NifTK  16.4.1 - 0798f20
CMIC's Translational Medical Imaging Platform
Public Types | Public Member Functions | Public Attributes | List of all members
InputParameters Class Reference
Collaboration diagram for InputParameters:
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Public Types

typedef tee_device< ostream,
ofstream > 		TeeDevice
 
typedef stream< TeeDevice > TeeStream
 
typedef tee_device< ostream,
ofstream > 		TeeDevice
 
typedef stream< TeeDevice > TeeStream
 
typedef tee_device
< std::ostream, std::ofstream > 		TeeDevice
 
typedef stream< TeeDevice > TeeStream
 

Public Member Functions

 InputParameters (TCLAP::CmdLine &commandLine, bool verbose, bool flgSave, bool compression, bool debug, bool overwrite, bool noRegistration, int minNSlices, std::string dInput, std::string dOutput, std::string logfile, std::string csvfile, std::string strT1, std::string strT2, std::string strADC, std::string strDCE, std::string segEM, QStringList aSegEM, std::string regAffine, QStringList aRegAffine, std::string regNonRigid, QStringList aRegNonRigid)
 
 ~InputParameters ()
 
void Print (void)
 
void PrintMessage (std::stringstream &message)
 
void PrintError (std::stringstream &message)
 
void PrintErrorAndExit (std::stringstream &message)
 
void PrintWarning (std::stringstream &message)
 
void PrintTag (const DictionaryType &dictionary, std::string entryId)
 
bool ReadImageFromFile (std::string inDir, std::string filename, std::string description, ImageType::Pointer &image)
 
bool ReadImageFromFile (std::string inDir, std::string filename, std::string description, nifti_image *&image)
 
void WriteImageToFile (std::string filename, std::string description, ImageType::Pointer image)
 
void WriteImageToFile (std::string filename, std::string description, nifti_image *image)
 
void DeleteFile (std::string filename)
 
 InputParameters (TCLAP::CmdLine &commandLine, bool verbose, bool flgRegister, bool flgSave, bool compression, bool debug, bool overwrite, bool computeMaskFromT2Only, bool excludeAxilla, bool cropFit, float coilCropDist, float maxNumberOfIterations, float nFittingLevels, bool doNotBiasFieldCorrectT1w, bool doNotBiasFieldCorrectT2w, std::string subdirMRI, std::string subdirData, std::string prefix, std::string dInput, std::string logfile, std::string csvfileT1w, std::string csvfileT2w, std::string strStructuralT2, std::string strFatSatT1, std::string strDixonWater, std::string strDixonFat, std::string segEM, QStringList aSegEM, std::string regAffine, QStringList aRegAffine, std::string regNonRigid, QStringList aRegNonRigid, std::string regResample, QStringList aRegResample)
 
 ~InputParameters ()
 
void Print (void)
 
void PrintMessage (std::stringstream &message)
 
void PrintError (std::stringstream &message)
 
void PrintErrorAndExit (std::stringstream &message)
 
void PrintWarning (std::stringstream &message)
 
void PrintTag (const DictionaryType &dictionary, std::string entryId)
 
bool ReadImageFromFile (std::string dirInput, std::string filename, std::string description, ImageType::Pointer &image)
 
bool ReadImageFromFile (std::string dirInput, std::string filename, std::string description, nifti_image *&image)
 
void WriteImageToFile (std::string filename, std::string description, ImageType::Pointer image)
 
void WriteImageToFile (std::string filename, std::string description, MaskImageType::Pointer image)
 
void WriteImageToFile (std::string filename, std::string description, nifti_image *image)
 
void DeleteFile (std::string filename)
 
 InputParameters (TCLAP::CmdLine &commandLine, bool verbose, bool compression, bool debug, bool overwrite, bool fatIsBright, std::string subDirMask, std::string fileMask, std::string subDirImage, std::string fileImage, std::string subDirData, std::string prefix, std::string dInput, std::string logfile, std::string csvfile, std::string segEM, QStringList aSegEM)
 
 ~InputParameters ()
 
void Print (void)
 
void PrintMessage (std::stringstream &message)
 
void PrintError (std::stringstream &message)
 
void PrintErrorAndExit (std::stringstream &message)
 
void PrintWarning (std::stringstream &message)
 
bool ReadImageFromFile (std::string fileInput, std::string description, ImageType::Pointer &image)
 
bool ReadImageFromFile (std::string dirInput, std::string filename, std::string description, ImageType::Pointer &image)
 
void WriteImageToFile (std::string filename, std::string description, ImageType::Pointer image, bool flgConcatenatePath=true)
 
void DeleteFile (std::string filename)
 

