MUA Detection

In [1]:

import datajoint as dj
from pathlib import Path

dj.config.load(
    Path("../dj_local_conf.json").absolute()
)  # load config for database connection info

from spyglass.mua.v1.mua import MuaEventsV1, MuaEventsParameters

import datajoint as dj from pathlib import Path dj.config.load( Path("../dj_local_conf.json").absolute() ) # load config for database connection info from spyglass.mua.v1.mua import MuaEventsV1, MuaEventsParameters

[2024-02-07 14:44:16,324][INFO]: Connecting edeno@lmf-db.cin.ucsf.edu:3306
[2024-02-07 14:44:16,357][INFO]: Connected edeno@lmf-db.cin.ucsf.edu:3306

In [2]:

MuaEventsParameters()

MuaEventsParameters()

Out[2]:

mua_param_name a name for this set of parameters	mua_param_dict dictionary of parameters
default	=BLOB=

Total: 1

In [3]:

MuaEventsV1()

MuaEventsV1()

Out[3]:

mua_param_name a name for this set of parameters	nwb_file_name name of the NWB file	unit_filter_params_name	sorted_spikes_group_name	pos_merge_id	detection_interval descriptive name of this interval list	analysis_file_name name of the file	mua_times_object_id
default	mediumnwb20230802_.nwb	default_exclusion	test_group	4eb59a18-045a-5768-d12e-b6473415ae1c	pos 0 valid times	mediumnwb20230802_235KSEV39O.nwb	a93532eb-2947-4552-8877-19ea0d2dcc4f

Total: 1

In [4]:

from spyglass.position import PositionOutput

nwb_copy_file_name = "mediumnwb20230802_.nwb"

trodes_s_key = {
    "nwb_file_name": nwb_copy_file_name,
    "interval_list_name": "pos 0 valid times",
    "trodes_pos_params_name": "single_led_upsampled",
}

pos_merge_id = (PositionOutput.TrodesPosV1 & trodes_s_key).fetch1("merge_id")
pos_merge_id

from spyglass.position import PositionOutput nwb_copy_file_name = "mediumnwb20230802_.nwb" trodes_s_key = { "nwb_file_name": nwb_copy_file_name, "interval_list_name": "pos 0 valid times", "trodes_pos_params_name": "single_led_upsampled", } pos_merge_id = (PositionOutput.TrodesPosV1 & trodes_s_key).fetch1("merge_id") pos_merge_id

Out[4]:

UUID('4eb59a18-045a-5768-d12e-b6473415ae1c')

In [5]:

from spyglass.spikesorting.analysis.v1.group import (
    SortedSpikesGroup,
)

sorted_spikes_group_key = {
    "nwb_file_name": nwb_copy_file_name,
    "sorted_spikes_group_name": "test_group",
    "unit_filter_params_name": "default_exclusion",
}

SortedSpikesGroup & sorted_spikes_group_key

from spyglass.spikesorting.analysis.v1.group import ( SortedSpikesGroup, ) sorted_spikes_group_key = { "nwb_file_name": nwb_copy_file_name, "sorted_spikes_group_name": "test_group", "unit_filter_params_name": "default_exclusion", } SortedSpikesGroup & sorted_spikes_group_key

Out[5]:

nwb_file_name name of the NWB file	unit_filter_params_name	sorted_spikes_group_name
mediumnwb20230802_.nwb	default_exclusion	test_group

Total: 1

In [6]:

mua_key = {
    "mua_param_name": "default",
    **sorted_spikes_group_key,
    "pos_merge_id": pos_merge_id,
    "detection_interval": "pos 0 valid times",
}

MuaEventsV1().populate(mua_key)
MuaEventsV1 & mua_key

mua_key = { "mua_param_name": "default", **sorted_spikes_group_key, "pos_merge_id": pos_merge_id, "detection_interval": "pos 0 valid times", } MuaEventsV1().populate(mua_key) MuaEventsV1 & mua_key

