mitkExtractSliceFilterTest.cpp

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/*============================================================================

The Medical Imaging Interaction Toolkit (MITK)

Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.

Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.

============================================================================*/

#include <itkImage.h>
#include <itkImageRegionIterator.h>
#include <mitkExtractSliceFilter.h>
#include <mitkIOUtil.h>
#include <mitkITKImageImport.h>
#include <mitkImageAccessByItk.h>
#include <mitkImageCast.h>
#include <mitkImagePixelReadAccessor.h>
#include <mitkInteractionConst.h>
#include <mitkNumericTypes.h>
#include <mitkRotationOperation.h>
#include <mitkStandardFileLocations.h>
#include <mitkTestingMacros.h>

#include <cstdlib>
#include <ctime>
#include <cmath>

#include <mitkGeometry3D.h>

#include <vtkActor.h>
#include <vtkImageActor.h>
#include <vtkImageData.h>
#include <vtkImageMapToColors.h>
#include <vtkImageMapper.h>
#include <vtkImageReslice.h>
#include <vtkInteractorStyleImage.h>
#include <vtkLookupTable.h>
#include <vtkPlaneSource.h>
#include <vtkPolyDataMapper.h>
#include <vtkRenderWindow.h>
#include <vtkRenderWindowInteractor.h>
#include <vtkRenderer.h>
#include <vtkSmartPointer.h>
#include <vtkTexture.h>

// use this to create the test volume on the fly
#define CREATE_VOLUME

// use this to save the created volume
//#define SAVE_VOLUME

// use this to calculate the error from the sphere mathematical model to our pixel based one
//#define CALC_TESTFAILURE_DEVIATION

// use this to render an oblique slice through a specified image
//#define SHOW_SLICE_IN_RENDER_WINDOW

// use this to have infos printed in mbilog
//#define EXTRACTOR_DEBUG

/*these are the deviations calculated by the function CalcTestFailureDeviation (see for details)*/
#define Testfailure_Deviation_Mean_128 0.853842

#define Testfailure_Deviation_Volume_128 0.145184
#define Testfailure_Deviation_Diameter_128 1.5625

#define Testfailure_Deviation_Mean_256 0.397693

#define Testfailure_Deviation_Volume_256 0.0141357
#define Testfailure_Deviation_Diameter_256 0.78125

#define Testfailure_Deviation_Mean_512 0.205277

#define Testfailure_Deviation_Volume_512 0.01993
#define Testfailure_Deviation_Diameter_512 0.390625

class mitkExtractSliceFilterTestClass
{
public:
  static void TestSlice(mitk::PlaneGeometry *planeGeometry, std::string testname)
  {
    TestPlane = planeGeometry;
    TestName = testname;

    mitk::ScalarType centerCoordValue = TestvolumeSize / 2.0;
    mitk::ScalarType center[3] = {centerCoordValue, centerCoordValue, centerCoordValue};
    mitk::Point3D centerIndex(center);

    double radius = TestvolumeSize / 4.0;
    if (TestPlane->Distance(centerIndex) >= radius)
      return; // outside sphere

    // feed ExtractSliceFilter
    mitk::ExtractSliceFilter::Pointer slicer = mitk::ExtractSliceFilter::New();

    slicer->SetInput(TestVolume);
    slicer->SetWorldGeometry(TestPlane);
    slicer->Update();

    MITK_TEST_CONDITION_REQUIRED(slicer->GetOutput() != nullptr, "Extractor returned a slice");

    mitk::Image::Pointer reslicedImage = slicer->GetOutput();

    AccessFixedDimensionByItk(reslicedImage, TestSphereRadiusByItk, 2);
    AccessFixedDimensionByItk(reslicedImage, TestSphereAreaByItk, 2);

    /*
    double devArea, devDiameter;
    if(TestvolumeSize == 128.0){ devArea = Testfailure_Deviation_Volume_128; devDiameter =
    Testfailure_Deviation_Diameter_128; }
    else if(TestvolumeSize == 256.0){devArea = Testfailure_Deviation_Volume_256; devDiameter =
    Testfailure_Deviation_Diameter_256;}
    else if (TestvolumeSize == 512.0){devArea = Testfailure_Deviation_Volume_512; devDiameter =
    Testfailure_Deviation_Diameter_512;}
    else{devArea = Testfailure_Deviation_Volume_128; devDiameter = Testfailure_Deviation_Diameter_128;}
    */

    std::string areatestName = TestName.append(" area");
    std::string diametertestName = TestName.append(" testing diameter");

    // TODO think about the deviation, 1% makes no sense at all
    MITK_TEST_CONDITION(std::abs(100 - testResults.percentageAreaCalcToPixel) < 1, areatestName);
    MITK_TEST_CONDITION(std::abs(100 - testResults.percentageRadiusToPixel) < 1, diametertestName);

#ifdef EXTRACTOR_DEBUG
    MITK_INFO << TestName << " >>> "
              << "planeDistanceToSphereCenter: " << testResults.planeDistanceToSphereCenter;
    MITK_INFO << "area in pixels: " << testResults.areaInPixel << " <-> area in mm: " << testResults.areaCalculated
              << " = " << testResults.percentageAreaCalcToPixel << "%";

