Skip to content

Commit

Permalink
Changed NWB files to hopefully save space on github actions runner
Browse files Browse the repository at this point in the history
  • Loading branch information
@rcpeene
rcpeene committed Apr 20, 2023
1 parent d191dba commit 723332c
Show file tree
Hide file tree
Showing 10 changed files with 934 additions and 903 deletions.
35 changes: 21 additions & 14 deletions docs/basics/read_nwb.ipynb
View file
Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,7 @@
"outputs": [],
"source": [
"dandiset_id = \"000021\"\n",
"dandi_filepath = \"sub-703279277/sub-703279277_ses-719161530.nwb\"\n",
"dandi_filepath = \"sub-699733573/sub-699733573_ses-715093703.nwb\"\n",
"download_loc = \".\""
]
},
Expand All @@ -83,11 +83,18 @@
"id": "da61049a",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"A newer version (0.53.0) of dandi/dandi-cli is available. You are using 0.46.6\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Downloaded file to ./sub-703279277_ses-719161530.nwb\n"
"Downloaded file to ./sub-699733573_ses-715093703.nwb\n"
]
}
],
Expand Down Expand Up @@ -131,7 +138,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"root pynwb.file.NWBFile at 0x2455969512992\n",
"root pynwb.file.NWBFile at 0x1716049481344\n",
"Fields:\n",
" acquisition: {\n",
" raw_running_wheel_rotation <class 'pynwb.base.TimeSeries'>,\n",
Expand All @@ -155,8 +162,8 @@
" probeF <class 'abc.EcephysElectrodeGroup'>\n",
" }\n",
" electrodes: electrodes <class 'hdmf.common.table.DynamicTable'>\n",
" file_create_date: [datetime.datetime(2020, 5, 26, 0, 53, 26, 986517, tzinfo=tzoffset(None, -25200))]\n",
" identifier: 719161530\n",
" file_create_date: [datetime.datetime(2020, 5, 26, 0, 53, 26, 986608, tzinfo=tzoffset(None, -25200))]\n",
" identifier: 715093703\n",
" institution: Allen Institute for Brain Science\n",
" intervals: {\n",
" drifting_gratings_presentations <class 'pynwb.epoch.TimeIntervals'>,\n",
Expand All @@ -177,20 +184,20 @@
" stimulus <class 'pynwb.base.ProcessingModule'>\n",
" }\n",
" session_description: Data and metadata for an Ecephys session\n",
" session_id: 719161530\n",
" session_start_time: 2019-01-08 16:25:16-08:00\n",
" session_id: 715093703\n",
" session_start_time: 2019-01-19 00:54:18-08:00\n",
" stimulus_notes: brain_observatory_1.1\n",
" subject: subject abc.EcephysSpecimen at 0x2455969512848\n",
" subject: subject abc.EcephysSpecimen at 0x1716049229424\n",
"Fields:\n",
" age: P122D\n",
" age_in_days: 122.0\n",
" age: P118D\n",
" age_in_days: 118.0\n",
" genotype: Sst-IRES-Cre/wt;Ai32(RCL-ChR2(H134R)_EYFP)/wt\n",
" sex: M\n",
" species: Mus musculus\n",
" specimen_name: Sst-IRES-Cre;Ai32-387858\n",
" subject_id: 703279277\n",
" specimen_name: Sst-IRES-Cre;Ai32-386129\n",
" subject_id: 699733573\n",
"\n",
" timestamps_reference_time: 2019-01-08 16:25:16-08:00\n",
" timestamps_reference_time: 2019-01-19 00:54:18-08:00\n",
" units: units <class 'pynwb.misc.Units'>\n",
"\n"
]
Expand Down Expand Up @@ -240,7 +247,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
"C:\\Users\\carter.peene\\AppData\\Local\\Temp\\ipykernel_1712\\3249629881.py:4: FutureWarning: Passing a negative integer is deprecated in version 1.0 and will not be supported in future version. Instead, use None to not limit the column width.\n",
"C:\\Users\\carter.peene\\AppData\\Local\\Temp\\ipykernel_16628\\3249629881.py:4: FutureWarning: Passing a negative integer is deprecated in version 1.0 and will not be supported in future version. Instead, use None to not limit the column width.\n",
" pd.set_option('display.max_colwidth', -1)\n"
]
}
Expand Down
11 changes: 9 additions & 2 deletions docs/basics/stream_nwb.ipynb
View file
Original file line number Diff line number Diff line change
Expand Up @@ -80,6 +80,13 @@
"id": "a51caf90",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"A newer version (0.53.0) of dandi/dandi-cli is available. You are using 0.46.6\n"
