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/*
*
* Copyright (C) 2002-2010, 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 the contents of a DICOM file to XML format
*
* Last Update: $Author: joergr $
* Update Date: $Date: 2010-10-14 13:13:30 $
* CVS/RCS Revision: $Revision: 1.39 $
* Status: $State: Exp $
*
* CVS/RCS Log at end of file
*
*/
#include "dcmtk/config/osconfig.h" /* make sure OS specific configuration is included first */
#include "dcmtk/dcmdata/dctk.h"
#include "dcmtk/dcmdata/cmdlnarg.h"
#include "dcmtk/ofstd/ofstd.h"
#include "dcmtk/ofstd/ofstream.h"
#include "dcmtk/ofstd/ofconapp.h"
#ifdef WITH_ZLIB
#include <zlib.h> /* for zlibVersion() */
#endif
#define OFFIS_CONSOLE_APPLICATION "dcm2xml"
#define OFFIS_CONSOLE_DESCRIPTION "Convert DICOM file and data set to XML"
#define DOCUMENT_TYPE_DEFINITION_FILE "dcm2xml.dtd"
static OFLogger dcm2xmlLogger = OFLog::getLogger("dcmtk.apps." OFFIS_CONSOLE_APPLICATION);
static char rcsid[] = "$dcmtk: " OFFIS_CONSOLE_APPLICATION " v"
OFFIS_DCMTK_VERSION " " OFFIS_DCMTK_RELEASEDATE " $";
// ********************************************
static OFCondition writeFile(STD_NAMESPACE ostream &out,
const char *ifname,
DcmFileFormat *dfile,
const E_FileReadMode readMode,
const OFBool loadIntoMemory,
const char *dtdFilename,
const char *defaultCharset,
const size_t writeFlags,
const OFBool checkAllStrings)
{
OFCondition result = EC_IllegalParameter;
if ((ifname != NULL) && (dfile != NULL))
{
DcmDataset *dset = dfile->getDataset();
if (loadIntoMemory)
dset->loadAllDataIntoMemory();
/* determine dataset character encoding */
OFString encString;
OFString csetString;
if (dset->findAndGetOFString(DCM_SpecificCharacterSet, csetString).good())
{
if (csetString == "ISO_IR 6")
encString = "UTF-8";
else if (csetString == "ISO_IR 192")
encString = "UTF-8";
else if (csetString == "ISO_IR 100")
encString = "ISO-8859-1";
else if (csetString == "ISO_IR 101")
encString = "ISO-8859-2";
else if (csetString == "ISO_IR 109")
encString = "ISO-8859-3";
else if (csetString == "ISO_IR 110")
encString = "ISO-8859-4";
else if (csetString == "ISO_IR 148")
encString = "ISO-8859-9";
else if (csetString == "ISO_IR 144")
encString = "ISO-8859-5";
else if (csetString == "ISO_IR 127")
encString = "ISO-8859-6";
else if (csetString == "ISO_IR 126")
encString = "ISO-8859-7";
else if (csetString == "ISO_IR 138")
encString = "ISO-8859-8";
else if (!csetString.empty())
OFLOG_WARN(dcm2xmlLogger, "(0008,0005) Specific Character Set '" << csetString << "' not supported");
} else {
/* SpecificCharacterSet is not present in the dataset */
if (dset->containsExtendedCharacters(checkAllStrings))
{
if (defaultCharset == NULL)
{
/* the dataset contains non-ASCII characters that really should not be there */
OFLOG_WARN(dcm2xmlLogger, OFFIS_CONSOLE_APPLICATION << ": (0008,0005) Specific Character Set absent "
<< "but extended characters used in file: " << ifname);
return EC_IllegalCall;
} else {
OFString charset(defaultCharset);
if (charset == "latin-1")
{
csetString = "ISO_IR 100";
encString = "ISO-8859-1";
}
else if (charset == "latin-2")
{
csetString = "ISO_IR 101";
encString = "ISO-8859-2";
}
else if (charset == "latin-3")
{
csetString = "ISO_IR 109";
encString = "ISO-8859-3";
}
else if (charset == "latin-4")
