Replace NaN with nan

omas/machine_mappings/d3d.py

@@ -1048,7 +1048,7 @@ def langmuir_probes_data(ods, pulse, _get_measurements=True):
                 printd('  Probe i={i:}, j={j:}, label={label:} passed the check; r={r:}, z={z:}'.format(**locals()), topic='machine')
                 ods['langmuir_probes.embedded'][j]['position.r'] = r
                 ods['langmuir_probes.embedded'][j]['position.z'] = z
-                ods['langmuir_probes.embedded'][j]['position.phi'] = np.NaN  # Didn't find this in MDSplus
+                ods['langmuir_probes.embedded'][j]['position.phi'] = np.nan  # Didn't find this in MDSplus
                 ods['langmuir_probes.embedded'][j]['identifier'] = 'PROBE_{:03d}: PNUM={}'.format(i, pnum)
                 ods['langmuir_probes.embedded'][j]['name'] = str(label).strip()
                 if _get_measurements:
@@ -1506,7 +1506,7 @@ def core_profiles_global_quantities_data(ods, pulse):
 
         m = mdsvalue('d3d', pulse=pulse, TDI=f"ptdata2(\"VLOOP\",{pulse})", treename=None)
 
-        gq['v_loop'] = interp1d(m.dim_of(0) * 1e-3, m.data(), bounds_error=False, fill_value=np.NaN)(t)
+        gq['v_loop'] = interp1d(m.dim_of(0) * 1e-3, m.data(), bounds_error=False, fill_value=np.nan)(t)
 
 
 # ================================

omas/machine_mappings/east.py

@@ -153,7 +153,7 @@ def setup_langmuir_probes_hardware_description_east(ods, pulse):
                     identifier = '{}{:02d}'.format(corner.upper(), probe_number)
                     ods['langmuir_probes.embedded'][j]['position.r'] = r[i]
                     ods['langmuir_probes.embedded'][j]['position.z'] = z[i]
-                    ods['langmuir_probes.embedded'][j]['position.phi'] = np.NaN  # Didn't find this in MDSplus
+                    ods['langmuir_probes.embedded'][j]['position.phi'] = np.nan  # Didn't find this in MDSplus
                     ods['langmuir_probes.embedded'][j]['identifier'] = identifier
                     ods['langmuir_probes.embedded'][j]['name'] = identifier
                     j += 1

omas/machine_mappings/python_tdi.py

@@ -25,7 +25,7 @@ def nan_where(a, b, n):
 
     a = a.data()
     b = b.data()
-    a[b == n] = np.NaN
+    a[b == n] = np.nan
     return a
 
 def get_largest_axis_value(a, b):

omas/omas_json.py

@@ -75,9 +75,9 @@ def base_class(x):
         clsODS = lambda: ODS(imas_version=imas_version, consistency_check=False)
         clsODC = lambda: ODC(imas_version=imas_version, consistency_check=False)
         try:
-            tmp = json_loader(x, clsODS, null_to=numpy.NaN)
+            tmp = json_loader(x, clsODS, null_to=numpy.nan)
         except Exception:
-            tmp = json_loader(x, clsODC, null_to=numpy.NaN)
+            tmp = json_loader(x, clsODC, null_to=numpy.nan)
         return tmp
 
     tmp = json.loads(json_string, object_pairs_hook=lambda x: base_class(x), **kw)

omas/omas_plot.py

@@ -3250,8 +3250,8 @@ def charge_exchange_overlay(ods, ax=None, which_pos='closest', **kw):
     label_dr, label_dz = label_shifter(nc, kw)
 
     # Get channel positions; each channel has a list of positions as it can vary with time as beams switch on/off.
-    r = [[numpy.NaN]] * nc
-    z = [[numpy.NaN]] * nc
+    r = [[numpy.nan]] * nc
+    z = [[numpy.nan]] * nc
     for i in range(nc):
         rs = ods['charge_exchange.channel'][i]['position.r.data']
         zs = ods['charge_exchange.channel'][i]['position.z.data']
@@ -3618,7 +3618,7 @@ def position_control_overlay(
     b = ods['pulse_schedule.position_control.boundary_outline']
     x = ods['pulse_schedule.position_control.x_point']
     s = ods['pulse_schedule.position_control.strike_point']
-    ikw = dict(bounds_error=False, fill_value=np.NaN)
+    ikw = dict(bounds_error=False, fill_value=np.nan)
     try:
         nbp = np.shape(b['[:].r.reference'])[0]
     except (IndexError, ValueError):
@@ -3656,7 +3656,7 @@ def position_control_overlay(
             rxm = [interp1d(eq['time'], eq['time_slice[:].boundary.x_point.{}.r'.format(i)], **ikw)(t) for i in range(nxm)]
             zxm = [interp1d(eq['time'], eq['time_slice[:].boundary.x_point.{}.z'.format(i)], **ikw)(t) for i in range(nxm)]
     else:
-        rxm = zxm = np.NaN
+        rxm = zxm = np.nan
     if timing_ref is not None:
         print(time.time() - timing_ref, 'position_control_overlay data unpacked')
 

