### A Pluto.jl notebook ###
# v0.19.16

using Markdown
using InteractiveUtils

# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error).
macro bind(def, element)
    quote
        local iv = try Base.loaded_modules[Base.PkgId(Base.UUID("6e696c72-6542-2067-7265-42206c756150"), "AbstractPlutoDingetjes")].Bonds.initial_value catch; b -> missing; end
        local el = $(esc(element))
        global $(esc(def)) = Core.applicable(Base.get, el) ? Base.get(el) : iv(el)
        el
    end
end

# ╔═╡ 67a5c3f5-5cd5-46e7-8b2a-83299387c18a
begin
	using ArgoData, Downloads, NCDatasets, Statistics
	using PrettyTables, PlutoUI
end

# ╔═╡ 708c3f0f-a8d4-45dd-85f2-c8bb934d2576
TableOfContents()

# ╔═╡ 52f89eed-0ab3-4082-b58f-45c90eaec205
md"""# MITprof Format & Cost Function

The `MITprof` format and cost function for [standard depth data](https://doi.org/10.7910/DVN/EE3C40) is defined in [Forget, et al 2015](http://dx.doi.org/10.5194/gmd-8-3071-2015).

Formatting native [Argo](https://argopy.readthedocs.io/en/latest/what_is_argo.html#what-is-argo) files into the MITprof format is done via `MITprof.format`
"""

# ╔═╡ 21062d00-f859-4d58-afed-d9748ca7f4f6
md"""## Cost Function

!!! note
    Cost functions are normalized distances between estimate and data. See [Forget, et al 2015](http://dx.doi.org/10.5194/gmd-8-3071-2015) for detail.
"""

# ╔═╡ f7950381-9ea8-4160-861b-dc0bf4b5bfe4
begin
	mywmo_bind = @bind wmo_txt confirm(TextField(default="6900900"))
	
	md"""## Select a Float
	\
	$(mywmo_bind)

	(default here is 6900900)
	
	## Alternate Floats (subset)	
	"""
end

# ╔═╡ 847f8175-0e8d-4fa7-8712-c6b47adbeab8
begin
	files_list=GDAC.files_list()
	nf=size(files_list,1)
	md"""Total number of identified floats is $(nf)"""
end

# ╔═╡ 89efaaca-e499-4367-bc23-c97a86f02d4b
begin
	pretty_table(files_list[1:2000:nf,:],
		header = names(files_list),
		header_crayon = crayon"yellow bold",
		highlighters  = ( hl_col(1, crayon"white"),hl_col(2, crayon"white") ),
	)
end

# ╔═╡ f094f531-57d9-4b8e-aa23-02b2c443bdf3
md"""## Julia packages"""

# ╔═╡ 39d1da64-217a-41b4-b2dc-07df1cfd3220
begin
	wmo=parse(Int,wmo_txt)
	folder=files_list[files_list.wmo.==wmo,"folder"][1]

	url0="https://data-argo.ifremer.fr/dac/$(folder)/"
	input_url=url0*"/$(wmo)/$(wmo)_prof.nc"
	input_file=joinpath(tempdir(),"$(wmo)_prof.nc")
	output_file=joinpath(tempdir(),"ncdev","$(wmo)_MITprof.nc")
	
	!isfile(input_file) ? fil=Downloads.download(input_url,input_file) : nothing
	!isdir(dirname(output_file)) ? mkdir(dirname(output_file)) : nothing
	isfile(output_file) ? rm(output_file) : nothing
	
	fil=joinpath(tempdir(),"ar_greylist.txt")
	isfile(fil) ? greylist=GDAC.grey_list(fil) : greylist=""

	"Done with Files Names"
end

# ╔═╡ ac23620a-b772-4bbb-95d2-d06ab497709c
begin
	meta=ArgoTools.meta(input_file,output_file)
	meta["greylist"]=greylist	
	gridded_fields=GriddedFields.load()
	"Done with initialization"
end

# ╔═╡ 48088d9f-3766-4b07-89dd-f57a9d8c7bd0
output_file2=MITprof.format(meta,gridded_fields,input_file,output_file)

# ╔═╡ 268c7d77-e2c2-48fa-a5c8-9c59e8fbc7f2
begin
	ds=Dataset(output_file2)
	
	println("Cost function values for float $(wmo) :")
	
	costT=ds["prof_Tweight"].* ((ds["prof_T"]-ds["prof_Testim"]).^2);
	ii=findall( ((!ismissing).(costT)).+(ds["prof_Tweight"].>0).>1 );

	costS=ds["prof_Sweight"].* ((ds["prof_S"]-ds["prof_Sestim"]).^2)
	ii=findall( ((!ismissing).(costS)).+(ds["prof_Sweight"].>0).>1 );
	
	println("mean T cost = $(mean(costT[ii])) ")
	println("mean S cost = $(mean(costS[ii])) ")

	if wmo==6900900
		println("")
		println("Reference values for default float (6900900) :")
		println("mean T cost = 1.4125672446566286")
		println("mean S cost = 1.365848840650727")
	end
end

