This library provides classes for input and output of images, transformations, and other types of objects. More...

Classes
class	cmtk::ClassStream
	Class for writing and reading various library classes to and from disk. More...
class	cmtk::ClassStreamStudyList
	StudyList with class stream file system interface. More...
class	cmtk::DICOM
	Reader/writer class for DICOM images. More...
struct	cmtk::FileFormatMagic
	Structure that holds information on magic file number. More...
class	cmtk::FileFormat
	Identify file (and directory) formats. More...
class	cmtk::FileHeader
	Access to fields in a binary file header. More...
class	cmtk::PGM
	Reader/writer class for PGM (portable graymap) files. More...
class	cmtk::ResourceFile
	Resource file is a map of sections accessed by section title. More...
class	cmtk::ScalarImageIO
	Read and write scalar 2d images. More...
class	cmtk::SQLite
	Wrapper class for SQLite database. More...
class	cmtk::Study
	Class for parameters of a general imaging study. More...
class	cmtk::StudyImageSet
	An imaging study that is constructed from multiple 2-D images. More...
class	cmtk::StudyList
class	cmtk::TypedStream
	Class for reading and writing og "typedstream" archives. More...
class	cmtk::TypedStreamStudylist
	Studylist with typedstream file system interface. More...
class	cmtk::VolumeFromFile
	Class to read uniform volume from disk file(s). More...
struct	cmtk::FileHeaderBioRad
	BioRad microscopy image file header. More...
class	cmtk::VolumeFromSlices
	Class for building 3D fields from slice image data. More...
class	cmtk::VolumeFromStudy
	Class for building 3D volumes from an Study object. More...
class	cmtk::VolumeIO
	Class for input/output of 3-D image data. More...
class	cmtk::XformIO
	Utility class for one-stop transformation import. More...
class	cmtk::XformListIO
	Utility class to generate a list of concatenated transformation objects. More...
Typedefs
typedef std::list< std::string >	cmtk::ResourceSection
	Resource file section is a list of strings.
typedef std::multimap < Study::SmartPtr, Xform::SmartPtr >	cmtk::StudyToXform
typedef std::map < Study::SmartPtr, StudyToXform >	cmtk::StudyToStudyToXform
Enumerations
enum	cmtk::AnalyzeDataType { cmtk::ANALYZE_TYPE_NONE = 0, cmtk::ANALYZE_TYPE_BINARY = 1, cmtk::ANALYZE_TYPE_UNSIGNED_CHAR = 2, cmtk::ANALYZE_TYPE_SIGNED_SHORT = 4, cmtk::ANALYZE_TYPE_SIGNED_INT = 8, cmtk::ANALYZE_TYPE_FLOAT = 16, cmtk::ANALYZE_TYPE_COMPLEX = 32, cmtk::ANALYZE_TYPE_DOUBLE = 64, cmtk::ANALYZE_TYPE_RGB = 128, cmtk::ANALYZE_TYPE_USHORT = 132, cmtk::ANALYZE_TYPE_UINT = 136, cmtk::ANALYZE_TYPE_ALL = 255 }
	IDs for data types in Analyze image file. More...
enum	cmtk::AnalyzeOrientation { cmtk::ANALYZE_AXIAL = 0, cmtk::ANALYZE_CORONAL = 1, cmtk::ANALYZE_SAGITTAL = 2, cmtk::ANALYZE_AXIAL_FLIP = 3, cmtk::ANALYZE_CORONAL_FLIP = 4, cmtk::ANALYZE_SAGITTAL_FLIP = 5, cmtk::ANALYZE_UNKNOWN = 255 }
	IDs for slice orientations in Analyze image file. More...
enum	cmtk::FileFormatID { cmtk::FILEFORMAT_NEXIST = 0, cmtk::FILEFORMAT_COMPRESSED_ARCHIVE = 1, cmtk::FILEFORMAT_STUDY = 2, cmtk::FILEFORMAT_STUDYLIST = 3, cmtk::FILEFORMAT_TYPEDSTREAM = 4, cmtk::FILEFORMAT_PGM = 5, cmtk::FILEFORMAT_DICOM = 6, cmtk::FILEFORMAT_VANDERBILT = 7, cmtk::FILEFORMAT_AMIRA = 8, cmtk::FILEFORMAT_RAW = 9, cmtk::FILEFORMAT_RAW3D = 10, cmtk::FILEFORMAT_BIORAD = 11, cmtk::FILEFORMAT_NIFTI_DETACHED = 12, cmtk::FILEFORMAT_NIFTI_SINGLEFILE = 13, cmtk::FILEFORMAT_ANALYZE_AVW = 14, cmtk::FILEFORMAT_METAIMAGE = 15, cmtk::FILEFORMAT_NRRD = 16, cmtk::FILEFORMAT_ANALYZE_HDR = 17, cmtk::FILEFORMAT_ANALYZE_HDR_BIGENDIAN = 18, cmtk::FILEFORMAT_ITK_TFM = 19, cmtk::FILEFORMAT_UNKNOWN }
	ID codes for known file formats. More...
enum	{ cmtk::PALETTE_GRAY = 0, cmtk::PALETTE_RED = 1, cmtk::PALETTE_GREEN = 2, cmtk::PALETTE_BLUE = 3, cmtk::PALETTE_RAINBOW = 4, cmtk::PALETTE_LABELS = 5 }
	Constants to identify color table. More...
Functions
ClassStream &	cmtk::operator<< (ClassStream &stream, const AffineXform &affineXform)
	Write affine transformation object.
ClassStream &	cmtk::operator>> (ClassStream &stream, AffineXform::SmartPtr &affineXform)
	Read affine transformation.
ClassStream &	cmtk::operator>> (ClassStream &stream, AffineXform &affineXform)
	Read affine transformation.
template<class TMetricFunctionalType >
ClassStream &	cmtk::operator<< (ClassStream &stream, const AffineMultiChannelRegistrationFunctional< TMetricFunctionalType > &functional)
	Write file names and transformations from affine multi-channel registration functional.
template<class TMetricFunctionalType >
ClassStream &	cmtk::operator>> (ClassStream &stream, AffineMultiChannelRegistrationFunctional< TMetricFunctionalType > &functional)
	Read file names and transformations from archive to multi-channel affine registration functional.
template<class TMetricFunctionalType >
ClassStream &	cmtk::operator<< (ClassStream &stream, const SplineWarpMultiChannelRegistrationFunctional< TMetricFunctionalType > &functional)
	Write file names and transformations from spline warp multi-channel registration functional.
ClassStream &	cmtk::operator<< (ClassStream &stream, const Xform &xform)
	Write transformation object.
ClassStream &	cmtk::operator<< (ClassStream &stream, const GroupwiseRegistrationFunctionalBase &func)
ClassStream &	cmtk::operator>> (ClassStream &stream, GroupwiseRegistrationFunctionalBase &func)
std::istream &	cmtk::operator>> (std::istream &stream, SegmentationLabelMap &lblMap)
	Operator to read a list of label IDs from a C++ stream.
	cmtk::TypedStream::TypedStream (const char *filename, const TypedStreamMode mode)
	Open constructor.
	cmtk::TypedStream::TypedStream (const char dir, const char archive, const TypedStreamMode mode)
	Open constructor for separate path and archive names.
virtual	cmtk::TypedStream::~TypedStream ()
	Destructor.
void	cmtk::TypedStream::Open (const char *filename, const TypedStreamMode mode)
	Open another archive without constructing a new object.
void	cmtk::TypedStream::Open (const char dir, const char archive, const TypedStreamMode mode)
	Open another archive in explicit directory.
void	cmtk::TypedStream::Close ()
	Close an open archive.
TypedStreamCondition	cmtk::TypedStream::Seek (const char *section, const bool forward=false)
	Move to a particular section in the open archive.
TypedStreamCondition	cmtk::TypedStream::Rewind ()
	Rewind archive.
int	cmtk::TypedStream::IsValid ()
	Return validity of archive.
TypedStreamStatus	cmtk::TypedStream::GetStatus () const
	Return status of last operation.
TypedStreamCondition	cmtk::TypedStream::Begin (const char *section=NULL)
	Begin a section.
TypedStreamCondition	cmtk::TypedStream::End (const bool flush=false)
	End a section.
bool	cmtk::TypedStream::ReadBool (const char *key, const bool defaultValue=false, const bool forward=false)
	Read boolean value from an open archive.
TypedStreamCondition	cmtk::TypedStream::ReadBoolArray (const char key, byte const array, const int size, const bool forward=false)
	Read array of boole values from an open archive.
int	cmtk::TypedStream::ReadInt (const char *key, const int defaultValue=0, const bool forward=false)
	Read integer value from an open archive.
TypedStreamCondition	cmtk::TypedStream::ReadIntArray (const char key, int const array, const int size, const bool forward=false)
	Read array of integer values from an open archive.
float	cmtk::TypedStream::ReadFloat (const char *key, const float defaultValue=0, const bool forward=false)
	Read single-precision value from an open archive.
TypedStreamCondition	cmtk::TypedStream::ReadFloatArray (const char key, float const array, const int size, const bool forward=false)
	Read array of single-precision values from an open archive.
double	cmtk::TypedStream::ReadDouble (const char *key, const double defaultValue=0, const bool forward=false)
	Read double-precision value from an open archive.
TypedStreamCondition	cmtk::TypedStream::ReadDoubleArray (const char key, double const array, const int size, const bool forward=false)
	Read array of double-precision values from an open archive.
Types::Coordinate	cmtk::TypedStream::ReadCoordinate (const char *key, const Types::Coordinate defaultValue=0, const bool forward=false)
	Read double- or single precision value from an open archive.
Types::DataItem	cmtk::TypedStream::ReadItem (const char *key, const Types::DataItem defaultValue=0, const bool forward=false)
	Read double- or single precision value from an open archive.
TypedStreamCondition	cmtk::TypedStream::ReadCoordinateArray (const char key, Types::Coordinate const array, const int size, const bool forward=false)
	Read array of double- or single precision values from an open archive.
TypedStreamCondition	cmtk::TypedStream::ReadItemArray (const char key, Types::DataItem const array, const int size, const bool forward=false)
	Read array of double- or single precision values from an open archive.
char *	cmtk::TypedStream::ReadString (const char key, const char defaultValue=NULL, const bool forward=false)
	Read null-terminated string from an open archive.
TypedStreamCondition	cmtk::TypedStream::WriteBool (const char *key, const bool value)
	Write a boolean value to an open archive.
TypedStreamCondition	cmtk::TypedStream::WriteInt (const char *key, const int value)
	Write an integer value to an open archive.
TypedStreamCondition	cmtk::TypedStream::WriteFloat (const char *key, const float value)
	Write a float value to an open archive.
TypedStreamCondition	cmtk::TypedStream::WriteDouble (const char *key, const double value)
	Write a double precision float value to an open archive.
TypedStreamCondition	cmtk::TypedStream::WriteCoordinate (const char *key, const Types::Coordinate value)
	Write an Types::Coordinate value to an open archive.
TypedStreamCondition	cmtk::TypedStream::WriteItem (const char *key, const Types::DataItem value)
	Write an Types::DataItem value to an open archive.
TypedStreamCondition	cmtk::TypedStream::WriteString (const char key, const char value)
	Write a string to an open archive.
TypedStreamCondition	cmtk::TypedStream::WriteString (const char *key, const std::string &value)
	Write a string to an open archive.
TypedStreamCondition	cmtk::TypedStream::WriteComment (const char *fmt,...)
	Write a formated comment to an open archive.
TypedStreamCondition	cmtk::TypedStream::WriteComment (const int argc, const char *argv[])
	Write string array as comment to an open archive.
TypedStreamCondition	cmtk::TypedStream::WriteComment (int argc, char *argv[])
	Write string array as comment to an open archive.
TypedStreamCondition	cmtk::TypedStream::WriteIntArray (const char key, const int array, const int size, const int valuesPerLine=10)
	Write array of integer values to an open archive.
TypedStreamCondition	cmtk::TypedStream::WriteBoolArray (const char key, const byte array, const int size, const int valuesPerLine=10)
	Write array of binay encoded boole values to an open archive.
TypedStreamCondition	cmtk::TypedStream::WriteFloatArray (const char key, const float array, const int size, const int valuesPerLine=10)
	Write array of single-precision values to an open archive.
TypedStreamCondition	cmtk::TypedStream::WriteDoubleArray (const char key, const double array, const int size, const int valuesPerLine=10)
	Write array of double-precision values to an open archive.
TypedStreamCondition	cmtk::TypedStream::WriteCoordinateArray (const char key, const Types::Coordinate array, const int size, const int valuesPerLine=10)
	Write array of double- or single precision values to an open archive.
TypedStreamCondition	cmtk::TypedStream::WriteItemArray (const char key, const Types::DataItem array, const int size, const int valuesPerLine=10)
	Write array of double- or single precision values to an open archive.
void	cmtk::TypedStream::SetDebugFlag (const TypedStreamDebugFlag debugFlag=TYPEDSTREAM_DEBUG_ON)
	Set debugging flag.
void	cmtk::TypedStream::InitInternals ()
	Initialize internal data structures.
TypedStreamCondition	cmtk::TypedStream::GenericReadArray (const char key, const int type, void const array, const int arraySize, const bool forward=false)
	Utility function: Read an array of arbitrary type.
TypedStreamToken	cmtk::TypedStream::ReadLineToken ()
	Read the next archive line to the buffer.
static int	cmtk::TypedStream::StringCmp (const char s1, const char s2)
	Compare two strings.
char *	cmtk::TypedStream::StringSplit (char *s1) const
	Separate next token.
static const char *	cmtk::TypedStream::GetTypedStreamIdent ()
	Return the identifier for the generated archive format (version).
void	cmtk::TypedStream::DebugOutput (const char *format,...)
	Output diagnostic message if debug flag is set.
ClassStream &	cmtk::ClassStream::operator<< (const LandmarkList *landmarkList)
	Write landmark list.
ClassStream &	cmtk::ClassStream::operator>> (WarpXform::SmartPtr &warpXform)
	Read (spline or linear) warp transformation.
ClassStream &	cmtk::ClassStream::operator>> (ParametricPlane *&parametricPlane)
	Read parametric plane.
ClassStream &	cmtk::ClassStream::operator<< (const ParametricPlane *parametricPlane)
	Write parametric plane object.
static StudyList *	cmtk::ClassStreamStudyList::Read (const char *path)
	Read studylist.
static StudyList *	cmtk::ClassStreamStudyList::Merge (const StudyList &studyList, const char *path)
	Merge with duplicated studylist.
static StudyList *	cmtk::ClassStreamStudyList::Merge (StudyList const studyList, const char path)
