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FullTextParser.java
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FullTextParser.java
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package org.grobid.core.engines;
import com.google.common.collect.Iterables;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.lang3.tuple.Pair;
import org.apache.commons.io.FileUtils;
import org.grobid.core.GrobidModels;
import org.grobid.core.data.BibDataSet;
import org.grobid.core.data.BiblioItem;
import org.grobid.core.data.Figure;
import org.grobid.core.data.Table;
import org.grobid.core.data.Equation;
import org.grobid.core.data.Metadata;
import org.grobid.core.data.Person;
import org.grobid.core.document.Document;
import org.grobid.core.document.DocumentPiece;
import org.grobid.core.document.DocumentPointer;
import org.grobid.core.document.DocumentSource;
import org.grobid.core.document.TEIFormatter;
import org.grobid.core.engines.citations.LabeledReferenceResult;
import org.grobid.core.engines.citations.ReferenceSegmenter;
import org.grobid.core.engines.config.GrobidAnalysisConfig;
import org.grobid.core.engines.counters.CitationParserCounters;
import org.grobid.core.engines.label.SegmentationLabels;
import org.grobid.core.engines.label.TaggingLabels;
import org.grobid.core.engines.label.TaggingLabel;
import org.grobid.core.engines.tagging.GenericTaggerUtils;
import org.grobid.core.exceptions.GrobidException;
import org.grobid.core.exceptions.GrobidResourceException;
import org.grobid.core.features.FeatureFactory;
import org.grobid.core.features.FeaturesVectorFulltext;
import org.grobid.core.lang.Language;
import org.grobid.core.layout.*;
import org.grobid.core.tokenization.TaggingTokenCluster;
import org.grobid.core.tokenization.TaggingTokenClusteror;
import org.grobid.core.utilities.LanguageUtilities;
import org.grobid.core.utilities.TextUtilities;
import org.grobid.core.utilities.KeyGen;
import org.grobid.core.utilities.LayoutTokensUtil;
import org.grobid.core.utilities.GrobidProperties;
import org.grobid.core.utilities.Consolidation;
import org.grobid.core.utilities.matching.ReferenceMarkerMatcher;
import org.grobid.core.utilities.matching.EntityMatcherException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.io.Writer;
import java.nio.charset.StandardCharsets;
import java.util.Arrays;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.HashMap;
import java.util.SortedSet;
import java.util.StringTokenizer;
import java.util.TreeSet;
import java.util.regex.Matcher;
import static org.apache.commons.lang3.StringUtils.*;
/**
* @author Patrice Lopez
*/
public class FullTextParser extends AbstractParser {
private static final Logger LOGGER = LoggerFactory.getLogger(FullTextParser.class);
//private LanguageUtilities languageUtilities = LanguageUtilities.getInstance();
// private String tmpPathName = null;
// private Document doc = null;
private File tmpPath = null;
// private String pathXML = null;
// private BiblioItem resHeader = null;
// default bins for relative position
private static final int NBBINS_POSITION = 12;
// default bins for inter-block spacing
private static final int NBBINS_SPACE = 5;
// default bins for block character density
private static final int NBBINS_DENSITY = 5;
// projection scale for line length
private static final int LINESCALE = 10;
private EngineParsers parsers;
/**
* TODO some documentation...
*/
public FullTextParser(EngineParsers parsers) {
super(GrobidModels.FULLTEXT);
this.parsers = parsers;
tmpPath = GrobidProperties.getTempPath();
}
public Document processing(File inputPdf,
GrobidAnalysisConfig config) throws Exception {
DocumentSource documentSource =
DocumentSource.fromPdf(inputPdf, config.getStartPage(), config.getEndPage(),
config.getPdfAssetPath() != null, true, false);
return processing(documentSource, config);
}
/**
* Machine-learning recognition of the complete full text structures.
