LIBERTY - Leaf Incorporating Biochemistry Exhibiting 
Reflectance and Transmittance Yields

Terence Dawson, 30th July 1998

Installation and user instructions
----------------------------------

Introduction
------------
LIBERTY is a general purpose radiative tranfer model for predicting 
the reflectance and transmittance spectra of a leaf, or stack of leaves in 
the visible and near infrared wavelengths (400 - 2500 nm). By treating 
a leaf as an aggregation of cells, with multiple radiation scattering 
between cells, output spectra is a function of three structural 
parameters and the combined absorption coefficients of leaf 
biochemicals. It is simple to use with the user being prompted for input 
values and the model output is written to an external file for use with 
graphing and spreadsheet packages as well as for coupling with 
vegetation canopy or ecosystem models. It is written in C which is a 
very flexible and portable language and, using external absorption 
coefficient files, has been successfully compiled for the following 
platforms:

MS-DOS
SUN Microsystems Solaris
Silicon Graphics IRIX

To compile, use the following command (note: this may vary between 
platforms - contact your system administrator if you are having 
problems):

cc liberty.c -lm

No header or make files are required, all calls to external libraries and  
function definitions are made at the beginning of the file.

File list
---------
LIBERTY uses external data files. This allows the user to easily 
modify the existing absorption coefficients or provide new ones. The 
full source file list is:

LIBERTY.C               Program code
PIGMENT.DAT             Absorption coefficient of in-vivo chlorophylls 
			and carotenoids
ALBINO.DAT              Absorption coefficient of dried albino leaf due to 
			lignin (visible wavelengths)
WATER.DAT               Water absorption coefficient
LIGCELL.DAT             Combined absorption coefficient of lignin and 
			cellulose
PROTEIN.DAT             Protein absorption coefficient

Additional utility files:

PLOT.C                  Plots LIBERTY output to display (MS-DOS with                                    
			VGA/EGA display only).                  
EGAVGA.BGI              Graphics driver for plot program.
LIBINV.C                Mathematical inversion of LIBERTY. By inputting a 
			measured spectra, gives a global absorption output.


Liberty generates an output file named LIBERTY.OUT which is a 
space delimited text file. When compiled, the full suite of files including 
executable and output files require less than 100 kbytes of disk storage.



Model inputs
------------
The following inputs are required from the user:
--------------------------------------------------------------------------
Variable        Description                             Typical values 
							  (and range)
--------------------------------------------------------------------------
Cell Diameter   Average leaf cell diameter (m-6)        40 (20 - 100)
--------------------------------------------------------------------------
Intercellular   Determinant for the amount of 
air space       radiative flux passing between cells    0.045 (0.01 - 0.1)
--------------------------------------------------------------------------
Leaf thickness  Arbitrary value to determine single 
		leaf reflectance and transmittance 
		from infinite reflectance criteria      1.6 (1 - 10)
--------------------------------------------------------------------------
Baseline        Wavelength independent absorption to 
absorption      compensate for changes in absolute      Fresh: 0.0006
		reflectance                             Dry: 0.0004
--------------------------------------------------------------------------
Albino          Absorption in the visible region due 
absorption      to lignin                               2 (0 - 4)
--------------------------------------------------------------------------
Chlorophyll 
content         Chlorophyll (pigment) content (mg.m-2)  200 (0 - 600)
--------------------------------------------------------------------------
Water 
content         Water content (g.m-2)                   100 (0 - 500)
--------------------------------------------------------------------------
Lignin and 
Cellulose       Combined lignin and cellulose 
content         content (g.m-2)                         40 (10 - 80)
--------------------------------------------------------------------------
Nitrogen        Nitrogen content
content         (g.m-2)                                 1 (0.3 - 2.0)
--------------------------------------------------------------------------

Model output
------------
LIBERTY produces a space delimited text file, example as below:

W R refl trans
400 0.029629 0.029592 0.035535
405 0.030031 0.029991 0.036120
	...
2500 0.517565 0.414745 0.394991

The first column is the wavelength, second column is the predicted 
spectra for infinite reflectance as demonstrated by stacked leaves, and 
the third and fourth column is the predicted single leaf reflectance and 
transmittance spectra, respectively.

Notes
-----

LIBERTY has been developed specifically for conifer needles so you will 
find the facility to estimate single leaf reflectance and transmittance
spectra from stacked needles particularly useful. However, the program
is equally valid for any leaf species with a minor caveat; The in-vivo
absorption coefficients used were determined from empirical work on various
pine species so you may need to re-calibrate variable values for other
vegetation types.

Utilities
---------

PLOT.C is a utility for plotting the liberty.out file to the screen. 
It displays all three spectra (infinite reflectance and single leaf
reflectance and transmittance with their respective maximum reflectance
values. This program requires the EGAVGA.BGI graphics driver included.

LIBINV.C performs a mathematical inversion of empirical spectra based
upon the structural variables used in LIBERTY (forward prediction). The 
output file, LIBINV.OUT provides a global absorption coefficient which
can facilitate determination of individual biochemical in-vivo absorption
coefficients. The input file must be a space separated text file and can 
be of variable wavelength (for inverting airborne data, such as AVIRIS). 
An example specification is as follows:


401.00 0.080285  
403.23 0.078268  
405.9 0.072514  
...

The output file, LIBINV.OUT provides a space separated text file of
the wavelength, reflectance and global absorption values.

Reference
---------
Dawson, T.P., Curran, P.J. and Plummer, S.E. (1998), LIBERTY - 
Modelling the effects of leaf biochemistry on reflectance spectra, 
Remote Sensing of Environment, 65, 50-60.

If you require further information or help, or discover any problems, 
please contact:

Name:       Terry Dawson              	University of Oxford
Email:      terry.dawson@ecu.ox.ac.uk   Environmental Change Unit
Telephone:  +44 (0)1865 281189       	1a Mansfield Road     
Fax:        +44 (0)1865 281181       	Oxford OX1 3TB, UK

