soma Namespace Reference

Namespaces
	internal

Classes
class	AffineTransformation3dBase
	Affine 3D transformation. More...
class	AllocatedVector
	A STL-like vector with a smart and slow allocation system for large data buffers. More...
class	AllocatorContext
	Allocation context. More...
class	AllocatorStrategy
	Determination of the allocation type depending of the buffer size to allocate and the disk format of data. More...
class	AsciiDataSourceTraits
class	AsciiDataSourceTraits< AimsVector< T, D > >
class	AsciiDataSourceTraits< carto::VoxelValue< T, C > >
class	AttributedChecker
	To check the syntax of an AttributedObject. More...
class	AttributedReader
	To read GenericObject from a file. More...
class	AttributedWriter
	To write an AttributedObject to a file. More...
class	BufferDataSource
class	ChainDataSource
	Abstract base DataSource class to operate on another DataSource (to transform it) More...
class	Creator
	Object creation / resize or other setup factory. More...
class	CStreamDataSource
	C stream data source: base class for all sources based on a FILE* (stdio streams) More...
class	DataSource
	Abstraction layer for various data sources (file, buffer, socket...). More...
class	DataSourceCapabilities
	Reading/Writing Capabilities of a FormatReader. More...
class	DataSourceInfo
	Informative object used by IO system. More...
class	DataSourceInfoLoader
	Generic information retreiver / checker for all data sources and file formats. More...
class	DataSourceList
	This class allows to manipulate "lists" of pointers to DataSource. More...
class	DefaultAsciiItemReader
class	DefaultAsciiItemWriter
class	DefaultBSwapItemReader
class	DefaultBSwapItemWriter
class	DefaultItemReader
	Default low-levels readers. More...
class	DefaultItemWriter
	Default low-levels writers. More...
class	DefaultMinfNodeExpander
class	DictionaryBuilder
class	FDDataSource
	File Descriptor data source: base class for all sources based on a file descriptor. More...
class	FileDataSource
class	FilteringDataSource
	Filtering data source: filters out comments and/or counts lines in a ASCII stream. More...
class	FormatChecker
	Format Checker. More...
class	FormatDictionary
	Formats holder for each format of Cartograph object, used by Reader and Writer. More...
class	FormatReader
	Low-level object IO reader specialized for a specific format. More...
class	FormatWriter
	Low-level object IO writer specialized for a specific format. More...
class	GenericWriter
class	HeaderTranslator
	Properties translator. More...
class	ImageReader
	ImageReader is a low level Image reader. More...
class	ImageWriter
	ImageWriter is a low level Image writer. More...
class	IOObjectTypesDictionary
	Global dictionary of supported object types for IO. More...
class	IStreamDataSource
	DataSource on a std::istream (read-only stream) More...
class	ItemReader
	Low-level "small item" reader, used by higher-level file readers. More...
class	ItemWriter
	Low-level "small item" writer, used by higher-level file writers. More...
class	JsonFormatChecker
class	JsonFormatReader
class	JsonFormatWriter
class	ListBuilder
class	LowLevelAllocator
	Abstract base class for actual allocators types. More...
class	MappingCopyAllocator
class	MappingROAllocator
class	MappingRWAllocator
class	MemoryAllocator
	Normal allocation mode: allocation in main memory. More...
class	MinfNodeExpander
class	MinfTreeExpander
class	MinfUtil
	Meta informations utilities. More...
class	MinfXMLReader
class	MultiFileFormat
struct	MultiFileFormatInfo
class	NullAllocator
	This allocator doesn't allocate anything. More...
class	ObjectListener
class	OStreamDataSource
	DataSource on a std::ostream (write-only stream) More...
class	PythonFormatChecker
class	PythonFormatReader
class	PythonFormatWriter
class	PythonReader
class	PythonWriter
class	Reader
	Generic reader for every format of Cartograph object. More...
class	ReaderAlgorithm
	Link mechanism between a data source or file and an algorithm operating on arbitrary data types. More...
class	ScaledEncoding
class	ScaledEncodingInfo
class	SingleDictionaryExpander
class	StreamDataSource
	DataSource on a std::iostream (read/write stream) More...
class	StreamUtil
class	Transformation
	Polymorphic base class for spatial transformations. More...
class	Transformation3d
	Polymorphic base class for spatial transformations in 3D. More...
class	Writer
	Generic writer for every format of Aims object. More...
class	XMLFormatChecker
class	XMLFormatReader

