Loopers

CHANGELOG.rst

@@ -21,11 +21,13 @@ Fixed
 
 - Fix bug in convolution(filter), lowest rows was replace by zeros in convolution computation.
   Important impact for tiny kernel
+- Fix method of sampling before contour fitting
 
 Added
 ^^^^^
 
 - Allow to replace mask by isnan method to manage nan data instead of masked data
+- Add drifter colocation example
 
 [3.5.0] - 2021-06-22
 --------------------

examples/06_grid_manipulation/pet_advect.py

@@ -50,7 +50,7 @@ def _repr_html_(self, *args, **kwargs):
 
     def save(self, *args, **kwargs):
         if args[0].endswith("gif"):
-            # In this case gif is use to create thumbnail which are not use but consume same time than video
+            # In this case gif is used to create thumbnail which is not used but consume same time than video
             # So we create an empty file, to save time
             with open(args[0], "w") as _:
                 pass

examples/06_grid_manipulation/pet_lavd.py

@@ -65,7 +65,7 @@ def _repr_html_(self, *args, **kwargs):
 
     def save(self, *args, **kwargs):
         if args[0].endswith("gif"):
-            # In this case gif is use to create thumbnail which are not use but consume same time than video
+            # In this case gif is used to create thumbnail which is not used but consume same time than video
             # So we create an empty file, to save time
             with open(args[0], "w") as _:
                 pass
@@ -159,11 +159,7 @@ def update(i_frame):
 # Format LAVD data
 lavd = RegularGridDataset.with_array(
     coordinates=("lon", "lat"),
-    datas=dict(
-        lavd=lavd.T,
-        lon=x_g,
-        lat=y_g,
-    ),
+    datas=dict(lavd=lavd.T, lon=x_g, lat=y_g,),
     centered=True,
 )
 

examples/07_cube_manipulation/pet_cube.py

@@ -31,7 +31,7 @@ def _repr_html_(self, *args, **kwargs):
 
     def save(self, *args, **kwargs):
         if args[0].endswith("gif"):
-            # In this case gif is use to create thumbnail which are not use but consume same time than video
+            # In this case gif is used to create thumbnail which is not used but consume same time than video
             # So we create an empty file, to save time
             with open(args[0], "w") as _:
                 pass

examples/08_tracking_manipulation/pet_track_anim_matplotlib_animation.py

@@ -30,7 +30,7 @@ def _repr_html_(self, *args, **kwargs):
 
     def save(self, *args, **kwargs):
         if args[0].endswith("gif"):
-            # In this case gif is use to create thumbnail which are not use but consume same time than video
+            # In this case gif is used to create thumbnail which is not used but consume same time than video
             # So we create an empty file, to save time
             with open(args[0], "w") as _:
                 pass

examples/10_tracking_diagnostics/pet_normalised_lifetime.py

@@ -65,14 +65,14 @@ def eddy_norm_lifetime(self, name, nb, factor=1):
 # %%
 # Figure
 # ------
-fig, axs = plt.subplots(nrows=2, figsize=(8, 6))
+fig, (ax0, ax1) = plt.subplots(nrows=2, figsize=(8, 6))
 
-axs[0].set_title("Normalised Mean Radius")
-axs[0].plot(*AC_radius), axs[0].plot(*CC_radius)
-axs[0].set_ylabel("Radius (km)"), axs[0].grid()
-axs[0].set_xlim(0, 1), axs[0].set_ylim(0, None)
+ax0.set_title("Normalised Mean Radius")
+ax0.plot(*AC_radius), ax0.plot(*CC_radius)
+ax0.set_ylabel("Radius (km)"), ax0.grid()
+ax0.set_xlim(0, 1), ax0.set_ylim(0, None)
 
