static void EnsureDataImageInCollection(mitk::DataCollection::Pointer collection, std::string origin, std::string target)
{
typedef itk::Image<double, 3> FeatureImage;
if (collection->HasElement(origin))
{
mitk::Image::Pointer originImage = dynamic_cast<mitk::Image*>(collection->GetMitkImage(origin).GetPointer());
FeatureImage::Pointer itkOriginImage = FeatureImage::New();
mitk::CastToItkImage(originImage,itkOriginImage);
if (!collection->HasElement(target) && itkOriginImage.IsNotNull())
{
FeatureImage::Pointer image = FeatureImage::New();
image->SetRegions(itkOriginImage->GetLargestPossibleRegion());
image->SetSpacing(itkOriginImage->GetSpacing());
image->SetOrigin(itkOriginImage->GetOrigin());
image->SetDirection(itkOriginImage->GetDirection());
image->Allocate();
collection->AddData(dynamic_cast<itk::DataObject*>(image.GetPointer()),target,"");
}
}
for (std::size_t i = 0; i < collection->Size();++i)
{
mitk::DataCollection* newCol = dynamic_cast<mitk::DataCollection*>(collection->GetData(i).GetPointer());
if (newCol != 0)
{
EnsureDataImageInCollection(newCol, origin, target);
}
}
}
int main(int argc, char *argv[])
{
mitkCommandLineParser parser;
parser.setTitle("Mri Normalization");
parser.setCategory("Preprocessing Tools");
parser.setDescription(
"Normalizes an MRI volume between medians of two given masks (e.g. ventricles and brain matter)");
parser.setContributor("MBI");
parser.setArgumentPrefix("--", "-");
// Add command line argument names
parser.addArgument("input", "i", mitkCommandLineParser::Image, "input image", "", us::Any(), false, false, false, mitkCommandLineParser::Input);
parser.addArgument("output", "o", mitkCommandLineParser::File, "output image", "", us::Any(), false, false, false, mitkCommandLineParser::Output);
parser.addArgument(
"maxMask", "m", mitkCommandLineParser::Image, "mask of which median is set as maximal value (1)", "", us::Any(), false, false, false, mitkCommandLineParser::Input);
parser.addArgument(
"minMask", "l", mitkCommandLineParser::Image, "mask of which median is set as minimal value (0)", "", us::Any(), false, false, false, mitkCommandLineParser::Input);
parser.addArgument(
"excludeMask", "e", mitkCommandLineParser::Image, "region which is exluded from the other two", "", us::Any(), false, false, false, mitkCommandLineParser::Input);
map<string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
// Show a help message
if (parsedArgs.size() == 0 || parsedArgs.count("help") || parsedArgs.count("h"))
{
std::cout << parser.helpText();
return EXIT_SUCCESS;
}
std::string outFile = us::any_cast<string>(parsedArgs["output"]);
mitk::Image::Pointer inputFile = mitk::IOUtil::Load<mitk::Image>(us::any_cast<string>(parsedArgs["input"]));
mitk::Image::Pointer maxMask = mitk::IOUtil::Load<mitk::Image>(us::any_cast<string>(parsedArgs["maxMask"]));
mitk::Image::Pointer minMask = mitk::IOUtil::Load<mitk::Image>(us::any_cast<string>(parsedArgs["minMask"]));
mitk::Image::Pointer excludeMask = mitk::IOUtil::Load<mitk::Image>(us::any_cast<string>(parsedArgs["excludeMask"]));
SeedImage::Pointer itkMaxImage = SeedImage::New();
SeedImage::Pointer itkMinImage = SeedImage::New();
SeedImage::Pointer itkExcludeImage = SeedImage::New();
FeatureImage::Pointer itkInputImage = FeatureImage::New();
mitk::CastToItkImage(inputFile, itkInputImage);
mitk::CastToItkImage(maxMask, itkMaxImage);
mitk::CastToItkImage(minMask, itkMinImage);
mitk::CastToItkImage(excludeMask, itkExcludeImage);
std::vector<mitk::ScalarType> medianMin;
std::vector<mitk::ScalarType> medianMax;
itk::ImageRegionIterator<FeatureImage> inputIt(itkInputImage, itkInputImage->GetLargestPossibleRegion());
itk::ImageRegionIterator<SeedImage> excludeIt(itkExcludeImage, itkExcludeImage->GetLargestPossibleRegion());
itk::ImageRegionIterator<SeedImage> minIt(itkMinImage, itkMinImage->GetLargestPossibleRegion());
