/*
 *
 *  Copyright (C) 2018-2021, OFFIS e.V.
 *  All rights reserved.  See COPYRIGHT file for details.
 *
 *  This software and supporting documentation were developed by
 *
 *    OFFIS e.V.
 *    R&D Division Health
 *    Escherweg 2
 *    D-26121 Oldenburg, Germany
 *
 *
 *  Module:  dcmdata
 *
 *  Author:  Pedro ArizpeGomez
 *
 *  Purpose: Implementation of Document encapsulation
 *
 */

//make sure OS specific configuration is included first
#include "dcmtk/config/osconfig.h"
#include "dcmtk/dcmdata/dcencdoc.h"

#include "dcmtk/ofstd/ofconapp.h"
#include "dcmtk/ofstd/ofxml.h"
#include "dcmtk/ofstd/oftypes.h"

#include "dcmtk/dcmdata/dcpath.h"
#include "dcmtk/dcmdata/dccodec.h"
#include "dcmtk/dcmdata/dcdeftag.h"
#include "dcmtk/dcmdata/dcuid.h"
#include "dcmtk/dcmdata/dcvrpobw.h"
#include "dcmtk/dcmdata/dcvrui.h"
#include "dcmtk/dcmdata/dcvrda.h"
#include "dcmtk/dcmdata/dcvrtm.h"

#define SHORTCOL 3
#define LONGCOL 21

// exit codes for this command line tool
// (common codes are defined in "ofexit.h" included from "ofconapp.h")

// general errors
#define EXITCODE_MEMORY_EXHAUSTED                4

DcmEncapsulatedDocument::DcmEncapsulatedDocument() :
        opt_patientBirthdate(),
        opt_patientID(),
        opt_patientName(),
        opt_patientSex(),

        opt_conceptCM(),
        opt_conceptCSD(),
        opt_conceptCV(),

        opt_documentTitle(),
        opt_seriesFile(),
        opt_seriesUID(),
        opt_studyUID(),

        opt_oenctype(EET_ExplicitLength),
        opt_writeMode(EWM_fileformat),
        opt_oglenc(EGL_withoutGL),
        opt_opadenc(EPD_withoutPadding),
        opt_oxfer(EXS_LittleEndianExplicit),
        opt_filepad(0),
        opt_itempad(0),

        opt_readSeriesInfo(OFFalse),
        opt_annotation(OFTrue),
        opt_increment(OFFalse),

        opt_instance(1),
        opt_overrideKeys(),

        cda_mediaTypes(),
        hl7_InstanceIdentifier(),
        opt_override(OFFalse),
        // Frame of Reference Module (STL)
        opt_frameOfReferenceUID(),
        opt_positionReferenceIndicator(),
        // Frame of Reference Module (STL)
        opt_manufacturer(),
        opt_manufacturerModelName(),
        opt_deviceSerialNumber(),
        opt_softwareVersions(),
        // Enhanced General Equipment Module (STL)
        opt_measurementUnitsCM(),
        opt_measurementUnitsCSD(),
        opt_measurementUnitsCV(),
        //encapsulation file type
        ftype()
{
}

OFBool DcmEncapsulatedDocument::XMLsearchAttribute(
        XMLNode currnode,
        OFList<OFString> *results,
        OFString attr)
{
  OFBool found = OFFalse;
#ifndef _XMLWIDECHAR
  if (currnode.nChildNode() == 0)
  {
    //"currnode has no children (leaf)";
    if (currnode.isAttributeSet(attr.c_str()))
    {
      //attribute found on leaf
      results->push_back(OFSTRING_GUARD(currnode.getAttribute(attr.c_str())));
      found = OFTrue;
    }
  }
  else
  {
    //"currnode has children (branch)";
    if (currnode.isAttributeSet(attr.c_str()))
    {
      //attribute found on branch
      results->push_back(OFSTRING_GUARD(currnode.getAttribute(attr.c_str())));
      found = OFTrue;
    }
    for (int i = 0; i < currnode.nChildNode(); i++)
    {
      //search all children recursively
      OFBool childfound = XMLsearchAttribute(currnode.getChildNode(i), results, attr);
      found |= childfound;
    }
  }
#endif
  return found;
}

OFString DcmEncapsulatedDocument::XMLgetAllAttributeValues(
        XMLNode fileNode,
        OFString attr)
{
  OFString attributeValues;
#ifndef _XMLWIDECHAR
  OFList<OFString> attributeValueslist;
  if (XMLsearchAttribute(fileNode, &attributeValueslist, attr))
  {
    //If the Attribute is mediaType, initialize with text/xml to exclude
    //the primary MIME Type of the encapsulated document
    if (attr == "mediaType") attributeValues.append("text/xml");
    while (!attributeValueslist.empty())
    {
      if (attributeValues.find(attributeValueslist.front()) == OFString_npos)
      {
        if (!attributeValues.empty()) attributeValues.append("\\");
        attributeValues.append(attributeValueslist.front());
      }
      attributeValueslist.pop_front();
    }
    //remove the primary MIME Type of the
    //encapsulated document
    if (attr == "mediaType")
    {
      if (attributeValues.size() > 9)
        attributeValues.erase(0, 9);
      else
        attributeValues = "";
    }
  }
#endif
  return attributeValues;
}

