FluspectB.h File Reference

#include <cstddef>
#include <string>
#include <vector>

Go to the source code of this file.

Data Structures
struct	helios::FluspectBiochemistry
	Fluspect-B leaf biochemistry inputs (PROSPECT-PRO + CX pigments + fluorescence parameters). More...
struct	helios::FluspectOptipar
struct	helios::FluspectKernel
	Output of Fluspect-B computation for one leaf biochemistry. More...

Functions
void	helios::loadFluspectOptipar (const std::string &xml_path, FluspectOptipar &optipar)
	Load Fluspect-B Optipar coefficients from a Helios spectral-library XML asset.
FluspectKernel	helios::computeFluspectKernel (const FluspectBiochemistry &biochem, const FluspectOptipar &optipar, float excitation_step_nm=5.f)
	Compute Fluspect-B leaf optics + fluorescence matrices for a single leaf biochemistry.

Detailed Description

Fluspect-B leaf fluorescence model (Vilfan et al. 2016) for Helios RadiationModel SIF plugin.

This module ports the fluspect_B_CX.m routine from SCOPE v2.0 (https://github.com/Christiaanvandertol/SCOPE) to C++. Given leaf biochemistry (PROSPECT-PRO + CX inputs) and Optipar specific-absorption coefficients, it computes: (a) PROSPECT-PRO-CX leaf reflectance and transmittance over 400-2400 nm (b) Forward and backward fluorescence excitation-emission matrices M_f[wlf, wle] and M_b[wlf, wle] (units: dimensionless fluorescence efficiency per excitation-emission wavelength pair). The M matrices, when multiplied by incoming excitation flux and the fluorescence quantum yield Phi_F, give the per-leaf fluorescence emission at each emission wavelength.

Inputs and outputs closely follow the MATLAB reference; see SCOPE's src/RTMs/fluspect_B_CX.m. Optipar specific-absorption coefficients are loaded from plugins/radiation/spectral_data/fluspect_B_optipar.xml.

Definition in file FluspectB.h.

Function Documentation

computeFluspectKernel()

FluspectKernel helios::computeFluspectKernel	(	const FluspectBiochemistry &	biochem,
		const FluspectOptipar &	optipar,
		float	excitation_step_nm = 5.f
	)

Compute Fluspect-B leaf optics + fluorescence matrices for a single leaf biochemistry.

Implements the doubling-method algorithm from fluspect_B_CX.m (SCOPE v2.0). The excitation grid is 400-750 nm at excitation_step_nm spacing (default 5 nm to match SCOPE's int=5 internal resolution). The emission grid is 640-848 nm at 4 nm spacing (Fluspect native; corresponds to wlf = 640:4:850 with MATLAB's inclusive/exclusive endpoint convention yielding 848 as the last sample).

Numerical agreement with MATLAB fluspect_B_CX is to within ~1e-6 per Mf/Mb element given identical Optipar coefficients.

Parameters

[in]	biochem	Leaf biochemistry inputs.
[in]	optipar	Optipar coefficients loaded via loadFluspectOptipar.
[in]	excitation_step_nm	Excitation wavelength grid spacing in nm. Must be > 0. The grid is 400 nm to 750 nm inclusive.

Returns

Filled FluspectKernel. If biochem.fqe <= 0, Mf/Mb are left empty (caller should treat as no fluorescence). Callers that want a quantum-yield-agnostic kernel can pass fqe = 1 and multiply by their own Phi_F externally — this is how RadiationModel uses the kernel so that leaves sharing biochemistry but differing in J/Jmax can share a cached kernel.

Definition at line 209 of file FluspectB.cpp.

loadFluspectOptipar()

void helios::loadFluspectOptipar	(	const std::string &	xml_path,
		FluspectOptipar &	optipar
	)

Load Fluspect-B Optipar coefficients from a Helios spectral-library XML asset.

Reads globaldata_vec2 entries named fluspect_optipar_<field> (nr, Kab, Kca, KcaV, KcaZ, Kdm, Kw, Ks, Kant, Kp, Kcbc, phi) from Context global data. If any entries are missing from Context global data but present in the named XML file on disk, loads them first via Context::loadXML.

Parameters

[in]	xml_path	Absolute path to fluspect_B_optipar.xml (resolved by caller).
[out]	optipar	Destination coefficient set.

Exceptions

helios_runtime_error

on any missing coefficient or grid-mismatch.

Definition at line 189 of file FluspectB.cpp.