svn commit: r1462648 - /ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/RunCorpusDiagnostics.java

[tm...@apache.org]

Author: tmill
Date: Fri Mar 29 21:15:31 2013
New Revision: 1462648

URL: http://svn.apache.org/r1462648
Log:
Code for inspecting training data and printing out statistics of interest. Right now correlates relation classes with time classes.

Added:
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/RunCorpusDiagnostics.java   (with props)

Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/RunCorpusDiagnostics.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/RunCorpusDiagnostics.java?rev=1462648&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/RunCorpusDiagnostics.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/RunCorpusDiagnostics.java Fri Mar 29 21:15:31 2013
@@ -0,0 +1,126 @@
+/**
+ * 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.utils;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import org.apache.ctakes.temporal.eval.CommandLine;
+import org.apache.ctakes.temporal.eval.Evaluation_ImplBase;
+import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.XMIReader;
+import org.apache.ctakes.temporal.eval.THYMEData;
+import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
+import org.apache.ctakes.typesystem.type.relation.TemporalTextRelation;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textsem.TimeMention;
+import org.apache.ctakes.utils.struct.CounterMap;
+import org.apache.uima.UIMAException;
+import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+import org.cleartk.util.ae.UriToDocumentTextAnnotator;
+import org.cleartk.util.cr.UriCollectionReader;
+import org.uimafit.factory.AggregateBuilder;
+import org.uimafit.factory.AnalysisEngineFactory;
+import org.uimafit.pipeline.JCasIterable;
+import org.uimafit.util.JCasUtil;
+
+import com.lexicalscope.jewel.cli.CliFactory;
+import com.lexicalscope.jewel.cli.Option;
+
+public class RunCorpusDiagnostics {
+	static interface Options {
+
+		@Option(longName = "text")
+		public File getRawTextDirectory();
+
+		@Option(longName = "xmi")
+		public File getXMIDirectory();
+
+		@Option(longName = "patients")
+		public CommandLine.IntegerRanges getPatients();
+
+		@Option(longName = "treebank", defaultToNull=true)
+		public File getTreebankDirectory();
+	}
+
+	/**
+	 * @param args
+	 * @throws IOException 
+	 * @throws UIMAException 
+	 */
+	public static void main(String[] args) throws UIMAException, IOException {
+		Options options = CliFactory.parseArguments(Options.class, args);
+		List<Integer> patientSets = options.getPatients().getList();
+		List<Integer> trainItems = THYMEData.getTrainPatientSets(patientSets);
+		CollectionReader reader = UriCollectionReader.getCollectionReaderFromFiles(getFilesFor(options.getRawTextDirectory(), trainItems));
+		AggregateBuilder aggregateBuilder = new AggregateBuilder();
+		aggregateBuilder.add(UriToDocumentTextAnnotator.getDescription());
+		aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(
+				XMIReader.class,
+				XMIReader.PARAM_XMI_DIRECTORY,
+				options.getXMIDirectory()));
+
+		CounterMap<String> timeClassCounts = new CounterMap<String>();
+		
+		JCasIterable casIter = new JCasIterable(reader, aggregateBuilder.createAggregate());
+		while(casIter.hasNext()){
+			JCas jcas = casIter.next();
+			JCas goldView = jcas.getView(Evaluation_ImplBase.GOLD_VIEW_NAME);
+			Collection<TemporalTextRelation> rels = JCasUtil.select(goldView, TemporalTextRelation.class);
+			for(BinaryTextRelation rel : rels){
+				Annotation arg1 = rel.getArg1().getArgument();
+				Annotation arg2 = rel.getArg2().getArgument();
+				String timeClass = null;
+				if(arg1 instanceof TimeMention && arg2 instanceof EventMention){
+					timeClass = ((TimeMention) arg1).getTimeClass();
+				}else if(arg1 instanceof EventMention && arg2 instanceof TimeMention){
+					timeClass = ((TimeMention) arg2).getTimeClass();
+				}
+				
+				if(timeClass != null){
+					timeClassCounts.add(rel.getCategory()+"--"+timeClass);
+				}
+//				System.out.println("Found relation: " + rel.getCategory());
+			}
+		}
+		
+		for(String key : timeClassCounts.keySet()){
+			System.out.println(key + " => " + timeClassCounts.get(key));
+		}
+	}
+
+	private static List<File> getFilesFor(File rawTextDirectory, List<Integer> patientSets) {
+		List<File> files = new ArrayList<File>();
+		for (Integer set : patientSets) {
+			File setTextDirectory = new File(rawTextDirectory, "doc" + set);
+			for (File file : setTextDirectory.listFiles()) {
+				// skip hidden files like .svn
+				if (!file.isHidden()) {
+					files.add(file);
+				}
+			}
+		}
+		return files;
+	}
+
+}

Propchange: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/RunCorpusDiagnostics.java
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