Public Attributes

bool flgVerbose
 
bool flgSaveImages
 
bool flgDebug
 
bool flgCompression
 
bool flgOverwrite
 
bool flgDoNotRegister
 
int minNumberOfSlices
 
std::string dirInput
 
std::string dirOutput
 
std::string fileLog
 
std::string fileOutputCSV
 
std::string strSeriesDescT1W
 
std::string strSeriesDescT2W
 
std::string strSeriesDescADC
 
std::string strSeriesDescDCE
 
std::string progSegEM
 
std::string progRegAffine
 
std::string progRegNonRigid
 
QStringList argsSegEM
 
QStringList argsRegAffine
 
QStringList argsRegNonRigid
 
std::ofstream * foutLog
 
std::ofstream * foutOutputCSV
 
std::ostream * newCout
 
TeeDevice * teeDevice
 
TeeStream * teeStream
 
bool flgRegisterImages
 
bool flgDoNotBiasFieldCorrectT1w
 
bool flgDoNotBiasFieldCorrectT2w
 
bool flgComputeMaskFromT2Only
 
bool flgExcludeAxilla
 
bool flgCropFit
 
float coilCropDistance
 
float MaximumNumberOfIterations
 
float NumberOfFittingLevels
 
std::string fileT1wOutputCSV
 
std::string fileT2wOutputCSV
 
std::string dirSubMRI
 
std::string dirSubData
 
std::string dirPrefix
 
std::string strSeriesDescStructuralT2
 
std::string strSeriesDescFatSatT1
 
std::string strSeriesDescDixonWater
 
std::string strSeriesDescDixonFat
 
std::string progRegResample
 
QStringList argsRegResample
 
std::ofstream * foutOutputT1wCSV
 
std::ofstream * foutOutputT2wCSV
 
bool flgFatIsBright
 
std::string fileMaskPattern
 
std::string fileImagePattern
 
std::string dirMask
 
std::string dirImage
 

Member Typedef Documentation

typedef tee_device<ostream, ofstream> InputParameters::TeeDevice
typedef tee_device<std::ostream, std::ofstream> InputParameters::TeeDevice
typedef tee_device<ostream, ofstream> InputParameters::TeeDevice
typedef stream<TeeDevice> InputParameters::TeeStream
typedef stream<TeeDevice> InputParameters::TeeStream
typedef stream<TeeDevice> InputParameters::TeeStream

Constructor & Destructor Documentation

InputParameters::InputParameters ( TCLAP::CmdLine &  commandLine,
bool  verbose,
bool  flgSave,
bool  compression,
bool  debug,
bool  overwrite,
bool  noRegistration,
int  minNSlices,
std::string  dInput,
std::string  dOutput,
std::string  logfile,
std::string  csvfile,
std::string  strT1,
std::string  strT2,
std::string  strADC,
std::string  strDCE,
std::string  segEM,
QStringList  aSegEM,
std::string  regAffine,
QStringList  aRegAffine,
std::string  regNonRigid,
QStringList  aRegNonRigid 
)
inline
InputParameters::~InputParameters ( )
inline
InputParameters::InputParameters ( TCLAP::CmdLine &  commandLine,
bool  verbose,
bool  flgRegister,
bool  flgSave,
bool  compression,
bool  debug,
bool  overwrite,
bool  computeMaskFromT2Only,
bool  excludeAxilla,
bool  cropFit,
float  coilCropDist,
float  maxNumberOfIterations,
float  nFittingLevels,
bool  doNotBiasFieldCorrectT1w,
bool  doNotBiasFieldCorrectT2w,
std::string  subdirMRI,
std::string  subdirData,
std::string  prefix,
std::string  dInput,
std::string  logfile,
std::string  csvfileT1w,
std::string  csvfileT2w,
std::string  strStructuralT2,
std::string  strFatSatT1,
std::string  strDixonWater,
std::string  strDixonFat,
std::string  segEM,
QStringList  aSegEM,
std::string  regAffine,
QStringList  aRegAffine,
std::string  regNonRigid,
QStringList  aRegNonRigid,
std::string  regResample,
QStringList  aRegResample 
)
inline
InputParameters::~InputParameters ( )
inline
InputParameters::InputParameters ( TCLAP::CmdLine &  commandLine,
bool  verbose,
bool  compression,
bool  debug,
bool  overwrite,
bool  fatIsBright,
std::string  subDirMask,
std::string  fileMask,
std::string  subDirImage,
std::string  fileImage,
std::string  subDirData,
std::string  prefix,
std::string  dInput,
std::string  logfile,
std::string  csvfile,
std::string  segEM,
QStringList  aSegEM 
)
inline
InputParameters::~InputParameters ( )
inline

