AntSimi · ludwigVonKoopa · May 16, 2021 · May 12, 2021 · May 12, 2021 · May 14, 2021
diff --git a/examples/16_network/pet_follow_particle.py b/examples/16_network/pet_follow_particle.py
@@ -8,14 +8,13 @@
 from matplotlib import colors
 from matplotlib import pyplot as plt
 from matplotlib.animation import FuncAnimation
-from numba import njit
-from numba import types as nb_types
-from numpy import arange, meshgrid, ones, unique, where, zeros
+from numpy import arange, meshgrid, ones, unique, zeros
 
 from py_eddy_tracker import start_logger
 from py_eddy_tracker.appli.gui import Anim
 from py_eddy_tracker.data import get_demo_path
 from py_eddy_tracker.dataset.grid import GridCollection
+from py_eddy_tracker.observations.groups import particle_candidate
 from py_eddy_tracker.observations.network import NetworkObservations
 from py_eddy_tracker.poly import group_obs
 
@@ -124,81 +123,6 @@ 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 +141,12 @@ 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))

diff --git a/examples/16_network/pet_ioannou_2017_case.py b/examples/16_network/pet_ioannou_2017_case.py
@@ -14,14 +14,13 @@
 from matplotlib import pyplot as plt
 from matplotlib.animation import FuncAnimation
 from matplotlib.ticker import FuncFormatter
-from numpy import arange, where, array, pi
+from numpy import arange, array, pi, where
 
 from py_eddy_tracker.appli.gui import Anim
 from py_eddy_tracker.data import get_demo_path
+from py_eddy_tracker.generic import coordinates_to_local
 from py_eddy_tracker.gui import GUI_AXES
 from py_eddy_tracker.observations.network import NetworkObservations
-
-from py_eddy_tracker.generic import coordinates_to_local
 from py_eddy_tracker.poly import fit_ellipse
 
 # %%

diff --git a/notebooks/python_module/01_general_things/pet_storage.ipynb b/notebooks/python_module/01_general_things/pet_storage.ipynb
@@ -230,7 +230,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.9.2"
+      "version": "3.7.9"
     }
   },
   "nbformat": 4,

diff --git a/notebooks/python_module/02_eddy_identification/pet_contour_circle.ipynb b/notebooks/python_module/02_eddy_identification/pet_contour_circle.ipynb
@@ -82,7 +82,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.7"
+      "version": "3.7.9"
     }
   },
   "nbformat": 4,

diff --git a/notebooks/python_module/02_eddy_identification/pet_display_id.ipynb b/notebooks/python_module/02_eddy_identification/pet_display_id.ipynb
@@ -129,7 +129,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.7"
+      "version": "3.7.9"
     }
   },
   "nbformat": 4,

diff --git a/notebooks/python_module/02_eddy_identification/pet_eddy_detection.ipynb b/notebooks/python_module/02_eddy_identification/pet_eddy_detection.ipynb
@@ -291,7 +291,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.7"
+      "version": "3.7.9"
     }
   },
   "nbformat": 4,

diff --git a/notebooks/python_module/02_eddy_identification/pet_eddy_detection_ACC.ipynb b/notebooks/python_module/02_eddy_identification/pet_eddy_detection_ACC.ipynb
@@ -161,7 +161,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.7"
+      "version": "3.7.9"
     }
   },
   "nbformat": 4,

diff --git a/notebooks/python_module/02_eddy_identification/pet_eddy_detection_gulf_stream.ipynb b/notebooks/python_module/02_eddy_identification/pet_eddy_detection_gulf_stream.ipynb
@@ -273,7 +273,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.7"
+      "version": "3.7.9"
     }
   },
   "nbformat": 4,

diff --git a/notebooks/python_module/02_eddy_identification/pet_filter_and_detection.ipynb b/notebooks/python_module/02_eddy_identification/pet_filter_and_detection.ipynb
@@ -176,7 +176,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.7"
+      "version": "3.7.9"
     }
   },
   "nbformat": 4,

diff --git a/notebooks/python_module/02_eddy_identification/pet_interp_grid_on_dataset.ipynb b/notebooks/python_module/02_eddy_identification/pet_interp_grid_on_dataset.ipynb
@@ -111,7 +111,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.7"
+      "version": "3.7.9"
     }
   },
   "nbformat": 4,

diff --git a/notebooks/python_module/02_eddy_identification/pet_radius_vs_area.ipynb b/notebooks/python_module/02_eddy_identification/pet_radius_vs_area.ipynb
@@ -107,7 +107,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.7"
+      "version": "3.7.9"
     }
   },
   "nbformat": 4,

diff --git a/notebooks/python_module/02_eddy_identification/pet_shape_gallery.ipynb b/notebooks/python_module/02_eddy_identification/pet_shape_gallery.ipynb
@@ -100,7 +100,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.7"
+      "version": "3.7.9"
     }
   },
   "nbformat": 4,

diff --git a/notebooks/python_module/02_eddy_identification/pet_sla_and_adt.ipynb b/notebooks/python_module/02_eddy_identification/pet_sla_and_adt.ipynb
@@ -223,7 +223,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.7"
+      "version": "3.7.9"
     }
   },
   "nbformat": 4,

diff --git a/notebooks/python_module/06_grid_manipulation/pet_advect.ipynb b/notebooks/python_module/06_grid_manipulation/pet_advect.ipynb
@@ -262,7 +262,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.9.2"
+      "version": "3.7.9"
     }
   },
   "nbformat": 4,

