Feature/add image types

cpp/mrd/hdf5/protocols.h

@@ -28,7 +28,7 @@ class MrdWriter : public mrd::MrdWriterBase, public yardl::hdf5::Hdf5Writer {
   void Flush() override;
 
   private:
-  std::unique_ptr<yardl::hdf5::UnionDatasetWriter<14>> data_dataset_state_;
+  std::unique_ptr<yardl::hdf5::UnionDatasetWriter<22>> data_dataset_state_;
 };
 
 // HDF5 reader for the Mrd protocol.
@@ -42,7 +42,7 @@ class MrdReader : public mrd::MrdReaderBase, public yardl::hdf5::Hdf5Reader {
   bool ReadDataImpl(mrd::StreamItem& value) override;
 
   private:
-  std::unique_ptr<yardl::hdf5::UnionDatasetReader<14>> data_dataset_state_;
+  std::unique_ptr<yardl::hdf5::UnionDatasetReader<22>> data_dataset_state_;
 };
 
 // HDF5 writer for the MrdNoiseCovariance protocol.

cpp/mrd/types.h

@@ -866,12 +866,13 @@ struct ImageFlags : yardl::BaseFlags<uint64_t, ImageFlags> {
   static const ImageFlags kLastInSet;
 };
 
-enum class ImageType {
-  kMagnitude = 1,
-  kPhase = 2,
-  kReal = 3,
-  kImag = 4,
-  kComplex = 5,
+enum class ImageType : uint64_t {
+  kMagnitude = 1ULL,
+  kPhase = 2ULL,
+  kReal = 3ULL,
+  kImag = 4ULL,
+  kComplex = 5ULL,
+  kRgbaMap = 6ULL,
 };
 
 template <typename Y>
@@ -1014,7 +1015,7 @@ struct NoiseCovariance {
   std::vector<mrd::CoilLabelType> coil_labels{};
   // Comes from Header.acquisitionSystemInformation.relativeReceiverNoiseBandwidth
   float receiver_noise_bandwidth{};
-  // Comes from Acquisition.sampleTimeNs
+  // Comes from Acquisition.sampleTimeUs
   uint64_t noise_dwell_time_ns{};
   // Number of samples used to compute matrix
   yardl::Size sample_count{};
@@ -1210,8 +1211,91 @@ using Array = yardl::DynamicNDArray<T>;
 
 using ArrayComplexFloat = mrd::Array<std::complex<float>>;
 
