static void Paint(mitk::Image::Pointer image, itk::Index<3> index, unsigned int timeStep)
{
// As soon as the ImagePixelWriteAccessor object goes out of scope at the
// end of this function, the image will be unlocked again (RAII).
mitk::ImagePixelWriteAccessor<T> writeAccessor(image, image->GetVolumeData(timeStep));
writeAccessor.SetPixelByIndex(index, std::numeric_limits<T>::min());
// Don't forget to update the modified time stamp of the image. Otherwise,
// everything downstream wouldn't recognize that the image changed,
// including the rendering system.
image->Modified();
}
// The tests all do the same, only in different directions
void testRoutine(mitk::SliceNavigationController::ViewDirection viewDirection)
{
int dim;
switch(viewDirection)
{
case(mitk::SliceNavigationController::Axial): dim = 2; break;
case(mitk::SliceNavigationController::Frontal): dim = 1; break;
case(mitk::SliceNavigationController::Sagittal): dim = 0; break;
case(mitk::SliceNavigationController::Original): dim = -1; break; // This is just to get rid of a warning
}
/* Fill segmentation
*
* 1st slice: 3x3 square segmentation
* 2nd slice: empty
* 3rd slice: 1x1 square segmentation in corner
* -> 2nd slice should become 2x2 square in corner
*
* put accessor in scope
*/
itk::Index<3> currentPoint;
{
mitk::ImagePixelWriteAccessor<mitk::Tool::DefaultSegmentationDataType, 3> writeAccessor(m_SegmentationImage);
// Fill 3x3 slice
currentPoint[dim] = m_CenterPoint[dim] - 1;
for (int i=-1; i<=1; ++i)
{
for (int j=-1; j<=1; ++j)
{
currentPoint[(dim+1)%3] = m_CenterPoint[(dim+1)%3] + i;
currentPoint[(dim+2)%3] = m_CenterPoint[(dim+2)%3] + j;
writeAccessor.SetPixelByIndexSafe(currentPoint, 1);
}
}
// Now i=j=1, set point two slices up
currentPoint[dim] = m_CenterPoint[dim] + 1;
writeAccessor.SetPixelByIndexSafe(currentPoint, 1);
}
// mitk::IOUtil::Save(m_SegmentationImage, "SOME PATH");
m_InterpolationController->SetSegmentationVolume(m_SegmentationImage);
m_InterpolationController->SetReferenceVolume(m_ReferenceImage);
// This could be easier...
mitk::SliceNavigationController::Pointer navigationController = mitk::SliceNavigationController::New();
navigationController->SetInputWorldTimeGeometry(m_SegmentationImage->GetTimeGeometry());
navigationController->Update(viewDirection);
mitk::Point3D pointMM;
m_SegmentationImage->GetTimeGeometry()->GetGeometryForTimeStep(0)->IndexToWorld(m_CenterPoint, pointMM);
navigationController->SelectSliceByPoint(pointMM);
auto plane = navigationController->GetCurrentPlaneGeometry();
mitk::Image::Pointer interpolationResult = m_InterpolationController->Interpolate(dim, m_CenterPoint[dim], plane, 0);
// mitk::IOUtil::Save(interpolationResult, "SOME PATH");
// Write result into segmentation image
vtkSmartPointer<mitkVtkImageOverwrite> reslicer = vtkSmartPointer<mitkVtkImageOverwrite>::New();
reslicer->SetInputSlice(interpolationResult->GetSliceData()->GetVtkImageAccessor(interpolationResult)->GetVtkImageData());
reslicer->SetOverwriteMode(true);
reslicer->Modified();
mitk::ExtractSliceFilter::Pointer extractor = mitk::ExtractSliceFilter::New(reslicer);
extractor->SetInput(m_SegmentationImage);
extractor->SetTimeStep(0);
extractor->SetWorldGeometry(plane);
extractor->SetVtkOutputRequest(true);
extractor->SetResliceTransformByGeometry(m_SegmentationImage->GetTimeGeometry()->GetGeometryForTimeStep(0));
