├── docs ├── src │ ├── guides │ │ └── tracks.md │ ├── topics │ │ ├── GEDI.md │ │ ├── ICESat-2.md │ │ └── ICESat.md │ ├── changelog.md │ ├── reference │ │ └── api.md │ ├── tutorial │ │ ├── installation.md │ │ └── usage.md │ ├── img │ │ └── favicon.svg │ ├── index.md │ ├── International_Space_Station.svg │ └── julia-dots.svg ├── versions.js ├── Project.toml ├── versions.json ├── make.jl ├── update_version.jl └── mkdocs.yml ├── .JuliaFormatter.toml ├── CITATION.cff ├── .gitignore ├── .github └── workflows │ ├── TagBot.yml │ ├── CompatHelper.yml │ ├── docs.yml │ └── CI.yml ├── src ├── geoid.jl ├── ICESat-2 │ ├── ATL12.jl │ ├── ICESat-2.jl │ ├── ATL03.jl │ ├── ATL08.jl │ └── blacklist.txt ├── geoarrays.jl ├── SpaceLiDAR.jl ├── GEDI │ ├── GEDI.jl │ └── L2A.jl ├── granule.jl ├── ICESat │ ├── ICESat.jl │ └── GLAH14.jl ├── laz.jl ├── interpolate.jl ├── s3.jl ├── geom.jl ├── geom_utils.jl ├── search.jl └── utils.jl ├── .cz.toml ├── .travis.yml ├── .appveyor.yml ├── Project.toml ├── test └── runtests.jl ├── README.md ├── notebooks └── juliacon_2021.jl ├── scripts └── outliers.jl └── LICENSE /docs/src/guides/tracks.md: -------------------------------------------------------------------------------- 1 | # Track filtering 2 | 3 | *Coming soon* 4 | -------------------------------------------------------------------------------- /docs/src/topics/GEDI.md: -------------------------------------------------------------------------------- 1 | # GEDI 2 | See their website at gedi.umd.edu 3 | -------------------------------------------------------------------------------- /docs/src/topics/ICESat-2.md: -------------------------------------------------------------------------------- 1 | # ICESat-2 2 | See their website at icesat-2.gsfc.nasa.gov 3 | 4 | -------------------------------------------------------------------------------- /docs/src/topics/ICESat.md: -------------------------------------------------------------------------------- 1 | # ICESat 2 | See their website at https://icesat.gsfc.nasa.gov/icesat/ -------------------------------------------------------------------------------- /docs/src/changelog.md: -------------------------------------------------------------------------------- 1 | ## Unreleased 2 | 3 | 4 | ## v0.1.3 5 | - Added interpolation for GeoArrays 6 | - Added FOSS4G notebook 7 | -------------------------------------------------------------------------------- /docs/src/reference/api.md: -------------------------------------------------------------------------------- 1 | # API reference 2 | 3 | ```@index 4 | ``` 5 | 6 | ```@autodocs 7 | Modules = [SpaceLiDAR] 8 | ``` 9 | -------------------------------------------------------------------------------- /docs/versions.js: -------------------------------------------------------------------------------- 1 | var DOC_VERSIONS = [ 2 | "stable", 3 | "v0.3", 4 | "v0.2", 5 | "v0.1", 6 | "dev", 7 | ]; 8 | -------------------------------------------------------------------------------- /docs/src/tutorial/installation.md: -------------------------------------------------------------------------------- 1 | # Installation 2 | Use the Julia built in package manager: 3 | ```julia 4 | ] add SpaceLiDAR 5 | ``` 6 | -------------------------------------------------------------------------------- /.JuliaFormatter.toml: -------------------------------------------------------------------------------- 1 | always_for_in = true 2 | always_use_return = true 3 | margin = 80 4 | remove_extra_newlines = true 5 | short_to_long_function_def = true 6 | -------------------------------------------------------------------------------- /docs/Project.toml: -------------------------------------------------------------------------------- 1 | [deps] 2 | Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" 3 | DocumenterMarkdown = "997ab1e6-3595-5248-9280-8efb232c3433" 4 | DocumenterTools = "35a29f4d-8980-5a13-9543-d66fff28ecb8" 5 | SpaceLiDAR = "29bf0bfc-420f-4fa5-b441-811fd9e6e11d" 6 | -------------------------------------------------------------------------------- /CITATION.cff: -------------------------------------------------------------------------------- 1 | cff-version: 1.2.0 2 | message: "If you use this software, please cite it using these metadata." 3 | authors: 4 | - affiliation: "Deltares, TU Delft" 5 | family-names: Pronk 6 | given-names: Maarten 7 | orcid: "https://orcid.org/0000-0001-8758-3939" 8 | date-released: 2021-07-30 9 | title: "SpaceLiDAR.jl" 10 | version: 1.0.0 11 | url: "https://github.com/evetion/SpaceLiDAR.jl" 12 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | *.jl.*.cov 2 | *.jl.cov 3 | *.jl.mem 4 | .DS_Store 5 | Manifest.toml 6 | /dev/ 7 | /docs/build/ 8 | /docs/site/ 9 | *.csv 10 | *.txt 11 | *.laz 12 | *.gpkg 13 | .pytest_cache 14 | .mypy_cache 15 | .ipynb_checkpoints 16 | *.pdf 17 | *.png 18 | *.tif 19 | *.tiff 20 | *.shp 21 | *.dbf 22 | *.prj 23 | *.qpj 24 | *.cpg 25 | *.shx 26 | *.vscode 27 | scripts 28 | *.h5 29 | /test/data 30 | /temp 31 | /output 32 | /data 33 | -------------------------------------------------------------------------------- /.github/workflows/TagBot.yml: -------------------------------------------------------------------------------- 1 | name: TagBot 2 | on: 3 | issue_comment: 4 | types: 5 | - created 6 | workflow_dispatch: 7 | jobs: 8 | TagBot: 9 | if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot' 10 | runs-on: ubuntu-latest 11 | steps: 12 | - uses: JuliaRegistries/TagBot@v1 13 | with: 14 | token: ${{ secrets.GITHUB_TOKEN }} 15 | ssh: ${{ secrets.DOCUMENTER_KEY }} 16 | -------------------------------------------------------------------------------- /src/geoid.jl: -------------------------------------------------------------------------------- 1 | using Proj4 2 | 3 | function to_egm2008!(table) 4 | egm08 = "./egm08_25.gtx" 5 | egm08 = isfile(egm08) ? abspath(egm08) : Base.download("https://github.com/OSGeo/proj-datumgrid/raw/master/world/egm08_25.gtx", egm08) 6 | wgs84 = Projection("+proj=longlat +datum=WGS84 +no_defs") 7 | egm2008 = Projection("+proj=vgridshift +grids=$egm08") 8 | data = hcat(Float64.(table.x), Float64.(table.y), Float64.(table.z)) 9 | transform!(wgs84, egm2008, data) 10 | table.z .= data[:,3] 11 | end 12 | -------------------------------------------------------------------------------- /.github/workflows/CompatHelper.yml: -------------------------------------------------------------------------------- 1 | name: CompatHelper 2 | on: 3 | schedule: 4 | - cron: 0 0 * * * 5 | workflow_dispatch: 6 | jobs: 7 | CompatHelper: 8 | runs-on: ubuntu-latest 9 | steps: 10 | - name: Pkg.add("CompatHelper") 11 | run: julia -e 'using Pkg; Pkg.add("CompatHelper")' 12 | - name: CompatHelper.main() 13 | env: 14 | GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} 15 | COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }} 16 | run: julia -e 'using CompatHelper; CompatHelper.main()' 17 | -------------------------------------------------------------------------------- /docs/versions.json: -------------------------------------------------------------------------------- 1 | [ 2 | { 3 | "aliases": [], 4 | "title": "stable", 5 | "version": "stable" 6 | }, 7 | { 8 | "aliases": [], 9 | "title": "v0.3", 10 | "version": "v0.3" 11 | }, 12 | { 13 | "aliases": [], 14 | "title": "v0.2", 15 | "version": "v0.2" 16 | }, 17 | { 18 | "aliases": [], 19 | "title": "v0.1", 20 | "version": "v0.1" 21 | }, 22 | { 23 | "aliases": [], 24 | "title": "dev", 25 | "version": "dev" 26 | } 27 | ] -------------------------------------------------------------------------------- /.cz.toml: -------------------------------------------------------------------------------- 1 | [tool.commitizen] 2 | name = "cz_conventional_commits" 3 | version = "0.1.0" 4 | version_files = [ 5 | "Project.toml:version", 6 | ] 7 | style = [ 8 | ["qmark", "fg:#ff9d00 bold"], 9 | ["question", "bold"], 10 | ["answer", "fg:#ff9d00 bold"], 11 | ["pointer", "fg:#ff9d00 bold"], 12 | ["highlighted", "fg:#ff9d00 bold"], 13 | ["selected", "fg:#cc5454"], 14 | ["separator", "fg:#cc5454"], 15 | ["instruction", ""], 16 | ["text", ""], 17 | ["disabled", "fg:#858585 italic"] 18 | ] 19 | changelog_file = "docs/src/changelog.md" 20 | -------------------------------------------------------------------------------- /docs/make.jl: -------------------------------------------------------------------------------- 1 | using Documenter, SpaceLiDAR 2 | using DocumenterMarkdown 3 | 4 | makedocs(; 5 | modules=[SpaceLiDAR], 6 | format=Markdown(), 7 | # pages=[ 8 | # "API" => "reference/api.md", 9 | # ], 10 | repo="https://github.com/evetion/SpaceLiDAR.jl/blob/{commit}{path}#L{line}", 11 | sitename="SpaceLiDAR.jl", 12 | authors="Maarten Pronk, Deltares", 13 | ) 14 | 15 | deploydocs(; 16 | repo="github.com/evetion/SpaceLiDAR.jl", 17 | deps=Deps.pip("mkdocs-material", "pygments", "python-markdown-math", "mkdocs-autorefs"), 18 | make=() -> run(`mkdocs build`), 19 | target="site" 20 | ) 21 | -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 1 | # Documentation: http://docs.travis-ci.com/user/languages/julia/ 2 | language: julia 3 | os: 4 | - linux 5 | - osx 6 | julia: 7 | - 1.0 8 | - nightly 9 | notifications: 10 | email: false 11 | after_success: 12 | - julia -e 'using Pkg; Pkg.add("Coverage"); using Coverage; Codecov.submit(process_folder())' 13 | jobs: 14 | allow_failures: 15 | - julia: nightly 16 | fast_finish: true 17 | include: 18 | - stage: Documentation 19 | julia: 1.0 20 | script: julia --project=docs -e ' 21 | using Pkg; 22 | Pkg.develop(PackageSpec(path=pwd())); 23 | Pkg.instantiate(); 24 | include("docs/make.jl");' 25 | after_success: skip 26 | -------------------------------------------------------------------------------- /docs/src/img/favicon.svg: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /.github/workflows/docs.yml: -------------------------------------------------------------------------------- 1 | name: Documentation 2 | 3 | on: 4 | push: 5 | branches: 6 | - master 7 | tags: '*' 8 | pull_request: 9 | 10 | jobs: 11 | build: 12 | runs-on: ubuntu-latest 13 | steps: 14 | - uses: actions/checkout@v2 15 | - uses: julia-actions/setup-julia@latest 16 | with: 17 | version: '1.6' 18 | - name: Install dependencies 19 | run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()' 20 | - name: Build and deploy 21 | env: 22 | GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token 23 | DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key 24 | run: julia --project=docs/ docs/make.jl 25 | -------------------------------------------------------------------------------- /.appveyor.yml: -------------------------------------------------------------------------------- 1 | # Documentation: https://github.com/JuliaCI/Appveyor.jl 2 | environment: 3 | matrix: 4 | - julia_version: 1.0 5 | - julia_version: nightly 6 | platform: 7 | - x86 8 | - x64 9 | matrix: 10 | allow_failures: 11 | - julia_version: nightly 12 | branches: 13 | only: 14 | - master 15 | - /release-.*/ 16 | notifications: 17 | - provider: Email 18 | on_build_success: false 19 | on_build_failure: false 20 | on_build_status_changed: false 21 | install: 22 | - ps: iex ((new-object net.webclient).DownloadString("https://raw.githubusercontent.com/JuliaCI/Appveyor.jl/version-1/bin/install.ps1")) 23 | build_script: 24 | - echo "%JL_BUILD_SCRIPT%" 25 | - C:\julia\bin\julia -e "%JL_BUILD_SCRIPT%" 26 | test_script: 27 | - echo "%JL_TEST_SCRIPT%" 28 | - C:\julia\bin\julia -e "%JL_TEST_SCRIPT%" 29 | on_success: 30 | - echo "%JL_CODECOV_SCRIPT%" 31 | - C:\julia\bin\julia -e "%JL_CODECOV_SCRIPT%" 32 | -------------------------------------------------------------------------------- /docs/update_version.jl: -------------------------------------------------------------------------------- 1 | # Post script to run to generate a mike compatible json file 2 | # from the javascripts versions file generated by Documenter. 3 | # This enables a version dropdown to be present in all documentation. 4 | using JSON 5 | 6 | versions = read("versions.js", String) 7 | re = r"DOC_VERSIONS\s?=\s?\[([^][]*)]" 8 | m = match(re, versions) 9 | if m === nothing 10 | error("Can't parse versions.js correctly") 11 | else 12 | group = String(m.captures[1]) 13 | group = replace(group, "\n" => "") 14 | group = replace(group, "\"" => "") 15 | group = replace(group, " " => "") 16 | json = [] 17 | for version in split(group, ",") 18 | if length(version) > 0 19 | push!