void transform(string inputFilename, string outputFilename)
{
typedef itk::Image< TPixelType, N > ImageType;
typedef itk::ImageFileReader< ImageType > ReaderType;
typedef itk::ImageFileWriter< ImageType > WriterType;
typename 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 ) {
std::cerr << "Exception caught while reading image " << std::endl;
std::cerr << e << std::endl;
}
typename WriterType::Pointer writer = WriterType::New();
writer->SetImageIO(io);
writer->SetFileName(outputFilename);
writer->SetInput(reader->GetOutput());
try {
writer->Update();
} catch( itk::ExceptionObject & e ) {
std::cerr << "Exception caught while writing image " << std::endl;
std::cerr << e << std::endl;
}
}
void ReadFile(std::string filename, typename TImageType::Pointer image)
{
typedef itk::ImageFileReader<TImageType> ReaderType;
typename ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(filename);
reader->Update();
image->Graft(reader->GetOutput());
}
template<class TImage> typename TImage::Pointer ttt::JSONTissueTrackingProject::readImage(const std::string & table, int frame) {
typedef itk::ImageFileReader<TImage> ReaderType;
typename ReaderType::Pointer reader = ReaderType::New();
std::stringstream ssQuery, ssFileName;
try {
ssQuery << "SELECT fileName FROM " << table << " WHERE " << table
<< ".idProject=? AND " << table << ".t=?";
std::auto_ptr<sql::PreparedStatement> prep_stmt(
m_DB->prepareStatement(ssQuery.str()));
prep_stmt->setInt(1, m_ProjectID); //IDproject==2
prep_stmt->setInt(2, frame); //IDproject==2
prep_stmt->execute();
std::auto_ptr<sql::ResultSet> res(prep_stmt->getResultSet());
assert(res->next());
std::string fileName = res->getString("fileName");
ssFileName << m_WorkingDirectory << "/" << fileName;
reader->SetFileName(ssFileName.str());
;
reader->Update();
reader->GetOutput()->SetSpacing(m_Spacing);
return reader->GetOutput();
} catch (sql::SQLException &e) {
/*
The MySQL Connector/C++ throws three different exceptions:
- sql::MethodNotImplementedException (derived from sql::SQLException)
- sql::InvalidArgumentException (derived from sql::SQLException)
- sql::SQLException (derived from std::runtime_error)
*/
cout << "# ERR: SQLException in " << __FILE__;
// cout << "(" << EXAMPLE_FUNCTION << ") on line " << __LINE__ << endl;
/* Use what() (derived from std::runtime_error) to fetch the error message */
cout << "# ERR: " << e.what();
cout << " (MySQL error code: " << e.getErrorCode();
cout << ", SQLState: " << e.getSQLState() << " )" << endl;
}
return NULL;
}
mitk::BaseData::Pointer mitk::RawImageFileReaderService::TypedRead(const std::string& path, EndianityType endianity, int* size)
{
typedef itk::Image< TPixel, VImageDimensions > ImageType;
typedef itk::ImageFileReader< ImageType > ReaderType;
typedef itk::RawImageIO< TPixel, VImageDimensions > IOType;
typename ReaderType::Pointer reader = ReaderType::New();
typename IOType::Pointer io = IOType::New();
io->SetFileDimensionality(VImageDimensions);
for (unsigned short int dim = 0; dim < VImageDimensions; ++dim)
{
io->SetDimensions(dim, size[dim] );
}
if (endianity == LITTLE)
{
io->SetByteOrderToLittleEndian();
}
else if (endianity == BIG)
{
io->SetByteOrderToBigEndian();
}
else
{
MITK_INFO << "Warning: endianity not properly set. Resulting image might be incorrect";
}
reader->SetImageIO( io );
reader->SetFileName(path);
try
{
reader->Update();
}
catch( itk::ExceptionObject & err )
{
MITK_ERROR <<"An error occurred during the raw image reading process: ";
MITK_INFO << err << std::endl;
}
mitk::Image::Pointer image = mitk::Image::New();
