/* ***** BEGIN LICENSE BLOCK *****
* Version: MPL 1.1/GPL 2.0/LGPL 2.1
*
* The contents of this file are subject to the Mozilla Public License Version
* 1.1 (the "License"); you may not use this file except in compliance with
* the License. You may obtain a copy of the License at
* http://www.mozilla.org/MPL/
*
* Software distributed under the License is distributed on an "AS IS" basis,
* WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License
* for the specific language governing rights and limitations under the
* License.
*
* The Original Code is part of dcm4che, an implementation of DICOM(TM) in
* Java(TM), hosted at http://sourceforge.net/projects/dcm4che.
*
* The Initial Developer of the Original Code is
* Gunter Zeilinger, Huetteldorferstr. 24/10, 1150 Vienna/Austria/Europe.
* Portions created by the Initial Developer are Copyright (C) 2002-2005
* the Initial Developer. All Rights Reserved.
*
* Contributor(s):
* Gunter Zeilinger <gunterze@gmail.com>
*
* Alternatively, the contents of this file may be used under the terms of
* either the GNU General Public License Version 2 or later (the "GPL"), or
* the GNU Lesser General Public License Version 2.1 or later (the "LGPL"),
* in which case the provisions of the GPL or the LGPL are applicable instead
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* decision by deleting the provisions above and replace them with the notice
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* the provisions above, a recipient may use your version of this file under
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*
* ***** END LICENSE BLOCK ***** */
package org.dcm4che3.tool.jpg2dcm;
import java.io.BufferedInputStream;
import java.io.DataInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.Date;
import java.util.List;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.OptionBuilder;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.commons.cli.PosixParser;
import org.dcm4che3.data.Attributes;
import org.dcm4che3.data.Tag;
import org.dcm4che3.data.UID;
import org.dcm4che3.data.VR;
import org.dcm4che3.io.DicomOutputStream;
import org.dcm4che3.io.SAXReader;
import org.dcm4che3.util.UIDUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* @author gunter zeilinger<gunterze@gmail.com>
* @author Hesham Elbadawi <bsdreko@gmail.com>
*
*/
public class Jpg2Dcm {
static final Logger LOG = LoggerFactory.getLogger(Jpg2Dcm.class);
private static final String USAGE = "jpg2dcm [Options] <jpgfile> <dcmfile>";
private static final String DESCRIPTION = "Encapsulate JPEG Image into DICOM Object.\nOptions:";
private static final String EXAMPLE = "--\nExample 1: Encapulate JPEG Image verbatim with default values "
+ "for mandatory DICOM attributes into DICOM Secondary Capture Image:"
+ "\n$ jpg2dcm -c jpg2dcm.xml image.jpg image.dcm"
+ "\n--\nExample 2: Encapulate JPEG Image without application segments "
+ "and additional DICOM attributes to mandatory defaults into DICOM "
+ "Image Object:"
+ "\n$ jpg2dcm --no-appn -c patattrs.cfg homer.jpg image.dcm"
+ "\n--\nExample 3: Encapulate MPEG2 Video with specified DICOM "
+ "attributes into DICOM Video Object:"
