void SuperPixelSegmentationGUI::slot_IterationComplete(unsigned int numberOfSegments)
{
std::stringstream ss;
ss << "Computed " << numberOfSegments << " segments." << std::endl;
this->statusBar()->showMessage(ss.str().c_str());
typedef itk::Image<itk::RGBPixel<unsigned char>, 2> RGBImageType;
RGBImageType::Pointer colorImage = RGBImageType::New();
colorImage->SetRegions(this->LabelImage->GetLargestPossibleRegion());
colorImage->Allocate();
unsigned int maxLabel = Helpers::MaxValue<LabelImageType>(this->LabelImage);
std::vector<RGBImageType::PixelType> segmentColors;
for(unsigned int labelId = 0; labelId <= maxLabel; ++labelId)
{
//std::cout << "Coloring label " << labelId << std::endl;
float rgb[3] = {0,0,0};
itk::ImageRegionIterator<LabelImageType> labelIterator(this->LabelImage, this->LabelImage->GetLargestPossibleRegion());
unsigned int counter = 0;
while(!labelIterator.IsAtEnd())
{
if(labelIterator.Get() == labelId)
{
rgb[0] += this->Image->GetPixel(labelIterator.GetIndex())[0];
rgb[1] += this->Image->GetPixel(labelIterator.GetIndex())[1];
rgb[2] += this->Image->GetPixel(labelIterator.GetIndex())[2];
counter++;
}// end if
++labelIterator;
} // end while
RGBImageType::PixelType colorPixel;
colorPixel[0] = rgb[0]/static_cast<float>(counter);
colorPixel[1] = rgb[1]/static_cast<float>(counter);
colorPixel[2] = rgb[2]/static_cast<float>(counter);
segmentColors.push_back(colorPixel);
} // end for
itk::ImageRegionIterator<LabelImageType> colorIterator(this->LabelImage, this->LabelImage->GetLargestPossibleRegion());
while(!colorIterator.IsAtEnd())
{
colorImage->SetPixel(colorIterator.GetIndex(), segmentColors[colorIterator.Get()]);
++colorIterator;
} // end while
QImage qimage = HelpersQt::GetQImageRGB<RGBImageType>(colorImage);
if(this->LabelImagePixmapItem)
{
this->Scene->removeItem(this->LabelImagePixmapItem);
}
this->LabelImagePixmapItem = this->Scene->addPixmap(QPixmap::fromImage(qimage));
Refresh();
}
void Initialisation::savePointAsAxialImage(ImageType::Pointer initialImage, string filename)
{
if (points_.size() > 0)
{
double radius = 2.0;
//if (initialRadius_/stretchingFactor_ > radius_) radius = radius_*stretchingFactor_; // initialRadius_ majored by radius_
//else radius = initialRadius_;
typedef itk::ImageDuplicator< ImageType > DuplicatorType3D;
DuplicatorType3D::Pointer duplicator = DuplicatorType3D::New();
duplicator->SetInputImage(initialImage);
duplicator->Update();
ImageType::Pointer clonedImage = duplicator->GetOutput();
// Intensity normalization
RescaleFilterType::Pointer rescaleFilter = RescaleFilterType::New();
rescaleFilter->SetInput(clonedImage);
rescaleFilter->SetOutputMinimum(0);
rescaleFilter->SetOutputMaximum(255);
try {
rescaleFilter->Update();
} catch( itk::ExceptionObject & e ) {
cerr << "Exception caught while normalizing input image " << endl;
cerr << e << endl;
}
clonedImage = rescaleFilter->GetOutput();
typedef itk::RGBPixel<unsigned char> RGBPixelType;
typedef itk::Image<RGBPixelType, 2> RGBImageType;
typedef itk::ExtractImageFilter< ImageType, RGBImageType > ExtractorTypeRGB;
PointType pt; pt[0] = initialPoint_[0]; pt[1] = initialPoint_[1]; pt[2] = initialPoint_[2];
ImageType::IndexType ind;
clonedImage->TransformPhysicalPointToIndex(pt,ind);
ImageType::SizeType desiredSize = clonedImage->GetLargestPossibleRegion().GetSize();
ImageType::IndexType desiredStart;
desiredStart[0] = 0; desiredStart[1] = ind[1]; desiredStart[2] = 0;
desiredSize[1] = 0;
ImageType::RegionType desiredRegion(desiredStart, desiredSize);
ExtractorTypeRGB::Pointer filter = ExtractorTypeRGB::New();
filter->SetExtractionRegion(desiredRegion);
filter->SetInput(clonedImage);
#if ITK_VERSION_MAJOR >= 4
filter->SetDirectionCollapseToIdentity(); // This is required.
#endif
try {
filter->Update();
} catch( itk::ExceptionObject & e ) {
std::cerr << "Exception caught while updating ExtractorTypeRGB " << std::endl;
std::cerr << e << std::endl;
}
RGBImageType::Pointer image = filter->GetOutput();
// draw cross
RGBPixelType pixel; pixel[0] = 255; pixel[1] = 255; pixel[2] = 255;
for (int x=-radius; x<=radius; x++) {
RGBImageType::IndexType ind_x, ind_y;
ind_x[0] = ind[0]+x; ind_x[1] = ind[2]; ind_y[0] = ind[0]; ind_y[1] = ind[2]+x;
image->SetPixel(ind_x, pixel);
image->SetPixel(ind_y, pixel);
}
typedef itk::ImageFileWriter< RGBImageType > WriterRGBType;
itk::PNGImageIO::Pointer ioPNG = itk::PNGImageIO::New();
WriterRGBType::Pointer writerPNG = WriterRGBType::New();
writerPNG->SetInput(image);
writerPNG->SetImageIO(ioPNG);
writerPNG->SetFileName(filename);
try {
writerPNG->Update();
}
catch( itk::ExceptionObject & e )
{
cout << "Exception thrown ! " << endl;
cout << "An error ocurred during Writing PNG" << endl;
cout << "Location = " << e.GetLocation() << endl;
cout << "Description = " << e.GetDescription() << endl;
}
}
else cout << "Error: Spinal cord center not detected" << endl;
}