Profile (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- ini.trakem2.persistence.DBObject
- - ini.trakem2.display.Displayable
  - - ini.trakem2.display.Profile

All Implemented Interfaces:

Paintable, VectorData
```
public class Profile
extends Displayable
implements VectorData
```
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. TODO - label not implemented yet. - can't paint segments in different colors yet - the whole curve is updated when only a particular set of points needs readjustment - also, points are smooth, and options should be given to make them non-smooth.

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 boolean`	`closed` Paint/behave as open or closed curve.
`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 double[][]`	`p_r` The array of right control points, one for each clicked point.

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
`Profile(Project project, long id, HashMap<String,String> ht, HashMap<Displayable,String> ht_links)` Construct a Bezier Profile from an XML entry.
`Profile(Project project, long id, String title, float alpha, boolean visible, Color color, double[][][] bezarr, boolean closed, boolean locked, AffineTransform at)` Construct a Bezier Profile from the database.
`Profile(Project project, long id, String title, float width, float height, float alpha, boolean visible, Color color, boolean closed, boolean locked, AffineTransform at)` Construct a Bezier Profile from the database, but the points will be loaded later, when actually needed, by calling setupForDisplay().
`Profile(Project project, String title, double x, double y)` A new user-requested Profile.
`Profile(Project project, String title, double x, double y, Point2D.Double[] points)` Construct a Bezier Profile object from a set of points mixed in this pattern: PCCPCCPCCPCCP , so, [PCC]n where P = backbone point and C = control point.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected int`	`addPoint(double x_p, double y_p, double magnification, double bezier_finess)` Add a point either at the end or between two existing points, with accuracy depending on magnification.
`protected void`	`addPointsAtBegin(double[][] new_p_l, double[][] new_p, double[][] new_p_r)`
`protected void`	`addPointsAtEnd(double[][] new_p_l, double[][] new_p, double[][] new_p_r)`
`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)`
`void`	`cache()` Cache this Profile if needed.
`protected void`	`calculateBoundingBox()`
`protected void`	`calculateBoundingBox(boolean adjust_position)` Calculate the bounding box of the curve in the shape of a Rectangle defined by x,y,width,height.
`boolean`	`canSendTo(Layer target_layer)` Returns false if the target_layer contains a profile that is directly linked to this profile.
`Displayable`	`clone(Project pr, boolean copy_id)` Performs a deep copy of this object, unlocked and visible.
`double`	`computeArea()` Calibrated, in units as specified at getLayerSet().getCalibration().getUnit() -- returns zero if this profile is not closed.
`double`	`computeLength()` Calibrated for pixel width only (that is, it assumes pixel aspect ratio 1:1), in units as specified at getLayerSet().getCalibration().getUnit()
`boolean`	`containsPoint(int x_p, int y_p)` Check if the given point (usually from a MOUSE_PRESSED MouseEvent) is contained within the boundaries of this object.
`void`	`destroy()` Release all memory resources taken by this object.
`protected double`	`distance(double x1, double y1, double x2, double y2)` Calculate distance from one point to another.
`protected void`	`dragControlPoint(int index, double x_d, double 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.
`protected void`	`enlargeArrays()` Increase the size of the arrays by 5 points.
`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)` The oid is this objects' id, whereas the 'id' tag will be the id of the wrapper Thing object.
`protected int`	`findClosestPoint(double x_p, double 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, double x_p, double y_p, double magnification)` Find a point in an array 'a', 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)`
`static List<Point3f>`	`generateTriangles(ProjectThing pt, double scale)` Takes a profile_list, scans for its Profile children, makes sublists of continuous profiles (if they happen to be branched), and then creates triangles for them using weighted vector strings.
`double[][][]`	`getBezierArrays()` Returns a triple array, each containing a [2][n_points] array specifiying the x,y of each left control point, backbone point and right control point respectively.
`protected double[][]`	`getFirstPoint()`
`protected double[][]`	`getLastPoint()`
`int`	`getNearestPointIndex(double x_p, double y_p)`
`Polygon`	`getPerimeter()` The perimeter of this profile, in integer precision.
`VectorString2D`	`getPerimeter2D()` Returns the interpolated points as a VectorString2D, calibrated.
`int`	`getPointCount()` Returns the number of backbone points.
`boolean`	`hasPoints()`
`void`	`insertBetween(int startIndex, int endIndex, double[][] tmp_p_l, double[][] tmp_p, double[][] tmp_p_r)`
`boolean`	`isClosed()`
`boolean`	`isDeletable()`
`boolean`	`isLinked()` Returns true if it's linked to at least one patch in the same Layer.
`boolean`	`isRoughlyInside(Layer layer, Rectangle r)` If this Displayable intersects with @param r or almost intersects, then returns true.
`void`	`keyPressed(KeyEvent ke)`
`static ij.measure.ResultsTable`	`measure(Profile[] profiles, ij.measure.ResultsTable rt, long profile_list_id)` Assumes Z-coord sorted list of profiles, as stored in a "profile_list" ProjectThing type.
`ij.measure.ResultsTable`	`measure(ij.measure.ResultsTable rt)` Measures the calibrated length, the lateral surface as the length times the layer thickness, and the volume (if closed) as the area times the layer thickness.
`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)` Execute the mouseDragged MouseEvent on this Profile.
`void`	`mousePressed(MouseEvent me, Layer layer, int x_p, int y_p, double mag)` Execute the mousePressed MouseEvent on this Profile.
`void`	`mouseReleased(MouseEvent me, Layer layer, int x_p, int y_p, int x_d, int y_d, int x_r, int y_r)` Execute the mouseReleased MouseEvent on this Profile.
`void`	`paint(Graphics2D g, Rectangle srcRect, double magnification, boolean active, int channels, Layer active_layer, List<Layer> layers)`
`void`	`printPoints()`
`protected boolean`	`remove2(boolean check)` Remove also from the trees if present; does nothing more than remove(boolean) unless overriden.
`protected void`	`removePoint(int index)` Remove a point from the bezier backbone and its two associated control points.
`void`	`repaint()` Repaint this Displayable in all Display instances that are showing it.
`void`	`repaint(boolean repaint_navigator)` Repaints in the given ImageCanvas only the area corresponding to the bounding box of this Profile.
`protected void`	`resetControlPoints(int index)` Set the control points to the same value as the backbone point which they control.
`void`	`setColor(Color c)`
`protected void`	`setPoints(double[][] p_l, double[][] p, double[][] p_r)`
`void`	`setPoints(double[][] p_l, double[][] p, double[][] p_r, boolean update)`
`void`	`snapTo(int cx, int cy, int x_p, int y_p)` x,y is the cursor position in offscreen coordinates.
`boolean`	`softRemove()` Does nothing.
`void`	`toggleClosed()` Toggle curve closed/open.
`void`	`toShapesFile(StringBuffer data, String group, String color, double z_scale)` Writes the data of this object as a Bezier object in the .shapes file represented by the 'data' StringBuffer.

