Ball (Fiji Javadocs 0-SNAPSHOT API)

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

All Implemented Interfaces:: Paintable, VectorData

public class Ball
extends ZDisplayable
implements VectorData

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

Field Summary

Fields
Modifier and Type	Field and Description
`protected int`	`n_points` The number of points.
`protected double[][]`	`p` The array of clicked points.
`protected long[]`	`p_layer` The array of Layers over which each point lives
`protected double[]`	`p_width` The width of each point.

Fields inherited from class ini.trakem2.display.ZDisplayable
layer_set

Fields inherited from class ini.trakem2.display.Displayable
alpha, annotation, at, color, COMPOSITE_ADD, COMPOSITE_COLOR_YCBCR, COMPOSITE_DIFFERENCE, COMPOSITE_MULTIPLY, COMPOSITE_NORMAL, COMPOSITE_SUBTRACT, compositeModes, height, hs_linked, last_color, layer, linked_props, linked_props_origins, locked, props, TAG_ATTR1, TAG_ATTR2, title, visible, width

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

Constructor Summary

Constructors
Constructor and Description
`Ball(Project project, long id, HashMap<String,String> ht, HashMap<Displayable,String> ht_links)` Construct a Ball from an XML entry.
`Ball(Project project, long id, String title, float width, float height, float alpha, boolean visible, Color color, boolean locked, AffineTransform at)` Construct an unloaded Ball from the database.
`Ball(Project project, String title, double x, double y)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addBall(double x, double y, double r, long layer_id)` Used to add individual ball objects when parsing.
`protected int`	`addPoint(double x_p, double y_p, long layer_id, double radius)` Add a point either at the end or between two existing points, with accuracy depending on magnification.
`void`	`adjustProperties()` Shows a dialog to adjust properties of this object.
`boolean`	`apply(Layer la, Area roi, CoordinateTransform ict)` Applies the 2D transform @ict (which is expected to operate on the world coordinates version of the data contained here) only to the data that falls within the @param roi (in world coords), and then recomputes the bounding box and affine transform (to a translation or identity).
`boolean`	`apply(VectorDataTransform vdt)`
`List<Point3f>`	`asWorldPoints()` Returns a Point3f for every x,y,z ball, in calibrated world space.
`protected boolean`	`calculateBoundingBox(Layer la)`
`Displayable`	`clone(Project pr, boolean copy_id)` Performs a deep copy of this object, without the links.
`boolean`	`contains(Layer layer, double x, double y)` Test whether the Ball contains the given point at the given layer.
`boolean`	`crop(List<Layer> range)` Retain the data within the layer range, and throw out all the rest.
`void`	`destroy()` Release all memory resources taken by this object.
`static void`	`exportDTD(StringBuilder sb_header, HashSet<String> hs, String indent)`
`void`	`exportSVG(StringBuffer data, double z_scale, String indent)` Does nothing unless overriden.
`void`	`exportXML(StringBuilder sb_body, String indent, XMLOptions options)` Similar to exportSVG but the layer_id is saved instead of the z.
`protected int`	`findPoint(double[][] a, int x_p, int y_p, double magnification, long lid)` Find a point in an array, with a precision dependent on the magnification.
`void`	`flush()` Release memory resources used by this object: namely the arrays of points, which can be reloaded with a call to setupForDisplay()
`static double[][][]`	`generateGlobe(int meridians, int parallels)` Generate a globe of radius 1.0 that can be used for any Ball.
`List<Point3f>`	`generateTriangles(double scale, double[][][] globe)` Put all balls as a single 'mesh'; the returned list contains all faces as three consecutive Point3f.
`Area`	`getAreaAt(Layer layer)` This area is meant to represent the entire area where a Displayable paints to in the @param layer.
`double[][]`	`getBalls()` Returns a [n_points][4] array, with x,y,z,radius on the second part; not transformed, but local! To obtain balls in world coordinates, calibrated, use getWorldBalls().
`int`	`getCount()` Return the number of balls.
`Layer`	`getFirstLayer()` Returns the layer of lowest Z coordinate where this ZDisplayable has a point in, or the creation layer if no points yet.
`String`	`getInfo()` Returns information on the number of ball objects per layer.
`Collection<Long>`	`getLayerIds()` Get the list of Layer ids on which this ZDisplayable has data on.
`Polygon`	`getPerimeter()` The exact perimeter of this Ball, in integer precision.
`String[]`	`getPointsForSQL()` Return the list of query statements needed to insert all the points in the database.
`Map<Layer,double[]>`	`getRawBalls()` Returns the raw data for the balls, sorted by Layer ID versus double[]{z,y,r} .
`double[][]`	`getWorldBalls()` Returns a [n_points][4] array, with x,y,z,radius on the second part, in world coordinates (that is, transformed with this AffineTransform and calibrated with the containing LayerSet's calibration).
`boolean`	`intersects(Area area, double z_first, double z_last)`
`boolean`	`isDeletable()`
`protected boolean`	`isRoughlyInside(Layer layer, Rectangle r)` If this Displayable intersects with @param r or almost intersects, then returns true.
`void`	`keyPressed(KeyEvent ke)`
`protected boolean`	`layerRemoved(Layer la)` Update internal datastructures to reflect the fact that @param layer has been removed from the containing LayerSet.
`boolean`	`linkPatches()` Link the Patch objects that lay underneath the part of the bounding box of this profile that shows in the current layer, so that they cannot be dragged independently.
`ij.measure.ResultsTable`	`measure(ij.measure.ResultsTable rt)` Returns a listing of all balls contained here, one per row with index, x, y, z, and radius, all calibrated.
`void`	`mouseDragged(MouseEvent me, Layer layer, int x_p, int y_p, int x_d, int y_d, int x_d_old, int y_d_old)`
`void`	`mousePressed(MouseEvent me, Layer layer, int x_p, int y_p, double mag)`
`void`	`mouseReleased(MouseEvent me, Layer layer, int x_p, int y_p, int x_d, int y_d, int x_r, int y_r)`
`void`	`paint(Graphics2D g, Rectangle srcRect, double magnification, boolean active, int channels, Layer active_layer, List<Layer> layers)`
`boolean`	`paintsAt(Layer layer)` Check if this instance will paint anything at the level of the given Layer.
`protected void`	`removePoint(int index)` Remove a point.
`void`	`repaint(boolean repaint_navigator, Layer layer)` Repaints in the given ImageCanvas only the area corresponding to the bounding box of this Profile.
`void`	`set(int i, double x, double y, Layer la, double radius)` Set the x,y,radius raw pixel values for the ball at index i.
`void`	`setRadius(int i, double radius)` Set the radius (raw pixel value) for the ball at index i.
`void`	`toShapesFile(StringBuffer data, String group, String color, double z_scale)` Writes the data of this object as a Ball object in the .shapes file represented by the 'data' StringBuffer.

