Package noduledistances.imagej

Class RootSegmentation

java.lang.Object

noduledistances.imagej.RootSegmentation

public class RootSegmentation
extends Object

Class for segmenting the roots from the rest of the image using Weka's Color Clustering segmentation method.

Author:

Brandin Farris

Field Summary

Fields

Modifier and Type	Field	Description
ij.ImagePlus	binarymap
ij.ImagePlus	skeletonMap

Constructor Summary

Constructors

Constructor	Description
RootSegmentation(trainableSegmentation.unsupervised.ColorClustering cluster, ij.gui.ShapeRoi[] rois)	performs color clustering segmentation to create a binary map of the root system.

Method Summary

Methods inherited from class java.lang.Object

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

Field Details

binarymap

public ij.ImagePlus binarymap

skeletonMap

public ij.ImagePlus skeletonMap

Constructor Details

RootSegmentation

public RootSegmentation(trainableSegmentation.unsupervised.ColorClustering cluster,
 ij.gui.ShapeRoi[] rois)

performs color clustering segmentation to create a binary map of the root system.

Parameters:

cluster - : clustering object that holds the model file used for segmentation. It's one of the biggest bottlenecks of the program. I'm using Weka's color clustering for this so I'm not sure what optimization I can do.