add test

Author: aTrotier

Project.toml

@@ -9,14 +9,24 @@ MRICoilSensitivities = "c57eb701-aafc-44a2-a53c-128049758959"
 MRIFiles = "5a6f062f-bf45-497d-b654-ad17aae2a530"
 MRIReco = "bdf86e05-2d2b-5731-a332-f3fe1f9e047f"
 NIfTI = "a3a9e032-41b5-5fc4-967a-a6b7a19844d3"
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 QuantitativeMRI = "659767e3-31a7-4dc1-8563-6e03f484b231"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
 [compat]
+JSON = "0.21"
+MRICoilSensitivities = "0.1.3"
+MRIFiles = "0.3.2"
+MRIReco = "0.9.0"
+NIfTI = "0.6.0"
+Pkg = "1.10"
+QuantitativeMRI = "0.1.3"
+Statistics = "1.10"
 julia = "1.10"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+LazyArtifacts = "4af54fe1-eca0-43a8-85a7-787d91b784e3"
 
 [targets]
-test = ["Test"]
+test = ["Test","LazyArtifacts"]

src/BIDS.jl

@@ -74,6 +74,11 @@ function write_bids_MP2RAGE(d::Dict,subname::AbstractString,folder="")
   p_MP2 = d["params_MP2RAGE"]
 
   # define JSON dict
+  proj = Pkg.project()
+  gen_dict = Dict{Any,Any}()
+  gen_dict["Name"] = proj.name
+  gen_dict["Version"] = string(proj.version)
+
   JSON_dict = Dict{Any,Any}()
   JSON_dict["InversonTime"]= [p_MP2.TI₁,p_MP2.TI₂] #s
   JSON_dict["RepetitionTimeExcitation"]= p_MP2.TR
@@ -82,10 +87,19 @@ function write_bids_MP2RAGE(d::Dict,subname::AbstractString,folder="")
   JSON_dict["FlipAngle"]= [p_MP2.α₁,p_MP2.α₂]
   JSON_dict["MagneticFieldStrength"] = MagneticField
   JSON_dict["Units"] = "arbitrary"
+  JSON_dict["GeneratedBy"]=gen_dict
+
 
   # Write the dictionary to a JSON file
   open(joinpath(folder,subname,"MP2RAGE.json"), "w") do f
     JSON.print(f, JSON_dict, 4)  # Indent 4 spaces for readability
   end
 
+  # Write dataset description
+
+
+  JSON_dict = Dict{Any,Any}()
+  JSON_dict["generatedBy"] = proj.name
+  JSON_dict["version"] = proj.version
+
 end

src/SEQ_BRUKER_a_MP2RAGE_CS_360.jl

@@ -8,9 +8,11 @@ using QuantitativeMRI
 using Statistics
 using JSON
 using NIfTI
+using Pkg
 
 # Write your package code here.
 include("bruker_sequence.jl")
 include("reconstruction.jl")
 include("BIDS.jl")
+
 end

src/reconstruction.jl

@@ -58,6 +58,7 @@ function reconstruction_MP2RAGE(path_bruker;mean_NR::Bool = false,paramsCS=Dict(
   params = merge(params,paramsCS)
 
   x_approx = reconstruction(acq, params).data
+  
   if mean_NR
     x_approx = mean(x_approx,dims=6) # average accross repetition
   end

test/Artifacts.toml

@@ -0,0 +1,6 @@
+[MP2RAGE_data]
+git-tree-sha1 = "04cd4c29bb9e2aeb5384fbc70a9af0e1a37ca369"
+
+    [[MP2RAGE_data.download]]
+    sha256 = "1f1b703c79db66ba6ef620651eca431cb0319d87f1eafa53826cb11a93afe4a8"
+    url = "https://zenodo.org/records/14051522/files/data.tar.gz"

test/runtests.jl

@@ -1,6 +1,24 @@
 using SEQ_BRUKER_a_MP2RAGE_CS_360
 using Test
+using LazyArtifacts
+using SEQ_BRUKER_a_MP2RAGE_CS_360.NIfTI
+using SEQ_BRUKER_a_MP2RAGE_CS_360.JSON
 
 @testset "SEQ_BRUKER_a_MP2RAGE_CS_360.jl" begin
-    # Write your tests here.
+    datadir = artifact"MP2RAGE_data"
+    @info "The test data is located at $datadir."
+
+    path_bruker = joinpath(datadir, "MP2RAGE_FULLY")
+    d = reconstruction_MP2RAGE(path_bruker; mean_NR=true)
+
+    @test size(d["im_reco"]) == (128,128,96,1,2)
+    @test size(d["T1map"]) == (128,128,96,1)
+    
+    write_bids_MP2RAGE(d,"sub","")
+
+    ni = niread(joinpath("sub","anat","sub_T1map.nii.gz")).raw
+    @test d["T1map"] == ni
+
+    JSON_dict = JSON.parsefile(joinpath("sub","MP2RAGE.json"))
+    @test JSON_dict["RepetitionTimePreparation"] == 5000
 end