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Posted to commits@ctakes.apache.org by se...@apache.org on 2017/04/10 20:56:04 UTC
svn commit: r1790896 [4/4] - in /ctakes/trunk:
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/
ctakes-a...
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/NeuralEventTimeRelationsCNNEvaluation.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/NeuralEventTimeRelationsCNNEvaluation.java?rev=1790896&r1=1790895&r2=1790896&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/NeuralEventTimeRelationsCNNEvaluation.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/NeuralEventTimeRelationsCNNEvaluation.java Mon Apr 10 20:56:02 2017
@@ -18,43 +18,23 @@
*/
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 com.google.common.base.Function;
+import com.google.common.collect.*;
+import com.lexicalscope.jewel.cli.CliFactory;
+import com.lexicalscope.jewel.cli.Option;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments;
import org.apache.ctakes.temporal.ae.EventTimeCNNAnnotator;
-import org.apache.ctakes.temporal.ae.TemporalRelationExtractorAnnotator;
-//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.keras.KerasStringOutcomeDataWriter;
import org.apache.ctakes.temporal.keras.ScriptStringFeatureDataWriter;
-//import org.apache.ctakes.temporal.ae.feature.selection.ZscoreNormalizationExtractor; //for normalization
-//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.syntax.WordToken;
-//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;
@@ -79,22 +59,29 @@ import org.cleartk.ml.CleartkAnnotator;
import org.cleartk.ml.jar.DefaultDataWriterFactory;
import org.cleartk.ml.jar.DirectoryDataWriterFactory;
import org.cleartk.ml.jar.GenericJarClassifierFactory;
-//import org.cleartk.ml.Instance; //for normalization
-//import org.cleartk.ml.feature.transform.InstanceDataWriter;//for normalization
-//import org.cleartk.ml.feature.transform.InstanceStream;//for normalization
import org.cleartk.ml.jar.JarClassifierBuilder;
-//import org.cleartk.ml.tksvmlight.TkSvmLightStringOutcomeDataWriter;
import org.cleartk.ml.tksvmlight.model.CompositeKernel.ComboOperator;
import org.cleartk.util.ViewUriUtil;
-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;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.PrintWriter;
+import java.net.URI;
+import java.util.*;
+
+//import java.util.HashSet;
+//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.feature.selection.ZscoreNormalizationExtractor; //for normalization
+//import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.WriteI2B2XML;
+//import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.XMLFormat;
+//import org.apache.ctakes.typesystem.type.relation.TemporalTextRelation;
+//import org.cleartk.ml.Instance; //for normalization
+//import org.cleartk.ml.feature.transform.InstanceDataWriter;//for normalization
+//import org.cleartk.ml.feature.transform.InstanceStream;//for normalization
+//import org.cleartk.ml.tksvmlight.TkSvmLightStringOutcomeDataWriter;
public class NeuralEventTimeRelationsCNNEvaluation extends
EvaluationOfTemporalRelations_ImplBase{
@@ -747,6 +734,13 @@ EvaluationOfTemporalRelations_ImplBase{
}
}
+ @PipeBitInfo(
+ name = "E-T Relation Overlapper",
+ description = "Adds Event-Time temporal relations for annotations overlapping those already having relations.",
+ role = PipeBitInfo.Role.SPECIAL,
+ dependencies = { PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION, PipeBitInfo.TypeProduct.TIMEX,
+ PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+ )
public static class AddPotentialRelations extends JCasAnnotator_ImplBase {
public static final String PARAM_RELATION_VIEW = "RelationView";
@ConfigurationParameter(name = PARAM_RELATION_VIEW,mandatory=false)
