add new features

examples/16_network/pet_relative.py

@@ -136,6 +136,51 @@
 ax.set_title(f"Clean network ({n_clean.infos()})")
 _ = n_clean.display_timeline(ax)
 
+
+# %%
+# change splittint-merging events
+# ------------------
+# change event where seg A split to B, then A merge into B, to A split to B then B merge into A
+fig, (ax1, ax2) = plt.subplots(2, 1, figsize=(15, 12), dpi=120)
+
+ax1.set_title(f"Clean network ({n_clean.infos()})")
+n_clean.display_timeline(ax1)
+
+clean_modified = n_clean.copy()
+clean_modified.correct_close_events(100)
+ax2.set_title(f"resplitted network ({clean_modified.infos()})")
+_ = clean_modified.display_timeline(ax2)
+
+
+# %%
+# keep only observations where water could propagate from an observation
+# ----------------------------------------------------------------------
+
+fig, (ax1, ax2) = plt.subplots(2, 1, figsize=(15, 12), dpi=120)
+i_observation = 600
+only_linked = n_clean.find_link(i_observation)
+
+for ax, dataset in zip([ax1, ax2], [n_clean, only_linked]):
+    dataset.display_timeline(
+        ax, field="segment", marker="+", lw=2, markersize=5, colors_mode="y"
+    )
+    ax.scatter(
+        n_clean.time[i_observation],
+        n_clean.segment[i_observation],
+        marker="s",
+        s=50,
+        color="black",
+        zorder=200,
+        label="observation start",
+        alpha=0.6,
+    )
+    ax.legend()
+
+ax1.set_title(f"full example ({n_clean.infos()})")
+ax2.set_title(f"only linked observations ({only_linked.infos()})")
+ax2.set_xlim(ax1.get_xlim())
+ax2.set_ylim(ax1.get_ylim())
+
 # %%
 # For further figure we will use clean path
 n = n_clean

src/py_eddy_tracker/observations/network.py

@@ -240,10 +240,188 @@ def from_split_network(cls, group_dataset, indexs, **kwargs):
     def infos(self, label=""):
         return f"{len(self)} obs {unique(self.segment).shape[0]} segments"
 
+    def correct_close_events(self, nb_days_max=20):
+        """
+        transform event where
+        segment A split to B, then A merge into B
+
+        to
+
+        segment A split to B, then B merge to A
+
+        these events are filtered with `nb_days_max`, which the event have to take place in less than `nb_days_max`
+
+        :param float nb_days_max: maximum time to search for splitting-merging event
+        """
+
+        _time = self.time
+        # segment used to correct and track changes
+        segment = self.segment_track_array.copy()
+        # final segment used to copy into self.segment
+        segment_copy = self.segment
+
+        segments_connexion = dict()
+
+        previous_obs, next_obs = self.previous_obs, self.next_obs
+
+        # record for every segments, the slice, indice of next obs & indice of previous obs
+        for i, seg, _ in self.iter_on(segment):
+            if i.start == i.stop:
+                continue
+
+            i_p, i_n = previous_obs[i.start], next_obs[i.stop - 1]
+            segments_connexion[seg] = [i, i_p, i_n]
+
+        for seg in sorted(segments_connexion.keys()):
+            seg_slice, i_seg_p, i_seg_n = segments_connexion[seg]
+
+            # the segment ID has to be corrected, because we may have changed it since
+            seg_corrected = segment[seg_slice.stop - 1]
+
+            # we keep the real segment number
+            seg_corrected_copy = segment_copy[seg_slice.stop - 1]
+
+            n_seg = segment[i_seg_n]
+
+            # if segment has splitting
+            if i_seg_n != -1:
+                seg2_slice, i2_seg_p, i2_seg_n = segments_connexion[n_seg]
+                p2_seg = segment[i2_seg_p]
+
+                # if it merge on the first in a certain time
+                if (p2_seg == seg_corrected) and (
+                    _time[i_seg_n] - _time[i2_seg_p] < nb_days_max
+                ):
+                    my_slice = slice(i_seg_n, seg2_slice.stop)
+                    # correct the factice segment
+                    segment[my_slice] = seg_corrected
+                    # correct the good segment
+                    segment_copy[my_slice] = seg_corrected_copy
+                    previous_obs[i_seg_n] = seg_slice.stop - 1
+
+                    segments_connexion[seg_corrected][0] = my_slice
+
+        self.segment[:] = segment_copy
+        self.previous_obs[:] = previous_obs
+
+        self.sort()
+
+    def sort(self, order=("track", "segment", "time")):
+        """
+        sort observations
+
+        :param tuple order: order or sorting. Passed to `np.argsort`
+        """
+
+        index_order = self.obs.argsort(order=order)
+        for field in self.elements:
+            self[field][:] = self[field][index_order]
+
+        translate = -ones(index_order.max() + 2, dtype="i4")
+        translate[index_order] = arange(index_order.shape[0])
+        self.next_obs[:] = translate[self.next_obs]
+        self.previous_obs[:] = translate[self.previous_obs]
+
     def obs_relative_order(self, i_obs):
         self.only_one_network()
         return self.segment_relative_order(self.segment[i_obs])
 
