update user guide

dandi · Oct 29, 2021 · c5e8cf0 · c5e8cf0
1 parent 0c67b47
commit c5e8cf0
Showing 1 changed file with 22 additions and 69 deletions.
diff --git a/DANDI User Guide.ipynb → DANDI User Guide, Part I.ipynb b/DANDI User Guide.ipynb → DANDI User Guide, Part I.ipynb
@@ -10,7 +10,9 @@
    "id": "404a40ef-a93d-4482-8249-f66967bc741c",
    "metadata": {},
    "source": [
-    "# Part 1, Converting data to NWB\n",
+    "# Part I\n",
+    "\n",
+    "## Converting data to NWB\n",
     "\n",
     "This is part 3 of the DANDI User Training on Nov 1, 2021.\n",
     "\n",
@@ -26,7 +28,7 @@
   },
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-   "execution_count": 22,
+   "execution_count": null,
    "id": "aa5bd1ad-cdb4-413e-8a8f-c8340fb8f739",
    "metadata": {},
    "outputs": [],
@@ -118,25 +120,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 20,
+   "execution_count": null,
    "id": "b9ebc17f-4b15-4c2c-b028-3b284785f22e",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "/home/jovyan/dandi-notebooks\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "!pwd"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": null,
    "id": "2fb3ab28-5e0a-4484-b0fa-9d4fc113e658",
    "metadata": {},
    "outputs": [],
@@ -176,7 +170,7 @@
    "id": "5594e0c8-fd05-4f9e-830d-a0380c6ade46",
    "metadata": {},
    "source": [
-    "# Part 2, Uploading to DANDI\n",
+    "# Uploading to DANDI\n",
     "\n",
     "When you register a dandiset, it creates a permenant ID. For instructional purposes, we will be using a staging version of DANDI, so that we do not create real IDs for pretend datasets.\n",
     "\n",
@@ -242,7 +236,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 26,
+   "execution_count": null,
    "id": "53cbeb15-679d-432b-8b9d-daf943829590",
    "metadata": {},
    "outputs": [],
@@ -271,32 +265,17 @@
    "id": "7d980104-839e-44ae-8031-ae3d20517eb7",
    "metadata": {},
    "source": [
-    "## Part 3, Visualization NWB files\n",
+    "## Visualization NWB files\n",
     "\n",
     "NWB Widgets is a library of interactive data visualizations that works automatically with any NWB file. This can be very useful for visually confirming any conversion."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "id": "b141a5a5-1e84-4796-b53e-ded9360ece51",
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "202325d29684459f9af43420939b054d",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "VBox(children=(HBox(children=(Label(value='session_description:', layout=Layout(max_height='40px', max_width='…"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "from nwbwidgets import nwb2widget\n",
     "\n",
@@ -313,7 +292,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": null,
    "id": "bbc614dc-577a-47fd-bbe6-51a45c263f21",
    "metadata": {},
    "outputs": [],
@@ -324,33 +303,23 @@
     "# neuropixel, Giocomo Lab (46 GB)\n",
     "#dandiset_id, filepath = \"000053\", \"sub-npI1/sub-npI1_ses-20190415_behavior+ecephys.nwb\"\n",
     "\n",
+    "# neuropixel, Allen Intitute\n",
+    "#dandiset_id, filepath = \"000022\", \"sub-744912845/sub-744912845_ses-766640955.nwb\"\n",
+    "\n",
     "# ecephys, Buzsaki Lab (15.2 GB)\n",
-    "dandiset_id, filepath = \"000003\", \"sub-YutaMouse41/sub-YutaMouse41_ses-YutaMouse41-150831_behavior+ecephys.nwb\""
+    "#dandiset_id, filepath = \"000003\", \"sub-YutaMouse41/sub-YutaMouse41_ses-YutaMouse41-150831_behavior+ecephys.nwb\""
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 27,
+   "execution_count": null,
    "id": "1fa74623-67c1-46af-8b06-6a6f33e721f1",
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "edce05c4de4d4cd7a3a9162b27fe2eda",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "VBox(children=(HBox(children=(Label(value='session_description:', layout=Layout(max_height='40px', max_width='…"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "from dandi.dandiapi import DandiAPIClient\n",
+    "from pynwb import NWBHDF5IO\n",
+    "from nwbwidgets import nwb2widget\n",
     "\n",
     "with DandiAPIClient() as client:\n",
     "    asset = client.get_dandiset(dandiset_id, \"draft\").get_asset_by_path(filepath)\n",
@@ -360,22 +329,6 @@
     "nwb = io.read()\n",
     "nwb2widget(nwb)"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "2c564363-710d-449b-9b4d-98e93504118f",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "c2b6b9ec-2f72-446d-bd50-3bc19e70befc",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -394,7 +347,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.6"
+   "version": "3.9.7"
   }
  },
  "nbformat": 4,