LeafOptics

This function updates leaf level reflectance, transmittance, and fluorescence spectra related parameters. Supported methods are

• Update leaf spectra based on pigment concentrations
• Update leaf spectra (reflectance and transmittance) to given broadband values
• Update leaf spectra based on pigment concentrations for the entire SPAC

leaf_spectra!(
            bio::HyperspectralLeafBiophysics{FT},
            wls::WaveLengthSet{FT},
            lha::HyperspectralAbsorption{FT},
            lwc::FT;
            APAR_car::Bool = true,
            reabsorb::Bool = true,
            α::FT = FT(40)
) where {FT<:AbstractFloat}

Update leaf reflectance and transmittance spectra, and fluorescence spectrum matrices, given

• bio HyperspectralLeafBiophysics type struct that contains leaf biophysical parameters
• wls WaveLengthSet type struct that contain wave length bins
• lha HyperspectralAbsorption type struct that contains absorption characteristic curves
• lwc Leaf water content [mol m⁻²]
• APAR_car If true, carotenoid absorption is accounted for in PPAR, default is true
• reabsorb If true, SIF reabsorption is enabled; otherwise, matb and matf should be based on the case with no reabsorption
• α Optimum angle of incidence (default is 40° as in PROSPECT-D, SCOPE uses 59°)

Examples

wls = ClimaCache.WaveLengthSet{Float64}();
bio = ClimaCache.HyperspectralLeafBiophysics{Float64}();
lha = ClimaCache.HyperspectralAbsorption{Float64}();
leaf_spectra!(bio, wls, lha, 50.0);
leaf_spectra!(bio, wls, lha, 50.0; APAR_car=false);
leaf_spectra!(bio, wls, lha, 50.0; APAR_car=false, α=59.0);

leaf_spectra!(bio::HyperspectralLeafBiophysics{FT}, wls::WaveLengthSet{FT}, ρ_par::FT, ρ_nir::FT, τ_par::FT, τ_nir::FT) where {FT<:AbstractFloat}

Update leaf reflectance and transmittance (e.g., prescribe broadband PAR and NIR values), given

• bio HyperspectralLeafBiophysics type struct that contains leaf biophysical parameters
• wls WaveLengthSet type struct that contain wave length bins
• ρ_par Reflectance at PAR region
• ρ_nir Reflectance at NIR region
• τ_par Transmittance at PAR region
• τ_nir Transmittance at NIR region

Examples

wls = ClimaCache.WaveLengthSet{Float64}();
bio = ClimaCache.HyperspectralLeafBiophysics{Float64}();
leaf_spectra!(bio, wls, 0.1, 0.45, 0.05, 0.25);

leaf_spectra!(spac::Union{MonoMLGrassSPAC{FT}, MonoMLPalmSPAC{FT}, MonoMLTreeSPAC{FT}}) where {FT<:AbstractFloat}

Update leaf reflectance and transmittance for SPAC, given

• spac MonoMLGrassSPAC, MonoMLPalmSPAC, or MonoMLTreeSPAC type SPAC

leaf_PAR(bio::HyperspectralLeafBiophysics{FT}, wls::WaveLengthSet{FT}, rad::HyperspectralRadiation{FT}; APAR_car::Bool = true) where {FT<:AbstractFloat}

Return leaf level PAR, APAR, and PPAR, given

• bio HyperspectralLeafBiophysics type struct that contains leaf biophysical parameters
• wls WaveLengthSet type struct that contains wave length bins
• rad HyperspectralRadiation type struct that contains incoming radiation information
• APAR_car If true (default), account carotenoid absorption as PPAR; otherwise, PPAR is only by chlorophyll

Examples

wls = ClimaCache.WaveLengthSet{Float64}();
bio = ClimaCache.HyperspectralLeafBiophysics{Float64}();
rad = ClimaCache.HyperspectralRadiation{Float64}();
par,apar,ppar = leaf_PAR(bio, wls, rad);
par,apar,ppar = leaf_PAR(bio, wls, rad; APAR_car=false);

leaf_SIF(bio::HyperspectralLeafBiophysics{FT}, wls::WaveLengthSet{FT}, rad::HyperspectralRadiation{FT}, ϕ::FT = FT(0.01); ϕ_photon::Bool = true) where {FT<:AbstractFloat}

Return the leaf level SIF at backward and forward directions, given

• bio HyperspectralLeafBiophysics type struct that contains leaf biophysical parameters
• wls WaveLengthSet type struct that contains wave length bins
• rad HyperspectralRadiation type struct that contains incoming radiation information
• ϕ Fluorescence quantum yield
• ϕ_photon If true (default), convert photon to photon when computing SIF; otherwise, convert energy to energy

Examples

wls = ClimaCache.WaveLengthSet{Float64}();
bio = ClimaCache.HyperspectralLeafBiophysics{Float64}();
rad = ClimaCache.HyperspectralRadiation{Float64}();
sif_b,sif_f = leaf_SIF(bio, wls, rad, 0.01);
sif_b,sif_f = leaf_SIF(bio, wls, rad, 0.01; ϕ_photon=false);

average_transmittance(α::FT, nr::FT) where {FT<:AbstractFloat}

Return the average transmittance of isotropic radiation across an interface between two dielectrics, given

• α angle of incidence
• nr Index of refraction

References

• Stern (1964) Transmission of isotropic radiation across an interface between two dielectrics. Applied Optics 3(1): 111-113.
• Allen (1973) Transmission of isotropic light across a dielectric surface in two and three dimensions. Journal of the Optical Society of America 63(6): 664-666.

photon(λ::FT, E::FT) where {FT<:AbstractFloat}

Return the number of moles of photons, given

• λ Wave length in [nm], converted to [m] by FAC
• E Joules of energy

photon!(λ::Vector{FT}, E::Vector{FT}, phot::Vector{FT}) where {FT<:AbstractFloat}
photon!(λ::Vector{FT}, E::Vector{FT}) where {FT<:AbstractFloat}

Compute and save the number of moles of photons, given

• λ Wave length in [nm], converted to [m] by FAC
• E Joules of energy (will be converted to moles of photons if phot in not given)
• phot Mole of photons (variable to save)

energy(λ::FT, phot::FT) where {FT<:AbstractFloat}

Return the energy, given

• λ Wave length in [nm], converted to [m] by FAC
• phot Number of moles of photon

energy!(λ::Vector{FT}, phot::Vector{FT}, E::Vector{FT}) where {FT<:AbstractFloat}
energy!(λ::Vector{FT}, phot::Vector{FT}) where {FT<:AbstractFloat}

Compute and save the number of moles of photons, given

• λ Wave length in [nm], converted to [m] by FAC
• phot Mole of photons (will be converted to moles of photons if E is not given)
• E Joules of energy (variable to save)