From de879ef412fb8b20ca1ae19cb4f71b60f09368d7 Mon Sep 17 00:00:00 2001 From: Heberto Mayorquin Date: Wed, 11 Mar 2026 01:39:44 -0600 Subject: [PATCH 1/5] draft --- src/probeinterface/__init__.py | 1 + src/probeinterface/neuropixels_tools.py | 748 +++++++++++++++++++----- tests/test_io/test_openephys.py | 58 ++ 3 files changed, 654 insertions(+), 153 deletions(-) diff --git a/src/probeinterface/__init__.py b/src/probeinterface/__init__.py index 3317c798..f1bf432f 100644 --- a/src/probeinterface/__init__.py +++ b/src/probeinterface/__init__.py @@ -28,6 +28,7 @@ parse_spikeglx_snsGeomMap, get_saved_channel_indices_from_spikeglx_meta, read_openephys, + read_openephys_binary, get_saved_channel_indices_from_openephys_settings, ) from .utils import combine_probes diff --git a/src/probeinterface/neuropixels_tools.py b/src/probeinterface/neuropixels_tools.py index e575ce54..8bfa699f 100644 --- a/src/probeinterface/neuropixels_tools.py +++ b/src/probeinterface/neuropixels_tools.py @@ -1003,59 +1003,260 @@ def get_saved_channel_indices_from_spikeglx_meta(meta_file: str | Path) -> np.ar ## -def read_openephys( +def _parse_probe_info_from_openephys_settings( settings_file: str | Path, - stream_name: Optional[str] = None, - probe_name: Optional[str] = None, - serial_number: Optional[str] = None, + stream_name: str, fix_x_position_for_oe_5: bool = True, - raise_error: bool = True, -) -> Probe: +) -> dict: """ - Read probe positions from Open Ephys folder when using the Neuropix-PXI plugin. - The reader assumes that the NP_PROBE fields are available in the settings file. - Open Ephys versions 0.5.x and 0.6.x are supported: - * For version 0.6.x, the probe names are inferred from the STREAM field. Probe - information is then populated sequentially with the NP_PROBE fields. - * For version 0.5.x, STREAMs are not available. In this case, if multiple probes - are available, they are named sequentially based on the nodeId. E.g. "100.0", - "100.1". These substrings are used for selection. + Parse an Open Ephys settings.xml and extract info for one probe matching stream_name. + + Navigates the XML to find the Neuropixels processor, matches the stream name to a + probe, and extracts the probe part number, electrode selection, and annotation + metadata. No raw XML elements are returned. Parameters ---------- - settings_file : Path, str, or None - If more than one settings.xml file is in the folder structure, this argument - is required to indicate which settings file to use - stream_name : str or None - If more than one probe is used, the 'stream_name' indicates which probe to load base on the - stream. For example, if there are 3 probes ('ProbeA', 'ProbeB', ProbeC) and the stream_name is - contains the substring 'ProbeC' (e.g. 'my-stream-ProbeC'), then the probe associated with - ProbeC is returned. If this argument is used, the 'probe_name' and 'serial_number' must be None. - probe_name : str or None - If more than one probe is used, the 'probe_name' indicates which probe to load base on the - probe name (e.g. "ProbeB"). If this argument is used, the 'stream_name' and 'serial_number' - must be None. - serial_number : str or None - If more than one probe is used, the 'serial_number' indicates which probe to load base on the - serial number. If this argument is used, the 'stream_name' and 'probe_name' - must be None. - fix_x_position_for_oe_5: bool - The neuropixels PXI plugin in the open-ephys < 0.6.0 contains a bug in the y position. This option allow to fix it. - raise_error: bool - If True, any error would raise an exception. If False, None is returned. Default True - - Note - ---- - The electrode positions are only available when recording using the Neuropix-PXI plugin version >= 0.3.3 + settings_file : Path or str + Path to the Open Ephys settings.xml file. + stream_name : str + The stream name used to select which probe to extract. The probe is + selected by substring match against probe names derived from STREAM + elements, with a fallback to serial number matching. + fix_x_position_for_oe_5 : bool + Fix a y-position bug in the Neuropix-PXI plugin for Open Ephys < 0.6.0. + Default True. Returns ------- - probe : Probe object + probe_info : dict + Dict with keys: + - probe_part_number : str + - serial_number : str or None + - name : str + - slot, port, dock : str or None + - selected_electrode_indices : list of int, or None (Path A) + - contact_ids : list of str, or None (Path B) + """ + ET = import_safely("xml.etree.ElementTree") + tree = ET.parse(str(settings_file)) + root = tree.getroot() + + info_chain = root.find("INFO") + oe_version = parse(info_chain.find("VERSION").text) + + # Find the Neuropixels processor + neuropix_pxi_processor = None + onebox_processor = None + onix_processor = None + for signal_chain in root.findall("SIGNALCHAIN"): + for processor in signal_chain: + if "PROCESSOR" == processor.tag: + pname = processor.attrib["name"] + if "Neuropix-PXI" in pname: + neuropix_pxi_processor = processor + if "OneBox" in pname: + onebox_processor = processor + if "ONIX" in pname: + onix_processor = processor + + if neuropix_pxi_processor is None and onebox_processor is None and onix_processor is None: + raise ValueError("Open Ephys settings.xml has no Neuropix-PXI, OneBox, or ONIX processor.") + if neuropix_pxi_processor is not None: + assert onebox_processor is None, "Only one processor should be present" + processor = neuropix_pxi_processor + neuropix_pxi_version = parse(neuropix_pxi_processor.attrib["libraryVersion"]) + if neuropix_pxi_version < parse("0.3.3"): + raise ValueError("Electrode locations are available from Neuropix-PXI version 0.3.3") + if onebox_processor is not None: + assert neuropix_pxi_processor is None, "Only one processor should be present" + processor = onebox_processor + if onix_processor is not None: + processor = onix_processor + + if "NodeId" in processor.attrib: + node_id = processor.attrib["NodeId"] + elif "nodeId" in processor.attrib: + node_id = processor.attrib["nodeId"] + else: + node_id = None + + # Read STREAM fields if present (>=0.6.x) + stream_fields = processor.findall("STREAM") + if len(stream_fields) > 0: + has_streams = True + probe_names_used = [] + for stream_field in stream_fields: + stream = stream_field.attrib["name"] + if "ADC" in stream: + continue + stream = stream.replace("-AP", "").replace("-LFP", "") + if stream not in probe_names_used: + probe_names_used.append(stream) + else: + has_streams = False + probe_names_used = None + + if onix_processor is not None: + probe_names_used = [pn for pn in probe_names_used if "Probe" in pn] + + # Find NP_PROBE elements + editor = processor.find("EDITOR") + if oe_version < parse("0.9.0"): + np_probes = editor.findall("NP_PROBE") + else: + custom_parameters = editor.find("CUSTOM_PARAMETERS") + if onix_processor is not None: + possible_probe_names = ["NEUROPIXELSV1E", "NEUROPIXELSV1F", "NEUROPIXELSV2E"] + parent_np_probe = "" + for possible_probe_name in possible_probe_names: + parent_np_probe = custom_parameters.findall(possible_probe_name) + if len(parent_np_probe) > 0: + break + if possible_probe_name == "NEUROPIXELSV2E": + np_probes = [parent_np_probe[0].findall(f"PROBE{a}")[0] for a in range(2)] + else: + np_probes = [parent_np_probe[0]] + else: + np_probes = custom_parameters.findall("NP_PROBE") + + if len(np_probes) == 0: + raise ValueError("NP_PROBE field not found in settings") + + np_probes = [probe for probe in np_probes if probe.attrib.get("isEnabled", "1") == "1"] + if len(np_probes) == 0: + raise ValueError("No enabled probes found in settings") + + if not has_streams: + probe_names_used = [f"{node_id}.{i}" for i in range(len(np_probes))] + + if has_streams and len(np_probes) < len(probe_names_used): + raise ValueError(f"Not enough NP_PROBE entries ({len(np_probes)}) for probes: {probe_names_used}") + + # Match stream_name to a probe + np_probe = None + probe_name = None + for np_p, pn in zip(np_probes, probe_names_used): + if pn in stream_name: + np_probe = np_p + probe_name = pn + break + if np_probe is None: + for np_p, pn in zip(np_probes, probe_names_used): + serial = np_p.attrib.get("probe_serial_number") or np_p.attrib.get("probeSerialNumber", "") + if serial and serial in stream_name: + np_probe = np_p + probe_name = pn + break + if np_probe is None: + raise ValueError(f"Stream '{stream_name}' does not match any available probe: {probe_names_used}") + + # Extract probe info from the matched NP_PROBE element + probe_part_number = np_probe.attrib.get("probe_part_number") or np_probe.attrib.get("probePartNumber") + probe_serial_number = np_probe.attrib.get("probe_serial_number") or np_probe.attrib.get("probeSerialNumber") + + if "custom_probe_name" in np_probe.attrib and np_probe.attrib["custom_probe_name"] != probe_serial_number: + name = np_probe.attrib["custom_probe_name"] + else: + name = probe_name + + info = { + "probe_part_number": probe_part_number, + "serial_number": probe_serial_number, + "name": name, + "slot": np_probe.attrib.get("slot"), + "port": np_probe.attrib.get("port"), + "dock": np_probe.attrib.get("dock"), + "selected_electrode_indices": None, + "positions": None, + } + + # Electrode selection + selected_electrodes = np_probe.find("SELECTED_ELECTRODES") + if selected_electrodes is not None: + # ONIX plugin provides electrode indices directly as SELECTED_ELECTRODES attributes. + # These are indices into the full probe's electrode array. + info["selected_electrode_indices"] = [int(ei) for ei in selected_electrodes.attrib.values()] + else: + # Neuropix-PXI and OneBox plugins provide CHANNELS (channel keys like CH0, CH1, ...) + # with ELECTRODE_XPOS/ELECTRODE_YPOS giving the physical position of each channel. + # We extract the positions so the caller can match them against the catalogue probe. + channels = np_probe.find("CHANNELS") + channel_names = np.array(list(channels.attrib.keys())) + channel_ids = np.array([int(ch[2:]) for ch in channel_names]) + channel_order = np.argsort(channel_ids) + + channel_names = channel_names[channel_order] + channel_values = np.array(list(channels.attrib.values()))[channel_order] + + if all(":" in val for val in channel_values): + shank_ids = np.array([int(val.split(":")[1]) for val in channel_values]) + elif all("_" in val for val in channel_names): + shank_ids = np.array([int(val.split("_")[1]) for val in channel_names]) + else: + shank_ids = None + + electrode_xpos = np_probe.find("ELECTRODE_XPOS") + electrode_ypos = np_probe.find("ELECTRODE_YPOS") + if electrode_xpos is None or electrode_ypos is None: + raise ValueError("ELECTRODE_XPOS or ELECTRODE_YPOS is not available in settings!") + + xpos = np.array([float(electrode_xpos.attrib[ch]) for ch in channel_names]) + ypos = np.array([float(electrode_ypos.attrib[ch]) for ch in channel_names]) + positions = np.array([xpos, ypos]).T + + probe_features = _load_np_probe_features() + pt_metadata, _, _ = get_probe_metadata_from_probe_features(probe_features, probe_part_number) + shank_pitch = pt_metadata["shank_pitch_um"] + + # Fix y-position bug in OE < 0.6.0 for multi-shank probes + if fix_x_position_for_oe_5 and oe_version < parse("0.6.0") and shank_ids is not None: + positions[:, 1] = positions[:, 1] - shank_pitch * shank_ids + + # Normalize x so the first column starts at 0 + offset = np.min(positions[:, 0]) + if shank_ids is not None: + offset -= np.min(shank_ids) * shank_pitch + positions[:, 0] -= offset + + info["positions"] = positions + + return info + + +def _parse_openephys_settings( + settings_file: str | Path, + fix_x_position_for_oe_5: bool = True, + raise_error: bool = True, +) -> Optional[list[dict]]: """ + Parse an Open Ephys settings.xml and extract per-probe metadata. + + Returns a list of dicts, one per enabled probe, containing the probe_part_number, + serial_number, name, slot/port/dock, and electrode selection info needed to + build the probe from the catalogue. + Parameters + ---------- + settings_file : Path or str + Path to the Open Ephys settings.xml file. + fix_x_position_for_oe_5 : bool + Fix position bug in open-ephys < 0.6.0. + raise_error : bool + If True, raise on error. If False, return None. + + Returns + ------- + probes_info : list of dict, or None + Each dict contains: + - probe_part_number, serial_number, name, slot, port, dock + - selected_electrode_indices: list of int (from SELECTED_ELECTRODES), or None + - contact_ids: list of str (reverse-engineered from CHANNELS), or None + - channel_names: np.array of str, or None + - elec_ids, shank_ids, pt_metadata, mux_info: for legacy fallback + """ ET = import_safely("xml.etree.ElementTree") - # parse xml tree = ET.parse(str(settings_file)) root = tree.getroot() @@ -1122,7 +1323,7 @@ def read_openephys( probe_names_used = None if onix_processor is not None: - probe_names_used = [probe_name for probe_name in probe_names_used if "Probe" in probe_name] + probe_names_used = [pn for pn in probe_names_used if "Probe" in pn] # for Open Ephys version < 1.0 np_probes is in the EDITOR field. # for Open Ephys version >= 1.0 np_probes is in the CUSTOM_PARAMETERS field. @@ -1158,14 +1359,12 @@ def read_openephys( raise Exception("No enabled probes found in settings") return None - # read probes info # If STREAMs are not available, probes are sequentially named based on the node id if not has_streams: probe_names_used = [f"{node_id}.