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

Methods inherited from class ini.trakem2.display.Displayable
areThereLayerCrossLinks, canSendTo, clone, clone, commonDTDChildren, contains, deselect, displacePoints, findById, findNearestPoint, findNearestPoint, getAffineTransform, getAffineTransformCopy, getAlpha, getAnnotation, getArea, getAreaForBucket, getBoundingBox, getBoundingBox, getBoundingBox, getBounds, getBounds, getColor, getComposite, getComposite, getCompositeMode, getHeight, getIntersection, getLayer, getLayersWithData, getLinked, getLinked, getLinkedBox, getLinkedGroup, getLinkedProperties, getLinkedProperties, getLinkedProperty, getLinkedProperty, getMinimalBoundingBox, getNameId, getPerimeter, 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, isVisible, link, link, makeAdjustPropertiesDialog, mouseWheelMoved, paintAsBox, paintOffscreen, paintSnapshot, preConcatenate, prePaint, preTransform, processAdjustPropertiesDialog, removeLinkedProperties, removeLinkedPropertiesFromOrigins, repaint, restXML, rotate, rotate, rotatePoints, scale, scale, scalePoints, setAffineTransform, setAlpha, setAlpha, setAnnotation, setCompositeMode, setDimensions, setDimensions, setLayer, setLinkedProperties, setLinkedProperty, setLocation, setLocked, setProperty, setTitle, setVisible, snapTo, toString, transform, transformPoint, transformPoint, transformPoints, transformPoints, transformPoints, transformPoints, transformPoints, transformPoints, transformPoints, transformPoints, transformPoints, transformRectangle, translate, translate, unlink, unlink, unlinkAll, updateInDatabase, xmlError, xmlError