Methods inherited from class ini.trakem2.display.Displayable
adjustProperties, areThereLayerCrossLinks, clone, clone, commonDTDChildren, contains, contains, deselect, displacePoints, exportDTD, findById, findNearestPoint, findNearestPoint, getAffineTransform, getAffineTransformCopy, getAlpha, getAnnotation, getArea, getAreaAt, getAreaForBucket, getBoundingBox, getBoundingBox, getBoundingBox, getBounds, getBounds, getBucketable, getColor, getComposite, getComposite, getCompositeMode, getHeight, getIntersection, getLayer, getLayerIds, getLayerSet, 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, isLocked, isLocked2, isOnlyLinkedTo, isOnlyLinkedTo, isOutOfRepaintingClip, isOutOfRepaintingClip, isVisible, link, link, linkPatches, makeAdjustPropertiesDialog, mouseWheelMoved, paintAsBox, paintOffscreen, paintSnapshot, preConcatenate, prePaint, preTransform, processAdjustPropertiesDialog, remove, removeLinkedProperties, removeLinkedPropertiesFromOrigins, restXML, rotate, rotate, rotatePoints, scale, scale, scalePoints, setAffineTransform, setAlpha, setAlpha, setAnnotation, setCompositeMode, setDimensions, setDimensions, setLayer, setLayer, setLinkedProperties, setLinkedProperty, setLocation, setLocked, setProperty, setTitle, setVisible, setVisible, toString, transform, transformPoint, transformPoint, transformPoints, transformPoints, transformPoints, transformPoints, transformPoints, transformPoints, transformPoints, transformPoints, transformPoints, transformRectangle, translate, translate, unlink, unlink, unlinkAll, updateBucket, updateInDatabase, xmlError, xmlError

Methods inherited from class ini.trakem2.persistence.DBObject
addToDatabase, getId, getInfo, 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_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.
- closed
```
protected boolean closed
```
  Paint/behave as open or closed curve.

