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package edu.stanford.nlp.pipeline;
import edu.stanford.nlp.ling.AnnotationLookup;
import edu.stanford.nlp.ling.CoreAnnotation;
import edu.stanford.nlp.ling.CoreAnnotations;
import edu.stanford.nlp.ling.CoreLabel;
import edu.stanford.nlp.process.CoreLabelTokenFactory;
import edu.stanford.nlp.process.CoreTokenFactory;
import edu.stanford.nlp.util.*;
import java.lang.reflect.Method;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.logging.Logger;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
/**
* Utility functions for annotating chunks
*
* @author Angel Chang
*/
public class ChunkAnnotationUtils {
private static final Logger logger = Logger.getLogger(ChunkAnnotationUtils.class.getName());
private static CoreLabelTokenFactory tokenFactory = new CoreLabelTokenFactory(true);
/**
* Checks if offsets of doc and sentence matches
* @param docAnnotation
* @return true if the offsets match, false otherwise
*/
public static boolean checkOffsets(CoreMap docAnnotation)
{
boolean okay = true;
String docText = docAnnotation.get(CoreAnnotations.TextAnnotation.class);
String docId = docAnnotation.get(CoreAnnotations.DocIDAnnotation.class);
List docTokens = docAnnotation.get(CoreAnnotations.TokensAnnotation.class);
List sentences = docAnnotation.get(CoreAnnotations.SentencesAnnotation.class);
for (CoreMap sentence:sentences) {
String sentText = sentence.get(CoreAnnotations.TextAnnotation.class);
List sentTokens = sentence.get(CoreAnnotations.TokensAnnotation.class);
int sentBeginChar = sentence.get(CoreAnnotations.CharacterOffsetBeginAnnotation.class);
int sentEndChar = sentence.get(CoreAnnotations.CharacterOffsetEndAnnotation.class);
int sentBeginToken = sentence.get(CoreAnnotations.TokenBeginAnnotation.class);
int sentEndToken = sentence.get(CoreAnnotations.TokenEndAnnotation.class);
String docTextSpan = docText.substring(sentBeginChar, sentEndChar);
List docTokenSpan = new ArrayList<>(docTokens.subList(sentBeginToken, sentEndToken));
logger.finer("Checking Document " + docId + " span (" + sentBeginChar + "," + sentEndChar + ") ");
if (!docTextSpan.equals(sentText) ) {
okay = false;
logger.finer("WARNING: Document " + docId + " span does not match sentence");
logger.finer("DocSpanText: " + docTextSpan);
logger.finer("SentenceText: " + sentText);
}
String sentTokenStr = getTokenText(sentTokens, CoreAnnotations.TextAnnotation.class);
String docTokenStr = getTokenText(docTokenSpan, CoreAnnotations.TextAnnotation.class);
if (!docTokenStr.equals(sentTokenStr) ) {
okay = false;
logger.finer("WARNING: Document " + docId + " tokens does not match sentence");
logger.finer("DocSpanTokens: " + docTokenStr);
logger.finer("SentenceTokens: " + sentTokenStr);
}
}
return okay;
}
/**
* Fix token offsets of sentences to match those in the document (assumes tokens are shared)
* sentence token indices may not match document token list if certain html elements are ignored
* @param docAnnotation
* @return true if fix was okay, false otherwise
*/
public static boolean fixTokenOffsets(CoreMap docAnnotation)
{
List docTokens = docAnnotation.get(CoreAnnotations.TokensAnnotation.class);
List sentences = docAnnotation.get(CoreAnnotations.SentencesAnnotation.class);
int i = 0;
CoreLabel curDocToken = docTokens.get(0);
for (CoreMap sentence:sentences) {
List sentTokens = sentence.get(CoreAnnotations.TokensAnnotation.class);
CoreLabel sentTokenFirst = sentTokens.get(0);
while (curDocToken != sentTokenFirst) {
i++;
if (i >= docTokens.size()) { return false; }
curDocToken = docTokens.get(i);
}
int sentTokenBegin = i;
CoreLabel sentTokenLast = sentTokens.get(sentTokens.size()-1);
while (curDocToken != sentTokenLast) {
i++;
if (i >= docTokens.size()) { return false; }
curDocToken = docTokens.get(i);
}
int sentTokenEnd = i+1;
sentence.set(CoreAnnotations.TokenBeginAnnotation.class, sentTokenBegin);
sentence.set(CoreAnnotations.TokenEndAnnotation.class, sentTokenEnd);
}
return true;
}
/**
* Copies annotation over to this coremap if not already set
*/
public static void copyUnsetAnnotations(CoreMap src, CoreMap dest) {
for (Class key : src.keySet()) {
if (!dest.has(key)) {
dest.set(key, src.get(key));
}
}
}
/**
* Give an list of character offsets for chunk, fix tokenization so tokenization occurs at
* boundary of chunks
* @param docAnnotation
* @param chunkCharOffsets
*/
public static boolean fixChunkTokenBoundaries(CoreMap docAnnotation, List chunkCharOffsets)
{
// First identify any tokens that need to be fixed
