| Package | Description |
|---|---|
| ini.trakem2 | |
| ini.trakem2.analysis | |
| ini.trakem2.display | |
| ini.trakem2.imaging | |
| ini.trakem2.persistence | |
| ini.trakem2.tree | |
| ini.trakem2.utils | |
| lenscorrection | |
| mpicbg.trakem2.align |
| Modifier and Type | Method and Description |
|---|---|
String |
Project.getMeaningfulTitle(Displayable d)
Searches upstream in the Project tree for things that have a user-defined name, stops at the first and returns it along with all the intermediate ones that only have a type and not a title, appended.
|
String |
Project.getMeaningfulTitle2(Displayable d) |
String |
Project.getParentTitle(Displayable d)
Returns the title of the enclosing abstract node in the ProjectTree.
|
String |
Project.getShortMeaningfulTitle(Displayable d)
Returns the first upstream user-defined name and type, and the id of the displayable tagged at the end.
|
String |
Project.getShortMeaningfulTitle(ProjectThing thing,
Displayable d) |
boolean |
Project.remove(Displayable d)
Removes an object from this Project.
|
void |
Project.select(Displayable d)
Find the node in any tree with a Thing that contains the given Displayable, and set it selected/highlighted, deselecting everything else first.
|
| Modifier and Type | Method and Description |
|---|---|
boolean |
Project.removeAll(Set<Displayable> col)
Calls Project.removeAll(col, null)
|
boolean |
Project.removeAll(Set<Displayable> col,
DefaultMutableTreeNode top_node)
Remove any set of Displayable objects from the Layer, LayerSet and Project Tree as necessary.
|
| Modifier and Type | Method and Description |
|---|---|
static <T extends Displayable> |
Graph.extractAndShowGraph(LayerSet ls,
Set<Class<T>> only)
Extract the graph based on connectors; leave @param only null to include all types.
|
static <T extends Displayable> |
Graph.extractGraph(LayerSet ls,
Set<Class<T>> only) |
| Modifier and Type | Class and Description |
|---|---|
class |
AreaList
A list of brush painted areas similar to a set of labelfields in Amira.
|
class |
AreaTree |
class |
Ball |
class |
Connector
A one-to-many connection, represented by one source point and one or more target points.
|
class |
Dissector
Implements the Double Dissector method with scale-invariant grouped labels.
|
class |
DLabel
This class is named funny to avoid confusion with java.awt.Label.
|
class |
LayerSet
A LayerSet is a container for a list of Layer.
|
class |
Patch |
class |
Pipe |
class |
Polyline
A sequence of points that make multiple chained line segments.
|
class |
Profile
A class to be a user-outlined profile over an image, which is painted with a particular color and also holds an associated text label.
|
class |
Stack |
class |
Tree<T>
A sequence of points ordered in a set of connected branches.
|
class |
Treeline |
class |
ZDisplayable
For Pipes and other objects that must be shown in all Layers of a LayerSet.
|
| Modifier and Type | Field and Description |
|---|---|
protected HashMap<Displayable,HashSet<Bucket>> |
LayerSet.LayerBucket.db_map |
protected HashSet<Displayable> |
Displayable.hs_linked
The Displayable objects this one is linked to.
|
protected Map<Displayable,Map<String,String>> |
Displayable.linked_props
The table of tables of properties: for any target Displayable, there is a set of properties specific of the relationship between this Displayable and the target one.
|
protected Set<Displayable> |
Displayable.linked_props_origins
The call back hooks to remove any linked properties in other Displayable instances when this Displayable is removed.
|
protected HashMap<Displayable,HashSet<Displayable>> |
Displayable.DataPackage.links |
protected HashMap<Displayable,HashSet<Displayable>> |
Displayable.DataPackage.links |
| Modifier and Type | Method and Description |
|---|---|
<T extends Displayable> |
Display.find()
Open a
GenericDialog to ask for parameters to find all Displayable that abide to them. |
<T extends Displayable> |
Display.find(String regex,
boolean visible_only,
Class<T> c,
int firstLayerIndex,
int lastLayerIndex) |
static <T extends Displayable> |
Display.find(String regex,
boolean visible_only,
Class<T> c,
List<Layer> layers) |
<T extends Displayable> |
Selection.get(Class<T> c)
Returns a list of selected Displayable of class c only.
|
<T extends Displayable> |
LayerSet.getAll(Class<T> c)
Get all Displayable or ZDisplayable of the given class.
|
<T extends Displayable> |
Layer.getAll(Class<T> c)
Returns a list of Displayable of class c only.
|
<T extends Displayable> |
Layer.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).
|
| Modifier and Type | Method and Description |
|---|---|
Displayable |
Displayable.clone()
Performs a deep copy of this object.
|
Displayable |
Displayable.clone(Project pr)
Performs a deep copy of this object but assigning to it the given project.
|
Displayable |
Stack.clone(Project pr,
boolean copy_id) |
Displayable |
Profile.clone(Project pr,
boolean copy_id)
Performs a deep copy of this object, unlocked and visible.
|
Displayable |
Polyline.clone(Project pr,
boolean copy_id)
Performs a deep copy of this object, without the links.
|
Displayable |
Pipe.clone(Project pr,
boolean copy_id)
Performs a deep copy of this object, without the links.
|
Displayable |
Patch.clone(Project pr,
boolean copy_id)
Performs a copy of this object, without the links, unlocked and visible, except for the image which is NOT duplicated.
