leafopticals.jl

###############################################################################
#
# Create LeafOpticals
#
###############################################################################
"""
    create_leaf_opticals(
                sWL::Array{FT,1},
                file::String = OPTI_2021
    ) where {FT<:AbstractFloat}

Create an `AbstractLeafOptiPara` struct, given
- `sWL` Standard wave length
- `opfn` File that saves optical parameters
"""
function create_leaf_opticals(
            sWL::Array{FT,1},
            opfn::String = OPTI_2021
) where {FT<:AbstractFloat}
    N = length(sWL) - 1;

    # reading data
    _opti   = matread(opfn)["optipar"];
    _nr     = _opti["nr"  ];
    _Km     = _opti["Kdm" ];
    _Kab    = _opti["Kab" ];
    _Kant   = _opti["Kant"];
    _Kcar   = _opti["Kca" ];
    _Kw     = _opti["Kw"  ];
    _KBrown = _opti["Ks"  ];
    _phi    = _opti["phi" ];
    _KcaV   = _opti["KcaV"];
    _KcaZ   = _opti["KcaZ"];
    _lambda = _opti["wl"  ];

    # create data to parse
    nr     = zeros(FT, N);
    Km     = zeros(FT, N);
    Kab    = zeros(FT, N);
    Kant   = zeros(FT, N);
    Kcar   = zeros(FT, N);
    Kw     = zeros(FT, N);
    KBrown = zeros(FT, N);
    phi    = zeros(FT, N);
    KcaV   = zeros(FT, N);
    KcaZ   = zeros(FT, N);
    lambda = zeros(FT, N);

    # fill in the data arrays
    # println("Reading Optical Parameters from ", sWL[1], " to ", sWL[end])
    @inbounds for i in 1:N
        wo = findall( (_lambda.>=sWL[i]) .& (_lambda.<sWL[i+1]) );
        if length(wo)==0
            @warn "Warning, some wavelengths out of bounds $(string(sWL[i]))";
        end

        nr[i]     = mean(    _nr[wo]);
        Km[i]     = mean(    _Km[wo]);
        Kab[i]    = mean(   _Kab[wo]);
        Kant[i]   = mean(  _Kant[wo]);
        Kcar[i]   = mean(  _Kcar[wo]);
        Kw[i]     = mean(    _Kw[wo]);
        KBrown[i] = mean(_KBrown[wo]);
        phi[i]    = mean(   _phi[wo]);
        KcaV[i]   = mean(  _KcaV[wo]);
        KcaZ[i]   = mean(  _KcaZ[wo]);
        lambda[i] = mean(_lambda[wo]);
    end

    # return the created struct
    return LeafOpticals{FT}(nr,
                            Km,
                            Kab,
                            Kant,
                            Kcar,
                            Kw,
                            KBrown,
                            phi,
                            KcaV,
                            KcaZ,
                            lambda)
end