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Pre-interpolate data loaders
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So that reprojection doesn't occur during model running
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@ctessum
ctessum committed Feb 28, 2025
1 parent 1141d8d commit a7c9609
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2 changes: 1 addition & 1 deletion Project.toml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
name = "EarthSciData"
uuid = "a293c155-435f-439d-9c11-a083b6b47337"
authors = ["EarthSciML Authors"]
version = "0.12.3"
version = "0.12.4"

[deps]
DataInterpolations = "82cc6244-b520-54b8-b5a6-8a565e85f1d0"
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80 changes: 67 additions & 13 deletions src/load.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -87,7 +87,7 @@ struct MetaData
"The index number of the z-dimension (e.g. vertical level)"
zdim::Int
"Grid staggering for each dimension. (true=edge-aligned, false=center-aligned)"
staggering::NTuple{3, Bool}
staggering::NTuple{3,Bool}
end

"""
Expand Down Expand Up @@ -176,8 +176,8 @@ mutable struct DataSetInterpolator{To,N,N2,FT,ITPT,DomT}
N = ndims(data)
N2 = N - 1
times = [DateTime(0, 1, 1) + Hour(i) for i ∈ 1:cache_size]
_, itp2 = create_interpolator!(To, interp_cache, data,
repeat([0:1], length(metadata.varsize)), times)
_, itp2 = create_interpolator!(interp_cache, data,
repeat([0:0.1:0.1], length(metadata.varsize)), times)
ITPT = typeof(itp2)

if domain.spatial_ref == metadata.native_sr
Expand All @@ -203,6 +203,14 @@ end
function replace_in_tuple(t::NTuple{N,T1}, index1::Int, v1::T2, index2::Int, v2::T2) where {T1,T2,N}
ntuple(i -> i == index1 ? T1(v1) : i == index2 ? T1(v2) : t[i], N)
end
function tuple_from_vals(index1::Int, v1::T, index2::Int, v2::T) where {T}
ntuple(i -> i == index1 ? v1 : i == index2 ? v2 :
throw(ArgumentError("missing index")), 2)
end
function tuple_from_vals(index1::Int, v1::T, index2::Int, v2::T, index3::Int, v3::T) where {T}
ntuple(i -> i == index1 ? v1 : i == index2 ? v2 : i == index3 ? v3 :
throw(ArgumentError("missing index")), 3)
end

function Base.show(io::IO, itp::DataSetInterpolator)
print(io, "DataSetInterpolator{$(typeof(itp.fs)), $(itp.varname)}")
Expand All @@ -227,8 +235,8 @@ function knots2range(knots, reltol=0.05)
end

"""Create a new interpolator, overwriting `interp_cache`."""
function create_interpolator!(To, interp_cache, data, coords, times)
grid = Tuple(knots2range.([coords..., datetime2unix.(times)]))
function create_interpolator!(interp_cache, data, coords, times)
grid = tuple(coords..., knots2range(datetime2unix.(times)))
copyto!(interp_cache, data)
itp = interpolate!(interp_cache, BSpline(Linear()))
itp = scale(itp, grid)
Expand All @@ -239,7 +247,8 @@ function update_interpolator!(itp::DataSetInterpolator{To}) where {To}
if size(itp.interp_cache) != size(itp.data)
itp.interp_cache = similar(itp.data)
end
grid, itp2 = create_interpolator!(To, itp.interp_cache, itp.data, itp.metadata.coords, itp.times)
coords = _model_grid(itp)
grid, itp2 = create_interpolator!(itp.interp_cache, itp.data, coords, itp.times)
@assert all([length(g) for g in grid] .== size(itp.data)) "invalid data size: $([length(g) for g in grid]) != $(size(itp.data))"
itp.itp = itp2
end
Expand Down Expand Up @@ -312,9 +321,25 @@ function async_loader(itp::DataSetInterpolator)
end
end

