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optogenetics.py

activate(schema_name, *, create_schema=True, create_tables=True, linking_module=None)

Activate this schema.

Parameters:

Name Type Description Default
schema_name str

schema name on the database server

 required
create_schema bool

when True (default), create schema in the database if it does not yet exist.

 True
create_tables bool

when True (default), create schema tables in the database if they do not yet exist.

 True
linking_module str

a module (or name) containing the required dependencies.

 None
Dependencies

Upstream tables: Device: Referenced by OptoProtocol. Pulse generator used for stimulation. Session: Referenced by OptoProtocol. Typically a recording session. Implantation: Referenced by OptoProtocol. Location of the implanted optical fiber.

Source code in element_optogenetics/optogenetics.py 
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def activate(
    schema_name: str,
    *,
    create_schema: bool = True,
    create_tables: bool = True,
    linking_module: str = None,
):
    """Activate this schema.

    Args:
        schema_name (str): schema name on the database server
        create_schema (bool): when True (default), create schema in the database if it
                            does not yet exist.
        create_tables (bool): when True (default), create schema tables in the database
                             if they do not yet exist.
        linking_module (str): a module (or name) containing the required dependencies.

    Dependencies:
        Upstream tables:
            Device: Referenced by OptoProtocol. Pulse generator used for stimulation.
            Session: Referenced by OptoProtocol. Typically a recording session.
            Implantation: Referenced by OptoProtocol. Location of the implanted optical fiber.
    """

    if isinstance(linking_module, str):
        linking_module = importlib.import_module(linking_module)
    assert inspect.ismodule(
        linking_module
    ), "The argument 'linking_module' must be a module's name or a module"

    global _linking_module
    _linking_module = linking_module

    schema.activate(
        schema_name,
        create_schema=create_schema,
        create_tables=create_tables,
        add_objects=_linking_module.__dict__,
    )

OptoWaveformType

Bases: Lookup

Stimulus waveform type (e.g., square, sine, etc.)

Attributes:

Name Type Description
waveform_type varchar(32)

Waveform type (e.g., square, sine)
Source code in element_optogenetics/optogenetics.py 
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@schema
class OptoWaveformType(dj.Lookup):
    """Stimulus waveform type (e.g., square, sine, etc.)

    Attributes:
        waveform_type ( varchar(32) ): Waveform type (e.g., square, sine)
    """

    definition = """
    waveform_type:    varchar(32)
    """
    contents = zip(["Square", "Ramp", "Sine"])

OptoWaveform

Bases: Lookup

OptoWaveform defines the shape of one cycle of the optogenetic stimulus

Child tables specify features of specific waveforms (e.g., square, sine, etc.)

Attributes:

Name Type Description
waveform_name varchar(32)

Name of waveform
OptoWaveformType foreign key

OptoWaveformType primary key
normalized_waveform longblob

For one cycle, normalized to peak
waveform_description varchar(255), optional

Description of waveform
Source code in element_optogenetics/optogenetics.py 
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@schema
class OptoWaveform(dj.Lookup):
    """OptoWaveform defines the shape of one cycle of the optogenetic stimulus

    Child tables specify features of specific waveforms (e.g., square, sine, etc.)

    Attributes:
        waveform_name ( varchar(32) ): Name of waveform
        OptoWaveformType (foreign key): OptoWaveformType primary key
        normalized_waveform (longblob, optional): For one cycle, normalized to peak
        waveform_description ( varchar(255), optional ): Description of waveform
    """

    definition = """
    # OptoWaveform defines the shape of one cycle of the optogenetic stimulus
    waveform_name            : varchar(32)
    ---
    -> OptoWaveformType
    normalized_waveform=null : longblob      # For one cycle, normalized to peak
    waveform_description=''  : varchar(255)  # description of the waveform
    """

    class Square(dj.Part):
        """Square waveform

        Attributes:
            OptoWaveform (foreign key): OptoWaveform primary key
            on_proportion ( decimal(2, 2) unsigned ): Proportion of stimulus on time within a cycle
            off_proportion ( decimal(2, 2) unsigned ): Proportion of stimulus off time within a cycle
        """

