- english correction

- refactoring

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

@@ -2,7 +2,7 @@
 Colocate looper with eddy from altimetry
 ========================================
 
-All loopers data used in this example are a subset from the dataset describe in this article
+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)
 """
 
@@ -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
@@ -71,15 +71,15 @@ def update_axes(ax, mappable=None):
 # %%
 # Global view
 # ===========
-ax = start_axes("All drifter available in med from Lumpkin dataset")
+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 (index used have no correspondance with original dataset).
+# 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")
@@ -138,7 +138,7 @@ def update_axes(ax, mappable=None):
 
 
 # %%
-# Animation which show drifter with colocated eddy
+# 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))

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,

notebooks/python_module/06_grid_manipulation/pet_lavd.ipynb

@@ -15,7 +15,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "\n# LAVD experiment\n\nNaive method to reproduce LAVD(Lagrangian-Averaged Vorticity deviation) method with a static velocity field.\nIn the current example we didn't remove a mean vorticity.\n\nMethod are described here:\n\n    - Abernathey, Ryan, and George Haller. \"Transport by Lagrangian Vortices in the Eastern Pacific\",\n      Journal of Physical Oceanography 48, 3 (2018): 667-685, accessed Feb 16, 2021,\n      https://doi.org/10.1175/JPO-D-17-0102.1\n    - `Transport by Coherent Lagrangian Vortices`_,\n      R. Abernathey, Sinha A., Tarshish N., Liu T., Zhang C., Haller G., 2019,\n      Talk a t the Sources and Sinks of Ocean Mesoscale Eddy Energy CLIVAR Workshop\n\n    https://usclivar.org/sites/default/files/meetings/2019/presentations/Aberernathey_CLIVAR.pdf\n"
+        "\nLAVD experiment\n===============\n\nNaive method to reproduce LAVD(Lagrangian-Averaged Vorticity deviation) method with a static velocity field.\nIn the current example we didn't remove a mean vorticity.\n\nMethod are described here:\n\n    - Abernathey, Ryan, and George Haller. \"Transport by Lagrangian Vortices in the Eastern Pacific\",\n      Journal of Physical Oceanography 48, 3 (2018): 667-685, accessed Feb 16, 2021,\n      https://doi.org/10.1175/JPO-D-17-0102.1\n    - `Transport by Coherent Lagrangian Vortices`_,\n      R. Abernathey, Sinha A., Tarshish N., Liu T., Zhang C., Haller G., 2019,\n      Talk a t the Sources and Sinks of Ocean Mesoscale Eddy Energy CLIVAR Workshop\n\n    https://usclivar.org/sites/default/files/meetings/2019/presentations/Aberernathey_CLIVAR.pdf\n"
       ]
     },
     {
@@ -48,14 +48,14 @@
       },
       "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": [
-        "## Data\nTo compute vorticity ($\\omega$) we compute u/v field with a stencil and apply the following equation with stencil\nmethod :\n\n\\begin{align}\\omega = \\frac{\\partial v}{\\partial x} - \\frac{\\partial u}{\\partial y}\\end{align}\n\n"
+        "Data\n----\nTo compute vorticity ($\\omega$) we compute u/v field with a stencil and apply the following equation with stencil\nmethod :\n\n\\begin{align}\\omega = \\frac{\\partial v}{\\partial x} - \\frac{\\partial u}{\\partial y}\\end{align}\n\n"
       ]
     },
     {
@@ -91,7 +91,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Particles\nParticles specification\n\n"
+        "Particles\n---------\nParticles specification\n\n"
       ]
     },
     {
@@ -109,7 +109,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## LAVD\n\n"
+        "LAVD\n----\n\n"
       ]
     },
     {
@@ -127,7 +127,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "### Anim\nMovie of LAVD integration at each integration time step.\n\n"
+        "Anim\n^^^^\nMovie of LAVD integration at each integration time step.\n\n"
       ]
     },
     {
@@ -138,14 +138,14 @@
       },
       "outputs": [],
       "source": [
-        "def update(i_frame):\n    global lavd, i\n    i += 1\n    x, y = particule.__next__()\n    # Interp vorticity on new_position\n    lavd += abs(g.interp(\"vort\", x, y).reshape(original_shape) * 1 / nb_time)\n    txt.set_text(f\"T0 + {i / step_by_day:.2f} days of advection\")\n    pcolormesh.set_array(lavd / i * nb_time)\n    return pcolormesh, txt\n\n\nkw_video = dict(frames=arange(nb_time), interval=1000.0 / step_by_day / 2, blit=True)\nfig, ax, txt = start_ax(dpi=60)\nx_g_, y_g_ = arange(0 - step / 2, 36 + step / 2, step), arange(\n    28 - step / 2, 46 + step / 2, step\n)\n# pcolorfast will be faster than pcolormesh, we could use pcolorfast due to x and y are regular\npcolormesh = ax.pcolorfast(x_g_, y_g_, lavd, **kw_vorticity)\nupdate_axes(ax, pcolormesh)\n_ = VideoAnimation(ax.figure, update, **kw_video)"
+        "def update(i_frame):\n    global lavd, i\n    i += 1\n    x, y = particule.__next__()\n    # Interp vorticity on new_position\n    lavd += abs(g.interp(\"vort\", x, y).reshape(original_shape) * 1 / nb_time)\n    txt.set_text(f\"T0 + {i / step_by_day:.2f} days of advection\")\n    pcolormesh.set_array(lavd / i * nb_time)\n    return pcolormesh, txt\n\n\nkw_video = dict(frames=arange(nb_time), interval=1000.0 / step_by_day / 2, blit=True)\nfig, ax, txt = start_ax(dpi=60)\nx_g_, y_g_ = (\n    arange(0 - step / 2, 36 + step / 2, step),\n    arange(28 - step / 2, 46 + step / 2, step),\n)\n# pcolorfast will be faster than pcolormesh, we could use pcolorfast due to x and y are regular\npcolormesh = ax.pcolorfast(x_g_, y_g_, lavd, **kw_vorticity)\nupdate_axes(ax, pcolormesh)\n_ = VideoAnimation(ax.figure, update, **kw_video)"
       ]
     },
     {
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "### Final LAVD\n\n"
+        "Final LAVD\n^^^^^^^^^^\n\n"
       ]
     },
     {
@@ -163,7 +163,7 @@
       },
       "outputs": [],
       "source": [
-        "lavd = RegularGridDataset.with_array(\n    coordinates=(\"lon\", \"lat\"),\n    datas=dict(\n        lavd=lavd.T,\n        lon=x_g,\n        lat=y_g,\n    ),\n    centered=True,\n)"
+        "lavd = RegularGridDataset.with_array(\n    coordinates=(\"lon\", \"lat\"),\n    datas=dict(lavd=lavd.T, lon=x_g, lat=y_g,),\n    centered=True,\n)"
       ]
     },
     {
@@ -201,7 +201,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.9"
+      "version": "3.7.7"
     }
   },
   "nbformat": 4,