Index

A B C D E F G H I J K L M N O P R S T U V W X Y Z
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

a - Variable in class signalprocesser.voronoi.eventqueue.VSiteEvent

AbstractAccumulator - Class in io.github.mianalysis.mia.process.houghtransform.accumulators

Created by sc13967 on 12/01/2018.

AbstractAccumulator(int[][]) - Constructor for class io.github.mianalysis.mia.process.houghtransform.accumulators.AbstractAccumulator

AbstractRepresentation - Class in signalprocesser.voronoi.representation

AbstractRepresentation() - Constructor for class signalprocesser.voronoi.representation.AbstractRepresentation

AbstractSphere - Class in io.github.mianalysis.mia.process.voxel

AbstractSphere() - Constructor for class io.github.mianalysis.mia.process.voxel.AbstractSphere

AbstractStatusStructure - Class in signalprocesser.voronoi.statusstructure

AbstractStatusStructure() - Constructor for class signalprocesser.voronoi.statusstructure.AbstractStatusStructure

AbstractTransform - Class in io.github.mianalysis.mia.process.houghtransform.transforms

Created by sc13967 on 12/01/2018.

AbstractTransform(ImageStack) - Constructor for class io.github.mianalysis.mia.process.houghtransform.transforms.AbstractTransform

AbstractTransform(ImageProcessor) - Constructor for class io.github.mianalysis.mia.process.houghtransform.transforms.AbstractTransform

accumulator - Variable in class io.github.mianalysis.mia.process.houghtransform.accumulators.AbstractAccumulator

accumulator - Variable in class io.github.mianalysis.mia.process.houghtransform.transforms.AbstractTransform

ACTION_NUMBER - Static variable in class io.github.mianalysis.mia.object.metadata.Metadata

add(Energy) - Method in class io.github.mianalysis.mia.process.activecontour.energies.EnergyCollection

add(Component) - Method in class signalprocesser.shared.JCollapsiblePanel

add(Component, int) - Method in class signalprocesser.shared.JCollapsiblePanel

add(Component, Object) - Method in class signalprocesser.shared.JCollapsiblePanel

add(Component, Object, int) - Method in class signalprocesser.shared.JCollapsiblePanel

add(String, Component) - Method in class signalprocesser.shared.JCollapsiblePanel

addBreak() - Method in class io.github.mianalysis.mia.process.skeleton.Skeleton

addCircleEvent(EventQueue) - Method in class signalprocesser.voronoi.statusstructure.VLinkedNode

addConnectedVertex(VHalfEdge) - Method in class signalprocesser.voronoi.representation.boundaryproblem.VVertex

addDetectedObjectsOverlay(ImagePlus, ArrayList<double[]>) - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.AbstractAccumulator

addDetectedObjectsOverlay(ImagePlus, ArrayList<double[]>) - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.CircleAccumulator

addDetectedObjectsOverlay(ImagePlus, ArrayList<double[]>) - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.LineAccumulator

addDetectedObjectsOverlay(ImagePlus, ArrayList<double[]>) - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.RectangleAccumulator

addDetectedObjectsOverlay(ImagePlus, ArrayList<double[]>) - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.SphereAccumulator

addDetectedObjectsOverlay(ImagePlus, ArrayList<double[]>) - Method in class io.github.mianalysis.mia.process.houghtransform.transforms.AbstractTransform

addEdge(VHalfEdge) - Method in class signalprocesser.voronoi.representation.triangulation.VVertex

addEvent(VEvent) - Method in class signalprocesser.voronoi.eventqueue.EventQueue

addFileCondition(FileCondition) - Method in class io.github.mianalysis.mia.process.system.FileCrawler

addFolderCondition(FileCondition) - Method in class io.github.mianalysis.mia.process.system.FileCrawler

addImagePath(String) - Method in class io.github.mianalysis.mia.process.io.VOCWriter

addImageSize(ImagePlus) - Method in class io.github.mianalysis.mia.process.io.VOCWriter

addMeasure(double) - Method in class io.github.mianalysis.mia.process.math.CumStat

addMeasure(double, boolean) - Method in class io.github.mianalysis.mia.process.math.CumStat

addMeasure(double, double) - Method in class io.github.mianalysis.mia.process.math.CumStat

addMeasure(double, double, boolean) - Method in class io.github.mianalysis.mia.process.math.CumStat

addMeasures(double[]) - Method in class io.github.mianalysis.mia.process.math.CumStat

addMeasures(double[], double[]) - Method in class io.github.mianalysis.mia.process.math.CumStat

addMeasures(float[]) - Method in class io.github.mianalysis.mia.process.math.CumStat

addMeasures(float[], float[]) - Method in class io.github.mianalysis.mia.process.math.CumStat

addObject(String, String, boolean, boolean, int[][]) - Method in class io.github.mianalysis.mia.process.io.VOCWriter

addOther(String, String) - Method in class io.github.mianalysis.mia.process.io.VOCWriter

addPoints(int[], double, int[][]) - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.AbstractAccumulator

addPoints(int[], double, int[][]) - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.CircleAccumulator

addPoints(int[], double, int[][]) - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.LineAccumulator

addPoints(int[], double, int[][]) - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.RectangleAccumulator

addPoints(int[], double, int[][]) - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.SphereAccumulator

addRandomPoints(ArrayList<VPoint>, boolean, int, int, int, int) - Static method in class signalprocesser.voronoi.shapegeneration.ShapeGeneration

addValueToConfusionMatrix(ImageStack, int, int, int, int, int, int) - Method in class io.github.mianalysis.mia.process.analysis.TextureCalculator

ALL - Static variable in interface io.github.mianalysis.mia.process.imagej.ImageTiler.TileAxes

AngularPersistenceCalculator - Class in io.github.mianalysis.mia.process.analysis

AngularPersistenceCalculator() - Constructor for class io.github.mianalysis.mia.process.analysis.AngularPersistenceCalculator

area - Variable in class signalprocesser.voronoi.representation.boundaryproblem.voronoicell.VVoronoiCell

area - Variable in class signalprocesser.voronoi.representation.voronoicell.VVoronoiCell

AREA_NAME - Static variable in class io.github.mianalysis.mia.object.metadata.Metadata

ArrayFunc - Class in io.github.mianalysis.mia.process.math

ArrayFunc() - Constructor for class io.github.mianalysis.mia.process.math.ArrayFunc

arrayListToArray(ArrayList<Double>) - Static method in class io.github.mianalysis.mia.process.math.ArrayFunc

AutoLocalThreshold3D - Class in io.github.mianalysis.mia.process.imagej

Created by sc13967 on 14/11/2017.

AutoLocalThreshold3D() - Constructor for class io.github.mianalysis.mia.process.imagej.AutoLocalThreshold3D

B

b - Variable in class signalprocesser.voronoi.eventqueue.VSiteEvent

beginAlgorithm(Collection<VPoint>) - Method in class signalprocesser.voronoi.representation.boundaryproblem.BoundaryProblemRepresentation

beginAlgorithm(Collection<VPoint>) - Method in class signalprocesser.voronoi.representation.boundaryproblem.voronoicell.VoronoiCellRepresentation

beginAlgorithm(Collection<VPoint>) - Method in interface signalprocesser.voronoi.representation.RepresentationInterface

beginAlgorithm(Collection<VPoint>) - Method in class signalprocesser.voronoi.representation.simpletriangulation.SimpleTriangulationRepresentation

beginAlgorithm(Collection<VPoint>) - Method in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

beginAlgorithm(Collection<VPoint>) - Method in class signalprocesser.voronoi.representation.voronoicell.VoronoiCellRepresentation

beginAlgorithm(Collection<VPoint>) - Method in class signalprocesser.voronoi.VoronoiTest.TestRepresentationWrapper

BendingEnergy - Class in io.github.mianalysis.mia.process.activecontour.energies

Created by Stephen on 16/09/2016.

BendingEnergy(double) - Constructor for class io.github.mianalysis.mia.process.activecontour.energies.BendingEnergy

BERNSEN - Static variable in class io.github.mianalysis.mia.process.imagej.AutoLocalThreshold3D

BestVoronoiCells - Class in signalprocesser.voronoi.representation.voronoicell

BestVoronoiCells(int) - Constructor for class signalprocesser.voronoi.representation.voronoicell.BestVoronoiCells

BestVoronoiCells(int, Collection<VPoint>) - Constructor for class signalprocesser.voronoi.representation.voronoicell.BestVoronoiCells

BlackFire() - Static method in class io.github.mianalysis.mia.object.imagej.LUTs

BlackIce() - Static method in class io.github.mianalysis.mia.object.imagej.LUTs

BlackSpectrum() - Static method in class io.github.mianalysis.mia.object.imagej.LUTs

BlackThermal() - Static method in class io.github.mianalysis.mia.object.imagej.LUTs

BOTTOMLEFT - Static variable in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

BOTTOMRIGHT - Static variable in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

BoundaryProblemRepresentation - Class in signalprocesser.voronoi.representation.boundaryproblem

BoundaryProblemRepresentation() - Constructor for class signalprocesser.voronoi.representation.boundaryproblem.BoundaryProblemRepresentation

BOX_FONT - Static variable in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.debug.DebugTree

BOX_HEIGHT - Static variable in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.debug.DebugTree

BOX_WIDTH - Static variable in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.debug.DebugTree

BreakFixer - Class in io.github.mianalysis.mia.process.skeleton

BreakFixer() - Constructor for class io.github.mianalysis.mia.process.skeleton.BreakFixer

BresenhamLine - Class in io.github.mianalysis.mia.process.voxel

Implements Bresenham's line algorithm to draw a straight line between two points.

BresenhamLine() - Constructor for class io.github.mianalysis.mia.process.voxel.BresenhamLine

BresenhamRectangle - Class in io.github.mianalysis.mia.process.voxel

BresenhamRectangle() - Constructor for class io.github.mianalysis.mia.process.voxel.BresenhamRectangle

BSTStatusStructure - Class in signalprocesser.voronoi.statusstructure.binarysearchtreeimpl

BSTStatusStructure() - Constructor for class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.BSTStatusStructure

buildContour(int[], int[]) - Static method in class io.github.mianalysis.mia.process.activecontour.ContourInitialiser

buildGrid() - Method in class io.github.mianalysis.mia.process.activecontour.GridInitialiser

BytePixelArray - Class in io.github.mianalysis.mia.process.houghtransform.pixelarrays

Created by sc13967 on 12/01/2018.

BytePixelArray(byte[], int[]) - Constructor for class io.github.mianalysis.mia.process.houghtransform.pixelarrays.BytePixelArray

C

c - Variable in class signalprocesser.voronoi.eventqueue.VSiteEvent

CalcCutOff() - Constructor for class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation.CalcCutOff

calcParabolaConstants(double) - Method in class signalprocesser.voronoi.eventqueue.VSiteEvent

calculate(double[], double[], double[], int[]) - Method in class io.github.mianalysis.mia.process.analysis.AngularPersistenceCalculator

calculate(double[], double[], double[], int[]) - Method in class io.github.mianalysis.mia.process.analysis.CumulativePathLengthCalculator

calculate(double[], double[], double[], int[]) - Method in class io.github.mianalysis.mia.process.analysis.DirectionalityRatioCalculator

calculate(double[], double[], double[], int[]) - Method in class io.github.mianalysis.mia.process.analysis.EuclideanDistanceCalculator

calculate(double[], double[], double[], int[]) - Method in class io.github.mianalysis.mia.process.analysis.InstantaneousSpeedCalculator

calculate(double[], double[], double[], int[]) - Method in class io.github.mianalysis.mia.process.analysis.InstantaneousStepSizeCalculator

calculate(double[], double[], double[], int[]) - Method in interface io.github.mianalysis.mia.process.analysis.SpatialCalculator

calculate(double[], double[], double[], int[]) - Method in interface io.github.mianalysis.mia.process.analysis.SummaryCalculator

calculate(double[], double[], double[], int[]) - Method in class io.github.mianalysis.mia.process.analysis.TotalPathLengthCalculator

calculate(int[], double[]) - Method in class io.github.mianalysis.mia.process.analysis.InstantaneousVelocityCalculator

calculate(int[], double[], double[], double[]) - Static method in class io.github.mianalysis.mia.process.analysis.DirectionalPersistenceCalculator

calculate(int[], double[], double[], double[]) - Static method in class io.github.mianalysis.mia.process.analysis.MSDCalculator

calculate(ImagePlus) - Static method in class io.github.mianalysis.mia.process.analysis.IntensityCalculator

Deprecated.

calculate(ImagePlus, CumStat) - Static method in class io.github.mianalysis.mia.process.analysis.IntensityCalculator

Deprecated.

calculate(ImageStack) - Static method in class io.github.mianalysis.mia.process.analysis.IntensityCalculator

calculate(ImageStack, int, int, int) - Method in class io.github.mianalysis.mia.process.analysis.TextureCalculator

calculate(ImageStack, ImageStack) - Static method in class io.github.mianalysis.mia.process.analysis.IntensityCalculator

calculate(ImageStack, CoordinateSet) - Static method in class io.github.mianalysis.mia.process.analysis.IntensityCalculator

calculate(ImageStack, CoordinateSet, int, int, int) - Method in class io.github.mianalysis.mia.process.analysis.TextureCalculator

calculate(ImageStack, CumStat) - Static method in class io.github.mianalysis.mia.process.analysis.IntensityCalculator

calculate(ImageStack, CumStat, ImageStack) - Static method in class io.github.mianalysis.mia.process.analysis.IntensityCalculator

calculate(ImageStack, CumStat, CoordinateSet) - Static method in class io.github.mianalysis.mia.process.analysis.IntensityCalculator

calculate(Track) - Method in interface io.github.mianalysis.mia.process.analysis.SpatialCalculator

calculate(Track) - Method in interface io.github.mianalysis.mia.process.analysis.SummaryCalculator

calculate(Track, Tracks) - Method in class io.github.mianalysis.mia.process.analysis.NearestNeighbourCalculator

calculate(CumStat[], int[], double[], double[], double[]) - Static method in class io.github.mianalysis.mia.process.analysis.DirectionalPersistenceCalculator

calculate(TreeMap<Integer, CumStat>, int[], double[], double[], double[]) - Static method in class io.github.mianalysis.mia.process.analysis.MSDCalculator

calculateAreaOfShape(PathIterator) - Static method in class signalprocesser.voronoi.VoronoiShared

calculateAreaOfShape(Shape) - Static method in class signalprocesser.voronoi.VoronoiShared

calculateAreaOfShape(ArrayList<VPoint>) - Static method in class signalprocesser.voronoi.VoronoiShared

calculateAreaOfTriangle(double, double, double) - Static method in class signalprocesser.voronoi.representation.boundaryproblem.voronoicell.VVoronoiCell

calculateAreaOfTriangle(double, double, double) - Static method in class signalprocesser.voronoi.representation.voronoicell.VVoronoiCell

calculateAverageDistanceFromLC() - Method in class io.github.mianalysis.mia.process.analysis.LongestChordCalculator

calculateAveragePoint() - Method in class signalprocesser.voronoi.representation.triangulation.VCluster

calculateCenter(VSiteEvent, VSiteEvent, VSiteEvent) - Static method in class signalprocesser.voronoi.VoronoiShared

calculateContinuous(double[], double[], double[]) - Static method in class io.github.mianalysis.mia.process.analysis.DirectionalPersistenceCalculator

calculateCurvature() - Method in class io.github.mianalysis.mia.process.analysis.CurvatureCalculator

calculateCutOff(TriangulationRepresentation) - Method in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation.CalcCutOff

calculateLengthCutoff() - Method in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

calculateMeanCentroid(CoordinateSet) - Static method in class io.github.mianalysis.mia.process.analysis.CentroidCalculator

calculatePerimeterOfShape(ArrayList<VPoint>) - Static method in class signalprocesser.voronoi.VoronoiShared

CELLTYPE - Static variable in class io.github.mianalysis.mia.object.metadata.Metadata

CentroidCalculator - Class in io.github.mianalysis.mia.process.analysis

CentroidCalculator() - Constructor for class io.github.mianalysis.mia.process.analysis.CentroidCalculator

CHANNEL - Static variable in class io.github.mianalysis.mia.object.metadata.Metadata

CHANNEL - Static variable in interface io.github.mianalysis.mia.process.imagej.ImageTiler.TileAxes

checkPath(String) - Static method in class io.github.mianalysis.mia.process.system.FileCrawler

CircleAccumulator - Class in io.github.mianalysis.mia.process.houghtransform.accumulators

Created by sc13967 on 13/01/2018.