|
Displayable |
LayerSet.clone(Project pr,
boolean copy_id) |
Displayable |
Dissector.clone(Project pr,
boolean copy_id)
Returns a deep copy.
|
abstract Displayable |
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 |
Ball.clone(Project pr,
boolean copy_id)
Performs a deep copy of this object, without the links.
|
Displayable |
AreaList.clone(Project pr,
boolean copy_id)
Performs a deep copy of this object, without the links.
|
Displayable |
LayerSet.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.
|
Displayable |
LayerSet.findDisplayable(long id)
Searches in all layers.
|
Displayable |
Layer.get(long id) |
Displayable |
Selection.getActive() |
Displayable |
Display.getActive() |
Displayable |
DisplayableChooser.getChosen() |
Displayable |
LayerSet.DoChangeTrees.getD() |
Displayable |
LayerSet.DoMoveZDisplayable.getD() |
Displayable |
Layer.DoMoveDisplayable.getD() |
Displayable |
DoStep.getD()
May return null.
|
Displayable |
Displayable.DoEdits.getD() |
Displayable |
Displayable.DoEdit.getD() |
Displayable |
Displayable.DoTransforms.getD() |
Displayable |
AreaWrapper.getSource() |
| Modifier and Type | Method and Description |
|---|---|
Collection<Displayable> |
LayerSet.addTransformStepWithDataForAll(Collection<Layer> layers)
Includes all ZDisplayable that paint at any of the given layers.
|
Collection<Displayable> |
Layer.find(Class<?> c,
double x,
double y) |
Collection<Displayable> |
Layer.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> |
Layer.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.
|
ArrayList<Displayable> |
LayerSet.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> |
LayerSet.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> |
LayerSet.find(Class<?> c,
Layer layer,
int x,
int y,
boolean visible_only) |
Collection<Displayable> |
Layer.find(Class<?> c,
Rectangle r,
boolean visible_only) |
Collection<Displayable> |
Layer.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> |
Layer.find(double x,
double y) |
Collection<Displayable> |
Layer.find(double x,
double y,
boolean visible_only)
Find the Displayable objects that contain the point.
|
Collection<Displayable> |
Layer.find(Rectangle r) |
Collection<Displayable> |
Layer.find(Rectangle r,
boolean visible_only)
Find the Displayable objects whose bounding box intersects with the given rectangle.
|
protected Map<Displayable,List<Area>> |
LayerSet.findAreas(Layer layer,
Rectangle box,
boolean visible)
Find all java.awt.geom.Area in layer that intersect with box, if visible.
|
Map<Node<T>,Collection<Displayable>> |
Tree.findIntersecting(Class<?> c) |
Collection<Displayable> |
Node.findLinkTargets(AffineTransform to_world)
Returns a list of Patch to link, which lay under the node.
|
Collection<Displayable> |
AreaTree.AreaNode.findLinkTargets(AffineTransform aff) |
Collection<Displayable> |
LayerSet.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> |
LayerSet.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> |
LayerSet.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> |
LayerSet.findZDisplayables(Class<?> c,
Layer layer,
Rectangle r,
boolean visible_only) |
Collection<Displayable> |
LayerSet.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> |
LayerSet.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> |
LayerSet.findZDisplayables(Layer layer,
Rectangle r,
boolean visible_only)
Find ZDisplayable objects that intersect the given rectangle in the given layer.
|
ArrayList<Displayable> |
LayerSet.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> |
LayerSet.get(Class<?> c)
Find, in this LayerSet and contained layers and their nested LayerSets if any, all Displayable instances of Class c.
|
Set<Displayable> |
Selection.getAffected()
Returns the set of all Displayable objects affected by this selection, that is, the selected ones and their linked ones.
|
Set<Displayable> |
Selection.getAffected(Class<?> c)
Returns the set of all Displayable objects of the given class affected by this selection, that is, among the selected ones and their linked ones.
|
HashMap<Displayable,HashSet<Bucket>> |
LayerSet.getBucketMap(Layer la) |
HashMap<Displayable,HashSet<Bucket>> |
Layer.getBucketMap(Layer layer) |
HashMap<Displayable,HashSet<Bucket>> |
Bucketable.getBucketMap(Layer layer) |
ArrayList<Displayable> |
Layer.getDisplayableList()
Returns the real list of displayables, not a copy.
|
ArrayList<? extends Displayable> |
Bucketable.getDisplayableList() |
ArrayList<Displayable> |
LayerSet.getDisplayables()
Return all the Displayable objects from all the layers of this LayerSet.
|
ArrayList<Displayable> |
Layer.getDisplayables()
Returns a copy of the list of Displayable objects.
|
ArrayList<Displayable> |
LayerSet.getDisplayables(Class<?> c)
Return all the Displayable objects from all the layers of this LayerSet of the given class.
|
ArrayList<Displayable> |
Layer.getDisplayables(Class<?> c)
Returns a list of Displayable of class c only.
|
ArrayList<Displayable> |
LayerSet.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.
|
Collection<Displayable> |
Layer.getDisplayables(Class<?> c,
Area aroi,
boolean visible_only)
Returns a list of all Displayable of class c that intersect the given area.
|
Collection<Displayable> |
Layer.getDisplayables(Class<?> c,
Area aroi,
boolean visible_only,
boolean instance_of)
Check class identity by instanceof instead of equality.
|
ArrayList<Displayable> |
Layer.getDisplayables(Class<?> c,
boolean visible_only)
Check class identity with equality, so no superclasses or interfaces are possible.
