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Posted to commits@ctakes.apache.org by tm...@apache.org on 2017/11/09 18:19:48 UTC
svn commit: r1814762 - in /ctakes/trunk:
ctakes-core/src/main/java/org/apache/ctakes/core/patient/
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/
Author: tmill
Date: Thu Nov 9 18:19:47 2017
New Revision: 1814762
URL: http://svn.apache.org/viewvc?rev=1814762&view=rev
Log:
WIP: Fixes compiler error but coref eval still not working.
Modified:
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/patient/PatientNoteStore.java
ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/patient/PatientNoteStore.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/patient/PatientNoteStore.java?rev=1814762&r1=1814761&r2=1814762&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/patient/PatientNoteStore.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/patient/PatientNoteStore.java Thu Nov 9 18:19:47 2017
@@ -55,7 +55,7 @@ public enum PatientNoteStore {
*/
synchronized public Collection<String> getCompletedPatientIds() {
return _wantedDocCounts.entrySet().stream()
- .filter( e -> _storedDocCounts.get( e.getKey() ).equals( e.getValue() ) )
+ .filter( e -> _storedDocCounts.getOrDefault( e.getKey(), 0 ).equals( e.getValue() ) )
.map( Map.Entry::getKey )
.collect( Collectors.toList() );
}
Modified: ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java?rev=1814762&r1=1814761&r2=1814762&view=diff
==============================================================================
--- ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java (original)
+++ ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java Thu Nov 9 18:19:47 2017
@@ -27,6 +27,7 @@ import org.apache.ctakes.core.config.Con
import org.apache.ctakes.core.patient.AbstractPatientConsumer;
import org.apache.ctakes.core.patient.PatientNoteCollector;
import org.apache.ctakes.core.patient.PatientNoteStore;
+import org.apache.ctakes.core.patient.PatientViewUtil;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.resource.FileLocator;
import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
@@ -1027,7 +1028,7 @@ public class EvaluationOfEventCoreferenc
@Override
protected void processPatientCas(JCas patientJcas) throws AnalysisEngineProcessException {
// scorer.process(patientJcas);
- for(JCas docView : notes.getDocumentViews(notes.getPreviousPatientName())){
+ for(JCas docView : PatientViewUtil.getDocumentViews(patientJcas)){
scorer.process(docView);
}
}
@@ -1073,7 +1074,7 @@ public class EvaluationOfEventCoreferenc
@Override
protected void processPatientCas(JCas patientJcas) throws AnalysisEngineProcessException {
- for(JCas docView : notes.getDocumentViews(notes.getPreviousPatientName())){
+ for(JCas docView : PatientViewUtil.getDocumentViews(patientJcas)){
delegate.process(docView);
}
}
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java?rev=1814762&r1=1814761&r2=1814762&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java Thu Nov 9 18:19:47 2017
@@ -61,6 +61,7 @@ import org.apache.ctakes.contexttokenize
import org.apache.ctakes.core.ae.OverlapAnnotator;
import org.apache.ctakes.core.ae.SentenceDetector;
import org.apache.ctakes.core.ae.TokenizerAnnotatorPTB;
+import org.apache.ctakes.core.patient.PatientNoteStore;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
import org.apache.ctakes.core.resource.FileLocator;
import org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE;
@@ -87,6 +88,7 @@ import org.apache.ctakes.typesystem.type
import org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.ctakes.utils.struct.CounterMap;
import org.apache.log4j.Logger;
import org.apache.uima.UIMAException;
import org.apache.uima.UimaContext;
@@ -127,6 +129,7 @@ import org.xml.sax.SAXException;
import com.google.common.collect.Lists;
import com.google.common.io.CharStreams;
import com.lexicalscope.jewel.cli.Option;
+import sun.reflect.generics.reflectiveObjects.NotImplementedException;
//import org.apache.ctakes.core.cleartk.ae.SentenceDetectorAnnotator;
//import org.threeten.bp.temporal.TemporalUnit;
@@ -437,23 +440,19 @@ org.cleartk.eval.Evaluation_ImplBase<Int
protected CollectionReader getCollectionReader( List<Integer> patientSets ) throws Exception {
List<File> collectedFiles = this.getFilesFor( patientSets );
Collections.sort(collectedFiles);
- // for(File file : collectedFiles){
- // System.err.println(file.getName());
- // }
- /**
- if(isTraining){
- final Collection<File> filesToRemove = new HashSet<>();
- for ( File xmiFile : collectedFiles ) {
- String fname = xmiFile.getName();
- if(this.badNotes.contains(fname)){
- LOGGER.error("Find Bad XMI file: "+fname);
- filesToRemove.add( xmiFile );
- }
- }
- collectedFiles.removeAll( filesToRemove );
- }
- isTraining = false;
- */
+
+ CounterMap<String> docCounts = new CounterMap<>();
+ for(File f : collectedFiles){
+ String ptidPrefix = null;
+ if(this.subcorpus == Subcorpus.Colon || this.subcorpus == Subcorpus.Brain){
+ ptidPrefix = f.getName().split("_")[0];
+ }else{
+ throw new UnsupportedOperationException("No prefix extraction method implemented in Evaluation_ImplBase collection reader getter.");
+ }
+ docCounts.add(ptidPrefix);
+ }
+ docCounts.forEach((k,v) -> PatientNoteStore.getInstance().setDocCount(k, v));
+
return UriCollectionReader.getCollectionReaderFromFiles( collectedFiles );
}