+enum class ArrayType {
+  kSpinDensityMap = 1,
+  kT1Map = 2,
+  kT2Map = 3,
+  kT2starMap = 4,
+  kAdcMap = 5,
+  kB0Map = 6,
+  kB1Map = 7,
+  kSensitivityMap = 8,
+  kGfactorMap = 9,
+  kUserMap = 10,
+};
+
+using ArrayMetaValue = std::variant<std::string, int64_t, double>;
+
+using ArrayMeta = std::unordered_map<std::string, std::vector<mrd::ArrayMetaValue>>;
+
+enum class ArrayDimension {
+  kChannel = 0,
+  kZ = 1,
+  kY = 2,
+  kX = 3,
+  kFrequency = 4,
+  kBasis = 5,
+  kSamples = 6,
+  kLoc = 7,
+  kS = 8,
+  kN = 9,
+  kE2 = 10,
+  kE1 = 11,
+  kE0 = 12,
+  kTime = 13,
+};
+
+struct NDArrayHeader {
+  std::vector<mrd::ArrayDimension> dimension_labels{};
+  mrd::ArrayType array_type{};
+  mrd::ArrayMeta meta{};
+
+  bool operator==(const NDArrayHeader& other) const {
+    return dimension_labels == other.dimension_labels &&
+      array_type == other.array_type &&
+      meta == other.meta;
+  }
+
+  bool operator!=(const NDArrayHeader& other) const {
+    return !(*this == other);
+  }
+};
+
+template <typename T>
+struct NDArray {
+  mrd::NDArrayHeader head{};
+  mrd::Array<T> data{};
+
+  bool operator==(const NDArray& other) const {
+    return head == other.head &&
+      data == other.data;
+  }
+
+  bool operator!=(const NDArray& other) const {
+    return !(*this == other);
+  }
+};
+
+using NDArrayUint16 = mrd::NDArray<uint16_t>;
+
+using NDArrayInt16 = mrd::NDArray<int16_t>;
+
+using NDArrayUint32 = mrd::NDArray<uint32_t>;
+
+using NDArrayInt32 = mrd::NDArray<int32_t>;
+
+using NDArrayFloat = mrd::NDArray<float>;
+
+using NDArrayDouble = mrd::NDArray<double>;
+
+using NDArrayComplexFloat = mrd::NDArray<std::complex<float>>;
+
+using NDArrayComplexDouble = mrd::NDArray<std::complex<double>>;
+
+using AnyNDArray = std::variant<mrd::NDArrayUint16, mrd::NDArrayInt16, mrd::NDArrayUint32, mrd::NDArrayInt32, mrd::NDArrayFloat, mrd::NDArrayDouble, mrd::NDArrayComplexFloat, mrd::NDArrayComplexDouble>;
+
 // Union of all primary types that can be streamed in the MRD Protocol
-using StreamItem = std::variant<mrd::Acquisition, mrd::WaveformUint32, mrd::ImageUint16, mrd::ImageInt16, mrd::ImageUint32, mrd::ImageInt32, mrd::ImageFloat, mrd::ImageDouble, mrd::ImageComplexFloat, mrd::ImageComplexDouble, mrd::AcquisitionBucket, mrd::ReconData, mrd::ArrayComplexFloat, mrd::ImageArray>;
+using StreamItem = std::variant<mrd::Acquisition, mrd::WaveformUint32, mrd::ImageUint16, mrd::ImageInt16, mrd::ImageUint32, mrd::ImageInt32, mrd::ImageFloat, mrd::ImageDouble, mrd::ImageComplexFloat, mrd::ImageComplexDouble, mrd::AcquisitionBucket, mrd::ReconData, mrd::ArrayComplexFloat, mrd::ImageArray, mrd::NDArrayUint16, mrd::NDArrayInt16, mrd::NDArrayUint32, mrd::NDArrayInt32, mrd::NDArrayFloat, mrd::NDArrayDouble, mrd::NDArrayComplexFloat, mrd::NDArrayComplexDouble>;
 
 } // namespace mrd
 

matlab/toolbox/+mrd/+binary/ImageHeaderSerializer.m

@@ -19,7 +19,7 @@
       field_serializers{14} = yardl.binary.OptionalSerializer(yardl.binary.Uint32Serializer);
       field_serializers{15} = yardl.binary.OptionalSerializer(yardl.binary.Uint64Serializer);
       field_serializers{16} = yardl.binary.VectorSerializer(yardl.binary.Uint64Serializer);
-      field_serializers{17} = yardl.binary.EnumSerializer('mrd.ImageType', @mrd.ImageType, yardl.binary.Int32Serializer);
+      field_serializers{17} = yardl.binary.EnumSerializer('mrd.ImageType', @mrd.ImageType, yardl.binary.Uint64Serializer);
       field_serializers{18} = yardl.binary.OptionalSerializer(yardl.binary.Uint32Serializer);
       field_serializers{19} = yardl.binary.OptionalSerializer(yardl.binary.Uint32Serializer);
       field_serializers{20} = yardl.binary.VectorSerializer(yardl.binary.Int32Serializer);

