int main(int argc, char* argv[]) {
CSimpleOpt::SOption specs[] = {
{ 0, "-o", SO_REQ_SEP },
SO_END_OF_OPTIONS
};
Options argParser;
StringVector args = argParser.ParseOptions(argc, argv, specs);
if (args.size() < 1) {
cout << argv[0] << " [input-vector] [output-rgb]" << endl;
return 1;
}
ImageIO<DeformFieldImageType> io;
DeformFieldImageType::Pointer img = io.ReadImage(args[0]);
// itk::UnaryFunctorImageFilter<DeformFieldImageType,RGBImageType> CastFilter;
typedef itk::UnaryFunctorImageFilter<DeformFieldImageType, RGBImageType, Vector2RGB> CastFilter;
CastFilter::Pointer caster = CastFilter::New();
caster->SetInput(img);
caster->Update();
RGBImageType::Pointer rgbImg = caster->GetOutput();
rgbImg->Print(cout);
io.WriteImageS<RGBImageType>(args[1], rgbImg);
return 0;
}
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();
}
bool TestCreateLuminanceImage()
{
// From RGB image
{
itk::Index<2> imageCorner = {{0,0}};
itk::Size<2> imageSize = {{100,100}};
itk::ImageRegion<2> imageRegion(imageCorner, imageSize);
typedef itk::Image<itk::RGBPixel<unsigned char>, 2> RGBImageType;
RGBImageType::Pointer rgbImage = RGBImageType::New();
rgbImage->SetRegions(imageRegion);
rgbImage->Allocate();
typedef itk::Image<float, 2> LuminanceImageType;
LuminanceImageType::Pointer luminanceImage = LuminanceImageType::New();
ITKHelpers::CreateLuminanceImage(rgbImage.GetPointer(), luminanceImage.GetPointer());
}
// From Vector image
{
itk::Index<2> imageCorner = {{0,0}};
itk::Size<2> imageSize = {{100,100}};
itk::ImageRegion<2> imageRegion(imageCorner, imageSize);
typedef itk::Image<itk::CovariantVector<unsigned char, 3>, 2> VectorImageType;
VectorImageType::Pointer vectorImage = VectorImageType::New();
vectorImage->SetRegions(imageRegion);
vectorImage->Allocate();
typedef itk::Image<float, 2> LuminanceImageType;
LuminanceImageType::Pointer luminanceImage = LuminanceImageType::New();
ITKHelpers::CreateLuminanceImage(vectorImage.GetPointer(), luminanceImage.GetPointer());
}
return true;
}
void LidarSegmentationWidget::on_action_Selections_SaveAsImage_triggered()
{
QString filename = QFileDialog::getSaveFileName(this,
"Save Image", ".", "PNG Files (*.png)");
if(filename.isEmpty())
{
return;
}
RGBImageType::Pointer selectionsImage = RGBImageType::New();
selectionsImage->SetRegions(this->ImageRegion);
selectionsImage->Allocate();
RGBPixelType whitePixel;
whitePixel.SetRed(255);
whitePixel.SetGreen(255);
whitePixel.SetBlue(255);
selectionsImage->FillBuffer(whitePixel);
RGBPixelType greenPixel;
greenPixel.SetRed(0);
greenPixel.SetGreen(255);
greenPixel.SetBlue(0);
ITKHelpers::SetPixels(selectionsImage.GetPointer(), this->Sources, greenPixel);
RGBPixelType redPixel;
redPixel.SetRed(255);
redPixel.SetGreen(0);
redPixel.SetBlue(0);
ITKHelpers::SetPixels(selectionsImage.GetPointer(), this->Sinks, redPixel);
typedef itk::ImageFileWriter< RGBImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName(filename.toStdString());
writer->SetInput(selectionsImage);
writer->Update();
}
void LidarSegmentationWidget::on_action_Selections_SaveBackgroundAsImage_triggered()
{
QString filename = QFileDialog::getSaveFileName(this,
"Save Image", "background.png", "PNG Files (*.png)");
if(filename.isEmpty())
{
return;
}
RGBImageType::Pointer selectionsImage = RGBImageType::New();
selectionsImage->SetRegions(this->ImageRegion);
selectionsImage->Allocate();
RGBPixelType blackPixel;
