Finished the 3d plot topology for images, added contour plots for images, added algebra, fixed image vertical flipping, experimental changes for a faster first boot

Manifest.toml

@@ -2,7 +2,7 @@
 
 julia_version = "1.11.2"
 manifest_format = "2.0"
-project_hash = "72412ae0f64cc39a16afe23fa1712ccaec97db17"
+project_hash = "d3959b0c3a38b987e17c2e3e73afbe28669615d7"
 
 [[deps.AbstractFFTs]]
 deps = ["LinearAlgebra"]
@@ -57,6 +57,44 @@ version = "1.2.0"
 uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
 version = "1.1.2"
 
+[[deps.ArnoldiMethod]]
+deps = ["LinearAlgebra", "Random", "StaticArrays"]
+git-tree-sha1 = "d57bd3762d308bded22c3b82d033bff85f6195c6"
+uuid = "ec485272-7323-5ecc-a04f-4719b315124d"
+version = "0.4.0"
+
+[[deps.ArrayInterface]]
+deps = ["Adapt", "LinearAlgebra"]
+git-tree-sha1 = "017fcb757f8e921fb44ee063a7aafe5f89b86dd1"
+uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
+version = "7.18.0"
+
+    [deps.ArrayInterface.extensions]
+    ArrayInterfaceBandedMatricesExt = "BandedMatrices"
+    ArrayInterfaceBlockBandedMatricesExt = "BlockBandedMatrices"
+    ArrayInterfaceCUDAExt = "CUDA"
+    ArrayInterfaceCUDSSExt = "CUDSS"
+    ArrayInterfaceChainRulesCoreExt = "ChainRulesCore"
+    ArrayInterfaceChainRulesExt = "ChainRules"
+    ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore"
+    ArrayInterfaceReverseDiffExt = "ReverseDiff"
+    ArrayInterfaceSparseArraysExt = "SparseArrays"
+    ArrayInterfaceStaticArraysCoreExt = "StaticArraysCore"
+    ArrayInterfaceTrackerExt = "Tracker"
+
+    [deps.ArrayInterface.weakdeps]
+    BandedMatrices = "aae01518-5342-5314-be14-df237901396f"
+    BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0"
+    CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
+    CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e"
+    ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2"
+    ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
+    GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527"
+    ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
+    SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+    StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c"
+    Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c"
+
 [[deps.Artifacts]]
 uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
 version = "1.11.0"
@@ -88,6 +126,12 @@ git-tree-sha1 = "0691e34b3bb8be9307330f88d1a3c3f25466c24d"
 uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35"
 version = "0.1.9"
 
+[[deps.BitTwiddlingConvenienceFunctions]]
+deps = ["Static"]
+git-tree-sha1 = "f21cfd4950cb9f0587d5067e69405ad2acd27b87"
+uuid = "62783981-4cbd-42fc-bca8-16325de8dc4b"
+version = "0.1.6"
+
 [[deps.BufferedStreams]]
 git-tree-sha1 = "6863c5b7fc997eadcabdbaf6c5f201dc30032643"
 uuid = "e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d"
@@ -104,6 +148,12 @@ git-tree-sha1 = "389ad5c84de1ae7cf0e28e381131c98ea87d54fc"
 uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82"
 version = "0.5.0"
 
+[[deps.CPUSummary]]
+deps = ["CpuId", "IfElse", "PrecompileTools", "Static"]
+git-tree-sha1 = "5a97e67919535d6841172016c9530fd69494e5ec"
+uuid = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9"
+version = "0.2.6"
+
 [[deps.CRC32c]]
 uuid = "8bf52ea8-c179-5cab-976a-9e18b702a9bc"
 version = "1.11.0"
@@ -128,9 +178,9 @@ version = "1.1.1"
 
 [[deps.CairoMakie]]
 deps = ["CRC32c", "Cairo", "Cairo_jll", "Colors", "FileIO", "FreeType", "GeometryBasics", "LinearAlgebra", "Makie", "PrecompileTools"]
-git-tree-sha1 = "0afa2b4ac444b9412130d68493941e1af462e26a"
+git-tree-sha1 = "77bc0964dd77811630e6c3329536a86b3b965cba"
 uuid = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
-version = "0.12.18"
+version = "0.13.0"
 
 [[deps.Cairo_jll]]
 deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"]
@@ -138,6 +188,12 @@ git-tree-sha1 = "009060c9a6168704143100f36ab08f06c2af4642"
 uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a"
 version = "1.18.2+1"
 
+[[deps.CatIndices]]
+deps = ["CustomUnitRanges", "OffsetArrays"]
+git-tree-sha1 = "a0f80a09780eed9b1d106a1bf62041c2efc995bc"
+uuid = "aafaddc9-749c-510e-ac4f-586e18779b91"
+version = "0.2.2"
+
 [[deps.ChainRulesCore]]
 deps = ["Compat", "LinearAlgebra"]
 git-tree-sha1 = "1713c74e00545bfe14605d2a2be1712de8fbcb58"
@@ -148,6 +204,18 @@ weakdeps = ["SparseArrays"]
     [deps.ChainRulesCore.extensions]
     ChainRulesCoreSparseArraysExt = "SparseArrays"
 
+[[deps.CloseOpenIntervals]]
+deps = ["Static", "StaticArrayInterface"]
+git-tree-sha1 = "05ba0d07cd4fd8b7a39541e31a7b0254704ea581"
+uuid = "fb6a15b2-703c-40df-9091-08a04967cfa9"
+version = "0.1.13"
+
+[[deps.Clustering]]
+deps = ["Distances", "LinearAlgebra", "NearestNeighbors", "Printf", "Random", "SparseArrays", "Statistics", "StatsBase"]
+git-tree-sha1 = "3e22db924e2945282e70c33b75d4dde8bfa44c94"
+uuid = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5"
+version = "0.15.8"
+
 [[deps.CodeTracking]]
 deps = ["InteractiveUtils", "UUIDs"]
 git-tree-sha1 = "7eee164f122511d3e4e1ebadb7956939ea7e1c77"
@@ -200,6 +268,11 @@ git-tree-sha1 = "3faae67b8899797592335832fccf4b3c80bb04fa"
 uuid = "a80b9123-70ca-4bc0-993e-6e3bcb318db6"
 version = "0.8.15"
 
+[[deps.CommonWorldInvalidations]]
+git-tree-sha1 = "ae52d1c52048455e85a387fbee9be553ec2b68d0"
+uuid = "f70d9fcc-98c5-4d4a-abd7-e4cdeebd8ca8"
+version = "1.0.0"
+
 [[deps.Compat]]
 deps = ["TOML", "UUIDs"]
 git-tree-sha1 = "8ae8d32e09f0dcf42a36b90d4e17f5dd2e4c4215"
@@ -215,6 +288,11 @@ deps = ["Artifacts", "Libdl"]
 uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
 version = "1.1.1+0"
 
+[[deps.ComputationalResources]]
+git-tree-sha1 = "52cb3ec90e8a8bea0e62e275ba577ad0f74821f7"
+uuid = "ed09eef8-17a6-5b46-8889-db040fac31e3"
+version = "0.3.2"
+
 [[deps.ConcurrentUtilities]]
 deps = ["Serialization", "Sockets"]
 git-tree-sha1 = "f36e5e8fdffcb5646ea5da81495a5a7566005127"
@@ -249,11 +327,28 @@ git-tree-sha1 = "439e35b0b36e2e5881738abc8857bd92ad6ff9a8"
 uuid = "d38c429a-6771-53c6-b99e-75d170b6e991"
 version = "0.6.3"
 
+[[deps.CoordinateTransformations]]
+deps = ["LinearAlgebra", "StaticArrays"]
+git-tree-sha1 = "f9d7112bfff8a19a3a4ea4e03a8e6a91fe8456bf"
+uuid = "150eb455-5306-5404-9cee-2592286d6298"
+version = "0.6.3"
+
+[[deps.CpuId]]
+deps = ["Markdown"]
+git-tree-sha1 = "fcbb72b032692610bfbdb15018ac16a36cf2e406"
+uuid = "adafc99b-e345-5852-983c-f28acb93d879"
+version = "0.3.1"
+
 [[deps.Crayons]]
 git-tree-sha1 = "249fe38abf76d48563e2f4556bebd215aa317e15"
 uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f"
 version = "4.1.1"
 
+[[deps.CustomUnitRanges]]
+git-tree-sha1 = "1a3f97f907e6dd8983b744d2642651bb162a3f7a"
+uuid = "dc8bdbbb-1ca9-579f-8c36-e416f6a65cce"
+version = "1.0.2"
+
 [[deps.DataAPI]]
 git-tree-sha1 = "abe83f3a2f1b857aac70ef8b269080af17764bbe"
 uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
@@ -299,6 +394,17 @@ git-tree-sha1 = "9e2f36d3c96a820c678f2f1f1782582fcf685bae"
 uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 version = "1.9.1"
 
+[[deps.Distances]]
+deps = ["LinearAlgebra", "Statistics", "StatsAPI"]
+git-tree-sha1 = "c7e3a542b999843086e2f29dac96a618c105be1d"
+uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
+version = "0.10.12"
+weakdeps = ["ChainRulesCore", "SparseArrays"]
+
+    [deps.Distances.extensions]
+    DistancesChainRulesCoreExt = "ChainRulesCore"
+    DistancesSparseArraysExt = "SparseArrays"
+
 [[deps.Distributed]]
 deps = ["Random", "Serialization", "Sockets"]
 uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
@@ -405,6 +511,12 @@ git-tree-sha1 = "74faea50c1d007c85837327f6775bea60b5492dd"
 uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5"
 version = "4.4.2+2"
 
+[[deps.FFTViews]]
+deps = ["CustomUnitRanges", "FFTW"]
+git-tree-sha1 = "cbdf14d1e8c7c8aacbe8b19862e0179fd08321c2"
+uuid = "4f61f5a4-77b1-5117-aa51-3ab5ef4ef0cd"
+version = "0.3.2"
+
 [[deps.FFTW]]
 deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"]
 git-tree-sha1 = "4820348781ae578893311153d69049a93d05f39d"
@@ -524,16 +636,16 @@ uuid = "781609d7-10c4-51f6-84f2-b8444358ff6d"
 version = "6.3.0+0"
 
