Complete plot with current and charge density. Need to fix the animation

simpegDCIP/Dev/JSAnimation/IPython_display.py

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+from .html_writer import HTMLWriter
+from matplotlib.animation import Animation
+import matplotlib.pyplot as plt
+import tempfile
+import random
+import os
+
+
+__all__ = ['anim_to_html', 'display_animation']
+
+
+class _NameOnlyTemporaryFile(object):
+    """A context-managed temporary file which is not opened.
+
+    The file should be accessible by name on any system.
+
+    Parameters
+    ----------
+    suffix : string
+        The suffix of the temporary file (default = '')
+    prefix : string
+        The prefix of the temporary file (default = '_tmp_')
+    hash_length : string
+        The length of the random hash.  The size of the hash space will
+        be 16 ** hash_length (default=8)
+    seed : integer
+        the seed for the random number generator.  If not specified, the
+        system time will be used as a seed.
+    absolute : boolean
+        If true, return an absolute path to a temporary file in the current
+        working directory.
+
+    Example
+    -------
+
+    >>> with _NameOnlyTemporaryFile(seed=0, absolute=False) as f:
+    ...     print(f)
+    ...
+    _tmp_d82c07cd
+    >>> os.path.exists('_tmp_d82c07cd')  # file removed after context
+    False
+
+    """
+    def __init__(self, prefix='_tmp_', suffix='', hash_length=8,
+                 seed=None, absolute=True):
+        rng = random.Random(seed)
+        self.name = '%s%0*x%s' % (prefix, hash_length,
+                                  rng.getrandbits(4 * hash_length), suffix)
+        if absolute:
+            self.name = os.path.abspath(self.name)
+
+    def __enter__(self):
+        return self
+
+    def __exit__(self, *exc_info):
+        if os.path.exists(self.name):
+            os.remove(self.name)
+
+
+def anim_to_html(anim, fps=None, embed_frames=True, default_mode='loop'):
+    """Generate HTML representation of the animation"""
+    if fps is None and hasattr(anim, '_interval'):
+        # Convert interval in ms to frames per second
+        fps = 1000. / anim._interval
+
+    plt.close(anim._fig)
+    if hasattr(anim, "_html_representation"):
+        return anim._html_representation
+    else:
+        # tempfile can't be used here: we need a filename, and this
+        # fails on windows.  Instead, we use a custom filename generator
+        #with tempfile.NamedTemporaryFile(suffix='.html') as f:
+        with _NameOnlyTemporaryFile(suffix='.html') as f:
+            anim.save(f.name,  writer=HTMLWriter(fps=fps,
+                                                 embed_frames=embed_frames,
+                                                 default_mode=default_mode))
+            html = open(f.name).read()
+
+        anim._html_representation = html
+        return html
+
+
+def display_animation(anim, **kwargs):
+    """Display the animation with an IPython HTML object"""
+    from IPython.display import HTML
+    return HTML(anim_to_html(anim, **kwargs))
+
+
+# This is the magic that makes animations display automatically in the
+# IPython notebook.  The _repr_html_ method is a special method recognized
+# by IPython.
+Animation._repr_html_ = anim_to_html

simpegDCIP/Dev/JSAnimation/__init__.py

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+from .html_writer import HTMLWriter

