diff --git a/extra/Manifest.toml b/extra/Manifest.toml index 962affa6..e19d92c1 100644 --- a/extra/Manifest.toml +++ b/extra/Manifest.toml @@ -1,854 +1,2206 @@ # This file is machine-generated - editing it directly is not advised -[[Adapt]] +julia_version = "1.9.0" +manifest_format = "2.0" +project_hash = "6e0892593020fbee926aa667f72677d6c75e8979" + +[[deps.ADTypes]] +git-tree-sha1 = "332e5d7baeff8497b923b730b994fa480601efc7" +uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" +version = "0.2.5" + +[[deps.AbstractFFTs]] deps = ["LinearAlgebra"] -git-tree-sha1 = "f1b523983a58802c4695851926203b36e28f09db" -uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.3.0" +git-tree-sha1 = "d92ad398961a3ed262d8bf04a1a2b8340f915fef" +uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" +version = "1.5.0" + + [deps.AbstractFFTs.extensions] + AbstractFFTsChainRulesCoreExt = "ChainRulesCore" + AbstractFFTsTestExt = "Test" -[[Artifacts]] + [deps.AbstractFFTs.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" + +[[deps.AbstractPlutoDingetjes]] deps = ["Pkg"] -git-tree-sha1 = "c30985d8821e0cd73870b17b0ed0ce6dc44cb744" +git-tree-sha1 = "793501dcd3fa7ce8d375a2c878dca2296232686e" +uuid = "6e696c72-6542-2067-7265-42206c756150" +version = "1.2.2" + +[[deps.Accessors]] +deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Test"] +git-tree-sha1 = "a7055b939deae2455aa8a67491e034f735dd08d3" +uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" +version = "0.1.33" + + [deps.Accessors.extensions] + AccessorsAxisKeysExt = "AxisKeys" + AccessorsIntervalSetsExt = "IntervalSets" + AccessorsStaticArraysExt = "StaticArrays" + AccessorsStructArraysExt = "StructArrays" + + [deps.Accessors.weakdeps] + AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5" + IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" + Requires = "ae029012-a4dd-5104-9daa-d747884805df" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" + +[[deps.Adapt]] +deps = ["LinearAlgebra", "Requires"] +git-tree-sha1 = "02f731463748db57cc2ebfbd9fbc9ce8280d3433" +uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" +version = "3.7.1" +weakdeps = ["StaticArrays"] + + [deps.Adapt.extensions] + AdaptStaticArraysExt = "StaticArrays" + +[[deps.ArgTools]] +uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" +version = "1.1.1" + +[[deps.ArnoldiMethod]] +deps = ["LinearAlgebra", "Random", "StaticArrays"] +git-tree-sha1 = "62e51b39331de8911e4a7ff6f5aaf38a5f4cc0ae" +uuid = "ec485272-7323-5ecc-a04f-4719b315124d" +version = "0.2.0" + +[[deps.Arpack]] +deps = ["Arpack_jll", "Libdl", "LinearAlgebra", "Logging"] +git-tree-sha1 = "9b9b347613394885fd1c8c7729bfc60528faa436" +uuid = "7d9fca2a-8960-54d3-9f78-7d1dccf2cb97" +version = "0.5.4" + +[[deps.Arpack_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "OpenBLAS_jll", "Pkg"] +git-tree-sha1 = "5ba6c757e8feccf03a1554dfaf3e26b3cfc7fd5e" +uuid = "68821587-b530-5797-8361-c406ea357684" +version = "3.5.1+1" + +[[deps.ArrayInterface]] +deps = ["Adapt", "LinearAlgebra", "Requires", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "247efbccf92448be332d154d6ca56b9fcdd93c31" +uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" +version = "7.6.1" + + [deps.ArrayInterface.extensions] + ArrayInterfaceBandedMatricesExt = "BandedMatrices" + ArrayInterfaceBlockBandedMatricesExt = "BlockBandedMatrices" + ArrayInterfaceCUDAExt = "CUDA" + ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore" + 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" + GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" + StaticArraysCore = 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"8e850ede-7688-5339-a07c-302acd2aaf8d" -version = "1.40.0+2" +version = "1.48.0+0" + +[[deps.p7zip_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" +version = "17.4.0+0" + +[[deps.prrte_jll]] +deps = ["Artifacts", "Hwloc_jll", "JLLWrappers", "Libdl", "PMIx_jll", "libevent_jll"] +git-tree-sha1 = "5adb2d7a18a30280feb66cad6f1a1dfdca2dc7b0" +uuid = "eb928a42-fffd-568d-ab9c-3f5d54fc65b9" +version = "3.0.2+0" -[[x264_jll]] +[[deps.x264_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "d713c1ce4deac133e3334ee12f4adff07f81778f" +git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" -version = "2020.7.14+2" +version = "2021.5.5+0" -[[x265_jll]] +[[deps.x265_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "487da2f8f2f0c8ee0e83f39d13037d6bbf0a45ab" +git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" -version = "3.0.0+3" +version = "3.5.0+0" -[[xkbcommon_jll]] +[[deps.xkbcommon_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] -git-tree-sha1 = "ece2350174195bb31de1a63bea3a41ae1aa593b6" +git-tree-sha1 = "9c304562909ab2bab0262639bd4f444d7bc2be37" uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" -version = "0.9.1+5" +version = "1.4.1+1" diff --git a/extra/Plot_output_julia.ipynb b/extra/Plot_output_julia.ipynb deleted file mode 100644 index 4ffe9a85..00000000 --- a/extra/Plot_output_julia.ipynb +++ /dev/null @@ -1,214 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "scrolled": true - }, - "outputs": [], - "source": [ - "using Plots\n", - "using HDF5\n", - "using Unitful\n", - "using UnitfulRecipes" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Load HDF5 output file" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "filename = \"particle_da.h5\"\n", - "fh = h5open(filename, \"r\")\n", - "\n", - "println(\"The following datasets found in file \", filename, \": \", keys(fh))\n", - "haskey(fh, \"data_syn\") && println(\"The following timestamps found: \", keys(fh[\"data_syn\"]))\n", - "haskey(fh[\"data_syn\"], \"t0\") && println(\"The following fields found: \", keys(fh[\"data_syn\"][\"t0\"]))" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Set these parameters to choose what to plot" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "timestamp = \"t1\" # Edit this value to plot a different time slice from the list above\n", - "field = \"height\" # Choose from the fields listed above" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Collect data from the output file" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "field_unit = read(fh[\"data_syn\"][timestamp][field][\"Unit\"])\n", - "var_unit = read(fh[\"data_var\"][timestamp][field][\"Unit\"])\n", - "x_unit = read(fh[\"grid\"][\"x\"][\"Unit\"])\n", - "y_unit = read(fh[\"grid\"][\"y\"][\"Unit\"])\n", - "x_st_unit = read(fh[\"stations\"][\"x\"][\"Unit\"])\n", - "y_st_unit = read(fh[\"stations\"][\"y\"][\"Unit\"])\n", - "\n", - "field_desc = read(fh[\"data_syn\"][timestamp][field][\"Description\"])\n", - "\n", - "x = read(fh[\"grid\"][\"x\"]) .* uparse(x_unit) .|> u\"km\"\n", - "y = read(fh[\"grid\"][\"y\"]) .* uparse(y_unit) .|> u\"km\"\n", - "z_t = read(fh[\"data_syn\"][timestamp][field]) .* uparse(field_unit)\n", - "z_avg = read(fh[\"data_avg\"][timestamp][field]) .* uparse(field_unit)\n", - "z_var = read(fh[\"data_var\"][timestamp][field]) .* uparse(var_unit)\n", - "z_std = sqrt.(z_var)\n", - "x_st = read(fh[\"stations\"][\"x\"]) .* uparse(x_st_unit) .|> u\"km\"\n", - "y_st = read(fh[\"stations\"][\"y\"]) .* uparse(y_st_unit) .|> u\"km\"" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Contour plots of surface height" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "function plot_data(x, y, z_t, z_avg, z_std, field_desc)\n", - " n_contours = 100\n", - " zmax = max(maximum(z_t), maximum(z_avg))\n", - " zmin = min(minimum(z_t), minimum(z_avg))\n", - " levels = range(zmin, zmax; length=n_contours)\n", - "\n", - " p1 = heatmap(x, y, z_t; title=\"True $(lowercase(field_desc))\")\n", - " p2 = heatmap(x, y, z_avg; title=\"Assimilated $(lowercase(field_desc))\")\n", - " p3 = heatmap(x, y, z_std; title=\"Std of assimilated $(lowercase(field_desc))\")\n", - "\n", - " for (i, plt) in enumerate((p1, p2, p3))\n", - " # Set labels\n", - " plot!(plt; xlabel=\"x\", ylabel=\"y\")\n", - " # Set range of color bar for first two plots\n", - " i ∈ (1, 2) && plot!(plt; clims=(ustrip(zmin), ustrip(zmax)))\n", - " # Add the positions of the stations\n", - " scatter!(plt, x_st, y_st, color=:red, marker=:star, label=\"\")\n", - " end\n", - "\n", - " plot(p1, p2, p3; titlefontsize=8, guidefontsize=8)\n", - "end\n", - "\n", - "plot_data(x, y, z_t, z_avg, z_std, field_desc)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Scatter plot of particle weights" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "weights = read(fh[\"weights\"][timestamp])\n", - "\n", - "p1 = scatter(weights, marker=:star)\n", - "p2 = scatter(weights, marker=:star, yscale=:log10)\n", - "\n", - "for plt in (p1, p2)\n", - " plot!(plt; xlabel=\"Particle ID\", ylabel=\"Weight\")\n", - "end\n", - "\n", - "plot(p1, p2, label=\"\")" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Time series of Estimated Sample Size" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "scrolled": false - }, - "outputs": [], - "source": [ - "plot([1 / sum(read(w) .^ 2) for w in fh[\"weights\"]];\n", - " label=\"\", marker=:o, xlabel=\"Time step\", ylabel=\"Estimated Sample Size (1 / sum(weight^2))\")" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Animation" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "animation = @animate for timestamp ∈ keys(fh[\"data_syn\"])\n", - " z_t = read(fh[\"data_syn\"][timestamp][field]) .* uparse(field_unit)\n", - " z_avg = read(fh[\"data_avg\"][timestamp][field]) .* uparse(field_unit)\n", - " z_var = read(fh[\"data_var\"][timestamp][field]) .* uparse(var_unit)\n", - " z_std = sqrt.(z_var)\n", - "\n", - " plot_data(x, y, z_t, z_avg, z_std, field_desc)\n", - "end\n", - "\n", - "mp4(animation, \"animation_jl.mp4\"; fps=5)" - ] - } - ], - "metadata": { - "@webio": { - "lastCommId": null, - "lastKernelId": null - }, - "kernelspec": { - "display_name": "Julia 1.6.0", - "language": "julia", - "name": "julia-1.6" - }, - "language_info": { - "file_extension": ".jl", - "mimetype": "application/julia", - "name": "julia", - "version": "1.6.0" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/extra/Plot_output_pluto.jl b/extra/Plot_output_pluto.jl deleted file mode 100644 index 211edf69..00000000 --- a/extra/Plot_output_pluto.jl +++ /dev/null @@ -1,183 +0,0 @@ -### A Pluto.jl notebook ### -# v0.14.5 - -using Markdown -using InteractiveUtils - -# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error). -macro bind(def, element) - quote - local el = $(esc(element)) - global $(esc(def)) = Core.applicable(Base.get, el) ? Base.get(el) : missing - el - end -end - -# ╔═╡ c7383ff4-ba4c-11eb-1977-b31b330b20d0 -begin - import Pkg - Pkg.activate(@__DIR__) - Pkg.instantiate() - using Plots - using HDF5 - using Unitful - using UnitfulRecipes - using PlutoUI -end - -# ╔═╡ 3e85f1c4-32ca-4e8e-ab9f-2fefaaabffb7 -md"## Load HDF5 output file" - -# ╔═╡ 72c703c9-3c32-45ab-b910-25a3c6652bdc -filename = "particle_da.h5" - -# ╔═╡ 7cbbad5a-3767-422c-9d6b-f32524d4bf04 -fh = h5open(filename, "r") - -# ╔═╡ 7c316637-defe-4f60-a7e5-2e10511f7044 -md"## Set these parameters to choose what to plot" - -# ╔═╡ e1acfe11-0ead-4ada-946e-eff674e6d44e -begin - timestamps = keys(fh["data_syn"]) - md""" - Select the timestamp - $(@bind timestamp_idx Slider(1:length(timestamps))) - """ -end - -# ╔═╡ 775fbb1e-a760-4862-829d-455051942255 -timestamp = timestamps[timestamp_idx] - -# ╔═╡ d442ef52-1566-484d-af31-ba3565307502 -md""" -Select the field -$(@bind field Select([f => f for f in keys(fh["data_syn"]["t0000"])])) -""" - -# ╔═╡ 384116c1-ed19-4a8c-85a7-6c0dfd9c164f -md"## Contour plots of surface height" - -# ╔═╡ 8f67e2b3-9a01-42a3-a56a-11b84776a5e1 -md"## Scatter plot of particle weights" - -# ╔═╡ a35f5895-5066-4e1d-b252-6172888aa92d -begin - weights = read(fh["weights"][timestamp]) - - p1 = scatter(weights, marker=:star) - p2 = scatter(weights, marker=:star, yscale=:log10) - - for plt in (p1, p2) - plot!