Merge branch 'cherry_pick_omas_viewer_dev' into test_new_EFIT_mapping…

…s_for_IDA

omas/examples/omas_units.py

@@ -31,7 +31,7 @@
 # how to manipulate data that has units
 ods.sample()
 with omas_environment(ods, unitsio=True):
-    ne = ods['core_profiles.profiles_1d.0.electrons.density_thermal']
+    ne = ods['core_profiles.profiles_1d.0.electrons.density']
     print(f'Mean density in  m^-3: {numpy.mean(ne.to("m^-3").magnitude):3.3g}')
     print(f'Mean density in cm^-3: {numpy.mean(ne.to("cm^-3").magnitude):3.3g}')
 

omas/machine_mappings/d3d.json

@@ -147,9 +147,6 @@
  "core_profiles.profiles_1d.:.electrons.density_fit.psi_norm": {
   "PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
  },
- "core_profiles.profiles_1d.:.electrons.density_thermal": {
-  "PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
- },
  "core_profiles.profiles_1d.:.electrons.temperature": {
   "PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r})"
  },

omas/machine_mappings/d3d.py

@@ -1408,7 +1408,6 @@ def core_profiles_profile_1d(ods, pulse, PROFILES_tree="OMFIT_PROFS"):
         query["electrons.temperature_fit.psi_norm"] = "PS_T_E"
         query["ion[1].density_fit.psi_norm"] = "PS_N_C"
         query["ion[1].temperature_fit.psi_norm"] = "PS_T_C"
-        query["ion[1].density_fit.psi_norm"] = "PS_T_C"
         query["ion[1].velocity.toroidal_fit.psi_norm"]= "PS_V_TOR_C"
         #query["j_total"] = "J_TOT"
         #query["pressure_perpendicular"] = "P_TOT"
@@ -1473,7 +1472,6 @@ def core_profiles_profile_1d(ods, pulse, PROFILES_tree="OMFIT_PROFS"):
         profiles_node = '\\TOP.PROFILES.'
         query = {
             "electrons.density": "EDENSFIT",
-            "electrons.density_thermal": "EDENSFIT",
             "electrons.temperature": "ETEMPFIT"
         }
         for entry in query:
@@ -1490,6 +1488,7 @@ def core_profiles_profile_1d(ods, pulse, PROFILES_tree="OMFIT_PROFS"):
                 continue
             for i_time, time in enumerate(data["time"]):
                 ods[f"core_profiles.profiles_1d[{i_time}]."+entry] = data[entry][i_time]
+
 # ================================
 @machine_mapping_function(__regression_arguments__, pulse=133221)
 def core_profiles_global_quantities_data(ods, pulse):

omas/machine_mappings/profiles_db_ccfe.json

@@ -10,7 +10,7 @@
  "core_profiles.profiles_1d.:": {
   "PYTHON": "profile_db_to_ODS(ods, {pulse}, {tok!r}, {db!r}, {ngrid!r})"
  },
- "core_profiles.profiles_1d.:.electrons.density_thermal": {
+ "core_profiles.profiles_1d.:.electrons.density": {
   "PYTHON": "profile_db_to_ODS(ods, {pulse}, {tok!r}, {db!r}, {ngrid!r})"
  },
  "core_profiles.profiles_1d.:.electrons.temperature": {

omas/machine_mappings/profiles_db_ccfe.py

@@ -82,7 +82,7 @@ def profile_db_to_ODS(ods, pulse, tok, db, ngrid):
         "['TWOD']['Q']": 'core_profiles.profiles_1d[0].q',
         "['TWOD']['TI']": 'core_profiles.profiles_1d[0].t_i_average',
         "['TWOD']['TE']": 'core_profiles.profiles_1d[0].electrons.temperature',
-        "['TWOD']['NE']": 'core_profiles.profiles_1d[0].electrons.density_thermal',
+        "['TWOD']['NE']": 'core_profiles.profiles_1d[0].electrons.density',
         "['TWOD']['CURTOT']": 'core_profiles.profiles_1d[0].j_tor',
         "['TWOD']['QNBII']": 'q_nbi_i',
         "['TWOD']['QNBIE']": 'q_nbi_e',

omas/omas_physics.py

@@ -987,7 +987,7 @@ def summary_greenwald(ods, update=True):
                 % time_index: ods['equilibrium.time_slice.%s.profiles_1d.rho_tor_norm' % time_index]
             },
         ):
-            ne = ods['core_profiles.profiles_1d.%d.electrons.density_thermal' % time_index]
+            ne = ods['core_profiles.profiles_1d.%d.electrons.density' % time_index]
             volume = ods['equilibrium.time_slice.%d.profiles_1d.volume' % time_index]
             ne_vol_avg = numpy.trapz(ne, x=volume) / volume[-1]
 
