Merge pull request #1 from ibaris/Outsourced_Soil

Soil reflectance in SAIL

examples/prospect_sail.py

@@ -19,9 +19,12 @@
 # select the coefficient values for the specific bands of ASTER (B1 - B9) or LANDSAT8 (B2 - B7). To access these bands
 # type prospect.L8.Bx (x = 2, 3, ..., 7) for Landsat 8 or prospect.ASTER.Bx (x = 1, 2, ..., 9) for ASTER.
 
+# To calculate the PROSAIL model we need some soil reflectance values. To obtain these we can use the LSM model:
+lsm = pyrism.LSM(reflectance=3.14 / 4, moisture=0.15)
 
-# To calculate the PROSAIL model we must call SAIL and specify the scattering and transmittance coefficients with these from PROSPECT like:
-prosail = pyrism.SAIL(iza=iza, vza=vza, raa=raa, ks=prospect.ks, kt=prospect.kt, lidf_type='campbell',
-                      lai=3, hotspot=0.25, soil_reflectance=3.14 / 4, soil_moisture=0.15)
+# Now we must call SAIL and specify the scattering and transmittance coefficients with these from PROSPECT like:
+prosail = pyrism.SAIL(iza=iza, vza=vza, raa=raa, ks=prospect.ks, kt=prospect.kt, rho_surface=lsm.ref,
+                      lidf_type='campbell',
+                      lai=3, hotspot=0.25)
 
 # The accessibility of the attributes are the same as the PROSPECT model.

pyrism/models/models.py

@@ -480,15 +480,15 @@ class SAIL(Kernel):
     iza, vza, raa : int, float or ndarray
         Incidence (iza) and scattering (vza) zenith angle, as well as relative azimuth (raa) angle.
     ks, kt : array_like
-        Continuous leaf reflection (ks) and leaf transmission (kt) values from from 400 until 2500 nm.
+        Continuous leaf reflection (ks) and leaf transmission (kt) values from from 400 until 2500 nm. One can use the
+        output from PROSPECT class instance.
     lai : float
         Leaf area index.
     hotspot : float
         The hotspot parameter.
-    soil_reflectance : int or float
-        Surface (Lambertian) reflectance in optical wavelength.
-    soil_moisture : int or float
-        Surface moisture content between 0 and 1.
+    rho_surface : array_like
+        Continuous surface reflectance values from from 400 until 2500 nm. One can use the
+        output from LSM class instance.
     lidf_type : {'verhoef', 'campbell'}, optional
         Define with which method the LIDF is calculated. Default is 'campbell'
     a, b : float, optional
@@ -525,25 +525,44 @@ class SAIL(Kernel):
 
     """
 
-    def __init__(self, iza, vza, raa, ks, kt, lai, hotspot, soil_reflectance, soil_moisture,
+    def __init__(self, iza, vza, raa, ks, kt, lai, hotspot, rho_surface,
                  lidf_type='campbell', a=57, b=0, normalize=False, nbar=0.0, angle_unit='DEG'):
+
         super(SAIL, self).__init__(iza=iza, vza=vza, raa=raa, normalize=normalize, nbar=nbar, angle_unit=angle_unit,
                                    align=True)
 
+        if len(ks) != 2101:
+            raise AssertionError(
+                "ks must contain continuous leaf reflectance values from from 400 until 2500 nm with a length of 2101. The actual length of ks is {0}".format(
+                    str(len(ks))))
+
+        elif len(kt) != 2101:
+            raise AssertionError(
+                "kt must contain continuous leaf transmitance values from from 400 until 2500 nm with a length of 2101. The actual length of kt is {0}".format(
+                    str(len(kt))))
+
+        elif len(rho_surface) != 2101:
+            raise AssertionError(
+                "rho_surface must contain continuous surface reflectance values from from 400 until 2500 nm with a length of 2101. The actual length of rho_surface is {0}".format(
+                    str(len(rho_surface))))
+
+        else:
+            pass
+
         self.ks = ks
         self.kt = kt
         self.lai = lai
         self.hotspot = hotspot
 
-        self.Soil = LSM(reflectance=soil_reflectance, moisture=soil_moisture)
+        self.rho_surface = rho_surface
         self.VollScat = VolScatt(iza, vza, raa, angle_unit)
 
         if lidf_type is 'verhoef':
             self.VollScat.coef(a=a, b=b, lidf_type='verhoef')
         elif lidf_type is 'campbell':
             self.VollScat.coef(a=a, lidf_type='campbell')
         else:
-            raise ValueError("The lidf_type must be 'verhoef' or 'campbell'")
+            raise AssertionError("The lidf_type must be 'verhoef' or 'campbell'")
 
         tss, too, tsstoo, rdd, tdd, rsd, tsd, rdo, tdo, rso, rsos, rsod, rddt, rsdt, rdot, rsodt, rsost, rsot, gammasdf, gammasdb, gammaso = self.__calc()
 
