A B C D E F G H I K L M N O P Q R S T U V W X Y

A

action(String) - Method in class fiji.help.Context_Help

actionPerformed(ActionEvent) - Method in class fiji.util.Recent_Commands

adjustmentValueChanged(AdjustmentEvent) - Method in class fiji.util.CurrentSlice

allIdentical(List<T>) - Method in class fiji.util.KDTree

apply(PathIterator) - Method in class fiji.geom.AreaCalculations.Calculation

area(PathIterator) - Static method in class fiji.geom.AreaCalculations

Computes the surface area of the path or multiple specified paths.

Area() - Constructor for class fiji.geom.AreaCalculations.Area

AreaCalculations - Class in fiji.geom

AreaCalculations() - Constructor for class fiji.geom.AreaCalculations

AreaCalculations.Area - Class in fiji.geom

AreaCalculations.Calculation - Class in fiji.geom

AreaCalculations.Centroid - Class in fiji.geom

AreaCalculations.Circumference - Class in fiji.geom

B

Binary_to_Point_Selection - Class in fiji.selection

This is a template for a plugin that requires one image to be opened, and takes it as parameter.

Binary_to_Point_Selection() - Constructor for class fiji.selection.Binary_to_Point_Selection

C

calculate(PathIterator) - Method in class fiji.geom.AreaCalculations.Calculation

calculateRoi() - Method in class fiji.util.Circle_Fitter

Computes and return the circle Roi that fits.

Calculation() - Constructor for class fiji.geom.AreaCalculations.Calculation

centroid(PathIterator) - Static method in class fiji.geom.AreaCalculations

Centroid() - Constructor for class fiji.geom.AreaCalculations.Centroid

changed() - Method in class fiji.util.CurrentSlice

check(ImagePlus) - Method in class fiji.util.CurrentSlice

checkWindow(Component) - Method in class fiji.util.CurrentSlice

choice - Variable in class fiji.stacks.Hyperstack_rearranger

Circle_Fitter - Class in fiji.util

Fit a circle selection to an image.

Circle_Fitter() - Constructor for class fiji.util.Circle_Fitter

circumference(PathIterator) - Static method in class fiji.geom.AreaCalculations

Computes the perimeter of the specified path or multiple paths.

Circumference() - Constructor for class fiji.geom.AreaCalculations.Circumference

commandExecuting(String) - Method in class fiji.util.Recent_Commands

compare(T, T) - Method in class fiji.util.DistanceComparator

CompositeConverter2 - Class in fiji.stacks

This is an incredibly stupid class, but I need the reference to the new ImagePlus, that's why I rewrote the CompositeConverter class here ...

CompositeConverter2() - Constructor for class fiji.stacks.CompositeConverter2

compute(ImageStack) - Method in class fiji.process3d.EDT

compute(ImageStack) - Method in class fiji.process3d.SEDT

Context_Help - Class in fiji.help

Context_Help() - Constructor for class fiji.help.Context_Help

Convert_Red_To_Magenta - Class in fiji.color

Convert all reds to magentas (to help red-green blind viewers).

Convert_Red_To_Magenta() - Constructor for class fiji.color.Convert_Red_To_Magenta

Convert_Red_To_Magenta_Clipboard - Class in fiji.color

Convert all reds to magentas in the system clipboard (to help red-green blind viewers)

Convert_Red_To_Magenta_Clipboard() - Constructor for class fiji.color.Convert_Red_To_Magenta_Clipboard

convertToHyperStack(ImagePlus) - Static method in class fiji.stacks.Hyperstack_rearranger

Converts this image to Hyperstack if it is RGB or 8-bit color

coordinate - Variable in class fiji.util.node.NonLeaf

copyImageToClipboard(ColorProcessor) - Static method in class fiji.color.Convert_Red_To_Magenta_Clipboard

createArray(int) - Method in interface fiji.util.node.Leaf

createArray(int) - Method in class fiji.util.node.SimpleNode

crop(ImageProcessor, Rectangle) - Static method in class fiji.selection.Select_Bounding_Box

crop(ImagePlus, Rectangle) - Static method in class fiji.selection.Select_Bounding_Box

