Index (noduledistances 0.5.0-SNAPSHOT API)

A B C D E F G I K M N O P R S T U
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

addEdge(Node[]) - Method in class noduledistances.imagej.RootGraph: Adds an edge to the graph.
addNodules(ArrayList<int[]>) - Method in class noduledistances.imagej.RootGraph: adds the set of nodules as Node objects to the graph by connecting each nodule node to the nearest node currently within the graph with an edge.
area - Variable in class noduledistances.imagej.Node
attachmentPoint(ShapeRoi, RootGraph) - Method in class noduledistances.imagej.RoiOverlay: Computes what we will use as the node for the given nodule.
averagePoint(Point[]) - Method in class noduledistances.imagej.RoiOverlay: Computes the average(or centroid) of the given array of points. i.e. it computes the mean of the X values and the mean of the Y values, and returns those as a point.

B

ballSubgraph(int, Point2D) - Method in class noduledistances.imagej.RootGraph: Find the numNodes closest Nodes to the given pt, and finds all edges that contain any of those nodes.
ballSubgraphLines(int, Point2D) - Method in class noduledistances.imagej.RootGraph: Find the numNods closest nodes to the given point, then creates an arrayList of lines that are all edges containing any of the closest nodes.
i.e. it records all edges containing the numNodes closest nodes, returning them as Roi objects.
binarymap - Variable in class noduledistances.imagej.RootSegmentation
blackenOutsideRectangle(ImagePlus) - Static method in class noduledistances.imagej.NoduleDistances: Method that asks the user to draw a rectangle around the part of the image containing the root system to remove any noise outside the root system.
breakupClump(ShapeRoi, int, List<CentroidCluster<ClumpClusterPoint>>) - Method in class noduledistances.imagej.RoiOverlay: Uses the computed clusters to breakup the given roi into an arrayList of individual Rois.

C

closestColorType(Node, RootGraph) - Method in class noduledistances.imagej.Statistics: computes what color the closest nodule is.
closestDistance(int, Node, RootGraph) - Method in class noduledistances.imagej.Statistics
ClumpClusterPoint - Class in noduledistances.imagej: An implementation of Apache Common's Clusterable interface to use Apache's clustering methods in RoiOverlay.breakupClump()
ClumpClusterPoint(double, double) - Constructor for class noduledistances.imagej.ClumpClusterPoint
ClumpClusterPoint(Point2D.Double) - Constructor for class noduledistances.imagej.ClumpClusterPoint
computeLengthOfPath(List<BaseVertex>) - Method in class noduledistances.imagej.RootGraph: Computes the length of the given path. i.e. the sum of the lengths of the lines between each arc in the path.
computeShortestDistances(int) - Method in class noduledistances.imagej.RootGraph: Computes and stores the all-pairs distance calculations between all Nodules numIteration times.
computeStatistics(int[], Node, RootGraph, ArrayList<Integer>) - Static method in class noduledistances.imagej.Statistics: Computes the number of nodules within a given radius of a given color.
containsEdge(int, int) - Method in class noduledistances.imagej.RootGraph: Checks whether the graph contains the edge [a,b].
convertToYanGraph() - Method in class noduledistances.imagej.RootGraph: creates a graph structure using Yan Qi's graph package to utilize their implementation of k shortest paths.

D

distance - Variable in class noduledistances.imagej.Node: DEPRECATED 2d array where each element A_ij is the distance to the j'th node on the i'th iteration of dijkstra's.
distance(Node) - Method in class noduledistances.imagej.Node: computes the euclidean distance between this node and the given node.

E

equals(Object) - Method in class noduledistances.imagej.Node: We say two nodes are equal when any of the following are true:
1. they reference the same object in memory
2. their x/y values are the same
3. if they are the same type of node( skeleton/nodule) AND are within 8 pixels

F

findPairs(int, int) - Static method in class noduledistances.imagej.NoduleDistances: Finds random sets of pairs of nodules.
FOLDER - Static variable in class noduledistances.imagej.Menu

