RED-6019: Remove hidden text when processing OCR

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 same color as background
     Any Text set to clipping with its many interactions with other elements

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

@@ -0,0 +1,54 @@
+package com.iqser.red.service.ocr.v1.server.model;
+
+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;
+
+@Data
+public class ClippingPathStack {
+
+    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) {
+        // Height or width are zero for straight lines, even though they are being rendered. Therefore, height or width must be at minimum >0.
+        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

@@ -0,0 +1,148 @@
+package com.iqser.red.service.ocr.v1.server.model;
+
+import com.pdftron.common.PDFNetException;
+import com.pdftron.pdf.Element;
+import com.pdftron.pdf.Rect;
+import lombok.*;
+import lombok.experimental.SuperBuilder;
+
+import java.awt.geom.Rectangle2D;
+
+@Data
+@SuperBuilder
+@NoArgsConstructor
+@AllArgsConstructor
+public abstract class ElementFeatures {
+    private int elementType;
+    private Rectangle2D boundingBox;
+
+    public boolean almostMatches(Element element) throws PDFNetException {
+        if (element.getType() != elementType) return false;
+        if (element.getBBox() == null) return false;
+        return rectsAlmostMatch(element.getBBox());
+    }
+
+    protected boolean almostEqual(double a, double b) {
+        double tolerance = 1e-3;
+        return Math.abs(a - b) < tolerance;
+    }
+
+    @SneakyThrows
+    private boolean rectsAlmostMatch(Rect bBox) {
+        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)
+    @Data
+    @SuperBuilder
+    @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 {
+            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)
+    @Data
+    @SuperBuilder
+    @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 true;
+        }
+    }
+
+    @EqualsAndHashCode(callSuper = true)
+    @Data
+    @SuperBuilder
+    @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 {
+            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 {
+        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/InvisibleElementService.java

@@ -0,0 +1,448 @@
+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.springframework.stereotype.Service;
+
+import java.awt.*;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.Rectangle2D;
+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 which is transparent or is set to not render
+            Text or Path or Images outside of clipping path
+            Text or Path or Images 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[] removeInvisibleElements(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);
+        }
+
+        return pdfDoc.save(SDFDoc.SaveMode.REMOVE_UNUSED, 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;
+    }
+
+
+    @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

@@ -1,49 +1,26 @@
 package com.iqser.red.service.ocr.v1.server.service;
 
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.InputStream;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeSet;
-
-import org.apache.commons.io.IOUtils;
-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.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.common.PDFNetException;
-import com.pdftron.pdf.Element;
-import com.pdftron.pdf.ElementReader;
-import com.pdftron.pdf.ElementWriter;
-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.PageIterator;
-import com.pdftron.pdf.Rect;
-import com.pdftron.pdf.RectCollection;
-import com.pdftron.sdf.Obj;
+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
@@ -59,36 +36,33 @@ public class OCRService {
 
     private final ObjectMapper objectMapper;
 
+    private final InvisibleElementService invisibleElementService;
+
 
-    @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);
+        byte[] fileWithoutInvisibleTextBytes = invisibleElementService.removeInvisibleElements(fileBytes, false);
+
+        var ocrBytes = ocr(fileWithoutInvisibleTextBytes, fileId, imageServiceResponse);
 
         return new ByteArrayInputStream(ocrBytes);
 
     }
 
 
-    @SuppressFBWarnings("REC_CATCH_EXCEPTION")
     private byte[] ocr(byte[] file, String fileId, ImageServiceResponse imageServiceResponse) {
-
         PDFDoc pdfDoc = null;
         try (ByteArrayOutputStream out = new ByteArrayOutputStream()) {
             pdfDoc = new PDFDoc(file);
-            removeInvisibleText(pdfDoc);
 
             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()),
@@ -103,18 +77,6 @@ public class OCRService {
 
             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();
-            }
-
             Optimizer.optimize(pdfDoc);
             pdfDoc.save(out, SDFDoc.SaveMode.LINEARIZED, null);
             pdfDoc.close();
@@ -178,7 +140,7 @@ public class OCRService {
                 rectCollection.clear();
 
             } catch (Exception e) {
-                log.warn("Failed to process PDF page {} - {}", pageEntry.getKey(), e);
+                log.warn("Failed to process PDF page {}", pageEntry.getKey());
             }
 
             rabbitTemplate.convertAndSend(MessagingConfiguration.OCR_STATUS_UPDATE_RESPONSE_QUEUE,
@@ -192,134 +154,4 @@ public class OCRService {
 