    MITK_INFO << "calculated diameter: " << testResults.diameterCalculated
              << " <-> diameter in mm: " << testResults.diameterInMM
              << " <-> diameter in pixel: " << testResults.diameterInPixel << " = "
              << testResults.percentageRadiusToPixel << "%";
#endif
  }

  /*
   * get the radius of the slice of a sphere based on pixel distance from edge to edge of the circle.
   */
  template <typename TPixel, unsigned int VImageDimension>
  static void TestSphereRadiusByItk(itk::Image<TPixel, VImageDimension> *inputImage)
  {
    typedef itk::Image<TPixel, VImageDimension> InputImageType;

    // set the index to the middle of the image's edge at x and y axis
    typename InputImageType::IndexType currentIndexX;
    currentIndexX[0] = (int)(TestvolumeSize / 2.0);
    currentIndexX[1] = 0;

    typename InputImageType::IndexType currentIndexY;
    currentIndexY[0] = 0;
    currentIndexY[1] = (int)(TestvolumeSize / 2.0);

    // remember the last pixel value
    double lastValueX = inputImage->GetPixel(currentIndexX);
    double lastValueY = inputImage->GetPixel(currentIndexY);

    // storage for the index marks
    std::vector<typename InputImageType::IndexType> indicesX;
    std::vector<typename InputImageType::IndexType> indicesY;

    /*Get four indices on the edge of the circle*/
    while (currentIndexX[1] < TestvolumeSize && currentIndexX[0] < TestvolumeSize)
    {
      // move x direction
      currentIndexX[1] += 1;

      // move y direction
      currentIndexY[0] += 1;

      if (inputImage->GetPixel(currentIndexX) > lastValueX)
      {
        // mark the current index
        typename InputImageType::IndexType markIndex;
        markIndex[0] = currentIndexX[0];
        markIndex[1] = currentIndexX[1];

        indicesX.push_back(markIndex);
      }
      else if (inputImage->GetPixel(currentIndexX) < lastValueX)
      {
        // mark the current index
        typename InputImageType::IndexType markIndex;
        markIndex[0] = currentIndexX[0];
        markIndex[1] = currentIndexX[1] - 1; // value inside the sphere

        indicesX.push_back(markIndex);
      }

      if (inputImage->GetPixel(currentIndexY) > lastValueY)
      {
        // mark the current index
        typename InputImageType::IndexType markIndex;
        markIndex[0] = currentIndexY[0];
        markIndex[1] = currentIndexY[1];

        indicesY.push_back(markIndex);
      }
      else if (inputImage->GetPixel(currentIndexY) < lastValueY)
      {
        // mark the current index
        typename InputImageType::IndexType markIndex;
        markIndex[0] = currentIndexY[0];
        markIndex[1] = currentIndexY[1] - 1; // value inside the sphere

        indicesY.push_back(markIndex);
      }

      // found both marks?
      if (indicesX.size() == 2 && indicesY.size() == 2)
        break;

      // the new 'last' values
      lastValueX = inputImage->GetPixel(currentIndexX);
      lastValueY = inputImage->GetPixel(currentIndexY);
    }

    /*
     *If we are here we found the four marks on the edge of the circle.
     *For the case our plane is rotated and shifted, we have to calculate the center of the circle,
     *else the center is the intersection of both straight lines between the marks.
     *When we have the center, the diameter of the circle will be checked to the reference value(math!).
     */

    // each distance from the first mark of each direction to the center of the straight line between the marks
    double distanceToCenterX = std::abs(indicesX[0][1] - indicesX[1][1]) / 2.0;
    // double distanceToCenterY = std::abs(indicesY[0][0] - indicesY[1][0]) / 2.0;

    // the center of the straight lines
    typename InputImageType::IndexType centerX;
    // typename InputImageType::IndexType centerY;

    centerX[0] = indicesX[0][0];
    centerX[1] = indicesX[0][1] + distanceToCenterX;
    // TODO think about implicit cast to int. this is not the real center of the image, which could be between two
    // pixels

    // centerY[0] = indicesY[0][0] + distanceToCenterY;
    // centerY[1] = inidcesY[0][1];

    typename InputImageType::IndexType currentIndex(centerX);
    lastValueX = inputImage->GetPixel(currentIndex);

    long sumpixels = 0;

    std::vector<typename InputImageType::IndexType> diameterIndices;

    // move up
    while (currentIndex[1] < TestvolumeSize)
    {
      currentIndex[1] += 1;

      if (inputImage->GetPixel(currentIndex) != lastValueX)
      {
        typename InputImageType::IndexType markIndex;
        markIndex[0] = currentIndex[0];
        markIndex[1] = currentIndex[1] - 1;

        diameterIndices.push_back(markIndex);
        break;
      }

      sumpixels++;
      lastValueX = inputImage->GetPixel(currentIndex);
    }

    currentIndex[1] -= sumpixels; // move back to center to go in the other direction
    lastValueX = inputImage->GetPixel(currentIndex);

    // move down
    while (currentIndex[1] >= 0)
    {
      currentIndex[1] -= 1;

      if (inputImage->GetPixel(currentIndex) != lastValueX)
      {
        typename InputImageType::IndexType markIndex;
        markIndex[0] = currentIndex[0];
        markIndex[1] = currentIndex[1]; // outside sphere because we want to calculate the distance from edge to edge

        diameterIndices.push_back(markIndex);
        break;
      }

      sumpixels++;
      lastValueX = inputImage->GetPixel(currentIndex);
    }

    /*
    *Now sumpixels should be the apromximate diameter of the circle. This is checked with the calculated diameter from
    *the plane transformation(math).
    */
    mitk::Point3D volumeCenter;
    volumeCenter[0] = volumeCenter[1] = volumeCenter[2] = TestvolumeSize / 2.0;

    double planeDistanceToSphereCenter = TestPlane->Distance(volumeCenter);

    double sphereRadius = TestvolumeSize / 4.0;

