RED-6019 InvisibleTex wip

ocr-service-image-v1/src/main/docker/Dockerfile

@@ -1,4 +1,4 @@
-FROM red/base-image:baseImageUser5
+FROM red/base-image:2.0.0
 
 COPY "libs/pdftron/OCRModuleLinux.tar.gz" .
 RUN tar xvzf OCRModuleLinux.tar.gz

ocr-service-v1/ocr-service-server-v1/pom.xml

@@ -86,6 +86,16 @@
     </dependencies>
     <build>
         <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <configuration>
+                    <annotationProcessors>
+                        <annotationProcessor>lombok.launch.AnnotationProcessorHider$AnnotationProcessor</annotationProcessor>
+                        <annotationProcessor>com.dslplatform.json.processor.CompiledJsonAnnotationProcessor</annotationProcessor>
+                    </annotationProcessors>
+                </configuration>
+            </plugin>
             <plugin>
                 <!-- generate git.properties for exposure in /info -->
                 <groupId>pl.project13.maven</groupId>
@@ -104,16 +114,6 @@
                     </execution>
                 </executions>
             </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-compiler-plugin</artifactId>
-                <configuration>
-                    <annotationProcessors>
-                        <annotationProcessor>lombok.launch.AnnotationProcessorHider$AnnotationProcessor</annotationProcessor>
-                        <annotationProcessor>com.dslplatform.json.processor.CompiledJsonAnnotationProcessor</annotationProcessor>
-                    </annotationProcessors>
-                </configuration>
-            </plugin>
             <plugin>
                 <!-- repackages the generated jar into a runnable fat-jar and makes it
                     executable -->

ocr-service-v1/ocr-service-server-v1/src/main/java/com/iqser/red/service/ocr/v1/server/model/ClippingPathStack.java

@@ -1,68 +1,54 @@
 package com.iqser.red.service.ocr.v1.server.model;
 
-import static com.iqser.red.service.ocr.v1.server.service.InvisibleElementRemovalService.TOLERANCE;
+import com.pdftron.pdf.Rect;
+import lombok.Data;
+import lombok.SneakyThrows;
 
 import java.awt.geom.Area;
 import java.awt.geom.GeneralPath;
 import java.awt.geom.Rectangle2D;
+import java.util.ArrayDeque;
 import java.util.Deque;
-import java.util.LinkedList;
-
-import com.pdftron.pdf.Rect;
-
-import lombok.Data;
-import lombok.SneakyThrows;
 
 @Data
 public class ClippingPathStack {
 
-    private Deque<Area> stack = new LinkedList<>();
-
+    private Deque<Area> stack = new ArrayDeque<>();
 
     @SneakyThrows
     public ClippingPathStack(Rect rectangle) {
-
         stack.push(new Area(new Rectangle2D.Double(rectangle.getX1(), rectangle.getY1(), rectangle.getWidth(), rectangle.getHeight()).getBounds2D()));
     }
 
 
     @SneakyThrows
     public void intersectClippingPath(GeneralPath path) {
-
         getCurrentClippingPath().intersect(new Area(path));
     }
 
-
     public boolean almostIntersects(double x, double y, double width, double height) {
-        // To address inconsistencies in the calculation of the bounding box we slightly increase the rectangle
         // Height or width are zero for straight lines, even though they are being rendered. Therefore, height or width must be at minimum >0.
-
-        double x_with_tolerance = x > 0 ? x - TOLERANCE : x + TOLERANCE;
-        double y_with_tolerance = y > 0 ? y - TOLERANCE : y + TOLERANCE;
-        double width_with_tolerance = width + (2 * TOLERANCE);
-        double height_with_tolerance = height + (2 * TOLERANCE);
+        double tolerance = 1e-3;
+        double x_with_tolerance = x > 0 ? x - tolerance : x + tolerance;
+        double y_with_tolerance = y > 0 ? y - tolerance : y + tolerance;
+        double width_with_tolerance = width + 2 * tolerance;
+        double height_with_tolerance = height + 2 * tolerance;
         return getCurrentClippingPath().intersects(x_with_tolerance, y_with_tolerance, width_with_tolerance, height_with_tolerance);
     }
 
-
     public Area getCurrentClippingPath() {
-
         return stack.peek();
     }
 
-
     public void enterNewGState() {
-
         Area current = stack.peek();
         Area cloned = new Area();
         cloned.add(current);
         stack.push(cloned);
     }
 
-
     public void leaveGState() {
-
         stack.pop();
     }
 
-}
+}

ocr-service-v1/ocr-service-server-v1/src/main/java/com/iqser/red/service/ocr/v1/server/model/ElementFeatures.java

@@ -1,170 +1,149 @@
 package com.iqser.red.service.ocr.v1.server.model;
 
-import static com.iqser.red.service.ocr.v1.server.service.InvisibleElementRemovalService.TOLERANCE;
-
-import java.awt.geom.Rectangle2D;
-
 import com.pdftron.common.PDFNetException;
 import com.pdftron.pdf.Element;
 import com.pdftron.pdf.Rect;
-
-import lombok.AccessLevel;
-import lombok.EqualsAndHashCode;
-import lombok.Getter;
-import lombok.SneakyThrows;
-import lombok.experimental.FieldDefaults;
+import lombok.*;
 import lombok.experimental.SuperBuilder;
 
-@Getter
+import java.awt.geom.Rectangle2D;
+
+@Data
 @SuperBuilder
-@FieldDefaults(makeFinal = true, level = AccessLevel.PRIVATE)
-public class ElementFeatures {
-
-    int elementType;
-    Rectangle2D boundingBox;
-
+@NoArgsConstructor
+@AllArgsConstructor
+public abstract class ElementFeatures {
+    private int elementType;
+    private Rectangle2D boundingBox;
 
     public boolean almostMatches(Element element) throws PDFNetException {
-
-        return element.getType() == elementType && //
-                element.getBBox() != null && //
-                rectsAlmostMatch(element.getBBox());
+        if (element.getType() != elementType) return false;
+        if (element.getBBox() == null) return false;
+        return rectsAlmostMatch(element.getBBox());
     }
 
-
     protected boolean almostEqual(double a, double b) {
-
-        return Math.abs(a - b) < TOLERANCE;
+        double tolerance = 1e-3;
+        return Math.abs(a - b) < tolerance;
     }
 
-
     @SneakyThrows
     private boolean rectsAlmostMatch(Rect bBox) {
-        // To address the inconsistencies in the calculation of the bounding box we check equality with a tolerance
-
-        return almostEqual(bBox.getX1(), boundingBox.getX()) && //
-                almostEqual(bBox.getY1(), boundingBox.getY()) && //
-                almostEqual(bBox.getWidth(), boundingBox.getWidth()) && //
-                almostEqual(bBox.getHeight(), boundingBox.getHeight());
+        if (!almostEqual(bBox.getX1(), boundingBox.getX())) return false;
+        if (!almostEqual(bBox.getY1(), boundingBox.getY())) return false;
+        if (!almostEqual(bBox.getWidth(), boundingBox.getWidth())) return false;
+        return almostEqual(bBox.getHeight(), boundingBox.getHeight());
     }
 
-
     @EqualsAndHashCode(callSuper = true)
-    @Getter
+    @Data
     @SuperBuilder
-    @FieldDefaults(makeFinal = true, level = AccessLevel.PRIVATE)
-    private static class Text extends ElementFeatures {
-
-        String text;
-        int font;
-        double fontsize;
-
+    @NoArgsConstructor
+    @AllArgsConstructor
+    public static class Text extends ElementFeatures {
+        private String text;
+        private int font;
+        private double fontsize;
 
         @Override
         public boolean almostMatches(Element element) throws PDFNetException {
-
-            return super.almostMatches(element) && //
-                    text.equals(element.getTextString()) && //
-                    font == element.getGState().getFont().getType() && //
-                    almostEqual(fontsize, element.getGState().getFontSize());
+            if (!super.almostMatches(element)) return false;
+            if (!text.equals(element.getTextString())) return false;
+            if (font != element.getGState().getFont().getType()) return false;
+            return almostEqual(fontsize, element.getGState().getFontSize());
         }
 
     }
 
     @EqualsAndHashCode(callSuper = true)
-    @Getter
+    @Data
     @SuperBuilder
-    @FieldDefaults(makeFinal = true, level = AccessLevel.PRIVATE)
-    private static class Path extends ElementFeatures {
-
-        boolean isClippingPath;
-        boolean isClipWindingFill;
-        boolean isStroked;
-        boolean isFilled;
-        boolean isWindingFill;
-
+    @NoArgsConstructor
+    @AllArgsConstructor
+    public static class Path extends ElementFeatures {
+        private boolean isClippingPath;
+        private boolean isClipWindingFill;
+        private boolean isStroked;
+        private boolean isFilled;
+        private boolean isWindingFill;
 
         @Override
         public boolean almostMatches(Element element) throws PDFNetException {
+            if (!super.almostMatches(element)) return false;
+            if (isClippingPath != element.isClippingPath()) return false;
+            if (isClipWindingFill != element.isClipWindingFill()) return false;
+            if (isStroked != element.isStroked()) return false;
+            if (isFilled != element.isFilled()) return false;
+            if (isWindingFill != element.isWindingFill()) return false;
 
-            return super.almostMatches(element) && //
-                    isClippingPath == element.isClippingPath() && //
-                    isClipWindingFill == element.isClipWindingFill() && //
-                    isStroked == element.isStroked() && //
-                    isFilled == element.isFilled() && //
-                    isWindingFill == element.isWindingFill();
-
+            return true;
         }
-
     }
 
     @EqualsAndHashCode(callSuper = true)
-    @Getter
+    @Data
     @SuperBuilder
-    @FieldDefaults(makeFinal = true, level = AccessLevel.PRIVATE)
-    private static class Image extends ElementFeatures {
-
-        int dataSize;
-        int height;
-        int width;
-        int renderingIntent;
-        int componentNum;
-        int bitsPerComponent;
-
+    @NoArgsConstructor
+    public static class Image extends ElementFeatures {
+        private int dataSize;
+        private int height;
+        private int width;
+        private int renderingIntent;
+        private int componentNum;
+        private int bitsPerComponent;
 
         @Override
         public boolean almostMatches(Element element) throws PDFNetException {
-
-            return super.almostMatches(element) && //
-                    dataSize == element.getImageDataSize() && //
-                    height == element.getImageHeight() && //
-                    width == element.getImageWidth() && //
-                    renderingIntent == element.getImageRenderingIntent() && //
-                    componentNum == element.getComponentNum() && //
-                    bitsPerComponent == element.getBitsPerComponent();
+            if (!super.almostMatches(element)) return false;
+            if (dataSize != element.getImageDataSize()) return false;
+            if (height != element.getImageHeight()) return false;
+            if (width != element.getImageWidth()) return false;
+            if (renderingIntent != element.getImageRenderingIntent()) return false;
+            if (componentNum != element.getComponentNum()) return false;
+            if (bitsPerComponent != element.getBitsPerComponent()) return false;
+            return true;
         }
-
     }
 
-
     public static ElementFeatures extractFeatures(Element element) throws PDFNetException {
-
-        return switch (element.getType()) {
-            case Element.e_path -> Path.builder()
-                    .elementType(element.getType())
-                    .boundingBox(toRectangle2D(element.getBBox()))
-                    .isClippingPath(element.isClippingPath())
-                    .isClipWindingFill(element.isClipWindingFill())
-                    .isStroked(element.isStroked())
-                    .isFilled(element.isFilled())
-                    .isWindingFill(element.isWindingFill())
-                    .build();
-            case Element.e_text -> Text.builder()
-                    .elementType(element.getType())
-                    .boundingBox(toRectangle2D(element.getBBox()))
-                    .text(element.getTextString())
-                    .font(element.getGState().getFont().getType())
-                    .fontsize(element.getGState().getFontSize())
-                    .build();
-            case Element.e_image, Element.e_inline_image -> Image.builder()
-                    .elementType(element.getType())
-                    .boundingBox(toRectangle2D(element.getBBox()))
-                    .dataSize(element.getImageDataSize())
-                    .height(element.getImageHeight())
-                    .width(element.getImageWidth())
-                    .renderingIntent(element.getImageRenderingIntent())
-                    .componentNum(element.getComponentNum())
-                    .bitsPerComponent(element.getBitsPerComponent())
-                    .build();
-            // This technically should never happen, it's a safetynet
-            default -> throw new RuntimeException("Feature Extraction is not supported for PDFTron.Element with type: " + element.getType());
-        };
+        switch (element.getType()) {
+            case Element.e_path:
+                return ElementFeatures.Path.builder()
+                        .elementType(element.getType())
+                        .boundingBox(toRectangle2D(element.getBBox()))
+                        .isClippingPath(element.isClippingPath())
+                        .isClipWindingFill(element.isClipWindingFill())
+                        .isStroked(element.isStroked())
+                        .isFilled(element.isFilled())
+                        .isWindingFill(element.isWindingFill())
+                        .build();
+            case Element.e_text:
+                return ElementFeatures.Text.builder()
+                        .elementType(element.getType())
+                        .boundingBox(toRectangle2D(element.getBBox()))
+                        .text(element.getTextString())
+                        .font(element.getGState().getFont().getType())
+                        .fontsize(element.getGState().getFontSize())
+                        .build();
+            case Element.e_image:
+            case Element.e_inline_image:
+                return Image.builder()
+                        .elementType(element.getType())
+                        .boundingBox(toRectangle2D(element.getBBox()))
+                        .dataSize(element.getImageDataSize())
+                        .height(element.getImageHeight())
+                        .width(element.getImageWidth())
+                        .renderingIntent(element.getImageRenderingIntent())
+                        .componentNum(element.getComponentNum())
+                        .bitsPerComponent(element.getBitsPerComponent())
+                        .build();
+            default:
+                throw new UnsupportedOperationException("Feature Extraction is not supported for PDFTron.Element with type: " + element.getType());
+        }
     }
 
-
     private static Rectangle2D toRectangle2D(Rect rect) throws PDFNetException {
-
         return new Rectangle2D.Double(rect.getX1(), rect.getY1(), rect.getWidth(), rect.getHeight());
     }
-
 }
+

ocr-service-v1/ocr-service-server-v1/src/main/java/com/iqser/red/service/ocr/v1/server/service/ImagePositionRetrievalService.java