blackPixel.SetRed(0);
blackPixel.SetGreen(0);
blackPixel.SetBlue(0);
RGBPixelType whitePixel;
whitePixel.SetRed(255);
whitePixel.SetGreen(255);
whitePixel.SetBlue(255);
ITKHelpers::SetPixelsInRegionToValue(selectionsImage.GetPointer(), selectionsImage->GetLargestPossibleRegion(),
blackPixel);
ITKHelpers::SetPixels(selectionsImage.GetPointer(), this->Sinks, whitePixel);
typedef itk::ImageFileWriter< RGBImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName(filename.toStdString());
writer->SetInput(selectionsImage);
writer->Update();
}
void LidarInpaintingHSVTextureVerification(TImage* const originalImage, Mask* const mask,
const unsigned int patchHalfWidth, const unsigned int numberOfKNN,
float slightBlurVariance = 1.0f, unsigned int searchRadius = 1000,
float localRegionSizeMultiplier = 3.0f, float maxAllowedUsedPixelsRatio = 0.5f)
{
itk::ImageRegion<2> fullRegion = originalImage->GetLargestPossibleRegion();
// Extract the RGB image
typedef itk::Image<itk::CovariantVector<float, 3>, 2> RGBImageType;
std::vector<unsigned int> firstThreeChannels = {0,1,2};
RGBImageType::Pointer rgbImage = RGBImageType::New();
ITKHelpers::ExtractChannels(originalImage, firstThreeChannels, rgbImage.GetPointer());
// Create the HSV image
typedef itk::Image<itk::CovariantVector<float, 3>, 2> HSVImageType;
HSVImageType::Pointer hsvImage = HSVImageType::New();
ITKVTKHelpers::ConvertRGBtoHSV(rgbImage.GetPointer(), hsvImage.GetPointer());
ITKHelpers::WriteImage(hsvImage.GetPointer(), "HSVImage.mha");
// Stack the HSV image with the original rest of the channels
typedef itk::Image<itk::CovariantVector<float, 5>, 2> HSVDxDyImageType;
HSVDxDyImageType::Pointer hsvDxDyImage = HSVDxDyImageType::New();
ITKHelpers::DeepCopy(originalImage, hsvDxDyImage.GetPointer());
ITKHelpers::ReplaceChannels(hsvDxDyImage.GetPointer(), firstThreeChannels, hsvImage.GetPointer());
// Blur the image for gradient computation stability (Criminisi's data term)
RGBImageType::Pointer blurredRGBImage = RGBImageType::New();
float blurVariance = 2.0f;
MaskOperations::MaskedBlur(rgbImage.GetPointer(), mask, blurVariance, blurredRGBImage.GetPointer());
ITKHelpers::WriteRGBImage(blurredRGBImage.GetPointer(), "BlurredRGBImage.png");
// Blur the image slightly so that the SSD comparisons are not so noisy
typename HSVDxDyImageType::Pointer slightlyBlurredHSVDxDyImage = TImage::New();
MaskOperations::MaskedBlur(hsvDxDyImage.GetPointer(), mask, slightBlurVariance, slightlyBlurredHSVDxDyImage.GetPointer());
ITKHelpers::WriteImage(slightlyBlurredHSVDxDyImage.GetPointer(), "SlightlyBlurredHSVDxDyImage.mha");
// Create the graph
typedef ImagePatchPixelDescriptor<TImage> ImagePatchPixelDescriptorType;
typedef boost::grid_graph<2> VertexListGraphType;
// We can't make this a signed type (size_t versus int) because we allow negative
boost::array<std::size_t, 2> graphSideLengths = { { fullRegion.GetSize()[0],
fullRegion.GetSize()[1] } };
VertexListGraphType graph(graphSideLengths);
typedef boost::graph_traits<VertexListGraphType>::vertex_descriptor VertexDescriptorType;
typedef boost::graph_traits<VertexListGraphType>::vertex_iterator VertexIteratorType;
// Get the index map
typedef boost::property_map<VertexListGraphType, boost::vertex_index_t>::const_type IndexMapType;
IndexMapType indexMap(get(boost::vertex_index, graph));
// Create the descriptor map. This is where the data for each pixel is stored.