(plt; xlabel="Particle ID", ylabel="Weight") - end - - plot(p1, p2, label="") -end - -# ╔═╡ e5335e14-bdb6-432c-94ab-c666c304efc6 -md"## Time series of Estimated Sample Size" - -# ╔═╡ 343a1d50-38f8-4457-81dc-5d962a2acb4a -plot([1 / sum(read(w) .^ 2) for w in fh["weights"]]; - label="", marker=:o, xlabel="Time step", ylabel="Estimated Sample Size (1 / sum(weight^2))") - -# ╔═╡ a52a3f7e-1d8e-4153-b0c2-2cb47584c447 -md"## Animation" - -# ╔═╡ 8520dcbb-0bd8-4020-aea3-009e24df2099 -md"## Collect data from the output file" - -# ╔═╡ cff1a64f-03ba-4150-9501-fa4803901808 -# All time-independent quantities -begin - field_unit = read(fh["data_syn"]["t0000"][field]["Unit"]) - var_unit = read(fh["data_var"]["t0000"][field]["Unit"]) - - field_desc = read(fh["data_syn"]["t0000"][field]["Description"]) - - x_unit = read(fh["grid"]["x"]["Unit"]) - y_unit = read(fh["grid"]["y"]["Unit"]) - x_st_unit = read(fh["stations"]["x"]["Unit"]) - y_st_unit = read(fh["stations"]["y"]["Unit"]) - - x = read(fh["grid"]["x"]) .* uparse(x_unit) .|> u"km" - y = read(fh["grid"]["y"]) .* uparse(y_unit) .|> u"km" - - x_st = read(fh["stations"]["x"]) .* uparse(x_st_unit) .|> u"km" - y_st = read(fh["stations"]["y"]) .* uparse(y_st_unit) .|> u"km" -end - -# ╔═╡ e17da3a7-39e4-4326-aa2e-08f70b574878 -function plot_data(x, y, z_t, z_avg, z_std, field_desc) - n_contours = 100 - zmax = max(maximum(z_t), maximum(z_avg)) - zmin = min(minimum(z_t), minimum(z_avg)) - levels = range(zmin, zmax; length=n_contours) - - # Note that for heatmaps we need to permute the dimensions of the z matrix - p1 = heatmap(x, y, z_t'; title="True $(lowercase(field_desc))") - p2 = heatmap(x, y, z_avg'; title="Assimilated $(lowercase(field_desc))") - p3 = heatmap(x, y, z_std'; title="Std of assimilated $(lowercase(field_desc))") - - for (i, plt) in enumerate((p1, p2, p3)) - # Set labels - plot!(plt; xlabel="x", ylabel="y") - # Set range of color bar for first two plots - i ∈ (1, 2) && plot!(plt; clims=(ustrip(zmin), ustrip(zmax))) - # Add the positions of the stations - scatter!(plt, x_st, y_st, color=:red, marker=:star, label="") - end - - plot(p1, p2, p3; titlefontsize=8, guidefontsize=8) -end - -# ╔═╡ ba33b9a1-7d73-4247-b298-ccf30acc8859 -function animate_data(fh, field, field_unit, var_unit, x, y) - animation = @animate for timestamp ∈ keys(fh["data_syn"]) - z_t = read(fh["data_syn"][timestamp][field]) .* uparse(field_unit) - z_avg = read(fh["data_avg"][timestamp][field]) .* uparse(field_unit) - z_std = sqrt.(read(fh["data_var"][timestamp][field]) .* uparse(var_unit)) - - plot_data(x, y, z_t, z_avg, z_std, field_desc) - end - - return mp4(animation, "animation_jl.mp4"; fps=5) -end - -# ╔═╡ a9343779-de40-4d33-8487-27d53ec095c0 -animate_data(fh, field, field_unit, var_unit, x, y) - -# ╔═╡ da1315e0-71de-4df6-9d74-259979571e1e -# Quantities specific to the current timestamp -begin - z_t = read(fh["data_syn"][timestamp][field]) .* uparse(field_unit) - z_avg = read(fh["data_avg"][timestamp][field]) .* uparse(field_unit) - z_std = sqrt.(read(fh["data_var"][timestamp][field]) .* uparse(var_unit)) -end - -# ╔═╡ 1d230245-5f29-4895-b0cb-4e49f6c125ff -plot_data(x, y, z_t, z_avg, z_std, field_desc) - -# ╔═╡ Cell order: -# ╠═c7383ff4-ba4c-11eb-1977-b31b330b20d0 -# ╟─3e85f1c4-32ca-4e8e-ab9f-2fefaaabffb7 -# ╠═72c703c9-3c32-45ab-b910-25a3c6652bdc -# ╟─7cbbad5a-3767-422c-9d6b-f32524d4bf04 -# ╟─7c316637-defe-4f60-a7e5-2e10511f7044 -# ╟─e1acfe11-0ead-4ada-946e-eff674e6d44e -# ╟─775fbb1e-a760-4862-829d-455051942255 -# ╟─d442ef52-1566-484d-af31-ba3565307502 -# ╟─384116c1-ed19-4a8c-85a7-6c0dfd9c164f -# ╟─e17da3a7-39e4-4326-aa2e-08f70b574878 -# ╟─1d230245-5f29-4895-b0cb-4e49f6c125ff -# ╟─8f67e2b3-9a01-42a3-a56a-11b84776a5e1 -# ╟─a35f5895-5066-4e1d-b252-6172888aa92d -# ╟─e5335e14-bdb6-432c-94ab-c666c304efc6 -# ╟─343a1d50-38f8-4457-81dc-5d962a2acb4a -# ╟─a52a3f7e-1d8e-4153-b0c2-2cb47584c447 -# ╟─ba33b9a1-7d73-4247-b298-ccf30acc8859 -# ╟─a9343779-de40-4d33-8487-27d53ec095c0 -# ╟─8520dcbb-0bd8-4020-aea3-009e24df2099 -# ╟─cff1a64f-03ba-4150-9501-fa4803901808 -# ╟─da1315e0-71de-4df6-9d74-259979571e1e diff --git a/extra/Plot_output_python.ipynb b/extra/Plot_output_python.ipynb deleted file mode 100644 index 2b57822d..00000000 --- a/extra/Plot_output_python.ipynb +++ /dev/null @@ -1,273 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "import numpy as np\n", - "import matplotlib.pyplot as plt\n", - "import h5py # if you get an error here, you may need to `pip install h5py` first\n", - "from pint import UnitRegistry # if you get an error here, you may need to `pip install pint` first" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Load HDF5 output file" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "filename = \"particle_da.h5\"\n", - "fh = h5py.File(filename,'r')\n", - "print(\"The following datasets found in file\",filename,\":\",list(fh))\n", - "if \"data_syn\" in list(fh): print(\"The following timestamps found: \", list(fh[\"data_syn\"]))\n", - "if \"t0\" in list(fh[\"data_syn\"]): print(\"The following fields found: \", list(fh[\"data_syn\"][\"t0\"]))" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Set these parameters to choose what to