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| [deps] | ||
| ArchGDAL = "c9ce4bd3-c3d5-55b8-8973-c0e20141b8c3" | ||
| DimensionalData = "0703355e-b756-11e9-17c0-8b28908087d0" | ||
| Extents = "411431e0-e8b7-467b-b5e0-f676ba4f2910" | ||
| GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a" | ||
| GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326" | ||
| NaturalEarth = "436b0209-26ab-4e65-94a9-6526d86fea76" | ||
| PyramidScheme = "ec211b67-1c2c-4319-878f-eaee078ee145" | ||
| RasterDataSources = "3cb90ccd-e1b6-4867-9617-4276c8b2ca36" | ||
| Rasters = "a3a2b9e3-a471-40c9-b274-f788e487c689" | ||
| WGLMakie = "276b4fcb-3e11-5398-bf8b-a0c2d153d008" | ||
| YAXArrays = "c21b50f5-aa40-41ea-b809-c0f5e47bfa5c" |
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| --- | ||
| engine: julia | ||
| title: "PyramidScheme.jl \n interactively plotting large raster data" | ||
| author: "Felix Cremer, Fabian Gans" | ||
| format: revealjs | ||
| execute: | ||
| echo: true | ||
| --- | ||
|
|
||
| ## What are pyramids? | ||
|
|
||
| ```{julia} | ||
| #| echo: false | ||
| using WGLMakie | ||
| using PyramidScheme | ||
| using DimensionalData.Dimensions | ||
| using DimensionalData | ||
| using Extents | ||
| @dim lat YDim "Latitude" | ||
| @dim lon XDim "Longitude" | ||
| replacenan(data) = data <= 0 ? NaN32 : Float32(data) | ||
| fullpyr = replacenan.(Pyramid(joinpath(@__DIR__,"..", "test/data/ESACCI-BIOMASS-L4-AGB-MERGED-100m-2020-fv4.0.zarr/"))) | ||
| europe= Extent(lon=(-10.0,35.0),lat=(33.0,70.0)) | ||
| europyr = Pyramid(fullpyr.base[lon = Between(europe.lon...), lat=Between(europe.lat...)], [l[lon = Between(europe.lon...), lat=Between(europe.lat...)] for l in fullpyr.levels], metadata(fullpyr)) | ||
| lim = Extent(X = (-63.36854472609895, -57.18529373390659), Y = (-2.666626089016638, -1.9161481184310643)) | ||
| subpyr = Pyramid(fullpyr.levels[3][lon = Between(lim.X...), lat=Between(lim.Y...)], [l[lon = Between(lim.X...), lat=Between(lim.Y...)] for l in fullpyr.levels[4:7]], metadata(fullpyr)) | ||
| function plotpyramid(fullpyr) | ||
| ps = Pyramid(fullpyr.levels[end-2], fullpyr.levels[end-1:end], metadata(fullpyr)) | ||
| n=4 | ||
| levelsizes = collect(size.(PyramidScheme.levels(ps))) | ||
| numlevels = PyramidScheme.nlevels(ps) | ||
| offsets = [(0.,0.)] | ||
| for i in 1:numlevels | ||
| s = size(PyramidScheme.levels(ps, i)) ./2 | ||
| push!(offsets, offsets[i] .+ s) | ||
| end | ||
| fig = Figure() | ||
| #globax = Axis(fig[1,1]) | ||
| #plot!(globax, fullpyr, colormap=:speed, colorscale=sqrt) | ||
| ax = Axis3(fig[1:2,1]) | ||
| for (i, offset) in enumerate(offsets) | ||
| axn = Axis(fig[3-i,2]) | ||
| l = levelsizes[i] | ||
| x = first(offset):(first(offset)+first(l)-1) | ||
| y = last(offset):last(offset) + last(l)-1 | ||
| r = Rect3(Point3f( offset..., 2*i), Vec3f(l..., 1)) | ||
| mesh!(ax, r, color=:grey80) | ||
| heatmap!(ax, reverse(x), y,PyramidScheme.levels(ps,i-1), transformation=(:xy, 2*i+1.2), colormap=:speed, colorscale=sqrt) | ||
| heatmap!(axn, PyramidScheme.levels(ps, i-1), colormap=:speed, colorscale=sqrt) | ||
| hidexdecorations!(axn) | ||
| axn.aspect = DataAspect() | ||
| end | ||
| hidedecorations!(ax) | ||
| hidespines!(ax) | ||
| colsize!(fig.layout, 2, Relative(0.3)) | ||
| fig | ||
| end | ||
| plotpyramid(europyr) | ||
| ``` | ||
|
|
||
|
|
||
| ## Compute the pyramids for your data | ||
| - In Memory data | ||
|
|
||
| ```{julia} | ||
| #| eval: false | ||
| using Rasters | ||
| using RasterDataSources | ||
| ras = Raster(WorldClim{Elevation},:elev, res="30s", lazy=true) | ||
| pyr = Pyramid(ras, resampling_method=mean) | ||
| Progress: 100%|████████████████████████████████████████████| Time: 0:00:47 | ||
| ``` | ||
|
|
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| - Larger data on disk | ||
|
|
||
| ```{julia} | ||
| #| eval: false | ||
| using YAXArrays | ||
| elevpath = getraster(WorldClim{Elevation},:elev, res="30s") | ||
| elev = Cube(elevpath) | ||
| zarrpath = tempname() * ".zarr" | ||
| savecube(elev, zarrpath) | ||
| PyramidScheme.buildpyramids(zarrpath) | ||
| ``` | ||
|
|
||
| ## Access Pyramiddata | ||
|
|
||
| - Zarr data | ||
| - Geotiff | ||
| - Locally or in the cloud | ||
| ```{julia} | ||
| agb2020 = replacenan.(Pyramid(joinpath(@__DIR__,"..", "test/data/ESACCI-BIOMASS-L4-AGB-MERGED-100m-2020-fv4.0.zarr/"))) | ||
| ``` | ||
|
|
||
| # Interactive visualisation | ||
|
|
||
| ```{julia} | ||
| #| eval: false | ||
| plot(agb2020, colormap=:speed, colorscale=sqrt) | ||
| ``` | ||
|
|
||
| # Computations on Pyramids | ||
| ```{julia} | ||
| #| eval: false | ||
| replacenan(data) = data <= 0 ? NaN32 : Float32(data) | ||
| agb2020 = replacenan.(Pyramid(joinpath(@__DIR__,"..", "test/data/ESACCI-BIOMASS-L4-AGB-MERGED-100m-2020-fv4.0.zarr/"))) | ||
| agb2017 = replacenan.(Pyramid(joinpath(@__DIR__,"..", "test/data/ESACCI-BIOMASS-L4-AGB-MERGED-100m-2017-fv4.0.zarr/"))) | ||
| agbdiff = agb2020 .- agb2017 | ||
| plot(agbdiff, colormap=:bukavu, colorrange=(-200, 200)) | ||
| ``` | ||
|
|
||
|
|
||
| # Outlook | ||
|
|
||
| - pyramids in multiple dimensions | ||
|
|
||
| - Understanding more formats | ||
|
|
||
| - Integrate DiskArrayEngine computations | ||
|
|
||
| - Open it up to more use cases | ||
|
|
||
| ```{julia} | ||
| #| eval:false | ||
| using YAXArrays, PyramidScheme | ||
| using GLMakie | ||
| import PyramidScheme as PS | ||
| using DiskArrays | ||
| import DimensionalData as DD | ||
| using DimensionalData.Dimensions | ||
| @dim lat YDim "Latitude" | ||
| @dim lon XDim "Longitude" | ||
| p2020 = PS.Pyramid("https://s3.bgc-jena.mpg.de:9000/pyramids/ESACCI-BIOMASS-L4-AGB-MERGED-100m-2020-fv4.0.zarr") | ||
| function DiskArrays.cache(a::YAXArray;maxsize=1000) | ||
| DD.rebuild(a,DiskArrays.cache(a.data;maxsize)) | ||
| end | ||
| function DiskArrays.cache(p::Pyramid;maxsize = 1000) | ||
| maxsize = maxsize ÷ (length(p.levels)+1) | ||
| Pyramid(DiskArrays.cache(p.base;maxsize),DiskArrays.cache.(p.levels;maxsize),p.metadata) | ||
| end | ||
| p2020 = DiskArrays.cache(p2020) | ||
| replacenan(nanval) = data -> <=(nanval)(data) ? NaN32 : Float32(data) | ||
| p2020nan = replacenan(0).(p2020) | ||
| plot(p2020nan, colormap=:speed, colorscale=sqrt) | ||
| ``` |
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