/*
* #%L
* BSD implementations of Bio-Formats readers and writers
* %%
* Copyright (C) 2005 - 2015 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.in;
import java.awt.color.CMMException;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import loci.common.ByteArrayHandle;
import loci.common.DataTools;
import loci.common.Location;
import loci.common.RandomAccessInputStream;
import loci.common.services.DependencyException;
import loci.common.services.ServiceException;
import loci.common.services.ServiceFactory;
import loci.formats.DelegateReader;
import loci.formats.FormatException;
import loci.formats.FormatTools;
import loci.formats.services.EXIFService;
import java.util.Date;
import java.util.HashMap;
import org.joda.time.DateTime;
import loci.formats.MetadataTools;
import loci.formats.meta.MetadataStore;
import ome.xml.model.primitives.Timestamp;
/**
* JPEGReader is the file format reader for JPEG images.
*
* @author Curtis Rueden ctrueden at wisc.edu
*/
public class JPEGReader extends DelegateReader {
// -- Constants --
private static final int MAX_SIZE = 8192;
// -- Constructor --
/** Constructs a new JPEGReader. */
public JPEGReader() {
super("JPEG", new String[] {"jpg", "jpeg", "jpe"});
nativeReader = new DefaultJPEGReader();
legacyReader = new TileJPEGReader();
nativeReaderInitialized = false;
legacyReaderInitialized = false;
domains = new String[] {FormatTools.GRAPHICS_DOMAIN};
suffixNecessary = false;
}
// -- FormatReader API methods --
/* @see FormatReader#setId(String) */
@Override
public void setId(String id) throws FormatException, IOException {
try {
super.setId(id);
}
catch (CMMException e) {
// strip out all but the first application marker
// ImageIO isn't too keen on supporting multiple application markers
// in the same stream, as evidenced by:
//
// http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6488904
in = new RandomAccessInputStream(id);
ByteArrayOutputStream v = new ByteArrayOutputStream();
byte[] tag = new byte[2];
in.read(tag);
v.write(tag);
in.read(tag);
int tagValue = DataTools.bytesToShort(tag, false) & 0xffff;
boolean appNoteFound = false;
while (tagValue != 0xffdb) {
if (!appNoteFound || (tagValue < 0xffe0 && tagValue >= 0xfff0)) {
v.write(tag);
in.read(tag);
int len = DataTools.bytesToShort(tag, false) & 0xffff;
byte[] tagContents = new byte[len - 2];
in.read(tagContents);
v.write(tag);
v.write(tagContents);
}
else {
in.read(tag);
int len = DataTools.bytesToShort(tag, false) & 0xffff;
in.skipBytes(len - 2);
}
if (tagValue >= 0xffe0 && tagValue < 0xfff0 && !appNoteFound) {
appNoteFound = true;
}
in.read(tag);
tagValue = DataTools.bytesToShort(tag, false) & 0xffff;
}
v.write(tag);
byte[] remainder = new byte[(int) (in.length() - in.getFilePointer())];
in.read(remainder);
v.write(remainder);
ByteArrayHandle bytes = new ByteArrayHandle(v.toByteArray());
Location.mapFile(currentId + ".fixed", bytes);
super.setId(currentId + ".fixed");
}
if (getSizeX() > MAX_SIZE && getSizeY() > MAX_SIZE &&
!legacyReaderInitialized)
{
close();
useLegacy = true;
super.setId(id);
}
if (currentId.endsWith(".fixed")) {
currentId = currentId.substring(0, currentId.lastIndexOf("."));
}
}
// -- IFormatReader API methods --
/* @see IFormatReader#getSeriesUsedFiles(boolean) */
@Override
public String[] getSeriesUsedFiles(boolean noPixels) {
FormatTools.assertId(currentId, true, 1);
return noPixels ? null : new String[] {currentId.replaceAll(".fixed", "")};
}
/* @see IFormatReader#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
Location.mapId(currentId, null);
}
// -- Helper reader --
static class DefaultJPEGReader extends ImageIOReader {
public DefaultJPEGReader() {
super("JPEG", new String[] {"jpg", "jpeg", "jpe"});
suffixNecessary = false;
suffixSufficient = false;
}
/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
@Override
public boolean isThisType(String name, boolean open) {
if (open) {
return super.isThisType(name, open);
}
return checkSuffix(name, getSuffixes());
}
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
MetadataStore store = makeFilterMetadata();
LOGGER.info("Parsing JPEG EXIF data");
try {
EXIFService exif = new ServiceFactory().getInstance(EXIFService.class);
if (exif == null) {
return;
}
exif.initialize(id);
// Set the acquisition date
Date date = exif.getCreationDate();
if (date != null) {
Timestamp timestamp = new Timestamp(new DateTime(date));
store.setImageAcquisitionDate(timestamp, 0);
}
HashMap<String, String> tags = exif.getTags();
for (String tagName : tags.keySet()) {
addGlobalMeta(tagName, tags.get(tagName));
}
}
catch (ServiceException e) {
LOGGER.debug("Could not parse EXIF data", e);
}
catch (DependencyException e) {
LOGGER.debug("Could not parse EXIF data", e);
}
}
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException
{
final int blockLen = 4;
if (!FormatTools.validStream(stream, blockLen, false)) return false;
byte[] signature = new byte[blockLen];
stream.read(signature);
if (signature[0] != (byte) 0xff || signature[1] != (byte) 0xd8 ||
signature[2] != (byte) 0xff || ((int) signature[3] & 0xf0) == 0)
{
return false;
}
return true;
}
}
}