Example usage for org.apache.commons.cli CommandLine getArgList

Introduction

In this page you can find the example usage for org.apache.commons.cli CommandLine getArgList.

Prototype

public List getArgList() 

Source Link

Document

Retrieve any left-over non-recognized options and arguments

Usage

From source file:org.dcm4che2.tool.rgb2ybr.Rgb2Ybr.java

public static void main(String[] args) {
    try {/*from www  . j  a v a2 s . co m*/
        CommandLine cl = parse(args);
        List argList = cl.getArgList();
        File ifile = new File((String) argList.get(0));
        File ofile = new File((String) argList.get(1));
        Rgb2Ybr rgb2ybr = new Rgb2Ybr();
        rgb2ybr.setPartial(cl.hasOption("p"));
        rgb2ybr.setInvers(cl.hasOption("i"));
        rgb2ybr.setOutput(ofile);
        long start = System.currentTimeMillis();
        rgb2ybr.convert(ifile);
        long fin = System.currentTimeMillis();
        System.out.println("Convert " + ifile + " to " + ofile + " in " + (fin - start) + "ms.");
    } catch (Exception e) {
        e.printStackTrace();
    }
}

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From source file:org.dcm4che2.tool.txt2dcmsr.Txt2DcmSR.java

public static void main(String[] args) {
    try {//from   w  ww  .  j  av  a  2  s  .c  om
        CommandLine cl = parse(args);
        Txt2DcmSR txt2dcmsr = new Txt2DcmSR();
        if (cl.hasOption("ivrle")) {
            txt2dcmsr.setTransferSyntax(UID.ImplicitVRLittleEndian);
        }
        if (cl.hasOption("cs")) {
            txt2dcmsr.setCharset(cl.getOptionValue("cs"));
        }
        if (cl.hasOption("c")) {
            txt2dcmsr.loadConfiguration(new File(cl.getOptionValue("c")));
        }
        if (cl.hasOption("uid")) {
            UIDUtils.setRoot(cl.getOptionValue("uid"));
        }
        txt2dcmsr.setParagraphs(cl.hasOption("para"));
        List argList = cl.getArgList();
        File txtFile = new File((String) argList.get(0));
        File dcmFile = new File((String) argList.get(1));
        long start = System.currentTimeMillis();
        txt2dcmsr.convert(txtFile, dcmFile);
        long fin = System.currentTimeMillis();
        System.out.println("Convert " + txtFile + " to " + dcmFile + " in " + (fin - start) + "ms.");
    } catch (IOException e) {
        e.printStackTrace();
    }
}

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From source file:org.dcm4che2.tool.txt2dcmsr.Txt2DcmSR.java

private static CommandLine parse(String[] args) {
    Options opts = new Options();

    OptionBuilder.withArgName("charset");
    OptionBuilder.hasArg();/*from   ww w. ja v  a  2 s. c o m*/
    OptionBuilder.withDescription("Specific Character Set, ISO_IR 100 by default");
    opts.addOption(OptionBuilder.create("cs"));

    OptionBuilder.withArgName("file");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription("Configuration file specifying DICOM attribute values");
    opts.addOption(OptionBuilder.create("c"));

    OptionBuilder.withArgName("prefix");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription("Generate UIDs with given prefix," + "1.2.40.0.13.1.<host-ip> by default.");
    opts.addOption(OptionBuilder.create("uid"));

    opts.addOption("para", false, "Separate text in paragraphs according line delimiters");

    opts.addOption("ivrle", false, "use Implicit VR Little Endian instead "
            + "Explicit VR Little Endian Transfer Syntax for DICOM encoding.");
    opts.addOption("h", "help", false, "print this message");

    opts.addOption("V", "version", false, "print the version information and exit");
    CommandLine cl = null;
    try {
        cl = new GnuParser().parse(opts, args);
    } catch (ParseException e) {
        exit("txt2dcmsr: " + e.getMessage());
        throw new RuntimeException("unreachable");
    }
    if (cl.hasOption('V')) {
        Package p = Txt2DcmSR.class.getPackage();
        System.out.println("txt2dcmsr 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;
}

