Review fixes for PR #65: map_channel_to_electrode, LFP boundaries, STTC, ImpedanceMeasurements

[MilagrosMarin]

Overview

This PR proposes fixes to be incorporated into PR #65 (Changes to Ephys Schema by @judewerth) before it merges to main. The diff shows only the review corrections on top of Jude's changes.

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Fixes Applied

A — Lazy imports for neo, quantities, elephant

import neo, import quantities as pq, and from elephant.spike_train_correlation import spike_time_tiling_coefficient moved from module level to lazy imports inside STTC.make().

Why: These are optional heavy dependencies used only by STTC.make(). Importing at module level causes ephys_no_curation to fail entirely on any environment without these packages (HPC nodes, minimal containers, dev machines not running spike sorting) — breaking LFP, frame analysis, and everything else that depends on this module. Follows the same lazy-import pattern applied to spikeinterface in the workflow repo.

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B — map_channel_to_electrode: restricted fetch + conflict detection + edge case guards

# Before (unrestricted — fetches ALL probe configs):
electrode_mapping, channel_mapping = probe.ElectrodeConfig.Electrode.fetch("electrode", "channel_idx")

# After:
electrode_mapping, channel_mapping = (
    probe.ElectrodeConfig.Electrode & {"probe_type": probe_type}
).fetch("electrode", "channel_idx")

if len(electrode_mapping) == 0:
    raise ValueError(f"No electrode configuration found for probe_type='{probe_type}'...")

pairs = np.unique(np.column_stack([electrode_mapping, channel_mapping]), axis=0)
if len(pairs) != len(np.unique(pairs[:, 0])):
    raise ValueError("Conflicting channel-electrode mappings found ...")
electrode_mapping, channel_mapping = pairs[:, 0], pairs[:, 1]

Also replaced np.empty(num_electrodes, dtype=int) with np.full(num_electrodes, -1, dtype=int).

Why:

• The original fetch was unrestricted — pulled mappings from all probe configs regardless of probe_type. Silently wrong the moment a second probe type is added.
• probe_type is already in ElectrodeConfig.Electrode's PK (via -> ProbeType.Electrode), so no join through ElectrodeConfig is needed.
• np.unique deduplication handles multiple configs for the same probe type that share the same mapping. Conflicting mappings raise a ValueError explicitly.
• Empty fetch guard: if no ElectrodeConfig exists yet, the fetch returns empty arrays and np.column_stack would crash with a cryptic message. Added explicit check first.
• np.empty → np.full(..., -1): np.empty produces uninitialized memory for indices not covered by the config. Sentinel value -1 makes uncovered positions detectable rather than silently returning garbage.

Non-blocking suggestion for @judewerth: The return variable electrode_ids and the docstring Returns: electrodes (array-like)... are misleading when electrode_to_channel=True — in that direction the function returns channel indices, not electrode indices. Worth updating in a follow-up.

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C — LFP boundary trimming: elif bug for single-file sessions

# Before (elif skips end trim when session is in a single file):
if file_relpath == file_paths[0]:
    lfps = lfps[:, start_idx:]
elif file_relpath == file_paths[-1]:   # never runs when first == last
    lfps = lfps[:, :end_idx]

# After (two independent if blocks, single slice):
start_idx = 0
end_idx = lfps.shape[1]
is_first_file = file_relpath == file_paths[0]
is_last_file = file_relpath == file_paths[-1]
if is_first_file or is_last_file:
    file_start = datetime.strptime(...)  # parsed once
    if is_first_file:
        start_idx = int((key['start_time'] - file_start).total_seconds() * fs)
    if is_last_file:
        end_idx = int((key['end_time'] - file_start).total_seconds() * fs)
lfps = lfps[:, start_idx:end_idx]

Why: When a session lives entirely within one .rhd file, file_paths[0] == file_paths[-1]. The elif means only the start boundary is trimmed — sessions in a single file silently include LFP data beyond end_time.

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D — # REMOVE LATER comment in STTC.make()

Replaced with: # clip spike times to session duration to guard against edge-case spikes beyond end_time. The line itself is necessary — without it, neo.SpikeTrain raises when spike times exceed t_stop.

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E — ImpedanceMeasurements.make(): existence check before fetch

Moved if not (EphysSessionProbe & key) before fetch("port_id"). Previously a missing EphysSessionProbe would cause port_id.pop() to raise KeyError instead of the intended ValueError.

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Test plan

• Verify from element_array_ephys.ephys_no_curation import map_channel_to_electrode, get_probe_type succeeds without neo/elephant installed
• Verify map_channel_to_electrode returns correct electrode indices for a known session
• Verify LFP extraction for a session within a single .rhd file produces the correct duration
• Verify STTC.make() runs end-to-end for a spike-sorted session

🤖 Generated with Claude Code

[MilagrosMarin]

Recreating with correct base targeting judewerth:main.