From 2cf75905089574b67646efa1adfc6e62d1c60558 Mon Sep 17 00:00:00 2001
From: Jose Gomez-Dans <jgomezdans@gmail.com>
Date: Tue, 11 Apr 2017 13:56:07 +0100
Subject: [PATCH] PROSPECT D as a option

I have added the PROSPECT-D model as an option. Currently, the
package allows you to select PROSPECT 5 and PROSPECT D. PROSPECT D
is exposed through the `prospect_d` function, which can also be
used to run PROSPECT5 through its options. I have also exposed the
surface incident angle. The PROSPECT models have also been coupled
to SAIL (which continues to be in Fortran), so you can see the
difference between PROSPECT model choices also at the canopy scale.

Version has been bumped up just because.
---
 prosail/__init__.py | 39 ++++++++++++++++++++++++++++++++++-----
 setup.py            |  4 +++-
 2 files changed, 37 insertions(+), 6 deletions(-)

diff --git a/prosail/__init__.py b/prosail/__init__.py
index 0ec6161..7c1d498 100644
--- a/prosail/__init__.py
+++ b/prosail/__init__.py
@@ -1,12 +1,16 @@
 import numpy as np
 from prosail_fortran import run_sailf as sail
 from prosail_fortran import run_prosailf as prosail
-from prosail_fortran import prospect_5b
+#from prosail_fortran import prospect_5b
+from prospect_d import prospect_d
 from prosail_fortran import mod_dataspec_p5b as spectral_libs
 
+import pkgutil
+from StringIO import StringIO
 
-def run_prosail(n, cab, car, cbrown, cw, cm, lai, lidfa, hspot,
-                tts, tto, psi, typelidf=2, lidfb=0., factor="SDR",
+def run_prosail(n, cab, car,  cbrown, cw, cm, lai, lidfa, hspot,
+                tts, tto, psi, ant=0.0, alpha=40., prospect_version="5", 
+                typelidf=2, lidfb=0., factor="SDR",
                 rsoil0=None, rsoil=None, psoil=None,
                 soil_spectrum1=None, soil_spectrum2=None):
     """Run the PROSPECT_5B and SAILh radiative transfer models. The soil
@@ -44,6 +48,13 @@ def run_prosail(n, cab, car, cbrown, cw, cm, lai, lidfa, hspot,
         Sensor zenith angle
     psi: float
         Relative sensor-solar azimuth angle ( saa - vaa )
+    ant: float
+        leaf anthocyanin concentration (default set to 0)
+    alpha: float
+        The alpha angle (in degrees) used in the surface scattering
+        calculations. By default it's set to 40 degrees.
+    prospect_version: str
+        Which PROSPECT version to use. We have "5" and "D"
     typelidf: int, optional
         The type of leaf angle distribution function to use. By default, is set
         to 2.
@@ -94,8 +105,26 @@ def run_prosail(n, cab, car, cbrown, cw, cm, lai, lidfa, hspot,
         rsoil0 = rsoil * (
         psoil * soil_spectrum1 + (1. - psoil) * soil_spectrum2)
 
-    rho = prosail(n, cab, car, cbrown, cw, cm, lai, lidfa, lidfb, rsoil0,
-                  hspot, tts, tto, psi, typelidf)
+    if prospect_version == "5":
+        wv, refl, trans = prospect_d (n, cab, car, cbrown, cw, cm, 0.0,
+                                      spectral_libs.refractive,
+                                      spectral_libs.k_cab, spectral_libs.k_car,
+                                      spectral_libs.k_brown, 
+                                      spectral_libs.k_cw, spectral_libs.k_cm,
+                                      np.zeros_like(spectral_libs.k_cm), 
+                                      alpha=alpha)
+    elif prospect_version.upper() == "D":
+        prospect_d_spectra = pkgutil.get_data('prosail', 'prospect_d_spectra.txt')
+        d = np.loadtxt( StringIO(prospect_d_spectra))
+        wv, refl, trans = prospect_d (n, cab, car, cbrown, cw, cm, ant,
+                                d[:,1], d[:,2], d[:,3], d[:,5], d[:,6], 
+                                d[:,7], d[:,4], alpha=alpha)
+
+    else:
+        raise ValueError("prospect_version can only be 5 or D!")
+    
+    rho = sail(refl, trans, lai, lidfa, lidfb, rsoil0, hspot, tts, tto, psi,
+               typelidf)
 
     if factor == "SDR":
         return rho[0, :]
diff --git a/setup.py b/setup.py
index e132df9..ee2caff 100644
--- a/setup.py
+++ b/setup.py
@@ -46,5 +46,7 @@ def configuration(parent_package='',top_path=None):
         author_email = author_email,
         classifiers = classifiers,
         configuration = configuration,
-        version="1.3.0",
+        package_data={"prosail":["*.txt"]},
+        include_package_data=True,
+        version="1.5.0",
         packages=["prosail"])