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/*
*
* Copyright (C) 2000-2024, 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: dcmsr
*
* Author: Joerg Riesmeier
*
* Purpose:
* convert the contents of a DICOM structured reporting file to XML format
*
*/
#include "dcmtk/config/osconfig.h" /* make sure OS specific configuration is included first */
#include "dcmtk/dcmsr/dsrdoc.h" /* for main interface class DSRDocument */
#include "dcmtk/dcmdata/dctk.h" /* for typical set of "dcmdata" headers */
#include "dcmtk/ofstd/ofstream.h"
#include "dcmtk/ofstd/ofconapp.h"
#ifdef WITH_ZLIB
#include <zlib.h> /* for zlibVersion() */
#endif
#ifdef DCMTK_ENABLE_CHARSET_CONVERSION
#include "dcmtk/ofstd/ofchrenc.h" /* for OFCharacterEncoding */
#endif
#define OFFIS_CONSOLE_APPLICATION "dsr2xml"
static OFLogger dsr2xmlLogger = OFLog::getLogger("dcmtk.apps." OFFIS_CONSOLE_APPLICATION);
static char rcsid[] = "$dcmtk: " OFFIS_CONSOLE_APPLICATION " v"
OFFIS_DCMTK_VERSION " " OFFIS_DCMTK_RELEASEDATE " $";
// ********************************************
static OFCondition checkCharacterSet(const char *ifname,
DcmFileFormat &dfile,
const char *defaultCharset,
const OFBool checkAllStrings)
{
OFCondition result = EC_IllegalParameter;
if (ifname != NULL)
{
DcmDataset *dset = dfile.getDataset();
/* determine character set encoding of the dataset */
OFString csetString;
if (dset->findAndGetOFStringArray(DCM_SpecificCharacterSet, csetString).good())
{
/* check whether character set is supported */
if (DSRTypes::definedTermToCharacterSet(csetString) == DSRTypes::CS_invalid)
{
if (!csetString.empty())
{
OFLOG_WARN(dsr2xmlLogger, OFFIS_CONSOLE_APPLICATION << ": SpecificCharacterSet (0008,0005) "
<< "value '" << csetString << "' not supported ... quoting non-ASCII characters");
#ifdef DCMTK_ENABLE_CHARSET_CONVERSION
OFLOG_DEBUG(dsr2xmlLogger, "using option --convert-to-utf8 to convert the DICOM file to "
"UTF-8 encoding might also help to solve this problem more appropriately");
#endif
}
}
/* no error */
result = EC_Normal;
} 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_ERROR(dsr2xmlLogger, OFFIS_CONSOLE_APPLICATION << ": SpecificCharacterSet (0008,0005) "
<< "element absent (on the main data set level) but extended characters used in file: " << ifname);
OFLOG_DEBUG(dsr2xmlLogger, "use option --charset-assume to manually specify an appropriate character set");
result = makeOFCondition(OFM_dcmdata, EC_CODE_CannotSelectCharacterSet, OF_error, "Missing Specific Character Set");
} else {
result = EC_Normal;
csetString = defaultCharset;
/* first, map "old" character set names to DICOM defined terms */
if (csetString == "latin-1")
csetString = "ISO_IR 100";
else if (csetString == "latin-2")
csetString = "ISO_IR 101";
else if (csetString == "latin-3")
csetString = "ISO_IR 109";
else if (csetString == "latin-4")
csetString = "ISO_IR 110";
else if (csetString == "latin-5")
csetString = "ISO_IR 148";
else if (csetString == "cyrillic")
csetString = "ISO_IR 144";
else if (csetString == "arabic")
csetString = "ISO_IR 127";
else if (csetString == "greek")
csetString = "ISO_IR 126";
else if (csetString == "hebrew")
csetString = "ISO_IR 138";
else if (csetString == "latin-9")
csetString = "ISO_IR 203";
/* then, check whether the character set is actually supported */
if (DSRTypes::definedTermToCharacterSet(csetString) == DSRTypes::CS_invalid)
{
OFLOG_FATAL(dsr2xmlLogger, OFFIS_CONSOLE_APPLICATION << ": Character set '"
<< defaultCharset << "' specified with option --charset-assume not supported");
result = makeOFCondition(OFM_dcmdata, EC_CODE_CannotSelectCharacterSet, OF_error, "Cannot select character set");
