Index

A B C D F G H I M N O R S T U V
All Classes and Interfaces|All Packages|Constant Field Values

A

addRoi(ShapeRoi) - Method in class noduledata.imagej.ColorData

add given roi to array of Rois

addRoi(ShapeRoi) - Method in class noduledata.imagej.MixedData

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

area - Variable in class noduledata.imagej.NoduleClump

averageArea() - Method in class noduledata.imagej.ColorData

calculates average area of the singular nodules.

averageLightness(Roi[]) - Method in class noduledata.imagej.NoduleData

calculates the average lightness of all nodules within the image.

B

binarymap - Variable in class noduledata.imagej.NoduleData

BOTTOMA - Static variable in class noduledata.imagej.NoduleData

BOTTOMB - Static variable in class noduledata.imagej.NoduleData

C

COLOR - Variable in class noduledata.imagej.ColorData

ColorData - Class in noduledata.imagej

This class handles the analysis of the segmented nodule Rois.

ColorData(RoiManager, int[], int, ImagePlus) - Constructor for class noduledata.imagej.ColorData

constructor method.

combinedMap() - Method in class noduledata.imagej.NoduleData

convertToBinary() - Method in class noduledata.imagej.ColorData

converts map to binary map.

correctClump(ImagePlus) - Method in class noduledata.imagej.NoduleClump

Prompts the user to correct (or not) the number of nodules within the clump.

createImageWithRoi(ImagePlus, Roi) - Static method in class noduledata.imagej.NoduleData

returns the given image cropped to the given roi.

createImageWithRoi(ImagePlus, Roi[]) - Static method in class noduledata.imagej.ColorData

Generates a map given a background image and ROIs.

D

drawRoi(ShapeRoi) - Method in class noduledata.imagej.MixedData

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

F

file - Variable in class noduledata.imagej.Menu

fillRect(Rectangle, ImageProcessor) - Static method in class noduledata.imagej.ColorData

fills given rect with given color.

findMixedNodules(ImagePlus, ColorData, ColorData) - Method in class noduledata.imagej.MixedData

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

FOLDER - Static variable in class noduledata.imagej.Menu

G

getArea() - Method in class noduledata.imagej.ColorData

areas[][[] is nx2 with n Rois.

getCircularity(int) - Method in class noduledata.imagej.ColorData

Returns the circularity of the roi at the given index.

getClump(int) - Method in class noduledata.imagej.ColorData

Returns clump at given index.

getClumped() - Method in class noduledata.imagej.MixedData

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

getClumps() - Method in class noduledata.imagej.ColorData

getData(boolean) - Method in class noduledata.imagej.ColorData

Method that generates the ResultsTable, ROI's, int[] areas, and numNodules.
Finds all ROIs using the measure method.
Finds any rois with large enough measure, and fills them in.

getFileType(File) - Static method in class noduledata.imagej.Menu

Returns:
1 for folder
2 for accepted image type
3 for .model file
4 for any other filetype.

getImageFromRoi(ShapeRoi, ImagePlus) - Static method in class noduledata.imagej.UserEditsHandler

Creates a zoomed in image of the given nodule.

getIndex(Roi) - Method in class noduledata.imagej.ColorData

returns index of given roi or -1 if Roi is not found.

getMap() - Method in class noduledata.imagej.ColorData

Returns the binary map for this ColorData object.

getPixelArea(int, String) - Method in class noduledata.imagej.MixedData

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

getPixels() - Method in class noduledata.imagej.ColorData

Returns the array of pixels that are nodule pixels of this type.

getRoi(int) - Method in class noduledata.imagej.ColorData

returns Roi at given index

getRois() - Method in class noduledata.imagej.ColorData

returns array of all rois.

getTable() - Method in class noduledata.imagej.ColorData

Returns the given ResultsTable

greenSingle - Variable in class noduledata.imagej.Menu

H

hasMixed - Variable in class noduledata.imagej.NoduleClump

I

image - Variable in class noduledata.imagej.ColorData

image - Variable in class noduledata.imagej.NoduleData

image - Static variable in class noduledata.imagej.NoduleSegmentation

IMAGE - Static variable in class noduledata.imagej.Menu

imageWithoutNodules() - Method in class noduledata.imagej.NoduleData

Returns an image with the segmented nodule pixels set to white.

index - Variable in class noduledata.imagej.NoduleClump

M

main(String...) - Static method in class noduledata.imagej.NoduleSegmentation

This main function serves for development purposes.

Menu - Class in noduledata.imagej

This class is an ImageJ Menu class for allowing the user to their files that this program will do the analysis on.

Menu() - Constructor for class noduledata.imagej.Menu

MixedData - Class in noduledata.imagej

This class handles mixed nodules specifically, as they're approached differently than the other nodules.

