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Posted to commits@ctakes.apache.org by cl...@apache.org on 2014/10/28 22:01:07 UTC
svn commit: r1634983 [3/3] - in
/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal: ae/
ae/feature/ eval/ pipelines/
Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfSelfEventTimeRelations.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfSelfEventTimeRelations.java?rev=1634983&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfSelfEventTimeRelations.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfSelfEventTimeRelations.java Tue Oct 28 21:01:06 2014
@@ -0,0 +1,984 @@
+/**
+ * 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.eval;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.PrintWriter;
+import java.net.URI;
+import java.util.ArrayDeque;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Deque;
+import java.util.HashMap;
+//import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments;
+import org.apache.ctakes.temporal.ae.EventTimeRelationAnnotator;
+import org.apache.ctakes.temporal.ae.EventTimeSelfRelationAnnotator;
+//import org.apache.ctakes.temporal.ae.EventTimeSyntacticAnnotator;
+//import org.apache.ctakes.temporal.ae.EventTimeRelationAnnotator;
+//import org.apache.ctakes.temporal.ae.EventEventRelationAnnotator;
+import org.apache.ctakes.temporal.ae.baselines.RecallBaselineEventTimeRelationAnnotator;
+import org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.ParameterSettings;
+import org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase.RemoveNonContainsRelations.RemoveGoldAttributes;
+//import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.WriteI2B2XML;
+//import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.XMLFormat;
+import org.apache.ctakes.temporal.utils.AnnotationIdCollection;
+import org.apache.ctakes.temporal.utils.TLinkTypeArray2;
+import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
+import org.apache.ctakes.typesystem.type.relation.RelationArgument;
+import org.apache.ctakes.typesystem.type.relation.TemporalTextRelation;
+//import org.apache.ctakes.typesystem.type.relation.TemporalTextRelation;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.TimeMention;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+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.apache.uima.jcas.tcas.Annotation;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.apache.uima.util.FileUtils;
+import org.cleartk.ml.jar.JarClassifierBuilder;
+import org.cleartk.ml.liblinear.LibLinearStringOutcomeDataWriter;
+//import org.cleartk.ml.libsvm.LibSvmStringOutcomeDataWriter;
+//import org.cleartk.ml.tksvmlight.TkSvmLightStringOutcomeDataWriter;
+import org.cleartk.ml.tksvmlight.model.CompositeKernel;
+import org.cleartk.ml.tksvmlight.model.CompositeKernel.ComboOperator;
+import org.cleartk.eval.AnnotationStatistics;
+import org.cleartk.util.ViewUriUtil;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.pipeline.JCasIterator;
+import org.apache.uima.fit.pipeline.SimplePipeline;
+import org.apache.uima.fit.util.JCasUtil;
+
+import com.google.common.base.Function;
+import com.google.common.collect.HashMultimap;
+import com.google.common.collect.Lists;
+import com.google.common.collect.Maps;
+import com.google.common.collect.Multimap;
+import com.google.common.collect.Sets;
+import com.lexicalscope.jewel.cli.CliFactory;
+import com.lexicalscope.jewel.cli.Option;
+
+public class EvaluationOfSelfEventTimeRelations extends
+EvaluationOfTemporalRelations_ImplBase{
+ static interface TempRelOptions extends Evaluation_ImplBase.Options{
+ @Option
+ public boolean getPrintFormattedRelations();
+
+ @Option
+ public boolean getBaseline();
+
+ @Option
+ public boolean getClosure();
+
+ @Option
+ public boolean getUseTmp();
+
+ @Option
+ public boolean getUseGoldAttributes();
+
+ @Option
+ public boolean getSkipTrain();
+ }
+
+ // protected static boolean DEFAULT_BOTH_DIRECTIONS = false;
+ // protected static float DEFAULT_DOWNSAMPLE = 1.0f;
+ // private static double DEFAULT_SVM_C = 1.0;
+ // private static double DEFAULT_SVM_G = 1.0;
+ // private static double DEFAULT_TK = 0.5;
+ // private static double DEFAULT_LAMBDA = 0.5;
+
+ // defaultParams = new ParameterSettings(DEFAULT_BOTH_DIRECTIONS, DEFAULT_DOWNSAMPLE, "tk",
+ // DEFAULT_SVM_C, DEFAULT_SVM_G, "polynomial", ComboOperator.SUM, DEFAULT_TK, DEFAULT_LAMBDA);
+ protected static ParameterSettings flatParams = new ParameterSettings(DEFAULT_BOTH_DIRECTIONS, DEFAULT_DOWNSAMPLE, "linear",
+ 10.0, 1.0, "linear", ComboOperator.VECTOR_ONLY, DEFAULT_TK, DEFAULT_LAMBDA);
+ protected static ParameterSettings allBagsParams = new ParameterSettings(DEFAULT_BOTH_DIRECTIONS, DEFAULT_DOWNSAMPLE, "tk",
+ 100.0, 0.1, "radial basis function", ComboOperator.SUM, 0.5, 0.5);
+ protected static ParameterSettings allParams = new ParameterSettings(DEFAULT_BOTH_DIRECTIONS, DEFAULT_DOWNSAMPLE, "tk",
+ 10.0, 1.0, "polynomial", ComboOperator.SUM, 0.1, 0.5); // (0.3, 0.4 for tklibsvm)
+ protected static ParameterSettings ftParams = new ParameterSettings(DEFAULT_BOTH_DIRECTIONS, DEFAULT_DOWNSAMPLE, "tk",
+ 1.0, 0.1, "radial basis function", ComboOperator.SUM, 0.5, 0.5);
+ private static Boolean recallModeEvaluation = true;
+
+ public static void main(String[] args) throws Exception {
+ TempRelOptions options = CliFactory.parseArguments(TempRelOptions.class, args);
+ List<Integer> trainItems = null;
+ List<Integer> devItems = null;
+ List<Integer> testItems = null;
+
+ List<Integer> patientSets = options.getPatients().getList();
+ if(options.getXMLFormat() == XMLFormat.I2B2){
+ trainItems = I2B2Data.getTrainPatientSets(options.getXMLDirectory());
+ devItems = I2B2Data.getDevPatientSets(options.getXMLDirectory());
+ testItems = I2B2Data.getTestPatientSets(options.getXMLDirectory());
+ }else{
+ trainItems = THYMEData.getPatientSets(patientSets, options.getTrainRemainders().getList());
+ devItems = THYMEData.getPatientSets(patientSets, options.getDevRemainders().getList());
+ testItems = THYMEData.getPatientSets(patientSets, options.getTestRemainders().getList());
+ }
+ ParameterSettings params = allParams;
+
+ // possibleParams.add(defaultParams);
+
+ // for(ParameterSettings params : possibleParams){
+ try{
+ File workingDir = new File("target/eval/thyme/");
+ if(!workingDir.exists()) workingDir.mkdirs();
+ if(options.getUseTmp()){
+ File tempModelDir = File.createTempFile("temporal", null, workingDir);
+ tempModelDir.delete();
+ tempModelDir.mkdir();
+ workingDir = tempModelDir;
+ }
+ EvaluationOfSelfEventTimeRelations evaluation = new EvaluationOfSelfEventTimeRelations(
+ workingDir,
+ options.getRawTextDirectory(),
+ options.getXMLDirectory(),
+ options.getXMLFormat(),
+ options.getXMIDirectory(),
+ options.getTreebankDirectory(),
+ options.getCoreferenceDirectory(),
+ options.getClosure(),
+ options.getPrintErrors(),
+ options.getPrintFormattedRelations(),
+ options.getBaseline(),
+ options.getUseGoldAttributes(),
+ options.getKernelParams(),
+ params);
+ evaluation.prepareXMIsFor(patientSets);
+ if(options.getI2B2Output()!=null) evaluation.setI2B2Output(options.getI2B2Output() + "/temporal-relations/event-time");
+ List<Integer> training = trainItems;
+ List<Integer> testing = null;
+ if(options.getTest()){
+ training.addAll(devItems);
+ testing = testItems;
+ }else{
+ testing = devItems;
+ }
+ //do closure on system, but not on gold, to calculate recall
+ evaluation.skipTrain = options.getSkipTrain();
+ params.stats = evaluation.trainAndRetrainAndTest(training, testing);//training);//
+ // System.err.println(options.getKernelParams() == null ? params : options.getKernelParams());
+ System.err.println("No closure on gold::Closure on System::Recall Mode");
+ System.err.println(params.stats);
+
+ //do closure on gold, but not on system, to calculate precision
+ evaluation.skipTrain = true;
+ recallModeEvaluation = false;
+ params.stats = evaluation.trainAndRetrainAndTest(training, testing);//training);//
+ // System.err.println(options.getKernelParams() == null ? params : options.getKernelParams());
+ System.err.println("No closure on System::Closure on Gold::Precision Mode");
+ System.err.println(params.stats);
+
+ //do closure on train, but not on test, to calculate plain results
+ evaluation.skipTrain = true;
+ evaluation.useClosure = false;
+ params.stats = evaluation.trainAndRetrainAndTest(training, testing);//training);//
+ // System.err.println(options.getKernelParams() == null ? params : options.getKernelParams());
+ System.err.println("Closure on train::No closure on Test::Plain Mode");
+ System.err.println(params.stats);
+
+
+ if(options.getUseTmp()){
+ // won't work because it's not empty. should we be concerned with this or is it responsibility of
+ // person invoking the tmp flag?
