GEOS STRTree versus libspatialindex RTree

rtree_profiling.ipynb

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   "cell_type": "code",
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   "source": [
    "import itertools\n",
    "\n",
    "import rtree\n",
    "import shapely\n",
    "from shapely.strtree import STRtree\n",
    "from shapely.geometry import Polygon, Point"
   ]
  },
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   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "```\n",
    "libspatialindex           1.9.0                he1b5a44_1    conda-forge\n",
    "geos                      3.7.1             hf484d3e_1000    conda-forge\n",
    "```"
   ]
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   "metadata": {},
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     "data": {
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     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
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   ],
   "source": [
    "rtree.__version__"
   ]
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   "metadata": {},
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     "data": {
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     "metadata": {},
     "output_type": "execute_result"
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   "source": [
    "shapely.__version__"
   ]
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  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "geoms = [\n",
    "    Polygon([(x, y), (x + 1, y), (x+1, y+1), (x, y+1)])\n",
    "    for x, y in itertools.product(range(200), range(200))\n",
    "]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "strtree = STRtree(geoms)\n",
    "rtree_idx = rtree.index.Index(((geom_idx, geom.bounds, None) for geom_idx, geom in enumerate(geoms)))"
   ]
  },
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   "cell_type": "code",
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     "text": [
      "129 ms ± 1.98 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)\n"
     ]
    }
   ],
   "source": [
    "%timeit STRtree(geoms)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2.03 s ± 84.4 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
     ]
    }
   ],
   "source": [
    "%timeit rtree.index.Index(((geom_idx, geom.bounds, None) for geom_idx, geom in enumerate(geoms)))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "search_pt = Point(139.2938371195723, 17.29550838723575)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "48.2 µs ± 427 ns per loop (mean ± std. dev. of 7 runs, 10000 loops each)\n"
     ]
    }
   ],
   "source": [
    "%timeit list(rtree_idx.intersection(search_pt.bounds))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.48 ms ± 57.4 µs per loop (mean ± std. dev. of 7 runs, 1000 loops each)\n"
     ]
    }
   ],
   "source": [
    "%timeit strtree.query(search_pt)"
   ]
  }
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