sc.fiji.snt.annotation

Class VFBUtils

java.lang.Object

sc.fiji.snt.annotation.VFBUtils

public class VFBUtils
extends java.lang.Object

Utility methods for accessing/handling Virtual Fly Brain (VFB) annotations

Author:

Tiago Ferreira

Method Summary

Modifier and Type	Method and Description
static SNTPoint	brainBarycentre(java.lang.String templateBrain) Returns the spatial centroid of an adult Drosophila template brain.
static OBJMesh	getMesh(java.lang.String vfbId) Retrieves the mesh associated with the specified VFB id.
static OBJMesh	getMesh(java.lang.String vfbId, org.scijava.util.ColorRGB color) Retrieves the mesh associated with the specified VFB id.
static OBJMesh	getRefBrain(java.lang.String templateBrain) Retrieves the surface mesh of an adult Drosophila template brain.
static boolean	isDatabaseAvailable() Checks whether a connection to the Virtual Fly Brain database can be established.
static void	main(java.lang.String[] args)

Methods inherited from class java.lang.Object

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

Method Detail

isDatabaseAvailable

public static boolean isDatabaseAvailable()

Checks whether a connection to the Virtual Fly Brain database can be established.

Returns:

true, if an HHTP connection could be established

brainBarycentre

public static SNTPoint brainBarycentre(java.lang.String templateBrain)

Returns the spatial centroid of an adult Drosophila template brain.

Parameters:

templateBrain - the template brain to be loaded (case-insensitive). Either "JFRC2" (AKA JFRC2010, VFB), "JFRC3" (AKA JFRC2013), or "FCWB" (FlyCircuit Whole Brain Template)

Returns:

the SNT point defining the (X,Y,Z) center of brain mesh.

getRefBrain

public static OBJMesh getRefBrain(java.lang.String templateBrain)
                           throws java.lang.IllegalArgumentException

Retrieves the surface mesh of an adult Drosophila template brain. No Internet connection is required, as these meshes (detailed on the nat.flybrains documentation) are bundled with SNT.

Parameters:

templateBrain - the template brain to be loaded (case-insensitive). Either "JFRC2" (AKA JFRC2010, VFB), "JFRC3" (AKA JFRC2013), or "FCWB" (FlyCircuit Whole Brain Template)

Returns:

the template mesh.

Throws:

java.lang.IllegalArgumentException - if templateBrain is not recognized

getMesh

public static OBJMesh getMesh(java.lang.String vfbId)

Retrieves the mesh associated with the specified VFB id.

Parameters:

vfbId - the VFB id, e.g., VFB_00017894, 00017894

Returns:

a reference to the retrieved mesh

getMesh

public static OBJMesh getMesh(java.lang.String vfbId,
                              org.scijava.util.ColorRGB color)

Retrieves the mesh associated with the specified VFB id.

Parameters:

vfbId - the VFB id, e.g., VFB_00017894, 00017894

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)