G

generateData(RootGraph, int[], String) - Method in class noduledistances.imagej.Statistics: Populates the String[][] data with computed statistics relevant to distance data.
getBoundaryPoints(ShapeRoi, ArrayList<ShapeRoi>) - Method in class noduledistances.imagej.RoiOverlay: For each line in intersections, it records the points of where that line intersects the given roi, if any.
getClumpData(ShapeRoi, int, RootGraph) - Method in class noduledistances.imagej.RoiOverlay: Uses k-means clustering to break up the given roi into several pieces.
getFileType(File) - Static method in class noduledistances.imagej.Menu: Returns 1 : folder
2 : accepted image type
3 : .model file
4 : any other filetype
getHaltonSequence(ShapeRoi) - Method in class noduledistances.imagej.RoiOverlay: Computes the halton sequence for a given ROI to create a sample of uniformly distributed points within the Roi polygon by intersecting the halton sequence with the polygon.
getHaltonVectors(int, Rectangle) - Method in class noduledistances.imagej.RoiOverlay: Computes generic halton vectors, and scales them to fill a bounding box.
getInstances(Point) - Method in class noduledistances.imagej.RootGraph: Finds searches for all in-arcs of the given node.
getNodules() - Method in class noduledistances.imagej.RootGraph
getPaths(int) - Method in class noduledistances.imagej.Node: Finds and returns the set of paths from this node to the given node.
getPoint() - Method in class noduledistances.imagej.ClumpClusterPoint
getRoiCentroids(RootGraph) - Method in class noduledistances.imagej.RoiOverlay: finds the centroid of all ROI's, and returns them in [color,x,y,area] format.
GraphOverlay - Class in noduledistances.imagej: This class is used to hold the image plus object that has the skeletonized root system on top of the image of the root.
GraphOverlay() - Constructor for class noduledistances.imagej.GraphOverlay
GREEN - Static variable in class noduledistances.imagej.Node
greenAttribute - Variable in class noduledistances.imagej.Menu

I

image - Static variable in class noduledistances.imagej.NoduleDistances
IMAGE - Static variable in class noduledistances.imagej.Menu
initialHeight - Static variable in class noduledistances.imagej.NoduleDistances
initialWidth - Static variable in class noduledistances.imagej.NoduleDistances

K

kMeansClustering(List<ClumpClusterPoint>, int) - Static method in class noduledistances.imagej.RoiOverlay: performs k-means clustering on a given set of points to break nodule clumps into k parts.

M

main(String...) - Static method in class noduledistances.imagej.NoduleDistances: This main function serves for development purposes.
meanDistance(int, Node, RootGraph) - Static method in class noduledistances.imagej.Statistics: Computes the mean distance from the given nodule to all other nodules of a given type.
Menu - Class in noduledistances.imagej
Menu() - Constructor for class noduledistances.imagej.Menu
mergeNonemptyComponents(ArrayList<int[]>) - Method in class noduledistances.imagej.RootGraph: Used to merge disconnected parts of the graph to create one connected graph.
MIXED - Static variable in class noduledistances.imagej.Node
MODEL - Static variable in class noduledistances.imagej.Menu
modelFile - Variable in class noduledistances.imagej.Menu

N

Node - Class in noduledistances.imagej
Node(int, int, int, double) - Constructor for class noduledistances.imagej.Node: constructor method
Node(int, int, int, double, int) - Constructor for class noduledistances.imagej.Node: constructor method
nodeIndex - Variable in class noduledistances.imagej.Node
nodeNumber - Variable in class noduledistances.imagej.Node: nodeNumber represents the number shown on the nodule csv data to easily associate a nodule node with it's nodule number.
nodes - Variable in class noduledistances.imagej.RootGraph: Node is an extension of java.awt.point that includes an identifier for the node, i.e.
NoduleDistances - Class in noduledistances.imagej
NoduleDistances() - Constructor for class noduledistances.imagej.NoduleDistances
noduledistances.imagej - package noduledistances.imagej
noduleFSRep() - Method in class noduledistances.imagej.RootGraph: Returns the subgraph that is all edges containing a nodule node as at least one of the nodes.
numIters - Variable in class noduledistances.imagej.Menu
numNodules - Variable in class noduledistances.imagej.RootGraph
numNodulesinBall(int, int, Node, RootGraph) - Method in class noduledistances.imagej.Statistics: Finds the number of nodules in the ball of given radius, centered at given node.

O

onBoundary(double, double, double, double, double, double) - Static method in class noduledistances.imagej.RoiOverlay: ChatGPT was used in making this method.
Determines whether a given point (x, y) is within 2 pixels from a line segment defined by the points (p1x, p1y) and (p2x, p2y).
OTHERFILETYPE - Static variable in class noduledistances.imagej.Menu
overlayedGraph - Variable in class noduledistances.imagej.GraphOverlay
overlayGraph(RootGraph, ColorProcessor) - Method in class noduledistances.imagej.GraphOverlay: overlays the graph and nodules onto the user-provided root system image.

