{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from scipy import misc\n",
    "from PIL import Image\n",
    "import numpy as np\n",
    "import matplotlib.pyplot as plt\n",
    "\n",
    "from mpl_toolkits.mplot3d import Axes3D\n",
    "\n",
    "import imagepers"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "im = np.loadtxt('paws.numpy')\n",
    "print(\"pre shape:\", im.shape)\n",
    "w, h = im.shape\n",
    "im = np.array(Image.fromarray(im).resize((h*2, w*2)))\n",
    "print(\"post shape:\", im.shape)\n",
    "im = im * (255 / np.max(im))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "g0 = imagepers.persistence(im)\n",
    "g0"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "fig = plt.figure()\n",
    "plt.imshow(im, interpolation=\"nearest\")\n",
    "plt.colorbar()\n",
    "xx, yy = np.mgrid[0:im.shape[0], 0:im.shape[1]]\n",
    "\n",
    "#fig = plt.figure()\n",
    "#plt.contourf(xx, yy, im, np.arange(0, 255, 20))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "fig = plt.figure()\n",
    "ax = fig.add_subplot(111)\n",
    "ax.set_title(\"Peristence diagram\")\n",
    "ax.plot([0,255], [0,255], '-', c='grey')\n",
    "for i, homclass in enumerate(g0):\n",
    "    p_birth, bl, pers, p_death = homclass\n",
    "    if pers <= 1.0:\n",
    "        continue\n",
    "    \n",
    "    x, y = bl, bl-pers\n",
    "    ax.plot([x], [y], '.', c='b')\n",
    "    ax.text(x, y+2, str(i+1), color='b')\n",
    "ax.set_xlabel(\"Birth level\")\n",
    "ax.set_ylabel(\"Death level\")\n",
    "ax.set_xlim((-5,260))\n",
    "ax.set_ylim((-5,260))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "fig = plt.figure()\n",
    "ax = fig.add_subplot(111)\n",
    "ax.set_title(\"Loci of births\")\n",
    "for i, homclass in enumerate(g0):\n",
    "    p_birth, bl, pers, p_death = homclass\n",
    "    if pers <= 20.0:\n",
    "        continue\n",
    "    y, x = p_birth\n",
    "    ax.plot([x], [y], '.', c='b')\n",
    "    ax.text(x, y+0.25, str(i+1), color='b')\n",
    "    \n",
    "ax.set_xlim((0,im.shape[1]))\n",
    "ax.set_ylim((0,im.shape[0]))\n",
    "plt.gca().invert_yaxis()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "fig = plt.figure(figsize=(6, 6))\n",
    "ax = fig.add_subplot(111, projection='3d')\n",
    "ax.set_zlim(0, 800)\n",
    "ax.plot_surface(xx, yy, im ,rstride=1, cstride=1, cmap=plt.cm.jet,\n",
    "        linewidth=0)\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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