Mercurial > hg > orthanc
view OrthancFramework/Sources/DicomParsing/FromDcmtkBridge.cpp @ 5647:f048683aa619
added "?whole" option to "/instances/{id}/tags" to access tags stored after pixel data
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Tue, 04 Jun 2024 17:50:45 +0200 |
| parents | f7adfb22e20e |
| children | dedbf019a707 |
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/** * Orthanc - A Lightweight, RESTful DICOM Store * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics * Department, University Hospital of Liege, Belgium * Copyright (C) 2017-2023 Osimis S.A., Belgium * Copyright (C) 2024-2024 Orthanc Team SRL, Belgium * Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium * * This program is free software: you can redistribute it and/or * modify it under the terms of the GNU Lesser General Public License * as published by the Free Software Foundation, either version 3 of * the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public * License along with this program. If not, see * <http://www.gnu.org/licenses/>. **/ #include "../PrecompiledHeaders.h" #ifndef NOMINMAX #define NOMINMAX #endif #if !defined(ORTHANC_SANDBOXED) # error The macro ORTHANC_SANDBOXED must be defined #endif #if !defined(DCMTK_VERSION_NUMBER) # error The macro DCMTK_VERSION_NUMBER must be defined #endif #include "FromDcmtkBridge.h" #include "ToDcmtkBridge.h" #include "../Compatibility.h" #include "../Logging.h" #include "../Toolbox.h" #include "../OrthancException.h" #if ORTHANC_SANDBOXED == 0 # include "../TemporaryFile.h" #endif #include <list> #include <limits> #include <boost/lexical_cast.hpp> #include <boost/filesystem.hpp> #include <boost/algorithm/string/predicate.hpp> #include <boost/algorithm/string/join.hpp> #include <dcmtk/dcmdata/dcdeftag.h> #include <dcmtk/dcmdata/dcdicent.h> #include <dcmtk/dcmdata/dcdict.h> #include <dcmtk/dcmdata/dcfilefo.h> #include <dcmtk/dcmdata/dcistrmb.h> #include <dcmtk/dcmdata/dcostrmb.h> #include <dcmtk/dcmdata/dcpixel.h> #include <dcmtk/dcmdata/dcuid.h> #include <dcmtk/dcmdata/dcxfer.h> #include <dcmtk/dcmdata/dcvrae.h> #include <dcmtk/dcmdata/dcvras.h> #include <dcmtk/dcmdata/dcvrat.h> #include <dcmtk/dcmdata/dcvrcs.h> #include <dcmtk/dcmdata/dcvrda.h> #include <dcmtk/dcmdata/dcvrds.h> #include <dcmtk/dcmdata/dcvrdt.h> #include <dcmtk/dcmdata/dcvrfd.h> #include <dcmtk/dcmdata/dcvrfl.h> #include <dcmtk/dcmdata/dcvris.h> #include <dcmtk/dcmdata/dcvrlo.h> #include <dcmtk/dcmdata/dcvrlt.h> #include <dcmtk/dcmdata/dcvrpn.h> #include <dcmtk/dcmdata/dcvrsh.h> #include <dcmtk/dcmdata/dcvrsl.h> #include <dcmtk/dcmdata/dcvrss.h> #include <dcmtk/dcmdata/dcvrst.h> #include <dcmtk/dcmdata/dcvrtm.h> #include <dcmtk/dcmdata/dcvrui.h> #include <dcmtk/dcmdata/dcvrul.h> #include <dcmtk/dcmdata/dcvrus.h> #include <dcmtk/dcmdata/dcvrut.h> #if DCMTK_VERSION_NUMBER >= 361 # include <dcmtk/dcmdata/dcvruc.h> # include <dcmtk/dcmdata/dcvrur.h> #endif #if DCMTK_USE_EMBEDDED_DICTIONARIES == 1 # if !defined(ORTHANC_FRAMEWORK_INCLUDE_RESOURCES) || (ORTHANC_FRAMEWORK_INCLUDE_RESOURCES == 1) # include <OrthancFrameworkResources.h> # endif #endif #if ORTHANC_ENABLE_DCMTK_JPEG == 1 # include <dcmtk/dcmjpeg/djdecode.h> # if ORTHANC_ENABLE_DCMTK_TRANSCODING == 1 # include <dcmtk/dcmjpeg/djencode.h> # endif #endif #if ORTHANC_ENABLE_DCMTK_JPEG_LOSSLESS == 1 # include <dcmtk/dcmjpls/djdecode.h> # if ORTHANC_ENABLE_DCMTK_TRANSCODING == 1 # include <dcmtk/dcmjpls/djencode.h> # endif #endif #include <dcmtk/dcmdata/dcrledrg.h> #if ORTHANC_ENABLE_DCMTK_TRANSCODING == 1 # include <dcmtk/dcmdata/dcrleerg.h> # include <dcmtk/dcmimage/diregist.h> // include to support color images #endif static bool hasExternalDictionaries_ = false; namespace Orthanc { static bool IsBinaryTag(const DcmTag& key) { return (key.isUnknownVR() || key.getEVR() == EVR_OB || key.getEVR() == EVR_OW || key.getEVR() == EVR_UN || key.getEVR() == EVR_ox); } #if DCMTK_USE_EMBEDDED_DICTIONARIES == 1 static void LoadEmbeddedDictionary(DcmDataDictionary& dictionary, FrameworkResources::FileResourceId resource) { std::string content; FrameworkResources::GetFileResource(content, resource); #if ORTHANC_SANDBOXED == 0 TemporaryFile tmp; tmp.Write(content); if (!dictionary.loadDictionary(tmp.GetPath().c_str())) { throw OrthancException(ErrorCode_InternalError, "Cannot read embedded dictionary. Under Windows, make sure that " "your TEMP directory does not contain special characters."); } #else if (!dictionary.loadFromMemory(content)) { throw OrthancException(ErrorCode_InternalError, "Cannot read embedded dictionary. Under Windows, make sure that " "your TEMP directory does not contain special characters."); } #endif } #endif namespace { class DictionaryLocker : public boost::noncopyable { private: DcmDataDictionary& dictionary_; public: DictionaryLocker() : dictionary_(dcmDataDict.wrlock()) { } ~DictionaryLocker() { #if DCMTK_VERSION_NUMBER >= 364 dcmDataDict.wrunlock(); #else dcmDataDict.unlock(); #endif } DcmDataDictionary& operator*() { return dictionary_; } DcmDataDictionary* operator->() { return &dictionary_; } }; ORTHANC_FORCE_INLINE static std::string FloatToString(float v) { /** * From "boost::lexical_cast" documentation: "For more involved * conversions, such as where precision or formatting need tighter * control than is offered by the default behavior of * lexical_cast, the conventional stringstream approach is * recommended." * https://www.boost.org/doc/libs/1_65_0/doc/html/boost_lexical_cast.html * http://www.gotw.ca/publications/mill19.htm * * The precision of 17 corresponds to "defaultRealPrecision" in JsonCpp: * https://github.com/open-source-parsers/jsoncpp/blob/master/include/json/value.h **/ //return boost::lexical_cast<std::string>(v); // This was used in Orthanc <= 1.9.0 std::ostringstream ss; ss << std::setprecision(17) << v; return ss.str(); } ORTHANC_FORCE_INLINE static std::string DoubleToString(double v) { //return boost::lexical_cast<std::string>(v); // This was used in Orthanc <= 1.9.0 std::ostringstream ss; ss << std::setprecision(17) << v; return ss.str(); } #define DCMTK_TO_CTYPE_CONVERTER(converter, cType, dcmtkType, getter, toStringFunction) \ \ struct converter \ { \ typedef cType CType; \ \ ORTHANC_FORCE_INLINE \ static bool Apply(CType& result, \ DcmElement& element, \ size_t i) \ { \ return dynamic_cast<dcmtkType&>(element).getter(result, i).good(); \ } \ \ ORTHANC_FORCE_INLINE \ static std::string ToString(CType value) \ { \ return toStringFunction(value); \ } \ }; DCMTK_TO_CTYPE_CONVERTER(DcmtkToSint32Converter, Sint32, DcmSignedLong, getSint32, boost::lexical_cast<std::string>) DCMTK_TO_CTYPE_CONVERTER(DcmtkToSint16Converter, Sint16, DcmSignedShort, getSint16, boost::lexical_cast<std::string>) DCMTK_TO_CTYPE_CONVERTER(DcmtkToUint32Converter, Uint32, DcmUnsignedLong, getUint32, boost::lexical_cast<std::string>) DCMTK_TO_CTYPE_CONVERTER(DcmtkToUint16Converter, Uint16, DcmUnsignedShort, getUint16, boost::lexical_cast<std::string>) DCMTK_TO_CTYPE_CONVERTER(DcmtkToFloat32Converter, Float32, DcmFloatingPointSingle, getFloat32, FloatToString) DCMTK_TO_CTYPE_CONVERTER(DcmtkToFloat64Converter, Float64, DcmFloatingPointDouble, getFloat64, DoubleToString) template <typename F> static DicomValue* ApplyDcmtkToCTypeConverter(DcmElement& element) { F f; typename F::CType value; if (element.getLength() > sizeof(typename F::CType) && (element.getLength() % sizeof(typename F::CType)) == 0) { size_t count = element.getLength() / sizeof(typename F::CType); std::vector<std::string> strings; for (size_t i = 0; i < count; i++) { if (f.Apply(value, element, i)) { strings.push_back(F::ToString(value)); } } return new DicomValue(boost::algorithm::join(strings, "\\"), false); } else if (f.Apply(value, element, 0)) { return new DicomValue(F::ToString(value), false); } else { return new DicomValue; } } } void FromDcmtkBridge::InitializeDictionary(bool loadPrivateDictionary) { CLOG(INFO, DICOM) << "Using DCMTK version: " << DCMTK_VERSION_NUMBER; #if DCMTK_USE_EMBEDDED_DICTIONARIES == 1 { DictionaryLocker locker; locker->clear(); CLOG(INFO, DICOM) << "Loading the embedded dictionaries"; /** * Do not load DICONDE dictionary, it breaks the other tags. The * command "strace storescu 2>&1 |grep dic" shows that DICONDE * dictionary is not loaded by storescu. **/ //LoadEmbeddedDictionary(*locker, FrameworkResources::DICTIONARY_DICONDE); LoadEmbeddedDictionary(*locker, FrameworkResources::DICTIONARY_DICOM); if (loadPrivateDictionary) { CLOG(INFO, DICOM) << "Loading the embedded dictionary of private tags"; LoadEmbeddedDictionary(*locker, FrameworkResources::DICTIONARY_PRIVATE); } else { CLOG(INFO, DICOM) << "The dictionary of private tags has not been loaded"; } } #else { std::vector<std::string> dictionaries; const char* env = std::getenv(DCM_DICT_ENVIRONMENT_VARIABLE); if (env != NULL) { // This mimics the behavior of DCMTK: // https://support.dcmtk.org/docs/file_envvars.html #if defined(_WIN32) Toolbox::TokenizeString(dictionaries, std::string(env), ';'); #else Toolbox::TokenizeString(dictionaries, std::string(env), ':'); #endif } else { boost::filesystem::path base = DCMTK_DICTIONARY_DIR; dictionaries.push_back((base / "dicom.dic").string()); if (loadPrivateDictionary) { dictionaries.push_back((base / "private.dic").string()); } } LoadExternalDictionaries(dictionaries); hasExternalDictionaries_ = false; // Fix the side-effect of "LoadExternalDictionaries()" } #endif /* make sure data dictionary is loaded */ if (!dcmDataDict.isDictionaryLoaded()) { throw OrthancException(ErrorCode_InternalError, "No DICOM dictionary loaded, check environment variable: " + std::string(DCM_DICT_ENVIRONMENT_VARIABLE)); } { // Test the dictionary with a simple DICOM tag DcmTag key(0x0010, 0x1030); // This is PatientWeight if (key.getEVR() != EVR_DS) { throw OrthancException(ErrorCode_InternalError, "The DICOM dictionary has not been correctly read"); } } } void FromDcmtkBridge::LoadExternalDictionaries(const std::vector<std::string>& dictionaries) { DictionaryLocker locker; CLOG(INFO, DICOM) << "Clearing the DICOM dictionary"; locker->clear(); for (size_t i = 0; i < dictionaries.size(); i++) { LOG(WARNING) << "Loading external DICOM dictionary: \"" << dictionaries[i] << "\""; if (!locker->loadDictionary(dictionaries[i].c_str())) { throw OrthancException(ErrorCode_InexistentFile); } } hasExternalDictionaries_ = true; } void FromDcmtkBridge::RegisterDictionaryTag(const DicomTag& tag, ValueRepresentation vr, const std::string& name, unsigned int minMultiplicity, unsigned int maxMultiplicity, const std::string& privateCreator) { if (minMultiplicity < 1) { throw OrthancException(ErrorCode_ParameterOutOfRange); } bool arbitrary = false; if (maxMultiplicity == 0) { maxMultiplicity = DcmVariableVM; arbitrary = true; } else if (maxMultiplicity < minMultiplicity) { throw OrthancException(ErrorCode_ParameterOutOfRange); } DcmEVR evr = ToDcmtkBridge::Convert(vr); CLOG(INFO, DICOM) << "Registering tag in dictionary: (" << tag.Format() << ") " << (DcmVR(evr).getValidVRName()) << " " << name << " (multiplicity: " << minMultiplicity << "-" << (arbitrary ? "n" : boost::lexical_cast<std::string>(maxMultiplicity)) << ")"; std::unique_ptr<DcmDictEntry> entry; if (privateCreator.empty()) { if (tag.GetGroup() % 2 == 1) { char buf[128]; sprintf(buf, "Warning: You are registering a private tag (%04x,%04x), " "but no private creator was associated with it", tag.GetGroup(), tag.GetElement()); LOG(WARNING) << buf; } entry.reset(new DcmDictEntry(tag.GetGroup(), tag.GetElement(), evr, name.c_str(), static_cast<int>(minMultiplicity), static_cast<int>(maxMultiplicity), NULL /* version */, OFTrue /* doCopyString */, NULL /* private creator */)); } else { // "Private Data Elements have an odd Group Number that is not // (0001,eeee), (0003,eeee), (0005,eeee), (0007,eeee), or // (FFFF,eeee)." if (tag.GetGroup() % 2 == 0 /* even */ || tag.GetGroup() == 0x0001 || tag.GetGroup() == 0x0003 || tag.GetGroup() == 0x0005 || tag.GetGroup() == 0x0007 || tag.GetGroup() == 0xffff) { char buf[128]; sprintf(buf, "Trying to register private tag (%04x,%04x), but it must have an odd group >= 0x0009", tag.GetGroup(), tag.GetElement()); throw OrthancException(ErrorCode_ParameterOutOfRange, std::string(buf)); } entry.reset(new DcmDictEntry(tag.GetGroup(), tag.GetElement(), evr, name.c_str(), static_cast<int>(minMultiplicity), static_cast<int>(maxMultiplicity), "private" /* version */, OFTrue /* doCopyString */, privateCreator.c_str())); } entry->setGroupRangeRestriction(DcmDictRange_Unspecified); entry->setElementRangeRestriction(DcmDictRange_Unspecified); { DictionaryLocker locker; if (locker->findEntry(DcmTagKey(tag.GetGroup(), tag.GetElement()), privateCreator.empty() ? NULL : privateCreator.c_str())) { throw OrthancException(ErrorCode_AlreadyExistingTag, "Cannot register twice the tag (" + tag.Format() + "), whose symbolic name is \"" + name + "\""); } else { locker->addEntry(entry.release()); } } } Encoding FromDcmtkBridge::DetectEncoding(bool& hasCodeExtensions, DcmItem& dataset, Encoding defaultEncoding) { // http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.12.html#sect_C.12.1.1.2 OFString tmp; if (dataset.findAndGetOFStringArray(DCM_SpecificCharacterSet, tmp).good()) { std::vector<std::string> tokens; Toolbox::TokenizeString(tokens, std::string(tmp.c_str()), '\\'); hasCodeExtensions = (tokens.size() > 1); for (size_t i = 0; i < tokens.size(); i++) { std::string characterSet = Toolbox::StripSpaces(tokens[i]); if (!characterSet.empty()) { Encoding encoding; if (GetDicomEncoding(encoding, characterSet.c_str())) { // The specific character set is supported by the Orthanc core return encoding; } else { LOG(WARNING) << "Value of Specific Character Set (0008,0005) is not supported: " << characterSet << ", fallback to ASCII (remove all special characters)"; return Encoding_Ascii; } } } } else { hasCodeExtensions = false; } // No specific character set tag: Use the default encoding return defaultEncoding; } Encoding FromDcmtkBridge::DetectEncoding(DcmItem &dataset, Encoding defaultEncoding) { bool hasCodeExtensions; // ignored return DetectEncoding(hasCodeExtensions, dataset, defaultEncoding); } void FromDcmtkBridge::ExtractDicomSummary(DicomMap& target, DcmItem& dataset, unsigned int maxStringLength, const std::set<DicomTag>& ignoreTagLength) { const Encoding defaultEncoding = GetDefaultDicomEncoding(); bool hasCodeExtensions; Encoding encoding = DetectEncoding(hasCodeExtensions, dataset, defaultEncoding); target.Clear(); for (unsigned long i = 0; i < dataset.card(); i++) { DcmElement* element = dataset.getElement(i); if (element && element->isLeaf()) { target.SetValueInternal(element->getTag().getGTag(), element->getTag().getETag(), ConvertLeafElement(*element, DicomToJsonFlags_Default, maxStringLength, encoding, hasCodeExtensions, ignoreTagLength)); } else { DcmSequenceOfItems* sequence = dynamic_cast<DcmSequenceOfItems*>(element); if (sequence) { Json::Value jsonSequence = Json::arrayValue; for (unsigned long s = 0; s < sequence->card(); s++) { DcmItem* child = sequence->getItem(s); Json::Value& v = jsonSequence.append(Json::objectValue); DatasetToJson(v, *child, DicomToJsonFormat_Full, DicomToJsonFlags_Default, maxStringLength, encoding, hasCodeExtensions, ignoreTagLength, 1); } target.SetSequenceValue(DicomTag(element->getTag().getGTag(), element->getTag().getETag()), jsonSequence); } } } } DicomTag FromDcmtkBridge::Convert(const DcmTag& tag) { return DicomTag(tag.getGTag(), tag.getETag()); } DicomTag FromDcmtkBridge::GetTag(const DcmElement& element) { return DicomTag(element.getGTag(), element.getETag()); } static DicomValue* CreateValueFromUtf8String(const DicomTag& tag, const std::string& utf8, unsigned int maxStringLength, const std::set<DicomTag>& ignoreTagLength) { if (maxStringLength != 0 && utf8.size() > maxStringLength && ignoreTagLength.find(tag) == ignoreTagLength.end()) { return new DicomValue; // Too long, create a NULL value } else { return new DicomValue(utf8, false); } } DicomValue* FromDcmtkBridge::ConvertLeafElement(DcmElement& element, DicomToJsonFlags flags, unsigned int maxStringLength, Encoding encoding, bool hasCodeExtensions, const std::set<DicomTag>& ignoreTagLength) { if (!element.isLeaf()) { // This function is only applicable to leaf elements throw OrthancException(ErrorCode_BadParameterType); } { char *c = NULL; if (element.isaString() && element.getString(c).good()) { if (c == NULL) // This case corresponds to the empty string { return new DicomValue("", false); } else { const std::string s(c); const std::string utf8 = Toolbox::ConvertToUtf8(s, encoding, hasCodeExtensions); return CreateValueFromUtf8String(GetTag(element), utf8, maxStringLength, ignoreTagLength); } } } if (element.getVR() == EVR_UN) { /** * Unknown value representation: Lookup in the dictionary. This * is notably the case for private tags registered with the * "Dictionary" configuration option, or for public tags with * "EVR_UN" in the case of Little Endian Implicit transfer * syntax (cf. DICOM CP 246). * ftp://medical.nema.org/medical/dicom/final/cp246_ft.pdf **/ DictionaryLocker locker; const DcmDictEntry* entry = locker->findEntry(element.getTag().getXTag(), element.getTag().getPrivateCreator()); if (entry != NULL && entry->getVR().isaString()) { Uint8* data = NULL; if (element.getUint8Array(data) == EC_Normal) { Uint32 length = element.getLength(); if (data == NULL || length == 0) { return new DicomValue("", false); // Empty string } // Remove the trailing padding, if any if (length > 0 && length % 2 == 0 && data[length - 1] == '\0') { length = length - 1; } if (element.getTag().isPrivate()) { // For private tags, we do not try and convert to UTF-8, // as nothing ensures that the encoding of the private tag // is the same as that of the remaining of the DICOM // dataset. Only go for ASCII strings. if (Toolbox::IsAsciiString(data, length)) { const std::string s(reinterpret_cast<const char*>(data), length); return CreateValueFromUtf8String(GetTag(element), s, maxStringLength, ignoreTagLength); } else { // Not a plain ASCII string: Consider it as a binary // value that is handled in the switch-case below } } else { // For public tags, convert to UTF-8 by using the // "SpecificCharacterSet" tag, if present. This branch is // new in Orthanc 1.9.1 (cf. DICOM CP 246). const std::string s(reinterpret_cast<const char*>(data), length); const std::string utf8 = Toolbox::ConvertToUtf8(s, encoding, hasCodeExtensions); return CreateValueFromUtf8String(GetTag(element), utf8, maxStringLength, ignoreTagLength); } } } } try { // http://support.dcmtk.org/docs/dcvr_8h-source.html switch (element.getVR()) { /** * Deal with binary data (including PixelData). **/ case EVR_OB: // other byte case EVR_OF: // other float case EVR_OW: // other word case EVR_UN: // unknown value representation case EVR_ox: // OB or OW depending on context case EVR_DS: // decimal string case EVR_IS: // integer string case EVR_AS: // age string case EVR_DA: // date string case EVR_DT: // date time string case EVR_TM: // time string case EVR_AE: // application entity title case EVR_CS: // code string case EVR_SH: // short string case EVR_LO: // long string case EVR_ST: // short text case EVR_LT: // long text case EVR_UT: // unlimited text case EVR_PN: // person name case EVR_UI: // unique identifier case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR { if (!