#!/usr/bin/env python3 import json import numpy as np import re import logging from sklearn.metrics import r2_score logger = logging.getLogger(__name__) class NpEncoder(json.JSONEncoder): def default(self, obj): if isinstance(obj, np.integer): return int(obj) elif isinstance(obj, np.floating): return float(obj) elif isinstance(obj, np.ndarray): return obj.tolist() else: return super(NpEncoder, self).default(obj) def running_mean(x: np.ndarray, N: int) -> np.ndarray: """ Compute `N` elements wide running average over `x`. :param x: 1-Dimensional NumPy array :param N: how many items to average """ # FIXME np.insert(x, 0, [x[0] for i in range(N/2)]) # FIXME np.insert(x, -1, [x[-1] for i in range(N/2)]) # (dabei ungerade N beachten) cumsum = np.cumsum(np.insert(x, 0, 0)) return (cumsum[N:] - cumsum[:-N]) / N def human_readable(value, unit): for prefix, factor in ( ("p", 1e-12), ("n", 1e-9), ("ยต", 1e-6), ("m", 1e-3), ("", 1), ("k", 1e3), ): if value < 1e3 * factor: return "{:.2f} {}{}".format(value * (1 / factor), prefix, unit) return "{:.2f} {}".format(value, unit) def is_numeric(n): """Check if `n` is numeric (i.e., it can be converted to float).""" if n is None: return False try: float(n) return True except ValueError: return False def is_power_of_two(n): """Check if `n` is a power of two (1, 2, 4, 8, 16, ...).""" return n > 0 and (n & (n - 1)) == 0 def float_or_nan(n): """Convert `n` to float (if numeric) or NaN.""" if n is None: return np.nan try: return float(n) except ValueError: return np.nan def soft_cast_int(n): """ Convert `n` to int (if numeric) or return it as-is. If `n` is empty, returns None. If `n` is not numeric, it is left unchanged. """ if n is None or n == "": return None try: return int(n) except ValueError: return n def soft_cast_float(n): """ Convert `n` to float (if numeric) or return it as-is. If `n` is empty, returns None. If `n` is not numeric, it is left unchanged. """ if n is None or n == "": return None try: return float(n) except ValueError: return n def flatten(somelist): """ Flatten a list. Example: flatten([[1, 2], [3], [4, 5]]) -> [1, 2, 3, 4, 5] """ return [item for sublist in somelist for item in sublist] def parse_conf_str(conf_str): """ Parse a configuration string `k1=v1,k2=v2`... and return a dict `{'k1': v1, 'k2': v2}`... Values are casted to float if possible and kept as-is otherwise. """ conf_dict = dict() for option in conf_str.split(","): key, value = option.split("=") conf_dict[key] = soft_cast_float(value) return conf_dict def remove_index_from_tuple(parameters, index): """ Remove the element at `index` from tuple `parameters`. :param parameters: tuple :param index: index of element which is to be removed :returns: parameters tuple without the element at index """ return (*parameters[:index], *parameters[index + 1 :]) def param_slice_eq(a, b, index): """ Check if by_param keys a and b are identical, ignoring the parameter at index. parameters: a, b -- (state/transition name, [parameter0 value, parameter1 value, ...]) index -- parameter index to ignore (0 -> parameter0, 1 -> parameter1, etc.) Returns True iff a and b have the same state/transition name, and all parameters at positions != index are identical. example: ('foo', [1, 4]), ('foo', [2, 4]), 0 -> True ('foo', [1, 4]), ('foo', [2, 4]), 1 -> False """ if (*a[:index], *a[index + 1 :]) == (*b[:index], *b[index + 1 :]): return True return False def match_parameter_values(input_param: dict, match_param: dict): """ Check whether one of the paramaters in `input_param` has the same value in `match_param`. :param input_param: parameter dict of a state/transition/... measurement :param match_param: parameter value filter :returns: True if for all parameters k in match_param: input_param[k] == match_param[k], or if match_param is None. """ if match_param is None: return True for k, v in match_param.items(): if k in input_param and input_param[k] != v: return False return True def