Member Function Documentation

void InputParameters::DeleteFile ( std::string  filename)
inline
void InputParameters::DeleteFile ( std::string  filename)
inline
void InputParameters::DeleteFile ( std::string  filename)
inline
void InputParameters::Print ( void  )
inline
void InputParameters::Print ( void  )
inline
void InputParameters::Print ( void  )
inline
void InputParameters::PrintError ( std::stringstream &  message)
inline
void InputParameters::PrintError ( std::stringstream &  message)
inline
void InputParameters::PrintError ( std::stringstream &  message)
inline
void InputParameters::PrintErrorAndExit ( std::stringstream &  message)
inline
void InputParameters::PrintErrorAndExit ( std::stringstream &  message)
inline
void InputParameters::PrintErrorAndExit ( std::stringstream &  message)
inline
void InputParameters::PrintMessage ( std::stringstream &  message)
inline
void InputParameters::PrintMessage ( std::stringstream &  message)
inline
void InputParameters::PrintMessage ( std::stringstream &  message)
inline
void InputParameters::PrintTag ( const DictionaryType &  dictionary,
std::string  entryId 
)
inline
void InputParameters::PrintTag ( const DictionaryType &  dictionary,
std::string  entryId 
)
inline
void InputParameters::PrintWarning ( std::stringstream &  message)
inline
void InputParameters::PrintWarning ( std::stringstream &  message)
inline
void InputParameters::PrintWarning ( std::stringstream &  message)
inline
bool InputParameters::ReadImageFromFile ( std::string  inDir,
std::string  filename,
std::string  description,
ImageType::Pointer &  image 
)
inline
bool InputParameters::ReadImageFromFile ( std::string  inDir,
std::string  filename,
std::string  description,
nifti_image *&  image 
)
inline
bool InputParameters::ReadImageFromFile ( std::string  fileInput,
std::string  description,
ImageType::Pointer &  image 
)
inline
bool InputParameters::ReadImageFromFile ( std::string  dirInput,
std::string  filename,
std::string  description,
ImageType::Pointer &  image 
)
inline
bool InputParameters::ReadImageFromFile ( std::string  dirInput,
std::string  filename,
std::string  description,
ImageType::Pointer &  image 
)
inline
bool InputParameters::ReadImageFromFile ( std::string  dirInput,
std::string  filename,
std::string  description,
nifti_image *&  image 
)
inline
void InputParameters::WriteImageToFile ( std::string  filename,
std::string  description,
ImageType::Pointer  image 
)
inline
void InputParameters::WriteImageToFile ( std::string  filename,
std::string  description,
nifti_image *  image 
)
inline
void InputParameters::WriteImageToFile ( std::string  filename,
std::string  description,
ImageType::Pointer  image,
bool  flgConcatenatePath = true 
)
inline
void InputParameters::WriteImageToFile ( std::string  filename,
std::string  description,
ImageType::Pointer  image 
)
inline
void InputParameters::WriteImageToFile ( std::string  filename,
std::string  description,
MaskImageType::Pointer  image 
)
inline
void InputParameters::WriteImageToFile ( std::string  filename,
std::string  description,
nifti_image *  image 
)
inline

Member Data Documentation

QStringList InputParameters::argsRegAffine
QStringList InputParameters::argsRegNonRigid
QStringList InputParameters::argsRegResample
QStringList InputParameters::argsSegEM
float InputParameters::coilCropDistance
std::string InputParameters::dirImage
std::string InputParameters::dirInput
std::string InputParameters::dirMask
std::string InputParameters::dirOutput
std::string InputParameters::dirPrefix
std::string InputParameters::dirSubData
std::string InputParameters::dirSubMRI
std::string InputParameters::fileImagePattern
std::string InputParameters::fileLog
std::string InputParameters::fileMaskPattern
std::string InputParameters::fileOutputCSV
std::string InputParameters::fileT1wOutputCSV
std::string InputParameters::fileT2wOutputCSV
bool InputParameters::flgCompression
bool InputParameters::flgComputeMaskFromT2Only
bool InputParameters::flgCropFit
bool InputParameters::flgDebug
bool InputParameters::flgDoNotBiasFieldCorrectT1w
bool InputParameters::flgDoNotBiasFieldCorrectT2w
bool InputParameters::flgDoNotRegister
bool InputParameters::flgExcludeAxilla
bool InputParameters::flgFatIsBright
bool InputParameters::flgOverwrite
bool InputParameters::flgRegisterImages
bool InputParameters::flgSaveImages
bool InputParameters::flgVerbose
std::ofstream * InputParameters::foutLog
std::ofstream * InputParameters::foutOutputCSV
std::ofstream* InputParameters::foutOutputT1wCSV
std::ofstream* InputParameters::foutOutputT2wCSV
float InputParameters::MaximumNumberOfIterations
int InputParameters::minNumberOfSlices
std::ostream * InputParameters::newCout
float InputParameters::NumberOfFittingLevels
std::string InputParameters::progRegAffine
std::string InputParameters::progRegNonRigid
std::string InputParameters::progRegResample
std::string InputParameters::progSegEM
std::string InputParameters::strSeriesDescADC
std::string InputParameters::strSeriesDescDCE
std::string InputParameters::strSeriesDescDixonFat
std::string InputParameters::strSeriesDescDixonWater
std::string InputParameters::strSeriesDescFatSatT1
std::string InputParameters::strSeriesDescStructuralT2
std::string InputParameters::strSeriesDescT1W
std::string InputParameters::strSeriesDescT2W
TeeDevice * InputParameters::teeDevice
TeeStream * InputParameters::teeStream
The documentation for this class was generated from the following files:
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