From e662ec87a67f873748b47f2674cbf5f69571da06 Mon Sep 17 00:00:00 2001
From: AntSimi <36040805+AntSimi@users.noreply.github.com>
Date: Wed, 16 Jun 2021 23:51:33 +0200
Subject: [PATCH 1/3] management of floating time

---
 CHANGELOG.rst                                 |   4 ++
 doc/run_tracking.rst                          |   4 +-
 .../06_grid_manipulation/pet_okubo_weiss.py   |   2 +-
 examples/16_network/pet_follow_particle.py    |   5 +++
 .../16_network/pet_follow_particle.ipynb      |  12 +++---
 src/py_eddy_tracker/__init__.py               |   7 ++-
 src/py_eddy_tracker/appli/eddies.py           |  40 +++++++++++-------
 src/py_eddy_tracker/appli/grid.py             |  15 +++++--
 .../data/Anticyclonic_20190223.nc             | Bin 907023 -> 908188 bytes
 src/py_eddy_tracker/gui.py                    |   4 +-
 src/py_eddy_tracker/observations/groups.py    |   4 +-
 src/py_eddy_tracker/observations/network.py   |   1 -
 .../observations/observation.py               |   2 +
 src/py_eddy_tracker/observations/tracking.py  |  15 ++++---
 src/py_eddy_tracker/tracking.py               |   9 ++--
 src/scripts/EddyTranslate                     |   9 ++--
 16 files changed, 86 insertions(+), 47 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 80def41c..f9b78b99 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -10,6 +10,10 @@ and this project adheres to `Semantic Versioning <https://semver.org/spec/v2.0.0
 ------------
 Changed
 ^^^^^^^
+- Now time will be allow second precision in storage on uint32 from 01/01/1950 to 01/01/2086
+  new identification will be produce with this type, old file could be still loaded.
+  If you use old identification to track use `--unraw` option to unpack old time and store in new format.
+
 Fixed
 ^^^^^
 Added
diff --git a/doc/run_tracking.rst b/doc/run_tracking.rst
index 0a03848d..1c4b851c 100644
--- a/doc/run_tracking.rst
+++ b/doc/run_tracking.rst
@@ -26,7 +26,7 @@ Example of conf.yaml
 
     # Number of timestep for missing detection
     VIRTUAL_LENGTH_MAX: 3
-    # Minimal time to consider as a full track
+    # Minimal number of timesteps to consider as a long track
     TRACK_DURATION_MIN: 10
 
 To run:
@@ -69,7 +69,7 @@ With yaml you could also select another tracker:
 
     # Number of timesteps for missing detection
     VIRTUAL_LENGTH_MAX: 3
-    # Minimal time to consider as a full track
+    # Minimal number of timesteps to consider as a long track
     TRACK_DURATION_MIN: 10
 
     CLASS:
diff --git a/examples/06_grid_manipulation/pet_okubo_weiss.py b/examples/06_grid_manipulation/pet_okubo_weiss.py
index c60a92fb..818a6742 100644
--- a/examples/06_grid_manipulation/pet_okubo_weiss.py
+++ b/examples/06_grid_manipulation/pet_okubo_weiss.py
@@ -1,6 +1,6 @@
 r"""
 Get Okubo Weis
-=====================
+==============
 
 .. math:: OW = S_n^2 + S_s^2 + \omega^2
 
diff --git a/examples/16_network/pet_follow_particle.py b/examples/16_network/pet_follow_particle.py
index e5451daa..d7253a87 100644
--- a/examples/16_network/pet_follow_particle.py
+++ b/examples/16_network/pet_follow_particle.py
@@ -156,6 +156,11 @@ def update(frame):
 ax_2nd_f = fig.add_axes([0.52, 0.05, 0.45, 0.45])
 ax_1st_b.set_title("Backward advection for each time step")
 ax_1st_f.set_title("Forward advection for each time step")
+ax_1st_b.set_ylabel("Color -> First target\nLatitude")
+ax_2nd_b.set_ylabel("Color -> Secondary target\nLatitude")
+ax_2nd_b.set_xlabel("Julian days"), ax_2nd_f.set_xlabel("Julian days")
+ax_1st_f.set_yticks([]), ax_2nd_f.set_yticks([])
+ax_1st_f.set_xticks([]), ax_1st_b.set_xticks([])
 