{stream_index}" for stream_index in range(len(np_probes))] # check consistency with stream names and other fields if has_streams: - # make sure we have at least as many NP_PROBE as the number of used probes if len(np_probes) < len(probe_names_used): if raise_error: raise Exception(f"Not enough NP_PROBE entries ({len(np_probes)}) for used probes: {probe_names_used}") @@ -1173,15 +1372,8 @@ def read_openephys( probe_features = _load_np_probe_features() - np_probes_info = [] - - # now load probe info from NP_PROBE fields - np_probes_info = [] + probes_info = [] for probe_idx, np_probe in enumerate(np_probes): - # selected_electrodes is the preferred way to instantiate the probe - # if this field is available, a full probe is created from the probe_part_number - # and then sliced using the selected electrodes. - # if not available, the xpos and ypos fields are used to create the probe slot = np_probe.attrib.get("slot") port = np_probe.attrib.get("port") dock = np_probe.attrib.get("dock") @@ -1192,40 +1384,37 @@ def read_openephys( pt_metadata, _, mux_info = get_probe_metadata_from_probe_features(probe_features, probe_part_number) - if selected_electrodes is not None: - selected_electrodes_values = selected_electrodes.attrib.values() - - num_shank = pt_metadata["num_shanks"] - contact_per_shank = pt_metadata["cols_per_shank"] * pt_metadata["rows_per_shank"] - - if num_shank == 1: - elec_ids = np.arange(contact_per_shank, dtype=int) - shank_ids = None - else: - elec_ids = np.concatenate([np.arange(contact_per_shank, dtype=int) for i in range(num_shank)]) - shank_ids = np.concatenate([np.zeros(contact_per_shank, dtype=int) + i for i in range(num_shank)]) - - full_probe = _make_npx_probe_from_description( - pt_metadata, probe_part_number, elec_ids, shank_ids, mux_info=mux_info - ) - - selected_electrode_indices = [int(electrode_index) for electrode_index in selected_electrodes_values] + # Assign probe name + if "custom_probe_name" in np_probe.attrib and np_probe.attrib["custom_probe_name"] != probe_serial_number: + name = np_probe.attrib["custom_probe_name"] + else: + name = probe_names_used[probe_idx] - sliced_probe = full_probe.get_slice(selection=selected_electrode_indices) + info = { + "probe_part_number": probe_part_number, + "serial_number": probe_serial_number, + "name": name, + "slot": slot, + "port": port, + "dock": dock, + "pt_metadata": pt_metadata, + "mux_info": mux_info, + "selected_electrode_indices": None, + "contact_ids": None, + "channel_names": None, + "elec_ids": None, + "shank_ids": None, + } - np_probe_dict = { - "pt_metadata": pt_metadata, - "serial_number": probe_serial_number, - "part_number": probe_part_number, - "mux_info": mux_info, - "probe": sliced_probe, - } + if selected_electrodes is not None: + # Newer plugin versions provide electrode indices directly + info["selected_electrode_indices"] = [int(ei) for ei in selected_electrodes.attrib.values()] else: + # Older plugin versions: reverse-engineer electrode IDs from positions channel_names = np.array(list(channels.attrib.keys())) channel_ids = np.array([int(ch[2:]) for ch in channel_names]) channel_order = np.argsort(channel_ids) - # sort channel_names and channel_values channel_names = channel_names[channel_order] channel_values = np.array(list(channels.attrib.values()))[channel_order] @@ -1255,30 +1444,22 @@ def read_openephys( # x offset so that the first column is at 0x offset = np.min(positions[:, 0]) - # if some shanks are not used, we need to adjust the offset if shank_ids is not None: offset -= np.min(shank_ids) * shank_pitch positions[:, 0] -= offset - # - y_pitch = pt_metadata[ - "electrode_pitch_vert_um" - ] # Vertical spacing between the centers of adjacent contacts - x_pitch = pt_metadata[ - "electrode_pitch_horz_um" - ] # Horizontal spacing between the centers of contacts within the same row + y_pitch = pt_metadata["electrode_pitch_vert_um"] + x_pitch = pt_metadata["electrode_pitch_horz_um"] number_of_columns = pt_metadata["cols_per_shank"] probe_stagger = ( pt_metadata["even_row_horz_offset_left_edge_to_leftmost_electrode_center_um"] - pt_metadata["odd_row_horz_offset_left_edge_to_leftmost_electrode_center_um"] ) num_shanks = pt_metadata["num_shanks"] - description = pt_metadata.get("description") elec_ids = [] for i, pos in enumerate(positions): - # Do not calculate contact ids if the model name is not known if description is None: elec_ids = None break @@ -1286,15 +1467,11 @@ def read_openephys( x_pos = pos[0] y_pos = pos[1] - # Adds a shift to rows in the staggered configuration is_row_staggered = np.mod(y_pos / y_pitch + 1, 2) == 1 row_stagger = probe_stagger if is_row_staggered else 0 - # Map the positions to the contacts ids shank_id = shank_ids[i] if num_shanks > 1 else 0 - # Electrode ids are computed from the positions of the electrodes. The computation - # is different for probes with one row of electrodes, or more than one. if x_pitch == 0: elec_id = int(number_of_columns * y_pos / y_pitch) else: @@ -1303,44 +1480,64 @@ def read_openephys( ) elec_ids.append(elec_id) - np_probe_dict = { - "shank_ids": shank_ids, - "elec_ids": elec_ids, - "channel_names": channel_names, - "pt_metadata": pt_metadata, - "slot": slot, - "port": port, - "dock": dock, - "serial_number": probe_serial_number, - "part_number": probe_part_number, - "mux_info": mux_info, - } - - # Sequentially assign probe names - if "custom_probe_name" in np_probe.attrib and np_probe.attrib["custom_probe_name"] != probe_serial_number: - name = np_probe.attrib["custom_probe_name"] - else: - name = probe_names_used[probe_idx] - np_probe_dict.update({"name": name}) - np_probes_info.append(np_probe_dict) + info["channel_names"] = channel_names + info["shank_ids"] = shank_ids + info["elec_ids"] = elec_ids + + # Build contact_ids from reverse-engineered electrode IDs + if elec_ids is not None: + shank_ids_iter = shank_ids if shank_ids is not None else [None] * len(elec_ids) + info["contact_ids"] = [ + _build_canonical_contact_id(eid, sid) for sid, eid in zip(shank_ids_iter, elec_ids) + ] + + probes_info.append(info) - # now