Single sweep detection

Detect spikes for a single sweep

import os
import matplotlib.pyplot as plt
from allensdk.api.queries.cell_types_api import CellTypesApi
from ipfx.data_set_utils import create_data_set
from ipfx.feature_extractor import SpikeFeatureExtractor

# 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)

# Get the data for the sweep into a format we can use
dataset = create_data_set(sweep_info=sweep_info, nwb_file=nwb_file)
sweep_number = 39
sweep = dataset.sweep(sweep_number)

# Extract information about the spikes
ext = SpikeFeatureExtractor()
results = ext.process(t=sweep.t, v=sweep.v, i=sweep.i)

# Plot the results, showing two features of the detected spikes
plt.plot(sweep.t, sweep.v)
plt.plot(results["peak_t"], results["peak_v"], 'r.')
plt.plot(results["threshold_t"], results["threshold_v"], 'k.')

# Set the plot limits to highlight where spikes are and set axis labels
plt.xlim(0.5, 2.5)
plt.xlabel("Time (s)")
plt.ylabel("Membrane potential (mV)")

plt.show()

Out:

/home/docs/checkouts/readthedocs.org/user_builds/ipfx/checkouts/v1.0.0.2/docs/gallery/spikes_examples/detect_spikes_single_sweep.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
  dataset = create_data_set(sweep_info=sweep_info, nwb_file=nwb_file)
/home/docs/checkouts/readthedocs.org/user_builds/ipfx/envs/v1.0.0.2/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/v1.0.0.2/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/v1.0.0.2/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,

Link to the example data used here: http://celltypes.brain-map.org/experiment/electrophysiology/488679042