improved preprocessing UI, added selective spectrum plot accordig to type (centroid, profile), potentially fixed a bug to retrieve folders on dropdown selectors in startup, improved preprocessing functions and test suite, testing a version control for preprocessing steps
This commit is contained in:
Pixelguy14
parent
edfbb77f58
commit
8fa92dc0e5
@ -2,7 +2,12 @@
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julia_version = "1.11.7"
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manifest_format = "2.0"
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project_hash = "38f13d997585a9af185f1863ff626d584a7e791e"
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project_hash = "7843f141174fe17a3abc4f25c3819d3195459b5a"
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[[deps.ANSIColoredPrinters]]
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git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c"
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uuid = "a4c015fc-c6ff-483c-b24f-f7ea428134e9"
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version = "0.0.1"
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[[deps.ATK_jll]]
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deps = ["Artifacts", "Glib_jll", "JLLWrappers", "Libdl"]
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@ -159,6 +164,11 @@ git-tree-sha1 = "bca794632b8a9bbe159d56bf9e31c422671b35e0"
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uuid = "18cc8868-cbac-4acf-b575-c8ff214dc66f"
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git-tree-sha1 = "4435559dc39793d53a9e3d278e185e920b4619ef"
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@ -289,6 +299,12 @@ git-tree-sha1 = "980f01d6d3283b3dbdfd7ed89405f96b7256ad57"
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git-tree-sha1 = "962834c22b66e32aa10f7611c08c8ca4e20749a9"
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@ -397,6 +413,12 @@ weakdeps = ["IntervalSets", "LinearAlgebra", "StaticArrays"]
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ConstructionBaseLinearAlgebraExt = "LinearAlgebra"
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ConstructionBaseStaticArraysExt = "StaticArrays"
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[[deps.ContinuousWavelets]]
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[[deps.Contour]]
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@ -434,6 +456,16 @@ git-tree-sha1 = "1a3f97f907e6dd8983b744d2642651bb162a3f7a"
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weakdeps = ["OffsetArrays"]
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[deps.DSP.extensions]
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OffsetArraysExt = "OffsetArrays"
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[[deps.DataAPI]]
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git-tree-sha1 = "abe83f3a2f1b857aac70ef8b269080af17764bbe"
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@ -516,6 +548,12 @@ git-tree-sha1 = "7442a5dfe1ebb773c29cc2962a8980f47221d76c"
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[[deps.Documenter]]
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deps = ["ANSIColoredPrinters", "AbstractTrees", "Base64", "CodecZlib", "Dates", "DocStringExtensions", "Downloads", "Git", "IOCapture", "InteractiveUtils", "JSON", "Logging", "Markdown", "MarkdownAST", "Pkg", "PrecompileTools", "REPL", "RegistryInstances", "SHA", "TOML", "Test", "Unicode"]
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git-tree-sha1 = "352b9a04e74edd16429aec79f033620cf8e780d4"
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[[deps.DotEnv]]
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deps = ["PrecompileTools"]
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git-tree-sha1 = "92e88cb68a5b10545234f46dfaeb2fa8a8a50c45"
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@ -651,12 +689,6 @@ git-tree-sha1 = "05882d6995ae5c12bb5f36dd2ed3f61c98cbb172"
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[[deps.FlameGraphs]]
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deps = ["AbstractTrees", "Colors", "FileIO", "FixedPointNumbers", "IndirectArrays", "LeftChildRightSiblingTrees", "Profile"]
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git-tree-sha1 = "0166baf81babb91cf78bfcc771d8e87c43d568df"
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[[deps.Fontconfig_jll]]
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git-tree-sha1 = "f85dac9a96a01087df6e3a749840015a0ca3817d"
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@ -804,6 +836,24 @@ git-tree-sha1 = "6570366d757b50fabae9f4315ad74d2e40c0560a"
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[[deps.Git]]
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deps = ["Git_LFS_jll", "Git_jll", "JLLWrappers", "OpenSSH_jll"]
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git-tree-sha1 = "824a1890086880696fc908fe12a17bcf61738bd8"
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version = "1.5.0"
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[[deps.Git_LFS_jll]]
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deps = ["Artifacts", "JLLWrappers", "Libdl"]
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git-tree-sha1 = "bb8471f313ed941f299aa53d32a94ab3bee08844"
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version = "3.7.0+0"
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[[deps.Git_jll]]
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deps = ["Artifacts", "Expat_jll", "JLLWrappers", "LibCURL_jll", "Libdl", "Libiconv_jll", "OpenSSL_jll", "PCRE2_jll", "Zlib_jll"]
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git-tree-sha1 = "b6a684587ebe896d9f68ae777f648205940f0f70"
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version = "2.51.3+0"
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[[deps.Glib_jll]]
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deps = ["Artifacts", "GettextRuntime_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"]
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git-tree-sha1 = "50c11ffab2a3d50192a228c313f05b5b5dc5acb2"
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@ -885,6 +935,12 @@ git-tree-sha1 = "68c173f4f449de5b438ee67ed0c9c748dc31a2ec"
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[[deps.IOCapture]]
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deps = ["Logging", "Random"]
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git-tree-sha1 = "b6d6bfdd7ce25b0f9b2f6b3dd56b2673a66c8770"
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[[deps.IfElse]]
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git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1"
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@ -1236,6 +1292,11 @@ git-tree-sha1 = "a9eaadb366f5493a5654e843864c13d8b107548c"
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uuid = "10f19ff3-798f-405d-979b-55457f8fc047"
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[[deps.LazilyInitializedFields]]
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version = "1.3.0"
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[[deps.LazyArtifacts]]
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deps = ["Artifacts", "Pkg"]
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uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3"
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@ -1436,6 +1497,12 @@ deps = ["Base64"]
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uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
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version = "1.11.0"
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[[deps.MarkdownAST]]
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deps = ["AbstractTrees", "Markdown"]
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git-tree-sha1 = "465a70f0fc7d443a00dcdc3267a497397b8a3899"
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[[deps.MathTeXEngine]]
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git-tree-sha1 = "a370fef694c109e1950836176ed0d5eabbb65479"
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@ -1785,10 +1852,6 @@ deps = ["Unicode"]
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uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
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version = "1.11.0"
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[[deps.Profile]]
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git-tree-sha1 = "fbb92c6c56b34e1a2c4c36058f68f332bec840e7"
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@ -1872,6 +1935,12 @@ git-tree-sha1 = "4618ed0da7a251c7f92e869ae1a19c74a7d2a7f9"
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uuid = "dee08c22-ab7f-5625-9660-a9af2021b33f"
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[[deps.RegistryInstances]]
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deps = ["LazilyInitializedFields", "Pkg", "TOML", "Tar"]
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git-tree-sha1 = "ffd19052caf598b8653b99404058fce14828be51"
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uuid = "2792f1a3-b283-48e8-9a74-f99dce5104f3"
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version = "0.1.0"
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[[deps.RelocatableFolders]]
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deps = ["SHA", "Scratch"]
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git-tree-sha1 = "ffdaf70d81cf6ff22c2b6e733c900c3321cab864"
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@ -2373,6 +2442,12 @@ git-tree-sha1 = "d1d9a935a26c475ebffd54e9c7ad11627c43ea85"
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uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f"
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version = "0.21.72"
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[[deps.Wavelets]]
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deps = ["DSP", "FFTW", "LinearAlgebra", "Reexport", "SpecialFunctions", "Statistics"]
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git-tree-sha1 = "d0ec97a100abbe47a5e9a02361841da49cce6029"
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uuid = "29a6e085-ba6d-5f35-a997-948ac2efa89a"
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version = "0.10.1"
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[[deps.Wayland_jll]]
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deps = ["Artifacts", "EpollShim_jll", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll"]
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git-tree-sha1 = "96478df35bbc2f3e1e791bc7a3d0eeee559e60e9"
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@ -7,12 +7,13 @@ Accessors = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697"
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Base64 = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
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CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
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CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
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CodecBase = "6c391c72-fb7b-5838-ba82-7cfb1bcfecbf"
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ColorSchemes = "35d6a980-a343-548e-a6ea-1d62b119f2f4"
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Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
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ContinuousWavelets = "96eb917e-2868-4417-9cb6-27e7ff17528f"
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DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
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Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
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FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
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FlameGraphs = "08572546-2f56-4bcf-ba4e-bab62c3a3f89"
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GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
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Genie = "c43c736e-a2d1-11e8-161f-af95117fbd1e"
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GenieFramework = "a59fdf5c-6bf0-4f5d-949c-a137c9e2f353"
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@ -25,6 +26,8 @@ ImageFiltering = "6a3955dd-da59-5b1f-98d4-e7296123deb5"
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ImageMorphology = "787d08f9-d448-5407-9aad-5290dd7ab264"
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ImageSegmentation = "80713f31-8817-5129-9cf8-209ff8fb23e1"
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Images = "916415d5-f1e6-5110-898d-aaa5f9f070e0"
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Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
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JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
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JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
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Libz = "2ec943e9-cfe8-584d-b93d-64dcb6d567b7"
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LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
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@ -47,7 +50,7 @@ Accessors = "0.1"
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Base64 = "1.11"
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CSV = "0.10"
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CairoMakie = "0.13"
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ColorSchemes = "3.31"
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ColorSchemes = "3.30"
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Colors = "0.12"
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DataFrames = "1.7"
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Dates = "1.11"
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33
app.jl
33
app.jl
@ -213,6 +213,7 @@ end
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# == Batch Processing & Registry Variables ==
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@private registry_init_done = false
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@in refetch_folders = false
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@in selected_files = String[]
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@in available_folders = String[]
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@in image_available_folders = String[]
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@ -1919,6 +1920,37 @@ end
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end
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end
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@onbutton refetch_folders begin
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# Re-load registry and update folder lists
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registry = load_registry(registry_path)
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all_folders = sort(collect(keys(registry)), lt=natural)
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img_folders = filter(folder -> get(get(registry, folder, Dict()), "is_imzML", false), all_folders)
