Use updated method in example

AntSimi · AntSimi · commit 0f189be164ec · 2020-10-12T10:53:45.000+02:00
Update docstring
diff --git a/.gitignore b/.gitignore
@@ -71,6 +71,7 @@ instance/
 # Sphinx documentation
 docs/_build/
 doc/gen_modules/
+doc/_autosummary/
 
 # PyBuilder
 target/
diff --git a/examples/02_eddy_identification/pet_eddy_detection.py b/examples/02_eddy_identification/pet_eddy_detection.py
@@ -141,11 +141,10 @@ def update_axes(ax, mappable=None):
 update_axes(ax, m)
 
 # %%
-# Display speed radius of eddies detected
+# Display speed radius of eddies detected with filled eddy contours
 ax = start_axes("Eddies speed radius (km)")
-a.filled(
-    ax, "radius_e", vmin=10, vmax=80, cmap="magma_r", factor=0.001, lut=14, ref=-10
-)
+kwargs = dict(vmin=10, vmax=80, cmap="magma_r", factor=0.001, lut=14, ref=-10)
+a.filled(ax, "radius_e", **kwargs)
 m = c.filled(
     ax, "radius_e", vmin=10, vmax=80, cmap="magma_r", factor=0.001, lut=14, ref=-10
 )
diff --git a/examples/02_eddy_identification/pet_interp_grid_on_dataset.py b/examples/02_eddy_identification/pet_interp_grid_on_dataset.py
@@ -54,11 +54,11 @@ def update_axes(ax, mappable=None):
 # %%
 # Get mean of eke in each effective contour
 
-ax = start_axes("EKE (cm²/s²)")
+ax = start_axes("EKE mean (cm²/s²)")
 a.display(ax, color="r", linewidth=0.5, label="Anticyclonic", ref=-10)
 c.display(ax, color="b", linewidth=0.5, label="Cyclonic", ref=-10)
 eke = a.interp_grid(aviso_map, "eke", method="mean", intern=False)
-ax.scatter((a.longitude + 10) % 360 - 10, a.latitude, c=eke, **eke_kwargs)
+a.filled(ax, eke, ref=-10, **eke_kwargs)
 eke = c.interp_grid(aviso_map, "eke", method="mean", intern=False)
-m = ax.scatter((c.longitude + 10) % 360 - 10, c.latitude, c=eke, **eke_kwargs)
+m = c.filled(ax, eke, ref=-10, **eke_kwargs)
 update_axes(ax, m)
diff --git a/examples/02_eddy_identification/pet_sla_and_adt.py b/examples/02_eddy_identification/pet_sla_and_adt.py
@@ -133,8 +133,9 @@ def update_axes(ax, mappable=None):
     ax.set_xlabel("Absolute Dynamic Topography")
     ax.set_ylabel("Sea Level Anomaly")
 
-    ax.plot(a_adt[field][i_a_adt] * factor, a_sla[field][i_a_sla] * factor, "r.")
-    ax.plot(c_adt[field][i_c_adt] * factor, c_sla[field][i_c_sla] * factor, "b.")
+    ax.plot(a_adt[field][i_a_adt] * factor, a_sla[field][i_a_sla] * factor, "r.", label='Anticyclonic')
+    ax.plot(c_adt[field][i_c_adt] * factor, c_sla[field][i_c_sla] * factor, "b.", label='Cyclonic')
     ax.set_aspect("equal"), ax.grid()
     ax.plot((0, 1000), (0, 1000), "g")
     ax.set_xlim(0, stop), ax.set_ylim(0, stop)
+    ax.legend()
diff --git a/notebooks/python_module/02_eddy_identification/pet_contour_circle.ipynb b/notebooks/python_module/02_eddy_identification/pet_contour_circle.ipynb
@@ -15,7 +15,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "\nDisplay contour & circle\n========================\n"
+        "\n# Display contour & circle\n"
       ]
     },
     {
diff --git a/notebooks/python_module/02_eddy_identification/pet_eddy_detection.ipynb b/notebooks/python_module/02_eddy_identification/pet_eddy_detection.ipynb
@@ -260,7 +260,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Display speed radius of eddies detected\n\n"
+        "Display speed radius of eddies detected with filled eddy contours\n\n"
       ]
     },
     {
@@ -271,7 +271,7 @@
       },
       "outputs": [],
       "source": [
