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Remove raster from mua figurl, update notebooks
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@edeno
edeno committed Feb 7, 2024
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141 changes: 60 additions & 81 deletions notebooks/51_MUA_Detection.ipynb
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Expand Up @@ -9,8 +9,8 @@
"name": "stderr",
"output_type": "stream",
"text": [
"[2024-02-06 13:11:28,336][INFO]: Connecting edeno@lmf-db.cin.ucsf.edu:3306\n",
"[2024-02-06 13:11:28,362][INFO]: Connected edeno@lmf-db.cin.ucsf.edu:3306\n"
"[2024-02-07 14:44:16,324][INFO]: Connecting edeno@lmf-db.cin.ucsf.edu:3306\n",
"[2024-02-07 14:44:16,357][INFO]: Connected edeno@lmf-db.cin.ucsf.edu:3306\n"
]
}
],
Expand Down Expand Up @@ -202,17 +202,24 @@
" <p id=\"nonprimary\">mua_times_object_id</p>\n",
" <span class=\"djtooltiptext\"></span>\n",
" </div> </th> </tr> </thead>\n",
" <tbody> <tr> </tr> </tbody>\n",
" <tbody> <tr> <td>default</td>\n",
"<td>mediumnwb20230802_.nwb</td>\n",
"<td>default_exclusion</td>\n",
"<td>test_group</td>\n",
"<td>4eb59a18-045a-5768-d12e-b6473415ae1c</td>\n",
"<td>pos 0 valid times</td>\n",
"<td>mediumnwb20230802_235KSEV39O.nwb</td>\n",
"<td>a93532eb-2947-4552-8877-19ea0d2dcc4f</td> </tr> </tbody>\n",
" </table>\n",
" \n",
" <p>Total: 0</p></div>\n",
" <p>Total: 1</p></div>\n",
" "
],
"text/plain": [
"*mua_param_nam *nwb_file_name *unit_filter_p *sorted_spikes *pos_merge_id *detection_int analysis_file_ mua_times_obje\n",
"+------------+ +------------+ +------------+ +------------+ +------------+ +------------+ +------------+ +------------+\n",
"\n",
" (Total: 0)"
"default mediumnwb20230 default_exclus test_group 4eb59a18-045a- pos 0 valid ti mediumnwb20230 a93532eb-2947-\n",
" (Total: 1)"
]
},
"execution_count": 3,
Expand Down Expand Up @@ -365,66 +372,6 @@
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"[13:11:30][WARNING] Spyglass: Upsampled position data, frame indices are invalid. Setting add_frame_ind=False\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-common' version 1.6.0 because version 1.5.1 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'core' version 2.6.0-alpha because version 2.5.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-experimental' version 0.3.0 because version 0.2.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-common' version 1.6.0 because version 1.5.1 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'core' version 2.6.0-alpha because version 2.5.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-experimental' version 0.3.0 because version 0.2.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-common' version 1.6.0 because version 1.5.1 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'core' version 2.6.0-alpha because version 2.5.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-experimental' version 0.3.0 because version 0.2.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-common' version 1.6.0 because version 1.5.1 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'core' version 2.6.0-alpha because version 2.5.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-experimental' version 0.3.0 because version 0.2.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-common' version 1.6.0 because version 1.5.1 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'core' version 2.6.0-alpha because version 2.5.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-experimental' version 0.3.0 because version 0.2.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-common' version 1.6.0 because version 1.5.1 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'core' version 2.6.0-alpha because version 2.5.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-experimental' version 0.3.0 because version 0.2.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-common' version 1.6.0 because version 1.5.1 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'core' version 2.6.0-alpha because version 2.5.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-experimental' version 0.3.0 because version 0.2.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-common' version 1.6.0 because version 1.5.1 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'core' version 2.6.0-alpha because version 2.5.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-experimental' version 0.3.0 because version 0.2.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/pynwb/ecephys.py:90: UserWarning: ElectricalSeries 'e-series': The second dimension of data does not match the length of electrodes. Your data may be transposed.\n",
" warnings.warn(\"%s '%s': The second dimension of data does not match the length of electrodes. \"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/pynwb/base.py:193: UserWarning: TimeSeries 'analog': Length of data does not match length of timestamps. Your data may be transposed. Time should be on the 0th dimension\n",
