Package fr.igred.omero.roi

Class ROIWrapper

java.lang.Object

fr.igred.omero.GenericObjectWrapper<T>

fr.igred.omero.AnnotatableWrapper<ROIData>

fr.igred.omero.roi.ROIWrapper

public class ROIWrapper
extends AnnotatableWrapper<ROIData>

Class containing a ROIData object.

Wraps function calls to the ROIData contained.

Field Summary

Fields

Modifier and Type	Field	Description
static String	ANNOTATION_LINK	Annotation link name for this type of object
static String	IJ_PROPERTY	Default IJ property to store ROI local labels / indices.

Fields inherited from class fr.igred.omero.GenericObjectWrapper

data

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
void	addShape(GenericShapeWrapper<?> shape)	Adds a ShapeData from a GenericShapeWrapper to the ROIData
void	addShapes(List<? extends GenericShapeWrapper<?>> shapes)	Adds ShapeData objects from a list of GenericShapeWrapper to the ROIData
protected String	annotationLinkType()	Returns the type of annotation link for this object.
ROIData	asROIData()	Deprecated. Returns the ROIData contained.
static String	checkProperty(String property)	Checks the provided property.
void	deleteShape(int pos)	Deletes a shape from the ROI.
void	deleteShape(ShapeData shape)	Deletes a ShapeData from the ROI.
static List<ROIWrapper>	fromImageJ(List<? extends Roi> ijRois)	Converts an ImageJ list of ROIs to a list of OMERO ROIs
static List<ROIWrapper>	fromImageJ(List<? extends Roi> ijRois, String property)	Converts an ImageJ list of ROIs to a list of OMERO ROIs
PixelsWrapper.Bounds	getBounds()	Returns the 5D bounds containing the ROI.
String	getName()	Gets the ROI name.
ShapeList	getShapes()	Returns the list of shapes contained in the ROIData.
static String	ijIDProperty(String property)	Returns the ID property corresponding to the input local index/label property (appends "_ID" to said property).
static String	ijNameProperty(String property)	Returns the ID property corresponding to the input local index/label property (appends "_NAME" to said property).
protected <A extends AnnotationData> void	link(Client client, A annotation)	Attach an AnnotationData to this object.
void	saveROI(Client client)	Saves the ROI.
void	setData(ROIData data)	Deprecated. Changes the wrapped data.
void	setImage(ImageWrapper image)	Sets the image linked to the ROI.
void	setName(String name)	Sets the ROI name.
List<Roi>	toImageJ()	Converts the ROI to a list of ImageJ ROIs.
List<Roi>	toImageJ(String property)	Converts the ROI to a list of ImageJ ROIs.
static List<Roi>	toImageJ(Collection<? extends ROIWrapper> rois, String property, boolean groupRois)	Converts an OMERO list of ROIs to a list of ImageJ ROIs
static List<Roi>	toImageJ(List<? extends ROIWrapper> rois)	Converts an OMERO list of ROIs to a list of ImageJ ROIs
static List<Roi>	toImageJ(List<? extends ROIWrapper> rois, String property)	Converts an OMERO list of ROIs to a list of ImageJ ROIs

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, getRatings, getTable, getTables, getTags, getValue, isLinked, link, link, linkIfNotLinked, rate, removeLink, removeLinks, unlink, unlink

Methods inherited from class fr.igred.omero.GenericObjectWrapper

asDataObject, canAnnotate, canChgrp, canChown, canDelete, canEdit, canLink, distinct, flatten, getCreated, getGroupId, getId, getOwner, getUpdated, 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

IJ_PROPERTY

public static final String IJ_PROPERTY

Default IJ property to store ROI local labels / indices.

See Also:

Constant Field Values

Constructor Detail

ROIWrapper

public ROIWrapper()

Constructor of the ROIWrapper class.

ROIWrapper

public ROIWrapper(Iterable<? extends GenericShapeWrapper<?>> 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

checkProperty

public static String checkProperty(String property)

Checks the provided property.

Parameters:

property - The property where the 4D ROI local index/label is stored.

Returns:

The property, or the default value IJ_PROPERTY (= "ROI") if it is null or empty.

ijIDProperty

public static String ijIDProperty(String property)

Returns the ID property corresponding to the input local index/label property (appends "_ID" to said property).

Parameters:

property - The property where the 4D ROI local index/label is stored. Defaults to "ROI" if null or empty.

Returns:

See above.

ijNameProperty

public static String ijNameProperty(String property)

Returns the ID property corresponding to the input local index/label property (appends "_NAME" to said property).

Parameters:

property - The property where the 4D ROI local index/label is stored. Defaults to "ROI" if null or empty.

Returns:

See above.

fromImageJ

public static List<ROIWrapper> fromImageJ(List<? extends Roi> ijRois)

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

Parameters:

ijRois - A list of ImageJ ROIs.

Returns:

The converted list of OMERO ROIs.

fromImageJ

public static List<ROIWrapper> fromImageJ(List<? extends Roi> ijRois,
                                          String property)

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

Parameters:

ijRois - A list 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.

toImageJ

public static List<Roi> toImageJ(List<? extends ROIWrapper> rois)

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

Parameters:

rois - A list of OMERO ROIs.

Returns:

The converted list of ImageJ ROIs.

toImageJ

public static List<Roi> toImageJ(List<? extends ROIWrapper> rois,
                                 String property)

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

Parameters:

rois - A list of OMERO 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 ImageJ ROIs.

toImageJ

public static List<Roi> toImageJ(Collection<? extends ROIWrapper> rois,
                                 String property,
                                 boolean groupRois)

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

Parameters:

rois - A list of OMERO ROIs.

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

groupRois - Whether ImageJ Rois belonging to the same OMERO ROI should be grouped or not.

Returns:

The converted list of ImageJ ROIs.

getName

public String getName()

Gets the ROI name.

Returns:

The ROI name (can be null).

setName

public void setName(String name)

Sets the ROI name.

Parameters:

name - The ROI name.

setData

@Deprecated
public void setData(ROIData data)

Deprecated.

Changes the wrapped data.

Parameters:

data - The ROI data.

addShapes

public void addShapes(List<? extends GenericShapeWrapper<?>> shapes)

Adds ShapeData objects from a list of GenericShapeWrapper to the ROIData

Parameters:

shapes - List of GenericShapeWrapper.

addShape

public void addShape(GenericShapeWrapper<?> shape)

Adds a ShapeData from a GenericShapeWrapper to the ROIData

Parameters:

shape - GenericShapeWrapper to add.

getShapes

public ShapeList getShapes()

Returns the list of shapes contained in the ROIData.

Returns:

list of shape contained in the ROIData.

setImage

public void setImage(ImageWrapper image)

Sets the image linked to the ROI.

Parameters:

image - Image linked to the ROIData.

asROIData

@Deprecated
public ROIData asROIData()

Deprecated.

Returns the ROIData contained. Use GenericObjectWrapper.asDataObject() instead.

Returns:

the ROIData contained.

deleteShape

public void deleteShape(ShapeData shape)

Deletes a ShapeData from the ROI.

Parameters:

shape - ShapeData to delete.

deleteShape

public void deleteShape(int pos)

Deletes a shape from the ROI.

Parameters:

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

Throws:

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

saveROI

public void saveROI(Client client)
             throws OMEROServerError,
                    ServiceException

Saves the ROI.

Parameters:

client - The client handling the connection.

Throws:

ServiceException - Cannot connect to OMERO.

OMEROServerError - Server error.

getBounds

public PixelsWrapper.Bounds getBounds()

Returns the 5D bounds containing the ROI.

Returns:

The 5D bounds.

toImageJ

public List<Roi> toImageJ()

Converts the ROI to a list of ImageJ ROIs.

Returns:

A list of ROIs.

toImageJ

public List<Roi> toImageJ(String property)

Converts the ROI to a list of ImageJ ROIs.

Parameters:

property - The property where the 4D ROI local index will be stored.

Returns:

A list of ROIs.

annotationLinkType

protected String annotationLinkType()

Returns the type of annotation link for this object.

Specified by:

annotationLinkType in class AnnotatableWrapper<ROIData>

Returns:

See above.

link

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

Attach an AnnotationData to this object.

Overrides:

link in class AnnotatableWrapper<ROIData>

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.