simpegDCIP/Dev/JSAnimation/examples.py

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+import numpy as np
+from matplotlib import pyplot as plt
+from matplotlib import animation
+from JSAnimation import IPython_display
+
+def basic_animation(frames=100, interval=30):
+    """Plot a basic sine wave with oscillating amplitude"""
+    fig = plt.figure()
+    ax = plt.axes(xlim=(0, 10), ylim=(-2, 2))
+    line, = ax.plot([], [], lw=2)
+
+    x = np.linspace(0, 10, 1000)
+
+    def init():
+        line.set_data([], [])
+        return line,
+
+    def animate(i):
+        y = np.cos(i * 0.02 * np.pi) * np.sin(x - i * 0.02 * np.pi)
+        line.set_data(x, y)
+        return line,
+
+    return animation.FuncAnimation(fig, animate, init_func=init,
+                                   frames=frames, interval=interval)
+
+
+def lorenz_animation(N_trajectories=20, rseed=1, frames=200, interval=30):
+    """Plot a 3D visualization of the dynamics of the Lorenz system"""
+    from scipy import integrate
+    from mpl_toolkits.mplot3d import Axes3D
+    from matplotlib.colors import cnames
+
+    def lorentz_deriv(coords, t0, sigma=10., beta=8./3, rho=28.0):
+        """Compute the time-derivative of a Lorentz system."""
+        x, y, z = coords
+        return [sigma * (y - x), x * (rho - z) - y, x * y - beta * z]
+
+    # Choose random starting points, uniformly distributed from -15 to 15
+    np.random.seed(rseed)
+    x0 = -15 + 30 * np.random.random((N_trajectories, 3))
+
+    # Solve for the trajectories
+    t = np.linspace(0, 2, 500)
+    x_t = np.asarray([integrate.odeint(lorentz_deriv, x0i, t)
+                      for x0i in x0])
+
+    # Set up figure & 3D axis for animation
+    fig = plt.figure()
+    ax = fig.add_axes([0, 0, 1, 1], projection='3d')
+    ax.axis('off')
+
+    # choose a different color for each trajectory
+    colors = plt.cm.jet(np.linspace(0, 1, N_trajectories))
+
+    # set up lines and points
+    lines = sum([ax.plot([], [], [], '-', c=c)
+                 for c in colors], [])
+    pts = sum([ax.plot([], [], [], 'o', c=c, ms=4)
+               for c in colors], [])
+
+    # prepare the axes limits
+    ax.set_xlim((-25, 25))
+    ax.set_ylim((-35, 35))
+    ax.set_zlim((5, 55))
+
+    # set point-of-view: specified by (altitude degrees, azimuth degrees)
+    ax.view_init(30, 0)
+
+    # initialization function: plot the background of each frame
+    def init():
+        for line, pt in zip(lines, pts):
+            line.set_data([], [])
+            line.set_3d_properties([])
+
+            pt.set_data([], [])
+            pt.set_3d_properties([])
+        return lines + pts
+
+    # animation function: called sequentially
+    def animate(i):
+        # we'll step two time-steps per frame.  This leads to nice results.
+        i = (2 * i) % x_t.shape[1]
+
+        for line, pt, xi in zip(lines, pts, x_t):
+            x, y, z = xi[:i + 1].T
+            line.set_data(x, y)
+            line.set_3d_properties(z)
+
+            pt.set_data(x[-1:], y[-1:])
+            pt.set_3d_properties(z[-1:])
+
+        ax.view_init(30, 0.3 * i)
+        fig.canvas.draw()
+        return lines + pts
+
+    return animation.FuncAnimation(fig, animate, init_func=init,
+                                   frames=frames, interval=interval)

