LayerSet (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- ini.trakem2.persistence.DBObject
- - ini.trakem2.display.Displayable
  - - ini.trakem2.display.LayerSet

All Implemented Interfaces:

Bucketable, Paintable
```
public final class LayerSet
extends Displayable
implements Bucketable
```
A LayerSet is a container for a list of Layer. LayerSet methods are NOT synchronized. It is your reponsibility to synchronize access to a LayerSet instance methods. Failure to do so may result in corrupted internal data structures and overall misbehavior.

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`protected static class`	`LayerSet.DoChangeTrees` Records the state of the LayerSet.al_layers, each Layer.al_displayables and all the trees and unique types of Project.
`protected static class`	`LayerSet.DoMoveZDisplayable`
`protected class`	`LayerSet.LayerBucket` A Bucket for the ZDisplayable parts that show in every Layer.

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

Field Summary

Fields
Modifier and Type	Field and Description
`static String[]`	`ANCHORS`
`protected boolean`	`area_color_cues`
`static int`	`BOTTOM`
`static int`	`CENTER`
`protected boolean`	`color_cues`
`static int`	`DOWN`
`static int`	`EAST`
`static int`	`FLIP_HORIZONTAL`
`static int`	`FLIP_VERTICAL`
`protected HashMap<Layer,LayerSet.LayerBucket>`	`lbucks` For fast search.
`protected int`	`n_layers_color_cue`
`static int`	`NORTH`
`static int`	`NORTHEAST`
`static int`	`NORTHWEST`
`protected boolean`	`paint_arrows`
`protected boolean`	`paint_edge_confidence_boxes`
`protected boolean`	`paint_tags`
`protected int`	`preload_ahead`
`protected boolean`	`prepaint`
`static int`	`R270`
`static int`	`R90`
`static String[]`	`ROTATIONS`
`static String[]`	`snapshot_modes`
`static int`	`SOUTH`
`static int`	`SOUTHEAST`
`static int`	`SOUTHWEST`
`protected Map<Integer,HashMap<String,Tag>>`	`tags` A set of unique tags, retrievable by their own identity.
`static int`	`TOP`
`static int`	`UP`
`protected boolean`	`use_color_cue_colors`
`static int`	`WEST`