|
ArrayList<Displayable> |
Layer.getDisplayables(Class<?> c,
boolean visible_only,
boolean instance_of) |
Collection<Displayable> |
Layer.getDisplayables(Class<?> c,
Rectangle roi)
Returns a list of all Displayable of class c that intersect the given rectangle.
|
List<Displayable> |
DisplayCanvas.getDisplayablesUnderMouse()
|
List<Displayable> |
DisplayCanvas.getDisplayablesUnderMouse(MouseEvent me)
Return the list of Displayable objects under the mouse,
sorted by proper stack order.
|
HashSet<Displayable> |
Displayable.getLinked()
Return the HashSet of directly linked Displayable objects.
|
HashSet<Displayable> |
Displayable.getLinked(Class<?> c)
Return those of Class c from among the directly linked.
|
HashSet<Displayable> |
Displayable.getLinkedGroup(HashSet<Displayable> hs)
Return the HashSet of all directly and indirectly linked objects.
|
Map<Displayable,Map<String,String>> |
Displayable.getLinkedProperties()
Returns a copy of this object's linked properties, which may be empty.
|
Set<Displayable> |
Connector.getOrigins()
Returns the set of Displayable objects under the origin point, or an empty set if none.
|
Set<Displayable> |
Connector.getOrigins(Class<?> c)
Returns the set of Displayable objects under the origin point, or an empty set if none.
|
Set<Displayable> |
Connector.getOrigins(Class<?> c,
boolean instance_of) |
ArrayList<Displayable> |
Selection.getSelected()
Returns a copy of the list of all selected Displayables (and not their linked ones).
|
static List<Displayable> |
Display.getSelected()
Return the list of selected Displayable objects of the front Display, or an emtpy list if no Display or none selected.
|
ArrayList<Displayable> |
Selection.getSelected(Class<?> c)
Returns a copy of the list of all selected Displayables (and not their linked ones) of the given class.
|
static List<? extends Displayable> |
Display.getSelected(Class<? extends Displayable> c)
Return the list of selected Displayable objects of class @param c of the front Display, or an emtpy list if no Display or none selected.
|
List<Displayable> |
Selection.getSelectedSorted(Class<? extends Displayable> c)
Returns the subset of selected objects of Class c, in the proper order according to the Layer.indexOf or the LayerSet.indexOf.
|
List<Set<Displayable>> |
Connector.getTargets()
Returns the list of sets of visible Displayable objects under each target, or an empty list if none.
|
List<Set<Displayable>> |
Connector.getTargets(Class<?> c)
Returns the list of sets of visible Displayable objects under each target, or an empty list if none.
|
List<Set<Displayable>> |
Connector.getTargets(Class<?> c,
boolean instance_of) |
HashSet<Displayable> |
LayerSet.hideExcept(ArrayList<Class<?>> type,
boolean repaint)
Hide all except those whose type is in 'type' list, whose visibility flag is left unchanged.
|
HashSet<Displayable> |
Layer.hideExcept(ArrayList<Class<?>> type,
boolean repaint)
Hide all except those whose type is in 'type' list, whose visibility flag is left unchanged.
|
List<Displayable> |
TransformationStep.remove(long id) |
Collection<Displayable> |
LayerSet.roughlyFindZDisplayables(Layer layer,
Rectangle r,
boolean visible_only)
Find ZDisplayable objects that intersect the given rectangle in the given layer.
|
Collection<Displayable> |
LayerSet.setAllVisible(boolean repaint)
Returns the collection of Displayable whose visibility state has changed.
|
Collection<Displayable> |
Layer.setAllVisible(boolean repaint)
Returns the collection of Displayable whose visibility state has changed.
|
Collection<Displayable> |
Selection.setVisible(boolean b)
Set all selected objects visible/hidden; returns a collection of those that changed state.
|
HashSet<Displayable> |
LayerSet.setVisible(String type,
boolean visible,
boolean repaint)
Returns the hash set of objects whose visibility has changed.
|
HashSet<Displayable> |
Layer.setVisible(String type,
boolean visible,
boolean repaint)
Note: Not recursive into embedded LayerSet objects.
|
| Modifier and Type | Method and Description |
|---|---|
void |
Selection.add(Displayable d) |
void |
Layer.add(Displayable displ)
Add a displayable and update all Display instances showing this Layer.
|
void |
Layer.add(Displayable displ,
boolean update_displays) |
void |
Layer.add(Displayable displ,
boolean update_displays,
boolean update_db) |
protected static void |
Display.add(Layer layer,
Displayable displ) |
protected static void |
Display.add(Layer layer,
Displayable displ,
boolean activate)
Find the displays that show the given Layer, and add the given Displayable to the GUI and sets it active only in the front Display and only if 'activate' is true.
|
void |
LayerSet.addUndoMoveStep(Displayable d)
To undo moving up/down/top/bottom.
|
boolean |
Selection.contains(Displayable d) |
boolean |
LayerSet.contains(Displayable zdispl) |
boolean |
Layer.contains(Displayable displ) |
Callable<Content> |
Display3D.createMesh(ProjectThing pt,
Displayable displ,
int resample)
Returns a function that returns a Content object.
|
DoStep |
LayerSet.createUndoMoveStep(Displayable d)
To undo moving up/down/top/bottom.
|
protected void |
Display.duplicateLinkAndSendTo(Displayable active,
int position,
Layer other_layer) |
boolean |
LayerSet.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 |
Display.flush(Displayable displ)
Cleanup internal lists that may contain the given Displayable.
|
<T extends Displayable> |
Layer.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).
