diff --git a/cpp/mrd/CMakeLists.txt b/cpp/mrd/CMakeLists.txt index c11f52b6..d67a01c7 100644 --- a/cpp/mrd/CMakeLists.txt +++ b/cpp/mrd/CMakeLists.txt @@ -43,4 +43,3 @@ endif() add_library(mrd_generated OBJECT ${Mrd_GENERATED_SOURCES}) target_link_libraries(mrd_generated ${Mrd_GENERATED_LINK_LIBRARIES}) -target_compile_features(mrd_generated PUBLIC cxx_std_17) diff --git a/cpp/mrd/binary/protocols.cc b/cpp/mrd/binary/protocols.cc index 0c73ba12..933b2caa 100644 --- a/cpp/mrd/binary/protocols.cc +++ b/cpp/mrd/binary/protocols.cc @@ -42,6 +42,7 @@ struct IsTriviallySerializable { IsTriviallySerializable::value && IsTriviallySerializable::value && IsTriviallySerializable::value && + IsTriviallySerializable::value && IsTriviallySerializable::value && IsTriviallySerializable::value && IsTriviallySerializable::value && @@ -57,8 +58,8 @@ struct IsTriviallySerializable { IsTriviallySerializable::value && IsTriviallySerializable::value && IsTriviallySerializable::value && - (sizeof(__T__) == (sizeof(__T__::flags) + sizeof(__T__::idx) + sizeof(__T__::measurement_uid) + sizeof(__T__::scan_counter) + sizeof(__T__::acquisition_time_stamp_ns) + sizeof(__T__::physiology_time_stamp_ns) + sizeof(__T__::channel_order) + sizeof(__T__::discard_pre) + sizeof(__T__::discard_post) + sizeof(__T__::center_sample) + sizeof(__T__::encoding_space_ref) + sizeof(__T__::sample_time_ns) + sizeof(__T__::position) + sizeof(__T__::read_dir) + sizeof(__T__::phase_dir) + sizeof(__T__::slice_dir) + sizeof(__T__::patient_table_position) + sizeof(__T__::user_int) + sizeof(__T__::user_float))) && - offsetof(__T__, flags) < offsetof(__T__, idx) && offsetof(__T__, idx) < offsetof(__T__, measurement_uid) && offsetof(__T__, measurement_uid) < offsetof(__T__, scan_counter) && offsetof(__T__, scan_counter) < offsetof(__T__, acquisition_time_stamp_ns) && offsetof(__T__, acquisition_time_stamp_ns) < offsetof(__T__, physiology_time_stamp_ns) && offsetof(__T__, physiology_time_stamp_ns) < offsetof(__T__, channel_order) && offsetof(__T__, channel_order) < offsetof(__T__, discard_pre) && offsetof(__T__, discard_pre) < offsetof(__T__, discard_post) && offsetof(__T__, discard_post) < offsetof(__T__, center_sample) && offsetof(__T__, center_sample) < offsetof(__T__, encoding_space_ref) && offsetof(__T__, encoding_space_ref) < offsetof(__T__, sample_time_ns) && offsetof(__T__, sample_time_ns) < offsetof(__T__, position) && offsetof(__T__, position) < offsetof(__T__, read_dir) && offsetof(__T__, read_dir) < offsetof(__T__, phase_dir) && offsetof(__T__, phase_dir) < offsetof(__T__, slice_dir) && offsetof(__T__, slice_dir) < offsetof(__T__, patient_table_position) && offsetof(__T__, patient_table_position) < offsetof(__T__, user_int) && offsetof(__T__, user_int) < offsetof(__T__, user_float); + (sizeof(__T__) == (sizeof(__T__::flags) + sizeof(__T__::idx) + sizeof(__T__::measurement_uid) + sizeof(__T__::scan_counter) + sizeof(__T__::acquisition_center_frequency) + sizeof(__T__::acquisition_time_stamp_ns) + sizeof(__T__::physiology_time_stamp_ns) + sizeof(__T__::channel_order) + sizeof(__T__::discard_pre) + sizeof(__T__::discard_post) + sizeof(__T__::center_sample) + sizeof(__T__::encoding_space_ref) + sizeof(__T__::sample_time_ns) + sizeof(__T__::position) + sizeof(__T__::read_dir) + sizeof(__T__::phase_dir) + sizeof(__T__::slice_dir) + sizeof(__T__::patient_table_position) + sizeof(__T__::user_int) + sizeof(__T__::user_float))) && + offsetof(__T__, flags) < offsetof(__T__, idx) && offsetof(__T__, idx) < offsetof(__T__, measurement_uid) && offsetof(__T__, measurement_uid) < offsetof(__T__, scan_counter) && offsetof(__T__, scan_counter) < offsetof(__T__, acquisition_center_frequency) && offsetof(__T__, acquisition_center_frequency) < offsetof(__T__, acquisition_time_stamp_ns) && offsetof(__T__, acquisition_time_stamp_ns) < offsetof(__T__, physiology_time_stamp_ns) && offsetof(__T__, physiology_time_stamp_ns) < offsetof(__T__, channel_order) && offsetof(__T__, channel_order) < offsetof(__T__, discard_pre) && offsetof(__T__, discard_pre) < offsetof(__T__, discard_post) && offsetof(__T__, discard_post) < offsetof(__T__, center_sample) && offsetof(__T__, center_sample) < offsetof(__T__, encoding_space_ref) && offsetof(__T__, encoding_space_ref) < offsetof(__T__, sample_time_ns) && offsetof(__T__, sample_time_ns) < offsetof(__T__, position) && offsetof(__T__, position) < offsetof(__T__, read_dir) && offsetof(__T__, read_dir) < offsetof(__T__, phase_dir) && offsetof(__T__, phase_dir) < offsetof(__T__, slice_dir) && offsetof(__T__, slice_dir) < offsetof(__T__, patient_table_position) && offsetof(__T__, patient_table_position) < offsetof(__T__, user_int) && offsetof(__T__, user_int) < offsetof(__T__, user_float); }; template <> @@ -68,9 +69,10 @@ struct IsTriviallySerializable { std::is_standard_layout_v<__T__> && IsTriviallySerializable::value && IsTriviallySerializable::value && + IsTriviallySerializable::value && IsTriviallySerializable::value && - (sizeof(__T__) == (sizeof(__T__::head) + sizeof(__T__::data) + sizeof(__T__::trajectory))) && - offsetof(__T__, head) < offsetof(__T__, data) && offsetof(__T__, data) < offsetof(__T__, trajectory); + (sizeof(__T__) == (sizeof(__T__::head) + sizeof(__T__::data) + sizeof(__T__::phase) + sizeof(__T__::trajectory))) && + offsetof(__T__, head) < offsetof(__T__, data) && offsetof(__T__, data) < offsetof(__T__, phase) && offsetof(__T__, phase) < offsetof(__T__, trajectory); }; template <> @@ -1026,6 +1028,24 @@ namespace { yardl::binary::ReadNDArray, yardl::binary::ReadFloatingPoint, 2>(stream, value); } +[[maybe_unused]] void WriteAcquisitionPhase(yardl::binary::CodedOutputStream& stream, mrd::AcquisitionPhase const& value) { + if constexpr (yardl::binary::IsTriviallySerializable::value) { + yardl::binary::WriteTriviallySerializable(stream, value); + return; + } + + yardl::binary::WriteNDArray(stream, value); +} + +[[maybe_unused]] void ReadAcquisitionPhase(yardl::binary::CodedInputStream& stream, mrd::AcquisitionPhase& value) { + if constexpr (yardl::binary::IsTriviallySerializable::value) { + yardl::binary::ReadTriviallySerializable(stream, value); + return; + } + + yardl::binary::ReadNDArray(stream, value); +} + [[maybe_unused]] void WriteTrajectoryData(yardl::binary::CodedOutputStream& stream, mrd::TrajectoryData const& value) { if constexpr (yardl::binary::IsTriviallySerializable::value) { yardl::binary::WriteTriviallySerializable(stream, value); @@ -1054,6 +1074,7 @@ namespace { mrd::binary::WriteEncodingCounters(stream, value.idx); yardl::binary::WriteInteger(stream, value.measurement_uid); yardl::binary::WriteOptional(stream, value.scan_counter); + yardl::binary::WriteOptional(stream, value.acquisition_center_frequency); yardl::binary::WriteOptional(stream, value.acquisition_time_stamp_ns); yardl::binary::WriteVector(stream, value.physiology_time_stamp_ns); yardl::binary::WriteVector(stream, value.channel_order); @@ -1081,6 +1102,7 @@ namespace { mrd::binary::ReadEncodingCounters(stream, value.idx); yardl::binary::ReadInteger(stream, value.measurement_uid); yardl::binary::ReadOptional(stream, value.scan_counter); + yardl::binary::ReadOptional(stream, value.acquisition_center_frequency); yardl::binary::ReadOptional(stream, value.acquisition_time_stamp_ns); yardl::binary::ReadVector(stream, value.physiology_time_stamp_ns); yardl::binary::ReadVector(stream, value.channel_order); @@ -1106,6 +1128,7 @@ namespace { mrd::binary::WriteAcquisitionHeader(stream, value.head); mrd::binary::WriteAcquisitionData(stream, value.data); + yardl::binary::WriteOptional(stream, value.phase); mrd::binary::WriteTrajectoryData(stream, value.trajectory); } @@ -1117,6 +1140,7 @@ namespace { mrd::binary::ReadAcquisitionHeader(stream, value.head); mrd::binary::ReadAcquisitionData(stream, value.data); + yardl::binary::ReadOptional(stream, value.phase); mrd::binary::ReadTrajectoryData(stream, value.trajectory); } diff --git a/cpp/mrd/hdf5/protocols.cc b/cpp/mrd/hdf5/protocols.cc index b333f6fd..2aad52d5 100644 --- a/cpp/mrd/hdf5/protocols.cc +++ b/cpp/mrd/hdf5/protocols.cc @@ -799,6 +799,7 @@ struct _Inner_AcquisitionHeader { idx(o.idx), measurement_uid(o.measurement_uid), scan_counter(o.scan_counter), + acquisition_center_frequency(o.acquisition_center_frequency), acquisition_time_stamp_ns(o.acquisition_time_stamp_ns), physiology_time_stamp_ns(o.physiology_time_stamp_ns), channel_order(o.channel_order), @@ -821,6 +822,7 @@ struct _Inner_AcquisitionHeader { yardl::hdf5::ToOuter(idx, o.idx); yardl::hdf5::ToOuter(measurement_uid, o.measurement_uid); yardl::hdf5::ToOuter(scan_counter, o.scan_counter); + yardl::hdf5::ToOuter(acquisition_center_frequency, o.acquisition_center_frequency); yardl::hdf5::ToOuter(acquisition_time_stamp_ns, o.acquisition_time_stamp_ns); yardl::hdf5::ToOuter(physiology_time_stamp_ns, o.physiology_time_stamp_ns); yardl::hdf5::ToOuter(channel_order, o.channel_order); @@ -842,6 +844,7 @@ struct _Inner_AcquisitionHeader { mrd::hdf5::_Inner_EncodingCounters idx; uint32_t measurement_uid; yardl::hdf5::InnerOptional scan_counter; + yardl::hdf5::InnerOptional acquisition_center_frequency; yardl::hdf5::InnerOptional acquisition_time_stamp_ns; yardl::hdf5::InnerVlen physiology_time_stamp_ns; yardl::hdf5::InnerVlen channel_order; @@ -864,17 +867,20 @@ struct _Inner_Acquisition { _Inner_Acquisition(mrd::Acquisition const& o) : head(o.head), data(o.data), + phase(o.phase), trajectory(o.trajectory) { } void ToOuter (mrd::Acquisition& o) const { yardl::hdf5::ToOuter(head, o.head); yardl::hdf5::ToOuter(data, o.data); + yardl::hdf5::ToOuter(phase, o.phase); yardl::hdf5::ToOuter(trajectory, o.trajectory); } mrd::hdf5::_Inner_AcquisitionHeader