diff --git a/notebooks/python_module/06_grid_manipulation/pet_filter.ipynb b/notebooks/python_module/06_grid_manipulation/pet_filter.ipynb
@@ -215,7 +215,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.7"
+      "version": "3.7.9"
     }
   },
   "nbformat": 4,

diff --git a/notebooks/python_module/06_grid_manipulation/pet_hide_pixel_out_eddies.ipynb b/notebooks/python_module/06_grid_manipulation/pet_hide_pixel_out_eddies.ipynb
@@ -111,7 +111,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.7"
+      "version": "3.7.9"
     }
   },
   "nbformat": 4,

diff --git a/notebooks/python_module/06_grid_manipulation/pet_lavd.ipynb b/notebooks/python_module/06_grid_manipulation/pet_lavd.ipynb
@@ -201,7 +201,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.9.2"
+      "version": "3.7.9"
     }
   },
   "nbformat": 4,

diff --git a/notebooks/python_module/06_grid_manipulation/pet_okubo_weiss.ipynb b/notebooks/python_module/06_grid_manipulation/pet_okubo_weiss.ipynb
@@ -201,7 +201,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.7"
+      "version": "3.7.9"
     }
   },
   "nbformat": 4,

diff --git a/notebooks/python_module/07_cube_manipulation/pet_cube.ipynb b/notebooks/python_module/07_cube_manipulation/pet_cube.ipynb
@@ -158,7 +158,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.9.2"
+      "version": "3.7.9"
     }
   },
   "nbformat": 4,

diff --git a/notebooks/python_module/07_cube_manipulation/pet_fsle_med.ipynb b/notebooks/python_module/07_cube_manipulation/pet_fsle_med.ipynb
@@ -33,7 +33,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## ADT in med\n:py:meth:`~py_eddy_tracker.dataset.grid.GridCollection.from_netcdf_cube` method is\nmade for data stores in time cube, you could use also \n:py:meth:`~py_eddy_tracker.dataset.grid.GridCollection.from_netcdf_list` method to\nload data-cube from multiple file.\n\n"
+        "## ADT in med\n:py:meth:`~py_eddy_tracker.dataset.grid.GridCollection.from_netcdf_cube` method is\nmade for data stores in time cube, you could use also\n:py:meth:`~py_eddy_tracker.dataset.grid.GridCollection.from_netcdf_list` method to\nload data-cube from multiple file.\n\n"
       ]
     },
     {
@@ -172,7 +172,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.9.2"
+      "version": "3.7.9"
     }
   },
   "nbformat": 4,

diff --git a/notebooks/python_module/07_cube_manipulation/pet_lavd_detection.ipynb b/notebooks/python_module/07_cube_manipulation/pet_lavd_detection.ipynb
@@ -194,7 +194,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.9.2"
+      "version": "3.7.9"
     }
   },
   "nbformat": 4,

diff --git a/notebooks/python_module/08_tracking_manipulation/pet_display_field.ipynb b/notebooks/python_module/08_tracking_manipulation/pet_display_field.ipynb
@@ -82,7 +82,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.7"
+      "version": "3.7.9"
     }
   },
   "nbformat": 4,

diff --git a/notebooks/python_module/08_tracking_manipulation/pet_display_track.ipynb b/notebooks/python_module/08_tracking_manipulation/pet_display_track.ipynb
@@ -118,7 +118,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.7"
+      "version": "3.7.9"
     }
   },
   "nbformat": 4,

diff --git a/notebooks/python_module/08_tracking_manipulation/pet_one_track.ipynb b/notebooks/python_module/08_tracking_manipulation/pet_one_track.ipynb
@@ -93,7 +93,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.7"
+      "version": "3.7.9"
     }
   },
   "nbformat": 4,

diff --git a/notebooks/python_module/08_tracking_manipulation/pet_run_a_tracking.ipynb b/notebooks/python_module/08_tracking_manipulation/pet_run_a_tracking.ipynb
@@ -154,7 +154,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.7"
+      "version": "3.7.9"
     }
   },
   "nbformat": 4,

diff --git a/notebooks/python_module/08_tracking_manipulation/pet_select_track_across_area.ipynb b/notebooks/python_module/08_tracking_manipulation/pet_select_track_across_area.ipynb
@@ -100,7 +100,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.7"
+      "version": "3.7.9"
     }
   },
   "nbformat": 4,

diff --git a/notebooks/python_module/08_tracking_manipulation/pet_track_anim.ipynb b/notebooks/python_module/08_tracking_manipulation/pet_track_anim.ipynb
@@ -82,7 +82,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.7"
+      "version": "3.7.9"
     }
   },
   "nbformat": 4,

diff --git a/notebooks/python_module/08_tracking_manipulation/pet_track_anim_matplotlib_animation.ipynb b/notebooks/python_module/08_tracking_manipulation/pet_track_anim_matplotlib_animation.ipynb
@@ -93,7 +93,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.7"
+      "version": "3.7.9"
     }
   },
   "nbformat": 4,

diff --git a/notebooks/python_module/10_tracking_diagnostics/pet_birth_and_death.ipynb b/notebooks/python_module/10_tracking_diagnostics/pet_birth_and_death.ipynb
@@ -144,7 +144,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.7"
+      "version": "3.7.9"
     }
   },
   "nbformat": 4,

diff --git a/notebooks/python_module/10_tracking_diagnostics/pet_center_count.ipynb b/notebooks/python_module/10_tracking_diagnostics/pet_center_count.ipynb
@@ -118,7 +118,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.7"
+      "version": "3.7.9"
     }
   },
   "nbformat": 4,