mitk::CastToMitkImage(reader->GetOutput(), image);
image->SetVolume( reader->GetOutput()->GetBufferPointer());
return image.GetPointer();
}
template <typename T> typename T::Pointer readImage(const char *filename)
{
printf("Reading %s ... \n",filename);
typedef typename itk::ImageFileReader<T> ReaderType;
typename ReaderType::Pointer reader = ReaderType::New();
ReaderType::GlobalWarningDisplayOff(); reader->SetFileName(filename);
try {
reader->Update();
}
catch(itk::ExceptionObject &err) {
std::cerr << "ExceptionObject caught!" <<std::endl;
std::cerr << err << std::endl;
_exit(0);
//return EXIT_FAILURE;
}
printf("Done\n"); return reader->GetOutput();
}
typename T::Pointer readImage(const std::string &filename)
{
std::cout << "Reading " << filename << " ..." << std::endl;
typedef typename itk::ImageFileReader<T> ReaderType;
typename ReaderType::Pointer reader = ReaderType::New();
ReaderType::GlobalWarningDisplayOff();
reader->SetFileName(filename);
try
{
reader->Update();
}
catch(itk::ExceptionObject &err)
{
std::cerr << "Exception object caught!" << std::endl;
std::cerr << err << std::endl;
}
std::cout << "Done." << std::endl;
return reader->GetOutput();
}
Volume* readScalarVolume(const std::string fileName) {
typedef itk::Image<T,3> ImageNDType;
typedef itk::ImageFileReader<ImageNDType> ReaderType;
typename ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(fileName.c_str());
int status = 1;
try
{
reader->Update();
status = 0;
}
catch(itk::ExceptionObject &excp)
{
throw tgt::FileException("ITK Exception: " + std::string(excp.GetDescription()), fileName);
}
if (status)
{
throw tgt::FileException("Other error reading file using ITK!", fileName);
}
return ITKToVoreenCopy<T>(reader->GetOutput());
}
int StartShConversion(int argc, char* argv[])
{
ctkCommandLineParser parser;
parser.setArgumentPrefix("--", "-");
parser.addArgument("input", "i", ctkCommandLineParser::String, "MITK SH image", us::Any(), false);
parser.addArgument("output", "o", ctkCommandLineParser::String, "MRtrix SH image", us::Any(), false);
parser.addArgument("shOrder", "sh", ctkCommandLineParser::Int, "spherical harmonics order");
map<string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
if (parsedArgs.size()==0)
return EXIT_FAILURE;
string inFile = us::any_cast<string>(parsedArgs["input"]);
string outFile = us::any_cast<string>(parsedArgs["output"]);
try
{
typedef itk::Image< float, 4 > OutImageType;
typedef itk::Image< itk::Vector< float, (shOrder*shOrder + shOrder + 2)/2 + shOrder >, 3 > InputImageType;
typename InputImageType::Pointer itkInImage = InputImageType::New();
typedef itk::ImageFileReader< InputImageType > ReaderType;
typename ReaderType::Pointer reader = ReaderType::New();
MITK_INFO << "reading " << inFile;
reader->SetFileName(inFile.c_str());
reader->Update();
itkInImage = reader->GetOutput();
// extract directions from fiber bundle
typename itk::ShCoefficientImageExporter<float, shOrder>::Pointer filter = itk::ShCoefficientImageExporter<float,shOrder>::New();
filter->SetInputImage(itkInImage);
filter->GenerateData();
OutImageType::Pointer outImage = filter->GetOutputImage();
typedef itk::ImageFileWriter< OutImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
MITK_INFO << "writing " << outFile;
writer->SetFileName(outFile.c_str());
writer->SetInput(outImage);
writer->Update();
MITK_INFO << "DONE";
}
catch (itk::ExceptionObject e)
{
MITK_INFO << e;
return EXIT_FAILURE;
}
catch (std::exception e)
{
MITK_INFO << e.what();
return EXIT_FAILURE;
}
catch (...)
{
MITK_INFO << "ERROR!?!";
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
