImage, sigmoidImage);
itk.simple.ThresholdImageFilter threshFilter2 = new ThresholdImageFilter();
threshFilter2.SetLower(0);
threshFilter2.SetUpper(0);
threshFilter2.SetOutsideValue(1);
itk.simple.Image threshImage2 = threshFilter2.Execute(substractImage);
itk.simple.BinaryErodeImageFilter erodeFilter = new BinaryErodeImageFilter();
erodeFilter.SetForegroundValue(1);
erodeFilter.SetBackgroundValue(0);
erodeFilter.SetKernelType(itk.simple.KernelEnum.sitkCross);
erodeFilter.SetKernelRadius(5);
itk.simple.Image erodeImage = erodeFilter.Execute(threshImage2);
itk.simple.ConnectedComponentImageFilter connFilter = new ConnectedComponentImageFilter();
connFilter.SetFullyConnected(true);
itk.simple.Image connImage = connFilter.Execute(erodeImage);
itk.simple.RelabelComponentImageFilter relabelFilter = new RelabelComponentImageFilter();
relabelFilter.SetMinimumObjectSize(5000);
itk.simple.Image relabelImage = relabelFilter.Execute(connImage);
itk.simple.BinaryThresholdImageFilter threshFilter3 = new BinaryThresholdImageFilter();
threshFilter3.SetInsideValue(1);
threshFilter3.SetOutsideValue(0);
threshFilter3.SetLowerThreshold(1);
threshFilter3.SetUpperThreshold(1);
itk.simple.Image threshImage3 = threshFilter3.Execute(relabelImage);
itk.simple.DilateObjectMorphologyImageFilter closeReconstructFilter = new DilateObjectMorphologyImageFilter();
closeReconstructFilter.SetKernelType(itk.simple.KernelEnum.sitkCross);
closeReconstructFilter.SetKernelRadius(5);
itk.simple.Image closeReconstructImage = closeReconstructFilter.Execute(threshImage3);
itk.simple.ImageFileWriter writer = new ImageFileWriter();
writer.SetFileName("SegmentujSledzione.dcm");
writer.Execute(closeReconstructImage);
return(closeReconstructImage);
}
public itk.simple.Image NalozObrazy(itk.simple.Image original, itk.simple.Image segmented)
{
itk.simple.MinimumMaximumImageFilter maxminFilter = new MinimumMaximumImageFilter();
maxminFilter.Execute(original);
double max = maxminFilter.GetMaximum();
itk.simple.CastImageFilter caster1 = new CastImageFilter();
caster1.SetOutputPixelType(itk.simple.PixelIDValueEnum.sitkInt16);
itk.simple.Image castImg = caster1.Execute(segmented);
itk.simple.MultiplyImageFilter multiplyFilter = new MultiplyImageFilter();
itk.simple.Image multiplyImage = multiplyFilter.Execute(castImg, max);
itk.simple.MaximumImageFilter maximumFilter = new MaximumImageFilter();
itk.simple.Image maximumImage = maximumFilter.Execute(original, multiplyImage);
//itk.simple.IntensityWindowingImageFilter windower = new IntensityWindowingImageFilter();
//windower.SetWindowMinimum(0);
//windower.SetWindowMaximum(255);
//windower.SetOutputMinimum(0);
//windower.SetOutputMaximum(1);
//itk.simple.Image window = windower.Execute(maximumImage);
itk.simple.ImageFileWriter writer = new ImageFileWriter();
writer.SetFileName("Wynik.dcm");
writer.Execute(maximumImage);
return maximumImage;
}
public itk.simple.Image SegmetacjaSledziony(itk.simple.Image image)
{
itk.simple.MorphologicalGradientImageFilter gradientFilter = new MorphologicalGradientImageFilter();
gradientFilter.SetKernelType(KernelEnum.sitkCross);
gradientFilter.SetKernelRadius(1);
itk.simple.Image gradientImage = gradientFilter.Execute(image);
itk.simple.SigmoidImageFilter sigmoidFilter = new SigmoidImageFilter();
sigmoidFilter.SetOutputMinimum(0);
sigmoidFilter.SetOutputMaximum(1);
sigmoidFilter.SetAlpha(1.5);
sigmoidFilter.SetBeta(100);
itk.simple.Image sigmoidImage = sigmoidFilter.Execute(gradientImage);
itk.simple.BinaryThresholdImageFilter threshFilter = new BinaryThresholdImageFilter();
threshFilter.SetLowerThreshold(100);
threshFilter.SetUpperThreshold(180);
threshFilter.SetOutsideValue(0);
threshFilter.SetInsideValue(1);
itk.simple.Image threshImage = threshFilter.Execute(image);
