// ------------------------------------------------------------------------
void LoadImage(const std::string &filename, ImageType::Pointer &image)
{
typedef itk::Image<unsigned short, 4> InImageType;
typedef itk::ImageFileReader<InImageType> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(filename);
reader->SetImageIO(itk::NrrdImageIO::New());
reader->Update();
typedef itk::ExtractImageFilter<InImageType, ImageType> ExtractorType;
ExtractorType::Pointer extractor = ExtractorType::New();
extractor->SetInput(reader->GetOutput());
InImageType::RegionType exRegion = reader->GetOutput()->GetLargestPossibleRegion();
InImageType::SizeType exSize = exRegion.GetSize();
InImageType::IndexType exIndex = exRegion.GetIndex();
exSize[3] = 0;
exIndex[3] = 0;
exRegion.SetSize(exSize);
exRegion.SetIndex(exIndex);
extractor->SetExtractionRegion(exRegion);
extractor->SetDirectionCollapseToSubmatrix();
extractor->Update();
image = extractor->GetOutput();
}
// ------------------------------------------------------------------------
void loadImageSeries(SeriesTransform &series,
const unsigned int &instanceNumbers)
{
// resize the image vector
series.images.resize(series.imageFilenames.size());
typedef itk::GDCMImageIO IOType;
typedef itk::ImageFileReader<ImageType> ReaderType;
for(unsigned int i = 0; i < instanceNumbers; i++)
{
ReaderType::Pointer reader = ReaderType::New();
reader->SetImageIO(IOType::New());
reader->SetFileName(series.imageFilenames[i]);
try
{
reader->Update();
}
catch(itk::ExceptionObject &e)
{
std::cout << e << std::endl;
exit(1);
}
series.images[i] = reader->GetOutput();
}
}
//read CT image
void CTImageTreeItem::retrieveITKImage(QProgressDialog *progress, int progressScale, int progressBase) {
//define and create file reader
typedef ReaderProgress::ReaderType ReaderType;
ReaderType::Pointer imageReader = ReaderType::New();
ReaderType::FileNamesContainer fc;
//assign filenames
fc.assign(m_fnList.begin(), m_fnList.end());
//set ImageIO and filenames
itk::GDCMImageIO::Pointer gdcmImageIO = itk::GDCMImageIO::New();
imageReader->SetImageIO( gdcmImageIO );
imageReader->SetFileNames(fc);
//create reader progress
ReaderProgress::Pointer progressor = ReaderProgress::New();
if (progress)
{
progressor->setDialog( progress, progressScale, progressBase );
imageReader->AddObserver(itk::AnyEvent(), progressor);
}
//try to read the images
try {
imageReader->Update();
}catch( itk::ExceptionObject & excep ) {
std::cerr << "Exception caught !" << std::endl;
std::cerr << excep << std::endl;
}
//assign the reader output to an image pointer
ImageType::Pointer imagePtr = imageReader->GetOutput();
setITKImage(imagePtr, 1);
//emit signal, that data has changed
m_model->dataChanged(m_model->createIndex(childNumber(),0,parent()),m_model->createIndex(childNumber(),columnCount()-1,parent()));
}
int main(int argc, char** argv) {
if(argc != 3){
std::cout << "Usage: Test2DImage inputFilename outputFilename";
return 1;
}
typedef signed int InputPixelType;
const unsigned int Dimension = 2;
typedef itk::Image<InputPixelType, Dimension> InputImageType;
typedef itk::RGBPixel<unsigned char> RGBPixelType;
typedef itk::Image<RGBPixelType, 2> RGBImageType;
typedef itk::ImageFileReader<InputImageType> ReaderType;
typedef itk::ImageFileWriter<RGBImageType> WriterType;
typedef itk::GDCMImageIO ImageIOType;
typedef itk::GradientAnisotropicDiffusionImageFilter<InputImageType,
InputImageType> DiffusionFilterType;
typedef itk::GradientMagnitudeImageFilter<InputImageType, InputImageType>
GradientMagnitudeFilterType;
typedef itk::Functor::ScalarToRGBPixelFunctor<int> ColorMapFunctorType;
typedef itk::UnaryFunctorImageFilter<InputImageType,
RGBImageType, ColorMapFunctorType> ColorMapFilterType;
typedef itk::JPEGImageIO JImageIOType;
ReaderType::Pointer reader = ReaderType::New();
WriterType::Pointer writer = WriterType::New();
ImageIOType::Pointer GDCMImageIO = ImageIOType::New();
JImageIOType::Pointer JPEGImageIO = JImageIOType::New();
ColorMapFilterType::Pointer colormapper = ColorMapFilterType::New();
reader->SetFileName(argv[1]);
reader->SetImageIO(GDCMImageIO);
try {
reader->Update();
}
catch (itk::ExceptionObject & e) {
std::cerr << "exception in file reader " << std::endl;
std::cerr << e << std::endl;
return 1;
}
DiffusionFilterType::Pointer diffusion = DiffusionFilterType::New();
diffusion->SetNumberOfIterations(1);
diffusion->SetConductanceParameter(4);
diffusion->SetTimeStep(0.125);
GradientMagnitudeFilterType::Pointer gradient = GradientMagnitudeFilterType::New();
diffusion->SetInput(reader->GetOutput());
gradient->SetInput(diffusion->GetOutput());
gradient->Update();
MyWatershedSegmenter<InputImageType> watershed(gradient->GetOutput());
watershed.buildLowerCompleteImage();
watershed.buildLabeledImage();
colormapper->SetInput(watershed.returnFinalImage());
writer->SetInput(colormapper->GetOutput());
writer->UseInputMetaDataDictionaryOff();
writer->SetImageIO(JPEGImageIO);
writer->SetFileName(argv[2]);
writer->Update();
}
bool extractPointAndNormalFromMask(string filename, CVector3 &point, CVector3 &normal1, CVector3 &normal2)
{
ReaderType::Pointer reader = ReaderType::New();
itk::NiftiImageIO::Pointer io = itk::NiftiImageIO::New();
reader->SetImageIO(io);
reader->SetFileName(filename);
try {
reader->Update();
} catch( itk::ExceptionObject & e ) {
cerr << "Exception caught while reading input image " << endl;
cerr << e << endl;
return false;
}
ImageType::Pointer image = reader->GetOutput();
vector<CVector3> result;
ImageType::IndexType ind;
itk::Point<double,3> pnt;
ImageIterator it( image, image->GetRequestedRegion() );
it.GoToBegin();
while(!it.IsAtEnd())
{
if (it.Get()!=0)
{
ind = it.GetIndex();
image->TransformIndexToPhysicalPoint(ind, pnt);
bool added = false;
if (result.size() == 0) {
result.push_back(CVector3(pnt[0],pnt[1],pnt[2]));
added = true;
}
else {
for (vector<CVector3>::iterator it=result.begin(); it!=result.end(); it++) {
if (pnt[2] < (*it)[2]) {
result.insert(it, CVector3(pnt[0],pnt[1],pnt[2]));
added = true;
break;
}
}
}
if (!added) result.push_back(CVector3(pnt[0],pnt[1],pnt[2]));
}
++it;
}
if (result.size() != 3) {
cerr << "Error: Not enough of too many points in the binary mask. Number of point needed = 3. Detected points = " << result.size() << endl;
return false;
}
point = result[1];
normal1 = (result[0]-result[1]).Normalize();
normal2 = (result[2]-result[1]).Normalize();
return true;
}
// ------------------------------------------------------------------------
void DicomParser::writeSeries(const DicomSeries &series, const QString &outputFolder)
{
// create the series name
QString name = QString::fromStdString(series.description);
name.replace(" ","_");
name += "_" + QString::number(series.images.front().seriesNumber);
name += ".nrrd";
QDir path(outputFolder);
QString fullPath = path.absoluteFilePath(name);
std::vector<DicomImage> images = series.images;
std::sort(images.begin(), images.end());
// write and build the output images
typedef itk::Image<unsigned short, 3> ImageType;
typedef itk::Image<unsigned short, 4> OutputImageType;
typedef itk::ImageFileReader<ImageType> ReaderType;
typedef itk::JoinSeriesImageFilter<ImageType, OutputImageType> JoinerType;
JoinerType::Pointer joiner = JoinerType::New();
ImageType::Pointer orig;
for(unsigned int i = 0; i < images.size(); i++)
{
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(images[i].filename);
std::cout << images[i].filename << std::endl;
reader->SetImageIO(itk::GDCMImageIO::New());
reader->Update();
ImageType::Pointer im = reader->GetOutput();
if(i == 0) orig = im;
im->SetOrigin(orig->GetOrigin());
im->SetDirection(orig->GetDirection());
im->SetSpacing(orig->GetSpacing());
joiner->SetInput(i, reader->GetOutput());
}
std::cout << joiner->GetOutput()->GetDirection() << std::endl;
typedef itk::ImageFileWriter<OutputImageType> WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetInput(joiner->GetOutput());
writer->SetFileName(fullPath.toStdString());
writer->SetImageIO(itk::NrrdImageIO::New());
writer->Update();
}
FilterImageType::Pointer getImage(const FileNamesContainer &filenames, DictionaryArray &dictArray) {
typedef itk::ImageSeriesReader< FilterImageType > ReaderType;
ReaderType::Pointer reader = ReaderType::New();
ImageIOType::Pointer gdcmImageIO = ImageIOType::New();
reader->SetImageIO( gdcmImageIO );
reader->SetFileNames(filenames);
reader->Update();
ReaderType::DictionaryArrayRawPointer dict;
dict = reader->GetMetaDataDictionaryArray();
for( ReaderType::DictionaryArrayType::const_iterator it = dict->begin(); it != dict->end(); ++it) {
dictArray.push_back( **it );
}
return reader->GetOutput();
}
itk::Image<unsigned char, 3>::Pointer boner::Importer::import(std::string path)
{
itk::Image<unsigned char, 3>::Pointer image;
typedef itk::ImageSeriesReader<itk::Image<unsigned char, 3>> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
itk::GDCMSeriesFileNames::Pointer namegenerator = itk::GDCMSeriesFileNames::New();
namegenerator->SetInputDirectory(path);
reader->SetImageIO(itk::GDCMImageIO::New());
reader->SetFileNames(namegenerator->GetInputFileNames());
image = reader->GetOutput();
image->Update();
return image;
}
// ------------------------------------------------------------------------
void InitialTransformExtractor::Compute()
{
GetFilenames(m_Filenames);
BuildMapping(m_Mapping);
std::string referenceFilename = GetReferenceImageFilename();
// load the reference file
typedef itk::ImageFileReader<ImageType> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(referenceFilename);
reader->SetImageIO(itk::GDCMImageIO::New());
reader->Update();
ImageType::Pointer refImage = reader->GetOutput();
// flip the x and y axis
typedef itk::PermuteAxesImageFilter<ImageType> FlipperType;
FlipperType::Pointer flipper = FlipperType::New();
itk::FixedArray<unsigned int, 3> order;
order[0] = 1;
order[1] = 0;
order[2] = 2;
flipper->SetOrder(order);
flipper->SetInput(refImage);
flipper->Update();
//refImage = flipper->GetOutput();
// transformation is the negative origin of the reference
ImageType::PointType origin = refImage->GetOrigin();
m_Translation[0] = -origin[0];
m_Translation[1] = -origin[1];
m_Translation[2] = -origin[2];
m_Rotation = refImage->GetDirection().GetInverse();
m_Reference = refImage;
}
void
NrrdPlugin::readSlice(int idx[3], int sz[3],
int nbytes, uchar *slice)
{
typedef itk::Image<T, 3> ImageType;
typedef itk::ImageFileReader<ImageType> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(m_fileName[0].toAscii().data());
typedef itk::NrrdImageIO NrrdIOType;
NrrdIOType::Pointer nrrdIO = NrrdIOType::New();
reader->SetImageIO(nrrdIO);
typedef itk::RegionOfInterestImageFilter<ImageType,ImageType> RegionExtractor;
ImageType::RegionType region;
ImageType::SizeType size;
ImageType::IndexType index;
index[2] = idx[2];
index[1] = idx[1];
index[0] = idx[0];
size[2] = sz[2];
size[1] = sz[1];
size[0] = sz[0];
region.SetIndex(index);
region.SetSize(size);
// Extract the relevant sub-region.