---

From source file:org.dcm4che3.tool.common.DetectEndOfOptionsPosixParser.java

@Override
public CommandLine parse(Options opts, String[] args, Properties props, boolean stopAtNonOption)
        throws ParseException {
    int i = args.length;
    while (--i >= 0 && !"--".equals(args[i]))
        ;/* w w w . j  av  a 2  s . c  o m*/
    CommandLine cl = super.parse(opts, i < 0 ? args : Arrays.copyOf(args, i), props, stopAtNonOption);
    if (i >= 0)
        while (++i < args.length)
            cl.getArgList().add(args[i]);
    return cl;
}

---

From source file:org.dcm4che3.tool.dcm2json.Dcm2Json.java

@SuppressWarnings("unchecked")
public static void main(String[] args) {
    try {/*from   w  w w  .j av a  2 s.co  m*/
        CommandLine cl = parseComandLine(args);
        Dcm2Json main = new Dcm2Json();
        main.setIndent(cl.hasOption("I"));
        configureBulkdata(main, cl);
        String fname = fname(cl.getArgList());
        if (fname.equals("-")) {
            main.convert(new DicomInputStream(System.in), System.out);
        } else {
            main.convert(new File(fname), System.out);
        }
    } catch (ParseException e) {
        System.err.println("dcm2xml: " + e.getMessage());
        System.err.println(rb.getString("try"));
        System.exit(2);
    } catch (Exception e) {
        System.err.println("dcm2xml: " + e.getMessage());
        e.printStackTrace();
        System.exit(2);
    }
}

---

From source file:org.dcm4che3.tool.dcm2xml.Dcm2Xml.java

@SuppressWarnings("unchecked")
public static void main(String[] args) {
    try {//  ww w. j  a v  a 2  s  .com
        CommandLine cl = parseComandLine(args);
        Dcm2Xml main = new Dcm2Xml();
        if (cl.hasOption("x"))
            main.setXSLTURL(toURL(cl.getOptionValue("x")));
        main.setIndent(cl.hasOption("I"));
        main.setIncludeKeyword(!cl.hasOption("K"));
        main.setIncludeNamespaceDeclaration(cl.hasOption("xmlns"));
        if (cl.hasOption("xml11"))
            main.setXMLVersion(XML_1_1);
        configureBulkdata(main, cl);
        String fname = fname(cl.getArgList());
        if (fname.equals("-")) {
            main.convert(new DicomInputStream(System.in), System.out);
        } else {
            main.convert(new File(fname), System.out);
        }
    } catch (ParseException e) {
        System.err.println("dcm2xml: " + e.getMessage());
        System.err.println(rb.getString("try"));
        System.exit(2);
    } catch (Exception e) {
        System.err.println("dcm2xml: " + e.getMessage());
        e.printStackTrace();
        System.exit(2);
    }
}

---

From source file:org.dcm4che3.tool.dcmdict.DcmDict.java

@SuppressWarnings("unchecked")
public static void main(String[] args) {
    CommandLine cl = null;
    try {//ww w  .j  av  a 2 s  .co m
        DcmDict main = new DcmDict();
        cl = parseComandLine(args);

        if (cl.hasOption("private-creator")) {
            String creator = cl.getOptionValue("private-creator");
            main.dict = ElementDictionary.getElementDictionary(creator);
        } else {
            main.dict = ElementDictionary.getStandardElementDictionary();
        }
        main.queryKeys = (LinkedList<String>) cl.getArgList();
        if (hasAbbreviation(main.queryKeys)) {
            buildCamelCaseMap(main);
        }
        buildMatches(main);
        if (!main.matches.isEmpty()) {
            printMatches(main);
        }
        if (!main.queryKeys.isEmpty()) {
            buildSuggestions(main);
            System.out.println(hashtag());
            printSuggestions(main);
        }
    } catch (ParseException e) {
        LOG.error("dcmdict\t" + e.getMessage());
        System.err.println(rb.getString("try"));
        System.exit(2);
    }
}

