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

S

saveElongationData() - Method in class snakeprogram3d.SnakeModel

Save all of the snakes elongation data

saveSnake() - Method in class snakeprogram3d.SnakeModel

Save all of the snakes data, so that they may be reloaded

selectNextSnake() - Method in class snakeprogram3d.SnakeModel

selectSnake(MouseEvent) - Method in class snakeprogram3d.SnakeModel

A MouseEvent version of the snake selector

selectSnake(ThreeDEvent) - Method in class snakeprogram3d.SnakeModel

Chooses the nearest snake.

set3DPanel(Component) - Method in class snakeprogram3d.SnakeFrame

The threed view is created afterwards, this set one of the variable panels to be the threed view.

setAlpha() - Method in class snakeprogram.SnakeFrame

setAlpha(double) - Method in class snakeprogram.TwoDDeformation

Set this before using

setAlpha() - Method in class snakeprogram3d.SnakeFrame

Trys to set the 'alpha' value.

setAlpha(double) - Method in class snakeprogram3d.SnakeModel

setAlpha(double) - Method in class snakeprogram3d.ThreeDDeformation

setBackgroundIntensity(double) - Method in class snakeprogram3d.SnakeModel

setBackInt(double) - Method in class snakeprogram.TwoDDeformation

This needs to be set

setBackInt(double) - Method in class snakeprogram3d.ThreeDDeformation

setBeta() - Method in class snakeprogram.SnakeFrame

setBeta(double) - Method in class snakeprogram.TwoDDeformation

Needs to be set

setBeta() - Method in class snakeprogram3d.SnakeFrame

Trys to set the 'beta' value.

setBeta(double) - Method in class snakeprogram3d.SnakeModel

setBeta(double) - Method in class snakeprogram3d.ThreeDDeformation

setColor(int) - Method in class snakeprogram3d.display3d.PolyLine

setConstants(HashMap<String, Double>) - Method in class snakeprogram.SnakeFrame

setConstants(HashMap<String, Double>) - Method in class snakeprogram3d.SnakeFrame

loads the default values for a HashMap

setCurrentSnake(Snake) - Method in class snakeprogram.SnakeImages

setCurrentSnake(Snake) - Method in class snakeprogram3d.SnakeImages

setDefaultConstants() - Method in class snakeprogram3d.SnakeModel

setDeformIterations(int) - Method in class snakeprogram3d.SnakeModel

setDrawSnake(boolean) - Method in class snakeprogram.SnakeImages

setDrawSnake(boolean) - Method in class snakeprogram3d.SnakeImages

setFixSnakePoints() - Method in class snakeprogram3d.SnakeModel

Sets the flag so the next click on the image pane extends the snake to the click location

setFollow(boolean) - Method in class snakeprogram.SnakeImages

setFollow(boolean) - Method in class snakeprogram3d.SnakeImages

setForegroundIntensity() - Method in class snakeprogram.SnakeFrame

setForegroundIntensity() - Method in class snakeprogram3d.SnakeFrame

Trys to set the 'foreground' value.

setForegroundIntensity(double) - Method in class snakeprogram3d.SnakeModel

setForInt(double) - Method in class snakeprogram.TwoDDeformation

This needs to be set

setForInt(double) - Method in class snakeprogram3d.ThreeDDeformation

setGamma() - Method in class snakeprogram.SnakeFrame

setGamma(double) - Method in class snakeprogram.TwoDDeformation

Needs to be set

setGamma() - Method in class snakeprogram3d.SnakeFrame

Trys to set the 'gamma' value.

setGamma(double) - Method in class snakeprogram3d.SnakeModel

setGamma(double) - Method in class snakeprogram3d.ThreeDDeformation

setGridLayout() - Method in class snakeprogram3d.SnakeFrame

sets the 2x2 layout with all three views.

setImageSmoothing(double) - Method in class snakeprogram3d.SnakeImages

setImageSmoothing(double) - Method in class snakeprogram3d.SnakeModel

sets the sigma of the image smoothing term.

