update examples, and add an example of eddy animation

Author: AntSimi

examples/08_tracking_manipulation/pet_track_anim.py

@@ -0,0 +1,69 @@
+"""
+Track animation
+===============
+
+Run in a terminal this script, which allow to watch eddy evolution
+
+"""
+from matplotlib import pyplot as plt
+from matplotlib.collections import LineCollection
+import matplotlib.transforms as mt
+from numpy import arange
+from py_eddy_tracker.observations.tracking import TrackEddiesObservations
+from py_eddy_tracker.poly import create_vertice
+import py_eddy_tracker_sample
+
+# %%
+# Load experimental atlas, and we select one eddy
+a = TrackEddiesObservations.load_file(
+    py_eddy_tracker_sample.get_path("eddies_med_adt_allsat_dt2018/Anticyclonic.zarr")
+)
+eddy = a.extract_ids([9672])
+t0, t1 = eddy.period
+t = eddy.time
+x = eddy["contour_lon_s"]
+y = eddy["contour_lat_s"]
+
+# %%
+# General value
+T = 25.0
+cmap = plt.get_cmap("viridis")
+COLORS = cmap(arange(T + 1) / T)
+
+
+# %%
+# plot
+fig = plt.figure(figsize=(12, 5))
+ax = fig.add_axes((0.05, 0.05, 0.9, 0.9))
+ax.set_xlim(16.5, 23)
+ax.set_ylim(34.5, 37)
+ax.set_aspect("equal")
+ax.grid()
+# init mappable
+txt = ax.text(16.6, 36.8, "", zorder=10)
+segs = list()
+c = LineCollection([], zorder=1)
+ax.add_collection(c)
+
+fig.canvas.draw()
+plt.show(block=False)
+# save background for future bliting
+bg_cache = fig.canvas.copy_from_bbox(ax.bbox)
+# display contour every 2 day
+for t_ in range(t0, t1 + 1, 2):
+    fig.canvas.restore_region(bg_cache)
+    # select contour for this time step
+    m = t == t_
+    segs.append(create_vertice(x[m][0], y[m][0]))
+    c.set_paths(segs)
+    c.set_color(COLORS[-len(segs) :])
+    txt.set_text(f"{t0} -> {t_} -> {t1}")
+    ax.draw_artist(c)
+    ax.draw_artist(txt)
+    # Remove first segment to keep only T contour
+    if len(segs) > T:
+        segs.pop(0)
+    # paint updated artist
+    fig.canvas.blit(ax.bbox)
+
+    fig.canvas.start_event_loop(1e-10)

examples/10_tracking_diagnostics/pet_center_count.py

@@ -27,7 +27,7 @@
 
 
 # %%
-# Plot 
+# Plot
 fig = plt.figure(figsize=(12, 18.5))
 ax_a = fig.add_axes([0.03, 0.75, 0.90, 0.25])
 ax_a.set_title("Anticyclonic center frequency")

notebooks/python_module/06_grid_manipulation/pet_hide_pixel_out_eddies.ipynb

@@ -26,7 +26,7 @@
       },
       "outputs": [],
       "source": [
-        "from matplotlib import pyplot as plt\nfrom matplotlib.path import Path\nfrom numpy import ones\nfrom py_eddy_tracker.observations.observation import EddiesObservations, custom_concat\nfrom py_eddy_tracker.dataset.grid import RegularGridDataset\nfrom py_eddy_tracker import data"
+        "from matplotlib import pyplot as plt\nfrom matplotlib.path import Path\nfrom numpy import ones\nfrom py_eddy_tracker.observations.observation import EddiesObservations\nfrom py_eddy_tracker.dataset.grid import RegularGridDataset\nfrom py_eddy_tracker.poly import create_vertice\nfrom py_eddy_tracker import data"
       ]
     },
     {
@@ -80,7 +80,7 @@
       },
       "outputs": [],
       "source": [
-        "fig = plt.figure(figsize=(12, 6))\nax = fig.add_axes((0.05, 0.05, 0.9, 0.9))\nax.set_aspect(\"equal\")\nax.set_xlim(10, 70)\nax.set_ylim(-50, -25)\n# We will used the outter contour\nx_name, y_name = a.intern(False)\nadt = g.grid(\"adt\")\nmask = ones(adt.shape, dtype='bool')\nfor eddy in a:\n    i, j = Path(custom_concat(eddy[x_name], eddy[y_name])).pixels_in(g)\n    mask[i, j] = False\nadt.mask[:] += ~mask\ng.display(ax, \"adt\")\na.display(ax, label=\"Anticyclonic\", color=\"g\", lw=1, extern_only=True)"
+        "fig = plt.figure(figsize=(12, 6))\nax = fig.add_axes((0.05, 0.05, 0.9, 0.9))\nax.set_aspect(\"equal\")\nax.set_xlim(10, 70)\nax.set_ylim(-50, -25)\n# We will used the outter contour\nx_name, y_name = a.intern(False)\nadt = g.grid(\"adt\")\nmask = ones(adt.shape, dtype='bool')\nfor eddy in a:\n    i, j = Path(create_vertice(eddy[x_name], eddy[y_name])).pixels_in(g)\n    mask[i, j] = False\nadt.mask[:] += ~mask\ng.display(ax, \"adt\")\na.display(ax, label=\"Anticyclonic\", color=\"g\", lw=1, extern_only=True)"
       ]
     },
     {

