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Posted to commits@ctakes.apache.org by se...@apache.org on 2017/11/08 14:52:07 UTC
svn commit: r1814586 - in /ctakes/trunk:
ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/pipeline/
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/
Author: seanfinan
Date: Wed Nov 8 14:52:06 2017
New Revision: 1814586
URL: http://svn.apache.org/viewvc?rev=1814586&view=rev
Log:
Add logging to common temporal engines
Modified:
ctakes/trunk/ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/pipeline/TemporalSubPipe.piper
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotator.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotator.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotator.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotator.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalRelationExtractorAnnotator.java
Modified: ctakes/trunk/ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/pipeline/TemporalSubPipe.piper
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/pipeline/TemporalSubPipe.piper?rev=1814586&r1=1814585&r2=1814586&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/pipeline/TemporalSubPipe.piper (original)
+++ ctakes/trunk/ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/pipeline/TemporalSubPipe.piper Wed Nov 8 14:52:06 2017
@@ -4,16 +4,16 @@
addDescription EventAnnotator
// Times. Use addLogged to log start and finish of processing. There aren't default models, so set specifically
-addLogged BackwardsTimeAnnotator classifierJarPath=/org/apache/ctakes/temporal/ae/timeannotator/model.jar
+add BackwardsTimeAnnotator classifierJarPath=/org/apache/ctakes/temporal/ae/timeannotator/model.jar
// DocTimeRel: the relation bin for Events to the Document Creation Time.
-addLogged DocTimeRelAnnotator classifierJarPath=/org/apache/ctakes/temporal/ae/doctimerel/model.jar
+add DocTimeRelAnnotator classifierJarPath=/org/apache/ctakes/temporal/ae/doctimerel/model.jar
// Event - Time binary relations.
-addLogged EventTimeRelationAnnotator classifierJarPath=/org/apache/ctakes/temporal/ae/eventtime/model.jar
+add EventTimeRelationAnnotator classifierJarPath=/org/apache/ctakes/temporal/ae/eventtime/model.jar
// Event - Event binary relations.
-addLogged EventEventRelationAnnotator classifierJarPath=/org/apache/ctakes/temporal/ae/eventevent/model.jar
+add EventEventRelationAnnotator classifierJarPath=/org/apache/ctakes/temporal/ae/eventevent/model.jar
// Need to improve. Generic Events (head words) should be replaced by overlapping subclasses with relations adjusted.
//add FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotator.java?rev=1814586&r1=1814585&r2=1814586&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotator.java Wed Nov 8 14:52:06 2017
@@ -20,12 +20,14 @@ package org.apache.ctakes.temporal.ae;
import com.google.common.collect.Lists;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
+import org.apache.ctakes.core.util.DotLogger;
import org.apache.ctakes.temporal.ae.feature.ParseSpanFeatureExtractor;
import org.apache.ctakes.temporal.ae.feature.TimeWordTypeExtractor;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.textsem.TimeMention;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.log4j.Logger;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -51,6 +53,7 @@ import org.cleartk.ml.jar.DirectoryDataW
import org.cleartk.ml.jar.GenericJarClassifierFactory;
import java.io.File;
+import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
@@ -65,6 +68,8 @@ import java.util.List;
)
public class BackwardsTimeAnnotator extends TemporalEntityAnnotator_ImplBase {
