Create an NWB DynamicTable with a column of object references

test_column_of_containers.ipynb

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  {
   "cell_type": "markdown",
   "id": "48be29fd-2005-4218-9901-39fc158352f7",
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   "source": [
    "## Create an NWB file with a DynamicTable with a column that contains references to container objects elsewhere in the file."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
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     "text": [
      "                                          test_column\n",
      "id                                                   \n",
      "0   test_ts1 pynwb.base.TimeSeries at 0x4357943120...\n",
      "1   test_ts2 pynwb.base.TimeSeries at 0x5233163520...\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "root pynwb.file.NWBFile at 0x5232280720\n",
       "Fields:\n",
       "  acquisition: {\n",
       "    test_dt <class 'hdmf.common.table.DynamicTable'>,\n",
       "    test_ts1 <class 'pynwb.base.TimeSeries'>,\n",
       "    test_ts2 <class 'pynwb.base.TimeSeries'>\n",
       "  }\n",
       "  file_create_date: [datetime.datetime(2023, 5, 30, 13, 6, 11, 52009, tzinfo=tzlocal())]\n",
       "  identifier: identifier\n",
       "  session_description: session_description\n",
       "  session_start_time: 2023-05-30 20:06:11.051719+00:00\n",
       "  timestamps_reference_time: 2023-05-30 20:06:11.051719+00:00"
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from pynwb import NWBFile, NWBHDF5IO, TimeSeries\n",
    "from hdmf.common import DynamicTable\n",
    "import datetime\n",
    "\n",
    "# create a test NWB file\n",
    "nwbfile = NWBFile(\n",
    "    session_description=\"session_description\",\n",
    "    identifier=\"identifier\",\n",
    "    session_start_time=datetime.datetime.now(datetime.timezone.utc),\n",
    ")\n",
    "\n",
    "# create two TimeSeries and add them to the file\n",
    "ts1 = TimeSeries(\n",
    "    name=\"test_ts1\",\n",
    "    data=[1, 2, 3],\n",
    "    unit=\"unit\",\n",
    "    rate=1.0\n",
    ")\n",
    "ts2 = TimeSeries(\n",
    "    name=\"test_ts2\",\n",
    "    data=[1, 2, 3],\n",
    "    unit=\"unit\",\n",
    "    rate=1.0\n",
    ")\n",
    "nwbfile.add_acquisition(ts1)\n",
    "nwbfile.add_acquisition(ts2)\n",
    "\n",
    "# create an empty DynamicTable and add a column\n",
    "dt = DynamicTable(\n",
    "    name=\"test_dt\",\n",
    "    description=\"test\"\n",
    ")\n",
    "dt.add_column(\n",
    "    name=\"test_column\",\n",
    "    description=\"test\"\n",
    ")\n",
    "\n",
    "# add two rows to the DynamicTable and set the values to be the two TimeSeries we created earlier\n",
    "dt.add_row(test_column=ts1)\n",
    "dt.add_row(test_column=ts2)\n",
    "\n",
    "print(dt.to_dataframe())\n",
    "\n",
    "# add the DynamicTable to the file\n",
    "nwbfile.add_acquisition(dt)\n",
    "\n",
    "nwbfile"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "f85a41b5-0537-4740-b71c-64b5e3b45897",
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    {
     "name": "stdout",
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     "text": [
      "root pynwb.file.NWBFile at 0x5233397040\n",
      "Fields:\n",
      "  acquisition: {\n",
      "    test_dt <class 'hdmf.common.table.DynamicTable'>,\n",
      "    test_ts1 <class 'pynwb.base.TimeSeries'>,\n",
      "    test_ts2 <class 'pynwb.base.TimeSeries'>\n",
      "  }\n",
      "  file_create_date: [datetime.datetime(2023, 5, 30, 13, 6, 11, 52009, tzinfo=tzoffset(None, -25200))]\n",
      "  identifier: identifier\n",
      "  session_description: session_description\n",
      "  session_start_time: 2023-05-30 20:06:11.051719+00:00\n",
      "  timestamps_reference_time: 2023-05-30 20:06:11.051719+00:00\n",
      "\n",
      "test_ts1 pynwb.base.TimeSeries at 0x5439904384\n",
      "Fields:\n",
      "  comments: no comments\n",
      "  conversion: 1.0\n",
      "  data: <HDF5 dataset \"data\": shape (3,), type \"<i8\">\n",
      "  description: no description\n",
      "  offset: 0.0\n",
      "  rate: 1.0\n",
      "  resolution: -1.0\n",
      "  starting_time: 0.0\n",
      "  starting_time_unit: seconds\n",
      "  unit: unit\n",
      "\n",
      "test_ts2 pynwb.base.TimeSeries at 0x5439905392\n",
      "Fields:\n",
      "  comments: no comments\n",
      "  conversion: 1.0\n",
      "  data: <HDF5 dataset \"data\": shape (3,), type \"<i8\">\n",
      "  description: no description\n",
      "  offset: 0.0\n",
      "  rate: 1.0\n",
      "  resolution: -1.0\n",
      "  starting_time: 0.0\n",
      "  starting_time_unit: seconds\n",
      "  unit: unit\n",
      "\n",
      "                                          test_column\n",
      "id                                                   \n",
      "0   test_ts1 pynwb.base.TimeSeries at 0x5439904384...\n",
      "1   test_ts2 pynwb.base.TimeSeries at 0x5439905392...\n"
     ]
    }
   ],
   "source": [
    "filename = \"test_column_of_containers.nwb\"\n",
    "\n",
    "# write the file to disk\n",
    "with NWBHDF5IO(filename, \"w\") as io:\n",
    "    io.write(nwbfile)\n",
    "\n",
    "# read the file from disk and inspect its contents\n",
    "with NWBHDF5IO(filename, \"r\") as io:\n",
    "    nwbfile = io.read()\n",
    "    print(nwbfile)\n",
    "    print(nwbfile.acquisition[\"test_ts1\"])\n",
    "    print(nwbfile.acquisition[\"test_ts2\"])\n",
    "    print(nwbfile.acquisition[\"test_dt\"].to_dataframe())\n",
    "    \n",
    "    assert nwbfile.acquisition[\"test_ts1\"] is nwbfile.acquisition[\"test_dt\"][\"test_column\"][0]\n",
    "    assert nwbfile.acquisition[\"test_ts2\"] is nwbfile.acquisition[\"test_dt\"][\"test_column\"][1]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "a2353bf4-7ceb-4e31-b5b8-e38463a0f3a2",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<HDF5 object reference>\n"
     ]
    }
   ],
   "source": [
    "# confirm using h5py that the HDF5 dataset contains object references\n",
    "import h5py\n",
    "f = h5py.File(filename, \"r\")\n",
    "print(f[\"acquisition/test_dt/test_column\"][0])"
   ]
  }
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