ibl_alignment_gui.loaders.data_loader

Classes

`DataLoader`	Abstract base class for loading processed data for the ibl_alignment_gui.
`DataLoaderLocal`	Data loader using local file system.
`DataLoaderOne`	Data loader using ONE.
`FeatureLoader`	Abstract base class for loading ephys atlas features.
`FeatureLoaderLocal`	Feature loader using the local file system.
`FeatureLoaderOne`	Feature loader using ONE.
`SpikeGLXLoader`	Abstract base class for loading SpikeGLX metadata and AP band snippets.
`SpikeGLXLoaderLocal`	SpikeGLX loader using local file system.
`SpikeGLXLoaderOne`	SpikeGLX loader using ONE.

class ibl_alignment_gui.loaders.data_loader.DataLoader[source] 

Bases: ABC

Abstract base class for loading processed data for the ibl_alignment_gui.

Loads spikesorted and raw ephys data.

Subclasses must implement the follow abstract methods: - load_passive_data - load_raw_passive_data - load_ephys_data - load_spikes_data

filter_raw_by_chns(data)[source] 

Filter ephys data to only include data relevant to channels present on selected shank.

Parameters:: data (dict) – Raw ephys data
Returns:: data – Filtered ephys data
Return type:: Bunch

filter_spikes_by_chns(spikes, clusters, channels)[source] 

Filter spikes to only include data relevant to channels present on selected shank.

Return type:

tuple[Bunch[str, Any], Bunch[str, Any], Bunch[str, Any]]

Returns:

spikes (Bunch) – Filtered spikes data
clusters (Bunch) – Filtered clusters data
channels (Bunch) – Filtered channels data

static filter_spikes_by_fr(spikes, clusters, min_fr=0.013888888888888888)[source] 

Remove low-firing clusters and filter spikes accordingly.

Parameters:

spikes (Bunch) – Spike data.
clusters (Bunch) – Cluster data.
min_fr (float) – Minimum firing rate in Hz.

Return type:

tuple[Bunch[str, Any], Bunch[str, Any]]

Returns:

spikes (Bunch) – Spikes data above fr threshold
clusters (Bunch) – Clusters data above fr threshold

get_data(shank_sites)[source] 

Load all relevant data associated with the probe.

Parameters:: shank_sites (Bunch) – A Bunch object containing the channels that correspond to the shank
Returns:: data – A Bunch object containing spikes, clusters, channels, RMS and PSD data, and passive stimulus data.
Return type:: Bunch

get_passive_data()[source] 

Load passive visual stimulus data including RF map, visual stimuli, and gabor events.

Return type:

tuple[Bunch[str, Any], Bunch[str, Any], Bunch[str, Any]]

Returns:

rf_data (Bunch) – RF map data including frames.
stim_data (Bunch) – Visual stimulus data.
vis_stim (Bunch) – Gabor event data for left and right gabors.

get_psd_data(alf_object)[source] 

Load power spectral density data for specified band.

Only returns data on channels present on selected shank.

Parameters:: alf_object (str) – The alf object to load
Returns:: psd_data – PSD data
Return type:: Bunch

get_rms_data(alf_object)[source] 

Load RMS data for specified band.

Only returns data on channels present on selected shank.

Parameters:: alf_object (str) – The alf object to load
Returns:: rms_data – RMS data
Return type:: Bunch

get_spikes_data()[source] 

Load spike sorting data and optionally filter by minimum firing rate threshold.

Only returns data on channels present on selected shank.

Return type:

tuple[Bunch[str, Any], Bunch[str, Any], Bunch[str, Any]]

Returns:

spikes (Bunch) – spikes data
clusters (Bunch) – clusters data
channels (Bunch) – channels data

static load_data(load_function, *args, raise_message=None, raise_exception=(<class 'one.alf.exceptions.ALFObjectNotFound'>, <class 'one.alf.exceptions.ALFMultipleCollectionsFound'>), raise_error=False, **kwargs)[source] 

Safely load data using a provided function.

Parameters:

load_function (Callable) – Function to load the data (e.g., ONE or alfio).
args (tuple) – Arguments for the loading function.
raise_message (str or None) – Message to log if an exception is raised.
raise_exception (Exception or ALFObjectNotFound) – Type of exception to catch.
raise_error (bool) – Whether to raise the exception after logging.

Returns:

The loaded data with an ‘exists’ flag.

Return type:

Bunch

abstractmethod load_ephys_data(alf_object, **kwargs)[source] 

Abstract method to load ephys data.

Return type:: Bunch[str, Any]

abstractmethod load_passive_data(alf_object, **kwargs)[source] 

Abstract method to load passive data.

Return type:: Bunch[str, Any]

abstractmethod load_raw_passive_data(alf_object, **kwargs)[source] 

Abstract method to load raw passive data.

Return type:: Bunch[str, Any]

abstractmethod load_spikes_data(alf_object, attributes, **kwargs)[source] 

Abstract method to load spike sorting data.