extractor->Modified();
extractor->Update();
// mitk::IOUtil::Save(m_SegmentationImage, "SOME PATH");
// Check a 4x4 square, the center of which needs to be filled
mitk::ImagePixelReadAccessor<mitk::Tool::DefaultSegmentationDataType, 3> readAccess(m_SegmentationImage);
currentPoint = m_CenterPoint;
for (int i=-1; i<=2; ++i)
{
for (int j=-1; j<=2; ++j)
{
currentPoint[(dim+1)%3] = m_CenterPoint[(dim+1)%3] + i;
currentPoint[(dim+2)%3] = m_CenterPoint[(dim+2)%3] + j;
if (i == -1 || i == 2 || j == -1 || j == 2)
{
CPPUNIT_ASSERT_MESSAGE("Have false positive segmentation.", readAccess.GetPixelByIndexSafe(currentPoint) == 0);
}
else
{
CPPUNIT_ASSERT_MESSAGE("Have false negative segmentation.", readAccess.GetPixelByIndexSafe(currentPoint) == 1);
}
}
}
}
ITK_THREAD_RETURN_TYPE ThreadMethod(void *data)
{
/* extract data pointer from Thread Info structure */
struct itk::MultiThreader::ThreadInfoStruct *pInfo = (struct itk::MultiThreader::ThreadInfoStruct *)data;
// some data validity checking
if (pInfo == NULL)
{
return ITK_THREAD_RETURN_VALUE;
}
if (pInfo->UserData == NULL)
{
return ITK_THREAD_RETURN_VALUE;
}
// obtain user data for processing
ThreadData *threadData = (ThreadData *)pInfo->UserData;
srand(pInfo->ThreadID);
mitk::Image::Pointer im = threadData->data;
int nrSlices = im->GetDimension(2);
// Create randomly a PixelRead- or PixelWriteAccessor for a slice and access all pixels in it.
try
{
if (rand() % 2)
{
testMutex.Lock();
mitk::ImageDataItem *iDi = im->GetSliceData(rand() % nrSlices);
testMutex.Unlock();
while (!iDi->IsComplete())
{
}
// MITK_INFO << "pixeltype: " << im->GetPixelType().GetComponentTypeAsString();
if ((im->GetPixelType().GetComponentTypeAsString() == "short") && (im->GetDimension() == 3))
{
// Use pixeltype&dimension specific read accessor
int xlength = im->GetDimension(0);
int ylength = im->GetDimension(1);
mitk::ImagePixelReadAccessor<short, 2> readAccessor(im, iDi);
itk::Index<2> idx;
for (int i = 0; i < xlength; ++i)
{
for (int j = 0; j < ylength; ++j)
{
idx[0] = i;
idx[1] = j;
readAccessor.GetPixelByIndexSafe(idx);
}
}
}
else
{
// use general accessor
mitk::ImageReadAccessor *iRA = new mitk::ImageReadAccessor(im, iDi);
delete iRA;
}
}
else
{
testMutex.Lock();
mitk::ImageDataItem *iDi = im->GetSliceData(rand() % nrSlices);
testMutex.Unlock();
while (!iDi->IsComplete())
{
}
if ((im->GetPixelType().GetComponentTypeAsString() == "short") && (im->GetDimension() == 3))
{
// Use pixeltype&dimension specific read accessor
int xlength = im->GetDimension(0);
int ylength = im->GetDimension(1);
mitk::ImagePixelWriteAccessor<short, 2> writeAccessor(im, iDi);
itk::Index<2> idx;
for (int i = 0; i < xlength; ++i)
{
for (int j = 0; j < ylength; ++j)
{
idx[0] = i;
idx[1] = j;
short newVal = rand() % 16000;
writeAccessor.SetPixelByIndexSafe(idx, newVal);
short val = writeAccessor.GetPixelByIndexSafe(idx);
if (val != newVal)
{
threadData->m_Successful = false;
}
}
}
}
else
{
// use general accessor
mitk::ImageWriteAccessor iB(im, iDi);
void *pointer = iB.GetData();
*((char *)pointer) = 0;
}
}
}
catch (mitk::MemoryIsLockedException &e)
{
threadData->m_Successful = false;
e.Print(std::cout);
}
catch (mitk::Exception &e)
{
threadData->m_Successful = false;
e.Print(std::cout);
}
// data processing end!
threadData->m_Barrier->Wait();
return ITK_THREAD_RETURN_VALUE;
}