@@ -598,12 +617,12 @@ def __calc(self):
             rso = 0
             rsos = 0
             rsod = 0
-            rddt = self.Soil.ref
-            rsdt = self.Soil.ref
-            rdot = self.Soil.ref
+            rddt = self.rho_surface
+            rsdt = self.rho_surface
+            rdot = self.rho_surface
             rsodt = 0
-            rsost = self.Soil.ref
-            rsot = self.Soil.ref
+            rsost = self.rho_surface
+            rsot = self.rho_surface
             gammasdf = 0
             gammaso = 0
             gammasdb = 0
@@ -689,18 +708,18 @@ def __calc(self):
             gammaso = gammasos + gammasod
 
             # Interaction with the soil
-            dn = 1. - self.Soil.ref * rdd
+            dn = 1. - self.rho_surface * rdd
 
             try:
                 dn[dn < 1e-36] = 1e-36
             except TypeError:
                 dn = max(1e-36, dn)
 
-            rddt = rdd + tdd * self.Soil.ref * tdd / dn
-            rsdt = rsd + (tsd + tss) * self.Soil.ref * tdd / dn
-            rdot = rdo + tdd * self.Soil.ref * (tdo + too) / dn
-            rsodt = ((tss + tsd) * tdo + (tsd + tss * self.Soil.ref * rdd) * too) * self.Soil.ref / dn
-            rsost = rso + tsstoo * self.Soil.ref
+            rddt = rdd + tdd * self.rho_surface * tdd / dn
+            rsdt = rsd + (tsd + tss) * self.rho_surface * tdd / dn
+            rdot = rdo + tdd * self.rho_surface * (tdo + too) / dn
+            rsodt = ((tss + tsd) * tdo + (tsd + tss * self.rho_surface * rdd) * too) * self.rho_surface / dn
+            rsost = rso + tsstoo * self.rho_surface
             rsot = rsost + rsodt
 
             return [tss, too, tsstoo, rdd, tdd, rsd, tsd, rdo, tdo,

setup.py

@@ -17,7 +17,7 @@ def get_packages():
 
 setup(name='pyrism',
 
-      version='0.0.2.1',
+      version='0.0.3',
 
       description='Python bindings for Remote Sensing Models',
 

tests/test_prospect_prosail.py

@@ -2,11 +2,11 @@
 from distutils import dir_util
 
 import pytest
-from numpy import allclose, loadtxt
+from numpy import allclose, loadtxt, atleast_1d
 from pytest import fixture
 from scipy.io import loadmat
 
-from pyrism import PROSPECT, SAIL
+from pyrism import PROSPECT, SAIL, LSM
 
 
 @fixture
@@ -79,9 +79,9 @@ def test_sdr_prosail5(self, datadir):
         fname = datadir("REFL_CAN.txt")
         w, resv, hdr, sdr, bhr, dhr = loadtxt(fname, unpack=True)
 
+        lsm = LSM(reflectance=1, moisture=1)
         prospect = PROSPECT(N=1.5, Cab=40, Cxc=8., Cbr=0.0, Cw=0.01, Cm=0.009, version="5")
-        sail = SAIL(iza=30, vza=10, raa=0, ks=prospect.ks, kt=prospect.kt, lai=3, hotspot=0.01, soil_reflectance=1,
-                    soil_moisture=1,
+        sail = SAIL(iza=30, vza=10, raa=0, ks=prospect.ks, kt=prospect.kt, lai=3, hotspot=0.01, rho_surface=lsm.ref,
                     a=-0.35, b=-0.15, lidf_type='verhoef')
 
         assert allclose(sdr, sail.BRF.ref, atol=0.01)
@@ -90,9 +90,9 @@ def test_hdr_prosail5(self, datadir):
         fname = datadir("REFL_CAN.txt")
         w, resv, hdr, sdr, bhr, dhr = loadtxt(fname, unpack=True)
 