-        "ax = start_axes(\"Eddies speed radius (km)\")\na.filled(\n    ax, \"radius_e\", vmin=10, vmax=80, cmap=\"magma_r\", factor=0.001, lut=14, ref=-10\n)\nm = c.filled(\n    ax, \"radius_e\", vmin=10, vmax=80, cmap=\"magma_r\", factor=0.001, lut=14, ref=-10\n)\nupdate_axes(ax, m)"
+        "ax = start_axes(\"Eddies speed radius (km)\")\nkwargs = dict(vmin=10, vmax=80, cmap=\"magma_r\", factor=0.001, lut=14, ref=-10)\na.filled(ax, \"radius_e\", **kwargs)\nm = c.filled(\n    ax, \"radius_e\", vmin=10, vmax=80, cmap=\"magma_r\", factor=0.001, lut=14, ref=-10\n)\nupdate_axes(ax, m)"
       ]
     }
   ],
diff --git a/notebooks/python_module/02_eddy_identification/pet_filter_and_detection.ipynb b/notebooks/python_module/02_eddy_identification/pet_filter_and_detection.ipynb
@@ -176,7 +176,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.0"
+      "version": "3.7.7"
     }
   },
   "nbformat": 4,
diff --git a/notebooks/python_module/02_eddy_identification/pet_interp_grid_on_dataset.ipynb b/notebooks/python_module/02_eddy_identification/pet_interp_grid_on_dataset.ipynb
@@ -37,7 +37,7 @@
       },
       "outputs": [],
       "source": [
-        "def start_axes(title):\n    fig = plt.figure(figsize=(13, 5))\n    ax = fig.add_axes([0.03, 0.03, 0.90, 0.94])\n    ax.set_xlim(-6, 36.5), ax.set_ylim(30, 46)\n    ax.set_aspect(\"equal\")\n    ax.set_title(title)\n    return ax\n\n\ndef update_axes(ax, mappable=None):\n    ax.grid()\n    ax.legend()\n    if mappable:\n        plt.colorbar(m, cax=ax.figure.add_axes([0.95, 0.05, 0.01, 0.9]))"
+        "def start_axes(title):\n    fig = plt.figure(figsize=(13, 5))\n    ax = fig.add_axes([0.03, 0.03, 0.90, 0.94])\n    ax.set_xlim(-6, 36.5), ax.set_ylim(30, 46)\n    ax.set_aspect(\"equal\")\n    ax.set_title(title)\n    return ax\n\n\ndef update_axes(ax, mappable=None):\n    ax.grid()\n    ax.legend()\n    if mappable:\n        plt.colorbar(mappable, cax=ax.figure.add_axes([0.95, 0.05, 0.01, 0.9]))"
       ]
     },
     {
@@ -55,7 +55,7 @@
       },
       "outputs": [],
       "source": [
-        "a = EddiesObservations.load_file(data.get_path(\"Anticyclonic_20160515.nc\"))\nc = EddiesObservations.load_file(data.get_path(\"Cyclonic_20160515.nc\"))\n\naviso_map = RegularGridDataset(\n    data.get_path(\"dt_med_allsat_phy_l4_20160515_20190101.nc\"), \"longitude\", \"latitude\"\n)\n# aviso_map.add_uv(\"adt\")\naviso_map.add_uv(\"sla\")"
+        "a = EddiesObservations.load_file(data.get_path(\"Anticyclonic_20160515.nc\"))\nc = EddiesObservations.load_file(data.get_path(\"Cyclonic_20160515.nc\"))\n\naviso_map = RegularGridDataset(\n    data.get_path(\"dt_med_allsat_phy_l4_20160515_20190101.nc\"), \"longitude\", \"latitude\"\n)\naviso_map.add_uv(\"adt\")"
       ]
     },
     {
@@ -91,7 +91,7 @@
       },
       "outputs": [],
       "source": [
-        "ax = start_axes(\"EKE (cm\u00b2/s\u00b2)\")\na.display(ax, color=\"r\", linewidth=0.5, label=\"Anticyclonic\", ref=-10)\nc.display(ax, color=\"b\", linewidth=0.5, label=\"Cyclonic\", ref=-10)\neke = a.interp_grid(aviso_map, \"eke\", method=\"mean\", intern=False)\nm = ax.scatter((a.longitude + 10) % 360 - 10, a.latitude, c=eke, **eke_kwargs)\neke = c.interp_grid(aviso_map, \"eke\", method=\"mean\", intern=False)\nm = ax.scatter((c.longitude + 10) % 360 - 10, c.latitude, c=eke, **eke_kwargs)\nupdate_axes(ax, m)"
+        "ax = start_axes(\"EKE mean (cm\u00b2/s\u00b2)\")\na.display(ax, color=\"r\", linewidth=0.5, label=\"Anticyclonic\", ref=-10)\nc.display(ax, color=\"b\", linewidth=0.5, label=\"Cyclonic\", ref=-10)\neke = a.interp_grid(aviso_map, \"eke\", method=\"mean\", intern=False)\na.filled(ax, eke, ref=-10, **eke_kwargs)\neke = c.interp_grid(aviso_map, \"eke\", method=\"mean\", intern=False)\nm = c.filled(ax, eke, ref=-10, **eke_kwargs)\nupdate_axes(ax, m)"