head; yardl::hdf5::InnerNdArray, std::complex, 2> data; + yardl::hdf5::InnerOptional, mrd::AcquisitionPhase> phase; yardl::hdf5::InnerNdArray trajectory; }; @@ -1710,6 +1716,7 @@ struct _Inner_ImageArray { t.insertMember("idx", HOFFSET(RecordType, idx), mrd::hdf5::GetEncodingCountersHdf5Ddl()); t.insertMember("measurementUid", HOFFSET(RecordType, measurement_uid), H5::PredType::NATIVE_UINT32); t.insertMember("scanCounter", HOFFSET(RecordType, scan_counter), yardl::hdf5::OptionalTypeDdl(H5::PredType::NATIVE_UINT32)); + t.insertMember("acquisitionCenterFrequency", HOFFSET(RecordType, acquisition_center_frequency), yardl::hdf5::OptionalTypeDdl(H5::PredType::NATIVE_UINT64)); t.insertMember("acquisitionTimeStampNs", HOFFSET(RecordType, acquisition_time_stamp_ns), yardl::hdf5::OptionalTypeDdl(H5::PredType::NATIVE_UINT64)); t.insertMember("physiologyTimeStampNs", HOFFSET(RecordType, physiology_time_stamp_ns), yardl::hdf5::InnerVlenDdl(H5::PredType::NATIVE_UINT64)); t.insertMember("channelOrder", HOFFSET(RecordType, channel_order), yardl::hdf5::InnerVlenDdl(H5::PredType::NATIVE_UINT32)); @@ -1733,6 +1740,7 @@ struct _Inner_ImageArray { H5::CompType t(sizeof(RecordType)); t.insertMember("head", HOFFSET(RecordType, head), mrd::hdf5::GetAcquisitionHeaderHdf5Ddl()); t.insertMember("data", HOFFSET(RecordType, data), yardl::hdf5::NDArrayDdl, std::complex, 2>(yardl::hdf5::ComplexTypeDdl())); + t.insertMember("phase", HOFFSET(RecordType, phase), yardl::hdf5::OptionalTypeDdl, mrd::AcquisitionPhase>(yardl::hdf5::InnerVlenDdl(H5::PredType::NATIVE_FLOAT))); t.insertMember("trajectory", HOFFSET(RecordType, trajectory), yardl::hdf5::NDArrayDdl(H5::PredType::NATIVE_FLOAT)); return t; } diff --git a/cpp/mrd/ndjson/protocols.cc b/cpp/mrd/ndjson/protocols.cc index 70357602..724e9773 100644 --- a/cpp/mrd/ndjson/protocols.cc +++ b/cpp/mrd/ndjson/protocols.cc @@ -796,6 +796,9 @@ void to_json(ordered_json& j, mrd::AcquisitionHeader const& value) { if (yardl::ndjson::ShouldSerializeFieldValue(value.scan_counter)) { j.push_back({"scanCounter", value.scan_counter}); } + if (yardl::ndjson::ShouldSerializeFieldValue(value.acquisition_center_frequency)) { + j.push_back({"acquisitionCenterFrequency", value.acquisition_center_frequency}); + } if (yardl::ndjson::ShouldSerializeFieldValue(value.acquisition_time_stamp_ns)) { j.push_back({"acquisitionTimeStampNs", value.acquisition_time_stamp_ns}); } @@ -856,6 +859,9 @@ void from_json(ordered_json const& j, mrd::AcquisitionHeader& value) { if (auto it = j.find("scanCounter"); it != j.end()) { it->get_to(value.scan_counter); } + if (auto it = j.find("acquisitionCenterFrequency"); it != j.end()) { + it->get_to(value.acquisition_center_frequency); + } if (auto it = j.find("acquisitionTimeStampNs"); it != j.end()) { it->get_to(value.acquisition_time_stamp_ns); } @@ -911,6 +917,9 @@ void to_json(ordered_json& j, mrd::Acquisition const& value) { if (yardl::ndjson::ShouldSerializeFieldValue(value.data)) { j.push_back({"data", value.data}); } + if (yardl::ndjson::ShouldSerializeFieldValue(value.phase)) { + j.push_back({"phase", value.phase}); + } if (yardl::ndjson::ShouldSerializeFieldValue(value.trajectory)) { j.push_back({"trajectory", value.trajectory}); } @@ -923,6 +932,9 @@ void from_json(ordered_json const& j, mrd::Acquisition& value) { if (auto it = j.find("data"); it != j.end()) { it->get_to(value.data); } + if (auto it = j.find("phase"); it != j.end()) { + it->get_to(value.phase); + } if (auto it = j.find("trajectory"); it != j.end()) { it->get_to(value.trajectory); } diff --git a/cpp/mrd/protocols.cc b/cpp/mrd/protocols.cc index 0040dccc..2caed957 100644 --- a/cpp/mrd/protocols.cc +++ b/cpp/mrd/protocols.cc @@ -39,7 +39,7 @@ void MrdReaderBaseInvalidState(uint8_t attempted, uint8_t current) { } // namespace -std::string MrdWriterBase::schema_ = 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std::vector MrdWriterBase::previous_schemas_ = { }; diff --git a/cpp/mrd/types.h b/cpp/mrd/types.h index 6153d206..6c6734d3 100644 --- a/cpp/mrd/types.h +++ b/cpp/mrd/types.h @@ -88,6 +88,8 @@ struct EncodingCounters { using AcquisitionData = yardl::NDArray, 2>; +using AcquisitionPhase = yardl::NDArray; + using TrajectoryData = yardl::NDArray; struct AcquisitionHeader { @@ -99,6 +101,8 @@ struct AcquisitionHeader { uint32_t measurement_uid{}; // Zero-indexed incrementing counter for readouts std::optional scan_counter{}; + // Acquisition center frequency in Hz + std::optional acquisition_center_frequency{}; // Clock time stamp (e.g. nanoseconds since midnight) std::optional acquisition_time_stamp_ns{}; // Time stamps relative to physiological triggering in nanoseconds @@ -137,6 +141,7 @@ struct AcquisitionHeader { idx == other.idx && measurement_uid == other.measurement_uid && scan_counter == other.scan_counter && + acquisition_center_frequency == other.acquisition_center_frequency && acquisition_time_stamp_ns == other.acquisition_time_stamp_ns && physiology_time_stamp_ns == other.physiology_time_stamp_ns && channel_order == other.channel_order && @@ -164,6 +169,8 @@ struct Acquisition { mrd::AcquisitionHeader head{}; // Raw k-space samples array mrd::AcquisitionData data{}; + // Phase offset array + std::optional phase{}; // Trajectory array mrd::TrajectoryData trajectory{}; @@ -190,6 +197,7 @@ struct Acquisition { bool operator==(const Acquisition& other) const { return head == other.head && data == other.data && + phase == other.phase && trajectory == other.trajectory; } diff --git a/cpp/mrd/yardl/detail/ndarray/impl.h b/cpp/mrd/yardl/detail/ndarray/impl.h index adef8090..53a966be 100644 --- a/cpp/mrd/yardl/detail/ndarray/impl.h +++ b/cpp/mrd/yardl/detail/ndarray/impl.h @@ -2,23 +2,10 @@ #include -#if __has_include() -#include -#else -#include -#endif - -#if XTENSOR_VERSION_MAJOR == 0 && XTENSOR_VERSION_MINOR <= 25 #include #include #include #include -#else -#include -#include -#include -#include -#endif namespace yardl { diff --git a/matlab/toolbox/+mrd/+binary/AcquisitionHeaderSerializer.m b/matlab/toolbox/+mrd/+binary/AcquisitionHeaderSerializer.m index 176900b5..00dffda9 100644 --- a/matlab/toolbox/+mrd/+binary/AcquisitionHeaderSerializer.m +++ b/matlab/toolbox/+mrd/+binary/AcquisitionHeaderSerializer.m @@ -8,20 +8,21 @@ field_serializers{3} = yardl.binary.Uint32Serializer; field_serializers{4} = yardl.binary.OptionalSerializer(yardl.binary.Uint32Serializer); field_serializers{5} = yardl.binary.OptionalSerializer(yardl.binary.Uint64Serializer); - field_serializers{6} = yardl.binary.VectorSerializer(yardl.binary.Uint64Serializer); - field_serializers{7} = yardl.binary.VectorSerializer(yardl.binary.Uint32Serializer); - field_serializers{8} = yardl.binary.OptionalSerializer(yardl.binary.Uint32Serializer); + field_serializers{6} = yardl.binary.OptionalSerializer(yardl.binary.Uint64Serializer); + field_serializers{7} = yardl.binary.VectorSerializer(yardl.binary.Uint64Serializer); + field_serializers{8} = yardl.binary.VectorSerializer(yardl.binary.Uint32Serializer); field_serializers{9} = yardl.binary.OptionalSerializer(yardl.binary.Uint32Serializer); field_serializers{10} = yardl.binary.OptionalSerializer(yardl.binary.Uint32Serializer); field_serializers{11} = yardl.binary.OptionalSerializer(yardl.binary.Uint32Serializer); - field_serializers{12} = yardl.binary.OptionalSerializer(yardl.binary.Uint64Serializer); - field_serializers{13} = yardl.binary.FixedNDArraySerializer(yardl.binary.Float32Serializer, [3]); + field_serializers{12} = yardl.binary.OptionalSerializer(yardl.binary.Uint32Serializer); + field_serializers{13} = yardl.binary.OptionalSerializer(yardl.binary.Uint64Serializer); field_serializers{14} = yardl.binary.FixedNDArraySerializer(yardl.binary.Float32Serializer, [3]); field_serializers{15} = yardl.binary.FixedNDArraySerializer(yardl.binary.Float32Serializer, [3]); field_serializers{16} = yardl.binary.FixedNDArraySerializer(yardl.binary.Float32Serializer, [3]); field_serializers{17} = yardl.binary.FixedNDArraySerializer(yardl.binary.Float32Serializer, [3]); - field_serializers{18} = yardl.binary.VectorSerializer(yardl.binary.Int32Serializer); - field_serializers{19} = yardl.binary.VectorSerializer(yardl.binary.Float32Serializer); + field_serializers{18} = yardl.binary.FixedNDArraySerializer(yardl.binary.Float32Serializer, [3]); + field_serializers{19} = yardl.binary.VectorSerializer(yardl.binary.Int32Serializer); + field_serializers{20} = yardl.binary.VectorSerializer(yardl.binary.Float32Serializer); self@yardl.binary.RecordSerializer('mrd.AcquisitionHeader', field_serializers); end @@ -31,12 +32,12 @@ function write(self, outstream, value) outstream (1,1) yardl.binary.CodedOutputStream value (1,1) mrd.AcquisitionHeader end - self.write_(outstream, value.flags, value.idx, value.measurement_uid, value.scan_counter, value.acquisition_time_stamp_ns, value.physiology_time_stamp_ns, value.channel_order, value.discard_pre, value.discard_post, value.center_sample, value.encoding_space_ref, value.sample_time_ns, value.position, value.read_dir, value.phase_dir, value.slice_dir, value.patient_table_position, value.user_int, value.user_float); + self.write_(outstream, value.flags, value.idx, value.measurement_uid, value.scan_counter, value.acquisition_center_frequency, value.acquisition_time_stamp_ns, value.physiology_time_stamp_ns, value.channel_order, value.discard_pre, value.discard_post, value.center_sample, value.encoding_space_ref, value.sample_time_ns, value.position, value.read_dir, value.phase_dir, value.slice_dir, value.patient_table_position, value.user_int, value.user_float); end function value = read(self, instream) fields = self.read_(instream); - value = mrd.AcquisitionHeader(flags=fields{1}, idx=fields{2}, measurement_uid=fields{3}, scan_counter=fields{4}, acquisition_time_stamp_ns=fields{5}, physiology_time_stamp_ns=fields{6}, channel_order=fields{7}, discard_pre=fields{8}, discard_post=fields{9}, center_sample=fields{10}, encoding_space_ref=fields{11}, sample_time_ns=fields{12}, position=fields{13}, read_dir=fields{14}, phase_dir=fields{15}, slice_dir=fields{16}, patient_table_position=fields{17}, user_int=fields{18}, user_float=fields{19}); + value = mrd.AcquisitionHeader(flags=fields{1}, idx=fields{2}, measurement_uid=fields{3}, scan_counter=fields{4}, acquisition_center_frequency=fields{5}, acquisition_time_stamp_ns=fields{6}, physiology_time_stamp_ns=fields{7}, channel_order=fields{8}, discard_pre=fields{9}, discard_post=fields{10}, center_sample=fields{11}, encoding_space_ref=fields{12}, sample_time_ns=fields{13}, position=fields{14}, read_dir=fields{15}, phase_dir=fields{16}, slice_dir=fields{17}, patient_table_position=fields{18}, user_int=fields{19}, user_float=fields{20}); end end end diff --git a/matlab/toolbox/+mrd/+binary/AcquisitionSerializer.m b/matlab/toolbox/+mrd/+binary/AcquisitionSerializer.m index 8191a748..d845be54 100644 --- a/matlab/toolbox/+mrd/+binary/AcquisitionSerializer.m +++ b/matlab/toolbox/+mrd/+binary/AcquisitionSerializer.m @@ -5,7 +5,8 @@ function self = AcquisitionSerializer() field_serializers{1} = mrd.binary.AcquisitionHeaderSerializer(); field_serializers{2} = yardl.binary.NDArraySerializer(yardl.binary.Complexfloat32Serializer, 2); - field_serializers{3} = yardl.binary.NDArraySerializer(yardl.binary.Float32Serializer, 2); + field_serializers{3} = yardl.binary.OptionalSerializer(yardl.binary.NDArraySerializer(yardl.binary.Float32Serializer, 1)); + field_serializers{4} = yardl.binary.NDArraySerializer(yardl.binary.Float32Serializer, 2); self@yardl.binary.RecordSerializer('mrd.Acquisition', field_serializers); end @@ -15,12 +16,12 @@ function write(self, outstream, value) outstream (1,1) yardl.binary.CodedOutputStream value (1,1) mrd.Acquisition end - self.write_(outstream, value.head, value.data, value.trajectory); + self.write_(outstream, value.head, value.data, value.phase, value.trajectory); end function value = read(self, instream) fields = self.read_(instream); - value = mrd.Acquisition(head=fields{1}, data=fields{2}, trajectory=fields{3}); + value = mrd.Acquisition(head=fields{1}, data=fields{2}, phase=fields{3}, trajectory=fields{4}); end end end diff --git a/matlab/toolbox/+mrd/Acquisition.m b/matlab/toolbox/+mrd/Acquisition.m index c2c0bdad..280e2125 100644 --- a/matlab/toolbox/+mrd/Acquisition.m +++ b/matlab/toolbox/+mrd/Acquisition.m @@ -6,6 +6,8 @@ head % Raw k-space samples array data + % Phase offset array + phase % Trajectory array trajectory end @@ -15,10 +17,12 @@ arguments kwargs.head = mrd.AcquisitionHeader(); kwargs.data = single.empty(); + kwargs.phase = yardl.None; kwargs.trajectory = single.empty(); end self.head = kwargs.head; self.data = kwargs.data; + self.phase = kwargs.phase; self.trajectory = kwargs.trajectory; end @@ -53,6 +57,7 @@ isa(other, "mrd.Acquisition") && ... isequal({self.head}, {other.head}) && ... isequal({self.data}, {other.data}) && ... + isequal({self.phase}, {other.phase}) && ... isequal({self.trajectory}, {other.trajectory}); end diff --git a/matlab/toolbox/+mrd/AcquisitionHeader.m b/matlab/toolbox/+mrd/AcquisitionHeader.m index 1a40e09d..0a2299ad 100644 --- a/matlab/toolbox/+mrd/AcquisitionHeader.m +++ b/matlab/toolbox/+mrd/AcquisitionHeader.m @@ -10,6 +10,8 @@ measurement_uid % Zero-indexed incrementing counter for readouts scan_counter + % Acquisition center frequency in Hz + acquisition_center_frequency % Clock time stamp (e.g. nanoseconds since midnight) acquisition_time_stamp_ns % Time stamps relative to physiological triggering in nanoseconds @@ -51,6 +53,7 @@ kwargs.idx = mrd.EncodingCounters(); kwargs.measurement_uid = uint32(0); kwargs.scan_counter = yardl.None; + kwargs.acquisition_center_frequency = yardl.None; kwargs.acquisition_time_stamp_ns = yardl.None; kwargs.physiology_time_stamp_ns = uint64.empty(); kwargs.channel_order = uint32.empty(); @@ -71,6 +74,7 @@ self.idx = kwargs.idx; self.measurement_uid = kwargs.measurement_uid; self.scan_counter = kwargs.scan_counter; + self.acquisition_center_frequency = kwargs.acquisition_center_frequency; self.acquisition_time_stamp_ns = kwargs.acquisition_time_stamp_ns; self.physiology_time_stamp_ns = kwargs.physiology_time_stamp_ns; self.channel_order = kwargs.channel_order; @@ -95,6 +99,7 @@ isequal({self.idx}, {other.idx}) && ... isequal({self.measurement_uid}, {other.measurement_uid}) && ... isequal({self.scan_counter}, {other.scan_counter}) && ... + isequal({self.acquisition_center_frequency}, {other.acquisition_center_frequency}) && ... isequal({self.acquisition_time_stamp_ns}, {other.acquisition_time_stamp_ns}) && ... isequal({self.physiology_time_stamp_ns}, {other.physiology_time_stamp_ns}) && ... isequal({self.channel_order}, {other.channel_order}) && ... diff --git a/matlab/toolbox/+mrd/MrdWriterBase.m b/matlab/toolbox/+mrd/MrdWriterBase.m index 4057451e..3c49e67d 100644 --- a/matlab/toolbox/+mrd/MrdWriterBase.m +++ b/matlab/toolbox/+mrd/MrdWriterBase.m @@ -51,7 +51,7 @@ function end_data(self) methods (Static) function res = schema() - res = string('{"protocol":{"name":"Mrd","sequence":[{"name":"header","type":[null,"Mrd.Header"]},{"name":"data","type":{"stream":{"items":"Mrd.StreamItem"}}}]},"types":[{"name":"AccelerationFactorType","fields":[{"name":"kspaceEncodingStep1","type":"uint32"},{"name":"kspaceEncodingStep2","type":"uint32"}]},{"name":"Acquisition","fields":[{"name":"head","type":"Mrd.AcquisitionHeader"},{"name":"data","type":"Mrd.AcquisitionData"},{"name":"trajectory","type":"Mrd.TrajectoryData"}]},{"name":"Acquisition","fields":[{"name":"head","type":"Mrd.AcquisitionHeader"},{"name":"data","type":"Mrd.AcquisitionData"},{"name":"trajectory","type":"Mrd.TrajectoryData"}]},{"name":"AcquisitionBucket","fields":[{"name":"data","type":{"vector":{"items":"Mrd.Acquisition"}}},{"name":"ref","type":{"vector":{"items":"Mrd.Acquisition"}}},{"name":"datastats","type":{"vector":{"items":"Mrd.EncodingLimitsType"}}},{"name":"refstats","type":{"vector":{"items":"Mrd.EncodingLimitsType"}}},{"name":"waveforms","type":{"vector":{"items":"Mrd.WaveformUint32"}}}]},{"name":"AcquisitionData","type":{"array":{"items":"complexfloat32","dimensions":[{"name":"coils"},{"name":"samples"}]}}},{"name":"AcquisitionFlags","base":"uint64","values":[{"symbol":"firstInEncodeStep1","value":1},{"symbol":"lastInEncodeStep1","value":2},{"symbol":"firstInEncodeStep2","value":4},{"symbol":"lastInEncodeStep2","value":8},{"symbol":"firstInAverage","value":16},{"symbol":"lastInAverage","value":32},{"symbol":"firstInSlice","value":64},{"symbol":"lastInSlice","value":128},{"symbol":"firstInContrast","value":256},{"symbol":"lastInContrast","value":512},{"symbol":"firstInPhase","value":1024},{"symbol":"lastInPhase","value":2048},{"symbol":"firstInRepetition","value":4096},{"symbol":"lastInRepetition","value":8192},{"symbol":"firstInSet","value":16384},{"symbol":"lastInSet","value":32768},{"symbol":"firstInSegment","value":65536},{"symbol":"lastInSegment","value":131072},{"symbol":"isNoiseMeasurement","value":262144},{"symbol":"isParallelCalibration","value":524288},{"symbol":"isParallelCalibrationAndImaging","value":1048576},{"symbol":"isReverse","value":2097152},{"symbol":"isNavigationData","value":4194304},{"symbol":"isPhasecorrData","value":8388608},{"symbol":"lastInMeasurement","value":16777216},{"symbol":"isHpfeedbackData","value":33554432},{"symbol":"isDummyscanData","value":67108864},{"symbol":"isRtfeedbackData","value":134217728},{"symbol":"isSurfacecoilcorrectionscanData","value":268435456},{"symbol":"isPhaseStabilizationReference","value":536870912},{"symbol":"isPhaseStabilization","value":1073741824}]},{"name":"AcquisitionHeader","fields":[{"name":"flags","type":"Mrd.AcquisitionFlags"},{"name":"idx","type":"Mrd.EncodingCounters"},{"name":"measurementUid","type":"uint32"},{"name":"scanCounter","type":[null,"uint32"]},{"name":"acquisitionTimeStampNs","type":[null,"uint64"]},{"name":"physiologyTimeStampNs","type":{"vector":{"items":"uint64"}}},{"name":"channelOrder","type":{"vector":{"items":"uint32"}}},{"name":"discardPre","type":[null,"uint32"]},{"name":"discardPost","type":[null,"uint32"]},{"name":"centerSample","type":[null,"uint32"]},{"name":"encodingSpaceRef","type":[null,"uint32"]},{"name":"sampleTimeNs","type":[null,"uint64"]},{"name":"position","type":{"array":{"items":"float32","dimensions":[{"length":3}]}}},{"name":"readDir","type":{"array":{"items":"float32","dimensions":[{"length":3}]}}},{"name":"phaseDir","type":{"array":{"items":"float32","dimensions":[{"length":3}]}}},{"name":"sliceDir","type":{"array":{"items":"float32","dimensions":[{"length":3}]}}},{"name":"patientTablePosition","type":{"array":{"items":"float32","dimensions":[{"length":3}]}}},{"name":"userInt","type":{"vector":{"items":"int32"}}},{"name":"userFloat","type":{"vector":{"items":"float32"}}}]},{"name":"AcquisitionSystemInformationType","fields":[{"name":"systemVendor","type":[null,"string"]},{"name":"systemModel","type":[null,"string"]},{"name":"systemFieldStrengthT","type":[null,"float32"]},{"name":"relativeReceiverNoiseBandwidth","type":[null,"float32"]},{"name":"receiverChannels","type":[null,"uint32"]},{"name":"coilLabel","type":{"vector":{"items":"Mrd.CoilLabelType"}}},{"name":"institutionName","type":[null,"string"]},{"name":"stationName","type":[null,"string"]},{"name":"deviceID","type":[null,"string"]},{"name":"deviceSerialNumber","type":[null,"string"]}]},{"name":"Array","typeParameters":["T"],"type":{"array":{"items":"T"}}},{"name":"ArrayComplexFloat","type":{"name":"Mrd.Array","typeArguments":["complexfloat32"]}},{"name":"Calibration","values":[{"symbol":"separable2D","value":0},{"symbol":"full3D","value":1},{"symbol":"other","value":2}]},{"name":"CalibrationMode","values":[{"symbol":"noacceleration","value":0},{"symbol":"embedded","value":1},{"symbol":"interleaved","value":2},{"symbol":"separate","value":3},{"symbol":"external","value":4},{"symbol":"other","value":5}]},{"name":"CoilLabelType","fields":[{"name":"coilNumber","type":"uint32"},{"name":"coilName","type":"string"}]},{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end