soma-io  4.5.0
soma Namespace Reference

Namespaces

 internal
 

Classes

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< 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 readers. 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  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  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 *)
 
template<typename T >
DataSourceoperator>> (DataSource &ds, T &x)
 
DataSourceoperator<< (DataSource &ds, const char &x)
 
DataSourceoperator<< (DataSource &ds, const int8_t &x)
 
DataSourceoperator<< (DataSource &ds, const uint8_t &x)
 
DataSourceoperator<< (DataSource &ds, const int16_t &x)
 
DataSourceoperator<< (DataSource &ds, const uint16_t &x)
 
DataSourceoperator<< (DataSource &ds, const int32_t &x)
 
DataSourceoperator<< (DataSource &ds, const uint32_t &x)
 
DataSourceoperator<< (DataSource &ds, const int64_t &x)
 
DataSourceoperator<< (DataSource &ds, const uint64_t &x)
 
DataSourceoperator<< (DataSource &ds, const long &x)
 
DataSourceoperator<< (DataSource &ds, const unsigned long &x)
 
DataSourceoperator<< (DataSource &ds, const float &x)
 
DataSourceoperator<< (DataSource &ds, const double &x)
 
DataSourceoperator<< (DataSource &ds, const std::string &x)
 
DataSourceoperator<< (DataSource &ds, const char *const &x)
 
template<typename T , unsigned int C>
DataSourceoperator<< (DataSource &ds, const carto::VoxelValue< T, C > &x)
 
DataSourceoperator<< (DataSource &ds, const carto::VoxelRGB &x)
 
DataSourceoperator<< (DataSource &ds, const carto::VoxelRGBA &x)
 
DataSourceoperator<< (DataSource &ds, const carto::VoxelHSV &x)
 
DataSourceoperator<< (DataSource &ds, const std::complex< float > &x)
 
DataSourceoperator<< (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...
 

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

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

Definition at line 214 of file reader_d.h.

typedef unsigned long long soma::offset_t

Offsets are 64 bits if supported.

Definition at line 51 of file datasource.h.

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.

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

Definition at line 215 of file reader_d.h.

Function Documentation

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.

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

std::ostream& soma::operator<< ( std::ostream &  os,
const MappingCopyAllocator &  thing 
)
std::ostream& soma::operator<< ( std::ostream &  os,
const MappingROAllocator &  thing 
)
std::ostream& soma::operator<< ( std::ostream &  os,
const MappingRWAllocator &  thing 
)
std::ostream& soma::operator<< ( std::ostream &  os,
const MemoryAllocator &  thing 
)
DataSource& soma::operator<< ( DataSource &  ds,
const char &  x 
)
inline
DataSource& soma::operator<< ( DataSource &  ds,
const int8_t &  x 
)
inline
DataSource& soma::operator<< ( DataSource &  ds,
const uint8_t &  x 
)
inline
DataSource& soma::operator<< ( DataSource &  ds,
const int16_t &  x 
)
inline
DataSource& soma::operator<< ( DataSource &  ds,
const uint16_t &  x 
)
inline
DataSource& soma::operator<< ( DataSource &  ds,
const int32_t &  x 
)
inline
DataSource& soma::operator<< ( DataSource &  ds,
const uint32_t &  x 
)
inline
DataSource& soma::operator<< ( DataSource &  ds,
const int64_t &  x 
)
inline
DataSource& soma::operator<< ( DataSource &  ds,
const uint64_t &  x 
)
inline
DataSource& soma::operator<< ( DataSource &  ds,
const long &  x 
)
inline
DataSource& soma::operator<< ( DataSource &  ds,
const unsigned long &  x 
)
inline
DataSource& soma::operator<< ( DataSource &  ds,
const float &  x 
)
inline
DataSource& soma::operator<< ( DataSource &  ds,
const double &  x 
)
inline
DataSource& soma::operator<< ( DataSource &  ds,
const std::string &  x 
)
inline
DataSource& soma::operator<< ( DataSource &  ds,
const char *const &  x 
)
inline
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.

DataSource& soma::operator<< ( DataSource &  ds,
const carto::VoxelRGB x 
)
inline
DataSource& soma::operator<< ( DataSource &  ds,
const carto::VoxelRGBA x 
)
inline
DataSource& soma::operator<< ( DataSource &  ds,
const carto::VoxelHSV x 
)
inline
DataSource& soma::operator<< ( DataSource &  ds,
const std::complex< float > &  x 
)
inline

Definition at line 866 of file asciidatasourcetraits.h.

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

Definition at line 897 of file asciidatasourcetraits.h.

template<typename T >
DataSource& soma::operator>> ( DataSource &  ds,
T &  x 
)
inline

Definition at line 580 of file asciidatasourcetraits.h.

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

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

Variable Documentation

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