Various manipulations on graphs. More...

#include <aims/graph/graphmanip.h>

Public Types
typedef BucketMap< Void > (	CreateBucketFunc) (GraphObject *, const std::string &)

Public Member Functions
std::vector< int >	attributeColor (const Graph &graph, const std::string &att)

Static Public Member Functions
static AffineTransformation3d	talairach (const Graph &g)
	Extract Talairach transformation (graph -> Talairach) More...

static void	storeTalairach (Graph &g, const AffineTransformation3d &m, bool force_old_attributes=false)
	Store Talairach transformation in graph. More...

static bool	hasOldTalairachTransform (const Graph &g)
	Test if a Graph has the old Talairach attributes. More...

static AffineTransformation3d	getICBMTransform (const Graph &g)
	Extract the transformation to the MNI ICBM152 space. More...

static AffineTransformation3d	getICBM2009cTemplateTransform (const Graph &g)
	Extract the transformation to the MNI ICBM152 space, shifted to the "most standard" field of view of the template image, the one from the ICBM2009c_nlin_asym template from the MNI. More...

static bool	buckets2Volume (Graph &g)
	converts internal representations of graph nodes from buckets to volume More...

static bool	volume2Buckets (Graph &g, CreateBucketFunc f=0)
	converts internal representations of graph nodes from volume to buckets. More...

static GraphElementCode &	graphElementCode (Graph &, const std::string &syntax, const std::string &id)

static GraphElementCode &	graphElementCodeByAtt (Graph &, const std::string &syntax, const std::string &attrib)

template<typename T >
static void	storeAims (Graph &graph, GraphObject *vertex, const std::string &attribute, carto::rc_ptr< T > obj)
	This template function stores the given object in the given Vertex / Edge of the graph and takes care of IO information to maintain in the graph. More...

template<typename T >
static Graph *	graphFromVolume (const carto::rc_ptr< carto::Volume< T > > &vol, T background=0, std::map< T, std::string > *trans=0)
	builds a ROI graph from a volume of labels More...

template<typename T >
static void	graphFromVolume (const carto::rc_ptr< carto::Volume< T > > &vol, Graph &g, T background=0, std::map< T, std::string > *trans=0, bool automaticBackgroundSearch=true)
	builds a ROI graph from a volume of labels More...

static void	setAttributeColor (Graph &graph, const std::string &att, const AimsRGB &)

static void	setAttributeColor (Graph &graph, const std::string &att, const AimsRGBA &)

static void	setAttributeColor (Graph &graph, const std::string &att, const std::vector< int > &)

static void	completeGraph (Graph &)
	Completes folds graph information. More...

static Graph *	mergeGraph (const std::string &, Graph &, Graph &, bool mergeMesh=true, bool invNormal=false)

static void	printGraphElementTable (const Graph &, std::ostream &ostr=std::cout)

static std::string	defaultExtensionForObjectType (const std::string &otype, const std::string &dtype)

static std::list< Edge * >	getPath (const Vertex from, const Vertex to)
	Get edges path from a vertex to another one. More...

Detailed Description

Various manipulations on graphs.

Definition at line 125 of file graphmanip.h.

Member Typedef Documentation

◆ CreateBucketFunc

typedef BucketMap<Void>*(* aims::GraphManip::CreateBucketFunc) (GraphObject *, const std::string &)

Definition at line 128 of file graphmanip.h.

Member Function Documentation

◆ attributeColor()

std::vector<int> aims::GraphManip::attributeColor	(	const Graph &	graph,
		const std::string &	att
	)

◆ buckets2Volume()

static bool aims::GraphManip::buckets2Volume ( Graph & g )

static

converts internal representations of graph nodes from buckets to volume

Returns: false if it fails: if all buckets have not been read from disk

◆ completeGraph()

static void aims::GraphManip::completeGraph ( Graph & )

static

Completes folds graph information.

Adds missing information to sulcal nodes, like meshes surface...

◆ defaultExtensionForObjectType()

static std::string aims::GraphManip::defaultExtensionForObjectType	(	const std::string &	otype,
		const std::string &	dtype
	)

static

Referenced by storeAims().

◆ getICBM2009cTemplateTransform()

static AffineTransformation3d aims::GraphManip::getICBM2009cTemplateTransform ( const Graph & g )

static

Extract the transformation to the MNI ICBM152 space, shifted to the "most standard" field of view of the template image, the one from the ICBM2009c_nlin_asym template from the MNI.

Actually we find various fields of view for the templates. The one we use here is (193, 229, 193). The transform to the "real" ICBM space (0 roughly at AC) is provided in the output transformation header. This space has a fixed transformation with our Aims Talairach, along with the template volume size and voxel size. Includes shifts and axes inversions.

◆ getICBMTransform()

static AffineTransformation3d aims::GraphManip::getICBMTransform ( const Graph & g )

static

Extract the transformation to the MNI ICBM152 space.

This space has a fixed transformation with our Aims Talairach.

◆ getPath()

static std::list<Edge *> aims::GraphManip::getPath	(	const Vertex *	from,
		const Vertex *	to
	)

static

Get edges path from a vertex to another one.

Adapted from Yann Leprince's code on: https://github.com/HumanBrainProject/hbp-spatial-backend/blob/fc79a6adc5d71fe6a02021f0d36698c5fde86b43/hbp_spatial_backend/transform_graph.py#L36

TODO: detect ambiguities (multiple same-length chains)

◆ graphElementCode()

static GraphElementCode& aims::GraphManip::graphElementCode	(	Graph &	,
		const std::string &	syntax,
		const std::string &	id
	)

static

◆ graphElementCodeByAtt()

static GraphElementCode& aims::GraphManip::graphElementCodeByAtt	(	Graph &	,
		const std::string &	syntax,
		const std::string &	attrib
	)

static

Referenced by storeAims().

◆ graphFromVolume() [1/2]

template<typename T >

static void aims::GraphManip::graphFromVolume	(	const carto::rc_ptr< carto::Volume< T > > &	vol,
		Graph &	g,
		T	background = `0`,
		std::map< T, std::string > *	trans = `0`,
		bool	automaticBackgroundSearch = `true`
	)

static

builds a ROI graph from a volume of labels

◆ graphFromVolume() [2/2]

template<typename T >

static Graph* aims::GraphManip::graphFromVolume	(	const carto::rc_ptr< carto::Volume< T > > &	vol,
		T	background = `0`,
		std::map< T, std::string > *	trans = `0`
	)

static

builds a ROI graph from a volume of labels

◆ hasOldTalairachTransform()

static bool aims::GraphManip::hasOldTalairachTransform ( const Graph & g )

static

Test if a Graph has the old Talairach attributes.

These attributes are "Talairach_translation", "Talairach_rotation" (both required), and "Talairach_scale" (optional). The modern way of storing the transformation to Talairach is in the "referentials" and "transformations" attributes.

◆ mergeGraph()

static Graph* aims::GraphManip::mergeGraph	(	const std::string &	,
		Graph &	,
		Graph &	,
		bool	mergeMesh = `true`,
		bool	invNormal = `false`
	)

static

◆ printGraphElementTable()

static void aims::GraphManip::printGraphElementTable	(	const Graph &	,
		std::ostream &	ostr = `std::cout`
	)

static

◆ setAttributeColor() [1/3]

static void aims::GraphManip::setAttributeColor	(	Graph &	graph,
		const std::string &	att,
		const AimsRGB &
	)

static

◆ setAttributeColor() [2/3]

static void aims::GraphManip::setAttributeColor	(	Graph &	graph,
		const std::string &	att,
		const AimsRGBA &
	)

static

◆ setAttributeColor() [3/3]

static void aims::GraphManip::setAttributeColor	(	Graph &	graph,
		const std::string &	att,
		const std::vector< int > &
	)

static

◆ storeAims()

template<typename T >

void aims::GraphManip::storeAims	(	Graph &	graph,
		GraphObject *	vertex,
		const std::string &	attribute,
		carto::rc_ptr< T >	obj
	)

static

This template function stores the given object in the given Vertex / Edge of the graph and takes care of IO information to maintain in the graph.

More precisely, it calls GraphObject::setProperty and fills the GraphElementTable accordingly in the graph

Definition at line 46 of file graphmanip_d.h.

References aims::GraphElementCode::attribute, aims::GraphElementCode::dataType, carto::DataTypeCode< class >::dataType(), defaultExtensionForObjectType(), aims::GraphElementCode::global_filename, aims::GraphElementCode::global_index_attribute, graphElementCodeByAtt(), aims::GraphElementCode::local_file_attribute, aims::GraphElementCode::objectType, and carto::DataTypeCode< class >::objectType().

Referenced by aims::Tex2Graph< T >::makeGraph().

◆ storeTalairach()

static void aims::GraphManip::storeTalairach	(	Graph &	g,
		const AffineTransformation3d &	m,
		bool	force_old_attributes = `false`
	)

static

Store Talairach transformation in graph.

The transformation is written in the modern attributes ("referentials" and "transformations"). It is also written to the legacy attributes ("Talairach_translation", "Talairach_rotation", and "Talairach_scale"), if these are already present, or if force_old_attributes is true.

◆ talairach()

static AffineTransformation3d aims::GraphManip::talairach ( const Graph & g )

static

Extract Talairach transformation (graph -> Talairach)

The transformation is returned from one of these sources, in order of priority:

The "transformations" attribute, corresponding to the "Talairach-AC/PC-Anatomist" referential.
The legacy "Talairach_translation", "Talairach_rotation", and "Talairach_scale" attributes.
Otherwise, identity is returned.

◆ volume2Buckets()

static bool aims::GraphManip::volume2Buckets	(	Graph &	g,
		CreateBucketFunc	f = `0`
	)

static

converts internal representations of graph nodes from volume to buckets.

Returns: false if it fails: if all volumes have not been read from disk

The documentation for this class was generated from the following files:

aims/graph/graphmanip.h
aims/graph/graphmanip_d.h

Public Types

Public Member Functions

Static Public Member Functions

Detailed Description

Member Typedef Documentation

◆ CreateBucketFunc

Member Function Documentation

◆ attributeColor()

◆ buckets2Volume()

◆ completeGraph()

◆ defaultExtensionForObjectType()

◆ getICBM2009cTemplateTransform()

◆ getICBMTransform()

◆ getPath()

◆ graphElementCode()

◆ graphElementCodeByAtt()

◆ graphFromVolume() [1/2]

◆ graphFromVolume() [2/2]

◆ hasOldTalairachTransform()

◆ mergeGraph()

◆ printGraphElementTable()

◆ setAttributeColor() [1/3]

◆ setAttributeColor() [2/3]

◆ setAttributeColor() [3/3]

◆ storeAims()

◆ storeTalairach()

◆ talairach()

◆ volume2Buckets()