+ static private final Logger LOGGER = Logger.getLogger( "BackwardsTimeAnnotator" );
+
public static final String PARAM_TIMEX_VIEW = "TimexView";
@ConfigurationParameter(
name = PARAM_TIMEX_VIEW,
@@ -149,33 +154,39 @@ public class BackwardsTimeAnnotator exte
@Override
public void initialize(UimaContext context) throws ResourceInitializationException {
- super.initialize(context);
-
- // define chunking
- this.timeChunking = new BioChunking<BaseToken, TimeMention>(BaseToken.class, TimeMention.class, "timeClass");
-
- CombinedExtractor1<BaseToken> allExtractors = new CombinedExtractor1<>(
- new CoveredTextExtractor<BaseToken>(),
- CharacterCategoryPatternFunction.<BaseToken>createExtractor(PatternType.REPEATS_MERGED),
- CharacterCategoryPatternFunction.<BaseToken>createExtractor(PatternType.ONE_PER_CHAR),
- new TypePathExtractor<>(BaseToken.class, "partOfSpeech"),
- new TimeWordTypeExtractor<BaseToken>());
+ LOGGER.info( "Initializing ..." );
+ try ( DotLogger dotter = new DotLogger() ) {
+ super.initialize( context );
+
+ // define chunking
+ this.timeChunking = new BioChunking<BaseToken, TimeMention>(BaseToken.class, TimeMention.class, "timeClass");
+
+ CombinedExtractor1<BaseToken> allExtractors = new CombinedExtractor1<>(
+ new CoveredTextExtractor<BaseToken>(),
+ CharacterCategoryPatternFunction.<BaseToken>createExtractor(PatternType.REPEATS_MERGED),
+ CharacterCategoryPatternFunction.<BaseToken>createExtractor(PatternType.ONE_PER_CHAR),
+ new TypePathExtractor<>(BaseToken.class, "partOfSpeech"),
+ new TimeWordTypeExtractor<BaseToken>());
// CombinedExtractor1 parseExtractors = new CombinedExtractor(
// new ParseSpanFeatureExtractor()
// );
- this.tokenFeatureExtractors = new ArrayList<FeatureExtractor1>();
- this.tokenFeatureExtractors.add(allExtractors);
+ this.tokenFeatureExtractors = new ArrayList<FeatureExtractor1>();
+ this.tokenFeatureExtractors.add(allExtractors);
- this.contextFeatureExtractors = new ArrayList<CleartkExtractor>();
- this.contextFeatureExtractors.add(new CleartkExtractor(
- BaseToken.class,
- allExtractors,
- new Preceding(3),
- new Following(3)));
+ this.contextFeatureExtractors = new ArrayList<CleartkExtractor>();
+ this.contextFeatureExtractors.add(new CleartkExtractor(
+ BaseToken.class,
+ allExtractors,
+ new Preceding(3),
+ new Following(3)));
// this.parseFeatureExtractors = new ArrayList<ParseSpanFeatureExtractor>();
// this.parseFeatureExtractors.add(new ParseSpanFeatureExtractor());
- parseExtractor = new ParseSpanFeatureExtractor();
+ parseExtractor = new ParseSpanFeatureExtractor();
+ } catch ( IOException ioE ) {
+ throw new ResourceInitializationException( ioE );
+ }
+ LOGGER.info( "Finished." );
}
@Override
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotator.java?rev=1814586&r1=1814585&r2=1814586&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotator.java Wed Nov 8 14:52:06 2017
@@ -18,32 +18,16 @@
*/
package org.apache.ctakes.temporal.ae;
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-//import java.io.IOException;
-import java.util.List;
-//import java.util.Map;
-import java.util.Map;
-
import org.apache.ctakes.core.pipeline.PipeBitInfo;
-import org.apache.ctakes.temporal.ae.feature.ClosestVerbExtractor;
-import org.apache.ctakes.temporal.ae.feature.ContinuousTextExtractor;
-import org.apache.ctakes.temporal.ae.feature.CoveredTextToValuesExtractor;
-import org.apache.ctakes.temporal.ae.feature.DateAndMeasurementExtractor;
-import org.apache.ctakes.temporal.ae.feature.EventPropertyExtractor;
-import org.apache.ctakes.temporal.ae.feature.NearbyVerbTenseXExtractor;
-import org.apache.ctakes.temporal.ae.feature.SectionHeaderExtractor;
-import org.apache.ctakes.temporal.ae.feature.TimeXExtractor;