@@ -1,195 +0,0 @@
-package com.iqser.red.service.ocr.v1.server.service;
-
-import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
-import java.awt.geom.RectangularShape;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-
-import org.springframework.stereotype.Service;
-
-import com.pdftron.common.Matrix2D;
-import com.pdftron.common.PDFNetException;
-import com.pdftron.pdf.Element;
-import com.pdftron.pdf.ElementReader;
-import com.pdftron.pdf.PDFDoc;
-import com.pdftron.pdf.Page;
-import com.pdftron.pdf.Rect;
-import com.pdftron.pdf.RectCollection;
-
-import lombok.SneakyThrows;
-
-@Service
-public class ImagePositionRetrievalService {
-
-    private static final double TOLERANCE = 1e-1;
-
-    // any image with smaller height and width than this gets thrown out, see everyPointInDashedLineIsImage.pdf
-    private static final int PIXEL_THRESHOLD = 10;
-
-
-    /**
-     * Iterates over all elements in a PDF Document and retrieves the bounding box for each image, that is larger than the pixel threshold of 10 in either dimension.
-     * Then it adjusts the bounding boxes for the page rotation.
-     * If the mirrorY flag is set, the Y Coordinates are mirrored and moved up by the page height. This is required for PDFTrons OCRModule.
-     *
-     * @param pdfDoc  a PDF File as PDFTron PDFDoc class
-     * @param mirrorY if this flag is set, all coordinates are calculated with upper left corner as (0,0), else initial user space
-     * @return a map with the page indices as keys and the image bounding boxes on that page as a RectCollection
-     */
-    @SneakyThrows
-    public Map<Integer, RectCollection> getImagePositionPerPage(PDFDoc pdfDoc, boolean mirrorY) {
-
-        Map<Integer, RectCollection> pageIdToImagePositions = new HashMap<>();
-        ElementReader reader = new ElementReader();
-        for (int pageId = 1; pageId <= pdfDoc.getPageCount(); ++pageId) {
-            RectCollection imagePositions = new RectCollection();
-            reader.begin(pdfDoc.getPage(pageId));
-
-            findImagePositionsOnPage(reader, imagePositions, pdfDoc.getPage(pageId), mirrorY);
-            imagePositions = mergeOverlappingRects(imagePositions);
-
-            reader.end();
-            if (imagePositions.getNumRects() > 0) {
-                pageIdToImagePositions.put(pageId, imagePositions);
-            }
-        }
-        return pageIdToImagePositions;
-    }
-
-
-    private void findImagePositionsOnPage(ElementReader reader, RectCollection imagePositions, Page currentPage, boolean mirrorY) throws PDFNetException {
-
-        Element element;
-        while ((element = reader.next()) != null) {
-            switch (element.getType()) {
-                case Element.e_image, Element.e_inline_image -> {
-                    // see everyPointInDashedLineIsImage.pdf TestFile
-                    if (element.getImageHeight() > PIXEL_THRESHOLD || element.getImageWidth() > PIXEL_THRESHOLD) {
-                        imagePositions.addRect(toRotationAdjustedRect(element.getBBox(), currentPage, mirrorY));
-                    }
-                }
-                case Element.e_form -> {
-                    reader.formBegin();
-                    findImagePositionsOnPage(reader, imagePositions, currentPage, mirrorY);
-                    reader.end();
-                }
-            }
-        }
-    }
-
-
-    @SneakyThrows
-    public RectCollection mergeOverlappingRects(RectCollection imagePositions) {
-
-        if (imagePositions.getNumRects() < 2) {
-            return imagePositions;
-        }
-
-        List<Rectangle2D> rectangleList = toSortedRectangleList(imagePositions);
-
-        mergeRectangleList(rectangleList);
-
-        return toRectCollection(rectangleList);
-    }
-
-
-    // Sometimes images are split up into stripes, here we merge the positions of aligned and intersecting rectangles into one larger rectangle
-    private void mergeRectangleList(List<Rectangle2D> rectangleList) {
-
-        for (int idx = 0; rectangleList.size() >= idx + 2; ) {
-
-            var rect1 = rectangleList.get(idx);
-            var rect2 = rectangleList.get(idx + 1);
-
-            if (intersects(rect1, rect2) && isAlignedXOrY(rect1, rect2)) {
-                rectangleList.remove(idx + 1);
-                rectangleList.remove(idx);
-                rectangleList.add(idx, rect1.createUnion(rect2));
-            } else {
-                ++idx;
-            }
-        }
-    }
-
-
-    private boolean intersects(Rectangle2D rect1, Rectangle2D rect2) {
-
-        return rect1.intersects(rect2.getMinX() - TOLERANCE, rect2.getMinY() - TOLERANCE, rect2.getWidth() + (2 * TOLERANCE), rect2.getHeight() + (2 * TOLERANCE));
-    }
-
-
-    private boolean isAlignedXOrY(Rectangle2D rect1, Rectangle2D rect2) {
-
-        boolean isAlignedX = Math.abs(rect1.getMinX() - rect2.getMinX()) < TOLERANCE && Math.abs(rect1.getMaxX() - rect2.getMaxX()) < TOLERANCE;
-        boolean isAlignedY = Math.abs(rect1.getMinY() - rect2.getMinY()) < TOLERANCE && Math.abs(rect1.getMaxY() - rect2.getMaxY()) < TOLERANCE;
-
-        return isAlignedX || isAlignedY;
-    }
-
-
-    private Rect toRotationAdjustedRect(Rect bbox, Page page, boolean mirrorY) throws PDFNetException {
-
-        int rotation = page.getRotation();
-        double height = page.getPageHeight();
-        double width = page.getPageWidth();
-
-        // Even though PDFTron almost always has the origin in the lower left corner, for some reason, the OCRModule's addTextZonesForPage() uses the upper left corner as origin...
-        Matrix2D mirrorMatrix;
-        if (mirrorY) {
-            mirrorMatrix = new Matrix2D(1, 0, 0, -1, 0, height);
-        } else {
-            mirrorMatrix = new Matrix2D();
-        }
-
-        // We need to rotate the rects to fit to the page rotation
-        Matrix2D rotationMatrix = switch (rotation) {
-            case 1 -> new Matrix2D(0, -1, 1, 0, 0, height);
-            case 2 -> new Matrix2D(-1, 0, 0, -1, width, height);
-            case 3 -> new Matrix2D(0, 1, -1, 0, width, 0);
-            default -> new Matrix2D();
-        };
-
-        Matrix2D finalMatrix = mirrorMatrix.multiply(rotationMatrix);
-
-        Point2D.Double p1 = finalMatrix.multPoint(bbox.getX1(), bbox.getY1());
-        Point2D.Double p2 = finalMatrix.multPoint(bbox.getX2(), bbox.getY2());
-
-        // PDFTron Rect *needs* lower left and upper right coordinates to calculate width and height correctly, even though the documentation states otherwise
-        Point2D.Double lowerLeft = new Point2D.Double(Math.min(p1.x, p2.x), Math.min(p1.y, p2.y));
-        Point2D.Double upperRight = new Point2D.Double(Math.max(p1.x, p2.x), Math.max(p1.y, p2.y));
-
-        return new Rect(lowerLeft.x, lowerLeft.y, upperRight.x, upperRight.y);
-    }
-
-
-    private RectCollection toRectCollection(List<Rectangle2D> rectangleList) {
-
-        RectCollection rectCollection = new RectCollection();
-        rectangleList.forEach(r -> {
-            try {
-                rectCollection.addRect(new Rect(r.getMinX(), r.getMinY(), r.getMaxX(), r.getMaxY()));
-            } catch (PDFNetException e) {
-                throw new RuntimeException(e);
-            }
-        });
-        return rectCollection;
-    }
-
-
-    @SneakyThrows
-    private List<Rectangle2D> toSortedRectangleList(RectCollection rectCollection) {
-
-        List<Rectangle2D> list = new LinkedList<>();
-        for (int i = 0; i < rectCollection.getNumRects(); ++i) {
-            Rect r = rectCollection.getRectAt(i);
-            list.add(new Rectangle2D.Double(r.getX1(), r.getY1(), r.getWidth(), r.getHeight()));
-        }
-        list.sort(Comparator.comparingDouble(RectangularShape::getMinY).thenComparing(RectangularShape::getMinX));
-        return list;
-    }
-
-}

ocr-service-v1/ocr-service-server-v1/src/main/java/com/iqser/red/service/ocr/v1/server/service/InvisibleElementRemovalService.java