typedef boost::vector_property_map<ImagePatchPixelDescriptorType, IndexMapType> ImagePatchDescriptorMapType;
ImagePatchDescriptorMapType imagePatchDescriptorMap(num_vertices(graph), indexMap);
// Create the patch inpainter.
typedef PatchInpainter<TImage> OriginalImageInpainterType;
OriginalImageInpainterType originalImagePatchInpainter(patchHalfWidth, originalImage, mask);
originalImagePatchInpainter.SetDebugImages(true);
originalImagePatchInpainter.SetImageName("RGB");
// Create an inpainter for the HSV image.
typedef PatchInpainter<HSVImageType> HSVImageInpainterType;
HSVImageInpainterType hsvImagePatchInpainter(patchHalfWidth, hsvImage, mask);
// Create an inpainter for the RGB image.
typedef PatchInpainter<RGBImageType> RGBImageInpainterType;
RGBImageInpainterType rgbImagePatchInpainter(patchHalfWidth, rgbImage, mask);
// Create an inpainter for the blurred image.
typedef PatchInpainter<RGBImageType> BlurredImageInpainterType;
BlurredImageInpainterType blurredRGBImagePatchInpainter(patchHalfWidth, blurredRGBImage, mask);
// Create an inpainter for the slightly blurred image.
typedef PatchInpainter<TImage> SlightlyBlurredHSVDxDyImageImageInpainterType;
SlightlyBlurredHSVDxDyImageImageInpainterType slightlyBlurredHSVDxDyImageImagePatchInpainter(patchHalfWidth, slightlyBlurredHSVDxDyImage, mask);
// Create a composite inpainter. (Note: the mask is inpainted in InpaintingVisitor::FinishVertex)
CompositePatchInpainter inpainter;
inpainter.AddInpainter(&originalImagePatchInpainter);
inpainter.AddInpainter(&hsvImagePatchInpainter);
inpainter.AddInpainter(&blurredRGBImagePatchInpainter);
inpainter.AddInpainter(&slightlyBlurredHSVDxDyImageImagePatchInpainter);
inpainter.AddInpainter(&rgbImagePatchInpainter);
// Create the priority function
typedef PriorityCriminisi<RGBImageType> PriorityType;
PriorityType priorityFunction(blurredRGBImage, mask, patchHalfWidth);
// priorityFunction.SetDebugLevel(1);
// Queue
typedef IndirectPriorityQueue<VertexListGraphType> BoundaryNodeQueueType;
BoundaryNodeQueueType boundaryNodeQueue(graph);
// Create the descriptor visitor (used for SSD comparisons).
typedef ImagePatchDescriptorVisitor<VertexListGraphType, TImage, ImagePatchDescriptorMapType>
ImagePatchDescriptorVisitorType;
// ImagePatchDescriptorVisitorType imagePatchDescriptorVisitor(originalImage, mask,
// imagePatchDescriptorMap, patchHalfWidth); // Use the non-blurred image for the SSD comparisons
ImagePatchDescriptorVisitorType imagePatchDescriptorVisitor(slightlyBlurredHSVDxDyImage, mask,
imagePatchDescriptorMap, patchHalfWidth); // Use the slightly blurred HSV image for the SSD comparisons. Make sure to use a *HSVSSD difference functor so the H differences are treated appropriately!
typedef DefaultAcceptanceVisitor<VertexListGraphType> AcceptanceVisitorType;
AcceptanceVisitorType acceptanceVisitor;
// Create the inpainting visitor. (The mask is inpainted in FinishVertex)
typedef InpaintingVisitor<VertexListGraphType, BoundaryNodeQueueType,
ImagePatchDescriptorVisitorType, AcceptanceVisitorType, PriorityType, TImage>
InpaintingVisitorType;
InpaintingVisitorType inpaintingVisitor(mask, boundaryNodeQueue,
imagePatchDescriptorVisitor, acceptanceVisitor,
&priorityFunction, patchHalfWidth, "InpaintingVisitor", originalImage);
inpaintingVisitor.SetDebugImages(true); // This produces PatchesCopied* images showing where patches were copied from/to at each iteration
// inpaintingVisitor.SetAllowNewPatches(false);
inpaintingVisitor.SetAllowNewPatches(true); // we can do this as long as we use one of the LinearSearchKNNProperty*Reuse (like LinearSearchKNNPropertyLimitLocalReuse) in the steps below
InitializePriority(mask, boundaryNodeQueue, &priorityFunction);
// Initialize the boundary node queue from the user provided mask image.
InitializeFromMaskImage<InpaintingVisitorType, VertexDescriptorType>(mask, &inpaintingVisitor);
std::cout << "PatchBasedInpaintingNonInteractive: There are " << boundaryNodeQueue.CountValidNodes()
<< " nodes in the boundaryNodeQueue" << std::endl;
#define DUseWeightedDifference
#ifdef DUseWeightedDifference
// The absolute value of the depth derivative range is usually about [0,12], so to make
// it comparable to to the color image channel range of [0,255], we multiply by 255/12 ~= 20.
// float depthDerivativeWeight = 20.0f;
// This should not be computed "by eye" by looking at the Dx and Dy channels of the PTX scan, because there are typically
// huge depth discontinuties around the objects that are going to be inpainted. We'd have to look at the masked version of this
// image to determine the min/max values of the unmasked pixels. They will be much smaller than the min/max values of the original
// image, which will make the depth derivative weights much higher (~100 or so)
// std::vector<typename TImage::PixelType> channelMins = ITKHelpers::ComputeMinOfAllChannels(originalImage);
// std::vector<typename TImage::PixelType> channelMaxs = ITKHelpers::ComputeMaxOfAllChannels(originalImage);
typename TImage::PixelType channelMins;
ITKHelpers::ComputeMinOfAllChannels(originalImage, channelMins);
typename TImage::PixelType channelMaxs;
ITKHelpers::ComputeMaxOfAllChannels(originalImage, channelMaxs);
float minX = fabs(channelMins[3]);
float maxX = fabs(channelMaxs[3]);
float maxValueX = std::max(minX, maxX);
std::cout << "maxValueX = " << maxValueX << std::endl;
float depthDerivativeWeightX = 255.0f / maxValueX;
std::cout << "Computed depthDerivativeWeightX = " << depthDerivativeWeightX << std::endl;
float minY = fabs(channelMins[4]);
float maxY = fabs(channelMaxs[4]);
float maxValueY = std::max(minY, maxY);
std::cout << "maxValueY = " << maxValueY << std::endl;
float depthDerivativeWeightY = 255.0f / maxValueY;
std::cout << "Computed depthDerivativeWeightY = " << depthDerivativeWeightY << std::endl;
// Use all channels
std::vector<float> weights = {1.0f, 1.0f, 1.0f, depthDerivativeWeightX, depthDerivativeWeightY};
// typedef WeightedSumSquaredPixelDifference<typename TImage::PixelType> PixelDifferenceType;
typedef WeightedHSVSSDFull<typename TImage::PixelType> FullPixelDifferenceType;
FullPixelDifferenceType fullPixelDifferenceFunctor(weights);
typedef ImagePatchDifference<ImagePatchPixelDescriptorType,
FullPixelDifferenceType > FullPatchDifferenceType;
FullPatchDifferenceType fullPatchDifferenceFunctor(fullPixelDifferenceFunctor);
// Use only the first 3 channels
typedef HSVSSD<typename TImage::PixelType> First3PixelDifferenceType;
First3PixelDifferenceType first3PixelDifferenceFunctor;
typedef ImagePatchDifference<ImagePatchPixelDescriptorType,
First3PixelDifferenceType > First3PatchDifferenceType;
First3PatchDifferenceType first3PatchDifferenceFunctor(first3PixelDifferenceFunctor);
#else
// Use an unweighted pixel difference
typedef ImagePatchDifference<ImagePatchPixelDescriptorType,
SumSquaredPixelDifference<typename TImage::PixelType> > PatchDifferenceType;
PatchDifferenceType patchDifferenceFunctor;
#endif
//#define DAllowReuse // comment/uncomment this line to toggle allowing patches to be used as the source patch more than once
#ifdef DAllowReuse
// Create the first (KNN) neighbor finder
typedef LinearSearchKNNProperty<ImagePatchDescriptorMapType, PatchDifferenceType> KNNSearchType;
