fr.igred.omero.roi

Interface ROI

All Superinterfaces:

Annotatable, RemoteObject

All Known Implementing Classes:

ROIWrapper

public interface ROI
extends Annotatable

Interface to handle ROIs on OMERO.

Field Summary

Fields

Modifier and Type	Field and Description
static String	IJ_PROPERTY Default IJ property to store ROI local labels / indices.

Method Summary

Modifier and Type	Method and Description
void	addShape(Shape shape) Adds a Shape to the ROI.
default void	addShapes(Iterable<? extends Shape> shapes) Adds shape objects from a list of shapes to the ROI.
ROIData	asDataObject() Returns a ROIData corresponding to the handled object.
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<ROI>	fromImageJ(Collection<? extends Roi> ijRois, String property, Supplier<? extends ROI> constructor, Function<? super Roi,? extends Iterable<? extends Shape>> converter) Converts a collection of ImageJ ROIs to a list of OMERO ROIs using the provided constructor and shape converter.
static List<ROI>	fromImageJ(Collection<? extends Roi> ijRois, Supplier<? extends ROI> constructor, Function<? super Roi,Iterable<? extends Shape>> converter) Converts an ImageJ list of ROIs to a list of OMERO ROIs using the provided constructor and shape converter.
default Bounds	getBounds() Returns the 5D bounds containing the ROI.
String	getName() Gets the ROI name.
List<Shape>	getShapes() Returns the list of shapes contained in the ROI.
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).
default <A extends AnnotationData> void	link(DataManager dm, A annotation) Attach an AnnotationData to this object.
void	saveROI(DataManager dm) Saves the ROI.
void	setImage(Image image) Sets the image linked to the ROI.
void	setName(String name) Sets the ROI name.
default List<Roi>	toImageJ() Converts the ROI to a list of ImageJ ROIs.
static List<Roi>	toImageJ(Collection<? extends ROI> rois) Converts a collection of OMERO ROIs to a list of ImageJ ROIs.
static List<Roi>	toImageJ(Collection<? extends ROI> rois, String property) Converts a collection of OMERO ROIs to a list of ImageJ ROIs.
static List<Roi>	toImageJ(Collection<? extends ROI> rois, String property, boolean groupRois) Converts a collection of OMERO ROIs to a list of ImageJ ROIs.
default List<Roi>	toImageJ(String property) Converts the ROI to a list of ImageJ ROIs.

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, distinct, flatten, getCreated, getElementsOf, getGroupId, getId, getOwner, getUpdated, saveAndUpdate

Field Detail

IJ_PROPERTY

static final String IJ_PROPERTY

Default IJ property to store ROI local labels / indices.

See Also:

Constant Field Values

Method Detail

checkProperty

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

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

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

static List<ROI> fromImageJ(Collection<? extends Roi> ijRois,
                            Supplier<? extends ROI> constructor,
                            Function<? super Roi,Iterable<? extends Shape>> converter)

Converts an ImageJ list of ROIs to a list of OMERO ROIs using the provided constructor and shape converter.

Parameters:

ijRois - A collection of ImageJ ROIs.

constructor - A constructor to create ROI instances.

converter - A function to convert an IJ Roi to a list of OMERO Shapes.

Returns:

The converted list of OMERO ROIs.

fromImageJ

static List<ROI> fromImageJ(Collection<? extends Roi> ijRois,
                            String property,
                            Supplier<? extends ROI> constructor,
                            Function<? super Roi,? extends Iterable<? extends Shape>> converter)

Converts a collection of ImageJ ROIs to a list of OMERO ROIs using the provided constructor and shape converter.

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.

constructor - A constructor to create ROI instances.

converter - A function to convert an IJ Roi to a list of OMERO Shapes.

Returns:

The converted list of OMERO ROIs.

toImageJ

static List<Roi> toImageJ(Collection<? extends ROI> rois)

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

Parameters:

rois - A collection of OMERO ROIs.

Returns:

The converted list of ImageJ ROIs.

toImageJ

static List<Roi> toImageJ(Collection<? extends ROI> rois,
                          String property)

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

Parameters:

rois - A collection 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

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

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

Parameters:

rois - A collection 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.

asDataObject

ROIData asDataObject()

Returns a ROIData corresponding to the handled object.

Specified by:

asDataObject in interface RemoteObject

Returns:

See above.

getName

String getName()

Gets the ROI name.

Returns:

The ROI name (can be null).

setName

void setName(String name)

Sets the ROI name.

Parameters:

name - The ROI name.

addShapes

default void addShapes(Iterable<? extends Shape> shapes)

Adds shape objects from a list of shapes to the ROI.

Parameters:

shapes - List of Shape.

addShape

void addShape(Shape shape)

Adds a Shape to the ROI.

Parameters:

shape - Shape to add.

getShapes

List<Shape> getShapes()

Returns the list of shapes contained in the ROI.

Returns:

See above.

setImage

void setImage(Image image)

Sets the image linked to the ROI.

Parameters:

image - Image linked to the ROI.

deleteShape

void deleteShape(ShapeData shape)

Deletes a ShapeData from the ROI.

Parameters:

shape - ShapeData to delete.

deleteShape

void deleteShape(int pos)

Deletes a shape from the ROI.

Parameters:

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

Throws:

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

saveROI

void saveROI(DataManager dm)
      throws ServiceException,
             AccessException,
             ExecutionException

Saves the ROI.

Parameters:

dm - The data manager.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getBounds

default Bounds getBounds()

Returns the 5D bounds containing the ROI.

Returns:

The 5D bounds.

toImageJ

default List<Roi> toImageJ()

Converts the ROI to a list of ImageJ ROIs.

Returns:

A list of ROIs.

toImageJ

default 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.

link

default <A extends AnnotationData> void link(DataManager dm,
                                             A annotation)
                                      throws ServiceException,
                                             AccessException,
                                             ExecutionException

Attach an AnnotationData to this object.

Specified by:

link in interface Annotatable

Type Parameters:

A - The type of the annotation.

Parameters:

dm - 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.