update animations to use pillow

.gitignore

@@ -1,4 +1,4 @@
-examples/images/animation/*/*.png
+examples/images/phase-animate/*/*.png
 examples/images/cobweb-animate/*.png
 .temp
 run_tests.bat

README.md

@@ -6,7 +6,7 @@
 
 **Python package for modeling, simulating, visualizing, and animating discrete nonlinear dynamical systems and chaos**
 
-It uses pandas, numpy, and numba for fast simulation, and matplotlib for beautiful visualizations and animations to explore system behavior. Compatible with Python 2/3.
+pynamical uses pandas, numpy, and numba for fast simulation, and matplotlib for beautiful visualizations and animations to explore system behavior. Compatible with Python 2+3.
 
 You can read/cite the journal article about pynamical: Boeing, G. 2016. "[Visual Analysis of Nonlinear Dynamical Systems: Chaos, Fractals, Self-Similarity and the Limits of Prediction](http://geoffboeing.com/publications/nonlinear-chaos-fractals-prediction/)." *Systems*, 4 (4), 37. doi:10.3390/systems4040037.
 
@@ -28,7 +28,7 @@ pip install pynamical
 
 First load pynamical. Then simulate some model and visualize its bifurcation diagram in just 2 lines of code:
 
-```
+```python
 from pynamical import logistic_map, simulate, bifurcation_plot
 pops = simulate(model=logistic_map, num_gens=100, rate_min=0, rate_max=4, num_rates=1000, num_discard=100)
 bifurcation_plot(pops)
@@ -38,15 +38,15 @@ bifurcation_plot(pops)
 
 Zoom into a slice of this bifurcation diagram to see its [fractal structure](examples/pynamical-demo-logistic-model.ipynb):
 
