You are viewing a plain text version of this content. The canonical link for it is here.
Posted to commits@ctakes.apache.org by dl...@apache.org on 2016/06/22 16:12:49 UTC
svn commit: r1749731 - in
/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn:
./ allPairsCandidateEventPrinter.java uniquePairsCandidateEventPrinter.java
Author: dligach
Date: Wed Jun 22 16:12:48 2016
New Revision: 1749731
URL: http://svn.apache.org/viewvc?rev=1749731&view=rev
Log:
training data printers for keras experiments
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/allPairsCandidateEventPrinter.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/uniquePairsCandidateEventPrinter.java
Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/allPairsCandidateEventPrinter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/allPairsCandidateEventPrinter.java?rev=1749731&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/allPairsCandidateEventPrinter.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/allPairsCandidateEventPrinter.java Wed Jun 22 16:12:48 2016
@@ -0,0 +1,278 @@
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.ctakes.temporal.nn;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Paths;
+import java.nio.file.StandardOpenOption;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.ctakes.temporal.duration.Utils;
+import org.apache.ctakes.temporal.eval.CommandLine;
+import org.apache.ctakes.temporal.eval.THYMEData;
+import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.uima.analysis_engine.AnalysisEngine;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.cas.CASException;
+import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
+import org.apache.uima.fit.util.JCasUtil;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+
+import com.lexicalscope.jewel.cli.CliFactory;
+import com.lexicalscope.jewel.cli.Option;
+
+/**
+ * Print gold standard relations and their context.
+ *
+ * @author dmitriy dligach
+ */
+public class allPairsCandidateEventPrinter {
+
+ static interface Options {
+
+ @Option(longName = "xmi-dir")
+ public File getInputDirectory();
+
+ @Option(longName = "patients")
+ public CommandLine.IntegerRanges getPatients();
+
+ @Option(longName = "output-train")
+ public File getTrainOutputDirectory();
+
+ @Option(longName = "output-test")
+ public File getTestOutputDirectory();
+ }
+
+ public static void main(String[] args) throws Exception {
+
+ Options options = CliFactory.parseArguments(Options.class, args);
+
+ File trainFile = options.getTrainOutputDirectory();
+ if(trainFile.exists()) {
+ trainFile.delete();
+ }
+ trainFile.createNewFile();
+ File devFile = options.getTestOutputDirectory();
+ if(devFile.exists()) {
+ devFile.delete();
+ }
+ devFile.createNewFile();
+
+ List<Integer> patientSets = options.getPatients().getList();
+ List<Integer> trainItems = THYMEData.getPatientSets(patientSets, THYMEData.TRAIN_REMAINDERS);
+ List<Integer> devItems = THYMEData.getPatientSets(patientSets, THYMEData.DEV_REMAINDERS);
+
+ List<File> trainFiles = Utils.getFilesFor(trainItems, options.getInputDirectory());
+ List<File> devFiles = Utils.getFilesFor(devItems, options.getInputDirectory());
+
+ // write training data to file
+ CollectionReader trainCollectionReader = Utils.getCollectionReader(trainFiles);
+ AnalysisEngine trainDataWriter = AnalysisEngineFactory.createEngine(
+ RelationSnippetPrinter.class,
+ "OutputFile",
+ trainFile.getAbsoluteFile());
+ SimplePipeline.runPipeline(trainCollectionReader, trainDataWriter);
+
+ // write dev data to file
+ CollectionReader devCollectionReader = Utils.getCollectionReader(devFiles);
+ AnalysisEngine devDataWriter = AnalysisEngineFactory.createEngine(
+ RelationSnippetPrinter.class,
+ "OutputFile",
+ devFile.getAbsolutePath());
+ SimplePipeline.runPipeline(devCollectionReader, devDataWriter);
+ }
+
+ /**
+ * Print gold standard relations and their context.