-import org.apache.ctakes.temporal.ae.feature.UmlsSingleFeatureExtractor;
-import org.apache.ctakes.temporal.ae.feature.duration.DurationExpectationFeatureExtractor;
+import org.apache.ctakes.core.util.DotLogger;
+import org.apache.ctakes.temporal.ae.feature.*;
import org.apache.ctakes.temporal.utils.SoftMaxUtil;
import org.apache.ctakes.typesystem.type.refsem.Event;
import org.apache.ctakes.typesystem.type.refsem.EventProperties;
-//import org.apache.ctakes.temporal.ae.feature.duration.DurationExpectationFeatureExtractor;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.log4j.Logger;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -57,24 +41,23 @@ import org.cleartk.ml.CleartkAnnotator;
import org.cleartk.ml.DataWriter;
import org.cleartk.ml.Feature;
import org.cleartk.ml.Instance;
-import org.cleartk.ml.feature.extractor.CleartkExtractor;
-import org.cleartk.ml.feature.extractor.CleartkExtractor.Bag;
-import org.cleartk.ml.feature.extractor.CleartkExtractor.Covered;
-import org.cleartk.ml.feature.extractor.CleartkExtractor.FirstCovered;
-import org.cleartk.ml.feature.extractor.CleartkExtractor.Following;
-import org.cleartk.ml.feature.extractor.CleartkExtractor.LastCovered;
-import org.cleartk.ml.feature.extractor.CleartkExtractor.Preceding;
+import org.cleartk.ml.feature.extractor.*;
+import org.cleartk.ml.feature.extractor.CleartkExtractor.*;
import org.cleartk.ml.feature.function.CharacterCategoryPatternFunction;
import org.cleartk.ml.feature.function.CharacterCategoryPatternFunction.PatternType;
-import org.cleartk.ml.feature.extractor.CleartkExtractorException;
-import org.cleartk.ml.feature.extractor.CombinedExtractor1;
-import org.cleartk.ml.feature.extractor.CoveredTextExtractor;
-import org.cleartk.ml.feature.extractor.TypePathExtractor;
import org.cleartk.ml.jar.DefaultDataWriterFactory;
import org.cleartk.ml.jar.DirectoryDataWriterFactory;
import org.cleartk.ml.jar.GenericJarClassifierFactory;
-import com.google.common.base.Charsets;
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+//import java.io.IOException;
+//import java.util.Map;
+//import org.apache.ctakes.temporal.ae.feature.duration.DurationExpectationFeatureExtractor;
//import com.google.common.base.Charsets;
@@ -86,6 +69,8 @@ import com.google.common.base.Charsets;
)
public class DocTimeRelAnnotator extends CleartkAnnotator<String> {
+ static private final Logger LOGGER = Logger.getLogger( "DocTimeRelAnnotator" );
+
public static AnalysisEngineDescription createDataWriterDescription(
Class<? extends DataWriter<String>> dataWriterClass,
File outputDirectory) throws ResourceInitializationException {
@@ -147,55 +132,61 @@ public class DocTimeRelAnnotator extends
@Override
public void initialize(UimaContext context) throws ResourceInitializationException {
- super.initialize(context);
- CombinedExtractor1<BaseToken> baseExtractor = new CombinedExtractor1<>(
- new CoveredTextExtractor<BaseToken>(),
- CharacterCategoryPatternFunction.<BaseToken>createExtractor(PatternType.ONE_PER_CHAR),
- new TypePathExtractor<>(BaseToken.class, "partOfSpeech"));
- this.contextExtractor = new CleartkExtractor<>(
- BaseToken.class,
- baseExtractor,
- new Preceding(3),
- new FirstCovered(1),
- new LastCovered(1),
- new Bag(new Covered()),
- new Following(3));
- final String vectorFile = "org/apache/ctakes/temporal/mimic_vectors.txt";
- final String vectorFile2 = "org/apache/ctakes/temporal/thyme_word2vec_mapped_50.vec";
- try {
- this.continuousText = new ContinuousTextExtractor(vectorFile);
- this.continuousText2 = new ContinuousTextExtractor(vectorFile2);
- } catch (CleartkExtractorException e) {
