Polyline (Fiji Javadocs 0-SNAPSHOT API)

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

All Implemented Interfaces:

Line3D, Paintable, VectorData
```
public class Polyline
extends ZDisplayable
implements Line3D, VectorData
```
A sequence of points that make multiple chained line segments.

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 static int`	`index` Helper vars for mouse events.
`protected int`	`n_points` The number of points.
`protected double[][]`	`p` The array of clicked x,y points as [2][n].
`protected long[]`	`p_layer` The array of Layers over which the points of this pipe live

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
`Polyline(Project project, long id, HashMap<String,String> ht_attr, HashMap<Displayable,String> ht_links)` Reconstruct from XML.
`Polyline(Project project, long id, String title, float width, float height, float alpha, boolean visible, Color color, boolean locked, AffineTransform at)`
`Polyline(Project project, String title)` New empty Polyline.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected int`	`addPoint(int x_p, int y_p, long layer_id, double magnification)` Add a point either at the end or between two existing points, with accuracy depending on magnification.
`protected int`	`appendPoint(int x_p, int y_p, long layer_id)` Append a point at the end.
`protected void`	`appendPoints(double[] px, double[] py, long[] p_layer_ids, int len)`
`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)`
`VectorString3D`	`asVectorString3D()` Returns a non-calibrated VectorString3D.
`protected boolean`	`calculateBoundingBox(boolean adjust_position, Layer la)`
`protected boolean`	`calculateBoundingBox(Layer la)`
`protected double[]`	`calculateDataBoundingBox()` Returns min_x, min_y, max_x, max_y.
`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)` Calls contains(x_p, y_p) unless overriden -- in ZDisplayable objects, it tests whether the given point is contained in the part of the ZDisplayable that shows in the given layer.
`protected boolean`	`containsLocal(Layer layer, double x, double y, double radius)`
`boolean`	`crop(List<Layer> range)` Retain the data within the layer range, and through out all the rest.
`void`	`destroy()` Release all memory resources taken by this object.
`void`	`dragPoint(int index, int dx, int dy)` Move backbone point by the given deltas.
`protected void`	`enlargeArrays()` Increase the size of the arrays by 5.
`protected void`	`enlargeArrays(int n_more)`
`static void`	`exportDTD(StringBuilder sb_header, HashSet<String> hs, String indent)` Exports to type t2_polyline.
`void`	`exportXML(StringBuilder sb_body, String indent, XMLOptions options)` Exports data.
`protected int`	`findClosestSegment(int x_p, int y_p, long layer_id, double mag)` Returns the index of the first point in the segment made of any two consecutive points.
`protected int`	`findNearestPoint(int x_p, int y_p, long layer_id)` Find closest point within the current layer.
`protected int`	`findPoint(int x_p, int y_p, long layer_id, double mag)` 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 void`	`flushTraceCache(Project project)`
`List<Point3f>`	`generateTriangles(double scale, int parallels, int resample)` Calibrated.
`List<Point3f>`	`generateTriangles(double scale, int parallels, int resample, ij.measure.Calibration cal)` Returns a list of Point3f that define a polyline in 3D, for usage with an ij3d CustomLineMesh CONTINUOUS.
`Area`	`getAreaAt(Layer layer)` A little square for each pixel in @param layer.
`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 id and project name; this method is meant to be overriden by any of the subclasses.
`Collection<Long>`	`getLayerIds()` Get the list of Layer ids on which this ZDisplayable has data on.
`Polygon`	`getPerimeter()` The exact perimeter of this polyline, in integer precision.
`void`	`insertPoint(int i, int x_p, int y_p, long layer_id)`
`boolean`	`intersects(Area area, double z_first, double z_last)`
`boolean`	`isDeletable()`
`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.
`int`	`length()` The number of points in this pipe.
`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)` Does nothing unless overriden.
`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)`
`protected void`	`removePoint(int index)` Remove a point from the bezier backbone and its two associated control points.
`void`	`repaint(boolean repaint_navigator, Layer la)` Repaints in the given ImageCanvas only the area corresponding to the bounding box of this Pipe.
`void`	`reverse()`
`static Object[]`	`simplify(double[] px, double[] py, long[] p_layer_ids, int max_iterations, LayerSet layer_set)` Resample the curve to, first, a number of points as resulting from resampling to a point interdistance of delta, and second, as adjustment by random walk of those points towards the original points.
`protected double[]`	`sqDistanceToEndPoints(double x_p, double y_p, long layer_id)`
`Polyline`	`sub(int start, int end)` Create a shorter Polyline, from start to end (inclusive); not added to the LayerSet.

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

Methods inherited from class ini.trakem2.display.Displayable
adjustProperties, areThereLayerCrossLinks, canSendTo, clone, clone, commonDTDChildren, contains, deselect, displacePoints, exportSVG, 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

Methods inherited from interface ini.trakem2.display.Line3D
getColor, getId, getLayerSet, getProject, toString

Field Detail
- n_points
```
protected int n_points
```
  The number of points.
- p
```
protected double[][] p
```
  The array of clicked x,y points as [2][n].
- p_layer
```
protected long[] p_layer
```
  The array of Layers over which the points of this pipe live
- index
```
protected static int index
```
  Helper vars for mouse events. It's safe to have them static since only one Pipe will be edited at a time.

Constructor Detail

Polyline

public Polyline(Project project,
                String title)

New empty Polyline.

Polyline

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

Polyline

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

Reconstruct from XML.