String text = docAnnotation.get(CoreAnnotations.TextAnnotation.class);
List tokens = docAnnotation.get(CoreAnnotations.TokensAnnotation.class);
List output = new ArrayList<>(tokens.size());
int i = 0;
CoreLabel token = tokens.get(i);
for (IntPair offsets:chunkCharOffsets) {
assert(token.beginPosition() >= 0);
assert(token.endPosition() >= 0);
int offsetBegin = offsets.getSource();
int offsetEnd = offsets.getTarget();
// Find tokens where token begins after chunk starts
// and token ends after chunk starts
while (offsetBegin < token.get(CoreAnnotations.CharacterOffsetBeginAnnotation.class)
|| offsetBegin >= token.get(CoreAnnotations.CharacterOffsetEndAnnotation.class)) {
output.add(token);
i++;
if (i >= tokens.size()) { return false; }
token = tokens.get(i);
}
// offsetBegin is now >= token begin and < token end
// go until we find a token that starts after our chunk has ended
while (offsetEnd > token.get(CoreAnnotations.CharacterOffsetBeginAnnotation.class)) {
// Check if chunk includes token
if (offsetBegin > token.get(CoreAnnotations.CharacterOffsetBeginAnnotation.class)) {
// Chunk starts in the middle of the token
if (offsetEnd < token.get(CoreAnnotations.CharacterOffsetEndAnnotation.class)) {
output.add(tokenFactory.makeToken(text.substring(token.beginPosition(), offsetBegin),
token.beginPosition(), offsetBegin-token.beginPosition()));
output.add(tokenFactory.makeToken(text.substring(offsetBegin,offsetEnd),
offsetBegin, offsetEnd-offsetBegin));
output.add(tokenFactory.makeToken(text.substring(offsetEnd,token.endPosition()),
offsetEnd, token.endPosition()-offsetEnd));
} else {
output.add(tokenFactory.makeToken(text.substring(token.beginPosition(), offsetBegin),
token.beginPosition(), offsetBegin-token.beginPosition()));
output.add(tokenFactory.makeToken(text.substring(offsetBegin,token.endPosition()),
offsetBegin, token.endPosition()-offsetBegin));
}
} else if (offsetEnd < token.get(CoreAnnotations.CharacterOffsetEndAnnotation.class)) {
output.add(tokenFactory.makeToken(text.substring(token.beginPosition(),offsetEnd),
token.beginPosition(), offsetEnd-token.beginPosition()));
output.add(tokenFactory.makeToken(text.substring(offsetEnd,token.endPosition()), offsetEnd,
token.endPosition()-offsetEnd));
} else {
// success! chunk contains token
output.add(token);
}
i++;
if (i >= tokens.size()) { return false; }
token = tokens.get(i);
}
}
// Add rest of the tokens
for (; i < tokens.size(); i++) {
token = tokens.get(i);
output.add(token);
}
docAnnotation.set(CoreAnnotations.TokensAnnotation.class, output);
return true;
}
/**
* Create chunk that is merged from chunkIndexStart to chunkIndexEnd (exclusive)
* @param chunkList - List of chunks
* @param origText - Text from which to extract chunk text
* @param chunkIndexStart - Index of first chunk to merge
* @param chunkIndexEnd - Index of last chunk to merge (exclusive)
* @param tokenFactory - factory for creating tokens (if we want to get a merged corelabel instead of something random)
* @return new merged chunk
*/
public static CoreMap getMergedChunk(List chunkList, String origText,
int chunkIndexStart, int chunkIndexEnd, CoreLabelTokenFactory tokenFactory)
{
CoreMap firstChunk = chunkList.get(chunkIndexStart);
CoreMap lastChunk = chunkList.get(chunkIndexEnd-1);
int firstCharOffset = firstChunk.get(CoreAnnotations.CharacterOffsetBeginAnnotation.class);
int lastCharOffset = lastChunk.get(CoreAnnotations.CharacterOffsetEndAnnotation.class);
int firstTokenIndex = firstChunk.get(CoreAnnotations.TokenBeginAnnotation.class);
int lastTokenIndex = lastChunk.get(CoreAnnotations.TokenEndAnnotation.class);
String chunkText = origText.substring(firstCharOffset, lastCharOffset);
CoreMap newChunk;
if (tokenFactory != null) {
newChunk = tokenFactory.makeToken(chunkText, firstCharOffset, lastCharOffset);
} else {
newChunk = new Annotation(chunkText);
}
newChunk.set(CoreAnnotations.CharacterOffsetBeginAnnotation.class, firstCharOffset);
newChunk.set(CoreAnnotations.CharacterOffsetEndAnnotation.class, lastCharOffset);
newChunk.set(CoreAnnotations.TokenBeginAnnotation.class, firstTokenIndex);
newChunk.set(CoreAnnotations.TokenEndAnnotation.class, lastTokenIndex);
List tokens = new ArrayList<>(lastTokenIndex - firstTokenIndex);
for (int i = chunkIndexStart; i < chunkIndexEnd; i++) {
CoreMap chunk = chunkList.get(i);
tokens.addAll(chunk.get(CoreAnnotations.TokensAnnotation.class));
}
newChunk.set(CoreAnnotations.TokensAnnotation.class, tokens);
// TODO: merge other keys into this new chunk ??
