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From seanfi...@apache.org
Subject svn commit: r1874146 - /ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/ae/BodySideFinder.java
Date Mon, 17 Feb 2020 18:41:20 GMT
Author: seanfinan
Date: Mon Feb 17 18:41:20 2020
New Revision: 1874146

URL: http://svn.apache.org/viewvc?rev=1874146&view=rev
Log:
example ae that assigns body sides to anatomic sites.

Added:
    ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/ae/BodySideFinder.java

Added: ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/ae/BodySideFinder.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/ae/BodySideFinder.java?rev=1874146&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/ae/BodySideFinder.java
(added)
+++ ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/ae/BodySideFinder.java
Mon Feb 17 18:41:20 2020
@@ -0,0 +1,174 @@
+package org.apache.ctakes.examples.ae;
+
+import org.apache.ctakes.core.ae.TokenizerAnnotatorPTB;
+import org.apache.ctakes.core.cr.TextBySentenceBuilder;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
+import org.apache.ctakes.core.pipeline.PipelineBuilder;
+import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
+import org.apache.ctakes.typesystem.type.syntax.WordToken;
+import org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention;
+import org.apache.ctakes.typesystem.type.textsem.BodySideModifier;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.log4j.Logger;
+import org.apache.uima.UIMAException;
+import org.apache.uima.analysis_engine.AnalysisEngineDescription;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.pipeline.SimplePipeline;
+import org.apache.uima.fit.util.JCasUtil;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.cas.FSArray;
+import org.apache.uima.jcas.tcas.Annotation;
+
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Comparator;
+import java.util.Map;
+import java.util.stream.Collectors;
+
+
+/**
+ * This is just an example ae that will assign body sides to anatomic sites.
+ * It will assign the closest preceding side to a site.
+ * This is just an example ( including main() ) of how one can:
+ * Create a pipeline with PipelineBuilder.
+ * Add Sentences with TextBySentenceBuilder.
+ * Create and add Annotations.
+ * Fetch annotations with JCasUtil.
+ * <p>
+ * If you are unfamiliar with the builder pattern
+ * or java streams or functional references then the flow may look a little strange,
+ * but the essential ctakes-related building blocks are more straightforward.
+ *
+ * @author SPF , chip-nlp
+ * @version %I%
+ * @since 2/17/2020
+ */
+@PipeBitInfo(
+      name = "BodySideFinder",
+      description = "Assigns Body Side to Anatomic Sites.",
+      role = PipeBitInfo.Role.ANNOTATOR
+)
+final public class BodySideFinder extends JCasAnnotator_ImplBase {
+
+   static private final Logger LOGGER = Logger.getLogger( "BodySideFinder" );
+
+   /**
+    * Holds a umls CUI and some synonyms for body sides.
+    * Has methods to detect a matching word token and create a BodySideModifier.
+    */
+   private enum Side {
+      RIGHT( "C0205090", "right", "dextro" ),
+      LEFT( "C0205091", "left", "levo" );
+      final private String _cui;
+      final private Collection<String> _patterns;
+
+      Side( final String cui, final String... patterns ) {
+         _cui = cui;
+         _patterns = Arrays.asList( patterns );
+      }
+
+      boolean isMatch( final WordToken word ) {
+         return _patterns.stream()
+                         .anyMatch( word.getCoveredText()::equalsIgnoreCase );
+      }
+
+      BodySideModifier createModifier( final JCas jCas, final WordToken word ) {
+         final BodySideModifier side = new BodySideModifier( jCas, word.getBegin(), word.getEnd()
);
+         final UmlsConcept umlsConcept = new UmlsConcept( jCas );
+         umlsConcept.setCui( _cui );
+         final FSArray conceptArr = new FSArray( jCas, 1 );
+         conceptArr.set( 0, umlsConcept );
+         side.setOntologyConceptArr( conceptArr );
+         side.addToIndexes( jCas );
+         return side;
+      }
+   }
+
+   /**
+    * Process Sentence -by- Sentence.
+    * If a sentence has anatomic site(s) and wordtokens that match a body side synonym,
+    * BodySideModifier(s) are created and attached to anatomic sites that follow in the sentence.
+    * {@inheritDoc}
+    */
+   @Override
+   public void process( final JCas jCas ) throws AnalysisEngineProcessException {
+      LOGGER.info( "Finding Body Side and Laterality ..." );
+
+      final Map<Sentence, Collection<AnatomicalSiteMention>> sentenceSiteMap
+            = JCasUtil.indexCovered( jCas, Sentence.class, AnatomicalSiteMention.class );
+
+      final Map<Sentence, Collection<WordToken>> sentenceWordMap
+            = JCasUtil.indexCovered( jCas, Sentence.class, WordToken.class );
+
+      sentenceSiteMap.entrySet().stream()
+                     .filter( e -> !e.getValue().isEmpty() )
+                     .forEach( e -> assignSides( jCas, e.getValue(), sentenceWordMap.get(
e.getKey() ) ) );
+
+      LOGGER.info( "Finished." );
+   }
+
+   /**
+    * Iterate through types of {@link}Side, calling {@link}findSide and {@link}setSide.
+    */
+   static private void assignSides( final JCas jCas,
+                                    final Collection<AnatomicalSiteMention> sites,
+                                    final Collection<WordToken> words ) {
+      Arrays.stream( Side.values() )
+            .map( s -> findSide( jCas, words, s ) )
+            .flatMap( Collection::stream )
+            .sorted( Comparator.comparingInt( Annotation::getBegin ) )
+            .forEach( s -> setSide( s, sites ) );
+   }
+
+   /**
+    * Iterate through WordTokens to find body sides and create BodySideModifiers representing
them.
+    */
+   static private Collection<BodySideModifier> findSide( final JCas jCas,
+                                                         final Collection<WordToken>
words,
+                                                         final Side side ) {
+      return words.stream()
+                  .filter( side::isMatch )
+                  .map( w -> side.createModifier( jCas, w ) )
+                  .collect( Collectors.toList() );
+   }
+
+   /**
+    * Assign a side to all following sites.
+    */
+   static private void setSide( final BodySideModifier side,
+                                final Collection<AnatomicalSiteMention> sites ) {
+      sites.stream()
+           .filter( s -> s.getEnd() > side.getEnd() )
+           .forEach( s -> s.setBodySide( side ) );
+   }
+
+
+   /**
+    * Demo
+    */
+   public static void main( final String... args ) {
+      final String sentence = "He had a slight fracture in the proximal right fibula";
+      final int index = sentence.indexOf( "fibula" );
+      try {
+         final AnalysisEngineDescription analysisEngine = new PipelineBuilder()
+               .add( TokenizerAnnotatorPTB.class )
+               .add( BodySideFinder.class )
+               .getAnalysisEngineDesc();
+         final JCas jCas = new TextBySentenceBuilder()
+               .addSentence( sentence )
+               .build();
+         final AnatomicalSiteMention site = new AnatomicalSiteMention( jCas, index, index
+ 6 );
+         site.addToIndexes( jCas );
+
+         SimplePipeline.runPipeline( jCas, analysisEngine );
+
+         LOGGER.info( site.getCoveredText() + " has body side " + site.getBodySide().getCoveredText()
);
+      } catch ( IOException | UIMAException uE ) {
+         LOGGER.error( uE.getMessage() );
+      }
+   }
+
+
+}



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