simpegDCIP/Dev/JSAnimation/html_writer.py

@@ -0,0 +1,327 @@
+import os
+import sys
+import random
+import string
+import warnings
+if sys.version_info < (3, 0):
+    from cStringIO import StringIO as InMemory
+else:
+    from io import BytesIO as InMemory
+from matplotlib.animation import writers, FileMovieWriter
+from base64 import b64encode
+
+
+ICON_DIR = os.path.join(os.path.dirname(__file__), 'icons')
+
+
+class _Icons(object):
+    """This class is a container for base64 representations of the icons"""
+    icons = ['first', 'prev', 'reverse', 'pause', 'play', 'next', 'last']
+
+    def __init__(self, icon_dir=ICON_DIR, extension='png'):
+        self.icon_dir = icon_dir
+        self.extension = extension
+        for icon in self.icons:
+            setattr(self, icon,
+                    self._load_base64('{0}.{1}'.format(icon, extension)))
+
+    def _load_base64(self, filename):
+        data = open(os.path.join(self.icon_dir, filename), 'rb').read()
+        return 'data:image/{0};base64,{1}'.format(self.extension,
+                                                  b64encode(data).decode('ascii'))
+
+
+JS_INCLUDE = """
+<script language="javascript">
+  /* Define the Animation class */
+  function Animation(frames, img_id, slider_id, interval, loop_select_id){
+    this.img_id = img_id;
+    this.slider_id = slider_id;
+    this.loop_select_id = loop_select_id;
+    this.interval = interval;
+    this.current_frame = 0;
+    this.direction = 0;
+    this.timer = null;
+    this.frames = new Array(frames.length);
+
+    for (var i=0; i<frames.length; i++)
+    {
+     this.frames[i] = new Image();
+     this.frames[i].src = frames[i];
+    }
+    document.getElementById(this.slider_id).max = this.frames.length - 1;
+    this.set_frame(this.current_frame);
+  }
+
+  Animation.prototype.get_loop_state = function(){
+    var button_group = document[this.loop_select_id].state;
+    for (var i = 0; i < button_group.length; i++) {
+        var button = button_group[i];
+        if (button.checked) {
+            return button.value;
+        }
+    }
+    return undefined;
+  }
+
+  Animation.prototype.set_frame = function(frame){
+    this.current_frame = frame;
+    document.getElementById(this.img_id).src = this.frames[this.current_frame].src;
+    document.getElementById(this.slider_id).value = this.current_frame;
+  }
+
+  Animation.prototype.next_frame = function()
+  {
+    this.set_frame(Math.min(this.frames.length - 1, this.current_frame + 1));
+  }
+
+  Animation.prototype.previous_frame = function()
+  {
+    this.set_frame(Math.max(0, this.current_frame - 1));
+  }
+
+  Animation.prototype.first_frame = function()
+  {
+    this.set_frame(0);
+  }
+
+  Animation.prototype.last_frame = function()
+  {
+    this.set_frame(this.frames.length - 1);
+  }
+
+  Animation.prototype.slower = function()
+  {
+    this.interval /= 0.7;
+    if(this.direction > 0){this.play_animation();}
+    else if(this.direction < 0){this.reverse_animation();}
+  }
+
+  Animation.prototype.faster = function()
+  {
+    this.interval *= 0.7;
+    if(this.direction > 0){this.play_animation();}
+    else if(this.direction < 0){this.reverse_animation();}
+  }
+
+  Animation.prototype.anim_step_forward = function()
+  {
+    this.current_frame += 1;
+    if(this.current_frame < this.frames.length){
+      this.set_frame(this.current_frame);
+    }else{
+      var loop_state = this.get_loop_state();
+      if(loop_state == "loop"){
+        this.first_frame();
+      }else if(loop_state == "reflect"){
+        this.last_frame();
+        this.reverse_animation();
+      }else{
+        this.pause_animation();
+        this.last_frame();
+      }
+    }
+  }
+
+  Animation.prototype.anim_step_reverse = function()
+  {
+    this.current_frame -= 1;
+    if(this.current_frame >= 0){
+      this.set_frame(this.current_frame);
+    }else{
+      var loop_state = this.get_loop_state();
+      if(loop_state == "loop"){
+        this.last_frame();
+      }else if(loop_state == "reflect"){
+        this.first_frame();
+        this.play_animation();
+      }else{
+        this.pause_animation();
+        this.first_frame();
+      }
+    }
+  }
+
+  Animation.prototype.pause_animation = function()
+  {
+    this.direction = 0;
+    if (this.timer){
+      clearInterval(this.timer);
+      this.timer = null;
+    }
+  }
+
+  Animation.prototype.play_animation = function()
+  {
+    this.pause_animation();
+    this.direction = 1;
+    var t = this;
+    if (!this.timer) this.timer = setInterval(function(){t.anim_step_forward();}, this.interval);
+  }
+
+  Animation.prototype.reverse_animation = function()
+  {
+    this.pause_animation();
+    this.direction = -1;
+    var t = this;
+    if (!this.timer) this.timer = setInterval(function(){t.anim_step_reverse();}, this.interval);
+  }
+</script>
+"""
+
+
+DISPLAY_TEMPLATE = """
+<div class="animation" align="center">
+    <img id="_anim_img{id}">
+    <br>
+    <input id="_anim_slider{id}" type="range" style="width:350px" name="points" min="0" max="1" step="1" value="0" onchange="anim{id}.set_frame(parseInt(this.value));"></input>
+    <br>
+    <button onclick="anim{id}.slower()">&#8211;</button>
+    <button onclick="anim{id}.first_frame()"><img class="anim_icon" src="{icons.first}"></button>
+    <button onclick="anim{id}.previous_frame()"><img class="anim_icon" src="{icons.prev}"></button>
+    <button onclick="anim{id}.reverse_animation()"><img class="anim_icon" src="{icons.reverse}"></button>
+    <button onclick="anim{id}.pause_animation()"><img class="anim_icon" src="{icons.pause}"></button>
+    <button onclick="anim{id}.play_animation()"><img class="anim_icon" src="{icons.play}"></button>
+    <button onclick="anim{id}.next_frame()"><img class="anim_icon" src="{icons.next}"></button>
