{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Cython for NumPy users"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "To follow the tutorial, see https://cython.readthedocs.io/en/latest/src/userguide/numpy_tutorial.html"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING: Disabling color, you really want to install colorlog.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0.29a0\n"
     ]
    }
   ],
   "source": [
    "from __future__ import print_function\n",
    "%load_ext cython\n",
    "import Cython\n",
    "print(Cython.__version__)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "array_1 = np.random.uniform(0, 1000, size=(3000, 2000)).astype(np.intc)\n",
    "array_2 = np.random.uniform(0, 1000, size=(3000, 2000)).astype(np.intc)\n",
    "a = 4\n",
    "b = 3\n",
    "c = 9"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### The first Cython program"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "##### Numpy version"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "def compute_np(array_1, array_2, a, b, c):\n",
    "    return np.clip(array_1, 2, 10) * a + array_2 * b + c"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "103 ms ± 2.68 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)\n"
     ]
    }
   ],
   "source": [
    "timeit_result = %timeit -o compute_np(array_1, array_2, a, b, c)\n",
    "np_time = timeit_result.average"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "np_result = compute_np(array_1, array_2, a, b, c)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "##### Pure Python version"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "def clip(a, min_value, max_value):\n",
    "    return min(max(a, min_value), max_value)\n",
    "\n",
    "\n",
    "def compute(array_1, array_2, a, b, c):\n",
    "    \"\"\"\n",
    "    This function must implement the formula\n",
    "    np.clip(array_1, 2, 10) * a + array_2 * b + c\n",
    "\n",
    "    array_1 and array_2 are 2D.\n",
    "    \"\"\"\n",
    "    x_max = array_1.shape[0]\n",
    "    y_max = array_1.shape[1]\n",
    "    \n",
    "    assert array_1.shape == array_2.shape\n",
    "\n",
    "    result = np.zeros((x_max, y_max), dtype=array_1.dtype)\n",
    "\n",
    "    for x in range(x_max):\n",
    "        for y in range(y_max):\n",
    "\n",
    "            tmp = clip(array_1[x, y], 2, 10)\n",
    "            tmp = tmp * a + array_2[x, y] * b\n",
    "            result[x, y] = tmp + c\n",
    "\n",
    "    return result"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "assert np.all(compute(array_1, array_2, a, b, c) == np_result)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1min 10s ± 844 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
     ]
    }
   ],
   "source": [
    "timeit_result = %timeit -o compute(array_1, array_2, a, b, c)\n",
    "py_time = timeit_result.average"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### We make a function to be able to easily compare timings with the NumPy version and the pure Python version."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "def compare_time(current, reference, name):\n",
    "    ratio = reference/current\n",
    "    if ratio > 1:\n",
    "        word = \"faster\"\n",
    "    else:\n",
    "        ratio = 1 / ratio \n",
    "        word = \"slower\"\n",
    "        \n",
    "    print(\"We are\", \"{0:.1f}\".format(ratio), \"times\", word, \"than the\", name, \"version.\")\n",
    "\n",
    "def print_report(compute_function):\n",
    "    assert np.all(compute_function(array_1, array_2, a, b, c) == np_result)\n",
    "    timeit_result = %timeit -o compute_function(array_1, array_2, a, b, c)\n",
    "    run_time = timeit_result.average\n",
    "    compare_time(run_time, py_time, \"pure Python\")\n",
    "    compare_time(run_time, np_time, \"NumPy\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "##### Pure Python version compiled with Cython:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "%%cython -a\n",
    "import numpy as np\n",
    "\n",
    "\n",
    "def clip(a, min_value, max_value):\n",
    "    return min(max(a, min_value), max_value)\n",
    "\n",
    "\n",
    "def compute(array_1, array_2, a, b, c):\n",
    "    \"\"\"\n",
    "    This function must implement the formula\n",
    "    np.clip(array_1, 2, 10) * a + array_2 * b + c\n",
    "\n",
    "    array_1 and array_2 are 2D.\n",
    "    \"\"\"\n",
    "    x_max = array_1.shape[0]\n",
    "    y_max = array_1.shape[1]\n",
    "    \n",
    "    assert array_1.shape == array_2.shape\n",
    "\n",
    "    result = np.zeros((x_max, y_max), dtype=array_1.dtype)\n",
