├── pyprosail ├── _prosail_model.so ├── prosail_model.so ├── PROSAIL_5B_Fortran.rar ├── Makefile ├── __init__.py ├── dladgen.f ├── MODULE_PRO4SAIL.f90 ├── tav_abs.f90 ├── LIDF.f90 ├── volscatt.f90 ├── PyPROSAIL.py ├── prospect_5B.f90 ├── PyPROSAIL.f90 └── PRO4SAIL.f90 ├── test.py ├── .gitignore ├── CITATION ├── README.md ├── appveyor.yml ├── setup.py ├── doc ├── make.bat ├── Makefile ├── index.rst └── conf.py ├── COPYING.LESSER └── COPYING /pyprosail/_prosail_model.so: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/robintw/PyProSAIL/HEAD/pyprosail/_prosail_model.so -------------------------------------------------------------------------------- /pyprosail/prosail_model.so: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/robintw/PyProSAIL/HEAD/pyprosail/prosail_model.so -------------------------------------------------------------------------------- /pyprosail/PROSAIL_5B_Fortran.rar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/robintw/PyProSAIL/HEAD/pyprosail/PROSAIL_5B_Fortran.rar -------------------------------------------------------------------------------- /test.py: -------------------------------------------------------------------------------- 1 | import pyprosail 2 | 3 | res = pyprosail.run(1.5, 40, 8, 0, 0.01, 0.009, 1, 3, 0.01, 30, 0, 10, 0, pyprosail.Planophile) 4 | print res -------------------------------------------------------------------------------- /pyprosail/Makefile: -------------------------------------------------------------------------------- 1 | mod: 2 | f2py -c -m prosail_model MODULE_PRO4SAIL.f90 dataSpec_P5B.f90 LIDF.f90 dladgen.f PRO4SAIL.f90 prospect_5B.f90 tav_abs.f90 volscatt.f90 PyPROSAIL.f90 -------------------------------------------------------------------------------- /pyprosail/__init__.py: -------------------------------------------------------------------------------- 1 | """A module that allows easy running of the ProSAIL (PROSPECT + SAIL) leaf and canopy 2 | reflectance model. 3 | 4 | The main function is `run`, which runs the ProSAIL model and returns the results as an array. 5 | 6 | """ 7 | 8 | from .PyProSAIL import * 9 | #__all__ = ['PyPROSAIL'] -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | tmp_in.txt 2 | *tmp.in* 3 | *.pyc 4 | .redcar 5 | build/* 6 | dist/* 7 | doc/build/* 8 | */._redcar/* 9 | ._redcar/ 10 | Output.txt 11 | Py6S.egg-info 12 | OutputsJ.txt 13 | src/GetSpectra.py 14 | src/Test.py 15 | Py6S/build 16 | CHL 17 | *.mie 18 | *.png 19 | .ropeproject 20 | /doc/_build/* 21 | *.pyd 22 | MANIFEST 23 | -------------------------------------------------------------------------------- /CITATION: -------------------------------------------------------------------------------- 1 | If you use PyProSAIL in your academic work then please cite it as follows: 2 | 3 | Wilson, R. T., PyProSAIL, Available from https://github.com/robintw/PyProSAIL 4 | 5 | In BibTeX format: 6 | 7 | @electronic{, 8 | author = {Wilson, R. T.}, 9 | year = {2013}, 10 | title = {PyProSAIL}, 11 | url = {https://github.com/robintw/PyProSAIL} 12 | } 13 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # PyProSAIL 2 | 3 | **This version of PyProSAIL is no longer supported. Please use [this version](https://github.com/EOA-team/PyProSAIL) instead.** 4 | 5 | PyProSAIL is a Python interface to the ProSAIL combined leaf and canopy optical model. 6 | 7 | This Pyhon interface (note: not the ProSAIL model itself) is released under the GNU Lesser General Public License. 8 | 9 | For more information see http://pyprosail.readthedocs.org. 10 | -------------------------------------------------------------------------------- /pyprosail/dladgen.f: -------------------------------------------------------------------------------- 1 | subroutine dladgen(a,b,freq) 2 | c 3 | real*8 a,b,freq(13),t 4 | real*8 dcum 5 | c 6 | do i1=1,8 7 | t=i1*10. 8 | freq(i1)=dcum(a,b,t) 9 | end do 10 | c 11 | do i2=9,12 12 | t=80.+(i2-8)*2. 13 | freq(i2)=dcum(a,b,t) 14 | end do 15 | c 16 | freq(13)=1. 17 | c 18 | do i=13,2,-1 19 | freq(i)=freq(i)-freq(i-1) 20 | end do 21 | c 22 | return 23 | end 24 | 25 | 26 | function dcum(a,b,t) 27 | c 28 | real*8 a,b,t,pi,rd,eps,delx,p,y,x,dx,dcum 29 | pi=atan(1.)*4. 30 | rd=pi/180. 31 | 32 | if (a.gt.1.) then 33 | c 34 | dcum=1.-cos(rd*t) 35 | c 36 | else 37 | 38 | eps=1.e-8 39 | delx=1. 40 | c 41 | x=2*rd*t 42 | p=x 43 | c 44 | do while (delx.gt.eps) 45 | y = a*sin(x)+.5*b*sin(2.*x) 46 | dx=.5*(y-x+p) 47 | x=x+dx 48 | delx=abs(dx) 49 | end do 50 | c 51 | dcum=(2.*y+p)/pi 52 | c 53 | endif 54 | c 55 | return 56 | end 57 | -------------------------------------------------------------------------------- /pyprosail/MODULE_PRO4SAIL.f90: -------------------------------------------------------------------------------- 1 | MODULE MOD_ANGLE 2 | REAL*8,SAVE :: pi,rd 3 | END MODULE 4 | 5 | !********************* 6 | 7 | MODULE MOD_staticvar 8 | REAL*8,SAVE :: cts,cto,ctscto 9 | REAL*8,SAVE :: ddb,ddf,dob,dof,dso 10 | REAL*8,SAVE :: ko,ks,sdb,sdf 11 | REAL*8,SAVE :: sob,sof,sumint 12 | REAL*8,ALLOCATABLE,SAVE :: sb(:),sf(:),vb(:),vf(:),w(:) 13 | REAL*8,ALLOCATABLE,SAVE :: m(:),m2(:),att(:),sigb(:),rinf(:),lidf(:) 14 | END MODULE 15 | 16 | !********************* 17 | 18 | MODULE MOD_output_PROSPECT 19 | REAL*8,ALLOCATABLE,SAVE :: LRT(:,:),rho(:),tau(:) 20 | END MODULE 21 | 22 | !********************* 23 | 24 | MODULE MOD_flag_util 25 | LOGICAL flag(7),init_completed,init_completed0 26 | LOGICAL delta_geom,delta_lai,delta_hot,delta_leaf,delta_skyl,delta_soil,delta_lidf 27 | REAL*8,ALLOCATABLE,SAVE :: lidf_old(:),rsoil_old(:) 28 | REAL*8,SAVE :: N_old,Cab_old,Car_old,Cbrown_old,Cw_old,Cm_old 29 | REAL*8,SAVE :: LIDFa_old,LIDFb_old,lai_old,q_old,skyl_old 30 | REAL*8,SAVE :: tts_old,tto_old,psi_old 31 | END MODULE 32 | 33 | !********************* 34 | 35 | MODULE MOD_SAIL 36 | REAL*8,SAVE :: tss,too,tsstoo 37 | REAL*8,ALLOCATABLE,SAVE :: tso(:),tsd(:),tdd(:),tdo(:),rsd(:),rdd(:),rso(:),rdo(:) 38 | REAL*8,ALLOCATABLE,SAVE :: rsos(:),rsod(:),rddt(:),rsdt(:),rdot(:),rsodt(:),rsost(:),rsot(:) 39 | END MODULE 40 | 41 | !********************* -------------------------------------------------------------------------------- /appveyor.yml: -------------------------------------------------------------------------------- 1 | environment: 2 | matrix: 3 | - PYTHON_VERSION: "2.7" 4 | - PYTHON_VERSION: "3.4" 5 | 6 | platform: 7 | - x86 8 | - x64 9 | 10 | matrix: 11 | fast_finish: true 12 | 13 | install: 14 | - set PATH=C:\Miniconda\Scripts 15 | - ps: If ($env:Platform -Match "x64") {$env:PATH="C:\Miniconda-x64\Scripts"} 16 | - conda config --set always_yes yes --set changeps1 no 17 | - conda update -q conda 18 | - conda create -q --name python%PYTHON_VERSION% python=%PYTHON_VERSION% 19 | - activate python%PYTHON_VERSION% 20 | - pip install -i https://pypi.anaconda.org/carlkl/simple mingwpy 21 | - conda install -q --name python%PYTHON_VERSION% setuptools numpy matplotlib nose pandas wheel scipy 22 | - python.exe setup.py config_fc 23 | - python.exe setup.py config --compiler=mingw32 --fcompiler=gfortran 24 | - python.exe setup.py build --compiler=mingw32 25 | - python.exe setup.py install 26 | 27 | build: off 28 | 29 | after_test: 30 | # This step builds your wheels. 31 | - python.exe setup.py bdist 32 | - python.exe setup.py sdist 33 | 34 | artifacts: 35 | # bdist_wheel puts your built wheel in the dist directory 36 | - path: dist\* 37 | 38 | #on_success: 39 | # You can use this step to upload your artifacts to a public website. 40 | # See Appveyor's documentation for more details. Or you can simply 41 | # access your wheels from the Appveyor "artifacts" tab for your build. 42 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | # File setup.py 2 | def configuration(parent_package='',top_path=None): 3 | from numpy.distutils.misc_util import Configuration 4 | config = Configuration('',parent_package,top_path, 5 | name = "PyPROSAIL", 6 | version = "1.0.1", 7 | description = """PyProSAIL is a Python interface to the ProSAIL combined leaf and canopy optical model. 