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

Class SampledFieldGeometryData

java.lang.Object

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

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

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

public class SampledFieldGeometryData
extends ImageGeometryData

The class SampledFieldGeometryData, which inherits ImageGeometryData and implements getSampledValues() and createImage() methods. This class contains following objects which are related to sampled field geometry.

• Geometry SampledFieldGeometry
• image size

This class is used in GeometryDatas, to visualize a model in 3D space. Date Created: Jun 26, 2015

Author:

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

Field Summary

Fields inherited from class jp.ac.keio.bio.fun.xitosbml.geometry.ImageGeometryData

g, hashSampledValue, img, raw

Constructor Summary

Constructors

Constructor and Description
SampledFieldGeometryData(org.sbml.jsbml.ext.spatial.GeometryDefinition gd, org.sbml.jsbml.ext.spatial.Geometry g) Instantiates a new sampled field geometry data with given GeometryDefinition and Geometry.

Method Summary

Modifier and Type	Method and Description
protected void	createImage() Create a stacked image from spatial image (3D).
protected void	getSampledValues() Get sampled value from Geometry (SampledFieldGeometry) and sets its value to the hashSampledValue (hashmap of sampled value).
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

Constructor Detail

SampledFieldGeometryData

public SampledFieldGeometryData(org.sbml.jsbml.ext.spatial.GeometryDefinition gd,
                                org.sbml.jsbml.ext.spatial.Geometry g)

Instantiates a new sampled field geometry data with given GeometryDefinition and Geometry.

Parameters:

gd - the GeometryDefinition

g - the Geometry

Method Detail

getSampledValues

protected void getSampledValues()

Get sampled value from Geometry (SampledFieldGeometry) and sets its value to the hashSampledValue (hashmap of sampled value).

createImage

protected void createImage()

Create a stacked image from spatial image (3D). The value of each pixel corresponds to the domain.

See Also:

ImageGeometryData.createImage()

getSpatialImage

public 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).

Specified by:

getSpatialImage in class ImageGeometryData

Returns:

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

See Also:

ImageGeometryData.getSpatialImage()