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
Modifier	Constructor and Description
`protected`	`LayerSet(Project project, long id)` Dummy.
	`LayerSet(Project project, long id, HashMap<String,String> ht_attributes, HashMap<Displayable,String> ht_links)` Reconstruct from an XML entry.
	`LayerSet(Project project, long id, String title, float width, float height, double rot_x, double rot_y, double rot_z, float layer_width, float layer_height, boolean locked, int snapshots_mode, AffineTransform at)` Reconstruct from the database.
	`LayerSet(Project project, String title, double x, double y, Layer parent, float layer_width, float layer_height)` Create a new LayerSet with a 0,0,0 rotation vector and default 20,20 px Displayable width,height.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`void`	`add(Layer layer)` Add a new Layer, inserted according to its Z.
`void`	`add(ZDisplayable zdispl)` Add a Displayable to be painted in all Layers, such as a Pipe.
`void`	`addAll(Collection<? extends ZDisplayable> coll)`
`LayerSet.DoChangeTrees`	`addChangeTreesStep()` Add a step to undo the addition or deletion of one or more objects in this project and LayerSet.
`LayerSet.DoChangeTrees`	`addChangeTreesStep(Set<DoStep> dependents)` Add a step to undo the addition or deletion of one or more objects in this project and LayerSet, along with an arbitrary set of steps that may alter, for example the data.
`boolean`	`addDataEditStep(Set<? extends Displayable> ds)` A new undo step for the "data" field of all Displayable in the set.
`void`	`addLayerContentStep(Layer la)` For the Displayable contained in a Layer: their number, and their stack order.
`void`	`addLayerEditedStep(Layer layer)` For the Z and thickness of a layer.
`void`	`addLayerEditedStep(List<Layer> al)` For the Z and thickness of a list of layers.
`void`	`addSilently(Layer layer)` Add a new Layer silently, ordering by z as well.
`void`	`addSilently(ZDisplayable zdispl)` Used for reconstruction purposes, avoids repainting or updating.
`void`	`addTransformStep()` Add an undo step for the transformations of all Displayable in all layers.
`void`	`addTransformStep(Collection<? extends Displayable> col)` Add an undo step for the transformations of all Displayable in hs.
`void`	`addTransformStep(Layer layer)` Add an undo step for the transformations of all Displayable in the layer.
`void`	`addTransformStep(List<Layer> layers)`
`Displayable.DoEdits`	`addTransformStepWithData(Collection<? extends Displayable> col)` Add an undo step for the transformations of all Displayable in col, with data as well (for Patch, data includes the CoordinateTransform).
`Collection<Displayable>`	`addTransformStepWithDataForAll(Collection<Layer> layers)` Includes all ZDisplayable that paint at any of the given layers.
`void`	`addUndoMoveStep(Displayable d)` To undo moving up/down/top/bottom.
`void`	`addUndoStep(DoStep step)`
`void`	`addZDisplayable(ZDisplayable zdispl)` Useful for typeless scripts so that a ZDisplayable can be added; the overloaded method add(Layer) and add(ZDisplayable) is not distinguishable otherwise.
`static void`	`applyTransforms(Map<Displayable,AffineTransform> m)`
`protected Tag`	`askForNewTag(int keyCode)`
`protected boolean`	`askToRemoveTag(int keyCode)` Returns false if the dialog was canceled or there wasn't any tag to remove.
`boolean`	`canRedo()`
`boolean`	`canUndo()`
`void`	`checkBuckets()` Checks only buckets for ZDisplayable, not any related to any layer.
`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.
`Displayable`	`clone(Project pr, Layer first, Layer last, Rectangle roi, boolean add_to_tree, boolean copy_id, boolean ignore_hidden_patches)` Clone the contents of this LayerSet, from first to last given layers, and cropping for the given rectangle; does NOT copy the ZDisplayable, which may be copied using the LayerSet.cloneInto method.
`static void`	`cloneInto(LayerSet src, Layer src_first, Layer src_last, Project pr, LayerSet copy, Rectangle roi, boolean copy_id)`
`boolean`	`contains(Class<?> c)` Returns true if any of the ZDisplayable objects are of the given class.
`boolean`	`contains(Displayable zdispl)`
`boolean`	`contains(Layer layer)`
`boolean`	`containsDisplayable(Class<?> c)` Check in all layers.
`LayerSet`	`create(Layer parent_layer)` Create a new LayerSet in the middle of the parent Layer.
`LayerStack`	`createLayerStack(Class<?> clazz, int type, int c_alphas)` Create a virtual layer stack that acts as a virtual ij.ImageStack, in RGB and set to a scale of max_dimension / Math.max(layer_width, layer_height).
`DoStep`	`createUndoMoveStep(Displayable d)` To undo moving up/down/top/bottom.
`void`	`destroy()` Release resources.
`void`	`enlargeToFit(Collection<? extends Displayable> ds)` Enlarge the 2D universe so that all Displayable in the collection fit in it; that is, that no Displayable has a negative x,y position or lays beyond bounds.
`boolean`	`enlargeToFit(Displayable d, int anchor)` Enlarges the display in the given direction; the anchor is the point to keep still, and can be any of LayerSet.NORTHWEST (top-left), etc.
`static void`	`exportDTD(StringBuilder sb_header, HashSet<String> hs, String indent)` Includes the !ELEMENT
`String`	`exportTags()`
`void`	`exportXML(Writer writer, String indent, XMLOptions options)`
`ArrayList<Displayable>`	`find(Class<?> c, Layer layer, Area aroi, boolean visible_only)` Find any Displayable or ZDisplayable objects of class C which intersect with the Area @param aroi.
`ArrayList<Displayable>`	`find(Class<?> c, Layer layer, Area aroi, boolean visible_only, boolean instance_of)` Find any Displayable or ZDisplayable objects of class C which intersect with the Area @param aroi.
`ArrayList<Displayable>`	`find(Class<?> c, Layer layer, int x, int y, boolean visible_only)`
`ArrayList<ZDisplayable>`	`find(Layer first, Layer last, Area area)` Find the ZDisplayable objects that intersect with the 3D roi defined by the first and last layers, and the area -all in world coordinates.
`protected Map<Displayable,List<Area>>`	`findAreas(Layer layer, Rectangle box, boolean visible)` Find all java.awt.geom.Area in layer that intersect with box, if visible.
`DBObject`	`findById(long id)` Searches in all ZDisplayables and in all layers, recursively into nested LayerSets.
`Displayable`	`findDisplayable(long id)` Searches in all layers.
`Collection<Displayable>`	`findZDisplayables(Class<?> c, Layer layer, Area aroi, boolean visible_only, boolean instance_of)` Find ZDisplayable objects of the given class that intersect the given area in the given layer.
`Collection<Displayable>`	`findZDisplayables(Class<?> c, Layer layer, int x, int y, boolean visible_only)` Find ZDisplayable objects of Class c that contain the point x,y in the given layer.
`Collection<Displayable>`	`findZDisplayables(Class<?> c, Layer layer, int x, int y, boolean visible_only, boolean instance_of)` Find ZDisplayable objects of Class c that contain the point x,y in the given layer.
`Collection<Displayable>`	`findZDisplayables(Class<?> c, Layer layer, Rectangle r, boolean visible_only)`
`Collection<Displayable>`	`findZDisplayables(Class<?> c, Layer layer, Rectangle r, boolean visible_only, boolean instance_of)` Find ZDisplayable objects of the given class that intersect the given rectangle in the given layer.
`Collection<Displayable>`	`findZDisplayables(Layer layer, int x, int y, boolean visible_only)` Find ZDisplayable objects that contain the point x,y in the given layer.
`Collection<Displayable>`	`findZDisplayables(Layer layer, Rectangle r, boolean visible_only)` Find ZDisplayable objects that intersect the given rectangle in the given layer.
`ArrayList<Displayable>`	`get(ArrayList<Displayable> all, Class<?> c)` Find, in this LayerSet and contained layers and their nested LayerSets if any, all Displayable instances of Class c, which are stored in the given ArrayList; returns the same ArrayList, or a new one if its null.
`ArrayList<Displayable>`	`get(Class<?> c)` Find, in this LayerSet and contained layers and their nested LayerSets if any, all Displayable instances of Class c.
`Rectangle`	`get2DBounds()` Returns a new Rectangle of 0, 0, layer_width, layer_height.
`<T extends Displayable> List<T>`	`getAll(Class<T> c)` Get all Displayable or ZDisplayable of the given class.
`HashMap<Displayable,HashSet<Bucket>>`	`getBucketMap(Layer la)`
`ij.measure.Calibration`	`getCalibration()`
`ij.measure.Calibration`	`getCalibrationCopy()`
`List<Layer>`	`getColorCueLayerRange(Layer active_layer)` Returns the list of layers to paint by considering the range of n_layers_color_cue around the active layer index.
`double`	`getDepth()` Returns the distance from the first layer's Z to the last layer's Z.
`ArrayList<ZDisplayable>`	`getDisplayableList()` Returns the real list of displayables, not a copy.
`ArrayList<Displayable>`	`getDisplayables()` Return all the Displayable objects from all the layers of this LayerSet.
`ArrayList<Displayable>`	`getDisplayables(Class<?> c)` Return all the Displayable objects from all the layers of this LayerSet of the given class.
`ArrayList<Displayable>`	`getDisplayables(Class<?> c, Area aroi, boolean visible_only)` Return all the Displayable objects from all the layers of this LayerSet of the given class that intersect the given area.
`Layer`	`getLayer(double z)` Returns the first layer found with the given Z coordinate, rounded to seventh decimal precision, or null if none found.
`Layer`	`getLayer(double z, double thickness, boolean create)` Returns null if none has the given z and thickness.
`Layer`	`getLayer(int i)` Find a layer by index, or null if none.
`Layer`	`getLayer(long id)` Find a layer with the given id, or null if none.
`Layer`	`getLayer(Long id)` Same as getLayer(long) but without box/unbox.
`float`	`getLayerHeight()`
`int`	`getLayerIndex(long id)`
`ArrayList<Layer>`	`getLayers()` Returns a copy of the layer list.
`List<Layer>`	`getLayers(int first, int last)` Returns a sublist of layers from first to last, both inclusive.
`List<Layer>`	`getLayers(Layer first, Layer last)` Returns the layer range from first to last, both included.
`float`	`getLayerWidth()`
`Rectangle`	`getMinimalBoundingBox(Class<?> c)` Returns the minimal 2D bounding box for Displayables of class @param c in all layers.
`Layer`	`getNearestLayer(double z)`
`ArrayList<Layer>`	`getNeighborLayers(Layer layer, int n)` Get up to 'n' layers before and after the given layers.
`Overlay`	`getOverlay()` Return the current Overlay or a new one if none yet.
`Layer`	`getParent()`
`int`	`getPixelsMaxDimension()`
`double`	`getRotX()`
`double`	`getRotY()`
`double`	`getRotZ()`
`int`	`getSnapshotsMode()`
`TreeSet<Tag>`	`getTags(int keyCode)` If there aren't any tags for keyCode, returns an empty TreeSet.
`double`	`getVirtualizationScale()` From 0.000...
`ArrayList<ZDisplayable>`	`getZDisplayables()` Returns a copy of the list of ZDisplayable objects.
`ArrayList<ZDisplayable>`	`getZDisplayables(Class<?> c)`
`ArrayList<ZDisplayable>`	`getZDisplayables(Class<?> c, boolean instance_of)` Returns a list of ZDisplayable of class c only.
`ArrayList<ZDisplayable>`	`getZDisplayables(Class<?> c, Layer layer, Area aroi, boolean visible_only)` Deprecated.
`ArrayList<ZDisplayable>`	`getZDisplayables(Class<?> c, Layer layer, Area aroi, boolean visible_only, boolean instance_of)` Deprecated.
`Object`	`grab(int first, int last, Rectangle r, double scale, Class<?> c, int c_alphas, int format, int type)` Returns the region defined by the rectangle as an image in the type and format specified.
`HashSet<Displayable>`	`hideExcept(ArrayList<Class<?>> type, boolean repaint)` Hide all except those whose type is in 'type' list, whose visibility flag is left unchanged.
`void`	`importTags(String path, boolean replace)`
`int`	`indexOf(Layer layer)` From zero to size-1.
`int`	`indexOf(ZDisplayable zd)` Returns the reverse index of ZDisplayable zd, which is the actual index as seen in the screen.
`protected boolean`	`isBottom(Displayable d)` Hub method: ZDisplayable or into the Displayable's Layer.
`boolean`	`isBottom(ZDisplayable zd)`
`boolean`	`isCalibrated()`
`boolean`	`isDeletable()`
`boolean`	`isEmptyAt(Layer layer)`
`boolean`	`isPixelsVirtualizationEnabled()`
`protected boolean`	`isTop(Displayable d)` Hub method: ZDisplayable or into the Displayable's Layer.
`boolean`	`isTop(ZDisplayable zd)`
`void`	`keyPressed(KeyEvent ke)`
`void`	`mouseDragged(MouseEvent me, int x_p, int y_p, int x_d, int y_d, int x_d_old, int y_d_old, Rectangle srcRect, double mag)`
`void`	`mousePressed(MouseEvent me, int x_p, int y_p, Rectangle srcRect, double mag)`
`void`	`mouseReleased(MouseEvent me, int x_p, int y_p, int x_d, int y_d, int x_r, int y_r, Rectangle srcRect, double mag)`
`protected void`	`move(int place, Displayable d)` Change z position in the layered stack, which defines the painting order.
`void`	`move(Set<Displayable> hs_d, Layer source, Layer target)` Move all Displayable objects in the HashSet to the given target layer.
`void`	`moveDown(Layer layer, Displayable d)` Move the given Displayable to the next layer if possible.
`void`	`moveUp(Layer layer, Displayable d)` Move the given Displayable to the previous layer if possible.
`Layer`	`next(Layer layer)`
`Layer`	`nextNonEmpty(Layer layer)`
`void`	`paint(Graphics2D g, Rectangle srcRect, double magnification, boolean active, int channels, Layer active_layer)`
`Layer`	`previous(Layer layer)`
`Layer`	`previousNonEmpty(Layer layer)`
`void`	`printDebugInfo()`
`Tag`	`putTag(String tag, int keyCode)` Returns an existing immutable Tag instance if already there, or stores a new one and returns it.
`void`	`recreateBuckets(boolean layer_buckets)` Recreate the ZDisplayable buckets, and also the Layer Displayable buckets if desired.
`void`	`recreateBuckets(Collection<Layer> layers, boolean layer_buckets)` Regenerate the quad-tree bucket system for the ZDisplayable instances that have data at each of the given layers, and optionally regenerate the buckets as well for the 2D Displayable instances of that layer as well.
`void`	`recreateBuckets(Layer layer, boolean layer_buckets)` Recreate the ZDisplayable buckets for `layer`, and also the `Layer` `Displayable` buckets if desired.
`boolean`	`redoOneStep()` Redoes one step of the ongoing transformation history, otherwise of the overall LayerSet history.
`boolean`	`remove(boolean check)` Remove from both the database and any Display that shows the Layer in which this Displayable is shown.
`void`	`remove(Layer layer)` Remove a child.
`boolean`	`remove(ZDisplayable zdispl)` Remove a child.
`protected boolean`	`remove2(boolean check)` Remove also from the trees if present; does nothing more than remove(boolean) unless overriden.
`boolean`	`removeAll(Set<ZDisplayable> zds)` Remove a child.
`void`	`removeAllTags()`
`void`	`removeFromOffscreens(Layer la)`
`protected boolean`	`removeLastUndoStep()`
`void`	`removeTag(String tag, int keyCode)` Removes the tag from the list of possible tags, and then from wherever it has been assigned.
`void`	`removeTag(Tag t)`
`protected void`	`reposition(Layer layer)` Used by the Layer.setZ method.
`void`	`restoreCalibration(HashMap<String,String> ht_attributes)` Restore calibration from the given XML attributes table.
`Collection<Displayable>`	`roughlyFindZDisplayables(Layer layer, Rectangle r, boolean visible_only)` Find ZDisplayable objects that intersect the given rectangle in the given layer.
`Collection<Displayable>`	`setAllVisible(boolean repaint)` Returns the collection of Displayable whose visibility state has changed.
`void`	`setAlpha(float alpha)` Overiding.
`void`	`setCalibration(ij.measure.Calibration cal)` Set the calibration to a clone of the given calibration.
`void`	`setDimensions(float x, float y, float layer_width, float layer_height)` May leave objects beyond the visible window.
`boolean`	`setDimensions(float layer_width, float layer_height, int anchor)` Returns false if any Displayables are being partially or totally cropped away.
`void`	`setLayer(Layer layer, boolean update)` 'update' in database or not.
`boolean`	`setMinimumDimensions()` Used by the Loader after loading blindly a lot of Patches.
`Overlay`	`setOverlay(Overlay o)` Set to null to remove the Overlay.
`void`	`setParent(Layer layer)`
`void`	`setPixelsMaxDimension(int d)`
`void`	`setPixelsVirtualizationEnabled(boolean b)`
`void`	`setRotVector(double rot_x, double rot_y, double rot_z)`
`void`	`setSnapshotsMode(int mode)`
`void`	`setSnapshotsQuality(boolean b)`
`void`	`setup()` For reconstruction purposes: set the active layer to the ZDisplayable objects.
`HashSet<Displayable>`	`setVisible(String type, boolean visible, boolean repaint)` Returns the hash set of objects whose visibility has changed.
`int`	`size()` The number of Layers in this LayerSet.
`boolean`	`snapshotsQuality()` For creating snapshots, using a very slow but much better scaling algorithm (the Image.SCALE_AREA_AVERAGING method).
`String`	`toString()` Minimal info that identifies this object as unique, for display on a JTree node.
`boolean`	`undoOneStep()` Undoes one step of the ongoing transformation history, otherwise of the overall LayerSet history.
`void`	`updateBucket(Displayable d, Layer layer)`
`void`	`updateLayerTree()` Recursive into nested LayerSet objects.