return newChunk;
}
/**
* Create chunk that is merged from chunkIndexStart to chunkIndexEnd (exclusive)
* @param chunkList - List of chunks
* @param chunkIndexStart - Index of first chunk to merge
* @param chunkIndexEnd - Index of last chunk to merge (exclusive)
* @param aggregators - Aggregators
* @param tokenFactory - factory for creating tokens (if we want to get a merged corelabel instead of something random)
* @return new merged chunk
*/
public static CoreMap getMergedChunk(List chunkList,
int chunkIndexStart, int chunkIndexEnd,
Map aggregators,
CoreLabelTokenFactory tokenFactory)
{
CoreMap newChunk;
if (tokenFactory != null) {
newChunk = tokenFactory.makeToken();
} else {
newChunk = new Annotation("");
}
for (Map.Entry entry:aggregators.entrySet()) {
if (chunkIndexEnd > chunkList.size()) {
assert(false);
}
Object value = entry.getValue().aggregate(entry.getKey(), chunkList.subList(chunkIndexStart, chunkIndexEnd));
newChunk.set(entry.getKey(), value);
}
if (newChunk instanceof CoreLabel) {
CoreLabel cl = (CoreLabel) newChunk;
cl.setValue(cl.word());
cl.setOriginalText(cl.word());
}
return newChunk;
}
/**
* Return chunk offsets
* @param chunkList - List of chunks
* @param charStart - character begin offset
* @param charEnd - character end offset
* @return chunk offsets
*/
public static Interval getChunkOffsetsUsingCharOffsets(List chunkList,
int charStart, int charEnd)
{
int chunkStart = 0;
int chunkEnd = chunkList.size();
// Find first chunk with start > charStart
for (int i = 0; i < chunkList.size(); i++) {
int start = chunkList.get(i).get(CoreAnnotations.CharacterOffsetBeginAnnotation.class);
if (start > charStart) {
break;
}
chunkStart = i;
}
// Find first chunk with start >= charEnd
for (int i = chunkStart; i < chunkList.size(); i++) {
int start = chunkList.get(i).get(CoreAnnotations.CharacterOffsetBeginAnnotation.class);
if (start >= charEnd) {
chunkEnd = i;
break;
}
}
return Interval.toInterval(chunkStart, chunkEnd, Interval.INTERVAL_OPEN_END);
}
/**
* Merge chunks from chunkIndexStart to chunkIndexEnd (exclusive) and replace them in the list
* @param chunkList - List of chunks
* @param origText - Text from which to extract chunk text
* @param chunkIndexStart - Index of first chunk to merge
* @param chunkIndexEnd - Index of last chunk to merge (exclusive)
*/
public static void mergeChunks(List chunkList, String origText,
int chunkIndexStart, int chunkIndexEnd)
{
CoreMap newChunk = getMergedChunk(chunkList, origText, chunkIndexStart, chunkIndexEnd, null);
int nChunksToRemove = chunkIndexEnd - chunkIndexStart - 1;
for (int i = 0; i < nChunksToRemove; i++) {
chunkList.remove(chunkIndexStart);
}
chunkList.set(chunkIndexStart, newChunk);
}
public static Character getFirstNonWsChar(CoreMap sent)
{
String sentText = sent.get(CoreAnnotations.TextAnnotation.class);
for (int j = 0; j < sentText.length(); j++) {
char c = sentText.charAt(j);
if (!Character.isWhitespace(c)) {
return c;
}
}
return null;
}
public static Integer getFirstNonWsCharOffset(CoreMap sent, boolean relative)
{
String sentText = sent.get(CoreAnnotations.TextAnnotation.class);
for (int j = 0; j < sentText.length(); j++) {
char c = sentText.charAt(j);
if (!Character.isWhitespace(c)) {
if (relative) {
return j;
} else {
return j + sent.get(CoreAnnotations.CharacterOffsetBeginAnnotation.class);
}
}
}
return null;
}
public static String getTrimmedText(CoreMap sent)
{
String sentText = sent.get(CoreAnnotations.TextAnnotation.class);
return sentText.trim();
}
/**
* Give an list of character offsets for chunk, fix sentence splitting
* so sentences doesn't break the chunks
* @param docAnnotation Document with sentences
* @param chunkCharOffsets ordered pairs of different chunks that should appear in sentences
* @return true if fix was okay (chunks are in all sentences), false otherwise
*/
public static boolean fixChunkSentenceBoundaries(CoreMap docAnnotation, List chunkCharOffsets)
{
return fixChunkSentenceBoundaries(docAnnotation, chunkCharOffsets, false, false, false);
}
/**
* Give an list of character offsets for chunk, fix sentence splitting
* so sentences doesn't break the chunks
* @param docAnnotation Document with sentences
* @param chunkCharOffsets ordered pairs of different chunks that should appear in sentences
* @param offsetsAreNotSorted Treat each pair of offsets as independent (look through all sentences again)
* @param extendedFixSentence Do extended sentence fixing based on some heuristics
* @param moreExtendedFixSentence Do even more extended sentence fixing based on some heuristics
* @return true if fix was okay (chunks are in all sentences), false otherwise
*/
