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jorisvandenbossche/pygeos-cython.ipynb

Created August 18, 2019 12:37
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pygeos-cython.ipynb
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Test cython algo using the pygeos geometry extension type"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"import pygeos"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"a = np.array([pygeos.points(i, i) for i in range(10000)], dtype=object)"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"array([<pygeos.Geometry POINT (0 0)>, <pygeos.Geometry POINT (1 1)>,\n",
" <pygeos.Geometry POINT (2 2)>, ...,\n",
" <pygeos.Geometry POINT (1e+04 1e+04)>,\n",
" <pygeos.Geometry POINT (1e+04 1e+04)>,\n",
" <pygeos.Geometry POINT (1e+04 1e+04)>], dtype=object)"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"a"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"<pygeos.Geometry POLYGON ((10 10, 10 100, 100 100, 100 10, 10 10))>"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"poly = pygeos.polygons([(10,10), (10,100), (100,100), (100, 10)])\n",
"poly"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Checking for a single polygon if it contains a bunch of points:"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"array([False, False, False, ..., False, False, False])"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"res1 = pygeos.contains(poly, a)\n",
"res1"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"177 µs ± 9.57 µs per loop (mean ± std. dev. of 7 runs, 10000 loops each)\n"
]
}
],
"source": [
"%timeit pygeos.contains(poly, a)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"---\n",
"\n",
"Let's now try to do the same using `cython` as illustrative exercise of interacting with the extension type from cython:"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
"%load_ext cython"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"First using plain loop and python API access to the pointers:"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
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"%%cython -l geos_c -L /home/joris/miniconda3/envs/geo-dev/lib -I /home/joris/miniconda3/envs/geo-dev/include -a\n",
"\n",
"import cython\n",
"\n",
"import numpy as np\n",
"cimport numpy as np\n",
"\n",
"cdef extern from \"geos_c.h\":\n",
" ctypedef void *GEOSContextHandle_t\n",
" ctypedef struct GEOSGeometry\n",
" char GEOSContains_r(GEOSContextHandle_t, const GEOSGeometry*, const GEOSGeometry*) nogil\n",
"\n",
"\n",
"cdef GEOSContextHandle_t get_geos_context_handle():\n",
" # Note: This requires that lgeos is defined, so needs to be imported as:\n",
" from shapely.geos import lgeos\n",
" cdef np.uintp_t handle = lgeos.geos_handle\n",
" return <GEOSContextHandle_t>handle\n",
"\n",
"\n",
"@cython.boundscheck(False)\n",
"@cython.wraparound(False)\n",
"def contains_cy(array, geometry):\n",
" \n",
" cdef Py_ssize_t idx\n",
" cdef unsigned int n = array.size\n",
" cdef np.ndarray[np.uint8_t, ndim=1, cast=True] result = np.empty(n, dtype=np.uint8)\n",
"\n",
" cdef GEOSContextHandle_t geos_handle\n",
" cdef GEOSGeometry *geom1\n",
" cdef GEOSGeometry *geom2\n",
" cdef np.intp_t geos_geom\n",
" cdef np.intp_t geos_geom1\n",
"\n",
" geos_handle = get_geos_context_handle()\n",
" geos_geom1 = geometry._ptr \n",
" geom1 = <GEOSGeometry *> geos_geom1\n",
" \n",
" for idx in xrange(n):\n",
" g = array[idx]\n",
" geos_geom = g._ptr\n",
" geom2 = <GEOSGeometry *>geos_geom\n",
"\n",
" # Put the result of whether the point is \"contained\" into the result array. \n",
" result[idx] = <np.uint8_t> GEOSContains_r(geos_handle, geom1, geom2)\n",
"\n",
" return result.view(dtype=np.bool)"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"array([False, False, False, ..., False, False, False])"
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"res2 = contains_cy(a, poly)\n",
"res2"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [],
"source": [
"np.testing.assert_allclose(res1, res2)"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"459 µs ± 27.1 µs per loop (mean ± std. dev. of 7 runs, 1000 loops each)\n"
]
}
],
"source": [
"%timeit contains_cy(a, poly)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"This is already a lot faster than if we would do that in pure python with shapely, but it is still quite a bit slower than pygeos' ufunc due to the python interaction for getting the element out of the array and getting the `_ptr` pointer to the GEOS object.\n",
