Dissector (Fiji Javadocs 0-SNAPSHOT API)

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

All Implemented Interfaces:

Paintable, VectorData
```
public class Dissector
extends ZDisplayable
implements VectorData
```
Implements the Double Dissector method with scale-invariant grouped labels. Each label is simply a cross marker with a number attached; labels are grouped; each member label of the group has the same number.

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
`Dissector(Project project, long id, HashMap<String,String> ht, HashMap<Displayable,String> ht_links)` Reconstruct from XML.
`Dissector(Project project, long id, String title, float width, float height, float alpha, boolean visible, Color color, boolean locked, AffineTransform at)`
`Dissector(Project project, String title, double x, double y)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addItem(int tag, int radius, String data)` For reconstruction purposes from XML.
`boolean`	`apply(Layer la, Area roi, CoordinateTransform ict)` Applies the 2D transform @ict (which is expected to operate on the world coordinates version of the data contained here) only to the data that falls within the @param roi (in world coords), and then recomputes the bounding box and affine transform (to a translation or identity).
`boolean`	`apply(VectorDataTransform vdt)`
`protected boolean`	`calculateBoundingBox(Layer la)`
`Displayable`	`clone(Project pr, boolean copy_id)` Returns a deep copy.
`boolean`	`contains(Layer layer, double x, double y)` Calls contains(x_p, y_p) unless overriden -- in ZDisplayable objects, it tests whether the given point is contained in the part of the ZDisplayable that shows in the given layer.
`boolean`	`crop(List<Layer> range)` Retain the data within the layer range, and through out all the rest.
`static void`	`exportDTD(StringBuilder sb_header, HashSet<String> hs, String indent)`
`void`	`exportXML(StringBuilder sb_body, String indent, XMLOptions options)` The oid is this objects' id, whereas the 'id' tag will be the id of the wrapper Thing object.
`Area`	`getAreaAt(Layer layer)` This area is meant to represent the entire area where a Displayable paints to in the @param layer.
`Layer`	`getFirstLayer()` Returns the layer of lowest Z coordinate where this ZDisplayable has a point in.
`String`	`getInfo()` Returns: - first line: the title of this dissector - second line: the number of items included in this dissector and then a list of 5 tab-separated columns: item tag, radius, x, y, z
`Collection<Long>`	`getLayerIds()` Get the list of Layer ids on which this ZDisplayable has data on.
`boolean`	`intersects(Area area, double z_first, double z_last)`
`boolean`	`isDeletable()`
`protected boolean`	`layerRemoved(Layer la)` Update internal datastructures to reflect the fact that @param layer has been removed from the containing LayerSet.
`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.
`ij.measure.ResultsTable`	`measure(ij.measure.ResultsTable rt)` Does nothing unless overriden.
`void`	`mouseDragged(MouseEvent me, Layer la, int x_p, int y_p, int x_d, int y_d, int x_d_old, int y_d_old)`
`void`	`mousePressed(MouseEvent me, Layer la, int x_p, int y_p, double mag)`
`void`	`mouseReleased(MouseEvent me, Layer la, int x_p, int y_p, int x_d, int y_d, int x_r, int y_r)`
`void`	`paint(Graphics2D g, Rectangle srcRect, double magnification, boolean active, int channels, Layer active_layer, List<Layer> layers)`
`void`	`paintSnapshot(Graphics2D g, Layer layer, List<Layer> layers, Rectangle srcRect, double mag)` Always paint as box.

Methods inherited from class ini.trakem2.display.ZDisplayable
exportDTD, getBucketable, getLayerSet, paintsAt, remove, remove2, setColor, setLayer, setLayerSet, setLayerSet, setVisible, softRemove, transformPoints, updateBucket, updateBucket

Methods inherited from class ini.trakem2.display.Displayable
adjustProperties, areThereLayerCrossLinks, canSendTo, clone, clone, commonDTDChildren, contains, deselect, destroy, displacePoints, exportSVG, findById, findNearestPoint, findNearestPoint, getAffineTransform, getAffineTransformCopy, getAlpha, getAnnotation, getArea, getAreaForBucket, getBoundingBox, getBoundingBox, getBoundingBox, getBounds, getBounds, getColor, getComposite, getComposite, getCompositeMode, getHeight, getIntersection, getLayer, getLayersWithData, getLinked, getLinked, getLinkedBox, getLinkedGroup, getLinkedProperties, getLinkedProperties, getLinkedProperty, getLinkedProperty, getMinimalBoundingBox, getNameId, getPerimeter, 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, mouseWheelMoved, paintAsBox, paintOffscreen, preConcatenate, prePaint, preTransform, processAdjustPropertiesDialog, removeLinkedProperties, removeLinkedPropertiesFromOrigins, repaint, restXML, rotate, rotate, rotatePoints, scale, scale, scalePoints, setAffineTransform, 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, getProject, getUniqueIdentifier, removeFromDatabase, updateInDatabase

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

Constructor Detail

Dissector

public Dissector(Project project,
                 String title,
                 double x,
                 double y)

Dissector

public Dissector(Project project,
                 long id,
                 String title,
                 float width,
                 float height,
                 float alpha,
                 boolean visible,
                 Color color,
                 boolean locked,
                 AffineTransform at)

Dissector

public Dissector(Project project,
                 long id,
                 HashMap<String,String> ht,
                 HashMap<Displayable,String> ht_links)

Reconstruct from XML.