-```
+```python
 pops = simulate(model=logistic_map, num_gens=100, rate_min=3.7, rate_max=3.9, num_rates=1000, num_discard=100)
 bifurcation_plot(pops, xmin=3.7, xmax=3.9)
 ```
 ![](examples/images/readme/logistic-map-bifurcation-3.png)
 
 Plot a two-dimensional [phase diagram](examples/pynamical-demo-phase-diagrams.ipynb) of the logistic map:
 
-```
+```python
 from pynamical import phase_diagram
 pops = simulate(model=logistic_map, num_gens=4000, rate_min=3.6, rate_max=4.0, num_rates=50, num_discard=100)
 phase_diagram(pops, xmin=0.25, xmax=0.75, ymin=0.8, ymax=1.01, size=7, color='viridis')
@@ -56,7 +56,7 @@ phase_diagram(pops, xmin=0.25, xmax=0.75, ymin=0.8, ymax=1.01, size=7, color='vi
 
 Or a three-dimensional phase diagram of the [cubic map](examples/pynamical-demo-other-models.ipynb):
 
-```
+```python
 from pynamical import cubic_map, phase_diagram_3d
 pops = simulate(model=cubic_map, num_gens=3000, rate_min=3.5, num_rates=30, num_discard=100)
 phase_diagram_3d(pops, xmin=-1, xmax=1, ymin=-1, ymax=1, zmin=-1, zmax=1, alpha=0.2, color='viridis', azim=330)
@@ -66,11 +66,11 @@ phase_diagram_3d(pops, xmin=-1, xmax=1, ymin=-1, ymax=1, zmin=-1, zmax=1, alpha=
 
 Animate the 3D phase diagram of the logistic map [to reveal](examples/pynamical-demo-3d-animation.ipynb) the strange attractor's structure:
 
-![](examples/images/animation/logistic-3d-phase-diagram-chaotic-regime.gif)
+![](examples/images/phase-animate/05-logistic-3d-phase-diagram-chaotic-regime.gif)
 
 Animate a cobweb plot of the logistic map's parameter space [to explore](examples/pynamical-demo-cobweb-plots.ipynb) sensitivity and behavior: 
 
-![](examples/images/cobweb-animate/animated-logistic-cobweb.gif)
+![](examples/images/animated-logistic-cobweb.gif)
 
 ## For more info:
   - [Read the journal article](http://geoffboeing.com/publications/nonlinear-chaos-fractals-prediction/)

examples/pynamical-demo-3d-animation.ipynb

@@ -8,12 +8,11 @@
     "\n",
     "Author: Geoff Boeing\n",
     "\n",
-    "\n",
-    "Journal article: http://geoffboeing.com/publications/nonlinear-chaos-fractals-prediction/\n",
+    "Journal article: Boeing, G. 2016. \"[Visual Analysis of Nonlinear Dynamical Systems: Chaos, Fractals, Self-Similarity and the Limits of Prediction](http://geoffboeing.com/publications/nonlinear-chaos-fractals-prediction/).\" *Systems*, 4 (4), 37. doi:10.3390/systems4040037.\n",
     "\n",
     "Blog post: http://geoffboeing.com/2015/04/animated-3d-plots-python/\n",
     "\n",
-    "This notebook demonstrates how to make animated GIFs that pan and zoom around 3-D phase diagrams to visualize fractal data sets, strange attractors, and chaos. If you get errors from images2gif, check out [this page](https://stackoverflow.com/questions/19149643/error-in-images2gif-py-with-globalpalette) or replace images2.gif.py with [this version](https://github.com/rec/echomesh/blob/master/code/python/external/images2gif.py). If you're on Python 3 you may need [this version](https://github.com/isaacgerg/images2gif) of images2gif."
+    "This notebook demonstrates how to make animated GIFs that pan and zoom around 3-D phase diagrams to visualize fractal data sets, strange attractors, and chaos."
    ]
   },
   {
@@ -25,9 +24,8 @@
    "outputs": [],
    "source": [
     "from pynamical import simulate, phase_diagram_3d, title_font, label_font\n",
-    "import pandas as pd, numpy as np, matplotlib.pyplot as plt, random, glob, IPython.display as IPdisplay\n",
-    "from PIL import Image as PIL_Image\n",
-    "from images2gif import writeGif\n",
+    "import pandas as pd, numpy as np, matplotlib.pyplot as plt, random, glob, os, IPython.display as IPdisplay\n",
+    "from PIL import Image\n",
     "%matplotlib inline"
    ]
   },
@@ -39,7 +37,7 @@
    },
    "outputs": [],
    "source": [
-    "save_folder = 'images/animation/'"
+    "save_folder = 'images/phase-animate'"
    ]
   },
   {
@@ -59,7 +57,7 @@
     {
      "data": {
       "text/html": [
-       "<img src=\"images/animation/pan-rotate-zoom-demo.gif\"/>"
+       "<img src=\"images/phase-animate/01-pan-rotate-zoom-demo.gif\"/>"
       ],
       "text/plain": [
        "<IPython.core.display.Image object>"
@@ -72,7 +70,11 @@
    ],
    "source": [
     "# set a filename, run the logistic model, and create the plot\n",
