Merge pull request #81 from bgilbert/icc

Support reading ICC color profiles

Author: bgilbert

org/openslide/OpenSlide.java

@@ -23,9 +23,17 @@
 package org.openslide;
 
 import java.awt.Color;
+import java.awt.color.ColorSpace;
+import java.awt.color.ICC_ColorSpace;
+import java.awt.color.ICC_Profile;
 import java.awt.Graphics2D;
 import java.awt.image.BufferedImage;
+import java.awt.image.ColorModel;
+import java.awt.image.DataBuffer;
 import java.awt.image.DataBufferInt;
+import java.awt.image.DirectColorModel;
+import java.awt.image.Raster;
+import java.awt.image.WritableRaster;
 import java.io.Closeable;
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -113,6 +121,8 @@ public void close() throws IOException {
 
     final private Map<String, AssociatedImage> associatedImages;
 
+    final private ColorModel colorModel;
+
     final private File canonicalFile;
 
     final private int hashCodeVal;
@@ -178,6 +188,8 @@ public OpenSlide(File file) throws IOException {
 
             associatedImages = Collections.unmodifiableMap(associated);
 
+            colorModel = readColorModel(null);
+
             // store info for hash and equals
             canonicalFile = file.getCanonicalFile();
             String quickhash1 = getProperties().get(PROPERTY_NAME_QUICKHASH1);
@@ -224,6 +236,10 @@ public long getLevelHeight(int level) {
         return levelHeights[level];
     }
 
+    public ColorModel getColorModel() {
+        return colorModel;
+    }
+
     public void paintRegionOfLevel(Graphics2D g, int dx, int dy, int sx,
             int sy, int w, int h, int level) throws IOException {
         paintRegion(g, dx, dy, sx, sy, w, h, levelDownsamples[level]);
@@ -246,6 +262,14 @@ public void paintRegionARGB(int dest[], long x, long y, int level, int w,
         }
     }
 
+    public BufferedImage readRegion(long x, long y, int level, int w, int h)
+            throws IOException {
+        BufferedImage img = createARGBBufferedImage(colorModel, w, h);
+        int data[] = getARGBPixels(img);
+        paintRegionARGB(data, x, y, level, w, h);
+        return img;
+    }
+
     public void paintRegion(Graphics2D g, int dx, int dy, long sx, long sy,
             int w, int h, double downsample) throws IOException {
         if (downsample < 1.0) {
@@ -288,14 +312,7 @@ public void paintRegion(Graphics2D g, int dx, int dy, long sx, long sy,
             return;
         }
 
-        BufferedImage img = new BufferedImage(levelW, levelH,
-                BufferedImage.TYPE_INT_ARGB_PRE);
-
-        int data[] = ((DataBufferInt) img.getRaster().getDataBuffer())
-                .getData();
-
-        paintRegionARGB(data, baseX, baseY, level, img.getWidth(), img
-                .getHeight());
+        BufferedImage img = readRegion(baseX, baseY, level, levelW, levelH);
 
         // g.scale(1.0 / relativeDS, 1.0 / relativeDS);
         g.drawImage(img, dx, dy, w, h, null);
@@ -396,11 +413,10 @@ BufferedImage getAssociatedImage(String name) throws IOException {
             throw new IOException("Failure reading associated image");
         }
 
-        BufferedImage img = new BufferedImage((int) dim[0], (int) dim[1],
-                BufferedImage.TYPE_INT_ARGB_PRE);
-
-        int data[] = ((DataBufferInt) img.getRaster().getDataBuffer())
-                .getData();
+        ColorModel cm = readColorModel(name);
+        BufferedImage img = createARGBBufferedImage(cm, (int) dim[0],
+                (int) dim[1]);
+        int data[] = getARGBPixels(img);
 
         try (errorCtx) {
             OpenSlideFFM.openslide_read_associated_image(errorCtx.getOsr(),
@@ -451,4 +467,57 @@ public boolean equals(Object obj) {
 
         return false;
     }
+
+    private static BufferedImage createARGBBufferedImage(ColorModel cm, int w,
+            int h) {
+        WritableRaster raster = Raster.createWritableRaster(
+                cm.createCompatibleSampleModel(w, h), null);
+        return new BufferedImage(cm, raster, true, null);
+    }
+
+    private static int[] getARGBPixels(BufferedImage img) {
+        DataBufferInt buf = (DataBufferInt) img.getRaster().getDataBuffer();
+        return buf.getData();
+    }
+
+    private ColorModel readColorModel(String associated) throws IOException {
+        ColorSpace space = readColorSpace(associated);
+        return new DirectColorModel(space, 32,
+                0x00ff0000, 0x0000ff00, 0x000000ff, 0xff000000, true,
+                DataBuffer.TYPE_INT);
+    }
+
+    private ColorSpace readColorSpace(String associated) throws IOException {
+        long size;
+        try (errorCtx) {
+            if (associated != null) {
+                size = OpenSlideFFM.openslide_get_associated_image_icc_profile_size(
+                        errorCtx.getOsr(), associated);
+            } else {
+                size = OpenSlideFFM.openslide_get_icc_profile_size(
+                        errorCtx.getOsr());
+            }
+        }
+        if (size <= 0) {
+            return ColorSpace.getInstance(ColorSpace.CS_sRGB);
+        } else if (size > Integer.MAX_VALUE) {
+            throw new IOException("ICC profile too large");
+        }
+
+        byte[] data = new byte[(int) size];
+        try (errorCtx) {
+            if (associated != null) {
+                OpenSlideFFM.openslide_read_associated_image_icc_profile(
+                        errorCtx.getOsr(), associated, data);
+            } else {
+                OpenSlideFFM.openslide_read_icc_profile(errorCtx.getOsr(),
+                        data);
+            }
+        }
+        try {
+            return new ICC_ColorSpace(ICC_Profile.getInstance(data));
+        } catch (IllegalArgumentException ex) {
+            throw new IOException("Invalid ICC profile", ex);
+        }
+    }
 }

org/openslide/OpenSlideFFM.java

@@ -330,6 +330,32 @@ static void openslide_read_region(OpenSlideRef osr, int dest[],
         }
     }
 
+    private static final MethodHandle get_icc_profile_size = function(
+            JAVA_LONG, "openslide_get_icc_profile_size", C_POINTER);
+
+    static long openslide_get_icc_profile_size(OpenSlideRef osr) {
+        try (Ref.ScopedLock l = osr.lock()) {
+            return (long) get_icc_profile_size.invokeExact(osr.getSegment());
+        } catch (Throwable ex) {
+            throw wrapException(ex);
+        }
+    }
+
+    private static final MethodHandle read_icc_profile = function(
+            null, "openslide_read_icc_profile", C_POINTER, C_POINTER);
+
+    static void openslide_read_icc_profile(OpenSlideRef osr, byte dest[]) {
+        try (Arena arena = Arena.ofConfined()) {
+            MemorySegment buf = arena.allocate(JAVA_BYTE, dest.length);
+            try (Ref.ScopedLock l = osr.lock()) {
+                read_icc_profile.invokeExact(osr.getSegment(), buf);
+            } catch (Throwable ex) {
+                throw wrapException(ex);
+            }
+            MemorySegment.copy(buf, JAVA_BYTE, 0, dest, 0, dest.length);
+        }
+    }
+
     private static final MethodHandle get_error = function(
             C_POINTER, "openslide_get_error", C_POINTER);
 
@@ -438,6 +464,44 @@ static void openslide_read_associated_image(OpenSlideRef osr, String name,
         }
     }
 
+    private static final MethodHandle get_associated_image_icc_profile_size = function(
+            JAVA_LONG, "openslide_get_associated_image_icc_profile_size",
+            C_POINTER, C_POINTER);
+
+    static long openslide_get_associated_image_icc_profile_size(
+            OpenSlideRef osr, String name) {
+        if (name == null) {
+            return -1;
+        }
+        try (Arena arena = Arena.ofConfined(); Ref.ScopedLock l = osr.lock()) {
+            return (long) get_associated_image_icc_profile_size.invokeExact(
+                    osr.getSegment(), arena.allocateFrom(name));
+        } catch (Throwable ex) {
+            throw wrapException(ex);
+        }
+    }
+
+    private static final MethodHandle read_associated_image_icc_profile = function(
+            null, "openslide_read_associated_image_icc_profile", C_POINTER,
+            C_POINTER, C_POINTER);
+
+    static void openslide_read_associated_image_icc_profile(OpenSlideRef osr,
+            String name, byte dest[]) {
+        if (name == null) {
+            return;
+        }
+        try (Arena arena = Arena.ofConfined()) {
+            MemorySegment buf = arena.allocate(JAVA_BYTE, dest.length);
+            try (Ref.ScopedLock l = osr.lock()) {
+                read_associated_image_icc_profile.invokeExact(osr.getSegment(),
+                        arena.allocateFrom(name), buf);
+            } catch (Throwable ex) {
+                throw wrapException(ex);
+            }
+            MemorySegment.copy(buf, JAVA_BYTE, 0, dest, 0, dest.length);
+        }
+    }
+
     private static final MethodHandle cache_create = function(
             C_POINTER, "openslide_cache_create", SIZE_T);