Add functions for getting parts of a file as struct (#97)

* Add functions for getting parts of a file as struct

* Add tests and further functions

* Fix tests

src/MDF.jl

@@ -401,7 +401,7 @@ measFramePermutation(f::MDFFileV1)::Union{Vector{Int64}, Nothing} = nothing
 measFramePermutation(f::MDFFileV2)::Union{Vector{Int64}, Nothing} = @keyoptional f["/measurement/framePermutation"]
 measSparsityTransformation(f::MDFFileV1)::Union{String, Nothing} = nothing
 measSparsityTransformation(f::MDFFileV2)::Union{String, Nothing} = @keyoptional f["/measurement/sparsityTransformation"]
-measSubsamplingIndices(f::MDFFileV2)::Union{Array{Integer, 4}, Nothing} = @keyoptional f["/measurement/subsamplingIndices"]
+measSubsamplingIndices(f::MDFFileV2)::Union{Array{Int64, 4}, Nothing} = @keyoptional f["/measurement/subsamplingIndices"]
 
 fullFramePermutation(f::MDFFile) = fullFramePermutation(f, calibIsMeanderingGrid(f))
 

src/MDFInMemory.jl

@@ -418,7 +418,7 @@ mutable struct MDFv2Measurement <: MDFv2InMemoryPart
   "Name of the applied sparsity transformation; optional if !isSparsityTransformed"
   sparsityTransformation::Union{String, Nothing}
   "Subsampling indices \\beta{j,c,k,b}; optional if !isSparsityTransformed"
-  subsamplingIndices::Union{Array{Integer, 4}, Nothing}
+  subsamplingIndices::Union{Array{Int64, 4}, Nothing}
 
   function MDFv2Measurement(;
     data = missing,
@@ -1303,6 +1303,57 @@ for (fieldname, fieldtype) in zip(fieldnames(MDFv2InMemory), fieldtypes(MDFv2InM
   end
 end
 
+# Extract individual parts of an MDFFile as in-memory parts
+for (partFieldnameStr, partPrefix) ∈ prefixes
+  partFieldnameSymbol = Symbol(partFieldnameStr)
+  partInMemorySymbol = Symbol(lowercase(partFieldnameStr[6:end]))
+  type_ = getfield(MPIFiles, partFieldnameSymbol)
+  fields = fieldnames(type_)
+  functionNames = [let fieldString=string(field_); partPrefix != "" ? Symbol(partPrefix*uppercase(fieldString[1])*fieldString[2:end]) : Symbol(fieldString) end for field_ ∈ fields if field_ ∉ [:drivefield, :receiver]]
+
+  @eval begin
+    @doc $"""
+      $partFieldnameStr(file::MDFFile)
+
+    Create a `$partFieldnameStr` from the respective section in the given `file`.
+    """
+    function $partFieldnameSymbol(file::MDFFile)::$type_
+      instance = $partFieldnameSymbol()
+      for (fieldname_, functionName_) in zip($fields, $functionNames)
+        setfield!(instance, fieldname_, eval(functionName_)(file))
+      end
+
+      return instance
+    end
+  end
+
+  if !(partFieldnameStr == "MDFv2Drivefield" || partFieldnameStr == "MDFv2Receiver")
+    @eval begin
+      @doc $"""
+        $partFieldnameStr(file::MDFv2InMemory)
+
+      Create a `$partFieldnameStr` from the respective section in the given `file`.
+      """
+      function $partFieldnameSymbol(file::MDFv2InMemory)::$type_
+        return file.$partInMemorySymbol
+      end
+    end
+  else
+    @eval begin
+      @doc $"""
+        $partFieldnameStr(file::MDFv2InMemory)
+
+      Create a `$partFieldnameStr` from the respective section in the given `file`.
+      """
+      function $partFieldnameSymbol(file::MDFv2InMemory)::$type_
+        return file.acquisition.$partInMemorySymbol
+      end
+    end
+  end
+end
+MDFv2Drivefield(part::MDFv2Acquisition) = part.drivefield
+MDFv2Receiver(part::MDFv2Acquisition) = part.receiver
+
 # And some utility functions
 measIsCalibProcessed(mdf::MDFv2InMemory)::Union{Bool, Missing} = measIsFramePermutation(mdf) && 
                                                                  measIsFourierTransformed(mdf) &&