8 | For more information see http://pyprosail.readthedocs.org.""", 9 | packages = ['pyprosail'], 10 | author = "Robin Wilson", 11 | author_email = "robin@rtwilson.com", 12 | url = "http://packages.python.org/PyPROSAIL", 13 | classifiers =[ 14 | "Development Status :: 5 - Production/Stable", 15 | "Intended Audience :: Science/Research", 16 | "Topic :: Scientific/Engineering :: Atmospheric Science", 17 | "Topic :: Scientific/Engineering :: Physics", 18 | "Topic :: Software Development :: Libraries :: Python Modules", 19 | "License :: OSI Approved :: GNU Library or Lesser General Public License (LGPL)", 20 | "Programming Language :: Python" 21 | 22 | ]) 23 | 24 | config.add_extension('_prosail_model', 25 | sources = ['./pyprosail/MODULE_PRO4SAIL.f90', './pyprosail/dataSpec_P5B.f90', 26 | './pyprosail/LIDF.f90', './pyprosail/dladgen.f', './pyprosail/PRO4SAIL.f90', 27 | './pyprosail/prospect_5B.f90', './pyprosail/tav_abs.f90', './pyprosail/volscatt.f90', 28 | './pyprosail/PyPROSAIL.f90']) 29 | return config 30 | 31 | if __name__ == "__main__": 32 | from numpy.distutils.core import setup 33 | setup(**configuration(top_path='').todict()) 34 | -------------------------------------------------------------------------------- /pyprosail/tav_abs.f90: -------------------------------------------------------------------------------- 1 | ! ******************************************************************************** 2 | ! tav_abs.f90 3 | ! ******************************************************************************** 4 | ! computation of the average transmittivity at the leaf surface within a given 5 | ! solid angle. teta is the incidence solid angle (in radian). The average angle 6 | ! that works in most cases is 40deg*pi/180. ref is the refaction index. 7 | ! ******************************************************************************** 8 | ! Stern F. (1964), Transmission of isotropic radiation across an interface between 9 | ! two dielectrics, Applied Optics, 3:111-113. 10 | ! Allen W.A. (1973), Transmission of isotropic light across a dielectric surface in 11 | ! two and three dimensions, Journal of the Optical Society of America, 63:664-666. 12 | ! ******************************************************************************** 13 | ! version 5.02 (25 July 2011) 14 | ! ******************************************************************************** 15 | 16 | subroutine tav_abs(theta,refr,res) 17 | 18 | USE MOD_dataSpec_P5B 19 | IMPLICIT none 20 | 21 | REAL*8, intent(in) :: theta, refr(nw) 22 | REAL*8, intent(out) :: res(nw) 23 | 24 | REAL*8 :: pi, thetarad 25 | REAL*8 :: refr2(nw) 26 | REAL*8 :: ax(nw),bx(nw),b0(nw),b1(nw),b2(nw) 27 | REAL*8 :: ts(nw),tp(nw),tp1(nw),tp2(nw),tp3(nw),tp4(nw),tp5(nw) 28 | 29 | pi=atan(1.)*4. 30 | thetarad=pi*theta/180. 31 | 32 | if (theta.eq.0.) then 33 | res=4.*refr/(refr+1.)**2 34 | return 35 | endif 36 | 37 | refr2=refr*refr 38 | ax=(refr+1.)**2/2. 39 | bx=-(refr2-1.)**2/4. 40 | 41 | if (thetarad.eq.pi/2.) then 42 | b1=0. 43 | else 44 | b1=dsqrt((sin(thetarad)**2-(refr2+1.)/2.)**2+bx) 45 | endif 46 | b2=sin(thetarad)**2-(refr2+1.)/2. 47 | b0=b1-b2 48 | ts=(bx**2/(6.*b0**3)+bx/b0-b0/2.)-(bx**2/(6.*ax**3)+bx/ax-ax/2.) 49 | tp1=-2.*refr2*(b0-ax)/(refr2+1.)**2 50 | tp2=-2.*refr2*(refr2+1.)*dlog(b0/ax)/(refr2-1.)**2 51 | tp3=refr2*(1./b0-1./ax)/2. 52 | tp4=16.*refr2**2*(refr2**2+1.)*dlog((2.*(refr2+1.)*b0-(refr2-1.)**2)/ & 53 | (2.*(refr2+1.)*ax-(refr2-1.)**2))/((refr2+1.)**3*(refr2-1.)**2) 54 | tp5=16.*refr2**3*(1./(2.*(refr2+1.)*b0-((refr2-1.)**2))-1./(2.*(refr2+1.) & 55 | *ax-(refr2-1.)**2))/(refr2+1.)**3 56 | tp=tp1+tp2+tp3+tp4+tp5 57 | res=(ts+tp)/(2.*sin(thetarad)**2) 58 | 59 | return 60 | end 61 | -------------------------------------------------------------------------------- /pyprosail/LIDF.f90: -------------------------------------------------------------------------------- 1 | !******************************************************************************** 2 | !* Campbell.f 3 | !* 4 | !* Computation of the leaf angle distribution function value (freq) 5 | !* Ellipsoidal distribution function caracterised by the average leaf 6 | !* inclination angle in degree (ala) 7 | !* Campbell 1986 8 | !* 9 | !******************************************************************************** 10 | 11 | SUBROUTINE campbell(n,ala,freq) 12 | 13 | IMPLICIT NONE 14 | 15 | INTEGER*4 :: i,n 16 | REAL*8 :: ala,freq(n),dum 17 | REAL*8 :: excent,tl1(n),tl2(n),x1,x2,alpha,alpha2 18 | REAL*8 :: tx1(13),tx2(13) 19 | REAL*8 :: x12,x22,almx1,almx2,alpx1,alpx2,sum0 20 | DATA tx2 /0, 10, 20, 30, 40, 50, 60, 70, 80, 82, 84, 86, 88/ 21 | DATA tx1 /10, 20, 30, 40, 50, 60, 70, 80, 82, 84, 86, 88, 90/ 22 | 23 | DO i=1,n 24 | tl1(i)=tx1(i)*ATAN(1.)/45. 25 | tl2(i)=tx2(i)*ATAN(1.)/45. 26 | ENDDO 27 | excent=EXP(-1.6184e-5*ala**3+2.1145e-3*ala**2-1.2390e-1*ala+3.2491) 28 | sum0 = 0. 29 | DO i=1,n 30 | x1 = excent/(SQRT(1.+excent**2*TAN(tl1(i))**2)) 31 | x2 = excent/(SQRT(1.+excent**2*TAN(tl2(i))**2)) 32 | IF (excent.eq.1.) THEN 33 | freq(i) = ABS(COS(tl1(i))-COS(tl2(i))) 34 | ELSE 35 | alpha = excent/SQRT(ABS(1.-excent**2)) 36 | alpha2 = alpha**2 37 | x12 = x1**2 38 | x22 = x2**2 39 | IF (excent.gt.1) THEN 40 | alpx1 = SQRT(alpha2+x12) 41 | alpx2 = SQRT(alpha2+x22) 42 | dum = x1*alpx1+alpha2*LOG(x1+alpx1) 43 | freq(i) = ABS(dum-(x2*alpx2+alpha2*LOG(x2+alpx2))) 44 | ELSE 45 | almx1 = SQRT(alpha2-x12) 46 | almx2 = SQRT(alpha2-x22) 47 | dum = x1*almx1+alpha2*ASIN(x1/alpha) 48 | freq(i) = ABS(dum-(x2*almx2+alpha2*ASIN(x2/alpha))) 49 | ENDIF 50 | ENDIF 51 | sum0 = sum0+freq(i) 52 | ENDDO 53 | DO i=1,n 54 | freq(i)=freq(i)/sum0 !*100. 55 | ENDDO 56 | 57 | RETURN 58 | END SUBROUTINE 59 | 60 | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 61 | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 62 | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 63 | 64 | SUBROUTINE calc_LIDF_ellipsoidal(na,alpha,freqvar) 65 | IMPLICIT NONE 66 | 67 | INTEGER*4 :: na,ia,icou,k 68 | REAL*8 :: opt,bemu,benu,alphadeg,alpha,freqvar(na),freq(na),pi 69 | !............................................................................... 70 | ! Call leaf angle distribution fonction 71 | !............................................................................... 72 | 73 | alphadeg=alpha 74 | 75 | CALL campbell(na,alphadeg,freq) 76 | DO ia=1,na 77 | freqvar(ia)=freq(ia) 78 | ENDDO 79 | 80 | RETURN 81 | END SUBROUTINE 82 | -------------------------------------------------------------------------------- /pyprosail/volscatt.f90: -------------------------------------------------------------------------------- 1 | SUBROUTINE volscatt(tts,tto,psi,ttl,chi_s,chi_o,frho,ftau) 2 | 3 | !******************************************************************************** 4 | !* tts = solar zenith 5 | !* tto = viewing zenith 6 | !* psi = azimuth 7 | !* ttl = leaf inclination angle 8 | !* chi_s = interception functions 9 | !* chi_o = interception functions 10 | !* frho = function to be multiplied by leaf reflectance rho 11 | !* ftau = functions to be multiplied by leaf transmittance tau 12 | !******************************************************************************** 13 | 14 | ! Compute volume scattering functions and interception coefficients 15 | ! for given solar zenith, viewing zenith, azimuth and leaf inclination angle. 16 | 17 | ! chi_s and chi_o are the interception functions. 18 | ! frho and ftau are the functions to be multiplied by leaf reflectance rho and 19 | ! leaf transmittance tau, respectively, in order to obtain the volume scattering 20 | ! function. 21 | 22 | ! Wout Verhoef, april 2001, for CROMA 23 | 24 | USE MOD_ANGLE 25 | IMPLICIT NONE 26 | 27 | REAL*8,INTENT(in) :: tts,tto,psi,ttl 28 | REAL*8,INTENT(inout) :: chi_s,chi_o,frho,ftau 29 | 30 | REAL*8 costs,costo,sints,sinto,cospsi 31 | REAL*8 psir 32 | REAL*8 costl,sintl,cs,co,ss,so,ds 33 | REAL*8 cosbts,cosbto,bts,bto 34 | REAL*8 btran1,btran2,bt1,bt2,bt3,t1,t2 35 | REAL*8 doo,denom 36 | 37 | costs=COS(rd*tts) 38 | costo=COS(rd*tto) 39 | sints=SIN(rd*tts) 40 | sinto=SIN(rd*tto) 41 | cospsi=COS(rd*psi) 42 | 43 | psir=rd*psi 44 | 45 | costl=COS(rd*ttl) 46 | sintl=SIN(rd*ttl) 47 | cs=costl*costs 48 | co=costl*costo 49 | ss=sintl*sints 50 | so=sintl*sinto 51 | 52 | !c .............................................................................. 53 | !c betas -bts- and betao -bto- computation 54 | !c Transition angles (beta) for solar (betas) and view (betao) directions 55 | !c if thetav+thetal>pi/2, bottom side of the leaves is observed for leaf azimut 56 | !c interval betao+phi. 16 | 17 | from . import _prosail_model 18 | import numpy as np 19 | 20 | # Common leaf distributions 21 | Planophile = (1, 0) 22 | Erectophile = (-1, 0) 23 | Plagiophile = (0, -1) 24 | Extremophile = (0, 1) 25 | Spherical = (-0.35, -0.15) 26 | Uniform = (0, 0) 27 | 28 | def run(N, chloro, caroten, brown, EWT, LMA, psoil, LAI, hot_spot, solar_zenith, solar_azimuth, view_zenith, view_azimuth, LIDF): 29 | """ 30 | Runs the ProSAIL model with the given parameters and returns a wavelength-reflectance 31 | array. 