@@ -908,6 +902,12 @@ EvaluationOfTemporalRelations_ImplBase{
}
}*/
+ @PipeBitInfo(
+ name = "Closed TLink Counter",
+ description = "Counts the number of TLinks that have shares Events or Times in the Gold view.",
+ role = PipeBitInfo.Role.SPECIAL,
+ dependencies = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+ )
public static class CountCloseRelation extends JCasAnnotator_ImplBase {
private String systemViewName = CAS.NAME_DEFAULT_SOFA;
@@ -981,6 +981,12 @@ EvaluationOfTemporalRelations_ImplBase{
}
}
+ @PipeBitInfo(
+ name = "Transitive Contains Adder",
+ description = "Adds Contains temporal relations for annotations / relations in contain other relations.",
+ role = PipeBitInfo.Role.SPECIAL,
+ dependencies = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+ )
public static class AddTransitiveContainsRelations extends JCasAnnotator_ImplBase {
@Override
@@ -1046,6 +1052,12 @@ EvaluationOfTemporalRelations_ImplBase{
}
+ @PipeBitInfo(
+ name = "TLink Overlap Adder",
+ description = "Adds an Overlap temporal relation for each Contains temporal relation.",
+ role = PipeBitInfo.Role.SPECIAL,
+ dependencies = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+ )
public static class AddContain2Overlap extends JCasAnnotator_ImplBase {
@Override
@@ -1072,6 +1084,12 @@ EvaluationOfTemporalRelations_ImplBase{
}
}
+ @PipeBitInfo(
+ name = "Reverse Overlap TLinker",
+ description = "Adds Overlap temporal relations with arguments flipped.",
+ role = PipeBitInfo.Role.SPECIAL,
+ dependencies = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+ )
public static class AddFlippedOverlap extends JCasAnnotator_ImplBase {
@Override
@@ -1182,6 +1200,12 @@ EvaluationOfTemporalRelations_ImplBase{
}
}
+ @PipeBitInfo(
+ name = "TLink Closure Engine",
+ description = "Performs closure on Temporal Relations",
+ role = PipeBitInfo.Role.SPECIAL,
+ dependencies = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+ )
public static class AddClosure extends JCasAnnotator_ImplBase {
@Override
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/NeuralEventTimeRelationsEvaluation.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/NeuralEventTimeRelationsEvaluation.java?rev=1790896&r1=1790895&r2=1790896&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/NeuralEventTimeRelationsEvaluation.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/NeuralEventTimeRelationsEvaluation.java Mon Apr 10 20:56:02 2017
@@ -18,47 +18,24 @@
*/
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 com.google.common.base.Function;
+import com.google.common.collect.*;
+import com.lexicalscope.jewel.cli.CliFactory;
+import com.lexicalscope.jewel.cli.Option;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments;
-import org.apache.ctakes.temporal.ae.EventTimeSelfRelationAnnotator;
import org.apache.ctakes.temporal.ae.NeuralEventTimeSelfRelationAnnotator;
import org.apache.ctakes.temporal.ae.TemporalRelationExtractorAnnotator;
-//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.ae.feature.selection.ZscoreNormalizationExtractor; //for normalization
-import org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase.RemoveGoldAttributes;
-import org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase.RemoveNonContainsRelations;
-import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.WriteAnaforaXML;
import org.apache.ctakes.temporal.keras.KerasStringOutcomeDataWriter;
import org.apache.ctakes.temporal.keras.ScriptStringOutcomeDataWriter;
-//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.syntax.WordToken;
-//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;
@@ -83,25 +60,29 @@ import org.cleartk.ml.CleartkAnnotator;
import org.cleartk.ml.jar.DefaultDataWriterFactory;
import org.cleartk.ml.jar.DirectoryDataWriterFactory;
