PatchStack (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- ij.ImagePlus
- - ini.trakem2.imaging.PatchStack

All Implemented Interfaces:

ij.measure.Measurements, ImageObserver, Cloneable
```
public class PatchStack
extends ij.ImagePlus
```
Assumed is all Patch instances in the array are of the same size, live in consecutive layers of the same thickness. The superclass ImagePlus uses the 'ip' pointer for a single ImageProcessor whose pixels get replaced every time a new slice is selected from the stack, when there is a stack. Here the 'ip' pointer is used for the current slice, which is the currently active Patch.

Field Summary
- Fields inherited from class ij.ImagePlus
  changes, CLOSED, COLOR_256, COLOR_RGB, compositeImage, currentSlice, dimensionsSet, flattenTitle, GRAY16, GRAY32, GRAY8, height, img, ip, locked, nChannels, nFrames, nSlices, OPENED, roi, setIJMenuBar, UPDATED, width, win
- Fields inherited from interface java.awt.image.ImageObserver
  ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH
- Fields inherited from interface ij.measure.Measurements
  ADD_TO_OVERLAY, ALL_STATS, AREA, AREA_FRACTION, CENTER_OF_MASS, CENTROID, CIRCULARITY, ELLIPSE, FERET, INTEGRATED_DENSITY, INVERT_Y, KURTOSIS, LABELS, LIMIT, MAX_STANDARDS, MEAN, MEDIAN, MIN_MAX, MODE, NaN_EMPTY_CELLS, PERIMETER, RECT, SCIENTIFIC_NOTATION, SHAPE_DESCRIPTORS, SKEWNESS, SLICE, STACK_POSITION, STD_DEV

Constructor Summary

Constructors
Constructor and Description

PatchStack(Patch[] patch, int currentSlice)

Constructors
Constructor and Description
`PatchStack(Patch[] patch, int currentSlice)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`close()`
`boolean`	`contains(Patch p)`
`void`	`copy(boolean cut)`
`ij.ImagePlus`	`createColor256Copy()` Does not respect local transform of the patches, this is intended for confocal stacks.
`ij.ImageStack`	`createEmptyStack()`
`ij.ImagePlus`	`createGray8Copy()` Does not respect local transform of the patches, this is intended for confocal stacks.
`ij.LookUpTable`	`createLut()`
`void`	`createNewRoi(int sx, int sy)`
`void`	`decacheAll()` Remove all awts and snaps from the loader's cache, and repaint (which will remake as many as needed)
`void`	`draw()`
`void`	`draw(int x, int y, int width, int height)`
`void`	`flush()`
`int`	`getBitDepth()`
`Rectangle`	`getBounds()` Assumes all patches are of the same dimensions.
`ij.measure.Calibration`	`getCalibration()`
`Patch`	`getCurrentPatch()` Returns the Patch corresponding to the current slice.
`int`	`getCurrentSlice()`
`int[]`	`getDimensions()` Override to return width, height, 1, patch.length, 1
`ij.io.FileInfo`	`getFileInfo()`
`Image`	`getImage()`
`ij.ImageStack`	`getImageStack()`
`ij.measure.Calibration`	`getLocalCalibration()`
`ij.process.ImageProcessor`	`getMask()`
`int`	`getNChannels()` Override to return 1.
`int`	`getNFrames()` Override to return 1.
`int`	`getNSlices()`
`Patch`	`getPatch(int i)` From 0 to getNSlices() -1, otherwise null.
`Patch`	`getPatch(Layer layer, Patch p)` If the 'p' is contained in this PatchStack, get the first Patch found to be contained here and in the given 'layer'
`int[]`	`getPixel(int x, int y)`
`ij.process.ImageProcessor`	`getProcessor()`
`Properties`	`getProperties()`
`Object`	`getProperty(String key)`
`Roi`	`getRoi()`
`ij.ImageStack`	`getStack()`
`int`	`getStackIndex(int channel, int slice, int frame)`
`int`	`getStackSize()`
`ij.process.ImageStatistics`	`getStatistics(int nOptions, int nBins, double histMin, double histMax)`
`String`	`getTitle()`
`int`	`getType()`
`void`	`hide()`
`void`	`invertLookupTable()`
`boolean`	`isInvertedLut()`
`boolean`	`isProcessor()`
`void`	`killRoi()`
`void`	`paste()`
`void`	`repaintWindow()`
`void`	`resetNonActive()` Reset temporary changes such as from dragging B&C sliders and so on, in the current slice (the current Patch).
`void`	`revert(Patch p)`
`void`	`revertAll()`
`void`	`saveImages()` Store working copies and remake the awts and repaint.
`void`	`saveRoi()`
`void`	`setCalibration(ij.measure.Calibration cal)`
`void`	`setColor(Color c)`
`void`	`setCurrentSlice(Patch p)`
`void`	`setDimensions(int nChannels, int nSlices, int nFrames)`
`void`	`setFileInfo(ij.io.FileInfo fi)`
`void`	`setImage(Image img)`
`void`	`setPosition(int channel, int slice, int frame)`
`void`	`setProcessor(String title, ij.process.ImageProcessor ip)`
`void`	`setProperty(String key, Object value)`
`void`	`setRoi(Rectangle r)`
`void`	`setRoi(Roi roi)`
`void`	`setSlice(int index)`
`void`	`setStack(String title, ij.ImageStack stack)`
`void`	`setTitle(String title)`
`protected void`	`setType(int type)`
`void`	`setWindow(Window win)`
`void`	`show()`
`void`	`show(String statusMessage)`
`void`	`trimProcessor()`
`void`	`updateAndDraw()`
`void`	`updateAndRepaintWindow()`
`void`	`updateImage()`