*
* @param documentSource input
* @param config config
* @return the document object with built TEI
*/
public Document processing(DocumentSource documentSource,
GrobidAnalysisConfig config) {
if (tmpPath == null) {
throw new GrobidResourceException("Cannot process pdf file, because temp path is null.");
}
if (!tmpPath.exists()) {
throw new GrobidResourceException("Cannot process pdf file, because temp path '" +
tmpPath.getAbsolutePath() + "' does not exists.");
}
try {
// general segmentation
Document doc = parsers.getSegmentationParser().processing(documentSource, config);
SortedSet<DocumentPiece> documentBodyParts = doc.getDocumentPart(SegmentationLabels.BODY);
// header processing
BiblioItem resHeader = new BiblioItem();
Pair<String, LayoutTokenization> featSeg = null;
if (GrobidProperties.isHeaderUseHeuristics()) {
parsers.getHeaderParser().processingHeaderBlock(config.getConsolidateHeader(), doc, resHeader);
}
// above the old version of the header block identification, because more robust
if ((resHeader.getTitle() == null) || (resHeader.getTitle().trim().length() == 0) ||
(resHeader.getAuthors() == null) || (resHeader.getFullAuthors() == null) ||
(resHeader.getFullAuthors().size() == 0) ) {
resHeader = new BiblioItem();
parsers.getHeaderParser().processingHeaderSection(config.getConsolidateHeader(), doc, resHeader);
// above, use the segmentation model result
if (doc.getMetadata() != null) {
Metadata metadata = doc.getMetadata();
if (metadata.getTitle() != null && resHeader.getTitle() == null)
resHeader.setTitle(metadata.getTitle());
if (metadata.getAuthor() != null) {
resHeader.setAuthors(metadata.getAuthor());
resHeader.setOriginalAuthors(metadata.getAuthor());
List<Person> localAuthors = parsers.getAuthorParser().processingHeader(metadata.getAuthor());
if (localAuthors != null) {
for (Person pers : localAuthors) {
resHeader.addFullAuthor(pers);
}
}
}
if ( (metadata.getTitle() != null) && (metadata.getAuthor() != null) ) {
parsers.getHeaderParser().consolidateHeader(resHeader, config.getConsolidateHeader());
}
}
}
// structure the abstract using the fulltext model
if (isNotBlank(resHeader.getAbstract())) {
List<LayoutToken> abstractTokens = resHeader.getLayoutTokens(TaggingLabels.HEADER_ABSTRACT);
if (CollectionUtils.isNotEmpty(abstractTokens)) {
SortedSet<DocumentPiece> documentParts = collectPiecesFromLayoutTokens(abstractTokens, doc);
featSeg = getBodyTextFeatured(doc, documentParts);
String rese2 = null;
List<LayoutToken> tokenizationsAbstract = null;
if (featSeg != null) {
// if featSeg is null, it usually means that no body segment is found in the
// document segmentation
String abstractText = featSeg.getLeft();
tokenizationsAbstract = featSeg.getRight().getTokenization();
if (isNotEmpty(trim(abstractText)))
rese2 = label(abstractText);
resHeader.setLabeledAbstract(rese2);
resHeader.setLayoutTokensForLabel(tokenizationsAbstract, TaggingLabels.HEADER_ABSTRACT);
}
}
}
// citation processing
// consolidation, if selected, is not done individually for each citation but
// in a second stage for all citations
List<BibDataSet> resCitations = parsers.getCitationParser().
processingReferenceSection(doc, parsers.getReferenceSegmenterParser(), 0);
// consolidate the set
if (config.getConsolidateCitations() != 0) {
Consolidation consolidator = Consolidation.getInstance();
if (consolidator.getCntManager() == null)
consolidator.setCntManager(Engine.getCntManager());
try {
Map<Integer,BiblioItem> resConsolidation = consolidator.consolidate(resCitations);
for(int i=0; i<resCitations.size(); i++) {
BiblioItem resCitation = resCitations.get(i).getResBib();
BiblioItem bibo = resConsolidation.get(i);
if (bibo != null) {
if (config.getConsolidateCitations() == 1)
BiblioItem.correct(resCitation, bibo);
else if (config.getConsolidateCitations() == 2)
BiblioItem.injectDOI(resCitation, bibo);
}
}
} catch(Exception e) {
throw new GrobidException(
"An exception occured while running consolidation on bibliographical references.", e);
}
}
//if (resCitations.size() == 0)
// System.out.println("!!!!!! article without citations !!!!");
doc.setBibDataSets(resCitations);
// full text processing
featSeg = getBodyTextFeatured(doc, documentBodyParts);
String rese = null;
LayoutTokenization layoutTokenization = null;
List<Figure> figures = null;
List<Table> tables = null;
List<Equation> equations = null;