    // calculate the radius of the circle cut from the sphere by the plane
    double diameter = 2.0 * std::sqrt(std::pow(sphereRadius, 2) - std::pow(planeDistanceToSphereCenter, 2));

    double percentageRadiusToPixel = 100 / diameter * sumpixels;

    /*
     *calculate the radius in mm by the both marks of the center line by using the world coordinates
     */
    // get the points as 3D coordinates
    mitk::Vector3D diameterPointRight, diameterPointLeft;

    diameterPointRight[2] = diameterPointLeft[2] = 0.0;

    diameterPointLeft[0] = diameterIndices[0][0];
    diameterPointLeft[1] = diameterIndices[0][1];

    diameterPointRight[0] = diameterIndices[1][0];
    diameterPointRight[1] = diameterIndices[1][1];

    // transform to worldcoordinates
    TestVolume->GetGeometry()->IndexToWorld(diameterPointLeft, diameterPointLeft);
    TestVolume->GetGeometry()->IndexToWorld(diameterPointRight, diameterPointRight);

    // euklidian distance
    double diameterInMM = ((diameterPointLeft * -1.0) + diameterPointRight).GetNorm();

    testResults.diameterInMM = diameterInMM;
    testResults.diameterCalculated = diameter;
    testResults.diameterInPixel = sumpixels;
    testResults.percentageRadiusToPixel = percentageRadiusToPixel;
    testResults.planeDistanceToSphereCenter = planeDistanceToSphereCenter;
  }

  /*brute force the area pixel by pixel*/
  template <typename TPixel, unsigned int VImageDimension>
  static void TestSphereAreaByItk(itk::Image<TPixel, VImageDimension> *inputImage)
  {
    typedef itk::Image<TPixel, VImageDimension> InputImageType;
    typedef itk::ImageRegionConstIterator<InputImageType> ImageIterator;

    ImageIterator imageIterator(inputImage, inputImage->GetLargestPossibleRegion());
    imageIterator.GoToBegin();

    int sumPixelsInArea = 0;

    while (!imageIterator.IsAtEnd())
    {
      if (inputImage->GetPixel(imageIterator.GetIndex()) == pixelValueSet)
        sumPixelsInArea++;
      ++imageIterator;
    }

    mitk::Point3D volumeCenter;
    volumeCenter[0] = volumeCenter[1] = volumeCenter[2] = TestvolumeSize / 2.0;

    double planeDistanceToSphereCenter = TestPlane->Distance(volumeCenter);

    double sphereRadius = TestvolumeSize / 4.0;

    // calculate the radius of the circle cut from the sphere by the plane
    double radius = std::sqrt(std::pow(sphereRadius, 2) - std::pow(planeDistanceToSphereCenter, 2));

    double areaInMM = 3.14159265358979 * std::pow(radius, 2);

    testResults.areaCalculated = areaInMM;
    testResults.areaInPixel = sumPixelsInArea;
    testResults.percentageAreaCalcToPixel = 100 / areaInMM * sumPixelsInArea;
  }

  /*
   * random a voxel. define plane through this voxel. reslice at the plane. compare the pixel vaues of the voxel
   * in the volume with the pixel value in the resliced image.
   * there are some indice shifting problems which causes the test to fail for oblique planes. seems like the chosen
   * worldcoordinate is not corrresponding to the index in the 2D image. and so the pixel values are not the same as
   * expected.
   */
  static void PixelvalueBasedTest()
  {
    /* setup itk image */
    typedef itk::Image<unsigned short, 3> ImageType;

    typedef itk::ImageRegionConstIterator<ImageType> ImageIterator;

    ImageType::Pointer image = ImageType::New();

    ImageType::IndexType start;
    start[0] = start[1] = start[2] = 0;

    ImageType::SizeType size;
    size[0] = size[1] = size[2] = 32;

    ImageType::RegionType imgRegion;
    imgRegion.SetSize(size);
    imgRegion.SetIndex(start);

    image->SetRegions(imgRegion);
    image->SetSpacing(1.0);
    image->Allocate();

    ImageIterator imageIterator(image, image->GetLargestPossibleRegion());
    imageIterator.GoToBegin();

    unsigned short pixelValue = 0;

    // fill the image with distinct values
    while (!imageIterator.IsAtEnd())
    {
      image->SetPixel(imageIterator.GetIndex(), pixelValue);
      ++imageIterator;
      ++pixelValue;
    }
    /* end setup itk image */

    mitk::Image::Pointer imageInMitk;
    CastToMitkImage(image, imageInMitk);

    /*mitk::ImageWriter::Pointer writer = mitk::ImageWriter::New();
    writer->SetInput(imageInMitk);
    std::string file = "C:\\Users\\schroedt\\Desktop\\cube.nrrd";
    writer->SetFileName(file);
    writer->Update();*/