+ FileUtils.deleteRecursive(workingDir);
+ }
+ }catch(ResourceInitializationException e){
+ System.err.println("Error with parameter settings: " + params);
+ e.printStackTrace();
+ }
+ }
+
+ public AnnotationStatistics<String> trainAndRetrainAndTest(List<Integer> trainItems, List<Integer> testItems)
+ throws Exception {
+ File trainDirectory = new File(this.baseDirectory, "train");
+ File retrainDirectory = new File(this.baseDirectory, "retrain_and_test");
+ trainDirectory.mkdirs();
+ retrainDirectory.mkdir();
+ this.train(this.getCollectionReader(trainItems), trainDirectory);
+ this.preTest(this.getCollectionReader(trainItems), trainDirectory, retrainDirectory);
+ return this.test(this.getCollectionReader(testItems), retrainDirectory);
+ }
+
+ // private ParameterSettings params;
+ private boolean baseline;
+ protected boolean useClosure;
+ protected boolean useGoldAttributes;
+ protected boolean skipTrain=false;
+ // protected boolean printRelations = false;
+
+ public EvaluationOfSelfEventTimeRelations(
+ File baseDirectory,
+ File rawTextDirectory,
+ File xmlDirectory,
+ XMLFormat xmlFormat,
+ File xmiDirectory,
+ File treebankDirectory,
+ File coreferenceDirectory,
+ boolean useClosure,
+ boolean printErrors,
+ boolean printRelations,
+ boolean baseline,
+ boolean useGoldAttributes,
+ String kernelParams,
+ ParameterSettings params){
+ super(
+ baseDirectory,
+ rawTextDirectory,
+ xmlDirectory,
+ xmlFormat,
+ xmiDirectory,
+ treebankDirectory,
+ coreferenceDirectory,
+ printErrors,
+ printRelations,
+ params);
+ this.params = params;
+ this.useClosure = useClosure;
+ this.printErrors = printErrors;
+ this.printRelations = printRelations;
+ this.useGoldAttributes = useGoldAttributes;
+ this.baseline = baseline;
+ this.kernelParams = kernelParams == null ? null : kernelParams.split(" ");
+ }
+
+ // public EvaluationOfTemporalRelations(File baseDirectory, File rawTextDirectory,
+ // File knowtatorXMLDirectory, File xmiDirectory) {
+ //
+ // super(baseDirectory, rawTextDirectory, knowtatorXMLDirectory, xmiDirectory, null);
+ // this.params = defaultParams;
+ // this.printErrors = false;
+ // }
+
+ @Override
+ protected void train(CollectionReader collectionReader, File directory) throws Exception {
+ // if(this.baseline) return;
+ if(this.skipTrain) return;
+ AggregateBuilder aggregateBuilder = this.getPreprocessorAggregateBuilder();
+ aggregateBuilder.add(CopyFromGold.getDescription(EventMention.class, TimeMention.class, BinaryTextRelation.class));
+ aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveCrossSentenceRelations.class));
+ if(!this.useGoldAttributes){
+ aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveGoldAttributes.class));
+ }
+ if (this.useClosure) {
+ aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(AddClosure.class));//aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(AddTransitiveContainsRelations.class));
+ // aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(AddContain2Overlap.class));
+ // aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(AddTransitiveBeforeAndOnRelations.class));
+ }
+ // aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(RemoveNonContainsRelations.class));
+ // aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(AddFlippedOverlap.class));//add flipped overlap instances to training data
+
+ aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveEventEventRelations.class));
+ aggregateBuilder.add(EventTimeRelationAnnotator.createDataWriterDescription(
+ LibLinearStringOutcomeDataWriter.class,
+ // LIBSVMStringOutcomeDataWriter.class,
+ // TKSVMlightStringOutcomeDataWriter.class,
+ // TKLIBSVMStringOutcomeDataWriter.class,
+ // SVMlightStringOutcomeDataWriter.class,
+ new File(directory,"event-time"),
+ params.probabilityOfKeepingANegativeExample));
+ // aggregateBuilder.add(EventEventRelationAnnotator.createDataWriterDescription(
+ // LIBSVMStringOutcomeDataWriter.class,
+ // new File(directory,"event-event"),
+ // params.probabilityOfKeepingANegativeExample));
+ SimplePipeline.runPipeline(collectionReader, aggregateBuilder.createAggregate());
+ String[] optArray;
+
+ if(this.kernelParams == null){
+ ArrayList<String> svmOptions = new ArrayList<>();
+ svmOptions.add("-c"); svmOptions.add(""+params.svmCost); // svm cost
+ svmOptions.add("-t"); svmOptions.add(""+params.svmKernelIndex); // kernel index
+ svmOptions.add("-d"); svmOptions.add("3"); // degree parameter for polynomial
+ svmOptions.add("-g"); svmOptions.add(""+params.svmGamma);
+ if(params.svmKernelIndex==ParameterSettings.SVM_KERNELS.indexOf("tk")){
+ svmOptions.add("-S"); svmOptions.add(""+params.secondKernelIndex); // second kernel index (similar to -t) for composite kernel
+ String comboFlag = (params.comboOperator == ComboOperator.SUM ? "+" : params.comboOperator == ComboOperator.PRODUCT ? "*" : params.comboOperator == ComboOperator.TREE_ONLY ? "T" : "V");
+ svmOptions.add("-C"); svmOptions.add(comboFlag);
+ svmOptions.add("-L"); svmOptions.add(""+params.lambda);
+ svmOptions.add("-T"); svmOptions.add(""+params.tkWeight);
+ svmOptions.add("-N"); svmOptions.add("3"); // normalize trees and features
+ }
+ optArray = svmOptions.toArray(new String[]{});
+ }else{
+ optArray = this.kernelParams;
+ for(int i = 0; i < optArray.length; i+=2){
+ optArray[i] = "-" + optArray[i];
+ }
+ }
+
+ // HideOutput hider = new HideOutput();
+ JarClassifierBuilder.trainAndPackage(new File(directory,"event-time"), "-w3","2","-w4","18","-w5","13","-w6","21","-w7","87","-w8","19","-c", optArray[1]);//"0.05");//"-h","0","-c", "1000");//optArray);
+ // JarClassifierBuilder.trainAndPackage(new File(directory,"event-event"), "-h","0","-c", "1000");
+ // hider.restoreOutput();
+ // hider.close();
+ }
+
+ @Override
+ protected AnnotationStatistics<String> test(CollectionReader collectionReader, File directory)
+ throws Exception {
+ AggregateBuilder aggregateBuilder = this.getPreprocessorAggregateBuilder();
+ aggregateBuilder.add(CopyFromGold.getDescription(EventMention.class, TimeMention.class));
+
+ aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(
+ RemoveCrossSentenceRelations.class,
+ RemoveCrossSentenceRelations.PARAM_SENTENCE_VIEW,
+ CAS.NAME_DEFAULT_SOFA,
+ RemoveCrossSentenceRelations.PARAM_RELATION_VIEW,
+ GOLD_VIEW_NAME));
+
+ if (!recallModeEvaluation && this.useClosure) { //closure for gold
+ aggregateBuilder.add(
+ AnalysisEngineFactory.createEngineDescription(AddClosure.class),//AnalysisEngineFactory.createPrimitiveDescription(AddTransitiveContainsRelations.class),
+ CAS.NAME_DEFAULT_SOFA,
+ GOLD_VIEW_NAME);
+ }
+
+ aggregateBuilder.add(
+ AnalysisEngineFactory.createEngineDescription(RemoveEventEventRelations.class),
+ CAS.NAME_DEFAULT_SOFA,
+ GOLD_VIEW_NAME);
+
+ aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveRelations.class));