import org.cleartk.ml.jar.GenericJarClassifierFactory;
-//import org.cleartk.ml.Instance; //for normalization
-//import org.cleartk.ml.feature.transform.InstanceDataWriter;//for normalization
-//import org.cleartk.ml.feature.transform.InstanceStream;//for normalization
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.util.ViewUriUtil;
-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;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.PrintWriter;
+import java.net.URI;
+import java.util.*;
+
+//import java.util.HashSet;
+//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.feature.selection.ZscoreNormalizationExtractor; //for normalization
+//import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.WriteI2B2XML;
+//import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.XMLFormat;
+//import org.apache.ctakes.typesystem.type.relation.TemporalTextRelation;
+//import org.cleartk.ml.Instance; //for normalization
+//import org.cleartk.ml.feature.transform.InstanceDataWriter;//for normalization
+//import org.cleartk.ml.feature.transform.InstanceStream;//for normalization
+//import org.cleartk.ml.tksvmlight.TkSvmLightStringOutcomeDataWriter;
public class NeuralEventTimeRelationsEvaluation extends
EvaluationOfTemporalRelations_ImplBase{
@@ -753,6 +734,13 @@ EvaluationOfTemporalRelations_ImplBase{
}
}
+ @PipeBitInfo(
+ name = "E-T Relation Overlapper",
+ description = "Adds Event-Time temporal relations for annotations overlapping those already having relations.",
+ role = PipeBitInfo.Role.SPECIAL,
+ dependencies = { PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION, PipeBitInfo.TypeProduct.TIMEX,
+ PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+ )
public static class AddPotentialRelations extends JCasAnnotator_ImplBase {
public static final String PARAM_RELATION_VIEW = "RelationView";
@ConfigurationParameter(name = PARAM_RELATION_VIEW,mandatory=false)
@@ -914,6 +902,12 @@ EvaluationOfTemporalRelations_ImplBase{
}
}*/
+ @PipeBitInfo(
+ name = "Closed TLink Counter",
+ description = "Counts the number of TLinks that have shares Events or Times in the Gold view.",
+ role = PipeBitInfo.Role.SPECIAL,
+ dependencies = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+ )
public static class CountCloseRelation extends JCasAnnotator_ImplBase {
private String systemViewName = CAS.NAME_DEFAULT_SOFA;
@@ -987,6 +981,12 @@ EvaluationOfTemporalRelations_ImplBase{
}
}
+ @PipeBitInfo(
+ name = "Transitive Contains Adder",
+ description = "Adds Contains temporal relations for annotations / relations in contain other relations.",
+ role = PipeBitInfo.Role.SPECIAL,
+ dependencies = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+ )
public static class AddTransitiveContainsRelations extends JCasAnnotator_ImplBase {
@Override
@@ -1052,6 +1052,12 @@ EvaluationOfTemporalRelations_ImplBase{
}
+ @PipeBitInfo(
+ name = "TLink Overlap Adder",
+ description = "Adds an Overlap temporal relation for each Contains temporal relation.",
+ role = PipeBitInfo.Role.SPECIAL,
+ dependencies = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+ )
public static class AddContain2Overlap extends JCasAnnotator_ImplBase {
@Override
@@ -1078,6 +1084,12 @@ EvaluationOfTemporalRelations_ImplBase{
}
}
+ @PipeBitInfo(
+ name = "Reverse Overlap TLinker",
+ description = "Adds Overlap temporal relations with arguments flipped.",
+ role = PipeBitInfo.Role.SPECIAL,
+ dependencies = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+ )
public static class AddFlippedOverlap extends JCasAnnotator_ImplBase {
@Override
@@ -1188,6 +1200,12 @@ EvaluationOfTemporalRelations_ImplBase{
}
}
+ @PipeBitInfo(
+ name = "TLink Closure Engine",
+ description = "Performs closure on Temporal Relations",
+ role = PipeBitInfo.Role.SPECIAL,