setInitializing(boolean) - Method in class snakeprogram.SnakeImages

setInitializing(boolean) - Method in class snakeprogram3d.display3d.InteractiveView

While initializing a line is drawn to the cursor.

setInitializing(boolean) - Method in class snakeprogram3d.SnakeImages

setInteractPanel(Component) - Method in class snakeprogram3d.SnakeFrame

The interactive view is created afterwards, this set one of the variable panels to be the interactive view.

setMarker(double[]) - Method in class snakeprogram.SnakeImages

setMaxDrawingBounds(int, int) - Method in class snakeprogram3d.SnakeImages

setMaxDrawingBounds(int, int) - Method in class snakeprogram3d.SnakeModel

When the view changes size this can be 800 or 400, should be scalable though.

setNumberOfSnakesLabel(int) - Method in class snakeprogram.SnakeFrame

setNumberOfSnakesLabel(int) - Method in class snakeprogram3d.SnakeFrame

Updates the number of snakes label

setOffset(double, double, double) - Method in class snakeprogram3d.display3d.BoundaryLine

setOffset(double, double, double) - Method in class snakeprogram3d.display3d.VariableTextured3dSurface

setPosition(double[]) - Method in class snakeprogram3d.display3d.VariableTextured3dSurface

setProperties() - Static method in class snakeprogram.SnakeApplication

setProperties() - Static method in class snakeprogram3d.SnakeApplication

Sets the Maximum Number of points in a filament.

setRawData(ArrayList<double[]>) - Method in class snakeprogram.SnakeImages

setRawData(ArrayList<double[]>) - Method in class snakeprogram3d.SnakeImages

setResolution(double) - Method in class snakeprogram3d.SnakeModel

setSelected(Snake) - Method in class snakeprogram3d.display3d.InteractiveView

There is a selected snake, it is red and clickable.

setSelected(Snake) - Method in class snakeprogram3d.display3d.ThreeDSnake

setSingleLayout(Component) - Method in class snakeprogram3d.SnakeFrame

places a single component in prominace.

setSnakes(MultipleSnakesStore) - Method in class snakeprogram.SnakeImages

setSnakes(MultipleSnakesStore) - Method in class snakeprogram3d.SnakeImages

setStretch() - Method in class snakeprogram.SnakeFrame

setStretch(double) - Method in class snakeprogram.TwoDDeformation

No default value needs to be set for TwoDCurveDeformations

setStretch() - Method in class snakeprogram3d.SnakeFrame

Trys to set the 'stretch' value.

setStretch(double) - Method in class snakeprogram3d.SnakeModel

setStretch(double) - Method in class snakeprogram3d.ThreeDDeformation

setStretchFix(boolean) - Method in class snakeprogram.SnakeImages

setTexture(Texture3D) - Method in class snakeprogram3d.display3d.ThreeDSurface

setTexture(Texture3D) - Method in class snakeprogram3d.display3d.VariableTextured3dSurface

setType(int) - Method in class snakeprogram3d.ThreeDEvent

setup(String, ImagePlus) - Method in class snakeprogram.SnakeApplication

setView() - Method in class snakeprogram3d.SnakeFrame

decides the componenet to be displayed then revalidates the main Frame

setWeight() - Method in class snakeprogram.SnakeFrame

setWeight(double) - Method in class snakeprogram.TwoDDeformation

This needs to be set

setWeight() - Method in class snakeprogram3d.SnakeFrame

Trys to set the 'weight' value.

setWeight(double) - Method in class snakeprogram3d.SnakeModel

setWeight(double) - Method in class snakeprogram3d.ThreeDDeformation

setZoomIn(boolean) - Method in class snakeprogram.SnakeImages

setZoomIn(boolean) - Method in class snakeprogram3d.SnakeImages

setZoomInBox(boolean) - Method in class snakeprogram.SnakeImages

setZoomInBox(boolean) - Method in class snakeprogram3d.SnakeImages

setZoomLocation(int, int) - Method in class snakeprogram.SnakeImages

setZoomLocation(int, int) - Method in class snakeprogram3d.SnakeImages

setZResolution(double) - Method in class snakeprogram3d.SnakeImages

returns the height in PIXELS zero height corresponds to frame 1

setZResolution(double) - Method in class snakeprogram3d.SnakeModel

Sets the zresolution and refreshes the display.

