toolsrtm.fluspect

FLUSPECT-B / FLUSPECT-B-Cx leaf model: PROSPECT reflectance/transmittance plus chlorophyll-fluorescence excitation-emission matrices. Direct port of ToolsRTM/R/fluspect_B.R (getFluspect.B) and fluspect_Cx.R (getFluspect.Cx).

FLUSPECT-B / FLUSPECT-B-Cx leaf model: PROSPECT reflectance/transmittance plus chlorophyll-fluorescence excitation-emission matrices, via Verhoef’s doubling method applied to the leaf mesophyll layer alone (leaf-air interfaces removed before doubling, re-added after).

Direct port of ToolsRTM/R/fluspect_B.R (getFluspect.B) and ToolsRTM/R/fluspect_Cx.R (getFluspect.Cx). These are two separate, duplicated R functions (not a shared core with a mode flag), so they’re ported as two separate Python functions here too, since their fluorescence-matrix output shapes genuinely differ (MbI/MbII/ MfI/MfII split by photosystem for the B version, vs a single Mb/Mf pair for the Cx version).

Reuses toolsrtm.leaf._one_layer() / toolsrtm.leaf._stokes_n_layers() for the PROSPECT part (identical math, alpha fixed at 59 degrees here instead of a caller-supplied angle, matching ToolsRTM::calctav(59, nr) in both R functions).

class toolsrtm.fluspect.FluspectBResult(lambda_: 'np.ndarray', refl: 'np.ndarray', tran: 'np.ndarray', kChlrel: 'np.ndarray', MbI: 'np.ndarray', MbII: 'np.ndarray', MfI: 'np.ndarray', MfII: 'np.ndarray')[source]

Bases: object

Parameters:
lambda_: ndarray
refl: ndarray
tran: ndarray
kChlrel: ndarray
MbI: ndarray
MbII: ndarray
MfI: ndarray
MfII: ndarray
class toolsrtm.fluspect.FluspectCxResult(lambda_: 'np.ndarray', refl: 'np.ndarray', tran: 'np.ndarray', kChlrel: 'np.ndarray', kCarrel: 'np.ndarray', Mb: 'np.ndarray', Mf: 'np.ndarray')[source]

Bases: object

Parameters:
lambda_: ndarray
refl: ndarray
tran: ndarray
kChlrel: ndarray
kCarrel: ndarray
Mb: ndarray
Mf: ndarray
toolsrtm.fluspect.fluspect_b(Cab, Car, EWT, LMA, Cs, N, fqe, Cx, Prot=None, CBC=None, Anth=None)[source]

FLUSPECT-B leaf model. Direct port of ToolsRTM::getFluspect.B.

Parameters:

  • Cab (float) – Chlorophyll a+b, carotenoid content (ug/cm2).

  • Car (float) – Chlorophyll a+b, carotenoid content (ug/cm2).

  • EWT (float) – Equivalent water thickness, leaf mass per area (g/cm2 both).

  • LMA (float) – Equivalent water thickness, leaf mass per area (g/cm2 both).

  • Cs (float) – Senescent/brown pigment content.

  • N (float) – Leaf structure parameter.

  • fqe (float) – Fluorescence quantum efficiency. If fqe <= 0, MbI/MbII/ MfI/MfII come back all-zero (no fluorescence) – refl/ tran are still computed and returned normally either way, since they never depend on fqe at all.

  • Cx (float) – Violaxanthin-zeaxanthin transition state, 0-1 (or -999 to use a fixed carotenoid absorption spectrum instead of the Cx-interpolated one).

  • Prot (float, optional) – If all three are given, matches R’s "Prot" %in% colnames(inputsLeaf) auto-detection: the PROSPECT-PRO Kall formula (with Anth/Prot/CBC terms) is used instead of the plain PROSPECT-D one. Note this auto-detection overrides any notion of a version argument in R too – there is no way to force PROSPECT-D once these are supplied, matching R exactly.

  • CBC (float, optional) – If all three are given, matches R’s "Prot" %in% colnames(inputsLeaf) auto-detection: the PROSPECT-PRO Kall formula (with Anth/Prot/CBC terms) is used instead of the plain PROSPECT-D one. Note this auto-detection overrides any notion of a version argument in R too – there is no way to force PROSPECT-D once these are supplied, matching R exactly.

  • Anth (float, optional) – If all three are given, matches R’s "Prot" %in% colnames(inputsLeaf) auto-detection: the PROSPECT-PRO Kall formula (with Anth/Prot/CBC terms) is used instead of the plain PROSPECT-D one. Note this auto-detection overrides any notion of a version argument in R too – there is no way to force PROSPECT-D once these are supplied, matching R exactly.

Return type:

FluspectBResult

Notes

R’s ToolsRTM::getFluspect.B used to have return(LRT) inside its if (fqe_ > 0) {...} block – since refl/tran are computed unconditionally above that block but the function’s only return statement lived inside it, fqe_ == 0 made the whole function silently return R’s NULL instead of a proper result (an implicit fall-through, not an error), which propagated into a zero-length rdot/rsot several calls downstream instead of failing loudly. This port originally mirrored that by returning None and required callers to check for it (toolsrtm.canopy._leaf_optics() used to raise ValueError on None rather than silently propagating a NULL like R did). Now that the R source computes and returns refl/tran/zero-Mb/Mf unconditionally (see ToolsRTM/R/fluspect_B.R’s own comment), this port matches that instead of raising.

toolsrtm.fluspect.fluspect_cx(Cab, Car, EWT, LMA, Cs, N, fqe, Cx, Prot, CBC, Anth)[source]

FLUSPECT-B-Cx leaf model. Direct port of ToolsRTM::getFluspect.Cx.

Always uses the PROSPECT-PRO Kall formula (Prot/CBC/Anth required, no auto-detection like fluspect_b()). If fqe <= 0, Mb/ Mf come back all-zero (no fluorescence) – refl/tran are still computed and returned normally either way (see fluspect_b()’s own docstring for why this isn’t a None return, like it used to be).

This function computes the physically-intended 640-850 nm fluorescence emission range (_IWLF_CORRECT).

Parameters:

  • Cab (float)

  • Car (float)

  • EWT (float)

  • LMA (float)

  • Cs (float)

  • N (float)

  • fqe (float)

  • Cx (float)

  • Prot (float)

  • CBC (float)

  • Anth (float)

Return type:

FluspectCxResult