CircleAccumulator(int[][]) - Constructor for class io.github.mianalysis.mia.process.houghtransform.accumulators.CircleAccumulator

circleEvent(VLinkedNode, VLinkedNode, VLinkedNode, int, int) - Method in class signalprocesser.voronoi.representation.boundaryproblem.BoundaryProblemRepresentation

circleEvent(VLinkedNode, VLinkedNode, VLinkedNode, int, int) - Method in class signalprocesser.voronoi.representation.boundaryproblem.voronoicell.VoronoiCellRepresentation

circleEvent(VLinkedNode, VLinkedNode, VLinkedNode, int, int) - Method in interface signalprocesser.voronoi.representation.RepresentationInterface

circleEvent(VLinkedNode, VLinkedNode, VLinkedNode, int, int) - Method in class signalprocesser.voronoi.representation.simpletriangulation.SimpleTriangulationRepresentation

circleEvent(VLinkedNode, VLinkedNode, VLinkedNode, int, int) - Method in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

circleEvent(VLinkedNode, VLinkedNode, VLinkedNode, int, int) - Method in class signalprocesser.voronoi.representation.voronoicell.VoronoiCellRepresentation

circleEvent(VLinkedNode, VLinkedNode, VLinkedNode, int, int) - Method in class signalprocesser.voronoi.VoronoiTest.TestRepresentationWrapper

CircleTransform - Class in io.github.mianalysis.mia.process.houghtransform.transforms

Created by sc13967 on 12/01/2018.

CircleTransform(ImageProcessor, String[]) - Constructor for class io.github.mianalysis.mia.process.houghtransform.transforms.CircleTransform

clearConnectedVertexs() - Method in class signalprocesser.voronoi.representation.boundaryproblem.VVertex

clearEdges() - Method in class signalprocesser.voronoi.representation.triangulation.VVertex

CLOCKWISE - Static variable in class io.github.mianalysis.mia.process.activecontour.minimisers.GreedyMinimiser

cloneCollection(Collection) - Static method in class signalprocesser.shared.Reflect

cloneCollection(Collection, int) - Static method in class signalprocesser.shared.Reflect

cloneLeafNode() - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VLeafNode

cloneLinkedNode() - Method in class signalprocesser.voronoi.statusstructure.VLinkedNode

cloneObject(Object) - Static method in class signalprocesser.shared.Reflect

cloneObject(Object, int) - Static method in class signalprocesser.shared.Reflect

cloneVector(Vector) - Static method in class signalprocesser.shared.Reflect

cloneVector(Vector, int) - Static method in class signalprocesser.shared.Reflect

COL - Static variable in class io.github.mianalysis.mia.object.metadata.Metadata

CombingCorrector - Class in io.github.mianalysis.mia.process.imagej

CombingCorrector() - Constructor for class io.github.mianalysis.mia.process.imagej.CombingCorrector

CommaSeparatedStringInterpreter - Class in io.github.mianalysis.mia.process.string

CommaSeparatedStringInterpreter() - Constructor for class io.github.mianalysis.mia.process.string.CommaSeparatedStringInterpreter

COMMENT - Static variable in class io.github.mianalysis.mia.object.metadata.Metadata

concatenateArrays(String[], String[]) - Static method in class io.github.mianalysis.mia.process.math.ArrayFunc

construct(Metadata) - Method in class io.github.mianalysis.mia.object.metadata.CV7000FilenameExtractor

contains(int[], int) - Static method in class io.github.mianalysis.mia.process.math.ArrayFunc

contains(ArrayList<Integer>, int) - Static method in class io.github.mianalysis.mia.process.math.ArrayFunc

ContourInitialiser - Class in io.github.mianalysis.mia.process.activecontour

Created by sc13967 on 31/01/2017.

ContourInitialiser() - Constructor for class io.github.mianalysis.mia.process.activecontour.ContourInitialiser

CONTRAST - Static variable in class io.github.mianalysis.mia.process.imagej.AutoLocalThreshold3D

convert(double) - Static method in class io.github.mianalysis.mia.process.math.WavelengthToColorConverter

convertPointsToBoundaryProblemPoints(ArrayList<VPoint>) - Static method in class signalprocesser.voronoi.representation.RepresentationFactory

convertPointsToSimpleTriangulationPoints(ArrayList<VPoint>) - Static method in class signalprocesser.voronoi.representation.RepresentationFactory

convertPointsToTriangulationPoints(ArrayList<VPoint>) - Static method in class signalprocesser.voronoi.representation.RepresentationFactory

convertPointsToVoronoiCellPoints(ArrayList<VPoint>) - Static method in class signalprocesser.voronoi.representation.RepresentationFactory

convertPointsToVPoints(ArrayList<VPoint>) - Static method in class signalprocesser.voronoi.representation.RepresentationFactory

convertTo8bit(double) - Static method in class io.github.mianalysis.mia.process.math.WavelengthToColorConverter

correspondingRows(double[], double) - Static method in class io.github.mianalysis.mia.process.math.ArrayFunc

CountryData - Class in signalprocesser.voronoi.tools

CountryData() - Constructor for class signalprocesser.voronoi.tools.CountryData

CountryListModel - Class in signalprocesser.voronoi.tools

CountryListModel(JComboBox, ArrayList<String>) - Constructor for class signalprocesser.voronoi.tools.CountryListModel

CountryListModel.CountryListRender - Class in signalprocesser.voronoi.tools

CountryListRender() - Constructor for class signalprocesser.voronoi.tools.CountryListModel.CountryListRender

counts - Variable in class io.github.mianalysis.mia.process.houghtransform.accumulators.AbstractAccumulator

createArea(ArrayList<VPoint>) - Static method in class signalprocesser.voronoi.shapegeneration.ShapeGeneration

createBoundaryProblemRepresentation() - Static method in class signalprocesser.voronoi.representation.RepresentationFactory

createDefaultStatusStructure() - Static method in class signalprocesser.voronoi.statusstructure.AbstractStatusStructure

createPoint(int, int) - Method in class signalprocesser.voronoi.representation.AbstractRepresentation

createPoint(int, int) - Method in class signalprocesser.voronoi.representation.boundaryproblem.BoundaryProblemRepresentation

createPoint(int, int) - Method in class signalprocesser.voronoi.representation.boundaryproblem.voronoicell.VoronoiCellRepresentation

createPoint(int, int) - Method in class signalprocesser.voronoi.representation.simpletriangulation.SimpleTriangulationRepresentation

createPoint(int, int) - Method in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

createPoint(int, int) - Method in class signalprocesser.voronoi.representation.voronoicell.VoronoiCellRepresentation

createShape(Area) - Static method in class signalprocesser.voronoi.shapegeneration.ShapeGeneration

createShape(PathIterator) - Static method in class signalprocesser.voronoi.shapegeneration.ShapeGeneration

createShape(ArrayList<VPoint>) - Static method in class signalprocesser.voronoi.shapegeneration.ShapeGeneration

createShapeOutline(String, Rectangle, Font) - Static method in class signalprocesser.voronoi.shapegeneration.ShapeGeneration

createSimpleTriangulationRepresentation() - Static method in class signalprocesser.voronoi.representation.RepresentationFactory

createTestCase() - Method in class signalprocesser.voronoi.tools.TestSuite

createTriangulationRepresentation() - Static method in class signalprocesser.voronoi.representation.RepresentationFactory

createVoronoiCellRepresentation() - Static method in class signalprocesser.voronoi.representation.RepresentationFactory

CumStat - Class in io.github.mianalysis.mia.process.math

CumStat() - Constructor for class io.github.mianalysis.mia.process.math.CumStat

CumStat(double[]) - Constructor for class io.github.mianalysis.mia.process.math.CumStat

CumStat(double[], boolean) - Constructor for class io.github.mianalysis.mia.process.math.CumStat

CumStat(double[], double[]) - Constructor for class io.github.mianalysis.mia.process.math.CumStat

CumStat(double[], double[], boolean) - Constructor for class io.github.mianalysis.mia.process.math.CumStat

CumStat(float[]) - Constructor for class io.github.mianalysis.mia.process.math.CumStat

CumStat(float[], boolean) - Constructor for class io.github.mianalysis.mia.process.math.CumStat

CumStat(float[], double[]) - Constructor for class io.github.mianalysis.mia.process.math.CumStat

CumStat(float[], double[], boolean) - Constructor for class io.github.mianalysis.mia.process.math.CumStat

CumStat(Collection<Double>) - Constructor for class io.github.mianalysis.mia.process.math.CumStat

CumulativePathLengthCalculator - Class in io.github.mianalysis.mia.process.analysis

Created by Stephen on 15/04/2017.

CumulativePathLengthCalculator() - Constructor for class io.github.mianalysis.mia.process.analysis.CumulativePathLengthCalculator

CurvatureCalculator - Class in io.github.mianalysis.mia.process.analysis

Created by sc13967 on 26/01/2018.

CurvatureCalculator(ArrayList<Point<Double>>, boolean, boolean) - Constructor for class io.github.mianalysis.mia.process.analysis.CurvatureCalculator

CurvatureCalculator.FittingMethod - Enum in io.github.mianalysis.mia.process.analysis

CV1000FilenameExtractor - Class in io.github.mianalysis.mia.object.metadata

Extracts names in the format W1F001T0001Z00C1.tif Created by stephen on 30/04/2017.

CV1000FilenameExtractor() - Constructor for class io.github.mianalysis.mia.object.metadata.CV1000FilenameExtractor

CV1000FoldernameExtractor - Class in io.github.mianalysis.mia.object.metadata

Extractor for the Yokogawa CV1000 format (e.g.

CV1000FoldernameExtractor() - Constructor for class io.github.mianalysis.mia.object.metadata.CV1000FoldernameExtractor

CV7000FilenameExtractor - Class in io.github.mianalysis.mia.object.metadata

CV7000FilenameExtractor() - Constructor for class io.github.mianalysis.mia.object.metadata.CV7000FilenameExtractor

D

DAY - Static variable in class io.github.mianalysis.mia.object.metadata.Metadata

DebugTree - Class in signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.debug

DebugTree(Frame) - Constructor for class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.debug.DebugTree

DebugTree.TreePanel - Class in signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.debug

determineMSTUsingPrimsAlgorithm(VVertex) - Static method in class signalprocesser.voronoi.representation.triangulation.SharedMinimumSpanningTree

determineMSTUsingPrimsAlgorithm(VVertex, double, ArrayList<VCluster>) - Static method in class signalprocesser.voronoi.representation.triangulation.SharedMinimumSpanningTree

DirectionalityRatioCalculator - Class in io.github.mianalysis.mia.process.analysis

Created by Stephen on 15/04/2017.

DirectionalityRatioCalculator() - Constructor for class io.github.mianalysis.mia.process.analysis.DirectionalityRatioCalculator

DirectionalPersistenceCalculator - Class in io.github.mianalysis.mia.process.analysis

Calculates the direction autocorrelation.

DirectionalPersistenceCalculator() - Constructor for class io.github.mianalysis.mia.process.analysis.DirectionalPersistenceCalculator

distanceTo(VVertex) - Method in class signalprocesser.voronoi.representation.boundaryproblem.VVertex

distanceTo(VVertex) - Method in class signalprocesser.voronoi.representation.triangulation.VVertex

distanceTo(VPoint) - Method in class signalprocesser.voronoi.VPoint

DLinkedListStatusStructure - Class in signalprocesser.voronoi.statusstructure.doublelinkedlistimpl

Implementation *not* working

DLinkedListStatusStructure() - Constructor for class signalprocesser.voronoi.statusstructure.doublelinkedlistimpl.DLinkedListStatusStructure

drawNode(Graphics2D, VNode, int, int, int) - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.debug.DebugTree.TreePanel

drawOverlay(VertexCollection, ImagePlus) - Method in class io.github.mianalysis.mia.process.skeleton.SkeletonVisualiser

drawOverlay(NodeCollection, ImagePlus) - Method in class io.github.mianalysis.mia.process.activecontour.visualisation.GridOverlay

drawPath(LinkedHashSet<Vertex>, ImagePlus) - Method in class io.github.mianalysis.mia.process.skeleton.SkeletonVisualiser

E

EITHER_TYPE - Static variable in interface io.github.mianalysis.mia.process.system.FileTools.FileTypes

ElasticEnergy - Class in io.github.mianalysis.mia.process.activecontour.energies

Created by Stephen on 16/09/2016.

ElasticEnergy(double) - Constructor for class io.github.mianalysis.mia.process.activecontour.energies.ElasticEnergy

endAlgorithm(Collection<VPoint>, int, VLinkedNode) - Method in class signalprocesser.voronoi.representation.boundaryproblem.BoundaryProblemRepresentation

endAlgorithm(Collection<VPoint>, int, VLinkedNode) - Method in class signalprocesser.voronoi.representation.boundaryproblem.voronoicell.VoronoiCellRepresentation

endAlgorithm(Collection<VPoint>, int, VLinkedNode) - Method in interface signalprocesser.voronoi.representation.RepresentationInterface

endAlgorithm(Collection<VPoint>, int, VLinkedNode) - Method in class signalprocesser.voronoi.representation.simpletriangulation.SimpleTriangulationRepresentation

endAlgorithm(Collection<VPoint>, int, VLinkedNode) - Method in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

endAlgorithm(Collection<VPoint>, int, VLinkedNode) - Method in class signalprocesser.voronoi.representation.voronoicell.VoronoiCellRepresentation

endAlgorithm(Collection<VPoint>, int, VLinkedNode) - Method in class signalprocesser.voronoi.VoronoiTest.TestRepresentationWrapper

Energy - Class in io.github.mianalysis.mia.process.activecontour.energies

Created by Stephen on 16/09/2016.

Energy(double) - Constructor for class io.github.mianalysis.mia.process.activecontour.energies.Energy

EnergyCollection - Class in io.github.mianalysis.mia.process.activecontour.energies

Created by Stephen on 07/09/2016.

EnergyCollection() - Constructor for class io.github.mianalysis.mia.process.activecontour.energies.EnergyCollection

EuclideanDistanceCalculator - Class in io.github.mianalysis.mia.process.analysis

Created by steph on 15/04/2017.

EuclideanDistanceCalculator() - Constructor for class io.github.mianalysis.mia.process.analysis.EuclideanDistanceCalculator

evaluateGreedy(NodeCollection) - Method in class io.github.mianalysis.mia.process.activecontour.minimisers.GreedyMinimiser

evaluateGreedy(Vertex) - Method in class io.github.mianalysis.mia.process.activecontour.minimisers.GreedyMinimiser

EventQueue - Class in signalprocesser.voronoi.eventqueue

EventQueue() - Constructor for class signalprocesser.voronoi.eventqueue.EventQueue

EventQueue(Collection<VEvent>) - Constructor for class signalprocesser.voronoi.eventqueue.EventQueue

EXC_COMPLETE - Enum constant in enum io.github.mianalysis.mia.process.system.FileCondition.Mode

EXC_PARTIAL - Enum constant in enum io.github.mianalysis.mia.process.system.FileCondition.Mode

exec(ImagePlus, String, int, int, double, double, double, boolean) - Method in class io.github.mianalysis.mia.process.imagej.AutoLocalThreshold3D

extendRangeToEnd(int[], int) - Static method in class io.github.mianalysis.mia.process.string.CommaSeparatedStringInterpreter

EXTENSION - Static variable in class io.github.mianalysis.mia.object.metadata.Metadata

ExtensionMatchesString - Class in io.github.mianalysis.mia.process.system

Checks the input file against a list of acceptable extensions Created by Stephen on 24/10/2016.

