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From tm...@apache.org
Subject svn commit: r1635138 - in /ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion: attributes/features/SubjectFeaturesExtractor.java medfacts/cleartk/SubjectCleartkAnalysisEngine.java
Date Wed, 29 Oct 2014 14:08:54 GMT
Author: tmill
Date: Wed Oct 29 14:08:53 2014
New Revision: 1635138

URL: http://svn.apache.org/r1635138
Log:
CTAKES-94: Changed tabs to spaces in subject extractor code.

Modified:
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/SubjectFeaturesExtractor.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/SubjectFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/SubjectFeaturesExtractor.java?rev=1635138&r1=1635137&r2=1635138&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/SubjectFeaturesExtractor.java
(original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/SubjectFeaturesExtractor.java
Wed Oct 29 14:08:53 2014
@@ -34,47 +34,47 @@ import org.cleartk.ml.feature.extractor.
 
 
 /** SubjectFeaturesExtractor
- * 		Ports the features and classification decisions of the first version (logic) of the
subject tool
+ *     Ports the features and classification decisions of the first version (logic) of the
subject tool
  * 
  * @author m081914
  *
  */
 public class SubjectFeaturesExtractor implements FeatureExtractor1<IdentifiedAnnotation>
{
-	
-	
-	@Override
-	public List<Feature> extract(JCas jCas, IdentifiedAnnotation arg) {
-		
-		List<Feature> features = new ArrayList<>();
-		
-		// Pull in general dependency-based features -- externalize to another extractor?
-	    ConllDependencyNode node = DependencyUtility.getNominalHeadNode(jCas, arg);
-	    if (node!= null) {
-	    	features.add(new Feature("DEPENDENCY_HEAD", node.getCoveredText()));
-	    	features.add(new Feature("DEPENDENCY_HEAD_deprel", node.getDeprel()));
-		}
-	    
-	    HashMap<String, Boolean> featsMap = SubjectAttributeClassifier.extract(jCas, arg);
+  
+  
+  @Override
+  public List<Feature> extract(JCas jCas, IdentifiedAnnotation arg) {
+    
+    List<Feature> features = new ArrayList<>();
+    
+    // Pull in general dependency-based features -- externalize to another extractor?
+      ConllDependencyNode node = DependencyUtility.getNominalHeadNode(jCas, arg);
+      if (node!= null) {
+        features.add(new Feature("DEPENDENCY_HEAD", node.getCoveredText()));
+        features.add(new Feature("DEPENDENCY_HEAD_deprel", node.getDeprel()));
+    }
+      
+      HashMap<String, Boolean> featsMap = SubjectAttributeClassifier.extract(jCas,
arg);
 
-	    if (!featsMap.isEmpty()) {
-	    	// Pull in all the features that were used for the rule-based module
-	    	features.addAll( hashToFeatureList(featsMap) );
-	    	// Pull in the result of the rule-based module as well
-	    	features.add(new Feature("SUBJECT_CLASSIFIER_LOGIC", SubjectAttributeClassifier.classifyWithLogic(featsMap)));
-	    }
-	    
-	    return features;
-	}
+      if (!featsMap.isEmpty()) {
+        // Pull in all the features that were used for the rule-based module
+        features.addAll( hashToFeatureList(featsMap) );
+        // Pull in the result of the rule-based module as well
+        features.add(new Feature("SUBJECT_CLASSIFIER_LOGIC", SubjectAttributeClassifier.classifyWithLogic(featsMap)));
+      }
+      
+      return features;
+  }
 
-	private static Collection<? extends Feature> hashToFeatureList(
-			HashMap<String, Boolean> featsIn) {
-		
-		Collection<Feature> featsOut = new HashSet<>();
-		for (String featName : featsIn.keySet()) {
-			featsOut.add(new Feature(featName,featsIn.get(featName)));
-		}
-		
-		return featsOut;
-	}
+  private static Collection<? extends Feature> hashToFeatureList(
+      HashMap<String, Boolean> featsIn) {
+    
+    Collection<Feature> featsOut = new HashSet<>();
+    for (String featName : featsIn.keySet()) {
+      featsOut.add(new Feature(featName,featsIn.get(featName)));
+    }
+    
+    return featsOut;
+  }
 
 }

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java?rev=1635138&r1=1635137&r2=1635138&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java
(original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java
Wed Oct 29 14:08:53 2014
@@ -32,68 +32,68 @@ import org.apache.uima.resource.Resource
 import org.cleartk.ml.Instance;
 
 public class SubjectCleartkAnalysisEngine extends
-		AssertionCleartkAnalysisEngine {
+    AssertionCleartkAnalysisEngine {
 