# Get the model grid for this interpolator.
function _model_grid(itp::DataSetInterpolator)
grid = EarthSciMLBase.grid(itp.domain, itp.metadata.staggering)
if length(itp.metadata.varsize) == 2 && itp.metadata.zdim <= 0
grid_size = tuple_from_vals(itp.metadata.xdim, grid[1],
itp.metadata.ydim, grid[2])
elseif length(itp.metadata.varsize) == 3
grid_size = tuple_from_vals(itp.metadata.xdim, grid[1],
itp.metadata.ydim, grid[2], itp.metadata.zdim, grid[3])
else
error("Invalid data size")
end
end

function initialize!(itp::DataSetInterpolator, t::DateTime)
itp.load_cache = zeros(eltype(itp.load_cache), itp.metadata.varsize...)
itp.data = zeros(eltype(itp.data), itp.metadata.varsize..., size(itp.data, length(size(itp.data)))) # Add a dimension for time.
grid_size = length.(_model_grid(itp))
itp.data = zeros(eltype(itp.data), grid_size...,
size(itp.data, length(size(itp.data)))) # Add a dimension for time.
Threads.@spawn async_loader(itp)
itp.initialized = true
end
Expand Down Expand Up @@ -343,6 +368,7 @@ function update!(itp::DataSetInterpolator, t::DateTime)
error("Unexpected time ordering, can't reorder indexes $(idxs_in_times) to $(idxs_in_cache)")
end

model_grid = EarthSciMLBase.grid(itp.domain, itp.metadata.staggering)
# Load the additional times we need
for idx in idxs_not_in_times
d = selectdim(itp.data, N, idx)
Expand All @@ -351,7 +377,7 @@ function update!(itp::DataSetInterpolator, t::DateTime)
if r != 0
throw(r)
end
interpolate_from!(itp, d, itp.load_cache) # Copy results to correct location
interpolate_from!(itp, d, itp.load_cache, model_grid) # Copy results to correct location
put!(itp.copyfinish, 0) # Let the loader know we've finished copying
end
itp.times = times
Expand All @@ -360,12 +386,40 @@ function update!(itp::DataSetInterpolator, t::DateTime)
update_interpolator!(itp)
end

function interpolate_from!(dsi::DataSetInterpolator, dst, src)
function interpolate_from!(dsi::DataSetInterpolator, dst::AbstractArray{T,N}, src::AbstractArray{T,N},
model_grid, extrapolate_type=Flat()) where {T,N}
data_grid = Tuple(knots2range.(dsi.metadata.coords))
model_grid = EarthSciMLBase.grid(dsi.domain, dsi.metadata.staggering)
dsi.metadata.xdim, dsi.metadata.ydim
itp = interpolate!(src, BSpline(Linear()))
itp = scale(itp, data_grid)
dst .= src
itp = extrapolate(scale(itp, data_grid), extrapolate_type)
if N == 3
for (i, x) in enumerate(model_grid[1])
for (j, y) in enumerate(model_grid[2])
for (k, z) in enumerate(model_grid[3])
idx = tuple_from_vals(dsi.metadata.xdim, i,
dsi.metadata.ydim, j, dsi.metadata.zdim, k)
locs = tuple_from_vals(dsi.metadata.xdim, x,
dsi.metadata.ydim, y, dsi.metadata.zdim, z)
locs = dsi.coord_trans(locs)
dst[idx...] = itp(locs...)
end
end
end
elseif N == 2 && dsi.metadata.zdim <= 0
for (i, x) in enumerate(model_grid[1])
for (j, y) in enumerate(model_grid[2])
idx = tuple_from_vals(dsi.metadata.xdim, i,
dsi.metadata.ydim, j)
locs = tuple_from_vals(dsi.metadata.xdim, x,
dsi.metadata.ydim, y)
locs = dsi.coord_trans(locs)
dst[idx...] = itp(locs...)
end
end
else
error("Invalid dimension configuration")
end
dst
end