(flags & DicomToJsonFlags_ConvertBinaryToNull)) { Uint8* data = NULL; Uint16* data16 = NULL; if (element.getUint8Array(data) == EC_Normal) { return new DicomValue(reinterpret_cast<const char*>(data), element.getLength(), true); } else if (element.getUint16Array(data16) == EC_Normal) { return new DicomValue(reinterpret_cast<const char*>(data16), element.getLength(), true); } } return new DicomValue; } /** * Numeric types **/ case EVR_SL: // signed long { return ApplyDcmtkToCTypeConverter<DcmtkToSint32Converter>(element); } case EVR_SS: // signed short { return ApplyDcmtkToCTypeConverter<DcmtkToSint16Converter>(element); } case EVR_UL: // unsigned long { return ApplyDcmtkToCTypeConverter<DcmtkToUint32Converter>(element); } case EVR_US: // unsigned short { return ApplyDcmtkToCTypeConverter<DcmtkToUint16Converter>(element); } case EVR_FL: // float single-precision { return ApplyDcmtkToCTypeConverter<DcmtkToFloat32Converter>(element); } case EVR_FD: // float double-precision { return ApplyDcmtkToCTypeConverter<DcmtkToFloat64Converter>(element); } /** * Attribute tag. **/ case EVR_AT: { DcmTagKey tag; if (dynamic_cast<DcmAttributeTag&>(element).getTagVal(tag, 0).good()) { DicomTag t(tag.getGroup(), tag.getElement()); return new DicomValue(t.Format(), false); } else { return new DicomValue; } } /** * Sequence types, should never occur at this point because of * "element.isLeaf()". **/ case EVR_SQ: // sequence of items return new DicomValue; /** * Internal to DCMTK. **/ case EVR_xs: // SS or US depending on context case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) case EVR_na: // na="not applicable", for data which has no VR case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor case EVR_item: // used internally for items case EVR_metainfo: // used internally for meta info datasets case EVR_dataset: // used internally for datasets case EVR_fileFormat: // used internally for DICOM files case EVR_dicomDir: // used internally for DICOMDIR objects case EVR_dirRecord: // used internally for DICOMDIR records case EVR_pixelSQ: // used internally for pixel sequences in a compressed image case EVR_pixelItem: // used internally for pixel items in a compressed image case EVR_PixelData: // used internally for uncompressed pixeld data case EVR_OverlayData: // used internally for overlay data return new DicomValue; /** * Default case. **/ default: return new DicomValue; } } catch (boost::bad_lexical_cast&) { return new DicomValue; } catch (std::bad_cast&) { return new DicomValue; } } static Json::Value& PrepareNode(Json::Value& parent, DcmElement& element, DicomToJsonFormat format) { assert(parent.type() == Json::objectValue); DicomTag tag(FromDcmtkBridge::GetTag(element)); const std::string formattedTag = tag.Format(); if (format == DicomToJsonFormat_Short) { parent[formattedTag] = Json::nullValue; return parent[formattedTag]; } // This code gives access to the name of the private tags std::string tagName = FromDcmtkBridge::GetTagName(element); switch (format) { case DicomToJsonFormat_Human: parent[tagName] = Json::nullValue; return parent[tagName]; case DicomToJsonFormat_Full: { parent[formattedTag] = Json::objectValue; Json::Value& node = parent[formattedTag]; if (element.isLeaf()) { node["Name"] = tagName; if (element.getTag().getPrivateCreator() != NULL) { node["PrivateCreator"] = element.getTag().getPrivateCreator(); } return node; } else { node["Name"] = tagName; node["Type"] = "Sequence"; node["Value"] = Json::nullValue; return node["Value"]; } } default: throw OrthancException(ErrorCode_ParameterOutOfRange); } } static void LeafValueToJson(Json::Value& target, const DicomValue& value, DicomToJsonFormat format, DicomToJsonFlags flags, unsigned int maxStringLength) { Json::Value* targetValue = NULL; Json::Value* targetType = NULL; switch (format) { case DicomToJsonFormat_Short: case DicomToJsonFormat_Human: { assert(target.type() == Json::nullValue); targetValue = ⌖ break; } case DicomToJsonFormat_Full: { assert(target.type() == Json::objectValue); target["Value"] = Json::nullValue; target["Type"] = Json::nullValue; targetType = &target["Type"]; targetValue = &target["Value"]; break; } default: throw OrthancException(ErrorCode_ParameterOutOfRange); } assert(targetValue != NULL); assert(targetValue->type() == Json::nullValue); assert(targetType == NULL || targetType->type() == Json::nullValue); if (value.IsNull()) { if (targetType != NULL) { *targetType = "Null"; } } else if (value.IsBinary()) { if (flags & DicomToJsonFlags_ConvertBinaryToAscii) { *targetValue = Toolbox::ConvertToAscii(value.GetContent()); } else { std::string s; value.FormatDataUriScheme(s); *targetValue = s; } if (targetType != NULL) { *targetType = "Binary"; } } else if (maxStringLength == 0 || value.GetContent().size() <= maxStringLength) { *targetValue = value.GetContent(); if (targetType != NULL) { *targetType = "String"; } } else { if (targetType != NULL) { *targetType = "TooLong"; } } } void FromDcmtkBridge::ElementToJson(Json::Value& parent, DcmElement& element, DicomToJsonFormat format, DicomToJsonFlags flags, unsigned int maxStringLength, Encoding encoding, bool hasCodeExtensions, const std::set<DicomTag>& ignoreTagLength, unsigned int depth) { if (parent.type() == Json::nullValue) { parent = Json::objectValue; } assert(parent.type() == Json::objectValue); Json::Value& target = PrepareNode(parent, element, format); if (element.isLeaf()) { // The "0" below lets "LeafValueToJson()" take care of "TooLong" values std::unique_ptr<DicomValue> v(FromDcmtkBridge::ConvertLeafElement (element, flags, 0, encoding, hasCodeExtensions, ignoreTagLength)); if (ignoreTagLength.find(GetTag(element)) == ignoreTagLength.end()) { LeafValueToJson(target, *v, format, flags, maxStringLength); } else { LeafValueToJson(target, *v, format, flags, 0); } } else { assert(target.type() == Json::nullValue); target = Json::arrayValue; // "All subclasses of DcmElement except for DcmSequenceOfItems // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset // etc. are not." The following dynamic_cast is thus OK. DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element); for (unsigned long i = 0; i < sequence.card(); i++) { DcmItem* child = sequence.getItem(i); Json::Value& v = target.append(Json::objectValue); DatasetToJson(v, *child, format, flags, maxStringLength, encoding, hasCodeExtensions, ignoreTagLength, depth + 1); } } } void FromDcmtkBridge::DatasetToJson(Json::Value& parent, DcmItem& item, DicomToJsonFormat format, DicomToJsonFlags flags, unsigned int maxStringLength, Encoding encoding, bool hasCodeExtensions, const std::set<DicomTag>& ignoreTagLength, unsigned int depth) { assert(parent.type() == Json::objectValue); for (unsigned long i = 0; i < item.card(); i++) { DcmElement* element = item.getElement(i); if (element == NULL) { throw OrthancException(ErrorCode_InternalError); } DicomTag tag(FromDcmtkBridge::Convert(element->getTag())); // New flag in Orthanc 1.9.1 if (depth == 0 && (flags & DicomToJsonFlags_StopAfterPixelData) && tag > DICOM_TAG_PIXEL_DATA) { continue; } // New flag in Orthanc 1.9.1 if ((flags & DicomToJsonFlags_SkipGroupLengths) && tag.GetElement() == 0x0000) { continue; } /*element->getTag().isPrivate()*/ if (tag.IsPrivate() && !(flags & DicomToJsonFlags_IncludePrivateTags)) { continue; } if (!(flags & DicomToJsonFlags_IncludeUnknownTags)) { DictionaryLocker locker; if (locker->findEntry(element->getTag(), element->getTag().getPrivateCreator()) == NULL) { continue; } } if (IsBinaryTag(element->getTag())) { // This is a binary tag if ((tag == DICOM_TAG_PIXEL_DATA && !(flags & DicomToJsonFlags_IncludePixelData)) || (tag != DICOM_TAG_PIXEL_DATA && !(flags & DicomToJsonFlags_IncludeBinary))) { continue; } } FromDcmtkBridge::ElementToJson(parent, *element, format, flags, maxStringLength, encoding, hasCodeExtensions, ignoreTagLength, depth); } } void FromDcmtkBridge::ExtractDicomAsJson(Json::Value& target, DcmDataset& dataset, DicomToJsonFormat format, DicomToJsonFlags flags, unsigned int maxStringLength, const std::set<DicomTag>& ignoreTagLength) { const Encoding defaultEncoding = GetDefaultDicomEncoding(); bool hasCodeExtensions; Encoding encoding = DetectEncoding(hasCodeExtensions, dataset, defaultEncoding); target = Json::objectValue; DatasetToJson(target, dataset, format, flags, maxStringLength, encoding, hasCodeExtensions, ignoreTagLength, 0); } void FromDcmtkBridge::ExtractHeaderAsJson(Json::Value& target, DcmMetaInfo& dataset, DicomToJsonFormat format, DicomToJsonFlags flags, unsigned int maxStringLength) { std::set<DicomTag> ignoreTagLength; target = Json::objectValue; DatasetToJson(target, dataset, format, flags, maxStringLength, Encoding_Ascii, false, ignoreTagLength, 0); } static std::string GetTagNameInternal(DcmTag& tag) { if (!hasExternalDictionaries_) { /** * Some patches for important tags because of different DICOM * dictionaries between DCMTK versions. Since Orthanc 1.9.4, we * don't apply these patches if external dictionaries are * loaded, notably for compatibility with DICONDE. In Orthanc <= * 1.9.3, this was done by method "DicomTag::GetMainTagsName()". **/ DicomTag tmp(tag.getGroup(), tag.getElement()); if (tmp == DICOM_TAG_ACCESSION_NUMBER) return "AccessionNumber"; if (tmp == DICOM_TAG_SOP_INSTANCE_UID) return "SOPInstanceUID"; if (tmp == DICOM_TAG_PATIENT_ID) return "PatientID"; if (tmp == DICOM_TAG_SERIES_INSTANCE_UID) return "SeriesInstanceUID"; if (tmp == DICOM_TAG_STUDY_INSTANCE_UID) return "StudyInstanceUID"; if (tmp == DICOM_TAG_PIXEL_DATA) return "PixelData"; if (tmp == DICOM_TAG_IMAGE_INDEX) return "ImageIndex"; if (tmp == DICOM_TAG_INSTANCE_NUMBER) return "InstanceNumber"; if (tmp == DICOM_TAG_NUMBER_OF_SLICES) return "NumberOfSlices"; if (tmp == DICOM_TAG_NUMBER_OF_FRAMES) return "NumberOfFrames"; if (tmp == DICOM_TAG_CARDIAC_NUMBER_OF_IMAGES) return "CardiacNumberOfImages"; if (tmp == DICOM_TAG_IMAGES_IN_ACQUISITION) return "ImagesInAcquisition"; if (tmp == DICOM_TAG_PATIENT_NAME) return "PatientName"; if (tmp == DICOM_TAG_IMAGE_POSITION_PATIENT) return "ImagePositionPatient"; if (tmp == DICOM_TAG_IMAGE_ORIENTATION_PATIENT) return "ImageOrientationPatient"; // New in Orthanc 1.6.0, as tagged as "RETIRED_" since DCMTK 3.6.4 if (tmp == DICOM_TAG_OTHER_PATIENT_IDS) return "OtherPatientIDs"; // End of patches } #if 0 // This version explicitly calls the dictionary const DcmDataDictionary& dict = dcmDataDict.rdlock(); const DcmDictEntry* entry = dict.findEntry(tag, NULL); std::string s(DcmTag_ERROR_TagName); if (entry != NULL) { s = std::string(entry->getTagName()); } dcmDataDict.unlock(); return s; #else const char* name = tag.getTagName(); if (name == NULL) { return DcmTag_ERROR_TagName; } else { return std::string(name); } #endif } static bool GetTagFromNameInternal(DicomTag& tag, const std::string& tagName) { // conversion from old tag names (ex: RETIRED_OtherPatientIDs is the new name for OtherPatientIDs that is still a valid name for DICOM_TAG_OTHER_PATIENT_IDS) if (tagName == "OtherPatientIDs") { tag = DICOM_TAG_OTHER_PATIENT_IDS; return true; } return false; } std::string FromDcmtkBridge::GetTagName(const DicomTag& t, const std::string& privateCreator) { DcmTag tag(t.GetGroup(), t.GetElement()); if (!privateCreator.empty()) { tag.setPrivateCreator(privateCreator.c_str()); } return GetTagNameInternal(tag); } std::string FromDcmtkBridge::GetTagName(const DcmElement& element) { // Copy the tag to ensure const-correctness of DcmElement. Note // that the private creator information is also copied. DcmTag tag(element.getTag()); return GetTagNameInternal(tag); } std::string FromDcmtkBridge::GetTagName(const DicomElement &element) { return GetTagName(element.GetTag(), ""); } DicomTag FromDcmtkBridge::ParseTag(const char* name) { DicomTag parsed(0, 0); if (DicomTag::ParseHexadecimal(parsed, name)) { return parsed; } #if 0 const DcmDataDictionary& dict = dcmDataDict.rdlock(); const DcmDictEntry* entry = dict.findEntry(name); if (entry == NULL) { dcmDataDict.unlock(); throw OrthancException(ErrorCode_UnknownDicomTag); } else { DcmTagKey key = entry->getKey(); DicomTag tag(key.getGroup(), key.getElement()); dcmDataDict.unlock(); return tag; } #else DcmTag tag; if (DcmTag::findTagFromName(name, tag).good()) { return DicomTag(tag.getGTag(), tag.getETag()); } else { DicomTag dcmTag(0, 0); if (GetTagFromNameInternal(dcmTag, name)) { return dcmTag; } CLOG(INFO, DICOM) << "Unknown DICOM tag: \"" << name << "\""; throw OrthancException(ErrorCode_UnknownDicomTag, name, false); } #endif } DicomTag FromDcmtkBridge::ParseTag(const std::string &name) { return ParseTag(name.c_str()); } bool FromDcmtkBridge::HasTag(const DicomMap &fields, const std::string &tagName) { return fields.HasTag(ParseTag(tagName)); } void FromDcmtkBridge::FormatListOfTags(std::string& output, const std::set<DicomTag>& tags) { std::set<std::string> values; for (std::set<DicomTag>::const_iterator it = tags.begin(); it != tags.end(); ++it) { values.insert(it->Format()); } Toolbox::JoinStrings(output, values, ";"); } void FromDcmtkBridge::FormatListOfTags(Json::Value& output, const std::set<DicomTag>& tags) { output = Json::arrayValue; for (std::set<DicomTag>::const_iterator it = tags.begin(); it != tags.end(); ++it) { output.append(it->Format()); } } // parses a list like "0010,0010;PatientBirthDate;0020,0020" void FromDcmtkBridge::ParseListOfTags(std::set<DicomTag>& result, const std::string& source) { result.clear(); std::vector<std::string> tokens; Toolbox::TokenizeString(tokens, source, ';'); for (std::vector<std::string>::const_iterator it = tokens.begin(); it != tokens.end(); ++it) { if (it->size() > 0) { DicomTag tag = FromDcmtkBridge::ParseTag(*it); result.insert(tag); } } } void FromDcmtkBridge::ParseListOfTags(std::set<DicomTag>& result, const Json::Value& source) { result.clear(); if (!source.isArray()) { throw OrthancException(ErrorCode_BadRequest, "List of tags is not an array"); } for (Json::ArrayIndex i = 0; i < source.size(); i++) { const std::string& value = source[i].asString(); DicomTag tag = FromDcmtkBridge::ParseTag(value); result.insert(tag); } } const DicomValue &FromDcmtkBridge::GetValue(const DicomMap &fields, const std::string &tagName) { return fields.GetValue(ParseTag(tagName)); } void FromDcmtkBridge::SetValue(DicomMap &target, const std::string &tagName, DicomValue *value) { const DicomTag tag = ParseTag(tagName); target.SetValueInternal(tag.GetGroup(), tag.GetElement(), value); } bool FromDcmtkBridge::IsUnknownTag(const DicomTag& tag) { DcmTag tmp(tag.GetGroup(), tag.GetElement()); return tmp.isUnknownVR(); } void FromDcmtkBridge::ToJson(Json::Value& result, const DicomMap& values, DicomToJsonFormat format) { if (result.type() != Json::objectValue) { throw OrthancException(ErrorCode_BadParameterType); } result.clear(); for (DicomMap::Content::const_iterator it = values.content_.begin(); it != values.content_.end(); ++it) { switch (format) { case DicomToJsonFormat_Human: { // TODO Inject PrivateCreator if some is available in the DicomMap? const std::string tagName = GetTagName(it->first, ""); if (it->second->IsNull()) { result[tagName] = Json::nullValue; } else if (it->second->IsSequence()) { result[tagName] = Json::arrayValue; const Json::Value& jsonSequence = it->second->GetSequenceContent(); for (Json::Value::ArrayIndex i = 0; i < jsonSequence.size(); ++i) { Json::Value target = Json::objectValue; Toolbox::SimplifyDicomAsJson(target, jsonSequence[i], DicomToJsonFormat_Human); result[tagName].append(target); } } else { // TODO IsBinary result[tagName] = it->second->GetContent(); } break; } case DicomToJsonFormat_Full: { // TODO Inject PrivateCreator if some is available in the DicomMap? const std::string tagName = GetTagName(it->first, ""); Json::Value value = Json::objectValue; value["Name"] = tagName; if (it->second->IsNull()) { value["Type"] = "Null"; value["Value"] = Json::nullValue; } else if (it->second->IsSequence()) { value["Type"] = "Sequence"; value["Value"] = it->second->GetSequenceContent(); } else { // TODO IsBinary value["Type"] = "String"; value["Value"] = it->second->GetContent(); } result[it->first.Format()] = value; break; } case DicomToJsonFormat_Short: { const std::string hex = it->first.Format(); if (it->second->IsNull()) { result[hex] = Json::nullValue; } else if (it->second->IsSequence()) { result[hex] = Json::arrayValue; const Json::Value& jsonSequence = it->second->GetSequenceContent(); for (Json::Value::ArrayIndex i = 0; i < jsonSequence.size(); ++i) { Json::Value target = Json::objectValue; Toolbox::SimplifyDicomAsJson(target, jsonSequence[i], DicomToJsonFormat_Short); result[hex].append(target); } } else { // TODO IsBinary result[hex] = it->second->GetContent(); } break; } default: throw OrthancException(ErrorCode_ParameterOutOfRange); } } } std::string FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType level) { char uid[100]; switch (level) { case ResourceType_Patient: // The "PatientID" field is of type LO (Long String), 64 // Bytes Maximum. An UUID is of length 36, thus it can be used // as a random PatientID. return Toolbox::GenerateUuid(); case ResourceType_Instance: return dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT); case ResourceType_Series: return dcmGenerateUniqueIdentifier(uid, SITE_SERIES_UID_ROOT); case ResourceType_Study: return dcmGenerateUniqueIdentifier(uid, SITE_STUDY_UID_ROOT); default: throw OrthancException(ErrorCode_ParameterOutOfRange); } } static bool SaveToMemoryBufferInternal(std::string& buffer, DcmFileFormat& dicom, E_TransferSyntax xfer, std::string& errorMessage) { E_EncodingType encodingType = /*opt_sequenceType*/ EET_ExplicitLength; // Create a memory buffer with the proper size { const uint32_t estimatedSize = dicom.calcElementLength(xfer, encodingType); // (*) buffer.resize(estimatedSize); } DcmOutputBufferStream ob(&buffer[0], buffer.size()); // Fill the memory buffer with the meta-header and the dataset dicom.transferInit(); OFCondition c = dicom.write(ob, xfer, encodingType, NULL, /*opt_groupLength*/ EGL_recalcGL, /*opt_paddingType*/ EPD_noChange, /*padlen*/ 0, /*subPadlen*/ 0, /*instanceLength*/ 0, EWM_updateMeta /* creates new SOP instance UID on lossy */); dicom.transferEnd(); if (c.good()) { // The DICOM file is successfully written, truncate the target // buffer if its size was overestimated by (*) ob.flush(); size_t effectiveSize = static_cast<size_t>(ob.tell()); if (effectiveSize < buffer.size()) { buffer.resize(effectiveSize); } return true; } else { // Error buffer.clear(); errorMessage = std::string(c.text()); return false; } } bool FromDcmtkBridge::SaveToMemoryBuffer(std::string& buffer, DcmDataset& dataSet) { std::string errorMessageNotUsed; return SaveToMemoryBuffer(buffer, dataSet, errorMessageNotUsed); } bool FromDcmtkBridge::SaveToMemoryBuffer(std::string& buffer, DcmDataset& dataSet, std::string& errorMessage) { // Determine the transfer syntax which shall be used to write the // information to the file. If not possible, switch to the Little // Endian syntax, with explicit length. // http://support.dcmtk.org/docs/dcxfer_8h-source.html /** * Note that up to Orthanc 0.7.1 (inclusive), the * "EXS_LittleEndianExplicit" was always used to save the DICOM * dataset into memory. We now keep the original transfer syntax * (if available). **/ E_TransferSyntax xfer = dataSet.getCurrentXfer(); if (xfer == EXS_Unknown) { // No information about the original transfer syntax: This is // most probably a DICOM dataset that was read from memory. xfer = EXS_LittleEndianExplicit; } // Create the meta-header information DcmFileFormat ff(&dataSet); ff.validateMetaInfo(xfer); ff.removeInvalidGroups(); return