	Merge studylist in place.
static void	cmtk::ClassStreamStudyList::Write (const char path, const StudyList studyList)
	Write studylist.
ClassStream &	cmtk::ClassStream::operator<< (const WarpXform *warpXform)
	Write generic transformation object.
ClassStream &	cmtk::ClassStream::PutWarp (const WarpXform *warpXform)
	Write actual warp transformation object.
ClassStream &	cmtk::ClassStream::Get (WarpXform::SmartPtr &warpXform, const AffineXform *affineXform=NULL)
	Actually read warp transformation object.
ClassStream &	cmtk::ClassStream::Get (WarpXform &warpXform, const AffineXform affineXform=NULL)
	Actually read warp transformation object.
ClassStream &	cmtk::ClassStream::operator>> (WarpXform *&warpXform)
	Read (spline or linear) warp transformation.
static ScalarImage *	cmtk::DICOM::Read (const char *path)
	Read ScalarImage from DICOM file.
static FileFormatID	cmtk::FileFormat::Identify (const char *path, const bool decompress=true)
	Identify file or directory with given path.
static FileFormatID	cmtk::FileFormat::GetID (const char *name)
	Return ID for given file format name.
static const char *	cmtk::FileFormat::Describe (const FileFormatID id)
	Return textual description of identified file format.
static FileFormatID	cmtk::FileFormat::IdentifyDirectory (const char *path)
	Identify directory with given path.
static FileFormatID	cmtk::FileFormat::IdentifyFile (const char *path, const bool decompress=true)
	Identify regular file with given path.
static ScalarImage *	cmtk::PGM::Read (const char *)
	Read image from PGM file directly.
static void	cmtk::PGM::Write (const char filename, const ScalarImage image, const Types::DataItem greyFrom, const Types::DataItem greyTo)
	Write scalar image to PGM file.
static void	cmtk::PGM::Write16bit (const char filename, const ScalarImage image, const Types::DataItem greyFrom=0, const Types::DataItem greyTo=65535)
	Write scalar image to 16bit PGM file.
void	cmtk::ResourceFile::Read (const char *fileName)
	Read from resource file.
void	cmtk::ResourceFile::Write (const char *fileName) const
	Write to resource file.
unsigned int	cmtk::ResourceFile::AddUnique (const char section, const char entry, const unsigned int maxItems=0)
	Add a unique (non-duplicate) string to resource section.
static ScalarImage *	cmtk::ScalarImageIO::ReadAnalyze (const char *)
	Read image from Analyze file.
static void	cmtk::ScalarImageIO::WriteAnalyze (const char filename, const ScalarImage image)
	Write scalar image to Analyze file.
	cmtk::Study::Study ()
	Default constructor.
	cmtk::Study::Study (const char fileSystemPath, const char name=NULL)
	Constructor: Construct study from image file.
virtual void	cmtk::Study::UpdateFromVolume ()
	Update from volume data, possibly after the data has been changed.
const char *	cmtk::Study::SetMakeName (const char *name=NULL, const int suffix=0)
	Set study name; create name if no name given.
virtual	cmtk::Study::~Study ()
	Destructor.
virtual bool	cmtk::Study::ReadVolume (const bool reRead=false, const char *orientation=NULL)
	Read volume data.
static Study *	cmtk::Study::Read (const char *path)
	Static study reader function.
virtual void	cmtk::Study::CopyColormap (const Study *other)
	Copy colormap information from another study object.
const Study *	cmtk::StudyList::GetStudy (const unsigned int studyIndex) const
	Get constant Study object by index.
Study::SmartPtr	cmtk::StudyList::GetStudy (const unsigned int studyIndex)
	Get non-constant Study object by index.
const Study *	cmtk::StudyList::FindStudyPath (const char *fileSystemPath) const
	Find constant Study object by file system path.
Study::SmartPtr	cmtk::StudyList::FindStudyPath (const char *fileSystemPath, const bool create=false)
	Find non-constant Study object by file system path.
const Study *	cmtk::StudyList::FindStudyName (const char *name) const
	Find constant Study object by file system path.
Study::SmartPtr	cmtk::StudyList::FindStudyName (const char *name)
	Find non-constant Study object by file system path.
Study::SmartPtr	cmtk::StudyList::AddStudy (const char *fileSystemPath)
	Add a new study entry.
void	cmtk::StudyList::AddStudy (Study::SmartPtr &study)
	Add an existing study object.
void	cmtk::StudyList::AddXform (const char fromStudyPath, const char toStudyPath, AffineXform::SmartPtr &affineXform, WarpXform::SmartPtr &warpXform=WarpXform::SmartPtr::Null)
	Add a coordinate transformation between two studies.
void	cmtk::StudyList::AddXform (Study::SmartPtr &fromStudy, Study::SmartPtr &toStudy, AffineXform::SmartPtr &affineXform, WarpXform::SmartPtr &warpXform=WarpXform::SmartPtr::Null)
	Add a coordinate transformation between two studies.
void	cmtk::StudyList::DeleteStudy (const Study *study)
	Remove and delete given study object.
	cmtk::TypedStream::TypedStream ()
	Default constructor.
	cmtk::TypedStreamStudylist::TypedStreamStudylist ()
	Default conctructor.
void	cmtk::TypedStreamStudylist::Clear ()
	Initialize all internal data structures.
	cmtk::TypedStreamStudylist::~TypedStreamStudylist ()
	Destructor.
bool	cmtk::TypedStreamStudylist::Read (const char *studylistpath)
	Read object from disk.
static void	cmtk::TypedStreamStudylist::Write (const char path, const char referenceStudy, const char floatingStudy, const Xform xform)
	Create studylist archive.
static const UniformVolume::SmartPtr	cmtk::VolumeFromFile::Read (const char *filename)
	Read volume from file automatically.
static const UniformVolume::SmartPtr	cmtk::VolumeFromFile::ReadAnalyzeHdr (const char *pathHdr, const bool bigEndian=false, const bool readData=true)
	Read Analyze 7.5 file (separate header file).
static void	cmtk::VolumeFromFile::WriteAnalyzeHdr (const char *pathHdr, const UniformVolume &volume, const bool verbose=false)
	Write Analyze 7.5 file (separate header file).
static const UniformVolume::SmartPtr	cmtk::VolumeFromFile::ReadBioRad (const char *path)
	Read BioRad PIC file (confocal microscopy image).
static void	cmtk::VolumeFromFile::WriteMetaImage (const char *pathHdr, const UniformVolume &volume)
	Write MetaImage file.
static const UniformVolume::SmartPtr	cmtk::VolumeFromFile::ReadNifti (const char *pathHdr, const bool detached, const bool readData=true)
	Read Nifti file.
static void	cmtk::VolumeFromFile::WriteNifti (const char *pathImg, const UniformVolume &volume, const bool verbose=false)
	Write Nifti file.
void	cmtk::VolumeFromSlices::InitSequence (const ScalarImage *image, const unsigned int numberOfSlices)
	Start creation of new volume.
virtual char *	cmtk::VolumeFromSlices::AllocDataArray (const int bytesperpixel, const int data_size) const
	Allocate memory for the 3D image data.
virtual TypedArray::SmartPtr	cmtk::VolumeFromSlices::EncapDataArray (const ScalarDataType dtype, void *const data, const int data_size) const
	Put image data into a custom data structure.
const char *	cmtk::VolumeFromSlices::FillPlane (unsigned int &plane, const ScalarImage *image)
	Copy one slice of data into field.
UniformVolume::SmartPtr	cmtk::VolumeFromSlices::FinishVolume (Types::Coordinate &sliceOffset, int &sliceDirection)
	Finish volume creation and free temporary storage.
const char *	cmtk::VolumeFromSlices::CheckImage (const int plane, const ScalarImage *image, const unsigned int frame=0)
	Check image consistency.
virtual UniformVolume::SmartPtr	cmtk::VolumeFromSlices::ConstructVolume (const DataGrid::IndexType &Dims, const UniformVolume::CoordinateVectorType &Size, const Types::Coordinate *Points[3], TypedArray::SmartPtr &Data) const
	Construct Volume object.
static const UniformVolume::SmartPtr	cmtk::VolumeFromStudy::Read (const Study *study, const bool verbose=false)
	Read from generic Study object.
virtual const UniformVolume::SmartPtr	cmtk::VolumeFromStudy::AssembleVolume (const StudyImageSet *study, const bool verbose=false)
	Build volume from slice images.
static UniformVolume::SmartPtr	cmtk::VolumeIO::Read (const char *path, const bool verbose=false)
	Read volume data from filesystem.
static UniformVolume::SmartPtr	cmtk::VolumeIO::ReadGrid (const char *path, const bool verbose=false)
	Read grid only from filesystem.
static UniformVolume::SmartPtr	cmtk::VolumeIO::ReadGridOriented (const char path, const char orientation, const bool verbose=false)
	Read grid only from filesystem and bring into standard "RAS" orientation.
static UniformVolume::SmartPtr	cmtk::VolumeIO::ReadOriented (const char path, const char orientation, const bool verbose=false)
	Read image from filesystem and reorient to align anatomy with coordinate axes.
static void	cmtk::VolumeIO::Write (const UniformVolume &volume, const char *pathAndFormat, const bool verbose=false)
	Write volume data to filesystem with automatic format parsing.
static void	cmtk::VolumeIO::Write (const UniformVolume &volume, const FileFormatID format, const char *path, const bool verbose=false)
	Write volume data to filesystem.
	cmtk::VolumeIO::Initializer::Initializer ()
	Default constructor: initialize VolumeIO settings.
static Xform::SmartPtr	cmtk::XformIO::Read (const char *path, const bool verbose=false)
	Read transformation from filesystem.
static void	cmtk::XformIO::Write (const Xform xform, const char path, const bool verbose=false)
	Write transformation to filesystem.
Variables
const char *	cmtk::FileFormatMagic::magicString
	Magic number as string of characters.
const size_t	cmtk::FileFormatMagic::magicStringLength
	Length of magic number string (necessary due to Null characters).
const FileFormatMagic	cmtk::FileFormatMagicNumbers []
	Magic number records for known file types.
const char *	cmtk::FileFormatName []
	Table of file format ID names.
FILE *	cmtk::TypedStream::File
	Pointer to the actual file.
gzFile	cmtk::TypedStream::GzFile
	Pointer to the compressed file in decompression mode.
TypedStreamMode	cmtk::TypedStream::Mode
	Mode the current archive was opened with.
TypedStreamStatus	cmtk::TypedStream::Status
	Holds the status of the last operation.
int	cmtk::TypedStream::PrecisionFloat
	Number of significant digits for "float" fields.
int	cmtk::TypedStream::PrecisionDouble
	Number of significant digits for "double" fields.
char	cmtk::TypedStream::Buffer [TYPEDSTREAM_LIMIT_BUFFER]
	Buffer for the current line read from the archive.
char *	cmtk::TypedStream::BufferKey
	Pointer to the "key" part of the line currently in Buffer.
char *	cmtk::TypedStream::BufferValue
	Pointer to the "value" part of the line currently in Buffer.
std::stack< int >	cmtk::TypedStream::LevelStack
	Stack of open section levels.
char *	cmtk::TypedStream::SplitPosition
	Internal position pointer for "StringSplit()".
TypedStreamDebugFlag	cmtk::TypedStream::DebugFlag
	Debug flag.
unsigned short	cmtk::FileHeaderBioRad::ny
short	cmtk::FileHeaderBioRad::npic
short	cmtk::FileHeaderBioRad::ramp1_min
short	cmtk::FileHeaderBioRad::ramp1_max
int	cmtk::FileHeaderBioRad::notes
short	cmtk::FileHeaderBioRad::byte_format
unsigned short	cmtk::FileHeaderBioRad::n
char	cmtk::FileHeaderBioRad::name [32]
short	cmtk::FileHeaderBioRad::merged
unsigned short	cmtk::FileHeaderBioRad::color1
unsigned short	cmtk::FileHeaderBioRad::file_id
short	cmtk::FileHeaderBioRad::ramp2_min
short	cmtk::FileHeaderBioRad::ramp2_max
unsigned short	cmtk::FileHeaderBioRad::color2
short	cmtk::FileHeaderBioRad::edited
short	cmtk::FileHeaderBioRad::lens
float	cmtk::FileHeaderBioRad::mag_factor
unsigned short	cmtk::FileHeaderBioRad::dummy [3]
const char *const	cmtk::CMTK_LEGACY_WRITE_IMAGES_RAS = "CMTK_LEGACY_WRITE_IMAGES_RAS"
	Environment variable that turns off writing output images in the array order of the input images.
static bool	cmtk::VolumeIO::WriteCompressedOn = true
	Global setting: write compressed images.
static Initializer	cmtk::VolumeIO::Initializer::Instance
	Instance of the initializer class.
TypedStream.h
enum	cmtk::TypedStreamMode { cmtk::TYPEDSTREAM_READ, cmtk::TYPEDSTREAM_WRITE, cmtk::TYPEDSTREAM_WRITE_ZLIB, cmtk::TYPEDSTREAM_APPEND }
	Access modes for archives. More...
enum	cmtk::TypedStreamCondition { cmtk::TYPEDSTREAM_ERROR, cmtk::TYPEDSTREAM_OK }
	Condition upon function return. More...
enum	cmtk::TypedStreamStatus { cmtk::TYPEDSTREAM_ERROR_NONE, cmtk::TYPEDSTREAM_ERROR_UNKNOWN, cmtk::TYPEDSTREAM_ERROR_SYSTEM, cmtk::TYPEDSTREAM_ERROR_FORMAT, cmtk::TYPEDSTREAM_ERROR_ARG, cmtk::TYPEDSTREAM_ERROR_MODE, cmtk::TYPEDSTREAM_ERROR_TYPE, cmtk::TYPEDSTREAM_ERROR_LIMIT, cmtk::TYPEDSTREAM_ERROR_LEVEL, cmtk::TYPEDSTREAM_ERROR_INVALID, cmtk::TYPEDSTREAM_ERROR_MAX }
	Classes of error conditions. More...
enum	cmtk::TypedStreamType { cmtk::TYPEDSTREAM_TYPE_INT, cmtk::TYPEDSTREAM_TYPE_BOOL, cmtk::TYPEDSTREAM_TYPE_BINARYBOOL, cmtk::TYPEDSTREAM_TYPE_FLOAT, cmtk::TYPEDSTREAM_TYPE_DOUBLE, cmtk::TYPEDSTREAM_TYPE_STRING }
	Identifiers for supported primitive data types. More...
enum	cmtk::TypedStreamToken { cmtk::TYPEDSTREAM_EOF, cmtk::TYPEDSTREAM_BEGIN, cmtk::TYPEDSTREAM_END, cmtk::TYPEDSTREAM_KEY, cmtk::TYPEDSTREAM_VALUE, cmtk::TYPEDSTREAM_COMMENT }
	Identifiers for tokens in archives. More...
enum	cmtk::TypedStreamDebugFlag { cmtk::TYPEDSTREAM_DEBUG_OFF, cmtk::TYPEDSTREAM_DEBUG_ON }
	Debug flag values. More...
#define	TYPEDSTREAM_LIMIT_BUFFER 1024
	Internal: Length of the read buffer for one archive line.
#define	TYPEDSTREAM_FLUSH true
	Constant for use with flush parameter of End() member function.
#define	TYPEDSTREAM_NOFLUSH false
	Constant for use with flush parameter of End() member function.

