Note
Click here to download the full example code
Peaks Widgets Gallery¶
Some widgets are useful before sorting and works with “peaks” given by detect_peaks() function.
They are useful to check drift before running sorters.
import matplotlib.pyplot as plt
import spikeinterface.full as si
First, let’s download a simulated dataset from the repo ‘https://gin.g-node.org/NeuralEnsemble/ephy_testing_data’
local_path = si.download_dataset(remote_path='mearec/mearec_test_10s.h5')
rec, sorting = si.read_mearec(local_path)
Lets filter and detect peak on it
from spikeinterface.sortingcomponents import detect_peaks
rec_filtred = si.bandpass_filter(rec, freq_min=300., freq_max=6000., margin_ms=5.0)
print(rec_filtred)
peaks = detect_peaks(
rec_filtred, method='locally_exclusive',
peak_sign='neg', detect_threshold=6, n_shifts=7,
local_radius_um=100,
noise_levels=None,
random_chunk_kwargs={},
chunk_memory='10M', n_jobs=1, progress_bar=True)
Traceback (most recent call last):
File "/home/docs/checkouts/readthedocs.org/user_builds/spikeinterface/checkouts/0.90.1/examples/modules/widgets/plot_4_peaks_gallery.py", line 30, in <module>
peaks = detect_peaks(
File "/home/docs/checkouts/readthedocs.org/user_builds/spikeinterface/conda/0.90.1/lib/python3.8/site-packages/spikeinterface/sortingcomponents/peak_detection.py", line 68, in detect_peaks
raise ModuleNotFoundError('"locally_exclusive" need numba which is not installed')
ModuleNotFoundError: "locally_exclusive" need numba which is not installed
- peaks is a numpy 1D array with structured dtype that contains several fields:
sample_ind/channel_ind/amplitude/segment_ind
print(peaks.dtype)
print(peaks.shape)
print(peaks.dtype.fields.keys())
- This “peaks” vector can be used in several widgets, for instance
plot_peak_activity_map()
si.plot_peak_activity_map(rec_filtred, peaks=peaks)
can be also animated with bin_duration_s=1.
si.plot_peak_activity_map(rec_filtred, bin_duration_s=1.)
- plot_drift_over_time’()
heatmap mode here bin_duration_s=1. because the rec is short (10s). a better value could 60s
si.plot_drift_over_time(rec_filtred, peaks=peaks, bin_duration_s=1.,
weight_with_amplitudes=True, mode='heatmap')
- plot_drift_over_time’()
in scatter mode
si.plot_drift_over_time(rec_filtred, peaks=peaks, weight_with_amplitudes=False, mode='scatter')
plt.show()
Total running time of the script: ( 0 minutes 0.186 seconds)