AreaTree (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- ini.trakem2.persistence.DBObject
- - ini.trakem2.display.Displayable
  - - ini.trakem2.display.ZDisplayable
    - - ini.trakem2.display.Tree<Area>
      - ini.trakem2.display.AreaTree

All Implemented Interfaces:: AreaContainer, Paintable, VectorData

public class AreaTree
extends Tree<Area>
implements AreaContainer

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class AreaTree.AreaNode
- Nested classes/interfaces inherited from class ini.trakem2.display.Tree
  Tree.MeasurementPair, Tree.MeasurePathDistance<I>, Tree.MeshData, Tree.NodePath, Tree.Pair
- Nested classes/interfaces inherited from class ini.trakem2.display.Displayable
  Displayable.DataPackage, Displayable.DoEdit, Displayable.DoEdits, Displayable.DoTransforms, Displayable.SliderListener

Nested Classes
Modifier and Type	Class and Description
`static class`	`AreaTree.AreaNode`

Field Summary
- Fields inherited from class ini.trakem2.display.Tree
  end_nodes, node_layer_map, root
- 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
`AreaTree(Project project, long id, HashMap<String,String> ht_attr, HashMap<Displayable,String> ht_links)` Reconstruct from XML.
`AreaTree(Project project, long id, String title, float width, float height, float alpha, boolean visible, Color color, boolean locked, AffineTransform at)` For cloning purposes, does not call addToDatabase()
`AreaTree(Project project, String title)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addWorldAreaTo(Node<?> nd, Area a)` Assumes `nd` is an AreaNode.
`boolean`	`calculateBoundingBox(Layer la)` May have the side effect of updating the buckets of the containing container of this Displayable.
`AreaTree`	`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.
`protected Tree.MeasurementPair`	`createMeasurementPair(Tree.NodePath np)`
`void`	`debug()`
`static void`	`exportDTD(StringBuilder sb_header, HashSet<String> hs, String indent)`
`protected boolean`	`exportXMLNodeAttributes(StringBuilder indent, StringBuilder sb, Node<Area> node)`
`protected boolean`	`exportXMLNodeData(StringBuilder indent, StringBuilder sb, Node<Area> node)`
`Tree.MeshData`	`generateMesh(double scale, int resample)`
`List<Area>`	`getAreas(Layer layer, Rectangle box)` Return the list of areas, in world coordinates, at the given layer, that intersect the given bounding box.
`protected Rectangle`	`getBounds(Collection<? extends Node<Area>> nodes)`
`boolean`	`interpolateAllGaps(boolean node_centric, boolean always_use_distance_map)` Processes shorter chains first.
`boolean`	`interpolateTowardsParent(Node<Area> nd, boolean node_centric, boolean always_use_distance_map)` Find the nearest parent with a non-null, non-empty Area, and interpolate from `nd` to it.
`protected boolean`	`isAnyNear(Collection<Node<Area>> nodes, float lx, float ly, float radius)` Returns true if the given point falls within a certain distance of any of the treeline segments, where a segment is defined as the line between a clicked point and the next.
`void`	`keyPressed(KeyEvent ke)`
`ij.measure.ResultsTable`	`measureAreas(ij.measure.ResultsTable rt)`
`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)`
`Tree<Area>`	`newInstance()` Create a new instance, intialized with same ZDisplayable-level parameters (affine, color, title, etc.).
`Node<Area>`	`newNode(float lx, float ly, Layer la, Node<?> modelNode)`
`Node<Area>`	`newNode(HashMap<String,String> ht_attr)` To reconstruct from XML.

