Peak_Counter_Tool (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- fiji.tool.AbstractTool
- - fiji.tool.AbstractTrackingTool
  - - sc.fiji.timelapse.Peak_Counter_Tool

All Implemented Interfaces:

SliceListener, ToolWithOptions, ij.ImageListener, ij.plugin.PlugIn, KeyListener, MouseListener, MouseMotionListener, WindowFocusListener, EventListener
```
public class Peak_Counter_Tool
extends AbstractTrackingTool
implements KeyListener, ToolWithOptions
```
A peak counter for profile stacks

Nested Class Summary
- Nested classes/interfaces inherited from class fiji.tool.AbstractTool
  AbstractTool.KeyProxy, AbstractTool.KeyProxyIfNotConsumed, AbstractTool.MouseMotionProxy, AbstractTool.MouseMotionProxyIfNotConsumed, AbstractTool.MouseProxy, AbstractTool.MouseWheelProxy, AbstractTool.MouseWheelProxyIfNotConsumed, AbstractTool.ToolbarMouseAdapter

Field Summary

Fields
Modifier and Type	Field and Description
`protected IntArray[]`	`allPeaks`
`protected Map<ProfileStack,IntArray[]>`	`allPeaksMap`
`protected Map<ProfileStack,Integer>`	`firstAdjustedSlice`
`protected int`	`handle`
`protected ProfileStack`	`image`
`protected int`	`maxSpeed`
`protected ij.ImagePlus`	`peakCountPlot`
`protected double[]`	`peakCountPlotLimits`
`protected IntArray`	`peaks`
`protected int`	`slice`

Fields inherited from class fiji.tool.AbstractTrackingTool
activeHandle, handCursor, latestCurrentSlice, map, originalCursor

Fields inherited from class fiji.tool.AbstractTool
clearToolsIfNecessary, ijKeyProxy, keyProxy, mouseMotionProxy, mouseProxy, mouseWheelProxy, savedToolName, sliceListener, sliceObservers, toolActive, toolbar, toolbarMouseListener, toolID, toolToggleListener

Constructor Summary

Constructors
Constructor and Description

Peak_Counter_Tool()

Constructors
Constructor and Description
`Peak_Counter_Tool()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected int`	`addPeak(int x)`
`protected int`	`closeToPeak(int x, int y)`
`protected int`	`closeToPeak(int x, int y, double tolerance)`
`protected boolean`	`getImage(ij.ImagePlus image)`
`protected boolean`	`getImage(MouseEvent e)`
`protected IntArray`	`getPeaks(int slice)`
`String`	`getToolIcon()` Return the string encoding of the tool icon as it will appear in the toolbar.
`protected void`	`initializePeaks()`
`void`	`initializePeaks(int slice)`
`void`	`initializePeaks(int slice, int window, double minimalSlope)`
`void`	`keyPressed(KeyEvent e)`
`void`	`keyReleased(KeyEvent e)`
`void`	`keyTyped(KeyEvent e)`
`protected OvalRoi`	`mark(int distance)`
`protected OvalRoi`	`mark(int distance, Color color)`
`void`	`mouseClicked(MouseEvent e)`
`void`	`mouseDragged(MouseEvent e)`
`void`	`mouseEntered(MouseEvent e)`
`void`	`mouseExited(MouseEvent e)`
`void`	`mouseMoved(MouseEvent e)`
`void`	`mousePressed(MouseEvent e)`
`void`	`mouseReleased(MouseEvent e)`
`protected int`	`movePeak(int index, int x)`
`Roi`	`optimizeRoi(Roi roi, ij.process.ImageProcessor ip)`
`protected int`	`peakPosition(int x)`
`void`	`showOptionDialog()` When called, this method displays the configuration panel for the concrete implementation of this tool.
`void`	`sliceChanged(ij.ImagePlus image)`
`protected int`	`snapAndAddPeak(int x)`
`protected int`	`snapPeak(int slice, int x)`
`protected void`	`snapPeaks()`
`protected void`	`snapPeaks(int adjustedSlice)`
`protected void`	`snapPeaks(int slice, IntArray initialPeaks)`
`protected PointRoi`	`toROI()`
`protected void`	`updatePeakCountPlot()`
`protected void`	`updateSlice()`

Methods inherited from class fiji.tool.AbstractTrackingTool
addIOButtons, clearROIs, exportToROIManager, exportToROIManager, getHandle, getROILabel, getRois, importFromROIManager, loadROIs, loadROIs, loadROIs, saveROIs, saveROIs, saveROIs, setRoi

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

peakCountPlot
```
protected ij.ImagePlus peakCountPlot
```

peakCountPlotLimits
```
protected double[] peakCountPlotLimits
```

image
```
protected ProfileStack image
```

slice
```
protected int slice
```

peaks
```
protected IntArray peaks
```

allPeaks
```
protected IntArray[] allPeaks
```

allPeaksMap

protected Map<ProfileStack,IntArray[]> allPeaksMap

maxSpeed
```
protected int maxSpeed
```

handle
```
protected int handle
```

firstAdjustedSlice

protected Map<ProfileStack,Integer> firstAdjustedSlice

Constructor Detail
- Peak_Counter_Tool
```
public Peak_Counter_Tool()
```

Method Detail
- getToolIcon
```
public String getToolIcon()
```
  Description copied from class: AbstractTool
  
  Return the string encoding of the tool icon as it will appear in the toolbar. See syntax for icon string.
  
