add docstring

Author: AntSimi

examples/02_eddy_identification/pet_display_id.py

@@ -13,6 +13,22 @@
 a = EddiesObservations.load_file(data.get_path("Anticyclonic_20190223.nc"))
 c = EddiesObservations.load_file(data.get_path("Cyclonic_20190223.nc"))
 
+# %%
+# filled contour with amplitude field
+fig = plt.figure(figsize=(15, 8))
+ax = fig.add_axes([0.03, 0.03, 0.90, 0.94])
+ax.set_aspect("equal")
+ax.set_xlim(0, 140)
+ax.set_ylim(-80, 0)
+kwargs = dict(extern_only=True, color="k", lw=1)
+a.display(ax, **kwargs), c.display(ax, **kwargs)
+a.filled(ax, "amplitude", cmap="magma_r", vmin=0, vmax=.5)
+m = c.filled(ax, "amplitude", cmap="magma_r", vmin=0, vmax=.5)
+colorbar = plt.colorbar(m, cax=ax.figure.add_axes([0.95, 0.05, 0.01, 0.9]))
+colorbar.set_label('Amplitude (m)')
+
+plt.show()
+
 # %%
 # draw contour
 fig = plt.figure(figsize=(15, 8))
@@ -24,17 +40,6 @@
 c.display(ax, label="Cyclonic", color="b", lw=1)
 ax.legend(loc="upper right")
 
-# %%
-# filled contour
-fig = plt.figure(figsize=(15, 8))
-ax = fig.add_axes([0.03, 0.03, 0.90, 0.94])
-ax.set_aspect("equal")
-ax.set_xlim(0, 140)
-ax.set_ylim(-80, 0)
-a.display(ax, label="Anticyclonic", color="r", lw=1)
-m = a.filled(ax, "amplitude", cmap="magma_r", vmin=0, vmax=.5)
-plt.colorbar(m, cax=ax.figure.add_axes([0.95, 0.05, 0.01, 0.9]))
-plt.show()
 # %%
 # Get general informations
 print(a)

notebooks/python_module/02_eddy_identification/pet_display_id.ipynb

@@ -51,7 +51,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "draw contour\n\n"
+        "filled contour with amplitude field\n\n"
       ]
     },
     {
@@ -62,14 +62,14 @@
       },
       "outputs": [],
       "source": [
-        "fig = plt.figure(figsize=(15, 8))\nax = fig.add_axes([0.03, 0.03, 0.94, 0.94])\nax.set_aspect(\"equal\")\nax.set_xlim(0, 360)\nax.set_ylim(-80, 80)\na.display(ax, label=\"Anticyclonic\", color=\"r\", lw=1)\nc.display(ax, label=\"Cyclonic\", color=\"b\", lw=1)\nax.legend(loc=\"upper right\")"
+        "fig = plt.figure(figsize=(15, 8))\nax = fig.add_axes([0.03, 0.03, 0.90, 0.94])\nax.set_aspect(\"equal\")\nax.set_xlim(0, 140)\nax.set_ylim(-80, 0)\nkwargs = dict(extern_only=True, color=\"k\", lw=1)\na.display(ax, **kwargs), c.display(ax, **kwargs)\na.filled(ax, \"amplitude\", cmap=\"magma_r\", vmin=0, vmax=.5)\nm = c.filled(ax, \"amplitude\", cmap=\"magma_r\", vmin=0, vmax=.5)\ncolorbar = plt.colorbar(m, cax=ax.figure.add_axes([0.95, 0.05, 0.01, 0.9]))\ncolorbar.set_label('Amplitude (m)')\n\nplt.show()"
       ]
     },
     {
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "filled contour\n\n"
+        "draw contour\n\n"
       ]
     },
     {
@@ -80,7 +80,7 @@
       },
       "outputs": [],
       "source": [
-        "fig = plt.figure(figsize=(15, 8))\nax = fig.add_axes([0.03, 0.03, 0.90, 0.94])\nax.set_aspect(\"equal\")\nax.set_xlim(0, 140)\nax.set_ylim(-80, 0)\na.display(ax, label=\"Anticyclonic\", color=\"r\", lw=1)\nm = a.filled(ax, \"amplitude\", cmap=\"magma_r\", vmin=0, vmax=.5)\nplt.colorbar(m, cax=ax.figure.add_axes([0.95, 0.05, 0.01, 0.9]))\nplt.show()"
+        "fig = plt.figure(figsize=(15, 8))\nax = fig.add_axes([0.03, 0.03, 0.94, 0.94])\nax.set_aspect(\"equal\")\nax.set_xlim(0, 360)\nax.set_ylim(-80, 80)\na.display(ax, label=\"Anticyclonic\", color=\"r\", lw=1)\nc.display(ax, label=\"Cyclonic\", color=\"b\", lw=1)\nax.legend(loc=\"upper right\")"
       ]
     },
     {

src/py_eddy_tracker/dataset/grid.py

@@ -593,6 +593,7 @@ def eddy_identification(
         :return: Return a list of 2 elements: Anticyclone and Cyclone
         :rtype: py_eddy_tracker.observations.observation.EddiesObservations
 
+        .. minigallery:: py_eddy_tracker.GridDataset.eddy_identification
         """
         if not isinstance(date, datetime):
             raise Exception("Date argument be a datetime object")

src/py_eddy_tracker/observations/observation.py

@@ -322,6 +322,11 @@ def add_rotation_type(self):
         return new
 
     def circle_contour(self):
+        """
+        Set contour like a circle with radius and center data
+
+        .. minigallery:: py_eddy_tracker.EddiesObservations.circle_contour
+        """
         angle = radians(linspace(0, 360, self.track_array_variables))
         x_norm, y_norm = cos(angle), sin(angle)
         for i, obs in enumerate(self):
@@ -1423,6 +1428,17 @@ def display(
             ax.plot(lon_e, lat_e, linestyle="-.", **kwargs_e)
 
     def grid_count(self, bins, intern=False, center=False):
+        """
+        Compute count of eddies in each bin (use of all pixel in each contour)
+
+        :param (numpy.array,numpy.array) bins: bins to compute count
+        :param bool intern: if True use speed contour only
+        :param bool center: if True use of center to count
+        :return: return grid of count
+        :rtype: py_eddy_tracker.dataset.grid.RegularGridDataset
+
+        .. minigallery:: py_eddy_tracker.EddiesObservations.grid_count
+        """
         x_name, y_name = self.intern(intern)
         x_bins, y_bins = arange(*bins[0]), arange(*bins[1])
         x0 = bins[0][0]