# README # Phillip Long # November 1, 2023 # Copied from Herman's MMT: https://github.com/salu133445/mmt/blob/main/mmt/utils.py # Contains utility (helper) functions # IMPORTS ################################################## import json import pathlib import warnings from os.path import exists from typing import Union, List, Tuple, Collection import numpy as np from re import sub ################################################## # CONSTANTS ################################################## NA_STRING = "NA" ################################################## # MISCELLANEOUS FUNCTIONS ################################################## def inverse_dict(d): """Return the inverse dictionary.""" return {v: k for k, v in d.items()} # implementation of R's rep function def rep(x: object, times: int, flatten: bool = False): """An implementation of R's rep() function. This can not be used to create a list of empty lists (see https://stackoverflow.com/questions/240178/list-of-lists-changes-reflected-across-sublists-unexpectedly).""" l = [x] * times if flatten: l = sum(l, []) return l # unique values in list while retaining order def unique(l: Union[List, Tuple]) -> list: """Returns the unique values from a list while retaining order.""" return list(dict.fromkeys(list(l))) # get the product of a list def product(l: Collection) -> float: """Returns the product of the elements in a list.""" return np.prod(a = np.array(object = l), axis = 0) ################################################## # DEAL WITH TEXT ################################################## # convert camel case to words def split_camel_case(string: str, sep: str = "-"): """Split a camelCase string.""" splitter = "_" if string is not None: string = [*string] # convert string to list of characters currently_in_digit = False # boolean flag for dealing with numbers for i, character in enumerate(string): if not character.isdigit() and currently_in_digit: # update whether we are inside of digit currently_in_digit = False if character.isupper(): string[i] = splitter + character elif character.isdigit() and not currently_in_digit: string[i] = splitter + character currently_in_digit = True words = "".join(string).split(splitter) # convert to list of words words = filter(lambda word: word != "", words) # filter out empty words return sep.join(words).lower() # join into one string return None ################################################## # SAVING AND LOADING FILES ################################################## def save_args(filepath: str, args): """Save the command-line arguments.""" args_dict = {} for key, value in vars(args).items(): if isinstance(value, pathlib.Path): args_dict[key] = str(value) else: args_dict[key] = value save_json(filepath = filepath, data = args_dict) def save_txt(filepath: str, data: list): """Save a list to a TXT file.""" with open(filepath, "w", encoding = "utf8") as f: for item in data: f.write(f"{item}\n") def load_txt(filepath: str): """Load a TXT file as a list.""" with open(filepath, encoding = "utf8") as f: return [line.strip() for line in f] def save_json(filepath: str, data: dict): """Save data as a JSON file.""" with open(filepath, "w", encoding = "utf8") as f: json.dump(obj = data, fp = f) def load_json(filepath: str): """Load data from a JSON file.""" with open(filepath, encoding = "utf8") as f: return json.load(fp = f) def save_csv(filepath: str, data, header: str = ""): """Save data as a CSV file.""" np.savetxt(fname = filepath, X = data, fmt = "%d", delimiter = ",", header = header, comments = "") def load_csv(filepath: str, skiprows: int = 1): """Load data from a CSV file.""" return np.loadtxt(fname = filepath, dtype = int, delimiter = ",", skiprows = skiprows) # make sure a string is valid for a csv file def validate_string_for_csv(string: str, sep: str = ",") -> str: """ Ensure a string is valid to be in a csv file, or any file delimetered by `sep`. Remove any newline characters as well as the delimeter itself. Get rid of wierd characters too. """ string = sub(pattern = "\n", repl = "", string = string) # get rid of newlines string = sub(pattern = sep, repl = "", string = string) # get rid of delimiters string = sub(pattern = r'[^ \w0-9,.?!/;:()&_+=\'\\<>\[\]\{\}-]', repl = "", string = string) # get wierd of funky characters string = " ".join(string.split()) # get rid of wierd whitespace return string # create a csv row item_is_NA = lambda item: (item is None) or (len(str(item)) == 0) # boolean to ensure an item is not NA def create_csv_row(info: list, sep: str = ",") -> str: """Create a csv row from a list.""" return sep.join((validate_string_for_csv(string = str(item), sep = sep) if not item_is_NA(item = item) else NA_STRING for item in info)) + "\n" # write a list to a file def write_to_file(info: dict, output_filepath: str, columns: list = None): """Write a dictionary (representing a row of data) to a file.""" # if there are provided columns if columns is not None: # reorder columns if possible columns = list(columns) info = {column: info[column] for column in columns} # write columns if they are not there yet if not exists(output_filepath): with open(output_filepath, "w") as output: output.write(create_csv_row(info = columns)) # write info with open(output_filepath, "a") as output: output.write(create_csv_row(info = list(info.values()))) ################################################## # DECORATORS ################################################## def ignore_exceptions(func): """Decorator that ignores all errors and warnings.""" def inner(*args, **kwargs): with warnings.catch_warnings(): warnings.simplefilter("ignore") try: return func(*args, **kwargs) except Exception: return None return inner ##################################################