org.apache.ctakes.necontexts
Class ContextAnnotator

java.lang.Object
  org.apache.uima.analysis_component.AnalysisComponent_ImplBase
      org.apache.uima.analysis_component.Annotator_ImplBase
          org.apache.uima.analysis_component.JCasAnnotator_ImplBase
              org.apache.ctakes.necontexts.ContextAnnotator

All Implemented Interfaces:

org.apache.uima.analysis_component.AnalysisComponent

public class ContextAnnotator
extends org.apache.uima.analysis_component.JCasAnnotator_ImplBase

The context annotator iterates through focus annotations and analyzes the surrounding context of each. The context is defined by a scope, window, and a maximum size (if applicable). The context can be further refined by boundary conditions as specified by the context analyzer used. For each focus annotation, a context is collected as a set of context annotations for each scope that is to be applied. The context annotations are passed to a context analyzer for analysis. If the context analyzer finds something of interest in the context annotations, then it will generate a context hit. Context hits are then passed to a context hit consumer which will perform an action on the hit such as updating an existing annotation or creating a new one.

Field Summary

static int	ALL_SCOPE The ALL_SCOPE scope provides the context annotation that are found in all three of the other scopes (LEFT, MIDDLE, and RIGHT).
static String	CONTEXT_ANALYZER_CLASS_PARAM "ContextAnalyzerClass" is a required, single, string parameter that specifies the context analyzer class that determines if a "hit" is found within a processed scope.
static String	CONTEXT_ANNOTATION_CLASS_PARAM "ContextAnnotationClass" is a required, single, string parameter that specifies the annotation type of the context annotations (often "tokens") that make up the context relative to a focus annotation within a scope that is being examined.
static String	CONTEXT_HIT_CONSUMER_CLASS_PARAM "ContextHitConsumerClass" is a required, single, string parameter that specifies the context hit consumer class that will process context hits that are found.
protected ContextAnalyzer	contextAnalyzer
protected ContextHitConsumer	contextConsumer
static String	FOCUS_ANNOTATION_CLASS_PARAM "FocusAnnotationClass" is a required, single, string parameter that specifies the annotation type of the focus annotations that are going to be examined by this annotator.
static int	LEFT_SCOPE
protected int	leftScopeSize
static String	MAX_LEFT_SCOPE_SIZE_PARAM "MaxLeftScopeSize" is a required, single, integer parameter that specifies the maximum size of the left scope.
static String	MAX_RIGHT_SCOPE_SIZE_PARAM "MaxRightScopeSize" is a required, single, integer parameter that specifies the maximum size of the right scope.
static int	MIDDLE_SCOPE Provides context annotations that are "inside" the focus annotation.
static int	RIGHT_SCOPE
protected int	rightScopeSize
static String	SCOPE_ORDER_PARAM "ScopeOrder" is a required, multiple, string parameter that specifies the order that the scopes should be processed in.
protected List<Integer>	scopes
static String	WINDOW_ANNOTATION_CLASS_PARAM "WindowAnnotationClass" is a required, single, string parameter that specifies the annotation type of the windows that specify the hard boundaries of scopes.

Constructor Summary

ContextAnnotator()

Method Summary

protected List<org.apache.uima.jcas.tcas.Annotation>	getLeftScopeContextAnnotations(org.apache.uima.jcas.JCas jCas, org.apache.uima.jcas.tcas.Annotation focus, org.apache.uima.jcas.tcas.Annotation window)
protected List<org.apache.uima.jcas.tcas.Annotation>	getMiddleScopeContextAnnotations(org.apache.uima.jcas.JCas jCas, org.apache.uima.jcas.tcas.Annotation focus)
protected List<org.apache.uima.jcas.tcas.Annotation>	getRightScopeContextAnnotations(org.apache.uima.jcas.JCas jCas, org.apache.uima.jcas.tcas.Annotation focus, org.apache.uima.jcas.tcas.Annotation window)
protected List<org.apache.uima.jcas.tcas.Annotation>	getScopeContextAnnotations(org.apache.uima.jcas.JCas jCas, org.apache.uima.jcas.tcas.Annotation focus, org.apache.uima.jcas.tcas.Annotation window, int scope)
void	initialize(org.apache.uima.UimaContext uimaContext)
void	process(org.apache.uima.jcas.JCas jCas)