SaveToMemoryBufferInternal(buffer, ff, xfer, errorMessage); } bool FromDcmtkBridge::Transcode(DcmFileFormat& dicom, DicomTransferSyntax syntax, const DcmRepresentationParameter* representation) { E_TransferSyntax xfer; if (!LookupDcmtkTransferSyntax(xfer, syntax)) { throw OrthancException(ErrorCode_InternalError); } else { DicomTransferSyntax sourceSyntax; bool known = LookupOrthancTransferSyntax(sourceSyntax, dicom); if (!dicom.chooseRepresentation(xfer, representation).good() || !dicom.canWriteXfer(xfer) || !dicom.validateMetaInfo(xfer, EWM_updateMeta).good()) { return false; } else { dicom.removeInvalidGroups(); if (known) { CLOG(INFO, DICOM) << "Transcoded an image from transfer syntax " << GetTransferSyntaxUid(sourceSyntax) << " to " << GetTransferSyntaxUid(syntax); } else { CLOG(INFO, DICOM) << "Transcoded an image from unknown transfer syntax to " << GetTransferSyntaxUid(syntax); } return true; } } } ValueRepresentation FromDcmtkBridge::LookupValueRepresentation(const DicomTag& tag) { DcmTag t(tag.GetGroup(), tag.GetElement()); return Convert(t.getEVR()); } ValueRepresentation FromDcmtkBridge::Convert(const DcmEVR vr) { switch (vr) { case EVR_AE: return ValueRepresentation_ApplicationEntity; case EVR_AS: return ValueRepresentation_AgeString; case EVR_AT: return ValueRepresentation_AttributeTag; case EVR_CS: return ValueRepresentation_CodeString; case EVR_DA: return ValueRepresentation_Date; case EVR_DS: return ValueRepresentation_DecimalString; case EVR_DT: return ValueRepresentation_DateTime; case EVR_FL: return ValueRepresentation_FloatingPointSingle; case EVR_FD: return ValueRepresentation_FloatingPointDouble; case EVR_IS: return ValueRepresentation_IntegerString; case EVR_LO: return ValueRepresentation_LongString; case EVR_LT: return ValueRepresentation_LongText; case EVR_OB: return ValueRepresentation_OtherByte; #if DCMTK_VERSION_NUMBER >= 361 case EVR_OD: return ValueRepresentation_OtherDouble; #endif case EVR_OF: return ValueRepresentation_OtherFloat; #if DCMTK_VERSION_NUMBER >= 362 case EVR_OL: return ValueRepresentation_OtherLong; #endif case EVR_OW: return ValueRepresentation_OtherWord; case EVR_PN: return ValueRepresentation_PersonName; case EVR_SH: return ValueRepresentation_ShortString; case EVR_SL: return ValueRepresentation_SignedLong; case EVR_SQ: return ValueRepresentation_Sequence; case EVR_SS: return ValueRepresentation_SignedShort; case EVR_ST: return ValueRepresentation_ShortText; case EVR_TM: return ValueRepresentation_Time; #if DCMTK_VERSION_NUMBER >= 361 case EVR_UC: return ValueRepresentation_UnlimitedCharacters; #endif case EVR_UI: return ValueRepresentation_UniqueIdentifier; case EVR_UL: return ValueRepresentation_UnsignedLong; case EVR_UN: return ValueRepresentation_Unknown; #if DCMTK_VERSION_NUMBER >= 361 case EVR_UR: return ValueRepresentation_UniversalResource; #endif case EVR_US: return ValueRepresentation_UnsignedShort; case EVR_UT: return ValueRepresentation_UnlimitedText; default: return ValueRepresentation_NotSupported; } } DcmElement* FromDcmtkBridge::CreateElementForTag(const DicomTag& tag, const std::string& privateCreator) { if (tag.IsPrivate() && privateCreator.empty()) { // This solves issue 140 (Modifying private tags with REST API // changes VR from LO to UN) // https://orthanc.uclouvain.be/bugs/show_bug.cgi?id=140 LOG(WARNING) << "Private creator should not be empty while creating a private tag: " << tag.Format(); } #if DCMTK_VERSION_NUMBER >= 362 DcmTag key(tag.GetGroup(), tag.GetElement()); if (tag.IsPrivate()) { return DcmItem::newDicomElement(key, privateCreator.c_str()); } else { return DcmItem::newDicomElement(key, NULL); } #else DcmTag key(tag.GetGroup(), tag.GetElement()); if (tag.IsPrivate()) { // https://forum.dcmtk.org/viewtopic.php?t=4527 LOG(WARNING) << "You are using DCMTK <= 3.6.1: All the private tags " "are considered as having a binary value representation"; key.setPrivateCreator(privateCreator.c_str()); return new DcmOtherByteOtherWord(key); } else { return newDicomElement(key); } #endif } void FromDcmtkBridge::FillElementWithString(DcmElement& element, const std::string& utf8Value, bool decodeDataUriScheme, Encoding dicomEncoding) { std::string binary; const std::string* decoded = &utf8Value; if (decodeDataUriScheme && boost::starts_with(utf8Value, URI_SCHEME_PREFIX_BINARY)) { std::string mime; if (!Toolbox::DecodeDataUriScheme(mime, binary, utf8Value)) { throw OrthancException(ErrorCode_BadFileFormat); } decoded = &binary; } else if (dicomEncoding != Encoding_Utf8) { binary = Toolbox::ConvertFromUtf8(utf8Value, dicomEncoding); decoded = &binary; } if (IsBinaryTag(element.getTag())) { bool ok; switch (element.getTag().getEVR()) { case EVR_OW: if (decoded->size() % sizeof(Uint16) != 0) { LOG(ERROR) << "A tag with OW VR must have an even number of bytes"; ok = false; } else { ok = element.putUint16Array((const Uint16*) decoded->c_str(), decoded->size() / sizeof(Uint16)).good(); } break; default: ok = element.putUint8Array((const Uint8*) decoded->c_str(), decoded->size()).good(); break; } if (ok) { return; } else { throw OrthancException(ErrorCode_InternalError); } } bool ok = false; try { switch (element.getTag().getEVR()) { // http://support.dcmtk.org/docs/dcvr_8h-source.html /** * TODO. **/ case EVR_OB: // other byte case EVR_OW: // other word throw OrthancException(ErrorCode_NotImplemented); case EVR_UN: // unknown value representation throw OrthancException(ErrorCode_ParameterOutOfRange); /** * String types. **/ case EVR_DS: // decimal string case EVR_IS: // integer string case EVR_AS: // age string case EVR_DA: // date string case EVR_DT: // date time string case EVR_TM: // time string case EVR_AE: // application entity title case EVR_CS: // code string case EVR_SH: // short string case EVR_LO: // long string case EVR_ST: // short text case EVR_LT: // long text case EVR_UT: // unlimited text case EVR_PN: // person name case EVR_UI: // unique identifier #if DCMTK_VERSION_NUMBER >= 361 case EVR_UC: // unlimited characters case EVR_UR: // URI/URL #endif { ok = element.putString(decoded->c_str()).good(); break; } /** * Numerical types **/ case EVR_SL: // signed long { ok = element.putSint32(boost::lexical_cast<Sint32>(*decoded)).good(); break; } case EVR_SS: // signed short { ok = element.putSint16(boost::lexical_cast<Sint16>(*decoded)).good(); break; } case EVR_UL: // unsigned long #if DCMTK_VERSION_NUMBER >= 362 case EVR_OL: // other long (requires byte-swapping) #endif { if (decoded->find('\\') != std::string::npos) { ok = element.putString(decoded->c_str()).good(); } else { ok = element.putUint32(boost::lexical_cast<Uint32>(*decoded)).good(); } break; } case EVR_xs: // unsigned short, signed short or multiple values { if (decoded->find('\\') != std::string::npos) { ok = element.putString(decoded->c_str()).good(); } else if (decoded->find('-') != std::string::npos) { ok = element.putSint16(boost::lexical_cast<Sint16>(*decoded)).good(); } else { ok = element.putUint16(boost::lexical_cast<Uint16>(*decoded)).good(); } break; } case EVR_US: // unsigned short { ok = element.putUint16(boost::lexical_cast<Uint16>(*decoded)).good(); break; } case EVR_FL: // float single-precision case EVR_OF: // other float (requires byte swapping) { ok = element.putFloat32(boost::lexical_cast<float>(*decoded)).good(); break; } case EVR_FD: // float double-precision #if DCMTK_VERSION_NUMBER >= 361 case EVR_OD: // other double (requires byte-swapping) #endif { ok = element.putFloat64(boost::lexical_cast<double>(*decoded)).good(); break; } /** * Other types **/ case EVR_AT: // attribute tag, new in Orthanc 1.9.4 { DicomTag value = ParseTag(utf8Value); ok = element.putTagVal(DcmTagKey(value.GetGroup(), value.GetElement())).good(); break; } /** * Sequence types, should never occur at this point. **/ case EVR_SQ: // sequence of items { ok = false; break; } /** * Internal to DCMTK. **/ case EVR_ox: // OB or OW depending on context case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) case EVR_na: // na="not applicable", for data which has no VR case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor case EVR_item: // used internally for items case EVR_metainfo: // used internally for meta info datasets case EVR_dataset: // used internally for datasets case EVR_fileFormat: // used internally for DICOM files case EVR_dicomDir: // used internally for DICOMDIR objects case EVR_dirRecord: // used internally for DICOMDIR records case EVR_pixelSQ: // used internally for pixel sequences in a compressed image case EVR_pixelItem: // used internally for pixel items in a compressed image case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) case EVR_PixelData: // used internally for uncompressed pixeld data case EVR_OverlayData: // used internally for overlay data case EVR_UNKNOWN2B: // used internally for elements with unknown VR with 2-byte length field in explicit VR default: break; } } catch (boost::bad_lexical_cast&) { ok = false; } if (!ok) { DicomTag tag(element.getTag().getGroup(), element.getTag().getElement()); throw OrthancException(ErrorCode_BadFileFormat, "While creating a DICOM instance, tag (" + tag.Format() + ") has out-of-range value: \"" + (*decoded) + "\""); } } DcmElement* FromDcmtkBridge::FromJson(const DicomTag& tag, const Json::Value& value, bool decodeDataUriScheme, Encoding dicomEncoding, const std::string& privateCreator) { std::unique_ptr<DcmElement> element; switch (value.type()) { case Json::stringValue: element.reset(CreateElementForTag(tag, privateCreator)); FillElementWithString(*element, value.asString(), decodeDataUriScheme, dicomEncoding); break; case Json::nullValue: element.reset(CreateElementForTag(tag, privateCreator)); FillElementWithString(*element, "", decodeDataUriScheme, dicomEncoding); break; case Json::arrayValue: { const char* p = NULL; if (tag.IsPrivate() && !privateCreator.empty()) { p = privateCreator.c_str(); } DcmTag key(tag.GetGroup(), tag.GetElement(), p); if (key.getEVR() != EVR_SQ) { throw OrthancException(ErrorCode_BadParameterType, "Bad Parameter type for tag " + tag.Format()); } DcmSequenceOfItems* sequence = new DcmSequenceOfItems(key); element.reset(sequence); for (Json::Value::ArrayIndex i = 0; i < value.size(); i++) { std::unique_ptr<DcmItem> item(new DcmItem); switch (value[i].type()) { case Json::objectValue: { Json::Value::Members members = value[i].getMemberNames(); for (Json::Value::ArrayIndex j = 0; j < members.size(); j++) { item->insert(FromJson(ParseTag(members[j]), value[i][members[j]], decodeDataUriScheme, dicomEncoding, privateCreator)); } break; } case Json::arrayValue: { // Lua cannot disambiguate between an empty dictionary // and an empty array if (value[i].size() != 0) { throw OrthancException(ErrorCode_BadParameterType); } break; } default: throw OrthancException(ErrorCode_BadParameterType); } sequence->append(item.release()); } break; } default: throw OrthancException(ErrorCode_BadParameterType, "Bad Parameter type for tag " + tag.Format()); } return element.release(); } DcmPixelSequence* FromDcmtkBridge::GetPixelSequence(DcmDataset& dataset) { DcmElement *element = NULL; if (!dataset.findAndGetElement(DCM_PixelData, element).good()) { throw OrthancException(ErrorCode_BadFileFormat); } DcmPixelData& pixelData = dynamic_cast<DcmPixelData&>(*element); E_TransferSyntax repType; const DcmRepresentationParameter *repParam = NULL; pixelData.getCurrentRepresentationKey(repType, repParam); DcmPixelSequence* pixelSequence = NULL; if (!pixelData.getEncapsulatedRepresentation(repType, repParam, pixelSequence).good()) { return NULL; } else { return pixelSequence; } } Encoding FromDcmtkBridge::ExtractEncoding(const Json::Value& json, Encoding defaultEncoding) { if (json.type() != Json::objectValue) { throw OrthancException(ErrorCode_BadParameterType); } Encoding encoding = defaultEncoding; const Json::Value::Members tags = json.getMemberNames(); // Look for SpecificCharacterSet (0008,0005) in the JSON file for (size_t i = 0; i < tags.size(); i++) { DicomTag tag = FromDcmtkBridge::ParseTag(tags[i]); if (tag == DICOM_TAG_SPECIFIC_CHARACTER_SET) { const Json::Value& value = json[tags[i]]; if (value.type() != Json::stringValue || (value.asString().length() != 0 && !GetDicomEncoding(encoding, value.asCString()))) { throw OrthancException(ErrorCode_BadRequest, "Unknown encoding while creating DICOM from JSON: " + value.toStyledString()); } if (value.asString().length() == 0) { return defaultEncoding; } } } return encoding; } static void SetString(DcmDataset& target, const DcmTag& tag, const std::string& value) { if (!target.putAndInsertString(tag, value.c_str()).good()) { throw OrthancException(ErrorCode_InternalError); } } DcmDataset* FromDcmtkBridge::FromJson(const Json::Value& json, // Encoded using UTF-8 bool generateIdentifiers, bool decodeDataUriScheme, Encoding defaultEncoding, const std::string& privateCreator) { std::unique_ptr<DcmDataset> result(new DcmDataset); Encoding encoding = ExtractEncoding(json, defaultEncoding); SetString(*result, DCM_SpecificCharacterSet, GetDicomSpecificCharacterSet(encoding)); const Json::Value::Members tags = json.getMemberNames(); bool hasPatientId = false; bool hasStudyInstanceUid = false; bool hasSeriesInstanceUid = false; bool hasSopInstanceUid = false; for (size_t i = 0; i < tags.size(); i++) { DicomTag tag = FromDcmtkBridge::ParseTag(tags[i]); const Json::Value& value = json[tags[i]]; if (tag == DICOM_TAG_PATIENT_ID) { hasPatientId = true; } else if (tag == DICOM_TAG_STUDY_INSTANCE_UID) { hasStudyInstanceUid = true; } else if (tag == DICOM_TAG_SERIES_INSTANCE_UID) { hasSeriesInstanceUid = true; } else if (tag == DICOM_TAG_SOP_INSTANCE_UID) { hasSopInstanceUid = true; } if (tag != DICOM_TAG_SPECIFIC_CHARACTER_SET) { std::unique_ptr<DcmElement> element(FromDcmtkBridge::FromJson(tag, value, decodeDataUriScheme, encoding, privateCreator)); result->findAndDeleteElement(element->getTag()); DcmElement* tmp = element.release(); if (!result->insert(tmp, false, false).good()) { delete tmp; throw OrthancException(ErrorCode_InternalError); } } } if (!hasPatientId && generateIdentifiers) { SetString(*result, DCM_PatientID, GenerateUniqueIdentifier(ResourceType_Patient)); } if (!hasStudyInstanceUid && generateIdentifiers) { SetString(*result, DCM_StudyInstanceUID, GenerateUniqueIdentifier(ResourceType_Study)); } if (!hasSeriesInstanceUid && generateIdentifiers) { SetString(*result, DCM_SeriesInstanceUID, GenerateUniqueIdentifier(ResourceType_Series)); } if (!hasSopInstanceUid && generateIdentifiers) { SetString(*result, DCM_SOPInstanceUID, GenerateUniqueIdentifier(ResourceType_Instance)); } return result.release(); } DcmFileFormat* FromDcmtkBridge::LoadFromMemoryBuffer(const void* buffer, size_t size) { DcmInputBufferStream is; if (size > 0) { is.setBuffer(buffer, size); } is.setEos(); std::unique_ptr<DcmFileFormat> result(new DcmFileFormat); result->transferInit(); /** * New in Orthanc 1.6.0: The "size" is given as an argument to the * "read()" method. This can avoid huge memory consumption if * parsing an invalid DICOM file, which can notably been observed * by executing the integration test "test_upload_compressed" on * valgrind running Orthanc. **/ if (!result->read(is, EXS_Unknown, EGL_noChange, size).good()) { throw OrthancException(ErrorCode_BadFileFormat, "Cannot parse an invalid DICOM file (size: " + boost::lexical_cast<std::string>(size) + " bytes)"); } result->loadAllDataIntoMemory(); result->transferEnd(); return result.release(); } void FromDcmtkBridge::FromJson(DicomMap& target, const Json::Value& source, const char* fieldName) { if (source.type() != Json::objectValue) { if (fieldName != NULL) { throw OrthancException(ErrorCode_BadFileFormat, std::string("Expecting an object in field '") + std::string(fieldName) + std::string("'")); } else { throw OrthancException(ErrorCode_BadFileFormat, "Expecting an object"); } } target.Clear(); Json::Value::Members members = source.getMemberNames(); for (size_t i = 0; i < members.size(); i++) { const Json::Value& value = source[members[i]]; if (value.type() != Json::stringValue) { throw OrthancException(ErrorCode_BadFileFormat, std::string("Expecting a string in field '") + members[i] + std::string("'")); } target.SetValue(ParseTag(members[i]), value.asString(), false); } } void FromDcmtkBridge::ChangeStringEncoding(DcmItem& dataset, Encoding source, bool hasSourceCodeExtensions, Encoding target) { // Recursive exploration of a dataset to change the encoding of // each string-like element if (source == target) { return; } for (unsigned long i = 0; i < dataset.card(); i++) { DcmElement* element = dataset.getElement(i); if (element) { if (element->isLeaf()) { char *c = NULL; if (element->isaString() && element->getString(c).good() && c != NULL) { std::string a = Toolbox::ConvertToUtf8(c, source, hasSourceCodeExtensions); std::string b = Toolbox::ConvertFromUtf8(a, target); element->putString(b.c_str()); } } else { // "All subclasses of DcmElement except for DcmSequenceOfItems // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset // etc. are not." The following dynamic_cast is thus OK. DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(*element); for (unsigned long j = 0; j < sequence.card(); j++) { ChangeStringEncoding(*sequence.getItem(j), source, hasSourceCodeExtensions, target); } } } } } void FromDcmtkBridge::InitializeCodecs() { #if ORTHANC_ENABLE_DCMTK_JPEG_LOSSLESS == 1 CLOG(INFO, DICOM) << "Registering JPEG Lossless codecs in DCMTK"; DJLSDecoderRegistration::registerCodecs(); # if ORTHANC_ENABLE_DCMTK_TRANSCODING == 1 DJLSEncoderRegistration::registerCodecs(); # endif #endif #if ORTHANC_ENABLE_DCMTK_JPEG == 1 CLOG(INFO, DICOM) << "Registering JPEG codecs in DCMTK"; DJDecoderRegistration::registerCodecs(); # if ORTHANC_ENABLE_DCMTK_TRANSCODING == 1 DJEncoderRegistration::registerCodecs(); # endif #endif CLOG(INFO, DICOM) << "Registering RLE codecs in DCMTK"; DcmRLEDecoderRegistration::registerCodecs(); #if ORTHANC_ENABLE_DCMTK_TRANSCODING == 1 DcmRLEEncoderRegistration::registerCodecs(); #endif } void FromDcmtkBridge::FinalizeCodecs() { #if ORTHANC_ENABLE_DCMTK_JPEG_LOSSLESS == 1 // Unregister JPEG-LS codecs DJLSDecoderRegistration::cleanup(); # if ORTHANC_ENABLE_DCMTK_TRANSCODING == 1 DJLSEncoderRegistration::cleanup(); # endif #endif #if ORTHANC_ENABLE_DCMTK_JPEG == 1 // Unregister JPEG codecs DJDecoderRegistration::cleanup(); # if ORTHANC_ENABLE_DCMTK_TRANSCODING == 1 DJEncoderRegistration::cleanup(); # endif #endif DcmRLEDecoderRegistration::cleanup(); #if ORTHANC_ENABLE_DCMTK_TRANSCODING == 1 DcmRLEEncoderRegistration::cleanup(); #endif } // Forward declaration static bool ApplyVisitorToElement(DcmElement& element, ITagVisitor& visitor, const std::vector<DicomTag>& parentTags, const std::vector<size_t>& parentIndexes, Encoding encoding, bool hasCodeExtensions); static void ApplyVisitorToDataset(DcmItem& dataset, ITagVisitor& visitor, const std::vector<DicomTag>& parentTags, const std::vector<size_t>& parentIndexes, Encoding encoding, bool hasCodeExtensions) { assert(parentTags.size() == parentIndexes.size()); std::set<DcmTagKey> toRemove; for (unsigned long i = 0; i < dataset.card(); i++) { DcmElement* element = dataset.getElement(i); if (element == NULL) { throw OrthancException(ErrorCode_InternalError); } else { if (!ApplyVisitorToElement(*element, visitor, parentTags, parentIndexes, encoding, hasCodeExtensions)) { toRemove.insert(element->getTag()); } } } // Remove all the tags that were planned for removal (cf. ITagVisitor::Action_Remove) for (std::set<DcmTagKey>::const_iterator