ONE-api 3.0b3__py3-none-any.whl → 3.0b4__py3-none-any.whl

one/alf/io.py

@@ -1,876 +1,876 @@
-"""I/O functions for ALyx Files.
-
-Provides support for time-series reading and interpolation as per the specifications
-For a full overview of the scope of the format, see:
-
-https://int-brain-lab.github.io/ONE/alf_intro.html
-"""
-
-import json
-import copy
-import logging
-import re
-from fnmatch import fnmatch
-from pathlib import Path
-from typing import Union
-from functools import partial
-from itertools import chain
-import warnings
-
-import numpy as np
-import pandas as pd
-import yaml
-
-from iblutil.util import Bunch
-from iblutil.io import parquet
-from iblutil.io import jsonable
-from .exceptions import ALFObjectNotFound
-from . import path, spec
-from .spec import FILE_SPEC
-
-_logger = logging.getLogger(__name__)
-
-
-class AlfBunch(Bunch):
-    """A dict-like object that supports dot indexing and conversion to DataFrame."""
-
-    @property
-    def check_dimensions(self):
-        """int: 0 for consistent dimensions, 1 for inconsistent dimensions."""
-        return check_dimensions(self)
-
-    def append(self, b, inplace=False):
-        """Appends one bunch to another, key by key.
-
-        Parameters
-        ----------
-        b : Bunch, dict
-            A Bunch of data to append
-        inplace : bool
-            If true, the data are appended in place, otherwise a copy is returned
-
-        Returns
-        -------
-        ALFBunch, None
-            An ALFBunch with the data appended, or None if inplace is True
-
-        """
-        # default is to return a copy
-        if inplace:
-            a = self
-        else:
-            a = AlfBunch(copy.deepcopy(self))
-        # handles empty bunches for convenience if looping
-        if b == {}:
-            return a
-        if a == {}:
-            return AlfBunch(b)
-        # right now supports only strictly matching keys. Will implement other cases as needed
-        if set(a.keys()) != set(b.keys()):
-            raise NotImplementedError('Append bunches only works with strictly matching keys'
-                                      'For more complex merges, convert to pandas dataframe.')
-        # do the merge; only concatenate lists and np arrays right now
-        for k in a:
-            if isinstance(a[k], np.ndarray):
-                a[k] = np.concatenate((a[k], b[k]), axis=0)
-            elif isinstance(a[k], list):
-                a[k].extend(b[k])
-            else:
-                _logger.warning(f'bunch key "{k}" is a {a[k].__class__}. I don\'t know how to'
-                                f' handle that. Use pandas for advanced features')
-        if a.check_dimensions != 0:
-            print_sizes = '\n'.join(f'{v.shape},\t{k}' for k, v in a.items())
-            _logger.warning(f'Inconsistent dimensions for object: \n{print_sizes}')
-
-        return a
-
-    def to_df(self) -> pd.DataFrame:
-        """Return DataFrame with data keys as columns."""
-        return dataframe(self)
-
-    @staticmethod
-    def from_df(df) -> 'AlfBunch':
-        data = dict(zip(df.columns, df.values.T))
-        split_keys = sorted(x for x in data.keys() if re.match(r'.+?_[01]$', x))
-        for x1, x2 in zip(*[iter(split_keys)] * 2):
-            data[x1[:-2]] = np.c_[data.pop(x1), data.pop(x2)]
-        return AlfBunch(data)
-
-
-def dataframe(adict):
-    """Convert an Bunch conforming to size conventions into a pandas DataFrame.
-
-    For 2-D arrays, stops at 10 columns per attribute.
-
-    Parameters
-    ----------
-    adict : dict, Bunch
-        A dict-like object of data to convert to DataFrame
-
-    Returns
-    -------
-    pd.DataFrame
-        A pandas DataFrame of data
-
-    """
-    if check_dimensions(adict) != 0:
-        raise ValueError('Can only convert to DataFrame objects with consistent size')
-    # easy case where there are only vectors
-    if all([len(adict[k].shape) == 1 for k in adict]):
-        return pd.DataFrame(adict)
-    # pandas has trouble with 2d data, chop it off with a limit of 10 columns per dataset
-    df = pd.DataFrame()
-    for k in adict.keys():
-        if adict[k].ndim == 1:
-            df[k] = adict[k]
-        elif adict[k].ndim == 2 and adict[k].shape[1] == 1:
-            df[k] = adict[k][:, 0]
-        elif adict[k].ndim == 2:
-            for i in np.arange(adict[k].shape[1]):
-                df[f"{k}_{i}"] = adict[k][:, i]
-                if i == 9:
-                    break
-        else:
-            _logger.warning(f'{k} attribute is 3D or more and won\'t convert to dataframe')
-            continue
-    return df
-
-
-def _find_metadata(file_alf) -> path.ALFPath:
-    """File path for an existing meta-data file for an alf_file.
-
-    Parameters
-    ----------
-    file_alf : str, pathlib.Path
-        A path of existing ALF.
-
-    Returns
-    -------
-    one.alf.path.ALFPath
-        Path of meta-data file if exists.
-
-    """
-    file_alf = path.ALFPath(file_alf)
-    ns, obj = file_alf.name.split('.')[:2]
-    return next(file_alf.parent.glob(f'{ns}.{obj}*.metadata*.json'), None)
-
-
-def read_ts(filename):
-    """Load time-series from ALF format.
-
-    Parameters
-    ----------
-    filename : str, pathlib.Path
-        An ALF path whose values to load
-
-    Returns
-    -------
-    numpy.ndarray
-        An array of timestamps belonging to the ALF path object
-    numpy.ndarray
-         An array of values in filename
-
-    Examples
-    --------
-    >>> t, d = read_ts(filename)
-
-    """
-    filename = path.ensure_alf_path(filename)
-
-    # alf format is object.attribute.extension, for example '_ibl_wheel.position.npy'
-    _, obj, attr, *_, ext = filename.dataset_name_parts
-
-    try:
-        # looking for matching object with attribute timestamps: '_ibl_wheel.timestamps.npy'
-        (time_file,), _ = filter_by(filename.parent, object=obj, attribute='times*', extension=ext)
-        assert time_file
-    except (ValueError, AssertionError):
-        name = spec.to_alf(obj, attr, ext)
-        raise FileNotFoundError(name + ' not found! No time-scale for ' + str(filename))
-
-    ts = np.load(filename.parent / time_file)
-    val = np.load(filename)
-    # Ensure timestamps
-    return ts2vec(ts, val.shape[0]), _ensure_flat(val)
-
-
-def _ensure_flat(arr):
-    """Given a single column array, returns a flat vector.  Other shapes are returned unchanged.
-
-    Parameters
-    ----------
-    arr : numpy.array
-        An array with shape (n, 1)
-
-    Returns
-    -------
-    numpy.ndarray
-        A vector with shape (n,)
-
-    """
-    return arr.flatten() if arr.ndim == 2 and arr.shape[1] == 1 else arr
-
-
-def ts2vec(ts: np.ndarray, n_samples: int) -> np.ndarray:
-    """Interpolate a continuous timeseries of the shape (2, 2).
-
-    Parameters
-    ----------
-    ts : numpy.array
-        a 2x2 numpy array of the form (sample, ts)
-    n_samples : int
-        Number of samples; i.e. the size of the resulting vector
-
-    Returns
-    -------
-    numpy.ndarray
-        A vector of interpolated timestamps
-
-    """
-    if len(ts.shape) == 1:
-        return ts
-    elif ts.ndim == 2 and ts.shape[1] == 1:
-        return ts.flatten()  # Deal with MATLAB single column array
-    if ts.ndim > 2 or ts.shape[1] != 2:
-        raise ValueError('Array shape should be (2, 2)')
-    # Linearly interpolate the times
-    x = np.arange(n_samples)
-    return np.interp(x, ts[:, 0], ts[:, 1])
-
-
-def check_dimensions(dico):
-    """Test for consistency of dimensions as per ALF specs in a dictionary.