ExtensionMatchesString(String) - Constructor for class io.github.mianalysis.mia.process.system.ExtensionMatchesString

ExtensionMatchesString(String[]) - Constructor for class io.github.mianalysis.mia.process.system.ExtensionMatchesString

ExtensionMatchesString(String[], FileCondition.Mode) - Constructor for class io.github.mianalysis.mia.process.system.ExtensionMatchesString

ExtensionMatchesString(String, FileCondition.Mode) - Constructor for class io.github.mianalysis.mia.process.system.ExtensionMatchesString

extract(Metadata, File) - Method in interface io.github.mianalysis.mia.object.metadata.FileExtractor

extract(Metadata, File) - Method in class io.github.mianalysis.mia.object.metadata.OperaFileExtractor

extract(Metadata, String) - Method in class io.github.mianalysis.mia.object.metadata.CV1000FilenameExtractor

extract(Metadata, String) - Method in class io.github.mianalysis.mia.object.metadata.CV1000FoldernameExtractor

extract(Metadata, String) - Method in class io.github.mianalysis.mia.object.metadata.CV7000FilenameExtractor

extract(Metadata, String) - Method in class io.github.mianalysis.mia.object.metadata.GenericExtractor

extract(Metadata, String) - Method in class io.github.mianalysis.mia.object.metadata.IncuCyteLongFilenameExtractor

extract(Metadata, String) - Method in class io.github.mianalysis.mia.object.metadata.IncuCyteShortFilenameExtractor

extract(Metadata, String) - Method in class io.github.mianalysis.mia.object.metadata.KeywordExtractor

extract(Metadata, String) - Method in interface io.github.mianalysis.mia.object.metadata.NameExtractor

extract(Metadata, String) - Method in class io.github.mianalysis.mia.object.metadata.OperaFilenameExtractor

extract(Metadata, String) - Method in class io.github.mianalysis.mia.object.metadata.OperaFoldernameExtractor

extract(Metadata, String, boolean) - Method in class io.github.mianalysis.mia.object.metadata.GenericExtractor

F

FIELD - Static variable in class io.github.mianalysis.mia.object.metadata.Metadata

FILE - Static variable in class io.github.mianalysis.mia.object.metadata.Metadata

FILE_TYPE - Static variable in interface io.github.mianalysis.mia.process.system.FileTools.FileTypes

FileCondition - Interface in io.github.mianalysis.mia.process.system

Created by sc13967 on 24/10/2016.

FileCondition.Mode - Enum in io.github.mianalysis.mia.process.system

FileCrawler - Class in io.github.mianalysis.mia.process.system

Created by Stephen on 16/10/2016.

FileCrawler(File) - Constructor for class io.github.mianalysis.mia.process.system.FileCrawler

FileExtractor - Interface in io.github.mianalysis.mia.object.metadata

Created by sc13967 on 20/07/2017.

FILENAME - Static variable in class io.github.mianalysis.mia.object.metadata.Metadata

FILEPATH - Static variable in class io.github.mianalysis.mia.object.metadata.Metadata

FileTools - Class in io.github.mianalysis.mia.process.system

FileTools() - Constructor for class io.github.mianalysis.mia.process.system.FileTools

FileTools.FileTypes - Interface in io.github.mianalysis.mia.process.system

findBest(Collection<VPoint>) - Method in class signalprocesser.voronoi.representation.voronoicell.BestVoronoiCells

firstValue(String) - Static method in class io.github.mianalysis.mia.process.string.CommaSeparatedStringInterpreter

fitGaussian2D(ImageProcessor, double[], double[][], int) - Static method in class io.github.mianalysis.mia.process.imagej.GaussianFitter

FloatPixelArray - Class in io.github.mianalysis.mia.process.houghtransform.pixelarrays

Created by sc13967 on 12/01/2018.

FloatPixelArray(float[], int[]) - Constructor for class io.github.mianalysis.mia.process.houghtransform.pixelarrays.FloatPixelArray

folder - Variable in class io.github.mianalysis.mia.process.system.FileCrawler

Folder - Class in io.github.mianalysis.mia.process.system

Created by Stephen on 16/10/2016.

Folder(File, Folder) - Constructor for class io.github.mianalysis.mia.process.system.Folder

FOLDER_TYPE - Static variable in interface io.github.mianalysis.mia.process.system.FileTools.FileTypes

formatHumanReadable(String) - Static method in class signalprocesser.voronoi.tools.CountryListModel

FRAME_HEIGHT - Static variable in class signalprocesser.voronoi.VoronoiTest

FRAME_WIDTH - Static variable in class signalprocesser.voronoi.VoronoiTest

G

GAP_BETWEENBOXES - Static variable in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.debug.DebugTree

GaussianDistribution2D - Class in io.github.mianalysis.mia.process.math

Created by sc13967 on 27/03/2018.

GaussianDistribution2D(double, double, double, double, double, double, double) - Constructor for class io.github.mianalysis.mia.process.math.GaussianDistribution2D

GaussianFitter - Class in io.github.mianalysis.mia.process.imagej

Created by sc13967 on 05/06/2017.

GaussianFitter() - Constructor for class io.github.mianalysis.mia.process.imagej.GaussianFitter

GeneralOps - Class in io.github.mianalysis.mia.process.math

Created by sc13967 on 16/08/2016.

GeneralOps() - Constructor for class io.github.mianalysis.mia.process.math.GeneralOps

generate(String, String, String, String) - Static method in class io.github.mianalysis.mia.object.metadata.IncuCyteShortFilenameExtractor

generateVoronoi(RepresentationInterface, Collection<VPoint>) - Static method in class signalprocesser.voronoi.VoronoiAlgorithm

generateVoronoi(RepresentationInterface, Collection<VPoint>, Graphics2D, VPoint, int) - Static method in class signalprocesser.voronoi.VoronoiAlgorithm

GenericExtractor - Class in io.github.mianalysis.mia.object.metadata

GenericExtractor(String, String[]) - Constructor for class io.github.mianalysis.mia.object.metadata.GenericExtractor

getAbsoluteRange(ImagePlus, int) - Static method in class io.github.mianalysis.mia.process.imagej.IntensityMinMax

getAbsoluteRange(ImagePlus, CoordinateSet, int, int) - Static method in class io.github.mianalysis.mia.process.imagej.IntensityMinMax

getAccumulatorAsImage() - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.AbstractAccumulator

getAccumulatorAsImage() - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.CircleAccumulator

getAccumulatorAsImage() - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.LineAccumulator

getAccumulatorAsImage() - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.RectangleAccumulator

getAccumulatorAsImage() - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.SphereAccumulator

getAccumulatorAsImage() - Method in class io.github.mianalysis.mia.process.houghtransform.transforms.AbstractTransform

getActionNumber() - Method in class io.github.mianalysis.mia.object.metadata.Metadata

getAllValidFilesInFolder() - Method in class io.github.mianalysis.mia.process.system.FileCrawler

getAndRemoveFirstEvent() - Method in class signalprocesser.voronoi.eventqueue.EventQueue

getAngleWeight() - Method in class io.github.mianalysis.mia.process.skeleton.BreakFixer

getAreaOfCell() - Method in class signalprocesser.voronoi.representation.boundaryproblem.voronoicell.VVoronoiCell

getAreaOfCell() - Method in class signalprocesser.voronoi.representation.voronoicell.VVoronoiCell

getASM() - Method in class io.github.mianalysis.mia.process.analysis.TextureCalculator

Calculates the angular second moment from the co-occurance matrix

getAsString(String) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

getAverage(int) - Method in class signalprocesser.voronoi.tools.TestSuite.ValueCollector

getAverageArea() - Method in class signalprocesser.voronoi.representation.voronoicell.BestVoronoiCells

getAverageDistanceMoved() - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.NodeCollection

getAverageX() - Method in class signalprocesser.voronoi.representation.voronoicell.BestVoronoiCells

getAverageY() - Method in class signalprocesser.voronoi.representation.voronoicell.BestVoronoiCells

getBestArea(int) - Method in class signalprocesser.voronoi.representation.voronoicell.BestVoronoiCells

getBestCell(int) - Method in class signalprocesser.voronoi.representation.voronoicell.BestVoronoiCells

getBestStored() - Method in class signalprocesser.voronoi.representation.voronoicell.BestVoronoiCells

getBottomNeighbour() - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

getBranchPoints() - Method in class io.github.mianalysis.mia.process.skeleton.Skeleton

getCalcCutOff() - Method in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

getCaption(int) - Method in class signalprocesser.voronoi.tools.TestSuite.ValueCollector

getCelltype() - Method in class io.github.mianalysis.mia.object.metadata.Metadata

getCenterY() - Method in class signalprocesser.voronoi.eventqueue.VCircleEvent

getChannel() - Method in class io.github.mianalysis.mia.object.metadata.Metadata

getCircle() - Method in class io.github.mianalysis.mia.process.voxel.MidpointCircle

getCircleEvents() - Method in class signalprocesser.voronoi.statusstructure.VLinkedNode

getCol() - Method in class io.github.mianalysis.mia.object.metadata.Metadata

getColumnClass(int) - Method in class signalprocesser.voronoi.tools.TestSuite.TestCaseTableModel

getColumnCount() - Method in class signalprocesser.voronoi.tools.TestSuite.TestCaseTableModel

getColumnName(int) - Method in class signalprocesser.voronoi.tools.TestSuite.TestCaseTableModel

getComment() - Method in class io.github.mianalysis.mia.object.metadata.Metadata

getConnectedEdgeString() - Method in class signalprocesser.voronoi.representation.triangulation.VVertex

getConnectedVertex() - Method in class signalprocesser.voronoi.representation.triangulation.VHalfEdge

getConnectedVertexs() - Method in class signalprocesser.voronoi.representation.boundaryproblem.VVertex

getConnectedVertexString() - Method in class signalprocesser.voronoi.representation.boundaryproblem.VVertex

getConnectedVertexString() - Method in class signalprocesser.voronoi.representation.triangulation.VVertex

getContrast() - Method in class io.github.mianalysis.mia.process.analysis.TextureCalculator

getCoOccurrenceMatrix() - Method in class io.github.mianalysis.mia.process.analysis.TextureCalculator

getCoord(int) - Method in class io.github.mianalysis.mia.process.math.Indexer

getCorrelation() - Method in class io.github.mianalysis.mia.process.analysis.TextureCalculator

getCountryData(String, Rectangle) - Static method in class signalprocesser.voronoi.tools.CountryData

getCountryList() - Static method in class signalprocesser.voronoi.tools.CountryData

getCurrentDepth() - Method in class io.github.mianalysis.mia.process.system.FileCrawler

Depth of the folder relative to the root folder.

getCurrentFileNumber() - Method in class io.github.mianalysis.mia.process.system.Folder

getCurrentFolderAsFile() - Method in class io.github.mianalysis.mia.process.system.FileCrawler

getCurrentFolderAsFolder() - Method in class io.github.mianalysis.mia.process.system.FileCrawler

getCurrentFolderNumber() - Method in class io.github.mianalysis.mia.process.system.Folder

getCurvature() - Method in class io.github.mianalysis.mia.process.analysis.CurvatureCalculator

getDay() - Method in class io.github.mianalysis.mia.object.metadata.Metadata

getDepth() - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VInternalNode

getDim() - Method in class io.github.mianalysis.mia.process.math.Indexer

getDistanceMoved() - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

getDistanceWeight() - Method in class io.github.mianalysis.mia.process.skeleton.BreakFixer

getEdge(int) - Method in class signalprocesser.voronoi.representation.triangulation.VVertex

getEdge(VVertex) - Method in class signalprocesser.voronoi.representation.triangulation.VVertex

getEdges() - Method in class signalprocesser.voronoi.representation.triangulation.VVertex

getElementAt(int) - Method in class signalprocesser.voronoi.tools.CountryListModel

getEndAngleRads(ArrayList<int[]>) - Static method in class io.github.mianalysis.mia.process.skeleton.BreakFixer

getEndPoints() - Method in class io.github.mianalysis.mia.process.skeleton.Skeleton

getEndWeight() - Method in class io.github.mianalysis.mia.process.skeleton.BreakFixer

getEnergy() - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

getEnergy(Vertex) - Method in class io.github.mianalysis.mia.process.activecontour.energies.BendingEnergy

getEnergy(Vertex) - Method in class io.github.mianalysis.mia.process.activecontour.energies.ElasticEnergy

getEnergy(Vertex) - Method in class io.github.mianalysis.mia.process.activecontour.energies.Energy

getEnergy(Vertex) - Method in class io.github.mianalysis.mia.process.activecontour.energies.EnergyCollection

getEnergy(Vertex) - Method in class io.github.mianalysis.mia.process.activecontour.energies.ImageEnergy

getEnergy(Vertex) - Method in class io.github.mianalysis.mia.process.activecontour.energies.ImageGradientEnergy

getEnergy(Vertex) - Method in class io.github.mianalysis.mia.process.activecontour.energies.PathEnergy

getEntropy() - Method in class io.github.mianalysis.mia.process.analysis.TextureCalculator

getExt() - Method in class io.github.mianalysis.mia.object.metadata.Metadata

getExts() - Method in class io.github.mianalysis.mia.process.system.ExtensionMatchesString

getfield(Object, String) - Static method in class signalprocesser.shared.Reflect

getField() - Method in class io.github.mianalysis.mia.object.metadata.Metadata

getFile() - Method in class io.github.mianalysis.mia.object.metadata.Metadata

getFilename() - Method in class io.github.mianalysis.mia.object.metadata.Metadata

getFilepath() - Method in class io.github.mianalysis.mia.object.metadata.Metadata

getFiles() - Method in class io.github.mianalysis.mia.process.system.Folder

getFirstCommonParent(VLeafNode) - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VLeafNode

getFirstEvent() - Method in class signalprocesser.voronoi.eventqueue.EventQueue

getFittingMethod() - Method in class io.github.mianalysis.mia.process.analysis.CurvatureCalculator

getFixEdges() - Method in class io.github.mianalysis.mia.process.activecontour.GridInitialiser

getFixedX() - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

getFixedY() - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

getFolderAsFile() - Method in class io.github.mianalysis.mia.process.system.Folder

getFolders() - Method in class io.github.mianalysis.mia.process.system.Folder

getGenericName(Metadata, String) - Static method in class io.github.mianalysis.mia.process.system.FileTools

getGenericNames(Metadata, String) - Static method in class io.github.mianalysis.mia.process.system.FileTools

getHeading(int) - Method in class signalprocesser.voronoi.tools.TestSuite.ValueCollector

getHeadNode() - Method in class signalprocesser.voronoi.statusstructure.AbstractStatusStructure

getHeadNode() - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.BSTStatusStructure

getHeadNode() - Method in class signalprocesser.voronoi.statusstructure.doublelinkedlistimpl.DLinkedListStatusStructure

getHour() - Method in class io.github.mianalysis.mia.object.metadata.Metadata

getID() - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

getID() - Method in class signalprocesser.voronoi.eventqueue.VEvent

getIgnoreCase() - Method in class io.github.mianalysis.mia.process.system.FileCrawler

getIncludeSubFolders() - Method in class io.github.mianalysis.mia.process.system.FileCrawler

getIndex(int[]) - Method in class io.github.mianalysis.mia.process.math.Indexer

getIndexer() - Method in class io.github.mianalysis.mia.process.analysis.TextureCalculator

getIndexer() - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.AbstractAccumulator

getinteger(Object, String) - Static method in class signalprocesser.shared.Reflect

getIntegerLengthCutoff() - Method in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

getIntersectWithNext(int) - Method in class signalprocesser.voronoi.statusstructure.VLinkedNode

getKeyword() - Method in class io.github.mianalysis.mia.object.metadata.Metadata

getLargestScorePixelIndex() - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.AbstractAccumulator

Returns the Indexer index for the pixel in the Accumulator with the largest score.

getLargestScorePixelIndex() - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.LineAccumulator

Returns the Indexer index for the pixel in the Accumulator with the largest score.

getLargestScorePixelIndex() - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.RectangleAccumulator

Returns the Indexer index for the pixel in the Accumulator with the largest score.