if (featSeg != null) {
// if featSeg is null, it usually means that no body segment is found in the
// document segmentation
String bodytext = featSeg.getLeft();
layoutTokenization = featSeg.getRight();
//tokenizationsBody = featSeg.getB().getTokenization();
//layoutTokensBody = featSeg.getB().getLayoutTokens();
if ( (bodytext != null) && (bodytext.trim().length() > 0) ) {
rese = label(bodytext);
} else {
LOGGER.debug("Fulltext model: The input to the CRF processing is empty");
}
// we apply now the figure and table models based on the fulltext labeled output
figures = processFigures(rese, layoutTokenization.getTokenization(), doc);
// further parse the caption
for(Figure figure : figures) {
if ((figure.getCaptionLayoutTokens() != null) && (figure.getCaptionLayoutTokens().size() > 0) ) {
Pair<String, List<LayoutToken>> captionProcess = processShort(figure.getCaptionLayoutTokens(), doc);
figure.setLabeledCaption(captionProcess.getLeft());
figure.setCaptionLayoutTokens(captionProcess.getRight());
}
}
tables = processTables(rese, layoutTokenization.getTokenization(), doc);
// further parse the caption
for(Table table : tables) {
if ( (table.getCaptionLayoutTokens() != null) && (table.getCaptionLayoutTokens().size() > 0) ) {
Pair<String, List<LayoutToken>> captionProcess = processShort(table.getCaptionLayoutTokens(), doc);
table.setLabeledCaption(captionProcess.getLeft());
table.setCaptionLayoutTokens(captionProcess.getRight());
}
}
equations = processEquations(rese, layoutTokenization.getTokenization(), doc);
} else {
LOGGER.debug("Fulltext model: The featured body is empty");
}
// possible annexes (view as a piece of full text similar to the body)
documentBodyParts = doc.getDocumentPart(SegmentationLabels.ANNEX);
featSeg = getBodyTextFeatured(doc, documentBodyParts);
String rese2 = null;
List<LayoutToken> tokenizationsBody2 = null;
if (featSeg != null) {
// if featSeg is null, it usually means that no body segment is found in the
// document segmentation
String bodytext = featSeg.getLeft();
tokenizationsBody2 = featSeg.getRight().getTokenization();
if (isNotEmpty(trim(bodytext)))
rese2 = label(bodytext);
//System.out.println(rese);
}
// final combination
toTEI(doc, // document
rese, rese2, // labeled data for body and annex
layoutTokenization, tokenizationsBody2, // tokenization for body and annex
resHeader, // header
figures, tables, equations,
config);
return doc;
} catch (GrobidException e) {
throw e;
} catch (Exception e) {
throw new GrobidException("An exception occurred while running Grobid.", e);
}
}
protected SortedSet<DocumentPiece> collectPiecesFromLayoutTokens(List<LayoutToken> tokensList, Document doc) {
SortedSet<DocumentPiece> documentParts = new TreeSet<>();
// identify continuous sequence of layout tokens in the token list
int positionStartPiece = -1;
int currentOffset = -1;
int startBlockPtr = -1;
LayoutToken previousAbstractToken = null;
for (LayoutToken currentToken : tokensList) {
if (currentOffset == -1) {
positionStartPiece = getDocIndexToken(doc, currentToken);
startBlockPtr = currentToken.getBlockPtr();
} else {
if (currentToken.getOffset() != currentOffset + previousAbstractToken.getText().length()) {
// new DocumentPiece to be added
DocumentPointer dp1 = new DocumentPointer(doc, startBlockPtr, positionStartPiece);
DocumentPointer dp2 = new DocumentPointer(doc,
previousAbstractToken.getBlockPtr(),
getDocIndexToken(doc, previousAbstractToken));
DocumentPiece piece = new DocumentPiece(dp1, dp2);
documentParts.add(piece);
// set index for the next DocumentPiece
positionStartPiece = getDocIndexToken(doc, currentToken);
startBlockPtr = currentToken.getBlockPtr();
}
}
currentOffset = currentToken.getOffset();
previousAbstractToken = currentToken;
}
// we still need to add the last document piece
// conditional below should always be true because abstract is not null if we reach this part, but paranoia is good when programming
if (positionStartPiece != -1) {
DocumentPointer dp1 = new DocumentPointer(doc, startBlockPtr, positionStartPiece);
DocumentPointer dp2 = new DocumentPointer(doc,
previousAbstractToken.getBlockPtr(),
getDocIndexToken(doc, previousAbstractToken));
DocumentPiece piece = new DocumentPiece(dp1, dp2);
documentParts.add(piece);
}
return documentParts;
}
/**
* Process a simple segment of layout tokens with the full text model.