itk::ImageRegionIterator<SeedImage> maxIt(itkMaxImage, itkMaxImage->GetLargestPossibleRegion());
while (!inputIt.IsAtEnd())
{
if (excludeIt.Get() == 0)
{
if (minIt.Get() != 0)
medianMin.push_back(inputIt.Get());
if (maxIt.Get() != 0)
medianMax.push_back(inputIt.Get());
}
++inputIt;
++excludeIt;
++minIt;
++maxIt;
}
std::sort(medianMax.begin(), medianMax.end());
std::sort(medianMin.begin(), medianMin.end());
mitk::ScalarType minVal = medianMin.at(medianMin.size() / 2);
mitk::ScalarType maxVal = medianMax.at(medianMax.size() / 2);
inputIt.GoToBegin();
// Create mapping
while (!inputIt.IsAtEnd())
{
inputIt.Set(1.0 * (inputIt.Get() - minVal) / (maxVal - minVal));
++inputIt;
}
mitk::Image::Pointer mitkResult = mitk::Image::New();
mitkResult = mitk::GrabItkImageMemory(itkInputImage);
mitk::IOUtil::Save(mitkResult, outFile);
return EXIT_SUCCESS;
}
int main(int argc, char *argv[])
{
mitkCommandLineParser parser;
parser.setTitle("Mri Normalization");
parser.setCategory("Preprocessing Tools");
parser.setDescription("Normalizes an MRI volume based on regions determined by Otsu.");
parser.setContributor("MBI");
parser.setArgumentPrefix("--", "-");
// Add command line argument names
parser.addArgument("input", "i", mitkCommandLineParser::InputImage, "input image", "input image");
parser.addArgument("output", "o", mitkCommandLineParser::OutputFile, "output image", "output image");
parser.addArgument("bins", "b", mitkCommandLineParser::Int, "number of regions (bins)", "number of regions (bins)");
parser.addArgument(
"minBin", "l", mitkCommandLineParser::Int, "bin of which median is set to 0", "bin of which median is set to 0");
parser.addArgument(
"maxBin", "h", mitkCommandLineParser::Int, "bin of which median is set to 1", "bin of which median is set to 1");
map<string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
// Show a help message
if (parsedArgs.size() == 0 || parsedArgs.count("help") || parsedArgs.count("h"))
{
std::cout << parser.helpText();
return EXIT_SUCCESS;
}
std::string outFile = us::any_cast<string>(parsedArgs["output"]);
mitk::Image::Pointer inputFile = mitk::IOUtil::Load<mitk::Image>(us::any_cast<string>(parsedArgs["input"]));
int numberOfThresholds = us::any_cast<int>(parsedArgs["bins"]);
int minBin = us::any_cast<int>(parsedArgs["minBin"]);
int maxBin = us::any_cast<int>(parsedArgs["maxBin"]);
FeatureImage::Pointer itkInputImage = FeatureImage::New();
mitk::CastToItkImage(inputFile, itkInputImage);
typedef itk::OtsuMultipleThresholdsImageFilter<FeatureImage, FeatureImage> FilterType;
FilterType::Pointer otsuFilter = FilterType::New();
otsuFilter->SetInput(itkInputImage);
otsuFilter->SetNumberOfThresholds(numberOfThresholds - 1);
otsuFilter->Update();
FeatureImage::Pointer itkLabelImage = otsuFilter->GetOutput();
std::vector<mitk::ScalarType> medianMin;
std::vector<mitk::ScalarType> medianMax;
itk::ImageRegionIterator<FeatureImage> inputIt(itkInputImage, itkInputImage->GetLargestPossibleRegion());
itk::ImageRegionIterator<FeatureImage> labelIt(itkLabelImage, itkLabelImage->GetLargestPossibleRegion());
while (!inputIt.IsAtEnd())
{
if (labelIt.Get() == minBin)
{
medianMin.push_back(inputIt.Get());
}
else if (labelIt.Get() == maxBin)
{
medianMax.push_back(inputIt.Get());
}
++inputIt;
++labelIt;
}
std::sort(medianMax.begin(), medianMax.end());
std::sort(medianMin.begin(), medianMin.end());
mitk::ScalarType minVal = medianMin.at(medianMin.size() / 2);
mitk::ScalarType maxVal = medianMax.at(medianMax.size() / 2);
inputIt.GoToBegin();
// labelIt.GoToBegin();
// Create mapping
while (!inputIt.IsAtEnd())
{
inputIt.Set(1.0 * (inputIt.Get() - minVal) / (maxVal - minVal));
// inputIt.Set(labelIt.Get());
++inputIt;
//++labelIt;
}
mitk::Image::Pointer mitkResult = mitk::Image::New();
mitkResult = mitk::GrabItkImageMemory(itkInputImage);
mitk::IOUtil::Save(mitkResult, outFile);
return EXIT_SUCCESS;
}