Typedefs
typedef unsigned long long	offset_t
	Offsets are 64 bits if supported. More...
typedef std::multimap< std::string, std::string >	multi_S
typedef std::set< std::string >	set_S
typedef std::pair< std::multimap< std::string, std::string >::const_iterator, std::multimap< std::string, std::string >::const_iterator >	pair_cit_S

Functions
std::ostream &	operator<< (std::ostream &os, const MemoryAllocator &thing)
std::ostream &	operator<< (std::ostream &os, const MappingCopyAllocator &thing)
std::ostream &	operator<< (std::ostream &os, const MappingROAllocator &thing)
std::ostream &	operator<< (std::ostream &os, const MappingRWAllocator &thing)
template<typename T >
bool	canEncodeAsScaledS16 (const T *vol, float &slope, float &offset, const std::vector< long > &strides, const std::vector< int > &sizes, bool enableoffset=true, double *maxerr=0)
	Checks if a volume can be encoded as 16 bit signed ints with a scale factor and optionally an offset. More...
template<>
bool	canEncodeAsScaledS16 (const float *vol, float &slope, float &offset, const std::vector< long > &strides, const std::vector< int > &sizes, bool enableoffset, double *)
template<>
bool	canEncodeAsScaledS16 (const double *vol, float &slope, float &offset, const std::vector< long > &strides, const std::vector< int > &sizes, bool enableoffset, double *)
soma::AffineTransformation3dBase	operator* (const soma::AffineTransformation3dBase &affineTransformation3d1, const soma::AffineTransformation3dBase &affineTransformation3d2)
std::ostream &	operator<< (std::ostream &os, const soma::AffineTransformation3dBase &thing)
template<typename T >
DataSource &	operator>> (DataSource &ds, T &x)
DataSource &	operator<< (DataSource &ds, const char &x)
DataSource &	operator<< (DataSource &ds, const int8_t &x)
DataSource &	operator<< (DataSource &ds, const uint8_t &x)
DataSource &	operator<< (DataSource &ds, const int16_t &x)
DataSource &	operator<< (DataSource &ds, const uint16_t &x)
DataSource &	operator<< (DataSource &ds, const int32_t &x)
DataSource &	operator<< (DataSource &ds, const uint32_t &x)
DataSource &	operator<< (DataSource &ds, const int64_t &x)
DataSource &	operator<< (DataSource &ds, const uint64_t &x)
DataSource &	operator<< (DataSource &ds, const long &x)
DataSource &	operator<< (DataSource &ds, const unsigned long &x)
DataSource &	operator<< (DataSource &ds, const float &x)
DataSource &	operator<< (DataSource &ds, const double &x)
DataSource &	operator<< (DataSource &ds, const std::string &x)
DataSource &	operator<< (DataSource &ds, const char *const &x)
template<typename T , unsigned int C>
DataSource &	operator<< (DataSource &ds, const carto::VoxelValue< T, C > &x)
DataSource &	operator<< (DataSource &ds, const carto::VoxelRGB &x)
DataSource &	operator<< (DataSource &ds, const carto::VoxelRGBA &x)
DataSource &	operator<< (DataSource &ds, const carto::VoxelHSV &x)
DataSource &	operator<< (DataSource &ds, const std::complex< float > &x)
DataSource &	operator<< (DataSource &ds, const std::complex< double > &x)
carto::Object	readDictionaryMinfXML (const std::string &fileName, carto::rc_ptr< carto::SyntaxSet > syntax=carto::rc_ptr< carto::SyntaxSet >())
carto::Object	readDictionaryMinfXML (DataSource &source, carto::rc_ptr< carto::SyntaxSet > syntax=carto::rc_ptr< carto::SyntaxSet >())
void	readDictionaryMinfXML (const std::string &fileName, carto::Object &dictionary, carto::rc_ptr< carto::SyntaxSet > syntax=carto::rc_ptr< carto::SyntaxSet >())
void	readDictionaryMinfXML (DataSource &source, carto::Object &dictionary, carto::rc_ptr< carto::SyntaxSet > syntax=carto::rc_ptr< carto::SyntaxSet >())
void	init_libXML ()
	just to force initializing libxml2, needs to be called once from the main thread in a multi-threaded environment. More...
template<typename T , int D>
DataSource &	operator<< (DataSource &ds, const AimsVector< T, D > &x)

