aims Namespace Reference

The class for EcatSino data write operation. More...

Namespaces
	DataManip
	internal
	strel

Classes
class	_convertedNiftiArrayValue
class	_convertedNiftiArrayValue< AimsVector< U, D > >
class	_convertedNiftiValue
class	_convertedNiftiValue< AimsVector< U, D > >
class	AffineTransformation3d
	Affine 3D transformation. More...
class	AimsApplication
class	AimsFastAllocationData
class	AimsGraphReader
	Reader / postprocessor for graph reading. More...
class	AimsGraphWriter
struct	AimsGraphWriter_Private
class	AimsRoi
class	AnyTypeReader
	A class to read an object of type T, even if the type on file is different. More...
class	AnyTypeReaderProcess
	A process to read an object of type T, even if the type on file is different. More...
class	APCReader
	Reads .APC (anterior/posterior commissures) files. More...
class	ArgFormat
class	ArgHeader
	Descriptor class for the .arg GRAPH file format header. More...
class	ArgReader
class	ArgWriter
class	BckFormat
class	BckHeader
	Descriptor class for the .bck BUCKET file format header. More...
class	BckMapFormat
class	BckMapReader
	BucketMap objects can be read / written by BckMapReader / BckMapWriter, these IO classes operate on the EXACT SAME FORMAT as the BCK format used by AimsBucket objects. More...
class	BckMapWriter
	BucketMap objects can be read / written by BckMapReader / BckMapWriter, these IO classes operate on the EXACT SAME FORMAT as the BCK format used by AimsBucket objects. More...
class	BckReader
class	BckWriter
class	Border
	The base class to manage borders on data containers. More...
class	BorderFiller
	This class contains static methods to fill the border of a VolumeRef with chosen values. More...
class	BorderIterator
	Represents the border of a volume. More...
class	BoundingBox
class	BucketMap
	An alternate, ordered, representation for buckets (voxels lists). More...
class	BucketMapGenerator
	Factory class for various common shapes of meshes. More...
class	Bundle
class	BundleFormatReader
	Virtual base class for bundles/fibers file formats support. More...
class	BundleInfo
class	BundleListener
	Serial processing of bundles. More...
class	BundleMotion
class	BundleProducer
	Serial processing of bundles. More...
class	BundleReader
	Reads a bundles file, and emits events while walking through its data. More...
class	BundleRegroup
class	BundleROISelect
class	BundleROISplit
class	Bundles
class	BundleSampler
	Filter fibers by randomly discarding a proportion of them. More...
class	BundlesFeatures
class	BundlesFusion
	Bundles fusionning: can merge several bundles producers (files...) into a single output, merging bundles split accross several producers, but having the same name. More...
class	BundleSlicesToMesh
class	BundlesSlicer
class	BundlesSlicerListener
class	BundleToGraph
	Bundles structure building as a Graph. More...
class	BundleToGraphWriter
class	BundleWriter
	Writes bundles information to a bundles file. More...
class	ChannelReader
	Reads a AimsData or carto::VolumeRef, with conversion if needed. More...
class	CiftiTools
	CIFTI-2 shaped matrices manipulation tools. More...
class	Clock
	The basic time tool. More...
class	CoarseReader
	Reads a AimsData<int16_t>, with conversion if needed. More...
class	ColorMap
class	ConnectedComponentEngine
class	ConnectedComponentEngine< AimsData< T >, AimsData< O > >
class	Connectivity
	Topology of a data container. More...
class	ConnectomistBundlesReader
	Connectomist .bundles format reader. More...
struct	CoordinatesLess
	Helper class for ordering Coordinates by their z, y, x coordinates. More...
struct	CoordinatesLess< T, 3 >
class	CurveOrientation
class	CurveSelection
class	CutMesh
	Cut meshes by a plane. More...
class	CutTexturedMesh
	Textured variant of CutMesh. More...
class	DecomposedAffineTransformation3d
class	DefaultAsciiItemReader
class	DefaultAsciiItemReader< AimsBucketItem< T > >
class	DefaultAsciiItemReader< DtiTensor >
class	DefaultAsciiItemReader< SparseMatrix >
class	DefaultAsciiItemReader< std::list< T > >
class	DefaultAsciiItemReader< std::vector< T > >
	Partial specialization for vectors. More...
class	DefaultAsciiItemReader< Tensor >
class	DefaultAsciiItemReader< Trieder >
class	DefaultAsciiItemWriter
class	DefaultAsciiItemWriter< AimsBucketItem< T > >
class	DefaultAsciiItemWriter< DtiTensor >
class	DefaultAsciiItemWriter< SparseMatrix >
class	DefaultAsciiItemWriter< std::list< T > >
class	DefaultAsciiItemWriter< std::vector< T > >
	Partial specialization for vectors. More...
class	DefaultAsciiItemWriter< Tensor >
class	DefaultAsciiItemWriter< Trieder >
class	DefaultBSwapItemReader
class	DefaultBSwapItemReader< AimsBucketItem< T > >
class	DefaultBSwapItemReader< AimsVector< T, D > >
	Partial specialization for vectors. More...
class	DefaultBSwapItemReader< DtiTensor >
class	DefaultBSwapItemReader< SparseMatrix >
class	DefaultBSwapItemReader< std::list< T > >
class	DefaultBSwapItemReader< std::vector< T > >
	Partial specialization for vectors. More...
class	DefaultBSwapItemReader< Tensor >
class	DefaultBSwapItemReader< Trieder >
class	DefaultBSwapItemWriter
class	DefaultBSwapItemWriter< AimsBucketItem< T > >
class	DefaultBSwapItemWriter< AimsVector< T, D > >
	Partial specialization for vectors. More...
class	DefaultBSwapItemWriter< DtiTensor >
class	DefaultBSwapItemWriter< SparseMatrix >
class	DefaultBSwapItemWriter< std::list< T > >
class	DefaultBSwapItemWriter< std::vector< T > >
	Partial specialization for vectors. More...
class	DefaultBSwapItemWriter< Tensor >
class	DefaultBSwapItemWriter< Trieder >
class	DefaultItemReader
	Default low-levels readers. More...
class	DefaultItemReader< AimsBucketItem< T > >
class	DefaultItemReader< AimsVector< T, D > >
	Partial specialization for vectors. More...
class	DefaultItemReader< DtiTensor >
class	DefaultItemReader< SparseMatrix >
class	DefaultItemReader< std::list< T > >
class	DefaultItemReader< std::vector< T > >
	Partial specialization for vectors. More...
class	DefaultItemReader< Tensor >
class	DefaultItemReader< Trieder >
class	DefaultItemWriter
	Default low-levels writers. More...
class	DefaultItemWriter< AimsBucketItem< T > >
class	DefaultItemWriter< AimsVector< T, D > >
	Partial specialization for vectors. More...
class	DefaultItemWriter< DtiTensor >
class	DefaultItemWriter< SparseMatrix >
class	DefaultItemWriter< std::list< T > >
class	DefaultItemWriter< std::vector< T > >
	Partial specialization for vectors. More...
class	DefaultItemWriter< Tensor >
class	DefaultItemWriter< Trieder >
class	EcatFormat
class	EcatHeader
	The descriptor class of the Ecat header. More...
class	EcatPlugin
class	EcatReader
	The class for Ecat data read operation. More...
class	EcatSinoHeader
	The descriptor class of the Ecat header. More...
class	EcatSinoReader
class	EcatSinoWriter
class	EcatWriter
	The class for VIDA data write operation. More...
class	FdfFormat
class	FdfHeader
class	FdfParType
class	FdfPlugin
class	FdfProcPar
class	FdfReader
class	FiberInfo
class	FiberOversampler
class	FileFormat
	Low-level object IO format: each specific format has such a reader / writer. More...
class	FileFormatDictionary
	Formats holder for each format of Aims object, used by Reader and Writer. More...
class	Finder
	Generic finder / checker for all data objects and file formats This will replace the old AimsFinder. More...
class	FinderBckFormat
class	FinderEcatFormat
class	FinderFdfFormat
class	FinderFormat
	Finder format checker. More...
class	FinderGenesisFormat
class	FinderGiftiFormat
class	FinderGraphFormat
class	FinderHieFormat
class	FinderImasFormat
class	FinderJpegFormat
class	FinderMeshFormat
class	FinderMniObjFormat
class	FinderPlyFormat
class	FinderSpmFormat
class	FinderTexFormat
class	FinderTiffFormat
class	FinderTriFormat
class	FinderTrmFormat
class	FinderVidaFormat
class	FinderWavefrontFormat
class	GenericWriter
class	GenesisFormat
class	GenesisHeader
	GE Genesis format header. More...
class	GenesisReader
class	GiftiHeader
	GIFTI Header class. More...
class	GiftiMeshFormat
class	GiftiPlugin
class	GiftiTextureFormat
class	GraphBundlesFormat
struct	GraphElementCode
	Describe how Aims objects are stored in graph objects. More...
class	GraphIterator
class	GraphManip
	Various manipulations on graphs. More...
class	GraphVolumeFormat
class	Header
class	HieFormat
class	Hierarchy
class	HierarchyReader
class	ImasFormat
class	ImasHeader
class	ImasSorDFormat
class	ImasVolFormat
class	IntegrableOf
class	IntegratorOf
class	Interpolator
class	IOObjectTypesDictionary
class	IOOptions
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	JpegFormat
class	JpegHeader
	The descriptor class of the .dim GIS header. More...
class	JpegPlugin
class	JpegReader
class	JpegWriter
class	LabelNodeFilter
class	LabelReader
class	LinearInterpolator
class	LowLevelArgReader
	Wrapper for a specific GraphReader. More...
class	LowLevelArgWriter
	Wrapper for a specific GraphWriter. More...
class	LowLevelRoiReader
class	LowLevelStandardArgReader
	Wrapper for the standard GraphReader. More...
class	LowLevelStandardArgWriter
	Wrapper for the standard GraphWriter. More...
class	MaskIterator
class	MaskIteratorOf
class	MaskIteratorOf< AimsData< T > >
class	MaskIteratorOf< Graph >
class	MathUtil
	Defines basic math functions that run on iterators. More...
class	MeshFormat
class	MeshHeader
class	MeshProjection
class	MeshProjectionFactory
class	MeshReader
	Mesh format readers for mesh objects. More...
class	MeshWriter
	Mesh format writer for mesh objects. More...
class	MinfFormat
class	MniObjFormat
class	MniObjHeader
class	MotionedMaskIterator
class	MotionedRoiIterator
class	MotionedVolumeROILabelMap
class	MotionWriter
	The class for motion write operation. More...
class	MRTrixBundleReader
	MRTrix .tck format reader. More...
class	NameNodeFilter
class	NodeFilter
class	Path
class	PlyFormat
class	PlyHeader
class	PlyPlugin
class	PlyReader
class	PlyWriter
class	PointSetFeatures
class	PointsInImageFeatures
class	Polyline
class	PolylinePolynomialInterpolator
class	PovFormat
class	PovWriter
	POV (http://www.povray.org) format writer for mesh objects. More...
class	Process
	Link mechanism between the Finder and a process operating on arbitrary data types. More...
struct	ProcessInput
class	ProgressInfo
	The template class used to display progression in text mode. More...
class	PythonHeader
	Attributed python-like header, stores all needed information about an object, currently used for volumes (AimsData). More...
class	Quaternion
class	Reader
	Generic reader for every format of Aims object. More...
class	ReaderAsObject
class	RoiDiff
	Differences between two labelled graphs (sulci...). More...
class	RoiFeatures
class	RoiIterator
class	RoiIteratorOf
class	RoiIteratorOf< AimsData< T > >
class	RoiIteratorOf< Graph >
class	ROILabelMap
class	RombergIntegratorOf
class	ScalarFeaturesProvider
	This class should be inherited by all subclasses that provides scalar features. More...
class	ScalarSetFeatures
class	ScaledEncoding
class	ScannerConf
	An attempt to efficiently manage view/sinogram acquisition PET data. More...
class	Selection
class	SelectionExpander
class	SelectionReader
class	SelectionSet
class	SelectionWriter
class	Selector
class	Settings
class	SimpleBundlesSlicer
class	SimpleVoxelSampler
class	Sinogram
class	SliceFormatHeader
	Header used for 2D image formats. More...
class	SomaIOAimsDataFormat
class	SparseMatrix
class	SparseMatrixUtil
class	SparseOrDenseMatrix
class	SparseVolume
class	SparseVolume< BucketMap< T > >
class	SparseVolume< BucketMap< Void > >
class	SparseVolume< carto::Volume< T > >
struct	specifiedLabels
class	SpmFormat
class	SpmHeader
	SPM Header class. More...
class	SpmReader
	The template class for SPM read operation. More...
class	SpmWriter
	The template class for SPM write operation. More...
class	StandardReferentials
class	StructuredConstVolume
class	StructuredVolume
	Class giving access to an iterator over the voxels of a volume inside of a structuring element. More...
class	StructuringElement
	aims::StructuringElement class representing a 3D structuring element. More...
class	StructuringElementRef
	Convenient handle for a StructuringElement. More...
class	StxFormat
class	SurfaceGenerator
	Factory class for various common shapes of meshes. More...
class	SurfaceManip
class	Tex2Graph
class	TexFormat
class	TexHeader
class	TexReader
	Tex format readers for texture objects. More...
class	TexWriter
	Tex format readers for texture objects. More...
class	TiffFormat
class	TiffHeader
	The descriptor class of the .dim GIS header. More...
class	TiffPlugin
class	TiffReader
class	TiffWriter
class	TrackvisBundleReader
	Trackvis .trk format reader. More...
class	TransformationChain3d
	Container for a composition of multiple transformations. More...
class	TrapezeIntegratorOf
class	TriFormat
class	TriHeader
class	TriReader
	Tri format readers for mesh objects. More...
class	TriWriter
class	TrmFormat
class	TrmHeader
	Descriptor class for the .trm Motion file format header. More...
class	VidaFormat
class	VidaHeader
	The descriptor class of the VIDA header. More...
class	VidaPlugin
class	VidaReader
	The class for VIDA data read operation. More...
class	VidaWriter
	The class for VIDA data write operation. More...
class	VolumeFormat
class	VolumeRefFormat
class	VolumeROILabelMap
class	VoxelSampler
class	Vrml1Format
class	WavefrontHeader
class	WavefrontMeshFormat
class	WavefrontMeshReader
class	WavefrontMeshWriter
class	WavefrontMeshWriter< D, Void >
class	Writer
	Generic writer for every format of Aims object. More...