matlab/toolbox/+mrd/+binary/MrdReader.m

@@ -17,7 +17,7 @@
       [email protected](skip_completed_check=options.skip_completed_check);
       [email protected](filename, mrd.MrdReaderBase.schema);
       self.header_serializer = yardl.binary.OptionalSerializer(mrd.binary.HeaderSerializer());
-      self.data_serializer = yardl.binary.StreamSerializer(yardl.binary.UnionSerializer('mrd.StreamItem', {mrd.binary.AcquisitionSerializer(), mrd.binary.WaveformSerializer(yardl.binary.Uint32Serializer), mrd.binary.ImageSerializer(yardl.binary.Uint16Serializer), mrd.binary.ImageSerializer(yardl.binary.Int16Serializer), mrd.binary.ImageSerializer(yardl.binary.Uint32Serializer), mrd.binary.ImageSerializer(yardl.binary.Int32Serializer), mrd.binary.ImageSerializer(yardl.binary.Float32Serializer), mrd.binary.ImageSerializer(yardl.binary.Float64Serializer), mrd.binary.ImageSerializer(yardl.binary.Complexfloat32Serializer), mrd.binary.ImageSerializer(yardl.binary.Complexfloat64Serializer), mrd.binary.AcquisitionBucketSerializer(), mrd.binary.ReconDataSerializer(), yardl.binary.DynamicNDArraySerializer(yardl.binary.Complexfloat32Serializer), mrd.binary.ImageArraySerializer()}, {@mrd.StreamItem.Acquisition, @mrd.StreamItem.WaveformUint32, @mrd.StreamItem.ImageUint16, @mrd.StreamItem.ImageInt16, @mrd.StreamItem.ImageUint32, @mrd.StreamItem.ImageInt32, @mrd.StreamItem.ImageFloat, @mrd.StreamItem.ImageDouble, @mrd.StreamItem.ImageComplexFloat, @mrd.StreamItem.ImageComplexDouble, @mrd.StreamItem.AcquisitionBucket, @mrd.StreamItem.ReconData, @mrd.StreamItem.ArrayComplexFloat, @mrd.StreamItem.ImageArray}));
+      self.data_serializer = yardl.binary.StreamSerializer(yardl.binary.UnionSerializer('mrd.StreamItem', {mrd.binary.AcquisitionSerializer(), mrd.binary.WaveformSerializer(yardl.binary.Uint32Serializer), mrd.binary.ImageSerializer(yardl.binary.Uint16Serializer), mrd.binary.ImageSerializer(yardl.binary.Int16Serializer), mrd.binary.ImageSerializer(yardl.binary.Uint32Serializer), mrd.binary.ImageSerializer(yardl.binary.Int32Serializer), mrd.binary.ImageSerializer(yardl.binary.Float32Serializer), mrd.binary.ImageSerializer(yardl.binary.Float64Serializer), mrd.binary.ImageSerializer(yardl.binary.Complexfloat32Serializer), mrd.binary.ImageSerializer(yardl.binary.Complexfloat64Serializer), mrd.binary.AcquisitionBucketSerializer(), mrd.binary.ReconDataSerializer(), yardl.binary.DynamicNDArraySerializer(yardl.binary.Complexfloat32Serializer), mrd.binary.ImageArraySerializer(), mrd.binary.NDArraySerializer(yardl.binary.Uint16Serializer), mrd.binary.NDArraySerializer(yardl.binary.Int16Serializer), mrd.binary.NDArraySerializer(yardl.binary.Uint32Serializer), mrd.binary.NDArraySerializer(yardl.binary.Int32Serializer), mrd.binary.NDArraySerializer(yardl.binary.Float32Serializer), mrd.binary.NDArraySerializer(yardl.binary.Float64Serializer), mrd.binary.NDArraySerializer(yardl.binary.Complexfloat32Serializer), mrd.binary.NDArraySerializer(yardl.binary.Complexfloat64Serializer)}, {@mrd.StreamItem.Acquisition, @mrd.StreamItem.WaveformUint32, @mrd.StreamItem.ImageUint16, @mrd.StreamItem.ImageInt16, @mrd.StreamItem.ImageUint32, @mrd.StreamItem.ImageInt32, @mrd.StreamItem.ImageFloat, @mrd.StreamItem.ImageDouble, @mrd.StreamItem.ImageComplexFloat, @mrd.StreamItem.ImageComplexDouble, @mrd.StreamItem.AcquisitionBucket, @mrd.StreamItem.ReconData, @mrd.StreamItem.ArrayComplexFloat, @mrd.StreamItem.ImageArray, @mrd.StreamItem.NdArrayUint16, @mrd.StreamItem.NdArrayInt16, @mrd.StreamItem.NdArrayUint32, @mrd.StreamItem.NdArrayInt32, @mrd.StreamItem.NdArrayFloat, @mrd.StreamItem.NdArrayDouble, @mrd.StreamItem.NdArrayComplexFloat, @mrd.StreamItem.NdArrayComplexDouble}));
     end
   end
 

matlab/toolbox/+mrd/+binary/MrdWriter.m

@@ -13,7 +13,7 @@
       [email protected]();
       [email protected](filename, mrd.MrdWriterBase.schema);
       self.header_serializer = yardl.binary.OptionalSerializer(mrd.binary.HeaderSerializer());
-      self.data_serializer = yardl.binary.StreamSerializer(yardl.binary.UnionSerializer('mrd.StreamItem', {mrd.binary.AcquisitionSerializer(), mrd.binary.WaveformSerializer(yardl.binary.Uint32Serializer), mrd.binary.ImageSerializer(yardl.binary.Uint16Serializer), mrd.binary.ImageSerializer(yardl.binary.Int16Serializer), mrd.binary.ImageSerializer(yardl.binary.Uint32Serializer), mrd.binary.ImageSerializer(yardl.binary.Int32Serializer), mrd.binary.ImageSerializer(yardl.binary.Float32Serializer), mrd.binary.ImageSerializer(yardl.binary.Float64Serializer), mrd.binary.ImageSerializer(yardl.binary.Complexfloat32Serializer), mrd.binary.ImageSerializer(yardl.binary.Complexfloat64Serializer), mrd.binary.AcquisitionBucketSerializer(), mrd.binary.ReconDataSerializer(), yardl.binary.DynamicNDArraySerializer(yardl.binary.Complexfloat32Serializer), mrd.binary.ImageArraySerializer()}, {@mrd.StreamItem.Acquisition, @mrd.StreamItem.WaveformUint32, @mrd.StreamItem.ImageUint16, @mrd.StreamItem.ImageInt16, @mrd.StreamItem.ImageUint32, @mrd.StreamItem.ImageInt32, @mrd.StreamItem.ImageFloat, @mrd.StreamItem.ImageDouble, @mrd.StreamItem.ImageComplexFloat, @mrd.StreamItem.ImageComplexDouble, @mrd.StreamItem.AcquisitionBucket, @mrd.StreamItem.ReconData, @mrd.StreamItem.ArrayComplexFloat, @mrd.StreamItem.ImageArray}));
+      self.data_serializer = yardl.binary.StreamSerializer(yardl.binary.UnionSerializer('mrd.StreamItem', {mrd.binary.AcquisitionSerializer(), mrd.binary.WaveformSerializer(yardl.binary.Uint32Serializer), mrd.binary.ImageSerializer(yardl.binary.Uint16Serializer), mrd.binary.ImageSerializer(yardl.binary.Int16Serializer), mrd.binary.ImageSerializer(yardl.binary.Uint32Serializer), mrd.binary.ImageSerializer(yardl.binary.Int32Serializer), mrd.binary.ImageSerializer(yardl.binary.Float32Serializer), mrd.binary.ImageSerializer(yardl.binary.Float64Serializer), mrd.binary.ImageSerializer(yardl.binary.Complexfloat32Serializer), mrd.binary.ImageSerializer(yardl.binary.Complexfloat64Serializer), mrd.binary.AcquisitionBucketSerializer(), mrd.binary.ReconDataSerializer(), yardl.binary.DynamicNDArraySerializer(yardl.binary.Complexfloat32Serializer), mrd.binary.ImageArraySerializer(), mrd.binary.NDArraySerializer(yardl.binary.Uint16Serializer), mrd.binary.NDArraySerializer(yardl.binary.Int16Serializer), mrd.binary.NDArraySerializer(yardl.binary.Uint32Serializer), mrd.binary.NDArraySerializer(yardl.binary.Int32Serializer), mrd.binary.NDArraySerializer(yardl.binary.Float32Serializer), mrd.binary.NDArraySerializer(yardl.binary.Float64Serializer), mrd.binary.NDArraySerializer(yardl.binary.Complexfloat32Serializer), mrd.binary.NDArraySerializer(yardl.binary.Complexfloat64Serializer)}, {@mrd.StreamItem.Acquisition, @mrd.StreamItem.WaveformUint32, @mrd.StreamItem.ImageUint16, @mrd.StreamItem.ImageInt16, @mrd.StreamItem.ImageUint32, @mrd.StreamItem.ImageInt32, @mrd.StreamItem.ImageFloat, @mrd.StreamItem.ImageDouble, @mrd.StreamItem.ImageComplexFloat, @mrd.StreamItem.ImageComplexDouble, @mrd.StreamItem.AcquisitionBucket, @mrd.StreamItem.ReconData, @mrd.StreamItem.ArrayComplexFloat, @mrd.StreamItem.ImageArray, @mrd.StreamItem.NdArrayUint16, @mrd.StreamItem.NdArrayInt16, @mrd.StreamItem.NdArrayUint32, @mrd.StreamItem.NdArrayInt32, @mrd.StreamItem.NdArrayFloat, @mrd.StreamItem.NdArrayDouble, @mrd.StreamItem.NdArrayComplexFloat, @mrd.StreamItem.NdArrayComplexDouble}));
     end
   end
 

