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Manifest.toml
View file @ fdcc7ea5
# This file is machine-generated - editing it directly is not advised # This file is machine-generated - editing it directly is not advised
julia_version = "1.10.4" julia_version = "1.10.5"
manifest_format = "2.0" manifest_format = "2.0"
project_hash = "170a37ab5d68a18e29bd757512b09ed22a40cf6c" project_hash = "170a37ab5d68a18e29bd757512b09ed22a40cf6c"
...@@ -16,39 +16,45 @@ uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" ...@@ -16,39 +16,45 @@ uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
[[deps.CSV]] [[deps.CSV]]
deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "PrecompileTools", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings", "WorkerUtilities"] deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "PrecompileTools", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings", "WorkerUtilities"]
git-tree-sha1 = "44dbf560808d49041989b8a96cae4cffbeb7966a" git-tree-sha1 = "deddd8725e5e1cc49ee205a1964256043720a6c3"
uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
version = "0.10.11" version = "0.10.15"
[[deps.CodecZlib]] [[deps.CodecZlib]]
deps = ["TranscodingStreams", "Zlib_jll"] deps = ["TranscodingStreams", "Zlib_jll"]
git-tree-sha1 = "02aa26a4cf76381be7f66e020a3eddeb27b0a092" git-tree-sha1 = "bce6804e5e6044c6daab27bb533d1295e4a2e759"
uuid = "944b1d66-785c-5afd-91f1-9de20f533193" uuid = "944b1d66-785c-5afd-91f1-9de20f533193"
version = "0.7.2" version = "0.7.6"
[[deps.ColorTypes]] [[deps.ColorTypes]]
deps = ["FixedPointNumbers", "Random"] deps = ["FixedPointNumbers", "Random"]
git-tree-sha1 = "eb7f0f8307f71fac7c606984ea5fb2817275d6e4" git-tree-sha1 = "c7acce7a7e1078a20a285211dd73cd3941a871d6"
uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f"
version = "0.11.4" version = "0.12.0"
[deps.ColorTypes.extensions]
StyledStringsExt = "StyledStrings"
[deps.ColorTypes.weakdeps]
StyledStrings = "f489334b-da3d-4c2e-b8f0-e476e12c162b"
[[deps.Colors]] [[deps.Colors]]
deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] deps = ["ColorTypes", "FixedPointNumbers", "Reexport"]
git-tree-sha1 = "fc08e5930ee9a4e03f84bfb5211cb54e7769758a" git-tree-sha1 = "64e15186f0aa277e174aa81798f7eb8598e0157e"
uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" uuid = "5ae59095-9a9b-59fe-a467-6f913c188581"
version = "0.12.10" version = "0.13.0"
[[deps.CommonSubexpressions]] [[deps.CommonSubexpressions]]
deps = ["MacroTools", "Test"] deps = ["MacroTools"]
git-tree-sha1 = "7b8a93dba8af7e3b42fecabf646260105ac373f7" git-tree-sha1 = "cda2cfaebb4be89c9084adaca7dd7333369715c5"
uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" uuid = "bbf7d656-a473-5ed7-a52c-81e309532950"
version = "0.3.0" version = "0.3.1"
[[deps.Compat]] [[deps.Compat]]
deps = ["UUIDs"] deps = ["TOML", "UUIDs"]
git-tree-sha1 = "e460f044ca8b99be31d35fe54fc33a5c33dd8ed7" git-tree-sha1 = "8ae8d32e09f0dcf42a36b90d4e17f5dd2e4c4215"
uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
version = "4.9.0" version = "4.16.0"
weakdeps = ["Dates", "LinearAlgebra"] weakdeps = ["Dates", "LinearAlgebra"]
[deps.Compat.extensions] [deps.Compat.extensions]
...@@ -65,21 +71,21 @@ uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" ...@@ -65,21 +71,21 @@ uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f"
version = "4.1.1" version = "4.1.1"
[[deps.DataAPI]] [[deps.DataAPI]]
git-tree-sha1 = "8da84edb865b0b5b0100c0666a9bc9a0b71c553c" git-tree-sha1 = "abe83f3a2f1b857aac70ef8b269080af17764bbe"
uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
version = "1.15.0" version = "1.16.0"
[[deps.DataFrames]] [[deps.DataFrames]]
deps = ["Compat", "DataAPI", "DataStructures", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrecompileTools", "PrettyTables", "Printf", "REPL", "Random", "Reexport", "SentinelArrays", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] deps = ["Compat", "DataAPI", "DataStructures", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrecompileTools", "PrettyTables", "Printf", "Random", "Reexport", "SentinelArrays", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"]
git-tree-sha1 = "04c738083f29f86e62c8afc341f0967d8717bdb8" git-tree-sha1 = "fb61b4812c49343d7ef0b533ba982c46021938a6"
uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
version = "1.6.1" version = "1.7.0"
[[deps.DataStructures]] [[deps.DataStructures]]
deps = ["Compat", "InteractiveUtils", "OrderedCollections"] deps = ["Compat", "InteractiveUtils", "OrderedCollections"]
git-tree-sha1 = "3dbd312d370723b6bb43ba9d02fc36abade4518d" git-tree-sha1 = "1d0a14036acb104d9e89698bd408f63ab58cdc82"
uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
version = "0.18.15" version = "0.18.20"
[[deps.DataValueInterfaces]] [[deps.DataValueInterfaces]]
git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6"
...@@ -115,41 +121,60 @@ version = "1.6.0" ...@@ -115,41 +121,60 @@ version = "1.6.0"
[[deps.FileIO]] [[deps.FileIO]]
deps = ["Pkg", "Requires", "UUIDs"] deps = ["Pkg", "Requires", "UUIDs"]
git-tree-sha1 = "299dc33549f68299137e51e6d49a13b5b1da9673" git-tree-sha1 = "2dd20384bf8c6d411b5c7370865b1e9b26cb2ea3"
uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
version = "1.16.1" version = "1.16.6"
[deps.FileIO.extensions]
HTTPExt = "HTTP"
[deps.FileIO.weakdeps]
HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
[[deps.FilePathsBase]] [[deps.FilePathsBase]]
deps = ["Compat", "Dates", "Mmap", "Printf", "Test", "UUIDs"] deps = ["Compat", "Dates"]
git-tree-sha1 = "e27c4ebe80e8699540f2d6c805cc12203b614f12" git-tree-sha1 = "7878ff7172a8e6beedd1dea14bd27c3c6340d361"
uuid = "48062228-2e41-5def-b9a4-89aafe57970f" uuid = "48062228-2e41-5def-b9a4-89aafe57970f"
version = "0.9.20" version = "0.9.22"
[deps.FilePathsBase.extensions]
FilePathsBaseMmapExt = "Mmap"
FilePathsBaseTestExt = "Test"
[deps.FilePathsBase.weakdeps]
Mmap = "a63ad114-7e13-5084-954f-fe012c677804"
Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
[[deps.FileWatching]] [[deps.FileWatching]]
uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
[[deps.FillArrays]] [[deps.FillArrays]]
deps = ["LinearAlgebra", "Random"] deps = ["LinearAlgebra"]
git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" git-tree-sha1 = "6a70198746448456524cb442b8af316927ff3e1a"
uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b"
version = "1.6.1" version = "1.13.0"
weakdeps = ["SparseArrays", "Statistics"]
[deps.FillArrays.extensions] [deps.FillArrays.extensions]
FillArraysPDMatsExt = "PDMats"
FillArraysSparseArraysExt = "SparseArrays" FillArraysSparseArraysExt = "SparseArrays"
FillArraysStatisticsExt = "Statistics" FillArraysStatisticsExt = "Statistics"
[deps.FillArrays.weakdeps]
PDMats = "90014a1f-27ba-587c-ab20-58faa44d9150"
SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
[[deps.FixedPointNumbers]] [[deps.FixedPointNumbers]]
deps = ["Statistics"] deps = ["Statistics"]
git-tree-sha1 = "335bfdceacc84c5cdf16aadc768aa5ddfc5383cc" git-tree-sha1 = "05882d6995ae5c12bb5f36dd2ed3f61c98cbb172"
uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93"
version = "0.8.4" version = "0.8.5"
[[deps.ForwardDiff]] [[deps.ForwardDiff]]
deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"] deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"]
