public class ROIHandler
extends java.lang.Object
Constructor and Description |
---|
ROIHandler() |
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.
|
public static void openROIs(IMetadata retrieve, ij.ImagePlus[] images)
public static void openROIs(IMetadata retrieve, ij.ImagePlus[] images, boolean isOMERO)
retrieve
- The OMEXML store.images
- The imageJ object.isOMERO
- true
if data stored in OMERO,
false
otherwise.public static void openROIs(IMetadata retrieve, ij.ImagePlus[] images, boolean isOMERO, java.lang.String roisMode)
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 RoiManagerpublic static ij.gui.Roi[] readFromRoiManager()
public static ij.gui.Roi[] readFromOverlays()
public static void saveROIs(MetadataStore store)
store
- Where to store the rois.private static ome.xml.model.primitives.NonNegativeInteger unwrap(int r)
r
- The value to wrap.private static void storeText(ij.gui.TextRoi roi, MetadataStore store, int roiNum, int shape, int c, int z, int t)
roi
- The roi to convert.store
- The store to handle.roiNum
- The roi numbershape
- The index of the shape.c
- The selected channel.z
- The selected slice.t
- The selected timepoint.private static void storePoint(ij.gui.PointRoi roi, MetadataStore store, int roiNum, int shape, int c, int z, int t)
roi
- The roi to convert.store
- The store to handle.roiNum
- The roi numbershape
- The index of the shape.c
- The selected channel.z
- The selected slice.t
- The selected timepoint.private static void storeLine(ij.gui.Line roi, MetadataStore store, int roiNum, int shape, int c, int z, int t)
roi
- The roi to convert.store
- The store to handle.roiNum
- The roi numbershape
- The index of the shape.c
- The selected channel.z
- The selected slice.t
- The selected timepoint.private static void storeRectangle(ij.gui.Roi roi, MetadataStore store, int roiNum, int shape, int c, int z, int t)
roi
- The roi to convert.store
- The store to handle.roiNum
- The roi numbershape
- The index of the shape.c
- The selected channel.z
- The selected slice.t
- The selected timepoint.private static void storePolygon(ij.gui.PolygonRoi roi, MetadataStore store, int roiNum, int shape, int c, int z, int t)
roi
- The roi to convert.store
- The store to handle.roiNum
- The roi numbershape
- The index of the shape.c
- The selected channel.z
- The selected slice.t
- The selected timepoint.private static void storeOval(ij.gui.OvalRoi roi, MetadataStore store, int roiNum, int shape, int c, int z, int t)
roi
- The roi to convert.store
- The store to handle.roiNum
- The roi numbershape
- The index of the shape.c
- The selected channel.z
- The selected slice.t
- The selected timepoint.private static int[][] parsePoints(java.lang.String points)
private static ome.xml.model.primitives.Color toOMExmlColor(java.awt.Color color)
color
- The color to convertCopyright © 2020 Open Microscopy Environment