# 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, rho_leaf, tau_leaf = 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, rho_leaf, tau_leaf = 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,hot_spot,LIDF,solar_zenith,view_zenith,solar_azimuth-view_azimuth,rho_leaf,tau_leaf,rho_soil)
# Simulate the canopy reflectance factor for a given difuse/total radiation condition (skyl)
rho_canopy = rdot*skyl+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/>.
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"description": "# pyPro4Sail\nVectorized vesions of the ProspectD and 4SAIL Radiative Transfer Models for simulating the transmission of radiation in leaves and canopies.\n\n## Synopsis\n\nThis project contains *Python* code for *Prospect* and *4SAIL* Radiative Transfer Models (**RTM**)\nfor simulating the transmission of optical and thermal electromagnetic radiation through \nleaves and vegetated canopies.\n\nThe package also include helpers for inverting the models, either using gradient-based optimization algorithms or regression-based approaches based of forward simulations.\n\nThe project consists of: \n\n1. lower-level modules with the basic functions needed in *Prospec5* and *4SAIL* RTMs.\n\n2. higher-level scripts for easily running ProSAIL in both forward and inverse mode.\n\n## Installation\n\nDownload the project to your local system, enter the download directory and then type.\n\n`python setup.py install` \n\nif you want to install pyTSEB and its low-level modules in your Python distribution. \n\nThe following Python library ir required for running Prospect and 4SAIL:\n\n- Numpy\n\nIn addition, the inversion of both RTMS requires.\n\n- Scipy\n\n- cma [Optional]\n\n\n## Code Example\n### High-level example\nYou can automatically run the coupled leaf+canopyt Prospect5+4SAIL RTM with *pyPro4Sail.py* module.\n\n```python\n[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)]\nimport pyPro4SAIL\nwl,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)\n```\n\nAlso it is possible to simulate the surface land-leaving thermal radiance with the function `run_TIR`.\n\n### Low-level example\n#### Prospect5 RTM\nYou can run *Prospect* by importing the module Prospect5.py and then either calling the function `Prospect5` \nfor simulating the full optical spectrum (400-2500nm), or the function `Prospect5_wl` for simulating\nthe leaf reflectance and transmittance for a given wavelength.\n\n```python\n# Running Prospect5\nimport Prospect5\n# Simulate leaf full optical spectrum (400-2500nm) \nwl, rho_leaf, tau_leaf = Prospect5.Prospect5(N, chloro, caroten, brown, EWT, LMA)\n\n```\n\nYou can type\n`help(Prospect5.Prospect5)`\nto understand better the inputs needed and the outputs returned\n\n#### 4SAIL RTM\nYou can run *4SAIL* by importing the module FourSAIL.py and then either calling the function `FourSAIL` \nfor simulating the reflectance and transmittance factor of a given canopy given a list of leaf reflectances \nand trasmittances, or you can call the function `FourSAIL_wl` for simulating the leaf reflectance and transmittance \nfactor of a given canopy at for a single wavelenght.\n\n```python\n# Running the coupled Prospect and 4SAIL\nimport Prospect5, FourSAIL\n# Simulate leaf full optical spectrum (400-2500nm) \nwl, rho_leaf, tau_leaf = Prospect5.Prospect5(N, chloro, caroten, brown, EWT, LMA)\n# Estimate the Leaf Inclination Distribution Function of a canopy\nLIDF = FourSAIL.CalcLIDF_Campbell(alpha)\n# Simulate leaf reflectance and transmittance factors of a canopy \ntss,too,tsstoo,rdd,tdd,rsd,tsd,rdo,tdo,rso,rsos,rsod,rddt,rsdt,rdot,rsodt,rsost,rsot,gammasdf,gammasdb,gammasowl = FourSAIL.FourSAIL(LAI,hot_spot,LIDF,solar_zenith,view_zenith,solar_azimuth-view_azimuth,rho_leaf,tau_leaf,rho_soil)\n# Simulate the canopy reflectance factor for a given difuse/total radiation condition (skyl)\nrho_canopy = rdot*skyl+rsot*(1-skyl)\n``` \n\nYou can type\n`help(FourSAIL.FourSAIL)`\nto understand better the inputs needed and the outputs returned\n \n## Basic Contents\n### High-level modules\n- *.src/pyPro4SAIL.py*\n> Runs the coupled Prospect5+4SAIL to estimate the canopy directional reflectance factor and 4SAIL to estimate the land-leaving broadband thermal radiance.\n\n### Low-level modules\nThe low-level modules in this project are aimed at providing customisation and more flexibility in running TSEB. \nThe following modules are included.\n\n- *.src/Prospect5.py*\n> core functions for running Prospect5 Leaf Radiative Transfer Model. \n\n- *.src/Prospect5Jacobian.py*\n> core functions for computing the Jacobian of Prospect5 Leaf Radiative Transfer Model. \n\n- *.src/FourSAIL.py*\n> core functions for running 4SAIL Canopy Radiative Transfer Model.\n\n- *.src/FourSAILJacobian.py*\n> core functions for computing the Jacobian of 4SAIL Canopy Radiative Transfer Model.\n\n- *.src/CostFunctionsPROSPECT4SAIL.py*\n> merit functions used to invert Prospect and/or 4SAIL from a given spectrum\n\n- *.src/cma.py*\n> Covariance Matrix Adaptation Evolution Strategy optimization method for inverting Prospect5 and/or 4SAIL.\n\n\n## API Reference\nhttp://pyPro4Sail.readthedocs.org/en/latest/index.html\n\n## Main Scientific References\n- 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.\n- Jean-Baptiste Feret, Christophe Fran\u00e7ois, Gregory P. Asner, Anatoly A. Gitelson, Roberta E. Martin, Luc P.R. Bidel, Susan L. Ustin, Guerric le Maire, St\u00e9phane 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.\n- 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.\n- W. Verhoef, L. Jia, Q. Xiao and Z. 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