getLC() - Method in class io.github.mianalysis.mia.process.analysis.LongestChordCalculator

getLCLength() - Method in class io.github.mianalysis.mia.process.analysis.LongestChordCalculator

getLeft() - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VInternalNode

getLeftNeighbour() - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

getLength() - Method in class io.github.mianalysis.mia.process.math.Indexer

getLength() - Method in class signalprocesser.voronoi.representation.triangulation.VHalfEdge

getLine(int, int, int, int) - Static method in class io.github.mianalysis.mia.process.voxel.BresenhamLine

getLinearFit(int[], double[], int) - Static method in class io.github.mianalysis.mia.process.analysis.MSDCalculator

getLinearFit(TreeMap<Integer, CumStat>, int) - Static method in class io.github.mianalysis.mia.process.analysis.MSDCalculator

getLoessAccuracy() - Method in class io.github.mianalysis.mia.process.analysis.CurvatureCalculator

getLoessBandwidth() - Method in class io.github.mianalysis.mia.process.analysis.CurvatureCalculator

getLoessIterations() - Method in class io.github.mianalysis.mia.process.analysis.CurvatureCalculator

getLongestPath() - Method in class io.github.mianalysis.mia.process.skeleton.Skeleton

getLowerThreshold() - Method in class io.github.mianalysis.mia.process.imagej.AutoLocalThreshold3D

getMag() - Method in class io.github.mianalysis.mia.object.metadata.Metadata

getMax() - Method in class io.github.mianalysis.mia.process.math.CumStat

getMaximumPointIntensity() - Method in class io.github.mianalysis.mia.process.analysis.SpotIntensity

getMaxLength() - Method in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

getMaxLengthOfMinimumSpanningTree() - Method in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

getMaxLengthOfSmallestTriangleEdge() - Method in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

getMean() - Method in class io.github.mianalysis.mia.process.math.CumStat

getMeanPointIntensity() - Method in class io.github.mianalysis.mia.process.analysis.SpotIntensity

getMin() - Method in class io.github.mianalysis.mia.object.metadata.Metadata

getMin() - Method in class io.github.mianalysis.mia.process.math.CumStat

getMinimumPointIntensity() - Method in class io.github.mianalysis.mia.process.analysis.SpotIntensity

getMinIncrement(double[]) - Static method in class io.github.mianalysis.mia.process.math.ArrayFunc

getMinLength() - Method in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

getMode() - Method in class io.github.mianalysis.mia.process.system.ExtensionMatchesString

getMode() - Method in class io.github.mianalysis.mia.process.system.NameContainsPattern

getMode() - Method in class io.github.mianalysis.mia.process.system.NameContainsString

getMode() - Method in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

getMonth() - Method in class io.github.mianalysis.mia.object.metadata.Metadata

getN() - Method in class io.github.mianalysis.mia.process.math.CumStat

getName() - Method in class io.github.mianalysis.mia.object.metadata.CV1000FilenameExtractor

getName() - Method in class io.github.mianalysis.mia.object.metadata.CV1000FoldernameExtractor

getName() - Method in class io.github.mianalysis.mia.object.metadata.CV7000FilenameExtractor

getName() - Method in interface io.github.mianalysis.mia.object.metadata.FileExtractor

getName() - Method in class io.github.mianalysis.mia.object.metadata.GenericExtractor

getName() - Method in class io.github.mianalysis.mia.object.metadata.IncuCyteLongFilenameExtractor

getName() - Method in class io.github.mianalysis.mia.object.metadata.IncuCyteShortFilenameExtractor

getName() - Method in class io.github.mianalysis.mia.object.metadata.KeywordExtractor

getName() - Method in interface io.github.mianalysis.mia.object.metadata.NameExtractor

getName() - Method in class io.github.mianalysis.mia.object.metadata.OperaFileExtractor

getName() - Method in class io.github.mianalysis.mia.object.metadata.OperaFilenameExtractor

getName() - Method in class io.github.mianalysis.mia.object.metadata.OperaFoldernameExtractor

getNCols() - Method in class io.github.mianalysis.mia.process.activecontour.GridInitialiser

getNext() - Method in class signalprocesser.voronoi.representation.boundaryproblem.voronoicell.VHalfEdge

getNext() - Method in class signalprocesser.voronoi.representation.voronoicell.VHalfEdge

getNext() - Method in class signalprocesser.voronoi.statusstructure.VLinkedNode

getNextConnectedEdge(int) - Method in class signalprocesser.voronoi.representation.boundaryproblem.VVertex

getNextConnectedEdge(VVertex) - Method in class signalprocesser.voronoi.representation.boundaryproblem.VVertex

getNextConnectedVertex(int) - Method in class signalprocesser.voronoi.representation.boundaryproblem.VVertex

getNextFile() - Method in class io.github.mianalysis.mia.process.system.Folder

getNextFileInFolder() - Method in class io.github.mianalysis.mia.process.system.FileCrawler

getNextFolder() - Method in class io.github.mianalysis.mia.process.system.Folder

getNextValidFileInFolder() - Method in class io.github.mianalysis.mia.process.system.FileCrawler

getNextValidFileInStructure() - Method in class io.github.mianalysis.mia.process.system.FileCrawler

getNNeighbours() - Method in class io.github.mianalysis.mia.process.analysis.CurvatureCalculator

getNObjects(int, int) - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.AbstractAccumulator

getNObjects(int, int) - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.CircleAccumulator

getNObjects(int, int) - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.LineAccumulator

getNObjects(int, int) - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.RectangleAccumulator

getNObjects(int, int) - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.SphereAccumulator

getNObjects(int, int) - Method in class io.github.mianalysis.mia.process.houghtransform.transforms.AbstractTransform

getNodeAboveSiteEvent(int, int) - Method in class signalprocesser.voronoi.statusstructure.AbstractStatusStructure

getNodeAboveSiteEvent(int, int) - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.BSTStatusStructure

getNodeAboveSiteEvent(int, int) - Method in class signalprocesser.voronoi.statusstructure.doublelinkedlistimpl.DLinkedListStatusStructure

getNodeAboveSiteEvent(VSiteEvent, int) - Method in class signalprocesser.voronoi.statusstructure.AbstractStatusStructure

getNodeCoordinates() - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.NodeCollection

Returns the coordinates of all nodes in the NodeCollection.

getNPointsMeasured() - Method in class io.github.mianalysis.mia.process.analysis.SpotIntensity

getNRows() - Method in class io.github.mianalysis.mia.process.activecontour.GridInitialiser

getnThreads() - Method in class io.github.mianalysis.mia.process.houghtransform.transforms.AbstractTransform

getNumberOfFiles() - Method in class io.github.mianalysis.mia.process.system.Folder

getNumberOfFolders() - Method in class io.github.mianalysis.mia.process.system.Folder

getNumberOfValidFilesInStructure() - Method in class io.github.mianalysis.mia.process.system.FileCrawler

getNumberOfValidFoldersInStructure() - Method in class io.github.mianalysis.mia.process.system.FileCrawler

getobject(Object, String) - Static method in class signalprocesser.shared.Reflect

getObjects(double, int) - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.AbstractAccumulator

getObjects(double, int) - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.CircleAccumulator

getObjects(double, int) - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.LineAccumulator

getObjects(double, int) - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.RectangleAccumulator

getObjects(double, int) - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.SphereAccumulator

getObjects(double, int) - Method in class io.github.mianalysis.mia.process.houghtransform.transforms.AbstractTransform

getParameters() - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.AbstractAccumulator

getParent() - Method in class io.github.mianalysis.mia.process.system.Folder

getParent() - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VInternalNode

getParent() - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VLeafNode

getParent() - Method in interface signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VNode

getPattern() - Method in class io.github.mianalysis.mia.object.metadata.CV1000FilenameExtractor

getPattern() - Method in class io.github.mianalysis.mia.object.metadata.CV1000FoldernameExtractor

getPattern() - Method in class io.github.mianalysis.mia.object.metadata.CV7000FilenameExtractor

getPattern() - Method in class io.github.mianalysis.mia.object.metadata.GenericExtractor

getPattern() - Method in class io.github.mianalysis.mia.object.metadata.IncuCyteLongFilenameExtractor

getPattern() - Method in class io.github.mianalysis.mia.object.metadata.IncuCyteShortFilenameExtractor

getPattern() - Method in interface io.github.mianalysis.mia.object.metadata.NameExtractor

getPattern() - Method in class io.github.mianalysis.mia.object.metadata.OperaFilenameExtractor

getPattern() - Method in class io.github.mianalysis.mia.object.metadata.OperaFoldernameExtractor

getPattern() - Method in class io.github.mianalysis.mia.process.system.NameContainsPattern

getPixels(ImagePlus, int) - Static method in class io.github.mianalysis.mia.process.imagej.IntensityMinMax

getPixels(ImagePlus, CoordinateSet, int, int) - Static method in class io.github.mianalysis.mia.process.imagej.IntensityMinMax

getPixelValue(int) - Method in class io.github.mianalysis.mia.process.houghtransform.pixelarrays.BytePixelArray

getPixelValue(int) - Method in class io.github.mianalysis.mia.process.houghtransform.pixelarrays.FloatPixelArray

getPixelValue(int) - Method in class io.github.mianalysis.mia.process.houghtransform.pixelarrays.PixelArray

getPixelValue(int) - Method in class io.github.mianalysis.mia.process.houghtransform.pixelarrays.ShortPixelArray

getPixelValue(int[]) - Method in class io.github.mianalysis.mia.process.houghtransform.pixelarrays.PixelArray

getPlateManufacturer() - Method in class io.github.mianalysis.mia.object.metadata.Metadata

getPlateModel() - Method in class io.github.mianalysis.mia.object.metadata.Metadata

getPlateName() - Method in class io.github.mianalysis.mia.object.metadata.Metadata

getPoint() - Method in class signalprocesser.voronoi.eventqueue.VSiteEvent

getPointsFormingOutterBoundary() - Method in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

getPreferredSize() - Method in class signalprocesser.voronoi.tools.CountryListModel.CountryListRender

getPrev() - Method in class signalprocesser.voronoi.representation.boundaryproblem.voronoicell.VHalfEdge

getPrev() - Method in class signalprocesser.voronoi.representation.voronoicell.VHalfEdge

getPrev() - Method in class signalprocesser.voronoi.statusstructure.VLinkedNode

getRandomNode() - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.NodeCollection

getRectangle(int, int, int) - Static method in class io.github.mianalysis.mia.process.voxel.BresenhamRectangle

getRight() - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VInternalNode

getRightNeighbour() - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

getROI() - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.NodeCollection

getRootFolderAsFile() - Method in class io.github.mianalysis.mia.process.system.FileCrawler

getRootFolderAsFolder() - Method in class io.github.mianalysis.mia.process.system.FileCrawler

getRootNode() - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.BSTStatusStructure

getRow() - Method in class io.github.mianalysis.mia.object.metadata.Metadata

getRowCount() - Method in class signalprocesser.voronoi.tools.TestSuite.TestCaseTableModel

getSampleN() - Method in class io.github.mianalysis.mia.process.activecontour.minimisers.GreedyMinimiser

getSec() - Method in class io.github.mianalysis.mia.object.metadata.Metadata

getSelectedCountry() - Method in class signalprocesser.voronoi.tools.CountryListModel

getSelectedItem() - Method in class signalprocesser.voronoi.tools.CountryListModel

getSeriesName() - Method in class io.github.mianalysis.mia.object.metadata.Metadata

getSeriesNumber() - Method in class io.github.mianalysis.mia.object.metadata.Metadata

getSize() - Method in class signalprocesser.voronoi.tools.CountryListModel.CountryListRender

getSize() - Method in class signalprocesser.voronoi.tools.CountryListModel

getSpecial() - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

getSpecialNode(int) - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.NodeCollection

getSphere() - Method in class io.github.mianalysis.mia.process.voxel.AbstractSphere

getSpline() - Method in class io.github.mianalysis.mia.process.analysis.CurvatureCalculator

getStandardDeviation(int) - Method in class signalprocesser.voronoi.tools.TestSuite.ValueCollector

getStd() - Method in class io.github.mianalysis.mia.process.math.CumStat

getStd(int) - Method in class io.github.mianalysis.mia.process.math.CumStat

getStdevPointIntensity() - Method in class io.github.mianalysis.mia.process.analysis.SpotIntensity

getstring(Object, String) - Static method in class signalprocesser.shared.Reflect

getSubArray(double[], int[]) - Static method in class io.github.mianalysis.mia.process.math.ArrayFunc

getSum() - Method in class io.github.mianalysis.mia.process.math.CumStat

getSumPointIntensity() - Method in class io.github.mianalysis.mia.process.analysis.SpotIntensity

getTestStr() - Method in class io.github.mianalysis.mia.process.system.NameContainsString

getTimelineNumber() - Method in class io.github.mianalysis.mia.object.metadata.Metadata

getTimepoint() - Method in class io.github.mianalysis.mia.object.metadata.Metadata

getTopNeighbour() - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

getTotalAreaOfBest() - Method in class signalprocesser.voronoi.representation.voronoicell.BestVoronoiCells

getUnits() - Method in class io.github.mianalysis.mia.object.metadata.Metadata

getUseActionWildcard() - Method in class io.github.mianalysis.mia.object.metadata.CV7000FilenameExtractor

getValueAt(int, int) - Method in class signalprocesser.voronoi.tools.TestSuite.TestCaseTableModel

getValues(double, double) - Method in class io.github.mianalysis.mia.process.math.GaussianDistribution2D

getVar() - Method in class io.github.mianalysis.mia.process.math.CumStat

getVar(int) - Method in class io.github.mianalysis.mia.process.math.CumStat

getWeight() - Method in class io.github.mianalysis.mia.process.activecontour.energies.Energy

getWeight() - Method in class io.github.mianalysis.mia.process.math.CumStat

getWeightedChannelRangeFast(ImagePlus, int, double, double) - Static method in class io.github.mianalysis.mia.process.imagej.IntensityMinMax

getWeightedChannelRangeFast(ImagePlus, CoordinateSet, int, int, double, double) - Static method in class io.github.mianalysis.mia.process.imagej.IntensityMinMax

getWeightedChannelRangePrecise(ImagePlus, int, double, double) - Static method in class io.github.mianalysis.mia.process.imagej.IntensityMinMax

getWeightedChannelRangePrecise(ImagePlus, CoordinateSet, int, int, double, double) - Static method in class io.github.mianalysis.mia.process.imagej.IntensityMinMax

getWell() - Method in class io.github.mianalysis.mia.object.metadata.Metadata

getWidth() - Method in class io.github.mianalysis.mia.process.activecontour.minimisers.GreedyMinimiser

getX() - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

getX() - Method in class io.github.mianalysis.mia.process.skeleton.Skeleton

getX() - Method in class io.github.mianalysis.mia.process.voxel.AbstractSphere

getX() - Method in class signalprocesser.voronoi.eventqueue.VCircleEvent

getX() - Method in class signalprocesser.voronoi.eventqueue.VEvent

getX() - Method in class signalprocesser.voronoi.eventqueue.VSiteEvent

getX() - Method in class signalprocesser.voronoi.representation.triangulation.VHalfEdge

getXCircle() - Method in class io.github.mianalysis.mia.process.voxel.MidpointCircle

getXCircleFill() - Method in class io.github.mianalysis.mia.process.voxel.MidpointCircle

getXHalf() - Method in class io.github.mianalysis.mia.process.voxel.MidpointCircle

getXHalfFill() - Method in class io.github.mianalysis.mia.process.voxel.MidpointCircle

getXMin() - Method in class io.github.mianalysis.mia.process.activecontour.GridInitialiser

getXOct() - Method in class io.github.mianalysis.mia.process.voxel.MidpointCircle

getXQuad() - Method in class io.github.mianalysis.mia.process.voxel.MidpointCircle

getXQuadFill() - Method in class io.github.mianalysis.mia.process.voxel.MidpointCircle

getXSpace() - Method in class io.github.mianalysis.mia.process.activecontour.GridInitialiser

getXYOrientationRads() - Method in class io.github.mianalysis.mia.process.analysis.LongestChordCalculator

getXYScaledZ(double) - Method in class io.github.mianalysis.mia.process.analysis.LongestChordCalculator

getY() - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

getY() - Method in class io.github.mianalysis.mia.process.skeleton.Skeleton

getY() - Method in class io.github.mianalysis.mia.process.voxel.AbstractSphere

getY() - Method in class signalprocesser.voronoi.eventqueue.VCircleEvent

getY() - Method in class signalprocesser.voronoi.eventqueue.VEvent

getY() - Method in class signalprocesser.voronoi.eventqueue.VSiteEvent

getY() - Method in class signalprocesser.voronoi.representation.triangulation.VHalfEdge

getYCircle() - Method in class io.github.mianalysis.mia.process.voxel.MidpointCircle

getYCircleFill() - Method in class io.github.mianalysis.mia.process.voxel.MidpointCircle

getYear() - Method in class io.github.mianalysis.mia.object.metadata.Metadata

getYHalf() - Method in class io.github.mianalysis.mia.process.voxel.MidpointCircle

getYHalfFill() - Method in class io.github.mianalysis.mia.process.voxel.MidpointCircle

getYMin() - Method in class io.github.mianalysis.mia.process.activecontour.GridInitialiser

getYOct() - Method in class io.github.mianalysis.mia.process.voxel.MidpointCircle

getYQuad() - Method in class io.github.mianalysis.mia.process.voxel.MidpointCircle

getYQuadFill() - Method in class io.github.mianalysis.mia.process.voxel.MidpointCircle

getYSpace() - Method in class io.github.mianalysis.mia.process.activecontour.GridInitialiser

getYValueOfParabola(double) - Method in class signalprocesser.voronoi.eventqueue.VSiteEvent

getYValueOfParabola(int) - Method in class signalprocesser.voronoi.eventqueue.VSiteEvent

getZ() - Method in class io.github.mianalysis.mia.object.metadata.Metadata

getZ() - Method in class io.github.mianalysis.mia.process.skeleton.Skeleton

getZ() - Method in class io.github.mianalysis.mia.process.voxel.AbstractSphere

goToNextFolder() - Method in class io.github.mianalysis.mia.process.system.FileCrawler

Sets the current folder as the next folder in the structure.

goToNextValidFolder() - Method in class io.github.mianalysis.mia.process.system.FileCrawler

GreedyMinimiser - Class in io.github.mianalysis.mia.process.activecontour.minimisers

Created by Stephen on 16/09/2016.

