Tests for MRIBase.rawdata and kDataCart

MRIBase/Project.toml

@@ -15,7 +15,8 @@ NFFTTools = "0.2.4"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 
 [targets]
-test = ["Test"]
+test = ["Test", "Random"]
 

MRIBase/test/Utils.jl

@@ -0,0 +1,82 @@
+module Utils
+using MRIBase
+
+export get_default_cartesian_raw_acq_data
+
+function get_default_cartesian_raw_acq_data_2d(n_profiles, n_samples_per_profile, data = nothing)
+	params = Dict{String, Any}()
+	params["trajectory"] = "Cartesian"
+	params["encodedSize"] = [n_samples_per_profile, n_profiles]
+	params["encodedFOV"] = [n_samples_per_profile, n_profiles, 1]
+
+	traj_nodes = kspaceNodes(trajectory(Float32, "Cartesian", n_profiles, n_samples_per_profile))
+	traj_nodes = reshape(traj_nodes, 2, n_samples_per_profile, n_profiles)
+	if data == nothing
+		data = rand(ComplexF32, n_samples_per_profile, n_profiles)
+	end
+
+	profiles = Vector{Profile}(undef, n_profiles)
+	for i_profile in 1:n_profiles
+		profile_head = AcquisitionHeader(idx = EncodingCounters(kspace_encode_step_1 = i_profile - 1), center_sample = div(n_samples_per_profile, 2))
+		profiles[i_profile] = Profile(
+			profile_head,
+			traj_nodes[:, :, i_profile],
+			reshape(data[:, i_profile], n_samples_per_profile, 1),
+		)
+	end
+
+	f = RawAcquisitionData(
+		params,
+		profiles,
+	)
+	return f
+end
+
+
+function get_default_cartesian_raw_acq_data_3d(n_slices, n_profiles, n_samples_per_profile, data = nothing, mask=nothing)
+	params = Dict{String, Any}()
+	params["trajectory"] = "Cartesian"
+	params["encodedSize"] = [n_samples_per_profile, n_profiles, n_slices]
+	params["encodedFOV"] = [n_samples_per_profile, n_profiles, n_slices]
+
+	traj_nodes = kspaceNodes(trajectory(Float32, "Cartesian3D", n_profiles, n_samples_per_profile, numSlices=n_slices))
+	traj_nodes = reshape(traj_nodes, 3, n_samples_per_profile, n_profiles, n_slices)
+	if data == nothing
+		data = rand(ComplexF32, n_samples_per_profile, n_profiles, n_slices)
+	end
+
+	n_elemens =  mask == nothing ? n_profiles*n_slices : sum(mask)
+	profiles = Vector{Profile}(undef, n_elemens)
+	i = 1
+	for i_profile in 1:n_profiles
+		for i_slice in 1:n_slices
+			if mask != nothing && !mask[1, i_profile, i_slice]
+				continue
+			end
+
+			profile_head = AcquisitionHeader(
+				idx = EncodingCounters(
+					kspace_encode_step_1 = i_profile - 1,
+					kspace_encode_step_2 = i_slice - 1,
+					), 
+				center_sample = div(n_samples_per_profile, 2),
+				trajectory_dimensions=3,
+			)
+			# profiles[(i_slice-1)*n_profiles+i_profile] = Profile(
+			profiles[i] = Profile(
+				profile_head,
+				traj_nodes[:, :, i_profile, i_slice],
+				reshape(data[:, i_profile, i_slice], n_samples_per_profile, 1),
+			)
+			i += 1
+		end
+	end
+
+	f = RawAcquisitionData(
+		params,
+		profiles,
+	)
+	return f
+end
+
+end

MRIBase/test/runtests.jl

@@ -1,5 +1,9 @@
 using Test, MRIBase
 
+include("Utils.jl")
+
 include("testTrajectories.jl")
 include("testFlags.jl")
-include("testConversion.jl")
+include("testRawAcqData.jl")
+include("testAcqData.jl")
+include("testConversion.jl")

MRIBase/test/testAcqData.jl

@@ -0,0 +1,34 @@
+using .Utils: get_default_cartesian_raw_acq_data_2d, get_default_cartesian_raw_acq_data_3d
+
+
+@testset "kDataCart restores the order when profiles are shuffled" begin
+	n_profiles = 10
+	n_samples_per_profile = 12
+	data = rand(ComplexF32, n_samples_per_profile, n_profiles)
+	f = get_default_cartesian_raw_acq_data_2d(n_profiles, n_samples_per_profile, data)
+	f.profiles = shuffle(f.profiles)
+	acq = AcquisitionData(f)
+	kdata = kDataCart(acq)[:, :, 1, 1, 1, 1]
+	@test isapprox(kdata, data)
+end
+
+
+@testset "kDataCart restores the order when profiles are shuffled for 3D data" begin
+	n_profiles = 10
+	n_samples_per_profile = 12
+	n_slices = 3
+	data = rand(ComplexF32, n_samples_per_profile, n_profiles, n_slices)
+	elipsoid_mask = zeros(Bool, 1, n_profiles, n_slices)
+	for i in 1:n_profiles
+		for j in 1:n_slices
+			elipsoid_mask[1, i, j] = (i-5)^2/25 + (j-2)^2/4 < 0.5
+		end
+	end
+	data .*= elipsoid_mask
+	f = get_default_cartesian_raw_acq_data_3d(n_slices, n_profiles, n_samples_per_profile, data, elipsoid_mask)
+	f.profiles = shuffle(f.profiles)
+	acq = AcquisitionData(f)
+	kdata = kDataCart(acq)[:, :, :, 1, 1, 1]
+
+	@test isapprox(kdata, data)
+end

MRIBase/test/testRawAcqData.jl

@@ -0,0 +1,26 @@
+using Random
+using MRIBase
+using .Utils: get_default_cartesian_raw_acq_data_2d
+
+
+@testset "MRIBase.rawdata with dense 2D cartesian data" begin
+	n_profiles = 10
+	n_samples_per_profile = 12
+	data = rand(ComplexF32, n_samples_per_profile, n_profiles)
+	f = get_default_cartesian_raw_acq_data_2d(n_profiles, n_samples_per_profile, data)
+	kdata = MRIBase.rawdata(f)
+	kdata = reshape(kdata, n_samples_per_profile, n_profiles)
+	@test isapprox(kdata, data)
+end
+
+
+@testset "MRIBase.rawdata is not supposed to handle shuffles profiles" begin
+	n_profiles = 10
+	n_samples_per_profile = 12
+	data = rand(ComplexF32, n_samples_per_profile, n_profiles)
+	f = get_default_cartesian_raw_acq_data_2d(n_profiles, n_samples_per_profile, data)
+    shuffle!(f.profiles)
+	kdata = MRIBase.rawdata(f)
+	kdata = reshape(kdata, n_samples_per_profile, n_profiles)
+	@test !isapprox(kdata, data)
+end