-axs[1].set_title("Normalised Mean Amplitude")
-axs[1].plot(*AC_amplitude, label="AC"), axs[1].plot(*CC_amplitude, label="CC")
-axs[1].set_ylabel("Amplitude (cm)"), axs[1].grid(), axs[1].legend()
-_ = axs[1].set_xlim(0, 1), axs[1].set_ylim(0, None)
+ax1.set_title("Normalised Mean Amplitude")
+ax1.plot(*AC_amplitude, label="AC"), ax1.plot(*CC_amplitude, label="CC")
+ax1.set_ylabel("Amplitude (cm)"), ax1.grid(), ax1.legend()
+_ = ax1.set_xlim(0, 1), ax1.set_ylim(0, None)

examples/12_external_data/pet_drifter_loopers.py

@@ -0,0 +1,153 @@
+"""
+Colocate looper with eddy from altimetry
+========================================
+
+All loopers data used in this example are a subset from the dataset described in this article
+[Lumpkin, R. : Global characteristics of coherent vortices from surface drifter trajectories](https://doi.org/10.1002/2015JC011435)
+"""
+
+import re
+
+import numpy as np
+import py_eddy_tracker_sample
+from matplotlib import pyplot as plt
+from matplotlib.animation import FuncAnimation
+
+from py_eddy_tracker import data
+from py_eddy_tracker.appli.gui import Anim
+from py_eddy_tracker.observations.tracking import TrackEddiesObservations
+
+
+# %%
+class VideoAnimation(FuncAnimation):
+    def _repr_html_(self, *args, **kwargs):
+        """To get video in html and have a player"""
+        content = self.to_html5_video()
+        return re.sub(
+            r'width="[0-9]*"\sheight="[0-9]*"', 'width="100%" height="100%"', content
+        )
+
+    def save(self, *args, **kwargs):
+        if args[0].endswith("gif"):
+            # In this case gif is used to create thumbnail which is not used but consume same time than video
+            # So we create an empty file, to save time
+            with open(args[0], "w") as _:
+                pass
+            return
+        return super().save(*args, **kwargs)
+
+
+def start_axes(title):
+    fig = plt.figure(figsize=(13, 5))
+    ax = fig.add_axes([0.03, 0.03, 0.90, 0.94], aspect="equal")
+    ax.set_xlim(-6, 36.5), ax.set_ylim(30, 46)
+    ax.set_title(title, weight="bold")
+    return ax
+
+
+def update_axes(ax, mappable=None):
+    ax.grid()
+    if mappable:
+        plt.colorbar(mappable, cax=ax.figure.add_axes([0.94, 0.05, 0.01, 0.9]))
+
+
+# %%
+# Load eddies dataset
+cyclonic_eddies = TrackEddiesObservations.load_file(
+    py_eddy_tracker_sample.get_demo_path("eddies_med_adt_allsat_dt2018/Cyclonic.zarr")
+)
+anticyclonic_eddies = TrackEddiesObservations.load_file(
+    py_eddy_tracker_sample.get_demo_path(
+        "eddies_med_adt_allsat_dt2018/Anticyclonic.zarr"
+    )
+)
+
+# %%
+# Load loopers dataset
+loopers_med = TrackEddiesObservations.load_file(
+    data.get_demo_path("loopers_lumpkin_med.nc")
+)
+
+# %%
+# Global view
+# ===========
+ax = start_axes("All drifters available in Med from Lumpkin dataset")
+loopers_med.plot(ax, lw=0.5, color="r", ref=-10)
+update_axes(ax)
+
+# %%
+# One segment of drifter
+# ======================
+#
+# Get a drifter segment (the indexes used have no correspondance with the original dataset).
+looper = loopers_med.extract_ids((3588,))
+fig = plt.figure(figsize=(16, 6))
+ax = fig.add_subplot(111, aspect="equal")
+looper.plot(ax, lw=0.5, label="Original position of drifter")
+looper_filtered = looper.copy()
+looper_filtered.position_filter(1, 13)
+s = looper_filtered.scatter(
+    ax,
+    "time",
+    cmap=plt.get_cmap("Spectral_r", 20),
+    label="Filtered position of drifter",
+)
+plt.colorbar(s).set_label("time (days from 1/1/1950)")
+ax.legend()
+ax.grid()
+
+# %%
+# Try to find a detected eddies with adt at same place. We used filtered track to simulate an eddy center
+match = looper_filtered.close_tracks(
+    anticyclonic_eddies, method="close_center", delta=0.1, nb_obs_min=50
+)
+fig = plt.figure(figsize=(16, 6))
+ax = fig.add_subplot(111, aspect="equal")
+looper.plot(ax, lw=0.5, label="Original position of drifter")
+looper_filtered.plot(ax, lw=1.5, label="Filtered position of drifter")
+match.plot(ax, lw=1.5, label="Matched eddy")
+ax.legend()
+ax.grid()
+
+# %%
+# Display radius of this 2 datasets.
+fig = plt.figure(figsize=(20, 8))
+ax = fig.add_subplot(111)
+ax.plot(looper.time, looper.radius_s / 1e3, label="loopers")
+looper_radius = looper.copy()
+looper_radius.median_filter(1, "time", "radius_s", inplace=True)
+looper_radius.loess_filter(13, "time", "radius_s", inplace=True)
+ax.plot(
+    looper_radius.time,
+    looper_radius.radius_s / 1e3,
+    label="loopers (filtered half window 13 days)",
+)
+ax.plot(match.time, match.radius_s / 1e3, label="altimetry")
+match_radius = match.copy()
+match_radius.median_filter(1, "time", "radius_s", inplace=True)
+match_radius.loess_filter(13, "time", "radius_s", inplace=True)
+ax.plot(
+    match_radius.time,
+    match_radius.radius_s / 1e3,
+    label="altimetry (filtered half window 13 days)",
+)
+ax.set_ylabel("radius(km)"), ax.set_ylim(0, 100)
+ax.legend()
+ax.set_title("Radius from loopers and altimeter")
+ax.grid()
+
+
+# %%
+# Animation of a drifter and its colocated eddy
+def update(frame):
+    # We display last 5 days of loopers trajectory
+    m = (looper.time < frame) * (looper.time > (frame - 5))
+    anim.func_animation(frame)
+    line.set_data(looper.lon[m], looper.lat[m])
+
+
+anim = Anim(match, intern=True, figsize=(8, 8), cmap="magma_r", nb_step=10, dpi=75)
+# mappable to show drifter in red
+line = anim.ax.plot([], [], "r", lw=4, zorder=100)[0]
+anim.fig.suptitle("")
+_ = VideoAnimation(anim.fig, update, frames=np.arange(*anim.period, 1), interval=125)

