viewspikes: examples on reproducible ephys

Author: oliche

viewspikes/examples_local.py

@@ -25,7 +25,7 @@
 "ce397420-3cd2-4a55-8fd1-5e28321981f4",
 
 # Example 1
-pid, t0 = ("8413c5c6-b42b-4ec6-b751-881a54413628", 810)
+pid, t0 = ("ce24bbe9-ae70-4659-9e9c-564d1a865de8", 810)
 bin_file = next(RAW_PATH.joinpath(pid).rglob("*.ap.bin"))
 sr = spikeglx.Reader(bin_file)
 sel = slice(int(t0 * sr.fs), int((t0 + 4) * sr.fs))

viewspikes/examples_reproducible.py

@@ -0,0 +1,92 @@
+import numpy as np
+import scipy
+import matplotlib.pyplot as plt
+from easyqc.gui import viewseis
+
+
+from oneibl.one import ONE
+from ibllib.ephys import neuropixel
+from ibllib.dsp import voltage
+from brainbox.plot import driftmap
+import alf.io
+
+from needles2 import run_needles2
+from viewspikes.data import stream, get_ks2, get_spikes
+from viewspikes.plots import plot_insertion, show_psd, overlay_spikes
+
+one = ONE()
+
+eids = ['56b57c38-2699-4091-90a8-aba35103155e',
+       '746d1902-fa59-4cab-b0aa-013be36060d5',
+       '7b26ce84-07f9-43d1-957f-bc72aeb730a3',
+       'dac3a4c1-b666-4de0-87e8-8c514483cacf',
+       '6f09ba7e-e3ce-44b0-932b-c003fb44fb89',
+       '73918ae1-e4fd-4c18-b132-00cb555b1ad2',
+       'f312aaec-3b6f-44b3-86b4-3a0c119c0438',
+       'dda5fc59-f09a-4256-9fb5-66c67667a466',
+       'ee40aece-cffd-4edb-a4b6-155f158c666a',
+       'ecb5520d-1358-434c-95ec-93687ecd1396',
+       '54238fd6-d2d0-4408-b1a9-d19d24fd29ce',
+       'e535fb62-e245-4a48-b119-88ce62a6fe67',
+       'b03fbc44-3d8e-4a6c-8a50-5ea3498568e0',
+       'db4df448-e449-4a6f-a0e7-288711e7a75a',
+       '064a7252-8e10-4ad6-b3fd-7a88a2db5463',
+       '41872d7f-75cb-4445-bb1a-132b354c44f0',
+       'dfd8e7df-dc51-4589-b6ca-7baccfeb94b4',
+       '4a45c8ba-db6f-4f11-9403-56e06a33dfa4',
+       '4b00df29-3769-43be-bb40-128b1cba6d35',
+       '862ade13-53cd-4221-a3fa-dda8643641f2',
+       '3638d102-e8b6-4230-8742-e548cd87a949',
+       'c7248e09-8c0d-40f2-9eb4-700a8973d8c8',
+       'aad23144-0e52-4eac-80c5-c4ee2decb198',
+       'd0ea3148-948d-4817-94f8-dcaf2342bbbe',
+       '7f6b86f9-879a-4ea2-8531-294a221af5d0',
+       'd23a44ef-1402-4ed7-97f5-47e9a7a504d9']
+
+insertions = one.alyx.rest('insertions', 'list', django=f'session__in,{eids}')
+
+## Example 1: Stream one second of ephys data
+# pid, t0 = ("e864fca7-40e3-4a80-b736-51d4662405e4", 2155)
+# pid, t0 = ('ce24bbe9-ae70-4659-9e9c-564d1a865de8', 610)
+
+pid, t0 = (insertions[10]['id'], 2500)
+
+
+sr, dsets = stream(pid, t0=t0, one=one, cache=True)
+raw = sr[:, :-1].T
+
+## Example: Plot Insertion for a given PID (todo: use Needles 2 for interactive)
+av = run_needles2.view(lazy=True)
+av.add_insertion_by_id(pid)
+
+## Example: Display the raw / pre-proc and KS2 parts -
+h = neuropixel.trace_header()
+sos = scipy.signal.butter(3, 300 / sr.fs / 2, btype='highpass', output='sos')
+butt = scipy.signal.sosfiltfilt(sos, raw)
+fk_kwargs ={'dx': 1, 'vbounds': [0, 1e6], 'ntr_pad': 160, 'ntr_tap': 0, 'lagc': .01, 'btype': 'lowpass'}
+destripe = voltage.destripe(raw, fs=sr.fs, fk_kwargs=fk_kwargs, tr_sel=np.arange(raw.shape[0]))
+ks2 = get_ks2(raw, dsets, one)
+eqc_butt = viewseis(butt.T, si=1 / sr.fs, h=h, t0=t0, title='butt', taxis=0)
+eqc_dest = viewseis(destripe.T, si=1 / sr.fs, h=h, t0=t0, title='destr', taxis=0)
+eqc_ks2 = viewseis(ks2.T, si=1 / sr.fs, h=h, t0=t0, title='ks2', taxis=0)
+
+
+## Example: overlay the spikes on the existing easyqc instances
+spikes, clusters, channels = get_spikes(dsets, one)
+_, tspi, xspi = overlay_spikes(eqc_butt, spikes, clusters, channels)
+overlay_spikes(eqc_dest, spikes, clusters, channels)
+overlay_spikes(eqc_ks2, spikes, clusters, channels)
+
+## Get the behaviour information
+eid = dsets[0]['session'][-36:]
+tdsets = one.alyx.rest('datasets', 'list', session=eid, django='name__icontains,trials.')
+one.download_datasets(tdsets)
+trials = alf.io.load_object(one.path_from_eid(eid).joinpath('alf'), 'trials')
+rewards = trials['feedback_times'][trials['feedbackType'] == 1]
+
+## Do the drift map with some task information overlaid
+fig, ax = plt.subplots()
+driftmap(spikes['times'], spikes['depths'], t_bin=0.1, d_bin=5, ax=ax)
+from ibllib.plots import vertical_lines
+vertical_lines(rewards, ymin=0, ymax=3800, ax=ax)
+

