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/*
*
* Copyright (C) 2003-2024, 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: Joerg Riesmeier
*
* Purpose: Convert XML document to DICOM file or data set
*
*/
#include "dcmtk/config/osconfig.h" /* make sure OS specific configuration is included first */
#include "dcmtk/dcmdata/dctk.h"
#include "dcmtk/dcmdata/dcpxitem.h" /* for class DcmPixelItem */
#include "dcmtk/dcmdata/cmdlnarg.h"
#include "dcmtk/ofstd/ofstd.h"
#include "dcmtk/ofstd/ofconapp.h"
#include "dcmtk/dcmdata/dcostrmz.h" /* for dcmZlibCompressionLevel */
#include "dcmtk/dcmdata/dcmxml/xml2dcm.h"
#ifdef WITH_ZLIB
#include <zlib.h> /* for zlibVersion() */
#endif
#define OFFIS_CONSOLE_APPLICATION "xml2dcm"
#define OFFIS_CONSOLE_DESCRIPTION "Convert XML document to DICOM file or data set"
// currently not used since DTD is always retrieved from XML document
//#define DOCUMENT_TYPE_DEFINITION_FILE "dcm2xml.dtd"
static char rcsid[] = "$dcmtk: " OFFIS_CONSOLE_APPLICATION " v"
OFFIS_DCMTK_VERSION " " OFFIS_DCMTK_RELEASEDATE " $";
// ********************************************
#ifdef WITH_LIBXML
static OFLogger xml2dcmLogger = OFLog::getLogger("dcmtk.apps." OFFIS_CONSOLE_APPLICATION);
#define SHORTCOL 3
#define LONGCOL 21
int main(int argc, char *argv[])
{
OFBool opt_metaInfo = OFTrue;
OFBool opt_namespace = OFFalse;
OFBool opt_validate = OFFalse;
OFBool opt_generateUIDs = OFFalse;
OFBool opt_overwriteUIDs = OFFalse;
OFBool opt_stopOnErrors = OFTrue;
E_TransferSyntax opt_xfer = EXS_Unknown;
E_EncodingType opt_enctype = EET_ExplicitLength;
E_GrpLenEncoding opt_glenc = EGL_recalcGL;
E_PaddingEncoding opt_padenc = EPD_withoutPadding;
E_FileWriteMode opt_writeMode = EWM_fileformat;
OFCmdUnsignedInt opt_filepad = 0;
OFCmdUnsignedInt opt_itempad = 0;
/* set-up command line parameters and options */
OFConsoleApplication app(OFFIS_CONSOLE_APPLICATION, OFFIS_CONSOLE_DESCRIPTION, rcsid);
OFCommandLine cmd;
cmd.setOptionColumns(LONGCOL, SHORTCOL);
cmd.setParamColumn(LONGCOL + SHORTCOL + 4);
cmd.addParam("xmlfile-in", "XML input filename to be converted\n(\"-\" for stdin)", OFCmdParam::PM_Mandatory);
cmd.addParam("dcmfile-out", "DICOM output filename\n(\"-\" for stdout)", OFCmdParam::PM_Mandatory);
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);
cmd.addGroup("input options:");
cmd.addSubGroup("input file format:");
cmd.addOption("--read-meta-info", "+f", "read meta information if present (default)");
cmd.addOption("--ignore-meta-info", "-f", "ignore file meta information");
cmd.addGroup("processing options:");
cmd.addSubGroup("validation:");
cmd.addOption("--validate-document", "+Vd", "validate XML document against DTD");
cmd.addOption("--check-namespace", "+Vn", "check XML namespace in document root");
cmd.addSubGroup("unique identifiers:");
cmd.addOption("--generate-new-uids", "+Ug", "generate new Study/Series/SOP Instance UID");
cmd.addOption("--dont-overwrite-uids", "-Uo", "do not overwrite existing UIDs (default)");
cmd.addOption("--overwrite-uids", "+Uo", "overwrite existing UIDs");