+    <button onclick="anim{id}.last_frame()"><img class="anim_icon" src="{icons.last}"></button>
+    <button onclick="anim{id}.faster()">+</button>
+  <form action="#n" name="_anim_loop_select{id}" class="anim_control">
+    <input type="radio" name="state" value="once" {once_checked}> Once </input>
+    <input type="radio" name="state" value="loop" {loop_checked}> Loop </input>
+    <input type="radio" name="state" value="reflect" {reflect_checked}> Reflect </input>
+  </form>
+</div>
+
+
+<script language="javascript">
+  /* Instantiate the Animation class. */
+  /* The IDs given should match those used in the template above. */
+  (function() {{
+    var img_id = "_anim_img{id}";
+    var slider_id = "_anim_slider{id}";
+    var loop_select_id = "_anim_loop_select{id}";
+    var frames = new Array({Nframes});
+    {fill_frames}
+
+    /* set a timeout to make sure all the above elements are created before
+       the object is initialized. */
+    setTimeout(function() {{
+        anim{id} = new Animation(frames, img_id, slider_id, {interval}, loop_select_id);
+    }}, 0);
+  }})()
+</script>
+"""
+
+INCLUDED_FRAMES = """
+  for (var i=0; i<{Nframes}; i++){{
+    frames[i] = "{frame_dir}/frame" + ("0000000" + i).slice(-7) + ".{frame_format}";
+  }}
+"""
+
+
+def _included_frames(frame_list, frame_format):
+    """frame_list should be a list of filenames"""
+    return INCLUDED_FRAMES.format(Nframes=len(frame_list),
+                                  frame_dir=os.path.dirname(frame_list[0]),
+                                  frame_format=frame_format)
+
+
+def _embedded_frames(frame_list, frame_format):
+    """frame_list should be a list of base64-encoded png files"""
+    template = '  frames[{0}] = "data:image/{1};base64,{2}"\n'
+    embedded = "\n"
+    for i, frame_data in enumerate(frame_list):
+        embedded += template.format(i, frame_format,
+                                    frame_data.replace('\n', '\\\n'))
+    return embedded
+
+
+@writers.register('html')
+class HTMLWriter(FileMovieWriter):
+    # we start the animation id count at a random number: this way, if two
+    # animations are meant to be included on one HTML page, there is a
+    # very small chance of conflict.
+    rng = random.Random()
+    exec_key = 'animation.ffmpeg_path'
+    args_key = 'animation.ffmpeg_args'
+    supported_formats = ['png', 'jpeg', 'tiff', 'svg']
+
+    @classmethod
+    def new_id(cls):
+        #return '%16x' % cls.rng.getrandbits(64)
+        return ''.join(cls.rng.choice(string.ascii_uppercase)
+                       for x in range(16))
+
+    def __init__(self, fps=30, codec=None, bitrate=None, extra_args=None,
+                 metadata=None, embed_frames=False, default_mode='loop'):
+        self.embed_frames = embed_frames
+        self.default_mode = default_mode.lower()
+
+        if self.default_mode not in ['loop', 'once', 'reflect']:
+            self.default_mode = 'loop'
+            warnings.warn("unrecognized default_mode: using 'loop'")
+
+        self._saved_frames = list()
+        super(HTMLWriter, self).__init__(fps, codec, bitrate,
+                                         extra_args, metadata)
+
+    def setup(self, fig, outfile, dpi, frame_dir=None):
+        if os.path.splitext(outfile)[-1] not in ['.html', '.htm']:
+            raise ValueError("outfile must be *.htm or *.html")
+
+        if not self.embed_frames:
+            if frame_dir is None:
+                frame_dir = outfile.rstrip('.html') + '_frames'
+            if not os.path.exists(frame_dir):
+                os.makedirs(frame_dir)
+            frame_prefix = os.path.join(frame_dir, 'frame')
+        else:
+            frame_prefix = None
+
+        super(HTMLWriter, self).setup(fig, outfile, dpi,
+                                      frame_prefix, clear_temp=False)
+
+    def grab_frame(self, **savefig_kwargs):
+        if self.embed_frames:
+            suffix = '.' + self.frame_format
+            f = InMemory()
+            self.fig.savefig(f, format=self.frame_format,
+                             dpi=self.dpi, **savefig_kwargs)
+            f.seek(0)
+            self._saved_frames.append(b64encode(f.read()).decode('ascii'))
+        else:
+            return super(HTMLWriter, self).grab_frame(**savefig_kwargs)
+
+    def _run(self):
+        # make a ducktyped subprocess standin
+        # this is called by the MovieWriter base class, but not used here.
+        class ProcessStandin(object):
+            returncode = 0
+            def communicate(self):
+                return ('', '')
+        self._proc = ProcessStandin()
+
+        # save the frames to an html file
+        if self.embed_frames:
+            fill_frames = _embedded_frames(self._saved_frames,
+                                           self.frame_format)
+        else:
+            # temp names is filled by FileMovieWriter
+            fill_frames = _included_frames(self._temp_names,
+                                           self.frame_format)
+
+        mode_dict = dict(once_checked='',
+                         loop_checked='',
+                         reflect_checked='')
+        mode_dict[self.default_mode + '_checked'] = 'checked'
+
+        interval = int(1000. / self.fps)
+
+        with open(self.outfile, 'w') as of:
+            of.write(JS_INCLUDE)
+            of.write(DISPLAY_TEMPLATE.format(id=self.new_id(),
+                                             Nframes=len(self._temp_names),
+                                             fill_frames=fill_frames,
+                                             interval=interval,
+                                             icons=_Icons(),
+                                             **mode_dict))