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Posted to commits@ctakes.apache.org by st...@apache.org on 2012/12/20 00:30:28 UTC
svn commit: r1424221 -
/incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/
Author: stevenbethard
Date: Wed Dec 19 23:30:27 2012
New Revision: 1424221
URL: http://svn.apache.org/viewvc?rev=1424221&view=rev
Log:
Moves patientSets out of Evaluation_ImplBase to make it easier to do train/dev/test experiments.
Modified:
incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfAnnotationSpans_ImplBase.java
incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKEventSpans.java
incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKTimeSpans.java
incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventProperties.java
incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventSpans.java
incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTimeSpans.java
incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java
Modified: incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfAnnotationSpans_ImplBase.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfAnnotationSpans_ImplBase.java?rev=1424221&r1=1424220&r2=1424221&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfAnnotationSpans_ImplBase.java (original)
+++ incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfAnnotationSpans_ImplBase.java Wed Dec 19 23:30:27 2012
@@ -70,9 +70,8 @@ public abstract class EvaluationOfAnnota
File baseDirectory,
File rawTextDirectory,
File knowtatorXMLDirectory,
- List<Integer> patientSets,
Set<AnnotatorType> annotatorFlags) {
- super(baseDirectory, rawTextDirectory, knowtatorXMLDirectory, patientSets, annotatorFlags);
+ super(baseDirectory, rawTextDirectory, knowtatorXMLDirectory, annotatorFlags);
}
protected abstract AnalysisEngineDescription getDataWriterDescription(File directory)
Modified: incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKEventSpans.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKEventSpans.java?rev=1424221&r1=1424220&r2=1424221&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKEventSpans.java (original)
+++ incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKEventSpans.java Wed Dec 19 23:30:27 2012
@@ -51,10 +51,11 @@ public class EvaluationOfClearTKEventSpa
EvaluationOfClearTKEventSpans evaluation = new EvaluationOfClearTKEventSpans(
new File("target/eval"),
options.getRawTextDirectory(),
- options.getKnowtatorXMLDirectory(),
- options.getPatients().getList());
+ options.getKnowtatorXMLDirectory());
evaluation.setLogging(Level.FINE, new File("target/eval/cleartk-event-errors.log"));
- List<AnnotationStatistics<String>> foldStats = evaluation.crossValidation(4);
+ List<AnnotationStatistics<String>> foldStats = evaluation.crossValidation(
+ options.getPatients().getList(),
+ 4);
for (AnnotationStatistics<String> stats : foldStats) {
System.err.println(stats);
}
@@ -65,13 +66,11 @@ public class EvaluationOfClearTKEventSpa
public EvaluationOfClearTKEventSpans(
File baseDirectory,
File rawTextDirectory,
- File knowtatorXMLDirectory,
- List<Integer> patientSets) {
+ File knowtatorXMLDirectory) {
super(
baseDirectory,
rawTextDirectory,
knowtatorXMLDirectory,
- patientSets,
EnumSet.noneOf(AnnotatorType.class));
}
Modified: incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKTimeSpans.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKTimeSpans.java?rev=1424221&r1=1424220&r2=1424221&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKTimeSpans.java (original)
+++ incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKTimeSpans.java Wed Dec 19 23:30:27 2012
@@ -50,10 +50,11 @@ public class EvaluationOfClearTKTimeSpan
EvaluationOfClearTKTimeSpans evaluation = new EvaluationOfClearTKTimeSpans(
new File("target/eval"),
options.getRawTextDirectory(),
- options.getKnowtatorXMLDirectory(),
- options.getPatients().getList());
+ options.getKnowtatorXMLDirectory());
evaluation.setLogging(Level.FINE, new File("target/eval/cleartk-time-errors.log"));
- List<AnnotationStatistics<String>> foldStats = evaluation.crossValidation(4);
+ List<AnnotationStatistics<String>> foldStats = evaluation.crossValidation(
+ options.getPatients().getList(),
+ 4);
for (AnnotationStatistics<String> stats : foldStats) {
System.err.println(stats);
}
@@ -64,13 +65,11 @@ public class EvaluationOfClearTKTimeSpan
public EvaluationOfClearTKTimeSpans(
File baseDirectory,
File rawTextDirectory,
- File knowtatorXMLDirectory,
- List<Integer> patientSets) {
+ File knowtatorXMLDirectory) {
super(
baseDirectory,
rawTextDirectory,
knowtatorXMLDirectory,
- patientSets,
EnumSet.noneOf(AnnotatorType.class));
}
Modified: incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventProperties.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventProperties.java?rev=1424221&r1=1424220&r2=1424221&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventProperties.java (original)
+++ incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventProperties.java Wed Dec 19 23:30:27 2012
@@ -60,9 +60,9 @@ public class EvaluationOfEventProperties
EvaluationOfEventProperties evaluation = new EvaluationOfEventProperties(
new File("target/eval"),
options.getRawTextDirectory(),