    PixelvalueBasedTestByPlane(imageInMitk, mitk::PlaneGeometry::Frontal);
    PixelvalueBasedTestByPlane(imageInMitk, mitk::PlaneGeometry::Sagittal);
    PixelvalueBasedTestByPlane(imageInMitk, mitk::PlaneGeometry::Axial);
  }

  static void PixelvalueBasedTestByPlane(mitk::Image *imageInMitk, mitk::PlaneGeometry::PlaneOrientation orientation)
  {
    typedef itk::Image<unsigned short, 3> ImageType;

    // set the seed of the rand function
    srand((unsigned)time(nullptr));

    /* setup a random orthogonal plane */
    int sliceindex = 17; // rand() % 32;
    bool isFrontside = true;
    bool isRotated = false;

    if (orientation == mitk::PlaneGeometry::Axial)
    {
      /*isFrontside = false;
      isRotated = true;*/
    }

    mitk::PlaneGeometry::Pointer plane = mitk::PlaneGeometry::New();

    plane->InitializeStandardPlane(imageInMitk->GetGeometry(), orientation, sliceindex, isFrontside, isRotated);

    mitk::Point3D origin = plane->GetOrigin();
    mitk::Vector3D normal;
    normal = plane->GetNormal();

    normal.Normalize();

    origin += normal * 0.5; // pixelspacing is 1, so half the spacing is 0.5

    plane->SetOrigin(origin);

    // we dont need this any more, because we are only testing orthogonal planes
    /*mitk::Vector3D rotationVector;
    rotationVector[0] = randFloat();
    rotationVector[1] = randFloat();
    rotationVector[2] = randFloat();


    float degree = randFloat() * 180.0;

    mitk::RotationOperation* op = new mitk::RotationOperation(mitk::OpROTATE, plane->GetCenter(), rotationVector,
    degree);
    plane->ExecuteOperation(op);
    delete op;*/

    /* end setup plane */

    /* define a point in the 3D volume.
     * add the two axis vectors of the plane (each multiplied with a
     * random number) to the origin. now the two random numbers
     * become our index coordinates in the 2D image, because the
     * length of the axis vectors is 1.
     */
    mitk::Point3D planeOrigin = plane->GetOrigin();
    mitk::Vector3D axis0, axis1;
    axis0 = plane->GetAxisVector(0);
    axis1 = plane->GetAxisVector(1);
    axis0.Normalize();
    axis1.Normalize();

    unsigned char n1 = 7;  // rand() % 32;
    unsigned char n2 = 13; // rand() % 32;

    mitk::Point3D testPoint3DInWorld;
    testPoint3DInWorld = planeOrigin + (axis0 * n1) + (axis1 * n2);

    // get the index of the point in the 3D volume
    ImageType::IndexType testPoint3DInIndex;
    imageInMitk->GetGeometry()->WorldToIndex(testPoint3DInWorld, testPoint3DInIndex);

    itk::Index<3> testPoint2DInIndex;

    /* end define a point in the 3D volume.*/

    // do reslicing at the plane
    mitk::ExtractSliceFilter::Pointer slicer = mitk::ExtractSliceFilter::New();
    slicer->SetInput(imageInMitk);
    slicer->SetWorldGeometry(plane);

    slicer->Update();

    mitk::Image::Pointer slice = slicer->GetOutput();

    // Get TestPoiont3D as Index in Slice
    slice->GetGeometry()->WorldToIndex(testPoint3DInWorld, testPoint2DInIndex);

    mitk::Point3D p, sliceIndexToWorld, imageIndexToWorld;
    p[0] = testPoint2DInIndex[0];
    p[1] = testPoint2DInIndex[1];
    p[2] = testPoint2DInIndex[2];
    slice->GetGeometry()->IndexToWorld(p, sliceIndexToWorld);

    p[0] = testPoint3DInIndex[0];
    p[1] = testPoint3DInIndex[1];
    p[2] = testPoint3DInIndex[2];
    imageInMitk->GetGeometry()->IndexToWorld(p, imageIndexToWorld);

    itk::Index<2> testPoint2DIn2DIndex;
    testPoint2DIn2DIndex[0] = testPoint2DInIndex[0];
    testPoint2DIn2DIndex[1] = testPoint2DInIndex[1];

    typedef mitk::ImagePixelReadAccessor<unsigned short, 3> VolumeReadAccessorType;
    typedef mitk::ImagePixelReadAccessor<unsigned short, 2> SliceReadAccessorType;
    VolumeReadAccessorType VolumeReadAccessor(imageInMitk);
    SliceReadAccessorType SliceReadAccessor(slice);

    // compare the pixelvalues of the defined point in the 3D volume with the value of the resliced image
    unsigned short valueAt3DVolume = VolumeReadAccessor.GetPixelByIndex(testPoint3DInIndex);
    unsigned short valueAtSlice = SliceReadAccessor.GetPixelByIndex(testPoint2DIn2DIndex);

    // valueAt3DVolume == valueAtSlice is not always working. because of rounding errors
    // indices are shifted
    MITK_TEST_CONDITION(valueAt3DVolume == valueAtSlice, "comparing pixelvalues for orthogonal plane");

    vtkSmartPointer<vtkImageData> imageInVtk = imageInMitk->GetVtkImageData();
    vtkSmartPointer<vtkImageData> sliceInVtk = slice->GetVtkImageData();

    double PixelvalueByMitkOutput = sliceInVtk->GetScalarComponentAsDouble(n1, n2, 0, 0);
    // double valueVTKinImage = imageInVtk->GetScalarComponentAsDouble(testPoint3DInIndex[0], testPoint3DInIndex[1],
    // testPoint3DInIndex[2], 0);

