Package qupath.lib.objects

Class PathCellObject

java.lang.Object

qupath.lib.objects.PathObject

qupath.lib.objects.PathROIObject

qupath.lib.objects.PathDetectionObject

qupath.lib.objects.PathCellObject

All Implemented Interfaces:

Externalizable, Serializable

public class PathCellObject
extends PathDetectionObject

A subclass of a PathDetectionObject, which also supports storing an (optional) extra ROI to represent the cell nucleus.

The primary ROI represents the cell boundary.

Author:

Pete Bankhead

See Also:

• PathDetectionObject
• Serialized Form

Constructor Summary

Constructors

Constructor	Description
PathCellObject()	Default constructor.

Method Summary

Modifier and Type	Method	Description
ROI	getNucleusROI()	Get the nucleus ROI for this cell.
boolean	hasNucleus()	Returns true if a nucleus ROI is stored for this cell.
void	readExternal(ObjectInput in)
void	writeExternal(ObjectOutput out)

Methods inherited from class qupath.lib.objects.PathDetectionObject

createEmptyMeasurementList, getMetadata, isEditable

Methods inherited from class qupath.lib.objects.PathROIObject

getClassProbability, getPathClass, getROI, isLocked, setLocked, setPathClass, setROI

Methods inherited from class qupath.lib.objects.PathObject

addChildObject, addChildObjects, addPathObject, addPathObjects, clearChildObjects, clearMetadataMap, clearPathObjects, getChildObjects, getChildObjects, getChildObjectsAsArray, getClassifications, getColor, getColorRGB, getDescendantObjects, getDisplayedName, getID, getLevel, getMeasurementList, getMeasurements, getName, getParent, getUnmodifiableMetadataMap, hasChildObjects, hasChildren, hasMeasurements, hasROI, isAnnotation, isCell, isDetection, isRootObject, isTile, isTMACore, nChildObjects, nDescendants, objectCountPostfix, refreshID, removeChildObject, removeChildObjects, removePathObject, removePathObjects, resetPathClass, retrieveMetadataKeys, retrieveMetadataValue, setClassifications, setColor, setColor, setColorRGB, setID, setName, setPathClass, storeMetadataValue, toString

Methods inherited from class java.lang.Object

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

Constructor Details

PathCellObject

public PathCellObject()

Default constructor. Should not be used directly, instead use PathObjects.createCellObject(ROI, ROI, PathClass, MeasurementList).

Method Details

hasNucleus

public boolean hasNucleus()

Returns true if a nucleus ROI is stored for this cell.

Returns:

getNucleusROI

public ROI getNucleusROI()

Get the nucleus ROI for this cell. This may be null, or may be a ROI stored in addition to PathROIObject.getROI(), which returns the overall cell boundary.

Returns:

writeExternal

public void writeExternal(ObjectOutput out)
                   throws IOException

Specified by:

writeExternal in interface Externalizable

Overrides:

writeExternal in class PathROIObject

Throws:

IOException

readExternal

public void readExternal(ObjectInput in)
                  throws IOException,
ClassNotFoundException

Specified by:

readExternal in interface Externalizable

Overrides:

readExternal in class PathROIObject

Throws:

IOException

ClassNotFoundException