de.unihalle.informatik.MiToBo.core.imageJ

Class RoiManagerAdapter

java.lang.Object

de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter

public class RoiManagerAdapter
extends Object

Convenience functions for interaction with ImageJ's ROI manager.

This class is implemented as singleton. To access its functionality, use the getAdapter() function to get the singleton instance and call its methods.

Author:

moeller

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
private static class	RoiManagerAdapter.RoiReader Class for parsing ImageJ roi files and zip archives.

Field Summary

Fields

Modifier and Type	Field and Description
private static Object	classLock Lock variable to make singleton thread-safe.
private static RoiManagerAdapter	roiAdapt The object instance.
private ij.plugin.frame.RoiManager	roiManager Reference to the current ImageJ roi manager.

Constructor Summary

Constructors

Modifier	Constructor and Description
private	RoiManagerAdapter() Hidden constructor, never called from outside.

Method Summary

Modifier and Type	Method and Description
void	addBordersToRoiManager(MTBBorder2DSet borders) Adds a set of 2D borders to the ROI manager.
void	addContoursToRoiManager(MTBContour2DSet conts) Adds a set of 2D contours to the ROI manager.
void	addPolygonsToRoiManager(MTBPolygon2DSet polys) Adds a set of polygons to the ROI manager.
void	addPolygonToRoiManager(MTBPolygon2D poly) Adds the given polygon to the ROI manager.
void	addRegionsToRoiManager(MTBRegion2DSet regs) Adds a set of 2D regions to the ROI manager.
boolean	areRegionsInManagerAvailable() Returns true if there are regions available in ROI manager.
private boolean	checkSelectionConsistency() Checks if a proper set of regions is selected in ImageJ ROI manager.
private boolean	checkSelectionConsistencyForLineSegments() Checks if a proper set of ROIs convertible to line segments is selected in ImageJ ROI manager.
MTBBorder2DSet	getBorderSetFromRoiManager() Reads a ROI manager selection into a set of borders.
MTBContour2DSet	getContourSetFromRoiManager() Reads a ROI manager selection into a set of contours.
static RoiManagerAdapter	getInstance() Single access point for singleton functionality.
MTBLineSegment2DSet	getLineSegmentSetFromRoiManager() Reads ROI manager selections into a set of line segments.
MTBPolygon2DSet	getPolygonSetFromRoiFile(String file, boolean asSnakes) Reads an ImageJ roi file into a set of polygons/snakes.
MTBPolygon2DSet	getPolygonSetFromRoiManager() Reads ROI manager selections into a set of polygons/snakes.
MTBRegion2DSet	getRegionSetFromRoiFile(String file) Reads an ImageJ roi file into a set of regions.
MTBRegion2DSet	getRegionSetFromRoiFile(String file, double xMin, double yMin, double xMax, double yMax) Reads an ImageJ roi file into a set of regions.
MTBRegion2DSet	getRegionSetFromRoiManager() Reads a ROI manager selection into a set of regions.
private void	openRoiManager() Gets an instance of the current ROI manager of ImageJ.

Methods inherited from class java.lang.Object

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

Field Detail

roiAdapt

private static RoiManagerAdapter roiAdapt

The object instance.

classLock

private static Object classLock

Lock variable to make singleton thread-safe.

roiManager

private ij.plugin.frame.RoiManager roiManager

Reference to the current ImageJ roi manager.

Constructor Detail

RoiManagerAdapter

private RoiManagerAdapter()

Hidden constructor, never called from outside.

Method Detail

getInstance

public static RoiManagerAdapter getInstance()

Single access point for singleton functionality.

Returns:

Reference to the singleton instance.

addPolygonToRoiManager

public void addPolygonToRoiManager(MTBPolygon2D poly)

Adds the given polygon to the ROI manager.

Parameters:

poly - Polygon to be added to ROI manager.

addPolygonsToRoiManager

public void addPolygonsToRoiManager(MTBPolygon2DSet polys)

Adds a set of polygons to the ROI manager.

Note that the set is destroyed by this operation, i.e. it cannot be recovered lateron from the ROI manager as it does not support to group several polygons into a logic entity.