Methods inherited from class ini.trakem2.display.Displayable
adjustProperties, areThereLayerCrossLinks, canSendTo, clone, clone, commonDTDChildren, contains, contains, deselect, displacePoints, exportDTD, exportSVG, exportXML, findNearestPoint, findNearestPoint, getAffineTransform, getAffineTransformCopy, getAlpha, getAnnotation, getArea, getAreaAt, getAreaForBucket, getBoundingBox, getBoundingBox, getBoundingBox, getBounds, getBounds, getBucketable, getColor, getComposite, getComposite, getCompositeMode, getHeight, getIntersection, getLayer, getLayerIds, getLayerSet, 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, link, link, linkPatches, makeAdjustPropertiesDialog, measure, mouseDragged, mousePressed, mouseReleased, mouseWheelMoved, paint, paintAsBox, paintOffscreen, paintSnapshot, preConcatenate, prePaint, preTransform, processAdjustPropertiesDialog, removeLinkedProperties, removeLinkedPropertiesFromOrigins, repaint, restXML, rotate, rotate, rotatePoints, scale, scale, scalePoints, setAffineTransform, setAlpha, setAnnotation, setColor, setCompositeMode, setDimensions, setDimensions, setLayer, setLinkedProperties, setLinkedProperty, setLocation, setLocked, setProperty, setTitle, setVisible, setVisible, snapTo, softRemove, transform, transformPoint, transformPoint, transformPoints, transformPoints, transformPoints, transformPoints, transformPoints, transformPoints, transformPoints, transformPoints, transformPoints, transformRectangle, translate, translate, unlink, unlink, unlinkAll, updateBucket, 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