(json,Dict( 20 | "version" => version, 21 | "title" => version, 22 | "aliases" => [] 23 | )) 24 | end 25 | end 26 | end 27 | write("versions.json", JSON.json(json)) 28 | -------------------------------------------------------------------------------- /src/ICESat-2/ATL12.jl: -------------------------------------------------------------------------------- 1 | 2 | function points(granule::ICESat2_Granule{:ATL12}, bbox=nothing, tracks=icesat2_tracks) 3 | dfs = Vector{NamedTuple}() 4 | HDF5.h5open(granule.url, "r") do file 5 | t_offset = read(file, "ancillary_data/atlas_sdp_gps_epoch")[1] + gps_offset 6 | orientation = read(file, "orbit_info/sc_orient")[1] 7 | 8 | for track ∈ tracks 9 | power = track_power(orientation, track) 10 | if in(track, keys(file)) && in("ssh_segments", keys(file[track])) && in("heights", keys(file[track]["ssh_segments"])) 11 | track_df = points(granule, file, track, power, t_offset) 12 | push!(dfs, track_df) 13 | end 14 | end 15 | end 16 | dfs 17 | end 18 | 19 | function points(::ICESat2_Granule{:ATL12}, file::HDF5.H5DataStore, track::AbstractString, power::AbstractString, t_offset::Real) 20 | z = read(file, "$track/ssh_segments/heights/h") 21 | x = read(file, "$track/ssh_segments/longitude") 22 | y = read(file, "$track/ssh_segments/latitude") 23 | t = read(file, "$track/ssh_segments/delta_time") 24 | 25 | times = unix2datetime.(t .+ t_offset) 26 | 27 | (x = x, y = y, z = z, t = times, track = Fill(track, length(times)), power = Fill(power, length(times))) 28 | end 29 | -------------------------------------------------------------------------------- /src/geoarrays.jl: -------------------------------------------------------------------------------- 1 | using Statistics 2 | using GeoArrays 3 | using StaticArrays 4 | 5 | function indices(ga::GeoArray, p::SVector{2,Float32}) 6 | map(x -> round(Int, x), inv(ga.f)(p)::SVector{2,Float64}) .+ 1 7 | end 8 | function indices(ga::GeoArray, p::SVector{2,Float64}) 9 | map(x -> round(Int, x), inv(ga.f)(p)::SVector{2,Float64}) .+ 1 10 | end 11 | function Base.getindex(ga::GeoArray, I::SVector{2,Float32}, buffer=0) 12 | (i, j) = indices(ga, I) 13 | return ga[i - buffer:i + buffer, j - buffer:j + buffer, :] 14 | end 15 | Base.getindex(ga::GeoArray, I::Vararg{Float32,2}) = Base.getindex(ga, SVector{2}(I)) 16 | 17 | function sample(ga::GeoArray, x::Real, y::Real, buffer=0, reducer=median) 18 | I = SVector{2}(x, y) 19 | i, j = indices(ga, I) 20 | 0 < i - buffer <= Base.size(ga.A)[1] || return NaN 21 | 0 < j - buffer <= Base.size(ga.A)[2] || return NaN 22 | 0 < i + buffer <= Base.size(ga.A)[1] || return NaN 23 | 0 < j + buffer <= Base.size(ga.A)[2] || return NaN 24 | # (all((i, j) .> (0, 0)) && all(Base.size(ga.A)[1:2] >= (i, j))) || return NaN 25 | data = ga.A[i - buffer:i + buffer, j - buffer:j + buffer, 1] 26 | mask = isfinite.(data) 27 | if sum(mask) == 0 28 | return NaN 29 | else 30 | return reducer(data[mask]) 31 | end 32 | end 33 | -------------------------------------------------------------------------------- /src/SpaceLiDAR.jl: -------------------------------------------------------------------------------- 1 | module SpaceLiDAR 2 | 3 | using Dates 4 | using CategoricalArrays 5 | using FillArrays 6 | using GeoDataFrames; const GDF = GeoDataFrames 7 | using HDF5 8 | 9 | include("granule.jl") 10 | include("utils.jl") 11 | include("search.jl") 12 | include("geom.jl") 13 | include("geom_utils.jl") 14 | include("s3.jl") 15 | include("geoarrays.jl") 16 | include("GEDI/GEDI.jl") 17 | include("GEDI/L2A.jl") 18 | include("ICESat-2/ICESat-2.jl") 19 | include("ICESat-2/ATL03.jl") 20 | include("ICESat-2/ATL08.jl") 21 | include("ICESat-2/ATL12.jl") 22 | include("ICESat/ICESat.jl") 23 | include("ICESat/GLAH14.jl") 24 | include("laz.jl") 25 | include("interpolate.jl") 26 | include("geoid.jl") 27 | 28 | export find, download!, netrc!, instantiate 29 | export xyz, lines, points, in_bbox, bounds 30 | export test, granule_from_file, granules_from_folder, write_granule_urls! 31 | 32 | precompile(find, (Symbol, String, NamedTuple, String)) 33 | precompile(find, (Symbol, String)) 34 | precompile(GeoArrays.read, (String,)) 35 | precompile(GeoArrays.read, (String, Bool)) 36 | precompile(instantiate, (Vector{ICESat2_Granule}, String)) 37 | precompile(instantiate, (Vector{GEDI_Granule}, String)) 38 | precompile(granules_from_folder, (String,)) 39 | precompile(granule_from_file, (String,)) 40 | precompile(download!, (ICESat2_Granule,)) 41 | precompile(download!, (GEDI_Granule,)) 42 | precompile(points, (GEDI_Granule,)) 43 | precompile(points, (ICESat2_Granule,)) 44 | precompile(lines, (GEDI_Granule,)) 45 | precompile(lines, (ICESat2_Granule,)) 46 | precompile(angle, (Vector{Float32}, Vector{Float32})) 47 | precompile(shift, (Float32, Float32, Float64, Float64)) 48 | 49 | end # module 50 | -------------------------------------------------------------------------------- /src/GEDI/GEDI.jl: -------------------------------------------------------------------------------- 1 | using Dates 2 | 3 | const gedi_tracks = ("BEAM0000", "BEAM0001", "BEAM0010", "BEAM0011", "BEAM0101", "BEAM0110", "BEAM1000", "BEAM1011") 4 | const gedi_date_format = dateformat"yyyymmddHHMMSS" 5 | const gedi_inclination = 51.6443 6 | 7 | mutable struct GEDI_Granule{product} <: Granule 8 | id::AbstractString 9 | url::AbstractString 10 | info::NamedTuple 11 | end 12 | GEDI_Granule(product, args...) = GEDI_Granule{product}(args...) 13 | 14 | function Base.copy(g::GEDI_Granule{product}) where product 15 | GEDI_Granule(product, g.id, g.url, g.info) 16 | end 17 | 18 | function info(g::GEDI_Granule) 19 | gedi_info(g.id) 20 | end 21 | 22 | """Derive info based on file id. 23 | 24 | The id is built up as follows, see section 2.4 in the user guide 25 | GEDI02_A_2019110014613_O01991_T04905_02_001_01.h5 26 | or newer (V2) 27 | GEDI02_A_2019242104318_O04046_01_T02343_02_003_02_V002.h5 28 | """ 29 | function gedi_info(filename) 30 | id, _ = splitext(filename) 31 | if endswith(id, "V002") 32 | type, name, datetime, orbit, segment, track, ppds, pge_version, revision, version = Base.split(id, "_") 33 | version = version[2:end] 34 | else 35 | type, name, datetime, orbit, track, ppds, version, revision = Base.split(id, "_") 36 | end 37 | days = Day(parse(Int, datetime[5:7]) - 1) # Stored as #days in year 38 | datetime = datetime[1:4] * "0101" * datetime[8:end] 39 | (type = Symbol(type * "_" * name), date = DateTime(datetime, gedi_date_format) + days, orbit = parse(Int, orbit[2:end]), track = parse(Int, track[2:end]), ppds = parse(Int, ppds), version = parse(Int, version), revision = parse(Int, revision)) 40 | end 41 | -------------------------------------------------------------------------------- /src/granule.jl: -------------------------------------------------------------------------------- 1 | using HDF5 2 | import Downloads 3 | 4 | """This is a method because it will segfault if precompiled.""" 5 | function _download(kwargs...) 6 | downloader = Downloads.Downloader() 7 | easy_hook = (easy, _) -> begin 8 | Downloads.Curl.setopt(easy, Downloads.Curl.CURLOPT_NETRC, Downloads.Curl.CURL_NETRC_OPTIONAL) 9 | Downloads.Curl.setopt(easy, Downloads.Curl.CURLOPT_COOKIEFILE, "") 10 | end 11 | downloader.easy_hook = easy_hook 12 | Downloads.download(kwargs...;downloader=downloader) 13 | end 14 | 15 | abstract type Granule end 16 | 17 | function HDF5.h5open(granule::Granule) 18 | HDF5.h5open(granule.url, "r") 19 | end 20 | 21 | function download!(granule::Granule, folder=".") 22 | fn = joinpath(abspath(folder), granule.id) 23 | if isfile(fn) 24 | granule.url = fn 25 | return fn 26 | end 27 | isfile(granule.url) && return granule 28 | if startswith(granule.url, "s3://") 29 | download_s3(granule.url, fn) 30 | elseif startswith(granule.url, "http") 31 | _download(granule.url, fn) 32 | else 33 | error("Can't determine how to download $(granule.url)") 34 | end 35 | granule.url = fn 36 | granule 37 | end 38 | 39 | function rm(granule::Granule) 40 | if isfile(granule.url) 41 | Base.rm(granule.url) 42 | else 43 | @warn("Can't delete $(granule.url)..") 44 | end 45 | end 46 | 47 | function download!(granules::Vector{Granule}, folder::AbstractString) 48 | for granule in granules 49 | download!(granule, folder) 50 | end 51 | end 52 | 53 | function filesize(granule::T) where T <: Granule 54 | filesize(granule.url) 55 | end 56 | -------------------------------------------------------------------------------- /.github/workflows/CI.yml: -------------------------------------------------------------------------------- 1 | name: CI 2 | on: 3 | - push 4 | - pull_request 5 | jobs: 6 | test: 7 | name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }} 8 | runs-on: ${{ matrix.os }} 9 | strategy: 10 | fail-fast: false 11 | matrix: 12 | version: 13 | - "1.5" 14 | - "1.6" 15 | os: 16 | - ubuntu-latest 17 | - macOS-latest 18 | - windows-latest 19 | arch: 20 | - x64 21 | steps: 22 | - uses: actions/checkout@v2 23 | - uses: julia-actions/setup-julia@v1 24 | with: 25 | version: ${{ matrix.version }} 26 | arch: ${{ matrix.arch }} 27 | 28 | - name: Create LFS file list 29 | run: git lfs ls-files -l | cut -d' ' -f1 | sort > .lfs-assets-id 30 | 31 | - name: Restore LFS cache 32 | uses: actions/cache@v2 33 | id: lfs-cache 34 | with: 35 | path: .git/lfs 36 | key: ${{ runner.os }}-lfs-${{ hashFiles('.lfs-assets-id') }}-v1 37 | 38 | - name: Git LFS Pull 39 | run: git lfs pull 40 | 41 | - uses: actions/cache@v1 42 | env: 43 | cache-name: cache-artifacts 44 | with: 45 | path: ~/.julia/artifacts 46 | key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }} 47 | restore-keys: | 48 | ${{ runner.os }}-test-${{ env.cache-name }}- 49 | ${{ runner.os }}-test- 50 | ${{ runner.os }}- 51 | - uses: julia-actions/julia-buildpkg@v1 52 | - uses: julia-actions/julia-runtest@v1 53 | - uses: julia-actions/julia-processcoverage@v1 54 | - uses: codecov/codecov-action@v1 55 | with: 56 | file: lcov.info 57 | -------------------------------------------------------------------------------- /src/ICESat/ICESat.jl: -------------------------------------------------------------------------------- 1 | using Dates 2 | 3 | const j2000_offset = datetime2unix(DateTime(2000, 1, 1, 12, 0, 0)) 4 | const fill_value = 3.4028235f38 5 | const icesat_inclination = 86.0 # actually 92, so this is 180. - 92. 6 | 7 | 8 | mutable struct ICESat_Granule{product} <: Granule 9 | id::String 10 | url::String 11 | info::NamedTuple 12 | end 13 | ICESat_Granule(product, args...) = ICESat_Granule{product}(args...) 14 | 15 | function Base.copy(g::ICESat_Granule{product}) where product 16 | ICESat_Granule(product, g.id, g.url, g.info) 17 | end 18 | 19 | function bounds(granule::ICESat_Granule) 20 | HDF5.h5open(granule.url, "r") do file 21 | nt = attributes(file) 22 | ntb = ( 23 | min_x = parse(Float64, read(nt["geospatial_lon_min"])), 24 | max_x = parse(Float64, read(nt["geospatial_lon_max"])), 25 | min_y = parse(Float64, read(nt["geospatial_lat_min"])), 26 | max_y = parse(Float64, read(nt["geospatial_lat_max"])), 27 | min_z = -1000, 28 | max_z = 8000 29 | ) 30 | @info ntb 31 | ntb 32 | end 33 | end 34 | 35 | 36 | Base.isfile(g::ICESat_Granule) = Base.isfile(g.url) 37 | 38 | """Derive info based on file id. 39 | 40 | The id is built up as follows, see 1.2.5 in the user guide 41 | ATL03_[yyyymmdd][hhmmss]_[ttttccss]_[vvv_rr].h5 42 | """ 43 | function info(g::ICESat_Granule) 44 | icesat_info(g.id) 45 | end 46 | 47 | function icesat_info(filename) 48 | id, _ = splitext(filename) 49 | type, revision, orbit, cycle, track, segment, version, filetype = split(id, "_") 50 | (type = Symbol(type), phase = parse(Int, orbit[1]), rgt = parse(Int, track[2]), instance = parse(Int, track[3:4]), cycle = parse(Int, cycle), segment = parse(Int, segment), version = parse(Int, version), revision = parse(Int, revision)) 51 | end 52 | -------------------------------------------------------------------------------- /docs/mkdocs.yml: -------------------------------------------------------------------------------- 1 | site_name: SpaceLiDAR.jl 2 | repo_url: https://github.com/evetion/SpaceLiDAR.jl 3 | site_description: Description... 