Return type:: Bunch[str, Any]

class ibl_alignment_gui.loaders.data_loader.DataLoaderLocal(data_paths)[source] 

Bases: DataLoader

Data loader using local file system.

Data are loaded from files on disk, from the dataset paths resolved from the session yaml.

Parameters:: data_paths (DatasetPaths) – The resolved dataset paths for the probe, holding the spike sorting, processed ephys, task, raw task and raw ephys directories.

get_passive_data()[source] 

Load passive data from local path.

Only attempts to load if both task_path and raw_task_path are defined.

Return type:: Bunch or None

load_ephys_data(alf_object, **kwargs)[source] 

Load ephys data from local path.

Return type:: Bunch

load_passive_data(alf_object, **kwargs)[source] 

Load passive data from local path.

Return type:: Bunch

load_raw_passive_data(alf_object, **kwargs)[source] 

Load raw passive data from local path.

Return type:: Bunch or None

load_spikes_data(alf_object, attributes, **kwargs)[source] 

Load spike sorting data from local path.

Return type:: Bunch

property spike_sorting_path: Path 

Return the path to the folder holding the spike sorting data.

Returns:: The path to the spike sorting folder.
Return type:: Path

class ibl_alignment_gui.loaders.data_loader.DataLoaderOne(insertion, one, session_path=None, spike_collection=None)[source] 

Bases: DataLoader

Data loader using ONE.

Data are downloaded using Alyx/ ONE.

Parameters:

insertion (dict) – Dictionary representing a probe insertion (must include ‘session’ and ‘name’).
one (ONE) – An ONE instance used to access data.
session_path (Path or None) – Path to the session folder. If None, it is resolved using the eid via one.eid2path.
spike_collection (str or None) – Spike sorting algorithm to load (e.g. ‘pykilosort’, ‘iblsorter’).

get_spike_sorting_path()[source] 

Determine the path to the spike sorting output.

Returns:: probe_path – A Path to the spike sorting folder for the probe.
Return type:: Path

load_ephys_data(alf_object, **kwargs)[source] 

Load ephys data using ONE.

Return type:: Bunch

load_passive_data(alf_object, **kwargs)[source] 

Load passive data using ONE.

Return type:: Bunch

load_raw_passive_data(alf_object, **kwargs)[source] 

Load raw passive data using ONE.

Return type:: Bunch

load_spikes_data(alf_object, attributes, **kwargs)[source] 

Load spike sorting data using ONE.

Return type:: Bunch

property spike_sorting_path: Path 

Return the path to the folder holding the spike sorting data.

Returns:: The path to the spike sorting folder.
Return type:: Path

class ibl_alignment_gui.loaders.data_loader.FeatureLoader[source] 

Bases: ABC

Abstract base class for loading ephys atlas features.

abstractmethod load_features(shank_sites=None)[source] 

Abstract method to load ephys atlas features.

Parameters:: shank_sites (Bunch or None) – The sites for the shank being loaded (see GeometryLoader.get_sites_for_shank()). When given, implementations that read a combined multi-shank file use it to keep only this shank’s channels.
Return type:: Bunch[str, Any]

class ibl_alignment_gui.loaders.data_loader.FeatureLoaderLocal(features_path)[source] 

Bases: FeatureLoader

Feature loader using the local file system.

Mirrors FeatureLoaderOne but reads a single per-channel feature parquet from disk instead of downloading the ephys-atlas feature table via ONE. Used in offline/yaml mode where the features file is supplied directly (e.g. by the local channel-prediction plugin dialog or the launcher script).

Parameters:: features_path (Path) – Path to a per-channel features parquet file (one row per channel).

load_features(shank_sites=None)[source] 

Load the per-channel features parquet from disk.

A single features file may hold every channel of a multi-shank probe. When shank_sites is given, the rows are split down to this shank by matching the file’s channel column against shank_sites['raw_ind'] (the raw-data channel indices for the shank). For a single-shank file (or a file already restricted to this shank) this is a no-op.

Parameters:: shank_sites (Bunch or None) – The sites for the shank being loaded (see GeometryLoader.get_sites_for_shank()). When None the full file is returned.
Returns:: feature_data – A Bunch with df (the features DataFrame) and exists=True if the file was found and non-empty, otherwise Bunch(exists=False).
Return type:: Bunch

class ibl_alignment_gui.loaders.data_loader.FeatureLoaderOne(insertion, one, feature_version, multi_area=False)[source] 

Bases: FeatureLoader

Feature loader using ONE.

Loads feature from ephys feature table.

download_features(project, feature, save_path)[source] 

Download the latest ephys atlas features from S3.

Parameters:

project (str) – The project name
feature (str) – The feature version
save_path (Path) – A path to save the downloaded file

Return type:

None

load_dataframe(project, feature, save_path)[source] 

Load the ephys-atlas feature table filtered to this insertion’s pid.

