Add method to extract period from network

Author: AntSimi

src/py_eddy_tracker/appli/network.py

@@ -61,11 +61,6 @@ def subset_network():
     parser = EddyParser("Subset network")
     parser.add_argument("input", help="input network file")
     parser.add_argument("out", help="output file")
-    parser.add_argument(
-        "--inverse_selection",
-        action="store_true",
-        help="Extract the inverse of selection",
-    )
     parser.add_argument(
         "-l",
         "--length",
@@ -80,10 +75,25 @@ def subset_network():
         type=int,
         help="Remove short dead end, first is for minimal obs number and second for minimal segment time to keep",
     )
+    parser.add_argument(
+        "--remove_trash",
+        action="store_true",
+        help="Remove trash (network id == 0)",
+    )
+    parser.add_argument(
+        "-p",
+        "--period",
+        nargs=2,
+        type=int,
+        help="Start day and end day, if it's negative value we will add to day min and add to day max,"
+        "if 0 it s not use",
+    )
     args = parser.parse_args()
-    n = NetworkObservations.load_file(args.input)
+    n = NetworkObservations.load_file(args.input, raw_data=True)
     if args.length is not None:
         n = n.longer_than(*args.length)
     if args.remove_dead_end is not None:
         n = n.remove_dead_end(*args.remove_dead_end)
+    if args.period is not None:
+        n = n.extract_with_period(args.period)
     n.write_file(filename=args.out)

src/py_eddy_tracker/generic.py

@@ -70,6 +70,11 @@ def build_index(groups):
     :param array groups: array which contain group to be separated
     :return: (first_index of each group, last_index of each group, value to shift group)
     :rtype: (array, array, int)
+
+    Examples
+    --------
+    >>> build_index(array((1, 1, 3, 4, 4)))
+    (array([0, 2, 2, 3]), array([2, 2, 3, 5]), 1)
     """
     i0, i1 = groups.min(), groups.max()
     amplitude = i1 - i0 + 1
@@ -78,7 +83,7 @@ def build_index(groups):
     for i, group in enumerate(groups[:-1]):
         # Get next value to compare
         next_group = groups[i + 1]
-        # if different we need to set index
+        # if different we need to set index for all group between the 2 values
         if group != next_group:
             first_index[group - i0 + 1 : next_group - i0 + 1] = i + 1
     last_index = zeros(amplitude, dtype=numba_types.int_)

src/py_eddy_tracker/observations/network.py

@@ -10,6 +10,7 @@
     arange,
     array,
     bincount,
+    bool_,
     concatenate,
     empty,
     in1d,
@@ -1237,6 +1238,30 @@ def extract_segment(self, segments, absolute=False):
                 mask[i] = False
         return self.extract_with_mask(mask)
 
+    def extract_with_period(self, period):
+        """
+        Extract within a time period
+
+        :param (int,int) period: two dates to define the period, must be specify from 1/1/1950
+        :return: Return all eddy tracks which are in bounds
+        :rtype: NetworkObservations
+
+        .. minigallery:: py_eddy_tracker.NetworkObservations.extract_with_period
+        """
+        dataset_period = self.period
+        p_min, p_max = period
+        if p_min > 0:
+            mask = self.time >= p_min
+        elif p_min < 0:
+            mask = self.time >= (dataset_period[0] - p_min)
+        else:
+            mask = ones(self.time.shape, dtype=bool_)
+        if p_max > 0:
+            mask *= self.time <= p_max
+        elif p_max < 0:
+            mask *= self.time <= (dataset_period[1] + p_max)
+        return self.extract_with_mask(mask)
+
     def extract_with_mask(self, mask):
         """
         Extract a subset of observations.

src/scripts/EddySubSetter

@@ -22,7 +22,7 @@ def id_parser():
         "--period",
         nargs=2,
         type=int,
-        help="Start day and end day, if it s negative value we will add to day min and add to day max, if 0 it s not use",
+        help="Start day and end day, if it's negative value we will add to day min and add to day max, if 0 it s not use",
     )
     group.add_argument(
         "-l",