matlab/toolbox/+mrd/+binary/NDArrayHeaderSerializer.m

@@ -0,0 +1,26 @@
+% This file was generated by the "yardl" tool. DO NOT EDIT.
+
+classdef NDArrayHeaderSerializer < yardl.binary.RecordSerializer
+  methods
+    function self = NDArrayHeaderSerializer()
+      field_serializers{1} = yardl.binary.VectorSerializer(yardl.binary.EnumSerializer('mrd.ArrayDimension', @mrd.ArrayDimension, yardl.binary.Int32Serializer));
+      field_serializers{2} = yardl.binary.EnumSerializer('mrd.ArrayType', @mrd.ArrayType, yardl.binary.Int32Serializer);
+      field_serializers{3} = yardl.binary.MapSerializer(yardl.binary.StringSerializer, yardl.binary.VectorSerializer(yardl.binary.UnionSerializer('mrd.ArrayMetaValue', {yardl.binary.StringSerializer, yardl.binary.Int64Serializer, yardl.binary.Float64Serializer}, {@mrd.ArrayMetaValue.String, @mrd.ArrayMetaValue.Int64, @mrd.ArrayMetaValue.Float64})));
+      [email protected]('mrd.NDArrayHeader', field_serializers);
+    end
+
+    function write(self, outstream, value)
+      arguments
+        self
+        outstream (1,1) yardl.binary.CodedOutputStream
+        value (1,1) mrd.NDArrayHeader
+      end
+      self.write_(outstream, value.dimension_labels, value.array_type, value.meta);
+    end
+
+    function value = read(self, instream)
+      fields = self.read_(instream);
+      value = mrd.NDArrayHeader(dimension_labels=fields{1}, array_type=fields{2}, meta=fields{3});
+    end
+  end
+end

matlab/toolbox/+mrd/+binary/NDArraySerializer.m

@@ -0,0 +1,25 @@
+% This file was generated by the "yardl" tool. DO NOT EDIT.
+
+classdef NDArraySerializer < yardl.binary.RecordSerializer
+  methods
+    function self = NDArraySerializer(t_serializer)
+      field_serializers{1} = mrd.binary.NDArrayHeaderSerializer();
+      field_serializers{2} = yardl.binary.DynamicNDArraySerializer(t_serializer);
+      [email protected]('mrd.NDArray', field_serializers);
+    end
+
+    function write(self, outstream, value)
+      arguments
+        self
+        outstream (1,1) yardl.binary.CodedOutputStream
+        value (1,1) mrd.NDArray
+      end
+      self.write_(outstream, value.head, value.data);
+    end
+
+    function value = read(self, instream)
+      fields = self.read_(instream);
+      value = mrd.NDArray(head=fields{1}, data=fields{2});
+    end
+  end
+end

