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     "from PIL import Image\n",
  11     "import numpy as np\n",
  12     "import matplotlib.pyplot as plt\n",
  13     "\n",
  14     "from mpl_toolkits.mplot3d import Axes3D\n",
  15     "\n",
  16     "import imagepers"
  17    ]
  18   },
  19   {
  20    "cell_type": "code",
  21    "execution_count": null,
  22    "metadata": {},
  23    "outputs": [],
  24    "source": [
  25     "im = np.loadtxt('paws.numpy')\n",
  26     "print(\"pre shape:\", im.shape)\n",
  27     "w, h = im.shape\n",
  28     "im = np.array(Image.fromarray(im).resize((h*2, w*2)))\n",
  29     "print(\"post shape:\", im.shape)\n",
  30     "im = im * (255 / np.max(im))"
  31    ]
  32   },
  33   {
  34    "cell_type": "code",
  35    "execution_count": null,
  36    "metadata": {},
  37    "outputs": [],
  38    "source": [
  39     "g0 = imagepers.persistence(im)\n",
  40     "g0"
  41    ]
  42   },
  43   {
  44    "cell_type": "code",
  45    "execution_count": null,
  46    "metadata": {},
  47    "outputs": [],
  48    "source": [
  49     "fig = plt.figure()\n",
  50     "plt.imshow(im, interpolation=\"nearest\")\n",
  51     "plt.colorbar()\n",
  52     "xx, yy = np.mgrid[0:im.shape[0], 0:im.shape[1]]\n",
  53     "\n",
  54     "#fig = plt.figure()\n",
  55     "#plt.contourf(xx, yy, im, np.arange(0, 255, 20))"
  56    ]
  57   },
  58   {
  59    "cell_type": "code",
  60    "execution_count": null,
  61    "metadata": {},
  62    "outputs": [],
  63    "source": [
  64     "fig = plt.figure()\n",
  65     "ax = fig.add_subplot(111)\n",
  66     "ax.set_title(\"Peristence diagram\")\n",
  67     "ax.plot([0,255], [0,255], '-', c='grey')\n",
  68     "for i, homclass in enumerate(g0):\n",
  69     "    p_birth, bl, pers, p_death = homclass\n",
  70     "    if pers <= 1.0:\n",
  71     "        continue\n",
  72     "    \n",
  73     "    x, y = bl, bl-pers\n",
  74     "    ax.plot([x], [y], '.', c='b')\n",
  75     "    ax.text(x, y+2, str(i+1), color='b')\n",
  76     "ax.set_xlabel(\"Birth level\")\n",
  77     "ax.set_ylabel(\"Death level\")\n",
  78     "ax.set_xlim((-5,260))\n",
  79     "ax.set_ylim((-5,260))"
  80    ]
  81   },
  82   {
  83    "cell_type": "code",
  84    "execution_count": null,
  85    "metadata": {},
  86    "outputs": [],
  87    "source": [
  88     "fig = plt.figure()\n",
  89     "ax = fig.add_subplot(111)\n",
  90     "ax.set_title(\"Loci of births\")\n",
  91     "for i, homclass in enumerate(g0):\n",
  92     "    p_birth, bl, pers, p_death = homclass\n",
  93     "    if pers <= 20.0:\n",
  94     "        continue\n",
  95     "    y, x = p_birth\n",
  96     "    ax.plot([x], [y], '.', c='b')\n",
  97     "    ax.text(x, y+0.25, str(i+1), color='b')\n",
  98     "    \n",
  99     "ax.set_xlim((0,im.shape[1]))\n",
 100     "ax.set_ylim((0,im.shape[0]))\n",
 101     "plt.gca().invert_yaxis()"
 102    ]
 103   },
 104   {
 105    "cell_type": "code",
 106    "execution_count": null,
 107    "metadata": {},
 108    "outputs": [],
 109    "source": [
 110     "fig = plt.figure(figsize=(6, 6))\n",
 111     "ax = fig.add_subplot(111, projection='3d')\n",
 112     "ax.set_zlim(0, 800)\n",
 113     "ax.plot_surface(xx, yy, im ,rstride=1, cstride=1, cmap=plt.cm.jet,\n",
 114     "        linewidth=0)\n",
 115     "plt.show()"
 116    ]
 117   },
 118   {
 119    "cell_type": "code",
 120    "execution_count": null,
 121    "metadata": {},
 122    "outputs": [],
 123    "source": []
 124   },
 125   {
 126    "cell_type": "code",
 127    "execution_count": null,
 128    "metadata": {},
 129    "outputs": [],
 130    "source": []
 131   }
 132  ],
 133  "metadata": {
 134   "kernelspec": {
 135    "display_name": "Python 3 (ipykernel)",
 136    "language": "python",
 137    "name": "python3"
 138   },
 139   "language_info": {
 140    "codemirror_mode": {
 141     "name": "ipython",
 142     "version": 3
 143    },
 144    "file_extension": ".py",
 145    "mimetype": "text/x-python",
 146    "name": "python",
 147    "nbconvert_exporter": "python",
 148    "pygments_lexer": "ipython3",
 149    "version": "3.11.8"
 150   }
 151  },
 152  "nbformat": 4,
 153  "nbformat_minor": 4
 154 }