git-tree-sha1 = "cf0fe81336da9fb90944683b8c41984b08793dad" git-tree-sha1 = "a2df1b776752e3f344e5116c06d75a10436ab853"
uuid = "f6369f11-7733-5829-9624-2563aa707210" uuid = "f6369f11-7733-5829-9624-2563aa707210"
version = "0.10.36" version = "0.10.38"
weakdeps = ["StaticArrays"] weakdeps = ["StaticArrays"]
[deps.ForwardDiff.extensions] [deps.ForwardDiff.extensions]
...@@ -160,19 +185,26 @@ deps = ["Random"] ...@@ -160,19 +185,26 @@ deps = ["Random"]
uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"
[[deps.InlineStrings]] [[deps.InlineStrings]]
deps = ["Parsers"] git-tree-sha1 = "45521d31238e87ee9f9732561bfee12d4eebd52d"
git-tree-sha1 = "9cc2baf75c6d09f9da536ddf58eb2f29dedaf461"
uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48" uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48"
version = "1.4.0" version = "1.4.2"
[deps.InlineStrings.extensions]
ArrowTypesExt = "ArrowTypes"
ParsersExt = "Parsers"
[deps.InlineStrings.weakdeps]
ArrowTypes = "31f734f8-188a-4ce0-8406-c8a06bd891cd"
Parsers = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
[[deps.InteractiveUtils]] [[deps.InteractiveUtils]]
deps = ["Markdown"] deps = ["Markdown"]
uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
[[deps.InvertedIndices]] [[deps.InvertedIndices]]
git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038" git-tree-sha1 = "6da3c4316095de0f5ee2ebd875df8721e7e0bdbe"
uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f" uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f"
version = "1.3.0" version = "1.3.1"
[[deps.IrrationalConstants]] [[deps.IrrationalConstants]]
git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2"
...@@ -186,14 +218,14 @@ version = "1.0.0" ...@@ -186,14 +218,14 @@ version = "1.0.0"
[[deps.JLLWrappers]] [[deps.JLLWrappers]]
deps = ["Artifacts", "Preferences"] deps = ["Artifacts", "Preferences"]
git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" git-tree-sha1 = "a007feb38b422fbdab534406aeca1b86823cb4d6"
uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210"
version = "1.5.0" version = "1.7.0"
[[deps.LaTeXStrings]] [[deps.LaTeXStrings]]
git-tree-sha1 = "f2355693d6778a178ade15952b7ac47a4ff97996" git-tree-sha1 = "dda21b8cbd6a6c40d9d02a73230f9d70fed6918c"
uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
version = "1.3.0" version = "1.4.0"
[[deps.LibCURL]] [[deps.LibCURL]]
deps = ["LibCURL_jll", "MozillaCACerts_jll"] deps = ["LibCURL_jll", "MozillaCACerts_jll"]
...@@ -224,15 +256,15 @@ uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" ...@@ -224,15 +256,15 @@ uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
[[deps.Libiconv_jll]] [[deps.Libiconv_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"] deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" git-tree-sha1 = "be484f5c92fad0bd8acfef35fe017900b0b73809"
uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531"
version = "1.17.0+0" version = "1.18.0+0"
[[deps.LightXML]] [[deps.LightXML]]
deps = ["Libdl", "XML2_jll"] deps = ["Libdl", "XML2_jll"]
git-tree-sha1 = "e129d9391168c677cd4800f5c0abb1ed8cb3794f" git-tree-sha1 = "3a994404d3f6709610701c7dabfc03fed87a81f8"
uuid = "9c8b4983-aa76-5018-a973-4c85ecc9e179" uuid = "9c8b4983-aa76-5018-a973-4c85ecc9e179"
version = "0.9.0" version = "0.9.1"
[[deps.LinearAlgebra]] [[deps.LinearAlgebra]]
deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"]
...@@ -240,9 +272,9 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" ...@@ -240,9 +272,9 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
[[deps.LogExpFunctions]] [[deps.LogExpFunctions]]
deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"]
git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" git-tree-sha1 = "13ca9e2586b89836fd20cccf56e57e2b9ae7f38f"
uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
version = "0.3.26" version = "0.3.29"
[deps.LogExpFunctions.extensions] [deps.LogExpFunctions.extensions]
LogExpFunctionsChainRulesCoreExt = "ChainRulesCore" LogExpFunctionsChainRulesCoreExt = "ChainRulesCore"
...@@ -258,10 +290,9 @@ version = "0.3.26" ...@@ -258,10 +290,9 @@ version = "0.3.26"
uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
[[deps.MacroTools]] [[deps.MacroTools]]
deps = ["Markdown", "Random"] git-tree-sha1 = "72aebe0b5051e5143a079a4685a46da330a40472"
git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48"
uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
version = "0.5.11" version = "0.5.15"
[[deps.Markdown]] [[deps.Markdown]]
deps = ["Base64"] deps = ["Base64"]
...@@ -274,9 +305,9 @@ version = "2.28.2+1" ...@@ -274,9 +305,9 @@ version = "2.28.2+1"
[[deps.Missings]] [[deps.Missings]]
deps = ["DataAPI"] deps = ["DataAPI"]
git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272" git-tree-sha1 = "ec4f7fbeab05d7747bdf98eb74d130a2a2ed298d"
uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28"
version = "1.1.0" version = "1.2.0"
[[deps.Mmap]] [[deps.Mmap]]
uuid = "a63ad114-7e13-5084-954f-fe012c677804" uuid = "a63ad114-7e13-5084-954f-fe012c677804"
...@@ -287,9 +318,9 @@ version = "2023.1.10" ...@@ -287,9 +318,9 @@ version = "2023.1.10"
[[deps.NaNMath]] [[deps.NaNMath]]
deps = ["OpenLibm_jll"] deps = ["OpenLibm_jll"]
git-tree-sha1 = "0877504529a3e5c3343c6f8b4c0381e57e4387e4" git-tree-sha1 = "030ea22804ef91648f29b7ad3fc15fa49d0e6e71"
uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
version = "1.0.2" version = "1.0.3"
[[deps.NetworkOptions]] [[deps.NetworkOptions]]
uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
...@@ -306,21 +337,21 @@ uuid = "05823500-19ac-5b8b-9628-191a04bc5112" ...@@ -306,21 +337,21 @@ uuid = "05823500-19ac-5b8b-9628-191a04bc5112"
version = "0.8.1+2" version = "0.8.1+2"
[[deps.OpenSpecFun_jll]] [[deps.OpenSpecFun_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl"]
git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1" git-tree-sha1 = "1346c9208249809840c91b26703912dff463d335"
uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e"
version = "0.5.5+0" version = "0.5.6+0"
[[deps.OrderedCollections]] [[deps.OrderedCollections]]
git-tree-sha1 = "2e73fe17cac3c62ad1aebe70d44c963c3cfdc3e3" git-tree-sha1 = "12f1439c4f986bb868acda6ea33ebc78e19b95ad"
uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
version = "1.6.2" version = "1.7.0"
[[deps.Parsers]] [[deps.Parsers]]
deps = ["Dates", "PrecompileTools", "UUIDs"] deps = ["Dates", "PrecompileTools", "UUIDs"]
git-tree-sha1 = "716e24b21538abc91f6205fd1d8363f39b442851" git-tree-sha1 = "8489905bcdbcfac64d1daa51ca07c0d8f0283821"
uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
version = "2.7.2" version = "2.8.1"
[[deps.Pkg]] [[deps.Pkg]]
deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
...@@ -329,27 +360,27 @@ version = "1.10.0" ...@@ -329,27 +360,27 @@ version = "1.10.0"
[[deps.PooledArrays]] [[deps.PooledArrays]]
deps = ["DataAPI", "Future"] deps = ["DataAPI", "Future"]
git-tree-sha1 = "a6062fe4063cdafe78f4a0a81cfffb89721b30e7" git-tree-sha1 = "36d8b4b899628fb92c2749eb488d884a926614d3"
uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720" uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720"
version = "1.4.2" version = "1.4.3"
[[deps.PrecompileTools]] [[deps.PrecompileTools]]