4 | site_author: evetion 5 | site_url: https://www.evetion.nl/SpaceLiDAR.jl/ 6 | 7 | extra_css: 8 | - assets/Documenter.css 9 | - css/earth.css 10 | 11 | extra_javascript: 12 | - https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS_HTML 13 | - assets/mathjaxhelper.js 14 | 15 | docs_dir: "build" 16 | 17 | nav: 18 | 19 | theme: 20 | name: material 21 | icon: 22 | logo: material/satellite-variant 23 | favicon: img/favicon.svg 24 | language: en 25 | palette: 26 | - media: "(prefers-color-scheme: light)" 27 | scheme: default 28 | primary: blue grey 29 | accent: indigo 30 | toggle: 31 | icon: material/lightbulb-outline 32 | name: Switch to dark mode 33 | - media: "(prefers-color-scheme: dark)" 34 | scheme: slate 35 | toggle: 36 | icon: material/lightbulb 37 | name: Switch to light mode 38 | features: 39 | - navigation.instant 40 | - navigation.tracking 41 | - navigation.tabs 42 | # - navigation.sections 43 | - navigation.expand 44 | - navigation.top 45 | plugins: 46 | - search 47 | - autorefs 48 | markdown_extensions: 49 | - extra 50 | - tables 51 | - fenced_code 52 | - mdx_math 53 | - pymdownx.highlight 54 | - admonition 55 | - toc: 56 | permalink: true 57 | edit_uri: edit/master/docs/ 58 | repo_name: evetion/SpaceLiDAR.jl 59 | extra: 60 | version: 61 | provider: mike 62 | social: 63 | - icon: fontawesome/brands/github 64 | link: https://github.com/evetion/SpaceLiDAR.jl 65 | name: Source code 66 | - icon: fontawesome/brands/gitter 67 | link: https://gitter.im/evetion/community 68 | name: Chat with me on Gitter 69 | copyright: Copyright © 2021 Maarten Pronk, Deltares 70 | -------------------------------------------------------------------------------- /src/laz.jl: -------------------------------------------------------------------------------- 1 | using LazIO 2 | using TypedTables 3 | using FillArrays 4 | 5 | function LazIO.write(fn::AbstractString, granule::ICESat2_Granule) 6 | meta = info(granule) 7 | id = "$(meta.type)_$(meta.rgt)_$(meta.cycle)_$(meta.segment)_$(meta.version)_$(meta.revision)" 8 | t = vcat(Table.(points(granule))...) 9 | nt = Table( 10 | X=t.x, 11 | Y=t.y, 12 | Z=t.z, 13 | intensity=round.(UInt16, min.(65535, t.u * 100)), 14 | gps_time=t.t, 15 | classification=t.classification, 16 | number_of_returns=t.number_of_returns, 17 | return_number=t.return_number, 18 | scan_angle_rank=map(==("strong"), t.power), 19 | point_source_ID=Fill(UInt16(meta.rgt), length(t)), 20 | user_data=Fill(UInt16(meta.cycle), length(t)) 21 | ) 22 | LazIO.write(fn, nt[.~isnan.(t.z)], bounds(granule), scalex=1e-6, scaley=1e-6, scalez=0.001, system_identifier=LazIO.writestring(id, 32), point_data_format=1, point_data_record_length=28, global_encoding=1) 23 | end 24 | 25 | function LazIO.write(fn::AbstractString, granule::GEDI_Granule) 26 | meta = info(granule) 27 | id = "$(meta.type)_$(meta.orbit)_$(meta.track)_$(meta.version)_$(meta.revision)" 28 | t = vcat(Table.(points(granule))...) 29 | nt = Table( 30 | X=t.x, 31 | Y=t.y, 32 | Z=t.z, 33 | intensity=round.(UInt16, min.(65535, t.u * 100)), 34 | gps_time=t.t, 35 | classification=t.classification, 36 | number_of_returns=t.number_of_returns, 37 | return_number=t.return_number, 38 | scan_angle_rank=map(==("strong"), t.power), 39 | point_source_ID=Fill(UInt16(meta.orbit), length(t)), 40 | ) 41 | LazIO.write(fn, nt[.~isnan.(t.z)], bounds(granule), scalex=1e-7, scaley=1e-7, scalez=0.001, system_identifier=LazIO.writestring(id, 32), point_data_format=1, point_data_record_length=28, global_encoding=1) 42 | end 43 | -------------------------------------------------------------------------------- /src/interpolate.jl: -------------------------------------------------------------------------------- 1 | using GeoArrays 2 | using StaticArrays 3 | using ProgressMeter 4 | using NearestNeighbors 5 | using StarTIN 6 | using Distances 7 | 8 | function interpolate!(ga::GeoArray, t, r=500.) 9 | tt = hcat(t.x, t.y) 10 | ttt = permutedims(tt) 11 | tree = BallTree(ttt, Haversine()) 12 | ui, uj = Base.size(ga)[1:2] 13 | p = Progress(length(ga), 1, "Interpolating...") 14 | Threads.@threads for i in 1:ui 15 | Threads.@threads for j in 1:uj 16 | coords = centercoords(ga, SVector{2}(i, j))::SArray{Tuple{2},Float64,1,2} 17 | ga.A[i, j, 1] = idw(coords, tree, r, t.z, ttt) 18 | next!(p) 19 | end 20 | end 21 | end 22 | 23 | function interpolate_nni!(ga::GeoArray, t, r=1., scale=100.0) 24 | tt = hcat(t.x .* scale, t.y .* scale, t.z) 25 | ttt = permutedims(tt) 26 | dt = DT() 27 | @time insert!(dt, ttt) 28 | StarTIN.info(dt) 29 | ui, uj = size(ga)[1:2] 30 | p = Progress(length(ga), 1, "Interpolating...") 31 | for i in 1:ui 32 | for j in 1:uj 33 | coords = centercoords(ga, SVector{2}(i, j))::SArray{Tuple{2},Float64,1,2} 34 | @inbounds ga.A[i, j, 1] = interpolate_laplace(dt, coords[1] * scale, coords[2] * scale) 35 | next!(p) 36 | end 37 | end 38 | end 39 | 40 | function idw(coords, tree, r, values, coordinates, power=2) 41 | idxs = inrange(tree, coords, r) 42 | if length(idxs) == 0 43 | return NaN32 44 | else 45 | distances = colwise(Haversine(), Float32.(coords), coordinates[:,idxs]) 46 | ws = 1.0f0 ./ distances.^power # .* view(uncertainty, idxs) 47 | Σw = sum(ws) 48 | 49 | if isinf(Σw) 50 | j = findfirst(iszero, distances) 51 | μ = values[idxs[j]] 52 | else 53 | ws ./= Σw 54 | vs = view(values, idxs) 55 | μ = sum(ws[i] * vs[i] for i in eachindex(vs)) 56 | end 57 | return μ 58 | end 59 | end 60 | -------------------------------------------------------------------------------- /docs/src/tutorial/usage.md: -------------------------------------------------------------------------------- 1 | # Usage 2 | Search for data 3 | ```julia 4 | using SpaceLiDAR 5 | # Find all ATL08 granules 6 | granules = find(:ICESat2, "ATL08") 7 | 8 | # Find only ATL03 granules in a part of Vietnam 9 | vietnam = (min_x = 102., min_y = 8.0, max_x = 107.0, max_y = 12.0) 10 | granules = find(:ICESat2, "ATL08", vietnam, "004") 11 | 12 | # Find GEDI granules in the same way 13 | granules = find(:GEDI, "GEDI02_A") 14 | 15 | # A granule is pretty simple 16 | granule = granules[1] 17 | granule.id # filename 18 | granule.url # download url 19 | granule.info # derived information from id 20 | 21 | # Downloading granules requires a setup .netrc with an NASA EarthData account 22 | # we provide a helper function, that creates/updates a ~/.netrc or ~/_netrc 23 | SpaceLiDAR.netrc!(, ) # replace with your credentials 24 | 25 | # Afterward you can download (requires curl to be available on PATH) 26 | fn = SpaceLiDAR.download!(granule) 27 | 28 | # You can also load a granule from disk 29 | granule = granule_from_file(fn) 30 | 31 | # Or from a folder 32 | local_granules = granules_from_folder() 33 | 34 | # Instantiate search results locally (useful for GEDI location indexing) 35 | local_granules = instantiate(granules, ) 36 | 37 | ``` 38 | 39 | Derive linestrings 40 | ```julia 41 | using TypedTables 42 | fn = "ATL03_20181110072251_06520101_003_01.h5" 43 | g = SpaceLiDAR.granule_from_file(fn) 44 | tlines = Table(SpaceLiDAR.lines(g, step=10000)) 45 | Table with 4 columns and 6 rows: 46 | geom sun_angle track t 47 | ┌─────────────────────────────────────────────────────────────────────────── 48 | 1 │ wkbLineString25D geometry 38.3864 gt1l_weak 2018-11-10T07:28:01.688 49 | 2 │ wkbLineString25D geometry 38.375 gt1r_strong 2018-11-10T07:28:02.266 50 | 3 │ wkbLineString25D geometry 38.2487 gt2l_weak 2018-11-10T07:28:04.474 51 | 4 │ wkbLineString25D geometry 38.1424 gt2r_strong 2018-11-10T07:28:07.374 52 | 5 │ wkbLineString25D geometry 38.2016 gt3l_weak 2018-11-10T07:28:05.051 53 | 6 │ wkbLineString25D geometry 38.1611 gt3r_strong 2018-11-10T07:28:06.344 54 | SpaceLiDAR.GDF.write("lines.gpkg", tlines) 55 | ``` 56 | -------------------------------------------------------------------------------- /src/s3.jl: -------------------------------------------------------------------------------- 1 | using AWSCore 2 | using AWSS3 3 | 4 | 5 | function download_s3(path::AbstractString, fn::AbstractString) 6 | # elements = split(path, "/") 7 | # bucket = elements[3] 8 | # path = join(elements[4:end], "/") 9 | # aws = AWSCore.aws_config(profile="default", region="eu-west-1") 10 | # AWSS3.s3_get_file(aws, bucket, path, fn) 11 | run(`aws s3 cp --only-show-errors $path $fn`) 12 | end 13 | 14 | """Change default download locatio n to a S3 bucket.""" 15 | function s3!(granule::Granule, bucket::String="s3://spacelidar", verify=false) 16 | fn = granule.id 17 | if verify && ~in(bucket, fn) 18 | return granule 19 | else 20 | granule.url = joinpath(bucket, fn) 21 | return granule 22 | end 23 | end 24 | s3!(granules::Vector{<:Granule}, args...) = map!(x -> s3!(x, args...), granules) 25 | 26 | function Base.in(granule::Granule, bucket::AbstractString="spacelidar") 27 | aws = AWSCore.aws_config(profile="default", region="eu-west-1") 28 | AWSS3.s3_exists(aws, bucket, granule.id) 29 | end 30 | 31 | function sync!(granules::Vector{<:Granule}, bucket="s3://spacelidar") 32 | mask = trues(length(granules)) 33 | while sum(mask) > 0 34 | in_bucket = map(x -> x["Key"], s3_list_objects(aws, bucket)) 35 | mask = map(g -> ~(g.id in in_bucket), granules) 36 | @info "Still checking $(sum(mask)) to sync granules..." 37 | for granule in granules[.~mask] 38 | granule.url = joinpath(bucket, granule.id) 39 | end 40 | download_to_s3(granules[mask], bucket) 41 | end 42 | granules 43 | end 44 | 45 | function download_to_s3(granules::Vector{<:Granule}, bucket="spacelidar") 46 | fn_hook = write_upload_hook!("s3_upload_hook.sh", bucket) 47 | fn_urls = write_granule_urls!("to_download.txt", granules) 48 | print(read(`aria2c --on-download-complete $fn_hook --file-allocation=none --continue=true --auto-file-renaming=false -j3 -x1 -i $fn_urls`)) 49 | end 50 | 51 | 52 | function write_upload_hook!(fn::String, bucket="spacelidar", rm=true) 53 | open(fn, "w") do f 54 | println(f, "#bin/sh") 55 | if rm 56 | println(f, "aws s3 cp \$3 s3://$bucket/ && rm \$3") 57 | else 58 | println(f, "aws s3 cp \$3 s3://$bucket/") 59 | end 60 | end 61 | chmod(fn, 0o775) 62 | abspath(fn) 63 | end 64 | -------------------------------------------------------------------------------- /Project.toml: -------------------------------------------------------------------------------- 1 | name = "SpaceLiDAR" 2 | uuid = "29bf0bfc-420f-4fa5-b441-811fd9e6e11d" 3 | authors = ["Maarten Pronk", "Deltares"] 4 | version = "0.1.3" 5 | 6 | [deps] 7 | AWSCore = "4f1ea46c-232b-54a6-9b17-cc2d0f3e6598" 8 | AWSS3 = "1c724243-ef5b-51ab-93f4-b0a88ac62a95" 9 | ArchGDAL = "c9ce4bd3-c3d5-55b8-8973-c0e20141b8c3" 10 | CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" 11 | CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597" 12 | Dates = "ade2ca70-3891-5945-98fb-dc099432e06a" 13 | Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" 14 | Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6" 15 | FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" 16 | GeoArrays = "2fb1d81b-e6a0-5fc5-82e6-8e06903437ab" 17 | GeoDataFrames = "62cb38b5-d8d2-4862-a48e-6a340996859f" 18 | HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f" 19 | HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3" 20 | ImageFiltering = "6a3955dd-da59-5b1f-98d4-e7296123deb5" 21 | JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" 22 | LazIO = "c3605908-9f0f-11e8-0a72-0d361c15a277" 23 | NearestNeighbors = "b8a86587-4115-5ab1-83bc-aa920d37bbce" 24 | PolygonOps = "647866c9-e3ac-4575-94e7-e3d426903924" 25 | Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7" 26 | ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca" 27 | Proj4 = "9a7e659c-8ee8-5706-894e-f68f43bc57ea" 28 | Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" 29 | RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" 30 | StarTIN = "152385ed-0447-47b3-b417-bbbf3d580ece" 31 | StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" 32 | Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" 33 | Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" 34 | TypedTables = "9d95f2ec-7b3d-5a63-8d20-e2491e220bb9" 35 | 36 | [compat] 37 | AWSCore = "^0.6" 38 | AWSS3 = "^0.8, 0.9" 39 | ArchGDAL = "^0.7" 40 | CSV = "^0.8, 0.9" 41 | CategoricalArrays = "^0.9, 0.10" 42 | Distances = "^0.10" 43 | FillArrays = "^0.11, 0.12" 44 | GeoArrays = "^0.5, 0.6" 45 | GeoDataFrames = "^0.1" 46 | HDF5 = "^0.15" 47 | HTTP = "^0.9" 48 | ImageFiltering = "^0.6, 0.7" 49 | JSON = "^0.21" 50 | LazIO = "^0.3" 51 | NearestNeighbors = "^0.4" 52 | PolygonOps = "^0.1" 53 | ProgressMeter = "^1.4" 54 | RecipesBase = "^1.1" 55 | StarTIN = "^0.1" 56 | StaticArrays = "^0.12, 1" 57 | Tables = "^1.4" 58 | TypedTables = "^1.3" 59 | julia = "^1.3" 60 | 61 | [extras] 62 | Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" 63 | 64 | [targets] 65 | test = ["Test"] 66 | -------------------------------------------------------------------------------- /docs/src/index.md: -------------------------------------------------------------------------------- 1 | 2 | [![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://evetion.github.io/SpaceLiDAR.jl/stable) 3 | [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://evetion.github.io/SpaceLiDAR.jl/dev) 4 | [![CI](https://github.com/evetion/SpaceLiDAR.jl/actions/workflows/CI.yml/badge.svg)](https://github.com/evetion/SpaceLiDAR.jl/actions/workflows/CI.yml) 5 | [![codecov](https://codecov.io/gh/evetion/SpaceLiDAR.jl/branch/master/graph/badge.svg?token=nztwnGtIcY)](https://codecov.io/gh/evetion/SpaceLiDAR.jl) 6 | 7 | # SpaceLiDAR 8 | A Julia toolbox for ICESat-2 and GEDI data. 9 | 10 | *This is a research package now, things are quick to change.* 11 | 12 | 13 | Currently supports the following data products: 14 | 15 | | data product | User Guide (UG) | Algorithm Theoretical Basis Document (ATBD)| 16 | |--- |--- |--- | 17 | | ICESat GLAH14 v34 | [UG](https://nsidc.org/sites/nsidc.org/files/MULTI-GLAH01-V033-V034-UserGuide.pdf) | [ATBD](https://eospso.nasa.gov/sites/default/files/atbd/ATBD-GLAS-02.pdf) | 18 | | ICESat-2 ATL03 v4 | [UG](https://nsidc.org/sites/nsidc.org/files/ATL03-V004-UserGuide.pdf) | [ATBD](https://icesat-2.gsfc.nasa.gov/sites/default/files/page_files/ICESat2_ATL03_ATBD_r004.pdf) | 19 | | ICESat-2 ATL08 v4 | [UG](https://nsidc.org/sites/nsidc.org/files/ATL08-V004-UserGuide.pdf) | [ATBD](https://icesat-2.gsfc.nasa.gov/sites/default/files/page_files/ICESat2_ATL08_ATBD_r004.pdf) | 20 | | ICESat-2 ATL12 v4 | [UG](https://nsidc.org/sites/nsidc.org/files/ATL12-V004-UserGuide.pdf) | [ATBD](https://icesat-2.gsfc.nasa.gov/sites/default/files/page_files/ICESat2_ATL12_ATBD_r004.pdf) | 21 | | GEDI L2A v2 | [UG](https://lpdaac.usgs.gov/documents/998/GEDI02_User_Guide_V2.pdf) | [ATBD](https://lpdaac.usgs.gov/documents/581/GEDI_WF_ATBD_v1.0.pdf) | 22 | 23 | 24 | For a quick overview, see the FOSS4G Pluto notebook [here](tutorial/foss4g_2021.jl.html) 25 | 26 | 27 | ## Papers 28 | Results are used (indirectly) in the following papers: 29 | 30 | Vernimmen, Ronald, Aljosja Hooijer, and Maarten Pronk. 2020. ‘New ICESat-2 Satellite LiDAR Data Allow First Global Lowland DTM Suitable for Accurate Coastal Flood Risk Assessment’. Remote Sensing 12 (17): 2827. [https://doi.org/10/gg9dg6](https://doi.org/10/gg9dg6). 31 | 32 | Hooijer, A., and R. Vernimmen. 2021. ‘Global LiDAR Land Elevation Data Reveal Greatest Sea-Level Rise Vulnerability in the Tropics’. Nature Communications 12 (1): 3592. [https://doi.org/10/gkzf49](https://doi.org/10/gkzf49). 33 | 34 | 35 | -------------------------------------------------------------------------------- /src/ICESat/GLAH14.jl: -------------------------------------------------------------------------------- 1 | const icesat_fill = 1.7976931348623157E308 2 | 3 | function points(granule::ICESat_Granule{:GLAH14}; step=1) 4 | HDF5.h5open(granule.url, "r") do file 5 | 6 | zt = file["Data_40HZ/Elevation_Surfaces/d_elev"][1:step:end]::Vector{Float64} 7 | m = zt .!= icesat_fill 8 | zc = file["Data_40HZ/Elevation_Corrections/d_satElevCorr"][1:step:end]::Vector{Float64} 9 | m .&= (zc .!= icesat_fill) 10 | zt .+= zc 11 | 12 | # tu = file["$track/land_segments/terrain/h_te_uncertainty"][1:step:end]::Array{Float32,1} 13 | 14 | x = file["Data_40HZ/Geolocation/d_lon"][1:step:end]::Vector{Float64} 15 | m .&= (x .!= icesat_fill) 16 | x[x .> 180] .= x[x .> 180] .- 360.0 # translate from 0 - 360 17 | y = file["Data_40HZ/Geolocation/d_lat"][1:step:end]::Vector{Float64} 18 | m .&= (y .!= icesat_fill) 19 | 20 | t = file["Data_40HZ/DS_UTCTime_40"][1:step:end][m]::Vector{Float64} 21 | # sensitivity = file["$track/land_segments/snr"][1:step:end]::Array{Float32,1} 22 | 23 | q = file["Data_40HZ/Quality/elev_use_flg"][1:step:end][m]::Vector{Int8} 24 | clouds = file["Data_40HZ/Elevation_Flags/elv_cloud_flg"][1:step:end][m]::Vector{Int8} 25 | sat_corr_flag = file["Data_40HZ/Quality/sat_corr_flg"][1:step:end][m]::Vector{Int8} 26 | att_flag = file["Data_40HZ/Quality/sigma_att_flg"][1:step:end][m]::Vector{Int8} 27 | ref_flag = file["Data_40HZ/Reflectivity/d_reflctUC"][1:step:end][m]::Vector{Float64} 28 | gain_value = file["Data_40HZ/Waveform/i_gval_rcv"][1:step:end][m]::Vector{Int32} 29 | 30 | dem = file["Data_40HZ/Geophysical/d_DEM_elv"][1:step:end][m]::Vector{Float64} 31 | dem[dem .== icesat_fill] .= NaN 32 | 33 | times = unix2datetime.(t .+ j2000_offset) 34 | 35 | gt = ( 36 | x = x[m], 37 | y = y[m], 38 | z = zt[m], 39 | # u = tu, 40 | t = times, 41 | q = .~(Bool.(q)), 42 | # sensitivity = sensitivity, 43 | cloud = Bool.(clouds), 44 | # classification = Fill("ground", length(times)), 45 | # return_number = Fill(2, length(times)), 46 | # number_of_returns = Fill(2, length(times)), 47 | reference = dem, 48 | gain = gain_value, 49 | reflectivity = ref_flag, 50 | attitude = att_flag, 51 | saturation = sat_corr_flag 52 | ) 53 | gt 54 | end 55 | end 56 | -------------------------------------------------------------------------------- /src/geom.jl: -------------------------------------------------------------------------------- 1 | using TypedTables 2 | 3 | const earth_radius_m = 6378.137 * 1000 4 | 5 | function makeline(x, y, z) 6 | mask = .~isnan.(z) 7 | if sum(mask) > 1 # skip creating invalid lines with 0 or 1 point 8 | line = GDF.AG.creategeom(GDF.AG.wkbLineString25D) 9 | GDF.AG.addpoint!.(Ref(line), x[mask], y[mask], z[mask]) 10 | @assert AG.isvalid(line) 11 | else 12 | line = AG.createlinestring() 13 | end 14 | line 15 | end 16 | 17 | function makepoint(x, y, z) 18 | GDF.AG.createpoint.(x, y, z) 19 | end 20 | 21 | # function Base.show(io::IO, geom::GDF.AG.AbstractGeometry) 22 | # if geom.ptr == C_NULL 23 | # print(io, "NULL Geometry") 24 | # else 25 | # print(io, "$(GDF.AG.getgeomtype(geom)) geometry") 26 | # end 27 | # end 28 | 29 | function envelope_polygon(geom::GDF.AG.AbstractGeometry) 30 | e = GDF.AG.envelope(geom) 31 | polygon = GDF.AG.createpolygon() 32 | ring = GDF.AG.createlinearring([(e.MinX, e.MinY), (e.MaxX, e.MinY), (e.MaxX, e.MaxY), (e.MinX, e.MaxY), (e.MinX, e.MinY)]) 33 | GDF.AG.addgeom!(polygon, ring) 34 | polygon 35 | end 36 | 37 | """Calculatitudee angle of direction in degrees where North is 0° for a Table.""" 38 | function angle!(t) 39 | # this assumes the table is ordered by time (ascending) 40 | t.angle = angle(t.x, t.y) 41 | t 42 | end 43 | 44 | """ 45 | angle(longitude::Vector{Number}, latitude::Vector{Number}) 46 | 47 | Calculate the angle of direction from previous points in degrees where North is 0°. 48 | Points are given as `longitude` and `latitude` pairs in their own vector. 49 | The angle for the first point is undefined and set to the second. 50 | 51 | Returns a `Vector{Number}` of angles 52 | """ 53 | function angle(longitude, latitude) 54 | length(longitude) == length(latitude) || error("`longitude` and `latitude` should have the same length.") 55 | angle = zeros(length(longitude)) 56 | prev = zeros(2) 57 | for i ∈ 1:length(longitude) 58 | angle[i] = rad2deg(atan(longitude[i] - prev[1], latitude[i] - prev[2])) 59 | prev[1] = longitude[i] 60 | prev[2] = latitude[i] 61 | end 62 | angle[1] = angle[2] 63 | return angle 64 | end 65 | 66 | """ 67 | shift(longitude, latitude, angle, distance) 68 | 69 | Shift `longitude` and `latitude` with `distance` m in direction `angle`, where North is 0°. 70 | Returns a tuple of the shifted coordinates: `(longitude, latitude)` 71 | """ 72 | function shift(longitude, latitude, angle, distance) 73 | θ = deg2rad(angle) 74 | δ = distance / earth_radius_m 75 | ϕ = deg2rad(latitude) 76 | λ = deg2rad(longitude) 77 | 78 | # Distances.jl only gives us Haversine, so this is the inverse 79 | ϕnew = asin( 80 | sin(ϕ) * cos(δ) + cos(ϕ) * sin(δ) * cos(θ) 81 | ) 82 | λnew = λ + atan( 83 | sin(θ) * sin(δ) * cos(ϕ), cos(δ) - sin(ϕ) * sin(ϕnew) 84 | ) 85 | return rad2deg(λnew), rad2deg(ϕnew) 86 | end 87 | -------------------------------------------------------------------------------- /src/geom_utils.jl: -------------------------------------------------------------------------------- 1 | using ArchGDAL; const AG = ArchGDAL 2 | using Distances 3 | using TypedTables 4 | 5 | function linpol(ax, bx, ay, by, x) 6 | # ax, bx = sort([ax, bx]) 7 | factor = (x - ax) / (bx - ax) 8 | ay + (by - ay) * factor 9 | end 10 | 11 | function z_along_line(line, point) 12 | x = AG.getx(point, 0) 13 | # point left of line, take first z 14 | fx, fy, fz = AG.getpoint(line, 0) 15 | lx, ly, lz = AG.getpoint(line, AG.ngeom(line) - 1) 16 | fx, lx = sort([fx, lx]) 17 | if x <= fx 18 | @info "Before line" 19 | return fz 20 | elseif x >= lx 21 | @info "Behind line" 22 | return lz 23 | else 24 | for i ∈ 0:AG.ngeom(line) - 2 25 | xa, ay, za = AG.getpoint(line, i) 26 | xb, by, zb = AG.getpoint(line, i + 1) 27 | if xa < x < xb || xa > x > xb 28 | return linpol(xa, xb, za, zb, x) 29 | end 30 | end 31 | end 32 | @error "Interpolation failed" 33 | NaN 34 | end 35 | 36 | """Split a linestring if the next point is further than `distance`. 37 | Not using Haversine here, as we want to split on meridians and such.""" 38 | function splitline(line::AG.IGeometry, distance=1.) 39 | points = [AG.getpoint(line, i - 1) for i in 1:AG.ngeom(line)] 40 | splits = Vector{Int}([0]) 41 | for i ∈ 1:length(points) - 1 42 | d = Euclidean()(points[i][1:2], points[i + 1][1:2]) 43 | if d > distance 44 | push!(splits, i) 45 | end 46 | end 47 | if length(splits) == 1 48 | return line 49 | else 50 | lines = Vector{Vector{Tuple{Float64,Float64,Float64}}}() 51 | push!(splits, length(points)) 52 | for i ∈ 1:length(splits) - 1 53 | line = points[splits[i] + 1:splits[i + 1]] 54 | push!(lines, line) 55 | end 56 | filter!(x -> length(x) > 1, lines) # filter out single point linestrings 57 | return AG.createmultilinestring(lines) 58 | end 59 | end 60 | 61 | function splitline(table::TypedTables.Table, distance=1.) 62 | rows = Vector{NamedTuple}() 63 | for row in table 64 | geom = splitline(row.geom, distance) 65 | if AG.getgeomtype(geom) == AG.GDAL.wkbMultiLineString25D 66 | for i in 1:AG.ngeom(geom) 67 | push!(rows, merge(row, (geom = AG.getgeom(geom, i - 1),))) 68 | end 69 | else 70 | push!(rows, merge(row, (geom = geom,))) 71 | end 72 | end 73 | Table(rows) 74 | end 75 | 76 | function clip!(table::TypedTables.Table, box::NamedTuple{(:min_x, :min_y, :max_x, :max_y),NTuple{4,Float64}}) 77 | polygon = createpolygon([[box.min_x, box.min_y], [box.max_x, box.min_y], [box.max_x, box.max_y], [box.min_x, box.max_y], [box.min_x, box.min_y]]) 78 | table.geom .= clip.(table.geom, Ref(polygon)) 79 | end 80 | 81 | function clip(geom::AG.IGeometry, polygon::AG.IGeometry) 82 | if AG.ngeom(geom) > 0 && AG.intersects(geom, polygon) 83 | AG.intersection(geom, polygon) 84 | else 85 | AG.createlinestring() 86 | end 87 | end 88 | 89 | function intersect(a::NamedTuple{(:min_x, :min_y, :max_x, :max_y),NTuple{4,Float64}}, b::NamedTuple{(:min_x, :min_y, :max_x, :max_y),NTuple{4,Float64}}) 90 | !(b.min_x > a.max_x || b.max_x < a.min_x || b.min_y > a.max_y || b.max_y < a.min_y) 91 | end 92 | -------------------------------------------------------------------------------- /test/runtests.jl: -------------------------------------------------------------------------------- 1 | using SpaceLiDAR 2 | using Test 3 | using LazIO 4 | using Distances 5 | import Downloads 6 | using Random 7 | 8 | const rng = MersenneTwister(54321) 9 | 10 | # ensure test data is present 11 | testdir = @__DIR__ 12 | datadir = joinpath(testdir, "data") 13 | isdir(datadir) || mkdir(datadir) 14 | 15 | function download_artifact(version, source_filename) 16 | local_path = joinpath(datadir, source_filename) 17 | url = "https://github.com/evetion/SpaceLiDAR-artifacts/releases/download/v$version/$source_filename" 18 | isfile(local_path) || Downloads.download(url, local_path) 19 | end 20 | 21 | download_artifact(v"0.1", "ATL03_20201121151145_08920913_004_01.h5") 22 | download_artifact(v"0.1", "ATL08_20201121151145_08920913_004_01.h5") 23 | download_artifact(v"0.1", "GEDI02_A_2019242104318_O04046_01_T02343_02_003_02_V002.h5") 24 | download_artifact(v"0.1", "GLAH14_634_1102_001_0071_0_01_0001.H5") 25 | 26 | @testset "SpaceLiDAR.jl" begin 27 | 28 | @testset "utils" begin 29 | @test SpaceLiDAR.track_power(0, "gt1l") == "strong" 30 | @test SpaceLiDAR.track_power(0, "gt1r") == "weak" 31 | @test SpaceLiDAR.track_power(1, "gt1l") == "weak" 32 | @test SpaceLiDAR.track_power(1, "gt1r") == "strong" 33 | @test SpaceLiDAR.track_power(2, "gt1l") == "transit" 34 | @test SpaceLiDAR.track_power(2, "gt1r") == "transit" 35 | end 36 | 37 | @testset "search" begin 38 | @test length(find(:ICESat, "GLAH14")) > 0 39 | @test length(find(:ICESat2, "ATL03", (min_x = 4., min_y = 40., max_x = 5., max_y = 50.))) > 0 40 | @test length(find(:ICESat2, "ATL08", (min_x = 4., min_y = 40., max_x = 5., max_y = 50.))) > 0 41 | @test length(find(:GEDI, "GEDI02_A", (min_x = 4., min_y = 40., max_x = 5., max_y = 