ScalarImageType::Pointer loadScalarImage(const std::string& filename) {
itk::ImageFileReader<ScalarImageType>::Pointer reader = itk::ImageFileReader<ScalarImageType>::New();
reader->SetFileName(filename);
reader->Update();
ScalarImageType::Pointer img = reader->GetOutput();
img->DisconnectPipeline();
return img;
}
WeightedLeastSquares::ImageListType WeightedLeastSquares::ComputeDifferenceImage(ImageListType PredImageList)
{
ImageListType DifferenceImageList;
int numOfImages = m_DWIListHR.size();
for (int i=0; i < numOfImages; i++)
{
SubtractImageFilterType::Pointer subtractImageFilter = SubtractImageFilterType::New();
subtractImageFilter->SetInput1(m_DWIListHR[i]);
subtractImageFilter->SetInput2(PredImageList[i]);
subtractImageFilter->Update();
ScalarImageType::Pointer diffImage = subtractImageFilter->GetOutput();
diffImage->DisconnectPipeline();
DifferenceImageList.push_back(diffImage);
}
return DifferenceImageList;
}
void LidarSegmentationWidget::on_action_View_DepthImage_triggered()
{
//Helpers::ITKImageChannelToVTKImage(thresholdFilter->GetOutput(), 3, this->OriginalImageData);
typedef itk::Image<ImageType::InternalPixelType, 2> ScalarImageType;
ScalarImageType::Pointer depthImage = ScalarImageType::New();
ITKHelpers::ExtractChannel(this->Image.GetPointer(), 3, depthImage.GetPointer());
typedef itk::ThresholdImageFilter<ScalarImageType> ThresholdImageFilterType;
float maxDepth = 20.0f;
ThresholdImageFilterType::Pointer thresholdFilter = ThresholdImageFilterType::New();
thresholdFilter->SetInput(depthImage);
thresholdFilter->ThresholdAbove(maxDepth);
thresholdFilter->SetOutsideValue(maxDepth);
thresholdFilter->Update();
ITKVTKHelpers::ITKScalarImageToScaledVTKImage(thresholdFilter->GetOutput(), this->OriginalImageData);
Refresh();
}
int testRepresenterForScalarImage(const std::string& datadir) {
typedef itk::StandardImageRepresenter<float, 2> RepresenterType;
typedef GenericRepresenterTest<RepresenterType> RepresenterTestType;
const std::string referenceFilename = datadir + "/hand_images/hand-1.vtk";
const std::string testDatasetFilename = datadir + "/hand_images/hand-2.vtk";
RepresenterType::Pointer representer = RepresenterType::New();
ScalarImageType::Pointer reference = loadScalarImage(referenceFilename);
representer->SetReference(reference);
// choose a test dataset, a point and its associate pixel value
ScalarImageType::Pointer testDataset = loadScalarImage(testDatasetFilename);
ScalarImageType::IndexType idx;
idx.Fill(0);
ScalarImageType::PointType testPt;
reference->TransformIndexToPhysicalPoint(idx, testPt);
ScalarImageType::PixelType testValue = testDataset->GetPixel(idx);
RepresenterTestType representerTest(representer, testDataset, std::make_pair(testPt, testValue));
return (representerTest.runAllTests() == true);
}
int main (int argc, char *argv[])
{
const unsigned int ImageDimension = 2;
GetPot cl (argc, const_cast<char**>(argv));
if( cl.size() == 1 || cl.search (2,"--help","-h") )
{
std::cout << "Not Enough Arguments" << std::endl;
std::cout << "Generate the Gradient Table" << std::endl;
std::cout << "Usage: return -1" << std::endl;
}
const string image_n = cl.follow("NoFile",1, "-i");
const string mask_n = cl.follow("NoFile", 1, "-m");
const string out_n = cl.follow("NoFile",1, "-o");
typedef itk::DiffusionTensor3D<float> DiffusionTensorType;
typedef itk::Image<DiffusionTensorType, 3> TensorImageType;
typedef itk::ImageFileReader<TensorImageType> TensorReaderType;
TensorReaderType::Pointer reader = TensorReaderType::New();
reader->SetFileName(image_n.c_str());
reader->Update();
TensorImageType::Pointer image = reader->GetOutput();
typedef itk::Image<float, 3> ScalarImageType;
typedef itk::ImageFileReader<ScalarImageType> ScalarReaderType;
ScalarReaderType::Pointer scalarReader = ScalarReaderType::New();
scalarReader->SetFileName(mask_n.c_str());