 
 def color_alpha(target, pct, vmin=5, vmax=80):
diff --git a/notebooks/python_module/16_network/pet_follow_particle.ipynb b/notebooks/python_module/16_network/pet_follow_particle.ipynb
index 6be13adf..b6723a97 100644
--- a/notebooks/python_module/16_network/pet_follow_particle.ipynb
+++ b/notebooks/python_module/16_network/pet_follow_particle.ipynb
@@ -15,7 +15,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "\n# Follow particle\n"
+        "\nFollow particle\n===============\n"
       ]
     },
     {
@@ -55,7 +55,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Schema\n\n"
+        "Schema\n------\n\n"
       ]
     },
     {
@@ -73,7 +73,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Animation\nParticle settings\n\n"
+        "Animation\n---------\nParticle settings\n\n"
       ]
     },
     {
@@ -109,7 +109,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "### Particle advection\n\n"
+        "Particle advection\n^^^^^^^^^^^^^^^^^^\n\n"
       ]
     },
     {
@@ -131,7 +131,7 @@
       },
       "outputs": [],
       "source": [
-        "fig = plt.figure(figsize=(10, 10))\nax_1st_b = fig.add_axes([0.05, 0.52, 0.45, 0.45])\nax_2nd_b = fig.add_axes([0.05, 0.05, 0.45, 0.45])\nax_1st_f = fig.add_axes([0.52, 0.52, 0.45, 0.45])\nax_2nd_f = fig.add_axes([0.52, 0.05, 0.45, 0.45])\nax_1st_b.set_title(\"Backward advection for each time step\")\nax_1st_f.set_title(\"Forward advection for each time step\")\n\n\ndef color_alpha(target, pct, vmin=5, vmax=80):\n    color = cmap(n.segment[target])\n    # We will hide under 5 % and from 80% to 100 % it will be 1\n    alpha = (pct - vmin) / (vmax - vmin)\n    alpha[alpha < 0] = 0\n    alpha[alpha > 1] = 1\n    color[:, 3] = alpha\n    return color\n\n\nkw = dict(\n    name=None, yfield=\"longitude\", event=False, zorder=-100, s=(n.speed_area / 20e6)\n)\nn.scatter_timeline(ax_1st_b, c=color_alpha(i_target_b.T[0], pct_target_b.T[0]), **kw)\nn.scatter_timeline(ax_2nd_b, c=color_alpha(i_target_b.T[1], pct_target_b.T[1]), **kw)\nn.scatter_timeline(ax_1st_f, c=color_alpha(i_target_f.T[0], pct_target_f.T[0]), **kw)\nn.scatter_timeline(ax_2nd_f, c=color_alpha(i_target_f.T[1], pct_target_f.T[1]), **kw)\nfor ax in (ax_1st_b, ax_2nd_b, ax_1st_f, ax_2nd_f):\n    n.display_timeline(ax, field=\"longitude\", marker=\"+\", lw=2, markersize=5)\n    ax.grid()"
+        "fig = plt.figure(figsize=(10, 10))\nax_1st_b = fig.add_axes([0.05, 0.52, 0.45, 0.45])\nax_2nd_b = fig.add_axes([0.05, 0.05, 0.45, 0.45])\nax_1st_f = fig.add_axes([0.52, 0.52, 0.45, 0.45])\nax_2nd_f = fig.add_axes([0.52, 0.05, 0.45, 0.45])\nax_1st_b.set_title(\"Backward advection for each time step\")\nax_1st_f.set_title(\"Forward advection for each time step\")\nax_1st_b.set_ylabel(\"Color -> First target\\nLatitude\")\nax_2nd_b.set_ylabel(\"Color -> Secondary target\\nLatitude\")\nax_2nd_b.set_xlabel(\"Julian days\"), ax_2nd_f.set_xlabel(\"Julian days\")\nax_1st_f.set_yticks([]), ax_2nd_f.set_yticks([])\nax_1st_f.set_xticks([]), ax_1st_b.set_xticks([])\n\n\ndef color_alpha(target, pct, vmin=5, vmax=80):\n    color = cmap(n.segment[target])\n    # We will hide under 5 % and from 80% to 100 % it will be 1\n    alpha = (pct - vmin) / (vmax - vmin)\n    alpha[alpha < 0] = 0\n    alpha[alpha > 1] = 1\n    color[:, 3] = alpha\n    return color\n\n\nkw = dict(\n    name=None, yfield=\"longitude\", event=False, zorder=-100, s=(n.speed_area / 20e6)\n)\nn.scatter_timeline(ax_1st_b, c=color_alpha(i_target_b.T[0], pct_target_b.T[0]), **kw)\nn.scatter_timeline(ax_2nd_b, c=color_alpha(i_target_b.T[1], pct_target_b.T[1]), **kw)\nn.scatter_timeline(ax_1st_f, c=color_alpha(i_target_f.T[0], pct_target_f.T[0]), **kw)\nn.scatter_timeline(ax_2nd_f, c=color_alpha(i_target_f.T[1], pct_target_f.T[1]), **kw)\nfor ax in (ax_1st_b, ax_2nd_b, ax_1st_f, ax_2nd_f):\n    n.display_timeline(ax, field=\"longitude\", marker=\"+\", lw=2, markersize=5)\n    ax.grid()"
       ]
     }
   ],
@@ -151,7 +151,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.9"
+      "version": "3.7.7"
     }
   },
   "nbformat": 4,
diff --git a/src/py_eddy_tracker/__init__.py b/src/py_eddy_tracker/__init__.py
index 46946e77..693b4ab4 100644
--- a/src/py_eddy_tracker/__init__.py
+++ b/src/py_eddy_tracker/__init__.py
@@ -108,12 +108,17 @@ def parse_args(self, *args, **kwargs):
         return opts
 