GreedyMinimiser(EnergyCollection) - Constructor for class io.github.mianalysis.mia.process.activecontour.minimisers.GreedyMinimiser

Grey() - Static method in class io.github.mianalysis.mia.object.imagej.LUTs

GreyFire() - Static method in class io.github.mianalysis.mia.object.imagej.LUTs

GridInitialiser - Class in io.github.mianalysis.mia.process.activecontour

Created by Stephen on 07/09/2016.

GridInitialiser() - Constructor for class io.github.mianalysis.mia.process.activecontour.GridInitialiser

GridInitialiser(int, int) - Constructor for class io.github.mianalysis.mia.process.activecontour.GridInitialiser

GridOverlay - Class in io.github.mianalysis.mia.process.activecontour.visualisation

Created by Stephen on 08/09/2016.

GridOverlay() - Constructor for class io.github.mianalysis.mia.process.activecontour.visualisation.GridOverlay

H

halfedge - Variable in class signalprocesser.voronoi.representation.boundaryproblem.voronoicell.VVoronoiCell

halfedge - Variable in class signalprocesser.voronoi.representation.voronoicell.VVoronoiCell

halfedge_in - Variable in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VInternalNode

halfedge_out - Variable in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VInternalNode

hasCircleEvents() - Method in class signalprocesser.voronoi.statusstructure.VLinkedNode

hasEdges() - Method in class signalprocesser.voronoi.representation.triangulation.VVertex

hasMoreFiles() - Method in class io.github.mianalysis.mia.process.system.Folder

hasMoreFilesInFolder() - Method in class io.github.mianalysis.mia.process.system.FileCrawler

hasMoreFolders() - Method in class io.github.mianalysis.mia.process.system.Folder

hasMoreFoldersInFolder() - Method in class io.github.mianalysis.mia.process.system.FileCrawler

hasStandardDeviation(int) - Method in class signalprocesser.voronoi.tools.TestSuite.ValueCollector

height - Variable in class io.github.mianalysis.mia.process.houghtransform.transforms.LineTransform

HiLo() - Static method in class io.github.mianalysis.mia.object.imagej.LUTs

HOUR - Static variable in class io.github.mianalysis.mia.object.metadata.Metadata

I

Ice() - Static method in class io.github.mianalysis.mia.object.imagej.LUTs

id - Variable in class signalprocesser.voronoi.eventqueue.VEvent

id - Variable in class signalprocesser.voronoi.representation.boundaryproblem.VVertex

id - Variable in class signalprocesser.voronoi.representation.triangulation.VVertex

id - Variable in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VInternalNode

id - Variable in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VLeafNode

ImageEnergy - Class in io.github.mianalysis.mia.process.activecontour.energies

Created by Stephen on 16/09/2016.

ImageEnergy(double, double[][]) - Constructor for class io.github.mianalysis.mia.process.activecontour.energies.ImageEnergy

ImageEnergy(double, ImagePlus) - Constructor for class io.github.mianalysis.mia.process.activecontour.energies.ImageEnergy

ImageGradientEnergy - Class in io.github.mianalysis.mia.process.activecontour.energies

Created by Stephen on 16/09/2016.

ImageGradientEnergy(double, double[][], double[][]) - Constructor for class io.github.mianalysis.mia.process.activecontour.energies.ImageGradientEnergy

ImageGradientEnergy(double, ImagePlus, ImagePlus) - Constructor for class io.github.mianalysis.mia.process.activecontour.energies.ImageGradientEnergy

ImageTiler - Class in io.github.mianalysis.mia.process.imagej

ImageTiler() - Constructor for class io.github.mianalysis.mia.process.imagej.ImageTiler

ImageTiler.TileAxes - Interface in io.github.mianalysis.mia.process.imagej

INC_COMPLETE - Enum constant in enum io.github.mianalysis.mia.process.system.FileCondition.Mode

INC_PARTIAL - Enum constant in enum io.github.mianalysis.mia.process.system.FileCondition.Mode

incrementedNumbers(double, double) - Static method in class io.github.mianalysis.mia.process.math.ArrayFunc

incrementedNumbers(int, int) - Static method in class io.github.mianalysis.mia.process.math.ArrayFunc

IncuCyteLongFilenameExtractor - Class in io.github.mianalysis.mia.object.metadata

Created by steph on 30/04/2017.

IncuCyteLongFilenameExtractor() - Constructor for class io.github.mianalysis.mia.object.metadata.IncuCyteLongFilenameExtractor

IncuCyteShortFilenameExtractor - Class in io.github.mianalysis.mia.object.metadata

Created by steph on 30/04/2017.

IncuCyteShortFilenameExtractor() - Constructor for class io.github.mianalysis.mia.object.metadata.IncuCyteShortFilenameExtractor

INDEX_FILE - Static variable in class signalprocesser.voronoi.tools.CountryData

indexer - Variable in class io.github.mianalysis.mia.process.houghtransform.accumulators.AbstractAccumulator

Indexer - Class in io.github.mianalysis.mia.process.math

Multidimensional indexing Created by sc13967 on 15/08/2016.

Indexer(int[]) - Constructor for class io.github.mianalysis.mia.process.math.Indexer

Indexer(int, int) - Constructor for class io.github.mianalysis.mia.process.math.Indexer

Indexer(int, int, int) - Constructor for class io.github.mianalysis.mia.process.math.Indexer

insertMetadataValues(String) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

insertNode(VLinkedNode, VSiteEvent) - Method in class signalprocesser.voronoi.statusstructure.AbstractStatusStructure

insertNode(VLinkedNode, VSiteEvent) - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.BSTStatusStructure

insertNode(VLinkedNode, VSiteEvent) - Method in class signalprocesser.voronoi.statusstructure.doublelinkedlistimpl.DLinkedListStatusStructure

inSphere(int, int, int, int) - Static method in class io.github.mianalysis.mia.process.voxel.AbstractSphere

InstantaneousSpeedCalculator - Class in io.github.mianalysis.mia.process.analysis

Created by Stephen on 15/04/2017.

InstantaneousSpeedCalculator() - Constructor for class io.github.mianalysis.mia.process.analysis.InstantaneousSpeedCalculator

InstantaneousStepSizeCalculator - Class in io.github.mianalysis.mia.process.analysis

Created by Stephen on 15/04/2017.

InstantaneousStepSizeCalculator() - Constructor for class io.github.mianalysis.mia.process.analysis.InstantaneousStepSizeCalculator

InstantaneousVelocityCalculator - Class in io.github.mianalysis.mia.process.analysis

Created by sc13967 on 18/04/2018.

InstantaneousVelocityCalculator() - Constructor for class io.github.mianalysis.mia.process.analysis.InstantaneousVelocityCalculator

IntensityCalculator - Class in io.github.mianalysis.mia.process.analysis

Created by sc13967 on 12/05/2017.

IntensityCalculator() - Constructor for class io.github.mianalysis.mia.process.analysis.IntensityCalculator

IntensityMinMax - Class in io.github.mianalysis.mia.process.imagej

Created by Stephen on 15/04/2017.

IntensityMinMax() - Constructor for class io.github.mianalysis.mia.process.imagej.IntensityMinMax

interpretIntegers(String, boolean, int) - Static method in class io.github.mianalysis.mia.process.string.CommaSeparatedStringInterpreter

INVALID_AREA - Static variable in class signalprocesser.voronoi.representation.boundaryproblem.voronoicell.VVoronoiCell

INVALID_AREA - Static variable in class signalprocesser.voronoi.representation.voronoicell.VVoronoiCell

io.github.mianalysis.mia.object.imagej - package io.github.mianalysis.mia.object.imagej

io.github.mianalysis.mia.object.metadata - package io.github.mianalysis.mia.object.metadata

io.github.mianalysis.mia.process.activecontour - package io.github.mianalysis.mia.process.activecontour

io.github.mianalysis.mia.process.activecontour.energies - package io.github.mianalysis.mia.process.activecontour.energies

io.github.mianalysis.mia.process.activecontour.minimisers - package io.github.mianalysis.mia.process.activecontour.minimisers

io.github.mianalysis.mia.process.activecontour.physicalmodel - package io.github.mianalysis.mia.process.activecontour.physicalmodel

io.github.mianalysis.mia.process.activecontour.visualisation - package io.github.mianalysis.mia.process.activecontour.visualisation

io.github.mianalysis.mia.process.analysis - package io.github.mianalysis.mia.process.analysis

io.github.mianalysis.mia.process.houghtransform.accumulators - package io.github.mianalysis.mia.process.houghtransform.accumulators

io.github.mianalysis.mia.process.houghtransform.pixelarrays - package io.github.mianalysis.mia.process.houghtransform.pixelarrays

io.github.mianalysis.mia.process.houghtransform.transforms - package io.github.mianalysis.mia.process.houghtransform.transforms

io.github.mianalysis.mia.process.imagej - package io.github.mianalysis.mia.process.imagej

io.github.mianalysis.mia.process.io - package io.github.mianalysis.mia.process.io

io.github.mianalysis.mia.process.math - package io.github.mianalysis.mia.process.math

io.github.mianalysis.mia.process.skeleton - package io.github.mianalysis.mia.process.skeleton

io.github.mianalysis.mia.process.string - package io.github.mianalysis.mia.process.string

io.github.mianalysis.mia.process.system - package io.github.mianalysis.mia.process.system

io.github.mianalysis.mia.process.voxel - package io.github.mianalysis.mia.process.voxel

isCaption(int) - Method in class signalprocesser.voronoi.tools.TestSuite.ValueCollector

isCircleEvent() - Method in class signalprocesser.voronoi.eventqueue.VCircleEvent

isCircleEvent() - Method in class signalprocesser.voronoi.eventqueue.VEvent

isCircleEvent() - Method in class signalprocesser.voronoi.eventqueue.VSiteEvent

isConnectedTo(VVertex) - Method in class signalprocesser.voronoi.representation.triangulation.VVertex

isdeleted - Variable in class signalprocesser.voronoi.representation.boundaryproblem.VHalfEdge

isEventQueueEmpty() - Method in class signalprocesser.voronoi.eventqueue.EventQueue

isInternalNode() - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VInternalNode

isInternalNode() - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VLeafNode

isInternalNode() - Method in interface signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VNode

isInternalNode() - Method in class signalprocesser.voronoi.statusstructure.VLinkedNode

isLeafNode() - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VInternalNode

isLeafNode() - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VLeafNode

isLeafNode() - Method in interface signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VNode

isLeafNode() - Method in class signalprocesser.voronoi.statusstructure.VLinkedNode

isOuterEdge() - Method in class signalprocesser.voronoi.representation.triangulation.VHalfEdge

isSiteEvent() - Method in class signalprocesser.voronoi.eventqueue.VCircleEvent

isSiteEvent() - Method in class signalprocesser.voronoi.eventqueue.VEvent

isSiteEvent() - Method in class signalprocesser.voronoi.eventqueue.VSiteEvent

isSpecial() - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

isStatusStructureEmpty() - Method in class signalprocesser.voronoi.statusstructure.AbstractStatusStructure

isStatusStructureEmpty() - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.BSTStatusStructure

isStatusStructureEmpty() - Method in class signalprocesser.voronoi.statusstructure.doublelinkedlistimpl.DLinkedListStatusStructure

isValue(int) - Method in class signalprocesser.voronoi.tools.TestSuite.ValueCollector

iterator() - Method in class io.github.mianalysis.mia.process.activecontour.energies.EnergyCollection

J

JCollapsiblePanel - Class in signalprocesser.shared

JCollapsiblePanel() - Constructor for class signalprocesser.shared.JCollapsiblePanel

JCollapsiblePanel(LayoutManager) - Constructor for class signalprocesser.shared.JCollapsiblePanel

Jet() - Static method in class io.github.mianalysis.mia.object.imagej.LUTs

K

KEYWORD - Static variable in class io.github.mianalysis.mia.object.metadata.Metadata

KeywordExtractor - Class in io.github.mianalysis.mia.object.metadata

Created by sc13967 on 07/02/2018.

KeywordExtractor(String) - Constructor for class io.github.mianalysis.mia.object.metadata.KeywordExtractor

L

leafnode - Variable in class signalprocesser.voronoi.eventqueue.VCircleEvent

length() - Method in class io.github.mianalysis.mia.process.houghtransform.pixelarrays.BytePixelArray

length() - Method in class io.github.mianalysis.mia.process.houghtransform.pixelarrays.FloatPixelArray

length() - Method in class io.github.mianalysis.mia.process.houghtransform.pixelarrays.PixelArray

length() - Method in class io.github.mianalysis.mia.process.houghtransform.pixelarrays.ShortPixelArray

LineAccumulator - Class in io.github.mianalysis.mia.process.houghtransform.accumulators

LineAccumulator(int[][]) - Constructor for class io.github.mianalysis.mia.process.houghtransform.accumulators.LineAccumulator

LineTransform - Class in io.github.mianalysis.mia.process.houghtransform.transforms

Created by sc13967 on 05/02/2025.

LineTransform(ImageProcessor, String[]) - Constructor for class io.github.mianalysis.mia.process.houghtransform.transforms.LineTransform

LOESS - Enum constant in enum io.github.mianalysis.mia.process.analysis.CurvatureCalculator.FittingMethod

LongestChordCalculator - Class in io.github.mianalysis.mia.process.analysis

Created by sc13967 on 20/06/2018.

LongestChordCalculator(CoordinateSet, double, double) - Constructor for class io.github.mianalysis.mia.process.analysis.LongestChordCalculator

LUTs - Class in io.github.mianalysis.mia.object.imagej

Created by Stephen on 19/08/2016.

LUTs() - Constructor for class io.github.mianalysis.mia.object.imagej.LUTs

M

MAGNIFICATION - Static variable in class io.github.mianalysis.mia.object.metadata.Metadata

max(int[]) - Static method in class io.github.mianalysis.mia.process.math.ArrayFunc

MAX_EDGES_TO_REMOVE - Static variable in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

MEAN - Static variable in class io.github.mianalysis.mia.process.imagej.AutoLocalThreshold3D

MEDIAN - Static variable in class io.github.mianalysis.mia.process.imagej.AutoLocalThreshold3D

Metadata - Class in io.github.mianalysis.mia.object.metadata

High-content result structure as an abstract class, which is extended on an experiment-by experiment basis Created by sc13967 on 25/10/2016.