showAbout() - Static method in class snakeprogram3d.HelpMessages

Shows 'about.html' which has some credits and

showHelp() - Static method in class snakeprogram3d.HelpMessages

Creats a JFrame containing a JEditor pane displaying 'parameters.html' which contains a list of the parameters used and a list of the button functions

sliceFromHeight(double) - Method in class snakeprogram3d.SnakeImages

returns the slice as a double, which gives the fraction between slices for interpolating.

SLICES - Variable in class snakeprogram3d.SnakeBufferedImages

SLICES - Variable in class snakeprogram3d.SnakeImages

Snake - Class in snakeprogram

Snake(int) - Constructor for class snakeprogram.Snake

Creates a new snake does not have any position data

Snake(ArrayList<double[]>, int, int) - Constructor for class snakeprogram.Snake

Creates a new snake with position data.

Snake - Class in snakeprogram3d

Basic snake, essentially a tree map containing all of the points of the snakes.

Snake() - Constructor for class snakeprogram3d.Snake

Snake(ArrayList<double[]>, int) - Constructor for class snakeprogram3d.Snake

SnakeActions - Enum in snakeprogram3d

The action commands for all of the buttons, menu items and parameters.

SnakeApplication - Class in snakeprogram

SnakeApplication() - Constructor for class snakeprogram.SnakeApplication

SnakeApplication - Class in snakeprogram3d

SnakeApplication() - Constructor for class snakeprogram3d.SnakeApplication

SnakeBufferedImages - Class in snakeprogram3d

Class for linking the 2D image plus image stack with the 3D volume stacks.

SnakeFrame - Class in snakeprogram

Main user interface.

SnakeFrame(SnakeModel) - Constructor for class snakeprogram.SnakeFrame

SnakeFrame - Class in snakeprogram3d

Main control panel, is divided into four regions, the Image/3D view region, a tabbed panel with controls, and a status region on the bottom.

SnakeFrame(SnakeModel) - Constructor for class snakeprogram3d.SnakeFrame

SnakeImages - Class in snakeprogram

A class for controlling the image data.

SnakeImages - Class in snakeprogram3d

A class for accessing original and or smoothed image data.

SnakeIO - Class in snakeprogram

This class is used for reading and writing snakes.

SnakeIO() - Constructor for class snakeprogram.SnakeIO

SnakeIO - Class in snakeprogram3d

Mostly static class for reading and writing snakes.

SnakeIO() - Constructor for class snakeprogram3d.SnakeIO

SnakeListener - Class in snakeprogram

starts actions that have been initiated via the UI are managed here.

SnakeModel - Class in snakeprogram3d

snakePanelMouseMoved(MouseEvent) - Method in class snakeprogram3d.SnakeModel

Handles two types of mouse moved events.

snakePanelMousePressed(MouseEvent) - Method in class snakeprogram3d.SnakeModel

When the mouse is pressed over the snake panel, transforms the click to a 3d event

snakeprogram - package snakeprogram

snakeprogram3d - package snakeprogram3d

snakeprogram3d.display3d - package snakeprogram3d.display3d

stopRunningNicely() - Method in class snakeprogram3d.SnakeModel

Causes a deform iterations

switchCards() - Method in class snakeprogram3d.SnakeFrame

Changes the display type by incrementing to the next one

switchCards() - Method in class snakeprogram3d.SnakeModel

For changing the view configuration.

synchronizeSnakes(MultipleSnakesStore) - Method in class snakeprogram3d.display3d.InteractiveView

Removes all old snakes and adds any snakes that need to be displayed in this frame.

synchronizeSnakes(MultipleSnakesStore) - Method in class snakeprogram3d.display3d.ThreeDSnake

Removes all snakes and displays the snakes in ss.