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Tidy up and remove old code
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- remove old unused code
- fix doc build
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@sjdaines
sjdaines committed Dec 29, 2024
1 parent 69fa57e commit 1b9daa5
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7 changes: 3 additions & 4 deletions docs/src/PALEOmodelOutput.md
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Expand Up @@ -69,20 +69,19 @@ OutputMemoryDomain
```@docs
save_netcdf
load_netcdf!
save_jld2
load_jld2!
```

## Field Array

```@meta
CurrentModule = PALEOmodel
```
[`FieldArray`](@ref) provides a generic array type with named dimensions `PALEOboxes.NamedDimension` and optional coordinates `PALEOboxes.FixedCoord` for processing of model output.
[`FieldArray`](@ref) provides a generic array type with named dimensions `PALEOboxes.NamedDimension` and optional coordinates [`PALEOmodel.FixedCoord`](@ref) for processing of model output.

```@docs
FieldArray
get_array(f::PB.Field{D, PB.ScalarSpace, V, N, M}; attributes=nothing) where {D, V, N, M}
get_array(fr::FieldRecord; coords=nothing)
FixedCoord
```

## Plotting output
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175 changes: 5 additions & 170 deletions src/CoordsDims.jl
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Expand Up @@ -8,6 +8,8 @@
A fixed (state independent) coordinate
These are generated from coordinate variables for use in output visualisation.
N = 1: a cell-centre coordinate, size(values) = (ncells, )
N = 2: a boundary coordinate, size(values) = (2, ncells)
"""
Expand All @@ -19,90 +21,11 @@ end

is_boundary_coordinate(fc::FixedCoord) = ndims(fc.values) == 2 && size(fc.values, 1) == 2

"""
append_units(name::AbstractString, attributes) -> "name (units)"
Utility function to append variable units string to a variable name for display.
"""
function append_units(name::AbstractString, attributes::Dict{Symbol, Any})
units = get(attributes, :units, "")
if isempty(units)
return name
else
return name*" ($units)"
end
end

append_units(name::AbstractString, attributes::Nothing) = name

"""
build_coords_edges(coords_vec::Vector{FixedCoord}) -> Vector{Float64}
Build a vector of coordinate edges (length `n+1``) from `coords_vec`, assuming the PALEO
convention that `coords_vec` contains three elements with
cell midpoints, lower edges, upper edges each of length `n`, in that order.
Falls back to just returning the first entry in `coords_vec` for other cases.
"""
function build_coords_edges(dim::PB.NamedDimension, coords_vec::Vector{FixedCoord})

if isempty(coords_vec)
# no coordinate - just return indices
co_values = collect(1:(dim.size+1))
co_label = dim.name
elseif length(coords_vec) == 1 && is_boundary_coordinate(coords_vec[1])
co = coords_vec[1]
co_values = vcat(co.values[1, :], co.values[2, end])
co_label = append_units(co.name, co.attributes)
elseif length(coords_vec) == 1 || length(coords_vec) > 3
# 1 coordinate or something we don't understand - take first
co = first(coords_vec)
co_values = co.values
co_label = append_units(co.name, co.attributes)
elseif length(coords_vec) == 2 && is_boundary_coordinate(coords_vec[2])
# assume mid, boundary
co = coords_vec[2]
co_values = vcat(co.values[1, :], co.values[2, end])
co_label = append_units(co.name, co.attributes)
elseif length(coords_vec) in (2, 3)
# 2 coordinates assume lower, upper edges
# 3 coordinates assume mid, lower, upper
co_lower = coords_vec[end-1]
co_upper = coords_vec[end]
co_label = append_units(co_lower.name*", "*co_upper.name, co_lower.attributes)
first(co_lower.values) < first(co_upper.values) ||
@warn "build_coords_edges: $co_label co_lower is > co_upper - check model grid"
if co_lower.values[end] > co_lower.values[1] # ascending order
co_lower.values[2:end] == co_upper.values[1:end-1] ||
@warn "build_coords_edges: $co_label lower and upper edges don't match"
co_values = [co_lower.values; co_upper.values[end]]
else # descending order
co_lower.values[1:end-1] == co_upper.values[2:end] ||
@warn "build_coords_edges: $co_label lower and upper edges don't match"
co_values = [co_upper.values[1]; co_lower.values]
end

