diff --git a/DANDI User Guide.ipynb b/DANDI User Guide, Part I.ipynb similarity index 99% rename from DANDI User Guide.ipynb rename to DANDI User Guide, Part I.ipynb index e6413f1..51de0a1 100644 --- a/DANDI User Guide.ipynb +++ b/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 @@ }, { "cell_type": "code", - "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,