+    def find_link(self, i_observations, forward=True, backward=False):
+        """
+        find all observations where obs `i_observation` could be
+        in future or past.
+
+        if forward=True, search all observation  where water
+        from obs "i_observation" could go
+
+        if backward=True, search all observation
+        where water from obs `i_observation` could come from
+
+        :param int,iterable(int) i_observation:
+            indices of observation. Can be
+            int, or iterable of int.
+        :param bool forward, backward:
+            if forward, search observations after obs.
+            else mode==backward search before obs
+
+        """
+
+        i_obs = (
+            [i_observations]
+            if not hasattr(i_observations, "__iter__")
+            else i_observations
+        )
+
+        segment = self.segment_track_array
+        previous_obs, next_obs = self.previous_obs, self.next_obs
+
+        segments_connexion = dict()
+
+        for i_slice, seg, _ in self.iter_on(segment):
+            if i_slice.start == i_slice.stop:
+                continue
+
+            i_p, i_n = previous_obs[i_slice.start], next_obs[i_slice.stop - 1]
+            p_seg, n_seg = segment[i_p], segment[i_n]
+
+            # dumping slice into dict
+            if seg not in segments_connexion:
+                segments_connexion[seg] = [i_slice, [], []]
+            else:
+                segments_connexion[seg][0] = i_slice
+
+            if i_p != -1:
+
+                if p_seg not in segments_connexion:
+                    segments_connexion[p_seg] = [None, [], []]
+
+                # backward
+                segments_connexion[seg][2].append((i_slice.start, i_p, p_seg))
+                # forward
+                segments_connexion[p_seg][1].append((i_p, i_slice.start, seg))
+
+            if i_n != -1:
+                if n_seg not in segments_connexion:
+                    segments_connexion[n_seg] = [None, [], []]
+
+                # forward
+                segments_connexion[seg][1].append((i_slice.stop - 1, i_n, n_seg))
+                # backward
+                segments_connexion[n_seg][2].append((i_n, i_slice.stop - 1, seg))
+
+        mask = zeros(segment.size, dtype=bool)
+
+        def func_forward(seg, indice):
+            seg_slice, _forward, _ = segments_connexion[seg]
+
+            mask[indice : seg_slice.stop] = True
+            for i_begin, i_end, seg2 in _forward:
+                if i_begin < indice:
+                    continue
+
+                if not mask[i_end]:
+                    func_forward(seg2, i_end)
+
+        def func_backward(seg, indice):
+            seg_slice, _, _backward = segments_connexion[seg]
+
+            mask[seg_slice.start : indice + 1] = True
+            for i_begin, i_end, seg2 in _backward:
+                if i_begin > indice:
+                    continue
+
+                if not mask[i_end]:
+                    func_backward(seg2, i_end)
+
+        for indice in i_obs:
+            if forward:
+                func_forward(segment[indice], indice)
+
+            if backward:
+                func_backward(segment[indice], indice)
+
+        return self.extract_with_mask(mask)
+
     def connexions(self, multi_network=False):
         """
         create dictionnary for each segments, gives the segments which interact with
@@ -490,14 +668,16 @@ def event_timeline(self, ax, field=None, method=None, factor=1, colors_mode="rol
 
         # TODO : fill mappables dict
         y_seg = dict()
+        _time = self.time
+
         if field is not None and method != "all":
             for i, b0, _ in self.iter_on("segment"):
                 y = self[field][i]
                 if y.shape[0] != 0:
                     y_seg[b0] = y.mean() * factor
         mappables = dict()
         for i, b0, b1 in self.iter_on("segment"):
-            x = self.time[i]
+            x = _time[i]
             if x.shape[0] == 0:
                 continue
 
@@ -532,7 +712,7 @@ def event_timeline(self, ax, field=None, method=None, factor=1, colors_mode="rol
                         else y_seg[seg_next]
                     )
                 )
-                ax.plot((x[-1], self.time[i_n]), (y0, y1), **event_kw)[0]
+                ax.plot((x[-1], _time[i_n]), (y0, y1), **event_kw)[0]
                 events["merging"].append((x[-1], y0))
 
             if i_p != -1:
@@ -548,7 +728,7 @@ def event_timeline(self, ax, field=None, method=None, factor=1, colors_mode="rol
                         else y_seg[seg_previous]
                     )
                 )
-                ax.plot((x[0], self.time[i_p]), (y0, y1), **event_kw)[0]
+                ax.plot((x[0], _time[i_p]), (y0, y1), **event_kw)[0]
                 events["spliting"].append((x[0], y0))
 
             j += 1
@@ -1045,7 +1225,7 @@ def extract_with_mask(self, mask):
             logger.warning("Empty dataset will be created")
         else:
             logger.info(
-                f"{nb_obs} observations will be extract ({nb_obs * 100. / self.shape[0]}%)"
+                f"{nb_obs} observations will be extract ({nb_obs / self.shape[0]:.3%})"
             )
             for field in self.obs.dtype.descr:
                 if field in ("next_obs", "previous_obs"):