Mercurial > hg > orthanc-wsi
changeset 131:3112e5edb8b6
sync
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Sat, 24 Mar 2018 11:30:05 +0100 |
| parents | 4f3945a2b725 |
| children | de866753a5fa |
| files | Resources/Orthanc/Core/DicomFormat/DicomTag.h Resources/Orthanc/Core/DicomParsing/FromDcmtkBridge.cpp Resources/Orthanc/Core/DicomParsing/FromDcmtkBridge.h Resources/Orthanc/Core/Enumerations.cpp Resources/Orthanc/Core/Enumerations.h Resources/Orthanc/Resources/CMake/DcmtkConfiguration.cmake Resources/Orthanc/Resources/Patches/dcmtk-3.6.2-cmath.patch Resources/SyncOrthancFolder.py |
| diffstat | 8 files changed, 465 insertions(+), 6 deletions(-) [+] |
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--- a/Resources/Orthanc/Core/DicomFormat/DicomTag.h Thu Mar 22 17:32:05 2018 +0100 +++ b/Resources/Orthanc/Core/DicomFormat/DicomTag.h Sat Mar 24 11:30:05 2018 +0100 @@ -123,6 +123,8 @@ static const DicomTag DICOM_TAG_MEDIA_STORAGE_SOP_CLASS_UID(0x0002, 0x0002); static const DicomTag DICOM_TAG_MEDIA_STORAGE_SOP_INSTANCE_UID(0x0002, 0x0003); static const DicomTag DICOM_TAG_DEIDENTIFICATION_METHOD(0x0012, 0x0063); + static const DicomTag DICOM_TAG_REFERENCED_SOP_INSTANCE_UID(0x0008, 0x1155); + static const DicomTag DICOM_TAG_FRAME_OF_REFERENCE_UID(0x0020, 0x0052); // DICOM tags used for fMRI (thanks to Will Ryder) static const DicomTag DICOM_TAG_NUMBER_OF_TEMPORAL_POSITIONS(0x0020, 0x0105);
--- a/Resources/Orthanc/Core/DicomParsing/FromDcmtkBridge.cpp Thu Mar 22 17:32:05 2018 +0100 +++ b/Resources/Orthanc/Core/DicomParsing/FromDcmtkBridge.cpp Sat Mar 24 11:30:05 2018 +0100 @@ -667,11 +667,11 @@ return new DicomValue; } } - catch (boost::bad_lexical_cast) + catch (boost::bad_lexical_cast&) { return new DicomValue; } - catch (std::bad_cast) + catch (std::bad_cast&) { return new DicomValue; } @@ -2096,4 +2096,322 @@ DJDecoderRegistration::cleanup(); #endif } + + + + // Forward declaration + static void ApplyVisitorToElement(DcmElement& element, + ITagVisitor& visitor, + const std::vector<DicomTag>& parentTags, + const std::vector<size_t>& parentIndexes, + Encoding encoding); + + static void ApplyVisitorToDataset(DcmItem& dataset, + ITagVisitor& visitor, + const std::vector<DicomTag>& parentTags, + const std::vector<size_t>& parentIndexes, + Encoding encoding) + { + assert(parentTags.size() == parentIndexes.size()); + + for (unsigned long i = 0; i < dataset.card(); i++) + { + DcmElement* element = dataset.getElement(i); + if (element == NULL) + { + throw OrthancException(ErrorCode_InternalError); + } + else + { + ApplyVisitorToElement(*element, visitor, parentTags, parentIndexes, encoding); + } + } + } + + + static void ApplyVisitorToLeaf(DcmElement& element, + ITagVisitor& visitor, + const std::vector<DicomTag>& parentTags, + const std::vector<size_t>& parentIndexes, + const DicomTag& tag, + Encoding encoding) + { + // TODO - Merge this function with ConvertLeafElement() + + assert(element.isLeaf()); + + DcmEVR evr = element.getTag().getEVR(); + ValueRepresentation vr = FromDcmtkBridge::Convert(evr); + + char *c = NULL; + if (element.isaString() && + element.getString(c).good()) + { + std::string utf8; + + if (c != NULL) // This case corresponds to the empty string + { + std::string s(c); + utf8 = Toolbox::ConvertToUtf8(s, encoding); + } + + std::string newValue; + ITagVisitor::Action action = visitor.VisitString + (newValue, parentTags, parentIndexes, tag, vr, utf8); + + switch (action) + { + case ITagVisitor::Action_None: + break; + + case ITagVisitor::Action_Replace: + { + std::string s = Toolbox::ConvertFromUtf8(newValue, encoding); + if (element.putString(s.c_str(), s.size()) != EC_Normal) + { + LOG(ERROR) << "Cannot replace value of tag: " << tag.Format(); + throw OrthancException(ErrorCode_InternalError); + } + + break; + } + + default: + throw OrthancException(ErrorCode_InternalError); + } + + return; // We're done + } + + + 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 + { + Uint8* data = NULL; + + if (element.getUint8Array(data) == EC_Normal) + { + visitor.VisitBinary(parentTags, parentIndexes, tag, vr, data, element.getLength()); + } + else + { + visitor.VisitUnknown(parentTags, parentIndexes, tag, vr); + } + + break; + } + + /** + * Numeric types + **/ + + case EVR_SL: // signed long + { + Sint32 f; + if (dynamic_cast<DcmSignedLong&>(element).getSint32(f).good()) + { + visitor.VisitInteger(parentTags, parentIndexes, tag, vr, f); + } + + break; + } + + case EVR_SS: // signed short + { + Sint16 f; + if (dynamic_cast<DcmSignedShort&>(element).getSint16(f).good()) + { + visitor.VisitInteger(parentTags, parentIndexes, tag, vr, f); + } + + break; + } + + case EVR_UL: // unsigned long + { + Uint32 f; + if (dynamic_cast<DcmUnsignedLong&>(element).getUint32(f).good()) + { + visitor.VisitInteger(parentTags, parentIndexes, tag, vr, f); + } + + break; + } + + case EVR_US: // unsigned short + { + Uint16 f; + if (dynamic_cast<DcmUnsignedShort&>(element).getUint16(f).good()) + { + visitor.VisitInteger(parentTags, parentIndexes, tag, vr, f); + } + + break; + } + + case EVR_FL: // float single-precision + { + Float32 f; + if (dynamic_cast<DcmFloatingPointSingle&>(element).getFloat32(f).good()) + { + visitor.VisitDouble(parentTags, parentIndexes, tag, vr, f); + } + + break; + } + + case EVR_FD: // float double-precision + { + Float64 f; + if (dynamic_cast<DcmFloatingPointDouble&>(element).getFloat64(f).good()) + { + visitor.VisitDouble(parentTags, parentIndexes, tag, vr, f); + } + + break; + } + + + /** + * Attribute tag. + **/ + + case EVR_AT: + { + DcmTagKey tagKey; + if (dynamic_cast<DcmAttributeTag&>(element).getTagVal(tagKey, 0).good()) + { + DicomTag t(tagKey.getGroup(), tagKey.getElement()); + visitor.VisitAttribute(parentTags, parentIndexes, tag, vr, t); + } + + break; + } + + + /** + * Sequence types, should never occur at this point because of + * "element.isLeaf()". + **/ + + case EVR_SQ: // sequence of items + return; + + + /** + * 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 + visitor.VisitUnknown(parentTags, parentIndexes, tag, vr); + return; + + + /** + * Default case. + **/ + + default: + return; + } + } + catch (boost::bad_lexical_cast&) + { + return; + } + catch (std::bad_cast&) + { + return; + } + } + + + static void ApplyVisitorToElement(DcmElement& element, + ITagVisitor& visitor, + const std::vector<DicomTag>& parentTags, + const std::vector<size_t>& parentIndexes, + Encoding encoding) + { + assert(parentTags.size() == parentIndexes.size()); + + DicomTag tag(FromDcmtkBridge::Convert(element.getTag())); + + if (element.isLeaf()) + { + ApplyVisitorToLeaf(element, visitor, parentTags, parentIndexes, tag, encoding); + } + 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); + + 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); + } + } + } + + + void FromDcmtkBridge::Apply(DcmItem& dataset, + ITagVisitor& visitor, + Encoding defaultEncoding) + { + std::vector<DicomTag> parentTags; + std::vector<size_t> parentIndexes; + Encoding encoding = DetectEncoding(dataset, defaultEncoding); + ApplyVisitorToDataset(dataset, visitor, parentTags, parentIndexes, encoding); + } }