  Overrides:
  
  getToolIcon in class AbstractTrackingTool
- getImage
```
protected boolean getImage(MouseEvent e)
```
- getImage
```
protected boolean getImage(ij.ImagePlus image)
```
- updateSlice
```
protected void updateSlice()
```
- getPeaks
```
protected IntArray getPeaks(int slice)
```
- updatePeakCountPlot
```
protected void updatePeakCountPlot()
```
- peakPosition
```
protected int peakPosition(int x)
```
  Returns:
  
  index of peak, or -1-insert where insert is the insert position
- initializePeaks
```
public void initializePeaks(int slice)
```
- initializePeaks
```
public void initializePeaks(int slice,
                            int window,
                            double minimalSlope)
```
- snapAndAddPeak
```
protected int snapAndAddPeak(int x)
```
- snapPeak
```
protected int snapPeak(int slice,
                       int x)
```
- addPeak
```
protected int addPeak(int x)
```
- movePeak
```
protected int movePeak(int index,
                       int x)
```
- closeToPeak
```
protected int closeToPeak(int x,
                          int y)
```
- closeToPeak
```
protected int closeToPeak(int x,
                          int y,
                          double tolerance)
```
- toROI
```
protected PointRoi toROI()
```
- optimizeRoi
```
public Roi optimizeRoi(Roi roi,
                       ij.process.ImageProcessor ip)
```
  Specified by:
  
  optimizeRoi in class AbstractTrackingTool
- snapPeaks
```
protected void snapPeaks(int adjustedSlice)
```
- snapPeaks
```
protected void snapPeaks()
```
- snapPeaks
```
protected void snapPeaks(int slice,
                         IntArray initialPeaks)
```
- mouseClicked
```
public void mouseClicked(MouseEvent e)
```
  Specified by:
  
  mouseClicked in interface MouseListener
  
  Overrides:
  
  mouseClicked in class AbstractTrackingTool
- mousePressed
```
public void mousePressed(MouseEvent e)
```
  Specified by:
  
  mousePressed in interface MouseListener
  
  Overrides:
  
  mousePressed in class AbstractTrackingTool
- mouseReleased
```
public void mouseReleased(MouseEvent e)
```
  Specified by:
  
  mouseReleased in interface MouseListener
  
  Overrides:
  
  mouseReleased in class AbstractTrackingTool
- mouseEntered
```
public void mouseEntered(MouseEvent e)
```
  Specified by:
  
  mouseEntered in interface MouseListener
  
  Overrides:
  
  mouseEntered in class AbstractTrackingTool
- mouseExited
```
public void mouseExited(MouseEvent e)
```
  Specified by:
  
  mouseExited in interface MouseListener
  
  Overrides:
  
  mouseExited in class AbstractTrackingTool
- keyPressed
```
public void keyPressed(KeyEvent e)
```
  Specified by:
  
  keyPressed in interface KeyListener
- keyTyped
```
public void keyTyped(KeyEvent e)
```
  Specified by:
  
  keyTyped in interface KeyListener
- keyReleased
```
public void keyReleased(KeyEvent e)
```
  Specified by:
  
  keyReleased in interface KeyListener
- mark
```
protected OvalRoi mark(int distance)
```
- mark
```
protected OvalRoi mark(int distance,
                       Color color)
```
- mouseMoved
```
public void mouseMoved(MouseEvent e)
```
  Specified by:
  
  mouseMoved in interface MouseMotionListener
  
  Overrides:
  
  mouseMoved in class AbstractTrackingTool
- mouseDragged
```
public void mouseDragged(MouseEvent e)
```
  Specified by:
  
  mouseDragged in interface MouseMotionListener
  
  Overrides:
  
  mouseDragged in class AbstractTrackingTool
- sliceChanged
```
public void sliceChanged(ij.ImagePlus image)
```
  Specified by:
  
  sliceChanged in interface SliceListener
  
  Overrides:
  
  sliceChanged in class AbstractTrackingTool
- initializePeaks
```
protected void initializePeaks()
```
- showOptionDialog
```
public void showOptionDialog()
```
  Description copied from interface: ToolWithOptions
  
  When called, this method displays the configuration panel for the concrete implementation of this tool. It is normally called when the user double-click the toolbar icon of this tool.
  
  Specified by:
  
  showOptionDialog in interface ToolWithOptions

Class Peak_Counter_Tool

Nested Class Summary

Nested classes/interfaces inherited from class fiji.tool.AbstractTool

Field Summary

Fields inherited from class fiji.tool.AbstractTrackingTool

Fields inherited from class fiji.tool.AbstractTool

Constructor Summary

Method Summary

Methods inherited from class fiji.tool.AbstractTrackingTool

Methods inherited from class fiji.tool.AbstractTool

Methods inherited from class java.lang.Object

Field Detail

peakCountPlot

peakCountPlotLimits

image

slice

peaks

allPeaks

allPeaksMap

maxSpeed

handle

firstAdjustedSlice

Constructor Detail

Peak_Counter_Tool

Method Detail

getToolIcon

getImage

getImage

updateSlice

getPeaks

updatePeakCountPlot

peakPosition

initializePeaks

initializePeaks

snapAndAddPeak

snapPeak

addPeak

movePeak

closeToPeak

closeToPeak

toROI

optimizeRoi

snapPeaks

snapPeaks

snapPeaks

mouseClicked

mousePressed

mouseReleased

mouseEntered

mouseExited

keyPressed

keyTyped

keyReleased

mark

mark

mouseMoved

mouseDragged

sliceChanged

initializePeaks

showOptionDialog