P

preprocessing(ImagePlus) - Method in class noduledistances.imagej.NoduleDistances: increases brightness and contrast in the image to improve segmentation of root system.
prevNode - Variable in class noduledistances.imagej.Node

R

RED - Static variable in class noduledistances.imagej.Node
redAttribute - Variable in class noduledistances.imagej.Menu
removeEdge(Node[]) - Method in class noduledistances.imagej.RootGraph: method for removing the given edge.
RoiOverlay - Class in noduledistances.imagej: This class object is used to extract the nodule information from the Nodule Segmentation plugin and incoporate that data with the rest of this plugin.
RoiOverlay(ImagePlus) - Constructor for class noduledistances.imagej.RoiOverlay: Extracts the Roi information from the loaded Tif image.
rootFile - Variable in class noduledistances.imagej.Menu
RootGraph - Class in noduledistances.imagej: The purpose of the class RootGraph is to hold all information related to the graph derived from the initial image, including the data and methods to translate between the abstract graph and the point and edges on the skeleton of the image.
RootGraph(ArrayList<ArrayList<int[]>>, GraphOverlay) - Constructor for class noduledistances.imagej.RootGraph: constructor.
RootSegmentation - Class in noduledistances.imagej: Class for segmenting the roots from the rest of the image using Weka's Color Clustering segmentation method.
RootSegmentation(ColorClustering, ShapeRoi[]) - Constructor for class noduledistances.imagej.RootSegmentation: performs color clustering segmentation to create a binary map of the root system.
run() - Method in class noduledistances.imagej.Menu: Method for starting the Menu display process.
run() - Method in class noduledistances.imagej.NoduleDistances

S

saveFile - Variable in class noduledistances.imagej.Menu
savePairwiseDistanceMatrices(RootGraph, String, int) - Method in class noduledistances.imagej.Statistics: Saves the pair-wise distance matrices as csv files.
saveRandomPaths(RootGraph, GraphOverlay, String, String) - Method in class noduledistances.imagej.NoduleDistances: Saves a set of images that are random computed shortest paths between the nodule nodes.
SCALEFACTOR - Static variable in class noduledistances.imagej.NoduleDistances
scaleImage(ImagePlus, double) - Static method in class noduledistances.imagej.Skeletonize: Scales the image according to the scale factor.
shortestPath(int, int, RootGraph, GraphOverlay) - Method in class noduledistances.imagej.NoduleDistances: Generates an image showing the shortest 5 paths between the two given nodes by \ coloring the paths taken 5 distinct colors
shortestPathsToList(List<Path>) - Method in class noduledistances.imagej.RootGraph: converts the list of computed shortest paths to an ArrayList of Arrays of ints.
showGraph() - Method in class noduledistances.imagej.GraphOverlay
skeleton - Variable in class noduledistances.imagej.RootGraph
SKELETON - Static variable in class noduledistances.imagej.Node: Node.type == 0 -> skeleton node type == 1 -> red nodule type == 2 -> green nodule type == 3 -> mixed nodule
skeletonize(ImagePlus) - Static method in class noduledistances.imagej.Skeletonize: Uses Ling Dong's skeletonization algorithm to find the skeleton of the root system.
Skeletonize - Class in noduledistances.imagej: Class using Ling Dong's skeletonization algorithm.
Skeletonize() - Constructor for class noduledistances.imagej.Skeletonize
skeletonMap - Variable in class noduledistances.imagej.RootSegmentation
Statistics - Class in noduledistances.imagej: A class that generates all of the statistical data for analysis, and saves it as one csv file.
Statistics(String, String, String) - Constructor for class noduledistances.imagej.Statistics: Initializer method for the Statistics class.

T

tifFile - Variable in class noduledistances.imagej.Menu
toString() - Method in class noduledistances.imagej.Node
trimArray(int[], int) - Method in class noduledistances.imagej.RoiOverlay: removes trailing zeros that result from the Power Diagram output.
type - Variable in class noduledistances.imagej.Node: type == 0 -> skeleton node
type == 1 -> red nodule
type == 2 -> green nodule
type == 3 -> mixed nodule

U

update(int) - Method in class noduledistances.imagej.Node: method for updating the nodule.
update(int, double, int) - Method in class noduledistances.imagej.Node: method for updating the node
update(int, int, int, double, int) - Method in class noduledistances.imagej.Node: method for updating the node.

A B C D E F G I K M N O P R S T U
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form