select find the selected probe (if multiple) - if len(np_probes) > 1: + return probes_info + + +def _select_openephys_probe_info( + probes_info: list[dict], + stream_name: Optional[str] = None, + probe_name: Optional[str] = None, + serial_number: Optional[str] = None, + raise_error: bool = True, +) -> Optional[dict]: + """ + Select one probe's info dict from the list returned by `_parse_openephys_settings`. + + Parameters + ---------- + probes_info : list of dict + List of per-probe info dicts from `_parse_openephys_settings`. + stream_name : str or None + Stream name for selection. + probe_name : str or None + Probe name for selection. + serial_number : str or None + Serial number for selection. + raise_error : bool + If True, raise on error. If False, return None. + + Returns + ------- + info : dict or None + """ + probe_names_used = [p["name"] for p in probes_info] + + if len(probes_info) > 1: found = False - probe_names = [p["name"] for p in np_probes_info] if stream_name is not None: assert probe_name is None and serial_number is None, ( "Use one of 'stream_name', 'probe_name', " "or 'serial_number'" ) - # Here we have to check if the probe name or the serial number is in the stream name - # If both are present, e.g., the name contains the serial number, the first match is used. - for probe_idx, probe_info in enumerate(np_probes_info): + for probe_info in probes_info: if probe_info["name"] in stream_name: found = True break if not found: - for probe_idx, probe_info in enumerate(np_probes_info): + for probe_info in probes_info: if probe_info["serial_number"] in stream_name: found = True break @@ -1354,7 +1551,7 @@ def read_openephys( assert stream_name is None and serial_number is None, ( "Use one of 'stream_name', 'probe_name', " "or 'serial_number'" ) - for probe_idx, probe_info in enumerate(np_probes_info): + for probe_info in probes_info: if probe_info["name"] == probe_name: found = True break @@ -1366,12 +1563,12 @@ def read_openephys( assert stream_name is None and probe_name is None, ( "Use one of 'stream_name', 'probe_name', " "or 'serial_number'" ) - for probe_idx, probe_info in enumerate(np_probes_info): + for probe_info in probes_info: if probe_info["serial_number"] == str(serial_number): found = True break if not found: - np_serial_numbers = [p["serial_number"] for p in probe_info] + np_serial_numbers = [p["serial_number"] for p in probes_info] if raise_error: raise Exception( f"The provided {serial_number} is not in the available serial numbers: {np_serial_numbers}" @@ -1380,13 +1577,12 @@ def read_openephys( else: raise Exception( f"More than one probe found. Use one of 'stream_name', 'probe_name', or 'serial_number' " - f"to select the right probe.\nProbe names: {probe_names}" + f"to select the right probe.\nProbe names: {probe_names_used}" ) + return probe_info else: - # in case of a single probe, make sure it is consistent with optional - # stream_name, probe_name, or serial number - available_probe_name = np_probes_info[0]["name"] - available_serial_number = np_probes_info[0]["serial_number"] + available_probe_name = probes_info[0]["name"] + available_serial_number = probes_info[0]["serial_number"] if stream_name: if available_probe_name not in stream_name: @@ -1412,43 +1608,289 @@ def read_openephys( f"{available_serial_number}" ) return None - probe_idx = 0 + return probes_info[0] - np_probe_info = np_probes_info[probe_idx] - np_probe = np_probes[probe_idx] - probe = np_probe_info.get("probe") - if probe is None: - # check if subset of channels - shank_ids = np_probe_info["shank_ids"] - elec_ids = np_probe_info["elec_ids"] - pt_metadata = np_probe_info["pt_metadata"] - mux_info = np_probe_info["mux_info"] +def _slice_catalogue_probe(full_probe: Probe, probe_info: dict) -> Probe: + """ + Slice a full catalogue probe using the electrode selection from probe_info. - probe = _make_npx_probe_from_description( - pt_metadata, probe_part_number, elec_ids, shank_ids=shank_ids, mux_info=mux_info - ) + For SELECTED_ELECTRODES (newer plugin), uses the indices directly. + For CHANNELS (older plugin), matches reverse-engineered contact_ids to the catalogue. + Falls back to legacy `_make_npx_probe_from_description` if matching fails. + + Parameters + ---------- + full_probe : Probe + Full catalogue probe from `build_neuropixels_probe`. + probe_info : dict + Probe info dict from `_parse_openephys_settings`. + + Returns + ------- + probe : Probe + """ + if probe_info["selected_electrode_indices"] is not None: + return full_probe.get_slice(selection=probe_info["selected_electrode_indices"]) + + contact_ids = probe_info["contact_ids"] + if contact_ids is not None: + catalogue_ids = set(full_probe.contact_ids) + if all(cid in catalogue_ids for cid in contact_ids): + contact_id_to_index = {cid: i for i, cid in enumerate(full_probe.contact_ids)} + selected_indices = np.array([contact_id_to_index[cid] for cid in contact_ids]) + return full_probe.get_slice(selection=selected_indices) + else: + warnings.warn( + "Could not match reverse-engineered electrode IDs to catalogue probe. " + "Falling back to legacy probe construction." + ) + + # Legacy fallback + return _make_npx_probe_from_description( + probe_info["pt_metadata"], + probe_info["probe_part_number"], + probe_info["elec_ids"], + shank_ids=probe_info["shank_ids"], + mux_info=probe_info["mux_info"], + ) + + +def _annotate_openephys_probe(probe: Probe, probe_info: dict) -> None: + """ + Annotate a probe with metadata from the parsed settings info. + + Parameters + ---------- + probe : Probe + The probe to annotate (modified in place). + probe_info : dict + Probe info dict from `_parse_openephys_settings`. + """ + if probe_info["channel_names"] is not None: + probe.annotate_contacts(channel_name=probe_info["channel_names"]) + + probe.serial_number = probe_info["serial_number"] + probe.name = probe_info["name"] + probe.annotate(part_number=probe_info["probe_part_number"]) + + if probe_info["slot"] is not None: + probe.annotate(slot=probe_info["slot"]) + if probe_info["port"] is not None: + probe.annotate(port=probe_info["port"]) + if probe_info["dock"] is not None: + probe.annotate(dock=probe_info["dock"]) + + +def read_openephys( + settings_file: str | Path, + stream_name: Optional[str] = None, + probe_name: Optional[str] = None, + serial_number: Optional[str] = None, + fix_x_position_for_oe_5: bool = True, + raise_error: bool = True, +) -> Probe: + """ + Read probe positions from Open