adding support for signals which use other signals as mappings, such as ppf/hrts/te (profile) and ppf/hrts/rho (rho coordinate)

Julian Kates-Harbeck · Julian Kates-Harbeck · commit bb58957f855a · 2017-12-14T00:28:10.000-05:00
diff --git a/data/signals.py b/data/signals.py
@@ -137,33 +137,33 @@ def fetch_nstx_data(signal_path,shot_num,c):
 
 profile_num_channels = 64
 #ZIPFIT comes from actual measurements
-etemp_profile = ProfileSignal("Electron temperature profile",["ZIPFIT01/PROFILES.ETEMPFIT"],[d3d],causal_shifts=[10],mapping_range=(0,1),num_channels=profile_num_channels,data_avail_tolerance=0.02)
-edens_profile = ProfileSignal("Electron density profile",["ZIPFIT01/PROFILES.EDENSFIT"],[d3d],causal_shifts=[10],mapping_range=(0,1),num_channels=profile_num_channels,data_avail_tolerance=0.02)
-itemp_profile = ProfileSignal("Ion temperature profile",["ZIPFIT01/PROFILES.ITEMPFIT"],[d3d],causal_shifts=[10],mapping_range=(0,1),num_channels=profile_num_channels,data_avail_tolerance=0.02)
-zdens_profile = ProfileSignal("Impurity density profile",["ZIPFIT01/PROFILES.ZDENSFIT"],[d3d],causal_shifts=[10],mapping_range=(0,1),num_channels=profile_num_channels,data_avail_tolerance=0.02)
-trot_profile = ProfileSignal("Rotation profile",["ZIPFIT01/PROFILES.TROTFIT"],[d3d],causal_shifts=[10],mapping_range=(0,1),num_channels=profile_num_channels,data_avail_tolerance=0.02)
-pthm_profile = ProfileSignal("Thermal pressure profile",["ZIPFIT01/PROFILES.PTHMFIT"],[d3d],causal_shifts=[10],mapping_range=(0,1),num_channels=profile_num_channels,data_avail_tolerance=0.02)# thermal pressure doesn't include fast ions
-neut_profile = ProfileSignal("Neutrals profile",["ZIPFIT01/PROFILES.NEUTFIT"],[d3d],causal_shifts=[10],mapping_range=(0,1),num_channels=profile_num_channels,data_avail_tolerance=0.02)
+etemp_profile = ProfileSignal("Electron temperature profile",["ppf/hrts/te","ZIPFIT01/PROFILES.ETEMPFIT"],[jet,d3d],mapping_paths=["ppf/hrts/rho",None],causal_shifts=[25,10],mapping_range=(0,1),num_channels=profile_num_channels,data_avail_tolerances=[0.05,0.02])
+edens_profile = ProfileSignal("Electron density profile",["ppf/hrts/ne","ZIPFIT01/PROFILES.EDENSFIT"],[jet,d3d],mapping_paths=["ppf/hrts/rho",None],causal_shifts=[25,10],mapping_range=(0,1),num_channels=profile_num_channels,data_avail_tolerances=[0.05,0.02])
+itemp_profile = ProfileSignal("Ion temperature profile",["ZIPFIT01/PROFILES.ITEMPFIT"],[d3d],causal_shifts=[10],mapping_range=(0,1),num_channels=profile_num_channels,data_avail_tolerances=[0.02])
+zdens_profile = ProfileSignal("Impurity density profile",["ZIPFIT01/PROFILES.ZDENSFIT"],[d3d],causal_shifts=[10],mapping_range=(0,1),num_channels=profile_num_channels,data_avail_tolerances=[0.02])
+trot_profile = ProfileSignal("Rotation profile",["ZIPFIT01/PROFILES.TROTFIT"],[d3d],causal_shifts=[10],mapping_range=(0,1),num_channels=profile_num_channels,data_avail_tolerances=[0.02])
+pthm_profile = ProfileSignal("Thermal pressure profile",["ZIPFIT01/PROFILES.PTHMFIT"],[d3d],causal_shifts=[10],mapping_range=(0,1),num_channels=profile_num_channels,data_avail_tolerances=[0.02])# thermal pressure doesn't include fast ions
+neut_profile = ProfileSignal("Neutrals profile",["ZIPFIT01/PROFILES.NEUTFIT"],[d3d],causal_shifts=[10],mapping_range=(0,1),num_channels=profile_num_channels,data_avail_tolerances=[0.02])
 
-q_profile = ProfileSignal("Q profile",["ZIPFIT01/PROFILES.BOOTSTRAP.QRHO"],[d3d],causal_shifts=[10],mapping_range=(0,1),num_channels=profile_num_channels,data_avail_tolerance=0.02)#compare to just q95
-bootstrap_current_profile = ProfileSignal("Rotation profile",["ZIPFIT01/PROFILES.BOOTSTRAP.JBS_SAUTER"],[d3d],causal_shifts=[10],mapping_range=(0,1),num_channels=profile_num_channels,data_avail_tolerance=0.02)
+q_profile = ProfileSignal("Q profile",["ZIPFIT01/PROFILES.BOOTSTRAP.QRHO"],[d3d],causal_shifts=[10],mapping_range=(0,1),num_channels=profile_num_channels,data_avail_tolerances=[0.02])#compare to just q95
+bootstrap_current_profile = ProfileSignal("Rotation profile",["ZIPFIT01/PROFILES.BOOTSTRAP.JBS_SAUTER"],[d3d],causal_shifts=[10],mapping_range=(0,1),num_channels=profile_num_channels,data_avail_tolerances=[0.02])
 
