Stack (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- ini.trakem2.persistence.DBObject
- - ini.trakem2.display.Displayable
  - - ini.trakem2.display.ZDisplayable
    - - ini.trakem2.display.Stack

All Implemented Interfaces:

ImageData, Paintable
```
public class Stack
extends ZDisplayable
implements ImageData
```
Author:

Stephan Saalfeld saalfeld@mpi-cbg.de

Nested Class Summary
- Nested classes/interfaces inherited from class ini.trakem2.display.Displayable
  Displayable.DataPackage, Displayable.DoEdit, Displayable.DoEdits, Displayable.DoTransforms, Displayable.SliderListener

Field Summary
- Fields inherited from class ini.trakem2.display.ZDisplayable
  layer_set
- Fields inherited from class ini.trakem2.display.Displayable
  alpha, annotation, at, color, COMPOSITE_ADD, COMPOSITE_COLOR_YCBCR, COMPOSITE_DIFFERENCE, COMPOSITE_MULTIPLY, COMPOSITE_NORMAL, COMPOSITE_SUBTRACT, compositeModes, height, hs_linked, last_color, layer, linked_props, linked_props_origins, locked, props, TAG_ATTR1, TAG_ATTR2, title, visible, width
- Fields inherited from class ini.trakem2.persistence.DBObject
  id, project

Constructor Summary

Constructors
Constructor and Description
`Stack(Project project, long id, HashMap<String,String> ht, HashMap<Displayable,String> ht_links)` Construct a Stack from an XML entry.
`Stack(Project project, String title, double x, double y, Layer initial_layer, String file_path)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected boolean`	`calculateBoundingBox(Layer la)`
`Displayable`	`clone(Project pr, boolean copy_id)` Performs a deep copy of this object, obtaining its unique id either from the given project or the exact same as this object's id.
`long`	`estimateImageFileSize()`
`static void`	`exportDTD(StringBuilder sb_header, HashSet<String> hs, String indent)`
`void`	`exportXML(StringBuilder sb_body, String indent, XMLOptions options)` Opens and closes the tag and exports data.
`protected Rectangle`	`getBounds(Rectangle rect)` Bounding box of the transformed data (or 0,0,0,0 when no data).
`String`	`getFilePath()`
`Layer`	`getFirstLayer()` Returns the layer of lowest Z coordinate where this ZDisplayable has a point in.
`InvertibleCoordinateTransform`	`getInvertibleCoordinateTransform()`
`Polygon`	`getPerimeter()` For now, just returns the bounding box---we can refine this later
`boolean`	`intersects(Area area, double z_first, double z_last)`
`boolean`	`isDeletable()`
`boolean`	`linkPatches()` Link the Patch objects that lay underneath the part of the bounding box of this profile that shows in the current layer, so that they cannot be dragged independently.
`void`	`paint(Graphics2D g, Rectangle srcRect, double magnification, boolean active, int channels, Layer active_layer, List<Layer> layers)` Slow paint: will wait until the image is generated and cached, then paint it.
`void`	`prePaint(Graphics2D g, Rectangle srcRect, double magnification, boolean active, int channels, Layer active_layer, List<Layer> _ignored)` Will not paint but fork a task to create an image to paint later, when not already cached.
`boolean`	`remove2(boolean check)` Avoid calling the trees: the stack exists only in the LayerSet ZDisplayable's list.
`void`	`setAffineTransform(AffineTransform at)` Sets the matrix values of this Displayable's AffineTransform to those of the given AffineTransform.
`void`	`setFilePath(String path)` Will decache the ImagePlus if loaded.
`void`	`setInvertibleCoordinateTransform(InvertibleCoordinateTransform ict)`
`void`	`setInvertibleCoordinateTransformSilently(InvertibleCoordinateTransform ict)` For reconstruction purposes, overwrites the present InvertibleCoordinateTransform, if any, with the given one.

