prosail 1.2.2

PROSAIL Python Bindings

J Gomez-Dans (NCEO & UCL) [e-mail]

Description

This repository contains the Python bindings to the PROSPECT and SAIL leaf and canopy reflectance models. The code is written in FORTRAN. The original fortran code was downloaded from Jussieu. I only added a function to simplify writing the wrappers, and you should go to that page to get newer versions of the code. A recent review of the use of both models is availabe in this paper_.

Installing the bindings

The installation of the bindings is quite straightforward: unpack the distribution and run the following command

python setup.py install

You can usually install it to your user’s directory (if you haven’t got superuser privileges) by

python setup.py install --user

Note

You will need a working FORTRAN compiler. I have only tested this with GCC on Linux, but it should work on other systems. You can also pass optimisation flags to the compiler:

python setup.py config_fc  --fcompiler=gnu95   --arch=-march=native --opt=-O3  install --user

Using the bindings

The bindings offer several functions, which will be described in detail below:.

• run_prospect: This function runs the PROSPECT 5B model in Feret et al 2008. The input parameters are the usual (n,cab,car,cbrown,cw,cm) (e.g. leaf layers, leaf Chlorophyll concentration, leaf Carotenoid concentration, leaf senescent fraction, Equivalent leaf water, leaf dry matter). It returns a spectrum between 400 and 2500 nm.
• run_sail: The SAILh model, which in this case requires leaf reflectance and transmittance to be fed to the model (e.g. you have already measured these spectra in the field). The rest of the parameters are (refl,trans,lai,lidfa,lidfb,rsoil,psoil,hspot,tts,tto,psi,typelidf). Additionally, there are two optional parameters, soil_spectrum1, soil_spectrum2, which allow you to set the soil spectra (otherwise, some default spectra get used). Output is a spectrum in the 400-2500 nm range.
• run_prosail: PROSPECT_5B and SAILh coupled together, with input parameters given by (n,cab,car,cbrown,cw,cm,lai,lidfa,lidfb,rsoil,psoil,hspot,tts,tto,psi,typelidf). Output is a spectrum in the 400-2500 nm range.

The parameters

The parameters used by the models and their units are introduced below:

Parameter	Description of parameter	Units	Typical min	Typical max
N	Leaf structure parameter	N/A	0.8	2.5
cab	Chlorophyll a+b concentration	ug/cm2	0	80
caw	Equivalent water thickiness	cm	0	200
car	Carotenoid concentration	ug/cm2	0	20
cbrown	Brown pigment	NA	0	1
cm	Dry matter content	g/cm2	0	200
lai	Leaf Area Index	N/A	0	10
lidfa	Leaf angle distribution	N/A
lidfb	Leaf angle distribution	N/A
psoil	Dry/Wet soil factor	N/A	0	1
rsoil	Soil brigthness factor	N/A
hspot	Hotspot parameter	N/A
tts	Solar zenith angle	deg	0	90
tto	Observer zenith angle	deg	0	90
phi	Relative azimuth angle	deg	0	360
typelidf	Leaf angle distribution type	Integer

Specifying the leaf angle distribution

The parameter typelidf regulates the leaf angle distribution family being used. The following options are understood:

• typelidf = 1: use the two parameter LAD parameterisation, where a and b control the average leaf slope and the distribution bimodality, respectively. Typical distributions are given by the following parameter choices:

LIDF type	LIDFa	LIDFb
Planophile	1	0
Erectophile	-1	0
Plagiophile	0	-1
Extremophile	0	1
Spherical	-0.35	-0.15
Uniform	0	0

• typelidf = 2 Ellipsoidal distribution, where LIDFa parameter stands for mean leaf angle (0 degrees is planophile, 90 degrees is erectophile). LIDFb parameter is ignored.

The soil model

The soil model is a fairly simple linear mixture model, where two spectra are mixed and then a brightness term added:

rho_soil = rsoil*(psoil*soil_spectrum1+(1-psoil)*soil_spectrum2)

The idea is that one of the spectra is a dry soil and the other a wet soil, so soil moisture is then contorlled by psoil. rsoil is just a brightness scaling term.