Package fr.igred.omero.roi

Class GenericShapeWrapper<T extends ShapeData>

java.lang.Object

fr.igred.omero.GenericObjectWrapper<T>

fr.igred.omero.AnnotatableWrapper<T>

fr.igred.omero.roi.GenericShapeWrapper<T>

Type Parameters:

T - Subclass of ShapeData

Direct Known Subclasses:

EllipseWrapper, LineWrapper, MaskWrapper, PointWrapper, PolygonWrapper, PolylineWrapper, RectangleWrapper, TextWrapper

public abstract class GenericShapeWrapper<T extends ShapeData>
extends AnnotatableWrapper<T>

Generic class containing a ShapeData (or a subclass) object.

Field Summary

Fields

Modifier and Type	Field	Description
static String	ANNOTATION_LINK	Annotation link name for this type of object

Fields inherited from class fr.igred.omero.GenericObjectWrapper

data

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	GenericShapeWrapper(T s)	Constructor of the GenericShapeWrapper class using a ShapeData.

Method Summary

Modifier and Type	Method	Description
protected String	annotationLinkType()	Returns the type of annotation link for this object.
T	asShapeData()	Deprecated. Gets the ShapeData object contained.
protected void	copyFromIJRoi(Roi ijRoi)	Copies details from an ImageJ ROI (position, stroke color, stroke width).
protected void	copyToIJRoi(Roi ijRoi)	Copies details to an ImageJ ROI (name, position, stroke color, fill color, stroke width).
Shape	createTransformedAWTShape()	Returns a new Shape defined by the geometry of the specified Shape after it has been transformed by the transform.
RectangleWrapper	getBoundingBox()	Returns a new RectangleWrapper corresponding to the bounding box of the shape, once the related AffineTransform has been applied.
int	getC()	Gets the channel.
Color	getFill()	Gets ShapeData fill color.
double	getFontSize()	Gets ShapeData font size.
Color	getStroke()	Gets the ShapeData stroke color.
int	getT()	Sets the time-point.
abstract String	getText()	Gets the text on the ShapeData.
int	getZ()	Gets the z-section.
<A extends AnnotationData> void	link(Client client, A annotation)	Attach an AnnotationData to this object.
void	setC(int c)	Sets the channel.
void	setCZT(int c, int z, int t)	Sets the channel, z-section and time-point at once.
void	setFill(Color fillColour)	Sets the ShapeData fill color.
void	setFontSize(double value)	Sets ShapeData font size.
void	setStroke(Color strokeColour)	Sets ShapeData stroke color.
void	setT(int t)	Sets the time-point.
abstract void	setText(String text)	Sets the text on the ShapeData.
void	setTransform(double a00, double a10, double a01, double a11, double a02, double a12)	Sets the transform to the matrix specified by the 6 double precision values.
void	setTransform(AffineTransform transform)	Sets the transform from a AffineTransform.
void	setZ(int z)	Sets the z-section.
abstract Shape	toAWTShape()	Converts the shape to an Shape.
AffineTransform	toAWTTransform()	Converts AffineTransform to AffineTransform.
Roi	toImageJ()	Converts shape to ImageJ ROI.

Methods inherited from class fr.igred.omero.AnnotatableWrapper

addAndReplaceFile, addAndReplaceFile, addAndReplaceTable, addAndReplaceTable, addFile, addFileAnnotation, addKeyValuePair, addMapAnnotation, addPairKeyValue, addTable, addTag, addTag, addTag, addTags, addTags, copyAnnotationLinks, getAnnotations, getFileAnnotations, getKeyValuePairs, getMapAnnotations, getMyRating, getTable, getTables, getTags, getValue, isLinked, link, link, linkIfNotLinked, rate, removeLink, unlink

Methods inherited from class fr.igred.omero.GenericObjectWrapper

asDataObject, canAnnotate, canChgrp, canChown, canDelete, canEdit, canLink, delete, distinct, flatten, getCreated, getGroupId, getId, getOwner, saveAndUpdate, toString, wrap, wrap

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

ANNOTATION_LINK

public static final String ANNOTATION_LINK

Annotation link name for this type of object

See Also:

Constant Field Values

Constructor Detail

GenericShapeWrapper

protected GenericShapeWrapper(T s)

Constructor of the GenericShapeWrapper class using a ShapeData.

Parameters:

s - The shape.

Method Detail

copyFromIJRoi

protected void copyFromIJRoi(Roi ijRoi)

Copies details from an ImageJ ROI (position, stroke color, stroke width).