# ╔═╡ 00000000-0000-0000-0000-000000000001
PLUTO_PROJECT_TOML_CONTENTS = """
[deps]
ArgoData = "9eb831cf-c491-48dc-bed4-6aca718df73c"
Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
PlutoUI = "7f904dfe-b85e-4ff6-b463-dae2292396a8"
PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"

[compat]
ArgoData = "~0.1.14"
NCDatasets = "~0.12.9"
PlutoUI = "~0.7.49"
PrettyTables = "~2.2.2"
"""

# ╔═╡ 00000000-0000-0000-0000-000000000002
PLUTO_MANIFEST_TOML_CONTENTS = """
# This file is machine-generated - editing it directly is not advised

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[[deps.MacroTools]]
deps = ["Markdown", "Random"]
git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2"
uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
version = "0.5.10"

[[deps.Markdown]]
deps = ["Base64"]
uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"

[[deps.MbedTLS_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
version = "2.28.0+0"

[[deps.MeshArrays]]
deps = ["CatViews", "Dates", "LazyArtifacts", "NearestNeighbors", "Pkg", "Printf", "SparseArrays", "Statistics", "Unitful"]
git-tree-sha1 = "81e21d78042b9b55e8b1ae39baf7d5436f138699"
uuid = "cb8c808f-1acf-59a3-9d2b-6e38d009f683"
version = "0.2.32"

[[deps.Missings]]
deps = ["DataAPI"]
git-tree-sha1 = "bf210ce90b6c9eed32d25dbcae1ebc565df2687f"
uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28"
version = "1.0.2"

[[deps.Mmap]]
uuid = "a63ad114-7e13-5084-954f-fe012c677804"

[[deps.MozillaCACerts_jll]]
uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
version = "2022.2.1"

[[deps.NCDatasets]]
deps = ["CFTime", "DataStructures", "Dates", "NetCDF_jll", "NetworkOptions", "Printf"]
git-tree-sha1 = "8d5cd8ff530228bf172f7d4e91d9ae9e8b8e8ad3"
uuid = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
version = "0.12.9"

[[deps.NearestNeighbors]]
deps = ["Distances", "StaticArrays"]
git-tree-sha1 = "440165bf08bc500b8fe4a7be2dc83271a00c0716"
uuid = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
version = "0.4.12"

[[deps.NetCDF]]
deps = ["DiskArrays", "Formatting", "NetCDF_jll"]
git-tree-sha1 = "328178762645783b20495d408ab317b4c2d25b1a"
uuid = "30363a11-5582-574a-97bb-aa9a979735b9"
version = "0.11.7"

[[deps.NetCDF_jll]]
deps = ["Artifacts", "HDF5_jll", "JLLWrappers", "LibCURL_jll", "Libdl", "Pkg", "XML2_jll", "Zlib_jll"]
git-tree-sha1 = "072f8371f74c3b9e1b26679de7fbf059d45ea221"
uuid = "7243133f-43d8-5620-bbf4-c2c921802cf3"
version = "400.902.5+1"

[[deps.NetworkOptions]]
uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
version = "1.2.0"

[[deps.OceanStateEstimation]]
deps = ["CodecZlib", "Distributed", "Downloads", "FortranFiles", "JLD2", "MITgcmTools", "MeshArrays", "NCDatasets", "Pkg", "Printf", "Scratch", "SharedArrays", "Statistics", "TOML", "Tar"]
git-tree-sha1 = "a4cab7532f422a2dfdff141695f2d5d16ced4593"
uuid = "891f6deb-a4f5-4bc5-a2e3-1e8f649cdd2c"
version = "0.3.1"

[[deps.OffsetArrays]]
deps = ["Adapt"]
git-tree-sha1 = "f71d8950b724e9ff6110fc948dff5a329f901d64"
uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
version = "1.12.8"

[[deps.OpenBLAS_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"]
uuid = "4536629a-c528-5b80-bd46-f80d51c5b363"
version = "0.3.20+0"

[[deps.OpenSSL_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "f6e9dba33f9f2c44e08a020b0caf6903be540004"
uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95"
version = "1.1.19+0"

[[deps.OrderedCollections]]
git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c"
uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
version = "1.4.1"

[[deps.PCRE2_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15"
version = "10.40.0+0"