KNNSearchType linearSearchKNN(imagePatchDescriptorMap, numberOfKNN, patchDifferenceFunctor);
#else
typedef LinearSearchKNNPropertyLimitLocalReuse<ImagePatchDescriptorMapType, FullPatchDifferenceType, RGBImageType> KNNSearchType;
KNNSearchType linearSearchKNN(imagePatchDescriptorMap, mask, numberOfKNN, localRegionSizeMultiplier, maxAllowedUsedPixelsRatio,
fullPatchDifferenceFunctor, inpaintingVisitor.GetSourcePixelMapImage(),
rgbImage.GetPointer());
linearSearchKNN.SetDebugImages(true);
linearSearchKNN.SetDebugScreenOutputs(true);
#endif
//#else // This works the best, but is less useful for demonstrations
// typedef LinearSearchKNNPropertyLimitLocalReuse<ImagePatchDescriptorMapType, FullPatchDifferenceType, RGBImageType> FullPixelKNNSearchType;
// FullPixelKNNSearchType fullPixelSearchKNN(imagePatchDescriptorMap, mask, numberOfKNN, localRegionSizeMultiplier, maxAllowedUsedPixelsRatio,
// fullPatchDifferenceFunctor, inpaintingVisitor.GetSourcePixelMapImage(),
// rgbImage.GetPointer());
// fullPixelSearchKNN.SetDebugImages(true);
// fullPixelSearchKNN.SetDebugScreenOutputs(true);
// typedef LinearSearchKNNPropertyLimitLocalReuse<ImagePatchDescriptorMapType, First3PatchDifferenceType, RGBImageType> First3PixelKNNSearchType;
// First3PixelKNNSearchType first3SearchKNN(imagePatchDescriptorMap, mask, numberOfKNN, localRegionSizeMultiplier, maxAllowedUsedPixelsRatio,
// first3PatchDifferenceFunctor, inpaintingVisitor.GetSourcePixelMapImage(),
// rgbImage.GetPointer());
// first3SearchKNN.SetDebugScreenOutputs(true);
//// typedef LinearSearchKNNProperty<ImagePatchDescriptorMapType, First3PatchDifferenceType> First3PixelKNNSearchType;
//// First3PixelKNNSearchType first3SearchKNN(imagePatchDescriptorMap, numberOfKNN,
//// first3PatchDifferenceFunctor);
//// first3SearchKNN.SetDebugImages(true);
// typedef LinearSearchKNNPropertyCombine<FullPixelKNNSearchType, First3PixelKNNSearchType> KNNSearchType;
// KNNSearchType linearSearchKNN(fullPixelSearchKNN, first3SearchKNN);
//#endif
// Setup the second (1-NN) neighbor finder
typedef std::vector<VertexDescriptorType>::iterator VertexDescriptorVectorIteratorType;
// This is templated on TImage because we need it to write out debug patches from this searcher (since we are not using an RGB image to compute the histograms)
// typedef LinearSearchBestTexture<ImagePatchDescriptorMapType, HSVImageType,
// VertexDescriptorVectorIteratorType, TImage> BestSearchType; // Use the histogram of the gradient magnitudes of a scalar represetnation of the image (e.g. magnitude image)
// typedef LinearSearchBestLidarTextureDerivatives<ImagePatchDescriptorMapType, HSVImageType,
// VertexDescriptorVectorIteratorType, TImage> BestSearchType; // Use the concatenated histograms of the absolute value of the derivatives of each channel
// typedef LinearSearchBestLidarHSVTextureGradient<ImagePatchDescriptorMapType, HSVDxDyImageType,
// VertexDescriptorVectorIteratorType, RGBImageType> BestSearchType; // Use the concatenated histograms of the gradient magnitudes of each channel. This HSVDxDyImageType must match the hsvDxDyImage provided below
typedef LinearSearchBestLidarHSVTextureGradientWithSort<ImagePatchDescriptorMapType, HSVDxDyImageType,
VertexDescriptorVectorIteratorType, RGBImageType> BestSearchType; // Use the concatenated histograms of the gradient magnitudes of each channel. This HSVDxDyImageType must match the hsvDxDyImage provided below. Also sort the patches for demonstrative output purposes.