Typedefs
typedef CoordinatesLess< Point3d, 3 >	BucketMapLess
typedef carto::rc_ptr< Bundle >	RBundle
typedef carto::rc_ptr< BundleListener >	RBundleListener
typedef carto::rc_ptr< BundleProducer >	RBundleProducer
typedef aims::Polyline::Point_t	FiberPoint
typedef std::vector< aims::FiberPoint >	Fiber
typedef std::vector< Fiber >	Fibers
typedef std::vector< Fibers >	BundlesSet
typedef std::map< std::string, std::map< std::string, GraphElementCode > >	GraphElementTable
	GraphElementCode table, stored in graphs in attribute "aims_objects_table" (carto::rc_ptr<GraphElementTable>) More...
typedef IntegrableOf< float >	Integrable
typedef IntegratorOf< float >	Integrator
typedef RombergIntegratorOf< float >	RombergIntegrator
typedef TrapezeIntegratorOf< float >	TrapezeIntegrator
typedef carto::AllocatorContext	Allocator
	compatibility typedef - NEVER USE IT More...
typedef boost::numeric::ublas::sparse_matrix< double >	boost_sparse_matrix
typedef boost::numeric::ublas::sparse_vector< double >	boost_sparse_vector
typedef ProgressInfo< double, double >	Progression