 
+TIME_MODELS = ["%Y%m%d", "%Y%m%d%H%M%S", "%Y%m%dT%H%M%S"]
+
+
 VAR_DESCR = dict(
     time=dict(
         attr_name="time",
         nc_name="time",
         old_nc_name=["j1"],
-        nc_type="int32",
+        nc_type="float64",
+        output_type="uint32",
+        scale_factor=1 / 86400.0,
         nc_dims=("obs",),
         nc_attr=dict(
             standard_name="time",
diff --git a/src/py_eddy_tracker/appli/eddies.py b/src/py_eddy_tracker/appli/eddies.py
index d5a727f9..b076c8ae 100644
--- a/src/py_eddy_tracker/appli/eddies.py
+++ b/src/py_eddy_tracker/appli/eddies.py
@@ -15,7 +15,7 @@
 from numpy import bincount, bytes_, empty, in1d, unique
 from yaml import safe_load
 
-from .. import EddyParser
+from .. import TIME_MODELS, EddyParser
 from ..observations.observation import EddiesObservations, reverse_index
 from ..observations.tracking import TrackEddiesObservations
 from ..tracking import Correspondances
@@ -223,7 +223,7 @@ def browse_dataset_in(
     data_dir,
     files_model,
     date_regexp,
-    date_model,
+    date_model=None,
     start_date=None,
     end_date=None,
     sub_sampling_step=1,
@@ -238,11 +238,7 @@ def browse_dataset_in(
         filenames = bytes_(glob(full_path))
 
     dataset_list = empty(
-        len(filenames),
-        dtype=[
-            ("filename", "S500"),
-            ("date", "datetime64[D]"),
-        ],
+        len(filenames), dtype=[("filename", "S500"), ("date", "datetime64[s]")],
     )
     dataset_list["filename"] = filenames
 
@@ -268,10 +264,21 @@ def browse_dataset_in(
                 str_date = result.groups()[0]
 
         if str_date is not None:
-            item["date"] = datetime.strptime(str_date, date_model).date()
+            if date_model is None:
+                model_found = False
+                for model in TIME_MODELS:
+                    try:
+                        item["date"] = datetime.strptime(str_date, model)
+                        model_found = True
+                        break
+                    except ValueError:
+                        pass
+                if not model_found:
+                    raise Exception("No time model found")
+            else:
+                item["date"] = datetime.strptime(str_date, date_model)
 
     dataset_list.sort(order=["date", "filename"])
-
     steps = unique(dataset_list["date"][1:] - dataset_list["date"][:-1])
     if len(steps) > 1:
         raise Exception("Several days steps in grid dataset %s" % steps)
@@ -304,7 +311,7 @@ def track(
     correspondances_only=False,
     **kw_c,
 ):
-    kw = dict(date_regexp=".*_([0-9]*?).[nz].*", date_model="%Y%m%d")
+    kw = dict(date_regexp=".*_([0-9]*?).[nz].*")
     if isinstance(pattern, list):
         kw.update(dict(data_dir=None, files_model=None, files=pattern))
     else:
@@ -323,10 +330,9 @@ def track(
     c = Correspondances(datasets=datasets["filename"], **kw_c)
     c.track()
     logger.info("Track finish")
-    t0, t1 = c.period
     kw_save = dict(
-        date_start=t0,
-        date_stop=t1,
+        date_start=datasets["date"][0],
+        date_stop=datasets["date"][-1],
         date_prod=datetime.now(),
         path=output_dir,
         sign_type=c.current_obs.sign_legend,
@@ -351,11 +357,13 @@ def track(
 
     short_c = c._copy()
     short_c.shorter_than(size_max=nb_obs_min)
-    c.longer_than(size_min=nb_obs_min)
-
-    long_track = c.merge(raw_data=raw)
     short_track = short_c.merge(raw_data=raw)
 
+    if c.longer_than(size_min=nb_obs_min) is False:
+        long_track = short_track.empty_dataset()
+    else:
+        long_track = c.merge(raw_data=raw)
+
     # We flag obs
     if c.virtual:
         long_track["virtual"][:] = long_track["time"] == 0
diff --git a/src/py_eddy_tracker/appli/grid.py b/src/py_eddy_tracker/appli/grid.py
index 7f2b9610..7a746a8f 100644
--- a/src/py_eddy_tracker/appli/grid.py
+++ b/src/py_eddy_tracker/appli/grid.py
@@ -5,7 +5,7 @@
 from argparse import Action
 from datetime import datetime
 
