Load cyclonic type if present

Author: AntSimi

src/py_eddy_tracker/appli.py

@@ -1,16 +1,21 @@
 # -*- coding: utf-8 -*-
 from py_eddy_tracker import EddyParser
 from py_eddy_tracker.observations.tracking import TrackEddiesObservations
+from netCDF4 import Dataset
 
 
 def merge_eddies():
     parser = EddyParser('Merge eddies')
     parser.add_argument('filename', nargs='+', help='all file to merge')
     parser.add_argument('out', help='output file')
     parser.add_argument('--add_rotation_variable', help='add rotation variables', action='store_true')
-    parser.add_argument('--include_var', nargs='+', type=str, help='use only listed variable, remove_var will be ignored')
+    parser.add_argument('--include_var', nargs='+', type=str, help='use only listed variable')
     args = parser.parse_args()
 
+    if args.include_var is None:
+        with Dataset(args.filename[0]) as h:
+            args.include_var = h.variables.keys()
+
     obs = TrackEddiesObservations.load_file(args.filename[0], raw_data=True, include_vars=args.include_var)
     if args.add_rotation_variable:
         obs = obs.add_rotation_type()

src/py_eddy_tracker/observations/observation.py

@@ -443,17 +443,13 @@ def load_from_zarr(cls, filename, raw_data=False, remove_vars=None, include_vars
         kwargs["track_extra_variables"] = []
         for variable in var_list:
             var_inv = VAR_DESCR_inv[variable]
-            if var_inv == "type_cyc":
-                continue
             if var_inv not in cls.ELEMENTS and var_inv not in array_variables:
                 kwargs["track_extra_variables"].append(var_inv)
         kwargs["raw_data"] = raw_data
         kwargs["only_variables"] = None if include_vars is None else [VAR_DESCR_inv[i] for i in include_vars]
         eddies = cls(size=nb_obs, **kwargs)
         for variable in var_list:
             var_inv = VAR_DESCR_inv[variable]
-            if var_inv == "type_cyc":
-                continue
             logger.debug('%s will be loaded', variable)
             # find unit factor
             factor = 1
@@ -524,17 +520,13 @@ def load_from_netcdf(cls, filename, raw_data=False, remove_vars=None, include_va
             kwargs["track_extra_variables"] = []
             for variable in var_list:
                 var_inv = VAR_DESCR_inv[variable]
-                if var_inv == "type_cyc":
-                    continue
                 if var_inv not in cls.ELEMENTS and var_inv not in array_variables:
                     kwargs["track_extra_variables"].append(var_inv)
             kwargs["raw_data"] = raw_data
             kwargs["only_variables"] = None if include_vars is None else [VAR_DESCR_inv[i] for i in include_vars]
             eddies = cls(size=nb_obs, **kwargs)
             for variable in var_list:
                 var_inv = VAR_DESCR_inv[variable]
-                if var_inv == "type_cyc":
-                    continue
                 # Patch
                 h_nc.variables[variable].set_auto_maskandscale(not raw_data)
                 logger.debug('Up load %s variable%s', variable, ', with raw mode' if raw_data else '')