|
Area |
Displayable.getIntersection(Displayable d)
Returns the intersection of this Displayable's area with the given one.
|
Map<String,String> |
Displayable.getLinkedProperties(Displayable target)
Returns a copy of this object's linked properties table for the given Displayable, which may be empty.
|
String |
Displayable.getLinkedProperty(Displayable target,
String key)
If the key is null or not found, or the aren't any properties linked to the target, returns null; otherwise returns the stored value for key and target.
|
String |
Displayable.getLinkedProperty(Displayable target,
String key,
String default_value)
If the key is null or not found, or the aren't any properties linked to the target, returns default_value; otherwise returns the stored value for key and target.
|
static Rectangle |
Displayable.getMinimalBoundingBox(Displayable[] d) |
static Content |
Display3D.getProfileContent(Displayable d)
Checks if the given Displayable is a Profile, and tries to find a possible Content object in the Image3DUniverse of its LayerSet according to the title as created from its profile_list ProjectThing.
|
int |
Layer.indexOf(Displayable d)
Returns -1 if not found.
|
boolean |
Patch.intersects(Displayable d) |
boolean |
Displayable.intersects(Displayable d)
Check if this perimeter's intersects that of the given Displayable.
|
boolean |
Patch.intersects(Displayable d,
boolean sloppy) |
protected boolean |
LayerSet.isBottom(Displayable d)
Hub method: ZDisplayable or into the Displayable's Layer.
|
boolean |
Layer.isBottom(Displayable d)
Within its own class only.
|
static boolean |
Display3D.isDisplayed(Displayable d)
Checks if there is any Display3D instance currently showing the given Displayable.
|
boolean |
Displayable.isLinked(Displayable d)
Check if thisobject is directly linked to the given Displayable.
|
boolean |
DisplayNavigator.isPainted(Displayable d)
Returns true if the given Displayable has been painted as an image and false if as a box or not at all.
|
boolean |
Display.isPartiallyWithinViewport(Displayable d)
Check if a panel for the given Displayable is partially visible in the JScrollPane
|
boolean |
Display.isSelected(Displayable d) |
protected boolean |
RollingPanel.isShowing(Displayable d) |
protected boolean |
LayerSet.isTop(Displayable d)
Hub method: ZDisplayable or into the Displayable's Layer.
|
boolean |
Layer.isTop(Displayable d)
Within its own class only.
|
static boolean |
Display.isTransforming(Displayable displ)
Find whether any Display is transforming the given Displayable.
|
boolean |
Display.isWithinViewport(Displayable d)
Check if a panel for the given Displayable is completely visible in the JScrollPane
|
void |
Displayable.link(Displayable d)
Link the given Displayable with this Displayable, and then tell the given Displayable to link this.
|
void |
Displayable.link(Displayable d,
boolean update_database)
Link the given Displayable with this Displayable, and then tell the given Displayable to link this.
|
VectorDataTransform |
VectorDataTransform.makeLocalTo(Displayable d)
Returns a copy whose roi and ct are local to the affine transform of @param d.
|
static String |
Display3D.makeTitle(Displayable d) |
protected void |
LayerSet.move(int place,
Displayable d)
Change z position in the layered stack, which defines the painting order.
|
void |
Layer.moveBottom(Displayable d)
Within its own class only.
|
void |
Layer.moveDown(Displayable d)
Within its own class only.
|
void |
LayerSet.moveDown(Layer layer,
Displayable d)
Move the given Displayable to the next layer if possible.
|
void |
Layer.moveTop(Displayable d)
Within its own class only.
|
void |
Layer.moveUp(Displayable d)
Within its own class only.
|
void |
LayerSet.moveUp(Layer layer,
Displayable d)
Move the given Displayable to the previous layer if possible.
|
BufferedImage |
DisplayCanvas.paintOffscreen(Layer active_layer,
int g_width,
int g_height,
Rectangle srcRect,
double magnification,
Displayable active,
int c_alphas,
Rectangle clipRect,
Loader loader,
HashMap<Color,Layer> hm,
ArrayList<LayerPanel> blending_list,
int mode,
GraphicsSource graphics_source,
boolean prepaint,
ArrayList<Displayable> al_top)
Deprecated.
|
BufferedImage |
DisplayCanvas.paintOffscreen(Layer active_layer,
List<Layer> layers,
ArrayList<Displayable> al_paint,
Displayable active,
int g_width,
int g_height,
int c_alphas,
Loader loader,
HashMap<Color,Layer> hm,
ArrayList<LayerPanel> blending_list,
int mode,
GraphicsSource graphics_source,
boolean prepaint,
int first_non_patch) |
BufferedImage |
DisplayCanvas.paintOffscreen(Layer active_layer,
List<Layer> layers,
int g_width,
int g_height,
Rectangle srcRect,
double magnification,
Displayable active,
int c_alphas,
Rectangle clipRect,
Loader loader,
HashMap<Color,Layer> hm,
ArrayList<LayerPanel> blending_list,
int mode,
GraphicsSource graphics_source,
boolean prepaint,
ArrayList<Displayable> al_top,
boolean preload)
This method uses data only from the arguments, and changes none.
|
boolean |
Display.paintsBelow(Displayable base,
Displayable other)
If the other paints under the base.
|
int |
Layer.relativeIndexOf(Displayable d)
Get the index of the given Displayable relative to the rest of its class.
|
void |
Selection.remove(Displayable d)
Remove the given displayable from this selection.
|
boolean |
Layer.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.