function lazyload!(itp::DataSetInterpolator, t::DateTime)
Expand Down Expand Up @@ -423,7 +477,7 @@ Interpolate without checking if the data has been correctly loaded for the given
@generated function interp_unsafe(itp::DataSetInterpolator{T1,N,N2}, t::DateTime, locs::Vararg{T2,N2}) where {T1,T2,N,N2}
if N2 == N - 1 # Number of locs has to be one less than the number of data dimensions so we can add the time in.
quote
locs = itp.coord_trans(locs)
#locs = itp.coord_trans(locs)
try
itp.itp(locs..., datetime2unix(t))
catch err
Expand Down
41 changes: 29 additions & 12 deletions test/load_test.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -14,8 +14,8 @@ te = DateTime(2022, 5, 3)
fs = EarthSciData.GEOSFPFileSet("4x5", "A3dyn", t, te)

domain = DomainInfo(t, te;
latrange=deg2rad(-85.0f0):deg2rad(2):deg2rad(85.0f0),
lonrange=deg2rad(-180.0f0):deg2rad(2.5):deg2rad(175.0f0),
lonrange=deg2rad(-175.0):deg2rad(2.5):deg2rad(175.0),
latrange=deg2rad(-85.0):deg2rad(2):deg2rad(85.0),
levrange=1:10, dtype=Float64)

@test EarthSciData.url(fs, t) == "https://geos-chem.s3-us-west-2.amazonaws.com/GEOS_4x5/GEOS_FP/2022/05/GEOSFP.20220501.A3dyn.4x5.nc"
Expand All @@ -39,6 +39,14 @@ itp = EarthSciData.DataSetInterpolator{Float32}(fs, "U", t, te, domain)
@test EarthSciData.dimnames(itp) == ["lon", "lat", "lev"]
@test issetequal(EarthSciData.varnames(fs), ["U", "OMEGA", "RH", "DTRAIN", "V"])

@testset "grid" begin
grd = EarthSciData._model_grid(itp)
length.(grd) == (142, 86, 10)
grd[1] ≈ deg2rad(-175.0 - 1.25):deg2rad(2.5):deg2rad(175.0 + 1.25)
grd[2] ≈ deg2rad(-85.0):deg2rad(2):deg2rad(85.0)
grd[3] ≈ 1:1.0:10
end

@testset "interpolation" begin
uvals = []
times = DateTime(2022, 5, 1):Hour(1):DateTime(2022, 5, 3)
Expand All @@ -48,8 +56,8 @@ itp = EarthSciData.DataSetInterpolator{Float32}(fs, "U", t, te, domain)
for i ∈ 4:3:length(uvals)-1
@test uvals[i] ≈ (uvals[i-1] + uvals[i+1]) / 2 atol = 1e-2
end
want_uvals = [-0.047425747f0, 0.064035736f0, 0.11166346f0, 0.09545743f0, 0.07925139f0,
-0.011301707f0, -0.17620188f0, -0.34110206f0, -0.501398f0, -0.65708977f0]
want_uvals = [-0.07933916f0, 0.03189625f0, 0.079422876f0, 0.06324073f0, 0.047058582f0,
-0.044040862f0, -0.21005762f0, -0.37607434f0, -0.53645617f0, -0.6912031f0]
@test uvals[1:10] ≈ want_uvals

# Test that shuffling the times doesn't change the results.
Expand Down Expand Up @@ -79,11 +87,13 @@ end
dfi = EarthSciData.DataFrequencyInfo(fs)
tt = dfi.centerpoints[EarthSciData.centerpoint_index(dfi, t)]
v = tv(fs, tt)
cache .= [v, v * 0.5, v * 2.0]
cache[:, 1] .= [v, v * 0.5, v * 2.0]
cache[:, 2] .= [v, v * 0.5, v * 2.0]
end
function EarthSciData.loadmetadata(fs::DummyFileSet, varname)
return EarthSciData.MetaData([[0.0, 0.5, 1.0]], u"m", "description", ["x"], [3],
"+proj=longlat +datum=WGS84 +no_defs", 1, 1, -1, (false, false, false))
return EarthSciData.MetaData([[0.0, 0.5, 1.0], [0.0, 1.0]], u"m",
"description", ["x"], [3, 2],
"+proj=longlat +datum=WGS84 +no_defs", 1, 2, -1, (false, false, false))
end

fs = DummyFileSet(DateTime(2022, 4, 30), DateTime(2022, 5, 4))
Expand All @@ -99,7 +109,8 @@ end