plot" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "timestamp = 't1' # Edit this value to plot a different time slice from the list above\n", - "field = 'height' # Choose from the fields listed above" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Collect data from the output file" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "ureg = UnitRegistry()\n", - "\n", - "field_unit = fh[\"data_syn\"][timestamp][field].attrs[\"Unit\"].decode('UTF-8')\n", - "var_unit = fh[\"data_var\"][timestamp][field].attrs[\"Unit\"].decode('UTF-8')\n", - "x_unit = fh[\"grid\"][\"x\"].attrs[\"Unit\"].decode('UTF-8')\n", - "y_unit = fh[\"grid\"][\"y\"].attrs[\"Unit\"].decode('UTF-8')\n", - "x_st_unit = fh[\"stations\"][\"x\"].attrs[\"Unit\"].decode('UTF-8')\n", - "y_st_unit = fh[\"stations\"][\"y\"].attrs[\"Unit\"].decode('UTF-8')\n", - "\n", - "field_desc = fh[\"data_syn\"][timestamp][field].attrs[\"Description\"].decode('UTF-8')\n", - "\n", - "x = (fh[\"grid\"][\"x\"][:] * ureg(x_unit)).to(ureg.km)\n", - "y = (fh[\"grid\"][\"y\"][:] * ureg(y_unit)).to(ureg.km)\n", - "z_t = fh[\"data_syn\"][timestamp][field][()] * ureg(field_unit)\n", - "z_avg = fh[\"data_avg\"][timestamp][field][()] * ureg(field_unit)\n", - "z_var = fh[\"data_var\"][timestamp][field][()] * ureg(var_unit)\n", - "z_std = np.sqrt(z_var)\n", - "x_st = (fh[\"stations\"][\"x\"][:] * ureg(x_st_unit)).to(ureg.km)\n", - "y_st = (fh[\"stations\"][\"y\"][:] * ureg(y_st_unit)).to(ureg.km)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Contour plots of surface height" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "scrolled": false - }, - "outputs": [], - "source": [ - "plt.rcParams[\"figure.figsize\"] = (18,6)\n", - "\n", - "n_contours = 100\n", - "zmax = max(np.max(z_t), np.max(z_avg)).magnitude\n", - "zmin = min(np.min(z_t), np.min(z_avg)).magnitude\n", - "levels = np.linspace(zmin, zmax, n_contours)\n", - "\n", - "fig, ax = plt.subplots(1,3)\n", - "i1 = ax[0].contourf(x,y,z_t,levels)\n", - "i2 = ax[1].contourf(x,y,z_avg,levels)\n", - "i3 = ax[2].contourf(x,y,z_std,n_contours)\n", - "\n", - "images = [i1,i2,i3]\n", - "\n", - "ax[0].set_title(f\"True {field_desc.lower()} [{z_t.units:~}]\")\n", - "ax[1].set_title(f\"Assimilated {field_desc.lower()} [{z_avg.units:~}]\")\n", - "ax[2].set_title(f\"Std of assimilated {field_desc.lower()} [{z_std.units:~}]\")\n", - "\n", - "for a,im in zip(ax,images):\n", - " a.scatter(x_st, y_st, color = 'r', marker = '*')\n", - " a.set_xlabel(f\"x [{y.units:~}]\")\n", - " a.set_ylabel(f\"y [{x.units:~}]\")\n", - " fig.colorbar(im,ax=a)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Scatter plot of particle weights" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "weights = fh[\"weights\"][timestamp][:]\n", - "fig, ax = plt.subplots(1,2)\n", - "\n", - "ax[0].plot(weights, '*')\n", - "ax[1].plot(weights, '*')\n", - "ax[1].set_yscale('log')\n", - "\n", - "for a in ax:\n", - " a.set_xlabel('Particle ID')\n", - " a.set_ylabel('Weight ('+a.get_yscale() + ')')" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Time series of Estimated Sample Size" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "ess = list()\n", - "for ts in list(fh[\"weights\"])[1:]:\n", - " ess.append(1/sum(fh[\"weights\"][ts][:]**2))\n", - "fig = plt.figure()\n", - "t = np.arange(1,np.size(ess)+1)\n", - "plt.plot(t,ess)\n", - "plt.xlabel('Time step')\n", - "plt.ylabel('Estimated Sample Size (1 / sum(weight^2))');" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Animation" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "from matplotlib import animation\n", - "\n", - "plt.rcParams[\"figure.figsize\"] = (18,6)\n", - "\n", - "n_contours = 100\n", - "\n", - "fig, ax = plt.subplots(1,3)\n", - "ax[0].set_title(f\"True {field_desc.lower()} [{z_t.units:~}]\")\n", - "ax[1].set_title(f\"Assimilated {field_desc.lower()} [{z_avg.units:~}]\")\n", - "ax[2].set_title(f\"Std of assimilated {field_desc.lower()} [{z_std.units:~}]\")\n", - "\n", - "cb = []\n", - "\n", - "def animate(i):\n", - " \n", - " for a in ax:\n", - " for c in a.collections:\n", - " c.remove()\n", - " \n", - " timestamp = f\"t{i}\"\n", - " z_t = fh[\"data_syn\"][timestamp][field][()] * ureg(field_unit)\n", - " z_avg = fh[\"data_avg\"][timestamp][field][()] * ureg(field_unit)\n", - " z_var = fh[\"data_var\"][timestamp][field][()] * ureg(var_unit)\n", - " z_std = np.sqrt(z_var)\n", - " \n", - " zmax = max(np.max(z_t), np.max(z_avg)).magnitude\n", - " zmin = min(np.min(z_t), np.min(z_avg)).magnitude\n", - " levels = np.linspace(zmin, zmax, n_contours) \n", - " \n", - " i1 = ax[0].contourf(x,y,z_t,levels)\n", - " i2 = ax[1].contourf(x,y,z_avg,levels)\n", - " i3 = ax[2].contourf(x,y,z_std,n_contours)\n", - " \n", - " images = [i1, i2, i3]\n", - " \n", - " for a,im in zip(ax,images):\n", - " a.scatter(x_st, y_st, color = 'r', marker = '*')\n", - " a.set_xlabel(f\"x [{y.units:~}]\")\n", - " a.set_ylabel(f\"y [{x.units:~}]\")\n", - " #if len(cb) < 3:\n", - " # cb.append(plt.colorbar(im, ax=a))\n", - " #else:\n", - " # for c in cb:\n", - " # c.update_normal(im)\n", - " \n", - " return images\n", - " \n", - "anim = animation.FuncAnimation(fig, animate, frames=50)\n", - "anim.save(\"animation.mp4\")" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "for key in fh[\"params\"].attrs:\n", - " try:\n", - " print(key, ':', fh[\"params\"].attrs[key])\n", - " except TypeError:\n", - " print(key, ':', 'N/A')" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.8.7" - } - }, - "nbformat": 4, - "nbformat_minor": 4 -} diff --git a/extra/Project.toml b/extra/Project.toml index f5896477..f4dabb0e 100644 --- a/extra/Project.toml +++ b/extra/Project.toml @@ -1,13 +1,14 @@ [deps] +DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab" +Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" +GaussianRandomFields = "e4b2fa32-6e09-5554-b718-106ed5adafe9" HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f" +OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" +PDMats = "90014a1f-27ba-587c-ab20-58faa44d9150" +ParticleDA = "61cd1fb4-f4c4-4bc8-80c6-ea5639a6ca2e" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" +Pluto = "c3e4b0f8-55cb-11ea-2926-15256bba5781" +PlutoLinks = "0ff47ea0-7a50-410d-8455-4348d5de0420" PlutoUI = "7f904dfe-b85e-4ff6-b463-dae2292396a8" -Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" -UnitfulRecipes = "42071c24-d89e-48dd-8a24-8a12d9b8861f" - -[compat] -HDF5 = "0.15" -Plots = "1.14" -Unitful = "1.7" -UnitfulRecipes = "1.2" -julia = "1.5" +SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462" +YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6" diff --git a/extra/llw2d_example.jl b/extra/llw2d_example.jl new file mode 100644 index 00000000..25709777 --- /dev/null +++ b/extra/llw2d_example.jl @@ -0,0 +1,139 @@ +### A Pluto.jl notebook ### +# v0.19.32 + +using Markdown +using InteractiveUtils + +# ╔═╡ 91e9009c-903f-11ee-2d75-653c9e327f0e +begin + using Pkg + Pkg.activate(".") + using ParticleDA + using PlutoLinks: @ingredients + using HDF5 + using Random + using YAML +end + +# ╔═╡ 104a7d46-ff7e-4a72-b741-a4ddb24eb183 +md"Load linear long-wave 2D (LLW2d) test model" + +# ╔═╡ 669e5aec-64d9-46c6-bee6-c567be942651 +LLW2d = @ingredients("../test/models/llw2d.jl").LLW2d + +# ╔═╡ e53ad67c-945a-4259-b246-dbf389a91f2a +md"Define simulation, filtering and model parameters" + +# ╔═╡ ecc9841a-1f37-4380-81a8-0e62a0f71969 +begin + const num_time_step = 100 # Number of time steps to simulate / filter + const num_particle = 200 # Number of particles to use when filtering + const filter_type = OptimalFilter # Particle filter proposal type + const statistics_type = ParticleDA.MeanAndVarSummaryStat + const simulation_seed = 122023 # Random number generator seed for simulation + const filtering_seed = 202312 # Random number generator seed for filtering + const parameters_output_file_path = "llw2d_parameters.yaml" # Parameters file + const simulated_output_file_path = "llw2d_simulated.h5" # Simulation output file + const filtering_output_file_path = "llw2d_filtered.h5" # Filtering output file + const model_parameters = Dict( # Parameters for LLW2d model + "llw2d" => Dict( + "x_length" => 200.0e3, + "y_length" => 200.0e3, + "nx" => 81, + "ny" => 81, + "n_stations_x" => 5, + "n_stations_y" => 5, + "station_boundary_x" => 20e3, + "station_boundary_y" => 20e3, + "station_distance_x" => 30e3, + "station_distance_y" => 30e3, + "obs_noise_std" => [0.05], + "nu" => 2.5, + "lambda" => 5.0e3, + "sigma" => [0.05, 0.5, 0.5], + "nu_initial_state" => 2.5, + "lambda_initial_state" => 5.0e3, + "sigma_initial_state" => [0.5, 5., 5.], + "n_integration_step" => 10, + "time_step" => 10., + "peak_height" => 30.0, + "peak_position" => [1e4, 1e4], + "observed_state_var_indices" => [1], + "use_peak_initial_state_mean" => true, + "padding" => 0, + ) + ) +end; + +# ╔═╡ 8bd3da51-e8a4-407f-89d4-579cb36e16fb +md"Write parameters to a YAML file" + +# ╔═╡ 4b430b41-ecde-4318-9ff3-9830c1d6b86a +YAML.write_file( + parameters_output_file_path, + Dict( + "simulate_observations" => Dict( + "seed" => simulation_seed, + "n_time_step" => num_time_step, + ), + "model" => model_parameters, + "filter" => Dict( + "seed" => filtering_seed, + "nprt" => num_particle + ), + ) +) + +# ╔═╡ 7f75e9af-455e-4c22-90bf-65de7f2eed26 +md"Simulate observations from LLW2d model to use in filtering and write to a HDF5 file" + +# ╔═╡ aef60dc3-2770-4736-a7aa-48be09ee5a4f +const model, observation_sequence = let + rng = Random.TaskLocalRNG() + Random.seed!(rng, simulation_seed) + model = LLW2d.init(model_parameters) + isfile(simulated_output_file_path) && rm(simulated_output_file_path) + observation_sequence = h5open(simulated_output_file_path, "cw") do output_file + simulate_observations_from_model( + model, num_time_step; output_file=output_file, rng=rng + ) + end + model, observation_sequence +end; + +# ╔═╡ f4821041-671e-499f-962d-e02f54849a9f +md"Perform filtering with simulated observations and write outputs to a HDF5 file" + +# ╔═╡ acbded08-c507-42c9-99ef-70f12685d02c +const final_particles, statistics = let + rng = Random.TaskLocalRNG() + Random.seed!(rng, filtering_seed) + filter_parameters = ParticleDA.FilterParameters( + nprt=num_particle, + verbose=true, + output_filename=filtering_output_file_path, + ) + isfile(filtering_output_file_path) && rm(filtering_output_file_path) + ParticleDA.run_particle_filter( + LLW2d.init, + filter_parameters, + model_parameters, + observation_sequence, + filter_type, + statistics_type; + rng=rng + ) +end; + +# ╔═╡ Cell order: +# ╠═91e9009c-903f-11ee-2d75-653c9e327f0e +# ╟─104a7d46-ff7e-4a72-b741-a4ddb24eb183 +# ╠═669e5aec-64d9-46c6-bee6-c567be942651 +# ╟─e53ad67c-945a-4259-b246-dbf389a91f2a +# ╠═ecc9841a-1f37-4380-81a8-0e62a0f71969 +# ╟─8bd3da51-e8a4-407f-89d4-579cb36e16fb +# ╠═4b430b41-ecde-4318-9ff3-9830c1d6b86a +# ╟─7f75e9af-455e-4c22-90bf-65de7f2eed26 +# ╠═aef60dc3-2770-4736-a7aa-48be09ee5a4f +# ╟─f4821041-671e-499f-962d-e02f54849a9f +# ╠═acbded08-c507-42c9-99ef-70f12685d02c diff --git a/extra/llw2d_visualizations.ipynb b/extra/llw2d_visualizations.ipynb new file mode 100644 index 00000000..170ef9f5 --- /dev/null +++ b/extra/llw2d_visualizations.ipynb @@ -0,0 +1,168 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "id": "f12b14aa-17c3-42d3-b3fc-561317c487ae", + "metadata": {}, + "outputs": [], + "source": [ + "import numpy as np\n", + "import matplotlib.pyplot as plt\n", + "from matplotlib.animation import FuncAnimation\n", + "import h5py\n", + "from IPython.display import HTML" + ] + }, + { + "cell_type": "markdown", + "id": "bc40c510-7697-4790-9b34-61b6477a9ce5", + "metadata": {}, + "source": [ + "## Load generated state and observation sequences and filtering estimates" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "acb41910-c6e2-47b7-b2f5-88929a66f911", + "metadata": {}, + "outputs": [], + "source": [ + "simulated_state_and_observations = h5py.File(\"llw2d_simulated.h5\", \"r\")\n", + "filtering_estimates = h5py.File(\"llw2d_filtered.h5\", \"r\")" + ] + }, + { + "cell_type": "markdown", + "id": "4e0bc147-df05-4ef2-b626-4f2719f7f251", + "metadata": {}, + "source": [ + "## Plot generated state sequence" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "6e983591-3d06-4101-9e46-669644fdff39", + "metadata": {}, + "outputs": [], + "source": [ + "n_timesteps = len(simulated_state_and_observations[\"state\"])\n", + "for timestep in range(0, n_timesteps, 20):\n", + " fig, axes = plt.subplots(1, 3, figsize=(11.5, 3), dpi=100)\n", + " for field_name, ax in zip((\"height\", \"vx\", \"vy\"), axes):\n", + " field = simulated_state_and_observations[\"state\"][f\"t{timestep:04}\"][field_name]\n", + " artist = ax.contourf(field, levels=50)\n", + " fig.colorbar(artist, ax=ax, label=f\"{field.attrs['Unit'].decode('utf-8')}\")\n", + " ax.set(title=field.attrs[\"Description\"].decode(\"utf-8\"), aspect=1, xticks=(), yticks=())\n", + " fig.suptitle(f\"Timestep {timestep}\")\n", + " fig.tight_layout()\n", + " plt.show(fig)\n", + " plt.close(fig)" + ] + }, + { + "cell_type": "markdown", + "id": "44e9673d-617d-4152-92fd-555734745f86", + "metadata": {}, + "source": [ + "## Plot filtering (mean) estimates of states" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "fd3d8768-07c2-4e34-beb5-befc9f9b6ddc", + "metadata": {}, + "outputs": [], + "source": [ + "n_timesteps = len(filtering_estimates[\"state_avg\"])\n", + "for timestep in range(0, n_timesteps, 20):\n", + " fig, axes = plt.subplots(1, 3, figsize=(11.5, 3), dpi=100)\n", + " for field_name, ax in zip((\"height\", \"vx\", \"vy\"), axes):\n", + " field = filtering_estimates[\"state_avg\"][f\"t{timestep:04}\"][field_name]\n", + " artist = ax.contourf(field, levels=50)\n", + " fig.colorbar(artist, ax=ax, label=f\"{field.attrs['Unit'].decode('utf-8')}\")\n", + " ax.set(title=field.attrs[\"Description\"].decode(\"utf-8\"), aspect=1, xticks=(), yticks=())\n", + " fig.suptitle(f\"Timestep {timestep}\")\n", + " fig.tight_layout()\n", + " plt.show(fig)\n", + " plt.close(fig)" + ] + }, + { + "cell_type": "markdown", + "id": "30304ccd-0d5f-4674-a0aa-232b127a5a39", + "metadata": {}, + "source": [ + "## Animate true and estimated fields" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "52833763-5a2b-48dc-a183-96dbf2619920", + "metadata": {}, + "outputs": [], + "source": [ + "fig, axes = plt.subplots(2, 3, figsize=(10, 6), dpi=100)\n", + "timestep = 0\n", + "artists = {}\n", + "state_sequences = {\n", + " \"True\": simulated_state_and_observations[\"state\"],\n", + " \"Filter mean\": filtering_estimates[\"state_avg\"],\n", + "}\n", + "field_display_ranges = {\n", + " \"height\": (-10, 10),\n", + " \"vx\": (-500, 500),\n", + " \"vy\": (-500, 500),\n", + "}\n", + "for (field_name, (lower, upper)), axes_col in zip(field_display_ranges.items(), axes.T):\n", + " for (label, state_sequence), ax in zip(state_sequences.items(), axes_col):\n", + " field = state_sequence[f\"t{timestep:04}\"][field_name]\n", + " artists[label, field_name] = ax.pcolormesh(field, vmin=lower, vmax=upper)\n", + " ax.set(aspect=1, xticks=(), yticks=())\n", + " ax.set_title(field.attrs[\"Description\"].decode(\"utf-8\") + f\"\\n({label})\", fontsize=9)\n", + "\n", + "def update(timestep):\n", + " for (label, field_name), artist in artists.items():\n", + " artist.set_array(state_sequences[label][f\"t{timestep:04}\"][field_name])\n", + " return tuple(artists.values())\n", + "\n", + "plt.close(fig)\n", + " \n", + "animation = FuncAnimation(fig=fig, func=update, frames=100)\n", + "HTML(animation.to_html5_video())" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.5" + }, + "widgets": { + "application/vnd.jupyter.widget-state+json": { + "state": {}, + "version_major": 2, + "version_minor": 0 + } + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/extra/llw2d_visualizations.jl b/extra/llw2d_visualizations.jl new file mode 100644 index 00000000..c6ee5df2 --- /dev/null +++ b/extra/llw2d_visualizations.jl @@ -0,0 +1,155 @@ +### A Pluto.jl notebook ### +# v0.19.32 + +using Markdown +using InteractiveUtils + +# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error). +macro bind(def, element) + quote + local iv = try Base.loaded_modules[Base.PkgId(Base.UUID("6e696c72-6542-2067-7265-42206c756150"), "AbstractPlutoDingetjes")].Bonds.initial_value catch; b -> missing; end + local el = $(esc(element)) + global $(esc(def)) = Core.applicable(Base.get, el) ? Base.get(el) : iv(el) + el + end +end + +# ╔═╡ 3508a798-905c-11ee-21fa-f5fff35793da +begin + using Pkg + Pkg.activate(".") + using ParticleDA + using Plots + using PlutoUI + using PlutoLinks: @ingredients + using HDF5 + using YAML +end + +# ╔═╡ bdf320a8-2581-4529-b279-b536d9720c89 +LLW2d = @ingredients("../test/models/llw2d.jl").LLW2d + +# ╔═╡ 03e16c11-7c81-4a1c-ac21-9f2640811882 +function plot_state_fields( + state, + model, + title; + show_station_locations=true, + size=(900, 320), +) + fields = LLW2d.flat_state_to_fields(state, model.parameters) + boundary_size = ( + floor(Int, model.parameters.absorber_thickness_fraction * model.parameters.nx), + floor(Int, model.parameters.absorber_thickness_fraction * model.parameters.ny) + ) + index_1_range = boundary_size[1]:model.parameters.nx-boundary_size[1] + index_2_range = boundary_size[2]:model.parameters.ny-boundary_size[2] + plots = [ + heatmap( + field[index_1_range, index_2_range], + aspect_ratio=:equal, + clims=(-scale, scale), + xticks=nothing, + yticks=nothing, + cmap=:deep, + legend=:none, + title=label, + xlims=(1, length(index_1_range)), + ylims=(1, length(index_2_range)), + ) + for (field, label, scale) in zip( + eachslice(fields, dims=3), + ("Surface height", "Velocity component 1", "Velocity component 2"), + (3, 300, 300), + ) + ] + if show_station_locations + station_grid_indices = LLW2d.get_station_grid_indices(model.parameters) + for observed_index in model.parameters.observed_state_var_indices + scatter!