end diff --git a/matlab/toolbox/+yardl/+binary/UnionSerializer.m b/matlab/toolbox/+yardl/+binary/UnionSerializer.m index 57b30ec7..ba935c9b 100644 --- a/matlab/toolbox/+yardl/+binary/UnionSerializer.m +++ b/matlab/toolbox/+yardl/+binary/UnionSerializer.m @@ -1,7 +1,7 @@ % Copyright (c) Microsoft Corporation. % Licensed under the MIT License. -classdef UnionSerializer < yardl.binary.TypeSerializer +classdef UnionSerializer < handle properties (Access=protected) classname_ diff --git a/model/mrd_acquisition.yml b/model/mrd_acquisition.yml index b6c55bd4..8159eee9 100644 --- a/model/mrd_acquisition.yml +++ b/model/mrd_acquisition.yml @@ -62,6 +62,11 @@ AcquisitionData: !array coils: samples: +AcquisitionPhase: !array + items: float + dimensions: + samples: + TrajectoryData: !array items: float dimensions: @@ -78,6 +83,8 @@ AcquisitionHeader: !record measurementUid: uint # Zero-indexed incrementing counter for readouts scanCounter: uint? + # Acquisition center frequency in Hz + acquisitionCenterFrequency: uint64? # Clock time stamp (e.g. nanoseconds since midnight) acquisitionTimeStampNs: uint64? # Time stamps relative to physiological triggering in nanoseconds @@ -117,6 +124,8 @@ Acquisition: !record head: AcquisitionHeader # Raw k-space samples array data: AcquisitionData + # Phase offset array + phase: AcquisitionPhase? # Trajectory array trajectory: TrajectoryData computedFields: @@ -124,4 +133,4 @@ Acquisition: !record samples: size(data, "samples") activeChannels: size(head.channelOrder) trajectoryDimensions: size(trajectory, "basis") - trajectorySamples: size(trajectory, "samples") \ No newline at end of file + trajectorySamples: size(trajectory, "samples") diff --git a/python/mrd/__init__.py b/python/mrd/__init__.py index 52e0c64d..c1fffdd4 100644 --- a/python/mrd/__init__.py +++ b/python/mrd/__init__.py @@ -26,6 +26,7 @@ def _parse_version(version: str) -> _Tuple[int, ...]: AcquisitionData, AcquisitionFlags, AcquisitionHeader, + AcquisitionPhase, AcquisitionSystemInformationType, AnyImage, Array, diff --git a/python/mrd/_binary.py b/python/mrd/_binary.py index 72182920..8c3c7d86 100644 --- a/python/mrd/_binary.py +++ b/python/mrd/_binary.py @@ -632,7 +632,7 @@ def write_numpy(self, stream: CodedOutputStream, value: np.complex64) -> None: stream.write(self._struct, value.real, value.imag) def read(self, stream: CodedInputStream) -> ComplexFloat: - return complex(*stream.read(self._struct)) + return ComplexFloat(*stream.read(self._struct)) def read_numpy(self, stream: CodedInputStream) -> np.complex64: real, imag = stream.read(self._struct) @@ -656,7 +656,7 @@ def write_numpy(self, stream: CodedOutputStream, value: np.complex128) -> None: stream.write(self._struct, value.real, value.imag) def read(self, stream: CodedInputStream) -> ComplexDouble: - return complex(*stream.read(self._struct)) + return ComplexDouble(*stream.read(self._struct)) def read_numpy(self, stream: CodedInputStream) -> np.complex128: real, imag = stream.read(self._struct) @@ -687,7 +687,7 @@ def read(self, stream: CodedInputStream) -> str: return str(view, "utf-8") def read_numpy(self, stream: CodedInputStream) -> np.object_: - return np.object_(self.read(stream)) # pyright: ignore [reportReturnType] + return np.object_(self.read(stream)) string_serializer = StringSerializer() @@ -770,7 +770,7 @@ def read_numpy(self, stream: CodedInputStream) -> np.timedelta64: time_serializer = TimeSerializer() DATETIME_NANOSECONDS_DTYPE = np.dtype("datetime64[ns]") -EPOCH_DATETIME = datetime.datetime.fromtimestamp(0, tz=datetime.timezone.utc) +EPOCH_DATETIME = datetime.datetime.utcfromtimestamp(0) class DateTimeSerializer(TypeSerializer[DateTime, np.datetime64]): @@ -1034,7 +1034,7 @@ def read(self, stream: CodedInputStream) -> list[T]: return [self._element_serializer.read(stream) for _ in range(length)] def read_numpy(self, stream: CodedInputStream) -> np.object_: - return np.object_(self.read(stream)) # pyright: ignore [reportReturnType] + return np.object_(self.read(stream)) TKey = TypeVar("TKey") @@ -1073,7 +1073,7 @@ def read(self, stream: CodedInputStream) -> dict[TKey, TValue]: } def read_numpy(self, stream: CodedInputStream) -> np.object_: - return np.object_(self.read(stream)) # pyright: ignore [reportReturnType] + return np.object_(self.read(stream)) class NDArraySerializerBase( diff --git a/python/mrd/_dtypes.py b/python/mrd/_dtypes.py index 4215d496..58417889 100644 --- a/python/mrd/_dtypes.py +++ b/python/mrd/_dtypes.py @@ -3,7 +3,6 @@ import datetime from types import GenericAlias -from typing import Annotated, Any import sys if sys.version_info >= (3, 10): @@ -16,13 +15,10 @@ def make_get_dtype_func( dtype_map: dict[ - Union[type, GenericAlias, Annotated[Any, Any]], + Union[type, GenericAlias], Union[np.dtype[Any], Callable[[tuple[type, ...]], np.dtype[Any]]], - ], -) -> Callable[ - [Union[type, GenericAlias, Annotated[Any, Any]]], - np.dtype[Any], -]: + ] +) -> Callable[[Union[type, GenericAlias]], np.dtype[Any]]: dtype_map[bool] = np.dtype(np.bool_) dtype_map[yardl.Int8] = np.dtype(np.int8) dtype_map[yardl.UInt8] = np.dtype(np.uint8) @@ -54,7 +50,7 @@ def make_get_dtype_func( def get_dtype_impl( dtype_map: dict[ - Union[type, GenericAlias, Annotated[Any, Any]], + Union[type, GenericAlias], Union[np.dtype[Any], Callable[[tuple[type, ...]], np.dtype[Any]]], ], t: Union[type, GenericAlias], @@ -69,8 +65,7 @@ def get_dtype_impl( origin = get_origin(t) if origin == Union or ( - sys.version_info >= (3, 10) - and isinstance(t, UnionType) # pyright: ignore[reportUnnecessaryIsInstance] + sys.version_info >= (3, 10) and isinstance(t, UnionType) ): return _get_union_dtype(get_args(t)) diff --git a/python/mrd/_ndjson.py b/python/mrd/_ndjson.py index 427708e3..7cb67c1d 100644 --- a/python/mrd/_ndjson.py +++ b/python/mrd/_ndjson.py @@ -568,7 +568,7 @@ def from_json(self, json_object: object) -> str: return cast(str, json_object) def from_json_to_numpy(self, json_object: object) -> np.object_: - return np.object_(json_object) # pyright: ignore [reportReturnType] + return np.object_(json_object) string_converter = StringConverter() diff --git a/python/mrd/binary.py b/python/mrd/binary.py index c8321d8e..a90cda9c 100644 --- a/python/mrd/binary.py +++ b/python/mrd/binary.py @@ -103,38 +103,38 @@ def read(self, stream: _binary.CodedInputStream) -> EncodingCounters: class AcquisitionHeaderSerializer(_binary.RecordSerializer[AcquisitionHeader]): def __init__(self) -> None: - super().__init__([("flags", _binary.EnumSerializer(_binary.uint64_serializer, AcquisitionFlags)), ("idx", EncodingCountersSerializer()), ("measurement_uid", _binary.uint32_serializer), ("scan_counter", _binary.OptionalSerializer(_binary.uint32_serializer)), ("acquisition_time_stamp_ns", _binary.OptionalSerializer(_binary.uint64_serializer)), ("physiology_time_stamp_ns", _binary.VectorSerializer(_binary.uint64_serializer)), ("channel_order", _binary.VectorSerializer(_binary.uint32_serializer)), ("discard_pre", _binary.OptionalSerializer(_binary.uint32_serializer)), ("discard_post", _binary.OptionalSerializer(_binary.uint32_serializer)), ("center_sample", _binary.OptionalSerializer(_binary.uint32_serializer)), ("encoding_space_ref", _binary.OptionalSerializer(_binary.uint32_serializer)), ("sample_time_ns", _binary.OptionalSerializer(_binary.uint64_serializer)), ("position", _binary.FixedNDArraySerializer(_binary.float32_serializer, (3,))), ("read_dir", _binary.FixedNDArraySerializer(_binary.float32_serializer, (3,))), ("phase_dir", _binary.FixedNDArraySerializer(_binary.float32_serializer, (3,))), ("slice_dir", _binary.FixedNDArraySerializer(_binary.float32_serializer, (3,))), ("patient_table_position", _binary.FixedNDArraySerializer(_binary.float32_serializer, (3,))), ("user_int", _binary.VectorSerializer(_binary.int32_serializer)), ("user_float", _binary.VectorSerializer(_binary.float32_serializer))]) + super().