+ aggregateBuilder.add(EventTimeRelationAnnotator.createEngineDescription(new File(directory,"event-time")));
+
+ if(this.i2b2Output != null){
+ aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(WriteI2B2XML.class, WriteI2B2XML.PARAM_OUTPUT_DIR, this.i2b2Output), "TimexView", CAS.NAME_DEFAULT_SOFA);
+ }
+
+ File outf = null;
+ if (recallModeEvaluation && this.useClosure) {//add closure for system output
+ aggregateBuilder.add(
+ AnalysisEngineFactory.createEngineDescription(AddClosure.class),//AnalysisEngineFactory.createPrimitiveDescription(AddTransitiveContainsRelations.class),
+ GOLD_VIEW_NAME,
+ CAS.NAME_DEFAULT_SOFA
+ );
+ aggregateBuilder.add(
+ AnalysisEngineFactory.createEngineDescription(RemoveEventEventRelations.class),
+ GOLD_VIEW_NAME,
+ CAS.NAME_DEFAULT_SOFA
+ );
+ outf = new File("target/eval/thyme/SystemError_eventTime_recall_dev.txt");
+ }else if (!recallModeEvaluation && this.useClosure){
+ outf = new File("target/eval/thyme/SystemError_eventTime_precision_dev.txt");
+ }else{
+ outf = new File("target/eval/thyme/SystemError_eventTime_plain_dev.txt");
+ }
+
+ PrintWriter outDrop =null;
+
+ outDrop = new PrintWriter(new BufferedWriter(new FileWriter(outf, false)));
+
+ Function<BinaryTextRelation, ?> getSpan = new Function<BinaryTextRelation, HashableArguments>() {
+ public HashableArguments apply(BinaryTextRelation relation) {
+ return new HashableArguments(relation);
+ }
+ };
+ Function<BinaryTextRelation, String> getOutcome = AnnotationStatistics.annotationToFeatureValue("category");
+
+ AnnotationStatistics<String> stats = new AnnotationStatistics<>();
+ JCasIterator jcasIter =new JCasIterator(collectionReader, aggregateBuilder.createAggregate());
+ JCas jCas = null;
+ while(jcasIter.hasNext()) {
+ jCas = jcasIter.next();
+ JCas goldView = jCas.getView(GOLD_VIEW_NAME);
+ JCas systemView = jCas.getView(CAS.NAME_DEFAULT_SOFA);
+ Collection<BinaryTextRelation> goldRelations = JCasUtil.select(
+ goldView,
+ BinaryTextRelation.class);
+ Collection<BinaryTextRelation> systemRelations = JCasUtil.select(
+ systemView,
+ BinaryTextRelation.class);
+
+ //newly add
+ // systemRelations = removeNonGoldRelations(systemRelations, goldRelations, getSpan);//for removing non-gold pairs
+ // systemRelations = correctArgOrder(systemRelations, goldRelations);//change the argument order of "OVERLAP" relation, if the order is flipped
+ //find duplicates in gold relations:
+ // Collection<BinaryTextRelation> duplicateGoldRelations = getDuplicateRelations(goldRelations, getSpan);
+ // if(!duplicateGoldRelations.isEmpty()){
+ // System.err.println("******Duplicate gold relations in : " + ViewURIUtil.getURI(jCas).toString());
+ // for (BinaryTextRelation rel : duplicateGoldRelations){
+ // System.err.println("Duplicate : "+ formatRelation(rel));
+ // }
+ // }
+ //end newly add
+
+ stats.add(goldRelations, systemRelations, getSpan, getOutcome);
+ if(this.printRelations){
+ URI uri = ViewUriUtil.getURI(jCas);
+ String[] path = uri.getPath().split("/");
+ printRelationAnnotations(path[path.length - 1], systemRelations);
+ }
+ if(this.printErrors){
+ Map<HashableArguments, BinaryTextRelation> goldMap = Maps.newHashMap();
+ for (BinaryTextRelation relation : goldRelations) {
+ goldMap.put(new HashableArguments(relation), relation);
+ }
+ Map<HashableArguments, BinaryTextRelation> systemMap = Maps.newHashMap();
+ for (BinaryTextRelation relation : systemRelations) {
+ systemMap.put(new HashableArguments(relation), relation);
+ }
+ Set<HashableArguments> all = Sets.union(goldMap.keySet(), systemMap.keySet());
+ List<HashableArguments> sorted = Lists.newArrayList(all);
+ Collections.sort(sorted);
+ outDrop.println("Doc id: " + ViewUriUtil.getURI(jCas).toString());
+ for (HashableArguments key : sorted) {
+ BinaryTextRelation goldRelation = goldMap.get(key);
+ BinaryTextRelation systemRelation = systemMap.get(key);
+ if (goldRelation == null) {
+ outDrop.println("System added: " + formatRelation(systemRelation));
+ } else if (systemRelation == null) {
+ outDrop.println("System dropped: " + formatRelation(goldRelation));
+ } else if (!systemRelation.getCategory().equals(goldRelation.getCategory())) {
+ String label = systemRelation.getCategory();
+ outDrop.printf("System labeled %s for %s\n", label, formatRelation(goldRelation));
+ } else{
+ outDrop.println("Nailed it! " + formatRelation(systemRelation));
+ }
+ }
+ }
+ }
+ outDrop.close();
+ return stats;
+ }
+
+ private void preTest(CollectionReader collectionReader, File directory, File retrainDirectory) throws Exception {
+ if(this.skipTrain) return;
+ AggregateBuilder aggregateBuilder = this.getPreprocessorAggregateBuilder();
+// aggregateBuilder.add(CopyFromGold.getDescription(EventMention.class,TimeMention.class));
+
+ aggregateBuilder.add(CopyFromGold.getDescription(EventMention.class, TimeMention.class, TemporalTextRelation.class));
+// aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveEventEventRelations.class));
+ // aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(
+ // RemoveCrossSentenceRelations.class,
+ // RemoveCrossSentenceRelations.PARAM_SENTENCE_VIEW,
+ // CAS.NAME_DEFAULT_SOFA,
+ // RemoveCrossSentenceRelations.PARAM_RELATION_VIEW,
+ // GOLD_VIEW_NAME));
+
+
+// aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveRelations.class));
+ //annotate on system-generated events, for event-time relations
+ aggregateBuilder.add(EventTimeSelfRelationAnnotator.createEngineDescription(new File(directory,"event-time")));
+
+ // //re-train:
+ //overwrite system-generated relations by gold temporal relations:
+// aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(OverwriteTemporalRelationToSystem.class));
+
+ //add closure for system output
+ aggregateBuilder.add(
+ AnalysisEngineFactory.createEngineDescription(AddClosure.class),//AnalysisEngineFactory.createPrimitiveDescription(AddTransitiveContainsRelations.class),
+ GOLD_VIEW_NAME,
+ CAS.NAME_DEFAULT_SOFA
+ );
+ aggregateBuilder.add(
+ AnalysisEngineFactory.createEngineDescription(RemoveEventEventRelations.class),
+ GOLD_VIEW_NAME,
+ CAS.NAME_DEFAULT_SOFA
+ );
+
+ // aggregateBuilder.add(CopyFromGold.getDescription(EventMention.class, TimeMention.class, BinaryTextRelation.class));//could not copy over, because it will remove all system generated relations
+ aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveCrossSentenceRelations.class));
+
+ if(!this.useGoldAttributes){
+ aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveGoldAttributes.class));
+ }
+
+ // aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveEventEventRelations.class));
+ aggregateBuilder.add(EventTimeSelfRelationAnnotator.createDataWriterDescription(
+ LibLinearStringOutcomeDataWriter.class,
+ // LIBSVMStringOutcomeDataWriter.class,