// BestSearchType linearSearchBest(imagePatchDescriptorMap, hsvDxDyImage.GetPointer(), mask); // use non-blurred for texture sorting
Debug bestSearchTypeDebug;
bestSearchTypeDebug.SetDebugScreenOutputs(true);
// bestSearchTypeDebug.SetDebugImages(true);
// linearSearchBest.SetDebugOutputs(true);
// linearSearchBest.SetDebugImages(true);
// use slightly blurred for texture sorting
BestSearchType linearSearchBest(imagePatchDescriptorMap, slightlyBlurredHSVDxDyImage.GetPointer(),
mask, rgbImage.GetPointer(), bestSearchTypeDebug);
// linearSearchBest.SetDebugImages(false);
linearSearchBest.SetDebugImages(true); // This produces BestPatch* images showing the list of the top K patches that were passed to the BestSearch functor
// Setup the two step neighbor finder
TwoStepNearestNeighbor<KNNSearchType, BestSearchType>
twoStepNearestNeighbor(linearSearchKNN, linearSearchBest);
// #define DFullSearch // comment/uncomment this line to set the search region
#ifdef DFullSearch
// Perform the inpainting (full search)
InpaintingAlgorithm(graph, inpaintingVisitor, &boundaryNodeQueue,
twoStepNearestNeighbor, &inpainter);
#else
NeighborhoodSearch<VertexDescriptorType, ImagePatchDescriptorMapType> neighborhoodSearch(originalImage->GetLargestPossibleRegion(),
searchRadius, imagePatchDescriptorMap);
// Perform the inpainting (local search)
bool algorithmDebug = true;
InpaintingAlgorithmWithLocalSearch(graph, inpaintingVisitor, &boundaryNodeQueue,
twoStepNearestNeighbor, &inpainter, neighborhoodSearch, algorithmDebug);
#endif
}
int main(int argc, char *argv[])
{
if(argc != 3)
{
std::cerr << "Required arguments: image mask" << std::endl;
return EXIT_FAILURE;
}
std::string imageFilename = argv[1];
std::string maskFilename = argv[2];
std::cout << "Reading image: " << imageFilename << std::endl;
std::cout << "Reading mask: " << maskFilename << std::endl;
typedef itk::ImageFileReader<FloatVectorImageType> ImageReaderType;
ImageReaderType::Pointer imageReader = ImageReaderType::New();
imageReader->SetFileName(imageFilename.c_str());
imageReader->Update();
std::cout << "Read image " << imageReader->GetOutput()->GetLargestPossibleRegion() << std::endl;
typedef itk::ImageFileReader<Mask> MaskReaderType;
MaskReaderType::Pointer maskReader = MaskReaderType::New();
maskReader->SetFileName(maskFilename.c_str());
maskReader->Update();
std::cout << "Read mask " << maskReader->GetOutput()->GetLargestPossibleRegion() << std::endl;
// Prepare image
RGBImageType::Pointer rgbImage = RGBImageType::New();
// TODO: update this to the new API
//Helpers::VectorImageToRGBImage(imageReader->GetOutput(), rgbImage);
OutputHelpers::WriteImage(rgbImage.GetPointer(), "Test/TestIsophotes.rgb.mha");
typedef itk::RGBToLuminanceImageFilter< RGBImageType, FloatScalarImageType > LuminanceFilterType;
LuminanceFilterType::Pointer luminanceFilter = LuminanceFilterType::New();
luminanceFilter->SetInput(rgbImage);
luminanceFilter->Update();
FloatScalarImageType::Pointer blurredLuminance = FloatScalarImageType::New();
// Blur with a Gaussian kernel
unsigned int kernelRadius = 5;
MaskOperations::MaskedBlur<FloatScalarImageType>(luminanceFilter->GetOutput(), maskReader->GetOutput(), kernelRadius,
blurredLuminance);