-
-    Alf broadcasting rules: only accepts consistent dimensions for a given axis
-    a dimension is consistent with another if it's empty, 1, or equal to the other arrays
-    dims [a, 1],  [1, b] and [a, b] are all consistent, [c, 1] is not
-
-    Parameters
-    ----------
-    dico : ALFBunch, dict
-        Dictionary containing data
-
-    Returns
-    -------
-    int
-        Status 0 for consistent dimensions, 1 for inconsistent dimensions
-
-    """
-    supported = (np.ndarray, pd.DataFrame)  # Data types that have a shape attribute
-    shapes = [dico[lab].shape for lab in dico
-              if isinstance(dico[lab], supported) and not lab.startswith('timestamps')]
-    first_shapes = [sh[0] for sh in shapes]
-    # Continuous timeseries are permitted to be a (2, 2)
-    timeseries = [k for k, v in dico.items()
-                  if k.startswith('timestamps') and isinstance(v, np.ndarray)]
-    if any(timeseries):
-        for key in timeseries:
-            if dico[key].ndim == 1 or (dico[key].ndim == 2 and dico[key].shape[1] == 1):
-                # Should be vector with same length as other attributes
-                first_shapes.append(dico[key].shape[0])
-            elif dico[key].ndim > 1 and dico[key].shape != (2, 2):
-                return 1  # ts not a (2, 2) arr or a vector
-
-    ok = len(first_shapes) == 0 or set(first_shapes).issubset({max(first_shapes), 1})
-    return int(ok is False)
-
-
-def load_file_content(fil):
-    """Return content of a file path.
-
-    Designed for very generic data file formats such as `json`, `npy`, `csv`, `(h)tsv`, `ssv`.
-
-    Parameters
-    ----------
-    fil : str, pathlib.Path
-        File to read
-
-    Returns
-    -------
-    Any
-        Array/json/pandas dataframe depending on format
-
-    """
-    if not fil:
-        return
-    fil = Path(fil)
-    if fil.stat().st_size == 0:
-        return
-    if fil.suffix == '.csv':
-        return pd.read_csv(fil).squeeze('columns')
-    if fil.suffix == '.json':
-        try:
-            with open(fil) as _fil:
-                return json.loads(_fil.read())
-        except Exception as e:
-            _logger.error(e)
-            return None
-    if fil.suffix == '.jsonable':
-        return jsonable.read(fil)
-    if fil.suffix == '.npy':
-        return _ensure_flat(np.load(file=fil, allow_pickle=True))
-    if fil.suffix == '.npz':
-        arr = np.load(file=fil)
-        # If single array with the default name ('arr_0') return individual array
-        return arr['arr_0'] if set(arr.files) == {'arr_0'} else arr
-    if fil.suffix == '.pqt':
-        return parquet.load(fil)[0]
-    if fil.suffix == '.ssv':
-        return pd.read_csv(fil, delimiter=' ').squeeze('columns')
-    if fil.suffix in ('.tsv', '.htsv'):
-        return pd.read_csv(fil, delimiter='\t').squeeze('columns')
-    if fil.suffix in ('.yml', '.yaml'):
-        with open(fil, 'r') as _fil:
-            return yaml.safe_load(_fil)
-    if fil.suffix == '.sparse_npz':
-        try:
-            import sparse
-            return sparse.load_npz(fil)
-        except ModuleNotFoundError:
-            warnings.warn(f'{Path(fil).name} requires the pydata sparse package to load.')
-            return path.ALFPath(fil)
-    return path.ALFPath(fil)
-
-
-def _ls(alfpath, object=None, **kwargs) -> (list, tuple):
-    """Given a path, an object and a filter, returns all files and associated attributes.
-
-    Parameters
-    ----------
-    alfpath : str, pathlib.Path
-        The folder to list
-    object : str, list
-        An ALF object name to filter by
-    wildcards : bool
-        If true uses unix shell style pattern matching, otherwise uses regular expressions
-    kwargs
-        Other ALF parts to filter, including namespace, attribute, etc.
-
-    Returns
-    -------
-    list of one.alf.path.ALFPath
-        A list of ALF paths.
-    tuple
-        A tuple of ALF attributes corresponding to the file paths.
-
-    Raises
-    ------
-    ALFObjectNotFound
-        No matching ALF object was found in the alfpath directory
-
-    """
-    alfpath = path.ALFPath(alfpath)
-    if not alfpath.exists():
-        files_alf = attributes = None
-    elif alfpath.is_dir():
-        if object is None:
-            # List all ALF files
-            files_alf, attributes = filter_by(alfpath, **kwargs)
-        else:
-            files_alf, attributes = filter_by(alfpath, object=object, **kwargs)
-    else:
-        object = alfpath.object
-        alfpath = alfpath.parent
-        files_alf, attributes = filter_by(alfpath, object=object, **kwargs)
-
-    # raise error if no files found
-    if not files_alf:
-        err_str = f'object "{object}"' if object else 'ALF files'
-        raise ALFObjectNotFound(f'No {err_str} found in {alfpath}')
-
-    return [alfpath.joinpath(f) for f in files_alf], attributes
-
-
-def iter_sessions(root_dir, pattern='*'):
-    """Recursively iterate over session paths in a given directory.
-
-    Parameters
-    ----------
-    root_dir : str, pathlib.Path
-        The folder to look for sessions.
-    pattern : str
-        Glob pattern to use. Default searches all folders.  Providing a more specific pattern makes
-        this more performant (see examples).
-
-    Yields
-    ------
-    pathlib.Path
-        The next session path in lexicographical order.
-
-    Examples
-    --------
-    Efficient iteration when `root_dir` contains <lab>/Subjects folders
-
-    >>> sessions = list(iter_sessions(root_dir, pattern='*/Subjects/*/????-??-??/*'))
-
-    Efficient iteration when `root_dir` contains subject folders
-
-    >>> sessions = list(iter_sessions(root_dir, pattern='*/????-??-??/*'))
-
-    """
-    if spec.is_session_path(root_dir):
-        yield path.ALFPath(root_dir)
-    for p in sorted(Path(root_dir).rglob(pattern)):
-        if p.is_dir() and spec.is_session_path(p):
-            yield path.ALFPath(p)
-
-
-def iter_datasets(session_path):
-    """Iterate over all files in a session, and yield relative dataset paths.
-
-    Parameters
-    ----------
-    session_path : str, pathlib.Path
-        The folder to look for datasets.
-
-    Yields
-    ------
-    one.alf.path.ALFPath
-        The next dataset path (relative to the session path) in lexicographical order.
-
-    """
-    for dataset in path.ALFPath(session_path).iter_datasets(recursive=True):
-        yield dataset.relative_to(session_path)
-
-
-def exists(alfpath, object, attributes=None, **kwargs) -> bool:
-    """Test if ALF object and optionally specific attributes exist in the given path.
-
-    Parameters
-    ----------
-    alfpath : str, pathlib.Path
-        The folder to look into
-    object : str
-        ALF object name
-    attributes : str, list
-        Wanted attributes
-    wildcards : bool
-        If true uses unix shell style pattern matching, otherwise uses regular expressions
-    kwargs
-        Other ALF parts to filter by
-
-    Returns
-    -------
-    bool
-        For multiple attributes, returns True only if all attributes are found
-
-    """
-    # if the object is not found, return False
-    try:
-        _, attributes_found = _ls(alfpath, object, **kwargs)
-    except (FileNotFoundError, ALFObjectNotFound):
-        return False
-
-    # if object found and no attribute provided, True
-    if not attributes:
-        return True
-
-    # if attributes provided, test if all are found
-    if isinstance(attributes, str):
-        attributes = [attributes]
-    attributes_found = set(part[2] for part in attributes_found)
-    return set(attributes).issubset(attributes_found)
-
-
-def load_object(alfpath, object=None, short_keys=False, **kwargs):
-    """Reads all files sharing the same object name.
