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 https://github.com/gunterze/dcm4che. * * The Initial Developer of the Original Code is * Agfa Healthcare. * Portions created by the Initial Developer are Copyright (C) 2013 * the Initial Developer. All Rights Reserved. * * Contributor(s): * See @authors listed below * * 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.dcm4che.tool.emf2sf; import java.io.File; import java.io.IOException; import java.text.DecimalFormat; import java.text.MessageFormat; import java.util.List; import java.util.ResourceBundle; import org.apache.commons.cli.CommandLine; import org.apache.commons.cli.OptionBuilder; import org.apache.commons.cli.Options; import org.apache.commons.cli.ParseException; import org.dcm4che.data.Attributes; import org.dcm4che.data.Tag; import org.dcm4che.emf.MultiframeExtractor; import org.dcm4che.io.DicomInputStream; import org.dcm4che.io.DicomInputStream.IncludeBulkData; import org.dcm4che.io.DicomOutputStream; import org.dcm4che.tool.common.CLIUtils; import org.dcm4che.util.SafeClose; /** * @author Gunter Zeilinger <gunterze@gmail.com> * */ public class Emf2sf { private static ResourceBundle rb = ResourceBundle.getBundle("org.dcm4che.tool.emf2sf.messages"); private MultiframeExtractor extractor = new MultiframeExtractor(); private int[] frames; private DecimalFormat outFileFormat; private File outDir; public final void setOutputDirectory(File outDir) { outDir.mkdirs(); this.outDir = outDir; } public final void setOutputFileFormat(String outFileFormat) { this.outFileFormat = new DecimalFormat(outFileFormat); } public final void setFrames(int[] frames) { this.frames = frames; } public void setPreserveSeriesInstanceUID(boolean PreserveSeriesInstanceUID) { extractor.setPreserveSeriesInstanceUID(PreserveSeriesInstanceUID); } public void setInstanceNumberFormat(String instanceNumberFormat) { extractor.setInstanceNumberFormat(instanceNumberFormat); } @SuppressWarnings("unchecked") public static void main(String[] args) { try { CommandLine cl = parseComandLine(args); Emf2sf main = new Emf2sf(); if (cl.hasOption("frame")) main.setFrames(toFrames(cl.getOptionValues("frame"))); main.setPreserveSeriesInstanceUID(cl.hasOption("not-chseries")); main.setOutputDirectory(new File(cl.getOptionValue("out-dir", "."))); if (cl.hasOption("out-file")) main.setOutputFileFormat(cl.getOptionValue("out-file")); long start = System.currentTimeMillis(); int n = main.extract(new File(fname(cl.getArgList()))); long end = System.currentTimeMillis(); System.out.println(); System.out.println(MessageFormat.format(rb.getString("extracted"), n, (end - start) / 1000f)); } catch (ParseException e) { System.err.println("emf2sf: " + e.getMessage()); System.err.println(rb.getString("try")); System.exit(2); } catch (Exception e) { System.err.println("emf2sf: " + e.getMessage()); e.printStackTrace(); System.exit(2); } } private static int[] toFrames(String[] ss) throws ParseException { if (ss == null) return null; int[] is = new int[ss.length]; for (int i = 0; i < is.length; i++) try { is[i] = Integer.parseInt(ss[i]) - 1; } catch (NumberFormatException e) { throw new ParseException("Invalid argument of option --frame: " + ss[i]); } return is; } private String fname(File srcFile, int frame) { if (outFileFormat != null) synchronized (outFileFormat) { return outFileFormat.format(frame); } return String.format(srcFile.getName() + "-%04d", frame); } public int extract(File file) throws IOException { Attributes src; DicomInputStream dis = new DicomInputStream(file); try { dis.setIncludeBulkData(IncludeBulkData.URI); src = dis.readDataset(-1, -1); } finally { SafeClose.close(dis); } Attributes fmi = dis.getFileMetaInformation(); if (frames == null) { int n = src.getInt(Tag.NumberOfFrames, 1); for (int frame = 0; frame < n; ++frame) extract(file, fmi, src, frame); return n; } else { for (int frame : frames) extract(file, fmi, src, frame); return frames.length; } } private void extract(File file, Attributes fmi, Attributes src, int frame) throws IOException { Attributes sf = extractor.extract(src, frame); DicomOutputStream out = new DicomOutputStream(new File(outDir, fname(file, frame + 1))); try { out.writeDataset( fmi != null ? sf.createFileMetaInformation(fmi.getString(Tag.TransferSyntaxUID)) : null, sf); System.out.print('.'); } finally { SafeClose.close(out); } } @SuppressWarnings("static-access") private static CommandLine parseComandLine(String[] args) throws ParseException { Options opts = new Options(); CLIUtils.addCommonOptions(opts); opts.addOption(OptionBuilder.withLongOpt("frame").hasArgs().withArgName("no[,..]").withValueSeparator(',') .withDescription(rb.getString("frame")).create("f")); opts.addOption(null, "not-chseries", false, rb.getString("not-chseries")); opts.addOption(OptionBuilder.withLongOpt("inst-no").hasArg().withArgName("format") .withDescription(rb.getString("inst-no")).create()); opts.addOption(OptionBuilder.withLongOpt("out-dir").hasArg().withArgName("directory") .withDescription(rb.getString("out-dir")).create()); opts.addOption(OptionBuilder.withLongOpt("out-file").hasArg().withArgName("name") .withDescription(rb.getString("out-file")).create()); return CLIUtils.parseComandLine(args, opts, rb, Emf2sf.class); } private static String fname(List<String> argList) throws ParseException { int numArgs = argList.size(); if (numArgs == 0) throw new ParseException(rb.getString("missing")); if (numArgs > 1) throw new ParseException(rb.getString("too-many")); return argList.get(0); } }