Allow to set the number of maxima in same contour

Add method to iterate on group of observation
Add method to align two dataset
Allow to load a slice instead of whole file
Add function to get bins statistic

Author: AntSimi

src/py_eddy_tracker/dataset/grid.py

@@ -53,7 +53,6 @@
     uniform_resample,
     coordinates_to_local,
     local_to_coordinates,
-    get_pixel_in_regular,
     nearest_grd_indice,
     bbox_indice_regular,
 )
@@ -63,6 +62,7 @@
     create_vertice,
     poly_area,
     fit_circle,
+    get_pixel_in_regular,
 )
 
 logger = logging.getLogger("pet")
@@ -577,6 +577,7 @@ def eddy_identification(
         precision=None,
         force_height_unit=None,
         force_speed_unit=None,
+        mle=1,
     ):
         """
         Compute eddy identification on specified grid
@@ -743,6 +744,7 @@ def eddy_identification(
                         anticyclonic_search=anticyclonic_search,
                         level=self.contours.levels[corrected_coll_index],
                         step=step,
+                        mle=mle,
                     )
                     # If we have a valid amplitude
                     if (not amp.within_amplitude_limits()) or (amp.amplitude == 0):
@@ -971,7 +973,13 @@ def _gaussian_filter(data, sigma, mode="reflect"):
 
     @staticmethod
     def get_amplitude(
-        contour, contour_height, data, anticyclonic_search=True, level=None, step=None
+        contour,
+        contour_height,
+        data,
+        anticyclonic_search=True,
+        level=None,
+        step=None,
+        mle=1,
     ):
         # Instantiate Amplitude object
         amp = Amplitude(
@@ -983,6 +991,8 @@ def get_amplitude(
             data=data,
             # Step by level
             interval=step,
+            # Set number max of local maxima
+            mle=mle,
         )
 
         if anticyclonic_search:
@@ -1821,7 +1831,9 @@ def regrid(self, other, grid_name, new_name=None):
             new_name = grid_name
         x, y = meshgrid(self.x_c, self.y_c)
         # interp and reshape
-        v_interp = other.interp(grid_name, x.reshape(-1), y.reshape(-1)).reshape(x.shape).T
+        v_interp = (
+            other.interp(grid_name, x.reshape(-1), y.reshape(-1)).reshape(x.shape).T
+        )
         v_interp = ma.array(v_interp, mask=isnan(v_interp))
         # and add it to self
         self.add_grid(new_name, v_interp)

src/py_eddy_tracker/eddy_feature.py

@@ -61,7 +61,7 @@ class Amplitude(object):
         "mle",
     )
 
-    def __init__(self, contour, contour_height, data, interval):
+    def __init__(self, contour, contour_height, data, interval, mle=1):
         # Height of the contour
         self.h_0 = contour_height
         # Step minimal to consider amplitude
@@ -97,7 +97,7 @@ def __init__(self, contour, contour_height, data, interval):
         # Amplitude which will be provide
         self.amplitude = 0
         # Maximum local extrema accepted
-        self.mle = 1
+        self.mle = mle
 
     def within_amplitude_limits(self):
         """Need update

src/py_eddy_tracker/generic.py

@@ -37,12 +37,10 @@
     zeros,
     isnan,
     bool_,
-    concatenate,
     radians,
     histogram,
 )
 from numba import njit, prange, types as numba_types
-from .poly import winding_number_grid_in_poly
 
 
 @njit(cache=True)
@@ -500,47 +498,6 @@ def bbox_indice_regular(vertices, x0, y0, xstep, ystep, N, circular, x_size):
     return slice_x, slice_y
 
 
-@njit(cache=True, fastmath=True)
-def get_pixel_in_regular(vertices, x_c, y_c, x_start, x_stop, y_start, y_stop):
-    """
-    Get a pixel list of a regular grid contain in a contour.
-
-    :param array_like vertices: contour vertice (N,2)
-    :param array_like x_c: longitude coordinate of grid
-    :param array_like y_c: latitude coordinate of grid
-    :param int x_start: west index of contour
-    :param int y_start: east index of contour
-    :param int x_stop: south index of contour
-    :param int y_stop: north index of contour
-    """
-    if x_stop < x_start:
-        x_ref = vertices[0, 0]
-        x_array = (
-            (concatenate((x_c[x_start:], x_c[:x_stop])) - x_ref + 180) % 360
-            + x_ref
-            - 180
-        )
-        return winding_number_grid_in_poly(
-            x_array,
-            y_c[y_start:y_stop],
-            x_start,
-            x_stop,
-            x_c.shape[0],
-            y_start,
-            vertices,
-        )
-    else:
-        return winding_number_grid_in_poly(
-            x_c[x_start:x_stop],
-            y_c[y_start:y_stop],
-            x_start,
-            x_stop,
-            x_c.shape[0],
-            y_start,
-            vertices,
-        )
-
-
 def build_circle(x0, y0, r):
     """
     Build circle from center coordinates.