Merge pull request #32 from open-AIMS/site-assessment

Add suitability raster assessment and site polygon assessment functionality

Manifest.toml

@@ -289,9 +289,9 @@ version = "0.7.6"
 
 [[deps.CodecZstd]]
 deps = ["TranscodingStreams", "Zstd_jll"]
-git-tree-sha1 = "5e41a52bec3b0881a7eb54f5391b779994504186"
+git-tree-sha1 = "d0073f473757f0d39ac9707f1eb03b431573cbd8"
 uuid = "6b39b394-51ab-5f42-8807-6242bab2b4c2"
-version = "0.8.5"
+version = "0.8.6"
 
 [[deps.ColorSchemes]]
 deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"]
@@ -414,10 +414,10 @@ uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
 version = "1.16.0"
 
 [[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"]
-git-tree-sha1 = "04c738083f29f86e62c8afc341f0967d8717bdb8"
+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 = "fb61b4812c49343d7ef0b533ba982c46021938a6"
 uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-version = "1.6.1"
+version = "1.7.0"
 
 [[deps.DataStructures]]
 deps = ["Compat", "InteractiveUtils", "OrderedCollections"]
@@ -452,10 +452,10 @@ uuid = "244e2a9f-e319-4986-a169-4d1fe445cd52"
 version = "0.1.2"
 
 [[deps.DelaunayTriangulation]]
-deps = ["AdaptivePredicates", "EnumX", "ExactPredicates", "Random"]
-git-tree-sha1 = "94eb20e6621600f4315813b1d1fc9b8a5a6a34db"
+deps = ["AdaptivePredicates", "EnumX", "ExactPredicates", "PrecompileTools", "Random"]
+git-tree-sha1 = "668bb97ea6df5e654e6288d87d2243591fe68665"
 uuid = "927a84f5-c5f4-47a5-9785-b46e178433df"
-version = "1.4.0"
+version = "1.6.0"
 
 [[deps.DiffResults]]
 deps = ["StaticArraysCore"]
@@ -512,9 +512,9 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 
 [[deps.Distributions]]
 deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"]
-git-tree-sha1 = "e6c693a0e4394f8fda0e51a5bdf5aef26f8235e9"
+git-tree-sha1 = "d7477ecdafb813ddee2ae727afa94e9dcb5f3fb0"
 uuid = "31c24e10-a181-5473-b8eb-7969acd0382f"
-version = "0.25.111"
+version = "0.25.112"
 
     [deps.Distributions.extensions]
     DistributionsChainRulesCoreExt = "ChainRulesCore"
@@ -585,9 +585,9 @@ version = "1.8.0"
 
 [[deps.FFTW_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "c6033cc3892d0ef5bb9cd29b7f2f0331ea5184ea"
+git-tree-sha1 = "4d81ed14783ec49ce9f2e168208a12ce1815aa25"
 uuid = "f5851436-0d7a-5f13-b9de-f02708fd171a"
-version = "3.3.10+0"
+version = "3.3.10+1"
 
 [[deps.FLoops]]
 deps = ["BangBang", "Compat", "FLoopsBase", "InitialValues", "JuliaVariables", "MLStyle", "Serialization", "Setfield", "Transducers"]
@@ -644,19 +644,21 @@ weakdeps = ["PDMats", "SparseArrays", "Statistics"]
     FillArraysStatisticsExt = "Statistics"
 
 [[deps.FiniteDiff]]
-deps = ["ArrayInterface", "LinearAlgebra", "Setfield", "SparseArrays"]
-git-tree-sha1 = "f9219347ebf700e77ca1d48ef84e4a82a6701882"
+deps = ["ArrayInterface", "LinearAlgebra", "Setfield"]
+git-tree-sha1 = "b10bdafd1647f57ace3885143936749d61638c3b"
 uuid = "6a86dc24-6348-571c-b903-95158fe2bd41"
-version = "2.24.0"
+version = "2.26.0"
 