+ dependencies = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+ )
public static class AddClosure extends JCasAnnotator_ImplBase {
@Override
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eval/EvaluationOfNeuralEEAndETRelations.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eval/EvaluationOfNeuralEEAndETRelations.java?rev=1790896&r1=1790895&r2=1790896&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eval/EvaluationOfNeuralEEAndETRelations.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eval/EvaluationOfNeuralEEAndETRelations.java Mon Apr 10 20:56:02 2017
@@ -18,48 +18,22 @@
*/
package org.apache.ctakes.temporal.nn.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.List;
-import java.util.Map;
-import java.util.Set;
-
+import com.google.common.base.Function;
+import com.google.common.collect.*;
+import com.lexicalscope.jewel.cli.CliFactory;
+import com.lexicalscope.jewel.cli.Option;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments;
-import org.apache.ctakes.temporal.ae.CrossSentenceTemporalRelationAnnotator;
import org.apache.ctakes.temporal.ae.DocTimeRelAnnotator;
-import org.apache.ctakes.temporal.ae.EventEventRelationAnnotator;
-import org.apache.ctakes.temporal.ae.EventTimeSelfRelationAnnotator;
-import org.apache.ctakes.temporal.ae.TemporalRelationExtractorAnnotator;
-import org.apache.ctakes.temporal.ae.WithinSentenceBeforeRelationAnnotator;
-//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.EvaluationOfEventEventThymeRelations.AddEEPotentialRelations;
-import org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.AddPotentialRelations;
-import org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.Overlap2Contains;
import org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.ParameterSettings;
-import org.apache.ctakes.temporal.keras.KerasStringOutcomeDataWriter;
-import org.apache.ctakes.temporal.keras.ScriptStringFeatureDataWriter;
-import org.apache.ctakes.temporal.nn.ae.EventEventTokenBasedAnnotator;
-//import org.apache.ctakes.temporal.nn.ae.EventTimeTokenAndPathBasedAnnotator;
-import org.apache.ctakes.temporal.nn.ae.EventTimeTokenBasedAnnotator;
-import org.apache.ctakes.temporal.nn.eval.EventTimeNeuralEvaluation.RemoveEventEventRelations;
import org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase;
import org.apache.ctakes.temporal.eval.Evaluation_ImplBase;
import org.apache.ctakes.temporal.eval.I2B2Data;
import org.apache.ctakes.temporal.eval.THYMEData;
-//import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.WriteI2B2XML;
-//import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.XMLFormat;
+import org.apache.ctakes.temporal.keras.KerasStringOutcomeDataWriter;
+import org.apache.ctakes.temporal.keras.ScriptStringFeatureDataWriter;
+import org.apache.ctakes.temporal.nn.ae.EventEventTokenBasedAnnotator;
+import org.apache.ctakes.temporal.nn.ae.EventTimeTokenBasedAnnotator;
import org.apache.ctakes.temporal.utils.AnnotationIdCollection;
import org.apache.ctakes.temporal.utils.TLinkTypeArray2;
import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
@@ -75,11 +49,9 @@ import org.apache.uima.cas.CAS;
import org.apache.uima.cas.CASException;
import org.apache.uima.collection.CollectionReader;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
-import org.apache.uima.fit.component.ViewCreatorAnnotator;
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.factory.ConfigurationParameterFactory;
import org.apache.uima.fit.pipeline.JCasIterator;
import org.apache.uima.fit.pipeline.SimplePipeline;
import org.apache.uima.fit.util.JCasUtil;
@@ -93,21 +65,25 @@ import org.cleartk.ml.jar.DefaultDataWri
import org.cleartk.ml.jar.DirectoryDataWriterFactory;
import org.cleartk.ml.jar.GenericJarClassifierFactory;
import org.cleartk.ml.jar.JarClassifierBuilder;