|
static void |
Display.remove(Layer layer,
Displayable displ)
Find the displays that show the given Layer, and remove the given Displayable from the GUI.
|
protected void |
Selection.removeFromPrev(Displayable d)
Removes the given Displayable from the selection and previous selection list.
|
Map<String,String> |
Displayable.removeLinkedProperties(Displayable target)
Removes and returns the table of properties lined to the target Displayable.
|
void |
DisplayNavigator.repaint(Displayable d)
Only its bounding box.
|
void |
DisplayCanvas.repaint(Displayable d)
Repaint as much as the bounding box around the given Displayable.
|
static void |
Display.repaint(Displayable d) |
void |
DisplayCanvas.repaint(Displayable displ,
int extra)
Repaint as much as the bounding box around the given Displayable plus the
extra padding.
|
void |
DisplayCanvas.repaint(Displayable displ,
int extra,
boolean update_graphics) |
static void |
Display.repaint(Layer layer,
Displayable displ)
Repaint the DisplayablePanel (and DisplayNavigator) only for the given Displayable, in all Displays showing the given Layer.
|
static void |
Display.repaint(Layer layer,
Displayable displ,
int extra) |
static void |
Display.repaint(Layer layer,
Displayable displ,
Rectangle r,
int extra) |
static void |
Display.repaint(Layer layer,
Displayable displ,
Rectangle r,
int extra,
boolean repaint_navigator)
Find the displays that show the given Layer, and repaint the given Displayable; does NOT update graphics for the offscreen image.
|
static void |
Display.repaint(Layer layer,
Displayable displ,
Rectangle r,
int extra,
boolean update_graphics,
boolean repaint_navigator) |
static void |
Display.repaint(LayerSet set,
Displayable displ,
int extra) |
static void |
Display.repaint(LayerSet set,
Displayable displ,
Rectangle r,
int extra) |
static void |
Display.repaint(LayerSet set,
Displayable displ,
Rectangle r,
int extra,
boolean repaint_navigator)
Repaint the Displayable in every Display that shows a Layer belonging to the given LayerSet.
|
static void |
Display.repaintSnapshot(Displayable displ)
Repaint the snapshot for the given Displayable both at the DisplayNavigator and on its panel,and only if it has not been painted before.
|
void |
RollingPanel.scrollToShow(Displayable d) |
void |
Display.select(Displayable d) |
void |
Display.select(Displayable d,
boolean shift_down)
Select/deselect accordingly to the current state and the shift key.
|
void |
SnapshotPanel.set(Displayable d) |
void |
DisplayablePanel.set(Displayable d)
For instance-recycling purposes.
|
void |
Selection.setActive(Displayable d) |
protected void |
Display.setActive(Displayable displ)
Used by the Selection exclusively.
|
static void |
Display.setActive(Object event,
Displayable displ) |
static Future<Boolean> |
Display3D.setColor(Displayable d,
Color color) |
static void |
Display.setFront(Layer layer,
Displayable displ)
Grab the last selected display (or create an new one if none) and show in it the layer,centered on the Displayable object.
|
void |
Displayable.setLinkedProperties(Displayable target,
Map<String,String> p)
Add all the properties in map p as properties linked to the target Displayable.
|
boolean |
Displayable.setLinkedProperty(Displayable target,
String key,
String value)
Add a property that is specific to the relationship between this Displayable and the target, and will be deleted when the target Displayable is deleted.
|
void |
AreaWrapper.setSource(Displayable source) |
static Future<Boolean> |
Display3D.setTransparency(Displayable d,
float alpha) |
static void |
Display.setUpdateGraphics(Layer layer,
Displayable displ)
Mark the canvas for updating the offscreen images if the given Displayable is NOT the active.
|
void |
Display.show(Layer layer,
Displayable displ,
boolean select,
boolean shift_down)
Set this Display to show the specific layer, centered at the @param displ, and perhaps selected,
adding to the selection instead of clearing it if @param shift_down is true.
|
static void |
Display.showCentered(Layer layer,
Displayable displ,
boolean select,
boolean shift_down)
Show the given Displayable centered and selected.
|
void |
Displayable.unlink(Displayable d)
Remove the link with the given Displayable, and tell the given Displayable to remove the link with this.
|
static Future<Content> |
Display3D.update(Displayable d)
Remake the mesh for the Displayable in a separate Thread, if it's included in a Display3D
(otherwise returns null).
|
void |
LayerSet.updateBucket(Displayable d,
Layer layer) |
void |
Layer.updateBucket(Displayable d,
Layer layer)
Update buckets of a position change for the given Displayable.
|
void |
Bucketable.updateBucket(Displayable d,
Layer layer) |
static void |
Display.updateCheckboxes(Displayable displ,
int cb,
boolean state)
Used by the Displayable to update the visibility and locking state checkboxes in other Displays.
|
static void |
Display.updatePanel(Layer layer,
Displayable displ) |
static void |
Display.updatePanelIndex(Layer layer,
Displayable displ)
Deprecated.
|
static void |
Display.updateTitle(Layer layer,
Displayable displ)
Update the title of the given Displayable in its DisplayablePanel, if any.
|
void |
Selection.updateTransform(Displayable d)
Update the bounding box of the whole selection.
|
static void |
Display.updateTransform(Displayable displ)
Update in all displays the Transform for the given Displayable if it's selected.
|
static boolean |
Display.willPaint(Displayable displ)
Check if any display will paint the given Displayable within its srcRect.