        definition = """
        -> master
        ---
        on_proportion  : decimal(2, 2) unsigned # Proportion of stimulus on time within a cycle
        off_proportion : decimal(2, 2) unsigned # Proportion of stimulus off time within a cycle
        """

    class Ramp(dj.Part):
        """Ramp waveform

        Attributes:
            OptoWaveform (foreign key): OptoWaveform primary key
            ramp_up_proportion ( decimal(2, 2) unsigned ): Ramp up proportion of the linear waveform
            ramp_down_proportion ( decimal(2, 2) unsigned ): Ramp down proportion of the linear waveform
        """

        definition = """
        -> master
        ---
        ramp_up_proportion   : decimal(2, 2) unsigned # Ramp up proportion of the linear waveform
        ramp_down_proportion : decimal(2, 2) unsigned # Ramp down proportion of the linear waveform
        """

    class Sine(dj.Part):
        """Sine Waveform. Starting_phase ranges (0, 2]. 0 for Sine, 0.5 for Cosine

        Attributes:
            OptoWaveform (foreign key): OptoWaveform primary key
            number_of_cycles (smallint): Number of cycles
            starting_phase (decimal(3, 2) ): Phase in pi at the beginning of the cycle.
                Defaults to 0
        """

        definition = """ # Starting_phase ranges (0, 2]. 0 for Sine, 0.5 for Cosine
        -> master
        ---
        number_of_cycles  : smallint
        starting_phase=0  : decimal(3, 2) # (pi) phase at the beginning of the cycle
        """

Square

Bases: Part

Square waveform

Attributes:

Name Type Description
OptoWaveform foreign key

OptoWaveform primary key
on_proportion decimal(2, 2) unsigned

Proportion of stimulus on time within a cycle
off_proportion decimal(2, 2) unsigned

Proportion of stimulus off time within a cycle
Source code in element_optogenetics/optogenetics.py 
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class Square(dj.Part):
    """Square waveform

    Attributes:
        OptoWaveform (foreign key): OptoWaveform primary key
        on_proportion ( decimal(2, 2) unsigned ): Proportion of stimulus on time within a cycle
        off_proportion ( decimal(2, 2) unsigned ): Proportion of stimulus off time within a cycle
    """

    definition = """
    -> master
    ---
    on_proportion  : decimal(2, 2) unsigned # Proportion of stimulus on time within a cycle
    off_proportion : decimal(2, 2) unsigned # Proportion of stimulus off time within a cycle
    """

Ramp

Bases: Part

Ramp waveform

Attributes:

Name Type Description
OptoWaveform foreign key

OptoWaveform primary key
ramp_up_proportion decimal(2, 2) unsigned

Ramp up proportion of the linear waveform
ramp_down_proportion decimal(2, 2) unsigned

Ramp down proportion of the linear waveform
Source code in element_optogenetics/optogenetics.py 
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class Ramp(dj.Part):
    """Ramp waveform

    Attributes:
        OptoWaveform (foreign key): OptoWaveform primary key
        ramp_up_proportion ( decimal(2, 2) unsigned ): Ramp up proportion of the linear waveform
        ramp_down_proportion ( decimal(2, 2) unsigned ): Ramp down proportion of the linear waveform
    """

    definition = """
    -> master
    ---
    ramp_up_proportion   : decimal(2, 2) unsigned # Ramp up proportion of the linear waveform
    ramp_down_proportion : decimal(2, 2) unsigned # Ramp down proportion of the linear waveform
    """

Sine

Bases: Part

Sine Waveform. Starting_phase ranges (0, 2]. 0 for Sine, 0.5 for Cosine

Attributes:

Name Type Description
OptoWaveform foreign key

OptoWaveform primary key
number_of_cycles smallint

Number of cycles
starting_phase decimal(3, 2)

Phase in pi at the beginning of the cycle. Defaults to 0
Source code in element_optogenetics/optogenetics.py 
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class Sine(dj.Part):
    """Sine Waveform. Starting_phase ranges (0, 2]. 0 for Sine, 0.5 for Cosine

    Attributes:
        OptoWaveform (foreign key): OptoWaveform primary key
        number_of_cycles (smallint): Number of cycles
        starting_phase (decimal(3, 2) ): Phase in pi at the beginning of the cycle.
            Defaults to 0
    """

    definition = """ # Starting_phase ranges (0, 2]. 0 for Sine, 0.5 for Cosine
    -> master
    ---
    number_of_cycles  : smallint
    starting_phase=0  : decimal(3, 2) # (pi) phase at the beginning of the cycle
    """

OptoStimParams

Bases: Manual

A single optical stimulus that repeats.

