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Posted to commits@ctakes.apache.org by cl...@apache.org on 2014/11/20 19:12:07 UTC
svn commit: r1640777 -
/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java
Author: clin
Date: Thu Nov 20 18:12:07 2014
New Revision: 1640777
URL: http://svn.apache.org/r1640777
Log:
make some adjustment for processing brain cander notes
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java
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=1640777&r1=1640776&r2=1640777&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 20 18:12:07 2014
@@ -60,6 +60,9 @@ import org.apache.ctakes.core.resource.L
import org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE;
import org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE;
import org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator;
+import org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator;
+import org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator;
+import org.apache.ctakes.dictionary.lookup2.ae.JCasTermAnnotator;
import org.apache.ctakes.lvg.ae.LvgAnnotator;
import org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl;
import org.apache.ctakes.postagger.POSTagger;
@@ -151,7 +154,7 @@ org.cleartk.eval.Evaluation_ImplBase<Int
@Option(longName = "dev-remainders", defaultValue = "3")
public CommandLine.IntegerRanges getDevRemainders();
- @Option(longName = "test-remainders", defaultValue = "4-5")
+ @Option(longName = "test-remainders", defaultValue = "6-7")
public CommandLine.IntegerRanges getTestRemainders();
@Option(longName = "treebank", defaultToNull=true)
@@ -280,7 +283,7 @@ org.cleartk.eval.Evaluation_ImplBase<Int
for (File dir : this.xmlDirectory.listFiles()) {
Set<String> ids = new HashSet<>();
for (Integer set : patientSets) {
- ids.add(String.format("ID%03d", set));
+ ids.add(String.format("doc%04d", set));
}
if (dir.isDirectory()) {
if (ids.contains(dir.getName().substring(0, 5))) {
@@ -325,7 +328,7 @@ org.cleartk.eval.Evaluation_ImplBase<Int
for (File file : rawTextDirectory.listFiles(new FilenameFilter(){
@Override
public boolean accept(File dir, String name) {
- return name.contains(String.format("ID%03d", setNum));
+ return name.contains(String.format("doc%04d", setNum));
}})) {
// skip hidden files like .svn
if (!file.isHidden()) {
@@ -423,11 +426,8 @@ org.cleartk.eval.Evaluation_ImplBase<Int
}
// identify segments
- if(this.xmlFormat == XMLFormat.I2B2){
- aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(SimpleSegmentAnnotator.class));
- }else{
- aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(SegmentsFromBracketedSectionTagsAnnotator.class));
- }
+ aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(SegmentsFromBracketedSectionTagsAnnotator.class));
+
// identify sentences
aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(
SentenceDetector.class,
@@ -486,9 +486,17 @@ org.cleartk.eval.Evaluation_ImplBase<Int
"DeleteAction",
new String[] { "selector=B" }));
// add UMLS on top of lookup windows
- aggregateBuilder.add(
- UmlsDictionaryLookupAnnotator.createAnnotatorDescription()
- );
+// aggregateBuilder.add(
+// UmlsDictionaryLookupAnnotator.createAnnotatorDescription()
+// );
+ aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(DefaultJCasTermAnnotator.class,
+ AbstractJCasTermAnnotator.PARAM_WINDOW_ANNOT_PRP,
+ "org.apache.ctakes.typesystem.type.textspan.Sentence",
+ JCasTermAnnotator.DICTIONARY_DESCRIPTOR_KEY,
+ ExternalResourceFactory.createExternalResourceDescription(
+ FileResourceImpl.class,
+ FileLocator.locateFile("org/apache/ctakes/dictionary/lookup/fast/cTakesHsql.xml"))
+ ));
/*
// add lvg annotator
@@ -658,6 +666,7 @@ org.cleartk.eval.Evaluation_ImplBase<Int
@Override
public void process(JCas jCas) throws AnalysisEngineProcessException {
+ boolean foundSections = false;
Matcher matcher = SECTION_PATTERN.matcher(jCas.getDocumentText());
while (matcher.find()) {
Segment segment = new Segment(jCas);
@@ -665,6 +674,14 @@ org.cleartk.eval.Evaluation_ImplBase<Int
segment.setEnd(matcher.end() - matcher.group(3).length());
segment.setId(matcher.group(2));
segment.addToIndexes();
+ foundSections = true;
+ }
+ if(!foundSections){
+ Segment segment = new Segment(jCas);
+ segment.setBegin(0);
+ segment.setEnd(jCas.getDocumentText().length());
+ segment.setId("SIMPLE_SEGMENT");
+ segment.addToIndexes();
}
}
}