partition_by_param(data, param_values): ret = dict() for i, parameters in enumerate(param_values): param_key = tuple(parameters) if param_key not in ret: ret[param_key] = list() ret[param_key].append(data[i]) return ret def by_name_to_by_param(by_name: dict): """ Convert aggregation by name to aggregation by name and parameter values. """ by_param = dict() for name in by_name.keys(): for i, parameters in enumerate(by_name[name]["param"]): param_key = (name, tuple(parameters)) if param_key not in by_param: by_param[param_key] = dict() for key in by_name[name].keys(): by_param[param_key][key] = list() by_param[param_key]["attributes"] = by_name[name]["attributes"] # special case for PTA models if "isa" in by_name[name]: by_param[param_key]["isa"] = by_name[name]["isa"] for attribute in by_name[name]["attributes"]: by_param[param_key][attribute].append(by_name[name][attribute][i]) if "supports" in by_name[name]: for support in by_name[name]["supports"]: by_param[param_key][support].append(by_name[name][support][i]) # Required for match_parameter_valuse in _try_fits by_param[param_key]["param"].append(by_name[name]["param"][i]) return by_param def by_param_to_by_name(by_param: dict) -> dict: """ Convert aggregation by name and parameter values to aggregation by name only. """ by_name = dict() for param_key in by_param.keys(): name, _ = param_key if name not in by_name: by_name[name] = dict() for key in by_param[param_key].keys(): by_name[name][key] = list() by_name[name]["attributes"] = by_param[param_key]["attributes"] # special case for PTA models if "isa" in by_param[param_key]: by_name[name]["isa"] = by_param[param_key]["isa"] for attribute in by_name[name]["attributes"]: by_name[name][attribute].extend(by_param[param_key][attribute]) if "supports" in by_param[param_key]: for support in by_param[param_key]["supports"]: by_name[name][support].extend(by_param[param_key][support]) by_name[name]["param"].extend(by_param[param_key]["param"]) for name in by_name.keys(): for attribute in by_name[name]["attributes"]: by_name[name][attribute] = np.array(by_name[name][attribute]) return by_name def filter_aggregate_by_param(aggregate, parameters, parameter_filter): """ Remove entries which do not have certain parameter values from `aggregate`. :param aggregate: aggregated measurement data, must be a dict conforming to aggregate[state or transition name]['param'] = (first parameter value, second parameter value, ...) and aggregate[state or transition name]['attributes'] = [list of keys with measurement data, e.g. 'power' or 'duration'] :param parameters: list of parameters, used to map parameter index to parameter name. parameters=['foo', ...] means 'foo' is the first parameter :param parameter_filter: [[name, value], [name, value], ...] list of parameter values to keep, all others are removed. Values refer to normalizad parameter data. """ for param_name_and_value in parameter_filter: param_index = parameters.index(param_name_and_value[0]) param_value = soft_cast_int(param_name_and_value[1]) names_to_remove = set() for name in aggregate.keys(): indices_to_keep = list( map(lambda x: x[param_index] == param_value, aggregate[name]["param"]) ) aggregate[name]["param"] = list( map( lambda iv: iv[1], filter( lambda iv: indices_to_keep[iv[0]], enumerate(aggregate[name]["param"]), ), ) ) if len(indices_to_keep) == 0: logger.debug("??? {}->{}".format(parameter_filter, name)) names_to_remove.add(name) else: for attribute in aggregate[name]["attributes"]: aggregate[name][attribute] = aggregate[name][attribute][ indices_to_keep ] if len(aggregate[name][attribute]) == 0: names_to_remove.add(name) for name in names_to_remove: aggregate.pop(name) def detect_outliers_in_aggregate(aggregate, z_limit=10, remove_outliers=False): for name in aggregate.keys(): indices_to_remove = set() attributes = list() for attribute in aggregate[name]["attributes"]: data = aggregate[name][attribute] z_scores = (data - np.mean(data)) / np.std(data) outliers = np.abs(z_scores) > z_limit if np.any(outliers) and remove_outliers: indices_to_remove = indices_to_remove.union( np.arange(len(outliers))[outliers] ) attributes.append(attribute) elif np.any(outliers): logger.info( f"{name} {attribute} has {len(z_scores[outliers])} outliers" ) if indices_to_remove: # Assumption: len(aggregate[name][attribute]) is the same for each # attribute. logger.info( f"Removing outliers {indices_to_remove} from {name}. Affected attributes: {attributes}" ) indices_to_keep = map( lambda x: x not in indices_to_remove, np.arange(len(outliers)) ) indices_to_keep = np.array(list(indices_to_keep)) for attribute in aggregate[name]["attributes"]: aggregate[name][attribute] = aggregate[name][attribute][indices_to_keep] aggregate[name]["param"] = list( map( lambda iv: iv[1], filter( lambda iv: indices_to_keep[iv[0]], enumerate(aggregate[name]["param"]), ), ) ) def aggregate_measures(aggregate: float, actual: list) -> dict: """ Calculate error measures for model value on data list. arguments: aggregate -- model value (float or int) actual -- real-world / reference values (list of float or int) return value: See regression_measures """ aggregate_array = np.array([aggregate] * len(actual)) return regression_measures(aggregate_array, np.array(actual)) def regression_measures(predicted: np.ndarray, actual: np.ndarray): """ Calculate error measures by comparing model values to reference values. arguments: predicted -- model values (np.ndarray) actual -- real-world / reference values (np.ndarray) Returns a dict containing the following measures: mae -- Mean Absolute Error mape -- Mean Absolute Percentage Error, if all items in actual are non-zero (NaN otherwise) smape -- Symmetric Mean Absolute Percentage Error, if no 0,0-pairs are present in actual and predicted (NaN otherwise) msd -- Mean Square Deviation rmsd -- Root Mean Square Deviation ssr -- Sum of Squared Residuals rsq -- R^2 measure, see sklearn.metrics.r2_score count -- Number of values """ if type(predicted) != np.ndarray: raise ValueError("first arg must be ndarray, is {}".format(type(predicted))) if type(actual) != np.ndarray: raise ValueError("second arg must be ndarray, is {}".format(type(actual))) deviations = predicted - actual # mean = np.mean(actual) if len(deviations) == 0: return {} measures = { "mae": np.mean(np.abs(deviations), dtype=np.float64), "msd": np.mean(deviations ** 2, dtype=np.float64), "rmsd": np.sqrt(np.mean(deviations ** 2), dtype=np.float64), "ssr": np.sum(deviations ** 2, dtype=np.float64), "rsq": r2_score(actual, predicted), "count": len(actual), } # rsq_quotient = np.sum((actual - mean)**2, dtype=np.float64) * np.sum((predicted - mean)**2, dtype=np.float64) if np.all(actual != 0): measures["mape"] = np.mean(np.abs(deviations / actual)) * 100 # bad measure else: measures["mape"] = np.nan if np.all(np.abs(predicted) + np.abs(actual) != 0): measures["smape"] = ( np.mean(np.abs(deviations) / ((np.abs(predicted) + np.abs(actual)) / 2)) * 100 ) else: measures["smape"] = np.nan # if np.all(rsq_quotient != 0): # measures['rsq'] = (np.sum((actual - mean) * (predicted - mean), dtype=np.float64)**2) / rsq_quotient return measures class OptionalTimingAnalysis: def __init__(self, enabled=True): self.enabled = enabled self.wrapped_lines = list() self.index = 1 def get_header(self): ret = "" if self.enabled: ret += "#define TIMEIT(index, functioncall) " ret += "counter.start(); " ret += "functioncall; " ret += "counter.stop();" ret += 'kout << endl << index << " :: " << counter.value << "/" << counter.overflow << endl;\n' return ret def wrap_codeblock(self, codeblock): if not self.enabled: return codeblock lines = codeblock.split("\n") ret = list() for line in lines: if re.fullmatch(".+;", line): ret.append("TIMEIT( {:d}, {} )".format(self.index, line)) self.wrapped_lines.append(line) self.index += 1 else: ret.append(line) return "\n".join(ret)