Merge pull request #24 from JuliaOcean/v0p1p11c

V0p1p11c

docs/make.jl

@@ -12,8 +12,8 @@ makedocs(;
     assets=String[],
 )
 
-list_files=GDAC.Argo_files_list()
-GDAC.CSV.write("Argo_float_files.csv",list_files)
+files_list=GDAC.files_list()
+GDAC.CSV.write("Argo_float_files.csv",files_list)
 mv("Argo_float_files.csv",joinpath(@__DIR__,"build", "Argo_float_files.csv"))
 
 deploydocs(;

examples/ArgoToMITprof.jl

@@ -20,7 +20,7 @@ meta=ArgoTools.meta(input_file,output_file)
 meta["greylist"]=greylist
 
 gridded_fields=GriddedFields.load()
-output_file=MITprof.MITprof_format(meta,gridded_fields,input_file,output_file)
+output_file=MITprof.format(meta,gridded_fields,input_file,output_file)
 
 ##
 

examples/ArgoToMITprof_step2.jl

@@ -121,7 +121,7 @@ ArgoTools.prof_test_set2!(prof_std,meta)
 meta["fileOut"]=joinpath(tempdir(),"MITprof_example.nc")
 isfile(meta["fileOut"]) ? rm(meta["fileOut"], force=true) : nothing
 
-MITprof.MITprof_write(meta,[prof],[prof_std])
+MITprof.write(meta,[prof],[prof_std])
 # -
 
 # ### Show Global Maps (via interpolation)

src/GDAC.jl

@@ -21,17 +21,17 @@ function grey_list()
 end
 
 """
-    Argo_files_list()
+    files_list()
 
 Get list of Argo float files from Ifremer GDAC server     
 <ftp://ftp.ifremer.fr/ifremer/argo/dac/>
 
 ```
 using ArgoData
-files_list=GDAC.Argo_files_list()
+files_list=GDAC.files_list()
 ```
 """
-function Argo_files_list()
+function files_list()
     ftp=FTP("ftp://ftp.ifremer.fr/ifremer/argo/dac/")
 
     files_list=DataFrame("folder" => [],"wmo" => [])
@@ -47,17 +47,17 @@ function Argo_files_list()
 end
 
 """
-    Argo_files_list(fil::String)
+    files_list(fil::String)
 
 Get list of Argo float files from csv file with columns two columns -- `folder` and `wmo`.
 
 ```
 using ArgoData
 fil="https://raw.githubusercontent.com/JuliaOcean/ArgoData.jl/gh-pages/dev/Argo_float_files.csv"
-files_list=GDAC.Argo_files_list(fil)
+files_list=GDAC.files_list(fil)
 ```
 """
-function Argo_files_list(fil::String)
+function files_list(fil::String)
     if isfile(fil)
         DataFrame(CSV.File(fil))
     else
@@ -66,7 +66,7 @@ function Argo_files_list(fil::String)
 end
 
 """
-    Argo_float_download(file::DataFrameRow,suff="prof",ftp=missing)
+    download_file(file::DataFrameRow,suff="prof",ftp=missing)
 
 Download Argo file from the GDAC server (`<ftp://ftp.ifremer.fr/ifremer/argo/dac/>` by default)
 to a temporary folder (`joinpath(tempdir(),"Argo_DAC_files")`)
@@ -84,16 +84,16 @@ Example :
 
 ```
 using ArgoData
-files_list=GDAC.Argo_files_list()
-GDAC.Argo_float_download(files_list[10000,:])
+files_list=GDAC.files_list()
+GDAC.download_file(files_list[10000,:])
 
 #or:
 
 ftp="ftp://usgodae.org/pub/outgoing/argo/dac/"
-GDAC.Argo_float_download(files_list[10000,:],"meta",ftp)
+GDAC.download_file(files_list[10000,:],"meta",ftp)
 ```
 """
-function Argo_float_download(file::DataFrameRow,suff="prof",ftp=missing)
+function download_file(file::DataFrameRow,suff="prof",ftp=missing)
     path=joinpath(tempdir(),"Argo_DAC_files")
     !isdir(path) ? mkdir(path) : nothing
     folder=file.folder

src/MITprof.jl

@@ -11,14 +11,8 @@ import ArgoData.GDAC
 
 ## reading MITprof files in bulk
 
-function ncread(f::String,v::String)
-    Dataset(f,"r") do ds
-        ds[v][:]
-    end
-end
-
 """
-    MITprof_read(f::String="MITprof/MITprof_mar2016_argo9506.nc")
+    read_positions(f::String="MITprof/MITprof_mar2016_argo9506.nc")
 