RegionExtractor::Pointer extractor = RegionExtractor::New();
extractor->SetInput(reader->GetOutput());
extractor->SetRegionOfInterest(region);
extractor->Update();
ImageType *dimg = extractor->GetOutput();
char *tdata = (char*)(dimg->GetBufferPointer());
memcpy(slice, tdata, nbytes);
}
int main(int, char ** argv)
{
OptionsData options;
readXMLValues(argv[2], options);
exit(1);
// parse the dicom directory
gdcm::Directory dir;
dir.Load(argv[1], true);
gdcm::Directory::FilenamesType filenames = dir.GetFilenames();
gdcm::Tag seriesDescription = gdcm::Tag(0x0008,0x103e);
gdcm::Tag seriesNumber = gdcm::Tag(0x0020,0x0011);
gdcm::Tag instanceNumber = gdcm::Tag(0x0020,0x0013);
gdcm::Tag sliceThickness = gdcm::Tag(0x0018,0x0050);
gdcm::Tag triggerTime = gdcm::Tag(0x0018,0x1060);
gdcm::Tag numberOfImages = gdcm::Tag(0x0018,0x1090);
gdcm::Tag slicePosition = gdcm::Tag(0x0019,0x1015);
gdcm::Tag imagePosition = gdcm::Tag(0x0020,0x0032);
gdcm::Tag imageOrientation = gdcm::Tag(0x0020,0x0037);
gdcm::Tag sliceLocation = gdcm::Tag(0x0020,0x1041);
gdcm::Tag rows = gdcm::Tag(0x0028,0x0010);
gdcm::Tag cols = gdcm::Tag(0x0028,0x0011);
gdcm::Tag pixelSpacing = gdcm::Tag(0x0028,0x0030);
gdcm::Scanner scanner;
scanner.AddTag(seriesDescription);
scanner.AddTag(seriesNumber);
scanner.AddTag(instanceNumber);
scanner.AddTag(sliceThickness);
scanner.AddTag(triggerTime);
scanner.AddTag(numberOfImages);
scanner.AddTag(slicePosition);
scanner.AddTag(imagePosition);
scanner.AddTag(imageOrientation);
scanner.AddTag(sliceLocation);
scanner.AddTag(rows);
scanner.AddTag(cols);
scanner.AddTag(pixelSpacing);
scanner.Scan(filenames);
gdcm::Scanner::MappingType mapping = scanner.GetMappings();
// extract all the images that are Short axis and are the first instance
gdcm::Directory::FilenamesType targetFilenames;
for(unsigned int i = 0; i < filenames.size(); i++)
{
const char * fname = filenames[i].c_str();
if(mapping.count(fname) == 0) continue;
// extract the image information
std::string descriptionStr = mapping[fname][seriesDescription];
std::string instanceNumberStr = mapping[fname][instanceNumber];
QString description = QString::fromStdString(descriptionStr);
unsigned int instanceNumber = QString::fromStdString(instanceNumberStr).toInt();
// check that the description is a short axis one and is instance 1
if(instanceNumber == 1 && description.contains("sa", Qt::CaseInsensitive))
{
targetFilenames.push_back(filenames[i]);
}
}
// sort the images based on their slice position
/*
gdcm::Sorter sorter;
sorter.SetSortFunction(position_sort);
sorter.StableSort(targetFilenames);
gdcm::Directory::FilenamesType sorted = sorter.GetFilenames();
for(unsigned int i = 0; i < sorted.size(); i++)
{
const char * fname = sorted[i].c_str();
std::string position = mapping[fname][imagePosition];
std::cout << position << std::endl;
std::cout << mapping[fname][sliceLocation] << std::endl;
}
*/
std::cout << targetFilenames.size() << std::endl;
// find the slice with the smallest slice position
double smallest = 1000000.0;
int smallestIndex;
for(unsigned int i = 0; i < targetFilenames.size(); i++)
{
const char * fname = targetFilenames[i].c_str();
std::string slicePosition = mapping[fname][sliceLocation];
double pos = QString::fromStdString(slicePosition).toDouble();
std::cout << pos << std::endl;
if(pos < smallest)
{
smallest = pos;
smallestIndex = i;
}
}
// load the image
typedef itk::Image<unsigned short, 3> ImageType;
typedef itk::ImageFileReader<ImageType> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(targetFilenames[smallestIndex]);
reader->SetImageIO(itk::GDCMImageIO::New());
reader->Update();
// flip the x and y axis
typedef itk::PermuteAxesImageFilter<ImageType> FlipperType;
FlipperType::Pointer flipper = FlipperType::New();
itk::FixedArray<unsigned int, 3> order;
order[0] = 1;
order[1] = 0;
order[2] = 2;
flipper->SetOrder(order);
flipper->SetInput(reader->GetOutput());
flipper->Update();
ImageType::Pointer referenceImage = flipper->GetOutput();
ImageType::DirectionType direction = referenceImage->GetDirection();
direction.SetIdentity();
referenceImage->SetDirection(direction);
ImageType::PointType origin = referenceImage->GetOrigin();
origin.Fill(20.0);
referenceImage->SetOrigin(origin);
ImageType::SpacingType spacing;
spacing.Fill(1.0);
referenceImage->SetSpacing(spacing);
flipper->GetOutput()->Print(std::cout);
typedef itk::ImageFileWriter<ImageType> WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetInput(referenceImage);
writer->SetImageIO(itk::NrrdImageIO::New());
writer->SetFileName("test.nrrd");
writer->Update();
std::cout << targetFilenames[smallestIndex] << std::endl;
return 0;
}
int main(int argc, char *argv[])
{
//print help
if( argc == 1 ) //argv[0]
{
PrintHelp(argv);
return 1;
}
if( argc == 2 ) //argv[0] -h
{
if( argv[1] == string("-h") || argv[1] == string("-H") || argv[1] == string("-help") )
{
PrintHelp(argv);
return 1;
}
else
{
cerr<< "For help: "<< argv[0] << " -h" <<endl;
return 0;
}
}
//tags used to name the converted 3d filename: PatientID_StudyID_StudyDate_Access#_Series#_SeriesDescription.mha
vector<string> tags;
tags.push_back("0010|0020");//patientID
tags.push_back("0020|0010");//studyID
tags.push_back("0008|0020");//studyDate
tags.push_back("0008|0050");//access#
tags.push_back("0020|0011");//series#
tags.push_back("0008|103e");//series description
//illegal filename chracters: \ / : * ? " < > | , which will be removed from tag value.
string illegalChars = "\\/:?\"<>|";
//accept output format, specified by -f
vector<string> acceptFormat;
acceptFormat.push_back("mha");
acceptFormat.push_back("nii");
acceptFormat.push_back("mhd");
acceptFormat.push_back("nrrd");
acceptFormat.push_back("hdr");
//timer start
const clock_t begin_time = clock();
//parse arguments
string dicomDirectory; // -i
string outputDirectory;// -o
bool write3D = false; //will be set to true, if outputDirectory is good
bool writeAllSeries = true; // default, if without -k
string outputFormat = "mha"; //default, if without -f
vector<string> seriesKeywords; //record series keywords specified by -f
string convertedList; //-l
bool writeConvertedList = false;
for (int ac = 1; ac < argc; ac++)
{
//-i
if( argv[ac] == string("-i") || argv[ac] == string("-I"))
{
if ( ++ac >= argc )
{
cerr<< "missing argument for -i" <<endl;
return 1;
}
dicomDirectory = argv[ac];
}
//-o
if( argv[ac] == string("-o") || argv[ac] == string("-O") )
{
if ( ++ac >= argc )
{
cerr<< "missing argument for -o" <<endl;
return 1;
}
outputDirectory = argv[ac];
}
//-f
if( argv[ac] == string("-f") || argv[ac] == string("-F") )
{
if ( ++ac >= argc )
{
cerr<< "missing argument for -f" <<endl;
return 1;
}
outputFormat = argv[ac];
transform(outputFormat.begin(), outputFormat.end(),outputFormat.begin(), tolower); //to lower case
}
//-k
if ( argv[ac] == string("-k") || argv[ac] == string("-K") )
{
if ( ++ac >= argc )
{
cerr<< "missing argument for -k" <<endl;
return 1;
}
//add elements after -f to vector serieskeywords
string seriesKeyword;
for( int i=ac; i<argc; i++ )
{
seriesKeyword=argv[i];
//push_back until next option
if( seriesKeyword == string("-l") || seriesKeyword == string("-i") || seriesKeyword == string("-o") || seriesKeyword == string("-f") )
{
break;
}
transform(seriesKeyword.begin(), seriesKeyword.end(), seriesKeyword.begin(), tolower);//to lower case
seriesKeyword = std::regex_replace(seriesKeyword, regex("^ +| +$|( ) +"), "$1");//remove leading,trailing and extra white space
seriesKeywords.push_back(seriesKeyword);
}
if( seriesKeywords.size() > 0 )
{
writeAllSeries = false;
}
}
//-l
if( argv[ac] == string("-l") || argv[ac] == string("-L") )
{
if ( ++ac >= argc )
{
cerr<< "missing argument for -l" <<endl;
return 1;
}
convertedList = argv[ac];
}
}
// Check if dicomDirectory is a directory and exist
bool exist = itksys::SystemTools::FileExists(dicomDirectory.c_str());
bool isDir = itksys::SystemTools::FileIsDirectory(dicomDirectory.c_str());
if ( !(exist && isDir) )
{
cerr << "ERROR: " << dicomDirectory << " does not exist or is no directory." << endl;
return 1;
}
//check if outputDirectory is good
if ( !(outputDirectory.empty()) )
{
//check if outputDirectory is a file
bool isFile = itksys::SystemTools::FileExists(outputDirectory.c_str(),true);
if ( isFile )
{
cerr << "ERROR: " << outputDirectory << " should be a directory!" << endl;
return 1;
}
// Check if outputDirectory exist
exist = itksys::SystemTools::FileExists( outputDirectory.c_str() );
if( !exist ) //create directory is not exist
{
try
{
itksys::SystemTools::MakeDirectory( outputDirectory.c_str() );
cout << outputDirectory << " created." << endl;
}
catch (itk::ExceptionObject &ex)
{
cout << ex << std::endl;
return 1;
}
}
//set write3D to ture when outputDirectory is good.