+        lsm = LSM(reflectance=1, moisture=1)
         prospect = PROSPECT(N=1.5, Cab=40, Cxc=8., Cbr=0.0, Cw=0.01, Cm=0.009, version="5")
-        sail = SAIL(iza=30, vza=10, raa=0, ks=prospect.ks, kt=prospect.kt, lai=3, hotspot=0.01, soil_reflectance=1,
-                    soil_moisture=1,
+        sail = SAIL(iza=30, vza=10, raa=0, ks=prospect.ks, kt=prospect.kt, lai=3, hotspot=0.01, rho_surface=lsm.ref,
                     a=-0.35, b=-0.15, lidf_type='verhoef')
 
         assert allclose(hdr, sail.HDR.ref, atol=0.01)
@@ -101,9 +101,9 @@ def test_bhr_prosail5(self, datadir):
         fname = datadir("REFL_CAN.txt")
         w, resv, hdr, sdr, bhr, dhr = loadtxt(fname, unpack=True)
 
+        lsm = LSM(reflectance=1, moisture=1)
         prospect = PROSPECT(N=1.5, Cab=40, Cxc=8., Cbr=0.0, Cw=0.01, Cm=0.009, version="5")
-        sail = SAIL(iza=30, vza=10, raa=0, ks=prospect.ks, kt=prospect.kt, lai=3, hotspot=0.01, soil_reflectance=1,
-                    soil_moisture=1,
+        sail = SAIL(iza=30, vza=10, raa=0, ks=prospect.ks, kt=prospect.kt, lai=3, hotspot=0.01, rho_surface=lsm.ref,
                     a=-0.35, b=-0.15, lidf_type='verhoef')
 
         assert allclose(bhr, sail.BHR.ref, atol=0.01)
@@ -112,9 +112,44 @@ def test_dhr_prosail5(self, datadir):
         fname = datadir("REFL_CAN.txt")
         w, resv, hdr, sdr, bhr, dhr = loadtxt(fname, unpack=True)
 
+        lsm = LSM(reflectance=1, moisture=1)
         prospect = PROSPECT(N=1.5, Cab=40, Cxc=8., Cbr=0.0, Cw=0.01, Cm=0.009, version="5")
-        sail = SAIL(iza=30, vza=10, raa=0, ks=prospect.ks, kt=prospect.kt, lai=3, hotspot=0.01, soil_reflectance=1,
-                    soil_moisture=1,
+        sail = SAIL(iza=30, vza=10, raa=0, ks=prospect.ks, kt=prospect.kt, lai=3, hotspot=0.01, rho_surface=lsm.ref,
                     a=-0.35, b=-0.15, lidf_type='verhoef')
 
         assert allclose(dhr, sail.DHR.ref, atol=0.01)
+
+
+class TestPROSAILError:
+    def test_ks(self, datadir):
+        fname = datadir("REFL_CAN.txt")
+        w, resv, hdr, sdr, bhr, dhr = loadtxt(fname, unpack=True)
+        ks = atleast_1d(0)
+
+        lsm = LSM(reflectance=1, moisture=1)
+        prospect = PROSPECT(N=1.5, Cab=40, Cxc=8., Cbr=0.0, Cw=0.01, Cm=0.009, version="5")
+        with pytest.raises(AssertionError):
+            sail = SAIL(iza=30, vza=10, raa=0, ks=ks, kt=prospect.kt, lai=3, hotspot=0.01, rho_surface=lsm.ref,
+                        a=-0.35, b=-0.15, lidf_type='verhoef')
+
+    def test_kt(self, datadir):
+        fname = datadir("REFL_CAN.txt")
+        w, resv, hdr, sdr, bhr, dhr = loadtxt(fname, unpack=True)
+        kt = atleast_1d(0)
+
+        lsm = LSM(reflectance=1, moisture=1)
+        prospect = PROSPECT(N=1.5, Cab=40, Cxc=8., Cbr=0.0, Cw=0.01, Cm=0.009, version="5")
+        with pytest.raises(AssertionError):
+            sail = SAIL(iza=30, vza=10, raa=0, ks=prospect.ks, kt=kt, lai=3, hotspot=0.01, rho_surface=lsm.ref,
+                        a=-0.35, b=-0.15, lidf_type='verhoef')
+
+    def test_surf(self, datadir):
+        fname = datadir("REFL_CAN.txt")
+        w, resv, hdr, sdr, bhr, dhr = loadtxt(fname, unpack=True)
+        kt = atleast_1d(0)
+
+        lsm = LSM(reflectance=1, moisture=1)
+        prospect = PROSPECT(N=1.5, Cab=40, Cxc=8., Cbr=0.0, Cw=0.01, Cm=0.009, version="5")
+        with pytest.raises(AssertionError):
+            sail = SAIL(iza=30, vza=10, raa=0, ks=prospect.ks, kt=prospect.kt, lai=3, hotspot=0.01, rho_surface=kt,
+                        a=-0.35, b=-0.15, lidf_type='verhoef')