loci.plugins.util

Class ROIHandler

java.lang.Object

loci.plugins.util.ROIHandler

public class ROIHandler
extends java.lang.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

Modifier and Type	Method and Description
static void	openROIs(IMetadata retrieve, ij.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, ij.ImagePlus[] images, boolean isOMERO) Opens the rois and converts them into ImageJ Rois.
static void	openROIs(IMetadata retrieve, ij.ImagePlus[] images, boolean isOMERO, java.lang.String roisMode) Opens the rois and converts them into ImageJ Rois.
private static int[][]	parsePoints(java.lang.String points) Parse (x, y) coordinates from a String returned by MetadataRetrieve.getPolygonpoints(...) or MetadataRetrieve.getPolylinepoints(...)
static ij.gui.Roi[]	readFromOverlays() Returns rois if any from the overlay.
static ij.gui.Roi[]	readFromRoiManager() Returns the rois if any stored in the ROI manager.
static void	saveROIs(MetadataStore store) Save ROIs in the ROI manager to the given MetadataStore.
private static void	storeLine(ij.gui.Line roi, MetadataStore store, int roiNum, int shape, int c, int z, int t) Stores the Line ROI into the specified metadata store.
private static void	storeOval(ij.gui.OvalRoi roi, MetadataStore store, int roiNum, int shape, int c, int z, int t) Stores the Oval ROI into the specified metadata store.
private static void	storePoint(ij.gui.PointRoi roi, MetadataStore store, int roiNum, int shape, int c, int z, int t) Stores the Point ROI into the specified metadata store.
private static void	storePolygon(ij.gui.PolygonRoi roi, MetadataStore store, int roiNum, int shape, int c, int z, int t) Stores the Polygon ROI into the specified metadata store.
private static void	storeRectangle(ij.gui.Roi roi, MetadataStore store, int roiNum, int shape, int c, int z, int t) Stores the Rectangle ROI into the specified metadata store.
private static void	storeText(ij.gui.TextRoi roi, MetadataStore store, int roiNum, int shape, int c, int z, int t) Stores the text ROI into the metadata stored.
private static ome.xml.model.primitives.Color	toOMExmlColor(java.awt.Color color) Converts the Java Color into an OME-XML Color.
private static ome.xml.model.primitives.NonNegativeInteger	unwrap(int r) Wraps the specified integer into a Non negative integer.

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,
                            ij.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,
                            ij.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(IMetadata retrieve,
                            ij.ImagePlus[] images,
                            boolean isOMERO,
                            java.lang.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 ij.gui.Roi[] readFromRoiManager()

Returns the rois if any stored in the ROI manager.

Returns:

See above.

readFromOverlays

public static ij.gui.Roi[] readFromOverlays()

Returns rois if any from the overlay.

Returns:

See above

saveROIs

public static void saveROIs(MetadataStore store)

Save ROIs in the ROI manager to the given MetadataStore.

Parameters:

store - Where to store the rois.

unwrap

private static ome.xml.model.primitives.NonNegativeInteger unwrap(int r)

Wraps the specified integer into a Non negative integer.

Parameters:

r - The value to wrap.

Returns:

See above.

storeText

private static void storeText(ij.gui.TextRoi roi,
                              MetadataStore store,
                              int roiNum,
                              int shape,
                              int c,
                              int z,
                              int t)

Stores the text ROI into the metadata stored.

Parameters:

roi - The roi to convert.

store - The store to handle.

roiNum - The roi number

shape - The index of the shape.

c - The selected channel.

z - The selected slice.

t - The selected timepoint.

storePoint

private static void storePoint(ij.gui.PointRoi roi,
                               MetadataStore store,
                               int roiNum,
                               int shape,
                               int c,
                               int z,
                               int t)

Stores the Point ROI into the specified metadata store.

Parameters:

roi - The roi to convert.

store - The store to handle.

roiNum - The roi number

shape - The index of the shape.

c - The selected channel.

z - The selected slice.

t - The selected timepoint.

storeLine

private static void storeLine(ij.gui.Line roi,
                              MetadataStore store,
                              int roiNum,
                              int shape,
                              int c,
                              int z,
                              int t)

Stores the Line ROI into the specified metadata store.

Parameters:

roi - The roi to convert.

store - The store to handle.

roiNum - The roi number

shape - The index of the shape.

c - The selected channel.

z - The selected slice.

t - The selected timepoint.

storeRectangle

private static void storeRectangle(ij.gui.Roi roi,
                                   MetadataStore store,
                                   int roiNum,
                                   int shape,
                                   int c,
                                   int z,
                                   int t)

Stores the Rectangle ROI into the specified metadata store.

Parameters:

roi - The roi to convert.

store - The store to handle.

roiNum - The roi number

shape - The index of the shape.

c - The selected channel.

z - The selected slice.

t - The selected timepoint.

storePolygon

private static void storePolygon(ij.gui.PolygonRoi roi,
                                 MetadataStore store,
                                 int roiNum,
                                 int shape,
                                 int c,
                                 int z,
                                 int t)

Stores the Polygon ROI into the specified metadata store.

Parameters:

roi - The roi to convert.

store - The store to handle.

roiNum - The roi number

shape - The index of the shape.

c - The selected channel.

z - The selected slice.

t - The selected timepoint.

storeOval

private static void storeOval(ij.gui.OvalRoi roi,
                              MetadataStore store,
                              int roiNum,
                              int shape,
                              int c,
                              int z,
                              int t)

Stores the Oval ROI into the specified metadata store.

Parameters:

roi - The roi to convert.

store - The store to handle.

roiNum - The roi number

shape - The index of the shape.

c - The selected channel.

z - The selected slice.

t - The selected timepoint.

parsePoints

private static int[][] parsePoints(java.lang.String points)

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

toOMExmlColor

private static ome.xml.model.primitives.Color toOMExmlColor(java.awt.Color color)

Converts the Java Color into an OME-XML Color.

Parameters:

color - The color to convert

Returns:

See above