         }
     }
-
-
-    /**
-     * There are 2 possibilities to have invisible Text in pdfs.
-     * 1. gState is set to invisible, this is ocr text.
-     * 2. Filled Path elements in front of the text.
-     */
-    @SneakyThrows
-    private void removeInvisibleText(PDFDoc pdfDoc) {
-
-        ElementWriter writer = new ElementWriter();
-        ElementReader reader = new ElementReader();
-        Set<Integer> visited = new TreeSet<>();
-
-        for (PageIterator iterator = pdfDoc.getPageIterator(); iterator.hasNext(); ) {
-            Page page = iterator.next();
-            removeOverlapText(page, reader, writer, visited);
-        }
-    }
-
-
-    @SneakyThrows
-    private void removeOverlapText(Page page, ElementReader reader, ElementWriter writer, Set<Integer> visited) {
-
-        visited.add((int) page.getSDFObj().getObjNum());
-        reader.begin(page);
-        writer.begin(page, ElementWriter.e_replacement, false, true, page.getResourceDict());
-        processElements(reader, writer, visited, false);
-        writer.end();
-        reader.end();
-    }
-
-
-    @SneakyThrows
-    private void processElements(ElementReader reader, ElementWriter writer, Set<Integer> visited, boolean isInForm) {
-
-        Set<Rect> filledRectangles = new HashSet<>();
-        for (Element element = reader.next(); element != null; element = reader.next())
-
-            switch (element.getType()) {
-                case Element.e_image:
-                case Element.e_inline_image:
-                    processImage(element, writer, isInForm);
-                    break;
-
-                case Element.e_text:
-                    processText(element, writer, filledRectangles);
-                    break;
-
-                case Element.e_path:
-                    processPath(element, writer, filledRectangles);
-                    break;
-
-                case Element.e_form:
-                    processForm(reader, writer, element, visited);
-                    break;
-
-                default:
-                    writer.writeElement(element);
-            }
-    }
-
-
-    @SneakyThrows
-    private void processImage(Element element, ElementWriter writer, boolean isInForm) {
-
-        if (!isInForm || !settings.isRemoveWatermark()) {
-            writer.writeElement(element);
-        }
-    }
-
-
-    @SneakyThrows
-    private void processText(Element element, ElementWriter writer, Set<Rect> filledRectangles) {
-
-        if (element.getBBox() == null) {
-            writer.writeElement(element);
-            return;
-        }
-
-        double x = element.getBBox().getX1();
-        double y = element.getBBox().getY1();
-        boolean filledRectangleIntersection = filledRectangles.stream().anyMatch(r -> {
-            try {
-                return r.contains(x, y);
-            } catch (PDFNetException e) {
-                throw new RuntimeException("Internal pdftron error during removal of overlap text", e);
-            }
-        });
-
-        var gState = element.getGState();
-
-        //See PDF Reference 5.3 Text rendering modes, 3 = Invisible, however this ocr does not use it.
-        if (!filledRectangleIntersection && gState.getTextRenderMode() != 3 || filledRectangleIntersection && gState.getTextRenderMode() == 0) {
-            writer.writeElement(element);
-        }
-    }
-
-
-    @SneakyThrows
-    private void processPath(Element element, ElementWriter writer, Set<Rect> filledRectangles) {
-
-        writer.writeElement(element);
-        if (element.getPathData() != null && element.getPathData().getPoints().length > 4) {
-            filledRectangles.add(element.getBBox());
-        }
-    }
-
-
-    @SneakyThrows
-    private void processForm(ElementReader reader, ElementWriter writer, Element element, Set<Integer> visited) {
-
-        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, true);
-            new_writer.end();
-            reader.end();
-        }
-    }
-
 }

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

@@ -0,0 +1,78 @@
+package com.iqser.red.service.ocr.v1.server;
+
+import com.iqser.red.service.ocr.v1.server.service.InvisibleElementService;
+import com.pdftron.pdf.PDFDoc;
+import com.pdftron.pdf.Page;
+import com.pdftron.pdf.PageIterator;
+import com.pdftron.pdf.TextExtractor;
+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;
+import static org.assertj.core.api.AssertionsForClassTypes.assertThat;
+
+@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.removeInvisibleElements(initialFileBytes, false);
+        var deltaFile = invisibleElementService.removeInvisibleElements(initialFileBytes, true);
+
+        String fileWithoutInvisibleTextLocation = getTemporaryDirectory() + "/" + fileName + ".pdf";
+        String deltaFileLocation = getTemporaryDirectory() + "/" + fileName + "_delta.pdf";
+
+        saveToFile(fileWithoutInvisibleTextLocation, fileWithoutInvisibleText);
+        saveToFile(deltaFileLocation, deltaFile);
+
+        System.out.println("Output File without invisible elements: " + fileWithoutInvisibleTextLocation);
+        System.out.println("Output Delta File: " + deltaFileLocation);
+        TextExtractor extractor = new TextExtractor();
+        PDFDoc pdfDoc = new PDFDoc(fileWithoutInvisibleText);
+        PageIterator iterator = pdfDoc.getPageIterator();
+        while (iterator.hasNext()) {
+            Page page = iterator.next();
+            extractor.begin(page);
+            String[] text = extractor.getAsText().split("\n");
+            assertThat(text).containsAnyOf("APPENDIX 16 Pathology Report", "Amendment 1", "Page 255 of 260");
+        }
+    }
+
+    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/resources/files/ComplexLayeredElements.IMAGE_INFO.json