-    "gif_filename = 'pan-rotate-zoom-demo'\n",
+    "gif_filename = '01-pan-rotate-zoom-demo'\n",
+    "working_folder = '{}/{}'.format(save_folder, gif_filename)\n",
+    "if not os.path.exists(working_folder):\n",
+    "    os.makedirs(working_folder)\n",
+    "    \n",
     "pops = simulate(num_gens=1000, rate_min=3.99, num_rates=1)\n",
     "fig, ax = phase_diagram_3d(pops, remove_ticks=False, show=False, save=False)\n",
     "\n",
@@ -99,17 +101,20 @@
     "    ax.dist = dist_range[int(azimuth/(360./steps))]\n",
     "    \n",
     "    # set the figure title to the viewing perspective, and save each figure as a .png\n",
-    "    fig.suptitle('elev=' + str(round(ax.elev,1)) + ', azim=' + str(round(ax.azim,1)) + ', dist=' + str(round(ax.dist,1)))\n",
-    "    plt.savefig(save_folder + gif_filename + '/img' + str(azimuth).zfill(3) + '.png')\n",
+    "    fig.suptitle('elev={:.1f}, azim={:.1f}, dist={:.1f}'.format(ax.elev, ax.azim, ax.dist))\n",
+    "    plt.savefig('{}/{}/img{:03d}.png'.format(save_folder, gif_filename, azimuth))\n",
     "    \n",
     "# don't display the static plot...\n",
     "plt.close()\n",
     "\n",
-    "# ...instead, create an animated gif of all the frames, then display it inline\n",
-    "images = [PIL_Image.open(image) for image in glob.glob(save_folder + gif_filename + '/*.png')]\n",
-    "file_path_name = save_folder + gif_filename + '.gif'\n",
-    "writeGif(file_path_name, images, duration=0.2)\n",
-    "IPdisplay.Image(url=file_path_name)"
+    "# load all the static images into a list then save as an animated gif\n",
+    "gif_filepath = '{}/{}.gif'.format(save_folder, gif_filename)\n",
+    "images = [Image.open(image) for image in glob.glob('{}/*.png'.format(working_folder))]\n",
+    "gif = images[0]\n",
+    "gif.info['duration'] = 20 #milliseconds per frame\n",
+    "gif.info['loop'] = 0 #how many times to loop (0=infinite)\n",
+    "gif.save(fp=gif_filepath, format='gif', save_all=True, append_images=images[1:])\n",
+    "IPdisplay.Image(url=gif_filepath)"
    ]
   },
   {
@@ -129,7 +134,7 @@
     {
      "data": {
       "text/html": [
-       "<img src=\"images/animation/pan-rotate-logistic-phase-diagram.gif\"/>"
+       "<img src=\"images/phase-animate/02-pan-rotate-logistic-phase-diagram.gif\"/>"
       ],
       "text/plain": [
        "<IPython.core.display.Image object>"
@@ -142,7 +147,11 @@
    ],
    "source": [
     "# set a filename, run the logistic model, and create the plot\n",
-    "gif_filename = 'pan-rotate-logistic-phase-diagram'\n",
+    "gif_filename = '02-pan-rotate-logistic-phase-diagram'\n",
+    "working_folder = '{}/{}'.format(save_folder, gif_filename)\n",
+    "if not os.path.exists(working_folder):\n",
+    "    os.makedirs(working_folder)\n",
+    "    \n",
     "pops = simulate(num_gens=1000, rate_min=3.99, num_rates=1)\n",
     "fig, ax = phase_diagram_3d(pops, color='#003399', xlabel='Population (t)', ylabel='Population (t + 1)', zlabel='', \n",
     "                           show=False, save=False)\n",
@@ -179,16 +188,19 @@
     "        \n",
     "    # add a figure title to each plot then save the figure to the disk\n",
     "    fig.suptitle('Logistic Map, r=3.99', fontsize=16, x=0.5, y=0.85)\n",
-    "    plt.savefig(save_folder + gif_filename + '/img' + str(n).zfill(3) + '.png', bbox_inches='tight')\n",
+    "    plt.savefig('{}/{}/img{:03d}.png'.format(save_folder, gif_filename, n), bbox_inches='tight')\n",
     "\n",
     "# don't display the static plot\n",
     "plt.close()\n",
     "\n",
-    "# create an animated gif of all the 3-D plot perspectives then display it inline\n",
-    "images = [PIL_Image.open(image) for image in glob.glob(save_folder + gif_filename + '/*.png')]\n",
-    "file_path_name = save_folder + gif_filename + '.gif'\n",
-    "writeGif(file_path_name, images, duration=0.1)\n",
-    "IPdisplay.Image(url=file_path_name)"
+    "# load all the static images into a list then save as an animated gif\n",
+    "gif_filepath = '{}/{}.gif'.format(save_folder, gif_filename)\n",
+    "images = [Image.open(image) for image in glob.glob('{}/*.png'.format(working_folder))]\n",
+    "gif = images[0]\n",
+    "gif.info['duration'] = 10 #milliseconds per frame\n",
+    "gif.info['loop'] = 0 #how many times to loop (0=infinite)\n",