Methods inherited from class ini.trakem2.display.ZDisplayable
crop, exportDTD, getBucketable, getLayerIds, getLayerSet, layerRemoved, paintsAt, remove, setColor, setLayer, setLayerSet, setLayerSet, setVisible, softRemove, transformPoints, updateBucket, updateBucket

Methods inherited from class ini.trakem2.display.Displayable
adjustProperties, areThereLayerCrossLinks, canSendTo, clone, clone, commonDTDChildren, contains, contains, deselect, destroy, displacePoints, exportSVG, findById, findNearestPoint, findNearestPoint, getAffineTransform, getAffineTransformCopy, getAlpha, getAnnotation, getArea, getAreaAt, getAreaForBucket, getBoundingBox, getBoundingBox, getBoundingBox, getBounds, getColor, getComposite, getComposite, getCompositeMode, getHeight, getIntersection, getLayer, getLayersWithData, getLinked, getLinked, getLinkedBox, getLinkedGroup, getLinkedProperties, getLinkedProperties, getLinkedProperty, getLinkedProperty, getMinimalBoundingBox, getNameId, getPerimeter, getProperties, getProperty, getProperty, getShortTitle, getTitle, getWidth, getX, getXMLSafeValue, getXMLSafeValue, getY, hasLinkedGroupWithinLayer, hasProperties, intersects, intersects, intersects, intersects, inverseTransformPoint, isLinked, isLinked, isLinked, isLocked, isLocked2, isOnlyLinkedTo, isOnlyLinkedTo, isOutOfRepaintingClip, isOutOfRepaintingClip, isRoughlyInside, isVisible, keyPressed, link, link, makeAdjustPropertiesDialog, measure, mouseDragged, mousePressed, mouseReleased, mouseWheelMoved, paintAsBox, paintOffscreen, paintSnapshot, preConcatenate, preTransform, processAdjustPropertiesDialog, removeLinkedProperties, removeLinkedPropertiesFromOrigins, repaint, restXML, rotate, rotate, rotatePoints, scale, scale, scalePoints, setAlpha, setAlpha, setAnnotation, setCompositeMode, setDimensions, setDimensions, setLayer, setLinkedProperties, setLinkedProperty, setLocation, setLocked, setProperty, setTitle, setVisible, snapTo, toString, transform, transformPoint, transformPoint, transformPoints, transformPoints, transformPoints, transformPoints, transformPoints, transformPoints, transformPoints, transformPoints, transformPoints, transformRectangle, translate, translate, unlink, unlink, unlinkAll, updateInDatabase, xmlError, xmlError

Methods inherited from class ini.trakem2.persistence.DBObject
addToDatabase, getId, getInfo, getProject, getUniqueIdentifier, removeFromDatabase, updateInDatabase

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

- Constructor Detail
  - Stack
```
public Stack(Project project,
             String title,
             double x,
             double y,
             Layer initial_layer,
             String file_path)
```
  - Stack
```
public Stack(Project project,
             long id,
             HashMap<String,String> ht,
             HashMap<Displayable,String> ht_links)
```
    Construct a Stack from an XML entry.
- Method Detail
  - getInvertibleCoordinateTransform
```
public InvertibleCoordinateTransform getInvertibleCoordinateTransform()
```
  - getFirstLayer
```
public Layer getFirstLayer()
```
    Description copied from class: ZDisplayable
    
    Returns the layer of lowest Z coordinate where this ZDisplayable has a point in.
    
    Specified by:
    
    getFirstLayer in class ZDisplayable
  - intersects
```
public boolean intersects(Area area,
                          double z_first,
                          double z_last)
```
    Specified by:
    
    intersects in class ZDisplayable
  - linkPatches
```
public boolean linkPatches()
```
    Description copied from class: ZDisplayable
    
    Link the Patch objects that lay underneath the part of the bounding box of this profile that shows in the current layer, so that they cannot be dragged independently.
    
    Specified by:
    
    linkPatches in class ZDisplayable
    
    Returns:
    
    whether the locking state changed.
  - clone
```
public Displayable clone(Project pr,
                         boolean copy_id)
```
    Description copied from class: Displayable
    
    Performs a deep copy of this object, obtaining its unique id either from the given project or the exact same as this object's id. The visibility, though, is set to true at all times.
    
