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surgery.py

activate(surgery_schema_name, subject_schema_name=None, *, create_schema=True, create_tables=True, linking_module=True)

Activate this schema.

Parameters:

Name Type Description Default
schema_name str

schema name on the database server to activate the subject element

 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 tables in the database if they do not yet exist.

 True
linking_module bool

a module name or a module containing the

 True
required dependencies to activate the `subject` element
required

Dependencies:

Upstream tables

User: the who conducted a particular surgery/implantation

Source code in element_animal/surgery.py 
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def activate(
    surgery_schema_name: str,
    subject_schema_name: str = None,
    *,
    create_schema: bool = True,
    create_tables: bool = True,
    linking_module: bool = True,
):
    """Activate this schema.

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

    Dependencies:
    Upstream tables:
        User: the who conducted a particular surgery/implantation
    """

    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

    subject.activate(
        subject_schema_name,
        create_schema=create_schema,
        create_tables=create_tables,
        linking_module=linking_module,
    )
    schema.activate(
        surgery_schema_name,
        create_schema=create_schema,
        create_tables=create_tables,
        add_objects=linking_module.__dict__,
    )

CoordinateReference

Bases: dj.Lookup

Coordinate reference system

Attributes:

Name Type Description
reference varchar(60)

Reference system (e.g., bregma, lambda, etc.)
Source code in element_animal/surgery.py 
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@schema
class CoordinateReference(dj.Lookup):
    """Coordinate reference system

    Attributes:
        reference ( varchar(60) ): Reference system (e.g., bregma, lambda, etc.)
    """

    definition = """
    reference   : varchar(32)
    """
    contents = zip(
        ["bregma", "lambda", "dura", "skull_surface", "sagittal_suture", "sinus"]
    )

BrainRegion

Bases: dj.Manual

Brain region of a given surgery

Attributes:

Name Type Description
region_acronym varchar(32) )

Brain region shorthand
region_name varchar(128) )

Brain region full name
Source code in element_animal/surgery.py 
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@schema
class BrainRegion(dj.Manual):
    """Brain region of a given surgery

    Attributes:
        region_acronym ( varchar(32) ) : Brain region shorthand
        region_name ( varchar(128) ) : Brain region full name
    """

    definition = """
    region_acronym : varchar(32)   # Brain region shorthand
    ---
    region_name    : varchar(256)  # Brain region full name
    """

Hemisphere

Bases: dj.Lookup

Brain region hemisphere

Attributes:

Name Type Description
hemisphere varchar(8)

Brain region hemisphere (e.g., left, right, middle)
Source code in element_animal/surgery.py 
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@schema
class Hemisphere(dj.Lookup):
    """Brain region hemisphere

    Attributes:
        hemisphere ( varchar(8) ): Brain region hemisphere (e.g., left, right, middle)
    """

    definition = """
    hemisphere: varchar(8) # Brain region hemisphere
    """

    contents = zip(["left", "right", "middle"])

ImplantationType

Bases: dj.Lookup

Type of implantation

Attributes:

Name Type Description
implant_type varchar(16)

Short name for type of implanted device
implant_description varchar(32)

Full description for implanted device
Source code in element_animal/surgery.py 
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@schema
class ImplantationType(dj.Lookup):
    """Type of implantation

    Attributes:
        implant_type ( varchar(16) ): Short name for type of implanted device
        implant_description ( varchar(32) ): Full description for implanted device
    """

    definition = """
    implant_type        : varchar(16) # Short name for type of implanted device
    ---
    implant_description : varchar(32) # Full description for implanted device
    """

    contents = (
        ("ephys", "electophysiology"),
        ("fiber", "fiber photometry"),
        ("opto", "optogenetic perturbation"),
    )

Implantation

Bases: dj.Manual

Implantation of a device

Attributes:

Name Type Description
Session foreign key

Session primary key
location_id int

ID of of brain location
ap float

In mm, Anterior/posterior; Anterior Positive
ap_reference projected attribute

Coordinate reference
ml float

In mm, medial axis; Right Positive
ml_reference projected attribute

Coordinate reference
dv float

In mm, dorso-ventral axis. Ventral negative
dv_reference projected attribute

Coordinate reference
theta float, nullable

Elevation in degrees. Rotation about ml-axis [0, 180] relative to z-axis
phi float, nullable

Azimuth in degrees. Rotations about dv-axis [0, 360] relative to x-axis
beta float, nullable

Rotation about shank in degrees. Rotation about the shank [-180, 180]. Clockwise is increasing. 0 is the probe-front facing anterior
Source code in element_animal/surgery.py 
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@schema
class Implantation(dj.Manual):
    """Implantation of a device

    Attributes:
        Session (foreign key): Session primary key
        location_id (int): ID of of brain location
        ap ( float ): In mm, Anterior/posterior; Anterior Positive
        ap_reference (projected attribute): Coordinate reference
        ml ( float ): In mm, medial axis; Right Positive
        ml_reference (projected attribute): Coordinate reference
        dv ( float ): In mm, dorso-ventral axis. Ventral negative
        dv_reference (projected attribute): Coordinate reference
        theta ( float, nullable ): Elevation in degrees.
            Rotation about ml-axis [0, 180] relative to z-axis
        phi ( float, nullable ): Azimuth in degrees.
            Rotations about dv-axis [0, 360] relative to x-axis
        beta ( float, nullable ): Rotation about shank in degrees.
            Rotation about the shank [-180, 180]. Clockwise is increasing.
            0 is the probe-front facing anterior
    """

    definition = """
    -> subject.Subject
    implant_date        : datetime       # surgery date
    -> ImplantationType
    -> BrainRegion.proj(target_region='region_acronym')
    -> Hemisphere.proj(target_hemisphere='hemisphere')
    ---
    -> User.proj(surgeon='user')         # surgeon
    implant_comment=''  : varchar(1024) # Comments about the implant
    """

    class Coordinate(dj.Part):
        definition = """
        -> master
        ---
        ap=null       : float  # (mm) anterior-posterior; ref is 0
        -> [nullable] CoordinateReference.proj(ap_ref='reference')
        ml=null       : float  # (mm) medial axis; ref is 0
        -> [nullable] CoordinateReference.proj(ml_ref='reference')
        dv=null       : float  # (mm) dorso-ventral axis; ventral negative
        -> [nullable] CoordinateReference.proj(dv_ref='reference')
        theta=null    : float  # (deg) rot about ml-axis [0, 180] wrt z
        phi=null      : float  # (deg) rot about dv-axis [0, 360] wrt x
        beta=null     : float  # (deg) rot about shank [-180, 180] wrt anterior
        """