introduction of a cost function

Author: adelepoulle

src/py_eddy_tracker/observations.py

@@ -236,14 +236,36 @@ def load_from_netcdf(filename):
             eddies.sign_type = h_nc.variables['cyc'][0]
         return eddies
 
+    def cost_function(self, records_in, records_out):
+        cost = ((records_in['amplitude'] - records_out['amplitude']
+                 ) / records_in['amplitude']
+                ) ** 2
+        cost += ((records_in['radius_s'] - records_out['radius_s']
+                  ) / records_in['radius_s']
+                 ) ** 2
+        return cost ** 0.5
+
     def tracking(self, other):
         """Track obs between self and other
         """
-        cost = self.distance(other)
+        dist = self.distance(other)
+        # Links available which are close (circle area selection)
+        mask_accept_dist = dist < 100
+        indexs_closest = where(mask_accept_dist)
+        cost_values = self.cost_function(
+            self.obs[indexs_closest[0]],
+            other.obs[indexs_closest[1]])
+
+        cost_mat = ma.empty(dist.shape, dtype='f4')
+        cost_mat.mask = -mask_accept_dist
+        cost_mat[mask_accept_dist] = cost_values
         # Links available which respect a maximal cost
-        mask_accept_cost = cost < 40
+        cost = dist
+        mask_accept_cost = cost < 100
         cost = ma.array(cost, mask=-mask_accept_cost, dtype='i2')
 
+        mask_accept_cost = mask_accept_dist
+        cost = cost_mat
         # Count number of link by self obs and other obs
         self_links = mask_accept_cost.sum(axis=1)
         other_links = mask_accept_cost.sum(axis=0)

src/py_eddy_tracker/tracking.py

@@ -186,7 +186,10 @@ def recense_dead_id_to_extend(self):
         self.previous_virtual_obs = self.virtual_obs
         # Creation of an virtual step for dead one
         self.virtual_obs = VirtualEddiesObservations(
-            size=nb_dead + nb_virtual_extend)
+            size=nb_dead + nb_virtual_extend, 
+            track_extra_variables=self.previous_obs.track_extra_variables,
+            track_array_variables=self.previous_obs.track_array_variables,
+            array_variables=self.previous_obs.array_variables)
 
         # Find mask/index on previous correspondance to extrapolate
         # position
@@ -200,6 +203,11 @@ def recense_dead_id_to_extend(self):
         # Position N-1 : B
         # Virtual Position : C
         # New position C = B + AB
+        for key in obs_b.dtype.fields.keys():
+            if key in ['lon', 'lat', 'time', 'track', 'segment_size',
+                       'dlon', 'dlat'] or 'contour_' in key:
+                continue
+            self.virtual_obs[key][:nb_dead] = obs_b[key]
         self.virtual_obs['dlon'][:nb_dead] = obs_b['lon'] - obs_a['lon']
         self.virtual_obs['dlat'][:nb_dead] = obs_b['lat'] - obs_a['lat']
         self.virtual_obs['lon'][:nb_dead