Functions
template<typename T >
void	AimsConnectedComponent (AimsData< T > &data, aims::Connectivity::Type connectivity, std::map< T, size_t > &valids, const T &backgrnd=0, bool bin=true, size_t minSize=0, size_t maxSize=0, size_t numMax=0, bool verbose=true)
template<typename T >
void	AimsConnectedComponent (AimsData< T > &data, aims::Connectivity::Type connectivity, const T &backgrnd=0, bool bin=true, size_t minSize=0, size_t maxSize=0, size_t numMax=0, bool verbose=true)
template<typename T >
void	AimsConnectedComponent (BucketMap< T > &data, aims::Connectivity::Type connectivity, const T &backgrnd=0, bool bin=true, size_t minSize=0, size_t maxSize=0, size_t numMax=0, bool verbose=true)
template<typename T >
void	AimsConnectedComponent (AimsBucket< Void > &component, const AimsData< T > &data, aims::Connectivity::Type connectivity, const T &backgrnd=0, bool bin=true, size_t minsize=0, size_t maxSize=0, size_t maxcomp=0, bool verbose=true)
template<typename T >
void	AimsConnectedComponent (AimsBucket< Void > &component, const BucketMap< T > &data, Connectivity::Type connectivity, const T &backgrnd=0, bool bin=true, size_t minsize=0, size_t maxSize=0, size_t maxcomp=0, bool verbose=true)
template<typename T >
AimsData< int16_t >	AimsLabeledConnectedComponent (AimsBucket< Void > &component, const AimsData< T > &data, aims::Connectivity::Type connectivity, const T &backgrnd=0, bool bin=true, size_t minsize=0, size_t maxSize=0, size_t maxcomp=0, bool verbose=true)
template<typename T >
AimsData< T >	diag (const AimsData< T > &thing)
template<typename T >
AimsData< T >	undiag (const AimsData< T > &thing)
template<typename T >
AimsData< T >	transpose (const AimsData< T > &thing)
template<typename T >
void	incSorting (AimsData< T > &thing)
template<typename T >
void	decSorting (AimsData< T > &thing)
template<typename T >
AimsData< int32_t >	incOrder (const AimsData< T > &thing)
template<typename T >
AimsData< int32_t >	decOrder (const AimsData< T > &thing)
template<typename T >
bool	hasSameDim (const AimsData< T > &v1, const AimsData< T > &v2)
template<typename T >
bool	hasSameSize (const AimsData< T > &v1, const AimsData< T > &v2)
template<typename T >
AimsData< T >	triInf (const AimsData< T > &thing)
template<typename T >
AimsData< T >	triSup (const AimsData< T > &thing)
std::string	aimsVersion ()
template<typename T >
AIMSDATA_API T	byteswap (const T &x)
template<typename T >
AIMSDATA_API T	byteswap16 (const T &x)
template<typename T >
AIMSDATA_API T	byteswap32 (const T &x)
template<typename T >
AIMSDATA_API T	byteswap64 (const T &x)
AIMSDATA_API short	byteswap (const short &x)
AIMSDATA_API unsigned short	byteswap (const unsigned short &x)
AIMSDATA_API int	byteswap (const int &x)
AIMSDATA_API unsigned int	byteswap (unsigned int x)
AIMSDATA_API float	byteswap (const float &x)
template<class T >
GenesisReader< T > &	operator>> (GenesisReader< T > &reader, AimsData< T > &thing)
AIMSDATA_API HierarchyReader &	operator>> (HierarchyReader &, Tree &)
HierarchyReader &	operator>> (HierarchyReader &reader, Hierarchy &thing)
MotionWriter &	operator<< (MotionWriter &writer, const AffineTransformation3d &thing) __attribute__((__deprecated__("OBSOLETE")))
	— OBSOLETE — More...
template<int D, class T >
AIMSDATA_API PovWriter< D, T > &	operator<< (PovWriter< D, T > &writer, const AimsTimeSurface< D, T > &thing)
template<typename T >
bool	canEncodeAsScaledS16 (const carto::Volume< T > &vol, float &slope, float &offset, 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 carto::Volume< float > &vol, float &slope, float &offset, bool enableoffset, double *)
template<>
bool	canEncodeAsScaledS16 (const carto::Volume< double > &vol, float &slope, float &offset, bool enableoffset, double *)
template<class T >
SpmReader< T > &	operator>> (SpmReader< T > &reader, AimsData< T > &thing)
template<class T >
SpmWriter< T > &	operator<< (SpmWriter< T > &writer, const AimsData< T > &thing)
void	spmAttributesConverter (carto::Object header)
void	spmAttributesConverter (carto::GenericObject &header)
template<class T >
aims::GenericWriter &	operator<< (aims::GenericWriter &writer, const T &thing)
template<class T >
aims::Writer< T > &	operator<< (aims::Writer< T > &writer, const T &thing)
template<int D, class T >
AIMSDATA_API MeshReader< D, T > &	operator>> (MeshReader< D, T > &reader, AimsTimeSurface< D, T > &thing)
template<int D, class T >
AIMSDATA_API MeshWriter< D, T > &	operator<< (MeshWriter< D, T > &writer, const AimsTimeSurface< D, T > &thing)
TriReader &	operator>> (TriReader &reader, AimsSurfaceTriangle &thing)
TriWriter &	operator<< (TriWriter &writer, AimsSurfaceTriangle &thing)
template<class T >
AIMSDATA_API TexReader< T > &	operator>> (TexReader< T > &r, TimeTexture< T > &thing)
template<class T >
AIMSDATA_API ItemWriter< T > &	operator>> (ItemWriter< T > &w, TimeTexture< T > &thing)
template<int D, class T >
WavefrontMeshWriter< D, T > &	operator<< (WavefrontMeshWriter< D, T > &writer, const AimsTimeSurface< D, T > &thing)
template<long D, typename T >
WavefrontMeshReader< D, T > &	operator>> (WavefrontMeshReader< D, T > &reader, AimsTimeSurface< D, T > &thing)
int	textureMax (const TimeTexture< short > &intex)
int	textureMin (const TimeTexture< short > &intex)
std::map< short, size_t > *	labelsHistogram (const TimeTexture< short > &intex, int maxlabel=32767, int minlabel=-32768, bool verbose=false)
carto::VolumeRef< AimsRGBA >	giftiColormap (const carto::Object header)
template<typename T >
carto::VolumeRef< AimsRGBA >	giftiColormap (const TimeTexture< T > &texture)
BucketMap< Void > *	mask (const BucketMap< Void > &src, const BucketMap< Void > &m, bool intersect=true)
	mask src object with m. More...
template<typename T >
BucketMap< Void > *	maskWithVolume (const BucketMap< Void > &src, const carto::rc_ptr< carto::Volume< T > > m, const T &val=0, bool insideval=false)
	mask src object with m, avoiding value val in m if insideval is true, keeping only val otherwise More...
carto::rc_ptr< Interpolator >	getLinearInterpolator (const std::string &)
template<typename T >
carto::rc_ptr< Interpolator >	getLinearInterpolator (const AimsData< T > &)
template carto::rc_ptr< Interpolator >	getLinearInterpolator (const AimsData< uint8_t > &)
template carto::rc_ptr< Interpolator >	getLinearInterpolator (const AimsData< int8_t > &)
template carto::rc_ptr< Interpolator >	getLinearInterpolator (const AimsData< uint16_t > &)
template carto::rc_ptr< Interpolator >	getLinearInterpolator (const AimsData< int16_t > &)
template carto::rc_ptr< Interpolator >	getLinearInterpolator (const AimsData< short > &)
template carto::rc_ptr< Interpolator >	getLinearInterpolator (const AimsData< uint32_t > &)
template carto::rc_ptr< Interpolator >	getLinearInterpolator (const AimsData< int32_t > &)
template carto::rc_ptr< Interpolator >	getLinearInterpolator (const AimsData< float > &)
template carto::rc_ptr< Interpolator >	getLinearInterpolator (const AimsData< double > &)
Quaternion	operator* (const Quaternion &a, const Quaternion &b)
template<typename T >
void	floodFill (carto::Volume< T > &vol, const Point3d &pos, T value, Connectivity::Type connectivity=Connectivity::CONNECTIVITY_18_XYZ, T tolerence=0, bool verbose=false)
carto::rc_ptr< MaskIterator >	getMaskIterator (const std::string &fileName)
carto::rc_ptr< MaskIterator >	getMaskIterator (const std::string &fileName, carto::rc_ptr< VoxelSampler > voxelSampler)
template<class T >
carto::rc_ptr< MaskIterator >	getMaskIterator (const AimsData< T > &data)
template<class T >
carto::rc_ptr< MaskIterator >	getMaskIterator (const AimsData< T > &data, carto::rc_ptr< VoxelSampler > voxelSampler)
carto::rc_ptr< MaskIterator >	getMaskIterator (const std::string &fileName, const Motion &motion)
carto::rc_ptr< MaskIterator >	getMaskIterator (const std::string &fileName, carto::rc_ptr< VoxelSampler > voxelSampler, const Motion &motion)
template<class T >
carto::rc_ptr< MaskIterator >	getMaskIterator (const AimsData< T > &data, const Motion &motion)
template<class T >
carto::rc_ptr< MaskIterator >	getMaskIterator (const AimsData< T > &data, carto::rc_ptr< VoxelSampler > voxelSampler, const Motion &motion)
carto::rc_ptr< RoiIterator >	getRoiIterator (const std::string &fileName, carto::rc_ptr< VoxelSampler > voxelSampler=carto::rc_ptr< VoxelSampler >())
template<class T >
carto::rc_ptr< RoiIterator >	getRoiIterator (const AimsData< T > &data, carto::rc_ptr< VoxelSampler > voxelSampler=carto::rc_ptr< VoxelSampler >())
carto::rc_ptr< RoiIterator >	getRoiIterator (const Graph &data, carto::rc_ptr< VoxelSampler > voxelSampler=carto::rc_ptr< VoxelSampler >())
carto::rc_ptr< RoiIterator >	getRoiIterator (const std::string &fileName, const Motion &)
carto::rc_ptr< RoiIterator >	getRoiIterator (const std::string &fileName, carto::rc_ptr< VoxelSampler > voxelSampler, const Motion &)
template<class T >
carto::rc_ptr< RoiIterator >	getRoiIterator (const AimsData< T > &data, const Motion &motion)
carto::rc_ptr< RoiIterator >	getRoiIterator (const Graph &data, const Motion &motion)
template<class T >
carto::rc_ptr< RoiIterator >	getRoiIterator (const AimsData< T > &data, carto::rc_ptr< VoxelSampler > voxelSampler, const Motion &motion)
carto::rc_ptr< RoiIterator >	getRoiIterator (const Graph &data, carto::rc_ptr< VoxelSampler > voxelSampler, const Motion &motion)
aims::SparseMatrix	operator+ (const aims::SparseMatrix &thing)
aims::SparseMatrix	operator- (const aims::SparseMatrix &thing)
aims::SparseMatrix	operator+ (const aims::SparseMatrix &thing1, const aims::SparseMatrix &thing2)
aims::SparseMatrix	operator- (const aims::SparseMatrix &thing1, const aims::SparseMatrix &thing2)
aims::SparseMatrix	operator* (const aims::SparseMatrix &thing1, const aims::SparseMatrix &thing2)
std::vector< double >	operator* (const aims::SparseMatrix &thing1, const std::vector< double > &thing2)
aims::SparseMatrix	operator* (const aims::SparseMatrix &thing1, const double &thing2)
aims::SparseMatrix	operator/ (const aims::SparseMatrix &thing1, const double &thing2)
aims::SparseOrDenseMatrix	operator- (const aims::SparseOrDenseMatrix &thing)
aims::SparseOrDenseMatrix	operator+ (const aims::SparseOrDenseMatrix &thing1, const aims::SparseOrDenseMatrix &thing2)
aims::SparseOrDenseMatrix	operator- (const aims::SparseOrDenseMatrix &thing1, const aims::SparseOrDenseMatrix &thing2)
aims::SparseOrDenseMatrix	operator* (const aims::SparseOrDenseMatrix &thing1, const double &thing2)
aims::SparseOrDenseMatrix	operator/ (const aims::SparseOrDenseMatrix &thing1, const double &thing2)
void	transformBoundingBox (const AffineTransformation3d &AffineTransformation3d, const Point3df &pmin1, const Point3df &pmax1, Point3df &pmin2, Point3df &pmax2)
AffineTransformation3d	operator* (const AffineTransformation3d &affineTransformation3d1, const AffineTransformation3d &affineTransformation3d2)
template<typename ObjectType , typename ValueType >
void	minmax (const ObjectType &, ValueType &min, ValueType &max)
template<typename ValueType >
void	minmax (const AimsData< ValueType > &volume, ValueType &min, ValueType &max)
template<typename ValueType >
void	minmax (const carto::Volume< ValueType > &volume, ValueType &min, ValueType &max)
template<typename ValueType >
void	minmax (const carto::rc_ptr< carto::Volume< ValueType > > &volume, ValueType &min, ValueType &max)
template<typename ValueType >
void	minmax (const carto::VolumeRef< ValueType > &volume, ValueType &min, ValueType &max)
template<class T1 , class T2 >
std::ostream &	operator<< (std::ostream &out, aims::ProgressInfo< T1, T2 > &progression)
template<class T >
EcatReader< T > &	operator>> (EcatReader< T > &reader, AimsData< T > &thing)
template<class T >
EcatSinoReader< T > &	operator>> (EcatSinoReader< T > &reader, std::vector< Sinogram< T > > &thing)
template<class T >
EcatSinoWriter< T > &	operator<< (EcatSinoWriter< T > &writer, Sinogram< T > &thing)
template<class T >
EcatSinoWriter< T > &	operator<< (EcatSinoWriter< T > &writer, const std::vector< Sinogram< T > > &thing)
EcatWriter &	operator<< (EcatWriter &writer, const AimsData< short > &thing)
EcatWriter &	operator<< (EcatWriter &writer, const AimsData< float > &thing)
template<class T >
VidaReader< T > &	operator>> (VidaReader< T > &reader, AimsData< T > &thing)
VidaWriter &	operator<< (VidaWriter &writer, const AimsData< short > &thing)
VidaWriter &	operator<< (VidaWriter &writer, const AimsData< float > &thing)
template<long D, typename T >
PlyReader< D, T > &	operator>> (PlyReader< D, T > &reader, AimsTimeSurface< D, T > &thing)
template<long D, typename T >
PlyWriter< D, T > &	operator<< (PlyWriter< D, T > &writer, const AimsTimeSurface< D, T > &thing)
template<class T >
AIMSDATA_API FdfReader< T > &	operator>> (FdfReader< T > &, AimsData< T > &)
template<class T >
FdfReader< T > &	operator>> (FdfReader< T > &reader, AimsData< T > &thing)
template<class T >
JpegReader< T > &	operator>> (JpegReader< T > &reader, AimsData< T > &thing)
template<class T >
JpegWriter< T > &	operator<< (JpegWriter< T > &writer, const AimsData< T > &thing)
template<class T >
TiffReader< T > &	operator>> (TiffReader< T > &reader, AimsData< T > &thing)
template<class T >
TiffWriter< T > &	operator<< (TiffWriter< T > &writer, const AimsData< T > &thing)
template<typename U >
U	convertedNiftiValue (void *data, int index, int dtype)
template<typename U >
U	convertedNiftiArrayValue (void *data, int index, int dtype, size_t size)
std::string	niftiDataType (int dt)
int	niftiIntDataType (const std::string &typecode)
std::string	giftiTextureDataType (int dtype, int &ndim, int *dims, int intent, int &ntime)
Lagrange's polynomial interpolation.
This implementation uses Neville's algorithm that is a recursive way.
template<class REAL >
AIMSDATA_API REAL	AimsLagrangeInterpolationOf (const AimsData< REAL > &xa, const AimsData< REAL > &ya, REAL x, REAL *dy)
	Returns the interpolation of a function defined at (xa,ya) points at x (dy is the error) More...
float	AimsLagrangeInterpolation (const AimsData< float > &xa, const AimsData< float > &ya, float x, float *dy)
Square, cube, ...
template<typename T >
T	sqr (const T &x)
	Get the square of x. More...
template<typename T >
T	cub (const T &x)
	Get the cube of x. More...
template<typename T >
float	sgn (const T &x)
	Get the sign of x. More...
template<typename T >
T	absdiff (const T &x, const T &y)
	Get the absolute difference between 2 values without having to take care of used type this is particularly useful for unsigned types. More...
Useful math functions for RGB, RGBA types
AimsRGB	absdiff (const AimsRGB &x, const AimsRGB &y)
	Get the absolute difference between 2 AimsRGB ie AimsRGB(abs(Rx - Ry), abs(Gx - Gy), abs(Bx - By)) More...
AimsRGBA	absdiff (const AimsRGBA &x, const AimsRGBA &y)
	Get the absolute difference between 2 AimsRGBA ie AimsRGBA(abs(Rx - Ry), abs(Gx - Gy), abs(Bx - By), abs(Ax - Ay)) More...