-import org.cleartk.ml.liblinear.LibLinearStringOutcomeDataWriter;
-//import org.cleartk.ml.libsvm.tk.TkLibSvmStringOutcomeDataWriter;
-//import org.cleartk.ml.libsvm.LIBSVMStringOutcomeDataWriter;
-//import org.cleartk.ml.tksvmlight.TKSVMlightStringOutcomeDataWriter;
import org.cleartk.ml.tksvmlight.model.CompositeKernel.ComboOperator;
import org.cleartk.util.ViewUriUtil;
-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;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.PrintWriter;
+import java.net.URI;
+import java.util.*;
+
+//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.nn.ae.EventTimeTokenAndPathBasedAnnotator;
+//import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.WriteI2B2XML;
+//import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.XMLFormat;
+//import org.cleartk.ml.libsvm.tk.TkLibSvmStringOutcomeDataWriter;
+//import org.cleartk.ml.libsvm.LIBSVMStringOutcomeDataWriter;
+//import org.cleartk.ml.tksvmlight.TKSVMlightStringOutcomeDataWriter;
public class EvaluationOfNeuralEEAndETRelations extends
EvaluationOfTemporalRelations_ImplBase{
@@ -455,8 +431,8 @@ EvaluationOfTemporalRelations_ImplBase{
// aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(WithinSentenceBeforeRelationAnnotator.class));
if(this.anaforaOutput != null){
- aed = AnalysisEngineFactory.createEngineDescription(WriteAnaforaXML.class, WriteAnaforaXML.PARAM_OUTPUT_DIR, this.anaforaOutput);
- aggregateBuilder.add(aed, "TimexView", CAS.NAME_DEFAULT_SOFA);
+ aed = AnalysisEngineFactory.createEngineDescription(WriteAnaforaXML.class, WriteAnaforaXML.PARAM_OUTPUT_DIR, this.anaforaOutput);
+ aggregateBuilder.add(aed, "TimexView", CAS.NAME_DEFAULT_SOFA);
}
File outf = null;
@@ -775,6 +751,12 @@ EvaluationOfTemporalRelations_ImplBase{
}
+ @PipeBitInfo(
+ name = "Transitive Contains Adder",
+ description = "Adds Contains temporal relations for annotations / relations in contain other relations.",
+ role = PipeBitInfo.Role.SPECIAL,
+ dependencies = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+ )
public static class AddTransitiveContainsRelations extends org.apache.uima.fit.component.JCasAnnotator_ImplBase {
@Override
@@ -840,6 +822,12 @@ EvaluationOfTemporalRelations_ImplBase{
}
+ @PipeBitInfo(
+ name = "TLink Overlap Adder",
+ description = "Adds an Overlap temporal relation for each Contains temporal relation.",
+ role = PipeBitInfo.Role.SPECIAL,
+ dependencies = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+ )
public static class AddContain2Overlap extends org.apache.uima.fit.component.JCasAnnotator_ImplBase {
@Override
@@ -866,6 +854,12 @@ EvaluationOfTemporalRelations_ImplBase{
}
}
+ @PipeBitInfo(
+ name = "Reverse Overlap TLinker",
+ description = "Adds Overlap temporal relations with arguments flipped.",
+ role = PipeBitInfo.Role.SPECIAL,
+ dependencies = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+ )
public static class AddFlippedOverlap extends org.apache.uima.fit.component.JCasAnnotator_ImplBase {
@Override
@@ -906,6 +900,12 @@ EvaluationOfTemporalRelations_ImplBase{
}
}
+ @PipeBitInfo(
+ name = "TLink Closure Engine",
+ description = "Performs closure on Temporal Relations",
+ role = PipeBitInfo.Role.SPECIAL,
+ dependencies = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+ )
public static class AddClosure extends JCasAnnotator_ImplBase {
@Override
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eval/EventEventNeuralEvaluation.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eval/EventEventNeuralEvaluation.java?rev=1790896&r1=1790895&r2=1790896&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eval/EventEventNeuralEvaluation.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eval/EventEventNeuralEvaluation.java Mon Apr 10 20:56:02 2017
@@ -17,21 +17,12 @@
* under the License.
