update reference of lavd example

Author: AntSimi

examples/06_grid_manipulation/pet_advect.py

@@ -79,7 +79,8 @@ def anim_ax(generator, **kw):
     ax = fig.add_axes([0, 0, 1, 1], projection="full_axes")
     ax.set_xlim(19, 30), ax.set_ylim(31, 36.5), ax.grid()
     a.filled(ax, facecolors="r", alpha=0.1), c.filled(ax, facecolors="b", alpha=0.1)
-    return fig, ax.text(21, 32.1, ""), ax.plot([], [], "k", **kw)[0], t
+    line = ax.plot([], [], "k", **kw)[0]
+    return fig, ax.text(21, 32.1, ""), line, t
 
 
 def update(i_frame, t_step):

examples/06_grid_manipulation/pet_lavd.py

@@ -7,8 +7,8 @@
 
 Method are described here:
 
-    - `Transport by Lagrangian Vortices in the Eastern Pacific <https://doi.org/10.1175/JPO-D-17-0102.1>`_
-    - `Transport by Coherent Lagrangian Vortices`_
+    - Abernathey, Ryan, and George Haller. " Transport by Lagrangian Vortices in the Eastern Pacific", Journal of Physical Oceanography 48, 3 (2018): 667-685, accessed Feb 16, 2021, https://doi.org/10.1175/JPO-D-17-0102.1
+    - `Transport by Coherent Lagrangian Vortices`_, R. Abernathey, Sinha A., Tarshish N., Liu T., Zhang C., Haller G., 2019, Talk a t the Sources and Sinks of Ocean Mesoscale Eddy Energy CLIVAR Workshop
 
 .. _Transport by Coherent Lagrangian Vortices:
     https://usclivar.org/sites/default/files/meetings/2019/presentations/Aberernathey_CLIVAR.pdf
@@ -74,7 +74,7 @@ def save(self, *args, **kwargs):
 # %%
 # Data
 # ----
-# To compute vorticity(:math:`\omega`) we compute u/v field with a stencil and apply the following equation with stencil
+# To compute vorticity (:math:`\omega`) we compute u/v field with a stencil and apply the following equation with stencil
 # method :
 #
 # .. math::
@@ -166,11 +166,11 @@ def update(i_frame):
 
 # %%
 # Display final LAVD with py eddy tracker detection.
-# Period used for LAVD integration(8 days) is too short for a real use, but choose for example efficiency.
+# Period used for LAVD integration (8 days) is too short for a real use, but choose for example efficiency.
 fig, ax, _ = start_ax()
 mappable = lavd.display(ax, "lavd", **kw_vorticity)
 NetworkObservations.load_file(get_path("Anticyclonic_20160515.nc")).display(
     ax, color="k"
 )
 NetworkObservations.load_file(get_path("Cyclonic_20160515.nc")).display(ax, color="k")
-update_axes(ax, mappable)
+_ = update_axes(ax, mappable)

