From f8c7a1662013ad298d0f73f4eb876f4ede02deee Mon Sep 17 00:00:00 2001 From: Markus Petters Date: Thu, 12 Nov 2020 20:21:15 -0500 Subject: [PATCH] update documentation --- docs/documentation/Manifest.toml | 97 +- docs/documentation/make.jl | 39 +- docs/documentation/src/assets/logo.svg | 5486 +++++++++++++++++ docs/documentation/src/lib/inversion.md | 7 +- docs/documentation/src/man/forward.md | 9 +- docs/documentation/src/man/inverse.md | 11 +- .../documentation/src/man/sizedistribution.md | 4 +- docs/documentation/src/man/tandem.md | 1 - docs/documentation/src/notebooks.md | 6 +- docs/documentation/versions.js | 1 + src/regularization.jl | 8 +- 11 files changed, 5587 insertions(+), 82 deletions(-) create mode 100644 docs/documentation/src/assets/logo.svg delete mode 100644 docs/documentation/src/man/tandem.md diff --git a/docs/documentation/Manifest.toml b/docs/documentation/Manifest.toml index a57be1b..95fe9b0 100644 --- a/docs/documentation/Manifest.toml +++ b/docs/documentation/Manifest.toml @@ -6,11 +6,17 @@ git-tree-sha1 = "051c95d6836228d120f5f4b984dd5aba1624f716" uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" version = "0.5.0" +[[Adapt]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "42c42f2221906892ceb765dbcb1a51deeffd86d7" +uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" +version = "2.3.0" + [[ArrayInterface]] deps = ["LinearAlgebra", "Requires", "SparseArrays"] -git-tree-sha1 = "920136b6b8ae5bd28a3c45d68e55421dec156d7f" +git-tree-sha1 = "bd09109dffaa3926a20178cb8432edd729be0db0" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "2.13.6" +version = "2.13.7" [[Artifacts]] deps = ["Pkg"] @@ -77,9 +83,9 @@ version = "0.3.0" [[Compat]] deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"] -git-tree-sha1 = "48608f94f3e1a755f65e7ef34684675bb3653030" +git-tree-sha1 = "a706ff10f1cd8dab94f59fd09c0e657db8e77ff0" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "3.21.0" +version = "3.23.0" [[CompilerSupportLibraries_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -106,9 +112,9 @@ uuid = "7ad07ef1-bdf2-5661-9d2b-286fd4296dac" version = "0.2.0" [[DataAPI]] -git-tree-sha1 = "176e23402d80e7743fc26c19c681bfb11246af32" +git-tree-sha1 = "ad84f52c0b8f05aa20839484dbaf01690b41ff84" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" -version = "1.3.0" +version = "1.4.0" [[DataFrames]] deps = ["CategoricalArrays", "Compat", "DataAPI", "Future", "InvertedIndices", "IteratorInterfaceExtensions", "Missings", "PooledArrays", "Printf", "REPL", "Reexport", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] @@ -118,9 +124,9 @@ version = "0.21.8" [[DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "db07bb22795762895b60e44d62b34b16c982a687" +git-tree-sha1 = "fb0aa371da91c1ff9dc7fbed6122d3e411420b9c" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.7" +version = "0.18.8" [[DataValueInterfaces]] git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" @@ -149,9 +155,9 @@ version = "1.0.1" [[Distances]] deps = ["LinearAlgebra", "Statistics"] -git-tree-sha1 = "a5b88815e6984e9f3256b6ca0dc63109b16a506f" +git-tree-sha1 = "e8b13ba5f166e11df2de6fc283e5db7864245df0" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.9.2" +version = "0.10.0" [[Distributed]] deps = ["Random", "Serialization", "Sockets"] @@ -170,10 +176,10 @@ uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" version = "0.8.3" [[Documenter]] -deps = ["Base64", "Dates", "DocStringExtensions", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"] -git-tree-sha1 = "fb1ff838470573adc15c71ba79f8d31328f035da" +deps = ["Base64", "Dates", "DocStringExtensions", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"] +git-tree-sha1 = "71e35e069daa9969b8af06cef595a1add76e0a11" uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4" -version = "0.25.2" +version = "0.25.3" [[Expat_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -201,9 +207,9 @@ version = "0.9.7" [[FiniteDiff]] deps = ["ArrayInterface", "LinearAlgebra", "Requires", "SparseArrays", "StaticArrays"] -git-tree-sha1 = "a78ee56e4636c20c2db9ccde8afe57065f6ab387" +git-tree-sha1 = "04e18906acf9c7f5b934a7ec3adc82280fb1953b" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.7.0" +version = "2.7.1" [[FixedPointNumbers]] deps = ["Statistics"] @@ -298,6 +304,12 @@ git-tree-sha1 = "0ec2e6e6a049eb8520c19cd8976085afcf2943fb" uuid = "a51ab1cf-af8e-5615-a023-bc2c838bba6b" version = "67.1.0+2" +[[IOCapture]] +deps = ["Logging"] +git-tree-sha1 = "377252859f740c217b936cebcd918a44f9b53b59" +uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" +version = "0.1.1" + [[IndirectArrays]] git-tree-sha1 = "c2a145a145dc03a7620af1444e0264ef907bd44f" uuid = "9b13fd28-a010-5f03-acff-a1bbcff69959" @@ -315,9 +327,9 @@ uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" [[Interpolations]] deps = ["AxisAlgorithms", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"] -git-tree-sha1 = "2b7d4e9be8b74f03115e64cf36ed2f48ae83d946" +git-tree-sha1 = "d2ff0813f0f110918db2537201686575fcf8d345" uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59" -version = "0.12.10" +version = "0.13.0" [[InvertedIndices]] deps = ["Test"] @@ -336,9 +348,9 @@ uuid = "82899510-4779-5014-852e-03e436cf321d" version = "1.0.0" [[JLLWrappers]] -git-tree-sha1 = "7cec881362e5b4e367ff0279dd99a06526d51a55" +git-tree-sha1 = "c70593677bbf2c3ccab4f7500d0f4dacfff7b75c" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.1.2" +version = "1.1.3" [[JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -354,9 +366,9 @@ version = "0.8.4" [[KernelDensity]] deps = ["Distributions", "DocStringExtensions", "FFTW", "Interpolations", "StatsBase"] -git-tree-sha1 = "2fdea3992af1bd7a90535d2937555d7b69d5e5ee" +git-tree-sha1 = "09aeec87bdc9c1fa70d0b508dfa94a21acd280d9" uuid = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b" -version = "0.6.1" +version = "0.6.2" [[LZO_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -412,10 +424,10 @@ deps = ["Libdl"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[Loess]] -deps = ["Distances", "Random", "Statistics", "Test"] -git-tree-sha1 = "0ee46caf683a422b595be4dfaed6cda28f541e25" +deps = ["Distances", "Statistics"] +git-tree-sha1 = "571701e0ccda39416b98c63813df551ec1745849" uuid = "4345ca2d-374a-55d4-8d30-97f9976e7612" -version = "0.5.0" +version = "0.5.2" [[Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" @@ -480,9 +492,10 @@ uuid = "6c575b1c-77cb-5640-a5dc-a54116c90507" version = "0.3.1" [[OffsetArrays]] -git-tree-sha1 = "a416e2f267e2c8729f25bcaf1ce19d2893faf393" +deps = ["Adapt"] +git-tree-sha1 = "9db93b990af57b3a56dca38476832f60d58f777b" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.3.1" +version = "1.4.0" [[OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -497,9 +510,9 @@ uuid = "87e2bd06-a317-5318-96d9-3ecbac512eee" version = "2.0.1" [[OrderedCollections]] -git-tree-sha1 = "16c08bf5dba06609fe45e30860092d6fa41fde7b" +git-tree-sha1 = "cf59cfed2e2c12e8a2ff0a4f1e9b2cd8650da6db" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -version = "1.3.1" +version = "1.3.2" [[PCRE_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -521,9 +534,9 @@ version = "1.42.4+10" [[Parsers]] deps = ["Dates"] -git-tree-sha1 = "6fa4202675c05ba0f8268a6ddf07606350eda3ce" +git-tree-sha1 = "b417be52e8be24e916e34b3d70ec2da7bdf56a68" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "1.0.11" +version = "1.0.12" [[Pixman_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -635,9 +648,9 @@ version = "0.10.3" [[StaticArrays]] deps = ["LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "016d1e1a00fabc556473b07161da3d39726ded35" +git-tree-sha1 = "da4cf579416c81994afd6322365d00916c79b8ae" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "0.12.4" +version = "0.12.5" [[Statistics]] deps = ["LinearAlgebra", "SparseArrays"] @@ -673,9 +686,9 @@ version = "1.0.0" [[Tables]] deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "TableTraits", "Test"] -git-tree-sha1 = "24a584cf65e2cfabdadc21694fb69d2e74c82b44" +git-tree-sha1 = "5131a624173d532299d1c7eb05341c18112b21b8" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.1.0" +version = "1.2.1" [[Test]] deps = ["Distributed", "InteractiveUtils", "Logging", "Random"] @@ -690,9 +703,9 @@ uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" [[WoodburyMatrices]] deps = ["LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "28ffe06d28b1ba8fdb2f36ec7bb079fac81bac0d" +git-tree-sha1 = "59e2ad8fd1591ea019a5259bd012d7aee15f995c" uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" -version = "0.5.2" +version = "0.5.3" [[XML2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] @@ -701,10 +714,10 @@ uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" version = "2.9.10+3" [[XSLT_jll]] -deps = ["Libdl", "Libgcrypt_jll", "Pkg", "XML2_jll"] -git-tree-sha1 = "8bb981a5c4a7efc799250c46ef757cbfd6c5ba9b" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Pkg", "XML2_jll"] +git-tree-sha1 = "2b3eac39df218762d2d005702d601cd44c997497" uuid = "aed1982a-8fda-507f-9586-7b0439959a61" -version = "1.1.33+3" +version = "1.1.33+4" [[Xorg_libX11_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] @@ -761,7 +774,7 @@ uuid = "83775a58-1f1d-513f-b197-d71354ab007a" version = "1.2.11+18" [[libpng_jll]] -deps = ["Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "0a93f3eae5b80f08dc789e549657c199f1da6417" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] +git-tree-sha1 = "6abbc424248097d69c0c87ba50fcb0753f93e0ee" uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" -version = "1.6.37+5" +version = "1.6.37+6" diff --git a/docs/documentation/make.jl b/docs/documentation/make.jl index abae87a..3fac63b 100644 --- a/docs/documentation/make.jl +++ b/docs/documentation/make.jl @@ -1,4 +1,3 @@ -push!(LOAD_PATH, "../src/") using Documenter, DifferentialMobilityAnalyzers, LinearAlgebra makedocs( @@ -11,24 +10,24 @@ makedocs( "Tutorial" => "tutorial.md", "Notebooks" => "notebooks.md" ], - "Manual" => Any[ - "Overview" => "man/overview.md", - "Size Distributions" => "man/sizedistribution.md", - "Initializing DMAs" => "man/dmas.md", - "Convolution Matrices" => "man/matrix.md", - "Forward Models" => "man/forward.md", - "Inverse Models" => "man/inverse.md", - "Performance Benchmarks" => "man/benchmarks.md", - ], - "Library" => Any[ - "Physics" => "lib/physics.md", - "Data Types" => "lib/types.md", - "Operators" => "lib/operators.md", - "Helper Functions" => "lib/helpers.md", - "Inversion Routines" => "lib/inversion.md", - "Benchmarks" => "lib/benchmarks.md" - ], - "References" => "references.md" + "Manual" => Any[ + "Overview" => "man/overview.md", + "Size Distributions" => "man/sizedistribution.md", + "Initializing DMAs" => "man/dmas.md", + "Convolution Matrices" => "man/matrix.md", + "Forward Models" => "man/forward.md", + "Inverse Models" => "man/inverse.md", + "Performance Benchmarks" => "man/benchmarks.md", + ], + "Library" => Any[ + "Physics" => "lib/physics.md", + "Data Types" => "lib/types.md", + "Operators" => "lib/operators.md", + "Helper Functions" => "lib/helpers.md", + "Inversion Routines" => "lib/inversion.md", + "Benchmarks" => "lib/benchmarks.md" + ], + + "References" => "references.md" ] ) - diff --git a/docs/documentation/src/assets/logo.svg b/docs/documentation/src/assets/logo.svg new file mode 100644 index 0000000..9b7af68 --- /dev/null +++ b/docs/documentation/src/assets/logo.svg @@ -0,0 +1,5486 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/docs/documentation/src/lib/inversion.md b/docs/documentation/src/lib/inversion.md index a4e8f1a..198a788 100644 --- a/docs/documentation/src/lib/inversion.md +++ b/docs/documentation/src/lib/inversion.md @@ -24,6 +24,11 @@ Ninv rinv ``` +### rinv2 +```@docs +rinv2 +``` + ### L1 ```@docs L1 @@ -37,4 +42,4 @@ L2 ### L1L2 ```@docs L1L2 -``` \ No newline at end of file +``` diff --git a/docs/documentation/src/man/forward.md b/docs/documentation/src/man/forward.md index 26c051c..a05c7dd 100644 --- a/docs/documentation/src/man/forward.md +++ b/docs/documentation/src/man/forward.md @@ -50,8 +50,8 @@ p1 = plot( # hide y = 𝕟ᶜⁿ.S, # hide Geom.step, # hide color = ["𝕟ᶜⁿ" for i in 𝕟ᶜⁿ.Dp], # hide - Guide.xlabel("Particle diameter (nm)"), # hide - Guide.ylabel("dN/dlnD (cm-3)"), # hide + Guide.xlabel("Particle diameter (nm)", orientation = :horizontal), # hide + Guide.ylabel("dN/dlnD (cm-3)", orientation = :vertical), # hide Guide.xticks( # hide ticks = log10.([10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600]), # hide ), # hide @@ -268,7 +268,6 @@ p1 = plot(#hide Guide.ylabel("Number concentration (cm-3)", orientation = :vertical),#hide Guide.xticks(ticks = (collect(100:10:220))),#hide Scale.x_continuous(labels = x -> x in xlabels ? @sprintf("%2i", (x)) : ""),#hide - Scale.color_discrete_manual("black"),#hide Coord.cartesian(xmin = 100, xmax = 220),#hide Theme(plot_padding = [2mm, 2mm, 2mm, 2mm]),#hide )#hide @@ -330,7 +329,6 @@ p1 = plot(#hide Guide.ylabel("Number concentration (cm-3)", orientation = :vertical),#hide Guide.xticks(ticks = (collect(0.8:0.1:3))),#hide Scale.x_continuous(labels = x -> x in xlabels ? @sprintf("%.1f", (x)) : ""),#hide - Scale.color_discrete_manual("black"),#hide Coord.cartesian(xmin = 0.8, xmax = 3),#hide Theme(plot_padding = [2mm, 2mm, 2mm, 2mm]),#hide )#hide @@ -404,14 +402,11 @@ p1 = plot(#hide Guide.ylabel("Number concentration (cm-3)", orientation = :vertical),#hide Guide.xticks(ticks = (collect(0.8:0.1:3))),#hide Scale.x_continuous(labels = x -> x in xlabels ? @sprintf("%.1f", (x)) : ""),#hide - Scale.color_discrete_manual("black"),#hide Coord.cartesian(xmin = 0.8, xmax = 3),#hide Theme(plot_padding = [2mm, 2mm, 2mm, 2mm]),#hide )#hide ``` - - ### Volatilty Tandem DMA See the [Manuscript](https://www.tandfonline.com/doi/full/10.1080/02786826.2018.1530724) and notebook S9 in the [Notebooks](@ref) section for examples involving the volatility tandem DMA. diff --git a/docs/documentation/src/man/inverse.md b/docs/documentation/src/man/inverse.md index b6384cf..431fc21 100644 --- a/docs/documentation/src/man/inverse.md +++ b/docs/documentation/src/man/inverse.md @@ -24,7 +24,7 @@ The regularization parameter ``\lambda`` "interpolates" between the noisy least- See session 3 of the [Tutorial](@ref) for an interactive explanation on how Tikhonov regularization works. ### Example -The L-curve search method is implemented in the [rinv](@ref) function. +The L-curve search method is implemented in the [rinv](@ref) function. Also check out the new [rinv2](@ref) function, which has much faster performance and is based on generalized cross validation. It also allows to specify higher order inversions. The default implementation gives near identical results to rinv. ```julia 𝕟ⁱⁿᵛ = rinv(𝕣.N, δ, λ₁=0.1, λ₂=1.0); @@ -44,8 +44,11 @@ r₁, r₂, l = 9.37e-3,1.961e-2,0.44369 𝕣 = (df,:Dp,:Rcn,δ) |> interpolateDataFrameOntoδ 𝕟ⁱⁿᵛ = rinv(𝕣.N, δ, λ₁=0.1, λ₂=1.0) - -df = DataFrame(Dp = 𝕟ⁱⁿᵛ.Dp, S = 𝕟ⁱⁿᵛ.S, Dist = ["𝕟ⁱⁿᵛ" for i = 1:length(𝕟ⁱⁿᵛ.Dp)]) #hide +𝕟ⁱⁿᵛ² = rinv2(𝕣.N, δ, λ₁=0.1, λ₂=1.0) + +df1 = DataFrame(Dp = 𝕟ⁱⁿᵛ.Dp, S = 𝕟ⁱⁿᵛ.S, Dist = ["𝕟ⁱⁿᵛ" for i = 1:length(𝕟ⁱⁿᵛ.Dp)]) #hide +df2 = DataFrame(Dp = 𝕟ⁱⁿᵛ².Dp, S = 𝕟ⁱⁿᵛ².S, Dist = ["𝕟ⁱⁿᵛ²" for i = 1:length(𝕟ⁱⁿᵛ².Dp)]) #hide +df = [df1;df2] #hide dfr = DataFrame(Dp = 𝕣.Dp, S = 𝕣.N, Dist = ["𝕣" for i = 1:length(𝕣.Dp)])#hide #hide xlabels = log10.([10, 100, 500])#hide @@ -212,4 +215,4 @@ p2 = plot(#hide )#hide set_default_plot_size(20cm, 8cm)#hide p = (hstack(p2, p1))#hide -``` \ No newline at end of file +``` diff --git a/docs/documentation/src/man/sizedistribution.md b/docs/documentation/src/man/sizedistribution.md index d16d3bf..fce2411 100644 --- a/docs/documentation/src/man/sizedistribution.md +++ b/docs/documentation/src/man/sizedistribution.md @@ -1,7 +1,7 @@ # Size Distributions ## Notation -Since this package is working a lot with size distributions, it is useful to highlight them. By convention we will use blackboard bold characters to denote size distributions +By convention blackboard bold characters denote size distributions !!! info **Blackboard bold font**: 𝕒, 𝕓, 𝕔, 𝕕, 𝕖, 𝕗, 𝕘, ... @@ -70,4 +70,4 @@ end # hide getplots1(𝕟₁, 𝕟₂, 𝕩) # hide ``` -The package implements a list of [Operators](@ref) for size distribution manipulation. Check out the [Tutorial](@ref) Session 1 and/or Notebook S3 in the [Notebooks](@ref) section for visualizations. \ No newline at end of file +The package implements a list of [Operators](@ref) for size distribution manipulation. Check out the [Tutorial](@ref) Session 1 and/or Notebook S3 in the [Notebooks](@ref) section for visualizations. diff --git a/docs/documentation/src/man/tandem.md b/docs/documentation/src/man/tandem.md deleted file mode 100644 index 57ae03c..0000000 --- a/docs/documentation/src/man/tandem.md +++ /dev/null @@ -1 +0,0 @@ -# Tandem DMA Setups \ No newline at end of file diff --git a/docs/documentation/src/notebooks.md b/docs/documentation/src/notebooks.md index 9f645b5..5352a79 100644 --- a/docs/documentation/src/notebooks.md +++ b/docs/documentation/src/notebooks.md @@ -1,5 +1,9 @@ # Notebooks +!!! warning + The notebooks were the original documentation of the project. Most of the material of the notebooks has been incorporated into the Manual section and is reproduced in the Tutorial. The notebooks are linked here for backward compatibility and to cover some content that is not yet included in the Manual section (e.g. the dual tandem DMA) or the FORTRAN integration. + + The project is documented in a journal manuscript. The original submission included 12 Supplementary Jupyter Notebooks. The links open the notebooks in viewer mode via NBViewer. The notebooks have been edited for compatibility and readability. @@ -62,4 +66,4 @@ This notebook presents an overview over coagulation theory. It is shown how to p This notebook demonstrates how to construct a convolution matrix using a DMA transfer function defined in a FORTRAN routine. The notebook explains how to compile the routine to a shared library and setup ```ccall``` to pass variables to and from the FORTRAN routine. -[Link to Virtual Machine](https://doi.org/10.5281/zenodo.2652893) \ No newline at end of file +[Link to Virtual Machine](https://doi.org/10.5281/zenodo.2652893) diff --git a/docs/documentation/versions.js b/docs/documentation/versions.js index 304a49d..ef6af60 100644 --- a/docs/documentation/versions.js +++ b/docs/documentation/versions.js @@ -1,5 +1,6 @@ var DOC_VERSIONS = [ "stable", + "v2.4", "v2.3", "latest", ]; diff --git a/src/regularization.jl b/src/regularization.jl index ad185e4..1f6cefc 100644 --- a/src/regularization.jl +++ b/src/regularization.jl @@ -261,7 +261,7 @@ stability and spreed. The default setting is 0th order + initial guess, which is to what is assumed in the rinv1 algorithm. Note that 0th order without initial guess produces poor results. -!! tip +!!! tip For fastest results use the sister function ```julia rinv2(R::AbstractVector; λ₁ = 1e-2, λ₂ = 1e1, order = 0, initial = true, n = 1) @@ -289,10 +289,10 @@ r₁, r₂, l = 9.37e-3,1.961e-2,0.44369 𝕣 = (df, :Dp, :Rcn, δ) |> interpolateDataFrameOntoδ # Compute the inverse with explicit DMA passing (slower) -𝕟ⁱⁿᵛ = rinv(𝕣.N, δ, λ₁ = 0.1, λ₂ = 1.0) +𝕟ⁱⁿᵛ = rinv2(𝕣.N, δ, λ₁ = 0.1, λ₂ = 1.0) # Compute the inverse without explicit DMA passing (much faster) -𝕟ⁱⁿᵛ = rinv(𝕣.N, λ₁ = 0.1, λ₂ = 1.0) +𝕟ⁱⁿᵛ = rinv2(𝕣.N, λ₁ = 0.1, λ₂ = 1.0) ``` """ function rinv2( @@ -358,4 +358,4 @@ function initializeDefaultMatrices() global Ψ₀ = setupRegularizationProblem(𝐀[:,:], 0) global Ψ₁ = setupRegularizationProblem(𝐀[:,:], 1) global Ψ₂ = setupRegularizationProblem(𝐀[:,:], 2) -end \ No newline at end of file +end