OFString DcmEncapsulatedDocument::XMLgetAttribute(
        XMLNode fileNode,
        DcmTagKey attr)
{
  OFString result = "";
#ifndef _XMLWIDECHAR
  if (attr == DCM_DocumentTitle)
  {
    if (fileNode.getChildNode("title").getText() != NULL)
    {
      result = OFString(OFSTRING_GUARD(fileNode.getChildNode("title").getText()));
    }
  }
  if (attr == DCM_HL7InstanceIdentifier)
  {
    result = OFString(OFSTRING_GUARD(fileNode.getChildNode("id").getAttribute("root"))) + "^"
             + OFString(OFSTRING_GUARD(fileNode.getChildNode("id").getAttribute("extension")));
  }
  /*PatientNameExtension could reflect the type of name (PHON, IDE, ABC)
  if (attr == DCM_PatientNameExtension)
  {
  result = OFString(OFSTRING_GUARD(fileNode.getChildNodeByPath("recordTarget/patientRole/patient/name").getAttribute("use")));
  }*/
  if (attr == DCM_PatientName)
  {
    result = OFString(
            OFSTRING_GUARD(fileNode.getChildNodeByPath("recordTarget/patientRole/patient/name/family").getText())) + "^"
             + OFString(OFSTRING_GUARD(
                                fileNode.getChildNodeByPath("recordTarget/patientRole/patient/name").getChildNode(
                                        "given", 0).getText())) + "^"
             + OFString(OFSTRING_GUARD(
                                fileNode.getChildNodeByPath("recordTarget/patientRole/patient/name").getChildNode(
                                        "given", 1).getText())) + "^"
             + OFString(
            OFSTRING_GUARD(fileNode.getChildNodeByPath("recordTarget/patientRole/patient/name/prefix").getText())) + "^"
             + OFString(
            OFSTRING_GUARD(fileNode.getChildNodeByPath("recordTarget/patientRole/patient/name/suffix").getText()));
  }
  if (attr == DCM_PatientSex)
  {
    result = OFString(OFSTRING_GUARD(fileNode.getChildNodeByPath(
            "recordTarget/patientRole/patient/administrativeGenderCode").getAttribute("code")));
  }
  if (attr == DCM_PatientBirthDate)
  {
    result = OFString(OFSTRING_GUARD(
                              fileNode.getChildNodeByPath("recordTarget/patientRole/patient/birthTime").getAttribute(
                                      "value")));
  }
  //Table A.8-1. Basic Code Attributes Mapping to HL7 V3 Code Data Types (CV, CS, CE and CD)
  if (attr == DCM_PatientID)
  {
    result = OFString(
            OFSTRING_GUARD(fileNode.getChildNodeByPath("recordTarget/patientRole/id").getAttribute("extension")));
  }
  if (attr == DCM_CodeValue)//Code Value
  {
    result = OFString(OFSTRING_GUARD(fileNode.getChildNode("code").getAttribute("code")));
  }
  if (attr == DCM_CodingSchemeUID)//Coding Scheme UID (PS3.16)
  {
    result = OFString(OFSTRING_GUARD(fileNode.getChildNode("code").getAttribute("codeSystem")));
  }
  if (attr == DCM_CodingSchemeDesignator)//Coding Scheme Designator (0008,0102)
  {
    OFString CSDtemp = OFString(OFSTRING_GUARD(fileNode.getChildNode("code").getAttribute("codeSystemName")));
    // Abbreviate most common CSNs
    if (CSDtemp == OFString("LOINC"))
    {
      result = OFString("LN");
    }
    else
    {
      if (CSDtemp == OFString("DICOM"))
      {
        result = OFString("DC");
      }
      else
      {
        if (CSDtemp == OFString("SNOMED"))
        {
          result = OFString("SRT");
        }
        else
        {
          result = CSDtemp;
        }
      }
    }
  }
  if (attr == DCM_CodingSchemeVersion)//Coding Scheme Version (0008,0103)
  {
    result = OFString(OFSTRING_GUARD(fileNode.getChildNode("code").getAttribute("codeSystemVersion")));
  }
  if (attr == DCM_CodeMeaning)//Code Meaning (0008,0104)
  {
    result = OFString(OFSTRING_GUARD(fileNode.getChildNode("code").getAttribute("displayName")));
  }
#endif
  return result;
}

int DcmEncapsulatedDocument::getCDAData(
        const char *filename,
        OFLogger &appLogger)
{
#ifdef _XMLWIDECHAR
#ifdef _MSC_VER
#pragma message("DCMTK compiled with 'wide char XML parser'. cda2dcm will be unable to read and encapsulate CDA documents.")
#else
#warning "DCMTK compiled with 'wide char XML parser'. cda2dcm will be unable to read and encapsulate CDA documents."
#endif
  OFLOG_ERROR(appLogger, "DCMTK compiled with \"wide char XML parser\". Cannot parse CDA data because of incompatible API.");
  return 99;
#else
  if (ftype != "cda")
  {
    OFLOG_WARN(appLogger, "Filetype mismatch or filetype not set. Current ftype is " << ftype);
  }
  XMLResults err;
  XMLNode fileNode = XMLNode::parseFile(filename, "ClinicalDocument", &err);
  OFLOG_TRACE(appLogger, "checking if the XML file is correctly formatted");
  if (0 != err.error)
  {
    OFLOG_ERROR(appLogger, fileNode.getError(err.error));
    return EXITCODE_INVALID_INPUT_FILE;
  }
  else
  {
    OFLOG_TRACE(appLogger, "XML file is correctly formatted");
  }
  OFLOG_TRACE(appLogger, "Getting all media types from CDA file");
  cda_mediaTypes = XMLgetAllAttributeValues(fileNode, "mediaType");
  OFLOG_TRACE(appLogger, "Following mediaTypes were found: " << cda_mediaTypes);
  OFLOG_TRACE(appLogger, "Getting HL7 Instance Identifier from CDA file");
  hl7_InstanceIdentifier = XMLgetAttribute(fileNode, DCM_HL7InstanceIdentifier);
  OFLOG_TRACE(appLogger, "Reading and comparing patient information between CDA File and options");
  OFString pID = XMLgetAttribute(fileNode, DCM_PatientID);
  if ((pID != "") && (opt_patientID != pID))
  {
    if (opt_patientID != "")
    {
      //if no-override option is inactive, return an error
      if (!opt_override)
      {
        OFLOG_ERROR(appLogger, "Patient ID mismatch:" << OFendl
                << "Found in the CDA file : " << pID << OFendl
                << "Entered (or found in DCM file): " << opt_patientID << OFendl
                << "If you wish to override, run again with +ov");
        return EXITCODE_COMMANDLINE_SYNTAX_ERROR;
      }
      else
      {
        OFLOG_WARN(appLogger, "Patient ID mismatch:" << OFendl
                << "Found in the CDA file : " << pID << OFendl
                << "Provided (in DCM file): " << opt_patientID);
      }
    }
    else
    {
      opt_patientID = pID;
    }
  }
  OFString pBirthDate = XMLgetAttribute(fileNode, DCM_PatientBirthDate);
  if ((pBirthDate != "") && (opt_patientBirthdate != pBirthDate))
  {
    if (opt_patientBirthdate != "")
    {
      if (!opt_override)
      {
        OFLOG_ERROR(appLogger, "Patient Birth Date mismatch:" << OFendl
                << "Found in the CDA file : " << pBirthDate << OFendl
                << "Provided (in DCM file): " << opt_patientBirthdate << OFendl
                << "If you wish to override, run again with +ov");
        return EXITCODE_COMMANDLINE_SYNTAX_ERROR;
      }
      else
      {
        OFLOG_WARN(appLogger, "Patient Birth Date mismatch:" << OFendl
                << "Found in the CDA file : " << pBirthDate << OFendl
                << "Provided (in DCM file): " << opt_patientBirthdate);
      }
    }
    else opt_patientBirthdate = pBirthDate;
  }
  OFString pSex = XMLgetAttribute(fileNode, DCM_PatientSex);
  if ((pSex != "") && (opt_patientSex != pSex))
  {
    if (opt_patientSex != "")
    {
      if (!opt_override)
      {
        OFLOG_ERROR(appLogger, "Patient Sex mismatch:" << OFendl
                << "Found in the CDA file : " << pSex << OFendl
                << "Provided (in DCM file): " << opt_patientSex << OFendl
                << "If you wish to override, run again with +ov");
        return EXITCODE_COMMANDLINE_SYNTAX_ERROR;
      }
      else
      {
        OFLOG_WARN(appLogger, "Patient Sex mismatch:" << OFendl
                << "Found in the CDA file : " << pSex << OFendl
                << "Provided (in DCM file): " << opt_patientSex);
      }
    }
    else opt_patientSex = pSex;
  }
  OFString pName = XMLgetAttribute(fileNode, DCM_PatientName);
  if ((pName != "^^^^") && (opt_patientName != pName))
  {
    if (opt_patientName != "")
    {
      if (!opt_override)
      {
        OFLOG_ERROR(appLogger, "Patient Name mismatch:" << OFendl
                << "Found in the CDA file : " << pName << OFendl
                << "Provided (in DCM file): " << opt_patientName << OFendl
                << "If you wish to override, run again with +ov");
        return EXITCODE_COMMANDLINE_SYNTAX_ERROR;
      }
      else
      {
        OFLOG_WARN(appLogger, "Patient Name mismatch:" << OFendl
                << "Found in the CDA file : " << pName << OFendl
                << "Provided (in DCM file): " << opt_patientName);
      }
    }
    else opt_patientName = pName;
  }
  //get document title from CDA
  OFString dTitle = XMLgetAttribute(fileNode, DCM_DocumentTitle);
  if (opt_documentTitle == "")
  {
    if (opt_conceptCSD != "") opt_documentTitle = opt_conceptCSD;
    if (opt_conceptCV != "") opt_documentTitle = opt_conceptCV;
    if (opt_conceptCM != "") opt_documentTitle = opt_conceptCM;
  }