    /* Test that everything is working equally if vtkoutput is used instead of the default output
     * from mitk ImageToImageFilter
     */
    mitk::ExtractSliceFilter::Pointer slicerWithVtkOutput = mitk::ExtractSliceFilter::New();
    slicerWithVtkOutput->SetInput(imageInMitk);
    slicerWithVtkOutput->SetWorldGeometry(plane);
    slicerWithVtkOutput->SetVtkOutputRequest(true);

    slicerWithVtkOutput->Update();
    vtkSmartPointer<vtkImageData> vtkImageByVtkOutput = slicerWithVtkOutput->GetVtkOutput();
    double PixelvalueByVtkOutput = vtkImageByVtkOutput->GetScalarComponentAsDouble(n1, n2, 0, 0);

    MITK_TEST_CONDITION(PixelvalueByMitkOutput == PixelvalueByVtkOutput,
                        "testing convertion of image output vtk->mitk by reslicer");

/*================ mbilog outputs ===========================*/
#ifdef EXTRACTOR_DEBUG
    MITK_INFO << "\n"
              << "TESTINFO index: " << sliceindex << " orientation: " << orientation << " frontside: " << isFrontside
              << " rotated: " << isRotated;
    MITK_INFO << "\n"
              << "slice index to world: " << sliceIndexToWorld;
    MITK_INFO << "\n"
              << "image index to world: " << imageIndexToWorld;

    MITK_INFO << "\n"
              << "vtk: slice: " << PixelvalueByMitkOutput << ", image: " << valueVTKinImage;

    MITK_INFO << "\n"
              << "testPoint3D InWorld" << testPoint3DInWorld << " is " << testPoint2DInIndex << " in 2D";
    MITK_INFO << "\n"
              << "randoms: " << ((int)n1) << ", " << ((int)n2);
    MITK_INFO << "\n"
              << "point is inside plane: " << plane->IsInside(testPoint3DInWorld)
              << " and volume: " << imageInMitk->GetGeometry()->IsInside(testPoint3DInWorld);

    MITK_INFO << "\n"
              << "volume idx: " << testPoint3DInIndex << " = " << valueAt3DVolume;
    MITK_INFO << "\n"
              << "volume world: " << testPoint3DInWorld << " = " << valueAt3DVolumeByWorld;
    MITK_INFO << "\n"
              << "slice idx: " << testPoint2DInIndex << " = " << valueAtSlice;

    itk::Index<3> curr;
    curr[0] = curr[1] = curr[2] = 0;

    for (int i = 0; i < 32; ++i)
    {
      for (int j = 0; j < 32; ++j)
      {
        ++curr[1];
        if (SliceReadAccessor.GetPixelByIndex(curr) == valueAt3DVolume)
        {
          MITK_INFO << "\n" << valueAt3DVolume << " MATCHED mitk " << curr;
        }
      }
      curr[1] = 0;
      ++curr[0];
    }

    typedef itk::Image<unsigned short, 2> Image2DType;

    Image2DType::Pointer img = Image2DType::New();
    CastToItkImage(slice, img);
    typedef itk::ImageRegionConstIterator<Image2DType> Iterator2D;

    Iterator2D iter(img, img->GetLargestPossibleRegion());
    iter.GoToBegin();
    while (!iter.IsAtEnd())
    {
      if (img->GetPixel(iter.GetIndex()) == valueAt3DVolume)
        MITK_INFO << "\n" << valueAt3DVolume << " MATCHED itk " << iter.GetIndex();

      ++iter;
    }
#endif // EXTRACTOR_DEBUG
  }

  /* random a float value */
  static float randFloat()
  {
    return (((float)rand() + 1.0) / ((float)RAND_MAX + 1.0)) +
           (((float)rand() + 1.0) / ((float)RAND_MAX + 1.0)) / ((float)RAND_MAX + 1.0);
  }

  /* create a sphere with the size of the given testVolumeSize*/
  static void InitializeTestVolume()
  {
#ifdef CREATE_VOLUME

    // do sphere creation
    ItkVolumeGeneration();

#ifdef SAVE_VOLUME
    // save in file
    mitk::ImageWriter::Pointer writer = mitk::ImageWriter::New();
    writer->SetInput(TestVolume);

    std::string file;

    std::ostringstream filename;
    filename << "C:\\home\\schroedt\\MITK\\Modules\\ImageExtraction\\Testing\\Data\\sphere_";
    filename << TestvolumeSize;
    filename << ".nrrd";

    file = filename.str();

    writer->SetFileName(file);
    writer->Update();
#endif // SAVE_VOLUME

#endif

#ifndef CREATE_VOLUME // read from file

    mitk::StandardFileLocations::Pointer locator = mitk::StandardFileLocations::GetInstance();

    std::string filename = locator->FindFile("sphere_512.nrrd.mhd", "Modules/ImageExtraction/Testing/Data");

    TestVolume = mitk::IOUtil::Load<mitk::Image>(filename);

#endif

#ifdef CALC_TESTFAILURE_DEVIATION
    // get the TestFailureDeviation in %
    AccessFixedDimensionByItk(TestVolume, CalcTestFailureDeviation, 3);
#endif
  }

