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Update example script and manifest
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@brenhinkeller
brenhinkeller committed Dec 25, 2024
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94 changes: 46 additions & 48 deletions examples/Manifest.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -165,9 +165,9 @@ version = "1.21.6+0"

[[deps.Bzip2_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "8873e196c2eb87962a2048b3b8e08946535864a1"
git-tree-sha1 = "35abeca13bc0425cff9e59e229d971f5231323bf"
uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0"
version = "1.0.8+2"
version = "1.0.8+3"

[[deps.CEnum]]
git-tree-sha1 = "389ad5c84de1ae7cf0e28e381131c98ea87d54fc"
Expand Down Expand Up @@ -420,9 +420,9 @@ version = "0.1.11"

[[deps.Expat_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "e51db81749b0777b2147fbe7b783ee79045b8e99"
git-tree-sha1 = "f42a5b1e20e009a43c3646635ed81a9fcaccb287"
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version = "2.6.4+1"
version = "2.6.4+2"

[[deps.FFMPEG]]
deps = ["FFMPEG_jll"]
Expand Down Expand Up @@ -450,9 +450,9 @@ version = "1.8.0"

[[deps.FFTW_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "4d81ed14783ec49ce9f2e168208a12ce1815aa25"
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uuid = "f5851436-0d7a-5f13-b9de-f02708fd171a"
version = "3.3.10+1"
version = "3.3.10+2"

[[deps.FileIO]]
deps = ["Pkg", "Requires", "UUIDs"]
Expand Down Expand Up @@ -550,15 +550,15 @@ version = "3.4.0+2"

[[deps.GR]]
deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Preferences", "Printf", "Qt6Wayland_jll", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "p7zip_jll"]
git-tree-sha1 = "52adc6828958ea8a0cf923d53aa10773dbca7d5f"
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uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71"
version = "0.73.9"
version = "0.73.10"

[[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"]
git-tree-sha1 = "4e9e2966af45b06f24fd952285841428f1d6e858"
git-tree-sha1 = "b90934c8cb33920a8dc66736471dc3961b42ec9f"
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version = "0.73.10+0"

[[deps.Gettext_jll]]
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Expand Down Expand Up @@ -651,9 +651,9 @@ version = "0.1.17"

[[deps.Hwloc_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "50aedf345a709ab75872f80a2779568dc0bb461b"
git-tree-sha1 = "290232556f4ffb60ac3e476acf28e1a46e764742"
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version = "2.11.2+1"
version = "2.11.2+2"

[[deps.HypergeometricFunctions]]
deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"]
Expand Down Expand Up @@ -873,9 +873,9 @@ version = "0.1.9"

[[deps.JLLWrappers]]
deps = ["Artifacts", "Preferences"]
git-tree-sha1 = "be3dc50a92e5a386872a493a10050136d4703f9b"
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version = "1.6.1"
version = "1.7.0"

[[deps.JSON]]
deps = ["Dates", "Mmap", "Parsers", "Unicode"]
Expand All @@ -891,9 +891,9 @@ version = "0.1.5"

[[deps.JpegTurbo_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "ef10afc9f4b942bcd75f4c3bc9d9e8d802944c23"
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version = "3.1.0+1"

[[deps.LAME_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
Expand All @@ -903,9 +903,9 @@ version = "3.100.2+0"

[[deps.LERC_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "36bdbc52f13a7d1dcb0f3cd694e01677a515655b"
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version = "4.0.0+2"

[[deps.LLVMOpenMP_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
Expand All @@ -915,9 +915,9 @@ version = "18.1.7+0"

[[deps.LZO_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
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[[deps.LaTeXStrings]]
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Expand Down Expand Up @@ -1017,9 +1017,9 @@ version = "1.17.0+1"

[[deps.Libmount_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "84eef7acd508ee5b3e956a2ae51b05024181dee0"
git-tree-sha1 = "d841749621f4dcf0ddc26a27d1f6484dfc37659a"
uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9"
version = "2.40.2+0"
version = "2.40.2+1"

[[deps.Libtiff_jll]]
deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"]
Expand All @@ -1029,9 +1029,9 @@ version = "4.7.0+0"

[[deps.Libuuid_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "edbf5309f9ddf1cab25afc344b1e8150b7c832f9"
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uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700"
version = "2.40.2+0"
version = "2.40.2+1"

[[deps.LinearAlgebra]]
deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"]
Expand Down Expand Up @@ -1089,9 +1089,9 @@ version = "0.15.0"

[[deps.Lz4_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "abf88ff67f4fd89839efcae2f4c39cbc4ecd0846"
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version = "1.10.0+1"
version = "1.10.0+2"

[[deps.MKL_jll]]
deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "oneTBB_jll"]
Expand Down Expand Up @@ -1277,15 +1277,15 @@ version = "1.4.3"

[[deps.OpenSSL_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "7493f61f55a6cce7325f197443aa80d32554ba10"
git-tree-sha1 = "f58782a883ecbf9fb48dcd363f9ccd65f36c23a8"
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version = "3.0.15+2"

[[deps.OpenSpecFun_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1"
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version = "0.5.5+1"

[[deps.Opus_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
Expand Down Expand Up @@ -1720,9 +1720,9 @@ weakdeps = ["OffsetArrays", "StaticArrays"]

[[deps.StaticArrays]]
deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"]
git-tree-sha1 = "777657803913ffc7e8cc20f0fd04b634f871af8f"
git-tree-sha1 = "7c01731da8ab6d3094c4d44c9057b00932459255"
uuid = "90137ffa-7385-5640-81b9-e52037218182"
version = "1.9.8"
version = "1.9.9"
weakdeps = ["ChainRulesCore", "Statistics"]

[deps.StaticArrays.extensions]
Expand Down Expand Up @@ -1803,11 +1803,9 @@ version = "1.11.0"

[[deps.Thermochron]]
deps = ["BangBang", "Distributions", "LinearAlgebra", "LoopVectorization", "LsqFit", "NaNStatistics", "ProgressMeter", "Reexport", "StatGeochemBase", "Statistics"]
git-tree-sha1 = "4aac9852980be2495ace0b98808c95c491ea4c3d"
repo-rev = "main"
repo-url = "https://github.com/OpenThermochronology/Thermochron.jl.git"
git-tree-sha1 = "564963d0e54783519627be48d6c25b1635a4ba33"
uuid = "b9a8379e-ee1a-4388-b7ca-7852af1cef08"
version = "0.11.0"
version = "0.11.1"
weakdeps = ["Plots"]

[deps.Thermochron.extensions]
Expand Down Expand Up @@ -1903,9 +1901,9 @@ version = "1.21.0+2"

[[deps.Wayland_protocols_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "93f43ab61b16ddfb2fd3bb13b3ce241cafb0e6c9"
git-tree-sha1 = "5db3e9d307d32baba7067b13fc7b5aa6edd4a19a"
uuid = "2381bf8a-dfd0-557d-9999-79630e7b1b91"
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version = "1.36.0+0"

[[deps.WoodburyMatrices]]
deps = ["LinearAlgebra", "SparseArrays"]
Expand All @@ -1927,9 +1925,9 @@ version = "1.1.42+0"

[[deps.XZ_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "15e637a697345f6743674f1322beefbc5dcd5cfc"
git-tree-sha1 = "ecda72ccaf6a67c190c9adf27034ee569bccbc3a"
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version = "5.6.3+1"

[[deps.Xorg_libICE_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
Expand Down Expand Up @@ -2082,9 +2080,9 @@ version = "1.2.13+1"

[[deps.Zstd_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "555d1076590a6cc2fdee2ef1469451f872d8b41b"
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[[deps.eudev_jll]]
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Expand All @@ -2106,9 +2104,9 @@ version = "3.1.1+1"

[[deps.libaec_jll]]
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version = "1.1.2+1"

[[deps.libaom_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
Expand Down Expand Up @@ -2153,15 +2151,15 @@ version = "1.18.0+0"

[[deps.libpng_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"]
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[[deps.libsixel_jll]]
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[[deps.libvorbis_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"]
Expand Down
22 changes: 14 additions & 8 deletions examples/tTinversion.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -28,25 +28,31 @@
# # # # # # # # # # Choice of regional thermochron data # # # # # # # # # #

# Literature samples from Guenthner et al. 2013 (AJS), Minnesota
# (23 ZirconHe, 11 ApatiteHe)
name = "Minnesota"
ds = importdataset("minnesota.csv", ',', importas=:Tuple)

# # Literature samples from McDannell et al. 2022 (doi: 10.1130/G50315.1), Manitoba
# # (12 ZirconHe, 5 ApatiteHe, 47 ApatiteFT, 269 ApatiteTrackLength)
# name = "Manitoba"
# ds = importdataset("manitoba.csv", ',', importas=:Tuple)

## --- Prepare problem

model = (
nsteps = 600000, # [n] How many steps of the Markov chain should we run?
nsteps = 1000000, # [n] How many steps of the Markov chain should we run?
burnin = 350000, # [n] How long should we wait for MC to converge (become stationary)
dr = 1.0, # [μm] Radius step size
dt = 8.0, # [Ma] Time step size
dTmax = 10.0, # [Ma/dt] Maximum reheating/burial per model timestep. If too high, may cause numerical problems in Crank-Nicholson solve
Tinit = 400.0, # [C] Initial model temperature (i.e., crystallization temperature)
ΔTinit = -50.0, # [C] Tinit can vary from Tinit to Tinit+ΔTinit
ΔTinit = -100.0, # [C] Tinit can vary from Tinit to Tinit+ΔTinit
Tnow = 0.0, # [C] Current surface temperature
ΔTnow = 20.0, # [Ma] Tnow may vary from Tnow to Tnow+ΔTnow
tnow = 0.0, # [Ma] Today
minpoints = 15, # [n] Minimum allowed number of t-T points
maxpoints = 50, # [n] Maximum allowed number of t-T points
dynamicsigma = true, # Update model uncertainties?
dynamicsigma = false, # Update model uncertainties?
dynamicjumping = true, # Update the t and t jumping (proposal) distributions based on previously accepted jumps
# Damage and annealing models for diffusivity (specify custom kinetics if desired)
adm = RDAAM(), # Flowers et al. 2009 (doi: 10.1016/j.gca.2009.01.015)
Expand All @@ -72,6 +78,7 @@
detail = DetailInterval()

# # Uncomment this section to require greater t-T node density in some time interval
# # (typically the youngest end of the total time interval, where you may expect the data more resolving power)
# detail = DetailInterval(
# agemin = 0.0, # Youngest end of detail interval
# agemax = 541.0, # Oldest end of detail interval
Expand Down Expand Up @@ -210,16 +217,15 @@

## --- Create image of paths

# Desired rsolution of tTing image
# Desired rsolution of tT image
xresolution = 2000
yresolution = 1000
burnin = model.burnin

# Resize the post-burnin part of the stationary distribution
tTdist = Array{Float64}(undef, xresolution, model.nsteps-burnin)
tTdist = Array{Float64}(undef, xresolution, model.nsteps)
xq = range(0, model.tinit, length=xresolution)
@time @inbounds for i = 1:model.nsteps-burnin
linterp1s!(view(tTdist,:,i), view(tT.tpointdist,:,i+burnin), view(tT.Tpointdist,:,i+burnin), xq)
@time @inbounds for i = 1:model.nsteps
linterp1s!(view(tTdist,:,i), view(tT.tpointdist,:,i), view(tT.Tpointdist,:,i), xq)
end

# Calculate composite image
Expand Down

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