itk.simple.CastImageFilter castThresh = new CastImageFilter();
castThresh.SetOutputPixelType(itk.simple.PixelIDValueEnum.sitkInt16);
itk.simple.Image castThreshImage = castThresh.Execute(threshImage);
itk.simple.SubtractImageFilter substractFilter = new SubtractImageFilter();
itk.simple.Image substractImage = substractFilter.Execute(castThreshImage, sigmoidImage);
itk.simple.ThresholdImageFilter threshFilter2 = new ThresholdImageFilter();
threshFilter2.SetLower(0);
threshFilter2.SetUpper(0);
threshFilter2.SetOutsideValue(1);
itk.simple.Image threshImage2 = threshFilter2.Execute(substractImage);
itk.simple.BinaryErodeImageFilter erodeFilter = new BinaryErodeImageFilter();
erodeFilter.SetForegroundValue(1);
erodeFilter.SetBackgroundValue(0);
erodeFilter.SetKernelType(itk.simple.KernelEnum.sitkCross);
erodeFilter.SetKernelRadius(5);
itk.simple.Image erodeImage = erodeFilter.Execute(threshImage2);
itk.simple.ConnectedComponentImageFilter connFilter = new ConnectedComponentImageFilter();
connFilter.SetFullyConnected(true);
itk.simple.Image connImage = connFilter.Execute(erodeImage);
itk.simple.RelabelComponentImageFilter relabelFilter = new RelabelComponentImageFilter();
relabelFilter.SetMinimumObjectSize(5000);
itk.simple.Image relabelImage = relabelFilter.Execute(connImage);
itk.simple.BinaryThresholdImageFilter threshFilter3 = new BinaryThresholdImageFilter();
threshFilter3.SetInsideValue(1);
threshFilter3.SetOutsideValue(0);
threshFilter3.SetLowerThreshold(1);
threshFilter3.SetUpperThreshold(1);
itk.simple.Image threshImage3 = threshFilter3.Execute(relabelImage);
itk.simple.DilateObjectMorphologyImageFilter closeReconstructFilter = new DilateObjectMorphologyImageFilter();
closeReconstructFilter.SetKernelType(itk.simple.KernelEnum.sitkCross);
closeReconstructFilter.SetKernelRadius(5);
itk.simple.Image closeReconstructImage = closeReconstructFilter.Execute(threshImage3);
itk.simple.ImageFileWriter writer = new ImageFileWriter();
writer.SetFileName("SegmentujSledzione.dcm");
writer.Execute(closeReconstructImage);
return closeReconstructImage;
}
static void Main(string[] args)
{
try {
if (args.Length < 1)
{
Console.WriteLine("Usage: RTKFirstReconstruction <output>");
return;
}
// Defines the RTK geometry object
ThreeDCircularProjectionGeometry geometry = new ThreeDCircularProjectionGeometry();
uint numberOfProjections = 360;
float firstAngle = 0;
float angularArc = 360;
float sid = 600; // source to isocenter distance in mm
float sdd = 1200; // source to detector distance in mm
float isox = 0; // X coordinate on the projection image of isocenter
float isoy = 0; // Y coordinate on the projection image of isocenter
for (int x = 0; x < numberOfProjections; x++)
{
float angle = firstAngle + x * angularArc / numberOfProjections;
geometry.AddProjection(sid, sdd, angle, isox, isoy);
}
ConstantImageSource constantImageSource = new ConstantImageSource();
VectorDouble origin = new VectorDouble(3);
origin.Add(-127.0);
origin.Add(-127.0);
origin.Add(-127.0);
VectorUInt32 sizeOutput = new VectorUInt32(3);
sizeOutput.Add(256);
sizeOutput.Add(256);
sizeOutput.Add(numberOfProjections);
VectorDouble spacing = new VectorDouble(3);
spacing.Add(1.0);
spacing.Add(1.0);
spacing.Add(1.0);
constantImageSource.SetOrigin(origin);
constantImageSource.SetSpacing(spacing);
constantImageSource.SetSize(sizeOutput);
constantImageSource.SetConstant(0.0);
Image source = constantImageSource.Execute();
RayEllipsoidIntersectionImageFilter rei = new RayEllipsoidIntersectionImageFilter();
VectorDouble semiprincipalaxis = new VectorDouble(3);
semiprincipalaxis.Add(50.0);
semiprincipalaxis.Add(50.0);
semiprincipalaxis.Add(50.0);
VectorDouble center = new VectorDouble(3);
center.Add(0.0);
center.Add(0.0);
center.Add(0.0);
// Set GrayScale value, axes, center...
