void TDimImage::fromItkImage( const ImageType *image ) {
ImageType::RegionType region;
region = image->GetBufferedRegion();
ImageType::SizeType size = region.GetSize();
ImageType::IndexType start = region.GetIndex();
unsigned int nx = size[0];
unsigned int ny = size[1];
// allocate this image
if (this->alloc( nx, ny, 1, sizeof(PixelType))<=0) return;
// copy data
typedef itk::ImageRegionConstIterator< ImageType > IteratorType;
IteratorType it( image, region );
it.GoToBegin();
const PixelType *data = (PixelType *) this->sampleBits(0);
while( !it.IsAtEnd() ) {
*data = it.Get();
++it;
++data;
}
}
void mitk::AutoCropImageFilter::ComputeNewImageBounds()
{
mitk::Image::ConstPointer inputMitk = this->GetInput();
if (m_OverrideCroppingRegion)
{
for (unsigned int i=0; i<3; ++i)
{
m_RegionIndex[i] = m_CroppingRegion.GetIndex()[i];
m_RegionSize[i] = m_CroppingRegion.GetSize()[i];
if (m_RegionIndex[i] >= inputMitk->GetDimension(i))
{
itkExceptionMacro("Cropping index is not inside the image. "
<< std::endl << "Index:"
<< std::endl << m_CroppingRegion.GetIndex()
<< std::endl << "Size:"
<< std::endl << m_CroppingRegion.GetSize());
}
if (m_RegionIndex[i] + m_RegionSize[i] >= inputMitk->GetDimension(i))
{
m_RegionSize[i] = inputMitk->GetDimension(i) - m_RegionIndex[i];
}
}
for (unsigned int i=0; i<3; ++i)
{
m_RegionIndex[i] = m_CroppingRegion.GetIndex()[i];
m_RegionSize[i] = m_CroppingRegion.GetSize()[i];
}
}
else
{
// Check if a 3D or 4D image is present
unsigned int timeSteps = 1;
if (inputMitk->GetDimension() == 4 )
timeSteps = inputMitk->GetDimension(3);
ImageType::IndexType minima,maxima;
if (inputMitk->GetDimension() == 4)
{
// initialize with time step 0
m_TimeSelector = mitk::ImageTimeSelector::New();
m_TimeSelector->SetInput( inputMitk );
m_TimeSelector->SetTimeNr( 0 );
m_TimeSelector->UpdateLargestPossibleRegion();
inputMitk = m_TimeSelector->GetOutput();
}
ImagePointer inputItk = ImageType::New();
mitk::CastToItkImage( inputMitk , inputItk );
// it is assumed that all volumes in a time series have the same 3D dimensions
ImageType::RegionType origRegion = inputItk->GetLargestPossibleRegion();
// Initialize min and max on the first (or only) time step
maxima = inputItk->GetLargestPossibleRegion().GetIndex();
minima[0] = inputItk->GetLargestPossibleRegion().GetSize()[0];
minima[1] = inputItk->GetLargestPossibleRegion().GetSize()[1];
minima[2] = inputItk->GetLargestPossibleRegion().GetSize()[2];
typedef itk::ImageRegionConstIterator< ImageType > ConstIteratorType;
for(unsigned int idx = 0; idx < timeSteps; ++idx)
{
// if 4D image, update time step and itk image
if( idx > 0)
{
m_TimeSelector->SetTimeNr( idx );
m_TimeSelector->UpdateLargestPossibleRegion();
inputMitk = m_TimeSelector->GetOutput();
mitk::CastToItkImage( inputMitk , inputItk );
}
ConstIteratorType inIt( inputItk, origRegion );
for ( inIt.GoToBegin(); !inIt.IsAtEnd(); ++inIt)
{
float pix_val = inIt.Get();
if ( fabs(pix_val - m_BackgroundValue) > mitk::eps )
{
for (int i=0; i < 3; i++)
{
minima[i] = vnl_math_min((int)minima[i],(int)(inIt.GetIndex()[i]));