Detailed Description

This library provides classes for input and output of images, transformations, and other types of objects.

Define Documentation

#define TYPEDSTREAM_FLUSH true

Constant for use with flush parameter of End() member function.

Definition at line 174 of file cmtkTypedStream.h.

#define TYPEDSTREAM_LIMIT_BUFFER 1024

Internal: Length of the read buffer for one archive line.

Definition at line 171 of file cmtkTypedStream.h.

Referenced by cmtk::TypedStream::Open(), and cmtk::TypedStream::ReadLineToken().

#define TYPEDSTREAM_NOFLUSH false

Constant for use with flush parameter of End() member function.

Definition at line 177 of file cmtkTypedStream.h.

Typedef Documentation

typedef std::list<std::string> cmtk::ResourceSection

Resource file section is a list of strings.

Definition at line 49 of file cmtkResourceFile.h.

typedef std::map< Study::SmartPtr, StudyToXform > cmtk::StudyToStudyToXform

Definition at line 54 of file cmtkStudyList.h.

typedef std::multimap<Study::SmartPtr, Xform::SmartPtr> cmtk::StudyToXform

Definition at line 53 of file cmtkStudyList.h.

Enumeration Type Documentation

anonymous enum

Constants to identify color table.

Enumerator:

PALETTE_GRAY	Grayscale color table.
PALETTE_RED	Red color table.
PALETTE_GREEN	Green color table.
PALETTE_BLUE	Blue color table.
PALETTE_RAINBOW	Rainbow color table.
PALETTE_LABELS	Color table for labels.

Definition at line 57 of file cmtkStudy.h.

enum cmtk::AnalyzeDataType

IDs for data types in Analyze image file.

Enumerator:

ANALYZE_TYPE_NONE
ANALYZE_TYPE_BINARY
ANALYZE_TYPE_UNSIGNED_CHAR
ANALYZE_TYPE_SIGNED_SHORT
ANALYZE_TYPE_SIGNED_INT
ANALYZE_TYPE_FLOAT
ANALYZE_TYPE_COMPLEX
ANALYZE_TYPE_DOUBLE
ANALYZE_TYPE_RGB
ANALYZE_TYPE_USHORT
ANALYZE_TYPE_UINT
ANALYZE_TYPE_ALL

Definition at line 45 of file cmtkAnalyze.h.

enum cmtk::AnalyzeOrientation

IDs for slice orientations in Analyze image file.

Enumerator:

ANALYZE_AXIAL
ANALYZE_CORONAL
ANALYZE_SAGITTAL
ANALYZE_AXIAL_FLIP
ANALYZE_CORONAL_FLIP
ANALYZE_SAGITTAL_FLIP
ANALYZE_UNKNOWN

Definition at line 61 of file cmtkAnalyze.h.

enum cmtk::FileFormatID

ID codes for known file formats.

Enumerator:

FILEFORMAT_NEXIST	File of this name does not exist.
FILEFORMAT_COMPRESSED_ARCHIVE	File is a compressed archive file.
FILEFORMAT_STUDY	Path is a typedstream study directory.
FILEFORMAT_STUDYLIST	Path is a typedstream studylist directory.
FILEFORMAT_TYPEDSTREAM	Path is a typedstream archive file.
FILEFORMAT_PGM	Path is a PGM image.
FILEFORMAT_DICOM	Path is a DICOM image.
FILEFORMAT_VANDERBILT	Path is a Vanderbilt image description file.
FILEFORMAT_AMIRA	Path is a Amira image file.
FILEFORMAT_RAW	Path is some raw binary file (2-D).
FILEFORMAT_RAW3D	Path is some raw binary file (3-D).
FILEFORMAT_BIORAD	Path is a BioRad .PIC image file.
FILEFORMAT_NIFTI_DETACHED	Path is a NRRD file.
FILEFORMAT_NIFTI_SINGLEFILE	Path is a NRRD file.
FILEFORMAT_ANALYZE_AVW	Path is an Analyze AVW file.
FILEFORMAT_METAIMAGE	Path is a MetaImage file.
FILEFORMAT_NRRD	Path is a NRRD file.
FILEFORMAT_ANALYZE_HDR	Path is an Analyze header file in little endian.
FILEFORMAT_ANALYZE_HDR_BIGENDIAN	Path is an Analyze header file in little endian.
FILEFORMAT_ITK_TFM	Path is an ITK transformation file.
FILEFORMAT_UNKNOWN	File type cannot be determined. This ID always has to be the last one!

Definition at line 46 of file cmtkFileFormat.h.

enum cmtk::TypedStreamCondition

Condition upon function return.

Enumerator:

TYPEDSTREAM_ERROR	There was an error.
TYPEDSTREAM_OK	No error encountered; operation completed successfully.

Definition at line 76 of file cmtkTypedStream.h.

enum cmtk::TypedStreamDebugFlag

Debug flag values.

Enumerator:

TYPEDSTREAM_DEBUG_OFF	There was an error.
TYPEDSTREAM_DEBUG_ON	No error encountered; operation completed successfully.

Definition at line 162 of file cmtkTypedStream.h.

enum cmtk::TypedStreamMode

Access modes for archives.

Enumerator:

TYPEDSTREAM_READ	Read-only access.
TYPEDSTREAM_WRITE	Write-only access.
TYPEDSTREAM_WRITE_ZLIB	Write-only access piped through zlib/gzip compression.
TYPEDSTREAM_APPEND	Open existing archive and append to it.

Definition at line 63 of file cmtkTypedStream.h.

enum cmtk::TypedStreamStatus

Classes of error conditions.

Enumerator:

TYPEDSTREAM_ERROR_NONE	No error.
TYPEDSTREAM_ERROR_UNKNOWN	Unknown error.
TYPEDSTREAM_ERROR_SYSTEM	A call to a system function returned an error condition. To find out more details, "errno" may be consulted.
TYPEDSTREAM_ERROR_FORMAT	Error in the format of the open archive.
TYPEDSTREAM_ERROR_ARG	Wrong or invalid arguments given to a function.
TYPEDSTREAM_ERROR_MODE	The requested operation is not available in the current stream mode. This usually means that a write access was requested on a read-only archive or a Seek() operation on a write-only archive.
TYPEDSTREAM_ERROR_TYPE	Error in a primitive data object. A value in the archive does not have the correct syntax for the expected type.
TYPEDSTREAM_ERROR_LIMIT	An internal limit was exhausted. As we are now using a proper STL stack for keeping track of open levels, this condition should not occur any more.
TYPEDSTREAM_ERROR_LEVEL	Close of a level was requested when none was open.
TYPEDSTREAM_ERROR_INVALID	The current stream is invalid. This condition is set when an access is tried without opening a file first.
TYPEDSTREAM_ERROR_MAX

Definition at line 85 of file cmtkTypedStream.h.

enum cmtk::TypedStreamToken

Identifiers for tokens in archives.

Enumerator:

TYPEDSTREAM_EOF	End-of-file.
TYPEDSTREAM_BEGIN	Section beginning "{".
TYPEDSTREAM_END	Section end "}".
TYPEDSTREAM_KEY	Key (field name).
TYPEDSTREAM_VALUE	Field value.
TYPEDSTREAM_COMMENT	Comment.

Definition at line 145 of file cmtkTypedStream.h.

enum cmtk::TypedStreamType

Identifiers for supported primitive data types.

Enumerator:

TYPEDSTREAM_TYPE_INT	Interger.
TYPEDSTREAM_TYPE_BOOL	Boolean (Yes/No).
TYPEDSTREAM_TYPE_BINARYBOOL	Binary boolean (0/1).
TYPEDSTREAM_TYPE_FLOAT	Single-precision float.
TYPEDSTREAM_TYPE_DOUBLE	Double-precision float.
TYPEDSTREAM_TYPE_STRING	String (char*).

Definition at line 128 of file cmtkTypedStream.h.

Function Documentation

Study::SmartPtr cmtk::StudyList::AddStudy ( const char * fileSystemPath ) [inherited]

Add a new study entry.

Parameters:

fileSystemPath Name of the study to add.

Definition at line 138 of file cmtkStudyList.cxx.

References NULL.

Referenced by cmtk::ClassStreamStudyList::Merge(), and cmtk::GroupwiseRegistrationOutput::WriteXformsSeparateArchives().

void cmtk::StudyList::AddStudy ( Study::SmartPtr & study ) [inherited]

Add an existing study object.

Parameters:

study Existing study object to add to the study list.

Definition at line 166 of file cmtkStudyList.cxx.

unsigned int cmtk::ResourceFile::AddUnique	(	const char *	section,
		const char *	entry,
		const unsigned int	maxItems = `0`
	)		`[inherited]`

Add a unique (non-duplicate) string to resource section.

Returns:: Number of entries that are in the section after adding new entry.

Definition at line 117 of file cmtkResourceFile.cxx.

void cmtk::StudyList::AddXform	(	const char *	fromStudyPath,
		const char *	toStudyPath,
		AffineXform::SmartPtr &	affineXform,
		WarpXform::SmartPtr &	warpXform = `WarpXform::SmartPtr::Null`
	)		`[inherited]`

Add a coordinate transformation between two studies.

Parameters:

fromStudyPath	Path of the study that the transformation maps from.
toStudyPath	Path of the study that the transformation maps to.
affineXform	Affine coordinate transformation between the given studies.
warpXform	Optional nonrigid transformation between the two given studies.

Definition at line 186 of file cmtkStudyList.cxx.

void cmtk::StudyList::AddXform	(	Study::SmartPtr &	fromStudy,
		Study::SmartPtr &	toStudy,
		AffineXform::SmartPtr &	affineXform,
		WarpXform::SmartPtr &	warpXform = `WarpXform::SmartPtr::Null`
	)		`[inherited]`

Add a coordinate transformation between two studies.

Definition at line 196 of file cmtkStudyList.cxx.

Referenced by cmtk::ClassStreamStudyList::Merge(), and cmtk::GroupwiseRegistrationOutput::WriteXformsSeparateArchives().

char * cmtk::VolumeFromSlices::AllocDataArray	(	const int	bytesperpixel,
		const int	data_size
	)		const `[protected, virtual, inherited]`

Allocate memory for the 3D image data.

Definition at line 92 of file cmtkVolumeFromSlices.cxx.

const UniformVolume::SmartPtr cmtk::VolumeFromStudy::AssembleVolume	(	const StudyImageSet *	study,
		const bool	verbose = `false`
	)		`[virtual, inherited]`

Build volume from slice images.

See also:: VolumeFromSlices::AssembleVolume

Definition at line 82 of file cmtkVolumeFromStudy.cxx.

References cmtk::AXIS_Z, NULL, cmtk::Console::printf(), and cmtk::StdErr.

Referenced by cmtk::VolumeFromStudy::Read().

TypedStreamCondition cmtk::TypedStream::Begin ( const char * section = NULL ) [inherited]

Begin a section.

In an archive opened for writing, this function will start a new section and increase the indentation level by one. For a read-only archive, this function will generate an error condition.

Parameters:

section Name of the new section.

Returns:: Error condition.

Definition at line 361 of file cmtkTypedStream.cxx.

References cmtk::TYPEDSTREAM_ERROR, cmtk::TYPEDSTREAM_ERROR_ARG, cmtk::TYPEDSTREAM_ERROR_INVALID, cmtk::TYPEDSTREAM_OK, and cmtk::TYPEDSTREAM_READ.

Referenced by cmtk::operator<<(), cmtk::ImagePairAffineRegistrationCommandLine::OutputResultList(), cmtk::AffineRegistrationCommandLine::OutputResultList(), cmtk::ImagePairNonrigidRegistrationCommandLine::OutputWarp(), cmtk::ElasticRegistrationCommandLine::OutputWarp(), cmtk::TypedStreamStudylist::Read(), cmtk::TypedStreamStudylist::Write(), cmtk::ClassStreamStudyList::Write(), cmtk::VoxelRegistration::ImagePreprocessor::WriteSettings(), and cmtk::ImagePairRegistration::ImagePreprocessor::WriteSettings().

const char * cmtk::VolumeFromSlices::CheckImage	(	const int	plane,
		const ScalarImage *	image,
		const unsigned int	frame = `0`
	)		`[protected, inherited]`

Check image consistency.

This function is used to verify that all images share the same matrix size, identical pixel calibrations, and the same primitive data type. Also, slices with zero distance and changing directions of the table position are detected and reported.

Parameters:

plane	Index of this image in the sequence.
image	A reference to a structure describing the next image.
frame	Index of frame within a multi-frame image.

Returns:: A pointer to an error message, of NULL if image was okay.

Definition at line 199 of file cmtkVolumeFromSlices.cxx.

References cmtk::AXIS_X, cmtk::AXIS_Y, CMTK_MAX_ANGLE_ERROR, CMTK_MAX_CALIB_ERROR, CMTK_MAX_LOCALIZE_ERROR, cmtk::ScalarImage::GetDims(), cmtk::ScalarImage::GetImageOrigin(), cmtk::FixedVector< NDIM, T >::MaxAbsValue(), NULL, cmtk::Console::printf(), and cmtk::StdErr.

void cmtk::TypedStreamStudylist::Clear ( ) [private, inherited]

Initialize all internal data structures.

Definition at line 59 of file cmtkTypedStreamStudylist.cxx.

References NULL.

void cmtk::TypedStream::Close ( ) [inherited]

Close an open archive.

Definition at line 310 of file cmtkTypedStream.cxx.

References NULL, cmtk::TYPEDSTREAM_APPEND, cmtk::TYPEDSTREAM_ERROR_NONE, and cmtk::TYPEDSTREAM_WRITE.

UniformVolume::SmartPtr cmtk::VolumeFromSlices::ConstructVolume	(	const DataGrid::IndexType &	Dims,
		const UniformVolume::CoordinateVectorType &	Size,
		const Types::Coordinate *	Points[3],
		TypedArray::SmartPtr &	Data
	)		const `[protected, virtual, inherited]`

Construct Volume object.

This function takes the geometry and data as read from the slice images. Its purpose is to compose an Volume object out of these components. By default, an instance of UniformVolume will be created for uniformly-spaced data, while an instance of igsRectilinearVolume is created for non-uniformly spaced images. Derived classes my override this function to create specialized volume classes derived from the aforementioned base classes.