 Standard Depth Argo Data Example.
 
@@ -31,7 +25,7 @@ The produced figure shows the number of profiles as function of time for a chose
 using ArgoData, Plots
 
 fi="MITprof/MITprof_mar2016_argo9506.nc"
-(lo,la,ye)=MITprof.MITprof_read(fi)
+(lo,la,ye)=MITprof.read_positions(fi)
 
 h = histogram(ye,bins=20,label=fi[end-10:end],title="Argo profiles")
 
@@ -40,7 +34,7 @@ kk=findall((ye.>ye0) .* (ye.<ye1))
 scatter(lo[kk],la[kk],label=fi[end-10:end],title="Argo profiles count")
 ```
 """
-function MITprof_read(f::String="MITprof/MITprof_mar2016_argo9506.nc")
+function read_positions(f::String="MITprof/MITprof_mar2016_argo9506.nc")
     #i = ncinfo(f)
     lo = ncread(f, "prof_lon")
     la = ncread(f, "prof_lat")
@@ -50,11 +44,11 @@ function MITprof_read(f::String="MITprof/MITprof_mar2016_argo9506.nc")
 end
 
 """
-    MITprof_read_loop(pth::String="profiles/")
+    read_positions_loop(pth::String="profiles/")
 
 Standard Depth Argo Data Collection -- see `?MITprof.read` for detail.
 """
-function MITprof_read_loop(pth::String="profiles/")
+function read_positions_loop(pth::String="profiles/")
     λ=("MITprof_mar2016_argo9506.nc","MITprof_mar2016_argo0708.nc",
     "MITprof_mar2016_argo0910.nc","MITprof_mar2016_argo1112.nc",
     "MITprof_mar2016_argo1314.nc","MITprof_mar2016_argo1515.nc")
@@ -73,15 +67,15 @@ end
 ## writing MITprof files
 
 """
-    MITprof.MITprof_write(meta,profiles,profiles_std;path="")
+    MITprof.write(meta,profiles,profiles_std;path="")
 
-Write to file.
+Create an MITprof file from meta data + profiles during `MIRprof.format`.
 
 ```
-MITprof.MITprof_write(meta,profiles,profiles_std)
+MITprof.write(meta,profiles,profiles_std)
 ```
 """
-function MITprof_write(meta::Dict,profiles::Array,profiles_std::Array;path="")
+function write(meta::Dict,profiles::Array,profiles_std::Array;path="")
 
     isempty(path) ? p=tempdir() : p=path
     fil=joinpath(p,meta["fileOut"])
@@ -176,62 +170,11 @@ end
 ##
 
 """
-    write(fil::String,mps::Vector{MITprofStandard})
+    write(fil::String,mp::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,mp::MITprofStandard) = write(fil,[mp])
 
 """
     write(fil::String,mps::Vector{MITprofStandard})
@@ -259,7 +202,7 @@ function write(fil::String,mps::Vector{MITprofStandard})
 
     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]
+    [defVar_fromVar(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")
@@ -280,6 +223,24 @@ end
 
 ##
 
+function ncread(f::String,v::String)
+    Dataset(f,"r") do ds
+        ds[v][:]
+    end
+end
+
+function defVar_fromVar(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
+
 function ncwrite_2d(data,fil,name,long_name,units)
     NCDataset(fil,"a") do ds
       defVar(ds,name,data,("iPROF","iDEPTH"),
@@ -305,15 +266,15 @@ end
 ##
 
 """
-    MITprof_format(meta,gridded_fields,input_file,output_file="")
+    format(meta,gridded_fields,input_file,output_file="")
 
 From Argo file name as input : read input file content, process into the MITprof format, and write to MITprof file.
 