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available_folders = deepcopy(all_folders)
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image_available_folders = deepcopy(img_folders)
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# For q-selects using image_available_folders
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if !isempty(image_available_folders)
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first_img_folder = first(image_available_folders)
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if isempty(selected_folder_main)
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selected_folder_main = first_img_folder
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end
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if isempty(selected_folder_compare_left)
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selected_folder_compare_left = first_img_folder
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end
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if isempty(selected_folder_compare_right)
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selected_folder_compare_right = first_img_folder
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end
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end
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# For q-selects using available_folders
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if !isempty(available_folders)
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if isempty(selected_folder_metadata)
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selected_folder_metadata = first(available_folders)
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end
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end
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end
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@mounted watchplots()
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@onchange isready @time begin
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@ -1967,7 +1999,6 @@ end
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image_available_folders = deepcopy(img_folders)
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println("UI lists updated. All: $(length(available_folders)), Images: $(length(image_available_folders))")
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catch e
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@warn "Registry synchronization failed: $e"
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available_folders = []
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392
app.jl.html
392
app.jl.html
@ -19,7 +19,7 @@
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<div class="text-h6">imzML & mzML Data Pre-Treatment</div>
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<div class="row items-center">
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<q-input standout="custom-standout" class="q-ma-sm cursor-pointer col" v-model="full_route" readonly
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:label="batch_file_count > 0 ? batch_file_count + ' file(s) in batch' : 'Select an imzML file'"
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:label="batch_file_count > 0 ? batch_file_count + ' file(s) in batch' : 'Select an imzMl / mzML file'"
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v-on:click="btnSearch=true">
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<template v-slot:append>
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<q-icon name="search" v-on:click="btnSearch=true" class="cursor-pointer" />
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@ -29,6 +29,22 @@
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<q-btn class="q-ma-sm" icon="clear" v-on:click="clear_batch_btn=true" :disable="batch_file_count === 0"
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label="Clear"></q-btn>
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</div>
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<q-list bordered separator v-if="selected_files.length > 0">
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<q-item v-for="(file, index) in selected_files" :key="index">
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<q-item-section>
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{{ file }}
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</q-item-section>
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<q-item-section side>
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<q-btn flat round icon="delete" size="sm" v-on:click="selected_files.splice(index, 1)"></q-btn>
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</q-item-section>
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</q-item>
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</q-list>
|
||||
<q-input standout="custom-standout" class="q-ma-sm cursor-pointer col" v-model="full_route_cal" readonly
|
||||
label="Select a calibration imzMl / mzML file" v-on:click="btnSearchCal=true">
|
||||
<template v-slot:append>
|
||||
<q-icon name="search" v-on:click="btnSearchCal=true" class="cursor-pointer" />
|
||||
</template>
|
||||
</q-input>-
|
||||
<br>
|
||||
<br>
|
||||
<q-tabs v-model="pre_tab" dense class="text-grey" indicator-color="primary" align="justify">
|
||||
@ -40,10 +56,176 @@
|
||||
<q-tab name="peak" label="Peak Detection"></q-tab>
|
||||
<q-tab name="binning" label="Binning"></q-tab>
|
||||
</q-tabs>
|
||||
<q-separator></q-separator>
|
||||
<q-separator />
|
||||
<q-tab-panels v-model="pre_tab" animated>
|
||||
<q-tab-panel name="stabilization">
|
||||
<p>HI!</p>
|
||||
<q-tab-panel name="stabilization" class="q-pa-md">
|
||||
<q-card class="q-mb-md">
|
||||
<q-card-section>
|
||||
<div class="text-h6">Method</div>
|
||||
</q-card-section>
|
||||
<q-card-section>
|
||||
<q-radio v-model="stabilization_method" val="sqrt" label="SQRT" /><br>
|
||||
<q-radio v-model="stabilization_method" val="log" label="LOG" /><br>
|
||||
<q-radio v-model="stabilization_method" val="log2" label="LOG 2" /><br>
|
||||
<q-radio v-model="stabilization_method" val="log10" label="LOG 10" /><br>
|
||||
</q-card-section>
|
||||
</q-card>
|
||||
<div class="row justify-end">
|
||||
<q-btn :loading="progressPrep" class="q-ma-sm btn-style" icon="play_arrow" v-on:click="acceptStab=true"
|
||||
padding="lg" label="Accept" />
|
||||
<q-btn :loading="progressPrep" class="q-ma-sm btn-style" icon="clear" v-on:click="undoPrep=true"
|
||||
padding="lg" label="Undo" />
|
||||
</div>
|
||||
</q-tab-panel>
|
||||
<q-tab-panel name="smoothing">
|
||||
<q-card class="q-mb-md">
|
||||
<q-card-section>
|
||||
<div class="text-h6">Method</div>
|
||||
</q-card-section>
|
||||
<q-card-section>
|
||||
<q-radio v-model="smoothing_method" val="sg" label="Savitzky-Golay" /><br>
|
||||
<q-radio v-model="smoothing_method" val="ma" label="Moving Average" /><br>
|
||||
</q-card-section>
|
||||
</q-card>
|
||||
<q-card>
|
||||
<q-card-section>
|
||||
<div class="text-h6">Parameters</div>
|
||||
</q-card-section>
|
||||
<q-card-section>
|
||||
<q-input standout="custom-standout" label="Half Window Size" type="number"
|
||||
v-model.number="smoothing_window"></q-input>
|
||||
</q-card-section>
|
||||
</q-card>
|
||||
<div class="row justify-end q-mt-md">
|
||||
<q-btn :loading="progressPrep" class="q-ma-sm btn-style" icon="play_arrow" v-on:click="acceptSmoo=true"
|
||||
padding="lg" label="Accept" />
|
||||
<q-btn :loading="progressPrep" class="q-ma-sm btn-style" icon="clear" v-on:click="undoPrep=true"
|
||||
padding="lg" label="Undo" />
|
||||
</div>
|
||||
</q-tab-panel>
|
||||
<q-tab-panel name="baseline">
|
||||
<q-card class="q-mb-md">
|
||||
<q-card-section>
|
||||
<div class="text-h6">Method</div>
|
||||
</q-card-section>
|
||||
<q-card-section>
|
||||
<q-radio v-model="baseline_method" val="snip" label="SNIP" /><br>
|
||||
<q-radio v-model="baseline_method" val="tophat" label="TOP HAT" /><br>
|
||||
<q-radio v-model="baseline_method" val="convex_hull" label="CONVEX HULL" /><br>
|
||||
<q-radio v-model="baseline_method" val="median" label="MEDIAN" /><br>
|
||||
</q-card-section>
|
||||
</q-card>
|
||||
<q-card>
|
||||
<q-card-section>
|
||||
<div class="text-h6">Parameters</div>
|
||||
</q-card-section>
|
||||
<q-card-section>
|
||||
<q-input standout="custom-standout" label="Iterations" type="number"
|
||||
v-model.number="baseline_iterations"></q-input>
|
||||
</q-card-section>
|
||||
</q-card>
|
||||
<div class="row justify-end q-mt-md">
|
||||
<q-btn :loading="progressPrep" class="q-ma-sm btn-style" icon="play_arrow" v-on:click="acceptBase=true"
|
||||
padding="lg" label="Accept" />
|
||||
<q-btn :loading="progressPrep" class="q-ma-sm btn-style" icon="clear" v-on:click="undoPrep=true"
|
||||
padding="lg" label="Undo" />
|
||||
</div>
|
||||
</q-tab-panel>
|
||||
<q-tab-panel name="calibration">
|
||||
<q-card class="q-mb-md">
|
||||
<q-card-section>
|
||||
<div class="text-h6">Method</div>
|
||||
</q-card-section>
|
||||
<q-card-section>
|
||||
<q-radio v-model="calibration_method" val="tic" label="TIC" /><br>
|
||||
<q-radio v-model="calibration_method" val="pqn" label="PQN" /><br>
|
||||
<q-radio v-model="calibration_method" val="median" label="MEDIAN" /><br>
|
||||
</q-card-section>
|
||||
</q-card>
|
||||
<div class="row justify-end q-mt-md">
|
||||
<q-btn :loading="progressPrep" class="q-ma-sm btn-style" icon="play_arrow" v-on:click="acceptCali=true"
|
||||
padding="lg" label="Accept" />
|
||||
<q-btn :loading="progressPrep" class="q-ma-sm btn-style" icon="clear" v-on:click="undoPrep=true"
|
||||
padding="lg" label="Undo" />
|
||||
</div>
|
||||
</q-tab-panel>
|
||||
<q-tab-panel name="warping">
|
||||
<q-card class="q-mb-md">
|
||||
<q-card-section>
|
||||
<div class="text-h6">Method</div>
|
||||
</q-card-section>
|
||||
<q-card-section>
|
||||
<q-radio v-model="warping_method" val="snip" label="SNIP" /><br>
|
||||
<q-radio v-model="warping_method" val="tophat" label="TOP HAT" /><br>
|
||||
<q-radio v-model="warping_method" val="convex_hull" label="CONVEX HULL" /><br>
|
||||
<q-radio v-model="warping_method" val="median" label="MEDIAN" /><br>
|
||||
</q-card-section>
|
||||
</q-card>
|
||||
<q-card>
|
||||
<q-card-section>
|
||||
<div class="text-h6">Parameters</div>
|
||||
</q-card-section>
|
||||
<q-card-section>
|
||||
<q-input standout="custom-standout" label="Iterations" type="number"
|
||||
v-model.number="warping_iterations"></q-input>
|
||||
</q-card-section>
|
||||
</q-card>
|
||||
<div class="row justify-end q-mt-md">
|
||||
<q-btn :loading="progressPrep" class="q-ma-sm btn-style" icon="play_arrow" v-on:click="acceptWarp=true"
|
||||
padding="lg" label="Accept" />
|
||||
<q-btn :loading="progressPrep" class="q-ma-sm btn-style" icon="clear" v-on:click="undoPrep=true"
|
||||
padding="lg" label="Undo" />
|
||||
</div>
|
||||
</q-tab-panel>
|
||||
<q-tab-panel name="peak">
|
||||
<p>Detect if profile or centroid to determine which elements to show.</p>
|
||||
<q-card class="q-mb-md">
|
||||
<q-card-section>
|
||||
<div class="text-h6">Method</div>
|
||||
</q-card-section>
|
||||
<q-card-section>
|
||||
<q-radio v-model="peak_method" val="mad" label="MAD" /><br>
|
||||
<q-radio v-model="peak_method" val="super_smoother" label="SUPER SMOOTHER" /><br>
|
||||
</q-card-section>
|
||||
</q-card>
|
||||
<q-card>
|
||||
<q-card-section>
|
||||
<div class="text-h6">Parameters</div>
|
||||
</q-card-section>
|
||||
<q-card-section>
|
||||
<q-input standout="custom-standout" label="Signal to Noise" type="number"
|
||||
v-model.number="peak_snr"></q-input>
|
||||
<q-input standout="custom-standout" label="Half Window Size" type="number" class="q-mt-md"
|
||||
v-model.number="peak_window"></q-input>
|
||||
<q-input standout="custom-standout" label="Intensity Threshold" type="number" class="q-mt-md"
|
||||
v-model.number="peak_threshold"></q-input>
|
||||
</q-card-section>
|
||||
</q-card>
|
||||
<div class="row justify-end q-mt-md">
|
||||
<q-btn :loading="progressPrep" class="q-ma-sm btn-style" icon="play_arrow" v-on:click="acceptPeak=true"
|
||||
padding="lg" label="Accept" />
|
||||
<q-btn :loading="progressPrep" class="q-ma-sm btn-style" icon="clear" v-on:click="undoPrep=true"
|
||||
padding="lg" label="Undo" />
|
||||
</div>
|
||||
</q-tab-panel>
|
||||
<q-tab-panel name="binning">
|
||||
<q-card>
|
||||
<q-card-section>
|
||||
<div class="text-h6">Parameters</div>
|
||||
</q-card-section>
|
||||
<q-card-section>
|
||||
<q-input standout="custom-standout" label="Tolerance" type="number"
|
||||
v-model.number="binning_tolerance"></q-input>
|
||||
<q-input standout="custom-standout" label="Frequency Threshold" type="number" class="q-mt-md"
|
||||
v-model.number="binning_threshold"></q-input>
|
||||
</q-card-section>
|
||||
</q-card>
|
||||
<div class="row justify-end q-mt-md">
|
||||
<q-btn :loading="progressPrep" class="q-ma-sm btn-style" icon="play_arrow" v-on:click="acceptBinn=true"
|
||||
padding="lg" label="Accept" />
|
||||
<q-btn :loading="progressPrep" class="q-ma-sm btn-style" icon="clear" v-on:click="undoPrep=true"
|
||||
padding="lg" label="Undo" />
|
||||
</div>
|
||||
</q-tab-panel>
|
||||
</q-tab-panels>
|
||||
</q-tab-panel>
|
||||
@ -56,7 +238,7 @@
|
||||
</p>
|
||||
<div class="row items-center">
|
||||
<q-input standout="custom-standout" class="q-ma-sm cursor-pointer col" v-model="full_route" readonly
|
||||
:label="batch_file_count > 0 ? batch_file_count + ' file(s) in batch' : 'Select an imzML file'"
|
||||
:label="batch_file_count > 0 ? batch_file_count + ' file(s) in batch' : 'Select an imzMl / mzML file'"
|
||||
v-on:click="btnSearch=true">
|
||||
<template v-slot:append>
|
||||
<q-icon name="search" v-on:click="btnSearch=true" class="cursor-pointer" />
|
||||
@ -171,10 +353,9 @@
|
||||
</q-btn>
|
||||
<q-btn icon="zoom_out_map" class="q-ma-sm on-right btn-style" v-on:click="compareBtn=true" padding="sm"
|
||||
label="Compare"></q-btn>
|
||||
<!--<q-btn class="q-ma-sm btn-style" :disable="btnMetadataDisable"
|
||||
v-on:click="showMetadataBtn=true" label="Show Metadata"></q-btn>-->
|
||||
<q-btn class="q-ma-sm btn-style" icon="edit" label="Mask Editor" href="/mask"></q-btn>
|
||||
<q-btn class="q-ma-sm btn-style" v-on:click="showMetadataBtn=true" label="Show Metadata"></q-btn>
|
||||
<q-btn class="q-ma-sm btn-style" icon="dashboard" v-on:click="showMetadataBtn=true"
|
||||
label="Show Metadata"></q-btn>
|
||||
<div class="q-pa-md row items-center" v-show="progress">
|
||||
<q-spinner color="primary" size="2em" class="q-mr-sm"></q-spinner>
|
||||
<div class="text-caption">{{ progress_message }}</div>
|
||||
@ -238,7 +419,6 @@
|
||||
<div class="text-h6">mzML to imzML Converter</div>
|
||||
<p>Select the .mzML file and the corresponding .txt synchronization file to convert them into an .imzML/.ibd
|
||||
pair.</p>
|
||||
|
||||
<q-input standout="custom-standout" class="q-ma-sm cursor-pointer" v-model="mzml_full_route" readonly
|
||||
label="Select your .mzML file" v-on:click="btnSearchMzml=true">
|
||||
<template v-slot:append>
|
||||
@ -268,96 +448,118 @@
|
||||
<div class="row col-6">
|
||||
<!-- Right DIV -->
|
||||
<div id="intDivStyle-right" class="st-col col-12 col-sm st-module">