Methods inherited from class org.apache.uima.analysis_component.JCasAnnotator_ImplBase

getRequiredCasInterface, process

Methods inherited from class org.apache.uima.analysis_component.Annotator_ImplBase

getCasInstancesRequired, hasNext, next

Methods inherited from class org.apache.uima.analysis_component.AnalysisComponent_ImplBase

batchProcessComplete, collectionProcessComplete, destroy, getContext, getResultSpecification, reconfigure, setResultSpecification

Methods inherited from class java.lang.Object

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

Field Detail

MAX_LEFT_SCOPE_SIZE_PARAM

public static final String MAX_LEFT_SCOPE_SIZE_PARAM

"MaxLeftScopeSize" is a required, single, integer parameter that specifies the maximum size of the left scope.

See Also:

Constant Field Values

MAX_RIGHT_SCOPE_SIZE_PARAM

public static final String MAX_RIGHT_SCOPE_SIZE_PARAM

"MaxRightScopeSize" is a required, single, integer parameter that specifies the maximum size of the right scope.

See Also:

Constant Field Values

SCOPE_ORDER_PARAM

public static final String SCOPE_ORDER_PARAM

"ScopeOrder" is a required, multiple, string parameter that specifies the order that the scopes should be processed in. Possible values are "LEFT", "MIDDLE", "RIGHT", and "ALL".

See Also:

Constant Field Values

WINDOW_ANNOTATION_CLASS_PARAM

public static final String WINDOW_ANNOTATION_CLASS_PARAM

"WindowAnnotationClass" is a required, single, string parameter that specifies the annotation type of the windows that specify the hard boundaries of scopes. Note that the entire window may not be used depending on the location of the focus annotation, the maximum scope size, and the boundary conditions specified by the context analyzer. A window encompasses all of the scopes (left, middle, and right). Examples of likely window types would be:

• DocumentAnnotation
• SentenceAnnotation
• SegmentAnnotation
• ...

See Also:

DocumentAnnotation, edu.mayo.bmi.common.type.Sentence, edu.mayo.bmi.common.type.Segment, Constant Field Values

FOCUS_ANNOTATION_CLASS_PARAM

public static final String FOCUS_ANNOTATION_CLASS_PARAM

"FocusAnnotationClass" is a required, single, string parameter that specifies the annotation type of the focus annotations that are going to be examined by this annotator. Examples of likely focus types would be:

• NamedEntityAnnotation
• Token
• ...

See Also:

edu.mayo.bmi.common.type.NamedEntity, edu.mayo.bmi.common.type.BaseToken, Constant Field Values

CONTEXT_ANNOTATION_CLASS_PARAM

public static final String CONTEXT_ANNOTATION_CLASS_PARAM

"ContextAnnotationClass" is a required, single, string parameter that specifies the annotation type of the context annotations (often "tokens") that make up the context relative to a focus annotation within a scope that is being examined. The context annotations are examined for context hits by the context analyzer. Examples of likely focus types would be:

• BaseToken
• WordToken
• NamedEntity

See Also:

edu.mayo.bmi.common.type.BaseToken, edu.mayo.bmi.common.type.WordToken, edu.mayo.bmi.common.type.NamedEntity, Constant Field Values

CONTEXT_ANALYZER_CLASS_PARAM

public static final String CONTEXT_ANALYZER_CLASS_PARAM

"ContextAnalyzerClass" is a required, single, string parameter that specifies the context analyzer class that determines if a "hit" is found within a processed scope.

See Also:

ContextAnalyzer, Constant Field Values

CONTEXT_HIT_CONSUMER_CLASS_PARAM

public static final String CONTEXT_HIT_CONSUMER_CLASS_PARAM

"ContextHitConsumerClass" is a required, single, string parameter that specifies the context hit consumer class that will process context hits that are found.

