implement alternative to missing values

docs/make.jl

@@ -16,6 +16,7 @@ makedocs(
         "Dimensions" => "dimensions.md",
         "Variables" => "variables.md",
         "Attributes" => "attributes.md",
+        "Fill values" => "fillvalue.md",
         "Performance tips" => "performance.md",
         "Known issues" => "issues.md",
         "Experimental features" => "experimental.md",

docs/src/index.md

@@ -36,7 +36,7 @@ To get started quickly see the [Quickstart](@ref) section. Otherwise see the fol
 * [Dimensions](@ref) : accessing/creating NetCDF dimensions
 * [Variables](@ref) : accessing/examining the variables (or dimensions) stored within a NetCDF dataset.
 * [Attributes](@ref) : accessing/creating NetCDF attributes
-* See [Performance tips](@ref performance_tips), [Known issues](@ref), [Experimental features](@ref) for more information.
+* See [Fill values and missing values](@ref), [Performance tips](@ref performance_tips), [Known issues](@ref), [Experimental features](@ref) for more information.
 
 ## Quick start
 

src/NCDatasets.jl

@@ -46,7 +46,8 @@ import CommonDataModel: AbstractDataset, AbstractVariable,
     iswritable, sync, CatArrays,
     SubDataset,
     @select, select, Near, coordinate_value, coordinate_names, split_by_and,
-    chunking, deflate, checksum
+    chunking, deflate, checksum,
+    _experimental_missing_value
 
 
 import DiskArrays

src/dataset.jl

@@ -28,6 +28,7 @@ const jlType = Dict(
 const ncType = Dict(value => key for (key, value) in jlType)
 
 iswritable(ds::NCDataset) = ds.iswritable
+_experimental_missing_value(ds::NCDataset) = ds._experimental_missing_value
 
 function isopen(ds::NCDataset)
     try
@@ -64,21 +65,25 @@ end
 function NCDataset(ncid::Integer,
                    iswritable::Bool,
                    isdefmode::Ref{Bool};
-                   parentdataset = nothing)
+                   parentdataset = nothing,
+                   _experimental_missing_value = missing,
+                   )
 
     function _finalize(ds)
         # only close open root group
         if (ds.ncid != -1) && (ds.parentdataset == nothing)
             close(ds)
         end
     end
-
-    ds = NCDataset{typeof(parentdataset)}(
+    @debug "_experimental_missing_value" _experimental_missing_value
+    ds = NCDataset{typeof(parentdataset),typeof(_experimental_missing_value)}(
         parentdataset,
         ncid,
         iswritable,
         isdefmode,
-        Dict{String,String}())
+        Dict{String,String}(),
+        _experimental_missing_value,
+    )
 
     if !iswritable
         initboundsmap!(ds)
@@ -169,6 +174,7 @@ function NCDataset(filename::AbstractString,
                    diskless::Bool = false,
                    persist::Bool = false,
                    memory::Union{Vector{UInt8},Nothing} = nothing,
+                   _experimental_missing_value = missing,
                    attrib = [])
 
     ncid = -1
@@ -226,7 +232,9 @@ function NCDataset(filename::AbstractString,
     end
 
     iswritable = mode != "r"
-    ds = NCDataset(ncid,iswritable,isdefmode)
+    ds = NCDataset(
+        ncid,iswritable,isdefmode,
+        _experimental_missing_value = _experimental_missing_value)
 
     # set global attributes
     for (attname,attval) in attrib

src/types.jl

@@ -24,7 +24,7 @@ struct Variable{NetCDFType,N,TDS} <: AbstractNCVariable{NetCDFType, N}
 end
 
 # must be mutable to register a finalizer
-mutable struct NCDataset{TDS} <: AbstractNCDataset where TDS <: Union{AbstractNCDataset,Nothing}
+mutable struct NCDataset{TDS,T_experimental_missing_value} <: AbstractNCDataset where TDS <: Union{AbstractNCDataset,Nothing}
     # parent_dataset is nothing for the root dataset
     parentdataset::TDS
     ncid::Cint
@@ -35,6 +35,7 @@ mutable struct NCDataset{TDS} <: AbstractNCDataset where TDS <: Union{AbstractNC
     # mapping between variables related via the bounds attribute
     # It is only used for read-only datasets to improve performance
     _boundsmap::Dict{String,String}
+    _experimental_missing_value::T_experimental_missing_value
 end
 
 "Alias to `NCDataset`"

test/test_fillvalue.jl

@@ -166,3 +166,31 @@ v = defVar(ds,"instrument_mode",String,("mode_items",),fillvalue = "UNDEFINED MO
 @test fillvalue(v) == "UNDEFINED MODE"
 close(ds)
 rm(filename)
+
+
+
+# Alternative to Missing for NetCDF fillvalue
+
+fname = tempname()
+data = randn(3,4)
+fv = 9999
+data[2,2] = fv
+
+ds = NCDataset(fname,"c")
+defDim(ds,"lon",size(data,1))
+defDim(ds,"lat",size(data,2))
+ncv = defVar(ds,"data",Float64,("lon","lat"),fillvalue = fv)
+ncv.var[:,:] = data
+
+ncv = cfvariable(ds,"data",_experimental_missing_value = NaN)
+@test eltype(ncv) == Float64
+@test ncv[1,1] == data[1,1]
+@test isnan(ncv[2,2])
+close(ds)
+
+
+ds = NCDataset(fname,"r",_experimental_missing_value = NaN)
+ncv = ds["data"]
+
+@test ncv[1,1] == data[1,1]
+@test isnan(ncv[2,2])