corrections for merge request

move particle_candidate in groups
add default values for shift_files
mistake with get_uv_quad correction still in comments
change delta_t to n_days
correct whitespaces

examples/16_network/pet_follow_particle.py

@@ -17,6 +17,7 @@
 from py_eddy_tracker.data import get_demo_path
 from py_eddy_tracker.dataset.grid import GridCollection
 from py_eddy_tracker.observations.network import NetworkObservations
+from py_eddy_tracker.observations.groups import particle_candidate
 from py_eddy_tracker.poly import group_obs
 
 start_logger().setLevel("ERROR")
@@ -124,81 +125,6 @@ def update(frame):
 ani = VideoAnimation(a.fig, update, frames=arange(20200, 20269, step), interval=200)
 
 
-# %%
-# In which observations are the particle
-# --------------------------------------
-def advect(x, y, c, t0, delta_t):
-    """
-    Advect particle from t0 to t0 + delta_t, with data cube.
-    """
-    kw = dict(nb_step=6, time_step=86400 / 6)
-    if delta_t < 0:
-        kw["backward"] = True
-        delta_t = -delta_t
-    p = c.advect(x, y, "u", "v", t_init=t0, **kw)
-    for _ in range(delta_t):
-        t, x, y = p.__next__()
-    return t, x, y
-
-
-def particle_candidate(x, y, c, eddies, t_start, i_target, pct, **kwargs):
-    # Obs from initial time
-    m_start = eddies.time == t_start
-    e = eddies.extract_with_mask(m_start)
-    # to be able to get global index
-    translate_start = where(m_start)[0]
-    # Identify particle in eddies (only in core)
-    i_start = e.contains(x, y, intern=True)
-    m = i_start != -1
-    x, y, i_start = x[m], y[m], i_start[m]
-    # Advect
-    t_end, x, y = advect(x, y, c, t_start, **kwargs)
-    # eddies at last date
-    m_end = eddies.time == t_end / 86400
-    e_end = eddies.extract_with_mask(m_end)
-    # to be able to get global index
-    translate_end = where(m_end)[0]
-    # Id eddies for each alive particle (in core and extern)
-    i_end = e_end.contains(x, y)
-    # compute matrix and fill target array
-    get_matrix(i_start, i_end, translate_start, translate_end, i_target, pct)
-
-
-@njit(cache=True)
-def get_matrix(i_start, i_end, translate_start, translate_end, i_target, pct):
-    nb_start, nb_end = translate_start.size, translate_end.size
-    # Matrix which will store count for every couple
-    count = zeros((nb_start, nb_end), dtype=nb_types.int32)
-    # Number of particles in each origin observation
-    ref = zeros(nb_start, dtype=nb_types.int32)
-    # For each particle
-    for i in range(i_start.size):
-        i_end_ = i_end[i]
-        i_start_ = i_start[i]
-        if i_end_ != -1:
-            count[i_start_, i_end_] += 1
-        ref[i_start_] += 1
-    for i in range(nb_start):
-        for j in range(nb_end):
-            pct_ = count[i, j]
-            # If there are particles from i to j
-            if pct_ != 0:
-                # Get percent
-                pct_ = pct_ / ref[i] * 100.0
-                # Get indices in full dataset
-                i_, j_ = translate_start[i], translate_end[j]
-                pct_0 = pct[i_, 0]
-                if pct_ > pct_0:
-                    pct[i_, 1] = pct_0
-                    pct[i_, 0] = pct_
-                    i_target[i_, 1] = i_target[i_, 0]
-                    i_target[i_, 0] = j_
-                elif pct_ > pct[i_, 1]:
-                    pct[i_, 1] = pct_
-                    i_target[i_, 1] = j_
-    return i_target, pct
-
-
 # %%
 # Particle advection
 # ^^^^^^^^^^^^^^^^^^
@@ -217,12 +143,12 @@ def get_matrix(i_start, i_end, translate_start, translate_end, i_target, pct):
 # Forward run
 i_target_f, pct_target_f = -ones(shape, dtype="i4"), zeros(shape, dtype="i1")
 for t in range(t_start, t_end - dt):
-    particle_candidate(x0, y0, c, n, t, i_target_f, pct_target_f, delta_t=dt)
+    particle_candidate(x0, y0, c, n, t, i_target_f, pct_target_f, n_days=dt)
 
 # Backward run
 i_target_b, pct_target_b = -ones(shape, dtype="i4"), zeros(shape, dtype="i1")
 for t in range(t_start + dt, t_end):
-    particle_candidate(x0, y0, c, n, t, i_target_b, pct_target_b, delta_t=-dt)
+    particle_candidate(x0, y0, c, n, t, i_target_b, pct_target_b, n_days=-dt)
 
 # %%
 fig = plt.figure(figsize=(10, 10))

src/py_eddy_tracker/dataset/grid.py

@@ -2264,7 +2264,7 @@ def from_netcdf_list(cls, filenames, t, x_name, y_name, indexs=None, heigth=None
             new.datasets.append((t, d))
         return new
 
-    def shift_files(self, t, filename, x_name, y_name, indexs, heigth):
+    def shift_files(self, t, filename, x_name, y_name, indexs=None, heigth=None):
         """Add next file to the list and remove the oldest"""
 
         self.datasets = self.datasets[1:]
@@ -2553,8 +2553,8 @@ def get_uv_quad(i0, j0, u, v, m, nb_x=0):
         i1 %= nb_x
     i_max, j_max = m.shape
 