* Return null if provided Layout Tokens is empty or if structuring failed.
*/
public Pair<String, List<LayoutToken>> processShortNew(List<LayoutToken> tokens, Document doc) {
if (CollectionUtils.isEmpty(tokens))
return null;
SortedSet<DocumentPiece> documentParts = collectPiecesFromLayoutTokens(tokens, doc);
Pair<String, LayoutTokenization> featSeg = getBodyTextFeatured(doc, documentParts);
String res = "";
List<LayoutToken> layoutTokenization = new ArrayList<>();
if (featSeg != null) {
String featuredText = featSeg.getLeft();
LayoutTokenization layouts = featSeg.getRight();
if (layouts != null)
layoutTokenization = layouts.getTokenization();
if (isNotBlank(featuredText)) {
res = label(featuredText);
}
} else
return null;
return Pair.of(res, layoutTokenization);
}
public Pair<String, List<LayoutToken>> processShort(List<LayoutToken> tokens, Document doc) {
if (CollectionUtils.isEmpty(tokens))
return null;
SortedSet<DocumentPiece> documentParts = new TreeSet<>();
// we need to identify all the continuous chunks of tokens, and ignore the others
List<List<LayoutToken>> tokenChunks = new ArrayList<>();
List<LayoutToken> currentChunk = new ArrayList<>();
int currentPos = 0;
for(LayoutToken token : tokens) {
if (currentChunk.size() == 0) {
currentChunk.add(token);
currentPos = token.getOffset() + token.getText().length();
} else {
int tokenPos = token.getOffset();
if (currentPos == tokenPos) {
// continous
currentChunk.add(token);
currentPos = token.getOffset() + token.getText().length();
} else {
// new chunk
tokenChunks.add(currentChunk);
currentChunk = new ArrayList<LayoutToken>();
currentChunk.add(token);
currentPos = token.getOffset() + token.getText().length();
}
}
}
// add last chunk
tokenChunks.add(currentChunk);
for(List<LayoutToken> chunk : tokenChunks) {
int endInd = chunk.size()-1;
int posStartAbstract = getDocIndexToken(doc, chunk.get(0));
int posEndAbstract = getDocIndexToken(doc, chunk.get(endInd));
DocumentPointer dp1 = new DocumentPointer(doc, chunk.get(0).getBlockPtr(), posStartAbstract);
DocumentPointer dp2 = new DocumentPointer(doc, chunk.get(endInd).getBlockPtr(), posEndAbstract);
DocumentPiece piece = new DocumentPiece(dp1, dp2);
documentParts.add(piece);
}
Pair<String, LayoutTokenization> featSeg = getBodyTextFeatured(doc, documentParts);
String res = null;
List<LayoutToken> layoutTokenization = null;
if (featSeg != null) {
String featuredText = featSeg.getLeft();
LayoutTokenization layouts = featSeg.getRight();
if (layouts != null)
layoutTokenization = layouts.getTokenization();
if ( (featuredText != null) && (featuredText.trim().length() > 0) ) {
res = label(featuredText);
}
}
return Pair.of(res, layoutTokenization);
}
static public Pair<String, LayoutTokenization> getBodyTextFeatured(Document doc,
SortedSet<DocumentPiece> documentBodyParts) {
if ((documentBodyParts == null) || (documentBodyParts.size() == 0)) {
return null;
}
FeatureFactory featureFactory = FeatureFactory.getInstance();
StringBuilder fulltext = new StringBuilder();
String currentFont = null;
int currentFontSize = -1;
List<Block> blocks = doc.getBlocks();
if ( (blocks == null) || blocks.size() == 0) {
return null;
}
// vector for features
FeaturesVectorFulltext features;
FeaturesVectorFulltext previousFeatures = null;
ReferenceMarkerMatcher referenceMarkerMatcher = null;
// if bibliographical references are available from the bibliographical reference section, we look if we have
// a numbering associated to the bibliographical references (bib. ref. callout will likely be numerical then)
String bibRefCalloutType = "UNKNOWN";
List<BibDataSet> bibDataSets = doc.getBibDataSets();
if (bibDataSets != null) {