+ *
+ * @author dmitriy dligach
+ */
+ public static class RelationSnippetPrinter extends JCasAnnotator_ImplBase {
+
+ @ConfigurationParameter(
+ name = "OutputFile",
+ mandatory = true,
+ description = "path to the output file")
+ private String outputFile;
+
+ @Override
+ public void process(JCas jCas) throws AnalysisEngineProcessException {
+
+ JCas goldView;
+ try {
+ goldView = jCas.getView("GoldView");
+ } catch (CASException e) {
+ throw new AnalysisEngineProcessException(e);
+ }
+
+ JCas systemView;
+ try {
+ systemView = jCas.getView("_InitialView");
+ } catch (CASException e) {
+ throw new AnalysisEngineProcessException(e);
+ }
+
+ // can't iterate over binary text relations in a sentence, so need
+ // a lookup from pair of annotations to binary text relation
+ Map<List<Annotation>, BinaryTextRelation> relationLookup = new HashMap<>();
+ for(BinaryTextRelation relation : JCasUtil.select(goldView, BinaryTextRelation.class)) {
+ Annotation arg1 = relation.getArg1().getArgument();
+ Annotation arg2 = relation.getArg2().getArgument();
+ relationLookup.put(Arrays.asList(arg1, arg2), relation);
+ }
+
+ // go over sentences, extracting event-event relation instances
+ for(Sentence sentence : JCasUtil.select(systemView, Sentence.class)) {
+ List<String> eventEventRelationsInSentence = new ArrayList<>();
+ List<EventMention> eventMentionsInSentence = JCasUtil.selectCovered(goldView, EventMention.class, sentence);
+
+ // retrieve event-event relations in this sentence
+ for(EventMention mention1 : eventMentionsInSentence) {
+ for(EventMention mention2 : eventMentionsInSentence) {
+ if(mention1 == mention2) {
+ continue;
+ }
+
+ BinaryTextRelation relation = relationLookup.get(Arrays.asList(mention1, mention2));
+
+ String label;
+ if(relation == null) {
+ label = "none";
+ } else {
+ label = relation.getCategory().toLowerCase();
+ }
+
+ String context;
+ if(mention1.getBegin() < mention2.getBegin()) {
+ // arg1 ... arg2, e.g. <arg1> biopsy </arg1> positive for <arg2> malignancy </arg2>
+ context = getTokensBetween(systemView, sentence, mention1, "arg1", mention2, "arg2", 2);
+ } else {
+ // arg2 ... arg1, e.g. <arg2> disease </arg2> seen on the <arg1> scan </arg1>
+ context = getTokensBetween(systemView, sentence, mention2, "arg2", mention1, "arg1", 2);
+ }
+
+ String text = String.format("%s|%s", label, context);
+ eventEventRelationsInSentence.add(text.toLowerCase());
+ }
+ }
+
+ try {
+ Files.write(Paths.get(outputFile), eventEventRelationsInSentence, StandardOpenOption.APPEND);
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+ }
+ }
+
+ /**
+ * Return tokens between arg1 and arg2 as string
+ * @param contextSize number of tokens to include on the left of arg1 and on the right of arg2
+ */
+ public static String getTokensBetween(
+ JCas jCas,
+ Sentence sent,
+ Annotation left,
+ String leftType,
+ Annotation right,
+ String rightType,
+ int contextSize)
+ throws AnalysisEngineProcessException {
+
+ List<String> tokens = new ArrayList<>();
+ for(BaseToken baseToken : JCasUtil.selectPreceding(jCas, BaseToken.class, left, contextSize)) {
+ if(sent.getBegin() <= baseToken.getBegin()) {
+ tokens.add(baseToken.getCoveredText());
+ }
+ }
+ tokens.add("<" + leftType + ">");
+ tokens.add(left.getCoveredText());
+ tokens.add("</" + leftType + ">");
+ for(BaseToken baseToken : JCasUtil.selectBetween(jCas, BaseToken.class, left, right)) {
+ tokens.add(baseToken.getCoveredText());
+ }
+ tokens.add("<" + rightType + ">");
+ tokens.add(right.getCoveredText());
+ tokens.add("</" + rightType + ">");
+ for(BaseToken baseToken : JCasUtil.selectFollowing(jCas, BaseToken.class, right, contextSize)) {
+ if(baseToken.getEnd() <= sent.getEnd()) {
+ tokens.add(baseToken.getCoveredText());
+ }
+ }
+
+ return String.join(" ", tokens).replaceAll("[\r\n]", " ");
+ }
+
+ /**
+ * If token is an event, add event markers. Otherwise, return as is.