 [[deps.GR]]
-deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Preferences", "Printf", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "p7zip_jll"]
+deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Preferences", "Printf", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "UUIDs", "p7zip_jll"]
-git-tree-sha1 = "ddda044ca260ee324c5fc07edb6d7cf3f0b9c350"
+git-tree-sha1 = "8e2d86e06ceb4580110d9e716be26658effc5bfd"
 uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71"
-version = "0.73.5"
+version = "0.72.8"
 
 [[deps.GR_jll]]
-deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "FreeType2_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Qt6Base_jll", "Zlib_jll", "libpng_jll"]
+deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Qt5Base_jll", "Zlib_jll", "libpng_jll"]
-git-tree-sha1 = "278e5e0f820178e8a26df3184fcb2280717c79b1"
+git-tree-sha1 = "da121cbdc95b065da07fbb93638367737969693f"
 uuid = "d2c73de3-f751-5644-a686-071e5b155ba9"
-version = "0.73.5+0"
+version = "0.72.8+0"
 
 [[deps.GarishPrint]]
 deps = ["Configurations", "Preferences"]
@@ -595,10 +707,10 @@ uuid = "cf35fbd7-0cd7-5166-be24-54bfbe79505f"
 version = "1.4.0"
 
 [[deps.GeometryBasics]]
-deps = ["EarCut_jll", "Extents", "GeoInterface", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"]
+deps = ["EarCut_jll", "Extents", "GeoInterface", "IterTools", "LinearAlgebra", "PrecompileTools", "Random", "StaticArrays"]
-git-tree-sha1 = "b62f2b2d76cee0d61a2ef2b3118cd2a3215d3134"
+git-tree-sha1 = "c1a9c159c3ac53aa09663d8662c7277ef3fa508d"
 uuid = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
-version = "0.4.11"
+version = "0.5.1"
 
 [[deps.Gettext_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"]
@@ -606,6 +718,12 @@ git-tree-sha1 = "9b02998aba7bf074d14de89f9d37ca24a1a0b046"
 uuid = "78b55507-aeef-58d4-861c-77aaff3498b1"
 version = "0.21.0+0"
 
+[[deps.Ghostscript_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "43ba3d3c82c18d88471cfd2924931658838c9d8f"
+uuid = "61579ee1-b43e-5ca0-a5da-69d92c66a64b"
+version = "9.55.0+4"
+
 [[deps.Giflib_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
 git-tree-sha1 = "6570366d757b50fabae9f4315ad74d2e40c0560a"
@@ -635,6 +753,12 @@ git-tree-sha1 = "01979f9b37367603e2848ea225918a3b3861b606"
 uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472"
 version = "1.3.14+1"
 
+[[deps.Graphs]]
+deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"]
+git-tree-sha1 = "1dc470db8b1131cfc7fb4c115de89fe391b9e780"
+uuid = "86223c79-3864-5bf0-83f7-82e725a168b6"
+version = "1.12.0"
+
 [[deps.GridLayoutBase]]
 deps = ["GeometryBasics", "InteractiveUtils", "Observables"]
 git-tree-sha1 = "dc6bed05c15523624909b3953686c5f5ffa10adc"
@@ -658,6 +782,18 @@ git-tree-sha1 = "55c53be97790242c29031e5cd45e8ac296dadda3"
 uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566"
 version = "8.5.0+0"
 
+[[deps.HistogramThresholding]]
+deps = ["ImageBase", "LinearAlgebra", "MappedArrays"]
+git-tree-sha1 = "7194dfbb2f8d945abdaf68fa9480a965d6661e69"
+uuid = "2c695a8d-9458-5d45-9878-1b8a99cf7853"
+version = "0.3.1"
+
+[[deps.HostCPUFeatures]]
+deps = ["BitTwiddlingConvenienceFunctions", "IfElse", "Libdl", "Static"]
+git-tree-sha1 = "8e070b599339d622e9a081d17230d74a5c473293"
+uuid = "3e5b6fbb-0976-4d2c-9146-d79de83f2fb0"
+version = "0.1.17"
+
 [[deps.HttpCommon]]
 deps = ["Dates", "Nullables", "Test", "URIParser"]
 git-tree-sha1 = "46313284237aa6ca67a6bce6d6fbd323d19cff59"
@@ -676,6 +812,11 @@ git-tree-sha1 = "7134810b1afce04bbc1045ca1985fbe81ce17653"
 uuid = "ac1192a8-f4b3-4bfe-ba22-af5b92cd3ab2"
 version = "0.9.5"
 
+[[deps.IfElse]]
+git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1"
+uuid = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173"
+version = "0.1.1"
+
 [[deps.ImageAxes]]
 deps = ["AxisArrays", "ImageBase", "ImageCore", "Reexport", "SimpleTraits"]
 git-tree-sha1 = "e12629406c6c4442539436581041d372d69c55ba"
@@ -688,24 +829,102 @@ git-tree-sha1 = "eb49b82c172811fd2c86759fa0553a2221feb909"
 uuid = "c817782e-172a-44cc-b673-b171935fbb9e"
 version = "0.1.7"
 
+[[deps.ImageBinarization]]
+deps = ["HistogramThresholding", "ImageCore", "LinearAlgebra", "Polynomials", "Reexport", "Statistics"]
+git-tree-sha1 = "33485b4e40d1df46c806498c73ea32dc17475c59"
+uuid = "cbc4b850-ae4b-5111-9e64-df94c024a13d"
+version = "0.3.1"
+
+[[deps.ImageContrastAdjustment]]
+deps = ["ImageBase", "ImageCore", "ImageTransformations", "Parameters"]
+git-tree-sha1 = "eb3d4365a10e3f3ecb3b115e9d12db131d28a386"
+uuid = "f332f351-ec65-5f6a-b3d1-319c6670881a"
+version = "0.3.12"
+
 [[deps.ImageCore]]
 deps = ["ColorVectorSpace", "Colors", "FixedPointNumbers", "MappedArrays", "MosaicViews", "OffsetArrays", "PaddedViews", "PrecompileTools", "Reexport"]
 git-tree-sha1 = "8c193230235bbcee22c8066b0374f63b5683c2d3"
 uuid = "a09fc81d-aa75-5fe9-8630-4744c3626534"
 version = "0.10.5"
 
+[[deps.ImageCorners]]
+deps = ["ImageCore", "ImageFiltering", "PrecompileTools", "StaticArrays", "StatsBase"]
+git-tree-sha1 = "24c52de051293745a9bad7d73497708954562b79"
+uuid = "89d5987c-236e-4e32-acd0-25bd6bd87b70"
+version = "0.1.3"
+
+[[deps.ImageDistances]]
+deps = ["Distances", "ImageCore", "ImageMorphology", "LinearAlgebra", "Statistics"]
+git-tree-sha1 = "08b0e6354b21ef5dd5e49026028e41831401aca8"
+uuid = "51556ac3-7006-55f5-8cb3-34580c88182d"
+version = "0.2.17"
+
+[[deps.ImageFiltering]]
+deps = ["CatIndices", "ComputationalResources", "DataStructures", "FFTViews", "FFTW", "ImageBase", "ImageCore", "LinearAlgebra", "OffsetArrays", "PrecompileTools", "Reexport", "SparseArrays", "StaticArrays", "Statistics", "TiledIteration"]
+git-tree-sha1 = "33cb509839cc4011beb45bde2316e64344b0f92b"
+uuid = "6a3955dd-da59-5b1f-98d4-e7296123deb5"
+version = "0.7.9"
+
 [[deps.ImageIO]]
 deps = ["FileIO", "IndirectArrays", "JpegTurbo", "LazyModules", "Netpbm", "OpenEXR", "PNGFiles", "QOI", "Sixel", "TiffImages", "UUIDs", "WebP"]
 git-tree-sha1 = "696144904b76e1ca433b886b4e7edd067d76cbf7"
 uuid = "82e4d734-157c-48bb-816b-45c225c6df19"
 version = "0.6.9"
 
+[[deps.ImageMagick]]
+deps = ["FileIO", "ImageCore", "ImageMagick_jll", "InteractiveUtils"]
+git-tree-sha1 = "c5c5478ae8d944c63d6de961b19e6d3324812c35"
+uuid = "6218d12a-5da1-5696-b52f-db25d2ecc6d1"
+version = "1.4.0"
+
+[[deps.ImageMagick_jll]]
+deps = ["Artifacts", "Ghostscript_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "OpenJpeg_jll", "Zlib_jll", "libpng_jll"]
+git-tree-sha1 = "fa01c98985be12e5d75301c4527fff2c46fa3e0e"
+uuid = "c73af94c-d91f-53ed-93a7-00f77d67a9d7"
+version = "7.1.1+1"
+
 [[deps.ImageMetadata]]
 deps = ["AxisArrays", "ImageAxes", "ImageBase", "ImageCore"]
 git-tree-sha1 = "2a81c3897be6fbcde0802a0ebe6796d0562f63ec"
 uuid = "bc367c6b-8a6b-528e-b4bd-a4b897500b49"
 version = "0.9.10"
 
