Sweep QC Features

Estimate sweep QC features

Out:

/home/docs/checkouts/readthedocs.org/user_builds/ipfx/checkouts/v1.0.0.1/docs/gallery/qc_examples/sweep_qc.py:25: VisibleDeprecationWarning: Function create_ephys_data_set is deprecated. Instead of using ipfx.data_set_utils.create_data_set, use ipfx.dataset.create.create_ephys_data_set
  data_set = create_data_set(sweep_info=sweep_info, nwb_file=nwb_file)
/home/docs/checkouts/readthedocs.org/user_builds/ipfx/envs/v1.0.0.1/lib/python3.7/site-packages/hdmf/spec/namespace.py:470: UserWarning: ignoring namespace 'hdmf-common' because it already exists
  warn("ignoring namespace '%s' because it already exists" % ns['name'])
/home/docs/checkouts/readthedocs.org/user_builds/ipfx/envs/v1.0.0.1/lib/python3.7/site-packages/hdmf/spec/namespace.py:470: UserWarning: ignoring namespace 'core' because it already exists
  warn("ignoring namespace '%s' because it already exists" % ns['name'])
/home/docs/checkouts/readthedocs.org/user_builds/ipfx/checkouts/v1.0.0.1/ipfx/dataset/create.py:124: VisibleDeprecationWarning: Class EphysDataSet is deprecated. Import EphysDataSet from ipfx.dataset.ephys_dataset rather than ipfx.ephys_dataset
  data=nwb_data,
   sweep_number stimulus_units  ...  tags  stimulus_amplitude
0             5             pA  ...    []             151.875
1             6             pA  ...    []             151.875
2             7             pA  ...    []             137.875
3             8             pA  ...    []             100.000
4             9             pA  ...    []             200.000

[5 rows x 28 columns]

from __future__ import print_function

import os
import pandas as pd
from ipfx.data_set_utils import create_data_set
from ipfx.qc_feature_extractor import sweep_qc_features
from allensdk.api.queries.cell_types_api import CellTypesApi

# Download and access the experimental data
ct = CellTypesApi()
nwb_file = os.path.join(
    os.path.dirname(os.getcwd()),
    "data",
    "nwb2_H17.03.008.11.03.05.nwb"
)
specimen_id = 595570553
sweep_info = ct.get_ephys_sweeps(specimen_id)

data_set = create_data_set(sweep_info=sweep_info, nwb_file=nwb_file)

# run sweep QC
sweep_features = sweep_qc_features(data_set)

print(pd.DataFrame(sweep_features).head())