snakeprogram3d
Class SnakeModel

java.lang.Object
  snakeprogram3d.SnakeModel

public class SnakeModel
extends java.lang.Object

Method Summary

void	addSnake() Starts the initialize snake process where SnakeRaw? are the transient snake coordinates.
void	autoDetectIntensities() Tries to determine the forground/background values automatically.
boolean	checkForCurrentSnake() This is used before attempting to modify the current snake such as with a fix or deform button press.
void	clearCurrentSnake()
void	clearScreen() removes all snakes from the current frame
void	decreaseMax() for adjusting brightness/contrast
void	decreaseMin() for adjusting brightness/contrast
void	deformRunning() Deforms the Current Snake.
void	deformSnake() Causes the deformation of a snake to occur
void	deleteEndFix() Disables UI and Deletes and end
void	deleteMiddleFix() Disables the UI and begins the Delete Middle fix
void	deleteSnake() deletes the current snake and selects the next one
void	deleteSnake(Snake s) Delets a snake
void	disableUI() stops any other input except for the MouseListener on the displayed Image
void	enableUI() enables buttons
void	finishDisplay() Creates volume data and submits the job to the main process.
java.lang.String	formatNumber(double value) Limits the display to two decimal points, or scientific notation if the number is out of a certain range.
void	getAndLoadImage() These are short access to images so the frame doesn't need to know about the SnakeImages class
void	getBackgroundIntensity() Sets the flag so the next time the snake panel is clicked background intesity will be calcularted
double[]	getClosestSnakePoint(double x, double y, double z) For getting the closest point on the current snake.
int	getDeformIterations()
int	getDrawHeight() short access to images so the frame doesn't need to know about the SnakeImages class
int	getDrawWidth() These are short access to images so the frame doesn't need to know about the SnakeImages class
void	getForegroundIntensity() Sets the flag so the next time the snake panel is clicked foreground intesity will be calcularted
javax.swing.JFrame	getFrame() Gets the frame used for dialogs.
java.awt.Image	getImage() short access to images so the frame doesn't need to know about the SnakeImages class
java.lang.String	getImageTitle() gets the filename of the open imageplus.
int	getNFrames()
int	getNSlices()
boolean	hasImage() After an image has been opened to make sure it has properly been loaded.
void	increaseMax() for adjusting brightness/contrast
void	increaseMin() for adjusting brightness/contrast
void	initializeZoomIn() Disables UI and begins a zoom in routine
void	loadImage(ij.ImagePlus implus) Loads an image from an existing image plus the principle useage of this function is to load an image when started through ImageJ.
void	loadSnake() Loads a snake from a file and sets the constant values in the snake panel.
void	mouseMoved(ThreeDEvent tde) Generated during a mouse move event, from 2d panel or the 3d views.
void	mousePressed(ThreeDEvent tde) Handles all mouse events in the 3d image coordnate space.
void	moveDown() Moves the YZ plane
void	moveUp() Moves the YZ plane
void	nextFrame() Next volume stack in time.
void	nextImage() moves to the next image
void	previousFrame() Previous volume stack in time.
void	previousImage() moves to the previous image
void	reduce3D(boolean t) Causes the model to use a reduced version of the 3d image.
void	saveElongationData() Save all of the snakes elongation data
void	saveSnake() Save all of the snakes data, so that they may be reloaded
void	selectNextSnake()
void	selectSnake(java.awt.event.MouseEvent evt) A MouseEvent version of the snake selector
void	selectSnake(ThreeDEvent tde) Chooses the nearest snake.
void	setAlpha(double a)
void	setBackgroundIntensity(double fim)
void	setBeta(double b)
void	setDefaultConstants()
void	setDeformIterations(int di)
void	setFixSnakePoints() Sets the flag so the next click on the image pane extends the snake to the click location
void	setForegroundIntensity(double f)
void	setGamma(double g)
void	setImageSmoothing(double v) sets the sigma of the image smoothing term.
void	setMaxDrawingBounds(int W, int H) When the view changes size this can be 800 or 400, should be scalable though.
void	setResolution(double res)
void	setStretch(double s)
void	setWeight(double w)
void	setZResolution(double mon) Sets the zresolution and refreshes the display.
void	snakePanelMouseMoved(java.awt.event.MouseEvent evt) Handles two types of mouse moved events.
void	snakePanelMousePressed(java.awt.event.MouseEvent evt) When the mouse is pressed over the snake panel, transforms the click to a 3d event
void	stopRunningNicely() Causes a deform iterations
void	switchCards() For changing the view configuration.
void	trackSnake() Goes to the next frame and copies the current snake.
void	trackSnakeBackwards() Goes to the previous frame and copies the current snake.
void	updateDisplay() Updates both displays.
void	updateFrame()
void	updateImagePanel() Updates the image panel and relevant properties.
void	updateThreeDDisplay() updates the snakes positions, should be called from the PROC thread.
void	validateSnakes()
void	wipeDown()
void	wipeUp()
void	zoomOut() resets the zoom to the orginal image size

