from .architype import (
    archetypes,
    archetypes_genes,
    find_spatial_archetypes,
    find_spatially_related_genes,
    get_genes_from_spatial_archetype,
)
from .cci_two_cluster import (
    find_cci_two_group,
    prepare_cci_cellpair_adata,
    prepare_cci_df,
)
from .cell_communication import niches, predict_ligand_activities, predict_target_genes
from .cluster import *
from .cluster.find_clusters import scc, spagcn_pyg
from .cluster_degs import (
    find_all_cluster_degs,
    find_cluster_degs,
    find_spatial_cluster_degs,
    top_n_degs,
)
from .cluster_lasso import *
from .coarse_align import AffineTrans, align_slices_pca, pca_align, procrustes
from .find_neighbors import (
    construct_geodesic_distance_matrix,
    construct_nn_graph,
    construct_spatial_distance_matrix,
    generate_spatial_weights_fixed_nbrs,
    generate_spatial_weights_fixed_radius,
    weighted_expr_neighbors_graph,
    weighted_spatial_graph,
)
from .glm import glm_degs

# from .image import add_image_layer
# from .interpolation_utils import *
from .labels import Label, create_label_class
from .lisa import GM_lag_model, lisa_geo_df, local_moran_i
from .live_wire import LiveWireSegmentation, compute_shortest_path, live_wire
from .paste import (
    center_align,
    generalized_procrustes_analysis,
    mapping_aligned_coords,
    mapping_center_coords,
    pairwise_align,
)
from .spatial_degs import cellbin_morani, moran_i
from .spatial_impute import *
from .spatial_impute.impute import STGNN
from .spatial_impute.run_impute import impute_and_downsample
from .ST_regression import *
from .ST_regression.generalized_lm import fit_glm
from .ST_regression.regression_utils import plot_prior_vs_data
from .ST_regression.spatial_regression import (
    Category_Model,
    Lagged_Model,
    Niche_LR_Model,
    Niche_Model,
)
from .three_dims_align import (
    get_align_labels,
    models_align,
    models_align_ref,
    models_center_align,
    models_center_align_ref,
    rigid_transform_2D,
    rigid_transform_3D,
)