  // the test result of the sphere reslice
  struct SliceProperties
  {
    double planeDistanceToSphereCenter;
    double diameterInMM;
    double diameterInPixel;
    double diameterCalculated;
    double percentageRadiusToPixel;
    double areaCalculated;
    double areaInPixel;
    double percentageAreaCalcToPixel;
  };

  static mitk::Image::Pointer TestVolume;
  static double TestvolumeSize;
  static mitk::PlaneGeometry::Pointer TestPlane;
  static std::string TestName;
  static unsigned char pixelValueSet;
  static SliceProperties testResults;
  static double TestFailureDeviation;

private:
  /*
   * Generate a sphere with a radius of TestvolumeSize / 4.0
   */
  static void ItkVolumeGeneration()
  {
    typedef itk::Image<unsigned char, 3> TestVolumeType;

    typedef itk::ImageRegionConstIterator<TestVolumeType> ImageIterator;

    TestVolumeType::Pointer sphereImage = TestVolumeType::New();

    TestVolumeType::IndexType start;
    start[0] = start[1] = start[2] = 0;

    TestVolumeType::SizeType size;
    size[0] = size[1] = size[2] = TestvolumeSize;

    TestVolumeType::RegionType imgRegion;
    imgRegion.SetSize(size);
    imgRegion.SetIndex(start);

    sphereImage->SetRegions(imgRegion);
    sphereImage->SetSpacing(1.0);
    sphereImage->Allocate();

    sphereImage->FillBuffer(0);

    mitk::Vector3D center;
    center[0] = center[1] = center[2] = TestvolumeSize / 2.0;

    double radius = TestvolumeSize / 4.0;

    double pixelValue = pixelValueSet;

    ImageIterator imageIterator(sphereImage, sphereImage->GetLargestPossibleRegion());
    imageIterator.GoToBegin();

    mitk::Vector3D currentVoxelInIndex;

    while (!imageIterator.IsAtEnd())
    {
      currentVoxelInIndex[0] = imageIterator.GetIndex()[0];
      currentVoxelInIndex[1] = imageIterator.GetIndex()[1];
      currentVoxelInIndex[2] = imageIterator.GetIndex()[2];

      double distanceToCenter = (center + (currentVoxelInIndex * -1.0)).GetNorm();

      // if distance to center is smaller then the radius of the sphere
      if (distanceToCenter < radius)
      {
        sphereImage->SetPixel(imageIterator.GetIndex(), pixelValue);
      }

      ++imageIterator;
    }

    CastToMitkImage(sphereImage, TestVolume);
  }

  /* calculate the devation of the voxel object to the mathematical sphere object.
   * this is use to make a statement about the accuracy of the resliced image, eg. the circle's diameter or area.
   */
  template <typename TPixel, unsigned int VImageDimension>
  static void CalcTestFailureDeviation(itk::Image<TPixel, VImageDimension> *inputImage)
  {
    typedef itk::Image<TPixel, VImageDimension> InputImageType;
    typedef itk::ImageRegionConstIterator<InputImageType> ImageIterator;

    ImageIterator iterator(inputImage, inputImage->GetLargestPossibleRegion());
    iterator.GoToBegin();

    int volumeInPixel = 0;

    while (!iterator.IsAtEnd())
    {
      if (inputImage->GetPixel(iterator.GetIndex()) == pixelValueSet)
        volumeInPixel++;
      ++iterator;
    }

    double diameter = TestvolumeSize / 2.0;
    double volumeCalculated = (1.0 / 6.0) * 3.14159265358979 * std::pow(diameter, 3);

    double volumeDeviation = std::abs(100 - (100 / volumeCalculated * volumeInPixel));

    typename InputImageType::IndexType index;
    index[0] = index[1] = TestvolumeSize / 2.0;
    index[2] = 0;

    int sumpixels = 0;
    while (index[2] < TestvolumeSize)
    {
      if (inputImage->GetPixel(index) == pixelValueSet)
        sumpixels++;
      index[2] += 1;
    }

    double diameterDeviation = std::abs(100 - (100 / diameter * sumpixels));
#ifdef DEBUG
    MITK_INFO << "volume deviation: " << volumeDeviation << " diameter deviation:" << diameterDeviation;
#endif
    mitkExtractSliceFilterTestClass::TestFailureDeviation = (volumeDeviation + diameterDeviation) / 2.0;
  }
};
/*================ #END class ================*/

/*================#BEGIN Instanciation of members ================*/
mitk::Image::Pointer mitkExtractSliceFilterTestClass::TestVolume = mitk::Image::New();
double mitkExtractSliceFilterTestClass::TestvolumeSize = 256.0;
mitk::PlaneGeometry::Pointer mitkExtractSliceFilterTestClass::TestPlane = mitk::PlaneGeometry::New();
std::string mitkExtractSliceFilterTestClass::TestName = "";
unsigned char mitkExtractSliceFilterTestClass::pixelValueSet = 255;
mitkExtractSliceFilterTestClass::SliceProperties mitkExtractSliceFilterTestClass::testResults = {
  -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0};
double mitkExtractSliceFilterTestClass::TestFailureDeviation = 0.0;
/*================ #END Instanciation of members ================*/