Variables
const std::string	minfTag
const std::string	noneTag
const std::string	trueTag
const std::string	falseTag
const std::string	numberTag
const std::string	stringTag
const std::string	listTag
const std::string	dictionaryTag
const std::string	factoryTag
const std::string	xhtmlTag
const std::string	referenceTag
const std::string	expanderAttribute
const std::string	lengthAttribute
const std::string	nameAttribute
const std::string	objectTypeAttribute
const std::string	identifierAttribute

Typedef Documentation

multi_S

typedef std::multimap< std::string, std::string > soma::multi_S

Definition at line 214 of file reader_d.h.

offset_t

typedef unsigned long long soma::offset_t

Offsets are 64 bits if supported.

Definition at line 51 of file datasource.h.

pair_cit_S

typedef std::pair< std::multimap< std::string, std::string >::const_iterator, std::multimap< std::string, std::string >::const_iterator > soma::pair_cit_S

Definition at line 217 of file reader_d.h.

set_S

typedef std::set< std::string > soma::set_S

Definition at line 215 of file reader_d.h.

Function Documentation

canEncodeAsScaledS16() [1/3]

template<typename T >

bool soma::canEncodeAsScaledS16 ( const T *  vol, float &  slope, float &  offset, const std::vector< long > &  strides, const std::vector< int > &  sizes, bool  enableoffset = true, double *  maxerr = 0  )

inline

Checks if a volume can be encoded as 16 bit signed ints with a scale factor and optionally an offset.

If so, the slope and offset are determined and set.

Definition at line 71 of file scaledcoding.h.

canEncodeAsScaledS16() [2/3]

template<>

bool soma::canEncodeAsScaledS16	(	const float *	vol,
		float &	slope,
		float &	offset,
		const std::vector< long > &	strides,
		const std::vector< int > &	sizes,
		bool	enableoffset,
		double *
	)

canEncodeAsScaledS16() [3/3]

template<>

bool soma::canEncodeAsScaledS16	(	const double *	vol,
		float &	slope,
		float &	offset,
		const std::vector< long > &	strides,
		const std::vector< int > &	sizes,
		bool	enableoffset,
		double *
	)

init_libXML()

void soma::init_libXML

(

)

just to force initializing libxml2, needs to be called once from the main thread in a multi-threaded environment.

Called from PluginLoader::load

operator*()

soma::AffineTransformation3dBase soma::operator*	(	const soma::AffineTransformation3dBase &	affineTransformation3d1,
		const soma::AffineTransformation3dBase &	affineTransformation3d2
	)

operator<<() [1/27]

std::ostream& soma::operator<<	(	std::ostream &	os,
		const MappingCopyAllocator &	thing
	)

operator<<() [2/27]

std::ostream& soma::operator<<	(	std::ostream &	os,
		const MappingROAllocator &	thing
	)

operator<<() [3/27]

std::ostream& soma::operator<<	(	std::ostream &	os,
		const MappingRWAllocator &	thing
	)

operator<<() [4/27]

std::ostream& soma::operator<<	(	std::ostream &	os,
		const MemoryAllocator &	thing
	)

operator<<() [5/27]

std::ostream& soma::operator<<	(	std::ostream &	os,
		const soma::AffineTransformation3dBase &	thing
	)

operator<<() [6/27]

DataSource& soma::operator<< ( DataSource &  ds, const char &  x  )

inline

Definition at line 588 of file asciidatasourcetraits.h.

