2Dpers.ipynb

   1 {
   2  "cells": [
   3   {
   4    "cell_type": "code",
   5    "execution_count": null,
   6    "metadata": {},
   7    "outputs": [],
   8    "source": [
   9     "from scipy import misc\n",
  10     "import numpy as np\n",
  11     "import matplotlib.pyplot as plt\n",
  12     "\n",
  13     "from mpl_toolkits.mplot3d import Axes3D\n",
  14     "\n",
  15     "import imagepers"
  16    ]
  17   },
  18   {
  19    "cell_type": "code",
  20    "execution_count": null,
  21    "metadata": {},
  22    "outputs": [],
  23    "source": [
  24     "im = np.loadtxt('paws.numpy')\n",
  25     "im = misc.imresize(im, 2.0)\n",
  26     "im = im * (255 / np.max(im))"
  27    ]
  28   },
  29   {
  30    "cell_type": "code",
  31    "execution_count": null,
  32    "metadata": {},
  33    "outputs": [],
  34    "source": [
  35     "g0 = imagepers.persistence(im)\n",
  36     "g0"
  37    ]
  38   },
  39   {
  40    "cell_type": "code",
  41    "execution_count": null,
  42    "metadata": {},
  43    "outputs": [],
  44    "source": [
  45     "fig = plt.figure()\n",
  46     "plt.imshow(im, interpolation=\"nearest\")\n",
  47     "plt.colorbar()\n",
  48     "xx, yy = np.mgrid[0:im.shape[0], 0:im.shape[1]]\n",
  49     "\n",
  50     "#fig = plt.figure()\n",
  51     "#plt.contourf(xx, yy, im, np.arange(0, 255, 20))"
  52    ]
  53   },
  54   {
  55    "cell_type": "code",
  56    "execution_count": null,
  57    "metadata": {},
  58    "outputs": [],
  59    "source": [
  60     "fig = plt.figure()\n",
  61     "ax = fig.add_subplot(111)\n",
  62     "ax.set_title(\"Peristence diagram\")\n",
  63     "ax.plot([0,255], [0,255], '-', c='grey')\n",
  64     "for i, homclass in enumerate(g0):\n",
  65     "    p_birth, bl, pers, p_death = homclass\n",
  66     "    if pers <= 1.0:\n",
  67     "        continue\n",
  68     "    \n",
  69     "    x, y = bl, bl-pers\n",
  70     "    ax.plot([x], [y], '.', c='b')\n",
  71     "    ax.text(x, y+2, str(i+1), color='b')\n",
  72     "ax.set_xlabel(\"Birth level\")\n",
  73     "ax.set_ylabel(\"Death level\")\n",
  74     "ax.set_xlim((-5,260))\n",
  75     "ax.set_ylim((-5,260))"
  76    ]
  77   },
  78   {
  79    "cell_type": "code",
  80    "execution_count": null,
  81    "metadata": {},
  82    "outputs": [],
  83    "source": [
  84     "fig = plt.figure()\n",
  85     "ax = fig.add_subplot(111)\n",
  86     "ax.set_title(\"Loci of births\")\n",
  87     "for i, homclass in enumerate(g0):\n",
  88     "    p_birth, bl, pers, p_death = homclass\n",
  89     "    if pers <= 20.0:\n",
  90     "        continue\n",
  91     "    y, x = p_birth\n",
  92     "    ax.plot([x], [y], '.', c='b')\n",
  93     "    ax.text(x, y+0.25, str(i+1), color='b')\n",
  94     "    \n",
  95     "ax.set_xlim((0,im.shape[1]))\n",
  96     "ax.set_ylim((0,im.shape[0]))\n",
  97     "plt.gca().invert_yaxis()"
  98    ]
  99   },
 100   {
 101    "cell_type": "code",
 102    "execution_count": null,
 103    "metadata": {},
 104    "outputs": [],
 105    "source": [
 106     "fig = plt.figure()\n",
 107     "ax = fig.gca(projection='3d')\n",
 108     "ax.plot_surface(xx, yy, im ,rstride=1, cstride=1, cmap=plt.cm.jet,\n",
 109     "        linewidth=0)"
 110    ]
 111   },
 112   {
 113    "cell_type": "code",
 114    "execution_count": null,
 115    "metadata": {},
 116    "outputs": [],
 117    "source": [
 118     "plt.show()"
 119    ]
 120   },
 121   {
 122    "cell_type": "code",
 123    "execution_count": null,
 124    "metadata": {
 125     "collapsed": true
 126    },
 127    "outputs": [],
 128    "source": []
 129   }
 130  ],
 131  "metadata": {
 132   "kernelspec": {
 133    "display_name": "Python 3",
 134    "language": "python3.5",
 135    "name": "python3"
 136   },
 137   "language_info": {
 138    "codemirror_mode": {
 139     "name": "ipython",
 140     "version": 3
 141    },
 142    "file_extension": ".py",
 143    "mimetype": "text/x-python",
 144    "name": "python",
 145    "nbconvert_exporter": "python",
 146    "pygments_lexer": "ipython3",
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 150  "nbformat": 4,
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 152 }