scalarReader->Update();
ScalarImageType::Pointer maskImage = scalarReader->GetOutput();
typedef itk::ImageRegionIterator<TensorImageType> TensorIterator;
typedef itk::ImageRegionIterator<ScalarImageType> ScalarIterator;
ScalarIterator itMask(maskImage, maskImage->GetLargestPossibleRegion());
TensorUtilities utilsTensor;
TensorImageType::Pointer logTensorImage = utilsTensor.LogTensorImageFilter(image, maskImage);
typedef itk::ImageFileWriter<TensorImageType> TensorImageWriterType;
TensorImageWriterType::Pointer tensorImageWriter = TensorImageWriterType::New();
tensorImageWriter->SetFileName("LogTensorImage_stupid.nii.gz");
tensorImageWriter->SetInput(logTensorImage);
tensorImageWriter->Update();
std::ofstream file;
file.open(out_n);
ScalarImageType::Pointer TraceImage = ScalarImageType::New();
CopyImage cpImage;
cpImage.CopyScalarImage(maskImage, TraceImage);
ScalarIterator itTr(TraceImage, TraceImage->GetLargestPossibleRegion());
TensorIterator itImg(logTensorImage, logTensorImage->GetLargestPossibleRegion());
for(itImg.GoToBegin(), itMask.GoToBegin(), itTr.GoToBegin(); !itTr.IsAtEnd(), !itImg.IsAtEnd(), !itMask.IsAtEnd(); ++itTr, ++itImg, ++itMask)
{
file << itImg.Get().GetTrace() << std::endl;
itTr.Set(itImg.Get().GetTrace()) ;
}
typedef itk::ImageFileWriter<ScalarImageType> WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName("LogTense_Trace.nii.gz");
writer->SetInput(TraceImage);
writer->Update();
file.close();
return 0;
}
int main(int argc, char *argv[])
{
GetPot cl(argc, const_cast<char**>(argv));
const string tensorImage_n = cl.follow("NoFile", 1, "-i");
const string outImage_n = cl.follow("NoFile",1, "-o");
const string maskImage_n = cl.follow("NoFile",1,"-m");
typedef itk::DiffusionTensor3D<float> DiffusionTensorType;
typedef itk::Image<DiffusionTensorType, 3> TensorImageType;
typedef itk::ImageFileReader<TensorImageType> TensorReaderType;
typedef itk::ImageFileWriter<TensorImageType> TensorWriterType;
TensorReaderType::Pointer tensorReader = TensorReaderType::New();
tensorReader->SetFileName(tensorImage_n.c_str());
tensorReader->Update();
TensorImageType::Pointer tensorImage = tensorReader->GetOutput();
typedef itk::Image<float, 3> ScalarImageType;
typedef itk::ImageFileReader<ScalarImageType> ScalarImageReaderType;
ScalarImageReaderType::Pointer scalarImageReader = ScalarImageReaderType::New();
scalarImageReader->SetFileName(maskImage_n.c_str());
scalarImageReader->Update();
ScalarImageType::Pointer maskImage = scalarImageReader->GetOutput();
TensorUtilities utilsTensor;
TensorImageType::Pointer tensor_replace_Nans = utilsTensor.ReplaceNaNsReverseEigenValue(tensorImage, maskImage);
TensorImageType::Pointer log_tensorImage = utilsTensor.LogTensorImageFilter(tensor_replace_Nans, maskImage);
TensorImageType::Pointer removed_nans_logTensorImage= utilsTensor.ReplaceNaNsInfs(log_tensorImage, maskImage);
typedef itk::ImageRegionIterator<TensorImageType> TensorIterator;
typedef itk::ImageRegionIterator<ScalarImageType> ScalarIterator;
TensorIterator itTens(removed_nans_logTensorImage, removed_nans_logTensorImage->GetLargestPossibleRegion());
ScalarIterator itMask(maskImage, maskImage->GetLargestPossibleRegion());
for (itMask.GoToBegin(), itTens.GoToBegin(); !itMask.IsAtEnd(), !itTens.IsAtEnd();
++itMask, ++itTens)
{
if (itMask.Get() !=0)
{
float Trace = itTens.Get().GetTrace();
if ( (isnan(Trace) == 1 ) || (isinf(Trace) == 1) )
{
std::cout << itMask.GetIndex() << std::endl;
}
}
}
std::cout << "Checking done " << std::endl;
TensorImageType::Pointer expedTensor = utilsTensor.ExpTensorImageFilter(removed_nans_logTensorImage, maskImage);
typedef itk::ImageFileWriter<TensorImageType> TensorWriterType;
TensorWriterType::Pointer tensorWriter = TensorWriterType::New();
tensorWriter->SetFileName(outImage_n.c_str());
tensorWriter->SetInput(expedTensor);
tensorWriter->Update();
return 0;
}