    "\n",
    "    for x in range(x_max):\n",
    "        for y in range(y_max):\n",
    "\n",
    "            tmp = clip(array_1[x, y], 2, 10)\n",
    "            tmp = tmp * a + array_2[x, y] * b\n",
    "            result[x, y] = tmp + c\n",
    "\n",
    "    return result"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "56.5 s ± 587 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n",
      "We are 1.2 times faster than the pure Python version.\n",
      "We are 546.0 times slower than the NumPy version.\n"
     ]
    }
   ],
   "source": [
    "print_report(compute)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Adding types:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "%%cython -a\n",
    "import numpy as np\n",
    "\n",
    "# We now need to fix a datatype for our arrays. I've used the variable\n",
    "# DTYPE for this, which is assigned to the usual NumPy runtime\n",
    "# type info object.\n",
    "DTYPE = np.intc\n",
    "\n",
    "# cdef means here that this function is a plain C function (so faster).\n",
    "# To get all the benefits, we type the arguments and the return value as int.\n",
    "cdef int clip(int a, int min_value, int max_value):\n",
    "    return min(max(a, min_value), max_value)\n",
    "\n",
    "\n",
    "def compute(array_1, array_2, int a, int b, int c):\n",
    "    \n",
    "    # The \"cdef\" keyword is also used within functions to type variables. It\n",
    "    # can only be used at the top indentation level (there are non-trivial\n",
    "    # problems with allowing them in other places, though we'd love to see\n",
    "    # good and thought out proposals for it).\n",
    "    cdef Py_ssize_t x_max = array_1.shape[0]\n",
    "    cdef Py_ssize_t y_max = array_1.shape[1]\n",
    "    \n",
    "    assert array_1.shape == array_2.shape\n",
    "    assert array_1.dtype == DTYPE\n",
    "    assert array_2.dtype == DTYPE\n",
    "\n",
    "    result = np.zeros((x_max, y_max), dtype=DTYPE)\n",
    "    \n",
    "    # It is very important to type ALL your variables. You do not get any\n",
    "    # warnings if not, only much slower code (they are implicitly typed as\n",
    "    # Python objects).\n",
    "    # For the \"tmp\" variable, we want to use the same data type as is\n",
    "    # stored in the array, so we use int because it correspond to np.intc.\n",
    "    # NB! An important side-effect of this is that if \"tmp\" overflows its\n",
    "    # datatype size, it will simply wrap around like in C, rather than raise\n",
    "    # an error like in Python.\n",
    "\n",
    "    cdef int tmp\n",
    "    cdef Py_ssize_t x, y\n",
    "\n",
    "    for x in range(x_max):\n",
    "        for y in range(y_max):\n",
    "\n",
    "            tmp = clip(array_1[x, y], 2, 10)\n",
    "            tmp = tmp * a + array_2[x, y] * b\n",
    "            result[x, y] = tmp + c\n",
    "\n",
    "    return result"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "26.5 s ± 422 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n",
      "We are 2.7 times faster than the pure Python version.\n",
      "We are 256.2 times slower than the NumPy version.\n"
     ]
    }
   ],
   "source": [
    "print_report(compute)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Efficient indexing with memoryviews:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "%%cython -a\n",
    "import numpy as np\n",
    "\n",
    "DTYPE = np.intc\n",
    "\n",
    "\n",
    "cdef int clip(int a, int min_value, int max_value):\n",
    "    return min(max(a, min_value), max_value)\n",
    "\n",
    "\n",
    "def compute(int[:, :] array_1, int[:, :] array_2, int a, int b, int c):\n",
    "     \n",
    "    cdef Py_ssize_t x_max = array_1.shape[0]\n",
    "    cdef Py_ssize_t y_max = array_1.shape[1]\n",
    "    \n",
    "    assert tuple(array_1.shape) == tuple(array_2.shape)\n",
    "\n",
    "    result = np.zeros((x_max, y_max), dtype=DTYPE)\n",
    "    cdef int[:, :] result_view = result\n",
    "\n",
    "    cdef int tmp\n",
    "    cdef Py_ssize_t x, y\n",
    "\n",
    "    for x in range(x_max):\n",
    "        for y in range(y_max):\n",
    "\n",
    "            tmp = clip(array_1[x, y], 2, 10)\n",
    "            tmp = tmp * a + array_2[x, y] * b\n",
    "            result_view[x, y] = tmp + c\n",
    "\n",
    "    return result"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "22.9 ms ± 197 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)\n",
      "We are 3081.0 times faster than the pure Python version.\n",
      "We are 4.5 times faster than the NumPy version.\n"
     ]
    }
   ],
   "source": [
