Mercurial > hg > orthanc
changeset 5816:3f10350b26da
DICOMWeb Json formatter: improve support for ill-formed DS values + DS values are now represented as strings instead of doubles
| author | Alain Mazy <am@orthanc.team> |
|---|---|
| date | Wed, 25 Sep 2024 19:36:43 +0200 |
| parents | 122fd5f97d39 |
| children | 86cd21ef81fb |
| files | NEWS OrthancFramework/Resources/CMake/OrthancFrameworkParameters.cmake OrthancFramework/Sources/DicomParsing/DicomWebJsonVisitor.cpp OrthancFramework/Sources/DicomParsing/DicomWebJsonVisitor.h OrthancFramework/UnitTestsSources/DicomMapTests.cpp OrthancFramework/UnitTestsSources/FromDcmtkTests.cpp |
| diffstat | 6 files changed, 85 insertions(+), 17 deletions(-) [+] |
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--- a/NEWS Wed Sep 25 16:36:04 2024 +0200 +++ b/NEWS Wed Sep 25 19:36:43 2024 +0200 @@ -4,8 +4,19 @@ REST API ----------- +* API version upgraded to 26 * Improved parsing of multiple numerical values in DICOM tags. https://discourse.orthanc-server.org/t/qido-includefield-with-sequences/4746/6 +* POSSIBLE BREAKING-CHANGES: + In DICOMWeb json, the "DS - Decimal String" values were represented by float numbers + and they are now represented as strings to avoid loss of precision when the decimal + number can not be exactly represented as a float. This is based on the DICOMWeb + standard https://dicom.nema.org/medical/dicom/current/output/chtml/part18/sect_F.2.3.html + - DS values can be represented as String or Number in Json. + - For IS, DS, SV and UV, a JSON String representation can be used to preserve the original + format during transformation of the representation, or if needed to avoid losing + precision of a decimal string. + https://discourse.orthanc-server.org/t/dicomwebplugin-does-not-return-series-metadata-properly/5195 Maintenance @@ -26,12 +37,11 @@ - added 2 metrics: orthanc_storage_cache_miss_count & orthanc_storage_cache_hit_count * Upgraded dependencies for static builds: - curl 8.9.0 + - boost 1.86.0 * Added a new fallback when trying to decode a frame: transcode the file using the plugin before decoding the frame. This solves some issues with JP2K Lossy compression: https://discourse.orthanc-server.org/t/decoding-displaying-jpeg2000-lossy-images/5117 * Added a new warning that can be disabled in the configuration: W003_DecoderFailure -* Upgraded dependencies for static builds: - - boost 1.86.0
--- a/OrthancFramework/Resources/CMake/OrthancFrameworkParameters.cmake Wed Sep 25 16:36:04 2024 +0200 +++ b/OrthancFramework/Resources/CMake/OrthancFrameworkParameters.cmake Wed Sep 25 19:36:43 2024 +0200 @@ -39,7 +39,7 @@ # Version of the Orthanc API, can be retrieved from "/system" URI in # order to check whether new URI endpoints are available even if using # the mainline version of Orthanc -set(ORTHANC_API_VERSION "24") +set(ORTHANC_API_VERSION "26") #####################################################################