+ * @param baseToken token to be considered
+ */
+ public static String convertToString(JCas jCas, BaseToken baseToken) throws AnalysisEngineProcessException {
+
+ JCas goldView;
+ try {
+ goldView = jCas.getView("GoldView");
+ } catch (CASException e) {
+ throw new AnalysisEngineProcessException(e);
+ }
+
+ List<EventMention> events = JCasUtil.selectCovering(goldView, EventMention.class, baseToken.getBegin(), baseToken.getEnd());
+ if(events.size() > 0) {
+ return "<e> " + baseToken.getCoveredText() + " </e>";
+ } else {
+ return baseToken.getCoveredText();
+ }
+ }
+
+ public static String getSentenceWithMarkedArgs(JCas jCas, Sentence sent, Annotation arg1, Annotation arg2) {
+
+ List<String> tokens = new ArrayList<>();
+ for(BaseToken baseToken : JCasUtil.selectCovered(jCas, BaseToken.class, sent)) {
+ // for a few hundred examples, begin/end offsets don't both match token begin/end
+ // so using an 'or' rather than 'and'
+ if(baseToken.getBegin() == arg1.getBegin() || (baseToken.getEnd() == arg1.getEnd())) {
+ tokens.add("<e>");
+ tokens.add(baseToken.getCoveredText());
+ tokens.add("</e>");
+ } else if(baseToken.getBegin() == arg2.getBegin() || (baseToken.getEnd() == arg2.getEnd())) {
+ tokens.add("<e>");
+ tokens.add(baseToken.getCoveredText());
+ tokens.add("</e>");
+ } else {
+ tokens.add(baseToken.getCoveredText());
+ }
+ }
+
+ return String.join(" ", tokens).replaceAll("[\r\n]", " ");
+ }
+}
Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/uniquePairsCandidateEventPrinter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/uniquePairsCandidateEventPrinter.java?rev=1749731&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/uniquePairsCandidateEventPrinter.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/uniquePairsCandidateEventPrinter.java Wed Jun 22 16:12:48 2016
@@ -0,0 +1,229 @@
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.ctakes.temporal.nn;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Paths;
+import java.nio.file.StandardOpenOption;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.ctakes.temporal.duration.Utils;
+import org.apache.ctakes.temporal.eval.CommandLine;
+import org.apache.ctakes.temporal.eval.THYMEData;
+import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.uima.analysis_engine.AnalysisEngine;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.cas.CASException;
+import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
+import org.apache.uima.fit.util.JCasUtil;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+
+import com.lexicalscope.jewel.cli.CliFactory;
+import com.lexicalscope.jewel.cli.Option;
+
+/**
+ * Print gold standard relations and their context.
+ *
+ * @author dmitriy dligach
+ */
+public class uniquePairsCandidateEventPrinter {
+
+ static interface Options {
+
+ @Option(longName = "xmi-dir")
+ public File getInputDirectory();
+
+ @Option(longName = "patients")
+ public CommandLine.IntegerRanges getPatients();
+
+ @Option(longName = "output-train")
+ public File getTrainOutputDirectory();
+
+ @Option(longName = "output-test")
+ public File getTestOutputDirectory();
+ }
+
+ public static void main(String[] args) throws Exception {
+
+ Options options = CliFactory.parseArguments(Options.class, args);
+
+ File trainFile = options.getTrainOutputDirectory();
+ if(trainFile.exists()) {
+ trainFile.delete();
+ }
+ trainFile.createNewFile();
+ File devFile = options.getTestOutputDirectory();
+ if(devFile.exists()) {
+ devFile.delete();
+ }
+ devFile.createNewFile();
+
+ List<Integer> patientSets = options.getPatients().getList();
+ List<Integer> trainItems = THYMEData.getPatientSets(patientSets, THYMEData.TRAIN_REMAINDERS);
+ List<Integer> devItems = THYMEData.getPatientSets(patientSets, THYMEData.DEV_REMAINDERS);
+
+ List<File> trainFiles = Utils.getFilesFor(trainItems, options.getInputDirectory());
+ List<File> devFiles = Utils.getFilesFor(devItems, options.getInputDirectory());
+
+ // write training data to file
+ CollectionReader trainCollectionReader = Utils.getCollectionReader(trainFiles);
+ AnalysisEngine trainDataWriter = AnalysisEngineFactory.createEngine(
+ RelationSnippetPrinter.class,
+ "OutputFile",
+ trainFile.getAbsoluteFile());
+ SimplePipeline.runPipeline(trainCollectionReader, trainDataWriter);
+
+ // write dev data to file
+ CollectionReader devCollectionReader = Utils.getCollectionReader(devFiles);
+ AnalysisEngine devDataWriter = AnalysisEngineFactory.createEngine(
+ RelationSnippetPrinter.class,
+ "OutputFile",
+ devFile.getAbsolutePath());
+ SimplePipeline.runPipeline(devCollectionReader, devDataWriter);
+ }
+
+ /**
+ * Print gold standard relations and their context.