|
||||
<st-tabs id="tabHeader-main" :ids="tabIDs" :labels="tabLabels" v-model="selectedTab" no-arrows></st-tabs>
|
||||
<q-tab-panels v-model="selectedTab">
|
||||
<q-tab-panel name="tab0">
|
||||
<!-- Content for Tab 0 -->
|
||||
<h6>Image visualizer</h6>
|
||||
<div class="row items-center">
|
||||
<q-select v-model="selected_folder_main" :options="image_available_folders" label="Select Dataset"
|
||||
class="q-ma-sm" style="min-width: 200px;"></q-select>
|
||||
<q-space></q-space>
|
||||
<q-btn icon="arrow_back" class="q-my-sm btn-style" v-on:click="imgMinus=true"></q-btn>
|
||||
<q-btn icon="arrow_forward" class="q-my-sm on-right btn-style" v-on:click="imgPlus=true"></q-btn>
|
||||
</div>
|
||||
<!-- Image manager -->
|
||||
<div id="image-container-normal" class="row st-col col-12">
|
||||
<div class="col-10 q-pa-none q-ma-none">
|
||||
<plotly id="plotImg" :data="plotdataImg" :layout="plotlayoutImg" class="q-pa-none q-ma-none sync_data"
|
||||
@click="data_click"></plotly>
|
||||
<div v-if="left_tab === 'pre_treatment'">
|
||||
<div class="text-h6 q-mb-md">Spectrum View</div>
|
||||
<q-card class="q-mb-md">
|
||||
<q-card-section>
|
||||
<div class="text-subtitle1">Before Preprocessing</div>
|
||||
</q-card-section>
|
||||
<q-card-section>
|
||||
<plotly id="plotSpectraBefore" :data="plotdata" :layout="plotlayout" class="q-pa-none q-ma-none"></plotly>
|
||||
</q-card-section>
|
||||
</q-card>
|
||||
<q-card>
|
||||
<q-card-section>
|
||||
<div class="text-subtitle1">After Preprocessing</div>
|
||||
</q-card-section>
|
||||
<q-card-section>
|
||||
<plotly id="plotSpectraAfter" :data="plotdata_after" :layout="plotlayout_after" class="q-pa-none q-ma-none">
|
||||
</plotly>
|
||||
</q-card-section>
|
||||
</q-card>
|
||||
</div>
|
||||
<div v-else>
|
||||
<st-tabs id="tabHeader-main" :ids="tabIDs" :labels="tabLabels" v-model="selectedTab" no-arrows></st-tabs>
|
||||
<q-tab-panels v-model="selectedTab">
|
||||
<q-tab-panel name="tab0">
|
||||
<!-- Content for Tab 0 -->
|
||||
<h6>Image visualizer</h6>
|
||||
<div class="row items-center">
|
||||
<q-select v-model="selected_folder_main" :options="image_available_folders" label="Select Dataset"
|
||||
class="q-ma-sm" style="min-width: 200px;" v-on:focus="refetch_folders = true"></q-select>
|
||||
<q-space></q-space>
|
||||
<q-btn icon="arrow_back" class="q-my-sm btn-style" v-on:click="imgMinus=true"></q-btn>
|
||||
<q-btn icon="arrow_forward" class="q-my-sm on-right btn-style" v-on:click="imgPlus=true"></q-btn>
|
||||
</div>
|
||||
<div class="col-2 q-pa-none q-ma-none">
|
||||
<q-img id="colorbar-normal" class="q-ma-none q-pa-none" :src="colorbar"></q-img>
|
||||
<!-- Image manager -->
|
||||
<div id="image-container-normal" class="row st-col col-12">
|
||||
<div class="col-10 q-pa-none q-ma-none">
|
||||
<plotly id="plotImg" :data="plotdataImg" :layout="plotlayoutImg" class="q-pa-none q-ma-none sync_data"
|
||||
@click="data_click"></plotly>
|
||||
</div>
|
||||
<div class="col-2 q-pa-none q-ma-none">
|
||||
<q-img id="colorbar-normal" class="q-ma-none q-pa-none" :src="colorbar"></q-img>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<p v-html="msgimg"></p>
|
||||
</q-tab-panel>
|
||||
<p v-html="msgimg"></p>
|
||||
</q-tab-panel>
|
||||
|
||||
<q-tab-panel name="tab1">
|
||||
<!-- Content for Tab 1 -->
|
||||
<h6>TrIQ visualizer</h6>
|
||||
<div class="row items-center">
|
||||
<q-select v-model="selected_folder_main" :options="image_available_folders" label="Select Dataset"
|
||||
class="q-ma-sm" style="min-width: 200px;"></q-select>
|
||||
<q-space></q-space>
|
||||
<q-btn icon="arrow_back" class="q-my-sm btn-style" v-on:click="imgMinusT=true"></q-btn>
|
||||
<q-btn icon="arrow_forward" class="q-my-sm on-right btn-style" v-on:click="imgPlusT=true"></q-btn>
|
||||
</div>
|
||||
<!-- Triq Image manager -->
|
||||
<div id="image-container-triq" class="row st-col col-12">
|
||||
<div class="col-10 q-pa-none q-ma-none ">
|
||||
<plotly id="plotImgT" :data="plotdataImgT" :layout="plotlayoutImgT" class="q-pa-none q-ma-none sync_data"
|
||||
@click="data_click"></plotly>
|
||||
<q-tab-panel name="tab1">
|
||||
<!-- Content for Tab 1 -->
|
||||
<h6>TrIQ visualizer</h6>
|
||||
<div class="row items-center">
|
||||
<q-select v-model="selected_folder_main" :options="image_available_folders" label="Select Dataset"
|
||||
class="q-ma-sm" style="min-width: 200px;" v-on:focus="refetch_folders = true"></q-select>
|
||||
<q-space></q-space>
|
||||
<q-btn icon="arrow_back" class="q-my-sm btn-style" v-on:click="imgMinusT=true"></q-btn>
|
||||
<q-btn icon="arrow_forward" class="q-my-sm on-right btn-style" v-on:click="imgPlusT=true"></q-btn>
|
||||
</div>
|
||||
<div class="col-2 q-pa-none q-ma-none ">
|
||||
<q-img id="colorbar-triq" class="q-ma-none q-pa-none" :src="colorbarT"></q-img>
|
||||
<!-- Triq Image manager -->
|
||||
<div id="image-container-triq" class="row st-col col-12">
|
||||
<div class="col-10 q-pa-none q-ma-none ">
|
||||
<plotly id="plotImgT" :data="plotdataImgT" :layout="plotlayoutImgT"
|
||||
class="q-pa-none q-ma-none sync_data" @click="data_click"></plotly>
|
||||
</div>
|
||||
<div class="col-2 q-pa-none q-ma-none ">
|
||||
<q-img id="colorbar-triq" class="q-ma-none q-pa-none" :src="colorbarT"></q-img>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<p v-html="msgtriq"></p>
|
||||
</q-tab-panel>
|
||||
<p v-html="msgtriq"></p>
|
||||
</q-tab-panel>
|
||||
|
||||
<q-tab-panel name="tab2">
|
||||
<div class="row items-center">
|
||||
<q-select v-model="selected_folder_main" :options="available_folders" label="Select Dataset" class="q-ma-sm"
|
||||
style="min-width: 200px;"></q-select>
|
||||
<q-btn-dropdown class="q-ma-sm btn-style" :loading="progressSpectraPlot" :disable="btnSpectraDisable"
|
||||
label="Generate Spectra" icon="play_arrow">
|
||||
<template v-slot:loading>
|
||||
<q-spinner-hourglass class="on-left" />
|
||||
Loading plot
|
||||
</template>
|
||||
<q-tab-panel name="tab2">
|
||||
<div class="row items-center">
|
||||
<q-select v-model="selected_folder_main" :options="available_folders" label="Select Dataset"
|
||||
class="q-ma-sm" style="min-width: 200px;" v-on:focus="refetch_folders = true"></q-select>
|
||||
<q-btn-dropdown class="q-ma-sm btn-style" :loading="progressSpectraPlot" :disable="btnSpectraDisable"
|
||||
label="Generate Spectra" icon="play_arrow">
|
||||
<template v-slot:loading>
|
||||
<q-spinner-hourglass class="on-left" />
|
||||
Loading plot
|
||||
</template>
|
||||
|
||||
<q-list>
|
||||
<q-item clickable v-close-popup v-on:click="createMeanPlot=true">
|
||||
<q-item-section>
|
||||
<q-item-label>Mean spectrum plot</q-item-label>
|
||||
</q-item-section>
|
||||
</q-item>
|
||||
<q-item clickable v-close-popup v-on:click="createSumPlot=true">
|
||||
<q-item-section>
|
||||
<q-item-label>Sum Spectrum plot</q-item-label>
|
||||
</q-item-section>
|
||||
</q-item>
|
||||
<q-item clickable v-close-popup v-on:click="createXYPlot=true">
|
||||
<q-item-section>
|
||||
<q-item-label>Spectrum plot (X,Y)</q-item-label>
|
||||
</q-item-section>
|
||||
</q-item>
|
||||
</q-list>
|
||||
</q-btn-dropdown>
|
||||
</div>
|
||||
<plotly id="plotSpectra" :data="plotdata" :layout="plotlayout" class="q-pa-none q-ma-none"></plotly>
|
||||
</q-tab-panel>
|
||||
<q-list>
|
||||
<q-item clickable v-close-popup v-on:click="createMeanPlot=true">
|
||||
<q-item-section>
|
||||
<q-item-label>Mean spectrum plot</q-item-label>
|
||||
</q-item-section>
|
||||
</q-item>
|
||||
<q-item clickable v-close-popup v-on:click="createSumPlot=true">
|
||||
<q-item-section>
|
||||
<q-item-label>Sum Spectrum plot</q-item-label>
|
||||
</q-item-section>
|
||||
</q-item>
|
||||
<q-item clickable v-close-popup v-on:click="createXYPlot=true">
|
||||
<q-item-section>
|
||||
<q-item-label>Spectrum plot (X,Y)</q-item-label>
|
||||
</q-item-section>
|
||||
</q-item>
|
||||
</q-list>
|
||||
</q-btn-dropdown>
|
||||
</div>
|
||||
<plotly id="plotSpectra" :data="plotdata" :layout="plotlayout" class="q-pa-none q-ma-none"></plotly>
|
||||
</q-tab-panel>
|
||||
|
||||
<q-tab-panel name="tab3">
|
||||
<!-- Content for Tab 3 -->
|
||||
<plotly id="plotTopo" :data="plotdataC" :layout="plotlayoutC" class="q-pa-none q-ma-none"></plotly>
|
||||
</q-tab-panel>
|
||||
<q-tab-panel name="tab4">
|
||||
<!-- Content for Tab 4 -->
|
||||
<plotly id="plot3d" :data="plotdata3d" :layout="plotlayout3d" class="q-pa-none q-ma-none"></plotly>
|
||||
</q-tab-panel>
|
||||
</q-tab-panels>
|
||||
<q-tab-panel name="tab3">
|
||||
<!-- Content for Tab 3 -->
|
||||
<plotly id="plotTopo" :data="plotdataC" :layout="plotlayoutC" class="q-pa-none q-ma-none"></plotly>
|
||||
</q-tab-panel>
|
||||
<q-tab-panel name="tab4">
|
||||
<!-- Content for Tab 4 -->
|
||||
<plotly id="plot3d" :data="plotdata3d" :layout="plotlayout3d" class="q-pa-none q-ma-none"></plotly>
|
||||
</q-tab-panel>
|
||||
</q-tab-panels>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
@ -395,7 +597,8 @@
|
||||
<div class="col-6">
|
||||
<div class="row items-center">
|
||||
<q-select v-model="selected_folder_compare_left" :options="image_available_folders"
|
||||
label="Select Left Dataset" class="q-ma-sm" style="min-width: 200px;"></q-select>
|
||||
label="Select Left Dataset" class="q-ma-sm" style="min-width: 200px;"
|
||||
v-on:focus="refetch_folders = true"></q-select>
|
||||
<q-space></q-space>
|
||||
<st-tabs id="tabHeaderCompareLeft" :ids="CompTabIDsLeft" :labels="CompTabLabelsLeft"
|
||||
v-model="CompSelectedTabLeft"></st-tabs>
|
||||
@ -464,7 +667,8 @@
|
||||
<div class="col-6">
|
||||
<div class="row items-center">
|
||||
<q-select v-model="selected_folder_compare_right" :options="image_available_folders"
|
||||
label="Select Right Dataset" class="q-ma-sm" style="min-width: 200px;"></q-select>
|
||||
label="Select Right Dataset" class="q-ma-sm" style="min-width: 200px;"
|
||||
v-on:focus="refetch_folders = true"></q-select>
|
||||
<q-space></q-space>
|
||||
<st-tabs id="tabHeaderCompareRight" :ids="CompTabIDsRight" :labels="CompTabLabelsRight"
|
||||
v-model="CompSelectedTabRight"></st-tabs>
|
||||
@ -561,7 +765,7 @@
|
||||
<div class="text-h6">Dataset Summary</div>
|
||||
<q-space />
|
||||
<q-select v-model="selected_folder_metadata" :options="available_folders" label="Select Dataset" class="q-ma-sm"
|
||||
style="min-width: 250px;" standout="custom-standout"></q-select>
|
||||
style="min-width: 250px;" standout="custom-standout" v-on:focus="refetch_folders = true"></q-select>
|
||||
</q-card-section>
|
||||
|
||||
<q-card-section class="q-pt-none">
|
||||
|
||||
@ -666,10 +666,10 @@ function xySpectrumPlot(data::MSIData, xCoord::Int, yCoord::Int, imgWidth::Int,
|
||||
# Downsample for plotting performance
|
||||
mz_down, int_down = MSI_src.downsample_spectrum(mz, intensity)
|
||||
|
||||
trace = if spectrum_mode == MSI_src.PROFILE
|
||||
PlotlyBase.scatter(x=mz_down, y=int_down, mode="lines", marker=attr(size=1, color="blue", opacity=0.5), name="Spectrum", hoverinfo="x", hovertemplate="<b>m/z</b>: %{x:.4f}<extra></extra>")
|
||||
else
|
||||
trace = if spectrum_mode == MSI_src.CENTROID
|
||||
PlotlyBase.stem(x=mz_down, y=int_down, marker=attr(size=1, color="blue", opacity=0.5), name="Spectrum", hoverinfo="x", hovertemplate="<b>m/z</b>: %{x:.4f}<extra></extra>")
|
||||
else
|
||||
PlotlyBase.scatter(x=mz_down, y=int_down, mode="lines", marker=attr(size=1, color="blue", opacity=0.5), name="Spectrum", hoverinfo="x", hovertemplate="<b>m/z</b>: %{x:.4f}<extra></extra>")
|
||||
end
|
||||
|
||||
plotdata = [trace]
|
||||
|
||||
18
mask.jl
18
mask.jl
@ -151,6 +151,7 @@ end
|
||||
@out available_folders = String[]
|
||||
@out image_available_folders = String[]
|
||||
@private registry_init_done = false
|
||||
@in refetch_folders = false
|
||||
|
||||
@out imgInt = "" # Path to current slice
|
||||
@out current_msi = ""
|
||||
@ -711,6 +712,23 @@ end
|
||||
end
|
||||
end
|
||||
|
||||
@onbutton refetch_folders begin
|
||||
# First, re-run the logic to populate the folder list
|
||||
registry = load_registry(registry_path)
|
||||
all_folders = sort(collect(keys(registry)), lt=natural)
|
||||
img_folders = filter(folder -> get(get(registry, folder, Dict()), "is_imzML", false), all_folders)
|
||||
|
||||
available_folders = deepcopy(all_folders)
|
||||
image_available_folders = deepcopy(img_folders)
|
||||
|
||||
# Apply the logic to select the first item if none is selected
|
||||
if !isempty(image_available_folders) && isempty(selected_folder_main)
|
||||
# This ensures the list is up-to-date
|
||||
image_available_folders = deepcopy(img_folders)
|
||||
selected_folder_main = first(image_available_folders)
|
||||
end
|
||||
end
|
||||
|
||||
@onchange isready begin
|
||||
if isready && !registry_init_done
|
||||
sleep(1.0) # Give frontend time to initialize
|
||||
|
||||
@ -15,7 +15,7 @@
|
||||
<div class="text-subtitle1 q-mt-md">Step 1: Select Slice</div>
|
||||
<div class="row items-center">
|
||||
<q-select v-model="selected_folder_main" :options="image_available_folders" label="Select Dataset"
|
||||
class="q-ma-sm col" standout="custom-standout" :disable="is_editing_mask"></q-select>
|
||||
class="q-ma-sm col" standout="custom-standout" :disable="is_editing_mask" v-on:focus="refetch_folders = true"></q-select>
|
||||
</div>
|
||||
<p class="text-center" v-html="msgimg"></p>
|
||||
|
||||
|
||||
@ -45,9 +45,10 @@
|
||||
color: #009f90;
|
||||
}
|
||||
|
||||
#intDivStyle-left {
|
||||
#intDivStyle-left, #intDivStyle-right {
|
||||
border-radius: 10px;
|
||||
padding: 10px;
|
||||
background-color: #fdfdfd; /* Add a background color to distinguish from the outer div */
|
||||
}
|
||||
|
||||
/* Tab styling to match your theme */
|
||||
@ -81,13 +82,13 @@
|
||||
font-size: 0.9rem;
|
||||
}
|
||||
|
||||
#intDivStyle-left .q-tab-panels {
|
||||
height: 700px; /* Set this to accommodate your tallest content */
|
||||
#intDivStyle-left .q-tab-panels, #intDivStyle-right .q-tab-panels {
|
||||
/* Removed fixed height */
|
||||
}
|
||||
|
||||
#intDivStyle-left .q-tab-panel {
|
||||
height: 100%;
|
||||
overflow-y: auto; /* Add scroll if content overflows */
|
||||
#intDivStyle-left .q-tab-panel, #intDivStyle-right .q-tab-panel {
|
||||
height: auto; /* Let content define height */
|
||||
overflow-y: hidden; /* Remove scrollbar */
|
||||
}
|
||||
|
||||
.pixelated-plot svg image {
|
||||
@ -99,3 +100,21 @@
|
||||
*{
|
||||
font-family: 'Roboto', 'Lato', sans-serif;
|
||||
}
|
||||
|
||||
.q-card {
|
||||
border-radius: 8px !important;
|
||||
box-shadow: 0 2px 4px rgba(0,0,0,0.1) !important;
|
||||
margin-bottom: 16px !important;
|
||||
}
|
||||
|
||||
.q-card__section--dark {
|
||||
background: #f7f7f7 !important;
|
||||
}
|
||||
|
||||
.q-radio__label {
|
||||
font-size: 1rem !important;
|
||||
}
|
||||
|
||||
.q-option-group > div {
|
||||
margin-bottom: 8px;
|
||||
}
|
||||
|
||||
@ -37,9 +37,20 @@ mutable struct StreamingBloomFilter
|
||||
end
|
||||
|
||||
"""
|
||||
BloomFilter(expected_elements::Int, false_positive_rate::Float64=0.01; seed::UInt64=0x12345678)
|
||||
BloomFilter{T}(expected_elements::Int, false_positive_rate::Float64=0.01; kwargs...) -> Return type
|
||||
|
||||
Creates a Bloom filter optimized for the expected number of elements and desired false positive rate.
|
||||
|
||||
# Arguments
|
||||
|
||||
- `expected_elements::Int`: Argument description
|
||||
- `false_positive_rate::Float64`: Argument description
|
||||
(**Default**: `0.01`)
|
||||
|
||||
# Keywords
|
||||
|
||||
- `seed::Union{UInt32,UInt64}`: Keyword description
|
||||
(**Default**: `0x12345678`)
|
||||
"""
|
||||
function BloomFilter{T}(expected_elements::Int, false_positive_rate::Float64=0.01; seed::Union{UInt32,UInt64}=0x12345678) where T
|
||||
# Convert seed to UInt64 for consistency
|
||||
@ -56,9 +67,12 @@ end
|
||||
"""
|
||||
optimal_bit_size(n::Int, p::Float64) -> Int
|
||||
|
||||
Calculates the optimal number of bits for a Bloom filter given:
|
||||
- n: expected number of elements
|
||||
- p: desired false positive rate
|
||||
Calculates the optimal number of bits for a Bloom filter
|
||||
|
||||
# Arguments
|
||||
|
||||
- `n::Int`: Expected number of elements
|
||||
- `p::Float64`: Desired false positive rate
|
||||
"""
|
||||
function optimal_bit_size(n::Int, p::Float64)::Int
|
||||
if p <= 0.0 || p >= 1.0
|
||||
@ -73,6 +87,11 @@ end
|
||||
optimal_hash_count(n::Int, m::Int) -> Int
|
||||
|
||||
Calculates the optimal number of hash functions for a Bloom filter.
|
||||
|
||||
# Arguments
|
||||
|
||||
- `n::Int`: Expected number of elements
|
||||
- `p::Float64`: Desired false positive rate
|
||||
"""
|
||||
function optimal_hash_count(n::Int, m::Int)::Int
|
||||
if n <= 0 || m <= 0
|
||||
@ -109,6 +128,11 @@ end
|
||||
Base.push!(bf::BloomFilter{T}, item::T)
|
||||
|
||||
Adds an element to the Bloom filter.
|
||||
|
||||
# Arguments
|
||||
|
||||
- `bf::BloomFilter{T}`: Argument description
|
||||
- `item::T`: Argument description
|
||||
"""
|
||||
function Base.push!(bf::BloomFilter{T}, item::T) where T
|
||||
hashes = hash_functions(item, bf.hash_count, bf.size, bf.seed)
|
||||
@ -169,27 +193,39 @@ function false_positive_rate(bf::BloomFilter)::Float64
|
||||
end
|
||||
|
||||
"""
|
||||
fill_ratio(bf::BloomFilter) -> Float64
|
||||
fill_ratio(bf::BloomFilter)::Float64 return count(bf.bits) / length(bf.bits) end -> Return type
|
||||
|
||||
Returns the fraction of bits that are set to 1.
|
||||
|
||||
# Arguments
|
||||
|
||||
- `bf::BloomFilter`: Argument description
|
||||
"""
|
||||
function fill_ratio(bf::BloomFilter)::Float64
|
||||
return count(bf.bits) / length(bf.bits)
|
||||
end
|
||||
|
||||
"""
|
||||
is_empty(bf::BloomFilter) -> Bool
|
||||
is_empty(bf::BloomFilter)::Bool return bf.count == 0 end -> Return type
|
||||
|
||||
Checks if the Bloom filter is empty (no elements added).
|
||||
|
||||
# Arguments
|
||||
|
||||
- `bf::BloomFilter`: Argument description
|
||||
"""
|
||||
function is_empty(bf::BloomFilter)::Bool
|
||||
return bf.count == 0
|
||||
end
|
||||
|
||||
"""
|
||||
reset!(bf::BloomFilter)
|
||||
reset!(bf::BloomFilter) fill!(bf.bits, false) bf.count = 0 return bf end -> Return type
|
||||
|
||||
Clears the Bloom filter, removing all elements.
|
||||
|
||||
# Arguments
|
||||
|
||||
- `bf::BloomFilter`: Argument description
|
||||
"""
|
||||
function reset!(bf::BloomFilter)
|
||||
fill!(bf.bits, false)
|
||||
@ -198,6 +234,20 @@ function reset!(bf::BloomFilter)
|
||||
end
|
||||
|
||||
# Specialized constructor for empty Bloom filters
|
||||
"""
|
||||
BloomFilter{T}(; kwargs...) -> Return type
|
||||
|
||||
Description of the function
|
||||
|
||||
# Keywords
|
||||
|
||||
- `size::Int`: Keyword description
|
||||
(**Default**: `100`)
|
||||
- `hash_count::Int`: Keyword description
|
||||
(**Default**: `3`)
|
||||
- `seed::Union{UInt32,UInt64}`: Keyword description
|
||||
(**Default**: `0x12345678`)
|
||||
"""
|
||||
function BloomFilter{T}(;size::Int=100, hash_count::Int=3, seed::Union{UInt32,UInt64}=0x12345678) where T
|
||||
seed_uint64 = UInt64(seed)
|
||||
bits = falses(size)
|
||||
|
||||
@ -420,6 +420,12 @@ function read_binary_vector(data::MSIData, io::IO, asset::SpectrumAsset)
|
||||
return out_array
|
||||
end
|
||||
|
||||
function read_binary_vector(data::MSIData, ts_handle::ThreadSafeFileHandle, asset::SpectrumAsset)
|
||||
lock(ts_handle.lock) do
|
||||
return read_binary_vector(data, ts_handle.handle, asset)
|
||||
end
|
||||
end
|
||||
|
||||
# Overload for different source types
|
||||
"""
|
||||
read_spectrum_from_disk(source::ImzMLSource, meta::SpectrumMetadata)
|
||||
|
||||
@ -28,8 +28,12 @@ export FeatureMatrix,
|
||||
snip_baseline,
|
||||
tic_normalize,
|
||||
pqn_normalize,
|
||||
median_normalize,
|
||||
detect_peaks_profile,
|
||||
detect_peaks_wavelet,
|
||||
detect_peaks_centroid,
|
||||
align_peaks_lowess,
|
||||
find_calibration_peaks,
|
||||
bin_peaks,
|
||||
plot_stage_spectrum,
|
||||
calculate_ppm_error,
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
446
src/PreprocessingVersioning.jl
Normal file
446
src/PreprocessingVersioning.jl
Normal file
@ -0,0 +1,446 @@
|
||||
# src/PreprocessingVersioning.jl
|
||||
|
||||
"""
|
||||
This module provides a versioning helper functions in our data preprocessing, module
|
||||
inspired by the functionality of the R package MALDIquant. It includes
|
||||
functions for quality control, intensity transformation, smoothing, baseline correction,
|
||||
normalization, peak picking, alignment, and feature matrix generation.
|
||||
|
||||
This module is unfinished and may not end up in the release version.
|
||||
"""
|
||||
|
||||
# =============================================================================
|
||||
# Dependencies
|
||||
# =============================================================================
|
||||
|
||||
using UUIDs, JLD2, CodecBase # For preprocessing versioning
|
||||
|
||||
# =============================================================================
|
||||
# Data Structures
|
||||
# =============================================================================
|
||||
|
||||
"""
|
||||
VersionedSpectralData
|
||||
|
||||
A struct to hold a snapshot of spectral data at a specific point in the
|
||||
preprocessing workflow. Each transformation creates a new instance of this
|
||||
struct, forming a history of all operations.
|
||||
|
||||
# Fields
|
||||
- `version_id::String`: A unique identifier for this version of the data.
|
||||
- `parent_id::String`: The identifier of the version from which this one was derived.
|
||||
- `spectra::Vector`: The spectral data itself, typically a vector of `(mz, intensity)` tuples.
|
||||
- `processing_step::String`: A description of the operation that created this version (e.g., "smooth", "baseline").
|
||||
- `timestamp::DateTime`: The time at which this version was created.
|
||||
- `parameters::Dict`: A dictionary of the parameters used in the processing step.
|
||||
"""
|
||||
struct VersionedSpectralData
|
||||
version_id::String
|
||||
parent_id::String
|
||||
spectra::Vector
|
||||
processing_step::String
|
||||
timestamp::DateTime
|
||||
parameters::Dict
|
||||
end
|
||||
|
||||
"""
|
||||
MSISession
|
||||
|
||||
Manages the state of a preprocessing session, including the history of all
|
||||
data versions and the current working version.
|
||||
|
||||
# Fields
|
||||
- `session_id::String`: A unique identifier for the entire session.
|
||||
- `original_data::VersionedSpectralData`: The initial, unprocessed spectral data.
|
||||
- `history::Vector{VersionedSpectralData}`: A chronological list of all data versions created during the session.
|
||||
- `current_version::VersionedSpectralData`: The version of the data currently being worked on or displayed.
|
||||
- `processing_steps::Vector{String}`: A human-readable log of the processing steps applied.
|
||||
"""
|
||||
mutable struct MSISession
|
||||
session_id::String
|
||||
original_data::VersionedSpectralData
|
||||
history::Vector{VersionedSpectralData}
|
||||
current_version::VersionedSpectralData
|
||||
processing_steps::Vector{String}
|
||||
end
|
||||
|
||||
# =============================================================================
|
||||
# Session Management
|
||||
# =============================================================================
|
||||
|
||||
"""
|
||||
initialize_session(raw_spectra::Vector, session_name::String) -> MSISession
|
||||
|
||||
Creates a new preprocessing session from raw spectral data.
|
||||
|
||||
# Arguments
|
||||
- `raw_spectra::Vector`: A vector of `(mz, intensity)` tuples representing the initial dataset.
|
||||
- `session_name::String`: A name for the session.
|
||||
|
||||
# Returns
|
||||
- `MSISession`: A new session object initialized with the provided data.
|
||||
"""
|
||||
function initialize_session(raw_spectra::Vector, session_name::String)::MSISession
|
||||
original = VersionedSpectralData(
|
||||
string(uuid4()),
|
||||
"root",
|
||||
raw_spectra,
|
||||
"Original Data",
|
||||
now(),
|
||||
Dict()
|
||||
)
|
||||
return MSISession(session_name, original, [original], original, [])
|
||||
end
|
||||
|
||||
"""
|
||||
get_processing_history(session::MSISession) -> Vector{String}
|
||||
|
||||
Returns a list of the processing steps applied during the session.
|
||||
"""
|
||||
get_processing_history(session::MSISession) = [v.processing_step for v in session.history]
|
||||
|
||||
"""
|
||||
undo_last_step!(session::MSISession)
|
||||
|
||||
Reverts the session to the state before the last processing step was applied.
|
||||
This modifies the session in place.
|
||||
"""
|
||||
function undo_last_step!(session::MSISession)
|
||||
if length(session.history) > 1
|
||||
pop!(session.history)
|
||||
pop!(session.processing_steps)
|
||||
session.current_version = last(session.history)
|
||||
end
|
||||
return session
|
||||
end
|
||||
|
||||
"""
|
||||
revert_to_version!(session::MSISession, version_id::String)
|
||||
|
||||
Reverts the session to a specific version in its history, discarding all
|
||||
subsequent changes. This modifies the session in place.
|
||||
"""
|
||||
function revert_to_version!(session::MSISession, version_id::String)
|
||||
target_idx = findfirst(v -> v.version_id == version_id, session.history)
|
||||
if !isnothing(target_idx)
|
||||
session.history = session.history[1:target_idx]
|
||||
session.current_version = session.history[end]
|
||||
# Also truncate the descriptive processing steps
|
||||
num_steps_to_keep = max(0, target_idx - 1)
|
||||
session.processing_steps = session.processing_steps[1:num_steps_to_keep]
|
||||
end
|
||||
return session
|
||||
end
|
||||
|
||||
# =============================================================================
|
||||
# Versioned Preprocessing
|
||||
# =============================================================================
|
||||
|
||||
"""
|
||||
apply_processing_step(spectra::Vector, step::Symbol, params::Dict) -> Vector
|
||||
|
||||
A dispatcher that applies a single, specified preprocessing function to a set of spectra.
|
||||
This is the core function called by the versioned workflow.
|
||||
|
||||
# Arguments
|
||||
- `spectra::Vector`: The input spectral data.
|
||||
- `step::Symbol`: The symbol representing the processing step (e.g., `:smooth`, `:baseline`).
|
||||
- `params::Dict`: A dictionary of parameters for the step.
|
||||
|
||||
# Returns
|
||||
- `Vector`: The processed spectral data.
|
||||
"""
|
||||
function apply_processing_step(spectra::Vector, step::Symbol, params::Dict)
|
||||
processed = deepcopy(spectra)
|
||||
params_sym = Dict(Symbol(k) => v for (k,v) in params) # Ensure keys are symbols
|
||||
|
||||
if step === :transform
|
||||
for i in eachindex(processed)
|
||||
mz, y = processed[i]
|
||||
processed[i] = (mz, transform_intensity(y; params_sym...))