       ]
     }
   ],
@@ -111,7 +111,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.0"
+      "version": "3.7.7"
     }
   },
   "nbformat": 4,
diff --git a/notebooks/python_module/02_eddy_identification/pet_radius_vs_area.ipynb b/notebooks/python_module/02_eddy_identification/pet_radius_vs_area.ipynb
@@ -107,7 +107,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.0"
+      "version": "3.7.7"
     }
   },
   "nbformat": 4,
diff --git a/notebooks/python_module/02_eddy_identification/pet_shape_gallery.ipynb b/notebooks/python_module/02_eddy_identification/pet_shape_gallery.ipynb
@@ -15,7 +15,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "\nShape error gallery\n===================\n\nGallery of contours with shape error\n"
+        "\n# Shape error gallery\n\nGallery of contours with shape error\n"
       ]
     },
     {
@@ -33,7 +33,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Method to compute circle path\n\n"
+        "Method to built circle from center coordinates\n\n"
       ]
     },
     {
@@ -69,7 +69,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Shape error gallery\n-------------------\nFor each contour display, we display circle fitted, we work at different latitude circle could have distorsion\n\n"
+        "## Shape error gallery\nFor each contour display, we display circle fitted, we work at different latitude circle could have distorsion\n\n"
       ]
     },
     {
diff --git a/notebooks/python_module/02_eddy_identification/pet_sla_and_adt.ipynb b/notebooks/python_module/02_eddy_identification/pet_sla_and_adt.ipynb
@@ -15,7 +15,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "\nEddy detection on SLA and ADT\n=============================\n"
+        "\n# Eddy detection on SLA and ADT\n"
       ]
     },
     {
@@ -145,7 +145,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Match\n-----------------------\nWhere cyclone meet anticyclone\n\n"
+        "## Match\nWhere cyclone meet anticyclone\n\n"
       ]
     },
     {
@@ -156,14 +156,14 @@
       },
       "outputs": [],
       "source": [
-        "i_c_adt, i_a_sla, c = c_adt.match(a_sla, 0.1)\ni_a_adt, i_c_sla, c = a_adt.match(c_sla, 0.1)\n\nax = start_axes(\"Cyclone share area with anticyclone\")\na_adt.index(i_a_adt).display(ax, **kwargs_a_adt)\nc_adt.index(i_c_adt).display(ax, **kwargs_c_adt)\na_sla.index(i_a_sla).display(ax, **kwargs_a_sla)\nc_sla.index(i_c_sla).display(ax, **kwargs_c_sla)\nax.legend()\nupdate_axes(ax)"
+        "i_c_adt, i_a_sla, c = c_adt.match(a_sla, cmin=0.01)\ni_a_adt, i_c_sla, c = a_adt.match(c_sla, cmin=0.01)\n\nax = start_axes(\"Cyclone share area with anticyclone\")\na_adt.index(i_a_adt).display(ax, **kwargs_a_adt)\nc_adt.index(i_c_adt).display(ax, **kwargs_c_adt)\na_sla.index(i_a_sla).display(ax, **kwargs_a_sla)\nc_sla.index(i_c_sla).display(ax, **kwargs_c_sla)\nax.legend()\nupdate_axes(ax)"
       ]
     },
     {
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Scatter plot\n------------\n\n"
+        "## Scatter plot\n\n"
       ]
     },
     {
@@ -174,7 +174,7 @@
       },
       "outputs": [],
       "source": [
-        "i_a_adt, i_a_sla, c = a_adt.match(a_sla, 0.1)\ni_c_adt, i_c_sla, c = c_adt.match(c_sla, 0.1)"
+        "i_a_adt, i_a_sla, c = a_adt.match(a_sla, cmin=0.1)\ni_c_adt, i_c_sla, c = c_adt.match(c_sla, cmin=0.1)"
       ]
     },
     {
@@ -203,7 +203,7 @@
       },
