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rcpeenercpeene
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Adjusted intro notebooks to run with example nwb
1 parent 529b7f7 commit 6a2b1d0

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4 files changed

+130
-28
lines changed

4 files changed

+130
-28
lines changed

‎docs/basics/download_nwb.ipynb‎

Lines changed: 36 additions & 13 deletions
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@@ -19,7 +19,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 1,
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"id": "8f34eecf",
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"metadata": {},
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"outputs": [],
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 2,
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"id": "67536d37",
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"metadata": {},
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"outputs": [],
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"source": [
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"dandiset_id = \"000021\"\n",
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"data_loc = \"~/data\"\n",
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"download_loc = \".\"\n",
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"authenticate = False\n",
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"dandi_api_key = \"your_api_key_here\""
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"dandi_api_key = \"\""
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 3,
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"id": "a309c067",
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"A newer version (0.46.6) of dandi/dandi-cli is available. You are using 0.46.3\n"
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]
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},
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Got dandiset DANDI:000021/draft\n"
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]
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}
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],
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"source": [
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"if authenticate:\n",
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" client = dandiapi.DandiAPIClient(token=dandi_api_key)\n",
@@ -76,7 +91,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 4,
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"id": "fe9aa40c",
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"metadata": {},
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"outputs": [],
@@ -86,17 +101,25 @@
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 5,
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"id": "a110beeb",
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Downloaded file to ./sub-699733573_ses-715093703.nwb\n"
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]
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}
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],
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"source": [
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"filename = filepath.split(\"/\")[-1]\n",
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"file = my_dandiset.get_asset_by_path(filepath)\n",
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"# this may take awhile, especially if the file to download is large\n",
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"file.download(f\"{data_loc}/{filename}\")\n",
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"file.download(f\"{download_loc}/{filename}\")\n",
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"\n",
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"print(f\"Downloaded file to {data_loc}/{filename}\")"
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"print(f\"Downloaded file to {download_loc}/{filename}\")"
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]
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},
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{
@@ -116,9 +139,9 @@
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"outputs": [],
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"source": [
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"# patience isn't just a virtue, it's a requirement\n",
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"my_dandiset.download_directory(\"./\", f\"{data_loc}/{dandiset_id}\")\n",
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"my_dandiset.download_directory(\"./\", f\"{download_loc}/{dandiset_id}\")\n",
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"\n",
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"print(f\"Downloaded directory to {data_loc}/{dandiset_id}\")"
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"print(f\"Downloaded directory to {download_loc}/{dandiset_id}\")"
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]
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}
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],