[[deps.Parsers]]
deps = ["Dates", "SnoopPrecompile"]
git-tree-sha1 = "b64719e8b4504983c7fca6cc9db3ebc8acc2a4d6"
uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
version = "2.5.1"

[[deps.Pkg]]
deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
version = "1.8.0"

[[deps.PlutoUI]]
deps = ["AbstractPlutoDingetjes", "Base64", "ColorTypes", "Dates", "FixedPointNumbers", "Hyperscript", "HypertextLiteral", "IOCapture", "InteractiveUtils", "JSON", "Logging", "MIMEs", "Markdown", "Random", "Reexport", "URIs", "UUIDs"]
git-tree-sha1 = "eadad7b14cf046de6eb41f13c9275e5aa2711ab6"
uuid = "7f904dfe-b85e-4ff6-b463-dae2292396a8"
version = "0.7.49"

[[deps.PooledArrays]]
deps = ["DataAPI", "Future"]
git-tree-sha1 = "a6062fe4063cdafe78f4a0a81cfffb89721b30e7"
uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720"
version = "1.4.2"

[[deps.Preferences]]
deps = ["TOML"]
git-tree-sha1 = "47e5f437cc0e7ef2ce8406ce1e7e24d44915f88d"
uuid = "21216c6a-2e73-6563-6e65-726566657250"
version = "1.3.0"

[[deps.PrettyTables]]
deps = ["Crayons", "Formatting", "LaTeXStrings", "Markdown", "Reexport", "StringManipulation", "Tables"]
git-tree-sha1 = "96f6db03ab535bdb901300f88335257b0018689d"
uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
version = "2.2.2"

[[deps.Printf]]
deps = ["Unicode"]
uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"

[[deps.REPL]]
deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"

[[deps.Random]]
deps = ["SHA", "Serialization"]
uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"

[[deps.Ratios]]
deps = ["Requires"]
git-tree-sha1 = "dc84268fe0e3335a62e315a3a7cf2afa7178a734"
uuid = "c84ed2f1-dad5-54f0-aa8e-dbefe2724439"
version = "0.4.3"

[[deps.Reexport]]
git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b"
uuid = "189a3867-3050-52da-a836-e630ba90ab69"
version = "1.2.2"

[[deps.Requires]]
deps = ["UUIDs"]
git-tree-sha1 = "838a3a4188e2ded87a4f9f184b4b0d78a1e91cb7"
uuid = "ae029012-a4dd-5104-9daa-d747884805df"
version = "1.3.0"

[[deps.SHA]]
uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
version = "0.7.0"

[[deps.Scratch]]
deps = ["Dates"]
git-tree-sha1 = "f94f779c94e58bf9ea243e77a37e16d9de9126bd"
uuid = "6c6a2e73-6563-6170-7368-637461726353"
version = "1.1.1"

[[deps.SentinelArrays]]
deps = ["Dates", "Random"]
git-tree-sha1 = "efd23b378ea5f2db53a55ae53d3133de4e080aa9"
uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c"
version = "1.3.16"

[[deps.Serialization]]
uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"

[[deps.SharedArrays]]
deps = ["Distributed", "Mmap", "Random", "Serialization"]
uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383"

[[deps.SnoopPrecompile]]
git-tree-sha1 = "f604441450a3c0569830946e5b33b78c928e1a85"
uuid = "66db9d55-30c0-4569-8b51-7e840670fc0c"
version = "1.0.1"

[[deps.Sockets]]
uuid = "6462fe0b-24de-5631-8697-dd941f90decc"

[[deps.SortingAlgorithms]]
deps = ["DataStructures"]
git-tree-sha1 = "a4ada03f999bd01b3a25dcaa30b2d929fe537e00"
uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c"
version = "1.1.0"

[[deps.SparseArrays]]
deps = ["LinearAlgebra", "Random"]
uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"

[[deps.StaticArrays]]
deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"]
git-tree-sha1 = "ffc098086f35909741f71ce21d03dadf0d2bfa76"
uuid = "90137ffa-7385-5640-81b9-e52037218182"
version = "1.5.11"

[[deps.StaticArraysCore]]
git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a"
uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c"
version = "1.4.0"

[[deps.Statistics]]
deps = ["LinearAlgebra", "SparseArrays"]
uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"

[[deps.StatsAPI]]
deps = ["LinearAlgebra"]
git-tree-sha1 = "f9af7f195fb13589dd2e2d57fdb401717d2eb1f6"
uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0"
version = "1.5.0"

[[deps.StringEncodings]]
deps = ["Libiconv_jll"]
git-tree-sha1 = "50ccd5ddb00d19392577902f0079267a72c5ab04"
uuid = "69024149-9ee7-55f6-a4c4-859efe599b68"
version = "0.3.5"

