Merge pull request #21 from PALEOtoolkit/outputwriters_fix

OutputWriter fixes

src/FieldRecord.jl

@@ -1,11 +1,18 @@
 """
-    FieldRecord{D <: AbstractData, S <: AbstractSpace, ...}
+    FieldRecord{D <: AbstractData, S <: AbstractSpace, V, N, M, R}
+    FieldRecord(
+        f::PB.Field{D, S, V, N, M}, attributes; 
+        coords_record, 
+        sizehint::Union{Nothing, Int}=nothing
+    ) -> fr
 
-A series of records each containing a `PALEOboxes.Field`.
+A series of `records::R` each containing the `values` from a `PALEOboxes.Field{D, S, N, V, M}`.
+
+A `coords_record` may be attached to provide a coordinate (eg model time) corresponding to `records`.
 
 # Implementation
-Fields with array values are stored in `records` as a Vector of arrays.
-Fields with single values (`field_single_element` true) are stored as a Vector of `eltype(Field.values)`. 
+Fields with array `values` are stored in `records` as a Vector of arrays.
+Fields with single `values` (`field_single_element` true) are stored as a Vector of `eltype(Field.values)`. 
 """
 struct FieldRecord{D <: PB.AbstractData, S <: PB.AbstractSpace, V, N, M, R}
     records::Vector{R}
@@ -44,7 +51,7 @@ field_single_element(::Type{PB.Field{D, S, V, N, M}}) where {D, S, V, N, M} = fi
 field_single_element(::Type{FR}) where {FR <: FieldRecord} = field_single_element(eltype(FR))
 field_single_element(f::T) where {T} = field_single_element(T)
 
-"create empty FieldRecord"
+
 function FieldRecord(
     f::PB.Field{D, S, V, N, M}, attributes;
     coords_record, 
@@ -63,9 +70,9 @@ function FieldRecord(
     return FieldRecord{D, S, V, N, M, eltype(records)}(records, f.data_dims, f.mesh, attributes, coords_record)
 end
 
-"create a new FieldRecord, containing supplied `existing_values` data arrays"
+"create a new FieldRecord, containing supplied `existing_values::Vector` data arrays"
 function wrap_fieldrecord(
-    existing_values, 
+    existing_values::Vector, 
     field_data::Type, 
     data_dims::NTuple{N, PB.NamedDimension},
     data_type::Union{DataType, Missing},
@@ -78,10 +85,10 @@ function wrap_fieldrecord(
     #    existing_values, field_data, data_dims, data_type, space, spatial_size(space, mesh), 
     # )
     if field_single_element(field_data, N, space, M)
-        # assume existing_values is a Vector, with element a Field value, to be stored in Field as a length-1 Vector
-        V = Array{eltype(existing_values), 1}
+        # assume existing_values is a Vector, with each element to be stored in Field values::V as a length 1 Vector
+        V = Vector{eltype(existing_values)}
     else
-        # assume existing_values is a Vector of Field values
+        # assume existing_values is a Vector of Field values::V
         V = eltype(existing_values)
     end
 

src/OutputWriters.jl

@@ -49,16 +49,18 @@ Implementations should define methods for:
 PALEOmodel.AbstractOutputWriter
 
 """
-    initialize!(output::PALEOmodel.AbstractOutputWriter, model, modeldata, nrecords [;rec_coord=:tmodel])
+    initialize!(
+        output::PALEOmodel.AbstractOutputWriter, model, modeldata, nrecords 
+        [;coords_record=:tmodel] [coords_record_units="yr"]
+    )
 
 Initialize from a PALEOboxes::Model, reserving memory for an assumed output dataset of `nrecords`.
 