Metadata() - Constructor for class io.github.mianalysis.mia.object.metadata.Metadata

MidpointCircle - Class in io.github.mianalysis.mia.process.voxel

MidpointCircle(int) - Constructor for class io.github.mianalysis.mia.process.voxel.MidpointCircle

migrateobj(Object, Class, Object) - Static method in class signalprocesser.shared.Reflect

MIN_ANGLE_TO_ALLOW - Static variable in class signalprocesser.voronoi.representation.boundaryproblem.BoundaryProblemRepresentation

MINUTE - Static variable in class io.github.mianalysis.mia.object.metadata.Metadata

MODE_DETERMINE_CLUSTERS - Static variable in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

MODE_DETERMINE_MINSPANNINGTREE - Static variable in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

MODE_GETSTATS_EXCLUDINGMSTSTATS - Static variable in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

MODE_REDUCE_OUTER_BOUNDARIES - Static variable in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

MONTH - Static variable in class io.github.mianalysis.mia.object.metadata.Metadata

mouseClicked(MouseEvent) - Method in class signalprocesser.shared.JCollapsiblePanel

mouseClicked(MouseEvent) - Method in class signalprocesser.voronoi.VoronoiTest.SignalPanel

mouseDragged(MouseEvent) - Method in class signalprocesser.voronoi.VoronoiTest.SignalPanel

mouseEntered(MouseEvent) - Method in class signalprocesser.shared.JCollapsiblePanel

mouseEntered(MouseEvent) - Method in class signalprocesser.voronoi.VoronoiTest.SignalPanel

mouseExited(MouseEvent) - Method in class signalprocesser.shared.JCollapsiblePanel

mouseExited(MouseEvent) - Method in class signalprocesser.voronoi.VoronoiTest.SignalPanel

mouseMoved(MouseEvent) - Method in class signalprocesser.voronoi.VoronoiTest.SignalPanel

mousePressed(MouseEvent) - Method in class signalprocesser.shared.JCollapsiblePanel

mousePressed(MouseEvent) - Method in class signalprocesser.voronoi.VoronoiTest.SignalPanel

mouseReleased(MouseEvent) - Method in class signalprocesser.shared.JCollapsiblePanel

mouseReleased(MouseEvent) - Method in class signalprocesser.voronoi.VoronoiTest.SignalPanel

MSDCalculator - Class in io.github.mianalysis.mia.process.analysis

Created by steph on 15/04/2017.

MSDCalculator() - Constructor for class io.github.mianalysis.mia.process.analysis.MSDCalculator

N

NameContainsPattern - Class in io.github.mianalysis.mia.process.system

Created by sc13967 on 24/10/2016.

NameContainsPattern(Pattern) - Constructor for class io.github.mianalysis.mia.process.system.NameContainsPattern

NameContainsPattern(Pattern[]) - Constructor for class io.github.mianalysis.mia.process.system.NameContainsPattern

NameContainsPattern(Pattern[], FileCondition.Mode) - Constructor for class io.github.mianalysis.mia.process.system.NameContainsPattern

NameContainsPattern(Pattern, FileCondition.Mode) - Constructor for class io.github.mianalysis.mia.process.system.NameContainsPattern

NameContainsString - Class in io.github.mianalysis.mia.process.system

Checks the input file against a list of acceptable extensions Created by sc13967 on 24/10/2016.

NameContainsString(String) - Constructor for class io.github.mianalysis.mia.process.system.NameContainsString

NameContainsString(String[]) - Constructor for class io.github.mianalysis.mia.process.system.NameContainsString

NameContainsString(String[], FileCondition.Mode) - Constructor for class io.github.mianalysis.mia.process.system.NameContainsString

NameContainsString(String, FileCondition.Mode) - Constructor for class io.github.mianalysis.mia.process.system.NameContainsString

NameExtractor - Interface in io.github.mianalysis.mia.object.metadata

Created by steph on 30/04/2017.

NearestNeighbourCalculator - Class in io.github.mianalysis.mia.process.analysis

Created by sc13967 on 22/01/2018.

NearestNeighbourCalculator() - Constructor for class io.github.mianalysis.mia.process.analysis.NearestNeighbourCalculator

newInstance(Class) - Static method in class signalprocesser.shared.Reflect

newInstance(Object) - Static method in class signalprocesser.shared.Reflect

newValue(int, double) - Method in class signalprocesser.voronoi.tools.TestSuite.ValueCollector

newValue(int, int) - Method in class signalprocesser.voronoi.tools.TestSuite.ValueCollector

newValue(int, String) - Method in class signalprocesser.voronoi.tools.TestSuite.ValueCollector

next - Variable in class signalprocesser.voronoi.representation.triangulation.VHalfEdge

NO_AREA_CALCULATED - Static variable in class signalprocesser.voronoi.representation.boundaryproblem.voronoicell.VVoronoiCell

NO_AREA_CALCULATED - Static variable in class signalprocesser.voronoi.representation.voronoicell.VVoronoiCell

NodeCollection - Class in io.github.mianalysis.mia.process.activecontour.physicalmodel

Created by Stephen on 07/09/2016.

NodeCollection() - Constructor for class io.github.mianalysis.mia.process.activecontour.physicalmodel.NodeCollection

normaliseScores() - Method in class io.github.mianalysis.mia.process.houghtransform.accumulators.AbstractAccumulator

normaliseScores() - Method in class io.github.mianalysis.mia.process.houghtransform.transforms.AbstractTransform

Normalises scores to the number of points that contribute to that position.

O

onShellSixWay(int, int, int, int) - Static method in class io.github.mianalysis.mia.process.voxel.SphereShell

onShellTwentySixWay(int, int, int, int) - Static method in class io.github.mianalysis.mia.process.voxel.SphereShell

OperaFileExtractor - Class in io.github.mianalysis.mia.object.metadata

Created by sc13967 on 20/07/2017.

OperaFileExtractor() - Constructor for class io.github.mianalysis.mia.object.metadata.OperaFileExtractor

OperaFilenameExtractor - Class in io.github.mianalysis.mia.object.metadata

Created by sc13967 on 18/07/2017.

OperaFilenameExtractor() - Constructor for class io.github.mianalysis.mia.object.metadata.OperaFilenameExtractor

OperaFoldernameExtractor - Class in io.github.mianalysis.mia.object.metadata

Created by sc13967 on 18/07/2017.

OperaFoldernameExtractor() - Constructor for class io.github.mianalysis.mia.object.metadata.OperaFoldernameExtractor

OUTER_VERTEXNUMBER - Static variable in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

P

p1 - Variable in class signalprocesser.voronoi.representation.simpletriangulation.VTriangle

p2 - Variable in class signalprocesser.voronoi.representation.simpletriangulation.VTriangle

p3 - Variable in class signalprocesser.voronoi.representation.simpletriangulation.VTriangle

padAlignArray(double[], double[], double[], double) - Static method in class io.github.mianalysis.mia.process.math.ArrayFunc

padArray(double[], int, double) - Static method in class io.github.mianalysis.mia.process.math.ArrayFunc

paint(Graphics) - Method in class signalprocesser.shared.JCollapsiblePanel

paint(Graphics2D) - Method in class signalprocesser.voronoi.representation.AbstractRepresentation

paint(Graphics2D) - Method in class signalprocesser.voronoi.representation.boundaryproblem.BoundaryProblemRepresentation

paint(Graphics2D) - Method in class signalprocesser.voronoi.representation.boundaryproblem.voronoicell.VoronoiCellRepresentation

paint(Graphics2D) - Method in class signalprocesser.voronoi.representation.simpletriangulation.SimpleTriangulationRepresentation

paint(Graphics2D) - Method in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

paint(Graphics2D) - Method in class signalprocesser.voronoi.representation.voronoicell.VoronoiCellRepresentation

paintComponent(Graphics) - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.debug.DebugTree.TreePanel

paintComponent(Graphics) - Method in class signalprocesser.voronoi.VoronoiTest.SignalPanel

parameters - Variable in class io.github.mianalysis.mia.process.houghtransform.accumulators.AbstractAccumulator

parent - Variable in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VInternalNode

parent - Variable in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VLeafNode

ParentContainsString - Class in io.github.mianalysis.mia.process.system

Checks the input file against a list of acceptable extensions Created by sc13967 on 24/10/2016.

ParentContainsString(String) - Constructor for class io.github.mianalysis.mia.process.system.ParentContainsString

ParentContainsString(String[]) - Constructor for class io.github.mianalysis.mia.process.system.ParentContainsString

ParentContainsString(String[], FileCondition.Mode) - Constructor for class io.github.mianalysis.mia.process.system.ParentContainsString

ParentContainsString(String, FileCondition.Mode) - Constructor for class io.github.mianalysis.mia.process.system.ParentContainsString

PATH_TO_COUNTRYDATA - Static variable in class signalprocesser.voronoi.tools.CountryData

PathEnergy - Class in io.github.mianalysis.mia.process.activecontour.energies

Created by sc13967 on 23/09/2016.

PathEnergy(double, double[][]) - Constructor for class io.github.mianalysis.mia.process.activecontour.energies.PathEnergy

PathEnergy(double, ImagePlus) - Constructor for class io.github.mianalysis.mia.process.activecontour.energies.PathEnergy

PATTERN_COORDLINE - Static variable in class signalprocesser.voronoi.tools.CountryData

PHANSALKAR - Static variable in class io.github.mianalysis.mia.process.imagej.AutoLocalThreshold3D

Physics() - Static method in class io.github.mianalysis.mia.object.imagej.LUTs

PixelArray - Class in io.github.mianalysis.mia.process.houghtransform.pixelarrays

Created by sc13967 on 12/01/2018.

PixelArray(int[]) - Constructor for class io.github.mianalysis.mia.process.houghtransform.pixelarrays.PixelArray

pixels - Variable in class io.github.mianalysis.mia.process.houghtransform.transforms.AbstractTransform

PLATE_MANUFACTURER - Static variable in class io.github.mianalysis.mia.object.metadata.Metadata

PLATE_MODEL - Static variable in class io.github.mianalysis.mia.object.metadata.Metadata

PLATE_NAME - Static variable in class io.github.mianalysis.mia.object.metadata.Metadata

POINT_SIZE - Static variable in class signalprocesser.voronoi.VoronoiTest

POPULATION - Static variable in class io.github.mianalysis.mia.process.math.CumStat

ppdist(double[], double[]) - Static method in class io.github.mianalysis.mia.process.math.GeneralOps

print(Graphics2D, VSiteEvent, int) - Method in class signalprocesser.voronoi.statusstructure.AbstractStatusStructure

printContents() - Method in class io.github.mianalysis.mia.process.system.Folder

printFiles() - Method in class io.github.mianalysis.mia.process.system.Folder

printFolders() - Method in class io.github.mianalysis.mia.process.system.Folder

printParameters() - Method in class io.github.mianalysis.mia.object.metadata.Metadata

process(ImageProcessor, int, int, double, boolean) - Method in class io.github.mianalysis.mia.process.skeleton.BreakFixer

process(ImageProcessor, int, int, double, boolean, double, double, double) - Static method in class io.github.mianalysis.mia.process.skeleton.BreakFixer

PROCESS_FAST - Static variable in class io.github.mianalysis.mia.process.imagej.IntensityMinMax

PROCESS_PRECISE - Static variable in class io.github.mianalysis.mia.process.imagej.IntensityMinMax

putKeyword(String) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

R

random - Static variable in class io.github.mianalysis.mia.object.imagej.LUTs

Random(boolean) - Static method in class io.github.mianalysis.mia.object.imagej.LUTs

Random(boolean, boolean) - Static method in class io.github.mianalysis.mia.object.imagej.LUTs

RANDOM - Static variable in class io.github.mianalysis.mia.process.activecontour.minimisers.GreedyMinimiser

randomVibrant - Static variable in class io.github.mianalysis.mia.object.imagej.LUTs

RandomVibrant(boolean) - Static method in class io.github.mianalysis.mia.object.imagej.LUTs

RandomVibrant(boolean, boolean) - Static method in class io.github.mianalysis.mia.object.imagej.LUTs

RectangleAccumulator - Class in io.github.mianalysis.mia.process.houghtransform.accumulators

RectangleAccumulator(int[][]) - Constructor for class io.github.mianalysis.mia.process.houghtransform.accumulators.RectangleAccumulator

Constructor for Accumulator object.

RectangleTransform - Class in io.github.mianalysis.mia.process.houghtransform.transforms

Created by sc13967 on 12/01/2018.

RectangleTransform(ImageProcessor, String[]) - Constructor for class io.github.mianalysis.mia.process.houghtransform.transforms.RectangleTransform

Reflect - Class in signalprocesser.shared

Reflect() - Constructor for class signalprocesser.shared.Reflect

remove(Energy) - Method in class io.github.mianalysis.mia.process.activecontour.energies.EnergyCollection

remove(Object) - Method in class io.github.mianalysis.mia.process.skeleton.Skeleton

removeCircleEvents(EventQueue) - Method in class signalprocesser.voronoi.statusstructure.VLinkedNode

removeEdge(VHalfEdge) - Method in class signalprocesser.voronoi.representation.triangulation.VVertex

removeEdgesInOrderFromOuterBoundary(VHalfEdge, int) - Static method in class signalprocesser.voronoi.representation.triangulation.SharedEdgeRemoval

removeEndRanges(String, int) - Static method in class io.github.mianalysis.mia.process.string.CommaSeparatedStringInterpreter

removeEvent(VEvent) - Method in class signalprocesser.voronoi.eventqueue.EventQueue

removeInterval(String) - Static method in class io.github.mianalysis.mia.process.string.CommaSeparatedStringInterpreter

removeNode(EventQueue, VLinkedNode) - Method in class signalprocesser.voronoi.statusstructure.AbstractStatusStructure

removeNode(EventQueue, VLinkedNode) - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.BSTStatusStructure

removeNode(EventQueue, VLinkedNode) - Method in class signalprocesser.voronoi.statusstructure.doublelinkedlistimpl.DLinkedListStatusStructure

RepresentationFactory - Class in signalprocesser.voronoi.representation

RepresentationInterface - Interface in signalprocesser.voronoi.representation

reset() - Method in class signalprocesser.voronoi.tools.TestSuite.ValueCollector

resetArea() - Method in class signalprocesser.voronoi.representation.boundaryproblem.voronoicell.VVoronoiCell

resetArea() - Method in class signalprocesser.voronoi.representation.voronoicell.VVoronoiCell

resetConfusionMatrix() - Method in class io.github.mianalysis.mia.process.analysis.TextureCalculator

resetCurrentFileNumber() - Method in class io.github.mianalysis.mia.process.system.Folder

resetCurrentFolderNumber() - Method in class io.github.mianalysis.mia.process.system.Folder

resetIterator() - Method in class io.github.mianalysis.mia.process.system.FileCrawler

RIGHTDOWN - Static variable in class io.github.mianalysis.mia.process.activecontour.minimisers.GreedyMinimiser

rootFolder - Variable in class io.github.mianalysis.mia.process.system.FileCrawler

ROW - Static variable in class io.github.mianalysis.mia.object.metadata.Metadata

run() - Method in class io.github.mianalysis.mia.process.houghtransform.transforms.AbstractTransform

Performs the Hough Transform on the image passed to the constructor.

run() - Method in class io.github.mianalysis.mia.process.houghtransform.transforms.CircleTransform

run() - Method in class io.github.mianalysis.mia.process.houghtransform.transforms.LineTransform

run() - Method in class io.github.mianalysis.mia.process.houghtransform.transforms.RectangleTransform

run() - Method in class io.github.mianalysis.mia.process.houghtransform.transforms.SphereTransform

run(ImagePlus, boolean) - Static method in class io.github.mianalysis.mia.process.imagej.IntensityMinMax

run(ImagePlus, boolean, double, double, int) - Static method in class io.github.mianalysis.mia.process.imagej.IntensityMinMax

run(ImagePlus, int, boolean) - Static method in class io.github.mianalysis.mia.process.imagej.CombingCorrector

run(String) - Method in class io.github.mianalysis.mia.process.imagej.AutoLocalThreshold3D

runTestSeries(JProgressBar, TestSuite.TestCase, int, int, File, int) - Method in class signalprocesser.voronoi.tools.TestSuite.RunTestSeries

RunTestSeries() - Constructor for class signalprocesser.voronoi.tools.TestSuite.RunTestSeries

