RED-9746: Document hardly editable

* revert quadtree lookup, since the lib does not seem to work reliably, also, no significant speed boost
* check each individual glyph instead of only a text run and remember past overlaps in glyph
* added logic to extract all glyphs exactly
* check for optional content or transparency in form objects and marked content

src/main/java/com/iqser/red/pdftronlogic/commons/InvisibleElementRemovalService.java

@@ -4,10 +4,8 @@ import static com.iqser.red.pdftronlogic.commons.VisualizationUtils.drawFeature;
 import static com.iqser.red.pdftronlogic.commons.VisualizationUtils.drawRect;
 
 import java.awt.Color;
-import java.awt.Shape;
 import java.awt.geom.Area;
 import java.awt.geom.GeneralPath;
-import java.awt.geom.Rectangle2D;
 import java.io.InputStream;
 import java.io.OutputStream;
 import java.util.ArrayList;
@@ -19,26 +17,21 @@ import java.util.TreeSet;
 
 import com.iqser.red.pdftronlogic.commons.features.ElementFeatureFactory;
 import com.iqser.red.pdftronlogic.commons.features.ElementFeatures;
-import com.iqser.red.pdftronlogic.commons.features.GlyphInfo;
 import com.iqser.red.pdftronlogic.commons.features.ImageFeatures;
 import com.iqser.red.pdftronlogic.commons.features.PathFeatures;
-import com.iqser.red.pdftronlogic.commons.features.TextFeatures;
 import com.iqser.red.pdftronlogic.commons.lookup.ElementFeatureLookup;
 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.Image;
 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.pdf.ocg.Group;
 import com.pdftron.sdf.Obj;
 import com.pdftron.sdf.SDFDoc;
 
@@ -254,7 +247,11 @@ public class InvisibleElementRemovalService {
             boolean inClippingPath = context.clippingPathStack().almostIntersects(rect.getX1(), rect.getY1(), rect.getWidth(), rect.getHeight());
             if (inClippingPath) {
                 ImageFeatures imageFeatures = ElementFeatureFactory.buildImage(imageElement);
-                if (!(context.markedContentStack.contextHasTransparency() || imageFeatures.isTransparent() || imageFeatures.isImageMask() || imageFeatures.isSoftMask())) {
+                if (!(context.markedContentStack.contextHasTransparency()
+                      || imageFeatures.isTransparent()
+                      || imageFeatures.isImageMask()
+                      || imageFeatures.isSoftMask()
+                      || imageFeatures.isMasked())) {
                     calculateOverlaps(context, imageFeatures);
                 }
                 context.visibleElements().add(imageFeatures);

src/main/java/com/iqser/red/pdftronlogic/commons/features/ElementFeatureFactory.java

@@ -13,6 +13,7 @@ import com.pdftron.pdf.CharIterator;
 import com.pdftron.pdf.Element;
 import com.pdftron.pdf.Font;
 import com.pdftron.pdf.GState;
+import com.pdftron.pdf.Image;
 import com.pdftron.pdf.PathData;
 
 import lombok.SneakyThrows;
@@ -61,10 +62,21 @@ public class ElementFeatureFactory {
 
     private ImageFeatures.ImageFeaturesBuilder<?, ?> buildImageBase(Element element) throws PDFNetException {
 
+        assert element.getType() == Element.e_image || element.getType() == Element.e_inline_image;
         try (var bbox = element.getBBox();) {
             boolean transparent = element.getGState().getBlendMode() != GState.e_bl_normal
                                   || element.getGState().getFillOpacity() > 1
                                   || element.getGState().getStrokeOpacity() > 1;
+
+            // see spec: 8.9.6.3 Explicit masking
+            boolean masked = false;
+            if (element.getType() == Element.e_image) {
+                Image image = new Image(element.getXObject());
+                if (image.getMask() != null) {
+                    Image imageMask = new Image(image.getMask());
+                    masked = imageMask.isImageMask();
+                }
+            }
             return ImageFeatures.builder()
                     .elementType(element.getType())
                     .boundingBox(Converter.toRectangle2D(bbox))
@@ -76,6 +88,7 @@ public class ElementFeatureFactory {
                     .bitsPerComponent(element.getBitsPerComponent())
                     .imageMask(element.isImageMask())
                     .softMask(element.getGState().getSoftMask() != null)
+                    .masked(masked)
                     .transparent(transparent);
         }
     }

src/main/java/com/iqser/red/pdftronlogic/commons/features/ImageFeatures.java

@@ -21,6 +21,7 @@ public class ImageFeatures extends ElementFeatures {
     int bitsPerComponent;
     boolean imageMask;
     boolean softMask;
+    boolean masked;
     boolean transparent;
     String hashOfImage;
 

src/test/java/com/iqser/red/pdftronlogic/commons/VisualEqualityTest.java

@@ -1,12 +1,13 @@
 package com.iqser.red.pdftronlogic.commons;
 
+import java.awt.geom.Rectangle2D;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
-import java.nio.IntBuffer;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.StandardCopyOption;
+import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.LinkedList;
 import java.util.List;
@@ -20,10 +21,18 @@ import org.junit.jupiter.api.Test;
 
 import com.iqser.red.pdftronlogic.commons.rendering.GhostScriptService;
 import com.iqser.red.pdftronlogic.commons.rendering.ImageFile;
+import com.pdftron.pdf.PDFDoc;
 import com.pdftron.pdf.PDFNet;
+import com.pdftron.sdf.SDFDoc;
+import com.sun.jna.Memory;
+import com.sun.jna.Native;
 import com.sun.jna.NativeLibrary;
+import com.sun.jna.Pointer;
+import com.sun.jna.ptr.PointerByReference;
 
 import lombok.SneakyThrows;
+import net.sourceforge.lept4j.Box;
+import net.sourceforge.lept4j.Boxa;
 import net.sourceforge.lept4j.Leptonica1;
 import net.sourceforge.lept4j.Pix;
 import net.sourceforge.lept4j.util.LeptUtils;
@@ -31,11 +40,22 @@ import net.sourceforge.lept4j.util.LeptUtils;
 @Disabled // requires leptonica and ghostscript to be installed locally
 public class VisualEqualityTest {
 
-    public static final double SIMILARITY_THRESHOLD = 0.015; // percentage of pixels which differ by more than 10 points in luminance
+    /*
-    public static final String LEPTONICA_DIR = "/home/kschuettler/software/leptonica/vcpkg/installed/x64-linux-dynamic/lib/";
+    We render both the origin and the processed file and then computes a diff per page, we then threshold and invert the diff.
+    This means, a visual difference of luminance greater than the threshold value shows up as a black pixel.
+    We then use Heckbert's Seed Fill Algorithm to detect connected black regions by recursively flooding connected pixels.
+    We then filter these error regions, ensuring their area is at least the threshold.
+    We do this, since single pixel errors are frequent, but cannot be perceived by a human. Most likely some float inaccuracies.
+    If there are any error regions left, we count the test as failed.
+     */
+    private static final int ERROR_REGION_AREA_THRESHOLD = 10;
+    public static final int LUMINANCE_DIFFERENCE_THRESHOLD = 170;
+
+    private static final Path TEST_OUTPUT_DIR = Path.of("/tmp/AAA_EQUALITY_TEST/");
+    private static final String LEPTONICA_DIR = "/home/kschuettler/software/leptonica/vcpkg/installed/x64-linux-dynamic/lib/";
+
     GhostScriptService ghostScriptService = new GhostScriptService();
     InvisibleElementRemovalService invisibleElementRemovalService = new InvisibleElementRemovalService();
-    Path TEST_OUTPUT_DIR = Path.of("/tmp/AAA_EQUALITY_TEST/");
 
 
     @BeforeEach
@@ -54,20 +74,22 @@ public class VisualEqualityTest {
     @SneakyThrows
     public void assertVisualEqualityOfProcessedFile() {
 
-        Path file = Path.of("/home/kschuettler/Dokumente/TestFiles/syn-dm-testfiles/SOLICITA_VICTRATO-GOLD-II_Item 20_Sensibilizacao_02.pdf");
+        Path file = Path.of("/home/kschuettler/Dokumente/TestFiles/full_syn_dm_testfiles/3977411_Final_Thiamethoxam_SL_MNLY.pdf");
         Context context = new Context(TEST_OUTPUT_DIR, new HashMap<>());
 
         runForFile(file, context);
 
