NDPI: support JPEG-XR and files larger than 4 GB

components/formats-bsd/pom.xml

@@ -103,6 +103,11 @@
 	    <artifactId>metadata-extractor</artifactId>
 	    <version>2.11.0</version>
     </dependency>
+    <dependency>
+      <groupId>ome</groupId>
+      <artifactId>jxrlib-all</artifactId>
+      <version>${jxrlib.version}</version>
+    </dependency>
 
     <!-- xerces is no longer a dependency of metadata-extractor, but it may be required by other BF components -->
     <dependency>

components/formats-gpl/src/loci/formats/codec/JPEGXRCodec.java → components/formats-bsd/src/loci/formats/codec/JPEGXRCodec.java

@@ -1,25 +1,32 @@
 /*
  * #%L
- * OME Bio-Formats package for reading and converting biological file formats.
+ * BSD implementations of Bio-Formats readers and writers
  * %%
  * Copyright (C) 2016 - 2017 Open Microscopy Environment:
  *   - Board of Regents of the University of Wisconsin-Madison
  *   - Glencoe Software, Inc.
  *   - University of Dundee
  * %%
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as
- * published by the Free Software Foundation, either version 2 of the 
- * License, or (at your option) any later version.
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
  * 
- * You should have received a copy of the GNU General Public 
- * License along with this program.  If not, see
- * <http://www.gnu.org/licenses/gpl-2.0.html>.
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
  * #L%
  */
 
@@ -81,17 +88,13 @@ public byte[] decompress(byte[] buf, CodecOptions options)
   {
     initialize();
 
-    byte[] uncompressed = service.decompress(buf);
-
-    if (options.interleaved) {
-      return uncompressed;
-    }
-
     int bpp = options.bitsPerSample / 8;
     int pixels = options.width * options.height;
+
+    byte[] uncompressed = service.decompress(buf);
     int channels = uncompressed.length / (pixels * bpp);
 
-    if (channels == 1) {
+    if (channels == 1 || options.interleaved) {
       return uncompressed;
     }
 
@@ -101,8 +104,9 @@ public byte[] decompress(byte[] buf, CodecOptions options)
       for (int c=0; c<channels; c++) {
         for (int b=0; b<bpp; b++) {
           int bb = options.littleEndian ? b : bpp - b - 1;
-          deinterleaved[bpp * (c * pixels + p) + bb] =
-            uncompressed[bpp * (p * channels + c) + b];
+          int src = bpp * (p * channels + c) + b;
+          int dest = bpp * (c * pixels + p) + bb;
+          deinterleaved[dest] = uncompressed[src];
         }
       }
     }

components/formats-bsd/src/loci/formats/services/JPEGXRService.java

@@ -0,0 +1,53 @@
+/*
+ * #%L
+ * BSD implementations of Bio-Formats readers and writers
+ * %%
+ * Copyright (C) 2016 - 2017 Open Microscopy Environment:
+ *   - Board of Regents of the University of Wisconsin-Madison
+ *   - Glencoe Software, Inc.
+ *   - University of Dundee
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package loci.formats.services;
+
+import loci.common.services.Service;
+import loci.formats.FormatException;
+
+/**
+ * Interface defining methods for working with JPEG-XR data
+ */
+public interface JPEGXRService extends Service {
+
+  /**
+   * Decompress the given JPEG-XR compressed byte array and return as a byte array.
+   * Opening and closing of decoders and streams is handled internally.
+   *
+   * @param compressed the complete JPEG-XR compressed data
+   * @return raw decompressed bytes
+   * @throws FormatException if an error occurs during decompression
+   */
+  byte[] decompress(byte[] compressed) throws FormatException;
+
+}

components/formats-bsd/src/loci/formats/services/JPEGXRServiceImpl.java

@@ -0,0 +1,118 @@
+/*
+ * #%L
+ * BSD implementations of Bio-Formats readers and writers
+ * %%
+ * Copyright (C) 2016 - 2017 Open Microscopy Environment:
+ *   - Board of Regents of the University of Wisconsin-Madison
+ *   - Glencoe Software, Inc.
+ *   - University of Dundee
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package loci.formats.services;
+
+import java.io.IOException;
+
+import loci.common.RandomAccessInputStream;
+import loci.common.services.AbstractService;
+import loci.formats.FormatException;
+import loci.formats.tiff.IFD;
+import loci.formats.tiff.TiffParser;
+
+import ome.jxrlib.Decode;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * Interface defining methods for working with JPEG-XR data
+ */
+public class JPEGXRServiceImpl extends AbstractService implements JPEGXRService {
+
+  // see table A.4 in ITU-T T.832
+  private static final int PIXEL_FORMAT_TAG = 0xbc01;
+
+  // see table A.6 in ITU-T T.832
+  private static final short BGR_24 = 0x0c;
+  private static final short BGR_32 = 0x0e;
+  private static final short BGRA_32 = 0x0f;
+  private static final short PBGRA_32 = 0x10;
+
+  private static final Logger LOGGER =
+    LoggerFactory.getLogger(JPEGXRServiceImpl.class);
+
+  public JPEGXRServiceImpl() {
+    checkClassDependency(ome.jxrlib.Decode.class);
+  }
+
+  /**
+   * @see JPEGXRServiceImpl#decompress(byte[])
+   */
+  public byte[] decompress(byte[] compressed) throws FormatException {
+      LOGGER.trace("begin tile decode; compressed size = {}", compressed.length);
+      try {
+        byte[] raw = Decode.decodeFirstFrame(compressed, 0, compressed.length);
+        short[] format = getPixelFormat(compressed);
+
+        if (isBGR(format)) {
+          int bpp = getBGRComponents(format);
+          // only happens with 8 bits per channel,
+          // 3 (BGR) or 4 (BGRA) channel data
+          for (int p=0; p<raw.length; p+=bpp) {
+            byte tmp = raw[p];
+            raw[p] = raw[p + 2];
+            raw[p + 2] = tmp;
+          }
+        }
+        return raw;
+      }
+      // really only want to catch ome.jxrlib.FormatError, but that doesn't compile
+      catch (Exception e) {
+        throw new FormatException(e);
+      }
+  }
+
+  private short[] getPixelFormat(byte[] stream) throws FormatException, IOException {
+    try (RandomAccessInputStream s = new RandomAccessInputStream(stream)) {
+      s.order(true);
+      s.seek(4);
+      long ifdPointer = s.readInt();
+      TiffParser p = new TiffParser(s);
+      IFD ifd = p.getIFD(ifdPointer);
+      return ifd.getIFDShortArray(PIXEL_FORMAT_TAG);
+    }
+  }
+
+  private boolean isBGR(short[] format) {
+    short lastByte = format[format.length - 1];
+    return lastByte == BGR_24 || lastByte == BGR_32 ||
+      lastByte == BGRA_32 || lastByte == PBGRA_32;
+  }
+
+  private int getBGRComponents(short[] format) {
+    short lastByte = format[format.length - 1];
+    return lastByte == BGR_24 || lastByte == BGR_32 ? 3 : 4;
+  }
+
+}

components/formats-bsd/src/loci/formats/tiff/TiffCompression.java

@@ -47,6 +47,7 @@
 import loci.formats.codec.JPEG2000Codec;
 import loci.formats.codec.JPEG2000CodecOptions;
 import loci.formats.codec.JPEGCodec;
+import loci.formats.codec.JPEGXRCodec;
 import loci.formats.codec.LZWCodec;
 import loci.formats.codec.LuraWaveCodec;
 import loci.formats.codec.NikonCodec;
@@ -193,7 +194,8 @@ public CodecOptions getCompressionCodecOptions(IFD ifd, CodecOptions opt)
 
   },
   NIKON(34713, new NikonCodec(), "Nikon"),
-  LURAWAVE(65535, new LuraWaveCodec(), "LuraWave");
+  LURAWAVE(65535, new LuraWaveCodec(), "LuraWave"),
+  JPEGXR(22610, new JPEGXRCodec(), "JPEG-XR");
 
   // -- Constants --
 

components/formats-bsd/src/loci/formats/tiff/TiffParser.java

@@ -542,7 +542,7 @@ public Object getIFDValue(TiffIFDEntry entry) throws IOException {
     }
 
     if (offset != in.getFilePointer()) {
-      if (fakeBigTiff && (offset < 0 || offset > in.getFilePointer())) {
+      if (fakeBigTiff && offset < 0) {
         offset &= 0xffffffffL;
         offset += 0x100000000L;
       }
@@ -1172,7 +1172,11 @@ public static void unpackBytes(byte[] samples, int startIndex, byte[] bytes,
 
     TiffCompression compression = ifd.getCompression();
     PhotoInterp photoInterp = ifd.getPhotometricInterpretation();
-    if (compression == TiffCompression.JPEG) photoInterp = PhotoInterp.RGB;
+    if (compression == TiffCompression.JPEG ||
+      compression == TiffCompression.JPEGXR)
+    {
+      photoInterp = PhotoInterp.RGB;
+    }
 
     int[] bitsPerSample = ifd.getBitsPerSample();
     int nChannels = bitsPerSample.length;

components/formats-gpl/pom.xml

@@ -63,11 +63,6 @@
       <artifactId>ome-poi</artifactId>
       <version>${ome-poi.version}</version>
     </dependency>
-    <dependency>
-      <groupId>ome</groupId>
-      <artifactId>jxrlib-all</artifactId>
-      <version>${jxrlib.version}</version>
-    </dependency>
     <dependency>
       <groupId>edu.ucar</groupId>
       <artifactId>cdm</artifactId>