deps = ["Preferences"] deps = ["Preferences"]
git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" git-tree-sha1 = "5aa36f7049a63a1528fe8f7c3f2113413ffd4e1f"
uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
version = "1.2.0" version = "1.2.1"
[[deps.Preferences]] [[deps.Preferences]]
deps = ["TOML"] deps = ["TOML"]
git-tree-sha1 = "7eb1686b4f04b82f96ed7a4ea5890a4f0c7a09f1" git-tree-sha1 = "9306f6085165d270f7e3db02af26a400d580f5c6"
uuid = "21216c6a-2e73-6563-6e65-726566657250" uuid = "21216c6a-2e73-6563-6e65-726566657250"
version = "1.4.0" version = "1.4.3"
[[deps.PrettyTables]] [[deps.PrettyTables]]
deps = ["Crayons", "LaTeXStrings", "Markdown", "Printf", "Reexport", "StringManipulation", "Tables"] deps = ["Crayons", "LaTeXStrings", "Markdown", "PrecompileTools", "Printf", "Reexport", "StringManipulation", "Tables"]
git-tree-sha1 = "ee094908d720185ddbdc58dbe0c1cbe35453ec7a" git-tree-sha1 = "1101cd475833706e4d0e7b122218257178f48f34"
uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
version = "2.2.7" version = "2.4.0"
[[deps.Printf]] [[deps.Printf]]
deps = ["Unicode"] deps = ["Unicode"]
...@@ -380,9 +411,9 @@ version = "0.7.0" ...@@ -380,9 +411,9 @@ version = "0.7.0"
[[deps.SentinelArrays]] [[deps.SentinelArrays]]
deps = ["Dates", "Random"] deps = ["Dates", "Random"]
git-tree-sha1 = "04bdff0b09c65ff3e06a05e3eb7b120223da3d39" git-tree-sha1 = "712fb0231ee6f9120e005ccd56297abbc053e7e0"
uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c" uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c"
version = "1.4.0" version = "1.4.8"
[[deps.Serialization]] [[deps.Serialization]]
uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
...@@ -392,9 +423,9 @@ uuid = "6462fe0b-24de-5631-8697-dd941f90decc" ...@@ -392,9 +423,9 @@ uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
[[deps.SortingAlgorithms]] [[deps.SortingAlgorithms]]
deps = ["DataStructures"] deps = ["DataStructures"]
git-tree-sha1 = "c60ec5c62180f27efea3ba2908480f8055e17cee" git-tree-sha1 = "66e0a8e672a0bdfca2c3f5937efb8538b9ddc085"
uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c"
version = "1.1.1" version = "1.2.1"
[[deps.SparseArrays]] [[deps.SparseArrays]]
deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"]
...@@ -403,9 +434,9 @@ version = "1.10.0" ...@@ -403,9 +434,9 @@ version = "1.10.0"
[[deps.SpecialFunctions]] [[deps.SpecialFunctions]]
deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"]
git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" git-tree-sha1 = "64cca0c26b4f31ba18f13f6c12af7c85f478cfde"
uuid = "276daf66-3868-5448-9aa4-cd146d93841b" uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
version = "2.3.1" version = "2.5.0"
[deps.SpecialFunctions.extensions] [deps.SpecialFunctions.extensions]
SpecialFunctionsChainRulesCoreExt = "ChainRulesCore" SpecialFunctionsChainRulesCoreExt = "ChainRulesCore"
...@@ -414,19 +445,23 @@ version = "2.3.1" ...@@ -414,19 +445,23 @@ version = "2.3.1"
ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
[[deps.StaticArrays]] [[deps.StaticArrays]]
deps = ["LinearAlgebra", "Random", "StaticArraysCore"] deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"]
git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab" git-tree-sha1 = "47091a0340a675c738b1304b58161f3b0839d454"
uuid = "90137ffa-7385-5640-81b9-e52037218182" uuid = "90137ffa-7385-5640-81b9-e52037218182"
version = "1.6.3" version = "1.9.10"
weakdeps = ["Statistics"]
[deps.StaticArrays.extensions] [deps.StaticArrays.extensions]
StaticArraysChainRulesCoreExt = "ChainRulesCore"
StaticArraysStatisticsExt = "Statistics" StaticArraysStatisticsExt = "Statistics"
[deps.StaticArrays.weakdeps]
ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
[[deps.StaticArraysCore]] [[deps.StaticArraysCore]]
git-tree-sha1 = "36b3d696ce6366023a0ea192b4cd442268995a0d" git-tree-sha1 = "192954ef1208c7019899fbf8049e717f92959682"
uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c"
version = "1.4.2" version = "1.4.3"
[[deps.Statistics]] [[deps.Statistics]]
deps = ["LinearAlgebra", "SparseArrays"] deps = ["LinearAlgebra", "SparseArrays"]
...@@ -435,9 +470,9 @@ version = "1.10.0" ...@@ -435,9 +470,9 @@ version = "1.10.0"
[[deps.StringManipulation]] [[deps.StringManipulation]]
deps = ["PrecompileTools"] deps = ["PrecompileTools"]
git-tree-sha1 = "a04cabe79c5f01f4d723cc6704070ada0b9d46d5" git-tree-sha1 = "a6b1675a536c5ad1a60e5a5153e1fee12eb146e3"
uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e"
version = "0.3.4" version = "0.4.0"
[[deps.SuiteSparse_jll]] [[deps.SuiteSparse_jll]]
deps = ["Artifacts", "Libdl", "libblastrampoline_jll"] deps = ["Artifacts", "Libdl", "libblastrampoline_jll"]
...@@ -456,25 +491,20 @@ uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" ...@@ -456,25 +491,20 @@ uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c"
version = "1.0.1" version = "1.0.1"
[[deps.Tables]] [[deps.Tables]]
deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"] deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "OrderedCollections", "TableTraits"]
git-tree-sha1 = "1544b926975372da01227b382066ab70e574a3ec" git-tree-sha1 = "598cd7c1f68d1e205689b1c2fe65a9f85846f297"
uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
version = "1.10.1" version = "1.12.0"
[[deps.Tar]] [[deps.Tar]]
deps = ["ArgTools", "SHA"] deps = ["ArgTools", "SHA"]
uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
version = "1.10.0" version = "1.10.0"
[[deps.Test]]
deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
[[deps.TranscodingStreams]] [[deps.TranscodingStreams]]
deps = ["Random", "Test"] git-tree-sha1 = "0c45878dcfdcfa8480052b6ab162cdd138781742"
git-tree-sha1 = "9a6ae7ed916312b41236fcef7e0af564ef934769"
uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
version = "0.9.13" version = "0.11.3"
[[deps.UUIDs]] [[deps.UUIDs]]
deps = ["Random", "SHA"] deps = ["Random", "SHA"]
...@@ -501,15 +531,15 @@ version = "1.6.1" ...@@ -501,15 +531,15 @@ version = "1.6.1"
[[deps.WriteVTK]] [[deps.WriteVTK]]
deps = ["Base64", "CodecZlib", "FillArrays", "LightXML", "TranscodingStreams", "VTKBase"] deps = ["Base64", "CodecZlib", "FillArrays", "LightXML", "TranscodingStreams", "VTKBase"]
git-tree-sha1 = "7b46936613e41cfe1c6a5897d243ddcab8feabec" git-tree-sha1 = "1d8042d58334ab7947ce505709df7009da6f3375"
uuid = "64499a7a-5c06-52f2-abe2-ccb03c286192" uuid = "64499a7a-5c06-52f2-abe2-ccb03c286192"
version = "1.18.0" version = "1.21.1"
[[deps.XML2_jll]] [[deps.XML2_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"]
git-tree-sha1 = "04a51d15436a572301b5abbb9d099713327e9fc4" git-tree-sha1 = "a2fccc6559132927d4c5dc183e3e01048c6dcbd6"
uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a"
version = "2.10.4+0" version = "2.13.5+0"
[[deps.Zlib_jll]] [[deps.Zlib_jll]]
deps = ["Libdl"] deps = ["Libdl"]
...@@ -519,7 +549,7 @@ version = "1.2.13+1" ...@@ -519,7 +549,7 @@ version = "1.2.13+1"
[[deps.libblastrampoline_jll]] [[deps.libblastrampoline_jll]]
deps = ["Artifacts", "Libdl"] deps = ["Artifacts", "Libdl"]
uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
version = "5.8.0+1" version = "5.11.0+0"
[[deps.nghttp2_jll]] [[deps.nghttp2_jll]]
deps = ["Artifacts", "Libdl"] deps = ["Artifacts", "Libdl"]
......