+ "\n$ jpg2dcm --mpeg -c mpg2dcm.xml video.mpg video.dcm";
private static final String LONG_OPT_CHARSET = "charset";
private static final String OPT_CHARSET_DESC = "Specific Character Set code string, ISO_IR 100 by default";
private static final String OPT_AUGMENT_CONFIG_DESC = "Specifies DICOM attributes included additional to mandatory defaults";
private static final String OPT_REPLACE_CONFIG_DESC = "Specifies DICOM attributes included instead of mandatory defaults";
private static final String LONG_OPT_TRANSFER_SYNTAX = "transfer-syntax";
private static final String OPT_TRANSFER_SYNTAX_DESC = "Transfer Syntax; 1.2.840.10008.1.2.4.50 (JPEG Baseline) by default.";
private static final String LONG_OPT_MPEG = "mpeg";
private static final String OPT_MPEG_DESC = "Same as --transfer-syntax 1.2.840.10008.1.2.4.100 (MPEG2).";
private static final String LONG_OPT_UID_PREFIX = "uid-prefix";
private static final String OPT_UID_PREFIX_DESC = "Generate UIDs with given prefix, 1.2.40.0.13.1.<host-ip> by default.";
private static final String LONG_OPT_NO_APPN = "no-appn";
private static final String OPT_NO_APPN_DESC = "Exclude application segments APPn from JPEG stream; "
+ "encapsulate JPEG stream verbatim by default.";
private static final String OPT_HELP_DESC = "Print this message";
private static final String OPT_VERSION_DESC = "Print the version information and exit";
private static int FF = 0xff;
private static int SOF = 0xc0;
private static int DHT = 0xc4;
private static int DAC = 0xcc;
private static int SOI = 0xd8;
private static int SOS = 0xda;
private static int APP = 0xe0;
private String charset = "ISO_IR 100";
private String transferSyntax = UID.JPEGBaseline1;
private byte[] buffer = new byte[8192];
private int jpgHeaderLen;
private int jpgLen;
private boolean noAPPn = false;
public Jpg2Dcm() {
}
public final void setCharset(String charset) {
this.charset = charset;
}
private final void setTransferSyntax(String uid) {
this.transferSyntax = uid;
}
private final void setNoAPPn(boolean noAPPn) {
this.noAPPn = noAPPn;
}
public void convert(CommandLine cl, File jpgFile, File dcmFile)
throws IOException {
jpgHeaderLen = 0;
jpgLen = (int) jpgFile.length();
DataInputStream jpgInput = new DataInputStream(new BufferedInputStream(
new FileInputStream(jpgFile)));
try {
Attributes attrs = new Attributes();
attrs.setString(Tag.SOPClassUID, VR.UI, UID.SecondaryCaptureImageStorage);
try {
if (cl.hasOption("mpeg") && cl.hasOption("c"))
attrs = SAXReader.parse(cl.getOptionValue("c"));
else if (cl.hasOption("c"))
attrs = SAXReader.parse(cl.getOptionValue("c"));
} catch (Exception e) {
throw new FileNotFoundException(
"Configuration XML file not found");
}
attrs.setString(Tag.SpecificCharacterSet, VR.CS, charset);
if (noAPPn || missingRowsColumnsSamplesPMI(attrs)) {
readHeader(attrs, jpgInput);
}
ensureUS(attrs, Tag.BitsAllocated, 8);
ensureUS(attrs, Tag.BitsStored, attrs.getInt(Tag.BitsAllocated,
(buffer[jpgHeaderLen] & 0xff) > 8 ? 16 : 8));
ensureUS(
attrs,
Tag.HighBit,
attrs.getInt(Tag.BitsStored, (buffer[jpgHeaderLen] & 0xff)) - 1);
ensureUS(attrs, Tag.PixelRepresentation, 0);
ensureUID(attrs, Tag.StudyInstanceUID);
ensureUID(attrs, Tag.SeriesInstanceUID);