Ephys folder when using the Neuropix-PXI plugin. + The reader assumes that the NP_PROBE fields are available in the settings file. + Open Ephys versions 0.5.x and 0.6.x are supported: + * For version 0.6.x, the probe names are inferred from the STREAM field. Probe + information is then populated sequentially with the NP_PROBE fields. + * For version 0.5.x, STREAMs are not available. In this case, if multiple probes + are available, they are named sequentially based on the nodeId. E.g. "100.0", + "100.1". These substrings are used for selection. + + Parameters + ---------- + settings_file : Path, str, or None + If more than one settings.xml file is in the folder structure, this argument + is required to indicate which settings file to use + stream_name : str or None + If more than one probe is used, the 'stream_name' indicates which probe to load base on the + stream. For example, if there are 3 probes ('ProbeA', 'ProbeB', ProbeC) and the stream_name is + contains the substring 'ProbeC' (e.g. 'my-stream-ProbeC'), then the probe associated with + ProbeC is returned. If this argument is used, the 'probe_name' and 'serial_number' must be None. + probe_name : str or None + If more than one probe is used, the 'probe_name' indicates which probe to load base on the + probe name (e.g. "ProbeB"). If this argument is used, the 'stream_name' and 'serial_number' + must be None. + serial_number : str or None + If more than one probe is used, the 'serial_number' indicates which probe to load base on the + serial number. If this argument is used, the 'stream_name' and 'probe_name' + must be None. + fix_x_position_for_oe_5: bool + The neuropixels PXI plugin in the open-ephys < 0.6.0 contains a bug in the y position. This option allow to fix it. + raise_error: bool + If True, any error would raise an exception. If False, None is returned. Default True - if "channel_names" in np_probe_info: - probe.annotate_contacts(channel_name=np_probe_info["channel_names"]) + Note + ---- + The electrode positions are only available when recording using the Neuropix-PXI plugin version >= 0.3.3 + + Returns + ------- + probe : Probe object + + """ + probes_info = _parse_openephys_settings(settings_file, fix_x_position_for_oe_5, raise_error) + if probes_info is None: + return None + + probe_info = _select_openephys_probe_info(probes_info, stream_name, probe_name, serial_number, raise_error) + if probe_info is None: + return None + + full_probe = build_neuropixels_probe(probe_info["probe_part_number"]) + probe = _slice_catalogue_probe(full_probe, probe_info) + _annotate_openephys_probe(probe, probe_info) chans_saved = get_saved_channel_indices_from_openephys_settings(settings_file, stream_name=stream_name) if chans_saved is not None: probe = probe.get_slice(chans_saved) - probe.serial_number = np_probe_info["serial_number"] - probe.name = np_probe_info["name"] + probe.set_device_channel_indices(np.arange(probe.get_contact_count())) + return probe - probe.annotate( - part_number=np_probe_info["part_number"], - ) - if "slot" in np_probe_info: - probe.annotate(slot=np_probe_info["slot"]) - if "port" in np_probe_info: - probe.annotate(port=np_probe_info["port"]) - if "dock" in np_probe_info: - probe.annotate(dock=np_probe_info["dock"]) +def read_openephys_binary( + settings_file: str | Path, + oebin_file: str | Path, + stream_name: str, + fix_x_position_for_oe_5: bool = True, +) -> Probe: + """ + Read probe positions from an Open Ephys binary format recording, using both the + settings.xml for probe geometry and the structure.oebin file for channel ordering. + + This function builds the probe geometry from settings.xml (which describes all probes + in the experiment), selects the probe matching the given stream, then uses the oebin + file to validate the channel count against the binary data layout. + + This is the recommended reader for Open Ephys binary recordings when the caller + has both the settings.xml and structure.oebin available, which is always the case + for the binary format. The ``stream_name`` parameter is required because the + settings.xml contains all probes in a single file and the oebin contains all + streams; a stream name is needed to select the correct probe and stream. + + Parameters + ---------- + settings_file : Path or str + Path to the Open Ephys settings.xml file. This file is located at the + Record Node level (e.g. ``Record Node 102/settings.xml``) and contains + the full signal chain configuration including all probe geometries. + oebin_file : Path or str + Path to the structure.oebin JSON file. This file is located at the + recording level (e.g. ``experiment1/recording1/structure.oebin``) and + describes the binary data layout including channel count per stream. + stream_name : str + The stream name used to select which probe to load from settings.xml + and which continuous stream to match in the oebin file. This is typically + the neo stream name constructed as ``"Record Node 102#Neuropix-PXI-100.ProbeA-AP"``. + The probe is selected by substring match: if the probe name (e.g. ``"ProbeA"``) + appears anywhere in the stream_name, that probe is selected. + fix_x_position_for_oe_5 : bool + Fix a y-position bug present in the Neuropix-PXI plugin for Open Ephys < 0.6.0 + where multi-shank probe y-coordinates included an erroneous shank pitch offset. + Despite the parameter name, this corrects the y (not x) position. Default True. + + Returns + ------- + probe : Probe + The probe with ``device_channel_indices`` set to identity mapping. + + Raises + ------ + ValueError + If the settings.xml cannot be parsed, no matching probe is found, or + the oebin channel count does not match the probe contact count. + """ + # Parse settings.xml for this stream's probe + probe_info = _parse_probe_info_from_openephys_settings(settings_file, stream_name, fix_x_position_for_oe_5) + + # Build probe from catalogue and slice to selected electrodes + full_probe = build_neuropixels_probe(probe_info["probe_part_number"]) + + if probe_info["selected_electrode_indices"] is not None: + # ONIX plugin provides electrode indices directly as SELECTED_ELECTRODES. + # These are indices into the full probe's contact array. + probe = full_probe.get_slice(selection=probe_info["selected_electrode_indices"]) + elif probe_info["positions"] is not None: + # Neuropix-PXI and OneBox plugins provide channel positions via + # CHANNELS + ELECTRODE_XPOS/ELECTRODE_YPOS. Match these positions against the + # catalogue