--- a/Resources/Orthanc/Core/DicomParsing/FromDcmtkBridge.h Thu Mar 22 17:32:05 2018 +0100 +++ b/Resources/Orthanc/Core/DicomParsing/FromDcmtkBridge.h Sat Mar 24 11:30:05 2018 +0100 @@ -33,6 +33,7 @@ #pragma once +#include "ITagVisitor.h" #include "../DicomFormat/DicomElement.h" #include "../DicomFormat/DicomMap.h" @@ -240,5 +241,9 @@ static void InitializeCodecs(); static void FinalizeCodecs(); + + static void Apply(DcmItem& dataset, + ITagVisitor& visitor, + Encoding defaultEncoding); }; }
--- a/Resources/Orthanc/Core/Enumerations.cpp Thu Mar 22 17:32:05 2018 +0100 +++ b/Resources/Orthanc/Core/Enumerations.cpp Sat Mar 24 11:30:05 2018 +0100 @@ -878,6 +878,112 @@ } + const char* EnumerationToString(ValueRepresentation vr) + { + switch (vr) + { + case ValueRepresentation_ApplicationEntity: // AE + return "AE"; + + case ValueRepresentation_AgeString: // AS + return "AS"; + + case ValueRepresentation_AttributeTag: // AT (2 x uint16_t) + return "AT"; + + case ValueRepresentation_CodeString: // CS + return "CS"; + + case ValueRepresentation_Date: // DA + return "DA"; + + case ValueRepresentation_DecimalString: // DS + return "DS"; + + case ValueRepresentation_DateTime: // DT + return "DT"; + + case ValueRepresentation_FloatingPointSingle: // FL (float) + return "FL"; + + case ValueRepresentation_FloatingPointDouble: // FD (double) + return "FD"; + + case ValueRepresentation_IntegerString: // IS + return "IS"; + + case ValueRepresentation_LongString: // LO + return "LO"; + + case ValueRepresentation_LongText: // LT + return "LT"; + + case ValueRepresentation_OtherByte: // OB + return "OB"; + + case ValueRepresentation_OtherDouble: // OD + return "OD"; + + case ValueRepresentation_OtherFloat: // OF + return "OF"; + + case ValueRepresentation_OtherLong: // OL + return "OL"; + + case ValueRepresentation_OtherWord: // OW + return "OW"; + + case ValueRepresentation_PersonName: // PN + return "PN"; + + case ValueRepresentation_ShortString: // SH + return "SH"; + + case ValueRepresentation_SignedLong: // SL (int32_t) + return "SL"; + + case ValueRepresentation_Sequence: // SQ + return "SQ"; + + case ValueRepresentation_SignedShort: // SS (int16_t) + return "SS"; + + case ValueRepresentation_ShortText: // ST + return "ST"; + + case ValueRepresentation_Time: // TM + return "TM"; + + case ValueRepresentation_UnlimitedCharacters: // UC + return "UC"; + + case ValueRepresentation_UniqueIdentifier: // UI (UID) + return "UI"; + + case ValueRepresentation_UnsignedLong: // UL (uint32_t) + return "UL"; + + case ValueRepresentation_Unknown: // UN + return "UN"; + + case ValueRepresentation_UniversalResource: // UR (URI or URL) + return "UR"; + + case ValueRepresentation_UnsignedShort: // US (uint16_t) + return "US"; + + case ValueRepresentation_UnlimitedText: // UT + return "UT"; + + case ValueRepresentation_NotSupported: + return "Not supported"; + + default: + throw OrthancException(ErrorCode_ParameterOutOfRange); + } + } + + Encoding StringToEncoding(const char* encoding) { std::string s(encoding);