} else {
OFLOG_INFO(dsr2xmlLogger, "inserting SpecificCharacterSet (0008,0005) element with value '" << csetString << "'");
/* insert the SpecificCharacterSet (0008,0005) element with new value */
result = dset->putAndInsertOFStringArray(DCM_SpecificCharacterSet, csetString);
}
}
} else {
if (defaultCharset != NULL)
{
/* use "debug" instead of "warn" in order to avoid too much output in default mode */
OFLOG_DEBUG(dsr2xmlLogger, "ignoring character set '" << defaultCharset
<< "' specified with option --charset-assume since it is not needed for this data set");
}
/* no error */
result = EC_Normal;
}
}
}
return result;
}
#ifdef DCMTK_ENABLE_CHARSET_CONVERSION
static OFCondition convertCharacterSet(const char *ifname,
DcmFileFormat &dfile,
const OFBool convertToUTF8)
{
OFCondition result = EC_IllegalParameter;
if (ifname != NULL)
{
/* convert all DICOM strings to UTF-8 (if requested) */
if (convertToUTF8)
{
OFLOG_INFO(dsr2xmlLogger, "converting all element values that are affected by SpecificCharacterSet (0008,0005) to UTF-8");
/* expect that SpecificCharacterSet contains the correct value (defined term) */
result = dfile.convertToUTF8();
if (result.bad())
OFLOG_FATAL(dsr2xmlLogger, OFFIS_CONSOLE_APPLICATION << ": error (" << result.text() << ") converting file to UTF-8: " << ifname);
} else {
/* no error */
result = EC_Normal;
}
}
return result;
}
#endif
static OFCondition writeFile(STD_NAMESPACE ostream &out,
const char *ifname,
DcmFileFormat &dfile,
const size_t readFlags,
const size_t writeFlags)
{
OFCondition result = EC_IllegalParameter;
if (ifname != NULL)
{
DSRDocument dsrdoc;
/* read SR data structures */
result = dsrdoc.read(*dfile.getDataset(), readFlags);
if (result.good())
{
/* write document in XML format and write it to the output stream */
result = dsrdoc.writeXML(out, writeFlags);
} else {
OFLOG_FATAL(dsr2xmlLogger, OFFIS_CONSOLE_APPLICATION << ": error (" << result.text() << ") parsing file: " << ifname);
/* make sure that the caller does not report this error, too */
result = EC_InternalError;
}
}
return result;
}
#define SHORTCOL 3
#define LONGCOL 22
int main(int argc, char *argv[])
{
size_t opt_readFlags = 0;
size_t opt_writeFlags = 0;
const char *opt_defaultCharset = NULL;
E_FileReadMode opt_readMode = ERM_autoDetect;
E_TransferSyntax opt_ixfer = EXS_Unknown;
OFBool opt_checkAllStrings = OFFalse;
#ifdef DCMTK_ENABLE_CHARSET_CONVERSION
OFBool opt_convertToUTF8 = OFFalse;
#endif
OFConsoleApplication app(OFFIS_CONSOLE_APPLICATION, "Convert DICOM SR file and data set to XML", rcsid);
OFCommandLine cmd;
cmd.setOptionColumns(LONGCOL, SHORTCOL);
cmd.setParamColumn(LONGCOL + SHORTCOL + 4);
cmd.addParam("dsrfile-in", "DICOM SR input filename to be converted\n(\"-\" for stdin)", 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.addGroup("processing options:");
cmd.addSubGroup("error handling:");
cmd.addOption("--unknown-relationship", "-Er", "accept unknown/missing relationship type");
cmd.addOption("--invalid-item-value", "-Ev", "accept invalid content item value\n(e.g. violation of VR or VM definition)");
cmd.addOption("--ignore-constraints", "-Ec", "ignore relationship content constraints");
cmd.addOption("--ignore-item-errors", "-Ee", "do not abort on content item errors, just warn\n(e.g. missing value type specific attributes)");
cmd.addOption("--skip-invalid-items", "-Ei", "skip invalid content items (incl. sub-tree)");
cmd.addOption("--disable-vr-checker", "-Dv", "disable check for VR-conformant string values");
cmd.addSubGroup("specific character set:");
cmd.addOption("--charset-require", "+Cr", "require declaration of ext. charset (default)");