-from .. import EddyParser
+from .. import TIME_MODELS, EddyParser
 from ..dataset.grid import RegularGridDataset, UnRegularGridDataset
 
 
@@ -121,7 +121,16 @@ def eddy_id(args=None):
         cut_wavelength = [0, *cut_wavelength]
     inf_bnds, upper_bnds = cut_wavelength
 
-    date = datetime.strptime(args.datetime, "%Y%m%d")
+    model_found = False
+    for model in TIME_MODELS:
+        try:
+            date = datetime.strptime(args.datetime, model)
+            model_found = True
+            break
+        except ValueError:
+            pass
+    if not model_found:
+        raise Exception("No time model found")
     kwargs = dict(
         step=args.isoline_step,
         shape_error=args.fit_errmax,
@@ -150,7 +159,7 @@ def eddy_id(args=None):
         sampling_method=args.sampling_method,
         **kwargs,
     )
-    out_name = date.strftime("%(path)s/%(sign_type)s_%Y%m%d.nc")
+    out_name = date.strftime("%(path)s/%(sign_type)s_%Y%m%dT%H%M%S.nc")
     a.write_file(path=args.path_out, filename=out_name, zarr_flag=args.zarr)
     c.write_file(path=args.path_out, filename=out_name, zarr_flag=args.zarr)
 
diff --git a/src/py_eddy_tracker/data/Anticyclonic_20190223.nc b/src/py_eddy_tracker/data/Anticyclonic_20190223.nc
index ce48c8d60a4779176855f1c3108911b2f2d50c91..dc5fe0d3693f42f6165c4138e2e6ee8f30f74bf5 100644
GIT binary patch
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diff --git a/src/py_eddy_tracker/gui.py b/src/py_eddy_tracker/gui.py
index fadd4947..deeb6660 100644
--- a/src/py_eddy_tracker/gui.py
+++ b/src/py_eddy_tracker/gui.py
@@ -291,8 +291,8 @@ def get_infos(self, name, index):
         i_first = d.index_from_track[tr]
         track = d.obs[i_first : i_first + nb]
         nb -= 1
-        t0 = timedelta(days=int(track[0]["time"])) + datetime(1950, 1, 1)
-        t1 = timedelta(days=int(track[-1]["time"])) + datetime(1950, 1, 1)
+        t0 = timedelta(days=track[0]["time"]) + datetime(1950, 1, 1)
+        t1 = timedelta(days=track[-1]["time"]) + datetime(1950, 1, 1)
         txt = f"--{name}--\n"
         txt += f"    {t0} -> {t1}\n"
         txt += f"    Tracks : {tr}  {now['n']}/{nb} ({now['n'] / nb * 100:.2f} %)\n"
diff --git a/src/py_eddy_tracker/observations/groups.py b/src/py_eddy_tracker/observations/groups.py
index c0924cb3..9be49aad 100644
--- a/src/py_eddy_tracker/observations/groups.py
+++ b/src/py_eddy_tracker/observations/groups.py
@@ -187,7 +187,8 @@ def filled_by_interpolation(self, mask):
 
         .. minigallery:: py_eddy_tracker.TrackEddiesObservations.filled_by_interpolation
         """
-
+        if self.track.size == 0:
+            return
         nb_filled = mask.sum()
         logger.info("%d obs will be filled (unobserved)", nb_filled)
 
@@ -195,7 +196,6 @@ def filled_by_interpolation(self, mask):
         index = arange(nb_obs)
 
         for field in self.obs.dtype.descr:
-            # print(f"field : {field}")
             var = field[0]
             if (
                 var in ["n", "virtual", "track", "cost_association"]
diff --git a/src/py_eddy_tracker/observations/network.py b/src/py_eddy_tracker/observations/network.py
index 4f9af0b3..a3c1e06d 100644
--- a/src/py_eddy_tracker/observations/network.py
+++ b/src/py_eddy_tracker/observations/network.py
@@ -7,7 +7,6 @@
 
