Package qupath.lib.objects

Class TMACoreObject

java.lang.Object

qupath.lib.objects.PathObject

qupath.lib.objects.PathROIObject

qupath.lib.objects.TMACoreObject

All Implemented Interfaces:

Externalizable, Serializable, MetadataStore

public class TMACoreObject
extends PathROIObject
implements MetadataStore

A special PathObject used exclusively to represent TMA cores.

Currently, these only contain circular (or elliptical) ROIs.

Author:

Pete Bankhead

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static final String	KEY_CASE_ID	Metadata key to store a case identify for the TMA core.
static final String	KEY_OS_CENSORED	Metadata key for an overall survival censored flag.
static final String	KEY_OVERALL_SURVIVAL	Metadata key for an overall survival (temporal) value.
static final String	KEY_RECURRENCE_FREE_SURVIVAL	Metadata key for an recurrence-free survival (temporal) value.
static final String	KEY_RFS_CENSORED	Metadata key for an recurrence-free survival censored flag.
static final String	LEGACY_KEY_UNIQUE_ID	Deprecated.

Constructor Summary

Constructors

Constructor	Description
TMACoreObject()	Default constructor.

Method Summary

Modifier and Type	Method	Description
void	clearMetadata()	Clear all associated metadata.
String	getCaseID()	Get the case ID metadata value.
Set<String>	getMetadataKeys()	Get all metadata keys.
Map<String,String>	getMetadataMap()	Returns an unmodifiable map containing the metadata.
String	getMetadataString(String key)	Get a metadata value, cast as a String if possible.
Object	getMetadataValue(String key)	Get a metadata value of any kind.
boolean	isMissing()	Query the 'missing' flag for this core.
Object	putMetadataValue(String key, String value)	Store a new metadata value.
void	readExternal(ObjectInput in)
void	setCaseID(String caseID)	Set the case ID metadata value.
void	setMissing(boolean missing)	Set the missing flag for this core, for example because insufficient tissue is present.
String	toString()
void	writeExternal(ObjectOutput out)

Methods inherited from class qupath.lib.objects.PathROIObject

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

Methods inherited from class qupath.lib.objects.PathObject

addChildObject, addChildObjects, addPathObject, addPathObjects, clearChildObjects, clearMetadataMap, clearPathObjects, createEmptyMeasurementList, getChildObjects, getChildObjects, getChildObjectsAsArray, getClassifications, getColor, getColorRGB, getDescendantObjects, getDisplayedName, getID, getLevel, getMeasurementList, getMeasurements, getMetadata, 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

Methods inherited from class java.lang.Object

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

Field Details

LEGACY_KEY_UNIQUE_ID

@Deprecated
public static final String LEGACY_KEY_UNIQUE_ID

Deprecated.

The key used before v0.4.0 to represent a unique (usually patient) ID. This was replaced by #KEY_CASE_ID.

See Also:

• Constant Field Values

KEY_CASE_ID

public static final String KEY_CASE_ID

Metadata key to store a case identify for the TMA core. This can be used to group cores that belong to the same case.

See Also:

• Constant Field Values

KEY_OVERALL_SURVIVAL

public static final String KEY_OVERALL_SURVIVAL

Metadata key for an overall survival (temporal) value.

See Also:

• Constant Field Values

KEY_RECURRENCE_FREE_SURVIVAL

public static final String KEY_RECURRENCE_FREE_SURVIVAL

Metadata key for an recurrence-free survival (temporal) value.

See Also:

• Constant Field Values

KEY_OS_CENSORED

public static final String KEY_OS_CENSORED

Metadata key for an overall survival censored flag.

See Also:

• Constant Field Values

KEY_RFS_CENSORED

public static final String KEY_RFS_CENSORED

Metadata key for an recurrence-free survival censored flag.

See Also:

• Constant Field Values

Constructor Details

TMACoreObject

public TMACoreObject()

Default constructor. Should not be used directly, instead use PathObjects.createTMACoreObject(double, double, double, boolean).

Method Details

isMissing

public boolean isMissing()

Query the 'missing' flag for this core.

Returns:

setMissing

public void setMissing(boolean missing)

Set the missing flag for this core, for example because insufficient tissue is present. 'Missing' cores are typically ignored during analysis.

Parameters:

missing -

getCaseID

public String getCaseID()

Get the case ID metadata value.

Returns:

See Also:

• setCaseID(String)

setCaseID

public void setCaseID(String caseID)

Set the case ID metadata value. This is typically used to store a patient identifier, and must be unique for the patient (but multiple cores may have the same ID if they correspond to the same patient).

Parameters:

caseID -

putMetadataValue

public Object putMetadataValue(String key,
 String value)

Description copied from interface: MetadataStore

Store a new metadata value.

Specified by:

putMetadataValue in interface MetadataStore

Parameters:

key -

value -

Returns:

getMetadataString

public String getMetadataString(String key)

Description copied from interface: MetadataStore

Get a metadata value, cast as a String if possible.

Specified by:

getMetadataString in interface MetadataStore

Parameters:

key -

Returns:

getMetadataValue

public Object getMetadataValue(String key)

Description copied from interface: MetadataStore

Get a metadata value of any kind.

Specified by:

getMetadataValue in interface MetadataStore

Parameters:

key -

Returns:

getMetadataKeys

public Set<String> getMetadataKeys()

Description copied from interface: MetadataStore

Get all metadata keys.

Specified by:

getMetadataKeys in interface MetadataStore

Returns:

getMetadataMap

public Map<String,String> getMetadataMap()

Description copied from interface: MetadataStore

Returns an unmodifiable map containing the metadata.

Specified by:

getMetadataMap in interface MetadataStore

Returns:

clearMetadata

public void clearMetadata()

Clear all associated metadata.

toString

public String toString()

Overrides:

toString in class PathObject

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