@@ -1,450 +0,0 @@
-package com.iqser.red.service.ocr.v1.server.service;
-
-import java.awt.Shape;
-import java.awt.geom.AffineTransform;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.Rectangle2D;
-import java.io.InputStream;
-import java.io.OutputStream;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Set;
-import java.util.TreeSet;
-
-import org.springframework.stereotype.Service;
-
-import com.google.common.primitives.Bytes;
-import com.google.common.primitives.Doubles;
-import com.iqser.red.service.ocr.v1.server.model.ClippingPathStack;
-import com.iqser.red.service.ocr.v1.server.model.ElementFeatures;
-import com.pdftron.common.Matrix2D;
-import com.pdftron.common.PDFNetException;
-import com.pdftron.pdf.ColorPt;
-import com.pdftron.pdf.ColorSpace;
-import com.pdftron.pdf.Element;
-import com.pdftron.pdf.ElementBuilder;
-import com.pdftron.pdf.ElementReader;
-import com.pdftron.pdf.ElementWriter;
-import com.pdftron.pdf.GState;
-import com.pdftron.pdf.PDFDoc;
-import com.pdftron.pdf.Page;
-import com.pdftron.pdf.PageIterator;
-import com.pdftron.pdf.PathData;
-import com.pdftron.pdf.Rect;
-import com.pdftron.sdf.Obj;
-import com.pdftron.sdf.SDFDoc;
-
-import lombok.Builder;
-import lombok.SneakyThrows;
-import lombok.extern.slf4j.Slf4j;
-
-@Slf4j
-@Service
-public class InvisibleElementRemovalService {
-
-    static public final double TOLERANCE = 1e-3;
-
-
-    /**
-     * Removes all hidden Text, Path and Image Elements from a PDF Document.
-     * handled cases:
-     * -Text which is transparent or is set to not render
-     * -Elements outside of clipping path
-     * -Elements that have been painted over by visible and filled Paths
-     * unhandled cases:
-     * -Elements covered by widely stroked path
-     * -Elements with the same color as background
-     * -Any Text set to clipping with its many interactions with other elements
-     *
-     * @param pdfFile The PDF file to process
-     * @param delta   If this flag is set only the removed Elements will be written to the output file.
-     *                The Elements are red if they are removed by clipping path, blue for transparency, and a green bounding box for overlap.
-     * @param out     OutputStream to write the resulting file to
-     **/
-    @SneakyThrows
-    public void removeInvisibleElements(InputStream pdfFile, OutputStream out, boolean delta) {
-
-        PDFDoc pdfDoc = new PDFDoc(pdfFile);
-
-        ElementWriter writer = new ElementWriter();
-        ElementReader reader = new ElementReader();
-        Set<Long> visitedXObjIds = new TreeSet<>();
-
-        for (PageIterator iterator = pdfDoc.getPageIterator(); iterator.hasNext(); ) {
-
-            Page page = iterator.next();
-
-            visitedXObjIds.add(page.getSDFObj().getObjNum());
-
-
-            InvisibleElementRemovalContext context = InvisibleElementRemovalContext.builder()
-                    .reader(reader)
-                    .clippingPathStack(new ClippingPathStack(page.getMediaBox()))
-                    .delta(delta)
-                    .overlappedElements(new ArrayList<>())
-                    .visibleElements(new ArrayList<>())
-                    .visitedXObjIds(visitedXObjIds)
-                    .build();
-
-            removeClippedElementsAndInvisibleTextAndRememberOverlappedElements(page, writer, context);
-
-            context.visitedXObjIds().clear();
-
-            removeOverlappedElements(page, writer, context);
-        }
-        pdfDoc.save(out, SDFDoc.SaveMode.REMOVE_UNUSED, null);
-    }
-
-
-    private void removeClippedElementsAndInvisibleTextAndRememberOverlappedElements(Page page,
-                                                                                    ElementWriter writer,
-                                                                                    InvisibleElementRemovalContext context) throws PDFNetException {
-
-        context.reader().begin(page);
-        writer.begin(page, ElementWriter.e_replacement, false, true, page.getResourceDict());
-        processElements(writer, context);
-        writer.end();
-        context.reader().end();
-    }
-
-
-    private void processElements(ElementWriter writer, InvisibleElementRemovalContext context) throws PDFNetException {
-
-        for (Element element = context.reader().next(); element != null; element = context.reader().next())
-            switch (element.getType()) {
-                case Element.e_image, Element.e_inline_image -> processImages(element, writer, context);
-                case Element.e_text -> processText(element, writer, context);
-                case Element.e_path -> processPath(element, writer, context);
-                case Element.e_form -> processForm(element, writer, context);
-                case Element.e_group_begin -> {
-                    context.clippingPathStack().enterNewGState();
-                    writer.writeElement(element);
-                }
-                case Element.e_group_end -> {
-                    context.clippingPathStack().leaveGState();
-                    writer.writeElement(element);
-                }
-                default -> writer.writeElement(element);
-            }
-    }
-
-
-    private void processImages(Element imageElement, ElementWriter writer, InvisibleElementRemovalContext context) throws PDFNetException {
-
-        Rect rect = imageElement.getBBox();
-
-        if (rect == null) {
-            return;
-        }
-
-        boolean inClippingPath = context.clippingPathStack().almostIntersects(rect.getX1(), rect.getY1(), rect.getWidth(), rect.getHeight());
-
-        if (!context.delta() && inClippingPath) {
-            context.visibleElements().add(ElementFeatures.extractFeatures(imageElement));
-        }
-
-        if (context.delta() ^ inClippingPath) {
-            writer.writeElement(imageElement);
-        }
-    }
-
-
-    private void processText(Element textElement, ElementWriter writer, InvisibleElementRemovalContext context) throws PDFNetException {
-
-        Rect rect = textElement.getBBox();
-
-        if (rect == null) {
-            writer.writeElement(textElement);
-            return;
-        }
-
-        GState gState = textElement.getGState();
-
-        boolean inClippingPath = context.clippingPathStack().almostIntersects(rect.getX1(), rect.getY1(), rect.getWidth(), rect.getHeight());
-
-        boolean isTextVisible = isTextRenderedVisibly(gState);
-
-        if (inClippingPath && isTextVisible) {
-            context.visibleElements().add(ElementFeatures.extractFeatures(textElement));
-        }
-        if (!context.delta()) {
-            if (inClippingPath && isTextVisible) {
-                writer.writeElement(textElement);
-            } else if (textElement.hasTextMatrix()) {
-                /*
-                PDFTron Element with type "text" refers to a Tj command. If a Tm command is just above it in the pdf file, PDFTron will join the two commands and treat them as one Element.
-                hasTextMatrix() checks for this case specifically. Also, Tm changes the position for a whole BT/ET segment, possibly containing multiple Tj commands.
-                Therefore, the position of a following Tj is affected by not writing the first Element.
-                This is why, we write only the Tm command:
-                */
-                writer.writeGStateChanges(textElement);
-            }
-        } else {
-            if (!inClippingPath) {
-                gState.setFillColorSpace(ColorSpace.createDeviceRGB());
-                // red for elements removed by clipping path
-                gState.setFillColor(new ColorPt(1, 0, 0));
-                writer.writeElement(textElement);
-            }
-            if (!isTextVisible) {
-                gState.setFillColorSpace(ColorSpace.createDeviceRGB());
-                // blue for elements removed due to transparency or not rendered
-                gState.setFillColor(new ColorPt(0, 0, 1));
-                gState.setTextRenderMode(GState.e_fill_text);
-                gState.setFillOpacity(1);
-                writer.writeElement(textElement);
-            }
-        }
-    }
-
-
-    private void processForm(Element formElement, ElementWriter writer, InvisibleElementRemovalContext context) throws PDFNetException {
-
-        writer.writeElement(formElement);
-        Obj formObj = formElement.getXObject();
-
-        if (!context.visitedXObjIds().contains(formObj.getObjNum())) {
-            context.visitedXObjIds().add(formObj.getObjNum());
-            // writer needs to be newly initialized when entering a new content stream
-            // see ElementEditTest in PDFTron (https://www.pdftron.com/documentation/samples/android/java/ElementEditTest)
-            ElementWriter formWriter = new ElementWriter();
-            context.reader().formBegin();
-            formWriter.begin(formObj);
-
-            context.reader().clearChangeList();
-            formWriter.setDefaultGState(context.reader());
-
-            processElements(formWriter, context);
-            formWriter.end();
-            context.reader().end();
-        }
-    }
-
-
-    private void processPath(Element pathElement, ElementWriter writer, InvisibleElementRemovalContext context) throws PDFNetException {
-        PathData pathData = pathElement.getPathData();
-
-        if (pathData.getOperators().length == 0 && pathData.getPoints().length == 0) {
-            writer.writeGStateChanges(pathElement);
-            return;
-        }
-
-        GeneralPath linePath = convertToGeneralPath(pathData);
-
-        //transform path to initial user space
-        var ctm = pathElement.getCTM();
-        var affineTransform = toAffineTransform(ctm);
-        linePath.transform(affineTransform);
-
-        var rect = linePath.getBounds2D();
-
-        boolean inClippingPath = context.clippingPathStack().almostIntersects(rect.getX(), rect.getY(), rect.getWidth(), rect.getHeight());
-
-        if (pathElement.isClippingPath()) {
-            if (pathElement.isClipWindingFill()) {
-                linePath.setWindingRule(GeneralPath.WIND_NON_ZERO);
-            } else {
-                linePath.setWindingRule(GeneralPath.WIND_EVEN_ODD);
-            }
-
-            context.clippingPathStack().intersectClippingPath(linePath);
-            pathElement.setPathClip(!context.delta());
-            writer.writeElement(pathElement);
-
-        } else {
-            if (pathElement.isWindingFill()) {
-                linePath.setWindingRule(GeneralPath.WIND_NON_ZERO);
-            } else {
-                linePath.setWindingRule(GeneralPath.WIND_EVEN_ODD);
-            }
-
-            if (inClippingPath) {
-                if (isFilledAndNonTransparent(pathElement)) {
-                    List<ElementFeatures> currentOverlappedElements = context.visibleElements()
-                            .stream()
-                            .filter(features -> almostContains(linePath, features.getBoundingBox()))
-                            .toList();
-                    context.overlappedElements().addAll(currentOverlappedElements);
-                    context.visibleElements().removeAll(currentOverlappedElements);
-                }
-                context.visibleElements().add(ElementFeatures.extractFeatures(pathElement));
-                if (!context.delta()) {
-                    writer.writeElement(pathElement);
-                }
-            }
-            if (context.delta() && !inClippingPath) {
-                pathElement.getGState().setFillColorSpace(ColorSpace.createDeviceRGB());
-                pathElement.getGState().setFillColor(new ColorPt(1, 0, 0));
-                pathElement.getGState().setStrokeColorSpace(ColorSpace.createDeviceRGB());
-                pathElement.getGState().setStrokeColor(new ColorPt(1, 0, 0));
-                writer.writeElement(pathElement);
-            }
-        }
-    }
-
-
-    private void removeOverlappedElements(Page page, ElementWriter writer, InvisibleElementRemovalContext context) throws PDFNetException {
-
-        context.reader().begin(page);
-        writer.begin(page, ElementWriter.e_replacement, false, true, page.getResourceDict());
-        if (context.delta()) {
-            // green for element removed due to overlapping
-            context.overlappedElements().forEach(feature -> drawBBox(writer, feature.getBoundingBox(), "#00FF00"));
-            context.overlappedElements().clear();
-        }
-        processOverlappedElements(writer, context);
-        writer.end();
-        context.reader().end();
-
-        if (context.overlappedElements().size() > 0) {
-            log.warn(context.overlappedElements().size() + " overlapped elements have not been found or removed");
-        }
-    }
-
-
-    private void processOverlappedElements(ElementWriter writer, InvisibleElementRemovalContext context) throws PDFNetException {
-
-        for (Element element = context.reader().next(); element != null; element = context.reader().next()) {
-            switch (element.getType()) {
-                case Element.e_form -> processFormOverlappedElements(writer, element, context);
-                case Element.e_path, Element.e_image, Element.e_inline_image, Element.e_text -> {
-                    boolean anyMatch = false;
-                    for (ElementFeatures elementToRemove : context.overlappedElements()) {
-                        if (elementToRemove.almostMatches(element)) {
-                            context.overlappedElements().remove(elementToRemove);
-                            anyMatch = true;
-                            break;
-                        }
-                    }
-                    if (!anyMatch) {
-                        writer.writeElement(element);
-                    } else if (element.getType() == 3 && element.hasTextMatrix()) {
-                        /*
-                        PDFTron Element with type "text" refers to a Tj command. If a Tm command is just above it in the pdf file, PDFTron will join the two commands and treat them as one Element.
-                        hasTextMatrix() checks for this case specifically. Also, Tm changes the position for a whole BT/ET segment, possibly containing multiple Tj commands.
-                        Therefore, the position of a following Tj is affected by not writing the first Element.
-                        This is why, we write only the Tm command:
-                        */
-                        writer.writeGStateChanges(element);
-                    }
-                }
-                default -> writer.writeElement(element);
-            }
-        }
-    }
-
-
-    private void processFormOverlappedElements(ElementWriter writer, Element formElement, InvisibleElementRemovalContext context) throws PDFNetException {
-
-        writer.writeElement(formElement);
-        Obj formObj = formElement.getXObject();
-
-        if (!context.visitedXObjIds().contains(formObj.getObjNum())) {
-            context.visitedXObjIds().add(formObj.getObjNum());
-            // writer needs to be newly initialized when entering a new content stream
-            // see ElementEditTest in PDFTron (https://www.pdftron.com/documentation/samples/android/java/ElementEditTest)
-            ElementWriter formWriter = new ElementWriter();
-            context.reader().formBegin();
-            formWriter.begin(formObj);
-
-            context.reader().clearChangeList();
-            formWriter.setDefaultGState(context.reader());
-
-            processOverlappedElements(formWriter, context);
-            formWriter.end();
-            context.reader().end();
-        }
-    }
-
-
-    private boolean isTextRenderedVisibly(GState gState) throws PDFNetException {
-
-        return gState.getTextRenderMode() != GState.e_invisible_text && //
-                !(gState.getTextRenderMode() == GState.e_fill_text && gState.getFillOpacity() == 0) && //
-                !(gState.getTextRenderMode() == GState.e_stroke_text && gState.getStrokeOpacity() == 0) && //
-                !(gState.getTextRenderMode() == GState.e_fill_stroke_text && gState.getFillOpacity() == 0 && gState.getStrokeOpacity() == 0);
-    }
-
-
-    private GeneralPath convertToGeneralPath(PathData pathData) throws PDFNetException {
-
-        GeneralPath linePath = new GeneralPath();
-        Iterator<Double> points = Doubles.asList(pathData.getPoints()).iterator();
-        Iterable<Byte> operators = Bytes.asList(pathData.getOperators());
-        for (var operator : operators) {
-            switch (operator) {
-                case PathData.e_moveto -> linePath.moveTo(points.next(), points.next());
-                case PathData.e_lineto -> linePath.lineTo(points.next(), points.next());
-                case PathData.e_cubicto -> linePath.curveTo(points.next(), points.next(), points.next(), points.next(), points.next(), points.next());
-                case PathData.e_closepath -> linePath.closePath();
-                case PathData.e_rect -> {
-                    double x = points.next();
-                    double y = points.next();
-                    double w = points.next();
-                    double h = points.next();
-                    linePath.moveTo(x, y);
-                    linePath.lineTo(x + w, y);
-                    linePath.lineTo(x + w, y + h);
-                    linePath.lineTo(x, y + h);
-                    linePath.closePath();
-                }
-                default -> throw new PDFNetException("Invalid Element Type", 0, "", "", "");
-            }
-        }
-        return linePath;
-    }
-
-
-    private boolean almostContains(Shape outer, Rectangle2D inner) {
-        //To address inconsistencies in the calculation of the bounding box we slightly shrink the inner rectangle
-
-        double x_with_tolerance = inner.getX() >= 0 ? inner.getX() + TOLERANCE : inner.getX() - TOLERANCE;
-        double y_with_tolerance = inner.getY() >= 0 ? inner.getY() + TOLERANCE : inner.getY() - TOLERANCE;
-        double height_with_tolerance = inner.getHeight() - (2 * TOLERANCE);
-        double width_with_tolerance = inner.getWidth() - (2 * TOLERANCE);
-        Rectangle2D innerRect = new Rectangle2D.Double(x_with_tolerance, y_with_tolerance, width_with_tolerance, height_with_tolerance);
-
-        return outer.contains(innerRect);
-    }
-
-
-    private boolean isFilledAndNonTransparent(Element element) throws PDFNetException {
-
-        return element.isFilled() && element.getGState().getFillOpacity() == 1;
-    }
-
-
-    @SneakyThrows
-    private void drawBBox(ElementWriter writer, Rectangle2D r, String hexcolor) {
-
-        ColorPt colorPt = new ColorPt(Integer.valueOf(hexcolor.substring(1, 3), 16) / 255d,
-                Integer.valueOf(hexcolor.substring(3, 5), 16) / 255d,
-                Integer.valueOf(hexcolor.substring(5, 7), 16) / 255d);
-        ElementBuilder eb = new ElementBuilder();
-        Element rect = eb.createRect(r.getX(), r.getY(), r.getWidth(), r.getHeight());
-        rect.setPathStroke(true);
-        rect.getGState().setStrokeColorSpace(ColorSpace.createDeviceRGB());
-        rect.getGState().setStrokeColor(colorPt);
-        writer.writePlacedElement(rect);
-    }
-
-
-    private static AffineTransform toAffineTransform(Matrix2D ctm) throws PDFNetException {
-
-        return new AffineTransform(ctm.getA(), ctm.getB(), ctm.getC(), ctm.getD(), ctm.getH(), ctm.getV());
-    }
-
-
-    @Builder
-    private record InvisibleElementRemovalContext(
-            boolean delta,
-            ElementReader reader,
-            ClippingPathStack clippingPathStack,
-            List<ElementFeatures> overlappedElements,
-            List<ElementFeatures> visibleElements,
-            Set<Long> visitedXObjIds) {
-
-    }
-
-}

ocr-service-v1/ocr-service-server-v1/src/main/java/com/iqser/red/service/ocr/v1/server/service/InvisibleElementService.java