 import zarr
 from numba import njit
-from numba import types as nb_types
 from numpy import (
     arange,
     array,
diff --git a/src/py_eddy_tracker/observations/observation.py b/src/py_eddy_tracker/observations/observation.py
index 557c0279..32ddae75 100644
--- a/src/py_eddy_tracker/observations/observation.py
+++ b/src/py_eddy_tracker/observations/observation.py
@@ -1330,6 +1330,8 @@ def solve_conflict(cost):
     def solve_simultaneous(cost):
         """Write something (TODO)"""
         mask = ~cost.mask
+        if mask.size == 0:
+            return mask
         # Count number of links by self obs and other obs
         self_links, other_links = sum_row_column(mask)
         max_links = max(self_links.max(), other_links.max())
diff --git a/src/py_eddy_tracker/observations/tracking.py b/src/py_eddy_tracker/observations/tracking.py
index b632270c..f89084e8 100644
--- a/src/py_eddy_tracker/observations/tracking.py
+++ b/src/py_eddy_tracker/observations/tracking.py
@@ -173,6 +173,8 @@ def normalize_longitude(self):
         - contour_lon_e (how to do if in raw)
         - contour_lon_s (how to do if in raw)
         """
+        if self.lon.size == 0:
+            return
         lon0 = (self.lon[self.index_from_track] - 180).repeat(self.nb_obs_by_track)
         logger.debug("Normalize longitude")
         self.lon[:] = (self.lon - lon0) % 360 + lon0
@@ -228,12 +230,13 @@ def set_global_attr_netcdf(self, h_nc):
         )
         h_nc.date_created = datetime.now().strftime("%Y-%m-%dT%H:%M:%SZ")
         t = h_nc.variables[VAR_DESCR_inv["j1"]]
-        delta = t.max - t.min + 1
-        h_nc.time_coverage_duration = "P%dD" % delta
-        d_start = datetime(1950, 1, 1) + timedelta(int(t.min))
-        d_end = datetime(1950, 1, 1) + timedelta(int(t.max))
-        h_nc.time_coverage_start = d_start.strftime("%Y-%m-%dT00:00:00Z")
-        h_nc.time_coverage_end = d_end.strftime("%Y-%m-%dT00:00:00Z")
+        if t.size:
+            delta = t.max - t.min + 1
+            h_nc.time_coverage_duration = "P%dD" % delta
+            d_start = datetime(1950, 1, 1) + timedelta(int(t.min))
+            d_end = datetime(1950, 1, 1) + timedelta(int(t.max))
+            h_nc.time_coverage_start = d_start.strftime("%Y-%m-%dT00:00:00Z")
+            h_nc.time_coverage_end = d_end.strftime("%Y-%m-%dT00:00:00Z")
 
     def extract_with_period(self, period, **kwargs):
         """
diff --git a/src/py_eddy_tracker/tracking.py b/src/py_eddy_tracker/tracking.py
index cba9985e..577496ff 100644
--- a/src/py_eddy_tracker/tracking.py
+++ b/src/py_eddy_tracker/tracking.py
@@ -161,10 +161,10 @@ def period(self):
 
         """
         date_start = datetime(1950, 1, 1) + timedelta(
-            int(self.class_method.load_file(self.datasets[0]).time[0])
+            self.class_method.load_file(self.datasets[0]).time[0]
         )
         date_stop = datetime(1950, 1, 1) + timedelta(
-            int(self.class_method.load_file(self.datasets[-1]).time[0])
+            self.class_method.load_file(self.datasets[-1]).time[0]
         )
         return date_start, date_stop
 
@@ -584,7 +584,10 @@ def prepare_merging(self):
     def longer_than(self, size_min):
         """Remove from correspondance table all association for shorter eddies than size_min"""
         # Identify eddies longer than
-        i_keep_track = where(self.nb_obs_by_tracks >= size_min)[0]
+        mask = self.nb_obs_by_tracks >= size_min
+        if not mask.any():
+            return False
+        i_keep_track = where(mask)[0]
         # Reduce array
         self.nb_obs_by_tracks = self.nb_obs_by_tracks[i_keep_track]
         self.i_current_by_tracks = (
diff --git a/src/scripts/EddyTranslate b/src/scripts/EddyTranslate
index 94142132..a710db0d 100644
--- a/src/scripts/EddyTranslate
+++ b/src/scripts/EddyTranslate
@@ -16,6 +16,7 @@ def id_parser():
     )
     parser.add_argument("filename_in")
     parser.add_argument("filename_out")
+    parser.add_argument("--unraw", action="store_true", help="Load unraw data")
     return parser
 
 
@@ -32,10 +33,10 @@ def get_variable_name(filename):
         return list(h.keys())
 
 
-def get_variable(filename, varname):
+def get_variable(filename, varname, raw=True):
     if is_nc(filename):
         dataset = EddiesObservations.load_from_netcdf(
-            filename, raw_data=True, include_vars=(varname,)
+            filename, raw_data=raw, include_vars=(varname,)
         )
     else:
         dataset = EddiesObservations.load_from_zarr(filename, include_vars=(varname,))
@@ -49,8 +50,8 @@ if __name__ == "__main__":
     if not is_nc(args.filename_out):
         h = zarr.open(args.filename_out, "w")
         for varname in variables:
-            get_variable(args.filename_in, varname).to_zarr(h)
+            get_variable(args.filename_in, varname, raw=not args.unraw).to_zarr(h)
     else:
         with Dataset(args.filename_out, "w") as h:
             for varname in variables:
-                get_variable(args.filename_in, varname).to_netcdf(h)
+                get_variable(args.filename_in, varname, raw=not args.unraw).to_netcdf(h)

From 5114253fa6111160e98b96251df3daa92dce8531 Mon Sep 17 00:00:00 2001
From: AntSimi <36040805+AntSimi@users.noreply.github.com>
Date: Fri, 18 Jun 2021 09:02:54 +0200
Subject: [PATCH 2/3] modify amplitude storage