Constructor Detail

Profile

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

A new user-requested Profile.

Profile
```
public Profile(Project project,
               String title,
               double x,
               double y,
               Point2D.Double[] points)
```
Construct a Bezier Profile object from a set of points mixed in this pattern: PCCPCCPCCPCCP , so, [PCC]n where P = backbone point and C = control point. This results from a BezierApproximation on a path of points as drawed with the mouse. Keep in mind the control points will NOT have the same tangents, but this may be either left like that or corrected with some smoothing algorithm.

Profile

public Profile(Project project,
               long id,
               String title,
               float alpha,
               boolean visible,
               Color color,
               double[][][] bezarr,
               boolean closed,
               boolean locked,
               AffineTransform at)

Construct a Bezier Profile from the database.

Profile

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

Construct a Bezier Profile from the database, but the points will be loaded later, when actually needed, by calling setupForDisplay().

Profile

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

Construct a Bezier Profile from an XML entry.

Method Detail

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

getPointCount
```
public int getPointCount()
```
Returns the number of backbone points.

isClosed
```
public boolean isClosed()
```

findPoint

protected int findPoint(double[][] a,
                        double x_p,
                        double y_p,
                        double magnification)

Find a point in an array 'a', with a precision dependent on the magnification.

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

distance

protected 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.

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,
                                double x_d,
                                double 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(double x_p,
                       double y_p,
                       double magnification,
                       double bezier_finess)
```
Add a point either at the end or between two existing points, with accuracy depending on magnification. Does not update the database. x_p,y_p are in the local space.

findClosestPoint

protected int findClosestPoint(double x_p,
                               double y_p,
                               double magnification,
                               double bezier_finess)

Find the closest point to an interpolated point with precision depending upon magnification. The point x_p,y_p is in local coordinates.

toggleClosed
```
public void toggleClosed()
```
Toggle curve closed/open.

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

mousePressed

public void mousePressed(MouseEvent me,
                         Layer layer,
                         int x_p,
                         int y_p,
                         double mag)

Execute the mousePressed MouseEvent on this Profile.

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)

Execute the mouseDragged MouseEvent on this Profile.

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)

Execute the mouseReleased MouseEvent on this Profile.

Overrides:: mouseReleased in class Displayable

calculateBoundingBox
```
protected void calculateBoundingBox()
```

calculateBoundingBox
```
protected void calculateBoundingBox(boolean adjust_position)
```
Calculate the bounding box of the curve in the shape of a Rectangle defined by x,y,width,height. If adjust_position is true, then points are made local to the minimal x,y.

repaint
```
public void repaint()
```
Description copied from class: Displayable

Repaint this Displayable in all Display instances that are showing it.

Overrides:

repaint in class Displayable

repaint
```
public void repaint(boolean repaint_navigator)
```
Repaints in the given ImageCanvas only the area corresponding to the bounding box of this Profile.

containsPoint
```
public boolean containsPoint(int x_p,
                             int y_p)
```
Check if the given point (usually from a MOUSE_PRESSED MouseEvent) is contained within the boundaries of this object. The point is expected as local coordinates.

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

Overrides:

destroy in class Displayable

cache
```
public void cache()
```
Cache this Profile if needed.

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 perimeter of this profile, 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 Bezier object in the .shapes file represented by the 'data' StringBuffer. The z_scale is added to manually correct for sample squashing under the coverslip.

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

getBezierArrays
```
public double[][][] getBezierArrays()
```
Returns a triple array, each containing a [2][n_points] array specifiying the x,y of each left control point, backbone point and right control point respectively. All of them are copies.

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

isDeletable in class Displayable

isLinked
```
public boolean isLinked()
```
Returns true if it's linked to at least one patch in the same Layer. Otherwise returns false.

Overrides:

isLinked in class Displayable

canSendTo
```
public boolean canSendTo(Layer target_layer)
```
Returns false if the target_layer contains a profile that is directly linked to this profile.

Overrides:

canSendTo in class Displayable

getFirstPoint
```
protected double[][] getFirstPoint()
```

getLastPoint
```
protected double[][] getLastPoint()
```

hasPoints
```
public boolean hasPoints()
```

setPoints

protected void setPoints(double[][] p_l,
                         double[][] p,
                         double[][] p_r)

setPoints

public void setPoints(double[][] p_l,
                      double[][] p,
                      double[][] p_r,
                      boolean update)

addPointsAtBegin

protected void addPointsAtBegin(double[][] new_p_l,
                                double[][] new_p,
                                double[][] new_p_r)

addPointsAtEnd

protected void addPointsAtEnd(double[][] new_p_l,
                              double[][] new_p,
                              double[][] new_p_r)

getNearestPointIndex

public int getNearestPointIndex(double x_p,
                                double y_p)

insertBetween

public void insertBetween(int startIndex,
                          int endIndex,
                          double[][] tmp_p_l,
                          double[][] tmp_p,
                          double[][] tmp_p_r)

printPoints
```
public void printPoints()
```

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)
```
Description copied from class: Displayable