-
-    For example, if the file provided to the function is `spikes.times`, the function will
-    load `spikes.times`, `spikes.clusters`, `spikes.depths`, `spike.amps` in a dictionary
-    whose keys will be `times`, `clusters`, `depths`, `amps`
-
-    Full Reference here: https://int-brain-lab.github.io/ONE/alf_intro.html
-
-    Simplified example: _namespace_object.attribute_timescale.part1.part2.extension
-
-    Parameters
-    ----------
-    alfpath : str, pathlib.Path, list
-        Any ALF path pertaining to the object OR directory containing ALFs OR list of paths.
-    object : str, list, None
-        The ALF object(s) to filter by.  If a directory is provided and object is None, all valid
-        ALF files returned.
-    short_keys : bool
-        By default, the output dictionary keys will be compounds of attributes, timescale and
-        any eventual parts separated by a dot. Use True to shorten the keys to the attribute
-        and timescale.
-    wildcards : bool
-        If true uses unix shell style pattern matching, otherwise uses regular expressions.
-    kwargs
-        Other ALF parts to filter by.
-
-    Returns
-    -------
-    AlfBunch
-        An ALFBunch (dict-like) of all attributes pertaining to the object.
-
-    Examples
-    --------
-        Load 'spikes' object
-
-        >>> spikes = load_object('full/path/to/my/alffolder/', 'spikes')
-
-        Load 'trials' object under the 'ibl' namespace
-
-        >>> trials = load_object('/subject/2021-01-01/001', 'trials', namespace='ibl')
-
-    """
-    if isinstance(alfpath, (Path, str)):
-        if Path(alfpath).is_dir() and object is None:
-            raise ValueError('If a directory is provided, the object name should be provided too')
-        files_alf, parts = _ls(alfpath, object, **kwargs)
-    else:  # A list of paths allows us to load an object from different revisions
-        files_alf = list(map(path.ALFPath, alfpath))
-        parts = [x.dataset_name_parts for x in files_alf]
-        assert len(set(p[1] for p in parts)) == 1
-        object = next(x[1] for x in parts)
-    # Take attribute and timescale from parts list
-    attributes = [p[2] if not p[3] else '_'.join(p[2:4]) for p in parts]
-    if not short_keys:  # Include extra parts in the keys
-        attributes = ['.'.join(filter(None, (attr, p[4]))) for attr, p in zip(attributes, parts)]
-        # TODO List duplicates; raise ALFError
-    assert len(set(attributes)) == len(attributes), (
-        f'multiple object {object} with the same attribute in {alfpath}, restrict parts/namespace')
-    out = AlfBunch({})
-
-    # load content for each file
-    for fil, att in zip(files_alf, attributes):
-        # if there is a corresponding metadata file, read it:
-        meta_data_file = _find_metadata(fil)
-        # if this is the actual meta-data file, skip and it will be read later
-        if meta_data_file == fil:
-            continue
-        out[att] = load_file_content(fil)
-        if meta_data_file:
-            meta = load_file_content(meta_data_file)
-            # the columns keyword splits array along the last dimension
-            if 'columns' in meta.keys():
-                out.update({v: out[att][::, k] for k, v in enumerate(meta['columns'])})
-                out.pop(att)
-                meta.pop('columns')
-            # if there is other stuff in the dictionary, save it, otherwise disregard
-            if meta:
-                out[att + 'metadata'] = meta
-    # Merge 'table' dataframe into bunch
-    table_key = next(filter(re.compile(r'^table([_.]|$)').match, out), None)  # py 3.8
-    if table_key:
-        table = out.pop(table_key)
-
-        def rename_columns(field):
-            """"Rename DataFrame fields to include timescale or extra ALF parts from table_key.
-
-            For example...
-                with table_key = table_clock, field1 -> field1_clock;
-                with table_key = table_clock.extra, field1_0 -> field1_clock.extra_0;
-                with table_key = table, field1 -> field1
-            """
-            return (field[:-2] + table_key[5:] + field[-2:]
-                    if re.match(r'.+?_[01]$', field)
-                    else field + table_key[5:])
-        table.rename(columns=rename_columns, inplace=True)
-        out.update(AlfBunch.from_df(table))
-    status = out.check_dimensions
-    timeseries = [k for k in out.keys() if 'timestamps' in k]
-    if any(timeseries) and len(out.keys()) > len(timeseries) and status == 0:
-        # Get length of one of the other arrays
-        ignore = ('timestamps', 'meta')
-        n_samples = next(v for k, v in out.items() if not any(x in k for x in ignore)).shape[0]
-        for key in timeseries:
-            # Expand timeseries if necessary
-            out[key] = ts2vec(out[key], n_samples)
-    if status != 0:
-        supported = (np.ndarray, pd.DataFrame)
-        print_sizes = '\n'.join(
-            f'{v.shape},\t{k}' for k, v in out.items() if isinstance(v, supported)
-        )
-        _logger.warning(f'Inconsistent dimensions for object: {object} \n{print_sizes}')
-    return out
-
-
-def save_object_npy(alfpath, dico, object, parts=None, namespace=None, timescale=None) -> list:
-    """Save dictionary in `ALF format`_ using dictionary keys as attribute names.
-
-    Dimensions have to be consistent.
-
-    Simplified ALF example: _namespace_object.attribute.part1.part2.extension.
-
-    Parameters
-    ----------
-    alfpath : str, pathlib.Path
-        Path of the folder to save data to.
-    dico : dict
-        Dictionary to save to npy; keys correspond to ALF attributes.
-    object : str
-        Name of the object to save.
-    parts : str, list, None
-        Extra parts to the ALF name.
-    namespace : str, None
-        The optional namespace of the object.
-    timescale : str, None
-        The optional timescale of the object.
-
-    Returns
-    -------
-    list of one.alf.path.ALFPath
-        List of written files.
-
-    Examples
-    --------
-    >>> spikes = {'times': np.arange(50), 'depths': np.random.random(50)}
-    >>> files = save_object_npy('/path/to/my/alffolder/', spikes, 'spikes')
-
-    .. _ALF format:
-        https://int-brain-lab.github.io/ONE/alf_intro.html
-
-    """
-    alfpath = path.ALFPath(alfpath)
-    status = check_dimensions(dico)
-    if status != 0:
-        raise ValueError('Dimensions are not consistent to save all arrays in ALF format: ' +
-                         str([(k, v.shape) for k, v in dico.items()]))
-    out_files = []
-    for k, v in dico.items():
-        out_file = alfpath / spec.to_alf(object, k, 'npy',
-                                         extra=parts, namespace=namespace, timescale=timescale)
-        np.save(out_file, v)
-        out_files.append(out_file)
-    return out_files
-
-
-def save_metadata(file_alf, dico) -> path.ALFPath:
-    """Writes a meta data file matching a current ALF file object.
-
-    For example given an alf file `clusters.ccfLocation.ssv` this will write a dictionary in JSON
-    format in `clusters.ccfLocation.metadata.json`
-
-    Reserved keywords:
-        - **columns**: column names for binary tables.
-        - **row**: row names for binary tables.
-        - **unit**
-
-    Parameters
-    ----------
-    file_alf : str, pathlib.Path
-        Full path to the alf object
-    dico : dict, ALFBunch
-        Dictionary containing meta-data
-
-    Returns
-    -------
-    one.alf.path.ALFPath
-        The saved metadata file path.
-
-    """
-    file_alf = path.ALFPath(file_alf)
-    assert file_alf.is_dataset, 'ALF filename not valid'
-    file_meta_data = file_alf.parent / (file_alf.stem + '.metadata.json')
-    with open(file_meta_data, 'w+') as fid:
-        fid.write(json.dumps(dico, indent=1))
-    return file_meta_data
-
-
-def next_num_folder(session_date_folder: Union[str, Path]) -> str:
-    """Return the next number for a session given a session_date_folder."""