       "outputs": [],
       "source": [
-        "fig = plt.figure(figsize=(12, 12))\nfig.suptitle(f\"Scatter plot (A : {i_a_adt.shape[0]}, C : {i_c_adt.shape[0]} matches)\")\n\nfor i, (label, field, factor, stop) in enumerate(\n    (\n        (\"speed radius (km)\", \"radius_s\", 0.001, 80),\n        (\"outter radius (km)\", \"radius_e\", 0.001, 120),\n        (\"amplitude (cm)\", \"amplitude\", 100, 25),\n        (\"speed max (cm/s)\", \"speed_average\", 100, 25),\n    )\n):\n    ax = fig.add_subplot(2, 2, i + 1, title=label)\n    ax.set_xlabel(\"Absolute Dynamic Topography\")\n    ax.set_ylabel(\"Sea Level Anomaly\")\n\n    ax.plot(a_adt[field][i_a_adt] * factor, a_sla[field][i_a_sla] * factor, \"r.\")\n    ax.plot(c_adt[field][i_c_adt] * factor, c_sla[field][i_c_sla] * factor, \"b.\")\n    ax.set_aspect(\"equal\"), ax.grid()\n    ax.plot((0, 1000), (0, 1000), \"g\")\n    ax.set_xlim(0, stop), ax.set_ylim(0, stop)"
+        "fig = plt.figure(figsize=(12, 12))\nfig.suptitle(f\"Scatter plot (A : {i_a_adt.shape[0]}, C : {i_c_adt.shape[0]} matches)\")\n\nfor i, (label, field, factor, stop) in enumerate(\n    (\n        (\"speed radius (km)\", \"radius_s\", 0.001, 80),\n        (\"outter radius (km)\", \"radius_e\", 0.001, 120),\n        (\"amplitude (cm)\", \"amplitude\", 100, 25),\n        (\"speed max (cm/s)\", \"speed_average\", 100, 25),\n    )\n):\n    ax = fig.add_subplot(2, 2, i + 1, title=label)\n    ax.set_xlabel(\"Absolute Dynamic Topography\")\n    ax.set_ylabel(\"Sea Level Anomaly\")\n\n    ax.plot(a_adt[field][i_a_adt] * factor, a_sla[field][i_a_sla] * factor, \"r.\", label='Anticyclonic')\n    ax.plot(c_adt[field][i_c_adt] * factor, c_sla[field][i_c_sla] * factor, \"b.\", label='Cyclonic')\n    ax.set_aspect(\"equal\"), ax.grid()\n    ax.plot((0, 1000), (0, 1000), \"g\")\n    ax.set_xlim(0, stop), ax.set_ylim(0, stop)\n    ax.legend()"
       ]
     }
   ],
diff --git a/notebooks/python_module/06_grid_manipulation/pet_filter.ipynb b/notebooks/python_module/06_grid_manipulation/pet_filter.ipynb
@@ -15,7 +15,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "\nGrid filtering in PET\n=====================\n\nHow filter work in py eddy tracker. This implementation maybe doesn't respect state art, but ...\n\nWe code a specific filter in order to filter grid with same wavelength at each pixel.\n"
+        "\n# Grid filtering in PET\n\nHow filter work in py eddy tracker. This implementation maybe doesn't respect state art, but ...\n\nWe code a specific filter in order to filter grid with same wavelength at each pixel.\n"
       ]
     },
     {
@@ -26,7 +26,7 @@
       },
       "outputs": [],
       "source": [
-        "from py_eddy_tracker.dataset.grid import RegularGridDataset\nfrom py_eddy_tracker import data\nfrom matplotlib import pyplot as plt\nfrom numpy import arange\n\n\ndef start_axes(title):\n    fig = plt.figure(figsize=(13, 5))\n    ax = fig.add_axes([0.03, 0.03, 0.90, 0.94])\n    ax.set_xlim(-6, 36.5), ax.set_ylim(30, 46)\n    ax.set_aspect(\"equal\")\n    ax.set_title(title)\n    return ax\n\n\ndef update_axes(ax, mappable=None):\n    ax.grid()\n    if mappable:\n        plt.colorbar(m, cax=ax.figure.add_axes([0.95, 0.05, 0.01, 0.9]))"
+        "from py_eddy_tracker.dataset.grid import RegularGridDataset\nfrom py_eddy_tracker import data\nfrom matplotlib import pyplot as plt\nfrom numpy import arange\n\n\ndef start_axes(title):\n    fig = plt.figure(figsize=(13, 5))\n    ax = fig.add_axes([0.03, 0.03, 0.90, 0.94])\n    ax.set_xlim(-6, 36.5), ax.set_ylim(30, 46)\n    ax.set_aspect(\"equal\")\n    ax.set_title(title)\n    return ax\n\n\ndef update_axes(ax, mappable=None):\n    ax.grid()\n    if mappable:\n        plt.colorbar(mappable, cax=ax.figure.add_axes([0.95, 0.05, 0.01, 0.9]))"
       ]
     },
     {
@@ -51,7 +51,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Kernel\n------\nShape of kernel will increase in x, when latitude increase\n\n"
+        "## Kernel\nShape of kernel will increase in x, when latitude increase\n\n"
       ]
     },
     {
@@ -87,7 +87,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Kernel applying\n---------------\nOriginal grid\n\n"
+        "## Kernel applying\nOriginal grid\n\n"
       ]
     },
     {
@@ -141,7 +141,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Clues\n-----\nwavelength : 80km\n\n"
+        "## Clues\nwavelength : 80km\n\n"
       ]
     },
     {
@@ -195,7 +195,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Old filter\n----------\nTo do ...\n\n"
+        "## Old filter\nTo do ...\n\n"
       ]
     }
   ],
diff --git a/notebooks/python_module/06_grid_manipulation/pet_hide_pixel_out_eddies.ipynb b/notebooks/python_module/06_grid_manipulation/pet_hide_pixel_out_eddies.ipynb
@@ -15,7 +15,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "\nSelect pixel in eddies\n======================\n"
+        "\n# Select pixel in eddies\n"
       ]
     },
     {
diff --git a/notebooks/python_module/08_tracking_manipulation/pet_display_field.ipynb b/notebooks/python_module/08_tracking_manipulation/pet_display_field.ipynb
@@ -15,7 +15,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "\nDisplay fields\n==============\n"
+        "\n# Display fields\n"
       ]
     },
     {
diff --git a/notebooks/python_module/08_tracking_manipulation/pet_display_track.ipynb b/notebooks/python_module/08_tracking_manipulation/pet_display_track.ipynb
@@ -51,7 +51,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "keep only eddies longer than 20 weeks\n\n"
+        "keep only eddies longer than 20 weeks, use -1 to have no upper limit\n\n"
       ]
     },
     {
diff --git a/notebooks/python_module/08_tracking_manipulation/pet_one_track.ipynb b/notebooks/python_module/08_tracking_manipulation/pet_one_track.ipynb
@@ -15,7 +15,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "\nOne Track\n===================\n"
+        "\n# One Track\n"
       ]
     },
     {
diff --git a/notebooks/python_module/08_tracking_manipulation/pet_run_a_tracking.ipynb b/notebooks/python_module/08_tracking_manipulation/pet_run_a_tracking.ipynb
@@ -33,7 +33,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Get remote data, we will keep only 180 first days\n`get_remote_sample` function is only to get demo dataset, in your own case give a list of identification filename\nand don't mix cyclonic and anticyclonic files\n\n"
+        "Get remote data, we will keep only 180 first days,\n`get_remote_sample` function is only to get demo dataset, in your own case give a list of identification filename\nand don't mix cyclonic and anticyclonic files.\n\n"
       ]
     },
     {
diff --git a/notebooks/python_module/08_tracking_manipulation/pet_select_track_across_area.ipynb b/notebooks/python_module/08_tracking_manipulation/pet_select_track_across_area.ipynb
@@ -15,7 +15,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "\nTracks which go through area\n============================\n"
+        "\n# Tracks which go through area\n"
       ]
     },
     {