( + plots[observed_index], + eachcol(station_grid_indices)..., + xlims=(1, length(index_1_range)), + ylims=(1, length(index_1_range)), + marker=2 + ) + end + end + plot( + plots..., + plot_title=title, + plot_titlevspan=-0.1, + layout=grid(1, 3), + size=size + ) +end + +# ╔═╡ 6c6b7457-d77a-44fe-b37b-a4f5e34f25b7 +function fields_to_state_vector(group) + vcat((vec(read(group, key)) for key in ("height", "vx", "vy"))...) +end + +# ╔═╡ e7d10ba9-1e28-4d2d-9b9b-bb7a9dfd345c +parameters = YAML.load_file("llw2d_parameters.yaml"); + +# ╔═╡ 746ef1cf-f99f-4cf4-9636-360fffe1dcdf +model = LLW2d.init(parameters["model"]); + +# ╔═╡ 861dd61a-6ec1-4bf3-8ccd-dbe1381b88c5 +num_time_step = parameters["simulate_observations"]["n_time_step"]; + +# ╔═╡ 847ec134-0807-49a3-8842-d81767a4dedb +state_true_sequence, state_mean_sequence, state_std_sequence = let + state_eltype = ParticleDA.get_state_eltype(model) + state_dimension = ParticleDA.get_state_dimension(model) + + state_true_seq = Matrix{state_eltype}(undef, num_time_step + 1, state_dimension) + state_mean_seq = Matrix{state_eltype}(undef, num_time_step + 1, state_dimension) + state_std_seq = Matrix{state_eltype}(undef, num_time_step + 1, state_dimension) + h5open("llw2d_simulated.h5", "r") do file + for t in 0:num_time_step + key = ParticleDA.time_index_to_hdf5_key(t) + state_true_seq[t + 1, :] = fields_to_state_vector(file["state"][key]) + end + end + h5open("llw2d_filtered.h5", "r") do file + for t in 0:num_time_step + key = ParticleDA.time_index_to_hdf5_key(t) + state_mean_seq[t + 1, :] = fields_to_state_vector(file["state_avg"][key]) + state_std_seq[t + 1, :] = sqrt.( + fields_to_state_vector(file["state_var"][key]) + ) + end + end + state_true_seq, state_mean_seq, state_std_seq +end; + +# ╔═╡ 33e6291a-7035-42df-aa6e-2870f5d1a830 +md""" +Timestep $(@bind timestep Slider(1:num_time_step; default=0, show_value=true)) +""" + +# ╔═╡ d25d3792-0a23-4e02-836b-6e3aa9060280 +let + plots = [ + plot_state_fields( + view(state_true_sequence, timestep, :), model, "True state" + ), + plot_state_fields( + view(state_mean_sequence, timestep, :), model, "Filtering estimate (mean)" + ) + ] + plot(plots..., layout=(2, 1), size=(900, 700)) +end + +# ╔═╡ Cell order: +# ╠═3508a798-905c-11ee-21fa-f5fff35793da +# ╠═bdf320a8-2581-4529-b279-b536d9720c89 +# ╠═03e16c11-7c81-4a1c-ac21-9f2640811882 +# ╠═6c6b7457-d77a-44fe-b37b-a4f5e34f25b7 +# ╠═e7d10ba9-1e28-4d2d-9b9b-bb7a9dfd345c +# ╠═746ef1cf-f99f-4cf4-9636-360fffe1dcdf +# ╠═861dd61a-6ec1-4bf3-8ccd-dbe1381b88c5 +# ╠═847ec134-0807-49a3-8842-d81767a4dedb +# ╟─33e6291a-7035-42df-aa6e-2870f5d1a830 +# ╠═d25d3792-0a23-4e02-836b-6e3aa9060280 diff --git a/extra/lorenz63_example.jl b/extra/lorenz63_example.jl new file mode 100644 index 00000000..56f85e9b --- /dev/null +++ b/extra/lorenz63_example.jl @@ -0,0 +1,254 @@ +### A Pluto.jl notebook ### +# v0.19.32 + +using Markdown +using InteractiveUtils + +# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error). +macro bind(def, element) + quote + local iv = try Base.loaded_modules[Base.PkgId(Base.UUID("6e696c72-6542-2067-7265-42206c756150"), "AbstractPlutoDingetjes")].Bonds.initial_value catch; b -> missing; end + local el = $(esc(element)) + global $(esc(def)) = Core.applicable(Base.get, el) ? Base.get(el) : iv(el) + el + end +end + +# ╔═╡ 86be08c2-5337-4b00-bdcc-26a2f04ff162 +begin + using Pkg + Pkg.activate(".") + using ParticleDA + using PlutoLinks: @ingredients + using PlutoUI + using Plots + using HDF5 + using Random + using Statistics + using YAML +end + +# ╔═╡ 7709ac00-728f-11ed-1f00-1f458e5ad3e2 +Lorenz63 = @ingredients("../test/models/lorenz63.jl").Lorenz63 + +# ╔═╡ 16a443e1-7b7f-4ba5-8999-2dd59eed50d3 +function load_simulation_outputs(output_filename) + h5open(output_filename, "r") do file + n_time_step = length(file["observations"]) + observation_dim = length(first(file["observations"])) + observation_eltype = eltype(first(file["observations"])) + state_dim = length(first(file["state"])) + state_eltype = eltype(first(file["state"])) + observation_sequence = Matrix{observation_eltype}( + undef, observation_dim, n_time_step + ) + state_true_sequence = Matrix{state_eltype}( + undef, state_dim, n_time_step + ) + for t in 1:n_time_step + key = ParticleDA.time_index_to_hdf5_key(t) + observation_sequence[:, t] = read(file["observations"][key]) + state_true_sequence[:, t] = read(file["state"][key]) + end + return observation_sequence, state_true_sequence + end +end + +# ╔═╡ cfb7be2d-772f-454f-b822-80899ed6ff55 +function load_filtering_outputs(output_filename) + h5open(output_filename, "r") do file + n_time_step = length(file["weights"]) - 1 + state_dim = length(first(file["state_avg"])) + state_eltype = eltype(first(file["state_avg"])) + n_particle = length(first(file["weights"])) + state_mean_sequence = Matrix{Float64}(undef, state_dim, n_time_step) + state_std_sequence = Matrix{Float64}(undef, state_dim, n_time_step) + weights_sequence = Matrix{Float64}(undef, n_particle, n_time_step) + for t in 1:n_time_step + key = ParticleDA.time_index_to_hdf5_key(t) + state_mean_sequence[:, t] = read(file["state_avg"][key]) + state_std_sequence[:, t] = read(file["state_var"][key]) + weights_sequence[:, t] = read(file["weights"][key]) + end + return state_mean_sequence, state_std_sequence, weights_sequence + end +end + +# ╔═╡ b10b319f-964a-43d0-a5fb-9847af748ae9 +function plot_effective_sample_sizes(weights_sequence) + n_time_step = size(weights_sequence, 2) + ess_sequence = 1 ./ sum(x -> x.^2, weights_sequence; dims=1)[1, :] + plot( + 1:n_time_step, + ess_sequence, + xlabel="Time index", + ylabel="Estimated ESS", + size=(800, 200), + legend=:none, + margin=20Plots.px, + ) +end + +# ╔═╡ 9243268a-daf7-450b-b275-ebebb3150c86 +function plot_rmses(state_true_sequence, state_mean_sequence) + n_time_step = size(state_mean_sequence, 2) + rmse_sequence = sqrt.( + mean(x -> x.^2, state_mean_sequence .- state_true_sequence; dims=1) + )[1, :] + plot( + 1:n_time_step, + rmse_sequence, + xlabel="Time index", + ylabel="RMSE(mean, truth)", + size=(800, 200), + legend=:none, + margin=20Plots.px, + ) +end + +# ╔═╡ 01da3a88-aa3c-4f32-b5c8-cd447665a3be +function plot_3d_comparison( + observed_indices, + observation_sequence, + state_true_sequence, + state_mean_sequence, +) + n_time_step = size(state_mean_sequence, 2) + p = plot(size=(800, 800), xlabel="x₁", ylabel="x₂", zlabel="x₃") + plot!(p, eachrow(state_true_sequence)..., label="True", ) + plot!(p, eachrow(state_mean_sequence)..., label="Filtering estimate (mean)") +end + +# ╔═╡ f9c5199a-3cd3-44c8-9bfc-8b90a8d8c9b9 +function plot_per_dimension_comparison( + observed_indices, + observation_sequence, + state_true_sequence, + state_mean_sequence, + state_std_sequence, +) + n_time_step = size(state_mean_sequence, 2) + plots = Array{Plots.Plot}(undef, 3) + for (i, (mean, std, state, label)) in enumerate(zip( + eachrow(state_mean_sequence), + eachrow(state_std_sequence), + eachrow(state_true_sequence), + ["x₁", "x₂", "x₃"] + )) + plots[i] = plot( + 1:n_time_step, + mean, + xlabel="Time index", + ylabel=label, + label="Filtering estimate", + ribbon=3 * std, + fillalpha=0.5, + legend=:outerright, + ) + if i in observed_indices + j = findfirst(isequal(i), observed_indices) + plot!( + plots[i], + 1:n_time_step, + observation_sequence[j, :], + seriestype=[:scatter], + label="Observations", + markersize=2, + markerstrokewidth=0, + ) + end + plot!(plots[i], 1:n_time_step, state, label="Truth") + end + plot( + plots..., + layout=(3, 1), + size=(800, 800), + margin=20Plots.px, + ) +end + +# ╔═╡ 4715bcaa-b726-4439-aa38-22708a918df4 +md""" +Number of particles $(@bind n_particle NumberField(1:1000, default=100))\ +Number of timesteps $(@bind n_time_step NumberField(1:1000, default=500))\ +Filter type $(@bind filter_type Select([OptimalFilter => "locally optimal", BootstrapFilter => "bootstrap"]))\ +Initial state std. $(@bind initial_state_std NumberField(0:0.1:10, default=0.5))\ +State noise std. $(@bind state_noise_std NumberField(0:0.1:10, default=0.5))\ +Observation noise std. $(@bind observation_noise_std NumberField(0:0.1:10, default=1.))\ +Observed state indices $(@bind observed_indices MultiCheckBox([1, 2, 3], default=[1,2,3])) +Show 3D plot $(@bind show_3d_plot CheckBox(default=true)) +""" + +# ╔═╡ 4d57d231-78fb-4383-a559-da84444ff7c1 +let + simulation_filename = tempname() + filtering_filename = tempname() + rng = Random.TaskLocalRNG() + Random.seed!(rng, 1234) + model_dict = Dict( + "observation_noise_std" => observation_noise_std, + "initial_state_std" => initial_state_std, + "state_noise_std" => state_noise_std, + "observed_indices" => observed_indices, + ) + model = Lorenz63.init(model_dict) + h5open(simulation_filename, "w") do file + ParticleDA.simulate_observations_from_model( + model, n_time_step; output_file=file, rng=rng + ) + end + observation_sequence, state_true_sequence = load_simulation_outputs( + simulation_filename + ) + filter_parameters = ParticleDA.FilterParameters( + nprt=n_particle, verbose=true, output_filename=filtering_filename, + ) + ParticleDA.run_particle_filter( + Lorenz63.init, + filter_parameters, + model_dict, + observation_sequence, + filter_type, + ParticleDA.MeanAndVarSummaryStat; + rng=rng + ) + state_mean_sequence, state_std_sequence, weights_sequence = load_filtering_outputs( + filtering_filename + ) + ess_plot = plot_effective_sample_sizes(weights_sequence) + rmse_plot = plot_rmses(state_true_sequence, state_mean_sequence) + if show_3d_plot + state_plot = plot_3d_comparison( + observed_indices, + observation_sequence, + state_true_sequence, + state_mean_sequence, + ) + else + state_plot = plot_per_dimension_comparison( + observed_indices, + observation_sequence, + state_true_sequence, + state_mean_sequence, + state_std_sequence + ) + end + plot( + ess_plot, rmse_plot, state_plot, + layout=grid(3, 1, heights=[0.15 ,0.15, 0.7]), + size=(800, 1200) + ) + +end + +# ╔═╡ Cell order: +# ╠═86be08c2-5337-4b00-bdcc-26a2f04ff162 +# ╠═7709ac00-728f-11ed-1f00-1f458e5ad3e2 +# ╠═16a443e1-7b7f-4ba5-8999-2dd59eed50d3 +# ╠═cfb7be2d-772f-454f-b822-80899ed6ff55 +# ╠═b10b319f-964a-43d0-a5fb-9847af748ae9 +# ╠═9243268a-daf7-450b-b275-ebebb3150c86 +# ╠═01da3a88-aa3c-4f32-b5c8-cd447665a3be +# ╠═f9c5199a-3cd3-44c8-9bfc-8b90a8d8c9b9 +# ╟─4715bcaa-b726-4439-aa38-22708a918df4 +# ╠═4d57d231-78fb-4383-a559-da84444ff7c1 diff --git a/extra/particle_da.h5 b/extra/particle_da.h5 deleted file mode 100644 index c72cb0a6..00000000 Binary files a/extra/particle_da.h5 and /dev/null differ