|
||||
end
|
||||
elseif step === :smooth
|
||||
for i in eachindex(processed)
|
||||
mz, y = processed[i]
|
||||
processed[i] = (mz, smooth_spectrum(y; params_sym...))
|
||||
end
|
||||
elseif step === :baseline
|
||||
for i in eachindex(processed)
|
||||
mz, y = processed[i]
|
||||
baseline = snip_baseline(y; params_sym...)
|
||||
processed[i] = (mz, max.(0.0, y .- baseline))
|
||||
end
|
||||
elseif step === :normalize
|
||||
mode = get(params, :normalize_method, :tic)
|
||||
if mode === :pqn
|
||||
matrix = hcat([float.(p[2]) for p in processed]...)
|
||||
matrix_norm = pqn_normalize(matrix)
|
||||
for i in eachindex(processed)
|
||||
mz, _ = processed[i]
|
||||
processed[i] = (mz, view(matrix_norm, :, i))
|
||||
end
|
||||
else # :tic or :median
|
||||
norm_func = (mode === :tic) ? tic_normalize : median_normalize
|
||||
for i in eachindex(processed)
|
||||
mz, y = processed[i]
|
||||
processed[i] = (mz, norm_func(y))
|
||||
end
|
||||
end
|
||||
elseif step === :peaks
|
||||
peak_results = Vector{Tuple{Vector{Float64},Vector{Float64}}}(undef, length(processed))
|
||||
for (i, (mz, y)) in enumerate(processed)
|
||||
pk_mz, pk_int = detect_peaks_profile(mz, y; params_sym...)
|
||||
peak_results[i] = (pk_mz, pk_int)
|
||||
end
|
||||
return peak_results
|
||||
elseif step === :peaks_wavelet
|
||||
peak_results = Vector{Tuple{Vector{Float64},Vector{Float64}}}(undef, length(processed))
|
||||
for (i, (mz, y)) in enumerate(processed)
|
||||
pk_mz, pk_int = detect_peaks_wavelet(mz, y; params_sym...)
|
||||
peak_results[i] = (pk_mz, pk_int)
|
||||
end
|
||||
return peak_results
|
||||
elseif step === :calibrate
|
||||
return calibrate_spectra(processed; params_sym...)
|
||||
else
|
||||
@warn "Unsupported processing step: $step"
|
||||
end
|
||||
return processed
|
||||
end
|
||||
|
||||
"""
|
||||
run_versioned_preprocessing(session::MSISession, step::Symbol, params::Dict) -> VersionedSpectralData
|
||||
|
||||
Creates a new version of spectral data by applying a single processing step to the
|
||||
current version in the session.
|
||||
|
||||
# Arguments
|
||||
- `session::MSISession`: The current processing session.
|
||||
- `step::Symbol`: The processing step to apply.
|
||||
- `params::Dict`: Parameters for the processing step.
|
||||
|
||||
# Returns
|
||||
- `VersionedSpectralData`: A new data version with the transformation applied.
|
||||
"""
|
||||
function run_versioned_preprocessing(session::MSISession, step::Symbol, params::Dict)
|
||||
# Create a new version based on the current one
|
||||
parent_version = session.current_version
|
||||
new_version_id = string(uuid4())
|
||||
|
||||
# Apply the processing step
|
||||
new_spectra = apply_processing_step(parent_version.spectra, step, params)
|
||||
|
||||
# Create the new versioned data object
|
||||
new_version = VersionedSpectralData(
|
||||
new_version_id,
|
||||
parent_version.version_id,
|
||||
new_spectra,
|
||||
string(step),
|
||||
now(),
|
||||
params
|
||||
)
|
||||
|
||||
return new_version
|
||||
end
|
||||
|
||||
"""
|
||||
apply_processing_with_version!(session::MSISession, step::Symbol, ui_params::Dict)
|
||||
|
||||
A high-level function to apply a processing step, create a new version, and
|
||||
update the session state in place.
|
||||
|
||||
# Arguments
|
||||
- `session::MSISession`: The session to modify.
|
||||
- `step::Symbol`: The processing step to apply.
|
||||
- `ui_params::Dict`: A dictionary of parameters, typically from a UI.
|
||||
"""
|
||||
function apply_processing_with_version!(session::MSISession, step::Symbol, ui_params::Dict)
|
||||
# In a real app, you would validate and convert UI params here.
|
||||
processing_params = ui_params
|
||||
|
||||
# Create the new version
|
||||
new_version = run_versioned_preprocessing(session, step, processing_params)
|
||||
|
||||
# Update the session
|
||||
push!(session.history, new_version)
|
||||
session.current_version = new_version
|
||||
|
||||
# Describe the step for the history log
|
||||
step_description = "$(string(step)) with params: " * join(["$k=$v" for (k,v) in processing_params], ", ")
|
||||
push!(session.processing_steps, step_description)
|
||||
|
||||
return session
|
||||
end
|
||||
|
||||
# =============================================================================
|
||||
# Data Serialization & Export
|
||||
# =============================================================================
|
||||
|
||||
"""
|
||||
save_spectral_version(data::VersionedSpectralData, filepath::String)
|
||||
|
||||
Saves a `VersionedSpectralData` object to a file using the JLD2 format.
|
||||
"""
|
||||
function save_spectral_version(data::VersionedSpectralData, filepath::String)
|
||||
JLD2.save_object(filepath, data)
|
||||
end
|
||||
|
||||
"""
|
||||
load_spectral_version(filepath::String) -> VersionedSpectralData
|
||||
|
||||
Loads a `VersionedSpectralData` object from a JLD2 file.
|
||||
"""
|
||||
function load_spectral_version(filepath::String)::VersionedSpectralData
|
||||
return JLD2.load_object(filepath)
|
||||
end
|
||||
|
||||
"""
|
||||
_encode_base64(data::AbstractVector{<:Real}) -> String
|
||||
|
||||
Helper function to convert a numeric vector into a Base64 encoded string.
|
||||
"""
|
||||
function _encode_base64(data::AbstractVector{T}) where T <: Real
|
||||
bytes = reinterpret(UInt8, data)
|
||||
return base64encode(bytes)
|
||||
end
|
||||
|
||||
"""
|
||||
export_to_mzml(session::MSISession, filepath::String)
|
||||
|
||||
Exports the current version of the spectral data in a session to a standard
|
||||
.mzML file.
|
||||
|
||||
# Arguments
|
||||
- `session::MSISession`: The current session.
|
||||
- `filepath::String`: The path for the output .mzML file.
|
||||
"""
|
||||
function export_to_mzml(session::MSISession, filepath::String)
|
||||
spectra_to_export = session.current_version.spectra
|
||||
|
||||
open(filepath, "w") do f
|
||||
# XML Header
|
||||
write(f, "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
|
||||
write(f, "<mzML xmlns=\"http://psi.hupo.org/ms/mzml\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd\" version=\"1.1\">\n")
|
||||
|
||||
# CV List
|
||||
write(f, " <cvList count=\"2\">\n")
|
||||
write(f, " <cv id=\"MS\" fullName=\"Proteomics Standards Initiative Mass Spectrometry Ontology\" version=\"4.1.123\" URI=\"https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo\"/>\n")
|
||||
write(f, " <cv id=\"UO\" fullName=\"Unit Ontology\" version=\"07:03:2022\" URI=\"https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo\"/>\n")
|
||||
write(f, " </cvList>\n")
|
||||
|
||||
# File Description
|
||||
write(f, " <fileDescription>\n <fileContent>\n")
|
||||
write(f, " <cvParam cvRef=\"MS\" accession=\"MS:1000579\" name=\"MS1 spectrum\"/>\n")
|
||||
write(f, " </fileContent>\n </fileDescription>\n")
|
||||
|
||||
# Run and Spectrum List
|
||||
write(f, " <run id=\"run1\" defaultInstrumentConfigurationRef=\"instrument1\">\n")
|
||||
write(f, " <spectrumList count=\"$(length(spectra_to_export))\" defaultDataProcessingRef=\"dp1\">\n")
|
||||
|
||||
for (i, (mz, intensity)) in enumerate(spectra_to_export)
|
||||
# Ensure data is in the correct format for encoding
|
||||
mz_64 = convert(Vector{Float64}, mz)
|
||||
int_32 = convert(Vector{Float32}, intensity)
|
||||
|
||||
# Base64 encode the binary data
|
||||
mz_b64 = _encode_base64(mz_64)
|
||||
int_b64 = _encode_base64(int_32)
|
||||
|
||||
write(f, " <spectrum index=\"$(i-1)\" id=\"scan=$(i)\" defaultArrayLength=\"$(length(mz))\">\n")
|
||||
write(f, " <cvParam cvRef=\"MS\" accession=\"MS:1000511\" name=\"ms level\" value=\"1\"/>\n")
|
||||
# Assuming profile mode for processed data, could be made dynamic
|
||||
write(f, " <cvParam cvRef=\"MS\" accession=\"MS:1000128\" name=\"profile spectrum\"/>\n")
|
||||
|
||||
write(f, " <binaryDataArrayList count=\"2\">\n")
|
||||
|
||||
# m/z array
|
||||
write(f, " <binaryDataArray encodedLength=\"$(length(mz_b64))\">\n")
|
||||
write(f, " <cvParam cvRef=\"MS\" accession=\"MS:1000514\" name=\"m/z array\" unitCvRef=\"MS\" unitAccession=\"MS:1000040\" unitName=\"m/z\"/>\n")
|
||||
write(f, " <cvParam cvRef=\"MS\" accession=\"MS:1000523\" name=\"64-bit float\"/>\n")
|
||||
write(f, " <cvParam cvRef=\"MS\" accession=\"MS:1000576\" name=\"no compression\"/>\n")
|
||||
write(f, " <binary>$(mz_b64)</binary>\n")
|
||||
write(f, " </binaryDataArray>\n")
|
||||
|
||||
# Intensity array
|
||||
write(f, " <binaryDataArray encodedLength=\"$(length(int_b64))\">\n")
|
||||
write(f, " <cvParam cvRef=\"MS\" accession=\"MS:1000515\" name=\"intensity array\" unitCvRef=\"MS\" unitAccession=\"MS:1000131\" unitName=\"number of detector counts\"/>\n")
|
||||
write(f, " <cvParam cvRef=\"MS\" accession=\"MS:1000521\" name=\"32-bit float\"/>\n")
|
||||
write(f, " <cvParam cvRef=\"MS\" accession=\"MS:1000576\" name=\"no compression\"/>\n")
|
||||
write(f, " <binary>$(int_b64)</binary>\n")
|
||||
write(f, " </binaryDataArray>\n")
|
||||
|
||||
write(f, " </binaryDataArrayList>\n")
|
||||
write(f, " </spectrum>\n")
|
||||
end
|
||||
|
||||
write(f, " </spectrumList>\n")
|
||||
write(f, " </run>\n")
|
||||
|
||||
# Dummy instrument and data processing info
|
||||
write(f, " <instrumentConfigurationList count=\"1\">\n")
|
||||
write(f, " <instrumentConfiguration id=\"instrument1\"/>\n")
|
||||
write(f, " </instrumentConfigurationList>\n")
|
||||
write(f, " <dataProcessingList count=\"1\">\n")
|
||||
write(f, " <dataProcessing id=\"dp1\"/>\n")
|
||||
write(f, " </dataProcessingList>\n")
|
||||
|
||||
write(f, "</mzML>\n")
|
||||
end
|
||||
println("Successfully exported current data to $filepath")
|
||||
end
|
||||
|
||||
|
||||
# =============================================================================
|
||||
# Stubs for UI Integration
|
||||
# =============================================================================
|
||||
|
||||
"""
|
||||
validate_ui_parameters(step::Symbol, ui_params::Dict) -> Tuple{Bool, String}
|
||||
|
||||
(Stub) Validates parameters from a UI before they are used in a processing step.
|
||||
"""
|
||||
function validate_ui_parameters(step::Symbol, ui_params::Dict)::Tuple{Bool, String}
|
||||
# In a real implementation, this would check types, ranges, etc.
|
||||
# For example, for :smooth, ensure 'sg_window' is an odd integer.
|
||||
println("Validating parameters for step: $step")
|
||||
return (true, "Parameters are valid.")
|
||||
end
|
||||
|
||||
"""
|
||||
run_processing_with_progress(session, step, params, progress_callback)
|
||||
|
||||
(Stub) A wrapper for running a processing step that includes a progress reporting callback.
|
||||
"""
|
||||
function run_processing_with_progress(session, step, params, progress_callback)
|
||||
progress_callback(0.0, "Starting $step...")
|
||||
|
||||
# This is a simplified example. Real implementation would need to
|
||||
# hook into the loops inside apply_processing_step.
|
||||
new_version = run_versioned_preprocessing(session, step, params)
|
||||
|
||||
progress_callback(1.0, "Finished $step.")
|
||||
return new_version
|
||||
end
|
||||
|
||||
"""
|
||||
safe_processing_application!(session::MSISession, step::Symbol, params::Dict)
|
||||
|
||||
(Stub) A safe wrapper to apply a processing step that includes error handling and rollback.
|
||||
"""
|
||||
function safe_processing_application!(session::MSISession, step::Symbol, params::Dict)
|
||||
num_history = length(session.history)
|
||||
try
|
||||
println("Safely applying step: $step")
|
||||
apply_processing_with_version!(session, step, params)
|
||||
catch e
|
||||
@error "Processing step '$step' failed!" exception=(e, catch_backtrace())
|
||||
# Roll back to the previous state
|
||||
while length(session.history) > num_history
|
||||
undo_last_step!(session)
|
||||
end
|
||||
println("Session has been rolled back to the previous state.")
|
||||
return session # Return the rolled-back session
|
||||
end
|
||||
return session # Return the updated session
|
||||
end
|
||||
|
||||
@ -40,10 +40,10 @@ Before running the tests, you must edit the `test/run_tests.jl` file to point to
|
||||
2. **Execute the Different Test Scripts**:
|
||||
Run the following command from the project's root directory. This will install the necessary dependencies and run the tests.
