2021-10-01_hdf5-bug.ipynb

{
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  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "00104246-c8b9-435e-bc02-304120b2693d",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Dataset shape = %s (1, 1, 2048, 2048, 36556)\n"
     ]
    },
    {
     "ename": "OSError",
     "evalue": "Can't read data (can't open directory: /opt/conda/lib/hdf5/plugin)",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mOSError\u001b[0m                                   Traceback (most recent call last)",
      "\u001b[0;32m/tmp/ipykernel_375/2585987517.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      4\u001b[0m     \u001b[0mds\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfd\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m\"0\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      5\u001b[0m     \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"Dataset shape = %s\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mds\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mshape\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 6\u001b[0;31m     \u001b[0mimg\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mds\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m1024\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;36m1025\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;36m1109\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;36m1609\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;36m19406\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;36m19906\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32mh5py/_objects.pyx\u001b[0m in \u001b[0;36mh5py._objects.with_phil.wrapper\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32mh5py/_objects.pyx\u001b[0m in \u001b[0;36mh5py._objects.with_phil.wrapper\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32m/opt/conda/lib/python3.9/site-packages/h5py/_hl/dataset.py\u001b[0m in \u001b[0;36m__getitem__\u001b[0;34m(self, args, new_dtype)\u001b[0m\n\u001b[1;32m    788\u001b[0m         \u001b[0mmspace\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mh5s\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcreate_simple\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mselection\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmshape\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    789\u001b[0m         \u001b[0mfspace\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mselection\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mid\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 790\u001b[0;31m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mid\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mread\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmspace\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfspace\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0marr\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmtype\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdxpl\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_dxpl\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    791\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    792\u001b[0m         \u001b[0;31m# Patch up the output for NumPy\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32mh5py/_objects.pyx\u001b[0m in \u001b[0;36mh5py._objects.with_phil.wrapper\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32mh5py/_objects.pyx\u001b[0m in \u001b[0;36mh5py._objects.with_phil.wrapper\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32mh5py/h5d.pyx\u001b[0m in \u001b[0;36mh5py.h5d.DatasetID.read\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32mh5py/_proxy.pyx\u001b[0m in \u001b[0;36mh5py._proxy.dset_rw\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;31mOSError\u001b[0m: Can't read data (can't open directory: /opt/conda/lib/hdf5/plugin)"
     ]
    }
   ],
   "source": [
    "import h5py\n",
    "url=\"https://dandiarchive.s3.amazonaws.com/blobs/9ce/1d4/9ce1d405-323f-4f6d-a5a8-63fd59c3dfe0\"\n",
    "with h5py.File(url, \"r\", driver=\"ros3\") as fd:\n",
    "    ds = fd[\"0\"]\n",
    "    print(\"Dataset shape = %s\", ds.shape)\n",
    "    img = ds[0, 0, 1024:1025,1109:1609,19406:19906]\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "99d3411e-67e3-4e32-8c4f-c5e7b357f67d",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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