cython-classes.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Naive Python implementation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "class PyAnimal:\n",
    "    i = 0\n",
    "    def do_stuff(self):\n",
    "        self.i += 1    \n",
    "    def state(self):\n",
    "        return self.i\n",
    "    \n",
    "class PyPopulation:\n",
    "    def __init__(self,animals):\n",
    "        self.animals = animals\n",
    "    def do_stuff(self):\n",
    "        for animal in self.animals:\n",
    "            animal.do_stuff()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "100 loops, best of 3: 17.9 ms per loop\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "411"
      ]
     },
     "execution_count": 32,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "animals = [PyAnimal() for i in range(100000)]\n",
    "population = PyPopulation(animals)\n",
    "%timeit population.do_stuff()\n",
    "population.animals[15].state()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Naive Cython implementation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "%load_ext cython"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "%%cython\n",
    "cdef class CyAnimal:\n",
    "    cdef int i\n",
    "    \n",
    "    cpdef void do_stuff(self):\n",
    "        self.i += 1\n",
    "        \n",
    "    cpdef int state(self):\n",
    "        return self.i\n",
    "\n",
    "cdef class CyPopulation:\n",
    "    cdef list animals\n",
    "    \n",
    "    def __init__(self,list animals):\n",
    "        self.animals = animals\n",
    "        \n",
    "    cpdef void do_stuff(self):\n",
    "        for animal in self.animals:\n",
    "            animal.do_stuff()\n",
    "            \n",
    "    cpdef list state(self):\n",
    "        return [animal.state() for animal in self.animals]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "100 loops, best of 3: 3.08 ms per loop\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "411"
      ]
     },
     "execution_count": 29,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "animals = [CyAnimal() for i in range(100000)]\n",
    "population = CyPopulation(animals)\n",
    "%timeit population.do_stuff()\n",
    "population.state()[15]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## C++ wrapper implementation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Overwriting cppanimal.h\n"
     ]
    }
   ],
   "source": [
    "%%writefile cppanimal.h\n",
    "\n",
    "class CppAnimal {\n",
    "    public:\n",
    "        int i;\n",
    "        CppAnimal():i(0) {}\n",
    "        void do_stuff() {\n",
    "            i++;\n",
    "        }\n",
    "        int state() {\n",
    "            return i;\n",
    "        }\n",
    "};"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "%%cython -+ -I .\n",
    "from libcpp.vector cimport vector\n",
    "from cython.operator cimport dereference as deref, preincrement as inc\n",
    "\n",
    "\"\"\"\n",
    "Expose interface from C++ class\n",
    "\"\"\"\n",
    "cdef extern from \"cppanimal.h\":\n",
    "    cdef cppclass CppAnimal:\n",
    "        CppAnimal()\n",
    "        void do_stuff()\n",
    "        int state()\n",
    "\n",
    "\"\"\"\n",
    "Since CppAnimal is a C++ class, we cannot interact with it from Python.\n",
    "The population class thus has to create the Animals through a method.\n",
    "\"\"\"\n",
    "cdef class CyPopulation2:\n",
    "    cdef vector[CppAnimal] animals\n",
    "    \n",
    "    cpdef create_animal(self):\n",
    "        self.animals.push_back(CppAnimal())\n",
    "        \n",
    "    cpdef void do_stuff(self):\n",
    "        cdef vector[CppAnimal].iterator it = self.animals.begin()\n",
    "        while it != self.animals.end():\n",
    "            deref(it).do_stuff()\n",
    "            inc(it)\n",
    "            \n",
    "    cpdef list state(self):\n",
    "        return [a.state() for a in self.animals]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "10000 loops, best of 3: 53.7 µs per loop\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "41111"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "population = CyPopulation2()\n",
    "[population.create_animal() for _ in range(100000)]\n",
    "%timeit population.do_stuff()\n",
    "population.state()[15]"
   ]
  }
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