32 | 33 | Arguments: 34 | 35 | * ``N`` -- Structure co-efficient 36 | * ``chloro`` -- Chlorophyll content (ug per cm^2) 37 | * ``caroten`` -- Carotenoid content (ug per cm^2) 38 | * ``brown`` -- Brown pigment content (arbitrary units) 39 | * ``EWT`` -- Equivalent Water Thickness (cm) 40 | * ``LMA`` -- Leaf Mass per unit area (g per cm^2) 41 | * ``soil_reflectance`` -- Soil reflectance: wet soil = 0, dry soil = 1 42 | * ``LAI`` -- Leaf Area Index 43 | * ``hot_spot`` -- Hot spot parameter 44 | * ``solar_zenith`` -- Solar zenith angle (degrees) 45 | * ``solar_azimuth`` -- Solar azimuth angle (degrees) 46 | * ``view_zenith`` -- View zenith angle (degrees) 47 | * ``view_azimuth`` -- View azimuth angle (degrees) 48 | * ``LIDF`` -- Leaf distibution function parameter(s) (see below) 49 | 50 | The leaf distribution function parameter(s) argument can be either: 51 | 52 | * A single number giving the average leaf angle (in degrees) for an elipsoidal distribution. 0 is planophile and 90 is erectophile. 53 | * A tuple giving (average leaf slope, bimodality parameter). These parameters must sum to be less than 1.0. For 54 | convenience a number of predefined options are given including: 55 | 56 | * Planophile 57 | * Erectophile 58 | * Plagiophile 59 | * Extremophile 60 | * Spherical 61 | * Uniform 62 | 63 | Examples of valid values for the leaf distribution function parameter include: 64 | 65 | * 30 (a 30 degree average leaf angle) 66 | * (0, -1) (an average leaf slope of 0 and a bimodality parameter of -1) 67 | * PyProsail.Planophile 68 | 69 | Example usage: 70 | 71 | 72 | 73 | """ 74 | 75 | try: 76 | l = len(LIDF) 77 | if l != 2: 78 | # Raise error 79 | pass 80 | 81 | TypeLidf = 1 82 | LIDFa = LIDF[0] 83 | LIDFb = LIDF[1] 84 | except TypeError: 85 | TypeLidf = 2 86 | LIDFa = LIDF 87 | LIDFb = 0 88 | 89 | return(_run_prosail(N, chloro, caroten, brown, EWT, LMA, psoil, LAI, hot_spot, solar_zenith, view_zenith, solar_azimuth, TypeLidf, LIDFa, LIDFb)) 90 | 91 | def _run_prosail(N, Cab, Car, Cbrown, Cw, Cm, psoil, LAI, hspot, tts, tto, psi, TypeLidf, LIDFa, LIDFb): 92 | # Check parameters here 93 | 94 | # TypeLidf must be either 1 or 2 95 | if TypeLidf not in [1, 2]: 96 | # Raise exception 97 | pass 98 | 99 | if TypeLidf == 1 and LIDFa + LIDFb > 1: 100 | # Raise exception 101 | pass 102 | 103 | wavelengths = np.arange(400, 2501) 104 | res = _prosail_model.run(N, Cab, Car, Cbrown, Cw, Cm, psoil, LAI, hspot, tts, tto, psi, TypeLidf, LIDFa, LIDFb) 105 | 106 | arr = np.transpose(np.vstack( (wavelengths/1000.0, res) )) 107 | return arr -------------------------------------------------------------------------------- /pyprosail/prospect_5B.f90: -------------------------------------------------------------------------------- 1 | ! ******************************************************************************** 2 | ! prospect_5B.f90 3 | ! ******************************************************************************** 4 | ! 5 | ! Jean-Baptiste FERET 6 | ! 7 | ! Department of Global Ecology / Carnegie Institution for Sciences 8 | ! 260 Panama Street 9 | ! Stanford, CA 94305, USA 10 | ! E-mail: jbferet@stanford.edu 11 | ! 12 | ! Stephane JACQUEMOUD 13 | ! 14 | ! Universite Paris Diderot / Institut de Physique du Globe de Paris 15 | ! 35 rue Helene Brion 16 | ! 75013 Paris, France 17 | ! E-mail: jacquemoud@ipgp.fr 18 | ! 19 | ! http://teledetection.ipgp.fr/prosail/ 20 | ! 21 | ! ******************************************************************************** 22 | ! Feret J.B., Francois C., Asner G.P., Gitelson A.A., Martin R.E., Bidel L.P.R., 23 | ! Ustin S.L., le Maire G., Jacquemoud S. (2008), PROSPECT-4 and 5: Advances in the 24 | ! leaf optical properties model separating photosynthetic pigments, Remote Sensing 25 | ! of Environment, 112:3030-3043. 26 | ! Jacquemoud S., Ustin S.L., Verdebout J., Schmuck G., Andreoli G., Hosgood B. 27 | ! (1996), Estimating leaf biochemistry using the PROSPECT leaf optical properties 28 | ! model, Remote Sensing of Environment, 56:194-202. 29 | ! Jacquemoud S., Baret F. (1990), PROSPECT: a model of leaf optical properties 30 | ! spectra, Remote Sensing of Environment, 34:75-91. 31 | ! ******************************************************************************** 32 | ! version 5.02 (25 July 2011) 33 | ! ******************************************************************************** 34 | 35 | SUBROUTINE prospect_5B(N,Cab,Car,Cbrown,Cw,Cm,RT) 36 | 37 | USE MOD_dataSpec_P5B 38 | IMPLICIT none 39 | 40 | REAL*8, intent(in) :: N,Cab,Car,Cbrown,Cw,Cm 41 | REAL*8, intent(out) :: RT(nw,2) 42 | 43 | REAL*8 :: k(nw), tau(nw), xx(nw), yy(nw) 44 | REAL*8 :: x1(nw),x2(nw),x3(nw),x4(nw),x5(nw),x6(nw) 45 | REAL*8 :: theta1, theta2, t1(nw),t2(nw) 46 | REAL*8 :: r(nw),t(nw),ra(nw),ta(nw) 47 | REAL*8 :: delta(nw),beta(nw),va(nw),vb(nw),s1(nw),s2(nw),s3(nw) 48 | 49 | k=(Cab*k_Cab+Car*k_Car+Cbrown*k_Brown+Cw*k_Cw+Cm*k_Cm)/N 50 | 51 | ! ******************************************************************************** 52 | ! reflectance and transmittance of one layer 53 | ! ******************************************************************************** 54 | ! Allen W.A., Gausman H.W., Richardson A.J., Thomas J.R. (1969), Interaction of 55 | ! isotropic ligth with a compact plant leaf, Journal of the Optical Society of 56 | ! American, 59:1376-1379. 57 | ! ******************************************************************************** 58 | 59 | ! exponential integral: S13AAF routine from the NAG library 60 | 61 | where (k.le.0.0) 62 | tau=1 63 | end where 64 | where (k.gt.0.0.and.k.le.4.0) 65 | xx=0.5*k-1.0 66 | yy=(((((((((((((((-3.60311230482612224d-13 & 67 | *xx+3.46348526554087424d-12)*xx-2.99627399604128973d-11) & 68 | *xx+2.57747807106988589d-10)*xx-2.09330568435488303d-9) & 69 | *xx+1.59501329936987818d-8)*xx-1.13717900285428895d-7) & 70 | *xx+7.55292885309152956d-7)*xx-4.64980751480619431d-6) & 71 | *xx+2.63830365675408129d-5)*xx-1.37089870978830576d-4) & 72 | *xx+6.47686503728103400d-4)*xx-2.76060141343627983d-3) & 73 | *xx+1.05306034687449505d-2)*xx-3.57191348753631956d-2) & 74 | *xx+1.07774527938978692d-1)*xx-2.96997075145080963d-1 75 | yy=(yy*xx+8.64664716763387311d-1)*xx+7.42047691268006429d-1 76 | yy=yy-log(k) 77 | tau=(1.0-k)*dexp(-k)+k**2*yy 78 | end where 79 | where (k.gt.4.0.and.k.le.85.0) 80 | xx=14.5/(k+3.25)-1.0 81 | yy=(((((((((((((((-1.62806570868460749d-12 & 82 | *xx-8.95400579318284288d-13)*xx-4.08352702838151578d-12) & 83 | *xx-1.45132988248537498d-11)*xx-8.35086918940757852d-11) & 84 | *xx-2.13638678953766289d-10)*xx-1.10302431467069770d-9) & 85 | *xx-3.67128915633455484d-9)*xx-1.66980544304104726d-8) & 86 | *xx-6.11774386401295125d-8)*xx-2.70306163610271497d-7) & 87 | *xx-1.05565006992891261d-6)*xx-4.72090467203711484d-6) & 88 | *xx-1.95076375089955937d-5)*xx-9.16450482931221453d-5) & 89 | *xx-4.05892130452128677d-4)*xx-2.14213055000334718d-3 90 | yy=((yy*xx-1.06374875116569657d-2)*xx-8.50699154984571871d-2)*xx+9.23755307807784058d-1 91 | yy=exp(-k)*yy/k 92 | tau=(1.0-k)*dexp(-k)+k**2*yy 93 | end where 94 | where (k.gt.85.0) 95 | tau=0 96 | end where 97 | 98 | ! transmissivity of the layer 99 | 100 | theta1=90. 101 | call tav_abs(theta1,refractive,t1) 102 | theta2=40. 103 | call tav_abs(theta2,refractive,t2) 104 | x1=1-t1 105 | x2=t1**2*tau**2*(refractive**2-t1) 106 | x3=t1**2*tau*refractive**2 107 | x4=refractive**4-tau**2*(refractive**2-t1)**2 108 | x5=t2/t1 109 | x6=x5*(t1-1)+1-t2 110 | r=x1+x2/x4 111 | t=x3/x4 112 | ra=x5*r+x6 113 | ta=x5*t 114 | 115 | ! ******************************************************************************** 116 | ! reflectance and transmittance of N layers 117 | ! ******************************************************************************** 118 | ! Stokes G.G. (1862), On the intensity of the light reflected from or transmitted 119 | ! through a pile of plates, Proceedings of the Royal Society of London, 11:545-556. 120 | ! ******************************************************************************** 121 | 122 | delta=(t**2-r**2-1)**2-4*r**2 123 | beta=(1+r**2-t**2-sqrt(delta))/(2*r) 124 | va=(1+r**2-t**2+sqrt(delta))/(2*r) 125 | vb=sqrt(beta*(va-r)/(va*(beta-r))) 126 | s1=ra*(va*vb**(N-1)-va**(-1)*vb**(-(N-1)))+(ta*t-ra*r)*(vb**(N-1)-vb**(-(N-1))) 127 | s2=ta*(va-va**(-1)) 128 | s3=va*vb**(N-1)-va**(-1)*vb**(-(N-1))-r*(vb**(N-1)-vb**(-(N-1))) 129 | RT(:,1)=s1/s3 130 | RT(:,2)=s2/s3 131 | 132 | end subroutine 133 | -------------------------------------------------------------------------------- /doc/make.bat: -------------------------------------------------------------------------------- 1 | @ECHO OFF 2 | 3 | REM Command file for Sphinx documentation 4 | 5 | if "%SPHINXBUILD%" == "" ( 6 | set SPHINXBUILD=sphinx-build 7 | ) 8 | set BUILDDIR=_build 9 | set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% . 10 | set I18NSPHINXOPTS=%SPHINXOPTS% . 