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

List of usage examples for org.apache.commons.cli CommandLine getArgList

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Introduction

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

Prototype

public List getArgList()

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Document

Retrieve any left-over non-recognized options and arguments

Usage

From source file:org.dcm4che2.tool.dcmsnd.DcmSnd.java

@SuppressWarnings("unchecked")
public static void execute(String[] args) throws Exception {
    CommandLine cl = parse(args);
    DcmSnd dcmsnd = new DcmSnd(cl.hasOption("device") ? cl.getOptionValue("device") : "DCMSND");
    final List<String> argList = cl.getArgList();
    String remoteAE = argList.get(0);
    String[] calledAETAddress = split(remoteAE, '@');
    dcmsnd.setCalledAET(calledAETAddress[0]);
    if (calledAETAddress[1] == null) {
        dcmsnd.setRemoteHost("127.0.0.1");
        dcmsnd.setRemotePort(104);//from  w  w  w . j  a v  a2s .  com
    } else {
        String[] hostPort = split(calledAETAddress[1], ':');
        dcmsnd.setRemoteHost(hostPort[0]);
        dcmsnd.setRemotePort(toPort(hostPort[1]));
    }
    if (cl.hasOption("L")) {
        String localAE = cl.getOptionValue("L");
        String[] localPort = split(localAE, ':');
        if (localPort[1] != null) {
            dcmsnd.setLocalPort(toPort(localPort[1]));
        }
        String[] callingAETHost = split(localPort[0], '@');
        dcmsnd.setCalling(callingAETHost[0]);
        if (callingAETHost[1] != null) {
            dcmsnd.setLocalHost(callingAETHost[1]);
        }
    }
    dcmsnd.setOfferDefaultTransferSyntaxInSeparatePresentationContext(cl.hasOption("ts1"));
    dcmsnd.setSendFileRef(cl.hasOption("fileref"));
    if (cl.hasOption("username")) {
        String username = cl.getOptionValue("username");
        UserIdentity userId;
        if (cl.hasOption("passcode")) {
            String passcode = cl.getOptionValue("passcode");
            userId = new UserIdentity.UsernamePasscode(username, passcode.toCharArray());
        } else {
            userId = new UserIdentity.Username(username);
        }
        userId.setPositiveResponseRequested(cl.hasOption("uidnegrsp"));
        dcmsnd.setUserIdentity(userId);
    }
    dcmsnd.setStorageCommitment(cl.hasOption("stgcmt"));
    String remoteStgCmtAE = null;
    if (cl.hasOption("stgcmtae")) {
        try {
            remoteStgCmtAE = cl.getOptionValue("stgcmtae");
            String[] aet_hostport = split(remoteStgCmtAE, '@');
            String[] host_port = split(aet_hostport[1], ':');
            dcmsnd.setStgcmtCalledAET(aet_hostport[0]);
            dcmsnd.setRemoteStgcmtHost(host_port[0]);
            dcmsnd.setRemoteStgcmtPort(toPort(host_port[1]));
        } catch (Exception e) {
            exit("illegal argument of option -stgcmtae");
        }
    }
    if (cl.hasOption("set")) {
        String[] vals = cl.getOptionValues("set");
        for (int i = 0; i < vals.length; i++, i++) {
            dcmsnd.addCoerceAttr(Tag.toTag(vals[i]), vals[i + 1]);
        }
    }
    if (cl.hasOption("setuid")) {
        dcmsnd.setSuffixUID(cl.getOptionValues("setuid"));
    }
    if (cl.hasOption("connectTO"))
        dcmsnd.setConnectTimeout(parseInt(cl.getOptionValue("connectTO"),
                "illegal argument of option -connectTO", 1, Integer.MAX_VALUE));
    if (cl.hasOption("reaper"))
        dcmsnd.setAssociationReaperPeriod(parseInt(cl.getOptionValue("reaper"),
                "illegal argument of option -reaper", 1, Integer.MAX_VALUE));
    if (cl.hasOption("rspTO"))
        dcmsnd.setDimseRspTimeout(parseInt(cl.getOptionValue("rspTO"), "illegal argument of option -rspTO", 1,
                Integer.MAX_VALUE));
    if (cl.hasOption("acceptTO"))
        dcmsnd.setAcceptTimeout(parseInt(cl.getOptionValue("acceptTO"), "illegal argument of option -acceptTO",
                1, Integer.MAX_VALUE));
    if (cl.hasOption("releaseTO"))
        dcmsnd.setReleaseTimeout(parseInt(cl.getOptionValue("releaseTO"),
                "illegal argument of option -releaseTO", 1, Integer.MAX_VALUE));
    if (cl.hasOption("soclosedelay"))
        dcmsnd.setSocketCloseDelay(parseInt(cl.getOptionValue("soclosedelay"),
                "illegal argument of option -soclosedelay", 1, 10000));
    if (cl.hasOption("shutdowndelay"))
        dcmsnd.setShutdownDelay(parseInt(cl.getOptionValue("shutdowndelay"),
                "illegal argument of option -shutdowndelay", 1, 10000));
    if (cl.hasOption("rcvpdulen"))
        dcmsnd.setMaxPDULengthReceive(
                parseInt(cl.getOptionValue("rcvpdulen"), "illegal argument of option -rcvpdulen", 1, 10000)
                        * KB);
    if (cl.hasOption("sndpdulen"))
        dcmsnd.setMaxPDULengthSend(
                parseInt(cl.getOptionValue("sndpdulen"), "illegal argument of option -sndpdulen", 1, 10000)
                        * KB);
    if (cl.hasOption("sosndbuf"))
        dcmsnd.setSendBufferSize(
                parseInt(cl.getOptionValue("sosndbuf"), "illegal argument of option -sosndbuf", 1, 10000) * KB);
    if (cl.hasOption("sorcvbuf"))
        dcmsnd.setReceiveBufferSize(
                parseInt(cl.getOptionValue("sorcvbuf"), "illegal argument of option -sorcvbuf", 1, 10000) * KB);
    if (cl.hasOption("bufsize"))
        dcmsnd.setTranscoderBufferSize(
                parseInt(cl.getOptionValue("bufsize"), "illegal argument of option -bufsize", 1, 10000) * KB);
    dcmsnd.setPackPDV(!cl.hasOption("pdv1"));
    dcmsnd.setTcpNoDelay(!cl.hasOption("tcpdelay"));
    if (cl.hasOption("async"))
        dcmsnd.setMaxOpsInvoked(
                parseInt(cl.getOptionValue("async"), "illegal argument of option -async", 0, 0xffff));
    if (cl.hasOption("lowprior"))
        dcmsnd.setPriority(CommandUtils.LOW);
    if (cl.hasOption("highprior"))
        dcmsnd.setPriority(CommandUtils.HIGH);
    System.out.println("Scanning files to send");
    long t1 = System.currentTimeMillis();
    for (int i = 1, n = argList.size(); i < n; ++i)
        dcmsnd.addFile(new File(argList.get(i)));
    long t2 = System.currentTimeMillis();
    if (dcmsnd.getNumberOfFilesToSend() == 0) {
        //System.exit( 2 );
        throw new RuntimeException();
    }
    System.out.println("\nScanned " + dcmsnd.getNumberOfFilesToSend() + " files in " + ((t2 - t1) / 1000F)
            + "s (=" + ((t2 - t1) / dcmsnd.getNumberOfFilesToSend()) + "ms/file)");
    dcmsnd.configureTransferCapability();
    if (cl.hasOption("tls")) {
        String cipher = cl.getOptionValue("tls");
        if ("NULL".equalsIgnoreCase(cipher)) {
            dcmsnd.setTlsWithoutEncyrption();
        } else if ("3DES".equalsIgnoreCase(cipher)) {
            dcmsnd.setTls3DES_EDE_CBC();
        } else if ("AES".equalsIgnoreCase(cipher)) {
            dcmsnd.setTlsAES_128_CBC();
        } else {
            exit("Invalid parameter for option -tls: " + cipher);
        }