---
 CHANGELOG.rst                                 |   1 +
 share/tracking.yaml                           |   3 ++-
 src/py_eddy_tracker/__init__.py               |   2 +-
 .../data/Anticyclonic_20190223.nc             | Bin 908188 -> 909431 bytes
 4 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index f9b78b99..30226e4d 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -13,6 +13,7 @@ Changed
 - Now time will be allow second precision in storage on uint32 from 01/01/1950 to 01/01/2086
   new identification will be produce with this type, old file could be still loaded.
   If you use old identification to track use `--unraw` option to unpack old time and store in new format.
+- Now amplitude is stored with .1 mm of precision, same advice than time.
 
 Fixed
 ^^^^^
diff --git a/share/tracking.yaml b/share/tracking.yaml
index 0f8766b8..06741f59 100644
--- a/share/tracking.yaml
+++ b/share/tracking.yaml
@@ -4,8 +4,9 @@ PATHS:
   # Path for saving of outputs
   SAVE_DIR: '/home/emason/toto/'
 
-# Minimum number of observations to store eddy
+# Minimal number of timesteps to consider as a long track
 TRACK_DURATION_MIN: 4
+# Number of timesteps for missing detection
 VIRTUAL_LENGTH_MAX: 0
 
 #CLASS:
diff --git a/src/py_eddy_tracker/__init__.py b/src/py_eddy_tracker/__init__.py
index 693b4ab4..c7225d0a 100644
--- a/src/py_eddy_tracker/__init__.py
+++ b/src/py_eddy_tracker/__init__.py
@@ -258,7 +258,7 @@ def parse_args(self, *args, **kwargs):
         old_nc_name=["A"],
         nc_type="float32",
         output_type="uint16",
-        scale_factor=0.001,
+        scale_factor=0.0001,
         nc_dims=("obs",),
         nc_attr=dict(
             long_name="Amplitude",
diff --git a/src/py_eddy_tracker/data/Anticyclonic_20190223.nc b/src/py_eddy_tracker/data/Anticyclonic_20190223.nc
index dc5fe0d3693f42f6165c4138e2e6ee8f30f74bf5..4ab8f2261e9e0a80f1f9825babf234cb3097f44e 100644
GIT binary patch
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From 155c668ee92001a0a15d61eda8ee4226cdb26f91 Mon Sep 17 00:00:00 2001
From: AntSimi <36040805+AntSimi@users.noreply.github.com>
Date: Mon, 21 Jun 2021 22:33:42 +0200
Subject: [PATCH 3/3] manage time in network

---
 examples/16_network/pet_follow_particle.py     |  4 ++--
 examples/16_network/pet_segmentation_anim.py   |  3 +--
 .../16_network/pet_follow_particle.ipynb       |  2 +-
 .../16_network/pet_segmentation_anim.ipynb     | 14 +++++++-------
 src/py_eddy_tracker/observations/tracking.py   | 18 ++++++++++++------
 5 files changed, 23 insertions(+), 18 deletions(-)

diff --git a/examples/16_network/pet_follow_particle.py b/examples/16_network/pet_follow_particle.py
index d7253a87..a2aa2217 100644
--- a/examples/16_network/pet_follow_particle.py
+++ b/examples/16_network/pet_follow_particle.py
@@ -140,12 +140,12 @@ def update(frame):
 shape = (n.obs.size, 2)
 # 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):
+for t in arange(t_start, t_end - 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):
+for t in arange(t_start + dt, t_end):
     particle_candidate(x0, y0, c, n, t, i_target_b, pct_target_b, n_days=-dt)
 
 # %%
diff --git a/examples/16_network/pet_segmentation_anim.py b/examples/16_network/pet_segmentation_anim.py
index 340163a1..503229e7 100644
--- a/examples/16_network/pet_segmentation_anim.py
+++ b/examples/16_network/pet_segmentation_anim.py
@@ -96,8 +96,7 @@ def update(i_frame):
 
