analysis.jl

### A Pluto.jl notebook ###
# v0.19.40

using Markdown
using InteractiveUtils

# ╔═╡ 6f6df7cc-2e6e-11ef-37a2-85991d0fbc5b
using PlutoUI: TableOfContents

# ╔═╡ bdaca39d-dfc8-4d3a-a0f4-0943bcd62e12
using CSV: read

# ╔═╡ e78bf131-14e6-4641-b60c-10b322f2a8e7
using DataFrames: DataFrame, groupby

# ╔═╡ 88f23085-659e-4ce1-92f0-37cbb46f4d48
using CairoMakie: Figure, Axis, barplot!, hlines!, axislegend, PolyElement, Legend, errorbars!, barplot

# ╔═╡ a25ff555-1b7f-4e80-a172-e6cabc108614
using CairoMakie

# ╔═╡ d1b9e06c-b0f6-4495-a379-c5ae336608fb
TableOfContents()

# ╔═╡ 08844e29-31ce-43b6-951b-1794de2a40b6
md"""
## Download CSVs
"""

# ╔═╡ 2e38bd34-7a05-4325-ba90-d0e764e5611b
root_dir = joinpath(pwd(), "data")

# ╔═╡ e2d5102b-1842-415c-b694-7f37be562937
c_df = read(joinpath(root_dir, "C_0bpm.csv"), DataFrame);

# ╔═╡ 98a9145b-0c7e-4277-b912-ffffd3b2b1a6
c_df_80, c_df_100, c_df_120 = groupby(c_df, :kV);

# ╔═╡ 5de7241a-e47b-4a5b-96a4-3e29ba918dab
d_df = read(joinpath(root_dir, "D_0bpm.csv"), DataFrame);

# ╔═╡ c13fec95-b46d-4dea-aeda-e08fb91a6bc5
d_df_80, d_df_100, d_df_120 = groupby(d_df, :kV);

# ╔═╡ 51be6bd8-46a7-42eb-b97f-934da59a7970
e_df = read(joinpath(root_dir, "E_0bpm.csv"), DataFrame);

# ╔═╡ d4de246a-dbdd-4a37-9d91-c936e4a8c120
e_df_80, e_df_100, e_df_120 = groupby(e_df, :kV);

# ╔═╡ ba29fa79-c096-4da9-b6db-61b8ff1d158a
f_df = read(joinpath(root_dir, "F_0bpm.csv"), DataFrame);

# ╔═╡ 72c80245-ba42-48d5-82ba-846feaa5f2b8
f_df_80, f_df_100, f_df_120 = groupby(f_df, :kV);

# ╔═╡ 2185ffbf-94da-45fa-99ca-3a8bce152c80
md"""
## Helper Functions
"""

# ╔═╡ 8ac1e3cf-bb6d-4d3f-b946-0b40086ce606
function find_highest_uncertain_mA(df, mass_col, bkg_col, std_col)
    for i in reverse(axes(df, 1))
        if df[i, mass_col] <= df[i, bkg_col] + df[i, std_col]
            return df[i, :mA]
        end
    end
    return 10.0
end

# ╔═╡ dbce0469-5484-4851-95f1-6c8e41fd7792
function count_uncertain_measurements(df, highest_uncertain_mA)
    count = 0
    for i in axes(df, 1)
        if (df[i, :mA] <= highest_uncertain_mA) && (df[i, :mA] != 10.0)
            count += 1
        end
    end
    return count
end

# ╔═╡ 78e9627a-33f2-4ee2-9318-336f8566e083
function analyze_uncertainties(df_80, df_100, df_120)
	# Create a DataFrame to store the results
	results_df = DataFrame(
		kV = ["80 kV", "100 kV", "120 kV"],
		vf_highest_uncertain_mA = zeros(3),
		agatston_highest_uncertain_mA = zeros(3),
		vf_uncertain_count = zeros(Int, 3),
		agatston_uncertain_count = zeros(Int, 3)
	)