        if (cl.hasOption("tls1")) {
            dcmsnd.setTlsProtocol(TLS1);
        } else if (cl.hasOption("ssl3")) {
            dcmsnd.setTlsProtocol(SSL3);
        } else if (cl.hasOption("no_tls1")) {
            dcmsnd.setTlsProtocol(NO_TLS1);
        } else if (cl.hasOption("no_ssl3")) {
            dcmsnd.setTlsProtocol(NO_SSL3);
        } else if (cl.hasOption("no_ssl2")) {
            dcmsnd.setTlsProtocol(NO_SSL2);
        }
        dcmsnd.setTlsNeedClientAuth(!cl.hasOption("noclientauth"));

        if (cl.hasOption("keystore")) {
            dcmsnd.setKeyStoreURL(cl.getOptionValue("keystore"));
        }
        if (cl.hasOption("keystorepw")) {
            dcmsnd.setKeyStorePassword(cl.getOptionValue("keystorepw"));
        }
        if (cl.hasOption("keypw")) {
            dcmsnd.setKeyPassword(cl.getOptionValue("keypw"));
        }
        if (cl.hasOption("truststore")) {
            dcmsnd.setTrustStoreURL(cl.getOptionValue("truststore"));
        }
        if (cl.hasOption("truststorepw")) {
            dcmsnd.setTrustStorePassword(cl.getOptionValue("truststorepw"));
        }
        try {
            dcmsnd.initTLS();
        } catch (Exception e) {
            System.err.println("ERROR: Failed to initialize TLS context:" + e.getMessage());
            //System.exit( 2 );
            throw new RuntimeException();
        }
    }
    try {
        dcmsnd.start();
    } catch (Exception e) {
        System.err.println("ERROR: Failed to start server for receiving " + "Storage Commitment results:"
                + e.getMessage());
        //System.exit( 2 );
        throw new RuntimeException();
    }
    try {
        t1 = System.currentTimeMillis();
        try {
            dcmsnd.open();
        } catch (Exception e) {
            System.err.println("ERROR: Failed to establish association:" + e.getMessage());
            //System.exit( 2 );
            throw new RuntimeException();
        }
        t2 = System.currentTimeMillis();
        System.out.println("Connected to " + remoteAE + " in " + ((t2 - t1) / 1000F) + "s");

