pipeline.py

import os

import datajoint as dj
from element_animal import subject
from element_animal.subject import Subject
from element_array_ephys import ephys_report, probe
from element_event import event, trial
from element_lab import lab, project
from element_lab.lab import Lab, Project, Protocol, Source, User
from element_session import session_with_datetime as session
from element_session.session_with_datetime import Session

from . import analysis
from .paths import (
    get_electrode_localization_dir,
    get_ephys_root_data_dir,
    get_processed_root_data_dir,
    get_session_directory,
)

if "custom" not in dj.config:
    dj.config["custom"] = {}

db_prefix = dj.config["custom"].get("database.prefix", "")

# ------------- Import the configured "ephys mode" -------------
ephys_mode = os.getenv("EPHYS_MODE", dj.config["custom"].get("ephys_mode", "acute"))
if ephys_mode == "acute":
    from element_array_ephys import ephys_acute as ephys
elif ephys_mode == "chronic":
    from element_array_ephys import ephys_chronic as ephys
elif ephys_mode == "no-curation":
    from element_animal.export.nwb import subject_to_nwb
    from element_array_ephys import ephys_no_curation as ephys
    from element_array_ephys.export.nwb import ecephys_session_to_nwb, write_nwb
    from element_lab.export.nwb import element_lab_to_nwb_dict
    from element_session.export.nwb import session_to_nwb
elif ephys_mode == "precluster":
    from element_array_ephys import ephys_precluster as ephys
else:
    raise ValueError(f"Unknown ephys mode: {ephys_mode}")


# ---------------- All items in namespace for linter -----------

__all__ = [
    # schemas
    "subject",
    "lab",
    "session",
    "trial",
    "event",
    "probe",
    "ephys",
    "ephys_report",
    # tables
    "Subject",
    "Source",
    "Lab",
    "Protocol",
    "User",
    "Project",
    "Session",
    # paths
    "get_ephys_root_data_dir",
    "get_session_directory",
    "get_electrode_localization_dir",
    # export
    "subject_to_nwb",
    "ecephys_session_to_nwb",
    "write_nwb",
    "element_lab_to_nwb_dict",
    "session_to_nwb",
]


# Activate "lab", "subject", "session" schema ---------------------------------

lab.activate(db_prefix + "lab")
project.activate(db_prefix + "project", linking_module=__name__)

subject.activate(db_prefix + "subject", linking_module=__name__)

Experimenter = lab.User

session.activate(db_prefix + "session", linking_module=__name__)


# Activate "event" and "trial" schema -----------------------------------------

trial.activate(db_prefix + "trial", db_prefix + "event", linking_module=__name__)


# Declare table "SkullReference" for use in element-array-ephys ---------------


@lab.schema
class SkullReference(dj.Lookup):
    definition = """
    skull_reference   : varchar(60)
    """
    contents = zip(["Bregma", "Lambda"])


# Activate "ephys" schema -----------------------------------------------------

ephys.activate(db_prefix + "ephys", db_prefix + "probe", linking_module=__name__)

# Activate "analysis" schema --------------------------------------------------

analysis.activate(db_prefix + "analysis", linking_module=__name__)