50.))) > 0 42 | end 43 | 44 | @testset "GLAH14" begin 45 | fn = joinpath(@__DIR__, "data/GLAH14_634_1102_001_0071_0_01_0001.H5") 46 | g = SpaceLiDAR.granule_from_file(fn) 47 | points = SpaceLiDAR.points(g) 48 | end 49 | @testset "ATL03" begin 50 | fn3 = joinpath(@__DIR__, "data/ATL03_20201121151145_08920913_004_01.h5") 51 | g3 = SpaceLiDAR.granule_from_file(fn3) 52 | points = SpaceLiDAR.points(g3) 53 | @test length(points) == 6 54 | lines = SpaceLiDAR.lines(g3, step=1000) 55 | @test length(lines) == 6 56 | SpaceLiDAR.classify(g3) 57 | end 58 | @testset "ATL08" begin 59 | fn8 = joinpath(@__DIR__, "data/ATL08_20201121151145_08920913_004_01.h5") 60 | g8 = SpaceLiDAR.granule_from_file(fn8) 61 | points = SpaceLiDAR.points(g8, step=1000) 62 | @test length(points) == 6 63 | lines = SpaceLiDAR.lines(g8, step=1000) 64 | @test length(lines) == 6 65 | LazIO.write("test.laz", g8) 66 | end 67 | @testset "L2A" begin 68 | fng = joinpath(@__DIR__, "data/GEDI02_A_2019242104318_O04046_01_T02343_02_003_02_V002.h5") 69 | gg = SpaceLiDAR.granule_from_file(fng) 70 | points = SpaceLiDAR.points(gg, step=1000) 71 | @test length(points) == 8 72 | points = SpaceLiDAR.points(gg, step=1000, canopy=true) 73 | @test length(points) == 16 74 | lines = SpaceLiDAR.lines(gg, step=1000) 75 | @test length(lines) == 8 76 | LazIO.write("test.laz", gg) 77 | end 78 | @testset "Geometry" begin 79 | @testset "shift" begin 80 | n = 100 81 | for (d, angle, x, y) ∈ zip(rand(rng, 0:1000, n), rand(rng, 1:360, n), rand(rng, -180:180, n), rand(-90:90, n)) 82 | o = (x, y) 83 | p = SpaceLiDAR.shift(o..., angle, d) 84 | @test isapprox(Haversine()(o, p), d; rtol=0.001 * d) 85 | end 86 | end 87 | end 88 | end 89 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | 2 | [![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://evetion.github.io/SpaceLiDAR.jl/stable) 3 | [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://evetion.github.io/SpaceLiDAR.jl/dev) 4 | [![CI](https://github.com/evetion/SpaceLiDAR.jl/actions/workflows/CI.yml/badge.svg)](https://github.com/evetion/SpaceLiDAR.jl/actions/workflows/CI.yml) 5 | [![codecov](https://codecov.io/gh/evetion/SpaceLiDAR.jl/branch/master/graph/badge.svg?token=nztwnGtIcY)](https://codecov.io/gh/evetion/SpaceLiDAR.jl) 6 | 7 | 8 | # SpaceLiDAR 9 | A Julia toolbox for ICESat-2 and GEDI data. 10 | 11 | *This is a research package now, things are quick to change.* 12 | 13 | Currently supports the following data products: 14 | 15 | | data product | User Guide (UG) | Algorithm Theoretical Basis Document (ATBD)| 16 | |--- |--- |--- | 17 | | ICESat GLAH14 v34 | [UG](https://nsidc.org/sites/nsidc.org/files/MULTI-GLAH01-V033-V034-UserGuide.pdf) | [ATBD](https://eospso.nasa.gov/sites/default/files/atbd/ATBD-GLAS-02.pdf) | 18 | | ICESat-2 ATL03 v4 | [UG](https://nsidc.org/sites/nsidc.org/files/ATL03-V004-UserGuide.pdf) | [ATBD](https://icesat-2.gsfc.nasa.gov/sites/default/files/page_files/ICESat2_ATL03_ATBD_r004.pdf) | 19 | | ICESat-2 ATL08 v4 | [UG](https://nsidc.org/sites/nsidc.org/files/ATL08-V004-UserGuide.pdf) | [ATBD](https://icesat-2.gsfc.nasa.gov/sites/default/files/page_files/ICESat2_ATL08_ATBD_r004.pdf) | 20 | | ICESat-2 ATL12 v4 | [UG](https://nsidc.org/sites/nsidc.org/files/ATL12-V004-UserGuide.pdf) | [ATBD](https://icesat-2.gsfc.nasa.gov/sites/default/files/page_files/ICESat2_ATL12_ATBD_r004.pdf) | 21 | | GEDI L2A v2 | [UG](https://lpdaac.usgs.gov/documents/998/GEDI02_User_Guide_V2.pdf) | [ATBD](https://lpdaac.usgs.gov/documents/581/GEDI_WF_ATBD_v1.0.pdf) | 22 | 23 | For a quick overview, see the FOSS4G Pluto notebook [here](https://www.evetion.nl/SpaceLiDAR.jl/dev/tutorial/foss4g_2021.jl.html) 24 | 25 | # Install 26 | ```julia 27 | ] add SpaceLiDAR 28 | ``` 29 | 30 | # Usage 31 | Search for data 32 | ```julia 33 | using SpaceLiDAR 34 | # Find all ATL08 granules 35 | granules = find(:ICESat2, "ATL08") 36 | 37 | # Find only ATL03 granules in a part of Vietnam 38 | vietnam = (min_x = 102., min_y = 8.0, max_x = 107.0, max_y = 12.0) 39 | granules = find(:ICESat2, "ATL08", vietnam, "004") 40 | 41 | # Find GEDI granules in the same way 42 | granules = find(:GEDI, "GEDI02_A") 43 | 44 | # A granule is pretty simple 45 | granule = granules[1] 46 | granule.id # filename 47 | granule.url # download url 48 | granule.info # derived information from id 49 | 50 | # Downloading granules requires a setup .netrc with an NASA EarthData account 51 | # we provide a helper function, that creates/updates a ~/.netrc or ~/_netrc 52 | SpaceLiDAR.netrc!(, ) # replace with your credentials 53 | 54 | # Afterward you can download (requires curl to be available on PATH) 55 | fn = SpaceLiDAR.download!(granule) 56 | 57 | # You can also load a granule from disk 58 | granule = granule_from_file(fn) 59 | 60 | # Or from a folder 61 | local_granules = granules_from_folder() 62 | 63 | # Instantiate search results locally (useful for GEDI location indexing) 64 | local_granules = instantiate(granules, ) 65 | ``` 66 | 67 | Derive linestrings 68 | ```julia 69 | using TypedTables 70 | fn = "ATL03_20181110072251_06520101_003_01.h5" 71 | g = SpaceLiDAR.granule_from_file(fn) 72 | tlines = Table(SpaceLiDAR.lines(g, step=10000)) 73 | Table with 4 columns and 6 rows: 74 | geom sun_angle track t 75 | ┌─────────────────────────────────────────────────────────────────────────── 76 | 1 │ wkbLineString25D geometry 38.3864 gt1l_weak 2018-11-10T07:28:01.688 77 | 2 │ wkbLineString25D geometry 38.375 gt1r_strong 2018-11-10T07:28:02.266 78 | 3 │ wkbLineString25D geometry 38.2487 gt2l_weak 2018-11-10T07:28:04.474 79 | 4 │ wkbLineString25D geometry 38.1424 gt2r_strong 2018-11-10T07:28:07.374 80 | 5 │ wkbLineString25D geometry 38.2016 gt3l_weak 2018-11-10T07:28:05.051 81 | 6 │ wkbLineString25D geometry 38.1611 gt3r_strong 2018-11-10T07:28:06.344 82 | SpaceLiDAR.GDF.write("lines.gpkg", tlines) 83 | ``` 84 | -------------------------------------------------------------------------------- /src/ICESat-2/ICESat-2.jl: -------------------------------------------------------------------------------- 1 | using Dates 2 | 3 | const icesat2_tracks = ("gt1l", "gt1r", "gt2l", "gt2r", "gt3l", "gt3r") 4 | const classification = Dict(0x03 => "low_canopy", 0x02 => "ground", 0x04 => "high_canopy", 0x05 => "unclassified", 0x01 => "noise") 5 | const icesat_date_format = dateformat"yyyymmddHHMMSS" 6 | const gps_offset = 315964800 7 | const fill_value = 3.4028235f38 8 | const blacklist = readlines(joinpath(@__DIR__, "blacklist.txt")) 9 | const icesat2_inclination = 88.0 # actually 92, so this is 180. - 92. 10 | 11 | 12 | mutable struct ICESat2_Granule{product} <: Granule 13 | id::String 14 | url::String 15 | bbox::NamedTuple 16 | info::NamedTuple 17 | end 18 | ICESat2_Granule(product, args...) = ICESat2_Granule{product}(args...) 19 | 20 | function Base.copy(g::ICESat2_Granule{product}) where product 21 | ICESat2_Granule(product, g.id, g.url, g.bbox, g.info) 22 | end 23 | 24 | function bounds(granule::ICESat2_Granule) 25 | HDF5.h5open(granule.url, "r") do file 26 | extent = attributes(file["METADATA/Extent"]) 27 | nt = (;collect(Symbol(x) => read(extent[x]) for x in keys(extent))...) 28 | ntb = (min_x = nt.westBoundLongitude, max_x = nt.eastBoundLongitude, min_y = nt.southBoundLatitude, max_y = nt.northBoundLatitude, min_z = -1000, max_z = 8000) 29 | granule.bbox = ntb 30 | ntb 31 | end 32 | end 33 | 34 | """Rough approximation of the track angle on a Euclidian lon/lat plot.""" 35 | function angle(::ICESat2_Granule, latitude=0.0) 36 | d = icesat2_inclination / (pi / 2) 37 | cos(latitude / d) * icesat2_inclination 38 | end 39 | 40 | """Return whether track is a strong or weak beam. 41 | See Section 7.5 The Spacecraft Orientation Parameter of the ATL03 ATDB.""" 42 | function track_power(orientation::Integer, track::String) 43 | # Backward orientation, left beam is strong 44 | if orientation == 0 45 | ifelse(occursin("r", track), "weak", "strong") 46 | # Forward orientation, right beam is strong 47 | elseif orientation == 1 48 | ifelse(occursin("r", track), "strong", "weak") 49 | # Orientation in transit, degradation could occur 50 | else 51 | "transit" 52 | end 53 | end 54 | 55 | Base.isfile(g::ICESat2_Granule) = Base.isfile(g.url) 56 | 57 | function Base.convert(product::Symbol, g::ICESat2_Granule{T}) where T 58 | g = ICESat2_Granule{product}( 59 | replace(replace(g.id, String(T) => String(product)), lowercase(String(T)) => lowercase(String(product))), 60 | replace(replace(g.url, String(T) => String(product)), lowercase(String(T)) => lowercase(String(product))), 61 | g.bbox, 62 | g.info 63 | ) 64 | # Check other version 65 | if !isfile(g) 66 | # TODO Also check higher versions 67 | url = replace(g.url, "01.h5" => "02.h5") 68 | if isfile(url) 69 | @warn "Used newer version available" 70 | g = ICESat2_Granule{product}(g.id, url, g.bbox, g.info) 71 | end 72 | end 73 | g 74 | end 75 | 76 | """Derive info based on file id. 77 | 78 | The id is built up as follows, see 1.2.5 in the user guide 79 | ATL03_[yyyymmdd][hhmmss]_[ttttccss]_[vvv_rr].h5 80 | """ 81 | function info(g::ICESat2_Granule) 82 | icesat2_info(g.id) 83 | end 84 | 85 | # Granule regions 1-14. Region 4 (North Pole) and region 11 (Sout Pole) are both ascending descending 86 | const ascending_segments = [true, true, true, true, false, false, false, false, false, false, true, true, true, true] 87 | const descending_segments = [false, false, false, true, true, true, true, true, true, true, true, false, false, false] 88 | 89 | function icesat2_info(filename) 90 | id, _ = splitext(filename) 91 | type, datetime, track, version, revision = split(id, "_") 92 | segment = parse(Int, track[7:end]) 93 | (type = Symbol(type), date = DateTime(datetime, icesat_date_format), rgt = parse(Int, track[1:4]), cycle = parse(Int, track[5:6]), segment = segment, version = parse(Int, version), revision = parse(Int, revision), ascending = ascending_segments[segment], descending = descending_segments[segment]) 94 | end 95 | 96 | function is_blacklisted(g::Granule) 97 | g.id in blacklist 98 | end 99 | -------------------------------------------------------------------------------- /notebooks/juliacon_2021.jl: -------------------------------------------------------------------------------- 1 | ### A Pluto.jl notebook ### 2 | # v0.14.8 3 | 4 | using Markdown 5 | using InteractiveUtils 6 | 7 | # ╔═╡ b7aa82f4-f38f-4dd2-9d86-984205cf95b9 8 | using SpaceLiDAR 9 | 10 | # ╔═╡ 2337d9f8-7615-43cc-9c8d-83176b685b8e 11 | using DataFrames 12 | 13 | # ╔═╡ 6a648fcf-0bd5-49ae-9cf8-0cf99867ca47 14 | using GeoDataFrames 15 | 16 | # ╔═╡ 7efc9e7e-58be-4fac-9eca-d571f1382b65 17 | using LazIO 18 | 19 | # ╔═╡ a5acd89a-320b-4cc8-81d3-16fbedb689b0 20 | md"""# SpaceLiDAR.jl @ JuliaCon 2021""" 21 | 22 | # ╔═╡ 8c11cb9b-ef88-48f3-a4c3-9dbfee1ccbce 23 | md""" 24 | An example of using SpaceLiDAR to retrieve and process ICESat-2 and GEDI satellite LiDAR data.""" 25 | 26 | # ╔═╡ 1d8c9cd5-544a-4267-9895-7d41a81146d8 27 | md"""#### Search""" 28 | 29 | # ╔═╡ 5c6b7711-5799-4a34-9cfc-14902d30bdd2 30 | md"""Let's find some data in Vietnam. We can define a (very rough) bounding box and search for data. This makes use of [NASA EarthData Search](https://search.earthdata.nasa.gov/).""" 31 | 32 | # ╔═╡ 9f611522-1c93-4d77-ac8e-49d7b90b1820 33 | vietnam = (min_x = 102., min_y = 8.0, max_x = 107.0, max_y = 12.0) 34 | 35 | # ╔═╡ 1729d09f-fa21-4da5-ac71-e1eb34f0ca11 36 | granules = find(:ICESat2, "ATL08", vietnam, "004") 37 | 38 | # ╔═╡ c7ed0663-0dd0-496e-bbcb-61f09e5691c5 39 | md"""These datasets (granules) come in the form of HDF5 (.h5) files, with *a lot* of attributes. Downloading them requires a working NASA EarthData account configured in an `~/.netrc` file.""" 40 | 41 | # ╔═╡ bf418df8-6923-44f3-a067-367a7c52afdf 42 | begin 43 | granule = copy(granules[1]) 44 | SpaceLiDAR.download!(granule) 45 | end 46 | 47 | # ╔═╡ 6da50bf6-fd03-479b-8d04-d9ccc41415c5 48 | md"""#### Extract""" 49 | 50 | # ╔═╡ 4e3e4815-778e-4339-bd9b-256bb4687804 51 | md"""Now that we have one granule locally, let's extract some data. This package is opiniated and does already apply some filters for you. It also converts dates and unnests where required.""" 52 | 53 | # ╔═╡ 4c04f1c2-c5d3-4f8e-9ba1-17088eb5ebbf 54 | t = vcat(DataFrame.(points(granule, canopy=true))...) 55 | 56 | # ╔═╡ 36d1438b-041a-4ea5-a4c6-e49b0fe9c4ff 57 | md"""ICESat-2 and GEDI have multiple beams, each is provided as its own Table, hence the `vcat`.""" 58 | 59 | # ╔═╡ 74e7ee28-de25-4393-b778-9766d58c189d 60 | tt = t[(t.sensitivity .>= 2) .& (t.u .<= 5) , :] 61 | 62 | # ╔═╡ 195ebb14-64e9-4d60-bada-e23aefb11ee8 63 | md"""#### Export""" 64 | 65 | # ╔═╡ 518bcb83-fa7e-42f6-a53e-240f94dd5d19 66 | md"""It's useful to inspect this data in other software such as QGIS, so let's save it as a GeoPackage. For this purpose I made `GeoDataFrames.jl`, built on top of `ArchGDAL.jl` and `GDAL`.""" 67 | 68 | # ╔═╡ 4e4c0925-a88f-447e-9a01-6847169d8325 69 | tt.geom=createpoint.(tt.x, tt.y, tt.z) 70 | 71 | # ╔═╡ a863a0bc-bd7b-421d-85f0-65b0b0572ac2 72 | GeoDataFrames.write("$(granule.id).gpkg", tt) 73 | 74 | # ╔═╡ da214c65-3a1b-4691-ae0b-6c00549f5423 75 | md"""For those more familiar with airborne LiDAR, you can also export to the `.laz` format by using `LazIO.jl`. Note that most attributes are lost this way.""" 76 | 77 | # ╔═╡ 21d2614e-de2a-4ede-bdd6-a3a862acddad 78 | LazIO.write("$(granule.id).laz", granule) 79 | 80 | # ╔═╡ Cell order: 81 | # ╟─a5acd89a-320b-4cc8-81d3-16fbedb689b0 82 | # ╟─8c11cb9b-ef88-48f3-a4c3-9dbfee1ccbce 83 | # ╠═b7aa82f4-f38f-4dd2-9d86-984205cf95b9 84 | # ╟─1d8c9cd5-544a-4267-9895-7d41a81146d8 85 | # ╟─5c6b7711-5799-4a34-9cfc-14902d30bdd2 86 | # ╟─9f611522-1c93-4d77-ac8e-49d7b90b1820 87 | # ╠═1729d09f-fa21-4da5-ac71-e1eb34f0ca11 88 | # ╟─c7ed0663-0dd0-496e-bbcb-61f09e5691c5 89 | # ╠═bf418df8-6923-44f3-a067-367a7c52afdf 90 | # ╟─6da50bf6-fd03-479b-8d04-d9ccc41415c5 91 | # ╟─4e3e4815-778e-4339-bd9b-256bb4687804 92 | # ╠═2337d9f8-7615-43cc-9c8d-83176b685b8e 93 | # ╠═4c04f1c2-c5d3-4f8e-9ba1-17088eb5ebbf 94 | # ╟─36d1438b-041a-4ea5-a4c6-e49b0fe9c4ff 95 | # ╠═74e7ee28-de25-4393-b778-9766d58c189d 96 | # ╟─195ebb14-64e9-4d60-bada-e23aefb11ee8 97 | # ╟─518bcb83-fa7e-42f6-a53e-240f94dd5d19 98 | # ╠═6a648fcf-0bd5-49ae-9cf8-0cf99867ca47 99 | # ╠═4e4c0925-a88f-447e-9a01-6847169d8325 100 | # ╠═a863a0bc-bd7b-421d-85f0-65b0b0572ac2 101 | # ╟─da214c65-3a1b-4691-ae0b-6c00549f5423 102 | # ╠═7efc9e7e-58be-4fac-9eca-d571f1382b65 103 | # ╠═21d2614e-de2a-4ede-bdd6-a3a862acddad 104 | -------------------------------------------------------------------------------- /src/search.jl: -------------------------------------------------------------------------------- 1 | using HTTP 2 | using JSON 3 | 4 | const world = (min_x = -180., min_y = -90., max_x = 180., max_y = 90.) 5 | 6 | struct Mission{x} 7 | end 8 | Mission(x) = Mission{x}() 9 | 10 | const url = "https://cmr.earthdata.nasa.gov/search/granules.json" 11 | 12 | # GEDIFinder has not been updated to v2 13 | # function find(::Mission{:GEDI}, product::String="GEDI02_A", bbox::NamedTuple{(:min_x, :min_y, :max_x, :max_y),NTuple{4,Float64}}=world, version::String="001") 14 | # # https://lpdaacsvc.cr.usgs.gov/services/gedifinder?product=GEDI02_A&version=001&bbox=[28.0,-83,24.0,-79] 15 | # url = "https://lpdaacsvc.cr.usgs.gov/services/gedifinder?" 16 | # q = Dict( 17 | # "bbox" => "[$(bbox.max_y),$(bbox.min_x),$(bbox.min_y),$(bbox.max_x)]", 18 | # "version" => version, 19 | # "product" => product 20 | # ) 21 | # # uri = HTTP.URI(;scheme="https", host="lpdaacsvc.cr.usgs.gov", path="/services/gedifinder", query=q) 22 | # r = HTTP.get(url, query=q, verbose=0) 23 | # data = JSON.parse(String(r.body)) 24 | 25 | # map(x -> GEDI_Granule( 26 | # Symbol(product), 27 | # basename(x), 28 | # x, 29 | # gedi_info(basename(x)) 30 | # ), 31 | # data["data"]) 32 | # end 33 | 34 | function find(::Mission{:GEDI}, product::String="GEDI02_A", bbox::NamedTuple{(:min_x, :min_y, :max_x, :max_y),NTuple{4,Float64}}=world, version::String="002") 35 | granules = earthdata_search(product, bbox, version; provider="LPDAAC_ECS") 36 | map(x -> GEDI_Granule( 37 | Symbol(product), 38 | x["producer_granule_id"], 39 | get(get(x, "links", [Dict()])[1], "href", ""), 40 | gedi_info(x["producer_granule_id"]) 41 | ), 42 | granules) 43 | end 44 | 45 | function find(::Mission{:ICESat2}, product::String="ATL03", bbox::NamedTuple{(:min_x, :min_y, :max_x, :max_y),NTuple{4,Float64}}=world, version::String="005") 46 | # https://cmr.earthdata.nasa.gov/search/granules.json?provider=NSIDC_ECS&page_size=2000&sort_key[]=-start_date&sort_key[]=producer_granule_id&short_name=ATL03&version=2&version=02&version=002&temporal[]=2018-10-13T00:00:00Z,2020-01-13T08:13:50Z&bounding_box=-180,-90,180,90 47 | granules = earthdata_search(product, bbox, version) 48 | map(x -> ICESat2_Granule( 49 | Symbol(product), 50 | x["producer_granule_id"], 51 | get(get(x, "links", [Dict()])[1], "href", ""), 52 | NamedTuple(), 53 | icesat2_info(x["producer_granule_id"]) 54 | ), 55 | granules) 56 | end 57 | 58 | function find(::Mission{:ICESat}, product::String="GLAH14", bbox::NamedTuple{(:min_x, :min_y, :max_x, :max_y),NTuple{4,Float64}}=world, version::String="034") 59 | # https://cmr.earthdata.nasa.gov/search/granules.json?provider=NSIDC_ECS&page_size=2000&sort_key[]=-start_date&sort_key[]=producer_granule_id&short_name=ATL03&version=2&version=02&version=002&temporal[]=2018-10-13T00:00:00Z,2020-01-13T08:13:50Z&bounding_box=-180,-90,180,90 60 | granules = earthdata_search(product, bbox, version) 61 | map(x -> ICESat_Granule( 62 | Symbol(product), 63 | x["producer_granule_id"], 64 | get(get(x, "links", [Dict()])[1], "href", ""), 65 | icesat_info(x["producer_granule_id"]) 66 | ), 67 | granules) 68 | end 69 | 70 | function parse_cmr_json(r) 71 | data = JSON.parse(String(r.body)) 72 | get(get(data, "feed", Dict()), "entry", []) 73 | end 74 | 75 | function find(mission::Symbol, args...) 76 | find(Mission(mission), args...) 77 | end 78 | 79 | function earthdata_search(product::String, bbox::NamedTuple{(:min_x, :min_y, :max_x, :max_y),NTuple{4,Float64}}, version::String; provider="NSIDC_ECS") 80 | page_size = 2000 81 | page_num = 1 82 | q = Dict( 83 | "provider" => provider, 84 | "page_num" => page_num, 85 | "page_size" => page_size, 86 | "short_name" => product, 87 | "version" => version, 88 | "bounding_box" => "$(bbox.min_x),$(bbox.min_y),$(bbox.max_x),$(bbox.max_y)" 89 | ) 90 | r = HTTP.get(url, query=q) 91 | cgranules = parse_cmr_json(r) 92 | granules = copy(cgranules) 93 | while length(cgranules) == page_size 94 | @warn "Found more than $page_size granules, requesting another $page_size..." 95 | q["page_num"] += 1 96 | r = HTTP.get(url, query=q) 97 | cgranules = parse_cmr_json(r) 98 | append!(granules, cgranules) 99 | end 100 | granules 101 | end 102 | -------------------------------------------------------------------------------- /src/utils.jl: -------------------------------------------------------------------------------- 1 | using Printf 2 | 3 | """Hacked version of Base.download which adds cookies and (optional) netrc parsing.""" 4 | function download_curl(url::AbstractString, filename::AbstractString) 5 | err = PipeBuffer() 6 | pipe = pipeline(`curl -s -b cookie.txt -c cookie.txt --netrc-optional -S -g -L -f -o $filename $url`, stderr=err) 7 | process = run(pipe, wait=false) 8 | if !success(process) 9 | error_msg = readline(err) 10 | @error "Download failed: $error_msg" 11 | Base.pipeline_error(process) 12 | end 13 | return filename 14 | end 15 | 16 | """Generate granule from .h5 file.""" 17 | function granule_from_file(filename::AbstractString) 18 | _, ext = splitext(filename) 19 | lowercase(ext) != ".h5" && error("Granule must be a .h5 file") 20 | 21 | name = basename(filename) 22 | if startswith(name, "ATL") 23 | info = icesat2_info(name) 24 | return ICESat2_Granule(info.type, name, filename, (x_min = 0.,), info) 25 | elseif startswith(name, "GEDI") 26 | info = gedi_info(name) 27 | return GEDI_Granule(info.type, name, filename, info) 28 | elseif startswith(name, "GLAH") 29 | info = icesat_info(name) 30 | return ICESat_Granule(info.type, name, filename, info) 31 | else 32 | error("Unknown granule.") 33 | end 34 | end 35 | 36 | """Generate granules from folder filled with .h5 files.""" 37 | function granules_from_folder(foldername::AbstractString) 38 | return [granule_from_file(joinpath(foldername, file)) for file in readdir(foldername) if lowercase(splitext(file)[end]) == ".h5"] 39 | end 40 | 41 | function instantiate(granules::Vector{T}, folder::AbstractString) where T <: Granule 42 | local_granules = Vector{eltype(granules)}() 43 | for granule in granules 44 | file = joinpath(folder, granule.id) 45 | if isfile(file) 46 | g = copy(granule) 47 | g.url = file 48 | push!(local_granules, g) 49 | end 50 | end 51 | @info "Found $(@sprintf("%.0f",(length(local_granules) / length(granules) * 100)))% of $(length(granules)) provided granules." 52 | local_granules 53 | end 54 | 55 | 56 | """Filter with bbox.""" 57 | function in_bbox(xyz, bbox::NamedTuple{(:min_x, :min_y, :max_x, :max_y),NTuple{4,Float64}}) 58 | filter(row -> ((bbox.min_x <= row.x <= bbox.max_x) && (bbox.min_y <= row.y <= bbox.max_y)), xyz) 59 | end 60 | function in_bbox!(xyz, bbox::NamedTuple{(:min_x, :min_y, :max_x, :max_y),NTuple{4,Float64}}) 61 | filter!(row -> ((bbox.min_x <= row.x <= bbox.max_x) && (bbox.min_y <= row.y <= bbox.max_y)), xyz) 62 | end 63 | 64 | function in_bbox(g::G, bbox::NamedTuple{(:min_x, :min_y, :max_x, :max_y),NTuple{4,Float64}}) where G <: Granule 65 | box = bounds(g) 66 | intersect((;box.min_x,box.min_y,box.max_x,box.max_y), bbox) 67 | end 68 | 69 | function in_bbox(g::Vector{G}, bbox::NamedTuple{(:min_x, :min_y, :max_x, :max_y),NTuple{4,Float64}}) where G <: Granule 70 | m = in_bbox.(g, Ref(bbox)) 71 | g[m] 72 | end 73 | 74 | function bounds(table) 75 | NamedTuple{(:min_x, :max_x, :min_y, :max_y, :min_z, :max_z)}((extrema(table.x)..., extrema(table.y)..., extrema(table.z)...)) 76 | end 77 | 78 | function write_granule_urls!(fn::String, granules::Vector{<:Granule}) 79 | open(fn, "w") do f 80 | for granule in granules 81 | println(f, granule.url) 82 | end 83 | end 84 | abspath(fn) 85 | end 86 | 87 | function test(granule::Granule) 88 | try 89 | HDF5.h5open(granule.url, "r") do file 90 | keys(file) 91 | end 92 | return true 93 | catch e 94 | @error "Granule at $(granule.url) failed with $e." 95 | return false 96 | end 97 | end 98 | 99 | """Writes/updates netrc file for ICESat-2 and GEDI downloads.""" 100 | function netrc!(username, password) 101 | if Sys.iswindows() 102 | fn = joinpath(homedir(), "_netrc") 103 | else 104 | fn = joinpath(homedir(), ".netrc") 105 | end 106 | 107 | open(fn, "a") do f 108 | write(f, "\n") 109 | write(f, "machine urs.earthdata.nasa.gov login $username password $(password)\n") 110 | write(f, "machine n5eil01u.ecs.nsidc.org login $username password $(password)\n") 111 | end 112 | fn 113 | end 114 | 115 | function filter_rgt(granules::Vector{<:Granule}, rgt::Int, cycle::Int) 116 | results = Vector{Granule}() 117 | for granule in granules 118 | i = info(granule) 119 | if i.rgt == rgt && i.cycle == cycle 120 | push!(results, granule) 121 | end 122 | end 123 | results 124 | end 125 | -------------------------------------------------------------------------------- /src/ICESat-2/ATL03.jl: -------------------------------------------------------------------------------- 1 | function points(granule::ICESat2_Granule{:ATL03}; bbox=nothing, tracks=icesat2_tracks, step=1) 2 | dfs = Vector{NamedTuple}() 3 | HDF5.h5open(granule.url, "r") do file 4 | t_offset = read(file, "ancillary_data/atlas_sdp_gps_epoch")[1]::Float64 + gps_offset 5 | orientation = read(file, "orbit_info/sc_orient")[1]::Int8 6 | 7 | for track ∈ tracks 8 | power = track_power(orientation, track) 9 | if in(track, keys(file)) && in("heights", keys(file[track])) 10 | track_df = points(granule, file, track, power, t_offset, step) 11 | push!(dfs, track_df) 12 | end 13 | end 14 | end 15 | for df in dfs 16 | df.z[df.z .== fill_value] .= NaN 17 | end 18 | dfs 19 | end 20 | 21 | function lines(granule::ICESat2_Granule{:ATL03}; tracks=icesat2_tracks, step=100) 22 | dfs = Vector{NamedTuple}() 23 | HDF5.h5open(granule.url, "r") do file 24 | t_offset = read(file, "ancillary_data/atlas_sdp_gps_epoch")[1]::Float64 + gps_offset 25 | orientation = read(file, "orbit_info/sc_orient")[1]::Int8 26 | 27 | for track ∈ tracks 28 | power = track_power(orientation, track) 29 | if in(track, keys(file)) && in("heights", keys(file[track])) 30 | track_df = points(granule, file, track, power, t_offset, step) 31 | line = makeline(track_df.x, track_df.y, track_df.z) 32 | i = div(length(track_df.t), 2) + 1 33 | nt = (geom = line, sun_angle = Float64(track_df.sun_angle[i]), track = track, power = power, t = track_df.t[i], granule = granule.id) 34 | push!