diff --git a/notebooks/python_module/08_tracking_manipulation/pet_track_anim.ipynb b/notebooks/python_module/08_tracking_manipulation/pet_track_anim.ipynb
@@ -15,7 +15,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "\nTrack animation\n===============\n\nRun in a terminal this script, which allow to watch eddy evolution\n"
+        "\n# Track animation\n\nRun in a terminal this script, which allow to watch eddy evolution\n"
       ]
     },
     {
diff --git a/notebooks/python_module/10_tracking_diagnostics/pet_geographic_stats.ipynb b/notebooks/python_module/10_tracking_diagnostics/pet_geographic_stats.ipynb
@@ -15,7 +15,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "\nGeographical statistics\n=======================\n"
+        "\n# Geographical statistics\n"
       ]
     },
     {
diff --git a/notebooks/python_module/10_tracking_diagnostics/pet_histo.ipynb b/notebooks/python_module/10_tracking_diagnostics/pet_histo.ipynb
@@ -15,7 +15,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "\nParameter Histogram\n===================\n"
+        "\n# Parameter Histogram\n"
       ]
     },
     {
diff --git a/notebooks/python_module/10_tracking_diagnostics/pet_pixel_used.ipynb b/notebooks/python_module/10_tracking_diagnostics/pet_pixel_used.ipynb
@@ -15,7 +15,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "\nCount pixel used\n======================\n"
+        "\n# Count pixel used\n"
       ]
     },
     {
@@ -62,7 +62,7 @@
       },
       "outputs": [],
       "source": [
-        "fig = plt.figure(figsize=(12, 18.5))\nax_a = fig.add_axes([0.03, 0.75, 0.90, 0.25])\nax_a.set_title(\"Anticyclonic frequency\")\nax_c = fig.add_axes([0.03, 0.5, 0.90, 0.25])\nax_c.set_title(\"Cyclonic frequency\")\nax_all = fig.add_axes([0.03, 0.25, 0.90, 0.25])\nax_all.set_title(\"All eddies frequency\")\nax_ratio = fig.add_axes([0.03, 0.0, 0.90, 0.25])\nax_ratio.set_title(\"Ratio cyclonic / Anticyclonic\")\n\n# Count pixel used for each contour\ng_a = a.grid_count(bins, intern=True)\ng_a.display(ax_a, **kwargs_pcolormesh)\ng_c = c.grid_count(bins, intern=True)\ng_c.display(ax_c, **kwargs_pcolormesh)\n# Compute a ratio Cyclonic / Anticyclonic\nratio = g_c.vars[\"count\"] / g_a.vars[\"count\"]\n\n# Mask manipulation to be able to sum the 2 grids\nm_c = g_c.vars[\"count\"].mask\nm = m_c & g_a.vars[\"count\"].mask\ng_c.vars[\"count\"][m_c] = 0\ng_c.vars[\"count\"] += g_a.vars[\"count\"]\ng_c.vars[\"count\"].mask = m\n\nm = g_c.display(ax_all, **kwargs_pcolormesh)\nplt.colorbar(m, cax=fig.add_axes([0.95, 0.27, 0.01, 0.7]))\n\ng_c.vars[\"count\"] = ratio\nm = g_c.display(ax_ratio, name=\"count\", vmin=0.1, vmax=10, norm=LogNorm())\nplt.colorbar(m, cax=fig.add_axes([0.95, 0.02, 0.01, 0.2]))\n\nfor ax in (ax_a, ax_c, ax_all, ax_ratio):\n    ax.set_aspect(\"equal\")\n    ax.set_xlim(-6, 36.5), ax.set_ylim(30, 46)\n    ax.grid()"
+        "fig = plt.figure(figsize=(12, 18.5))\nax_a = fig.add_axes([0.03, 0.75, 0.90, 0.25])\nax_a.set_title(\"Anticyclonic frequency\")\nax_c = fig.add_axes([0.03, 0.5, 0.90, 0.25])\nax_c.set_title(\"Cyclonic frequency\")\nax_all = fig.add_axes([0.03, 0.25, 0.90, 0.25])\nax_all.set_title(\"All eddies frequency\")\nax_ratio = fig.add_axes([0.03, 0.0, 0.90, 0.25])\nax_ratio.set_title(\"Ratio cyclonic / Anticyclonic\")\n\n# Count pixel used for each contour\ng_a = a.grid_count(bins, intern=True)\ng_a.display(ax_a, **kwargs_pcolormesh)\ng_c = c.grid_count(bins, intern=True)\ng_c.display(ax_c, **kwargs_pcolormesh)\n# Compute a ratio Cyclonic / Anticyclonic\nratio = g_c.vars[\"count\"] / g_a.vars[\"count\"]\n\n# Mask