@@ -0,0 +1,463 @@
+package com.iqser.red.service.ocr.v1.server.service;
+
+import com.iqser.red.service.ocr.v1.server.model.ClippingPathStack;
+import com.iqser.red.service.ocr.v1.server.model.ElementFeatures;
+import com.pdftron.common.Matrix2D;
+import com.pdftron.common.PDFNetException;
+import com.pdftron.pdf.*;
+import com.pdftron.sdf.Obj;
+import com.pdftron.sdf.SDFDoc;
+import lombok.SneakyThrows;
+import lombok.extern.slf4j.Slf4j;
+import org.apache.commons.io.FileUtils;
+import org.springframework.stereotype.Service;
+
+import java.awt.*;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.Rectangle2D;
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
+import java.util.TreeSet;
+import java.util.stream.Collectors;
+
+@Slf4j
+@Service
+public class InvisibleElementService {
+
+    /*
+    handled cases:
+        Text or Path outside of clipping path
+        Text which is transparent or is set to not render
+        Text or Path that have been painted over by visible and filled Paths
+    unhandled cases:
+        Text covered by widely stroked path
+        Text same color as background
+        Any Text set to clipping with its many interactions with other elements
+     */
+    @SneakyThrows
+    public byte[] removeInvisibleTextOrPathElements(byte[] pdfFile, boolean delta) {
+        PDFDoc pdfDoc = new PDFDoc(pdfFile);
+
+        ElementWriter writer = new ElementWriter();
+        ElementReader reader = new ElementReader();
+        Set<Integer> visited = new TreeSet<>();
+
+        for (PageIterator iterator = pdfDoc.getPageIterator(); iterator.hasNext(); ) {
+            Page page = iterator.next();
+            List<ElementFeatures> overlappedElements = removeClippedElementsAndInvisibleTextAndRememberOverlappedElements(page, reader, writer, visited, delta);
+            visited.clear();
+            removeOverlappedElements(page, reader, writer, visited, overlappedElements, delta);
+        }
+
+        if (delta) {
+            debugSave(pdfDoc.save(SDFDoc.SaveMode.LINEARIZED, null));
+        }
+
+        return pdfDoc.save(SDFDoc.SaveMode.LINEARIZED, null);
+    }
+
+    private List<ElementFeatures> removeClippedElementsAndInvisibleTextAndRememberOverlappedElements(Page page, ElementReader reader, ElementWriter writer, Set<Integer> visited, boolean delta)
+            throws PDFNetException {
+        var overlappedElements = new ArrayList<ElementFeatures>();
+        var visibleElements = new ArrayList<ElementFeatures>();
+        ClippingPathStack clippingPathStack = new ClippingPathStack(page.getMediaBox());
+        visited.add((int) page.getSDFObj().getObjNum());
+        reader.begin(page);
+        writer.begin(page, ElementWriter.e_replacement, false, true, page.getResourceDict());
+        processElements(reader, writer, visited, clippingPathStack, delta, overlappedElements, visibleElements);
+        writer.end();
+        reader.end();
+        return overlappedElements;
+    }
+
+    private void processElements(ElementReader reader, ElementWriter writer, Set<Integer> visited, ClippingPathStack clippingPathStack, Boolean delta,
+                                 List<ElementFeatures> coveredElements, List<ElementFeatures> visibleElements)
+            throws PDFNetException {
+
+        for (Element element = reader.next(); element != null; element = reader.next())
+            switch (element.getType()) {
+
+                case Element.e_image:
+                case Element.e_inline_image:
+                    processImages(element, writer, clippingPathStack, delta, visibleElements);
+                    break;
+
+                case Element.e_text:
+                    processText(element, writer, clippingPathStack, delta, visibleElements);
+                    break;
+
+                case Element.e_path:
+                    processPath(element, writer, clippingPathStack, delta, coveredElements, visibleElements);
+                    break;
+
+                case Element.e_form:
+                    processForm(reader, writer, element, visited, clippingPathStack, delta, coveredElements, visibleElements);
+                    break;
+
+                case Element.e_group_begin:
+                    clippingPathStack.enterNewGState();
+                    writer.writeElement(element);
+                    break;
+
+                case Element.e_group_end:
+                    clippingPathStack.leaveGState();
+                    writer.writeElement(element);
+                    break;
+
+                default:
+                    writer.writeElement(element);
+            }
+    }
+
+    private void processImages(Element imageElement, ElementWriter writer, ClippingPathStack clippingPathStack, Boolean delta, List<ElementFeatures> visibleElements)
+            throws PDFNetException {
+
+        Rect rect = imageElement.getBBox();
+
+        if (rect == null) {
+            return;
+        }
+
+        boolean inClippingPath = clippingPathStack.almostIntersects(rect.getX1(), rect.getY1(), rect.getWidth(), rect.getHeight());
+
+        if (!delta && inClippingPath) {
+            visibleElements.add(ElementFeatures.extractFeatures(imageElement));
+            writer.writeElement(imageElement);
+        }
+
+        if (delta && !inClippingPath) {
+            writer.writeElement(imageElement);
+        }
+    }
+
+    private void processText(Element textElement, ElementWriter writer, ClippingPathStack clippingPathStack,
+                             Boolean delta, List<ElementFeatures> visibleElements)
+            throws PDFNetException {
+
+        Rect rect = textElement.getBBox();
+
+        if (rect == null) {
+            writer.writeElement(textElement);
+            return;
+        }
+
+        GState gState = textElement.getGState();
+
+        boolean inClippingPath = clippingPathStack.almostIntersects(rect.getX1(), rect.getY1(), rect.getWidth(), rect.getHeight());
+
+        boolean isTextVisible = isTextRenderedVisibly(gState);
+
+        if (inClippingPath && isTextVisible) {
+            visibleElements.add(ElementFeatures.extractFeatures(textElement));
+        }
+        if (!delta) {
+            if (inClippingPath && isTextVisible) {
+                writer.writeElement(textElement);
+            } else if (textElement.hasTextMatrix()) {
+                /*
+                PDFTron Element with type "text" refers to a Tj command. If a Tm command is just above it in the pdf file, PDFTron will join the two commands and treat them as one Element.
+                hasTextMatrix() checks for this case specifically. Also, Tm changes the position for a whole BT/ET segment, possibly containing multiple Tj commands.
+                Therefore, the position of a following Tj is affected by not writing the first Element.
+                This is why, we write only the Tm command:
+                */
+                writer.writeGStateChanges(textElement);
+            }
+        } else {
+            if (!inClippingPath) {
+                gState.setFillColorSpace(ColorSpace.createDeviceRGB());
+                gState.setFillColor(new ColorPt(1, 0, 0));
+                writer.writeElement(textElement);
+            }
+            if (!isTextVisible) {
+                gState.setFillColorSpace(ColorSpace.createDeviceRGB());
+                gState.setFillColor(new ColorPt(0, 0, 1));
+                gState.setTextRenderMode(GState.e_fill_text);
+                gState.setFillOpacity(1);
+                writer.writeElement(textElement);
+            }
+        }
+    }
+
+    private void processForm(ElementReader reader, ElementWriter writer, Element element, Set<Integer> visited, ClippingPathStack clippingPathStack, Boolean delta,
+                             List<ElementFeatures> coveredElements, List<ElementFeatures> allElements)
+            throws PDFNetException {
+
+        writer.writeElement(element);
+        Obj formObj = element.getXObject();
+
+        if (!visited.contains((int) formObj.getObjNum())) {
+            visited.add((int) formObj.getObjNum());
+            ElementWriter new_writer = new ElementWriter();
+            reader.formBegin();
+            new_writer.begin(formObj);
+
+            reader.clearChangeList();
+            new_writer.setDefaultGState(reader);
+
+            processElements(reader, new_writer, visited, clippingPathStack, delta, coveredElements, allElements);
+            new_writer.end();
+            reader.end();
+        }
+    }
+
+    private void processPath(Element pathElement, ElementWriter writer, ClippingPathStack clippingPathStack, Boolean delta,
+                             List<ElementFeatures> overlappedElements, List<ElementFeatures> visibleElements)
+            throws PDFNetException {
+
+        GeneralPath linePath = convertToGeneralPath(pathElement.getPathData());
+
+        //transform path to initial user space
+        var ctm = pathElement.getCTM();
+        var affineTransform = getAffineTransform(ctm);
+        linePath.transform(affineTransform);
+
+        var rect = linePath.getBounds2D();
+
+        boolean inClippingPath = clippingPathStack.almostIntersects(rect.getX(), rect.getY(), rect.getWidth(), rect.getHeight());
+
+        if (pathElement.isClippingPath()) {
+            if (pathElement.isClipWindingFill()) {
+                linePath.setWindingRule(GeneralPath.WIND_NON_ZERO);
+            } else {
+                linePath.setWindingRule(GeneralPath.WIND_EVEN_ODD);
+            }
+
+            clippingPathStack.intersectClippingPath(linePath);
+            pathElement.setPathClip(!delta);
+            writer.writeElement(pathElement);
+
+        } else {
+            if (inClippingPath) {
+                if (isFilledAndNonTransparent(pathElement)) {
+                    List<ElementFeatures> currentOverlappedElements = visibleElements.stream()
+                            .filter(features -> almostContains(linePath, features.getBoundingBox()))
+                            .collect(Collectors.toList());
+                    overlappedElements.addAll(currentOverlappedElements);
+                    visibleElements.removeAll(currentOverlappedElements);
+                }
+                visibleElements.add(ElementFeatures.extractFeatures(pathElement));
+                if (!delta) {
+                    writer.writeElement(pathElement);
+                }
+            }
+            if (delta && !inClippingPath) {
+                pathElement.getGState().setFillColorSpace(ColorSpace.createDeviceRGB());
+                pathElement.getGState().setFillColor(new ColorPt(1, 0, 0));
+                pathElement.getGState().setStrokeColorSpace(ColorSpace.createDeviceRGB());
+                pathElement.getGState().setStrokeColor(new ColorPt(1, 0, 0));
+                writer.writeElement(pathElement);
+            }
+        }
+    }
+
+    private static AffineTransform getAffineTransform(Matrix2D ctm) throws PDFNetException {
+        return new AffineTransform(ctm.getA(), ctm.getB(), ctm.getC(), ctm.getD(), ctm.getH(), ctm.getV());
+    }
+
+    private void removeOverlappedElements(Page page, ElementReader reader, ElementWriter writer, Set<Integer> visited, List<ElementFeatures> overlappedElements, boolean delta)
+            throws PDFNetException {
+        reader.begin(page);
+        writer.begin(page, ElementWriter.e_replacement, false, true, page.getResourceDict());
+        if (delta) {
+            overlappedElements.forEach(feature -> drawBBox(writer, feature.getBoundingBox(), "#00FF00"));
+            overlappedElements.clear();
+        }
+        processOverlappedElements(reader, writer, visited, overlappedElements, delta);
+        writer.end();
+        reader.end();
+
+        if (overlappedElements.size() > 0) {
+            log.warn(overlappedElements.size() + " overlapped elements have not been found and removed");
+        }
+    }
+
+    private void processOverlappedElements(ElementReader reader, ElementWriter writer, Set<Integer> visited, List<ElementFeatures> coveredElements, boolean delta)
+            throws PDFNetException {
+        for (Element element = reader.next(); element != null; element = reader.next()) {
+            switch (element.getType()) {
+                case Element.e_form:
+                    processFormOverlappedElements(reader, writer, element, visited, coveredElements, delta);
+                    break;
+                case Element.e_path:
+                case Element.e_image:
+                case Element.e_inline_image:
+                case Element.e_text:
+                    boolean anyMatch = false;
+                    for (ElementFeatures elementToRemove : coveredElements) {
+                        if (elementToRemove.almostMatches(element)) {
+                            coveredElements.remove(elementToRemove);
+                            anyMatch = true;
+                            break;
+                        }
+                    }
+                    if (!anyMatch) {
+                        writer.writeElement(element);
+                    } else if (element.getType() == 3 && element.hasTextMatrix()) {
+                        /*
+                        PDFTron Element with type "text" refers to a Tj command. If a Tm command is just above it in the pdf file, PDFTron will join the two commands and treat them as one Element.
+                        hasTextMatrix() checks for this case specifically. Also, Tm changes the position for a whole BT/ET segment, possibly containing multiple Tj commands.
+                        Therefore, the position of a following Tj is affected by not writing the first Element.
+                        This is why, we write only the Tm command:
+                        */
+                        writer.writeGStateChanges(element);
+                    }
+                    break;
+
+                default:
+                    writer.writeElement(element);
+
+            }
+        }
+    }
+
+    private void processFormOverlappedElements(ElementReader reader, ElementWriter writer, Element element, Set<Integer> visited, List<ElementFeatures> elementsToRemove, boolean delta)
+            throws PDFNetException {
+
+        writer.writeElement(element);
+        Obj formObj = element.getXObject();
+
+        if (!visited.contains((int) formObj.getObjNum())) {
+            visited.add((int) formObj.getObjNum());
+            ElementWriter new_writer = new ElementWriter();
+            reader.formBegin();
+            new_writer.begin(formObj);
+
+            reader.clearChangeList();
+            new_writer.setDefaultGState(reader);
+
+            processOverlappedElements(reader, new_writer, visited, elementsToRemove, delta);
+            new_writer.end();
+            reader.end();
+        }
+    }
+
+    private boolean isTextRenderedVisibly(GState gState) throws PDFNetException {
+        if (gState.getTextRenderMode() == GState.e_invisible_text) return false;
+        if (gState.getTextRenderMode() == GState.e_fill_text && gState.getFillOpacity() == 0) return false;
+        if (gState.getTextRenderMode() == GState.e_stroke_text && gState.getStrokeOpacity() == 0) return false;
+        if (gState.getTextRenderMode() == GState.e_fill_stroke_text && gState.getFillOpacity() == 0 && gState.getStrokeOpacity() == 0) return false;
+        return true;
+    }
+
+    private GeneralPath convertToGeneralPath(PathData pathData) throws PDFNetException {
+        GeneralPath linePath = new GeneralPath();
+
+        double[] dataPoints = pathData.getPoints();
+        byte[] opr = pathData.getOperators();
+
+        double x1;
+        double y1;
+        double x2;
+        double y2;
+        double x3;
+        double y3;
+
+        int data_index = 0;
+        for (int opr_index = 0; opr_index < opr.length; ++opr_index) {
+            switch (opr[opr_index]) {
+                case PathData.e_moveto:
+                    x1 = dataPoints[data_index];
+                    ++data_index;
+                    y1 = dataPoints[data_index];
+                    ++data_index;
+
+                    linePath.moveTo(x1, y1);
+                    break;
+                case PathData.e_lineto:
+                    x1 = dataPoints[data_index];
+                    ++data_index;
+                    y1 = dataPoints[data_index];
+                    ++data_index;
+
+                    linePath.lineTo(x1, y1);
+                    break;
+                case PathData.e_cubicto:
+                    x1 = dataPoints[data_index];
+                    ++data_index;
+                    y1 = dataPoints[data_index];
+                    ++data_index;
+                    x2 = dataPoints[data_index];
+                    ++data_index;
+                    y2 = dataPoints[data_index];
+                    ++data_index;
+                    x3 = dataPoints[data_index];
+                    ++data_index;
+                    y3 = dataPoints[data_index];
+                    ++data_index;
+
+                    linePath.curveTo(x1, y1, x2, y2, x3, y3);
+                    break;
+                case PathData.e_rect:
+                    x1 = dataPoints[data_index];
+                    ++data_index;
+                    y1 = dataPoints[data_index];
+                    ++data_index;
+                    double w = dataPoints[data_index];
+                    ++data_index;
+                    double h = dataPoints[data_index];
+                    ++data_index;
+                    x2 = x1 + w;
+                    y2 = y1;
+                    x3 = x2;
+                    y3 = y1 + h;
+                    double x4 = x1;
+                    double y4 = y3;
+
+                    linePath.moveTo(x1, y1);
+                    linePath.lineTo(x2, y2);
+                    linePath.lineTo(x3, y3);
+                    linePath.lineTo(x4, y4);
+                    break;
+                case PathData.e_closepath:
+                    linePath.closePath();
+                    break;
+                default:
+                    throw new PDFNetException("Invalid Element Type", 0, "", "", "");
+            }
+        }
+        return linePath;
+    }
+
+    private boolean almostContains(Shape outer, Rectangle2D inner) {
+        double tolerance = 1e-3;
+
+        double x_with_tolerance = inner.getX() >= 0 ? inner.getX() + tolerance : inner.getX() - tolerance;
+        double y_with_tolerance = inner.getY() >= 0 ? inner.getY() + tolerance : inner.getY() - tolerance;
+        double height_with_tolerance = inner.getHeight() - (2 * tolerance);
+        double width_with_tolerance = inner.getWidth() - (2 * tolerance);
+        Rectangle2D innerRect = new Rectangle2D.Double(x_with_tolerance, y_with_tolerance, width_with_tolerance, height_with_tolerance);
+
+        return outer.contains(innerRect);
+    }
+
+    private boolean isFilledAndNonTransparent(Element element) throws PDFNetException {
+        return element.isFilled() && element.getGState().getFillOpacity() == 1;
+    }
+
+
+    private void debugSave(byte[] pdfFile) {
+        String fileLocation = "/tmp/delta.pdf";
+        try (var f_out = FileUtils.openOutputStream(new File(fileLocation))) {
+            f_out.write(pdfFile);
+        } catch (IOException e) {
+            throw new RuntimeException("File location: " + fileLocation + "could not be openend, no file will be saved");
+        }
+    }
+
+    @SneakyThrows
+    private void drawBBox(ElementWriter writer, Rectangle2D r, String hexcolor) {
+        ColorPt colorPt = new ColorPt(Integer.valueOf(hexcolor.substring(1, 3), 16) / 255d,
+                Integer.valueOf(hexcolor.substring(3, 5), 16) / 255d,
+                Integer.valueOf(hexcolor.substring(5, 7), 16) / 255d);
+        ElementBuilder eb = new ElementBuilder();
+        Element rect = eb.createRect(r.getX(), r.getY(), r.getWidth(), r.getHeight());
+        rect.setPathStroke(true);
+        rect.getGState().setStrokeColorSpace(ColorSpace.createDeviceRGB());
+        rect.getGState().setStrokeColor(colorPt);
+        writer.writePlacedElement(rect);
+    }
+}

ocr-service-v1/ocr-service-server-v1/src/main/java/com/iqser/red/service/ocr/v1/server/service/OCRService.java

@@ -1,34 +1,29 @@
 package com.iqser.red.service.ocr.v1.server.service;
 