MixedData(RoiManager, int[], int, ImagePlus) - Constructor for class noduledata.imagej.MixedData

Uses the ColorData constructor method.

mixedSingle - Variable in class noduledata.imagej.Menu

MODEL - Static variable in class noduledata.imagej.Menu

modelFile - Variable in class noduledata.imagej.Menu

mouseClicked(Point, double, ImagePlus) - Method in class noduledata.imagej.UserEditsHandler

Handles when the user clicks anywhere on the GUI.
Checks if the user clicked on any nodule on the image, and if so, calls a sub menu to allow user to edit that nodule.

N

NoduleClump - Class in noduledata.imagej

An object of this class represents a nodule clump and the data that separates the nodule into separated nodules via various methods.

NoduleClump() - Constructor for class noduledata.imagej.NoduleClump

NoduleClump(int, ShapeRoi, double, int, ImagePlus) - Constructor for class noduledata.imagej.NoduleClump

constructor

NoduleData - Class in noduledata.imagej

This class manages the segmentation of the image and the saving of the data.

NoduleData(ColorClustering, int, int, int) - Constructor for class noduledata.imagej.NoduleData

generate a segmentation map using using a ColorClustering model.

noduledata.imagej - package noduledata.imagej

NoduleSegmentation - Class in noduledata.imagej

This is the parent class or 'main' class for this project.

NoduleSegmentation() - Constructor for class noduledata.imagej.NoduleSegmentation

numInstances - Variable in class noduledata.imagej.NoduleData

numNodules - Variable in class noduledata.imagej.ColorData

numNodules - Variable in class noduledata.imagej.NoduleClump

O

OTHERFILETYPE - Static variable in class noduledata.imagej.Menu

R

redSingle - Variable in class noduledata.imagej.Menu

removeArrayOfRois(int[]) - Method in class noduledata.imagej.ColorData

removes the data for the given indices.

removeRoi(ShapeRoi) - Method in class noduledata.imagej.ColorData

removeRoi(ShapeRoi) - Method in class noduledata.imagej.MixedData

Attempts to find the given roi in the array of roi's, and removes it if it's present.

removeRoots() - Method in class noduledata.imagej.ColorData

Uses aspect ratio and area to locate and remove fluoresced roots caught in initial segmentation

roi - Variable in class noduledata.imagej.NoduleClump

roiPixelCount(int) - Method in class noduledata.imagej.MixedData

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

run() - Method in class noduledata.imagej.Menu

run() - Method in class noduledata.imagej.NoduleSegmentation

run(String) - Method in class noduledata.imagej.NoduleData

This is what is called to compute the data for the given image.

run(String) - Method in class noduledata.imagej.UserEditsHandler

Method that's called to initialize part of the program allowing the user to make manual changes.

S

saveFile - Variable in class noduledata.imagej.Menu

saveTable() - Method in class noduledata.imagej.ColorData

save data as CSV file.

scaleImage(ImageIcon, int, int) - Method in class noduledata.imagej.UserEditsHandler

returns the scaled image icon according to the given newWidth and newHeight

setClumped(int[][]) - Method in class noduledata.imagej.MixedData

public setter method for clumped nodules array.

setMap(ImagePlus) - Method in class noduledata.imagej.ColorData

Sets or updates the binary map.

setPixels(int[]) - Method in class noduledata.imagej.ColorData

Sets the pixels that are counted as nodule pixels of this type.

setRoi(int, ShapeRoi) - Method in class noduledata.imagej.ColorData

Replaces ROI at the given index with new ROI Does nothing if index is invalid.

setRoi(int, ShapeRoi) - Method in class noduledata.imagej.MixedData

public method for setting roi at given index.

setRois(ShapeRoi[]) - Method in class noduledata.imagej.ColorData

updater method for the array of ROI's

setTable(ResultsTable) - Method in class noduledata.imagej.ColorData

Sets the ImageJ ResultsTable object.

showAnnotatedMap() - Method in class noduledata.imagej.ColorData

Creates an annotated version of the map and displays it.

showMap() - Method in class noduledata.imagej.ColorData

Show's the map using ImageJ API.

T

TOPB - Static variable in class noduledata.imagej.NoduleData

TOPCUTOFFSLOPE - Static variable in class noduledata.imagej.NoduleData

U

UserEditsHandler - Class in noduledata.imagej

This class was created to allow the user to make manual adjustments to the programs segmentation and outlines of the nodules.

UserEditsHandler(ImagePlus, ColorData, ColorData, MixedData) - Constructor for class noduledata.imagej.UserEditsHandler

constructor method

V

Visualize() - Method in class noduledata.imagej.NoduleData

VisualizeRoi(ImagePlus, Roi, boolean) - Method in class noduledata.imagej.ColorData

Shows the RG color distribution graph for the given Roi

A B C D F G H I M N O R S T U V
All Classes and Interfaces|All Packages|Constant Field Values