+[[deps.ImageMorphology]]
+deps = ["DataStructures", "ImageCore", "LinearAlgebra", "LoopVectorization", "OffsetArrays", "Requires", "TiledIteration"]
+git-tree-sha1 = "6f0a801136cb9c229aebea0df296cdcd471dbcd1"
+uuid = "787d08f9-d448-5407-9aad-5290dd7ab264"
+version = "0.4.5"
+
+[[deps.ImageQualityIndexes]]
+deps = ["ImageContrastAdjustment", "ImageCore", "ImageDistances", "ImageFiltering", "LazyModules", "OffsetArrays", "PrecompileTools", "Statistics"]
+git-tree-sha1 = "783b70725ed326340adf225be4889906c96b8fd1"
+uuid = "2996bd0c-7a13-11e9-2da2-2f5ce47296a9"
+version = "0.3.7"
+
+[[deps.ImageSegmentation]]
+deps = ["Clustering", "DataStructures", "Distances", "Graphs", "ImageCore", "ImageFiltering", "ImageMorphology", "LinearAlgebra", "MetaGraphs", "RegionTrees", "SimpleWeightedGraphs", "StaticArrays", "Statistics"]
+git-tree-sha1 = "b217d9ded4a95052ffc09acc41ab781f7f72c7ba"
+uuid = "80713f31-8817-5129-9cf8-209ff8fb23e1"
+version = "1.8.3"
+
+[[deps.ImageShow]]
+deps = ["Base64", "ColorSchemes", "FileIO", "ImageBase", "ImageCore", "OffsetArrays", "StackViews"]
+git-tree-sha1 = "3b5344bcdbdc11ad58f3b1956709b5b9345355de"
+uuid = "4e3cecfd-b093-5904-9786-8bbb286a6a31"
+version = "0.3.8"
+
+[[deps.ImageTransformations]]
+deps = ["AxisAlgorithms", "CoordinateTransformations", "ImageBase", "ImageCore", "Interpolations", "OffsetArrays", "Rotations", "StaticArrays"]
+git-tree-sha1 = "e0884bdf01bbbb111aea77c348368a86fb4b5ab6"
+uuid = "02fcd773-0e25-5acc-982a-7f6622650795"
+version = "0.10.1"
+
+[[deps.Images]]
+deps = ["Base64", "FileIO", "Graphics", "ImageAxes", "ImageBase", "ImageBinarization", "ImageContrastAdjustment", "ImageCore", "ImageCorners", "ImageDistances", "ImageFiltering", "ImageIO", "ImageMagick", "ImageMetadata", "ImageMorphology", "ImageQualityIndexes", "ImageSegmentation", "ImageShow", "ImageTransformations", "IndirectArrays", "IntegralArrays", "Random", "Reexport", "SparseArrays", "StaticArrays", "Statistics", "StatsBase", "TiledIteration"]
+git-tree-sha1 = "12fdd617c7fe25dc4a6cc804d657cc4b2230302b"
+uuid = "916415d5-f1e6-5110-898d-aaa5f9f070e0"
+version = "0.26.1"
+
 [[deps.Imath_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
 git-tree-sha1 = "0936ba688c6d201805a83da835b55c61a180db52"
@@ -741,6 +960,12 @@ version = "1.4.2"
     ArrowTypes = "31f734f8-188a-4ce0-8406-c8a06bd891cd"
     Parsers = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
 
+[[deps.IntegralArrays]]
+deps = ["ColorTypes", "FixedPointNumbers", "IntervalSets"]
+git-tree-sha1 = "b842cbff3f44804a84fda409745cc8f04c029a20"
+uuid = "1d092043-8f09-5a30-832f-7509e371ab51"
+version = "0.1.6"
+
 [[deps.IntelOpenMP_jll]]
 deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl"]
 git-tree-sha1 = "10bd689145d2c3b2a9844005d01087cc1194e79e"
@@ -827,6 +1052,12 @@ git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856"
 uuid = "82899510-4779-5014-852e-03e436cf321d"
 version = "1.0.0"
 
+[[deps.JLD2]]
+deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "PrecompileTools", "Requires", "TranscodingStreams"]
+git-tree-sha1 = "91d501cb908df6f134352ad73cde5efc50138279"
+uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
+version = "0.5.11"
+
 [[deps.JLFzf]]
 deps = ["Pipe", "REPL", "Random", "fzf_jll"]
 git-tree-sha1 = "71b48d857e86bf7a1838c4736545699974ce79a2"
@@ -932,6 +1163,12 @@ version = "0.16.5"
     SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
     SymEngine = "123dc426-2d89-5057-bbad-38513e3affd8"
 
+[[deps.LayoutPointers]]
+deps = ["ArrayInterface", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface"]
+git-tree-sha1 = "a9eaadb366f5493a5654e843864c13d8b107548c"
+uuid = "10f19ff3-798f-405d-979b-55457f8fc047"
+version = "0.1.17"
+
 [[deps.LazilyInitializedFields]]
 git-tree-sha1 = "0f2da712350b020bc3957f269c9caad516383ee0"
 uuid = "0e77f7df-68c5-4e49-93ce-4cd80f5598bf"
@@ -1013,10 +1250,10 @@ uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9"
 version = "2.40.3+0"
 
 [[deps.Libtiff_jll]]
-deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"]
+deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "Pkg", "Zlib_jll", "Zstd_jll"]
-git-tree-sha1 = "2da088d113af58221c52828a80378e16be7d037a"
+git-tree-sha1 = "3eb79b0ca5764d4799c06699573fd8f533259713"
 uuid = "89763e89-9b03-5906-acba-b20f662cd828"
-version = "4.5.1+1"
+version = "4.4.0+0"
 
 [[deps.Libuuid_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
@@ -1035,6 +1272,12 @@ deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"]
 uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 version = "1.11.0"
 
+[[deps.LittleCMS_jll]]
+deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pkg"]
+git-tree-sha1 = "110897e7db2d6836be22c18bffd9422218ee6284"
+uuid = "d3a379c0-f9a3-5b72-a4c0-6bf4d2e8af0f"
+version = "2.12.0+0"
+
 [[deps.LogExpFunctions]]
 deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"]
 git-tree-sha1 = "13ca9e2586b89836fd20cccf56e57e2b9ae7f38f"
@@ -1061,6 +1304,21 @@ git-tree-sha1 = "f02b56007b064fbfddb4c9cd60161b6dd0f40df3"
 uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36"
 version = "1.1.0"
 
+[[deps.LoopVectorization]]
+deps = ["ArrayInterface", "CPUSummary", "CloseOpenIntervals", "DocStringExtensions", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "PrecompileTools", "SIMDTypes", "SLEEFPirates", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"]
+git-tree-sha1 = "8084c25a250e00ae427a379a5b607e7aed96a2dd"
+uuid = "bdcacae8-1622-11e9-2a5c-532679323890"
+version = "0.12.171"
+
+    [deps.LoopVectorization.extensions]
+    ForwardDiffExt = ["ChainRulesCore", "ForwardDiff"]
+    SpecialFunctionsExt = "SpecialFunctions"
+
+    [deps.LoopVectorization.weakdeps]
+    ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
+    ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
+    SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
+
 [[deps.LoweredCodeUtils]]
 deps = ["JuliaInterpreter"]
 git-tree-sha1 = "688d6d9e098109051ae33d126fcfc88c4ce4a021"
@@ -1084,16 +1342,16 @@ uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
 version = "0.5.15"
 
 [[deps.Makie]]
-deps = ["Animations", "Base64", "CRC32c", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "Contour", "Dates", "DelaunayTriangulation", "Distributions", "DocStringExtensions", "Downloads", "FFMPEG_jll", "FileIO", "FilePaths", "FixedPointNumbers", "Format", "FreeType", "FreeTypeAbstraction", "GeometryBasics", "GridLayoutBase", "ImageBase", "ImageIO", "InteractiveUtils", "Interpolations", "IntervalSets", "InverseFunctions", "Isoband", "KernelDensity", "LaTeXStrings", "LinearAlgebra", "MacroTools", "MakieCore", "Markdown", "MathTeXEngine", "Observables", "OffsetArrays", "Packing", "PlotUtils", "PolygonOps", "PrecompileTools", "Printf", "REPL", "Random", "RelocatableFolders", "Scratch", "ShaderAbstractions", "Showoff", "SignedDistanceFields", "SparseArrays", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "TriplotBase", "UnicodeFun", "Unitful"]
+deps = ["Animations", "Base64", "CRC32c", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "Contour", "Dates", "DelaunayTriangulation", "Distributions", "DocStringExtensions", "Downloads", "FFMPEG_jll", "FileIO", "FilePaths", "FixedPointNumbers", "Format", "FreeType", "FreeTypeAbstraction", "GeometryBasics", "GridLayoutBase", "ImageBase", "ImageIO", "InteractiveUtils", "Interpolations", "IntervalSets", "InverseFunctions", "Isoband", "KernelDensity", "LaTeXStrings", "LinearAlgebra", "MacroTools", "MakieCore", "Markdown", "MathTeXEngine", "Observables", "OffsetArrays", "PNGFiles", "Packing", "PlotUtils", "PolygonOps", "PrecompileTools", "Printf", "REPL", "Random", "RelocatableFolders", "Scratch", "ShaderAbstractions", "Showoff", "SignedDistanceFields", "SparseArrays", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "TriplotBase", "UnicodeFun", "Unitful"]
-git-tree-sha1 = "be3051d08b78206fb5e688e8d70c9e84d0264117"
+git-tree-sha1 = "021b6b64b68f6ee09fb35a1528a2b5a7f48ac00c"
 uuid = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
-version = "0.21.18"
+version = "0.22.0"
 
 [[deps.MakieCore]]
 deps = ["ColorTypes", "GeometryBasics", "IntervalSets", "Observables"]
-git-tree-sha1 = "9019b391d7d086e841cbeadc13511224bd029ab3"
+git-tree-sha1 = "c731269d5a2c85ffdc689127a9ba6d73e978a4b1"
 uuid = "20f20a25-4f0e-4fdf-b5d1-57303727442b"
-version = "0.8.12"
+version = "0.9.0"
 
 [[deps.Malt]]
 deps = ["Distributed", "Logging", "RelocatableFolders", "Serialization", "Sockets"]
@@ -1101,6 +1359,11 @@ git-tree-sha1 = "02a728ada9d6caae583a0f87c1dd3844f99ec3fd"
 uuid = "36869731-bdee-424d-aa32-cab38c994e3b"
 version = "1.1.2"
 
+[[deps.ManualMemory]]
+git-tree-sha1 = "bcaef4fc7a0cfe2cba636d84cda54b5e4e4ca3cd"
+uuid = "d125e4d3-2237-4719-b19c-fa641b8a4667"
+version = "0.1.8"
+
 [[deps.MappedArrays]]
 git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e"
 uuid = "dbb5928d-eab1-5f90-85c2-b9b0edb7c900"
@@ -1133,6 +1396,12 @@ git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102"
 uuid = "442fdcdd-2543-5da2-b0f3-8c86c306513e"
 version = "0.3.2"
 
