void LabelsVolumeGenerator::postProcessTargetITK()
{
typedef unsigned char PixelType;
typedef Image<PixelType, 3> ImageType;
// create a new image from the target data
ImageType::Pointer input = ImageType::New();
ImageType::IndexType start;
start.Fill(0);
ImageType::SizeType size;
for (int i = 0; i < 3; ++i) size[i] = m_targetVolume->dimensions[i];
ImageType::RegionType region;
region.SetSize(size);
region.SetIndex(start);
input->SetRegions(region);
input->SetSpacing(m_targetVolume->spacing.data());
input->Allocate();
memcpy(input->GetBufferPointer(), m_targetVolume->data, m_bufferSize);
// create a grayscale dilation filter and a structuring element
typedef BinaryBallStructuringElement<PixelType, 3> StructureType;
typedef GrayscaleDilateImageFilter<ImageType, ImageType, StructureType> DilateFilterType;
DilateFilterType::Pointer filter = DilateFilterType::New();
StructureType structure;
structure.SetRadius(1);
filter->SetKernel(structure);
// set up progress reporting
if (m_progressReporter)
{
CStyleCommand::Pointer command = CStyleCommand::New();
command->SetClientData(m_progressReporter);
command->SetCallback(ProgressCallback);
filter->AddObserver(ProgressEvent(), command);
m_progressReporter->start("Post-Processing Label volume",
"Dilating label field...");
}
// hook up the filters and run
filter->SetInput(input);
filter->Update();
if (m_progressReporter)
m_progressReporter->finish();
// copy back into the target volume data
memcpy(m_targetVolume->data, filter->GetOutput()->GetBufferPointer(), m_bufferSize);
// threshold and gaussian blur to put a smooth version into the alpha channel
typedef BinaryThresholdImageFilter<ImageType, ImageType> ThresholderType;
// typedef DiscreteGaussianImageFilter<ImageType, ImageType> SmoothFilterType;
typedef SmoothingRecursiveGaussianImageFilter<ImageType, ImageType> SmoothFilterType;
ThresholderType::Pointer thresholder = ThresholderType::New();
thresholder->SetLowerThreshold(1);
thresholder->SetUpperThreshold(255);
thresholder->SetInsideValue(255);
thresholder->SetOutsideValue(0);
SmoothFilterType::Pointer smoother = SmoothFilterType::New();
// smoother->SetVariance(0.05); // in physical units
// smoother->SetMaximumKernelWidth(5);
smoother->SetSigma(0.2);
// set up progress reporting (again)
if (m_progressReporter)
{
CStyleCommand::Pointer command = CStyleCommand::New();
command->SetClientData(m_progressReporter);
command->SetCallback(ProgressCallback);
smoother->AddObserver(ProgressEvent(), command);
m_progressReporter->start("Post-Processing Label volume",
"Smoothing alpha mask...");
}
// hook up the filters and run
thresholder->SetInput(input);
smoother->SetInput(thresholder->GetOutput());
smoother->Update();
// copy back into the target volume data
memcpy(m_targetMask->data, smoother->GetOutput()->GetBufferPointer(), m_bufferSize);
if (m_progressReporter)
m_progressReporter->finish();
}
int main(int, char ** argv)
{
// load the input nifti image
std::string inputFolderName = argv[1];
std::string outputFilename = argv[2];
// get the set of images from the input folder
QStringList nameFilters;
nameFilters << "phiContour*_t=*_final.nii";
QDir inputFolder(QString::fromStdString(inputFolderName));
QStringList inputFiles = inputFolder.entryList(nameFilters);
unsigned int numTimeSteps = inputFiles.size();
qSort(inputFiles.begin(), inputFiles.end(), file_sort);
std::cout << "--> Found " << numTimeSteps << " segmentations" << std::endl;
std::cout << "--> Loading images and thresholding " << std::endl;
utils::LabelVolumeList labels;
for(unsigned int i = 0; i < numTimeSteps; i++)
{
std::cout << "\t" << inputFiles[i].toStdString() << std::endl;
typedef itk::Image<float,3> InputImageType;
typedef itk::ImageFileReader<InputImageType> ReaderType;
std::string filename = inputFolderName + "/" + inputFiles[i].toStdString();
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(filename);
reader->SetImageIO(itk::NiftiImageIO::New());
reader->Update();
typedef itk::BinaryThresholdImageFilter<InputImageType, utils::LabelVolume> ThresholderType;
ThresholderType::Pointer thresholder = ThresholderType::New();
thresholder->SetInput(reader->GetOutput());
thresholder->SetOutsideValue(0);
thresholder->SetInsideValue(1);
thresholder->SetLowerThreshold(0);
thresholder->SetUpperThreshold(255);
thresholder->Update();
labels.push_back(thresholder->GetOutput());
}
// build the output image
typedef itk::Image<unsigned char, 4> OutputType;
OutputType::Pointer output = OutputType::New();
typedef itk::JoinSeriesImageFilter<utils::LabelVolume, OutputType> JoinerType;
JoinerType::Pointer joiner = JoinerType::New();
joiner->SetSpacing(1.0);
joiner->SetOrigin(0);
for(unsigned int i = 0; i < labels.size(); i++)
{
joiner->SetInput(i, labels[i]);
}
joiner->Update();
output = joiner->GetOutput();
// save the output
typedef itk::ImageFileWriter<OutputType> WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetInput(output);
writer->SetFileName(outputFilename);
writer->Update();
/*
utils::LabelVolume::Pointer ref = labels[0];
OutputType::SpacingType outSpacing;
OutputType::DirectionType outDirection;
outDirection.SetIdentity();
OutputType::PointType outOrigin;
for(unsigned int i = 0; i < 3; i++)
{
outSpacing[i] = ref->GetSpacing()[i];
outOrigin[i] = ref->GetOrigin()[i];
}
return 0;
utils::LabelVolumeIO::Write(outputFilename, thresholder->GetOutput());
*/
return 0;
}