__init__([("flags", _binary.EnumSerializer(_binary.uint64_serializer, AcquisitionFlags)), ("idx", EncodingCountersSerializer()), ("measurement_uid", _binary.uint32_serializer), ("scan_counter", _binary.OptionalSerializer(_binary.uint32_serializer)), ("acquisition_center_frequency", _binary.OptionalSerializer(_binary.uint64_serializer)), ("acquisition_time_stamp_ns", _binary.OptionalSerializer(_binary.uint64_serializer)), ("physiology_time_stamp_ns", _binary.VectorSerializer(_binary.uint64_serializer)), ("channel_order", _binary.VectorSerializer(_binary.uint32_serializer)), ("discard_pre", _binary.OptionalSerializer(_binary.uint32_serializer)), ("discard_post", _binary.OptionalSerializer(_binary.uint32_serializer)), ("center_sample", _binary.OptionalSerializer(_binary.uint32_serializer)), ("encoding_space_ref", _binary.OptionalSerializer(_binary.uint32_serializer)), ("sample_time_ns", _binary.OptionalSerializer(_binary.uint64_serializer)), ("position", _binary.FixedNDArraySerializer(_binary.float32_serializer, (3,))), ("read_dir", _binary.FixedNDArraySerializer(_binary.float32_serializer, (3,))), ("phase_dir", _binary.FixedNDArraySerializer(_binary.float32_serializer, (3,))), ("slice_dir", _binary.FixedNDArraySerializer(_binary.float32_serializer, (3,))), ("patient_table_position", _binary.FixedNDArraySerializer(_binary.float32_serializer, (3,))), ("user_int", _binary.VectorSerializer(_binary.int32_serializer)), ("user_float", _binary.VectorSerializer(_binary.float32_serializer))]) def write(self, stream: _binary.CodedOutputStream, value: AcquisitionHeader) -> None: if isinstance(value, np.void): self.write_numpy(stream, value) return - self._write(stream, value.flags, value.idx, value.measurement_uid, value.scan_counter, value.acquisition_time_stamp_ns, value.physiology_time_stamp_ns, value.channel_order, value.discard_pre, value.discard_post, value.center_sample, value.encoding_space_ref, value.sample_time_ns, value.position, value.read_dir, value.phase_dir, value.slice_dir, value.patient_table_position, value.user_int, value.user_float) + self._write(stream, value.flags, value.idx, value.measurement_uid, value.scan_counter, value.acquisition_center_frequency, value.acquisition_time_stamp_ns, value.physiology_time_stamp_ns, value.channel_order, value.discard_pre, value.discard_post, value.center_sample, value.encoding_space_ref, value.sample_time_ns, value.position, value.read_dir, value.phase_dir, value.slice_dir, value.patient_table_position, value.user_int, value.user_float) def write_numpy(self, stream: _binary.CodedOutputStream, value: np.void) -> None: - self._write(stream, value['flags'], value['idx'], value['measurement_uid'], value['scan_counter'], value['acquisition_time_stamp_ns'], value['physiology_time_stamp_ns'], value['channel_order'], value['discard_pre'], value['discard_post'], value['center_sample'], value['encoding_space_ref'], value['sample_time_ns'], value['position'], value['read_dir'], value['phase_dir'], value['slice_dir'], value['patient_table_position'], value['user_int'], value['user_float']) + self._write(stream, value['flags'], value['idx'], value['measurement_uid'], value['scan_counter'], value['acquisition_center_frequency'], value['acquisition_time_stamp_ns'], value['physiology_time_stamp_ns'], value['channel_order'], value['discard_pre'], value['discard_post'], value['center_sample'], value['encoding_space_ref'], value['sample_time_ns'], value['position'], value['read_dir'], value['phase_dir'], value['slice_dir'], value['patient_table_position'], value['user_int'], value['user_float']) def read(self, stream: _binary.CodedInputStream) -> AcquisitionHeader: field_values = self._read(stream) - return AcquisitionHeader(flags=field_values[0], idx=field_values[1], measurement_uid=field_values[2], scan_counter=field_values[3], acquisition_time_stamp_ns=field_values[4], physiology_time_stamp_ns=field_values[5], channel_order=field_values[6], discard_pre=field_values[7], discard_post=field_values[8], center_sample=field_values[9], encoding_space_ref=field_values[10], sample_time_ns=field_values[11], position=field_values[12], read_dir=field_values[13], phase_dir=field_values[14], slice_dir=field_values[15], patient_table_position=field_values[16], user_int=field_values[17], user_float=field_values[18]) + return AcquisitionHeader(flags=field_values[0], idx=field_values[1], measurement_uid=field_values[2], scan_counter=field_values[3], acquisition_center_frequency=field_values[4], acquisition_time_stamp_ns=field_values[5], physiology_time_stamp_ns=field_values[6], channel_order=field_values[7], discard_pre=field_values[8], discard_post=field_values[9], center_sample=field_values[10], encoding_space_ref=field_values[11], sample_time_ns=field_values[12], position=field_values[13], read_dir=field_values[14], phase_dir=field_values[15], slice_dir=field_values[16], patient_table_position=field_values[17], user_int=field_values[18], user_float=field_values[19]) class AcquisitionSerializer(_binary.RecordSerializer[Acquisition]): def __init__(self) -> None: - super().__init__([("head", AcquisitionHeaderSerializer()), ("data", _binary.NDArraySerializer(_binary.complexfloat32_serializer, 2)), ("trajectory", _binary.NDArraySerializer(_binary.float32_serializer, 2))]) + super().__init__([("head", AcquisitionHeaderSerializer()), ("data", _binary.NDArraySerializer(_binary.complexfloat32_serializer, 2)), ("phase", _binary.OptionalSerializer(_binary.NDArraySerializer(_binary.float32_serializer, 1))), ("trajectory", _binary.NDArraySerializer(_binary.float32_serializer, 2))]) def write(self, stream: _binary.CodedOutputStream, value: Acquisition) -> None: if isinstance(value, np.void): self.write_numpy(stream, value) return - self._write(stream, value.head, value.data, value.trajectory) + self._write(stream, value.head, value.data, value.phase, value.trajectory) def write_numpy(self, stream: _binary.CodedOutputStream, value: np.void) -> None: - self._write(stream, value['head'], value['data'], value['trajectory']) + self._write(stream, value['head'], value['data'], value['phase'], value['trajectory']) def read(self, stream: _binary.CodedInputStream) -> Acquisition: field_values = self._read(stream) - return Acquisition(head=field_values[0], data=field_values[1], trajectory=field_values[2]) + return Acquisition(head=field_values[0], data=field_values[1], phase=field_values[2], trajectory=field_values[3]) class SubjectInformationTypeSerializer(_binary.RecordSerializer[SubjectInformationType]): diff --git a/python/mrd/ndjson.py b/python/mrd/ndjson.py index 88926aa7..6a323a91 100644 --- a/python/mrd/ndjson.py +++ b/python/mrd/ndjson.py @@ -170,6 +170,7 @@ def __init__(self) -> None: self._idx_converter = EncodingCountersConverter() self._measurement_uid_converter = _ndjson.uint32_converter self._scan_counter_converter = _ndjson.OptionalConverter(_ndjson.uint32_converter) + self._acquisition_center_frequency_converter = _ndjson.OptionalConverter(_ndjson.uint64_converter) self._acquisition_time_stamp_ns_converter = _ndjson.OptionalConverter(_ndjson.uint64_converter) self._physiology_time_stamp_ns_converter = _ndjson.VectorConverter(_ndjson.uint64_converter) self._channel_order_converter = _ndjson.VectorConverter(_ndjson.uint32_converter) @@ -190,6 +191,7 @@ def __init__(self) -> None: ("idx", self._idx_converter.overall_dtype()), ("measurement_uid", self._measurement_uid_converter.overall_dtype()), ("scan_counter", self._scan_counter_converter.overall_dtype()), + ("acquisition_center_frequency", self._acquisition_center_frequency_converter.overall_dtype()), ("acquisition_time_stamp_ns", self._acquisition_time_stamp_ns_converter.overall_dtype()), ("physiology_time_stamp_ns", self._physiology_time_stamp_ns_converter.overall_dtype()), ("channel_order", self._channel_order_converter.overall_dtype()), @@ -217,6 +219,8 @@ def to_json(self, value: AcquisitionHeader) -> object: json_object["measurementUid"] = self._measurement_uid_converter.to_json(value.measurement_uid) if value.scan_counter is not None: json_object["scanCounter"] = self._scan_counter_converter.to_json(value.scan_counter) + if value.acquisition_center_frequency is not None: + json_object["acquisitionCenterFrequency"] = self._acquisition_center_frequency_converter.to_json(value.acquisition_center_frequency) if value.acquisition_time_stamp_ns is not None: json_object["acquisitionTimeStampNs"] = self._acquisition_time_stamp_ns_converter.to_json(value.acquisition_time_stamp_ns) json_object["physiologyTimeStampNs"] = self._physiology_time_stamp_ns_converter.to_json(value.physiology_time_stamp_ns) @@ -250,6 +254,8 @@ def numpy_to_json(self, value: np.void) -> object: json_object["measurementUid"] = self._measurement_uid_converter.numpy_to_json(value["measurement_uid"]) if (field_val := value["scan_counter"]) is not None: json_object["scanCounter"] = self._scan_counter_converter.numpy_to_json(field_val) + if (field_val := value["acquisition_center_frequency"]) is not None: + json_object["acquisitionCenterFrequency"] = self._acquisition_center_frequency_converter.numpy_to_json(field_val) if (field_val := value["acquisition_time_stamp_ns"]) is not None: json_object["acquisitionTimeStampNs"] = self._acquisition_time_stamp_ns_converter.numpy_to_json(field_val) json_object["physiologyTimeStampNs"] = self._physiology_time_stamp_ns_converter.numpy_to_json(value["physiology_time_stamp_ns"]) @@ -281,6 +287,7 @@ def from_json(self, json_object: object) -> AcquisitionHeader: idx=self._idx_converter.from_json(json_object["idx"],), measurement_uid=self._measurement_uid_converter.from_json(json_object["measurementUid"],), scan_counter=self._scan_counter_converter.from_json(json_object.get("scanCounter")), + acquisition_center_frequency=self._acquisition_center_frequency_converter.from_json(json_object.get("acquisitionCenterFrequency")), acquisition_time_stamp_ns=self._acquisition_time_stamp_ns_converter.from_json(json_object.get("acquisitionTimeStampNs")), physiology_time_stamp_ns=self._physiology_time_stamp_ns_converter.from_json(json_object["physiologyTimeStampNs"],), channel_order=self._channel_order_converter.from_json(json_object["channelOrder"],), @@ -306,6 +313,7 @@ def from_json_to_numpy(self, json_object: object) -> np.void: self._idx_converter.from_json_to_numpy(json_object["idx"]), self._measurement_uid_converter.from_json_to_numpy(json_object["measurementUid"]), self._scan_counter_converter.from_json_to_numpy(json_object.get("scanCounter")), + self._acquisition_center_frequency_converter.from_json_to_numpy(json_object.get("acquisitionCenterFrequency")), self._acquisition_time_stamp_ns_converter.from_json_to_numpy(json_object.get("acquisitionTimeStampNs")), self._physiology_time_stamp_ns_converter.from_json_to_numpy(json_object["physiologyTimeStampNs"]), self._channel_order_converter.from_json_to_numpy(json_object["channelOrder"]), @@ -328,10 +336,12 @@ class AcquisitionConverter(_ndjson.JsonConverter[Acquisition, np.void]): def __init__(self) -> None: self._head_converter = AcquisitionHeaderConverter() self._data_converter = _ndjson.NDArrayConverter(_ndjson.complexfloat32_converter, 2) + self._phase_converter = _ndjson.OptionalConverter(_ndjson.NDArrayConverter(_ndjson.float32_converter, 1)) self._trajectory_converter = _ndjson.NDArrayConverter(_ndjson.float32_converter, 2) super().