Error in the set_probes function in spikeinterface ?

[Kayv-cmb]

Hi Spikeinterface,

There seems to be an issue in the spikeinterface set_probes function in the core packages.

I am trying to set a probes to a recording but I get this error :

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[1], [line 50](vscode-notebook-cell:?execution_count=1&line=50)
     [48](vscode-notebook-cell:?execution_count=1&line=48) recording_b = recording.remove_channels(remove_channel_ids=missing_numbers)
     [49](vscode-notebook-cell:?execution_count=1&line=49) #probe.set_device_channel_indices(recording_b.get_channel_ids())
---> [50](vscode-notebook-cell:?execution_count=1&line=50) recording_clean = recording_b.set_probe(probe)
     [51](vscode-notebook-cell:?execution_count=1&line=51) #recording = recording.remove_channels(remove_channel_ids=bad_channel['index_pixels'])
     [52](vscode-notebook-cell:?execution_count=1&line=52) # setting the channel location
     [53](vscode-notebook-cell:?execution_count=1&line=53) #recording.set_channel_locations(positions) to check...
     [54](vscode-notebook-cell:?execution_count=1&line=54) rec_dict = dict(filt=recording_clean)

File [~/.conda/envs/CHIME_kayvan/lib/python3.9/site-packages/spikeinterface/core/baserecordingsnippets.py:96](https://vscode-remote+ssh-002dremote-002bvis-005fnode2.vscode-resource.vscode-cdn.net/camp/home/combadk/working/combadk/ScriptKC/CHIME_script/~/.conda/envs/CHIME_kayvan/lib/python3.9/site-packages/spikeinterface/core/baserecordingsnippets.py:96), in BaseRecordingSnippets.set_probe(self, probe, group_mode, in_place)
     [94](https://vscode-remote+ssh-002dremote-002bvis-005fnode2.vscode-resource.vscode-cdn.net/camp/home/combadk/working/combadk/ScriptKC/CHIME_script/~/.conda/envs/CHIME_kayvan/lib/python3.9/site-packages/spikeinterface/core/baserecordingsnippets.py:94) probegroup = ProbeGroup()
     [95](https://vscode-remote+ssh-002dremote-002bvis-005fnode2.vscode-resource.vscode-cdn.net/camp/home/combadk/working/combadk/ScriptKC/CHIME_script/~/.conda/envs/CHIME_kayvan/lib/python3.9/site-packages/spikeinterface/core/baserecordingsnippets.py:95) probegroup.add_probe(probe)
---> [96](https://vscode-remote+ssh-002dremote-002bvis-005fnode2.vscode-resource.vscode-cdn.net/camp/home/combadk/working/combadk/ScriptKC/CHIME_script/~/.conda/envs/CHIME_kayvan/lib/python3.9/site-packages/spikeinterface/core/baserecordingsnippets.py:96) return self.set_probes(probegroup, group_mode=group_mode, in_place=in_place)

File [~/.conda/envs/CHIME_kayvan/lib/python3.9/site-packages/spikeinterface/core/baserecordingsnippets.py:170](https://vscode-remote+ssh-002dremote-002bvis-005fnode2.vscode-resource.vscode-cdn.net/camp/home/combadk/working/combadk/ScriptKC/CHIME_script/~/.conda/envs/CHIME_kayvan/lib/python3.9/site-packages/spikeinterface/core/baserecordingsnippets.py:170), in BaseRecordingSnippets.set_probes(self, probe_or_probegroup, group_mode, in_place)
    [163](https://vscode-remote+ssh-002dremote-002bvis-005fnode2.vscode-resource.vscode-cdn.net/camp/home/combadk/working/combadk/ScriptKC/CHIME_script/~/.conda/envs/CHIME_kayvan/lib/python3.9/site-packages/spikeinterface/core/baserecordingsnippets.py:163) if number_of_device_channel_indices >= self.get_num_channels():
    [164](https://vscode-remote+ssh-002dremote-002bvis-005fnode2.vscode-resource.vscode-cdn.net/camp/home/combadk/working/combadk/ScriptKC/CHIME_script/~/.conda/envs/CHIME_kayvan/lib/python3.9/site-packages/spikeinterface/core/baserecordingsnippets.py:164)     error_msg = (
    [165](https://vscode-remote+ssh-002dremote-002bvis-005fnode2.vscode-resource.vscode-cdn.net/camp/home/combadk/working/combadk/ScriptKC/CHIME_script/~/.conda/envs/CHIME_kayvan/lib/python3.9/site-packages/spikeinterface/core/baserecordingsnippets.py:165)         f"The given Probe have 'device_channel_indices' that do not match channel count \n"
    [166](https://vscode-remote+ssh-002dremote-002bvis-005fnode2.vscode-resource.vscode-cdn.net/camp/home/combadk/working/combadk/ScriptKC/CHIME_script/~/.conda/envs/CHIME_kayvan/lib/python3.9/site-packages/spikeinterface/core/baserecordingsnippets.py:166)         f"{number_of_device_channel_indices} vs {self.get_num_channels()} \n"
    [167](https://vscode-remote+ssh-002dremote-002bvis-005fnode2.vscode-resource.vscode-cdn.net/camp/home/combadk/working/combadk/ScriptKC/CHIME_script/~/.conda/envs/CHIME_kayvan/lib/python3.9/site-packages/spikeinterface/core/baserecordingsnippets.py:167)         f"device_channel_indices are the following: {device_channel_indices} \n"
    [168](https://vscode-remote+ssh-002dremote-002bvis-005fnode2.vscode-resource.vscode-cdn.net/camp/home/combadk/working/combadk/ScriptKC/CHIME_script/~/.conda/envs/CHIME_kayvan/lib/python3.9/site-packages/spikeinterface/core/baserecordingsnippets.py:168)         f"recording channels are the following: {self.get_channel_ids()} \n"
    [169](https://vscode-remote+ssh-002dremote-002bvis-005fnode2.vscode-resource.vscode-cdn.net/camp/home/combadk/working/combadk/ScriptKC/CHIME_script/~/.conda/envs/CHIME_kayvan/lib/python3.9/site-packages/spikeinterface/core/baserecordingsnippets.py:169)     )
--> [170](https://vscode-remote+ssh-002dremote-002bvis-005fnode2.vscode-resource.vscode-cdn.net/camp/home/combadk/working/combadk/ScriptKC/CHIME_script/~/.conda/envs/CHIME_kayvan/lib/python3.9/site-packages/spikeinterface/core/baserecordingsnippets.py:170)     raise ValueError(error_msg)
...
ValueError: The given Probe have 'device_channel_indices' that do not match channel count 
110 vs 52 
device_channel_indices are the following: [  1   2   4   5   6   7   9  10  11  13  18  19  20  24  28  35  37  38  39  40  41  44  47  49  50  52  54  58  59  63  68  70  72  79  81  83  84  86  87  88  89  90  91  92  94  97 100 104 106 107 108 110] 
recording channels are the following: [  1   2   4   5   6   7   9  10  11  13  18  19  20  24  28  35  37  38  39  40  41  44  47  49  50  52  54  58  59  63  68  70  72  79  81  83  84  86  87  88  89  90  91  92  94  97 100 104 106 107 108 110]