-    # if i1 >= i_max or j1 >= j_max:
-    #     return True, nan, nan, nan, nan, nan, nan, nan, nan
+    if i1 >= i_max or j1 >= j_max:
+        return True, nan, nan, nan, nan, nan, nan, nan, nan
 
     if m[i0, j0] or m[i0, j1] or m[i1, j0] or m[i1, j1]:
         return True, nan, nan, nan, nan, nan, nan, nan, nan

src/py_eddy_tracker/observations/groups.py

@@ -1,8 +1,8 @@
 import logging
 from abc import ABC, abstractmethod
 
-from numba import njit
-from numpy import arange, int32, interp, median, zeros
+from numba import njit, types as nb_types
+from numpy import arange, int32, interp, median, zeros, where
 
 from .observation import EddiesObservations
 
@@ -65,6 +65,111 @@ def get_missing_indices(
     return indices
 
 
+
+def advect(x, y, c, t0, n_days):
+    """
+    Advect particle from t0 to t0 + n_days, with data cube.
+
+    :param np.array(float) x: longitude of particles
+    :param np.array(float) y: latitude  of particles
+    :param `~py_eddy_tracker.dataset.grid.GridCollection` c: GridCollection with speed for particles
+    :param int t0: julian day of advection start
+    :param int n_days: number of days to advect
+    """
+
+    kw = dict(nb_step=6, time_step=86400 / 6)
+    if n_days < 0:
+        kw["backward"] = True
+        n_days = -n_days
+    p = c.advect(x, y, "u", "v", t_init=t0, **kw)
+    for _ in range(n_days):
+        t, x, y = p.__next__()
+    return t, x, y
+
+
+def particle_candidate(x, y, c, eddies, t_start, i_target, pct, **kwargs):
+    """Select particles within eddies, advect them, return target observation and associated percentages
+
+    :param np.array(float) x: longitude of particles
+    :param np.array(float) y: latitude  of particles
+    :param `~py_eddy_tracker.dataset.grid.GridCollection` c: GridCollection with speed for particles
+    :param GroupEddiesObservations eddies: GroupEddiesObservations considered
+    :param int t_start: julian day of the advection
+    :param np.array(int) i_target: corresponding obs where particles are advected
+    :param np.array(int) pct: corresponding percentage of avected particles
+    :params dict kwargs: dict of params given to `advect`
+
+    """
+
+    # Obs from initial time
+    m_start = eddies.time == t_start
+
+    e = eddies.extract_with_mask(m_start)
+    # to be able to get global index
+    translate_start = where(m_start)[0]
+    # Identify particle in eddies (only in core)
+    i_start = e.contains(x, y, intern=True)
+    m = i_start != -1
+
+    x, y, i_start = x[m], y[m], i_start[m]
+    # Advect
+    t_end, x, y = advect(x, y, c, t_start, **kwargs)
+    # eddies at last date
+    m_end = eddies.time == t_end / 86400
+    e_end = eddies.extract_with_mask(m_end)
+    # to be able to get global index
+    translate_end = where(m_end)[0]
+    # Id eddies for each alive particle (in core and extern)
+    i_end = e_end.contains(x, y)
+    # compute matrix and fill target array
+    get_matrix(i_start, i_end, translate_start, translate_end, i_target, pct)
+
+
+@njit(cache=True)
+def get_matrix(i_start, i_end, translate_start, translate_end, i_target, pct):
+    """Compute target observation and associated percentages
+
+    :param np.array(int) i_start: indices of associated contours at starting advection day
+    :param np.array(int) i_end: indices of associated contours after advection
+    :param np.array(int) translate_start: corresponding global indices at starting advection day
+    :param np.array(int) translate_end: corresponding global indices after advection
+    :param np.array(int) i_target: corresponding obs where particles are advected
+    :param np.array(int) pct: corresponding percentage of avected particles
+    """
+
+    nb_start, nb_end = translate_start.size, translate_end.size
+    # Matrix which will store count for every couple
+    count = zeros((nb_start, nb_end), dtype=nb_types.int32)
+    # Number of particles in each origin observation
+    ref = zeros(nb_start, dtype=nb_types.int32)
+    # For each particle
+    for i in range(i_start.size):
+        i_end_ = i_end[i]
+        i_start_ = i_start[i]
+        if i_end_ != -1:
+            count[i_start_, i_end_] += 1
+        ref[i_start_] += 1
+    for i in range(nb_start):
+        for j in range(nb_end):
+            pct_ = count[i, j]
+            # If there are particles from i to j
+            if pct_ != 0:
+                # Get percent
+                pct_ = pct_ / ref[i] * 100.0
+                # Get indices in full dataset
+                i_, j_ = translate_start[i], translate_end[j]
+                pct_0 = pct[i_, 0]
+                if pct_ > pct_0:
+                    pct[i_, 1] = pct_0
+                    pct[i_, 0] = pct_
+                    i_target[i_, 1] = i_target[i_, 0]
+                    i_target[i_, 0] = j_
+                elif pct_ > pct[i_, 1]:
+                    pct[i_, 1] = pct_
+                    i_target[i_, 1] = j_
+    return i_target, pct
+
+
 class GroupEddiesObservations(EddiesObservations, ABC):
     @abstractmethod
     def fix_next_previous_obs(self):