" warn(\"%s '%s': Length of data does not match length of timestamps. Your data may be transposed. \"\n",
"[13:11:34][INFO] Spyglass: Writing new NWB file mediumnwb20230802_235KSEV39O.nwb\n"
]
},
{
"data": {
"text/html": [
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"name": "stderr",
"output_type": "stream",
"text": [
"[13:11:36][WARNING] Spyglass: Upsampled position data, frame indices are invalid. Setting add_frame_ind=False\n",
"[13:11:40][WARNING] Spyglass: Upsampled position data, frame indices are invalid. Setting add_frame_ind=False\n"
"[14:44:19][WARNING] Spyglass: Upsampled position data, frame indices are invalid. Setting add_frame_ind=False\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-common' version 1.6.0 because version 1.5.1 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'core' version 2.6.0-alpha because version 2.5.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-experimental' version 0.3.0 because version 0.2.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-common' version 1.6.0 because version 1.5.1 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'core' version 2.6.0-alpha because version 2.5.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-experimental' version 0.3.0 because version 0.2.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-common' version 1.6.0 because version 1.5.1 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'core' version 2.6.0-alpha because version 2.5.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-experimental' version 0.3.0 because version 0.2.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-common' version 1.6.0 because version 1.5.1 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'core' version 2.6.0-alpha because version 2.5.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-experimental' version 0.3.0 because version 0.2.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-common' version 1.6.0 because version 1.5.1 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'core' version 2.6.0-alpha because version 2.5.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-experimental' version 0.3.0 because version 0.2.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-common' version 1.6.0 because version 1.5.1 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'core' version 2.6.0-alpha because version 2.5.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-experimental' version 0.3.0 because version 0.2.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-common' version 1.6.0 because version 1.5.1 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'core' version 2.6.0-alpha because version 2.5.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"/home/edeno/miniconda3/envs/spyglass/lib/python3.9/site-packages/hdmf/spec/namespace.py:531: UserWarning: Ignoring cached namespace 'hdmf-experimental' version 0.3.0 because version 0.2.0 is already loaded.\n",
" warn(\"Ignoring cached namespace '%s' version %s because version %s is already loaded.\"\n",
"[14:44:24][WARNING] Spyglass: Upsampled position data, frame indices are invalid. Setting add_frame_ind=False\n"
]
},
{
Expand Down Expand Up @@ -906,8 +895,8 @@
"name": "stderr",
"output_type": "stream",
"text": [
"[13:11:40][WARNING] Spyglass: Upsampled position data, frame indices are invalid. Setting add_frame_ind=False\n",
"[13:11:43][WARNING] Spyglass: Upsampled position data, frame indices are invalid. Setting add_frame_ind=False\n"
"[14:44:25][WARNING] Spyglass: Upsampled position data, frame indices are invalid. Setting add_frame_ind=False\n",
"[14:44:29][WARNING] Spyglass: Upsampled position data, frame indices are invalid. Setting add_frame_ind=False\n"
]
},
{
Expand All @@ -920,7 +909,7 @@
{
"data": {
"text/plain": [
"'https://figurl.org/f?v=gs://figurl/spikesortingview-10&d=sha1://ad1b2f082a47f72cf1ecca346f3a9e953319b07c&label=Multiunit%20Detection&zone=franklab.default'"
"'https://figurl.org/f?v=gs://figurl/spikesortingview-10&d=sha1://08d7c35434e8469686fca8aff3ec9319bccb44f9&label=Multiunit%20Detection&zone=franklab.default'"
]
},
"execution_count": 9,
Expand All @@ -931,19 +920,9 @@
"source": [
"(MuaEventsV1 & mua_key).create_figurl(\n",
" zscore_mua=True,\n",
" plot_speed=True,\n",
")"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [],
"source": [
"# need to figure out how to exclude time in position time"
]
},
{
"cell_type": "code",
"execution_count": null,
Expand Down
5 changes: 0 additions & 5 deletions notebooks/py_scripts/51_MUA_Detection.py
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Expand Up @@ -107,9 +107,4 @@

(MuaEventsV1 & mua_key).create_figurl(
zscore_mua=True,
plot_speed=True,
)

# +
# need to figure out how to exclude time in position time
# -
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