Namespaces
	internal

Classes
class	LowLevelAllocator
	Abstract base class for actual allocators types. More...

class	MemoryAllocator
	Normal allocation mode: allocation in main memory. More...

class	NullAllocator
	This allocator doesn't allocate anything. More...

class	AllocatorStrategy
	Determination of the allocation type depending of the buffer size to allocate and the disk format of data. More...

class	AllocatorContext
	Allocation context. More...

class	MappingCopyAllocator

class	MappingROAllocator

class	MappingRWAllocator

class	AttributedChecker
	To check the syntax of an AttributedObject. More...

class	FormatChecker
	Format Checker. More...

class	JsonFormatChecker

class	PythonFormatChecker

class	XMLFormatChecker

class	BufferDataSource

class	ChainDataSource
	Abstract base DataSource class to operate on another DataSource (to transform it) 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	DataSourceList
	This class allows to manipulate "lists" of pointers to DataSource. More...

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	StreamDataSource
	DataSource on a std::iostream (read/write stream) More...

class	IStreamDataSource
	DataSource on a std::istream (read-only stream) More...

class	OStreamDataSource
	DataSource on a std::ostream (write-only stream) 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	ImageReader
	ImageReader is a low level Image reader. More...

class	ImageWriter
	ImageWriter is a low level Image 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	FormatDictionary
	Formats holder for each format of Cartograph object, used by Reader and Writer. More...

class	IOObjectTypesDictionary
	Global dictionary of supported object types for IO. More...

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	ScaledEncodingInfo

class	ScaledEncoding

class	GenericWriter

class	Writer
	Generic writer for every format of Aims object. More...

class	AttributedReader
	To read GenericObject from a file. More...

class	ItemReader
	Low-level "small item" reader, used by higher-level file readers. More...

class	DefaultItemReader
	Default low-levels readers. More...

class	DefaultAsciiItemReader

class	DefaultBSwapItemReader

class	JsonFormatReader

class	PythonFormatReader

class	PythonReader

class	XMLFormatReader

class	AffineTransformation3dBase
	Affine 3D transformation. More...

class	Transformation
	Polymorphic base class for spatial transformations. More...

class	Transformation3d
	Polymorphic base class for spatial transformations in 3D. More...

class	AllocatedVector
	A STL-like vector with a smart and slow allocation system for large data buffers. More...

class	AsciiDataSourceTraits

class	StreamUtil

class	AsciiDataSourceTraits< carto::VoxelValue< T, C > >

class	Creator
	Object creation / resize or other setup factory. More...

class	MinfUtil
	Meta information utilities. More...

class	HeaderTranslator
	Properties translator. More...

struct	MultiFileFormatInfo

class	MultiFileFormat

class	ObjectListener

class	MinfNodeExpander

class	MinfTreeExpander

class	DefaultMinfNodeExpander

class	SingleDictionaryExpander

class	ListBuilder

class	DictionaryBuilder

class	MinfXMLReader

class	AsciiDataSourceTraits< AimsVector< T, D > >

class	AttributedWriter
	To write an AttributedObject to a file. More...

class	ItemWriter
	Low-level "small item" writer, used by higher-level file writers. More...

class	DefaultItemWriter
	Default low-levels writers. More...

class	DefaultAsciiItemWriter

class	DefaultBSwapItemWriter

class	JsonFormatWriter

class	PythonFormatWriter

class	PythonWriter

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 216 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 219 of file reader_d.h.

◆ set_S

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

Definition at line 217 of file reader_d.h.

Function Documentation

◆ canEncodeAsScaledS16() [1/3]

template<>

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

◆ 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<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.

◆ 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]

template<typename T , int D>

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

inline

Definition at line 1247 of file vector.h.

◆ operator<<() [2/27]

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

inline

Definition at line 834 of file asciidatasourcetraits.h.

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

◆ operator<<() [3/27]

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

inline

Definition at line 788 of file asciidatasourcetraits.h.

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

◆ operator<<() [4/27]

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

inline

Definition at line 811 of file asciidatasourcetraits.h.

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

◆ operator<<() [5/27]

template<typename T , unsigned int C>

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

inline

Definition at line 765 of file asciidatasourcetraits.h.

◆ operator<<() [6/27]

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

inline

Definition at line 587 of file asciidatasourcetraits.h.

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

◆ operator<<() [7/27]

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

inline

Definition at line 689 of file asciidatasourcetraits.h.

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

◆ operator<<() [8/27]

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

inline

Definition at line 675 of file asciidatasourcetraits.h.

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

◆ operator<<() [9/27]

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

inline

Definition at line 668 of file asciidatasourcetraits.h.

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

◆ operator<<() [10/27]

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

inline

Definition at line 609 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 623 of file asciidatasourcetraits.h.