try {
referenceMarkerMatcher = doc.getReferenceMarkerMatcher();
// we look at the exising extracted labels in the bibliographical section (if available and if any) and set
// the value based on the majority of labels
int nbNumbType = 0;
int nbAuthorType = 0;
for(BibDataSet bibDataSet : bibDataSets) {
if ((bibDataSet == null) || (bibDataSet.getRefSymbol() == null))
continue;
boolean isNumb = referenceMarkerMatcher.isNumberedCitationReference(bibDataSet.getRefSymbol());
if (isNumb) {
nbNumbType++;
continue;
}
boolean isAuthor = referenceMarkerMatcher.isAuthorCitationStyle(bibDataSet.getRefSymbol());
if (isAuthor)
nbAuthorType++;
}
if (nbNumbType > (bibDataSets.size() / 2))
bibRefCalloutType = "NUMBER";
else if (nbNumbType > (bibDataSets.size() / 2))
bibRefCalloutType = "AUTHOR";
} catch(EntityMatcherException e) {
e.printStackTrace();
LOGGER.info("Could not build the bibliographical matcher", e);
}
}
boolean endblock;
boolean endPage = true;
boolean newPage = true;
//boolean start = true;
int mm = 0; // page position
int nn = 0; // document position
double lineStartX = Double.NaN;
boolean indented = false;
int fulltextLength = 0;
int pageLength = 0; // length of the current page
double lowestPos = 0.0;
double spacingPreviousBlock = 0.0;
int currentPage = 0;
List<LayoutToken> layoutTokens = new ArrayList<LayoutToken>();
fulltextLength = getFulltextLength(doc, documentBodyParts, fulltextLength);
// System.out.println("fulltextLength: " + fulltextLength);
for(DocumentPiece docPiece : documentBodyParts) {
DocumentPointer dp1 = docPiece.getLeft();
DocumentPointer dp2 = docPiece.getRight();
//int blockPos = dp1.getBlockPtr();
for(int blockIndex = dp1.getBlockPtr(); blockIndex <= dp2.getBlockPtr(); blockIndex++) {
boolean graphicVector = false;
boolean graphicBitmap = false;
Block block = blocks.get(blockIndex);
// length of the page where the current block is
double pageHeight = block.getPage().getHeight();
int localPage = block.getPage().getNumber();
if (localPage != currentPage) {
newPage = true;
currentPage = localPage;
mm = 0;
lowestPos = 0.0;
spacingPreviousBlock = 0.0;
}
/*if (start) {
newPage = true;
start = false;
}*/
boolean newline;
boolean previousNewline = false;
endblock = false;
/*if (endPage) {
newPage = true;
mm = 0;
lowestPos = 0.0;
}*/
if (lowestPos > block.getY()) {
// we have a vertical shift, which can be due to a change of column or other particular layout formatting
spacingPreviousBlock = doc.getMaxBlockSpacing() / 5.0; // default
}
else
spacingPreviousBlock = block.getY() - lowestPos;
String localText = block.getText();
if (TextUtilities.filterLine(localText)) {
continue;
}
/*if (localText != null) {
if (localText.contains("@PAGE")) {
mm = 0;
// pageLength = 0;
endPage = true;
newPage = false;
} else {
endPage = false;
}
}*/
// character density of the block
double density = 0.0;
if ( (block.getHeight() != 0.0) && (block.getWidth() != 0.0) &&
(localText != null) && (!localText.contains("@PAGE")) &&
(!localText.contains("@IMAGE")) )
density = (double)localText.length() / (block.getHeight() * block.getWidth());
// check if we have a graphical object connected to the current block
List<GraphicObject> localImages = Document.getConnectedGraphics(block, doc);
if (localImages != null) {
for(GraphicObject localImage : localImages) {
if (localImage.getType() == GraphicObjectType.BITMAP)
graphicVector = true;
if (localImage.getType() == GraphicObjectType.VECTOR)
graphicBitmap = true;
}
}
List<LayoutToken> tokens = block.getTokens();
if (tokens == null) {
continue;
}
int n = 0;// token position in current block
if (blockIndex == dp1.getBlockPtr()) {