/*================ #BEGIN test main ================*/
int mitkExtractSliceFilterTest(int /*argc*/, char * /*argv*/ [])
{
  MITK_TEST_BEGIN("mitkExtractSliceFilterTest")

  // pixelvalue based testing
  mitkExtractSliceFilterTestClass::PixelvalueBasedTest();

  // initialize sphere test volume
  mitkExtractSliceFilterTestClass::InitializeTestVolume();

  mitk::Vector3D spacing = mitkExtractSliceFilterTestClass::TestVolume->GetGeometry()->GetSpacing();

  // the center of the sphere = center of image
  double sphereCenter = mitkExtractSliceFilterTestClass::TestvolumeSize / 2.0;

  double planeSize = mitkExtractSliceFilterTestClass::TestvolumeSize;

  /* axial plane */
  mitk::PlaneGeometry::Pointer geometryAxial = mitk::PlaneGeometry::New();
  geometryAxial->InitializeStandardPlane(
    planeSize, planeSize, spacing, mitk::PlaneGeometry::Axial, sphereCenter, false, true);
  geometryAxial->ChangeImageGeometryConsideringOriginOffset(true);

  mitk::Point3D origin = geometryAxial->GetOrigin();
  mitk::Vector3D normal;
  normal = geometryAxial->GetNormal();

  normal.Normalize();

  origin += normal * 0.5; // pixelspacing is 1, so half the spacing is 0.5

  // geometryAxial->SetOrigin(origin);

  mitkExtractSliceFilterTestClass::TestSlice(geometryAxial, "Testing axial plane");
  /* end axial plane */

  /* sagittal plane */
  mitk::PlaneGeometry::Pointer geometrySagital = mitk::PlaneGeometry::New();
  geometrySagital->InitializeStandardPlane(
    planeSize, planeSize, spacing, mitk::PlaneGeometry::Sagittal, sphereCenter, true, false);
  geometrySagital->ChangeImageGeometryConsideringOriginOffset(true);

  origin = geometrySagital->GetOrigin();
  normal = geometrySagital->GetNormal();

  normal.Normalize();

  origin += normal * 0.5; // pixelspacing is 1, so half the spacing is 0.5

  // geometrySagital->SetOrigin(origin);

  mitkExtractSliceFilterTestClass::TestSlice(geometrySagital, "Testing sagittal plane");
  /* sagittal plane */

  /* sagittal shifted plane */
  mitk::PlaneGeometry::Pointer geometrySagitalShifted = mitk::PlaneGeometry::New();
  geometrySagitalShifted->InitializeStandardPlane(
    planeSize, planeSize, spacing, mitk::PlaneGeometry::Sagittal, (sphereCenter - 14), true, false);
  geometrySagitalShifted->ChangeImageGeometryConsideringOriginOffset(true);

  origin = geometrySagitalShifted->GetOrigin();
  normal = geometrySagitalShifted->GetNormal();

  normal.Normalize();

  origin += normal * 0.5; // pixelspacing is 1, so half the spacing is 0.5

  // geometrySagitalShifted->SetOrigin(origin);

  mitkExtractSliceFilterTestClass::TestSlice(geometrySagitalShifted, "Testing sagittal plane shifted");
  /* end sagittal shifted plane */

  /* coronal plane */
  mitk::PlaneGeometry::Pointer geometryCoronal = mitk::PlaneGeometry::New();
  geometryCoronal->InitializeStandardPlane(
    planeSize, planeSize, spacing, mitk::PlaneGeometry::Frontal, sphereCenter, true, false);
  geometryCoronal->ChangeImageGeometryConsideringOriginOffset(true);

  origin = geometryCoronal->GetOrigin();
  normal = geometryCoronal->GetNormal();

  normal.Normalize();

  origin += normal * 0.5; // pixelspacing is 1, so half the spacing is 0.5

  // geometryCoronal->SetOrigin(origin);

  mitkExtractSliceFilterTestClass::TestSlice(geometryCoronal, "Testing coronal plane");
  /* end coronal plane */

  /* oblique plane */
  mitk::PlaneGeometry::Pointer obliquePlane = mitk::PlaneGeometry::New();
  obliquePlane->InitializeStandardPlane(
    planeSize, planeSize, spacing, mitk::PlaneGeometry::Sagittal, sphereCenter, true, false);
  obliquePlane->ChangeImageGeometryConsideringOriginOffset(true);

  origin = obliquePlane->GetOrigin();
  normal = obliquePlane->GetNormal();

  normal.Normalize();

  origin += normal * 0.5; // pixelspacing is 1, so half the spacing is 0.5

  // obliquePlane->SetOrigin(origin);

  mitk::Vector3D rotationVector;
  rotationVector[0] = 0.2;
  rotationVector[1] = 0.4;
  rotationVector[2] = 0.62;

  float degree = 37.0;

  mitk::RotationOperation *op =
    new mitk::RotationOperation(mitk::OpROTATE, obliquePlane->GetCenter(), rotationVector, degree);
  obliquePlane->ExecuteOperation(op);
  delete op;

  mitkExtractSliceFilterTestClass::TestSlice(obliquePlane, "Testing oblique plane");
/* end oblique plane */

#ifdef SHOW_SLICE_IN_RENDER_WINDOW
  /*================ #BEGIN vtk render code ================*/