+    "gif.save(fp=gif_filepath, format='gif', save_all=True, append_images=images[1:])\n",
+    "IPdisplay.Image(url=gif_filepath)"
    ]
   },
   {
@@ -221,39 +233,39 @@
        "    <tr>\n",
        "      <th>995</th>\n",
        "      <td>0.247214</td>\n",
-       "      <td>0.324087</td>\n",
+       "      <td>0.563377</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>996</th>\n",
        "      <td>0.742535</td>\n",
-       "      <td>0.091102</td>\n",
+       "      <td>0.453418</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>997</th>\n",
        "      <td>0.762795</td>\n",
-       "      <td>0.001077</td>\n",
+       "      <td>0.384585</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>998</th>\n",
        "      <td>0.721947</td>\n",
-       "      <td>0.206058</td>\n",
+       "      <td>0.304216</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>999</th>\n",
        "      <td>0.800951</td>\n",
-       "      <td>0.786185</td>\n",
+       "      <td>0.272667</td>\n",
        "    </tr>\n",
        "  </tbody>\n",
        "</table>\n",
        "</div>"
       ],
       "text/plain": [
        "        chaos    random\n",
-       "995  0.247214  0.324087\n",
-       "996  0.742535  0.091102\n",
-       "997  0.762795  0.001077\n",
-       "998  0.721947  0.206058\n",
-       "999  0.800951  0.786185"
+       "995  0.247214  0.563377\n",
+       "996  0.742535  0.453418\n",
+       "997  0.762795  0.384585\n",
+       "998  0.721947  0.304216\n",
+       "999  0.800951  0.272667"
       ]
      },
      "execution_count": 5,
@@ -280,7 +292,7 @@
     {
      "data": {
       "text/html": [
-       "<img src=\"images/animation/pan-rotate-logistic-random.gif\"/>"
+       "<img src=\"images/phase-animate/03-pan-rotate-logistic-random.gif\"/>"
       ],
       "text/plain": [
        "<IPython.core.display.Image object>"
@@ -293,7 +305,11 @@
    ],
    "source": [
     "# set a filename and then create the plot\n",
-    "gif_filename = 'pan-rotate-logistic-random'\n",
+    "gif_filename = '03-pan-rotate-logistic-random'\n",
+    "working_folder = '{}/{}'.format(save_folder, gif_filename)\n",
+    "if not os.path.exists(working_folder):\n",
+    "    os.makedirs(working_folder)\n",
+    "    \n",
     "fig, ax = phase_diagram_3d(pops, color=['#003399','#cc0000'], xlabel='Population (t)', ylabel='Population (t + 1)', \n",
     "                           zlabel='', legend=True, legend_bbox_to_anchor=(0.94, 0.96), show=False, save=False)\n",
     "\n",
@@ -329,16 +345,19 @@
     "        \n",
     "    # add a figure title to each plot then save the figure to the disk\n",
     "    fig.suptitle(u'3-D phase diagram, chaos vs random', fontsize=16, x=0.5, y=0.85)\n",
-    "    plt.savefig(save_folder + gif_filename + '/img' + str(n).zfill(3) + '.png', bbox_inches='tight')\n",
+    "    plt.savefig('{}/{}/img{:03d}.png'.format(save_folder, gif_filename, n), bbox_inches='tight')\n",
     "\n",
     "# don't display the static plot\n",
     "plt.close()\n",
     "\n",
-    "# create an animated gif of all the 3-D plot perspectives then display it inline\n",
-    "images = [PIL_Image.open(image) for image in glob.glob(save_folder + gif_filename + '/*.png')]\n",
-    "file_path_name = save_folder + gif_filename + '.gif'\n",
-    "writeGif(file_path_name, images, duration=0.1)\n",
-    "IPdisplay.Image(url=file_path_name)"
+    "# load all the static images into a list then save as an animated gif\n",
+    "gif_filepath = '{}/{}.gif'.format(save_folder, gif_filename)\n",
+    "images = [Image.open(image) for image in glob.glob('{}/*.png'.format(working_folder))]\n",
+    "gif = images[0]\n",
+    "gif.info['duration'] = 10 #milliseconds per frame\n",
+    "gif.info['loop'] = 0 #how many times to loop (0=infinite)\n",
+    "gif.save(fp=gif_filepath, format='gif', save_all=True, append_images=images[1:])\n",
+    "IPdisplay.Image(url=gif_filepath)"
    ]
   },
   {
@@ -370,7 +389,7 @@
     {
      "data": {
       "text/html": [
-       "<img src=\"images/animation/pan-rotate-chaotic-regime.gif\"/>"
+       "<img src=\"images/phase-animate/04-pan-rotate-chaotic-regime.gif\"/>"
       ],
       "text/plain": [
        "<IPython.core.display.Image object>"
@@ -383,7 +402,11 @@
    ],
    "source": [