Methods inherited from class java.lang.Object

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

Method Detail

deformRunning

public void deformRunning()
                   throws java.lang.IllegalAccessException

Deforms the Current Snake. This method should not be executed on the event thread but instead should be placed on the Snake event loop, PROC.

Throws:

java.lang.IllegalAccessException - occurs when the snake is too short.

snakePanelMousePressed

public void snakePanelMousePressed(java.awt.event.MouseEvent evt)

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

Parameters:

evt - the generated mouse event.

mousePressed

public void mousePressed(ThreeDEvent tde)

Handles all mouse events in the 3d image coordnate space.

Parameters:

tde - Event that is handled in 3d image space.

snakePanelMouseMoved

public void snakePanelMouseMoved(java.awt.event.MouseEvent evt)

Handles two types of mouse moved events. 2d Events are processed for zooming and adding a snake. Then a 3d event is generated for updating the 3d views.

Parameters:

evt - mouse event.

mouseMoved

public void mouseMoved(ThreeDEvent tde)

Generated during a mouse move event, from 2d panel or the 3d views.

Parameters:

tde - event in image space

getClosestSnakePoint

public double[] getClosestSnakePoint(double x,
                                     double y,
                                     double z)

For getting the closest point on the current snake.

Parameters:

x - cnet

y - cnet

z - cnet

Returns:

xyz array.

formatNumber

public java.lang.String formatNumber(double value)

Limits the display to two decimal points, or scientific notation if the number is out of a certain range.

Parameters:

value - number to be represented by a string

Returns:

string

selectSnake

public void selectSnake(java.awt.event.MouseEvent evt)

A MouseEvent version of the snake selector

Parameters:

evt - original mouse event.

selectSnake

public void selectSnake(ThreeDEvent tde)

Chooses the nearest snake. This method is called by another listener added by the snake_frame which is enabled or disable along with the rest of the GUI.

Parameters:

tde - image space

saveElongationData

public void saveElongationData()

Save all of the snakes elongation data

saveSnake

public void saveSnake()

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

loadSnake

public void loadSnake()

Loads a snake from a file and sets the constant values in the snake panel.

trackSnake

public void trackSnake()

Goes to the next frame and copies the current snake. then deforms that snake.

trackSnakeBackwards

public void trackSnakeBackwards()

Goes to the previous frame and copies the current snake. then deforms that snake.

deleteMiddleFix

public void deleteMiddleFix()

Disables the UI and begins the Delete Middle fix

deleteEndFix

public void deleteEndFix()

Disables UI and Deletes and end

previousImage

public void previousImage()

moves to the previous image

nextImage

public void nextImage()

moves to the next image

initializeZoomIn

public void initializeZoomIn()

Disables UI and begins a zoom in routine

deleteSnake

public void deleteSnake()

deletes the current snake and selects the next one

deleteSnake

public void deleteSnake(Snake s)

Delets a snake

Parameters:

s - the snake that will be deleted.

clearScreen

public void clearScreen()

removes all snakes from the current frame

getForegroundIntensity

public void getForegroundIntensity()

Sets the flag so the next time the snake panel is clicked foreground intesity will be calcularted

getBackgroundIntensity

public void getBackgroundIntensity()

Sets the flag so the next time the snake panel is clicked background intesity will be calcularted

zoomOut

public void zoomOut()

resets the zoom to the orginal image size

addSnake

public void addSnake()

Starts the initialize snake process where SnakeRaw? are the transient snake coordinates.

deformSnake

public void deformSnake()

Causes the deformation of a snake to occur

setFixSnakePoints

public void setFixSnakePoints()