Methods inherited from interface ini.trakem2.display.Bucketable
getProject

Field Detail

NORTH
```
public static final int NORTH
```
See Also:

Constant Field Values

NORTHEAST
```
public static final int NORTHEAST
```
See Also:

Constant Field Values

EAST
```
public static final int EAST
```
See Also:

Constant Field Values

SOUTHEAST
```
public static final int SOUTHEAST
```
See Also:

Constant Field Values

SOUTH
```
public static final int SOUTH
```
See Also:

Constant Field Values

SOUTHWEST
```
public static final int SOUTHWEST
```
See Also:

Constant Field Values

WEST
```
public static final int WEST
```
See Also:

Constant Field Values

NORTHWEST
```
public static final int NORTHWEST
```
See Also:

Constant Field Values

CENTER
```
public static final int CENTER
```
See Also:

Constant Field Values

R90
```
public static final int R90
```
See Also:

Constant Field Values

R270
```
public static final int R270
```
See Also:

Constant Field Values

FLIP_HORIZONTAL
```
public static final int FLIP_HORIZONTAL
```
See Also:

Constant Field Values

FLIP_VERTICAL
```
public static final int FLIP_VERTICAL
```
See Also:

Constant Field Values

TOP
```
public static final int TOP
```
See Also:

Constant Field Values

UP
```
public static final int UP
```
See Also:

Constant Field Values

DOWN
```
public static final int DOWN
```
See Also:

Constant Field Values

BOTTOM
```
public static final int BOTTOM
```
See Also:

Constant Field Values

snapshot_modes

public static final String[] snapshot_modes

ANCHORS
```
public static final String[] ANCHORS
```

ROTATIONS
```
public static final String[] ROTATIONS
```

color_cues
```
protected boolean color_cues
```

area_color_cues
```
protected boolean area_color_cues
```

use_color_cue_colors
```
protected boolean use_color_cue_colors
```

paint_arrows
```
protected boolean paint_arrows
```

paint_tags
```
protected boolean paint_tags
```

paint_edge_confidence_boxes

protected boolean paint_edge_confidence_boxes

n_layers_color_cue
```
protected int n_layers_color_cue
```

prepaint
```
protected boolean prepaint
```

preload_ahead
```
protected int preload_ahead
```

lbucks

protected HashMap<Layer,LayerSet.LayerBucket> lbucks

For fast search.

tags
```
protected final Map<Integer,HashMap<String,Tag>> tags
```
A set of unique tags, retrievable by their own identity.

Constructor Detail

LayerSet

protected LayerSet(Project project,
                   long id)

Dummy.

LayerSet

public LayerSet(Project project,
                String title,
                double x,
                double y,
                Layer parent,
                float layer_width,
                float layer_height)

Create a new LayerSet with a 0,0,0 rotation vector and default 20,20 px Displayable width,height.

LayerSet

public LayerSet(Project project,
                long id,
                String title,
                float width,
                float height,
                double rot_x,
                double rot_y,
                double rot_z,
                float layer_width,
                float layer_height,
                boolean locked,
                int snapshots_mode,
                AffineTransform at)

Reconstruct from the database.