+ // TKSVMlightStringOutcomeDataWriter.class,
+ // TKLIBSVMStringOutcomeDataWriter.class,
+ // SVMlightStringOutcomeDataWriter.class,
+ new File(retrainDirectory,"event-time"),
+ params.probabilityOfKeepingANegativeExample));
+ // aggregateBuilder.add(EventEventRelationAnnotator.createDataWriterDescription(
+ // LIBSVMStringOutcomeDataWriter.class,
+ // new File(directory,"event-event"),
+ // params.probabilityOfKeepingANegativeExample));
+ SimplePipeline.runPipeline(collectionReader, aggregateBuilder.createAggregate());
+ String[] optArray;
+
+ if(this.kernelParams == null){
+ ArrayList<String> svmOptions = new ArrayList<>();
+ svmOptions.add("-c"); svmOptions.add(""+params.svmCost); // svm cost
+ svmOptions.add("-t"); svmOptions.add(""+params.svmKernelIndex); // kernel index
+ svmOptions.add("-d"); svmOptions.add("3"); // degree parameter for polynomial
+ svmOptions.add("-g"); svmOptions.add(""+params.svmGamma);
+ if(params.svmKernelIndex==ParameterSettings.SVM_KERNELS.indexOf("tk")){
+ svmOptions.add("-S"); svmOptions.add(""+params.secondKernelIndex); // second kernel index (similar to -t) for composite kernel
+ String comboFlag = (params.comboOperator == ComboOperator.SUM ? "+" : params.comboOperator == ComboOperator.PRODUCT ? "*" : params.comboOperator == ComboOperator.TREE_ONLY ? "T" : "V");
+ svmOptions.add("-C"); svmOptions.add(comboFlag);
+ svmOptions.add("-L"); svmOptions.add(""+params.lambda);
+ svmOptions.add("-T"); svmOptions.add(""+params.tkWeight);
+ svmOptions.add("-N"); svmOptions.add("3"); // normalize trees and features
+ }
+ optArray = svmOptions.toArray(new String[]{});
+ }else{
+ optArray = this.kernelParams;
+ for(int i = 0; i < optArray.length; i+=2){
+ optArray[i] = "-" + optArray[i];
+ }
+ }
+
+ // HideOutput hider = new HideOutput();
+ JarClassifierBuilder.trainAndPackage(new File(retrainDirectory,"event-time"), "-w1","0.6","-c", optArray[1]);//"-w1","0.6","-w3","28","-w4","8","-w5","2","-w6","9","-w7","9","-w8","12","-c", optArray[1]);//"0.05");//"-h","0","-c", "1000");//optArray);
+ // JarClassifierBuilder.trainAndPackage(new File(directory,"event-event"), "-h","0","-c", "1000");
+ // hider.restoreOutput();
+ // hider.close();
+ // TODO Auto-generated method stub
+
+ }
+
+
+ public static class RemoveEventEventRelations extends JCasAnnotator_ImplBase {
+ public static final String PARAM_RELATION_VIEW = "RelationView";
+ @ConfigurationParameter(name = PARAM_RELATION_VIEW,mandatory=false)
+ private String relationViewName = CAS.NAME_DEFAULT_SOFA;
+
+ @Override
+ public void process(JCas jCas) throws AnalysisEngineProcessException {
+ JCas relationView;
+ try {
+ relationView = jCas.getView(this.relationViewName);
+ } catch (CASException e) {
+ throw new AnalysisEngineProcessException(e);
+ }
+
+ for(BinaryTextRelation relation : Lists.newArrayList(JCasUtil.select(relationView, BinaryTextRelation.class))){
+ // if(relation.getCategory().equals("CONTAINS")){
+ RelationArgument arg1 = relation.getArg1();
+ RelationArgument arg2 = relation.getArg2();
+ if(arg1.getArgument() instanceof TimeMention && arg2.getArgument() instanceof EventMention ||
+ arg1.getArgument() instanceof EventMention && arg2.getArgument() instanceof TimeMention){
+ // these are the kind we keep.
+ continue;
+ }
+ // if(arg1.getArgument() instanceof EventMention && arg2.getArgument() instanceof EventMention){
+ arg1.removeFromIndexes();
+ arg2.removeFromIndexes();
+ relation.removeFromIndexes();
+ }
+ // }
+
+ }
+ }
+
+ public static class OverwriteTemporalRelationToSystem extends JCasAnnotator_ImplBase {
+
+ @Override
+ public void process(JCas jCas) throws AnalysisEngineProcessException {
+ JCas systemView;
+ JCas goldView;
+ try {
+ systemView = jCas.getView(CAS.NAME_DEFAULT_SOFA);
+ goldView = jCas.getView(GOLD_VIEW_NAME);
+ } catch (CASException e) {
+ throw new AnalysisEngineProcessException(e);
+ }
+
+ Map<List<Integer>, TemporalTextRelation> goldRelationLookup = new HashMap<>();
+
+ for(TemporalTextRelation relation: JCasUtil.select(goldView, TemporalTextRelation.class)){
+ Annotation arg1 = relation.getArg1().getArgument();
+ Annotation arg2 = relation.getArg2().getArgument();
+
+ //populate gold relation hashmap:
+ goldRelationLookup.put(Arrays.asList(arg1.getBegin(),arg1.getEnd(),arg2.getBegin(),arg2.getEnd()), relation);
+ }
+
+ //iterate system relations to update any conflicts with gold
+ for(TemporalTextRelation relation: JCasUtil.select(systemView, TemporalTextRelation.class)){
+ Annotation arg1 = relation.getArg1().getArgument();
+ Annotation arg2 = relation.getArg2().getArgument();
+ String sysLabel = relation.getCategory();
+ int arg1Beg = arg1.getBegin();
+ int arg1End = arg1.getEnd();
+ int arg2Beg = arg2.getBegin();
+ int arg2End = arg2.getEnd();
+ TemporalTextRelation goldRel = goldRelationLookup.get(Arrays.asList(arg1Beg,arg1End,arg2Beg,arg2End));
+ String goldLabel = null;
+ if(goldRel != null){
+ goldLabel = goldRel.getCategory();
+ if(!goldLabel.equals(sysLabel)){
+ relation.setCategory(goldLabel);
+ }
+ }else{//gold relation is not found
+ goldRel = goldRelationLookup.get(Arrays.asList(arg2Beg,arg2End, arg1Beg,arg1End));
+ if(goldRel != null){
+ RelationArgument tempArg = (RelationArgument) relation.getArg1().clone();
+ relation.setArg1((RelationArgument) relation.getArg2().clone());
+ relation.setArg2(tempArg);
+ goldLabel = goldRel.getCategory();
+ relation.setCategory(goldLabel);
+ }
+ }
+ }
+
+ }
+ }
+
+
+ public static class RemoveCrossSentenceRelations extends JCasAnnotator_ImplBase {
+
+ public static final String PARAM_SENTENCE_VIEW = "SentenceView";
+
+ @ConfigurationParameter(name = PARAM_SENTENCE_VIEW,mandatory=false)
+ private String sentenceViewName = CAS.NAME_DEFAULT_SOFA;
+
+ public static final String PARAM_RELATION_VIEW = "RelationView";
+
+ @ConfigurationParameter(name = PARAM_RELATION_VIEW,mandatory=false)
+ private String relationViewName = CAS.NAME_DEFAULT_SOFA;
+
+ @Override
+ public void process(JCas jCas) throws AnalysisEngineProcessException {
+ JCas sentenceView, relationView;
+ try {
+ sentenceView = jCas.getView(this.sentenceViewName);
+ relationView = jCas.getView(this.relationViewName);
+ } catch (CASException e) {
+ throw new AnalysisEngineProcessException(e);
+ }
+
+ // map events and times to the sentences that contain them
+ Map<IdentifiedAnnotation, Integer> sentenceIndex = Maps.newHashMap();
+ int index = -1;
+ for (Sentence sentence : JCasUtil.select(sentenceView, Sentence.class)) {
+ ++index;
+ for (EventMention event : JCasUtil.selectCovered(relationView, EventMention.class, sentence)) {
+ sentenceIndex.put(event, index);
+ }
+ for (TimeMention time : JCasUtil.selectCovered(relationView, TimeMention.class, sentence)) {
+ sentenceIndex.put(time, index);
+ }
+ }
+
+ // remove any relations that are in different sentences.