scripts/Manifest.toml
View file @ fdcc7ea5
This diff is collapsed.
scripts/run_experiments.jl
View file @ fdcc7ea5
...@@ -609,21 +609,45 @@ end ...@@ -609,21 +609,45 @@ end
huber(x, gamma) = abs(x) < gamma ? x^2 / (2 * gamma) : abs(x) - gamma / 2 huber(x, gamma) = abs(x) < gamma ? x^2 / (2 * gamma) : abs(x) - gamma / 2
# TODO: finish! function globally_refine!(hmesh::HMesh, st::L1L2TVState)
function refine_and_estimate_pd(st::L1L2TVState)
# globally refine
marked_cells = Set(axes(st.mesh.cells, 2)) marked_cells = Set(axes(st.mesh.cells, 2))
mesh_new, fs_new = refine(st.mesh, marked_cells; mesh_new, fs_new = refine!(hmesh, marked_cells;
st.est, st.g, st.u, st.p1, st.p2, st.du, st.dp1, st.dp2) st.tdata, st.est, st.g, st.u, st.p1, st.p2, st.du, st.dp1, st.dp2)
st_new = L1L2TVState(st; mesh = mesh_new, st_new = L1L2TVState(st; mesh = mesh_new,
fs_new.tdata,
fs_new.est, fs_new.g, fs_new.u, fs_new.p1, fs_new.p2, fs_new.est, fs_new.g, fs_new.u, fs_new.p1, fs_new.p2,
fs_new.du, fs_new.dp1, fs_new.dp2) fs_new.du, fs_new.dp1, fs_new.dp2)
return st_new
end
function refine_and_estimate_pd!(st, ctx, i, interpolate_image_data!, f0 = nothing, f1 = nothing)
hmesh = HMesh(st.mesh)
hmesh_coarse_cells = cells(hmesh)
st_new = globally_refine!(hmesh, st)
# compute primal dual error indicators # compute primal dual error indicators
if isnothing(f0) && isnothing(f1)
interpolate_image_data!(st_new)
else
# TODO: we should maybe create a distinct state object for optflow and
# have f0, f1 be part of it to avoid this special casing.
interpolate_image_data!(f0, f1)
end
estimate_pd!(st_new) estimate_pd!(st_new)
# Output optional fine data
if i == 1
# Hack to get numbering from 0 as the other vtu data.
output(st_new, joinpath(ctx.outdir, "output_pd_fine_$(lpad(0, 5, '0')).vtu"), st_new.g, st_new.est)
end
output(st_new, joinpath(ctx.outdir, "output_pd_fine_$(lpad(i, 5, '0')).vtu"), st_new.g, st_new.est)
# transfer data to old state # transfer data to old state
# mesh_coarse, fs_coarse = coarsen(hmesh, hmesh_coarse_cells; st_new.est)
@assert cells(st.mesh) == cells(mesh_coarse)
st.est.data .= fs_coarse.est.data
end end
# this computes the primal-dual error indicator which is not really useful # this computes the primal-dual error indicator which is not really useful
...@@ -1359,7 +1383,7 @@ function inpaint(ctx) ...@@ -1359,7 +1383,7 @@ function inpaint(ctx)
ctx.params.lambda, ctx.params.beta, ctx.params.lambda, ctx.params.beta,
ctx.params.gamma1, ctx.params.gamma2) ctx.params.gamma1, ctx.params.gamma2)
function interpolate_image_data!() function interpolate_image_data!(st)
println("interpolate image data ...") println("interpolate image data ...")
if ctx.params.n_refine == 0 if ctx.params.n_refine == 0
# if we use a grid at image resolution, we wan't to avoid # if we use a grid at image resolution, we wan't to avoid
...@@ -1381,7 +1405,7 @@ function inpaint(ctx) ...@@ -1381,7 +1405,7 @@ function inpaint(ctx)
pvd = paraview_collection(joinpath(ctx.outdir, "output.pvd")) do pvd pvd = paraview_collection(joinpath(ctx.outdir, "output.pvd")) do pvd
interpolate_image_data!() interpolate_image_data!(st)
pvd[0] = save_step(0) pvd[0] = save_step(0)
...@@ -1403,7 +1427,11 @@ function inpaint(ctx) ...@@ -1403,7 +1427,11 @@ function inpaint(ctx)
# plot # plot
i += 1 i += 1
display(plot(grayclamp.(to_img(sample(st.u))))) display(plot(grayclamp.(to_img(sample(st.u)))))
estimate_res!(st) if hasproperty(ctx.params, :estimator) && ctx.params.estimator == :primal_dual
refine_and_estimate_pd!(st, ctx, i, interpolate_image_data!)