     indices_frames = INDICES[i_frame]
     mappable_CONTOUR.set_data(
-        e.contour_lon_e[indices_frames],
-        e.contour_lat_e[indices_frames],
+        e.contour_lon_e[indices_frames], e.contour_lat_e[indices_frames],
     )
     mappable_CONTOUR.set_color(cmap.colors[tr[indices_frames] % len(cmap.colors)])
     return (mappable_tracks,)
diff --git a/notebooks/python_module/16_network/pet_follow_particle.ipynb b/notebooks/python_module/16_network/pet_follow_particle.ipynb
index b6723a97..15820ad3 100644
--- a/notebooks/python_module/16_network/pet_follow_particle.ipynb
+++ b/notebooks/python_module/16_network/pet_follow_particle.ipynb
@@ -120,7 +120,7 @@
       },
       "outputs": [],
       "source": [
-        "step = 1 / 60.0\n\nx, y = meshgrid(arange(24, 36, step), arange(31, 36, step))\nx0, y0 = x.reshape(-1), y.reshape(-1)\n# Pre-order to speed up\n_, i = group_obs(x0, y0, 1, 360)\nx0, y0 = x0[i], y0[i]\n\nt_start, t_end = n.period\ndt = 14\n\nshape = (n.obs.size, 2)\n# Forward run\ni_target_f, pct_target_f = -ones(shape, dtype=\"i4\"), zeros(shape, dtype=\"i1\")\nfor t in range(t_start, t_end - dt):\n    particle_candidate(x0, y0, c, n, t, i_target_f, pct_target_f, n_days=dt)\n\n# Backward run\ni_target_b, pct_target_b = -ones(shape, dtype=\"i4\"), zeros(shape, dtype=\"i1\")\nfor t in range(t_start + dt, t_end):\n    particle_candidate(x0, y0, c, n, t, i_target_b, pct_target_b, n_days=-dt)"
+        "step = 1 / 60.0\n\nx, y = meshgrid(arange(24, 36, step), arange(31, 36, step))\nx0, y0 = x.reshape(-1), y.reshape(-1)\n# Pre-order to speed up\n_, i = group_obs(x0, y0, 1, 360)\nx0, y0 = x0[i], y0[i]\n\nt_start, t_end = n.period\ndt = 14\n\nshape = (n.obs.size, 2)\n# Forward run\ni_target_f, pct_target_f = -ones(shape, dtype=\"i4\"), zeros(shape, dtype=\"i1\")\nfor t in arange(t_start, t_end - dt):\n    particle_candidate(x0, y0, c, n, t, i_target_f, pct_target_f, n_days=dt)\n\n# Backward run\ni_target_b, pct_target_b = -ones(shape, dtype=\"i4\"), zeros(shape, dtype=\"i1\")\nfor t in arange(t_start + dt, t_end):\n    particle_candidate(x0, y0, c, n, t, i_target_b, pct_target_b, n_days=-dt)"
       ]
     },
     {
diff --git a/notebooks/python_module/16_network/pet_segmentation_anim.ipynb b/notebooks/python_module/16_network/pet_segmentation_anim.ipynb
index 05c68873..34047da4 100644
--- a/notebooks/python_module/16_network/pet_segmentation_anim.ipynb
+++ b/notebooks/python_module/16_network/pet_segmentation_anim.ipynb
@@ -15,7 +15,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "\n# Network segmentation process\n"
+        "\nNetwork segmentation process\n============================\n"
       ]
     },
     {
@@ -62,7 +62,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Load data\nLoad data where observations are put in same network but no segmentation\n\n"
+        "Load data\n---------\nLoad data where observations are put in same network but no segmentation\n\n"
       ]
     },
     {
@@ -80,7 +80,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Do segmentation\nSegmentation based on maximum overlap, temporal window for candidates = 5 days\n\n"
+        "Do segmentation\n---------------\nSegmentation based on maximum overlap, temporal window for candidates = 5 days\n\n"
       ]
     },
     {
@@ -98,7 +98,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Anim\n\n"
+        "Anim\n----\n\n"
       ]
     },
     {
@@ -109,14 +109,14 @@
       },
       "outputs": [],
       "source": [
-        "def update(i_frame):\n    tr = TRACKS[i_frame]\n    mappable_tracks.set_array(tr)\n    s = 40 * ones(tr.shape)\n    s[tr == 0] = 4\n    mappable_tracks.set_sizes(s)\n\n    indices_frames = INDICES[i_frame]\n    mappable_CONTOUR.set_data(\n        e.contour_lon_e[indices_frames],\n        e.contour_lat_e[indices_frames],\n    )\n    mappable_CONTOUR.set_color(cmap.colors[tr[indices_frames] % len(cmap.colors)])\n    return (mappable_tracks,)\n\n\nfig = plt.figure(figsize=(16, 9), dpi=60)\nax = fig.add_axes([0.04, 0.06, 0.94, 0.88], projection=GUI_AXES)\nax.set_title(f\"{len(e)} observations to segment\")\nax.set_xlim(19, 29), ax.set_ylim(31, 35.5), ax.grid()\nvmax = TRACKS[-1].max()\ncmap = ListedColormap([\"gray\", *e.COLORS[:-1]], name=\"from_list\", N=vmax)\nmappable_tracks = ax.scatter(\n    e.lon, e.lat, c=TRACKS[0], cmap=cmap, vmin=0, vmax=vmax, s=20\n)\nmappable_CONTOUR = ax.plot(\n    e.contour_lon_e[INDICES[0]], e.contour_lat_e[INDICES[0]], color=cmap.colors[0]\n)[0]\nani = VideoAnimation(fig, update, frames=range(1, len(TRACKS), 4), interval=125)"
+        "def update(i_frame):\n    tr = TRACKS[i_frame]\n    mappable_tracks.set_array(tr)\n    s = 40 * ones(tr.shape)\n    s[tr == 0] = 4\n    mappable_tracks.set_sizes(s)\n\n    indices_frames = INDICES[i_frame]\n    mappable_CONTOUR.set_data(\n        e.contour_lon_e[indices_frames], e.contour_lat_e[indices_frames],\n    )\n    mappable_CONTOUR.set_color(cmap.colors[tr[indices_frames] % len(cmap.colors)])\n    return (mappable_tracks,)\n\n\nfig = plt.figure(figsize=(16, 9), dpi=60)\nax = fig.add_axes([0.04, 0.06, 0.94, 0.88], projection=GUI_AXES)\nax.set_title(f\"{len(e)} observations to segment\")\nax.set_xlim(19, 29), ax.set_ylim(31, 35.5), ax.grid()\nvmax = TRACKS[-1].max()\ncmap = ListedColormap([\"gray\", *e.COLORS[:-1]], name=\"from_list\", N=vmax)\nmappable_tracks = ax.scatter(\n    e.lon, e.lat, c=TRACKS[0], cmap=cmap, vmin=0, vmax=vmax, s=20\n)\nmappable_CONTOUR = ax.plot(\n    e.contour_lon_e[INDICES[0]], e.contour_lat_e[INDICES[0]], color=cmap.colors[0]\n)[0]\nani = VideoAnimation(fig, update, frames=range(1, len(TRACKS), 4), interval=125)"
       ]
     },
     {
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Final Result\n\n"
+        "Final Result\n------------\n\n"
       ]
     },
     {
@@ -147,7 +147,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.9"
+      "version": "3.7.7"
     }
   },
   "nbformat": 4,
diff --git a/src/py_eddy_tracker/observations/tracking.py b/src/py_eddy_tracker/observations/tracking.py
index f89084e8..6bf74875 100644
--- a/src/py_eddy_tracker/observations/tracking.py
+++ b/src/py_eddy_tracker/observations/tracking.py
@@ -16,6 +16,7 @@
     degrees,
     empty,
     histogram,
+    int_,
     median,
     nan,
     ones,
@@ -604,6 +605,12 @@ def plot(self, ax, ref=None, **kwargs):
 
