Fixed endless processing

Ignore failing Ruling expansion
Fixed text parsing orientation problem
2021-06-02 13:49:48 +02:00 · 2021-06-02 13:00:51 +02:00 · 2021-06-02 11:19:34 +02:00 · 2021-06-01 15:41:14 +02:00 · 2021-06-01 15:40:41 +02:00 · 2021-05-12 12:23:03 +02:00
12 changed files with 142 additions and 17 deletions
@@ -0,0 +1,6 @@
+package com.iqser.red.service.redaction.v1.server.classification.model;
+
+public enum Orientation {
+
+    NONE, LEFT, RIGHT
+}
@@ -32,6 +32,7 @@ public class TextBlock extends AbstractTextContainer {

    private String classification;

+
    public TextBlock(float minX, float maxX, float minY, float maxY, List<TextPositionSequence> sequences, int rotation) {
        this.minX = minX;
        this.maxX = maxX;
@@ -1,6 +1,7 @@
 package com.iqser.red.service.redaction.v1.server.classification.service;

 import com.iqser.red.service.redaction.v1.server.classification.model.FloatFrequencyCounter;
+import com.iqser.red.service.redaction.v1.server.classification.model.Orientation;
 import com.iqser.red.service.redaction.v1.server.classification.model.Page;
 import com.iqser.red.service.redaction.v1.server.classification.model.StringFrequencyCounter;
 import com.iqser.red.service.redaction.v1.server.classification.model.TextBlock;
@@ -11,16 +12,21 @@ import com.iqser.red.service.redaction.v1.server.tableextraction.model.Cell;
 import com.iqser.red.service.redaction.v1.server.tableextraction.model.Rectangle;
 import com.iqser.red.service.redaction.v1.server.tableextraction.model.Ruling;
 import com.iqser.red.service.redaction.v1.server.tableextraction.model.Table;
+
 import org.springframework.stereotype.Service;

 import java.util.ArrayList;
+import java.util.Iterator;
 import java.util.List;

@Service
@SuppressWarnings("all")
 public class BlockificationService {

-    public Page blockify(List<TextPositionSequence> textPositions, List<Ruling> horizontalRulingLines, List<Ruling> verticalRulingLines) {
+    static final float THRESHOLD = 1f;
+
+    public Page blockify(List<TextPositionSequence> textPositions, List<Ruling> horizontalRulingLines,
+                         List<Ruling> verticalRulingLines) {

        List<TextPositionSequence> chunkWords = new ArrayList<>();
        List<AbstractTextContainer> chunkBlockList1 = new ArrayList<>();
@@ -28,21 +34,46 @@ public class BlockificationService {
        float minX = 1000, maxX = 0, minY = 1000, maxY = 0;
        TextPositionSequence prev = null;

+        boolean wasSplitted = false;
+        Float splitX1 = null;
        for (TextPositionSequence word : textPositions) {

            boolean lineSeparation = minY - word.getY2() > word.getHeight() * 1.25;
            boolean startFromTop = word.getY1() > maxY + word.getHeight();
+            boolean splitByX = prev != null && maxX + 50 < word.getX1() && prev.getY1() == word.getY1();
+            boolean newLineAfterSplit = prev != null && word.getY1() != prev.getY1() && wasSplitted && splitX1 != word.getX1();
+            boolean splittedByRuling = word.getRotation() == 0 && isSplittedByRuling(maxX, minY, word.getX1(), word.getY1(), verticalRulingLines) || word
+                    .getRotation() == 0 && isSplittedByRuling(minX, minY, word.getX1(), word.getY2(), horizontalRulingLines) || word
+                    .getRotation() == 90 && isSplittedByRuling(maxX, minY, word.getX1(), word.getY1(), horizontalRulingLines) || word
+                    .getRotation() == 90 && isSplittedByRuling(minX, minY, word.getX1(), word.getY2(), verticalRulingLines);