        t1 = System.currentTimeMillis();
        dcmsnd.send();
        t2 = System.currentTimeMillis();
        prompt(dcmsnd, (t2 - t1) / 1000F);
        if (dcmsnd.isStorageCommitment()) {
            t1 = System.currentTimeMillis();
            if (dcmsnd.commit()) {
                t2 = System.currentTimeMillis();
                System.out.println(
                        "Request Storage Commitment from " + remoteAE + " in " + ((t2 - t1) / 1000F) + "s");
                System.out.println("Waiting for Storage Commitment Result..");
                try {
                    DicomObject cmtrslt = dcmsnd.waitForStgCmtResult();
                    t1 = System.currentTimeMillis();
                    promptStgCmt(cmtrslt, ((t1 - t2) / 1000F));
                } catch (InterruptedException e) {
                    System.err.println("ERROR:" + e.getMessage());
                }
            }
        }
        dcmsnd.close();
        System.out.println("Released connection to " + remoteAE);
        if (remoteStgCmtAE != null) {
            t1 = System.currentTimeMillis();
            try {
                dcmsnd.openToStgcmtAE();
            } catch (Exception e) {
                System.err.println("ERROR: Failed to establish association:" + e.getMessage());
                //System.exit( 2 );
                throw new RuntimeException();
            }
            t2 = System.currentTimeMillis();
            System.out.println("Connected to " + remoteStgCmtAE + " in " + ((t2 - t1) / 1000F) + "s");
            t1 = System.currentTimeMillis();
            if (dcmsnd.commit()) {
                t2 = System.currentTimeMillis();
                System.out.println("Request Storage Commitment from " + remoteStgCmtAE + " in "
                        + ((t2 - t1) / 1000F) + "s");
                System.out.println("Waiting for Storage Commitment Result..");
                try {
                    DicomObject cmtrslt = dcmsnd.waitForStgCmtResult();
                    t1 = System.currentTimeMillis();
                    promptStgCmt(cmtrslt, ((t1 - t2) / 1000F));
                } catch (InterruptedException e) {
                    System.err.println("ERROR:" + e.getMessage());
                }
            }
            dcmsnd.close();
            System.out.println("Released connection to " + remoteStgCmtAE);
        }
    } finally {
        dcmsnd.stop();
    }
}

From source file:org.dcm4che2.tool.dcmups.DcmUPS.java

@SuppressWarnings("unchecked")
public static void main(String[] args) {
    CommandLine cl = parse(args);
    DcmUPS dcmups = new DcmUPS(cl.hasOption("device") ? cl.getOptionValue("device") : "DCMUPSSCU");
    final List<String> argList = cl.getArgList();
    Operation op = null;//from www .j av a 2 s  .  c  o m
    String remoteAE = null;
    if (!argList.isEmpty()) {
        op = toOperation(argList.get(0));
        dcmups.setSOPClassUID(op.sopClassUID);
        if (argList.size() < 2)
            exit("Missing <aet>[@<host>[:<port>]] after <operation>.");
        remoteAE = argList.get(1);
        String[] calledAETAddress = split(remoteAE, '@');
        dcmups.setCalledAET(calledAETAddress[0]);
        if (calledAETAddress[1] == null) {
            dcmups.setRemoteHost("127.0.0.1");
            dcmups.setRemotePort(104);
        } else {
            String[] hostPort = split(calledAETAddress[1], ':');
            dcmups.setRemoteHost(hostPort[0]);
            dcmups.setRemotePort(toPort(hostPort[1]));
        }
        if (argList.size() > 2)
            exit("Too many arguments.");
    }
    if (cl.hasOption("L")) {
        String localAE = cl.getOptionValue("L");
        String[] localPort = split(localAE, ':');
        if (localPort[1] != null)
            dcmups.setLocalPort(toPort(localPort[1]));
        String[] callingAETHost = split(localPort[0], '@');
        dcmups.setCalling(callingAETHost[0]);
        if (callingAETHost[1] != null) {
            dcmups.setLocalHost(callingAETHost[1]);
        }
    }
    if (cl.hasOption("username")) {
        String username = cl.getOptionValue("username");
        UserIdentity userId;
        if (cl.hasOption("passcode")) {
            String passcode = cl.getOptionValue("passcode");
            userId = new UserIdentity.UsernamePasscode(username, passcode.toCharArray());
        } else {
            userId = new UserIdentity.Username(username);
        }
        userId.setPositiveResponseRequested(cl.hasOption("uidnegrsp"));
        dcmups.setUserIdentity(userId);
    }
    if (cl.hasOption("connectTO"))
        dcmups.setConnectTimeout(parseInt(cl.getOptionValue("connectTO"),
                "illegal argument of option -connectTO", 1, Integer.MAX_VALUE));
    if (cl.hasOption("reaper"))
        dcmups.setAssociationReaperPeriod(parseInt(cl.getOptionValue("reaper"),
                "illegal argument of option -reaper", 1, Integer.MAX_VALUE));
    if (cl.hasOption("cfindrspTO"))
        dcmups.setDimseRspTimeout(parseInt(cl.getOptionValue("cfindrspTO"),
                "illegal argument of option -cfindrspTO", 1, Integer.MAX_VALUE));
    if (cl.hasOption("acceptTO"))
        dcmups.setAcceptTimeout(parseInt(cl.getOptionValue("acceptTO"), "illegal argument of option -acceptTO",
                1, Integer.MAX_VALUE));
    if (cl.hasOption("releaseTO"))
        dcmups.setReleaseTimeout(parseInt(cl.getOptionValue("releaseTO"),
                "illegal argument of option -releaseTO", 1, Integer.MAX_VALUE));
    if (cl.hasOption("soclosedelay"))
        dcmups.setSocketCloseDelay(parseInt(cl.getOptionValue("soclosedelay"),
                "illegal argument of option -soclosedelay", 1, 10000));
    if (cl.hasOption("rcvpdulen"))
        dcmups.setMaxPDULengthReceive(
                parseInt(cl.getOptionValue("rcvpdulen"), "illegal argument of option -rcvpdulen", 1, 10000)
                        * KB);
    if (cl.hasOption("sndpdulen"))
        dcmups.setMaxPDULengthSend(
                parseInt(cl.getOptionValue("sndpdulen"), "illegal argument of option -sndpdulen", 1, 10000)
                        * KB);
    if (cl.hasOption("sosndbuf"))
        dcmups.setSendBufferSize(
                parseInt(cl.getOptionValue("sosndbuf"), "illegal argument of option -sosndbuf", 1, 10000) * KB);
    if (cl.hasOption("sorcvbuf"))
        dcmups.setReceiveBufferSize(
                parseInt(cl.getOptionValue("sorcvbuf"), "illegal argument of option -sorcvbuf", 1, 10000) * KB);
    dcmups.setPackPDV(!cl.hasOption("pdv1"));
    dcmups.setTcpNoDelay(!cl.hasOption("tcpdelay"));
    if (cl.hasOption("findprior"))
        dcmups.setPriority(toPriority(cl.getOptionValue("findprior")));

    if (cl.hasOption("r")) {
        String[] returnKeys = cl.getOptionValues("r");
        for (int i = 0; i < returnKeys.length; i++)
            dcmups.addReturnKey(Tag.toTagPath(returnKeys[i]));
    } else if (op == Operation.find)
        dcmups.addDefReturnKeys();

    if (cl.hasOption("q")) {
        String[] matchingKeys = cl.getOptionValues("q");
        for (int i = 1; i < matchingKeys.length; i++, i++)
            dcmups.addMatchingKey(Tag.toTagPath(matchingKeys[i - 1]), matchingKeys[i]);
    }

    dcmups.configureTransferCapability(cl.hasOption("ivrle") ? IVRLE_TS : NATIVE_LE_TS);

    if (cl.hasOption("tls")) {
        String cipher = cl.getOptionValue("tls");
        if ("NULL".equalsIgnoreCase(cipher)) {
            dcmups.setTlsWithoutEncyrption();
        } else if ("3DES".equalsIgnoreCase(cipher)) {
            dcmups.setTls3DES_EDE_CBC();
        } else if ("AES".equalsIgnoreCase(cipher)) {
            dcmups.setTlsAES_128_CBC();
        } else {
            exit("Invalid parameter for option -tls: " + cipher);
        }
        if (cl.hasOption("tls1")) {
            dcmups.setTlsProtocol(TLS1);
        } else if (cl.hasOption("ssl3")) {
            dcmups.setTlsProtocol(SSL3);
        } else if (cl.hasOption("no_tls1")) {
            dcmups.setTlsProtocol(NO_TLS1);
        } else if (cl.hasOption("no_ssl3")) {
            dcmups.setTlsProtocol(NO_SSL3);
        } else if (cl.hasOption("no_ssl2")) {
            dcmups.setTlsProtocol(NO_SSL2);
        }
        dcmups.setTlsNeedClientAuth(!cl.hasOption("noclientauth"));
        if (cl.hasOption("keystore")) {
            dcmups.setKeyStoreURL(cl.getOptionValue("keystore"));
        }
        if (cl.hasOption("keystorepw")) {
            dcmups.setKeyStorePassword(cl.getOptionValue("keystorepw"));
        }
        if (cl.hasOption("keypw")) {
            dcmups.setKeyPassword(cl.getOptionValue("keypw"));
        }
        if (cl.hasOption("truststore")) {
            dcmups.setTrustStoreURL(cl.getOptionValue("truststore"));
        }
        if (cl.hasOption("truststorepw")) {
            dcmups.setTrustStorePassword(cl.getOptionValue("truststorepw"));
        }
        long t1 = System.currentTimeMillis();
        try {
            dcmups.initTLS();
        } catch (Exception e) {
            System.err.println("ERROR: Failed to initialize TLS context:" + e.getMessage());
            System.exit(2);
        }
        long t2 = System.currentTimeMillis();
        LOG.info("Initialize TLS context in {} s", Float.valueOf((t2 - t1) / 1000f));
    }