LayerSet

public LayerSet(Project project,
                long id,
                HashMap<String,String> ht_attributes,
                HashMap<Displayable,String> ht_links)

Reconstruct from an XML entry.

Method Detail

setup
```
public void setup()
```
For reconstruction purposes: set the active layer to the ZDisplayable objects. Recurses through LayerSets in the children layers.

create
```
public LayerSet create(Layer parent_layer)
```
Create a new LayerSet in the middle of the parent Layer.

addSilently
```
public void addSilently(Layer layer)
```
Add a new Layer silently, ordering by z as well.

add
```
public void add(Layer layer)
```
Add a new Layer, inserted according to its Z.

printDebugInfo
```
public void printDebugInfo()
```

getParent
```
public Layer getParent()
```

setLayer

public void setLayer(Layer layer,
                     boolean update)

'update' in database or not.

Overrides:: setLayer in class Displayable

setParent
```
public void setParent(Layer layer)
```

mousePressed

public void mousePressed(MouseEvent me,
                         int x_p,
                         int y_p,
                         Rectangle srcRect,
                         double mag)

mouseDragged

public void mouseDragged(MouseEvent me,
                         int x_p,
                         int y_p,
                         int x_d,
                         int y_d,
                         int x_d_old,
                         int y_d_old,
                         Rectangle srcRect,
                         double mag)

mouseReleased

public void mouseReleased(MouseEvent me,
                          int x_p,
                          int y_p,
                          int x_d,
                          int y_d,
                          int x_r,
                          int y_r,
                          Rectangle srcRect,
                          double mag)

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

keyPressed in class Displayable

toString
```
public String toString()
```
Description copied from class: Displayable

Minimal info that identifies this object as unique, for display on a JTree node.

Overrides:

toString in class Displayable

paint

public void paint(Graphics2D g,
                  Rectangle srcRect,
                  double magnification,
                  boolean active,
                  int channels,
                  Layer active_layer)

getLayerWidth
```
public float getLayerWidth()
```
Specified by:

getLayerWidth in interface Bucketable

getLayerHeight
```
public float getLayerHeight()
```
Specified by:

getLayerHeight in interface Bucketable

getRotX
```
public double getRotX()
```

getRotY
```
public double getRotY()
```

getRotZ
```
public double getRotZ()
```

size
```
public int size()
```
The number of Layers in this LayerSet.

setRotVector

public void setRotVector(double rot_x,
                         double rot_y,
                         double rot_z)

setMinimumDimensions
```
public boolean setMinimumDimensions()
```
Used by the Loader after loading blindly a lot of Patches. Will crop the canvas to the minimum size possible.

enlargeToFit
```
public void enlargeToFit(Collection<? extends Displayable> ds)
```
Enlarge the 2D universe so that all Displayable in the collection fit in it; that is, that no Displayable has a negative x,y position or lays beyond bounds.

enlargeToFit
```
public boolean enlargeToFit(Displayable d,
                            int anchor)
```
Enlarges the display in the given direction; the anchor is the point to keep still, and can be any of LayerSet.NORTHWEST (top-left), etc.

setDimensions

public void setDimensions(float x,
                          float y,
                          float layer_width,
                          float layer_height)

May leave objects beyond the visible window.

setDimensions

public boolean setDimensions(float layer_width,
                             float layer_height,
                             int anchor)

Returns false if any Displayables are being partially or totally cropped away.

remove2
```
protected boolean remove2(boolean check)
```
Description copied from class: Displayable

Remove also from the trees if present; does nothing more than remove(boolean) unless overriden.

Overrides:

remove2 in class Displayable

remove
```
public boolean remove(boolean check)
```
Description copied from class: Displayable

Remove from both the database and any Display that shows the Layer in which this Displayable is shown.

Overrides:

remove in class Displayable

remove
```
public void remove(Layer layer)
```
Remove a child. Does not destroy it or delete it from the database.

next
```
public Layer next(Layer layer)
```

previous
```
public Layer previous(Layer layer)
```

nextNonEmpty

public Layer nextNonEmpty(Layer layer)

previousNonEmpty

public Layer previousNonEmpty(Layer layer)

getLayerIndex
```
public int getLayerIndex(long id)
```

getLayer
```
public Layer getLayer(int i)
```
Find a layer by index, or null if none.

getLayer
```
public Layer getLayer(long id)
```
Find a layer with the given id, or null if none.

getLayer
```
public Layer getLayer(Long id)
```
Same as getLayer(long) but without box/unbox.

getLayer
```
public Layer getLayer(double z)
```
Returns the first layer found with the given Z coordinate, rounded to seventh decimal precision, or null if none found.

getNearestLayer

public Layer getNearestLayer(double z)

getLayer
```
public Layer getLayer(double z,
                      double thickness,
                      boolean create)
```
Returns null if none has the given z and thickness. If 'create' is true and no layer is found, a new one with the given Z is created and added to the LayerTree.

addZDisplayable
```
public void addZDisplayable(ZDisplayable zdispl)
```
Useful for typeless scripts so that a ZDisplayable can be added; the overloaded method add(Layer) and add(ZDisplayable) is not distinguishable otherwise.

add
```
public void add(ZDisplayable zdispl)
```
Add a Displayable to be painted in all Layers, such as a Pipe. Also updates open displays of the fact.

addAll

public void addAll(Collection<? extends ZDisplayable> coll)

addSilently
```
public void addSilently(ZDisplayable zdispl)
```
Used for reconstruction purposes, avoids repainting or updating.

remove
```
public boolean remove(ZDisplayable zdispl)
```
Remove a child. Does not destroy the child nor remove it from the database, only from the LayerSet and the Display.

removeAll
```
public boolean removeAll(Set<ZDisplayable> zds)
```
Remove a child. Does not destroy the child nor remove it from the database, only from the LayerSet and the Display. Returns false if at least one failed to be removed.

contains
```
public boolean contains(Layer layer)
```

contains

public boolean contains(Displayable zdispl)

getLayers
```
public ArrayList<Layer> getLayers()
```
Returns a copy of the layer list.

getLayers
```
public List<Layer> getLayers(int first,
                             int last)
```
Returns a sublist of layers from first to last, both inclusive. If last is larger than first, the order is reversed.

getLayers

public List<Layer> getLayers(Layer first,
                             Layer last)

Returns the layer range from first to last, both included. If last.getZ() < first.getZ(), the order is reversed.

getColorCueLayerRange
```
public List<Layer> getColorCueLayerRange(Layer active_layer)
```
Returns the list of layers to paint by considering the range of n_layers_color_cue around the active layer index.

isDeletable
```
public boolean isDeletable()
```
Specified by:

isDeletable in class Displayable

setAlpha
```
public void setAlpha(float alpha)
```
Overiding. The alpha is used to show whether the LayerSet object is selected or not.

Overrides:

setAlpha in class Displayable

moveDown

public void moveDown(Layer layer,
                     Displayable d)

Move the given Displayable to the next layer if possible.

moveUp

public void moveUp(Layer layer,
                   Displayable d)

Move the given Displayable to the previous layer if possible.

move

public void move(Set<Displayable> hs_d,
                 Layer source,
                 Layer target)

Move all Displayable objects in the HashSet to the given target layer.

setVisible

public HashSet<Displayable> setVisible(String type,
                                       boolean visible,
                                       boolean repaint)

Returns the hash set of objects whose visibility has changed.

hideExcept
```
public HashSet<Displayable> hideExcept(ArrayList<Class<?>> type,
                                       boolean repaint)
```
Hide all except those whose type is in 'type' list, whose visibility flag is left unchanged. Returns the list of displayables made hidden.

setAllVisible
```
public Collection<Displayable> setAllVisible(boolean repaint)
```
Returns the collection of Displayable whose visibility state has changed.

contains
```
public boolean contains(Class<?> c)
```
Returns true if any of the ZDisplayable objects are of the given class.

containsDisplayable

public boolean containsDisplayable(Class<?> c)

Check in all layers.

getDepth
```
public double getDepth()
```
Returns the distance from the first layer's Z to the last layer's Z.

getDisplayables
```
public ArrayList<Displayable> getDisplayables()
```
Return all the Displayable objects from all the layers of this LayerSet. Does not include the ZDisplayables.

getDisplayables
```
public ArrayList<Displayable> getDisplayables(Class<?> c)
```
Return all the Displayable objects from all the layers of this LayerSet of the given class. Does not include the ZDisplayables.

getDisplayables

public ArrayList<Displayable> getDisplayables(Class<?> c,
                                              Area aroi,
                                              boolean visible_only)

Return all the Displayable objects from all the layers of this LayerSet of the given class that intersect the given area. Does not include the ZDisplayables.

indexOf
```
public int indexOf(Layer layer)
```
From zero to size-1.

exportXML

public void exportXML(Writer writer,
                      String indent,
                      XMLOptions options)
               throws Exception

Throws:: Exception

exportDTD

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

Includes the !ELEMENT

setSnapshotsMode

public void setSnapshotsMode(int mode)

getSnapshotsMode
```
public int getSnapshotsMode()
```

destroy
```
public void destroy()
```
Description copied from class: Displayable

Release resources.

Overrides:

destroy in class Displayable

reposition

protected void reposition(Layer layer)

Used by the Layer.setZ method.

getNeighborLayers

public ArrayList<Layer> getNeighborLayers(Layer layer,
                                          int n)

Get up to 'n' layers before and after the given layers.

isTop

public boolean isTop(ZDisplayable zd)

isBottom

public boolean isBottom(ZDisplayable zd)

isTop
```
protected boolean isTop(Displayable d)
```
Hub method: ZDisplayable or into the Displayable's Layer.

isBottom
```
protected boolean isBottom(Displayable d)
```
Hub method: ZDisplayable or into the Displayable's Layer.

move

protected void move(int place,
                    Displayable d)

Change z position in the layered stack, which defines the painting order.

indexOf
```
public int indexOf(ZDisplayable zd)
```
Returns the reverse index of ZDisplayable zd, which is the actual index as seen in the screen.

isEmptyAt

public boolean isEmptyAt(Layer layer)

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

clone

public Displayable clone(Project pr,
                         Layer first,
                         Layer last,
                         Rectangle roi,
                         boolean add_to_tree,
                         boolean copy_id,
                         boolean ignore_hidden_patches)

Clone the contents of this LayerSet, from first to last given layers, and cropping for the given rectangle; does NOT copy the ZDisplayable, which may be copied using the LayerSet.cloneInto method.

cloneInto

public static void cloneInto(LayerSet src,
                             Layer src_first,
                             Layer src_last,
                             Project pr,
                             LayerSet copy,
                             Rectangle roi,
                             boolean copy_id)
                      throws Exception

Throws:: Exception

createLayerStack
```
public LayerStack createLayerStack(Class<?> clazz,
                                   int type,
                                   int c_alphas)
```
Create a virtual layer stack that acts as a virtual ij.ImageStack, in RGB and set to a scale of max_dimension / Math.max(layer_width, layer_height).

getPixelsMaxDimension
```
public int getPixelsMaxDimension()
```

getVirtualizationScale
```
public double getVirtualizationScale()
```
From 0.000... to 1.

setPixelsMaxDimension

public void setPixelsMaxDimension(int d)

setPixelsVirtualizationEnabled

public void setPixelsVirtualizationEnabled(boolean b)

isPixelsVirtualizationEnabled

public boolean isPixelsVirtualizationEnabled()

get2DBounds
```
public Rectangle get2DBounds()
```
Returns a new Rectangle of 0, 0, layer_width, layer_height.

setCalibration
```
public void setCalibration(ij.measure.Calibration cal)
```
Set the calibration to a clone of the given calibration.

getCalibration

public ij.measure.Calibration getCalibration()

getCalibrationCopy

public ij.measure.Calibration getCalibrationCopy()

isCalibrated
```
public boolean isCalibrated()
```

restoreCalibration
```
public void restoreCalibration(HashMap<String,String> ht_attributes)
```
Restore calibration from the given XML attributes table.

snapshotsQuality
```
public boolean snapshotsQuality()
```
For creating snapshots, using a very slow but much better scaling algorithm (the Image.SCALE_AREA_AVERAGING method).

setSnapshotsQuality

public void setSnapshotsQuality(boolean b)

get
```
public ArrayList<Displayable> get(Class<?> c)
```
Find, in this LayerSet and contained layers and their nested LayerSets if any, all Displayable instances of Class c. Includes the ZDisplayables.