  if ((dTitle != "") && (opt_documentTitle != dTitle))
  {
    if (opt_documentTitle != "")
    {
      if (!opt_override)
      {
        OFLOG_ERROR(appLogger, "Document Title mismatch:" << OFendl
                << "Found in the CDA file : " << dTitle << OFendl
                << "Provided (in DCM file): " << opt_documentTitle << OFendl
                << "If you wish to override, run again with +ov");
        return EXITCODE_COMMANDLINE_SYNTAX_ERROR;
      }
      else
      {
        OFLOG_WARN(appLogger, "Document Title mismatch:" << OFendl
                << "Found in the CDA file : " << dTitle << OFendl
                << "Provided (in DCM file): " << opt_documentTitle);
      }
    }
    else opt_documentTitle = dTitle;
  }
  //get Concept information from CDA
  OFString cCSD = XMLgetAttribute(fileNode, DCM_CodingSchemeDesignator);
  if ((cCSD != "") && (opt_conceptCSD != cCSD))
  {
    if (opt_conceptCSD != "")
    {
      if (!opt_override)
      {
        OFLOG_ERROR(appLogger, "concept CSD mismatch:" << OFendl
                << "Found in the CDA file : " << cCSD << OFendl
                << "Provided (in DCM file): " << opt_conceptCSD << OFendl
                << "If you wish to override, run again with +ov");
        return EXITCODE_COMMANDLINE_SYNTAX_ERROR;
      }
      else
      {
        OFLOG_WARN(appLogger, "concept CSD mismatch:" << OFendl
                << "Found in the CDA file : " << cCSD << OFendl
                << "Provided (in DCM file): " << opt_conceptCSD);
      }
    }
    else opt_conceptCSD = cCSD;
  }
  OFString cCV = XMLgetAttribute(fileNode, DCM_CodeValue);
  if ((cCV != "") && (opt_conceptCV != cCV))
  {
    if (opt_conceptCV != "")
    {
      if (!opt_override)
      {
        OFLOG_ERROR(appLogger, "concept CV mismatch:" << OFendl
                << "Found in the CDA file : " << cCV << OFendl
                << "Provided (in DCM file): " << opt_conceptCV << OFendl
                << "If you wish to override, run again with +ov");
        return EXITCODE_COMMANDLINE_SYNTAX_ERROR;
      }
      else
      {
        OFLOG_WARN(appLogger, "concept CV mismatch:" << OFendl
                << "Found in the CDA file : " << cCV << OFendl
                << "Provided (in DCM file): " << opt_conceptCV);
      }
    }
    else opt_conceptCV = cCV;
  }
  OFString cCM = XMLgetAttribute(fileNode, DCM_CodeMeaning);
  if ((cCM != "") && (opt_conceptCM != cCM))
  {
    if (opt_conceptCM != "")
    {
      if (!opt_override)
      {
        OFLOG_ERROR(appLogger, "concept CM mismatch:" << OFendl
                << "Found in the CDA file : " << cCM << OFendl
                << "Provided (in DCM file): " << opt_conceptCM << OFendl
                << "If you wish to override, run again with +ov");
        return EXITCODE_COMMANDLINE_SYNTAX_ERROR;
      }
      else
      {
        OFLOG_WARN(appLogger, "concept CM mismatch:" << OFendl
                << "Found in the CDA file : " << cCM << OFendl
                << "Provided (in DCM file): " << opt_conceptCM);
      }
    }
    else opt_conceptCM = cCM;
  }
  return EXITCODE_NO_ERROR;
#endif
}

void DcmEncapsulatedDocument::addCDACommandlineOptions(OFCommandLine &cmd)
{
  ftype = "cda";
  cmd.setOptionColumns(LONGCOL, SHORTCOL);
  cmd.setParamColumn(LONGCOL + SHORTCOL + 4);
  cmd.addParam("cdafile-in", "CDA input filename to be converted");
  cmd.addParam("dcmfile-out", "DICOM output filename");
  addGeneralOptions(cmd);
  addDocumentOptions(cmd);
  cmd.addSubGroup("override CDA data:");
  cmd.addOption("--no-override", "-ov",
                "CDA patient and document data must match study,\nseries or manually entered information (default)");
  cmd.addOption("--override", "+ov",
                "CDA's data will be overwritten by study, series\nor manually entered information");
  addOutputOptions(cmd);
}

void DcmEncapsulatedDocument::addPDFCommandlineOptions(OFCommandLine &cmd)
{
  ftype = "pdf";
  cmd.setOptionColumns(LONGCOL, SHORTCOL);
  cmd.setParamColumn(LONGCOL + SHORTCOL + 4);
  cmd.addParam("pdffile-in", "PDF input filename to be converted");
  cmd.addParam("dcmfile-out", "DICOM output filename");
  addGeneralOptions(cmd);
  addDocumentOptions(cmd);
  addOutputOptions(cmd);
}

void DcmEncapsulatedDocument::addSTLCommandlineOptions(OFCommandLine &cmd)
{
  ftype = "stl";
  cmd.setOptionColumns(LONGCOL, SHORTCOL);
  cmd.setParamColumn(LONGCOL + SHORTCOL + 4);
  cmd.addParam("stlfile-in", "STL input filename to be converted");
  cmd.addParam("dcmfile-out", "DICOM output filename");
  addGeneralOptions(cmd);
  addDocumentOptions(cmd);
  cmd.addSubGroup("enhanced general equipment:");
  cmd.addOption("--manufacturer", "+mn", 1, "[n]ame: string",
                "manufacturer's name");
  cmd.addOption("--manufacturer-model", "+mm", 1, "[n]ame: string",
                "manufacturer's model name");
  cmd.addOption("--device-serial", "+ds", 1, "[n]umber: string",
                "device serial number");
  cmd.addOption("--software-versions", "+sv", 1, "[v]ersions: string",
                "software versions");
  cmd.addSubGroup("3d model measurement units:");
  cmd.addOption("--measurement-units", "+mu", 3, "[CSD] [CV] [CM]: string (default: UCUM, um, um)",
                "measurement units defined by coding scheme\ndesignator CSD, code value CV, code meaning CM");
  addOutputOptions(cmd);
}

void DcmEncapsulatedDocument::addGeneralOptions(OFCommandLine &cmd)
{
  cmd.addGroup("general options:", LONGCOL, SHORTCOL + 2);
  cmd.addOption("--help", "-h", "print this help text and exit", OFCommandLine::AF_Exclusive);
  cmd.addOption("--version", "print version information and exit", OFCommandLine::AF_Exclusive);
  OFLog::addOptions(cmd);
}

