Package noduledata.imagej

Class MixedData

java.lang.Object

noduledata.imagej.ColorData

noduledata.imagej.MixedData

public class MixedData
extends ColorData

This class handles mixed nodules specifically, as they're approached differently than the other nodules. I identify mixed nodules by looking for yellow pixels in the segmented binary map. This works because the images we took of the root system were more zoomed out, and may not work for more high definition images, as mixed nodules themselves are not always yellow, and are often green and red next to each other.

Author:

Indefiables

Field Summary

Fields inherited from class noduledata.imagej.ColorData

COLOR, image, numNodules

Constructor Summary

Constructors

Constructor	Description
MixedData(ij.plugin.frame.RoiManager manager, int[] color, int colorThreshold, ij.ImagePlus im)	Uses the ColorData constructor method.

Method Summary

Modifier and Type	Method	Description
void	addRoi(ij.gui.ShapeRoi roi)	public method for appending new roi to end of the array.
void	drawRoi(ij.gui.ShapeRoi roi)	shows the given roi as a white blob overlaying the original image.
void	findMixedNodules(ij.ImagePlus im, ColorData red, ColorData green)	Identifies mixed nodules by checking for yellow pixels or by calculating the distance between red and green rois.
int[][]	getClumped()	indices of clumped nodules. clumped[mixedRoiIndex][0/1] where 0 == red, 1 == green
int	getPixelArea(int index, String color)	returns the number of pixels of the chosen color for the nodule at the given index.
boolean	removeRoi(ij.gui.ShapeRoi roi)	Attempts to find the given roi in the array of roi's, and removes it if it's present.
String	roiPixelCount(int index)	returns the counts of red and green pixels of the mixed nodule roi at the given index.
void	setClumped(int[][] clumped)	public setter method for clumped nodules array.
void	setRoi(int index, ij.gui.ShapeRoi roi)	public method for setting roi at given index.

Methods inherited from class noduledata.imagej.ColorData

averageArea, convertToBinary, createImageWithRoi, fillRect, getArea, getCircularity, getClump, getClumps, getData, getIndex, getMap, getPixels, getRoi, getRois, getTable, removeArrayOfRois, removeRoots, saveTable, setMap, setPixels, setRois, setTable, showAnnotatedMap, showMap, VisualizeRoi

Methods inherited from class java.lang.Object

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

Constructor Details

MixedData

public MixedData(ij.plugin.frame.RoiManager manager,
 int[] color,
 int colorThreshold,
 ij.ImagePlus im)

Uses the ColorData constructor method.

Parameters:

manager - : RoiManager object.

color - : rgb of the nodule type.

colorThreshold - : pixel threshold for a singular noduel area

im - : image we're doing analysis on.

Method Details

getPixelArea

public int getPixelArea(int index,
 String color)

returns the number of pixels of the chosen color for the nodule at the given index.

setRoi

public void setRoi(int index,
 ij.gui.ShapeRoi roi)

public method for setting roi at given index.

Overrides:

setRoi in class ColorData

addRoi

public void addRoi(ij.gui.ShapeRoi roi)

public method for appending new roi to end of the array.

Overrides:

addRoi in class ColorData

removeRoi

public boolean removeRoi(ij.gui.ShapeRoi roi)

Attempts to find the given roi in the array of roi's, and removes it if it's present. Returns true if the removal was succesful, false if the roi wasn't found.

Overrides:

removeRoi in class ColorData

Parameters:

roi - removes the given ROI from list of rois.

findMixedNodules

public void findMixedNodules(ij.ImagePlus im,
 ColorData red,
 ColorData green)

Identifies mixed nodules by checking for yellow pixels or by calculating the distance between red and green rois.

drawRoi

public void drawRoi(ij.gui.ShapeRoi roi)

shows the given roi as a white blob overlaying the original image.

Parameters:

roi -

roiPixelCount

public String roiPixelCount(int index)

returns the counts of red and green pixels of the mixed nodule roi at the given index.

getClumped

public int[][] getClumped()

indices of clumped nodules. clumped[mixedRoiIndex][0/1] where 0 == red, 1 == green

setClumped

public void setClumped(int[][] clumped)

public setter method for clumped nodules array.

Parameters:

clumped -