  // set reslicer for renderwindow

  mitk::Image::Pointer pic = mitk::IOUtil::Load<mitk::Image>(filename);
  vtkSmartPointer<vtkImageReslice> slicer = vtkSmartPointer<vtkImageReslice>::New();

  slicer->SetInput(pic->GetVtkImageData());

  mitk::PlaneGeometry::Pointer obliquePl = mitk::PlaneGeometry::New();
  obliquePl->InitializeStandardPlane(
    pic->GetGeometry(), mitk::PlaneGeometry::Sagittal, pic->GetGeometry()->GetCenter()[0], true, false);
  obliquePl->ChangeImageGeometryConsideringOriginOffset(true);

  mitk::Point3D origin2 = obliquePl->GetOrigin();
  mitk::Vector3D n;
  n = obliquePl->GetNormal();

  n.Normalize();

  origin2 += n * 0.5; // pixelspacing is 1, so half the spacing is 0.5

  obliquePl->SetOrigin(origin2);

  mitk::Vector3D rotation;
  rotation[0] = 0.534307;
  rotation[1] = 0.000439605;
  rotation[2] = 0.423017;
  MITK_INFO << rotation;

  mitk::RotationOperation *operation =
    new mitk::RotationOperation(mitk::OpROTATE, obliquePl->GetCenter(), rotationVector, degree);
  obliquePl->ExecuteOperation(operation);
  delete operation;

  double origin[3];
  origin[0] = obliquePl->GetOrigin()[0];
  origin[1] = obliquePl->GetOrigin()[1];
  origin[2] = obliquePl->GetOrigin()[2];
  slicer->SetResliceAxesOrigin(origin);

  mitk::Vector3D right, bottom, normal;
  right = obliquePl->GetAxisVector(0);
  bottom = obliquePl->GetAxisVector(1);
  normal = obliquePl->GetNormal();

  right.Normalize();
  bottom.Normalize();
  normal.Normalize();

  double cosines[9];

  mitk::vnl2vtk(right.GetVnlVector(), cosines); // x

  mitk::vnl2vtk(bottom.GetVnlVector(), cosines + 3); // y

  mitk::vnl2vtk(normal.GetVnlVector(), cosines + 6); // n

  slicer->SetResliceAxesDirectionCosines(cosines);

  slicer->SetOutputDimensionality(2);
  slicer->Update();

  // set vtk renderwindow
  vtkSmartPointer<vtkPlaneSource> vtkPlane = vtkSmartPointer<vtkPlaneSource>::New();
  vtkPlane->SetOrigin(0.0, 0.0, 0.0);

  // These two points define the axes of the plane in combination with the origin.
  // Point 1 is the x-axis and point 2 the y-axis.
  // Each plane is transformed according to the view (axial, coronal and saggital) afterwards.
  vtkPlane->SetPoint1(1.0, 0.0, 0.0); // P1: (xMax, yMin, depth)
  vtkPlane->SetPoint2(0.0, 1.0, 0.0); // P2: (xMin, yMax, depth)
  // these are not the correct values for all slices, only a square plane by now

  vtkSmartPointer<vtkPolyDataMapper> imageMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
  imageMapper->SetInputConnection(vtkPlane->GetOutputPort());

  vtkSmartPointer<vtkLookupTable> lookupTable = vtkSmartPointer<vtkLookupTable>::New();

  // built a default lookuptable
  lookupTable->SetRampToLinear();
  lookupTable->SetSaturationRange(0.0, 0.0);
  lookupTable->SetHueRange(0.0, 0.0);
  lookupTable->SetValueRange(0.0, 1.0);
  lookupTable->Build();
  // map all black values to transparent
  lookupTable->SetTableValue(0, 0.0, 0.0, 0.0, 0.0);
  lookupTable->SetRange(-255.0, 255.0);
  // lookupTable->SetRange(-1022.0, 1184.0);//pic3D range

  vtkSmartPointer<vtkTexture> texture = vtkSmartPointer<vtkTexture>::New();

  texture->SetInput(slicer->GetOutput());

  texture->SetLookupTable(lookupTable);

  texture->SetMapColorScalarsThroughLookupTable(true);

  vtkSmartPointer<vtkActor> imageActor = vtkSmartPointer<vtkActor>::New();
  imageActor->SetMapper(imageMapper);
  imageActor->SetTexture(texture);

  // Setup renderers
  vtkSmartPointer<vtkRenderer> renderer = vtkSmartPointer<vtkRenderer>::New();
  renderer->AddActor(imageActor);

  // Setup render window
  vtkSmartPointer<vtkRenderWindow> renderWindow = vtkSmartPointer<vtkRenderWindow>::New();
  renderWindow->AddRenderer(renderer);

  // Setup render window interactor
  vtkSmartPointer<vtkRenderWindowInteractor> renderWindowInteractor = vtkSmartPointer<vtkRenderWindowInteractor>::New();
  vtkSmartPointer<vtkInteractorStyleImage> style = vtkSmartPointer<vtkInteractorStyleImage>::New();
  renderWindowInteractor->SetInteractorStyle(style);

  // Render and start interaction
  renderWindowInteractor->SetRenderWindow(renderWindow);
  // renderer->AddViewProp(imageActor);

  renderWindow->Render();
  renderWindowInteractor->Start();
// always end with this!
/*================ #END vtk render code ================*/
#endif // SHOW_SLICE_IN_RENDER_WINDOW

  MITK_TEST_END()
}