Package fr.igred.omero.roi

Class ROIWrapper

java.lang.Object

fr.igred.omero.ObjectWrapper<T>

fr.igred.omero.AnnotatableWrapper<ROIData>

fr.igred.omero.roi.ROIWrapper

All Implemented Interfaces:

Annotatable, RemoteObject, ROI

public class ROIWrapper
extends AnnotatableWrapper<ROIData>
implements ROI

Class containing a ROIData object.

Wraps function calls to the ROIData contained.

Field Summary

Fields

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

Fields inherited from class fr.igred.omero.ObjectWrapper

data

Fields inherited from interface fr.igred.omero.roi.ROI

IJ_PROPERTY

Constructor Summary

Constructors

Constructor	Description
ROIWrapper()	Constructor of the ROIWrapper class.
ROIWrapper(java.lang.Iterable<? extends Shape> shapes)	Constructor of the ROIWrapper class.
ROIWrapper(ROIData roi)	Constructor of the ROIWrapper class.

Method Summary

Modifier and Type	Method	Description
void	addShape(Shape shape)	Adds a Shape to the ROI.
protected java.lang.String	annotationLinkType()	Returns the type of annotation link for this object.
void	deleteShape(int pos)	Deletes a shape from the ROI.
void	deleteShape(ShapeData shape)	Deletes a ShapeData from the ROI.
static java.util.List<ROI>	fromImageJ(java.util.Collection<? extends Roi> ijRois)	Converts a collection of ImageJ ROIs to a list of OMERO ROIs
static java.util.List<ROI>	fromImageJ(java.util.Collection<? extends Roi> ijRois, java.lang.String property)	Converts a collection of ImageJ ROIs to a list of OMERO ROIs
java.lang.String	getName()	Gets the ROI name.
java.util.List<Shape>	getShapes()	Returns the list of shapes contained in the ROI.
void	saveROI(DataManager dm)	Saves the ROI.
void	setImage(Image image)	Sets the image linked to the ROI.
void	setName(java.lang.String name)	Sets the ROI name.

Methods inherited from class fr.igred.omero.AnnotatableWrapper

addAndReplaceFile, addAndReplaceTable, addKeyValuePair, addTag, addTag, getAnnotations, getFileAnnotations, getMapAnnotations, getMyRating, getTable, getTags, rate, removeLink, unlink

Methods inherited from class fr.igred.omero.ObjectWrapper

asDataObject, canAnnotate, canChgrp, canChown, canDelete, canEdit, canLink, 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

Methods inherited from interface fr.igred.omero.Annotatable

addAndReplaceFile, addAndReplaceFile, addAndReplaceTable, addAndReplaceTable, addFile, addKeyValuePair, addTable, addTag, addTag, addTags, copyAnnotationLinks, getAnnotationData, getAnnotations, getFileAnnotations, getKeyValuePairs, getMapAnnotations, getMyRating, getTable, getTables, getTags, getValues, isLinked, link, link, linkIfNotLinked, rate, unlink

Methods inherited from interface fr.igred.omero.RemoteObject

canAnnotate, canChgrp, canChown, canDelete, canEdit, canLink, getCreated, getGroupId, getId, getOwner, saveAndUpdate

Methods inherited from interface fr.igred.omero.roi.ROI

addShapes, asDataObject, getBounds, link, toImageJ, toImageJ

Field Detail

ANNOTATION_LINK

public static final java.lang.String ANNOTATION_LINK

Annotation link name for this type of object

See Also:

Constant Field Values

Constructor Detail

ROIWrapper

public ROIWrapper()

Constructor of the ROIWrapper class.

ROIWrapper

public ROIWrapper(java.lang.Iterable<? extends Shape> shapes)

Constructor of the ROIWrapper class.

Parameters:

shapes - List of shapes to add to the ROIData.

ROIWrapper

public ROIWrapper(ROIData roi)

Constructor of the ROIWrapper class.

Parameters:

roi - The ROIData to wrap.

Method Detail

fromImageJ

public static java.util.List<ROI> fromImageJ(java.util.Collection<? extends Roi> ijRois)

Converts a collection of ImageJ ROIs to a list of OMERO ROIs

Parameters:

ijRois - A collection of ImageJ ROIs.

Returns:

The converted list of OMERO ROIs.

fromImageJ

public static java.util.List<ROI> fromImageJ(java.util.Collection<? extends Roi> ijRois,
                                             java.lang.String property)

Converts a collection of ImageJ ROIs to a list of OMERO ROIs

Parameters:

ijRois - A collection of ImageJ ROIs.

property - The property used to store the 4D ROI local index/label. Defaults to "ROI" if null or empty.

Returns:

The converted list of OMERO ROIs.

getName

public java.lang.String getName()

Gets the ROI name.

Specified by:

getName in interface ROI

Returns:

The ROI name (can be null).

setName

public void setName(java.lang.String name)

Sets the ROI name.

Specified by:

setName in interface ROI

Parameters:

name - The ROI name.

addShape

public void addShape(Shape shape)

Adds a Shape to the ROI.

Specified by:

addShape in interface ROI

Parameters:

shape - Shape to add.

getShapes

public java.util.List<Shape> getShapes()

Returns the list of shapes contained in the ROI.

Specified by:

getShapes in interface ROI

Returns:

See above.

setImage

public void setImage(Image image)

Sets the image linked to the ROI.

Specified by:

setImage in interface ROI

Parameters:

image - Image linked to the ROI.

deleteShape

public void deleteShape(ShapeData shape)

Deletes a ShapeData from the ROI.

Specified by:

deleteShape in interface ROI

Parameters:

shape - ShapeData to delete.

deleteShape

public void deleteShape(int pos)

Deletes a shape from the ROI.

Specified by:

deleteShape in interface ROI

Parameters:

pos - Position of the ShapeData in the ShapeData list from the ROI.

Throws:

java.lang.IndexOutOfBoundsException - If pos is out of the ShapeData list bounds.

saveROI

public void saveROI(DataManager dm)
             throws ServiceException,
                    AccessException,
                    java.util.concurrent.ExecutionException

Saves the ROI.

Specified by:

saveROI in interface ROI

Parameters:

dm - The data manager.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

annotationLinkType

protected java.lang.String annotationLinkType()

Returns the type of annotation link for this object.

Specified by:

annotationLinkType in class AnnotatableWrapper<ROIData>

Returns:

See above.