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From shalg...@apache.org
Subject svn commit: r1520631 - in /ctakes/trunk: ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/ ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/ ctakes-assertion/src/main/java/org/apache/ctakes/assertion/att...
Date Fri, 06 Sep 2013 17:00:44 GMT
Author: shalgrim
Date: Fri Sep  6 17:00:43 2013
New Revision: 1520631

URL: http://svn.apache.org/r1520631
Log:
Added post as cue word in historyOf.psv
Added In History Sections feature

Added:
    ctakes/trunk/ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/historyOf.psv
Modified:
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/HistoryFeaturesExtractor.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/history/HistoryAttributeClassifier.java
    ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/subject/SubjectAttributeClassifier.java

Added: ctakes/trunk/ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/historyOf.psv
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/historyOf.psv?rev=1520631&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/historyOf.psv
(added)
+++ ctakes/trunk/ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/historyOf.psv
Fri Sep  6 17:00:43 2013
@@ -0,0 +1,11 @@
+has been|historyOf|historyOf
+had|historyOf|historyOf
+hx of recent|historyOf|historyOf
+hx of|historyOf|historyOf
+hx|historyOf|historyOf
+recent|historyOf|historyOf
+s/p|historyOf|historyOf
+status post|historyOf|historyOf
+post|historyOf|historyOf
+previous|historyOf|historyOf
+prior|historyOf|historyOf

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/HistoryFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/HistoryFeaturesExtractor.java?rev=1520631&r1=1520630&r2=1520631&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/HistoryFeaturesExtractor.java
(original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/HistoryFeaturesExtractor.java
Fri Sep  6 17:00:43 2013
@@ -63,9 +63,12 @@ public class HistoryFeaturesExtractor im
 
 	    // 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("HISTORY_CLASSIFIER_LOGIC", HistoryAttributeClassifier.classifyWithLogic(featsMap)));
-
+	    
+	    // Add whether it is token preceded by "h/o"
+	    //features.add(new Feature("PRECEDED_BY_H_SLASH_O", HistoryAttributeClassifier.precededByH_O(jCas,
arg)));
 	    
 	    return features;
 	}

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/history/HistoryAttributeClassifier.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/history/HistoryAttributeClassifier.java?rev=1520631&r1=1520630&r2=1520631&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/history/HistoryAttributeClassifier.java
(original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/history/HistoryAttributeClassifier.java
Fri Sep  6 17:00:43 2013
@@ -21,6 +21,8 @@ package org.apache.ctakes.assertion.attr
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.Collections;
+import java.util.Comparator;
 import java.util.HashMap;
 import java.util.List;
 import java.util.regex.Matcher;
@@ -29,6 +31,7 @@ import java.util.regex.Pattern;
 import org.apache.uima.UIMAException;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
+import org.apache.uima.jcas.tcas.DocumentAnnotation;
 import org.uimafit.util.JCasUtil;
 import org.xml.sax.SAXException;
 
@@ -53,7 +56,8 @@ public class HistoryAttributeClassifier 
 	private static final String POSTCOORD_NMOD = "donor_srlarg";
 	private static final String DISCUSSION_DEPPATH = "discussion_deppath";
 	private static final String SUBSUMED_CHUNK = "other_token"; 
-	private static final String SUBSUMED_ANNOT = "other_deppath"; 
+	private static final String SUBSUMED_ANNOT = "other_deppath";
+	private static final String IN_HIST_SECTION = "in_history_section";
     public static ArrayList<String> FeatureIndex = new ArrayList<String>();
     static{
             FeatureIndex.add(POSTCOORD_NMOD);
@@ -61,6 +65,19 @@ public class HistoryAttributeClassifier 
             FeatureIndex.add(SUBSUMED_CHUNK);
             FeatureIndex.add(SUBSUMED_ANNOT);
     }
+    
+    private static final String[] GHC_HIST_SECTIONS = 
+    	{
+    	"fh",
+    	"sh",
+    	//"hpi",  // based on 8/30 review of errors, this is a pretty lousy indicator of history

+    	"pmh", // missed a bunch of these in 8/20 run reviewed on 8/30. am i forgetting lowercase?
+    	"psh",
+    	"social history:",
+    	"family history",
+    	"past medical history",
+    	"pmh/psh" // missed a bunch of these in 8/20 run reviewed on 8/30. am i forgetting lowercase?
+    	};
 
 	// currently goes from entityMention to Sentence to SemanticArgument
 	public static Boolean getHIstory(JCas jCas, IdentifiedAnnotation mention) {
@@ -96,6 +113,49 @@ public class HistoryAttributeClassifier 
 		}
 		return false;
 	}
+	
+	/*
+	 * SRH adding 8/19/13
+	 * Idea is that I want to know if I am in a "sentence" that starts with
+	 * a GH history section name.
+	 * There's some work to be done here.
+	 * Let's define paragraphs as what's delimited by \n in GH docs
+	 * Then we can define these sections as I've seen them by what's in a
+	 * paragraph.
+	 * But a paragraph may have more than one sentence in it.
+	 * So I have to actually not find the first part of the sentence that 
+	 * contains the thing, but the paragraph.
+	 * So actually I have to start from the sentence and search backwards
+	 * for a newline.
+	 * So what's written below works (untested/unerified) in the case that I have
+	 * the starting sentence of a paragraph.
+	 * But I still have to find that first sentence.
+	 */
+	private static boolean isInHistSection(Sentence s) {
+		String sText = s.getCoveredText();
+		
+		for (String secStart : GHC_HIST_SECTIONS)
+		{
+			int slen = secStart.length();
+			
+			if (sText.length() >= slen)
+			{
+				String sentStart = sText.trim().substring(0, slen).toLowerCase();
+				if (sentStart.equals(secStart))
+				{
+					return true;
+				}
+			}
+		}
+		
+		return false;
+	}
+	
+	public static class SentComparator implements Comparator<Sentence> {
+		public int compare(Sentence s1, Sentence s2) {
+			return s1.getBegin() - s2.getBegin();
+		}
+	}
 