Parameters:

Dims	Dimensions of the 3D data, ie. number of voxels in x-, y-, and z-direction.
Size	Extents of data in [mm] in x-, y-, and z-direction.
Points	Positions of the grid points (voxels) with respect to the three spatial coordinates. In case the points are uniformly spaced in all three dimensions, an instance of UniformVolume is created with grid spacing as defined by the uniform spacings in this array. Otherwise, an instance of igsRectilinearVolume is created with precisely this array as its "Points" field.
Data	Pixel data array for the new volume.

See also:: igsRectilinearVolume::Points

Returns:: The newly created instance of a class derived from Volume.

See also:: Volume

Definition at line 273 of file cmtkVolumeFromSlices.cxx.

References cmtk::StdErr.

void cmtk::Study::CopyColormap ( const Study * other ) [virtual, inherited]

Copy colormap information from another study object.

Definition at line 235 of file cmtkStudy.cxx.

void cmtk::TypedStream::DebugOutput	(	const char *	format,
			...
	)		`[private, inherited]`

Output diagnostic message if debug flag is set.

Parameters:

format printf-style format string for the remaining variable number of function arguments.

Definition at line 1554 of file cmtkTypedStream.cxx.

References cmtk::TYPEDSTREAM_DEBUG_ON.

void cmtk::StudyList::DeleteStudy ( const Study * study ) [inherited]

Remove and delete given study object.

Parameters:

study Study object to delete from the list.

Definition at line 213 of file cmtkStudyList.cxx.

const char * cmtk::FileFormat::Describe ( const FileFormatID id ) [static, inherited]

Return textual description of identified file format.

Definition at line 170 of file cmtkFileFormat.cxx.

References cmtk::FILEFORMAT_AMIRA, cmtk::FILEFORMAT_ANALYZE_AVW, cmtk::FILEFORMAT_ANALYZE_HDR, cmtk::FILEFORMAT_ANALYZE_HDR_BIGENDIAN, cmtk::FILEFORMAT_BIORAD, cmtk::FILEFORMAT_DICOM, cmtk::FILEFORMAT_NEXIST, cmtk::FILEFORMAT_NIFTI_DETACHED, cmtk::FILEFORMAT_NIFTI_SINGLEFILE, cmtk::FILEFORMAT_NRRD, cmtk::FILEFORMAT_PGM, cmtk::FILEFORMAT_RAW, cmtk::FILEFORMAT_STUDY, cmtk::FILEFORMAT_STUDYLIST, cmtk::FILEFORMAT_UNKNOWN, and cmtk::FILEFORMAT_VANDERBILT.

Referenced by cmtk::FileFormat::Describe(), and cmtk::Study::Study().

TypedArray::SmartPtr cmtk::VolumeFromSlices::EncapDataArray	(	const ScalarDataType	dtype,
		void *const	data,
		const int	data_size
	)		const `[protected, virtual, inherited]`

Put image data into a custom data structure.

By default, the image data is encapsulated into a newly created TypedArray object.

Definition at line 98 of file cmtkVolumeFromSlices.cxx.

TypedStreamCondition cmtk::TypedStream::End ( const bool flush = false ) [inherited]

End a section.

In the open archive, this function will close the last section and decrease the nesting level by one.

Parameters:

flush If this flag is set, the output file buffer will be flushed after closing the section.

Returns:: Error condition.

Definition at line 413 of file cmtkTypedStream.cxx.

References cmtk::TYPEDSTREAM_BEGIN, cmtk::TYPEDSTREAM_END, cmtk::TYPEDSTREAM_EOF, cmtk::TYPEDSTREAM_ERROR, cmtk::TYPEDSTREAM_ERROR_INVALID, cmtk::TYPEDSTREAM_ERROR_LEVEL, cmtk::TYPEDSTREAM_OK, and cmtk::TYPEDSTREAM_READ.

Referenced by cmtk::operator<<(), cmtk::operator>>(), cmtk::ImagePairAffineRegistrationCommandLine::OutputResultList(), cmtk::AffineRegistrationCommandLine::OutputResultList(), cmtk::ImagePairNonrigidRegistrationCommandLine::OutputWarp(), cmtk::ElasticRegistrationCommandLine::OutputWarp(), cmtk::TypedStreamStudylist::Write(), cmtk::ClassStreamStudyList::Write(), cmtk::VoxelRegistration::ImagePreprocessor::WriteSettings(), and cmtk::ImagePairRegistration::ImagePreprocessor::WriteSettings().

const char * cmtk::VolumeFromSlices::FillPlane	(	unsigned int &	plane,
		const ScalarImage *	image
	)		`[protected, inherited]`

Copy one slice of data into field.

This function rearranges the bytes in the given 2D image so that after all slices have been copied to the 3D array, the xy-plane is always axial with respect to the patient.

Definition at line 106 of file cmtkVolumeFromSlices.cxx.

References NULL.

const Study * cmtk::StudyList::FindStudyName ( const char * name ) const [inherited]

Find constant Study object by file system path.

Parameters:

name	Name of the study to find.

Definition at line 106 of file cmtkStudyList.cxx.

References NULL.

Study::SmartPtr cmtk::StudyList::FindStudyName ( const char * name ) [inherited]

Find non-constant Study object by file system path.

Parameters:

name	Name of the study to find.

Definition at line 122 of file cmtkStudyList.cxx.

Study::SmartPtr cmtk::StudyList::FindStudyPath	(	const char *	fileSystemPath,
		const bool	create = `false`
	)		`[inherited]`

Find non-constant Study object by file system path.

Parameters:

fileSystemPath	Path of study to find in filesystem
create	Flag whether to create a study that does not exist already

Definition at line 84 of file cmtkStudyList.cxx.

const Study * cmtk::StudyList::FindStudyPath ( const char * fileSystemPath ) const [inherited]

Find constant Study object by file system path.

Definition at line 68 of file cmtkStudyList.cxx.

References NULL.

UniformVolume::SmartPtr cmtk::VolumeFromSlices::FinishVolume	(	Types::Coordinate &	sliceOffset,
		int &	sliceDirection
	)		`[protected, inherited]`

Finish volume creation and free temporary storage.

Parameters:

sliceOffset	This reference is set to the absolute slice coordinate of the original image that became the first plane in the resulting volume. This can be used to write images with precisely the same absolute positions later.
sliceDirection	This reference is set to a flag indicating whether in the original images the slice positions increased (+1) or decreased (-1) with increasing slice index.

Returns:: The newly created volume object as returned by ConstructVolume().

Definition at line 128 of file cmtkVolumeFromSlices.cxx.

References cmtk::Memory::DeleteArray(), cmtk::META_IMAGE_ORIENTATION, cmtk::META_IMAGE_ORIENTATION_ORIGINAL, cmtk::META_SPACE, cmtk::META_SPACE_ORIGINAL, cmtk::META_SPACE_UNITS_STRING, and cmtk::SelectDataTypeInteger().

TypedStreamCondition cmtk::TypedStream::GenericReadArray	(	const char *	key,
		const int	type,
		void *const	array,
		const int	arraySize,
		const bool	forward = `false`
	)		`[private, inherited]`

Utility function: Read an array of arbitrary type.

This function is called by all reader functions. Internally, a "switch" statement selects the correct code for the effective data type to be read. Besides, common functions such as the skipping of inserted sections are implemented as shared code for all data types.

Parameters:

key	Field key (name)
type	Array data type ID
array	Target storage space for read data
arraySize	Number of array elements
forward	Flag: read forward from current position in stream (if false, reset to current section start)

Definition at line 1150 of file cmtkTypedStream.cxx.

References NULL, cmtk::TYPEDSTREAM_BEGIN, cmtk::TYPEDSTREAM_END, cmtk::TYPEDSTREAM_EOF, cmtk::TYPEDSTREAM_ERROR, cmtk::TYPEDSTREAM_ERROR_ARG, cmtk::TYPEDSTREAM_ERROR_NONE, cmtk::TYPEDSTREAM_ERROR_SYSTEM, cmtk::TYPEDSTREAM_ERROR_TYPE, cmtk::TYPEDSTREAM_KEY, cmtk::TYPEDSTREAM_OK, cmtk::TYPEDSTREAM_TYPE_BINARYBOOL, cmtk::TYPEDSTREAM_TYPE_BOOL, cmtk::TYPEDSTREAM_TYPE_DOUBLE, cmtk::TYPEDSTREAM_TYPE_FLOAT, cmtk::TYPEDSTREAM_TYPE_INT, and cmtk::TYPEDSTREAM_TYPE_STRING.

ClassStream & cmtk::ClassStream::Get	(	WarpXform::SmartPtr &	warpXform,
		const AffineXform *	affineXform = `NULL`
	)		`[inherited]`

Actually read warp transformation object.

Definition at line 82 of file cmtkClassStreamWarpXform.cxx.

Referenced by cmtk::ClassStreamStudyList::Merge(), and cmtk::TypedStreamStudylist::Read().

ClassStream & cmtk::ClassStream::Get	(	WarpXform *&	warpXform,
		const AffineXform *	affineXform = `NULL`
	)		`[inherited]`

Actually read warp transformation object.

Definition at line 92 of file cmtkClassStreamWarpXform.cxx.

References cmtk::FixedVector< NDIM, T >::begin(), cmtk::Memory::DeleteArray(), cmtk::MetaInformationObject::m_MetaInformation, cmtk::AffineXform::MakeInverse(), cmtk::META_SPACE, NULL, and cmtk::TYPEDSTREAM_OK.

FileFormatID cmtk::FileFormat::GetID ( const char * name ) [static, inherited]

Return ID for given file format name.

Definition at line 156 of file cmtkFileFormat.cxx.

References cmtk::FILEFORMAT_UNKNOWN.

TypedStreamStatus cmtk::TypedStream::GetStatus ( ) const [inline, inherited]

Return status of last operation.

Definition at line 249 of file cmtkTypedStream.h.

const Study * cmtk::StudyList::GetStudy ( const unsigned int studyIndex ) const [inherited]

Get constant Study object by index.

Definition at line 46 of file cmtkStudyList.cxx.

References NULL.

Study::SmartPtr cmtk::StudyList::GetStudy ( const unsigned int studyIndex ) [inherited]

Get non-constant Study object by index.

Definition at line 57 of file cmtkStudyList.cxx.

static const char* cmtk::TypedStream::GetTypedStreamIdent ( ) [inline, static, private, inherited]

Return the identifier for the generated archive format (version).

Definition at line 637 of file cmtkTypedStream.h.

FileFormatID cmtk::FileFormat::Identify	(	const char *	path,
		const bool	decompress = `true`
	)		`[static, inherited]`

Identify file or directory with given path.

Compressed files as supported by CompressedStream are handled. If both an uncompressed and a compressed file exist for the same path prefix, then the uncompressed file has precedence.

Parameters:

path	Image path.
decompress	If set, compressed files are decompressed before determining their file type.

Definition at line 141 of file cmtkFileFormat.cxx.

References cmtk::FILEFORMAT_NEXIST.

Referenced by cmtk::FileFormat::Describe().

FileFormatID cmtk::FileFormat::IdentifyDirectory ( const char * path ) [static, private, inherited]

Identify directory with given path.

Definition at line 212 of file cmtkFileFormat.cxx.

References cmtk::FILEFORMAT_STUDY, cmtk::FILEFORMAT_STUDYLIST, and cmtk::FILEFORMAT_UNKNOWN.

FileFormatID cmtk::FileFormat::IdentifyFile	(	const char *	path,
		const bool	decompress = `true`
	)		`[static, private, inherited]`

Identify regular file with given path.

Parameters:

path	Image path.
decompress	If set, compressed files are decompressed before determining their file type.

Definition at line 237 of file cmtkFileFormat.cxx.

References cmtk::FILEFORMAT_COMPRESSED_ARCHIVE, cmtk::FILEFORMAT_NEXIST, cmtk::FILEFORMAT_UNKNOWN, cmtk::CompressedStream::IsCompressed(), cmtk::CompressedStream::IsValid(), and cmtk::CompressedStream::Read().

cmtk::VolumeIO::Initializer::Initializer ( ) [private, inherited]

Default constructor: initialize VolumeIO settings.

Definition at line 419 of file cmtkVolumeIO.cxx.

void cmtk::TypedStream::InitInternals ( ) [private, inherited]

Initialize internal data structures.

This function is called from both constructors to initialize the internal data structures of this object.

Definition at line 86 of file cmtkTypedStream.cxx.

References NULL, cmtk::TYPEDSTREAM_DEBUG_OFF, and cmtk::TYPEDSTREAM_ERROR_NONE.

void cmtk::VolumeFromSlices::InitSequence	(	const ScalarImage *	image,
		const unsigned int	numberOfSlices
	)		`[protected, inherited]`

Start creation of new volume.

Definition at line 54 of file cmtkVolumeFromSlices.cxx.

References cmtk::AXIS_X, cmtk::AXIS_Y, cmtk::ScalarImage::GetDims(), and cmtk::ScalarImage::GetImageOrigin().

int cmtk::TypedStream::IsValid ( ) [inline, inherited]

Return validity of archive.

Returns:: 1 if an archive is currently open, 0 if not.

Definition at line 242 of file cmtkTypedStream.h.

References NULL.

StudyList * cmtk::ClassStreamStudyList::Merge	(	const StudyList &	studyList,
		const char *	path
	)		`[static, inherited]`

Merge with duplicated studylist.

Definition at line 56 of file cmtkClassStreamStudyList.cxx.

StudyList * cmtk::ClassStreamStudyList::Merge	(	StudyList *const	studyList,
		const char *	path
	)		`[static, inherited]`

Merge studylist in place.

Definition at line 63 of file cmtkClassStreamStudyList.cxx.

References cmtk::StudyList::AddStudy(), cmtk::StudyList::AddXform(), cmtk::TypedStream::Close(), cmtk::ClassStream::Get(), cmtk::TypedStream::IsValid(), cmtk::META_XFORM_FIXED_IMAGE_PATH, cmtk::META_XFORM_MOVING_IMAGE_PATH, NULL, cmtk::ClassStream::Open(), cmtk::TypedStream::ReadString(), and cmtk::TypedStream::Seek().

void cmtk::TypedStream::Open	(	const char *	filename,
		const TypedStreamMode	mode
	)		`[inherited]`

Open another archive without constructing a new object.

Definition at line 149 of file cmtkTypedStream.cxx.

References NULL, cmtk::FileUtils::RecursiveMkPrefixDir(), cmtk::TYPEDSTREAM_APPEND, cmtk::TYPEDSTREAM_ERROR_ARG, cmtk::TYPEDSTREAM_ERROR_FORMAT, cmtk::TYPEDSTREAM_ERROR_NONE, cmtk::TYPEDSTREAM_ERROR_SYSTEM, TYPEDSTREAM_LIMIT_BUFFER, cmtk::TYPEDSTREAM_READ, cmtk::TYPEDSTREAM_WRITE, and cmtk::TYPEDSTREAM_WRITE_ZLIB.

void cmtk::TypedStream::Open	(	const char *	dir,
		const char *	archive,
		const TypedStreamMode	mode
	)		`[inherited]`

Open another archive in explicit directory.