omas/omas_sample.py

@@ -586,19 +586,19 @@ def langmuir_probes(ods):
     ods['langmuir_probes.embedded.1.name'] = 'p23'
     ods['langmuir_probes.embedded.1.position.r'] = 0.9
     ods['langmuir_probes.embedded.1.position.z'] = -0.9
-    ods['langmuir_probes.embedded.1.position.phi'] = numpy.NaN
+    ods['langmuir_probes.embedded.1.position.phi'] = numpy.nan
 
     ods['langmuir_probes.embedded.2.identifier'] = -2
     ods['langmuir_probes.embedded.2.name'] = 'blah'
     ods['langmuir_probes.embedded.2.position.r'] = 1.5
     ods['langmuir_probes.embedded.2.position.z'] = -1.25
-    ods['langmuir_probes.embedded.2.position.phi'] = numpy.NaN
+    ods['langmuir_probes.embedded.2.position.phi'] = numpy.nan
 
     ods['langmuir_probes.embedded.3.identifier'] = -3
     ods['langmuir_probes.embedded.3.name'] = 'donkey!'
     ods['langmuir_probes.embedded.3.position.r'] = 1.525
     ods['langmuir_probes.embedded.3.position.z'] = -1.25
-    ods['langmuir_probes.embedded.3.position.phi'] = numpy.NaN
+    ods['langmuir_probes.embedded.3.position.phi'] = numpy.nan
 
     ods['langmuir_probes.embedded.4.identifier'] = -4
     ods['langmuir_probes.embedded.4.name'] = 'zzz'
@@ -610,7 +610,7 @@ def langmuir_probes(ods):
     ods['langmuir_probes.embedded.5.name'] = "it's just a test"
     ods['langmuir_probes.embedded.5.position.r'] = 2.45
     ods['langmuir_probes.embedded.5.position.z'] = 0.25
-    ods['langmuir_probes.embedded.5.position.phi'] = numpy.NaN
+    ods['langmuir_probes.embedded.5.position.phi'] = numpy.nan
 
     return ods
 
@@ -691,10 +691,10 @@ def add_position_control(ods_):
             bdry[i]['r.reference_name'] = bdry[i]['z.reference_name'] = 'seg{}'.format(i)
 
         strk = ods_['pulse_schedule.position_control.strike_point']
-        strk[0]['r.reference'] = numpy.array([numpy.NaN, 1.35, 1.35, 1.35, 1.35, 1.35, 1.35, 1.35, numpy.NaN, numpy.NaN])
-        strk[0]['z.reference'] = numpy.array([numpy.NaN, -1.35, -1.35, -1.35, -1.35, -1.35, -1.35, -1.35, numpy.NaN, numpy.NaN])
-        strk[1]['r.reference'] = numpy.array([numpy.NaN, 1.02, 1.02, 1.02, 1.02, 1.02, 1.02, 1.02, numpy.NaN, numpy.NaN])
-        strk[1]['z.reference'] = numpy.array([numpy.NaN, -1.2, -1.2, -1.2, -1.2, -1.2, -1.2, -1.2, numpy.NaN, numpy.NaN])
+        strk[0]['r.reference'] = numpy.array([numpy.nan, 1.35, 1.35, 1.35, 1.35, 1.35, 1.35, 1.35, numpy.nan, numpy.nan])
+        strk[0]['z.reference'] = numpy.array([numpy.nan, -1.35, -1.35, -1.35, -1.35, -1.35, -1.35, -1.35, numpy.nan, numpy.nan])
+        strk[1]['r.reference'] = numpy.array([numpy.nan, 1.02, 1.02, 1.02, 1.02, 1.02, 1.02, 1.02, numpy.nan, numpy.nan])
+        strk[1]['z.reference'] = numpy.array([numpy.nan, -1.2, -1.2, -1.2, -1.2, -1.2, -1.2, -1.2, numpy.nan, numpy.nan])
 
         for i in range(2):
             strk[i]['r.reference_type'] = strk[i]['z.reference_type'] = 1
@@ -703,8 +703,8 @@ def add_position_control(ods_):
         xpt = ods_['pulse_schedule.position_control.x_point']
         xpt[0]['r.reference'] = numpy.array([1.1, 1.34, 1.34, 1.43, 1.43, 1.43, 1.43, 1.43, 1.13, 1.13])
         xpt[0]['z.reference'] = numpy.array([-1.6, -1.21, -1.21, -1.15, -1.15, -1.15, -1.15, -1.15, -1.41, -1.41])
-        xpt[1]['r.reference'] = numpy.array([numpy.NaN] * len(t))
-        xpt[1]['z.reference'] = numpy.array([numpy.NaN] * len(t))
+        xpt[1]['r.reference'] = numpy.array([numpy.nan] * len(t))
+        xpt[1]['z.reference'] = numpy.array([numpy.nan] * len(t))
 
         for i in range(2):
             xpt[i]['r.reference_type'] = xpt[i]['z.reference_type'] = 1