References soma::AsciiDataSourceTraits< T >::write().

operator<<() [7/27]

DataSource& soma::operator<< ( DataSource &  ds, const int8_t &  x  )

inline

Definition at line 596 of file asciidatasourcetraits.h.

References soma::AsciiDataSourceTraits< T >::write().

operator<<() [8/27]

DataSource& soma::operator<< ( DataSource &  ds, const uint8_t &  x  )

inline

Definition at line 603 of file asciidatasourcetraits.h.

References soma::AsciiDataSourceTraits< T >::write().

operator<<() [9/27]

DataSource& soma::operator<< ( DataSource &  ds, const int16_t &  x  )

inline

Definition at line 610 of file asciidatasourcetraits.h.

References soma::AsciiDataSourceTraits< T >::write().

operator<<() [10/27]

DataSource& soma::operator<< ( DataSource &  ds, const uint16_t &  x  )

inline

Definition at line 617 of file asciidatasourcetraits.h.

References soma::AsciiDataSourceTraits< T >::write().

operator<<() [11/27]

DataSource& soma::operator<< ( DataSource &  ds, const int32_t &  x  )

inline

Definition at line 624 of file asciidatasourcetraits.h.

References soma::AsciiDataSourceTraits< T >::write().

operator<<() [12/27]

DataSource& soma::operator<< ( DataSource &  ds, const uint32_t &  x  )

inline

Definition at line 631 of file asciidatasourcetraits.h.

References soma::AsciiDataSourceTraits< T >::write().

operator<<() [13/27]

DataSource& soma::operator<< ( DataSource &  ds, const int64_t &  x  )

inline

Definition at line 638 of file asciidatasourcetraits.h.

References soma::AsciiDataSourceTraits< T >::write().

operator<<() [14/27]

DataSource& soma::operator<< ( DataSource &  ds, const uint64_t &  x  )

inline

Definition at line 645 of file asciidatasourcetraits.h.

References soma::AsciiDataSourceTraits< T >::write().

operator<<() [15/27]

DataSource& soma::operator<< ( DataSource &  ds, const long &  x  )

inline

Definition at line 654 of file asciidatasourcetraits.h.

References soma::AsciiDataSourceTraits< T >::write().

operator<<() [16/27]

DataSource& soma::operator<< ( DataSource &  ds, const unsigned long &  x  )

inline

Definition at line 661 of file asciidatasourcetraits.h.

References soma::AsciiDataSourceTraits< T >::write().

operator<<() [17/27]

DataSource& soma::operator<< ( DataSource &  ds, const float &  x  )

inline

Definition at line 669 of file asciidatasourcetraits.h.

References soma::AsciiDataSourceTraits< T >::write().

operator<<() [18/27]

DataSource& soma::operator<< ( DataSource &  ds, const double &  x  )

inline

Definition at line 676 of file asciidatasourcetraits.h.

References soma::AsciiDataSourceTraits< T >::write().

operator<<() [19/27]

DataSource& soma::operator<< ( DataSource &  ds, const std::string &  x  )

inline

Definition at line 683 of file asciidatasourcetraits.h.

References soma::AsciiDataSourceTraits< T >::write().

operator<<() [20/27]

DataSource& soma::operator<< ( DataSource &  ds, const char *const &  x  )

inline

Definition at line 690 of file asciidatasourcetraits.h.