manipulation to be able to sum the 2 grids\nm_c = g_c.vars[\"count\"].mask\nm = m_c & g_a.vars[\"count\"].mask\ng_c.vars[\"count\"][m_c] = 0\ng_c.vars[\"count\"] += g_a.vars[\"count\"]\ng_c.vars[\"count\"].mask = m\n\nm = g_c.display(ax_all, **kwargs_pcolormesh)\nplt.colorbar(m, cax=fig.add_axes([0.95, 0.27, 0.01, 0.7]))\n\ng_c.vars[\"count\"] = ratio\nm = g_c.display(ax_ratio, name=\"count\", vmin=0.1, vmax=10, norm=LogNorm(), cmap='coolwarm_r')\nplt.colorbar(m, cax=fig.add_axes([0.95, 0.02, 0.01, 0.2]))\n\nfor ax in (ax_a, ax_c, ax_all, ax_ratio):\n    ax.set_aspect(\"equal\")\n    ax.set_xlim(-6, 36.5), ax.set_ylim(30, 46)\n    ax.grid()"
       ]
     }
   ],
diff --git a/src/py_eddy_tracker/appli/__init__.py b/src/py_eddy_tracker/appli/__init__.py
@@ -0,0 +1,4 @@
+# -*- coding: utf-8 -*-
+"""
+Entry point
+"""
diff --git a/src/py_eddy_tracker/dataset/grid.py b/src/py_eddy_tracker/dataset/grid.py
@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 """
+Class to load and manipulate RegularGrid and UnRegularGrid
 """
 import logging
 from numpy import (
diff --git a/src/py_eddy_tracker/eddy_feature.py b/src/py_eddy_tracker/eddy_feature.py
@@ -593,7 +593,7 @@ def display(
             bins argument must be define
         :param array bins: bins use to colorize contour
         :param str cmap: Name of cmap to use for field display
-        :param dict kwargs: look at :py:method:`matplotlib.collections.LineCollection`
+        :param dict kwargs: look at :py:meth:`matplotlib.collections.LineCollection`
 
         .. minigallery:: py_eddy_tracker.Contours.display
         """
diff --git a/src/py_eddy_tracker/gui.py b/src/py_eddy_tracker/gui.py
diff --git a/src/py_eddy_tracker/observations/observation.py b/src/py_eddy_tracker/observations/observation.py
diff --git a/src/py_eddy_tracker/observations/tracking.py b/src/py_eddy_tracker/observations/tracking.py

Original file line number	Diff line number	Diff line change
`@@ -15,7 +15,7 @@`
`15`	`15`	`"cell_type": "markdown",`
`16`	`16`	`"metadata": {},`
`17`	`17`	`"source": [`
`18`		`- "\nDisplay contour & circle\n========================\n"`
	`18`	`+ "\n# Display contour & circle\n"`
`19`	`19`	`]`
`20`	`20`	`},`
`21`	`21`	`{`
Original file line number	Diff line number	Diff line change
`@@ -260,7 +260,7 @@`
`260`	`260`	`"cell_type": "markdown",`
`261`	`261`	`"metadata": {},`
`262`	`262`	`"source": [`
`263`		`- "Display speed radius of eddies detected\n\n"`
	`263`	`+ "Display speed radius of eddies detected with filled eddy contours\n\n"`
`264`	`264`	`]`
`265`	`265`	`},`
`266`	`266`	`{`
`@@ -271,7 +271,7 @@`
`271`	`271`	`},`
`272`	`272`	`"outputs": [],`
`273`	`273`	`"source": [`
`274`		`- "ax = start_axes(\"Eddies speed radius (km)\")\na.filled(\n ax, \"radius_e\", vmin=10, vmax=80, cmap=\"magma_r\", factor=0.001, lut=14, ref=-10\n)\nm = c.filled(\n ax, \"radius_e\", vmin=10, vmax=80, cmap=\"magma_r\", factor=0.001, lut=14, ref=-10\n)\nupdate_axes(ax, m)"`
	`274`	`+ "ax = start_axes(\"Eddies speed radius (km)\")\nkwargs = dict(vmin=10, vmax=80, cmap=\"magma_r\", factor=0.001, lut=14, ref=-10)\na.filled(ax, \"radius_e\", **kwargs)\nm = c.filled(\n ax, \"radius_e\", vmin=10, vmax=80, cmap=\"magma_r\", factor=0.001, lut=14, ref=-10\n)\nupdate_axes(ax, m)"`
`275`	`275`	`]`
`276`	`276`	`}`
`277`	`277`	`],`
Original file line number	Diff line number	Diff line change
`@@ -176,7 +176,7 @@`
`176`	`176`	`"name": "python",`
`177`	`177`	`"nbconvert_exporter": "python",`
`178`	`178`	`"pygments_lexer": "ipython3",`
`179`		`- "version": "3.7.0"`