    if (cl.hasOption("f"))
        try {
            dcmups.load(new File(cl.getOptionValue("f")));
        } catch (Exception e) {
            exit(e.getMessage());
        }
    else if (op == Operation.create || op == Operation.set)
        exit("Missing option -f");

    if (cl.hasOption("iuid"))
        dcmups.setSOPInstanceUID(cl.getOptionValue("iuid"));
    else if (op == Operation.set || op == Operation.get || op == Operation.chstate)
        exit("Missing option -iuid");

    if (cl.hasOption("state"))
        dcmups.setState(cl.getOptionValue("state"));
    else if (op == Operation.chstate)
        exit("Missing option -state");

    if (op == Operation.subscribe || op == Operation.unsubscribe || op == Operation.suspend
            || op == Operation.reqcancel) {
        if (cl.hasOption("aet"))
            if (op == Operation.reqcancel)
                dcmups.setRequestingAE(cl.getOptionValue("aet"));
            else {
                dcmups.setReceivingAE(cl.getOptionValue("aet"));
                if (op == Operation.subscribe)
                    dcmups.setDeletionLock(cl.hasOption("dellock"));
            }
        else
            exit("Missing option -aet");
    }

    if (cl.hasOption("tuid"))
        dcmups.setTransactionUID(cl.getOptionValue("tuid"));
    else if (op == Operation.chstate)
        exit("Missing option -tuid");

    if (cl.hasOption("upspush"))
        dcmups.setSOPClassUID(UID.UnifiedProcedureStepPushSOPClass);

    if (cl.hasOption("upspull"))
        dcmups.setSOPClassUID(UID.UnifiedProcedureStepPullSOPClass);

    if (cl.hasOption("upswatch"))
        dcmups.setSOPClassUID(UID.UnifiedProcedureStepWatchSOPClass);

    try {
        if (!dcmups.start() && op == null)
            exit("Missing -L aet[@host]:port");
    } catch (Exception e) {
        System.err.println(
                "ERROR: Failed to start server for receiving " + "requested objects:" + e.getMessage());
        System.exit(2);
    }
    if (op != null) {
        long t1 = System.currentTimeMillis();
        try {
            dcmups.open();
        } catch (Exception e) {
            LOG.error("Failed to establish association:", e);
            System.exit(2);
        }
        long t2 = System.currentTimeMillis();
        LOG.info("Connected to {} in {} s", remoteAE, Float.valueOf((t2 - t1) / 1000f));
        try {
            op.execute(dcmups);
        } catch (IOException e) {
            LOG.error(e.getMessage(), e);
        } catch (InterruptedException e) {
            LOG.error(e.getMessage(), e);
        } finally {
            try {
                dcmups.close();
            } catch (InterruptedException e) {
                LOG.error(e.getMessage(), e);
            }
            LOG.info("Released connection to {}", remoteAE);
        }
    }
}

From source file:org.dcm4che2.tool.dcmwado.DcmWado.java

private static CommandLine parse(String[] args) {
    Options opts = new Options();
    OptionBuilder.withArgName("suid:Suid:iuid");
    OptionBuilder.hasArgs(3);/*from w w w .  j a  va 2s. co m*/
    OptionBuilder.withValueSeparator(':');
    OptionBuilder.withDescription(
            "Retrieve object with given Study " + "Instance UID, Series Instance UID and SOP Instance UID.");
    opts.addOption(OptionBuilder.create("uid"));

    OptionBuilder.withArgName("Suid:iuid");
    OptionBuilder.hasArgs(2);
    OptionBuilder.withValueSeparator(':');
    OptionBuilder.withDescription("Series Instance UID and SOP Instance UID "
            + "of the presentation state storage object to be applied to the " + "image.");
    opts.addOption(OptionBuilder.create("pr"));

    opts.addOption("dcm", false, "Request DICOM object. (MIME type: application/dicom)");
    opts.addOption("jpeg", false, "Request JPEG image. (MIME type: image/jpeg)");
    opts.addOption("gif", false, "Request GIF image. (MIME type: image/gif)");
    opts.addOption("png", false, "Request PNG image. (MIME type: image/png)");
    opts.addOption("jp2", false, "Request JPEG 2000 image. (MIME type: image/jp2)");
    opts.addOption("mpeg", false, "Request MPEG video. (MIME type: video/mpeg)");
    opts.addOption("txt", false, "Request plain text document. (MIME type: text/plain)");
    opts.addOption("html", false, "Request HTML document. (MIME type: text/html)");
    opts.addOption("xml", false, "Request XML document. (MIME type: text/xml)");
    opts.addOption("rtf", false, "Request RTF document. (MIME type: text/rtf)");
    opts.addOption("pdf", false, "Request PDF document. (MIME type: application/pdf)");
    opts.addOption("cda1", false,
            "Request CDA Level 1 document. " + "(MIME type: application/x-hl7-cda-level-one+xml)");

    OptionBuilder.withArgName("type");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription("Request document with the specified MIME type."
            + "Alternative MIME types can be specified by additional -mime options.");
    opts.addOption(OptionBuilder.create("mime"));

    OptionBuilder.withArgName("uid");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription("Returned object shall be encoded with "
            + "the specified Transfer Syntax. Alternative Transfer Syntaxes "
            + "can be specified by additional -ts options.");
    opts.addOption(OptionBuilder.create("ts"));

    OptionBuilder.withArgName("name");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription(
            "Returned object shall be encoded with " + "specified Character set. Alternative Character sets "
                    + "can be specified by additional -charset options.");
    opts.addOption(OptionBuilder.create("charset"));

    opts.addOption("anonymize", false,
            "Remove all patient identification" + "information from returned DICOM Object");

    OptionBuilder.withArgName("type");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription(
            "Burn in patient information" + "(-annotation=patient) and/or technique information "
                    + "(-annotation=technique) in returned pixel data.");
    opts.addOption(OptionBuilder.create("annotation"));

    OptionBuilder.withArgName("num");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription("Maximal number of pixel rows in returned image.");
    opts.addOption(OptionBuilder.create("rows"));

    OptionBuilder.withArgName("num");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription("Maximal number of pixel columns in returned image.");
    opts.addOption(OptionBuilder.create("columns"));

    OptionBuilder.withArgName("num");
    OptionBuilder.hasArg();
    OptionBuilder
            .withDescription("Return single frame with that number " + "within a multi-frame image object.");
    opts.addOption(OptionBuilder.create("frame"));

    OptionBuilder.withArgName("x1:y1:x2:y2");
    OptionBuilder.hasArgs(4);
    OptionBuilder.withValueSeparator(':');
    OptionBuilder.withDescription("Return rectangular region of image "
            + "matrix specified by top left (x1,y1) and bottom right (x2,y2) "
            + "corner in relative coordinates within the range 0.0 to 1.0.");
    opts.addOption(OptionBuilder.create("window"));

    OptionBuilder.withArgName("center/width");
    OptionBuilder.hasArgs(2);
    OptionBuilder.withValueSeparator('/');
    OptionBuilder
            .withDescription("Specifies center and width of the " + "VOI window to be applied to the image.");
    opts.addOption(OptionBuilder.create("window"));

    OptionBuilder.withArgName("num");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription(
            "Quality of the image to be returned " + "within the range 1 to 100, 100 being the best quality.");
    opts.addOption(OptionBuilder.create("quality"));

    OptionBuilder.withArgName("path");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription("Directory to store retrieved objects, " + "working directory by default");
    opts.addOption(OptionBuilder.create("dir"));

    OptionBuilder.withArgName("dirpath");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription("Directory to store retrieved objects, " + "working directory by default");
    opts.addOption(OptionBuilder.create("dir"));

    OptionBuilder.withArgName("file");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription("Store retrieved object to specified file, "
            + "use SOP Instance UID + format specific file extension as " + "file name by default.");
    opts.addOption(OptionBuilder.create("o"));

    opts.addOption("nostore", false, "Do not store retrieved objects to files.");
    opts.addOption("nokeepalive", false, "Close TCP connection after each response.");
    opts.addOption("noredirect", false, "Disable HTTP redirects.");

    OptionBuilder.withArgName("kB");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription(
            "Size of byte buffer in KB " + "used for copying the retrieved object to disk, 8 KB by default.");
    opts.addOption(OptionBuilder.create("buffersize"));

    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 (MissingOptionException e) {
        exit("dcmwado: Missing required option " + e.getMessage());
        throw new RuntimeException("unreachable");
    } catch (ParseException e) {
        exit("dcmwado: " + e.getMessage());
        throw new RuntimeException("unreachable");
    }
    if (cl.hasOption('V')) {
        Package p = DcmWado.class.getPackage();
        System.out.println("dcmwado v" + p.getImplementationVersion());
        System.exit(0);
    }
    if (cl.hasOption('h') || cl.getArgList().isEmpty()) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(USAGE, DESCRIPTION, opts, EXAMPLE);
        System.exit(0);
    }
    int narg = cl.getArgList().size();
    if (narg == 0)
        exit("Missing url of WADO server");
    if (narg == 1) {
        if (!cl.hasOption("uid")) {
            exit("You must either option -uid <uids> or <file>|<directory> specify");
        }
    } else {
        if (cl.hasOption("uid")) {
            exit("You may not specify option -uid <uids> together with " + "<file>|<directory>.");
        }
    }
    return cl;
}

From source file:org.dcm4che2.tool.dcmwado.DcmWado.java

public static void main(String[] args) {
    DcmWado dcmwado = new DcmWado();
    try {/*from www .  ja v a 2  s.c o  m*/
        CommandLine cl = parse(args);
        if (cl.hasOption("pr")) {
            dcmwado.setPresentation(cl.getOptionValues("pr"));
        }
        if (cl.hasOption("dcm")) {
            dcmwado.addContentType("application/dicom");
        }
        if (cl.hasOption("jpeg")) {
            dcmwado.addContentType("image/jpeg");
        }
        if (cl.hasOption("gif")) {
            dcmwado.addContentType("image/gif)");
        }
        if (cl.hasOption("png")) {
            dcmwado.addContentType("image/png");
        }
        if (cl.hasOption("jp2")) {
            dcmwado.addContentType("image/jp2");
        }
        if (cl.hasOption("mpeg")) {
            dcmwado.addContentType("video/mpeg");
        }
        if (cl.hasOption("txt")) {
            dcmwado.addContentType("text/plain");
        }
        if (cl.hasOption("html")) {
            dcmwado.addContentType("text/html");
        }
        if (cl.hasOption("xml")) {
            dcmwado.addContentType("text/xml");
        }
        if (cl.hasOption("rtf")) {
            dcmwado.addContentType("text/rtf");
        }
        if (cl.hasOption("pdf")) {
            dcmwado.addContentType("application/pdf");
        }
        if (cl.hasOption("cda1")) {
            dcmwado.addContentType("application/x-hl7-cda-level-one+xml");
        }
        if (cl.hasOption("mime")) {
            dcmwado.addContentType(cl.getOptionValues("mime"));
        }
        if (cl.hasOption("ts")) {
            dcmwado.setTransferSyntax(cl.getOptionValues("ts"));
        }
        dcmwado.setTransferSyntaxSameAsFile(cl.hasOption("tsfile"));
        if (cl.hasOption("charset")) {
            dcmwado.setCharset(cl.getOptionValues("charset"));
        }
        dcmwado.setAnonymize(cl.hasOption("anonymize"));
        if (cl.hasOption("annotation")) {
            dcmwado.setAnnotation(cl.getOptionValues("annotation"));
        }
        if (cl.hasOption("rows")) {
            dcmwado.setRows(parseInt(cl.getOptionValue("h"), "Invalid value of -h", 1, Integer.MAX_VALUE));
        }
        if (cl.hasOption("columns")) {
            dcmwado.setColumns(parseInt(cl.getOptionValue("w"), "Invalid value of -w", 1, Integer.MAX_VALUE));
        }
        if (cl.hasOption("frame")) {
            dcmwado.setFrameNumber(
                    parseInt(cl.getOptionValue("f"), "Invalid value of -f", 1, Integer.MAX_VALUE));
        }
        if (cl.hasOption("region")) {
            dcmwado.setRegion(cl.getOptionValues("reg"));
        }
        if (cl.hasOption("window")) {
            dcmwado.setWindow(cl.getOptionValues("voi"));
        }
        if (cl.hasOption("quality")) {
            dcmwado.setImageQuality(
                    parseInt(cl.getOptionValue("q"), "Invalid value of -q", 1, Integer.MAX_VALUE));
        }
        if (cl.hasOption("dir")) {
            dcmwado.setDirectory(new File(cl.getOptionValue("dir")));
        }
        if (cl.hasOption("o")) {
            dcmwado.setOutput(new File(cl.getOptionValue("o")));
        }
        if (cl.hasOption("nostore")) {
            dcmwado.setDirectory(null);
        }
        dcmwado.setNoKeepAlive(cl.hasOption("nokeepalive"));
        dcmwado.setFollowsRedirect(!cl.hasOption("noredirect"));
        if (cl.hasOption("buffersize")) {
            dcmwado.setBufferSize(parseInt(cl.getOptionValue("bs"), "Invalid value of -bs", 1, 1000) * KB);
        }
        List argList = cl.getArgList();
        dcmwado.setBaseURL((String) argList.get(0));
        if (cl.hasOption("uid")) {
            dcmwado.setUIDs(cl.getOptionValues("uid"));
        } else {

            System.out.println("Scanning files for uids");
            long t1 = System.currentTimeMillis();
            for (int i = 1, n = argList.size(); i < n; i++) {
                dcmwado.addFile(new File((String) argList.get(i)));
            }
            long t2 = System.currentTimeMillis();
            System.out.println(
                    "\nScanned " + dcmwado.getNumberOfRequests() + " files in " + ((t2 - t1) / 1000F) + "s");
        }
    } catch (Exception e) {
        exit(e.getMessage());
    }
    long t1 = System.currentTimeMillis();
    dcmwado.fetchObjects();
    long t2 = System.currentTimeMillis();
    float seconds = (t2 - t1) / 1000F;
    System.out.println(
            "\nFetch " + dcmwado.getNumberOfRequests() + " objects (=" + promptBytes(dcmwado.getTotalSize())
                    + ") in " + seconds + "s (=" + promptBytes(dcmwado.getTotalSize() / seconds) + "/s)");
}

From source file:org.dcm4che2.tool.fixjpegls.FixJpegLS.java

@SuppressWarnings("unchecked")
public static void main(String[] args) {
    try {//from   w  w  w  .jav  a2 s  .c o m
        CommandLine cl = parseCommandLine(args);
        if (cl == null)
            return;
        List<String> argList = cl.getArgList();
        File target = removeTarget(argList);
        FixJpegLS fixJpegLS = new FixJpegLS();
        if (cl.hasOption("no-check-impl-cuid"))
            fixJpegLS.setImplClassUID(null);
        else if (cl.hasOption("check-impl-cuid"))
            fixJpegLS.setImplClassUID(cl.getOptionValue("check-impl-cuid"));
        if (cl.hasOption("no-new-impl-cuid"))
            fixJpegLS.setNewImplClassUID(null);
        else if (cl.hasOption("new-impl-cuid"))
            fixJpegLS.setNewImplClassUID(cl.getOptionValue("new-impl-cuid"));
        int[] counts = new int[2];
        long start = System.currentTimeMillis();
        for (String arg : argList)
            fixJpegLS.fix(new File(arg), target, counts);
        long end = System.currentTimeMillis();
        System.out.println();
        System.out.println("Fix " + counts[1] + " of " + counts[0] + " scanned files in "
                + ((end - start) / 1000.f) + " s.");
    } catch (ParseException e) {
        System.err.println("fixjpegls: " + e.getMessage());
        System.err.println("Try `fixjpegls --help' for more information.");
        System.exit(1);
    } catch (Exception e) {
        System.err.println("fixjpegls: " + e.getMessage());
        System.exit(1);
    }

}

From source file:org.dcm4che2.tool.jpg2dcm.Jpg2Dcm.java

@SuppressWarnings("rawtypes")
public static void main(String[] args) {
    try {/*from  w w w .j  a  v a  2s .c o m*/
        CommandLine cl = parse(args);
        Jpg2Dcm jpg2Dcm = new Jpg2Dcm();
        if (cl.hasOption(LONG_OPT_CHARSET)) {
            jpg2Dcm.setCharset(cl.getOptionValue(LONG_OPT_CHARSET));
        }
        if (cl.hasOption("c")) {
            jpg2Dcm.loadConfiguration(new File(cl.getOptionValue("c")), true);
        }
        if (cl.hasOption("C")) {
            jpg2Dcm.loadConfiguration(new File(cl.getOptionValue("C")), false);
        }
        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));

        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(jpgFile, dcmFile, 1);
        long fin = System.currentTimeMillis();
        System.out.println("Encapsulated " + jpgFile + " to " + dcmFile + " in " + (fin - start) + "ms.");
    } catch (IOException e) {
        e.printStackTrace();
    }
}

From source file:org.dcm4che2.tool.jpg2dcm.Jpg2Dcm.java

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

    OptionBuilder.withArgName("code");
    OptionBuilder.hasArg();/*from   www  .  j  a v a  2  s .  c om*/
    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();
        System.out.println("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;
}

From source file:org.dcm4che2.tool.pdf2dcm.Pdf2Dcm.java

public static void main(String[] args) {
    try {//w ww.j av  a  2s  .c  o m
        CommandLine cl = parse(args);
        Pdf2Dcm pdf2Dcm = new Pdf2Dcm();
        if (cl.hasOption("ivrle")) {
            pdf2Dcm.setTransferSyntax(UID.ImplicitVRLittleEndian);
        }
        if (cl.hasOption("cs")) {
            pdf2Dcm.setCharset(cl.getOptionValue("cs"));
        }
        if (cl.hasOption("bs")) {
            pdf2Dcm.setBufferSize(Integer.parseInt(cl.getOptionValue("bs")));
        }
        if (cl.hasOption("c")) {
            pdf2Dcm.loadConfiguration(new File(cl.getOptionValue("c")));
        }
        if (cl.hasOption("uid")) {
            UIDUtils.setRoot(cl.getOptionValue("uid"));
        }
        List argList = cl.getArgList();
        File pdfFile = new File((String) argList.get(0));
        File dcmFile = new File((String) argList.get(1));
        long start = System.currentTimeMillis();
        pdf2Dcm.convert(pdfFile, dcmFile);
        long fin = System.currentTimeMillis();
        System.out.println("Encapsulated " + pdfFile + " to " + dcmFile + " in " + (fin - start) + "ms.");
    } catch (IOException e) {
        e.printStackTrace();
    }
}

From source file:org.dcm4che2.tool.pdf2dcm.Pdf2Dcm.java

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

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

    OptionBuilder.withArgName("size");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription("Buffer size used for copying PDF to DICOM file, 8192 by default");
    opts.addOption(OptionBuilder.create("bs"));

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

    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");

    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("V", "version", false, "print the version information and exit");
    CommandLine cl = null;
    try {
        cl = new GnuParser().parse(opts, args);
    } catch (ParseException e) {
        exit("pdf2dcm: " + e.getMessage());
        throw new RuntimeException("unreachable");
    }
    if (cl.hasOption('V')) {
        Package p = Pdf2Dcm.class.getPackage();
        System.out.println("pdf2dcm 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.dcm4che2.tool.rgb2ybr.Rgb2Ybr.java

private static CommandLine parse(String[] args) {
    Options opts = new Options();
    opts.addOption("p", "partial", false, "convert to YBR_PARTIAL instead to YBR_FULL (=default)");
    opts.addOption("i", "invers", false, "convert from YBR_* to RGB");
    opts.addOption("h", "help", false, "print this message");
    opts.addOption("V", "version", false, "print the version information and exit");
    CommandLine cl = null;
    try {//  w  w  w  .ja va  2s .c om
        cl = new PosixParser().parse(opts, args);
    } catch (ParseException e) {
        exit("rgb2ybr: " + e.getMessage());
        throw new RuntimeException("unreachable");
    }
    if (cl.hasOption('V')) {
        Package p = Rgb2Ybr.class.getPackage();
        System.out.println("rgb2ybr 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;
}