public static boolean fixChunkSentenceBoundaries(CoreMap docAnnotation, List chunkCharOffsets,
boolean offsetsAreNotSorted,
boolean extendedFixSentence, boolean moreExtendedFixSentence)
{
String text = docAnnotation.get(CoreAnnotations.TextAnnotation.class);
List sentences = docAnnotation.get(CoreAnnotations.SentencesAnnotation.class);
if (sentences == null || sentences.size() == 0) return true;
if (chunkCharOffsets != null) {
int i = 0;
CoreMap sentence = sentences.get(i);
for (IntPair offsets:chunkCharOffsets) {
int offsetBegin = offsets.getSource();
int offsetEnd = offsets.getTarget();
// Find sentence where sentence begins after chunk starts
// and sentence ends after chunk starts
while (offsetBegin < sentence.get(CoreAnnotations.CharacterOffsetBeginAnnotation.class)
|| offsetBegin >= sentence.get(CoreAnnotations.CharacterOffsetEndAnnotation.class)) {
i++;
if (i >= sentences.size()) { return false; }
sentence = sentences.get(i);
}
// offsetBegin is now >= sentence begin and < sentence end
// Check if sentence end includes chunk
if (sentence.get(CoreAnnotations.CharacterOffsetEndAnnotation.class) >= offsetEnd) {
// success! sentence contains chunk
} else {
// hmm, sentence contains beginning of chunk, but not end
// Lets find sentence that contains end of chunk and merge sentences
int startSentIndex = i;
while (offsetEnd > sentence.get(CoreAnnotations.CharacterOffsetEndAnnotation.class)) {
i++;
if (i >= sentences.size()) { return false; }
sentence = sentences.get(i);
}
Integer firstNonWsCharOffset = getFirstNonWsCharOffset(sentence, false);
if (firstNonWsCharOffset != null && firstNonWsCharOffset >= offsetEnd) {
// Ends before first real character of this sentence, don't include this sentence
i--;
sentence = sentences.get(i);
}
// Okay, now let's merge sentences from startSendIndex to i (includes i)
mergeChunks(sentences, text, startSentIndex, i+1);
// Reset our iterating index i to startSentIndex
i = startSentIndex;
sentence = sentences.get(i);
}
if (extendedFixSentence) {
//System.err.println("Doing extended fixing of sentence:" + text.substring(offsetBegin,offsetEnd));
if (i+1 < sentences.size()) {
// Extended sentence fixing:
// Check if entity is at the end of this sentence and if next sentence starts with uppercase
// If not uppercase, merge with next sentence
boolean entityAtSentEnd = true;
int sentCharBegin = sentence.get(CoreAnnotations.CharacterOffsetBeginAnnotation.class);
String sentText = sentence.get(CoreAnnotations.TextAnnotation.class);
int offsetEndInSentText = offsetEnd - sentCharBegin;
for (int j = offsetEndInSentText; j < sentText.length(); j++) {
char c = sentText.charAt(j);
if (!Character.isWhitespace(c)) {
entityAtSentEnd = false;
break;
}
}
boolean doMerge = false;
if (entityAtSentEnd) {
CoreMap nextSentence = sentences.get(i+1);
Character c = getFirstNonWsChar(nextSentence);
if (c != null) {
doMerge = !Character.isUpperCase(c);
if (!doMerge) {
logger.finer("No merge: c is '" + c + "'");
}
} else {
logger.finer("No merge: no char");
}
} else {
logger.finer("No merge: entity not at end");
}
if (doMerge) {
logger.finer("Merge chunks");
mergeChunks(sentences, text, i, i+2);
}
}
}
if (offsetsAreNotSorted) {
i = 0;
}
sentence = sentences.get(i);
}
}
// Do a bit more sentence fixing
if (moreExtendedFixSentence) {
int i = 0;
while (i+1 < sentences.size()) {
boolean doMerge = false;
CoreMap sentence = sentences.get(i);
CoreMap nextSentence = sentences.get(i+1);
String sentTrimmedText = getTrimmedText(sentence);
String nextSentTrimmedText = getTrimmedText(nextSentence);
if (sentTrimmedText.length() <= 1 || nextSentTrimmedText.length() <= 1) {
// Merge
doMerge = true;
} else {
// List sentTokens = sentence.get(CoreAnnotations.TokensAnnotation.class);
// CoreLabel lastSentToken = sentTokens.get(sentTokens.size()-1);
Character c = getFirstNonWsChar(nextSentence);
// List nextSentTokens = nextSentence.get(CoreAnnotations.TokensAnnotation.class);
if (c != null && !Character.isUpperCase(c)) {
if (c == ',' || (Character.isLowerCase(c))) {
doMerge = true;
}
}
}
if (doMerge) {
mergeChunks(sentences, text, i, i+2);
} else {
i++;
}
}
}
// Set sentence indices
for (int i = 0; i < sentences.size(); i++) {
CoreMap sentence = sentences.get(i);
sentence.set(CoreAnnotations.SentenceIndexAnnotation.class, i);
}
return true;
}
/**
* Annotates a CoreMap representing a chunk with basic chunk information
* CharacterOffsetBeginAnnotation - set to CharacterOffsetBeginAnnotation of first token in chunk
* CharacterOffsetEndAnnotation - set to CharacterOffsetEndAnnotation of last token in chunk
* TokensAnnotation - List of tokens in this chunk
* TokenBeginAnnotation - Index of first token in chunk (index in original list of tokens)