-import static java.lang.String.format;
-
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.OutputStream;
-import java.util.Map;
-
-import org.springframework.amqp.rabbit.core.RabbitTemplate;
-import org.springframework.stereotype.Service;
-
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.iqser.red.service.ocr.v1.api.model.OCRStatusUpdateResponse;
 import com.iqser.red.service.ocr.v1.server.configuration.MessagingConfiguration;
+import com.iqser.red.service.ocr.v1.server.model.ImagePosition;
+import com.iqser.red.service.ocr.v1.server.model.image.ImageServiceResponse;
 import com.iqser.red.service.ocr.v1.server.settings.OcrServiceSettings;
-import com.pdftron.common.PDFNetException;
-import com.pdftron.pdf.OCRModule;
-import com.pdftron.pdf.OCROptions;
-import com.pdftron.pdf.Optimizer;
-import com.pdftron.pdf.PDFDoc;
-import com.pdftron.pdf.Page;
-import com.pdftron.pdf.RectCollection;
+import com.iqser.red.service.persistence.service.v1.api.utils.SuppressFBWarnings;
+import com.iqser.red.service.redaction.v1.model.Point;
+import com.iqser.red.service.redaction.v1.model.Rectangle;
+import com.pdftron.pdf.*;
 import com.pdftron.sdf.SDFDoc;
-
 import io.micrometer.core.annotation.Timed;
 import lombok.RequiredArgsConstructor;
 import lombok.SneakyThrows;
 import lombok.extern.slf4j.Slf4j;
+import org.apache.commons.io.IOUtils;
+import org.springframework.amqp.rabbit.core.RabbitTemplate;
+import org.springframework.stereotype.Service;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.InputStream;
+import java.util.*;
+
 
 @Slf4j
 @Service
@@ -44,141 +39,139 @@ public class OCRService {
 
     private final ObjectMapper objectMapper;
 
-    private final InvisibleElementRemovalService invisibleElementRemovalService;
+    private final InvisibleElementService invisibleElementService;
 
-    private final ImagePositionRetrievalService imagePositionRetrievalService;
+    @Timed("redactmanager_PDFTron-ocrDocument")
+    @SneakyThrows
+    public InputStream ocrDocument(String dossierId, String fileId) {
+
+        var fileStream = fileStorageService.getOriginalFileAsStream(dossierId, fileId);
+
+        var imageServiceResponse = fileStorageService.getImageServiceResponse(dossierId, fileId);
+
+        var fileBytes = IOUtils.toByteArray(fileStream);
+
+        var ocrBytes = ocr(fileBytes, fileId, imageServiceResponse);
+
+        return new ByteArrayInputStream(ocrBytes);
+
+    }
 
 
-    /**
-     * First loads the PDF Document from storage.
-     * Then removes all invisible Elements from the PDF, check InvisibleElementRemovalService for details.
-     * Then gets Image Position Information, check ImagePositionRetrievalService for details.
-     * Then runs OCR page by page, exclusively on pages which have images on them. It does so, by creating a new PDFDoc and inserting a single page at a time.
-     * This is because PDFTron OCROptions overlays all regions where OCR should not be run with white images. It does not check for empty pages.
-     * For Documents with many pages but few Images this results in major performance improvements.
-     * It then re-adds the OCRed Pages to the original document and saves it.
-     *
-     * @param dossierId The dossier id
-     * @param fileId    The file id
-     * @param out       OutputStream to write the file to
-     */
-    @Timed("redactmanager_runOcrOnDocument")
-    public void runOcrOnDocument(String dossierId, String fileId, OutputStream out) throws IOException {
+    @SuppressFBWarnings("REC_CATCH_EXCEPTION")
+    private byte[] ocr(byte[] file, String fileId, ImageServiceResponse imageServiceResponse) {
 
-        try (ByteArrayOutputStream transferOutputStream = new ByteArrayOutputStream()) {
-            try (InputStream fileStream = fileStorageService.getOriginalFileAsStream(dossierId, fileId)) {
-                long start = System.currentTimeMillis();
-                log.debug("Start invisible element removal for file with dossierId {} and fileId {}", dossierId, fileId);
-                invisibleElementRemovalService.removeInvisibleElements(fileStream, transferOutputStream, false);
-                long end = System.currentTimeMillis();
-                log.debug("Invisible element removal successful for file with dossierId {} and fileId {}, took {}s", dossierId, fileId, format("%.1f", (end - start) / 1000.0));
+        PDFDoc pdfDoc = null;
+
+        var fileWithoutInvisibleText = invisibleElementService.removeInvisibleTextOrPathElements(file, false);
+
+        try (ByteArrayOutputStream out = new ByteArrayOutputStream()) {
+            pdfDoc = new PDFDoc(fileWithoutInvisibleText);
+
+            Map<Integer, List<ImagePosition>> pages = new HashMap<>();
+
+            // TODO take logic to ignore small and combine images from image-service.
+            // TODO Then replace logic so ocr-service is independent from image-service.
+            imageServiceResponse.getData()
+                    .forEach(imageMetadata -> pages.computeIfAbsent(imageMetadata.getPosition().getPageNumber(), x -> new ArrayList<>())
+                            .add(new ImagePosition(new Rectangle(new Point(imageMetadata.getPosition().getX1(), imageMetadata.getPosition().getY1()),
+                                    imageMetadata.getGeometry().getWidth(),
+                                    imageMetadata.getGeometry().getHeight(),
+                                    imageMetadata.getPosition().getPageNumber()), imageMetadata.isAlpha())));
+
+            Map<Integer, PDFDoc> pdfDocMap = Collections.synchronizedMap(new HashMap<>());
+
+            rabbitTemplate.convertAndSend(MessagingConfiguration.OCR_STATUS_UPDATE_RESPONSE_QUEUE,
+                    objectMapper.writeValueAsString(OCRStatusUpdateResponse.builder().fileId(fileId).numberOfPagesToOCR(pages.keySet().size()).build()));
+
+            ocrPages(pdfDoc, fileId, pages, pdfDocMap);
+
+            for (var entry : pdfDocMap.entrySet()) {
+
+                var ocrDoc = entry.getValue();
+                var page = entry.getKey();
+
+                Page ocrPage = ocrDoc.getPageIterator(1).next();
+                pdfDoc.pageInsert(pdfDoc.getPageIterator(page), ocrPage);
+                pdfDoc.pageRemove(pdfDoc.getPageIterator(page + 1));
+
+                ocrDoc.close();
             }
-            try (InputStream transferInputStream = new ByteArrayInputStream(transferOutputStream.toByteArray())) {
-                long start = System.currentTimeMillis();
-                runOcr(transferInputStream, out, fileId);
-                long end = System.currentTimeMillis();
-                log.info("ocr successful for file with dossierId {} and fileId {}, took {}s", dossierId, fileId, format("%.1f", (end - start) / 1000.0));
+            Optimizer.optimize(pdfDoc);
+            pdfDoc.save(out, SDFDoc.SaveMode.LINEARIZED, null);
+            pdfDoc.close();
+
+            rabbitTemplate.convertAndSend(MessagingConfiguration.OCR_STATUS_UPDATE_RESPONSE_QUEUE,
+                    objectMapper.writeValueAsString(OCRStatusUpdateResponse.builder()
+                            .fileId(fileId)
+                            .numberOfPagesToOCR(pages.keySet().size())
+                            .numberOfOCRedPages(pages.keySet().size())
+                            .ocrFinished(true)
+                            .build()));
+
+            return out.toByteArray();
+        } catch (Exception e) {
+            throw new RuntimeException(e);
+        } finally {
+            if (pdfDoc != null) {
+                try {
+                    pdfDoc.close();
+                } catch (Exception e) {
+                    log.debug("Failed to close document", e);
+                }
             }
         }
     }
 
 
     @SneakyThrows
-    private void runOcr(InputStream fileStream, OutputStream out, String fileId) {
+    private void ocrPages(PDFDoc pdfDoc, String fileId, Map<Integer, List<ImagePosition>> pages, Map<Integer, PDFDoc> pdfDocMap) {
 
-        PDFDoc pdfDoc = new PDFDoc(fileStream);
+        int numberOfOCRedPages = 0;
+        for (var pageEntry : pages.entrySet()) {
 
-        Map<Integer, RectCollection> pageIdToRectCollection = imagePositionRetrievalService.getImagePositionPerPage(pdfDoc, true);
-
-        // Optimization:
-        // When a page does not have a TextZone, PDFTron whites out the page. But, PDFTron scans it anyway, resulting in a longer runtime.
-        // So, we need to remove pages without images.
-        // Furthermore, creating a new document is *much* faster than reusing the same document and adding/removing pages one by one.
-        // Therefore, we create a new Document with a single page for every page that contains text.
-        int numProcessedPages = 0;
-        for (Integer pageId : pageIdToRectCollection.keySet()) {
             try {
-                PDFDoc singlePagePdfDoc = extractSinglePagePdfDoc(pdfDoc, pageId);
-                processOcr(pageIdToRectCollection, pageId, singlePagePdfDoc);
-                ++numProcessedPages;
+                RectCollection rectCollection = new RectCollection();
 
-                log.info("{}/{} Page {} done, OCR regions {}",
-                        numProcessedPages,
-                        pageIdToRectCollection.size(),
-                        pageId,
-                        getAllOcrTextZonesAsString(pageIdToRectCollection, pageId));
+                var page = pageEntry.getKey();
 
-                replaceOriginalPageWithOcrPage(pdfDoc, pageId, singlePagePdfDoc);
-                singlePagePdfDoc.close();
+                Page pdfPage = pdfDoc.getPageIterator(page).next();
 
-                rabbitTemplate.convertAndSend(MessagingConfiguration.OCR_STATUS_UPDATE_RESPONSE_QUEUE,
-                        objectMapper.writeValueAsString(OCRStatusUpdateResponse.builder()
-                                .fileId(fileId)
-                                .numberOfPagesToOCR(pageIdToRectCollection.size())
-                                .numberOfOCRedPages(numProcessedPages)
-                                .build()));
+                pdfPage.setMediaBox(pdfPage.getCropBox());
 
-            } catch (PDFNetException e) {
-                log.error("Failed to process page {}", pageId);
-                throw new RuntimeException(e);
+                for (ImagePosition imagePosition : pageEntry.getValue()) {
+                    Rectangle rectangle = imagePosition.getRectangle();
+
+                    // Warning coordinate system is different in this call macOs/Linux
+                    double y = -rectangle.getTopLeft().getY() + pdfPage.getCropBox().getY2() - rectangle.getHeight();
+                    rectCollection.addRect(rectangle.getTopLeft().getX(), y, rectangle.getTopLeft().getX() + rectangle.getWidth(), y + rectangle.getHeight());
+                }
+
+                PDFDoc ocrDoc = new PDFDoc();
+                ocrDoc.pagePushBack(pdfPage);
+                pdfDocMap.put(pageEntry.getKey(), ocrDoc);
+
+                OCROptions options = new OCROptions();
+                options.addTextZonesForPage(rectCollection, 1);
+                options.addLang(ENGLISH);
+                options.addDPI(settings.getOcrDPI());
+                OCRModule.processPDF(ocrDoc, options);
+
+                rectCollection.clear();
+
+            } catch (Exception e) {
+                log.warn("Failed to process PDF page {} - {}", pageEntry.getKey(), e);
             }
-        }
 
-        rabbitTemplate.convertAndSend(MessagingConfiguration.OCR_STATUS_UPDATE_RESPONSE_QUEUE,
-                objectMapper.writeValueAsString(OCRStatusUpdateResponse.builder()
-                        .fileId(fileId)
-                        .numberOfPagesToOCR(pageIdToRectCollection.size())
-                        .numberOfOCRedPages(numProcessedPages)
-                        .ocrFinished(true)
-                        .build()));
+            rabbitTemplate.convertAndSend(MessagingConfiguration.OCR_STATUS_UPDATE_RESPONSE_QUEUE,
+                    objectMapper.writeValueAsString(OCRStatusUpdateResponse.builder()
+                            .fileId(fileId)
+                            .numberOfPagesToOCR(pages.keySet().size())
+                            .numberOfOCRedPages(++numberOfOCRedPages)
+                            .build()));
+
+            log.warn("Done page {}", pageEntry);
 
-        Optimizer.optimize(pdfDoc);
-        try {
-            pdfDoc.save(out, SDFDoc.SaveMode.LINEARIZED, null);
-        } catch (Exception e) {
-            log.error("Processed File with fileId {} could not be saved", fileId);
-            throw new RuntimeException(e);
         }
     }
-
-
-    private void processOcr(Map<Integer, RectCollection> pageIdToRectCollection, Integer pageId, PDFDoc singlePagePdfDoc) throws PDFNetException {
-
-        OCROptions options = new OCROptions();
-        options.addTextZonesForPage(pageIdToRectCollection.get(pageId), 1);
-        options.addLang(ENGLISH);
-        options.addDPI(settings.getOcrDPI());
-
-        OCRModule.processPDF(singlePagePdfDoc, options);
-    }
-
-
-    private static PDFDoc extractSinglePagePdfDoc(PDFDoc pdfDoc, Integer pageId) throws PDFNetException {
-
-        PDFDoc singlePagePdfDoc = new PDFDoc();
-        Page page = pdfDoc.getPage(pageId);
-        page.setMediaBox(page.getCropBox()); // this line ensures the ocr text is placed correctly by PDFTron, see TestFile MediaBoxBiggerThanCropBox.pdf
-        singlePagePdfDoc.pagePushBack(page);
-        return singlePagePdfDoc;
-    }
-
-
-    private static void replaceOriginalPageWithOcrPage(PDFDoc pdfDoc, Integer pageId, PDFDoc ocrPageDoc) throws PDFNetException {
-
-        Page ocrPage = ocrPageDoc.getPage(1);
-        pdfDoc.pageInsert(pdfDoc.getPageIterator(pageId), ocrPage);
-        pdfDoc.pageRemove(pdfDoc.getPageIterator(pageId + 1));
-    }
-
-
-    private static StringBuilder getAllOcrTextZonesAsString(Map<Integer, RectCollection> pageIdToRectCollection, Integer pageId) throws PDFNetException {
-
-        StringBuilder zonesString = new StringBuilder();
-        for (int j = 0; j < pageIdToRectCollection.get(pageId).getNumRects(); ++j) {
-            var r = pageIdToRectCollection.get(pageId).getRectAt(j);
-            zonesString.append(format("[lower left (%.1f|%.1f) upper right (%.1f|%.1f)]", r.getX1(), r.getY1(), r.getX2(), r.getY2()));
-        }
-        return zonesString;
-    }
-
 }

ocr-service-v1/ocr-service-server-v1/src/main/java/com/iqser/red/service/ocr/v1/server/service/OcrMessageReceiver.java

@@ -1,9 +1,5 @@
 package com.iqser.red.service.ocr.v1.server.service;
 
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.IOException;
-
 import org.springframework.amqp.AmqpRejectAndDontRequeueException;
 import org.springframework.amqp.rabbit.annotation.RabbitHandler;
 import org.springframework.amqp.rabbit.annotation.RabbitListener;
@@ -12,9 +8,9 @@ import org.springframework.stereotype.Service;
 
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
-import com.iqser.red.service.ocr.v1.api.model.DocumentRequest;
 import com.iqser.red.service.ocr.v1.server.client.FileStatusProcessingUpdateClient;
 import com.iqser.red.service.ocr.v1.server.configuration.MessagingConfiguration;
+import com.iqser.red.service.ocr.v1.api.model.DocumentRequest;
 
 import feign.FeignException;
 import lombok.RequiredArgsConstructor;
@@ -38,6 +34,7 @@ public class OcrMessageReceiver {
 
         DocumentRequest ocrRequestMessage = objectMapper.readValue(in, DocumentRequest.class);
 
+        long start = System.currentTimeMillis();
         log.info("Start ocr for file with dossierId {} and fileId {}", ocrRequestMessage.getDossierId(), ocrRequestMessage.getFileId());
 
         setStatusOcrProcessing(ocrRequestMessage.getDossierId(), ocrRequestMessage.getFileId());
@@ -47,18 +44,14 @@ public class OcrMessageReceiver {
             fileStorageService.storeUntouchedFile(ocrRequestMessage.getDossierId(), ocrRequestMessage.getFileId(), originalFile);
         }
 
-        try (var transferStream = new ByteArrayOutputStream()) {
-            ocrService.runOcrOnDocument(ocrRequestMessage.getDossierId(), ocrRequestMessage.getFileId(), transferStream);
-            try (var inputStream = new ByteArrayInputStream(transferStream.toByteArray())) {
-                fileStorageService.storeOriginalFile(ocrRequestMessage.getDossierId(), ocrRequestMessage.getFileId(), inputStream);
-            }
-        } catch (IOException e) {
-            log.error("Failed to store file with dossierId {} and fileId {}", ocrRequestMessage.getDossierId(), ocrRequestMessage.getFileId());
-            throw new RuntimeException(e);
-        }
+        var ocrResult = ocrService.ocrDocument(ocrRequestMessage.getDossierId(), ocrRequestMessage.getFileId());
+
+        fileStorageService.storeOriginalFile(ocrRequestMessage.getDossierId(), ocrRequestMessage.getFileId(), ocrResult);
+
+        long end = System.currentTimeMillis();
+        log.info("Successfully processed ocr for file with dossierId {} and fileId {}, took {}", ocrRequestMessage.getDossierId(), ocrRequestMessage.getFileId(), end - start);
 
         fileStatusProcessingUpdateClient.ocrSuccessful(ocrRequestMessage.getDossierId(), ocrRequestMessage.getFileId());
-
     }
 
 

ocr-service-v1/ocr-service-server-v1/src/main/resources/application.yml

@@ -35,7 +35,7 @@ management:
     metrics.enabled: ${monitoring.enabled:false}
     prometheus.enabled: ${monitoring.enabled:false}
     health.enabled: true
-  endpoints.web.exposure.include: prometheus, health, metrics
+  endpoints.web.exposure.include: prometheus, health
   metrics.export.prometheus.enabled: ${monitoring.enabled:false}
 
 
@@ -46,4 +46,4 @@ storage:
   endpoint: 'https://s3.amazonaws.com'
   backend: 's3'
 
-pdftron.license: ${PDFTRON_LICENSE}
+pdftron.license: ${PDFTRON_LICENSE}

ocr-service-v1/ocr-service-server-v1/src/test/java/com/iqser/red/service/ocr/v1/server/InvisibleElementServiceTest.java

@@ -0,0 +1,64 @@
+package com.iqser.red.service.ocr.v1.server;
+
+import com.iqser.red.service.ocr.v1.server.service.InvisibleElementService;
+import lombok.SneakyThrows;
+import org.apache.commons.io.FileUtils;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.springframework.amqp.rabbit.core.RabbitTemplate;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.boot.test.mock.mockito.MockBean;
+import org.springframework.context.annotation.Import;
+import org.springframework.core.io.ClassPathResource;
+import org.springframework.test.context.junit.jupiter.SpringExtension;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+
+import static com.iqser.red.service.ocr.v1.server.utils.OsUtils.getTemporaryDirectory;
+
+@ExtendWith(SpringExtension.class)
+@SpringBootTest(classes = Application.class, webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT //
+        , properties = {"pdftron.ocrmodule.path=/YourOCRModulePath"})
+@Import(OcrServiceIntegrationTest.TestConfiguration.class)
+public class InvisibleElementServiceTest {
+
+    @Autowired
+    private InvisibleElementService invisibleElementService;
+
+    @MockBean
+    protected RabbitTemplate rabbitTemplate;
+
+    @Test
+    @SneakyThrows
+    public void testRemoveInvisibleText() {
+        String fileName = "InvisibleText";
+
+        ClassPathResource pdfFileResource = new ClassPathResource("files/" + fileName + ".pdf");
+
+        var initialFileBytes = Files.readAllBytes(pdfFileResource.getFile().toPath());
+
+        var fileWithoutInvisibleText = invisibleElementService.removeInvisibleTextOrPathElements(initialFileBytes, false);
+        var deltaFile = invisibleElementService.removeInvisibleTextOrPathElements(initialFileBytes, true);
+
+        String fileWithoutInvisibleTextLocation = getTemporaryDirectory() + "/" + fileName + ".pdf";
+        String deltaFileLocation = getTemporaryDirectory() + "/" + fileName + "_delta.pdf";
+
+        saveToFile(fileWithoutInvisibleTextLocation, fileWithoutInvisibleText);
+        saveToFile(deltaFileLocation, deltaFile);
+
+        System.out.println("File:" + fileWithoutInvisibleTextLocation);
+        System.out.println("File:" + deltaFileLocation);
+    }
+
+    private void saveToFile(String location, byte[] fileBytes) {
+        try (var f_out = FileUtils.openOutputStream(new File(location))) {
+            f_out.write(fileBytes);
+        } catch (IOException e) {
+            throw new RuntimeException("File location: " + location + "could not be openend, no file will be saved");
+        }
+
+    }
+}

ocr-service-v1/ocr-service-server-v1/src/test/java/com/iqser/red/service/ocr/v1/server/OcrServiceIntegrationTest.java

@@ -1,18 +1,16 @@
 package com.iqser.red.service.ocr.v1.server;
 
-import static com.iqser.red.service.ocr.v1.server.utils.OsUtils.getTemporaryDirectory;
-import static org.assertj.core.api.Assertions.assertThat;
-
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.concurrent.TimeUnit;
-
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.iqser.red.service.ocr.v1.server.service.FileStorageService;
+import com.iqser.red.service.ocr.v1.server.service.OCRService;
+import com.iqser.red.service.ocr.v1.server.utils.FileSystemBackedStorageService;
+import com.iqser.red.service.persistence.service.v1.api.model.dossiertemplate.dossier.file.FileType;
+import com.iqser.red.storage.commons.StorageAutoConfiguration;
+import com.iqser.red.storage.commons.service.StorageService;
+import lombok.SneakyThrows;
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.IOUtils;
 import org.junit.jupiter.api.AfterEach;
-import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.ExtendWith;
@@ -29,23 +27,10 @@ import org.springframework.context.annotation.Primary;
 import org.springframework.core.io.ClassPathResource;
 import org.springframework.test.context.junit.jupiter.SpringExtension;
 
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.iqser.red.service.ocr.v1.server.service.FileStorageService;
-import com.iqser.red.service.ocr.v1.server.service.OCRService;
-import com.iqser.red.service.ocr.v1.server.utils.FileSystemBackedStorageService;
-import com.iqser.red.service.persistence.service.v1.api.model.dossiertemplate.dossier.file.FileType;
-import com.iqser.red.storage.commons.StorageAutoConfiguration;
-import com.iqser.red.storage.commons.service.StorageService;
-import com.pdftron.common.PDFNetException;
-import com.pdftron.pdf.OCRModule;
-import com.pdftron.pdf.PDFDoc;
-import com.pdftron.pdf.Page;
-import com.pdftron.pdf.PageIterator;
-import com.pdftron.pdf.TextExtractor;
+import java.io.File;
 
-import io.micrometer.prometheus.PrometheusMeterRegistry;
-import io.micrometer.prometheus.PrometheusTimer;
-import lombok.SneakyThrows;
+import static com.iqser.red.service.ocr.v1.server.utils.OsUtils.getTemporaryDirectory;
+import static org.assertj.core.api.Assertions.assertThat;
 
 @ExtendWith(SpringExtension.class)
 @SpringBootTest(classes = Application.class, webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT //
@@ -68,131 +53,62 @@ public class OcrServiceIntegrationTest {
     @Autowired
     private OCRService ocrService;
 
-    @Autowired
-    private PrometheusMeterRegistry registry;
 
-
-    @BeforeEach
+    @Test
+    @Disabled // OCRModule is not available on build server. If you want to run the test set the property at the top.
     @SneakyThrows
-    @Disabled // OCRModule is not available on build server. If you want to run the test set the property at the top.
-    public void assertOCRModuleIsLoaded() {
+    public void testOCR() {
 
-        assert OCRModule.isModuleAvailable();
-    }
-
-
-    @Test
-    @Disabled // OCRModule is not available on build server. If you want to run the test set the property at the top.
-    public void testOCRMetrics() {
-
-        testOCR("Watermark");
-        testOCR("Watermark");
-        testOCR("Watermark");
-
-        var ocrOnDocumentMeter = registry.getMeters().stream().filter(m -> m.getId().getName().equalsIgnoreCase("redactmanager_runOcrOnDocument")).findAny();
-        assertThat(ocrOnDocumentMeter.isPresent()).isTrue();
-        PrometheusTimer timer = (PrometheusTimer) ocrOnDocumentMeter.get();
-        assertThat(timer.count()).isEqualTo(3);
-        assertThat(timer.mean(TimeUnit.SECONDS)).isGreaterThan(0.1);
-    }
-
-
-    @Test
-    @Disabled // OCRModule is not available on build server. If you want to run the test set the property at the top.
-    public void testOcr() {
-        // check visually for most of the images containing text, the resulting text is kind of nonsense, just ensure it is there
-        String text = testOCR("StitchedImagesMultiPage");
-    }
-
-
-    @Test
-    @Disabled // OCRModule is not available on build server. If you want to run the test set the property at the top.
-    public void testManyRotatedImages() {
-        // check visually for most of the images containing text, the resulting text is kind of nonsense, just ensure it is there
-        String text = testOCR("manyRotatedImages");
-        assertThat(text).contains("Michela", "Gregori", "DVM", "PhD", "Pathologist");
-    }
-
-
-    @Test
-    @Disabled // OCRModule is not available on build server. If you want to run the test set the property at the top.
-    public void testMergeImages() {
-        // check visually for most of the images containing text, the resulting text is kind of nonsense, just ensure it is there
-        String text = testOCR("merge_images");
-        assertThat(text).contains("Bodyweight change of dams with live young - group mean values",
-                "Control",
-                "mg/g day",
-                "10 mg/kg/day",
-                "20 mg/kg/",
-                "Days",
-                "50",
-                "-200",
-                "—250",
-                "150",
-                "200",
-                "250",
-                "—150");
-    }
-
-
-    @Test
-    @Disabled // OCRModule is not available on build server. If you want to run the test set the property at the top.
-    public void testOCRWatermark() {
-
-        assertThat(testOCR("Watermark")).contains("syngenta");
-    }
-
-
-    @Test
-    @Disabled // OCRModule is not available on build server. If you want to run the test set the property at the top.
-    public void testOCRInvisibleText() {
-
-        String text = testOCR("InvisibleText");
-        assertThat(text).contains("Michela", "Gregori", "DVM", "PhD", "Pathologist", "SIGNATURE PAGE");
-        assertThat(text).doesNotContain("COMPLETION DATE:", "LABORATORY PROJECT ID:", "AUTHOR(S):", "Substance");
-    }
-
-
-    @SneakyThrows
-    private String testOCR(String fileName) {
+        String fileName = "Watermark";
 
+        ClassPathResource imageInfoResource = new ClassPathResource("files/" + fileName + ".IMAGE_INFO.json");
         ClassPathResource pdfFileResource = new ClassPathResource("files/" + fileName + ".pdf");
+
         var originId = FileStorageService.getStorageId("dossier", "file", FileType.ORIGIN);
-        try (var fileStream = pdfFileResource.getInputStream()) {
-            storageService.storeObject(originId, fileStream);
-        }
-        try (var out = new FileOutputStream(getTemporaryDirectory() + "/" + fileName + ".pdf")) {
-            ocrService.runOcrOnDocument("dossier", "file", out);
-        }
+        storageService.storeObject(originId, pdfFileResource.getInputStream());
+
+        var imageId = FileStorageService.getStorageId("dossier", "file", FileType.IMAGE_INFO);
+        storageService.storeObject(imageId, imageInfoResource.getInputStream());
+
+        var response = ocrService.ocrDocument("dossier", "file");
+
+        var out = FileUtils.openOutputStream(new File(getTemporaryDirectory() + "/" + fileName + ".pdf"));
+        IOUtils.copy(response, out);
 
         System.out.println("File:" + getTemporaryDirectory() + "/" + fileName + ".pdf");
-        try (var fileStream = new FileInputStream(getTemporaryDirectory() + "/" + fileName + ".pdf")) {
-            return extractAllTextFromDocument(fileStream);
-        }
     }
 
 
-    private static String extractAllTextFromDocument(InputStream fileStream) throws IOException, PDFNetException {
+    @Test
+    @Disabled // OCRModule is not available on build server. If you want to run the test set the property at the top.
+    @SneakyThrows
+    public void testRemoveInvisibleText() {
 
-        PDFDoc pdfDoc = new PDFDoc(fileStream);
-        TextExtractor extractor = new TextExtractor();
-        List<String> texts = new ArrayList<>();
+        String fileName = "ocr/OCR Docs/MK244 - Fitness of Analytical Method - Physical-Chemical Pro";
+//        String fileName = "InvisiblePathElements";
 
-        PageIterator iterator = pdfDoc.getPageIterator();
-        while (iterator.hasNext()) {
-            Page page = iterator.next();
-            extractor.begin(page);
-            texts.add(extractor.getAsText());
-        }
+        ClassPathResource imageInfoResource = new ClassPathResource("files/InvisibleText.IMAGE_INFO.json");
+        ClassPathResource pdfFileResource = new ClassPathResource("files/" + fileName + ".pdf");
 
-        return String.join("\n", texts);
+        var originId = FileStorageService.getStorageId("dossier", "file", FileType.ORIGIN);
+        storageService.storeObject(originId, pdfFileResource.getInputStream());
+
+        var imageId = FileStorageService.getStorageId("dossier", "file", FileType.IMAGE_INFO);
+        storageService.storeObject(imageId, imageInfoResource.getInputStream());
+
+        var response = ocrService.ocrDocument("dossier", "file");
+
+        var out = FileUtils.openOutputStream(new File(getTemporaryDirectory() + "/" + fileName + ".pdf"));
+        IOUtils.copy(response, out);
+
+        System.out.println("File:" + getTemporaryDirectory() + "/" + fileName + ".pdf");
     }
 
 
     @SneakyThrows
     public void dummyTest() {
 
-        // Build needs one test to not fail.
+        // Build needs one text to not fail.
         assertThat(1).isEqualTo(1);
     }
 
@@ -212,7 +128,7 @@ public class OcrServiceIntegrationTest {
 
         @Bean
         @Primary
-        public StorageService inMemoryStorage() {
+        public StorageService inmemoryStorage() {
 
             return new FileSystemBackedStorageService();
         }

ocr-service-v1/ocr-service-server-v1/src/test/java/com/iqser/red/service/ocr/v1/server/service/ImagePositionRetrievalServiceTest.java

@@ -1,236 +0,0 @@
-package com.iqser.red.service.ocr.v1.server.service;
-
-import static com.iqser.red.service.ocr.v1.server.utils.OsUtils.getTemporaryDirectory;
-import static org.assertj.core.api.Assertions.assertThat;
-
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-import java.util.stream.Collectors;
-
-import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.extension.ExtendWith;
-import org.springframework.amqp.rabbit.core.RabbitTemplate;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.boot.test.context.SpringBootTest;
-import org.springframework.boot.test.mock.mockito.MockBean;
-import org.springframework.context.annotation.Import;
-import org.springframework.core.io.ClassPathResource;
-import org.springframework.test.context.junit.jupiter.SpringExtension;
-
-import com.iqser.red.service.ocr.v1.server.Application;
-import com.iqser.red.service.ocr.v1.server.OcrServiceIntegrationTest;
-import com.pdftron.common.PDFNetException;
-import com.pdftron.pdf.ColorPt;
-import com.pdftron.pdf.ColorSpace;
-import com.pdftron.pdf.Element;
-import com.pdftron.pdf.ElementBuilder;
-import com.pdftron.pdf.ElementWriter;
-import com.pdftron.pdf.PDFDoc;
-import com.pdftron.pdf.Page;
-import com.pdftron.pdf.Rect;
-import com.pdftron.pdf.RectCollection;
-import com.pdftron.sdf.SDFDoc;
-
-import lombok.SneakyThrows;
-
-@ExtendWith(SpringExtension.class)
-@SpringBootTest(classes = Application.class, webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT)
-@Import(OcrServiceIntegrationTest.TestConfiguration.class)
-class ImagePositionRetrievalServiceTest {
-
-    @Autowired
-    private ImagePositionRetrievalService imagePositionRetrievalService;
-
-    @MockBean
-    protected RabbitTemplate rabbitTemplate;
-
-
-    @Test
-    @SneakyThrows
-    public void testImagePositionRetrievalForRotateTestFileWithImages() {
-
-        String fileName = "RotateTestFileWithImages";
-
-        List<int[]> allRectCoords = testImagePositionDetection(fileName);
-
-        assertThat(allRectCoords).contains(new int[]{48, 572, 295, 721},
-                new int[]{54, 279, 301, 428},
-                new int[]{360, 173, 509, 419},
-                new int[]{362, 522, 511, 768},
-                new int[]{459, 354, 608, 600},
-                new int[]{145, 404, 392, 553},
-                new int[]{151, 111, 398, 260},
-                new int[]{457, 5, 606, 251},
-                new int[]{395, 480, 545, 726},
-                new int[]{393, 130, 542, 377},
-                new int[]{88, 236, 334, 386},
-                new int[]{82, 530, 328, 679},
-                new int[]{465, 11, 614, 257},
-                new int[]{159, 117, 406, 266},
-                new int[]{467, 360, 617, 607},
-                new int[]{153, 410, 400, 559});
-    }
-
-
-    @Test
-    @SneakyThrows
-    public void testImagePositionRetrievalForRotateTestFileWithImagesExtremeCropbox() {
-
-        String fileName = "RotateTestFileWithImagesExtremeCropbox";
-
-        List<int[]> allRectCoords = testImagePositionDetection(fileName);
-        assertThat(allRectCoords).contains(new int[]{48, 572, 295, 721},
-                new int[]{362, 522, 511, 768},
-                new int[]{360, 173, 509, 419},
-                new int[]{54, 279, 301, 428},
-                new int[]{145, 192, 392, 341},
-                new int[]{459, 142, 608, 388},
-                new int[]{457, -207, 606, 39},
-                new int[]{151, -101, 398, 48},
-                new int[]{-30, 238, 216, 387},
-                new int[]{283, 188, 433, 434},
-                new int[]{281, -162, 430, 85},
-                new int[]{-24, -56, 222, 94},
-                new int[]{-39, 410, 208, 559},
-                new int[]{275, 360, 425, 607},
-                new int[]{273, 11, 422, 257},
-                new int[]{-33, 117, 214, 266});
-    }
-
-
-    @Test
-    @SneakyThrows
-    public void testMergeImages() {
-
-        String fileName = "merge_images";
-        List<int[]> allRectCoords = testImagePositionDetection(fileName);
-        assertThat(allRectCoords).contains(new int[]{90, 284, 398, 770});
-    }
-
-
-    @Test
-    @SneakyThrows
-    public void testStitchedImagesMultiPage() {
-
-        String fileName = "StitchedImagesMultiPage";
-        List<int[]> allRectCoords = testImagePositionDetection(fileName);
-        assertThat(allRectCoords.size()).isEqualTo(48);
-    }
-
-    @Test
-    @SneakyThrows
-    public void testEveryPointInDashedLineIsImage() {
-        String fileName = "everyPointInDashedLineIsImage";
-        List<int[]> allRectCoords = testImagePositionDetection(fileName);
-        assertThat(allRectCoords.size()).isEqualTo(0);
-    }
-
-
-    private List<int[]> testImagePositionDetection(String fileName) throws IOException, PDFNetException {
-
-        InputStream fileStream = new FileInputStream(new ClassPathResource("files/" + fileName + ".pdf").getFile().getAbsolutePath());
-        PDFDoc pdfDoc = new PDFDoc(fileStream);
-
-        Map<Integer, RectCollection> pageIdToRectCollection = imagePositionRetrievalService.getImagePositionPerPage(pdfDoc, false);
-
-        ElementWriter writer = new ElementWriter();
-        pageIdToRectCollection.forEach((pageId, rectCollection) -> {
-            try {
-                writer.begin(pdfDoc.getPage(pageId));
-                drawRectCollection(writer, rectCollection, pdfDoc.getPage(pageId));
-                drawGrid(writer, pdfDoc.getPage(pageId));
-                writer.end();
-                StringBuilder zonesString = new StringBuilder();
-                for (int j = 0; j < rectCollection.getNumRects(); ++j) {
-                    var r = rectCollection.getRectAt(j);
-                    zonesString.append(String.format("%d:[lower left (%.1f|%.1f) upper right (%.1f|%.1f)]; ", j, r.getX1(), r.getY1(), r.getX2(), r.getY2()));
-                }
-                System.out.printf("Page %d: rotation: %d OCR regions %s \n", pageId, pdfDoc.getPage(pageId).getRotation(), zonesString);
-            } catch (PDFNetException e) {
-                throw new RuntimeException(e);
-            }
-        });
-
-        // Check visually for red Rectangles to match images in the saved pdf file
-        try (var out = new FileOutputStream(getTemporaryDirectory() + "/" + fileName + "_IMAGE_BBOX.pdf")) {
-            out.write(pdfDoc.save(SDFDoc.SaveMode.LINEARIZED, null));
-        }
-        System.out.println("result file: " + getTemporaryDirectory() + "/" + fileName + "_IMAGE_BBOX.pdf");
-        fileStream.close();
-        // round all coords to nearest int to account for inconsistencies with the calculation of the bounding box
-        return pageIdToRectCollection.values().stream().map(this::toRoundedCoordinateArrayList).flatMap(List::stream).collect(Collectors.toList());
-    }
-
-
-    @SneakyThrows
-    private List<int[]> toRoundedCoordinateArrayList(RectCollection rectCollection) {
-
-        List<int[]> coords = new ArrayList<>(rectCollection.getNumRects());
-        for (int i = 0; i < rectCollection.getNumRects(); ++i) {
-            var r = rectCollection.getRectAt(i);
-            coords.add(new int[]{(int) Math.round(r.getX1()), (int) Math.round(r.getY1()), (int) Math.round(r.getX2()), (int) Math.round(r.getY2())});
-        }
-        return coords;
-    }
-
-
-    @SneakyThrows
-    private void drawGrid(ElementWriter writer, Page page) {
-
-        ElementBuilder eb = new ElementBuilder();
-        double dX = 15;
-        double dY = 15;
-        int nRows = (int) (page.getPageHeight() / dY) + 1;
-        int nCols = (int) (page.getPageWidth() / dX) + 1;
-        for (int row = 0; row < nRows; ++row) {
-            for (int col = 0; col < nCols; ++col) {
-                Element cell = eb.createRect(col * dX, row * dY, dX, dY);
-                cell.setPathStroke(true);
-                cell.getGState().setLineWidth(1);
-                cell.getGState().setStrokeOpacity(0.1);
-                cell.getGState().setStrokeColorSpace(ColorSpace.createDeviceRGB());
-                if (row == 0 && col == 0) {
-                    cell.getGState().setStrokeColor(new ColorPt(0, 0, 1));
-                    cell.setPathFill(true);
-                    cell.getGState().setFillOpacity(0.8);
-                    cell.getGState().setFillColorSpace(ColorSpace.createDeviceRGB());
-                    cell.getGState().setFillColor(new ColorPt(0, 0, 1));
-                } else {
-                    cell.setPathFill(false);
-                    cell.getGState().setStrokeColor(new ColorPt(0.1, 0.1, 0.1));
-                }
-                writer.writePlacedElement(cell);
-            }
-        }
-    }
-
-
-    @SneakyThrows
-    public static void drawRectCollection(ElementWriter writer, RectCollection rectCollection, Page page) {
-
-        ColorPt colorPt = new ColorPt(1, 0, 0);
-        ElementBuilder eb = new ElementBuilder();
-        for (int i = 0; i < rectCollection.getNumRects(); ++i) {
-            Rect r = rectCollection.getRectAt(i);
-            Element rect = eb.createRect(r.getX1(), r.getY1(), r.getWidth(), r.getHeight());
-
-            rect.setPathStroke(true);
-            rect.getGState().setLineWidth(5);
-            rect.getGState().setStrokeColorSpace(ColorSpace.createDeviceRGB());
-            rect.getGState().setStrokeColor(colorPt);
-
-            rect.setPathFill(true);
-            rect.getGState().setFillColorSpace(ColorSpace.createDeviceRGB());
-            rect.getGState().setFillColor(colorPt);
-            rect.getGState().setFillOpacity(0.5);
-
-            writer.writePlacedElement(rect);
-        }
-    }
-
-}

ocr-service-v1/ocr-service-server-v1/src/test/java/com/iqser/red/service/ocr/v1/server/service/InvisibleElementRemovalServiceTest.java

@@ -1,73 +0,0 @@
-package com.iqser.red.service.ocr.v1.server.service;
-
-import static com.iqser.red.service.ocr.v1.server.utils.OsUtils.getTemporaryDirectory;
-import static org.assertj.core.api.AssertionsForClassTypes.assertThat;
-
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-
-import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.extension.ExtendWith;
-import org.springframework.amqp.rabbit.core.RabbitTemplate;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.boot.test.context.SpringBootTest;
-import org.springframework.boot.test.mock.mockito.MockBean;
-import org.springframework.context.annotation.Import;
-import org.springframework.core.io.ClassPathResource;
-import org.springframework.test.context.junit.jupiter.SpringExtension;
-
-import com.iqser.red.service.ocr.v1.server.Application;
-import com.iqser.red.service.ocr.v1.server.OcrServiceIntegrationTest;
-import com.pdftron.pdf.PDFDoc;
-import com.pdftron.pdf.Page;
-import com.pdftron.pdf.PageIterator;
-import com.pdftron.pdf.TextExtractor;
-
-import lombok.SneakyThrows;
-
-@ExtendWith(SpringExtension.class)
-@SpringBootTest(classes = Application.class, webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT)
-@Import(OcrServiceIntegrationTest.TestConfiguration.class)
-public class InvisibleElementRemovalServiceTest {
-
-    @Autowired
-    private InvisibleElementRemovalService invisibleElementRemovalService;
-
-    @MockBean
-    protected RabbitTemplate rabbitTemplate;
-
-
-    @Test
-    @SneakyThrows
-    public void testRemoveInvisibleText() {
-
-        String fileName = "InvisibleText";
-
-        ClassPathResource pdfFileResource = new ClassPathResource("files/" + fileName + ".pdf");
-
-        try (var initialFileStream = pdfFileResource.getInputStream(); var out = new FileOutputStream(getTemporaryDirectory() + "/" + fileName + ".pdf")) {
-            invisibleElementRemovalService.removeInvisibleElements(initialFileStream, out,false);
-        }
-
-        try (var initialFileStream = pdfFileResource.getInputStream(); var out = new FileOutputStream(getTemporaryDirectory() + "/" + fileName + "_delta.pdf")) {
-            invisibleElementRemovalService.removeInvisibleElements(initialFileStream, out,true);
-        }
-
-        System.out.println("Output File without invisible elements: files/" + fileName + ".pdf");
-        System.out.println("Output Delta File without invisible elements: files/" + fileName + "_delta.pdf");
-        TextExtractor extractor = new TextExtractor();
-
-        PDFDoc pdfDoc;
-        try(var fileStream = new FileInputStream(getTemporaryDirectory() + "/" + fileName + ".pdf")) {
-            pdfDoc = new PDFDoc(fileStream);
-        }
-
-        PageIterator iterator = pdfDoc.getPageIterator();
-        while (iterator.hasNext()) {
-            Page page = iterator.next();
-            extractor.begin(page);
-            String[] text = extractor.getAsText().split("\n");
-            assertThat(text).contains("APPENDIX 16 Pathology Report", "Amendment 1", "Page 255 of 260");
-        }
-    }
-}

ocr-service-v1/ocr-service-server-v1/src/test/resources/application.yml

@@ -5,13 +5,4 @@ spring:
     allow-circular-references: true # FIXME
 
 
-pdftron.license: demo:1650351709282:7bd235e003000000004ec28a6743e1163a085e2115de2536ab6e2cfe5a
-
-
-management:
-  endpoint:
-    metrics.enabled: true
-    prometheus.enabled: true
-    health.enabled: true
-  endpoints.web.exposure.include: prometheus, health, metrics
-  metrics.export.prometheus.enabled: true
+pdftron.license: demo:1650351709282:7bd235e003000000004ec28a6743e1163a085e2115de2536ab6e2cfe5a

ocr-service-v1/ocr-service-server-v1/src/test/resources/files/CropboxNotEqualToMediaBox.IMAGE_INFO.json

@@ -0,0 +1 @@
+{"dossierId": "55547c91-6b0e-4aa6-9009-2e7c4cd90f13", "fileId": "917b9d9c9f548f85fef3679db45ff46c", "targetFileExtension": "ORIGIN.pdf.gz", "responseFileExtension": "IMAGE_INFO.json.gz", "data": [{"classification": {"label": "signature", "probabilities": {"signature": 0.9927, "logo": 0.0038, "other": 0.0034, "formula": 0.0}}, "representation": "FFF2CF0F7C74FFC1070830FFF", "position": {"x1": -7, "x2": 603, "y1": 0, "y2": 852, "pageNumber": 1}, "geometry": {"width": 610, "height": 852}, "alpha": false, "filters": {"geometry": {"imageSize": {"quotient": 1.0096, "tooLarge": true, "tooSmall": false}, "imageFormat": {"quotient": 0.716, "tooTall": false, "tooWide": false}}, "probability": {"unconfident": false}, "allPassed": false}}], "dataCV": []}

ocr-service-v1/ocr-service-server-v1/src/test/resources/files/Fm1Debug1.IMAGE_INFO.json

