adding parameters to bash tools

- expose underlying parameters to users (min_overlapp, minimal_area)
- correction of some docstrings

Author: ludwigVonKoopa

src/py_eddy_tracker/appli/network.py

@@ -21,6 +21,16 @@ def build_network():
     parser.add_argument(
         "--window", "-w", type=int, help="Half time window to search eddy", default=1
     )
+
+    parser.add_argument(
+        "--min-overlap", "-p", type=float, help="minimum overlap area to associate observations", default=0.2
+    )
+    parser.add_argument(
+        "--minimal-area",
+            action="store_true",
+            help="If True, use intersection/little polygon, else intersection/union",
+    )
+
     parser.contour_intern_arg()
 
     parser.memory_arg()
@@ -32,7 +42,7 @@ def build_network():
         intern=args.intern,
         memory=args.memory,
     )
-    group = n.group_observations(minimal_area=True)
+    group = n.group_observations(min_overlap=args.min_overlap, minimal_area=args.minimal_area)
     n.build_dataset(group).write_file(filename=args.out)
 
 
@@ -44,6 +54,14 @@ def divide_network():
     parser.add_argument(
         "--window", "-w", type=int, help="Half time window to search eddy", default=1
     )
+    parser.add_argument(
+        "--min-overlap", "-p", type=float, help="minimum overlap area to associate observations", default=0.2
+    )
+    parser.add_argument(
+        "--minimal-area",
+            action="store_true",
+            help="If True, use intersection/little polygon, else intersection/union",
+    )
     args = parser.parse_args()
     contour_name = TrackEddiesObservations.intern(args.intern, public_label=True)
     e = TrackEddiesObservations.load_file(
@@ -52,7 +70,7 @@ def divide_network():
     )
     n = NetworkObservations.from_split_network(
         TrackEddiesObservations.load_file(args.input, raw_data=True),
-        e.split_network(intern=args.intern, window=args.window),
+        e.split_network(intern=args.intern, window=args.window, min_overlap=args.min_overlap, minimal_area=args.minimal_area),
     )
     n.write_file(filename=args.out)
 

src/py_eddy_tracker/observations/network.py

@@ -1701,7 +1701,23 @@ def group_translator(nb, duos):
                 apply_replace(translate, gr_i, gr_j)
         return translate
 
-    def group_observations(self, **kwargs):
+    def group_observations(self, min_overlap=0.2, minimal_area=False):
+        """Store every interaction between identifications
+
+        Parameters
+        ----------
+        minimal_area : bool, optional
+            If True, function will compute intersection/little polygon, else intersection/union, by default False
+
+        min_overlap : float, optional
+            minimum overlap area to associate observations, by default 0.2
+
+        Returns
+        -------
+        TrackEddiesObservations
+            netcdf with interactions
+        """
+
         results, nb_obs = list(), list()
         # To display print only in INFO
         display_iteration = logger.getEffectiveLevel() == logging.INFO
@@ -1715,7 +1731,7 @@ def group_observations(self, **kwargs):
             for j in range(i + 1, min(self.window + i + 1, self.nb_input)):
                 xj, yj = self.buffer.load_contour(self.filenames[j])
                 ii, ij = bbox_intersection(xi, yi, xj, yj)
-                m = vertice_overlap(xi[ii], yi[ii], xj[ij], yj[ij], **kwargs) > 0.2
+                m = vertice_overlap(xi[ii], yi[ii], xj[ij], yj[ij], minimal_area=minimal_area) > min_overlap
                 results.append((i, j, ii[m], ij[m]))
         if display_iteration:
             print()

src/py_eddy_tracker/observations/tracking.py

@@ -656,12 +656,12 @@ def split_network(self, intern=True, **kwargs):
 
     def set_tracks(self, x, y, ids, window, **kwargs):
         """
-        Will split one group (network) in segments
+        Split one group (network) in segments
 
         :param array x: coordinates of group
         :param array y: coordinates of group
         :param ndarray ids: several fields like time, group, ...
-        :param int windows: number of days where observations could missed
+        :param int window: number of days where observations could missed
         """
         time_index = build_index((ids["time"]).astype("i4"))
         nb = x.shape[0]
@@ -713,8 +713,8 @@ def get_previous_obs(
         time_e,
         time_ref,
         window,
-        min_overlap=0.01,
-        **kwargs,
+        min_overlap=0.2,
+        minimal_area=False,
     ):
         """Backward association of observations to the segments"""
         time_cur = int_(ids["time"][i_current])
@@ -730,7 +730,7 @@ def get_previous_obs(
             if len(ii) == 0:
                 continue
             c = zeros(len(xj))
-            c[ij] = vertice_overlap(xi[ii], yi[ii], xj[ij], yj[ij], **kwargs)
+            c[ij] = vertice_overlap(xi[ii], yi[ii], xj[ij], yj[ij], minimal_area=minimal_area)
             # We remove low overlap
             c[c < min_overlap] = 0
             # We get index of maximal overlap
@@ -753,8 +753,8 @@ def get_next_obs(
         time_e,
         time_ref,
         window,
-        min_overlap=0.01,
-        **kwargs,
+        min_overlap=0.2,
+        minimal_area=False,
     ):
         """Forward association of observations to the segments"""
         time_max = time_e.shape[0] - 1
@@ -773,7 +773,7 @@ def get_next_obs(
             if len(ii) == 0:
                 continue
             c = zeros(len(xj))
-            c[ij] = vertice_overlap(xi[ii], yi[ii], xj[ij], yj[ij], **kwargs)
+            c[ij] = vertice_overlap(xi[ii], yi[ii], xj[ij], yj[ij], minimal_area=minimal_area)
             # We remove low overlap
             c[c < min_overlap] = 0
             # We get index of maximal overlap