-#equilibrium_image = 2DSignal("2D Magnetic Equilibrium",["EFIT01/RESULTS.GEQDSK.PSIRZ"],[d3d],causal_shifts=[10],mapping_range=(0,1),num_channels=profile_num_channels,data_avail_tolerance=0.02)
+#equilibrium_image = 2DSignal("2D Magnetic Equilibrium",["EFIT01/RESULTS.GEQDSK.PSIRZ"],[d3d],causal_shifts=[10],mapping_range=(0,1),num_channels=profile_num_channels,data_avail_tolerances=[0.02])
 
 #EFIT is the inverse problem from external magnetic measurements
-#pressure_profile = ProfileSignal("Pressure profile",["EFIT01/RESULTS.GEQDSK.PRES"],[d3d],causal_shifts=[10],mapping_range=(0,1),num_channels=profile_num_channels,data_avail_tolerance=0.02)# pressure might be unphysical since it is not constrained by measurements, only the EFIT which does not know about density and temperature
-q_psi_profile = ProfileSignal("Q(psi) profile",["EFIT01/RESULTS.GEQDSK.QPSI"],[d3d],causal_shifts=[10],mapping_range=(0,1),num_channels=profile_num_channels,data_avail_tolerance=0.02)
+#pressure_profile = ProfileSignal("Pressure profile",["EFIT01/RESULTS.GEQDSK.PRES"],[d3d],causal_shifts=[10],mapping_range=(0,1),num_channels=profile_num_channels,data_avail_tolerances=[0.02])# pressure might be unphysical since it is not constrained by measurements, only the EFIT which does not know about density and temperature
+q_psi_profile = ProfileSignal("Q(psi) profile",["EFIT01/RESULTS.GEQDSK.QPSI"],[d3d],causal_shifts=[10],mapping_range=(0,1),num_channels=profile_num_channels,data_avail_tolerances=[0.02])
 
 
 # epress_profile_spatial = ProfileSignal("Electron pressure profile",["ppf/hrts/pe/"],[jet],causal_shifts=[25],mapping_range=(2,4),num_channels=profile_num_channels)
-etemp_profile_spatial = ProfileSignal("Electron temperature profile",["ppf/hrts/te"],[jet],causal_shifts=[25],mapping_range=(2,4),num_channels=profile_num_channels,data_avail_tolerance=0.05)
-edens_profile_spatial = ProfileSignal("Electron density profile",["ppf/hrts/ne"],[jet],causal_shifts=[25],mapping_range=(2,4),num_channels=profile_num_channels,data_avail_tolerance=0.05)
-rho_profile_spatial = ProfileSignal("Rho at spatial positions",["ppf/hrts/rho"],[jet],causal_shifts=[25],mapping_range=(2,4),num_channels=profile_num_channels,data_avail_tolerance=0.05)
+etemp_profile_spatial = ProfileSignal("Electron temperature profile",["ppf/hrts/te"],[jet],causal_shifts=[25],mapping_range=(2,4),num_channels=profile_num_channels,data_avail_tolerances=[0.05])
+edens_profile_spatial = ProfileSignal("Electron density profile",["ppf/hrts/ne"],[jet],causal_shifts=[25],mapping_range=(2,4),num_channels=profile_num_channels,data_avail_tolerances=[0.05])
+rho_profile_spatial = ProfileSignal("Rho at spatial positions",["ppf/hrts/rho"],[jet],causal_shifts=[25],mapping_range=(2,4),num_channels=profile_num_channels,data_avail_tolerances=[0.05])
 
-etemp = Signal("electron temperature",["ppf/hrtx/te0"],[jet],causal_shifts=[25],data_avail_tolerance=0.05)
+etemp = Signal("electron temperature",["ppf/hrtx/te0"],[jet],causal_shifts=[25],data_avail_tolerances=[0.05])
 # epress = Signal("electron pressure",["ppf/hrtx/pe0/"],[jet],causal_shifts=[25])
 
