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Posted to commits@ctakes.apache.org by sw...@apache.org on 2013/06/18 16:20:09 UTC
svn commit: r1494148 - in
/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion:
eval/AssertionEvaluation.java
medfacts/cleartk/AssertionCleartkAnalysisEngine.java
Author: swu
Date: Tue Jun 18 14:20:09 2013
New Revision: 1494148
URL: http://svn.apache.org/r1494148
Log:
assertion evaluation allows multiple input directories
Modified:
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java?rev=1494148&r1=1494147&r2=1494148&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java Tue Jun 18 14:20:09 2013
@@ -116,7 +116,7 @@ public class AssertionEvaluation extends
name = "--train-dir",
usage = "specify the directory containing the XMI training files (for example, /NLP/Corpus/Relations/mipacq/xmi/train)",
required = true)
- public File trainDirectory;
+ public String trainDirectory;
@Option(
name = "--test-dir",
@@ -250,7 +250,13 @@ protected static Options options = new O
// System.err.println("forcing skipping of conditional processing!!!");
// options.runConditional = false;
printOptionsForDebugging(options);
- List<File> trainFiles = Arrays.asList(options.trainDirectory.listFiles());
+ String[] dirs = options.trainDirectory.split("[;:]");
+ List<File> trainFiles = new ArrayList<File>();
+ for (String dir : dirs) {
+ File trainDir = new File(dir);
+ trainFiles.addAll(Arrays.asList(trainDir.listFiles()));
+ System.out.println(trainFiles.toString());
+ }
//File modelsDir = new File("models/modifier");
File modelsDir = options.modelsDirectory;
File evaluationOutputDirectory = options.evaluationOutputDirectory;
@@ -364,7 +370,7 @@ protected static Options options = new O
"ignore generic: %b%n" +
"ignore history: %b%n" +
"%n%n",
- options.trainDirectory.getAbsolutePath(),
+ options.trainDirectory,
(options.testDirectory != null) ? options.testDirectory.getAbsolutePath() : "",
options.modelsDirectory.getAbsolutePath(),
options.crossValidationFolds,
@@ -429,8 +435,18 @@ public static void printScore(Map<String
public static void preprocess(File preprocessDir ) throws ResourceInitializationException, UIMAException, IOException {
// File devDirectory = new File(options.trainDirectory.getParentFile() + File.separator + "dev");
- GoldEntityAndAttributeReaderPipelineForSeedCorpus.readSharpUmlsCem(
- preprocessDir, options.trainDirectory, options.testDirectory, options.devDirectory);
+ File trainDir = null;
+ if (options.trainDirectory.split("[;:]").length>1) {
+ throw new IOException("Assertion preprocess wants to write to one train directory, but you've supplied multiple.");
+ } else {
+ trainDir = new File(options.trainDirectory);
+ }
+ if (preprocessDir.getName().contains("i2b2")) {
+
+ } else {
+ GoldEntityAndAttributeReaderPipelineForSeedCorpus.readSharpUmlsCem(
+ preprocessDir, trainDir, options.testDirectory, options.devDirectory);
+ }
}
@Override
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java?rev=1494148&r1=1494147&r2=1494148&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java Tue Jun 18 14:20:09 2013
@@ -91,19 +91,20 @@ public abstract class AssertionCleartkAn
protected Random coin = new Random(0);
- public ConllDependencyNode findAnnotationHead(JCas jcas, Annotation annotation) {
-
- for (ConllDependencyNode depNode : JCasUtil.selectCovered(jcas, ConllDependencyNode.class, annotation)) {
-
- ConllDependencyNode head = depNode.getHead();
- if (head == null || head.getEnd() <= annotation.getBegin() || head.getBegin() > annotation.getEnd()) {
- // The head is outside the bounds of the annotation, so this node must be the annotation's head
- return depNode;
- }
- }
- // Can this happen?
- return null;
- }
+/* DEPRECATED: STW 2013/03/28. Use DependencyUtility:getNominalHeadNode(jCas,annotation) instead */
+// public ConllDependencyNode findAnnotationHead(JCas jcas, Annotation annotation) {
+//
+// for (ConllDependencyNode depNode : JCasUtil.selectCovered(jcas, ConllDependencyNode.class, annotation)) {
+//
+// ConllDependencyNode head = depNode.getHead();
+// if (head == null || head.getEnd() <= annotation.getBegin() || head.getBegin() > annotation.getEnd()) {
+// // The head is outside the bounds of the annotation, so this node must be the annotation's head
+// return depNode;
+// }
+// }
+// // Can this happen?
+// return null;
+// }