All Analysis

Run analysis for all stimulus types on data in the NWB file

Out:

/home/docs/checkouts/readthedocs.org/user_builds/ipfx/envs/latest/lib/python3.6/site-packages/hdmf/spec/namespace.py:485: UserWarning: Ignoring cached namespace 'hdmf-common' version 1.1.0 because version 1.3.0 is already loaded.
  % (ns['name'], ns['version'], self.__namespaces.get(ns['name'])['version']))
/home/docs/checkouts/readthedocs.org/user_builds/ipfx/envs/latest/lib/python3.6/site-packages/hdmf/spec/namespace.py:485: UserWarning: Ignoring cached namespace 'core' version 2.2.0 because version 2.2.5 is already loaded.
  % (ns['name'], ns['version'], self.__namespaces.get(ns['name'])['version']))
WARNING:root:sweep 61: ['Recording stopped before completing the experiment epoch']
WARNING:root:sweep 62: ['Recording stopped before completing the experiment epoch']
WARNING:root:sweep 63: ['Recording stopped before completing the experiment epoch']
WARNING:root:sweep 64: ['Recording stopped before completing the experiment epoch']
WARNING:root:sweep 65: ['Recording stopped before completing the experiment epoch']
WARNING:root:sweep 66: ['Recording stopped before completing the experiment epoch']
WARNING:root:sweep 67: ['Recording stopped before completing the experiment epoch']
WARNING:root:sweep 68: ['Recording stopped before completing the experiment epoch']
WARNING:root:sweep 69: ['Recording stopped before completing the experiment epoch']
WARNING:root:sweep 70: ['Recording stopped before completing the experiment epoch']
WARNING:root:Warning: stimulus_name Noise 1 not found.
STIMULUS_TYPE_NAME_MAPPING: {<StimulusType.RAMP: 'ramp'>: {'Ramp'}, <StimulusType.LONG_SQUARE: 'long_square'>: {'Long Square Threshold', 'Long Square SupraThreshold', 'Long Square SubThreshold', 'Long Square'}, <StimulusType.COARSE_LONG_SQUARE: 'coarse_long_square'>: {'C1LSCOARSE'}, <StimulusType.SHORT_SQUARE_TRIPLE: 'short_square_triple'>: {'Short Square - Triple'}, <StimulusType.SHORT_SQUARE: 'short_square'>: {'Short Square - Hold -80mV', 'Short Square - Hold -70mV', 'Short Square - Hold -60mV', 'Short Square Threshold', 'Short Square'}, <StimulusType.CHIRP: 'chirp'>: {'Chirp C - Hold -60mV', 'Chirp A Threshold', 'Chirp', 'Chirp D - Hold -55mV', 'Chirp B - Hold -65mV'}, <StimulusType.SEARCH: 'search'>: {'Search'}, <StimulusType.TEST: 'test'>: {'Test'}, <StimulusType.BLOWOUT: 'blowout'>: {'EXTPBLWOUT'}, <StimulusType.BATH: 'bath'>: {'EXTPINBATH'}, <StimulusType.SEAL: 'seal'>: {'EXTPCllATT'}, <StimulusType.BREAKIN: 'breakin'>: {'EXTPBREAKN'}, <StimulusType.EXTP: 'extp'>: {'EXTP'}}
Using default detection parameters
WARNING:root:Warning: stimulus_name Noise 2 not found.
STIMULUS_TYPE_NAME_MAPPING: {<StimulusType.RAMP: 'ramp'>: {'Ramp'}, <StimulusType.LONG_SQUARE: 'long_square'>: {'Long Square Threshold', 'Long Square SupraThreshold', 'Long Square SubThreshold', 'Long Square'}, <StimulusType.COARSE_LONG_SQUARE: 'coarse_long_square'>: {'C1LSCOARSE'}, <StimulusType.SHORT_SQUARE_TRIPLE: 'short_square_triple'>: {'Short Square - Triple'}, <StimulusType.SHORT_SQUARE: 'short_square'>: {'Short Square - Hold -80mV', 'Short Square - Hold -70mV', 'Short Square - Hold -60mV', 'Short Square Threshold', 'Short Square'}, <StimulusType.CHIRP: 'chirp'>: {'Chirp C - Hold -60mV', 'Chirp A Threshold', 'Chirp', 'Chirp D - Hold -55mV', 'Chirp B - Hold -65mV'}, <StimulusType.SEARCH: 'search'>: {'Search'}, <StimulusType.TEST: 'test'>: {'Test'}, <StimulusType.BLOWOUT: 'blowout'>: {'EXTPBLWOUT'}, <StimulusType.BATH: 'bath'>: {'EXTPINBATH'}, <StimulusType.SEAL: 'seal'>: {'EXTPCllATT'}, <StimulusType.BREAKIN: 'breakin'>: {'EXTPBREAKN'}, <StimulusType.EXTP: 'extp'>: {'EXTP'}}
Using default detection parameters
{'rheobase_sweep_num': 34, 'thumbnail_sweep_num': 36, 'vrest': -67.84906877790179, 'ri': 161.2471640110016, 'sag': 0.1976964920759201, 'tau': 16.20768335673351, 'vm_for_sag': -86.21875, 'f_i_curve_slope': 0.3530456831503806, 'adaptation': 0.05018917956237554, 'latency': 0.028179999999999872, 'avg_isi': 44.4504761904762, 'upstroke_downstroke_ratio_long_square': 2.7872165672263765, 'peak_v_long_square': 38.28125, 'peak_t_long_square': 0.56728, 'trough_v_long_square': -52.343753814697266, 'trough_t_long_square': 0.5685800000000001, 'fast_trough_v_long_square': -52.3125, 'fast_trough_t_long_square': 0.5685199999999999, 'slow_trough_v_long_square': None, 'slow_trough_t_long_square': None, 'threshold_v_long_square': -38.312503814697266, 'threshold_i_long_square': 70, 'threshold_t_long_square': 0.56688, 'upstroke_downstroke_ratio_ramp': 2.8088185451956593, 'peak_v_ramp': 39.395832, 'peak_t_ramp': 5.09762, 'trough_v_ramp': -54.96875, 'trough_t_ramp': 5.099006666666667, 'fast_trough_v_ramp': -54.9375, 'fast_trough_t_ramp': 5.098966666666667, 'slow_trough_v_ramp': -52.645835876464844, 'slow_trough_t_ramp': 5.123726666666667, 'threshold_v_ramp': -38.875, 'threshold_i_ramp': 115.0, 'threshold_t_ramp': 5.097200000000001, 'upstroke_downstroke_ratio_short_square': 2.8238712481895005, 'peak_v_short_square': 40.04018, 'peak_t_short_square': 0.5033514285714286, 'trough_v_short_square': -69.11607, 'trough_t_short_square': 0.6062599999999999, 'fast_trough_v_short_square': -52.54018, 'fast_trough_t_short_square': 0.5044228571428572, 'slow_trough_v_short_square': None, 'slow_trough_t_short_square': None, 'threshold_v_short_square': -43.339287, 'threshold_i_short_square': 540.0, 'threshold_t_short_square': 0.5029971428571428}

import os

from ipfx.dataset.create import create_ephys_data_set
from ipfx.data_set_features import extract_data_set_features
from ipfx.utilities import drop_failed_sweeps

# Download and access the experimental data from DANDI archive per instructions in the documentation
# Example below will use an nwb file provided with the package

nwb_file = os.path.join(
    os.path.dirname(os.getcwd()),
    "data",
    "nwb2_H17.03.008.11.03.05.nwb"
)

# Create Ephys Data Set
data_set = create_ephys_data_set(nwb_file=nwb_file)

# Drop failed sweeps: sweeps with incomplete recording or failing QC criteria
drop_failed_sweeps(data_set)

# Calculate ephys features
cell_features, sweep_features, cell_record, sweep_records, _, _ = \
    extract_data_set_features(data_set, subthresh_min_amp=-100.0)

print(cell_record)