+        System.out.println(context);
 
         assert context.failedFiles.isEmpty();
     }
 
+
     @Test
     @SneakyThrows
     public void assertVisualEqualityOfProcessedFolder() {
 
-        Path folder = Path.of("/home/kschuettler/Dokumente/TestFiles/syn-dm-testfiles");
+        Path folder = Path.of("/home/kschuettler/Dokumente/TestFiles/full_syn_dm_testfiles");
         Context context = new Context(TEST_OUTPUT_DIR, new HashMap<>());
 
         Files.walk(folder)
@@ -78,7 +100,6 @@ public class VisualEqualityTest {
                 .peek(file -> runForFile(file, context))
                 .forEach(f -> System.out.println(context));
 
-
         assert context.failedFiles.isEmpty();
     }
 
@@ -91,17 +112,20 @@ public class VisualEqualityTest {
         Files.createDirectories(fileFolder);
         Path processedFile = fileFolder.resolve("processed.pdf");
         Path deltaFile = fileFolder.resolve("delta.pdf");
-        Path copiedOriginFile = fileFolder.resolve("origin.pdf");
+        Path savedOriginFile = fileFolder.resolve("origin.pdf");
-        Files.copy(originFile, copiedOriginFile, StandardCopyOption.REPLACE_EXISTING);
+        try (var in = new FileInputStream(originFile.toFile()); var out = new FileOutputStream(savedOriginFile.toFile())) {
+            PDFDoc pdfDoc = new PDFDoc(in);
+            pdfDoc.save(out, SDFDoc.SaveMode.LINEARIZED, null);
+        }
 
-        try (var in = new FileInputStream(copiedOriginFile.toFile()); var out = new FileOutputStream(processedFile.toFile())) {
+        try (var in = new FileInputStream(originFile.toFile()); var out = new FileOutputStream(processedFile.toFile())) {
             invisibleElementRemovalService.removeInvisibleElements(in, out, false);
         }
-        try (var in = new FileInputStream(copiedOriginFile.toFile()); var out = new FileOutputStream(deltaFile.toFile())) {
+        try (var in = new FileInputStream(originFile.toFile()); var out = new FileOutputStream(deltaFile.toFile())) {
             invisibleElementRemovalService.removeInvisibleElements(in, out, true);
         }
         System.out.println("removed invisible elements");
-        assertVisualEquality(originFile, processedFile, context);
+        assertVisualEquality(savedOriginFile, processedFile, context);
         System.out.println("finished visual equality check");
     }
 
@@ -147,10 +171,10 @@ public class VisualEqualityTest {
             }
 
             String errorFile = context.getErrorFolder(originFile).resolve(originalPage.pageNumber() + ".tiff").toFile().toString();
-            double diffRatio = detectErrors(originalPagePix, processedPagePix, errorFile);
+            List<Rectangle2D> errorRegions = detectErrors(originalPagePix, processedPagePix, errorFile);
 
-            if (diffRatio > SIMILARITY_THRESHOLD) {
+            if (!errorRegions.isEmpty()) {
-                context.getFailedFile(originFile).addErrorMessage("Page " + originalPage.pageNumber() + " differs by " + formatPercentage(diffRatio) + "%!");
+                context.getFailedFile(originFile).addErrorMessage("Page " + originalPage.pageNumber() + " has " + errorRegions.size() + " errors!");
             }
 
             synchronized (VisualEqualityTest.class) {
@@ -161,37 +185,66 @@ public class VisualEqualityTest {
     }
 
 
-    private static String formatPercentage(double diffRatio) {
+    synchronized public List<Rectangle2D> detectErrors(Pix pix1, Pix pix2, String errorFile) {
 
