Source code

001/* ***** BEGIN LICENSE BLOCK *****
002 * Version: MPL 1.1/GPL 2.0/LGPL 2.1
003 *
004 * The contents of this file are subject to the Mozilla Public License Version
005 * 1.1 (the "License"); you may not use this file except in compliance with
006 * the License. You may obtain a copy of the License at
007 * http://www.mozilla.org/MPL/
008 *
009 * Software distributed under the License is distributed on an "AS IS" basis,
010 * WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License
011 * for the specific language governing rights and limitations under the
012 * License.
013 *
014 * The Original Code is part of dcm4che, an implementation of DICOM(TM) in
015 * Java(TM), hosted at https://github.com/gunterze/dcm4che.
016 *
017 * The Initial Developer of the Original Code is
018 * Agfa Healthcare.
019 * Portions created by the Initial Developer are Copyright (C) 2011
020 * the Initial Developer. All Rights Reserved.
021 *
022 * Contributor(s):
023 * See @authors listed below
024 *
025 * Alternatively, the contents of this file may be used under the terms of
026 * either the GNU General Public License Version 2 or later (the "GPL"), or
027 * the GNU Lesser General Public License Version 2.1 or later (the "LGPL"),
028 * in which case the provisions of the GPL or the LGPL are applicable instead
029 * of those above. If you wish to allow use of your version of this file only
030 * under the terms of either the GPL or the LGPL, and not to allow others to
031 * use your version of this file under the terms of the MPL, indicate your
032 * decision by deleting the provisions above and replace them with the notice
033 * and other provisions required by the GPL or the LGPL. If you do not delete
034 * the provisions above, a recipient may use your version of this file under
035 * the terms of any one of the MPL, the GPL or the LGPL.
036 *
037 * ***** END LICENSE BLOCK ***** */
038
039package org.dcm4che3.tool.dcm2xml;
040
041import java.io.BufferedOutputStream;
042import java.io.File;
043import java.io.FileOutputStream;
044import java.io.IOException;
045import java.io.OutputStream;
046import java.net.MalformedURLException;
047import java.net.URL;
048import java.util.List;
049import java.util.ResourceBundle;
050
051import javax.xml.parsers.SAXParser;
052import javax.xml.parsers.SAXParserFactory;
053import javax.xml.transform.OutputKeys;
054import javax.xml.transform.Transformer;
055import javax.xml.transform.TransformerConfigurationException;
056import javax.xml.transform.TransformerFactory;
057import javax.xml.transform.sax.SAXTransformerFactory;
058import javax.xml.transform.sax.TransformerHandler;
059import javax.xml.transform.stream.StreamResult;
060import javax.xml.transform.stream.StreamSource;
061
062import org.apache.commons.cli.CommandLine;
063import org.apache.commons.cli.OptionBuilder;
064import org.apache.commons.cli.OptionGroup;
065import org.apache.commons.cli.Options;
066import org.apache.commons.cli.ParseException;
067import org.dcm4che3.data.Attributes;
068import org.dcm4che3.io.BulkDataDescriptor;
069import org.dcm4che3.io.ContentHandlerAdapter;
070import org.dcm4che3.io.DicomInputStream;
071import org.dcm4che3.io.DicomInputStream.IncludeBulkData;
072import org.dcm4che3.io.SAXWriter;
073import org.dcm4che3.tool.common.CLIUtils;
074
075/**
076 * Tool for converting DICOM to XML presentation and optionally apply XSLT
077 * stylesheet on it.
078 * 
079 * @author Gunter Zeilinger <gunterze@gmail.com>
080 */
081public class Dcm2Xml {
082
083    private static final String XML_1_0 = "1.0";
084    private static final String XML_1_1 = "1.1";
085
086    private static ResourceBundle rb =
087        ResourceBundle.getBundle("org.dcm4che3.tool.dcm2xml.messages");
088
089    private String xsltURL;
090    private boolean indent = false;
091    private boolean includeKeyword = true;
092    private boolean includeNamespaceDeclaration = false;
093    private IncludeBulkData includeBulkData = IncludeBulkData.URI;
094    private boolean catBlkFiles = false;
095    private String blkFilePrefix = "blk";
096    private String blkFileSuffix;
097    private File blkDirectory;
098    private Attributes blkAttrs;
099    private String xmlVersion = XML_1_0;
100
101    public final void setXSLTURL(String xsltURL) {
102        this.xsltURL = xsltURL;
103    }
104
105    public final void setIndent(boolean indent) {
106        this.indent = indent;
107    }
108
109    public final void setIncludeKeyword(boolean includeKeyword) {
110        this.includeKeyword = includeKeyword;
111    }
112
113    public final void setIncludeNamespaceDeclaration(boolean includeNamespaceDeclaration) {
114        this.includeNamespaceDeclaration = includeNamespaceDeclaration;
115    }
116
117    public final void setIncludeBulkData(IncludeBulkData includeBulkData) {
118        this.includeBulkData = includeBulkData;
119    }
120
121    public final void setConcatenateBulkDataFiles(boolean catBlkFiles) {
122        this.catBlkFiles = catBlkFiles;
123    }
124
125    public final void setBulkDataFilePrefix(String blkFilePrefix) {
126        this.blkFilePrefix = blkFilePrefix;
127    }
128
129    public final void setBulkDataFileSuffix(String blkFileSuffix) {
130        this.blkFileSuffix = blkFileSuffix;
131    }
132
133    public final void setBulkDataDirectory(File blkDirectory) {
134        this.blkDirectory = blkDirectory;
135    }
136
137    public final void setBulkDataAttributes(Attributes blkAttrs) {
138        this.blkAttrs = blkAttrs;
139    }
140
141    public final void setXMLVersion(String xmlVersion) {
142        this.xmlVersion = xmlVersion;
143    }
144
145    @SuppressWarnings("static-access")
146    private static CommandLine parseComandLine(String[] args)
147            throws ParseException {
148        Options opts = new Options();
149        CLIUtils.addCommonOptions(opts);
150        opts.addOption(OptionBuilder
151                .withLongOpt("xsl")
152                .hasArg()
153                .withArgName("xsl-file")
154                .withDescription(rb.getString("xsl"))
155                .create("x"));
156        opts.addOption("I", "indent", false, rb.getString("indent"));
157        opts.addOption("K", "no-keyword", false, rb.getString("no-keyword"));
158        opts.addOption(null, "xmlns", false, rb.getString("xmlns"));
159        opts.addOption(null, "xml11", false, rb.getString("xml11"));
160        addBulkdataOptions(opts);
161
162        return CLIUtils.parseComandLine(args, opts, rb, Dcm2Xml.class);
163    }
164
165    @SuppressWarnings("static-access")
166    private static void addBulkdataOptions(Options opts) {
167        OptionGroup group = new OptionGroup();
168        group.addOption(OptionBuilder
169                .withLongOpt("no-bulkdata")
170                .withDescription(rb.getString("no-bulkdata"))
171                .create("B"));
172        group.addOption(OptionBuilder
173                .withLongOpt("with-bulkdata")
174                .withDescription(rb.getString("with-bulkdata"))
175                .create("b"));
176        opts.addOptionGroup(group);
177        opts.addOption(OptionBuilder
178                .withLongOpt("blk-file-dir")
179                .hasArg()
180                .withArgName("directory")
181                .withDescription(rb.getString("blk-file-dir"))
182                .create("d"));
183        opts.addOption(OptionBuilder
184                .withLongOpt("blk-file-prefix")
185                .hasArg()
186                .withArgName("prefix")
187                .withDescription(rb.getString("blk-file-prefix"))
188                .create());
189        opts.addOption(OptionBuilder
190                .withLongOpt("blk-file-suffix")
191                .hasArg()
192                .withArgName("suffix")
193                .withDescription(rb.getString("blk-file-dir"))
194                .create());
195        opts.addOption("c", "cat-blk-files", false,
196                rb.getString("cat-blk-files"));
197        opts.addOption(OptionBuilder
198                .withLongOpt("blk-spec")
199                .hasArg()
200                .withArgName("xml-file")
201                .withDescription(rb.getString("blk-spec"))
202                .create("X"));
203    }
204
205    @SuppressWarnings("unchecked")
206    public static void main(String[] args) {
207        try {
208            CommandLine cl = parseComandLine(args);
209            Dcm2Xml main = new Dcm2Xml();
210            if (cl.hasOption("x"))
211                main.setXSLTURL(toURL(cl.getOptionValue("x")));
212            main.setIndent(cl.hasOption("I"));