    Specified by:
    
    clone in class Displayable
  - isDeletable
```
public boolean isDeletable()
```
    Specified by:
    
    isDeletable in class Displayable
  - getFilePath
```
public String getFilePath()
```
  - setFilePath
```
public void setFilePath(String path)
```
    Will decache the ImagePlus if loaded.
  - estimateImageFileSize
```
public long estimateImageFileSize()
```
  - paint
```
public void paint(Graphics2D g,
                  Rectangle srcRect,
                  double magnification,
                  boolean active,
                  int channels,
                  Layer active_layer,
                  List<Layer> layers)
```
    Slow paint: will wait until the image is generated and cached, then paint it.
    
    Specified by:
    
    paint in interface Paintable
    
    Overrides:
    
    paint in class Displayable
  - prePaint
```
public void prePaint(Graphics2D g,
                     Rectangle srcRect,
                     double magnification,
                     boolean active,
                     int channels,
                     Layer active_layer,
                     List<Layer> _ignored)
```
    Will not paint but fork a task to create an image to paint later, when not already cached.
    
    Specified by:
    
    prePaint in interface Paintable
    
    Overrides:
    
    prePaint in class Displayable
  - exportDTD
```
public static final void exportDTD(StringBuilder sb_header,
                                   HashSet<String> hs,
                                   String indent)
```
  - exportXML
```
public void exportXML(StringBuilder sb_body,
                      String indent,
                      XMLOptions options)
```
    Opens and closes the tag and exports data. The image is saved in the directory provided in @param any as a String.
    
    Overrides:
    
    exportXML in class ZDisplayable
  - getBounds
```
protected Rectangle getBounds(Rectangle rect)
```
    Description copied from class: Displayable
    
    Bounding box of the transformed data (or 0,0,0,0 when no data). Returns the same Rectangle, modified.
    
    Overrides:
    
    getBounds in class Displayable
  - getPerimeter
```
public Polygon getPerimeter()
```
    For now, just returns the bounding box---we can refine this later
    
    Overrides:
    
    getPerimeter in class Displayable
  - setInvertibleCoordinateTransformSilently
```
public void setInvertibleCoordinateTransformSilently(InvertibleCoordinateTransform ict)
```
    For reconstruction purposes, overwrites the present InvertibleCoordinateTransform, if any, with the given one.
  - setInvertibleCoordinateTransform
```
public void setInvertibleCoordinateTransform(InvertibleCoordinateTransform ict)
```
  - setAffineTransform
```
public void setAffineTransform(AffineTransform at)
```
    Description copied from class: Displayable
    
    Sets the matrix values of this Displayable's AffineTransform to those of the given AffineTransform.
    
    Overrides:
    
    setAffineTransform in class Displayable
  - remove2
```
public boolean remove2(boolean check)
```
    Avoid calling the trees: the stack exists only in the LayerSet ZDisplayable's list.
    
    Overrides:
    
    remove2 in class ZDisplayable
  - calculateBoundingBox
```
protected boolean calculateBoundingBox(Layer la)
```
    Specified by:
    
    calculateBoundingBox in class ZDisplayable

Class Stack

Nested Class Summary

Nested classes/interfaces inherited from class ini.trakem2.display.Displayable

Field Summary

Fields inherited from class ini.trakem2.display.ZDisplayable

Fields inherited from class ini.trakem2.display.Displayable

Fields inherited from class ini.trakem2.persistence.DBObject

Constructor Summary

Method Summary

Methods inherited from class ini.trakem2.display.ZDisplayable

Methods inherited from class ini.trakem2.display.Displayable

Methods inherited from class ini.trakem2.persistence.DBObject

Methods inherited from class java.lang.Object

Constructor Detail

Stack

Stack

Method Detail

getInvertibleCoordinateTransform

getFirstLayer

intersects

linkPatches

clone

isDeletable

getFilePath

setFilePath

estimateImageFileSize

paint

prePaint

exportDTD

exportXML

getBounds

getPerimeter

setInvertibleCoordinateTransformSilently

setInvertibleCoordinateTransform

setAffineTransform

remove2

calculateBoundingBox