- System.err.println("cannot find file: "+ vectorFile);
- e.printStackTrace();
- }
- this.tokenVectorContext = new CleartkExtractor<>(
- BaseToken.class,
- continuousText,
- new Preceding(5),
- new Covered(),
- new Following(5));
- this.tokenVectorContext2 = new CleartkExtractor<>(
- BaseToken.class,
- continuousText2,
- new Covered());
- this.sectionIDExtractor = new SectionHeaderExtractor();
- this.closestVerbExtractor = new ClosestVerbExtractor();
- this.timeXExtractor = new TimeXExtractor();
- this.genericExtractor = new EventPropertyExtractor();
-// this.umlsExtractor = new UmlsSingleFeatureExtractor();
- this.verbTensePatternExtractor = new NearbyVerbTenseXExtractor();
-
- this.dateExtractor = new DateAndMeasurementExtractor();
-
-// try {
-// Map<String, double[]> word_disSem = CoveredTextToValuesExtractor.parseTextDoublesMap(new File("src/main/resources/embeddings.size25.txt"), Charsets.UTF_8);
-// this.disSemExtractor = new CoveredTextToValuesExtractor("DisSemFeat", word_disSem);
-// } catch (IOException e) {
-// e.printStackTrace();
-// }
-// this.durationExtractor = new DurationExpectationFeatureExtractor();
- }
+ LOGGER.info( "Initializing ..." );
+ try ( DotLogger dotter = new DotLogger() ) {
+ super.initialize( context );
+ CombinedExtractor1<BaseToken> baseExtractor = new CombinedExtractor1<>(
+ new CoveredTextExtractor<BaseToken>(),
+ CharacterCategoryPatternFunction.<BaseToken>createExtractor( PatternType.ONE_PER_CHAR ),
+ new TypePathExtractor<>( BaseToken.class, "partOfSpeech" ) );
+ this.contextExtractor = new CleartkExtractor<>(
+ BaseToken.class,
+ baseExtractor,
+ new Preceding( 3 ),
+ new FirstCovered( 1 ),
+ new LastCovered( 1 ),
+ new Bag( new Covered() ),
+ new Following( 3 ) );
+ final String vectorFile = "org/apache/ctakes/temporal/mimic_vectors.txt";
+ final String vectorFile2 = "org/apache/ctakes/temporal/thyme_word2vec_mapped_50.vec";
+ try {
+ this.continuousText = new ContinuousTextExtractor( vectorFile );
+ this.continuousText2 = new ContinuousTextExtractor( vectorFile2 );
+ } catch ( CleartkExtractorException e ) {
+ System.err.println( "cannot find file: " + vectorFile );
+ e.printStackTrace();
+ }
+ this.tokenVectorContext = new CleartkExtractor<>(
+ BaseToken.class,
+ continuousText,
+ new Preceding( 5 ),
+ new Covered(),
+ new Following( 5 ) );
+ this.tokenVectorContext2 = new CleartkExtractor<>(
+ BaseToken.class,
+ continuousText2,
+ new Covered() );
+ this.sectionIDExtractor = new SectionHeaderExtractor();
+ this.closestVerbExtractor = new ClosestVerbExtractor();
+ this.timeXExtractor = new TimeXExtractor();
+ this.genericExtractor = new EventPropertyExtractor();
+ // this.umlsExtractor = new UmlsSingleFeatureExtractor();
+ this.verbTensePatternExtractor = new NearbyVerbTenseXExtractor();
+
+ this.dateExtractor = new DateAndMeasurementExtractor();
+
+ // try {
+ // Map<String, double[]> word_disSem = CoveredTextToValuesExtractor.parseTextDoublesMap(new File("src/main/resources/embeddings.size25.txt"), Charsets.UTF_8);
+ // this.disSemExtractor = new CoveredTextToValuesExtractor("DisSemFeat", word_disSem);
+ // } catch (IOException e) {
+ // e.printStackTrace();
+ // }
+ // this.durationExtractor = new DurationExpectationFeatureExtractor();
+ } catch ( IOException ioE ) {
+ throw new ResourceInitializationException( ioE );
+ }
+ LOGGER.info( "Finished." );
+ }
@Override
public void process(JCas jCas) throws AnalysisEngineProcessException {
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java?rev=1814586&r1=1814585&r2=1814586&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java Wed Nov 8 14:52:06 2017
@@ -19,14 +19,11 @@ package org.apache.ctakes.temporal.ae;
* under the License.