213            main.setIncludeKeyword(!cl.hasOption("K"));
214            main.setIncludeNamespaceDeclaration(cl.hasOption("xmlns")); if (cl.hasOption("xml11"))
215                main.setXMLVersion(XML_1_1);
216            configureBulkdata(main, cl);
217            String fname = fname(cl.getArgList());
218            if (fname.equals("-")) {
219                main.convert(new DicomInputStream(System.in), System.out);
220            } else {
221                main.convert(new File(fname), System.out);
222            }
223        } catch (ParseException e) {
224            System.err.println("dcm2xml: " + e.getMessage());
225            System.err.println(rb.getString("try"));
226            System.exit(2);
227        } catch (Exception e) {
228            System.err.println("dcm2xml: " + e.getMessage());
229            e.printStackTrace();
230            System.exit(2);
231        }
232    }
233
234    private static String toURL(String fileOrURL) {
235        try {
236            new URL(fileOrURL);
237            return fileOrURL;
238        } catch (MalformedURLException e) {
239            return new File(fileOrURL).toURI().toString();
240        }
241    }
242
243    private static void configureBulkdata(Dcm2Xml dcm2xml, CommandLine cl)
244            throws Exception {
245        if (cl.hasOption("b")) {
246            dcm2xml.setIncludeBulkData(IncludeBulkData.YES);
247        }
248        if (cl.hasOption("B")) {
249            dcm2xml.setIncludeBulkData(IncludeBulkData.NO);
250        }
251        if (cl.hasOption("blk-file-prefix")) {
252            dcm2xml.setBulkDataFilePrefix(
253                    cl.getOptionValue("blk-file-prefix"));
254        }
255        if (cl.hasOption("blk-file-suffix")) {
256            dcm2xml.setBulkDataFileSuffix(
257                    cl.getOptionValue("blk-file-suffix"));
258        }
259        if (cl.hasOption("d")) {
260            File tempDir = new File(cl.getOptionValue("d"));
261            dcm2xml.setBulkDataDirectory(tempDir);
262        }
263        dcm2xml.setConcatenateBulkDataFiles(cl.hasOption("c"));
264        if (cl.hasOption("X")) {
265            dcm2xml.setBulkDataAttributes(
266                    parseXML(cl.getOptionValue("X")));
267        }
268    }
269
270    private static Attributes parseXML(String fname) throws Exception {
271        Attributes attrs = new Attributes();
272        ContentHandlerAdapter ch = new ContentHandlerAdapter(attrs);
273        SAXParserFactory f = SAXParserFactory.newInstance();
274        SAXParser p = f.newSAXParser();
275        p.parse(new File(fname), ch);
276        return attrs;
277    }
278
279    private static String fname(List<String> argList) throws ParseException {
280        int numArgs = argList.size();
281        if (numArgs == 0)
282            throw new ParseException(rb.getString("missing"));
283        if (numArgs > 1)
284            throw new ParseException(rb.getString("too-many"));
285        return argList.get(0);
286    }
287
288    public void convert(DicomInputStream dis, OutputStream out) throws IOException,
289            TransformerConfigurationException {
290        dis.setIncludeBulkData(includeBulkData);
291        if (blkAttrs != null)
292            dis.setBulkDataDescriptor(BulkDataDescriptor.valueOf(blkAttrs));
293        dis.setBulkDataDirectory(blkDirectory);
294        dis.setBulkDataFilePrefix(blkFilePrefix);
295        dis.setBulkDataFileSuffix(blkFileSuffix);
296        dis.setConcatenateBulkDataFiles(catBlkFiles);
297        TransformerHandler th = getTransformerHandler();
298        Transformer t = th.getTransformer();
299        t.setOutputProperty(OutputKeys.INDENT, indent ? "yes" : "no");
300        t.setOutputProperty(OutputKeys.VERSION, xmlVersion);
301        th.setResult(new StreamResult(out));
302        SAXWriter saxWriter = new SAXWriter(th);
303        saxWriter.setIncludeKeyword(includeKeyword);
304        saxWriter.setIncludeNamespaceDeclaration(includeNamespaceDeclaration);
305        dis.setDicomInputHandler(saxWriter);
306        dis.readDataset(-1, -1);
307    }
308
309    public void convert(File dicomFile, OutputStream out) throws IOException,
310            TransformerConfigurationException {
311        DicomInputStream dis = new DicomInputStream(dicomFile);
312        try {
313            convert(dis, out);
314        } finally {
315            dis.close();
316        }
317    }
318
319    public void convert(File dicomFile, File xmlFile) throws IOException,
320            TransformerConfigurationException {
321        OutputStream out = new BufferedOutputStream(new FileOutputStream(xmlFile));
322        try {
323            convert(dicomFile, out);
324        } finally {
325            out.close();
326        }
327    }
328
329    private TransformerHandler getTransformerHandler()
330            throws TransformerConfigurationException, IOException {
331        SAXTransformerFactory tf = (SAXTransformerFactory)
332                TransformerFactory.newInstance();
333        if (xsltURL == null)
334            return tf.newTransformerHandler();
335
336        TransformerHandler th = tf.newTransformerHandler(
337                new StreamSource(xsltURL));
338        return th;
339    }
340}