Package qupath.lib.objects

Class PathROIObject

java.lang.Object

qupath.lib.objects.PathObject

qupath.lib.objects.PathROIObject

All Implemented Interfaces:

Externalizable, Serializable, MinimalMetadataStore

Direct Known Subclasses:

PathAnnotationObject, PathDetectionObject, TMACoreObject

public abstract class PathROIObject
extends PathObject

Abstract class used for PathObjects that have ROIs associated with them.

In practice, this is almost all PathObjects (with the notable exception of PathRootObjects).

See Also:

• Serialized Form

Method Summary

Modifier and Type	Method	Description
double	getClassProbability()	Request the classification probability, or Double.NaN if no probability is available.
PathClass	getPathClass()	Get the classification of the object.
ROI	getROI()	Get the region of interest (ROI) for the object.
boolean	isEditable()	Deprecated. since v0.4.0
boolean	isLocked()	Query the locked status for the object, indicating whether it should be editable or not.
void	readExternal(ObjectInput in)
void	setLocked(boolean locked)	Set locked flag, indicating that the object ROI should not be modified.
void	setPathClass(PathClass pathClass, double classProbability)	Set the classification of the object, specifying a classification probability.
void	setROI(ROI roi)	Set the ROI for this object.
void	writeExternal(ObjectOutput out)

Methods inherited from class qupath.lib.objects.PathObject

addChildObject, addChildObjects, clearChildObjects, clearMetadataMap, createEmptyMeasurementList, getChildObjects, getChildObjects, getChildObjectsAsArray, getClassification, getClassifications, getColor, getDescendantObjects, getDisplayedName, getID, getLevel, getMeasurementList, getMeasurements, getMetadata, getName, getParent, getUnmodifiableMetadataMap, hasChildObjects, hasMeasurements, hasMetadata, hasROI, isAnnotation, isCell, isDetection, isRootObject, isTile, isTMACore, nChildObjects, nDescendants, objectCountPostfix, refreshID, removeChildObject, removeChildObjects, resetPathClass, retrieveMetadataKeys, retrieveMetadataValue, setClassification, setClassification, setClassifications, setColor, setColor, setID, setName, setPathClass, storeMetadataValue, toString

Methods inherited from class java.lang.Object

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

Method Details

setROI

public void setROI(ROI roi)

Set the ROI for this object. If this is called, one should remember to update any associated hierarchy to notify it of the change.

Parameters:

roi -

setLocked

public void setLocked(boolean locked)

Set locked flag, indicating that the object ROI should not be modified. It directly impacts on isEditable()

Note that this is only a hint that other code should pay attention to - it is not enforced locally.

TODO: Consider shifting this method into PathObject rather than PathROIObject (even if it doesn't really do anything there).

Overrides:

setLocked in class PathObject

Parameters:

locked -

isLocked

public boolean isLocked()

Query the locked status for the object, indicating whether it should be editable or not.

Overrides:

isLocked in class PathObject

Returns:

isEditable

@Deprecated
public boolean isEditable()

Deprecated.

since v0.4.0

Return true if isLocked() is false, otherwise returns false.

This method existed before isLocked() to try to automatically determine whether an object should be locked or not. Now the isLocked() flag should be used instead.

Specified by:

isEditable in class PathObject

Returns:

setPathClass

public void setPathClass(PathClass pathClass,
 double classProbability)

Description copied from class: PathObject

Set the classification of the object, specifying a classification probability.

The probability is expected to be between 0 and 1, or Double.NaN if no probability should be set.

Specified by:

setPathClass in class PathObject

Parameters:

pathClass -

classProbability -

See Also:

• PathObject.setPathClass(PathClass)
• PathObject.setClassification(String)
• PathObject.setClassifications(Collection)

getClassProbability

public double getClassProbability()

Description copied from class: PathObject

Request the classification probability, or Double.NaN if no probability is available.

Specified by:

getClassProbability in class PathObject

Returns:

getPathClass

public PathClass getPathClass()

Description copied from class: PathObject

Get the classification of the object.

The PathClass object is used as the internal representation of the object's classification, encapsulating both the different string components of the classification and the color used for display.

For convenience, PathObject.getClassification() and PathObject.getClassifications() provide a simpler way to interact with classifications as one or more strings.

Specified by:

getPathClass in class PathObject

Returns:

See Also:

• PathObject.setPathClass(PathClass)
• PathObject.getClassification()
• PathObject.getClassifications()

getROI

public ROI getROI()

Description copied from class: PathObject

Get the region of interest (ROI) for the object.

Specified by:

getROI in class PathObject

Returns:

writeExternal

public void writeExternal(ObjectOutput out)
                   throws IOException

Specified by:

writeExternal in interface Externalizable

Overrides:

writeExternal in class PathObject

Throws:

IOException

readExternal

public void readExternal(ObjectInput in)
                  throws IOException,
ClassNotFoundException

Specified by:

readExternal in interface Externalizable

Overrides:

readExternal in class PathObject

Throws:

IOException

ClassNotFoundException