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

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

- Field Detail
  - n_points
```
protected int n_points
```
    The number of points.
  - p
```
protected double[][] p
```
    The array of clicked points.
  - p_layer
```
protected long[] p_layer
```
    The array of Layers over which each point lives
  - p_width
```
protected double[] p_width
```
    The width of each point.
- Constructor Detail
  - Ball
```
public Ball(Project project,
            String title,
            double x,
            double y)
```
  - Ball
```
public Ball(Project project,
            long id,
            String title,
            float width,
            float height,
            float alpha,
            boolean visible,
            Color color,
            boolean locked,
            AffineTransform at)
```
    Construct an unloaded Ball from the database. Points will be loaded later, when needed.
  - Ball
```
public Ball(Project project,
            long id,
            HashMap<String,String> ht,
            HashMap<Displayable,String> ht_links)
```
    Construct a Ball from an XML entry.
- Method Detail
  - addBall
```
public void addBall(double x,
                    double y,
                    double r,
                    long layer_id)
```
    Used to add individual ball objects when parsing.
  - findPoint
```
protected int findPoint(double[][] a,
                        int x_p,
                        int y_p,
                        double magnification,
                        long lid)
```
    Find a point in an array, with a precision dependent on the magnification.
  - removePoint
```
protected void removePoint(int index)
```
    Remove a point.
  - addPoint
```
protected int addPoint(double x_p,
                       double y_p,
                       long layer_id,
                       double radius)
```
    Add a point either at the end or between two existing points, with accuracy depending on magnification. The width of the new point is that of the closest point after which it is inserted.
  - paint
```
public void paint(Graphics2D g,
                  Rectangle srcRect,
                  double magnification,
                  boolean active,
                  int channels,
                  Layer active_layer,
                  List<Layer> layers)
```
    Specified by:
    
    paint in interface Paintable
    
    Overrides:
    
    paint in class Displayable
  - keyPressed
```
public void keyPressed(KeyEvent ke)
```
    Overrides:
    
    keyPressed in class Displayable
  - mousePressed
```
public void mousePressed(MouseEvent me,
                         Layer layer,
                         int x_p,
                         int y_p,
                         double mag)
```
    Overrides:
    
    mousePressed in class Displayable
  - mouseDragged
```
public void mouseDragged(MouseEvent me,
                         Layer layer,
                         int x_p,
                         int y_p,
                         int x_d,
                         int y_d,
                         int x_d_old,
                         int y_d_old)
```
    Overrides:
    
    mouseDragged in class Displayable
  - mouseReleased
```
public void mouseReleased(MouseEvent me,
                          Layer layer,
                          int x_p,
                          int y_p,
                          int x_d,
                          int y_d,
                          int x_r,
                          int y_r)
```
    Overrides:
    
    mouseReleased in class Displayable
  - calculateBoundingBox
```
protected boolean calculateBoundingBox(Layer la)
```
    Specified by:
    
    calculateBoundingBox in class ZDisplayable
  - destroy
```
public void destroy()
```
    Release all memory resources taken by this object.
    
    Overrides:
    
    destroy in class Displayable
  - repaint
```
public void repaint(boolean repaint_navigator,
                    Layer layer)
```
    Repaints in the given ImageCanvas only the area corresponding to the bounding box of this Profile.
  - flush
```
public void flush()
```
    Release memory resources used by this object: namely the arrays of points, which can be reloaded with a call to setupForDisplay()
  - getPerimeter
```
public Polygon getPerimeter()
```
    The exact perimeter of this Ball, in integer precision.
    
    Overrides:
    
    getPerimeter in class Displayable
  - toShapesFile
```
public void toShapesFile(StringBuffer data,
                         String group,
                         String color,
                         double z_scale)
```
    Writes the data of this object as a Ball object in the .shapes file represented by the 'data' StringBuffer.
  - getPointsForSQL
```
public String[] getPointsForSQL()
```
    Return the list of query statements needed to insert all the points in the database.
  - isDeletable
```
public boolean isDeletable()
```
    Specified by:
    
    isDeletable in class Displayable
  - contains
```
public boolean contains(Layer layer,
                        double x,
                        double y)
```
    Test whether the Ball contains the given point at the given layer. What it does: and tests whether the point is contained in any of the balls present in the given layer.
    