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

getAndLoadImage

public void getAndLoadImage()

These are short access to images so the frame doesn't need to know about the SnakeImages class

autoDetectIntensities

public void autoDetectIntensities()

Tries to determine the forground/background values automatically. Usually fails.

getDrawHeight

public int getDrawHeight()

short access to images so the frame doesn't need to know about the SnakeImages class

Returns:

height of space for drawing image.

getImage

public java.awt.Image getImage()

short access to images so the frame doesn't need to know about the SnakeImages class

Returns:

awt version of image.

getDrawWidth

public int getDrawWidth()

These are short access to images so the frame doesn't need to know about the SnakeImages class

Returns:

width available for drawing image.

getFrame

public javax.swing.JFrame getFrame()

Gets the frame used for dialogs.

Returns:

main frame of application

getNSlices

public int getNSlices()

Returns:

number of slices per frame

getNFrames

public int getNFrames()

Returns:

number of frames.

hasImage

public boolean hasImage()

After an image has been opened to make sure it has properly been loaded.

Returns:

image ready

getDeformIterations

public int getDeformIterations()

Returns:

the number of iterations when deform iterations is clicked.

setDeformIterations

public void setDeformIterations(int di)

Parameters:

di - number of iterations per deform iteration click.

setZResolution

public void setZResolution(double mon)

Sets the zresolution and refreshes the display.

Parameters:

mon - zspacing

setResolution

public void setResolution(double res)

setBackgroundIntensity

public void setBackgroundIntensity(double fim)

setForegroundIntensity

public void setForegroundIntensity(double f)

setAlpha

public void setAlpha(double a)

setBeta

public void setBeta(double b)

setGamma

public void setGamma(double g)

setWeight

public void setWeight(double w)

setStretch

public void setStretch(double s)

setImageSmoothing

public void setImageSmoothing(double v)

sets the sigma of the image smoothing term.

Parameters:

v - standard deviation of the gaussian filter.

loadImage

public void loadImage(ij.ImagePlus implus)

Loads an image from an existing image plus the principle useage of this function is to load an image when started through ImageJ.

Parameters:

implus - the ImagePlus preloaded via ImageJ

finishDisplay

public void finishDisplay()

Creates volume data and submits the job to the main process. this is called whenever the zresolution changes, image smoothing changes, +/- MIN & MAX changes.

updateDisplay

public void updateDisplay()

Updates both displays.

updateImagePanel

public void updateImagePanel()

Updates the image panel and relevant properties.

updateThreeDDisplay

public void updateThreeDDisplay()

updates the snakes positions, should be called from the PROC thread.

disableUI

public void disableUI()

stops any other input except for the MouseListener on the displayed Image

enableUI

public void enableUI()

enables buttons

checkForCurrentSnake

public boolean checkForCurrentSnake()

This is used before attempting to modify the current snake such as with a fix or deform button press.

Returns:

current snake is set.

stopRunningNicely

public void stopRunningNicely()

Causes a deform iterations

getImageTitle

public java.lang.String getImageTitle()

gets the filename of the open imageplus.

Returns:

name of image

moveUp

public void moveUp()

Moves the YZ plane

moveDown

public void moveDown()

Moves the YZ plane

wipeDown

public void wipeDown()

wipeUp

public void wipeUp()

switchCards

public void switchCards()

For changing the view configuration.

setMaxDrawingBounds

public void setMaxDrawingBounds(int W,
                                int H)

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

Parameters:

W - width

H - height

nextFrame

public void nextFrame()

Next volume stack in time.

previousFrame

public void previousFrame()

Previous volume stack in time.

increaseMax

public void increaseMax()

for adjusting brightness/contrast

decreaseMax

public void decreaseMax()

for adjusting brightness/contrast

increaseMin

public void increaseMin()

for adjusting brightness/contrast

decreaseMin

public void decreaseMin()

for adjusting brightness/contrast

updateFrame

public void updateFrame()

setDefaultConstants

public void setDefaultConstants()

reduce3D

public void reduce3D(boolean t)

Causes the model to use a reduced version of the 3d image.

Parameters:

t - Real resolution when false, and reduced resolution when true.

selectNextSnake

public void selectNextSnake()

clearCurrentSnake

public void clearCurrentSnake()

validateSnakes

public void validateSnakes()