examples/16_network/pet_follow_particle.py

@@ -31,7 +31,7 @@ def _repr_html_(self, *args, **kwargs):
 
     def save(self, *args, **kwargs):
         if args[0].endswith("gif"):
-            # In this case gif is used to create thumbnail which are not used but consumes same time than video
+            # In this case gif is used to create thumbnail which is not used but consume same time than video
             # So we create an empty file, to save time
             with open(args[0], "w") as _:
                 pass

examples/16_network/pet_group_anim.py

@@ -29,7 +29,7 @@ def _repr_html_(self, *args, **kwargs):
 
     def save(self, *args, **kwargs):
         if args[0].endswith("gif"):
-            # In this case gif is use to create thumbnail which are not use but consume same time than video
+            # In this case gif is used to create thumbnail which is not used but consume same time than video
             # So we create an empty file, to save time
             with open(args[0], "w") as _:
                 pass

examples/16_network/pet_ioannou_2017_case.py

@@ -36,7 +36,7 @@ def _repr_html_(self, *args, **kwargs):
 
     def save(self, *args, **kwargs):
         if args[0].endswith("gif"):
-            # In this case gif is use to create thumbnail which are not use but consume same time than video
+            # In this case gif is used to create thumbnail which is not used but consume same time than video
             # So we create an empty file, to save time
             with open(args[0], "w") as _:
                 pass

