import scanpy as sc
import anndata as ad
import squidpy as sq
import pandas as pd
import seaborn as sns
import numpy as np
import warnings
from matplotlib import pyplot as plt
warnings.filterwarnings("ignore")
from _utils import *


class SG(object):
    """ Spatial Enrichment Analysis of Gene Association using L-index.
    """
    def __init__(self, 
                 count_path = "", meta_path = "",
                 visium_path="/mnt/atlas_local/linhua/data/SEAGAL/test_data/"):
        
        data = load_raw(self, count_path, meta_path, visium_path)
            
        ## preprocess, and QC
        data = process_st(self, data, min_counts=150, min_cells=10)
        ## spatial process
        self.adata = spatial_process(data)
        self.co_expression = None
        self.co_expression_grouped = None
        self.hotspot = None
        self.hotspot_names = None
        # self.plot =  plot()
    