-q95 = Signal("q95 safety factor",['ppf/efit/q95',"EFIT01/RESULTS.AEQDSK.Q95"],[jet,d3d],causal_shifts=[15,10],normalize=False,data_avail_tolerance=0.03)
+q95 = Signal("q95 safety factor",['ppf/efit/q95',"EFIT01/RESULTS.AEQDSK.Q95"],[jet,d3d],causal_shifts=[15,10],normalize=False,data_avail_tolerances=[0.03,0.02])
 
 ip = Signal("plasma current",["jpf/da/c2-ipla","d3d/ipspr15V"],[jet,d3d],is_ip=True) #"d3d/ipsip" was used before, ipspr15V seems to be available for a superset of shots.
 iptarget = Signal("plasma current target",["d3d/ipsiptargt"],[d3d])
diff --git a/plasma/primitives/data.py b/plasma/primitives/data.py
@@ -15,7 +15,10 @@
 #           self.signals.append(Signal(signal_descriptions[i],signal_paths[i]))
 
 class Signal(object):
-    def __init__(self,description,paths,machines,tex_label=None,causal_shifts=None,is_ip=False,normalize=True,data_avail_tolerance=0,is_strictly_positive=False):
+    def __init__(self,description,paths,machines,tex_label=None,
+        causal_shifts=None,is_ip=False,normalize=True,
+        data_avail_tolerances=None,is_strictly_positive=False,
+        mapping_paths=None):
         assert(len(paths) == len(machines))
         self.description = description
         self.paths = paths
@@ -26,8 +29,11 @@ def __init__(self,description,paths,machines,tex_label=None,causal_shifts=None,i
         self.is_ip = is_ip
         self.num_channels = 1
         self.normalize = normalize
-        self.data_avail_tolerance = data_avail_tolerance
+        if data_avail_tolerances == None:
+            data_avail_tolerances = [0 for m in machines]
+        self.data_avail_tolerances = data_avail_tolerances
         self.is_strictly_positive=is_strictly_positive
+        self.mapping_paths = mapping_paths
 
     def is_strictly_positive_fn(self):
         return self.is_strictly_positive
@@ -112,10 +118,21 @@ def get_path(self,machine):
         idx = self.get_idx(machine)
         return self.paths[idx]
 
+    def get_mapping_path(self,machine):
+        if self.mapping_paths is None:
+            return None
+        else:
+            idx = self.get_idx(machine)
+            return self.mapping_paths[idx]    
+
     def get_causal_shift(self,machine):
         idx = self.get_idx(machine)
         return self.causal_shifts[idx]
 
+    def get_data_avail_tolerance(self,machine):
+        idx = self.get_idx(machine)
+        return self.data_avail_tolerances[idx]
+
     def get_idx(self,machine):
         assert(machine in self.machines)
         idx = self.machines.index(machine)  
@@ -143,8 +160,8 @@ def __repr__(self):
         return self.description
 
 class ProfileSignal(Signal):
-    def __init__(self,description,paths,machines,tex_label=None,causal_shifts=None,mapping_range=(0,1),num_channels=32,data_avail_tolerance=0,is_strictly_positive=False):
-        super(ProfileSignal, self).__init__(description,paths,machines,tex_label,causal_shifts,is_ip=False,data_avail_tolerance=data_avail_tolerance,is_strictly_positive=is_strictly_positive)
+    def __init__(self,description,paths,machines,tex_label=None,causal_shifts=None,mapping_range=(0,1),num_channels=32,data_avail_tolerances=None,is_strictly_positive=False,mapping_paths=None):
+        super(ProfileSignal, self).__init__(description,paths,machines,tex_label,causal_shifts,is_ip=False,data_avail_tolerance=data_avail_tolerance,is_strictly_positive=is_strictly_positive,mapping_paths=mapping_paths)
         self.mapping_range = mapping_range
         self.num_channels = num_channels
 
@@ -195,10 +212,18 @@ def get_connection(self):
 
     def fetch_data(self,signal,shot_num,c):
         path = signal.get_path(self)
+        mapping_path = signal.get_mapping_path(self)
         success = False
         mapping = None
         try:
             time,data,mapping,success = self.fetch_data_fn(path,shot_num,c)
+            if mapping_path is not None:
+                time_map,data_map,mapping_map,success_map = self.fetch_data_fn(mapping_path,shot_num,c)
+                assert(time == time_map), "time for signal {} and mapping {} don't align: \n{}\n\n{}\n".format(path,mapping_path,time,time_map)
+                success = (success and success_map)
+                if not success:
+                    print("No success for signal {} and mapping {}".format(path,mapping_path))
+                mapping = data_map
         except Exception as e:
             time,data = create_missing_value_filler()
             print(e)
diff --git a/plasma/primitives/shots.py b/plasma/primitives/shots.py
@@ -401,11 +401,11 @@ def get_signals_and_times_from_file(self,conf):
                 signal_arrays.append(sig)
                 time_arrays.append(t)
                 if self.is_disruptive and self.t_disrupt > np.max(t):
-                    if self.t_disrupt > np.max(t) + signal.data_avail_tolerance:
+                    if self.t_disrupt > np.max(t) + signal.get_data_avail_tolerance(self.machine):
                         print('Shot {}: disruption event is not contained in valid time region of signal {} by {}s, omitting.'.format(self.number,signal,self.t_disrupt - np.max(t)))
                         valid = False 
                     else:
-                        t_max = np.max(t) + signal.data_avail_tolerance
+                        t_max = np.max(t) + signal.get_data_avail_tolerance(self.machine)
                 else:
                     t_max = min(t_max,np.max(t))
 
