Package loci.plugins.util

Class ROIHandler

java.lang.Object

loci.plugins.util.ROIHandler

public class ROIHandler
extends Object

Utility class for managing regions of interest within ImageJ. Capable of constructing ROIs within ImageJ's ROI manager matching those specified in an OME metadata store, and vice versa.

Constructor Summary

Constructors

Constructor	Description
ROIHandler()

Method Summary

Modifier and Type	Method	Description
static void	openROIs(loci.formats.meta.IMetadata retrieve, ImagePlus[] images)	Look for ROIs in the given OMEXMLMetadata; if any are present, apply them to the given images and display them in the ROI manager.
static void	openROIs(loci.formats.meta.IMetadata retrieve, ImagePlus[] images, boolean isOMERO)	Opens the rois and converts them into ImageJ Rois.
static void	openROIs(loci.formats.meta.IMetadata retrieve, ImagePlus[] images, boolean isOMERO, String roisMode)	Opens the rois and converts them into ImageJ Rois.
static Roi[]	readFromOverlays()	Returns rois if any from the overlay.
static Roi[]	readFromRoiManager()	Returns the rois if any stored in the ROI manager.
static void	saveROIs(loci.formats.meta.MetadataStore store)	Save ROIs in the ROI manager to the given MetadataStore.

Methods inherited from class java.lang.Object

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

Constructor Details

ROIHandler

public ROIHandler()

Method Details

openROIs

public static void openROIs(loci.formats.meta.IMetadata retrieve,
 ImagePlus[] images)

Look for ROIs in the given OMEXMLMetadata; if any are present, apply them to the given images and display them in the ROI manager.

openROIs

public static void openROIs(loci.formats.meta.IMetadata retrieve,
 ImagePlus[] images,
 boolean isOMERO)

Opens the rois and converts them into ImageJ Rois.

Parameters:

retrieve - The OMEXML store.

images - The imageJ object.

isOMERO - true if data stored in OMERO, false otherwise.

openROIs

public static void openROIs(loci.formats.meta.IMetadata retrieve,
 ImagePlus[] images,
 boolean isOMERO,
 String roisMode)

Opens the rois and converts them into ImageJ Rois.

Parameters:

retrieve - The OMEXML store.

images - The imageJ object.

isOMERO - true if data stored in OMERO, false otherwise.

roisMode - Determines whether to import Rois to overlay or RoiManager

readFromRoiManager

public static Roi[] readFromRoiManager()

Returns the rois if any stored in the ROI manager.

Returns:

See above.

readFromOverlays

public static Roi[] readFromOverlays()

Returns rois if any from the overlay.

Returns:

See above

saveROIs

public static void saveROIs(loci.formats.meta.MetadataStore store)

Save ROIs in the ROI manager to the given MetadataStore.

Parameters:

store - Where to store the rois.