current - Variable in class fiji.geom.AreaCalculations.Calculation

currentSlice - Variable in class fiji.color.Convert_Red_To_Magenta

CurrentSlice - Class in fiji.util

CurrentSlice() - Constructor for class fiji.util.CurrentSlice

D

dealWithCalibration() - Method in class fiji.stacks.Dynamic_Reslice

debug - Static variable in class fiji.util.KDTree

defaultIndexChannels - Static variable in class fiji.stacks.Hyperstack_rearranger

defaultIndexFrames - Static variable in class fiji.stacks.Hyperstack_rearranger

defaultIndexSlices - Static variable in class fiji.stacks.Hyperstack_rearranger

denoise(FloatProcessor, float) - Static method in class fiji.denoise.ROF_Denoise

denoise(FloatProcessor, float, float, float, int) - Static method in class fiji.denoise.ROF_Denoise

deriveX(ImageProcessor) - Static method in class fiji.geom.Shape_Index_Map

deriveY(ImageProcessor) - Static method in class fiji.geom.Shape_Index_Map

dimension - Variable in class fiji.util.KDTree

dispose() - Method in class fiji.util.CurrentSlice

DistanceComparator<T extends Leaf<T>> - Class in fiji.util

Compares which Leaf is closer to another Leaf

DistanceComparator(T) - Constructor for class fiji.util.DistanceComparator

distanceTo(N) - Method in interface fiji.util.node.Leaf

distanceTo(SimpleNode) - Method in class fiji.util.node.SimpleNode

duplicates - Variable in class fiji.util.KDTree

Dynamic_Reslice - Class in fiji.stacks

Dynamic reslice of a stack.

Dynamic_Reslice() - Constructor for class fiji.stacks.Dynamic_Reslice

Empty constructor, needed by ImageJ.

Dynamic_Reslice(ImagePlus) - Constructor for class fiji.stacks.Dynamic_Reslice

Create a new instance of this plugin, linked to the ImagePlus given in argument.

E

EDT - Class in fiji.process3d

EDT() - Constructor for class fiji.process3d.EDT

equals(SimpleNode) - Method in class fiji.util.node.SimpleNode

exec(ImagePlus, int, int, int, float) - Method in class Retinex_

F

fiji.color - package fiji.color

fiji.denoise - package fiji.denoise

fiji.drawing - package fiji.drawing

fiji.geom - package fiji.geom

fiji.help - package fiji.help

fiji.process3d - package fiji.process3d

fiji.selection - package fiji.selection

fiji.stacks - package fiji.stacks

fiji.util - package fiji.util

fiji.util.node - package fiji.util.node

findNearestNeighbor(T) - Method in class fiji.util.NearestNeighborSearch

findNearestNeighbor(T, Node<T>, int) - Method in class fiji.util.NearestNeighborSearch

findNeighbors(T, Node<T>, int) - Method in class fiji.util.RadiusNeighborSearch

findNeighborsSorted(T, double) - Method in class fiji.util.RadiusNeighborSearch

findNeighborsUnsorted(T, double) - Method in class fiji.util.RadiusNeighborSearch

findNNearestNeighbors(T, int) - Method in class fiji.util.NNearestNeighborSearch

findNNearestNeighbors(T, Node<T>, int, int, T[]) - Method in class fiji.util.NNearestNeighborSearch

frequentListSize - Static variable in class fiji.util.Recent_Commands

G

gaussianBlur - Static variable in class fiji.geom.Shape_Index_Map

get(int) - Method in interface fiji.util.node.Leaf

get(int) - Method in class fiji.util.node.SimpleNode

getBoundingBox(ImageProcessor, Rectangle, double) - Static method in class fiji.selection.Select_Bounding_Box

getClipboardImage() - Static method in class fiji.color.Convert_Red_To_Magenta_Clipboard

getDefaultThreshold() - Method in class fiji.util.Circle_Fitter

The default threshold is determined like this: as a circle is a linear structure, we want the _square root_ of the total number of pixels to contribute.

getDimension() - Method in class fiji.util.KDTree

getDuplicates() - Method in class fiji.util.KDTree

getFlip() - Method in class fiji.stacks.Dynamic_Reslice

Get the flip state for this instance.

getImageChunk(ImagePlus, int, int) - Static method in class fiji.stacks.Hyperstack_rearranger