11 | if NOT "%PAPER%" == "" ( 12 | set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS% 13 | set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS% 14 | ) 15 | 16 | if "%1" == "" goto help 17 | 18 | if "%1" == "help" ( 19 | :help 20 | echo.Please use `make ^` where ^ is one of 21 | echo. html to make standalone HTML files 22 | echo. dirhtml to make HTML files named index.html in directories 23 | echo. singlehtml to make a single large HTML file 24 | echo. pickle to make pickle files 25 | echo. json to make JSON files 26 | echo. htmlhelp to make HTML files and a HTML help project 27 | echo. qthelp to make HTML files and a qthelp project 28 | echo. devhelp to make HTML files and a Devhelp project 29 | echo. epub to make an epub 30 | echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter 31 | echo. text to make text files 32 | echo. man to make manual pages 33 | echo. texinfo to make Texinfo files 34 | echo. gettext to make PO message catalogs 35 | echo. changes to make an overview over all changed/added/deprecated items 36 | echo. linkcheck to check all external links for integrity 37 | echo. doctest to run all doctests embedded in the documentation if enabled 38 | goto end 39 | ) 40 | 41 | if "%1" == "clean" ( 42 | for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i 43 | del /q /s %BUILDDIR%\* 44 | goto end 45 | ) 46 | 47 | if "%1" == "html" ( 48 | %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html 49 | if errorlevel 1 exit /b 1 50 | echo. 51 | echo.Build finished. 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This program allows modeling reflectance data from canopy 3 | ! - modeling leaf optical properties with PROSPECT-5 (feret et al. 2008) 4 | ! - modeling leaf inclination distribution function with the subroutine campbell 5 | ! (Ellipsoidal distribution function caracterised by the average leaf 6 | ! inclination angle in degree), or dladgen (2 parameters LIDF) 7 | ! - modeling canopy reflectance with 4SAIL (Verhoef et al., 2007) 8 | 9 | ! This version has been implemented by Jean-Baptiste Feret 10 | ! Jean-Baptiste Feret takes the entire responsibility for this version 11 | ! All comments, changes or questions should be sent to: 12 | ! jbferet@stanford.edu 13 | 14 | ! References: 15 | ! Verhoef et al. (2007) Unified Optical-Thermal Four-Stream Radiative 16 | ! Transfer Theory for Homogeneous Vegetation Canopies, IEEE TRANSACTIONS 17 | ! ON GEOSCIENCE AND REMOTE SENSING, VOL. 45, NO. 6, JUNE 2007 18 | ! Feret et al. (2008), PROSPECT-4 and 5: Advances in the Leaf Optical 19 | ! Properties Model Separating Photosynthetic Pigments, REMOTE SENSING OF 20 | ! ENVIRONMENT 21 | ! The specific absorption coefficient corresponding to brown pigment is 22 | ! provided by Frederic Baret (EMMAH, INRA Avignon, baret@avignon.inra.fr) 23 | ! and used with his autorization. 24 | ! the model PRO4SAIL is based on a version provided by 25 | ! Wout Verhoef 26 | ! NLR 27 | ! April/May 2003 28 | 29 | ! The original 2-parameter LIDF model is developed by and described in: 30 | ! W. Verhoef, 1998, "Theory of radiative transfer models applied in 31 | ! optical remote sensing of vegetation canopies", Wageningen Agricultural 32 | ! University, The Netherlands, 310 pp. (Ph. D. thesis) 33 | ! the Ellipsoidal LIDF is taken from: 34 | ! Campbell (1990), Derivtion of an angle density function for canopies 35 | ! with ellipsoidal leaf angle distribution, Agricultural and Forest 36 | ! Meteorology, 49 173-176 37 | 38 | subroutine run(N, Cab, Car, Cbrown, Cw, Cm, psoil, LAI, hspot, tts, tto, psi, TypeLidf, LIDFa, LIDFb, result) 39 | USE MOD_ANGLE ! defines pi & rad conversion 40 | USE MOD_staticvar ! static variables kept in memory for optimization 41 | USE MOD_flag_util ! flags for optimization 42 | USE MOD_output_PROSPECT ! output variables of PROSPECT 43 | USE MOD_SAIL ! variables of SAIL 44 | USE MOD_dataSpec_P5B 45 | IMPLICIT NONE 46 | 47 | REAL*8, intent(in) :: N,Cab, Car,Cbrown,Cw,Cm, psoil, LAI, hspot, tts, tto, psi, LIDFa,LIDFb 48 | INTEGER, intent(in) :: TypeLidf 49 | REAL*8, intent(out) :: result(nw) 50 | 51 | 52 | ! LEAF BIOCHEMISTRY 53 | !REAL*8 :: N,Car,Cbrown,Cw,Cm 54 | ! CANOPY 55 | REAL*8 :: skyl,ihot 56 | REAL*8,ALLOCATABLE,SAVE :: resh(:),resv(:) 57 | REAL*8,ALLOCATABLE,SAVE :: rsoil0(:),PARdiro(:),PARdifo(:) 58 | INTEGER :: ii 59 | 60 | ! ANGLE CONVERSION 61 | pi=ATAN(1.)*4. 62 | rd=pi/180. 63 | 64 | ! PROSPECT output 65 | ALLOCATE (LRT(nw,2),rho(nw),tau(nw)) 66 | ! SAIL 67 | ALLOCATE (sb(nw),sf(nw),vb(nw),vf(nw),w(nw)) 68 | ALLOCATE (m(nw),m2(nw),att(nw),sigb(nw),rinf(nw)) 69 | ALLOCATE (PARdiro(nw),PARdifo(nw)) 70 | ALLOCATE(tsd(nw),tdd(nw),tdo(nw),rsd(nw),rdd(nw),rso(nw),rdo(nw)) 71 | ALLOCATE(rddt(nw),rsdt(nw),rdot(nw),rsodt(nw),rsost(nw),rsot(nw),rsos(nw),rsod(nw)) 72 | ALLOCATE(lidf(13)) 73 | ! resh : hemispherical reflectance 74 | ! resv : directional reflectance 75 | ALLOCATE (resh(nw),resv(nw)) 76 | ALLOCATE (rsoil_old(nw)) 77 | 78 | !TypeLidf=1 79 | ! if 2-parameters LIDF: TypeLidf=1 80 | !IF (TypeLidf.EQ.1) THEN 81 | ! LIDFa LIDF parameter a, which controls the average leaf slope 82 | ! LIDFb LIDF parameter b, which controls the distribution's bimodality 83 | ! LIDF type a b 84 | ! Planophile 1 0 85 | ! Erectophile -1 0 86 | ! Plagiophile 0 -1 87 | ! Extremophile 0 1 88 | ! Spherical -0.35 -0.15 89 | ! Uniform 0 0 90 | ! requirement: |LIDFa| + |LIDFb| < 1 91 | !LIDFa = -0.35 92 | !LIDFb = -0.15 93 | ! if ellipsoidal distribution: TypeLidf=2 94 | !ELSEIF (TypeLidf.EQ.2) THEN 95 | ! LIDFa = average leaf angle (degrees) 0 = planophile / 90 = erectophile 96 | ! LIDFb = 0 97 | !LIDFa = 30 98 | !LIDFb = 0 99 | !ENDIF 100 | 101 | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 102 | !!LEAF CHEM & STR PROPERTIES!! 103 | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 104 | ! INITIAL PARAMETERS 105 | !Cab = 40. ! chlorophyll content (ug.cm-2) 106 | !Car = 8. ! carotenoid content (ug.cm-2) 107 | !Cbrown = 0.0 ! brown pigment content (arbitrary units) 108 | !Cw = 0.01 ! EWT (cm) 109 | !Cm = 0.009 ! LMA (g.cm-2) 110 | !N = 1.5 ! structure coefficient 111 | 112 | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 113 | !! Soil Reflectance Properties !! 114 | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 115 | ! rsoil1 = dry soil 116 | ! rsoil2 = wet soil 117 | ALLOCATE (rsoil0(nw)) 118 | !psoil = 1. ! soil factor (psoil=0: wet soil / psoil=1: dry soil) 119 | rsoil0=psoil*Rsoil1+(1-psoil)*Rsoil2 120 | 121 | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 122 | !! 4SAIL canopy structure parm !! 123 | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 124 | !LAI = 3. ! leaf area index (m^2/m^2) 125 | !hspot = 0.01 ! hot spot 126 | !tts = 30. ! solar zenith angle (degrees) 127 | !tto = 10. ! observer zenith angle (degrees) 128 | !psi = 0. ! azimuth (degrees) 129 | 130 | init_completed=.false. ! only at first call of PRO4SAIL 131 | 132 | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 133 | !! CALL PRO4SAIL !! 134 | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 135 | CALL PRO4SAIL(N,Cab,Car,Cbrown,Cw,Cm,LIDFa,LIDFb,TypeLIDF,LAI,hspot,tts,tto,psi,rsoil0) 136 | 137 | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 138 | !! direct / diffuse light !! 139 | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 140 | ! the direct and diffuse light are taken into account as proposed by: 141 | ! Francois et al. (2002) Conversion of 400-1100 nm vegetation albedo 142 | ! measurements into total shortwave broadband albedo using a canopy 143 | ! radiative transfer model, Agronomie 144 | skyl = 0.847- 1.61*sin((90-tts)*rd)+ 1.04*sin((90-tts)*rd)*sin((90-tts)*rd) ! % diffuse radiation 145 | ! Es = direct 146 | ! Ed = diffuse 147 | ! PAR direct 148 | PARdiro = (1-skyl)*Es 149 | ! PAR diffus 150 | PARdifo = (skyl)*Ed 151 | ! resv : directional reflectance 152 | resv = (rdot*PARdifo+rsot*PARdiro)/(PARdiro+PARdifo) 153 | 154 | result = resv 155 | 156 | ! PROSPECT output 157 | DEALLOCATE(LRT, rho, tau) 158 | ! SAIL 159 | DEALLOCATE(sb,sf,vb,vf,w) 160 | DEALLOCATE(m,m2,att,sigb,rinf) 161 | DEALLOCATE(PARdiro,PARdifo) 162 | DEALLOCATE(tsd,tdd,tdo,rsd,rdd,rso,rdo) 163 | DEALLOCATE(rddt,rsdt,rdot,rsodt,rsost,rsot,rsos,rsod) 164 | DEALLOCATE(lidf) 165 | ! resh : hemispherical reflectance 166 | ! resv : directional reflectance 167 | DEALLOCATE(resh,resv) 168 | DEALLOCATE(rsoil_old) 169 | DEALLOCATE(rsoil0) 170 | 171 | END 172 | -------------------------------------------------------------------------------- /doc/index.rst: -------------------------------------------------------------------------------- 1 | .. PyProSAIL documentation master file, created by 2 | sphinx-quickstart on Tue Jan 1 18:02:06 2013. 3 | You can adapt this file completely to your liking, but it should at least 4 | contain the root `toctree` directive. 5 | 6 | Welcome to PyProSAIL's documentation! 7 | ===================================== 8 | 9 | **Warning: PyProSAIL is no longer supported. It may work for you, or it may not, but I am no longer doing 10 | any updates, and will not be able to provide support.