OutputHelpers::WriteImage<FloatScalarImageType>(blurredLuminance, "Test/TestIsophotes.blurred.mha");
//inpainting.ComputeMaskedIsophotes(blurredLuminance, maskReader->GetOutput());
//Helpers::WriteImage<FloatVector2ImageType>(inpainting.GetIsophoteImage(), );
//HelpersOutput::Write2DVectorImage(inpainting.GetIsophoteImage(), "Test/TestIsophotes.isophotes.mha");
itk::Size<2> size;
size.Fill(21);
// Target
itk::Index<2> targetIndex;
targetIndex[0] = 187;
targetIndex[1] = 118;
itk::ImageRegion<2> targetRegion(targetIndex, size);
// Source
itk::Index<2> sourceIndex;
sourceIndex[0] = 176;
sourceIndex[1] = 118;
itk::ImageRegion<2> sourceRegion(sourceIndex, size);
//PatchPair patchPair(Patch(sourceRegion), Patch(targetRegion));
//PatchPair patchPair;
// Patch sourcePatch(sourceRegion);
// Patch targetPatch(targetRegion);
// PatchPair patchPair(sourcePatch, targetPatch);
//inpainting.FindBoundary();
// std::vector<itk::Index<2> > borderPixels =
// ITKHelpers::GetNonZeroPixels(inpainting.GetBoundaryImage(), targetRegion);
itk::RGBPixel<unsigned char> black;
black.SetRed(0);
black.SetGreen(0);
black.SetBlue(0);
itk::RGBPixel<unsigned char> red;
red.SetRed(255);
red.SetGreen(0);
red.SetBlue(0);
itk::RGBPixel<unsigned char> darkRed;
darkRed.SetRed(100);
darkRed.SetGreen(0);
darkRed.SetBlue(0);
itk::RGBPixel<unsigned char> yellow;
yellow.SetRed(255);
yellow.SetGreen(255);
yellow.SetBlue(0);
itk::RGBPixel<unsigned char> green;
green.SetRed(0);
green.SetGreen(255);
green.SetBlue(0);
itk::RGBPixel<unsigned char> darkGreen;
darkGreen.SetRed(0);
darkGreen.SetGreen(100);
darkGreen.SetBlue(0);
itk::RGBPixel<unsigned char> blue;
blue.SetRed(0);
blue.SetGreen(0);
blue.SetBlue(255);
RGBImageType::Pointer output = RGBImageType::New();
output->SetRegions(imageReader->GetOutput()->GetLargestPossibleRegion());
output->Allocate();
output->FillBuffer(black);
ITKHelpers::BlankAndOutlineRegion(output.GetPointer(), targetRegion, black, red);
ITKHelpers::BlankAndOutlineRegion(output.GetPointer(), sourceRegion, black, green);
RGBImageType::Pointer target = RGBImageType::New();
target->SetRegions(imageReader->GetOutput()->GetLargestPossibleRegion());
target->Allocate();
ITKHelpers::BlankAndOutlineRegion(target.GetPointer(), targetRegion, black, red);
RGBImageType::Pointer source = RGBImageType::New();
source->SetRegions(imageReader->GetOutput()->GetLargestPossibleRegion());
source->Allocate();
ITKHelpers::BlankAndOutlineRegion(source.GetPointer(), sourceRegion, black, green);
// itk::Offset<2> offset = targetIndex - sourceIndex;
/*
for(unsigned int pixelId = 0; pixelId < borderPixels.size(); ++pixelId)
{
itk::Index<2> targetPatchSourceSideBoundaryPixel = borderPixels[pixelId];
itk::Index<2> sourcePatchTargetSideBoundaryPixel;
//bool valid = GetAdjacentBoundaryPixel(currentPixel, candidatePairs[sourcePatchId], adjacentBoundaryPixel);
bool valid = inpainting.GetAdjacentBoundaryPixel(targetPatchSourceSideBoundaryPixel, patchPair, sourcePatchTargetSideBoundaryPixel);
target->SetPixel(targetPatchSourceSideBoundaryPixel, darkRed);
source->SetPixel(sourcePatchTargetSideBoundaryPixel, darkGreen);
if(!valid)
{
continue;
}
// Bring the adjacent pixel back to the target region.
