Author: tmill
Date: Tue Nov 12 20:37:21 2013
New Revision: 1541221
URL: http://svn.apache.org/r1541221
Log:
Fixes CTAKES-264. Switched to using UIMAFit's JCasUtil selectCovered methods.
Added annotation-based version (rather than span-based version) for further
speedup.
Modified:
ctakes/trunk/ctakes-chunker/src/main/java/org/apache/ctakes/chunker/ae/adjuster/ChunkAdjuster.java
Modified:
ctakes/trunk/ctakes-chunker/src/main/java/org/apache/ctakes/chunker/ae/adjuster/ChunkAdjuster.java
URL:
http://svn.apache.org/viewvc/ctakes/trunk/ctakes-chunker/src/main/java/org/apache/ctakes/chunker/ae/adjuster/ChunkAdjuster.java?rev=1541221&r1=1541220&r2=1541221&view=diff
==============================================================================
---
ctakes/trunk/ctakes-chunker/src/main/java/org/apache/ctakes/chunker/ae/adjuster/ChunkAdjuster.java
(original)
+++
ctakes/trunk/ctakes-chunker/src/main/java/org/apache/ctakes/chunker/ae/adjuster/ChunkAdjuster.java
Tue Nov 12 20:37:21 2013
@@ -19,20 +19,20 @@
package org.apache.ctakes.chunker.ae.adjuster;
import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import org.apache.ctakes.typesystem.type.syntax.Chunk;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
import org.apache.log4j.Logger;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import
org.apache.uima.analysis_engine.annotator.AnnotatorConfigurationException;
import org.apache.uima.analysis_engine.annotator.AnnotatorProcessException;
-import org.apache.uima.cas.FSIterator;
import org.apache.uima.jcas.JCas;
-import org.apache.uima.jcas.JFSIndexRepository;
import org.apache.uima.resource.ResourceInitializationException;
-
-import org.apache.ctakes.typesystem.type.syntax.Chunk;
-import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.uimafit.util.JCasUtil;
/**
* UIMA annotator that uses a pattern and a rule about that pattern to adjust
@@ -89,7 +89,8 @@ public class ChunkAdjuster extends JCasA
*
* @see
org.apache.uima.analysis_engine.annotator.BaseAnnotator#initialize(AnnotatorContext)
*/
- public void initialize(UimaContext aContext)
+ @Override
+ public void initialize(UimaContext aContext)
throws ResourceInitializationException {
super.initialize(aContext);
@@ -132,67 +133,76 @@ public class ChunkAdjuster extends JCasA
* processed. For each Sentence, look for the pattern, and adjust a
chunk if
* the pattern is found.
*/
- public void process(JCas jcas)
+ @Override
+ public void process(JCas jcas)
throws AnalysisEngineProcessException {
logger.info(" process(JCas)");
- String text = jcas.getDocumentText();
-
try {
- JFSIndexRepository indexes =
jcas.getJFSIndexRepository();
- FSIterator sentenceItr =
indexes.getAnnotationIndex(Sentence.type)
- .iterator();
- while (sentenceItr.hasNext()) {
- Sentence sentence = (Sentence)
sentenceItr.next();
- int start = sentence.getBegin();
- int end = sentence.getEnd();
- annotateRange(jcas, text, start, end);
+ Collection<Sentence> sentences = JCasUtil.select(jcas,
Sentence.class);
+ for(Sentence sentence : sentences){
+ annotateSentence(jcas, sentence);
}
} catch (Exception e) {
throw new AnalysisEngineProcessException(e);
}
}
+ protected void annotateSentence(JCas jcas, Sentence sent) throws
AnalysisEngineProcessException{
+ List<Chunk> chunkList = new ArrayList<Chunk>(JCasUtil.selectCovered(jcas,
Chunk.class, sent));
+
+ // For each chunk in the Sentence, see if the chunk is the start of a
+ // matching pattern
+ // If so, extend the end offset of the <code>i</code> +
+ // <code>indexOfTokenToInclude</code>
+ for (int i = 0; i < chunkList.size(); i++) {
+
+ boolean matches = true;
+ Chunk chunk = chunkList.get(i);
+
+ while (matches == true) {
+ matches = compareToPattern(chunkList, i);
+ if (matches) {
+ extendChunk(chunk, chunkList.get(i + indexOfTokenToInclude)
+ .getEnd());
+ removeEnvelopedChunks(chunkList, i); // to check again on next
+ // iteration of while loop
+ }
+ }
+ }
+
+ }
+
/**
* A utility method that annotates a given range.