@@ -0,0 +1 @@
+{"dossierId": "55547c91-6b0e-4aa6-9009-2e7c4cd90f13", "fileId": "917b9d9c9f548f85fef3679db45ff46c", "targetFileExtension": "ORIGIN.pdf.gz", "responseFileExtension": "IMAGE_INFO.json.gz", "data": []}

ocr-service-v1/ocr-service-server-v1/src/test/resources/files/InvisiblePathElements.IMAGE_INFO.json

@@ -0,0 +1 @@
+{"dossierId": "55547c91-6b0e-4aa6-9009-2e7c4cd90f13", "fileId": "917b9d9c9f548f85fef3679db45ff46c", "targetFileExtension": "ORIGIN.pdf.gz", "responseFileExtension": "IMAGE_INFO.json.gz", "data": []}

ocr-service-v1/ocr-service-server-v1/src/test/resources/files/InvisibleText.IMAGE_INFO.json

@@ -0,0 +1 @@
+{"dossierId": "55547c91-6b0e-4aa6-9009-2e7c4cd90f13", "fileId": "917b9d9c9f548f85fef3679db45ff46c", "targetFileExtension": "ORIGIN.pdf.gz", "responseFileExtension": "IMAGE_INFO.json.gz", "data": []}

ocr-service-v1/ocr-service-server-v1/src/test/resources/files/InvisibleTextWStar1.IMAGE_INFO.json

@@ -0,0 +1 @@
+{"dossierId": "55547c91-6b0e-4aa6-9009-2e7c4cd90f13", "fileId": "917b9d9c9f548f85fef3679db45ff46c", "targetFileExtension": "ORIGIN.pdf.gz", "responseFileExtension": "IMAGE_INFO.json.gz", "data": []}

ocr-service-v1/ocr-service-server-v1/src/test/resources/files/MediaBoxBiggerThanCropBox.IMAGE_INFO.json

@@ -0,0 +1 @@
+{"dossierId": "55547c91-6b0e-4aa6-9009-2e7c4cd90f13", "fileId": "d7f1e0e37cba4e28ebdf894a79d3bd67", "targetFileExtension": "ORIGIN.pdf.gz", "responseFileExtension": "IMAGE_INFO.json.gz", "data": [{"classification": {"label": "signature", "probabilities": {"signature": 0.9872, "logo": 0.0064, "other": 0.0063, "formula": 0.0001}}, "representation": "FFFCF10608F6F89747BFFC301", "position": {"x1": -9, "x2": 584, "y1": 9, "y2": 849, "pageNumber": 1}, "geometry": {"width": 593, "height": 840}, "alpha": false, "filters": {"geometry": {"imageSize": {"quotient": 0.9992, "tooLarge": true, "tooSmall": false}, "imageFormat": {"quotient": 0.706, "tooTall": false, "tooWide": false}}, "probability": {"unconfident": false}, "allPassed": false}}], "dataCV": []}

ocr-service-v1/ocr-service-server-v1/src/test/resources/files/PathOperatorDebugFile.IMAGE_INFO.json

@@ -0,0 +1 @@
+{"dossierId": "55547c91-6b0e-4aa6-9009-2e7c4cd90f13", "fileId": "917b9d9c9f548f85fef3679db45ff46c", "targetFileExtension": "ORIGIN.pdf.gz", "responseFileExtension": "IMAGE_INFO.json.gz", "data": []}

ocr-service-v1/ocr-service-server-v1/src/test/resources/files/PathOperatorDebugFileText.IMAGE_INFO.json

@@ -0,0 +1 @@
+{"dossierId": "55547c91-6b0e-4aa6-9009-2e7c4cd90f13", "fileId": "917b9d9c9f548f85fef3679db45ff46c", "targetFileExtension": "ORIGIN.pdf.gz", "responseFileExtension": "IMAGE_INFO.json.gz", "data": []}

ocr-service-v1/ocr-service-server-v1/src/test/resources/files/Watermark.IMAGE_INFO.json

@@ -0,0 +1 @@
+{"dossierId": "55547c91-6b0e-4aa6-9009-2e7c4cd90f13", "fileId": "32b19ec38896f5105c09041def470c90", "targetFileExtension": "ORIGIN.pdf.gz", "responseFileExtension": "IMAGE_INFO.json.gz", "data": [{"classification": {"label": "logo", "probabilities": {"logo": 0.9999, "signature": 0.0001, "formula": 0.0, "other": 0.0}}, "representation": "307EF8F6E9833CE9D7AF9EFFF", "position": {"x1": 26, "x2": 586, "y1": -2, "y2": 794, "pageNumber": 1}, "geometry": {"width": 560, "height": 796}, "alpha": false, "filters": {"geometry": {"imageSize": {"quotient": 0.959, "tooLarge": true, "tooSmall": false}, "imageFormat": {"quotient": 0.7035, "tooTall": false, "tooWide": false}}, "probability": {"unconfident": false}, "allPassed": false}}, {"classification": {"label": "logo", "probabilities": {"logo": 1.0, "formula": 0.0, "other": 0.0, "signature": 0.0}}, "representation": "FFF7FFD2000000018F3FFEFFF", "position": {"x1": 90, "x2": 210, "y1": 676, "y2": 720, "pageNumber": 1}, "geometry": {"width": 120, "height": 44}, "alpha": false, "filters": {"geometry": {"imageSize": {"quotient": 0.1044, "tooLarge": false, "tooSmall": false}, "imageFormat": {"quotient": 2.7273, "tooTall": false, "tooWide": false}}, "probability": {"unconfident": false}, "allPassed": true}}], "dataCV": []}

ocr-service-v1/ocr-service-server-v1/src/test/resources/files/abc

@@ -0,0 +1,235 @@
+
+0 TL
+q
+    q
+        150 0 m
+        400 0 l
+        400 300 l
+        150 300 l
+        h
+        58 50 m
+        58 200 l
+        570 200 l
+        570 50 l
+        F
+        W
+        n
+        BT
+        -0.011 Tc
+        0 Tw
+        100 Tz
+        /C2_0 12 Tf
+        0 Tr
+        0 Ts
+        485.52 66.48 Td
+        (\0003\000D\000J\000H\000\003) Tj
+        0 Tc
+        26.4 0 Td
+        (\000\024) Tj
+        0.24 Tc
+        8.88 0 Td
+        (\000R\000I) Tj
+        0 Tc
+        9.84 0 Td
+        [(\000\003)-10(\000\030)] TJ
+        0.078 Tc
+        -440.88 -27.6 Td
+        (\0006\000W\000X\000G\000\\) Tj
+        -0.007 Tc
+        30.96 0 Td
+        (\0001\000X\000P\000E\000H\000U\000\035\000\003\000\003) Tj
+        -0.014 Tc
+        48.72 0 Td
+        (\0007\0000\0005\000\023\000\024\000\027\000\025) Tj
+        ET
+        q
+            154.32 0 0 76.32 385.68 643.68 cm
+            /Im0 Do
+        Q
+        BT
+        0.013 Tc
+        /C2_1 12 Tf
+        288.96 601.44 Td
+        (\0006\000X\000E\000V\000W\000D\000Q\000F\000H) Tj
+        0 Tc
+        -168.24 -27.6 Td
+        [(\0006\000<\0001\000\030\000\027\000\031\000\026\000\026\000\023\000\003)-10(\000\261)] TJ
+        ET
+        q
+            192.96 584.88 317.52 -13.92  re
+            W
+            n
+            BT
+            -0.006 Tc
+            192.96 573.84 Td
+            (\0007\000R\000[\000L\000F\000L\000W\000\\\000\003\0006\000W\000X\000G\000\\\000\003\000E\000\\\000\003\000'\000H\000U\000P\000D\000O\000\003\000$\000G\000P\000L\000Q\000L\000V\000W\000U\000D\000W\000L\000R\000Q\000\003\000W\000R\000\003\000+\000D\000Q\000\003\000:\000L\000V\000W\000D\000U\000\003\0005\000D\000W\000V\000\003) Tj
+            ET
+        Q
+        BT
+        -0.024 Tc
+        284.4 560.16 Td
+        (\000I\000R\000U\000\003\000\027\000\003\000:\000H\000H\000N\000V) Tj
+        -0.011 Tc
+        -14.4 -27.6 Td
+        (\0003\000D\000W\000K\000R\000O\000R\000J\000\\\000\003\0005\000H\000S\000R\000U\000W) Tj
+        ET
+        117.12 630 0.72 -3.6  re
+        f*
+        117.12 630 2.16 -0.72  re
+        f*
+        118.56 628.56 0.72 -2.16  re
+        f*
+        118.56 628.56 0.72 -0.72  re
+        f*
+        119.28 630 390.96 -0.72  re
+        f*
+        119.28 628.56 390.96 -0.72  re
+        f*
+        511.68 630 0.72 -3.6  re
+        f*
+        510.24 630 2.16 -0.72  re
+        f*
+        510.24 628.56 0.72 -2.16  re
+        f*
+        510.24 628.56 0.72 -0.72  re
+        f*
+        118.56 626.4 0.72 -111.84  re
+        f*
+        117.12 626.4 0.72 -111.84  re
+        f*
+        117.12 514.56 0.72 -2.16  re
+        f*
+        117.12 513.12 2.16 -0.72  re
+        f*
+        118.56 514.56 0.72 -0.72  re
+        f*
+        118.56 514.56 0.72 -0.72  re
+        f*
+        119.28 513.12 390.96 -0.72  re
+        f*
+        119.28 514.56 390.96 -0.72  re
+        f*
+        511.68 626.4 0.72 -111.84  re
+        f*
+        510.24 626.4 0.72 -111.84  re
+        f*
+        511.68 514.56 0.72 -2.16  re
+        f*
+        510.24 513.12 2.16 -0.72  re
+        f*
+        510.24 514.56 0.72 -0.72  re
+        f*
+        510.24 514.56 0.72 -0.72  re
+        f*
+        BT
+        0.011 Tc
+        89.76 266.64 Td
+        (\000$\0008\0007\000+\0002\0005\000\013\0006\000\f\000\035) Tj
+        -0.012 Tc
+        /C2_0 12 Tf
+        184.8 0.24 Td
+        (\0000\000L\000F\000K\000H\000O\000D\000\003\000*\000U\000H\000J\000R\000U\000L\000\003) Tj
+        -0.037 Tc
+        82.56 0 Td
+        (\000'\0009\0000\000\003\0003\000K\000'\000\003) Tj
+        0.101 Tc
+        55.2 0 Td
+        (\0003\000D\000W\000K\000R\000O) Tj
+        -0.02 Tc
+        30.72 0 Td
+        (\000R\000J\000L\000V\000W) Tj
+        -0.01 Tc
+        /C2_1 12 Tf
+        -353.28 -27.84 Td
+        (\000&\0002\0000\0003\000/\000\(\0007\000,\0002\0001\000\003\000'\000$\0007\000\(\000\035) Tj
+        -0.009 Tc
+        /C2_0 12 Tf
+        184.8 0.24 Td
+        (\000\023\000\030\000\003\0000\000D\000U\000F\000K\000\003\000\025\000\023\000\024\000\033) Tj
+        /C2_1 12 Tf
+        -184.8 -27.84 Td
+        (\000/\000$\000%\0002\0005\000$\0007\0002\0005\000<\000\003\0003\0005\0002\000-\000\(\000&\0007\000\003\000,) Tj
+        -0.026 Tc
+        152.4 0 Td
+        (\000'\000\035) Tj
+        0.009 Tc
+        /C2_0 12 Tf
+        32.4 0.24 Td
+        (\0005\000H\000S\000R\000U\000W\000\003\0001\000X\000P\000E) Tj
+        0.021 Tc
+        65.52 0 Td
+        (\000H\000U\000\035\000\003) Tj
+        -0.014 Tc
+        15.84 0 Td
+        (\0007\0000\0005\000\023\000\024\000\027\000\025) Tj
+        0.078 Tc
+        -81.36 -13.68 Td
+        (\0006\000W\000X\000G\000\\) Tj
+        -0.011 Tc
+        27.84 0 Td
+        (\000\003\0001\000X\000P\000E\000H\000U\000\035) Tj
+        -0.014 Tc
+        48.72 0 Td
+        (\0007\0000\0005\000\023\000\024\000\027\000\025) Tj
+        -0.008 Tc
+        -76.56 -13.92 Td
+        (\0007\000D\000V\000N\000\003\0001\000X\000P\000E\000H\000U\000\035\000\003) Tj
+        -0.019 Tc
+        72 0 Td
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+        0 Tc
+        /C2_1 12 Tf
+        -256.8 -27.84 Td
+        [(\0009\0002\000/\0008\0000\000\(\000\003)-10(\000\024)] TJ
+        -0.052 Tc
+        66.24 0 Td
+        (\0002\000\)\000\003) Tj
+        0 Tc
+        19.68 0 Td
+        (\000\024) Tj
+        -0.01 Tc
+        8.88 0 Td
+        (\0002\000\)\000\003\0006\0007\0008\000'\000<) Tj
+        ET
+        146.88 155.04 6 -1.2  re
+        f*
+        175.68 155.04 5.76 -1.2  re
+        f*
+        BT
+        -0.053 Tc
+        89.76 142.56 Td
+        (\0003\000$\000*\000\(\000\003) Tj
+        0 Tc
+        36.24 0 Td
+        (\000\024) Tj
+        -0.052 Tc
+        9.12 0 Td
+        (\0002\000\)\000\003) Tj
+        0 Tc
+        19.68 0 Td
+        (\000\030) Tj
+        ET
+        126 141.36 6 -1.2  re
+        f*
+        154.8 141.36 6 -1.2  re
+        f*
+        /Artifact <</Subtype/Watermark/Type/Pagination>> BDC
+        q
+            /G0 gs
+            0.940613 0 0 0.940613 26.0628 0 cm
+            0 0 0 RG
+            0 w
+            /Fm0 Do
+        Q
+        EMC
+        /Artifact <</Contents( Page 250 of 256)/Subtype/Header/Type/Pagination>> BDC
+        q
+            /G0 gs
+            1 0 0 1 458.67 48.412 cm
+            0 0 0 RG
+            0 w
+            /Fm1 Do
+        Q
+        EMC
+    Q
+Q

ocr-service-v1/ocr-service-server-v1/src/test/resources/log4j2-test.xml

@@ -1,16 +0,0 @@
-<Configuration>
-
-    <Appenders>
-        <Console name="CONSOLE" target="SYSTEM_OUT">
-            <PatternLayout pattern="%d{HH:mm:ss.SSS} [%t] %-5level %logger{36} - %msg%n"/>
-        </Console>
-    </Appenders>
-
-    <Loggers>
-        <Root level="warn">
-            <AppenderRef ref="CONSOLE"/>
-        </Root>
-        <Logger name="com.iqser" level="info"/>
-    </Loggers>
-
-</Configuration>

ocr-service-v1/pom.xml

@@ -7,7 +7,7 @@
     <parent>
         <groupId>com.iqser.red</groupId>
         <artifactId>platform-dependency</artifactId>
-        <version>1.16.0</version>
+        <version>1.14.0</version>
         <relativePath/>
     </parent>