benchmark-tiffslide-tcga.ipynb

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  {
   "cell_type": "markdown",
   "id": "30a2e806",
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   "source": [
    "# Benchmark openslide vs tiffslide\n",
    "\n",
    "With CMU images from OpenSlide test data, Tiffslide is generally faster than Openslide. With SVS slides from TCGA, however, Tiffslide is much slower."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "cdb427ed",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "tiffslide  2.1.2\n",
      "openslide  1.2.0\n",
      "tifffile   2023.7.4\n",
      "numpy      1.25.0\n",
      "PIL        9.5.0\n",
      "Python 3.10.12 | packaged by conda-forge | (main, Jun 23 2023, 22:40:32) [GCC 12.3.0]\n"
     ]
    }
   ],
   "source": [
    "import tiffslide\n",
    "import openslide\n",
    "import tifffile\n",
    "import numpy as np\n",
    "import PIL\n",
    "\n",
    "for m in [tiffslide, openslide, tifffile, np, PIL]:\n",
    "    print(f\"{m.__name__:<11}{m.__version__}\")\n",
    "    \n",
    "import sys\n",
    "print(\"Python\", sys.version)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "43bad576",
   "metadata": {},
   "outputs": [],
   "source": [
    "def benchmark(wsi_path):\n",
    "    t = tiffslide.TiffSlide(wsi_path)\n",
    "    o = openslide.OpenSlide(wsi_path)\n",
    "    \n",
    "    print(\"Openslide -- get thumbnail\")\n",
    "    %timeit o.get_thumbnail((256, 256))\n",
    "    print(\"Tiffslide -- get thumbnail\")\n",
    "    %timeit t.get_thumbnail((256, 256))\n",
    "    print()\n",
    "    \n",
    "    kwargs = dict(location=(20_000, 15_000), level=0, size=(256, 256))\n",
    "    print(\"Openslide -- read region at level 0\")\n",
    "    %timeit o.read_region(**kwargs)\n",
    "    print(\"Tiffslide -- read region at level 0\")\n",
    "    %timeit t.read_region(**kwargs)\n",
    "    print()\n",
    "    \n",
    "    kwargs = dict(location=(20_000, 15_000), level=2, size=(256, 256))\n",
    "    print(\"Openslide -- read region at level 2\")\n",
    "    %timeit o.read_region(**kwargs)\n",
    "    print(\"Tiffslide -- read region at level 2\")\n",
    "    %timeit t.read_region(**kwargs)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "c12da821",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Openslide -- get thumbnail\n",
      "711 ms ± 18.5 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n",
      "Tiffslide -- get thumbnail\n",
      "2.27 s ± 38.2 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n",
      "\n",
      "Openslide -- read region at level 0\n",
      "1.89 ms ± 17.8 µs per loop (mean ± std. dev. of 7 runs, 1,000 loops each)\n",
      "Tiffslide -- read region at level 0\n",
      "77.5 ms ± 2.1 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)\n",
      "\n",
      "Openslide -- read region at level 2\n",
      "6.93 ms ± 250 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)\n",
      "Tiffslide -- read region at level 2\n",
      "73.5 ms ± 1.21 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)\n"
     ]
    }
   ],
   "source": [
    "# From https://portal.gdc.cancer.gov/files/d46167af-6c29-49c7-95cf-3a801181aca4\n",
    "benchmark(\"/tmp/tiffslide/images/TCGA-SVS/TCGA-3C-AALI-01Z-00-DX1.F6E9A5DF-D8FB-45CF-B4BD-C6B76294C291.svs\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "e6d1017d",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Openslide -- get thumbnail\n",
      "215 ms ± 14.8 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n",
      "Tiffslide -- get thumbnail\n",
      "117 ms ± 1.25 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)\n",
      "\n",
      "Openslide -- read region at level 0\n",
      "1.86 ms ± 20.3 µs per loop (mean ± std. dev. of 7 runs, 1,000 loops each)\n",
      "Tiffslide -- read region at level 0\n",
      "2.46 ms ± 110 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)\n",
      "\n",
      "Openslide -- read region at level 2\n",
      "6.86 ms ± 149 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)\n",
      "Tiffslide -- read region at level 2\n",
      "2.67 ms ± 60 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)\n"
     ]
    }
   ],
   "source": [
    "# From https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/CMU-1.svs\n",
    "benchmark(\"/tmp/tiffslide/images/Aperio/CMU-1.svs\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "11b22c45",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Openslide -- get thumbnail\n",
      "5.03 ms ± 125 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)\n",
      "Tiffslide -- get thumbnail\n",
      "5.04 ms ± 158 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)\n",
      "\n",
      "Openslide -- read region at level 0\n",
      "1.84 ms ± 7.96 µs per loop (mean ± std. dev. of 7 runs, 1,000 loops each)\n",
      "Tiffslide -- read region at level 0\n",
      "1.65 ms ± 30.3 µs per loop (mean ± std. dev. of 7 runs, 1,000 loops each)\n",
      "\n",
      "Openslide -- read region at level 2\n",
      "7.09 ms ± 198 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)\n",
      "Tiffslide -- read region at level 2\n",
      "1.93 ms ± 22.2 µs per loop (mean ± std. dev. of 7 runs, 1,000 loops each)\n"
     ]
    }
   ],
   "source": [
    "# From https://openslide.cs.cmu.edu/download/openslide-testdata/Generic-TIFF/CMU-1.tiff\n",
    "benchmark(\"/tmp/tiffslide/images/Generic-TIFF/CMU-1.tiff\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "8a930846",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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