@@ -0,0 +1 @@
+{"dossierId": "c8553cbd-409f-4e1a-baf4-34b11d49deac", "fileId": "bd6f93ed896dd0e2f641b0568f13ddf1", "targetFileExtension": "ORIGIN.pdf.gz", "responseFileExtension": "IMAGE_INFO.json.gz", "data": [{"classification": {"label": "other", "probabilities": {"other": 0.9999, "logo": 0.0001, "formula": 0.0, "signature": 0.0}}, "representation": "FFFFFEFBF7EFCFFFFFFFFFFFF", "position": {"x1": -3, "x2": 795, "y1": 0, "y2": 612, "pageNumber": 1}, "geometry": {"width": 798, "height": 612}, "alpha": false, "filters": {"geometry": {"imageSize": {"quotient": 1.0038, "tooLarge": true, "tooSmall": false}, "imageFormat": {"quotient": 1.3039, "tooTall": false, "tooWide": false}}, "probability": {"unconfident": false}, "allPassed": false}}, {"classification": {"label": "logo", "probabilities": {"logo": 0.9966, "other": 0.0025, "signature": 0.0005, "formula": 0.0003}}, "representation": "FFC33D3C323CCF3390C1F8C72", "position": {"x1": 120, "x2": 131, "y1": 264, "y2": 380, "pageNumber": 1}, "geometry": {"width": 11, "height": 116}, "alpha": true, "filters": {"geometry": {"imageSize": {"quotient": 0.0513, "tooLarge": false, "tooSmall": false}, "imageFormat": {"quotient": 0.0948, "tooTall": true, "tooWide": false}}, "probability": {"unconfident": false}, "allPassed": false}}, {"classification": {"label": "other", "probabilities": {"other": 1.0, "formula": 0.0, "logo": 0.0, "signature": 0.0}}, "representation": "EF8FF6381060800318F0E187", "position": {"x1": 152, "x2": 205, "y1": 115, "y2": 533, "pageNumber": 1}, "geometry": {"width": 53, "height": 418}, "alpha": true, "filters": {"geometry": {"imageSize": {"quotient": 0.2138, "tooLarge": false, "tooSmall": false}, "imageFormat": {"quotient": 0.1268, "tooTall": false, "tooWide": false}}, "probability": {"unconfident": false}, "allPassed": true}}, {"classification": {"label": "other", "probabilities": {"other": 0.5967, "logo": 0.1756, "signature": 0.1218, "formula": 0.106}}, "representation": "EC9377C9170E1070C3070C30F", "position": {"x1": 196, "x2": 221, "y1": 121, "y2": 245, "pageNumber": 1}, "geometry": {"width": 25, "height": 124}, "alpha": true, "filters": {"geometry": {"imageSize": {"quotient": 0.08, "tooLarge": false, "tooSmall": false}, "imageFormat": {"quotient": 0.2016, "tooTall": false, "tooWide": false}}, "probability": {"unconfident": false}, "allPassed": true}}, {"classification": {"label": "logo", "probabilities": {"logo": 1.0, "formula": 0.0, "other": 0.0, "signature": 0.0}}, "representation": "CF1F1F70F140036860F1441B5", "position": {"x1": 707, "x2": 718, "y1": 481, "y2": 531, "pageNumber": 1}, "geometry": {"width": 11, "height": 50}, "alpha": true, "filters": {"geometry": {"imageSize": {"quotient": 0.0337, "tooLarge": false, "tooSmall": true}, "imageFormat": {"quotient": 0.22, "tooTall": false, "tooWide": false}}, "probability": {"unconfident": false}, "allPassed": false}}, {"classification": {"label": "logo", "probabilities": {"logo": 0.9704, "other": 0.0223, "formula": 0.0044, "signature": 0.0029}}, "representation": "CF0F1C70F1C7090081F7CF073", "position": {"x1": 732, "x2": 744, "y1": 118, "y2": 241, "pageNumber": 1}, "geometry": {"width": 12, "height": 123}, "alpha": true, "filters": {"geometry": {"imageSize": {"quotient": 0.0552, "tooLarge": false, "tooSmall": false}, "imageFormat": {"quotient": 0.0976, "tooTall": true, "tooWide": false}}, "probability": {"unconfident": false}, "allPassed": false}}], "dataCV": []}

