Port #100 to master and commit.

MRIFiles/src/ISMRMRD/HDF5Types.jl

@@ -219,6 +219,10 @@ struct HDF5_Acquisition
   data::HVL_T{Float32} #for some reason this is stored as float
 end
 
+struct HDF5_AcquisitionHeaderOnly
+  head::AcquisitionHeaderImmutable
+end
+
 function get_hdf5type_acquisition()
   off = i -> Cint(fieldoffset(HDF5_Acquisition,i))
   datatype = h5t_create(H5T_COMPOUND, sizeof(HDF5_Acquisition) )
@@ -240,6 +244,15 @@ function get_hdf5type_acquisition()
   return datatype
 end
 
+function get_hdf5type_acquisition_header_only()
+  off = i -> Cint(fieldoffset(HDF5_AcquisitionHeaderOnly,i))
+  datatype = h5t_create(H5T_COMPOUND, sizeof(HDF5_AcquisitionHeaderOnly) )
+  d1 = get_hdf5type_acquisitionheader()
+  h5t_insert(datatype, "head", off(1), d1)
+  h5t_close(d1)
+
+  return datatype
+end
 
 function writeProfiles(file, dataset, profiles::Vector{Profile})
 

MRIFiles/src/ISMRMRD/ISMRMRD.jl

@@ -12,30 +12,41 @@ end
 
 reads the `ISMRMRDFile` f and stores the result in a `RawAcquisitionDataObject`
 """
-function MRIBase.RawAcquisitionData(f::ISMRMRDFile, dataset="dataset")
+function MRIBase.RawAcquisitionData(f::ISMRMRDFile, dataset="dataset"; 
+                                    slice=nothing, repetition=nothing, contrast=nothing)
 
   h5open(f.filename) do h
     headerStr = read(h["/$(dataset)/xml"])
     params = GeneralParameters(headerStr[1])
 
-    d = read(h["/$(dataset)/data"])
-    M = length(d)
-    profiles = Profile[]
-
-    for m=1:M
-      head = read_header(d[m].head)
-      D = Int(head.trajectory_dimensions)
-      chan = Int(head.active_channels)
+    M = size(h["/$(dataset)/data"]) # for some reason this is a matrix 
 
-      traj = isempty(d[m].traj) ? Matrix{Float32}(undef,0,0) : reshape(d[m].traj, D, :)
+    # In the next lines we only read the headers of the profiles such that
+    # we can later filter on them
+    dTypeHeader = get_hdf5type_acquisition_header_only()
+    headerData = Array{HDF5_AcquisitionHeaderOnly}(undef, M)
+    HDF5.API.h5d_read(h["/$(dataset)/data"], dTypeHeader, H5S_ALL, H5S_ALL, H5P_DEFAULT, headerData)
 
-      if !isempty(d[m].data)
-        dat = reshape(reinterpret(ComplexF32,d[m].data), :, chan)
-      else
-        dat = Matrix{ComplexF32}(undef,0,0)
-      end
+    profiles = Profile[]
 
-      push!(profiles, Profile(head,traj,dat) )
+    for m in CartesianIndices(M)
+      if (repetition == nothing || headerData[m].head.idx.repetition in repetition) &&
+          (slice == nothing || headerData[m].head.idx.slice in slice) &&
+          (contrast == nothing || headerData[m].head.idx.contrast in contrast)
+         d = h["/$(dataset)/data"][m] # Here we read the header again. This could/should be avoided
+         head = read_header(d.head)
+         D = Int(head.trajectory_dimensions)
+         chan = Int(head.active_channels)
+         traj = isempty(d.traj) ? Matrix{Float32}(undef, 0, 0) : reshape(d.traj, D, :)
+
+         if !isempty(d.data)
+           dat = reshape(reinterpret(ComplexF32, d.data), :, chan)
+         else
+           dat = Matrix{ComplexF32}(undef,0,0)
+         end
+
+         push!(profiles, Profile(head, traj, dat) )
+       end
     end
     return RawAcquisitionData(params, profiles)
   end

MRIFiles/test/testISMRMRD.jl

@@ -36,6 +36,14 @@ IrecoCopy = reconstruction(AcquisitionData(acqCopy), params)
 
 @test IrecoCopy == Ireco
 
+### test partial read
+
+acqPartial = RawAcquisitionData(f, slice=1) # slice 1 is not contained in the file
+
+@test length(acqPartial.profiles) == 0
+
+### test spiral data
+
 filename = joinpath(datadir, "simple_spiral.h5")
 
 f = ISMRMRDFile(filename)