Detailed Description

The class for EcatSino data write operation.

Typedef Documentation

Allocator

typedef carto::AllocatorContext aims::Allocator

compatibility typedef - NEVER USE IT

Definition at line 51 of file allocator.h.

boost_sparse_matrix

typedef boost::numeric::ublas::sparse_matrix< double > aims::boost_sparse_matrix

Definition at line 52 of file sparseMatrix.h.

boost_sparse_vector

typedef boost::numeric::ublas::sparse_vector< double > aims::boost_sparse_vector

Definition at line 53 of file sparseMatrix.h.

BucketMapLess

typedef CoordinatesLess<Point3d, 3> aims::BucketMapLess

Definition at line 73 of file bucketMap.h.

BundlesSet

typedef std::vector< Fibers > aims::BundlesSet

Definition at line 52 of file bundleRegroup.h.

Fiber

typedef std::vector< aims::FiberPoint > aims::Fiber

Definition at line 50 of file bundleRegroup.h.

FiberPoint

typedef aims::Polyline::Point_t aims::FiberPoint

Definition at line 89 of file bundles.h.

Fibers

typedef std::vector< Fiber > aims::Fibers

Definition at line 51 of file bundleRegroup.h.

GraphElementTable

typedef std::map<std::string, std::map<std::string,GraphElementCode> > aims::GraphElementTable

GraphElementCode table, stored in graphs in attribute "aims_objects_table" (carto::rc_ptr<GraphElementTable>)

Definition at line 101 of file graphmanip.h.

Integrable

typedef IntegrableOf<float> aims::Integrable

Definition at line 67 of file integrator.h.

Integrator

typedef IntegratorOf<float> aims::Integrator

Definition at line 68 of file integrator.h.

Progression

typedef ProgressInfo<double, double> aims::Progression

Definition at line 128 of file progress.h.

RBundle

typedef carto::rc_ptr<Bundle> aims::RBundle

Definition at line 83 of file bundles.h.

RBundleListener

typedef carto::rc_ptr<BundleListener> aims::RBundleListener

Definition at line 86 of file bundles.h.

RBundleProducer

typedef carto::rc_ptr<BundleProducer> aims::RBundleProducer

Definition at line 87 of file bundles.h.

RombergIntegrator

typedef RombergIntegratorOf<float> aims::RombergIntegrator

Definition at line 104 of file rombergitg.h.

TrapezeIntegrator

typedef TrapezeIntegratorOf<float> aims::TrapezeIntegrator

Definition at line 116 of file trapezeitg.h.