     "# set a filename and create the plot\n",
-    "gif_filename = 'pan-rotate-chaotic-regime'\n",
+    "gif_filename = '04-pan-rotate-chaotic-regime'\n",
+    "working_folder = '{}/{}'.format(save_folder, gif_filename)\n",
+    "if not os.path.exists(working_folder):\n",
+    "    os.makedirs(working_folder)\n",
+    "    \n",
     "fig, ax = phase_diagram_3d(pops, color='viridis', color_reverse=False,\n",
     "                           xlabel='Population (t)', ylabel='Population (t + 1)', zlabel='', \n",
     "                           show=False, save=False)\n",
@@ -421,16 +444,19 @@
     "    \n",
     "    # add a figure title to each plot then save the figure to the disk\n",
     "    fig.suptitle('Logistic Map, r=3.6 to r=4.0', fontsize=16, x=0.5, y=0.85)\n",
-    "    plt.savefig(save_folder + gif_filename + '/img' + str(n).zfill(3) + '.png', bbox_inches='tight')\n",
+    "    plt.savefig('{}/{}/img{:03d}.png'.format(save_folder, gif_filename, n), bbox_inches='tight')\n",
     "\n",
     "# don't display the static plot\n",
     "plt.close()\n",
     "\n",
-    "# create an animated gif of all the 3-D plot perspectives then display it inline\n",
-    "images = [PIL_Image.open(image) for image in glob.glob(save_folder + gif_filename + '/*.png')]\n",
-    "file_path_name = save_folder + gif_filename + '.gif'\n",
-    "writeGif(file_path_name, images, duration=0.1)\n",
-    "IPdisplay.Image(url=file_path_name)"
+    "# load all the static images into a list then save as an animated gif\n",
+    "gif_filepath = '{}/{}.gif'.format(save_folder, gif_filename)\n",
+    "images = [Image.open(image) for image in glob.glob('{}/*.png'.format(working_folder))]\n",
+    "gif = images[0]\n",
+    "gif.info['duration'] = 10 #milliseconds per frame\n",
+    "gif.info['loop'] = 0 #how many times to loop (0=infinite)\n",
+    "gif.save(fp=gif_filepath, format='gif', save_all=True, append_images=images[1:])\n",
+    "IPdisplay.Image(url=gif_filepath)"
    ]
   },
   {
@@ -465,7 +491,7 @@
     {
      "data": {
       "text/html": [
-       "<img src=\"images/animation/logistic-3d-phase-diagram-chaotic-regime.gif\"/>"
+       "<img src=\"images/phase-animate/05-logistic-3d-phase-diagram-chaotic-regime.gif\"/>"
       ],
       "text/plain": [
        "<IPython.core.display.Image object>"
@@ -478,7 +504,11 @@
    ],
    "source": [
     "# set a filename and create the plot\n",
-    "gif_filename = 'logistic-3d-phase-diagram-chaotic-regime'\n",
+    "gif_filename = '05-logistic-3d-phase-diagram-chaotic-regime'\n",
+    "working_folder = '{}/{}'.format(save_folder, gif_filename)\n",
+    "if not os.path.exists(working_folder):\n",
+    "    os.makedirs(working_folder)\n",
+    "    \n",
     "fig, ax = phase_diagram_3d(pops, color='viridis', color_reverse=False, show=False, save=False)\n",
     "\n",
     "# configure the initial viewing perspective\n",
@@ -507,16 +537,19 @@
     "    \n",
     "    # add a figure title to each plot then save the figure to the disk\n",
     "    fig.suptitle('Logistic Map, r=3.6 to r=4.0', fontsize=16, x=0.5, y=0.85)\n",
-    "    plt.savefig(save_folder + gif_filename + '/img' + str(n).zfill(3) + '.png', bbox_inches='tight')\n",
+    "    plt.savefig('{}/{}/img{:03d}.png'.format(save_folder, gif_filename, n), bbox_inches='tight')\n",
     "\n",
     "# don't display the static plot\n",
     "plt.close()\n",
     "\n",
-    "# create an animated gif of all the 3-D plot perspectives then display it inline\n",
-    "images = [PIL_Image.open(image) for image in glob.glob(save_folder + gif_filename + '/*.png')]\n",
-    "file_path_name = save_folder + gif_filename + '.gif'\n",
-    "writeGif(file_path_name, images, duration=0.1)\n",
-    "IPdisplay.Image(url=file_path_name)"
+    "# load all the static images into a list then save as an animated gif\n",
+    "gif_filepath = '{}/{}.gif'.format(save_folder, gif_filename)\n",
+    "images = [Image.open(image) for image in glob.glob('{}/*.png'.format(working_folder))]\n",
+    "gif = images[0]\n",
+    "gif.info['duration'] = 10 #milliseconds per frame\n",
+    "gif.info['loop'] = 0 #how many times to loop (0=infinite)\n",
+    "gif.save(fp=gif_filepath, format='gif', save_all=True, append_images=images[1:])\n",
+    "IPdisplay.Image(url=gif_filepath)"
    ]
   },
   {