+ for (BinaryTextRelation relation : Lists.newArrayList(JCasUtil.select(
+ relationView,
+ BinaryTextRelation.class))) {
+ Integer sent1 = sentenceIndex.get(relation.getArg1().getArgument());
+ Integer sent2 = sentenceIndex.get(relation.getArg2().getArgument());
+ if (sent1 == null || sent2 == null || !sent1.equals(sent2)) {
+ relation.getArg1().removeFromIndexes();
+ relation.getArg2().removeFromIndexes();
+ relation.removeFromIndexes();
+ }
+ }
+ }
+ }
+
+
+ public static class RemoveRelations extends JCasAnnotator_ImplBase {
+ @Override
+ public void process(JCas jCas) throws AnalysisEngineProcessException {
+ for (BinaryTextRelation relation : Lists.newArrayList(JCasUtil.select(
+ jCas,
+ BinaryTextRelation.class))) {
+ relation.getArg1().removeFromIndexes();
+ relation.getArg2().removeFromIndexes();
+ relation.removeFromIndexes();
+ }
+ }
+ }
+
+
+
+ public static class AddContain2Overlap extends JCasAnnotator_ImplBase {
+
+ @Override
+ public void process(JCas jCas) throws AnalysisEngineProcessException {
+
+ Set<BinaryTextRelation> containsRelations = Sets.newHashSet();
+ for (BinaryTextRelation relation : JCasUtil.select(jCas, BinaryTextRelation.class)) {
+ if (relation.getCategory().equals("CONTAINS")) {
+ containsRelations.add(relation);
+ }
+ }
+
+ for (BinaryTextRelation relation : containsRelations) {
+ RelationArgument arg1 = (RelationArgument) relation.getArg1().clone();
+ RelationArgument arg2 = (RelationArgument) relation.getArg2().clone();
+ BinaryTextRelation newrelation = new BinaryTextRelation(jCas);
+ newrelation.setArg1(arg1);
+ newrelation.setArg2(arg2);
+ newrelation.setCategory("OVERLAP");
+ arg1.addToIndexes();
+ arg2.addToIndexes();
+ newrelation.addToIndexes();
+ }
+ }
+ }
+
+ public static class AddFlippedOverlap extends JCasAnnotator_ImplBase {
+
+ @Override
+ public void process(JCas jCas) throws AnalysisEngineProcessException {
+
+ Set<BinaryTextRelation> overlapRelations = Sets.newHashSet();
+ Multimap<Annotation, Annotation> overlaps = HashMultimap.create();
+ for (BinaryTextRelation relation : JCasUtil.select(jCas, BinaryTextRelation.class)) {
+ if (relation.getCategory().equals("OVERLAP")) {
+ overlapRelations.add(relation);
+ Annotation arg1 = relation.getArg1().getArgument();
+ Annotation arg2 = relation.getArg2().getArgument();
+ overlaps.put(arg1, arg2);
+ }
+ }
+
+ for (BinaryTextRelation orelation : overlapRelations) {
+ Annotation argA = orelation.getArg1().getArgument();
+ Annotation argB = orelation.getArg2().getArgument();
+ //add overlap
+ if (!overlaps.containsEntry(argB, argA)) {
+ //create a new flipped relation:
+ RelationArgument arg1 = new RelationArgument(jCas);
+ arg1.setArgument(argB);
+ RelationArgument arg2 = new RelationArgument(jCas);
+ arg2.setArgument(argA);
+ BinaryTextRelation relation = new BinaryTextRelation(jCas);
+ relation.setArg1(arg1);
+ relation.setArg2(arg2);
+ relation.setCategory("OVERLAP");
+ arg1.addToIndexes();
+ arg2.addToIndexes();
+ relation.addToIndexes();
+ overlaps.put(argB, argA);
+ }
+
+ }
+ }
+ }
+
+ public static class AddClosure extends JCasAnnotator_ImplBase {
+
+ @Override
+ public void process(JCas jCas) throws AnalysisEngineProcessException {
+
+ Multimap<List<Annotation>, BinaryTextRelation> annotationsToRelation = HashMultimap.create();
+ for (BinaryTextRelation relation : JCasUtil.select(jCas, BinaryTextRelation.class)){
+ String relationType = relation.getCategory();
+ if(validTemporalType(relationType)){
+ Annotation arg1 = relation.getArg1().getArgument();
+ Annotation arg2 = relation.getArg2().getArgument();
+ annotationsToRelation.put(Arrays.asList(arg1, arg2), relation);
+ }
+ }
+ for (List<Annotation> span: Lists.newArrayList(annotationsToRelation.keySet())){
+ Collection<BinaryTextRelation> relations = annotationsToRelation.get(span);
+ if(relations.size()>1){//if same span maps to multiple relations
+ Set<String> types = Sets.newHashSet();
+ for(BinaryTextRelation relation: relations){
+ types.add(relation.getCategory());
+ }
+ if(types.size()>1){
+ for(BinaryTextRelation relation: Lists.newArrayList(relations)){
+ annotationsToRelation.remove(span, relation);
+ relation.getArg1().removeFromIndexes();
+ relation.getArg2().removeFromIndexes();
+ relation.removeFromIndexes();
+ }
+ }else if(types.size()==1){
+ for (int i =1; i< relations.size(); i++){
+ BinaryTextRelation relation = (BinaryTextRelation) relations.toArray()[i];
+ annotationsToRelation.remove(span, relation);
+ relation.getArg1().removeFromIndexes();
+ relation.getArg2().removeFromIndexes();
+ relation.removeFromIndexes();
+ }
+ }
+ }
+ }
+
+ ArrayList<BinaryTextRelation> temporalRelation = new ArrayList<>(annotationsToRelation.values());//new ArrayList<BinaryTextRelation>();
+ // Map<List<Annotation>, BinaryTextRelation> temporalRelationLookup = new HashMap<List<Annotation>, BinaryTextRelation>();
+ //
+ // for (BinaryTextRelation relation : JCasUtil.select(jCas, BinaryTextRelation.class)){
+ // String relationType = relation.getCategory();
+ // if(validTemporalType(relationType)){
+ // Annotation arg1 = relation.getArg1().getArgument();
+ // Annotation arg2 = relation.getArg2().getArgument();
+ // BinaryTextRelation tempRelation = temporalRelationLookup.get(Arrays.asList(arg1, arg2));
+ // if( tempRelation == null){
+ // temporalRelation.add(relation);
+ // temporalRelationLookup.put(Arrays.asList(arg1, arg2), relation);
+ // }else{//if there is duplicate
+ // relation.getArg1().removeFromIndexes();
+ // relation.getArg2().removeFromIndexes();
+ // relation.removeFromIndexes();
+ // }
+ //
+ // }
+ // }
+
+ if (!temporalRelation.isEmpty()){
+ TLinkTypeArray2 relationArray = new TLinkTypeArray2(temporalRelation, new AnnotationIdCollection(temporalRelation));
+
+ int addedCount = 0;
+ for (BinaryTextRelation relation : relationArray.getClosedTlinks(jCas)) {
+ RelationArgument arg1 = relation.getArg1();
+ RelationArgument arg2 = relation.getArg2();
+ String relationType = relation.getCategory();
+ if(relationType.equals("CONTAINED-BY")||relationType.equals("AFTER")){//ignore these two categories, because their reciprocal already exist.
