Layer (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- ini.trakem2.persistence.DBObject
- - ini.trakem2.display.Layer

All Implemented Interfaces:: Bucketable, Comparable<Layer>

public final class Layer
extends DBObject
implements Bucketable, Comparable<Layer>

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

protected static class Layer.DoMoveDisplayable

Nested Classes
Modifier and Type	Class and Description
`protected static class`	`Layer.DoMoveDisplayable`

Field Summary

Fields
Modifier and Type	Field and Description
`static Comparator<Layer>`	`COMPARATOR` Compare layers by Z.
`static int`	`IMAGE`
`static int`	`IMAGEPLUS`
`static int`	`IMAGEPROCESSOR`
`static int`	`PIXELARRAY`

Fields inherited from class ini.trakem2.persistence.DBObject
id, project

Constructor Summary

Constructors
Constructor and Description
`Layer(Project project, double z, double thickness, LayerSet parent)`
`Layer(Project project, long id, double z, double thickness)` Reconstruct from database
`Layer(Project project, long id, HashMap<String,String> ht_attributes)` Reconstruct from XML file.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`add(Displayable displ)` Add a displayable and update all Display instances showing this Layer.
`void`	`add(Displayable displ, boolean update_displays)`
`void`	`add(Displayable displ, boolean update_displays, boolean update_db)`
`void`	`addSilently(DBObject displ)` Used for reconstruction purposes.
`void`	`apply(Class<?> c, AffineTransform at)` Preconcatenate the given AffineTransform to all Displayable objects of class c, without respecting their links.
`void`	`checkBuckets()`
`Layer`	`clone(Project pr, LayerSet ls, Rectangle roi, boolean copy_id, boolean ignore_hidden_patches)` Make a copy of this layer into the given LayerSet, enclosing only Displayable objects within the roi, and translating them for that roi x,y.
`int`	`compareTo(Layer layer)`
`boolean`	`contains(Class<?> c)` Returns true if any of the Displayable objects are of the given class.
`boolean`	`contains(Class<?> c, boolean visible_only)` Returns true if any of the Displayable objects are of the given class; if `visible_only` is true, will return true only if at least one of the matched objects is visible.
`boolean`	`contains(Displayable displ)`
`boolean`	`contains(int x, int y, int inset)`
`int`	`count(Class<?> c)` Count instances of the given Class.
`static Layer`	`create(Project project, LayerSet parent)` Creates a new Layer asking for z and thickness, and adds it to the parent and returns it.
`static List<Layer>`	`createMany(Project project, LayerSet parent)` Pops up a dialog to choose the first Z coord, the thickness, the number of layers, and whether to skip the creation of any layers whose Z and thickness match that of existing layers.
`void`	`destroy()`
`static void`	`exportDTD(StringBuilder sb_header, HashSet<String> hs, String indent)` Includes all Displayable objects in the list of possible children.
`void`	`exportXML(StringBuilder sb_body, String indent, XMLOptions options)` Subclasses can override this method to store the instance as XML.
`Collection<Displayable>`	`find(Class<?> c, double x, double y)`
`Collection<Displayable>`	`find(Class<?> c, double x, double y, boolean visible_only)` Find the Displayable objects of Class c that contain the point, with class equality.
`Collection<Displayable>`	`find(Class<?> c, double x, double y, boolean visible_only, boolean instance_of)` Find the Displayable objects of Class c that contain the point, with instanceof if instance_of is true.
`Collection<Displayable>`	`find(Class<?> c, Rectangle r, boolean visible_only)`
`Collection<Displayable>`	`find(Class<?> c, Rectangle r, boolean visible_only, boolean instance_of)` Find the Displayable objects whose bounding box intersects with the given rectangle.
`Collection<Displayable>`	`find(double x, double y)`
`Collection<Displayable>`	`find(double x, double y, boolean visible_only)` Find the Displayable objects that contain the point.
`Collection<Displayable>`	`find(Rectangle r)`
`Collection<Displayable>`	`find(Rectangle r, boolean visible_only)` Find the Displayable objects whose bounding box intersects with the given rectangle.
`DBObject`	`findById(long id)`
`Displayable`	`get(long id)`
`<T extends Displayable> ArrayList<T>`	`getAll(Class<T> c)` Returns a list of Displayable of class c only.
`HashMap<Displayable,HashSet<Bucket>>`	`getBucketMap(Layer layer)`
`double`	`getCalibratedThickness()`
`double`	`getCalibratedZ()`