{
csetString = "ISO_IR 110";
encString = "ISO-8859-4";
}
else if (charset == "latin-5")
{
csetString = "ISO_IR 148";
encString = "ISO-8859-9";
}
else if (charset == "cyrillic")
{
csetString = "ISO_IR 144";
encString = "ISO-8859-5";
}
else if (charset == "arabic")
{
csetString = "ISO_IR 127";
encString = "ISO-8859-6";
}
else if (charset == "greek")
{
csetString = "ISO_IR 126";
encString = "ISO-8859-7";
}
else if (charset == "hebrew")
{
csetString = "ISO_IR 138";
encString = "ISO-8859-8";
}
dset->putAndInsertString(DCM_SpecificCharacterSet, csetString.c_str());
}
}
}
/* write XML document header */
out << "<?xml version=\"1.0\"";
/* optional character set */
if (encString.length() > 0)
out << " encoding=\"" << encString << "\"";
out << "?>" << OFendl;
/* add document type definition (DTD) */
if (writeFlags & DCMTypes::XF_addDocumentType)
{
out << "<!DOCTYPE ";
if (readMode == ERM_dataset)
out << "data-set";
else
out << "file-format";
/* embed DTD */
if (writeFlags & DCMTypes::XF_embedDocumentType)
{
out << " [" << OFendl;
/* copy content from DTD file */
#ifdef HAVE_IOS_NOCREATE
STD_NAMESPACE ifstream dtdFile(dtdFilename, STD_NAMESPACE ios::in | STD_NAMESPACE ios::nocreate);
#else
STD_NAMESPACE ifstream dtdFile(dtdFilename, STD_NAMESPACE ios::in);
#endif
if (dtdFile)
{
char c;
/* copy all characters */
while (dtdFile.get(c))
out << c;
}
else
{
OFLOG_WARN(dcm2xmlLogger, OFFIS_CONSOLE_APPLICATION << ": cannot open DTD file: " << dtdFilename);
}
out << "]";
} else { /* reference DTD */
out << " SYSTEM \"" << DOCUMENT_TYPE_DEFINITION_FILE << "\"";
}
out << ">" << OFendl;
}
/* write XML document content */
if (readMode == ERM_dataset)
result = dset->writeXML(out, writeFlags);
else
result = dfile->writeXML(out, writeFlags);
}
return result;
}
#define SHORTCOL 3
#define LONGCOL 20
int main(int argc, char *argv[])
{
size_t opt_writeFlags = 0;
OFBool opt_loadIntoMemory = OFFalse;
OFBool opt_checkAllStrings = OFFalse;
const char *opt_defaultCharset = NULL;
E_FileReadMode opt_readMode = ERM_autoDetect;
E_TransferSyntax opt_ixfer = EXS_Unknown;
OFCmdUnsignedInt opt_maxReadLength = 4096; // default is 4 KB
const char *opt_dtdFilename = DEFAULT_SUPPORT_DATA_DIR DOCUMENT_TYPE_DEFINITION_FILE;
OFString optStr;
OFConsoleApplication app(OFFIS_CONSOLE_APPLICATION, OFFIS_CONSOLE_DESCRIPTION, rcsid);
OFCommandLine cmd;
cmd.setOptionColumns(LONGCOL, SHORTCOL);
cmd.setParamColumn(LONGCOL + SHORTCOL + 4);
cmd.addParam("dcmfile-in", "DICOM input filename to be converted", OFCmdParam::PM_Mandatory);
cmd.addParam("xmlfile-out", "XML output filename (default: stdout)", OFCmdParam::PM_Optional);
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-file", "+f", "read file format or data set (default)");
cmd.addOption("--read-file-only", "+fo", "read file format only");
cmd.addOption("--read-dataset", "-f", "read data set without file meta information");
cmd.addSubGroup("input transfer syntax:");
cmd.addOption("--read-xfer-auto", "-t=", "use TS recognition (default)");
cmd.addOption("--read-xfer-detect", "-td", "ignore TS specified in the file meta header");
cmd.addOption("--read-xfer-little", "-te", "read with explicit VR little endian TS");
cmd.addOption("--read-xfer-big", "-tb", "read with explicit VR big endian TS");
cmd.addOption("--read-xfer-implicit", "-ti", "read with implicit VR little endian TS");
cmd.addSubGroup("long tag values:");
cmd.addOption("--load-all", "+M", "load very long tag values (e.g. pixel data)");
cmd.addOption("--load-short", "-M", "do not load very long values (default)");
cmd.addOption("--max-read-length", "+R", 1, "[k]bytes: integer (4..4194302, default: 4)",
"set threshold for long values to k kbytes");
cmd.addGroup("processing options:");
cmd.addSubGroup("character set:");
cmd.addOption("--charset-require", "+Cr", "require declaration of extended charset (default)");
cmd.addOption("--charset-assume", "+Ca", 1, "[c]harset: string constant",
"(latin-1 to -5, cyrillic, arabic, greek, hebrew)\n"
"assume charset c if no extended charset declared");
cmd.addOption("--charset-check-all", "+Cc", "check all data elements with string values\n(default: only PN, LO, LT, SH, ST and UT)");
cmd.addGroup("output options:");
cmd.addSubGroup("XML structure:");
cmd.addOption("--add-dtd-reference", "+Xd", "add reference to document type definition (DTD)");
cmd.addOption("--embed-dtd-content", "+Xe", "embed document type definition into XML document");
optStr = "use specified DTD file (only with +Xe)\n(default: ";
optStr += opt_dtdFilename;
optStr += ")";
cmd.addOption("--use-dtd-file", "+Xf", 1, "[f]ilename: string",
optStr.c_str());
cmd.addOption("--use-xml-namespace", "+Xn", "add XML namespace declaration to root element");
cmd.addSubGroup("DICOM data elements:");
cmd.addOption("--write-element-name", "+Wn", "write name of the DICOM data elements (default)");
cmd.addOption("--no-element-name", "-Wn", "do not write name of the DICOM data elements");
cmd.addOption("--write-binary-data", "+Wb", "write binary data of OB and OW elements\n(default: off, be careful with --load-all)");
cmd.addOption("--encode-hex", "+Eh", "encode binary data as hex numbers (default)");
cmd.addOption("--encode-base64", "+Eb", "encode binary data as Base64 (RFC 2045, MIME)");
/* evaluate command line */
prepareCmdLineArgs(argc, argv, OFFIS_CONSOLE_APPLICATION);
if (app.parseCommandLine(cmd, argc, argv, OFCommandLine::PF_ExpandWildcards))
{
/* check exclusive options first */
if (cmd.hasExclusiveOption())
{
if (cmd.findOption("--version"))
{
app.printHeader(OFTrue /*print host identifier*/);
COUT << OFendl << "External libraries used:";
#ifdef WITH_ZLIB
COUT << OFendl << "- ZLIB, Version " << zlibVersion() << OFendl;
#else
COUT << " none" << OFendl;
#endif
return 0;
}
}
/* general options */
OFLog::configureFromCommandLine(cmd, app);
/* input options */
cmd.beginOptionBlock();
if (cmd.findOption("--read-file")) opt_readMode = ERM_autoDetect;
if (cmd.findOption("--read-file-only")) opt_readMode = ERM_fileOnly;
if (cmd.findOption("--read-dataset")) opt_readMode = ERM_dataset;
cmd.endOptionBlock();
cmd.beginOptionBlock();
if (cmd.findOption("--read-xfer-auto"))
opt_ixfer = EXS_Unknown;
if (cmd.findOption("--read-xfer-detect"))
dcmAutoDetectDatasetXfer.set(OFTrue);
if (cmd.findOption("--read-xfer-little"))
{
app.checkDependence("--read-xfer-little", "--read-dataset", opt_readMode == ERM_dataset);
opt_ixfer = EXS_LittleEndianExplicit;
}
if (cmd.findOption("--read-xfer-big"))
{
app.checkDependence("--read-xfer-big", "--read-dataset", opt_readMode == ERM_dataset);