rei.SetDensity(20);
rei.SetAngle(0);
rei.SetCenter(center);
rei.SetAxis(semiprincipalaxis);
rei.SetGeometry(geometry);
Image reiImage = rei.Execute(source);
// Create reconstructed image
ConstantImageSource constantImageSource2 = new ConstantImageSource();
VectorUInt32 sizeOutput2 = new VectorUInt32(3);
sizeOutput2.Add(256);
sizeOutput2.Add(256);
sizeOutput2.Add(256);
constantImageSource2.SetOrigin(origin);
constantImageSource2.SetSpacing(spacing);
constantImageSource2.SetSize(sizeOutput2);
constantImageSource2.SetConstant(0.0);
Image source2 = constantImageSource2.Execute();
Console.WriteLine("Performing reconstruction");
FDKConeBeamReconstructionFilter feldkamp = new FDKConeBeamReconstructionFilter();
feldkamp.SetGeometry(geometry);
feldkamp.SetTruncationCorrection(0.0);
feldkamp.SetHannCutFrequency(0.0);
Image image = feldkamp.Execute(source2, reiImage);
ImageFileWriter writer = new ImageFileWriter();
writer.SetFileName(args[0]);
writer.Execute(image);
} catch (Exception ex) {
Console.WriteLine(ex);
}
}
static void Main(string[] args)
{
try {
if (args.Length < 1) {
Console.WriteLine("Usage: RTKFirstReconstruction <output>");
return;
}
// Defines the RTK geometry object
ThreeDCircularProjectionGeometry geometry = new ThreeDCircularProjectionGeometry();
uint numberOfProjections = 360;
float firstAngle = 0;
float angularArc = 360;
float sid = 600; // source to isocenter distance in mm
float sdd = 1200; // source to detector distance in mm
float isox = 0; // X coordinate on the projection image of isocenter
float isoy = 0; // Y coordinate on the projection image of isocenter
for (int x = 0; x < numberOfProjections; x++)
{
float angle = firstAngle + x * angularArc / numberOfProjections;
geometry.AddProjection(sid, sdd, angle, isox, isoy);
}
ConstantImageSource constantImageSource = new ConstantImageSource();
VectorDouble origin = new VectorDouble(3);
origin.Add(-127.0);
origin.Add(-127.0);
origin.Add(-127.0);
VectorUInt32 sizeOutput = new VectorUInt32(3);
sizeOutput.Add(256);
sizeOutput.Add(256);
sizeOutput.Add(numberOfProjections);
VectorDouble spacing = new VectorDouble(3);
spacing.Add(1.0);
spacing.Add(1.0);
spacing.Add(1.0);
constantImageSource.SetOrigin(origin);
constantImageSource.SetSpacing(spacing);
constantImageSource.SetSize(sizeOutput);
constantImageSource.SetConstant(0.0);
Image source = constantImageSource.Execute();
RayEllipsoidIntersectionImageFilter rei = new RayEllipsoidIntersectionImageFilter();
VectorDouble semiprincipalaxis = new VectorDouble(3);
semiprincipalaxis.Add(50.0);
semiprincipalaxis.Add(50.0);
semiprincipalaxis.Add(50.0);
VectorDouble center = new VectorDouble(3);
center.Add(0.0);
center.Add(0.0);
center.Add(0.0);
// Set GrayScale value, axes, center...
rei.SetDensity(20);
rei.SetAngle(0);
rei.SetCenter(center);
rei.SetAxis(semiprincipalaxis);
rei.SetGeometry(geometry);
Image reiImage = rei.Execute(source);
// Create reconstructed image
ConstantImageSource constantImageSource2 = new ConstantImageSource();
VectorUInt32 sizeOutput2 = new VectorUInt32(3);
sizeOutput2.Add(256);
sizeOutput2.Add(256);
sizeOutput2.Add(256);
constantImageSource2.SetOrigin(origin);
constantImageSource2.SetSpacing(spacing);
constantImageSource2.SetSize(sizeOutput2);
constantImageSource2.SetConstant(0.0);
Image source2 = constantImageSource2.Execute();
Console.WriteLine("Performing reconstruction");
FDKConeBeamReconstructionFilter feldkamp = new FDKConeBeamReconstructionFilter();
feldkamp.SetGeometry(geometry);
feldkamp.SetTruncationCorrection(0.0);
feldkamp.SetHannCutFrequency(0.0);
Image image = feldkamp.Execute(source2, reiImage);
ImageFileWriter writer = new ImageFileWriter();
writer.SetFileName(args[0]);
writer.Execute(image);
} catch (Exception ex) {
Console.WriteLine(ex);
}
}
