Add animation example

Author: AntSimi

doc/conf.py

@@ -63,6 +63,7 @@
     },
     "line_numbers": False,
     "filename_pattern": "/pet",
+    "matplotlib_animations": True,
     "binder": {
         # Required keys
         "org": "AntSimi",

examples/08_tracking_manipulation/pet_track_anim.py

@@ -14,7 +14,8 @@
 a = TrackEddiesObservations.load_file(
     py_eddy_tracker_sample.get_path("eddies_med_adt_allsat_dt2018/Anticyclonic.zarr")
 )
-eddy = a.extract_ids([9672])
+# We get only 300 first step to save time of documentation builder
+eddy = a.extract_ids([9672]).index(slice(0, 300))
 
 # %%
 # Run animation

examples/08_tracking_manipulation/pet_track_anim_matplotlib_animation.py

@@ -0,0 +1,33 @@
+"""
+Track animation
+===============
+
+Run in a terminal this script, which allow to watch eddy evolution
+
+"""
+from py_eddy_tracker.observations.tracking import TrackEddiesObservations
+from py_eddy_tracker.appli.gui import Anim
+import py_eddy_tracker_sample
+from matplotlib.animation import FuncAnimation
+from numpy import arange
+
+# %%
+# 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])
+
+# %%
+# Run animation
+a = Anim(eddy, intern=True, figsize=(8, 3.5), cmap="magma_r", nb_step=6)
+a.txt.set_position((17, 34.6))
+a.ax.set_xlim(16.5, 23)
+a.ax.set_ylim(34.5, 37)
+
+# arguments to get full animation
+# kwargs = dict(frames=arange(*a.period), interval=50)
+# arguments to reduce compute cost for doucmentation, we display only every 10 days
+kwargs = dict(frames=arange(*a.period)[200:800:10], save_count=60, interval=200)
+
+ani = FuncAnimation(a.fig, a.func_animation, **kwargs)

notebooks/python_module/08_tracking_manipulation/pet_track_anim.ipynb

@@ -44,7 +44,7 @@
       },
       "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])"
+        "a = TrackEddiesObservations.load_file(\n    py_eddy_tracker_sample.get_path(\"eddies_med_adt_allsat_dt2018/Anticyclonic.zarr\")\n)\n# We get only 300 first step to save time of documentation builder\neddy = a.extract_ids([9672]).index(slice(0, 300))"
       ]
     },
     {

notebooks/python_module/08_tracking_manipulation/pet_track_anim_matplotlib_animation.ipynb

@@ -0,0 +1,90 @@
+{
+  "cells": [
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "%matplotlib inline"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "\n# Track animation\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 py_eddy_tracker.observations.tracking import TrackEddiesObservations\nfrom py_eddy_tracker.appli.gui import Anim\nimport py_eddy_tracker_sample\nfrom matplotlib.animation import FuncAnimation\nfrom numpy import arange"
+      ]
+    },
+    {
+      "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])"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "Run animation\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "a = Anim(eddy, intern=True, figsize=(8, 3.5), cmap=\"magma_r\", nb_step=6)\na.txt.set_position((17, 34.6))\na.ax.set_xlim(16.5, 23)\na.ax.set_ylim(34.5, 37)\n\n# arguments to get full animation\nkwargs = dict(frames=arange(*a.period), interval=50)\n# arguments to reduce compute cost for doucmentation, we display only every 10 days\nkwargs = dict(frames=arange(*a.period)[200:800:10], save_count=60, interval=200)\n\nani = FuncAnimation(a.fig, a.func_animation, **kwargs)"
+      ]
+    }
+  ],
+  "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
+}

src/py_eddy_tracker/appli/gui.py

@@ -33,18 +33,19 @@
 
 
 class Anim:
-    def __init__(self, eddy, intern=False, sleep_event=0.1, **kwargs):
+    def __init__(self, eddy, intern=False, sleep_event=0.1, graphic_information=False, **kwargs):
         self.eddy = eddy
         x_name, y_name = eddy.intern(intern)
         self.t, self.x, self.y = eddy.time, eddy[x_name], eddy[y_name]
         self.x_core, self.y_core, self.track = eddy["lon"], eddy["lat"], eddy["track"]
+        self.graphic_informations = graphic_information
         self.pause = False
         self.period = self.eddy.period
         self.sleep_event = sleep_event
         self.mappables = list()
         self.setup(**kwargs)
 
