Add new method of observation display

Author: AntSimi

doc/conf.py

@@ -326,4 +326,8 @@
 
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {"https://docs.python.org/": None}
+intersphinx_mapping = {
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "python": ("https://docs.python.org/3/", None),
+    "matplotlib": ("https://matplotlib.org/", None),
+}

examples/02_eddy_identification/pet_display_id.py

@@ -14,12 +14,29 @@
 c = EddiesObservations.load_file(data.get_path("Cyclonic_20190223.nc"))
 
 # %%
-# Plot
+# draw contour
 fig = plt.figure(figsize=(15, 8))
-ax = fig.add_subplot(111)
+ax = fig.add_axes([0.03, 0.03, 0.94, 0.94])
 ax.set_aspect("equal")
 ax.set_xlim(0, 360)
 ax.set_ylim(-80, 80)
 a.display(ax, label="Anticyclonic", color="r", lw=1)
 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)
+# %%
+print(c)

notebooks/python_module/02_eddy_identification/pet_display_id.ipynb

@@ -15,7 +15,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "\nDisplay identification\n======================\n"
+        "\n# Display identification\n"
       ]
     },
     {
@@ -51,7 +51,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Plot\n\n"
+        "draw contour\n\n"
       ]
     },
     {
@@ -62,7 +62,54 @@
       },
       "outputs": [],
       "source": [
-        "fig = plt.figure(figsize=(15, 8))\nax = fig.add_subplot(111)\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, 0.94, 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\")"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "filled contour\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "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()"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "Get general informations\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "print(a)"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "print(c)"
       ]
     }
   ],

src/py_eddy_tracker/observations/observation.py

@@ -60,6 +60,9 @@
 from tokenize import TokenError
 from tarfile import ExFileObject
 from matplotlib.path import Path as BasePath
+from matplotlib.collections import PolyCollection
+from matplotlib.cm import get_cmap
+from matplotlib.colors import Normalize
 from .. import VAR_DESCR, VAR_DESCR_inv, __version__
 from ..generic import (
     distance_grid,
@@ -1342,9 +1345,62 @@ def scatter(self, ax, name, ref=None, factor=1, **kwargs):
             x = (x - ref) % 360 + ref
         return ax.scatter(x, self.latitude, c=self[name] * factor, **kwargs)
 
+    def filled(
+        self,
+        ax,
+        varname,
+        intern=False,
+        cmap="magma_r",
+        lut=10,
+        vmin=None,
+        vmax=None,
+        **kwargs,
+    ):
+        """
+        :param matplotlib.axes.Axes ax: matplotlib axes use to draw
+        :param str varname: var which will be use to fill contour
+        :param bool intern: if True draw speed contour instead of effective contour
+        :param str cmap: matplotlib colormap name
+        :param int,None lut: Number of division of colormaps
+        :param float,None vmin:
+        :param float,None vmax:
+        :return: Collection drawed
+        :rtype: matplotlib.collections.PolyCollection
+
+        .. minigallery:: py_eddy_tracker.EddiesObservations.filled
+        """
+        cmap = get_cmap(cmap, lut)
+        x_name, y_name = self.intern(intern)
+        x, y, v = self[x_name], self[y_name], self[varname]
+        if vmin is None:
+            vmin = v.min()
+        if vmax is None:
+            vmax = v.max()
+        v = (v - vmin) / (vmax - vmin)
+        verts = list()
+        colors = list()
+        for x_, y_, v_ in zip(x, y, v):
+            verts.append(create_vertice(x_, y_))
+            colors.append(cmap(v_))
+        c = PolyCollection(verts, facecolors=colors, **kwargs)
+        ax.add_collection(c)
+        c.cmap = cmap
+        c.norm = Normalize(vmin=vmin, vmax=vmax)
+        return c
+
     def display(
         self, ax, ref=None, extern_only=False, intern_only=False, nobs=True, **kwargs
     ):
+        """
+        :param matplotlib.axes.Axes ax: matplotlib axes use to draw
+        :param float,None ref: if define use like west bound
+        :param bool extern_only: if True draw effective contour only
+        :param bool intern_only: if True draw speed contour only
+        :param bool nobs: if True add number of eddies in label
+        :param dict kwargs: look at :py:meth:`matplotlib.axes.Axes.plot`
+
+        .. minigallery:: py_eddy_tracker.EddiesObservations.display
+        """
         if not extern_only:
             lon_s = flatten_line_matrix(self.obs["contour_lon_s"])
             lat_s = flatten_line_matrix(self.obs["contour_lat_s"])

src/py_eddy_tracker/observations/tracking.py

@@ -237,7 +237,7 @@ def extract_with_area(self, area, **kwargs):
         :return: Return all eddy tracks which are in bounds
         :rtype: TrackEddiesObservations
 
-        .. minigallery:: py_eddy_tracker.observations.tracking.TrackEddiesObservations.extract_with_area
+        .. minigallery:: py_eddy_tracker.TrackEddiesObservations.extract_with_area
         """
         mask = (self.latitude > area["llcrnrlat"]) * (self.latitude < area["urcrnrlat"])
         lon0 = area["llcrnrlon"]
@@ -254,7 +254,7 @@ def extract_with_period(self, period, **kwargs):
         :return: Return all eddy tracks which are in bounds
         :rtype: TrackEddiesObservations
 
-        .. minigallery:: py_eddy_tracker.observations.tracking.TrackEddiesObservations.extract_with_period
+        .. minigallery:: py_eddy_tracker.TrackEddiesObservations.extract_with_period
         """
         dataset_period = self.period
         p_min, p_max = period
@@ -336,7 +336,7 @@ def extract_with_length(self, bounds):
         :return: Return all eddy tracks which have length between bounds
         :rtype: TrackEddiesObservations
 
-        .. minigallery:: py_eddy_tracker.observations.tracking.TrackEddiesObservations.extract_with_length
+        .. minigallery:: py_eddy_tracker.TrackEddiesObservations.extract_with_length
         """
         b0, b1 = bounds
         if b0 >= 0 and b1 >= 0: