Pipe (Fiji Javadocs 0-SNAPSHOT API)

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

All Implemented Interfaces:: Line3D, Paintable, VectorData

public class Pipe
extends ZDisplayable
implements Line3D, 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 double[][]`	`p_i` The array of interpolated points generated from p, p_l and p_r.
`protected double[][]`	`p_l` The array of left control points, one for each clicked point.
`protected long[]`	`p_layer` The array of Layers over which the points of this pipe live
`protected double[][]`	`p_r` The array of right control points, one for each clicked point.
`protected double[]`	`p_width` The width of each point.
`protected double[]`	`p_width_i` The interpolated width for each interpolated 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
`Pipe(Project project, long id, HashMap<String,String> ht, HashMap<Displayable,String> ht_links)` Construct a Pipe from an XML entry.
`Pipe(Project project, long id, String title, float width, float height, float alpha, boolean visible, Color color, boolean locked, AffineTransform at)` Construct an unloaded Pipe from the database.
`Pipe(Project project, String title, double x, double y)`

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, double magnification, double bezier_finess, long layer_id)` Add a point either at the end or between two existing points, with accuracy depending on magnification.
`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)`
`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 Pipe contains the given point at the given layer.
`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.
`static double`	`distance(double x1, double y1, double x2, double y2)` Calculate distance from one point to another.
`protected void`	`dragControlPoint(int index, int x_d, int y_d, double[][] p_dragged, double[][] p_adjusted, boolean symmetric)` Drag a control point and adjust the other, dependent one, in a symmetric way or not.
`protected void`	`dragPoint(int index, int dx, int dy)` Move backbone point by the given deltas.
`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)` Exports data, the tag is not opened nor closed.
`protected int`	`findClosestPoint(int x_p, int y_p, double magnification, double bezier_finess)` Find the closest point to an interpolated point with precision depending upon magnification.
`protected int`	`findPoint(double[][] a, long[] p_layer, int x_p, int y_p, long lid, double magnification)` 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()
`protected void`	`generateInterpolatedPoints(double bezier_finess)`
`double[][][]`	`generateMesh(double scale)`
`static List<Point3f>`	`generateTriangles(double[][][] all_points, double scale)` Accepts an arrays as that returned from methods generateJoints and makeTube: first dimension is the list of points, second dimension is the number of vertices defining the circular cross section of the tube, and third dimension is the x,y,z of each vertex.
`List<Point3f>`	`generateTriangles(double scale, int parallels, int resample)` Calibrated.
`Area`	`getAreaAt(Layer layer)` This area is meant to represent the entire area where a Displayable paints to in the @param layer.
`double[][]`	`getBackbone()` Returns a [p_i[0].length][4] array, with x,y,z,radius on the second part.
`Rectangle`	`getBounds(Rectangle r, Layer layer)` Returns the bounds of this object as it shows in the given layer, set into @param r.
`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 pipe, in integer precision.
`String[]`	`getPointsForSQL()` Return the list of query statements needed to insert all the points in the database.
`String`	`getUpdatePointForSQL(int index)`
`boolean`	`intersects(Area area, double z_first, double z_last)`
`boolean`	`intersects(Layer layer, Area area)` Expects Area in world coords.
`boolean`	`intersects(Layer layer, Rectangle r)` Expects Rectangle in world coords.
`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 clicked, backbone points in this pipe.
`boolean`	`linkPatches()` Scan the Display and link Patch objects that lay under this Pipe's bounding box.
`static double[][][]`	`makeTube(double[] px, double[] py, double[] pz, double[] p_width_i, int resample, int parallels, ij.measure.Calibration cal)`
`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.
`protected void`	`resetControlPoints(int index)` Set the control points to the same value as the backbone point which they control.
`void`	`reverse()` Reverses the order of the points in the arrays.
`void`	`snapTo(int cx, int cy, int x_p, int y_p)` x,y is the cursor position in offscreen coordinates.
`void`	`toShapesFile(StringBuffer data, String group, String color, double z_scale)` Writes the data of this object as a Pipe object in the .shapes file represented by the 'data' StringBuffer.

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, findById, findNearestPoint, findNearestPoint, getAffineTransform, getAffineTransformCopy, getAlpha, getAnnotation, getArea, getAreaForBucket, getBoundingBox, getBoundingBox, getBoundingBox, 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, 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, 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, toString, 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 points.
- p_l
```
protected double[][] p_l
```
  The array of left control points, one for each clicked point.
- p_r
```
protected double[][] p_r
```
  The array of right control points, one for each clicked point.
- p_i
```
protected double[][] p_i
```
  The array of interpolated points generated from p, p_l and p_r.
- p_layer
```
protected long[] p_layer
```
  The array of Layers over which the points of this pipe live
- p_width
```
protected double[] p_width
```
  The width of each point.
- p_width_i
```
protected double[] p_width_i
```
  The interpolated width for each interpolated point.

Constructor Detail

Pipe

public Pipe(Project project,
            String title,
            double x,
            double y)

Pipe

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

Construct an unloaded Pipe from the database. Points will be loaded later, when needed.

Pipe

public Pipe(Project project,
            long id,
            HashMap<String,String> ht,
            HashMap<Displayable,String> ht_links)

Construct a Pipe from an XML entry.

Method Detail
- findPoint
```
protected int findPoint(double[][] a,
                        long[] p_layer,
                        int x_p,
                        int y_p,
                        long lid,
                        double magnification)
```
  Find a point in an array, with a precision dependent on the magnification. Only points in the current layer are found, the rest are ignored. Returns -1 if none found.
- removePoint
```
protected void removePoint(int index)
```
  Remove a point from the bezier backbone and its two associated control points.
- distance
```
public static double distance(double x1,
                              double y1,
                              double x2,
                              double y2)
```
  Calculate distance from one point to another.
- dragPoint
```
protected void dragPoint(int index,
                         int dx,
                         int dy)
```
  Move backbone point by the given deltas.
- resetControlPoints
```
protected void resetControlPoints(int index)
```
  Set the control points to the same value as the backbone point which they control.
- dragControlPoint
```
protected void dragControlPoint(int index,
                                int x_d,
                                int y_d,
                                double[][] p_dragged,
                                double[][] p_adjusted,
                                boolean symmetric)
```
  Drag a control point and adjust the other, dependent one, in a symmetric way or not.
- addPoint
```
protected int addPoint(int x_p,
                       int y_p,
                       double magnification,
                       double bezier_finess,
                       long layer_id)
```
  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.
- findClosestPoint
```
protected int findClosestPoint(int x_p,
                               int y_p,
                               double magnification,
                               double bezier_finess)
```
  Find the closest point to an interpolated point with precision depending upon magnification.
- generateInterpolatedPoints
```
protected void generateInterpolatedPoints(double bezier_finess)
```
- 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
- calculateBoundingBox
```
protected boolean calculateBoundingBox(boolean adjust_position,
                                       Layer la)
```
- 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 pipe, 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 Pipe 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.
- getUpdatePointForSQL
```
public String getUpdatePointForSQL(int index)
```
- isDeletable
```
public boolean isDeletable()
```
  Specified by:
  
  isDeletable in class Displayable
- length
```
public int length()
```
  The number of clicked, backbone points in this pipe.
  
  Specified by:
  
  length in interface Line3D
- contains
```
public boolean contains(Layer layer,
                        double x,
                        double y)
```
  Test whether the Pipe contains the given point at the given layer. What it does: generates subpolygons that are present in the given layer, and tests whether the point is contained in any of them.
  
  Overrides:
  
  contains in class Displayable
- linkPatches
```
public boolean linkPatches()
```
  Scan the Display and link Patch objects that lay under this Pipe's bounding box.
  
  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
- 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
- getBackbone
```
public double[][] getBackbone()
```
  Returns a [p_i[0].length][4] array, with x,y,z,radius on the second part. Not translated to x,y but local!
- snapTo
```
public void snapTo(int cx,
                   int cy,
                   int x_p,
                   int y_p)
```
  x,y is the cursor position in offscreen coordinates.
  
  Overrides:
  
  snapTo in class Displayable
- exportXML
```
public void exportXML(StringBuilder sb_body,
                      String indent,
                      XMLOptions options)
```
  Exports data, the tag is not opened nor closed.
  
  Overrides:
  
  exportXML in class ZDisplayable
- exportDTD
```
public static void exportDTD(StringBuilder sb_header,
                             HashSet<String> hs,
                             String indent)
```
- generateMesh
```
public double[][][] generateMesh(double scale)
```
- 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 static List<Point3f> generateTriangles(double[][][] all_points,
                                              double scale)
```
  Accepts an arrays as that returned from methods generateJoints and makeTube: first dimension is the list of points, second dimension is the number of vertices defining the circular cross section of the tube, and third dimension is the x,y,z of each vertex.
- makeTube
```
public static double[][][] makeTube(double[] px,
                                    double[] py,
                                    double[] pz,
                                    double[] p_width_i,
                                    int resample,
                                    int parallels,
                                    ij.measure.Calibration cal)
```
- 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
- 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.
- intersects
```
public boolean intersects(Layer layer,
                          Rectangle r)
```
  Expects Rectangle in world coords.
  
  Overrides:
  
  intersects in class Displayable
- intersects
```
public boolean intersects(Layer layer,
                          Area area)
```
  Expects Area in world coords.
  
  Overrides:
  
  intersects in class Displayable
- getBounds
```
public Rectangle getBounds(Rectangle r,
                           Layer layer)
```
  Returns the bounds of this object as it shows in the given layer, set into @param r.
  
  Overrides:
  
  getBounds in class Displayable
- measure
```
public ij.measure.ResultsTable measure(ij.measure.ResultsTable rt)
```
  Description copied from class: Displayable
  
  Does nothing unless overriden.
  
  Overrides:
  
  measure in class Displayable
- reverse
```
public void reverse()
```
  Reverses the order of the points in the arrays.
- 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
- 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
- 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
```
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

Class Pipe

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_l

p_r

p_i

p_layer

p_width

p_width_i

Constructor Detail

Pipe

Pipe

Pipe

Method Detail

findPoint

removePoint

distance

dragPoint

resetControlPoints

dragControlPoint

addPoint

findClosestPoint

generateInterpolatedPoints

paint

keyPressed

mousePressed

mouseDragged

mouseReleased

calculateBoundingBox

calculateBoundingBox

destroy

flush

repaint

getPerimeter

toShapesFile

getPointsForSQL

getUpdatePointForSQL

isDeletable

length

contains

linkPatches

getFirstLayer

exportSVG

getBackbone

snapTo

exportXML

exportDTD

generateMesh

clone

generateTriangles

generateTriangles

makeTube

asVectorString3D

getInfo

intersects

intersects

intersects

getBounds

measure

reverse

crop

layerRemoved

apply

apply

getLayerIds

getAreaAt