`ArrayList<Displayable>`	`getDisplayableList()` Returns the real list of displayables, not a copy.
`ArrayList<Displayable>`	`getDisplayables()` Returns a copy of the list of Displayable objects.
`ArrayList<Displayable>`	`getDisplayables(Class<?> c)` Returns a list of Displayable of class c only.
`Collection<Displayable>`	`getDisplayables(Class<?> c, Area aroi, boolean visible_only)` Returns a list of all Displayable of class c that intersect the given area.
`Collection<Displayable>`	`getDisplayables(Class<?> c, Area aroi, boolean visible_only, boolean instance_of)` Check class identity by instanceof instead of equality.
`ArrayList<Displayable>`	`getDisplayables(Class<?> c, boolean visible_only)` Check class identity with equality, so no superclasses or interfaces are possible.
`ArrayList<Displayable>`	`getDisplayables(Class<?> c, boolean visible_only, boolean instance_of)`
`Collection<Displayable>`	`getDisplayables(Class<?> c, Rectangle roi)` Returns a list of all Displayable of class c that intersect the given rectangle.
`<T extends Displayable> Collection<T>`	`getIntersecting(Displayable d, Class<T> target)` Find the Displayable objects of class 'target' whose perimeter (not just the bounding box) intersect the given Displayable (which is itself included if present in this very Layer).
`float`	`getLayerHeight()`
`protected String`	`getLayerThingTitle()`
`float`	`getLayerWidth()`
`Rectangle`	`getMinimalBoundingBox(Class<?> c)` Returns null if no Displayable objects of class c exist.
`Rectangle`	`getMinimalBoundingBox(Class<?> c, boolean visible_only)` Returns null if no Displayable objects of class c exist (or are visible if `visible_only` is true).
`int`	`getNDisplayables()`
`Overlay`	`getOverlay()` Return the current Overlay or a new one if none yet.
`LayerSet`	`getParent()`
`Area`	`getPatchArea(boolean visible_only)` Returns an Area in world coordinates that represents the inside of all Patches.
`ArrayList<Patch>`	`getPatches(boolean visible_only)`
`int[]`	`getPixel(int x, int y, double mag)` Don't use this for fast pixel grabbing; this is intended for the dropper tool and status bar reporting by mouse motion.
`String`	`getPrintableTitle()` Returns a title such as 018__4-K4_2__z1.67 , which is [layer_set index]__[title]__[z coord] .
`double`	`getThickness()`
`String`	`getTitle()` Sublcasses can override this method to provide a proper String, otherwise calls toString()
`double`	`getZ()`
`Object`	`grab(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.
`int`	`indexOf(Displayable d)` Returns -1 if not found.
`boolean`	`isBottom(Displayable d)` Within its own class only.
`boolean`	`isEmpty()` Checks if there are any Displayable or if any ZDisplayable paints in this layer.
`boolean`	`isTop(Displayable d)` Within its own class only.
`void`	`moveBottom(Displayable d)` Within its own class only.
`void`	`moveDown(Displayable d)` Within its own class only.
`void`	`moveTop(Displayable d)` Within its own class only.
`void`	`moveUp(Displayable d)` Within its own class only.
`void`	`recreateBuckets()`
`int`	`relativeIndexOf(Displayable d)` Get the index of the given Displayable relative to the rest of its class.
`boolean`	`remove(boolean check)` Remove this layer and all its contents from the project.
`boolean`	`remove(Displayable displ)` Will recreate the buckets; if you intend to remove many, use "removeAll" instead, so that the expensive operation of recreating the buckets is done only once.
`boolean`	`removeAll(Set<Displayable> ds)` Remove a set of children.
`Collection<Displayable>`	`setAllVisible(boolean repaint)` Returns the collection of Displayable whose visibility state has changed.
`void`	`setBucketsEnabled(boolean b)`
`Overlay`	`setOverlay(Overlay o)` Set to null to remove the Overlay.
`void`	`setParent(LayerSet layer_set)`
`void`	`setParentSilently(LayerSet layer_set)` Used for reconstruction purposes.
`void`	`setThickness(double thickness)`
`HashSet<Displayable>`	`setVisible(String type, boolean visible, boolean repaint)` Note: Not recursive into embedded LayerSet objects.
`void`	`setZ(double z)`
`Coordinate<Patch>`	`toPatchCoordinate(double world_x, double world_y)` Transfer the world coordinate specified by `world_x`,`world_y` in pixels, to the local coordinate of the `Patch` immediately present under it.
`String`	`toString()`
`void`	`updateBucket(Displayable d, Layer layer)` Update buckets of a position change for the given Displayable.
`void`	`updateLayerTree()` Recursive into nested LayerSet objects.