answerdata = [tv(fs, t) * v for t ∈ dfi.centerpoints, v ∈ [1.0, 0.5, 2.0]]

grid = Tuple(EarthSciData.knots2range.([datetime2unix.(dfi.centerpoints), [0.0, 0.5, 1.0]]))
grid = Tuple(EarthSciData.knots2range.([datetime2unix.(dfi.centerpoints),
[0.0, 0.5, 1.0]]))
answer_itp = scale(interpolate(answerdata, BSpline(Linear())), grid)

times = DateTime(2022, 5, 1):Hour(1):DateTime(2022, 5, 3)
Expand All @@ -109,14 +120,14 @@ end
answers = zeros(Float32, length(times), length(xs))
for (i, tt) ∈ enumerate(times)
for (j, x) ∈ enumerate(xs)
uvals[i, j] = interp!(itp, tt, x)
uvals[i, j] = interp!(itp, tt, (x, x)...)
answers[i, j] = answer_itp(datetime2unix(tt), x)
end
end

@test uvals ≈ answers

interp!(itp, times[end], xs[end])
interp!(itp, times[end], xs[end], xs[end])
@test length(itp.times) == 2
@test itp.times == [DateTime("2022-05-02T22:30:00"), DateTime("2022-05-03T01:30:00")]

Expand All @@ -126,7 +137,7 @@ end
tt = times[i]
for j ∈ randperm(length(xs))
x = xs[j]
uvals[i, j] = interp!(itp, tt, x)
uvals[i, j] = interp!(itp, tt, x, x)
answers[i, j] = answer_itp(datetime2unix(tt), x)
end
end
Expand All @@ -140,7 +151,7 @@ end
answers = zeros(Float32, length(times), length(xs))
for (i, tt) ∈ enumerate(times)
for (j, x) ∈ enumerate(xs)
uvals[i, j] = interp!(itp, tt, x)
uvals[i, j] = interp!(itp, tt, x, x)
answers[i, j] = answer_itp(datetime2unix(tt), x)
end
end
Expand Down Expand Up @@ -170,3 +181,9 @@ end
true
end
end

@testset "tuple_from_vals" begin
@test EarthSciData.tuple_from_vals(1, 1, 2, 2, 3, 3) == (1, 2, 3)
@test EarthSciData.tuple_from_vals(2, 2, 1, 1, 3, 3) == (1, 2, 3)
@test EarthSciData.tuple_from_vals(3, 3, 2, 2, 1, 1) == (1, 2, 3)
end
4 changes: 2 additions & 2 deletions test/nei2016monthly_test.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ sample_time = DateTime(2016, 5, 1)

@testset "correct projection" begin
itp = EarthSciData.DataSetInterpolator{Float32}(fileset, "NOX", ts, te, domain)
@test interp!(itp, sample_time, deg2rad(-97.0f0), deg2rad(40.0f0)) ≈ 9.211331f-10
@test interp!(itp, sample_time, deg2rad(-97.0f0), deg2rad(40.0f0)) ≈ 1.256768f-9
end

@testset "incorrect projection" begin
Expand All @@ -42,7 +42,7 @@ end

@testset "Out of domain" begin
itp = EarthSciData.DataSetInterpolator{Float32}(fileset, "NOX", ts, te, domain)
@test_throws BoundsError interp!(itp, sample_time, deg2rad(0.0f0), deg2rad(40.0f0))
@test interp!(itp, sample_time, deg2rad(0.0f0), deg2rad(40.0f0)) ≈ 0.0
end


Expand Down
2 changes: 1 addition & 1 deletion test/solve_test.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@ end
DateTime("2016-04-16T00:00:00"), DateTime("2016-05-16T12:00:00")]
prob = ODEProblem(sys2, [], get_tspan(domain), [])
sol = solve(prob)
@test only(sol.u[end]) ≈ 6.3645540358326396e-6
@test only(sol.u[end]) ≈ 5.322912896619149e-6
end

emis = NEI2016MonthlyEmis("mrggrid_withbeis_withrwc", domain)
Expand Down

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Registration pull request created: JuliaRegistries/General/126054

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Release notes:

## Breaking changes

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Tagging

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