     [deps.FiniteDiff.extensions]
     FiniteDiffBandedMatricesExt = "BandedMatrices"
     FiniteDiffBlockBandedMatricesExt = "BlockBandedMatrices"
+    FiniteDiffSparseArraysExt = "SparseArrays"
     FiniteDiffStaticArraysExt = "StaticArrays"
 
     [deps.FiniteDiff.weakdeps]
     BandedMatrices = "aae01518-5342-5314-be14-df237901396f"
     BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0"
+    SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
     StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 
 [[deps.FixedPointNumbers]]
@@ -721,9 +723,9 @@ version = "0.4.2"
 
 [[deps.GeoInterface]]
 deps = ["Extents", "GeoFormatTypes"]
-git-tree-sha1 = "5921fc0704e40c024571eca551800c699f86ceb4"
+git-tree-sha1 = "2f6fce56cdb8373637a6614e14a5768a88450de2"
 uuid = "cf35fbd7-0cd7-5166-be24-54bfbe79505f"
-version = "1.3.6"
+version = "1.3.7"
 
 [[deps.GeoInterfaceMakie]]
 deps = ["GeoInterface", "GeometryBasics", "MakieCore"]
@@ -763,9 +765,9 @@ version = "0.4.11"
 
 [[deps.GeometryOps]]
 deps = ["CoordinateTransformations", "DataAPI", "DelaunayTriangulation", "ExactPredicates", "GeoInterface", "GeometryBasics", "InteractiveUtils", "LinearAlgebra", "SortTileRecursiveTree", "Statistics", "Tables"]
-git-tree-sha1 = "54a1777d49f40dccd749b6df98b8cbe178dee0b9"
+git-tree-sha1 = "51857a37476d46ff9ee99d188de1b4ce0382594d"
 uuid = "3251bfac-6a57-4b6d-aa61-ac1fef2975ab"
-version = "0.1.12"
+version = "0.1.13"
 
     [deps.GeometryOps.extensions]
     GeometryOpsFlexiJoinsExt = "FlexiJoins"
@@ -802,9 +804,9 @@ version = "1.1.2"
 
 [[deps.Graphs]]
 deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"]
-git-tree-sha1 = "ebd18c326fa6cee1efb7da9a3b45cf69da2ed4d9"
+git-tree-sha1 = "1dc470db8b1131cfc7fb4c115de89fe391b9e780"
 uuid = "86223c79-3864-5bf0-83f7-82e725a168b6"
-version = "1.11.2"
+version = "1.12.0"
 
 [[deps.HDF5_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "LazyArtifacts", "LibCURL_jll", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "OpenSSL_jll", "TOML", "Zlib_jll", "libaec_jll"]
@@ -832,9 +834,9 @@ version = "0.1.17"
 
 [[deps.Hwloc_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "5e19e1e4fa3e71b774ce746274364aef0234634e"
+git-tree-sha1 = "dd3b49277ec2bb2c6b94eb1604d4d0616016f7a6"
 uuid = "e33a78d0-f292-5ffc-b300-72abe9b543c8"
-version = "2.11.1+0"
+version = "2.11.2+0"
 
 [[deps.HypergeometricFunctions]]
 deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"]
@@ -867,9 +869,9 @@ version = "0.1.5"
 
 [[deps.ImageBinarization]]
 deps = ["HistogramThresholding", "ImageCore", "LinearAlgebra", "Polynomials", "Reexport", "Statistics"]
-git-tree-sha1 = "f5356e7203c4a9954962e3757c08033f2efe578a"
+git-tree-sha1 = "33485b4e40d1df46c806498c73ea32dc17475c59"
 uuid = "cbc4b850-ae4b-5111-9e64-df94c024a13d"
-version = "0.3.0"
+version = "0.3.1"
 
 [[deps.ImageContrastAdjustment]]
 deps = ["ImageBase", "ImageCore", "ImageTransformations", "Parameters"]
@@ -1030,9 +1032,9 @@ version = "0.15.1"
 