    Overrides:
    
    contains in class Displayable
  - linkPatches
```
public boolean linkPatches()
```
    Description copied from class: ZDisplayable
    
    Link the Patch objects that lay underneath the part of the bounding box of this profile that shows in the current layer, so that they cannot be dragged independently.
    
    Specified by:
    
    linkPatches in class ZDisplayable
    
    Returns:
    
    whether the locking state changed.
  - getFirstLayer
```
public Layer getFirstLayer()
```
    Returns the layer of lowest Z coordinate where this ZDisplayable has a point in, or the creation layer if no points yet.
    
    Specified by:
    
    getFirstLayer in class ZDisplayable
  - getRawBalls
```
public Map<Layer,double[]> getRawBalls()
```
    Returns the raw data for the balls, sorted by Layer ID versus double[]{z,y,r} .
  - getBalls
```
public double[][] getBalls()
```
    Returns a [n_points][4] array, with x,y,z,radius on the second part; not transformed, but local! To obtain balls in world coordinates, calibrated, use getWorldBalls().
  - getWorldBalls
```
public double[][] getWorldBalls()
```
    Returns a [n_points][4] array, with x,y,z,radius on the second part, in world coordinates (that is, transformed with this AffineTransform and calibrated with the containing LayerSet's calibration).
  - asWorldPoints
```
public List<Point3f> asWorldPoints()
```
    Returns a Point3f for every x,y,z ball, in calibrated world space.
  - exportSVG
```
public void exportSVG(StringBuffer data,
                      double z_scale,
                      String indent)
```
    Description copied from class: Displayable
    
    Does nothing unless overriden.
    
    Overrides:
    
    exportSVG in class Displayable
  - exportXML
```
public void exportXML(StringBuilder sb_body,
                      String indent,
                      XMLOptions options)
```
    Similar to exportSVG but the layer_id is saved instead of the z. The convention is my own, a ball_ob that contains ball objects and links.
    
    Overrides:
    
    exportXML in class ZDisplayable
  - exportDTD
```
public static void exportDTD(StringBuilder sb_header,
                             HashSet<String> hs,
                             String indent)
```
  - paintsAt
```
public boolean paintsAt(Layer layer)
```
    Description copied from class: ZDisplayable
    
    Check if this instance will paint anything at the level of the given Layer.
    
    Overrides:
    
    paintsAt in class ZDisplayable
  - getInfo
```
public String getInfo()
```
    Returns information on the number of ball objects per layer.
    
    Overrides:
    
    getInfo in class DBObject
  - clone
```
public Displayable clone(Project pr,
                         boolean copy_id)
```
    Performs a deep copy of this object, without the links.
    
    Specified by:
    
    clone in class Displayable
  - generateGlobe
```
public static double[][][] generateGlobe(int meridians,
                                         int parallels)
```
    Generate a globe of radius 1.0 that can be used for any Ball. First dimension is Z, then comes a double array x,y. Minimal accepted meridians and parallels is 3.
  - generateTriangles
```
public List<Point3f> generateTriangles(double scale,
                                       double[][][] globe)
```
    Put all balls as a single 'mesh'; the returned list contains all faces as three consecutive Point3f. The mesh is also translated by x,y,z of this Displayable.
  - intersects
```
public boolean intersects(Area area,
                          double z_first,
                          double z_last)
```
    Specified by:
    
    intersects in class ZDisplayable
    
    Parameters:
    
    area - is expected in world coordinates.
  - getAreaAt
```
public Area getAreaAt(Layer layer)
```
    Description copied from class: Displayable
    
    This area is meant to represent the entire area where a Displayable paints to in the @param layer. But for some this is reduced to areas with data, not with interpolated data. For example, a Polyine would show a list of little 1x1 rectangles for each point in the @param layer.
    
    Overrides:
    
    getAreaAt in class Displayable
  - isRoughlyInside
```
protected boolean isRoughlyInside(Layer layer,
                                  Rectangle r)
```
    Description copied from class: Displayable
    
    If this Displayable intersects with @param r or almost intersects, then returns true. This method is meant to be very fast, and err on the "yes" and never on the "no".
    
