public void Apply()
{
if (this.SelectedImageGraphicProvider == null)
{
return;
}
ImageGraphic image = this.SelectedImageGraphicProvider.ImageGraphic;
if (image == null)
{
return;
}
if (!(image is GrayscaleImageGraphic))
{
return;
}
itkImageBase input = ItkHelper.CreateItkImage(image as GrayscaleImageGraphic);
itkImageBase output = itkImage.New(input);
ItkHelper.CopyToItkImage(image as GrayscaleImageGraphic, input);
String mangledType = input.MangledTypeString;
CastImageFilterType castToIF2 = CastImageFilterType.New(mangledType + "IF2");
SmoothingFilterType smoothingFilter = SmoothingFilterType.New("IF2IF2");
smoothingFilter.TimeStep = 0.125;
smoothingFilter.NumberOfIterations = 5;
smoothingFilter.ConductanceParameter = 9.0;
GradientMagnitudeFilterType gradientMagnitudeFilter = GradientMagnitudeFilterType.New("IF2IF2");
gradientMagnitudeFilter.Sigma = 1.0;
SigmoidFilterType sigmoidFilter = SigmoidFilterType.New("IF2IF2");
sigmoidFilter.OutputMinimum = 0.0;
sigmoidFilter.OutputMaximum = 1.0;
sigmoidFilter.Alpha = -0.5; //-0.3
sigmoidFilter.Beta = 3.0; //2.0
FastMarchingFilterType fastMarchingFilter = FastMarchingFilterType.New("IF2IF2");
double seedValue = 0.0;
int[] seedPosition = { 256, 256 };// user input
itkIndex seedIndex = new itkIndex(seedPosition);
itkLevelSetNode[] trialPoints = { new itkLevelSetNode(seedValue, seedIndex) };
fastMarchingFilter.TrialPoints = trialPoints;
fastMarchingFilter.StoppingValue = 100;
BinaryThresholdFilterType binaryThresholdFilter = BinaryThresholdFilterType.New("IF2" + mangledType); //to UC2?
binaryThresholdFilter.UpperThreshold = 100.0; //200
binaryThresholdFilter.LowerThreshold = 0.0;
binaryThresholdFilter.OutsideValue = 0;
if (image.BitsPerPixel == 16)
{
binaryThresholdFilter.InsideValue = (image as GrayscaleImageGraphic).ModalityLut.MaxInputValue;//32767;
}
else
{
binaryThresholdFilter.InsideValue = 255;
}
//intensityFilterType intensityFilter = intensityFilterType.New("UC2" + mangledType);
//intensityFilter.OutputMinimum = 0;
//if (image.BitsPerPixel == 16)
// intensityFilter.OutputMaximum = (image as GrayscaleImageGraphic).ModalityLut.MaxInputValue;//32767;
//else
// intensityFilter.OutputMaximum = 255;
// Make data stream connections
castToIF2.SetInput(input);
smoothingFilter.SetInput(castToIF2.GetOutput());
gradientMagnitudeFilter.SetInput(smoothingFilter.GetOutput());
sigmoidFilter.SetInput(gradientMagnitudeFilter.GetOutput());
fastMarchingFilter.SetInput(sigmoidFilter.GetOutput());
binaryThresholdFilter.SetInput(fastMarchingFilter.GetOutput());
//intensityFilter.SetInput(binaryThresholdFilter.GetOutput());
//smoothingFilter.Update();
fastMarchingFilter.OutputSize = input.BufferedRegion.Size;//?
