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.

Author:

Melissa Linkert melissa at glencoesoftware.com

Constructor Summary

Constructors

Constructor and Description
ROIHandler()

Method Summary

Methods

Modifier and Type	Method and Description
static void	openROIs(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(IMetadata retrieve, ImagePlus[] images, boolean isOMERO)
private static int[][]	parsePoints(String points) Parse (x, y) coordinates from a String returned by MetadataRetrieve.getPolygonpoints(...) or MetadataRetrieve.getPolylinepoints(...)
static Roi[]	readFromOverlays()
static Roi[]	readFromRoiManager()
static void	saveROIs(MetadataStore store) Save ROIs in the ROI manager to the given MetadataStore.
private static void	storeLine(Line roi, MetadataStore store, int roiNum, int shape) Store a Line ROI in the given MetadataStore.
private static void	storeOval(OvalRoi roi, MetadataStore store, int roiNum, int shape) Store an Oval ROI in the given MetadataStore.
private static void	storePoint(PointRoi roi, MetadataStore store, int roiNum, int shape)
private static void	storePolygon(PolygonRoi roi, MetadataStore store, int roiNum, int shape) Store a Polygon ROI in the given MetadataStore.
private static void	storeRectangle(Roi roi, MetadataStore store, int roiNum, int shape) Store an Roi (rectangle) in the given MetadataStore.
private static void	storeText(TextRoi roi, MetadataStore store, int roiNum, int shape)
private static Color	toOMExmlColor(Color color)
private static NonNegativeInteger	unwrap(int r)

Methods inherited from class java.lang.Object

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

Constructor Detail

ROIHandler

public ROIHandler()

Method Detail

openROIs

public static void openROIs(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(IMetadata retrieve,
            ImagePlus[] images,
            boolean isOMERO)

readFromRoiManager

public static Roi[] readFromRoiManager()

readFromOverlays

public static Roi[] readFromOverlays()

saveROIs

public static void saveROIs(MetadataStore store)

Save ROIs in the ROI manager to the given MetadataStore.

unwrap

private static NonNegativeInteger unwrap(int r)

storeText

private static void storeText(TextRoi roi,
             MetadataStore store,
             int roiNum,
             int shape)

storePoint

private static void storePoint(PointRoi roi,
              MetadataStore store,
              int roiNum,
              int shape)

storeLine

private static void storeLine(Line roi,
             MetadataStore store,
             int roiNum,
             int shape)

Store a Line ROI in the given MetadataStore.

storeRectangle

private static void storeRectangle(Roi roi,
                  MetadataStore store,
                  int roiNum,
                  int shape)

Store an Roi (rectangle) in the given MetadataStore.

storePolygon

private static void storePolygon(PolygonRoi roi,
                MetadataStore store,
                int roiNum,
                int shape)

Store a Polygon ROI in the given MetadataStore.

storeOval

private static void storeOval(OvalRoi roi,
             MetadataStore store,
             int roiNum,
             int shape)

Store an Oval ROI in the given MetadataStore.

parsePoints

private static int[][] parsePoints(String points)

Parse (x, y) coordinates from a String returned by MetadataRetrieve.getPolygonpoints(...) or MetadataRetrieve.getPolylinepoints(...)

toOMExmlColor

private static Color toOMExmlColor(Color color)