"\n",
"But since the pygeos.Geometry object is a python extension type, we can access its struct from cython without python overhead.\n",
"\n",
"I created a `src/pygeos.h` with the following content (the current definition is in `src/ufuncs.c`):\n",
"\n",
"```c\n",
"#include <Python.h>\n",
"\n",
"typedef struct {\n",
" PyObject_HEAD\n",
" void *ptr;\n",
"} GeometryObject;\n",
"```\n",
"\n",
"so we can let cython know about this:"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
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"static PyObject *__pyx_pw_46_cython_magic_a9838a4c03c47d83fcfca3e26fdbda41_1contains_cy2(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {\n",
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},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"%%cython -l geos_c -L /home/joris/miniconda3/envs/geo-dev/lib -I /home/joris/miniconda3/envs/geo-dev/include -I /home/joris/scipy/repos/pygeos/src/ -a\n",
"\n",
"import cython\n",
"\n",
"import numpy as np\n",
"cimport numpy as np\n",
"\n",
"cdef extern from \"geos_c.h\":\n",
" ctypedef void *GEOSContextHandle_t\n",
" ctypedef struct GEOSGeometry\n",
" char GEOSContains_r(GEOSContextHandle_t, const GEOSGeometry*, const GEOSGeometry*) nogil\n",
"\n",
"\n",
"cdef GEOSContextHandle_t get_geos_context_handle():\n",
" # Note: This requires that lgeos is defined, so needs to be imported as:\n",
" from shapely.geos import lgeos\n",
" cdef np.uintp_t handle = lgeos.geos_handle\n",
" return <GEOSContextHandle_t>handle\n",
"\n",
"\n",
"#cdef extern class pygeos.ufuncs.Geometry:\n",
"# pass\n",
"\n",
"cdef extern from \"pygeos.h\":\n",
" \n",
" ctypedef struct GeometryObject:\n",
" np.intp_t ptr\n",
"\n",
" ctypedef class pygeos.ufuncs.Geometry [object GeometryObject]:\n",
" cdef np.intp_t _ptr \"ptr\"\n",
"\n",
"\n",
"@cython.boundscheck(False)\n",
"@cython.wraparound(False)\n",
"def contains_cy2(np.ndarray[object, ndim=1, cast=True] array, geometry):\n",
" \n",
" cdef Py_ssize_t idx\n",
" cdef unsigned int n = array.size\n",
" cdef np.ndarray[np.uint8_t, ndim=1, cast=True] result = np.empty(n, dtype=np.uint8)\n",
"\n",
" cdef GEOSContextHandle_t geos_handle\n",
" cdef GeometryObject *pygeom1\n",
" cdef GeometryObject *pygeom2\n",
" cdef GEOSGeometry *geom1\n",
" cdef GEOSGeometry *geom2\n",
" cdef np.intp_t geos_geom\n",
" cdef np.intp_t geos_geom1\n",
" #cdef np.ndarray[GeometryObject, ndim=1, cast=True] object_array = array\n",
" \n",
" geos_handle = get_geos_context_handle()\n",
"\n",
" pygeom1 = <GeometryObject *> geometry\n",
" geos_geom1 = <np.uintp_t> pygeom1.ptr\n",
" geom1 = <GEOSGeometry *> geos_geom1\n",
"\n",
" for idx in xrange(n):\n",
" pygeom2 = <GeometryObject *> array[idx]\n",
" geos_geom = pygeom2.ptr\n",
" geom2 = <GEOSGeometry *>geos_geom\n",
"\n",
" # Put the result of whether the point is \"contained\" into the result array. \n",
" result[idx] = <np.uint8_t> GEOSContains_r(geos_handle, geom1, geom2)\n",
"\n",
" return result.view(dtype=np.bool)"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"array([False, False, False, ..., False, False, False])"
]
},
"execution_count": 13,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"res3 = contains_cy2(a, poly)\n",
"res3"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [],
"source": [
"np.testing.assert_allclose(res1, res3)"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"138 µs ± 16.8 µs per loop (mean ± std. dev. of 7 runs, 10000 loops each)\n"
]
}
],
"source": [
"%timeit contains_cy2(a, poly)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"So this is a further performance improvement, now in the same order as pygeos (even faster here, but the timing is quite variable, it's more or less the same). We can see that\n",
"\n",
"- accessing the pointer from the pygeos.Geometry object now happens without python overhead (no yellow in the annotations)\n",
"- but, getting an element out of the object array still does .. (the `pygeom2 = <GeometryObject *> array[idx]` line in the loop)\n",
"\n",
"This doesn't seem to bother performance-wise that much, but, the consequence is that we can't put the loop in a `nogil` context to release the GIL (which is critical to use this algo in a parallel setting).\n"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python (geo-dev)",
"language": "python",
"name": "geo-dev"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.3"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
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