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
A special PathObject used exclusively to represent TMA cores.
Currently, these only contain circular (or elliptical) ROIs.
- Author:
- Pete Bankhead
- See Also:
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final StringMetadata key to store a case identify for the TMA core.static final StringMetadata key for an overall survival censored flag.static final StringMetadata key for an overall survival (temporal) value.static final StringMetadata key for an recurrence-free survival (temporal) value.static final StringMetadata key for an recurrence-free survival censored flag.static final StringDeprecated. -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoidClear all associated metadata.Get the case ID metadata value.Get all metadata keys.Returns an unmodifiable map containing the metadata.getMetadataString(String key) Get a metadata value, cast as a String if possible.getMetadataValue(String key) Get a metadata value of any kind.booleanQuery the 'missing' flag for this core.putMetadataValue(String key, String value) Store a new metadata value.voidvoidSet the case ID metadata value.voidsetMissing(boolean missing) Set the missing flag for this core, for example because insufficient tissue is present.toString()voidMethods inherited from class qupath.lib.objects.PathROIObject
getClassProbability, getPathClass, getROI, isEditable, isLocked, setLocked, setPathClass, setROIMethods 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
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Field Details
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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:
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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:
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KEY_OVERALL_SURVIVAL
Metadata key for an overall survival (temporal) value.- See Also:
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KEY_RECURRENCE_FREE_SURVIVAL
Metadata key for an recurrence-free survival (temporal) value.- See Also:
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KEY_OS_CENSORED
Metadata key for an overall survival censored flag.- See Also:
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KEY_RFS_CENSORED
Metadata key for an recurrence-free survival censored flag.- See Also:
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Constructor Details
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TMACoreObject
public TMACoreObject()Default constructor. Should not be used directly, instead usePathObjects.createTMACoreObject(double, double, double, boolean).
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Method Details
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isMissing
public boolean isMissing()Query the 'missing' flag for this core.- Returns:
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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-
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getCaseID
Get the case ID metadata value.- Returns:
- See Also:
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setCaseID
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-
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putMetadataValue
Description copied from interface:MetadataStoreStore a new metadata value.- Specified by:
putMetadataValuein interfaceMetadataStore- Returns:
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getMetadataString
Description copied from interface:MetadataStoreGet a metadata value, cast as a String if possible.- Specified by:
getMetadataStringin interfaceMetadataStore- Returns:
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getMetadataValue
Description copied from interface:MetadataStoreGet a metadata value of any kind.- Specified by:
getMetadataValuein interfaceMetadataStore- Returns:
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getMetadataKeys
Description copied from interface:MetadataStoreGet all metadata keys.- Specified by:
getMetadataKeysin interfaceMetadataStore- Returns:
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getMetadataMap
Description copied from interface:MetadataStoreReturns an unmodifiable map containing the metadata.- Specified by:
getMetadataMapin interfaceMetadataStore- Returns:
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clearMetadata
public void clearMetadata()Clear all associated metadata. -
toString
- Overrides:
toStringin classPathObject
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writeExternal
- Specified by:
writeExternalin interfaceExternalizable- Overrides:
writeExternalin classPathROIObject- Throws:
IOException
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readExternal
- Specified by:
readExternalin interfaceExternalizable- Overrides:
readExternalin classPathROIObject- Throws:
IOExceptionClassNotFoundException
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