// n = dp1.getTokenDocPos() - block.getStartToken();
n = dp1.getTokenBlockPos();
}
int lastPos = tokens.size();
// if it's a last block from a document piece, it may end earlier
if (blockIndex == dp2.getBlockPtr()) {
lastPos = dp2.getTokenBlockPos();
if (lastPos >= tokens.size()) {
LOGGER.error("DocumentPointer for block " + blockIndex + " points to " +
dp2.getTokenBlockPos() + " token, but block token size is " +
tokens.size());
lastPos = tokens.size();
}
}
while (n < lastPos) {
if (blockIndex == dp2.getBlockPtr()) {
//if (n > block.getEndToken()) {
if (n > dp2.getTokenDocPos() - block.getStartToken()) {
break;
}
}
LayoutToken token = tokens.get(n);
layoutTokens.add(token);
features = new FeaturesVectorFulltext();
features.token = token;
double coordinateLineY = token.getY();
String text = token.getText();
if ( (text == null) || (text.length() == 0)) {
n++;
//mm++;
//nn++;
continue;
}
//text = text.replaceAll("\\s+", "");
text = text.replace(" ", "");
if (text.length() == 0) {
n++;
mm++;
nn++;
continue;
}
//if (text.equals("\n") || text.equals("\r") ) {
if (text.equals("\n")) {
newline = true;
previousNewline = true;
n++;
mm++;
nn++;
continue;
} else
newline = false;
// final sanitisation and filtering
text = text.replaceAll("[ \n]", "");
if (TextUtilities.filterLine(text)) {
n++;
continue;
}
if (previousNewline) {
newline = true;
previousNewline = false;
if ((token != null) && (previousFeatures != null)) {
double previousLineStartX = lineStartX;
lineStartX = token.getX();
double characterWidth = token.width / text.length();
if (!Double.isNaN(previousLineStartX)) {
if (previousLineStartX - lineStartX > characterWidth)
indented = false;
else if (lineStartX - previousLineStartX > characterWidth)
indented = true;
// Indentation ends if line start is > 1 character width to the left of previous line start
// Indentation starts if line start is > 1 character width to the right of previous line start
// Otherwise indentation is unchanged
}
}
}
//System.out.println(text + "\t" + token.getX() + "\t" + lineStartX + "\t" + indented);
features.string = text;
if (graphicBitmap) {
features.bitmapAround = true;
}
if (graphicVector) {
features.vectorAround = true;
}
if (newline) {
features.lineStatus = "LINESTART";
if (token != null)
lineStartX = token.getX();
// be sure that previous token is closing a line, except if it's a starting line
if (previousFeatures != null) {
if (!previousFeatures.lineStatus.equals("LINESTART"))
previousFeatures.lineStatus = "LINEEND";
}
}
Matcher m0 = featureFactory.isPunct.matcher(text);
if (m0.find()) {
features.punctType = "PUNCT";
}
if (text.equals("(") || text.equals("[")) {
features.punctType = "OPENBRACKET";
} else if (text.equals(")") || text.equals("]")) {
features.punctType = "ENDBRACKET";
} else if (text.equals(".")) {
features.punctType = "DOT";
} else if (text.equals(",")) {
features.punctType = "COMMA";
} else if (text.equals("-")) {
features.punctType = "HYPHEN";
} else if (text.equals("\"") || text.equals("\'") || text.equals("`")) {
features.punctType = "QUOTE";
}
if (indented) {
features.alignmentStatus = "LINEINDENT";
}
else {
features.alignmentStatus = "ALIGNEDLEFT";
}
if (n == 0) {
features.lineStatus = "LINESTART";
// be sure that previous token is closing a line, except if it's a starting line
if (previousFeatures != null) {
if (!previousFeatures.lineStatus.equals("LINESTART"))
previousFeatures.lineStatus = "LINEEND";
}
if (token != null)
lineStartX = token.getX();
features.blockStatus = "BLOCKSTART";
} else if (n == tokens.size() - 1) {
features.lineStatus = "LINEEND";
previousNewline = true;
features.blockStatus = "BLOCKEND";
endblock = true;
} else {
// look ahead...