write3D = true;
}
//check if ouput format is accept
if ( !(find(acceptFormat.begin(), acceptFormat.end(), outputFormat) != acceptFormat.end()) )
{
cerr<< "accepted output formats:mha, nii, mhd, nrrd, hdr" <<endl;
return 1;
}
//open convertedList file specified by -l
ofstream convertedListFile;
if ( !convertedList.empty() )
{
convertedListFile.exceptions ( ofstream::failbit | ofstream::badbit );
try
{
convertedListFile.open( outputDirectory + string(PATH_SEP) + convertedList, ios::out | ios::app);
writeConvertedList = true;
}
catch (std::ofstream::failure e)
{
cerr << "Exception opening file."<<endl;
return 1;
}
}
cout<<"Analyzing "<<dicomDirectory<<endl;
//image type to read 2d dicom image, used to get the dicom tags of patientID,studyId,etc...
typedef itk::Image< signed short, 2 > ImageType2D;
typedef itk::ImageFileReader< ImageType2D > ReaderType2D;
ReaderType2D::Pointer reader2D = ReaderType2D::New();
//image type to write 3d mha image
typedef signed short PixelType;
const unsigned int Dimension = 3;
typedef itk::Image< PixelType, Dimension > ImageType;
typedef itk::ImageSeriesReader< ImageType > ReaderType;
typedef itk::GDCMSeriesFileNames NamesGeneratorType;
NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();
ReaderType::Pointer reader = ReaderType::New();
typedef itk::GDCMImageIO ImageIOType;
ImageIOType::Pointer dicomIO = ImageIOType::New();
nameGenerator->SetRecursive(true);
nameGenerator->SetUseSeriesDetails(true);
nameGenerator->AddSeriesRestriction("0008|0021");
nameGenerator->SetDirectory(dicomDirectory);
//get all the series (by series UID) under the input folder
typedef std::vector< std::string > SeriesIdContainer;
const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();
SeriesIdContainer::const_iterator seriesItr = seriesUID.begin();
SeriesIdContainer::const_iterator seriesEnd = seriesUID.end();
//get the correspondence between series UID and PatientID,studyId,studyDate,accessNumber,seriesNumber,seriesDescription
//key is series UID, vector<string> is PatientID,studyID,studyDate,accessNumber,seriesNumber,seriesDescription
map< string, vector<string> > seriesUidToOtherStuff;
seriesItr = seriesUID.begin();
while (seriesItr != seriesUID.end())
{
string seriesIdentifier = seriesItr->c_str();
//get file names belong to specific series
vector< string > fileNames = nameGenerator->GetFileNames(seriesIdentifier);
vector< string > otherStuff;
//read tags(PatientID StudyID StudyDate Access# Series# SeriesDescription) value from the first file of each series
if (!fileNames.empty())
{
reader2D->SetFileName(fileNames[0]);
reader2D->SetImageIO(dicomIO);
try
{
reader2D->UpdateLargestPossibleRegion(); //do not use reader->Update(),since image size is different across series.
}
catch (itk::ExceptionObject &ex)
{
cout << ex << endl;
return 1;
}
typedef itk::MetaDataDictionary DictionaryType;
const DictionaryType & dictionary = dicomIO->GetMetaDataDictionary();
typedef itk::MetaDataObject< std::string > MetaDataStringType;
DictionaryType::ConstIterator itr = dictionary.Begin();
DictionaryType::ConstIterator end = dictionary.End();
for (int i = 0; i < tags.size(); i++)
{
string entryId = tags[i];
DictionaryType::ConstIterator tagItr = dictionary.Find( entryId );
if( tagItr != end )
{
MetaDataStringType::ConstPointer entryvalue =dynamic_cast<const MetaDataStringType *>(tagItr->second.GetPointer() );
if( entryvalue )//entry found
{
string tagvalue = entryvalue->GetMetaDataObjectValue();
tagvalue = regex_replace(tagvalue, regex("^ +| +$|( ) +"), "$1");//remove leading,trailing and extra white space
otherStuff.push_back(tagvalue);
}
else
{
otherStuff.push_back("EntryNotFound");
}
}
}//end for
}//end if (!fileNames.empty())
seriesUidToOtherStuff[seriesIdentifier] = otherStuff;
seriesItr++;
}//end while
//list series number and description for each patient and access#
/*patientID, access#, series#, series descrition hierarchy:
patientid
access#
series#:series description
series#:series description
...
access#
series#:series description
series#:series description
...
patientid
...
...
*/
//create 2d vector for sorting
vector<string> vs;
vector< vector<string> > vvs;
for( map< string,vector<string> >::iterator ii=seriesUidToOtherStuff.begin(); ii!=seriesUidToOtherStuff.end(); ++ii)
{
vector<string> vsNew;
vs = (*ii).second;
vsNew.push_back(vs[0]);//patientID
vsNew.push_back(vs[3]);//access#
vsNew.push_back(vs[4]);//series#
vsNew.push_back(vs[5]);//series description
vvs.push_back(vsNew);
}
//sort: patientID and access# by string lexicographical order, series# by integer
sort(vvs.begin(),vvs.end(),comparator);
//print series number and description for each patient and access#
string patientID;
string accessNumber;
vector<string> patientIDVector;
vector<string> accessNumberVector;
if ( vvs.size()>0 )
{
cout <<dicomDirectory<<" contains the following DICOM Series:"<<endl;
for( int i = 0; i < vvs.size(); i++)
{
patientID = vvs[i][0];
accessNumber = vvs[i][1];
if (find(patientIDVector.begin(), patientIDVector.end(), patientID) == patientIDVector.end() ) // a new patientID
{
patientIDVector.push_back(patientID);
cout<<"patient ID: "<<patientID<<endl;
}
if (find(accessNumberVector.begin(), accessNumberVector.end(), accessNumber) == accessNumberVector.end() ) // a new accessNumber
{
accessNumberVector.push_back(accessNumber);
cout<<" "<<"access#: "<<accessNumber<<endl;
}
cout<<" "<<vvs[i][2]<<": "<<vvs[i][3]<<endl; //list series#:series description
}
}
else
{
cout << "The directory: "<<dicomDirectory<<" contains no DICOM Series! InputDirectory correct?"<<endl;
return 0;
}
//write 3D volume
if (write3D)
{
typedef std::vector< std::string > FileNamesContainer;
FileNamesContainer fileNames;
typedef itk::ImageFileWriter< ImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
string outFileName;
seriesItr = seriesUID.begin();
while (seriesItr != seriesUID.end())
{
string seriesIdentifier;
if (writeAllSeries) //without -k option
{
seriesIdentifier = seriesItr->c_str();
}
else //with -k option
{
//get sereisDescription according to seriesUID
string seriesDescription = seriesUidToOtherStuff[*seriesItr][5];
transform(seriesDescription.begin(), seriesDescription.end(), seriesDescription.begin(), tolower);//to lower case
//check if series Description contains the specified keyword (by -k)
for( int i = 0; i < seriesKeywords.size(); i++)
{
if (seriesDescription.find(seriesKeywords[i]) != string::npos)
{
seriesIdentifier = seriesItr->c_str();
}
}
}//end if (writeAllSeries)
if ( !seriesIdentifier.empty() )
{
//get file names belong to specific series
fileNames = nameGenerator->GetFileNames(seriesIdentifier);
reader->SetImageIO(dicomIO);
reader->SetFileNames(fileNames);
//get output file name:PatientID_StudyID_StudyDate_Access#_Series#_SeriesDescription
vector<string> vs = seriesUidToOtherStuff[seriesIdentifier];
string temp = vs[0]+"_"+vs[1]+"_"+vs[2]+"_"+vs[3]+"_"+vs[4]+"_"+vs[5];
string tempNew;
//remove illegal characters
for (string::iterator it = temp.begin(); it < temp.end(); ++it)
{
bool found = illegalChars.find(*it) != string::npos;
if(!found){
tempNew=tempNew+(*it);
}
}
//repace space with . . Many series descriptions come with spaces. But, filenames with spaces is not good.
