+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "from scipy import misc\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",
+ "im = misc.imresize(im, 2.0)\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()\n",
+ "ax = fig.gca(projection='3d')\n",
+ "ax.plot_surface(xx, yy, im ,rstride=1, cstride=1, cmap=plt.cm.jet,\n",
+ " linewidth=0)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "plt.show()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "collapsed": true
+ },
+ "outputs": [],
+ "source": []
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python3.5",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.5.5"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 1
+}