-        return String.format("%.2f", diffRatio * 100);
-    }
-
-
-    public double detectErrors(Pix pix1, Pix pix2, String errorFile) {
-        // First, check if dimensions are the same
-        if (pix1.w != pix2.w || pix1.h != pix2.h || pix1.d != pix2.d) {
-            return 1;
-        }
-
-        // Create a new Pix for the absolute difference
         Pix pixDiff = Leptonica1.pixAbsDifference(pix1, pix2);
 
-        // Set a threshold for pixel difference (e.g., 10 out of 255)
+        Pix pixThresh = Leptonica1.pixThresholdToBinary(pixDiff, LUMINANCE_DIFFERENCE_THRESHOLD);
-        int threshold = 10;
+        Leptonica1.pixInvert(pixThresh, pixThresh);
-        Pix pixThresh = Leptonica1.pixThresholdToBinary(pixDiff, threshold);
+        // checks for connected black regions and outputs them as a list of boxes, a boxa
+        Boxa boxa = Leptonica1.pixConnComp(pixThresh, null, 8);
 
-        IntBuffer pCount = IntBuffer.allocate(1);
+        List<Rectangle2D> errorRegions = readRectsFromBoxa(boxa).stream()
-        Leptonica1.pixCountPixels(pixThresh, pCount, null);
+                .filter(box -> box.getWidth() * box.getHeight() >= ERROR_REGION_AREA_THRESHOLD)
-        long totalPixels = (long) pix1.w * pix1.h;
+                .toList();
-        long samePixels = pCount.get();
+
-        double percentDifference = 1 - (double) samePixels / totalPixels;
+        if (!errorRegions.isEmpty()) {
-        if (percentDifference > SIMILARITY_THRESHOLD) {
+            System.out.println("Found error(s) on page " + Path.of(errorFile).getFileName().toString().replace(".tiff", "") + ", writing error file.");
-            Leptonica1.pixWrite(errorFile, pixThresh, 5);
+//            Boxa errorRegionsBoxa = pushRectsIntoBoxa(errorRegions); // this does not work
+//            Pix errorPix = Leptonica1.pixDrawBoxa(pixThresh, errorRegionsBoxa, 2, -1); // somehow this runs forever
+            Leptonica1.pixWrite(errorFile, pixThresh, 4);
+//            LeptUtils.disposePix(errorPix);
+//            LeptUtils.dispose(errorRegionsBoxa);
         }
 
+        LeptUtils.dispose(boxa);
         LeptUtils.disposePix(pixDiff);
         LeptUtils.disposePix(pixThresh);
-        return percentDifference;
+        return errorRegions;
+    }
+
+
+    private static List<Rectangle2D> readRectsFromBoxa(Boxa boxa) {
+
+        Pointer[] pointers = boxa.box.getPointer().getPointerArray(0, boxa.n);
+        List<Rectangle2D> boxes = new ArrayList<>(boxa.n);
+        for (int i = 0; i < boxa.n; i++) {
+            Box box = new Box(pointers[i]);
+            boxes.add(new Rectangle2D.Double(box.x, box.y, box.w, box.h));
+            LeptUtils.dispose(box);
+        }
+        return boxes;
+    }
+
+
+    private static Boxa pushRectsIntoBoxa(List<Rectangle2D> rects) {
+
+        Boxa boxa = new Boxa();
+        boxa.n = rects.size();
+        boxa.nalloc = rects.size();
+
+        Memory boxMemory = new Memory((long) Native.POINTER_SIZE * rects.size());
+
+        for (int i = 0; i < rects.size(); i++) {
+            Rectangle2D rect = rects.get(i);
+            Box box = new Box((int) rect.getX(), (int) rect.getY(), (int) rect.getWidth(), (int) rect.getHeight(), 0);
+
+            boxMemory.setPointer((long) i * Native.POINTER_SIZE, box.getPointer());
+        }
+
+        boxa.box = new PointerByReference(boxMemory);
+
+        return boxa;
     }
 
 

src/test/java/com/iqser/red/pdftronlogic/commons/rendering/GhostScriptService.java

@@ -30,7 +30,7 @@ public class GhostScriptService {
     int BATCH_SIZE = 256;
     String FORMAT = ".tiff";
     String DEVICE = "tiffgray";
-    int DPI = 125;
+    int DPI = 100;
     int PROCESS_COUNT = 1;