end

return co_values, co_label
end

"guess coordinate edges from midpoints, assuming uniform spacing"
function guess_coords_edges(x_midpoints)
first_x = x_midpoints[1] - 0.5*(x_midpoints[2] - x_midpoints[1])
last_x = x_midpoints[end] + 0.5*(x_midpoints[end] - x_midpoints[end-1])
return [first_x; 0.5.*(x_midpoints[1:end-1] .+ x_midpoints[2:end]); last_x]
end


function get_region(fc::FixedCoord, indices::AbstractVector)
return FixedCoord(fc.name, fc.values[indices], fc.attributes)
end

function get_region(fcv::Vector{FixedCoord}, indices::AbstractVector)
return [FixedCoord(fc.name, fc.values[indices], fc.attributes) for fc in fcv]
end

##################################################################
# Coordinate filtering and selection
################################################################

"find indices of coord from first before range[1] to first after range[2]"
function find_indices(coord::AbstractVector, range)
Expand Down Expand Up @@ -180,91 +103,3 @@ function dimscoord_subset(dim::PB.NamedDimension, coords::Vector{FixedCoord}, se
return cidx, dim_subset, coords_subset, coords_used
end


#=
#################################################
# Dimensions
#####################################################
"""
NamedDimension
A named dimension, with optional attached fixed coordinates `coords`
PALEO convention is that where possible `coords` contains three elements, for cell
midpoints, lower edges, upper edges, in that order.
"""
mutable struct NamedDimension
name::String
size::Int64
coords::Vector{FixedCoord} # may be empty
end
"create from size only (no coords)"
function NamedDimension(name, size::Integer)
return NamedDimension(
name,
size,
FixedCoord[],
)
end
"create from coord mid-points"
function NamedDimension(name, coord::AbstractVector)
return NamedDimension(
name,
length(coord),
[
FixedCoord(name, coord, Dict{Symbol, Any}()),
]
)
end
"create from coord mid-points and edges"
function NamedDimension(name, coord::AbstractVector, coord_edges::AbstractVector)
if coord[end] > coord[1]
# ascending order
coord_lower = coord_edges[1:end-1]
coord_upper = coord_edges[2:end]
else
# descending order
coord_lower = coord_edges[2:end]
coord_upper = coord_edges[1:end-1]
end
return NamedDimension(
name,
length(coord),
[
FixedCoord(name, coord, Dict{Symbol, Any}()),
FixedCoord(name*"_lower", coord_lower, Dict{Symbol, Any}()),
FixedCoord(name*"_upper", coord_upper, Dict{Symbol, Any}()),
]
)
end
function get_region(nd::NamedDimension, indices::AbstractVector)
return NamedDimension(nd.name, length(indices), get_region(nd.coords, indices))
end
"""
build_coords_edges(nd::NamedDimension) -> Vector{Float64}
Call [`build_coords_edges`](@ref)(nd.coords), or fallback to just returning indices
if no coords present.
"""
function build_coords_edges(nd::NamedDimension)
if !isempty(nd.coords)
return build_coords_edges(nd.coords)
else
@warn "no coords for NamedDimension $(nd.name), returning indices"
return collect(1:nd.size), nd.name*" (indices)"
end
end
function Base.show(io::IO, nd::NamedDimension)
print(io, "NamedDimension(name=", nd.name, ", size=", nd.size, ", coords=(")
join(io, [c.name for c in nd.coords], ", ")
print(io, "))")
return nothing
end
=#
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