@@ -1051,11 +1051,11 @@ def summary_lineaverage_density(ods, line_grid=2000, time_index=None, update=Tru
     Zgrid = ods['equilibrium']['time_slice'][time_index]['profiles_2d'][0]['grid']['dim2']
 
     psi2d = ods['equilibrium']['time_slice'][time_index]['profiles_2d'][0]['psi']
-    psi_interp = scipy.interpolate.interp2d(Zgrid, Rgrid, psi2d)
+    psi_spl = RectBivariateSpline(Rgrid, Zgrid, psi2d)
     psi_eq = ods['equilibrium']['time_slice'][time_index]['profiles_1d']['psi']
     rhon_eq = ods['equilibrium']['time_slice'][time_index]['profiles_1d']['rho_tor_norm']
     rhon_cp = ods['core_profiles']['profiles_1d'][time_index]['grid']['rho_tor_norm']
-    ne = ods['core_profiles']['profiles_1d'][time_index]['electrons']['density_thermal']
+    ne = ods['core_profiles']['profiles_1d'][time_index]['electrons']['density']
     ne = numpy.interp(rhon_eq, rhon_cp, ne)
     tck = scipy.interpolate.splrep(psi_eq, ne, k=3)
 
@@ -1105,7 +1105,7 @@ def summary_lineaverage_density(ods, line_grid=2000, time_index=None, update=Tru
             i1 = zero_crossings[0]
             i2 = zero_crossings[-1]
 
-            psival = [psi_interp(Zline[i], Rline[i])[0] for i in range(i1, i2, numpy.sign(i2 - i1))]
+            psival = [psi_spl(Rline[i], Zline[i], grid=False).item() for i in range(i1, i2, numpy.sign(i2 - i1))]
             ne_interp = scipy.interpolate.splev(psival, tck)
             ne_line = numpy.trapz(ne_interp)
             ne_line /= abs(i2 - i1)
@@ -1239,7 +1239,7 @@ def summary_taue(ods, thermal=True, update=True):
         with omas_environment(ods, coordsio={'equilibrium.time_slice.0.profiles_1d.psi': psi}):
             volume = equilibrium_ods['profiles_1d']['volume']
             kappa = volume[-1] / 2 / numpy.pi / numpy.pi / a / a / r_major
-            ne = ods['core_profiles']['profiles_1d'][time_index]['electrons']['density_thermal']
+            ne = ods['core_profiles']['profiles_1d'][time_index]['electrons']['density']
             ne_vol_avg = numpy.trapz(ne, x=volume) / volume[-1]
 
             if 'interferometer' in ods:
@@ -1542,7 +1542,7 @@ def core_profiles_pressures(ods, update=True):
 
         __p__ = None
         if 'density_thermal' in prof1d['electrons'] and 'temperature' in prof1d['electrons']:
-            __p__ = nominal_values(prof1d['electrons']['density_thermal'] * prof1d['electrons']['temperature'] * constants.e)
+            __p__ = nominal_values(prof1d['electrons']['density'] * prof1d['electrons']['temperature'] * constants.e)
         elif 'pressure_thermal' in prof1d['electrons']:
             __p__ = nominal_values(prof1d['electrons']['pressure_thermal'])
 

omas/omas_plot.py

@@ -762,7 +762,10 @@ def get2d(contour_quantity):
     if levels is None and value_1d is not None:
         if contour_quantity == 'q':
             max_q = int(numpy.round(omas_interp1d(0.95, x_value_1d, value_1d)))
-            levels = numpy.arange(max_q)
+            levels = numpy.arange(numpy.abs(max_q))
+            if max_q < 0:
+                levels *= -1
+                levels = levels[::-1]
         else:
             levels = numpy.linspace(numpy.min(value_1d), numpy.max(value_1d), 11)[1:-1]
             levels = numpy.hstack((levels, levels[-1] + (levels[1] - levels[0]) * numpy.arange(100)[1:]))
@@ -799,8 +802,10 @@ def get2d(contour_quantity):
             r = scipy.ndimage.zoom(r, sf)
             z = scipy.ndimage.zoom(z, sf)
             value_2d = scipy.ndimage.zoom(value_2d, sf)
-
-        cs = ax.contour(r, z, value_2d, levels, **kw)
+        if levels is not None:
+            cs = ax.contour(r, z, value_2d, levels, **kw)
+        else:
+            cs = ax.contour(r, z, value_2d, **kw)
 
         if label_contours or ((label_contours is None) and (contour_quantity == 'q')):
             ax.clabel(cs)
@@ -1186,7 +1191,7 @@ def core_profiles_currents_summary(ods, time_index=None, time=None, ax=None, **k
 
 @add_to__ODS__
 def core_profiles_summary(ods, time_index=None, time=None, fig=None, 
-                          ods_species=None, quantities=['density_thermal', 'temperature'], 
+                          ods_species=None, quantities=['density', 'temperature'], 
                           x_axis = "rho_tor_norm", **kw):
     """
     Plot densities and temperature profiles for electrons and all ion species
@@ -1280,7 +1285,8 @@ def core_profiles_summary(ods, time_index=None, time=None, fig=None,
                     #     plotting_list.append(prof1d[specie][q]*scale * prof1d[specie]['element[0].z_n'])
                     #     label_name_z.append(r'$\times$' + f" {int(prof1d[specie]['element[0].z_n'])}")
                     # else:
-                    if len(prof1d[specie][q]) == len(prof1d[specie][q + "_error_upper"]):
+
+                    if q + "_error_upper" in prof1d[specie] and len(prof1d[specie][q]) == len(prof1d[specie][q + "_error_upper"]):
                         plotting_list.append(unumpy.uarray(prof1d[specie][q]*scale,
                                              prof1d[specie][q + "_error_upper"]*scale))
                     else:
@@ -1292,6 +1298,8 @@ def core_profiles_summary(ods, time_index=None, time=None, fig=None,
                                               prof1d[specie][q + "_fit.measured_error_upper"]*scale])
                         except Exception as e:
                             data_list.append(None)
+                    else:
+                        data_list.append(None)
                     label_name_z.append("")
                     label_name.append(f'{names[index]} {q.capitalize()}')
         elif "e_field.radial" not in q:

omas/omas_symbols.py

@@ -13,7 +13,7 @@
 _symbols['.b_field_r'] = r'$B_{r}$'
 _symbols['.b_field_tor'] = r'$B_{\phi}$'
 _symbols['.b_field_z'] = r'$B_{z}$'
-_symbols['.electrons.density_thermal'] = '$n_e$'
+_symbols['.electrons.density'] = '$n_e$'
 _symbols['.ion.:.density'] = r'$n_{i:}$'
 _symbols['.n_e'] = '$n_e$'
 _symbols['.potential_floating'] = r'$\phi_f'

omas/samples/sample_core_profiles_ods.json

@@ -14,7 +14,7 @@
 "profiles_1d": [
 {
 "electrons": {
-"density_thermal": [
+"density": [
 6.153301513064224e+19,
 6.072762281483232e+19,
 5.885729236754774e+19,

omas/tests/test_omas_core.py

@@ -503,7 +503,7 @@ def test_latexit(self):
         assert latexit['.n_e'] == '$n_e$'
         assert latexit['n_e'] == '$n_e$'
 
-        assert latexit['core_profiles.profiles_1d[:].electrons.density_thermal'] == '$n_e$'
+        assert latexit['core_profiles.profiles_1d[:].electrons.density'] == '$n_e$'
         assert latexit['barometry.gauge[:].pressure.data'] == '$P$'
         assert latexit['equilibrium.time_slice[0].ggd[1].b_field_tor[0].values'] == r'$B_{\phi}$'
         assert latexit['core_profiles.profiles_1d[4].ion[0].density'] == '$n_{i0}$'

omas/tests/test_omas_physics.py

@@ -343,9 +343,9 @@ def test_coordsio(self):
         ods5 = ODS()
         ods5['core_profiles.profiles_1d[0].grid.rho_tor_norm'] = data5
         with omas_environment(ods5, coordsio={'core_profiles.profiles_1d[0].grid.rho_tor_norm': data10}):
-            ods5['core_profiles.profiles_1d[0].electrons.density_thermal'] = data10
+            ods5['core_profiles.profiles_1d[0].electrons.density'] = data10
         assert len(ods5['core_profiles.profiles_1d[0].grid.rho_tor_norm']) == 5
-        assert len(ods5['core_profiles.profiles_1d[0].electrons.density_thermal']) == 5
+        assert len(ods5['core_profiles.profiles_1d[0].electrons.density']) == 5
 
         ods6 = ODS()
         ods6['core_profiles.profiles_1d[0].grid.rho_tor_norm'] = data5

omas/tests/test_omas_plot.py

@@ -52,7 +52,7 @@ def tearDown(self):
         pyplot.close()
 
     def test_quantity(self):
-        self.ods.plot_quantity('core_profiles.profiles_1d.0.electrons.density_thermal', '$n_e$', lw=2)
+        self.ods.plot_quantity('core_profiles.profiles_1d.0.electrons.density', '$n_e$', lw=2)
         self.ods.plot_quantity('@core.*elec.*dens', '$n_e$', lw=2)
         try:
             self.ods.plot_quantity('@core.*')

omas/tests/test_omas_utils.py

@@ -49,7 +49,7 @@ def test_different_ods(self):
         assert isinstance(diff_prof2, list)
         assert 'core_profiles' in ' '.join(diff_prof2)
         ods2.sample_core_profiles()
-        ods2['core_profiles.profiles_1d.0.electrons.density_thermal'][0] = 1.5212
+        ods2['core_profiles.profiles_1d.0.electrons.density'][0] = 1.5212
         diff_prof3 = ods2.diff(ods3)
         assert isinstance(diff_prof3, list)
         assert 'value' in ' '.join(diff_prof3)

sphinx/source/how.rst

@@ -102,13 +102,13 @@ The `ODS` class extends native Python dictionary and list classes with:
 
     .. code-block:: python
 
-        ods['core_profiles.profiles_1d.0.electrons.density_thermal'].xarray()
+        ods['core_profiles.profiles_1d.0.electrons.density'].xarray()
 
 14. Conveniently **plot individual quantities**:
 
     .. code-block:: python
 
-        ods.plot_quantity('core_profiles.profiles_1d.0.electrons.density_thermal')
+        ods.plot_quantity('core_profiles.profiles_1d.0.electrons.density')
 
 15. **Use regular expressions** with ``@`` construct for accessing data and plotting: