cleanup

src/constantinople_lab_to_nwb/fiber_photometry/tutorials/fiber_photometry_example_notebook.ipynb

@@ -42,64 +42,6 @@
     "nwbfile = io.read()"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "44c16af5-b5bd-455a-b678-2e46776ec5ce",
-   "metadata": {},
-   "source": [
-    "# Streaming an NWB file\n",
-    "\n",
-    "This section demonstrates how to access the files on the [DANDI Archive](https://dandiarchive.org) without downloading them. Based on the [Streaming NWB files](https://pynwb.readthedocs.io/en/stable/tutorials/advanced_io/streaming.html) tutorial from [PyNWB](https://pynwb.readthedocs.io/en/stable/#).\n",
-    "\n",
-    "The `dandi.dandiapi.DandiAPIClient` can be used to get the S3 URL of the NWB file stored in the DANDI Archive.\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "id": "66a8d2ca-6ed6-4816-83af-e7f687f1f82e",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# from dandi.dandiapi import DandiAPIClient\n",
-    "\n",
-    "# client = DandiAPIClient.for_dandi_instance(\"dandi\")\n",
-    "\n",
-    "# dandiset_id = \"001265\"\n",
-    "# file_path = \"sub-G026/sub-G026_ses-RWTautowait2-20210528-101504.nwb\"\n",
-    "\n",
-    "# with DandiAPIClient() as client:\n",
-    "#     asset = client.get_dandiset(dandiset_id, 'draft').get_asset_by_path(file_path)\n",
-    "#     s3_url = asset.get_content_url(follow_redirects=1, strip_query=True)\n"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "0cbbef68-7cdf-441c-b911-d887d1d58642",
-   "metadata": {},
-   "source": [
-    "We will use `remfile` for streaming the file. You can read more about `remfile` at [this tutorial section](https://pynwb.readthedocs.io/en/stable/tutorials/advanced_io/streaming.html#method-3-remfile)."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 4,
-   "id": "95ac6631-3cc4-4db0-9b2b-f9ec7d17290f",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# import h5py\n",
-    "# from pynwb import NWBHDF5IO\n",
-    "# import remfile\n",
-    "\n",
-    "# # We stream the file using remfile and open it with h5py and pynwb\n",
-    "# file = remfile.File(s3_url)\n",
-    "# h5_file = h5py.File(file, \"r\")\n",
-    "# io = NWBHDF5IO(file=h5_file, load_namespaces=True)\n",
-    "\n",
-    "# nwbfile = io.read()"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "7ee4f8ff-42b9-463e-b4ee-cf79a5e5276a",

src/constantinople_lab_to_nwb/schierek_embargo_2024/tutorials/ephys_example_notebook.ipynb

@@ -46,64 +46,6 @@
     "nwbfile = io.read()\n"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "4781be7e-7af0-492e-bfb0-a4af09ecf0c2",
-   "metadata": {},
-   "source": [
-    "# Streaming an NWB file\n",
-    "\n",
-    "This section demonstrates how to access the files on the [DANDI Archive](https://dandiarchive.org) without downloading them. Based on the [Streaming NWB files](https://pynwb.readthedocs.io/en/stable/tutorials/advanced_io/streaming.html) tutorial from [PyNWB](https://pynwb.readthedocs.io/en/stable/#).\n",
-    "\n",
-    "The `dandi.dandiapi.DandiAPIClient` can be used to get the S3 URL of the NWB file stored in the DANDI Archive.\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "id": "f402c0a8-285a-4270-9c46-c3ff2d24b13a",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# from dandi.dandiapi import DandiAPIClient\n",
-    "\n",
-    "# client = DandiAPIClient.for_dandi_instance(\"dandi\")\n",
-    "\n",
-    "# dandiset_id = \"001264\"\n",
-    "# file_path = \"sub-J076/sub-J076_ses-RWTautowait2-20231212-145250_ecephys.nwb\"\n",
-    "\n",
-    "# with DandiAPIClient() as client:\n",
-    "#     asset = client.get_dandiset(dandiset_id, 'draft').get_asset_by_path(file_path)\n",
-    "#     s3_url = asset.get_content_url(follow_redirects=1, strip_query=True)\n"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "5b5f586b-c337-4c13-8a69-a83c640d1ebf",
-   "metadata": {},
-   "source": [
-    "We will use `remfile` for streaming the file. You can read more about `remfile` at [this tutorial section](https://pynwb.readthedocs.io/en/stable/tutorials/advanced_io/streaming.html#method-3-remfile)."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 4,
-   "id": "25469dcf-3453-4391-be40-a1b9b199d31e",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# import h5py\n",
-    "# from pynwb import NWBHDF5IO\n",
-    "# import remfile\n",
-    "\n",
-    "# # We stream the file using remfile and open it with h5py and pynwb\n",
-    "# file = remfile.File(s3_url)\n",
-    "# h5_file = h5py.File(file, \"r\")\n",
-    "# io = NWBHDF5IO(file=h5_file, load_namespaces=True)\n",
-    "\n",
-    "# nwbfile = io.read()"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "25a5bb56-7dd1-4d4e-b56c-a65543811c89",
@@ -435,16 +377,18 @@
   },
   {
    "cell_type": "code",
+   "execution_count": 1,
    "id": "281be40d-1a73-4b97-ad78-cf6ddbb8e0e7",
    "metadata": {
     "ExecuteTime": {
      "end_time": "2024-12-04T12:41:53.499609Z",
      "start_time": "2024-12-04T12:41:53.497410Z"
     }
    },
-   "source": "nwbfile.processing[\"ecephys\"]",
    "outputs": [],
-   "execution_count": 1
+   "source": [
+    "nwbfile.processing[\"ecephys\"]"
+   ]
   },
   {
    "cell_type": "code",