__init__(np.dtype([ ("head", self._head_converter.overall_dtype()), ("data", self._data_converter.overall_dtype()), + ("phase", self._phase_converter.overall_dtype()), ("trajectory", self._trajectory_converter.overall_dtype()), ])) @@ -342,6 +352,8 @@ def to_json(self, value: Acquisition) -> object: json_object["head"] = self._head_converter.to_json(value.head) json_object["data"] = self._data_converter.to_json(value.data) + if value.phase is not None: + json_object["phase"] = self._phase_converter.to_json(value.phase) json_object["trajectory"] = self._trajectory_converter.to_json(value.trajectory) return json_object @@ -352,6 +364,8 @@ def numpy_to_json(self, value: np.void) -> object: json_object["head"] = self._head_converter.numpy_to_json(value["head"]) json_object["data"] = self._data_converter.numpy_to_json(value["data"]) + if (field_val := value["phase"]) is not None: + json_object["phase"] = self._phase_converter.numpy_to_json(field_val) json_object["trajectory"] = self._trajectory_converter.numpy_to_json(value["trajectory"]) return json_object @@ -361,6 +375,7 @@ def from_json(self, json_object: object) -> Acquisition: return Acquisition( head=self._head_converter.from_json(json_object["head"],), data=self._data_converter.from_json(json_object["data"],), + phase=self._phase_converter.from_json(json_object.get("phase")), trajectory=self._trajectory_converter.from_json(json_object["trajectory"],), ) @@ -370,6 +385,7 @@ def from_json_to_numpy(self, json_object: object) -> np.void: return ( self._head_converter.from_json_to_numpy(json_object["head"]), self._data_converter.from_json_to_numpy(json_object["data"]), + self._phase_converter.from_json_to_numpy(json_object.get("phase")), self._trajectory_converter.from_json_to_numpy(json_object["trajectory"]), ) # type:ignore diff --git a/python/mrd/protocols.py b/python/mrd/protocols.py index 191d38fe..3180532b 100644 --- a/python/mrd/protocols.py +++ b/python/mrd/protocols.py @@ -24,7 +24,7 @@ class MrdWriterBase(abc.ABC): def __init__(self) -> None: self._state = 0 - schema = r"""{"protocol":{"name":"Mrd","sequence":[{"name":"header","type":[null,"Mrd.Header"]},{"name":"data","type":{"stream":{"items":"Mrd.StreamItem"}}}]},"types":[{"name":"AccelerationFactorType","fields":[{"name":"kspaceEncodingStep1","type":"uint32"},{"name":"kspaceEncodingStep2","type":"uint32"}]},{"name":"Acquisition","fields":[{"name":"head","type":"Mrd.AcquisitionHeader"},{"name":"data","type":"Mrd.AcquisitionData"},{"name":"trajectory","type":"Mrd.TrajectoryData"}]},{"name":"Acquisition","fields":[{"name":"head","type":"Mrd.AcquisitionHeader"},{"name":"data","type":"Mrd.AcquisitionData"},{"name":"trajectory","type":"Mrd.TrajectoryData"}]},{"name":"AcquisitionBucket","fields":[{"name":"data","type":{"vector":{"items":"Mrd.Acquisition"}}},{"name":"ref","type":{"vector":{"items":"Mrd.Acquisition"}}},{"name":"datastats","type":{"vector":{"items":"Mrd.EncodingLimitsType"}}},{"name":"refstats","type":{"vector":{"items":"Mrd.EncodingLimitsType"}}},{"name":"waveforms","type":{"vector":{"items":"Mrd.WaveformUint32"}}}]},{"name":"AcquisitionData","type":{"array":{"items":"complexfloat32","dimensions":[{"name":"coils"},{"name":"samples"}]}}},{"name":"AcquisitionFlags","base":"uint64","values":[{"symbol":"firstInEncodeStep1","value":1},{"symbol":"lastInEncodeStep1","value":2},{"symbol":"firstInEncodeStep2","value":4},{"symbol":"lastInEncodeStep2","value":8},{"symbol":"firstInAverage","value":16},{"symbol":"lastInAverage","value":32},{"symbol":"firstInSlice","value":64},{"symbol":"lastInSlice","value":128},{"symbol":"firstInContrast","value":256},{"symbol":"lastInContrast","value":512},{"symbol":"firstInPhase","value":1024},{"symbol":"lastInPhase","value":2048},{"symbol":"firstInRepetition","value":4096},{"symbol":"lastInRepetition","value":8192},{"symbol":"firstInSet","value":16384},{"symbol":"lastInSet","value":32768},{"symbol":"firstInSegment","value":65536},{"symbol":"lastInSegment","value":131072},{"symbol":"isNoiseMeasurement","value":262144},{"symbol":"isParallelCalibration","value":524288},{"symbol":"isParallelCalibrationAndImaging","value":1048576},{"symbol":"isReverse","value":2097152},{"symbol":"isNavigationData","value":4194304},{"symbol":"isPhasecorrData","value":8388608},{"symbol":"lastInMeasurement","value":16777216},{"symbol":"isHpfeedbackData","value":33554432},{"symbol":"isDummyscanData","value":67108864},{"symbol":"isRtfeedbackData","value":134217728},{"symbol":"isSurfacecoilcorrectionscanData","value":268435456},{"symbol":"isPhaseStabilizationReference","value":536870912},{"symbol":"isPhaseStabilization","value":1073741824}]},{"name":"AcquisitionHeader","fields":[{"name":"flags","type":"Mrd.AcquisitionFlags"},{"name":"idx","type":"Mrd.EncodingCounters"},{"name":"measurementUid","type":"uint32"},{"name":"scanCounter","type":[null,"uint32"]},{"name":"acquisitionTimeStampNs","type":[null,"uint64"]},{"name":"physiologyTimeStampNs","type":{"vector":{"items":"uint64"}}},{"name":"channelOrder","type":{"vector":{"items":"uint32"}}},{"name":"discardPre","type":[null,"uint32"]},{"name":"discardPost","type":[null,"uint32"]},{"name":"centerSample","type":[null,"uint32"]},{"name":"encodingSpaceRef","type":[null,"uint32"]},{"name":"sampleTimeNs","type":[null,"uint64"]},{"name":"position","type":{"array":{"items":"float32","dimensions":[{"length":3}]}}},{"name":"readDir","type":{"array":{"items":"float32","dimensions":[{"length":3}]}}},{"name":"phaseDir","type":{"array":{"items":"float32","dimensions":[{"length":3}]}}},{"name":"sliceDir","type":{"array":{"items":"float32","dimensions":[{"length":3}]}}},{"name":"patientTablePosition","type":{"array":{"items":"float32","dimensions":[{"length":3}]}}},{"name":"userInt","type":{"vector":{"items":"int32"}}},{"name":"userFloat","type":{"vector":{"items":"float32"}}}]},{"name":"AcquisitionSystemInformationType","fields":[{"name":"systemVendor","type":[null,"string"]},{"name":"systemModel","type":[null,"string"]},{"name":"systemFieldStrengthT","type":[null,"float32"]},{"name":"relativeReceiverNoiseBandwidth","type":[null,"float32"]},{"name":"receiverChannels","type":[null,"uint32"]},{"name":"coilLabel","type":{"vector":{"items":"Mrd.CoilLabelType"}}},{"name":"institutionName","type":[null,"string"]},{"name":"stationName","type":[null,"string"]},{"name":"deviceID","type":[null,"string"]},{"name":"deviceSerialNumber","type":[null,"string"]}]},{"name":"Array","typeParameters":["T"],"type":{"array":{"items":"T"}}},{"name":"ArrayComplexFloat","type":{"name":"Mrd.Array","typeArguments":["complexfloat32"]}},{"name":"Calibration","values":[{"symbol":"separable2D","value":0},{"symbol":"full3D","value":1},{"symbol":"other","value":2}]},{"name":"CalibrationMode","values":[{"symbol":"noacceleration","value":0},{"symbol":"embedded","value":1},{"symbol":"interleaved","value":2},{"symbol":"separate","value":3},{"symbol":"external","value":4},{"symbol":"other","value":5}]},{"name":"CoilLabelType","fields":[{"name":"coilNumber","type":"uint32"},{"name":"coilName","type":"string"}]},{"nam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,"value":1},{"symbol":"hFDR","value":2},{"symbol":"hFDL","value":3},{"symbol":"fFP","value":4},{"symbol":"fFS","value":5},{"symbol":"fFDR","value":6},{"symbol":"fFDL","value":7}]},{"name":"ReconAssembly","fields":[{"name":"data","type":"Mrd.ReconBuffer"},{"name":"ref","type":[null,"Mrd.ReconBuffer"]}]},{"name":"ReconBuffer","fields":[{"name":"data","type":{"array":{"items":"complexfloat32","dimensions":[{"name":"loc"},{"name":"s"},{"name":"n"},{"name":"chan"},{"name":"e2"},{"name":"e1"},{"name":"e0"}]}}},{"name":"trajectory","type":{"array":{"items":"float32","dimensions":[{"name":"loc"},{"name":"s"},{"name":"n"},{"name":"e2"},{"name":"e1"},{"name":"basis"},{"name":"samples"}]}}},{"name":"density","type":[null,{"array":{"items":"float32","dimensions":[{"name":"loc"},{"name":"s"},{"name":"n"},{"name":"e2"},{"name":"e1"},{"name":"e0"}]}}]},{"name":"headers","type":{"array":{"items":"Mrd.AcquisitionHeader","dimensions":[{"name":"loc"},{"name":"s"},{"name":"n"},{"name":"e2"},{"name":"e1"}]}}},{"name":"sampling","type":"Mrd.SamplingDescription"}]},{"name":"ReconData","fields":[{"name":"buffers","type":{"vector":{"items":"Mrd.ReconAssembly"}}}]},{"name":"ReferencedImageSequenceType","fields":[{"name":"referencedSOPInstanceUID","type":{"vector":{"items":"string"}}}]},{"name":"SamplingDescription","fields":[{"name":"encodedFOV","type":"Mrd.FieldOfViewMm"},{"name":"reconFOV","type":"Mrd.FieldOfViewMm"},{"name":"encodedMatrix","type":"Mrd.MatrixSizeType"},{"name":"reconMatrix","type":"Mrd.MatrixSizeType"},{"name":"samplingLimits","type":"Mrd.SamplingLimits"}]},{"name":"SamplingLimits","fields":[{"name":"kspaceEncodingStep0","type":"Mrd.LimitType"},{"name":"kspaceEncodingStep1","type":"Mrd.LimitType"},{"name":"kspaceEncodingStep2","type":"Mrd.LimitType"}]},{"name":"SequenceParametersType","fields":[{"name":"tR","type":{"vector":