mitkManualSegmentationToSurfaceFilter.cpp

Go to the documentation of this file.

/*=========================================================================
 
Program:   Medical Imaging & Interaction Toolkit
Language:  C++
Date:      $Date$
Version:   $Revision$
 
Copyright (c) German Cancer Research Center, Division of Medical and
Biological Informatics. All rights reserved.
See MITKCopyright.txt or https://www.mitk.org/copyright.html for details.
 
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE.  See the above copyright notices for more information.
 
=========================================================================*/

#include <mitkManualSegmentationToSurfaceFilter.h>

#include <vtkSmartPointer.h>

#include "mitkProgressBar.h"

mitk::ManualSegmentationToSurfaceFilter::ManualSegmentationToSurfaceFilter() 
{
  m_MedianFilter3D = false;
  m_MedianKernelSizeX = 3;
  m_MedianKernelSizeY = 3;
  m_MedianKernelSizeZ = 3;
  m_UseGaussianImageSmooth = false;
  m_GaussianStandardDeviation = 1.5;
  m_Interpolation = false;
  m_InterpolationX = 1.0f;
  m_InterpolationY = 1.0f;
  m_InterpolationZ = 1.0f;
};


mitk::ManualSegmentationToSurfaceFilter::~ManualSegmentationToSurfaceFilter(){};

void mitk::ManualSegmentationToSurfaceFilter::GenerateData() 
{
  mitk::Surface *surface = this->GetOutput();
  mitk::Image * image    =  (mitk::Image*)GetInput();
  mitk::Image::RegionType outputRegion = image->GetRequestedRegion();

  int tstart=outputRegion.GetIndex(3);
  int tmax=tstart+outputRegion.GetSize(3); //GetSize()==1 - will aber 0 haben, wenn nicht zeitaufgeloest

  ScalarType thresholdExpanded = this->m_Threshold;

  if ((tmax-tstart) > 0)
  {
    ProgressBar::GetInstance()->AddStepsToDo( 7 * (tmax - tstart)  );
  }

  for( int t=tstart; t<tmax; t++ )
  {

    vtkSmartPointer<vtkImageData> vtkimage = image->GetVtkImageData(t);

    // Median -->smooth 3D 
    MITK_INFO << (m_MedianFilter3D ? "Applying median..." : "No median filtering");
    if(m_MedianFilter3D)
    {
      vtkImageMedian3D *median = vtkImageMedian3D::New();
      median->SetInput(vtkimage); //RC++ (VTK < 5.0)
      median->SetKernelSize(m_MedianKernelSizeX,m_MedianKernelSizeY,m_MedianKernelSizeZ);//Std: 3x3x3
      median->ReleaseDataFlagOn();
      median->UpdateInformation();
      median->Update();
      vtkimage = median->GetOutput(); //->Out
      median->Delete();
    }
    ProgressBar::GetInstance()->Progress();

    //Interpolate image spacing 
    MITK_INFO << (m_Interpolation ? "Resampling..." : "No resampling");
    if(m_Interpolation)
    {
      vtkImageResample * imageresample = vtkImageResample::New();
      imageresample->SetInput(vtkimage);

      //Set Spacing Manual to 1mm in each direction (Original spacing is lost during image processing)      
      imageresample->SetAxisOutputSpacing(0, m_InterpolationX);
      imageresample->SetAxisOutputSpacing(1, m_InterpolationY);
      imageresample->SetAxisOutputSpacing(2, m_InterpolationZ);
      imageresample->UpdateInformation();
      imageresample->Update();
      vtkimage=imageresample->GetOutput();//->Output
      imageresample->Delete();
    }
    ProgressBar::GetInstance()->Progress();

    MITK_INFO << (m_UseGaussianImageSmooth ? "Applying gaussian smoothing..." : "No gaussian smoothing");
    if(m_UseGaussianImageSmooth)//gauss
    {
      vtkImageThreshold* vtkimagethreshold = vtkImageThreshold::New();
      vtkimagethreshold->SetInput(vtkimage);
      vtkimagethreshold->SetInValue( 100 );
      vtkimagethreshold->SetOutValue( 0 );
      vtkimagethreshold->ThresholdByUpper( this->m_Threshold ); 
      thresholdExpanded = 49;

      vtkimagethreshold->SetOutputScalarTypeToUnsignedChar();
      vtkimagethreshold->ReleaseDataFlagOn();

      vtkImageGaussianSmooth *gaussian = vtkImageGaussianSmooth::New();
      gaussian->SetInput(vtkimagethreshold->GetOutput()); 
      gaussian->SetDimensionality(3);
      gaussian->SetRadiusFactor(0.49);
      gaussian->SetStandardDeviation( m_GaussianStandardDeviation );
      gaussian->ReleaseDataFlagOn();
      gaussian->UpdateInformation();
      gaussian->Update();
      vtkimage = gaussian->GetOutput(); //->Out
      gaussian->Delete();
      vtkimagethreshold->Delete();
    }
    ProgressBar::GetInstance()->Progress();

    // Create sureface for t-Slice
    CreateSurface(t, vtkimage, surface, thresholdExpanded);
    ProgressBar::GetInstance()->Progress();
  }
};


void mitk::ManualSegmentationToSurfaceFilter::SetMedianKernelSize(int x, int y, int z)
{
  m_MedianKernelSizeX = x;
  m_MedianKernelSizeY = y;
  m_MedianKernelSizeZ = z;
 }

void mitk::ManualSegmentationToSurfaceFilter::SetInterpolation(vtkDouble x, vtkDouble y, vtkDouble z)
{
  m_InterpolationX = x;
  m_InterpolationY = y;
  m_InterpolationZ = z;
}