---

From source file:org.dcm4che3.tool.dcmgen.DcmGen.java

public static void main(String[] args) {
    CommandLine cl = null;
    try {/*from w w w.j  av a2 s .  c  o  m*/
        DcmGen main = new DcmGen();
        cl = parseComandLine(args);
        Attributes overrideAttrs = new Attributes();

        if (cl.getArgList().size() < 2) {
            throw new ParseException("Missing required arguments");
        } else {
            if (cl.hasOption("override")) {
                CLIUtils.addAttributes(overrideAttrs, cl.getOptionValues("override"));
            }
            if (cl.getArgs()[0].contains(":"))
                setCounts(cl, main, true);
            else
                setCounts(cl, main, false);
            if (cl.getArgList().size() == 3) {
                main.seedFile = new File(cl.getArgs()[1]);
                main.outputDir = new File(cl.getArgs()[2]);
            } else if (cl.getArgList().size() == 2) {
                main.seedFile = new File(cl.getArgs()[1]);
                main.outputDir = new File("./");
            }

            else {
                throw new ParseException("Too many arguments specified");
            }
            if (main.seriesCount > main.instanceCount) {
                throw new ParseException("Series count can not exceeed instance count");
            }
            main.generateDICOM(overrideAttrs);
        }

    } catch (ParseException e) {
        LOG.error("DcmGen\t" + e.getMessage());
        System.err.println(rb.getString("try"));
        System.exit(2);
    }
}

---

From source file:org.dcm4che3.tool.hl7snd.HL7Snd.java

@SuppressWarnings("unchecked")
public static void main(String[] args) {
    try {/* w  ww .j  a v a 2 s.  c o  m*/
        CommandLine cl = parseComandLine(args);
        HL7Snd main = new HL7Snd();
        configureConnect(main.remote, cl);
        configureBind(main.conn, cl);
        CLIUtils.configure(main.conn, cl);
        main.remote.setTlsProtocols(main.conn.getTlsProtocols());
        main.remote.setTlsCipherSuites(main.conn.getTlsCipherSuites());
        try {
            main.open();
            main.sendFiles(cl.getArgList());
        } finally {
            main.close();
        }
    } catch (ParseException e) {
        System.err.println("hl7snd: " + e.getMessage());
        System.err.println(rb.getString("try"));
        System.exit(2);
    } catch (Exception e) {
        System.err.println("hl7snd: " + e.getMessage());
        e.printStackTrace();
        System.exit(2);
    }
}