Out[6]:

mua_param_name a name for this set of parameters	nwb_file_name name of the NWB file	unit_filter_params_name	sorted_spikes_group_name	pos_merge_id	detection_interval descriptive name of this interval list	analysis_file_name name of the file	mua_times_object_id
default	mediumnwb20230802_.nwb	default_exclusion	test_group	4eb59a18-045a-5768-d12e-b6473415ae1c	pos 0 valid times	mediumnwb20230802_235KSEV39O.nwb	a93532eb-2947-4552-8877-19ea0d2dcc4f

Total: 1

In [7]:

mua_times = (MuaEventsV1 & mua_key).fetch1_dataframe()
mua_times

mua_times = (MuaEventsV1 & mua_key).fetch1_dataframe() mua_times

Out[7]:

	start_time	end_time	duration	mean_zscore	median_zscore	max_zscore	min_zscore	speed_at_start	speed_at_end	max_speed	min_speed	median_speed	mean_speed
id
0	1.625936e+09	1.625936e+09	0.238	1.204139	1.220925	2.258331	0.028349	2.760825	1.517296	3.576624	1.427160	2.851154	2.616020
1	1.625936e+09	1.625936e+09	0.120	1.364368	1.349665	2.412096	0.015503	1.803533	0.497099	1.803533	0.464203	0.553494	0.722099
2	1.625936e+09	1.625936e+09	0.082	1.350428	1.490812	2.229001	0.016666	0.639882	0.830598	0.838116	0.639882	0.791716	0.772154
3	1.625936e+09	1.625936e+09	0.074	1.609420	1.803123	2.578417	0.013637	2.690052	0.684351	2.690052	0.684351	1.327693	1.451886
4	1.625936e+09	1.625936e+09	0.208	1.459232	1.441996	2.610289	0.040791	0.208621	1.136773	1.298535	0.162133	1.088990	0.935486
...	...	...	...	...	...	...	...	...	...	...	...	...	...
160	1.625937e+09	1.625937e+09	0.212	3.099559	3.296528	5.312823	0.013042	1.183369	0.500407	1.183369	0.386452	0.827476	0.791367
161	1.625937e+09	1.625937e+09	0.406	2.234536	2.555549	4.133360	0.013230	0.483370	0.415434	0.967244	0.170981	0.615845	0.603776
162	1.625937e+09	1.625937e+09	0.106	1.272785	1.090846	2.567647	0.029594	1.173970	1.531232	1.586072	1.173970	1.533011	1.472277
163	1.625937e+09	1.625937e+09	0.130	2.206783	2.288842	3.916084	0.000061	1.843658	2.197606	2.263417	1.843658	2.212691	2.156476
164	1.625937e+09	1.625937e+09	0.088	1.682973	1.689252	3.048358	0.021588	1.288769	1.058330	1.334759	1.058330	1.296841	1.260912

165 rows × 13 columns

In [8]:

import matplotlib.pyplot as plt
import numpy as np

fig, axes = plt.subplots(2, 1, sharex=True, figsize=(15, 4))
speed = MuaEventsV1.get_speed(mua_key).to_numpy()
time = speed.index.to_numpy()
multiunit_firing_rate = MuaEventsV1.get_firing_rate(mua_key, time)

time_slice = slice(
    np.searchsorted(time, mua_times.loc[10].start_time) - 1_000,
    np.searchsorted(time, mua_times.loc[10].start_time) + 5_000,
)

axes[0].plot(
    time[time_slice],
    multiunit_firing_rate[time_slice],
    color="black",
)
axes[0].set_ylabel("firing rate (Hz)")
axes[0].set_title("multiunit")
axes[1].fill_between(time[time_slice], speed[time_slice], color="lightgrey")
axes[1].set_ylabel("speed (cm/s)")
axes[1].set_xlabel("time (s)")

for id, mua_time in mua_times.loc[
    np.logical_and(
        mua_times["start_time"] > time[time_slice].min(),
        mua_times["end_time"] < time[time_slice].max(),
    )
].iterrows():
    axes[0].axvspan(
        mua_time["start_time"], mua_time["end_time"], color="red", alpha=0.5
    )