else
estimate_res!(st)
end
pvd[i] = save_step(i) pvd[i] = save_step(i)
#break #break
...@@ -1424,11 +1452,15 @@ function inpaint(ctx) ...@@ -1424,11 +1452,15 @@ function inpaint(ctx)
# manually mark all cell within inpainting domain, since the # manually mark all cell within inpainting domain, since the
# estimator is not reliable there # estimator is not reliable there
for cell in cells(mesh) if !hasproperty(ctx.params, :estimator) || ctx.params.estimator != :primal_dual
bind!(st.tdata, cell) # The primal-dual estimator seems reliable inside the
maskv = evaluate(st.tdata, SA[1/3, 1/3]) # inpainting domain
if abs(maskv[begin] - 1.) > 1e-8 for cell in cells(mesh)
push!(marked_cells, cell) bind!(st.tdata, cell)
maskv = evaluate(st.tdata, SA[1/3, 1/3])
if abs(maskv[begin] - 1.) > 1e-8
push!(marked_cells, cell)
end
end end
end end
#marked_cells = Set(axes(mesh.cells, 2)) #marked_cells = Set(axes(mesh.cells, 2))
...@@ -1436,7 +1468,7 @@ function inpaint(ctx) ...@@ -1436,7 +1468,7 @@ function inpaint(ctx)
st.est, st.g, st.u, st.p1, st.p2, st.du, st.dp1, st.dp2, st.tdata) st.est, st.g, st.u, st.p1, st.p2, st.du, st.dp1, st.dp2, st.tdata)
st = L1L2TVState(st; mesh, fs.tdata, st = L1L2TVState(st; mesh, fs.tdata,
fs.est, fs.g, fs.u, fs.p1, fs.p2, fs.du, fs.dp1, fs.dp2) fs.est, fs.g, fs.u, fs.p1, fs.p2, fs.du, fs.dp1, fs.dp2)
interpolate_image_data!() interpolate_image_data!(st)
end end
end end
end # @elapsed end # @elapsed
...@@ -1462,6 +1494,7 @@ function experiment_inpaint_adaptive(ctx) ...@@ -1462,6 +1494,7 @@ function experiment_inpaint_adaptive(ctx)
params = ( params = (
name = "test", name = "test",
n_refine = coarsen, n_refine = coarsen,
#estimator = :primal_dual,
g_arr, mask_arr, mesh, g_arr, mask_arr, mesh,
#alpha1 = 0.2, alpha2 = 8., lambda = 1., #alpha1 = 0.2, alpha2 = 8., lambda = 1.,
alpha1 = 0., alpha2 = 50., lambda = 1., alpha1 = 0., alpha2 = 50., lambda = 1.,
...@@ -1582,7 +1615,7 @@ function optflow(ctx) ...@@ -1582,7 +1615,7 @@ function optflow(ctx)
interpolate!(st.g, g_optflow; u0 = st.u, f0, fw, st.tdata) interpolate!(st.g, g_optflow; u0 = st.u, f0, fw, st.tdata)
end end
function interpolate_image_data!() function interpolate_image_data!(f0, f1)
println("interpolate image data ...") println("interpolate image data ...")
project_image!(f0, imgf0) project_image!(f0, imgf0)
project_image!(f1, imgf1) project_image!(f1, imgf1)
...@@ -1596,7 +1629,7 @@ function optflow(ctx) ...@@ -1596,7 +1629,7 @@ function optflow(ctx)
pvd = paraview_collection(joinpath(ctx.outdir, "output.pvd")) do pvd pvd = paraview_collection(joinpath(ctx.outdir, "output.pvd")) do pvd
interpolate_image_data!() interpolate_image_data!(f0, f1)
warp!() # in the first step just to fill st.g warp!() # in the first step just to fill st.g
pvd[0] = save_step(0) pvd[0] = save_step(0)
...@@ -1640,7 +1673,11 @@ function optflow(ctx) ...@@ -1640,7 +1673,11 @@ function optflow(ctx)
k_refine += 1 k_refine += 1
k_refine > ctx.params.n_refine && break k_refine > ctx.params.n_refine && break
println("refine ...") println("refine ...")
estimate_res!(st) if hasproperty(ctx.params, :estimator) && ctx.params.estimator == :primal_dual
refine_and_estimate_pd!(st, ctx, i, interpolate_image_data!, f0, f1)
else
estimate_res!(st)
end
marked_cells = mark(st; theta = 0.5) marked_cells = mark(st; theta = 0.5)
#marked_cells = Set(axes(mesh.cells, 2)) #marked_cells = Set(axes(mesh.cells, 2))
mesh, fs = refine(mesh, marked_cells; mesh, fs = refine(mesh, marked_cells;
...@@ -1649,7 +1686,7 @@ function optflow(ctx) ...@@ -1649,7 +1686,7 @@ function optflow(ctx)
st = L1L2TVState(st; mesh, fs.tdata, st = L1L2TVState(st; mesh, fs.tdata,
fs.est, fs.g, fs.u, fs.p1, fs.p2, fs.du, fs.dp1, fs.dp2) fs.est, fs.g, fs.u, fs.p1, fs.p2, fs.du, fs.dp1, fs.dp2)
f0, f1, fw = (fs.f0, fs.f1, fs.fw) f0, f1, fw = (fs.f0, fs.f1, fs.fw)
interpolate_image_data!() interpolate_image_data!(f0, f1)
end end
end end
#CSV.write(joinpath(ctx.outdir, "energies.csv"), df) #CSV.write(joinpath(ctx.outdir, "energies.csv"), df)
...@@ -1684,7 +1721,7 @@ function experiment_optflow_middlebury(ctx) ...@@ -1684,7 +1721,7 @@ function experiment_optflow_middlebury(ctx)
imgf0 = loadimg(joinpath(ctx.indir, "frame10.png")) imgf0 = loadimg(joinpath(ctx.indir, "frame10.png"))
imgf1 = loadimg(joinpath(ctx.indir, "frame11.png")) imgf1 = loadimg(joinpath(ctx.indir, "frame11.png"))
gtflow = FileIO.load(joinpath(ctx.indir, "flow10.flo")) gtflow = FileIO.load(joinpath(ctx.indir, "flow10.flo"))
maxflow = OpticalFlowUtils._maxflow(gtflow) maxflow = OpticalFlowUtils.maxflow(gtflow)
ctx = Util.Context(ctx; imgf0, imgf1, maxflow, gtflow) ctx = Util.Context(ctx; imgf0, imgf1, maxflow, gtflow)
saveimg(joinpath(ctx.outdir, "ground_truth.png"), colorflow(gtflow; maxflow)) saveimg(joinpath(ctx.outdir, "ground_truth.png"), colorflow(gtflow; maxflow))
...@@ -1700,12 +1737,6 @@ function experiment_optflow_middlebury_all_benchmarks(ctx) ...@@ -1700,12 +1737,6 @@ function experiment_optflow_middlebury_all_benchmarks(ctx)
end end
end end
# FIXME: legacy
function experiment_optflow_middlebury_all(ctx)
experiment_optflow_middlebury_all_benchmarks(
Util.Context(ctx; warp = true, refine = true, n_refine = 6))
end
function experiment_optflow_middlebury_warping_comparison(ctx) function experiment_optflow_middlebury_warping_comparison(ctx)
ctx(experiment_optflow_middlebury_all_benchmarks, "vanilla"; ctx(experiment_optflow_middlebury_all_benchmarks, "vanilla";
warp = false, refine = false, n_refine = 0) warp = false, refine = false, n_refine = 0)
...@@ -1720,6 +1751,8 @@ function experiment_optflow_middlebury_warping_comparison_adaptive(ctx) ...@@ -1720,6 +1751,8 @@ function experiment_optflow_middlebury_warping_comparison_adaptive(ctx)
warp = true, refine = false, n_refine = 0) warp = true, refine = false, n_refine = 0)
ctx(experiment_optflow_middlebury_all_benchmarks, "adaptive-warping"; ctx(experiment_optflow_middlebury_all_benchmarks, "adaptive-warping";
warp = true, refine = true, n_refine = 6) warp = true, refine = true, n_refine = 6)
#ctx(experiment_optflow_middlebury_all_benchmarks, "adaptive-warping";
# warp = true, refine = true, n_refine = 6, estimator = :residual)
end end
function experiment_optflow_schoice(ctx) function experiment_optflow_schoice(ctx)
......
