pyPro4Sail

Vectorized vesions of the ProspectD and 4SAIL Radiative Transfer Models for simulating the transmission of radiation in leaves and canopies.

Synopsis

This project contains Python code for Prospect and 4SAIL Radiative Transfer Models (RTM) for simulating the transmission of optical and thermal electromagnetic radiation through leaves and vegetated canopies.

The package also include helpers for inverting the models, either using gradient-based optimization algorithms or regression-based approaches based of forward simulations.

The project consists of:

1. lower-level modules with the basic functions needed in Prospec5 and 4SAIL RTMs.

2. higher-level scripts for easily running ProSAIL in both forward and inverse mode.

Installation

Download the project to your local system, enter the download directory and then type.

python setup.py install

if you want to install pyTSEB and its low-level modules in your Python distribution.

The following Python library ir required for running Prospect and 4SAIL:

• Numpy

In addition, the inversion of both RTMS requires.

• Scipy

• cma [Optional]

Code Example

High-level example

You can automatically run the coupled leaf+canopyt Prospect5+4SAIL RTM with pyPro4Sail.py module.

python [N, chloro, caroten, brown, EWT, LMA, LAI, hot_spot, solar_zenith, solar_azimuth, view_zenith, view_azimuth, LIDF]=[1.5,40,8,0.0,0.01,0.009,3,0.01,30,180,10,180,(-0.35,-0.15)] import pyPro4SAIL wl,rho=pyPro4SAIL.run(N, chloro, caroten, brown, EWT, LMA, LAI, hot_spot, solar_zenith, solar_azimuth, view_zenith, view_azimuth, LIDF, skyl=0.2, soilType=pyPro4SAIL.DEFAULT_SOIL)

Also it is possible to simulate the surface land-leaving thermal radiance with the function run_TIR.

Low-level example

Prospect5 RTM

You can run Prospect by importing the module Prospect5.py and then either calling the function Prospect5 for simulating the full optical spectrum (400-2500nm), or the function Prospect5_wl for simulating the leaf reflectance and transmittance for a given wavelength.

```python

Running Prospect5

import Prospect5

Simulate leaf full optical spectrum (400-2500nm)

wl, rholeaf, tauleaf = Prospect5.Prospect5(N, chloro, caroten, brown, EWT, LMA)

```

You can type help(Prospect5.Prospect5) to understand better the inputs needed and the outputs returned

4SAIL RTM

You can run 4SAIL by importing the module FourSAIL.py and then either calling the function FourSAIL for simulating the reflectance and transmittance factor of a given canopy given a list of leaf reflectances and trasmittances, or you can call the function FourSAIL_wl for simulating the leaf reflectance and transmittance factor of a given canopy at for a single wavelenght.

```python

Running the coupled Prospect and 4SAIL

import Prospect5, FourSAIL

Simulate leaf full optical spectrum (400-2500nm)

wl, rholeaf, tauleaf = Prospect5.Prospect5(N, chloro, caroten, brown, EWT, LMA)

Estimate the Leaf Inclination Distribution Function of a canopy

LIDF = FourSAIL.CalcLIDF_Campbell(alpha)

Simulate leaf reflectance and transmittance factors of a canopy

tss,too,tsstoo,rdd,tdd,rsd,tsd,rdo,tdo,rso,rsos,rsod,rddt,rsdt,rdot,rsodt,rsost,rsot,gammasdf,gammasdb,gammasowl = FourSAIL.FourSAIL(LAI,hotspot,LIDF,solarzenith,viewzenith,solarazimuth-viewazimuth,rholeaf,tauleaf,rhosoil)

Simulate the canopy reflectance factor for a given difuse/total radiation condition (skyl)

rho_canopy = rdotskyl+rsot(1-skyl) ```

You can type help(FourSAIL.FourSAIL) to understand better the inputs needed and the outputs returned

Basic Contents

High-level modules

• .src/pyPro4SAIL.py > Runs the coupled Prospect5+4SAIL to estimate the canopy directional reflectance factor and 4SAIL to estimate the land-leaving broadband thermal radiance.

Low-level modules

The low-level modules in this project are aimed at providing customisation and more flexibility in running TSEB. The following modules are included.

• .src/Prospect5.py

  core functions for running Prospect5 Leaf Radiative Transfer Model.

• .src/Prospect5Jacobian.py

  core functions for computing the Jacobian of Prospect5 Leaf Radiative Transfer Model.

• .src/FourSAIL.py

  core functions for running 4SAIL Canopy Radiative Transfer Model.

• .src/FourSAILJacobian.py

  core functions for computing the Jacobian of 4SAIL Canopy Radiative Transfer Model.

• .src/CostFunctionsPROSPECT4SAIL.py

  merit functions used to invert Prospect and/or 4SAIL from a given spectrum

• .src/cma.py

  Covariance Matrix Adaptation Evolution Strategy optimization method for inverting Prospect5 and/or 4SAIL.

API Reference

http://pyPro4Sail.readthedocs.org/en/latest/index.html

Main Scientific References

• S. Jacquemoud, F. Baret, PROSPECT: A model of leaf optical properties spectra, Remote Sensing of Environment, Volume 34, Issue 2, November 1990, Pages 75-91, ISSN 0034-4257, http://dx.doi.org/10.1016/0034-4257(90)90100-Z.
• Jean-Baptiste Feret, Christophe François, Gregory P. Asner, Anatoly A. Gitelson, Roberta E. Martin, Luc P.R. Bidel, Susan L. Ustin, Guerric le Maire, Stéphane Jacquemoud, PROSPECT-4 and 5: Advances in the leaf optical properties model separating photosynthetic pigments, Remote Sensing of Environment, Volume 112, Issue 6, 16 June 2008, Pages 3030-3043, ISSN 0034-4257, http://dx.doi.org/10.1016/j.rse.2008.02.012.
• W. Verhoef, Light scattering by leaf layers with application to canopy reflectance modeling: The SAIL model, Remote Sensing of Environment, Volume 16, Issue 2, October 1984, Pages 125-141, ISSN 0034-4257, http://dx.doi.org/10.1016/0034-4257(84)90057-9.
• W. Verhoef, L. Jia, Q. Xiao and Z. Su, Unified Optical-Thermal Four-Stream Radiative Transfer Theory for Homogeneous Vegetation Canopies, IEEE Transactions on Geoscience and Remote Sensing, vol. 45, no. 6, pp. 1808-1822, June 2007. http://dx.doi.org/10.1109/TGRS.2007.895844.

Tests

to be included

Contributors

• Hector Nieto hnieto@ias.csic.es hector.nieto.solana@gmail.com main developer
• Radoslaw Guzinski
• Robin Wilson robin@rtwilson.com main developer of pyProSail https://github.com/robintw/PyProSAIL

License

pyPro4Sail: a Python Two Source Energy Balance Model

Copyright 2016 Hector Nieto and contributors.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.