	# Find the highest uncertain mA values and count uncertain measurements for each kV and technique
	for (i, df) in enumerate([df_80, df_100, df_120])
		results_df[i, :vf_highest_uncertain_mA] = find_highest_uncertain_mA(df, :vf_mass, :vf_mass_bkg_mean, :vf_mass_bkg_std)
		results_df[i, :agatston_highest_uncertain_mA] = find_highest_uncertain_mA(df, :agatston_mass, :agatston_mass_bkg_mean, :agatston_mass_bkg_std)
		results_df[i, :vf_uncertain_count] = count_uncertain_measurements(df, results_df[i, :vf_highest_uncertain_mA])
		results_df[i, :agatston_uncertain_count] = count_uncertain_measurements(df, results_df[i, :agatston_highest_uncertain_mA])
	end

	return results_df
end

# ╔═╡ 686b9462-9a3b-4f52-90d1-52b46fc9c998
function plot_mass_comparison(
	df_80, df_100, df_120;
	ylims = (-10, 100), yticks = 0:25:100
)
	f = Figure(size = (800, 1000))

	for (i, (df, kv)) in enumerate(zip([df_80, df_100, df_120], ["80 kV", "100 kV", "120 kV"]))
		xs = eachindex(df[:, :mA])
		elements_per_xtick = 4  # Number of elements per x-tick (excluding ground truth line)
		dodge = 1 / (elements_per_xtick + 1)  # Calculate dodge value
		barwidth = dodge * 1.1  # Calculate bar width (110% of dodge value)
		ax = Axis(
			f[i, 1],
			title = "$kv",
			ylabel = "Mass (mg)",
			xlabel = "mA",
			xticks = (xs, string.(Int.(df[:, :mA]))),
			yticks = yticks
		)
		ylims!(low = ylims[1], high = ylims[2])

		barplot!(
			xs .- dodge * 1.5,
			df[:, :vf_mass_bkg_mean];
			label="Volume Fraction Background Mass",
			width = barwidth,
			color = :lightcyan2
		)
		errorbars!(
			xs .- dodge * 1.5,
			df[:, :vf_mass_bkg_mean],
			df[:, :vf_mass_bkg_std];
			whiskerwidth = 10,
			linewidth = 1,
			color = :black,
		)
		barplot!(
			xs .- dodge * 0.5,
			df[:, :vf_mass];
			label="Volume Fraction Mass",
			width = barwidth,
			color = :cyan3
		)
		barplot!(
			xs .+ dodge * 0.5,
			df[:, :agatston_mass_bkg_mean];
			label="Agatston Background Mass",
			width = barwidth,
			color = :palevioletred2
		)
		errorbars!(
			xs .+ dodge * 0.5,
			df[:, :agatston_mass_bkg_mean],
			df[:, :agatston_mass_bkg_std];
			whiskerwidth = 10,
			linewidth = 1,
			color = :black
		)
		barplot!(
			xs .+ dodge * 1.5,
			df[:, :agatston_mass];
			label="Agatston Mass",
			width = barwidth,
			color = :palevioletred4
		)

		hlines!(
			df[:, :gt_mass][1];
			xmin = 0,
			xmax = xs[end] + 0.5,
			label = "Ground Truth Mass",
			color = :green,
			linestyle = :dash
		)
	end

	elements = [
		PolyElement(color = :lightcyan2),
		PolyElement(color = :cyan3),
		PolyElement(color = :palevioletred2),
		PolyElement(color = :palevioletred4),
		LineElement(color = :green, linestyle = :dash)
	]
	labels = [
		"Volume Fraction \nBackground Mass",
		"Volume Fraction \nMass",
		"Agatston \nBackground Mass",
		"Agatston Mass",
		"Ground Truth \nMass"
	]
	legend = Legend(f[2, 2], elements, labels, "Legend", framevisible = false)

	return f
end

# ╔═╡ 9281994e-f515-4877-829c-2fadc7a1f9a4
md"""
## Analysis
"""

# ╔═╡ fb5641cc-e158-4181-9c6c-819733d044bb
md"""
### (C) Density: 50 mg/cc, Diameter: 5.0 mm
"""

# ╔═╡ d6c226b9-8a6f-49ee-b5ff-3d80eb6f1fb6
plot_mass_comparison(
	c_df_80, c_df_100, c_df_120;
	ylims = (-10, 100), yticks = 0:25:100
)

# ╔═╡ a36fcd41-33a0-47cc-ac4f-a07203f9771d
results_c_df = analyze_uncertainties(c_df_80, c_df_100, c_df_120)

# ╔═╡ 5d536775-3ccf-4fd4-a560-472ef7f2abfd
md"""
### (D) Density: 100 mg/cc, Diameter: 1.2 mm
"""

# ╔═╡ b5fc2168-006c-4a3c-9d86-49d70b4f30f7
plot_mass_comparison(
	d_df_80, d_df_100, d_df_120;
	ylims = (-1, 5), yticks = 0:5
)

# ╔═╡ 48489a26-0b14-4228-b464-97e2696cefcd
results_d_df = analyze_uncertainties(d_df_80, d_df_100, d_df_120)

# ╔═╡ fb379775-62b9-4357-9fda-57c1040e6ff9
md"""
### (E) Density: 100 mg/cc, Diameter: 3.0 mm
"""

# ╔═╡ a984a9aa-4a05-4713-833a-6d44d4db6870
plot_mass_comparison(
	e_df_80, e_df_100, e_df_120;
	ylims = (-10, 35), yticks = 0:5:35
)