 [[deps.IntervalArithmetic]]
 deps = ["CRlibm_jll", "MacroTools", "RoundingEmulator"]
-git-tree-sha1 = "fe30dec78e68f27fc416901629c6e24e9d5f057b"
+git-tree-sha1 = "8e125d40cae3a9f4276cdfeb4fcdb1828888a4b3"
 uuid = "d1acc4aa-44c8-5952-acd4-ba5d80a2a253"
-version = "0.22.16"
+version = "0.22.17"
 weakdeps = ["DiffRules", "ForwardDiff", "IntervalSets", "LinearAlgebra", "RecipesBase"]
 
     [deps.IntervalArithmetic.extensions]
@@ -1127,9 +1129,9 @@ version = "0.1.5"
 
 [[deps.JpegTurbo_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "c84a835e1a09b289ffcd2271bf2a337bbdda6637"
+git-tree-sha1 = "25ee0be4d43d0269027024d75a24c24d6c6e590c"
 uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8"
-version = "3.0.3+0"
+version = "3.0.4+0"
 
 [[deps.JuliaVariables]]
 deps = ["MLStyle", "NameResolution"]
@@ -1166,9 +1168,9 @@ weakdeps = ["Serialization"]
 
 [[deps.LZO_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "70c5da094887fd2cae843b8db33920bac4b6f07d"
+git-tree-sha1 = "854a9c268c43b77b0a27f22d7fab8d33cdb3a731"
 uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac"
-version = "2.10.2+0"
+version = "2.10.2+1"
 
 [[deps.LaTeXStrings]]
 git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec"
@@ -1259,9 +1261,9 @@ version = "4.5.1+1"
 
 [[deps.LightBSON]]
 deps = ["DataStructures", "Dates", "DecFP", "FNVHash", "JSON3", "Sockets", "StructTypes", "Transducers", "UUIDs", "UnsafeArrays", "WeakRefStrings"]
-git-tree-sha1 = "1c98cccebf21f97c5a0cc81ff8cebffd1e14fb0f"
+git-tree-sha1 = "ce253ad53efeed8201656971874d8cd9dad0227e"
 uuid = "a4a7f996-b3a6-4de6-b9db-2fa5f350df41"
-version = "0.2.20"
+version = "0.2.21"
 
 [[deps.LineSearches]]
 deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"]
@@ -1317,9 +1319,9 @@ weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"]
 
 [[deps.Lz4_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "7f26c8fc5229e68484e0b3447312c98e16207d11"
+git-tree-sha1 = "abf88ff67f4fd89839efcae2f4c39cbc4ecd0846"
 uuid = "5ced341a-0733-55b8-9ab6-a4889d929147"
-version = "1.10.0+0"
+version = "1.10.0+1"
 
 [[deps.MIMEs]]
 git-tree-sha1 = "65f28ad4b594aebe22157d6fac869786a255b7eb"
@@ -1339,9 +1341,9 @@ version = "0.4.17"
 
 [[deps.MPICH_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"]
-git-tree-sha1 = "19d4bd098928a3263693991500d05d74dbdc2004"
+git-tree-sha1 = "7715e65c47ba3941c502bffb7f266a41a7f54423"
 uuid = "7cb0a576-ebde-5e09-9194-50597f1243b4"
-version = "4.2.2+0"
+version = "4.2.3+0"
 
 [[deps.MPIPreferences]]
 deps = ["Libdl", "Preferences"]
@@ -1351,9 +1353,9 @@ version = "0.1.11"
 
 [[deps.MPItrampoline_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"]
-git-tree-sha1 = "8c35d5420193841b2f367e658540e8d9e0601ed0"
+git-tree-sha1 = "70e830dab5d0775183c99fc75e4c24c614ed7142"
 uuid = "f1f71cc9-e9ae-5b93-9b94-4fe0e1ad3748"
-version = "5.4.0+0"
+version = "5.5.1+0"
 