The oid is this objects' id, whereas the 'id' tag will be the id of the wrapper Thing object.

Overrides:

exportXML in class Displayable

exportDTD

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

getPerimeter2D
```
public VectorString2D getPerimeter2D()
```
Returns the interpolated points as a VectorString2D, calibrated. Returns null if there aren't any points.

keyPressed
```
public void keyPressed(KeyEvent ke)
```
Overrides:

keyPressed in class Displayable

setColor
```
public void setColor(Color c)
```
Overrides:

setColor in class Displayable

clone
```
public Displayable clone(Project pr,
                         boolean copy_id)
```
Performs a deep copy of this object, unlocked and visible.

Specified by:

clone in class Displayable

generateTriangles
```
public static List<Point3f> generateTriangles(ProjectThing pt,
                                              double scale)
```
Takes a profile_list, scans for its Profile children, makes sublists of continuous profiles (if they happen to be branched), and then creates triangles for them using weighted vector strings.

softRemove
```
public boolean softRemove()
```
Does nothing.

Overrides:

softRemove in class Displayable

remove2
```
protected boolean remove2(boolean check)
```
Description copied from class: Displayable

Remove also from the trees if present; does nothing more than remove(boolean) unless overriden.

Overrides:

remove2 in class Displayable

computeLength
```
public double computeLength()
```
Calibrated for pixel width only (that is, it assumes pixel aspect ratio 1:1), in units as specified at getLayerSet().getCalibration().getUnit()

computeArea
```
public double computeArea()
```
Calibrated, in units as specified at getLayerSet().getCalibration().getUnit() -- returns zero if this profile is not closed.

measure
```
public ij.measure.ResultsTable measure(ij.measure.ResultsTable rt)
```
Measures the calibrated length, the lateral surface as the length times the layer thickness, and the volume (if closed) as the area times the layer thickness.

Overrides:

measure in class Displayable

measure

public static ij.measure.ResultsTable measure(Profile[] profiles,
                                              ij.measure.ResultsTable rt,
                                              long profile_list_id)

Assumes Z-coord sorted list of profiles, as stored in a "profile_list" ProjectThing type. .

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

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 Profile

Nested Class Summary

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

Field Summary

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.Displayable

Methods inherited from class ini.trakem2.persistence.DBObject

Methods inherited from class java.lang.Object

Field Detail

n_points

p

p_l

p_r

p_i

closed

Constructor Detail

Profile

Profile

Profile

Profile

Profile

Method Detail

enlargeArrays

getPointCount

isClosed

findPoint

removePoint

distance

dragPoint

resetControlPoints

dragControlPoint

addPoint

findClosestPoint

toggleClosed

generateInterpolatedPoints

paint

mousePressed

mouseDragged

mouseReleased

calculateBoundingBox

calculateBoundingBox

repaint

repaint

containsPoint

destroy

cache

flush

getPerimeter

toShapesFile

exportSVG

getBezierArrays

isDeletable

isLinked

canSendTo

getFirstPoint

getLastPoint

hasPoints

setPoints

setPoints

addPointsAtBegin

addPointsAtEnd

getNearestPointIndex

insertBetween

printPoints

snapTo

exportXML

exportDTD

getPerimeter2D

keyPressed

setColor

clone

generateTriangles

softRemove

remove2

computeLength

computeArea

measure