(dfs, nt) 35 | end 36 | end 37 | end 38 | dfs 39 | end 40 | 41 | function points(::ICESat2_Granule{:ATL03}, file::HDF5.H5DataStore, track::AbstractString, power::AbstractString, t_offset::Float64, step=1) 42 | z = file["$track/heights/h_ph"][1:step:end]::Vector{Float32} 43 | x = file["$track/heights/lon_ph"][1:step:end]::Vector{Float64} 44 | y = file["$track/heights/lat_ph"][1:step:end]::Vector{Float64} 45 | t = file["$track/heights/delta_time"][1:step:end]::Vector{Float64} 46 | c = file["$track/heights/signal_conf_ph"][1,1:step:end]::Vector{Int8} 47 | q = file["$track/heights/quality_ph"][1:step:end]::Vector{Int8} 48 | 49 | # Segment calc 50 | segment_counts = read(file, "$track/geolocation/segment_ph_cnt")::Vector{Int32} 51 | 52 | segment = read(file, "$track/geolocation/segment_id")::Vector{Int32} 53 | segments = map_counts(segment, segment_counts)[1:step:end] 54 | 55 | sun_angle = read(file, "$track/geolocation/solar_elevation")::Vector{Float32} 56 | sun_angles = map_counts(sun_angle, segment_counts)[1:step:end] 57 | 58 | u = read(file, "$track/geolocation/sigma_h")::Vector{Float32} 59 | uu = map_counts(u, segment_counts)[1:step:end] 60 | 61 | dem = read(file, "$track/geophys_corr/dem_h")::Vector{Float32} 62 | demd = map_counts(dem, segment_counts)[1:step:end] 63 | 64 | times = unix2datetime.(t .+ t_offset) 65 | 66 | ( 67 | x = x, 68 | y = y, 69 | z = z, 70 | q = q, 71 | u = uu, 72 | t = times, 73 | confidence = c, 74 | segment = segments, 75 | track = Fill(track, length(sun_angles)), 76 | power = Fill(power, length(sun_angles)), 77 | sun_angle = sun_angles, 78 | reference = demd 79 | ) 80 | end 81 | 82 | function map_counts(values, counts) 83 | c = fill(zero(eltype(values)), sum(counts)) 84 | ref = 1 85 | for i in eachindex(counts) 86 | value = values[i] 87 | count = counts[i] 88 | c[ref:ref + count - 1] .= value 89 | ref += count 90 | end 91 | c 92 | end 93 | 94 | """Retrieve all points as classified as ground in ATL08.""" 95 | function classify(granule::ICESat2_Granule{:ATL03}, atl08::Union{ICESat2_Granule{:ATL08},Nothing}=nothing; tracks=icesat2_tracks) 96 | if isnothing(atl08) 97 | atl08 = convert(:ATL08, granule) 98 | end 99 | 100 | dfs = Vector{NamedTuple}() 101 | HDF5.h5open(granule.url, "r") do file 102 | t_offset = read(file, "ancillary_data/atlas_sdp_gps_epoch")[1]::Float64 + gps_offset 103 | orientation = read(file, "orbit_info/sc_orient")[1]::Int8 104 | 105 | for track ∈ tracks 106 | power = track_power(orientation, track) 107 | if in(track, keys(file)) && in("heights", keys(file[track])) 108 | track_df = points(granule, file, track, power, t_offset) 109 | 110 | mapping = atl03_mapping(atl08, track) 111 | 112 | unique_segments = unique(mapping.segment) 113 | index_map = create_mapping(track_df.segment, unique_segments) 114 | 115 | class = fill("unclassified", length(track_df.x)) 116 | for i in 1:length(mapping.segment) 117 | index = get(index_map, mapping.segment[i], nothing) 118 | isnothing(index) && continue 119 | offset = mapping.index[i] - 1 120 | class[index + offset] = classification[mapping.classification[i] + 1] 121 | end 122 | track_dfc = merge(track_df, (classification = class,)) 123 | push!(dfs, track_dfc) 124 | end 125 | end 126 | end 127 | dfs 128 | end 129 | 130 | function create_mapping(dfsegment, unique_segments) 131 | index_map = Dict{Int64,Int64}() 132 | for unique_segment in unique_segments 133 | pos = searchsortedfirst(dfsegment, unique_segment) 134 | if (pos <= length(dfsegment)) && (dfsegment[pos] == unique_segment) 135 | index_map[unique_segment] = pos 136 | end 137 | end 138 | index_map 139 | end 140 | -------------------------------------------------------------------------------- /src/ICESat-2/ATL08.jl: -------------------------------------------------------------------------------- 1 | function points(granule::ICESat2_Granule{:ATL08}; tracks=icesat2_tracks, step=1, canopy=false, ground=true) 2 | dfs = Vector{NamedTuple}() 3 | HDF5.h5open(granule.url, "r") do file 4 | t_offset = read(file, "ancillary_data/atlas_sdp_gps_epoch")[1]::Float64 + gps_offset 5 | orientation = read(file, "orbit_info/sc_orient")[1]::Int8 6 | 7 | for (i, track) ∈ enumerate(tracks) 8 | power = track_power(orientation, track) 9 | if in(track, keys(file)) && in("land_segments", keys(file[track])) 10 | for track_nt ∈ points(granule, file, track, power, t_offset, step, canopy, ground) 11 | track_nt.z[track_nt.z .== fill_value] .= NaN 12 | push!(dfs, track_nt) 13 | end 14 | end 15 | end 16 | end 17 | dfs 18 | end 19 | 20 | function points(::ICESat2_Granule{:ATL08}, file::HDF5.H5DataStore, track::AbstractString, power::AbstractString, t_offset::Float64, step=1, canopy=false, ground=true) 21 | if ground 22 | zt = file["$track/land_segments/terrain/h_te_median"][1:step:end]::Vector{Float32} 23 | tu = file["$track/land_segments/terrain/h_te_uncertainty"][1:step:end]::Vector{Float32} 24 | end 25 | if canopy 26 | zc = file["$track/land_segments/canopy/h_mean_canopy_abs"][1:step:end]::Vector{Float32} 27 | cu = file["$track/land_segments/canopy/h_canopy_uncertainty"][1:step:end]::Vector{Float32} 28 | end 29 | x = file["$track/land_segments/longitude"][1:step:end]::Vector{Float32} 30 | y = file["$track/land_segments/latitude"][1:step:end]::Vector{Float32} 31 | t = file["$track/land_segments/delta_time"][1:step:end]::Vector{Float64} 32 | sensitivity = file["$track/land_segments/snr"][1:step:end]::Vector{Float32} 33 | clouds = file["$track/land_segments/layer_flag"][1:step:end]::Vector{Int8} 34 | scattered = file["$track/land_segments/msw_flag"][1:step:end]::Vector{Int8} 35 | saturated = file["$track/land_segments/sat_flag"][1:step:end]::Vector{Int8} 36 | q = file["$track/land_segments/terrain_flg"][1:step:end]::Vector{Int32} 37 | phr = file["$track/land_segments/ph_removal_flag"][1:step:end]::Vector{Int8} 38 | dem = file["$track/land_segments/dem_h"][1:step:end]::Vector{Float32} 39 | times = unix2datetime.(t .+ t_offset) 40 | 41 | if ground 42 | gt = ( 43 | x = x, 44 | y = y, 45 | z = zt, 46 | u = tu, 47 | t = times, 48 | q = q, 49 | phr = Int16.(phr), 50 | sensitivity = sensitivity, 51 | scattered = Int16.(scattered), 52 | saturated = Int16.(saturated), 53 | clouds = Bool.(clouds), 54 | track = Fill(track, length(times)), 55 | power = Fill(power, length(times)), 56 | classification = Fill("ground", length(times)), 57 | return_number = Fill(2, length(times)), 58 | number_of_returns = Fill(2, length(times)), 59 | reference = dem, 60 | ) 61 | end 62 | if canopy 63 | ct = ( 64 | x = x, 65 | y = y, 66 | z = zc, 67 | u = cu, 68 | t = times, 69 | q = q, 70 | phr = Int16.(phr), 71 | sensitivity = sensitivity, 72 | scattered = Int16.(scattered), 73 | saturated = Int16.(saturated), 74 | clouds = Bool.(clouds), 75 | track = Fill(track, length(times)), 76 | power = Fill(power, length(times)), 77 | classification = Fill("high_canopy", length(times)), 78 | return_number = Fill(1, length(times)), 79 | number_of_returns = Fill(2, length(times)), 80 | reference = dem, 81 | ) 82 | end 83 | if canopy && ground 84 | ct, gt 85 | elseif canopy 86 | (ct,) 87 | elseif ground 88 | (gt,) 89 | else 90 | () 91 | end 92 | end 93 | 94 | function lines(granule::ICESat2_Granule{:ATL08}; tracks=icesat2_tracks, step=100, quality=1) 95 | dfs = Vector{NamedTuple}() 96 | HDF5.h5open(granule.url, "r") do file 97 | # t_offset = read(file, "ancillary_data/atlas_sdp_gps_epoch")[1]::Float64 + gps_offset 98 | orientation = read(file, "orbit_info/sc_orient")[1]::Int8 99 | 100 | for track ∈ tracks 101 | power = track_power(orientation, track) 102 | if in(track, keys(file)) && in("land_segments", keys(file[track])) 103 | z = file["$track/land_segments/terrain/h_te_median"][1:step:end]::Array{Float32,1} 104 | x = file["$track/land_segments/longitude"][1:step:end]::Array{Float32,1} 105 | y = file["$track/land_segments/latitude"][1:step:end]::Array{Float32,1} 106 | # t = file["$track/land_segments/delta_time"][1:step:end]::Array{Float64,1} 107 | # times = unix2datetime.(t .+ t_offset) 108 | z[z .== fill_value] .= NaN 109 | line = makeline(x, y, z) 110 | # i = div(length(t), 2) + 1 111 | nt = (geom = line, track = track, power = power, granule = granule.id) 112 | push!(dfs, nt) 113 | end 114 | end 115 | end 116 | dfs 117 | end 118 | 119 | function atl03_mapping(granule::ICESat2_Granule{:ATL08}) 120 | dfs = Vector{NamedTuple}() 121 | HDF5.h5open(granule.url, "r") do file 122 | for track ∈ icesat2_tracks 123 | if in(track, keys(file)) && in("signal_photons", keys(file[track])) 124 | df = atl03_mapping(file, track) 125 | push!(dfs, df) 126 | end 127 | end 128 | end 129 | dfs 130 | end 131 | 132 | function atl03_mapping(granule::ICESat2_Granule{:ATL08}, track::AbstractString) 133 | HDF5.h5open(granule.url, "r") do file 134 | if in(track, keys(file)) && in("signal_photons", keys(file[track])) 135 | df = atl03_mapping(file, track) 136 | end 137 | end 138 | end 139 | 140 | function atl03_mapping(file::HDF5.H5DataStore, track::AbstractString) 141 | c = read(file, "$track/signal_photons/classed_pc_flag")::Array{Int8,1} 142 | i = read(file, "$track/signal_photons/classed_pc_indx")::Array{Int32,1} 143 | s = read(file, "$track/signal_photons/ph_segment_id")::Array{Int32,1} 144 | (segment = s, index = i, classification = c, track = track) 145 | end 146 | -------------------------------------------------------------------------------- /src/GEDI/L2A.jl: -------------------------------------------------------------------------------- 1 | const t_offset = 1514764800 # Time delta since Jan 1 00:00 2018. 2 | 3 | function bounds(::GEDI_Granule) 4 | (min_x = -180., max_x = 180., min_y = -63., max_y = 63., min_z = -1000., max_z = 25000.) 5 | end 6 | 7 | function points(granule::GEDI_Granule{:GEDI02_A}; tracks=gedi_tracks, step=1, ground=true, canopy=false, quality=1) 8 | dfs = Vector{NamedTuple}() 9 | HDF5.h5open(granule.url, "r") do file 10 | 11 | for (i, track) ∈ enumerate(tracks) 12 | power = i > 4 ? "strong" : "weak" 13 | if in(track, keys(file)) 14 | for track_df ∈ points(granule, file, track, power, step, ground, canopy, quality) 15 | push!(dfs, track_df) 16 | end 17 | end 18 | end 19 | end 20 | dfs 21 | end 22 | 23 | 24 | function points(g::GEDI_Granule{:GEDI02_A}, file, track, power, step, ground, canopy, quality::Union{Nothing,Integer}=1, degraded=false) 25 | zu = file["$track/elevation_bin0_error"][1:step:end]::Vector{Float32} 26 | dem = file["$track/digital_elevation_model"][1:step:end]::Vector{Float32} 27 | intensity = file["$track/energy_total"][1:step:end]::Vector{Float32} 28 | aid = file["$track/selected_algorithm"][1:step:end]::Vector{UInt8} 29 | 30 | if canopy 31 | xt = file["$track/lon_highestreturn"][1:step:end]::Vector{Float64} 32 | yt = file["$track/lat_highestreturn"][1:step:end]::Vector{Float64} 33 | zt = file["$track/elev_highestreturn"][1:step:end]::Vector{Float32} 34 | zt[(zt .< -1000.0) .& (zt .> 25000.0)] .= NaN 35 | end 36 | if ground 37 | xb = file["$track/lon_lowestmode"][1:step:end]::Vector{Float64} 38 | yb = file["$track/lat_lowestmode"][1:step:end]::Vector{Float64} 39 | zb = file["$track/elev_lowestmode"][1:step:end]::Vector{Float32} 40 | # zzb = similar(aid, Float32) 41 | # for algorithm in 1:6 42 | # zzb[aid .== algorithm] = file["$track/geolocation/elev_lowestreturn_a$algorithm"][1:step:end][aid .== algorithm] 43 | # end 44 | zb[(zb .< -1000.0) .& (zb .> 25000.0)] .= NaN 45 | # zzb[(zb .< -1000.0) .& (zb .> 25000.0)] .= NaN 46 | end 47 | t = file["$track/delta_time"][1:step:end]::Vector{Float64} 48 | 49 | # Quality 50 | q = file["$track/quality_flag"][1:step:end]::Vector{UInt8} 51 | aq = file["$track/rx_assess/quality_flag"][1:step:end]::Vector{UInt8} 52 | d = file["$track/degrade_flag"][1:step:end]::Vector{UInt8} 53 | stale = file["$track/geolocation/stale_return_flag"][1:step:end]::Vector{UInt8} 54 | s = file["$track/surface_flag"][1:step:end]::Vector{UInt8} 55 | 56 | minel, maxel = zeros(size(s)), zeros(size(s)) 57 | for algorithm in 1:6 58 | z = file["$track/geolocation/elev_lowestmode_a$algorithm"][1:step:end]::Vector{Float32} 59 | minel .= min.(minel, z) 60 | maxel .= max.(maxel, z) 61 | end 62 | zarange = maxel .- minel 63 | 64 | a = file["$track/rx_assess/rx_maxamp"][1:step:end]::Vector{Float32} 65 | sd = file["$track/rx_assess/sd_corrected"][1:step:end]::Vector{Float32} 66 | f = a ./ sd 67 | 68 | # # Algorithm 69 | zcross = similar(aid, Float32) 70 | toploc = similar(aid, Float32) 71 | for algorithm in 1:6 72 | zcross[aid .== algorithm] = file["$track/rx_processing_a$algorithm/zcross"][1:step:end][aid .== algorithm] 73 | toploc[aid .== algorithm] = file["$track/rx_processing_a$algorithm/toploc"][1:step:end][aid .== algorithm] 74 | end 75 | 76 | zs = file["$track/sensitivity"][1:step:end]::Vector{Float32} 77 | sun_angle = file["$track/solar_elevation"][1:step:end]::Vector{Float32} 78 | if isnothing(quality) 79 | m = trues(length(q)) 80 | else 81 | m = q .