replace( tempNew.begin(), tempNew.end(), ' ', '.');
//get full path file name
outFileName = outputDirectory + string(PATH_SEP) + tempNew + "."+outputFormat;
//write
writer->SetFileName(outFileName);
writer->UseCompressionOn();
writer->SetInput(reader->GetOutput());
cout << "Writing: " << outFileName << endl;
try
{
writer->Update();
}
catch (itk::ExceptionObject &ex)
{
cout << ex << std::endl;
continue;
}
//writing converted files full path to convertedList
if ( writeConvertedList )
{
try
{
convertedListFile << outFileName <<endl;
}
catch (std::ofstream::failure e)
{
cerr << "Exception writing file"<<endl;
}
}
}
seriesItr++;
}//end while
}//end if write3D
//close convertedList file
if (convertedListFile.is_open())
{
try
{
convertedListFile.close();
}
catch (std::ofstream::failure e)
{
cerr << "Exception closing file"<<endl;
}
}
//print elasped time
cout << "Elapsed time: "<<float( clock () - begin_time )/CLOCKS_PER_SEC<<" Seconds";
return 0;
}
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;
}
}
}
// ------------------------------------------------------------------------
void DicomParser::loadImages()
{
// group the series into sa and not sa
DicomSeriesList saList;
DicomSeriesList otherList;
for(unsigned int i = 0; i < series.size(); i++)
{
std::string description = series[i].description;
QString desc = QString::fromStdString(description);
if(desc.contains("Cine_SA"))
saList.push_back(series[i]);
else if(desc.contains("cine_SA"))
saList.push_back(series[i]);
else if(desc.contains("Cine_sa"))
saList.push_back(series[i]);
else if(desc.contains("Cine_ipat SA"))
saList.push_back(series[i]);
//else if(desc.contains("sa"))
//saList.push_back(series[i]);
else
otherList.push_back(series[i]);
}
// sort the sa list based on position
std::sort(saList.begin(), saList.end(), series_sort);
std::sort(otherList.begin(), otherList.end(), series_sort);
for(unsigned int i = 0; i < saList.size(); i++)
{
seriesAgain.push_back(saList[i]);
}
for(unsigned int i = 0; i < otherList.size(); i++)
{
seriesAgain.push_back(otherList[i]);
}
for(unsigned int i = 0; i < seriesAgain.size(); i++)
{
std::string filename = seriesAgain[i].images.front().filename;
typedef itk::Image<unsigned short,3> ImageType;
typedef itk::ImageFileReader<ImageType> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetImageIO(itk::GDCMImageIO::New());
reader->SetFileName(filename);
typedef itk::ImageToVTKImageFilter<ImageType> VTKFilterType;
VTKFilterType::Pointer vtkFilter = VTKFilterType::New();
vtkFilter->SetInput(reader->GetOutput());
vtkFilter->Update();
vtkSmartPointer<vtkImageData> image =
vtkSmartPointer<vtkImageData>::New();
image->DeepCopy(vtkFilter->GetOutput());
image->Print(std::cout);
vtkSmartPointer<vtkImageSliceMapper> mapper =
vtkSmartPointer<vtkImageSliceMapper>::New();
mapper->SetInputData(image);
vtkSmartPointer<vtkImageSlice> actor =
vtkSmartPointer<vtkImageSlice>::New();
actor->SetMapper(mapper);
actor->GetProperty()->SetColorLevel(177.48);
actor->GetProperty()->SetColorWindow(512.04);
images.push_back(actor);
}
}
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 argc, char ** argv)
{
std::string folderName = argv[1];
std::string filter = argv[2];
typedef utils::Directory Directory;
Directory::FilenamesType filenames = Directory::GetFiles(folderName, ".nrrd");
Directory::FilenamesType goodFilenames;
filterFilenames(filenames, filter, goodFilenames);
// load the images
std::vector<ImageType::Pointer> imageList;
for(unsigned int i = 0; i < goodFilenames.size(); i++)
{
std::cout << goodFilenames[i] << std::endl;
typedef itk::ImageFileReader<ImageType> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(goodFilenames[i]);
reader->SetImageIO(itk::NrrdImageIO::New());
reader->Update();
imageList.push_back(reader->GetOutput());
}
std::sort(imageList.begin(), imageList.end(), imageSort);
ImageType::Pointer outputImage = ImageType::New();
ImageType::RegionType outputRegion;
ImageType::SizeType outputSize = imageList.front()->GetLargestPossibleRegion().GetSize();
outputSize[2] = imageList.size();
ImageType::IndexType outputIndex;
outputIndex.Fill(0);
outputRegion.SetSize(outputSize);
outputRegion.SetIndex(outputIndex);
// compute the spacing
double meanSpacing = 0.0;
for(unsigned int i = 1; i < imageList.size(); i++)
{
ImageType::Pointer im1 = imageList[i-1];
ImageType::Pointer im2 = imageList[i];
meanSpacing += (im1->GetOrigin()-im2->GetOrigin()).GetNorm();
}
meanSpacing /= (double) (imageList.size()-1);
ImageType::SpacingType spacing = imageList.front()->GetSpacing();
spacing[2] = meanSpacing;
outputImage->SetRegions(outputRegion);
outputImage->SetSpacing(spacing);
outputImage->SetOrigin(imageList.front()->GetOrigin());
outputImage->SetDirection(imageList.front()->GetDirection());
outputImage->Allocate();
itk::ImageRegionIterator<ImageType> outIt(outputImage, outputImage->GetLargestPossibleRegion());
outIt.GoToBegin();
while(!outIt.IsAtEnd())
{
ImageType::IndexType index = outIt.GetIndex();
ImageType::IndexType testIndex = index;
testIndex[2] = 0;
outIt.Set(imageList[index[2]]->GetPixel(testIndex));
++outIt;
}
std::string stackFilename = folderName + "/stack.nrrd";
typedef itk::ImageFileWriter<ImageType> WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetInput(outputImage);
writer->SetFileName(stackFilename);
writer->SetImageIO(itk::NrrdImageIO::New());
writer->Update();
return 0;
}
bool
NrrdPlugin::setFile(QStringList files)
{
m_fileName = files;
typedef itk::Image<unsigned char, 3> ImageType;
typedef itk::ImageFileReader<ImageType> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(m_fileName[0].toAscii().data());
typedef itk::NrrdImageIO NrrdIOType;
NrrdIOType::Pointer nrrdIO = NrrdIOType::New();
reader->SetImageIO(nrrdIO);
reader->Update();
itk::ImageIOBase::Pointer imageIO = reader->GetImageIO();
m_height = imageIO->GetDimensions(0);
m_width = imageIO->GetDimensions(1);
m_depth = imageIO->GetDimensions(2);
m_voxelSizeX = imageIO->GetSpacing(0);
m_voxelSizeY = imageIO->GetSpacing(1);
m_voxelSizeZ = imageIO->GetSpacing(2);
int et = imageIO->GetComponentType();
if (et == itk::ImageIOBase::UCHAR) m_voxelType = _UChar;
if (et == itk::ImageIOBase::CHAR) m_voxelType = _Char;
if (et == itk::ImageIOBase::USHORT) m_voxelType = _UShort;
if (et == itk::ImageIOBase::SHORT) m_voxelType = _Short;
if (et == itk::ImageIOBase::INT) m_voxelType = _Int;
if (et == itk::ImageIOBase::FLOAT) m_voxelType = _Float;
m_skipBytes = m_headerBytes = 0;
m_bytesPerVoxel = 1;
if (m_voxelType == _UChar) m_bytesPerVoxel = 1;
else if (m_voxelType == _Char) m_bytesPerVoxel = 1;
else if (m_voxelType == _UShort) m_bytesPerVoxel = 2;
else if (m_voxelType == _Short) m_bytesPerVoxel = 2;
else if (m_voxelType == _Int) m_bytesPerVoxel = 4;
else if (m_voxelType == _Float) m_bytesPerVoxel = 4;
if (m_4dvol) // do not perform further calculations.
return true;
if (m_voxelType == _UChar ||
m_voxelType == _Char ||
m_voxelType == _UShort ||
m_voxelType == _Short)
{
findMinMaxandGenerateHistogram();
}
else
{
findMinMax();
generateHistogram();
}
return true;
}
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;
}
int main() {
typedef unsigned short PixelType;
const unsigned int Dimension = 3;
typedef itk::Image< PixelType, Dimension > ImageType;
typedef itk::VTKImageExport<ImageType> ImageExportType;
typedef itk::ImageSeriesReader< ImageType > ReaderType;
ReaderType::Pointer reader = ReaderType::New();
typedef itk::GDCMImageIO ImageIOType;
ImageIOType::Pointer dicomIO = ImageIOType::New();
reader->SetImageIO( dicomIO );
typedef itk::GDCMSeriesFileNames NamesGeneratorType;
NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();
nameGenerator->SetUseSeriesDetails( true );
nameGenerator->AddSeriesRestriction("0008|0021" );
nameGenerator->SetDirectory( "/Users/mac/BIOMED/Subjects/testSubject");
typedef std::vector< std::string > SeriesIdContainer;
const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();
std::cout << seriesUID.size() << std::endl;
SeriesIdContainer::const_iterator seriesItr = seriesUID.begin();
SeriesIdContainer::const_iterator seriesEnd = seriesUID.end();
while( seriesItr != seriesEnd )
{
std::cout << seriesItr->c_str() << std::endl;
seriesItr++;
}
std::string seriesIdentifier;
seriesIdentifier = seriesUID.begin()->c_str();
std::cout << seriesIdentifier.c_str() << std::endl;
typedef std::vector< std::string > FileNamesContainer;
FileNamesContainer fileNames;
fileNames = nameGenerator->GetFileNames( seriesIdentifier );
reader->SetFileNames( fileNames );
try
{
reader->Update();
}
catch (itk::ExceptionObject &ex)
{
std::cout << ex << std::endl;
}
//------------------------------------------------------------------------
// ITK to VTK pipeline connection.
//------------------------------------------------------------------------
// Create the itk::VTKImageExport instance and connect it to the
// itk::CurvatureFlowImageFilter.
ImageExportType::Pointer exporter = ImageExportType::New();
exporter->SetInput(reader->GetOutput());
exporter->Update();
// Create the vtkImageImport and connect it to the
// itk::VTKImageExport instance.
vtkImageImport* importer = vtkImageImport::New();
ConnectPipelines(exporter, importer);
//------------------------------------------------------------------------
// VTK pipeline.
//------------------------------------------------------------------------
//Demo Display DICOM Image
/*
string folder = "/Users/mac/BIOMED/Subjects/testSubject";
// Read all the DICOM files in the specified directory.