matlab/toolbox/+mrd/AnyNDArray.m

@@ -0,0 +1,97 @@
+% This file was generated by the "yardl" tool. DO NOT EDIT.
+
+classdef AnyNDArray < yardl.Union
+  methods (Static)
+    function res = NDArrayUint16(value)
+      res = mrd.AnyNDArray(1, value);
+    end
+
+    function res = NDArrayInt16(value)
+      res = mrd.AnyNDArray(2, value);
+    end
+
+    function res = NDArrayUint32(value)
+      res = mrd.AnyNDArray(3, value);
+    end
+
+    function res = NDArrayInt32(value)
+      res = mrd.AnyNDArray(4, value);
+    end
+
+    function res = NDArrayFloat(value)
+      res = mrd.AnyNDArray(5, value);
+    end
+
+    function res = NDArrayDouble(value)
+      res = mrd.AnyNDArray(6, value);
+    end
+
+    function res = NDArrayComplexFloat(value)
+      res = mrd.AnyNDArray(7, value);
+    end
+
+    function res = NDArrayComplexDouble(value)
+      res = mrd.AnyNDArray(8, value);
+    end
+
+    function z = zeros(varargin)
+      elem = mrd.AnyNDArray(0, yardl.None);
+      if nargin == 0
+        z = elem;
+        return;
+      end
+      sz = [varargin{:}];
+      if isscalar(sz)
+        sz = [sz, sz];
+      end
+      z = reshape(repelem(elem, prod(sz)), sz);
+    end
+  end
+
+  methods
+    function res = isNDArrayUint16(self)
+      res = self.index == 1;
+    end
+
+    function res = isNDArrayInt16(self)
+      res = self.index == 2;
+    end
+
+    function res = isNDArrayUint32(self)
+      res = self.index == 3;
+    end
+
+    function res = isNDArrayInt32(self)
+      res = self.index == 4;
+    end
+
+    function res = isNDArrayFloat(self)
+      res = self.index == 5;
+    end
+
+    function res = isNDArrayDouble(self)
+      res = self.index == 6;
+    end
+
+    function res = isNDArrayComplexFloat(self)
+      res = self.index == 7;
+    end
+
+    function res = isNDArrayComplexDouble(self)
+      res = self.index == 8;
+    end
+
+    function eq = eq(self, other)
+      eq = isa(other, "mrd.AnyNDArray") && all([self.index_] == [other.index_], 'all') && all([self.value] == [other.value], 'all');
+    end
+
+    function ne = ne(self, other)
+      ne = ~self.eq(other);
+    end
+
+    function t = tag(self)
+      tags_ = ["NDArrayUint16", "NDArrayInt16", "NDArrayUint32", "NDArrayInt32", "NDArrayFloat", "NDArrayDouble", "NDArrayComplexFloat", "NDArrayComplexDouble"];
+      t = tags_(self.index_);
+    end
+  end
+end

matlab/toolbox/+mrd/ArrayDimension.m

@@ -0,0 +1,61 @@
+% This file was generated by the "yardl" tool. DO NOT EDIT.
+
+classdef ArrayDimension < uint64
+  methods (Static)
+    function v = CHANNEL
+      v = mrd.ArrayDimension(0);
+    end
+    function v = Z
+      v = mrd.ArrayDimension(1);
+    end
+    function v = Y
+      v = mrd.ArrayDimension(2);
+    end
+    function v = X
+      v = mrd.ArrayDimension(3);
+    end
+    function v = FREQUENCY
+      v = mrd.ArrayDimension(4);
+    end
+    function v = BASIS
+      v = mrd.ArrayDimension(5);
+    end
+    function v = SAMPLES
+      v = mrd.ArrayDimension(6);
+    end
+    function v = LOC
+      v = mrd.ArrayDimension(7);
+    end
+    function v = S
+      v = mrd.ArrayDimension(8);
+    end
+    function v = N
+      v = mrd.ArrayDimension(9);
+    end
+    function v = E2
+      v = mrd.ArrayDimension(10);
+    end
+    function v = E1
+      v = mrd.ArrayDimension(11);
+    end
+    function v = E0
+      v = mrd.ArrayDimension(12);
+    end
+    function v = TIME
+      v = mrd.ArrayDimension(13);
+    end
+
+    function z = zeros(varargin)
+      elem = mrd.ArrayDimension(0);
+      if nargin == 0
+        z = elem;
+        return;
+      end
+      sz = [varargin{:}];
+      if isscalar(sz)
+        sz = [sz, sz];
+      end
+      z = reshape(repelem(elem, prod(sz)), sz);
+    end
+  end
+end

matlab/toolbox/+mrd/ArrayMeta.m

@@ -0,0 +1,4 @@
+% This file was generated by the "yardl" tool. DO NOT EDIT.
+
+classdef ArrayMeta < yardl.Map
+end