	`179`	`+ "version": "3.7.7"`
`180`	`180`	`}`
`181`	`181`	`},`
`182`	`182`	`"nbformat": 4,`
Original file line number	Diff line number	Diff line change
`@@ -37,7 +37,7 @@`
`37`	`37`	`},`
`38`	`38`	`"outputs": [],`
`39`	`39`	`"source": [`
`40`		`- "def start_axes(title):\n fig = plt.figure(figsize=(13, 5))\n ax = fig.add_axes([0.03, 0.03, 0.90, 0.94])\n ax.set_xlim(-6, 36.5), ax.set_ylim(30, 46)\n ax.set_aspect(\"equal\")\n ax.set_title(title)\n return ax\n\n\ndef update_axes(ax, mappable=None):\n ax.grid()\n ax.legend()\n if mappable:\n plt.colorbar(m, cax=ax.figure.add_axes([0.95, 0.05, 0.01, 0.9]))"`
	`40`	`+ "def start_axes(title):\n fig = plt.figure(figsize=(13, 5))\n ax = fig.add_axes([0.03, 0.03, 0.90, 0.94])\n ax.set_xlim(-6, 36.5), ax.set_ylim(30, 46)\n ax.set_aspect(\"equal\")\n ax.set_title(title)\n return ax\n\n\ndef update_axes(ax, mappable=None):\n ax.grid()\n ax.legend()\n if mappable:\n plt.colorbar(mappable, cax=ax.figure.add_axes([0.95, 0.05, 0.01, 0.9]))"`
`41`	`41`	`]`
`42`	`42`	`},`
`43`	`43`	`{`
`@@ -55,7 +55,7 @@`
`55`	`55`	`},`
`56`	`56`	`"outputs": [],`
`57`	`57`	`"source": [`
`58`		`- "a = EddiesObservations.load_file(data.get_path(\"Anticyclonic_20160515.nc\"))\nc = EddiesObservations.load_file(data.get_path(\"Cyclonic_20160515.nc\"))\n\naviso_map = RegularGridDataset(\n data.get_path(\"dt_med_allsat_phy_l4_20160515_20190101.nc\"), \"longitude\", \"latitude\"\n)\n# aviso_map.add_uv(\"adt\")\naviso_map.add_uv(\"sla\")"`
	`58`	`+ "a = EddiesObservations.load_file(data.get_path(\"Anticyclonic_20160515.nc\"))\nc = EddiesObservations.load_file(data.get_path(\"Cyclonic_20160515.nc\"))\n\naviso_map = RegularGridDataset(\n data.get_path(\"dt_med_allsat_phy_l4_20160515_20190101.nc\"), \"longitude\", \"latitude\"\n)\naviso_map.add_uv(\"adt\")"`
`59`	`59`	`]`
`60`	`60`	`},`
`61`	`61`	`{`
`@@ -91,7 +91,7 @@`
`91`	`91`	`},`
`92`	`92`	`"outputs": [],`
`93`	`93`	`"source": [`
`94`		- "ax = start_axes(\"EKE (cm\u00b2/s\u00b2)\")\na.display(ax, color=\"r\", linewidth=0.5, label=\"Anticyclonic\", ref=-10)\nc.display(ax, color=\"b\", linewidth=0.5, label=\"Cyclonic\", ref=-10)\neke = a.interp_grid(aviso_map, \"eke\", method=\"mean\", intern=False)\nm = ax.scatter((a.longitude + 10) % 360 - 10, a.latitude, c=eke, eke_kwargs)\neke = c.interp_grid(aviso_map, \"eke\", method=\"mean\", intern=False)\nm = ax.scatter((c.longitude + 10) % 360 - 10, c.latitude, c=eke, eke_kwargs)\nupdate_axes(ax, m)"
	`94`	`+ "ax = start_axes(\"EKE mean (cm\u00b2/s\u00b2)\")\na.display(ax, color=\"r\", linewidth=0.5, label=\"Anticyclonic\", ref=-10)\nc.display(ax, color=\"b\", linewidth=0.5, label=\"Cyclonic\", ref=-10)\neke = a.interp_grid(aviso_map, \"eke\", method=\"mean\", intern=False)\na.filled(ax, eke, ref=-10, eke_kwargs)\neke = c.interp_grid(aviso_map, \"eke\", method=\"mean\", intern=False)\nm = c.filled(ax, eke, ref=-10, eke_kwargs)\nupdate_axes(ax, m)"`
`95`	`95`	`]`
`96`	`96`	`}`
`97`	`97`	`],`
`@@ -111,7 +111,7 @@`
`111`	`111`	`"name": "python",`
`112`	`112`	`"nbconvert_exporter": "python",`
`113`	`113`	`"pygments_lexer": "ipython3",`
`114`		`- "version": "3.7.0"`
	`114`	`+ "version": "3.7.7"`
`115`	`115`	`}`
`116`	`116`	`},`
`117`	`117`	`"nbformat": 4,`
Original file line number	Diff line number	Diff line change
`@@ -107,7 +107,7 @@`
`107`	`107`	`"name": "python",`
`108`	`108`	`"nbconvert_exporter": "python",`
`109`	`109`	`"pygments_lexer": "ipython3",`
`110`		`- "version": "3.7.0"`
	`110`	`+ "version": "3.7.7"`
`111`	`111`	`}`
`112`	`112`	`},`
`113`	`113`	`"nbformat": 4,`