]
},
{
"name": "stdout",
"output_type": "stream",
Expand Down Expand Up @@ -108,7 +115,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"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%2F20230419%2Fus-east-2%2Fs3%2Faws4_request&X-Amz-Date=20230419T212302Z&X-Amz-Expires=3600&X-Amz-SignedHeaders=host&X-Amz-Signature=8adf393c56367137b7a9b30b4dec0f51dc53bb1c644e0fc39e2bda5f8212772d\n"
"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%2F20230420%2Fus-east-2%2Fs3%2Faws4_request&X-Amz-Date=20230420T201648Z&X-Amz-Expires=3600&X-Amz-SignedHeaders=host&X-Amz-Signature=6088e2110f82ce358dec90e827468a37fd995c34e80089139ff1056659e1ccb8\n"
]
}
],
Expand Down Expand Up @@ -194,7 +201,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "68ddf60862604864ae406df6da33989b",
"model_id": "770645b2edf24149ad7158e0ea7c3096",
"version_major": 2,
"version_minor": 0
},
Expand Down
37 changes: 22 additions & 15 deletions docs/basics/use_nwbwidgets.ipynb
View file
Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@
"outputs": [],
"source": [
"dandiset_id = \"000021\"\n",
"dandi_filepath = \"sub-707296975/sub-707296975_ses-721123822.nwb\"\n",
"dandi_filepath = \"sub-699733573/sub-699733573_ses-715093703.nwb\"\n",
"download_loc = \".\""
]
},
Expand All @@ -82,11 +82,18 @@
"id": "1c5db129",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"A newer version (0.53.0) of dandi/dandi-cli is available. You are using 0.46.6\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Downloaded file to ./sub-707296975_ses-721123822.nwb\n"
"Downloaded file to ./sub-699733573_ses-715093703.nwb\n"
]
}
],
Expand Down Expand Up @@ -132,7 +139,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"root pynwb.file.NWBFile at 0x2656323972736\n",
"root pynwb.file.NWBFile at 0x2285253481232\n",
"Fields:\n",
" acquisition: {\n",
" raw_running_wheel_rotation <class 'pynwb.base.TimeSeries'>,\n",
Expand All @@ -156,8 +163,8 @@
" probeF <class 'abc.EcephysElectrodeGroup'>\n",
" }\n",
" electrodes: electrodes <class 'hdmf.common.table.DynamicTable'>\n",
" file_create_date: [datetime.datetime(2020, 5, 26, 0, 53, 26, 832332, tzinfo=tzoffset(None, -25200))]\n",
" identifier: 721123822\n",
" file_create_date: [datetime.datetime(2020, 5, 26, 0, 53, 26, 986608, tzinfo=tzoffset(None, -25200))]\n",
" identifier: 715093703\n",
" institution: Allen Institute for Brain Science\n",
" intervals: {\n",
" drifting_gratings_presentations <class 'pynwb.epoch.TimeIntervals'>,\n",
Expand All @@ -178,20 +185,20 @@
" stimulus <class 'pynwb.base.ProcessingModule'>\n",
" }\n",
" session_description: Data and metadata for an Ecephys session\n",
" session_id: 721123822\n",
" session_start_time: 2019-01-08 16:25:35-08:00\n",
" session_id: 715093703\n",
" session_start_time: 2019-01-19 00:54:18-08:00\n",
" stimulus_notes: brain_observatory_1.1\n",
" subject: subject abc.EcephysSpecimen at 0x2656348756528\n",
" subject: subject abc.EcephysSpecimen at 0x2285271628048\n",
"Fields:\n",
" age: P125D\n",
" age_in_days: 125.0\n",
" genotype: Pvalb-IRES-Cre/wt;Ai32(RCL-ChR2(H134R)_EYFP)/wt\n",
" age: P118D\n",
" age_in_days: 118.0\n",
" genotype: Sst-IRES-Cre/wt;Ai32(RCL-ChR2(H134R)_EYFP)/wt\n",
" sex: M\n",
" species: Mus musculus\n",
" specimen_name: Pvalb-IRES-Cre;Ai32-388521\n",
" subject_id: 707296975\n",
" specimen_name: Sst-IRES-Cre;Ai32-386129\n",
" subject_id: 699733573\n",
"\n",
" timestamps_reference_time: 2019-01-08 16:25:35-08:00\n",
" timestamps_reference_time: 2019-01-19 00:54:18-08:00\n",
" units: units <class 'pynwb.misc.Units'>\n",
"\n"
]
Expand All @@ -213,7 +220,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "cb26375efbbc48298b11bee1a7af2fbb",
"model_id": "ff394f60aa434277a364cc6bd96495c5",
"version_major": 2,
"version_minor": 0
},
Expand Down

0 comments on commit 723332c

Please sign in to comment.