 
 	public static HashMap<String, Boolean> extract(JCas jCas,
@@ -114,11 +174,89 @@ public class HistoryAttributeClassifier 
 				break;
 			}
 		}
-//		if (sEntity==null)
-//			return null;
+		
+		DocumentAnnotation docAnnot = null;
+		
+		Collection<DocumentAnnotation> docAnnots = 
+				JCasUtil.select(jCas, DocumentAnnotation.class);
+		
+		if (!docAnnots.isEmpty())
+		{
+			Object[] docAnnotArray = docAnnots.toArray();
+			docAnnot = (DocumentAnnotation) docAnnotArray[0];
+		}
 		
 		if (sEntity!=null) {
 			
+			// but I actually need to find out if this sentence is preceded by
+			// a newline or if I have to find the preceding one that does.
+			if (docAnnot != null)
+			{
+				String doctext = docAnnot.getCoveredText();
+				int sentStart = sEntity.getBegin();
+				
+				if (sentStart > 0)
+				{
+					boolean argInHistSection = false;
+					
+					// TOFIX:
+					// What I have to do here is not get the preceding char
+					// but rather get the chars in between prior sent and this
+					// and then check for newline therein.
+					String precedingChar =
+							doctext.substring(sentStart-1, sentStart);
+
+					// sort the sentences
+					// TODO: make it so you don't sort every time for same sentence.
+					ArrayList<Sentence> sentList = new ArrayList<Sentence>(sentences);
+					Collections.sort(sentList, new SentComparator());
+					
+					// get index of sEntity
+					int currind = sentList.indexOf(sEntity);
+					
+					if (currind == 0) {
+						argInHistSection = isInHistSection(sEntity);						
+					} else {
+						currind--;
+						Sentence prevSent = sentList.get(currind);
+						String tweenSents = doctext.substring(prevSent.getEnd(), sentStart);
+						if (tweenSents.indexOf("\n") != -1) {
+							// there is a newline between this sentence and prior sentence
+							argInHistSection = isInHistSection(sEntity);
+						} else if (currind == 0) {
+							argInHistSection = isInHistSection(prevSent);
+						} else {
+							while (currind > 0) {
+								Sentence currSent = prevSent;
+								currind--;
+								prevSent = sentList.get(currind);
+
+								sentStart = currSent.getBegin();
+								int prevSentEnd = prevSent.getEnd();
+								
+								try {
+									tweenSents = doctext.substring(prevSentEnd, sentStart);
+								} catch (StringIndexOutOfBoundsException e) {
+									System.err.println("wtf");
+								}
+
+								if (tweenSents.indexOf("\n") != -1 || currind == 0) {
+									argInHistSection = isInHistSection(currSent);
+									break;
+								} else if (currind == 0) {
+									argInHistSection = isInHistSection(prevSent);
+									break;										
+								}
+							}
+						}
+					}
+
+					// and here do something with argInHistSection.
+					// ie, create the feature
+					vfeat.put(IN_HIST_SECTION, argInHistSection);
+				}
+				
+			}
 
 			// 2) some other identified annotation subsumes this one?
 			List<IdentifiedAnnotation> lsmentions = JCasUtil.selectCovering(jCas, IdentifiedAnnotation.class,
arg.getBegin(), arg.getEnd());
@@ -157,15 +295,14 @@ public class HistoryAttributeClassifier 
 			for (Chunk chunk : lschunks) {
 				if ( chunk.getBegin()>arg.getBegin()) {
 					break;
-				} else {
-					if ( chunk.getEnd()<arg.getEnd()) {
-						continue;
-					} else if ( !DependencyUtility.equalCoverage(
-							DependencyUtility.getNominalHeadNode(jCas, chunk), 
-							DependencyUtility.getNominalHeadNode(jCas, arg)) ) {
-						// the case that annot is a superset
-						vfeat.put(SUBSUMED_CHUNK, true);
-					}
+				}
+				if ( chunk.getEnd()<arg.getEnd()) {
+					continue;
+				} else if ( !DependencyUtility.equalCoverage(
+						DependencyUtility.getNominalHeadNode(jCas, chunk), 
+						DependencyUtility.getNominalHeadNode(jCas, arg)) ) {
+					// the case that annot is a superset
+					vfeat.put(SUBSUMED_CHUNK, true);
 				}
 			}
 		}

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/subject/SubjectAttributeClassifier.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/subject/SubjectAttributeClassifier.java?rev=1520631&r1=1520630&r2=1520631&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/subject/SubjectAttributeClassifier.java
(original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/subject/SubjectAttributeClassifier.java
Fri Sep  6 17:00:43 2013
@@ -211,7 +211,6 @@ public class SubjectAttributeClassifier 
 		return vfeat;
 	}
 	
-	
 	public static String classifyWithLogic(HashMap<String, Boolean> vfeat) {
 		
 		if (vfeat==null) {



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