* tokenStartIndex + totalTokenOffset
* TokenEndAnnotation - Index of last token in chunk (index in original list of tokens)
* tokenEndIndex + totalTokenOffset
* @param chunk - CoreMap to be annotated
* @param tokens - List of tokens to look for chunks
* @param tokenStartIndex - Index (relative to current list of tokens) at which this chunk starts
* @param tokenEndIndex - Index (relative to current list of tokens) at which this chunk ends (not inclusive)
* @param totalTokenOffset - Index of tokens to offset by
*/
public static void annotateChunk(CoreMap chunk,
List tokens, int tokenStartIndex, int tokenEndIndex, int totalTokenOffset)
{
List chunkTokens = new ArrayList<>(tokens.subList(tokenStartIndex, tokenEndIndex));
chunk.set(CoreAnnotations.CharacterOffsetBeginAnnotation.class,
chunkTokens.get(0).get(CoreAnnotations.CharacterOffsetBeginAnnotation.class));
chunk.set(CoreAnnotations.CharacterOffsetEndAnnotation.class,
chunkTokens.get(chunkTokens.size()-1).get(CoreAnnotations.CharacterOffsetEndAnnotation.class));
chunk.set(CoreAnnotations.TokensAnnotation.class, chunkTokens);
chunk.set(CoreAnnotations.TokenBeginAnnotation.class, tokenStartIndex+totalTokenOffset);
chunk.set(CoreAnnotations.TokenEndAnnotation.class, tokenEndIndex+totalTokenOffset);
}
public static String getTokenText(List tokens, Class tokenTextKey)
{
return getTokenText(tokens, tokenTextKey, " ");
}
public static String getTokenText(List tokens, Class tokenTextKey, String delimiter)
{
StringBuilder sb = new StringBuilder();
int prevEndIndex = -1;
for (CoreMap cm:tokens) {
Object obj = cm.get(tokenTextKey);
boolean includeDelimiter = sb.length() > 0;
if (cm.containsKey(CoreAnnotations.CharacterOffsetBeginAnnotation.class) &&
cm.containsKey(CoreAnnotations.CharacterOffsetEndAnnotation.class)) {
int beginIndex = cm.get(CoreAnnotations.CharacterOffsetBeginAnnotation.class);
int endIndex = cm.get(CoreAnnotations.CharacterOffsetEndAnnotation.class);
if (prevEndIndex == beginIndex) {
// No spaces
includeDelimiter = false;
}
prevEndIndex = endIndex;
}
if (obj != null) {
if (includeDelimiter) {
sb.append(delimiter);
}
sb.append(obj);
}
}
return sb.toString();
}
/**
* Annotates a CoreMap representing a chunk with text information
* TextAnnotation - String representing tokens in this chunks (token text separated by space)
* @param chunk - CoreMap to be annotated
* @param tokenTextKey - Key to use to find the token text
*/
public static void annotateChunkText(CoreMap chunk, Class tokenTextKey)
{
List chunkTokens = chunk.get(CoreAnnotations.TokensAnnotation.class);
String text = getTokenText(chunkTokens, tokenTextKey);
chunk.set(CoreAnnotations.TextAnnotation.class, text);
}
public static boolean hasCharacterOffsets(CoreMap chunk)
{
return (chunk.get(CoreAnnotations.CharacterOffsetBeginAnnotation.class) != null &&
chunk.get(CoreAnnotations.CharacterOffsetEndAnnotation.class) != null);
}
/**
* Annotates a CoreMap representing a chunk with text information
* TextAnnotation - String extracted from the origAnnotation using character offset information for this chunk
* @param chunk - CoreMap to be annotated
* @param origAnnotation - Annotation from which to extract the text for this chunk
*/
public static boolean annotateChunkText(CoreMap chunk, CoreMap origAnnotation)
{
String annoText = origAnnotation.get(CoreAnnotations.TextAnnotation.class);
if (annoText == null) return false;
if (!hasCharacterOffsets(chunk)) return false;
Integer annoBeginCharOffset = origAnnotation.get(CoreAnnotations.CharacterOffsetBeginAnnotation.class);
if (annoBeginCharOffset == null) { annoBeginCharOffset = 0; }
int chunkBeginCharOffset = chunk.get(CoreAnnotations.CharacterOffsetBeginAnnotation.class) - annoBeginCharOffset;
int chunkEndCharOffset = chunk.get(CoreAnnotations.CharacterOffsetEndAnnotation.class) - annoBeginCharOffset;
if (chunkBeginCharOffset < 0) {
logger.fine("Adjusting begin char offset from " + chunkBeginCharOffset + " to 0");
logger.fine("Chunk begin offset: " + chunk.get(CoreAnnotations.CharacterOffsetBeginAnnotation.class) +
", Source text begin offset " + annoBeginCharOffset);
chunkBeginCharOffset = 0;
}
if (chunkBeginCharOffset > annoText.length()) {
logger.fine("Adjusting begin char offset from " + chunkBeginCharOffset + " to " + annoText.length());
logger.fine("Chunk begin offset: " + chunk.get(CoreAnnotations.CharacterOffsetBeginAnnotation.class) +
", Source text begin offset " + annoBeginCharOffset);
chunkBeginCharOffset = annoText.length();
}
if (chunkEndCharOffset < 0) {
logger.fine("Adjusting end char offset from " + chunkEndCharOffset + " to 0");