binaryThresholdFilter.Update();
binaryThresholdFilter.GetOutput(output);
ItkHelper.CopyFromItkImage(image as GrayscaleImageGraphic, output);
image.Draw();
input.Dispose();
output.Dispose();
}
public void Apply()
{
if (this.SelectedImageGraphicProvider == null)
{
return;
}
ImageGraphic image = this.SelectedImageGraphicProvider.ImageGraphic;
if (image == null)
{
return;
}
if (!(image is GrayscaleImageGraphic))
{
return;
}
byte[] pixels = image.PixelData.Raw;
itkImageBase input = ItkHelper.CreateItkImage(image as GrayscaleImageGraphic);
itkImageRegion region = input.LargestPossibleRegion;
itkImageBase output = itkImage.New(input);
ItkHelper.CopyToItkImage(image as GrayscaleImageGraphic, input);
String mangledType = input.MangledTypeString;
CastImageFilterType castToIF2 = CastImageFilterType.New(mangledType + "IF2");
castToIF2.SetInput(input);
FilterType filter = FilterType.New("IF2IF2");
filter.SetInput(castToIF2.GetOutput());
// TODO: need to allow user to set parameters of filter
filter.LowerThreshold = 90;
filter.UpperThreshold = 127;
//filter.OutsideValue = 0;
// smoothing the edge
double[] error = { 0.01, 0.01 };
filter.MaximumError = error;
double[] var = { 1.0, 1.0 };
filter.Variance = var;
intensityFilterType intensityFilter = intensityFilterType.New("IF2" + mangledType);
intensityFilter.SetInput(filter.GetOutput());
intensityFilter.OutputMinimum = 0;
if (image.BitsPerPixel == 16)
{
intensityFilter.OutputMaximum = (image as GrayscaleImageGraphic).ModalityLut.MaxInputValue;//32767;
}
else
{
intensityFilter.OutputMaximum = 255;
}
intensityFilter.Update();
#if DEBUG
bool debug = false;
if (debug)
{
itkImageBase outputIF2 = itkImage.New("IF2");
filter.GetOutput(outputIF2);
float min = float.MaxValue, max = float.MinValue;
unsafe
{
fixed(byte *pDstByte = image.PixelData.Raw)
{
itkImageRegionConstIterator_IF2 itkIt = new itkImageRegionConstIterator_IF2(outputIF2, region);
byte *pDst = (byte *)pDstByte;
int height = image.Rows;
int width = image.Columns;
for (int y = 0; y < height; y++)
{
for (int x = 0; x < width; x++)
{
float f = itkIt.Get().ValueAsF;
if (f > max)
{
max = f;
}
if (f < min)
{
min = f;
}
pDst[0] = (byte)itkIt.Get().ValueAsF;
pDst++;
itkIt++;
}
}
}
}
Console.WriteLine("min max "); Console.Write(min); Console.Write(" "); Console.WriteLine(max);
}
#endif
intensityFilter.GetOutput(output);
ItkHelper.CopyFromItkImage(image as GrayscaleImageGraphic, output);
image.Draw();
filter.Dispose();
intensityFilter.Dispose();
input.Dispose();
output.Dispose();
}
public void Apply()
{
if (this.SelectedImageGraphicProvider == null)
{
return;
}
ImageGraphic image = this.SelectedImageGraphicProvider.ImageGraphic;
if (image == null)
{
return;
}
if (!(image is GrayscaleImageGraphic))
{
return;
}
byte[] pixels = image.PixelData.Raw;
itkImageBase input = ItkHelper.CreateItkImage(image as GrayscaleImageGraphic);
itkImageRegion region = input.LargestPossibleRegion;
itkImageBase output = itkImage.New(input);
ItkHelper.CopyToItkImage(image as GrayscaleImageGraphic, input);
string mangledType = input.MangledTypeString;
string mangledType2 = input.PixelType.MangledTypeString;
CastImageFilterType castToIF2 = CastImageFilterType.New(mangledType + "IF2");
castToIF2.SetInput(input);
FilterType filter = FilterType.New("IF2IF2");
filter.SetInput(castToIF2.GetOutput());
intensityFilterType intensityFilter = intensityFilterType.New("IF2" + mangledType);
intensityFilter.SetInput(filter.GetOutput());
intensityFilter.OutputMinimum = 0;
if (image.BitsPerPixel == 16)
{
intensityFilter.OutputMaximum = (image as GrayscaleImageGraphic).ModalityLut.MaxInputValue;
}
else
{
intensityFilter.OutputMaximum = 255;
}
intensityFilter.Update();
intensityFilter.GetOutput(output);
ItkHelper.CopyFromItkImage(image as GrayscaleImageGraphic, output);
image.Draw();
filter.Dispose();
intensityFilter.Dispose();
input.Dispose();
output.Dispose();
}
static void Main(string[] args) {
try {
// Get input parameters
if (args.Length < 3) {
Console.WriteLine("Missing Parameters");
Console.Write("Usage: " + Environment.GetCommandLineArgs()[0] + " ");
Console.Write("fixedImageFile movingImageFile ");
Console.Write("outputImagefile ");
Console.WriteLine("[checkerBoardBefore] [checkerBoardAfter]");
return;
}
// Create components
TransformType transform = TransformType.New();
OptimizerType optimizer = OptimizerType.New();
InterpolatorType interpolator = InterpolatorType.New();
MetricType metric = MetricType.New();
RegistrationType registration = RegistrationType.New();