See Also:

ContextHitConsumer, Constant Field Values

LEFT_SCOPE

public static final int LEFT_SCOPE

See Also:

Constant Field Values

MIDDLE_SCOPE

public static final int MIDDLE_SCOPE

Provides context annotations that are "inside" the focus annotation. For example, if the focus annotation type is a named entity mention and the context annotation is a token type, then the middle scope will examine the tokens that fall within the named entity mention.

See Also:

Constant Field Values

RIGHT_SCOPE

public static final int RIGHT_SCOPE

See Also:

Constant Field Values

ALL_SCOPE

public static final int ALL_SCOPE

The ALL_SCOPE scope provides the context annotation that are found in all three of the other scopes (LEFT, MIDDLE, and RIGHT).

See Also:

Constant Field Values

leftScopeSize

protected int leftScopeSize

rightScopeSize

protected int rightScopeSize

scopes

protected List<Integer> scopes

contextAnalyzer

protected ContextAnalyzer contextAnalyzer

contextConsumer

protected ContextHitConsumer contextConsumer

Constructor Detail

ContextAnnotator

public ContextAnnotator()

Method Detail

initialize

public void initialize(org.apache.uima.UimaContext uimaContext)
                throws org.apache.uima.resource.ResourceInitializationException

Specified by:

initialize in interface org.apache.uima.analysis_component.AnalysisComponent

Overrides:

initialize in class org.apache.uima.analysis_component.AnalysisComponent_ImplBase

Throws:

org.apache.uima.resource.ResourceInitializationException

process

public void process(org.apache.uima.jcas.JCas jCas)
             throws org.apache.uima.analysis_engine.AnalysisEngineProcessException

Specified by:

process in class org.apache.uima.analysis_component.JCasAnnotator_ImplBase

Throws:

org.apache.uima.analysis_engine.AnalysisEngineProcessException

getScopeContextAnnotations

protected List<org.apache.uima.jcas.tcas.Annotation> getScopeContextAnnotations(org.apache.uima.jcas.JCas jCas,
                                                                                org.apache.uima.jcas.tcas.Annotation focus,
                                                                                org.apache.uima.jcas.tcas.Annotation window,
                                                                                int scope)
                                                                         throws org.apache.uima.analysis_engine.AnalysisEngineProcessException

Throws:

org.apache.uima.analysis_engine.AnalysisEngineProcessException

getLeftScopeContextAnnotations

protected List<org.apache.uima.jcas.tcas.Annotation> getLeftScopeContextAnnotations(org.apache.uima.jcas.JCas jCas,
                                                                                    org.apache.uima.jcas.tcas.Annotation focus,
                                                                                    org.apache.uima.jcas.tcas.Annotation window)
                                                                             throws org.apache.uima.analysis_engine.AnalysisEngineProcessException

Throws:

org.apache.uima.analysis_engine.AnalysisEngineProcessException

getRightScopeContextAnnotations

protected List<org.apache.uima.jcas.tcas.Annotation> getRightScopeContextAnnotations(org.apache.uima.jcas.JCas jCas,
                                                                                     org.apache.uima.jcas.tcas.Annotation focus,
                                                                                     org.apache.uima.jcas.tcas.Annotation window)
                                                                              throws org.apache.uima.analysis_engine.AnalysisEngineProcessException

Throws:

org.apache.uima.analysis_engine.AnalysisEngineProcessException

getMiddleScopeContextAnnotations

protected List<org.apache.uima.jcas.tcas.Annotation> getMiddleScopeContextAnnotations(org.apache.uima.jcas.JCas jCas,
                                                                                      org.apache.uima.jcas.tcas.Annotation focus)
                                                                               throws org.apache.uima.analysis_engine.AnalysisEngineProcessException

Throws:

org.apache.uima.analysis_engine.AnalysisEngineProcessException