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Posted to commits@ctakes.apache.org by se...@apache.org on 2016/10/19 21:37:33 UTC
svn commit: r1765723 -
/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngineFit.java
Author: seanfinan
Date: Wed Oct 19 21:37:33 2016
New Revision: 1765723
URL: http://svn.apache.org/viewvc?rev=1765723&view=rev
Log:
uimafit version of assertion, with minor change and refactoring
Added:
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngineFit.java
Added: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngineFit.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngineFit.java?rev=1765723&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngineFit.java (added)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngineFit.java Wed Oct 19 21:37:33 2016
@@ -0,0 +1,216 @@
+package org.apache.ctakes.assertion.medfacts;
+
+import org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl;
+import org.apache.ctakes.assertion.medfacts.i2b2.api.SingleDocumentProcessorCtakes;
+import org.apache.ctakes.assertion.medfacts.types.Concept;
+import org.apache.ctakes.core.resource.FileLocator;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.log4j.Logger;
+import org.apache.uima.UimaContext;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.util.JCasUtil;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.mitre.jcarafe.jarafe.JarafeMEDecoder;
+import org.mitre.medfacts.i2b2.annotation.PartOfSpeechTagger;
+import org.mitre.medfacts.i2b2.annotation.ScopeParser;
+import org.mitre.medfacts.i2b2.api.ApiConcept;
+import org.mitre.medfacts.i2b2.api.AssertionDecoderConfiguration;
+import org.mitre.medfacts.i2b2.cli.BatchRunner;
+import org.mitre.medfacts.zoner.CharacterOffsetToLineTokenConverter;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.util.*;
+
+import static org.apache.ctakes.typesystem.type.constants.CONST.ATTR_SUBJECT_FAMILY_MEMBER;
+import static org.apache.ctakes.typesystem.type.constants.CONST.ATTR_SUBJECT_PATIENT;
+
+
+/**
+ * @author SPF , chip-nlp
+ * @version %I%
+ * @since 10/19/2016
+ */
+public class AssertionAnalysisEngineFit extends JCasAnnotator_ImplBase {
+
+ static private final Logger LOGGER = Logger.getLogger( "AssertionAnalysisEngineFit" );
+
+ static public final String ASSERTION_MODEL_PARAM = "assertionModelResource";
+ static public final String SCOPE_MODEL_PARAM = "scopeModelResource";
+ static public final String CUE_MODEL_PARAM = "cueModelResource";
+ static public final String POS_MODEL_PARAM = "posModelResource";
+ static public final String ENABLED_FEATURES_PARAM = "enabledFeaturesResource";
+
+
+ @ConfigurationParameter(
+ name = ASSERTION_MODEL_PARAM,
+ defaultValue = "org/apache/ctakes/assertion/models/i2b2.model" )
+ private String _assertionModelPath;
+
+ @ConfigurationParameter(
+ name = SCOPE_MODEL_PARAM,
+ defaultValue = "org/apache/ctakes/assertion/models/scope.model" )
+ private String _scopeModelPath;
+
+ @ConfigurationParameter(
+ name = CUE_MODEL_PARAM,
+ defaultValue = "org/apache/ctakes/assertion/models/cue.model" )
+ private String _cueModelPath;
+
+ @ConfigurationParameter(
+ name = POS_MODEL_PARAM,
+ defaultValue = "org/apache/ctakes/assertion/models/pos.model" )
+ private String _posModelPath;
+
+ @ConfigurationParameter(
+ name = ENABLED_FEATURES_PARAM,
+ defaultValue = "org/apache/ctakes/assertion/models/featureFile11b" )
+ private String _enabledFeaturesPath;
+
+ private AssertionDecoderConfiguration _assertionDecoderConfiguration;
+
+ @Override
+ public void initialize( final UimaContext uimaContext ) throws ResourceInitializationException {
+ super.initialize( uimaContext );
+ // byte assertionModelContents[];
+ File assertionModelFile;
+ String scopeModelFilePath;
+ String cueModelFilePath;
+ String posModelFilePath;
+ File enabledFeaturesFile;
+ try {
+ assertionModelFile = FileLocator.locateFile( _assertionModelPath );
+ // assertionModelContents = StringHandling.readEntireContentsBinary(assertionModelFile);
+ scopeModelFilePath = FileLocator.getFullPath( _scopeModelPath );
+ cueModelFilePath = FileLocator.getFullPath( _cueModelPath );
+ posModelFilePath = FileLocator.getFullPath( _posModelPath );
+ enabledFeaturesFile = FileLocator.locateFile( _enabledFeaturesPath );
+ } catch ( FileNotFoundException fnfE ) {
+ throw new ResourceInitializationException( fnfE );
+ }
+ LOGGER.info( "scope model file: " + scopeModelFilePath );
+ LOGGER.info( "cue model file: " + cueModelFilePath );
+ LOGGER.info( "pos model file: " + posModelFilePath );
+ final AssertionDecoderConfiguration assertionDecoderConfiguration = new AssertionDecoderConfiguration();
+ final ScopeParser scopeParser = new ScopeParser( scopeModelFilePath, cueModelFilePath );
+ assertionDecoderConfiguration.setScopeParser( scopeParser );
+ final PartOfSpeechTagger posTagger = new PartOfSpeechTagger( posModelFilePath );
+ assertionDecoderConfiguration.setPosTagger( posTagger );