-The default for `rec_coord` is `:tmodel`, for a sequence of records following the time evolution
+The default for `coords_record` is `:tmodel`, for a sequence of records following the time evolution
 of the model.
 """
 function initialize!(
-    output::PALEOmodel.AbstractOutputWriter, model::PB.Model, modeldata::PB.ModelData, nrecords;
-    rec_coord::Symbol=:tmodel
+    output::PALEOmodel.AbstractOutputWriter, model::PB.Model, modeldata::PB.ModelData, nrecords
 )
 end
 
@@ -222,8 +224,8 @@ Base.length(output::OutputMemoryDomain) = output._nrecs
 
 "create from a PALEOboxes::Domain"
 function OutputMemoryDomain(
-    dom::PB.Domain, modeldata::PB.ModelData, nrecords; 
-    coords_record=:tmodel, coords_units="yr"
+    dom::PB.Domain, modeldata::PB.ModelData, nrecords::Integer; 
+    coords_record::Symbol=:tmodel, coords_record_units::AbstractString="yr"
 )
 
     odom =  OutputMemoryDomain(
@@ -271,7 +273,7 @@ function OutputMemoryDomain(
     odom.metadata[String(coords_record)] = Dict(
         :var_name=>String(coords_record), :domain_name=>dom.name,
         :vfunction=>PB.VF_Undefined, :description=>"output record coordinate",
-        :field_data=>PB.ScalarData, :space=>PB.ScalarSpace, :data_dims=>(), :units=>coords_units,
+        :field_data=>PB.ScalarData, :space=>PB.ScalarSpace, :data_dims=>(), :units=>coords_record_units,
     )
 
     # add variables
@@ -304,8 +306,8 @@ end
 "create from a DataFrames DataFrame containing scalar data"
 function OutputMemoryDomain(
     name::AbstractString, data::DataFrames.DataFrame;
-    metadata::Dict{String, Dict{Symbol, Any}}=Dict("tmodel"=>Dict{Symbol, Any}(:units=>"yr")),
-    coords_record=:tmodel,
+    coords_record::Symbol=:tmodel, coords_record_units::AbstractString="yr",
+    metadata::Dict{String, Dict{Symbol, Any}}=Dict(coords_record=>Dict{Symbol, Any}(:units=>coords_record_units)),    
 )
     # create minimal metadata for scalar Variables
     for vname in DataFrames.names(data)
@@ -413,7 +415,9 @@ function PB.get_field(odom::OutputMemoryDomain, varname)
     varname in DataFrames.names(df) || 
         error("Variable $varname not found in output (no column '$varname' in Dataframe output.domains[\"$(odom.name)\"].data)")
 
-    vdata = df[!, Symbol(varname)]
+    use_all_records = DataFrames.nrow(df) == odom._nrecs
+    # vdata = df[!, Symbol(varname)]
+    vdata = use_all_records ? df[!, Symbol(varname)] : df[1:odom._nrecs, Symbol(varname)]
 
     attributes = get(odom.metadata, varname, nothing)
 
@@ -438,12 +442,15 @@ function PB.get_field(odom::OutputMemoryDomain, varname)
         coords_record=[
             PB.FixedCoord(
                 String(odom.coords_record),
-                df[!, odom.coords_record],
+                # df[!, odom.coords_record],
+                use_all_records ? df[!, odom.coords_record] : df[1:odom._nrecs, odom.coords_record],
                 odom.metadata[String(odom.coords_record)]
             ),
         ]
     )
 
+    # @Infiltrator.infiltrate
+
     return fr
 end
 
@@ -656,15 +663,17 @@ end
 
 function initialize!(
     output::OutputMemory, model::PB.Model, modeldata::PB.ModelData, nrecords;
-    rec_coord::Symbol=:tmodel
+    rec_coord::Symbol=:tmodel, # deprecated
+    coords_record::Symbol=rec_coord, coords_record_units::AbstractString="yr",    
 )
 
     # Create Dict of DataFrames with output
     empty!(output.domains)
     for dom in model.domains
         output.domains[dom.name] = OutputMemoryDomain(
             dom, modeldata, nrecords,
-            coords_record=rec_coord,
+            coords_record=coords_record,
+            coords_record_units=coords_record_units,
         )
     end