    Overrides:
    
    isRoughlyInside in class Displayable
  - measure
```
public ij.measure.ResultsTable measure(ij.measure.ResultsTable rt)
```
    Returns a listing of all balls contained here, one per row with index, x, y, z, and radius, all calibrated. 'name-id' is a column that displays the title of this Ball object only when such title is purely a number.
    
    Overrides:
    
    measure in class Displayable
  - crop
```
public boolean crop(List<Layer> range)
```
    Retain the data within the layer range, and throw out all the rest.
    
    Overrides:
    
    crop in class ZDisplayable
  - layerRemoved
```
protected boolean layerRemoved(Layer la)
```
    Description copied from class: ZDisplayable
    
    Update internal datastructures to reflect the fact that @param layer has been removed from the containing LayerSet.
    
    Overrides:
    
    layerRemoved in class ZDisplayable
  - apply
```
public boolean apply(Layer la,
                     Area roi,
                     CoordinateTransform ict)
              throws Exception
```
    Description copied from interface: VectorData
    
    Applies the 2D transform @ict (which is expected to operate on the world coordinates version of the data contained here) only to the data that falls within the @param roi (in world coords), and then recomputes the bounding box and affine transform (to a translation or identity). Does not consider links.
    
    Specified by:
    
    apply in interface VectorData
    
    Parameters:
    
    la - Only data at this Layer may be transformed.
    
    roi - Only data inside this world-coordinates Area may be transformed.
    
    ict - The transform to apply to the data that is in @param la and within @param roi.
    
    Throws:
    
    Exception
  - apply
```
public boolean apply(VectorDataTransform vdt)
              throws Exception
```
    Specified by:
    
    apply in interface VectorData
    
    Throws:
    
    Exception
  - getLayerIds
```
public Collection<Long> getLayerIds()
```
    Description copied from class: ZDisplayable
    
    Get the list of Layer ids on which this ZDisplayable has data on.
    
    Overrides:
    
    getLayerIds in class ZDisplayable
  - adjustProperties
```
public void adjustProperties()
```
    Description copied from class: Displayable
    
    Shows a dialog to adjust properties of this object.
    
    Overrides:
    
    adjustProperties in class Displayable
  - set
```
public void set(int i,
                double x,
                double y,
                Layer la,
                double radius)
```
    Set the x,y,radius raw pixel values for the ball at index i. When done setting values, call repaint(true, null).
    
    Throws:
    
    IndexOutOfBoundsException - if i < 0 or i >= the number of points.
  - getCount
```
public int getCount()
```
    Return the number of balls.
  - setRadius
```
public void setRadius(int i,
                      double radius)
```
    Set the radius (raw pixel value) for the ball at index i. When done setting values, call repaint(true, null).
    
    Throws:
    
    IndexOutOfBoundsException - if i < 0 or i >= the number of points.

Class Ball

Nested Class Summary

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

Field Summary

Fields inherited from class ini.trakem2.display.ZDisplayable

Fields inherited from class ini.trakem2.display.Displayable

Fields inherited from class ini.trakem2.persistence.DBObject

Constructor Summary

Method Summary

Methods inherited from class ini.trakem2.display.ZDisplayable

Methods inherited from class ini.trakem2.display.Displayable

Methods inherited from class ini.trakem2.persistence.DBObject

Methods inherited from class java.lang.Object

Field Detail

n_points

p

p_layer

p_width

Constructor Detail

Ball

Ball

Ball

Method Detail

addBall

findPoint

removePoint

addPoint

paint

keyPressed

mousePressed

mouseDragged

mouseReleased

calculateBoundingBox

destroy

repaint

flush

getPerimeter

toShapesFile

getPointsForSQL

isDeletable

contains

linkPatches

getFirstLayer

getRawBalls

getBalls

getWorldBalls

asWorldPoints

exportSVG

exportXML

exportDTD

paintsAt

getInfo

clone

generateGlobe

generateTriangles

intersects

getAreaAt

isRoughlyInside

measure

crop

layerRemoved

apply

apply

getLayerIds

adjustProperties

set

getCount

setRadius