AllenUtils (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- sc.fiji.snt.annotation.AllenUtils

```
public class AllenUtils
extends Object
```
Utility methods for accessing/handling AllenCompartments

Author:

Tiago Ferreira, Cameron Arshadi

Field Summary

Fields
Modifier and Type Field and Description

protected static int BRAIN_ROOT_ID

static String VERSION
The version of the Common Coordinate Framework currently used by SNT

Fields
Modifier and Type	Field and Description
`protected static int`	`BRAIN_ROOT_ID`
`static String`	`VERSION` The version of the Common Coordinate Framework currently used by SNT

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static void`	`assignHemisphereTags(DirectedWeightedGraph graph)`
`static void`	`assignHemisphereTags(Tree tree)`
`static void`	`assignToLeftHemisphere(Tree tree)`
`static void`	`assignToRightHemisphere(Tree tree)`
`static SNTPoint`	`brainCenter()` Returns the spatial centroid of the Allen CCF.
`static int`	`getAxisDefiningMidSagittalPlane()` Gets the axis defining mid sagittal plane.
`protected static org.json.JSONObject`	`getBrainAreasByStructureId()`
`protected static org.json.JSONObject`	`getBrainAreasByUUID()`
`protected static org.json.JSONArray`	`getBrainAreasList()`
`static AllenCompartment`	`getCompartment(int id)` Constructs a compartment from its CCF id
`static AllenCompartment`	`getCompartment(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 List<AllenCompartment>`	`getOntologies()` Gets the Allen CCF as a flat (non-hierarchical) collection of ontologies.
`static List<AllenCompartment>`	`getOntologies(int depth, boolean meshes)` Gets a flat (non-hierarchical) list of all the compartments of the specified ontology depth.
`static OBJMesh`	`getRootMesh(ColorRGB color)` Retrieves the surface contours for the Allen Mouse Brain Atlas (CCF), bundled with SNT.
`static DefaultTreeModel`	`getTreeModel(boolean meshesOnly)` Retrieves the Allen CCF hierarchical tree data.
`static boolean`	`isLeftHemisphere(double x, double y, double z)`
`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(String[] args)`
`static List<DirectedWeightedSubgraph>`	`splitByHemisphere(DirectedWeightedGraph graph)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - VERSION
```
public static final String VERSION
```
    The version of the Common Coordinate Framework currently used by SNT
    
    See Also:
    
    Constant Field Values
  - BRAIN_ROOT_ID
```
protected static final int BRAIN_ROOT_ID
```
    See Also:
    
    Constant Field Values
- Method Detail
  - getBrainAreasList
```
protected static org.json.JSONArray getBrainAreasList()
```
  - getBrainAreasByStructureId
```
protected static org.json.JSONObject getBrainAreasByStructureId()
```
  - getBrainAreasByUUID
```
protected static org.json.JSONObject getBrainAreasByUUID()
```
  - 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(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
  - assignHemisphereTags
```
public static void assignHemisphereTags(DirectedWeightedGraph graph)
```
  - getAxisDefiningMidSagittalPlane
```
public static int getAxisDefiningMidSagittalPlane()
```
    Gets the axis defining mid sagittal plane.
    
    Returns:
    
    the axis defining mid sagittal plane where X=0; Y=1; Z=2;
  - assignHemisphereTags
```
public static void assignHemisphereTags(Tree tree)
```
  - splitByHemisphere
```
public static List<DirectedWeightedSubgraph> splitByHemisphere(DirectedWeightedGraph graph)
```
  - 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
  - isLeftHemisphere
```
public static boolean isLeftHemisphere(double x,
                                       double y,
                                       double z)
```
  - 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 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 List<AllenCompartment> getOntologies()
```
    Gets the Allen CCF as a flat (non-hierarchical) collection of ontologies.
    
    Returns:
    
    the "flattened" ontologies list
  - getOntologies
```
public static List<AllenCompartment> getOntologies(int depth,
                                                   boolean meshes)
```
    Gets a flat (non-hierarchical) list of all the compartments of the specified ontology depth.
    
    Parameters:
    
    depth - the ontology depth
    
    meshes - If true, only compartments with known meshes are retrieved
    
    Returns:
    
    the "flattened" list of compartment
  - getRootMesh
```
public static OBJMesh getRootMesh(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(String[] args)
```

Class AllenUtils

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

VERSION

BRAIN_ROOT_ID

Method Detail

getBrainAreasList

getBrainAreasByStructureId

getBrainAreasByUUID

getCompartment

getCompartment

assignToLeftHemisphere

assignToRightHemisphere

isLeftHemisphere

assignHemisphereTags

getAxisDefiningMidSagittalPlane

assignHemisphereTags

splitByHemisphere

isLeftHemisphere

isLeftHemisphere

brainCenter

getHighestOntologyDepth

getTreeModel

getOntologies

getOntologies

getRootMesh

main