jp.ac.keio.bio.fun.xitosbml.visual

Class Viewer

java.lang.Object

jp.ac.keio.bio.fun.xitosbml.visual.Viewer

public class Viewer
extends Object

The class Viewer, which visualizes a SpatialImage object on ImageJ 3D Viewer. This class also contains some methods to handle ImageJ image object (ImagePlus). Date Created: Feb 21, 2017

Author:

Kaito Ii <ii@fun.bio.keio.ac.jp>, Akira Funahashi <funa@bio.keio.ac.jp>

Constructor Summary

Constructors

Constructor and Description
Viewer()

Method Summary

Modifier and Type	Method and Description
void	findPoints() Find points in the 3D universe.
HashMap<String,org.scijava.vecmath.Point3d>	gethashBound() Gets the hashmap of boundary.
HashMap<String,List<org.scijava.vecmath.Point3d>>	gethashVertices() Gets the hashmap of vertices.
void	view(SpatialImage spImg) Visualize SpatialImage object on ImageJ 3D Viewer

Methods inherited from class java.lang.Object

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

Constructor Detail

Viewer

public Viewer()

Method Detail

view

public void view(SpatialImage spImg)

Visualize SpatialImage object on ImageJ 3D Viewer

Parameters:

spImg - the The SpatialImage, which is a class for handling spatial image in XitoSBML.

findPoints

public void findPoints()

Find points in the 3D universe. If the 3D space contains MethGroup, then add all the vertices of the mesh to hashmap of vertices. Minimum and Maximum boundary is also assigned as points.

gethashVertices

public HashMap<String,List<org.scijava.vecmath.Point3d>> gethashVertices()

Gets the hashmap of vertices.

Returns:

the hashmap of vertices

gethashBound

public HashMap<String,org.scijava.vecmath.Point3d> gethashBound()

Gets the hashmap of boundary.

Returns:

the hashmap of boundary