Methods inherited from class ij.ImagePlus
addImageListener, clone, convertIndexToPosition, copy, copyAttributes, copyScale, copyToSystem, createHyperStack, createImagePlus, createRoiMask, createThresholdMask, crop, crop, crop, crop, cropAndSave, cut, deleteRoi, duplicate, flatten, flattenStack, getAllStatistics, getBufferedImage, getBytesPerPixel, getC, getCanvas, getChannel, getChannelProcessor, getClipboard, getCompositeMode, getDefault16bitRange, getDimensions, getDisplayMode, getDisplayRangeMax, getDisplayRangeMin, getFrame, getGlobalCalibration, getHeight, getHideOverlay, getID, getImageProperties, getImageStackSize, getInfoProperty, getLocationAsString, getLuts, getNDimensions, getNumericProp, getNumericProperty, getOpenAsHyperStack, getOriginalFileInfo, getOverlay, getPlot, getProp, getPropertiesAsArray, getPropsInfo, getRawStatistics, getShortTitle, getSizeInBytes, getSlice, getStartTime, getStaticGlobalCalibration, getStatistics, getStatistics, getStatistics, getStringProperty, getT, getWidth, getWindow, getZ, imageUpdate, isComposite, isDisplayedHyperStack, isHyperStack, isLocked, isLockedByAnotherThread, isStack, isThreshold, isVisible, killStack, lock, lockSilently, logImageListeners, mouseMoved, notifyListeners, okToDeleteRoi, paste, plotHistogram, plotHistogram, removeImageListener, resetClipboard, resetDisplayRange, resetStack, resize, resize, restoreRoi, revert, setActivated, setActiveChannels, setAntialiasRendering, setC, setDefault16bitRange, setDisplayMode, setDisplayRange, setDisplayRange, setGlobalCalibration, setHideOverlay, setIgnoreFlush, setIgnoreGlobalCalibration, setIJMenuBar, setIJMenuBar, setImage, setLut, setOpenAsHyperStack, setOverlay, setOverlay, setOverlay, setPlot, setPosition, setPositionWithoutUpdate, setProcessor, setProp, setProp, setProperties, setRoi, setRoi, setSliceWithoutUpdate, setStack, setStack, setT, setTypeToColor256, setWindow, setZ, startTiming, tempOverlay, toString, unlock, updateChannelAndDraw, updatePosition, updateStatusbarValue, updateVirtualSlice

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

- Constructor Detail
  - PatchStack
```
public PatchStack(Patch[] patch,
                  int currentSlice)
```
- Method Detail
  - getBounds
```
public Rectangle getBounds()
```
    Assumes all patches are of the same dimensions.
  - contains
```
public boolean contains(Patch p)
```
  - getPatch
```
public Patch getPatch(Layer layer,
                      Patch p)
```
    If the 'p' is contained in this PatchStack, get the first Patch found to be contained here and in the given 'layer'
  - getPatch
```
public Patch getPatch(int i)
```
    From 0 to getNSlices() -1, otherwise null.
  - getCurrentPatch
```
public Patch getCurrentPatch()
```
    Returns the Patch corresponding to the current slice.
  - setCurrentSlice
```
public void setCurrentSlice(Patch p)
```
  - revert
```
public void revert(Patch p)
```
  - revertAll
```
public void revertAll()
```
  - resetNonActive
```
public void resetNonActive()
```
    Reset temporary changes such as from dragging B&C sliders and so on, in the current slice (the current Patch).
  - saveImages
```
public void saveImages()
```
    Store working copies and remake the awts and repaint.
  - draw
```
public void draw()
```
    Overrides:
    
    draw in class ij.ImagePlus
  - draw
```
public void draw(int x,
                 int y,
                 int width,
                 int height)
```
    Overrides:
    