Parameters:

polys - Set of polygons to be added to ROI manager.

addRegionsToRoiManager

public void addRegionsToRoiManager(MTBRegion2DSet regs)

Adds a set of 2D regions to the ROI manager.

Parameters:

regs - Set of regions to be added to ROI manager.

addContoursToRoiManager

public void addContoursToRoiManager(MTBContour2DSet conts)

Adds a set of 2D contours to the ROI manager.

Parameters:

conts - Set of contours to be added to ROI manager.

addBordersToRoiManager

public void addBordersToRoiManager(MTBBorder2DSet borders)

Adds a set of 2D borders to the ROI manager.

Parameters:

borders - Set of borders to be added to ROI manager.

getRegionSetFromRoiFile

public MTBRegion2DSet getRegionSetFromRoiFile(String file)
                                       throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                              de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Reads an ImageJ roi file into a set of regions.

Parameters:

file - Input file.

Returns:

Set of regions; always non-null, but probably empty.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown in case of failure.

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException - Thrown in case of failure.

getRegionSetFromRoiFile

public MTBRegion2DSet getRegionSetFromRoiFile(String file,
                                              double xMin,
                                              double yMin,
                                              double xMax,
                                              double yMax)
                                       throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                              de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Reads an ImageJ roi file into a set of regions.

Parameters:

file - Input file.

xMin - Minimal x value of user-specified domain.

yMin - Minimal y value of user-specified domain.

xMax - Maximal x value of user-specified domain.

yMax - Maximal y value of user-specified domain.

Returns:

Set of regions; always non-null, but probably empty.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown in case of failure.

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException - Thrown in case of failure.

getPolygonSetFromRoiFile

public MTBPolygon2DSet getPolygonSetFromRoiFile(String file,
                                                boolean asSnakes)
                                         throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                                de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Reads an ImageJ roi file into a set of polygons/snakes.

Parameters:

file - Input file.

asSnakes - If true, function returns snakes, otherwise polygons.

Returns:

Set of polygons/snakes; always non-null, but probably empty.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown in case of failure.

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException - Thrown in case of failure.

getLineSegmentSetFromRoiManager

public MTBLineSegment2DSet getLineSegmentSetFromRoiManager()

Reads ROI manager selections into a set of line segments.

Note that polylines are not automatically closed, i.e. the first and last point are not identical even if ImageJ shows a closed polygon.

Returns:

Set of line segments; always non-null, but probably empty.

getPolygonSetFromRoiManager

public MTBPolygon2DSet getPolygonSetFromRoiManager()

Reads ROI manager selections into a set of polygons/snakes.

Returns:

Set of polygons; always non-null, but probably empty.

getRegionSetFromRoiManager

public MTBRegion2DSet getRegionSetFromRoiManager()

Reads a ROI manager selection into a set of regions.

Returns:

Set of regions; always non-null, but probably empty.

getContourSetFromRoiManager

public MTBContour2DSet getContourSetFromRoiManager()

Reads a ROI manager selection into a set of contours.

Returns:

Set of contours; always non-null, but probably empty.

getBorderSetFromRoiManager

public MTBBorder2DSet getBorderSetFromRoiManager()

Reads a ROI manager selection into a set of borders.

Returns:

Set of borders; always non-null, but probably empty.

areRegionsInManagerAvailable

public boolean areRegionsInManagerAvailable()

Returns true if there are regions available in ROI manager.

Returns:

True, if region manager contains at least one region.

checkSelectionConsistency

private boolean checkSelectionConsistency()

Checks if a proper set of regions is selected in ImageJ ROI manager.

Returns:

True, if a proper set, i.e. at least one region, is selected and the region(s) is/are of correct type.

checkSelectionConsistencyForLineSegments

private boolean checkSelectionConsistencyForLineSegments()

Checks if a proper set of ROIs convertible to line segments is selected in ImageJ ROI manager.

Returns:

True, if a proper set, i.e. at least one ROI, is selected and the ROI(s) is/are of correct type.

openRoiManager

private void openRoiManager()

Gets an instance of the current ROI manager of ImageJ.

If there is already a roi manager open, get a reference to that one, otherwise open a new one.