import org.itk.itkanisotropicsmoothing.itkCurvatureAnisotropicDiffusionImageFilterIF2IF2;

import org.itk.itkcommon.itkImageUC2;

import org.itk.itkcommon.itkIndex2;

import org.itk.itkfastmarching.itkFastMarchingImageFilterIF2IF2;

import org.itk.itkfastmarching.itkLevelSetNodeF2;

import org.itk.itkfastmarching.itkVectorContainerUILSNF2;

import org.itk.itkimagefilterbase.itkCastImageFilterIF2IUC2;

import org.itk.itkimagefilterbase.itkCastImageFilterIUC2IF2;

import org.itk.itkimagegradient.itkGradientMagnitudeImageFilterIF2IF2;

import org.itk.itkimageintensity.itkSigmoidImageFilterIF2IF2;

import org.itk.itkioimagebase.itkImageFileReaderIUC2;

import org.itk.itkioimagebase.itkImageFileWriterIUC2;

public class itkImageIO {

// use .png images for this example

// more information: 

    // www.itk.org/Doxygen/html/Examples_2Segmentation_2GeodesicActiveContourImageFilter_8cxx-example.html

public static void main( String argv[] )

 {

String inFile = argv[0];

String outFile = argv[1];

   itkImageFileReaderIUC2 reader = new itkImageFileReaderIUC2();

   itkImageFileWriterIUC2 writer = new itkImageFileWriterIUC2();

   reader.SetFileName( inFile );

   reader.Update();

   itkImageUC2 img = reader.GetOutput();

   int sx = (int) img.GetLargestPossibleRegion().GetSize().GetElement(0);

   int sy = (int) img.GetLargestPossibleRegion().GetSize().GetElement(1);

   System.out.println("Dim x: " + Integer.valueOf(sx) + "\tDim y: " + Integer.valueOf(sy));

    // cast unsigned char image to float for active contour level set segmentation

   System.out.println("Casting to float.");

   itkCastImageFilterIUC2IF2 castFloat = new itkCastImageFilterIUC2IF2();

   castFloat.SetInput(reader.GetOutput());

   castFloat.Update();

   // instantiate objects

   //smoothing

   System.out.println("Smoothing image.");

   itkCurvatureAnisotropicDiffusionImageFilterIF2IF2 uniso = new itkCurvatureAnisotropicDiffusionImageFilterIF2IF2();

   uniso.SetInput(castFloat.GetOutput());

   uniso.SetTimeStep(0.125);

   uniso.SetNumberOfIterations(5);

   uniso.SetConductanceParameter(9);

   uniso.Update();

   //gradient and sigmoid

   System.out.println("Calculating gradient magnitude.");

   itkGradientMagnitudeImageFilterIF2IF2 gradMag = new itkGradientMagnitudeImageFilterIF2IF2();

   gradMag.SetInput(uniso.GetOutput());

   gradMag.Update();

   System.out.println("Applying sigmoid filter.");

   itkSigmoidImageFilterIF2IF2 sigmoid = new itkSigmoidImageFilterIF2IF2();

   sigmoid.SetInput(gradMag.GetOutput());

   sigmoid.SetAlpha(-0.3);

   sigmoid.SetBeta(2);

   sigmoid.SetOutputMinimum(0.0f);

   sigmoid.SetOutputMaximum(1.0f);

   sigmoid.Update();

   //fast marching as level set initialization for active contours level set filter

   System.out.println("Starting fast marching image filter.");

   itkFastMarchingImageFilterIF2IF2 fast = new itkFastMarchingImageFilterIF2IF2();

   fast.SetInput(sigmoid.GetOutput());

   //56 92 5 1 -0,3 2,0 10

   itkIndex2 idx = new itkIndex2();

   itkLevelSetNodeF2 node = new itkLevelSetNodeF2();

   idx.SetElement(0, 56);

   idx.SetElement(1, 92);

   node.SetIndex(idx);

   node.SetValue(-5);

   itkVectorContainerUILSNF2 container = new itkVectorContainerUILSNF2();

   container.Initialize();

   container.InsertElement(0, node);    

   fast.SetTrialPoints(container);

   fast.SetSpeedConstant(1.0f);

   fast.SetOutputSize(castFloat.GetOutput().GetLargestPossibleRegion().GetSize());

   fast.Update();

   //cast back to unsigned char

   itkCastImageFilterIF2IUC2 castUC = new itkCastImageFilterIF2IUC2();

   castUC.SetInput(fast.GetOutput());

   castUC.Update();

   //write to output

   writer.SetFileName( outFile );

   writer.SetInput( castUC.GetOutput() );

   writer.Update();

 }

}