vtkSmartPointer<vtkDICOMImageReader> reader2 =
vtkSmartPointer<vtkDICOMImageReader>::New();
reader2->SetDirectoryName(folder.c_str());
reader2->Update();
*/
vtkSmartPointer<vtkImageSliceMapper> imageSliceMapper = vtkSmartPointer<vtkImageSliceMapper>::New();
imageSliceMapper->SetInputConnection(importer->GetOutputPort());
//imageSliceMapper->SetInputData(importer->GetOutput());
imageSliceMapper->Update();
vtkSmartPointer<vtkImageSlice> imageSlice = vtkSmartPointer<vtkImageSlice>::New();
imageSlice->SetMapper(imageSliceMapper);
vtkSmartPointer<vtkSmartVolumeMapper> volumeMapper =
vtkSmartPointer<vtkSmartVolumeMapper>::New();
volumeMapper->SetBlendModeToComposite();
volumeMapper->SetInputConnection(importer->GetOutputPort());
vtkSmartPointer<vtkVolumeProperty> volumeProperty =
vtkSmartPointer<vtkVolumeProperty>::New();
volumeProperty->ShadeOff();
volumeProperty->SetInterpolationType(VTK_LINEAR_INTERPOLATION);
// Setup renderers
vtkSmartPointer<vtkRenderer> renderer = vtkSmartPointer<vtkRenderer>::New();
renderer->AddViewProp(imageSlice);
renderer->ResetCamera();
renderer->SetBackground(0.1,0.4,0.2);
// Setup render window
vtkSmartPointer<vtkRenderWindow> renderWindow = vtkSmartPointer<vtkRenderWindow>::New();
renderWindow->SetSize(500, 500);
renderWindow->AddRenderer(renderer);
vtkSmartPointer<vtkVolume> volume = vtkSmartPointer<vtkVolume>::New();
volume->SetMapper(volumeMapper);
volume->SetProperty(volumeProperty);
renderer->AddViewProp(volume);
renderer->ResetCamera();
volumeMapper->SetRequestedRenderModeToRayCast();
volumeMapper->SetBlendModeToMinimumIntensity();
renderWindow->Render();
vtkSmartPointer<vtkRenderWindowInteractor> renderWindowInteractor =
vtkSmartPointer<vtkRenderWindowInteractor>::New();
// Render and start interaction
renderWindowInteractor->SetRenderWindow(renderWindow);
renderWindowInteractor->Initialize();
renderWindowInteractor->Start();
return 0;
}
int main(int argc, char *argv[])
{
srand (time(NULL));
if (argc == 1)
{
help();
return EXIT_FAILURE;
}
string inputFilename = "", outputPath = "", outputFilenameBinary = "", outputFilenameMesh = "", outputFilenameBinaryCSF = "", outputFilenameMeshCSF = "", outputFilenameAreas = "", outputFilenameAreasCSF = "", outputFilenameCenterline = "", outputFilenameCenterlineBinary = "", inputCenterlineFilename = "", initMaskFilename = "";
double typeImageFactor = 0.0, initialisation = 0.5;
int downSlice = -10000, upSlice = 10000;
string suffix;
bool input_dicom = false, output_detection = false, output_mesh = false, output_centerline_binary = false, output_centerline_coord = false, output_cross = false, init_with_centerline = false, init_with_mask = false, verbose = false, output_init_tube = false, completeCenterline = false, init_validation = false, low_res_mesh = false, CSF_segmentation = false;
int gapInterSlices = 4, nbSlicesInitialisation = 5;
double radius = 4.0;
int numberOfPropagationIteration = 200;
double maxDeformation = 0.0, maxArea = 0.0, minContrast = 50.0, tradeoff_d;
bool tradeoff_d_bool = false;
for (int i = 0; i < argc; ++i) {
if (strcmp(argv[i],"-i")==0) {
i++;
inputFilename = argv[i];
}
else if (strcmp(argv[i],"-i-dicom")==0) {
i++;
//inputFilename = argv[i];
//input_dicom = true;
}
else if (strcmp(argv[i],"-o")==0) {
i++;
outputPath = argv[i];
}
else if (strcmp(argv[i],"-t")==0) {
i++;
if (strcmp(argv[i],"t1")==0) {
typeImageFactor = -1.0;
if (verbose) cout << endl << "WARNING: be sure your image is a T1-weighted image." << endl << endl;
}
else if (strcmp(argv[i],"t2")==0) {
typeImageFactor = 1.0;
if (verbose) cout << endl << "WARNING: be sure your image is a T2-weighted image." << endl << endl;
}
else {
cout << "Error: Invalid type or image (need to be \"t1\" or \"t2\")" << endl << endl;
help();
return EXIT_FAILURE;
}
}
else if (strcmp(argv[i],"-init")==0) {
i++;
initialisation = atof(argv[i]);
}
else if (strcmp(argv[i],"-down")==0) {
i++;
downSlice = atoi(argv[i]);
}
else if (strcmp(argv[i],"-up")==0) {
i++;
upSlice = atoi(argv[i]);
}
else if (strcmp(argv[i],"-detect-display")==0) {
output_detection = true;
}
else if (strcmp(argv[i],"-mesh")==0) {
output_mesh = true;
}
else if (strcmp(argv[i],"-centerline-binary")==0) {
output_centerline_binary = true;
}
else if (strcmp(argv[i],"-centerline-coord")==0) {
output_centerline_coord = true;
}
else if (strcmp(argv[i],"-cross")==0) {
output_cross = true;
}
else if (strcmp(argv[i],"-detect-n")==0) {
i++;
nbSlicesInitialisation = atoi(argv[i]);
}
else if (strcmp(argv[i],"-detect-gap")==0) {
i++;
gapInterSlices = atoi(argv[i]);
}
else if (strcmp(argv[i],"-detect-radius")==0) {
i++;
radius = atof(argv[i]);
}
else if (strcmp(argv[i],"-init-centerline")==0) {
i++;
inputCenterlineFilename = argv[i];
init_with_centerline = true;
}
else if (strcmp(argv[i],"-nbiter")==0) {
i++;
numberOfPropagationIteration = atoi(argv[i]);
}
else if (strcmp(argv[i],"-init-mask")==0) {
i++;
initMaskFilename = argv[i];
init_with_mask = true;
}
else if (strcmp(argv[i],"-init-tube")==0) {
output_init_tube = true;
}
else if (strcmp(argv[i],"-init-validation")==0) {
init_validation = true;
}
else if (strcmp(argv[i],"-low-resolution-mesh")==0) {
low_res_mesh = true;
}
else if (strcmp(argv[i],"-max-deformation")==0) {
i++;
maxDeformation = atof(argv[i]);
}
else if (strcmp(argv[i],"-max-area")==0) {
i++;
maxArea = atof(argv[i]);
}
else if (strcmp(argv[i],"-min-contrast")==0) {
i++;
minContrast = atof(argv[i]);
}
else if (strcmp(argv[i],"-d")==0) {
i++;
tradeoff_d = atof(argv[i]);
tradeoff_d_bool = true;
}
else if (strcmp(argv[i],"-CSF")==0) {
CSF_segmentation = true;
if (maxArea == 0.0) maxArea = 120;
if (maxDeformation == 0.0) maxDeformation = 2.5;
}
else if (strcmp(argv[i],"-verbose")==0) {
verbose = true;
}
else if (strcmp(argv[i],"-help")==0) {
help();
return EXIT_FAILURE;
}
}
if (inputFilename == "")
{
cerr << "Input filename or folder (if DICOM) not provided" << endl;
help();
return EXIT_FAILURE;
}
if (typeImageFactor == 0)
{
cerr << "Error: The type of contrast not provided (option -t)" << endl;
help();
return EXIT_FAILURE;
}
// output files must have the same extension as input file
string nii=".nii", niigz=".nii.gz"; suffix=niigz;
size_t pos = inputFilename.find(niigz);
if (pos == string::npos) {
pos = inputFilename.find(nii);
suffix = nii;
}
if (outputPath!="" && outputPath.compare(outputPath.length()-1,1,"/")) outputPath += "/"; // add "/" if missing
outputFilenameBinary = outputPath+"segmentation_binary"+suffix;
outputFilenameMesh = outputPath+"segmentation_mesh.vtk";
outputFilenameBinaryCSF = outputPath+"segmentation_CSF_binary"+suffix;
outputFilenameMeshCSF = outputPath+"segmentation_CSF_mesh.vtk";
outputFilenameAreas = outputPath+"cross_sectional_areas.txt";
outputFilenameAreasCSF = outputPath+"cross_sectional_areas_CSF.txt";
outputFilenameCenterline = outputPath+"segmentation_centerline.txt";
outputFilenameCenterlineBinary = outputPath+"segmentation_centerline_binary"+suffix;
// if output path doesn't exist, we create it
if (outputPath!="") itk::FileTools::CreateDirectory(outputPath.c_str());
// Image reading - image can be T1 or T2 (or Tx-like) depending on contrast between spinal cord and CSF
// typeImageFactor depend of contrast type and is equal to +1 when CSF is brighter than spinal cord and equal to -1 inversely
ImageType::Pointer initialImage, image = ImageType::New();
if (input_dicom)
{
/*ImageIOType::Pointer gdcmIO = ImageIOType::New();
InputNamesGeneratorType::Pointer inputNames = InputNamesGeneratorType::New();
inputNames->SetInputDirectory( inputFilename );
const DICOMReaderType::FileNamesContainer & filenames = inputNames->GetInputFileNames();
DICOMReaderType::Pointer reader = DICOMReaderType::New();
reader->SetImageIO( gdcmIO );
reader->SetFileNames( filenames );
try
{
reader->Update();
} catch (itk::ExceptionObject &excp) {
std::cerr << "Exception thrown while reading the DICOM series" << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
initialImage = reader->GetOutput();*/
}
else
{
ReaderType::Pointer reader = ReaderType::New();
itk::NiftiImageIO::Pointer io = itk::NiftiImageIO::New();
reader->SetImageIO(io);
reader->SetFileName(inputFilename);
try {
reader->Update();
} catch( itk::ExceptionObject & e ) {
cerr << "Exception caught while reading input image" << endl;
cerr << e << endl;
return EXIT_FAILURE;
}
initialImage = reader->GetOutput();
}
// Change orientation of input image to AIL. Output images will have the same orientation as input image
OrientImage<ImageType> orientationFilter;
orientationFilter.setInputImage(initialImage);
orientationFilter.orientation(itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_AIL);
initialImage = orientationFilter.getOutputImage();
// Crop image if it is too large in left-right direction. No need to compute the initialization on the whole image. We assume the spinal cord is included in a 5cm large region.
ImageType::SizeType desiredSize = initialImage->GetLargestPossibleRegion().GetSize();
ImageType::SpacingType spacingI = initialImage->GetSpacing();
if (desiredSize[2]*spacingI[2] > 60 && !init_with_mask && !init_with_centerline)
{
SymmetricalCropping symCroppingFilter;
symCroppingFilter.setInputImage(initialImage);
symCroppingFilter.setInitSlice(initialisation);
int crop_slice = -1;
try {
crop_slice = symCroppingFilter.symmetryDetection();
} catch(exception & e) {
cerr << "Exception caught while computing symmetry" << endl;
cerr << e.what() << endl;
return EXIT_FAILURE;
}
if (crop_slice != -1) {
if (verbose) cout << "Cropping input image in left-right direction around slice = " << crop_slice << endl;
image = symCroppingFilter.cropping();
} else {
if (verbose) cout << "Image non cropped for symmetry" << endl;
image = initialImage;
}
}
else image = initialImage;
// Intensity normalization
RescaleFilterType::Pointer rescaleFilter = RescaleFilterType::New();
rescaleFilter->SetInput(image);
rescaleFilter->SetOutputMinimum(0);
rescaleFilter->SetOutputMaximum(1000);
try {
rescaleFilter->Update();
} catch( itk::ExceptionObject & e ) {
cerr << "Exception caught while normalizing input image " << endl;
cerr << e << endl;
return EXIT_FAILURE;
}
image = rescaleFilter->GetOutput();
// computing magnitude and direction of gradient image
GradientMFilterType::Pointer gradientMagnitudeFilter = GradientMFilterType::New();
gradientMagnitudeFilter->SetInput(image);
try {
gradientMagnitudeFilter->Update();
} catch( itk::ExceptionObject & e ) {
cerr << "Exception caught while updating gradientMagnitudeFilter " << endl;
cerr << e << endl;
return EXIT_FAILURE;
}
ImageType::Pointer imageGradient = gradientMagnitudeFilter->GetOutput();
VectorGradientFilterType::Pointer gradientMapFilter = VectorGradientFilterType::New();
gradientMapFilter->SetInput( image );
try {
gradientMapFilter->Update();
} catch( itk::ExceptionObject & e ) {
cerr << "Exception caught while updating gradientMapFilter " << endl;
cerr << e << endl;
return EXIT_FAILURE;
}
GradientImageType::Pointer imageVectorGradient = gradientMapFilter->GetOutput();
// Creation of 3D image with origin, orientation and scaling, containing original image, gradient image, vector gradient image
ImageType::SizeType regionSize = image->GetLargestPossibleRegion().GetSize();
ImageType::PointType origineI = image->GetOrigin();
CVector3 origine = CVector3(origineI[0],origineI[1],origineI[2]);
ImageType::DirectionType directionI = image->GetInverseDirection();
CVector3 directionX = CVector3(directionI[0][0],directionI[0][1],directionI[0][2]),
directionY = CVector3(directionI[1][0],directionI[1][1],directionI[1][2]),
directionZ = CVector3(directionI[2][0],directionI[2][1],directionI[2][2]);
CVector3 spacing = CVector3(spacingI[0],spacingI[1],spacingI[2]);
Image3D* image3DGrad = new Image3D(imageVectorGradient,regionSize[0],regionSize[1],regionSize[2],origine,directionX,directionY,directionZ,spacing,typeImageFactor);
image3DGrad->setImageOriginale(initialImage);
image3DGrad->setCroppedImageOriginale(image);
image3DGrad->setImageMagnitudeGradient(imageGradient);
/******************************************
// Initialization of Propagated Deformable Model of Spinal Cord
******************************************/
int radialResolution, axialResolution, numberOfDeformIteration = 3;
double axialStep, propagationLength = 800.0;
// Definition of parameters for T1 and T2 images. T1 need better resolution to provide accurate segmentation.