get
```
public ArrayList<Displayable> get(ArrayList<Displayable> all,
                                  Class<?> c)
```
Find, in this LayerSet and contained layers and their nested LayerSets if any, all Displayable instances of Class c, which are stored in the given ArrayList; returns the same ArrayList, or a new one if its null. Includes the ZDisplayables.

grab
```
public Object grab(int first,
                   int last,
                   Rectangle r,
                   double scale,
                   Class<?> c,
                   int c_alphas,
                   int format,
                   int type)
```
Returns the region defined by the rectangle as an image in the type and format specified. The type is either ImagePlus.GRAY8 or ImagePlus.COLOR_RGB. The format is either Layer.IMAGE (an array) or Layer.ImagePlus (it returns an ImagePlus containing an ImageStack), from which any ImageProcessor or pixel arrays can be retrieved trivially.

findDisplayable
```
public Displayable findDisplayable(long id)
```
Searches in all layers. Ignores the ZDisplaybles.

findById
```
public DBObject findById(long id)
```
Searches in all ZDisplayables and in all layers, recursively into nested LayerSets.

Overrides:

findById in class Displayable

updateLayerTree
```
public void updateLayerTree()
```
Recursive into nested LayerSet objects.

find

public ArrayList<ZDisplayable> find(Layer first,
                                    Layer last,
                                    Area area)

Find the ZDisplayable objects that intersect with the 3D roi defined by the first and last layers, and the area -all in world coordinates.

getZDisplayables
```
public ArrayList<ZDisplayable> getZDisplayables()
```
Returns a copy of the list of ZDisplayable objects.

getDisplayableList
```
public ArrayList<ZDisplayable> getDisplayableList()
```
Returns the real list of displayables, not a copy. If you modify this list, Thor may ground you with His lightning.

Specified by:

getDisplayableList in interface Bucketable

getBucketMap

public HashMap<Displayable,HashSet<Bucket>> getBucketMap(Layer la)

Specified by:: getBucketMap in interface Bucketable

updateBucket

public void updateBucket(Displayable d,
                         Layer layer)

Specified by:: updateBucket in interface Bucketable

recreateBuckets
```
public void recreateBuckets(boolean layer_buckets)
```
Recreate the ZDisplayable buckets, and also the Layer Displayable buckets if desired.

recreateBuckets
```
public void recreateBuckets(Layer layer,
                            boolean layer_buckets)
```
Recreate the ZDisplayable buckets for layer, and also the Layer Displayable buckets if desired.

Parameters:

layer - The Layer to recreate ZDisplayable buckets for.

layer_buckets - Whether to also recreate the Layer-specific buckets for images and text labels.

recreateBuckets
```
public void recreateBuckets(Collection<Layer> layers,
                            boolean layer_buckets)
```
Regenerate the quad-tree bucket system for the ZDisplayable instances that have data at each of the given layers, and optionally regenerate the buckets as well for the 2D Displayable instances of that layer as well.

checkBuckets
```
public void checkBuckets()
```
Checks only buckets for ZDisplayable, not any related to any layer.

getMinimalBoundingBox
```
public Rectangle getMinimalBoundingBox(Class<?> c)
```
Returns the minimal 2D bounding box for Displayables of class @param c in all layers.

addDataEditStep
```
public boolean addDataEditStep(Set<? extends Displayable> ds)
```
A new undo step for the "data" field of all Displayable in the set.

addTransformStep
```
public void addTransformStep(Layer layer)
```
Add an undo step for the transformations of all Displayable in the layer.

addTransformStep

public void addTransformStep(List<Layer> layers)

addTransformStep
```
public void addTransformStep(Collection<? extends Displayable> col)
```
Add an undo step for the transformations of all Displayable in hs.

addTransformStepWithData
```
public Displayable.DoEdits addTransformStepWithData(Collection<? extends Displayable> col)
```
Add an undo step for the transformations of all Displayable in col, with data as well (for Patch, data includes the CoordinateTransform).

addTransformStepWithDataForAll
```
public Collection<Displayable> addTransformStepWithDataForAll(Collection<Layer> layers)
```
Includes all ZDisplayable that paint at any of the given layers.

addTransformStep
```
public void addTransformStep()
```
Add an undo step for the transformations of all Displayable in all layers.

addChangeTreesStep
```
public LayerSet.DoChangeTrees addChangeTreesStep()
```
Add a step to undo the addition or deletion of one or more objects in this project and LayerSet.

addChangeTreesStep
```
public LayerSet.DoChangeTrees addChangeTreesStep(Set<DoStep> dependents)
```
Add a step to undo the addition or deletion of one or more objects in this project and LayerSet, along with an arbitrary set of steps that may alter, for example the data.

addLayerContentStep
```
public void addLayerContentStep(Layer la)
```
For the Displayable contained in a Layer: their number, and their stack order.

addLayerEditedStep
```
public void addLayerEditedStep(Layer layer)
```
For the Z and thickness of a layer.

addLayerEditedStep
```
public void addLayerEditedStep(List<Layer> al)
```
For the Z and thickness of a list of layers.

addUndoStep
```
public void addUndoStep(DoStep step)
```

canUndo
```
public boolean canUndo()
```

canRedo
```
public boolean canRedo()
```

undoOneStep
```
public boolean undoOneStep()
```
Undoes one step of the ongoing transformation history, otherwise of the overall LayerSet history.

removeLastUndoStep

protected boolean removeLastUndoStep()

redoOneStep
```
public boolean redoOneStep()
```
Redoes one step of the ongoing transformation history, otherwise of the overall LayerSet history.

applyTransforms

public static void applyTransforms(Map<Displayable,AffineTransform> m)

createUndoMoveStep

public DoStep createUndoMoveStep(Displayable d)

To undo moving up/down/top/bottom.

addUndoMoveStep
```
public void addUndoMoveStep(Displayable d)
```
To undo moving up/down/top/bottom.

getOverlay
```
public Overlay getOverlay()
```
Return the current Overlay or a new one if none yet.

setOverlay
```
public Overlay setOverlay(Overlay o)
```
Set to null to remove the Overlay.