-    session_date_folder = Path(session_date_folder)
-    if not session_date_folder.exists():
-        return '001'
-    session_nums = [
-        int(x.name) for x in session_date_folder.iterdir()
-        if x.is_dir() and not x.name.startswith('.') and x.name.isdigit()
-    ]
-    out = f'{max(session_nums or [0]) + 1:03d}'
-    assert len(out) == 3, 'ALF spec does not support session numbers > 999'
-    return out
-
-
-def remove_empty_folders(folder: Union[str, Path]) -> None:
-    """Iteratively remove any empty child folders."""
-    all_folders = sorted(x for x in Path(folder).rglob('*') if x.is_dir())
-    for f in reversed(all_folders):  # Reversed sorted ensures we remove deepest first
-        try:
-            f.rmdir()
-        except Exception:
-            continue
-
-
-def filter_by(alf_path, wildcards=True, **kwargs):
-    """Given a path and optional filters, returns all ALF files and their associated parts.
-
-    The filters constitute a logical AND.  For all but `extra`, if a list is provided, one or more
-    elements must match (a logical OR).
-
-    Parameters
-    ----------
-    alf_path : str, pathlib.Path
-        A path to a folder containing ALF datasets.
-    wildcards : bool
-        If true, kwargs are matched as unix-style patterns, otherwise as regular expressions.
-    object : str, list
-        Filter by a given object (e.g. 'spikes').
-    attribute : str, list
-        Filter by a given attribute (e.g. 'intervals').
-    extension : str, list
-        Filter by extension (e.g. 'npy').
-    namespace : str, list
-        Filter by a given namespace (e.g. 'ibl') or None for files without one.
-    timescale : str, list
-        Filter by a given timescale (e.g. 'bpod') or None for files without one.
-    extra : str, list
-        Filter by extra parameters (e.g. 'raw') or None for files without extra parts
-        NB: Wild cards not permitted here.
-
-    Returns
-    -------
-    alf_files : list of one.alf.path.ALFPath
-        A Path to a directory containing ALF files.
-    attributes : list of dicts
-        A list of parsed file parts.
-
-    Examples
-    --------
-    Filter files with universal timescale
-
-    >>> filter_by(alf_path, timescale=None)
-
-    Filter files by a given ALF object
-
-    >>> filter_by(alf_path, object='wheel')
-
-    Filter using wildcard, e.g. 'wheel' and 'wheelMoves' ALF objects
-
-    >>> filter_by(alf_path, object='wh*')
-
-    Filter all intervals that are in bpod time
-
-    >>> filter_by(alf_path, attribute='intervals', timescale='bpod')
-
-    Filter all files containing either 'intervals' OR 'timestamps' attributes
-
-    >>> filter_by(alf_path, attribute=['intervals', 'timestamps'])
-
-    Filter all files using a regular expression
-
-    >>> filter_by(alf_path, object='^wheel.*', wildcards=False)
-    >>> filter_by(alf_path, object=['^wheel$', '.*Moves'], wildcards=False)
-
-    """
-    alf_files = [f.relative_to(alf_path) for f in path.ALFPath(alf_path).iter_datasets()]
-    attributes = list(map(path.ALFPath.parse_alf_name, alf_files))
-
-    if kwargs:
-        # Validate keyword arguments against regex group names
-        invalid = kwargs.keys() - spec.regex(FILE_SPEC).groupindex.keys()
-        if invalid:
-            raise TypeError('%s() got an unexpected keyword argument "%s"'
-                            % (__name__, set(invalid).pop()))
-
-        # # Ensure 'extra' input is a list; if str split on dot
-        if 'extra' in kwargs and isinstance(kwargs['extra'], str):
-            kwargs['extra'] = kwargs['extra'].split('.')
-
-        def _match(part, pattern, split=None):
-            if pattern is None or part is None:
-                # If either is None, both should be None to match
-                return pattern is part
-            elif split:
-                # Check all provided extra fields match those in ALF
-                return all(elem in part.split(split) for elem in pattern if elem)
-            elif not isinstance(pattern, str):
-                if wildcards:
-                    return any(_match(part, x, split) for x in pattern)
-                else:
-                    return re.match('|'.join(pattern), part) is not None
-            else:
-                # Check given attribute matches, allowing wildcards
-                return fnmatch(part, pattern) if wildcards else re.match(pattern, part) is not None
-
-        # Iterate over ALF files
-        for file, attr in zip(alf_files.copy(), attributes.copy()):
-            for k, v in kwargs.items():  # Iterate over attributes
-                match = _match(attr[k], v, '.' if k == 'extra' else None)
-
-                if not match:  # Remove file from list and move on to next file
-                    alf_files.remove(file)
-                    attributes.remove(attr)
-                    break
-
-    return alf_files, [tuple(attr.values()) for attr in attributes]
-
-
-def find_variants(file_list, namespace=True, timescale=True, extra=True, extension=True):
-    """Find variant datasets.
-
-    Finds any datasets on disk that are considered a variant of the input datasets. At minimum, a
-    dataset is uniquely defined by session path, collection, object and attribute. Therefore,
-    datasets with the same name and collection in a different revision folder are considered a
-    variant. If any of the keyword arguments are set to False, those parts are ignored when
-    comparing datasets.
-
-    Parameters
-    ----------
-    file_list : list of str, list of pathlib.Path
-        A list of ALF paths to find variants of.
-    namespace : bool
-        If true, treat datasets with a different namespace as unique.
-    timescale : bool
-        If true, treat datasets with a different timescale as unique.
-    extra : bool
-        If true, treat datasets with a different extra parts as unique.
-    extension : bool
-        If true, treat datasets with a different extension as unique.
-
-    Returns
-    -------
-    Dict[pathlib.Path, list of pathlib.Path]
-        A map of input file paths to a list variant dataset paths.
-
-    Raises
-    ------
-    ValueError
-        One or more input file paths are not valid ALF datasets.
-
-    Examples
-    --------
-    Find all datasets with an identical name and collection in a different revision folder
-
-    >>> find_variants(['/sub/2020-10-01/001/alf/#2020-01-01#/obj.attr.npy'])
-    {Path('/sub/2020-10-01/001/alf/#2020-01-01#/obj.attr.npy'): [
-        Path('/sub/2020-10-01/001/alf/obj.attr.npy')
-    ]}
-
-    Find all datasets with different namespace or revision
-
-    >>> find_variants(['/sub/2020-10-01/001/alf/#2020-01-01#/obj.attr.npy'], namespace=False)
-    {Path('/sub/2020-10-01/001/#2020-01-01#/obj.attr.npy'): [
-        Path('/sub/2020-10-01/001/#2020-01-01#/_ns_obj.attr.npy'),
-        Path('/sub/2020-10-01/001/obj.attr.npy'),
-    ]}
-
-    """
-    # Initialize map of unique files to their duplicates
-    duplicates = {}
-    # Determine which parts to filter
-    variables = locals()
-    filters = {'namespace', 'timescale', 'extra', 'extension'}
-    to_compare = ('lab', 'subject', 'date', 'number', 'collection', 'object', 'attribute',
-                  *(arg for arg in filters if variables[arg]))
-
-    def parts_match(parts, file):
-        """Compare a file's unique parts to a given file."""
-        other = file.parse_alf_path()
-        return all(parts[k] == other[k] for k in to_compare)
-
-    # iterate over unique files and their parts
-    for f in map(path.ALFPath, file_list):
-        parts = f.parse_alf_path()
-        # first glob for files matching object.attribute (including revisions)
-        pattern = f'*{parts["object"]}.{parts["attribute"]}*'
-        # this works because revision will always be last folder;
-        # i.e. revisions can't contain collections
-        globbed = map(f.without_revision().parent.glob, (pattern, '#*#/' + pattern))
-        globbed = chain.from_iterable(globbed)  # unite revision and non-revision globs
-        # refine duplicates based on other parts (this also ensures we don't catch similar objects)
-        globbed = filter(partial(parts_match, parts), globbed)
-        # key = f.relative_to_session().as_posix()
-        duplicates[f] = [x for x in globbed if x != f]  # map file to list of its duplicates
-    return duplicates
+"""I/O functions for ALyx Files.