S

SAMPLE - Static variable in class io.github.mianalysis.mia.process.math.CumStat

SAVE_FILE - Static variable in class signalprocesser.voronoi.VoronoiTest

scanFolders() - Method in class io.github.mianalysis.mia.process.system.FileCrawler

Runs through all folders, listing files and folder

SECOND - Static variable in class io.github.mianalysis.mia.object.metadata.Metadata

SERIES_NAME - Static variable in class io.github.mianalysis.mia.object.metadata.Metadata

SERIES_NUMBER - Static variable in class io.github.mianalysis.mia.object.metadata.Metadata

setActionNumber(int) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

setAngleWeight(double) - Method in class io.github.mianalysis.mia.process.skeleton.BreakFixer

setBottomNeighbour(Vertex) - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

setCalcCutOff(TriangulationRepresentation.CalcCutOff) - Method in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

setCelltype(String) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

setCenterY(int) - Method in class signalprocesser.voronoi.eventqueue.VCircleEvent

setChannel(int) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

setCol(int) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

setCollapsed(boolean) - Method in class signalprocesser.shared.JCollapsiblePanel

setComment(String) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

setDay(int) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

setDepthForRootNode() - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VInternalNode

setDetermineClustersMode() - Method in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

setDetermineMinSpanningTreeMode() - Method in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

setDistanceMoved(double) - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

setDistanceMoved(double, double, double, double) - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

setDistanceWeight(double) - Method in class io.github.mianalysis.mia.process.skeleton.BreakFixer

setEndWeight(double) - Method in class io.github.mianalysis.mia.process.skeleton.BreakFixer

setEnergy(double) - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

setExt(String) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

setfield(Object, String, Object) - Static method in class signalprocesser.shared.Reflect

setfield(Object, String, Object, String) - Static method in class signalprocesser.shared.Reflect

setField(int) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

setFile(File) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

setFilename(String) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

setFilepath(String) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

setFittingMethod(CurvatureCalculator.FittingMethod) - Method in class io.github.mianalysis.mia.process.analysis.CurvatureCalculator

setFixEdges(boolean) - Method in class io.github.mianalysis.mia.process.activecontour.GridInitialiser

setFixedX(boolean) - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.NodeCollection

setFixedX(boolean) - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

setFixedY(boolean) - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.NodeCollection

setFixedY(boolean) - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

setGetStatsExcludingMSTStatsMode() - Method in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

setGetStatsMode() - Method in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

setHeading(int, String, boolean) - Method in class signalprocesser.voronoi.tools.TestSuite.ValueCollector

setHour(int) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

setID(int) - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

setIgnoreCase(boolean) - Method in class io.github.mianalysis.mia.process.system.FileCrawler

setIncludeSubFolders(boolean) - Method in class io.github.mianalysis.mia.process.system.FileCrawler

setinteger(Object, String, Object) - Static method in class signalprocesser.shared.Reflect

setIntegerLengthCutoff(int) - Method in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

setLayout(LayoutManager) - Method in class signalprocesser.shared.JCollapsiblePanel

setLeft(VNode) - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VInternalNode

setLeftNeighbour(Vertex) - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

setLineCol(Color) - Method in class io.github.mianalysis.mia.process.activecontour.visualisation.GridOverlay

setLineCol(Color) - Method in class io.github.mianalysis.mia.process.skeleton.SkeletonVisualiser

setLoessAccuracy(double) - Method in class io.github.mianalysis.mia.process.analysis.CurvatureCalculator

setLoessIterations(int) - Method in class io.github.mianalysis.mia.process.analysis.CurvatureCalculator

setLowerThreshold(int) - Method in class io.github.mianalysis.mia.process.imagej.AutoLocalThreshold3D

setMag(String) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

setMin(int) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

setMonth(int) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

setNCols(int) - Method in class io.github.mianalysis.mia.process.activecontour.GridInitialiser

setNext(VHalfEdge) - Method in class signalprocesser.voronoi.representation.boundaryproblem.voronoicell.VHalfEdge

setNext(VHalfEdge) - Method in class signalprocesser.voronoi.representation.voronoicell.VHalfEdge

setNext(VLinkedNode) - Method in class signalprocesser.voronoi.statusstructure.VLinkedNode

setNNeighbours(int) - Method in class io.github.mianalysis.mia.process.analysis.CurvatureCalculator

setNodeCol(Color) - Method in class io.github.mianalysis.mia.process.activecontour.visualisation.GridOverlay

setNodeCol(Color) - Method in class io.github.mianalysis.mia.process.skeleton.SkeletonVisualiser

setNodeRadius(double) - Method in class io.github.mianalysis.mia.process.activecontour.visualisation.GridOverlay

setNRows(int) - Method in class io.github.mianalysis.mia.process.activecontour.GridInitialiser

setnThreads(int) - Method in class io.github.mianalysis.mia.process.houghtransform.transforms.AbstractTransform

setParent(VInternalNode) - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VInternalNode

setParent(VInternalNode) - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VLeafNode

setParent(VInternalNode) - Method in interface signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VNode

setPlateManufacturer(String) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

setPlateModel(String) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

setPlateName(String) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

setReduceOuterBoundariesMode() - Method in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

setRight(VNode) - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VInternalNode

setRightNeighbour(Vertex) - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

setRootFolder(File) - Method in class io.github.mianalysis.mia.process.system.FileCrawler

setRootNode(VSiteEvent) - Method in class signalprocesser.voronoi.statusstructure.AbstractStatusStructure

setRootNode(VSiteEvent) - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.BSTStatusStructure

setRootNode(VSiteEvent) - Method in class signalprocesser.voronoi.statusstructure.doublelinkedlistimpl.DLinkedListStatusStructure

setRootNode(VNode) - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.BSTStatusStructure

setRootNode(VNode, int) - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.debug.DebugTree

setRootNode(VLinkedNode) - Method in class signalprocesser.voronoi.statusstructure.doublelinkedlistimpl.DLinkedListStatusStructure

setRow(int) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

setSampleN(double) - Method in class io.github.mianalysis.mia.process.activecontour.minimisers.GreedyMinimiser

setSec(int) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

setSelectedItem(Object) - Method in class signalprocesser.voronoi.tools.CountryListModel

setSequence(int) - Method in class io.github.mianalysis.mia.process.activecontour.minimisers.GreedyMinimiser

setSeriesName(String) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

setSeriesNumber(int) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

setSiteEvents(VSiteEvent, VSiteEvent) - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VInternalNode

setSpecial(int) - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

setTimelineNumber(int) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

setTimepoint(int) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

setTopNeighbour(Vertex) - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

setToUseActionWildcard(boolean) - Method in class io.github.mianalysis.mia.object.metadata.CV7000FilenameExtractor

setUnits(String) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

setVertexRadius(double) - Method in class io.github.mianalysis.mia.process.skeleton.SkeletonVisualiser

setWeight(double) - Method in class io.github.mianalysis.mia.process.activecontour.energies.Energy

setWell(String) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

setWidth(double) - Method in class io.github.mianalysis.mia.process.activecontour.minimisers.GreedyMinimiser

setX(double) - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

setX(int) - Method in class signalprocesser.voronoi.eventqueue.VCircleEvent

setXMin(double) - Method in class io.github.mianalysis.mia.process.activecontour.GridInitialiser

setXSpace(double) - Method in class io.github.mianalysis.mia.process.activecontour.GridInitialiser

setXY(double, double) - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

setXY(int, int) - Method in class signalprocesser.voronoi.representation.boundaryproblem.voronoicell.VHalfEdge

setXY(int, int) - Method in class signalprocesser.voronoi.representation.voronoicell.VHalfEdge

setY(double) - Method in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

setY(int) - Method in class signalprocesser.voronoi.eventqueue.VCircleEvent

setYear(int) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

setYMin(double) - Method in class io.github.mianalysis.mia.process.activecontour.GridInitialiser

setYSpace(double) - Method in class io.github.mianalysis.mia.process.activecontour.GridInitialiser

setZ(int) - Method in class io.github.mianalysis.mia.object.metadata.Metadata

ShapeGeneration - Class in signalprocesser.voronoi.shapegeneration

ShapeGeneration() - Constructor for class signalprocesser.voronoi.shapegeneration.ShapeGeneration

ShapeGenerationException - Exception Class in signalprocesser.voronoi.shapegeneration

ShapeGenerationException(String) - Constructor for exception class signalprocesser.voronoi.shapegeneration.ShapeGenerationException

SHAPEMARGIN_LEFTRIGHT - Static variable in class signalprocesser.voronoi.VoronoiTest

SHAPEMARGIN_TOPBOTTOM - Static variable in class signalprocesser.voronoi.VoronoiTest

SharedEdgeRemoval - Class in signalprocesser.voronoi.representation.triangulation

SharedEdgeRemoval() - Constructor for class signalprocesser.voronoi.representation.triangulation.SharedEdgeRemoval

SharedMinimumSpanningTree - Class in signalprocesser.voronoi.representation.triangulation

SharedMinimumSpanningTree() - Constructor for class signalprocesser.voronoi.representation.triangulation.SharedMinimumSpanningTree

ShortPixelArray - Class in io.github.mianalysis.mia.process.houghtransform.pixelarrays

Created by sc13967 on 12/01/2018.

ShortPixelArray(short[], int[]) - Constructor for class io.github.mianalysis.mia.process.houghtransform.pixelarrays.ShortPixelArray

SHOW_DEBUG_INFO - Static variable in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

SHOW_EDGE_LENGTHS - Static variable in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

SHOW_INTERNAL_TRIANGLES - Static variable in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

shownonminimumspanningtree - Variable in class signalprocesser.voronoi.representation.triangulation.VHalfEdge

showOverlay(ImagePlus, double, int[], double) - Method in class io.github.mianalysis.mia.process.analysis.CurvatureCalculator

showOverlay(ImagePlus, int[], int) - Method in class io.github.mianalysis.mia.process.analysis.CurvatureCalculator

SignalPanel() - Constructor for class signalprocesser.voronoi.VoronoiTest.SignalPanel

signalprocesser.shared - package signalprocesser.shared

signalprocesser.voronoi - package signalprocesser.voronoi

signalprocesser.voronoi.eventqueue - package signalprocesser.voronoi.eventqueue

signalprocesser.voronoi.representation - package signalprocesser.voronoi.representation

signalprocesser.voronoi.representation.boundaryproblem - package signalprocesser.voronoi.representation.boundaryproblem

signalprocesser.voronoi.representation.boundaryproblem.voronoicell - package signalprocesser.voronoi.representation.boundaryproblem.voronoicell

signalprocesser.voronoi.representation.simpletriangulation - package signalprocesser.voronoi.representation.simpletriangulation

signalprocesser.voronoi.representation.triangulation - package signalprocesser.voronoi.representation.triangulation

signalprocesser.voronoi.representation.voronoicell - package signalprocesser.voronoi.representation.voronoicell

signalprocesser.voronoi.shapegeneration - package signalprocesser.voronoi.shapegeneration

signalprocesser.voronoi.statusstructure - package signalprocesser.voronoi.statusstructure

signalprocesser.voronoi.statusstructure.binarysearchtreeimpl - package signalprocesser.voronoi.statusstructure.binarysearchtreeimpl

signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.debug - package signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.debug

signalprocesser.voronoi.statusstructure.doublelinkedlistimpl - package signalprocesser.voronoi.statusstructure.doublelinkedlistimpl

signalprocesser.voronoi.tools - package signalprocesser.voronoi.tools

SimpleTriangulationRepresentation - Class in signalprocesser.voronoi.representation.simpletriangulation

SimpleTriangulationRepresentation() - Constructor for class signalprocesser.voronoi.representation.simpletriangulation.SimpleTriangulationRepresentation

siteevent - Variable in class signalprocesser.voronoi.statusstructure.VLinkedNode

siteEvent(VLinkedNode, VLinkedNode, VLinkedNode) - Method in class signalprocesser.voronoi.representation.boundaryproblem.BoundaryProblemRepresentation

siteEvent(VLinkedNode, VLinkedNode, VLinkedNode) - Method in class signalprocesser.voronoi.representation.boundaryproblem.voronoicell.VoronoiCellRepresentation

siteEvent(VLinkedNode, VLinkedNode, VLinkedNode) - Method in interface signalprocesser.voronoi.representation.RepresentationInterface

siteEvent(VLinkedNode, VLinkedNode, VLinkedNode) - Method in class signalprocesser.voronoi.representation.simpletriangulation.SimpleTriangulationRepresentation

siteEvent(VLinkedNode, VLinkedNode, VLinkedNode) - Method in class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

siteEvent(VLinkedNode, VLinkedNode, VLinkedNode) - Method in class signalprocesser.voronoi.representation.voronoicell.VoronoiCellRepresentation

siteEvent(VLinkedNode, VLinkedNode, VLinkedNode) - Method in class signalprocesser.voronoi.VoronoiTest.TestRepresentationWrapper

SIX - Enum constant in enum io.github.mianalysis.mia.process.voxel.SphereShell.Connectivity

size() - Method in class io.github.mianalysis.mia.process.activecontour.energies.EnergyCollection

Skeleton - Class in io.github.mianalysis.mia.process.skeleton

Created by sc13967 on 24/01/2018.

Skeleton(int[], int[], int[]) - Constructor for class io.github.mianalysis.mia.process.skeleton.Skeleton

Skeleton(ImagePlus) - Constructor for class io.github.mianalysis.mia.process.skeleton.Skeleton

SkeletonVisualiser - Class in io.github.mianalysis.mia.process.skeleton

Created by sc13967 on 25/01/2018.

SkeletonVisualiser() - Constructor for class io.github.mianalysis.mia.process.skeleton.SkeletonVisualiser

solveQuadratic(double, double, double) - Static method in class signalprocesser.voronoi.VoronoiShared

SpatialCalculator - Interface in io.github.mianalysis.mia.process.analysis

Created by sc13967 on 20/01/2018.

Spectrum() - Static method in class io.github.mianalysis.mia.object.imagej.LUTs

SphereAccumulator - Class in io.github.mianalysis.mia.process.houghtransform.accumulators

Created by sc13967 on 13/01/2018.

SphereAccumulator(int[][]) - Constructor for class io.github.mianalysis.mia.process.houghtransform.accumulators.SphereAccumulator

Constructor for Accumulator object.

SphereShell - Class in io.github.mianalysis.mia.process.voxel

SphereShell(int, SphereShell.Connectivity) - Constructor for class io.github.mianalysis.mia.process.voxel.SphereShell

SphereShell.Connectivity - Enum in io.github.mianalysis.mia.process.voxel

SphereSolid - Class in io.github.mianalysis.mia.process.voxel

SphereSolid(int) - Constructor for class io.github.mianalysis.mia.process.voxel.SphereSolid

SphereTransform - Class in io.github.mianalysis.mia.process.houghtransform.transforms

Created by sc13967 on 12/01/2018.