[[deps.StringManipulation]]
git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123"
uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e"
version = "0.3.0"

[[deps.Suppressor]]
git-tree-sha1 = "c6ed566db2fe3931292865b966d6d140b7ef32a9"
uuid = "fd094767-a336-5f1f-9728-57cf17d0bbfb"
version = "0.2.1"

[[deps.TOML]]
deps = ["Dates"]
uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
version = "1.0.0"

[[deps.TableTraits]]
deps = ["IteratorInterfaceExtensions"]
git-tree-sha1 = "c06b2f539df1c6efa794486abfb6ed2022561a39"
uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c"
version = "1.0.1"

[[deps.Tables]]
deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"]
git-tree-sha1 = "c79322d36826aa2f4fd8ecfa96ddb47b174ac78d"
uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
version = "1.10.0"

[[deps.Tar]]
deps = ["ArgTools", "SHA"]
uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
version = "1.10.0"

[[deps.Test]]
deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

[[deps.TranscodingStreams]]
deps = ["Random", "Test"]
git-tree-sha1 = "e4bdc63f5c6d62e80eb1c0043fcc0360d5950ff7"
uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
version = "0.9.10"

[[deps.Tricks]]
git-tree-sha1 = "6bac775f2d42a611cdfcd1fb217ee719630c4175"
uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775"
version = "0.1.6"

[[deps.URIParser]]
deps = ["Unicode"]
git-tree-sha1 = "53a9f49546b8d2dd2e688d216421d050c9a31d0d"
uuid = "30578b45-9adc-5946-b283-645ec420af67"
version = "0.4.1"

[[deps.URIs]]
git-tree-sha1 = "ac00576f90d8a259f2c9d823e91d1de3fd44d348"
uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4"
version = "1.4.1"

[[deps.UUIDs]]
deps = ["Random", "SHA"]
uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"

[[deps.Unicode]]
uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"

[[deps.Unitful]]
deps = ["ConstructionBase", "Dates", "LinearAlgebra", "Random"]
git-tree-sha1 = "d670a70dd3cdbe1c1186f2f17c9a68a7ec24838c"
uuid = "1986cc42-f94f-5a68-af5c-568840ba703d"
version = "1.12.2"

[[deps.WeakRefStrings]]
deps = ["DataAPI", "InlineStrings", "Parsers"]
git-tree-sha1 = "b1be2855ed9ed8eac54e5caff2afcdb442d52c23"
uuid = "ea10d353-3f73-51f8-a26c-33c1cb351aa5"
version = "1.4.2"

[[deps.WoodburyMatrices]]
deps = ["LinearAlgebra", "SparseArrays"]
git-tree-sha1 = "de67fa59e33ad156a590055375a30b23c40299d3"
uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6"
version = "0.5.5"

[[deps.XML2_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"]
git-tree-sha1 = "58443b63fb7e465a8a7210828c91c08b92132dff"
uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a"
version = "2.9.14+0"

[[deps.YAML]]
deps = ["Base64", "Dates", "Printf", "StringEncodings"]
git-tree-sha1 = "dbc7f1c0012a69486af79c8bcdb31be820670ba2"
uuid = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
version = "0.4.8"

[[deps.Zlib_jll]]
deps = ["Libdl"]
uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
version = "1.2.12+3"

[[deps.libblastrampoline_jll]]
deps = ["Artifacts", "Libdl", "OpenBLAS_jll"]
uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
version = "5.1.1+0"

[[deps.nghttp2_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
version = "1.48.0+0"

[[deps.p7zip_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"
version = "17.4.0+0"
"""

# ╔═╡ Cell order:
# ╟─708c3f0f-a8d4-45dd-85f2-c8bb934d2576
# ╟─52f89eed-0ab3-4082-b58f-45c90eaec205
# ╟─48088d9f-3766-4b07-89dd-f57a9d8c7bd0
# ╟─21062d00-f859-4d58-afed-d9748ca7f4f6
# ╟─268c7d77-e2c2-48fa-a5c8-9c59e8fbc7f2
# ╟─f7950381-9ea8-4160-861b-dc0bf4b5bfe4
# ╟─89efaaca-e499-4367-bc23-c97a86f02d4b
# ╟─847f8175-0e8d-4fa7-8712-c6b47adbeab8
# ╟─f094f531-57d9-4b8e-aa23-02b2c443bdf3
# ╠═67a5c3f5-5cd5-46e7-8b2a-83299387c18a
# ╟─39d1da64-217a-41b4-b2dc-07df1cfd3220
# ╟─ac23620a-b772-4bbb-95d2-d06ab497709c
# ╟─00000000-0000-0000-0000-000000000001
# ╟─00000000-0000-0000-0000-000000000002