+
+Provides support for time-series reading and interpolation as per the specifications
+For a full overview of the scope of the format, see:
+
+https://int-brain-lab.github.io/ONE/alf_intro.html
+"""
+
+import json
+import copy
+import logging
+import re
+from fnmatch import fnmatch
+from pathlib import Path
+from typing import Union
+from functools import partial
+from itertools import chain
+import warnings
+
+import numpy as np
+import pandas as pd
+import yaml
+
+from iblutil.util import Bunch
+from iblutil.io import parquet
+from iblutil.io import jsonable
+from .exceptions import ALFObjectNotFound
+from . import path, spec
+from .spec import FILE_SPEC
+
+_logger = logging.getLogger(__name__)
+
+
+class AlfBunch(Bunch):
+    """A dict-like object that supports dot indexing and conversion to DataFrame."""
+
+    @property
+    def check_dimensions(self):
+        """int: 0 for consistent dimensions, 1 for inconsistent dimensions."""
+        return check_dimensions(self)
+
+    def append(self, b, inplace=False):
+        """Appends one bunch to another, key by key.
+
+        Parameters
+        ----------
+        b : Bunch, dict
+            A Bunch of data to append
+        inplace : bool
+            If true, the data are appended in place, otherwise a copy is returned
+
+        Returns
+        -------
+        ALFBunch, None
+            An ALFBunch with the data appended, or None if inplace is True
+
+        """
+        # default is to return a copy
+        if inplace:
+            a = self
+        else:
+            a = AlfBunch(copy.deepcopy(self))
+        # handles empty bunches for convenience if looping
+        if b == {}:
+            return a
+        if a == {}:
+            return AlfBunch(b)
+        # right now supports only strictly matching keys. Will implement other cases as needed
+        if set(a.keys()) != set(b.keys()):
+            raise NotImplementedError('Append bunches only works with strictly matching keys'
+                                      'For more complex merges, convert to pandas dataframe.')
+        # do the merge; only concatenate lists and np arrays right now
+        for k in a:
+            if isinstance(a[k], np.ndarray):
+                a[k] = np.concatenate((a[k], b[k]), axis=0)
+            elif isinstance(a[k], list):
+                a[k].extend(b[k])
+            else:
+                _logger.warning(f'bunch key "{k}" is a {a[k].__class__}. I don\'t know how to'
+                                f' handle that. Use pandas for advanced features')
+        if a.check_dimensions != 0:
+            print_sizes = '\n'.join(f'{v.shape},\t{k}' for k, v in a.items())
+            _logger.warning(f'Inconsistent dimensions for object: \n{print_sizes}')
+
+        return a
+
+    def to_df(self) -> pd.DataFrame:
+        """Return DataFrame with data keys as columns."""
+        return dataframe(self)
+
+    @staticmethod
+    def from_df(df) -> 'AlfBunch':
+        data = dict(zip(df.columns, df.values.T))
+        split_keys = sorted(x for x in data.keys() if re.match(r'.+?_[01]$', x))
+        for x1, x2 in zip(*[iter(split_keys)] * 2):
+            data[x1[:-2]] = np.c_[data.pop(x1), data.pop(x2)]
+        return AlfBunch(data)
+
+
+def dataframe(adict):
+    """Convert an Bunch conforming to size conventions into a pandas DataFrame.
+
+    For 2-D arrays, stops at 10 columns per attribute.
+
+    Parameters
+    ----------
+    adict : dict, Bunch
+        A dict-like object of data to convert to DataFrame
+
+    Returns
+    -------
+    pd.DataFrame
+        A pandas DataFrame of data
+
+    """
+    if check_dimensions(adict) != 0:
+        raise ValueError('Can only convert to DataFrame objects with consistent size')
+    # easy case where there are only vectors
+    if all([len(adict[k].shape) == 1 for k in adict]):
+        return pd.DataFrame(adict)
+    # pandas has trouble with 2d data, chop it off with a limit of 10 columns per dataset
+    df = pd.DataFrame()
+    for k in adict.keys():
+        if adict[k].ndim == 1:
+            df[k] = adict[k]
+        elif adict[k].ndim == 2 and adict[k].shape[1] == 1:
+            df[k] = adict[k][:, 0]
+        elif adict[k].ndim == 2:
+            for i in np.arange(adict[k].shape[1]):
+                df[f"{k}_{i}"] = adict[k][:, i]
+                if i == 9:
+                    break
+        else:
+            _logger.warning(f'{k} attribute is 3D or more and won\'t convert to dataframe')
+            continue
+    return df
+
+
+def _find_metadata(file_alf) -> path.ALFPath:
+    """File path for an existing meta-data file for an alf_file.
+
+    Parameters
+    ----------
+    file_alf : str, pathlib.Path
+        A path of existing ALF.
+
+    Returns
+    -------
+    one.alf.path.ALFPath
+        Path of meta-data file if exists.
+
+    """
+    file_alf = path.ALFPath(file_alf)
+    ns, obj = file_alf.name.split('.')[:2]
+    return next(file_alf.parent.glob(f'{ns}.{obj}*.metadata*.json'), None)
+
+
+def read_ts(filename):
+    """Load time-series from ALF format.
+
+    Parameters
+    ----------
+    filename : str, pathlib.Path
+        An ALF path whose values to load
+
+    Returns
+    -------
+    numpy.ndarray
+        An array of timestamps belonging to the ALF path object
+    numpy.ndarray
+         An array of values in filename
+
+    Examples
+    --------
+    >>> t, d = read_ts(filename)
+
+    """
+    filename = path.ensure_alf_path(filename)
+
+    # alf format is object.attribute.extension, for example '_ibl_wheel.position.npy'
+    _, obj, attr, *_, ext = filename.dataset_name_parts
+
+    try:
+        # looking for matching object with attribute timestamps: '_ibl_wheel.timestamps.npy'
+        (time_file,), _ = filter_by(filename.parent, object=obj, attribute='times*', extension=ext)
+        assert time_file
+    except (ValueError, AssertionError):
+        name = spec.to_alf(obj, attr, ext)
+        raise FileNotFoundError(name + ' not found! No time-scale for ' + str(filename))
+
+    ts = np.load(filename.parent / time_file)
+    val = np.load(filename)
+    # Ensure timestamps
+    return ts2vec(ts, val.shape[0]), _ensure_flat(val)
+
+
+def _ensure_flat(arr):
+    """Given a single column array, returns a flat vector.  Other shapes are returned unchanged.
+
+    Parameters
+    ----------
+    arr : numpy.array
+        An array with shape (n, 1)
+
+    Returns
+    -------
+    numpy.ndarray
+        A vector with shape (n,)
+
+    """
+    return arr.flatten() if arr.ndim == 2 and arr.shape[1] == 1 else arr
+
+
+def ts2vec(ts: np.ndarray, n_samples: int) -> np.ndarray:
+    """Interpolate a continuous timeseries of the shape (2, 2).
+
+    Parameters
+    ----------
+    ts : numpy.array
+        a 2x2 numpy array of the form (sample, ts)
+    n_samples : int
+        Number of samples; i.e. the size of the resulting vector
+
+    Returns
+    -------
+    numpy.ndarray
+        A vector of interpolated timestamps
+
+    """
+    if len(ts.shape) == 1:
+        return ts
+    elif ts.ndim == 2 and ts.shape[1] == 1:
+        return ts.flatten()  # Deal with MATLAB single column array
+    if ts.ndim > 2 or ts.shape[1] != 2:
+        raise ValueError('Array shape should be (2, 2)')
+    # Linearly interpolate the times
+    x = np.arange(n_samples)
+    return np.interp(x, ts[:, 0], ts[:, 1])
+
+
+def check_dimensions(dico):
+    """Test for consistency of dimensions as per ALF specs in a dictionary.