{"items":"float32"}}},{"name":"tE","type":{"vector":{"items":"float32"}}},{"name":"tI","type":{"vector":{"items":"float32"}}},{"name":"flipAngleDeg","type":{"vector":{"items":"float32"}}},{"name":"sequenceType","type":[null,"string"]},{"name":"echoSpacing","type":{"vector":{"items":"float32"}}},{"name":"diffusionDimension","type":[null,"Mrd.DiffusionDimension"]},{"name":"diffusion","type":{"vector":{"items":"Mrd.DiffusionType"}}},{"name":"diffusionScheme","type":[null,"string"]}]},{"name":"StreamItem","type":[{"tag":"Acquisition","type":"Mrd.Acquisition"},{"tag":"WaveformUint32","type":"Mrd.WaveformUint32"},{"tag":"ImageUint16","type":"Mrd.ImageUint16"},{"tag":"ImageInt16","type":"Mrd.ImageInt16"},{"tag":"ImageUint32","type":"Mrd.ImageUint32"},{"tag":"ImageInt32","type":"Mrd.ImageInt32"},{"tag":"ImageFloat","type":"Mrd.ImageFloat"},{"tag":"ImageDouble","type":"Mrd.ImageDouble"},{"tag":"ImageComplexFloat","type":"Mrd.ImageComplexFloat"},{"tag":"ImageComplexDouble","type":"Mrd.ImageComplexDouble"},{"tag":"AcquisitionBucket","type":"Mrd.AcquisitionBucket"},{"tag":"ReconData","type":"Mrd.ReconData"},{"tag":"ArrayComplexFloat","type":"Mrd.ArrayComplexFloat"},{"tag":"ImageArray","type":"Mrd.ImageArray"}]},{"name":"StudyInformationType","fields":[{"name":"studyDate","type":[null,"date"]},{"name":"studyTime","type":[null,"time"]},{"name":"studyID","type":[null,"string"]},{"name":"accessionNumber","type":[null,"int64"]},{"name":"referringPhysicianName","type":[null,"string"]},{"name":"studyDescription","type":[null,"string"]},{"name":"studyInstanceUID","type":[null,"string"]},{"name":"bodyPartExamined","type":[null,"string"]}]},{"name":"SubjectInformationType","fields":[{"name":"patientName","type":[null,"string"]},{"name":"patientWeightKg","type":[null,"float32"]},{"name":"patientHeightM","type":[null,"float32"]},{"name":"patientID","type":[null,"string"]},{"name":"patientBirthdate","type":[null,"date"]},{"name":"patientGender","type":[null,"Mrd.PatientGender"]}]},{"name":"ThreeDimensionalFloat","fields":[{"name":"x","type":"float32"},{"name":"y","type":"float32"},{"name":"z","type":"float32"}]},{"name":"Trajectory","values":[{"symbol":"cartesian","value":0},{"symbol":"epi","value":1},{"symbol":"radial","value":2},{"symbol":"goldenangle","value":3},{"symbol":"spiral","value":4},{"symbol":"other","value":5}]},{"name":"TrajectoryData","type":{"array":{"items":"float32","dimensions":[{"name":"basis"},{"name":"samples"}]}}},{"name":"TrajectoryDescriptionType","fields":[{"name":"identifier","type":"string"},{"name":"userParameterLong","type":{"vector":{"items":"Mrd.UserParameterLongType"}}},{"name":"userParameterDouble","type":{"vector":{"items":"Mrd.UserParameterDoubleType"}}},{"name":"userParameterString","type":{"vector":{"items":"Mrd.UserParameterStringType"}}},{"name":"comment","type":[null,"string"]}]},{"name":"UserParameterBase64Type","fields":[{"name":"name","type":"string"},{"name":"value","type":"string"}]},{"name":"UserParameterDoubleType","fields":[{"name":"name","type":"string"},{"name":"value","type":"float64"}]},{"name":"UserParameterLongType","fields":[{"name":"name","type":"string"},{"name":"value","type":"int64"}]},{"name":"UserParameterStringType","fields":[{"name":"name","type":"string"},{"name":"value","type":"string"}]},{"name":"UserParametersType","fields":[{"name":"userParameterLong","type":{"vector":{"items":"Mrd.UserParameterLongType"}}},{"name":"userParameterDouble","type":{"vector":{"items":"Mrd.UserParameterDoubleType"}}},{"name":"userParameterString","type":{"vector":{"items":"Mrd.UserParameterStringType"}}},{"name":"userParameterBase64","type":{"vector":{"items":"Mrd.UserParameterBase64Type"}}}]},{"name":"Waveform","typeParameters":["T"],"fields":[{"name":"flags","type":"uint64"},{"name":"measurementUid","type":"uint32"},{"name":"scanCounter","type":"uint32"},{"name":"timeStampNs","type":"uint64"},{"name":"sampleTimeNs","type":"uint64"},{"name":"waveformId","type":"uint32"},{"name":"data","type":{"name":"Mrd.WaveformSamples","typeArguments":["T"]}}]},{"name":"WaveformInformationType","fields":[{"name":"waveformName","type":"string"},{"name":"waveformType","type":"Mrd.WaveformType"},{"name":"userParameters","type":"Mrd.UserParametersType"}]},{"name":"WaveformSamples","typeParameters":["T"],"type":{"array":{"items":"T","dimensions":[{"name":"channels"},{"name":"samples"}]}}},{"name":"WaveformType","values":[{"symbol":"ecg","value":0},{"symbol":"pulse","value":1},{"symbol":"respiratory","value":2},{"symbol":"trigger","value":3},{"symbol":"gradientwaveform","value":4},{"symbol":"other","value":5}]},{"name":"WaveformUint32","type":{"name":"Mrd.Waveform","typeArguments":["uint32"]}},{"name":"WaveformUint32","type":{"name":"Mrd.Waveform","typeArguments":["uint32"]}}]}""" def close(self) -> None: if self._state == 3: diff --git a/python/mrd/types.py b/python/mrd/types.py index bcddc28f..3dcde358 100644 --- a/python/mrd/types.py +++ b/python/mrd/types.py @@ -143,6 +143,8 @@ def __repr__(self) -> str: AcquisitionData = npt.NDArray[np.complex64] +AcquisitionPhase = npt.NDArray[np.float32] + TrajectoryData = npt.NDArray[np.float32] class AcquisitionHeader: @@ -158,6 +160,9 @@ class AcquisitionHeader: scan_counter: typing.Optional[yardl.UInt32] """Zero-indexed incrementing counter for readouts""" + acquisition_center_frequency: typing.Optional[yardl.UInt64] + """Acquisition center frequency in Hz""" + acquisition_time_stamp_ns: typing.Optional[yardl.UInt64] """Clock time stamp (e.g. nanoseconds since midnight)""" @@ -213,6 +218,7 @@ def __init__(self, *, idx: typing.Optional[EncodingCounters] = None, measurement_uid: yardl.UInt32 = 0, scan_counter: typing.Optional[yardl.UInt32] = None, + acquisition_center_frequency: typing.Optional[yardl.UInt64] = None, acquisition_time_stamp_ns: typing.Optional[yardl.UInt64] = None, physiology_time_stamp_ns: typing.Optional[list[yardl.UInt64]] = None, channel_order: typing.Optional[list[yardl.UInt32]] = None, @@ -233,6 +239,7 @@ def __init__(self, *, self.idx = idx if idx is not None else EncodingCounters() self.measurement_uid = measurement_uid self.scan_counter = scan_counter + self.acquisition_center_frequency = acquisition_center_frequency self.acquisition_time_stamp_ns = acquisition_time_stamp_ns self.physiology_time_stamp_ns = physiology_time_stamp_ns if physiology_time_stamp_ns is not None else [] self.channel_order = channel_order if channel_order is not None else [] @@ -256,6 +263,7 @@ def __eq__(self, other: object) -> bool: and self.idx == other.idx and self.measurement_uid == other.measurement_uid and self.scan_counter == other.scan_counter + and self.acquisition_center_frequency == other.acquisition_center_frequency and self.acquisition_time_stamp_ns == other.acquisition_time_stamp_ns and self.physiology_time_stamp_ns == other.physiology_time_stamp_ns and self.channel_order == other.channel_order @@ -274,10 +282,10 @@ def __eq__(self, other: object) -> bool: ) def __str__(self) -> str: - return f"AcquisitionHeader(flags={self.flags}, idx={self.idx}, measurement_uid={self.measurement_uid}, scan_counter={self.scan_counter}, acquisition_time_stamp_ns={self.acquisition_time_stamp_ns}, physiology_time_stamp_ns={self.physiology_time_stamp_ns}, channel_order={self.channel_order}, discard_pre={self.discard_pre}, discard_post={self.discard_post}, center_sample={self.center_sample}, encoding_space_ref={self.encoding_space_ref}, sample_time_ns={self.sample_time_ns}, position={self.position}, read_dir={self.read_dir}, phase_dir={self.phase_dir}, slice_dir={self.slice_dir}, patient_table_position={self.patient_table_position}, user_int={self.user_int}, user_float={self.user_float})" + return f"AcquisitionHeader(flags={self.flags}, idx={self.idx}, measurement_uid={self.measurement_uid}, scan_counter={self.scan_counter}, acquisition_center_frequency={self.acquisition_center_frequency}, acquisition_time_stamp_ns={self.acquisition_time_stamp_ns}, physiology_time_stamp_ns={self.physiology_time_stamp_ns}, channel_order={self.channel_order}, discard_pre={self.discard_pre}, discard_post={self.discard_post}, center_sample={self.center_sample}, encoding_space_ref={self.encoding_space_ref}, sample_time_ns={self.sample_time_ns}, position={self.position}, read_dir={self.read_dir}, phase_dir={self.phase_dir}, slice_dir={self.slice_dir}, patient_table_position={self.patient_table_position}, user_int={self.user_int}, user_float={self.user_float})" def __repr__(self) -> str: - return f"AcquisitionHeader(flags={repr(self.flags)}, idx={repr(self.idx)}, measurement_uid={repr(self.measurement_uid)}, scan_counter={repr(self.scan_counter)}, acquisition_time_stamp_ns={repr(self.acquisition_time_stamp_ns)}, physiology_time_stamp_ns={repr(self.physiology_time_stamp_ns)}, channel_order={repr(self.channel_order)}, discard_pre={repr(self.discard_pre)}, discard_post={repr(self.discard_post)}, center_sample={repr(self.center_sample)}, encoding_space_ref={repr(self.encoding_space_ref)}, sample_time_ns={repr(self.sample_time_ns)}, position={repr(self.position)}, read_dir={repr(self.read_dir)}, phase_dir={repr(self.phase_dir)}, slice_dir={repr(self.slice_dir)}, patient_table_position={repr(self.patient_table_position)}, user_int={repr(self.user_int)}, user_float={repr(self.user_float)})" + return f"AcquisitionHeader(flags={repr(self.flags)}, idx={repr(self.idx)}, measurement_uid={repr(self.measurement_uid)}, scan_counter={repr(self.scan_counter)}, acquisition_center_frequency={repr(self.acquisition_center_frequency)}, acquisition_time_stamp_ns={repr(self.acquisition_time_stamp_ns)}, physiology_time_stamp_ns={repr(self.physiology_time_stamp_ns)}, channel_order={repr(self.channel_order)}, discard_pre={repr(self.discard_pre)}, discard_post={repr(self.discard_post)}, center_sample={repr(self.center_sample)}, encoding_space_ref={repr(self.encoding_space_ref)}, sample_time_ns={repr(self.sample_time_ns)}, position={repr(self.position)}, read_dir={repr(self.read_dir)}, phase_dir={repr(self.phase_dir)}, slice_dir={repr(self.slice_dir)}, patient_table_position={repr(self.patient_table_position)}, user_int={repr(self.user_int)}, user_float={repr(self.user_float)})" class Acquisition: @@ -287,6 +295,9 @@ class Acquisition: data: AcquisitionData """Raw k-space samples array""" + phase: typing.Optional[AcquisitionPhase] + """Phase offset array""" + trajectory: TrajectoryData """Trajectory array""" @@ -294,10 +305,12 @@ class Acquisition: def __init__(self, *, head: typing.Optional[AcquisitionHeader] = None, data: typing.Optional[AcquisitionData] = None, + phase: typing.Optional[AcquisitionPhase] = None, trajectory: typing.Optional[TrajectoryData] = None, ): self.head = head if head is not None else AcquisitionHeader() self.data = data if data is not None else np.zeros((0, 0), dtype=np.dtype(np.complex64)) + self.phase = phase self.trajectory = trajectory if trajectory is not None else np.zeros((0, 0), dtype=np.dtype(np.float32)) def coils(self) -> yardl.Size: @@ -320,14 +333,15 @@ def __eq__(self, other: object) -> bool: isinstance(other, Acquisition) and self.head == other.head and yardl.structural_equal(self.data, other.data) + and (other.phase is None if self.phase is None else (other.phase is not None and yardl.structural_equal(self.phase, other.phase))) and yardl.structural_equal(self.trajectory, other.trajectory) ) def __str__(self) -> str: - return f"Acquisition(head={self.head}, data={self.data}, trajectory={self.trajectory})" + return f"Acquisition(head={self.head}, data={self.data}, phase={self.phase}, trajectory={self.trajectory})" def __repr__(self) -> str: - return f"Acquisition(head={repr(self.head)}, data={repr(self.data)}, trajectory={repr(self.trajectory)})" + return f"Acquisition(head={repr(self.head)}, data={repr(self.data)}, phase={repr(self.phase)}, trajectory={repr(self.trajectory)})" class PatientGender(yardl.OutOfRangeEnum): @@ -2124,13 +2138,13 @@ class StreamItemUnionCase(StreamItem, yardl.UnionCase[_T]): del StreamItemUnionCase def _mk_get_dtype(): - dtype_map: dict[typing.Union[type, types.GenericAlias, typing.Annotated[typing.Any, typing.Any]], typing.Union[np.dtype[typing.Any], typing.Callable[[tuple[type, ...]], np.dtype[typing.Any]]]] = {} + dtype_map: dict[typing.Union[type, types.GenericAlias], typing.Union[np.dtype[typing.Any], typing.Callable[[tuple[type, ...]], np.dtype[typing.Any]]]] = {} get_dtype = _dtypes.make_get_dtype_func(dtype_map) dtype_map.setdefault(AcquisitionFlags, np.dtype(np.uint64)) dtype_map.setdefault(EncodingCounters, np.dtype([('kspace_encode_step_1', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.uint32))], align=True)), ('kspace_encode_step_2', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.uint32))], align=True)), ('average', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.uint32))], align=True)), ('slice', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.uint32))], align=True)), ('contrast', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.uint32))], align=True)), ('phase', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.uint32))], align=True)), ('repetition', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.uint32))], align=True)), ('set', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.uint32))], align=True)), ('segment', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.uint32))], align=True)), ('user', np.dtype(np.object_))], align=True)) - dtype_map.setdefault(AcquisitionHeader, np.dtype([('flags', get_dtype(AcquisitionFlags)), ('idx', get_dtype(EncodingCounters)), ('measurement_uid', np.dtype(np.uint32)), ('scan_counter', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.uint32))], align=True)), ('acquisition_time_stamp_ns', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.uint64))], align=True)), ('physiology_time_stamp_ns', np.dtype(np.object_)), ('channel_order', np.dtype(np.object_)), ('discard_pre', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.uint32))], align=True)), ('discard_post', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.uint32))], align=True)), ('center_sample', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.uint32))], align=True)), ('encoding_space_ref', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.uint32))], align=True)), ('sample_time_ns', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.uint64))], align=True)), ('position', np.dtype(np.float32), (3,)), ('read_dir', np.dtype(np.float32), (3,)), ('phase_dir', np.dtype(np.float32), (3,)), ('slice_dir', np.dtype(np.float32), (3,)), ('patient_table_position', np.dtype(np.float32), (3,)), ('user_int', np.dtype(np.object_)), ('user_float', np.dtype(np.object_))], align=True)) - dtype_map.setdefault(Acquisition, np.dtype([('head', get_dtype(AcquisitionHeader)), ('data', np.dtype(np.object_)), ('trajectory', np.dtype(np.object_))], align=True)) + dtype_map.setdefault(AcquisitionHeader, np.dtype([('flags', get_dtype(AcquisitionFlags)), ('idx', get_dtype(EncodingCounters)), ('measurement_uid', np.dtype(np.uint32)), ('scan_counter', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.uint32))], align=True)), ('acquisition_center_frequency', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.uint64))], align=True)), ('acquisition_time_stamp_ns', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.uint64))], align=True)), ('physiology_time_stamp_ns', np.dtype(np.object_)), ('channel_order', np.dtype(np.object_)), ('discard_pre', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.uint32))], align=True)), ('discard_post', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.uint32))], align=True)), ('center_sample', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.uint32))], align=True)), ('encoding_space_ref', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.uint32))], align=True)), ('sample_time_ns', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.uint64))], align=True)), ('position', np.dtype(np.float32), (3,)), ('read_dir', np.dtype(np.float32), (3,)), ('phase_dir', np.dtype(np.float32), (3,)), ('slice_dir', np.dtype(np.float32), (3,)), ('patient_table_position', np.dtype(np.float32), (3,)), ('user_int', np.dtype(np.object_)), ('user_float', np.dtype(np.object_))], align=True)) + dtype_map.setdefault(Acquisition, np.dtype([('head', get_dtype(AcquisitionHeader)), ('data', np.dtype(np.object_)), ('phase', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.object_))], align=True)), ('trajectory', np.dtype(np.object_))], align=True)) dtype_map.setdefault(PatientGender, np.dtype(np.int32)) dtype_map.setdefault(SubjectInformationType, np.dtype([('patient_name', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.object_))], align=True)), ('patient_weight_kg', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.float32))], align=True)), ('patient_height_m', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.float32))], align=True)), ('patient_id', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.object_))], align=True)), ('patient_birthdate', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.datetime64))], align=True)), ('patient_gender', np.dtype([('has_value', np.dtype(np.bool_)), ('value', get_dtype(PatientGender))], align=True))], align=True)) dtype_map.setdefault(StudyInformationType, np.dtype([('study_date', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.datetime64))], align=True)), ('study_time', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.timedelta64))], align=True)), ('study_id', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.object_))], align=True)), ('accession_number', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.int64))], align=True)), ('referring_physician_name', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.object_))], align=True)), ('study_description', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.object_))], align=True)), ('study_instance_uid', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.object_))], align=True)), ('body_part_examined', np.dtype([('has_value', np.dtype(np.bool_)), ('value', np.dtype(np.object_))], align=True))], align=True)) diff --git a/python/mrd/yardl_types.py b/python/mrd/yardl_types.py index 019c5ca6..40693d23 100644 --- a/python/mrd/yardl_types.py +++ b/python/mrd/yardl_types.py @@ -56,7 +56,7 @@ class DateTime: def __init__(self, nanoseconds_from_epoch: Union[int, np.datetime64] = 0): if isinstance(nanoseconds_from_epoch, np.datetime64): if nanoseconds_from_epoch.dtype != "datetime64[ns]": - self._value = np.datetime64(nanoseconds_from_epoch, "ns") # type: ignore + self._value = np.datetime64(nanoseconds_from_epoch, "ns") else: self._value = nanoseconds_from_epoch else: @@ -67,9 +67,7 @@ def numpy_value(self) -> np.datetime64: return self._value def to_datetime(self) -> datetime.datetime: - return datetime.datetime.fromtimestamp( - self._value.astype(int) / 1e9, tz=datetime.timezone.utc - ) + return datetime.datetime.utcfromtimestamp(self._value.astype(int) / 1e9) @staticmethod def from_components( @@ -271,7 +269,8 @@ def structural_equal(a: object, b: object) -> bool: if not isinstance(b, np.void): return b == a return a.dtype == b.dtype and all( - structural_equal(x, y) for x, y in zip(a, b) # type: ignore + structural_equal(x, y) + for x, y in zip(a, b) # pyright: ignore [reportGeneralTypeIssues] ) if isinstance(b, np.void):