test/MDFInMemory.jl

@@ -41,6 +41,7 @@ end
 
   fnMeasV2_converted = joinpath(tmpdir,"mdfim","measurement_V2_converted.mdf")
   fnSMV2_converted = joinpath(tmpdir,"mdfim","systemMatrix_V2_converted.mdf")
+  fnPart_converted = joinpath(tmpdir,"mdfim","imparts.mdf")
 
   @testset "Conversion" begin
     @testset "Fields" begin
@@ -396,7 +397,8 @@ end
       order = "xyz",
       positions = fill(0.0, (3, O)),
       size = [1, 1, 1],
-      snr = fill(0.0, (K, C, J))
+      snr = fill(0.0, (K, C, J)),
+      isMeanderingGrid = false # Not in specs for MDF v2!
     )
     mdf.reconstruction = MDFv2Reconstruction(
       data = fill(0, (S, P, Q)),
@@ -582,4 +584,148 @@ end
       test_mdf_replacement(mdf, :recoSize, [1, 1, 2], "The product of `size` with `[1, 1, 2]` must equal P.")
     end
   end
+
+  @testset "Part retrieval" begin
+    A = 1 # tracer materials/injections for multi-color MPI
+    N = 2 # acquired frames (N = O + E), same as a spatial position for calibration
+    E = 1 # acquired background frames (E = N − O)
+    O = 1 # acquired foreground frames (O = N − E)
+    B = 1 # coefficients stored after sparsity transformation (B \\le O)
+    J = 1 # periods within one frame
+    Y = 1 # partitions of each patch position
+    C = 1 # receive channels
+    D = 1 # drive-field channels
+    F = 1 # frequencies describing the drive-field waveform
+    V = 800 # points sampled at receiver during one drive-field period
+    W = V # sampling points containing processed data (W = V if no frequency selection or bandwidth reduction has been applied)
+    K = Int(V/2 + 1)# frequencies describing the processed data (K = V/2 + 1 if no frequency selection or bandwidth reduction has been applied)
+    Q = 1 # frames in the reconstructed MPI data set
+    P = 1 # voxels in the reconstructed MPI data set
+    S = 1 # channels in the reconstructed MPI data set
+
+    mdf = MDFv2InMemory()
+    mdf.root = MDFv2Root(
+      time=DateTime("2021-04-26T17:12:21.686"),
+      uuid=UUID("946a039e-48de-47ee-957e-a15af437e0be"),
+      version=VersionNumber("2.1.0")
+    )
+    mdf.study = MDFv2Study(
+      description = "n.a.",
+      name = "n.a.",
+      number = 1,
+      time = DateTime("2021-04-26T17:12:21.686"),
+      uuid = UUID("f2f3ae66-2fc3-49f7-91f9-71c1c2dc15e7")
+    )
+    mdf.experiment = MDFv2Experiment(
+      description = "n.a.",
+      isSimulation = true,
+      name = "n.a.",
+      number = 1,
+      subject = "n.a.",
+      uuid = UUID("3076d4bc-a2ef-46ef-8a99-dcd047379b8a")
+    )
+    mdf.tracer = MDFv2Tracer(
+      batch = fill("n.a.", A),
+      concentration = fill(1.0, A),
+      injectionTime = fill(DateTime("2021-04-26T17:12:21.686"), A),
+      name = fill("MyAwesomeTracer", A),
+      solute = fill("n.a.", A),
+      vendor = fill("Me", A),
+      volume = fill(1.0, A),
+    )
+    mdf.scanner = MDFv2Scanner(
+      boreSize = 0.3,
+      facility = "MyAwesomeInstitute",
+      manufacturer = "MeMyselfAndI",
+      name = "MyAwesomeScanner",
+      operator = "JustMe",
+      topology = "FFL" # Of course ;)
+    )
+    drivefield = MDFv2Drivefield(
+      baseFrequency = 40e3,
+      cycle = 1600/40e3,