Method Detail

enlargeArrays
```
protected void enlargeArrays()
```
Increase the size of the arrays by 5.

enlargeArrays

protected void enlargeArrays(int n_more)

findClosestSegment

protected int findClosestSegment(int x_p,
                                 int y_p,
                                 long layer_id,
                                 double mag)

Returns the index of the first point in the segment made of any two consecutive points.

findPoint
```
protected int findPoint(int x_p,
                        int y_p,
                        long layer_id,
                        double mag)
```
Find a point in an array, with a precision dependent on the magnification. Only points in the given layer are considered, the rest are ignored. Returns -1 if none found.

findNearestPoint

protected int findNearestPoint(int x_p,
                               int y_p,
                               long layer_id)

Find closest point within the current layer.

removePoint
```
protected void removePoint(int index)
```
Remove a point from the bezier backbone and its two associated control points.

dragPoint

public void dragPoint(int index,
                      int dx,
                      int dy)

Move backbone point by the given deltas.

sqDistanceToEndPoints

protected double[] sqDistanceToEndPoints(double x_p,
                                         double y_p,
                                         long layer_id)

Parameters:: x_p,y_p - in local coords.

insertPoint

public void insertPoint(int i,
                        int x_p,
                        int y_p,
                        long layer_id)

appendPoint

protected int appendPoint(int x_p,
                          int y_p,
                          long layer_id)

Append a point at the end. Returns the index of the new point.

addPoint
```
protected int addPoint(int x_p,
                       int y_p,
                       long layer_id,
                       double magnification)
```
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.

appendPoints

protected void appendPoints(double[] px,
                            double[] py,
                            long[] p_layer_ids,
                            int len)

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

flushTraceCache

public static void flushTraceCache(Project project)

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

calculateBoundingBox

protected boolean calculateBoundingBox(boolean adjust_position,
                                       Layer la)

calculateDataBoundingBox
```
protected double[] calculateDataBoundingBox()
```
Returns min_x, min_y, max_x, max_y.

destroy
```
public void destroy()
```
Release all memory resources taken by this object.

Overrides:

destroy in class Displayable

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()

repaint

public void repaint(boolean repaint_navigator,
                    Layer la)

Repaints in the given ImageCanvas only the area corresponding to the bounding box of this Pipe.

getPerimeter
```
public Polygon getPerimeter()
```
The exact perimeter of this polyline, in integer precision.

Overrides:

getPerimeter in class Displayable

getAreaAt
```
public Area getAreaAt(Layer layer)
```
A little square for each pixel in @param layer.

Overrides:

getAreaAt in class Displayable

isRoughlyInside
```
public 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

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

isDeletable in class Displayable

length
```
public int length()
```
The number of points in this pipe.

Specified by:

length in interface Line3D

contains
```
public boolean contains(Layer layer,
                        double x,
                        double y)
```
Description copied from class: Displayable

Calls contains(x_p, y_p) unless overriden -- in ZDisplayable objects, it tests whether the given point is contained in the part of the ZDisplayable that shows in the given layer.

Overrides:

contains in class Displayable

containsLocal

protected boolean containsLocal(Layer layer,
                                double x,
                                double y,
                                double radius)

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

exportXML

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

Exports data.

Overrides:: exportXML in class ZDisplayable

exportDTD

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

Exports to type t2_polyline.

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

generateTriangles

public List<Point3f> generateTriangles(double scale,
                                       int parallels,
                                       int resample)

Calibrated.

Specified by:: generateTriangles in interface Line3D

generateTriangles

public List<Point3f> generateTriangles(double scale,
                                       int parallels,
                                       int resample,
                                       ij.measure.Calibration cal)

Returns a list of Point3f that define a polyline in 3D, for usage with an ij3d CustomLineMesh CONTINUOUS. @param parallels is ignored.

intersects

public boolean intersects(Area area,
                          double z_first,
                          double z_last)

Specified by:: intersects in class ZDisplayable

asVectorString3D
```
public VectorString3D asVectorString3D()
```
Returns a non-calibrated VectorString3D.

Specified by:

asVectorString3D in interface Line3D

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

Returns id and project name; this method is meant to be overriden by any of the subclasses.

Overrides:

getInfo in class DBObject

measure
```
public ij.measure.ResultsTable measure(ij.measure.ResultsTable rt)
```
Description copied from class: Displayable

Does nothing unless overriden.

Overrides:

measure in class Displayable

simplify

public static Object[] simplify(double[] px,
                                double[] py,
                                long[] p_layer_ids,
                                int max_iterations,
                                LayerSet layer_set)
                         throws Exception

Resample the curve to, first, a number of points as resulting from resampling to a point interdistance of delta, and second, as adjustment by random walk of those points towards the original points.

Throws:: Exception

crop
```
public boolean crop(List<Layer> range)
```
Retain the data within the layer range, and through out all the rest.

Overrides:

crop in class ZDisplayable

sub
```
public Polyline sub(int start,
                    int end)
```
Create a shorter Polyline, from start to end (inclusive); not added to the LayerSet.

reverse
```
public void reverse()
```

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

Class Polyline

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

Methods inherited from interface ini.trakem2.display.Line3D

Field Detail

n_points

p

p_layer

index

Constructor Detail

Polyline

Polyline

Polyline

Method Detail

enlargeArrays

enlargeArrays

findClosestSegment

findPoint

findNearestPoint

removePoint

dragPoint

sqDistanceToEndPoints

insertPoint

appendPoint

addPoint

appendPoints

paint

keyPressed

flushTraceCache

mousePressed

mouseDragged

mouseReleased

calculateBoundingBox

calculateBoundingBox

calculateDataBoundingBox

destroy

flush

repaint

getPerimeter

getAreaAt

isRoughlyInside

isDeletable

length

contains

containsLocal

linkPatches

getFirstLayer

exportXML

exportDTD

clone

generateTriangles

generateTriangles

intersects

asVectorString3D

getInfo

measure

simplify

crop

sub

reverse

layerRemoved

apply

apply

getLayerIds