diff --git a/.readthedocs.yml b/.readthedocs.yml index 5ac02e12..ba36f8ea 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -9,3 +9,5 @@ python: install: - method: pip path: . +sphinx: + configuration: doc/conf.py \ No newline at end of file diff --git a/CHANGELOG.rst b/CHANGELOG.rst index f8eee72f..6d6d6a30 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -11,14 +11,23 @@ and this project adheres to `Semantic Versioning big).sum()} network with more than {big} obs and the biggest have {nb_by_network.max()} observations ({nb_by_network[nb_by_network> big].sum()} observations cumulate)", + f" with {(nb_by_network > big).sum()} network with more than {big} obs and the biggest have {nb_by_network.max()} observations ({nb_by_network[nb_by_network > big].sum()} observations cumulate)", f" {nb_trash} observations in trash", + f" {lifetime.max()} days max of lifetime", ] return "\n".join(infos) @@ -200,6 +205,13 @@ def ref_segment_track_index(self): @property def ref_index(self): return self.index_network[2] + + @property + def lifetime(self): + """Return lifetime for each observation""" + lt=self.networks_period.astype("int") + nb_by_network=self.network_size() + return lt.repeat(nb_by_network) def network_segment_size(self, id_networks=None): """Get number of segment by network @@ -225,6 +237,15 @@ def network_size(self, id_networks=None): i = id_networks - self.index_network[2] return self.index_network[1][i] - self.index_network[0][i] + @property + def networks_period(self): + """ + Return period for each network + """ + return get_period_with_index(self.time, *self.index_network[:2]) + + + def unique_segment_to_id(self, id_unique): """Return id network and id segment for a unique id @@ -274,7 +295,7 @@ def astype(self, cls): new[k][:] = self[k][:] new.sign_type = self.sign_type return new - + def longer_than(self, nb_day_min=-1, nb_day_max=-1): """ Select network on time duration @@ -1125,23 +1146,29 @@ def segment_track_array(self): self._segment_track_array = build_unique_array(self.segment, self.track) return self._segment_track_array - def birth_event(self): + def birth_event(self, only_index=False): """Extract birth events.""" i_start, _, _ = self.index_segment_track indices = i_start[self.previous_obs[i_start] == -1] if self.first_is_trash(): indices = indices[1:] - return self.extract_event(indices) - + if only_index: + return indices + else : + return self.extract_event(indices) + generation_event = birth_event - def death_event(self): + def death_event(self, only_index=False): """Extract death events.""" _, i_stop, _ = self.index_segment_track indices = i_stop[self.next_obs[i_stop - 1] == -1] - 1 if self.first_is_trash(): indices = indices[1:] - return self.extract_event(indices) + if only_index: + return indices + else : + return self.extract_event(indices) dissipation_event = death_event @@ -1452,7 +1479,7 @@ def plot(self, ax, ref=None, color_cycle=None, **kwargs): j += 1 return mappables - def remove_dead_end(self, nobs=3, ndays=0, recursive=0, mask=None): + def remove_dead_end(self, nobs=3, ndays=0, recursive=0, mask=None, return_mask=False): """ Remove short segments that don't connect several segments @@ -1478,6 +1505,8 @@ def remove_dead_end(self, nobs=3, ndays=0, recursive=0, mask=None): ) # get mask for selected obs m = ~self.segment_mask(segments_keep) + if return_mask: + return ~m self.track[m] = 0 self.segment[m] = 0 self.previous_obs[m] = -1 @@ -1495,6 +1524,8 @@ def remove_dead_end(self, nobs=3, ndays=0, recursive=0, mask=None): self.sort() if recursive > 0: self.remove_dead_end(nobs, ndays, recursive - 1) + + def extract_segment(self, segments, absolute=False): """Extract given segments @@ -1788,8 +1819,8 @@ def date2file(julian_day): ) logger.info( ( - f"coherence {_t} / {range_end-1} ({(_t - range_start) / (range_end - range_start-1):.1%})" - f" : {time.time()-_timestamp:5.2f}s" + f"coherence {_t} / {range_end - 1} ({(_t - range_start) / (range_end - range_start - 1):.1%})" + f" : {time.time() - _timestamp:5.2f}s" ) ) @@ -1865,8 +1896,8 @@ def date2file(julian_day): ) logger.info( ( - f"coherence {_t} / {range_end-1} ({(_t - range_start) / (range_end - range_start-1):.1%})" - f" : {time.time()-_timestamp:5.2f}s" + f"coherence {_t} / {range_end - 1} ({(_t - range_start) / (range_end - range_start - 1):.1%})" + f" : {time.time() - _timestamp:5.2f}s" ) ) return itf_final, ptf_final @@ -2035,6 +2066,7 @@ def group_observations(self, min_overlap=0.2, minimal_area=False, **kwargs): results, nb_obs = list(), list() # To display print only in INFO display_iteration = logger.getEffectiveLevel() == logging.INFO + for i, filename in enumerate(self.filenames): if display_iteration: print(f"{filename} compared to {self.window} next", end="\r") @@ -2065,7 +2097,7 @@ def group_observations(self, min_overlap=0.2, minimal_area=False, **kwargs): nb_alone, nb_obs, nb_gr = (gr == self.NOGROUP).sum(), len(gr), len(unique(gr)) logger.info( f"{nb_alone} alone / {nb_obs} obs, {nb_gr} groups, " - f"{nb_alone *100./nb_obs:.2f} % alone, {(nb_obs - nb_alone) / (nb_gr - 1):.1f} obs/group" + f"{nb_alone * 100. / nb_obs:.2f} % alone, {(nb_obs - nb_alone) / (nb_gr - 1):.1f} obs/group" ) return gr @@ -2316,3 +2348,21 @@ def mask_follow_obs(m, next_obs, time, indexs, dt=3): m[i_next] = True i_next = next_obs[i_next] dt_ = abs(time[i_next] - t0) + + +@njit(cache=True) +def get_period_with_index(t, i0, i1): + """Return peek to peek cover by each slice define by i0 and i1 + + :param array t: array which contain values to estimate spread + :param array i0: index which determine start of slice + :param array i1: index which determine end of slice + :return array: Peek to peek of t + """ + periods = np.empty(i0.size, t.dtype) + for i in range(i0.size): + if i1[i] == i0[i]: + periods[i] = 0 + continue + periods[i] = t[i0[i] : i1[i]].ptp() + return periods diff --git a/src/py_eddy_tracker/observations/tracking.py b/src/py_eddy_tracker/observations/tracking.py index 164f9724..fa1c1f93 100644 --- a/src/py_eddy_tracker/observations/tracking.py +++ b/src/py_eddy_tracker/observations/tracking.py @@ -380,7 +380,7 @@ def extract_toward_direction(self, west=True, delta_lon=None): d_lon = lon[i1] - lon[i0] m = d_lon < 0 if west else d_lon > 0 if delta_lon is not None: - m *= delta_lon < d_lon + m *= delta_lon < abs(d_lon) m = m.repeat(nb) return self.extract_with_mask(m)