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

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

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

Field Detail
- COMPARATOR
```
public static final Comparator<Layer> COMPARATOR
```
  Compare layers by Z.
- IMAGEPROCESSOR
```
public static final int IMAGEPROCESSOR
```
  See Also:
  
  Constant Field Values
- PIXELARRAY
```
public static final int PIXELARRAY
```
  See Also:
  
  Constant Field Values
- IMAGE
```
public static final int IMAGE
```
  See Also:
  
  Constant Field Values
- IMAGEPLUS
```
public static final int IMAGEPLUS
```
  See Also:
  
  Constant Field Values

Constructor Detail

Layer

public Layer(Project project,
             double z,
             double thickness,
             LayerSet parent)

Layer

public Layer(Project project,
             long id,
             double z,
             double thickness)

Reconstruct from database

Layer

public Layer(Project project,
             long id,
             HashMap<String,String> ht_attributes)

Reconstruct from XML file.

Method Detail

create
```
public static Layer create(Project project,
                           LayerSet parent)
```
Creates a new Layer asking for z and thickness, and adds it to the parent and returns it. Returns null if the dialog was canceled.

createMany
```
public static List<Layer> createMany(Project project,
                                     LayerSet parent)
```
Pops up a dialog to choose the first Z coord, the thickness, the number of layers, and whether to skip the creation of any layers whose Z and thickness match that of existing layers.

Returns:

The newly created layers.

getPrintableTitle
```
public String getPrintableTitle()
```
Returns a title such as 018__4-K4_2__z1.67 , which is [layer_set index]__[title]__[z coord] . The ordinal number starts at 1 and finishes at parent's length, inclusive.

toString
```
public String toString()
```
Overrides:

toString in class Object

add
```
public void add(Displayable displ)
```
Add a displayable and update all Display instances showing this Layer.

add

public void add(Displayable displ,
                boolean update_displays)

add

public void add(Displayable displ,
                boolean update_displays,
                boolean update_db)

getBucketMap

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

Specified by:: getBucketMap in interface Bucketable

addSilently
```
public void addSilently(DBObject displ)
```
Used for reconstruction purposes. Assumes the displ are given in the proper order!

remove
```
public boolean remove(Displayable displ)
```
Will recreate the buckets; if you intend to remove many, use "removeAll" instead, so that the expensive operation of recreating the buckets is done only once.

removeAll
```
public boolean removeAll(Set<Displayable> ds)
```
Remove a set of children. Does not destroy the children nor remove them from the database, only from the Layer and the Display.

setParentSilently

public void setParentSilently(LayerSet layer_set)

Used for reconstruction purposes.

setParent

public void setParent(LayerSet layer_set)

getParent
```
public LayerSet getParent()
```

getZ
```
public double getZ()
```

getThickness
```
public double getThickness()
```

getCalibratedZ
```
public double getCalibratedZ()
```

getCalibratedThickness

public double getCalibratedThickness()

remove
```
public boolean remove(boolean check)
```
Remove this layer and all its contents from the project.