Returns an ImagePlus for a 2d or 3d stack where ImageProcessors are not copied but just added.

getImagePlus() - Method in class fiji.stacks.Dynamic_Reslice

getKDTree() - Method in class fiji.util.NearestNeighborSearch

getKDTree() - Method in class fiji.util.NNearestNeighborSearch

getKDTree() - Method in class fiji.util.RadiusNeighborSearch

getListIndex() - Method in class fiji.util.Recent_Commands

getMostFrequent(int) - Method in class fiji.util.Recent_Commands

getMostRecent(int) - Method in class fiji.util.Recent_Commands

getNumDimensions() - Method in interface fiji.util.node.Leaf

getNumDimensions() - Method in class fiji.util.node.SimpleNode

getResult() - Method in class fiji.geom.AreaCalculations.Centroid

getRoot() - Method in class fiji.util.KDTree

getRotate() - Method in class fiji.stacks.Dynamic_Reslice

Get the rotate state for this instance.

getShapeIndex(ImageProcessor) - Static method in class fiji.geom.Shape_Index_Map

The formula is: dnx_x + dny_y s = 2 / PI * arctan --------------------------------------- sqrt((dnx_x - dny_y)^2 + 4 dny_x dnx_y) where _x and _y are the x and y components of the partial derivatives of the normal vector of the surface defined by the intensities of the image.

getShapeIndexMap(ImagePlus, double) - Static method in class fiji.geom.Shape_Index_Map

getSlice(ImagePlus, Roi) - Method in class fiji.stacks.Dynamic_Reslice

Create an ImageProcessor containing the reslice of the current stack in the given ImagePlus, for the Roi given as second argument (not necessary the ImagePlus's Roi).

getThreshold() - Method in class fiji.util.Circle_Fitter

Returns threshold used by this plugin.

getTitle() - Method in class fiji.help.Context_Help

gp - Variable in class fiji.selection.Rounded_Rectangle

guessBackground(ImageProcessor) - Method in class fiji.selection.Select_Bounding_Box

H

handleImage(ImagePlus, boolean) - Method in class fiji.util.CurrentSlice

handleImages(boolean) - Method in class fiji.util.CurrentSlice

handleSegment() - Method in class fiji.geom.AreaCalculations.Area

handleSegment() - Method in class fiji.geom.AreaCalculations.Calculation

handleSegment() - Method in class fiji.geom.AreaCalculations.Centroid

handleSegment() - Method in class fiji.geom.AreaCalculations.Circumference

hasDuplicates() - Method in class fiji.util.KDTree

Hyperstack_rearranger - Class in fiji.stacks

Hyperstack_rearranger() - Constructor for class fiji.stacks.Hyperstack_rearranger

I

image - Variable in class fiji.color.Convert_Red_To_Magenta

image - Variable in class fiji.denoise.ROF_Denoise

image - Variable in class fiji.geom.Shape_Index_Map

image - Variable in class fiji.selection.Binary_to_Point_Selection

image - Variable in class fiji.util.CurrentSlice

imageClosed(ImagePlus) - Method in class fiji.util.CurrentSlice

imageOpened(ImagePlus) - Method in class fiji.util.CurrentSlice

imageUpdated(ImagePlus) - Method in class fiji.util.CurrentSlice

install() - Method in class fiji.util.Recent_Commands

ip - Variable in class fiji.util.CurrentSlice

isLeaf() - Method in interface fiji.util.node.Node

isLeaf() - Method in class fiji.util.node.NonLeaf

isLeaf() - Method in class fiji.util.node.SimpleNode

K

kappa - Static variable in class fiji.selection.Rounded_Rectangle

KDTree<T extends Leaf<T>> - Class in fiji.util

KDTree(List<T>) - Constructor for class fiji.util.KDTree

Construct a KDTree from the elements in the given list.