Parameters:

project (str) – The project name.
feature (str) – The feature version label.
save_path (Path) – Directory under which the <project>/<feature> tables are stored.

Returns:

The feature table rows for this insertion’s pid.

Return type:

pd.DataFrame

load_features(shank_sites=None)[source] 

Load ephys atlas features from ONE.

Parameters:: shank_sites (Bunch or None) – Unused here — the ONE table is already filtered to this insertion’s pid. Accepted to keep the FeatureLoader interface uniform across loaders.
Returns:: feature_data – A Bunch containing a dataFrame containing ephys atlas features for the probe.
Return type:: Bunch

read_full_dataframe(project, feature, save_path)[source] 

Read the full ephys-atlas feature table for all insertions, downloading if needed.

Parameters:

project (str) – The project name.
feature (str) – The feature version label.
save_path (Path) – Directory under which the <project>/<feature> tables are stored.

Returns:

The full feature table across all insertions, or an empty frame if the tables are not cached and ephysatlas is unavailable to download them.

Return type:

pd.DataFrame

class ibl_alignment_gui.loaders.data_loader.SpikeGLXLoader(save_path=None)[source] 

Bases: ABC

Abstract base class for loading SpikeGLX metadata and AP band snippets.

Subclasses must implement the follow abstract methods: - load_meta_data - load_ap_data

Parameters:: save_path (Path or None) – Directory where cached snippet data will be saved.

get_meta_data()[source] 

Load and parse metadata for the AP band.

Returns:: A Bunch containing geometry info and an ‘exists’ flag.
Return type:: Bunch

static get_time_snippets(sr, n=3, pad=200)[source] 

Return n time points across the file duration, excluding pad seconds from start and end.

Parameters:

sr (spikeglx.Reader or Streamer) – The raw data reader
n (int) – Number of time points to extract.
pad (int) – Time (seconds) to exclude from beginning and end.

Returns:

Array of time points in seconds.

Return type:

np.ndarray

abstractmethod load_ap_data()[source] 

Abstract method to return a SpikeGLX reader or Streamer object.

Return type:: spikeglx.Reader | Streamer | None

load_ap_snippets(twin=1)[source] 

Load AP snippets centered around selected time points.

Also computes channel quality metrics across snippets to detect dead, noisy and outside channels.

Parameters:: twin (float) – Time window in seconds for each snippet.
Returns:: data – Snippets of raw data for three timepoints in addition to metadata (exists, fs).
Return type:: Bunch

abstractmethod load_lf_data()[source] 

Abstract method to return a SpikeGLX reader or Streamer object.

Return type:: spikeglx.Reader | Streamer | None

load_lf_snippets(twin=5)[source] 

Load LF snippets centered around selected time points.

Also computes channel quality metrics across snippets to detect dead, noisy and outside channels.

Parameters:: twin (float) – Time window in seconds for each snippet.
Returns:: data – Snippets of raw data for three timepoints in addition to metadata (exists, fs).
Return type:: Bunch

abstractmethod load_meta_data()[source] 

Abstract method to load AP metadata.

Return type:: dict | None

class ibl_alignment_gui.loaders.data_loader.SpikeGLXLoaderLocal(meta_path)[source] 

Bases: SpikeGLXLoader

SpikeGLX loader using local file system.

Parameters:

probe_path (Path) – Root directory of probe data
meta_collection (str) – Name of subfolder containing meta and binary files.

load_ap_data()[source] 

Load binary AP data from local path.

Returns:: A spikeglx.Reader instance to load the raw data, or None if not found.
Return type:: spikeglx.Reader or None

load_lf_data()[source] 

Load binary LF data from local path.

Returns:: A spikeglx.Reader instance to load the raw data, or None if not found.
Return type:: spikeglx.Reader or None

load_meta_data()[source] 

Load AP metadata from local path.

Returns:: A dict containing the spikeglx AP band metadata, or None if not found.
Return type:: dict or None

class ibl_alignment_gui.loaders.data_loader.SpikeGLXLoaderOne(insertion, one, session_path=None, force=False)[source] 

Bases: SpikeGLXLoader

SpikeGLX loader using ONE.

Raw data is streamed via ONE

Parameters:

insertion (dict) – Dictionary representing a probe insertion (must include ‘session’ and ‘name’).
one (ONE) – An ONE instance used to access data.
session_path (Path or None) – Path to the session folder. If None, it is resolved using the eid via one.eid2path.
force (bool) – If True, forces removal of cached data before streaming.

load_ap_data()[source] 

Load AP data using ONE.

Returns:: A streamer object for AP band.
Return type:: Streamer

load_lf_data()[source] 

Load LF data using ONE.

Returns:: A streamer object for LF band.
Return type:: Streamer

load_meta_data()[source] 

Load AP metadata using ONE.

Returns:: A dict containing the spikeglx AP band metadata, or None if not found.
Return type:: dict or None