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Folder

pynapple.io.folder

The Folder class helps to navigate a hierarchical data tree.

Folder

Bases: UserDict

Base class for all type of folders (i.e. Project, Subject, Sessions, ...). Handles files and sub-folders discovery

Attributes:

Name Type Description
data dict

Dictionary holidng all the pynapple objects found in the folder.

name str

Name of the folder

npz_files list

List of npz files found in the folder

nwb_files list

List of nwb files found in the folder

path str

Absolute path of the folder

subfolds dict

Dictionary of all the subfolders

Source code in pynapple/io/folder.py
class Folder(UserDict):
    """
    Base class for all type of folders (i.e. Project, Subject, Sessions, ...).
    Handles files and sub-folders discovery

    Attributes
    ----------
    data : dict
        Dictionary holidng all the pynapple objects found in the folder.
    name : str
        Name of the folder
    npz_files : list
        List of npz files found in the folder
    nwb_files : list
        List of nwb files found in the folder
    path : str
        Absolute path of the folder
    subfolds : dict
        Dictionary of all the subfolders

    """

    def __init__(self, path):  # , exclude=(), max_depth=4):
        """Initialize the Folder object

        Parameters
        ----------
        path : str
            Path to the folder
        """
        path = path.rstrip("/")
        self.path = path
        self.name = os.path.basename(path)
        self._basic_view = Tree(
            ":open_file_folder: {}".format(self.name), guide_style="blue"
        )
        self._full_view = None

        # Search sub-folders
        subfolds = [
            f.path
            for f in os.scandir(path)
            if f.is_dir() and not f.name.startswith(".")
        ]
        subfolds.sort()

        self.subfolds = {}

        for s in subfolds:
            sub = os.path.basename(s)
            self.subfolds[sub] = Folder(s)
            self._basic_view.add(":open_file_folder: [blue]" + sub)

        # Search files
        self.npz_files = _find_files(path, "npz")
        self.nwb_files = _find_files(path, "nwb")

        for filename, file in self.npz_files.items():
            self._basic_view.add("[green]" + file.name + " \t|\t " + file.type)

        for file in self.nwb_files.values():
            self._basic_view.add("[magenta]" + file.name + " \t|\t NWB file")

        # Putting everything together
        self.data = {**self.npz_files, **self.nwb_files, **self.subfolds}

        UserDict.__init__(self, self.data)

    def __str__(self):
        """View of the object"""
        with Console() as console:
            console.print(self._basic_view)
        return ""

    # def __repr__(self):
    #     """View of the object"""
    #     print(self._basic_view)

    def __getitem__(self, key):
        """Get subfolder or load file.

        Parameters
        ----------
        key : str

        Returns
        -------
        (Ts, Tsd, TsdFrame, TsGroup, IntervalSet, Folder or NWBFile)

        Raises
        ------
        KeyError
            If key is not in the dictionary
        """
        if key.__hash__:
            if self.__contains__(key):
                if isinstance(self.data[key], NPZFile):
                    data = self.data[key].load()
                    self.data[key] = data
                    # setattr(self, key, data)
                    return data
                elif isinstance(self.data[key], NWBFile):
                    return self.data[key]
                else:
                    return self.data[key]
            else:
                raise KeyError("Can't find key {} in group index.".format(key))

    # # # Gets called when an attribute is accessed
    # def __getattribute__(self, item):
    #     value = super(Folder, self).__getattribute__(item)

    #     if isinstance(value, NPZFile):
    #         data = value.load()
    #         setattr(self, item, data)
    #         self.data[item] = data
    #         return data
    #     else:
    #         return value

    def _generate_tree_view(self):
        tree = Tree(":open_file_folder: {}".format(self.name), guide_style="blue")

        # Folder
        for fold in self.subfolds.keys():
            tree.add(":open_file_folder: " + fold)
            _walk_folder(tree.children[-1], self.subfolds[fold])

        # NPZ files
        for file in self.npz_files.values():
            tree.add("[green]" + file.name + " \t|\t " + file.type)

        # NWB files
        for file in self.nwb_files.values():
            tree.add("[magenta]" + file.name + " \t|\t NWB file")

        self._full_view = tree

    def expand(self):
        """Display the full tree view. Equivalent to Folder.view"""
        if not isinstance(self._full_view, Tree):
            self._generate_tree_view()

        with Console() as console:
            console.print(self._full_view)

        return None

    @property
    def view(self):
        """Summary"""
        return self.expand()

    def save(self, name, obj, description=""):
        """Save a pynapple object in the folder in a single file in uncompressed ``.npz`` format.
        By default, the save function overwrite previously save file with the same name.

