Source code for immuneML.util.NumpyHelper

import json
from enum import Enum

import numpy as np

[docs] class NumpyHelper: SIMPLE_TYPES = [str, int, float, bool, np.str_, np.int_, np.float_, np.bool_]
[docs] @staticmethod def group_structured_array_by(data, field): for col in data.dtype.names: data[col][np.argwhere(data[col] == None)] = "" sorted_data = np.sort(data, order=[field], axis=0) grouped_lists = np.split(sorted_data, np.cumsum(np.unique(sorted_data[field], return_counts=True)[1])[:-1]) return grouped_lists
[docs] @staticmethod def is_simple_type(t): """returns if the type t is string or a number so that it does not use pickle if serialized""" return t in NumpyHelper.SIMPLE_TYPES
[docs] @staticmethod def get_numpy_representation(obj): """converts object to representation that can be stored without pickle enables in numpy arrays; if it is an object or a dict, it will be serialized to a json string""" if obj is None: return '' elif type(obj) in NumpyHelper.SIMPLE_TYPES: return obj elif isinstance(obj, Enum): return elif not isinstance(obj, dict) and not isinstance(obj, list) and not isinstance(obj, Enum): representation = vars(obj) else: representation = obj return json.dumps(representation, default=lambda x: if isinstance(x, Enum) else str(x))
[docs] @staticmethod def is_nan_or_empty(value): return value == 'nan' or value is None or (not isinstance(value, str) and np.isnan(value)) or value == ''