|
| Modifier and Type | Method and Description |
|---|---|
protected static void |
Display.addAll(Layer layer,
Collection<? extends Displayable> coll) |
boolean |
LayerSet.addDataEditStep(Set<? extends Displayable> ds)
A new undo step for the "data" field of all Displayable in the set.
|
void |
LayerSet.addTransformStep(Collection<? extends Displayable> col)
Add an undo step for the transformations of all Displayable in hs.
|
Displayable.DoEdits |
LayerSet.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).
|
void |
Display.adjustGroupProperties(Collection<Displayable> col)
Pops up a dialog to adjust the alpha, visible, color, locked and compositeMode of all Displayables in
col. |
static void |
LayerSet.applyTransforms(Map<Displayable,AffineTransform> m) |
static void |
Display.centerAt(Coordinate<Displayable> c,
boolean select,
boolean shift_down) |
protected static void |
Patch.crosslink(Collection<Displayable> patches,
boolean overlapping_only) |
static <A extends Tree<?>> |
Tree.duplicateAs(Collection<Displayable> col,
Class<A> target)
Takes a collection of Tree instances and creates duplicate siblings of the target class.
|
void |
LayerSet.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.
|
static void |
AreaList.exportAsLabels(List<Displayable> listToPaint,
Roi roi,
float scale,
int first_layer,
int last_layer,
boolean visible_only,
boolean to_file,
boolean as_amira_labels)
Export all given AreaLists as one per pixel value, what is called a "labels" file; a file dialog is offered to save the image as a tiff stack.
|
ArrayList<Displayable> |
LayerSet.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.
|
static Rectangle |
Displayable.getBoundingBox(Collection<? extends Displayable> ds,
Rectangle r)
Bounding box of a collection of transformed
Displayables. |
HashSet<Displayable> |
Displayable.getLinkedGroup(HashSet<Displayable> hs)
Return the HashSet of all directly and indirectly linked objects.
|
static List<? extends Displayable> |
Display.getSelected(Class<? extends Displayable> c)
Return the list of selected Displayable objects of class @param c of the front Display, or an emtpy list if no Display or none selected.
|
List<Displayable> |
Selection.getSelectedSorted(Class<? extends Displayable> c)
Returns the subset of selected objects of Class c, in the proper order according to the Layer.indexOf or the LayerSet.indexOf.
|
static AreaList |
AreaList.merge(ArrayList<Displayable> al)
Merge all arealists contained in the ArrayList to the first one found, and remove the others from the project, and only if they belong to the same LayerSet.
|
void |
LayerSet.move(Set<Displayable> hs_d,
Layer source,
Layer target)
Move all Displayable objects in the HashSet to the given target layer.
|
BufferedImage |
DisplayCanvas.paintOffscreen(Layer active_layer,
int g_width,
int g_height,
Rectangle srcRect,
double magnification,
Displayable active,
int c_alphas,
Rectangle clipRect,
Loader loader,
HashMap<Color,Layer> hm,
ArrayList<LayerPanel> blending_list,
int mode,
GraphicsSource graphics_source,
boolean prepaint,
ArrayList<Displayable> al_top)
Deprecated.
|
BufferedImage |
DisplayCanvas.paintOffscreen(Layer active_layer,
List<Layer> layers,
ArrayList<Displayable> al_paint,
Displayable active,
int g_width,
int g_height,
int c_alphas,
Loader loader,
HashMap<Color,Layer> hm,
ArrayList<LayerPanel> blending_list,
int mode,
GraphicsSource graphics_source,
boolean prepaint,
int first_non_patch) |
BufferedImage |
DisplayCanvas.paintOffscreen(Layer active_layer,
List<Layer> layers,
int g_width,
int g_height,
Rectangle srcRect,
double magnification,
Displayable active,
int c_alphas,
Rectangle clipRect,
Loader loader,
HashMap<Color,Layer> hm,
ArrayList<LayerPanel> blending_list,
int mode,
GraphicsSource graphics_source,
boolean prepaint,
ArrayList<Displayable> al_top,
boolean preload)
This method uses data only from the arguments, and changes none.
|
static void |
Displayable.preConcatenate(AffineTransform at,
Collection<Displayable> ds)
Preconcatenate the
at to every Displayable in ds,
without touching their links; then the buckets are updated for all necessary layers. |
void |
Connector.readLegacyXML(LayerSet ls,
HashMap<String,String> ht_attr,
HashMap<Displayable,String> ht_links) |
void |
Selection.removeAll(Collection<Displayable> col)
Remove all given displayables from this selection.
|
boolean |
Layer.removeAll(Set<Displayable> ds)
Remove a set of children.
|
void |
DisplayCanvas.repaint(HashSet<Displayable> hs)
Repaint the clip corresponding to the sum of all boundingboxes of
Displayable objects in the hashset.
|
void |
Selection.selectAll(Collection<? extends Displayable> al) |
static ArrayList<AreaList> |
AreaList.split(List<Displayable> al)
For each AreaList in the list, find disconnected volumes within each and make an AreaList out of each.
|
static void |
Display.updateCheckboxes(Collection<Displayable> displs,
int cb)
Update the checkbox @param cb state to an appropriate value for each Displayable.
|
static void |
Display.updateCheckboxes(Collection<Displayable> displs,
int cb,
boolean state)
Set the checkbox @param cb state to @param state value, for each Displayable.
|
| Constructor and Description |
|---|
AreaWrapper(Displayable source,
Area area) |
Display(Project project,
Layer layer,
Displayable displ)
Open a new Display centered around the given Displayable.