|
||||
```bash
|
||||
julia --project=. test/run_tests.jl
|
||||
julia --threads auto --project=. test/run_tests.jl
|
||||
```
|
||||
```bash
|
||||
julia --project=. test/run_preprocessing.jl
|
||||
julia --threads auto --project=. test/run_preprocessing.jl
|
||||
```
|
||||
|
||||
3. **Check the Results**:
|
||||
|
||||
@ -1,468 +1,371 @@
|
||||
# test/run_preprocessing.jl
|
||||
|
||||
# ===================================================================
|
||||
# Test Environment for the Preprocessing.jl Module
|
||||
# Preprocessing Test Suite for JuliaMSI
|
||||
# ===================================================================
|
||||
# This script tests the full preprocessing pipeline on single spectra
|
||||
# and total spectra from both .mzML and .imzML files.
|
||||
# It generates an overlay plot showing all preprocessing stages and
|
||||
# saves the resulting feature matrix to a CSV file.
|
||||
# This script provides a customizable workflow to test and visualize
|
||||
# the effects of different preprocessing steps on individual spectra
|
||||
# from .mzML or .imzML files.
|
||||
#
|
||||
# Instructions:
|
||||
# 1. Ensure the file paths in the "CONFIG" section are correct.
|
||||
# 1. Configure the file paths and parameters in the "CONFIG" section.
|
||||
# 2. Run the script from the project's root directory:
|
||||
# julia test/run_preprocessing.jl
|
||||
# 3. Check the `test/results/` folder for output plots and CSVs.
|
||||
# julia --threads auto --project=. test/run_preprocessing.jl
|
||||
# 3. Check the configured `RESULTS_DIR` for output plots and CSV files.
|
||||
# ===================================================================
|
||||
|
||||
using Printf
|
||||
using CairoMakie
|
||||
using DataFrames
|
||||
using CSV
|
||||
using Statistics
|
||||
using Interpolations
|
||||
import Pkg
|
||||
using DataFrames # For saving FeatureMatrix to CSV
|
||||
using CSV # For saving FeatureMatrix to CSV
|
||||
using Statistics # For mean()
|
||||
|
||||
# --- Load Modules ---
|
||||
# Activate the project environment to access dependencies
|
||||
# --- Load the MSI_src Module ---
|
||||
# Activate the project environment at the parent directory of this test script
|
||||
Pkg.activate(joinpath(@__DIR__, ".."))
|
||||
using MSI_src # This brings in Preprocessing.jl functions via export
|
||||
using MSI_src
|
||||
|
||||
|
||||
# ===================================================================
|
||||
# CONFIG: Test files and parameters
|
||||
# CONFIG: CUSTOMIZE YOUR PREPROCESSING WORKFLOW HERE
|
||||
# ===================================================================
|
||||
|
||||
# --- Test Files ---
|
||||
# An mzML file for testing spectrum-based processing
|
||||
# const TEST_MZML_FILE = "/home/pixel/Documents/Cinvestav_2025/Analisis/CE4_BF_R1/CE4_BF_R1.mzML"
|
||||
# const TEST_MZML_FILE = "/home/pixel/Documents/Cinvestav_2025/Analisis/set de datos MS/Leaf_profile_LD_LTP_MS.mzML"
|
||||
const TEST_MZML_FILE = "/home/pixel/Documents/Cinvestav_2025/Analisis/set de datos MS/Escopolamina_tuneo_fraq_20ev.mzML"
|
||||
#const TEST_MZML_FILE = "/home/pixel/Documents/Cinvestav_2025/Analisis/set de datos MS/Atropina_tuneo_fraq_20ev.mzML"
|
||||
# --- Input and Output ---
|
||||
const TEST_FILE = "/home/pixel/Documents/Cinvestav_2025/Analisis/salida/Stomach_DHB_uncompressed.imzML" # Can be .mzML or .imzML
|
||||
const RESULTS_DIR = "test/results/preprocessing"
|
||||
const NUM_SPECTRA_TO_PROCESS = nothing # Set to `nothing` to process all spectra
|
||||
|
||||
const MZML_SPECTRUM_ID = 1
|
||||
# --- Internal Standards for Calibration and QC ---
|
||||
# replace these with m/z values of known compounds present in your dataset.
|
||||
const INTERNAL_STANDARDS = Dict(
|
||||
"P13" => 432.6584,
|
||||
"P15" => 464.6059,
|
||||
"P17" => 526.5534,
|
||||
"P21" => 650.4485,
|
||||
"P25" => 774.3435,
|
||||
"P29" => 898.2385,
|
||||
"P31" => 950.1861,
|
||||
"P33" => 1022.1336,
|
||||
"P37" => 1146.0286,
|
||||
"P45" => 1593.8187,
|
||||
"Unknown 1" => 772.433,
|
||||
"Unknown 2" => 772.5253
|
||||
)
|
||||
|
||||
# An imzML file for testing
|
||||
# const TEST_IMZML_FILE = "/home/pixel/Documents/Cinvestav_2025/Analisis/CE4_BF_R1/CE4_BF_R1.imzML"
|
||||
# const IMZML_COORDS = (50, 50)
|
||||
const TEST_IMZML_FILE = "/home/pixel/Documents/Cinvestav_2025/Analisis/salida/Stomach_DHB_uncompressed.imzML"
|
||||
const IMZML_COORDS = (1997, 639)
|
||||
# --- Preprocessing Step Parameters ---
|
||||
|
||||
# --- Output Directory ---
|
||||
const RESULTS_DIR = "test/results"
|
||||
# Step 0: Quality Control (QC)
|
||||
const QC_PARAMS = (
|
||||
ppm_tolerance = 5.0, # PPM tolerance for matching internal standards
|
||||
)
|
||||
|
||||
# Step 1: Calibration
|
||||
const CALIBRATION_PARAMS = (
|
||||
enabled = true,
|
||||
ppm_tolerance = 5.0, # PPM tolerance for finding calibration peaks
|
||||
)
|
||||
|
||||
# Step 2: Smoothing
|
||||
# Note: Smoothing is less effective and often unnecessary for centroid data.
|
||||
const SMOOTHING_PARAMS = (
|
||||
enabled = false,
|
||||
window = 9,
|
||||
order = 2,
|
||||
)
|
||||
|
||||
# Step 3: Baseline Correction
|
||||
# Note: Baseline correction is less effective and often unnecessary for centroid data.
|
||||
const BASELINE_CORRECTION_PARAMS = (
|
||||
enabled = false,
|
||||
iterations = 100,
|
||||
)
|
||||
|
||||
# Step 4: Normalization
|
||||
const NORMALIZATION_PARAMS = (
|
||||
enabled = true,
|
||||
method = :tic, # :tic, :median, or :none
|
||||
)
|
||||
|
||||
# Step 5: Peak Detection
|
||||
const PEAK_DETECTION_PARAMS = (
|
||||
enabled = true,
|
||||
method = :centroid, # Use :centroid for centroided data, :profile for profile data
|
||||
# --- Parameters for :centroid method ---
|
||||
intensity_threshold = 0.0, # Filters out peaks below this absolute intensity
|
||||
# --- Parameters for :profile method ---
|
||||
half_window = 10,
|
||||
snr_threshold = 3.0,
|
||||
min_peak_prominence = 0.05,
|
||||
merge_peaks_tolerance = 0.002,
|
||||
)
|
||||
|
||||
# Step 6: Peak Alignment (Warping)
|
||||
# This is performed after collecting peaks from all spectra.
|
||||
const PEAK_ALIGNMENT_PARAMS = (
|
||||
enabled = true,
|
||||
tolerance = 0.002,
|
||||
tolerance_unit = :mz, # :mz or :ppm
|
||||
min_matched_peaks = 3, # Lowered for sparse centroid data
|
||||
)
|
||||
|
||||
# Step 7: Peak Binning
|
||||
const PEAK_BINNING_PARAMS = (
|
||||
enabled = true,
|
||||
tolerance = 0.1,
|
||||
tolerance_unit = :mz, # :mz or :ppm
|
||||
frequency_threshold = 0.1, # Min fraction of spectra a peak must be in
|
||||
)
|
||||
|
||||
# ===================================================================
|
||||
# HELPER FUNCTIONS FOR PLOTTING
|
||||
# HELPER FUNCTIONS
|
||||
# ===================================================================
|
||||
|
||||
"""
|
||||
plot_overlay_stages(collected_data, output_path, title)
|
||||
plot_spectrum_on_fig(fig_pos, mz, intensity, title)
|
||||
|
||||
Creates a single plot overlaying spectra from different preprocessing stages.
|
||||
Helper function to plot a spectrum on a specific position of a CairoMakie figure.
|
||||
"""
|
||||
function plot_overlay_stages(collected_data, output_path, title)
|
||||
fig = Figure(size = (1400, 800))
|
||||
ax = Axis(fig[1, 1], title=title, xlabel="m/z", ylabel="Intensity")
|
||||
|
||||
colors = Makie.wong_colors() # A good set of distinct colors
|
||||
|
||||
for (i, (stage, mz, intensity)) in enumerate(collected_data)
|
||||
color = colors[mod1(i, length(colors))] # Cycle through colors
|
||||
|
||||
# Plot the spectrum as a line
|
||||
lines!(ax, mz, intensity, color=color, label=string(stage))
|
||||
|
||||
# If it's the peaks stage, also mark the peak tops
|
||||
if stage == :peaks
|
||||
scatter!(ax, mz, intensity, color=color, marker=:circle, markersize=8, label="$(string(stage)) (tops)")
|
||||
end
|
||||
end
|
||||
axislegend(ax, position=:rt) # Right top position
|
||||
save(output_path, fig)
|
||||
println("SUCCESS: Overlay plot saved to $output_path")
|
||||
function plot_spectrum_on_fig(fig_pos, mz, intensity, title)
|
||||
ax = Axis(fig_pos, title=title, xlabel="m/z", ylabel="Intensity")
|
||||
lines!(ax, mz, intensity)
|
||||
end
|
||||
|
||||
|
||||
# ===================================================================
|
||||
# TEST DEFINITIONS
|
||||
# MAIN PROCESSING SCRIPT
|
||||
# ===================================================================
|
||||
|
||||
"""
|
||||
test_full_pipeline(msi_data, spectrum_id; output_dir, file_type_prefix)
|
||||
function run_preprocessing_suite()
|
||||
println("Starting Preprocessing Test Suite...")
|
||||
mkpath(RESULTS_DIR)
|
||||
|
||||
Tests the full preprocessing pipeline on a single spectrum and saves a plot
|
||||
for each intermediate step using the `on_stage` callback.
|
||||
`spectrum_id` can be an `Int` (for mzML) or a `Tuple{Int, Int}` (for imzML).
|
||||
"""
|
||||
function test_full_pipeline(msi_data, spectrum_id; output_dir, file_type_prefix, mz_tolerance=0.002)
|
||||
println("\n--- Testing Full Preprocessing Pipeline on Spectrum: $spectrum_id (File Type: $file_type_prefix) ---")
|
||||
# --- Load Data ---
|
||||
println("Loading data from: $TEST_FILE")
|
||||
if !isfile(TEST_FILE)
|
||||
println("ERROR: Test file not found. Please check the path in the CONFIG section.")
|
||||
return
|
||||
end
|
||||
msi_data = @time OpenMSIData(TEST_FILE)
|
||||
println("Data loaded successfully. Found $(length(msi_data.spectra_metadata)) spectra.")
|
||||
|
||||
# 1. Determine the spectrum index
|
||||
local spec_idx
|
||||
if spectrum_id isa Int
|
||||
spec_idx = spectrum_id
|
||||
else # Tuple for imzML
|
||||
spec_idx = msi_data.coordinate_map[spectrum_id...]
|
||||
# --- Determine which spectra to process ---
|
||||
total_spectra = length(msi_data.spectra_metadata)
|
||||
indices_to_process = if NUM_SPECTRA_TO_PROCESS === nothing
|
||||
1:total_spectra
|
||||
else
|
||||
unique(round.(Int, range(1, total_spectra, length=min(NUM_SPECTRA_TO_PROCESS, total_spectra))))
|
||||
end
|
||||
println("Will process $(length(indices_to_process)) spectra.")
|
||||
|
||||
# --- Data storage for results ---
|
||||
qc_results = DataFrame(spectrum_idx=Int[], metric=String[], value=Float64[], compound=String[])
|
||||
all_processed_peaks_mz = Vector{Vector{Float64}}()
|
||||
all_processed_peaks_int = Vector{Vector{Float64}}()
|
||||
spectrum_indices_with_peaks = Int[]
|
||||
|
||||
# --- Main Loop: Process each spectrum individually ---
|
||||
println("\n" * "="^20 * " Processing Individual Spectra " * "="^20)
|
||||
for (i, idx) in enumerate(indices_to_process)
|
||||
print("\rProcessing spectrum #$idx ($(i)/$(length(indices_to_process)))...")