maxima[i] = vnl_math_max((int)maxima[i],(int)(inIt.GetIndex()[i]));
}
}
}
}
typedef ImageType::RegionType::SizeType::SizeValueType SizeValueType;
m_RegionSize[0] = (SizeValueType)(m_MarginFactor * (maxima[0] - minima[0] + 1 ));
m_RegionSize[1] = (SizeValueType)(m_MarginFactor * (maxima[1] - minima[1] + 1 ));
m_RegionSize[2] = (SizeValueType)(m_MarginFactor * (maxima[2] - minima[2] + 1 ));
m_RegionIndex = minima;
m_RegionIndex[0] -= (m_RegionSize[0] - maxima[0] + minima[0] - 1 )/2;
m_RegionIndex[1] -= (m_RegionSize[1] - maxima[1] + minima[1] - 1 )/2;
m_RegionIndex[2] -= (m_RegionSize[2] - maxima[2] + minima[2] - 1 )/2;
ImageType::RegionType cropRegion(m_RegionIndex,m_RegionSize);
origRegion.Crop(cropRegion);
m_RegionSize[0] = origRegion.GetSize()[0];
m_RegionSize[1] = origRegion.GetSize()[1];
m_RegionSize[2] = origRegion.GetSize()[2];
m_RegionIndex[0] = origRegion.GetIndex()[0];
m_RegionIndex[1] = origRegion.GetIndex()[1];
m_RegionIndex[2] = origRegion.GetIndex()[2];
m_CroppingRegion = origRegion;
}
}
virtual ReadResult readImage(const std::string& file, const osgDB::ReaderWriter::Options* options) const
{
std::string ext = osgDB::getLowerCaseFileExtension(file);
if (!acceptsExtension(ext)) return ReadResult::FILE_NOT_HANDLED;
std::string fileName = osgDB::findDataFile( file, options );
if (fileName.empty()) return ReadResult::FILE_NOT_FOUND;
notice()<<"Reading DICOM file "<<fileName<<std::endl;
typedef unsigned short PixelType;
const unsigned int Dimension = 3;
typedef itk::Image< PixelType, Dimension > ImageType;
typedef itk::ImageFileReader< ImageType > ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName( fileName.c_str() );
typedef itk::GDCMImageIO ImageIOType;
ImageIOType::Pointer gdcmImageIO = ImageIOType::New();
reader->SetImageIO( gdcmImageIO );
try
{
reader->Update();
}
catch (itk::ExceptionObject & e)
{
std::cerr << "exception in file reader " << std::endl;
std::cerr << e.GetDescription() << std::endl;
std::cerr << e.GetLocation() << std::endl;
return ReadResult::ERROR_IN_READING_FILE;
}
ImageType::Pointer inputImage = reader->GetOutput();
ImageType::RegionType region = inputImage->GetBufferedRegion();
ImageType::SizeType size = region.GetSize();
ImageType::IndexType start = region.GetIndex();
//inputImage->GetSpacing();
//inputImage->GetOrigin();
unsigned int width = size[0];
unsigned int height = size[1];
unsigned int depth = size[2];
osg::RefMatrix* matrix = new osg::RefMatrix;
notice()<<"width = "<<width<<" height = "<<height<<" depth = "<<depth<<std::endl;
for(unsigned int i=0; i<Dimension; ++i)
{
(*matrix)(i,i) = inputImage->GetSpacing()[i];
(*matrix)(3,i) = inputImage->GetOrigin()[i];
}
osg::Image* image = new osg::Image;
image->allocateImage(width, height, depth, GL_LUMINANCE, GL_UNSIGNED_BYTE, 1);
unsigned char* data = image->data();
typedef itk::ImageRegionConstIterator< ImageType > IteratorType;
IteratorType it(inputImage, region);
it.GoToBegin();
while (!it.IsAtEnd())
{
*data = it.Get();
++data;
++it;
}
image->setUserData(matrix);
matrix->preMult(osg::Matrix::scale(double(image->s()), double(image->t()), double(image->r())));
