depreciate the atmosphere argument in Model.run

smrt/atmosphere/test_atmosphere.py

@@ -2,8 +2,7 @@
 
 import numpy as np
 
-from smrt import make_snowpack, make_model, sensor, make_soil
-from smrt import sensor_list
+from smrt import make_snowpack, make_model, sensor_list
 from smrt.atmosphere.simple_isotropic_atmosphere import SimpleIsotropicAtmosphere, make_atmosphere
 
 
@@ -14,33 +13,34 @@ def test_simple_isotropic_atmosphere():
     temperature = [265, 265]
     thickness = [0.4, 10]
     radius = [200e-6, 400e-6]
-    #stickiness = [1000, 1000]
     stickiness = [0.2, 0.2]
 
     rads = sensor_list.amsre('36V')
 
     atmos = SimpleIsotropicAtmosphere(30., 6., 0.90)
 
-    snowpack = make_snowpack(thickness, "sticky_hard_spheres",
-                            density=density, temperature=temperature, radius=radius, stickiness=stickiness)
+    snowpack = make_snowpack(thickness, "sticky_hard_spheres", density=density,
+                             temperature=temperature, radius=radius, stickiness=stickiness)
 
     # create the EM Model - Equivalent DMRTML
     iba = make_model("iba", "dort")
 
     res1 = iba.run(rads, snowpack)
-    res2 = iba.run(rads, snowpack, atmosphere=atmos)
+
+    snowpack.atmosphere = atmos
+    res2 = iba.run(rads, snowpack)
 
     print('TB 1: ', res1.TbV(), 'TB2: ', res2.TbV())
 
-    #absorption with effective permittivity
+    # absorption with effective permittivity
     assert abs(res1.TbV() - 227.61318467710458) < 1e-2
     assert abs(res2.TbV() - 214.66092232541834) < 1e-2
 
 
 def test_frequency_dependent_atmosphere():
 
     mu = np.cos(np.arange(0, 90))
-    atmos = make_atmosphere(tbdown={10e9: 15, 21e9: 23}, tbup={10e9:5, 21e9:6}, trans={10e9:1, 21e9:0.95})
+    atmos = make_atmosphere(tbdown={10e9: 15, 21e9: 23}, tbup={10e9: 5, 21e9: 6}, trans={10e9: 1, 21e9: 0.95})
 
     assert np.all(atmos.tbup(frequency=10e9, costheta=mu, npol=2) == 5)
     assert np.all(atmos.tbdown(frequency=21e9, costheta=mu, npol=2) == 23)

smrt/core/model.py

@@ -7,7 +7,7 @@
 The :py:mod:`smrt.rtsolver` is responsible for propagation of the incident or emitted energy through the layers, up to the surface, and eventually 
 through the atmosphere.
 
-To build a model, use the :py:func:`make_model` function with the type of emmodel and type of rtsolver as arguments.
+To build a model, use the :py:meth:`make_model` function with the type of emmodel and type of rtsolver as arguments.
 Then call the :py:meth:`Model.run` method of the model instance by specifying the sensor (:py:class:`smrt.core.sensor.Sensor`),
 snowpack (:py:class:`smrt.core.snowpack.Snowpack`) and optionally atmosphere (see :py:mod:`smrt.atmosphere`).
 The results are returned as a :py:class:`~smrt.core.result.Result` which can then been interrogated to retrieve brightness temperature,
@@ -172,6 +172,10 @@ def run(self, sensor, snowpack, atmosphere=None, snowpack_dimension=None, progre
             :returns: result of the calculation(s) as a :py:class:`Results` instance
         """
 
+        if atmosphere is not None:
+            raise DeprecationWarning("The atmosphere argument of the run method is going to be depreciated."
+                " Setting the 'atmosphere' with make_snowpack (and similar functions) is now the recommended way.")
+
         if not isinstance(sensor, SensorBase):
             raise SMRTError("the first argument of 'run' must be a sensor")
 

smrt/test/test_physics_law.py

@@ -10,19 +10,23 @@
 def test_isothermal_universe_highscatt():
     _do_test_isothermal_universe(0.8e-3, 10)
 
+
 def test_isothermal_universe_lowscatt():
     _do_test_isothermal_universe(0.05e-3, 10)
 
+
 def test_isothermal_universe_shallow():
     _do_test_isothermal_universe(0.8e-3, 0.1)
 
 
 def test_kirchoff_law_highscatt():
     _do_test_kirchoff_law(0.8e-3, 10)
 
+
 def test_kirchoff_law_lowscatt():
     _do_test_kirchoff_law(0.05e-3, 10)
 
+
 def test_kirchoff_law_shallow():
     _do_test_kirchoff_law(0.8e-3, 0.1)
 
@@ -31,13 +35,14 @@ def _do_test_isothermal_universe(pc, thickness_1):
 
     T = 265
 
-    substrate = make_soil('soil_wegmuller',permittivity_model=complex(10,1), roughness_rms=0.001, temperature=T)
-
-    snowpack = make_snowpack([0.3, thickness_1], "exponential",
-                            density=[200, 300], temperature=T, corr_length=pc, substrate=substrate)
+    substrate = make_soil('soil_wegmuller', permittivity_model=complex(10,1), roughness_rms=0.001, temperature=T)
 
     atmosphere = SimpleIsotropicAtmosphere(tbdown=T, tbup=0, trans=1)
 
+    snowpack = make_snowpack([0.3, thickness_1], "exponential",
+                             density=[200, 300], temperature=T, corr_length=pc,
+                             substrate=substrate, atmosphere=atmosphere)
+
     # create the sensor
     theta = range(10, 80, 5)
     radiometer = sensor_list.passive(37e9, theta)
@@ -46,7 +51,7 @@ def _do_test_isothermal_universe(pc, thickness_1):
     m = make_model("iba", "dort")
 
     # run the model
-    sresult = m.run(radiometer, snowpack, atmosphere)
+    sresult = m.run(radiometer, snowpack)
 
     np.testing.assert_allclose(sresult.TbV(), T, atol=0.01)
     np.testing.assert_allclose(sresult.TbH(), T, atol=0.01)
@@ -58,11 +63,12 @@ def _do_test_kirchoff_law(pc, thickness_1):
 
     substrate = make_soil('soil_wegmuller', permittivity_model=complex(10, 1), roughness_rms=0.001, temperature=T)
 
-    snowpack = make_snowpack([0.3, thickness_1], "exponential",
-                             density=[200, 300], temperature=T, corr_length=pc, substrate=substrate)
-
     atmosphere1K = SimpleIsotropicAtmosphere(tbdown=1, tbup=0, trans=1)
 
+    snowpack = make_snowpack([0.3, thickness_1], "exponential",
+                             density=[200, 300], temperature=T, corr_length=pc,
+                             substrate=substrate)
+
     # create the sensor
     theta = range(10, 80, 5)
     radiometer = sensor_list.passive(37e9, theta)
@@ -72,17 +78,18 @@ def _do_test_kirchoff_law(pc, thickness_1):
 
     # run the model
     sresult_0 = m.run(radiometer, snowpack)
-    sresult_1 = m.run(radiometer, snowpack, atmosphere1K)
+    snowpack.atmosphere = atmosphere1K
+    sresult_1 = m.run(radiometer, snowpack)
 
     # V-pol
-    emissivity_V = (sresult_0.TbV() + sresult_1.TbV())/2/T
+    emissivity_V = (sresult_0.TbV() + sresult_1.TbV()) / 2 / T
     reflectivity_V = (sresult_1.TbV() - sresult_0.TbV())
 
     print(emissivity_V, 1 - reflectivity_V)
     np.testing.assert_allclose(emissivity_V, 1 - reflectivity_V, atol=0.002)
 
     # H-pol
-    emissivity_H = (sresult_0.TbH() + sresult_1.TbH())/2/T
+    emissivity_H = (sresult_0.TbH() + sresult_1.TbH()) / 2 / T
     reflectivity_H = (sresult_1.TbH() - sresult_0.TbH())
 
     print(emissivity_H, 1 - reflectivity_H)