|
||||
|
||||
process_spectrum(msi_data, idx) do mz, intensity
|
||||
if qc_is_empty(mz, intensity) || !qc_is_regular(mz)
|
||||
# @warn "Skipping empty or irregular spectrum #$idx"
|
||||
return
|
||||
end
|
||||
|
||||
original_mz, original_intensity = copy(mz), copy(intensity)
|
||||
processed_mz, processed_intensity = copy(mz), copy(intensity)
|
||||
|
||||
# --- Step 0: QC (PPM and Resolution) ---
|
||||
# This happens before any modification to the m/z axis
|
||||
let ref_masses = collect(values(INTERNAL_STANDARDS))
|
||||
matched_peaks = find_calibration_peaks(processed_mz, processed_intensity, ref_masses, ppm_tolerance=QC_PARAMS.ppm_tolerance)
|
||||
|
||||
for (compound, theoretical_mz) in INTERNAL_STANDARDS
|
||||
# Find the measured m/z that corresponds to this theoretical_mz
|
||||
measured_mz = 0.0
|
||||
for (theo, meas) in matched_peaks
|
||||
if theo == theoretical_mz
|
||||
measured_mz = meas
|
||||
break
|
||||
end
|
||||
end
|
||||
|
||||
if measured_mz > 0
|
||||
# PPM Error
|
||||
ppm_error = calculate_ppm_error(measured_mz, theoretical_mz)
|
||||
push!(qc_results, (idx, "ppm_error", ppm_error, compound))
|
||||
|
||||
# Resolution
|
||||
resolution = calculate_resolution_fwhm(measured_mz, processed_mz, processed_intensity)
|
||||
if !isnan(resolution)
|
||||
push!(qc_results, (idx, "resolution", resolution, compound))
|
||||
end
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
# --- Step 1: Calibration ---
|
||||
if CALIBRATION_PARAMS.enabled
|
||||
ref_masses = collect(values(INTERNAL_STANDARDS))
|
||||
matched_peaks = find_calibration_peaks(processed_mz, processed_intensity, ref_masses, ppm_tolerance=CALIBRATION_PARAMS.ppm_tolerance)
|
||||
if length(matched_peaks) >= 2
|
||||
measured = sort(collect(values(matched_peaks)))
|
||||
theoretical = sort(collect(keys(matched_peaks)))
|
||||
itp = linear_interpolation(measured, theoretical, extrapolation_bc=Line())
|
||||
processed_mz = itp(processed_mz)
|
||||
end
|
||||
end
|
||||
|
||||
# --- Step 2: Smoothing ---
|
||||
if SMOOTHING_PARAMS.enabled
|
||||
processed_intensity = smooth_spectrum(processed_intensity, window=SMOOTHING_PARAMS.window, order=SMOOTHING_PARAMS.order)
|
||||
end
|
||||
|
||||
# --- Step 3: Baseline Correction ---
|
||||
if BASELINE_CORRECTION_PARAMS.enabled
|
||||
baseline = snip_baseline(processed_intensity, iterations=BASELINE_CORRECTION_PARAMS.iterations)
|
||||
processed_intensity .-= baseline
|
||||
processed_intensity = max.(0, processed_intensity) # Ensure non-negativity
|
||||
end
|
||||
|
||||
# --- Step 4: Normalization ---
|
||||
if NORMALIZATION_PARAMS.enabled && NORMALIZATION_PARAMS.method != :none
|
||||
if NORMALIZATION_PARAMS.method == :tic
|
||||
processed_intensity = tic_normalize(processed_intensity)
|
||||
elseif NORMALIZATION_PARAMS.method == :median
|
||||
processed_intensity = median_normalize(processed_intensity)
|
||||
end
|
||||
end
|
||||
|
||||
# --- Step 5: Peak Detection ---
|
||||
local pk_mz, pk_int
|
||||
pk_mz, pk_int = Float64[], Float64[] # Initialize empty
|
||||
if PEAK_DETECTION_PARAMS.enabled
|
||||
if PEAK_DETECTION_PARAMS.method == :profile
|
||||
pk_mz, pk_int = detect_peaks_profile(processed_mz, processed_intensity,
|
||||
half_window=PEAK_DETECTION_PARAMS.half_window,
|
||||
snr_threshold=PEAK_DETECTION_PARAMS.snr_threshold,
|
||||
min_peak_prominence=PEAK_DETECTION_PARAMS.min_peak_prominence,
|
||||
merge_peaks_tolerance=PEAK_DETECTION_PARAMS.merge_peaks_tolerance)
|
||||
elseif PEAK_DETECTION_PARAMS.method == :wavelet
|
||||
pk_mz, pk_int = detect_peaks_wavelet(processed_mz, processed_intensity)
|
||||
else # :centroid
|
||||
pk_mz, pk_int = detect_peaks_centroid(processed_mz, processed_intensity)
|
||||
end
|
||||
|
||||
if !isempty(pk_mz)
|
||||
push!(all_processed_peaks_mz, pk_mz)
|
||||
push!(all_processed_peaks_int, pk_int)
|
||||
push!(spectrum_indices_with_peaks, idx)
|
||||
end
|
||||
end
|
||||
|
||||
# --- Visualization of a sample spectrum ---
|
||||
if i == 1 # Only plot the first processed spectrum
|
||||
println("\nGenerating example plots for spectrum #$idx...")
|
||||
fig = Figure(size=(1200, 800))
|
||||
|
||||
plot_spectrum_on_fig(fig[1,1], original_mz, original_intensity, "1. Original Spectrum")
|
||||
plot_spectrum_on_fig(fig[2,1], processed_mz, processed_intensity, "2. After All Steps (Before Peak Picking)")
|
||||
|
||||
# Plot detected peaks
|
||||
ax = Axis(fig[3,1], title="3. Detected Peaks")
|
||||
if !isempty(pk_mz)
|
||||
stem!(ax, pk_mz, pk_int)
|
||||
end
|
||||
|
||||
save(joinpath(RESULTS_DIR, "example_spectrum_processing.png"), fig)
|
||||
println("Saved example processing plots.")
|
||||
end
|
||||
end
|
||||
end
|
||||
println("\nIndividual spectrum processing complete.")
|
||||
|
||||
# --- Save QC Results ---
|
||||
if !isempty(qc_results)
|
||||
println("\n" * "="^20 * " Generating QC Report " * "="^20)
|
||||
CSV.write(joinpath(RESULTS_DIR, "qc_results.csv"), qc_results)
|
||||
println("QC results saved to qc_results.csv")
|
||||
|
||||
# Generate summary plots for QC
|
||||
fig = Figure(size=(1200, 600))
|
||||
|
||||
# PPM Error Histogram
|
||||
ppm_errors = filter(row -> row.metric == "ppm_error", qc_results).value
|
||||
if !isempty(ppm_errors)
|
||||
ax1 = Axis(fig[1,1], title="PPM Error Distribution", xlabel="PPM Error")
|
||||
hist!(ax1, ppm_errors, bins=30)
|
||||
end
|
||||
|
||||
# Resolution Histogram
|
||||
resolutions = filter(row -> row.metric == "resolution", qc_results).value
|
||||
if !isempty(resolutions)
|
||||
ax2 = Axis(fig[1,2], title="Resolution Distribution", xlabel="Resolution (FWHM)")
|
||||
hist!(ax2, resolutions, bins=30)
|
||||
end
|
||||
|
||||
save(joinpath(RESULTS_DIR, "qc_summary_plots.png"), fig)
|
||||
println("QC summary plots saved.")
|
||||
end
|
||||
|
||||
if spec_idx == 0
|
||||
println("SKIPPED: No spectrum found at coordinates $spectrum_id.")
|
||||
if isempty(all_processed_peaks_mz)
|
||||
@warn "No peaks were detected in any of the processed spectra. Skipping alignment and binning."
|
||||
return
|
||||
end
|
||||
|
||||
# 2. Define the pipeline steps in the desired order
|
||||
pipeline_steps = [
|
||||
:qc,
|
||||
:transform,
|
||||
:smooth,
|
||||
:baseline,
|
||||
:normalize,
|
||||
:peaks,
|
||||
:align, # Align requires multiple spectra, but we'll run it on a single one for now (will warn)
|
||||
:bin
|
||||
]
|
||||
# --- Step 6: Peak Alignment ---
|
||||
println("\n" * "="^20 * " Aligning Peaks " * "="^20)
|
||||
aligned_peaks_mz = copy(all_processed_peaks_mz)
|
||||
if PEAK_ALIGNMENT_PARAMS.enabled
|
||||
# Create a reference peak list (e.g., from the spectrum with the most peaks)
|
||||
ref_idx = argmax(length.(all_processed_peaks_mz))
|
||||
reference_peaks = all_processed_peaks_mz[ref_idx]
|
||||
println("Using spectrum $(spectrum_indices_with_peaks[ref_idx]) as alignment reference.")
|
||||
|
||||
# Define parameters for each step
|
||||
params = Dict(
|
||||
:transform_method => :sqrt,
|
||||
:sg_window => 15,
|
||||
:sg_order => 2,
|
||||
:snip_iterations => 100,
|
||||
:normalize_method => :tic,
|
||||
:peak_half_window => 10,
|
||||
:peak_snr => 3.0,
|
||||
:peak_intensity_threshold => 0.0, # For centroid peak detection
|
||||
:align_tolerance => mz_tolerance,
|
||||
:bin_tolerance => mz_tolerance,
|
||||
:bin_min_frequency => 0.0 # Keep all bins for a single spectrum
|
||||
)
|
||||
for i in 1:length(aligned_peaks_mz)
|
||||
if i == ref_idx continue end
|
||||
alignment_func = align_peaks_lowess(reference_peaks, aligned_peaks_mz[i],
|
||||
tolerance=PEAK_ALIGNMENT_PARAMS.tolerance,
|
||||
tolerance_unit=PEAK_ALIGNMENT_PARAMS.tolerance_unit,
|
||||
min_matched_peaks=PEAK_ALIGNMENT_PARAMS.min_matched_peaks)
|
||||
|
||||
# 3. Define the on_stage callback to collect data for overlay plot and save separate plots
|
||||
collected_stage_data = []
|
||||
stage_counter = Ref(0) # Initialize counter for sequential naming
|
||||
normalized_spectrum = nothing # Variable to hold the normalized spectrum
|
||||
aligned_peaks_mz[i] = alignment_func(aligned_peaks_mz[i])
|
||||
end
|
||||
println("Peak alignment complete.")
|
||||
end
|
||||
|
||||
function stage_callback(stage; idx, mz, intensity)
|
||||
stage_counter[] += 1 # Increment counter
|
||||
println(" -> Generating plot for stage: $stage")
|
||||
# --- Step 7: Peak Binning & Feature Matrix Generation ---
|
||||
println("\n" * "="^20 * " Binning Peaks " * "="^20)
|
||||
if PEAK_BINNING_PARAMS.enabled
|
||||
feature_matrix, mz_bins = bin_peaks(aligned_peaks_mz, all_processed_peaks_int,
|
||||
PEAK_BINNING_PARAMS.tolerance,
|
||||
tolerance_unit=PEAK_BINNING_PARAMS.tolerance_unit,
|
||||
frequency_threshold=PEAK_BINNING_PARAMS.frequency_threshold)
|
||||
|
||||
local fig # Make fig available in the whole function scope
|
||||
if !isempty(feature_matrix)
|
||||
df = DataFrame(feature_matrix, :auto)
|
||||
rename!(df, ["bin_$(i)" for i in 1:size(df, 2)])
|
||||
insertcols!(df, 1, :spectrum_idx => spectrum_indices_with_peaks)
|
||||
|
||||
if stage == :normalize
|
||||
normalized_spectrum = (mz, intensity)
|
||||
fig = plot_stage_spectrum(mz, intensity, title="Stage: $stage (Spectrum $spectrum_id)")
|
||||
elseif stage == :peaks && normalized_spectrum !== nothing
|
||||
# For the peaks stage, plot the normalized spectrum as a base layer
|
||||
fig = Figure(size = (1400, 500))
|
||||
ax = Axis(fig[1, 1], title="Stage: Peaks (Spectrum $spectrum_id)", xlabel="m/z", ylabel="Intensity")
|
||||
lines!(ax, normalized_spectrum[1], normalized_spectrum[2], color=:gray, label="Normalized Spectrum")
|
||||
scatter!(ax, mz, intensity, color=:red, marker=:circle, markersize=8, label="Detected Peaks")
|
||||
axislegend(ax)
|
||||
CSV.write(joinpath(RESULTS_DIR, "feature_matrix.csv"), df)
|
||||
println("Feature matrix saved to feature_matrix.csv")
|
||||
|
||||
# Save bin m/z ranges
|
||||
bin_df = DataFrame(bin_index=1:length(mz_bins), mz_start=[b[1] for b in mz_bins], mz_end=[b[2] for b in mz_bins])
|
||||
CSV.write(joinpath(RESULTS_DIR, "bin_definitions.csv"), bin_df)
|
||||
println("Bin definitions saved to bin_definitions.csv")
|
||||
else
|
||||
# Default plotting for all other stages
|
||||
fig = plot_stage_spectrum(mz, intensity, title="Stage: $stage (Spectrum $spectrum_id)")
|
||||
@warn "Feature matrix was empty after binning."
|
||||
end
|
||||
|
||||
# Save the figure
|
||||
stage_output_path = joinpath(output_dir, "$(file_type_prefix)_$(spectrum_id)_$(stage_counter[])_$(stage).png")
|
||||
save(stage_output_path, fig)
|
||||
|
||||
# Collect data for overlay plot
|
||||
push!(collected_stage_data, (stage, mz, intensity))
|
||||
end
|
||||
|
||||
# 4. Run the pipeline on the single spectrum
|
||||
println("Running pipeline with steps: $pipeline_steps")
|
||||
processed_result = run_preprocessing_pipeline(
|
||||
msi_data,
|
||||
[spec_idx], # The pipeline expects a vector of indices
|
||||
steps=pipeline_steps,
|
||||
params=params,
|
||||
on_stage=stage_callback
|
||||
)
|
||||
|
||||
# 5. Generate and save the overlay plot
|
||||
overlay_output_path = joinpath(output_dir, "$(file_type_prefix)_$(spectrum_id)_all_stages_overlay.png")
|
||||
plot_overlay_stages(collected_stage_data, overlay_output_path, "Preprocessing Stages Overlay (Spectrum $spectrum_id)")
|
||||
|
||||
# 6. Save feature matrix if generated
|
||||
if processed_result isa FeatureMatrix
|
||||
feature_matrix_output_path = joinpath(output_dir, "$(file_type_prefix)_$(spectrum_id)_feature_matrix.csv")
|
||||
# Convert mz_bins to a more readable format for CSV
|
||||
mz_labels = ["$(round(b[1], digits=4))_$(round(b[2], digits=4))" for b in processed_result.mz_bins]
|
||||
df = DataFrame(processed_result.matrix, Symbol.(mz_labels))
|
||||
CSV.write(feature_matrix_output_path, df)
|
||||
println("SUCCESS: Feature matrix saved to $feature_matrix_output_path")
|
||||
else
|
||||
@warn "Pipeline did not return a FeatureMatrix for Spectrum $spectrum_id."
|
||||
processed_result
|
||||
end
|
||||
|
||||
println("--- Pipeline test finished for Spectrum: $spectrum_id (File Type: $file_type_prefix) ---")
|
||||
println("Check the '$(output_dir)' directory for output plots and CSVs.")
|
||||
println("\nPreprocessing Test Suite finished successfully!")
|
||||
end
|
||||
|
||||
"""
|
||||
test_full_pipeline_on_total_spectrum(msi_data; output_dir, file_type_prefix)
|
||||
|
||||
Tests the full preprocessing pipeline on the *total spectrum* (sum of all spectra)
|
||||
and saves a plot for each intermediate step.