*/
package org.apache.ctakes.temporal.nn.eval;
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.PrintWriter;
-import java.net.URI;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
+import com.google.common.base.Function;
+import com.google.common.collect.*;
+import com.lexicalscope.jewel.cli.CliFactory;
+import com.lexicalscope.jewel.cli.Option;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments;
import org.apache.ctakes.temporal.ae.baselines.RecallBaselineEventTimeRelationAnnotator;
import org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.RemoveCrossSentenceRelations;
@@ -75,14 +66,12 @@ import org.cleartk.ml.jar.JarClassifierB
import org.cleartk.ml.tksvmlight.model.CompositeKernel.ComboOperator;
import org.cleartk.util.ViewUriUtil;
-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;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.PrintWriter;
+import java.net.URI;
+import java.util.*;
public class EventEventNeuralEvaluation extends
EvaluationOfTemporalRelations_ImplBase{
@@ -438,6 +427,13 @@ EvaluationOfTemporalRelations_ImplBase{
return stats;
}
+ @PipeBitInfo(
+ name = "Event-Event TLinker",
+ description = "Adds Event -to- Event temporal relations.",
+ role = PipeBitInfo.Role.ANNOTATOR,
+ dependencies = { PipeBitInfo.TypeProduct.EVENT },
+ products = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+ )
public static class AddEEPotentialRelations extends org.apache.uima.fit.component.JCasAnnotator_ImplBase {
public static final String PARAM_RELATION_VIEW = "RelationView";
@ConfigurationParameter(name = PARAM_RELATION_VIEW,mandatory=false)
@@ -517,6 +513,12 @@ EvaluationOfTemporalRelations_ImplBase{
}
}
+ @PipeBitInfo(
+ name = "Closed TLink Counter",
+ description = "Counts the number of TLinks that have shares Events or Times in the Gold view.",
+ role = PipeBitInfo.Role.SPECIAL,
+ dependencies = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+ )
public static class CountCloseRelation extends JCasAnnotator_ImplBase {
private String systemViewName = CAS.NAME_DEFAULT_SOFA;
@@ -661,6 +663,12 @@ EvaluationOfTemporalRelations_ImplBase{
}
}
+ @PipeBitInfo(
+ name = "TLink Closure Engine",
+ description = "Performs closure on Temporal Relations",
+ role = PipeBitInfo.Role.SPECIAL,
+ dependencies = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+ )
public static class AddClosure extends JCasAnnotator_ImplBase {
@Override
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eval/EventTimeNeuralEvaluation.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eval/EventTimeNeuralEvaluation.java?rev=1790896&r1=1790895&r2=1790896&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eval/EventTimeNeuralEvaluation.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eval/EventTimeNeuralEvaluation.java Mon Apr 10 20:56:02 2017
@@ -18,22 +18,11 @@
*/
package org.apache.ctakes.temporal.nn.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.List;
-import java.util.Map;
-import java.util.Set;
-
+import com.google.common.base.Function;
+import com.google.common.collect.*;
+import com.lexicalscope.jewel.cli.CliFactory;
+import com.lexicalscope.jewel.cli.Option;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments;
import org.apache.ctakes.temporal.ae.baselines.RecallBaselineEventTimeRelationAnnotator;
import org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.ParameterSettings;
@@ -78,14 +67,12 @@ import org.cleartk.ml.jar.JarClassifierB
import org.cleartk.ml.tksvmlight.model.CompositeKernel.ComboOperator;
import org.cleartk.util.ViewUriUtil;
-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;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.PrintWriter;
+import java.net.URI;
+import java.util.*;
public class EventTimeNeuralEvaluation extends
EvaluationOfTemporalRelations_ImplBase{
@@ -511,6 +498,13 @@ EvaluationOfTemporalRelations_ImplBase{
}
}
+ @PipeBitInfo(
+ name = "E-T Relation Overlapper",
+ description = "Adds Event-Time temporal relations for annotations overlapping those already having relations.",
+ role = PipeBitInfo.Role.SPECIAL,
+ dependencies = { PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION, PipeBitInfo.TypeProduct.TIMEX,
+ PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+ )
public static class AddPotentialRelations extends JCasAnnotator_ImplBase {
public static final String PARAM_RELATION_VIEW = "RelationView";
@ConfigurationParameter(name = PARAM_RELATION_VIEW,mandatory=false)
@@ -621,6 +615,12 @@ EvaluationOfTemporalRelations_ImplBase{
}
}
+ @PipeBitInfo(
+ name = "Closed TLink Counter",
+ description = "Counts the number of TLinks that have shares Events or Times in the Gold view.",
+ role = PipeBitInfo.Role.SPECIAL,
+ dependencies = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+ )
public static class CountCloseRelation extends JCasAnnotator_ImplBase {
private String systemViewName = CAS.NAME_DEFAULT_SOFA;
@@ -694,6 +694,12 @@ EvaluationOfTemporalRelations_ImplBase{
}
}
+ @PipeBitInfo(
+ name = "Transitive Contains Adder",
+ description = "Adds Contains temporal relations for annotations / relations in contain other relations.",
+ role = PipeBitInfo.Role.SPECIAL,
+ dependencies = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+ )
public static class AddTransitiveContainsRelations extends JCasAnnotator_ImplBase {
@Override
@@ -759,6 +765,12 @@ EvaluationOfTemporalRelations_ImplBase{
}
+ @PipeBitInfo(
+ name = "TLink Overlap Adder",
+ description = "Adds an Overlap temporal relation for each Contains temporal relation.",
+ role = PipeBitInfo.Role.SPECIAL,
+ dependencies = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+ )
public static class AddContain2Overlap extends JCasAnnotator_ImplBase {
@Override
@@ -785,6 +797,12 @@ EvaluationOfTemporalRelations_ImplBase{
}
}
+ @PipeBitInfo(
+ name = "Reverse Overlap TLinker",
+ description = "Adds Overlap temporal relations with arguments flipped.",
+ role = PipeBitInfo.Role.SPECIAL,
+ dependencies = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+ )
public static class AddFlippedOverlap extends JCasAnnotator_ImplBase {
@Override
@@ -895,6 +913,12 @@ EvaluationOfTemporalRelations_ImplBase{
}
}
+ @PipeBitInfo(
+ name = "TLink Closure Engine",
+ description = "Performs closure on Temporal Relations",
+ role = PipeBitInfo.Role.SPECIAL,
+ dependencies = { PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
+ )
public static class AddClosure extends JCasAnnotator_ImplBase {
@Override
Modified: ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/DBCollectionReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/DBCollectionReader.java?rev=1790896&r1=1790895&r2=1790896&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/DBCollectionReader.java (original)
+++ ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/DBCollectionReader.java Mon Apr 10 20:56:02 2017
@@ -18,18 +18,9 @@
*/
package org.apache.ctakes.ytex.uima;
-import java.io.IOException;
-import java.sql.Driver;
-import java.sql.ResultSet;
-import java.sql.SQLException;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import javax.sql.DataSource;
-
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
+import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.ytex.uima.types.DocKey;
import org.apache.ctakes.ytex.uima.types.KeyValuePair;
import org.apache.uima.cas.CAS;
@@ -54,6 +45,15 @@ import org.springframework.transaction.T
import org.springframework.transaction.support.TransactionCallback;
import org.springframework.transaction.support.TransactionTemplate;
+import javax.sql.DataSource;
+import java.io.IOException;
+import java.sql.Driver;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
/**
*
* Read documents from db. Config parameters:
@@ -72,6 +72,10 @@ import org.springframework.transaction.s
* @author vijay
*
*/
+@PipeBitInfo(
+ name = "Database Reader",
+ description = "Read documents from a database.",
+ role = PipeBitInfo.Role.READER )
public class DBCollectionReader extends CollectionReader_ImplBase {
private static final Log log = LogFactory.getLog(DBCollectionReader.class);