+ final Set<String> enabledFeatureIdSet = BatchRunner.loadEnabledFeaturesFromFile( enabledFeaturesFile );
+ assertionDecoderConfiguration.setEnabledFeatureIdSet( enabledFeatureIdSet );
+ final JarafeMEDecoder assertionDecoder = new JarafeMEDecoder( assertionModelFile );
+ assertionDecoderConfiguration.setAssertionDecoder( assertionDecoder );
+ _assertionDecoderConfiguration = assertionDecoderConfiguration;
+ }
+
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public void process( final JCas jcas ) throws AnalysisEngineProcessException {
+ LOGGER.info( "Starting processing" );
+ final String documentText = jcas.getDocumentText();
+ final List<ApiConcept> apiConceptList = new ArrayList<>();
+ final Collection<Concept> concepts = JCasUtil.select( jcas, Concept.class );
+ for ( Concept concept : concepts ) {
+ final int begin = concept.getBegin();
+ final int end = concept.getEnd();
+ final String conceptText = documentText.substring( begin, end );
+ final ApiConcept apiConcept = new ApiConcept();
+ apiConcept.setBegin( begin );
+ apiConcept.setEnd( end );
+ apiConcept.setText( conceptText );
+ apiConcept.setType( concept.getConceptType() );
+ apiConcept.setExternalId( concept.getAddress() );
+ apiConceptList.add( apiConcept );
+ }
+ final SingleDocumentProcessorCtakes processor = new SingleDocumentProcessorCtakes();
+ processor.setJcas( jcas );
+ processor.setAssertionDecoderConfiguration( _assertionDecoderConfiguration );
+ processor.setContents( documentText );
+ final CharacterOffsetToLineTokenConverter converter = new CharacterOffsetToLineTokenConverterCtakesImpl( jcas );
+ processor.setConverter2( converter );
+ apiConceptList.forEach( processor::addConcept );
+ LOGGER.debug( "BEFORE CALLING processor.processSingleDocument()" );
+ processor.processSingleDocument();
+ LOGGER.debug( "AFTER CALLING processor.processSingleDocument()" );
+ final Map<Integer, String> assertionTypeMap = processor.getAssertionTypeMap();
+ final CasIndexer<Annotation> indexer = new CasIndexer<>( jcas, null );
+ for ( Map.Entry<Integer, String> current : assertionTypeMap.entrySet() ) {
+ final Integer currentIndex = current.getKey();
+ final String currentAssertionType = current.getValue();
+ final ApiConcept originalConcept = apiConceptList.get( currentIndex );
+ final Concept associatedConcept = (Concept)indexer.lookupByAddress( originalConcept.getExternalId() );
+ final int entityAddress = associatedConcept.getOriginalEntityExternalId();
+ final IdentifiedAnnotation annotation = (IdentifiedAnnotation)indexer.lookupByAddress( entityAddress );
+ mapI2B2AssertionValueToCtakes( currentAssertionType, annotation );
+ }
+ LOGGER.info( "Processing Finished" );
+ }
+
+
+ static private void fillProperties( final IdentifiedAnnotation annotation,
+ final int polarity, final int uncertainty,
+ final boolean generic, final boolean conditional,
+ final String subject, final float confidence ) {
+ annotation.setPolarity( polarity );
+ annotation.setUncertainty( uncertainty );
+ annotation.setGeneric( generic );
+ annotation.setConditional( conditional );
+ annotation.setSubject( subject );
+ annotation.setConfidence( confidence );
+ }
+
+
+ // possible values for currentAssertionType:
+ // present
+ // absent
+ // associated_with_someone_else
+ // conditional
+ // hypothetical
+ // possible
+ // Changed from original implementation by information in https://www.mitre.org/sites/default/files/pdf/10_4676.pdf
+ static private void mapI2B2AssertionValueToCtakes( final String assertionType,
+ final IdentifiedAnnotation annotation )
+ throws AnalysisEngineProcessException {
+ if ( assertionType == null ) {
+ LOGGER.error( "current assertion type is null" );
+ fillProperties( annotation, -2, -2, false, false, "skipped", -2.0f );
+ return;
+ }
+ switch ( assertionType ) {
+ case "present":
+ fillProperties( annotation, 1, 0, false, false, ATTR_SUBJECT_PATIENT, 1.0f );
+ break;
+ case "absent":
+ fillProperties( annotation, -1, 0, false, false, ATTR_SUBJECT_PATIENT, 1.0f );
+ break;
+ case "associated_with_someone_else":
+ // OLD: annotation.setSubject( "CONST.ATTR_SUBJECT_FAMILY_MEMBER" );
+ fillProperties( annotation, 1, 0, false, false, ATTR_SUBJECT_FAMILY_MEMBER, 1.0f );
+ break;
+ case "conditional":
+ // OLD: currently no mapping to sharp type...all sharp properties are defaults!
+ // OLD: annotation.setConditional( false );
+ fillProperties( annotation, 1, 0, false, true, ATTR_SUBJECT_PATIENT, 1.0f );
+ break;
+ case "hypothetical":
+ // OLD: annotation.setConditional( true ); annotation.setGeneric( false );
+ fillProperties( annotation, 1, 0, true, false, ATTR_SUBJECT_PATIENT, 1.0f );
+ break;
+ case "possible":
+ fillProperties( annotation, 1, 1, false, false, ATTR_SUBJECT_PATIENT, 1.0f );
+ break;
+ default:
+ LOGGER.error( "unexpected assertion value returned: " + assertionType );
+ fillProperties( annotation, -2, -2, false, false, "skipped", -2.0f );
+ break;
+ }
+ }
+
+}