svn commit: r1516499 - /ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/SignSymptomDurations.java

[dl...@apache.org]

Author: dligach
Date: Thu Aug 22 16:12:30 2013
New Revision: 1516499

URL: http://svn.apache.org/r1516499
Log:
first shot at finding durations of sign/symptoms

Added:
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/SignSymptomDurations.java   (with props)

Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/SignSymptomDurations.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/SignSymptomDurations.java?rev=1516499&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/SignSymptomDurations.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/SignSymptomDurations.java Thu Aug 22 16:12:30 2013
@@ -0,0 +1,112 @@
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.ctakes.temporal.data.analysis;
+
+import java.io.File;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.List;
+
+import org.apache.ctakes.relationextractor.eval.XMIReader;
+import org.apache.ctakes.typesystem.type.structured.DocumentID;
+import org.apache.ctakes.typesystem.type.textsem.SignSymptomMention;
+import org.apache.ctakes.typesystem.type.textsem.TimeMention;
+import org.apache.uima.analysis_engine.AnalysisEngine;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.cas.CAS;
+import org.apache.uima.cas.CASException;
+import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.jcas.JCas;
+import org.cleartk.util.Options_ImplBase;
+import org.kohsuke.args4j.Option;
+import org.uimafit.component.JCasAnnotator_ImplBase;
+import org.uimafit.factory.AnalysisEngineFactory;
+import org.uimafit.factory.CollectionReaderFactory;
+import org.uimafit.pipeline.SimplePipeline;
+import org.uimafit.util.JCasUtil;
+
+/**
+ * ...
+ * 
+ * @author dmitriy dligach
+ */
+public class SignSymptomDurations {
+
+  public static class Options extends Options_ImplBase {
+
+    @Option(
+        name = "--input-dir",
+        usage = "specify the path to the directory containing the xmi files",
+        required = true)
+    public File inputDirectory;
+  }
+  
+	public static void main(String[] args) throws Exception {
+		
+		Options options = new Options();
+		options.parseOptions(args);
+
+		List<File> trainFiles = Arrays.asList(options.inputDirectory.listFiles());
+    CollectionReader collectionReader = getCollectionReader(trainFiles);
+		
+    AnalysisEngine durationPrinter = AnalysisEngineFactory.createPrimitive(
+    		DurationPrinter.class);
+    		
+		SimplePipeline.runPipeline(collectionReader, durationPrinter);
+	}
+  
+  public static class DurationPrinter extends JCasAnnotator_ImplBase {
+
+    @Override
+    public void process(JCas jCas) throws AnalysisEngineProcessException {
+
+      JCas systemView;
+      try {
+        systemView = jCas.getView(CAS.NAME_DEFAULT_SOFA);
+      } catch (CASException e) {
+        throw new AnalysisEngineProcessException(e);
+      }   
+
+      Collection<DocumentID> ids = JCasUtil.select(systemView, DocumentID.class);
+      String fileName = ids.iterator().next().getDocumentID();
+      String signSymptomText = fileName.split("\\.")[0]; // e.g. "smoker.txt"
+      
+      for(SignSymptomMention signSymptomMention : JCasUtil.select(systemView, SignSymptomMention.class)) {
+        if(signSymptomMention.getCoveredText().equals(signSymptomText)) {
+          for(TimeMention timeMention : JCasUtil.selectFollowing(systemView, TimeMention.class, signSymptomMention, 1)) {
+            System.out.println(signSymptomMention.getCoveredText() + ": " + timeMention.getCoveredText());
+          }
+        }
+      }
+    }
+  }
+  
+  private static CollectionReader getCollectionReader(List<File> items) throws Exception {
+
+    String[] paths = new String[items.size()];
+    for (int i = 0; i < paths.length; ++i) {
+      paths[i] = items.get(i).getPath();
+    }
+    
+    return CollectionReaderFactory.createCollectionReader(
+        XMIReader.class,
+        XMIReader.PARAM_FILES,
+        paths);
+  }
+}

Propchange: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/SignSymptomDurations.java
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