registration.SetOptimizer(optimizer);
registration.SetTransform(transform);
registration.SetInterpolator(interpolator);
registration.SetMetric(metric);
// Set metric parameters
metric.FixedImageStandardDeviation = 0.4;
metric.MovingImageStandardDeviation = 0.4;
// Read input images
ImageType fixedImage = ImageType.New();
fixedImage.Read(args[0]);
ImageType movingImage = ImageType.New();
movingImage.Read(args[1]);
// Normailize
NormalizeFilterType fixedNormalizer = NormalizeFilterType.New();
NormalizeFilterType movingNormalizer = NormalizeFilterType.New();
GaussianFilterType fixedSmoother = GaussianFilterType.New();
GaussianFilterType movingSmoother = GaussianFilterType.New();
fixedSmoother.Variance = new double[] { 2.0, 2.0 };
movingSmoother.Variance = new double[] { 2.0, 2.0 };
// Setup pipeline
fixedNormalizer.SetInput(fixedImage);
movingNormalizer.SetInput(movingImage);
fixedSmoother.SetInput(fixedNormalizer.GetOutput());
movingSmoother.SetInput(movingNormalizer.GetOutput());
ImageType fixedSmootherOutput = ImageType.New();
fixedSmoother.GetOutput(fixedSmootherOutput);
ImageType movingSmootherOutput = ImageType.New();
movingSmoother.GetOutput(movingSmootherOutput);
registration.SetFixedImage(fixedSmootherOutput);
registration.SetMovingImage(movingSmootherOutput);
// Set requested region
fixedNormalizer.Update();
ImageType fixedNormalizerOutput = ImageType.New();
fixedNormalizer.GetOutput(fixedNormalizerOutput);
RegionType fixedImageRegion = fixedNormalizerOutput.BufferedRegion;
fixedImage.RequestedRegion = fixedImageRegion;
//registration.FixedImageRegion = fixedImageRegion
// Set initial parameters
ParametersType initialParameters =
new ParametersType(transform.NumberOfParameters);
initialParameters[0] = 0.0;
initialParameters[1] = 0.0;
registration.InitialTransformParameters = initialParameters;
// Set metric sampling
int numberOfPixels = fixedImageRegion.Size[0] * fixedImageRegion.Size[1];
int numberOfSamples = (int)((double)numberOfPixels * 0.01);
metric.NumberOfSpatialSamples = (uint)numberOfSamples;
// Setup optimizer
optimizer.LearningRate = 15.0;
optimizer.NumberOfIterations = 200;
optimizer.Maximize = true;
// Listen for iteration events
optimizer.Iteration += OnOptimizerIterationEvent;
// Start registration
registration.StartRegistration();
Console.WriteLine(optimizer.StopCondition);
// Get results
ParametersType finalParameters = registration.LastTransformParameters;
double TranslationAlongX = finalParameters[0];
double TranslationAlongY = finalParameters[1];
uint numberOfIterations = optimizer.NumberOfIterations;
double bestValue = optimizer.GetValue();
// Print results
Console.WriteLine("Result=");
Console.WriteLine(String.Format(" Translation X = {0}", TranslationAlongX));
Console.WriteLine(String.Format(" Translation Y = {0}", TranslationAlongY));
Console.WriteLine(String.Format(" Iterations = {0}", numberOfIterations));
Console.WriteLine(String.Format(" Metric value = {0}", bestValue));
Console.WriteLine(String.Format(" Numb. Samples = {0}", numberOfSamples));
// Setup resample filter
TransformType finalTransform = TransformType.New();
finalTransform.Parameters = finalParameters;
//finalTransform.FixedParameters = transform.FixedParameters;
ResampleFilterType resample = ResampleFilterType.New();
resample.SetTransform(finalTransform);
resample.SetInput(movingImage);
resample.OutputSize = fixedImage.LargestPossibleRegion.Size;
resample.OutputSpacing = fixedImage.Spacing;
resample.OutputOrigin = fixedImage.Origin;
resample.DefaultPixelValue = 100;
// Write resampled output
OutputImageType output = OutputImageType.New();
CastFilterType caster = CastFilterType.New(movingImage, output);
caster.SetInput(resample.GetOutput());
caster.Update();
caster.GetOutput(output);
output.Write(args[2]);
// Generate checkerboards before registration
CheckerBoardType checker = CheckerBoardType.New();
checker.SetInput1(fixedImage);
checker.SetInput2(movingImage);
checker.Update();
ImageType checkerOut = ImageType.New();
checker.GetOutput(checkerOut);
caster.SetInput(checkerOut);
caster.Update();
caster.GetOutput(output);
if (args.Length > 3) {
output.Write(args[3]);
}
// Generate checkerboards after registration
checker.SetInput1(fixedImage);
checker.SetInput2(resample.GetOutput());
checker.Update();
checker.GetOutput(checkerOut);
caster.SetInput(checkerOut);
caster.Update();
caster.GetOutput(output);
if (args.Length > 4) {
output.Write(args[4]);
}
}
catch (Exception ex)
{
Console.WriteLine(ex.ToString());
}
}