KDTree(List<T>, int) - Constructor for class fiji.util.KDTree

kdTree - Variable in class fiji.util.NearestNeighborSearch

kdTree - Variable in class fiji.util.NNearestNeighborSearch

kdTree - Variable in class fiji.util.RadiusNeighborSearch

keyPressed(KeyEvent) - Method in class fiji.util.Recent_Commands

keyReleased(KeyEvent) - Method in class fiji.util.Recent_Commands

keyTyped(KeyEvent) - Method in class fiji.util.Recent_Commands

L

Leaf<N extends Leaf<N>> - Interface in fiji.util.node

left - Variable in class fiji.util.node.NonLeaf

Linear_Gradient - Class in fiji.drawing

Linear_Gradient() - Constructor for class fiji.drawing.Linear_Gradient

M

main(String[]) - Static method in class fiji.geom.AreaCalculations

main(String[]) - Static method in class fiji.util.TestKDTree

makeComposite(ImagePlus) - Method in class fiji.stacks.CompositeConverter2

makeLinearGradient(ImageProcessor, int, int, Line) - Static method in class fiji.drawing.Linear_Gradient

makeNode(List<T>, int) - Method in class fiji.util.KDTree

MAX_GAUSSIAN_SCALE - Static variable in class Retinex_

MAX_RETINEX_SCALES - Static variable in class Retinex_

maxLRUSize - Static variable in class fiji.util.Recent_Commands

median(List<T>, int) - Method in class fiji.util.KDTree

medianLength - Variable in class fiji.util.KDTree

MIN_GAUSSIAN_SCALE - Static variable in class Retinex_

mouseDragged(MouseEvent) - Method in class fiji.stacks.Dynamic_Reslice

mouseMoved(MouseEvent) - Method in class fiji.stacks.Dynamic_Reslice

N

NearestNeighborSearch<T extends Leaf<T>> - Class in fiji.util

NearestNeighborSearch(KDTree<T>) - Constructor for class fiji.util.NearestNeighborSearch

NNearestNeighborSearch<T extends Leaf<T>> - Class in fiji.util

NNearestNeighborSearch(KDTree<T>) - Constructor for class fiji.util.NNearestNeighborSearch

Node<N extends Node<N>> - Interface in fiji.util.node

NonLeaf<T extends Leaf<T>> - Class in fiji.util.node

NonLeaf(float, int, Node<T>, Node<T>) - Constructor for class fiji.util.node.NonLeaf

numSlices - Variable in class fiji.color.Convert_Red_To_Magenta

O

obsolete() - Method in class fiji.util.CurrentSlice

P

pointsWithinRadius - Variable in class fiji.util.RadiusNeighborSearch

PREFS_KEY - Static variable in class fiji.util.Recent_Commands

previous - Variable in class fiji.geom.AreaCalculations.Calculation

process(ColorProcessor) - Static method in class fiji.color.Convert_Red_To_Magenta

processSystemClipboard() - Static method in class fiji.color.Convert_Red_To_Magenta_Clipboard

putRow(ImageProcessor, int, int, float[], int) - Method in class fiji.stacks.Radial_Reslice

Q

quarterCircle(int, int) - Method in class fiji.selection.Rounded_Rectangle

R

Radial_Gradient - Class in fiji.drawing

Radial_Gradient() - Constructor for class fiji.drawing.Radial_Gradient

Radial_Reslice - Class in fiji.stacks

Implements the Radial Reslice command.

Radial_Reslice() - Constructor for class fiji.stacks.Radial_Reslice

radius - Variable in class fiji.util.RadiusNeighborSearch

RadiusNeighborSearch<T extends Leaf<T>> - Class in fiji.util

RadiusNeighborSearch(KDTree<T>) - Constructor for class fiji.util.RadiusNeighborSearch

radreslice(ImagePlus) - Method in class fiji.stacks.Radial_Reslice

Recent_Commands - Class in fiji.util

Recent_Commands() - Constructor for class fiji.util.Recent_Commands

recentListSize - Static variable in class fiji.util.Recent_Commands

reorderHyperstack(ImagePlus, String, boolean, boolean) - Static method in class fiji.stacks.Hyperstack_rearranger

Creates a new Hyperstack with a different order of dimensions, the ImageProcessors are not copied but just linked from the input ImagePlus

reorderHyperstack(ImagePlus, int, int, int, boolean, boolean) - Static method in class fiji.stacks.Hyperstack_rearranger

Creates a new Hyperstack with a different order of dimensions, the ImageProcessors are not copied but just linked from the input ImagePlus id's used here, reflecting (XY)CZT: channel = 0 slices = 1 frames = 2

reslice() - Method in class fiji.stacks.Dynamic_Reslice

Main method that actually dispatch the work.

result - Variable in class fiji.geom.AreaCalculations.Calculation

Retinex_ - Class in <Unnamed>

Retinex_() - Constructor for class Retinex_

RETINEX_HIGH - Static variable in class Retinex_

RETINEX_LOW - Static variable in class Retinex_

RETINEX_UNIFORM - Static variable in class Retinex_

right - Variable in class fiji.util.node.NonLeaf

ROF_Denoise - Class in fiji.denoise

This denoising method is based on total-variation, originally proposed by Rudin, Osher and Fatemi.