‎docs/basics/read_nwb.ipynb‎

Lines changed: 84 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -19,7 +19,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 1,
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"id": "d76f08a6",
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"metadata": {},
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"outputs": [],
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 2,
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"id": "400c411d",
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"metadata": {},
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"outputs": [],
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"source": [
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"nwb_filepath = \"~/data/sub-699733573_ses-715093703.nwb\""
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"nwb_filepath = \"./sub-699733573_ses-715093703.nwb\""
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 3,
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"id": "7628e758",
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"C:\\Users\\carter.peene\\AppData\\Local\\Programs\\Python\\Python39\\lib\\site-packages\\hdmf\\spec\\namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-common' version 1.1.3 because version 1.5.1 is already loaded.\n",
60+
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
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"C:\\Users\\carter.peene\\AppData\\Local\\Programs\\Python\\Python39\\lib\\site-packages\\hdmf\\spec\\namespace.py:531: UserWarning: Ignoring cached namespace 'core' version 2.2.2 because version 2.5.0 is already loaded.\n",
62+
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n"
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]
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},
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"root pynwb.file.NWBFile at 0x2647013427664\n",
70+
"Fields:\n",
71+
" acquisition: {\n",
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" raw_running_wheel_rotation <class 'pynwb.base.TimeSeries'>,\n",
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" running_wheel_signal_voltage <class 'pynwb.base.TimeSeries'>,\n",
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" running_wheel_supply_voltage <class 'pynwb.base.TimeSeries'>\n",
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" }\n",
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" devices: {\n",
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" probeA <class 'abc.EcephysProbe'>,\n",
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" probeB <class 'abc.EcephysProbe'>,\n",
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" probeC <class 'abc.EcephysProbe'>,\n",
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" probeD <class 'abc.EcephysProbe'>,\n",
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" probeE <class 'abc.EcephysProbe'>,\n",
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" probeF <class 'abc.EcephysProbe'>\n",
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" }\n",
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" electrode_groups: {\n",
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" probeA <class 'abc.EcephysElectrodeGroup'>,\n",
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" probeB <class 'abc.EcephysElectrodeGroup'>,\n",
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" probeC <class 'abc.EcephysElectrodeGroup'>,\n",
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" probeD <class 'abc.EcephysElectrodeGroup'>,\n",
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" probeE <class 'abc.EcephysElectrodeGroup'>,\n",
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" probeF <class 'abc.EcephysElectrodeGroup'>\n",
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" }\n",
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" electrodes: electrodes <class 'hdmf.common.table.DynamicTable'>\n",
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" file_create_date: [datetime.datetime(2020, 5, 26, 0, 53, 26, 986608, tzinfo=tzoffset(None, -25200))]\n",
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" identifier: 715093703\n",
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" institution: Allen Institute for Brain Science\n",
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" intervals: {\n",
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" drifting_gratings_presentations <class 'pynwb.epoch.TimeIntervals'>,\n",
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" flashes_presentations <class 'pynwb.epoch.TimeIntervals'>,\n",
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" gabors_presentations <class 'pynwb.epoch.TimeIntervals'>,\n",
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" invalid_times <class 'pynwb.epoch.TimeIntervals'>,\n",
101+
" natural_movie_one_presentations <class 'pynwb.epoch.TimeIntervals'>,\n",
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" natural_movie_three_presentations <class 'pynwb.epoch.TimeIntervals'>,\n",
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" natural_scenes_presentations <class 'pynwb.epoch.TimeIntervals'>,\n",
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" spontaneous_presentations <class 'pynwb.epoch.TimeIntervals'>,\n",
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" static_gratings_presentations <class 'pynwb.epoch.TimeIntervals'>\n",
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" }\n",
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" invalid_times: invalid_times <class 'pynwb.epoch.TimeIntervals'>\n",
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" processing: {\n",
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" eye_tracking_rig_metadata <class 'pynwb.base.ProcessingModule'>,\n",
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" optotagging <class 'pynwb.base.ProcessingModule'>,\n",
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" running <class 'pynwb.base.ProcessingModule'>,\n",
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" stimulus <class 'pynwb.base.ProcessingModule'>\n",
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" }\n",
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" session_description: Data and metadata for an Ecephys session\n",
115+
" session_id: 715093703\n",
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" session_start_time: 2019-01-19 00:54:18-08:00\n",
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" stimulus_notes: brain_observatory_1.1\n",
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" subject: subject abc.EcephysSpecimen at 0x2647012943904\n",
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"Fields:\n",
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" age: P118D\n",
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" age_in_days: 118.0\n",
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" genotype: Sst-IRES-Cre/wt;Ai32(RCL-ChR2(H134R)_EYFP)/wt\n",
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" sex: M\n",
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" species: Mus musculus\n",
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" specimen_name: Sst-IRES-Cre;Ai32-386129\n",
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" subject_id: 699733573\n",
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"\n",
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" timestamps_reference_time: 2019-01-19 00:54:18-08:00\n",
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" units: units <class 'pynwb.misc.Units'>\n",
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"\n"
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]
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}
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],
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"source": [
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"io = NWBHDF5IO(nwb_filepath, mode=\"r\", load_namespaces=True)\n",
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"nwb = io.read()\n",

‎docs/basics/stream_nwb.ipynb‎

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -19,7 +19,7 @@
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"cell_type": "code",
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"execution_count": 1,
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},
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{
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},
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},
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"cell_type": "code",
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{
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"text": [
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"Retrieved file url https://dandiarchive.s3.amazonaws.com/blobs/f5f/175/f5f1752f-5227-47d5-8f75-cd71937878aa?response-content-disposition=attachment%3B%20filename%3D%22sub-699733573_ses-715093703.nwb%22&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAUBRWC5GAEKH3223E%2F20221118%2Fus-east-2%2Fs3%2Faws4_request&X-Amz-Date=20221118T201449Z&X-Amz-Expires=3600&X-Amz-SignedHeaders=host&X-Amz-Signature=dd1f57c2d1b0a34cd5223cc0671d6a41dcea82917769a0befe6fc22de7247b3d\n"
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"Retrieved file url https://dandiarchive.s3.amazonaws.com/blobs/f5f/175/f5f1752f-5227-47d5-8f75-cd71937878aa?response-content-disposition=attachment%3B%20filename%3D%22sub-699733573_ses-715093703.nwb%22&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAUBRWC5GAEKH3223E%2F20221130%2Fus-east-2%2Fs3%2Faws4_request&X-Amz-Date=20221130T215329Z&X-Amz-Expires=3600&X-Amz-SignedHeaders=host&X-Amz-Signature=9edb7bb8f4263cd27cdcc37b27cc23cc7e79b8dbc3a0c9d6b4ae2a74da30c63a\n"
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]
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}
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],
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},
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{
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"cell_type": "code",
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"id": "d15db3bb",
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"metadata": {
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"scrolled": true
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},
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"cell_type": "code",
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},
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"execution_count": 7,
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"id": "3e06b964",
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"metadata": {},
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"outputs": [
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "ea3fdc0704e549fdb98aaf1b164c4203",
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"model_id": "682abdb6aeef48f4a3164f618072cbc1",
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"version_major": 2,
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"version_minor": 0
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},

‎docs/basics/use_nwbwidgets.ipynb‎

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"metadata": {},
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"outputs": [],
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"source": [
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"nwb_filepath = \"~/data/your_file.nwb\""
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"nwb_filepath = \"./sub-699733573_ses-715093703.nwb\""
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]
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},
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{

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