retina
Class OIDStackWindow

java.lang.Object
  |
  +--java.awt.Component
        |
        +--java.awt.Container
              |
              +--java.awt.Window
                    |
                    +--java.awt.Frame
                          |
                          +--ij.gui.ImageWindow
                                |
                                +--ij.gui.StackWindow
                                      |
                                      +--retina.OIDStackWindow
All Implemented Interfaces:
javax.accessibility.Accessible, java.awt.event.ActionListener, java.awt.event.AdjustmentListener, java.util.EventListener, java.awt.event.FocusListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.lang.Runnable, java.io.Serializable, java.awt.event.WindowListener
Direct Known Subclasses:
OIDWindow

public class OIDStackWindow
extends ij.gui.StackWindow
implements java.lang.Runnable

Optical Imaging frame sequence analysis. Many methods to aggregate and analyze the frames in epochs acoording to different methods using ImageJ. (c) 2003 Michael Abramoff. All rights reserved.

See Also:
Serialized Form

Inner classes inherited from class java.awt.Frame
java.awt.Frame.AccessibleAWTFrame
 
Inner classes inherited from class java.awt.Window
java.awt.Window.AccessibleAWTWindow
 
Inner classes inherited from class java.awt.Container
java.awt.Container.AccessibleAWTContainer
 
Inner classes inherited from class java.awt.Component
java.awt.Component.AccessibleAWTComponent, java.awt.Component.AWTTreeLock
 
Field Summary
 OIDProcessor processor
           
 
Fields inherited from class ij.gui.StackWindow
done, slice, sliceSelector, thread
 
Fields inherited from class ij.gui.ImageWindow
closed, ic, ij, imp, running, running2
 
Fields inherited from class java.awt.Frame
CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, HAND_CURSOR, icon, ICONIFIED, mbManagement, menuBar, MOVE_CURSOR, N_RESIZE_CURSOR, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, ownedWindows, resizable, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, SW_RESIZE_CURSOR, TEXT_CURSOR, title, W_RESIZE_CURSOR, WAIT_CURSOR
 
Fields inherited from class java.awt.Window
inputContext, OPENED, ownedWindowList, state, warningString, windowListener
 
Fields inherited from class java.awt.Container
component, containerListener, layoutMgr, listeningBoundsChildren, listeningChildren, ncomponents
 
Fields inherited from class java.awt.Component
accessibleContext, actionListenerK, adjustmentListenerK, appContext, background, BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, componentListener, componentListenerK, componentOrientation, containerListenerK, cursor, dropTarget, enabled, eventMask, focusListener, focusListenerK, font, foreground, graphicsConfig, hasFocus, height, hierarchyBoundsListener, hierarchyBoundsListenerK, hierarchyListener, hierarchyListenerK, incRate, inputMethodListener, inputMethodListenerK, isInc, isPacked, itemListenerK, keyListener, keyListenerK, LEFT_ALIGNMENT, locale, LOCK, metrics, minSize, mouseListener, mouseListenerK, mouseMotionListener, mouseMotionListenerK, newEventsOnly, ownedWindowK, parent, peer, peerFont, popups, prefSize, RIGHT_ALIGNMENT, textListenerK, TOP_ALIGNMENT, valid, visible, width, windowClosingException, windowListenerK, x, y
 
Fields inherited from interface java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH
 
Constructor Summary
OIDStackWindow(ij.ImagePlus imp)
          Start an OIDProcessor for imp.
OIDStackWindow(ij.ImagePlus imp, ij.gui.ImageCanvas ic, ij.io.FileInfo fi, java.lang.String[] epochNames)
          Start an OIDProcessor for imp.
 
Method Summary
 float[][] diffPairwise(float[][] a, int length, int start, int end)
          Perform pairwise differencing on all conditions.
 void run()
           
 void saveTimecourse(int length, int start, int end)
          Save the timecourse as a TIFF file.
 
Methods inherited from class ij.gui.StackWindow
actionPerformed, adjustmentValueChanged, close, showSlice, updateSliceSelector
 
Methods inherited from class ij.gui.ImageWindow
, centerNextImage, copy, drawInfo, focusGained, focusLost, getCanvas, getClipboard, getImagePlus, getInitialMagnification, getInsets, isClosed, mouseMoved, paint, paste, setImagePlus, toString, updateImage, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened
 
Methods inherited from class java.awt.Frame
addNotify, addToFrameList, constructComponentName, finalize, getAccessibleContext, getCursorType, getFrames, getIconImage, getMenuBar, getState, getTitle, isResizable, paramString, postProcessKeyEvent, remove, removeFromFrameList, removeNotify, setCursor, setIconImage, setMenuBar, setResizable, setState, setTitle
 
Methods inherited from class java.awt.Window
addOwnedWindow, addWindowListener, adjustListeningChildren, applyResourceBundle, applyResourceBundle, connectOwnedWindow, dispatchEventImpl, dispose, eventEnabled, getFocusOwner, getGraphicsConfiguration, getInputContext, getListeners, getLocale, getOwnedWindows, getOwner, getToolkit, getWarningString, hide, isActive, isShowing, nextFocus, pack, postEvent, postWindowEvent, preProcessKeyEvent, processEvent, processWindowEvent, removeOwnedWindow, removeWindowListener, resetGC, setCursor, setFocusOwner, show, toBack, toFront, transferFocus
 
Methods inherited from class java.awt.Container
add, add, add, add, add, addContainerListener, addImpl, applyOrientation, checkGD, countComponents, createChildHierarchyEvents, createHierarchyEvents, deliverEvent, dispatchEventToSelf, doLayout, findComponentAt, findComponentAt, findComponentAt, getAccessibleAt, getAccessibleChild, getAccessibleChildrenCount, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents_NoClientCode, getComponents, getLayout, getMaximumSize, getMinimumSize, getMouseEventTarget, getPreferredSize, getWindow, insets, invalidate, invalidateTree, isAncestorOf, layout, lightweightPaint, lightweightPrint, list, list, locate, minimumSize, numListening, paintComponents, paintHeavyweightComponents, postsOldMouseEvents, preferredSize, print, printComponents, printHeavyweightComponents, processContainerEvent, proxyEnableEvents, proxyRequestFocus, remove, remove, removeAll, removeContainerListener, setFont, setLayout, update, validate, validateTree
 
Methods inherited from class java.awt.Component
action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addPropertyChangeListener, addPropertyChangeListener, areInputMethodsEnabled, bounds, checkImage, checkImage, checkWindowClosingException, coalesceEvents, contains, contains, createImage, createImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, getAccessibleIndexInParent, getAccessibleStateSet, getBackground, getBounds, getBounds, getColorModel, getComponentOrientation, getCursor, getDropTarget, getFont_NoClientCode, getFont, getFontMetrics, getForeground, getGraphics, getHeight, getInputMethodRequests, getLocation, getLocation, getLocationOnScreen_NoTreeLock, getLocationOnScreen, getName, getNativeContainer, getParent_NoClientCode, getParent, getPeer, getSize, getSize, getToolkitImpl, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isDisplayable, isDoubleBuffered, isEnabled, isEnabledImpl, isFocusTraversable, isLightweight, isOpaque, isRecursivelyVisible, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, reshape, resize, resize, setBackground, setBounds, setBounds, setComponentOrientation, setDropTarget, setEnabled, setForeground, setLocale, setLocation, setLocation, setName, setSize, setSize, setVisible, show, size, transferFocus
 
Methods inherited from class java.lang.Object
clone, equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface java.awt.MenuContainer
getFont, postEvent
 

Field Detail

processor

public OIDProcessor processor
Constructor Detail

OIDStackWindow

public OIDStackWindow(ij.ImagePlus imp,
                      ij.gui.ImageCanvas ic,
                      ij.io.FileInfo fi,
                      java.lang.String[] epochNames)
Start an OIDProcessor for imp.
Parameters:
imp - the ImagePlus that contains the frames (or the first ImagePlus if there are multiple).

OIDStackWindow

public OIDStackWindow(ij.ImagePlus imp)
Start an OIDProcessor for imp.
Parameters:
imp - the ImagePlus that contains the frames (or the first ImagePlus if there are multiple).
Method Detail

run

public void run()
Specified by:
run in interface java.lang.Runnable
Overrides:
run in class ij.gui.StackWindow

saveTimecourse

public void saveTimecourse(int length,
                           int start,
                           int end)
Save the timecourse as a TIFF file.

diffPairwise

public float[][] diffPairwise(float[][] a,
                              int length,
                              int start,
                              int end)
Perform pairwise differencing on all conditions.
Parameters:
a - the frames.
length - the number of frames per conditions.
start - the start frame of the stimulus
end - the last frame for the stimulus
Returns:
a float[][] containg the pairwise subtraction of each condition.