Uses of Class
noduledistances.imagej.RootGraph

Uses of RootGraph in noduledistances.imagej

Methods in noduledistances.imagej with parameters of type RootGraph

Modifier and Type	Method	Description
double[]	RoiOverlay.attachmentPoint(ij.gui.ShapeRoi roi, RootGraph graph)	Computes what we will use as the node for the given nodule.
protected int	Statistics.closestColorType(Node node, RootGraph graph)	computes what color the closest nodule is.
protected int	Statistics.closestDistance(int color, Node node, RootGraph graph)
protected static HashMap<Integer,double[]>	Statistics.computeStatistics(int[] radii, Node node, RootGraph graph, ArrayList<Integer> options)	Computes the number of nodules within a given radius of a given color.
void	Statistics.generateData(RootGraph graph, int[] radii, String saveFile)	Populates the String[][] data with computed statistics relevant to distance data.
int[]	RoiOverlay.getClumpData(ij.gui.ShapeRoi roi, int numNods, RootGraph graph)	Uses k-means clustering to break up the given roi into several pieces.
ArrayList<int[]>	RoiOverlay.getRoiCentroids(RootGraph graph)	finds the centroid of all ROI's, and returns them in [color,x,y,area] format.
protected static double	Statistics.meanDistance(int color, Node node, RootGraph graph)	Computes the mean distance from the given nodule to all other nodules of a given type.
protected int	Statistics.numNodulesinBall(int color, int radius, Node node, RootGraph graph)	Finds the number of nodules in the ball of given radius, centered at given node.
void	GraphOverlay.overlayGraph(RootGraph graph, ij.process.ColorProcessor cp)	overlays the graph and nodules onto the user-provided root system image.
void	Statistics.savePairwiseDistanceMatrices(RootGraph graph, String saveFile, int numIters)	Saves the pair-wise distance matrices as csv files.
void	NoduleDistances.saveRandomPaths(RootGraph graph, GraphOverlay graphOverlay, String saveFile, String title)	Saves a set of images that are random computed shortest paths between the nodule nodes.
ij.ImagePlus	NoduleDistances.shortestPath(int startNodeIndex, int endNodeIndex, RootGraph graph, GraphOverlay graphOverlay)	Generates an image showing the shortest 5 paths between the two given nodes by \ coloring the paths taken 5 distinct colors