"""
DynaCLR Visualization Package

A modular package for visualizing cell embeddings and infection status
with interactive microscopy image viewing.
"""

from .config import (
    DATA_PATH,
    OME_ZARR_PATH,
    ANNDATA_PATH,
    INFECTION_ANNOTATIONS_PATH,
    INFECTION_COLOR_MAP,
    DEFAULT_CROP_SIZE,
    DEFAULT_CONTRAST,
    DEFAULT_OPACITY,
)
from .data import (
    load_ome_dataset,
    load_anndata,
    get_embedding_data,
    get_all_embeddings,
    get_fov_choices,
    get_tracks_for_fov,
    is_track_annotated,
)
from .image import extract_track_images, normalize_channel_image
from .plot import create_embedding_plot
from .handlers import (
    update_plot_and_selector,
    update_track_selector,
    on_cell_selected,
    update_channel_images,
)
from .ui import create_app

__all__ = [
    # Config
    "DATA_PATH",
    "OME_ZARR_PATH",
    "ANNDATA_PATH",
    "INFECTION_ANNOTATIONS_PATH",
    "INFECTION_COLOR_MAP",
    "DEFAULT_CROP_SIZE",
    "DEFAULT_CONTRAST",
    "DEFAULT_OPACITY",
    # Data
    "load_ome_dataset",
    "load_anndata",
    "get_embedding_data",
    "get_all_embeddings",
    "get_fov_choices",
    "get_tracks_for_fov",
    "is_track_annotated",
    # Image
    "extract_track_images",
    "normalize_channel_image",
    # Plot
    "create_embedding_plot",
    # Handlers
    "update_plot_and_selector",
    "update_track_selector",
    "on_cell_selected",
    "update_channel_images",
    # UI
    "create_app",
]