void DcmEncapsulatedDocument::addDocumentOptions(OFCommandLine &cmd)
{
  cmd.addGroup("DICOM document options:");
  cmd.addSubGroup("document title:");
  cmd.addOption("--title", "+t", 1, "[t]itle: string (default: empty)",
                "document title");
  cmd.addOption("--concept-name", "+cn", 3, "[CSD] [CV] [CM]: string (default: empty)",
                "coded representation of document title defined\nby coding scheme designator CSD,\n"
                "code value CV and code meaning CM");
  cmd.addSubGroup("patient data:");
  cmd.addOption("--patient-name", "+pn", 1, "[n]ame: string",
                "patient's name in DICOM PN syntax");
  cmd.addOption("--patient-id", "+pi", 1, "[i]d: string",
                "patient identifier");
  cmd.addOption("--patient-birthdate", "+pb", 1, "[d]ate: string (YYYYMMDD)",
                "patient's birth date");
  cmd.addOption("--patient-sex", "+ps", 1, "[s]ex: string (M, F or O)",
                "patient's sex");
  cmd.addSubGroup("study and series:");
  cmd.addOption("--generate", "+sg", "generate new study and\nseries UIDs (default)");
  cmd.addOption("--study-from", "+st", 1, "[f]ilename: string",
                "read patient/study data from DICOM file");
  cmd.addOption("--series-from", "+se", 1, "[f]ilename: string",
                "read patient/study/series data from DICOM file");
  cmd.addSubGroup("instance number:");
  cmd.addOption("--instance-one", "+i1", "use instance number 1\n(default, not with +se)");
  cmd.addOption("--instance-inc", "+ii", "increment instance number (only with +se)");
  cmd.addOption("--instance-set", "+is", 1, "[i]nstance number: integer", "use instance number i");
  cmd.addSubGroup("burned-in annotation:");
  cmd.addOption("--annotation-yes", "+an", "document contains patient identifying data\n(default)");
  cmd.addOption("--annotation-no", "-an", "document does not contain patient identif. data");
}

void DcmEncapsulatedDocument::addOutputOptions(OFCommandLine &cmd)
{
  cmd.addGroup("processing options:");
  cmd.addSubGroup("other processing options:");
  cmd.addOption("--key", "-k", 1, "[k]ey: gggg,eeee=\"str\", path or dict. name=\"str\"",
                "add further attribute");
  cmd.addGroup("output options:");
  cmd.addSubGroup("output transfer syntax:");
  cmd.addOption("--write-xfer-little", "+te", "write with explicit VR little endian (default)");
  cmd.addOption("--write-xfer-big", "+tb", "write with explicit VR big endian TS");
  cmd.addOption("--write-xfer-implicit", "+ti", "write with implicit VR little endian TS");
  cmd.addSubGroup("group length encoding:");
  cmd.addOption("--group-length-recalc", "+g=", "recalculate group lengths if present (default)");
  cmd.addOption("--group-length-create", "+g", "always write with group length elements");
  cmd.addOption("--group-length-remove", "-g", "always write without group length elements");
  cmd.addSubGroup("length encoding in sequences and items:");
  cmd.addOption("--length-explicit", "+e", "write with explicit lengths (default)");
  cmd.addOption("--length-undefined", "-e", "write with undefined lengths");
  cmd.addSubGroup("data set trailing padding (not with --write-dataset):");
  cmd.addOption("--padding-retain", "-p=", "do not change padding (default)");
  cmd.addOption("--padding-off", "-p", "no padding (implicit if --write-dataset)");
  cmd.addOption("--padding-create", "+p", 2, "[f]ile-pad [i]tem-pad: integer",
                "align file on multiple of f bytes\nand items on multiple of i bytes");
}

void DcmEncapsulatedDocument::parseArguments(
        OFConsoleApplication &app,
        OFCommandLine &cmd)
{
  //command line parameters and options
  cmd.getParam(1, opt_ifname);
  cmd.getParam(2, opt_ofname);

  OFLog::configureFromCommandLine(cmd, app);

  dcmEnableGenerationOfNewVRs();

  // Override keys are applied at the very end of the conversion "pipeline"
  OFList<OFString> overrideKeys;

  cmd.beginOptionBlock();
  if (cmd.findOption("--generate"))
  {
    opt_seriesFile = "";
    opt_readSeriesInfo = OFFalse;
  }

  if (cmd.findOption("--series-from"))
  {
    app.checkValue(cmd.getValue(opt_seriesFile));
    opt_readSeriesInfo = OFTrue;
  }

  if (cmd.findOption("--study-from"))
  {
    app.checkValue(cmd.getValue(opt_seriesFile));
    opt_readSeriesInfo = OFFalse;
  }
  cmd.endOptionBlock();
  if (cmd.findOption("--title"))
  {
    app.checkValue(cmd.getValue(opt_documentTitle));
  }
  if (cmd.findOption("--concept-name"))
  {
    app.checkValue(cmd.getValue(opt_conceptCSD));
    app.checkValue(cmd.getValue(opt_conceptCV));
    app.checkValue(cmd.getValue(opt_conceptCM));
  }
  if (cmd.findOption("--patient-name"))
  {
    app.checkValue(cmd.getValue(opt_patientName));
    app.checkConflict("--patient-name", "--study-from or --series-from",
                      opt_seriesFile != "");
  }
  if (cmd.findOption("--patient-id"))
  {
    app.checkValue(cmd.getValue(opt_patientID));
    app.checkConflict("--patient-id", "--study-from or --series-from",
                      opt_seriesFile != "");
  }
  if (cmd.findOption("--patient-birthdate"))
  {
    app.checkValue(cmd.getValue(opt_patientBirthdate));
    app.checkConflict("--patient-birthdate", "--study-from or --series-from", opt_seriesFile != "");
  }
  if (cmd.findOption("--patient-sex"))
  {
    app.checkValue(cmd.getValue(opt_patientSex));
    app.checkConflict("--patient-sex", "--study-from or --series-from", opt_seriesFile != "");
  }
  cmd.beginOptionBlock();
  if (cmd.findOption("--annotation-yes"))
  {
    opt_annotation = OFTrue;
  }
  if (cmd.findOption("--annotation-no"))
  {
    opt_annotation = OFFalse;
  }
  cmd.endOptionBlock();
  if (ftype == "cda")
  {
    cmd.beginOptionBlock();
    if (cmd.findOption("--override"))
    {
      opt_override = OFTrue;
    }
    if (cmd.findOption("--no-override"))
    {
      opt_override = OFFalse;
    }
    cmd.endOptionBlock();
  }
  if (ftype == "stl")
  {
    if (cmd.findOption("--measurement-units"))
    {
      app.checkValue(cmd.getValue(opt_measurementUnitsCSD));
      app.checkValue(cmd.getValue(opt_measurementUnitsCV));
      app.checkValue(cmd.getValue(opt_measurementUnitsCM));
    }
    if (cmd.findOption("--manufacturer")) app.checkValue(cmd.getValue(opt_manufacturer));
    if (cmd.findOption("--manufacturer-model")) app.checkValue(cmd.getValue(opt_manufacturerModelName));
    if (cmd.findOption("--device-serial")) app.checkValue(cmd.getValue(opt_deviceSerialNumber));
    if (cmd.findOption("--software-versions")) app.checkValue(cmd.getValue(opt_softwareVersions));
  }
  cmd.beginOptionBlock();
  if (cmd.findOption("--write-xfer-little")) opt_oxfer = EXS_LittleEndianExplicit;
  if (cmd.findOption("--write-xfer-big")) opt_oxfer = EXS_BigEndianExplicit;
  if (cmd.findOption("--write-xfer-implicit")) opt_oxfer = EXS_LittleEndianImplicit;
  cmd.endOptionBlock();

