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Merge pull request #3505 from melissalinkert/new-ndpi
NDPI: support JPEG-XR and files larger than 4 GB
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53 changes: 53 additions & 0 deletions
53
components/formats-bsd/src/loci/formats/services/JPEGXRService.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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% | ||
| */ | ||
|
|
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| package loci.formats.services; | ||
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| import loci.common.services.Service; | ||
| import loci.formats.FormatException; | ||
|
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| /** | ||
| * Interface defining methods for working with JPEG-XR data | ||
| */ | ||
| public interface JPEGXRService extends Service { | ||
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| /** | ||
| * 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; | ||
|
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| } |
118 changes: 118 additions & 0 deletions
118
components/formats-bsd/src/loci/formats/services/JPEGXRServiceImpl.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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% | ||
| */ | ||
|
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| package loci.formats.services; | ||
|
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| import java.io.IOException; | ||
|
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| import loci.common.RandomAccessInputStream; | ||
| import loci.common.services.AbstractService; | ||
| import loci.formats.FormatException; | ||
| import loci.formats.tiff.IFD; | ||
| import loci.formats.tiff.TiffParser; | ||
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| import ome.jxrlib.Decode; | ||
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| import org.slf4j.Logger; | ||
| import org.slf4j.LoggerFactory; | ||
|
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| /** | ||
| * Interface defining methods for working with JPEG-XR data | ||
| */ | ||
| public class JPEGXRServiceImpl extends AbstractService implements JPEGXRService { | ||
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| // see table A.4 in ITU-T T.832 | ||
| private static final int PIXEL_FORMAT_TAG = 0xbc01; | ||
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| // 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; | ||
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| private static final Logger LOGGER = | ||
| LoggerFactory.getLogger(JPEGXRServiceImpl.class); | ||
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| public JPEGXRServiceImpl() { | ||
| checkClassDependency(ome.jxrlib.Decode.class); | ||
| } | ||
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| /** | ||
| * @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); | ||
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| 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); | ||
| } | ||
| } | ||
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| 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); | ||
| } | ||
| } | ||
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| private boolean isBGR(short[] format) { | ||
| short lastByte = format[format.length - 1]; | ||
| return lastByte == BGR_24 || lastByte == BGR_32 || | ||
| lastByte == BGRA_32 || lastByte == PBGRA_32; | ||
| } | ||
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| private int getBGRComponents(short[] format) { | ||
| short lastByte = format[format.length - 1]; | ||
| return lastByte == BGR_24 || lastByte == BGR_32 ? 3 : 4; | ||
| } | ||
|
|
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| } |
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