logger.fine("Chunk end offset: " + chunk.get(CoreAnnotations.CharacterOffsetEndAnnotation.class) +
", Source text begin offset " + annoBeginCharOffset);
chunkEndCharOffset = 0;
}
if (chunkEndCharOffset > annoText.length()) {
logger.fine("Adjusting end char offset from " + chunkEndCharOffset + " to " + annoText.length());
logger.fine("Chunk end offset: " + chunk.get(CoreAnnotations.CharacterOffsetEndAnnotation.class) +
", Source text begin offset " + annoBeginCharOffset);
chunkEndCharOffset = annoText.length();
}
if (chunkEndCharOffset < chunkBeginCharOffset) {
logger.fine("Adjusting end char offset from " + chunkEndCharOffset + " to " + chunkBeginCharOffset);
logger.fine("Chunk end offset: " + chunk.get(CoreAnnotations.CharacterOffsetEndAnnotation.class) +
", Source text begin offset " + annoBeginCharOffset);
chunkEndCharOffset = chunkBeginCharOffset;
}
String chunkText = annoText.substring(chunkBeginCharOffset, chunkEndCharOffset);
chunk.set(CoreAnnotations.TextAnnotation.class, chunkText);
return true;
}
/**
* Annotates tokens in chunk
* @param chunk - CoreMap representing chunk (should have TextAnnotation and TokensAnnotation)
* @param tokenChunkKey - If not null, each token is annotated with the chunk using this key
* @param tokenLabelKey - If not null, each token is annotated with the text associated with the chunk using this key
*/
public static void annotateChunkTokens(CoreMap chunk, Class tokenChunkKey, Class tokenLabelKey)
{
List chunkTokens = chunk.get(CoreAnnotations.TokensAnnotation.class);
if (tokenLabelKey != null) {
String text = chunk.get(CoreAnnotations.TextAnnotation.class);
for (CoreLabel t: chunkTokens) {
t.set(tokenLabelKey, text);
}
}
if (tokenChunkKey != null) {
for (CoreLabel t: chunkTokens) {
t.set(tokenChunkKey, chunk);
}
}
}
/**
* Create a new chunk Annotation with basic chunk information
* CharacterOffsetBeginAnnotation - set to CharacterOffsetBeginAnnotation of first token in chunk
* CharacterOffsetEndAnnotation - set to CharacterOffsetEndAnnotation of last token in chunk
* TokensAnnotation - List of tokens in this chunk
* TokenBeginAnnotation - Index of first token in chunk (index in original list of tokens)
* tokenStartIndex + totalTokenOffset
* TokenEndAnnotation - Index of last token in chunk (index in original list of tokens)
* tokenEndIndex + totalTokenOffset
* @param tokens - List of tokens to look for chunks
* @param tokenStartIndex - Index (relative to current list of tokens) at which this chunk starts
* @param tokenEndIndex - Index (relative to current list of tokens) at which this chunk ends (not inclusive)
* @param totalTokenOffset - Index of tokens to offset by
* @return Annotation representing new chunk
*/
public static Annotation getAnnotatedChunk(List tokens, int tokenStartIndex, int tokenEndIndex, int totalTokenOffset)
{
Annotation chunk = new Annotation("");
annotateChunk(chunk, tokens, tokenStartIndex, tokenEndIndex, totalTokenOffset);
return chunk;
}
/**
* Create a new chunk Annotation with basic chunk information
* CharacterOffsetBeginAnnotation - set to CharacterOffsetBeginAnnotation of first token in chunk
* CharacterOffsetEndAnnotation - set to CharacterOffsetEndAnnotation of last token in chunk
* TokensAnnotation - List of tokens in this chunk
* TokenBeginAnnotation - Index of first token in chunk (index in original list of tokens)
* tokenStartIndex + totalTokenOffset
* TokenEndAnnotation - Index of last token in chunk (index in original list of tokens)
* tokenEndIndex + totalTokenOffset
* TextAnnotation - String extracted from the origAnnotation using character offset information for this chunk
* @param tokens - List of tokens to look for chunks
* @param tokenStartIndex - Index (relative to current list of tokens) at which this chunk starts
* @param tokenEndIndex - Index (relative to current list of tokens) at which this chunk ends (not inclusive)
* @param totalTokenOffset - Index of tokens to offset by
* @param tokenChunkKey - If not null, each token is annotated with the chunk using this key
* @param tokenTextKey - Key to use to find the token text
* @param tokenLabelKey - If not null, each token is annotated with the text associated with the chunk using this key
* @return Annotation representing new chunk
*/
public static Annotation getAnnotatedChunk(List tokens, int tokenStartIndex, int tokenEndIndex, int totalTokenOffset,
Class tokenChunkKey, Class tokenTextKey, Class tokenLabelKey)
{
Annotation chunk = getAnnotatedChunk(tokens, tokenStartIndex, tokenEndIndex, totalTokenOffset);
annotateChunkText(chunk, tokenTextKey);
annotateChunkTokens(chunk, tokenChunkKey, tokenLabelKey);
return chunk;
}
/**
* Create a new chunk Annotation with basic chunk information