# ╔═╡ 8101daa2-c556-4f3f-8321-7572663750c9
results_e_df = analyze_uncertainties(e_df_80, e_df_100, e_df_120)

# ╔═╡ 3f4ef699-35bf-4fd2-ad26-db546209d955
md"""
### (F) Density: 100 mg/cc, Diameter: 5.0 mm
"""

# ╔═╡ 1a0f5672-a427-4081-8bc1-60abe1c70dd3
plot_mass_comparison(
	f_df_80, f_df_100, f_df_120;
	ylims = (-20, 120), yticks = 0:20:120
)

# ╔═╡ 5c3fac6f-b4b5-4256-a7da-987a9ac197ca
results_f_df = analyze_uncertainties(f_df_80, f_df_100, f_df_120)

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[[deps.SpecialFunctions]]
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weakdeps = ["ChainRulesCore"]

    [deps.SpecialFunctions.extensions]
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[[deps.StackViews]]
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git-tree-sha1 = "46e589465204cd0c08b4bd97385e4fa79a0c770c"
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weakdeps = ["ChainRulesCore", "Statistics"]

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    StaticArraysChainRulesCoreExt = "ChainRulesCore"
    StaticArraysStatisticsExt = "Statistics"

[[deps.StaticArraysCore]]
git-tree-sha1 = "192954ef1208c7019899fbf8049e717f92959682"
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[[deps.Statistics]]
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[[deps.StatsAPI]]
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[[deps.StatsBase]]
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git-tree-sha1 = "5cf7606d6cef84b543b483848d4ae08ad9832b21"
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deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"]
git-tree-sha1 = "cef0472124fab0695b58ca35a77c6fb942fdab8a"
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    StatsFunsInverseFunctionsExt = "InverseFunctions"

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    StructArraysGPUArraysCoreExt = "GPUArraysCore"
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    StructArraysStaticArraysExt = "StaticArrays"

    [deps.StructArrays.weakdeps]
    Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
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[[deps.SuiteSparse]]
deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"]
uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9"

[[deps.SuiteSparse_jll]]
deps = ["Artifacts", "Libdl", "libblastrampoline_jll"]
uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c"
version = "7.2.1+1"

[[deps.TOML]]
deps = ["Dates"]
uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
version = "1.0.3"

[[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"]
git-tree-sha1 = "cb76cf677714c095e535e3501ac7954732aeea2d"
uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
version = "1.11.1"

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

[[deps.TensorCore]]
deps = ["LinearAlgebra"]
git-tree-sha1 = "1feb45f88d133a655e001435632f019a9a1bcdb6"
uuid = "62fd8b95-f654-4bbd-a8a5-9c27f68ccd50"
version = "0.1.1"

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

[[deps.TiffImages]]
deps = ["ColorTypes", "DataStructures", "DocStringExtensions", "FileIO", "FixedPointNumbers", "IndirectArrays", "Inflate", "Mmap", "OffsetArrays", "PkgVersion", "ProgressMeter", "SIMD", "UUIDs"]
git-tree-sha1 = "bc7fd5c91041f44636b2c134041f7e5263ce58ae"
uuid = "731e570b-9d59-4bfa-96dc-6df516fadf69"
version = "0.10.0"

[[deps.TranscodingStreams]]
git-tree-sha1 = "a947ea21087caba0a798c5e494d0bb78e3a1a3a0"
uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
version = "0.10.9"
weakdeps = ["Random", "Test"]

    [deps.TranscodingStreams.extensions]
    TestExt = ["Test", "Random"]

[[deps.Tricks]]
git-tree-sha1 = "eae1bb484cd63b36999ee58be2de6c178105112f"
uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775"
version = "0.1.8"

[[deps.TriplotBase]]
git-tree-sha1 = "4d4ed7f294cda19382ff7de4c137d24d16adc89b"
uuid = "981d1d27-644d-49a2-9326-4793e63143c3"
version = "0.1.0"

[[deps.URIs]]
git-tree-sha1 = "67db6cc7b3821e19ebe75791a9dd19c9b1188f2b"
uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4"
version = "1.5.1"

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

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

[[deps.UnicodeFun]]
deps = ["REPL"]
git-tree-sha1 = "53915e50200959667e78a92a418594b428dffddf"
uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1"
version = "0.4.1"

