if not perform: sys.exit( "Config file set to perform=False, not performing {}".format(__file__)) # Forced overwrite can be achieved in one of two ways. # The command line overrides the config file, check here if it is provided if not force: force = args.force barcode_foci_cols = id_cols + location_cols + spot_parent_cols all_foci_cols = list( set(id_cols + location_cols + foci_cols + spot_score_cols + barcode_cols + gene_cols)) cell_quality = CellQuality(quality_func, category_class_name=quality_col, category_col_index=quality_idx) cell_category_dict = cell_quality.define_cell_quality() cell_category_df = pd.DataFrame(cell_category_dict, index=[quality_col]) sites = [ x.name for x in input_platedir.iterdir() if x.name not in ignore_files ] num_sites = len(sites) image_list = [] for site in sites: print(f"Now processing spots for {site}...") # Load image metadata per site try:
cell_config = config["options"]["preprocess"]["process-cells"] cell_sort_col = cell_config["sort_col"] merge_info = cell_config["merge_columns"] foci_site_col = cell_config["foci_site_col"] force = cell_config["force_overwrite"] metadata_merge_foci_cols = cell_config["metadata_merge_columns"]["foci_cols"] metadata_merge_cell_cols = cell_config["metadata_merge_columns"]["cell_cols"] # Forced overwrite can be achieved in one of two ways. # The command line overrides the config file, check here if it is provided if not force: force = args.force cell_quality = CellQuality(quality_func, category_class_name=quality_col, category_col_index=quality_idx) cell_category_dict = cell_quality.define_cell_quality() empty_cell_category = len(cell_category_dict) + 1 cell_category_dict[empty_cell_category] = "Empty" cell_category_df = pd.DataFrame(cell_category_dict, index=[quality_col]).transpose() # Enables feature filtering by loading the Cell Painting feature file. # 0.prefilter-features.py must be run first try: all_feature_df = pd.read_csv(prefilter_file, sep="\t").query("not prefilter_column") except FileNotFoundError: raise FileNotFoundError( "Error",