woSource

Class MIPSviewer

java.lang.Object

woSource.ScreenSelectorClass

woSource.MIPSviewer

All Implemented Interfaces:

ij.plugin.PlugIn

Direct Known Subclasses:

MIPSviewerColor

public class MIPSviewer
extends ScreenSelectorClass
implements ij.plugin.PlugIn

WO 11/11/2011-1/2013 implements a user-interactive Maximum Intentisy Projection (MIP) viewer

11/16/11 works well: spins in real time, can throw the mouse to get automatic rotation, etc.

This permits one to display the 3D maximum intensity projection of an object in an image stack.
1. The object can be rotated in any direction using a mouse-drag (hold left button down while "dragging in the direction of rotation and while the HAND icon is selected on the ImageJ toolbar).
2. The object can be rotated hands-free (continuously, without input = spinning) by 'throwing' "the mouse cursor (release the mouse button while dragging in the desired direction). To stop "the automatic rotation, click the mouse anywhere on the window or hit the space bar.
3. Clipping permitted as a % of total viewing depth, where max depth is when viewing dataset "from the side or from the top (phi or theta = 90 degrees).
4. A movie (AVI) can be created by getting the object in continuous motion in the "desired direction and hitting the AVI button.
The projection calculation is done in real-time. Large datasets may need to be cropped or resized (Toolbar->Image->Scale) beforehand to speed up the interaction.\n\n");

See Also:

MIPSviewerColor

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected class	MIPSviewer.Updater

Field Summary

Fields

Modifier and Type	Field and Description
GenericRecallableDialog	gd
protected static ScreenSelectorCanvas	MIPs_canvas
protected MIPSviewer.Updater	updater

Constructor Summary

Constructors

Constructor and Description
MIPSviewer()

Method Summary

Modifier and Type	Method and Description
void	destroy()
void	getHeaderInfo(float sliceRatio)
protected void	getInitView()
protected ij.gui.Roi	getRoi()
void	hideGUI()
void	mouseDragged(java.awt.event.MouseEvent e)
void	mouseMoved(java.awt.event.MouseEvent e)
void	mousePressed(java.awt.event.MouseEvent e)
void	mouseReleased(java.awt.event.MouseEvent e)
void	redisplay()
void	resetView()
void	run(java.lang.String arg) This method is called when the plugin is loaded.
void	runGUI()
void	saveImage(java.lang.String type)
void	setup(boolean[][][] A)
void	setup(boolean[][][] A, float sliceRatio)
void	setup(boolean[][][] A, float sliceRatio, ij.ImagePlus passedimp)
void	setup(boolean[][][] A, float sliceRatio, ij.ImagePlus passedimp, java.util.Properties[] props)
void	setup(boolean[][][] A, float sliceRatio, java.util.Properties[] props)
void	setup(boolean[][][] A, ij.ImagePlus passedimp)
void	setup(byte[][][] A)
void	setup(byte[][][] A, float sliceRatio)
void	setup(byte[][][] A, float sliceRatio, ij.ImagePlus passedimp)
void	setup(byte[][][] A, float sliceRatio, ij.ImagePlus passedimp, java.util.Properties[] props)
void	setup(byte[][][] A, float sliceRatio, java.util.Properties[] props)
void	setup(byte[][][] A, ij.ImagePlus passedimp)
void	setup(short[][][] A)
void	setup(short[][][] A, float sliceRatio)
void	setup(short[][][] A, float sliceRatio, ij.ImagePlus passedimp)
void	setup(short[][][] A, float sliceRatio, ij.ImagePlus passedimp, java.util.Properties[] props)
void	setup(short[][][] A, float sliceRatio, java.util.Properties[] props)
void	setup(short[][][] A, ij.ImagePlus passedimp)
void	setupView(ij.ImagePlus passedimp, java.util.Properties[] props)
void	stop() WO 1/10/2015 I found and fixed a problem that when trying to destroy this MIPsviewer, it calls updater.quit(), which calls updater.inturrupt() and then sets the updater=null and viewAd=null, however the thread could still be inside called the spinning/resetview loop and/or computing the mipsviewbyte such that it will then try to write to the viewAd inside resetview() after the viewAd is killed.
void	toBack()
void	toFront()
void	UpdateSelection(int a, int b, java.lang.String keytype)
void	winLevel()
void	zoomIn()
void	zoomOut()

Methods inherited from class woSource.ScreenSelectorClass

keyPressed, UpdateScreen

Methods inherited from class java.lang.Object

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

Field Detail

gd

public GenericRecallableDialog gd

MIPs_canvas

protected static ScreenSelectorCanvas MIPs_canvas

updater

protected MIPSviewer.Updater updater

Constructor Detail

MIPSviewer

public MIPSviewer()

Method Detail

setup

public void setup(short[][][] A)

setup

public void setup(short[][][] A,
                  float sliceRatio)

setup

public void setup(short[][][] A,
                  ij.ImagePlus passedimp)

setup

public void setup(short[][][] A,
                  float sliceRatio,
                  ij.ImagePlus passedimp)

setup

public void setup(short[][][] A,
                  float sliceRatio,
                  java.util.Properties[] props)

setup

public void setup(short[][][] A,
                  float sliceRatio,
                  ij.ImagePlus passedimp,
                  java.util.Properties[] props)

setup

public void setup(boolean[][][] A)

setup

public void setup(boolean[][][] A,
                  float sliceRatio)

setup

public void setup(boolean[][][] A,
                  ij.ImagePlus passedimp)

setup

public void setup(boolean[][][] A,
                  float sliceRatio,
                  ij.ImagePlus passedimp)

setup

public void setup(boolean[][][] A,
                  float sliceRatio,
                  java.util.Properties[] props)

setup

public void setup(boolean[][][] A,
                  float sliceRatio,
                  ij.ImagePlus passedimp,
                  java.util.Properties[] props)

setup

public void setup(byte[][][] A)

setup

public void setup(byte[][][] A,
                  float sliceRatio)

setup

public void setup(byte[][][] A,
                  ij.ImagePlus passedimp)

setup

public void setup(byte[][][] A,
                  float sliceRatio,
                  ij.ImagePlus passedimp)

setup

public void setup(byte[][][] A,
                  float sliceRatio,
                  java.util.Properties[] props)

setup

public void setup(byte[][][] A,
                  float sliceRatio,
                  ij.ImagePlus passedimp,
                  java.util.Properties[] props)

setupView

public void setupView(ij.ImagePlus passedimp,
                      java.util.Properties[] props)

getInitView

protected void getInitView()

getHeaderInfo

public void getHeaderInfo(float sliceRatio)

run

public void run(java.lang.String arg)

Description copied from interface: ij.plugin.PlugIn

This method is called when the plugin is loaded. 'arg', which may be blank, is the argument specified for this plugin in IJ_Props.txt.

Specified by:

run in interface ij.plugin.PlugIn

runGUI

public void runGUI()

destroy

public void destroy()

hideGUI

public void hideGUI()

saveImage

public void saveImage(java.lang.String type)

winLevel

public void winLevel()

redisplay

public void redisplay()

resetView

public void resetView()

zoomIn

public void zoomIn()

zoomOut

public void zoomOut()

toFront

public void toFront()

toBack

public void toBack()

UpdateSelection

public void UpdateSelection(int a,
                            int b,
                            java.lang.String keytype)

Overrides:

UpdateSelection in class ScreenSelectorClass

mouseMoved

public void mouseMoved(java.awt.event.MouseEvent e)

Overrides:

mouseMoved in class ScreenSelectorClass

mousePressed

public void mousePressed(java.awt.event.MouseEvent e)

Overrides:

mousePressed in class ScreenSelectorClass

mouseReleased

public void mouseReleased(java.awt.event.MouseEvent e)

Overrides:

mouseReleased in class ScreenSelectorClass

mouseDragged

public void mouseDragged(java.awt.event.MouseEvent e)

Overrides:

mouseDragged in class ScreenSelectorClass

getRoi

protected ij.gui.Roi getRoi()

stop

public void stop()

WO 1/10/2015 I found and fixed a problem that when trying to destroy this MIPsviewer, it calls updater.quit(), which calls updater.inturrupt() and then sets the updater=null and viewAd=null, however the thread could still be inside called the spinning/resetview loop and/or computing the mipsviewbyte such that it will then try to write to the viewAd inside resetview() after the viewAd is killed. This either throws an exception error in updater, or creates a new zombie viewAd (depending on the code used in resetview). So I added the flag wantQuit that is set when updater.quit() is invoked, and read inside the spinning loop and inside resetview right before drawing to viewAd. This is a helper class for Orthogonal_Views that delegates the repainting of the destination windows to another thread.