** 11 | 12 | PyProSAIL is a Python interface to the ProSAIL combined leaf optical properties (PROSPECT) and canopy bi-directional reflectance (SAIL) model. The Python code simply interfaces with the Fortran code provided `here `_ and, currently at least, does nothing more than let you run it easily from code. 13 | 14 | This interface is released under the GNU Lesser General Public License. 15 | 16 | (Very) Quickstart 17 | ----------------- 18 | Install it from PyPI:: 19 | 20 | pip install pyprosail 21 | 22 | Run it with some parameters, and look at the results:: 23 | 24 | >>> import pyprosail 25 | >>> result = pyprosail.run(1.5, 40, 8, 0, 0.01, 0.009, 1, 3, 0.01, 30, 10, 0, pyprosail.Planophile) 26 | >>> result[:,0] # These are the wavelengths (in micrometres) 27 | array([ 0.4 , 0.401, 0.402, ..., 2.498, 2.499, 2.5 ]) 28 | >>> result[:,1] # These are the reflectances (as a fraction) 29 | array([ 0.02119318, 0.02121176, 0.0212236 , ..., 0.02039977, 30 | 0.02024749, 0.02028665]) 31 | 32 | That's basically it! For more details on how to install it, exactly what parameters you can give the ``run`` method, and how to use PyProSAIL with Py6S, then read on. 33 | 34 | Installation 35 | ------------ 36 | PyProSAIL is available on the Python Package Index (PyPI), and can therefore be installed using easy_install or pip:: 37 | 38 | pip install pyprosail 39 | # or 40 | easy_install pyprosail 41 | 42 | Or a Windows Installer can be downloaded from the `PyPI page `_. It depends on the ``numpy`` and ``scipy`` modules - which you are likely to already have installed if you do any scientific programming with Python. If not, I would suggest installing something like the `Enthought Python Distribution `_, or `Pythonxy `_. 43 | 44 | The actual installation process is a little more complicated than it is for many pure Python modules, as it involves compiling the original Fortran code of the ProSAIL model. If running the installation commands above does not give any errors then you can assume everything is working fine - but if it does, then read on below. 45 | 46 | As the installation requires compiling some Fortran code, it will need to be able to find a Fortran compiler. Thus, the most likely reason for the install to fail is because a Fortran compiler can't be found. The installation routine is fairly good at finding Fortran compilers (searching various sensible places - depending on the operating system), so simply installing one of the compilers listed below should make it all work: 47 | 48 | * **Windows:** The easiest way is to use the `Windows installer `_, but if you want to compile from the Fortran source then follow the steps 1-4 `here `_ to install the GFortran compiler and set it up so that it can be used by the PyProSAIL installation procedure. 49 | * **OS X:** Install GCC by following the instructions `here `_. 50 | * **Linux:** Install GFortran using the package manager for your system, for example ``apt-get install gfortran``. 51 | 52 | If you have any issues with installation, please contact me using the details in the Support section below. 53 | 54 | Running the model 55 | ----------------- 56 | To run the model using some parameters, simply import the model:: 57 | 58 | import pyprosail 59 | 60 | and then call the run method, as documented below. 61 | 62 | .. py:function:: pyprosail.run(N, chloro, caroten, brown, EWT, LMA, psoil, LAI, hot_spot, solar_zenith, solar_azimuth, view_zenith, view_azimuth, LIDF) 63 | 64 | Runs the ProSAIL model with the given parameters and returns a 2D array with two columns: wavelengths and reflectances. The model is always run for the entire wavelength range of 0.4--2.5 micrometres. 65 | 66 | Arguments: 67 | 68 | * ``N`` -- Structure co-efficient 69 | * ``chloro`` -- Chlorophyll content (ug per cm^2) 70 | * ``caroten`` -- Carotenoid content (ug per cm^2) 71 | * ``brown`` -- Brown pigment content (arbitrary units) 72 | * ``EWT`` -- Equivalent Water Thickness (cm) 73 | * ``LMA`` -- Leaf Mass per unit area (g per cm^2) 74 | * ``soil_reflectance`` -- Soil reflectance: wet soil = 0, dry soil = 1 75 | * ``LAI`` -- Leaf Area Index 76 | * ``hot_spot`` -- Hot spot parameter 77 | * ``solar_zenith`` -- Solar zenith angle (degrees) 78 | * ``solar_azimuth`` -- Solar azimuth angle (degrees) 79 | * ``view_zenith`` -- View zenith angle (degrees) 80 | * ``view_azimuth`` -- View azimuth angle (degrees) 81 | * ``LIDF`` -- Leaf distibution function parameter(s) (see below) 82 | 83 | The leaf distribution function parameter(s) argument can be either: 84 | 85 | * A single number giving the average leaf angle (in degrees) for an elipsoidal distribution. 0 is planophile and 90 is erectophile. 86 | * A tuple giving (average leaf slope, bimodality parameter). These parameters must sum to be less than 1.0. For convenience a number of predefined options are given including: 87 | 88 | * ``pyprosail.Planophile`` 89 | * ``pyprosail.Erectophile`` 90 | * ``pyprosail.Plagiophile`` 91 | * ``pyprosail.Extremophile`` 92 | * ``pyprosail.Spherical`` 93 | * ``pyprosail.Uniform`` 94 | 95 | Examples of valid values for the leaf distribution function parameter include: 96 | 97 | * ``30`` (a 30 degree average leaf angle) 98 | * ``(0, -1)`` (an average leaf slope of 0 and a bimodality parameter of -1) 99 | * ``PyProsail.Planophile`` 100 | 101 | Using with Py6S 102 | --------------- 103 | PyProSAIL is very easy to use with Py6S (a Python interface to the 6S Radiative Transfer Model - see `here `_). PyProSAIL can be used to create a spectrum, which can then be used by Py6S as the ground reflectance for a simulation:: 104 | 105 | # Make sure you have both PyProSAIL and Py6S installed 106 | import pyprosail 107 | from Py6S import * 108 | 109 | spectrum = pyprosail.run(1.5, 40, 8, 0, 0.01, 0.009, 1, 3, 0.01, 30, 0, 10, 0, pyprosail.Planophile) 110 | s = SixS() 111 | s.ground_reflectance = GroundReflectance.HomogeneousLambertian(spectrum) 112 | s.run() 113 | 114 | It's as simple as that! For more information on the parameters that you can pass to the GroundReflectance functions, see the `Py6S documentation `_. 115 | 116 | Support 117 | ------- 118 | Py6S was developed by the author as part of his PhD (which has not yet finished). He is still developing the software, but has many other demands on his time. He will try to answer any support queries as soon as possible, but he cannot guarantee a quick response. 119 | 120 | **Email:** robin@rtwilson.com -------------------------------------------------------------------------------- /COPYING.LESSER: -------------------------------------------------------------------------------- 1 | GNU LESSER GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | 9 | This version of the GNU Lesser General Public License incorporates 10 | the terms and conditions of version 3 of the GNU General Public 11 | License, supplemented by the additional permissions listed below. 12 | 13 | 0. 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Revised Versions of the GNU Lesser General Public License. 145 | 146 | The Free Software Foundation may publish revised and/or new versions 147 | of the GNU Lesser General Public License from time to time. Such new 148 | versions will be similar in spirit to the present version, but may 149 | differ in detail to address new problems or concerns. 150 | 151 | Each version is given a distinguishing version number. If the 152 | Library as you received it specifies that a certain numbered version 153 | of the GNU Lesser General Public License "or any later version" 154 | applies to it, you have the option of following the terms and 155 | conditions either of that published version or of any later version 156 | published by the Free Software Foundation. If the Library as you 157 | received it does not specify a version number of the GNU Lesser 158 | General Public License, you may choose any version of the GNU Lesser 159 | General Public License ever published by the Free Software Foundation. 160 | 161 | If the Library as you received it specifies that a proxy can decide 162 | whether future versions of the GNU Lesser General Public License shall 163 | apply, that proxy's public statement of acceptance of any version is 164 | permanent authorization for you to choose that version for the 165 | Library. 166 | -------------------------------------------------------------------------------- /doc/conf.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | # 3 | # PyProSAIL documentation build configuration file, created by 4 | # sphinx-quickstart on Tue Jan 1 18:02:06 2013. 