probe to find which electrodes are active. + xml_positions = probe_info["positions"] + catalogue_positions = full_probe.contact_positions + + matched_indices = [] + for xml_pos in xml_positions: + distances = np.sum(np.abs(catalogue_positions - xml_pos), axis=1) + best_index = np.argmin(distances) + matched_indices.append(best_index) + + matched_indices = np.array(matched_indices) + + # Validate: all matches should be exact (within floating point tolerance) + # and each XML position should match a unique catalogue contact + max_distance = max( + np.sum(np.abs(catalogue_positions[matched_indices[i]] - xml_positions[i])) + for i in range(len(matched_indices)) + ) + n_unique = len(np.unique(matched_indices)) + + if max_distance > 0.1 or n_unique != len(matched_indices): + raise ValueError( + f"Could not match XML electrode positions to catalogue probe '{probe_info['probe_part_number']}'. " + f"Max position distance: {max_distance:.2f} um, " + f"unique matches: {n_unique}/{len(matched_indices)}. " + f"The probe part number in settings.xml may be incorrect, or the probe model " + f"may not be in the catalogue." + ) + + probe = full_probe.get_slice(selection=matched_indices) + else: + raise ValueError( + f"No electrode selection found in settings.xml for probe '{probe_info['name']}'. " + f"Expected either SELECTED_ELECTRODES or CHANNELS with ELECTRODE_XPOS/ELECTRODE_YPOS." + ) + + # Annotate + probe.serial_number = probe_info["serial_number"] + probe.name = probe_info["name"] + probe.annotate(part_number=probe_info["probe_part_number"]) + for attr in ("slot", "port", "dock"): + if probe_info[attr] is not None: + probe.annotate(**{attr: probe_info[attr]}) + + # Apply saved channel subsetting + chans_saved = get_saved_channel_indices_from_openephys_settings(settings_file, stream_name=stream_name) + if chans_saved is not None: + probe = probe.get_slice(chans_saved) + + # Read oebin and validate channel count + oebin_file = Path(oebin_file) + with open(oebin_file, "r") as f: + oebin = json.load(f) + + continuous_streams = oebin.get("continuous", []) + matched_stream = None + for cs in continuous_streams: + folder_name = cs.get("folder_name", "") + if stream_name in folder_name or folder_name in stream_name: + matched_stream = cs + break + + if matched_stream is None: + available = [cs.get("folder_name", "unknown") for cs in continuous_streams] + raise ValueError(f"Could not find matching stream in oebin file. Available streams: {available}") + + num_channels = matched_stream.get("num_channels", 0) + num_contacts = probe.get_contact_count() + if num_channels != num_contacts and num_channels > 0: + raise ValueError( + f"Channel count mismatch: oebin has {num_channels} channels but probe has {num_contacts} contacts." + ) + + probe.set_device_channel_indices(np.arange(probe.get_contact_count())) return probe diff --git a/tests/test_io/test_openephys.py b/tests/test_io/test_openephys.py index 37002358..eae0c796 100644 --- a/tests/test_io/test_openephys.py +++ b/tests/test_io/test_openephys.py @@ -5,6 +5,8 @@ import pytest from probeinterface import read_openephys +from probeinterface.neuropixels_tools import _parse_openephys_settings, _select_openephys_probe_info +from probeinterface.neuropixels_tools import _slice_catalogue_probe, build_neuropixels_probe from probeinterface.testing import validate_probe_dict data_path = Path(__file__).absolute().parent.parent / "data" / "openephys" @@ -355,6 +357,62 @@ def test_onix_np2(): assert probe_1.get_shank_count() == 4 +def _build_probe_from_settings(settings_file, **kwargs): + """Helper: parse settings, select probe, build from catalogue, slice.""" + probes_info = _parse_openephys_settings(settings_file) + info = _select_openephys_probe_info(probes_info, **kwargs) + full_probe = build_neuropixels_probe(info["probe_part_number"]) + return _slice_catalogue_probe(full_probe, info) + + +def test_build_openephys_probe_no_wiring(): + # Path A (SELECTED_ELECTRODES): ONIX dataset + probe_a = _build_probe_from_settings(data_path / "OE_ONIX-NP" / "settings_bankA.xml") + assert probe_a is not None + assert probe_a.device_channel_indices is None + + # Path B (CHANNELS): Neuropix-PXI dataset + probe_b = _build_probe_from_settings(data_path / "OE_Neuropix-PXI" / "settings.xml") + assert probe_b is not None + assert probe_b.device_channel_indices is None + + +def test_build_openephys_probe_uses_catalogue(): + # Path A (SELECTED_ELECTRODES): OE 1.0 dataset + probe_a = _build_probe_from_settings( + data_path / "OE_1.0_Neuropix-PXI-multi-probe" / "settings.xml", probe_name="ProbeA" + ) + assert probe_a is not None + for cid in probe_a.contact_ids: + assert cid.startswith("e") or cid.startswith("s"), f"Unexpected contact_id format: {cid}" + + # Path B (CHANNELS): NP2 dataset (single shank, canonical IDs should be "eN") + probe_b = _build_probe_from_settings(data_path / "OE_Neuropix-PXI" / "settings.xml") + assert probe_b is not None + for cid in probe_b.contact_ids: + assert cid.startswith("e") or cid.startswith("s"), f"Unexpected contact_id format: {cid}" + + +def test_read_openephys_backward_compatible(): + # Verify read_openephys still produces valid probes with device_channel_indices set + # Path B dataset + probe = read_openephys(data_path / "OE_Neuropix-PXI" / "settings.xml") + probe_dict = probe.to_dict(array_as_list=True) + validate_probe_dict(probe_dict) + assert probe.device_channel_indices is not None + assert len(probe.device_channel_indices) == probe.get_contact_count() + assert np.array_equal(probe.device_channel_indices, np.arange(probe.get_contact_count())) + + # Path A dataset + probe_a = read_openephys( + data_path / "OE_1.0_Neuropix-PXI-multi-probe" / "settings.xml", probe_name="ProbeA" + ) + probe_dict = probe_a.to_dict(array_as_list=True) + validate_probe_dict(probe_dict) + assert probe_a.device_channel_indices is not None + assert np.array_equal(probe_a.device_channel_indices, np.arange(probe_a.get_contact_count())) + + if __name__ == "__main__": # test_multiple_probes() # test_NP_Ultra() From 56be30e237375539817a29da132f0365a84740b7 Mon Sep 17 00:00:00 2001 From: Heberto Mayorquin Date: Wed, 11 Mar 2026 11:26:28 -0600 Subject: [PATCH 2/5] new test and bette error message --- src/probeinterface/neuropixels_tools.py | 75 +- .../experiment1/recording1/structure.oebin | 8105 ++++++++ .../Record_Node_101/settings.xml | 493 + .../experiment4/recording2/structure.oebin | 15495 ++++++++++++++++ .../Record_Node_101/settings.xml | 1309 ++ tests/test_io/test_openephys.py | 181 +- 6 files changed, 25633 insertions(+), 25 deletions(-) create mode 100644 tests/data/openephys/OE_Neuropix-PXI-NP1-binary/Record_Node_101/experiment1/recording1/structure.oebin create mode 100644 tests/data/openephys/OE_Neuropix-PXI-NP1-binary/Record_Node_101/settings.xml create mode 100644 tests/data/openephys/OE_Neuropix-PXI-NP2-4shank-binary/Record_Node_101/experiment4/recording2/structure.oebin create mode 100644 tests/data/openephys/OE_Neuropix-PXI-NP2-4shank-binary/Record_Node_101/settings.xml diff --git a/src/probeinterface/neuropixels_tools.py b/src/probeinterface/neuropixels_tools.py index 8bfa699f..0afe015d 100644 --- a/src/probeinterface/neuropixels_tools.py +++ b/src/probeinterface/neuropixels_tools.py @@ -1183,17 +1183,17 @@ def _parse_probe_info_from_openephys_settings( # with ELECTRODE_XPOS/ELECTRODE_YPOS giving the physical position of each channel. # We extract the positions so the caller can match them against the catalogue probe. channels = np_probe.find("CHANNELS") - channel_names = np.array(list(channels.attrib.keys())) - channel_ids = np.array([int(ch[2:]) for ch in channel_names]) + plugin_channel_keys = np.array(list(channels.attrib.keys())) + channel_ids = np.array([int(ch[2:]) for ch in plugin_channel_keys]) channel_order = np.argsort(channel_ids) - channel_names = channel_names[channel_order] + plugin_channel_keys = plugin_channel_keys[channel_order] channel_values = np.array(list(channels.attrib.values()))[channel_order] if all(":" in val for val in channel_values): shank_ids = np.array([int(val.split(":")[1]) for val in channel_values]) - elif all("_" in val for val in channel_names): - shank_ids = np.array([int(val.split("_")[1]) for val in channel_names]) + elif all("_" in val for val in plugin_channel_keys): + shank_ids = np.array([int(val.split("_")[1]) for val in plugin_channel_keys]) else: shank_ids = None @@ -1202,8 +1202,8 @@ def _parse_probe_info_from_openephys_settings( if electrode_xpos is None or electrode_ypos is None: raise ValueError("ELECTRODE_XPOS or ELECTRODE_YPOS is not available in settings!") - xpos = np.array([float(electrode_xpos.attrib[ch]) for ch in channel_names]) - ypos = np.array([float(electrode_ypos.attrib[ch]) for ch in channel_names]) + xpos = np.array([float(electrode_xpos.attrib[ch]) for ch in plugin_channel_keys]) + ypos = np.array([float(electrode_ypos.attrib[ch]) for ch in plugin_channel_keys]) positions = np.array([xpos, ypos]).T probe_features = _load_np_probe_features() @@ -1221,6 +1221,7 @@ def _parse_probe_info_from_openephys_settings( positions[:, 0] -= offset info["positions"] = positions + info["plugin_channel_keys"] = plugin_channel_keys return info @@ -1839,7 +1840,8 @@ def read_openephys_binary( if max_distance > 0.1 or n_unique != len(matched_indices): raise ValueError( - f"Could not match XML electrode positions to catalogue probe '{probe_info['probe_part_number']}'. " + f"Could not match XML electrode positions to catalogue probe '{probe_info['probe_part_number']}' " + f"in settings '{settings_file}'. " f"Max position distance: {max_distance:.2f} um, " f"unique matches: {n_unique}/{len(matched_indices)}. " f"The probe part number in settings.xml may be incorrect, or the probe model " @@ -1849,7 +1851,7 @@ def read_openephys_binary( probe = full_probe.get_slice(selection=matched_indices) else: raise ValueError( - f"No electrode selection found in settings.xml for probe '{probe_info['name']}'. " + f"No electrode selection found in '{settings_file}' for probe '{probe_info['name']}'. " f"Expected either SELECTED_ELECTRODES or CHANNELS with ELECTRODE_XPOS/ELECTRODE_YPOS." ) @@ -1860,6 +1862,8 @@ def read_openephys_binary( for attr in ("slot", "port", "dock"): if probe_info[attr] is not None: probe.annotate(**{attr: probe_info[attr]}) + if probe_info.get("plugin_channel_keys") is not None: + probe.annotate_contacts(plugin_channel_key=probe_info["plugin_channel_keys"]) # Apply saved channel subsetting chans_saved = get_saved_channel_indices_from_openephys_settings(settings_file, stream_name=stream_name) @@ -1881,16 +1885,59 @@ def read_openephys_binary( if matched_stream is None: available = [cs.get("folder_name", "unknown") for cs in continuous_streams] - raise ValueError(f"Could not find matching stream in oebin file. Available streams: {available}") + raise ValueError( + f"Could not find stream matching '{stream_name}' in oebin file '{oebin_file}'. " + f"Available streams: {available}" + ) - num_channels = matched_stream.get("num_channels", 0) + oebin_channels = matched_stream.get("channels", []) num_contacts = probe.get_contact_count() - if num_channels != num_contacts and num_channels > 0: + + # Extract electrode_index metadata from oebin channels. + # This was added in neuropixels-pxi plugin v0.5.0 (January 2023). + oebin_electrode_indices = [] + for ch in oebin_channels: + electrode_index = None + for m in ch.get("channel_metadata", []): + if m.get("name") == "electrode_index": + electrode_index = m["value"][0] + break + oebin_electrode_indices.append(electrode_index) + + # Filter out non-electrode channels (e.g. AP_SYNC) that lack electrode_index + electrode_channel_indices = [i for i, ei in enumerate(oebin_electrode_indices) if ei is not None] + oebin_electrode_indices = [oebin_electrode_indices[i] for i in electrode_channel_indices] + + if len(oebin_electrode_indices) != num_contacts: raise ValueError( - f"Channel count mismatch: oebin has {num_channels} channels but probe has {num_contacts} contacts." + f"Channel count mismatch: oebin '{oebin_file}' has {len(oebin_electrode_indices)} electrode channels " + f"but probe from settings '{settings_file}' has {num_contacts} contacts." ) - probe.set_device_channel_indices(np.arange(probe.get_contact_count())) + # Check if electrode_index values are valid (not all zeros). + # All-zero values occur in recordings from neuropixels-pxi < 0.5.0. + has_valid_electrode_indices = not all(ei == 0 for ei in oebin_electrode_indices) + + if has_valid_electrode_indices: + # Map each probe contact to its binary file column using electrode_index. + electrode_index_to_column = {ei: col for col, ei in enumerate(oebin_electrode_indices)} + device_channel_indices = np.zeros(num_contacts, dtype=int) + for i, contact_id in enumerate(probe.contact_ids): + electrode_index = int(contact_id.split("e")[-1]) + if electrode_index not in electrode_index_to_column: + warnings.warn( + f"Contact {contact_id} has