        Parameters
        ----------
        name : str
            Filename
        obj : Ts, Tsd, TsdFrame, TsGroup or IntervalSet
            Pynapple object.
        description : str, optional
            Metainformation added as a json sidecar.
        """
        filepath = os.path.join(self.path, name)
        obj.save(filepath)
        self.npz_files[name] = NPZFile(filepath + ".npz")
        self.data[name] = obj

        metadata = {"time": str(datetime.now()), "info": str(description)}

        with open(os.path.join(self.path, name + ".json"), "w") as ff:
            json.dump(metadata, ff, indent=2)

        # regenerate the tree view
        self._generate_tree_view()

    def load(self):
        """Load all compatible NPZ files."""
        for k in self.npz_files.keys():
            self[k] = self.npz_files[k].load()

    # def add_metadata(self):
    #     """Summary"""
    #     pass

    def info(self, name):
        """Display the metadata within the json sidecar of a NPZ file

        Parameters
        ----------
        name : str
            Name of the npz file
        """
        self.metadata(name)

    def doc(self, name):
        """Display the metadata within the json sidecar of a NPZ file

        Parameters
        ----------
        name : str
            Name of the npz file
        """
        self.metadata(name)

    def metadata(self, name):
        """Display the metadata within the json sidecar of a NPZ file

        Parameters
        ----------
        name : str
            Name of the npz file
        """
        # Search for json first
        json_filename = os.path.join(self.path, name + ".json")
        if os.path.isfile(json_filename):
            with open(json_filename, "r") as ff:
                metadata = json.load(ff)
                text = "\n".join([" : ".join(it) for it in metadata.items()])
            panel = Panel.fit(
                text, border_style="green", title=os.path.join(self.path, name + ".npz")
            )
        else:
            panel = Panel.fit(
                "No metadata",
                border_style="red",
                title=os.path.join(self.path, name + ".npz"),
            )
        with Console() as console:
            console.print(panel)

        return None

view property

view

Summary

__init__

__init__(path)

Initialize the Folder object

Parameters:

Name Type Description Default
path str

Path to the folder

required
Source code in pynapple/io/folder.py
def __init__(self, path):  # , exclude=(), max_depth=4):
    """Initialize the Folder object

    Parameters
    ----------
    path : str
        Path to the folder
    """
    path = path.rstrip("/")
    self.path = path
    self.name = os.path.basename(path)
    self._basic_view = Tree(
        ":open_file_folder: {}".format(self.name), guide_style="blue"
    )
    self._full_view = None

    # Search sub-folders
    subfolds = [
        f.path
        for f in os.scandir(path)
        if f.is_dir() and not f.name.startswith(".")
    ]
    subfolds.sort()

    self.subfolds = {}

    for s in subfolds:
        sub = os.path.basename(s)
        self.subfolds[sub] = Folder(s)
        self._basic_view.add(":open_file_folder: [blue]" + sub)

    # Search files
    self.npz_files = _find_files(path, "npz")
    self.nwb_files = _find_files(path, "nwb")

    for filename, file in self.npz_files.items():
        self._basic_view.add("[green]" + file.name + " \t|\t " + file.type)

    for file in self.nwb_files.values():
        self._basic_view.add("[magenta]" + file.name + " \t|\t NWB file")

    # Putting everything together
    self.data = {**self.npz_files, **self.nwb_files, **self.subfolds}

    UserDict.__init__(self, self.data)

__str__

__str__()

View of the object

Source code in pynapple/io/folder.py
def __str__(self):
    """View of the object"""
    with Console() as console:
        console.print(self._basic_view)
    return ""

__getitem__

__getitem__(key)

Get subfolder or load file.