    "print_report(compute)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Tuning indexing further:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "%%cython -a\n",
    "import numpy as np\n",
    "cimport cython\n",
    "\n",
    "DTYPE = np.intc\n",
    "\n",
    "\n",
    "cdef int clip(int a, int min_value, int max_value):\n",
    "    return min(max(a, min_value), max_value)\n",
    "\n",
    "@cython.boundscheck(False)\n",
    "@cython.wraparound(False)\n",
    "def compute(int[:, :] array_1, int[:, :] array_2, int a, int b, int c):\n",
    "     \n",
    "    cdef Py_ssize_t x_max = array_1.shape[0]\n",
    "    cdef Py_ssize_t y_max = array_1.shape[1]\n",
    "    \n",
    "    assert tuple(array_1.shape) == tuple(array_2.shape)\n",
    "\n",
    "    result = np.zeros((x_max, y_max), dtype=DTYPE)\n",
    "    cdef int[:, :] result_view = result\n",
    "\n",
    "    cdef int tmp\n",
    "    cdef Py_ssize_t x, y\n",
    "\n",
    "    for x in range(x_max):\n",
    "        for y in range(y_max):\n",
    "\n",
    "            tmp = clip(array_1[x, y], 2, 10)\n",
    "            tmp = tmp * a + array_2[x, y] * b\n",
    "            result_view[x, y] = tmp + c\n",
    "\n",
    "    return result"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "16.8 ms ± 25.4 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)\n",
      "We are 4200.7 times faster than the pure Python version.\n",
      "We are 6.2 times faster than the NumPy version.\n"
     ]
    }
   ],
   "source": [
    "print_report(compute)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Declaring the NumPy arrays as contiguous."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%cython\n",
    "import numpy as np\n",
    "cimport cython\n",
    "\n",
    "DTYPE = np.intc\n",
    "\n",
    "\n",
    "cdef int clip(int a, int min_value, int max_value):\n",
    "    return min(max(a, min_value), max_value)\n",
    "\n",
    "\n",
    "@cython.boundscheck(False)\n",
    "@cython.wraparound(False)\n",
    "def compute(int[:, ::1] array_1, int[:, ::1] array_2, int a, int b, int c):\n",
    "     \n",
    "    cdef Py_ssize_t x_max = array_1.shape[0]\n",
    "    cdef Py_ssize_t y_max = array_1.shape[1]\n",
    "    \n",
    "    assert tuple(array_1.shape) == tuple(array_2.shape)\n",
    "\n",
    "    result = np.zeros((x_max, y_max), dtype=DTYPE)\n",
    "    cdef int[:, ::1] result_view = result\n",
    "\n",
    "    cdef int tmp\n",
    "    cdef Py_ssize_t x, y\n",
    "\n",
    "    for x in range(x_max):\n",
    "        for y in range(y_max):\n",
    "\n",
    "            tmp = clip(array_1[x, y], 2, 10)\n",
    "            tmp = tmp * a + array_2[x, y] * b\n",
    "            result_view[x, y] = tmp + c\n",
    "\n",
    "    return result"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "11.1 ms ± 30.2 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)\n",
      "We are 6350.9 times faster than the pure Python version.\n",
      "We are 9.3 times faster than the NumPy version.\n"
     ]
    }
   ],
   "source": [
    "print_report(compute)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Making the function cleaner"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%cython -a\n",
    "# cython: infer_types=True\n",
    "import numpy as np\n",
    "cimport cython\n",
    "\n",
    "DTYPE = np.intc\n",
    "\n",
    "\n",
    "cdef int clip(int a, int min_value, int max_value):\n",
    "    return min(max(a, min_value), max_value)\n",
    "\n",
    "\n",
    "@cython.boundscheck(False)\n",
    "@cython.wraparound(False)\n",
    "def compute(int[:, ::1] array_1, int[:, ::1] array_2, int a, int b, int c):\n",
    "     \n",
    "    x_max = array_1.shape[0]\n",
    "    y_max = array_1.shape[1]\n",
    "    \n",
    "    assert tuple(array_1.shape) == tuple(array_2.shape)\n",
    "\n",
    "    result = np.zeros((x_max, y_max), dtype=DTYPE)\n",
    "    cdef int[:, ::1] result_view = result\n",
    "\n",
    "    cdef int tmp\n",
    "    cdef Py_ssize_t x, y\n",
    "\n",
    "    for x in range(x_max):\n",
    "        for y in range(y_max):\n",
    "\n",
    "            tmp = clip(array_1[x, y], 2, 10)\n",
    "            tmp = tmp * a + array_2[x, y] * b\n",
    "            result_view[x, y] = tmp + c\n",
    "\n",
    "    return result"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "11.5 ms ± 261 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)\n",
      "We are 6131.2 times faster than the pure Python version.\n",
      "We are 9.0 times faster than the NumPy version.\n"
     ]
    }
   ],
   "source": [