ensureUID(attrs, Tag.SOPInstanceUID);
Date now = new Date();
attrs.setDate(Tag.InstanceCreationDate, VR.DA, now);
attrs.setDate(Tag.InstanceCreationTime, VR.TM, now);
Attributes fmi = attrs.createFileMetaInformation(transferSyntax);
DicomOutputStream dos = new DicomOutputStream(dcmFile);
try {
dos.writeDataset(fmi, attrs);
dos.writeHeader(Tag.PixelData, VR.OB, -1);
if (!cl.hasOption("mpeg")) {
dos.writeHeader(Tag.Item, null, 0);
dos.writeHeader(Tag.Item, null, (jpgLen + 1) & ~1);
dos.write(buffer, 0, jpgHeaderLen);
}
int r;
while ((r = jpgInput.read(buffer)) > 0) {
dos.write(buffer, 0, r);
}
if (!cl.hasOption("mpeg")) {
if ((jpgLen & 1) != 0) {
dos.write(0);
}
}
dos.writeHeader(Tag.SequenceDelimitationItem, null, 0);
} finally {
dos.close();
}
} finally {
jpgInput.close();
}
}
private boolean missingRowsColumnsSamplesPMI(Attributes attrs) {
return !(attrs.containsValue(Tag.Rows)
&& attrs.containsValue(Tag.Columns)
&& attrs.containsValue(Tag.SamplesPerPixel) && attrs
.containsValue(Tag.PhotometricInterpretation));
}
private void readHeader(Attributes attrs, DataInputStream jpgInput)
throws IOException {
if (jpgInput.read() != FF || jpgInput.read() != SOI
|| jpgInput.read() != FF) {
throw new IOException("JPEG stream does not start with FF D8 FF");
}
int marker = jpgInput.read();
int segmLen;
boolean seenSOF = false;
buffer[0] = (byte) FF;
buffer[1] = (byte) SOI;
buffer[2] = (byte) FF;
buffer[3] = (byte) marker;
jpgHeaderLen = 4;
while (marker != SOS) {
segmLen = jpgInput.readUnsignedShort();
if (buffer.length < jpgHeaderLen + segmLen + 2) {
growBuffer(jpgHeaderLen + segmLen + 2);
}
buffer[jpgHeaderLen++] = (byte) (segmLen >>> 8);
buffer[jpgHeaderLen++] = (byte) segmLen;
jpgInput.readFully(buffer, jpgHeaderLen, segmLen - 2);
if ((marker & 0xf0) == SOF && marker != DHT && marker != DAC) {
seenSOF = true;
int p = buffer[jpgHeaderLen] & 0xff;
int y = ((buffer[jpgHeaderLen + 1] & 0xff) << 8)
| (buffer[jpgHeaderLen + 2] & 0xff);
int x = ((buffer[jpgHeaderLen + 3] & 0xff) << 8)
| (buffer[jpgHeaderLen + 4] & 0xff);
int nf = buffer[jpgHeaderLen + 5] & 0xff;
attrs.setInt(Tag.SamplesPerPixel, VR.US, nf);
if (nf == 3) {
attrs.setString(Tag.PhotometricInterpretation, VR.CS,
"YBR_FULL_422");
attrs.setInt(Tag.PlanarConfiguration, VR.US, 0);
} else {
attrs.setString(Tag.PhotometricInterpretation, VR.CS,
"MONOCHROME2");
}
attrs.setInt(Tag.Rows, VR.US, y);
attrs.setInt(Tag.Columns, VR.US, x);
attrs.setInt(Tag.BitsAllocated, VR.US, p > 8 ? 16 : 8);
attrs.setInt(Tag.BitsStored, VR.US, p);
attrs.setInt(Tag.HighBit, VR.US, p - 1);
attrs.setInt(Tag.PixelRepresentation, VR.US, 0);
}
if (noAPPn & (marker & 0xf0) == APP) {
jpgLen -= segmLen + 2;
jpgHeaderLen -= 4;
} else {
jpgHeaderLen += segmLen - 2;
}
if (jpgInput.read() != FF) {
throw new IOException("Missing SOS segment in JPEG stream");
}
marker = jpgInput.read();
buffer[jpgHeaderLen++] = (byte) FF;
buffer[jpgHeaderLen++] = (byte) marker;
}
if (!seenSOF) {
throw new IOException("Missing SOF segment in JPEG stream");
}
}
private void growBuffer(int minSize) {
int newSize = buffer.length << 1;
while (newSize < minSize) {
newSize <<= 1;
}
byte[] tmp = new byte[newSize];