if (typeImageFactor == 1.0) { // T2
radialResolution = 15;
axialResolution = 3;
axialStep = 6.0;
}
else { // T1
radialResolution = 20; //30
axialResolution = 3; //5
axialStep = 6.0; //8
}
CVector3 point, normal1, normal2; // normal1 and normal2 and normals in both direction from initial point
double stretchingFactor = 1.0;
vector<CVector3> centerline;
if (init_with_centerline)
{
if (verbose) cout << "Initialization - using given centerline" << endl;
centerline = extractCenterline(inputCenterlineFilename);
if (centerline.size() == 0) return EXIT_FAILURE;
}
else if (init_with_mask)
{
if (verbose) cout << "Initialization - using given mask" << endl;
bool result_init = extractPointAndNormalFromMask(initMaskFilename, point, normal1, normal2);
if (!result_init) return EXIT_FAILURE;
if (verbose) {
cout << "Point = " << point << endl;
cout << "Normal 1 = " << normal1 << endl;
cout << "Normal 2 = " << normal2 << endl;
}
}
else
{
bool isSpinalCordDetected = false;
int countFailure = 0;
double step = 0.025; // step of displacement in pourcentage of the image
do
{
if (verbose) cout << "Initialization - spinal cord detection on axial slices" << endl;
Initialisation init(image,typeImageFactor);
init.setVerbose(verbose);
init.setGap(gapInterSlices); // gap between slices is necessary to provide good normals
init.setRadius(radius); // approximate radius of spinal cord. This parameter is used to initiate Hough transform
init.setNumberOfSlices(nbSlicesInitialisation);
// if the initialization fails at the first position in the image, an other spinal cord detection process is launch higher.
int d = rand() % 2; if (d==0) d = -1;
isSpinalCordDetected = init.computeInitialParameters(initialisation+(double)countFailure*step*(double)d);
//if (!isSpinalCordDetected) isSpinalCordDetected = init.computeInitialParameters(0.7);
if(isSpinalCordDetected)
{
if (output_detection) init.savePointAsAxialImage(image,outputPath+"result_detection.png");
init.getPoints(point,normal1,normal2,radius,stretchingFactor);
if (normal2 == CVector3::ZERO) normal2 = -normal1;
if (verbose) {
cout << "Initialization - Spinal Cord Detection:" << endl;
cout << "Point = " << point << endl;
cout << "Normal 1 = " << normal1 << endl;
cout << "Normal 2 = " << normal2 << endl;
cout << "Radius = " << radius << endl;
}
if(init_validation)
{
// Definition of discrimination surface for the validation of the spinal cord detection module
double K_T1 = 15.7528, K_T2 = 3.2854;
CVector3 L_T1 = CVector3(-0.0762,-2.5921,0.3472), L_T2 = CVector3(-0.0022,-1.2995,0.4909);
CMatrix3x3 Q_T1, Q_T2;
Q_T1[0] = 0.0; Q_T1[1] = 0.0; Q_T1[2] = 0.0; Q_T1[3] = 0.0; Q_T1[4] = 0.1476; Q_T1[5] = 0.0; Q_T1[6] = 0.0; Q_T1[7] = 0.0; Q_T1[8] = 0.6082;
Q_T2[0] = 0.0; Q_T2[1] = 0.0; Q_T2[2] = 0.0; Q_T2[3] = 0.0; Q_T2[4] = 0.0687; Q_T2[5] = 0.0; Q_T2[6] = 0.0; Q_T2[7] = 0.0; Q_T2[8] = 0.3388;
double contrast = 0.0, mean_distance = 0.0, std_distance = 0.0;
// validation of the spinal cord detetion
int *sizeDesired = new int[3];
double *spacingDesired = new double[3];
sizeDesired[0] = 61; sizeDesired[1] = 61; sizeDesired[2] = 11;
spacingDesired[0] = 0.5; spacingDesired[1] = 0.5; spacingDesired[2] = 0.5;
SCRegion* spinal_cord_verif = new SCRegion();
spinal_cord_verif->setSize(sizeDesired);
spinal_cord_verif->setSpacing(spacingDesired);
spinal_cord_verif->setOrigin(point[0],point[1],point[2]);
spinal_cord_verif->setNormal(normal1[0],normal1[1],normal1[2]);
spinal_cord_verif->setFactor(typeImageFactor);
try {
spinal_cord_verif->readImage(initialImage);
spinal_cord_verif->createImage();
contrast = spinal_cord_verif->computeContrast(mean_distance,std_distance,15);
} catch (string const& e) {
cerr << e << endl;
contrast = -1.0;
}
CVector3 vec = CVector3(contrast,mean_distance,std_distance);
double discrim = 0.0;
if (typeImageFactor == -1) // if T1
{
CVector3 temp = vec*Q_T1;
double quad = 0.0;
for(int r=0; r<3; r++) {
quad += temp[r]*vec[r];
}
discrim = K_T1 + vec*L_T1 + quad;
}
else{
CVector3 temp = vec*Q_T2;
double quad = 0.0;
for(int r=0; r<3; r++) {
quad += temp[r]*vec[r];
}
discrim = K_T2 + vec*L_T2 + quad;
}
if (discrim > 0.0)
{
countFailure++;
isSpinalCordDetected = false;
if (verbose) cout << "WARNING: Bad initialization. Attempt to locate spinal cord at an other level." << endl << endl;
}
else
{
isSpinalCordDetected = true;
}
delete sizeDesired, spacingDesired, spinal_cord_verif;
}
else {
isSpinalCordDetected = true;
}
} else {
countFailure++;
}
}
while (!isSpinalCordDetected && countFailure<10);
if (!isSpinalCordDetected)
{
cerr << "Error: Enable to detect the spinal cord. Please provide the initial position and orientation of the spinal cord (-init, -init-mask)" << endl;
return EXIT_FAILURE;
}
}
/******************************************
// Launch of Propagated Deformable Model of Spinal Cord. Propagation have to be done in both direction
******************************************/
PropagatedDeformableModel* prop = new PropagatedDeformableModel(radialResolution,axialResolution,radius,numberOfDeformIteration,numberOfPropagationIteration,axialStep,propagationLength);
if (maxDeformation != 0.0) prop->setMaxDeformation(maxDeformation);
if (maxArea != 0.0) prop->setMaxArea(maxArea);
prop->setMinContrast(minContrast);
prop->setInitialPointAndNormals(point,normal1,normal2);
prop->setStretchingFactor(stretchingFactor);
prop->setUpAndDownLimits(downSlice,upSlice);
prop->setImage3D(image3DGrad);
if (init_with_centerline) {
prop->propagationWithCenterline();
for (unsigned int k=0; k<centerline.size(); k++) prop->addPointToCenterline(centerline[k]);
if (initialisation <= 1) prop->setInitPosition(initialisation);
}
if (tradeoff_d_bool) {
prop->setTradeOffDistanceFeature(tradeoff_d);
}
prop->setVerbose(verbose);
prop->computeMeshInitial();
if (output_init_tube) {
SpinalCord *tube1 = prop->getInitialMesh(), *tube2 = prop->getInverseInitialMesh();
tube1->save(outputPath+"InitialTube1.vtk");
tube2->save(outputPath+"InitialTube2.vtk");
}
prop->adaptationGlobale(); // Propagation
// Saving low resolution mesh
if (low_res_mesh)
{
SpinalCord *meshOutputLowResolution = prop->getOutput();
meshOutputLowResolution->save(outputPath+"segmentation_mesh_low_resolution.vtk",initialImage);
//meshOutput->computeCenterline(true,path+"LowResolution");
//meshOutput->computeCrossSectionalArea(true,path+"LowResolution");
//image3DGrad->TransformMeshToBinaryImage(meshOutput,path+"LowResolution",orientationFilter.getInitialImageOrientation());
//meshOutput->saveCenterlineAsBinaryImage(initialImage,path+"LowResolution",orientationFilter.getInitialImageOrientation());
}
/******************************************
// High Resolution Deformation
******************************************/
prop->rafinementGlobal();
SpinalCord* meshOutputFinal = prop->getOutputFinal();
if (output_mesh) meshOutputFinal->save(outputFilenameMesh,initialImage);
if (output_centerline_coord) meshOutputFinal->computeCenterline(true,outputFilenameCenterline,true);
if (output_cross) meshOutputFinal->computeCrossSectionalArea(true,outputFilenameAreas,true,image3DGrad);
image3DGrad->TransformMeshToBinaryImage(meshOutputFinal,outputFilenameBinary,orientationFilter.getInitialImageOrientation());
if (output_centerline_binary) meshOutputFinal->saveCenterlineAsBinaryImage(initialImage,outputFilenameCenterlineBinary,orientationFilter.getInitialImageOrientation());
if (verbose) {
double lengthPropagation = meshOutputFinal->getLength();
cout << "Total propagation length = " << lengthPropagation << " mm" << endl;
}
if (CSF_segmentation)
{
/******************************************
// Launch of Propagated Deformable Model on the CSF. Propagation have to be done in both direction
******************************************/
double factor_CSF = 2;
PropagatedDeformableModel* prop_CSF = new PropagatedDeformableModel(radialResolution,axialResolution,radius*factor_CSF,numberOfDeformIteration,numberOfPropagationIteration,axialStep,propagationLength);
if (maxDeformation != 0.0) prop_CSF->setMaxDeformation(maxDeformation*factor_CSF);
if (maxArea != 0.0) prop_CSF->setMaxArea(maxArea*factor_CSF*2);
prop->setMinContrast(minContrast);
prop_CSF->setInitialPointAndNormals(point,normal1,normal2);
prop_CSF->setStretchingFactor(stretchingFactor);
prop_CSF->setUpAndDownLimits(downSlice,upSlice);
image3DGrad->setTypeImageFactor(-image3DGrad->getTypeImageFactor());
prop_CSF->setImage3D(image3DGrad);
if (init_with_centerline) {
prop_CSF->propagationWithCenterline();
for (unsigned int k=0; k<centerline.size(); k++) prop->addPointToCenterline(centerline[k]);
if (initialisation <= 1) prop->setInitPosition(initialisation);
}
prop_CSF->setVerbose(verbose);
prop_CSF->computeMeshInitial();
if (output_init_tube) {
SpinalCord *tube1 = prop_CSF->getInitialMesh(), *tube2 = prop_CSF->getInverseInitialMesh();
tube1->save(outputPath+"InitialTubeCSF1.vtk");
tube2->save(outputPath+"InitialTubeCSF2.vtk");
}
prop_CSF->adaptationGlobale(); // Propagation
// Saving low resolution mesh
if (low_res_mesh)
{
SpinalCord *meshOutputLowResolution = prop_CSF->getOutput();
meshOutputLowResolution->save(outputPath+"segmentation_CSF_mesh_low_resolution.vtk",initialImage);
//meshOutput->computeCenterline(true,path+"LowResolution");
//meshOutput->computeCrossSectionalArea(true,path+"LowResolution");
//image3DGrad->TransformMeshToBinaryImage(meshOutput,path+"LowResolution",orientationFilter.getInitialImageOrientation());