  cmd.beginOptionBlock();
  if (cmd.findOption("--group-length-recalc")) opt_oglenc = EGL_recalcGL;
  if (cmd.findOption("--group-length-create")) opt_oglenc = EGL_withGL;
  if (cmd.findOption("--group-length-remove")) opt_oglenc = EGL_withoutGL;
  cmd.endOptionBlock();

  cmd.beginOptionBlock();
  if (cmd.findOption("--length-explicit")) opt_oenctype = EET_ExplicitLength;
  if (cmd.findOption("--length-undefined")) opt_oenctype = EET_UndefinedLength;
  cmd.endOptionBlock();

  cmd.beginOptionBlock();
  if (cmd.findOption("--padding-retain"))
  {
    app.checkConflict("--padding-retain", "--write-dataset",
                      opt_writeMode == EWM_dataset);
    opt_opadenc = EPD_noChange;
  }
  if (cmd.findOption("--padding-off")) opt_opadenc = EPD_withoutPadding;
  if (cmd.findOption("--padding-create"))
  {
    app.checkConflict("--padding-create", "--write-dataset",
                      opt_writeMode == EWM_dataset);
    app.checkValue(cmd.getValueAndCheckMin(opt_filepad, 0));
    app.checkValue(cmd.getValueAndCheckMin(opt_itempad, 0));
    opt_opadenc = EPD_withPadding;
  }
  cmd.endOptionBlock();

  // create override attribute dataset (copied from findscu code)
  if (cmd.findOption("--key", 0, OFCommandLine::FOM_FirstFromLeft))
  {
    const char *ovKey = NULL;
    do
    {
      app.checkValue(cmd.getValue(ovKey));
      overrideKeys.push_back(ovKey);
    } while (cmd.findOption("--key", 0, OFCommandLine::FOM_NextFromLeft));
  }
  DcmEncapsulatedDocument::setOverrideKeys(overrideKeys);
  // initialize default for --series-from
  if (opt_seriesFile != "" && opt_readSeriesInfo) opt_increment = OFTrue;

  cmd.beginOptionBlock();
  if (cmd.findOption("--instance-one"))
  {
    app.checkConflict("--instance-one", "--series-from",
                      (opt_seriesFile != "") && opt_readSeriesInfo);
    opt_increment = OFFalse;
    opt_instance = 1;
  }
  if (cmd.findOption("--instance-inc"))
  {
    app.checkDependence("--instance-inc", "--series-from",
                        (opt_seriesFile != "") && opt_readSeriesInfo);
    opt_increment = OFTrue;
  }
  if (cmd.findOption("--instance-set"))
  {
    opt_increment = OFFalse;
    app.checkValue(cmd.getValueAndCheckMin(opt_instance, 1));
  }
  cmd.endOptionBlock();
}

OFCondition DcmEncapsulatedDocument::createIdentifiers(OFLogger &appLogger)
{
  char buf[100];
  OFCondition cond = EC_Normal;
  Sint32 incrementedInstance = 0;
  if (opt_seriesFile != "")
  {
    DcmFileFormat dfile;
    cond = dfile.loadFile(opt_seriesFile, EXS_Unknown, EGL_noChange);
    if (cond.bad())
    {
      OFLOG_WARN(appLogger, cond.text()
              << ": reading file: " << opt_seriesFile);
    }
    else
    {
      const char *c = NULL;
      DcmDataset *dset = dfile.getDataset();
      if (dset)
      {
        OFLOG_TRACE(appLogger, "reading patient attributes");
        c = NULL;
        if (dset->findAndGetString(DCM_PatientName, c).good() && c)
        {
          opt_patientName = c;
        }
        c = NULL;
        if (dset->findAndGetString(DCM_PatientID, c).good() && c)
        {
          opt_patientID = c;
        }
        c = NULL;
        if (dset->findAndGetString(DCM_PatientBirthDate, c).good() && c)
        {
          opt_patientBirthdate = c;
        }
        c = NULL;
        if (dset->findAndGetString(DCM_PatientSex, c).good() && c)
        {
          opt_patientSex = c;
        }
        OFLOG_TRACE(appLogger, "reading study attributes");
        c = NULL;
        if (dset->findAndGetString(DCM_StudyInstanceUID, c).good() && c)
        {
          opt_studyUID = c;
        }
        OFLOG_TRACE(appLogger, "reading series attributes");
        if (opt_readSeriesInfo)
        {
          c = NULL;
          if (dset->findAndGetString(DCM_SeriesInstanceUID, c).good() && c)
          {
            opt_seriesUID = c;
          }
          if (dset->findAndGetSint32(DCM_InstanceNumber,
                                     incrementedInstance).good())
          {
            ++incrementedInstance;
          }
          else
          {
            incrementedInstance = 0;
          }
          if (opt_increment) opt_instance = incrementedInstance;
        }
        if (ftype == "stl")
        {
          OFLOG_TRACE(appLogger, "reading STL specific information");
          c = NULL;
          OFLOG_TRACE(appLogger, "reading Frame of Reference Info");
          if (dset->findAndGetString(DCM_FrameOfReferenceUID, c).good() && c)
          {
            opt_frameOfReferenceUID = c;
          }
          c = NULL;
          if (dset->findAndGetString(DCM_PositionReferenceIndicator, c).good() && c)
          {
            opt_positionReferenceIndicator = c;
          }
          OFLOG_TRACE(appLogger, "reading Enhanced Equipment info");
          c = NULL;
          if (dset->findAndGetString(DCM_Manufacturer, c).good() && c)
          {
            opt_manufacturer = c;
          }
          c = NULL;
          if (dset->findAndGetString(DCM_ManufacturerModelName, c).good() && c)
          {
            opt_manufacturerModelName = c;
          }
          c = NULL;
          if (dset->findAndGetString(DCM_DeviceSerialNumber, c).good() && c)
          {
            opt_deviceSerialNumber = c;
          }
          c = NULL;
          if (dset->findAndGetString(DCM_SoftwareVersions, c).good() && c)
          {
            opt_softwareVersions = c;
          }
          OFLOG_TRACE(appLogger, "reading manufacturing 3d model info");
          {

            OFLOG_TRACE(appLogger, "manufacturing 3d model info read successfully");
          }
        }
      }
    }
  }
  if (opt_studyUID.empty())
  {
    dcmGenerateUniqueIdentifier(buf, SITE_STUDY_UID_ROOT);
    opt_studyUID = buf;
  }
  if (opt_seriesUID.empty())
  {
    dcmGenerateUniqueIdentifier(buf, SITE_SERIES_UID_ROOT);
    opt_seriesUID = buf;
  }
  return cond;
}

int DcmEncapsulatedDocument::insertEncapsulatedDocument(
        DcmItem *dataset,
        OFLogger &appLogger)
{
  char buf[100];
  size_t fileSize = 0;
  size_t buflen = 100;
  struct stat fileStat;

  if (0 == stat(opt_ifname.c_str(), &fileStat))
  {
    fileSize = OFstatic_cast(size_t, fileStat.st_size);
  }
  else
  {
    OFLOG_ERROR(appLogger, "file " << opt_ifname << " not found");
    return EXITCODE_NO_INPUT_FILES;
  }
  if (fileSize == 0)
  {
    OFLOG_ERROR(appLogger, "file " << opt_ifname << " is empty");
    return EXITCODE_INVALID_INPUT_FILE;
  }
  FILE *encapfile = fopen(opt_ifname.c_str(), "rb");
  if (encapfile == NULL)
  {
    OFLOG_ERROR(appLogger, "unable to read file " << opt_ifname);
    return EXITCODE_CANNOT_READ_INPUT_FILE;
  }
  if (fileSize < buflen)
  {
    buflen = fileSize;
  }
  if (buflen != fread(buf, 1, buflen, encapfile))
  {
    OFLOG_ERROR(appLogger, "read error in file " << opt_ifname);
    fclose(encapfile);
    return EXITCODE_INVALID_INPUT_FILE;
  }
  if (ftype == "pdf")
  {
    // check magic word for PDF file
    if (0 != strncmp("%PDF-", buf, 5))
    {
      OFLOG_ERROR(appLogger, "file " << opt_ifname << " is not a PDF file");
      fclose(encapfile);
      return EXITCODE_INVALID_INPUT_FILE;
    }
    // check PDF version number
    char *version = buf + 5;
    OFBool found = OFFalse;
    for (int i = 0; i < 5; ++i)
    {
      if (version[i] == 10 || version[i] == 13)
      {
        version[i] = 0; // insert end of string
        found = OFTrue;
        break;
      }
    }
    if (!found)
    {
      OFLOG_ERROR(appLogger, "file " << opt_ifname
              << ": unable to decode PDF version number");
      fclose(encapfile);
      return EXITCODE_INVALID_INPUT_FILE;
    }
    OFLOG_INFO(appLogger, "file " << opt_ifname
            << ": PDF " << version << ", "
            << (fileSize + 1023) / 1024 << "kB");
  }
  else
  {
    if (ftype == "cda")
    {
      //xml validation occurs when getting data
      OFLOG_INFO(appLogger, "file " << opt_ifname
              << ": HL7 CDA file (XML Format)" << ", "
              << (fileSize + 1023) / 1024 << "kB");
    }
    else
    {
      if (ftype == "stl")
      {
        // Each facet contains:
        //  - Normals: 3 floats (4 bytes)
        //  - Vertices: 3x floats (4 byte each, 12 bytes total)
        //  - AttributeCount: 1 short (2 bytes)
        // Total: 50 bytes per facet
        const size_t facetSize32 = 3 * sizeof(Float32)
                                   + 3 * 3 * sizeof(Float32)
                                   + sizeof(Uint16);
        const size_t facetSize64 = 3 * sizeof(Float64)
                                   + 3 * 3 * sizeof(Float64)
                                   + sizeof(Uint16);
        // STL validation for ASCII CODE
        if (fileSize < 15)
        {
          // "solid " and "endsolid " markers for an ASCII file
          OFLOG_ERROR(appLogger, "The STL file is not long enough"
                  << " (" << fileSize << "kB)");
          fclose(encapfile);
          return EXITCODE_INVALID_INPUT_FILE;
        }
        // Binary files should never start with "solid ",
        // but just in case, check for ASCII,
        // and if not valid then check for binary...
        // Look for text "solid " in first 6 bytes,
        // indicating the possibility that this is an
        // ASCII STL format.
        if (0 == strncmp("solid ", buf, 6))
        {
          OFLOG_ERROR(appLogger, "File " << opt_ifname
                  << " starts with 'solid '. "
                  << "It is a valid STL file but it is in ASCII Code"
                  << "and DICOM only accepts binary STL");
          return EXITCODE_INVALID_INPUT_FILE;
        }
          //////STL validation for Binary Format
        else
        {
          OFLOG_DEBUG(appLogger, "Magic word 'solid ' not found. "
                  << "Validating STL file "
                  << "in Binary format");
          // 80-byte header + 4-byte "number of triangles" for a binary file
          if (fileSize < 84)
          {
            OFLOG_ERROR(appLogger, "The binary STL file is not long enough"
                    << " (" << fileSize << "kB)");
            fclose(encapfile);
            return EXITCODE_INVALID_INPUT_FILE;
          }
          // Header is from bytes 0-79
          // The number of Triangles starts at byte offset 80 and is a uint32 (4 Bytes)
          char ntriangleschar[5];
          for (int j = 0; j < 4; j++)
            ntriangleschar[j] = buf[80 + j];
          ntriangleschar[4] = 0;
          Uint32 *nTriangles = OFreinterpret_cast(Uint32*, ntriangleschar);
          // Verify that file size equals the sum of
          // header + nTriangles value + all triangles
          OFLOG_DEBUG(appLogger, "verifying if the file size is consistent");
          if (fileSize == (84 + *OFconst_cast(Uint32*, nTriangles) * facetSize32) ||
              fileSize == (84 + *OFconst_cast(Uint32*, nTriangles) * facetSize64))
          {
            OFLOG_DEBUG(appLogger, "File " << opt_ifname
                    << " passed binary STL validation." << OFendl
                    << "Assuming valid STL file "
                    << "in binary format"
            );
            OFLOG_TRACE(appLogger, "The binary STL file is:" << OFendl
                    << fileSize << " kB " << " as expected." << OFendl
                    << (84 + *OFconst_cast(Uint32 * , nTriangles) * facetSize32) << " kB for x86" << OFendl
                    << (84 + *OFconst_cast(Uint32 * , nTriangles) * facetSize64) << " kB for x64" << OFendl
                    << "(84 + triangles number * facet size)" << OFendl
                    << " number of Triangles " << *OFconst_cast(Uint32 * , nTriangles) << OFendl
                    << " nTriangles (Uint32): " << nTriangles << OFendl
                    << " facetSize32: " << facetSize32 << OFendl
                    << " facetSize64: " << facetSize64 << OFendl
            );
          }
          else
          {
            OFLOG_ERROR(appLogger, "The binary STL file is not consistent." << OFendl
                    << (84 + *OFconst_cast(Uint32 * , nTriangles) * facetSize32) << " kB for x86 and "
                    << (84 + *OFconst_cast(Uint32 * , nTriangles) * facetSize64) << " kB for x64 " << OFendl
                    << "(84 + triangles number * facet size)" << OFendl
                    << " number of Triangles " << *OFconst_cast(Uint32 * , nTriangles) << OFendl
                    << " nTriangles (Uint32): " << nTriangles << OFendl
                    << " facetSize32: " << facetSize32 << OFendl
                    << " facetSize64: " << facetSize64 << OFendl
            );
            fclose(encapfile);
            return EXITCODE_INVALID_INPUT_FILE;
          }
        }
      }
      else
      {
        OFLOG_WARN(appLogger, "Filetype not supported or filetype not set. Current ftype is " << ftype << OFendl
                << "The name of the passed logger is: " << appLogger.getName());
      }
    }
  }
  if (0 != fseek(encapfile, 0, SEEK_SET))
  {
    OFLOG_ERROR(appLogger, "file " << opt_ifname << ": seek error");
    fclose(encapfile);
    return EXITCODE_CANNOT_READ_INPUT_FILE;
  }
  OFCondition result = EC_Normal;
  DcmPolymorphOBOW *elem = new DcmPolymorphOBOW(DCM_EncapsulatedDocument);
  if (elem)
  {
    size_t numBytes = fileSize;
    // according to CP 1851
    result = dataset->putAndInsertUint32(DCM_EncapsulatedDocumentLength, OFstatic_cast(Uint32, numBytes));
    if (numBytes & 1) ++numBytes;
    Uint8 *bytes = NULL;
    if (result.good())
    {
      result = elem->createUint8Array(OFstatic_cast(Uint32, numBytes), bytes);
    }
    else
    {
      return EXITCODE_CANNOT_WRITE_OUTPUT_FILE;
    }
    if (result.good())
    {
      // blank pad byte
      bytes[numBytes - 1] = 0;
      // read file content
      if (fileSize != fread(bytes, 1, fileSize, encapfile))
      {
        OFLOG_ERROR(appLogger, "read error in file " << opt_ifname);
        return EXITCODE_CANNOT_READ_INPUT_FILE;
      }
    }
    else
    {
      return EXITCODE_MEMORY_EXHAUSTED;
    }
  }
  else
  {
    fclose(encapfile);
    return EXITCODE_MEMORY_EXHAUSTED;
  }
  // if successful, insert element into dataset
  if (result.good())
  {
    result = dataset->insert(elem);
  }
  else
  {
    delete elem;
    OFLOG_ERROR(appLogger, "Unsuccessful, did not insert element.");
    return EXITCODE_CANNOT_WRITE_OUTPUT_FILE;
  }
  // close file
  fclose(encapfile);
  if (result.good())
  {
    return EXITCODE_NO_ERROR;
  }
  else
  {
    return EXITCODE_CANNOT_WRITE_OUTPUT_FILE;
  }
}