== quality 82 | end 83 | 84 | # Ignore degraded 85 | m .&= d .== 0 86 | m .&= aq .!= 0 87 | m .&= stale .== 0 88 | m .&= f .>= 4 89 | m .&= zcross .> 0 90 | m .&= toploc .> 0 91 | m .&= zarange .<= 2 92 | # # Ignore values outside of 300m of reference surface 93 | m .&= s .!= 0 94 | 95 | times = unix2datetime.(t .+ t_offset) 96 | 97 | if canopy 98 | nt_canopy = ( 99 | x = xt[m], 100 | y = yt[m], 101 | z = zt[m], 102 | # zl = zt[m], 103 | u = zu[m], 104 | intensity = intensity[m], 105 | sensitivity = zs[m], 106 | t = times[m], 107 | surface = Bool.(s[m]), 108 | quality = Bool.(q[m]), 109 | track = Fill(track, length(q))[m], 110 | power = Fill(power, length(q))[m], 111 | classification = Fill("high_canopy", length(q))[m], 112 | sun_angle = sun_angle[m], 113 | return_number = Fill(1, length(sun_angle))[m], 114 | number_of_returns = Fill(2, length(sun_angle))[m], 115 | reference = dem[m], 116 | # range = zarange[m] 117 | ) 118 | end 119 | if ground 120 | nt_ground = ( 121 | x = xb[m], 122 | y = yb[m], 123 | z = zb[m], 124 | # zl = zzb[m], 125 | u = zu[m], 126 | intensity = intensity[m], 127 | sensitivity = zs[m], 128 | t = times[m], 129 | surface = Bool.(s[m]), 130 | quality = Bool.(q[m]), 131 | track = Fill(track, length(q))[m], 132 | power = Fill(power, length(q))[m], 133 | classification = Fill("ground", length(q))[m], 134 | sun_angle = sun_angle[m], 135 | return_number = Fill(2, length(sun_angle))[m], 136 | number_of_returns = Fill(2, length(sun_angle))[m], 137 | reference = dem[m], 138 | # range = zarange[m] 139 | ) 140 | end 141 | if canopy && ground 142 | nt_canopy, nt_ground 143 | elseif canopy 144 | (nt_canopy,) 145 | elseif ground 146 | (nt_ground,) 147 | else 148 | () 149 | end 150 | end 151 | 152 | 153 | function lines(granule::GEDI_Granule{:GEDI02_A}; tracks=gedi_tracks, step=1, ground=true, canopy=false, quality=nothing) 154 | dfs = Vector{NamedTuple}() 155 | HDF5.h5open(granule.url, "r") do file 156 | for (i, track) ∈ enumerate(tracks) 157 | power = i > 4 ? "strong" : "weak" 158 | if in(track, keys(file)) 159 | for track_df ∈ points(granule, file, track, power, step, ground, canopy, quality) 160 | line = makeline(track_df.x, track_df.y, track_df.z) 161 | nt = (geom = line, track = track, power = power, granule = granule.id) 162 | push!(dfs, nt) 163 | end 164 | end 165 | end 166 | end 167 | dfs 168 | end 169 | -------------------------------------------------------------------------------- /scripts/outliers.jl: -------------------------------------------------------------------------------- 1 | """Try to detect outliers in ICESat-2 & GEDI granules 2 | by cross comparing them.""" 3 | 4 | using SpaceLiDAR 5 | using Glob 6 | using GeoDataFrames; const GDF = GeoDataFrames 7 | using TypedTables 8 | using ArchGDAL; const AG = ArchGDAL 9 | using Dates 10 | using ProgressMeter 11 | using Combinatorics 12 | using GeoArrays 13 | using Statistics 14 | using CSV 15 | 16 | limit = 100 17 | # const seasia = (min_x = 92., min_y = -10.0, max_x = 142.0, max_y = 21.0) 18 | const seasia = (min_x = 102., min_y = 8.0, max_x = 107.0, max_y = 12.0) # vietnam 19 | 20 | # Based on SE Asia 21 | bad = [ 22 | "ATL08_20190308110827_10690208_003_01.h5", 23 | "ATL08_20200514143433_07490708_003_01.h5", 24 | "ATL08_20181206155406_10540108_003_01.h5", 25 | "ATL08_20181129035056_09390114_003_01.h5", 26 | "ATL08_20200705141328_01560807_003_01.h5", # segment 7? 27 | "ATL08_20200705142030_01560808_003_01.h5", # segment 8? 28 | "ATL08_20200618151228_12840707_003_01.h5", # segment 7? 29 | "ATL08_20200618151930_12840708_003_01.h5", # segment 8? 30 | "ATL08_20200806130651_06440807_003_01.h5", # segment 7? 31 | "ATL08_20200806131353_06440808_003_01.h5", # segment 8? 32 | "ATL08_20191219120550_12760514_003_01.h5", # segment 14? 33 | "ATL08_20191219103835_12760501_003_01.h5", # segment 1? 34 | "ATL08_20191129010015_09640507_003_01.h5", # segment 7? 35 | "ATL08_20191129010717_09640508_003_01.h5", # segment 8? 36 | "ATL08_20191102115253_05590501_003_01.h5", # segment 1? 37 | "ATL08_20191102132008_05590514_003_01.h5", # segment 14? 38 | "ATL08_20200313054344_11840601_003_01.h5", # segment 1 39 | "ATL08_20200313071058_11840614_003_01.h5", # segment 14 40 | "ATL08_20191102013254_05520507_003_01.h5", 41 | "ATL08_20191102013956_05520508_003_01.h5", 42 | "ATL08_20200417062841_03320701_003_01.h5", 43 | ] 44 | 45 | # These are large, worldwide granules, so limit or search for them 46 | gedi_path = "/mnt/ec66e171-5639-4c62-9d2c-08e81c462669/gedi/L2A/v1" 47 | # gedi_granules = granules_from_folder(gedi_path)[1:limit] 48 | 49 | # If you've downloaded everything locally: 50 | gedi_granules = find(:GEDI, "GEDI02_A", seasia) 51 | gedi_granules = SpaceLiDAR.instantiate(gedi_granules, gedi_path) 52 | 53 | # These are smaller, already cut out granules 54 | icesat_path = "/mnt/ec66e171-5639-4c62-9d2c-08e81c462669/icesat2/ATL08/v03" 55 | # icesat_granules = granules_from_folder(icesat_path)[1:limit * 50] 56 | # If you've downloaded everything locally: 57 | icesat_granules = find(:ICESat2, "ATL08", seasia) 58 | icesat_granules = SpaceLiDAR.instantiate(icesat_granules, icesat_path) 59 | filter!(!SpaceLiDAR.is_blacklisted, icesat_granules) 60 | filter!(!g -> g.id in bad, icesat_granules) 61 | 62 | granules = vcat(icesat_granules, gedi_granules) 63 | granules_v = in_bbox(granules, seasia) # bbox filtering based on header information, works only for ICESat-2 64 | 65 | 66 | # Retrieve linestrings from granules, note the decimation by step=10 67 | alllines = Vector{Table}() 68 | @showprogress 1 "Reading..." for granule in granules_v 69 | if SpaceLiDAR.test(granule) 70 | try 71 | lines = Table(SpaceLiDAR.lines(granule, step=1, quality=1)) 72 | push!(alllines, lines) 73 | catch e 74 | if e isa InterruptException 75 | break 76 | else 77 | @warn "$(granule.id) failed with $e" 78 | end 79 | end 80 | end 81 | end 82 | 83 | t = vcat(alllines...) 84 | SpaceLiDAR.clip!(t, seasia) 85 | t = SpaceLiDAR.splitline(t, 0.1) 86 | tt = t[AG.ngeom.(t.geom) .> 0] # skip empty linestrings 87 | GDF.write("alllines.gpkg", tt) 88 | 89 | 90 | intersections = Vector{NamedTuple}() 91 | @showprogress 1 "Intersections..." for (a, b) in combinations(t, 2) 92 | if a.granule == b.granule 93 | continue 94 | else 95 | if (AG.ngeom(a.geom) > 1) && (AG.ngeom(b.geom) > 1) && AG.intersects(a.geom, b.geom) 96 | points = AG.intersection(a.geom, b.geom) 97 | else 98 | continue 99 | end 100 | type = AG.getgeomtype(points) 101 | if type == AG.GDAL.wkbMultiPoint25D 102 | for i ∈ 1:AG.ngeom(points) 103 | # An intersection points of 2 2.5D lines gets a Z halfway between the lines 104 | p = AG.getgeom(points, i - 1) # starts with 0 105 | z = SpaceLiDAR.z_along_line(a.geom, p) 106 | z = (z - AG.getz(p, 0)) * 2 107 | push!(intersections, (a = a.granule, b = b.granule, diff = z, geom = p)) 108 | end 109 | elseif type == AG.GDAL.wkbPoint25D 110 | p = points 111 | z = SpaceLiDAR.z_along_line(a.geom, p) 112 | z = (z - AG.getz(p, 0)) * 2 113 | push!(intersections, (a = a.granule, b = b.granule, diff = z, geom = p)) 114 | elseif type == AG.GDAL.wkbLineString25D 115 | continue # no intersection 116 | end 117 | end 118 | end 119 | 120 | df = Table(intersections) 121 | GDF.write("intersections.gpkg", df) 122 | 123 | 124 | 125 | # Find the granules that should be blacklisted 126 | 127 | # n_outlier = 25 128 | mean_threshold = 10 # Only for lowland, we can expect 10m errors in sloped terrain! 129 | 130 | # If you already have an intersections gpkg 131 | # fn = "intersections.gpkg" 132 | # df = TypedTables.Table(GDF.read(fn)) 133 | 134 | # Generate mask with land polygons (I've used Natural Earth) 135 | # gdal_rasterize -l ne_10m_land -burn 1.0 -tr 0.005 0.005 -init 0.0 -te -180.0 -90.0 180.0 90.0 -ot Byte -at -of GTiff -co COMPRESS=DEFLATE -co TILED=yes ne_10m_land.shp 136 | mask_fn = "world_mask.tif" 137 | mask = GeoArrays.read(mask_fn) 138 | 139 | function Base.in(point::ArchGDAL.IGeometry, mask::GeoArray) 140 | x = ArchGDAL.getx(point, 0) 141 | y = ArchGDAL.gety(point, 0) 142 | try 143 | Bool(mask[x,y][1]) 144 | catch BoundsError 145 | false 146 | end 147 | end 148 | df = df[in.(df.geom, Ref(mask))] 149 | 150 | function unify(t) 151 | ids = unique(vcat(t.a, t.b)) 152 | list = Dict{String,Vector{Float64}}() 153 | for row in df 154 | haskey(list, row.a) || (list[row.a] = Vector{Float64}()) 155 | haskey(list, row.b) || (list[row.b] = Vector{Float64}()) 156 | push!(list[row.a], row.diff) 157 | push!(list[row.b], -row.diff) 158 | end 159 | r = collect(values(list)) 160 | t = GDF.DataFrame(granule=collect(keys(list)), diff=sum.(r), med=Statistics.median.(r), mean=Statistics.mean.(r), count=length.(r)) 161 | end 162 | # Dump to csv for manual checks 163 | CSV.write("outlier_granules.csv", unify(df)) 164 | 165 | outliers = Vector{String}() 166 | xm = 9999 167 | while xm >= mean_threshold 168 | t = unify(df) 169 | t.mean .= abs.(t.mean) 170 | sort!(t, :mean, rev=true) 171 | xm = t.mean[1] 172 | x = t.granule[1] 173 | push!(outliers, x) 174 | mask = (df.a .!= x) .& (df.b .!= x) 175 | df = df[mask] 176 | end 177 | @info "We think these outliers are bad:" 178 | @info outliers 179 | -------------------------------------------------------------------------------- /docs/src/International_Space_Station.svg: -------------------------------------------------------------------------------- 1 | 2 | 13 | 15 | 18 | 21 | 22 | 23 | 25 | 26 | 28 | image/svg+xml 29 | 31 | 32 | 33 | 34 | 35 | 38 | 41 | 44 | 47 | 50 | 54 | 55 | 58 | 62 | 63 | 66 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | -------------------------------------------------------------------------------- /docs/src/julia-dots.svg: -------------------------------------------------------------------------------- 1 | 2 | 14 | 16 | 19 | 22 | 23 | 24 | 43 | 45 | 49 | 53 | 57 | 58 | 62 | 66 | 70 | 74 | 75 | 79 | 83 | 84 | 88 | 92 | 93 | 94 | 95 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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Such new versions will 567 | be similar in spirit to the present version, but may differ in detail to 568 | address new problems or concerns. 569 | 570 | Each version is given a distinguishing version number. If the 571 | Program specifies that a certain numbered version of the GNU General 572 | Public License "or any later version" applies to it, you have the 573 | option of following the terms and conditions either of that numbered 574 | version or of any later version published by the Free Software 575 | Foundation. 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Interpretation of Sections 15 and 16. 613 | 614 | If the disclaimer of warranty and limitation of liability provided 615 | above cannot be given local legal effect according to their terms, 616 | reviewing courts shall apply local law that most closely approximates 617 | an absolute waiver of all civil liability in connection with the 618 | Program, unless a warranty or assumption of liability accompanies a 619 | copy of the Program in return for a fee. 620 | 621 | END OF TERMS AND CONDITIONS 622 | 623 | How to Apply These Terms to Your New Programs 624 | 625 | If you develop a new program, and you want it to be of the greatest 626 | possible use to the public, the best way to achieve this is to make it 627 | free software which everyone can redistribute and change under these terms. 628 | 629 | To do so, attach the following notices to the program. It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | 635 | Copyright (C) 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | Copyright (C) 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | -------------------------------------------------------------------------------- /src/ICESat-2/blacklist.txt: -------------------------------------------------------------------------------- 1 | ATL03_20190914031358_11920403_003_01.h5 2 | ATL03_20190914031923_11920404_003_01.h5 3 | ATL03_20190914032432_11920405_003_01.h5 4 | ATL03_20190914032957_11920406_003_01.h5 5 | ATL03_20190914033827_11920407_003_01.h5 6 | ATL03_20190914034529_11920408_003_01.h5 7 | ATL03_20190914035231_11920409_003_01.h5 8 | ATL03_20190914035833_11920410_003_01.h5 9 | ATL03_20190914040614_11920411_003_01.h5 10 | ATL03_20190914041157_11920412_003_01.h5 11 | ATL03_20190914041938_11920413_003_01.h5 12 | ATL03_20190914042540_11920414_003_01.h5 13 | ATL03_20191005003226_01240503_003_01.h5 14 | ATL03_20191005003751_01240504_003_01.h5 15 | ATL03_20191005004300_01240505_003_01.h5 16 | ATL03_20191005004825_01240506_003_01.h5 17 | ATL03_20191005005655_01240507_003_01.h5 18 | 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