return image;
}
int main(int, char ** argv)
{
std::string inputFolder = argv[1];
std::string outputFolder = argv[2];
std::string lookupFilename = argv[3];
// load the lookup file and read the image filenames
LookupMap lookup;
FilenamesType imageFilenames;
readFilenames(inputFolder, imageFilenames);
loadLookupFile(lookupFilename, lookup);
// looop through the list of images
for(unsigned int i = 0; i < imageFilenames.size(); i++)
{
std::string fname = imageFilenames[i];
QFileInfo finfo(QString::fromStdString(fname));
std::string basename = finfo.completeBaseName().toStdString() + ".nrrd";
FilenamesType dicomFilenames = lookup[basename];
// slice up the input image to recreate the output
typedef utils::ImageVolume ImageType;
ImageType::Pointer input = utils::ImageVolumeIO::Read(fname);
const unsigned int slices = input->GetLargestPossibleRegion().GetSize()[2];
for(unsigned int slice = 0; slice < slices; slice++)
{
typedef itk::RegionOfInterestImageFilter<ImageType, ImageType> ROIFilter;
ROIFilter::Pointer roiFilter = ROIFilter::New();
roiFilter->SetInput(input);
ImageType::RegionType roi = input->GetLargestPossibleRegion();
ImageType::IndexType roiIndex = roi.GetIndex();
ImageType::SizeType roiSize = roi.GetSize();
roiIndex[2] = slice;
roiSize[2] = 1;
roi.SetSize(roiSize);
roi.SetIndex(roiIndex);
roiFilter->SetRegionOfInterest(roi);
roiFilter->Update();
ImageType::Pointer imSlice = roiFilter->GetOutput();
// load the dicom file
std::string dicomFilename = dicomFilenames[slice];
DcmFileFormat fileFormat;
fileFormat.loadFile(dicomFilename.c_str());
unsigned int numberOfPixels = imSlice->GetLargestPossibleRegion().GetNumberOfPixels();
unsigned short * buffer = new unsigned short[numberOfPixels];
fileFormat.getDataset()->putAndInsertUint16Array(DCM_PixelData, buffer, imSlice->GetLargestPossibleRegion().GetNumberOfPixels());
// reset the pixel values
itk::ImageRegionConstIterator<ImageType> it(imSlice, imSlice->GetLargestPossibleRegion());
unsigned int count = 0;
while(!it.IsAtEnd())
{
buffer[count] = it.Get();
++it; ++count;
}
fileFormat.getDataset()->putAndInsertUint16Array(DCM_PixelData, buffer, imSlice->GetLargestPossibleRegion().GetNumberOfPixels());
// create the output filename
std::stringstream ss;
ss << outputFolder << "/dicom_" << i << "_" << slice << ".dcm";
fileFormat.saveFile(ss.str().c_str());
}
}
return 0;
}
void MyImageClass::SaveDICOMSeries(QString save_path, std::string subfolder)
{
std::string output_directory = save_path.toStdString();
output_directory +=subfolder;
itksys::SystemTools::MakeDirectory( output_directory.c_str() );
typedef signed short OutputPixelType;
const unsigned int output_pixel_dimension = 2;
typedef itk::Image < OutputPixelType, output_pixel_dimension > Image2Dtype;
typedef itk::CastImageFilter<InternalImageType, ImageType> CastFilterType;
typedef itk::ImageSeriesWriter < ImageType, Image2Dtype> SeriesWriterType;
CastFilterType::Pointer caster = CastFilterType::New();
SeriesWriterType::Pointer series_writer = SeriesWriterType::New();