-            if (prev != null && (lineSeparation || startFromTop || word.getRotation() == 0 && isSplittedByRuling(maxX, minY, word
-                    .getX1(), word.getY1(), verticalRulingLines) || word.getRotation() == 0 && isSplittedByRuling(minX, minY, word
-                    .getX1(), word.getY2(), horizontalRulingLines) || word.getRotation() == 90 && isSplittedByRuling(maxX, minY, word
-                    .getX1(), word.getY1(), horizontalRulingLines) || word.getRotation() == 90 && isSplittedByRuling(minX, minY, word
-                    .getX1(), word.getY2(), verticalRulingLines))) {
+            if (prev != null && (lineSeparation || startFromTop || splitByX || newLineAfterSplit || splittedByRuling)) {
+
+                Orientation prevOrientation = null;
+                if(!chunkBlockList1.isEmpty()) {
+                    prevOrientation = chunkBlockList1.get(chunkBlockList1.size() - 1).getOrientation();
+                }

                TextBlock cb1 = buildTextBlock(chunkWords);
                chunkBlockList1.add(cb1);
                chunkWords = new ArrayList<>();

+                if (splitByX && !splittedByRuling) {
+                    wasSplitted = true;
+                    cb1.setOrientation(Orientation.LEFT);
+                    splitX1 = word.getX1();
+                } else
+
+                if (newLineAfterSplit && !splittedByRuling) {
+                    wasSplitted = false;
+                    cb1.setOrientation(Orientation.RIGHT);
+                    splitX1 = null;
+                } else
+
+                if(prevOrientation != null && prevOrientation.equals(Orientation.RIGHT) && (lineSeparation || !startFromTop || !splitByX || !newLineAfterSplit || !splittedByRuling)){
+                    cb1.setOrientation(Orientation.LEFT);
+                }
+
                minX = 1000;
                maxX = 0;
                minY = 1000;
@@ -72,9 +103,62 @@ public class BlockificationService {
            chunkBlockList1.add(cb1);
        }

+        Iterator<AbstractTextContainer> itty = chunkBlockList1.iterator();
+
+        TextBlock previousLeft = null;
+        TextBlock previousRight = null;
+        while (itty.hasNext()) {
+            TextBlock block = (TextBlock) itty.next();
+
+            if(previousLeft != null && block.getOrientation().equals(Orientation.LEFT)){
+                if (previousLeft.getMinY() > block.getMinY() && block.getMaxY() + block.getMostPopularWordHeight() > previousLeft.getMinY()){
+                    previousLeft.add(block);
+                    itty.remove();
+                    continue;
+                }
+            }
+
+            if(previousRight != null && block.getOrientation().equals(Orientation.RIGHT)){
+                if (previousRight.getMinY() > block.getMinY() && block.getMaxY() + block.getMostPopularWordHeight() > previousRight.getMinY()){
+                    previousRight.add(block);
+                    itty.remove();
+                    continue;
+                }
+            }
+
+            if (block.getOrientation().equals(Orientation.LEFT)) {
+                previousLeft = block;
+            } else if (block.getOrientation().equals(Orientation.RIGHT)) {
+                previousRight = block;
+            }
+        }
+
+
+        itty = chunkBlockList1.iterator();
+        TextBlock previous = null;
+        while (itty.hasNext()) {
+            TextBlock block = (TextBlock) itty.next();
+
+            if(previous != null && previous.getOrientation().equals(Orientation.LEFT) && block.getOrientation().equals(Orientation.LEFT) && equalsWithThreshold(block.getMaxY(), previous
+                    .getMaxY())||
+                    previous != null && previous.getOrientation().equals(Orientation.LEFT) && block.getOrientation().equals(Orientation.RIGHT) && equalsWithThreshold(block.getMaxY(), previous
+                    .getMaxY())){
+                previous.add(block);
+                itty.remove();
+                continue;
+            }
+
+            previous = block;
+        }
+
+
        return new Page(chunkBlockList1);
    }

+    private boolean equalsWithThreshold(float f1, float f2){
+        return Math.abs(f1 - f2) < THRESHOLD;
+    }
+

    private TextBlock buildTextBlock(List<TextPositionSequence> wordBlockList) {

@@ -117,7 +201,8 @@ public class BlockificationService {
    }


-    private boolean isSplittedByRuling(float previousX2, float previousY1, float currentX1, float currentY1, List<Ruling> rulingLines) {
+    private boolean isSplittedByRuling(float previousX2, float previousY1, float currentX1, float currentY1,
+                                       List<Ruling> rulingLines) {

        for (Ruling ruling : rulingLines) {
            if (ruling.intersectsLine(previousX2, previousY1, currentX1, currentY1)) {
@@ -128,7 +213,8 @@ public class BlockificationService {
    }


-    public Rectangle calculateBodyTextFrame(List<Page> pages, FloatFrequencyCounter documentFontSizeCounter, boolean landscape) {
+    public Rectangle calculateBodyTextFrame(List<Page> pages, FloatFrequencyCounter documentFontSizeCounter,
+                                            boolean landscape) {

        float minX = 10000;
        float maxX = -100;
@@ -46,6 +46,17 @@ public class PDFAreaTextStripper extends PDFTextStripperByArea {
                startIndex = i;
            }

+
+            if (textPositions.get(i).getRotation() == 0 && i > 0 && textPositions.get(i).getX() > textPositions.get(i - 1).getEndX() + 1) {
+                List<TextPosition> sublist = textPositions.subList(startIndex, i);
+                if (!(sublist.isEmpty() || sublist.size() == 1 && (sublist.get(0)
+                        .getUnicode()
+                        .equals(" ") || sublist.get(0).getUnicode().equals("\u00A0")))) {
+                    textPositionSequences.add(new TextPositionSequence(sublist, pageNumber));
+                }
+                startIndex = i;
+            }
+
            if (i > 0 && (textPositions.get(i).getUnicode().equals(" ") || textPositions.get(i)
                    .getUnicode()
                    .equals("\u00A0")) && i <= textPositions.size() - 2) {
@@ -300,6 +300,18 @@ public class PDFLinesTextStripper extends PDFTextStripper {
                startIndex = i;
            }

+
+            if (textPositions.get(i).getRotation() == 0 && i > 0 && textPositions.get(i).getX() > textPositions.get(i - 1).getEndX() + 1) {
+                List<TextPosition> sublist = textPositions.subList(startIndex, i);
+                if (!(sublist.isEmpty() || sublist.size() == 1 && (sublist.get(0)
+                        .getUnicode()
+                        .equals(" ") || sublist.get(0).getUnicode().equals("\u00A0")))) {
+                    textPositionSequences.add(new TextPositionSequence(sublist, pageNumber));
+                }
+                startIndex = i;
+            }
+
+
            if (i > 0 && (textPositions.get(i).getUnicode().equals(" ") || textPositions.get(i)
                    .getUnicode()
                    .equals("\u00A0")) && i <= textPositions.size() - 2) {
@@ -21,7 +21,7 @@ public class MessagingConfiguration {

        return QueueBuilder.durable(REDACTION_QUEUE)
                .withArgument("x-dead-letter-exchange", "")
-                .withArgument("x-dead-letter-routing-key", REDACTION_QUEUE)
+                .withArgument("x-dead-letter-routing-key", REDACTION_DQL)
                .maxPriority(2)
                .build();
    }
@@ -237,8 +237,7 @@ public class ReanalyzeService {
        }

        redactionLog.getRedactionLogEntry()
-                .removeIf(entry -> sectionsToReanalyse.contains(entry.getSectionNumber()) && !entry.isImage() || entry.getSectionNumber() == 0 && !entry
-                        .isImage());
+                .removeIf(entry -> sectionsToReanalyse.contains(entry.getSectionNumber()));
        redactionLog.getRedactionLogEntry().addAll(newRedactionLogEntries);
        return finalizeAnalysis(analyzeRequest, startTime, redactionLog, text, dictionaryIncrement);

@@ -2,6 +2,8 @@ package com.iqser.red.service.redaction.v1.server.tableextraction.model;

 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.iqser.red.service.redaction.v1.model.Rectangle;
+import com.iqser.red.service.redaction.v1.server.classification.model.Orientation;
+
 import lombok.AllArgsConstructor;
 import lombok.Data;
 import lombok.NoArgsConstructor;
@@ -18,6 +20,8 @@ public abstract class AbstractTextContainer {
    protected String classification;
    protected int page;

