Freq jac (#867)

atmtools · Nov 21, 2024 · 876b242 · 876b242
2 parents dabc79e + bb0a748
commit 876b242
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diff --git a/examples/getting-started/2-clearsky-radiative-transfer/2.zeeman-sensor.py b/examples/getting-started/2-clearsky-radiative-transfer/2.zeeman-sensor.py
@@ -35,23 +35,21 @@
 ws.spectral_radiance_space_agendaSet(option="UniformCosmicBackground")
 ws.spectral_radiance_surface_agendaSet(option="Blackbody")
 ws.ray_path_observer_agendaSet(option="Geometric")
-ws.spectral_radiance_observer_agendaSet(option="EmissionUnits")
+ws.spectral_radiance_observer_agendaSet(option="Emission")
 
-# %% Set up a sensor with Gaussian channel widths on individual frequency ranges
+# %% Set up a sensor with Gaussian standard deviation channel widths on individual frequency ranges
 
 pos = [100e3, 0, 0]
 los = [180.0, 0.0]
-ws.measurement_sensorSimpleGaussian(fwhm=1e5, pos=pos, los=los, pol="RC")
+ws.measurement_sensorSimpleGaussian(std=1e5, pos=pos, los=los, pol="RC")
 
 # %% Core calculations
 
-result = pyarts.arts.Vector()
-result_jac = pyarts.arts.Matrix()
-ws.measurement_vectorFromSensor(result, result_jac)
+ws.measurement_vectorFromSensor()
 
 # %% Show results
 
-plt.plot((ws.frequency_grid - line_f0) / 1e6, result)
+plt.plot((ws.frequency_grid - line_f0) / 1e6, ws.measurement_vector)
 plt.xlabel("Frequency offset [MHz]")
 plt.ylabel("Spectral radiance [K]")
 plt.title(
@@ -61,20 +59,20 @@
 # %% Test
 
 assert np.allclose(
-    result[::100],
+    ws.measurement_vector[::100],
     np.array(
         [
-            227.78646795,
-            230.8638575,
-            234.80652899,
-            240.36081974,
-            249.78247057,
-            207.62113428,
-            249.78190355,
-            240.35972683,
-            234.80495168,
-            230.86180615,
-            227.78395156,
+            227.85626271,
+            230.93430882,
+            234.89998118,
+            240.50100578,
+            250.05272664,
+            209.9140708,
+            249.51258095,
+            240.21976958,
+            234.71155853,
+            230.79135297,
+            227.73970752,
         ]
     ),
 )
diff --git a/examples/getting-started/3-disort/1.clearsky-radiance.py b/examples/getting-started/3-disort/1.clearsky-radiance.py
@@ -32,7 +32,6 @@
     toa=toa, basename="planets/Earth/afgl/tropical/", missing_is_zero=1
 )
 ws.atmospheric_fieldIGRF(time="2000-03-11 14:39:37")
-# ws.atmospheric_field[pyarts.arts.AtmKey.t] = 300.0
 
 # %% Checks and settings
 
@@ -42,7 +41,7 @@
 
 # %% Core Disort calculations
 
-ws.disort_spectral_radiance_fieldClearsky(
+ws.disort_spectral_radiance_fieldSunlessClearsky(
     longitude=lon,
     latitude=lat,
     disort_quadrature_dimension=NQuad,

diff --git a/examples/getting-started/3-disort/2.clearsky-flux.py b/examples/getting-started/3-disort/2.clearsky-flux.py
@@ -41,7 +41,7 @@
 
 # %% Core Disort calculations
 
-ws.disort_settings_agendaSet(option="Clearsky")
+ws.disort_settings_agendaSet(option="SunlessClearsky")
 
 ws.ray_pathGeometricDownlooking(longitude=lon, latitude=lat, max_step=40_000)
 ws.ray_path_atmospheric_pointFromPath()

diff --git a/python/src/pyarts/plots/ppvar_atm.py b/python/src/pyarts/plots/ppvar_atm.py
@@ -41,22 +41,22 @@ def plt_info(atm, keys=[]):
     for key in keys:
         if isinstance(key, pyarts.arts.ArrayOfSpeciesTag):
             out[key] = Info("linear", f"VMR {key} [-]", 1)
-        elif isinstance(key, pyarts.arts.options.AtmKey):
-            if key == pyarts.arts.options.AtmKey.t:
+        elif isinstance(key, pyarts.arts.AtmKey):
+            if key == pyarts.arts.AtmKey.t:
                 out[key] = Info("linear", "Temperature [K]", 1)
-            elif key == pyarts.arts.options.AtmKey.p:
+            elif key == pyarts.arts.AtmKey.p:
                 out[key] = Info("log", "Pressure [Pa]", 1)
-            elif key == pyarts.arts.options.AtmKey.mag_u:
+            elif key == pyarts.arts.AtmKey.mag_u:
                 out[key] = Info("linear", "Magnetic u-component [µT]", 1e6)
-            elif key == pyarts.arts.options.AtmKey.mag_v:
+            elif key == pyarts.arts.AtmKey.mag_v:
                 out[key] = Info("linear", "Magnetic v-component [µT]", 1e6)
-            elif key == pyarts.arts.options.AtmKey.mag_w:
+            elif key == pyarts.arts.AtmKey.mag_w:
                 out[key] = Info("linear", "Magnetic w-component [µT]", 1e6)
-            elif key == pyarts.arts.options.AtmKey.wind_u:
+            elif key == pyarts.arts.AtmKey.wind_u:
                 out[key] = Info("linear", "Wind u-component [m/s]", 1)
-            elif key == pyarts.arts.options.AtmKey.wind_v:
+            elif key == pyarts.arts.AtmKey.wind_v:
                 out[key] = Info("linear", "Wind v-component [m/s]", 1)
-            elif key == pyarts.arts.options.AtmKey.wind_w:
+            elif key == pyarts.arts.AtmKey.wind_w:
                 out[key] = Info("linear", "Wind w-component [m/s]", 1)
             else:
                 assert False, "Unknown key type"

diff --git a/python/test/workspace/test_variables.py b/python/test/workspace/test_variables.py
@@ -169,6 +169,7 @@ def test_method_agenda_variables_io(self):
         vars = list(allvars.keys())
         mets = pyarts.arts.globals.workspace_methods()
         ages = pyarts.arts.globals.workspace_agendas()
+        opts = pyarts.arts.globals.option_groups()
 
         res = {}
         for var in vars:
@@ -189,13 +190,19 @@ def test_method_agenda_variables_io(self):
                     if var in ages[ag].input or var in ages[ag].output:
                         ok_anyways = True
                         break
+
+                # Allow options to be pure input
+                if nout == 0 and allvars[var].type in opts:
+                    ok_anyways = True                            
 
+                # Allow agendas to be pure input
                 if nin != 0 and allvars[var].type == "Agenda":
                     ok_anyways = True
 
                 if not ok_anyways:
                     bad_vars.append(f"{var}")
 
+
         bad_vars.sort()
         assert len(bad_vars) == 0, (
             "Should have no pure input/output variables,\n"

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -22,6 +22,7 @@ add_custom_target(UtilityHeadersArts SOURCES ${HEADERFILES})
 add_library(workspace_group STATIC
   workspace_groups.cpp
 )
+target_link_libraries(workspace_group PRIVATE arts_options)
 
 add_executable(make_auto_wsg make_auto_wsg.cpp)
 add_custom_command(OUTPUT

diff --git a/src/core/CMakeLists.txt b/src/core/CMakeLists.txt
@@ -21,6 +21,7 @@ add_subdirectory(matpack)
 add_subdirectory(rtepack)
 add_subdirectory(predefined)
 add_subdirectory(operators)
+add_subdirectory(jacobian)
 add_subdirectory(fwd)
 add_subdirectory(lbl)
 add_subdirectory(lookup)
@@ -48,7 +49,6 @@ add_library(artscore STATIC
   geodetic.cc
   igrf13.cc
   interpolation.cc
-  jacobian.cc
   jpl_species.cc
   lineshapemodel.cc
   mc_antenna.cc
@@ -60,7 +60,6 @@ add_library(artscore STATIC
   radiation_field.cc
   raw.cc
   refraction.cc
-  retrieval_target.cc
   sensor.cc
   special_interp.cc
   sun.cc
@@ -93,6 +92,7 @@ target_link_libraries(artscore PUBLIC
   util
   disort-cpp
   legendre
+  jacobian
 )
 
 target_include_directories(artscore PUBLIC "${CMAKE_CURRENT_SOURCE_DIR}")

diff --git a/src/core/absorption/CMakeLists.txt b/src/core/absorption/CMakeLists.txt
@@ -5,4 +5,4 @@ add_library(absorption STATIC
   predefined_absorption_models.cc
 )
 target_link_libraries(absorption PUBLIC path predef physics lbl)
-target_include_directories(absorption PUBLIC ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/..)
+target_include_directories(absorption PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
diff --git a/src/core/atm/CMakeLists.txt b/src/core/atm/CMakeLists.txt
@@ -1,4 +1,4 @@
 add_library(atm STATIC atm.cpp)
 
 target_link_libraries(atm PUBLIC matpack operators quantum species physics)
-target_include_directories(atm PUBLIC ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/..)
+target_include_directories(atm PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
diff --git a/src/core/fwd/CMakeLists.txt b/src/core/fwd/CMakeLists.txt
@@ -7,4 +7,4 @@ add_library(fwd STATIC
   fwd_spectral_radiance.cpp
 )
 target_link_libraries(fwd PUBLIC path absorption)
-target_include_directories(fwd PUBLIC ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/..)
+target_include_directories(fwd PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
diff --git a/src/core/jacobian/CMakeLists.txt b/src/core/jacobian/CMakeLists.txt
@@ -0,0 +1,6 @@
+add_library(jacobian STATIC
+jacobian.cc
+)
+
+target_link_libraries(jacobian PUBLIC atm sensor scattering lbl)
+target_include_directories(jacobian PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})