* CharacterOffsetBeginAnnotation - set to CharacterOffsetBeginAnnotation of first token in chunk
* CharacterOffsetEndAnnotation - set to CharacterOffsetEndAnnotation of last token in chunk
* TokensAnnotation - List of tokens in this chunk
* TokenBeginAnnotation - Index of first token in chunk (index in original list of tokens)
* tokenStartIndex + annotation's TokenBeginAnnotation
* TokenEndAnnotation - Index of last token in chunk (index in original list of tokens)
* tokenEndIndex + annotation's TokenBeginAnnotation
* TextAnnotation - String extracted from the origAnnotation using character offset information for this chunk
* @param annotation - Annotation from which to extract the text for this chunk
* @param tokenStartIndex - Index (relative to current list of tokens) at which this chunk starts
* @param tokenEndIndex - Index (relative to current list of tokens) at which this chunk ends (not inclusive)
* @return Annotation representing new chunk
*/
public static Annotation getAnnotatedChunk(CoreMap annotation, int tokenStartIndex, int tokenEndIndex)
{
Integer annoTokenBegin = annotation.get(CoreAnnotations.TokenBeginAnnotation.class);
if (annoTokenBegin == null) { annoTokenBegin = 0; }
List tokens = annotation.get(CoreAnnotations.TokensAnnotation.class);
Annotation chunk = getAnnotatedChunk(tokens, tokenStartIndex, tokenEndIndex, annoTokenBegin);
boolean annotatedTextFromCharOffsets = annotateChunkText(chunk, annotation);
if (!annotatedTextFromCharOffsets) {
// Use tokens to get text annotation
annotateChunkText(chunk, CoreAnnotations.TextAnnotation.class);
}
return chunk;
}
/**
* Create a new chunk Annotation with basic chunk information
* CharacterOffsetBeginAnnotation - set to CharacterOffsetBeginAnnotation of first token in chunk
* CharacterOffsetEndAnnotation - set to CharacterOffsetEndAnnotation of last token in chunk
* TokensAnnotation - List of tokens in this chunk
* TokenBeginAnnotation - Index of first token in chunk (index in original list of tokens)
* tokenStartIndex + annotation's TokenBeginAnnotation
* TokenEndAnnotation - Index of last token in chunk (index in original list of tokens)
* tokenEndIndex + annotation's TokenBeginAnnotation
* TextAnnotation - String extracted from the origAnnotation using character offset information for this chunk
* @param annotation - Annotation from which to extract the text for this chunk
* @param tokenStartIndex - Index (relative to current list of tokens) at which this chunk starts
* @param tokenEndIndex - Index (relative to current list of tokens) at which this chunk ends (not inclusive)
* @param tokenChunkKey - If not null, each token is annotated with the chunk using this key
* @param tokenLabelKey - If not null, each token is annotated with the text associated with the chunk using this key
* @return Annotation representing new chunk
*/
public static Annotation getAnnotatedChunk(CoreMap annotation, int tokenStartIndex, int tokenEndIndex,
Class tokenChunkKey, Class tokenLabelKey)
{
Annotation chunk = getAnnotatedChunk(annotation, tokenStartIndex, tokenEndIndex);
annotateChunkTokens(chunk, tokenChunkKey, tokenLabelKey);
return chunk;
}
public static CoreMap getAnnotatedChunkUsingCharOffsets(CoreMap annotation, int charOffsetStart, int charOffsetEnd)
{
// TODO: make more efficient search
List cm = getAnnotatedChunksUsingSortedCharOffsets(annotation,
CollectionUtils.makeList(new IntPair(charOffsetStart, charOffsetEnd)));
if (cm != null && cm.size() > 0) {
return cm.get(0);
} else {
return null;
}
}
public static List getAnnotatedChunksUsingSortedCharOffsets(
CoreMap annotation, List charOffsets)
{
return getAnnotatedChunksUsingSortedCharOffsets(annotation, charOffsets, true, null, null, true);
}
/**
* Create a list of new chunk Annotation with basic chunk information
* CharacterOffsetBeginAnnotation - set to CharacterOffsetBeginAnnotation of first token in chunk
* CharacterOffsetEndAnnotation - set to CharacterOffsetEndAnnotation of last token in chunk
* TokensAnnotation - List of tokens in this chunk
* TokenBeginAnnotation - Index of first token in chunk (index in original list of tokens)
* tokenStartIndex + annotation's TokenBeginAnnotation
* TokenEndAnnotation - Index of last token in chunk (index in original list of tokens)
* tokenEndIndex + annotation's TokenBeginAnnotation
* TextAnnotation - String extracted from the origAnnotation using character offset information for this chunk
* @param annotation - Annotation from which to extract the text for this chunk
* @param charOffsets - List of start and end (not inclusive) character offsets
* Note: assume char offsets are sorted and nonoverlapping!!!