--- a/OrthancFramework/Sources/DicomParsing/DicomWebJsonVisitor.cpp Wed Sep 25 16:36:04 2024 +0200 +++ b/OrthancFramework/Sources/DicomParsing/DicomWebJsonVisitor.cpp Wed Sep 25 19:36:43 2024 +0200 @@ -28,6 +28,7 @@ #include "../Logging.h" #include "../OrthancException.h" #include "../Toolbox.h" +#include "../SerializationToolbox.h" #include "FromDcmtkBridge.h" #include <boost/math/special_functions/round.hpp> @@ -341,6 +342,31 @@ } } + Json::Value DicomWebJsonVisitor::FormatDecimalString(double value, const std::string& originalString) + { + try + { + long long a = boost::math::llround<double>(value); + + double d = fabs(value - static_cast<double>(a)); + + if (d <= std::numeric_limits<double>::epsilon() * 100.0) + { + return FormatInteger(a); // if the decimal number is an integer, you can represent it as an integer + } + else + { + return Json::Value(originalString); // keep the original string to avoid rounding errors e.g, transforming "0.143" into 0.14299999999999 + } + } + catch (boost::math::rounding_error&) + { + // Can occur if "long long" is too small to receive this value + // (e.g. infinity) + return Json::Value(originalString); + } + } + DicomWebJsonVisitor::DicomWebJsonVisitor() : formatter_(NULL) { @@ -677,14 +703,33 @@ case ValueRepresentation_DecimalString: { std::string t = Toolbox::StripSpaces(tokens[i]); + boost::replace_all(t, ",", "."); // some invalid files uses "," instead of "." + + // remove invalid/useless trailing decimal separator + if (t.size() > 0 && t[t.size()-1] == '.') + { + t.resize(t.size() -1); + } + if (t.empty()) { node[KEY_VALUE].append(Json::nullValue); } else { - double tmp = boost::lexical_cast<double>(t); - node[KEY_VALUE].append(FormatDouble(tmp)); + // https://dicom.nema.org/medical/dicom/current/output/chtml/part18/sect_F.2.3.html + // DS values can be represented as String or Number in Json. + // For IS, DS, SV and UV, a JSON String representation can be used to preserve the original format during transformation of the representation, or if needed to avoid losing precision of a decimal string. + // Since 1.12.5, always use the string repesentation. Before, decimal numbers were represented as double which led to loss of precision (e.g: 0.143 represented as 0.1429999999) + double tmp; + if (SerializationToolbox::ParseDouble(tmp, t)) // make sure that the string contains a valid decimal number + { + node[KEY_VALUE].append(t); + } + else + { + throw boost::bad_lexical_cast(); + } } break;
--- a/OrthancFramework/Sources/DicomParsing/DicomWebJsonVisitor.h Wed Sep 25 16:36:04 2024 +0200 +++ b/OrthancFramework/Sources/DicomParsing/DicomWebJsonVisitor.h Wed Sep 25 19:36:43 2024 +0200 @@ -74,6 +74,8 @@ static Json::Value FormatDouble(double value); + static Json::Value FormatDecimalString(double value, const std::string& originalString); + public: DicomWebJsonVisitor();
--- a/OrthancFramework/UnitTestsSources/DicomMapTests.cpp Wed Sep 25 16:36:04 2024 +0200 +++ b/OrthancFramework/UnitTestsSources/DicomMapTests.cpp Wed Sep 25 19:36:43 2024 +0200 @@ -804,6 +804,7 @@ dicom.ReplacePlainString(DICOM_TAG_PATIENT_NAME, "SB1^SB2^SB3^SB4^SB5"); dicom.ReplacePlainString(DICOM_TAG_IMAGE_ORIENTATION_PATIENT, "1\\2.3\\4"); dicom.ReplacePlainString(DICOM_TAG_IMAGE_POSITION_PATIENT, ""); + dicom.ReplacePlainString(DICOM_TAG_PIXEL_SPACING, "0,143\\0,143"); // seen in https://discourse.orthanc-server.org/t/dicomwebplugin-does-not-return-series-metadata-properly/5195 DicomWebJsonVisitor visitor; dicom.Apply(visitor); @@ -815,10 +816,10 @@ ASSERT_EQ(EnumerationToString(ValueRepresentation_DecimalString), tag["vr"].asString()); ASSERT_EQ(2u, tag.getMemberNames().size()); ASSERT_EQ(3u, value.size()); - ASSERT_EQ(Json::realValue, value[1].type()); - ASSERT_FLOAT_EQ(1.0f, value[0].asFloat()); - ASSERT_FLOAT_EQ(2.3f, value[1].asFloat()); - ASSERT_FLOAT_EQ(4.0f, value[2].asFloat()); + ASSERT_EQ(Json::stringValue, value[1].type()); // since Orthanc 1.12.5, this is now stored as a string + ASSERT_EQ("1", value[0].asString()); + ASSERT_EQ("2.3", value[1].asString()); + ASSERT_EQ("4", value[2].asString()); } { @@ -827,13 +828,23 @@ ASSERT_EQ(1u, tag.getMemberNames().size()); } + { + const Json::Value& tag = visitor.GetResult() ["00280030"]; // PixelSpacing + const Json::Value& value = tag["Value"]; + + ASSERT_EQ(EnumerationToString(ValueRepresentation_DecimalString), tag["vr"].asString()); + ASSERT_EQ(2u, value.size()); + ASSERT_EQ("0.143", value[0].asString()); + ASSERT_EQ("0.143", value[1].asString()); + } + std::string xml; visitor.FormatXml(xml); { DicomMap m; m.FromDicomWeb(visitor.GetResult()); - ASSERT_EQ(3u, m.GetSize()); + ASSERT_EQ(4u, m.GetSize()); std::string s; ASSERT_TRUE(m.LookupStringValue(s, DICOM_TAG_PATIENT_NAME, false)); @@ -869,12 +880,12 @@ ASSERT_EQ(EnumerationToString(ValueRepresentation_DecimalString), tag["vr"].asString()); ASSERT_EQ(2u, tag.getMemberNames().size()); ASSERT_EQ(4u, value.size()); - ASSERT_EQ(Json::realValue, value[0].type()); + ASSERT_EQ(Json::stringValue, value[0].type()); ASSERT_EQ(Json::nullValue, value[1].type()); ASSERT_EQ(Json::nullValue, value[2].type()); - ASSERT_EQ(Json::realValue, value[3].type()); - ASSERT_FLOAT_EQ(1.5f, value[0].asFloat()); - ASSERT_FLOAT_EQ(2.5f, value[3].asFloat()); + ASSERT_EQ(Json::stringValue, value[3].type()); + ASSERT_EQ("1.5", value[0].asString()); + ASSERT_EQ("2.5", value[3].asString()); } std::string xml; @@ -912,8 +923,8 @@ target.FromDicomWeb(visitor.GetResult()); ASSERT_EQ("DS", visitor.GetResult() ["00280030"]["vr"].asString()); - ASSERT_FLOAT_EQ(1.5f, visitor.GetResult() ["00280030"]["Value"][0].asFloat()); - ASSERT_FLOAT_EQ(1.3f, visitor.GetResult() ["00280030"]["Value"][1].asFloat()); + ASSERT_EQ("1.5", visitor.GetResult() ["00280030"]["Value"][0].asString()); + ASSERT_EQ("1.3", visitor.GetResult() ["00280030"]["Value"][1].asString()); std::string s; ASSERT_TRUE(target.LookupStringValue(s, DICOM_TAG_PIXEL_SPACING, false));
--- a/OrthancFramework/UnitTestsSources/FromDcmtkTests.cpp Wed Sep 25 16:36:04 2024 +0200 +++ b/OrthancFramework/UnitTestsSources/FromDcmtkTests.cpp Wed Sep 25 19:36:43 2024 +0200 @@ -2043,7 +2043,7 @@ ASSERT_EQ("DA", visitor.GetResult() ["00080012"]["vr"].asString()); ASSERT_EQ("DA", visitor.GetResult() ["00080012"]["Value"][0].asString()); ASSERT_EQ("DS", visitor.GetResult() ["00101020"]["vr"].asString()); - ASSERT_FLOAT_EQ(42.0f, visitor.GetResult() ["00101020"]["Value"][0].asFloat()); + ASSERT_EQ("42", visitor.GetResult() ["00101020"]["Value"][0].asString()); ASSERT_EQ("DT", visitor.GetResult() ["0008002A"]["vr"].asString()); ASSERT_EQ("DT", visitor.GetResult() ["0008002A"]["Value"][0].asString()); ASSERT_EQ("FL", visitor.GetResult() ["00109431"]["vr"].asString());