examples/16_network/pet_segmentation_anim.py

@@ -27,7 +27,7 @@ def _repr_html_(self, *args, **kwargs):
 
     def save(self, *args, **kwargs):
         if args[0].endswith("gif"):
-            # In this case gif is use to create thumbnail which are not use but consume same time than video
+            # In this case gif is used to create thumbnail which is not used but consume same time than video
             # So we create an empty file, to save time
             with open(args[0], "w") as _:
                 pass
@@ -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,)

notebooks/python_module/06_grid_manipulation/pet_advect.ipynb

@@ -15,7 +15,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "\n# Grid advection\n\nDummy advection which use only static geostrophic current, which didn't solve the complex circulation of the ocean.\n"
+        "\nGrid advection\n==============\n\nDummy advection which use only static geostrophic current, which didn't solve the complex circulation of the ocean.\n"
       ]
     },
     {
@@ -91,14 +91,14 @@
       },
       "outputs": [],
       "source": [
-        "class VideoAnimation(FuncAnimation):\n    def _repr_html_(self, *args, **kwargs):\n        \"\"\"To get video in html and have a player\"\"\"\n        content = self.to_html5_video()\n        return re.sub(\n            r'width=\"[0-9]*\"\\sheight=\"[0-9]*\"', 'width=\"100%\" height=\"100%\"', content\n        )\n\n    def save(self, *args, **kwargs):\n        if args[0].endswith(\"gif\"):\n            # In this case gif is use to create thumbnail which are not use but consume same time than video\n            # So we create an empty file, to save time\n            with open(args[0], \"w\") as _:\n                pass\n            return\n        return super().save(*args, **kwargs)"
+        "class VideoAnimation(FuncAnimation):\n    def _repr_html_(self, *args, **kwargs):\n        \"\"\"To get video in html and have a player\"\"\"\n        content = self.to_html5_video()\n        return re.sub(\n            r'width=\"[0-9]*\"\\sheight=\"[0-9]*\"', 'width=\"100%\" height=\"100%\"', content\n        )\n\n    def save(self, *args, **kwargs):\n        if args[0].endswith(\"gif\"):\n            # In this case gif is used to create thumbnail which is not used but consume same time than video\n            # So we create an empty file, to save time\n            with open(args[0], \"w\") as _:\n                pass\n            return\n        return super().save(*args, **kwargs)"
       ]
     },
     {
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Anim\nParticles setup\n\n"
+        "Anim\n----\nParticles setup\n\n"
       ]
     },
     {
@@ -152,7 +152,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "### Filament forward\nDraw 3 last position in one path for each particles.,\nit could be run backward with `backward=True` option in filament method\n\n"
+        "Filament forward\n^^^^^^^^^^^^^^^^\nDraw 3 last position in one path for each particles.,\nit could be run backward with `backward=True` option in filament method\n\n"
       ]
     },
     {
@@ -170,7 +170,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "### Particle forward\nForward advection of particles\n\n"
+        "Particle forward\n^^^^^^^^^^^^^^^^^\nForward advection of particles\n\n"
       ]
     },
     {
@@ -206,14 +206,14 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Particles stat\n\n"
+        "Particles stat\n--------------\n\n"
       ]
     },
     {
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "### Time_step settings\nDummy experiment to test advection precision, we run particles 50 days forward and backward with different time step\nand we measure distance between new positions and original positions.\n\n"
+        "Time_step settings\n^^^^^^^^^^^^^^^^^^\nDummy experiment to test advection precision, we run particles 50 days forward and backward with different time step\nand we measure distance between new positions and original positions.\n\n"
       ]
     },
     {
@@ -231,7 +231,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "### Time duration\nWe keep same time_step but change time duration\n\n"
+        "Time duration\n^^^^^^^^^^^^^\nWe keep same time_step but change time duration\n\n"
       ]
     },
     {
@@ -262,7 +262,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.9"
+      "version": "3.7.7"
     }
   },
   "nbformat": 4,