it = toRemove.begin(); it != toRemove.end(); ++it) { std::unique_ptr<DcmElement> tmp(dataset.remove(*it)); } } // Returns "true" iff the element must be kept. If "false" is // returned, the element will be removed. static bool ApplyVisitorToLeaf(DcmElement& element, ITagVisitor& visitor, const std::vector<DicomTag>& parentTags, const std::vector<size_t>& parentIndexes, const DicomTag& tag, Encoding encoding, bool hasCodeExtensions) { // TODO - Merge this function, that is more recent, with ConvertLeafElement() assert(element.isLeaf()); DcmEVR evr = element.getTag().getEVR(); /** * Fix the EVR for types internal to DCMTK **/ if (evr == EVR_ox) // OB or OW depending on context { evr = EVR_OB; } else if (evr == EVR_xs) // SS or US depending on context { // So far we assume that it's alway US (as a best guess: https://forum.dcmtk.org/viewtopic.php?t=932) // However, e.g. in a LUTDescriptor (3 values), the middle value can be a SS depending on other tag values while first and third value are always US. // This patch, although not perfect fixes https://orthanc.uclouvain.be/bugs/show_bug.cgi?id=214. // It might need some rework once we encounter a LUTDescriptor with a SS value. ref: https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.11.2.html#sect_C.11.2.1.1 evr = EVR_US; } else if (evr == EVR_lt) // US, SS or OW depending on context, used for LUT Data (thus the name) { // best guess is OW: final user should be able to interpret it correctly depending on the context evr = EVR_OW; } if (evr == EVR_UNKNOWN || // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR) evr == EVR_UNKNOWN2B) // used internally for elements with unknown VR with 2-byte length field in explicit VR { evr = EVR_UN; } if (evr == EVR_UN) { // New in Orthanc 1.9.5 DictionaryLocker locker; const DcmDictEntry* entry = locker->findEntry(element.getTag().getXTag(), element.getTag().getPrivateCreator()); if (entry != NULL) { evr = entry->getEVR(); } } const ValueRepresentation vr = FromDcmtkBridge::Convert(evr); /** * Deal with binary data (including PixelData). **/ if (evr == EVR_OB || // other byte evr == EVR_OW || // other word evr == EVR_UN) // unknown value representation { Uint16* data16 = NULL; Uint8* data = NULL; ITagVisitor::Action action; if ((element.getTag() == DCM_PixelData || // (*) New in Orthanc 1.9.1 evr == EVR_OW) && element.getUint16Array(data16) == EC_Normal) { action = visitor.VisitBinary(parentTags, parentIndexes, tag, vr, data16, element.getLength()); } else if (evr != EVR_OW && element.getUint8Array(data) == EC_Normal) { /** * WARNING: The call to "getUint8Array()" crashes * (segmentation fault) on big-endian architectures if applied * to pixel data, during the call to "swapIfNecessary()" in * "DcmPolymorphOBOW::getUint8Array()" (this method is not * reimplemented in derived class "DcmPixelData"). However, * "getUint16Array()" works correctly, hence (*). **/ action = visitor.VisitBinary(parentTags, parentIndexes, tag, vr, data, element.getLength()); } else { action = visitor.VisitNotSupported(parentTags, parentIndexes, tag, vr); } switch (action) { case ITagVisitor::Action_None: return true; // We're done case ITagVisitor::Action_Remove: return false; case ITagVisitor::Action_Replace: throw OrthancException(ErrorCode_NotImplemented, "Iterator cannot replace binary data"); default: throw OrthancException(ErrorCode_ParameterOutOfRange); } } /** * Deal with plain strings (and convert them to UTF-8) **/ char *c = NULL; if (element.isaString() && element.getString(c).good()) { std::string utf8; if (c != NULL) // This case corresponds to the empty string { if (element.getTag() == DCM_SpecificCharacterSet) { utf8.assign(c); } else { std::string s(c); utf8 = Toolbox::ConvertToUtf8(s, encoding, hasCodeExtensions); } } std::string newValue; ITagVisitor::Action action = visitor.VisitString (newValue, parentTags, parentIndexes, tag, vr, utf8); switch (action) { case ITagVisitor::Action_None: return true; case ITagVisitor::Action_Remove: return false; case ITagVisitor::Action_Replace: { std::string s = Toolbox::ConvertFromUtf8(newValue, encoding); if (element.putString(s.c_str()) != EC_Normal) { throw OrthancException(ErrorCode_InternalError, "Iterator cannot replace value of tag: " + tag.Format()); } return true; } default: throw OrthancException(ErrorCode_InternalError); } } ITagVisitor::Action action; try { // http://support.dcmtk.org/docs/dcvr_8h-source.html switch (evr) { /** * Plain string values. **/ case EVR_DS: // decimal string case EVR_IS: // integer string case EVR_AS: // age string case EVR_DA: // date string case EVR_DT: // date time string case EVR_TM: // time string case EVR_AE: // application entity title case EVR_CS: // code string case EVR_SH: // short string case EVR_LO: // long string case EVR_ST: // short text case EVR_LT: // long text case EVR_UT: // unlimited text case EVR_PN: // person name case EVR_UI: // unique identifier { Uint8* data = NULL; if (element.getUint8Array(data) == EC_Normal) { const Uint32 length = element.getLength(); Uint32 l = 0; while (l < length && data[l] != 0) { l++; } std::string ignored; std::string s(reinterpret_cast<const char*>(data), l); action = visitor.VisitString(ignored, parentTags, parentIndexes, tag, vr, Toolbox::ConvertToUtf8(s, encoding, hasCodeExtensions)); } else { action = visitor.VisitNotSupported(parentTags, parentIndexes, tag, vr); } if (action == ITagVisitor::Action_Replace) { LOG(WARNING) << "Iterator cannot replace this string tag: " << FromDcmtkBridge::GetTagName(element) << " (" << tag.Format() << ")"; return true; } break; } /** * Numeric types **/ case EVR_SL: // signed long { DcmSignedLong& content = dynamic_cast<DcmSignedLong&>(element); std::vector<int64_t> values; values.reserve(content.getVM()); for (unsigned long i = 0; i < content.getVM(); i++) { Sint32 f; if (content.getSint32(f, i).good()) { values.push_back(f); } } action = visitor.VisitIntegers(parentTags, parentIndexes, tag, vr, values); break; } case EVR_SS: // signed short { DcmSignedShort& content = dynamic_cast<DcmSignedShort&>(element); std::vector<int64_t> values; values.reserve(content.getVM()); for (unsigned long i = 0; i < content.getVM(); i++) { Sint16 f; if (content.getSint16(f, i).good()) { values.push_back(f); } } action = visitor.VisitIntegers(parentTags, parentIndexes, tag, vr, values); break; } case EVR_UL: // unsigned long #if DCMTK_VERSION_NUMBER >= 362 case EVR_OL: #endif { DcmUnsignedLong& content = dynamic_cast<DcmUnsignedLong&>(element); std::vector<int64_t> values; values.reserve(content.getVM()); for (unsigned long i = 0; i < content.getVM(); i++) { Uint32 f; if (content.getUint32(f, i).good()) { values.push_back(f); } } action = visitor.VisitIntegers(parentTags, parentIndexes, tag, vr, values); break; } case EVR_US: // unsigned short { DcmUnsignedShort& content = dynamic_cast<DcmUnsignedShort&>(element); std::vector<int64_t> values; values.reserve(content.getVM()); for (unsigned long i = 0; i < content.getVM(); i++) { Uint16 f; if (content.getUint16(f, i).good()) { values.push_back(f); } } action = visitor.VisitIntegers(parentTags, parentIndexes, tag, vr, values); break; } case EVR_FL: // float single-precision case EVR_OF: { DcmFloatingPointSingle& content = dynamic_cast<DcmFloatingPointSingle&>(element); std::vector<double> values; values.reserve(content.getVM()); for (unsigned long i = 0; i < content.getVM(); i++) { Float32 f; if (content.getFloat32(f, i).good()) { values.push_back(f); } } action = visitor.VisitDoubles(parentTags, parentIndexes, tag, vr, values); break; } case EVR_FD: // float double-precision #if DCMTK_VERSION_NUMBER >= 361 case EVR_OD: #endif { DcmFloatingPointDouble& content = dynamic_cast<DcmFloatingPointDouble&>(element); std::vector<double> values; values.reserve(content.getVM()); for (unsigned long i = 0; i < content.getVM(); i++) { Float64 f; if (content.getFloat64(f, i).good()) { values.push_back(f); } } action = visitor.VisitDoubles(parentTags, parentIndexes, tag, vr, values); break; } /** * Attribute tag. **/ case EVR_AT: { DcmAttributeTag& content = dynamic_cast<DcmAttributeTag&>(element); std::vector<DicomTag> values; values.reserve(content.getVM()); for (unsigned long i = 0; i < content.getVM(); i++) { DcmTagKey f; if (content.getTagVal(f, i).good()) { DicomTag t(f.getGroup(), f.getElement()); values.push_back(t); } } assert(vr == ValueRepresentation_AttributeTag); action = visitor.VisitAttributes(parentTags, parentIndexes, tag, values); break; } /** * Sequence types, should never occur at this point because of * "element.isLeaf()". **/ case EVR_SQ: // sequence of items { return true; } /** * Internal to DCMTK. **/ case EVR_xs: // SS or US depending on context case EVR_lt: // US, SS or OW depending on context, used for LUT Data (thus the name) case EVR_na: // na="not applicable", for data which has no VR case EVR_up: // up="unsigned pointer", used internally for DICOMDIR suppor case EVR_item: // used internally for items case EVR_metainfo: // used internally for meta info datasets case EVR_dataset: // used internally for datasets case EVR_fileFormat: // used internally for DICOM files case EVR_dicomDir: // used internally for DICOMDIR objects case EVR_dirRecord: // used internally for DICOMDIR records case EVR_pixelSQ: // used internally for pixel sequences in a compressed image case EVR_pixelItem: // used internally for pixel items in a compressed image case EVR_PixelData: // used internally for uncompressed pixeld data case EVR_OverlayData: // used internally for overlay data { action = visitor.VisitNotSupported(parentTags, parentIndexes, tag, vr); break; } /** * Default case. **/ default: return true; } switch (action) { case ITagVisitor::Action_None: return true; // We're done case ITagVisitor::Action_Remove: return false; case ITagVisitor::Action_Replace: throw OrthancException(ErrorCode_NotImplemented, "Iterator cannot replace non-string-like data"); default: throw OrthancException(ErrorCode_ParameterOutOfRange); } } catch (boost::bad_lexical_cast&) { return true; } catch (std::bad_cast&) { return true; } } // Returns "true" iff the element must be kept. If "false" is // returned, the element will be removed. static bool ApplyVisitorToElement(DcmElement& element, ITagVisitor& visitor, const std::vector<DicomTag>& parentTags, const std::vector<size_t>& parentIndexes, Encoding encoding, bool hasCodeExtensions) { assert(parentTags.size() == parentIndexes.size()); DicomTag tag(FromDcmtkBridge::Convert(element.getTag())); if (element.isLeaf()) { return ApplyVisitorToLeaf(element, visitor, parentTags, parentIndexes, tag, encoding, hasCodeExtensions); } else { // "All subclasses of DcmElement except for DcmSequenceOfItems // are leaf nodes, while DcmSequenceOfItems, DcmItem, DcmDataset // etc. are not." The following dynamic_cast is thus OK. DcmSequenceOfItems& sequence = dynamic_cast<DcmSequenceOfItems&>(element); ITagVisitor::Action action = visitor.VisitSequence(parentTags, parentIndexes, tag, sequence.card()); switch (action) { case ITagVisitor::Action_None: if (sequence.card() != 0) // Minor optimization to avoid creating "tags" and "indexes" if not needed { std::vector<DicomTag> tags = parentTags; std::vector<size_t> indexes = parentIndexes; tags.push_back(tag); indexes.push_back(0); for (unsigned long i = 0; i < sequence.card(); i++) { indexes.back() = static_cast<size_t>(i); DcmItem* child = sequence.getItem(i); ApplyVisitorToDataset(*child, visitor, tags, indexes, encoding, hasCodeExtensions); } } return true; // Keep case ITagVisitor::Action_Remove: return false; case ITagVisitor::Action_Replace: throw OrthancException(ErrorCode_NotImplemented, "Iterator cannot replace sequences"); default: throw OrthancException(ErrorCode_ParameterOutOfRange); } } } void FromDcmtkBridge::Apply(DcmItem& dataset, ITagVisitor& visitor, Encoding defaultEncoding) { std::vector<DicomTag> parentTags; std::vector<size_t> parentIndexes; bool hasCodeExtensions; Encoding encoding = DetectEncoding(hasCodeExtensions, dataset, defaultEncoding); ApplyVisitorToDataset(dataset, visitor, parentTags, parentIndexes, encoding, hasCodeExtensions); } bool FromDcmtkBridge::LookupOrthancTransferSyntax(DicomTransferSyntax& target, DcmFileFormat& dicom) { if (dicom.getDataset() == NULL) { throw OrthancException(ErrorCode_InternalError); } else { return LookupOrthancTransferSyntax(target, *dicom.getDataset()); } } bool FromDcmtkBridge::LookupOrthancTransferSyntax(DicomTransferSyntax& target, DcmDataset& dataset) { E_TransferSyntax xfer = dataset.getCurrentXfer(); if (xfer == EXS_Unknown) { dataset.updateOriginalXfer(); xfer = dataset.getOriginalXfer(); if (xfer == EXS_Unknown) { throw OrthancException(ErrorCode_BadFileFormat, "Cannot determine the transfer syntax of the DICOM instance"); } } return FromDcmtkBridge::LookupOrthancTransferSyntax(target, xfer); } void FromDcmtkBridge::LogMissingTagsForStore(DcmDataset& dicom) { std::string patientId, studyInstanceUid, seriesInstanceUid, sopInstanceUid; const char* c = NULL; if (dicom.findAndGetString(DCM_PatientID, c).good() && c != NULL) { patientId.assign(c); } c = NULL; if (dicom.findAndGetString(DCM_StudyInstanceUID, c).good() && c != NULL) { studyInstanceUid.assign(c); } c = NULL; if (dicom.findAndGetString(DCM_SeriesInstanceUID, c).good() && c != NULL) { seriesInstanceUid.assign(c); } c = NULL; if (dicom.findAndGetString(DCM_SOPInstanceUID, c).good() && c != NULL) { sopInstanceUid.assign(c); } DicomMap::LogMissingTagsForStore(patientId, studyInstanceUid, seriesInstanceUid, sopInstanceUid); } void FromDcmtkBridge::IDicomPathVisitor::ApplyInternal(FromDcmtkBridge::IDicomPathVisitor& visitor, DcmItem& item, const DicomPath& pattern, const DicomPath& actualPath) { const size_t level = actualPath.GetPrefixLength(); if (level == pattern.GetPrefixLength()) { visitor.Visit(item, actualPath); } else { assert(level < pattern.GetPrefixLength()); const DicomTag& tmp = pattern.GetPrefixTag(level); DcmTagKey tag(tmp.GetGroup(), tmp.GetElement()); DcmSequenceOfItems *sequence = NULL; if (item.findAndGetSequence(tag, sequence).good() && sequence != NULL) { for (unsigned long i = 0; i < sequence->card(); i++) { if (pattern.IsPrefixUniversal(level) || pattern.GetPrefixIndex(level) == static_cast<size_t>(i)) { DcmItem *child = sequence->getItem(i); if (child != NULL) { DicomPath childPath = actualPath; childPath.AddIndexedTagToPrefix(pattern.GetPrefixTag(level), static_cast<size_t>(i)); ApplyInternal(visitor, *child, pattern, childPath); } } } } } } void FromDcmtkBridge::IDicomPathVisitor::Apply(IDicomPathVisitor& visitor, DcmDataset& dataset, const DicomPath& path) { DicomPath actualPath(path.GetFinalTag()); ApplyInternal(visitor, dataset, path, actualPath); } void FromDcmtkBridge::RemovePath(DcmDataset& dataset, const DicomPath& path) { class Visitor : public FromDcmtkBridge::IDicomPathVisitor { public: virtual void Visit(DcmItem& item, const DicomPath& path) ORTHANC_OVERRIDE { DcmTagKey key(path.GetFinalTag().GetGroup(), path.GetFinalTag().GetElement()); std::unique_ptr<DcmElement> removed(item.remove(key)); } }; Visitor visitor; IDicomPathVisitor::Apply(visitor, dataset, path); } void FromDcmtkBridge::ClearPath(DcmDataset& dataset, const DicomPath& path, bool onlyIfExists) { class Visitor : public FromDcmtkBridge::IDicomPathVisitor { public: bool onlyIfExists_; public: explicit Visitor(bool onlyIfExists) : onlyIfExists_(onlyIfExists) { } virtual void Visit(DcmItem& item, const DicomPath& path) ORTHANC_OVERRIDE { DcmTagKey key(path.GetFinalTag().GetGroup(), path.GetFinalTag().GetElement()); if (onlyIfExists_ && !item.tagExists(key)) { // The tag is non-existing, do not clear it } else { if (!item.insertEmptyElement(key, OFTrue /* replace old value */).good()) { throw OrthancException(ErrorCode_InternalError); } } } }; Visitor visitor(onlyIfExists); IDicomPathVisitor::Apply(visitor, dataset, path); } void FromDcmtkBridge::ReplacePath(DcmDataset& dataset, const DicomPath& path, const DcmElement& element, DicomReplaceMode mode) { class Visitor : public FromDcmtkBridge::IDicomPathVisitor { private: std::unique_ptr<DcmElement> element_; DicomReplaceMode mode_; public: Visitor(const DcmElement& element, DicomReplaceMode mode) : element_(dynamic_cast<DcmElement*>(element.clone())), mode_(mode) { if (element_.get() == NULL) { throw OrthancException(ErrorCode_InternalError, "Cannot clone DcmElement"); } } virtual void Visit(DcmItem& item, const DicomPath& path) ORTHANC_OVERRIDE { std::unique_ptr<DcmElement> cloned(dynamic_cast<DcmElement*>(element_->clone())); if (cloned.get() == NULL) { throw OrthancException(ErrorCode_InternalError, "Cannot clone DcmElement"); } else { DcmTagKey key(path.GetFinalTag().GetGroup(), path.GetFinalTag().GetElement()); if (!item.tagExists(key)) { switch (mode_) { case DicomReplaceMode_InsertIfAbsent: break; // Fine, we can proceed with insertion case DicomReplaceMode_ThrowIfAbsent: throw OrthancException(ErrorCode_InexistentItem, "Cannot replace inexistent tag: " + GetTagName(*element_)); case DicomReplaceMode_IgnoreIfAbsent: return; // Don't proceed with insertion default: throw OrthancException(ErrorCode_ParameterOutOfRange); } } if (!item.insert(cloned.release(), OFTrue /* replace old */).good()) { throw OrthancException(ErrorCode_InternalError, "Cannot replace an element: " + GetTagName(*element_)); } } } }; DcmTagKey key(path.GetFinalTag().GetGroup(), path.GetFinalTag().GetElement()); if (element.getTag() != key) { throw OrthancException(ErrorCode_ParameterOutOfRange, "The final tag must be the same as the tag of the element during a replacement"); } else { Visitor visitor(element, mode); IDicomPathVisitor::Apply(visitor, dataset, path); } } bool FromDcmtkBridge::LookupSequenceItem(DicomMap& target, DcmDataset& dataset, const DicomPath& path, size_t sequenceIndex) { class Visitor : public FromDcmtkBridge::IDicomPathVisitor { private: bool found_; DicomMap& target_; size_t sequenceIndex_; public: Visitor(DicomMap& target, size_t sequenceIndex) : found_(false), target_(target), sequenceIndex_(sequenceIndex) { } virtual void Visit(DcmItem& item, const DicomPath& path) ORTHANC_OVERRIDE { DcmTagKey tag(path.GetFinalTag().GetGroup(), path.GetFinalTag().GetElement()); DcmSequenceOfItems *sequence = NULL; if (item.findAndGetSequence(tag, sequence).good() && sequence != NULL && sequenceIndex_ < sequence->card()) { std::set<DicomTag> ignoreTagLength; ExtractDicomSummary(target_, *sequence->getItem(sequenceIndex_), 0, ignoreTagLength); found_ = true; } } bool HasFound() const { return found_; } }; Visitor visitor(target, sequenceIndex); IDicomPathVisitor::Apply(visitor, dataset, path); return visitor.HasFound(); } bool FromDcmtkBridge::LookupStringValue(std::string& target, DcmDataset& dataset, const DicomTag& key) { DcmTagKey dcmkey(key.GetGroup(), key.GetElement()); const char* str = NULL; const Uint8* data = NULL; unsigned long size = 0; if (dataset.findAndGetString(dcmkey, str).good() && str != NULL) { target.assign(str); return true; } else if (dataset.findAndGetUint8Array(dcmkey, data, &size).good() && data != NULL && size > 0) { /** * This special case is necessary for borderline DICOM files * that have DICOM tags have the "UN" value representation. New * in Orthanc 1.10.1. * https://groups.google.com/g/orthanc-users/c/86fobx3ZyoM/m/KBG17un6AQAJ **/ unsigned long l = 0; while (l < size && data[l] != 0) { l++; } target.assign(reinterpret_cast<const char*>(data), l); return true; } else { return false; } } } #include "./FromDcmtkBridge_TransferSyntaxes.impl.h"