OFCondition DcmEncapsulatedDocument::createHeader(
        DcmItem *dataset,
        OFLogger &logger)
{
  OFCondition result = EC_Normal;
  char buf[80];
  // insert empty type 2 attributes
  if (result.good()) result = dataset->insertEmptyElement(DCM_StudyDate);
  if (result.good()) result = dataset->insertEmptyElement(DCM_StudyTime);
  if (result.good()) result = dataset->insertEmptyElement(DCM_AccessionNumber);
  if (result.good()) result = dataset->insertEmptyElement(DCM_Manufacturer);
  if (result.good()) result = dataset->insertEmptyElement(DCM_ReferringPhysicianName);
  if (result.good()) result = dataset->insertEmptyElement(DCM_StudyID);
  if (result.good()) result = dataset->insertEmptyElement(DCM_ContentDate);
  if (result.good()) result = dataset->insertEmptyElement(DCM_ContentTime);
  if (result.good()) result = dataset->insertEmptyElement(DCM_AcquisitionDateTime);
  if (result.good())
  {
    if (opt_conceptCSD != "" && opt_conceptCV != "" && opt_conceptCM != "")
    {
      result = DcmCodec::insertCodeSequence(dataset, DCM_ConceptNameCodeSequence,
                                            opt_conceptCSD.c_str(),
                                            opt_conceptCV.c_str(),
                                            opt_conceptCM.c_str());
    }
    else
    {
      result = dataset->insertEmptyElement(DCM_ConceptNameCodeSequence);
    }
  }
  // insert const value attributes
  if (result.good())
  {
    result = dataset->putAndInsertString(DCM_SpecificCharacterSet, "ISO_IR 100");
  }
  //insert encapsulated file storage UID (CDA/PDF/STL)
  if (result.good())
  {
    if (ftype == "pdf")
    {
      OFLOG_TRACE(logger, "Inserting SOPClassUID to dataset");
      result = dataset->putAndInsertString(DCM_SOPClassUID, UID_EncapsulatedPDFStorage);
    }
    if (ftype == "cda")
    {
      OFLOG_TRACE(logger, "Inserting SOPClassUID to dataset");
      result = dataset->putAndInsertString(DCM_SOPClassUID, UID_EncapsulatedCDAStorage);
    }
    if (ftype == "stl")
    {//STL Specific modules
      OFLOG_TRACE(logger, "Validating Frame of Reference UID value");
      if (opt_frameOfReferenceUID.empty())
      {
        OFLOG_DEBUG(logger, "Frame of Reference UID "
                << DCM_FrameOfReferenceUID
                << " value was empty, generating a new one."
        );
        dcmGenerateUniqueIdentifier(buf, SITE_SERIES_UID_ROOT);
        opt_frameOfReferenceUID = buf;
      }
      else
      {
        if (DcmUniqueIdentifier::checkStringValue(opt_frameOfReferenceUID, "1").bad())
        {
          OFLOG_DEBUG(logger, "Frame of Reference UID "
                  << DCM_FrameOfReferenceUID
                  << " value was faulty, generating a new one."
          );
          dcmGenerateUniqueIdentifier(buf, SITE_SERIES_UID_ROOT);
          opt_frameOfReferenceUID = buf;
        }
      }
      if (result.good())
      {
        OFLOG_TRACE(logger, "Inserting Frame of Reference info to dataset");
        result = dataset->putAndInsertOFStringArray(DCM_FrameOfReferenceUID, opt_frameOfReferenceUID);
      }
      if (result.good())
        result = dataset->putAndInsertOFStringArray(DCM_PositionReferenceIndicator, opt_positionReferenceIndicator);
      OFLOG_TRACE(logger, "Validating and inserting Enhanced General Equipment fields");
      if (result.good())
      {
        if (opt_manufacturer.empty())
        {
          opt_manufacturer = "DCMTK_MANUFACTURING";
          OFLOG_WARN(logger, "No Manufacturer "
                  << DCM_Manufacturer
                  << " provided nor found in series. This attribute is "
                  << "required for Enhanced General Equipment module. "
                  << opt_manufacturer
                  << " will be inserted as dummy value."
          );
        }
        result = dataset->putAndInsertOFStringArray(DCM_Manufacturer, opt_manufacturer);
      }
      if (result.good())
      {
        if (opt_manufacturerModelName.empty())
        {
          opt_manufacturerModelName = "DCMTK_3DMODEL_3";
          OFLOG_WARN(logger, "No Manufacturer Model Name "
                  << DCM_ManufacturerModelName
                  << " provided nor found in series. This attribute is "
                  << "required for Enhanced General Equipment module. "
                  << opt_manufacturerModelName
                  << " will be inserted as dummy value."
          );
        }
        result = dataset->putAndInsertOFStringArray(DCM_ManufacturerModelName, opt_manufacturerModelName);
      }
      if (result.good())
      {
        if (opt_deviceSerialNumber.empty())
        {
          opt_deviceSerialNumber = "DCMTK01234567890";
          OFLOG_WARN(logger, "No Device Serial Number "
                  << DCM_DeviceSerialNumber
                  << " provided nor found in series. This attribute is "
                  << "required for Enhanced General Equipment module. "
                  << opt_deviceSerialNumber
                  << " will be inserted as dummy value."
          );
        }
        result = dataset->putAndInsertOFStringArray(DCM_DeviceSerialNumber, opt_deviceSerialNumber);
      }
      if (result.good())
      {
        if (opt_softwareVersions.empty())
        {
          opt_softwareVersions = OFFIS_DCMTK_VERSION;
          OFLOG_WARN(logger, "No Software Versions "
                  << DCM_SoftwareVersions
                  << " provided nor found in series. This attribute is "
                  << "required for Enhanced General Equipment module. "
                  << opt_softwareVersions
                  << " will be inserted as dummy value."
          );
        }
        result = dataset->putAndInsertOFStringArray(DCM_SoftwareVersions, opt_softwareVersions);
      }
      if (result.good())
      {
        if (opt_measurementUnitsCSD != "" && opt_measurementUnitsCV != "" && opt_measurementUnitsCM != "")
        {
          result = DcmCodec::insertCodeSequence(dataset, DCM_MeasurementUnitsCodeSequence,
                                                opt_measurementUnitsCSD.c_str(),
                                                opt_measurementUnitsCV.c_str(),
                                                opt_measurementUnitsCM.c_str());
        }
        else
        {
          OFLOG_DEBUG(logger, "Measurement Units Code Sequence "
                  << DCM_FrameOfReferenceUID
                  << "had one or more empty values, generating default values."
          );
          result = DcmCodec::insertCodeSequence(dataset, DCM_MeasurementUnitsCodeSequence, "UCUM", "um", "um");
        }
      }
      if (result.good())
      {
        OFLOG_TRACE(logger, "Inserting SOPClassUID to dataset");
        result = dataset->putAndInsertString(DCM_SOPClassUID, UID_EncapsulatedSTLStorage);
      }
    }
  }
  if (result.good())
  {
    if (ftype == "stl")
    {
      result = dataset->putAndInsertString(DCM_Modality, "M3D");
    }
    else
    {
      // we are now using "DOC" for the modality, which seems to be more appropriate than "OT" (see CP-749)
      result = dataset->putAndInsertString(DCM_Modality, "DOC");
    }
  }
  if (result.good())
  {
    if (ftype != "stl")
    {
      OFLOG_TRACE(logger, "Inserting default Conversion type: Workstation (WSD) to dataset");
      result = dataset->putAndInsertString(DCM_ConversionType, "WSD");
    }
    else
    {
      OFLOG_TRACE(logger, "STL has no Conversion Type");
      result = EC_Normal;
    }
  }
  if (result.good())
  {
    // according to C.24.2.1 on part 3, (0042,0012) is text/XML for CDA.
    if (ftype == "cda")
      result = dataset->putAndInsertString(DCM_MIMETypeOfEncapsulatedDocument, "text/XML");
    // according to A.45.1.4.1 on part 3, MIME Type is application/pdf for PDF.
    if (ftype == "pdf")
      result = dataset->putAndInsertString(DCM_MIMETypeOfEncapsulatedDocument, "application/pdf");
    // according to A.85.1.4.2 on part 3, MIME Type is model/stl.
    if (ftype == "stl")
      result = dataset->putAndInsertString(DCM_MIMETypeOfEncapsulatedDocument, "model/stl");
  }
  // there is no way we could determine a meaningful series number, so we just use a constant.
  if (result.good()) result = dataset->putAndInsertString(DCM_SeriesNumber, "1");
  // insert variable value attributes
  if (result.good()) result = dataset->putAndInsertString(DCM_DocumentTitle, opt_documentTitle.c_str());
  if (result.good()) result = dataset->putAndInsertString(DCM_PatientName, opt_patientName.c_str());
  if (result.good()) result = dataset->putAndInsertString(DCM_PatientID, opt_patientID.c_str());
  if (result.good()) result = dataset->putAndInsertString(DCM_PatientBirthDate, opt_patientBirthdate.c_str());
  if (result.good()) result = dataset->putAndInsertString(DCM_PatientSex, opt_patientSex.c_str());
  if (result.good()) result = dataset->putAndInsertString(DCM_BurnedInAnnotation, opt_annotation ? "YES" : "NO");
  if (strlen(cda_mediaTypes.c_str()) > 0)
  {
    if (result.good()) result = dataset->putAndInsertString(DCM_ListOfMIMETypes, cda_mediaTypes.c_str());
  }
  if (hl7_InstanceIdentifier.size() > 0)
  {
    if (result.good()) result = dataset->putAndInsertString(DCM_HL7InstanceIdentifier, hl7_InstanceIdentifier.c_str());
  }
  sprintf(buf, "%ld", OFstatic_cast(long, opt_instance));
  if (result.good()) result = dataset->putAndInsertString(DCM_InstanceNumber, buf);
  dcmGenerateUniqueIdentifier(buf, SITE_INSTANCE_UID_ROOT);
  if (result.good()) result = dataset->putAndInsertString(DCM_StudyInstanceUID, opt_studyUID.c_str());
  if (result.good()) result = dataset->putAndInsertString(DCM_SeriesInstanceUID, opt_seriesUID.c_str());
  if (result.good()) result = dataset->putAndInsertString(DCM_SOPInstanceUID, buf);
  // set instance creation date and time
  OFString s;
  if (result.good()) result = DcmDate::getCurrentDate(s);
  if (result.good()) result = dataset->putAndInsertOFStringArray(DCM_InstanceCreationDate, s);
  if (result.good()) result = DcmTime::getCurrentTime(s);
  if (result.good()) result = dataset->putAndInsertOFStringArray(DCM_InstanceCreationTime, s);
  return result;
}