opt_ixfer = EXS_BigEndianExplicit;
}
if (cmd.findOption("--read-xfer-implicit"))
{
app.checkDependence("--read-xfer-implicit", "--read-dataset", opt_readMode == ERM_dataset);
opt_ixfer = EXS_LittleEndianImplicit;
}
cmd.endOptionBlock();
if (cmd.findOption("--max-read-length"))
{
app.checkValue(cmd.getValueAndCheckMinMax(opt_maxReadLength, 4, 4194302));
opt_maxReadLength *= 1024; // convert kbytes to bytes
}
cmd.beginOptionBlock();
if (cmd.findOption("--load-all"))
opt_loadIntoMemory = OFTrue;
if (cmd.findOption("--load-short"))
opt_loadIntoMemory = OFFalse;
cmd.endOptionBlock();
/* processing options */
cmd.beginOptionBlock();
if (cmd.findOption("--charset-require"))
opt_defaultCharset = NULL;
if (cmd.findOption("--charset-assume"))
{
app.checkValue(cmd.getValue(opt_defaultCharset));
OFString charset(opt_defaultCharset);
if (charset != "latin-1" && charset != "latin-2" && charset != "latin-3" &&
charset != "latin-4" && charset != "latin-5" && charset != "cyrillic" &&
charset != "arabic" && charset != "greek" && charset != "hebrew")
{
app.printError("unknown value for --charset-assume. known values are latin-1 to -5, cyrillic, arabic, greek, hebrew.");
}
}
cmd.endOptionBlock();
if (cmd.findOption("--charset-check-all"))
opt_checkAllStrings = OFTrue;
/* output options */
cmd.beginOptionBlock();
if (cmd.findOption("--add-dtd-reference"))
opt_writeFlags |= DCMTypes::XF_addDocumentType;
if (cmd.findOption("--embed-dtd-content"))
opt_writeFlags |= DCMTypes::XF_addDocumentType | DCMTypes::XF_embedDocumentType;
cmd.endOptionBlock();
if (cmd.findOption("--use-dtd-file"))
{
app.checkDependence("--use-dtd-file", "--embed-dtd-content", (opt_writeFlags & DCMTypes::XF_embedDocumentType) > 0);
app.checkValue(cmd.getValue(opt_dtdFilename));
}
if (cmd.findOption("--use-xml-namespace"))
opt_writeFlags |= DCMTypes::XF_useDcmtkNamespace;
cmd.beginOptionBlock();
if (cmd.findOption("--write-element-name"))
opt_writeFlags &= ~DCMTypes::XF_omitDataElementName;
if (cmd.findOption("--no-element-name"))
opt_writeFlags |= DCMTypes::XF_omitDataElementName;
cmd.endOptionBlock();
if (cmd.findOption("--write-binary-data"))
opt_writeFlags |= DCMTypes::XF_writeBinaryData;
cmd.beginOptionBlock();
if (cmd.findOption("--encode-hex"))
{
app.checkDependence("--encode-hex", "--write-binary-data", (opt_writeFlags & DCMTypes::XF_writeBinaryData) > 0);
opt_writeFlags &= ~DCMTypes::XF_encodeBase64;
}
if (cmd.findOption("--encode-base64"))
{
app.checkDependence("--encode-base64", "--write-binary-data", (opt_writeFlags & DCMTypes::XF_writeBinaryData) > 0);
opt_writeFlags |= DCMTypes::XF_encodeBase64;
}
cmd.endOptionBlock();
}
/* print resource identifier */
OFLOG_DEBUG(dcm2xmlLogger, rcsid << OFendl);
/* make sure data dictionary is loaded */
if (!dcmDataDict.isDictionaryLoaded())
{
OFLOG_WARN(dcm2xmlLogger, "no data dictionary loaded, check environment variable: "
<< DCM_DICT_ENVIRONMENT_VARIABLE);
}
/* make sure document type definition file exists */
if ((opt_writeFlags & DCMTypes::XF_embedDocumentType) && !OFStandard::fileExists(opt_dtdFilename))
{
OFLOG_WARN(dcm2xmlLogger, OFFIS_CONSOLE_APPLICATION << ": DTD file \"" << opt_dtdFilename
<< "\" does not exist ... adding reference instead");
opt_writeFlags &= ~DCMTypes::XF_embedDocumentType;
