mSCOPE

mSCOPE is an integrated multi-layer model of vegetation reflectance, photosynthesis, fluorescence, temperature and energy balance.

Brief introduction

This version of the mSCOPE model (mSCOPE_v1_beta) is based upon the SCOPE model (v1.61). It simulates the light interaction and energy balance of vertically heterogeneous canopies. mSCOPE keeps the same model structure and output of SCOPE, but uses a different solution for the radiative transfer of incident and emitted radiation in vegetation canopies.
Questions related to mSCOPE, please contact p.yang@utwente.nl; or peiqiyangweb@gmail.com (Peiqi Yang).

Prerequisites

The model is written in Matlab codes. It was developed and tested using Matlab 2017. Using older versions may lead to some problems.

For example, the matrix multiplication used in RTMo_m.m and RTMf_m.m. 
To do the multiplication of two matrices with the dimension of 60x2162 (A) and 60x1 (B), in the older versions, one may need to use a loop 
for j=1:60
C(j,:) = A(j,:)*B(j)
end
While, in Matlab 2017 or later versions, it is simply computed as A*B;

The input data are structured in a excel spreadsheet. The users are expected to have the Microsoft installed. If there is not, please contact p.yang@utwente.nl. This issue can be easily fixed by giving alternative inpute options.

What will you receive when you download the model

In the main folder, you will find

manuals - SCOPE manuals - SCOPE and mSCOPE presetations

inputdata - input - soil_spectrum (reflectance spectra of several typic soils) soilnew.txt. soil_field.txt. Note: the users can also replace with their own soil spectra in the model.

  		-  radiationdata
  			Esun_.dat. 					Incoming direct solar light spectrum
  			Esky_.dat. 					Incomging direct diffuse light spectrum
  			FLEX-S3_std.atm. 		T18 system 
  			T18 system: Verhoef, W., van der Tol, C., & Middleton, E. M. (2018). Hyperspectral radiative transfer modeling to explore the combined retrieval of biophysical parameters and canopy fluorescence from FLEX–Sentinel-3 tandem mission multi-sensor data. Remote sensing of environment, 204, 942-963.
  	
  		-  fluspect_parameters  (absorption coefficients of constituents of a leaf, and fluroescence emission basic spectra)
  			optipar_fluspect.txt
  			Optipar_fluspect_2014.txt
  	
  		-  directional 				(for directional simulation, the angles in the files will be simulated)
  			brdf_angles.dat. 	oversampling in the hot spot position
  			brdf_angles_no_oversampling.dat
  				
  		-  dataset for_verification
  
  	- measured  					(you will not need these files for the use of mSCOPE, because it is for time series simulation which is not available yet in mSCOPE)
  		-	dataset for_verification

output Note: the output is saved in the directory

mSCOPE_code_v1 - Input_data.xlsx. You change the input parameters in this file - mSCOPE.m. The main function

  	- RTMs. 							leaf and canopy radiative transfer models
  		-	fluspect_b.  			simulating leaf reflectance, transmittance and fluorescence emission matrices
  		-	RTMo_m.    			canopy radiative transfer in the solar domain. 
  		- 	RTMf_m. 				canopy radiative transfer model for fluorescence 
  		- 	RTMt. 						canopy radiative transfer for emitted thermal radiation	
  		
  	- Supporting.  
  		-	Brightness_T.  		converting radiant emittance(energy per time per area) to temperature for backbody by inverting Stefan–Boltzmann law	
  		-  calczenithangle. 	computing solar position based on the location and time
  		- 	e2phot.					calculating the number of moles of photons corresponding to E Joules of energy of wavelength lambda
  		-  ephoton. 			 	calculating the energy content (J) of 1 photon of wavelength lambda (m)
  		
  	- IO. 								reading inputdata, exporting and ploting (optional) simulation results
  	
  	- Fluxes 							Computing photosynthesis, latent and sensible heat, leaf temperature

Summary of the main changes in mSCOPE

a. input_mSCOPE.m It reads the vertical profiles of leaf optical properties (e.g. Cab, Cw) from input_data.xlsx in spratsheet 'mSCOPE' The input_mSCOPE is called in the main function mSCOPE.m L61 before executing fluspect_mSCOPE and canopy RTMs.

b. fluspect_mSCOPE.m It runs fluspect_b for different layers to obtain leaf reflectance, transmittance, Mb and Mf fluspect_mSCOPE is called in the main function mSCOPE.m L249

c. RTMo_m.m It is a replacement of the RTMo.m in SCOPE. Many changes have been made here. RTMo_m.m is called in the main function mSCOPE.m L279

d. RTMf_m.m It is a replacement of the RTMf.m in SCOPE. Many changes have been made here. RTMf_m is called in the main function mSCOPE.m L279

References

The origial SCOPE paper

Van der Tol, C., Verhoef, W., Timmermans, J., Verhoef, A., & Su, Z. (2009). An integrated model of soil-canopy spectral radiances, photosynthesis, fluorescence, temperature and energy balance. Biogeosciences, 6(12), 3109-3129.

The mSCOPE paper

Yang, P., Verhoef, W., & Van Der Tol, C. (2017). The mSCOPE model: A simple adaptation to the SCOPE model to describe reflectance, fluorescence and photosynthesis of vertically heterogeneous canopies. Remote sensing of environment, 201, 1-11.

Authors

Peiqi Yang (p.yang@utwente.nl; peiqiyangweb@gmail.com)

Wout Verhoef (w.verhoef@utwente.nl)

Christiaan van der Tol (c.vandertol@utwente.nl)

License

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 any later version.

dipankar05 / mSCOPE