-	boolean USE_DEFAULT_EXTRACTORS = false;
-	
-	@Override
-	public void initialize(UimaContext context) throws ResourceInitializationException {
-		super.initialize(context);
-		probabilityOfKeepingADefaultExample = 0.1;
-
-		if (this.isTraining() && this.goldViewName == null) {
-			throw new IllegalArgumentException(PARAM_GOLD_VIEW_NAME + " must be defined during training");
-		}
-		
-		initialize_subject_extractor();
-		initializeFeatureSelection();
-
-	}
-
-
-	private void initialize_subject_extractor() {
-		this.entityFeatureExtractors.add( new SubjectFeaturesExtractor());
-	}
-	
-	@Override
-	public void setClassLabel(IdentifiedAnnotation entityOrEventMention,
-			Instance<String> instance) throws AnalysisEngineProcessException {
-		if (this.isTraining())
-	      {
-	        String subj = entityOrEventMention.getSubject();
-	        
-	        // downsampling. initialize probabilityOfKeepingADefaultExample to 1.0 for no downsampling
-	        if ("patient".equals(subj) 
-	        		&& coin.nextDouble() >= this.probabilityOfKeepingADefaultExample) {
-	        	return;
-	        }
-	        instance.setOutcome(subj);
-	        logger.log(Level.DEBUG,  String.format("[%s] expected: ''; actual: ''; features:
%s",
-		      		  this.getClass().getSimpleName(),
-		      		  instance.toString()
-		      		  ));
-	      } else
-	      {
-	        String label = this.classifier.classify(instance.getFeatures());
-	        entityOrEventMention.setSubject(label);
-	        logger.log(Level.DEBUG, "SUBJECT is being set on an IdentifiedAnnotation: "+label+"
"+entityOrEventMention.getSubject());
-	      }
-	}
-	public static FeatureSelection<String> createFeatureSelection(double threshold) {
-		return new Chi2FeatureSelection<>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME,
threshold, false);
-	}
-
-	public static URI createFeatureSelectionURI(File outputDirectoryName) {
-		return new File(outputDirectoryName, FEATURE_SELECTION_NAME + "_Chi2_extractor.dat").toURI();
-	}
-	
-	@Override
-	protected void initializeFeatureSelection() throws ResourceInitializationException {
-	    if (featureSelectionThreshold == 0) {
-	    	this.featureSelection = null;
-	    } else {
-	    	this.featureSelection = createFeatureSelection(this.featureSelectionThreshold);
-	    }		
-	}
-	  
+  boolean USE_DEFAULT_EXTRACTORS = false;
+  
+  @Override
+  public void initialize(UimaContext context) throws ResourceInitializationException {
+    super.initialize(context);
+    probabilityOfKeepingADefaultExample = 0.1;
+
+    if (this.isTraining() && this.goldViewName == null) {
+      throw new IllegalArgumentException(PARAM_GOLD_VIEW_NAME + " must be defined during
training");
+    }
+    
+    initialize_subject_extractor();
+    initializeFeatureSelection();
+
+  }
+
+
+  private void initialize_subject_extractor() {
+    this.entityFeatureExtractors.add( new SubjectFeaturesExtractor());
+  }
+  
+  @Override
+  public void setClassLabel(IdentifiedAnnotation entityOrEventMention,
+      Instance<String> instance) throws AnalysisEngineProcessException {
+    if (this.isTraining())
+        {
+          String subj = entityOrEventMention.getSubject();
+          
+          // downsampling. initialize probabilityOfKeepingADefaultExample to 1.0 for no downsampling
+          if ("patient".equals(subj) 
+              && coin.nextDouble() >= this.probabilityOfKeepingADefaultExample)
{
+            return;
+          }
+          instance.setOutcome(subj);
+          logger.log(Level.DEBUG,  String.format("[%s] expected: ''; actual: ''; features:
%s",
+                this.getClass().getSimpleName(),
+                instance.toString()
+                ));
+        } else
+        {
+          String label = this.classifier.classify(instance.getFeatures());
+          entityOrEventMention.setSubject(label);
+          logger.log(Level.DEBUG, "SUBJECT is being set on an IdentifiedAnnotation: "+label+"
"+entityOrEventMention.getSubject());
+        }
+  }
+  public static FeatureSelection<String> createFeatureSelection(double threshold) {
+    return new Chi2FeatureSelection<>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME,
threshold, false);
+  }
+
+  public static URI createFeatureSelectionURI(File outputDirectoryName) {
+    return new File(outputDirectoryName, FEATURE_SELECTION_NAME + "_Chi2_extractor.dat").toURI();
+  }
+  
+  @Override
+  protected void initializeFeatureSelection() throws ResourceInitializationException {
+      if (featureSelectionThreshold == 0) {
+        this.featureSelection = null;
+      } else {
+        this.featureSelection = createFeatureSelection(this.featureSelectionThreshold);
+      }    
+  }
+    
 }



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