+ continue;
+ }
+ //check if the inferred relation new:
+ Collection<BinaryTextRelation> relations = annotationsToRelation.get(Arrays.asList(arg1.getArgument(), arg2.getArgument()));
+ if(relations.isEmpty()){ //if haven't seen this inferred relation before, then add this relation
+ arg1.addToIndexes();
+ arg2.addToIndexes();
+ relation.addToIndexes();
+ addedCount++;
+ }
+ }
+
+ System.out.println( "**************************************************************");
+ System.out.println( "Finally added closure relations: " + addedCount );
+ System.out.println( "**************************************************************");
+ }
+
+ }
+
+ private static boolean validTemporalType(String relationType) {
+ if(relationType.equals("CONTAINS")||relationType.equals("OVERLAP")||relationType.equals("BEFORE")||relationType.equals("ENDS-ON")||relationType.equals("BEGINS-ON"))
+ return true;
+ return false;
+ }
+ }
+
+ // public static class AddTransitiveBeforeAndOnRelations extends JCasAnnotator_ImplBase {
+ //
+ // @Override
+ // public void process(JCas jCas) throws AnalysisEngineProcessException {
+ //
+ // // collect many-to-many mappings of containment relations
+ // Multimap<Annotation, Annotation> contains = HashMultimap.create();
+ // Multimap<Annotation, Annotation> before = HashMultimap.create();
+ // Multimap<Annotation, Annotation> endson = HashMultimap.create();
+ // Multimap<Annotation, Annotation> beginson = HashMultimap.create();
+ // Set<BinaryTextRelation> beforeRel = Sets.newHashSet();
+ //
+ // for (BinaryTextRelation relation : JCasUtil.select(jCas, BinaryTextRelation.class)) {
+ // if (relation.getCategory().equals("CONTAINS")) {
+ // Annotation arg1 = relation.getArg1().getArgument();
+ // Annotation arg2 = relation.getArg2().getArgument();
+ // contains.put(arg1, arg2);
+ // }else if (relation.getCategory().equals("BEFORE")) {
+ // Annotation arg1 = relation.getArg1().getArgument();
+ // Annotation arg2 = relation.getArg2().getArgument();
+ // before.put(arg1, arg2);
+ // beforeRel.add(relation);
+ // }else if (relation.getCategory().equals("ENDS-ON")) {
+ // Annotation arg1 = relation.getArg1().getArgument();
+ // Annotation arg2 = relation.getArg2().getArgument();
+ // endson.put(arg1, arg2);
+ // if (!endson.containsEntry(arg2, arg1)) {
+ // endson.put(arg2, arg1);
+ // }
+ // }else if (relation.getCategory().equals("BEGINS-ON")) {
+ // Annotation arg1 = relation.getArg1().getArgument();
+ // Annotation arg2 = relation.getArg2().getArgument();
+ // beginson.put(arg1, arg2);
+ // if (!beginson.containsEntry(arg2, arg1)) {
+ // beginson.put(arg2, arg1);
+ // }
+ // }
+ // }
+ //
+ // // for A BEFORE B, check if A and B Contain anything
+ // for (BinaryTextRelation brelation : beforeRel) {
+ // Annotation argA = brelation.getArg1().getArgument();
+ // Annotation argB = brelation.getArg2().getArgument();
+ // //add contained before
+ // for (Annotation childA : contains.get(argA)) {
+ // for (Annotation childB : contains.get(argB)) {
+ // if (!before.containsEntry(childA, childB)) {
+ // //create a new before relation:
+ // RelationArgument arg1 = new RelationArgument(jCas);
+ // arg1.setArgument(childA);
+ // RelationArgument arg2 = new RelationArgument(jCas);
+ // arg2.setArgument(childB);
+ // BinaryTextRelation relation = new BinaryTextRelation(jCas);
+ // relation.setArg1(arg1);
+ // relation.setArg2(arg2);
+ // relation.setCategory("BEFORE");
+ // arg1.addToIndexes();
+ // arg2.addToIndexes();
+ // relation.addToIndexes();
+ // before.put(childA, childB);
+ // }
+ // }
+ // }
+ // //add ends-on A
+ // for (Annotation endsOnA : endson.get(argA)) {
+ // if (!before.containsEntry(endsOnA, argB)) {
+ // //create a new before relation:
+ // RelationArgument arg1 = new RelationArgument(jCas);
+ // arg1.setArgument(endsOnA);
+ // RelationArgument arg2 = new RelationArgument(jCas);
+ // arg2.setArgument(argB);
+ // BinaryTextRelation relation = new BinaryTextRelation(jCas);
+ // relation.setArg1(arg1);
+ // relation.setArg2(arg2);
+ // relation.setCategory("BEFORE");
+ // arg1.addToIndexes();
+ // arg2.addToIndexes();
+ // relation.addToIndexes();
+ // before.put(endsOnA, argB);
+ // }
+ // }
+ // //add begins-on B
+ // for (Annotation beginsOnB : beginson.get(argB)) {
+ // if (!before.containsEntry(argA, beginsOnB)) {
+ // //create a new before relation:
+ // RelationArgument arg1 = new RelationArgument(jCas);
+ // arg1.setArgument(argA);
+ // RelationArgument arg2 = new RelationArgument(jCas);
+ // arg2.setArgument(beginsOnB);
+ // BinaryTextRelation relation = new BinaryTextRelation(jCas);
+ // relation.setArg1(arg1);
+ // relation.setArg2(arg2);
+ // relation.setCategory("BEFORE");
+ // arg1.addToIndexes();
+ // arg2.addToIndexes();
+ // relation.addToIndexes();
+ // before.put(argA, beginsOnB);
+ // }
+ // }
+ // }
+ // }
+ //
+ // }
+}
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations.java?rev=1634983&r1=1634982&r2=1634983&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations.java Tue Oct 28 21:01:06 2014
@@ -349,7 +349,7 @@ EvaluationOfTemporalRelations_ImplBase{
aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveRelations.class));
aggregateBuilder.add(this.baseline ? RecallBaselineEventTimeRelationAnnotator.createAnnotatorDescription(directory) :
- EventTimeRelationAnnotator.createAnnotatorDescription(new File(directory,EVENT_TIME)));
+ EventTimeRelationAnnotator.createEngineDescription(new File(directory,EVENT_TIME)));
aggregateBuilder.add(EventEventRelationAnnotator.createAnnotatorDescription(new File(directory,EVENT_EVENT)));
aggregateBuilder.add(EventDischargeTimeAnnotator.createAnnotatorDescription(new File(directory,EVENT_DISCHARGE)));
aggregateBuilder.add(EventAdmissionTimeAnnotator.createAnnotatorDescription(new File(directory,EVENT_ADMISSION)));
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations_ImplBase.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations_ImplBase.java?rev=1634983&r1=1634982&r2=1634983&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations_ImplBase.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations_ImplBase.java Tue Oct 28 21:01:06 2014
@@ -47,204 +47,242 @@ import com.lexicalscope.jewel.cli.Option
public abstract class EvaluationOfTemporalRelations_ImplBase extends
Evaluation_ImplBase<AnnotationStatistics<String>> {
- static interface TempRelOptions extends Evaluation_ImplBase.Options{
- @Option
- public boolean getTest();
-
- @Option
- public boolean getPrintFormattedRelations();
-
- @Option
- public boolean getBaseline();
-
- @Option
- public boolean getClosure();
-
- @Option
- public boolean getClassificationOnly();
-
- }
-
- protected static boolean DEFAULT_BOTH_DIRECTIONS = false;
- protected static float DEFAULT_DOWNSAMPLE = 1.0f;
- protected static double DEFAULT_SVM_C = 1.0;
- protected static double DEFAULT_SVM_G = 1.0;
- protected static double DEFAULT_TK = 0.5;
- protected static double DEFAULT_LAMBDA = 0.5;
-
- protected static ParameterSettings defaultParams = new ParameterSettings(DEFAULT_BOTH_DIRECTIONS, DEFAULT_DOWNSAMPLE, "linear",
- DEFAULT_SVM_C, DEFAULT_SVM_G, "polynomial", ComboOperator.SUM, DEFAULT_TK, DEFAULT_LAMBDA);
-
-
- protected ParameterSettings params = null;
- protected boolean printRelations = false;
-
- public EvaluationOfTemporalRelations_ImplBase(File baseDirectory,
- File rawTextDirectory, File xmlDirectory, XMLFormat xmlFormat,
- File xmiDirectory, File treebankDirectory, File coreferenceDirectory, boolean printErrors, boolean printRelations, ParameterSettings params) {
- super(baseDirectory, rawTextDirectory, xmlDirectory, xmlFormat, xmiDirectory,
- treebankDirectory, coreferenceDirectory);
- this.params = params;
- this.printRelations = printRelations;
- this.printErrors = printErrors;
- }
-
- public EvaluationOfTemporalRelations_ImplBase(File baseDirectory,
- File rawTextDirectory, File xmlDirectory, XMLFormat xmlFormat,
- File xmiDirectory, File treebankDirectory, boolean printErrors, boolean printRelations, ParameterSettings params) {
- super(baseDirectory, rawTextDirectory, xmlDirectory, xmlFormat, xmiDirectory,
- treebankDirectory);
- this.params = params;
- this.printRelations = printRelations;
- this.printErrors = printErrors;
- }
-
- public static class PreserveEventEventRelations extends JCasAnnotator_ImplBase {
- public static final String PARAM_GOLD_VIEW = "GoldView";
-
- @ConfigurationParameter(name = PARAM_GOLD_VIEW,mandatory=false)
- private String goldViewName = CAS.NAME_DEFAULT_SOFA;
-
- @Override
- public void process(JCas jCas) throws AnalysisEngineProcessException {
- for(BinaryTextRelation relation : Lists.newArrayList(JCasUtil.select(jCas, BinaryTextRelation.class))){
- RelationArgument arg1 = relation.getArg1();
- RelationArgument arg2 = relation.getArg2();
- if(arg1.getArgument() instanceof EventMention && arg2.getArgument() instanceof EventMention && relation instanceof TemporalTextRelation){
- // these are the kind we keep.