src/function.jl
View file @ fdcc7ea5
...@@ -24,7 +24,7 @@ evaluate_basis(::DP1, x) = evaluate_basis(P1(), x) ...@@ -24,7 +24,7 @@ evaluate_basis(::DP1, x) = evaluate_basis(P1(), x)
struct FeSpace{M, Fe, S} struct FeSpace{M, Fe, S}
mesh::M mesh::M
element::Fe element::Fe
dofmap::Array{Int, 3} # (rdim, eldof, cell) -> gdof dofmap::Array{Int, 3} # (rangedim, eldof, cell) -> gdof
ndofs::Int # = maximum(dofmap) ndofs::Int # = maximum(dofmap)
end end
...@@ -64,7 +64,7 @@ function FeSpace(mesh, el::DP1, size_=(1,)) ...@@ -64,7 +64,7 @@ function FeSpace(mesh, el::DP1, size_=(1,))
end end
Base.show(io::IO, ::MIME"text/plain", x::FeSpace) = Base.show(io::IO, ::MIME"text/plain", x::FeSpace) =
print("$(nameof(typeof(x))), $(nameof(typeof(x.element))) elements, size $(x.size), $(ndofs(x)) dofs") print(io, "$(nameof(typeof(x))), $(nameof(typeof(x.element))) elements, size $(x.size), $(ndofs(x)) dofs")
function Base.getproperty(obj::FeSpace{<:Any, <:Any, S}, sym::Symbol) where S function Base.getproperty(obj::FeSpace{<:Any, <:Any, S}, sym::Symbol) where S
if sym === :size if sym === :size
...@@ -104,7 +104,7 @@ function FeFunction(space; name=string(gensym("f"))) ...@@ -104,7 +104,7 @@ function FeFunction(space; name=string(gensym("f")))
end end
Base.show(io::IO, ::MIME"text/plain", f::FeFunction) = Base.show(io::IO, ::MIME"text/plain", f::FeFunction) =
print("$(nameof(typeof(f))), size $(f.space.size) with $(length(f.data)) dofs") print(io, "$(nameof(typeof(f))), size $(f.space.size) with $(length(f.data)) dofs")
interpolate!(dst::FeFunction, expr::Function; params...) = interpolate!(dst::FeFunction, expr::Function; params...) =
interpolate!(dst, dst.space.element, expr; params...) interpolate!(dst, dst.space.element, expr; params...)
...@@ -256,7 +256,7 @@ struct Derivative{F, M} ...@@ -256,7 +256,7 @@ struct Derivative{F, M}
end end
Base.show(io::IO, ::MIME"text/plain", x::Derivative) = Base.show(io::IO, ::MIME"text/plain", x::Derivative) =
print("$(nameof(typeof(x))) of $(typeof(x.f))") print(io, "$(nameof(typeof(x))) of $(typeof(x.f))")
# TODO: should be called "derivative" # TODO: should be called "derivative"
function nabla(f) function nabla(f)
...@@ -380,6 +380,9 @@ function prolong!(new_f, old_f, old_cell, new_cells, ::DP0) ...@@ -380,6 +380,9 @@ function prolong!(new_f, old_f, old_cell, new_cells, ::DP0)
end end
# IO
vtk_append!(vtkfile, f::FeFunction, fs::FeFunction...) = vtk_append!(vtkfile, f::FeFunction, fs::FeFunction...) =
(vtk_append!(vtkfile, f); vtk_append!(vtkfile, fs...)) (vtk_append!(vtkfile, f); vtk_append!(vtkfile, fs...))
......
src/mesh.jl
View file @ fdcc7ea5
export init_grid, init_hgrid, save, refine!, refine, cells, vertices, export HMesh, init_grid, init_hgrid, save, refine!, refine, cells, vertices,
ndims_domain, ndims_space, nvertices, nvertices_cell, ncells ndims_domain, ndims_space, nvertices, nvertices_cell, ncells, coarsen
using LinearAlgebra: norm using LinearAlgebra: norm
...@@ -9,12 +9,14 @@ using StaticArrays: SVector ...@@ -9,12 +9,14 @@ using StaticArrays: SVector
struct HMesh struct HMesh
vertices::Vector{SVector{2, Float64}} vertices::Vector{SVector{2, Float64}}
cells::Vector{NTuple{3, Int}} cells::Vector{NTuple{3, Int}}
"direct descendents of a cell"
children::Vector{Union{NTuple{2, Int}, Nothing}}
"refinement depth below each cell" "refinement depth below each cell"
levels::Vector{Int} levels::Vector{Int}
end end
Base.show(io::IO, ::MIME"text/plain", x::HMesh) = Base.show(io::IO, ::MIME"text/plain", x::HMesh) =
print("$(nameof(typeof(x))), $(ncells(x)) cells") print(io, "$(nameof(typeof(x))), $(ncells(x)) cells")
ndims_domain(::HMesh) = 2 ndims_domain(::HMesh) = 2
ndims_space(::HMesh) = 2 ndims_space(::HMesh) = 2
...@@ -44,8 +46,10 @@ function init_hgrid(m::Int, n::Int = m, v0 = (0., 0.), v1 = (1., 1.)) ...@@ -44,8 +46,10 @@ function init_hgrid(m::Int, n::Int = m, v0 = (0., 0.), v1 = (1., 1.))
push!(cells, (vidx[I], vidx[I + e1], vidx[I + e1 + e2])) push!(cells, (vidx[I], vidx[I + e1], vidx[I + e1 + e2]))
push!(cells, (vidx[I], vidx[I + e1 + e2], vidx[I + e2])) push!(cells, (vidx[I], vidx[I + e1 + e2], vidx[I + e2]))
end end
children = fill(nothing, axes(cells))
levels = zeros(Int, axes(cells))
return HMesh(vertices, cells, zeros(Int, axes(cells))) return HMesh(vertices, cells, children, levels)
end end
function init_hgrid(img::Array{<:Any, 2}; type=:vertex) function init_hgrid(img::Array{<:Any, 2}; type=:vertex)
...@@ -79,13 +83,14 @@ function HMesh(mesh::Mesh) ...@@ -79,13 +83,14 @@ function HMesh(mesh::Mesh)
for c in axes(mesh.cells, 2) for c in axes(mesh.cells, 2)
push!(cells, NTuple{3}(mesh.cells[:, c])) push!(cells, NTuple{3}(mesh.cells[:, c]))
end end
children = fill(nothing, axes(cells))
levels = zeros(Int, axes(cells)) levels = zeros(Int, axes(cells))
return HMesh(vertices, cells, levels) return HMesh(vertices, cells, children, levels)
end end
Base.show(io::IO, ::MIME"text/plain", x::Mesh) = Base.show(io::IO, ::MIME"text/plain", x::Mesh) =
print("$(nameof(typeof(x))), $(ncells(x)) cells") print(io, "$(nameof(typeof(x))), $(ncells(x)) cells")
ndims_domain(::Mesh) = 2 ndims_domain(::Mesh) = 2
ndims_space(::Mesh) = 2 ndims_space(::Mesh) = 2
...@@ -156,10 +161,10 @@ function init_grid(a::Array{<:Any, 2}, m::Int, n::Int = m; type=:vertex) ...@@ -156,10 +161,10 @@ function init_grid(a::Array{<:Any, 2}, m::Int, n::Int = m; type=:vertex)
init_grid((m, n)..., (0.5, 0.5), s .- (0.5, 0.5)) init_grid((m, n)..., (0.5, 0.5), s .- (0.5, 0.5))
end end