+[[deps.MetaGraphs]]
+deps = ["Graphs", "JLD2", "Random"]
+git-tree-sha1 = "e9650bea7f91c3397eb9ae6377343963a22bf5b8"
+uuid = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
+version = "0.8.0"
+
 [[deps.Millboard]]
 git-tree-sha1 = "ea6a5b7e56e76d8051023faaa11d91d1d881dac3"
 uuid = "39ec1447-df44-5f4c-beaa-866f30b4d3b2"
@@ -1181,6 +1450,12 @@ git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21"
 uuid = "c020b1a1-e9b0-503a-9c33-f039bfc54a85"
 version = "1.0.0"
 
+[[deps.NearestNeighbors]]
+deps = ["Distances", "StaticArrays"]
+git-tree-sha1 = "8a3271d8309285f4db73b4f662b1b290c715e85e"
+uuid = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
+version = "0.4.21"
+
 [[deps.Netpbm]]
 deps = ["FileIO", "ImageCore", "ImageMetadata"]
 git-tree-sha1 = "d92b107dbb887293622df7697a2223f9f8176fcd"
@@ -1245,6 +1520,12 @@ git-tree-sha1 = "8292dd5c8a38257111ada2174000a33745b06d4e"
 uuid = "18a262bb-aa17-5467-a713-aee519bc75cb"
 version = "3.2.4+0"
 
+[[deps.OpenJpeg_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Libtiff_jll", "LittleCMS_jll", "Pkg", "libpng_jll"]
+git-tree-sha1 = "76374b6e7f632c130e78100b166e5a48464256f8"
+uuid = "643b3616-a352-519d-856d-80112ee9badc"
+version = "2.4.0+0"
+
 [[deps.OpenLibm_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "05823500-19ac-5b8b-9628-191a04bc5112"
@@ -1378,9 +1659,9 @@ version = "0.8.19"
 
 [[deps.Plots]]
 deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "TOML", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"]
-git-tree-sha1 = "dae01f8c2e069a683d3a6e17bbae5070ab94786f"
+git-tree-sha1 = "f202a1ca4f6e165238d8175df63a7e26a51e04dc"
 uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
-version = "1.40.9"
+version = "1.40.7"
 
     [deps.Plots.extensions]
     FileIOExt = "FileIO"
@@ -1408,11 +1689,35 @@ git-tree-sha1 = "e0864c15334d2c4bac8137ce3359f1174565e719"
 uuid = "72656b73-756c-7461-726b-72656b6b696b"
 version = "1.2.0"
 
+[[deps.PolyesterWeave]]
+deps = ["BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "Static", "ThreadingUtilities"]
+git-tree-sha1 = "645bed98cd47f72f67316fd42fc47dee771aefcd"
+uuid = "1d0040c9-8b98-4ee7-8388-3f51789ca0ad"
+version = "0.2.2"
+
 [[deps.PolygonOps]]
 git-tree-sha1 = "77b3d3605fc1cd0b42d95eba87dfcd2bf67d5ff6"
 uuid = "647866c9-e3ac-4575-94e7-e3d426903924"
 version = "0.1.2"
 
+[[deps.Polynomials]]
+deps = ["LinearAlgebra", "OrderedCollections", "RecipesBase", "Requires", "Setfield", "SparseArrays"]
+git-tree-sha1 = "27f6107dc202e2499f0750c628a848ce5d6e77f5"
+uuid = "f27b6e38-b328-58d1-80ce-0feddd5e7a45"
+version = "4.0.13"
+
+    [deps.Polynomials.extensions]
+    PolynomialsChainRulesCoreExt = "ChainRulesCore"
+    PolynomialsFFTWExt = "FFTW"
+    PolynomialsMakieCoreExt = "MakieCore"
+    PolynomialsMutableArithmeticsExt = "MutableArithmetics"
+
+    [deps.Polynomials.weakdeps]
+    ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
+    FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
+    MakieCore = "20f20a25-4f0e-4fdf-b5d1-57303727442b"
+    MutableArithmetics = "d8a4904e-b15c-11e9-3269-09a3773c0cb0"
+
 [[deps.PooledArrays]]
 deps = ["DataAPI", "Future"]
 git-tree-sha1 = "36d8b4b899628fb92c2749eb488d884a926614d3"
@@ -1476,11 +1781,11 @@ git-tree-sha1 = "8b3fc30bc0390abdce15f8822c889f669baed73d"
 uuid = "4b34888f-f399-49d4-9bb3-47ed5cae4e65"
 version = "1.0.1"
 
-[[deps.Qt6Base_jll]]
+[[deps.Qt5Base_jll]]
-deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Vulkan_Loader_jll", "Xorg_libSM_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_cursor_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "libinput_jll", "xkbcommon_jll"]
+deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"]
-git-tree-sha1 = "7c29f0e8c575428bd84dc3c72ece5178caa67336"
+git-tree-sha1 = "0c03844e2231e12fda4d0086fd7cbe4098ee8dc5"
-uuid = "c0090381-4147-56d7-9ebc-da0b1113ec56"
+uuid = "ea2cea3b-5b76-57ae-a6ef-0a8af62496e1"
-version = "6.5.2+2"
+version = "5.15.3+2"
 
 [[deps.QuadGK]]
 deps = ["DataStructures", "LinearAlgebra"]
@@ -1494,6 +1799,12 @@ version = "2.11.1"
     [deps.QuadGK.weakdeps]
     Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9"
 
+[[deps.Quaternions]]
+deps = ["LinearAlgebra", "Random", "RealDot"]
+git-tree-sha1 = "994cc27cdacca10e68feb291673ec3a76aa2fae9"
+uuid = "94ee1d12-ae83-5a48-8b1c-48b8ff168ae0"
+version = "0.7.6"
+
 [[deps.REPL]]
 deps = ["InteractiveUtils", "Markdown", "Sockets", "StyledStrings", "Unicode"]
 uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
@@ -1519,6 +1830,12 @@ weakdeps = ["FixedPointNumbers"]
     [deps.Ratios.extensions]
     RatiosFixedPointNumbersExt = "FixedPointNumbers"
 
+[[deps.RealDot]]
+deps = ["LinearAlgebra"]
+git-tree-sha1 = "9f0a1b71baaf7650f4fa8a1d168c7fb6ee41f0c9"
+uuid = "c1ae055f-0cd5-4b69-90a6-9a35b1a98df9"
+version = "0.1.0"
+
 [[deps.RecipesBase]]
 deps = ["PrecompileTools"]
 git-tree-sha1 = "5c3d09cc4f31f5fc6af001c250bf1278733100ff"
@@ -1536,6 +1853,12 @@ git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b"
 uuid = "189a3867-3050-52da-a836-e630ba90ab69"
 version = "1.2.2"
 
+[[deps.RegionTrees]]
+deps = ["IterTools", "LinearAlgebra", "StaticArrays"]
+git-tree-sha1 = "4618ed0da7a251c7f92e869ae1a19c74a7d2a7f9"
+uuid = "dee08c22-ab7f-5625-9660-a9af2021b33f"
+version = "0.3.2"
+
 [[deps.RegistryInstances]]
 deps = ["LazilyInitializedFields", "Pkg", "TOML", "Tar"]
 git-tree-sha1 = "ffd19052caf598b8653b99404058fce14828be51"
@@ -1588,6 +1911,16 @@ git-tree-sha1 = "58cdd8fb2201a6267e1db87ff148dd6c1dbd8ad8"
 uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f"
 version = "0.5.1+0"
 
+[[deps.Rotations]]
+deps = ["LinearAlgebra", "Quaternions", "Random", "StaticArrays"]
+git-tree-sha1 = "5680a9276685d392c87407df00d57c9924d9f11e"
+uuid = "6038ab10-8711-5258-84ad-4b1120ba62dc"
+version = "1.7.1"
+weakdeps = ["RecipesBase"]
+
+    [deps.Rotations.extensions]
+    RotationsRecipesBaseExt = "RecipesBase"
+
 [[deps.RoundingEmulator]]
 git-tree-sha1 = "40b9edad2e5287e05bd413a38f61a8ff55b9557b"
 uuid = "5eaf0fd0-dfba-4ccb-bf02-d820a40db705"
@@ -1603,6 +1936,17 @@ git-tree-sha1 = "fea870727142270bdf7624ad675901a1ee3b4c87"
 uuid = "fdea26ae-647d-5447-a871-4b548cad5224"
 version = "3.7.1"
 
+[[deps.SIMDTypes]]
+git-tree-sha1 = "330289636fb8107c5f32088d2741e9fd7a061a5c"
+uuid = "94e857df-77ce-4151-89e5-788b33177be4"
+version = "0.1.0"
+
+[[deps.SLEEFPirates]]
+deps = ["IfElse", "Static", "VectorizationBase"]
+git-tree-sha1 = "456f610ca2fbd1c14f5fcf31c6bfadc55e7d66e0"
+uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa"
+version = "0.6.43"
+
 [[deps.Scratch]]
 deps = ["Dates"]
 git-tree-sha1 = "3bac05bc7e74a75fd9cba4295cde4045d9fe2386"
@@ -1619,11 +1963,17 @@ version = "1.4.8"
 uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 version = "1.11.0"
 
+[[deps.Setfield]]
+deps = ["ConstructionBase", "Future", "MacroTools", "StaticArraysCore"]
+git-tree-sha1 = "e2cc6d8c88613c05e1defb55170bf5ff211fbeac"
+uuid = "efcf1570-3423-57d1-acb7-fd33fddbac46"
+version = "1.1.1"
+
 [[deps.ShaderAbstractions]]
-deps = ["ColorTypes", "FixedPointNumbers", "GeometryBasics", "LinearAlgebra", "Observables", "StaticArrays", "StructArrays", "Tables"]
+deps = ["ColorTypes", "FixedPointNumbers", "GeometryBasics", "LinearAlgebra", "Observables", "StaticArrays"]
-git-tree-sha1 = "79123bc60c5507f035e6d1d9e563bb2971954ec8"
+git-tree-sha1 = "818554664a2e01fc3784becb2eb3a82326a604b6"
 uuid = "65257c39-d410-5151-9873-9b3e5be5013e"
-version = "0.4.1"
+version = "0.5.0"
 