Methods inherited from class ini.trakem2.display.Tree
addNode, addToLinkLater, adjustEdgeConfidence, adjustNodeColors, apply, apply, asPoint, asVertices, cacheSubtree, canJoin, clearCache, clearState, colorizeByBranchBetweennessCentrality, colorizeByNodeBetweennessCentrality, computeAllDegrees, computeCentrality, contains, copyAs, createCoordinate, createMultiTableView, createNewNode, createReviewStack, crop, deselect, destroy, dropAllTags, duplicateAs, exportXML, findClosestNode, findClosestNodeW, findClosestNodeW, findConnectors, findFirstIntersectingNode, findIntersecting, findNearAndGetNext, findNearAndGetPrevious, findNearestEdge, findNearestEndNode, findNearestNode, findNextBranchOrEndPoint, findNode, findNodeNear, findNodeNear, findPreviousBranchOrRootPoint, findTaggedPairs, findTags, fireNodeRemoved, firstIntersectingNode, fix, flyThrough, flyThroughMarked, generateAllReviewStacks, generateRegions, generateReviewStackForSlab, generateReviewStackForSlab, generateSkeleton, generateSubtreeReviewStacks, generateSubtreeReviewStacks, generateTriangles, getActive, getAreaAt, getBounds, getBranchAndEndNodes, getBranchNodes, getEndNodes, getFirstLayer, getLastAdded, getLastEdited, getLastVisited, getLayerIds, getLayersWithData, getMarked, getNodesAt, getNodesToPaint, getNodesToPaint, getOriginPoint, getPaintingBounds, getRoot, getShortTitle, insertNode, intersects, intersects, intersects, isDeletable, isRoughlyInside, isTagging, join, layerRemoved, linkPatches, markNear, measure, measurePathDistance, measurePathDistance, measureTaggedPairs, mouseWheelMoved, paint, paint, paintsAt, paintSnapshot, popNode, remove2, removeFromLinkLater, removeNode, removeReviews, repaint, reRoot, reRoot, setActive, setEdgeConfidence, setLastAdded, setLastEdited, setLastMarked, setLastVisited, setRoot, splitAt, splitNear, toClosestPaintedNode, unmark, updateCache, updateView, updateViewData

Methods inherited from class ini.trakem2.display.ZDisplayable
exportDTD, getBucketable, getLayerSet, 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, displacePoints, exportSVG, findById, findNearestPoint, findNearestPoint, getAffineTransform, getAffineTransformCopy, getAlpha, getAnnotation, getArea, getAreaForBucket, getBoundingBox, getBoundingBox, getBoundingBox, getBounds, getColor, getComposite, getComposite, getCompositeMode, getHeight, getIntersection, getLayer, getLinked, getLinked, getLinkedBox, getLinkedGroup, getLinkedProperties, getLinkedProperties, getLinkedProperty, getLinkedProperty, getMinimalBoundingBox, getNameId, getPerimeter, getPerimeter, getProperties, getProperty, getProperty, getTitle, getWidth, getX, getXMLSafeValue, getXMLSafeValue, getY, hasLinkedGroupWithinLayer, hasProperties, intersects, intersects, inverseTransformPoint, isLinked, isLinked, isLinked, isLocked, isLocked2, isOnlyLinkedTo, isOnlyLinkedTo, isOutOfRepaintingClip, isOutOfRepaintingClip, isVisible, link, link, makeAdjustPropertiesDialog, 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, getInfo, getProject, getUniqueIdentifier, removeFromDatabase, updateInDatabase

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

Constructor Detail

AreaTree

public AreaTree(Project project,
                String title)

AreaTree

public AreaTree(Project project,
                long id,
                HashMap<String,String> ht_attr,
                HashMap<Displayable,String> ht_links)

Reconstruct from XML.

AreaTree

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

For cloning purposes, does not call addToDatabase()

Method Detail

newInstance
```
public Tree<Area> newInstance()
```
Description copied from class: Tree

Create a new instance, intialized with same ZDisplayable-level parameters (affine, color, title, etc.).

Specified by:

newInstance in class Tree<Area>

newNode

public Node<Area> newNode(float lx,
                          float ly,
                          Layer la,
                          Node<?> modelNode)

Specified by:: newNode in class Tree<Area>

newNode
```
public Node<Area> newNode(HashMap<String,String> ht_attr)
```
Description copied from class: Tree

To reconstruct from XML.

