Remove reference to obs or observation to be easily replace by store later

Author: AntSimi

src/py_eddy_tracker/observations/groups.py

@@ -292,15 +292,14 @@ def filled_by_interpolation(self, mask):
         nb_obs = len(self)
         index = arange(nb_obs)
 
-        for field in self.obs.dtype.descr:
-            var = field[0]
+        for field in self.fields:
             if (
-                var in ["n", "virtual", "track", "cost_association"]
-                or var in self.array_variables
+                field in ["n", "virtual", "track", "cost_association"]
+                or field in self.array_variables
             ):
                 continue
-            self.obs[var][mask] = interp(
-                index[mask], index[~mask], self.obs[var][~mask]
+            self.obs[field][mask] = interp(
+                index[mask], index[~mask], self.obs[field][~mask]
             )
 
     def insert_virtual(self):

src/py_eddy_tracker/observations/observation.py

@@ -264,7 +264,7 @@ def get_infos(self):
             bins_lat=(-90, -60, -15, 15, 60, 90),
             bins_amplitude=array((0, 1, 2, 3, 4, 5, 10, 500)),
             bins_radius=array((0, 15, 30, 45, 60, 75, 100, 200, 2000)),
-            nb_obs=self.observations.shape[0],
+            nb_obs=len(self),
         )
         t0, t1 = self.period
         infos["t0"], infos["t1"] = t0, t1
@@ -341,7 +341,7 @@ def __repr__(self):
         bins_lat = (-90, -60, -15, 15, 60, 90)
         bins_amplitude = array((0, 1, 2, 3, 4, 5, 10, 500))
         bins_radius = array((0, 15, 30, 45, 60, 75, 100, 200, 2000))
-        nb_obs = self.observations.shape[0]
+        nb_obs = len(self)
 
         return f"""    | {nb_obs} observations from {t0} to {t1} ({period} days, ~{nb_obs / period:.0f} obs/day)
     |   Speed area      : {self.speed_area.sum() / period / 1e12:.2f} Mkm²/day
@@ -416,7 +416,7 @@ def remove_fields(self, *fields):
         """
         Copy with fields listed remove
         """
-        nb_obs = self.obs.shape[0]
+        nb_obs = len(self)
         fields = set(fields)
         only_variables = set(self.fields) - fields
         track_extra_variables = set(self.track_extra_variables) - fields
@@ -439,7 +439,7 @@ def add_fields(self, fields=list(), array_fields=list()):
         """
         Add a new field.
         """
-        nb_obs = self.obs.shape[0]
+        nb_obs = len(self)
         new = self.__class__(
             size=nb_obs,
             track_extra_variables=list(
@@ -547,9 +547,9 @@ def merge(self, other):
         nb_obs_self = len(self)
         nb_obs = nb_obs_self + len(other)
         eddies = self.new_like(self, nb_obs)
-        other_keys = other.obs.dtype.fields.keys()
-        self_keys = self.obs.dtype.fields.keys()
-        for key in eddies.obs.dtype.fields.keys():
+        other_keys = other.fields
+        self_keys = self.fields
+        for key in eddies.fields:
             eddies.obs[key][:nb_obs_self] = self.obs[key][:]
             if key in other_keys:
                 eddies.obs[key][nb_obs_self:] = other.obs[key][:]
@@ -657,8 +657,8 @@ def insert_observations(self, other, index):
         """Insert other obs in self at the given index."""
         if not self.coherence(other):
             raise Exception("Observations with no coherence")
-        insert_size = len(other.obs)
-        self_size = len(self.obs)
+        insert_size = len(other)
+        self_size = len(self)
         new_size = self_size + insert_size
         if self_size == 0:
             self.observations = other.obs
@@ -1542,8 +1542,7 @@ def to_zarr(self, handler, **kwargs):
             handler.attrs["track_array_variables"] = self.track_array_variables
             handler.attrs["array_variables"] = ",".join(self.array_variables)
         # Iter on variables to create:
-        fields = [field[0] for field in self.observations.dtype.descr]
-        for ori_name in fields:
+        for ori_name in self.fields:
             # Patch for a transition
             name = ori_name
             #
@@ -1588,12 +1587,11 @@ def to_netcdf(self, handler, **kwargs):
             handler.track_array_variables = self.track_array_variables
             handler.array_variables = ",".join(self.array_variables)
         # Iter on variables to create:
-        fields = [field[0] for field in self.observations.dtype.descr]
         fields_ = array(
-            [VAR_DESCR[field[0]]["nc_name"] for field in self.observations.dtype.descr]
+            [VAR_DESCR[field]["nc_name"] for field in self.fields]
         )
         i = fields_.argsort()
-        for ori_name in array(fields)[i]:
+        for ori_name in array(self.fields)[i]:
             # Patch for a transition
             name = ori_name
             #
@@ -1865,10 +1863,9 @@ def extract_with_mask(self, mask):
         if nb_obs == 0:
             logger.warning("Empty dataset will be created")
         else:
-            for field in self.obs.dtype.descr:
+            for field in self.fields:
                 logger.debug("Copy of field %s ...", field)
-                var = field[0]
-                new.obs[var] = self.obs[var][mask]
+                new.obs[field] = self.obs[field][mask]
         return new
 