    draw in class ij.ImagePlus
  - updateAndDraw
```
public void updateAndDraw()
```
    Overrides:
    
    updateAndDraw in class ij.ImagePlus
  - repaintWindow
```
public void repaintWindow()
```
    Overrides:
    
    repaintWindow in class ij.ImagePlus
  - updateAndRepaintWindow
```
public void updateAndRepaintWindow()
```
    Overrides:
    
    updateAndRepaintWindow in class ij.ImagePlus
  - updateImage
```
public void updateImage()
```
    Overrides:
    
    updateImage in class ij.ImagePlus
  - hide
```
public void hide()
```
    Overrides:
    
    hide in class ij.ImagePlus
  - close
```
public void close()
```
    Overrides:
    
    close in class ij.ImagePlus
  - show
```
public void show()
```
    Overrides:
    
    show in class ij.ImagePlus
  - show
```
public void show(String statusMessage)
```
    Overrides:
    
    show in class ij.ImagePlus
  - invertLookupTable
```
public void invertLookupTable()
```
  - getImage
```
public Image getImage()
```
    Overrides:
    
    getImage in class ij.ImagePlus
  - setImage
```
public void setImage(Image img)
```
    Overrides:
    
    setImage in class ij.ImagePlus
  - setProcessor
```
public void setProcessor(String title,
                         ij.process.ImageProcessor ip)
```
    Overrides:
    
    setProcessor in class ij.ImagePlus
  - setStack
```
public void setStack(String title,
                     ij.ImageStack stack)
```
    Overrides:
    
    setStack in class ij.ImagePlus
  - setFileInfo
```
public void setFileInfo(ij.io.FileInfo fi)
```
    Overrides:
    
    setFileInfo in class ij.ImagePlus
  - setWindow
```
public void setWindow(Window win)
```
  - setColor
```
public void setColor(Color c)
```
    Overrides:
    
    setColor in class ij.ImagePlus
  - isProcessor
```
public boolean isProcessor()
```
    Overrides:
    
    isProcessor in class ij.ImagePlus
  - getProcessor
```
public ij.process.ImageProcessor getProcessor()
```
    Overrides:
    
    getProcessor in class ij.ImagePlus
  - trimProcessor
```
public void trimProcessor()
```
    Overrides:
    
    trimProcessor in class ij.ImagePlus
  - getMask
```
public ij.process.ImageProcessor getMask()
```
    Overrides:
    
    getMask in class ij.ImagePlus
  - getStatistics
```
public ij.process.ImageStatistics getStatistics(int nOptions,
                                                int nBins,
                                                double histMin,
                                                double histMax)
```
    Overrides:
    
    getStatistics in class ij.ImagePlus
  - getTitle
```
public String getTitle()
```
    Overrides:
    
    getTitle in class ij.ImagePlus
  - setTitle
```
public void setTitle(String title)
```
    Overrides:
    
    setTitle in class ij.ImagePlus
  - getStackSize
```
public int getStackSize()
```
    Overrides:
    
    getStackSize in class ij.ImagePlus
  - setDimensions
```
public void setDimensions(int nChannels,
                          int nSlices,
                          int nFrames)
```
    Overrides:
    
    setDimensions in class ij.ImagePlus
  - getNChannels
```
public int getNChannels()
```
    Override to return 1.
    
    Overrides:
    
    getNChannels in class ij.ImagePlus
  - getNSlices
```
public int getNSlices()
```
    Overrides:
    
    getNSlices in class ij.ImagePlus
  - getNFrames
```
public int getNFrames()
```
    Override to return 1.
    
    Overrides:
    
    getNFrames in class ij.ImagePlus
  - getDimensions
```
public int[] getDimensions()
```
    Override to return width, height, 1, patch.length, 1
    
    Overrides:
    
    getDimensions in class ij.ImagePlus
  - getType
```
public int getType()
```
    Overrides:
    
    getType in class ij.ImagePlus
  - getBitDepth
```
public int getBitDepth()
```
    Overrides:
    
    getBitDepth in class ij.ImagePlus
  - setType
```
protected void setType(int type)
```
    Overrides:
    
    setType in class ij.ImagePlus
  - setProperty
```
public void setProperty(String key,
                        Object value)
```
    Overrides:
    
    setProperty in class ij.ImagePlus
  - getProperty
```
public Object getProperty(String key)
```
    Overrides:
    
    getProperty in class ij.ImagePlus
  - getProperties
```
public Properties getProperties()
```
    Overrides:
    
    getProperties in class ij.ImagePlus
  - createLut
```
public ij.LookUpTable createLut()
```
    Overrides:
    