* @param charOffsetIsRelative - Whether the character offsets are relative to the current annotation or absolute offsets
* @param tokenChunkKey - If not null, each token is annotated with the chunk using this key
* @param tokenLabelKey - If not null, each token is annotated with the text associated with the chunk using this key
* @param allowPartialTokens - Whether to allow partial tokens or not
* @return List of annotation representing new chunks
*/
public static List getAnnotatedChunksUsingSortedCharOffsets(
CoreMap annotation, List charOffsets, boolean charOffsetIsRelative,
Class tokenChunkKey, Class tokenLabelKey, boolean allowPartialTokens)
{
String annoText = annotation.get(CoreAnnotations.TextAnnotation.class);
List chunks = new ArrayList<>(charOffsets.size());
List annoTokens = annotation.get(CoreAnnotations.TokensAnnotation.class);
Integer annoCharBegin = annotation.get(CoreAnnotations.CharacterOffsetBeginAnnotation.class);
if (annoCharBegin == null) { annoCharBegin = 0; }
Integer annoTokenBegin = annotation.get(CoreAnnotations.TokenBeginAnnotation.class);
if (annoTokenBegin == null) { annoTokenBegin = 0; }
int i = 0;
for (IntPair p:charOffsets) {
int beginRelCharOffset = charOffsetIsRelative? p.getSource():p.getSource()-annoCharBegin;
int endRelCharOffset = charOffsetIsRelative? p.getTarget():p.getTarget()-annoCharBegin;
int beginCharOffset = beginRelCharOffset + annoCharBegin;
int endCharOffset = endRelCharOffset + annoCharBegin;
if (beginRelCharOffset >= annoText.length()) { break; }
if (endRelCharOffset > annoText.length()) { endRelCharOffset = annoText.length(); }
if (allowPartialTokens) {
while (i < annoTokens.size() && annoTokens.get(i).endPosition() <= beginCharOffset) {
i++;
}
} else {
while (i < annoTokens.size() && annoTokens.get(i).beginPosition() < beginCharOffset) {
i++;
}
}
if (i >= annoTokens.size()) break;
int tokenBegin = i;
int j = i;
if (allowPartialTokens) {
while (j < annoTokens.size() && annoTokens.get(j).beginPosition() < endCharOffset) {
j++;
}
} else {
while (j < annoTokens.size() && annoTokens.get(j).endPosition() <= endCharOffset) {
assert(annoTokens.get(j).beginPosition() >= beginCharOffset);
j++;
}
}
int tokenEnd = j;
List chunkTokens = new ArrayList<>(annoTokens.subList(tokenBegin, tokenEnd));
String chunkText = annoText.substring(beginRelCharOffset, endRelCharOffset);
Annotation chunk = new Annotation(chunkText);
chunk.set(CoreAnnotations.CharacterOffsetBeginAnnotation.class, beginCharOffset);
chunk.set(CoreAnnotations.CharacterOffsetEndAnnotation.class, endCharOffset);
chunk.set(CoreAnnotations.TokensAnnotation.class, chunkTokens);
chunk.set(CoreAnnotations.TokenBeginAnnotation.class, tokenBegin + annoTokenBegin);
chunk.set(CoreAnnotations.TokenEndAnnotation.class, tokenEnd + annoTokenBegin);
annotateChunkTokens(chunk, tokenChunkKey, tokenLabelKey);
chunks.add(chunk);
if (j >= annoTokens.size()) break;
}
if (chunks.size() != charOffsets.size()) {
logger.warning("WARNING: Only " + chunks.size() + "/" + charOffsets.size()
+ " chunks found. Check if offsets are sorted/nonoverlapping");
}
return chunks;
}
public static void annotateChunk(CoreMap annotation, Class newAnnotationKey,
Class aggrKey, CoreMapAttributeAggregator aggregator)
{
Object v = aggregator.aggregate(aggrKey, annotation.get(CoreAnnotations.TokensAnnotation.class));
annotation.set(newAnnotationKey, v);
}
public static void annotateChunk(CoreMap chunk, Map attributes)
{
for (String attr:attributes.keySet()) {
String value = attributes.get(attr);
AnnotationLookup.KeyLookup lookup = AnnotationLookup.getCoreKey(attr);
if (attr != null) {
if (value != null) {
try {
Class valueClass = AnnotationLookup.getValueType(lookup.coreKey);
if (valueClass == String.class) {
chunk.set(lookup.coreKey, value);
} else {
Method valueOfMethod = valueClass.getMethod("valueOf", String.class);
if (valueOfMethod != null) {
chunk.set(lookup.coreKey, valueOfMethod.invoke(valueClass, value));
}
}
} catch (Exception ex) {
throw new RuntimeException("Unable to annotate attribute " + attr, ex);
}
} else {
chunk.set(lookup.coreKey, null);
}
} else {
throw new UnsupportedOperationException("Unknown attributes: " + attr);
}
}
}
public static void annotateChunks(List chunks, int start, int end, Map attributes)
{
for (int i = start; i < end; i++) {
annotateChunk(chunks.get(i), attributes);
}
}
public static void annotateChunks(List chunks, Map attributes)
{
for (CoreMap chunk:chunks) {
annotateChunk(chunk, attributes);
}
}
public static T createCoreMap(CoreMap cm, String text, int start, int end,
CoreTokenFactory factory) {
if (end > start) {
T token = factory.makeToken();
Integer cmCharStart = cm.get(CoreAnnotations.CharacterOffsetBeginAnnotation.class);
if (cmCharStart == null) cmCharStart = 0;
token.set(CoreAnnotations.TextAnnotation.class, text.substring(start, end));
token.set(CoreAnnotations.CharacterOffsetBeginAnnotation.class, cmCharStart + start);
token.set(CoreAnnotations.CharacterOffsetEndAnnotation.class, cmCharStart + end);
return token;
} else {
return null;
}
}
public static void appendCoreMap(List res,
CoreMap cm, String text, int start, int end,
CoreTokenFactory factory) {
T scm = createCoreMap(cm, text, start, end, factory);
if (scm != null) {
res.add(scm);
}
}
public static List splitCoreMap(Pattern p, boolean includeMatched,
CoreMap cm, CoreTokenFactory factory)
{
List res = new ArrayList<>();
String text = cm.get(CoreAnnotations.TextAnnotation.class);
Matcher m = p.matcher(text);
int index = 0;
while (m.find()) {
int start = m.start();
int end = m.end();
// Include characters from index to m.start()
appendCoreMap(res, cm, text, index, start, factory);
// Include matched pattern
if (includeMatched) {
appendCoreMap(res, cm, text, start, end, factory);
}
index = end;
}
appendCoreMap(res, cm, text, index, text.length(), factory);
return res;
}
}