Parameters:

Name Type Description Default
key str
required

Returns:

Type Description
(Ts, Tsd, TsdFrame, TsGroup, IntervalSet, Folder or NWBFile)

Raises:

Type Description
KeyError

If key is not in the dictionary

Source code in pynapple/io/folder.py
def __getitem__(self, key):
    """Get subfolder or load file.

    Parameters
    ----------
    key : str

    Returns
    -------
    (Ts, Tsd, TsdFrame, TsGroup, IntervalSet, Folder or NWBFile)

    Raises
    ------
    KeyError
        If key is not in the dictionary
    """
    if key.__hash__:
        if self.__contains__(key):
            if isinstance(self.data[key], NPZFile):
                data = self.data[key].load()
                self.data[key] = data
                # setattr(self, key, data)
                return data
            elif isinstance(self.data[key], NWBFile):
                return self.data[key]
            else:
                return self.data[key]
        else:
            raise KeyError("Can't find key {} in group index.".format(key))

expand

expand()

Display the full tree view. Equivalent to Folder.view

Source code in pynapple/io/folder.py
def expand(self):
    """Display the full tree view. Equivalent to Folder.view"""
    if not isinstance(self._full_view, Tree):
        self._generate_tree_view()

    with Console() as console:
        console.print(self._full_view)

    return None

save

save(name, obj, description='')

Save a pynapple object in the folder in a single file in uncompressed .npz format. By default, the save function overwrite previously save file with the same name.

Parameters:

Name Type Description Default
name str

Filename

required
obj (Ts, Tsd, TsdFrame, TsGroup or IntervalSet)

Pynapple object.

required
description str

Metainformation added as a json sidecar.

''
Source code in pynapple/io/folder.py
def save(self, name, obj, description=""):
    """Save a pynapple object in the folder in a single file in uncompressed ``.npz`` format.
    By default, the save function overwrite previously save file with the same name.

    Parameters
    ----------
    name : str
        Filename
    obj : Ts, Tsd, TsdFrame, TsGroup or IntervalSet
        Pynapple object.
    description : str, optional
        Metainformation added as a json sidecar.
    """
    filepath = os.path.join(self.path, name)
    obj.save(filepath)
    self.npz_files[name] = NPZFile(filepath + ".npz")
    self.data[name] = obj

    metadata = {"time": str(datetime.now()), "info": str(description)}

    with open(os.path.join(self.path, name + ".json"), "w") as ff:
        json.dump(metadata, ff, indent=2)

    # regenerate the tree view
    self._generate_tree_view()

load

load()

Load all compatible NPZ files.

Source code in pynapple/io/folder.py
def load(self):
    """Load all compatible NPZ files."""
    for k in self.npz_files.keys():
        self[k] = self.npz_files[k].load()

info

info(name)

Display the metadata within the json sidecar of a NPZ file

Parameters:

Name Type Description Default
name str

Name of the npz file

required
Source code in pynapple/io/folder.py
def info(self, name):
    """Display the metadata within the json sidecar of a NPZ file

    Parameters
    ----------
    name : str
        Name of the npz file
    """
    self.metadata(name)

doc

doc(name)

Display the metadata within the json sidecar of a NPZ file

Parameters:

Name Type Description Default
name str

Name of the npz file

required
Source code in pynapple/io/folder.py
def doc(self, name):
    """Display the metadata within the json sidecar of a NPZ file

    Parameters
    ----------
    name : str
        Name of the npz file
    """
    self.metadata(name)

metadata

metadata(name)

Display the metadata within the json sidecar of a NPZ file

Parameters:

Name Type Description Default
name str

Name of the npz file

required
Source code in pynapple/io/folder.py
def metadata(self, name):
    """Display the metadata within the json sidecar of a NPZ file

    Parameters
    ----------
    name : str
        Name of the npz file
    """
    # Search for json first
    json_filename = os.path.join(self.path, name + ".json")
    if os.path.isfile(json_filename):
        with open(json_filename, "r") as ff:
            metadata = json.load(ff)
            text = "\n".join([" : ".join(it) for it in metadata.items()])
        panel = Panel.fit(
            text, border_style="green", title=os.path.join(self.path, name + ".npz")
        )
    else:
        panel = Panel.fit(
            "No metadata",
            border_style="red",
            title=os.path.join(self.path, name + ".npz"),
        )
    with Console() as console:
        console.print(panel)

    return None