|
DisplayablePanel(Display display,
Displayable d) |
SnapshotPanel(Display display,
Displayable d) |
| Constructor and Description |
|---|
AreaList(Project project,
long id,
HashMap<String,String> ht_attributes,
HashMap<Displayable,String> ht_links)
Reconstruct from XML.
|
AreaTree(Project project,
long id,
HashMap<String,String> ht_attr,
HashMap<Displayable,String> ht_links)
Reconstruct from XML.
|
Ball(Project project,
long id,
HashMap<String,String> ht,
HashMap<Displayable,String> ht_links)
Construct a Ball from an XML entry.
|
Connector(Project project,
long id,
HashMap<String,String> ht_attr,
HashMap<Displayable,String> ht_links)
Reconstruct from XML.
|
ContrastAdjustmentMode(Display display,
List<Displayable> selected) |
Displayable(Project project,
long id,
HashMap<String,String> ht,
HashMap<Displayable,String> ht_links)
Reconstruct a Displayable from an XML entry.
|
DisplayableChooser(Collection<Displayable> al_under,
Object lock) |
Dissector(Project project,
long id,
HashMap<String,String> ht,
HashMap<Displayable,String> ht_links)
Reconstruct from XML.
|
DLabel(Project project,
long id,
HashMap<String,String> ht,
HashMap<Displayable,String> ht_links)
To reconstruct from an XML entry.
|
GroupingMode(Display display,
List<Displayable> selected) |
LayerSet(Project project,
long id,
HashMap<String,String> ht_attributes,
HashMap<Displayable,String> ht_links)
Reconstruct from an XML entry.
|
NonLinearTransformMode(Display display,
List<Displayable> selected) |
Patch(Project project,
long id,
HashMap<String,String> ht_attributes,
HashMap<Displayable,String> ht_links)
Reconstruct from an XML entry.
|
Pipe(Project project,
long id,
HashMap<String,String> ht,
HashMap<Displayable,String> ht_links)
Construct a Pipe from an XML entry.
|
Polyline(Project project,
long id,
HashMap<String,String> ht_attr,
HashMap<Displayable,String> ht_links)
Reconstruct from XML.
|
Profile(Project project,
long id,
HashMap<String,String> ht,
HashMap<Displayable,String> ht_links)
Construct a Bezier Profile from an XML entry.
|
Stack(Project project,
long id,
HashMap<String,String> ht,
HashMap<Displayable,String> ht_links)
Construct a Stack from an XML entry.
|
Tree(Project project,
long id,
HashMap<String,String> ht_attr,
HashMap<Displayable,String> ht_links)
Reconstruct from XML.
|
Treeline(Project project,
long id,
HashMap<String,String> ht_attr,
HashMap<Displayable,String> ht_links)
Reconstruct from XML.
|
ZDisplayable(Project project,
long id,
HashMap<String,String> ht,
HashMap<Displayable,String> ht_links)
For reconstruction from an XML file.
|
| Modifier and Type | Method and Description |
|---|---|
boolean |
ContrastEnhancerWrapper.apply(Collection<Displayable> patches_) |
| Modifier and Type | Field and Description |
|---|---|
protected Set<Displayable> |
Loader.hs_unloadable |
| Modifier and Type | Method and Description |
|---|---|
void |
Loader.cache(Displayable d,
ij.ImagePlus imp)
Add to the cache, or if already there, make it be the last (to be flushed the last).
|
<I> ij.ImagePlus |
Loader.createLazyFlyThrough(List<? extends Region<I>> regions,
double magnification,
int type,
Displayable active)
Each slice is generated on demand, one slice per Region instance.
|
Image |
Loader.getFlatAWTImage(Layer layer,
Rectangle srcRect_,
double scale,
int c_alphas,
int type,
Class<?> clazz,
List<? extends Displayable> al_displ,
boolean quality,
Color background,
Displayable active) |
ij.ImagePlus |
Loader.getFlatImage(Layer layer,
Rectangle srcRect_,
double scale,
int c_alphas,
int type,
Class<?> clazz,
List<? extends Displayable> al_displ,
boolean quality,
Color background,
Displayable active) |
boolean |
Loader.isUnloadable(Displayable p) |
static double |
Loader.maxDim(Displayable d) |
void |
Loader.removeFromUnloadable(Displayable p) |
| Modifier and Type | Method and Description |
|---|---|
Bureaucrat |
Loader.enhanceContrast(Collection<Displayable> patches,
Patch reference)
Homogenize contrast for all patches, optionally using the @param reference Patch (can be null).
|
Bureaucrat |
Loader.generateMipMaps(ArrayList<Displayable> al)
Returns generateMipMaps(al, false).
|
Bureaucrat |
Loader.generateMipMaps(ArrayList<Displayable> al,
boolean overwrite)
Does nothing and returns null unless overriden.
|
Bureaucrat |
FSLoader.generateMipMaps(Collection<Displayable> patches,
boolean overwrite)
Generate image pyramids and store them into files under the dir_mipmaps for each Patch object in the Project.