typedef itk::NumericSeriesFileNames NumericNamesGeneratorType;
NumericNamesGeneratorType::Pointer namesGenerator = NumericNamesGeneratorType::New();
itk::MetaDataDictionary &dict = gdcmIO_->GetMetaDataDictionary();
std::string tagkey,value;
tagkey = "0008|0060";
value = "MR";
itk::EncapsulateMetaData<std::string>(dict,tagkey,value);
tagkey = "0008|0008";
value = "DERIVED\\SECONDARY";
itk::EncapsulateMetaData<std::string>(dict,tagkey,value);
tagkey = "0008|0064";
value = "DV";
itk::EncapsulateMetaData<std::string>(dict,tagkey,value);
caster->SetInput(reader_->GetOutput());
series_writer->SetInput( caster->GetOutput());
series_writer->SetImageIO(gdcmIO_);
ImageType::RegionType region = reader_->GetOutput()->GetLargestPossibleRegion();
ImageType::IndexType start = region.GetIndex();
ImageType::SizeType size = region.GetSize();
std::string format = output_directory;
format += "/image%03d.dcm";
namesGenerator->SetSeriesFormat(format.c_str());
namesGenerator->SetStartIndex(start[2]);
namesGenerator->SetEndIndex(start[2]+size[2]-1);
namesGenerator->SetIncrementIndex(1);
series_writer->SetFileNames (namesGenerator->GetFileNames());
series_writer->SetMetaDataDictionaryArray(reader_->GetMetaDataDictionaryArray());
try
{
series_writer->Update();
}
catch( itk::ExceptionObject &excp)
{
msg_box_.setText(excp.GetDescription());
msg_box_.exec();
}
}
bool VolumeProcess::DialateImage(int iterations)
{
int border = 2;
ImageType::Pointer tempImg = ImageType::New();
tempImg->SetRegions( m_outputImage->GetLargestPossibleRegion() );
tempImg->Allocate();
tempImg->FillBuffer(0);
ImageType::RegionType fullRegion = m_outputImage->GetBufferedRegion();
ImageType::RegionType borderRegion;
borderRegion.SetIndex(0, fullRegion.GetIndex(0)+border);
borderRegion.SetIndex(1, fullRegion.GetIndex(1)+border);
borderRegion.SetIndex(2, fullRegion.GetIndex(2)+border);
borderRegion.SetSize(0, fullRegion.GetSize(0)-(2*border));
borderRegion.SetSize(1, fullRegion.GetSize(1)-(2*border));
borderRegion.SetSize(2, fullRegion.GetSize(2)-(2*border));
itk::ImageRegionIteratorWithIndex< ImageType > itr( m_outputImage, borderRegion );
while(iterations > 0)
{
for(itr.GoToBegin(); !itr.IsAtEnd(); ++itr)
{
double blockMax = itr.Get();
for(int k=-1; k<=1; k++)
{
for(int j=-1; j<=1; j++)
{
for(int i=-1; i<=1; i++)
{
ImageType::IndexType index = itr.GetIndex();
index[0] += i;
index[1] += j;
index[2] += k;
ImageType::PixelType pix = m_outputImage->GetPixel(index);
if((double)pix > blockMax)
{
blockMax = (double)pix;
}
}
}
}
// Keep the peak of the original intensity
if (blockMax == itr.Get() && blockMax != 0)
{
blockMax = blockMax + 1;
}
tempImg->SetPixel(itr.GetIndex(), blockMax);
}
//Copy temp img back to image for next dialation
itk::ImageRegionIterator< ImageType > itr1( tempImg, tempImg->GetLargestPossibleRegion() );
itk::ImageRegionIterator< ImageType > itr2( m_outputImage, m_outputImage->GetLargestPossibleRegion() );
for(itr1.GoToBegin(), itr2.GoToBegin() ; !itr1.IsAtEnd(); ++itr1, ++itr2)
{
itr2.Set( itr1.Get() );
}
iterations--;
}
if(debug)
std::cerr << "Dialation Done" << std::endl;
return true;
}