itk::Index<2> targetPatchTargetSideBoundaryPixel = sourcePatchTargetSideBoundaryPixel + offset;
output->SetPixel(targetPatchSourceSideBoundaryPixel, darkRed);
output->SetPixel(targetPatchTargetSideBoundaryPixel, blue);
output->SetPixel(sourcePatchTargetSideBoundaryPixel, darkGreen);
}
*/
// OutputHelpers::WriteImage(output.GetPointer(), "Test/FollowIsophotes.Output.mha");
// OutputHelpers::WriteImage(target.GetPointer(), "Test/FollowIsophotes.Target.mha");
// OutputHelpers::WriteImage(source.GetPointer(), "Test/FollowIsophotes.Source.mha");
return EXIT_SUCCESS;
}
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;
}
int main(int argc, char *argv[])
{
if(argc != 3)
{
std::cerr << "Required arguments: image mask" << std::endl;
return EXIT_FAILURE;
}
std::string imageFilename = argv[1];
std::string maskFilename = argv[2];
std::cout << "Reading image: " << imageFilename << std::endl;
std::cout << "Reading mask: " << maskFilename << std::endl;
typedef itk::ImageFileReader<FloatVectorImageType> ImageReaderType;
ImageReaderType::Pointer imageReader = ImageReaderType::New();
imageReader->SetFileName(imageFilename.c_str());
imageReader->Update();
std::cout << "Read image " << imageReader->GetOutput()->GetLargestPossibleRegion() << std::endl;
typedef itk::ImageFileReader<Mask> MaskReaderType;
MaskReaderType::Pointer maskReader = MaskReaderType::New();
maskReader->SetFileName(maskFilename.c_str());
maskReader->Update();
std::cout << "Read mask " << maskReader->GetOutput()->GetLargestPossibleRegion() << std::endl;
// Prepare image
RGBImageType::Pointer rgbImage = RGBImageType::New();
// Helpers::VectorImageToRGBImage(imageReader->GetOutput(), rgbImage);
// TODO: Update this call to new API
//maskReader->GetOutput()->ApplyToImage(rgbImage.GetPointer(), Qt::black);
ITKHelpers::WriteImage(rgbImage.GetPointer(), "Test/TestIsophotes.rgb.mha");
typedef itk::RGBToLuminanceImageFilter< RGBImageType, FloatScalarImageType > LuminanceFilterType;
LuminanceFilterType::Pointer luminanceFilter = LuminanceFilterType::New();
luminanceFilter->SetInput(rgbImage);
luminanceFilter->Update();
ITKHelpers::WriteImage(luminanceFilter->GetOutput(), "Test/Luminance.mha");
// PatchBasedInpainting inpainting;
// inpainting.SetDebugImages(true);
// inpainting.SetMask(maskReader->GetOutput());
// inpainting.SetImage(imageReader->GetOutput());
//Helpers::Write2DVectorImage(inpainting.GetIsophoteImage(), "Test/TestIsophotes.isophotes.mha");
//inpainting.FindBoundary();
// After blurVariance == 4, you cannot tell the difference in the output.
for(unsigned int blurVariance = 0; blurVariance < 5; ++blurVariance)
{
std::string fileNumber = Helpers::ZeroPad(blurVariance, 2);
FloatScalarImageType::Pointer blurredLuminance = FloatScalarImageType::New();
// Blur with a Gaussian kernel
MaskOperations::MaskedBlur(luminanceFilter->GetOutput(), maskReader->GetOutput(),
blurVariance, blurredLuminance.GetPointer());
std::stringstream ssBlurredLuminance;
ssBlurredLuminance << "Test/BlurredLuminance_" << fileNumber << ".mha";
ITKHelpers::WriteImage(blurredLuminance.GetPointer(), ssBlurredLuminance.str());
//Helpers::WriteImage<FloatScalarImageType>(blurredLuminance, "Test/TestIsophotes.blurred.mha");
FloatVector2ImageType::Pointer gradient = FloatVector2ImageType::New();
Derivatives::MaskedGradient(blurredLuminance.GetPointer(), maskReader->GetOutput(), gradient.GetPointer());
// Boundary gradient
typedef itk::MaskImageFilter< FloatVector2ImageType, UnsignedCharScalarImageType, FloatVector2ImageType > MaskFilterType;
MaskFilterType::Pointer maskFilter = MaskFilterType::New();
maskFilter->SetInput(gradient);
//maskFilter->SetMaskImage(inpainting.GetBoundaryImage());
maskFilter->Update();
vtkSmartPointer<vtkPolyData> boundaryGradient = vtkSmartPointer<vtkPolyData>::New();
// TODO: Convert this call to new API
//Helpers::ConvertNonZeroPixelsToVectors(maskFilter->GetOutput(), boundaryGradient);
std::stringstream ssPolyData;
ssPolyData << "Test/BoundaryGradient_" << fileNumber << ".vtp";
VTKHelpers::WritePolyData(boundaryGradient, ssPolyData.str());
}
return EXIT_SUCCESS;
}