     def scatter(self, ax, name=None, ref=None, factor=1, **kwargs):

src/py_eddy_tracker/observations/tracking.py

@@ -118,7 +118,7 @@ def __repr__(self):
         t0, t1 = self.period
         period = t1 - t0 + 1
         nb = self.nb_obs_by_track
-        nb_obs = self.observations.shape[0]
+        nb_obs = len(self)
         m = self.virtual.astype("bool")
         nb_m = m.sum()
         bins_t = (1, 30, 90, 180, 270, 365, 1000, 10000)
@@ -147,7 +147,7 @@ def __repr__(self):
 
     def add_distance(self):
         """Add a field of distance (m) between two consecutive observations, 0 for the last observation of each track"""
-        if "distance_next" in self.observations.dtype.descr:
+        if "distance_next" in self.fields:
             return self
         new = self.add_fields(("distance_next",))
         new["distance_next"][:1] = self.distance_to_next()
@@ -205,10 +205,9 @@ def extract_longer_eddies(self, nb_min, nb_obs, compress_id=True):
         logger.info("Selection of %d observations", nb_obs_select)
         eddies = self.__class__.new_like(self, nb_obs_select)
         eddies.sign_type = self.sign_type
-        for field in self.obs.dtype.descr:
+        for field in self.fields:
             logger.debug("Copy of field %s ...", field)
-            var = field[0]
-            eddies.obs[var] = self.obs[var][mask]
+            eddies.obs[field] = self.obs[field][mask]
         if compress_id:
             list_id = unique(eddies.obs.track)
             list_id.sort()
@@ -387,13 +386,13 @@ def extract_toward_direction(self, west=True, delta_lon=None):
 
     def extract_first_obs_in_box(self, res):
         data = empty(
-            self.obs.shape, dtype=[("lon", "f4"), ("lat", "f4"), ("track", "i4")]
+            len(self), dtype=[("lon", "f4"), ("lat", "f4"), ("track", "i4")]
         )
         data["lon"] = self.longitude - self.longitude % res
         data["lat"] = self.latitude - self.latitude % res
         data["track"] = self.track
         _, indexs = unique(data, return_index=True)
-        mask = zeros(self.obs.shape, dtype="bool")
+        mask = zeros(len(self), dtype="bool")
         mask[indexs] = True
         return self.extract_with_mask(mask)
 
@@ -508,10 +507,9 @@ def extract_with_mask(
         if nb_obs == 0:
             logger.info("Empty dataset will be created")
         else:
-            for field in self.obs.dtype.descr:
+            for field in self.fields:
                 logger.debug("Copy of field %s ...", field)
-                var = field[0]
-                new.obs[var] = self.obs[var][mask]
+                new.obs[field] = self.obs[field][mask]
             if compress_id:
                 list_id = unique(new.track)
                 list_id.sort()