+
+    Alf broadcasting rules: only accepts consistent dimensions for a given axis
+    a dimension is consistent with another if it's empty, 1, or equal to the other arrays
+    dims [a, 1],  [1, b] and [a, b] are all consistent, [c, 1] is not
+
+    Parameters
+    ----------
+    dico : ALFBunch, dict
+        Dictionary containing data
+
+    Returns
+    -------
+    int
+        Status 0 for consistent dimensions, 1 for inconsistent dimensions
+
+    """
+    supported = (np.ndarray, pd.DataFrame)  # Data types that have a shape attribute
+    shapes = [dico[lab].shape for lab in dico
+              if isinstance(dico[lab], supported) and not lab.startswith('timestamps')]
+    first_shapes = [sh[0] for sh in shapes]
+    # Continuous timeseries are permitted to be a (2, 2)
+    timeseries = [k for k, v in dico.items()
+                  if k.startswith('timestamps') and isinstance(v, np.ndarray)]
+    if any(timeseries):
+        for key in timeseries:
+            if dico[key].ndim == 1 or (dico[key].ndim == 2 and dico[key].shape[1] == 1):
+                # Should be vector with same length as other attributes
+                first_shapes.append(dico[key].shape[0])
+            elif dico[key].ndim > 1 and dico[key].shape != (2, 2):
+                return 1  # ts not a (2, 2) arr or a vector
+
+    ok = len(first_shapes) == 0 or set(first_shapes).issubset({max(first_shapes), 1})
+    return int(ok is False)
+
+
+def load_file_content(fil):
+    """Return content of a file path.
+
+    Designed for very generic data file formats such as `json`, `npy`, `csv`, `(h)tsv`, `ssv`.
+
+    Parameters
+    ----------
+    fil : str, pathlib.Path
+        File to read
+
+    Returns
+    -------
+    Any
+        Array/json/pandas dataframe depending on format
+
+    """
+    if not fil:
+        return
+    fil = Path(fil)
+    if fil.stat().st_size == 0:
+        return
+    if fil.suffix == '.csv':
+        return pd.read_csv(fil).squeeze('columns')
+    if fil.suffix == '.json':
+        try:
+            with open(fil) as _fil:
+                return json.loads(_fil.read())
+        except Exception as e:
+            _logger.error(e)
+            return None
+    if fil.suffix == '.jsonable':
+        return jsonable.read(fil)
+    if fil.suffix == '.npy':
+        return _ensure_flat(np.load(file=fil, allow_pickle=True))
+    if fil.suffix == '.npz':
+        arr = np.load(file=fil)
+        # If single array with the default name ('arr_0') return individual array
+        return arr['arr_0'] if set(arr.files) == {'arr_0'} else arr
+    if fil.suffix == '.pqt':
+        return parquet.load(fil)[0]
+    if fil.suffix == '.ssv':
+        return pd.read_csv(fil, delimiter=' ').squeeze('columns')
+    if fil.suffix in ('.tsv', '.htsv'):
+        return pd.read_csv(fil, delimiter='\t').squeeze('columns')
+    if fil.suffix in ('.yml', '.yaml'):
+        with open(fil, 'r') as _fil:
+            return yaml.safe_load(_fil)
+    if fil.suffix == '.sparse_npz':
+        try:
+            import sparse
+            return sparse.load_npz(fil)
+        except ModuleNotFoundError:
+            warnings.warn(f'{Path(fil).name} requires the pydata sparse package to load.')
+            return path.ALFPath(fil)
+    return path.ALFPath(fil)
+
+
+def _ls(alfpath, object=None, **kwargs) -> (list, tuple):
+    """Given a path, an object and a filter, returns all files and associated attributes.
+
+    Parameters
+    ----------
+    alfpath : str, pathlib.Path
+        The folder to list
+    object : str, list
+        An ALF object name to filter by
+    wildcards : bool
+        If true uses unix shell style pattern matching, otherwise uses regular expressions
+    kwargs
+        Other ALF parts to filter, including namespace, attribute, etc.
+
+    Returns
+    -------
+    list of one.alf.path.ALFPath
+        A list of ALF paths.
+    tuple
+        A tuple of ALF attributes corresponding to the file paths.
+
+    Raises
+    ------
+    ALFObjectNotFound
+        No matching ALF object was found in the alfpath directory
+
+    """
+    alfpath = path.ALFPath(alfpath)
+    if not alfpath.exists():
+        files_alf = attributes = None
+    elif alfpath.is_dir():
+        if object is None:
+            # List all ALF files
+            files_alf, attributes = filter_by(alfpath, **kwargs)
+        else:
+            files_alf, attributes = filter_by(alfpath, object=object, **kwargs)
+    else:
+        object = alfpath.object
+        alfpath = alfpath.parent
+        files_alf, attributes = filter_by(alfpath, object=object, **kwargs)
+
+    # raise error if no files found
+    if not files_alf:
+        err_str = f'object "{object}"' if object else 'ALF files'
+        raise ALFObjectNotFound(f'No {err_str} found in {alfpath}')
+
+    return [alfpath.joinpath(f) for f in files_alf], attributes
+
+
+def iter_sessions(root_dir, pattern='*'):
+    """Recursively iterate over session paths in a given directory.
+
+    Parameters
+    ----------
+    root_dir : str, pathlib.Path
+        The folder to look for sessions.
+    pattern : str
+        Glob pattern to use. Default searches all folders.  Providing a more specific pattern makes
+        this more performant (see examples).
+
+    Yields
+    ------
+    pathlib.Path
+        The next session path in lexicographical order.
+
+    Examples
+    --------
+    Efficient iteration when `root_dir` contains <lab>/Subjects folders
+
+    >>> sessions = list(iter_sessions(root_dir, pattern='*/Subjects/*/????-??-??/*'))
+
+    Efficient iteration when `root_dir` contains subject folders
+
+    >>> sessions = list(iter_sessions(root_dir, pattern='*/????-??-??/*'))
+
+    """
+    if spec.is_session_path(root_dir):
+        yield path.ALFPath(root_dir)
+    for p in sorted(Path(root_dir).rglob(pattern)):
+        if p.is_dir() and spec.is_session_path(p):
+            yield path.ALFPath(p)
+
+
+def iter_datasets(session_path):
+    """Iterate over all files in a session, and yield relative dataset paths.
+
+    Parameters
+    ----------
+    session_path : str, pathlib.Path
+        The folder to look for datasets.
+
+    Yields
+    ------
+    one.alf.path.ALFPath
+        The next dataset path (relative to the session path) in lexicographical order.
+
+    """
+    for dataset in path.ALFPath(session_path).iter_datasets(recursive=True):
+        yield dataset.relative_to(session_path)
+
+
+def exists(alfpath, object, attributes=None, **kwargs) -> bool:
+    """Test if ALF object and optionally specific attributes exist in the given path.
+
+    Parameters
+    ----------
+    alfpath : str, pathlib.Path
+        The folder to look into
+    object : str
+        ALF object name
+    attributes : str, list
+        Wanted attributes
+    wildcards : bool
+        If true uses unix shell style pattern matching, otherwise uses regular expressions
+    kwargs
+        Other ALF parts to filter by
+
+    Returns
+    -------
+    bool
+        For multiple attributes, returns True only if all attributes are found
+
+    """
+    # if the object is not found, return False
+    try:
+        _, attributes_found = _ls(alfpath, object, **kwargs)
+    except (FileNotFoundError, ALFObjectNotFound):
+        return False
+
+    # if object found and no attribute provided, True
+    if not attributes:
+        return True
+
+    # if attributes provided, test if all are found
+    if isinstance(attributes, str):
+        attributes = [attributes]
+    attributes_found = set(part[2] for part in attributes_found)
+    return set(attributes).issubset(attributes_found)
+
+
+def load_object(alfpath, object=None, short_keys=False, **kwargs):
+    """Reads all files sharing the same object name.
+
+    For example, if the file provided to the function is `spikes.times`, the function will
+    load `spikes.times`, `spikes.clusters`, `spikes.depths`, `spike.amps` in a dictionary
+    whose keys will be `times`, `clusters`, `depths`, `amps`
+
+    Full Reference here: https://int-brain-lab.github.io/ONE/alf_intro.html
+
+    Simplified example: _namespace_object.attribute_timescale.part1.part2.extension
+
+    Parameters
+    ----------
+    alfpath : str, pathlib.Path, list
+        Any ALF path pertaining to the object OR directory containing ALFs OR list of paths.
+    object : str, list, None
+        The ALF object(s) to filter by.  If a directory is provided and object is None, all valid
+        ALF files returned.
+    short_keys : bool
+        By default, the output dictionary keys will be compounds of attributes, timescale and
+        any eventual parts separated by a dot. Use True to shorten the keys to the attribute
+        and timescale.
+    wildcards : bool
+        If true uses unix shell style pattern matching, otherwise uses regular expressions.
+    kwargs
+        Other ALF parts to filter by.
+
+    Returns
+    -------
+    AlfBunch
+        An ALFBunch (dict-like) of all attributes pertaining to the object.
+
+    Examples
+    --------
+        Load 'spikes' object
+
+        >>> spikes = load_object('full/path/to/my/alffolder/', 'spikes')
+
+        Load 'trials' object under the 'ibl' namespace
+
+        >>> trials = load_object('/subject/2021-01-01/001', 'trials', namespace='ibl')
+
+    """
+    if isinstance(alfpath, (Path, str)):
+        if Path(alfpath).is_dir() and object is None:
+            raise ValueError('If a directory is provided, the object name should be provided too')
+        files_alf, parts = _ls(alfpath, object, **kwargs)
+    else:  # A list of paths allows us to load an object from different revisions
+        files_alf = list(map(path.ALFPath, alfpath))
+        parts = [x.dataset_name_parts for x in files_alf]
+        assert len(set(p[1] for p in parts)) == 1
+        object = next(x[1] for x in parts)
+    # Take attribute and timescale from parts list
+    attributes = [p[2] if not p[3] else '_'.join(p[2:4]) for p in parts]
+    if not short_keys:  # Include extra parts in the keys
+        attributes = ['.'.join(filter(None, (attr, p[4]))) for attr, p in zip(attributes, parts)]
+        # TODO List duplicates; raise ALFError
+    assert len(set(attributes)) == len(attributes), (
+        f'multiple object {object} with the same attribute in {alfpath}, restrict parts/namespace')
+    out = AlfBunch({})
+
+    # load content for each file
+    for fil, att in zip(files_alf, attributes):
+        # if there is a corresponding metadata file, read it:
+        meta_data_file = _find_metadata(fil)
+        # if this is the actual meta-data file, skip and it will be read later
+        if meta_data_file == fil:
+            continue
+        out[att] = load_file_content(fil)
+        if meta_data_file:
+            meta = load_file_content(meta_data_file)
+            # the columns keyword splits array along the last dimension
+            if 'columns' in meta.keys():
+                out.update({v: out[att][::, k] for k, v in enumerate(meta['columns'])})
+                out.pop(att)
+                meta.pop('columns')
+            # if there is other stuff in the dictionary, save it, otherwise disregard
+            if meta:
+                out[att + 'metadata'] = meta
+    # Merge 'table' dataframe into bunch
+    table_key = next(filter(re.compile(r'^table([_.]|$)').match, out), None)  # py 3.8
+    if table_key:
+        table = out.pop(table_key)
+
+        def rename_columns(field):
+            """"Rename DataFrame fields to include timescale or extra ALF parts from table_key.
+
+            For example...
+                with table_key = table_clock, field1 -> field1_clock;
+                with table_key = table_clock.extra, field1_0 -> field1_clock.extra_0;
+                with table_key = table, field1 -> field1
+            """
+            return (field[:-2] + table_key[5:] + field[-2:]
+                    if re.match(r'.+?_[01]$', field)
+                    else field + table_key[5:])
+        table.rename(columns=rename_columns, inplace=True)
+        out.update(AlfBunch.from_df(table))
+    status = out.check_dimensions
+    timeseries = [k for k in out.keys() if 'timestamps' in k]
+    if any(timeseries) and len(out.keys()) > len(timeseries) and status == 0:
+        # Get length of one of the other arrays
+        ignore = ('timestamps', 'meta')
+        n_samples = next(v for k, v in out.items() if not any(x in k for x in ignore)).shape[0]
+        for key in timeseries:
+            # Expand timeseries if necessary
+            out[key] = ts2vec(out[key], n_samples)
+    if status != 0:
+        supported = (np.ndarray, pd.DataFrame)
+        print_sizes = '\n'.join(
+            f'{v.shape},\t{k}' for k, v in out.items() if isinstance(v, supported)
+        )
+        _logger.warning(f'Inconsistent dimensions for object: {object} \n{print_sizes}')
+    return out
+
+
+def save_object_npy(alfpath, dico, object, parts=None, namespace=None, timescale=None) -> list:
+    """Save dictionary in `ALF format`_ using dictionary keys as attribute names.
+
+    Dimensions have to be consistent.
+
+    Simplified ALF example: _namespace_object.attribute.part1.part2.extension.
+
+    Parameters
+    ----------
+    alfpath : str, pathlib.Path
+        Path of the folder to save data to.
+    dico : dict
+        Dictionary to save to npy; keys correspond to ALF attributes.
+    object : str
+        Name of the object to save.
+    parts : str, list, None
+        Extra parts to the ALF name.
+    namespace : str, None
+        The optional namespace of the object.
+    timescale : str, None
+        The optional timescale of the object.
+
+    Returns
+    -------
+    list of one.alf.path.ALFPath
+        List of written files.
+
+    Examples
+    --------
+    >>> spikes = {'times': np.arange(50), 'depths': np.random.random(50)}
+    >>> files = save_object_npy('/path/to/my/alffolder/', spikes, 'spikes')
+
+    .. _ALF format:
+        https://int-brain-lab.github.io/ONE/alf_intro.html
+
+    """
+    alfpath = path.ALFPath(alfpath)
+    status = check_dimensions(dico)
+    if status != 0:
+        raise ValueError('Dimensions are not consistent to save all arrays in ALF format: ' +
+                         str([(k, v.shape) for k, v in dico.items()]))
+    out_files = []
+    for k, v in dico.items():
+        out_file = alfpath / spec.to_alf(object, k, 'npy',
+                                         extra=parts, namespace=namespace, timescale=timescale)
+        np.save(out_file, v)
+        out_files.append(out_file)
+    return out_files
+
+
+def save_metadata(file_alf, dico) -> path.ALFPath:
+    """Writes a meta data file matching a current ALF file object.
+
+    For example given an alf file `clusters.ccfLocation.ssv` this will write a dictionary in JSON
+    format in `clusters.ccfLocation.metadata.json`
+
+    Reserved keywords:
+        - **columns**: column names for binary tables.
+        - **row**: row names for binary tables.
+        - **unit**
+
+    Parameters
+    ----------
+    file_alf : str, pathlib.Path
+        Full path to the alf object
+    dico : dict, ALFBunch
+        Dictionary containing meta-data
+
+    Returns
+    -------
+    one.alf.path.ALFPath
+        The saved metadata file path.
+
+    """
+    file_alf = path.ALFPath(file_alf)
+    assert file_alf.is_dataset, 'ALF filename not valid'
+    file_meta_data = file_alf.parent / (file_alf.stem + '.metadata.json')
+    with open(file_meta_data, 'w+') as fid:
+        fid.write(json.dumps(dico, indent=1))
+    return file_meta_data
+
+
+def next_num_folder(session_date_folder: Union[str, Path]) -> str:
+    """Return the next number for a session given a session_date_folder."""
+    session_date_folder = Path(session_date_folder)
+    if not session_date_folder.exists():
+        return '001'
+    session_nums = [
+        int(x.name) for x in session_date_folder.iterdir()
+        if x.is_dir() and not x.name.startswith('.') and x.name.isdigit()
+    ]
+    out = f'{max(session_nums or [0]) + 1:03d}'
+    assert len(out) == 3, 'ALF spec does not support session numbers > 999'
+    return out
+
+
+def remove_empty_folders(folder: Union[str, Path]) -> None:
+    """Iteratively remove any empty child folders."""
+    all_folders = sorted(x for x in Path(folder).rglob('*') if x.is_dir())
+    for f in reversed(all_folders):  # Reversed sorted ensures we remove deepest first
+        try:
+            f.rmdir()
+        except Exception:
+            continue
+
+
+def filter_by(alf_path, wildcards=True, **kwargs):
+    """Given a path and optional filters, returns all ALF files and their associated parts.
+
+    The filters constitute a logical AND.  For all but `extra`, if a list is provided, one or more
+    elements must match (a logical OR).
+
+    Parameters
+    ----------
+    alf_path : str, pathlib.Path
+        A path to a folder containing ALF datasets.
+    wildcards : bool
+        If true, kwargs are matched as unix-style patterns, otherwise as regular expressions.
+    object : str, list
+        Filter by a given object (e.g. 'spikes').
+    attribute : str, list
+        Filter by a given attribute (e.g. 'intervals').
+    extension : str, list
+        Filter by extension (e.g. 'npy').
+    namespace : str, list
+        Filter by a given namespace (e.g. 'ibl') or None for files without one.
+    timescale : str, list
+        Filter by a given timescale (e.g. 'bpod') or None for files without one.
+    extra : str, list
+        Filter by extra parameters (e.g. 'raw') or None for files without extra parts
+        NB: Wild cards not permitted here.
+
+    Returns
+    -------
+    alf_files : list of one.alf.path.ALFPath
+        A Path to a directory containing ALF files.
+    attributes : list of dicts
+        A list of parsed file parts.
+
+    Examples
+    --------
+    Filter files with universal timescale
+
+    >>> filter_by(alf_path, timescale=None)
+
+    Filter files by a given ALF object
+
+    >>> filter_by(alf_path, object='wheel')
+
+    Filter using wildcard, e.g. 'wheel' and 'wheelMoves' ALF objects
+
+    >>> filter_by(alf_path, object='wh*')
+
+    Filter all intervals that are in bpod time
+
+    >>> filter_by(alf_path, attribute='intervals', timescale='bpod')
+
+    Filter all files containing either 'intervals' OR 'timestamps' attributes
+
+    >>> filter_by(alf_path, attribute=['intervals', 'timestamps'])
+
+    Filter all files using a regular expression
+
+    >>> filter_by(alf_path, object='^wheel.*', wildcards=False)
+    >>> filter_by(alf_path, object=['^wheel$', '.*Moves'], wildcards=False)
+
+    """
+    alf_files = [f.relative_to(alf_path) for f in path.ALFPath(alf_path).iter_datasets()]
+    attributes = list(map(path.ALFPath.parse_alf_name, alf_files))
+
+    if kwargs:
+        # Validate keyword arguments against regex group names
+        invalid = kwargs.keys() - spec.regex(FILE_SPEC).groupindex.keys()
+        if invalid:
+            raise TypeError('%s() got an unexpected keyword argument "%s"'
+                            % (__name__, set(invalid).pop()))
+
+        # # Ensure 'extra' input is a list; if str split on dot
+        if 'extra' in kwargs and isinstance(kwargs['extra'], str):
+            kwargs['extra'] = kwargs['extra'].split('.')
+
+        def _match(part, pattern, split=None):
+            if pattern is None or part is None:
+                # If either is None, both should be None to match
+                return pattern is part
+            elif split:
+                # Check all provided extra fields match those in ALF
+                return all(elem in part.split(split) for elem in pattern if elem)
+            elif not isinstance(pattern, str):
+                if wildcards:
+                    return any(_match(part, x, split) for x in pattern)
+                else:
+                    return re.match('|'.join(pattern), part) is not None
+            else:
+                # Check given attribute matches, allowing wildcards
+                return fnmatch(part, pattern) if wildcards else re.match(pattern, part) is not None
+
+        # Iterate over ALF files
+        for file, attr in zip(alf_files.copy(), attributes.copy()):
+            for k, v in kwargs.items():  # Iterate over attributes
+                match = _match(attr[k], v, '.' if k == 'extra' else None)
+
+                if not match:  # Remove file from list and move on to next file
+                    alf_files.remove(file)
+                    attributes.remove(attr)
+                    break
+
+    return alf_files, [tuple(attr.values()) for attr in attributes]
+
+
+def find_variants(file_list, namespace=True, timescale=True, extra=True, extension=True):
+    """Find variant datasets.
+
+    Finds any datasets on disk that are considered a variant of the input datasets. At minimum, a
+    dataset is uniquely defined by session path, collection, object and attribute. Therefore,
+    datasets with the same name and collection in a different revision folder are considered a
+    variant. If any of the keyword arguments are set to False, those parts are ignored when
+    comparing datasets.
+
+    Parameters
+    ----------
+    file_list : list of str, list of pathlib.Path
+        A list of ALF paths to find variants of.
+    namespace : bool
+        If true, treat datasets with a different namespace as unique.
+    timescale : bool
+        If true, treat datasets with a different timescale as unique.
+    extra : bool
+        If true, treat datasets with a different extra parts as unique.
+    extension : bool
+        If true, treat datasets with a different extension as unique.
+
+    Returns
+    -------
+    Dict[pathlib.Path, list of pathlib.Path]
+        A map of input file paths to a list variant dataset paths.
+
+    Raises
+    ------
+    ValueError
+        One or more input file paths are not valid ALF datasets.
+
+    Examples
+    --------
+    Find all datasets with an identical name and collection in a different revision folder
+
+    >>> find_variants(['/sub/2020-10-01/001/alf/#2020-01-01#/obj.attr.npy'])
+    {Path('/sub/2020-10-01/001/alf/#2020-01-01#/obj.attr.npy'): [
+        Path('/sub/2020-10-01/001/alf/obj.attr.npy')
+    ]}
+
+    Find all datasets with different namespace or revision
+
+    >>> find_variants(['/sub/2020-10-01/001/alf/#2020-01-01#/obj.attr.npy'], namespace=False)
+    {Path('/sub/2020-10-01/001/#2020-01-01#/obj.attr.npy'): [
+        Path('/sub/2020-10-01/001/#2020-01-01#/_ns_obj.attr.npy'),
+        Path('/sub/2020-10-01/001/obj.attr.npy'),
+    ]}
+
+    """
+    # Initialize map of unique files to their duplicates
+    duplicates = {}
+    # Determine which parts to filter
+    variables = locals()
+    filters = {'namespace', 'timescale', 'extra', 'extension'}
+    to_compare = ('lab', 'subject', 'date', 'number', 'collection', 'object', 'attribute',
+                  *(arg for arg in filters if variables[arg]))
+
+    def parts_match(parts, file):
+        """Compare a file's unique parts to a given file."""
+        other = file.parse_alf_path()
+        return all(parts[k] == other[k] for k in to_compare)
+
+    # iterate over unique files and their parts
+    for f in map(path.ALFPath, file_list):
+        parts = f.parse_alf_path()
+        # first glob for files matching object.attribute (including revisions)
+        pattern = f'*{parts["object"]}.{parts["attribute"]}*'
+        # this works because revision will always be last folder;
+        # i.e. revisions can't contain collections
+        globbed = map(f.without_revision().parent.glob, (pattern, '#*#/' + pattern))
+        globbed = chain.from_iterable(globbed)  # unite revision and non-revision globs
+        # refine duplicates based on other parts (this also ensures we don't catch similar objects)
+        globbed = filter(partial(parts_match, parts), globbed)
+        # key = f.relative_to_session().as_posix()
+        duplicates[f] = [x for x in globbed if x != f]  # map file to list of its duplicates
+    return duplicates