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Workaround for issue in NCDatasets v0.14 #82

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Feb 9, 2024
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Workaround for issue in NCDatasets v0.14 #82

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16 changes: 13 additions & 3 deletions src/OutputWriters.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -812,6 +812,7 @@ function save_netcdf(
# Fails with variables with missing values eg that are Union{Missing, Float64}
# appears to be a NCDatasets.jl limitation (at least in v0.12.17) - the logic to map these to netcdf is
# combined with that to write the data, and the alternate form with just the type fails
# TODO may not work with NCDatasets v0.13 and later due to variable indexing changes ?
define_all_first = false
# define_all_first = true

Expand Down Expand Up @@ -896,6 +897,7 @@ function save_netcdf(

# write data (only used if define_all_first==true)
for (nc_v, nc_vdata) in nc_all_vdata
# TODO may not work with NCDatasets v0.13 and later ?
nc_v[:] = nc_vdata
end
end
Expand Down Expand Up @@ -1235,7 +1237,15 @@ end
function subdomain_to_netcdf!(ds, name::AbstractString, subdom::PB.Grids.InteriorSubdomain)
NCDatasets.defDim(ds, "subdomain_"*name, length(subdom.indices))

v = NCDatasets.defVar(ds, "subdomain_"*name, subdom.indices .- 1, ("subdomain_"*name,)) # convert to zero based
# v = NCDatasets.defVar(ds, "subdomain_"*name, subdom.indices .- 1, ("subdomain_"*name,)) # convert to zero based

# workaround for issue in NCDatasets v0.14 (and probably in v0.13 as well)
# https://github.com/Alexander-Barth/NCDatasets.jl/issues/246
# "v0.14 cannot create variable from an Int64 array with missing values"


si32_zerobased = [ismissing(i) ? missing : Int32(i-1) for i in subdom.indices]
v = NCDatasets.defVar(ds, "subdomain_"*name, si32_zerobased, ("subdomain_"*name,)) # convert to zero based
v.attrib["subdomain_type"] = "InteriorSubdomain"
end

Expand All @@ -1246,9 +1256,9 @@ function netcdf_to_subdomains(dsvars)
if haskey(v.attrib, "subdomain_type")
subdomain_type = v.attrib["subdomain_type"]
if subdomain_type == "BoundarySubdomain"
subdom = PB.Grids.BoundarySubdomain(v[:])
subdom = PB.Grids.BoundarySubdomain(Array(v))
elseif subdomain_type == "InteriorSubdomain"
subdom = PB.Grids.InteriorSubdomain(v[:])
subdom = PB.Grids.InteriorSubdomain(Array(v))
else
error("invalid subdomain_type = $subdomain_type")
end
Expand Down
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