Add catalogue-based probe construction for OpenEphys

[h-mayorquin]

This adds read_openephys_binary(settings_file, oebin_file, stream_name), a new reader for Open Ephys binary format recordings that uses both settings.xml (probe geometry) and structure.oebin (binary data layout) to build probes. It also refactors read_openephys to use catalogue-based probe construction, fixing contact_id consistency with SpikeGLX. See #405 for the broader discussion on separating probe construction from wiring.

Both readers now follow the same pattern as read_spikeglx (introduced in PR #383): build the full probe from the catalogue via build_neuropixels_probe, then combine it with data from the source files to determine which electrodes are active and how they map to the data. For SpikeGLX, the source file is the .meta file (IMRO table). For Open Ephys, the settings.xml provides electrode positions (via ELECTRODE_XPOS/ELECTRODE_YPOS) or electrode indices (via SELECTED_ELECTRODES), which are matched against the catalogue probe geometry to select the active contacts. read_openephys_binary additionally reads the structure.oebin to set device_channel_indices. As proposed in SpikeInterface/spikeinterface#4435, the oebin contains per-channel electrode_index metadata (added in neuropixels-pxi plugin v0.5.0, January 2023) that maps each binary file column to its electrode index. When available and non-zero, read_openephys_binary uses this for wiring. For older recordings where electrode_index is missing or all zeros, it falls back to identity wiring, which is correct because the binary .dat file is always written in channel-number order (as confirmed by Josh Siegle). The existing read_openephys is kept for backward compatibility and always sets identity wiring since it has no oebin.

Because both readers now derive contact_ids from the catalogue probe, this also fixes #394 (OpenEphys contact_ids inconsistent with SpikeGLX). The previous code reverse-engineered electrode IDs from positions, which produced different IDs than SpikeGLX for probes where OpenEphys positions don't exactly match the canonical geometry. @chrishalcrow identified the affected datasets in the existing test data (OE_Neuropix-PXI-NP-Ultra, OE_6.7_enabled_disabled_Neuropix-PXI, OE_Neuropix-PXI-QuadBase). A new consistency test verifies that for these and other datasets, the contact_ids from read_openephys are a subset of the catalogue probe's contact_ids.

Other changes:

• Each contact in read_openephys_binary is annotated with plugin_channel_key (the XML CHANNELS key, e.g. "CH0", "CH29"), distinct from neo's channel_name which comes from the oebin and uses different naming conventions.
• Two new test datasets (NP2014 single-shank, NP1032 4-shank) with paired settings.xml + structure.oebin files.
• There is an edge case described in Test data labeled NP1100 has electrode positions inconsistent with NP1100 catalogue geometry #407 which I am addressing here.

[alejoe91]

@h-mayorquin I reviewed this carefully and made som last changes.

• The new read_openephys was not loading ADC info anymore! I centralized the logic betwee spikeglx and openephys and added a check that this annotation exists in the tests
• Removed channel_name from probe info and contact annotation
• Renamed _slice_catalogue_probe to _slice_openephys_catalogue_probe
• Renamed plugin_channel_keys to settings_channel_keys
• Simplified a bit the logic in extracting electrode_index (we don't need the break + append(None) and then remove the Nones)

[alejoe91]

@jsiegle confirmed that electrode_index is left->right / bottom->top / left shank->right shank

[h-mayorquin]

@h-mayorquin I reviewed this carefully and made som last changes.

• The new read_openephys was not loading ADC info anymore! I centralized the logic betwee spikeglx and openephys and added a check that this annotation exists in the tests

Thanks

• Removed channel_name from probe info and contact annotation
  Make sense.
• Renamed _slice_catalogue_probe to _slice_openephys_catalogue_probe
  Yes, this is a better name.
• Renamed plugin_channel_keys to settings_channel_keys
  I think this is a better name as well.
• Simplified a bit the logic in extracting electrode_index (we don't need the break + append(None) and then remove the Nones)
  Thanks, this is something that I always have to clean and sometimes I forget. Agents produce overly defensive code.

This LGTM. I added Josh's comment on the code as well.

[alejoe91]

@h-mayorquin I further simplified the stream_name logic: it's not up to probeinterface to figure out the correct oe_stream_name, so let's just check for stream_name == folder_name and move the logic to spikeinterface

[alejoe91]

@h-mayorquin with the last commit I added a re-ordering of the ADC annotations (adc_group, adc_sample_order) to match the device_channel_index.

Exploring this a bit more, it seems that the channel order in the oebin file corresponds 1-1 to this CUSTOM_PARAMETER field of the STREAM in the settings file: https://github.com/h-mayorquin/probeinterface/blob/separate_open_ephys/tests/data/openephys/OE_OneBox-NP2014-binary/Record_Node_101/settings.xml#L58C4-L445C18

Maybe an even simpler solution would be to use that field to slice and re-order contacts?

[h-mayorquin]

Yes, we agreed in meeting that #409 makes more sense. A solution that uses less files is better.