Function Documentation

absdiff() [1/3]

AimsRGB aims::absdiff ( const AimsRGB &  x, const AimsRGB &  y  )

inline

Get the absolute difference between 2 AimsRGB ie AimsRGB(abs(Rx - Ry), abs(Gx - Gy), abs(Bx - By))

Definition at line 56 of file mathelemrgb.h.

References absdiff().

absdiff() [2/3]

AimsRGBA aims::absdiff ( const AimsRGBA &  x, const AimsRGBA &  y  )

inline

Get the absolute difference between 2 AimsRGBA ie AimsRGBA(abs(Rx - Ry), abs(Gx - Gy), abs(Bx - By), abs(Ax - Ay))

Definition at line 71 of file mathelemrgb.h.

References absdiff().

absdiff() [3/3]

template<typename T >

T aims::absdiff ( const T &  x, const T &  y  )

inline

Get the absolute difference between 2 values without having to take care of used type this is particularly useful for unsigned types.

Definition at line 80 of file mathelem.h.

Referenced by absdiff().

AimsConnectedComponent() [1/5]

template<typename T >

void aims::AimsConnectedComponent ( AimsData< T > &  data, aims::Connectivity::Type  connectivity, std::map< T, size_t > &  valids, const T &  backgrnd = 0, bool  bin = true, size_t  minSize = 0, size_t  maxSize = 0, size_t  numMax = 0, bool  verbose = true  )

inline

Definition at line 116 of file component.h.

References verbose.

Referenced by AimsConnectedComponent().

AimsConnectedComponent() [2/5]

template<typename T >

void aims::AimsConnectedComponent ( AimsData< T > &  data, aims::Connectivity::Type  connectivity, const T &  backgrnd = 0, bool  bin = true, size_t  minSize = 0, size_t  maxSize = 0, size_t  numMax = 0, bool  verbose = true  )

inline

Definition at line 133 of file component.h.

References AimsConnectedComponent(), AimsLabeledConnectedComponent(), and verbose.

AimsConnectedComponent() [3/5]

template<typename T >

void aims::AimsConnectedComponent	(	BucketMap< T > &	data,
		aims::Connectivity::Type	connectivity,
		const T &	backgrnd = 0,
		bool	bin = true,
		size_t	minSize = 0,
		size_t	maxSize = 0,
		size_t	numMax = 0,
		bool	verbose = true
	)

Definition at line 477 of file component_d.h.

References AimsConnectedComponent().

AimsConnectedComponent() [4/5]

template<typename T >

void aims::AimsConnectedComponent	(	AimsBucket< Void > &	component,
		const AimsData< T > &	data,
		aims::Connectivity::Type	connectivity,
		const T &	backgrnd = 0,
		bool	bin = true,
		size_t	minsize = 0,
		size_t	maxSize = 0,
		size_t	maxcomp = 0,
		bool	verbose = true
	)

Definition at line 243 of file component_d.h.

References AimsData< T >::dimT(), AimsData< T >::dimX(), AimsData< T >::dimY(), AimsData< T >::dimZ(), ForEach3d, AimsVector< T, D >::item(), AimsBucketItem< T >::location(), aims::Border::oLine(), and aims::Border::oSlice().

AimsConnectedComponent() [5/5]

template<typename T >

void aims::AimsConnectedComponent	(	AimsBucket< Void > &	component,
		const BucketMap< T > &	data,
		Connectivity::Type	connectivity,
		const T &	backgrnd = 0,
		bool	bin = true,
		size_t	minsize = 0,
		size_t	maxSize = 0,
		size_t	maxcomp = 0,
		bool	verbose = true
	)

Definition at line 380 of file component_d.h.

References aims::internal::_nulltesttemplate_iseq(), AimsBucketItem< T >::location(), aims::Connectivity::nbNeighbors(), and aims::Connectivity::xyzOffset().

AimsLabeledConnectedComponent()

template<typename T >

AimsData< int16_t > aims::AimsLabeledConnectedComponent	(	AimsBucket< Void > &	component,
		const AimsData< T > &	data,
		aims::Connectivity::Type	connectivity,
		const T &	backgrnd = 0,
		bool	bin = true,
		size_t	minsize = 0,
		size_t	maxSize = 0,
		size_t	maxcomp = 0,
		bool	verbose = true
	)

Definition at line 505 of file component_d.h.

References AimsData< T >::dimT(), AimsData< T >::dimX(), AimsData< T >::dimY(), AimsData< T >::dimZ(), ForEach3d, AimsVector< T, D >::item(), AimsBucketItem< T >::location(), aims::Border::oLine(), and aims::Border::oSlice().

Referenced by AimsConnectedComponent().

AimsLagrangeInterpolation()

float aims::AimsLagrangeInterpolation ( const AimsData< float > &  xa, const AimsData< float > &  ya, float  x, float *  dy  )

inline

Definition at line 97 of file lagrange.h.

AimsLagrangeInterpolationOf()

template<class REAL >

AIMSDATA_API REAL aims::AimsLagrangeInterpolationOf	(	const AimsData< REAL > &	xa,
		const AimsData< REAL > &	ya,
		REAL	x,
		REAL *	dy
	)

Returns the interpolation of a function defined at (xa,ya) points at x (dy is the error)

Definition at line 55 of file lagrange.h.

References ASSERT, and AimsData< T >::dimX().

aimsVersion()

std::string aims::aimsVersion

(

)

byteswap() [1/6]

template<typename T >

AIMSDATA_API T aims::byteswap ( const T &  x )

inline

Definition at line 44 of file byteswap.h.

References ASSERT, byteswap16(), byteswap32(), and byteswap64().

byteswap() [2/6]

AIMSDATA_API short aims::byteswap ( const short &  x )

inline

Definition at line 102 of file byteswap.h.

References byteswap16().

byteswap() [3/6]

AIMSDATA_API unsigned short aims::byteswap ( const unsigned short &  x )

inline

Definition at line 107 of file byteswap.h.

References byteswap16().

byteswap() [4/6]

AIMSDATA_API int aims::byteswap ( const int &  x )

inline

Definition at line 112 of file byteswap.h.

References byteswap32().

byteswap() [5/6]

AIMSDATA_API unsigned int aims::byteswap ( unsigned int  x )

inline

Definition at line 117 of file byteswap.h.

References byteswap32().

byteswap() [6/6]

AIMSDATA_API float aims::byteswap ( const float &  x )

inline

Definition at line 122 of file byteswap.h.

References byteswap32().

byteswap16()

template<typename T >

AIMSDATA_API T aims::byteswap16 ( const T &  x )

inline

Definition at line 55 of file byteswap.h.

Referenced by byteswap().

byteswap32()

template<typename T >

AIMSDATA_API T aims::byteswap32 ( const T &  x )

inline

Definition at line 67 of file byteswap.h.

Referenced by byteswap().

byteswap64()

template<typename T >

AIMSDATA_API T aims::byteswap64 ( const T &  x )

inline

Definition at line 81 of file byteswap.h.

Referenced by byteswap().

canEncodeAsScaledS16() [1/3]

template<typename T >

bool aims::canEncodeAsScaledS16 ( const carto::Volume< T > &  vol, float &  slope, float &  offset, 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 69 of file scaledcoding.h.

Referenced by aims::SpmWriter< T >::write().

canEncodeAsScaledS16() [2/3]

template<>

bool aims::canEncodeAsScaledS16	(	const carto::Volume< float > &	vol,
		float &	slope,
		float &	offset,
		bool	enableoffset,
		double *
	)

canEncodeAsScaledS16() [3/3]

template<>

bool aims::canEncodeAsScaledS16	(	const carto::Volume< double > &	vol,
		float &	slope,
		float &	offset,
		bool	enableoffset,
		double *
	)

convertedNiftiArrayValue()

template<typename U >

U aims::convertedNiftiArrayValue ( void *  data, int  index, int  dtype, size_t  size  )

inline

Definition at line 129 of file giftiutil.h.

References giftiTextureDataType(), niftiDataType(), and niftiIntDataType().

convertedNiftiValue()

template<typename U >

U aims::convertedNiftiValue ( void *  data, int  index, int  dtype  )

inline

Definition at line 122 of file giftiutil.h.

cub()

template<typename T >

T aims::cub ( const T &  x )

inline

Get the cube of x.

Definition at line 65 of file mathelem.h.

decOrder()

template<typename T >

AimsData<int32_t> aims::decOrder ( const AimsData< T > &  thing )

inline

Definition at line 172 of file volumemanip.h.

References ASSERT, AimsData< T >::clone(), AimsData< T >::dimT(), AimsData< T >::dimX(), AimsData< T >::dimY(), and AimsData< T >::dimZ().

decSorting()

template<typename T >

void aims::decSorting ( AimsData< T > &  thing )

inline

Definition at line 116 of file volumemanip.h.

References ASSERT, AimsData< T >::dimT(), AimsData< T >::dimX(), AimsData< T >::dimY(), and AimsData< T >::dimZ().

diag()

template<typename T >

AimsData<T> aims::diag ( const AimsData< T > &  thing )

inline

Definition at line 44 of file volumemanip.h.