Specified by:

newNode in class Tree<Area>

clone
```
public AreaTree 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

getAreas
```
public List<Area> getAreas(Layer layer,
                           Rectangle box)
```
Return the list of areas, in world coordinates, at the given layer, that intersect the given bounding box.

Specified by:

getAreas in interface AreaContainer

exportDTD

public static void exportDTD(StringBuilder sb_header,
                             HashSet<String> hs,
                             String indent)

exportXMLNodeAttributes

protected boolean exportXMLNodeAttributes(StringBuilder indent,
                                          StringBuilder sb,
                                          Node<Area> node)

Specified by:: exportXMLNodeAttributes in class Tree<Area>

exportXMLNodeData

protected boolean exportXMLNodeData(StringBuilder indent,
                                    StringBuilder sb,
                                    Node<Area> node)

Specified by:: exportXMLNodeData in class Tree<Area>

calculateBoundingBox
```
public boolean calculateBoundingBox(Layer la)
```
Description copied from interface: AreaContainer

May have the side effect of updating the buckets of the containing container of this Displayable.

Specified by:

calculateBoundingBox in interface AreaContainer

Overrides:

calculateBoundingBox in class Tree<Area>

Returns:

Whether this Displayable's bounding box was modified.

mousePressed

public void mousePressed(MouseEvent me,
                         Layer la,
                         int x_p,
                         int y_p,
                         double mag)

Overrides:: mousePressed in class Tree<Area>

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 Tree<Area>

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 Tree<Area>

keyPressed
```
public void keyPressed(KeyEvent ke)
```
Overrides:

keyPressed in class Tree<Area>

getBounds

protected Rectangle getBounds(Collection<? extends Node<Area>> nodes)

Overrides:: getBounds in class Tree<Area>

generateMesh

public Tree.MeshData generateMesh(double scale,
                                  int resample)

debug
```
public void debug()
```

isAnyNear
```
protected boolean isAnyNear(Collection<Node<Area>> nodes,
                            float lx,
                            float ly,
                            float radius)
```
Returns true if the given point falls within a certain distance of any of the treeline segments, where a segment is defined as the line between a clicked point and the next.

Overrides:

isAnyNear in class Tree<Area>

measureAreas

public ij.measure.ResultsTable measureAreas(ij.measure.ResultsTable rt)

Specified by:: measureAreas in interface AreaContainer

interpolateTowardsParent
```
public boolean interpolateTowardsParent(Node<Area> nd,
                                        boolean node_centric,
                                        boolean always_use_distance_map)
                                 throws Exception
```
Find the nearest parent with a non-null, non-empty Area, and interpolate from nd to it.

Parameters:

nd - The node to start interpolating from, towards its nearest parent with an area.

node_centric - If true, consider areas relative to the node coordinates. If false, relative to the overall AreaTree.

Throws:

Exception

interpolateAllGaps

public boolean interpolateAllGaps(boolean node_centric,
                                  boolean always_use_distance_map)
                           throws Exception

Processes shorter chains first.

Throws:: Exception

addWorldAreaTo

public void addWorldAreaTo(Node<?> nd,
                           Area a)

Assumes nd is an AreaNode. Otherwise fails with ClassCastException.

Parameters:: nd - An AreaNode.

createMeasurementPair

protected Tree.MeasurementPair createMeasurementPair(Tree.NodePath np)

Specified by:: createMeasurementPair in class Tree<Area>

Class AreaTree

Nested Class Summary

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

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

Field Summary

Fields inherited from class ini.trakem2.display.Tree

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.Tree

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

AreaTree

AreaTree

AreaTree

Method Detail

newInstance

newNode

newNode

clone

getAreas

exportDTD

exportXMLNodeAttributes

exportXMLNodeData

calculateBoundingBox

mousePressed

mouseDragged

mouseReleased

keyPressed

getBounds

generateMesh

debug

isAnyNear

measureAreas

interpolateTowardsParent

interpolateAllGaps

addWorldAreaTo

createMeasurementPair