}
int result = 0;
/* first parameter is treated as the input filename */
const char *ifname = NULL;
cmd.getParam(1, ifname);
/* check input file */
if ((ifname != NULL) && (strlen(ifname) > 0))
{
/* read DICOM file or data set */
DcmFileFormat dfile;
OFCondition status = dfile.loadFile(ifname, opt_ixfer, EGL_noChange, opt_maxReadLength, opt_readMode);
if (status.good())
{
/* if second parameter is present, it is treated as the output filename ("stdout" otherwise) */
if (cmd.getParamCount() == 2)
{
const char *ofname = NULL;
cmd.getParam(2, ofname);
STD_NAMESPACE ofstream stream(ofname);
if (stream.good())
{
/* write content in XML format to file */
if (writeFile(stream, ifname, &dfile, opt_readMode, opt_loadIntoMemory, opt_dtdFilename,
opt_defaultCharset, opt_writeFlags, opt_checkAllStrings).bad())
result = 2;
} else
result = 1;
} else {
/* write content in XML format to standard output */
if (writeFile(COUT, ifname, &dfile, opt_readMode, opt_loadIntoMemory, opt_dtdFilename,
opt_defaultCharset, opt_writeFlags, opt_checkAllStrings).bad())
result = 3;
}
} else
OFLOG_WARN(dcm2xmlLogger, OFFIS_CONSOLE_APPLICATION << ": (" << status.text() << ") reading file: "<< ifname);
} else
OFLOG_WARN(dcm2xmlLogger, OFFIS_CONSOLE_APPLICATION << ": invalid filename: <empty string>");
return result;
}
/*
* CVS/RCS Log:
* $Log: dcm2xml.cc,v $
* Revision 1.39 2010-10-14 13:13:30 joergr
* Updated copyright header. Added reference to COPYRIGHT file.
*
* Revision 1.38 2009-11-13 13:20:23 joergr
* Fixed minor issues in log output.
*
* Revision 1.37 2009-11-04 09:58:05 uli
* Switched to logging mechanism provided by the "new" oflog module
*
* Revision 1.36 2009-04-24 12:20:41 joergr
* Fixed minor inconsistencies regarding layout/formatting in syntax usage.
*
* Revision 1.35 2009-04-21 14:02:49 joergr
* Fixed minor inconsistencies in manpage / syntax usage.
*
* Revision 1.34 2009-03-25 17:54:35 joergr
* Added parentheses in order to keep MSVC quiet.
*
* Revision 1.33 2009-03-11 13:06:12 joergr
* Added support for specifying the filename of the DTD on the command line.
* Added command line option for quiet mode (print no warnings and errors).
*
* Revision 1.32 2009-02-04 18:08:18 joergr
* Fixed various layout and formatting issues.
*
* Revision 1.31 2008-09-25 14:38:48 joergr
* Moved output of resource identifier in order to avoid printing the same
* information twice.
*
* Revision 1.30 2008-09-25 11:19:48 joergr
* Added support for printing the expanded command line arguments.
* Always output the resource identifier of the command line tool in debug mode.
*
* Revision 1.29 2008-01-23 15:09:26 joergr
* Restructured code in order to avoid empty output file in case the input file
* could not be read.
*
* Revision 1.28 2006/12/13 14:21:56 joergr
* Removed dependence of the new command line option "--charset-check-all" from
* option "--charset-assume".
*
* Revision 1.27 2006/12/13 13:55:38 joergr
* Added new command line option that allows to check all data elements with
* string values for extended characters, not only those affected by Specific
* CharacterSet (0008,0005).
*
* Revision 1.26 2006/08/15 15:50:56 meichel
* Updated all code in module dcmdata to correctly compile when
* all standard C++ classes remain in namespace std.
*
* Revision 1.25 2006/07/27 13:52:42 joergr
* Changed parameter "exclusive" of method addOption() from type OFBool into an
* integer parameter "flags". Prepended prefix "PF_" to parseLine() flags.
* Option "--help" is no longer an exclusive option by default.
*
* Revision 1.24 2006/05/11 08:44:57 joergr
* Added new option that allows to omit the element name in the XML output.
* Moved checkForNonASCIICharacters() from application to library.
*
* Revision 1.23 2006/02/23 12:46:51 joergr
* Added new default option --encode-hex. Fixed layout and formatting issues.
*
* Revision 1.22 2005/12/08 15:40:42 meichel
* Changed include path schema for all DCMTK header files
*
* Revision 1.21 2005/12/07 16:42:49 onken
* Changed default and minimum value of --max-read-length to 4 KB
*
* Revision 1.20 2005/12/02 08:58:44 joergr
* Added new command line option that ignores the transfer syntax specified in
* the meta header and tries to detect the transfer syntax automatically from
* the dataset.
* Added new command line option that checks whether a given file starts with a
* valid DICOM meta header.
* Removed superfluous local variable. Changed type of variable "maxReadLength".
* Made description of option --max-read-length more consistent with the other
* command line tools.
*
* Revision 1.19 2005/12/01 11:25:44 joergr
* Removed superfluous local variable. Changed type of variable "maxReadLength".
*
* Revision 1.18 2005/11/28 15:28:54 meichel
* File dcdebug.h is not included by any other header file in the toolkit
* anymore, to minimize the risk of name clashes of macro debug().
*
* Revision 1.17 2005/11/17 11:26:11 onken
* Option --max-read-length now uses OFCommandLine to check, whether option
* value is in range
*
* Revision 1.16 2005/11/16 14:59:11 onken
* *** empty log message ***
*
* Revision 1.15 2005/11/16 14:55:56 onken
* Added "--max-read-length" option to dcmdump and dcm2xml to override
* DCMTK-internal threshold (4096K) for long attribute values.
*
* Revision 1.14 2005/06/24 10:06:46 joergr
* Check dependence between command line options --write-binary-data and
* --encode-base64.
*
* Revision 1.13 2004/11/29 17:02:17 joergr
* Added warning message when character set is unknown, unsupported or cannot
* be mapped to the output format. Added support for UTF-8 character set.
*
* Revision 1.12 2004/11/22 16:30:19 meichel
* Now checking whether extended characters are present in a DICOM dataset,
* preventing generation of incorrect XML if undeclared extended charset used.
*
* Revision 1.11 2003/04/22 08:23:33 joergr
* Added new command line option which allows to embed the content of the DTD
* instead of referencing the DTD file.
*
* Revision 1.10 2003/04/01 14:56:14 joergr
* Added support for XML namespaces.
*
* Revision 1.9 2002/11/26 08:42:58 meichel
* Replaced all includes for "zlib.h" with <zlib.h>
* to avoid inclusion of zlib.h in the makefile dependencies.
*
* Revision 1.8 2002/09/23 17:52:01 joergr
* Prepared code for future support of 'config.guess' host identifiers.
*
* Revision 1.7 2002/09/23 13:50:39 joergr
* Added new command line option "--version" which prints the name and version
* number of external libraries used.
*
* Revision 1.6 2002/08/21 10:14:13 meichel
* Adapted code to new loadFile and saveFile methods, thus removing direct
* use of the DICOM stream classes.
*
* Revision 1.5 2002/06/10 17:35:47 joergr
* Fixed inconsistency regarding spelling of the "file-format" element.
*
* Revision 1.4 2002/05/14 08:19:22 joergr
* Added support for Base64 (MIME) encoded binary data.
*
* Revision 1.3 2002/05/07 12:47:41 joergr
* Fixed bug in an error message.
*
* Revision 1.2 2002/04/25 14:56:35 joergr
* Removed unused function parameter to keep Sun CC 2.0.1 quiet.
*
* Revision 1.1 2002/04/25 10:08:35 joergr
* Added new command line tool to convert DICOM files to XML.
*
*
*/
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