niftkBreastDicomSeriesReadImageWrite.cxx File Reference

Include dependency graph for niftkBreastDicomSeriesReadImageWrite.cxx:

Classes
struct	arguments

Typedefs
typedef signed short	PixelType
typedef itk::Image< PixelType, Dimension >	ImageType
typedef itk::ImageSeriesReader < ImageType >	ReaderType
typedef itk::GDCMSeriesFileNames	NamesGeneratorType
typedef itk::MetaDataDictionary	DictionaryType
typedef itk::MetaDataObject < std::string >	MetaDataStringType
typedef std::vector< std::string >	FileNamesContainer
typedef itk::SpatialOrientation::ValidCoordinateOrientationFlags	SO_OrientationType

Enumerations
enum	{   O_VERBOSE, O_DEBUG, O_SERIES, O_FILENAME_FILTER,   O_TAGS, O_ORIENTATION, O_OUTPUT_FILESTEM, O_OUTPUT_FILESUFFIX,   O_INPUT_DICOM_DIRECTORY }

Functions
bool	WriteSeriesAsVolume (std::fstream &fout, bool flgVerbose, bool flgDebug, int orientation, std::string seriesIdentifier, std::string filenameFilter, std::string fileOutputStem, std::string fileOutputSuffix, std::string fileOutput, FileNamesContainer &fileNames, ReaderType *reader, std::string tagModalityValue)
std::string	SO_OrientationToString (SO_OrientationType in)
template<class ImageType >
void	DumpDirections (const std::string &prompt, const typename ImageType::Pointer &image)
void	AppendTag (std::string &fileOutputFilename, const DictionaryType &dictionary, std::string entryId, bool flgVerbose)
std::string	SeriesOutputFilename (std::fstream &fout, std::string fileInputImage, std::string fileOutputStem, bool flgVerbose, std::string &tagModalityValue)
bool	WriteSeriesAsVolume (std::fstream &fout, bool flgVerbose, bool flgDebug, int orientation, std::string seriesIdentifier, std::string filenameFilter, std::string fileOutputStem, std::string fileOutputSuffix, std::string fileOutput, NamesGeneratorType *nameGenerator, ReaderType *reader, std::string tagModalityValue)
int	main (int argc, char *argv[])

Variables
struct niftk::CommandLineArgumentDescription	clArgList []
const char *	orientationCodeName [49]
const unsigned int	Dimension = 3

Typedef Documentation

typedef itk::MetaDataDictionary DictionaryType

typedef std::vector< std::string > FileNamesContainer

typedef itk::Image< PixelType, Dimension > ImageType

typedef itk::MetaDataObject< std::string > MetaDataStringType

typedef itk::GDCMSeriesFileNames NamesGeneratorType

typedef signed short PixelType

typedef itk::ImageSeriesReader< ImageType > ReaderType

typedef itk::SpatialOrientation::ValidCoordinateOrientationFlags SO_OrientationType

Enumeration Type Documentation

anonymous enum

Enumerator
O_VERBOSE
O_DEBUG
O_SERIES
O_FILENAME_FILTER
O_TAGS
O_ORIENTATION
O_OUTPUT_FILESTEM
O_OUTPUT_FILESUFFIX
O_INPUT_DICOM_DIRECTORY

Function Documentation

void AppendTag	(	std::string &	fileOutputFilename,
		const DictionaryType &	dictionary,
		std::string	entryId,
		bool	flgVerbose
	)

template<class ImageType >

void DumpDirections	(	const std::string &	prompt,
		const typename ImageType::Pointer &	image
	)

int main	(	int	argc,
		char *	argv[]
	)

std::string SeriesOutputFilename	(	std::fstream &	fout,
		std::string	fileInputImage,
		std::string	fileOutputStem,
		bool	flgVerbose,
		std::string &	tagModalityValue
	)

std::string SO_OrientationToString

(

SO_OrientationType

in

)

bool WriteSeriesAsVolume	(	std::fstream &	fout,
		bool	flgVerbose,
		bool	flgDebug,
		int	orientation,
		std::string	seriesIdentifier,
		std::string	filenameFilter,
		std::string	fileOutputStem,
		std::string	fileOutputSuffix,
		std::string	fileOutput,
		FileNamesContainer &	fileNames,
		ReaderType *	reader,
		std::string	tagModalityValue
	)

bool WriteSeriesAsVolume	(	std::fstream &	fout,
		bool	flgVerbose,
		bool	flgDebug,
		int	orientation,
		std::string	seriesIdentifier,
		std::string	filenameFilter,
		std::string	fileOutputStem,
		std::string	fileOutputSuffix,
		std::string	fileOutput,
		NamesGeneratorType *	nameGenerator,
		ReaderType *	reader,
		std::string	tagModalityValue
	)

Variable Documentation

struct niftk::CommandLineArgumentDescription clArgList[]

Initial value:

= {

  {OPT_SWITCH, "v", NULL, "Verbose output."},
  {OPT_SWITCH, "dbg", NULL, "Output debugging info."},

  {OPT_STRING, "series", "name", "The input series name required."},
  {OPT_STRING, "filter", "pattern", "Only consider DICOM files that contain the string 'pattern'."},
  {OPT_STRING, "tags",   "DICOM tags", "File of additional DICOM tags  eg. '0008|0060' used to split the series."},

  {OPT_INT, "orient", "value", 
   "Orient the image according to itk::SpatialOrientation::ValidCoordinateOrientationFlags.\n"
   "\t e.g. RAI (19): x axis runs from R to L, y from A to P and z from I to S.\n"
   "\t  1=RIP,  2=LIP,  3=RSP,  4=LSP,  5=RIA,  6=LIA,  7=RSA,  8=LSA,\n"
   "\t  9=IRP, 10=ILP, 11=SRP, 12=SLP, 13=IRA, 14=ILA, 15=SRA, 16=SLA,\n"
   "\t 17=RPI, 18=LPI, 19=RAI, 20=LAI, 21=RPS, 22=LPS, 23=RAS, 24=LAS,\n"
   "\t 25=PRI, 26=PLI, 27=ARI, 28=ALI, 29=PRS, 30=PLS, 31=ARS, 32=ALS,\n"
   "\t 33=IPR, 34=SPR, 35=IAR, 36=SAR, 37=IPL, 38=SPL, 39=IAL, 40=SAL,\n"
   "\t 41=PIR, 42=PSR, 43=AIR, 44=ASR, 45=PIL, 46=PSL, 47=AIL, 48=ASL."
  },

  {OPT_STRING, "of", "filestem", "The output filestem or directory (filename will be: 'filestem%s.suffix')."},
  {OPT_STRING|OPT_REQ, "os", "suffix",   "The output image suffix to use when using option '-of'."},

  {OPT_STRING|OPT_REQ|OPT_LONELY, NULL, "directory", "Input DICOM directory."},

  {OPT_DONE, NULL, NULL, 
   "Program to convert the content of a DICOM directory into breast image volumes.\n"
  }
}

const unsigned int Dimension = 3

const char* orientationCodeName[49]