ROF_Denoise() - Constructor for class fiji.denoise.ROF_Denoise

root - Variable in class fiji.util.KDTree

Rounded_Rectangle - Class in fiji.selection

Rounded_Rectangle() - Constructor for class fiji.selection.Rounded_Rectangle

run(ImageProcessor) - Method in class fiji.color.Convert_Red_To_Magenta

This method is run when the current image was accepted.

run(String) - Method in class fiji.color.Convert_Red_To_Magenta_Clipboard

run(ImageProcessor) - Method in class fiji.denoise.ROF_Denoise

This method is run when the current image was accepted.

run(ImageProcessor) - Method in class fiji.drawing.Linear_Gradient

run(ImageProcessor) - Method in class fiji.drawing.Radial_Gradient

run(ImageProcessor) - Method in class fiji.geom.Shape_Index_Map

This method is run when the current image was accepted.

run(ImageProcessor) - Method in class fiji.process3d.EDT

run(ImageProcessor) - Method in class fiji.process3d.SEDT

run(ImageProcessor) - Method in class fiji.selection.Binary_to_Point_Selection

This method is run when the current image was accepted.

run(ImageProcessor) - Method in class fiji.selection.Rounded_Rectangle

run(ImageProcessor) - Method in class fiji.selection.Select_Bounding_Box

run(String) - Method in class fiji.stacks.Dynamic_Reslice

Main method, called when the plugin is launched from ImageJ menu.

run(String) - Method in class fiji.stacks.Hyperstack_rearranger

run(ImageProcessor) - Method in class fiji.stacks.Radial_Reslice

run(ImageProcessor) - Method in class fiji.util.Circle_Fitter

run(String) - Method in class fiji.util.Recent_Commands

run(String) - Method in class Retinex_

runInteractively() - Method in class fiji.util.Recent_Commands

runSelectedCommand() - Method in class fiji.util.Recent_Commands

S

SEDT - Class in fiji.process3d

SEDT() - Constructor for class fiji.process3d.SEDT

Select_Bounding_Box - Class in fiji.selection

Select_Bounding_Box() - Constructor for class fiji.selection.Select_Bounding_Box

setAutoThreshold() - Method in class fiji.util.Circle_Fitter

Sets the threshold used by this plugin to be the default one.

setFlip(boolean) - Method in class fiji.stacks.Dynamic_Reslice

Set the flip state for this instance.

setImageProcessor(ImageProcessor) - Method in class fiji.util.Circle_Fitter

Set the ImageProcessor that will be fitted.

setRotate(boolean) - Method in class fiji.stacks.Dynamic_Reslice

Set the flip state for this instance.

setThreshold(float) - Method in class fiji.util.Circle_Fitter

Sets the threshold for the fit.

setup(String, ImagePlus) - Method in class fiji.color.Convert_Red_To_Magenta

This method gets called by ImageJ / Fiji to determine whether the current image is of an appropriate type.

setup(String, ImagePlus) - Method in class fiji.denoise.ROF_Denoise

This method gets called by ImageJ / Fiji to determine whether the current image is of an appropriate type.

setup(String, ImagePlus) - Method in class fiji.drawing.Linear_Gradient

setup(String, ImagePlus) - Method in class fiji.drawing.Radial_Gradient

setup(String, ImagePlus) - Method in class fiji.geom.Shape_Index_Map

This method gets called by ImageJ / Fiji to determine whether the current image is of an appropriate type.

setup(String, ImagePlus) - Method in class fiji.process3d.EDT

setup(String, ImagePlus) - Method in class fiji.process3d.SEDT

setup(String, ImagePlus) - Method in class fiji.selection.Binary_to_Point_Selection

