SimpleITK  2.0.0rc1.post255
FastMarchingSegmentation/FastMarchingSegmentation.cs
/*=========================================================================
*
* Copyright NumFOCUS
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
// This example is based on ITK's FastMarchingImageFilter.cxx example
//INPUTS: {BrainProtonDensitySlice.png}
// OUTPUTS: {FastMarchingImageFilterOutput5.png}
// ARGUMENTS: 81 114 1.0 -0.5 3.0 100 100
using System;
using SitkImage = itk.simple.Image;
using System.Globalization;
namespace itk.simple.examples
{
public class FastMarchingSegmentation
{
static void Main(string[] args)
{
if (args.Length < 9)
{
Console.WriteLine("Missing Parameters ");
Console.WriteLine("Usage: " + System.AppDomain.CurrentDomain.FriendlyName +
" inputImage outputImage seedX seedY " +
" Sigma SigmoidAlpha SigmoidBeta TimeThreshold");
return;
}
string inputFilename = args[0];
string outputFilename = args[1];
uint[] seedPosition = { Convert.ToUInt32(args[2]), Convert.ToUInt32(args[3]),0 };
double sigma = double.Parse(args[4], CultureInfo.InvariantCulture);
double alpha = double.Parse(args[5], CultureInfo.InvariantCulture); ;
double beta = double.Parse(args[6], CultureInfo.InvariantCulture);
double timeThreshold = double.Parse(args[7], CultureInfo.InvariantCulture);
double stoppingTime = double.Parse(args[8], CultureInfo.InvariantCulture);
// Read input image
SitkImage inputImage = SimpleITK.ReadImage(inputFilename, PixelIDValueEnum.sitkFloat32);
// The input image will be processed with a few iterations of
// feature-preserving diffusion. We create a filter and set the
// appropriate parameters.
CurvatureAnisotropicDiffusionImageFilter smoothing = new CurvatureAnisotropicDiffusionImageFilter();
smoothing.SetTimeStep(0.125);
smoothing.SetNumberOfIterations(5);
smoothing.SetConductanceParameter(9.0);
SitkImage smoothingOutput = smoothing.Execute(inputImage);
SitkImage gradientMagnitudeOutput = SimpleITK.GradientMagnitudeRecursiveGaussian(smoothingOutput, sigma);
SitkImage sigmoidOutput = SimpleITK.Sigmoid(gradientMagnitudeOutput, alpha, beta, 1.0, 0.0);
FastMarchingImageFilter fastMarching = new FastMarchingImageFilter();
//VectorUIntList trialPoints; Add trialPoints into list if using multiple seeds. Here we only use one seedpoint
VectorUInt32 trialPoint = new VectorUInt32(3);
trialPoint.Add(seedPosition[0]);
trialPoint.Add(seedPosition[1]);
trialPoint.Add(seedPosition[2]);
fastMarching.AddTrialPoint(trialPoint);
// Since the front representing the contour will propagate continuously
// over time, it is desirable to stop the process once a certain time has
// been reached. This allows us to save computation time under the
// assumption that the region of interest has already been computed. The
// value for stopping the process is defined with the method
// SetStoppingValue(). In principle, the stopping value should be a
// little bit higher than the threshold value.
fastMarching.SetStoppingValue(stoppingTime);
SitkImage fastmarchingOutput = fastMarching.Execute(sigmoidOutput);
BinaryThresholdImageFilter thresholder = new BinaryThresholdImageFilter();
thresholder.SetLowerThreshold(0.0);
thresholder.SetUpperThreshold(timeThreshold);
thresholder.SetOutsideValue(0);
thresholder.SetInsideValue(255);
SitkImage result = thresholder.Execute(fastmarchingOutput);
SimpleITK.WriteImage(result, outputFilename);
}
}
}
itk::simple::Image
The Image class for SimpleITK.
Definition: sitkImage.h:75
itk::simple::PixelIDValueEnum
PixelIDValueEnum
Enumerated values of pixelIDs.
Definition: sitkPixelIDValues.h:90
itk
itk::simple
Definition: sitkAdditionalProcedures.h:29