+    private Orientation orientation = Orientation.NONE;
+
    public abstract String getText();

    public boolean contains(AbstractTextContainer other) {
@@ -246,8 +246,12 @@ public class Ruling extends Line2D.Float {

    public Ruling expand(float amount) {
        Ruling r = (Ruling) this.clone();
-        r.setStart(this.getStart() - amount);
-        r.setEnd(this.getEnd() + amount);
+        try {
+            r.setStart(this.getStart() - amount);
+            r.setEnd(this.getEnd() + amount);
+        } catch (UnsupportedOperationException e){
+            log.warn("Could not expand ruling!");
+        }
        return r;
    }

@@ -102,7 +102,7 @@ public class PdfVisualisationService {

            contentStream.newLineAtOffset(textBlock.getMinX(), textBlock.getMaxY());

-            contentStream.showText(textBlock.getClassification());
+            contentStream.showText(textBlock.getClassification() + textBlock.getOrientation());

            contentStream.endText();
        }
@@ -676,8 +676,8 @@ public class RedactionIntegrationTest {
        dictionary.get(AUTHOR).add("physical");
        reanlysisVersions.put("physical", 2L);

-        dictionary.get(VERTEBRATE).add("s-metolachlor");
-        reanlysisVersions.put("s-metolachlor", 3L);
+//        dictionary.get(VERTEBRATE).add("s-metolachlor");
+//        reanlysisVersions.put("s-metolachlor", 3L);

        when(dictionaryClient.getVersion(TEST_RULESET_ID, DictionaryResource.GLOBAL_DOSSIER)).thenReturn(3L);

@@ -801,7 +801,7 @@ public class RedactionIntegrationTest {
    public void classificationTest() throws IOException {

        System.out.println("classificationTest");
-        ClassPathResource pdfFileResource = new ClassPathResource("files/Trinexapac/93 Trinexapac-ethyl_RAR_03_Volume_3CA_B-1_2017-03-31.pdf");
+        ClassPathResource pdfFileResource = new ClassPathResource("files/new/Single Study - Oral (Gavage) Mouse.pdf");


        AnalyzeRequest request = prepareStorage(pdfFileResource.getInputStream());
@@ -1652,3 +1652,5 @@ Zoecon Corp.
 Zoecon Corp., Palo Alto, USA
 Zyma SA
 Zyma SA, Nyon, Switzerland
+Mambo-Tox Ltd. Biomedical Sciences Building Bassett Crescent East Southampton SO16 7PX UK
+Syngenta Environmental Sciences Jealott’s Hill International Research Centre Bracknell, Berkshire RG42 6EY UK
Author	SHA1	Message	Date
Dominique Eifländer	a14f2fa4cf	Fixed endless processing	2021-06-02 13:49:48 +02:00
Dominique Eifländer	69f68273d1	Ignore failing Ruling expansion	2021-06-02 13:00:51 +02:00
Dominique Eifländer	541a55798c	Fixed text parsing orientation problem	2021-06-02 11:19:34 +02:00
Dominique Eifländer	5a9b86ba76	RED-1535: Improved document parsing, added orientation to textblock	2021-06-01 15:41:14 +02:00
Dominique Eifländer	d18003736b	Fixed missing whitespaces	2021-06-01 15:40:41 +02:00
Dominique Eiflaender	b16b56daf1	Pull request #154 : RED-1477: Fixed duplicate images Merge in RED/redaction-service from RED-1477 to master * commit 'bdf40f5e4eec9984306516790eb8c4eb106b0aa1': RED-1477: Fixed duplicate images	2021-05-12 12:23:03 +02:00
Dominique Eifländer	bdf40f5e4e	RED-1477: Fixed duplicate images	2021-05-12 11:28:17 +02:00
Dominique Eiflaender	e281ab98fa	Pull request #153 : Fixed dossier dictionary renalaysis Merge in RED/redaction-service from dossierReanalysisFix to master * commit '184f55535aa07123a80a78e7a0aff949c2827465': Fixed dossier dictionary renalaysis	2021-04-30 14:00:54 +02:00