+ *
+ * @author dmitriy dligach
+ */
+ public static class RelationSnippetPrinter extends JCasAnnotator_ImplBase {
+
+ @ConfigurationParameter(
+ name = "OutputFile",
+ mandatory = true,
+ description = "path to the output file")
+ private String outputFile;
+
+ @Override
+ public void process(JCas jCas) throws AnalysisEngineProcessException {
+
+ JCas goldView;
+ try {
+ goldView = jCas.getView("GoldView");
+ } catch (CASException e) {
+ throw new AnalysisEngineProcessException(e);
+ }
+
+ JCas systemView;
+ try {
+ systemView = jCas.getView("_InitialView");
+ } catch (CASException e) {
+ throw new AnalysisEngineProcessException(e);
+ }
+
+ // can't iterate over binary text relations in a sentence, so need
+ // a lookup from pair of annotations to binary text relation
+ Map<List<Annotation>, BinaryTextRelation> relationLookup = new HashMap<>();
+ for(BinaryTextRelation relation : JCasUtil.select(goldView, BinaryTextRelation.class)) {
+ Annotation arg1 = relation.getArg1().getArgument();
+ Annotation arg2 = relation.getArg2().getArgument();
+ relationLookup.put(Arrays.asList(arg1, arg2), relation);
+ }
+
+ // go over sentences, extracting event-event relation instances
+ for(Sentence sentence : JCasUtil.select(systemView, Sentence.class)) {
+ List<String> eventEventRelationsInSentence = new ArrayList<>();
+ ArrayList<EventMention> eventMentionsInSentence = new ArrayList<>(JCasUtil.selectCovered(goldView, EventMention.class, sentence));
+
+ // retrieve event-event relations in this sentence
+ for(int i = 0; i < eventMentionsInSentence.size(); i++) {
+ for(int j = i + 1; j < eventMentionsInSentence.size(); j++) {
+ EventMention mention1 = eventMentionsInSentence.get(i);
+ EventMention mention2 = eventMentionsInSentence.get(j);
+ BinaryTextRelation forwardRelation = relationLookup.get(Arrays.asList(mention1, mention2));
+ BinaryTextRelation reverseRelation = relationLookup.get(Arrays.asList(mention2, mention1));
+
+ String label;
+ if(forwardRelation != null) {
+ if(forwardRelation.getCategory().equals("CONTAINS")) {
+ label = "contains"; // this is contains relation
+ } else {
+ label = "none"; // this is some other relation
+ }
+ } else if(reverseRelation != null) {
+ if(reverseRelation.getCategory().equals("CONTAINS")) {
+ label = "contains-1"; // this is contains relation
+ } else {
+ label = "none"; // this is some other relation
+ }
+ } else {
+ label = "none"; // no relation between mentions
+ }
+
+ String context = getTokensBetween(systemView, sentence, mention1, mention2, 0);
+ String text = String.format("%s|%s", label, context);
+ eventEventRelationsInSentence.add(text.toLowerCase());
+ }
+ }
+
+ try {
+ Files.write(Paths.get(outputFile), eventEventRelationsInSentence, StandardOpenOption.APPEND);
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+ }
+ }
+
+ /**
+ * Return tokens between arg1 and arg2 as string
+ * @param contextSize number of tokens to include on the left of arg1 and on the right of arg2
+ */
+ public static String getTokensBetween(
+ JCas jCas,
+ Sentence sent,
+ Annotation left,
+ Annotation right,
+ int contextSize) {
+
+ List<String> tokens = new ArrayList<>();
+ for(BaseToken baseToken : JCasUtil.selectPreceding(jCas, BaseToken.class, left, contextSize)) {
+ if(sent.getBegin() <= baseToken.getBegin()) {
+ tokens.add(baseToken.getCoveredText());
+ }
+ }
+ tokens.add(left.getCoveredText());
+ for(BaseToken baseToken : JCasUtil.selectBetween(jCas, BaseToken.class, left, right)) {
+ tokens.add(baseToken.getCoveredText());
+ }
+ tokens.add(right.getCoveredText());
+ for(BaseToken baseToken : JCasUtil.selectFollowing(jCas, BaseToken.class, right, contextSize)) {
+ if(baseToken.getEnd() <= sent.getEnd()) {
+ tokens.add(baseToken.getCoveredText());
+ }
+ }
+
+ return String.join(" ", tokens).replaceAll("[\r\n]", " ");
+ }
+}