- continue;
- }
- arg1.removeFromIndexes();
- arg2.removeFromIndexes();
- relation.removeFromIndexes();
- }
- }
- }
-
- public static class RemoveNonContainsRelations extends JCasAnnotator_ImplBase {
- public static final String PARAM_RELATION_VIEW = "RelationView";
-
- @ConfigurationParameter(name = PARAM_RELATION_VIEW,mandatory=false)
- private String relationViewName = CAS.NAME_DEFAULT_SOFA;
- @Override
- public void process(JCas jCas) throws AnalysisEngineProcessException {
- JCas relationView = null;
-
- try {
- relationView = jCas.getView(relationViewName);
- } catch (CASException e) {
- e.printStackTrace();
- }
- for (BinaryTextRelation relation : Lists.newArrayList(JCasUtil.select(
- relationView,
- BinaryTextRelation.class))) {
- if (!relation.getCategory().startsWith("CONTAINS")) {
- relation.getArg1().removeFromIndexes();
- relation.getArg2().removeFromIndexes();
- relation.removeFromIndexes();
- }
- }
- }
-
- public static class RemoveGoldAttributes extends JCasAnnotator_ImplBase {
- @Override
- public void process(JCas jCas) throws AnalysisEngineProcessException {
- for(EventMention event : JCasUtil.select(jCas, EventMention.class)){
- if(event.getEvent() != null && event.getEvent().getProperties() != null){
- event.getEvent().getProperties().setContextualAspect("UNK");
- event.getEvent().getProperties().setContextualModality("UNK");
- }
- }
- for(TimeMention timex : JCasUtil.select(jCas, TimeMention.class)){
- timex.setTimeClass("UNK");
- }
- }
- }
- }
-
- protected static Collection<BinaryTextRelation> correctArgOrder(
- Collection<BinaryTextRelation> systemRelations,
- Collection<BinaryTextRelation> goldRelations) {
- Set<BinaryTextRelation> goodSys = Sets.newHashSet();
-
- for(BinaryTextRelation sysrel : systemRelations){
- Annotation sysArg1 = sysrel.getArg1().getArgument();
- Annotation sysArg2 = sysrel.getArg2().getArgument();
- for(BinaryTextRelation goldrel : goldRelations){
- Annotation goldArg1 = goldrel.getArg1().getArgument();
- Annotation goldArg2 = goldrel.getArg2().getArgument();
- if (matchSpan(sysArg2, goldArg1) && matchSpan(sysArg1, goldArg2)){//the order of system pair was flipped
- if(sysrel.getCategory().equals("OVERLAP")){ //if the relation is overlap, and the arg order was flipped, then change back the order
- RelationArgument tempArg = (RelationArgument) sysrel.getArg1().clone();
- sysrel.setArg1((RelationArgument) sysrel.getArg2().clone());
- sysrel.setArg2(tempArg);
- }//for other types of relation, still maintain the type.
- continue;
- }
- }
- goodSys.add(sysrel);
- }
-
- return goodSys;
- }
-
- private static boolean matchSpan(Annotation arg1, Annotation arg2) {
- boolean result = false;
- result = arg1.getBegin() == arg2.getBegin() && arg1.getEnd() == arg2.getEnd();
- return result;
- }
-
- protected static void printRelationAnnotations(String fileName, Collection<BinaryTextRelation> relations) {
-
- for(BinaryTextRelation binaryTextRelation : relations) {
-
- Annotation arg1 = binaryTextRelation.getArg1().getArgument();
- Annotation arg2 = binaryTextRelation.getArg2().getArgument();
-
- String arg1Type = arg1.getClass().getSimpleName();
- String arg2Type = arg2.getClass().getSimpleName();
-
- int arg1Begin = arg1.getBegin();
- int arg1End = arg1.getEnd();
- int arg2Begin = arg2.getBegin();
- int arg2End = arg2.getEnd();
-
- String category = binaryTextRelation.getCategory();
-
- System.out.format("%s\t%s\t%s\t%d\t%d\t%s\t%d\t%d\n",
- fileName, category, arg1Type, arg1Begin, arg1End, arg2Type, arg2Begin, arg2End);
- }
- }
-
- protected static String formatRelation(BinaryTextRelation relation) {
- IdentifiedAnnotation arg1 = (IdentifiedAnnotation)relation.getArg1().getArgument();
- IdentifiedAnnotation arg2 = (IdentifiedAnnotation)relation.getArg2().getArgument();
- String arg1Type ="E";
- String arg2Type ="T";
- if(arg1 instanceof TimeMention) arg1Type = "T";
- if(arg2 instanceof EventMention) arg2Type = "E";
- String text = arg1.getCAS().getDocumentText();
- int begin = Math.min(arg1.getBegin(), arg2.getBegin());
- int end = Math.max(arg1.getBegin(), arg2.getBegin());
- begin = Math.max(0, begin - 50);
- end = Math.min(text.length(), end + 50);
- return String.format(
- "%s(%s(type=%d!%d-%d!%s), %s(type=%d!%d-%d!%s)) in ...%s...",
- relation.getCategory(),
- arg1.getCoveredText(),
- arg1.getTypeID(),
- //add extra
- arg1.getBegin(),
- arg1.getEnd(),
- arg1Type,
-
- arg2.getCoveredText(),
- arg2.getTypeID(),
- //add extra
- arg2.getBegin(),
- arg2.getEnd(),
- arg2Type,
- text.substring(begin, end).replaceAll("[\r\n]", " "));
- }
+ static interface TempRelOptions extends Evaluation_ImplBase.Options{
+ @Option
+ public boolean getTest();
+
+ @Option
+ public boolean getPrintFormattedRelations();
+
+ @Option
+ public boolean getBaseline();
+
+ @Option
+ public boolean getClosure();
+
+ @Option
+ public boolean getClassificationOnly();
+
+ }
+
+ protected static boolean DEFAULT_BOTH_DIRECTIONS = false;
+ protected static float DEFAULT_DOWNSAMPLE = 1.0f;
+ protected static double DEFAULT_SVM_C = 1.0;
+ protected static double DEFAULT_SVM_G = 1.0;
+ protected static double DEFAULT_TK = 0.5;
+ protected static double DEFAULT_LAMBDA = 0.5;
+
+ protected static ParameterSettings defaultParams = new ParameterSettings(DEFAULT_BOTH_DIRECTIONS, DEFAULT_DOWNSAMPLE, "linear",
+ DEFAULT_SVM_C, DEFAULT_SVM_G, "polynomial", ComboOperator.SUM, DEFAULT_TK, DEFAULT_LAMBDA);
+
+
+ protected ParameterSettings params = null;
+ protected boolean printRelations = false;
+
+ public EvaluationOfTemporalRelations_ImplBase(File baseDirectory,
+ File rawTextDirectory, File xmlDirectory, XMLFormat xmlFormat,
+ File xmiDirectory, File treebankDirectory, File coreferenceDirectory, boolean printErrors, boolean printRelations, ParameterSettings params) {
+ super(baseDirectory, rawTextDirectory, xmlDirectory, xmlFormat, xmiDirectory,
+ treebankDirectory, coreferenceDirectory);
+ this.params = params;
+ this.printRelations = printRelations;
+ this.printErrors = printErrors;
+ }
+
+ public EvaluationOfTemporalRelations_ImplBase(File baseDirectory,
+ File rawTextDirectory, File xmlDirectory, XMLFormat xmlFormat,
+ File xmiDirectory, File treebankDirectory, boolean printErrors, boolean printRelations, ParameterSettings params) {
+ super(baseDirectory, rawTextDirectory, xmlDirectory, xmlFormat, xmiDirectory,
+ treebankDirectory);
+ this.params = params;
+ this.printRelations = printRelations;
+ this.printErrors = printErrors;
+ }
+
+ public static class PreserveEventEventRelations extends JCasAnnotator_ImplBase {
+ public static final String PARAM_GOLD_VIEW = "GoldView";
+
+ @ConfigurationParameter(name = PARAM_GOLD_VIEW,mandatory=false)
+ private String goldViewName = CAS.NAME_DEFAULT_SOFA;
+
+ @Override
+ public void process(JCas jCas) throws AnalysisEngineProcessException {
+ for(BinaryTextRelation relation : Lists.newArrayList(JCasUtil.select(jCas, BinaryTextRelation.class))){
+ RelationArgument arg1 = relation.getArg1();
+ RelationArgument arg2 = relation.getArg2();
+ if(arg1.getArgument() instanceof EventMention && arg2.getArgument() instanceof EventMention && relation instanceof TemporalTextRelation){
+ // these are the kind we keep.