cmd.addGroup("output options:");
cmd.addSubGroup("output file format:");
cmd.addOption("--write-file", "+F", "write file format (default)");
cmd.addOption("--write-dataset", "-F", "write data set without file meta information");
cmd.addOption("--update-meta-info", "+Fu", "update particular file meta information");
cmd.addSubGroup("output transfer syntax:");
cmd.addOption("--write-xfer-same", "+t=", "write with same TS as input (default)");
cmd.addOption("--write-xfer-little", "+te", "write with explicit VR little endian TS");
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");
#ifdef WITH_ZLIB
cmd.addOption("--write-xfer-deflated", "+td", "write with deflated expl. VR little endian TS");
#endif
cmd.addSubGroup("error handling:");
cmd.addOption("--stop-on-error", "-E", "do not write if document is invalid (default)");
cmd.addOption("--ignore-errors", "+E", "attempt to write even if document is invalid");
cmd.addSubGroup("post-1993 value representations:");
cmd.addOption("--enable-new-vr", "+u", "enable support for new VRs (UN/UT) (default)");
cmd.addOption("--disable-new-vr", "-u", "disable support for new VRs, convert to OB");
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\n(default if not --write-dataset)");
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");
#ifdef WITH_ZLIB
cmd.addSubGroup("deflate compression level (only with --write-xfer-deflated):");
cmd.addOption("--compression-level", "+cl", 1, "[l]evel: integer (default: 6)",
"0=uncompressed, 1=fastest, 9=best compression");
#endif
/* evaluate command line */
prepareCmdLineArgs(argc, argv, OFFIS_CONSOLE_APPLICATION);
if (app.parseCommandLine(cmd, argc, argv))
{
/* check exclusive options first */
if (cmd.hasExclusiveOption())
{
if (cmd.findOption("--version"))
{
app.printHeader(OFTrue /*print host identifier*/);
COUT << OFendl << "External libraries used:" << OFendl;
#ifdef WITH_ZLIB
COUT << "- ZLIB, Version " << zlibVersion() << OFendl;
#endif
COUT << "- LIBXML, Version " << LIBXML_DOTTED_VERSION << OFendl;
#if defined(LIBXML_ICONV_ENABLED) && defined(LIBXML_ZLIB_ENABLED)
COUT << " with built-in LIBICONV and ZLIB support" << OFendl;
#elif defined(LIBXML_ICONV_ENABLED)
COUT << " with built-in LIBICONV support" << OFendl;
#elif defined(LIBXML_ZLIB_ENABLED)
COUT << " with built-in ZLIB support" << OFendl;
#endif
return 0;
}
}
/* general options */
OFLog::configureFromCommandLine(cmd, app);
/* input options */
cmd.beginOptionBlock();
if (cmd.findOption("--read-meta-info"))
opt_metaInfo = OFTrue;
if (cmd.findOption("--ignore-meta-info"))
opt_metaInfo = OFFalse;
cmd.endOptionBlock();
/* processing options */
if (cmd.findOption("--validate-document"))
opt_validate = OFTrue;
if (cmd.findOption("--check-namespace"))
opt_namespace = OFTrue;
if (cmd.findOption("--generate-new-uids"))
opt_generateUIDs = OFTrue;
cmd.beginOptionBlock();
if (cmd.findOption("--dont-overwrite-uids"))
{
app.checkDependence("--dont-overwrite-uids", "--generate-new-uids", opt_generateUIDs);
opt_overwriteUIDs = OFFalse;
}
if (cmd.findOption("--overwrite-uids"))
{
