Source code for ibl_alignment_gui.app.main

import os
import sys

# The spatial-encoder (torch) and inference (xgboost, via ephysatlas.regionclassifier) plugins
# each bundle their own OpenMP runtime. On macOS, having both loaded in one process leaves two
# independent libomp.dylib copies mapped in-process; as soon as either does a parallel OpenMP
# region (e.g. XGBoost's model loading), their internal thread-pool state collides and segfaults
# - confirmed via crash log + reproduction, independent of xgboost's own n_jobs setting. Forcing
# a single OpenMP thread avoids the thread-pool bring-up that triggers the corruption. Must be
# set before torch/xgboost are ever imported (they're lazily imported by the plugins later), so
# this needs to happen at process start, before those imports occur anywhere.
# Only macOS is affected; applying the limit elsewhere would needlessly single-thread the
# OpenMP-backed numpy/scipy work that the rest of the GUI depends on.
if sys.platform == 'darwin':
    os.environ.setdefault('OMP_NUM_THREADS', '1')

import argparse

from qtpy import QtWidgets

from ibl_alignment_gui.app.controllers.app_controller import AlignmentGUIController
from ibl_alignment_gui.utils.optional import (
    ALLEN_EXTRA_HINT,
    IBL_EXTRA_HINT,
    has_allen,
    has_ibllib,
)
from iblutil.util import setup_logger


def _setup_logging() -> None:
    """Attach a stream handler to the package logger so progress messages are visible.

    Without this the package's ``logger.info`` calls go nowhere: a library configures no
    handlers of its own, and Python's fallback handler only emits WARNING and above. Every
    launcher calls this so the GUI always reports what it is loading. Scoped to the
    ``ibl_alignment_gui`` logger so third-party log levels are left alone.
    """
    setup_logger('ibl_alignment_gui', level='INFO')


def _require_extra(available: bool, hint: str) -> None:
    """Exit with an actionable message if a required optional dependency is missing.

    Parameters
    ----------
    available : bool
        Whether the required optional dependency is installed.
    hint : str
        The install instructions shown when the dependency is missing.

    Raises
    ------
    SystemExit
        If ``available`` is False, exiting the process with the hint as the message.
    """
    if not available:
        raise SystemExit(hint)




def launch_app() -> None:
    """Launch the alignment GUI application in offline mode with optional YAML file."""
    parser = argparse.ArgumentParser()

    parser.add_argument('-y', '--yaml', required=False, type=str, help='Path to the YAML file')

    args = parser.parse_args()

    _setup_logging()
    app = QtWidgets.QApplication([])
    mainapp = AlignmentGUIController(offline=True, csv=None, yaml=args.yaml)
    mainapp.view.show()
    app.exec_()





def launch_app_ibl() -> None:
    """Launch the alignment GUI application in IBL mode.

    Optionally accepts a CSV file or a probe insertion id (pid) to auto-load. When a pid is
    given the subject, session and shank dropdowns are configured to that insertion and its
    data is loaded automatically.
    """
    # IBL online mode requires ibllib (raw-data streaming, alignment upload/QC).
    _require_extra(has_ibllib(), IBL_EXTRA_HINT)

    parser = argparse.ArgumentParser()

    parser.add_argument('-c', '--csv', required=False, type=str, help='Path to the CSV file')
    parser.add_argument(
        '-p', '--pid', required=False, type=str, help='Probe insertion id to auto-load'
    )

    args = parser.parse_args()

    if args.csv is not None and args.pid is not None:
        parser.error('--pid cannot be used together with --csv')

    _setup_logging()
    app = QtWidgets.QApplication([])
    try:
        mainapp = AlignmentGUIController(offline=False, csv=args.csv, yaml=None, pid=args.pid)
    except ValueError as err:
        parser.error(str(err))
    mainapp.view.show()
    app.exec_()





def launch_app_allen() -> None:
    """Launch the alignment GUI in Allen/Code Ocean mode with DocDB support.

    Runs offline from a session YAML (chosen from the source button, or passed with ``-y``) and
    adds a DocDB checkbox that toggles whether previous alignments are read from, and results
    written to, the Allen DocDB (ticked) or the local files (unticked).
    """
    # Allen mode requires the aind/DocDB dependency stack.
    _require_extra(has_allen(), ALLEN_EXTRA_HINT)

    parser = argparse.ArgumentParser()

    parser.add_argument('-y', '--yaml', required=False, type=str, help='Path to the YAML file')

    args = parser.parse_args()

    _setup_logging()
    app = QtWidgets.QApplication([])
    mainapp = AlignmentGUIController(offline=True, csv=None, yaml=args.yaml, allen=True)
    mainapp.view.show()
    app.exec_()



if __name__ == '__main__':
    launch_app()