|
||||
"""
|
||||
function test_full_pipeline_on_total_spectrum(msi_data; output_dir, file_type_prefix, mz_tolerance=0.002)
|
||||
println("\n--- Testing Full Preprocessing Pipeline on TOTAL Spectrum (File Type: $file_type_prefix) ---")
|
||||
|
||||
# 1. Get the total spectrum
|
||||
total_mz, total_intensity = get_total_spectrum(msi_data)
|
||||
total_spectrum = (total_mz, total_intensity)
|
||||
|
||||
if qc_is_empty(total_mz, total_intensity)
|
||||
println("SKIPPED: Total spectrum is empty.")
|
||||
return
|
||||
end
|
||||
|
||||
# 2. Define the pipeline steps and parameters (same as for single spectrum)
|
||||
pipeline_steps = [
|
||||
:qc,
|
||||
:transform,
|
||||
:smooth,
|
||||
:baseline,
|
||||
:normalize,
|
||||
:peaks,
|
||||
:align, # Align requires multiple spectra, but we'll run it on a single one for now (will warn)
|
||||
:bin
|
||||
]
|
||||
|
||||
params = Dict(
|
||||
:transform_method => :sqrt,
|
||||
:sg_window => 15,
|
||||
:sg_order => 2,
|
||||
:snip_iterations => 100,
|
||||
:normalize_method => :tic,
|
||||
:peak_half_window => 10,
|
||||
:peak_snr => 3.0,
|
||||
:align_tolerance => mz_tolerance,
|
||||
:bin_tolerance => mz_tolerance,
|
||||
:bin_min_frequency => 0.0 # Keep all bins for a single spectrum
|
||||
)
|
||||
|
||||
# 3. Define the on_stage callback
|
||||
collected_stage_data = []
|
||||
stage_counter = Ref(0) # Initialize counter for sequential naming
|
||||
normalized_spectrum_total = nothing # Variable to hold the normalized spectrum
|
||||
|
||||
function stage_callback_total(stage; idx, mz, intensity)
|
||||
stage_counter[] += 1 # Increment counter
|
||||
println(" -> Generating plot for stage: $stage (Total Spectrum)")
|
||||
|
||||
local fig
|
||||
|
||||
if stage == :normalize
|
||||
normalized_spectrum_total = (mz, intensity)
|
||||
fig = plot_stage_spectrum(mz, intensity, title="Stage: $stage (Total Spectrum)")
|
||||
elseif stage == :peaks && normalized_spectrum_total !== nothing
|
||||
fig = Figure(size = (1400, 500))
|
||||
ax = Axis(fig[1, 1], title="Stage: Peaks (Total Spectrum)", xlabel="m/z", ylabel="Intensity")
|
||||
lines!(ax, normalized_spectrum_total[1], normalized_spectrum_total[2], color=:gray, label="Normalized Spectrum")
|
||||
scatter!(ax, mz, intensity, color=:red, marker=:circle, markersize=8, label="Detected Peaks")
|
||||
axislegend(ax)
|
||||
else
|
||||
fig = plot_stage_spectrum(mz, intensity, title="Stage: $stage (Total Spectrum)")
|
||||
end
|
||||
|
||||
# Save separate plot with sequential name
|
||||
stage_output_path = joinpath(output_dir, "$(file_type_prefix)_total_$(stage_counter[])_$(stage).png")
|
||||
save(stage_output_path, fig)
|
||||
|
||||
# Collect data for overlay plot
|
||||
push!(collected_stage_data, (stage, mz, intensity))
|
||||
end
|
||||
|
||||
# 4. Run the pipeline on the single total spectrum
|
||||
println("Running pipeline with steps: $pipeline_steps")
|
||||
processed_result = run_preprocessing_pipeline(
|
||||
[total_spectrum], # Pass the total spectrum as a vector of one spectrum
|
||||
steps=pipeline_steps,
|
||||
params=params,
|
||||
on_stage=stage_callback_total
|
||||
)
|
||||
|
||||
# 5. Generate and save the overlay plot
|
||||
overlay_output_path = joinpath(output_dir, "$(file_type_prefix)_total_all_stages_overlay.png")
|
||||
plot_overlay_stages(collected_stage_data, overlay_output_path, "Preprocessing Stages Overlay (Total Spectrum)")
|
||||
|
||||
# 6. Save feature matrix if generated
|
||||
if processed_result isa FeatureMatrix
|
||||
feature_matrix_output_path = joinpath(output_dir, "$(file_type_prefix)_total_feature_matrix.csv")
|
||||
# Convert mz_bins to a more readable format for CSV
|
||||
mz_labels = ["$(round(b[1], digits=4))_$(round(b[2], digits=4))" for b in processed_result.mz_bins]
|
||||
df = DataFrame(processed_result.matrix, Symbol.(mz_labels))
|
||||
CSV.write(feature_matrix_output_path, df)
|
||||
println("SUCCESS: Feature matrix saved to $feature_matrix_output_path")
|
||||
else
|
||||
@warn "Pipeline did not return a FeatureMatrix for Total Spectrum."
|
||||
processed_result
|
||||
end
|
||||
|
||||
println("--- Pipeline test finished for TOTAL Spectrum (File Type: $file_type_prefix) ---")
|
||||
println("Check the '$(output_dir)' directory for output plots and CSVs.")
|
||||
end
|
||||
|
||||
|
||||
# ===================================================================
|
||||
# TEST RUNNER
|
||||
# ===================================================================
|
||||
|
||||
function run_preprocessing_tests()
|
||||
println("="^80)
|
||||
println("STARTING PREPROCESSING TEST SUITE")
|
||||
println("="^80)
|
||||
|
||||
# --- Test Case 1: Run full pipeline on a single mzML spectrum ---
|
||||
println("\n" * "="^20 * " Test Case 1: Full Pipeline on .mzML Spectrum " * "="^20)
|
||||
println("FILE: ", TEST_MZML_FILE)
|
||||
if isfile(TEST_MZML_FILE)
|
||||
try
|
||||
msi_data_mzml = OpenMSIData(TEST_MZML_FILE)
|
||||
|
||||
# Dynamically determine tolerance
|
||||
println("\n--- Calculating optimal tolerance for .mzML data ---")
|
||||
report_mzml = analyze_mass_accuracy(msi_data_mzml, get_common_calibration_standards(:maldi_pos))
|
||||
mz_tolerance_mzml = 0.002 # Default
|
||||
if haskey(report_mzml, :optimal_ppm) && !isnan(report_mzml.optimal_ppm) && !isempty(report_mzml.matched_peaks)
|
||||
avg_mz = mean([p[1] for p in report_mzml.matched_peaks])
|
||||
mz_tolerance_mzml = avg_mz * report_mzml.optimal_ppm / 1e6
|
||||
println("Optimal PPM: $(round(report_mzml.optimal_ppm, digits=2)), Average m/z: $(round(avg_mz, digits=2))")
|
||||
println("Calculated m/z tolerance: $(round(mz_tolerance_mzml, digits=5))")
|
||||
else
|
||||
println("Could not determine optimal tolerance, using default: $mz_tolerance_mzml")
|
||||
end
|
||||
|
||||
# Create a dedicated subdirectory for the output plots
|
||||
mzml_output_dir = joinpath(RESULTS_DIR, "mzml_pipeline_stages")
|
||||
mkpath(mzml_output_dir)
|
||||
|
||||
test_full_pipeline(msi_data_mzml, MZML_SPECTRUM_ID, output_dir=mzml_output_dir, file_type_prefix="mzml", mz_tolerance=mz_tolerance_mzml)
|
||||
test_full_pipeline_on_total_spectrum(msi_data_mzml, output_dir=mzml_output_dir, file_type_prefix="mzml", mz_tolerance=mz_tolerance_mzml)
|
||||
catch e
|
||||
println("ERROR in .mzML pipeline test: $e")
|
||||
showerror(stdout, e, catch_backtrace())
|
||||
end
|
||||
else
|
||||
println("SKIPPED: File not found: $TEST_MZML_FILE")
|
||||
end
|
||||
|
||||
# --- Test Case 2: Run full pipeline on a single imzML spectrum ---
|
||||
println("\n" * "="^20 * " Test Case 2: Full Pipeline on .imzML Spectrum " * "="^20)
|
||||
println("FILE: ", TEST_IMZML_FILE)
|
||||
if isfile(TEST_IMZML_FILE)
|
||||
try
|
||||
msi_data_imzml = OpenMSIData(TEST_IMZML_FILE)
|
||||
|
||||
# Dynamically determine tolerance
|
||||
println("\n--- Calculating optimal tolerance for .imzML data ---")
|
||||
report_imzml = analyze_mass_accuracy(msi_data_imzml, get_common_calibration_standards(:maldi_pos))
|
||||
mz_tolerance_imzml = 0.002 # Default
|
||||
if haskey(report_imzml, :optimal_ppm) && !isnan(report_imzml.optimal_ppm) && !isempty(report_imzml.matched_peaks)
|
||||
avg_mz = mean([p[1] for p in report_imzml.matched_peaks])
|
||||
mz_tolerance_imzml = avg_mz * report_imzml.optimal_ppm / 1e6
|
||||
println("Optimal PPM: $(round(report_imzml.optimal_ppm, digits=2)), Average m/z: $(round(avg_mz, digits=2))")
|
||||
println("Calculated m/z tolerance: $(round(mz_tolerance_imzml, digits=5))")
|
||||
else
|
||||
println("Could not determine optimal tolerance, using default: $mz_tolerance_imzml")
|
||||
end
|
||||
|
||||
# Create a dedicated subdirectory for the output plots
|
||||
imzml_output_dir = joinpath(RESULTS_DIR, "imzml_pipeline_stages")
|
||||
mkpath(imzml_output_dir)
|
||||
|
||||
test_full_pipeline(msi_data_imzml, IMZML_COORDS, output_dir=imzml_output_dir, file_type_prefix="imzml", mz_tolerance=mz_tolerance_imzml)
|
||||
test_full_pipeline_on_total_spectrum(msi_data_imzml, output_dir=imzml_output_dir, file_type_prefix="imzml", mz_tolerance=mz_tolerance_imzml)
|
||||
# generate_qc_report(msi_data_imzml, TEST_IMZML_FILE, output_dir=imzml_output_dir)
|
||||
custom_reference_peaks = Dict(
|
||||
31.974 => "Red Phosphorus",
|
||||
432.6584 => "P13",
|
||||
464.6059 => "P15",
|
||||
526.5534 => "P17",
|
||||
650.4485 => "P21",
|
||||
774.3435 => "P25",
|
||||
898.2385 => "P29",
|
||||
950.1861 => "P31",
|
||||
1022.1336 => "P33",
|
||||
1146.0286 => "P37",
|
||||
1593.8187 => "P45",
|
||||
772.433 => "Unknown 1",
|
||||
772.5253 => "Unknown 2"
|
||||
)
|
||||
n_samples = length(msi_data_imzml.spectra_metadata)
|
||||
generate_qc_report(msi_data_imzml, TEST_IMZML_FILE, reference_peaks=custom_reference_peaks, output_dir=imzml_output_dir, sample_spectra=n_samples)
|
||||
catch e
|
||||
println("ERROR in .imzML pipeline test: $e")
|
||||
showerror(stdout, e, catch_backtrace())
|
||||
end
|
||||
else
|
||||
println("SKIPPED: File not found: $TEST_IMZML_FILE")
|
||||
end
|
||||
|
||||
# --- Test Case 3: Generate QC Report for .imzML data ---
|
||||
println("\n" * "="^20 * " Test Case 3: QC Report Generation for .imzML " * "="^20)
|
||||
println("FILE: ", TEST_IMZML_FILE)
|
||||
if isfile(TEST_IMZML_FILE)
|
||||
try
|
||||
msi_data_imzml = OpenMSIData(TEST_IMZML_FILE)
|
||||
|
||||
# Create a dedicated subdirectory for the QC report
|
||||
qc_output_dir = joinpath(RESULTS_DIR, "qc_report")
|
||||
mkpath(qc_output_dir)
|
||||
|
||||
println("\n--- Generating comprehensive QC report ---")
|
||||
custom_reference_peaks = Dict(
|
||||
31.974 => "Red Phosphorus",
|
||||
432.6584 => "P13",
|
||||
464.6059 => "P15",
|
||||
526.5534 => "P17",
|
||||
650.4485 => "P21",
|
||||
774.3435 => "P25",
|
||||
898.2385 => "P29",
|
||||
950.1861 => "P31",
|
||||
1022.1336 => "P33",
|
||||
1146.0286 => "P37",
|
||||
1593.8187 => "P45",
|
||||
772.433 => "Unknown 1",
|
||||
772.5253 => "Unknown 2"
|
||||
)
|
||||
# You can control the number of spectra sampled for the QC report.
|
||||
# For the most accurate results, you can sample all spectra, but it will take longer.
|
||||
# To sample all, use: n_samples = length(msi_data_imzml.spectra_metadata)
|
||||
n_samples = length(msi_data_imzml.spectra_metadata)
|
||||
|
||||
#generate_qc_report(msi_data_imzml, TEST_IMZML_FILE, output_dir=qc_output_dir)
|
||||
generate_qc_report(msi_data_imzml, TEST_IMZML_FILE, reference_peaks=custom_reference_peaks, output_dir=qc_output_dir, sample_spectra=n_samples)
|
||||
|
||||
println("\n--- Analyzing specific reference peaks ---")
|
||||
#=
|
||||
reference_peaks = Dict(
|
||||
104.10754 => "Imidazole",
|
||||
175.11995 => "GPC fragment",
|
||||
226.15687 => "Phosphocholine"
|
||||
)
|
||||
=#
|
||||
report = analyze_mass_accuracy(msi_data_imzml, custom_reference_peaks)
|
||||
if haskey(report, :optimal_ppm)
|
||||
println("Optimal PPM tolerance with specific peaks: $(round(report.optimal_ppm, digits=2)) ppm")
|
||||
else
|
||||
println("Could not determine optimal PPM with specific peaks.")
|
||||
end
|
||||
|
||||
catch e
|
||||
println("ERROR in QC report generation test: $e")
|
||||
showerror(stdout, e, catch_backtrace())
|
||||
end
|
||||
else
|
||||
println("SKIPPED: File not found: $TEST_IMZML_FILE")
|
||||
end
|
||||
|
||||
println("\nPreprocessing tests finished.")
|
||||
end
|
||||
|
||||
# --- Execute ---
|
||||
# Ensure the results directory exists
|
||||
mkpath(RESULTS_DIR)
|
||||
@time run_preprocessing_tests()
|
||||
run_preprocessing_suite()
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user