Overrides:

remove in class DBObject

setZ
```
public void setZ(double z)
```

setThickness

public void setThickness(double thickness)

contains

public boolean contains(int x,
                        int y,
                        int inset)

contains

public boolean contains(Displayable displ)

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

contains
```
public boolean contains(Class<?> c,
                        boolean visible_only)
```
Returns true if any of the Displayable objects are of the given class; if visible_only is true, will return true only if at least one of the matched objects is visible.

count
```
public int count(Class<?> c)
```
Count instances of the given Class.

isEmpty
```
public boolean isEmpty()
```
Checks if there are any Displayable or if any ZDisplayable paints in this layer.

getDisplayables
```
public ArrayList<Displayable> getDisplayables()
```
Returns a copy of the list of Displayable objects.

getDisplayableList
```
public final ArrayList<Displayable> 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

getNDisplayables
```
public int getNDisplayables()
```

getAll

public <T extends Displayable> ArrayList<T> getAll(Class<T> c)

Returns a list of Displayable of class c only.

getDisplayables

public ArrayList<Displayable> getDisplayables(Class<?> c)

Returns a list of Displayable of class c only.

getDisplayables

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

getPatches

public ArrayList<Patch> getPatches(boolean visible_only)

getDisplayables
```
public Collection<Displayable> getDisplayables(Class<?> c,
                                               Rectangle roi)
```
Returns a list of all Displayable of class c that intersect the given rectangle. Expensive: will use an Area(roi) to compare against the Displayable.getArea(), which can be very expensive when using e.g. non-linear transforms in a Patch instance, potentially requiring the loading and non-linear transform of the mask.

getDisplayables

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

Returns a list of all Displayable of class c that intersect the given area.

getDisplayables

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

Check class identity by instanceof instead of equality.

getDisplayables

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

Check class identity with equality, so no superclasses or interfaces are possible.

get
```
public Displayable get(long id)
```

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

getLayerWidth in interface Bucketable

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

getLayerHeight in interface Bucketable

find

public Collection<Displayable> find(double x,
                                    double y)

find

public Collection<Displayable> find(double x,
                                    double y,
                                    boolean visible_only)

Find the Displayable objects that contain the point.

find

public Collection<Displayable> find(Class<?> c,
                                    double x,
                                    double y)

find

public Collection<Displayable> find(Class<?> c,
                                    double x,
                                    double y,
                                    boolean visible_only)

Find the Displayable objects of Class c that contain the point, with class equality.

find

public Collection<Displayable> find(Class<?> c,
                                    double x,
                                    double y,
                                    boolean visible_only,
                                    boolean instance_of)

Find the Displayable objects of Class c that contain the point, with instanceof if instance_of is true.

find

public Collection<Displayable> find(Rectangle r)

find
```
public Collection<Displayable> find(Rectangle r,
                                    boolean visible_only)
```
Find the Displayable objects whose bounding box intersects with the given rectangle. Cheap: will only compare against the Rectangle bounding box of each Displayable. In addition, will use buckets when present.

find

public Collection<Displayable> find(Class<?> c,
                                    Rectangle r,
                                    boolean visible_only)

find

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

Find the Displayable objects whose bounding box intersects with the given rectangle.

getIntersecting

public <T extends Displayable> Collection<T> getIntersecting(Displayable d,
                                                             Class<T> target)

Find the Displayable objects of class 'target' whose perimeter (not just the bounding box) intersect the given Displayable (which is itself included if present in this very Layer).

indexOf

public final int indexOf(Displayable d)

Returns -1 if not found.

moveUp
```
public void moveUp(Displayable d)
```
Within its own class only. 'up' is at the last element of the ArrayList (since when painting, the first one gets painted first, and thus gets buried the most while the last paints last, on top).

moveDown
```
public void moveDown(Displayable d)
```
Within its own class only.

moveTop
```
public void moveTop(Displayable d)
```
Within its own class only.

moveBottom

public void moveBottom(Displayable d)

Within its own class only.

isTop
```
public boolean isTop(Displayable d)
```
Within its own class only.

isBottom

public boolean isBottom(Displayable d)

Within its own class only.

relativeIndexOf
```
public int relativeIndexOf(Displayable d)
```
Get the index of the given Displayable relative to the rest of its class. Beware that the order of the al_displayables is bottom at zero, top at last, but the relative index returned here is inverted: top at zero, bottom at last -to match the tabs' vertical orientation in a Display.

setVisible

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

Note: Not recursive into embedded LayerSet objects. Returns the hash set of objects whose visibility has changed.

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

exportXML

public void exportXML(StringBuilder sb_body,
                      String indent,
                      XMLOptions options)

Description copied from class: DBObject

Subclasses can override this method to store the instance as XML.

Overrides:: exportXML in class DBObject

exportDTD

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

Includes all Displayable objects in the list of possible children.

getLayerThingTitle
```
protected String getLayerThingTitle()
```

getTitle
```
public String getTitle()
```
Description copied from class: DBObject

Sublcasses can override this method to provide a proper String, otherwise calls toString()

Overrides:

getTitle in class DBObject

destroy
```
public void destroy()
```

getMinimalBoundingBox
```
public Rectangle getMinimalBoundingBox(Class<?> c)
```
Returns null if no Displayable objects of class c exist.

getMinimalBoundingBox

public Rectangle getMinimalBoundingBox(Class<?> c,
                                       boolean visible_only)

Returns null if no Displayable objects of class c exist (or are visible if visible_only is true).

getPatchArea
```
public Area getPatchArea(boolean visible_only)
```
Returns an Area in world coordinates that represents the inside of all Patches.

apply
```
public void apply(Class<?> c,
                  AffineTransform at)
```
Preconcatenate the given AffineTransform to all Displayable objects of class c, without respecting their links.

clone

public Layer clone(Project pr,
                   LayerSet ls,
                   Rectangle roi,
                   boolean copy_id,
                   boolean ignore_hidden_patches)

Make a copy of this layer into the given LayerSet, enclosing only Displayable objects within the roi, and translating them for that roi x,y.

grab
```
public Object grab(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.IMAGEPROCESSOR, Layer.IMAGEPLUS, Layer.PIXELARRAY or Layer.IMAGE.