References ASSERT, AimsData< T >::dimT(), AimsData< T >::dimX(), AimsData< T >::dimY(), and AimsData< T >::dimZ().

floodFill()

template<typename T >

void aims::floodFill	(	carto::Volume< T > &	vol,
		const Point3d &	pos,
		T	value,
		Connectivity::Type	connectivity = Connectivity::CONNECTIVITY_18_XYZ,
		T	tolerence = 0,
		bool	verbose = false
	)

Definition at line 43 of file fill_d.h.

References carto::Volume< T >::at(), carto::VolumeRef< T >::at(), carto::VolumeRef< T >::fill(), carto::VolumeProxy< T >::getSize(), aims::Connectivity::nbNeighbors(), aims::Connectivity::offset(), and aims::Connectivity::xyzOffset().

getLinearInterpolator() [1/11]

carto::rc_ptr< Interpolator > aims::getLinearInterpolator

(

const std::string &

)

Referenced by getLinearInterpolator(), and aims::Interpolator::values().

getLinearInterpolator() [2/11]

template<typename T >

carto::rc_ptr< Interpolator > aims::getLinearInterpolator ( const AimsData< T > &  image )

inline

Definition at line 211 of file linearInterpolator.h.

References getLinearInterpolator().

getLinearInterpolator() [3/11]

template carto::rc_ptr< Interpolator > aims::getLinearInterpolator

(

const AimsData< uint8_t > &

)

getLinearInterpolator() [4/11]

template carto::rc_ptr< Interpolator > aims::getLinearInterpolator

(

const AimsData< int8_t > &

)

getLinearInterpolator() [5/11]

template carto::rc_ptr< Interpolator > aims::getLinearInterpolator

(

const AimsData< uint16_t > &

)

getLinearInterpolator() [6/11]

template carto::rc_ptr< Interpolator > aims::getLinearInterpolator

(

const AimsData< int16_t > &

)

getLinearInterpolator() [7/11]

template carto::rc_ptr< Interpolator > aims::getLinearInterpolator

(

const AimsData< short > &

)

getLinearInterpolator() [8/11]

template carto::rc_ptr< Interpolator > aims::getLinearInterpolator

(

const AimsData< uint32_t > &

)

getLinearInterpolator() [9/11]

template carto::rc_ptr< Interpolator > aims::getLinearInterpolator

(

const AimsData< int32_t > &

)

getLinearInterpolator() [10/11]

template carto::rc_ptr< Interpolator > aims::getLinearInterpolator

(

const AimsData< float > &

)

getLinearInterpolator() [11/11]

template carto::rc_ptr< Interpolator > aims::getLinearInterpolator

(

const AimsData< double > &

)

getMaskIterator() [1/8]

carto::rc_ptr< MaskIterator > aims::getMaskIterator

(

const std::string &

fileName

)

Referenced by getMaskIterator(), and aims::MaskIteratorOf< AimsData< T > >::regionName().

getMaskIterator() [2/8]

carto::rc_ptr< MaskIterator > aims::getMaskIterator	(	const std::string &	fileName,
		carto::rc_ptr< VoxelSampler >	voxelSampler
	)

getMaskIterator() [3/8]

template<class T >

carto::rc_ptr< MaskIterator > aims::getMaskIterator

(

const AimsData< T > &

data

)

Definition at line 598 of file maskIterator.h.

getMaskIterator() [4/8]

template<class T >

carto::rc_ptr< MaskIterator > aims::getMaskIterator	(	const AimsData< T > &	data,
		carto::rc_ptr< VoxelSampler >	voxelSampler
	)

Definition at line 607 of file maskIterator.h.

References getMaskIterator().

getMaskIterator() [5/8]

carto::rc_ptr< MaskIterator > aims::getMaskIterator	(	const std::string &	fileName,
		const Motion &	motion
	)

getMaskIterator() [6/8]

carto::rc_ptr< MaskIterator > aims::getMaskIterator	(	const std::string &	fileName,
		carto::rc_ptr< VoxelSampler >	voxelSampler,
		const Motion &	motion
	)

getMaskIterator() [7/8]

template<class T >

carto::rc_ptr< MaskIterator > aims::getMaskIterator	(	const AimsData< T > &	data,
		const Motion &	motion
	)

Definition at line 626 of file maskIterator.h.

References getMaskIterator().

getMaskIterator() [8/8]

template<class T >

carto::rc_ptr< MaskIterator > aims::getMaskIterator	(	const AimsData< T > &	data,
		carto::rc_ptr< VoxelSampler >	voxelSampler,
		const Motion &	motion
	)

Definition at line 636 of file maskIterator.h.

References getMaskIterator().

getRoiIterator() [1/9]

carto::rc_ptr< RoiIterator > aims::getRoiIterator	(	const std::string &	fileName,
		carto::rc_ptr< VoxelSampler >	voxelSampler = carto::rc_ptr< VoxelSampler >()
	)

Referenced by getRoiIterator(), and aims::RoiIteratorOf< AimsData< T > >::regionName().

getRoiIterator() [2/9]

template<class T >

carto::rc_ptr< RoiIterator > aims::getRoiIterator	(	const AimsData< T > &	data,
		carto::rc_ptr< VoxelSampler >	voxelSampler = carto::rc_ptr< VoxelSampler >()
	)

Definition at line 375 of file roiIterator.h.

References getRoiIterator().

getRoiIterator() [3/9]

carto::rc_ptr< RoiIterator > aims::getRoiIterator	(	const Graph &	data,
		carto::rc_ptr< VoxelSampler >	voxelSampler = carto::rc_ptr< VoxelSampler >()
	)

getRoiIterator() [4/9]

carto::rc_ptr< RoiIterator > aims::getRoiIterator	(	const std::string &	fileName,
		const Motion &
	)

getRoiIterator() [5/9]

carto::rc_ptr< RoiIterator > aims::getRoiIterator	(	const std::string &	fileName,
		carto::rc_ptr< VoxelSampler >	voxelSampler,
		const Motion &
	)

getRoiIterator() [6/9]

template<class T >

carto::rc_ptr< RoiIterator > aims::getRoiIterator	(	const AimsData< T > &	data,
		const Motion &	motion
	)

Definition at line 401 of file roiIterator.h.

References getRoiIterator().

getRoiIterator() [7/9]

carto::rc_ptr< RoiIterator > aims::getRoiIterator	(	const Graph &	data,
		const Motion &	motion
	)

getRoiIterator() [8/9]

template<class T >

carto::rc_ptr< RoiIterator > aims::getRoiIterator	(	const AimsData< T > &	data,
		carto::rc_ptr< VoxelSampler >	voxelSampler,
		const Motion &	motion
	)

Definition at line 416 of file roiIterator.h.

References getRoiIterator().

getRoiIterator() [9/9]

carto::rc_ptr< RoiIterator > aims::getRoiIterator	(	const Graph &	data,
		carto::rc_ptr< VoxelSampler >	voxelSampler,
		const Motion &	motion
	)

giftiColormap() [1/2]

carto::VolumeRef<AimsRGBA> aims::giftiColormap

(

const carto::Object

header

)

Referenced by giftiColormap().

giftiColormap() [2/2]

template<typename T >

carto::VolumeRef<AimsRGBA> aims::giftiColormap

(

const TimeTexture< T > &

texture

)

Definition at line 22 of file texturetools.h.

References giftiColormap(), TimeTexture< T >::header(), and carto::Object::reference().

giftiTextureDataType()

std::string aims::giftiTextureDataType	(	int	dtype,
		int &	ndim,
		int *	dims,
		int	intent,
		int &	ntime
	)

Referenced by convertedNiftiArrayValue().

hasSameDim()

template<typename T >

bool aims::hasSameDim ( const AimsData< T > &  v1, const AimsData< T > &  v2  )

inline

Definition at line 205 of file volumemanip.h.

References AimsData< T >::dimT(), AimsData< T >::dimX(), AimsData< T >::dimY(), and AimsData< T >::dimZ().

hasSameSize()

template<typename T >

bool aims::hasSameSize ( const AimsData< T > &  v1, const AimsData< T > &  v2  )

inline

Definition at line 216 of file volumemanip.h.

References AimsData< T >::sizeT(), AimsData< T >::sizeX(), AimsData< T >::sizeY(), and AimsData< T >::sizeZ().

incOrder()

template<typename T >

AimsData<int32_t> aims::incOrder ( const AimsData< T > &  thing )

inline

Definition at line 139 of file volumemanip.h.

References ASSERT, AimsData< T >::clone(), AimsData< T >::dimT(), AimsData< T >::dimX(), AimsData< T >::dimY(), and AimsData< T >::dimZ().

incSorting()

template<typename T >

void aims::incSorting ( AimsData< T > &  thing )

inline

Definition at line 93 of file volumemanip.h.

