Add and test oxideconversion for tuple datasets

src/utilities/Geochemistry.jl

@@ -195,6 +195,15 @@
 
 ## --- Oxide conversions
 
+    function fillifnan!(dest::AbstractArray, source::AbstractArray, factor::Number=1.0)
+        @inbounds for i in eachindex(dest, source)
+            if isnan(dest[i]) && !isnan(source[i])
+                dest[i] = source[i] * factor
+            end
+        end
+        return dest
+    end
+
     """
     ```julia
     dataset = oxideconversion(dataset::Dict; unitratio::Number=10000)
@@ -209,6 +218,7 @@
         return oxideconversion!(result)
     end
     export oxideconversion
+
     """
     ```julia
     dataset = oxideconversion!(dataset::Dict; unitratio::Number=10000)
@@ -225,18 +235,47 @@
         # end
 
         # Array of elements to convert
-        source = ["Si","Ti","Al","Fe","Fe","Mg","Ca","Mn","Li","Na","K","P","Cr","Ni","Co","C","S","H"]
-        dest = ["SiO2","TiO2","Al2O3","FeOT","Fe2O3T","MgO","CaO","MnO","Li2O","Na2O","K2O","P2O5","Cr2O3","NiO","CoO","CO2","SO2","H2O"]
-        conversionfactor = [2.13932704290547,1.66847584248889,1.88944149488507,1.28648836426407,1.42973254639611,1.65825961736268,1.39919258253823,1.29121895771597,2.1526657060518732,1.34795912485574,1.20459963614796,2.29133490474735,1.46154369861159,1.27258582901258,1.27147688434143,3.66405794688203,1.99806612601372,8.93601190476191]
+        source = ("Si","Ti","Al","Fe","Fe","Mg","Ca","Mn","Li","Na","K","P","Cr","Ni","Co","C","S","H")
+        dest = ("SiO2","TiO2","Al2O3","FeOT","Fe2O3T","MgO","CaO","MnO","Li2O","Na2O","K2O","P2O5","Cr2O3","NiO","CoO","CO2","SO2","H2O")
+        conversionfactor = (2.13932704290547,1.66847584248889,1.88944149488507,1.28648836426407,1.42973254639611,1.65825961736268,1.39919258253823,1.29121895771597,2.1526657060518732,1.34795912485574,1.20459963614796,2.29133490474735,1.46154369861159,1.27258582901258,1.27147688434143,3.66405794688203,1.99806612601372,8.93601190476191)
 
         # If source field exists, fill in destination from source
         for i ∈ eachindex(source)
             if haskey(dataset, source[i])
                 if ~haskey(dataset, dest[i]) # If destination field doesn't exist, make it.
                     dataset[dest[i]] = fill(NaN, size(dataset[source[i]]))
+                    if haskey(dataset, "elements")
+                        dataset["elements"] = dataset["elements"] ∪ (dest[i],)
+                    end
+                end
+                oxide = dataset[dest[i]]
+                metal = dataset[source[i]]
+                fillifnan!(oxide, metal, conversionfactor[i]/unitratio)
+            end
+        end
+
+        return dataset
+    end
+
+    function oxideconversion!(dataset::NamedTuple; unitratio::Number=10000)
+        # Convert major elements (Ti, Al, etc.) into corresponding oxides (TiO2, Al2O3)...
+        # for i ∈ eachindex(source)
+        #     conversionfactor(i)=mass.percation.(dest[i])./mass.(source[i]);
+        # end
+
+        # Array of elements to convert
+        source = (:Si, :Ti, :Al, :Fe, :Fe, :Mg, :Ca, :Mn, :Li, :Na, :K, :P, :Cr, :Ni, :Co, :C, :S, :H)
+        dest = (:SiO2, :TiO2, :Al2O3, :FeOT, :Fe2O3T, :MgO, :CaO, :MnO, :Li2O, :Na2O, :K2O, :P2O5, :Cr2O3, :NiO, :CoO, :CO2, :SO2, :H2O)
+        conversionfactor = (2.13932704290547,1.66847584248889,1.88944149488507,1.28648836426407,1.42973254639611,1.65825961736268,1.39919258253823,1.29121895771597,2.1526657060518732,1.34795912485574,1.20459963614796,2.29133490474735,1.46154369861159,1.27258582901258,1.27147688434143,3.66405794688203,1.99806612601372,8.93601190476191)
+
+        # If source field exists, fill in destination from source
+        for i ∈ eachindex(source)
+            if haskey(dataset, source[i])
+                if haskey(dataset, dest[i]) # If destination field doesn't exist, make it.
+                    oxide = dataset[dest[i]]
+                    metal = dataset[source[i]]
+                    fillifnan!(oxide, metal, conversionfactor[i]/unitratio)
                 end
-                t = isnan.(dataset[dest[i]]) .& (.~ isnan.(dataset[source[i]]))
-                dataset[dest[i]][t] = dataset[source[i]][t] .* (conversionfactor[i] / unitratio)
             end
         end
 

test/testGeochemistry.jl

@@ -22,6 +22,17 @@
     @test all(D["CaO"] .≈ (molarmass["Ca"]+molarmass["O"])/molarmass["Ca"])
     @test all(D["P2O5"] .≈ (molarmass["P"]+2.5*molarmass["O"])/molarmass["P"])
 
+
+    DT = elementify(unelementify(D), importas=:Tuple)
+    for e in (:FeOT, :MgO, :CaO, :P2O5)
+        DT[e] .= NaN 
+    end
+    oxideconversion!(DT)
+    @test all(DT.FeOT .≈ (molarmass["Fe"]+molarmass["O"])/molarmass["Fe"])
+    @test all(DT.MgO .≈ (molarmass["Mg"]+molarmass["O"])/molarmass["Mg"])
+    @test all(DT.CaO .≈ (molarmass["Ca"]+molarmass["O"])/molarmass["Ca"])
+    @test all(DT.P2O5 .≈ (molarmass["P"]+2.5*molarmass["O"])/molarmass["P"])
+
     # Weathering indices
     @test CIA(14.8577, 4.5611, 3.29641, 2.3992) ≈ 47.66582778067264
     @test WIP(3.2964, 4.5611, 2.3992, 5.9121) ≈ 78.40320264846837

test/testImport.jl

@@ -43,7 +43,7 @@
     @test importdataset("tupledataset.csv", ',', importas=:Tuple, elements=(elements...,), skipstart=1) == datatuple
 
     @test exportdataset(datatuple, "tupledataset.tsv") == nothing
-    @test importdataset("tupledataset.csv", importas=:Tuple) == datatuple
+    @test importdataset("tupledataset.tsv", '\t', importas=:Tuple) == datatuple
 
     @test exportdataset(datatuple, "tupledataset.csv", ',', digits=6) == nothing
     @test importdataset("tupledataset.csv", ',', importas=:Tuple).Lv == round.(datatuple.Lv, digits=6)
@@ -151,4 +151,10 @@
     @test isa(darray, Array{Float64,2})
     @test size(darray) == (5, length(keys(d)))
 
-## ---
+## --- Clean up
+
+    rm("dictdataset.csv")
+    rm("tupledataset.csv")
+    rm("tupledataset.tsv")
+
+## --- End of File

test/testUtilities.jl

@@ -47,7 +47,7 @@
     @test data == [-9999 -9999 5 2; -9999 20 100 36; 3 8 35 10; 32 42 50 6; 88 75 27 9; 13 5 1 -9999]
     @test metadata["nodata"] == -9999
 
-
+    rm("grid.asc")
 
     # Random lat-lon generation
     @test isa(randlatlon(), Tuple{Float64,Float64})