boolean endline = false;
int ii = 1;
boolean endloop = false;
while ((n + ii < tokens.size()) && (!endloop)) {
LayoutToken tok = tokens.get(n + ii);
if (tok != null) {
String toto = tok.getText();
if (toto != null) {
if (toto.equals("\n")) {
endline = true;
endloop = true;
} else {
if ((toto.length() != 0)
&& (!(toto.startsWith("@IMAGE")))
&& (!(toto.startsWith("@PAGE")))
&& (!text.contains(".pbm"))
&& (!text.contains(".svg"))
&& (!text.contains(".png"))
&& (!text.contains(".jpg"))) {
endloop = true;
}
}
}
}
if (n + ii == tokens.size() - 1) {
endblock = true;
endline = true;
}
ii++;
}
if ((!endline) && !(newline)) {
features.lineStatus = "LINEIN";
}
else if (!newline) {
features.lineStatus = "LINEEND";
previousNewline = true;
}
if ((!endblock) && (features.blockStatus == null))
features.blockStatus = "BLOCKIN";
else if (features.blockStatus == null) {
features.blockStatus = "BLOCKEND";
//endblock = true;
}
}
if (text.length() == 1) {
features.singleChar = true;
}
if (Character.isUpperCase(text.charAt(0))) {
features.capitalisation = "INITCAP";
}
if (featureFactory.test_all_capital(text)) {
features.capitalisation = "ALLCAP";
}
if (featureFactory.test_digit(text)) {
features.digit = "CONTAINSDIGITS";
}
Matcher m = featureFactory.isDigit.matcher(text);
if (m.find()) {
features.digit = "ALLDIGIT";
}
if (currentFont == null) {
currentFont = token.getFont();
features.fontStatus = "NEWFONT";
} else if (!currentFont.equals(token.getFont())) {
currentFont = token.getFont();
features.fontStatus = "NEWFONT";
} else
features.fontStatus = "SAMEFONT";
int newFontSize = (int) token.getFontSize();
if (currentFontSize == -1) {
currentFontSize = newFontSize;
features.fontSize = "HIGHERFONT";
} else if (currentFontSize == newFontSize) {
features.fontSize = "SAMEFONTSIZE";
} else if (currentFontSize < newFontSize) {
features.fontSize = "HIGHERFONT";
currentFontSize = newFontSize;
} else if (currentFontSize > newFontSize) {
features.fontSize = "LOWERFONT";
currentFontSize = newFontSize;
}
if (token.getBold())
features.bold = true;
if (token.getItalic())
features.italic = true;
if (features.capitalisation == null)
features.capitalisation = "NOCAPS";
if (features.digit == null)
features.digit = "NODIGIT";
if (features.punctType == null)
features.punctType = "NOPUNCT";
features.relativeDocumentPosition = featureFactory
.linearScaling(nn, fulltextLength, NBBINS_POSITION);
// System.out.println(mm + " / " + pageLength);
features.relativePagePositionChar = featureFactory
.linearScaling(mm, pageLength, NBBINS_POSITION);
int pagePos = featureFactory
.linearScaling(coordinateLineY, pageHeight, NBBINS_POSITION);
if (pagePos > NBBINS_POSITION)
pagePos = NBBINS_POSITION;
features.relativePagePosition = pagePos;
//System.out.println((coordinateLineY) + " " + (pageHeight) + " " + NBBINS_POSITION + " " + pagePos);
if (spacingPreviousBlock != 0.0) {
features.spacingWithPreviousBlock = featureFactory
.linearScaling(spacingPreviousBlock - doc.getMinBlockSpacing(),
doc.getMaxBlockSpacing() - doc.getMinBlockSpacing(), NBBINS_SPACE);
}
if (density != -1.0) {
features.characterDensity = featureFactory
.linearScaling(density - doc.getMinCharacterDensity(), doc.getMaxCharacterDensity() - doc.getMinCharacterDensity(), NBBINS_DENSITY);
//System.out.println((density-doc.getMinCharacterDensity()) + " " + (doc.getMaxCharacterDensity()-doc.getMinCharacterDensity()) + " " + NBBINS_DENSITY + " " + features.characterDensity);
}
features.calloutType = bibRefCalloutType;
// check of the token is a known bib ref label
if ((referenceMarkerMatcher != null) && ( referenceMarkerMatcher.isKnownLabel(text) || referenceMarkerMatcher.isKnownFirstAuthor(text) ))
features.calloutKnown = true;
// fulltext.append(features.printVector());
if (previousFeatures != null) {
if (features.blockStatus.equals("BLOCKSTART") &&
previousFeatures.blockStatus.equals("BLOCKIN")) {
// this is a post-correction due to the fact that the last character of a block
// can be a space or EOL character
previousFeatures.blockStatus = "BLOCKEND";
previousFeatures.lineStatus = "LINEEND";
