void SeriesReader::readSeriesData(unsigned int minSlices) {
nameGenerator->SetUseSeriesDetails( true );
nameGenerator->SetDirectory( inputDir );
typedef std::vector< std::string > SeriesIdContainer;
const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();
SeriesIdContainer::const_iterator seriesItr = seriesUID.begin();
SeriesIdContainer::const_iterator seriesEnd = seriesUID.end();
while( seriesItr != seriesEnd ) {
FileNamesContainer fileNames = nameGenerator->GetFileNames(seriesItr->c_str());
if (fileNames.size() >= minSlices)
slist.push_back( fileNames );
seriesItr++;
}
}
SeriesFilelist getSeriesFileNames(const std::string &inputDir, unsigned int minSlices) {
NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();
nameGenerator->SetUseSeriesDetails( true );
nameGenerator->SetDirectory( inputDir );
SeriesFilelist slist;
typedef std::vector< std::string > SeriesIdContainer;
const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();
SeriesIdContainer::const_iterator seriesItr = seriesUID.begin();
SeriesIdContainer::const_iterator seriesEnd = seriesUID.end();
while( seriesItr != seriesEnd ) {
FileNamesContainer fileNames = nameGenerator->GetFileNames(seriesItr->c_str());
if (fileNames.size() >= minSlices)
slist.push_back( fileNames );
seriesItr++;
}
return slist;
}
bool ITKImplicit::loadDicom(const std::string & directory)
{
nameGenerator->SetInputDirectory( directory.c_str() );
typedef std::vector< std::string > FileNamesContainer;
FileNamesContainer fileNames;
fileNames = nameGenerator->GetInputFileNames( );
unsigned int numberOfFilenames = fileNames.size();
for(unsigned int fni = 0; fni<numberOfFilenames; fni++)
{
std::cout << "filename # " << fni << " = ";
std::cout << fileNames[fni] << std::endl;
}
reader->SetFileNames( fileNames );
try
{
reader->Update();
}
catch (itk::ExceptionObject &excp)
{
std::cerr << "Exception thrown while reading the image" << std::endl;
std::cerr << excp << std::endl;
return false;
}
//
// At this point we would have the volumetric data loaded in memory and we can
// get access to it by invoking the \code{GetOutput()} method in the reader.
//
myImage = reader->GetOutput();
return true;
}
void SeriesReader::getSeriesFileNames(unsigned int num, FileNamesContainer &fc) {
if (slist.size() > num) fc = slist[num];
else fc.clear();
};
void QtDcmConvert::convert()
{
if (QtDcmPreferences::instance()->useDcm2nii())
{
QString program = QtDcmPreferences::instance()->getDcm2niiPath();
QStringList arguments;
arguments << "-x" << "N";
arguments << "-r" << "N";
arguments << "-g" << "N";
arguments << "-o" << d->outputDirectory << d->inputDirectory;
QProcess * process = new QProcess(this);
process->setStandardOutputFile(d->tempDirectory + QDir::separator() + "logs" + QDir::separator() + d->serieUID + ".txt");
process->start(program, arguments);
process->waitForFinished();
delete process;
}
else
{
typedef signed short PixelType;
const unsigned int Dimension = 3;
typedef itk::Image< PixelType, Dimension > ImageType;
typedef itk::ImageSeriesReader< ImageType > ReaderType;
typedef itk::ImageFileWriter<ImageType> WriterType;
typedef itk::GDCMImageIO ImageIOType;
typedef itk::GDCMSeriesFileNames NamesGeneratorType;
typedef std::vector< std::string > FileNamesContainer;
typedef std::vector< std::string > SeriesIdContainer;
// ImageType::Pointer image = 0;
ReaderType::Pointer reader = ReaderType::New();
ImageIOType::Pointer dicomIO = ImageIOType::New();
NamesGeneratorType::Pointer inputNames = NamesGeneratorType::New();
inputNames->SetUseSeriesDetails ( true );
inputNames->AddSeriesRestriction ( "0008|0021" );
inputNames->AddSeriesRestriction ( "0020,0037" );
inputNames->LoadSequencesOn();
inputNames->LoadPrivateTagsOn();
inputNames->SetInputDirectory ( d->inputDirectory.toStdString() );
try
{
const SeriesIdContainer & seriesUID = inputNames->GetSeriesUIDs();
std::string seriesIdentifier = seriesUID.begin()->c_str();
FileNamesContainer filenames = inputNames->GetFileNames ( seriesIdentifier );
dicomIO->SetFileName ( filenames.begin()->c_str() );
try
{
dicomIO->ReadImageInformation();
}
catch ( itk::ExceptionObject &e )
{
qDebug() << e.GetDescription();
return;
}
reader->UseStreamingOn();
reader->SetFileNames ( filenames );
reader->SetImageIO ( dicomIO );
try
{
reader->Update();
}
catch ( itk::ExceptionObject &excp )
{
std::cerr << excp << std::endl;
return;
}
// IteratorType itOut;
//
// image = reader->GetOutput();
//
// RegionType region;
// region.SetSize ( 0, image->GetLargestPossibleRegion().GetSize() [0] );
// region.SetSize ( 1, image->GetLargestPossibleRegion().GetSize() [1] );
// region.SetSize ( 2, image->GetLargestPossibleRegion().GetSize() [2] );
// image->SetRegions ( region );
// image->Allocate();
// SpacingType spacing;
// spacing[0] = image->GetSpacing() [0];
// spacing[1] = image->GetSpacing() [1];
// spacing[2] = image->GetSpacing() [2];
// spacing[3] = 1;
// image->SetSpacing ( spacing );
// PointType origin;
// origin[0] = image->GetOrigin() [0];
// origin[1] = image->GetOrigin() [1];
// origin[2] = image->GetOrigin() [2];
// origin[3] = 0;
// image->SetOrigin ( origin );
// DirectionType direction;
// for ( unsigned int i=0; i<4; i++ )
// for ( unsigned int j=0; j<4; j++ )
// {
// if ( ( i < 3 ) && ( j < 3 ) )
// direction[i][j] = image->GetDirection() [i][j];
// else
// direction[i][j] = ( i == j ) ? 1 : 0;
// }
// image->SetDirection ( direction );
// itOut = IteratorType ( image, region );
//
// image->SetMetaDataDictionary ( dicomIO->GetMetaDataDictionary() );
//
//
// itk::ImageRegionIterator<ImageType> itIn ( image, image->GetLargestPossibleRegion() );
// while ( !itIn.IsAtEnd() )
// {
// itOut.Set ( itIn.Get() );
// ++itIn;
// ++itOut;
// }
WriterType::Pointer writer = WriterType::New();
QString completeFilename = d->outputDirectory + QDir::separator() + d->outputFilename;
writer->SetFileName ( completeFilename.toStdString() );
writer->SetInput ( reader->GetOutput() );
// writer->SetInput ( image );
try
{
writer->Update();
}
catch ( itk::ExceptionObject &ex )
{
std::cout << ex << std::endl;
return;
}
}
catch ( itk::ExceptionObject &ex )
{
std::cout << ex << std::endl;
return;
}
}
}
