snakeprogram3d
Class SnakeImages

java.lang.Object
  snakeprogram3d.SnakeImages

public class SnakeImages
extends java.lang.Object

A class for accessing original and or smoothed image data.

Field Summary

int	FRAMES
double	MAXPIXEL
double	MINPIXEL
int	SLICES

Method Summary

boolean	checkSnake()
void	drawRawSnake(ij.process.ImageProcessor improc) This method is called by updateDisplay() and draws the points in SnakeRaw to the screen connected by a line.
void	drawSnake(Snake s, ij.process.ImageProcessor improc)
void	drawSnakes(ij.process.ImageProcessor imp) Draws all of the snakes in SnakeStore
double	fromZoomX(double newX) this method takes an X coordinates and returns its position in the original, un-zoomed, image
double	fromZoomY(double newY) this method takes an Y coordinates and returns position in the original, un-zoomed, image
ij.ImagePlus	getAndLoadImage(javax.swing.JFrame xx) Gets a file name via the swing file chooser dialog
double[]	getAutoIntensities() not a good function
int	getCurrentFrame()
int	getCurrentSlice()
double	getDepth()
java.io.File	getFile()
int	getHeight()
int	getNFrames()
int	getNSlices() Returns the total number of slices
ij.ImagePlus	getOriginalPlus()
double	getPixel(double x, double y, double z) Gets the Smoothed pixel value from the image.
java.lang.String	getTitle()
int	getWidth()
double	getZResolution()
boolean	hasImage()
double	heightFromSlice() finds the height using the current slice as the reference
double	heightFromSlice(double slice) returns the height in PIXELS zero height corresponds to frame 1
void	loadImage(ij.ImagePlus implus)
void	nextFrame()
void	nextImage()
void	previousFrame()
void	previousImage()
void	resetZoom() Sets the zoom box to be the whole image
void	setCurrentSnake(Snake cs)
void	setDrawSnake(boolean v)
void	setFollow(boolean v)
void	setImageSmoothing(double v)
void	setInitializing(boolean v)
void	setMaxDrawingBounds(int w, int h)
void	setRawData(java.util.ArrayList<double[]> xv)
void	setSnakes(MultipleSnakesStore mss)
void	setZoomIn(boolean v)
void	setZoomInBox(boolean v)
void	setZoomLocation(int x, int y)
void	setZResolution(double value) returns the height in PIXELS zero height corresponds to frame 1
double	sliceFromHeight(double height) returns the slice as a double, which gives the fraction between slices for interpolating.
double	toZoomX(double oldX) this method takes an X coordinate on the original image and finds its new position on a zoomed image
double	toZoomY(double oldY) takes an Y coordinate on the original image and finds its new position on a zoomed image
void	trackingZoomBox(int x, int y)
void	updateImagePanel()
void	updateMousePosition(double x, double y) This is used for following the mouse it requres the image coordinates

Methods inherited from class java.lang.Object

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

Field Detail

SLICES

public int SLICES

FRAMES

public int FRAMES

MAXPIXEL

public double MAXPIXEL

MINPIXEL

public double MINPIXEL

Method Detail

hasImage

public boolean hasImage()

getZResolution

public double getZResolution()

updateImagePanel

public void updateImagePanel()

trackingZoomBox

public void trackingZoomBox(int x,
                            int y)

setZoomInBox

public void setZoomInBox(boolean v)

setZoomIn

public void setZoomIn(boolean v)

setRawData

public void setRawData(java.util.ArrayList<double[]> xv)

checkSnake

public boolean checkSnake()

setDrawSnake

public void setDrawSnake(boolean v)

setFollow

public void setFollow(boolean v)

getOriginalPlus

public ij.ImagePlus getOriginalPlus()

updateMousePosition

public void updateMousePosition(double x,
                                double y)

This is used for following the mouse it requres the image coordinates

drawRawSnake

public void drawRawSnake(ij.process.ImageProcessor improc)

This method is called by updateDisplay() and draws the points in SnakeRaw to the screen connected by a line. Before doing this, it transforms the coordinates in these vectors based on the current zoom status. The new coordinates are then stored in the vectors, SnakeDrawX and SnakeDrawY. If the program is drawing a closed contour, the program will connect the first and last points of the snake.

drawSnake

public void drawSnake(Snake s,
                      ij.process.ImageProcessor improc)

drawSnakes

public void drawSnakes(ij.process.ImageProcessor imp)

Draws all of the snakes in SnakeStore

resetZoom

public void resetZoom()

Sets the zoom box to be the whole image

setZoomLocation

public void setZoomLocation(int x,
                            int y)

fromZoomX

public double fromZoomX(double newX)

this method takes an X coordinates and returns its position in the original, un-zoomed, image

fromZoomY

public double fromZoomY(double newY)

this method takes an Y coordinates and returns position in the original, un-zoomed, image

toZoomX

public double toZoomX(double oldX)

this method takes an X coordinate on the original image and finds its new position on a zoomed image

toZoomY

public double toZoomY(double oldY)

takes an Y coordinate on the original image and finds its new position on a zoomed image

getAndLoadImage

public ij.ImagePlus getAndLoadImage(javax.swing.JFrame xx)

Gets a file name via the swing file chooser dialog

getNSlices

public int getNSlices()

Returns the total number of slices

getNFrames

public int getNFrames()

getCurrentFrame

public int getCurrentFrame()

getCurrentSlice

public int getCurrentSlice()

nextImage

public void nextImage()

previousImage

public void previousImage()

nextFrame

public void nextFrame()

previousFrame

public void previousFrame()

loadImage

public void loadImage(ij.ImagePlus implus)

setInitializing

public void setInitializing(boolean v)

setCurrentSnake

public void setCurrentSnake(Snake cs)

setSnakes

public void setSnakes(MultipleSnakesStore mss)

getAutoIntensities

public double[] getAutoIntensities()

not a good function

heightFromSlice

public double heightFromSlice(double slice)

returns the height in PIXELS zero height corresponds to frame 1

Parameters:

slice - frame number starts at 1.

heightFromSlice

public double heightFromSlice()

finds the height using the current slice as the reference

sliceFromHeight

public double sliceFromHeight(double height)

returns the slice as a double, which gives the fraction between slices for interpolating. a height of zero corresponds to slice of 1, as per ImageJ slice.

setZResolution

public void setZResolution(double value)

returns the height in PIXELS zero height corresponds to frame 1

Parameters:

value - frame number starts at 1.

getPixel

public double getPixel(double x,
                       double y,
                       double z)

Gets the Smoothed pixel value from the image. This value is smoothed in all three directions.

Parameters:

x - cnet in pixels.

y - cnet in pixels.

z - cnet in pixels.

Returns:

pixel value

getHeight

public int getHeight()

Returns:

height of original image in px

getWidth

public int getWidth()

Returns:

width of original image in px

getDepth

public double getDepth()

Returns:

slices times zresolution

getTitle

public java.lang.String getTitle()

getFile

public java.io.File getFile()

setImageSmoothing

public void setImageSmoothing(double v)

setMaxDrawingBounds

public void setMaxDrawingBounds(int w,
                                int h)