*/
-import java.io.File;
-import java.io.IOException;
-import java.net.URI;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-import java.util.Random;
-
+import com.google.common.base.Predicate;
+import com.google.common.collect.HashMultimap;
+import com.google.common.collect.Iterables;
+import com.google.common.collect.Lists;
+import com.google.common.collect.Multimap;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.temporal.ae.feature.ChunkingExtractor;
import org.apache.ctakes.temporal.ae.feature.PredicateArgumentExtractor;
@@ -54,24 +51,22 @@ import org.cleartk.ml.CleartkAnnotator;
import org.cleartk.ml.Feature;
import org.cleartk.ml.Instance;
import org.cleartk.ml.chunking.BioChunking;
-import org.cleartk.ml.feature.extractor.CleartkExtractor;
+import org.cleartk.ml.feature.extractor.*;
import org.cleartk.ml.feature.extractor.CleartkExtractor.Following;
import org.cleartk.ml.feature.extractor.CleartkExtractor.Preceding;
-import org.cleartk.ml.feature.extractor.CombinedExtractor1;
-import org.cleartk.ml.feature.extractor.CoveredTextExtractor;
-import org.cleartk.ml.feature.extractor.FeatureExtractor1;
-import org.cleartk.ml.feature.extractor.TypePathExtractor;
import org.cleartk.ml.feature.function.CharacterCategoryPatternFunction;
import org.cleartk.ml.feature.function.CharacterCategoryPatternFunction.PatternType;
import org.cleartk.ml.jar.DefaultDataWriterFactory;
import org.cleartk.ml.jar.DirectoryDataWriterFactory;
import org.cleartk.ml.jar.GenericJarClassifierFactory;
-import com.google.common.base.Predicate;
-import com.google.common.collect.HashMultimap;
-import com.google.common.collect.Iterables;
-import com.google.common.collect.Lists;
-import com.google.common.collect.Multimap;
+import java.io.File;
+import java.io.IOException;
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.Random;
@PipeBitInfo(
name = "Event Annotator",
@@ -246,10 +241,9 @@ public class EventAnnotator extends Temp
BaseToken lastToken = tokens.get(tokens.size() - 1);
String value = String.format("%s_%s", entity.getClass().getSimpleName(), entity.getTypeID());
endOfEntityFeatures.put(lastToken, new Feature("EndOf", value));
- }
+ }
}
}
-
Random rand = new Random();
//TRY SMOTE algorithm here to generate more minority class samples
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotator.java?rev=1814586&r1=1814585&r2=1814586&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotator.java Wed Nov 8 14:52:06 2017
@@ -18,59 +18,24 @@
*/
package org.apache.ctakes.temporal.ae;
-import java.io.File;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
+import com.google.common.collect.Lists;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
+import org.apache.ctakes.core.util.DotLogger;
import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator;
import org.apache.ctakes.relationextractor.ae.features.PartOfSpeechFeaturesExtractor;
import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
-import org.apache.ctakes.relationextractor.ae.features.TokenFeaturesExtractor;
-import org.apache.ctakes.temporal.ae.feature.CheckSpecialWordRelationExtractor;
-import org.apache.ctakes.temporal.ae.feature.ConjunctionRelationFeaturesExtractor;
-//import org.apache.ctakes.temporal.ae.feature.DependencyParseUtils;
-import org.apache.ctakes.temporal.ae.feature.DependencyPathFeaturesExtractor;
-import org.apache.ctakes.temporal.ae.feature.CoordinateFeaturesExtractor;
-import org.apache.ctakes.temporal.ae.feature.DependingVerbsFeatureExtractor;
-import org.apache.ctakes.temporal.ae.feature.EmptyFeaturesExtractor;
-import org.apache.ctakes.temporal.ae.feature.MultiTokenFeaturesExtractor;
-//import org.apache.ctakes.temporal.ae.feature.EventInBetweenPropertyExtractor;
-//import org.apache.ctakes.temporal.ae.feature.EventOutsidePropertyExtractor;
-import org.apache.ctakes.temporal.ae.feature.SpecialAnnotationRelationExtractor;
-import org.apache.ctakes.temporal.ae.feature.TemporalPETFlatExtractor;
-import org.apache.ctakes.temporal.ae.feature.TokenPropertyFeaturesExtractor;
-import org.apache.ctakes.temporal.ae.feature.DeterminerRelationFeaturesExtractor;