--- a/Resources/Orthanc/Core/Enumerations.h Thu Mar 22 17:32:05 2018 +0100 +++ b/Resources/Orthanc/Core/Enumerations.h Sat Mar 24 11:30:05 2018 +0100 @@ -620,6 +620,8 @@ const char* EnumerationToString(DicomVersion version); + const char* EnumerationToString(ValueRepresentation vr); + Encoding StringToEncoding(const char* encoding); ResourceType StringToResourceType(const char* type);
--- a/Resources/Orthanc/Resources/CMake/DcmtkConfiguration.cmake Thu Mar 22 17:32:05 2018 +0100 +++ b/Resources/Orthanc/Resources/CMake/DcmtkConfiguration.cmake Sat Mar 24 11:30:05 2018 +0100 @@ -81,8 +81,18 @@ message(FATAL_ERROR "Error while patching a file") endif() - else (FirstRun()) - message("No need to apply a patch for speed in DCMTK") + else() + message("Applying patch to detect mathematic primitives in DCMTK 3.6.2") + execute_process( + COMMAND ${PATCH_EXECUTABLE} -p0 -N -i + ${ORTHANC_ROOT}/Resources/Patches/dcmtk-3.6.2-cmath.patch + WORKING_DIRECTORY ${CMAKE_BINARY_DIR} + RESULT_VARIABLE Failure + ) + + if (Failure) + message(FATAL_ERROR "Error while patching a file") + endif() endif() else() message("The patches for DCMTK have already been applied") @@ -99,8 +109,6 @@ if ("${CMAKE_SYSTEM_VERSION}" STREQUAL "LinuxStandardBase") SET(DCMTK_ENABLE_CHARSET_CONVERSION "iconv" CACHE STRING "") - SET(HAVE_PROTOTYPE_STD__ISINF 1 CACHE INTERNAL "") - SET(HAVE_PROTOTYPE_STD__ISNAN 1 CACHE INTERNAL "") SET(HAVE_SYS_GETTID 0 CACHE INTERNAL "") execute_process(
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Resources/Orthanc/Resources/Patches/dcmtk-3.6.2-cmath.patch Sat Mar 24 11:30:05 2018 +0100 @@ -0,0 +1,17 @@ +diff -urEb dcmtk-3.6.2.orig/CMake/GenerateDCMTKConfigure.cmake dcmtk-3.6.2/CMake/GenerateDCMTKConfigure.cmake +--- dcmtk-3.6.2.orig/CMake/GenerateDCMTKConfigure.cmake 2018-03-24 11:19:13.705396611 +0100 ++++ dcmtk-3.6.2/CMake/GenerateDCMTKConfigure.cmake 2018-03-24 11:19:33.429286501 +0100 +@@ -571,9 +571,9 @@ + CHECK_FUNCTIONWITHHEADER_EXISTS(isinf "${HEADERS}" HAVE_PROTOTYPE_ISINF) + CHECK_FUNCTIONWITHHEADER_EXISTS(isnan "${HEADERS}" HAVE_PROTOTYPE_ISNAN) + CHECK_FUNCTIONWITHHEADER_EXISTS(finite "${HEADERS}" HAVE_PROTOTYPE_FINITE) +- CHECK_FUNCTIONWITHHEADER_EXISTS(std::isinf "${HEADERS}" HAVE_PROTOTYPE_STD__ISINF) +- CHECK_FUNCTIONWITHHEADER_EXISTS(std::isnan "${HEADERS}" HAVE_PROTOTYPE_STD__ISNAN) +- CHECK_FUNCTIONWITHHEADER_EXISTS(std::finite "${HEADERS}" HAVE_PROTOTYPE_STD__FINITE) ++ CHECK_FUNCTIONWITHHEADER_EXISTS(std::isinf<double> "${HEADERS}" HAVE_PROTOTYPE_STD__ISINF) ++ CHECK_FUNCTIONWITHHEADER_EXISTS(std::isnan<double> "${HEADERS}" HAVE_PROTOTYPE_STD__ISNAN) ++ CHECK_FUNCTIONWITHHEADER_EXISTS(std::finite<double> "${HEADERS}" HAVE_PROTOTYPE_STD__FINITE) + CHECK_FUNCTIONWITHHEADER_EXISTS(flock "${HEADERS}" HAVE_PROTOTYPE_FLOCK) + CHECK_FUNCTIONWITHHEADER_EXISTS(gethostbyname "${HEADERS}" HAVE_PROTOTYPE_GETHOSTBYNAME) + CHECK_FUNCTIONWITHHEADER_EXISTS(gethostbyname_r "${HEADERS}" HAVE_PROTOTYPE_GETHOSTBYNAME_R) +Only in dcmtk-3.6.2/CMake: GenerateDCMTKConfigure.cmake~
--- a/Resources/SyncOrthancFolder.py Thu Mar 22 17:32:05 2018 +0100 +++ b/Resources/SyncOrthancFolder.py Sat Mar 24 11:30:05 2018 +0100 @@ -130,6 +130,7 @@ 'Resources/Patches/dcmtk-3.6.0-mingw64.patch', 'Resources/Patches/dcmtk-3.6.0-speed.patch', 'Resources/Patches/dcmtk-3.6.2-linux-standard-base.patch', + 'Resources/Patches/dcmtk-3.6.2-cmath.patch', 'Resources/ThirdParty/VisualStudio/stdint.h', 'Resources/ThirdParty/base64/base64.cpp', 'Resources/ThirdParty/base64/base64.h',