5 | # 6 | # This file is execfile()d with the current directory set to its containing dir. 7 | # 8 | # Note that not all possible configuration values are present in this 9 | # autogenerated file. 10 | # 11 | # All configuration values have a default; values that are commented out 12 | # serve to show the default. 13 | 14 | import sys, os 15 | 16 | # If extensions (or modules to document with autodoc) are in another directory, 17 | # add these directories to sys.path here. If the directory is relative to the 18 | # documentation root, use os.path.abspath to make it absolute, like shown here. 19 | #sys.path.insert(0, os.path.abspath('.')) 20 | 21 | # -- General configuration ----------------------------------------------------- 22 | 23 | # If your documentation needs a minimal Sphinx version, state it here. 24 | #needs_sphinx = '1.0' 25 | 26 | # Add any Sphinx extension module names here, as strings. They can be extensions 27 | # coming with Sphinx (named 'sphinx.ext.*') or your custom ones. 28 | extensions = ['sphinx.ext.autodoc', 'sphinx.ext.intersphinx', 'sphinx.ext.coverage', 'sphinx.ext.viewcode'] 29 | 30 | # Add any paths that contain templates here, relative to this directory. 31 | templates_path = ['_templates'] 32 | 33 | # The suffix of source filenames. 34 | source_suffix = '.rst' 35 | 36 | # The encoding of source files. 37 | #source_encoding = 'utf-8-sig' 38 | 39 | # The master toctree document. 40 | master_doc = 'index' 41 | 42 | # General information about the project. 43 | project = u'PyProSAIL' 44 | copyright = u'2013, Robin Wilson' 45 | 46 | # The version info for the project you're documenting, acts as replacement for 47 | # |version| and |release|, also used in various other places throughout the 48 | # built documents. 49 | # 50 | # The short X.Y version. 51 | version = '1.0' 52 | # The full version, including alpha/beta/rc tags. 53 | release = '1.0' 54 | 55 | # The language for content autogenerated by Sphinx. Refer to documentation 56 | # for a list of supported languages. 57 | #language = None 58 | 59 | # There are two options for replacing |today|: either, you set today to some 60 | # non-false value, then it is used: 61 | #today = '' 62 | # Else, today_fmt is used as the format for a strftime call. 63 | #today_fmt = '%B %d, %Y' 64 | 65 | # List of patterns, relative to source directory, that match files and 66 | # directories to ignore when looking for source files. 67 | exclude_patterns = ['_build'] 68 | 69 | # The reST default role (used for this markup: `text`) to use for all documents. 70 | #default_role = None 71 | 72 | # If true, '()' will be appended to :func: etc. cross-reference text. 73 | #add_function_parentheses = True 74 | 75 | # If true, the current module name will be prepended to all description 76 | # unit titles (such as .. function::). 77 | #add_module_names = True 78 | 79 | # If true, sectionauthor and moduleauthor directives will be shown in the 80 | # output. They are ignored by default. 81 | #show_authors = False 82 | 83 | # The name of the Pygments (syntax highlighting) style to use. 84 | pygments_style = 'sphinx' 85 | 86 | # A list of ignored prefixes for module index sorting. 87 | #modindex_common_prefix = [] 88 | 89 | 90 | # -- Options for HTML output --------------------------------------------------- 91 | 92 | # The theme to use for HTML and HTML Help pages. See the documentation for 93 | # a list of builtin themes. 94 | html_theme = 'default' 95 | 96 | # Theme options are theme-specific and customize the look and feel of a theme 97 | # further. For a list of options available for each theme, see the 98 | # documentation. 99 | #html_theme_options = {} 100 | 101 | # Add any paths that contain custom themes here, relative to this directory. 102 | #html_theme_path = [] 103 | 104 | # The name for this set of Sphinx documents. If None, it defaults to 105 | # " v documentation". 106 | #html_title = None 107 | 108 | # A shorter title for the navigation bar. Default is the same as html_title. 109 | #html_short_title = None 110 | 111 | # The name of an image file (relative to this directory) to place at the top 112 | # of the sidebar. 113 | #html_logo = None 114 | 115 | # The name of an image file (within the static path) to use as favicon of the 116 | # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 117 | # pixels large. 118 | #html_favicon = None 119 | 120 | # Add any paths that contain custom static files (such as style sheets) here, 121 | # relative to this directory. They are copied after the builtin static files, 122 | # so a file named "default.css" will overwrite the builtin "default.css". 123 | html_static_path = ['_static'] 124 | 125 | # If not '', a 'Last updated on:' timestamp is inserted at every page bottom, 126 | # using the given strftime format. 127 | #html_last_updated_fmt = '%b %d, %Y' 128 | 129 | # If true, SmartyPants will be used to convert quotes and dashes to 130 | # typographically correct entities. 131 | #html_use_smartypants = True 132 | 133 | # Custom sidebar templates, maps document names to template names. 134 | #html_sidebars = {} 135 | 136 | # Additional templates that should be rendered to pages, maps page names to 137 | # template names. 138 | #html_additional_pages = {} 139 | 140 | # If false, no module index is generated. 141 | #html_domain_indices = True 142 | 143 | # If false, no index is generated. 144 | #html_use_index = True 145 | 146 | # If true, the index is split into individual pages for each letter. 147 | #html_split_index = False 148 | 149 | # If true, links to the reST sources are added to the pages. 150 | #html_show_sourcelink = True 151 | 152 | # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. 153 | #html_show_sphinx = True 154 | 155 | # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. 156 | #html_show_copyright = True 157 | 158 | # If true, an OpenSearch description file will be output, and all pages will 159 | # contain a tag referring to it. The value of this option must be the 160 | # base URL from which the finished HTML is served. 161 | #html_use_opensearch = '' 162 | 163 | # This is the file name suffix for HTML files (e.g. ".xhtml"). 164 | #html_file_suffix = None 165 | 166 | # Output file base name for HTML help builder. 167 | htmlhelp_basename = 'PyProSAILdoc' 168 | 169 | 170 | # -- Options for LaTeX output -------------------------------------------------- 171 | 172 | latex_elements = { 173 | # The paper size ('letterpaper' or 'a4paper'). 174 | #'papersize': 'letterpaper', 175 | 176 | # The font size ('10pt', '11pt' or '12pt'). 177 | #'pointsize': '10pt', 178 | 179 | # Additional stuff for the LaTeX preamble. 180 | #'preamble': '', 181 | } 182 | 183 | # Grouping the document tree into LaTeX files. List of tuples 184 | # (source start file, target name, title, author, documentclass [howto/manual]). 185 | latex_documents = [ 186 | ('index', 'PyProSAIL.tex', u'PyProSAIL Documentation', 187 | u'Robin Wilson', 'manual'), 188 | ] 189 | 190 | # The name of an image file (relative to this directory) to place at the top of 191 | # the title page. 192 | #latex_logo = None 193 | 194 | # For "manual" documents, if this is true, then toplevel headings are parts, 195 | # not chapters. 196 | #latex_use_parts = False 197 | 198 | # If true, show page references after internal links. 199 | #latex_show_pagerefs = False 200 | 201 | # If true, show URL addresses after external links. 202 | #latex_show_urls = False 203 | 204 | # Documents to append as an appendix to all manuals. 205 | #latex_appendices = [] 206 | 207 | # If false, no module index is generated. 208 | #latex_domain_indices = True 209 | 210 | 211 | # -- Options for manual page output -------------------------------------------- 212 | 213 | # One entry per manual page. List of tuples 214 | # (source start file, name, description, authors, manual section). 215 | man_pages = [ 216 | ('index', 'pyprosail', u'PyProSAIL Documentation', 217 | [u'Robin Wilson'], 1) 218 | ] 219 | 220 | # If true, show URL addresses after external links. 221 | #man_show_urls = False 222 | 223 | 224 | # -- Options for Texinfo output ------------------------------------------------ 225 | 226 | # Grouping the document tree into Texinfo files. List of tuples 227 | # (source start file, target name, title, author, 228 | # dir menu entry, description, category) 229 | texinfo_documents = [ 230 | ('index', 'PyProSAIL', u'PyProSAIL Documentation', 231 | u'Robin Wilson', 'PyProSAIL', 'One line description of project.', 232 | 'Miscellaneous'), 233 | ] 234 | 235 | # Documents to append as an appendix to all manuals. 236 | #texinfo_appendices = [] 237 | 238 | # If false, no module index is generated. 239 | #texinfo_domain_indices = True 240 | 241 | # How to display URL addresses: 'footnote', 'no', or 'inline'. 