    "print_report(compute)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### More generic code:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "%%cython\n",
    "# cython: infer_types=True\n",
    "import numpy as np\n",
    "cimport cython\n",
    "\n",
    "ctypedef fused my_type:\n",
    "    int\n",
    "    double\n",
    "    long long\n",
    "\n",
    "\n",
    "cdef my_type clip(my_type a, my_type min_value, my_type max_value):\n",
    "    return min(max(a, min_value), max_value)\n",
    "\n",
    "\n",
    "@cython.boundscheck(False)\n",
    "@cython.wraparound(False)\n",
    "def compute(my_type[:, ::1] array_1, my_type[:, ::1] array_2, my_type a, my_type b, my_type c):\n",
    "     \n",
    "    x_max = array_1.shape[0]\n",
    "    y_max = array_1.shape[1]\n",
    "    \n",
    "    assert tuple(array_1.shape) == tuple(array_2.shape)\n",
    "    \n",
    "    if my_type is int:\n",
    "        dtype = np.intc\n",
    "    elif my_type is double:\n",
    "        dtype = np.double\n",
    "    elif my_type is cython.longlong:\n",
    "        dtype = np.double\n",
    "        \n",
    "    result = np.zeros((x_max, y_max), dtype=dtype)\n",
    "    cdef my_type[:, ::1] result_view = result\n",
    "\n",
    "    cdef my_type tmp\n",
    "    cdef Py_ssize_t x, y\n",
    "\n",
    "    for x in range(x_max):\n",
    "        for y in range(y_max):\n",
    "\n",
    "            tmp = clip(array_1[x, y], 2, 10)\n",
    "            tmp = tmp * a + array_2[x, y] * b\n",
    "            result_view[x, y] = tmp + c\n",
    "\n",
    "    return result"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 45,
   "metadata": {},
   "outputs": [],
   "source": [
    "arr_1_float = array_1.astype(np.float64)\n",
    "arr_2_float = array_2.astype(np.float64)\n",
    "\n",
    "float_cython_result = compute(arr_1_float, arr_2_float, a, b, c)\n",
    "float_numpy_result = compute_np(arr_1_float, arr_2_float, a, b, c)\n",
    "\n",
    "assert np.all(float_cython_result == float_numpy_result)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 46,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "11.5 ms ± 258 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)\n",
      "We are 6153.1 times faster than the pure Python version.\n",
      "We are 9.0 times faster than the NumPy version.\n"
     ]
    }
   ],
   "source": [
    "print_report(compute)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Using multiple threads"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 56,
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "%%cython --force\n",
    "# distutils: extra_compile_args=-fopenmp\n",
    "# distutils: extra_link_args=-fopenmp\n",
    "import numpy as np\n",
    "cimport cython\n",
    "from cython.parallel import prange\n",
    "\n",
    "ctypedef fused my_type:\n",
    "    int\n",
    "    double\n",
    "    long long\n",
    "\n",
    "\n",
    "# We declare our plain c function nogil\n",
    "cdef my_type clip(my_type a, my_type min_value, my_type max_value) nogil:\n",
    "    return min(max(a, min_value), max_value)\n",
    "\n",
    "\n",
    "@cython.boundscheck(False)\n",
    "@cython.wraparound(False)\n",
    "def compute(my_type[:, ::1] array_1, my_type[:, ::1] array_2, my_type a, my_type b, my_type c):\n",
    "     \n",
    "    cdef Py_ssize_t x_max = array_1.shape[0]\n",
    "    cdef Py_ssize_t y_max = array_1.shape[1]\n",
    "    \n",
    "    assert tuple(array_1.shape) == tuple(array_2.shape)\n",
    "    \n",
    "    if my_type is int:\n",
    "        dtype = np.intc\n",
    "    elif my_type is double:\n",
    "        dtype = np.double\n",
    "    elif my_type is cython.longlong:\n",
    "        dtype = np.longlong\n",
    "        \n",
    "    result = np.zeros((x_max, y_max), dtype=dtype)\n",
    "    cdef my_type[:, ::1] result_view = result\n",
    "\n",
    "    cdef my_type tmp\n",
    "    cdef Py_ssize_t x, y\n",
    "\n",
    "    # We use prange here.\n",
    "    for x in prange(x_max, nogil=True):\n",
    "        for y in range(y_max):\n",
    "\n",
    "            tmp = clip(array_1[x, y], 2, 10)\n",
    "            tmp = tmp * a + array_2[x, y] * b\n",
    "            result_view[x, y] = tmp + c\n",
    "\n",
    "    return result"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 57,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "9.33 ms ± 412 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)\n",
      "We are 7559.0 times faster than the pure Python version.\n",
      "We are 11.1 times faster than the NumPy version.\n"
     ]
    }
   ],
   "source": [
    "print_report(compute)"
   ]
  }
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