Parameters:

ijRoi - An ImageJ Roi.

copyToIJRoi

protected void copyToIJRoi(Roi ijRoi)

Copies details to an ImageJ ROI (name, position, stroke color, fill color, stroke width).

Parameters:

ijRoi - An ImageJ Roi.

asShapeData

@Deprecated
public T asShapeData()

Deprecated.

Gets the ShapeData object contained.

Returns:

the shape.

getC

public int getC()

Gets the channel.

Returns:

the channel. -1 if the shape applies to all channels of the image.

setC

public void setC(int c)

Sets the channel.

Parameters:

c - the channel. Pass -1 to remove z value, i.e. shape applies to all channels of the image.

getZ

public int getZ()

Gets the z-section.

Returns:

the z-section. -1 if the shape applies to all z-sections of the image.

setZ

public void setZ(int z)

Sets the z-section.

Parameters:

z - the z-section. Pass -1 to remove z value, i.e. shape applies to all z-sections of the image.

getT

public int getT()

Sets the time-point.

Returns:

the time-point. -1 if the shape applies to all time-points of the image.

setT

public void setT(int t)

Sets the time-point.

Parameters:

t - the time-point. Pass -1 to remove t value, i.e. shape applies to all time-points of the image.

setCZT

public void setCZT(int c,
                   int z,
                   int t)

Sets the channel, z-section and time-point at once.

Parameters:

c - the channel. Pass -1 to remove z value, i.e. shape applies to all channels of the image.

z - the z-section. Pass -1 to remove z value, i.e. shape applies to all z-sections of the image.

t - the time-point. Pass -1 to remove t value, i.e. shape applies to all time-points of the image.

getFontSize

public double getFontSize()

Gets ShapeData font size.

Returns:

The font size (in typography points)

setFontSize

public void setFontSize(double value)

Sets ShapeData font size.

Parameters:

value - The font size (in typography points)

getStroke

public Color getStroke()

Gets the ShapeData stroke color.

Returns:

The stroke color

setStroke

public void setStroke(Color strokeColour)

Sets ShapeData stroke color.

Parameters:

strokeColour - The stroke color

getFill

public Color getFill()

Gets ShapeData fill color.

Returns:

The fill color

setFill

public void setFill(Color fillColour)

Sets the ShapeData fill color.

Parameters:

fillColour - The fill color

getText

public abstract String getText()

Gets the text on the ShapeData.

Returns:

the text

setText

public abstract void setText(String text)

Sets the text on the ShapeData.

Parameters:

text - the text

toAWTShape

public abstract Shape toAWTShape()

Converts the shape to an Shape.

Returns:

The converted AWT Shape.

setTransform

public void setTransform(double a00,
                         double a10,
                         double a01,
                         double a11,
                         double a02,
                         double a12)

Sets the transform to the matrix specified by the 6 double precision values.

Parameters:

a00 - the X coordinate scaling element of the 3x3 matrix

a10 - the Y coordinate shearing element of the 3x3 matrix

a01 - the X coordinate shearing element of the 3x3 matrix

a11 - the Y coordinate scaling element of the 3x3 matrix

a02 - the X coordinate translation element of the 3x3 matrix

a12 - the Y coordinate translation element of the 3x3 matrix

setTransform

public void setTransform(AffineTransform transform)

Sets the transform from a AffineTransform.

Parameters:

transform - A Java AffineTransform.

toAWTTransform

public AffineTransform toAWTTransform()

Converts AffineTransform to AffineTransform.

Returns:

The converted affine transform.

createTransformedAWTShape

public Shape createTransformedAWTShape()

Returns a new Shape defined by the geometry of the specified Shape after it has been transformed by the transform.

Returns:

A new transformed Shape.

getBoundingBox

public RectangleWrapper getBoundingBox()

Returns a new RectangleWrapper corresponding to the bounding box of the shape, once the related AffineTransform has been applied.

Returns:

The bounding box.

toImageJ

public Roi toImageJ()

Converts shape to ImageJ ROI.

Returns:

An ImageJ ROI.

annotationLinkType

protected String annotationLinkType()

Returns the type of annotation link for this object.

Specified by:

annotationLinkType in class AnnotatableWrapper<T extends ShapeData>

Returns:

See above.

link

public <A extends AnnotationData> void link(Client client,
                                            A annotation)
                                     throws ServiceException,
                                            AccessException,
                                            ExecutionException

Attach an AnnotationData to this object.

Overrides:

link in class AnnotatableWrapper<T extends ShapeData>

Type Parameters:

A - The type of the annotation.

Parameters:

client - The client handling the connection.

annotation - The AnnotationData.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.