242 | #texinfo_show_urls = 'footnote' 243 | 244 | 245 | # Example configuration for intersphinx: refer to the Python standard library. 246 | intersphinx_mapping = {'http://docs.python.org/': None} 247 | -------------------------------------------------------------------------------- /pyprosail/PRO4SAIL.f90: -------------------------------------------------------------------------------- 1 | SUBROUTINE PRO4SAIL(N,Cab,Car,Cbrown,Cw,Cm,LIDFa,LIDFb,TypeLIDF,lai,q,tts,tto,psi,rsoil) 2 | 3 | ! This version has been implemented by Jean-Baptiste Feret 4 | ! Jean-Baptiste Feret takes the entire responsibility for this version 5 | ! All comments, changes or questions should be sent to: 6 | ! jbferet@stanford.edu 7 | 8 | ! Jean-Baptiste Feret 9 | ! Institut de Physique du Globe de Paris 10 | ! Space and Planetary Geophysics 11 | ! October 2009 12 | 13 | ! this model PRO4SAIL is based on a version provided by 14 | ! Wout Verhoef 15 | ! NLR 16 | ! April/May 2003, 17 | ! original version downloadable at http://teledetection.ipgp.jussieu.fr/prosail/ 18 | ! Improved and extended version of SAILH model that avoids numerical singularities 19 | ! and works more efficiently if only few parameters change. 20 | ! References: 21 | ! Verhoef et al. (2007) Unified Optical-Thermal Four-Stream Radiative 22 | ! Transfer Theory for Homogeneous Vegetation Canopies, IEEE TRANSACTIONS 23 | ! ON GEOSCIENCE AND REMOTE SENSING, VOL. 45, NO. 6, JUNE 2007 24 | 25 | ! The module "staticvar" is meant for internal use in order to keep 26 | ! several variables static between successive calls of the subroutine. 27 | ! For calculation of vertical flux profiles inside the canopy, the quantities 28 | ! m, sb, sf, ks, and rinf are needed by the calling routine, so in this case 29 | ! this module must also be declared in the calling routine. 30 | 31 | USE MOD_ANGLE 32 | USE MOD_dataSpec_P5B 33 | USE MOD_output_PROSPECT 34 | USE MOD_SAIL 35 | USE MOD_flag_util 36 | USE MOD_staticvar 37 | IMPLICIT NONE 38 | 39 | !!!!!!!! INPUT / OUTPUT !!!!!!!! 40 | REAL*8,INTENT(in) :: N,Cab,Car,Cbrown,Cw,Cm 41 | REAL*8,INTENT(in) :: LIDFa,LIDFb,lai,q,rsoil(nw) 42 | REAL*8,INTENT(in) :: tts,tto,psi 43 | INTEGER*4,INTENT(in) :: TypeLIDF 44 | !!!!!!!! END INPUT / OUTPUT !!!!!!!! 45 | 46 | REAL*8 :: chi_o,chi_s,ctl,sto,sts,tanto,tants,cospsi,koli,ksli,bf,bfli,alf,litab(13) 47 | REAL*8 :: f1,f2,g1(nw),g2(nw),ttl,sigf(nw),sobli,sofli,x1,x2,y1,y2,z 48 | REAL*8 :: fhot,fint,frho,ftau,J1ko(nw),J1ks(nw),J2ko(nw),J2ks(nw),Jfunc3 49 | REAL*8 :: T1(nw),T2(nw),T3(nw),Tv1(nw),Tv2(nw) 50 | REAL*8 :: e1(nw),e2(nw),rinf2(nw),re(nw),denom(nw) 51 | REAL*8 :: Ps(nw),Qs(nw),Pv(nw),Qv(nw),dn(nw) 52 | INTEGER*4 :: na 53 | data litab/5.,15.,25.,35.,45.,55.,65.,75.,81.,83.,85.,87.,89./ 54 | 55 | ! Raise all flags if we arrive here for the first time, lower them at other times 56 | DO i=1,7 57 | flag(i)=.not.init_completed 58 | ENDDO 59 | 60 | IF (init_completed) THEN 61 | ! Detect which inputs have changed (if it is not the first time) 62 | delta_lai = (lai.ne.lai_old) 63 | delta_hot = (q.ne.q_old) 64 | delta_geom = (tts.ne.tts_old).or.(tto.ne.tto_old).or.& 65 | (psi.ne.psi_old) 66 | delta_soil = (SUM((rsoil-rsoil_old)**2).ne.0) 67 | delta_lidf = (LIDFa.ne.LIDFa_old).or.(LIDFb.ne.LIDFb_old) 68 | delta_leaf = (N.ne.N_old).or.(Cab.ne.Cab_old).or.(Car.ne.Car_old).or.& 69 | (Cbrown.ne.Cbrown_old).or.(Cw.ne.Cw_old).or.(Cm.ne.Cm_old) 70 | 71 | ! Raise the flags for the modules to be executed 72 | flag(1) = delta_geom 73 | flag(2) = delta_lidf 74 | flag(3) = delta_geom.or.delta_lidf 75 | flag(4) = flag(3).or.delta_leaf 76 | flag(5) = flag(4).or.delta_lai.or.delta_soil 77 | flag(6) = flag(3).or.delta_lai.or.delta_hot 78 | flag(7) = delta_leaf 79 | ENDIF 80 | 81 | ! Make sure that on next occasions init is regarded as being completed 82 | init_completed=.true. 83 | 84 | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 85 | !!LEAF CHEM & STR PROPERTIES!! 86 | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 87 | IF(flag(7)) THEN !! 88 | CALL prospect_5B(N,Cab,Car,Cbrown,Cw,Cm,LRT) 89 | rho = LRT(:,1) 90 | tau = LRT(:,2) 91 | ENDIF 92 | 93 | IF(flag(1)) THEN 94 | ! Geometric quantities 95 | cts = COS(rd*tts) 96 | cto = COS(rd*tto) 97 | ctscto = cts*cto 98 | tants = TAN(rd*tts) 99 | tanto = TAN(rd*tto) 100 | cospsi = COS(rd*psi) 101 | dso = SQRT(tants*tants+tanto*tanto-2.*tants*tanto*cospsi) 102 | ENDIF 103 | 104 | na=13 105 | IF (flag(2)) THEN 106 | ! Generate leaf angle distribution from average leaf angle (ellipsoidal) or (a,b) parameters 107 | IF(TypeLidf.EQ.1) THEN 108 | CALL dladgen(LIDFa,LIDFb,lidf) 109 | ELSEIF(TypeLidf.EQ.2) THEN 110 | CALL calc_LIDF_ellipsoidal(na,LIDFa,lidf) 111 | ENDIF 112 | ENDIF 113 | 114 | ! angular distance, compensation of shadow length 115 | IF (flag(3)) THEN 116 | ! Calculate geometric factors associated with extinction and scattering 117 | ! Initialise sums 118 | ks = 0 119 | ko = 0 120 | bf = 0 121 | sob = 0 122 | sof = 0 123 | 124 | ! Weighted sums over LIDF 125 | DO i=1,na 126 | ttl = litab(i) ! leaf inclination discrete values 127 | ctl = COS(rd*ttl) 128 | ! SAIL volume scattering phase function gives interception and portions to be 129 | ! multiplied by rho and tau 130 | CALL volscatt(tts,tto,psi,ttl,chi_s,chi_o,frho,ftau) 131 | 132 | !******************************************************************************** 133 | !* SUITS SYSTEM COEFFICIENTS 134 | !* 135 | !* ks : Extinction coefficient for direct solar flux 136 | !* ko : Extinction coefficient for direct observed flux 137 | !* att : Attenuation coefficient for diffuse flux 138 | !* sigb : Backscattering coefficient of the diffuse downward flux 139 | !* sigf : Forwardscattering coefficient of the diffuse upward flux 140 | !* sf : Scattering coefficient of the direct solar flux for downward diffuse flux 141 | !* sb : Scattering coefficient of the direct solar flux for upward diffuse flux 142 | !* vf : Scattering coefficient of upward diffuse flux in the observed direction 143 | !* vb : Scattering coefficient of downward diffuse flux in the observed direction 144 | !* w : Bidirectional scattering coefficient 145 | !******************************************************************************** 146 | 147 | ! Extinction coefficients 148 | ksli = chi_s/cts 149 | koli = chi_o/cto 150 | 151 | ! Area scattering coefficient fractions 152 | sobli = frho*pi/ctscto 153 | sofli = ftau*pi/ctscto 154 | bfli = ctl*ctl 155 | ks = ks+ksli*lidf(i) 156 | ko = ko+koli*lidf(i) 157 | bf = bf+bfli*lidf(i) 158 | sob = sob+sobli*lidf(i) 159 | sof = sof+sofli*lidf(i) 160 | 161 | ENDDO 162 | ! Geometric factors to be used later with rho and tau 163 | sdb = 0.5*(ks+bf) 164 | sdf = 0.5*(ks-bf) 165 | dob = 0.5*(ko+bf) 166 | dof = 0.5*(ko-bf) 167 | ddb = 0.5*(1.+bf) 168 | ddf = 0.5*(1.-bf) 169 | ENDIF 170 | 171 | IF(flag(4)) THEN 172 | ! Here rho and tau come in 173 | sigb= ddb*rho+ddf*tau 174 | sigf= ddf*rho+ddb*tau 175 | att = 1.-sigf 176 | m2=(att+sigb)*(att-sigb) 177 | WHERE (m2.LT.0) 178 | m2=0 179 | ENDWHERE 180 | m=SQRT(m2) 181 | sb = sdb*rho+sdf*tau 182 | sf = sdf*rho+sdb*tau 183 | vb = dob*rho+dof*tau 184 | vf = dof*rho+dob*tau 185 | w = sob*rho+sof*tau 186 | ENDIF 187 | 188 | IF (flag(5)) THEN 189 | ! Here the LAI comes in 190 | ! Outputs for the case LAI = 0 191 | IF (lai.le.0) THEN 192 | tss = 1.; too = 1.; tsstoo = 1. 193 | rdd = 0.; tdd = 1.; rsd = 0. 194 | tsd = 0.; rdo = 0.; tdo = 0. 195 | rso = 0.; rsos = 0.; rsod = 0. 196 | 197 | rddt = rsoil; rsdt = rsoil; rdot = rsoil 198 | rsodt = 0.; rsost = rsoil; rsot = rsoil 199 | RETURN 200 | ENDIF 201 | 202 | ! Other cases (LAI > 0) 203 | e1 = EXP(-m*lai) 204 | e2 = e1*e1 205 | rinf = (att-m)/sigb 206 | rinf2 = rinf*rinf 207 | re = rinf*e1 208 | denom = 1.-rinf2*e2 209 | 210 | CALL Jfunc1(ks,m,lai,J1ks) 211 | CALL Jfunc2(ks,m,lai,J2ks) 212 | CALL Jfunc1(ko,m,lai,J1ko) 213 | CALL Jfunc2(ko,m,lai,J2ko) 214 | 215 | Ps = (sf+sb*rinf)*J1ks 216 | Qs = (sf*rinf+sb)*J2ks 217 | Pv = (vf+vb*rinf)*J1ko 218 | Qv = (vf*rinf+vb)*J2ko 219 | 220 | rdd = rinf*(1.-e2)/denom 221 | tdd = (1.-rinf2)*e1/denom 222 | tsd = (Ps-re*Qs)/denom 223 | rsd = (Qs-re*Ps)/denom 224 | tdo = (Pv-re*Qv)/denom 225 | rdo = (Qv-re*Pv)/denom 226 | 227 | tss = EXP(-ks*lai) 228 | too = EXP(-ko*lai) 229 | z = Jfunc3(ks,ko,lai) 230 | g1 = (z-J1ks*too)/(ko+m) 231 | g2 = (z-J1ko*tss)/(ks+m) 232 | 233 | Tv1 = (vf*rinf+vb)*g1 234 | Tv2 = (vf+vb*rinf)*g2 235 | T1 = Tv1*(sf+sb*rinf) 236 | T2 = Tv2*(sf*rinf+sb) 237 | T3 = (rdo*Qs+tdo*Ps)*rinf 238 | 239 | ! Multiple scattering contribution to bidirectional canopy reflectance 240 | rsod = (T1+T2-T3)/(1.-rinf2) 241 | ENDIF 242 | 243 | IF (flag(6)) THEN 244 | ! Treatment of the hotspot-effect 245 | alf=1e6 246 | ! Apply correction 2/(K+k) suggested by F.