pipeline.py

get_miniscope_root_data_dir()

Return root directory for miniscope from 'miniscope_root_data_dir' config as list

Returns:

Name	Type	Description
path	any	List of path(s) if available or None

Source code in workflow_miniscope/paths.py

def get_miniscope_root_data_dir() -> Union[list, None]:
    """Return root directory for miniscope from 'miniscope_root_data_dir' config as list

    Returns:
        path (any): List of path(s) if available or None
    """
    mini_root_dirs = dj.config.get("custom", {}).get("miniscope_root_data_dir")

    if not mini_root_dirs:
        return None
    elif not isinstance(mini_root_dirs, abc.Sequence):
        return list(mini_root_dirs)
    else:
        return mini_root_dirs

Device

Bases: dj.Lookup

Table for managing lab Devices.

Attributes:

Name	Type	Description
device	varchar(32)	Device short name.
modality	varchar(64)	Modality for which this device is used.
description	varchar(256)	Optional. Description of device.

Source code in workflow_miniscope/reference.py

@schema
class Device(dj.Lookup):
    """Table for managing lab Devices.

    Attributes:
        device ( varchar(32) ): Device short name.
        modality ( varchar(64) ): Modality for which this device is used.
        description ( varchar(256) ): Optional. Description of device.
    """

    definition = """
    device             : varchar(32)
    ---
    modality           : varchar(64)
    description=''     : varchar(256)
    """
    contents = [
        ["Miniscope_V4_BNO", "Miniscope", "V4 Miniscope with head orientation sensor."],
    ]

get_session_directory(session_key)

Return relative path from SessionDirectory table given key

Parameters:

Name	Type	Description	Default
session_key	dict	Key uniquely identifying a session	required

Returns:

Name	Type	Description
path	str	Relative path of session directory

Source code in workflow_miniscope/paths.py

def get_session_directory(session_key: dict) -> str:
    """Return relative path from SessionDirectory table given key

    Args:
        session_key (dict): Key uniquely identifying a session

    Returns:
        path (str): Relative path of session directory
    """
    from .pipeline import session

    session_dir = (session.SessionDirectory & session_key).fetch1("session_dir")
    return session_dir

AnatomicalLocation

Bases: dj.Manual

Lookup table for anatomical location

Attributes:

Name	Type	Description
recording_location_id	( varchar(16)	Lookup id for location
anatomical_description	varchar(256)	Location full description

Source code in workflow_miniscope/reference.py

@schema
class AnatomicalLocation(dj.Manual):
    """Lookup table for anatomical location

    Attributes:
        recording_location_id  ( varchar(16) ): Lookup id for location
        anatomical_description ( varchar(256) ): Location full description
    """

    definition = """
    recording_location_id : varchar(16) # Lookup id for location
    ---
    anatomical_description: varchar(256) # Location full description
    """