app.checkDependence("--overwrite-uids", "--generate-new-uids", opt_generateUIDs);
opt_overwriteUIDs = OFTrue;
}
cmd.endOptionBlock();
/* output options */
cmd.beginOptionBlock();
if (cmd.findOption("--write-file"))
opt_writeMode = EWM_fileformat;
if (cmd.findOption("--write-dataset"))
opt_writeMode = EWM_dataset;
cmd.endOptionBlock();
if (cmd.findOption("--update-meta-info"))
{
app.checkConflict("--update-meta-info", "--write-dataset", opt_writeMode == EWM_dataset);
opt_writeMode = EWM_updateMeta;
}
cmd.beginOptionBlock();
if (cmd.findOption("--write-xfer-same"))
opt_xfer = EXS_Unknown;
if (cmd.findOption("--write-xfer-little"))
opt_xfer = EXS_LittleEndianExplicit;
if (cmd.findOption("--write-xfer-big"))
opt_xfer = EXS_BigEndianExplicit;
if (cmd.findOption("--write-xfer-implicit"))
opt_xfer = EXS_LittleEndianImplicit;
#ifdef WITH_ZLIB
if (cmd.findOption("--write-xfer-deflated"))
opt_xfer = EXS_DeflatedLittleEndianExplicit;
#endif
cmd.endOptionBlock();
cmd.beginOptionBlock();
if (cmd.findOption("--stop-on-error")) opt_stopOnErrors = OFTrue;
if (cmd.findOption("--ignore-errors")) opt_stopOnErrors = OFFalse;
cmd.endOptionBlock();
cmd.beginOptionBlock();
if (cmd.findOption("--enable-new-vr"))
dcmEnableGenerationOfNewVRs();
if (cmd.findOption("--disable-new-vr"))
dcmDisableGenerationOfNewVRs();
cmd.endOptionBlock();
cmd.beginOptionBlock();
if (cmd.findOption("--group-length-recalc"))
opt_glenc = EGL_recalcGL;
if (cmd.findOption("--group-length-create"))
opt_glenc = EGL_withGL;
if (cmd.findOption("--group-length-remove"))
opt_glenc = EGL_withoutGL;
cmd.endOptionBlock();
cmd.beginOptionBlock();
if (cmd.findOption("--length-explicit"))
opt_enctype = EET_ExplicitLength;
if (cmd.findOption("--length-undefined"))
opt_enctype = EET_UndefinedLength;
cmd.endOptionBlock();
cmd.beginOptionBlock();
if (cmd.findOption("--padding-retain"))
{
app.checkConflict("--padding-retain", "--write-dataset", opt_writeMode == EWM_dataset);
opt_padenc = EPD_noChange;
}
if (cmd.findOption("--padding-off"))
opt_padenc = 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_padenc = EPD_withPadding;
}
cmd.endOptionBlock();
#ifdef WITH_ZLIB
if (cmd.findOption("--compression-level"))
{
OFCmdUnsignedInt comprLevel = 0;
app.checkDependence("--compression-level", "--write-xfer-deflated", opt_xfer == EXS_DeflatedLittleEndianExplicit);
app.checkValue(cmd.getValueAndCheckMinMax(comprLevel, 0, 9));
dcmZlibCompressionLevel.set(OFstatic_cast(int, comprLevel));
}
#endif
}
/* print resource identifier */
OFLOG_DEBUG(xml2dcmLogger, rcsid << OFendl);
/* make sure data dictionary is loaded */
if (!dcmDataDict.isDictionaryLoaded())
{
OFLOG_WARN(xml2dcmLogger, "no data dictionary loaded, check environment variable: "
<< DCM_DICT_ENVIRONMENT_VARIABLE);
}
// initialize XML parser
DcmXMLParseHelper::initLibrary();
OFCondition result = EC_Normal;
const char *opt_ifname = NULL;
const char *opt_ofname = NULL;
cmd.getParam(1, opt_ifname);
cmd.getParam(2, opt_ofname);
/* check filenames */
if ((opt_ifname == NULL) || (strlen(opt_ifname) == 0))
{
OFLOG_ERROR(xml2dcmLogger, OFFIS_CONSOLE_APPLICATION << ": invalid input filename: <empty string>");
