adding dktnames to module and adding as default to ADNIDatasets

src/ADNIDatasets.jl

@@ -4,6 +4,8 @@ using CSV, DataFrames
 using Setfield
 using Dates
 
+include("dktnames.jl")
+
 struct ADNIScanData
     Date::Date
     SUVR::Vector{Float64}
@@ -24,16 +26,16 @@ struct ADNIDataset
     rois::Vector{String}
 end
 
-function ADNISubject(subid, df::DataFrame, dktnames, reference_region::String)
+function ADNISubject(subid, df::DataFrame, roi_names, reference_region::String)
     sub = filter( x -> x.RID == subid, df )
 
     if "EXAMDATE" ∈ names(sub)
         subdate = sub[!, :EXAMDATE]
     elseif "SCANDATE" ∈ names(sub)
         subdate = sub[!, :SCANDATE]
     end
-    subsuvr = sub[!, suvr_name.(dktnames)] |> dropmissing |> disallowmissing |> Array
-    subvol = sub[!, vol_name.(dktnames)] |> dropmissing |> disallowmissing |> Array
+    subsuvr = sub[!, suvr_name.(roi_names)] |> dropmissing |> disallowmissing |> Array
+    subvol = sub[!, vol_name.(roi_names)] |> dropmissing |> disallowmissing |> Array
     subref = sub[!, suvr_name.(reference_region)]
     n_scans = length(subdate)
     if n_scans == size(subsuvr, 1) == size(subvol, 1)
@@ -46,23 +48,23 @@ function ADNISubject(subid, df::DataFrame, dktnames, reference_region::String)
     end
 end
 
-function ADNIDataset(df::DataFrame, dktnames; min_scans=1, max_scans=Inf, reference_region="inferiorcerebellum")
+function ADNIDataset(df::DataFrame, roi_names=dktnames; min_scans=1, max_scans=Inf, reference_region="inferiorcerebellum")
     subjects = unique(df.RID)
 
     n_scans = [count(==(sub), df.RID) for sub in subjects]
     multi_subs = subjects[findall(x -> min_scans <= x <= max_scans, n_scans)]
 
     adnisubjects = Vector{ADNISubject}()
     for sub in multi_subs 
-        sub = ADNISubject(sub, df, dktnames, reference_region)
+        sub = ADNISubject(sub, df, roi_names, reference_region)
         if sub isa ADNISubject
             push!(adnisubjects, sub)
         end
     end
     ADNIDataset(
         length(adnisubjects),
         adnisubjects,
-        dktnames
+        roi_names
     )
 end
 

src/dktnames.jl

@@ -0,0 +1,83 @@
+dktnames = ["ctx_rh_lateralorbitofrontal",
+"ctx_rh_parsorbitalis",
+"ctx_rh_frontalpole",
+"ctx_rh_medialorbitofrontal",
+"ctx_rh_parstriangularis",
+"ctx_rh_parsopercularis",
+"ctx_rh_rostralmiddlefrontal",
+"ctx_rh_superiorfrontal",
+"ctx_rh_caudalmiddlefrontal",
+"ctx_rh_precentral",
+"ctx_rh_paracentral",
+"ctx_rh_rostralanteriorcingulate",
+"ctx_rh_caudalanteriorcingulate",
+"ctx_rh_posteriorcingulate",
+"ctx_rh_isthmuscingulate",
+"ctx_rh_postcentral",
+"ctx_rh_supramarginal",
+"ctx_rh_superiorparietal",
+"ctx_rh_inferiorparietal",
+"ctx_rh_precuneus",
+"ctx_rh_cuneus",
+"ctx_rh_pericalcarine",
+"ctx_rh_lateraloccipital",
+"ctx_rh_lingual",
+"ctx_rh_fusiform",
+"ctx_rh_parahippocampal",
+"ctx_rh_entorhinal",
+"ctx_rh_temporalpole",
+"ctx_rh_inferiortemporal",
+"ctx_rh_middletemporal",
+"ctx_rh_bankssts",
+"ctx_rh_superiortemporal",
+"ctx_rh_transversetemporal",
+"ctx_rh_insula",
+"Right_Thalamus_Proper",
+"Right_Caudate",
+"Right_Putamen",
+"Right_Pallidum",
+"Right_Accumbens_area",
+"Right_Hippocampus",
+"Right_Amygdala",
+"ctx_lh_lateralorbitofrontal",
+"ctx_lh_parsorbitalis",
+"ctx_lh_frontalpole",
+"ctx_lh_medialorbitofrontal",
+"ctx_lh_parstriangularis",
+"ctx_lh_parsopercularis",
+"ctx_lh_rostralmiddlefrontal",
+"ctx_lh_superiorfrontal",
+"ctx_lh_caudalmiddlefrontal",
+"ctx_lh_precentral",
+"ctx_lh_paracentral",
+"ctx_lh_rostralanteriorcingulate",
+"ctx_lh_caudalanteriorcingulate",
+"ctx_lh_posteriorcingulate",
+"ctx_lh_isthmuscingulate",
+"ctx_lh_postcentral",
+"ctx_lh_supramarginal",
+"ctx_lh_superiorparietal",
+"ctx_lh_inferiorparietal",
+"ctx_lh_precuneus",
+"ctx_lh_cuneus",
+"ctx_lh_pericalcarine",
+"ctx_lh_lateraloccipital",
+"ctx_lh_lingual",
+"ctx_lh_fusiform",
+"ctx_lh_parahippocampal",
+"ctx_lh_entorhinal",
+"ctx_lh_temporalpole",
+"ctx_lh_inferiortemporal",
+"ctx_lh_middletemporal",
+"ctx_lh_bankssts",
+"ctx_lh_superiortemporal",
+"ctx_lh_transversetemporal",
+"ctx_lh_insula",
+"Left_Thalamus_Proper",
+"Left_Caudate",
+"Left_Putamen",
+"Left_Pallidum",
+"Left_Accumbens_area",
+"Left_Hippocampus",
+"Left_Amygdala",
+"brainstem"]

test/runtests.jl

@@ -8,14 +8,12 @@ using Test
 
 testpath = dirname(relpath(@__FILE__))
 datapath = joinpath(testpath, "adni-test.csv")
-dktpath = joinpath(testpath, "dktnames.csv")
 
 datadf = CSV.read(datapath, DataFrame)
-dktdf = CSV.read(dktpath, DataFrame)
 
-data_scans_3 = ADNIDataset(datadf, dktdf.region; min_scans=3)
-data_scans_1 = ADNIDataset(datadf, dktdf.region; min_scans=1)
-data_scans_2 = ADNIDataset(datadf, dktdf.region; min_scans=2, max_scans=2)
+data_scans_3 = ADNIDataset(datadf; min_scans=3)
+data_scans_1 = ADNIDataset(datadf; min_scans=1)
+data_scans_2 = ADNIDataset(datadf; min_scans=2, max_scans=2)
 
 @testset "ADNIDatasets.jl" begin
     # test number of subjects are correct