viewspikes/examples_stream.py

@@ -21,8 +21,13 @@
 "f86e9571-63ff-4116-9c40-aa44d57d2da9",  # CSHL049_2020-01-08_probe00 a bit stripy but fine
 "675952a4-e8b3-4e82-a179-cc970d5a8b01",  # CSH_ZAD_029_2020-09-19_probe01 a bit stripy as well
 
-## Example 1: Stream one second of ephys data
-pid, t0 = ("e864fca7-40e3-4a80-b736-51d4662405e4", 2155)
+# Example 1: Stream one second of ephys data
+# pid, t0 = ("e864fca7-40e3-4a80-b736-51d4662405e4", 2155)
+# pid, t0 = ('ce24bbe9-ae70-4659-9e9c-564d1a865de8', 610)
+
+pid, t0 = ("0ece5c6a-7d1e-4365-893d-ac1cc04f1d7b", 3000)
+
+
 sr, dsets = stream(pid, t0=t0, one=one, cache=True)
 
 ## Example 2: Plot Insertion for a given PID (todo: use Needles 2 for interactive)
@@ -41,8 +46,13 @@
 butt = scipy.signal.sosfiltfilt(sos, raw)
 fk_kwargs ={'dx': 1, 'vbounds': [0, 1e6], 'ntr_pad': 160, 'ntr_tap': 0, 'lagc': .01, 'btype': 'lowpass'}
 destripe = voltage.destripe(raw, fs=sr.fs, fk_kwargs=fk_kwargs, tr_sel=np.arange(raw.shape[0]))
+ks2 = get_ks2(raw, dsets, one)
 eqc_butt = viewseis(butt.T, si=1 / sr.fs, h=h, t0=t0, title='butt', taxis=0)
 eqc_dest = viewseis(destripe.T, si=1 / sr.fs, h=h, t0=t0, title='destr', taxis=0)
+eqc_ks2 = viewseis(ks2.T, si=1 / sr.fs, h=h, t0=t0, title='ks2', taxis=0)
+
+
+
 
 # Example 5: overlay the spikes on the existing easyqc instances
 spikes, clusters, channels = get_spikes(dsets, one)