electrode_index {electrode_index} not found in oebin. " + f"Falling back to identity wiring." + ) + device_channel_indices = np.arange(num_contacts) + break + device_channel_indices[i] = electrode_index_to_column[electrode_index] + else: + # Fallback: identity wiring. The binary .dat file is written in channel-number order + # (confirmed in https://github.com/open-ephys-plugins/neuropixels-pxi/issues/39). + device_channel_indices = np.arange(num_contacts) + + probe.set_device_channel_indices(device_channel_indices) return probe diff --git a/tests/data/openephys/OE_Neuropix-PXI-NP1-binary/Record_Node_101/experiment1/recording1/structure.oebin b/tests/data/openephys/OE_Neuropix-PXI-NP1-binary/Record_Node_101/experiment1/recording1/structure.oebin new file mode 100644 index 00000000..17532415 --- /dev/null +++ b/tests/data/openephys/OE_Neuropix-PXI-NP1-binary/Record_Node_101/experiment1/recording1/structure.oebin @@ -0,0 +1,8105 @@ +{ + "GUI version": "1.0.1", + "continuous": [ + { + "folder_name": "Neuropix-PXI-100.ProbeA/", + "sample_rate": 30000.0, + "source_processor_name": "Neuropix-PXI", + "source_processor_id": 100, + "stream_name": "ProbeA", + "recorded_processor": "Record Node", + "recorded_processor_id": 101, + "num_channels": 384, + "channels": [ + { + "channel_name": "CH0", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 0 + ] + } + ] + }, + { + "channel_name": "CH1", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 1 + ] + } + ] + }, + { + "channel_name": "CH2", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 2 + ] + } + ] + }, + { + "channel_name": "CH3", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 3 + ] + } + ] + }, + { + "channel_name": "CH4", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 4 + ] + } + ] + }, + { + "channel_name": "CH5", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 5 + ] + } + ] + }, + { + "channel_name": "CH6", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 6 + ] + } + ] + }, + { + "channel_name": "CH7", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 7 + ] + } + ] + }, + { + "channel_name": "CH8", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 8 + ] + } + ] + }, + { + "channel_name": "CH9", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 9 + ] + } + ] + }, + { + "channel_name": "CH10", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 10 + ] + } + ] + }, + { + "channel_name": "CH11", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 11 + ] + } + ] + }, + { + "channel_name": "CH12", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 12 + ] + } + ] + }, + { + "channel_name": "CH13", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 13 + ] + } + ] + }, + { + "channel_name": "CH14", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 14 + ] + } + ] + }, + { + "channel_name": "CH15", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 15 + ] + } + ] + }, + { + "channel_name": "CH16", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 16 + ] + } + ] + }, + { + "channel_name": "CH17", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 17 + ] + } + ] + }, + { + "channel_name": "CH18", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 18 + ] + } + ] + }, + { + "channel_name": "CH19", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 19 + ] + } + ] + }, + { + "channel_name": "CH20", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 20 + ] + } + ] + }, + { + "channel_name": "CH21", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 21 + ] + } + ] + }, + { + "channel_name": "CH22", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 22 + ] + } + ] + }, + { + "channel_name": "CH23", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 23 + ] + } + ] + }, + { + "channel_name": "CH24", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 24 + ] + } + ] + }, + { + "channel_name": "CH25", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 25 + ] + } + ] + }, + { + "channel_name": "CH26", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 26 + ] + } + ] + }, + { + "channel_name": "CH27", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 27 + ] + } + ] + }, + { + "channel_name": "CH28", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 28 + ] + } + ] + }, + { + "channel_name": "CH29", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 29 + ] + } + ] + }, + { + "channel_name": "CH30", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 30 + ] + } + ] + }, + { + "channel_name": "CH31", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 31 + ] + } + ] + }, + { + "channel_name": "CH32", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 32 + ] + } + ] + }, + { + "channel_name": "CH33", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 33 + ] + } + ] + }, + { + "channel_name": "CH34", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 34 + ] + } + ] + }, + { + "channel_name": "CH35", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 35 + ] + } + ] + }, + { + "channel_name": "CH36", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 36 + ] + } + ] + }, + { + "channel_name": "CH37", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 37 + ] + } + ] + }, + { + "channel_name": "CH38", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 38 + ] + } + ] + }, + { + "channel_name": "CH39", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 39 + ] + } + ] + }, + { + "channel_name": "CH40", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 40 + ] + } + ] + }, + { + "channel_name": "CH41", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 41 + ] + } + ] + }, + { + "channel_name": "CH42", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 42 + ] + } + ] + }, + { + "channel_name": "CH43", + "description": 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"value": [ + 80 + ] + } + ] + }, + { + "channel_name": "CH129", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 81 + ] + } + ] + }, + { + "channel_name": "CH130", + "description": "Neuropixels electrode", + "identifier": "neuropixels.electrode", + "history": "Neuropix-PXI -> Neuropixels CAR -> Record Node", + "bit_volts": 0.1949999928, + "units": "uV", + "type": 0, + "channel_metadata": [ + { + "name": "electrode_index", + "description": "Electrode index for this channel", + "identifier": "neuropixels.electrode_index", + "type": "uint16", + "length": 1, + "value": [ + 82 + ] + } + ] + }, + { + "channel_name": "CH131", + 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