# horribly implemented, please don't curse me # TODO: cleanup
function bisect!(mesh::HMesh, marked_cells::Set) function bisect!(mesh::HMesh, marked_cells::Set)
refined_cells = Pair{Int, NTuple{2, Int}}[] refined_cells = Pair{Int, NTuple{2, Int}}[]
# assemble edge -> cells map # assemble mapping: edge -> cells
edgemap = Dict{NTuple{2, Int}, Vector{Int}}() edgemap = Dict{NTuple{2, Int}, Vector{Int}}()
for cell in cells(mesh) for cell in cells(mesh)
vs = sort(SVector(vertices(mesh, cell))) vs = sort(SVector(vertices(mesh, cell)))
...@@ -173,8 +178,6 @@ function bisect!(mesh::HMesh, marked_cells::Set) ...@@ -173,8 +178,6 @@ function bisect!(mesh::HMesh, marked_cells::Set)
edgemap[e3] = push!(get!(edgemap, e3, []), cell) edgemap[e3] = push!(get!(edgemap, e3, []), cell)
end end
#return edgemap
function refine_cell(c1) function refine_cell(c1)
c2 = -1 c2 = -1
# c1 -> c11 + c12 # c1 -> c11 + c12
...@@ -208,6 +211,7 @@ function bisect!(mesh::HMesh, marked_cells::Set) ...@@ -208,6 +211,7 @@ function bisect!(mesh::HMesh, marked_cells::Set)
# take care to produce positively oriented cells # take care to produce positively oriented cells
push!(mesh.cells, Tuple(replace(SVector(vertices(mesh, c1)), c1_vs[1] => vbisect))) push!(mesh.cells, Tuple(replace(SVector(vertices(mesh, c1)), c1_vs[1] => vbisect)))
push!(mesh.levels, 0) push!(mesh.levels, 0)
push!(mesh.children, nothing)
c3 = lastindex(mesh.cells) c3 = lastindex(mesh.cells)
@assert(length(setdiff(c1_vs, c1_vs[1])) == 2) @assert(length(setdiff(c1_vs, c1_vs[1])) == 2)
replace!(edgemap[NTuple{2}(setdiff(c1_vs, c1_vs[1]))], c1 => c3) replace!(edgemap[NTuple{2}(setdiff(c1_vs, c1_vs[1]))], c1 => c3)
...@@ -215,6 +219,7 @@ function bisect!(mesh::HMesh, marked_cells::Set) ...@@ -215,6 +219,7 @@ function bisect!(mesh::HMesh, marked_cells::Set)
# take care to produce positively oriented cells # take care to produce positively oriented cells
push!(mesh.cells, Tuple(replace(SVector(vertices(mesh, c1)), c1_vs[2] => vbisect))) push!(mesh.cells, Tuple(replace(SVector(vertices(mesh, c1)), c1_vs[2] => vbisect)))
push!(mesh.levels, 0) push!(mesh.levels, 0)
push!(mesh.children, nothing)
c4 = lastindex(mesh.cells) c4 = lastindex(mesh.cells)
@assert(length(setdiff(c1_vs, c1_vs[2])) == 2) @assert(length(setdiff(c1_vs, c1_vs[2])) == 2)
replace!(edgemap[NTuple{2}(setdiff(c1_vs, c1_vs[2]))], c1 => c4) replace!(edgemap[NTuple{2}(setdiff(c1_vs, c1_vs[2]))], c1 => c4)
...@@ -227,11 +232,13 @@ function bisect!(mesh::HMesh, marked_cells::Set) ...@@ -227,11 +232,13 @@ function bisect!(mesh::HMesh, marked_cells::Set)
mesh.levels[c1] += 1 mesh.levels[c1] += 1
delete!(marked_cells, c1) delete!(marked_cells, c1)
push!(refined_cells, c1 => (c3, c4)) push!(refined_cells, c1 => (c3, c4))
mesh.children[c1] = (c3, c4)
if c2 > 0 if c2 > 0
# take care to produce positively oriented cells # take care to produce positively oriented cells
push!(mesh.cells, Tuple(replace(SVector(vertices(mesh, c2)), c1_vs[1] => vbisect))) # c1_vs is correct push!(mesh.cells, Tuple(replace(SVector(vertices(mesh, c2)), c1_vs[1] => vbisect))) # c1_vs is correct
push!(mesh.levels, 0) push!(mesh.levels, 0)
push!(mesh.children, nothing)
c5 = lastindex(mesh.cells) c5 = lastindex(mesh.cells)
@assert(length(setdiff(c2_vs, c1_vs[1])) == 2) @assert(length(setdiff(c2_vs, c1_vs[1])) == 2)
replace!(edgemap[NTuple{2}(setdiff(c2_vs, c1_vs[1]))], c2 => c5) replace!(edgemap[NTuple{2}(setdiff(c2_vs, c1_vs[1]))], c2 => c5)
...@@ -239,6 +246,7 @@ function bisect!(mesh::HMesh, marked_cells::Set) ...@@ -239,6 +246,7 @@ function bisect!(mesh::HMesh, marked_cells::Set)
# take care to produce positively oriented cells # take care to produce positively oriented cells
push!(mesh.cells, Tuple(replace(SVector(vertices(mesh, c2)), c1_vs[2] => vbisect))) # c1_vs is correct push!(mesh.cells, Tuple(replace(SVector(vertices(mesh, c2)), c1_vs[2] => vbisect))) # c1_vs is correct
push!(mesh.levels, 0) push!(mesh.levels, 0)
push!(mesh.children, nothing)
c6 = lastindex(mesh.cells) c6 = lastindex(mesh.cells)
@assert(length(setdiff(c2_vs, c1_vs[2])) == 2) @assert(length(setdiff(c2_vs, c1_vs[2])) == 2)
replace!(edgemap[NTuple{2}(setdiff(c2_vs, c1_vs[2]))], c2 => c6) replace!(edgemap[NTuple{2}(setdiff(c2_vs, c1_vs[2]))], c2 => c6)
...@@ -251,6 +259,7 @@ function bisect!(mesh::HMesh, marked_cells::Set) ...@@ -251,6 +259,7 @@ function bisect!(mesh::HMesh, marked_cells::Set)
mesh.levels[c2] += 1 mesh.levels[c2] += 1
delete!(marked_cells, c2) delete!(marked_cells, c2)
push!(refined_cells, c2 => (c5, c6)) push!(refined_cells, c2 => (c5, c6))
mesh.children[c2] = (c5, c6)
end end
end end
...@@ -265,46 +274,64 @@ end ...@@ -265,46 +274,64 @@ end
# TODO: cleanup and optimize # TODO: cleanup and optimize
# FIXME: this assumes hmesh was created from f.mesh # FIXME: this assumes hmesh was created from f.mesh
function refine!(hmesh::HMesh, marked_cells::Set; fs...) function refine!(hmesh::HMesh, marked_cells::Set; fs...)
fs = NamedTuple(fs)
old_mesh = sub_mesh(hmesh) old_mesh = sub_mesh(hmesh)
hmesh_old_leaf_cells = cells(hmesh)
@assert allequal(x -> x.space.mesh, fs) "Functions living on different meshes."
for f in fs
# Note this is only a superficial check. We don't spend the effort to
# check that meshes match structurally as well.
@assert length(cells(f.space.mesh)) == length(hmesh_old_leaf_cells) "Mismatching number of cells for mesh function and lowest layer of hierarchical mesh: $(length(cells(f.space.mesh))) vs $(length(hmesh_leaf_cells))."