+      divider = fill(1600, (F, D)),
+      numChannels = D,
+      phase = fill(0.0, (F, D, J)),
+      strength = fill(1.0, (F, D, J)),
+      waveform = fill("sine", (F, D)),
+    )
+    receiver = MDFv2Receiver(
+      bandwidth = 20e3,
+      dataConversionFactor = repeat([1/2^16 0]', outer=(1, C)),
+      inductionFactor = fill(1.0, C),
+      numChannels = C,
+      numSamplingPoints = V,
+      transferFunction = fill(1+0.5im, (K, C)),
+      unit = "V"
+    )
+    mdf.acquisition = MDFv2Acquisition(
+      gradient = fill(0.0, (3, 3, Y, J)),
+      numAverages = 1,
+      numFrames = N,
+      numPeriodsPerFrame = J,
+      offsetField = fill(0.0, (3, Y, J)),
+      startTime = DateTime("2021-04-26T17:12:21.686"),
+      drivefield = drivefield,
+      receiver = receiver
+    )
+    mdf.measurement = MDFv2Measurement(;
+      data = fill(0, (K, C, J, N)),
+      # framePermutation = fill(0, N),
+      # frequencySelection = collect(1:K),
+      isBackgroundCorrected = false,
+      isBackgroundFrame = vcat(fill(true, E), fill(false, O)),
+      isFastFrameAxis = false,
+      isFourierTransformed = false,
+      isFramePermutation = false,
+      isFrequencySelection = false,
+      isSparsityTransformed = false,
+      isSpectralLeakageCorrected = false,
+      isTransferFunctionCorrected = false,
+      # sparsityTransformation = "DCT-I",
+      # subsamplingIndices = fill(0, (B, K, C, J))
+    )
+    mdf.calibration = MDFv2Calibration(
+      deltaSampleSize = fill(0.001, 3),
+      fieldOfView = fill(0.2, 3),
+      fieldOfViewCenter = fill(0.0, 3),
+      method = "robot",
+      offsetFields = fill(0.0, (3, O)),
+      order = "xyz",
+      positions = fill(0.0, (3, O)),
+      size = [1, 1, 1],
+      snr = fill(0.0, (K, C, J)),
+      isMeanderingGrid = false
+    )
+    mdf.reconstruction = MDFv2Reconstruction(
+      data = fill(0, (S, P, Q)),
+      fieldOfView = fill(0.2, 3),
+      fieldOfViewCenter = fill(0.0, 3),
+      isOverscanRegion = fill(false, P),
+      order = "xyz",
+      positions = fill(0.0, (3, P)),
+      size = [1, 1, 1]
+    )
+
+    saveasMDF(fnPart_converted, mdf)
+    file = MPIFile(fnPart_converted)
+
+    for partFieldnameStr in keys(MPIFiles.prefixes)
+      partInMemorySymbol = Symbol(lowercase(partFieldnameStr[6:end]))
+
+      partim = eval(Symbol(partFieldnameStr))(mdf)
+      part = eval(Symbol(partFieldnameStr))(file)
+
+      if !(partFieldnameStr == "MDFv2Drivefield" || partFieldnameStr == "MDFv2Receiver")
+        @test partim == getfield(mdf, partInMemorySymbol)
+        @test all([getfield(part, fieldname_) == getfield(getfield(mdf, partInMemorySymbol), fieldname_) for fieldname_ ∈ fieldnames(typeof(part)) if fieldname_ ∉ [:drivefield, :receiver]])
+      else
+        @test partim == getfield(mdf.acquisition, partInMemorySymbol)
+        @test all([getfield(part, fieldname_) == getfield(getfield(mdf.acquisition, partInMemorySymbol), fieldname_) for fieldname_ ∈ fieldnames(typeof(part))])
+      end 
+    end
+
+    @test MDFv2Drivefield(MDFv2Acquisition(mdf)) == drivefield
+    @test MDFv2Receiver(MDFv2Acquisition(mdf)) == receiver
+  end
 end