 ```
-MITprof.MITprof_format(meta,gridded_fields,input_file)
+MITprof.format(meta,gridded_fields,input_file)
 ```
 """
-function MITprof_format(meta,gridded_fields,input_file,output_file="")
+function format(meta,gridded_fields,input_file,output_file="")
     @unpack Γ,msk,T,S,σT,σS = gridded_fields
     z_std = meta["z_std"]
 
@@ -391,23 +352,23 @@ function MITprof_format(meta,gridded_fields,input_file,output_file="")
         profiles_std[m]=prof_std
     end
 
-    MITprof.MITprof_write(meta,profiles,profiles_std)
+    MITprof.write(meta,profiles,profiles_std)
 
     output_file
 end
 
 """
-    Mitprof_format_loop(II)
+    format_loop(II)
 
-Loop over files and call `MITprof_format`.
+Loop over files and call `format`.
 
 ```
 gridded_fields=GriddedFields.load()
-files_list=GDAC.Argo_files_list()
-MITprof.MITprof_format_loop(gridded_fields,files_list,1:10)
+files_list=GDAC.files_list()
+MITprof.format_loop(gridded_fields,files_list,1:10)
 ```   
 """
-function MITprof_format_loop(gridded_fields,files_list,II)
+function format_loop(gridded_fields,files_list,II)
 
     pth0=joinpath(tempdir(),"Argo_MITprof_files")
     pth1=joinpath(pth0,"input")
@@ -429,7 +390,7 @@ function MITprof_format_loop(gridded_fields,files_list,II)
         if isfile(input_file)
             ds=Dataset(input_file)
             if haskey(ds,"PSAL")*haskey(ds,"TEMP")
-                output_file=MITprof.MITprof_format(meta,gridded_fields,input_file,output_file)
+                output_file=MITprof.format(meta,gridded_fields,input_file,output_file)
                 println("✔ $(wmo)")
             else
                 io = open(output_file[1:end-3]*".txt", "w")

src/tools.jl

@@ -4,11 +4,11 @@ using Dates, YAML, NCDatasets, CSV, DataFrames, Interpolations, Printf
 import ArgoData.ProfileNative
 
 """
-    mitprof_interp_setup(fil::String)
+    meta_init(fil::String)
 
-Get parameters to call `MITprof_format` from yaml file (`fil`, e.g. "../examples/ArgoToMITprof.yml").
+Get parameters to call `MITprof.format` from yaml file (`fil`, e.g. "../examples/ArgoToMITprof.yml").
 """
-function mitprof_interp_setup(fil="")
+function meta_init(fil="")
 
     if !isempty(fil)
         meta=YAML.load(open(fil))
@@ -94,10 +94,10 @@ end
 """
     meta(input_file,output_file)
 
-Get parameters to call `MITprof_format` which will read from `input_file` to create `output_file`.
+Get parameters to call `MITprof.format` which will read from `input_file` to create `output_file`.
 """
 function meta(input_file,output_file)
-    meta=ArgoTools.mitprof_interp_setup()
+    meta=ArgoTools.meta_init()
     #f=1
     #input_file=meta["dirIn"]*meta["fileInList"][f]
     meta["fileOut"]=output_file

test/runtests.jl

@@ -3,11 +3,11 @@ using Test
 
 @testset "ArgoData.jl" begin
 
-    files_list=GDAC.Argo_files_list()
-    GDAC.Argo_float_download(files_list[10000,:])
+    files_list=GDAC.files_list()
+    GDAC.download_file(files_list[10000,:])
 
     ftp="ftp://usgodae.org/pub/outgoing/argo/dac/"
-    fil=GDAC.Argo_float_download(files_list[10000,:],"meta",ftp)
+    fil=GDAC.download_file(files_list[10000,:],"meta",ftp)
 
     @test isfile(fil)