findById
```
public DBObject findById(long id)
```

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

getPixel
```
public int[] getPixel(int x,
                      int y,
                      double mag)
```
Don't use this for fast pixel grabbing; this is intended for the dropper tool and status bar reporting by mouse motion.

recreateBuckets
```
public void recreateBuckets()
```

updateBucket
```
public void updateBucket(Displayable d,
                         Layer layer)
```
Update buckets of a position change for the given Displayable.

Specified by:

updateBucket in interface Bucketable

checkBuckets
```
public void checkBuckets()
```

setBucketsEnabled

public void setBucketsEnabled(boolean b)

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.

compareTo
```
public int compareTo(Layer layer)
```
Specified by:

compareTo in interface Comparable<Layer>

toPatchCoordinate

public Coordinate<Patch> toPatchCoordinate(double world_x,
                                           double world_y)
                                    throws NoninvertibleTransformException,
                                           NoninvertibleModelException

Transfer the world coordinate specified by world_x,world_y in pixels, to the local coordinate of the Patch immediately present under it.

Returns:: null if no Patch is under the coordinate, else the Coordinate with the x, y, Layer and the Patch.
Throws:: NoninvertibleModelException; NoninvertibleTransformException

Class Layer

Nested Class Summary

Field Summary

Fields inherited from class ini.trakem2.persistence.DBObject

Constructor Summary

Method Summary

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

COMPARATOR

IMAGEPROCESSOR

PIXELARRAY

IMAGE

IMAGEPLUS

Constructor Detail

Layer

Layer

Layer

Method Detail

create

createMany

getPrintableTitle

toString

add

add

add

getBucketMap

addSilently

remove

removeAll

setParentSilently

setParent

getParent

getZ

getThickness

getCalibratedZ

getCalibratedThickness

remove

setZ

setThickness

contains

contains

contains

contains

count

isEmpty

getDisplayables

getDisplayableList

getNDisplayables

getAll

getDisplayables

getDisplayables

getPatches

getDisplayables

getDisplayables

getDisplayables

getDisplayables

get

getLayerWidth

getLayerHeight

find

find

find

find

find

find

find

find

find

getIntersecting

indexOf

moveUp

moveDown

moveTop

moveBottom

isTop

isBottom

relativeIndexOf

setVisible