References ASSERT, AimsData< T >::dimT(), AimsData< T >::dimX(), AimsData< T >::dimY(), and AimsData< T >::dimZ().

labelsHistogram()

std::map<short, size_t>* aims::labelsHistogram	(	const TimeTexture< short > &	intex,
		int	maxlabel = 32767,
		int	minlabel = -32768,
		bool	verbose = false
	)

mask()

BucketMap<Void>* aims::mask	(	const BucketMap< Void > &	src,
		const BucketMap< Void > &	m,
		bool	intersect = true
	)

mask src object with m.

Parameters

intersect

if true, the result is the intersection between both buckets. If false, m is removed from src.

Referenced by aims::AimsGraphReader::PostProcessor::elementInfo(), and AimsMerge< T, U >::~AimsMerge().

maskWithVolume()

template<typename T >

BucketMap< Void > * aims::maskWithVolume	(	const BucketMap< Void > &	src,
		const carto::rc_ptr< carto::Volume< T > >	m,
		const T &	val = 0,
		bool	insideval = false
	)

mask src object with m, avoiding value val in m if insideval is true, keeping only val otherwise

Definition at line 42 of file mask_d.h.

References carto::TypedObject< T >::getProperty(), aims::BucketMap< T >::header(), aims::BucketMap< T >::setHeader(), and aims::BucketMap< T >::setSizeXYZT().

minmax() [1/5]

template<typename ObjectType , typename ValueType >

void aims::minmax	(	const ObjectType &	,
		ValueType &	min,
		ValueType &	max
	)

Definition at line 50 of file minmax.h.

Referenced by minmax().

minmax() [2/5]

template<typename ValueType >

void aims::minmax	(	const AimsData< ValueType > &	volume,
		ValueType &	min,
		ValueType &	max
	)

Definition at line 60 of file minmax.h.

References AimsData< T >::begin(), AimsData< T >::dimT(), AimsData< T >::dimX(), AimsData< T >::dimY(), AimsData< T >::dimZ(), aims::Border::oFirstPoint(), aims::Border::oLineBetweenSlice(), aims::Border::oPointBetweenLine(), and aims::Border::oSliceBetweenVolume().

minmax() [3/5]

template<typename ValueType >

void aims::minmax	(	const carto::Volume< ValueType > &	volume,
		ValueType &	min,
		ValueType &	max
	)

Definition at line 88 of file minmax.h.

References carto::Volume< T >::at(), carto::VolumeProxy< T >::getSizeT(), carto::VolumeProxy< T >::getSizeX(), carto::VolumeProxy< T >::getSizeY(), and carto::VolumeProxy< T >::getSizeZ().

minmax() [4/5]

template<typename ValueType >

void aims::minmax	(	const carto::rc_ptr< carto::Volume< ValueType > > &	volume,
		ValueType &	min,
		ValueType &	max
	)

Definition at line 121 of file minmax.h.

References minmax().

minmax() [5/5]

template<typename ValueType >

void aims::minmax	(	const carto::VolumeRef< ValueType > &	volume,
		ValueType &	min,
		ValueType &	max
	)

Definition at line 132 of file minmax.h.

References minmax().

niftiDataType()

std::string aims::niftiDataType

(

int

dt

)

Referenced by convertedNiftiArrayValue().

niftiIntDataType()

int aims::niftiIntDataType

(

const std::string &

typecode

)

Referenced by convertedNiftiArrayValue().

operator*() [1/6]

Quaternion aims::operator*	(	const Quaternion &	a,
		const Quaternion &	b
	)

Referenced by aims::SparseMatrix::getSparseColumn(), and aims::SparseOrDenseMatrix::getSparseColumn().

operator*() [2/6]

AffineTransformation3d aims::operator*	(	const AffineTransformation3d &	affineTransformation3d1,
		const AffineTransformation3d &	affineTransformation3d2
	)

operator*() [3/6]

aims::SparseOrDenseMatrix aims::operator*	(	const aims::SparseOrDenseMatrix &	thing1,
		const double &	thing2
	)

operator*() [4/6]

aims::SparseMatrix aims::operator*	(	const aims::SparseMatrix &	thing1,
		const aims::SparseMatrix &	thing2
	)

operator*() [5/6]

std::vector<double> aims::operator*	(	const aims::SparseMatrix &	thing1,
		const std::vector< double > &	thing2
	)

operator*() [6/6]

aims::SparseMatrix aims::operator*	(	const aims::SparseMatrix &	thing1,
		const double &	thing2
	)

operator+() [1/3]

aims::SparseMatrix aims::operator+

(

const aims::SparseMatrix &

thing

)

Referenced by aims::SparseMatrix::getSparseColumn(), and aims::SparseOrDenseMatrix::getSparseColumn().

operator+() [2/3]

aims::SparseMatrix aims::operator+	(	const aims::SparseMatrix &	thing1,
		const aims::SparseMatrix &	thing2
	)

operator+() [3/3]

aims::SparseOrDenseMatrix aims::operator+	(	const aims::SparseOrDenseMatrix &	thing1,
		const aims::SparseOrDenseMatrix &	thing2
	)

operator-() [1/4]

aims::SparseMatrix aims::operator-

(

const aims::SparseMatrix &

thing

)

Referenced by aims::SparseMatrix::getSparseColumn(), and aims::SparseOrDenseMatrix::getSparseColumn().

operator-() [2/4]

aims::SparseOrDenseMatrix aims::operator-

(

const aims::SparseOrDenseMatrix &

thing

)

operator-() [3/4]

aims::SparseOrDenseMatrix aims::operator-	(	const aims::SparseOrDenseMatrix &	thing1,
		const aims::SparseOrDenseMatrix &	thing2
	)

operator-() [4/4]

aims::SparseMatrix aims::operator-	(	const aims::SparseMatrix &	thing1,
		const aims::SparseMatrix &	thing2
	)

operator/() [1/2]

aims::SparseOrDenseMatrix aims::operator/	(	const aims::SparseOrDenseMatrix &	thing1,
		const double &	thing2
	)

operator/() [2/2]

aims::SparseMatrix aims::operator/	(	const aims::SparseMatrix &	thing1,
		const double &	thing2
	)

Referenced by aims::SparseMatrix::getSparseColumn(), and aims::SparseOrDenseMatrix::getSparseColumn().

operator<<() [1/18]

VidaWriter& aims::operator<<	(	VidaWriter &	writer,
		const AimsData< short > &	thing
	)

operator<<() [2/18]

VidaWriter& aims::operator<<	(	VidaWriter &	writer,
		const AimsData< float > &	thing
	)

operator<<() [3/18]

EcatWriter& aims::operator<<	(	EcatWriter &	writer,
		const AimsData< short > &	thing
	)

operator<<() [4/18]

EcatWriter& aims::operator<<	(	EcatWriter &	writer,
		const AimsData< float > &	thing
	)

operator<<() [5/18]

MotionWriter & aims::operator<< ( MotionWriter &  writer, const AffineTransformation3d &  thing  )

inline

— OBSOLETE —

Output stream operator.

Definition at line 87 of file motionW.h.

References aims::MotionWriter::write().

Referenced by aims::SparseMatrix::getSparseColumn().

operator<<() [6/18]

TriWriter& aims::operator<< ( TriWriter &  writer, AimsSurfaceTriangle &  thing  )

inline

Definition at line 62 of file triW.h.

References aims::TriWriter::write().

operator<<() [7/18]

template<class T >

EcatSinoWriter<T>& aims::operator<<	(	EcatSinoWriter< T > &	writer,
		Sinogram< T > &	thing
	)

operator<<() [8/18]

template<class T >

EcatSinoWriter<T>& aims::operator<<	(	EcatSinoWriter< T > &	writer,
		const std::vector< Sinogram< T > > &	thing
	)

Definition at line 95 of file ecatSinoW.h.

References aims::EcatSinoWriter< T >::write().

operator<<() [9/18]

template<class T >

JpegWriter<T>& aims::operator<< ( JpegWriter< T > &  writer, const AimsData< T > &  thing  )

inline

Definition at line 76 of file jpegW.h.

operator<<() [10/18]

template<long D, typename T >

PlyWriter<D,T>& aims::operator<< ( PlyWriter< D, T > &  writer, const AimsTimeSurface< D, T > &  thing  )

inline

Definition at line 71 of file plyw.h.

operator<<() [11/18]

template<int D, class T >

AIMSDATA_API PovWriter<D,T>& aims::operator<< ( PovWriter< D, T > &  writer, const AimsTimeSurface< D, T > &  thing  )

inline

Definition at line 72 of file povW.h.

operator<<() [12/18]

template<int D, class T >

AIMSDATA_API MeshWriter<D,T>& aims::operator<< ( MeshWriter< D, T > &  writer, const AimsTimeSurface< D, T > &  thing  )

inline

Definition at line 78 of file meshW.h.

operator<<() [13/18]

template<class T >

SpmWriter< T > & aims::operator<< ( SpmWriter< T > &  writer, const AimsData< T > &  thing  )

inline

Definition at line 100 of file spmW.h.

References aims::SpmWriter< T >::write().

operator<<() [14/18]

template<int D, class T >

WavefrontMeshWriter<D,T>& aims::operator<< ( WavefrontMeshWriter< D, T > &  writer, const AimsTimeSurface< D, T > &  thing  )

inline

Definition at line 176 of file wavefrontmeshW.h.

operator<<() [15/18]

template<class T >

aims::GenericWriter& aims::operator<< ( aims::GenericWriter &  writer, const T &  thing  )

inline

Definition at line 117 of file writer.h.

References aims::GenericWriter::write().

operator<<() [16/18]

template<class T >

aims::Writer<T>& aims::operator<< ( aims::Writer< T > &  writer, const T &  thing  )

inline

Definition at line 126 of file writer.h.

References aims::Writer< T >::write().

operator<<() [17/18]

template<class T1 , class T2 >

std::ostream& aims::operator<< ( std::ostream &  out, aims::ProgressInfo< T1, T2 > &  progression  )

inline

Definition at line 131 of file progress.h.

References aims::ProgressInfo< T1, T2 >::render().

operator<<() [18/18]

template<class T >

TiffWriter<T>& aims::operator<< ( TiffWriter< T > &  writer, const AimsData< T > &  thing  )

inline

Definition at line 72 of file tiffW.h.

operator>>() [1/17]

template<class T >

VidaReader< T > & aims::operator>> ( VidaReader< T > &  reader, AimsData< T > &  thing  )

inline

Definition at line 88 of file vidaR.h.

References aims::VidaReader< T >::read().

operator>>() [2/17]

AIMSDATA_API HierarchyReader& aims::operator>>	(	HierarchyReader &	,
		Tree &
	)

operator>>() [3/17]

template<class T >

EcatReader< T > & aims::operator>> ( EcatReader< T > &  reader, AimsData< T > &  thing  )

inline

Definition at line 88 of file ecatR.h.

References aims::EcatReader< T >::read().

operator>>() [4/17]

template<class T >

AIMSDATA_API FdfReader< T >& aims::operator>> ( FdfReader< T > &  , AimsData< T > &    )

inline

Definition at line 82 of file fdfR.h.

References AimsData< T >::allocator(), aims::FdfReader< T >::read(), and carto::Object::value().

operator>>() [5/17]

template<class T >

SpmReader< T > & aims::operator>> ( SpmReader< T > &  reader, AimsData< T > &  thing  )

inline

Definition at line 110 of file spmR.h.

References aims::SpmReader< T >::read().

operator>>() [6/17]

TriReader& aims::operator>> ( TriReader &  reader, AimsSurfaceTriangle &  thing  )

inline

Definition at line 69 of file triR.h.

References aims::TriReader::read().

operator>>() [7/17]

template<class T >

GenesisReader<T>& aims::operator>> ( GenesisReader< T > &  reader, AimsData< T > &  thing  )

inline

Definition at line 70 of file genesisR.h.

References aims::GenesisReader< T >::read().

operator>>() [8/17]

template<class T >

EcatSinoReader<T>& aims::operator>> ( EcatSinoReader< T > &  reader, std::vector< Sinogram< T > > &  thing  )

inline

Definition at line 70 of file ecatSinoR.h.

References aims::EcatSinoReader< T >::read().

operator>>() [9/17]

HierarchyReader& aims::operator>> ( HierarchyReader &  reader, Hierarchy &  thing  )

inline

Definition at line 73 of file hieR.h.

References aims::HierarchyReader::read().

operator>>() [10/17]

template<class T >

JpegReader<T>& aims::operator>> ( JpegReader< T > &  reader, AimsData< T > &  thing  )

inline

Definition at line 74 of file jpegR.h.

References aims::JpegReader< T >::read().

operator>>() [11/17]

template<class T >

AIMSDATA_API ItemWriter<T>& aims::operator>> ( ItemWriter< T > &  w, TimeTexture< T > &  thing  )

inline

Definition at line 74 of file texW.h.

References aims::ItemWriter< T >::write().

operator>>() [12/17]

template<class T >

TiffReader<T>& aims::operator>> ( TiffReader< T > &  reader, AimsData< T > &  thing  )

inline

Definition at line 75 of file tiffR.h.

References AimsData< T >::allocator(), aims::TiffReader< T >::read(), and carto::Object::value().

operator>>() [13/17]

template<long D, typename T >

PlyReader<D,T>& aims::operator>> ( PlyReader< D, T > &  reader, AimsTimeSurface< D, T > &  thing  )

inline

Definition at line 75 of file plyr.h.

References AimsTimeSurface< D, T >::normal(), ply_get_argument_property(), ply_get_argument_user_data(), ply_get_argument_value(), AimsTimeSurface< D, T >::polygon(), aims::PlyReader< D, T >::read(), carto::Object::value(), and AimsTimeSurface< D, T >::vertex().

operator>>() [14/17]

template<class T >

AIMSDATA_API TexReader<T>& aims::operator>> ( TexReader< T > &  r, TimeTexture< T > &  thing  )

inline

Definition at line 76 of file texR.h.

References aims::TexReader< T >::read().

operator>>() [15/17]

template<int D, class T >

AIMSDATA_API MeshReader<D,T>& aims::operator>> ( MeshReader< D, T > &  reader, AimsTimeSurface< D, T > &  thing  )

inline

Definition at line 81 of file meshR.h.

References aims::MeshReader< D, T >::read().

operator>>() [16/17]

template<class T >

FdfReader< T >& aims::operator>> ( FdfReader< T > &  reader, AimsData< T > &  thing  )

inline

Definition at line 82 of file fdfR.h.

References AimsData< T >::allocator(), aims::FdfReader< T >::read(), and carto::Object::value().

operator>>() [17/17]

template<long D, typename T >

WavefrontMeshReader<D,T>& aims::operator>> ( WavefrontMeshReader< D, T > &  reader, AimsTimeSurface< D, T > &  thing  )

inline

Definition at line 123 of file wavefrontmeshR.h.

References carto::DictionaryInterface::copyProperties(), carto::FileUtil::dirname(), soma::IStreamDataSource::eof(), rc_ptr< GenericObject >::get(), soma::StreamUtil::getline(), carto::TypedObject< T >::getProperty(), AimsTimeSurface< D, T >::normal(), AimsTimeSurface< D, T >::polygon(), aims::Reader< T >::read(), aims::WavefrontMeshReader< D, T >::read(), carto::FileUtil::separator(), carto::TypedObject< T >::setProperty(), AimsTimeSurface< D, T >::texture(), carto::Object::value(), and AimsTimeSurface< D, T >::vertex().

sgn()

template<typename T >

float aims::sgn ( const T &  x )

inline

Get the sign of x.

Definition at line 71 of file mathelem.h.

spmAttributesConverter() [1/2]

void aims::spmAttributesConverter ( carto::Object  header )

inline

Definition at line 46 of file spmattribconverter.h.

spmAttributesConverter() [2/2]

void aims::spmAttributesConverter

(

carto::GenericObject &

header

)

sqr()

template<typename T >

T aims::sqr ( const T &  x )

inline

Get the square of x.

Definition at line 59 of file mathelem.h.

textureMax()

int aims::textureMax

(

const TimeTexture< short > &

intex

)

textureMin()

int aims::textureMin

(

const TimeTexture< short > &

intex

)

transformBoundingBox()

void aims::transformBoundingBox	(	const AffineTransformation3d &	AffineTransformation3d,
		const Point3df &	pmin1,
		const Point3df &	pmax1,
		Point3df &	pmin2,
		Point3df &	pmax2
	)

transpose()

template<typename T >

AimsData<T> aims::transpose ( const AimsData< T > &  thing )

inline

Definition at line 76 of file volumemanip.h.

References ASSERT, AimsData< T >::dimT(), AimsData< T >::dimX(), AimsData< T >::dimY(), and AimsData< T >::dimZ().

triInf()

template<typename T >

AimsData<T> aims::triInf ( const AimsData< T > &  thing )

inline

Definition at line 227 of file volumemanip.h.

References ASSERT, aims::Border::borderWidth(), AimsData< T >::dimT(), AimsData< T >::dimX(), AimsData< T >::dimY(), and AimsData< T >::dimZ().

triSup()

template<typename T >

AimsData<T> aims::triSup ( const AimsData< T > &  thing )

inline

Definition at line 246 of file volumemanip.h.

References ASSERT, aims::Border::borderWidth(), AimsData< T >::dimT(), AimsData< T >::dimX(), AimsData< T >::dimY(), and AimsData< T >::dimZ().

undiag()

template<typename T >

AimsData<T> aims::undiag ( const AimsData< T > &  thing )

inline

Definition at line 60 of file volumemanip.h.

References ASSERT, AimsData< T >::dimT(), AimsData< T >::dimX(), AimsData< T >::dimY(), and AimsData< T >::dimZ().