Definition at line 110 of file cmtkTypedStream.cxx.

References NULL, cmtk::StdErr, cmtk::TYPEDSTREAM_APPEND, cmtk::TYPEDSTREAM_WRITE, and cmtk::TYPEDSTREAM_WRITE_ZLIB.

ClassStream & cmtk::operator<<	(	ClassStream &	stream,
		const GroupwiseRegistrationFunctionalBase &	func
	)

Definition at line 48 of file cmtkGroupwiseRegistrationFunctionalIO.cxx.

References cmtk::FixedVector< NDIM, T >::begin(), cmtk::TypedStream::Begin(), cmtk::UniformVolume::Deltas(), cmtk::TypedStream::End(), cmtk::DataGrid::GetDims(), cmtk::MetaInformationObject::m_MetaInformation, cmtk::Volume::m_Offset, cmtk::META_FS_PATH, cmtk::Volume::Size, cmtk::TypedStream::WriteCoordinateArray(), cmtk::TypedStream::WriteIntArray(), and cmtk::TypedStream::WriteString().

ClassStream & cmtk::ClassStream::operator<< ( const WarpXform * warpXform ) [inherited]

Write generic transformation object.

This function determines the virtual type of the transformation object (spline or linear deformation) using a dynamic_cast. It then calls the appropriate specialized output function.

Definition at line 45 of file cmtkClassStreamWarpXform.cxx.

template<class TMetricFunctionalType >

ClassStream & cmtk::operator<<	(	ClassStream &	stream,
		const AffineMultiChannelRegistrationFunctional< TMetricFunctionalType > &	functional
	)

Write file names and transformations from affine multi-channel registration functional.

Definition at line 45 of file cmtkClassStreamMultiChannelRegistration.txx.

References cmtk::TypedStream::Begin(), cmtk::TypedStream::End(), cmtk::META_FS_PATH, cmtk::TypedStream::WriteInt(), and cmtk::TypedStream::WriteString().

template<class TMetricFunctionalType >

ClassStream & cmtk::operator<<	(	ClassStream &	stream,
		const SplineWarpMultiChannelRegistrationFunctional< TMetricFunctionalType > &	functional
	)

Write file names and transformations from spline warp multi-channel registration functional.

Definition at line 113 of file cmtkClassStreamMultiChannelRegistration.txx.

References cmtk::TypedStream::Begin(), cmtk::TypedStream::End(), cmtk::META_FS_PATH, cmtk::TypedStream::WriteInt(), and cmtk::TypedStream::WriteString().

ClassStream & cmtk::ClassStream::operator<< ( const ParametricPlane * parametricPlane ) [inherited]

Write parametric plane object.

Definition at line 64 of file cmtkClassStreamParametricPlane.cxx.

References cmtk::ParametricPlane::GetNormal(), cmtk::ParametricPlane::GetPhi(), cmtk::ParametricPlane::GetRho(), and cmtk::ParametricPlane::GetTheta().

ClassStream & cmtk::operator<<	(	ClassStream &	stream,
		const AffineXform &	affineXform
	)

Write affine transformation object.

Definition at line 43 of file cmtkClassStreamAffineXform.cxx.

References cmtk::TypedStream::Begin(), cmtk::TypedStream::End(), cmtk::AffineXform::GetUseLogScaleFactors(), cmtk::AffineXform::RetAngles(), cmtk::AffineXform::RetCenter(), cmtk::AffineXform::RetScales(), cmtk::AffineXform::RetShears(), cmtk::AffineXform::RetXlate(), and cmtk::TypedStream::WriteCoordinateArray().

ClassStream& cmtk::operator<<	(	ClassStream &	stream,
		const Xform &	xform
	)

Write transformation object.

Definition at line 49 of file cmtkClassStreamXform.h.

ClassStream & cmtk::ClassStream::operator<< ( const LandmarkList * landmarkList ) [inherited]

Write landmark list.

Definition at line 43 of file cmtkClassStreamLandmarkList.cxx.

ClassStream & cmtk::operator>>	(	ClassStream &	stream,
		AffineXform::SmartPtr &	affineXform
	)

Read affine transformation.

Definition at line 60 of file cmtkClassStreamAffineXform.cxx.

ClassStream & cmtk::ClassStream::operator>> ( WarpXform *& warpXform ) [inherited]

Read (spline or linear) warp transformation.

Definition at line 212 of file cmtkClassStreamWarpXform.cxx.

ClassStream& cmtk::operator>>	(	ClassStream &	stream,
		GroupwiseRegistrationFunctionalBase &	func
	)

std::istream & cmtk::operator>>	(	std::istream &	stream,
		SegmentationLabelMap &	lblMap
	)

Operator to read a list of label IDs from a C++ stream.

Definition at line 46 of file cmtkSegmentationLabelIO.cxx.

template<class TMetricFunctionalType >

ClassStream & cmtk::operator>>	(	ClassStream &	stream,
		AffineMultiChannelRegistrationFunctional< TMetricFunctionalType > &	functional
	)

Read file names and transformations from archive to multi-channel affine registration functional.

Definition at line 69 of file cmtkClassStreamMultiChannelRegistration.txx.

References cmtk::TypedStream::End(), NULL, cmtk::TypedStream::ReadInt(), cmtk::TypedStream::ReadString(), cmtk::TypedStream::Seek(), and cmtk::StdErr.

ClassStream & cmtk::operator>>	(	ClassStream &	stream,
		AffineXform &	affineXform
	)

Read affine transformation.

Definition at line 75 of file cmtkClassStreamAffineXform.cxx.

References cmtk::Vector< T >::Elements, cmtk::TypedStream::End(), cmtk::MetaInformationObject::m_MetaInformation, cmtk::META_SPACE, cmtk::META_XFORM_FIXED_IMAGE_PATH, cmtk::META_XFORM_MOVING_IMAGE_PATH, NULL, cmtk::TypedStream::ReadCoordinateArray(), cmtk::TypedStream::ReadString(), cmtk::TypedStream::Rewind(), cmtk::TypedStream::Seek(), cmtk::MetaInformationObject::SetMetaInfo(), cmtk::AffineXform::SetParamVector(), cmtk::AffineXform::SetUseLogScaleFactors(), and cmtk::TYPEDSTREAM_OK.

ClassStream & cmtk::ClassStream::operator>> ( WarpXform::SmartPtr & warpXform ) [inherited]

Read (spline or linear) warp transformation.

Definition at line 61 of file cmtkClassStreamLandmarkList.cxx.

ClassStream & cmtk::ClassStream::operator>> ( ParametricPlane *& parametricPlane ) [inherited]

Read parametric plane.

Definition at line 43 of file cmtkClassStreamParametricPlane.cxx.

References NULL, cmtk::ParametricPlane::SetPhi(), cmtk::ParametricPlane::SetRho(), cmtk::ParametricPlane::SetTheta(), and cmtk::TYPEDSTREAM_OK.

ClassStream & cmtk::ClassStream::PutWarp ( const WarpXform * warpXform ) [private, inherited]

Write actual warp transformation object.

Definition at line 52 of file cmtkClassStreamWarpXform.cxx.

References cmtk::FixedVector< NDIM, T >::begin(), cmtk::WarpXform::Domain, cmtk::BitVector::GetBitVector(), cmtk::WarpXform::m_Dims, cmtk::Xform::m_NumberOfParameters, cmtk::WarpXform::m_Offset, and cmtk::Xform::m_Parameters.

StudyList * cmtk::ClassStreamStudyList::Read ( const char * path ) [static, inherited]

Read studylist.

Definition at line 49 of file cmtkClassStreamStudyList.cxx.

Xform::SmartPtr cmtk::XformIO::Read	(	const char *	path,
		const bool	verbose = `false`
	)		`[static, inherited]`

Read transformation from filesystem.

Definition at line 52 of file cmtkXformIO.cxx.

References cmtk::FILEFORMAT_ITK_TFM, cmtk::FILEFORMAT_NRRD, cmtk::FILEFORMAT_STUDYLIST, cmtk::FILEFORMAT_TYPEDSTREAM, cmtk::TypedStreamStudylist::GetAffineXform(), cmtk::TypedStreamStudylist::GetWarpXform(), NULL, cmtk::ClassStream::Open(), and cmtk::StdErr.

Referenced by cmtk::AffineRegistrationCommandLine::AffineRegistrationCommandLine(), cmtk::ImagePairAffineRegistrationCommandLine::ImagePairAffineRegistrationCommandLine(), and cmtk::XformListIO::MakeFromStringList().

ScalarImage * cmtk::DICOM::Read ( const char * path ) [static, inherited]

Read ScalarImage from DICOM file.

Definition at line 65 of file cmtkDICOM.cxx.

References cmtk::AXIS_X, cmtk::AXIS_Y, cmtk::ScalarImage::GetDims(), NULL, cmtk::Console::printf(), cmtk::ScalarImage::SetImageOrigin(), cmtk::StdErr, cmtk::TYPE_BYTE, cmtk::TYPE_CHAR, cmtk::TYPE_SHORT, and cmtk::TYPE_USHORT.

ScalarImage * cmtk::PGM::Read ( const char * filename ) [static, inherited]

Read image from PGM file directly.

Definition at line 57 of file cmtkPGM.cxx.

References cmtk::CompressedStream::Get(), isspace, cmtk::CompressedStream::IsValid(), NULL, cmtk::Console::printf(), cmtk::CompressedStream::Read(), cmtk::StdErr, cmtk::TYPE_BYTE, cmtk::TYPE_INT, and cmtk::TYPE_USHORT.

void cmtk::ResourceFile::Read ( const char * fileName ) [inherited]

Read from resource file.

Definition at line 50 of file cmtkResourceFile.cxx.

References isspace, cmtk::Console::printf(), and cmtk::StdErr.

UniformVolume::SmartPtr cmtk::VolumeIO::Read	(	const char *	path,
		const bool	verbose = `false`
	)		`[static, inherited]`

Read volume data from filesystem.

Definition at line 73 of file cmtkVolumeIO.cxx.

References cmtk::DataTypeName, cmtk::FILEFORMAT_ANALYZE_HDR, cmtk::FILEFORMAT_ANALYZE_HDR_BIGENDIAN, cmtk::FILEFORMAT_BIORAD, cmtk::FILEFORMAT_DICOM, cmtk::FILEFORMAT_NIFTI_DETACHED, cmtk::FILEFORMAT_NIFTI_SINGLEFILE, cmtk::FILEFORMAT_NRRD, cmtk::FILEFORMAT_VANDERBILT, cmtk::TypedArray::GetRange(), cmtk::TypedArray::GetType(), cmtk::Types::Range< T >::m_LowerBound, cmtk::Types::Range< T >::m_UpperBound, cmtk::META_FILEFORMAT_ORIGINAL, cmtk::META_FS_PATH, NULL, cmtk::Console::printf(), cmtk::StdErr, cmtk::TYPE_DOUBLE, and cmtk::TYPE_FLOAT.

Referenced by cmtk::Study::ReadVolume().

Study * cmtk::Study::Read ( const char * path ) [static, inherited]

Static study reader function.

Definition at line 229 of file cmtkStudy.cxx.

References cmtk::Study::Study().

const UniformVolume::SmartPtr cmtk::VolumeFromStudy::Read	(	const Study *	study,
		const bool	verbose = `false`
	)		`[static, inherited]`

Read from generic Study object.

Definition at line 66 of file cmtkVolumeFromStudy.cxx.

References cmtk::VolumeFromStudy::AssembleVolume(), and NULL.

bool cmtk::TypedStreamStudylist::Read ( const char * studylistpath ) [inherited]

Read object from disk.

Definition at line 74 of file cmtkTypedStreamStudylist.cxx.

References cmtk::TypedStream::Begin(), cmtk::TypedStream::Close(), cmtk::ClassStream::Get(), cmtk::TypedStream::IsValid(), cmtk::META_XFORM_FIXED_IMAGE_PATH, cmtk::META_XFORM_MOVING_IMAGE_PATH, cmtk::ClassStream::Open(), cmtk::Console::printf(), cmtk::TypedStream::ReadString(), cmtk::TypedStream::Seek(), cmtk::StdErr, and cmtk::StrCmp().

const UniformVolume::SmartPtr cmtk::VolumeFromFile::Read ( const char * filename ) [static, inherited]

Read volume from file automatically.

Definition at line 49 of file cmtkVolumeFromFile.cxx.

References cmtk::FILEFORMAT_ANALYZE_HDR, cmtk::FILEFORMAT_ANALYZE_HDR_BIGENDIAN, cmtk::FILEFORMAT_DICOM, cmtk::FILEFORMAT_VANDERBILT, and NULL.

ScalarImage * cmtk::ScalarImageIO::ReadAnalyze ( const char * pathHdr ) [static, inherited]

const UniformVolume::SmartPtr cmtk::VolumeFromFile::ReadAnalyzeHdr	(	const char *	pathHdr,
		const bool	bigEndian = `false`,
		const bool	readData = `true`
	)		`[static, inherited]`

Read Analyze 7.5 file (separate header file).

Definition at line 71 of file cmtkVolumeFromFileAnalyze.cxx.

const UniformVolume::SmartPtr cmtk::VolumeFromFile::ReadBioRad ( const char * path ) [static, inherited]

Read BioRad PIC file (confocal microscopy image).

Definition at line 73 of file cmtkVolumeFromFileBioRad.cxx.

References cmtk::AXIS_X, cmtk::AXIS_Y, cmtk::AXIS_Z, cmtk::FileHeaderBioRad::byte_format, cmtk::Memory::ByteSwap(), cmtk::CompressedStream::Feof(), cmtk::FileHeaderBioRad::file_id, cmtk::FileHeaderBioRad::notes, cmtk::FileHeaderBioRad::npic, NULL, cmtk::FileHeaderBioRad::nx, cmtk::FileHeaderBioRad::ny, cmtk::CompressedStream::Read(), cmtk::StdErr, cmtk::TYPE_BYTE, and cmtk::TYPE_USHORT.

bool cmtk::TypedStream::ReadBool	(	const char *	key,
		const bool	defaultValue = `false`,
		const bool	forward = `false`
	)		`[inherited]`

Read boolean value from an open archive.

This function recognizes both yes/no and 0/1 entries in the archive. First, "yes" and "no" is tried, if that doesn't work the function reads an integer value from the same key.

Returns:: If reading was succesful, the value from the archive is returned. Otherwise the value given as the "defaultValue" parameter is returned.