---

From source file:org.dcm4che3.tool.ihe.modality.Modality.java

@SuppressWarnings({ "unchecked" })
public static void main(String[] args) {
    try {/*from   w  ww.j  a  v a2s.com*/
        CommandLine cl = parseComandLine(args);
        if (cl.getArgList().isEmpty())
            throw new MissingOptionException(rb.getString("missing-i-file"));
        final Device device = new Device("modality");
        final Connection conn = new Connection();
        final ApplicationEntity ae = new ApplicationEntity("MODALITY");
        checkOptions(cl);
        CLIUtils.configureBind(conn, ae, cl);
        CLIUtils.configure(conn, cl);
        device.addConnection(conn);
        device.addApplicationEntity(ae);
        ae.addConnection(conn);
        final MppsSCU mppsscu = new MppsSCU(ae);
        final StoreSCU storescu = new StoreSCU(ae);
        final StgCmtSCU stgcmtscu = new StgCmtSCU(ae);
        CLIUtils.configureConnect(mppsscu.getRemoteConnection(), mppsscu.getAAssociateRQ(), cl);
        CLIUtils.configureConnect(stgcmtscu.getRemoteConnection(), stgcmtscu.getAAssociateRQ(), cl);
        CLIUtils.configureConnect(storescu.getRemoteConnection(), storescu.getAAssociateRQ(), cl);
        calledAET = storescu.getAAssociateRQ().getCalledAET();
        mppsscu.setTransferSyntaxes(CLIUtils.transferSyntaxesOf(cl));
        mppsscu.setCodes(
                CLIUtils.loadProperties(cl.getOptionValue("code-config", "resource:code.properties"), null));
        if (cl.hasOption("dc"))
            mppsscu.setFinalStatus("DISCONTINUED");
        if (cl.hasOption("dc-reason"))
            mppsscu.setDiscontinuationReason(cl.getOptionValue("dc-reason"));
        stgcmtscu.setTransferSyntaxes(CLIUtils.transferSyntaxesOf(cl));
        stgcmtscu.setStorageDirectory(StgCmtSCU.getStorageDirectory(cl));
        StoreSCU.configureRelatedSOPClass(storescu, cl);
        storescu.setUIDSuffix(StoreSCU.uidSuffixOf(cl));
        Attributes attrs = new Attributes();
        CLIUtils.addAttributes(attrs, cl.getOptionValues("s"));
        mppsscu.setAttributes(attrs);
        storescu.setAttributes(attrs);
        stgcmtscu.setAttributes(attrs);
        setTlsParams(mppsscu.getRemoteConnection(), conn);
        setTlsParams(storescu.getRemoteConnection(), conn);
        setTlsParams(stgcmtscu.getRemoteConnection(), conn);
        String tmpPrefix = "iocmtest-";
        String tmpSuffix = null;
        File tmpDir = null;
        configureTmpFile(storescu, tmpPrefix, tmpSuffix, tmpDir, cl);
        String mppsiuid = UIDUtils.createUID();
        mppsscu.setPPSUID(mppsiuid);
        if (cl.hasOption("kos-title")) {
            List<String> fname = Arrays.asList(mkkos(cl));
            scanFiles(fname, tmpPrefix, tmpSuffix, tmpDir, mppsscu, storescu, stgcmtscu);
        } else {
            stgcmtscu.setUIDSuffix(cl.getOptionValue("uid-suffix"));
            storescu.setUIDSuffix(cl.getOptionValue("uid-suffix"));
            mppsscu.setUIDSuffix(cl.getOptionValue("uid-suffix"));
            scanFiles(cl.getArgList(), tmpPrefix, tmpSuffix, tmpDir, mppsscu, storescu, stgcmtscu);
        }
        ExecutorService executorService = Executors.newCachedThreadPool();
        ScheduledExecutorService scheduledExecutorService = Executors.newSingleThreadScheduledExecutor();
        device.setExecutor(executorService);
        device.setScheduledExecutor(scheduledExecutorService);
        device.bindConnections();
        try {
            boolean sendMpps = cl.hasOption("mpps");
            boolean sendLateMpps = cl.hasOption("mpps-late");
            if (sendMpps || sendLateMpps) {
                sendMpps(mppsscu, sendMpps);
                addReferencedPerformedProcedureStepSequence(mppsiuid, storescu);
            } else {
                nullifyReferencedPerformedProcedureStepSequence(storescu);
            }
            sendObjects(storescu);
            if (sendLateMpps)
                sendMppsNSet(mppsscu);
            if (cl.hasOption("stgcmt"))
                sendStgCmt(stgcmtscu);
        } finally {
            if (conn.isListening()) {
                device.waitForNoOpenConnections();
                device.unbindConnections();
            }
            executorService.shutdown();
            scheduledExecutorService.shutdown();
        }
    } catch (ParseException e) {
        System.err.println(e.getMessage());
        System.err.println(rb.getString("try"));
        System.exit(2);
    } catch (Exception e) {
        System.err.println(e.getMessage());
        e.printStackTrace();
        System.exit(2);
    }
}

---

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