notebooks/python_module/08_tracking_manipulation/pet_track_anim.ipynb

@@ -0,0 +1,108 @@
+{
+  "cells": [
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "%matplotlib inline"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "\nTrack animation\n===============\n\nRun in a terminal this script, which allow to watch eddy evolution\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "from matplotlib import pyplot as plt\nfrom matplotlib.collections import LineCollection\nimport matplotlib.transforms as mt\nfrom numpy import arange\nfrom py_eddy_tracker.observations.tracking import TrackEddiesObservations\nfrom py_eddy_tracker.poly import create_vertice\nimport py_eddy_tracker_sample"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "Load experimental atlas, and we select one eddy\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "a = TrackEddiesObservations.load_file(\n    py_eddy_tracker_sample.get_path(\"eddies_med_adt_allsat_dt2018/Anticyclonic.zarr\")\n)\neddy = a.extract_ids([9672])\nt0, t1 = eddy.period\nt = eddy.time\nx = eddy[\"contour_lon_s\"]\ny = eddy[\"contour_lat_s\"]"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "General value\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "T = 25.0\ncmap = plt.get_cmap(\"viridis\")\nCOLORS = cmap(arange(T + 1) / T)"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "plot\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "fig = plt.figure(figsize=(12, 5))\nax = fig.add_axes((0.05, 0.05, 0.9, 0.9))\nax.set_xlim(16.5, 23)\nax.set_ylim(34.5, 37)\nax.set_aspect(\"equal\")\nax.grid()\n# init mappable\ntxt = ax.text(16.6, 36.8, \"\", zorder=10)\nsegs = list()\nc = LineCollection([], zorder=1)\nax.add_collection(c)\n\nfig.canvas.draw()\nplt.show(block=False)\n# save background for future bliting\nbg_cache = fig.canvas.copy_from_bbox(ax.bbox)\n# display contour every 2 day\nfor t_ in range(t0, t1 + 1, 2):\n    fig.canvas.restore_region(bg_cache)\n    # select contour for this time step\n    m = t == t_\n    segs.append(create_vertice(x[m][0], y[m][0]))\n    c.set_paths(segs)\n    c.set_color(COLORS[-len(segs) :])\n    txt.set_text(f\"{t0} -> {t_} -> {t1}\")\n    ax.draw_artist(c)\n    ax.draw_artist(txt)\n    # Remove first segment to keep only T contour\n    if len(segs) > T:\n        segs.pop(0)\n    # paint updated artist\n    fig.canvas.blit(ax.bbox)\n\n    fig.canvas.start_event_loop(1e-10)"
+      ]
+    }
+  ],
+  "metadata": {
+    "kernelspec": {
+      "display_name": "Python 3",
+      "language": "python",
+      "name": "python3"
+    },
+    "language_info": {
+      "codemirror_mode": {
+        "name": "ipython",
+        "version": 3
+      },
+      "file_extension": ".py",
+      "mimetype": "text/x-python",
+      "name": "python",
+      "nbconvert_exporter": "python",
+      "pygments_lexer": "ipython3",
+      "version": "3.7.7"
+    }
+  },
+  "nbformat": 4,
+  "nbformat_minor": 0
+}

notebooks/python_module/10_tracking_diagnostics/pet_center_count.ipynb

@@ -51,7 +51,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Plot \n\n"
+        "Plot\n\n"
       ]
     },
     {