//meshOutput->saveCenterlineAsBinaryImage(initialImage,path+"LowResolution",orientationFilter.getInitialImageOrientation());
}
/******************************************
// High Resolution Deformation
******************************************/
prop_CSF->rafinementGlobal();
SpinalCord* meshOutputFinal = prop_CSF->getOutputFinal();
if (output_mesh) meshOutputFinal->save(outputFilenameMeshCSF,initialImage);
if (output_cross) meshOutputFinal->computeCrossSectionalArea(true,outputFilenameAreasCSF,true,image3DGrad);
image3DGrad->TransformMeshToBinaryImage(meshOutputFinal,outputFilenameBinaryCSF,orientationFilter.getInitialImageOrientation());
if (verbose) {
double lengthPropagation = meshOutputFinal->getLength();
cout << "Total propagation length = " << lengthPropagation << " mm" << endl;
}
delete prop_CSF;
}
delete image3DGrad, prop;
return EXIT_SUCCESS;
}
bool itkDataTensorImageReaderBase::read (const QString &path)
{
if (this->io.IsNull())
return false;
this->readInformation ( path );
qDebug() << "Read with: " << this->identifier();
if (medAbstractData *medData = dynamic_cast<medAbstractData*>(this->data()) ) {
if (medData->identifier()=="itkDataTensorImageDouble3") {
if (this->io->GetNumberOfComponents()==6) {
typedef itk::Tensor<double, 3> TensorType;
typedef itk::Image<TensorType, 3> TensorImageType;
typedef itk::Vector<double, 6> VectorType;
typedef itk::Image<VectorType, 3> VectorImageType;
typedef itk::ImageFileReader<VectorImageType> ReaderType;
VectorImageType::Pointer image = 0;
{
ReaderType::Pointer reader = ReaderType::New();
reader->SetImageIO (this->io);
reader->SetFileName ( path.toAscii().constData() );
try {
reader->Update();
}
catch (itk::ExceptionObject &e) {
qDebug() << e.GetDescription();
return false;
}
image = reader->GetOutput();
}
TensorImageType::Pointer tensors = TensorImageType::New();
TensorImageType::RegionType region = image->GetLargestPossibleRegion();
tensors->SetRegions (region);
tensors->SetSpacing (image->GetSpacing());
tensors->SetOrigin (image->GetOrigin());
tensors->SetDirection (image->GetDirection());
try {
tensors->Allocate();
}
catch (itk::ExceptionObject &e) {
qDebug() << e.GetDescription();
return false;
}
itk::ImageRegionConstIteratorWithIndex<VectorImageType> itIn (image,
image->GetLargestPossibleRegion());
itk::ImageRegionIteratorWithIndex<TensorImageType> itOut(tensors,
tensors->GetLargestPossibleRegion());
while(!itOut.IsAtEnd()) {
VectorType vec = itIn.Get();
TensorType tensor;
for( unsigned int j=0; j<6; j++) {
tensor[j] = vec[j];
}
itOut.Set (tensor);
++itOut;
++itIn;
}
medData->setData (tensors);
}
else if (this->io->GetNumberOfComponents()==9) {
typedef itk::Tensor<double, 3> TensorType;
typedef itk::Image<TensorType, 3> TensorImageType;
typedef itk::Vector<double, 9> VectorType;
typedef itk::Image<VectorType, 3> VectorImageType;
typedef itk::ImageFileReader<VectorImageType> ReaderType;
VectorImageType::Pointer image = 0;
{
ReaderType::Pointer reader = ReaderType::New();
reader->SetImageIO (this->io);
reader->SetFileName ( path.toAscii().constData() );
try {
reader->Update();
}
catch (itk::ExceptionObject &e) {
qDebug() << e.GetDescription();
return false;
}
image = reader->GetOutput();
}
TensorImageType::Pointer tensors = TensorImageType::New();
TensorImageType::RegionType region = image->GetLargestPossibleRegion();
tensors->SetRegions (region);
tensors->SetSpacing (image->GetSpacing());
tensors->SetOrigin (image->GetOrigin());
tensors->SetDirection (image->GetDirection());
try {
tensors->Allocate();
}
catch (itk::ExceptionObject &e) {
qDebug() << e.GetDescription();
return false;
}
itk::ImageRegionConstIteratorWithIndex<VectorImageType> itIn (image,
image->GetLargestPossibleRegion());
itk::ImageRegionIteratorWithIndex<TensorImageType> itOut(tensors,
tensors->GetLargestPossibleRegion());
while(!itOut.IsAtEnd()) {
VectorType vec = itIn.Get();
TensorType tensor;
for (unsigned int i=0; i<3; i++)
for (unsigned int j=0; j<3; j++)
tensor.SetComponent (i, j, vec[i*3+j]);
itOut.Set (tensor);
++itOut;
++itIn;
}
medData->setData (tensors);
}
else {
qDebug() << "Unsupported number of components";
return false;
}
}
else if (medData->identifier()=="itkDataTensorImageFloat3") {
if (this->io->GetNumberOfComponents()==6) {
typedef itk::Tensor<float, 3> TensorType;
typedef itk::Image<TensorType, 3> TensorImageType;
typedef itk::Vector<float, 6> VectorType;
typedef itk::Image<VectorType, 3> VectorImageType;
typedef itk::ImageFileReader<VectorImageType> ReaderType;
VectorImageType::Pointer image = 0;
{
ReaderType::Pointer reader = ReaderType::New();
reader->SetImageIO (this->io);
reader->SetFileName ( path.toAscii().constData() );
try {
reader->Update();
}
catch (itk::ExceptionObject &e) {
qDebug() << e.GetDescription();
return false;
}
image = reader->GetOutput();
}
TensorImageType::Pointer tensors = TensorImageType::New();
TensorImageType::RegionType region = image->GetLargestPossibleRegion();
tensors->SetRegions (region);
tensors->SetSpacing (image->GetSpacing());
tensors->SetOrigin (image->GetOrigin());
tensors->SetDirection (image->GetDirection());
try {
tensors->Allocate();
}
catch (itk::ExceptionObject &e) {
qDebug() << e.GetDescription();
return false;
}
itk::ImageRegionConstIteratorWithIndex<VectorImageType> itIn (image,
image->GetLargestPossibleRegion());
itk::ImageRegionIteratorWithIndex<TensorImageType> itOut(tensors,
tensors->GetLargestPossibleRegion());
while(!itOut.IsAtEnd()) {
VectorType vec = itIn.Get();
TensorType tensor;
for( unsigned int j=0; j<6; j++) {
tensor[j] = vec[j];
}
itOut.Set (tensor);
++itOut;
++itIn;
}
medData->setData (tensors);
}
else if (this->io->GetNumberOfComponents()==9) {
typedef itk::Tensor<float, 3> TensorType;
typedef itk::Image<TensorType, 3> TensorImageType;
typedef itk::Vector<float, 9> VectorType;
typedef itk::Image<VectorType, 3> VectorImageType;
typedef itk::ImageFileReader<VectorImageType> ReaderType;
VectorImageType::Pointer image = 0;
{
ReaderType::Pointer reader = ReaderType::New();
reader->SetImageIO (this->io);
reader->SetFileName ( path.toAscii().constData() );
try {
reader->Update();
}
catch (itk::ExceptionObject &e) {
qDebug() << e.GetDescription();
return false;
}
image = reader->GetOutput();
}
TensorImageType::Pointer tensors = TensorImageType::New();
TensorImageType::RegionType region = image->GetLargestPossibleRegion();
tensors->SetRegions (region);
tensors->SetSpacing (image->GetSpacing());
tensors->SetOrigin (image->GetOrigin());
tensors->SetDirection (image->GetDirection());
try {
tensors->Allocate();
}
catch (itk::ExceptionObject &e) {
qDebug() << e.GetDescription();
return false;
}
itk::ImageRegionConstIteratorWithIndex<VectorImageType> itIn (image,
image->GetLargestPossibleRegion());
itk::ImageRegionIteratorWithIndex<TensorImageType> itOut(tensors,
tensors->GetLargestPossibleRegion());
while(!itOut.IsAtEnd()) {
VectorType vec = itIn.Get();
TensorType tensor;
for (unsigned int i=0; i<3; i++)
for (unsigned int j=0; j<3; j++)
tensor.SetComponent (i, j, vec[i*3+j]);
itOut.Set (tensor);
++itOut;
++itIn;
}
medData->setData (tensors);
}
else {
qDebug() << "Unsupported number of components";
return false;
}
}
else {
qDebug() << "Unsupported data type";
return false;
}
}
else {
qDebug() << "No data set or could not create one";
return false;
}
return true;
}
vector<CVector3> extractCenterline(string filename)
{
vector<CVector3> result;
string nii=".nii", niigz=".nii.gz", txt=".txt", suffix="";
size_t pos_niigz = filename.find(niigz), pos_nii = filename.find(nii), pos_txt = filename.find(txt);
if (pos_niigz != string::npos || pos_nii != string::npos)
{
ReaderType::Pointer reader = ReaderType::New();
itk::NiftiImageIO::Pointer io = itk::NiftiImageIO::New();
reader->SetImageIO(io);
reader->SetFileName(filename);
try {
reader->Update();
} catch( itk::ExceptionObject & e ) {
cerr << "Exception caught while reading centerline input image " << endl;
cerr << e << endl;
}
ImageType::Pointer image_centerline = reader->GetOutput();
OrientImage<ImageType> orientationFilter;
orientationFilter.setInputImage(image_centerline);
orientationFilter.orientation(itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_AIL);
image_centerline = orientationFilter.getOutputImage();
ImageType::IndexType ind;
itk::Point<double,3> point;
ImageIterator it( image_centerline, image_centerline->GetRequestedRegion() );
it.GoToBegin();
while(!it.IsAtEnd())
{
if (it.Get()!=0)
{
ind = it.GetIndex();
image_centerline->TransformIndexToPhysicalPoint(ind, point);
bool added = false;
if (result.size() == 0) {
result.push_back(CVector3(point[0],point[1],point[2]));
added = true;
}
else {
for (vector<CVector3>::iterator it=result.begin(); it!=result.end(); it++) {
if (point[2] < (*it)[2]) {
result.insert(it, CVector3(point[0],point[1],point[2]));
added = true;
break;
}
}
}
if (!added) result.push_back(CVector3(point[0],point[1],point[2]));
}
++it;
}
/*// spline approximation to produce correct centerline
double range = result.size()/4.0 ;
const unsigned int ParametricDimension = 1; const unsigned int DataDimension = 3;
typedef double RealType;
typedef itk::Vector<RealType, DataDimension> VectorType; typedef itk::Image<VectorType, ParametricDimension> ImageType;
typedef itk::PointSet <VectorType , ParametricDimension > PointSetType; PointSetType::Pointer pointSet = PointSetType::New();
// Sample the helix.
int nb = result.size();
for (unsigned long i=0; i<nb; i++) {
PointSetType::PointType point; point[0] = (double)i/(double)(nb-1);
pointSet ->SetPoint( i, point );
VectorType V;
V[0] = result[i][0]; V[1] = result[i][1]; V[2] = result[i][2];
pointSet ->SetPointData( i, V );
}
typedef itk::BSplineScatteredDataPointSetToImageFilter <PointSetType , ImageType > FilterType;
FilterType::Pointer filter = FilterType::New();
ImageType::SpacingType spacing; spacing.Fill( 1.0 ); ImageType::SizeType size; size.Fill( 2.0); ImageType::PointType origin; origin.Fill( 0.0 );
ImageType::RegionType region(size); FilterType::ArrayType closedim; closedim.Fill(0);
filter->SetSize( size ); filter->SetOrigin( origin ); filter->SetSpacing( spacing ); filter->SetInput( pointSet );
int splineOrder = 3; filter->SetSplineOrder( splineOrder ); FilterType::ArrayType ncps;
ncps.Fill( splineOrder + 1 ); filter->SetNumberOfControlPoints( ncps ); filter->SetNumberOfLevels( 5 ); filter->SetGenerateOutputImage( false );
try
{ filter->Update();
} catch( itk::ExceptionObject & e ) {
std::cerr << "Exception caught while reading input image " << std::endl;
std::cerr << e << std::endl;
}
typedef itk::BSplineControlPointImageFunction < ImageType, double > BSplineType;
BSplineType::Pointer bspline = BSplineType::New();
bspline->SetSplineOrder(filter->GetSplineOrder());
bspline->SetOrigin(origin);
bspline->SetSpacing(spacing);
bspline->SetSize(size);
bspline->SetInputImage(filter->GetPhiLattice());
result.clear();
for (double i=0; i<=2.0*range; i++) {
PointSetType::PointType point; point[0] = i/(2.0*range);
VectorType V = bspline->Evaluate( point );
result.push_back(CVector3(V[0],V[1],V[2]));
}*/
}
else if (pos_txt != string::npos)
{
ifstream myfile;
string l;
double x, y, z;
CVector3 point, pointPrecedent;
int i = 0;
myfile.open(filename.c_str());
if (myfile.is_open())
{
while (myfile.good())
{
getline(myfile,l);
stringstream ss(l);
ss >> x >> z >> y;
point = CVector3(x,y,z);
if ((point-pointPrecedent).Norm() > 0) {
pointPrecedent = point;
//point[1] = -point[1];
result.push_back(point);
}
i++;
}
}
myfile.close();
}
int main(int argc, char *argv[])
{
printf("STARTING\n");
srand (time(NULL));
if (argc == 1)
{
help();
return EXIT_FAILURE;
}
// Initialization of parameters
string inputFilename = "", outputPath = "", outputFilenameBinary = "", outputFilenameMesh = "", outputFilenameBinaryCSF = "", outputFilenameMeshCSF = "", outputFilenameAreas = "", outputFilenameAreasCSF = "", outputFilenameCenterline = "", outputFilenameCenterlineBinary = "", inputCenterlineFilename = "", initMaskFilename = "";
double typeImageFactor = 0.0, initialisation = 0.5;
int downSlice = -10000, upSlice = 10000;
string suffix;
bool input_dicom = false, output_detection = false, output_detection_nii = false, output_mesh = false, output_centerline_binary = false, output_centerline_coord = false, output_cross = false, init_with_centerline = false, init_with_mask = false, verbose = false, output_init_tube = false, completeCenterline = false, init_validation = false, low_res_mesh = false, CSF_segmentation = false;
int gapInterSlices = 4, nbSlicesInitialisation = 5;
double radius = 4.0;
int numberOfPropagationIteration = 200;
double maxDeformation = 0.0, maxArea = 0.0, minContrast = 50.0, tradeoff_d = 25, tradeoff_K = 200;
bool tradeoff_d_bool = false;
int nbiter_GGVF = 2;
// Initialization with Vesselness Filter and Minimal Path
bool init_with_minimalpath = true;
double minimalPath_alpha=0.1;
double minimalPath_beta=1.0;
double minimalPath_gamma=5.0;
double minimalPath_sigmaMinimum=1.5;
double minimalPath_sigmaMaximum=4.5;
unsigned int minimalPath_numberOfSigmaSteps=10;
double minimalPath_sigmaDistance=30.0;
// Reading option parameters from user input
cout << argc;
for (int i = 0; i < argc; ++i) {
if (strcmp(argv[i],"-i")==0) {
i++;
inputFilename = argv[i];
}
else if (strcmp(argv[i],"-i-dicom")==0) {
i++;
//inputFilename = argv[i];
//input_dicom = true;
}
else if (strcmp(argv[i],"-o")==0) {
i++;
outputPath = argv[i];
}
else if (strcmp(argv[i],"-t")==0) {
i++;
if (strcmp(argv[i],"t1")==0) {
typeImageFactor = -1.0;
if (verbose) cout << endl << "WARNING: be sure your image is a T1-weighted image." << endl << endl;
}
else if (strcmp(argv[i],"t2")==0) {
typeImageFactor = 1.0;
if (verbose) cout << endl << "WARNING: be sure your image is a T2-weighted image." << endl << endl;
}
else {
cout << "Error: Invalid type or image (need to be \"t1\" or \"t2\")" << endl << endl;
help();
return EXIT_FAILURE;
}
}
else if (strcmp(argv[i],"-param-init")==0)
{
printf("\nPARAM INIT\n");
// param structure delimited by commas:
// minimalPath_alpha,minimalPath_beta,minimalPath_gamma,minimalPath_sigmaMinimum,minimalPath_sigmaMaximum,minimalPath_numberOfSigmaSteps,minimalPath_sigmaDistance
vector<string> param_init = split(argv[i], ',');
minimalPath_alpha = atof(param_init[0].c_str());
printf("%f\n", minimalPath_alpha);
minimalPath_beta = atof(param_init[1].c_str());
printf("%f\n", minimalPath_beta);
minimalPath_gamma = atof(param_init[2].c_str());
printf("%f\n", minimalPath_gamma);
minimalPath_sigmaMinimum = atof(param_init[3].c_str());
printf("%f\n", minimalPath_sigmaMinimum);
minimalPath_sigmaMaximum = atof(param_init[4].c_str());
printf("%f\n", minimalPath_sigmaMaximum);
minimalPath_numberOfSigmaSteps = atoi(param_init[5].c_str());
printf("%i\n", minimalPath_numberOfSigmaSteps);
minimalPath_sigmaDistance = atof(param_init[6].c_str());
printf("%f\n", minimalPath_sigmaDistance);
}
else if (strcmp(argv[i],"-verbose")==0) {
verbose = true;
}
else if (strcmp(argv[i],"-help")==0) {
help();
return EXIT_FAILURE;
}
}
// Checking if user added mandatory arguments
if (inputFilename == "")
{
cerr << "Input filename not provided" << endl;
help();
return EXIT_FAILURE;
}
if (typeImageFactor == 0)
{
cerr << "Error: The type of contrast not provided (option -t)" << endl;
help();
return EXIT_FAILURE;
}
// output files must have the same extension as input file
string nii=".nii", niigz=".nii.gz";
suffix=niigz;
size_t pos = inputFilename.find(niigz);
if (pos == string::npos) {
pos = inputFilename.find(nii);
suffix = nii;
}
// Extract the input file name
unsigned found_slash = inputFilename.find_last_of("/\\");
string inputFilename_nameonly = inputFilename.substr(found_slash+1);
unsigned found_point = inputFilename_nameonly.find_first_of(".");
inputFilename_nameonly = inputFilename_nameonly.substr(0,found_point);
// Check if output folder ends with /
if (outputPath!="" && outputPath.compare(outputPath.length()-1,1,"/")) outputPath += "/"; // add "/" if missing
// Set output filenames
outputFilenameBinary = outputPath+inputFilename_nameonly+"_seg"+suffix;
outputFilenameMesh = outputPath+inputFilename_nameonly+"_mesh.vtk";
outputFilenameBinaryCSF = outputPath+inputFilename_nameonly+"_CSF_seg"+suffix;
outputFilenameMeshCSF = outputPath+inputFilename_nameonly+"_CSF_mesh.vtk";
outputFilenameAreas = outputPath+inputFilename_nameonly+"_cross_sectional_areas.txt";
outputFilenameAreasCSF = outputPath+inputFilename_nameonly+"_cross_sectional_areas_CSF.txt";
outputFilenameCenterline = outputPath+inputFilename_nameonly+"_centerline.txt";
outputFilenameCenterlineBinary = outputPath+inputFilename_nameonly+"_centerline"+suffix;
// if output path doesn't exist, we create it
if (outputPath!="") itk::FileTools::CreateDirectory(outputPath.c_str());
// Image reading - image can be T1 or T2 (or Tx-like) depending on contrast between spinal cord and CSF
// typeImageFactor depend of contrast type and is equal to +1 when CSF is brighter than spinal cord and equal to -1 inversely
ImageType::Pointer initialImage, image = ImageType::New();
ReaderType::Pointer reader = ReaderType::New();
itk::NiftiImageIO::Pointer io = itk::NiftiImageIO::New();
reader->SetImageIO(io);
reader->SetFileName(inputFilename);
try {
reader->Update();
} catch( itk::ExceptionObject & e ) {
cerr << "ERROR: Exception caught while reading input image (-i option). Are you sure the image exist?" << endl;
cerr << e << endl;
return EXIT_FAILURE;
}
initialImage = reader->GetOutput();
ImageType::SizeType desiredSize = initialImage->GetLargestPossibleRegion().GetSize();
ImageType::SpacingType spacingI = initialImage->GetSpacing();
// Intensity normalization
RescaleFilterType::Pointer rescaleFilter = RescaleFilterType::New();
rescaleFilter->SetInput(initialImage);
rescaleFilter->SetOutputMinimum(0);
rescaleFilter->SetOutputMaximum(1000);
try {
rescaleFilter->Update();
} catch( itk::ExceptionObject & e ) {
cerr << "Exception caught while normalizing input image " << endl;
cerr << e << endl;
return EXIT_FAILURE;
}
image = rescaleFilter->GetOutput();
vesselnessFilter(image, typeImageFactor, minimalPath_alpha, minimalPath_beta, minimalPath_gamma, minimalPath_sigmaMinimum, minimalPath_sigmaMaximum, minimalPath_numberOfSigmaSteps, minimalPath_sigmaDistance);
return EXIT_SUCCESS;
}