Returns:

the previous Overlay, if any.

removeFromOffscreens

public final void removeFromOffscreens(Layer la)

findAreas
```
protected Map<Displayable,List<Area>> findAreas(Layer layer,
                                                Rectangle box,
                                                boolean visible)
```
Find all java.awt.geom.Area in layer that intersect with box, if visible. Areas are returned as they are, with coords local to the Displayable they come from. Modifying the Area instances will modify the actual data in the AreaContainer Displayable.

putTag
```
public Tag putTag(String tag,
                  int keyCode)
```
Returns an existing immutable Tag instance if already there, or stores a new one and returns it.

getTags
```
public TreeSet<Tag> getTags(int keyCode)
```
If there aren't any tags for keyCode, returns an empty TreeSet.

askForNewTag

protected Tag askForNewTag(int keyCode)

askToRemoveTag
```
protected boolean askToRemoveTag(int keyCode)
```
Returns false if the dialog was canceled or there wasn't any tag to remove.

removeTag
```
public void removeTag(String tag,
                      int keyCode)
```
Removes the tag from the list of possible tags, and then from wherever it has been assigned. The @param tag is duck-typed.

removeTag
```
public void removeTag(Tag t)
```

removeAllTags
```
public void removeAllTags()
```

exportTags
```
public String exportTags()
```

importTags

public void importTags(String path,
                       boolean replace)

getZDisplayables

public ArrayList<ZDisplayable> getZDisplayables(Class<?> c)

getZDisplayables
```
public ArrayList<ZDisplayable> getZDisplayables(Class<?> c,
                                                boolean instance_of)
```
Returns a list of ZDisplayable of class c only. If @param instance_of, use c.isInstance(...) instead of class equality.

getZDisplayables

@Deprecated
public ArrayList<ZDisplayable> getZDisplayables(Class<?> c,
                                                            Layer layer,
                                                            Area aroi,
                                                            boolean visible_only)

Deprecated.

Use method findZDisplayables(...) instead.

getZDisplayables

@Deprecated
public ArrayList<ZDisplayable> getZDisplayables(Class<?> c,
                                                            Layer layer,
                                                            Area aroi,
                                                            boolean visible_only,
                                                            boolean instance_of)

Deprecated.

Use method findZDisplayables(...) instead.

find

public ArrayList<Displayable> find(Class<?> c,
                                   Layer layer,
                                   Area aroi,
                                   boolean visible_only)

Find any Displayable or ZDisplayable objects of class C which intersect with the Area @param aroi. If @param visible_only, then only those that are not hidden.

find

public ArrayList<Displayable> find(Class<?> c,
                                   Layer layer,
                                   Area aroi,
                                   boolean visible_only,
                                   boolean instance_of)

Find any Displayable or ZDisplayable objects of class C which intersect with the Area @param aroi. If @param visible_only, then only those that are not hidden. If @param instance_of is true, then classes are not check by equality but by instanceof.

find

public ArrayList<Displayable> find(Class<?> c,
                                   Layer layer,
                                   int x,
                                   int y,
                                   boolean visible_only)

findZDisplayables

public Collection<Displayable> findZDisplayables(Layer layer,
                                                 int x,
                                                 int y,
                                                 boolean visible_only)

Find ZDisplayable objects that contain the point x,y in the given layer.

findZDisplayables

public Collection<Displayable> findZDisplayables(Class<?> c,
                                                 Layer layer,
                                                 int x,
                                                 int y,
                                                 boolean visible_only)

Find ZDisplayable objects of Class c that contain the point x,y in the given layer.

findZDisplayables

public Collection<Displayable> findZDisplayables(Class<?> c,
                                                 Layer layer,
                                                 int x,
                                                 int y,
                                                 boolean visible_only,
                                                 boolean instance_of)

Find ZDisplayable objects of Class c that contain the point x,y in the given layer.

findZDisplayables

public Collection<Displayable> findZDisplayables(Class<?> c,
                                                 Layer layer,
                                                 Rectangle r,
                                                 boolean visible_only)

findZDisplayables

public Collection<Displayable> findZDisplayables(Class<?> c,
                                                 Layer layer,
                                                 Rectangle r,
                                                 boolean visible_only,
                                                 boolean instance_of)

Find ZDisplayable objects of the given class that intersect the given rectangle in the given layer.

findZDisplayables

public Collection<Displayable> findZDisplayables(Class<?> c,
                                                 Layer layer,
                                                 Area aroi,
                                                 boolean visible_only,
                                                 boolean instance_of)

Find ZDisplayable objects of the given class that intersect the given area in the given layer. If @param instance_of is true, use c.isAssignableFrom instead of class equality.

findZDisplayables

public Collection<Displayable> findZDisplayables(Layer layer,
                                                 Rectangle r,
                                                 boolean visible_only)

Find ZDisplayable objects that intersect the given rectangle in the given layer.

roughlyFindZDisplayables

public Collection<Displayable> roughlyFindZDisplayables(Layer layer,
                                                        Rectangle r,
                                                        boolean visible_only)

Find ZDisplayable objects that intersect the given rectangle in the given layer. May return false positives but never false negatives.

getAll
```
public <T extends Displayable> List<T> getAll(Class<T> c)
```
Get all Displayable or ZDisplayable of the given class. Classes are tested by equality, except for ZDisplayable.class. Will also consider Displayable.class and subclasses in a similar fashion, by calling Layer.getAll(c).

Class LayerSet

Nested Class Summary

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

Field Summary

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.Displayable

Methods inherited from class ini.trakem2.persistence.DBObject

Methods inherited from class java.lang.Object

Methods inherited from interface ini.trakem2.display.Bucketable

Field Detail

NORTH

NORTHEAST

EAST

SOUTHEAST

SOUTH

SOUTHWEST

WEST

NORTHWEST

CENTER

R90

R270

FLIP_HORIZONTAL

FLIP_VERTICAL

TOP

UP

DOWN

BOTTOM

snapshot_modes

ANCHORS

ROTATIONS

color_cues

area_color_cues

use_color_cue_colors

paint_arrows

paint_tags

paint_edge_confidence_boxes

n_layers_color_cue

prepaint

preload_ahead

lbucks

tags

Constructor Detail

LayerSet

LayerSet

LayerSet

LayerSet

Method Detail

setup

create

addSilently

add

printDebugInfo

getParent

setLayer

setParent

mousePressed

mouseDragged

mouseReleased

keyPressed

toString

paint

getLayerWidth

getLayerHeight

getRotX

getRotY

getRotZ

size

setRotVector

setMinimumDimensions

enlargeToFit

enlargeToFit

setDimensions

setDimensions

remove2

remove

remove

next