System.arraycopy(buffer, 0, tmp, 0, jpgHeaderLen);
buffer = tmp;
}
private void ensureUID(Attributes attrs, int tag) {
if (!attrs.containsValue(tag)) {
attrs.setString(tag, VR.UI, UIDUtils.createUID());
}
}
private void ensureUS(Attributes attrs, int tag, int val) {
if (!attrs.containsValue(tag)) {
attrs.setInt(tag, VR.US, val);
}
}
public static void main(String[] args) {
try {
CommandLine cl = parse(args);
Jpg2Dcm jpg2Dcm = new Jpg2Dcm();
if (cl.hasOption(LONG_OPT_CHARSET)) {
jpg2Dcm.setCharset(cl.getOptionValue(LONG_OPT_CHARSET));
}
if (cl.hasOption(LONG_OPT_UID_PREFIX)) {
UIDUtils.setRoot(cl.getOptionValue(LONG_OPT_UID_PREFIX));
}
if (cl.hasOption(LONG_OPT_MPEG)) {
jpg2Dcm.setTransferSyntax(UID.MPEG2);
}
if (cl.hasOption(LONG_OPT_TRANSFER_SYNTAX)) {
jpg2Dcm.setTransferSyntax(cl
.getOptionValue(LONG_OPT_TRANSFER_SYNTAX));
}
jpg2Dcm.setNoAPPn(cl.hasOption(LONG_OPT_NO_APPN));
@SuppressWarnings("rawtypes")
List argList = cl.getArgList();
File jpgFile = new File((String) argList.get(0));
File dcmFile = new File((String) argList.get(1));
long start = System.currentTimeMillis();
jpg2Dcm.convert(cl, jpgFile, dcmFile);
long fin = System.currentTimeMillis();
LOG.info("Encapsulated " + jpgFile + " to " + dcmFile + " in "
+ (fin - start) + "ms.");
} catch (IOException e) {
e.printStackTrace();
}
}
private static CommandLine parse(String[] args) {
Options opts = new Options();
OptionBuilder.withArgName("code");
OptionBuilder.hasArg();
OptionBuilder.withDescription(OPT_CHARSET_DESC);
OptionBuilder.withLongOpt(LONG_OPT_CHARSET);
opts.addOption(OptionBuilder.create());
OptionBuilder.withArgName("file");
OptionBuilder.hasArg();
OptionBuilder.withDescription(OPT_AUGMENT_CONFIG_DESC);
opts.addOption(OptionBuilder.create("c"));
OptionBuilder.withArgName("file");
OptionBuilder.hasArg();
OptionBuilder.withDescription(OPT_REPLACE_CONFIG_DESC);
opts.addOption(OptionBuilder.create("C"));
OptionBuilder.withArgName("prefix");
OptionBuilder.hasArg();
OptionBuilder.withDescription(OPT_UID_PREFIX_DESC);
OptionBuilder.withLongOpt(LONG_OPT_UID_PREFIX);
opts.addOption(OptionBuilder.create());
OptionBuilder.withArgName("uid");
OptionBuilder.hasArg();
OptionBuilder.withDescription(OPT_TRANSFER_SYNTAX_DESC);
OptionBuilder.withLongOpt(LONG_OPT_TRANSFER_SYNTAX);
opts.addOption(OptionBuilder.create());
opts.addOption(null, LONG_OPT_MPEG, false, OPT_MPEG_DESC);
opts.addOption(null, LONG_OPT_NO_APPN, false, OPT_NO_APPN_DESC);
opts.addOption("h", "help", false, OPT_HELP_DESC);
opts.addOption("V", "version", false, OPT_VERSION_DESC);
CommandLine cl = null;
try {
cl = new PosixParser().parse(opts, args);
} catch (ParseException e) {
exit("jpg2dcm: " + e.getMessage());
throw new RuntimeException("unreachable");
}
if (cl.hasOption('V')) {
Package p = Jpg2Dcm.class.getPackage();
LOG.info("jpg2dcm v" + p.getImplementationVersion());
System.exit(0);
}
if (cl.hasOption('h') || cl.getArgList().size() != 2) {
HelpFormatter formatter = new HelpFormatter();
formatter.printHelp(USAGE, DESCRIPTION, opts, EXAMPLE);
System.exit(0);
}
return cl;
}
private static void exit(String msg) {
LOG.error(msg);
LOG.error("Try 'jpg2dcm -h' for more information.");
System.exit(1);
}
}