-M. Breon 247 | IF (q.gt.0.) THEN 248 | alf=(dso/q)*2./(ks+ko) 249 | ENDIF 250 | IF (alf.GT.200.) THEN !inserted H. Bach 1/3/04 251 | alf=200. 252 | ENDIF 253 | IF (alf.eq.0.) THEN 254 | ! The pure hotspot - no shadow 255 | tsstoo = tss 256 | sumint = (1-tss)/(ks*lai) 257 | ELSE 258 | ! Outside the hotspot 259 | fhot=lai*SQRT(ko*ks) 260 | ! Integrate by exponential Simpson method in 20 steps 261 | ! the steps are arranged according to equal partitioning 262 | ! of the slope of the joint probability function 263 | x1=0. 264 | y1=0. 265 | f1=1. 266 | fint=(1.-EXP(-alf))*.05 267 | sumint=0. 268 | 269 | DO i=1,20 270 | IF (i.lt.20) THEN 271 | x2=-LOG(1.-i*fint)/alf 272 | ELSE 273 | x2=1. 274 | ENDIF 275 | y2=-(ko+ks)*lai*x2+fhot*(1.-EXP(-alf*x2))/alf 276 | f2=EXP(y2) 277 | sumint=sumint+(f2-f1)*(x2-x1)/(y2-y1) 278 | x1=x2 279 | y1=y2 280 | f1=f2 281 | ENDDO 282 | tsstoo=f1 283 | ENDIF 284 | ENDIF 285 | 286 | ! Bidirectional reflectance 287 | ! Single scattering contribution 288 | rsos = w*lai*sumint 289 | 290 | ! Total canopy contribution 291 | rso=rsos+rsod 292 | 293 | ! Interaction with the soil 294 | dn=1.-rsoil*rdd 295 | 296 | ! rddt: bi-hemispherical reflectance factor 297 | rddt=rdd+tdd*rsoil*tdd/dn 298 | ! rsdt: directional-hemispherical reflectance factor for solar incident flux 299 | rsdt=rsd+(tsd+tss)*rsoil*tdd/dn 300 | ! rdot: hemispherical-directional reflectance factor in viewing direction 301 | rdot=rdo+tdd*rsoil*(tdo+too)/dn 302 | ! rsot: bi-directional reflectance factor 303 | rsodt=rsod+((tss+tsd)*tdo+(tsd+tss*rsoil*rdd)*too)*rsoil/dn 304 | rsost=rsos+tsstoo*rsoil 305 | rsot=rsost+rsodt 306 | 307 | ! Before returning, save current parameters as old ones 308 | N_old = N ; Cab_old = Cab; Car_old = Car 309 | Cbrown_old = Cbrown; Cw_old = Cw; Cm_old = Cm 310 | lai_old = lai; LIDFa_old = LIDFa; LIDFb_old = LIDFb 311 | tts_old = tts; tto_old = tto; psi_old = psi 312 | q_old = q; rsoil_old = rsoil 313 | 314 | RETURN 315 | END 316 | 317 | 318 | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 319 | !**************************************************** 320 | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 321 | 322 | 323 | SUBROUTINE Jfunc1(k,l,t,Jout) 324 | 325 | USE MOD_dataSpec_P5B 326 | IMPLICIT NONE 327 | 328 | ! J1 function with avoidance of singularity problem 329 | ! 330 | REAL*8,INTENT(in) :: k,l(nw),t 331 | REAL*8,INTENT(out) :: Jout(nw) 332 | REAL*8 :: del(nw) 333 | 334 | 335 | del=(k-l)*t 336 | WHERE (ABS(del)>1e-3) 337 | Jout=(EXP(-l*t)-EXP(-k*t))/(k-l) 338 | ELSEWHERE 339 | Jout=0.5*t*(EXP(-k*t)+EXP(-l*t))*(1.-del*del/12.) 340 | END WHERE 341 | 342 | END 343 | 344 | 345 | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 346 | !**************************************************** 347 | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 348 | 349 | 350 | SUBROUTINE Jfunc2(k,l,t,Jout) 351 | 352 | USE MOD_dataSpec_P5B 353 | IMPLICIT NONE 354 | 355 | ! J2 function 356 | 357 | REAL*8,INTENT(in) :: k,l(nw),t 358 | REAL*8,INTENT(out) :: Jout(nw) 359 | REAL*8 :: del(nw) 360 | 361 | Jout=(1.-EXP(-(k+l)*t))/(k+l) 362 | 363 | END 364 | 365 | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 366 | !**************************************************** 367 | !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 368 | 369 | 370 | FUNCTION Jfunc3(k,l,t) 371 | 372 | USE MOD_dataSpec_P5B 373 | IMPLICIT NONE 374 | 375 | ! J2 function 376 | 377 | REAL*8 :: k,l,t 378 | REAL*8 :: Jfunc3 379 | 380 | Jfunc3=(1.-EXP(-(k+l)*t))/(k+l) 381 | 382 | END -------------------------------------------------------------------------------- /COPYING: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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No Surrender of Others' Freedom. 541 | 542 | If conditions are imposed on you (whether by court order, agreement or 543 | otherwise) that contradict the conditions of this License, they do not 544 | excuse you from the conditions of this License. If you cannot convey a 545 | covered work so as to satisfy simultaneously your obligations under this 546 | License and any other pertinent obligations, then as a consequence you may 547 | not convey it at all. For example, if you agree to terms that obligate you 548 | to collect a royalty for further conveying from those to whom you convey 549 | the Program, the only way you could satisfy both those terms and this 550 | License would be to refrain entirely from conveying the Program. 551 | 552 | 13. Use with the GNU Affero General Public License. 553 | 554 | Notwithstanding any other provision of this License, you have 555 | permission to link or combine any covered work with a work licensed 556 | under version 3 of the GNU Affero General Public License into a single 557 | combined work, and to convey the resulting work. The terms of this 558 | License will continue to apply to the part which is the covered work, 559 | but the special requirements of the GNU Affero General Public License, 560 | section 13, concerning interaction through a network will apply to the 561 | combination as such. 562 | 563 | 14. Revised Versions of this License. 564 | 565 | The Free Software Foundation may publish revised and/or new versions of 566 | the GNU General Public License from time to time. Such new versions will 567 | be similar in spirit to the present version, but may differ in detail to 568 | address new problems or concerns. 569 | 570 | Each version is given a distinguishing version number. If the 571 | Program specifies that a certain numbered version of the GNU General 572 | Public License "or any later version" applies to it, you have the 573 | option of following the terms and conditions either of that numbered 574 | version or of any later version published by the Free Software 575 | Foundation. If the Program does not specify a version number of the 576 | GNU General Public License, you may choose any version ever published 577 | by the Free Software Foundation. 578 | 579 | If the Program specifies that a proxy can decide which future 580 | versions of the GNU General Public License can be used, that proxy's 581 | public statement of acceptance of a version permanently authorizes you 582 | to choose that version for the Program. 583 | 584 | Later license versions may give you additional or different 585 | permissions. However, no additional obligations are imposed on any 586 | author or copyright holder as a result of your choosing to follow a 587 | later version. 588 | 589 | 15. Disclaimer of Warranty. 590 | 591 | THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY 592 | APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT 593 | HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY 594 | OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, 595 | THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR 596 | PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM 597 | IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF 598 | ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 599 | 600 | 16. Limitation of Liability. 601 | 602 | IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING 603 | WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS 604 | THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY 605 | GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE 606 | USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF 607 | DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD 608 | PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), 609 | EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF 610 | SUCH DAMAGES. 611 | 612 | 17. Interpretation of Sections 15 and 16. 613 | 614 | If the disclaimer of warranty and limitation of liability provided 615 | above cannot be given local legal effect according to their terms, 616 | reviewing courts shall apply local law that most closely approximates 617 | an absolute waiver of all civil liability in connection with the 618 | Program, unless a warranty or assumption of liability accompanies a 619 | copy of the Program in return for a fee. 620 | 621 | END OF TERMS AND CONDITIONS 622 | 623 | How to Apply These Terms to Your New Programs 624 | 625 | If you develop a new program, and you want it to be of the greatest 626 | possible use to the public, the best way to achieve this is to make it 627 | free software which everyone can redistribute and change under these terms. 628 | 629 | To do so, attach the following notices to the program. It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | 635 | Copyright (C) 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | Copyright (C) 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . --------------------------------------------------------------------------------