}
fulltext.append(previousFeatures.printVector());
}
n++;
mm += text.length();
nn += text.length();
previousFeatures = features;
}
// lowest position of the block
lowestPos = block.getY() + block.getHeight();
//blockPos++;
}
}
if (previousFeatures != null) {
fulltext.append(previousFeatures.printVector());
}
return Pair.of(fulltext.toString(),
new LayoutTokenization(layoutTokens));
}
/**
* Evaluate the length of the fulltext
*/
private static int getFulltextLength(Document doc, SortedSet<DocumentPiece> documentBodyParts, int fulltextLength) {
for(DocumentPiece docPiece : documentBodyParts) {
DocumentPointer dp1 = docPiece.getLeft();
DocumentPointer dp2 = docPiece.getRight();
int tokenStart = dp1.getTokenDocPos();
int tokenEnd = dp2.getTokenDocPos();
for (int i = tokenStart; i <= tokenEnd && i < doc.getTokenizations().size(); i++) {
//tokenizationsBody.add(tokenizations.get(i));
fulltextLength += doc.getTokenizations().get(i).getText().length();
}
}
return fulltextLength;
}
/**
* Return the index of a token in a document tokenization
*/
private static int getDocIndexToken(Document doc, LayoutToken token) {
int blockPtr = token.getBlockPtr();
Block block = doc.getBlocks().get(blockPtr);
int startTokenBlockPos = block.getStartToken();
List<LayoutToken> tokens = doc.getTokenizations();
int i = startTokenBlockPos;
for(; i < tokens.size(); i++) {
int offset = tokens.get(i).getOffset();
if (offset >= token.getOffset())
break;
}
return i;
}
/**
* Process the specified pdf and format the result as training data for all the models.
*
* @param inputFile input file
* @param pathFullText path to fulltext
* @param pathTEI path to TEI
* @param id id
*/
public Document createTraining(File inputFile,
String pathFullText,
String pathTEI,
int id) {
if (tmpPath == null)
throw new GrobidResourceException("Cannot process pdf file, because temp path is null.");
if (!tmpPath.exists()) {
throw new GrobidResourceException("Cannot process pdf file, because temp path '" +
tmpPath.getAbsolutePath() + "' does not exists.");
}
DocumentSource documentSource = null;
try {
if (!inputFile.exists()) {
throw new GrobidResourceException("Cannot train for fulltext, becuase file '" +
inputFile.getAbsolutePath() + "' does not exists.");
}
String pdfFileName = inputFile.getName();
// SEGMENTATION MODEL
documentSource = DocumentSource.fromPdf(inputFile, -1, -1, false, true, true);
Document doc = new Document(documentSource);
doc.addTokenizedDocument(GrobidAnalysisConfig.defaultInstance());
if (doc.getBlocks() == null) {
throw new Exception("PDF parsing resulted in empty content");
}
doc.produceStatistics();
String fulltext = //getAllTextFeatured(doc, false);
parsers.getSegmentationParser().getAllLinesFeatured(doc);
List<LayoutToken> tokenizations = doc.getTokenizationsFulltext();
// we write first the full text untagged (but featurized with segmentation features)
String outPathFulltext = pathFullText + File.separator +
pdfFileName.replace(".pdf", ".training.segmentation");
Writer writer = new OutputStreamWriter(new FileOutputStream(new File(outPathFulltext), false), "UTF-8");
writer.write(fulltext + "\n");
writer.close();
// also write the raw text as seen before segmentation
StringBuffer rawtxt = new StringBuffer();
for(LayoutToken txtline : tokenizations) {
rawtxt.append(txtline.getText());
}
String outPathRawtext = pathFullText + File.separator +
pdfFileName.replace(".pdf", ".training.segmentation.rawtxt");
FileUtils.writeStringToFile(new File(outPathRawtext), rawtxt.toString(), "UTF-8");
if (isNotBlank(fulltext)) {
String rese = parsers.getSegmentationParser().label(fulltext);
StringBuffer bufferFulltext = parsers.getSegmentationParser().trainingExtraction(rese, tokenizations, doc);
// write the TEI file to reflect the extact layout of the text as extracted from the pdf
writer = new OutputStreamWriter(new FileOutputStream(new File(pathTEI +
File.separator +
pdfFileName.replace(".pdf", ".training.segmentation.tei.xml")), false), "UTF-8");
writer.write("<?xml version=\"1.0\" ?>\n<tei>\n\t<teiHeader>\n\t\t<fileDesc xml:id=\"" + id +