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

@@ -0,0 +1 @@
+{"dossierId": "c8553cbd-409f-4e1a-baf4-34b11d49deac", "fileId": "bd6f93ed896dd0e2f641b0568f13ddf1", "targetFileExtension": "ORIGIN.pdf.gz", "responseFileExtension": "IMAGE_INFO.json.gz", "data": [{"classification": {"label": "other", "probabilities": {"other": 0.9999, "logo": 0.0001, "formula": 0.0, "signature": 0.0}}, "representation": "FFFFFEFBF7EFCFFFFFFFFFFFF", "position": {"x1": -3, "x2": 795, "y1": 0, "y2": 612, "pageNumber": 1}, "geometry": {"width": 798, "height": 612}, "alpha": false, "filters": {"geometry": {"imageSize": {"quotient": 1.0038, "tooLarge": true, "tooSmall": false}, "imageFormat": {"quotient": 1.3039, "tooTall": false, "tooWide": false}}, "probability": {"unconfident": false}, "allPassed": false}}, {"classification": {"label": "logo", "probabilities": {"logo": 0.9966, "other": 0.0025, "signature": 0.0005, "formula": 0.0003}}, "representation": "FFC33D3C323CCF3390C1F8C72", "position": {"x1": 120, "x2": 131, "y1": 264, "y2": 380, "pageNumber": 1}, "geometry": {"width": 11, "height": 116}, "alpha": true, "filters": {"geometry": {"imageSize": {"quotient": 0.0513, "tooLarge": false, "tooSmall": false}, "imageFormat": {"quotient": 0.0948, "tooTall": true, "tooWide": false}}, "probability": {"unconfident": false}, "allPassed": false}}, {"classification": {"label": "other", "probabilities": {"other": 1.0, "formula": 0.0, "logo": 0.0, "signature": 0.0}}, "representation": "EF8FF6381060800318F0E187", "position": {"x1": 152, "x2": 205, "y1": 115, "y2": 533, "pageNumber": 1}, "geometry": {"width": 53, "height": 418}, "alpha": true, "filters": {"geometry": {"imageSize": {"quotient": 0.2138, "tooLarge": false, "tooSmall": false}, "imageFormat": {"quotient": 0.1268, "tooTall": false, "tooWide": false}}, "probability": {"unconfident": false}, "allPassed": true}}, {"classification": {"label": "other", "probabilities": {"other": 0.5967, "logo": 0.1756, "signature": 0.1218, "formula": 0.106}}, "representation": "EC9377C9170E1070C3070C30F", "position": {"x1": 196, "x2": 221, "y1": 121, "y2": 245, "pageNumber": 1}, "geometry": {"width": 25, "height": 124}, "alpha": true, "filters": {"geometry": {"imageSize": {"quotient": 0.08, "tooLarge": false, "tooSmall": false}, "imageFormat": {"quotient": 0.2016, "tooTall": false, "tooWide": false}}, "probability": {"unconfident": false}, "allPassed": true}}, {"classification": {"label": "logo", "probabilities": {"logo": 1.0, "formula": 0.0, "other": 0.0, "signature": 0.0}}, "representation": "CF1F1F70F140036860F1441B5", "position": {"x1": 707, "x2": 718, "y1": 481, "y2": 531, "pageNumber": 1}, "geometry": {"width": 11, "height": 50}, "alpha": true, "filters": {"geometry": {"imageSize": {"quotient": 0.0337, "tooLarge": false, "tooSmall": true}, "imageFormat": {"quotient": 0.22, "tooTall": false, "tooWide": false}}, "probability": {"unconfident": false}, "allPassed": false}}, {"classification": {"label": "logo", "probabilities": {"logo": 0.9704, "other": 0.0223, "formula": 0.0044, "signature": 0.0029}}, "representation": "CF0F1C70F1C7090081F7CF073", "position": {"x1": 732, "x2": 744, "y1": 118, "y2": 241, "pageNumber": 1}, "geometry": {"width": 12, "height": 123}, "alpha": true, "filters": {"geometry": {"imageSize": {"quotient": 0.0552, "tooLarge": false, "tooSmall": false}, "imageFormat": {"quotient": 0.0976, "tooTall": true, "tooWide": false}}, "probability": {"unconfident": false}, "allPassed": false}}], "dataCV": []}