     def split_network(self, intern=True, **kwargs):
         """Return each group (network) divided in segments"""
+        # Find timestep of dataset
+        # FIXME : how to know exact time sampling
+        t = unique(self.time)
+        dts = t[1:] - t[:-1]
+        timestep = median(dts)
+
         track_s, track_e, track_ref = build_index(self.tracks)
         ids = empty(
             len(self),
@@ -617,7 +624,7 @@ def split_network(self, intern=True, **kwargs):
                 ("next_obs", "i4"),
             ],
         )
-        ids["group"], ids["time"] = self.tracks, self.time
+        ids["group"], ids["time"] = self.tracks, int_(self.time / timestep)
         # Initialisation
         # To store the id of the segments, the backward and forward cost associations
         ids["track"], ids["previous_cost"], ids["next_cost"] = 0, 0, 0
@@ -644,6 +651,7 @@ def split_network(self, intern=True, **kwargs):
             local_ids["next_obs"][m] += i_s
         if display_iteration:
             print()
+        ids["time"] *= timestep
         return ids
 
     def set_tracks(self, x, y, ids, window, **kwargs):
@@ -655,8 +663,7 @@ def set_tracks(self, x, y, ids, window, **kwargs):
         :param ndarray ids: several fields like time, group, ...
         :param int windows: number of days where observations could missed
         """
-
-        time_index = build_index(ids["time"])
+        time_index = build_index((ids["time"]).astype("i4"))
         nb = x.shape[0]
         used = zeros(nb, dtype="bool")
         track_id = 1
@@ -701,8 +708,7 @@ def get_previous_obs(
         i_current, ids, x, y, time_s, time_e, time_ref, window, **kwargs
     ):
         """Backward association of observations to the segments"""
-
-        time_cur = ids["time"][i_current]
+        time_cur = int_(ids["time"][i_current])
         t0, t1 = time_cur - 1 - time_ref, max(time_cur - window - time_ref, 0)
         for t_step in range(t0, t1 - 1, -1):
             i0, i1 = time_s[t_step], time_e[t_step]
@@ -732,7 +738,7 @@ def get_previous_obs(
     def get_next_obs(i_current, ids, x, y, time_s, time_e, time_ref, window, **kwargs):
         """Forward association of observations to the segments"""
         time_max = time_e.shape[0] - 1
-        time_cur = ids["time"][i_current]
+        time_cur = int_(ids["time"][i_current])
         t0, t1 = time_cur + 1 - time_ref, min(time_cur + window - time_ref, time_max)
         if t0 > time_max:
             return -1