Parameters:

key	The name of the boolean entry in the archive.
defaultValue	Default value returned if no valid entry can be read. This parameter can be omitted and defaults to false.
forward	Flag: read forward from current position in stream (if false, reset to current section start)

Definition at line 640 of file cmtkTypedStream.cxx.

References cmtk::TYPEDSTREAM_OK, cmtk::TYPEDSTREAM_TYPE_BOOL, and cmtk::TYPEDSTREAM_TYPE_INT.

TypedStreamCondition cmtk::TypedStream::ReadBoolArray	(	const char *	key,
		byte *const	array,
		const int	size,
		const bool	forward = `false`
	)		`[inherited]`

Read array of boole values from an open archive.

For a description of parameters and return value see ReadBool.

Parameters:

key	The name of the array in the archive.
array	Pointer to allocated storage for the array to be read into.
size	Size of the array.
forward	Flag: read forward from current position in stream (if false, reset to current section start)

Definition at line 653 of file cmtkTypedStream.cxx.

References cmtk::TYPEDSTREAM_TYPE_BINARYBOOL.

Types::Coordinate cmtk::TypedStream::ReadCoordinate	(	const char *	key,
		const Types::Coordinate	defaultValue = `0`,
		const bool	forward = `false`
	)		`[inline, inherited]`

Read double- or single precision value from an open archive.

Whether double- or single-precision data is read depends on the definition of the CMTK_COORDINATES_DOUBLE preprocessor symbol. This function is thus guaranteed to always match the Types::Coordinate type.

See also:: CMTK_COORDINATES_DOUBLE; Types::Coordinate

Parameters:

key	The name of the field in the archive.
defaultValue	Default value if the field is not found.
forward	Flag: read forward from current position in stream (if false, reset to current section start)

Definition at line 343 of file cmtkTypedStream.h.

TypedStreamCondition cmtk::TypedStream::ReadCoordinateArray	(	const char *	key,
		Types::Coordinate *const	array,
		const int	size,
		const bool	forward = `false`
	)		`[inline, inherited]`

Read array of double- or single precision values from an open archive.

Whether double- or single-precision data is read depends on the definition of the CMTK_COORDINATES_DOUBLE preprocessor symbol. This function is thus guaranteed to always match the Types::Coordinate type.

See also:: CMTK_COORDINATES_DOUBLE; Types::Coordinate

Parameters:

key	The name of the array in the archive.
array	Pointer to allocated storage for the array to be read into.
size	Size of the array.
forward	Flag: read forward from current position in stream (if false, reset to current section start)

Definition at line 379 of file cmtkTypedStream.h.

Referenced by cmtk::operator>>().

double cmtk::TypedStream::ReadDouble	(	const char *	key,
		const double	defaultValue = `0`,
		const bool	forward = `false`
	)		`[inherited]`

Read double-precision value from an open archive.

For a description of parameters and return value see ReadBool.

Parameters:

key	The name of the field in the archive.
defaultValue	Default value returned if the field is not found in the archive.
forward	Flag: read forward from current position in stream (if false, reset to current section start)

Definition at line 696 of file cmtkTypedStream.cxx.

References cmtk::TYPEDSTREAM_OK, and cmtk::TYPEDSTREAM_TYPE_DOUBLE.

TypedStreamCondition cmtk::TypedStream::ReadDoubleArray	(	const char *	key,
		double *const	array,
		const int	size,
		const bool	forward = `false`
	)		`[inherited]`

Read array of double-precision values from an open archive.

For a description of parameters and return value see ReadBool.

Parameters:

key	The name of the array in the archive.
array	Pointer to allocated storage for the array to be read into.
size	Size of the array.
forward	Flag: read forward from current position in stream (if false, reset to current section start)

Definition at line 707 of file cmtkTypedStream.cxx.

References cmtk::TYPEDSTREAM_TYPE_DOUBLE.

float cmtk::TypedStream::ReadFloat	(	const char *	key,
		const float	defaultValue = `0`,
		const bool	forward = `false`
	)		`[inherited]`

Read single-precision value from an open archive.

For a description of parameters and return value see ReadBool.

Parameters:

key	The name of the field in the archive.
defaultValue	Default value returned if no valid entry can be read. This parameter can be omitted and defaults to zero.
forward	Flag: read forward from current position in stream (if false, reset to current section start)

Definition at line 678 of file cmtkTypedStream.cxx.

References cmtk::TYPEDSTREAM_OK, and cmtk::TYPEDSTREAM_TYPE_FLOAT.

TypedStreamCondition cmtk::TypedStream::ReadFloatArray	(	const char *	key,
		float *const	array,
		const int	size,
		const bool	forward = `false`
	)		`[inherited]`

Read array of single-precision values from an open archive.

For a description of parameters and return value see ReadBool.

Parameters:

key	The name of the array in the archive.
array	Pointer to allocated storage for the array to be read into.
size	Size of the array.
forward	Flag: read forward from current position in stream (if false, reset to current section start)

Definition at line 689 of file cmtkTypedStream.cxx.

References cmtk::TYPEDSTREAM_TYPE_FLOAT.

UniformVolume::SmartPtr cmtk::VolumeIO::ReadGrid	(	const char *	path,
		const bool	verbose = `false`
	)		`[static, inherited]`

Read grid only from filesystem.

Definition at line 169 of file cmtkVolumeIO.cxx.

References cmtk::FILEFORMAT_ANALYZE_HDR, cmtk::FILEFORMAT_ANALYZE_HDR_BIGENDIAN, cmtk::FILEFORMAT_NIFTI_DETACHED, cmtk::FILEFORMAT_NIFTI_SINGLEFILE, cmtk::META_FS_PATH, NULL, cmtk::Console::printf(), and cmtk::StdErr.

UniformVolume::SmartPtr cmtk::VolumeIO::ReadGridOriented	(	const char *	path,
		const char *	orientation,
		const bool	verbose = `false`
	)		`[static, inherited]`

Read grid only from filesystem and bring into standard "RAS" orientation.

Definition at line 213 of file cmtkVolumeIO.cxx.

References cmtk::META_IMAGE_ORIENTATION, and cmtk::StdErr.

int cmtk::TypedStream::ReadInt	(	const char *	key,
		const int	defaultValue = `0`,
		const bool	forward = `false`
	)		`[inherited]`

Read integer value from an open archive.

For a description of parameters and return value see ReadBool.

Parameters:

key	The name of the field in the archive.
defaultValue	Default value returned if no valid entry can be read. This parameter can be omitted and defaults to zero.
forward	Flag: read forward from current position in stream (if false, reset to current section start)

Definition at line 660 of file cmtkTypedStream.cxx.

References cmtk::TYPEDSTREAM_OK, and cmtk::TYPEDSTREAM_TYPE_INT.

Referenced by cmtk::operator>>().

TypedStreamCondition cmtk::TypedStream::ReadIntArray	(	const char *	key,
		int *const	array,
		const int	size,
		const bool	forward = `false`
	)		`[inherited]`

Read array of integer values from an open archive.

For a description of parameters and return value see ReadBool.

Parameters:

key	The name of the array in the archive.
array	Pointer to allocated storage for the array to be read into.
size	Size of the array.
forward	Flag: read forward from current position in stream (if false, reset to current section start)

Definition at line 671 of file cmtkTypedStream.cxx.

References cmtk::TYPEDSTREAM_TYPE_INT.

Referenced by cmtk::operator>>().

Types::DataItem cmtk::TypedStream::ReadItem	(	const char *	key,
		const Types::DataItem	defaultValue = `0`,
		const bool	forward = `false`
	)		`[inline, inherited]`

Read double- or single precision value from an open archive.

Whether double- or single-precision data is read depends on the definition of the CMTK_DATA_DOUBLE preprocessor symbol. This function is thus guaranteed to always match the Types::DataItem type.

See also:: CMTK_DATA_DOUBLE; Types::DataItem

Parameters:

key	The name of the field in the archive.
defaultValue	Default value returned if the field is not found in the archive.
forward	Flag: read forward from current position in stream (if false, reset to current section start)

Definition at line 361 of file cmtkTypedStream.h.

TypedStreamCondition cmtk::TypedStream::ReadItemArray	(	const char *	key,
		Types::DataItem *const	array,
		const int	size,
		const bool	forward = `false`
	)		`[inline, inherited]`

Read array of double- or single precision values from an open archive.

Whether double- or single-precision data is read depends on the definition of the CMTK_DATA_DOUBLE preprocessor symbol. This function is thus guaranteed to always match the Types::DataItem type.

See also:: CMTK_DATA_DOUBLE; Types::DataItem

Parameters:

key	The name of the array in the archive.
array	Pointer to allocated storage for the array to be read into.
size	Size of the array.
forward	Flag: read forward from current position in stream (if false, reset to current section start)

Definition at line 398 of file cmtkTypedStream.h.

TypedStreamToken cmtk::TypedStream::ReadLineToken ( ) [private, inherited]

Read the next archive line to the buffer.

Definition at line 1415 of file cmtkTypedStream.cxx.

References cmtk::TYPEDSTREAM_BEGIN, cmtk::TYPEDSTREAM_COMMENT, cmtk::TYPEDSTREAM_END, cmtk::TYPEDSTREAM_EOF, cmtk::TYPEDSTREAM_KEY, TYPEDSTREAM_LIMIT_BUFFER, and cmtk::TYPEDSTREAM_VALUE.

const UniformVolume::SmartPtr cmtk::VolumeFromFile::ReadNifti	(	const char *	pathHdr,
		const bool	detached,
		const bool	readData = `true`
	)		`[static, inherited]`

UniformVolume::SmartPtr cmtk::VolumeIO::ReadOriented	(	const char *	path,
		const char *	orientation,
		const bool	verbose = `false`
	)		`[static, inherited]`

Read image from filesystem and reorient to align anatomy with coordinate axes.

Parameters:

path	Filesystem path of the image to read.
orientation	Three-character orientation code. The image will be brought into the orientation specified by this string. Default is "RAS", i.e., the returned image will be oriented so that the positive x axis is aligned with the anatomical L/R (left/right) direction, the y axis is aligned with the P/A (posterior/anterior) direction, and the y axis is aligned with the I/S (inferior/superior) direction.
verbose	Flag for verbose operation: if true, write status information to standard error.

Definition at line 243 of file cmtkVolumeIO.cxx.

References cmtk::META_IMAGE_ORIENTATION, and cmtk::StdErr.

Referenced by cmtk::AffineRegistrationCommandLine::AffineRegistrationCommandLine(), cmtk::ImagePairAffineRegistrationCommandLine::ImagePairAffineRegistrationCommandLine(), cmtk::SimpleLevelsetCommandLineBase::Init(), cmtk::ImageOperationApplyMask::ReadMaskFile(), cmtk::Study::ReadVolume(), and cmtk::ImageSymmetryPlaneCommandLineBase::Run().

char * cmtk::TypedStream::ReadString	(	const char *	key,
		const char *	defaultValue = `NULL`,
		const bool	forward = `false`
	)		`[inherited]`

Read null-terminated string from an open archive.

The string returned is newly allocated by this function. So unless NULL is returner, the string must later be freed by the caller in order to avoid memory leaks.

Returns:: A pointer to a newly allocated string is returned if reading was succesful. If no valid entry could be read from the archive, a copy of the string given as "defaultValue" parameter is returned. If that parameter was NULL, the same value is also returned.

Parameters:

key	The name of the field in the archive.
defaultValue	Default value returned if the field is not found in the archive.
forward	Flag: read forward from current position in stream (if false, reset to current section start)

Definition at line 714 of file cmtkTypedStream.cxx.

References NULL, cmtk::TYPEDSTREAM_OK, and cmtk::TYPEDSTREAM_TYPE_STRING.

Referenced by cmtk::AffineRegistrationCommandLine::AffineRegistrationCommandLine(), cmtk::ElasticRegistrationCommandLine::ElasticRegistrationCommandLine(), cmtk::ImagePairAffineRegistrationCommandLine::ImagePairAffineRegistrationCommandLine(), cmtk::ImagePairNonrigidRegistrationCommandLine::ImagePairNonrigidRegistrationCommandLine(), cmtk::ClassStreamStudyList::Merge(), cmtk::operator>>(), and cmtk::TypedStreamStudylist::Read().

bool cmtk::Study::ReadVolume	(	const bool	reRead = `false`,
		const char *	orientation = `NULL`
	)		`[virtual, inherited]`

Read volume data.

Parameters:

reRead	If this is false, then the volume is only read if it has not been read before. Otherwise, it is re-read in any case.
orientation	Optional three-letter anatomical image orientation.

Returns:: True if reading was successful; the "Volume" field has a pointer to the resulting image volume.

Definition at line 174 of file cmtkStudy.cxx.

References cmtk::AXIS_Z, cmtk::TypedArray::GetData(), cmtk::TypedArray::GetPercentile(), cmtk::TypedArray::GetRange(), cmtk::Study::m_Dims, cmtk::Types::Range< T >::m_LowerBound, cmtk::Types::Range< T >::m_UpperBound, NULL, cmtk::VolumeIO::Read(), and cmtk::VolumeIO::ReadOriented().

TypedStreamCondition cmtk::TypedStream::Rewind ( ) [inherited]

Rewind archive.

This function resets filepointer of an open archive to the beginning of the current section.

Definition at line 585 of file cmtkTypedStream.cxx.

References cmtk::TYPEDSTREAM_ERROR, cmtk::TYPEDSTREAM_ERROR_INVALID, cmtk::TYPEDSTREAM_ERROR_MODE, cmtk::TYPEDSTREAM_ERROR_SYSTEM, cmtk::TYPEDSTREAM_OK, and cmtk::TYPEDSTREAM_READ.

Referenced by cmtk::operator>>().

TypedStreamCondition cmtk::TypedStream::Seek	(	const char *	section,
		const bool	forward = `false`
	)		`[inherited]`

Move to a particular section in the open archive.

The named section is found if it is either inside the currently open section or after it on the same level.

This function may only be called for read-only archive, ie. for such that were opened in TYPEDSTREAM_READONLY mode. For writeable archive, it will return an error.

Parameters:

section	Name of the section whose beginning stream pointer is moved to.
forward	Flag: read forward from current position in stream (if false, reset to current section start)

Definition at line 485 of file cmtkTypedStream.cxx.

References cmtk::TYPEDSTREAM_BEGIN, cmtk::TYPEDSTREAM_END, cmtk::TYPEDSTREAM_EOF, cmtk::TYPEDSTREAM_ERROR, cmtk::TYPEDSTREAM_ERROR_ARG, cmtk::TYPEDSTREAM_ERROR_INVALID, cmtk::TYPEDSTREAM_ERROR_LEVEL, cmtk::TYPEDSTREAM_ERROR_MODE, cmtk::TYPEDSTREAM_ERROR_NONE, cmtk::TYPEDSTREAM_OK, and cmtk::TYPEDSTREAM_READ.