This method gets called by ImageJ / Fiji to determine whether the current image is of an appropriate type.

setup(String, ImagePlus) - Method in class fiji.selection.Rounded_Rectangle

setup(String, ImagePlus) - Method in class fiji.selection.Select_Bounding_Box

setup(String, ImagePlus) - Method in class fiji.stacks.Radial_Reslice

setup(String, ImagePlus) - Method in class fiji.util.Circle_Fitter

Shape_Index_Map - Class in fiji.geom

Calculate the shape index as defined in J Koenderink and A van Doorn, “Surface shape and curvature scales,” Image Vision Comput, vol. 10, no. 8, pp. 557–565, 1992

Shape_Index_Map() - Constructor for class fiji.geom.Shape_Index_Map

shutdown() - Method in class fiji.stacks.Dynamic_Reslice

Shut down the Dynamic reslice, that is, remove itself from the listener list.

SimpleNode - Class in fiji.util.node

SimpleNode(SimpleNode) - Constructor for class fiji.util.node.SimpleNode

SimpleNode(float[]) - Constructor for class fiji.util.node.SimpleNode

slice - Variable in class fiji.util.CurrentSlice

stack - Variable in class fiji.color.Convert_Red_To_Magenta

start - Variable in class fiji.geom.AreaCalculations.Calculation

start(int, int) - Method in class fiji.selection.Rounded_Rectangle

start() - Method in class fiji.stacks.Dynamic_Reslice

Method to start the dynamic reslice process after all parameters have been set.

straight(int, int) - Method in class fiji.selection.Rounded_Rectangle

suppressRepeatedCommands - Static variable in class fiji.util.Recent_Commands

T

TestKDTree - Class in fiji.util

TestKDTree() - Constructor for class fiji.util.TestKDTree

testNearestNeighbor(int, int, int, float, float) - Static method in class fiji.util.TestKDTree

testNNearestNeighbor(int, int, int, int, float, float) - Static method in class fiji.util.TestKDTree

toString(Node<T>, String) - Method in class fiji.util.KDTree

toString() - Method in class fiji.util.KDTree

toString(T) - Method in class fiji.util.NNearestNeighborSearch

toString(T[], int) - Method in class fiji.util.NNearestNeighborSearch

toString(Node<T>) - Method in class fiji.util.node.NonLeaf

toString() - Method in class fiji.util.node.NonLeaf

toString() - Method in class fiji.util.node.SimpleNode

triangleArea(double[], double[], double[]) - Static method in class fiji.geom.AreaCalculations

U

update() - Method in class fiji.stacks.Dynamic_Reslice

Refresh the output display with the current roi.

url - Static variable in class fiji.help.Context_Help

V

valueChanged(ListSelectionEvent) - Method in class fiji.util.Recent_Commands

W

windowActivated(WindowEvent) - Method in class fiji.stacks.Dynamic_Reslice

windowActivated(WindowEvent) - Method in class fiji.util.CurrentSlice

windowClosed(WindowEvent) - Method in class fiji.stacks.Dynamic_Reslice

windowClosed(WindowEvent) - Method in class fiji.util.CurrentSlice

windowClosing(WindowEvent) - Method in class fiji.stacks.Dynamic_Reslice

windowClosing(WindowEvent) - Method in class fiji.util.CurrentSlice

windowDeactivated(WindowEvent) - Method in class fiji.stacks.Dynamic_Reslice

windowDeactivated(WindowEvent) - Method in class fiji.util.CurrentSlice

windowDeiconified(WindowEvent) - Method in class fiji.stacks.Dynamic_Reslice

windowDeiconified(WindowEvent) - Method in class fiji.util.CurrentSlice

windowIconified(WindowEvent) - Method in class fiji.stacks.Dynamic_Reslice

windowIconified(WindowEvent) - Method in class fiji.util.CurrentSlice

windowOpened(WindowEvent) - Method in class fiji.stacks.Dynamic_Reslice

windowOpened(WindowEvent) - Method in class fiji.util.CurrentSlice

X

x - Variable in class fiji.selection.Rounded_Rectangle

Y

y - Variable in class fiji.selection.Rounded_Rectangle

A B C D E F G H I K L M N O P Q R S T U V W X Y