jp.ac.keio.bio.fun.xitosbml.geometry

Class ImageGeometryData

java.lang.Object

jp.ac.keio.bio.fun.xitosbml.geometry.AbstractData

jp.ac.keio.bio.fun.xitosbml.geometry.ImageGeometryData

Direct Known Subclasses:

AnalyticGeometryData, SampledFieldGeometryData

public abstract class ImageGeometryData
extends AbstractData

The class ImageGeometryData, which is an abstract class and be used to create data objects for geometry objects (AnalyticGeometryData, SampledFieldGeometryData and ParametricGeometryData). The inherited class should implement getSampledValues(), createImage() and getSpatialImage() methods. Date Created: Jun 25, 2015

Author:

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

Field Summary

Fields

Modifier and Type	Field and Description
protected org.sbml.jsbml.ext.spatial.Geometry	g The Geometry object.
protected HashMap<String,Integer>	hashSampledValue The hashmap of sampled value of spatial image.
protected ij.ImagePlus	img The ImageJ image object.
protected byte[]	raw The raw data of spatial image in 1D array.

Method Summary

Modifier and Type	Method and Description
abstract SpatialImage	getSpatialImage() Create and return a new spatial image.

Methods inherited from class java.lang.Object

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

Field Detail

g

protected org.sbml.jsbml.ext.spatial.Geometry g

The Geometry object.

hashSampledValue

protected HashMap<String,Integer> hashSampledValue

The hashmap of sampled value of spatial image.

img

protected ij.ImagePlus img

The ImageJ image object.

raw

protected byte[] raw

The raw data of spatial image in 1D array.

Method Detail

getSpatialImage

public abstract SpatialImage getSpatialImage()

Create and return a new spatial image. SpatialImage object is generated with the ImagePlus object (img) and the hashmap of sampled value (pixel value of a SampledVolume).

Returns:

spatial image object, which is an object for handling spatial image in XitoSBML.