 [[deps.SharedArrays]]
 deps = ["Distributed", "Mmap", "Random", "Serialization"]
@@ -1653,6 +2003,12 @@ git-tree-sha1 = "5d7e3f4e11935503d3ecaf7186eac40602e7d231"
 uuid = "699a6c99-e7fa-54fc-8d76-47d257e15c1d"
 version = "0.9.4"
 
+[[deps.SimpleWeightedGraphs]]
+deps = ["Graphs", "LinearAlgebra", "Markdown", "SparseArrays"]
+git-tree-sha1 = "4b33e0e081a825dbfaf314decf58fa47e53d6acb"
+uuid = "47aef6b3-ad0c-573a-a1e2-d07658019622"
+version = "1.4.0"
+
 [[deps.Sixel]]
 deps = ["Dates", "FileIO", "ImageCore", "IndirectArrays", "OffsetArrays", "REPL", "libsixel_jll"]
 git-tree-sha1 = "2da10356e31327c7096832eb9cd86307a50b1eb6"
@@ -1696,6 +2052,23 @@ git-tree-sha1 = "46e589465204cd0c08b4bd97385e4fa79a0c770c"
 uuid = "cae243ae-269e-4f55-b966-ac2d0dc13c15"
 version = "0.1.1"
 
+[[deps.Static]]
+deps = ["CommonWorldInvalidations", "IfElse", "PrecompileTools"]
+git-tree-sha1 = "87d51a3ee9a4b0d2fe054bdd3fc2436258db2603"
+uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3"
+version = "1.1.1"
+
+[[deps.StaticArrayInterface]]
+deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "PrecompileTools", "Static"]
+git-tree-sha1 = "96381d50f1ce85f2663584c8e886a6ca97e60554"
+uuid = "0d7ed370-da01-4f52-bd93-41d350b8b718"
+version = "1.8.0"
+weakdeps = ["OffsetArrays", "StaticArrays"]
+
+    [deps.StaticArrayInterface.extensions]
+    StaticArrayInterfaceOffsetArraysExt = "OffsetArrays"
+    StaticArrayInterfaceStaticArraysExt = "StaticArrays"
+
 [[deps.StaticArrays]]
 deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"]
 git-tree-sha1 = "47091a0340a675c738b1304b58161f3b0839d454"
@@ -1809,9 +2182,9 @@ version = "0.4.0"
 
 [[deps.StructArrays]]
 deps = ["ConstructionBase", "DataAPI", "Tables"]
-git-tree-sha1 = "9537ef82c42cdd8c5d443cbc359110cbb36bae10"
+git-tree-sha1 = "5a3a31c41e15a1e042d60f2f4942adccba05d3c9"
 uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a"
-version = "0.6.21"
+version = "0.7.0"
 
     [deps.StructArrays.extensions]
     StructArraysAdaptExt = "Adapt"
@@ -1885,12 +2258,24 @@ git-tree-sha1 = "43044b737fa70bc12f6105061d3da38f881a3e3c"
 uuid = "b718987f-49a8-5099-9789-dcd902bef87d"
 version = "1.0.2"
 
+[[deps.ThreadingUtilities]]
+deps = ["ManualMemory"]
+git-tree-sha1 = "eda08f7e9818eb53661b3deb74e3159460dfbc27"
+uuid = "8290d209-cae3-49c0-8002-c8c24d57dab5"
+version = "0.5.2"
+
 [[deps.TiffImages]]
 deps = ["ColorTypes", "DataStructures", "DocStringExtensions", "FileIO", "FixedPointNumbers", "IndirectArrays", "Inflate", "Mmap", "OffsetArrays", "PkgVersion", "ProgressMeter", "SIMD", "UUIDs"]
 git-tree-sha1 = "3c0faa42f2bd3c6d994b06286bba2328eae34027"
 uuid = "731e570b-9d59-4bfa-96dc-6df516fadf69"
 version = "0.11.2"
 
+[[deps.TiledIteration]]
+deps = ["OffsetArrays", "StaticArrayInterface"]
+git-tree-sha1 = "1176cc31e867217b06928e2f140c90bd1bc88283"
+uuid = "06e1c1a7-607b-532d-9fad-de7d9aa2abac"
+version = "0.5.0"
+
 [[deps.Tokenize]]
 git-tree-sha1 = "468b4685af4abe0e9fd4d7bf495a6554a6276e75"
 uuid = "0796e94c-ce3b-5d07-9a54-7f471281c624"
@@ -1964,17 +2349,17 @@ git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78"
 uuid = "41fe7b60-77ed-43a1-b4f0-825fd5a5650d"
 version = "0.2.0"
 
+[[deps.VectorizationBase]]
+deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static", "StaticArrayInterface"]
+git-tree-sha1 = "4ab62a49f1d8d9548a1c8d1a75e5f55cf196f64e"
+uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f"
+version = "0.21.71"
+
 [[deps.VersionParsing]]
 git-tree-sha1 = "58d6e80b4ee071f5efd07fda82cb9fbe17200868"
 uuid = "81def892-9a0e-5fdd-b105-ffc91e053289"
 version = "1.3.0"
 
-[[deps.Vulkan_Loader_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Wayland_jll", "Xorg_libX11_jll", "Xorg_libXrandr_jll", "xkbcommon_jll"]
-git-tree-sha1 = "2f0486047a07670caad3a81a075d2e518acc5c59"
-uuid = "a44049a8-05dd-5a78-86c9-5fde0876e88c"
-version = "1.3.243+0"
-
 [[deps.Wayland_jll]]
 deps = ["Artifacts", "EpollShim_jll", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"]
 git-tree-sha1 = "85c7811eddec9e7f22615371c3cc81a504c508ee"
@@ -2011,24 +2396,6 @@ git-tree-sha1 = "7d1671acbe47ac88e981868a078bd6b4e27c5191"
 uuid = "aed1982a-8fda-507f-9586-7b0439959a61"
 version = "1.1.42+0"
 
-[[deps.XZ_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "beef98d5aad604d9e7d60b2ece5181f7888e2fd6"
-uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800"
-version = "5.6.4+0"
-
-[[deps.Xorg_libICE_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "326b4fea307b0b39892b3e85fa451692eda8d46c"
-uuid = "f67eecfb-183a-506d-b269-f58e52b52d7c"
-version = "1.1.1+0"
-
-[[deps.Xorg_libSM_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libICE_jll"]
-git-tree-sha1 = "3796722887072218eabafb494a13c963209754ce"
-uuid = "c834827a-8449-5923-a945-d239c165b7dd"
-version = "1.2.4+0"
-
 [[deps.Xorg_libX11_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxcb_jll", "Xorg_xtrans_jll"]
 git-tree-sha1 = "9dafcee1d24c4f024e7edc92603cedba72118283"
@@ -2107,12 +2474,6 @@ git-tree-sha1 = "dbc53e4cf7701c6c7047c51e17d6e64df55dca94"
 uuid = "cc61e674-0454-545c-8b26-ed2c68acab7a"
 version = "1.1.2+1"
 
-[[deps.Xorg_xcb_util_cursor_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_jll", "Xorg_xcb_util_renderutil_jll"]
-git-tree-sha1 = "04341cb870f29dcd5e39055f895c39d016e18ccd"
-uuid = "e920d4aa-a673-5f3a-b3d7-f755a4d47c43"
-version = "0.1.4+0"
-
 [[deps.Xorg_xcb_util_image_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"]
 git-tree-sha1 = "0fab0a40349ba1cba2c1da699243396ff8e94b97"
@@ -2178,24 +2539,12 @@ git-tree-sha1 = "622cf78670d067c738667aaa96c553430b65e269"
 uuid = "3161d3a3-bdf6-5164-811a-617609db77b4"
 version = "1.5.7+0"
 
-[[deps.eudev_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "gperf_jll"]
-git-tree-sha1 = "431b678a28ebb559d224c0b6b6d01afce87c51ba"
-uuid = "35ca27e7-8b34-5b7f-bca9-bdc33f59eb06"
-version = "3.2.9+0"
-
 [[deps.fzf_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
 git-tree-sha1 = "6e50f145003024df4f5cb96c7fce79466741d601"
 uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09"
 version = "0.56.3+0"
 
-[[deps.gperf_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "0ba42241cb6809f1a278d0bcb976e0483c3f1f2d"
-uuid = "1a1c6b14-54f6-533d-8383-74cd7377aa70"
-version = "3.1.1+1"
-
 [[deps.isoband_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "51b5eeb3f98367157a7a12a1fb0aa5328946c03c"
@@ -2233,24 +2582,12 @@ git-tree-sha1 = "9bf7903af251d2050b467f76bdbe57ce541f7f4f"
 uuid = "1183f4f0-6f2a-5f1a-908b-139f9cdfea6f"
 version = "0.2.2+0"
 
-[[deps.libevdev_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "141fe65dc3efabb0b1d5ba74e91f6ad26f84cc22"
-uuid = "2db6ffa8-e38f-5e21-84af-90c45d0032cc"
-version = "1.11.0+0"
-
 [[deps.libfdk_aac_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
 git-tree-sha1 = "8a22cf860a7d27e4f3498a0fe0811a7957badb38"
 uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280"
 version = "2.0.3+0"
 
-[[deps.libinput_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "eudev_jll", "libevdev_jll", "mtdev_jll"]
-git-tree-sha1 = "ad50e5b90f222cfe78aa3d5183a20a12de1322ce"
-uuid = "36db933b-70db-51c0-b978-0f229ee0e533"
-version = "1.18.0+0"
-
 [[deps.libpng_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"]
 git-tree-sha1 = "d7b5bbf1efbafb5eca466700949625e07533aff2"
@@ -2275,12 +2612,6 @@ git-tree-sha1 = "ccbb625a89ec6195856a50aa2b668a5c08712c94"
 uuid = "c5f90fcd-3b7e-5836-afba-fc50a0988cb2"
 version = "1.4.0+0"
 