Power and intensity are both optional. Users may wish to document one or the other.

Attributes:

Name Type Description
opto_params_id smallint

Stimulus parameter ID
OptoWaveform foreign key

OptoWaveform primary key
wavelength int

Wavelength in nm of optical stimulation light
power decimal(6, 2), optional

Total power in mW from light source
light_intensity decimal(6, 2), optional

Power for given area
frequency decimal(5, 1)

Frequency in Hz of the waveform
duration decimal(5, 1)

Duration in ms of each optical stimulus
Source code in element_optogenetics/optogenetics.py 
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@schema
class OptoStimParams(dj.Manual):
    """A single optical stimulus that repeats.

    Power and intensity are both optional. Users may wish to document one or the other.

    Attributes:
        opto_params_id (smallint): Stimulus parameter ID
        OptoWaveform (foreign key): OptoWaveform primary key
        wavelength (int): Wavelength in nm of optical stimulation light
        power ( decimal(6, 2), optional ): Total power in mW from light source
        light_intensity ( decimal(6, 2), optional ): Power for given area
        frequency ( decimal(5, 1) ): Frequency in Hz of the waveform
        duration ( decimal(5, 1) ): Duration in ms of each optical stimulus
    """

    definition = """
    # Defines a single optical stimulus that repeats.
    opto_params_id     : smallint
    ---
    -> OptoWaveform
    wavelength           : int             # (nm) wavelength of optical stimulation light
    power=null           : decimal(6, 2)   # (mW) total power from light source
    light_intensity=null : decimal(6, 2)   # (mW/mm2) power for given area
    frequency            : decimal(5, 1)   # (Hz) frequency of the waveform
    duration             : decimal(5, 1)   # (ms) duration of each optical stimulus
    """

OptoProtocol

Bases: Manual

Protocol for a given session. This table ties together the fiber location, pulse generator, and stimulus parameters.

Attributes:

Name Type Description
Session foreign key

Session primary key
protocol_id int

Protocol ID
OptoStimParams foreign key

OptoStimParams primary key
Implantation foreign key

Implantation primary key
Device (foreign key

Device primary key
protocol_description varchar(255), optional

Description of optogenetics protocol
Source code in element_optogenetics/optogenetics.py 
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@schema
class OptoProtocol(dj.Manual):
    """Protocol for a given session.  This table ties together the fiber location, pulse generator, and stimulus parameters.

    Attributes:
        Session (foreign key): Session primary key
        protocol_id (int): Protocol ID
        OptoStimParams (foreign key): OptoStimParams primary key
        Implantation (foreign key): Implantation primary key
        Device  (foreign key, optional): Device  primary key
        protocol_description ( varchar(255), optional ): Description of optogenetics protocol
    """

    definition = """
    -> Session
    protocol_id: int
    ---
    -> OptoStimParams
    -> Implantation
    -> [nullable] Device
    protocol_description='' : varchar(255) # description of optogenetics protocol
    """

OptoEvent

Bases: Manual

Start and end time of the stimulus within a session

Attributes:

Name Type Description
OptoProtocol foreign key

OptoProtocol primary key
stim_start_time float

Stimulus start time in seconds relative to session start
stim_end_time float

Stimulus end time in seconds relative to session start
Source code in element_optogenetics/optogenetics.py 
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@schema
class OptoEvent(dj.Manual):
    """Start and end time of the stimulus within a session

    Attributes:
        OptoProtocol (foreign key): OptoProtocol primary key
        stim_start_time (float): Stimulus start time in seconds relative to session start
        stim_end_time (float): Stimulus end time in seconds relative to session start
    """

    definition = """
    -> OptoProtocol
    stim_start_time  : float  # (s) stimulus start time relative to session start
    ---
    stim_end_time    : float  # (s) stimulus end time relative session start
    """