|
Image |
Loader.getFlatAWTImage(Layer layer,
Rectangle srcRect_,
double scale,
int c_alphas,
int type,
Class<?> clazz,
List<? extends Displayable> al_displ,
boolean quality,
Color background) |
Image |
Loader.getFlatAWTImage(Layer layer,
Rectangle srcRect_,
double scale,
int c_alphas,
int type,
Class<?> clazz,
List<? extends Displayable> al_displ,
boolean quality,
Color background,
Displayable active) |
ij.ImagePlus |
Loader.getFlatImage(Layer layer,
Rectangle srcRect_,
double scale,
int c_alphas,
int type,
Class<?> clazz,
List<? extends Displayable> al_displ) |
ij.ImagePlus |
Loader.getFlatImage(Layer layer,
Rectangle srcRect_,
double scale,
int c_alphas,
int type,
Class<?> clazz,
List<? extends Displayable> al_displ,
boolean quality) |
ij.ImagePlus |
Loader.getFlatImage(Layer layer,
Rectangle srcRect_,
double scale,
int c_alphas,
int type,
Class<?> clazz,
List<? extends Displayable> al_displ,
boolean quality,
Color background)
Returns a screenshot of the given layer for the given magnification and srcRect.
|
ij.ImagePlus |
Loader.getFlatImage(Layer layer,
Rectangle srcRect_,
double scale,
int c_alphas,
int type,
Class<?> clazz,
List<? extends Displayable> al_displ,
boolean quality,
Color background,
Displayable active) |
ProjectThing |
DBLoader.getRootProjectThing(Project project,
TemplateThing root_tt,
TemplateThing project_tt,
HashMap<Long,Displayable> hs_d)
Get all the Thing objects, recursively, for the root, and their corresponding encapsulated objects.
|
Bureaucrat |
Loader.maskBorders(Collection<Displayable> patches,
int left,
int top,
int right,
int bottom)
Make the border have an alpha of zero.
|
ArrayList<Future<?>> |
Loader.maskBorders(int left,
int top,
int right,
int bottom,
Collection<Displayable> patches)
Make the border have an alpha of zero.
|
Bureaucrat |
Loader.regenerateMipMaps(Collection<? extends Displayable> patches)
Does nothing and returns null unless overriden.
|
Bureaucrat |
FSLoader.regenerateMipMaps(Collection<? extends Displayable> patches)
Order the regeneration of all mipmaps for the Patch instances in
patches, setting up a task that blocks input until all completed. |
Bureaucrat |
Loader.setMinAndMax(Collection<? extends Displayable> patches,
double min,
double max) |
| Modifier and Type | Method and Description |
|---|---|
Displayable |
RenameThingStep.getD() |
| Modifier and Type | Method and Description |
|---|---|
Set<Displayable> |
ProjectTree.remove(Set<? extends Displayable> displayables,
DefaultMutableTreeNode top)
Remove the Thing and DefaultMutableTreeNode that wrap each of the Displayable;
calls softRemove on each Displayable, and does NOT call remove on the Displayable.
|
| Modifier and Type | Method and Description |
|---|---|
DefaultMutableTreeNode |
ProjectTree.addChild(ProjectThing parent,
String childType,
Displayable d)
|
DefaultMutableTreeNode |
ProjectTree.addSibling(Displayable elder,
Displayable sibling)
Finds the node for the elder and adds the sibling next to it, under the same parent.
|
Connector |
ProjectTree.tryAddNewConnector(Displayable d,
boolean selectNode)
|
| Modifier and Type | Method and Description |
|---|---|
void |
ProjectTree.insertSegmentations(Collection<? extends Displayable> al)
Creates a new node of basic type for each AreaList, Ball, Pipe or Polyline present in the ArrayList.
|
Set<Displayable> |
ProjectTree.remove(Set<? extends Displayable> displayables,
DefaultMutableTreeNode top)
Remove the Thing and DefaultMutableTreeNode that wrap each of the Displayable;
calls softRemove on each Displayable, and does NOT call remove on the Displayable.
|
| Modifier and Type | Method and Description |
|---|---|
static List<Point3f> |
AreaUtils.generateTriangles(Displayable d,
double scale,
int resample_,
Map<Layer,Area> areas)
Expects areas in local coordinates to the Displayable @param d.
|
static Bureaucrat |
Utils.launchTPlugIn(KeyEvent ke,
String menu,
Project project,
Displayable active)
Returns null if no plugin was launched.
|
static void |
Search.remove(Displayable displ)
Remove from the tables if there.
|
| Modifier and Type | Method and Description |
|---|---|
static boolean |
Utils.addPlugIns(JPopupMenu popup,
String menu,
Project project,
Callable<Displayable> active)
Returns false if none to add.
|
static JMenu |
Utils.addPlugIns(String menu,
Project project,
Callable<Displayable> active)
Returns null if none to add.
|
| Modifier and Type | Method and Description |
|---|---|
static void |
DistortionCorrectionTask.run(DistortionCorrectionTask.CorrectDistortionFromSelectionParam p,
List<Patch> patches,
Displayable active,
Layer layer) |
static void |
DistortionCorrectionTask.run(DistortionCorrectionTask.CorrectDistortionFromSelectionParam p,
List<Patch> patches,
Displayable active,
Layer layer,
Worker worker) |
| Modifier and Type | Method and Description |
|---|---|
static AlignTask.ReferenceData |
AlignTask.createTransformPropertiesTable(List<Displayable> src_vdata,
List<Displayable> tgt_vdata,
Set<Long> lids_to_operate)
Creates a map only for visible patches that intersect vdata.
|
static AlignTask.ReferenceData |
AlignTask.createTransformPropertiesTable(List<Displayable> src_vdata,
List<Displayable> tgt_vdata,
Set<Long> lids_to_operate)
Creates a map only for visible patches that intersect vdata.
|
static void |
AlignTask.transformVectorData(AlignTask.ReferenceData rd,
Collection<Displayable> vdata,
LayerSet target_layerset) |
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