notebooks/python_module/06_grid_manipulation/pet_advect.ipynb

@@ -109,7 +109,7 @@
       },
       "outputs": [],
       "source": [
-        "x, y = np.meshgrid(np.arange(13, 36, 0.125), np.arange(28, 40, 0.125))\nx, y = x.reshape(-1), y.reshape(-1)\n# Remove all original position that we can't advect at first place\nm = ~np.isnan(g.interp(\"u\", x, y))\nx, y = x[m], y[m]\n\n# Movie properties\nkwargs = dict(frames=np.arange(51), interval=90)\nkw_p = dict(nb_step=2, time_step=21600)\nframe_t = kw_p[\"nb_step\"] * kw_p[\"time_step\"] / 86400.0\n\n\ndef anim_ax(generator, **kw):\n    t = 0\n    for _ in range(4):\n        generator.__next__()\n        t += frame_t\n\n    fig = plt.figure(figsize=(10, 5), dpi=64)\n    ax = fig.add_axes([0, 0, 1, 1], projection=\"full_axes\")\n    ax.set_xlim(19, 30), ax.set_ylim(31, 36.5), ax.grid()\n    a.filled(ax, facecolors=\"r\", alpha=0.1), c.filled(ax, facecolors=\"b\", alpha=0.1)\n    return fig, ax.text(21, 32.1, \"\"), ax.plot([], [], \"k\", **kw)[0], t\n\n\ndef update(i_frame, t_step):\n    global t\n    x, y = p.__next__()\n    t += t_step\n    l.set_data(x, y)\n    txt.set_text(f\"T0 + {t:.1f} days\")"
+        "x, y = np.meshgrid(np.arange(13, 36, 0.125), np.arange(28, 40, 0.125))\nx, y = x.reshape(-1), y.reshape(-1)\n# Remove all original position that we can't advect at first place\nm = ~np.isnan(g.interp(\"u\", x, y))\nx, y = x[m], y[m]\n\n# Movie properties\nkwargs = dict(frames=np.arange(51), interval=90)\nkw_p = dict(nb_step=2, time_step=21600)\nframe_t = kw_p[\"nb_step\"] * kw_p[\"time_step\"] / 86400.0\n\n\ndef anim_ax(generator, **kw):\n    t = 0\n    for _ in range(4):\n        generator.__next__()\n        t += frame_t\n\n    fig = plt.figure(figsize=(10, 5), dpi=64)\n    ax = fig.add_axes([0, 0, 1, 1], projection=\"full_axes\")\n    ax.set_xlim(19, 30), ax.set_ylim(31, 36.5), ax.grid()\n    a.filled(ax, facecolors=\"r\", alpha=0.1), c.filled(ax, facecolors=\"b\", alpha=0.1)\n    line = ax.plot([], [], \"k\", **kw)[0]\n    return fig, ax.text(21, 32.1, \"\"), line, t\n\n\ndef update(i_frame, t_step):\n    global t\n    x, y = p.__next__()\n    t += t_step\n    l.set_data(x, y)\n    txt.set_text(f\"T0 + {t:.1f} days\")"
       ]
     },
     {

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    - `Transport by Lagrangian Vortices in the Eastern Pacific <https://doi.org/10.1175/JPO-D-17-0102.1>`_\n    - `Transport by Coherent Lagrangian Vortices`_\n\n    https://usclivar.org/sites/default/files/meetings/2019/presentations/Aberernathey_CLIVAR.pdf\n"
+        "\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\", Journal of Physical Oceanography 48, 3 (2018): 667-685, accessed Feb 16, 2021, https://doi.org/10.1175/JPO-D-17-0102.1\n    - `Transport by Coherent Lagrangian Vortices`_, R. Abernathey, Sinha A., Tarshish N., Liu T., Zhang C., Haller G., 2019, 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"
       ]
     },
     {
@@ -55,7 +55,7 @@
       "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\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"
       ]
     },
     {
@@ -170,7 +170,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Display final LAVD with py eddy tracker detection.\nPeriod used for LAVD integration(8 days) is too short for a real use, but choose for example efficiency.\n\n"
+        "Display final LAVD with py eddy tracker detection.\nPeriod used for LAVD integration (8 days) is too short for a real use, but choose for example efficiency.\n\n"
       ]
     },
     {
@@ -181,7 +181,7 @@
       },
       "outputs": [],
       "source": [
-        "fig, ax, _ = start_ax()\nmappable = lavd.display(ax, \"lavd\", **kw_vorticity)\nNetworkObservations.load_file(get_path(\"Anticyclonic_20160515.nc\")).display(\n    ax, color=\"k\"\n)\nNetworkObservations.load_file(get_path(\"Cyclonic_20160515.nc\")).display(ax, color=\"k\")\nupdate_axes(ax, mappable)"
+        "fig, ax, _ = start_ax()\nmappable = lavd.display(ax, \"lavd\", **kw_vorticity)\nNetworkObservations.load_file(get_path(\"Anticyclonic_20160515.nc\")).display(\n    ax, color=\"k\"\n)\nNetworkObservations.load_file(get_path(\"Cyclonic_20160515.nc\")).display(ax, color=\"k\")\n_ = update_axes(ax, mappable)"
       ]
     }
   ],