3D probes are not handeled

[vonaviv]

Hi,

The GUI expects only 2D probes. I have identified locations where only 2D contact position is expected:

Lines 52, 54, 125, 131, 431 in spikeinterface_gui/probeview.py
Line 77, 515 in spikeinterface_gui/waveformview.py

After I have handled these (by self.contact_positions[:, 0:2]) I go the following error and I am not sure if it's related to the issue from above:

Traceback (most recent call last):
  File "/home/vivanov/Workspace/spikesorting/dev/spikeinterface-gui.py", line 86, in <module>
    run_mainwindow(sorting_analyzer, mode="desktop", curation=False)
  File "/home/vivanov/Workspace/spikeinterface-gui/spikeinterface_gui/main.py", line 185, in run_mainwindow
    win = QtMainWindow(controller, layout_dict=layout_dict, user_settings=user_settings)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/vivanov/Workspace/spikeinterface-gui/spikeinterface_gui/backend_qt.py", line 178, in __init__
    view._refresh()
  File "/home/vivanov/Workspace/spikeinterface-gui/spikeinterface_gui/view_base.py", line 128, in _refresh
    self._qt_refresh(**kwargs)
  File "/home/vivanov/Workspace/spikeinterface-gui/spikeinterface_gui/basescatterview.py", line 306, in _qt_refresh
    spike_times, spike_data, hist_count, hist_bins, ymin, ymax, inds = self.get_unit_data(
                                                                       ^^^^^^^^^^^^^^^^^^^
  File "/home/vivanov/Workspace/spikeinterface-gui/spikeinterface_gui/basescatterview.py", line 60, in get_unit_data
    min_bin_size = np.min(np.diff(np.unique(spike_data)))
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/vivanov/anaconda3/envs/spikesorting/lib/python3.12/site-packages/numpy/_core/fromnumeric.py", line 3261, in min
    return _wrapreduction(a, np.minimum, 'min', axis, None, out,
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/vivanov/anaconda3/envs/spikesorting/lib/python3.12/site-packages/numpy/_core/fromnumeric.py", line 83, in _wrapreduction
    return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: zero-size array to reduction operation minimum which has no identity

[chrishalcrow]

Hello, thanks for reporting this. I'll make a PR about the 3D locations later today.
But I think this issue is that spike_data is empty. This contains all your spike data, e.g. spike times, spike locations and spike amplitudes. Would you be able to check if you have any empty units (units with no spikes)? E.g. in another script load your analyzer, and check

analyzer.sorting.count_num_spikes_per_unit()

Alternatively, it could be that something went wrong with the computation of the spike locations or amplitudes.

[chrishalcrow]

Hey @vonaviv - I just made a PR to allow for 3D probes. Would you be able to try out the PR on your data? Thanks!