OFCondition DcmEncapsulatedDocument::applyOverrideKeys(DcmDataset *outputDset)
{
  // replace specific keys by those in overrideKeys, copied from findscu
  OFListConstIterator(OFString) path = opt_overrideKeys.begin();
  OFListConstIterator(OFString) endOfList = opt_overrideKeys.end();
  OFCondition cond;
  DcmPathProcessor proc;
  while (path != endOfList)
  {
    cond = proc.applyPathWithValue(outputDset, *path);
    if (cond.bad())
    {
      OFString err;
      err += "Bad override key/path: ";
      err += *path;
      err += ": ";
      err += cond.text();
      return makeOFCondition(OFM_dcmdata, 18, OF_error, err.c_str());
    }
    path++;
  }
  return cond;
}

void DcmEncapsulatedDocument::setOverrideKeys(const OFList<OFString> &ovkeys)
{
  OFListConstIterator(OFString) it = ovkeys.begin();
  OFListConstIterator(OFString) end = ovkeys.end();
  while (it != end)
  {
    opt_overrideKeys.push_back(*it);
    it++;
  }
}

OFCondition DcmEncapsulatedDocument::saveFile(DcmFileFormat fileformat)
{
  return fileformat.saveFile(opt_ofname, opt_oxfer, opt_oenctype, opt_oglenc,
                             opt_opadenc, OFstatic_cast(Uint32, opt_filepad),
                             OFstatic_cast(Uint32, opt_itempad));
}

OFString DcmEncapsulatedDocument::getInputFileName()
{
  return opt_ifname;
}

void DcmEncapsulatedDocument::setInputFileName(OFString fName)
{
  opt_ifname = fName;
}

OFString DcmEncapsulatedDocument::getOutputFileName()
{
  return opt_ofname;
}

void DcmEncapsulatedDocument::setOutputFileName(OFString fName)
{
  opt_ofname = fName;
}

OFString DcmEncapsulatedDocument::getFileType()
{
  return ftype;
}

void DcmEncapsulatedDocument::setFileType(OFString fType)
{
  ftype = fType;
}

E_TransferSyntax DcmEncapsulatedDocument::getTransferSyntax()
{
  return opt_oxfer;
}

DcmEncapsulatedDocument::~DcmEncapsulatedDocument()
{
}