Referenced by cmtk::AffineRegistrationCommandLine::AffineRegistrationCommandLine(), cmtk::ElasticRegistrationCommandLine::ElasticRegistrationCommandLine(), cmtk::ImagePairAffineRegistrationCommandLine::ImagePairAffineRegistrationCommandLine(), cmtk::ImagePairNonrigidRegistrationCommandLine::ImagePairNonrigidRegistrationCommandLine(), cmtk::ClassStreamStudyList::Merge(), cmtk::operator>>(), and cmtk::TypedStreamStudylist::Read().

void cmtk::TypedStream::SetDebugFlag ( const TypedStreamDebugFlag debugFlag = TYPEDSTREAM_DEBUG_ON ) [inline, inherited]

Set debugging flag.

Parameters:

debugFlag Set the debug flag to this value.

Definition at line 545 of file cmtkTypedStream.h.

const char * cmtk::Study::SetMakeName	(	const char *	name = `NULL`,
		const int	suffix = `0`
	)		`[inherited]`

Set study name; create name if no name given.

This function sets the name of this study. If no name is given (name parameter is NULL pointer), then a name is constructed from the file system path of this study.

Parameters:

name	New study name
suffix	Unique numerical suffix to be added to study name if other studies with the same name exist.

Definition at line 115 of file cmtkStudy.cxx.

Referenced by cmtk::Study::Study().

int cmtk::TypedStream::StringCmp	(	const char *	s1,
		const char *	s2
	)		`[static, private, inherited]`

Compare two strings.

Other than the standard library's strcmp() function, this implementation ignores upper and lowercase. Also, strings are terminated by either NULL characters or any white space or newline.

Returns:: 0 for identical strings (up to upper-/lowercase), 1 for non-identical strings.

Definition at line 1464 of file cmtkTypedStream.cxx.

char * cmtk::TypedStream::StringSplit ( char * s1 ) const [private, inherited]

Separate next token.

This function identifies the next token in the given string, sets a NULL character to mark its end and returns a pointer to the token's first character. The state between calls is saved in the "SplitPosition" field. Calling the function with NULL as a parameter resets the internal state.

Parameters:

s1	String to split into tokens.

Definition at line 1497 of file cmtkTypedStream.cxx.

References NULL.

cmtk::Study::Study	(	const char *	fileSystemPath,
		const char *	name = `NULL`
	)		`[inherited]`

Constructor: Construct study from image file.

Definition at line 64 of file cmtkStudy.cxx.

References cmtk::FileFormat::Describe(), and cmtk::Study::SetMakeName().

cmtk::Study::Study ( ) [inherited]

Default constructor.

Definition at line 49 of file cmtkStudy.cxx.

Referenced by cmtk::Study::Read().

cmtk::TypedStream::TypedStream	(	const char *	dir,
		const char *	archive,
		const TypedStreamMode	mode
	)		`[inherited]`

Open constructor for separate path and archive names.

Parameters:

dir	Directory to open archive in.
archive	Name of the archive to open.
mode	Access mode, ie. read-only, write-only, etc.

Definition at line 78 of file cmtkTypedStream.cxx.

cmtk::TypedStream::TypedStream ( ) [inherited]

Default constructor.

Definition at line 63 of file cmtkTypedStream.cxx.

cmtk::TypedStream::TypedStream	(	const char *	filename,
		const TypedStreamMode	mode
	)		`[inherited]`

Open constructor.

Parameters:

filename	Name of the archive to open.
mode	Access mode, ie. read-only, write-only, etc.

Definition at line 70 of file cmtkTypedStream.cxx.

cmtk::TypedStreamStudylist::TypedStreamStudylist ( ) [inherited]

Default conctructor.

Definition at line 54 of file cmtkTypedStreamStudylist.cxx.

void cmtk::Study::UpdateFromVolume ( ) [virtual, inherited]

Update from volume data, possibly after the data has been changed.

Definition at line 97 of file cmtkStudy.cxx.

References cmtk::TypedArray::GetData(), cmtk::TypedArray::GetPercentile(), cmtk::TypedArray::GetRange(), cmtk::Types::Range< T >::m_LowerBound, and cmtk::Types::Range< T >::m_UpperBound.

void cmtk::VolumeIO::Write	(	const UniformVolume &	volume,
		const FileFormatID	format,
		const char *	path,
		const bool	verbose = `false`
	)		`[static, inherited]`

Write volume data to filesystem.

Parameters:

volume	Image object that is written to disk.
format	Selector for output file format.
path	Filesystem path of the image to write.
verbose	Flag for verbose operation: if true, write status information to standard error.

Definition at line 366 of file cmtkVolumeIO.cxx.

References cmtk::FILEFORMAT_ANALYZE_HDR, cmtk::FILEFORMAT_METAIMAGE, cmtk::FILEFORMAT_NIFTI_DETACHED, cmtk::FILEFORMAT_NIFTI_SINGLEFILE, cmtk::FILEFORMAT_NRRD, cmtk::MetaInformationObject::GetMetaInfo(), cmtk::UniformVolume::GetReoriented(), cmtk::MetaInformationObject::m_MetaInformation, cmtk::META_FS_PATH, cmtk::META_IMAGE_ORIENTATION, cmtk::META_IMAGE_ORIENTATION_ORIGINAL, cmtk::MetaInformationObject::MetaKeyExists(), NULL, and cmtk::FileUtils::RecursiveMkPrefixDir().

Referenced by cmtk::SimpleLevelsetCommandLine< TImpl >::Execute(), cmtk::ImagePairAffineRegistrationCommandLine::OutputResult(), cmtk::AffineRegistrationCommandLine::OutputResult(), cmtk::ImageSymmetryPlaneCommandLineBase::WriteAligned(), cmtk::ImageSymmetryPlaneCommandLineBase::WriteDifference(), cmtk::ImageSymmetryPlaneCommandLineBase::WriteMarkPlane(), and cmtk::ImageSymmetryPlaneCommandLineBase::WriteMirror().

void cmtk::TypedStreamStudylist::Write	(	const char *	path,
		const char *	referenceStudy,
		const char *	floatingStudy,
		const Xform *	xform
	)		`[static, inherited]`

Create studylist archive.

Definition at line 158 of file cmtkTypedStreamStudylist.cxx.

References cmtk::TypedStream::Begin(), cmtk::TypedStream::Close(), cmtk::TypedStream::End(), cmtk::AffineXform::GetInverse(), cmtk::TypedStream::IsValid(), cmtk::ClassStream::Open(), cmtk::TypedStream::WriteInt(), and cmtk::TypedStream::WriteString().

void cmtk::PGM::Write	(	const char *	filename,
		const ScalarImage *	image,
		const Types::DataItem	greyFrom,
		const Types::DataItem	greyTo
	)		`[static, inherited]`

Write scalar image to PGM file.

Definition at line 144 of file cmtkPGM.cxx.

References cmtk::Memory::DeleteArray(), cmtk::ScalarImage::GetDims(), and cmtk::ScalarImage::GetNumberOfPixels().

void cmtk::ResourceFile::Write ( const char * fileName ) const [inherited]

Write to resource file.

Definition at line 91 of file cmtkResourceFile.cxx.

References cmtk::Console::printf(), and cmtk::StdErr.

void cmtk::ClassStreamStudyList::Write	(	const char *	path,
		const StudyList *	studyList
	)		`[static, inherited]`

Write studylist.

Definition at line 140 of file cmtkClassStreamStudyList.cxx.

References cmtk::TypedStream::Begin(), cmtk::TypedStream::Close(), cmtk::TypedStream::End(), cmtk::ClassStream::Open(), and cmtk::TypedStream::WriteString().

void cmtk::VolumeIO::Write	(	const UniformVolume &	volume,
		const char *	pathAndFormat,
		const bool	verbose = `false`
	)		`[static, inherited]`

Write volume data to filesystem with automatic format parsing.

The output file format is determined automatically from the output name suffix.

Note:: Note that using ".hdr" will write a deprecated Analyze 7.5 hdr/img format pair with private extensions and questionable assumptions regarding the anatomical orientation of the image. To write a NIFTI hdr/img pair that avoids these problems, use the filename suffix ".img" (or write a single-file NIFTI using the ".nii" suffix).

Parameters:

volume	Image object that is written to disk.
pathAndFormat	Filesystem path of the image to write.
verbose	Flag for verbose operation: if true, write status information to standard error.

Definition at line 272 of file cmtkVolumeIO.cxx.

References cmtk::FILEFORMAT_ANALYZE_HDR, cmtk::FILEFORMAT_METAIMAGE, cmtk::FILEFORMAT_NIFTI_DETACHED, cmtk::FILEFORMAT_NIFTI_SINGLEFILE, cmtk::FILEFORMAT_NRRD, cmtk::FILEFORMAT_UNKNOWN, cmtk::FileUtils::GetAbsolutePath(), NULL, and cmtk::StdErr.

void cmtk::XformIO::Write	(	const Xform *	xform,
		const char *	path,
		const bool	verbose = `false`
	)		`[static, inherited]`

Write transformation to filesystem.

Definition at line 117 of file cmtkXformIO.cxx.

References cmtk::FILEFORMAT_ITK_TFM, cmtk::FILEFORMAT_NRRD, cmtk::FILEFORMAT_TYPEDSTREAM, cmtk::FileUtils::GetAbsolutePath(), and cmtk::StdErr.

Referenced by cmtk::ImageSymmetryPlaneCommandLineBase::Run().

void cmtk::PGM::Write16bit	(	const char *	filename,
		const ScalarImage *	image,
		const Types::DataItem	greyFrom = `0`,
		const Types::DataItem	greyTo = `65535`
	)		`[static, inherited]`

Write scalar image to 16bit PGM file.

Definition at line 186 of file cmtkPGM.cxx.

References cmtk::Memory::DeleteArray(), cmtk::TypedArray::Get(), cmtk::ScalarImage::GetDims(), and cmtk::ScalarImage::GetNumberOfPixels().

void cmtk::ScalarImageIO::WriteAnalyze	(	const char *	filename,
		const ScalarImage *	image
	)		`[static, inherited]`

void cmtk::VolumeFromFile::WriteAnalyzeHdr	(	const char *	pathHdr,
		const UniformVolume &	volume,
		const bool	verbose = `false`
	)		`[static, inherited]`

Write Analyze 7.5 file (separate header file).

Definition at line 268 of file cmtkVolumeFromFileAnalyze.cxx.

TypedStreamCondition cmtk::TypedStream::WriteBool	(	const char *	key,
		const bool	value
	)		`[inherited]`

Write a boolean value to an open archive.

Parameters:

key	The name of the field under which to write this value in the archive.
value	Value to write to the archive under the given key.

Definition at line 730 of file cmtkTypedStream.cxx.

References cmtk::TYPEDSTREAM_OK.

Referenced by cmtk::AffineRegistrationCommandLine::OutputResultList(), cmtk::ImagePairNonrigidRegistrationCommandLine::OutputWarp(), cmtk::ElasticRegistrationCommandLine::OutputWarp(), cmtk::VoxelRegistration::ImagePreprocessor::WriteSettings(), and cmtk::ImagePairRegistration::ImagePreprocessor::WriteSettings().

TypedStreamCondition cmtk::TypedStream::WriteBoolArray	(	const char *	key,
		const byte *	array,
		const int	size,
		const int	valuesPerLine = `10`
	)		`[inherited]`

Write array of binay encoded boole values to an open archive.

Parameters:

key	The name of the field under which to write this array in the archive.
array	Pointer to the array to be written.
size	Number of values in the array. This is the number of values written to the archive.
valuesPerLine	Optional number of values per line of text written to the archive. This improves readability of the resulting archive as a text.

Definition at line 985 of file cmtkTypedStream.cxx.

References cmtk::TYPEDSTREAM_ERROR, cmtk::TYPEDSTREAM_ERROR_ARG, and cmtk::TYPEDSTREAM_OK.

TypedStreamCondition cmtk::TypedStream::WriteComment	(	const char *	fmt,
			...
	)		`[inherited]`

Write a formated comment to an open archive.

Parameters:

fmt	printf-style format string for the remaining variable number of parameters

Definition at line 867 of file cmtkTypedStream.cxx.

References cmtk::TYPEDSTREAM_ERROR, cmtk::TYPEDSTREAM_ERROR_MODE, cmtk::TYPEDSTREAM_OK, and cmtk::TYPEDSTREAM_WRITE.

TypedStreamCondition cmtk::TypedStream::WriteComment	(	const int	argc,
		const char *	argv[]
	)		`[inherited]`

Write string array as comment to an open archive.

Parameters:

argc	Number of strings in the array.
argv	Array of string pointers.

Definition at line 899 of file cmtkTypedStream.cxx.

References cmtk::TYPEDSTREAM_ERROR, cmtk::TYPEDSTREAM_ERROR_MODE, cmtk::TYPEDSTREAM_OK, and cmtk::TYPEDSTREAM_WRITE.

TypedStreamCondition cmtk::TypedStream::WriteComment	(	int	argc,
		char *	argv[]
	)		`[inherited]`

Write string array as comment to an open archive.

Parameters:

argc	Number of strings in the array.
argv	Array of string pointers.

Definition at line 892 of file cmtkTypedStream.cxx.

TypedStreamCondition cmtk::TypedStream::WriteCoordinate	(	const char *	key,
		const Types::Coordinate	value
	)		`[inline, inherited]`

Write an Types::Coordinate value to an open archive.

Parameters:

key	The name of the field under which to write this value in the archive.
value	Value to write to the archive under the given key.

Definition at line 440 of file cmtkTypedStream.h.

TypedStreamCondition cmtk::TypedStream::WriteCoordinateArray	(	const char *	key,
		const Types::Coordinate *	array,
		const int	size,
		const int	valuesPerLine = `10`
	)		`[inline, inherited]`

Write array of double- or single precision values to an open archive.

Whether double- or single-precision data is written depends on the definition of the CMTK_COORDINATES_DOUBLE preprocessor symbol. This function is thus guaranteed to always match the Types::Coordinate type.

See also:: CMTK_COORDINATES_DOUBLE; Types::Coordinate

Parameters:

key	The name of the field under which to write this array in the archive.
array	Pointer to the array to be written.
size	Number of values in the array. This is the number of values written to the archive.
valuesPerLine	Optional number of values per line of text written to the archive. This improves readability of the resulting archive as a text.

Definition at line 513 of file cmtkTypedStream.h.

Referenced by cmtk::operator<<().

TypedStreamCondition cmtk::TypedStream::WriteDouble	(	const char *	key,
		const double	value
	)		`[inherited]`

Write a double precision float value to an open archive.