import matplotlib.pyplot as plt import numpy as np fig, axes = plt.subplots(2, 1, sharex=True, figsize=(15, 4)) speed = MuaEventsV1.get_speed(mua_key).to_numpy() time = speed.index.to_numpy() multiunit_firing_rate = MuaEventsV1.get_firing_rate(mua_key, time) time_slice = slice( np.searchsorted(time, mua_times.loc[10].start_time) - 1_000, np.searchsorted(time, mua_times.loc[10].start_time) + 5_000, ) axes[0].plot( time[time_slice], multiunit_firing_rate[time_slice], color="black", ) axes[0].set_ylabel("firing rate (Hz)") axes[0].set_title("multiunit") axes[1].fill_between(time[time_slice], speed[time_slice], color="lightgrey") axes[1].set_ylabel("speed (cm/s)") axes[1].set_xlabel("time (s)") for id, mua_time in mua_times.loc[ np.logical_and( mua_times["start_time"] > time[time_slice].min(), mua_times["end_time"] < time[time_slice].max(), ) ].iterrows(): axes[0].axvspan( mua_time["start_time"], mua_time["end_time"], color="red", alpha=0.5 )

[14:44:19][WARNING] Spyglass: Upsampled position data, frame indices are invalid. Setting add_frame_ind=False
/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.
  warn("Ignoring cached namespace '%s' version %s because version %s is already loaded."
/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.
  warn("Ignoring cached namespace '%s' version %s because version %s is already loaded."
/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.
  warn("Ignoring cached namespace '%s' version %s because version %s is already loaded."
/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.
  warn("Ignoring cached namespace '%s' version %s because version %s is already loaded."
/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.
  warn("Ignoring cached namespace '%s' version %s because version %s is already loaded."
/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.
  warn("Ignoring cached namespace '%s' version %s because version %s is already loaded."
/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.
  warn("Ignoring cached namespace '%s' version %s because version %s is already loaded."
/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.
  warn("Ignoring cached namespace '%s' version %s because version %s is already loaded."
/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.
  warn("Ignoring cached namespace '%s' version %s because version %s is already loaded."
/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.
  warn("Ignoring cached namespace '%s' version %s because version %s is already loaded."
/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.
  warn("Ignoring cached namespace '%s' version %s because version %s is already loaded."
/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.
  warn("Ignoring cached namespace '%s' version %s because version %s is already loaded."
/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.
  warn("Ignoring cached namespace '%s' version %s because version %s is already loaded."
/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.
  warn("Ignoring cached namespace '%s' version %s because version %s is already loaded."
/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.
  warn("Ignoring cached namespace '%s' version %s because version %s is already loaded."
/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.
  warn("Ignoring cached namespace '%s' version %s because version %s is already loaded."
/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.
  warn("Ignoring cached namespace '%s' version %s because version %s is already loaded."
/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.
  warn("Ignoring cached namespace '%s' version %s because version %s is already loaded."
/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.
  warn("Ignoring cached namespace '%s' version %s because version %s is already loaded."
/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.
  warn("Ignoring cached namespace '%s' version %s because version %s is already loaded."
/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.
  warn("Ignoring cached namespace '%s' version %s because version %s is already loaded."
[14:44:24][WARNING] Spyglass: Upsampled position data, frame indices are invalid. Setting add_frame_ind=False

In [9]:

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

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

[14:44:25][WARNING] Spyglass: Upsampled position data, frame indices are invalid. Setting add_frame_ind=False
[14:44:29][WARNING] Spyglass: Upsampled position data, frame indices are invalid. Setting add_frame_ind=False

WARNING: TimeseriesGraph::_add_series y argument is not 1D array. Using squeeze.

Out[9]:

'https://figurl.org/f?v=gs://figurl/spikesortingview-10&d=sha1://08d7c35434e8469686fca8aff3ec9319bccb44f9&label=Multiunit%20Detection&zone=franklab.default'

In [ ]: