sc.fiji.snt.annotation

Class AllenUtils

java.lang.Object

sc.fiji.snt.annotation.AllenUtils

public class AllenUtils
extends java.lang.Object

Utility methods for accessing/handling AllenCompartments

Author:

Tiago Ferreira

Field Summary

Fields

Modifier and Type	Field and Description
static int	VERSION The version of the Common Coordinate Framework currently used by SNT

Method Summary

Modifier and Type	Method and Description
static void	assignToLeftHemisphere(Tree tree)
static void	assignToRightHemisphere(Tree tree)
static SNTPoint	brainCenter() Returns the spatial centroid of the Allen CCF.
static AllenCompartment	getCompartment(int id) Constructs a compartment from its CCF id
static AllenCompartment	getCompartment(java.lang.String nameOrAcronym) Constructs a compartment from its CCF name or acronym
static int	getHighestOntologyDepth() Gets the maximum number of ontology levels in the Allen CCF.
static java.util.Collection<AllenCompartment>	getOntologies() Gets the Allen CCF as a flat (non-hierarchical) collection of ontologies.
static OBJMesh	getRootMesh(org.scijava.util.ColorRGB color) Retrieves the surface contours for the Allen Mouse Brain Atlas (CCF), bundled with SNT.
static javax.swing.tree.DefaultTreeModel	getTreeModel(boolean meshesOnly) Retrieves the Allen CCF hierarchical tree data.
static boolean	isLeftHemisphere(SNTPoint point) Checks the hemisphere a reconstruction node belongs to.
static boolean	isLeftHemisphere(Tree tree) Checks the hemisphere a neuron belongs to.
static void	main(java.lang.String[] args)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

VERSION

public static final int VERSION

The version of the Common Coordinate Framework currently used by SNT

See Also:

Constant Field Values

Method Detail

getCompartment

public static AllenCompartment getCompartment(int id)

Constructs a compartment from its CCF id

Parameters:

id - the integer identifier

Returns:

the compartment matching the id or null if id is not valid

getCompartment

public static AllenCompartment getCompartment(java.lang.String nameOrAcronym)

Constructs a compartment from its CCF name or acronym

Parameters:

nameOrAcronym - the name or acronym (case insensitive) identifying the compartment

Returns:

the compartment whose name or acronym matches the specified string or null if no match was found

assignToLeftHemisphere

public static void assignToLeftHemisphere(Tree tree)

assignToRightHemisphere

public static void assignToRightHemisphere(Tree tree)

isLeftHemisphere

public static boolean isLeftHemisphere(Tree tree)

Checks the hemisphere a neuron belongs to.

Parameters:

tree - the Tree to be tested

Returns:

true, if soma (or root node) is in the left hemisphere, false otherwise

isLeftHemisphere

public static boolean isLeftHemisphere(SNTPoint point)

Checks the hemisphere a reconstruction node belongs to.

Parameters:

point - the point

Returns:

true, if is left hemisphere, false otherwise

brainCenter

public static SNTPoint brainCenter()

Returns the spatial centroid of the Allen CCF.

Returns:

the SNT point defining the (X,Y,Z) center of the ARA

getHighestOntologyDepth

public static int getHighestOntologyDepth()

Gets the maximum number of ontology levels in the Allen CCF.

Returns:

the max number of ontology levels.

getTreeModel

public static javax.swing.tree.DefaultTreeModel getTreeModel(boolean meshesOnly)

Retrieves the Allen CCF hierarchical tree data.

Parameters:

meshesOnly - Whether only compartments with known meshes should be included

Returns:

the Allen CCF tree data model

getOntologies

public static java.util.Collection<AllenCompartment> getOntologies()

Gets the Allen CCF as a flat (non-hierarchical) collection of ontologies.

Returns:

the "flattened" ontologies list

getRootMesh

public static OBJMesh getRootMesh(org.scijava.util.ColorRGB color)

Retrieves the surface contours for the Allen Mouse Brain Atlas (CCF), bundled with SNT.

Parameters:

color - the color to be assigned to the mesh

Returns:

a reference to the retrieved mesh

main

public static void main(java.lang.String[] args)