-    def setup(self, cmap="jet", nb_step=25, figsize=(8, 6)):
+    def setup(self, cmap="jet", nb_step=25, figsize=(8, 6), **kwargs):
         cmap = pyplot.get_cmap(cmap)
         self.colors = cmap(arange(nb_step + 1) / nb_step)
         self.nb_step = nb_step
@@ -54,7 +55,7 @@ def setup(self, cmap="jet", nb_step=25, figsize=(8, 6)):
         y_min, y_max = self.y_core.min() - 2, self.y_core.max() + 2
         d_y = y_max - y_min
         # plot
-        self.fig = pyplot.figure(figsize=figsize)
+        self.fig = pyplot.figure(figsize=figsize, **kwargs)
         t0, t1 = self.period
         self.fig.suptitle(f"{t0} -> {t1}")
         self.ax = self.fig.add_axes((0.05, 0.05, 0.9, 0.9))
@@ -63,6 +64,7 @@ def setup(self, cmap="jet", nb_step=25, figsize=(8, 6)):
         self.ax.grid()
         # init mappable
         self.txt = self.ax.text(x_min + 0.05 * d_x, y_min + 0.05 * d_y, "", zorder=10)
+        self.segs = list()
         self.contour = LineCollection([], zorder=1)
         self.ax.add_collection(self.contour)
 
@@ -90,7 +92,6 @@ def show(self, infinity_loop=False):
         loop = True
         t0, t1 = self.period
         while loop:
-            self.segs = list()
             self.now = t0
             while True:
                 dt = self.sleep_event
@@ -119,13 +120,17 @@ def prev(self):
         self.now -= 1
         return self.draw_contour()
 
-    def draw_contour(self):
-        # t0, t1 = self.period
-        # select contour for this time step
+    def func_animation(self, frame):
         while self.mappables:
             self.mappables.pop().remove()
+        self.now = frame
+        self.update()
+        artists = [self.contour, self.txt]
+        artists.extend(self.mappables)
+        return artists
+
+    def update(self):
         m = self.t == self.now
-        self.ax.figure.canvas.restore_region(self.bg_cache)
         if m.sum():
             self.segs.append(
                 create_vertice(
@@ -137,7 +142,10 @@ def draw_contour(self):
         self.contour.set_paths(self.segs)
         self.contour.set_color(self.colors[-len(self.segs) :])
         self.contour.set_lw(arange(len(self.segs)) / len(self.segs) * 2.5)
-        self.txt.set_text(f"{self.now} - {1/self.sleep_event:.0f} frame/s")
+        txt = f"{self.now}"
+        if self.graphic_informations:
+            txt += f"- {1/self.sleep_event:.0f} frame/s"
+        self.txt.set_text(txt)
         for i in where(m)[0]:
             mappable = self.ax.text(
                 self.x_core[i], self.y_core[i], self.track[i], fontsize=8
@@ -149,6 +157,14 @@ def draw_contour(self):
         # Remove first segment to keep only T contour
         if len(self.segs) > self.nb_step:
             self.segs.pop(0)
+
+    def draw_contour(self):
+        # t0, t1 = self.period
+        # select contour for this time step
+        while self.mappables:
+            self.mappables.pop().remove()
+        self.ax.figure.canvas.restore_region(self.bg_cache)
+        self.update()
         # paint updated artist
         self.ax.figure.canvas.blit(self.ax.bbox)