References soma::AsciiDataSourceTraits< T >::write().

operator<<() [21/27]

template<typename T , unsigned int C>

DataSource& soma::operator<< ( DataSource &  ds, const carto::VoxelValue< T, C > &  x  )

inline

Definition at line 766 of file asciidatasourcetraits.h.

References soma::AsciiDataSourceTraits< T >::write().

operator<<() [22/27]

DataSource& soma::operator<< ( DataSource &  ds, const carto::VoxelRGB &  x  )

inline

Definition at line 789 of file asciidatasourcetraits.h.

References soma::AsciiDataSourceTraits< T >::write().

operator<<() [23/27]

DataSource& soma::operator<< ( DataSource &  ds, const carto::VoxelRGBA &  x  )

inline

Definition at line 812 of file asciidatasourcetraits.h.

References soma::AsciiDataSourceTraits< T >::write().

operator<<() [24/27]

DataSource& soma::operator<< ( DataSource &  ds, const carto::VoxelHSV &  x  )

inline

Definition at line 835 of file asciidatasourcetraits.h.

References soma::AsciiDataSourceTraits< T >::write().

operator<<() [25/27]

DataSource& soma::operator<< ( DataSource &  ds, const std::complex< float > &  x  )

inline

Definition at line 866 of file asciidatasourcetraits.h.

References soma::AsciiDataSourceTraits< T >::write().

operator<<() [26/27]

DataSource& soma::operator<< ( DataSource &  ds, const std::complex< double > &  x  )

inline

Definition at line 897 of file asciidatasourcetraits.h.

References soma::AsciiDataSourceTraits< T >::write().

operator<<() [27/27]

template<typename T , int D>

DataSource& soma::operator<< ( DataSource &  ds, const AimsVector< T, D > &  x  )

inline

Definition at line 1212 of file vector.h.

operator>>()

template<typename T >

DataSource& soma::operator>> ( DataSource &  ds, T &  x  )

inline

Definition at line 580 of file asciidatasourcetraits.h.

References soma::AsciiDataSourceTraits< T >::read().

readDictionaryMinfXML() [1/4]

carto::Object soma::readDictionaryMinfXML	(	const std::string &	fileName,
		carto::rc_ptr< carto::SyntaxSet >	syntax = carto::rc_ptr< carto::SyntaxSet >()
	)

readDictionaryMinfXML() [2/4]

carto::Object soma::readDictionaryMinfXML	(	DataSource &	source,
		carto::rc_ptr< carto::SyntaxSet >	syntax = carto::rc_ptr< carto::SyntaxSet >()
	)

readDictionaryMinfXML() [3/4]

void soma::readDictionaryMinfXML	(	const std::string &	fileName,
		carto::Object &	dictionary,
		carto::rc_ptr< carto::SyntaxSet >	syntax = carto::rc_ptr< carto::SyntaxSet >()
	)

readDictionaryMinfXML() [4/4]

void soma::readDictionaryMinfXML	(	DataSource &	source,
		carto::Object &	dictionary,
		carto::rc_ptr< carto::SyntaxSet >	syntax = carto::rc_ptr< carto::SyntaxSet >()
	)

Variable Documentation

dictionaryTag

const std::string soma::dictionaryTag

expanderAttribute

const std::string soma::expanderAttribute

factoryTag

const std::string soma::factoryTag

falseTag

const std::string soma::falseTag

identifierAttribute

const std::string soma::identifierAttribute

lengthAttribute

const std::string soma::lengthAttribute

listTag

const std::string soma::listTag

minfTag

const std::string soma::minfTag

nameAttribute

const std::string soma::nameAttribute

noneTag

const std::string soma::noneTag

numberTag

const std::string soma::numberTag

objectTypeAttribute

const std::string soma::objectTypeAttribute

referenceTag

const std::string soma::referenceTag

stringTag

const std::string soma::stringTag

trueTag

const std::string soma::trueTag

xhtmlTag

const std::string soma::xhtmlTag