-[[deps.mtdev_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "814e154bdb7be91d78b6802843f76b6ece642f11"
-uuid = "009596ad-96f7-51b1-9f1b-5ce2d5e8a71e"
-version = "1.1.6+0"
-
 [[deps.nghttp2_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"

Project.toml

@@ -1,13 +1,11 @@
 [deps]
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
-Genie = "c43c736e-a2d1-11e8-161f-af95117fbd1e"
 GenieFramework = "a59fdf5c-6bf0-4f5d-949c-a137c9e2f353"
+Images = "916415d5-f1e6-5110-898d-aaa5f9f070e0"
 Libz = "2ec943e9-cfe8-584d-b93d-64dcb6d567b7"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 NaturalSort = "c020b1a1-e9b0-503a-9c33-f039bfc54a85"
 PlotlyBase = "a03496cd-edff-5a9b-9e67-9cda94a718b5"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 julia_mzML_imzML = "38eb50d3-2fb6-4afa-992a-964ed8562ed9"
-
-[Genie]
-instantiated_pwd = "/var/home/pixelguy14/Documentos/CINVESTAV_2025/Julia_msi_GUI"

app.jl

@@ -9,7 +9,8 @@ using Colors
 using julia_mzML_imzML
 using Statistics
 using NaturalSort
-# using ImageMagick
+using Images
+using LinearAlgebra
 @genietools
 
 # == Code import ==
@@ -19,6 +20,9 @@ rgb_ViridisPalette = reinterpret(ColorTypes.RGB24, ViridisPalette)
 
 # == Search functions ==
 function increment_image(current_image, image_list)
+    if isempty(image_list)
+        return nothing
+    end
     current_index = findfirst(isequal(current_image), image_list)
     if current_index == nothing || current_index == length(image_list) || current_image === ""
         return image_list[length(image_list)]  # Return the current image if it's the last one or not found
@@ -28,6 +32,9 @@ function increment_image(current_image, image_list)
 end
 
 function decrement_image(current_image, image_list)
+    if isempty(image_list)
+        return nothing
+    end
     current_index = findfirst(isequal(current_image), image_list)
     if current_index == nothing || current_index == 1 || current_image === ""
         return image_list[1]  # Return the current image if it's the first one or not found
@@ -65,6 +72,8 @@ end
     @in createSumPlot = false # To generate sum spectrum plot
     @in image3dPlot = false # To generate 3d plot based on current image
     @in triq3dPlot = false # To generate 3d plot based on current triq image
+    @in imageCPlot = false # To generate contour plots of current image
+    @in triqCPlot = false # To generate contour plots of current triq image
     @in progress = false
     @in progressPlot = false
     @in triqEnabled = false
@@ -133,7 +142,12 @@ end
         scene = attr(
             xaxis_title = "X",
             yaxis_title = "Y",
-            zaxis_title = "Z"
+            zaxis_title = "Z",
+            xaxis_nticks = 20, 
+            yaxis_nticks = 20, 
+            zaxis_nticks = 4, 
+            camera = attr(eye = attr(x = 0, y = -1, z = 0.5)), 
+            aspectratio = attr(x = 1, y = 1, z = 0.2)
         )
     )
 
@@ -141,7 +155,7 @@ end
     x = 1:10
     y = 1:10
     z = [sin(i * j / 10) for i in x, j in y]
-    trace3D = PlotlyBase.surface(x=x, y=y, z=z,
+    trace3D = PlotlyBase.surface(x=[], y=[], z=[],
                                 contours_z=attr(
                                     show=true,
                                     usecolormap=true,
@@ -157,15 +171,7 @@ end
     # == Reactive handlers ==
     # Reactive handlers watch a variable and execute a block of code when its value changes
     # The onbutton handler will set the variable to false after the block is executed
-    @onchange triqEnabled begin
-        # just in case that they remove an image manually, we use the least intensive button to get all images and re-order them.
-        msi_bmp = sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
-        col_msi_png = sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir("public")),lt=natural)
-        triq_bmp = sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
-        col_triq_png = sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir("public")),lt=natural)
-    end
     
-
     @onchange file_name begin
         msg = ""
         progress = false
@@ -219,7 +225,12 @@ end
                         msg = "Incorrect TrIQ values, please adjust accordingly and try again."
                         warning_msg = true
                     else
+                        image_path = joinpath("./public", "TrIQ_$(text_nmass).bmp")
                         SaveBitmap(joinpath("public", "TrIQ_$(text_nmass).bmp"),TrIQ(slice, Int(triqColor), triqProb),ViridisPalette)
+                        # Flip te image vertically then save it again
+                        img = load(image_path) 
+                        flipped_img = reverse(img, dims=1)
+                        save(image_path, flipped_img)
                         # Use timestamp to refresh image interface container
                         imgIntT = "/TrIQ_$(text_nmass).bmp?t=$(timestamp)"
                         # Get current image 
@@ -241,7 +252,12 @@ end
                         #println("all col msi in folder= ",col_triq_png)
                     end
                 else # If we don't use TrIQ
+                    image_path = joinpath("./public", "MSI_$(text_nmass).bmp")
                     SaveBitmap(joinpath("public", "MSI_$(text_nmass).bmp"),IntQuant(slice),ViridisPalette)
+                    # Flip te image vertically then save it again
+                    img = load(image_path) 
+                    flipped_img = reverse(img, dims=1)
+                    save(image_path, flipped_img)
                     # Use timestamp to refresh image interface container
                     imgInt = "/MSI_$(text_nmass).bmp?t=$(timestamp)"
                     # Get current image 
@@ -293,11 +309,23 @@ end
                 btnPlotDisable = true
                 msg = "Loading plot..."
                 spectraMz = LoadMzml(full_routeMz)
+                layoutSpectra = PlotlyBase.Layout(
+                    title = "SUM Spectrum plot",
+                    xaxis = PlotlyBase.attr(
+                        title = "<i>m/z</i>",
+                        showgrid = true
+                    ),
+                    yaxis = PlotlyBase.attr(
+                        title = "Intensity",
+                        showgrid = true
+                    )
+                )
                 # dims = size(spectraMz)
                 # scansMax = dims[2] # we get the total of scansMax
                 # traceSpectra = PlotlyBase.scatter(x = spectraMz[1, 1], y = spectraMz[2, 1], mode="lines")
                 traceSpectra = PlotlyBase.scatter(x = mean(spectraMz[1,:]), y = mean(spectraMz[2,:]), mode="lines")
                 plotdata = [traceSpectra] # We add the data from spectra to the plot
+                plotlayout = layoutSpectra
                 spectraMz = nothing # Important for memory cleaning
                 GC.gc() # Trigger garbage collection
                 if Sys.islinux()
@@ -319,6 +347,10 @@ end
     @onbutton ImgMinus begin
         # Append a query string to force the image to refresh 
         timestamp = string(time_ns()) 
+        # Update the array of images listed in the public folder
+        msi_bmp = sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
+        col_msi_png = sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir("public")),lt=natural)
+        
         new_msi = decrement_image(current_msi, msi_bmp)
         new_col_msi = decrement_image(current_col_msi, col_msi_png)
         
@@ -333,7 +365,11 @@ end
     end
     @onbutton ImgPlus begin
         # Append a query string to force the image to refresh 
-        timestamp = string(time_ns()) 
+        timestamp = string(time_ns())
+        # Update the array of images listed in the public folder
+        msi_bmp = sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
+        col_msi_png = sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir("public")),lt=natural)
+        
         new_msi = increment_image(current_msi, msi_bmp)
         new_col_msi = increment_image(current_col_msi, col_msi_png)
 
@@ -352,6 +388,9 @@ end
         timestamp = string(time_ns()) 
         new_msi = decrement_image(current_triq, triq_bmp)
         new_col_msi = decrement_image(current_col_triq, col_triq_png)
+        # Update the array of images with TrIQ filter listed in the public folder
+        triq_bmp = sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
+        col_triq_png = sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir("public")),lt=natural)
 
         current_triq = new_msi
         current_col_triq = new_col_msi
@@ -368,7 +407,10 @@ end
         timestamp = string(time_ns()) 
         new_msi = increment_image(current_triq, triq_bmp)
         new_col_msi = increment_image(current_col_triq, col_triq_png)
-
+        # Update the array of images with TrIQ filter listed in the public folder
+        triq_bmp = sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
+        col_triq_png = sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir("public")),lt=natural)
+        
         current_triq = new_msi
         current_col_triq = new_col_msi
         imgIntT = "/$(current_triq)"
@@ -379,77 +421,270 @@ end
         msgtriq = "image with the Nmass of $(replace(text_nmass, "_" => "."))"
     end
 