end
cell_refinements = bisect!(hmesh, marked_cells) cell_refinements = bisect!(hmesh, marked_cells)
# we use a extended mesh containing all cells (both fine and hmesh_new_leaf_cells = cells(hmesh)
# coarse) since a cell might have been refinemened multiple times and the
# intermediate cells will not be present in the final mesh for direct # We use an extended mesh containing all cells and build functions on top
# prolongation of data # of that since prolongation across multiple levels becomes more convenient
# when having a single set of cells to index with `cell_refinements`.
extended_mesh = sub_mesh(hmesh, axes(hmesh.cells, 1)) extended_mesh = sub_mesh(hmesh, axes(hmesh.cells, 1))
# Final leaf mesh, reindexed.
new_mesh = sub_mesh(hmesh) new_mesh = sub_mesh(hmesh)
refined_cells = map(x -> first(x), cell_refinements) refined_cells = map(x -> first(x), cell_refinements)
# extended functions onto newly created cells # create extended functions on all cells of extended mesh
extended_fs = map(NamedTuple(fs)) do f extended_fs = map(fs) do f
space = FeSpace(extended_mesh, f.space.element, f.space.size) space = FeSpace(extended_mesh, f.space.element, f.space.size)
return FeFunction(space; f.name) return FeFunction(space; f.name)
end end
# copy over previous data for unmodified cells # copy over data for unmodified cells
for (f, extended_f) in zip(NamedTuple(fs), extended_fs) for (cell, h_cell) in enumerate(hmesh_old_leaf_cells)
copyto!(extended_f.data, f.data) for (ext_f, f) in zip(extended_fs, fs)
gdofs = f.space.dofmap[:, :, cell]
ext_gdofs = ext_f.space.dofmap[:, :, h_cell]
ext_f.data[ext_gdofs] .= f.data[gdofs]
end
end end
# prolong data for refined cells # prolong data for refined cells
# TODO: use hmesh.children instead of `cell_refinements`.
for (old_cell, extended_cells) in cell_refinements for (old_cell, extended_cells) in cell_refinements
for extended_f in extended_fs for extended_f in extended_fs
prolong!(extended_f, extended_f, old_cell, extended_cells) prolong!(extended_f, extended_f, old_cell, extended_cells)
end end
end end
# retain only non-refined cells # create final functions on the new leaf mesh
new_fs = map(NamedTuple(extended_fs)) do f new_fs = map(extended_fs) do f
space = FeSpace(new_mesh, f.space.element, f.space.size) space = FeSpace(new_mesh, f.space.element, f.space.size)
return FeFunction(space; f.name) return FeFunction(space; f.name)
end end
retained_cells = setdiff(cells(extended_mesh), refined_cells) # copy over all leaf cell data into newly indexed mesh
@assert(retained_cells == cells(hmesh)) for (new_cell, old_cell) in enumerate(hmesh_new_leaf_cells)
for (new_cell, old_cell) in enumerate(retained_cells)
for (f, new_f) in zip(extended_fs, new_fs) for (f, new_f) in zip(extended_fs, new_fs)
gdofs = f.space.dofmap[:, :, old_cell] gdofs = f.space.dofmap[:, :, old_cell]
new_gdofs = new_f.space.dofmap[:, :, new_cell] new_gdofs = new_f.space.dofmap[:, :, new_cell]
new_f.data[new_gdofs] .= f.data[gdofs] new_f.data[new_gdofs] .= f.data[gdofs]
end end
end end
return new_mesh, new_fs return new_mesh, new_fs
end end
...@@ -314,6 +341,47 @@ function refine(mesh::Mesh, marked_cells; fs...) ...@@ -314,6 +341,47 @@ function refine(mesh::Mesh, marked_cells; fs...)
return refine!(hmesh, Set(marked_cells); fs...) return refine!(hmesh, Set(marked_cells); fs...)
end end
"""
Coarsen functions to a new coarse mesh.
Assumptions:
- `hmesh` contains the coarse mesh with the given cell indices,
- The meshes of `fs...` are exactly the finest level of `hmesh`.
"""
function coarsen(hmesh::HMesh, hmesh_coarse_cells; fs...)
fs = NamedTuple(fs)
coarse_mesh = sub_mesh(hmesh, hmesh_coarse_cells)
hmesh_fine_cells = cells(hmesh)
coarse_fs = map(fs) do f
@assert length(cells(f.space.mesh)) == count(==(0), hmesh.levels)
space = FeSpace(coarse_mesh, f.space.element, f.space.size)
return FeFunction(space; f.name)
end
function coarse_dofs(hcell, f)
if hmesh.levels[hcell] == 0
# reverse cell index map
fine_cell = findfirst(==(hcell), hmesh_fine_cells)
@assert f.space.element isa DP0 "only DP0 implemented"
gdofs = f.space.dofmap[:, 1, fine_cell]
return f.data[gdofs]
else
return sum(coarse_dofs(subhcell, f) for subhcell in hmesh.children[hcell]) / length(hmesh.children[hcell])
end
end
for coarse_cell in cells(coarse_mesh)
for (f, coarse_f) in zip(fs, coarse_fs)
# need to map to `hmesh` indexing
coarse_gdofs = coarse_f.space.dofmap[:, 1, coarse_cell]
coarse_f.data[coarse_gdofs] .= coarse_dofs(hmesh_coarse_cells[coarse_cell], f)
end
end
return coarse_mesh, coarse_fs
end
function geo_tolocal(A, v) function geo_tolocal(A, v)
J = jacobian(x -> A * [1 - x[1] - x[2], x[1], x[2]], [0., 0.]) J = jacobian(x -> A * [1 - x[1] - x[2], x[1], x[2]], [0., 0.])
return J \ (v - A[:, 1]) return J \ (v - A[:, 1])
......
test/Manifest.toml
View file @ fdcc7ea5
# This file is machine-generated - editing it directly is not advised # This file is machine-generated - editing it directly is not advised
julia_version = "1.7.0" julia_version = "1.10.5"
manifest_format = "2.0" manifest_format = "2.0"
project_hash = "a87db4a96b9f8108c69768cc4f6470d5533e4e6e"
[[deps.Base64]] [[deps.Base64]]
uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
...@@ -18,11 +19,12 @@ deps = ["Base64"] ...@@ -18,11 +19,12 @@ deps = ["Base64"]
uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
[[deps.Random]] [[deps.Random]]
deps = ["SHA", "Serialization"] deps = ["SHA"]
uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
[[deps.SHA]] [[deps.SHA]]
uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
version = "0.7.0"
[[deps.Serialization]] [[deps.Serialization]]
uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
......
test/runtests.jl
View file @ fdcc7ea5
...@@ -53,23 +53,38 @@ end ...@@ -53,23 +53,38 @@ end
@test img == img_sampled @test img == img_sampled
end end
@testset "mesh refinement" begin @testset "hierarchical mesh" begin
# simple hashing # simple hashing
val(f) = integrate(f.space.mesh, (x; f) -> sum(f .* f); f) val(f) = integrate(f.space.mesh, (x; f) -> sum(f .* f); f)
mesh = init_grid(zeros(5, 5)) mesh = init_grid(zeros(5, 5))
hmesh = HMesh(mesh)
f = FeFunction(FeSpace(mesh, P1(), (2, 3))) f = FeFunction(FeSpace(mesh, DP0(), (2, 3)))
f.data .= rand(size(f.data)...) f.data .= rand(size(f.data)...)
for i = 1:2 hmesh_cells_per_refinement = Vector{Int}[]
# refine roughly half of all cells n = 5
cells_ref = Set(findall(_ -> rand(Bool), cells(mesh)))
mesh_new, (f_new,) = refine(mesh, cells_ref; f) @testset "refinement $i" for i in 1:n
push!(hmesh_cells_per_refinement, cells(hmesh))
# Random set of cells on the finest level.
cells_ref = Set(filter(_ -> rand(Bool), cells(hmesh)))
mesh_new, (f_new,) = refine!(hmesh, cells_ref; f)
@test isapprox(val(f), val(f_new)) @test all(isnothing, hmesh.children[iszero.(hmesh.levels)])
@test all(!isnothing, hmesh.children[hmesh.levels .> 0])
@test isapprox(val(f_new), val(f))
(mesh, f) = (mesh_new, f_new) (mesh, f) = (mesh_new, f_new)
end end
@testset "coarsening" for i in n:-1:1
(mesh_coarse, (f_coarse,)) = coarsen(hmesh, hmesh_cells_per_refinement[i]; f)
@test isapprox(val(f_coarse), val(f))
#(mesh, f) = (mesh_coarse, f_coarse)
end
end end