SphereTransform(ImageStack, String[]) - Constructor for class io.github.mianalysis.mia.process.houghtransform.transforms.SphereTransform

SpotIntensity - Class in io.github.mianalysis.mia.process.analysis

SpotIntensity(ImageProcessor, double, double, double) - Constructor for class io.github.mianalysis.mia.process.analysis.SpotIntensity

STANDARD - Enum constant in enum io.github.mianalysis.mia.process.analysis.CurvatureCalculator.FittingMethod

start(Window, String, String, Thread) - Static method in class signalprocesser.shared.StatusDialog

StatusDialog - Class in signalprocesser.shared

StatusDialog(Dialog, String, String) - Constructor for class signalprocesser.shared.StatusDialog

StatusDialog(Frame, String, String) - Constructor for class signalprocesser.shared.StatusDialog

stitch(ImagePlus, int, int, int, int, int, int, String) - Static method in class io.github.mianalysis.mia.process.imagej.ImageTiler

strDoublyLinkedList(int) - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.BSTStatusStructure

sum(int[]) - Static method in class io.github.mianalysis.mia.process.math.ArrayFunc

SummaryCalculator - Interface in io.github.mianalysis.mia.process.analysis

T

T - Static variable in interface io.github.mianalysis.mia.process.imagej.ImageTiler.TileAxes

test(File, boolean) - Method in class io.github.mianalysis.mia.process.system.ExtensionMatchesString

test(File, boolean) - Method in interface io.github.mianalysis.mia.process.system.FileCondition

test(File, boolean) - Method in class io.github.mianalysis.mia.process.system.NameContainsPattern

test(File, boolean) - Method in class io.github.mianalysis.mia.process.system.NameContainsString

test(File, boolean) - Method in class io.github.mianalysis.mia.process.system.ParentContainsString

test(String, boolean) - Method in class io.github.mianalysis.mia.process.system.NameContainsString

TestCase() - Constructor for class signalprocesser.voronoi.tools.TestSuite.TestCase

TestCase(int, int, int) - Constructor for class signalprocesser.voronoi.tools.TestSuite.TestCase

TestCase(String, int, int, int) - Constructor for class signalprocesser.voronoi.tools.TestSuite.TestCase

TestCase(String, Font, int, int, int) - Constructor for class signalprocesser.voronoi.tools.TestSuite.TestCase

TestCase(String, String, int, int, int) - Constructor for class signalprocesser.voronoi.tools.TestSuite.TestCase

TestCaseTableModel() - Constructor for class signalprocesser.voronoi.tools.TestSuite.TestCaseTableModel

testCurrentFolderIsValid() - Method in class io.github.mianalysis.mia.process.system.FileCrawler

testFileConditions(File) - Method in class io.github.mianalysis.mia.process.system.FileCrawler

testFolderConditions(File) - Method in class io.github.mianalysis.mia.process.system.FileCrawler

TestRepresentationWrapper() - Constructor for class signalprocesser.voronoi.VoronoiTest.TestRepresentationWrapper

TestSuite - Class in signalprocesser.voronoi.tools

TestSuite(boolean, Frame) - Constructor for class signalprocesser.voronoi.tools.TestSuite

TestSuite.RunTestSeries - Class in signalprocesser.voronoi.tools

TestSuite.TestCase - Class in signalprocesser.voronoi.tools

TestSuite.TestCaseTableModel - Class in signalprocesser.voronoi.tools

TestSuite.ValueCollector - Class in signalprocesser.voronoi.tools

TextToolkit - Class in signalprocesser.shared

TextToolkit() - Constructor for class signalprocesser.shared.TextToolkit

TextureCalculator - Class in io.github.mianalysis.mia.process.analysis

Texture measures, largely from Robert M.

TextureCalculator() - Constructor for class io.github.mianalysis.mia.process.analysis.TextureCalculator

Thermal() - Static method in class io.github.mianalysis.mia.object.imagej.LUTs

tile(ImagePlus, int, int, int, int, String) - Static method in class io.github.mianalysis.mia.process.imagej.ImageTiler

TIMELINE_NUMBER - Static variable in class io.github.mianalysis.mia.object.metadata.Metadata

TIMEPOINT - Static variable in class io.github.mianalysis.mia.object.metadata.Metadata

TOPLEFT - Static variable in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

TOPRIGHT - Static variable in class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

toString() - Method in class signalprocesser.voronoi.eventqueue.VCircleEvent

toString() - Method in class signalprocesser.voronoi.eventqueue.VEvent

toString() - Method in class signalprocesser.voronoi.eventqueue.VSiteEvent

toString() - Method in class signalprocesser.voronoi.representation.boundaryproblem.voronoicell.VHalfEdge

toString() - Method in class signalprocesser.voronoi.representation.triangulation.VVertex

toString() - Method in class signalprocesser.voronoi.representation.voronoicell.VHalfEdge

toString() - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.BSTStatusStructure

toString() - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VInternalNode

toString() - Method in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VLeafNode

toString() - Method in class signalprocesser.voronoi.statusstructure.doublelinkedlistimpl.DLinkedListStatusStructure

toString() - Method in class signalprocesser.voronoi.VPoint

TotalPathLengthCalculator - Class in io.github.mianalysis.mia.process.analysis

TotalPathLengthCalculator() - Constructor for class io.github.mianalysis.mia.process.analysis.TotalPathLengthCalculator

treedialog - Static variable in class signalprocesser.voronoi.VoronoiTest

TreePanel() - Constructor for class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.debug.DebugTree.TreePanel

TriangulationRepresentation - Class in signalprocesser.voronoi.representation.triangulation

TriangulationRepresentation() - Constructor for class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

TriangulationRepresentation(int) - Constructor for class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

TriangulationRepresentation(TriangulationRepresentation.CalcCutOff) - Constructor for class signalprocesser.voronoi.representation.triangulation.TriangulationRepresentation

TriangulationRepresentation.CalcCutOff - Class in signalprocesser.voronoi.representation.triangulation

TWENTY_SIX - Enum constant in enum io.github.mianalysis.mia.process.voxel.SphereShell.Connectivity

U

uniqueid - Static variable in class signalprocesser.voronoi.eventqueue.VEvent

uniqueid - Static variable in class signalprocesser.voronoi.representation.boundaryproblem.VVertex

uniqueid - Static variable in class signalprocesser.voronoi.representation.triangulation.VVertex

uniqueid - Static variable in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.BSTStatusStructure

uniqueRows(double[][]) - Static method in class io.github.mianalysis.mia.process.math.ArrayFunc

uniqueRows(int[]) - Static method in class io.github.mianalysis.mia.process.math.ArrayFunc

uniqueVals(double[]) - Static method in class io.github.mianalysis.mia.process.math.ArrayFunc

uniqueVals(float[]) - Static method in class io.github.mianalysis.mia.process.math.ArrayFunc

uniqueVals(int[]) - Static method in class io.github.mianalysis.mia.process.math.ArrayFunc

uniqueVals(String[]) - Static method in class io.github.mianalysis.mia.process.math.ArrayFunc

UNITS - Static variable in class io.github.mianalysis.mia.object.metadata.Metadata

V

v1 - Variable in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VInternalNode

v2 - Variable in class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VInternalNode

validate(RealVector) - Method in class io.github.mianalysis.mia.process.math.Validator

Validator - Class in io.github.mianalysis.mia.process.math

Created by sc13967 on 21/06/2017.

Validator(RealMatrix) - Constructor for class io.github.mianalysis.mia.process.math.Validator

ValueCollector(int) - Constructor for class signalprocesser.voronoi.tools.TestSuite.ValueCollector

valueOf(String) - Static method in enum io.github.mianalysis.mia.process.analysis.CurvatureCalculator.FittingMethod

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum io.github.mianalysis.mia.process.system.FileCondition.Mode

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum io.github.mianalysis.mia.process.voxel.SphereShell.Connectivity

Returns the enum constant of this type with the specified name.

values() - Static method in enum io.github.mianalysis.mia.process.analysis.CurvatureCalculator.FittingMethod

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum io.github.mianalysis.mia.process.system.FileCondition.Mode

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum io.github.mianalysis.mia.process.voxel.SphereShell.Connectivity

Returns an array containing the constants of this enum type, in the order they are declared.

VCircleEvent - Class in signalprocesser.voronoi.eventqueue

VCircleEvent() - Constructor for class signalprocesser.voronoi.eventqueue.VCircleEvent

VCircleEvent(int, int) - Constructor for class signalprocesser.voronoi.eventqueue.VCircleEvent

VCluster - Class in signalprocesser.voronoi.representation.triangulation

VCluster() - Constructor for class signalprocesser.voronoi.representation.triangulation.VCluster

vertex - Variable in class signalprocesser.voronoi.representation.boundaryproblem.VHalfEdge

vertex - Variable in class signalprocesser.voronoi.representation.triangulation.VHalfEdge

Vertex - Class in io.github.mianalysis.mia.process.activecontour.physicalmodel

Vertex(double, double) - Constructor for class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

Vertex(double, double, int) - Constructor for class io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex

vertexnumber - Variable in class signalprocesser.voronoi.representation.boundaryproblem.VHalfEdge

vertexnumber - Variable in class signalprocesser.voronoi.representation.triangulation.VHalfEdge

VEvent - Class in signalprocesser.voronoi.eventqueue

VEvent() - Constructor for class signalprocesser.voronoi.eventqueue.VEvent

VHalfEdge - Class in signalprocesser.voronoi.representation.boundaryproblem

VHalfEdge - Class in signalprocesser.voronoi.representation.boundaryproblem.voronoicell

VHalfEdge - Class in signalprocesser.voronoi.representation.triangulation

VHalfEdge - Class in signalprocesser.voronoi.representation.voronoicell

VHalfEdge() - Constructor for class signalprocesser.voronoi.representation.boundaryproblem.voronoicell.VHalfEdge

VHalfEdge() - Constructor for class signalprocesser.voronoi.representation.voronoicell.VHalfEdge

VHalfEdge(int, int) - Constructor for class signalprocesser.voronoi.representation.boundaryproblem.voronoicell.VHalfEdge

VHalfEdge(int, int) - Constructor for class signalprocesser.voronoi.representation.voronoicell.VHalfEdge

VHalfEdge(int, VVertex) - Constructor for class signalprocesser.voronoi.representation.boundaryproblem.VHalfEdge

VHalfEdge(int, VVertex) - Constructor for class signalprocesser.voronoi.representation.triangulation.VHalfEdge

VHalfEdge(int, VVertex, VHalfEdge) - Constructor for class signalprocesser.voronoi.representation.triangulation.VHalfEdge

VInternalNode - Class in signalprocesser.voronoi.statusstructure.binarysearchtreeimpl

VInternalNode() - Constructor for class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VInternalNode

VInternalNode(VNode, VNode) - Constructor for class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VInternalNode

VLeafNode - Class in signalprocesser.voronoi.statusstructure.binarysearchtreeimpl

VLeafNode() - Constructor for class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VLeafNode

VLeafNode(VSiteEvent) - Constructor for class signalprocesser.voronoi.statusstructure.binarysearchtreeimpl.VLeafNode

VLinkedNode - Class in signalprocesser.voronoi.statusstructure

VLinkedNode() - Constructor for class signalprocesser.voronoi.statusstructure.VLinkedNode

VLinkedNode(VSiteEvent) - Constructor for class signalprocesser.voronoi.statusstructure.VLinkedNode

VNode - Interface in signalprocesser.voronoi.statusstructure.binarysearchtreeimpl

VOCWriter - Class in io.github.mianalysis.mia.process.io

VOCWriter() - Constructor for class io.github.mianalysis.mia.process.io.VOCWriter

VoronoiAlgorithm - Class in signalprocesser.voronoi

VORONOICELLAREA_CUTOFF - Static variable in class signalprocesser.voronoi.representation.boundaryproblem.BoundaryProblemRepresentation

VoronoiCellRepresentation - Class in signalprocesser.voronoi.representation.boundaryproblem.voronoicell

VoronoiCellRepresentation - Class in signalprocesser.voronoi.representation.voronoicell

VoronoiCellRepresentation() - Constructor for class signalprocesser.voronoi.representation.boundaryproblem.voronoicell.VoronoiCellRepresentation

VoronoiCellRepresentation() - Constructor for class signalprocesser.voronoi.representation.voronoicell.VoronoiCellRepresentation

VoronoiShared - Class in signalprocesser.voronoi

VoronoiShared() - Constructor for class signalprocesser.voronoi.VoronoiShared

VoronoiTest - Class in signalprocesser.voronoi

VoronoiTest() - Constructor for class signalprocesser.voronoi.VoronoiTest

Creates new form MainFrame

VoronoiTest.SignalPanel - Class in signalprocesser.voronoi

VoronoiTest.TestRepresentationWrapper - Class in signalprocesser.voronoi

VPoint - Class in signalprocesser.voronoi

VPoint() - Constructor for class signalprocesser.voronoi.VPoint

VPoint(int, int) - Constructor for class signalprocesser.voronoi.VPoint

VPoint(VPoint) - Constructor for class signalprocesser.voronoi.VPoint

VSiteEvent - Class in signalprocesser.voronoi.eventqueue

VSiteEvent(VPoint) - Constructor for class signalprocesser.voronoi.eventqueue.VSiteEvent

VTriangle - Class in signalprocesser.voronoi.representation.simpletriangulation

VTriangle() - Constructor for class signalprocesser.voronoi.representation.simpletriangulation.VTriangle

VTriangle(int, int) - Constructor for class signalprocesser.voronoi.representation.simpletriangulation.VTriangle

VTriangle(VPoint) - Constructor for class signalprocesser.voronoi.representation.simpletriangulation.VTriangle

VVertex - Class in signalprocesser.voronoi.representation.boundaryproblem

VVertex - Class in signalprocesser.voronoi.representation.triangulation

VVertex() - Constructor for class signalprocesser.voronoi.representation.boundaryproblem.VVertex

VVertex() - Constructor for class signalprocesser.voronoi.representation.triangulation.VVertex

VVertex(int, int) - Constructor for class signalprocesser.voronoi.representation.boundaryproblem.VVertex

VVertex(int, int) - Constructor for class signalprocesser.voronoi.representation.triangulation.VVertex

VVertex(VPoint) - Constructor for class signalprocesser.voronoi.representation.boundaryproblem.VVertex

VVertex(VPoint) - Constructor for class signalprocesser.voronoi.representation.triangulation.VVertex

VVoronoiCell - Class in signalprocesser.voronoi.representation.boundaryproblem.voronoicell

VVoronoiCell - Class in signalprocesser.voronoi.representation.voronoicell

VVoronoiCell() - Constructor for class signalprocesser.voronoi.representation.boundaryproblem.voronoicell.VVoronoiCell

VVoronoiCell() - Constructor for class signalprocesser.voronoi.representation.voronoicell.VVoronoiCell

VVoronoiCell(int, int) - Constructor for class signalprocesser.voronoi.representation.boundaryproblem.voronoicell.VVoronoiCell

VVoronoiCell(int, int) - Constructor for class signalprocesser.voronoi.representation.voronoicell.VVoronoiCell

VVoronoiCell(VPoint) - Constructor for class signalprocesser.voronoi.representation.boundaryproblem.voronoicell.VVoronoiCell

VVoronoiCell(VPoint) - Constructor for class signalprocesser.voronoi.representation.voronoicell.VVoronoiCell

W

WavelengthToColorConverter - Class in io.github.mianalysis.mia.process.math

WavelengthToColorConverter() - Constructor for class io.github.mianalysis.mia.process.math.WavelengthToColorConverter

weight - Variable in class io.github.mianalysis.mia.process.activecontour.energies.Energy

WELL - Static variable in class io.github.mianalysis.mia.object.metadata.Metadata

width - Variable in class io.github.mianalysis.mia.process.houghtransform.transforms.LineTransform

write(String) - Method in class io.github.mianalysis.mia.process.io.VOCWriter

writeFromLeft(Graphics2D, Font, Color, String, Rectangle) - Static method in class signalprocesser.shared.TextToolkit

writeFromLeftCentered(Graphics2D, Font, Color, String, Rectangle) - Static method in class signalprocesser.shared.TextToolkit

writeFromRight(Graphics2D, Font, Color, String, Rectangle) - Static method in class signalprocesser.shared.TextToolkit

writeFromTop(Graphics2D, Font, Color, String, Rectangle) - Static method in class signalprocesser.shared.TextToolkit

writeFromTop(Graphics2D, Font, Color, String, Rectangle, int) - Static method in class signalprocesser.shared.TextToolkit

writeSummary(BufferedWriter, boolean) - Method in class signalprocesser.voronoi.tools.TestSuite.ValueCollector

X

x - Variable in class io.github.mianalysis.mia.process.voxel.AbstractSphere

x - Variable in class signalprocesser.voronoi.representation.boundaryproblem.voronoicell.VHalfEdge

x - Variable in class signalprocesser.voronoi.representation.voronoicell.VHalfEdge

x - Variable in class signalprocesser.voronoi.VPoint

Y

y - Variable in class io.github.mianalysis.mia.process.voxel.AbstractSphere

y - Variable in class signalprocesser.voronoi.representation.boundaryproblem.voronoicell.VHalfEdge

y - Variable in class signalprocesser.voronoi.representation.voronoicell.VHalfEdge

y - Variable in class signalprocesser.voronoi.VPoint

YEAR - Static variable in class io.github.mianalysis.mia.object.metadata.Metadata

Z

z - Variable in class io.github.mianalysis.mia.process.voxel.AbstractSphere

Z - Static variable in interface io.github.mianalysis.mia.process.imagej.ImageTiler.TileAxes

ZPOSITION - Static variable in class io.github.mianalysis.mia.object.metadata.Metadata

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