cmd.addOption("--charset-assume", "+Ca", 1, "[c]harset: string",
"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, UC and UT)");
#ifdef DCMTK_ENABLE_CHARSET_CONVERSION
cmd.addOption("--convert-to-utf8", "+U8", "convert all element values that are affected\nby Specific Character Set (0008,0005) to UTF-8");
#endif
cmd.addGroup("output options:");
cmd.addSubGroup("encoding:");
cmd.addOption("--attr-all", "+Ea", "encode everything as XML attribute\n(shortcut for +Ec, +Er, +Ev and +Et)");
cmd.addOption("--attr-code", "+Ec", "encode code value, coding scheme designator\nand coding scheme version as XML attribute");
cmd.addOption("--attr-relationship", "+Er", "encode relationship type as XML attribute");
cmd.addOption("--attr-value-type", "+Ev", "encode value type as XML attribute");
cmd.addOption("--attr-template-id", "+Et", "encode template id as XML attribute");
cmd.addOption("--template-envelope", "+Ee", "template element encloses content items\n(requires +Wt, implies +Et)");
cmd.addSubGroup("XML structure:");
cmd.addOption("--add-schema-reference", "+Xs", "add reference to XML Schema \"" DCMSR_XML_XSD_FILE "\"\n(not with +Ea, +Ec, +Er, +Ev, +Et, +Ee, +We)");
cmd.addOption("--use-xml-namespace", "+Xn", "add XML namespace declaration to root element");
cmd.addSubGroup("writing:");
cmd.addOption("--write-empty-tags", "+We", "write all tags even if their value is empty");
cmd.addOption("--write-item-id", "+Wi", "always write item identifier");
cmd.addOption("--write-template-id", "+Wt", "write template identification information");
/* 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:";
#if !defined(WITH_ZLIB) && !defined(DCMTK_ENABLE_CHARSET_CONVERSION)
COUT << " none" << OFendl;
#else
COUT << OFendl;
#endif
#ifdef WITH_ZLIB
COUT << "- ZLIB, Version " << zlibVersion() << OFendl;
#endif
#ifdef DCMTK_ENABLE_CHARSET_CONVERSION
COUT << "- " << OFCharacterEncoding::getLibraryVersionString() << 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();
/* processing options */
if (cmd.findOption("--unknown-relationship"))
opt_readFlags |= DSRTypes::RF_acceptUnknownRelationshipType;
if (cmd.findOption("--invalid-item-value"))
opt_readFlags |= DSRTypes::RF_acceptInvalidContentItemValue;
if (cmd.findOption("--ignore-constraints"))
opt_readFlags |= DSRTypes::RF_ignoreRelationshipConstraints;
if (cmd.findOption("--ignore-item-errors"))
opt_readFlags |= DSRTypes::RF_ignoreContentItemErrors;
if (cmd.findOption("--skip-invalid-items"))
opt_readFlags |= DSRTypes::RF_skipInvalidContentItems;
if (cmd.findOption("--disable-vr-checker"))
dcmEnableVRCheckerForStringValues.set(OFFalse);
cmd.beginOptionBlock();
if (cmd.findOption("--charset-require"))
opt_defaultCharset = NULL;
if (cmd.findOption("--charset-assume"))
app.checkValue(cmd.getValue(opt_defaultCharset));
cmd.endOptionBlock();
if (cmd.findOption("--charset-check-all"))
opt_checkAllStrings = OFTrue;
#ifdef DCMTK_ENABLE_CHARSET_CONVERSION
if (cmd.findOption("--convert-to-utf8"))
opt_convertToUTF8 = OFTrue;
#endif
/* output options */
if (cmd.findOption("--attr-all"))
opt_writeFlags |= DSRTypes::XF_encodeEverythingAsAttribute;
if (cmd.findOption("--attr-code"))
opt_writeFlags |= DSRTypes::XF_codeComponentsAsAttribute;
if (cmd.findOption("--attr-relationship"))
opt_writeFlags |= DSRTypes::XF_relationshipTypeAsAttribute;
if (cmd.findOption("--attr-value-type"))
opt_writeFlags |= DSRTypes::XF_valueTypeAsAttribute;
if (cmd.findOption("--attr-template-id"))
opt_writeFlags |= DSRTypes::XF_templateIdentifierAsAttribute;
if (cmd.findOption("--template-envelope"))
opt_writeFlags |= DSRTypes::XF_templateElementEnclosesItems;