[[deps.Unitful]]
deps = ["Dates", "LinearAlgebra", "Random"]
git-tree-sha1 = "dd260903fdabea27d9b6021689b3cd5401a57748"
uuid = "1986cc42-f94f-5a68-af5c-568840ba703d"
version = "1.20.0"

    [deps.Unitful.extensions]
    ConstructionBaseUnitfulExt = "ConstructionBase"
    InverseFunctionsUnitfulExt = "InverseFunctions"

    [deps.Unitful.weakdeps]
    ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
    InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112"

[[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 = "c1a7aa6219628fcd757dede0ca95e245c5cd9511"
uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6"
version = "1.0.0"

[[deps.WorkerUtilities]]
git-tree-sha1 = "cd1659ba0d57b71a464a29e64dbc67cfe83d54e7"
uuid = "76eceee3-57b5-4d4a-8e66-0e911cebbf60"
version = "1.6.1"

[[deps.XML2_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"]
git-tree-sha1 = "52ff2af32e591541550bd753c0da8b9bc92bb9d9"
uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a"
version = "2.12.7+0"

[[deps.XSLT_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"]
git-tree-sha1 = "91844873c4085240b95e795f692c4cec4d805f8a"
uuid = "aed1982a-8fda-507f-9586-7b0439959a61"
version = "1.1.34+0"

[[deps.Xorg_libX11_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxcb_jll", "Xorg_xtrans_jll"]
git-tree-sha1 = "afead5aba5aa507ad5a3bf01f58f82c8d1403495"
uuid = "4f6342f7-b3d2-589e-9d20-edeb45f2b2bc"
version = "1.8.6+0"

[[deps.Xorg_libXau_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "6035850dcc70518ca32f012e46015b9beeda49d8"
uuid = "0c0b7dd1-d40b-584c-a123-a41640f87eec"
version = "1.0.11+0"

[[deps.Xorg_libXdmcp_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "34d526d318358a859d7de23da945578e8e8727b7"
uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05"
version = "1.1.4+0"

[[deps.Xorg_libXext_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"]
git-tree-sha1 = "d2d1a5c49fae4ba39983f63de6afcbea47194e85"
uuid = "1082639a-0dae-5f34-9b06-72781eeb8cb3"
version = "1.3.6+0"

[[deps.Xorg_libXrender_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"]
git-tree-sha1 = "47e45cd78224c53109495b3e324df0c37bb61fbe"
uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa"
version = "0.9.11+0"

[[deps.Xorg_libpthread_stubs_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "8fdda4c692503d44d04a0603d9ac0982054635f9"
uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74"
version = "0.1.1+0"

[[deps.Xorg_libxcb_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"]
git-tree-sha1 = "b4bfde5d5b652e22b9c790ad00af08b6d042b97d"
uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b"
version = "1.15.0+0"

[[deps.Xorg_xtrans_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "e92a1a012a10506618f10b7047e478403a046c77"
uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10"
version = "1.5.0+0"

[[deps.Zlib_jll]]
deps = ["Libdl"]
uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
version = "1.2.13+1"

[[deps.isoband_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "51b5eeb3f98367157a7a12a1fb0aa5328946c03c"
uuid = "9a68df92-36a6-505f-a73e-abb412b6bfb4"
version = "0.2.3+0"

[[deps.libaom_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "1827acba325fdcdf1d2647fc8d5301dd9ba43a9d"
uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b"
version = "3.9.0+0"

[[deps.libass_jll]]
deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"]
git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47"
uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0"
version = "0.15.1+0"

[[deps.libblastrampoline_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
version = "5.8.0+1"

[[deps.libfdk_aac_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55"
uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280"
version = "2.0.2+0"

[[deps.libpng_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"]
git-tree-sha1 = "d7015d2e18a5fd9a4f47de711837e980519781a4"
uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f"
version = "1.6.43+1"

[[deps.libsixel_jll]]
deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Pkg", "libpng_jll"]
git-tree-sha1 = "d4f63314c8aa1e48cd22aa0c17ed76cd1ae48c3c"
uuid = "075b6546-f08a-558a-be8f-8157d0f608a5"
version = "1.10.3+0"

[[deps.libvorbis_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"]
git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c"
uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a"
version = "1.3.7+1"

[[deps.nghttp2_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
version = "1.52.0+1"

[[deps.oneTBB_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "7d0ea0f4895ef2f5cb83645fa689e52cb55cf493"
uuid = "1317d2d5-d96f-522e-a858-c73665f53c3e"
version = "2021.12.0+0"

[[deps.p7zip_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"
version = "17.4.0+2"

[[deps.x264_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2"
uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a"
version = "2021.5.5+0"

[[deps.x265_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9"
uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76"
version = "3.5.0+0"
"""

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