+ continue;
+ }
+ arg1.removeFromIndexes();
+ arg2.removeFromIndexes();
+ relation.removeFromIndexes();
+ }
+ }
+ }
+
+ public static class RemoveNonContainsRelations extends JCasAnnotator_ImplBase {
+ public static final String PARAM_RELATION_VIEW = "RelationView";
+
+ @ConfigurationParameter(name = PARAM_RELATION_VIEW,mandatory=false)
+ private String relationViewName = CAS.NAME_DEFAULT_SOFA;
+ @Override
+ public void process(JCas jCas) throws AnalysisEngineProcessException {
+ JCas relationView = null;
+
+ try {
+ relationView = jCas.getView(relationViewName);
+ } catch (CASException e) {
+ e.printStackTrace();
+ }
+ for (BinaryTextRelation relation : Lists.newArrayList(JCasUtil.select(
+ relationView,
+ BinaryTextRelation.class))) {
+ if (!relation.getCategory().startsWith("CONTAINS")) {
+ relation.getArg1().removeFromIndexes();
+ relation.getArg2().removeFromIndexes();
+ relation.removeFromIndexes();
+ }
+ }
+ }
+
+ public static class RemoveGoldAttributes extends JCasAnnotator_ImplBase {
+ @Override
+ public void process(JCas jCas) throws AnalysisEngineProcessException {
+ for(EventMention event : JCasUtil.select(jCas, EventMention.class)){
+ if(event.getEvent() != null && event.getEvent().getProperties() != null){
+ event.getEvent().getProperties().setContextualAspect("UNK");
+ event.getEvent().getProperties().setContextualModality("UNK");
+ }
+ }
+ for(TimeMention timex : JCasUtil.select(jCas, TimeMention.class)){
+ timex.setTimeClass("UNK");
+ }
+ }
+ }
+ }
+
+ protected static Collection<BinaryTextRelation> correctArgOrder(
+ Collection<BinaryTextRelation> systemRelations,
+ Collection<BinaryTextRelation> goldRelations) {
+ Set<BinaryTextRelation> goodSys = Sets.newHashSet();
+
+ for(BinaryTextRelation sysrel : systemRelations){
+ Annotation sysArg1 = sysrel.getArg1().getArgument();
+ Annotation sysArg2 = sysrel.getArg2().getArgument();
+ for(BinaryTextRelation goldrel : goldRelations){
+ Annotation goldArg1 = goldrel.getArg1().getArgument();
+ Annotation goldArg2 = goldrel.getArg2().getArgument();
+ if (matchSpan(sysArg2, goldArg1) && matchSpan(sysArg1, goldArg2)){//the order of system pair was flipped
+ if(sysrel.getCategory().equals("OVERLAP")){ //if the relation is overlap, and the arg order was flipped, then change back the order
+ RelationArgument tempArg = (RelationArgument) sysrel.getArg1().clone();
+ sysrel.setArg1((RelationArgument) sysrel.getArg2().clone());
+ sysrel.setArg2(tempArg);
+ }//for other types of relation, still maintain the type.
+ continue;
+ }
+ }
+ goodSys.add(sysrel);
+ }
+
+ return goodSys;
+ }
+
+ private static boolean matchSpan(Annotation arg1, Annotation arg2) {
+ boolean result = false;
+ result = arg1.getBegin() == arg2.getBegin() && arg1.getEnd() == arg2.getEnd();
+ return result;
+ }
+
+ protected static void printRelationAnnotations(String fileName, Collection<BinaryTextRelation> relations) {
+
+ for(BinaryTextRelation binaryTextRelation : relations) {
+
+ Annotation arg1 = binaryTextRelation.getArg1().getArgument();
+ Annotation arg2 = binaryTextRelation.getArg2().getArgument();
+
+ String arg1Type = arg1.getClass().getSimpleName();
+ String arg2Type = arg2.getClass().getSimpleName();
+
+ int arg1Begin = arg1.getBegin();
+ int arg1End = arg1.getEnd();
+ int arg2Begin = arg2.getBegin();
+ int arg2End = arg2.getEnd();
+
+ String category = binaryTextRelation.getCategory();
+
+ System.out.format("%s\t%s\t%s\t%d\t%d\t%s\t%d\t%d\n",
+ fileName, category, arg1Type, arg1Begin, arg1End, arg2Type, arg2Begin, arg2End);
+ }
+ }
+
+ protected static String formatRelation(BinaryTextRelation relation) {
+ IdentifiedAnnotation arg1 = (IdentifiedAnnotation)relation.getArg1().getArgument();
+ IdentifiedAnnotation arg2 = (IdentifiedAnnotation)relation.getArg2().getArgument();
+ String arg1Type ="E";
+ String arg2Type ="T";
+ if(arg1 instanceof TimeMention) arg1Type = "T";
+ if(arg2 instanceof EventMention) arg2Type = "E";
+ String text = arg1.getCAS().getDocumentText();
+ int begin = Math.min(arg1.getBegin(), arg2.getBegin());
+ int end = Math.max(arg1.getEnd(), arg2.getEnd());
+ int begin1 = 0;
+ int end1 = 0;
+ int begin2 = 0;
+ int end2 = 0;
+ if(arg1.getBegin()< arg2.getBegin()){
+ begin1 = arg1.getBegin();
+ end1 = arg1.getEnd();
+ begin2 = arg2.getBegin();
+ end2 = arg2.getEnd();
+ }else{ //arg1 is after arg2
+ begin1 = arg2.getBegin();
+ end1 = arg2.getEnd();
+ begin2 = arg1.getBegin();
+ end2 = arg1.getEnd();
+ }
+ begin = Math.max(0, begin - 200);
+ end = Math.min(text.length(), end + 200);
+ StringBuilder between = new StringBuilder();
+ if(begin<begin1) between.append(text.substring(begin, begin1).replaceAll("[\r\n]", " "));
+ between.append(" [" + text.substring(begin1, end1) + "] ");
+ if(begin2<=end1){
+ between.append(text.substring(begin,begin1).replaceAll("[\r\n]", " ")+" ["+ text.substring(begin1,begin2)+" [");
+ if(end1<end2){
+ between.append(text.substring(begin2,end1) + "]" + text.substring(end1,end2) + "]" + text.substring(end2,end));
+ }else{
+ between.append(text.substring(begin2,end2) + "]" + text.substring(end2,end1) + "]" + text.substring(end1,end));
+ }
+
+ }else if(begin2-end1 <=400){
+ between.append(text.substring(end1, begin2).replaceAll("[\r\n]", " "));
+ }else{
+ between.append(text.substring(end1, end1+200).replaceAll("[\r\n]", " ")+ "...");
+ int extra = (begin2-end1-400)/10;
+ for (int i = 1; i<extra; i++){
+ between.append(".");
+ }
+ between.append(text.substring(begin2-200, begin2).replaceAll("[\r\n]", " "));
+ }
+ between.append(" [" + text.substring(begin2, end2)+ "] ");
+ if(end2 < end) between.append(text.substring(end2, end).replaceAll("[\r\n]", " ") );
+ return String.format(
+ "%s(%s(type=%d!%d-%d!%s), %s(type=%d!%d-%d!%s)) in ...%s...",
+ relation.getCategory(),
+ arg1.getCoveredText(),
+ arg1.getTypeID(),
+ //add extra
+ arg1.getBegin(),
+ arg1.getEnd(),
+ arg1Type,
+
+ arg2.getCoveredText(),
+ arg2.getTypeID(),
+ //add extra
+ arg2.getBegin(),
+ arg2.getEnd(),
+ arg2Type,
+ between.toString());
+ }
}
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/FullTemporalExtractionPipeline.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/FullTemporalExtractionPipeline.java?rev=1634983&r1=1634982&r2=1634983&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/FullTemporalExtractionPipeline.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/FullTemporalExtractionPipeline.java Tue Oct 28 21:01:06 2014
@@ -69,13 +69,13 @@ public class FullTemporalExtractionPipel
@Option(
shortName = "r",
description = "Specify the path to the directory where the trained event-time relation model is located",
- defaultValue="target/eval/temporal-relations/event-time/train_and_test/")
+ defaultValue="target/eval/thyme/train_and_test/event-time/")
public String getEventTimeRelationModelDirectory();
@Option(
shortName = "s",
description = "Specify the path to the directory where the trained event-event relation model is located",
- defaultToNull=true) // add in default value once we have a satisfying trained model
+ defaultValue="target/eval/thyme/train_and_test/event-event/") // add in default value once we have a satisfying trained model
public String getEventEventRelationModelDirectory();
@Option(
@@ -102,7 +102,7 @@ public class FullTemporalExtractionPipel
aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(CopyPropertiesToTemporalEventAnnotator.class));
aggregateBuilder.add(DocTimeRelAnnotator.createAnnotatorDescription(options.getDoctimerelModelDirectory() + File.separator + "model.jar"));
aggregateBuilder.add(BackwardsTimeAnnotator.createAnnotatorDescription(options.getTimeModelDirectory() + File.separator + "model.jar"));
- aggregateBuilder.add(EventTimeRelationAnnotator.createAnnotatorDescription(options.getEventTimeRelationModelDirectory() + File.separator + "model.jar"));
+ aggregateBuilder.add(EventTimeRelationAnnotator.createEngineDescription(options.getEventTimeRelationModelDirectory() + File.separator + "model.jar"));
if(options.getEventEventRelationModelDirectory()!=null){
aggregateBuilder.add(EventEventRelationAnnotator.createAnnotatorDescription(options.getEventEventRelationModelDirectory() + File.separator + "model.jar"));
}