deformablemesh.util

Class MeshAnalysis

java.lang.Object

deformablemesh.util.MeshAnalysis

public class MeshAnalysis
extends Object

Created by msmith on 2/9/16.

Constructor Summary

Constructors

Constructor and Description
MeshAnalysis(Map<Integer,DeformableMesh3D> meshes, Map<Integer,Furrow3D> furrows, MeshImageStack stack)

Method Summary

Modifier and Type	Method and Description
static void	calculateAllVolumes(List<Track> tracks, MeshImageStack stack) Generates a text window with the time series for all of the tracks provided.
void	calculateAverageIntensity(int i, double cortex_thickness)
void	calculateLineScans(int frame, double cortex_thickness)
void	createOutput(double cortex_thickness)
void	measureVolume()
static void	plotDisplacementHistogram(List<Track> tracks, MeshImageStack meshImageStack)
static void	plotDisplacementsVsTime(List<Track> tracks, MeshImageStack meshImageStack)
static void	plotElongationsVsTime(List<Track> tracks)
static void	plotMeshesOverTime(List<Track> tracks, MeshImageStack mis) Plots the number of meshes over time.
static void	plotVolumesOverTime(List<Track> tracks, MeshImageStack mis) Creates a plot of the volumes over time.
static double	radius(double v, double rc)

Methods inherited from class java.lang.Object

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

Constructor Detail

MeshAnalysis

public MeshAnalysis(Map<Integer,DeformableMesh3D> meshes,
                    Map<Integer,Furrow3D> furrows,
                    MeshImageStack stack)

Method Detail

plotElongationsVsTime

public static void plotElongationsVsTime(List<Track> tracks)

Parameters:

tracks -

meshImageStack -

createOutput

public void createOutput(double cortex_thickness)

calculateAverageIntensity

public void calculateAverageIntensity(int i,
                                      double cortex_thickness)

calculateLineScans

public void calculateLineScans(int frame,
                               double cortex_thickness)

radius

public static double radius(double v,
                            double rc)

measureVolume

public void measureVolume()

plotMeshesOverTime

public static void plotMeshesOverTime(List<Track> tracks,
                                      MeshImageStack mis)

Plots the number of meshes over time.

Parameters:

tracks -

mis -

plotVolumesOverTime

public static void plotVolumesOverTime(List<Track> tracks,
                                       MeshImageStack mis)

Creates a plot of the volumes over time. Tracked cells are connected.

Parameters:

tracks -

mis -

plotDisplacementHistogram

public static void plotDisplacementHistogram(List<Track> tracks,
                                             MeshImageStack meshImageStack)

plotDisplacementsVsTime

public static void plotDisplacementsVsTime(List<Track> tracks,
                                           MeshImageStack meshImageStack)

calculateAllVolumes

public static void calculateAllVolumes(List<Track> tracks,
                                       MeshImageStack stack)

Generates a text window with the time series for all of the tracks provided.

Parameters:

tracks -

stack -