    createLut in class ij.ImagePlus
  - isInvertedLut
```
public boolean isInvertedLut()
```
    Overrides:
    
    isInvertedLut in class ij.ImagePlus
  - getPixel
```
public int[] getPixel(int x,
                      int y)
```
    Overrides:
    
    getPixel in class ij.ImagePlus
  - createEmptyStack
```
public ij.ImageStack createEmptyStack()
```
    Overrides:
    
    createEmptyStack in class ij.ImagePlus
  - getStack
```
public ij.ImageStack getStack()
```
    Overrides:
    
    getStack in class ij.ImagePlus
  - getImageStack
```
public ij.ImageStack getImageStack()
```
    Overrides:
    
    getImageStack in class ij.ImagePlus
  - getCurrentSlice
```
public int getCurrentSlice()
```
    Overrides:
    
    getCurrentSlice in class ij.ImagePlus
  - setSlice
```
public void setSlice(int index)
```
    Overrides:
    
    setSlice in class ij.ImagePlus
  - getRoi
```
public Roi getRoi()
```
    Overrides:
    
    getRoi in class ij.ImagePlus
  - setRoi
```
public void setRoi(Roi roi)
```
    Overrides:
    
    setRoi in class ij.ImagePlus
  - setRoi
```
public void setRoi(Rectangle r)
```
    Overrides:
    
    setRoi in class ij.ImagePlus
  - createNewRoi
```
public void createNewRoi(int sx,
                         int sy)
```
    Overrides:
    
    createNewRoi in class ij.ImagePlus
  - killRoi
```
public void killRoi()
```
    Overrides:
    
    killRoi in class ij.ImagePlus
  - saveRoi
```
public void saveRoi()
```
    Overrides:
    
    saveRoi in class ij.ImagePlus
  - getFileInfo
```
public ij.io.FileInfo getFileInfo()
```
    Overrides:
    
    getFileInfo in class ij.ImagePlus
  - flush
```
public void flush()
```
    Overrides:
    
    flush in class ij.ImagePlus
  - getCalibration
```
public ij.measure.Calibration getCalibration()
```
    Overrides:
    
    getCalibration in class ij.ImagePlus
  - setCalibration
```
public void setCalibration(ij.measure.Calibration cal)
```
    Overrides:
    
    setCalibration in class ij.ImagePlus
  - getLocalCalibration
```
public ij.measure.Calibration getLocalCalibration()
```
    Overrides:
    
    getLocalCalibration in class ij.ImagePlus
  - copy
```
public void copy(boolean cut)
```
    Overrides:
    
    copy in class ij.ImagePlus
  - paste
```
public void paste()
```
    Overrides:
    
    paste in class ij.ImagePlus
  - decacheAll
```
public void decacheAll()
```
    Remove all awts and snaps from the loader's cache, and repaint (which will remake as many as needed)
  - setPosition
```
public void setPosition(int channel,
                        int slice,
                        int frame)
```
    Overrides:
    
    setPosition in class ij.ImagePlus
  - getStackIndex
```
public int getStackIndex(int channel,
                         int slice,
                         int frame)
```
    Overrides:
    
    getStackIndex in class ij.ImagePlus
  - createGray8Copy
```
public ij.ImagePlus createGray8Copy()
```
    Does not respect local transform of the patches, this is intended for confocal stacks.
  - createColor256Copy
```
public ij.ImagePlus createColor256Copy()
```
    Does not respect local transform of the patches, this is intended for confocal stacks.

Class PatchStack

Field Summary

Fields inherited from class ij.ImagePlus

Fields inherited from interface java.awt.image.ImageObserver

Fields inherited from interface ij.measure.Measurements

Constructor Summary

Method Summary

Methods inherited from class ij.ImagePlus

Methods inherited from class java.lang.Object

Constructor Detail

PatchStack

Method Detail

getBounds

contains

getPatch

getPatch

getCurrentPatch

setCurrentSlice

revert

revertAll

resetNonActive

saveImages

draw

draw

updateAndDraw

repaintWindow

updateAndRepaintWindow

updateImage

hide

close

show

show

invertLookupTable

getImage

setImage

setProcessor

setStack

setFileInfo

setWindow

setColor

isProcessor

getProcessor

trimProcessor

getMask

getStatistics

getTitle

setTitle

getStackSize

setDimensions

getNChannels

getNSlices

getNFrames

getDimensions

getType

getBitDepth

setType

setProperty

getProperty

getProperties

createLut

isInvertedLut

getPixel

createEmptyStack

getStack

getImageStack

getCurrentSlice

setSlice

getRoi

setRoi

setRoi

createNewRoi

killRoi

saveRoi

getFileInfo

flush

getCalibration

setCalibration

getLocalCalibration

copy

paste