result = EC_IllegalParameter;
}
if ((opt_ofname == NULL) || (strlen(opt_ofname) == 0))
{
OFLOG_ERROR(xml2dcmLogger, OFFIS_CONSOLE_APPLICATION << ": invalid output filename: <empty string>");
result = EC_IllegalParameter;
}
if (result.good())
{
DcmFileFormat fileformat;
E_TransferSyntax xfer;
DcmXMLParseHelper parser;
OFLOG_INFO(xml2dcmLogger, "reading XML input file: " << opt_ifname);
/* read XML file and feed data into DICOM fileformat */
result = parser.readXmlFile(opt_ifname, fileformat, xfer, opt_metaInfo, opt_namespace, opt_validate, opt_stopOnErrors);
if (result.good())
{
DcmDataset *dataset = fileformat.getDataset();
/* generate new UIDs (if required) */
if (opt_generateUIDs)
{
char uid[100];
if (opt_overwriteUIDs || !dataset->tagExistsWithValue(DCM_StudyInstanceUID))
{
OFLOG_INFO(xml2dcmLogger, "generating new Study Instance UID");
dataset->putAndInsertString(DCM_StudyInstanceUID, dcmGenerateUniqueIdentifier(uid, SITE_STUDY_UID_ROOT));
}
if (opt_overwriteUIDs || !dataset->tagExistsWithValue(DCM_SeriesInstanceUID))
{
OFLOG_INFO(xml2dcmLogger, "generating new Series Instance UID");
dataset->putAndInsertString(DCM_SeriesInstanceUID, dcmGenerateUniqueIdentifier(uid, SITE_SERIES_UID_ROOT));
}
if (opt_overwriteUIDs || !dataset->tagExistsWithValue(DCM_SOPInstanceUID))
{
OFLOG_INFO(xml2dcmLogger, "generating new SOP Instance UID");
dataset->putAndInsertString(DCM_SOPInstanceUID, dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT));
}
}
OFLOG_INFO(xml2dcmLogger, "writing DICOM output file: " << opt_ofname);
/* determine transfer syntax to write the file */
if ((opt_xfer == EXS_Unknown) && (xfer != EXS_Unknown))
opt_xfer = xfer;
/* check whether this is possible */
if (fileformat.canWriteXfer(opt_xfer))
{
/* check whether pixel data is compressed */
if ((opt_writeMode == EWM_dataset) && DcmXfer(xfer).usesEncapsulatedFormat())
{
OFLOG_WARN(xml2dcmLogger, "encapsulated pixel data require file format, ignoring --write-dataset");
opt_writeMode = EWM_fileformat;
}
/* write DICOM file */
result = fileformat.saveFile(opt_ofname, opt_xfer, opt_enctype, opt_glenc, opt_padenc,
OFstatic_cast(Uint32, opt_filepad), OFstatic_cast(Uint32, opt_itempad), opt_writeMode);
if (result.bad())
OFLOG_ERROR(xml2dcmLogger, result.text() << ": writing file: " << opt_ofname);
} else {
OFLOG_ERROR(xml2dcmLogger, "no conversion to transfer syntax " << DcmXfer(opt_xfer).getXferName() << " possible!");
result = EC_CannotChangeRepresentation;
}
}
}
/* clean up XML library before quitting */
DcmXMLParseHelper::cleanupLibrary();
return result.status();
}
#else /* WITH_LIBXML */
int main(int, char *[])
{
CERR << rcsid << OFendl << OFFIS_CONSOLE_DESCRIPTION << OFendl << OFendl
<< OFFIS_CONSOLE_APPLICATION " requires the libxml library." << OFendl
<< "This " OFFIS_CONSOLE_APPLICATION " has been configured and compiled without libxml." << OFendl
<< "Please reconfigure your system and recompile if appropriate." << OFendl;
return 0;
}
#endif /* WITH_LIBXML */
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