-import org.apache.ctakes.temporal.ae.feature.RelationEmbeddingFeatureExtractor;
-import org.apache.ctakes.temporal.ae.feature.RelationSyntacticETEmbeddingFeatureExtractor;
-import org.apache.ctakes.temporal.ae.feature.RelationSyntacticEmbeddingFeatureExtractor;
-import org.apache.ctakes.temporal.ae.feature.EventArgumentPropertyExtractor;
-import org.apache.ctakes.temporal.ae.feature.EventTimeRelationFeatureExtractor;
-import org.apache.ctakes.temporal.ae.feature.EventPositionRelationFeaturesExtractor;
-import org.apache.ctakes.temporal.ae.feature.NumberOfEventsInTheSameSentenceExtractor;
-import org.apache.ctakes.temporal.ae.feature.NearbyVerbTenseRelationExtractor;
-import org.apache.ctakes.temporal.ae.feature.NumberOfEventTimeBetweenCandidatesExtractor;
-import org.apache.ctakes.temporal.ae.feature.OverlappedHeadFeaturesExtractor;
-import org.apache.ctakes.temporal.ae.feature.SRLRelationFeaturesExtractor;
-import org.apache.ctakes.temporal.ae.feature.TimeXRelationFeaturesExtractor;
-import org.apache.ctakes.temporal.ae.feature.SectionHeaderRelationExtractor;
-//import org.apache.ctakes.temporal.ae.feature.TemporalAttributeFeatureExtractor;
-import org.apache.ctakes.temporal.ae.feature.UmlsFeatureExtractor;
-import org.apache.ctakes.temporal.ae.feature.UnexpandedTokenFeaturesExtractor;
-//import org.apache.ctakes.temporal.ae.feature.UnexpandedTokenFeaturesExtractor;
-//import org.apache.ctakes.temporal.ae.feature.treekernel.TemporalPETExtractor;
+import org.apache.ctakes.temporal.ae.feature.*;
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.syntax.ConllDependencyNode;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.log4j.Logger;
+import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.tcas.Annotation;
import org.apache.uima.resource.ResourceInitializationException;
@@ -80,11 +45,21 @@ import org.cleartk.ml.feature.extractor.
import org.cleartk.ml.jar.DefaultDataWriterFactory;
import org.cleartk.ml.jar.DirectoryDataWriterFactory;
import org.cleartk.ml.jar.GenericJarClassifierFactory;
-import org.cleartk.util.ViewUriUtil;
-import org.apache.uima.fit.factory.AnalysisEngineFactory;
-import org.apache.uima.fit.util.JCasUtil;
-import com.google.common.collect.Lists;
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
+
+//import org.apache.ctakes.temporal.ae.feature.DependencyParseUtils;
+//import org.apache.ctakes.temporal.ae.feature.EventInBetweenPropertyExtractor;
+//import org.apache.ctakes.temporal.ae.feature.EventOutsidePropertyExtractor;
+//import org.apache.ctakes.temporal.ae.feature.TemporalAttributeFeatureExtractor;
+//import org.apache.ctakes.temporal.ae.feature.UnexpandedTokenFeaturesExtractor;
+//import org.apache.ctakes.temporal.ae.feature.treekernel.TemporalPETExtractor;
+//import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
@PipeBitInfo(
name = "E-E TLinker",
@@ -95,6 +70,8 @@ import com.google.common.collect.Lists;
)
public class EventEventRelationAnnotator extends TemporalRelationExtractorAnnotator {
+ static private final Logger LOGGER = Logger.getLogger( "EventEventRelationAnnotator" );
+
public static AnalysisEngineDescription createDataWriterDescription(
Class<? extends DataWriter<String>> dataWriterClass,
File outputDirectory,
@@ -140,6 +117,17 @@ public class EventEventRelationAnnotator
private RelationSyntacticETEmbeddingFeatureExtractor embedingExtractor;
+ @Override
+ public void initialize( final UimaContext context ) throws ResourceInitializationException {
+ LOGGER.info( "Initializing ..." );
+ try ( DotLogger dotter = new DotLogger() ) {
+ super.initialize( context );
+ } catch ( IOException ioE ) {
+ throw new ResourceInitializationException( ioE );
+ }
+ LOGGER.info( "Finished." );
+ }
+
@Override
protected List<RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation>> getFeatureExtractors() {
final String vectorFile = "org/apache/ctakes/temporal/gloveresult_3";
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotator.java?rev=1814586&r1=1814585&r2=1814586&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotator.java Wed Nov 8 14:52:06 2017
@@ -18,41 +18,14 @@
*/
package org.apache.ctakes.temporal.ae;
-import java.io.File;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Map;
-
+import com.google.common.collect.Lists;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
+import org.apache.ctakes.core.util.DotLogger;
import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator;
import org.apache.ctakes.relationextractor.ae.features.PartOfSpeechFeaturesExtractor;
import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
import org.apache.ctakes.relationextractor.ae.features.TokenFeaturesExtractor;
-import org.apache.ctakes.temporal.ae.feature.CheckSpecialWordRelationExtractor;
-import org.apache.ctakes.temporal.ae.feature.ConjunctionRelationFeaturesExtractor;
-import org.apache.ctakes.temporal.ae.feature.DependencyFeatureExtractor;
-import org.apache.ctakes.temporal.ae.feature.DependencyPathFeaturesExtractor;
-import org.apache.ctakes.temporal.ae.feature.EventArgumentPropertyExtractor;
-//import org.apache.ctakes.temporal.ae.feature.EventIndexOfSameSentenceRelationFeaturesExtractor;
-//import org.apache.ctakes.temporal.ae.feature.EventPositionRelationFeaturesExtractor;
-//import org.apache.ctakes.temporal.ae.feature.EventTimeRelationFeatureExtractor;
-import org.apache.ctakes.temporal.ae.feature.NearbyVerbTenseRelationExtractor;
-import org.apache.ctakes.temporal.ae.feature.NearestFlagFeatureExtractor;
-import org.apache.ctakes.temporal.ae.feature.NumberOfEventTimeBetweenCandidatesExtractor;
-import org.apache.ctakes.temporal.ae.feature.OverlappedHeadFeaturesExtractor;
-//import org.apache.ctakes.temporal.ae.feature.SRLRelationFeaturesExtractor;
-//import org.apache.ctakes.temporal.ae.feature.SectionHeaderRelationExtractor;
-import org.apache.ctakes.temporal.ae.feature.TemporalAttributeFeatureExtractor;
-import org.apache.ctakes.temporal.ae.feature.TemporalPETFlatExtractor;
-//import org.apache.ctakes.temporal.ae.feature.TimeWordTypeRelationExtractor;
-import org.apache.ctakes.temporal.ae.feature.TimeXPropertyRelationFeaturesExtractor;
-import org.apache.ctakes.temporal.ae.feature.TimeXRelationFeaturesExtractor;
-//import org.apache.ctakes.temporal.ae.feature.UnexpandedTokenFeaturesExtractor;
-//import org.apache.ctakes.temporal.ae.feature.TemporalAttributeFeatureExtractor;
-//import org.apache.ctakes.temporal.ae.feature.treekernel.EventTimeFlatTreeFeatureExtractor;
-//import org.apache.ctakes.temporal.ae.feature.treekernel.EventVerbRelationTreeExtractor;
-//import org.apache.ctakes.temporal.ae.feature.treekernel.TemporalPETExtractor;
-//import org.apache.ctakes.temporal.ae.feature.treekernel.TemporalPathExtractor;
+import org.apache.ctakes.temporal.ae.feature.*;
import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
import org.apache.ctakes.typesystem.type.relation.RelationArgument;
import org.apache.ctakes.typesystem.type.relation.TemporalTextRelation;
@@ -60,7 +33,11 @@ import org.apache.ctakes.typesystem.type
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.log4j.Logger;
+import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.tcas.Annotation;
import org.apache.uima.resource.ResourceInitializationException;
@@ -69,10 +46,25 @@ import org.cleartk.ml.DataWriter;
import org.cleartk.ml.jar.DefaultDataWriterFactory;
import org.cleartk.ml.jar.DirectoryDataWriterFactory;
import org.cleartk.ml.jar.GenericJarClassifierFactory;
-import org.apache.uima.fit.factory.AnalysisEngineFactory;
-import org.apache.uima.fit.util.JCasUtil;
-import com.google.common.collect.Lists;
+import java.io.File;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
+
+//import org.apache.ctakes.temporal.ae.feature.EventIndexOfSameSentenceRelationFeaturesExtractor;
+//import org.apache.ctakes.temporal.ae.feature.EventPositionRelationFeaturesExtractor;
+//import org.apache.ctakes.temporal.ae.feature.EventTimeRelationFeatureExtractor;
+//import org.apache.ctakes.temporal.ae.feature.SRLRelationFeaturesExtractor;
+//import org.apache.ctakes.temporal.ae.feature.SectionHeaderRelationExtractor;
+//import org.apache.ctakes.temporal.ae.feature.TimeWordTypeRelationExtractor;
