Java tutorial
/* ***** 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 * of those above. If you wish to allow use of your version of this file only * under the terms of either the GPL or the LGPL, and not to allow others to * use your version of this file under the terms of the MPL, indicate your * decision by deleting the provisions above and replace them with the notice * and other provisions required by the GPL or the LGPL. If you do not delete * the provisions above, a recipient may use your version of this file under * the terms of any one of the MPL, the GPL or the LGPL. * * ***** 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(); 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); } }