Method Detail
- paint
```
public void paint(Graphics2D g,
                  Rectangle srcRect,
                  double magnification,
                  boolean active,
                  int channels,
                  Layer active_layer,
                  List<Layer> layers)
```
  Specified by:
  
  paint in interface Paintable
  
  Overrides:
  
  paint in class Displayable
- 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
- 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.
- contains
```
public boolean contains(Layer layer,
                        double x,
                        double y)
```
  Description copied from class: Displayable
  
  Calls contains(x_p, y_p) unless overriden -- in ZDisplayable objects, it tests whether the given point is contained in the part of the ZDisplayable that shows in the given layer.
  
  Overrides:
  
  contains in class Displayable
- clone
```
public Displayable clone(Project pr,
                         boolean copy_id)
```
  Returns a deep copy.
  
  Specified by:
  
  clone in class Displayable
- isDeletable
```
public boolean isDeletable()
```
  Specified by:
  
  isDeletable in class Displayable
- mousePressed
```
public void mousePressed(MouseEvent me,
                         Layer la,
                         int x_p,
                         int y_p,
                         double mag)
```
  Overrides:
  
  mousePressed in class Displayable
- mouseDragged
```
public void mouseDragged(MouseEvent me,
                         Layer la,
                         int x_p,
                         int y_p,
                         int x_d,
                         int y_d,
                         int x_d_old,
                         int y_d_old)
```
  Overrides:
  
  mouseDragged in class Displayable
- mouseReleased
```
public void mouseReleased(MouseEvent me,
                          Layer la,
                          int x_p,
                          int y_p,
                          int x_d,
                          int y_d,
                          int x_r,
                          int y_r)
```
  Overrides:
  
  mouseReleased in class Displayable
- calculateBoundingBox
```
protected boolean calculateBoundingBox(Layer la)
```
  Specified by:
  
  calculateBoundingBox in class ZDisplayable
- exportDTD
```
public static void exportDTD(StringBuilder sb_header,
                             HashSet<String> hs,
                             String indent)
```
- exportXML
```
public void exportXML(StringBuilder sb_body,
                      String indent,
                      XMLOptions options)
```
  Description copied from class: Displayable
  
  The oid is this objects' id, whereas the 'id' tag will be the id of the wrapper Thing object.
  
  Overrides:
  
  exportXML in class ZDisplayable
- addItem
```
public void addItem(int tag,
                    int radius,
                    String data)
```
  For reconstruction purposes from XML.
- getInfo
```
public String getInfo()
```
  Returns: - first line: the title of this dissector - second line: the number of items included in this dissector and then a list of 5 tab-separated columns: item tag, radius, x, y, z
  
  Overrides:
  
  getInfo in class DBObject
- paintSnapshot
```
public void paintSnapshot(Graphics2D g,
                          Layer layer,
                          List<Layer> layers,
                          Rectangle srcRect,
                          double mag)
```
  Always paint as box. TODO paint as the area of an associated ROI.
  
  Overrides:
  
  paintSnapshot in class Displayable
- intersects
```
public boolean intersects(Area area,
                          double z_first,
                          double z_last)
```
  Specified by:
  
  intersects in class ZDisplayable
- measure
```
public ij.measure.ResultsTable measure(ij.measure.ResultsTable rt)
```
  Description copied from class: Displayable
  
  Does nothing unless overriden.
  
  Overrides:
  
  measure in class Displayable
- crop
```
public boolean crop(List<Layer> range)
```
  Retain the data within the layer range, and through out all the rest.
  
  Overrides:
  
  crop in class ZDisplayable
- layerRemoved
```
protected boolean layerRemoved(Layer la)
```
  Description copied from class: ZDisplayable
  
  Update internal datastructures to reflect the fact that @param layer has been removed from the containing LayerSet.
  
  Overrides:
  
  layerRemoved in class ZDisplayable
- apply
```
public boolean apply(Layer la,
                     Area roi,
                     CoordinateTransform ict)
              throws Exception
```
  Description copied from interface: VectorData
  
  Applies the 2D transform @ict (which is expected to operate on the world coordinates version of the data contained here) only to the data that falls within the @param roi (in world coords), and then recomputes the bounding box and affine transform (to a translation or identity). Does not consider links.
  
  Specified by:
  
  apply in interface VectorData
  
  Parameters:
  
  la - Only data at this Layer may be transformed.
  
  roi - Only data inside this world-coordinates Area may be transformed.
  
  ict - The transform to apply to the data that is in @param la and within @param roi.
  
  Throws:
  
  Exception
- apply
```
public boolean apply(VectorDataTransform vdt)
              throws Exception
```
  Specified by:
  
  apply in interface VectorData
  
  Throws:
  
  Exception
- getLayerIds
```
public Collection<Long> getLayerIds()
```
  Description copied from class: ZDisplayable
  
  Get the list of Layer ids on which this ZDisplayable has data on.
  
  Overrides:
  
  getLayerIds in class ZDisplayable
- getAreaAt
```
public Area getAreaAt(Layer layer)
```
  Description copied from class: Displayable
  
  This area is meant to represent the entire area where a Displayable paints to in the @param layer. But for some this is reduced to areas with data, not with interpolated data. For example, a Polyine would show a list of little 1x1 rectangles for each point in the @param layer.
  
  Overrides:
  
  getAreaAt in class Displayable

Class Dissector

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

Dissector

Dissector

Dissector

Method Detail

paint

getFirstLayer

linkPatches

contains

clone

isDeletable

mousePressed

mouseDragged

mouseReleased

calculateBoundingBox

exportDTD

exportXML

addItem

getInfo

paintSnapshot

intersects

measure

crop

layerRemoved

apply

apply

getLayerIds

getAreaAt