+//import org.apache.ctakes.temporal.ae.feature.UnexpandedTokenFeaturesExtractor;
+//import org.apache.ctakes.temporal.ae.feature.TemporalAttributeFeatureExtractor;
+//import org.apache.ctakes.temporal.ae.feature.treekernel.EventTimeFlatTreeFeatureExtractor;
+//import org.apache.ctakes.temporal.ae.feature.treekernel.EventVerbRelationTreeExtractor;
+//import org.apache.ctakes.temporal.ae.feature.treekernel.TemporalPETExtractor;
+//import org.apache.ctakes.temporal.ae.feature.treekernel.TemporalPathExtractor;
@PipeBitInfo(
name = "E-T TLinker",
@@ -83,6 +75,8 @@ import com.google.common.collect.Lists;
)
public class EventTimeRelationAnnotator extends RelationExtractorAnnotator {
+ static private final Logger LOGGER = Logger.getLogger( "EventTimeRelationAnnotator" );
+
public static AnalysisEngineDescription createDataWriterDescription(
Class<? extends DataWriter<String>> dataWriterClass,
File outputDirectory,
@@ -125,6 +119,17 @@ public class EventTimeRelationAnnotator
new File(modelDirectory, "model.jar"));
}
+ @Override
+ public void initialize( final UimaContext context ) throws ResourceInitializationException {
+ LOGGER.info( "Initializing ..." );
+ try ( DotLogger dotter = new DotLogger() ) {
+ super.initialize( context );
+ } catch ( IOException ioE ) {
+ throw new ResourceInitializationException( ioE );
+ }
+ LOGGER.info( "Finished." );
+ }
+
@Override
protected List<RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation>> getFeatureExtractors() {
return Lists.newArrayList(
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalRelationExtractorAnnotator.java?rev=1814586&r1=1814585&r2=1814586&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalRelationExtractorAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalRelationExtractorAnnotator.java Wed Nov 8 14:52:06 2017
@@ -21,31 +21,15 @@ package org.apache.ctakes.temporal.ae;
//import java.io.File; //for normalization
//import java.io.IOException;//for normalization
//import java.net.URI;//for normalization
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Random;
-
-import org.apache.ctakes.relationextractor.ae.features.DependencyPathFeaturesExtractor;
-import org.apache.ctakes.relationextractor.ae.features.DependencyTreeFeaturesExtractor;
-import org.apache.ctakes.relationextractor.ae.features.NamedEntityFeaturesExtractor;
-import org.apache.ctakes.relationextractor.ae.features.PartOfSpeechFeaturesExtractor;
-import org.apache.ctakes.relationextractor.ae.features.PhraseChunkingExtractor;
-import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
-import org.apache.ctakes.relationextractor.ae.features.TokenFeaturesExtractor;
-//import org.apache.ctakes.temporal.ae.feature.selection.ZscoreNormalizationExtractor;//for normalization
-import org.apache.ctakes.temporal.utils.SoftMaxUtil;
+
+import com.google.common.collect.Lists;
+import org.apache.ctakes.relationextractor.ae.features.*;
import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
import org.apache.ctakes.typesystem.type.relation.RelationArgument;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.uima.UimaContext;
import org.apache.uima.UimaContextAdmin;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
-import org.apache.uima.cas.CASException;
import org.apache.uima.fit.descriptor.ConfigurationParameter;
import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
@@ -59,7 +43,10 @@ import org.cleartk.ml.Instance;
import org.cleartk.ml.jar.GenericJarClassifierFactory;
import org.cleartk.util.ViewUriUtil;
-import com.google.common.collect.Lists;
+import java.net.URL;
+import java.util.*;
+
+//import org.apache.ctakes.temporal.ae.feature.selection.ZscoreNormalizationExtractor;//for normalization
public abstract class TemporalRelationExtractorAnnotator extends CleartkAnnotator<String> {
@@ -160,7 +147,8 @@ public abstract class TemporalRelationEx
@Override
public void initialize(UimaContext context) throws ResourceInitializationException {
- allowClassifierModelOnClasspath(context);
+
+ allowClassifierModelOnClasspath(context);
super.initialize(context);
// minmaxExtractor = createMinMaxNormalizationExtractor();
/**for normalization