Merge pull request #23 from JuliaOcean/v0p1p11b

V0p1p11b

src/MITprof.jl

@@ -4,6 +4,7 @@ using Dates, MeshArrays, NCDatasets, OrderedCollections, UnPack
 
 import ArgoData.ProfileNative
 import ArgoData.ProfileStandard
+import ArgoData.MITprofStandard
 import ArgoData.ArgoTools
 import ArgoData.GriddedFields
 import ArgoData.GDAC
@@ -174,6 +175,111 @@ end
 
 ##
 
+"""
+    write(fil::String,mps::Vector{MITprofStandard})
+
+Create an MITprof file from an MITprofStandard input.  
+"""
+function write(fil::String,mp::MITprofStandard)
+
+    iPROF = size(mp.T,1)
+    iDEPTH = size(mp.T,2)
+    iINTERP = 4
+    lTXT = 30
+
+    NCDataset(fil,"c") do ds
+        defDim(ds,"iPROF",iPROF)
+        defDim(ds,"iDEPTH",iDEPTH)
+        defDim(ds,"iINTERP",iINTERP)
+        defDim(ds,"lTXT",lTXT)
+        ds.attrib["title"] = "MITprof file created by ArgoData.jl (WIP)"
+    end
+
+    ##
+
+    NCDataset(fil,"a") do ds
+        defVar(ds,"prof_depth",mp.depth[:],("iDEPTH",),
+              attrib = OrderedDict(
+           "units" => "m",
+           "_FillValue" => -9999.,
+           "long_name" => "Depth"
+        ))
+    end
+
+    ncwrite_1d(mp.lon[:],fil,"prof_lon","Longitude (degree East)","degrees_east")
+    ncwrite_1d(mp.lat[:],fil,"prof_lat","Latitude (degree North)","degrees_north")
+    ncwrite_1d(mp.date[:],fil,"prof_date","Julian day since Jan-1-0000"," ") ##need units
+#    ncwrite_1d(mp.ymd[;],fil,"prof_YYYYMMDD","year (4 digits), month (2 digits), day (2 digits)"," ") ##need units
+#    ncwrite_1d(mp.hms[:],fil,"prof_HHMMSS","hour (2 digits), minute (2 digits), second (2 digits)"," ") ##need units
+
+    ncwrite_2d(mp.T[:,:],fil,"prof_T","Temperature","degree_Celsius")
+    ncwrite_2d(mp.Tw[:,:],fil,"prof_Tweight","Temperature least-square weight","(degree C)^-2")
+    ncwrite_2d(mp.Te[:,:],fil,"prof_Testim","Temperature atlas (monthly clim.)","degree_Celsius")
+
+    ncwrite_2d(mp.S[:,:],fil,"prof_S","Salinity","psu")
+    ncwrite_2d(mp.Sw[:,:],fil,"prof_Sweight","Salinity least-square weight","(psu)^-2")
+    ncwrite_2d(mp.Se[:,:],fil,"prof_Sestim","Salinity atlas (monthly clim.)","psu")
+end
+
+function my_defVar(fil,var)
+    T=eltype(skipmissing(var))
+    NCDataset(fil,"a") do ds
+        defVar(ds,name(var),T,dimnames(var),
+            attrib = OrderedDict(
+            "units" => var.attrib["units"],
+            "_FillValue" => var.attrib["_FillValue"],
+            "long_name" => var.attrib["long_name"]
+        ))
+    end
+end
+
+"""
+    write(fil::String,mps::Vector{MITprofStandard})
+
+Create an MITprof file from a vector of MITprofStandard inputs.  
+"""
+function write(fil::String,mps::Vector{MITprofStandard})
+
+    nps=cumsum([size(mps[i].T,1) for i in 1:length(mps)])
+
+    iPROF = nps[end]
+    iDEPTH = size(mps[1].T,2)
+    iINTERP = 4
+    lTXT = 30
+
+    NCDataset(fil,"c") do ds
+        defDim(ds,"iPROF",iPROF)
+        defDim(ds,"iDEPTH",iDEPTH)
+        defDim(ds,"iINTERP",iINTERP)
+        defDim(ds,"lTXT",lTXT)
+        ds.attrib["title"] = "MITprof file created by ArgoData.jl (WIP)"
+    end
+
+    ##
+
+    list_variables=(:lon,:lat,:date,:depth,:T,:Te,:Tw,:S,:Se,:Sw)
+    #to be added : ID, ymd, hms, and maybe more
+    [my_defVar(fil,getfield(mps[1],var)) for var in list_variables]
+
+    list_variables=(:lon,:lat,:date,:T,:Te,:Tw,:S,:Se,:Sw)
+    ds=NCDataset(fil,"a")
+    for var in list_variables
+        for ii in 1:length(mps)
+            tmp=getfield(mps[ii],var)
+            ii==1 ? jj=collect(1:nps[1]) : jj=collect(nps[ii-1]+1:nps[ii])
+            if ndims(tmp)==1
+                ds[name(tmp)][jj]=tmp[:]
+            else
+                ds[name(tmp)][jj,:]=tmp[:,:]
+            end
+        end
+    end
+    close(ds)
+
+end
+
+##
+
 function ncwrite_2d(data,fil,name,long_name,units)
     NCDataset(fil,"a") do ds
       defVar(ds,name,data,("iPROF","iDEPTH"),

src/data_structures.jl

@@ -99,7 +99,7 @@ function MITprofStandard(fil::String)
     ds=Dataset(fil)
     haskey(ds,"prof_descr") ? ID=ds["prof_descr"] : ID=split(basename(fil),"_")[1]
     MITprofStandard(fil,
-        ds["prof_lon"],ds["prof_lat"],ds["prof_depth"],ds["prof_date"],
+        ds["prof_lon"],ds["prof_lat"],ds["prof_date"],ds["prof_depth"],
         fill(ID,size(ds["prof_lon"])),
         ds["prof_T"],ds["prof_Testim"],ds["prof_Tweight"],
         ds["prof_S"],ds["prof_Sestim"],ds["prof_Sweight"]

test/runtests.jl

@@ -21,5 +21,8 @@ using Test
 
     mp=MITprofStandard(output_file)
 
+    MITprof.write(output_file*".tmp1",mp);
+    MITprof.write(output_file*".tmp2",[mp,mp]);
+
     @test isa(mp,MITprofStandard)
 end