Parameters:

key	The name of the field under which to write this value in the archive.
value	Value to write to the archive under the given key.

Definition at line 790 of file cmtkTypedStream.cxx.

References cmtk::TYPEDSTREAM_OK.

Referenced by cmtk::ImagePairAffineRegistrationCommandLine::OutputResultList(), cmtk::AffineRegistrationCommandLine::OutputResultList(), cmtk::ImagePairNonrigidRegistrationCommandLine::OutputWarp(), cmtk::ElasticRegistrationCommandLine::OutputWarp(), cmtk::VoxelRegistration::ImagePreprocessor::WriteSettings(), and cmtk::ImagePairRegistration::ImagePreprocessor::WriteSettings().

TypedStreamCondition cmtk::TypedStream::WriteDoubleArray	(	const char *	key,
		const double *	array,
		const int	size,
		const int	valuesPerLine = `10`
	)		`[inherited]`

Write array of double-precision values to an open archive.

Parameters:

key	The name of the field under which to write this array in the archive.
array	Pointer to the array to be written.
size	Number of values in the array. This is the number of values written to the archive.
valuesPerLine	Optional number of values per line of text written to the archive. This improves readability of the resulting archive as a text.

Definition at line 1095 of file cmtkTypedStream.cxx.

References cmtk::TYPEDSTREAM_ERROR, cmtk::TYPEDSTREAM_ERROR_ARG, and cmtk::TYPEDSTREAM_OK.

TypedStreamCondition cmtk::TypedStream::WriteFloat	(	const char *	key,
		const float	value
	)		`[inherited]`

Write a float value to an open archive.

Parameters:

key	The name of the field under which to write this value in the archive.
value	Value to write to the archive under the given key.

Definition at line 770 of file cmtkTypedStream.cxx.

References cmtk::TYPEDSTREAM_OK.

TypedStreamCondition cmtk::TypedStream::WriteFloatArray	(	const char *	key,
		const float *	array,
		const int	size,
		const int	valuesPerLine = `10`
	)		`[inherited]`

Write array of single-precision values to an open archive.

Parameters:

key	The name of the field under which to write this array in the archive.
array	Pointer to the array to be written.
size	Number of values in the array. This is the number of values written to the archive.
valuesPerLine	Optional number of values per line of text written to the archive. This improves readability of the resulting archive as a text.

Definition at line 1040 of file cmtkTypedStream.cxx.

References cmtk::TYPEDSTREAM_ERROR, cmtk::TYPEDSTREAM_ERROR_ARG, and cmtk::TYPEDSTREAM_OK.

TypedStreamCondition cmtk::TypedStream::WriteInt	(	const char *	key,
		const int	value
	)		`[inherited]`

Write an integer value to an open archive.

Parameters:

key	The name of the field under which to write this value in the archive.
value	Value to write to the archive under the given key.

Definition at line 750 of file cmtkTypedStream.cxx.

References cmtk::TYPEDSTREAM_OK.

Referenced by cmtk::operator<<(), cmtk::ImagePairAffineRegistrationCommandLine::OutputResultList(), cmtk::AffineRegistrationCommandLine::OutputResultList(), cmtk::ImagePairNonrigidRegistrationCommandLine::OutputWarp(), cmtk::ElasticRegistrationCommandLine::OutputWarp(), cmtk::TypedStreamStudylist::Write(), cmtk::VoxelRegistration::ImagePreprocessor::WriteSettings(), and cmtk::ImagePairRegistration::ImagePreprocessor::WriteSettings().

TypedStreamCondition cmtk::TypedStream::WriteIntArray	(	const char *	key,
		const int *	array,
		const int	size,
		const int	valuesPerLine = `10`
	)		`[inherited]`

Write array of integer values to an open archive.

Parameters:

key	The name of the field under which to write this array in the archive.
array	Pointer to the array to be written.
size	Number of values in the array. This is the number of values written to the archive.
valuesPerLine	Optional number of values per line of text written to the archive. This improves readability of the resulting archive as a text.

Definition at line 930 of file cmtkTypedStream.cxx.

References cmtk::TYPEDSTREAM_ERROR, cmtk::TYPEDSTREAM_ERROR_ARG, and cmtk::TYPEDSTREAM_OK.

Referenced by cmtk::operator<<().

TypedStreamCondition cmtk::TypedStream::WriteItem	(	const char *	key,
		const Types::DataItem	value
	)		`[inline, inherited]`

Write an Types::DataItem value to an open archive.

Parameters:

key	The name of the field under which to write this value in the archive.
value	Value to write to the archive under the given key.

Definition at line 451 of file cmtkTypedStream.h.

TypedStreamCondition cmtk::TypedStream::WriteItemArray	(	const char *	key,
		const Types::DataItem *	array,
		const int	size,
		const int	valuesPerLine = `10`
	)		`[inline, inherited]`

Write array of double- or single precision values to an open archive.

Whether double- or single-precision data is written depends on the definition of the CMTK_DATA_DOUBLE preprocessor symbol. This function is thus guaranteed to always match the Types::DataItem type.

See also:: CMTK_DATA_DOUBLE; Types::DataItem

Parameters:

key	The name of the field under which to write this array in the archive.
array	Pointer to the array to be written.
size	Number of values in the array. This is the number of values written to the archive.
valuesPerLine	Optional number of values per line of text written to the archive. This improves readability of the resulting archive as a text.

Definition at line 532 of file cmtkTypedStream.h.

void cmtk::VolumeFromFile::WriteMetaImage	(	const char *	pathHdr,
		const UniformVolume &	volume
	)		`[static, inherited]`

void cmtk::VolumeFromFile::WriteNifti	(	const char *	pathImg,
		const UniformVolume &	volume,
		const bool	verbose = `false`
	)		`[static, inherited]`

TypedStreamCondition cmtk::TypedStream::WriteString	(	const char *	key,
		const char *	value
	)		`[inherited]`

Write a string to an open archive.

Parameters:

key	The name of the field under which to write this string in the archive.
value	String to write to the archive under the given key.

Definition at line 817 of file cmtkTypedStream.cxx.

References cmtk::TYPEDSTREAM_OK.

Referenced by cmtk::operator<<(), cmtk::ImagePairAffineRegistrationCommandLine::OutputResultList(), cmtk::AffineRegistrationCommandLine::OutputResultList(), cmtk::ImagePairNonrigidRegistrationCommandLine::OutputWarp(), cmtk::ElasticRegistrationCommandLine::OutputWarp(), cmtk::TypedStreamStudylist::Write(), cmtk::ClassStreamStudyList::Write(), cmtk::VoxelRegistration::ImagePreprocessor::WriteSettings(), and cmtk::ImagePairRegistration::ImagePreprocessor::WriteSettings().

TypedStreamCondition cmtk::TypedStream::WriteString	(	const char *	key,
		const std::string &	value
	)		`[inherited]`

Write a string to an open archive.

Parameters:

key	The name of the field under which to write this string in the archive.
value	String to write to the archive under the given key.

Definition at line 810 of file cmtkTypedStream.cxx.

cmtk::Study::~Study ( ) [virtual, inherited]

Destructor.

Definition at line 166 of file cmtkStudy.cxx.

cmtk::TypedStream::~TypedStream ( ) [virtual, inherited]

Destructor.

Close() is called to close a possibly open archive.

Definition at line 101 of file cmtkTypedStream.cxx.

cmtk::TypedStreamStudylist::~TypedStreamStudylist ( ) [inherited]

Destructor.

Definition at line 67 of file cmtkTypedStreamStudylist.cxx.

Variable Documentation

char cmtk::TypedStream::Buffer[TYPEDSTREAM_LIMIT_BUFFER] [private, inherited]

Buffer for the current line read from the archive.

Definition at line 587 of file cmtkTypedStream.h.

char* cmtk::TypedStream::BufferKey [private, inherited]

Pointer to the "key" part of the line currently in Buffer.

Definition at line 590 of file cmtkTypedStream.h.

char* cmtk::TypedStream::BufferValue [private, inherited]

Pointer to the "value" part of the line currently in Buffer.

Definition at line 593 of file cmtkTypedStream.h.

short cmtk::FileHeaderBioRad::byte_format [inherited]

Definition at line 57 of file cmtkVolumeFromFileBioRad.cxx.

Referenced by cmtk::VolumeFromFile::ReadBioRad().

const char* const cmtk::CMTK_LEGACY_WRITE_IMAGES_RAS = "CMTK_LEGACY_WRITE_IMAGES_RAS"

Environment variable that turns off writing output images in the array order of the input images.

Definition at line 67 of file cmtkVolumeIO.cxx.

unsigned short cmtk::FileHeaderBioRad::color1 [inherited]

Definition at line 61 of file cmtkVolumeFromFileBioRad.cxx.

unsigned short cmtk::FileHeaderBioRad::color2 [inherited]

Definition at line 65 of file cmtkVolumeFromFileBioRad.cxx.

TypedStreamDebugFlag cmtk::TypedStream::DebugFlag [private, inherited]

Debug flag.

Definition at line 643 of file cmtkTypedStream.h.

unsigned short cmtk::FileHeaderBioRad::dummy[3] [inherited]

Definition at line 69 of file cmtkVolumeFromFileBioRad.cxx.

short cmtk::FileHeaderBioRad::edited [inherited]

Definition at line 66 of file cmtkVolumeFromFileBioRad.cxx.

FILE* cmtk::TypedStream::File [private, inherited]

Pointer to the actual file.

Definition at line 558 of file cmtkTypedStream.h.

unsigned short cmtk::FileHeaderBioRad::file_id [inherited]

Definition at line 62 of file cmtkVolumeFromFileBioRad.cxx.

Referenced by cmtk::VolumeFromFile::ReadBioRad().

const FileFormatMagic cmtk::FileFormatMagicNumbers[]

Initial value:

 {
  { 0, NULL, 0 }, 
  { 0, NULL, 0 }, 
  { 0, NULL, 0 }, 
  { 0, NULL, 0 }, 
  { 0, "! TYPEDSTREAM", 13 }, 
  { 0, "P5", 2 }, 
  { 128, "DICM", 4 }, 
  { 0, "Modality :=", 11 }, 
  { 0, "# AmiraMesh 3D", 14 },
  { 0, NULL, 0 }, 
  { 0, NULL, 0 }, 
  { 54, "\x39\x30", 2 }, 
  { 344, "ni1\x00", 4 }, 
  { 344, "n+1\x00", 4 }, 
  { 0, "AVW_ImageFile", 13 }, 
  { 0, NULL, 0 }, 
  { 0, "NRRD", 4 }, 
  { 0, "\x5C\x01\x00\x00", 4 }, 
  { 0, "\x00\x00\x01\x5C", 4 }, 
  { 0, "#Insight Transform File V1.0", 28 }, 
  { 0, NULL, 0 }  
}

Magic number records for known file types.

Definition at line 70 of file cmtkFileFormat.cxx.

const char * cmtk::FileFormatName

Table of file format ID names.

Definition at line 94 of file cmtkFileFormat.cxx.

gzFile cmtk::TypedStream::GzFile [private, inherited]

Pointer to the compressed file in decompression mode.

Definition at line 561 of file cmtkTypedStream.h.

VolumeIO::Initializer cmtk::VolumeIO::Initializer::Instance [static, private, inherited]

Instance of the initializer class.

Definition at line 169 of file cmtkVolumeIO.h.

short cmtk::FileHeaderBioRad::lens [inherited]

Definition at line 67 of file cmtkVolumeFromFileBioRad.cxx.

std::stack<int> cmtk::TypedStream::LevelStack [private, inherited]

Stack of open section levels.

This stack holds the starting positions of all currently open sections. The entries are byte positions relative to the beginning of the file.

Definition at line 599 of file cmtkTypedStream.h.

float cmtk::FileHeaderBioRad::mag_factor [inherited]

Definition at line 68 of file cmtkVolumeFromFileBioRad.cxx.

const char* cmtk::FileFormatMagic::magicString [inherited]

Magic number as string of characters.

Definition at line 64 of file cmtkFileFormat.cxx.

const size_t cmtk::FileFormatMagic::magicStringLength [inherited]

Length of magic number string (necessary due to Null characters).

Definition at line 66 of file cmtkFileFormat.cxx.

short cmtk::FileHeaderBioRad::merged [inherited]

Definition at line 60 of file cmtkVolumeFromFileBioRad.cxx.

TypedStreamMode cmtk::TypedStream::Mode [private, inherited]

Mode the current archive was opened with.

Definition at line 564 of file cmtkTypedStream.h.

unsigned short cmtk::FileHeaderBioRad::n [inherited]

Definition at line 58 of file cmtkVolumeFromFileBioRad.cxx.

char cmtk::FileHeaderBioRad::name[32] [inherited]

Definition at line 59 of file cmtkVolumeFromFileBioRad.cxx.

int cmtk::FileHeaderBioRad::notes [inherited]

Definition at line 56 of file cmtkVolumeFromFileBioRad.cxx.

Referenced by cmtk::VolumeFromFile::ReadBioRad().

short cmtk::FileHeaderBioRad::npic [inherited]

Definition at line 53 of file cmtkVolumeFromFileBioRad.cxx.

Referenced by cmtk::VolumeFromFile::ReadBioRad().

unsigned short cmtk::FileHeaderBioRad::ny [inherited]

Definition at line 52 of file cmtkVolumeFromFileBioRad.cxx.

Referenced by cmtk::VolumeFromFile::ReadBioRad().

int cmtk::TypedStream::PrecisionDouble [private, inherited]

Number of significant digits for "double" fields.

As all float numbers are written to the archive as strings, part of the native resolution is lost. This field determines, how many significant digits are preserved when converting double precision float numbers to strings.

Definition at line 584 of file cmtkTypedStream.h.

int cmtk::TypedStream::PrecisionFloat [private, inherited]

Number of significant digits for "float" fields.

As all float numbers are written to the archive as strings, part of the native resolution is lost. This field determines, how many significant digits are preserved when converting single precision float numbers to strings.

Definition at line 576 of file cmtkTypedStream.h.

short cmtk::FileHeaderBioRad::ramp1_max [inherited]

Definition at line 55 of file cmtkVolumeFromFileBioRad.cxx.

short cmtk::FileHeaderBioRad::ramp1_min [inherited]

Definition at line 54 of file cmtkVolumeFromFileBioRad.cxx.

short cmtk::FileHeaderBioRad::ramp2_max [inherited]

Definition at line 64 of file cmtkVolumeFromFileBioRad.cxx.

short cmtk::FileHeaderBioRad::ramp2_min [inherited]

Definition at line 63 of file cmtkVolumeFromFileBioRad.cxx.

char* cmtk::TypedStream::SplitPosition [mutable, private, inherited]

Internal position pointer for "StringSplit()".

Definition at line 634 of file cmtkTypedStream.h.