- options.getKnowtatorXMLDirectory(),
- options.getPatients().getList());
- List<Map<String, AnnotationStatistics<String>>> foldStats = evaluation.crossValidation(4);
+ options.getKnowtatorXMLDirectory());
+ List<Map<String, AnnotationStatistics<String>>> foldStats = evaluation.crossValidation(
+ options.getPatients().getList(), 4);
Map<String, AnnotationStatistics<String>> overallStats = new HashMap<String, AnnotationStatistics<String>>();
for (String name : PROPERTY_NAMES) {
overallStats.put(name, new AnnotationStatistics<String>());
@@ -89,13 +89,11 @@ public class EvaluationOfEventProperties
public EvaluationOfEventProperties(
File baseDirectory,
File rawTextDirectory,
- File knowtatorXMLDirectory,
- List<Integer> patientSets) {
+ File knowtatorXMLDirectory) {
super(
baseDirectory,
rawTextDirectory,
knowtatorXMLDirectory,
- patientSets,
EnumSet.of(AnnotatorType.PART_OF_SPEECH_TAGS));
}
Modified: incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventSpans.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventSpans.java?rev=1424221&r1=1424220&r2=1424221&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventSpans.java (original)
+++ incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventSpans.java Wed Dec 19 23:30:27 2012
@@ -65,11 +65,12 @@ public class EvaluationOfEventSpans exte
new File("target/eval"),
options.getRawTextDirectory(),
options.getKnowtatorXMLDirectory(),
- options.getPatients().getList(),
options.getProbabilityOfKeepingANegativeExample(),
options.getFeatureSelectionThreshold());
evaluation.setLogging(Level.FINE, new File("target/eval/ctakes-event-errors.log"));
- List<AnnotationStatistics<String>> foldStats = evaluation.crossValidation(2);
+ List<AnnotationStatistics<String>> foldStats = evaluation.crossValidation(
+ options.getPatients().getList(),
+ 2);
for (AnnotationStatistics<String> stats : foldStats) {
System.err.println(stats);
}
@@ -85,10 +86,9 @@ public class EvaluationOfEventSpans exte
File baseDirectory,
File rawTextDirectory,
File knowtatorXMLDirectory,
- List<Integer> patientSets,
float probabilityOfKeepingANegativeExample,
float featureSelectionThreshold) {
- super(baseDirectory, rawTextDirectory, knowtatorXMLDirectory, patientSets, EnumSet.of(
+ super(baseDirectory, rawTextDirectory, knowtatorXMLDirectory, EnumSet.of(
AnnotatorType.PART_OF_SPEECH_TAGS));
//AnnotatorType.UMLS_NAMED_ENTITIES,
//AnnotatorType.LEXICAL_VARIANTS,
Modified: incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTimeSpans.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTimeSpans.java?rev=1424221&r1=1424220&r2=1424221&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTimeSpans.java (original)
+++ incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTimeSpans.java Wed Dec 19 23:30:27 2012
@@ -44,10 +44,11 @@ public class EvaluationOfTimeSpans exten
EvaluationOfTimeSpans evaluation = new EvaluationOfTimeSpans(
new File("target/eval"),
options.getRawTextDirectory(),
- options.getKnowtatorXMLDirectory(),
- options.getPatients().getList());
+ options.getKnowtatorXMLDirectory());
evaluation.setLogging(Level.FINE, new File("target/eval/ctakes-time-errors.log"));
- List<AnnotationStatistics<String>> foldStats = evaluation.crossValidation(4);
+ List<AnnotationStatistics<String>> foldStats = evaluation.crossValidation(
+ options.getPatients().getList(),
+ 4);
for (AnnotationStatistics<String> stats : foldStats) {
System.err.println(stats);
}
@@ -58,13 +59,11 @@ public class EvaluationOfTimeSpans exten
public EvaluationOfTimeSpans(
File baseDirectory,
File rawTextDirectory,
- File knowtatorXMLDirectory,
- List<Integer> patientSets) {
+ File knowtatorXMLDirectory) {
super(
baseDirectory,
rawTextDirectory,
knowtatorXMLDirectory,
- patientSets,
EnumSet.of(AnnotatorType.PART_OF_SPEECH_TAGS));
}
Modified: incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java?rev=1424221&r1=1424220&r2=1424221&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java (original)
+++ incubator/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java Wed Dec 19 23:30:27 2012
@@ -90,31 +90,23 @@ public abstract class Evaluation_ImplBas
protected File knowtatorXMLDirectory;
- protected List<Integer> patientSets;
-
private Set<AnnotatorType> annotatorFlags;
public Evaluation_ImplBase(
File baseDirectory,
File rawTextDirectory,
File knowtatorXMLDirectory,
- List<Integer> patientSets,
Set<AnnotatorType> annotatorFlags) {
super(baseDirectory);
this.rawTextDirectory = rawTextDirectory;
this.knowtatorXMLDirectory = knowtatorXMLDirectory;
- this.patientSets = patientSets;
this.annotatorFlags = annotatorFlags;
}
- public List<STATISTICS_TYPE> crossValidation(int nFolds) throws Exception {
- return this.crossValidation(this.patientSets, nFolds);
- }
-
@Override
- protected CollectionReader getCollectionReader(List<Integer> selectedPatientSets) throws Exception {
+ protected CollectionReader getCollectionReader(List<Integer> patientSets) throws Exception {
List<File> files = new ArrayList<File>();
- for (Integer set : selectedPatientSets) {
+ for (Integer set : patientSets) {
File setTextDirectory = new File(this.rawTextDirectory, "doc" + set);
for (File file : setTextDirectory.listFiles()) {
files.add(file);