-    # 3d plot 
+    # 3d plot
     @onbutton image3dPlot begin
         msg = "Image 3D plot selected"
         cleaned_imgInt = replace(imgInt, r"\?.*" => "")
         cleaned_imgInt = lstrip(cleaned_imgInt, '/')
-        var1 = joinpath( "public", cleaned_imgInt )
+        var = joinpath( "./public", cleaned_imgInt )
-        if isfile(var1)
+
+        if isfile(var)
             try
-                img = FileIO.load(File{DataFormat{:BMP}}(var1))
+                img = load(var)
-                img_gray = Gray.(img) # Convert to grayscale 
+                #println("Image type:", typeof(img))
+                img_gray = Gray.(img) # Convert to grayscale
+                #println("Grayscale image type:", typeof(img_gray)) 
                 img_array = Array(img_gray)
+                elevation = Float32.(Array(img_gray)) ./ 255.0 # Normalize between 0 and 1
+                #println("Elevation size:", size(elevation)) 
+                # Smooth the image 
+                sigma = 4.0
+                kernel = Kernel.gaussian(sigma)
+                #println(size(kernel))
+                elevation_smoothed = imfilter(elevation, kernel) 
+                #println("Smoothed elevation size:", size(elevation_smoothed))
+                # Transpose the elevation_smoothed array
+                # Create the X, Y meshgrid coordinates 
+                x = 1:size(elevation_smoothed, 2) 
+                y = 1:size(elevation_smoothed, 1)
+                X = repeat(reshape(x, 1, length(x)), length(y), 1)
+                #println("Size of X:", size(X))
+                Y = repeat(reshape(y, length(y), 1), 1, length(x))
+                #println("Size of Y:", size(Y))
+                # Calculate the number of ticks and aspect ratio for the 3d plot
+                x_nticks = min(20, length(x))
+                y_nticks = min(20, length(y))
+                z_nticks = 5
+                aspect_ratio = attr(x = 1, y = length(y) / length(x), z = 0.5)
+
+                # Define the layout for the 3D plot
+                layout3D = PlotlyBase.Layout(
+                    title = "3D Surface Plot",
+                    scene = attr(
+                        xaxis_nticks = x_nticks,
+                        yaxis_nticks = y_nticks,
+                        zaxis_nticks = z_nticks, 
+                        camera = attr(eye = attr(x = 0, y = -1, z = 0.5)), 
+                        aspectratio = aspect_ratio
+                    )
+                )
+                if size(elevation_smoothed, 1) < size(elevation_smoothed, 2)
+                    # Transpose the elevation_smoothed array if Y axis is longer than X axis to fix chopping
+                    elevation_smoothed = transpose(elevation_smoothed)
+                    Y = -Y
+                end
+
+                trace3D = PlotlyBase.surface(x = X[1, :], y = Y[:, 1], z = elevation_smoothed,
+                contours_z = attr(
+                    show = true,
+                    usecolormap = true,
+                    highlightcolor = "limegreen",
+                    project_z = true
+                ), colorscale = "Viridis")
+                plotdata3d = [trace3D] # We add the data from the image to the plot
+                plotlayout3d = layout3D # we update the style of the plot to fit the image.
+                spectraMz = nothing # Important for memory cleaning
+                GC.gc() # Trigger garbage collection
+                if Sys.islinux()
+                    ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure julia returns the freed memory to OS
+                end
+                msg = "Plot loaded."
             catch e 
                 msg = "Failed to load and process image: $e" 
                 warning_msg = true 
-                println(msg) 
+                println(msg)
             end
-            elevation = img_array / 255.0 # Normalize between 0 and 1
+        else
-            # Smooth the image 
+            msg = "image could not be 3d plotted"
-            sigma = 4.0 
+            warning_msg = true
-            elevation_smoothed = imfilter(elevation, Kernel.gaussian(sigma)) 
+        end
-            # Create the X, Y meshgrid coordinates 
+    end
-            x = 1:size(elevation_smoothed, 2) 
+    # 3d plot for TrIQ
-            y = 1:size(elevation_smoothed, 1) 
+    @onbutton triq3dPlot begin
-            X, Y = ndgrid(x, y)
+        msg = "TrIQ 3D plot selected"
-            trace3D = PlotlyBase.scatter(x = X[1, :], y =Y[:, 1], z=elevation_smoothed, colorscale="Viridis")
+        cleaned_imgIntT = replace(imgIntT, r"\?.*" => "")
-            plotdata3d = [trace3D] # We add the data from the image to the plot
+        cleaned_imgIntT = lstrip(cleaned_imgIntT, '/')
-            spectraMz = nothing # Important for memory cleaning
+        var = joinpath( "./public", cleaned_imgIntT )
-            GC.gc() # Trigger garbage collection
+
-            if Sys.islinux()
+        if isfile(var)
-                ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure julia returns the freed memory to OS
+            try
+                img = load(var)
+                img_gray = Gray.(img) # Convert to grayscale
+                img_array = Array(img_gray)
+                elevation = Float32.(Array(img_gray)) ./ 255.0 # Normalize between 0 and 1
+                # Smooth the image 
+                sigma = 4.0
+                kernel = Kernel.gaussian(sigma)
+                elevation_smoothed = imfilter(elevation, kernel) 
+                
+                # Create the X, Y meshgrid coordinates 
+                x = 1:size(elevation_smoothed, 2) 
+                y = 1:size(elevation_smoothed, 1)
+                X = repeat(reshape(x, 1, length(x)), length(y), 1)
+                Y = repeat(reshape(y, length(y), 1), 1, length(x))
+                
+                # Calculate the number of ticks and aspect ratio for the 3d plot
+                x_nticks = min(20, length(x))
+                y_nticks = min(20, length(y))
+                z_nticks = 5
+                aspect_ratio = attr(x = 1, y = length(y) / length(x), z = 0.5)
+
+                # Define the layout for the 3D plot
+                layout3D = PlotlyBase.Layout(
+                    title = "3D Surface Plot",
+                    scene = attr(
+                        xaxis_nticks = x_nticks,
+                        yaxis_nticks = y_nticks,
+                        zaxis_nticks = z_nticks, 
+                        camera = attr(eye = attr(x = 0, y = -1, z = 0.5)), 
+                        aspectratio = aspect_ratio
+                    )
+                )
+                if size(elevation_smoothed, 1) < size(elevation_smoothed, 2)
+                    # Transpose the elevation_smoothed array if Y axis is longer than X axis to fix chopping
+                    elevation_smoothed = transpose(elevation_smoothed)
+                    Y = -Y
+                end
+
+                trace3D = PlotlyBase.surface(x = X[1, :], y = Y[:, 1], z = elevation_smoothed,
+                contours_z = attr(
+                    show = true,
+                    usecolormap = true,
+                    highlightcolor = "limegreen",
+                    project_z = true
+                ), colorscale = "Viridis")
+                plotdata3d = [trace3D] # We add the data from the image to the plot
+                plotlayout3d = layout3D # we update the style of the plot to fit the image.
+                spectraMz = nothing # Important for memory cleaning
+                GC.gc() # Trigger garbage collection
+                if Sys.islinux()
+                    ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure julia returns the freed memory to OS
+                end
+                msg = "Plot loaded."
+            catch e 
+                msg = "Failed to load and process image: $e" 
+                warning_msg = true 
+                println(msg)
             end
-             msg = "Plot loaded."
         else
             msg = "image could not be 3d plotted"
             warning_msg = true
         end
     end
 
-    @onbutton triq3dPlot begin
+    # Contour 2d plot
-        msg = "TrIQ 3D plot selected"
+    @onbutton imageCPlot begin
+        msg = "Image 2D plot selected"
+        cleaned_imgInt = replace(imgInt, r"\?.*" => "")
+        cleaned_imgInt = lstrip(cleaned_imgInt, '/')
+        var = joinpath("./public", cleaned_imgInt)
+    
+        if isfile(var)
+            try
+                img = load(var)
+                # Convert to grayscale
+                img_gray = Gray.(img)
+                img_array = Array(img_gray)
+                elevation = Float32.(Array(img_gray)) ./ 255.0  # Normalize between 0 and 1
+    
+                # Smooth the image
+                sigma = 4.0
+                kernel = Kernel.gaussian(sigma)
+                elevation_smoothed = imfilter(elevation, kernel)
+    
+                # Create the X, Y meshgrid coordinates
+                x = 1:size(elevation_smoothed, 2)
+                y = 1:size(elevation_smoothed, 1)
+                X = repeat(reshape(x, 1, length(x)), length(y), 1)
+                Y = repeat(reshape(y, length(y), 1), 1, length(x))
+                
+                layoutContour = PlotlyBase.Layout(
+                    title = "2D Topographic Map",
+                    xaxis_title = "X",
+                    yaxis_title = "Y",
+                    margin = attr(l = 65, r = 50, b = 65, t = 90)
+                )
+                traceContour = PlotlyBase.contour(
+                    z = elevation_smoothed,
+                    x = X[1, :],  # Use the first row
+                    y = -Y[:, 1],  # Use the first column
+                    contours_coloring = "lines",
+                    colorscale = "Viridis"
+                )
+                plotdata = [traceContour]
+                plotlayout = layoutContour
+    
+                spectraMz = nothing  # Important for memory cleaning
+                GC.gc()  # Trigger garbage collection
+                if Sys.islinux()
+                    ccall(:malloc_trim, Int32, (Int32,), 0)  # Ensure Julia returns the freed memory to OS
+                end
+                msg = "Plot loaded."
+            catch e
+                msg = "Failed to load and process image: $e"
+                warning_msg = true
+                println(msg)
+            end
+        else
+            msg = "Image could not be 2D plotted"
+            warning_msg = true
+        end
+    end
+    # Contour 2d plot for TrIQ
+    @onbutton triqCPlot begin
+        msg = "Image 2D plot selected"
         cleaned_imgIntT = replace(imgIntT, r"\?.*" => "")
         cleaned_imgIntT = lstrip(cleaned_imgIntT, '/')
-        var1 = joinpath( "public", cleaned_imgIntT )
+        var = joinpath("./public", cleaned_imgIntT)
-        if isfile(var1)
+    
+        if isfile(var)
             try
-                img = FileIO.load(File{DataFormat{:BMP}}(var1))
+                img = load(var)
-                img_gray = Gray.(img) # Convert to grayscale 
+                # Convert to grayscale
+                img_gray = Gray.(img)
                 img_array = Array(img_gray)
-            catch e 
+                elevation = Float32.(Array(img_gray)) ./ 255.0  # Normalize between 0 and 1
-                msg = "Failed to load and process image: $e" 
+    
-                warning_msg = true 
+                # Smooth the image
-                println(msg) 
+                sigma = 4.0
+                kernel = Kernel.gaussian(sigma)
+                elevation_smoothed = imfilter(elevation, kernel)
+    
+                # Create the X, Y meshgrid coordinates
+                x = 1:size(elevation_smoothed, 2)
+                y = 1:size(elevation_smoothed, 1)
+                X = repeat(reshape(x, 1, length(x)), length(y), 1)
+                Y = repeat(reshape(y, length(y), 1), 1, length(x))
+                
+                layoutContour = PlotlyBase.Layout(
+                    title = "2D Topographic Map",
+                    xaxis_title = "X",
+                    yaxis_title = "Y",
+                    margin = attr(l = 65, r = 50, b = 65, t = 90)
+                )
+                traceContour = PlotlyBase.contour(
+                    z = elevation_smoothed,
+                    x = X[1, :],  # Use the first row
+                    y = -Y[:, 1],  # Use the first column
+                    contours_coloring = "lines",
+                    colorscale = "Viridis"
+                )
+                plotdata = [traceContour]
+                plotlayout = layoutContour
+    
+                spectraMz = nothing  # Important for memory cleaning
+                GC.gc()  # Trigger garbage collection
+                if Sys.islinux()
+                    ccall(:malloc_trim, Int32, (Int32,), 0)  # Ensure Julia returns the freed memory to OS
+                end
+                msg = "Plot loaded."
+            catch e
+                msg = "Failed to load and process image: $e"
+                warning_msg = true
+                println(msg)
             end
-            elevation = img_array / 255.0 # Normalize between 0 and 1
-            # Smooth the image 
-            sigma = 4.0 
-            elevation_smoothed = imfilter(elevation, Kernel.gaussian(sigma)) 
-            # Create the X, Y meshgrid coordinates 
-            x = 1:size(elevation_smoothed, 2) 
-            y = 1:size(elevation_smoothed, 1) 
-            X, Y = ndgrid(x, y)
-            trace3D = PlotlyBase.scatter(x = X[1, :], y =Y[:, 1], z=elevation_smoothed, colorscale="Viridis")
-            plotdata3d = [trace3D] # We add the data from the image to the plot
-            spectraMz = nothing # Important for memory cleaning
-            GC.gc() # Trigger garbage collection
-            if Sys.islinux()
-                ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure julia returns the freed memory to OS
-            end
-             msg = "Plot loaded."
         else
-            msg = "image could not be 3d plotted"
+            msg = "Image could not be 2D plotted"
             warning_msg = true
         end
     end

app.jl.html

@@ -5,17 +5,17 @@
             <h4>Julia mzML imzML analysis GUI&nbsp;</h4>
             <h6>Please make sure the ibd, the mzML and the imzML files are located in the same directory and have the same name.</h6>
             <h6>It may take a while to generate the image and the plot, please be patient.</h6>
+            <h6>To generate the contour or 3D plot, you have to select it using the User Interface</h6>
         </div>
     </header>
     <!-- TOP -->
-    <div class="row">
+        <div id="extDivStyle" class="row col-12 q-pa-xl">
-        <div id="extDivStyle" class="st-col col-12 col-sm st-module">
+            <div class="row col-6">
-            <div class="row">
                 <!-- Left DIV -->
-                <div id="intDivStyle" class="st-col col-12 col-sm st-module">
+                <div id="intDivStyle" class="st-col col-12 st-module">
                     <!--<q-file v-model="file_route" filled="" label="Select your imzML file" accept=".imzML"></q-file>-->
                     <q-input id="textRoute" standout="custom-standout" v-model="file_route" label="Insert the route to your imzML file"></q-input>
-                    <div class="row st-col col-12 col-sm">
+                    <div class="row st-col col-12">
                         <q-input id="textName" class="col-9" standout="custom-standout" v-model="file_name" label="Insert the name of your imzML file"></q-input>
                         <q-btn-dropdown
                         id="btnStyle"
@@ -36,7 +36,19 @@
                               <q-item-label>Sum Spectrum Plot</q-item-label>
                             </q-item-section>
                           </q-item>
+
+                          <q-item clickable v-close-popup v-on:click="imageCPlot = true">
+                            <q-item-section>
+                              <q-item-label>Image Contour Plot</q-item-label>
+                            </q-item-section>
+                          </q-item>
                           
+                          <q-item clickable v-close-popup v-on:click="triqCPlot = true">
+                            <q-item-section>
+                              <q-item-label>TrIQ Contour Plot</q-item-label>
+                            </q-item-section>
+                          </q-item>
+
                           <q-item clickable v-close-popup v-on:click="image3dPlot = true">
                             <q-item-section>
                               <q-item-label>Image 3D Plot</q-item-label>
@@ -88,12 +100,10 @@
                     </q-btn>
                     <p>{{msg}}</p>
                 </div>
-            </div><!--        <plotly :data="plotdata" :layout="plotlayout"> </plotly>-->
+            </div>
-        </div>
+            <div class="row col-6">
-        <div id="extDivStyle" class="st-col col-12 col-sm st-module">
-            <div class="row">
                 <!-- Right DIV -->
-                <div id="intDivStyle" class="st-col col-12 col-sm st-module">
+                <div id="intDivStyle" class="st-col col-12 st-module">
                     <h6>Image Visualizer</h6>
                     <!-- Btn image changer -->
                     <div>
@@ -101,8 +111,8 @@
                         <q-btn id="btnStyle" icon="arrow_forward" rounded v-on:click="ImgPlus = true"></q-btn>
                     </div>
                     <!-- Image manager -->
-                    <div id="image-container" class="row st-col col-12 col-sm items-center">
+                    <div id="image-container" class="row st-col col-12 items-center">
-                        <div style="max-height: 500px; overflow: auto;" class="st-col col-10">
+                        <div class="st-col col-10">
                             <q-img id="imgInt" class="q-ma-none q-pa-none" :src="imgInt" fit="scale-down"></q-img>
                         </div>
                         <div class="st-col col-2">
@@ -116,11 +126,11 @@
                         <q-btn id="btnStyle" icon="arrow_forward" rounded v-on:click="ImgPlusT = true"></q-btn>
                     </div>
                     <!-- Triq Image manager -->
-                    <div id="image-container" class="row st-col col-12 col-sm items-center">
+                    <div id="image-container" class="row st-col col-12 items-center">
-                        <div style="max-height: 500px; overflow: auto;" class="st-col col-10">
+                        <div class="col-10">
                             <q-img id="imgInt" class="q-ma-none q-pa-none" :src="imgIntT" fit="scale-down"></q-img>
                         </div>
-                        <div class="st-col col-2">
+                        <div class="col-2">
                             <q-img id="colorbar" class="q-ma-none q-pa-none" :src="colorbarT"></q-img>
                         </div>
                     </div>
@@ -128,16 +138,15 @@
                 </div>
             </div>
         </div>
-    </div>
+        <!-- Bottom -->
-    <!-- Bottom -->
+    <div id="extDivStyle" class="row col-12 q-pa-xl">
-    <div class="row">
         <!-- Bottom Left Div -->
-        <div class="st-col col-12 col-sm st-module" >
+        <div class="st-col col-12 st-module q-pa-none" >
-            <plotly id="plotStyle" :data="plotdata" :layout="plotlayout" class="st-col col-12 col-sm-12"></plotly>
+            <plotly id="plotStyle" :data="plotdata" :layout="plotlayout" class="col-12"></plotly>
         </div>
         <!-- Bottom Right Div -->
-        <div class="st-col col-12 col-sm st-module" >
+        <div class="st-col col-12 st-module q-pa-none" >
-            <plotly id="plotStyle3d" :data="plotdata3d" :layout="plotlayout3d" class="st-col col-12 col-sm-12"></plotly>
+            <plotly id="plotStyle3d" :data="plotdata3d" :layout="plotlayout3d" class="col-12"></plotly>
         </div>
     </div>
 

ongoing_tasks.txt

@@ -4,9 +4,11 @@ PENDING
         avoid image enlargement -> CURRENT WIP
         image flip upside down
         colorbar revamp
-    3d topography for images -> CURRENT WIP
     Multiple plot types
-
+    Tag for time it takes in creating image and creating plots -> CURRENT WIP
+    Create function that makes the imzML from mzML files
+    Possibility to add multiple imzML to process at once ?
+    Pixel selection marks 
 
 DONE
     Quicker start for julia GUI
@@ -16,4 +18,5 @@ DONE
         UI functionality added
     Code cleanse
         better code readability
-    Better blind search for images 
+    Better blind search for images
+    3d topography for images 

public/css/autogenerated.css

@@ -1 +1 @@
- #btnStyle{background:#009f90;color:rgb(229, 236, 246);}#imgInt{float:left;}#header{display:flex;align-items:center;}#imgLogo{width:100px;height:80px;margin-right:10px;margin-left:10px;}#extDivStyle{background-color:#c9cdb1;}#intDivStyle{padding-top:10px;padding-right:10px;padding-bottom:10px;padding-left:10px;background-color:rgb(229, 236, 246);}#colorbar{float:left;}.custom-standout{background-color:#ccd2db!important;color:rgb(229, 236, 246)!important;}
+#btnStyle{background:#009f90;color:rgb(229, 236, 246);}#imgInt{float:left;}#header{display:flex;align-items:center;}#imgLogo{width:100px;height:80px;margin-right:10px;margin-left:10px;}#extDivStyle{background-color:#c9cdb1;border-radius: 10px;}#intDivStyle{padding-top:10px;padding-right:10px;padding-bottom:10px;padding-left:10px;}#colorbar{float:left;}.custom-standout{background-color:#ccd2db!important;color:rgb(229, 236, 246)!important;}

start_MSI_GUI.jl

@@ -1,7 +1,11 @@
 using Pkg
 Pkg.activate(".")
-Pkg.add("Libz") ; Pkg.add("PlotlyBase") ; Pkg.add("CairoMakie") ; Pkg.add("Colors") ; Pkg.add("Statistics") ; Pkg.add("NaturalSort")
+Pkg.instantiate()
+Pkg.update()
+Pkg.gc()
+Pkg.add("Libz") ; Pkg.add("PlotlyBase") ; Pkg.add("CairoMakie") ; Pkg.add("Colors") ; Pkg.add("Statistics") ; Pkg.add("NaturalSort") ; Pkg.add("GenieFramework")
 Pkg.add(url="https://github.com/CINVESTAV-LABI/julia_mzML_imzML") # With this we ensure it uses the latest library iteration
+Pkg.add("Images") ; Pkg.add("LinearAlgebra")
 Pkg.instantiate()
 Pkg.update()