*/
- protected void annotateRange(JCas jcas, String text, int rangeBegin,
+ protected void annotateRange(JCas jcas, int rangeBegin,
int rangeEnd)
throws AnalysisEngineProcessException {
- JFSIndexRepository indexes = jcas.getJFSIndexRepository();
-
// logger.info("Adjuster: from " + rangeBegin + " to " +
rangeEnd);
// Find the Chunks in this Sentence
// For each Chunk, there is a corresponding more specific such
as NP,
// PP, etc
- FSIterator chunkItr =
indexes.getAnnotationIndex(Chunk.type).iterator();
- ArrayList<Chunk> list = new ArrayList<Chunk>();
- while (chunkItr.hasNext()) {
- Chunk baseChunk = (Chunk) chunkItr.next();
- if (baseChunk.getBegin() >= rangeBegin
- && baseChunk.getEnd() <= rangeEnd) {
- list.add(baseChunk);
- }
- }
+ List<Chunk> chunkList = new
ArrayList<Chunk>(JCasUtil.selectCovered(jcas, Chunk.class, rangeBegin,
rangeEnd));
// For each chunk in the Sentence, see if the chunk is the
start of a
// matching pattern
// If so, extend the end offset of the <code>i</code> +
// <code>indexOfTokenToInclude</code>
- for (int i = 0; i < list.size(); i++) {
+ for (int i = 0; i < chunkList.size(); i++) {
boolean matches = true;
- Chunk chunk = list.get(i);
+ Chunk chunk = chunkList.get(i);
while (matches == true) {
- matches = compareToPattern(list, i);
+ matches = compareToPattern(chunkList, i);
if (matches) {
- extendChunk(chunk, list.get(i +
indexOfTokenToInclude)
+ extendChunk(chunk, chunkList.get(i +
indexOfTokenToInclude)
.getEnd());
- removeEnvelopedChunks(list, i); // to
check again on next
+ removeEnvelopedChunks(chunkList, i); //
to check again on next
// iteration of while loop
}
}
@@ -205,11 +215,11 @@ public class ChunkAdjuster extends JCasA
* This allows the rule to be applied again.
*
*/
- private void removeEnvelopedChunks(ArrayList<Chunk> list, int i) {
+ private void removeEnvelopedChunks(List<Chunk> list, int i) {
for (int j = 0; j < indexOfTokenToInclude; j++) {
- Chunk chunk = list.remove(i + 1);
- if (false)
- logger.info("removed '" +
chunk.getCoveredText() + "'");
+ list.remove(i + 1);
+// if (false)
+// logger.info("removed '" +
chunk.getCoveredText() + "'");
}
}
@@ -228,8 +238,8 @@ public class ChunkAdjuster extends JCasA
* false.
* @throws AnnotatorProcessException
*/
- private boolean compareToPattern(ArrayList<Chunk> list, int i)
- throws AnalysisEngineProcessException {
+ private boolean compareToPattern(List<Chunk> list, int i)
+ {
boolean match = true;
int len = list.size();
@@ -257,7 +267,7 @@ public class ChunkAdjuster extends JCasA
* @return The updated Chunk
* @throws AnnotatorProcessException
*/
- private Chunk extendChunk(Chunk chunk, int newEnd)
+ private static Chunk extendChunk(Chunk chunk, int newEnd)
throws AnalysisEngineProcessException {
if (newEnd < chunk.getBegin()) {
