Add catalogue-based probe construction for OpenEphys and channel map ordering#409
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h-mayorquin merged 46 commits intoSpikeInterface:mainfrom Mar 18, 2026
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… adc check in tests, plugin_channe_keys -> settings_channel_keys
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…-map-ordering' into openephys-channel-map-ordering
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LGTM
I removed a function that I introduced for the oebin structure _contact_id_to_global_electrode_index and modified the relates tests.
…annel-map-ordering
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Replaces #406
In #406, the
read_openephyswas refactored to use the probe from the catalogue and then slice it. In addition, it attempts to solve a mismatch between the channel order in the settings file and structure.oebin file (see SpikeInterface/spikeinterface#4394), by using thestructure.oebinfileelectrode_indexfield to set device channel indices. This comes with a lot of additional logic (that we thought was required).I was checking again the
settings.xmland had a eureka moment! The mismatch is not random, but it's due to a "Channel Map" processor preceding the "Record Node"! If we simply read the custom channel map and apply it when we slice the probe, this magically fix all issues, with a much simpler solution and without requiring the additional oebin file. Then we can apply the defaultarangefor device channel indices.You can see the changes with #406 here
All tests with the
structure.oebinare kept!