Add a debugging script.

Author: JoeZiminski

debugging/debugging_session_displacement.py

@@ -0,0 +1,83 @@
+"""
+TODO: some notes on this debugging script.
+"""
+import spikeinterface.full as si
+from spikeinterface.generation.session_displacement_generator import generate_session_displacement_recordings
+import matplotlib.pyplot as plt
+import numpy as np
+from spikeinterface.sortingcomponents.peak_detection import detect_peaks
+from spikeinterface.sortingcomponents.peak_localization import localize_peaks
+
+# Generate a ground truth recording where every unit is firing a lot,
+# with high amplitude, and is close to the spike, so all picked up.
+# This just makes it easy to play around with the units, e.g.
+# if specifying 5 units, 5 unit peaks are clearly visible, none are lost
+# because their position is too far from probe.
+
+default_unit_params_range = dict(
+    alpha=(100.0, 500.0),
+    depolarization_ms=(0.09, 0.14),
+    repolarization_ms=(0.5, 0.8),
+    recovery_ms=(1.0, 1.5),
+    positive_amplitude=(0.1, 0.25),
+    smooth_ms=(0.03, 0.07),
+    spatial_decay=(20, 40),
+    propagation_speed=(250.0, 350.0),
+    b=(0.1, 1),
+    c=(0.1, 1),
+    x_angle=(0, np.pi),
+    y_angle=(0, np.pi),
+    z_angle=(0, np.pi),
+)
+
+default_unit_params_range["alpha"] = (500, 500)  # do this or change the margin on generate_unit_locations_kwargs
+default_unit_params_range["b"] = (0.5, 1) # and make the units fatter, easier to receive signal!
+default_unit_params_range["c"] = (0.5, 1)
+
+scale_ = [np.array([0.25, 0.5, 1, 1, 0])] * 2
+scale_ = [np.ones(5)] + scale_
+
+rec_list, _ = generate_session_displacement_recordings(
+    non_rigid_gradient=None,  # 0.05, TODO: note this will set nonlinearity to both x and y (the same)
+    num_units=5,
+    recording_durations=(25, 25, 25),  # TODO: checks on inputs
+    recording_shifts=(
+        (0, 0),
+        (0, 0),
+        (0, 0),
+    ),
+    recording_amplitude_scalings= {
+        "method": "by_amplitude_and_firing_rate",
+        "scalings": scale_,
+    },
+    generate_sorting_kwargs=dict(firing_rates=(0, 200), refractory_period_ms=4.0),
+    generate_templates_kwargs=dict(unit_params=default_unit_params_range, ms_before=1.5, ms_after=3),
+    seed=None,
+    generate_unit_locations_kwargs=dict(
+        margin_um=0.0,  # if this is say 20, then units go off the edge of the probe and are such low amplitude they are not picked up.
+        minimum_z=5.0,
+        maximum_z=45.0,
+        minimum_distance=18.0,
+        max_iteration=100,
+        distance_strict=False,
+    ),
+)
+
+# Iterate through each recording, plotting the raw traces then
+# detecting and plotting the peaks.
+
+for rec in rec_list:
+
+    si.plot_traces(rec, time_range=(0, 1))
+    plt.show()
+
+    peaks = detect_peaks(rec, method="locally_exclusive")
+    peak_locs = localize_peaks(rec, peaks, method="grid_convolution")
+
+    si.plot_drift_raster_map(
+        peaks=peaks,
+        peak_locations=peak_locs,
+        recording=rec,
+        clim=(-300, 0)  # fix clim for comparability across plots
+    )
+    plt.show()