When I had a look at the code, it seems to check the max of the device_channel_indices against the number of channel in the recording should it be comparing size?

        number_of_device_channel_indices = np.max(list(device_channel_indices) + [0])
        if number_of_device_channel_indices >= self.get_num_channels():
            error_msg = (
                f"The given Probe have 'device_channel_indices' that do not match channel count \n"
                f"{number_of_device_channel_indices} vs {self.get_num_channels()} \n"
                f"device_channel_indices are the following: {device_channel_indices} \n"
                f"recording channels are the following: {self.get_channel_ids()} \n"
            )
            raise ValueError(error_msg)

[alejoe91]

Hi @Kayv-cmb

The device_channel_indices is an index, so it's maximum value cannot exceed num_channels - 1

How are you setting the device_channel_indices? Can you paste your script?

[Kayv-cmb]

I am setting it like this, but basically I have a lot of preprocessing before actually creating a recording and which end up of
with having a positions array (x,y,z) for the probe with channel indices like this
array([ 74, 99, 25, 58, 72, 107, 91, 59, 63, 35, 90, 44, 42, 108, 97, 41, 87, 66, 19, 84, 37, 43, 88, 81, 104, 110, 57, 93, 106, 89, 24, 48, 2, 5, 52, 111, 28, 61, 102, 9, 68, 4, 11, 70, 40, 6, 75, 47, 79, 86, 94, 13, 49, 100, 92, 20, 7, 10, 1, 39, 18, 38, 50, 54, 83])

exp = Experiment(directory, ct= dic)

recording = extractor.read_chime(exp)
num_channel = recording.get_num_channels()
tip_min_um = exp.ct.tip_min*exp.ct.voxel[0]

positions,bad_channel,df_min_noises = exp.channel_map(exp.wire_map,tip_min_um)
missing_numbers = find_missing_numbers(df_min_noises['index_pixels'],num_channel)

#positions,bad_channel = exp.channel_map(exp.wire_map,exp.ct.tip_min)
# Creation of a custom prob linked to the channel map
if positions.shape[1]==3:
    probe = Probe(ndim = 3, si_units='um')
    # Setting the position of the probes
    plane_axes_xy = np.zeros((len(positions), 2, 3))
    # xy axis will be:
    plane_axes_xy[:, 0, 0] = 1
    plane_axes_xy[:, 1, 1] = 1
    probe.set_contacts(positions=positions, shapes='circle', shape_params={'radius': 8}, plane_axes =plane_axes_xy)
    #probe.set_global_device_channel_indices(np.arrange(position.shape[0]))
    #probe.set_device_channel_indices(np.arange(positions.shape[0]))
    probe.set_device_channel_indices(df_min_noises['index_pixels'])

# removing channel that got higher noise level
recording_b = recording.remove_channels(remove_channel_ids=missing_numbers)
#probe.set_device_channel_indices(recording_b.get_channel_ids())
recording_clean = recording_b.set_probe(probe)

[Kayv-cmb]

and when I compare this

ValueError: The given Probe have 'device_channel_indices' that do not match channel count 
110 vs 52 
device_channel_indices are the following: [  1   2   4   5   6   7   9  10  11  13  18  19  20  24  28  35  37  38  39  40  41  44  47  49  50  52  54  58  59  63  68  70  72  79  81  83  84  86  87  88  89  90  91  92  94  97 100 104 106 107 108 110] 
recording channels are the following: [  1   2   4   5   6   7   9  10  11  13  18  19  20  24  28  35  37  38  39  40  41  44  47  49  50  52  54  58  59  63  68  70  72  79  81  83  84  86  87  88  89  90  91  92  94  97 100 104 106 107 108 110]

I have exactly the same channel inside both and the same number of channel but the match check give different output

[Kayv-cmb]

I changed my way of doing it so that it would not trigger this error so I will close