if (cmd.findOption("--add-schema-reference"))
opt_writeFlags |= DSRTypes::XF_addSchemaReference;
if (cmd.findOption("--use-xml-namespace"))
opt_writeFlags |= DSRTypes::XF_useDcmsrNamespace;
if (cmd.findOption("--write-empty-tags"))
opt_writeFlags |= DSRTypes::XF_writeEmptyTags;
if (cmd.findOption("--write-item-id"))
opt_writeFlags |= DSRTypes::XF_alwaysWriteItemIdentifier;
if (cmd.findOption("--write-template-id"))
opt_writeFlags |= DSRTypes::XF_writeTemplateIdentification;
/* check conflicts and dependencies */
if (opt_writeFlags & DSRTypes::XF_addSchemaReference)
{
app.checkConflict("--add-schema-reference", "--attr-all", (opt_writeFlags & DSRTypes::XF_encodeEverythingAsAttribute) == DSRTypes::XF_encodeEverythingAsAttribute);
app.checkConflict("--add-schema-reference", "--attr-code", (opt_writeFlags & DSRTypes::XF_codeComponentsAsAttribute) > 0);
app.checkConflict("--add-schema-reference", "--attr-relationship", (opt_writeFlags & DSRTypes::XF_relationshipTypeAsAttribute) > 0);
app.checkConflict("--add-schema-reference", "--attr-value-type", (opt_writeFlags & DSRTypes::XF_valueTypeAsAttribute) > 0);
app.checkConflict("--add-schema-reference", "--attr-template-id", (opt_writeFlags & DSRTypes::XF_templateIdentifierAsAttribute) > 0);
app.checkConflict("--add-schema-reference", "--template-envelope", (opt_writeFlags & DSRTypes::XF_templateElementEnclosesItems) > 0);
app.checkConflict("--add-schema-reference", "--write-empty-tags", (opt_writeFlags & DSRTypes::XF_writeEmptyTags) > 0);
}
if (opt_writeFlags & DSRTypes::XF_templateIdentifierAsAttribute)
app.checkDependence("--attr-template-id", "--write-template-id", (opt_writeFlags & DSRTypes::XF_writeTemplateIdentification) > 0);
if (opt_writeFlags & DSRTypes::XF_templateElementEnclosesItems)
app.checkDependence("--template-envelope", "--write-template-id", (opt_writeFlags & DSRTypes::XF_writeTemplateIdentification) > 0);
}
/* print resource identifier */
OFLOG_DEBUG(dsr2xmlLogger, rcsid << OFendl);
/* make sure data dictionary is loaded */
if (!dcmDataDict.isDictionaryLoaded())
{
OFLOG_WARN(dsr2xmlLogger, "no data dictionary loaded, check environment variable: "
<< DCM_DICT_ENVIRONMENT_VARIABLE);
}
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, DCM_MaxReadLength /* default */, opt_readMode);
if (status.good())
{
/* check specific character set (and possibly fix it) */
if (checkCharacterSet(ifname, dfile, opt_defaultCharset, opt_checkAllStrings).good())
{
#ifdef DCMTK_ENABLE_CHARSET_CONVERSION
/* convert character set of dataset, e.g. to UTF-8 */
if (convertCharacterSet(ifname, dfile, opt_convertToUTF8).bad())
result = 4;
#endif
} else
result = 7;
if (result == 0)
{
/* 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 */
status = writeFile(stream, ifname, dfile, opt_readFlags, opt_writeFlags);
if (status.bad() && (status != EC_InternalError))
{
OFLOG_FATAL(dsr2xmlLogger, OFFIS_CONSOLE_APPLICATION << ": error (" << status.text() << ") writing file: "<< ofname);
result = 2;
}
} else
result = 1;
} else {
/* write content in XML format to standard output */
status = writeFile(COUT, ifname, dfile, opt_readFlags, opt_writeFlags);
if (status.bad() && (status != EC_InternalError))
{
OFLOG_FATAL(dsr2xmlLogger, OFFIS_CONSOLE_APPLICATION << ": error (" << status.text() << ") writing to standard output");
result = 3;
}
}
}
} else {
OFLOG_FATAL(dsr2xmlLogger, OFFIS_CONSOLE_APPLICATION << ": error (" << status.text() << ") reading file: " << ifname);
result = 5;
}
} else {
OFLOG_FATAL(dsr2xmlLogger, OFFIS_CONSOLE_APPLICATION << ": invalid filename: <empty string>");
result = 6;
}
return result;
}
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