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

◆ operator<<() [12/27]

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

inline

Definition at line 637 of file asciidatasourcetraits.h.

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

◆ operator<<() [13/27]

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

inline

Definition at line 595 of file asciidatasourcetraits.h.

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

◆ operator<<() [14/27]

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

inline

Definition at line 653 of file asciidatasourcetraits.h.

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

◆ operator<<() [15/27]

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

inline

Definition at line 896 of file asciidatasourcetraits.h.

◆ operator<<() [16/27]

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

inline

Definition at line 865 of file asciidatasourcetraits.h.

◆ operator<<() [17/27]

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

inline

Definition at line 682 of file asciidatasourcetraits.h.

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

◆ operator<<() [18/27]

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

inline

Definition at line 616 of file asciidatasourcetraits.h.

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

◆ operator<<() [19/27]

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

inline

Definition at line 630 of file asciidatasourcetraits.h.

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

◆ operator<<() [20/27]

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

inline

Definition at line 644 of file asciidatasourcetraits.h.

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

◆ operator<<() [21/27]

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

inline

Definition at line 602 of file asciidatasourcetraits.h.

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

◆ operator<<() [22/27]

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

inline

Definition at line 660 of file asciidatasourcetraits.h.

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

◆ operator<<() [23/27]

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

◆ operator<<() [24/27]

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

◆ operator<<() [25/27]

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

◆ operator<<() [26/27]

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

◆ operator<<() [27/27]

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

◆ 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]

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

◆ readDictionaryMinfXML() [2/4]

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

◆ readDictionaryMinfXML() [3/4]

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

◆ readDictionaryMinfXML() [4/4]

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

Variable Documentation

◆ dictionaryTag

const std::string soma::dictionaryTag

extern

◆ expanderAttribute

const std::string soma::expanderAttribute

extern

◆ factoryTag

const std::string soma::factoryTag

extern

◆ falseTag

const std::string soma::falseTag

extern

◆ identifierAttribute

const std::string soma::identifierAttribute

extern

◆ lengthAttribute

const std::string soma::lengthAttribute

extern

◆ listTag

const std::string soma::listTag

extern

◆ minfTag

const std::string soma::minfTag

extern

◆ nameAttribute

const std::string soma::nameAttribute

extern

◆ noneTag

const std::string soma::noneTag

extern

◆ numberTag

const std::string soma::numberTag

extern

◆ objectTypeAttribute

const std::string soma::objectTypeAttribute

extern

◆ referenceTag

const std::string soma::referenceTag

extern

◆ stringTag

const std::string soma::stringTag

extern

◆ trueTag

const std::string soma::trueTag

extern

◆ xhtmlTag

const std::string soma::xhtmlTag

extern

Namespaces

Classes

Typedefs

Functions

Variables

Typedef Documentation

◆ multi_S

◆ offset_t

◆ pair_cit_S

◆ set_S

Function Documentation

◆ canEncodeAsScaledS16() [1/3]

◆ canEncodeAsScaledS16() [2/3]

◆ canEncodeAsScaledS16() [3/3]

◆ init_libXML()

◆ operator*()

◆ operator<<() [1/27]

◆ operator<<() [2/27]

◆ operator<<() [3/27]

◆ operator<<() [4/27]

◆ operator<<() [5/27]

◆ operator<<() [6/27]

◆ operator<<() [7/27]

◆ operator<<() [8/27]

◆ operator<<() [9/27]

◆ operator<<() [10/27]

◆ operator<<() [11/27]

◆ operator<<() [12/27]

◆ operator<<() [13/27]

◆ operator<<() [14/27]

◆ operator<<() [15/27]

◆ operator<<() [16/27]

◆ operator<<() [17/27]

◆ operator<<() [18/27]

◆ operator<<() [19/27]

◆ operator<<() [20/27]

◆ operator<<() [21/27]

◆ operator<<() [22/27]

◆ operator<<() [23/27]

◆ operator<<() [24/27]

◆ operator<<() [25/27]

◆ operator<<() [26/27]

◆ operator<<() [27/27]

◆ operator>>()

◆ readDictionaryMinfXML() [1/4]

◆ readDictionaryMinfXML() [2/4]

◆ readDictionaryMinfXML() [3/4]

◆ readDictionaryMinfXML() [4/4]

Variable Documentation

◆ dictionaryTag

◆ expanderAttribute

◆ factoryTag

◆ falseTag

◆ identifierAttribute

◆ lengthAttribute

◆ listTag

◆ minfTag

◆ nameAttribute

◆ noneTag

◆ numberTag

◆ objectTypeAttribute

◆ referenceTag

◆ stringTag

◆ trueTag

◆ xhtmlTag