 [[deps.MacroTools]]
 deps = ["Markdown", "Random"]
@@ -1363,9 +1365,9 @@ version = "0.5.13"
 
 [[deps.MakieCore]]
 deps = ["ColorTypes", "GeometryBasics", "IntervalSets", "Observables"]
-git-tree-sha1 = "b0e2e3473af351011e598f9219afb521121edd2b"
+git-tree-sha1 = "4604f03e5b057e8e62a95a44929cafc9585b0fe9"
 uuid = "20f20a25-4f0e-4fdf-b5d1-57303727442b"
-version = "0.8.6"
+version = "0.8.9"
 
 [[deps.ManualMemory]]
 git-tree-sha1 = "bcaef4fc7a0cfe2cba636d84cda54b5e4e4ca3cd"
@@ -1515,9 +1517,9 @@ version = "1.7.1"
 
 [[deps.OnlineStatsBase]]
 deps = ["AbstractTrees", "Dates", "LinearAlgebra", "OrderedCollections", "Statistics", "StatsBase"]
-git-tree-sha1 = "9a067a4ea67d1ebab4554b73792dd429f098387c"
+git-tree-sha1 = "a5a5a68d079ce531b0220e99789e0c1c8c5ed215"
 uuid = "925886fa-5bf2-5e8e-b522-a9147a512338"
-version = "1.7.0"
+version = "1.7.1"
 
 [[deps.OpenBLAS_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"]
@@ -1666,10 +1668,22 @@ uuid = "1d0040c9-8b98-4ee7-8388-3f51789ca0ad"
 version = "0.2.2"
 
 [[deps.Polynomials]]
-deps = ["LinearAlgebra", "RecipesBase"]
-git-tree-sha1 = "a14a99e430e42a105c898fcc7f212334bc7be887"
+deps = ["LinearAlgebra", "RecipesBase", "Requires", "Setfield", "SparseArrays"]
+git-tree-sha1 = "1a9cfb2dc2c2f1bd63f1906d72af39a79b49b736"
 uuid = "f27b6e38-b328-58d1-80ce-0feddd5e7a45"
-version = "3.2.4"
+version = "4.0.11"
+
+    [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"]
@@ -1702,9 +1716,9 @@ version = "0.2.0"
 
 [[deps.PrettyTables]]
 deps = ["Crayons", "LaTeXStrings", "Markdown", "PrecompileTools", "Printf", "Reexport", "StringManipulation", "Tables"]
-git-tree-sha1 = "66b20dd35966a748321d3b2537c4584cf40387c7"
+git-tree-sha1 = "1101cd475833706e4d0e7b122218257178f48f34"
 uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
-version = "2.3.2"
+version = "2.4.0"
 
 [[deps.Printf]]
 deps = ["Unicode"]
@@ -2058,9 +2072,9 @@ weakdeps = ["ChainRulesCore", "InverseFunctions"]
 
 [[deps.StringManipulation]]
 deps = ["PrecompileTools"]
-git-tree-sha1 = "a04cabe79c5f01f4d723cc6704070ada0b9d46d5"
+git-tree-sha1 = "a6b1675a536c5ad1a60e5a5153e1fee12eb146e3"
 uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e"
-version = "0.3.4"
+version = "0.4.0"
 
 [[deps.StructArrays]]
 deps = ["ConstructionBase", "DataAPI", "Tables"]
@@ -2170,9 +2184,9 @@ uuid = "06e1c1a7-607b-532d-9fad-de7d9aa2abac"
 version = "0.5.0"
 
 [[deps.TranscodingStreams]]
-git-tree-sha1 = "e84b3a11b9bece70d14cce63406bbc79ed3464d2"
+git-tree-sha1 = "0c45878dcfdcfa8480052b6ab162cdd138781742"
 uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
-version = "0.11.2"
+version = "0.11.3"
 
 [[deps.Transducers]]
 deps = ["Accessors", "Adapt", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "ConstructionBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "SplittablesBase", "Tables"]
@@ -2242,9 +2256,9 @@ version = "0.6.3"
 
 [[deps.WellKnownGeometry]]
 deps = ["GeoFormatTypes", "GeoInterface"]
-git-tree-sha1 = "af8adada82cfd2791bb1e39a87cbf538bb76fdaf"
+git-tree-sha1 = "5b29dedd69787822220775b8baaea377173a2b02"
 uuid = "0f680547-7be7-4555-8820-bb198eeb646b"
-version = "0.2.3"
+version = "0.2.4"
 
 [[deps.WoodburyMatrices]]
 deps = ["LinearAlgebra", "SparseArrays"]
@@ -2306,9 +2320,9 @@ version = "1.2.13+1"
 
 [[deps.Zstd_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "e678132f07ddb5bfa46857f0d7620fb9be675d3b"
+git-tree-sha1 = "555d1076590a6cc2fdee2ef1469451f872d8b41b"
 uuid = "3161d3a3-bdf6-5164-811a-617609db77b4"
-version = "1.5.6+0"
+version = "1.5.6+1"
 
 [[deps.boost_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"]
@@ -2335,15 +2349,15 @@ version = "100.701.300+0"
 
 [[deps.libpng_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"]
-git-tree-sha1 = "d7015d2e18a5fd9a4f47de711837e980519781a4"
+git-tree-sha1 = "b70c870239dc3d7bc094eb2d6be9b73d27bef280"
 uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f"
-version = "1.6.43+1"
+version = "1.6.44+0"
 
 [[deps.libsixel_jll]]
 deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Pkg", "libpng_jll"]
-git-tree-sha1 = "d4f63314c8aa1e48cd22aa0c17ed76cd1ae48c3c"
+git-tree-sha1 = "7dfa0fd9c783d3d0cc43ea1af53d69ba45c447df"
 uuid = "075b6546-f08a-558a-be8f-8157d0f608a5"
-version = "1.10.3+0"
+version = "1.10.3+1"
 
 [[deps.libzip_jll]]
 deps = ["Artifacts", "Bzip2_jll", "GnuTLS_jll", "JLLWrappers", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"]

README.md

@@ -120,7 +120,7 @@ Locally, write times with four threads configured range from 10 to 15 seconds.
 
 ## Reef edge alignment for site searching
 
-`identify_potential_sites_edges()` can be used to identify potential sites that only align with
+`identify_edge_aligned_sites()` can be used to identify potential sites that only align with
 the nearest reef edge (or specified rotations away from this angle).
 This method works by identifying the closest edge of reef polygon geometries that have been
 converted into lines.
@@ -140,7 +140,7 @@ The following processing is required before use:
 - `lon` and `lat` columns (FLoat64) must be added to the GeoDataFrame.
   - E.g. `valid_pixels.lon = first.(GI.coordinates.(valid_pixels.geometry))`
   The column used for masking should be the same as the column specified as geometry_col in
-  `identify_potential_sites_edges` (default = `:geometry`).
+  `identify_edge_aligned_sites` (default = `:geometry`).
 
 ## Docker build and run
 

docs/src/getting_started.md

@@ -139,7 +139,7 @@ Locally, write times with four threads configured range from 10 to 15 seconds.
 
 ## Reef edge alignment for site searching
 
-`identify_potential_sites_edges()` can be used to identify potential sites that only align with
+`identify_edge_aligned_sites()` can be used to identify potential sites that only align with
 the nearest reef edge (or specified rotations away from this angle).
 This method works by identifying the closest edge of reef polygon geometries that have been
 converted into lines.
@@ -159,4 +159,4 @@ The following processing is required before use:
 - `lon` and `lat` columns (FLoat64) must be added to the GeoDataFrame.
   - E.g. `valid_pixels.lon = first.(GI.coordinates.(valid_pixels.geometry))`
   The column used for masking should be the same as the column specified as geometry_col in
-  `identify_potential_sites_edges` (default = `:geometry`).
+  `identify_edge_aligned_sites` (default = `:geometry`).