# -*- coding: utf-8 -*- """ Created on Tue Jul 12 11:05:57 2016 some help functions to perform basic tasks @author: tb00083 """ import os import sys import csv import socket import numpy as np import json import pickle # python3.x import time from datetime import timedelta, datetime from typing import Any, List, Tuple, Union import subprocess import struct import errno from pprint import pprint import glob from threading import Thread def welcome_message(): """ get welcome message including hostname and command line arguments """ hostname = socket.gethostname() all_args = ' '.join(sys.argv) out_text = 'On server {}: {}\n'.format(hostname, all_args) return out_text class EasyDict(dict): """Convenience class that behaves like a dict but allows access with the attribute syntax.""" def __init__(self, dict_to_convert=None): if dict_to_convert is not None: for key, val in dict_to_convert.items(): self[key] = val def __getattr__(self, name: str) -> Any: try: return self[name] except KeyError: raise AttributeError(name) def __setattr__(self, name: str, value: Any) -> None: self[name] = value def __delattr__(self, name: str) -> None: del self[name] def get_time_id_str(): """ returns a string with DDHHM format, where M is the minutes cut to the tenths """ now = datetime.now() time_str = "{:02d}{:02d}{:02d}".format(now.day, now.hour, now.minute) time_str = time_str[:-1] return time_str def time_format(t): m, s = divmod(t, 60) h, m = divmod(m, 60) m, h, s = int(m), int(h), int(s) if m == 0 and h == 0: return "{}s".format(s) elif h == 0: return "{}m{}s".format(m, s) else: return "{}h{}m{}s".format(h, m, s) def get_all_files(dir_path, trim=0, extension=''): """ Recursively get list of all files in the given directory trim = 1 : trim the dir_path from results, 0 otherwise extension: get files with specific format """ file_paths = [] # List which will store all of the full filepaths. # Walk the tree. for root, directories, files in os.walk(dir_path): for filename in files: # Join the two strings in order to form the full filepath. filepath = os.path.join(root, filename) file_paths.append(filepath) # Add it to the list. if trim == 1: # trim dir_path from results if dir_path[-1] != os.sep: dir_path += os.sep trim_len = len(dir_path) file_paths = [x[trim_len:] for x in file_paths] if extension: # select only file with specific extension extension = extension.lower() tlen = len(extension) file_paths = [x for x in file_paths if x[-tlen:] == extension] return file_paths # Self-explanatory. def get_all_dirs(dir_path, trim=0): """ Recursively get list of all directories in the given directory excluding the '.' and '..' directories trim = 1 : trim the dir_path from results, 0 otherwise """ out = [] # Walk the tree. for root, directories, files in os.walk(dir_path): for dirname in directories: # Join the two strings in order to form the full filepath. dir_full = os.path.join(root, dirname) out.append(dir_full) # Add it to the list. if trim == 1: # trim dir_path from results if dir_path[-1] != os.sep: dir_path += os.sep trim_len = len(dir_path) out = [x[trim_len:] for x in out] return out def read_list(file_path, delimeter=' ', keep_original=True): """ read list column wise deprecated, should use pandas instead """ out = [] with open(file_path, 'r') as f: reader = csv.reader(f, delimiter=delimeter) for row in reader: out.append(row) out = zip(*out) if not keep_original: for col in range(len(out)): if out[col][0].isdigit(): # attempt to convert to numerical array out[col] = np.array(out[col]).astype(np.int64) return out def save_pickle2(file_path, **kwargs): """ save variables to file (using pickle) """ # check if any variable is a dict var_count = 0 for key in kwargs: var_count += 1 if isinstance(kwargs[key], dict): sys.stderr.write('Opps! Cannot write a dictionary into pickle') sys.exit(1) with open(file_path, 'wb') as f: pickler = pickle.Pickler(f, -1) pickler.dump(var_count) for key in kwargs: pickler.dump(key) pickler.dump(kwargs[key]) def load_pickle2(file_path, varnum=0): """ load variables that previously saved using self.save() varnum : number of variables u want to load (0 mean it will load all) Note: if you are loading class instance(s), you must have it defined in advance """ with open(file_path, 'rb') as f: pickler = pickle.Unpickler(f) var_count = pickler.load() if varnum: var_count = min([var_count, varnum]) out = {} for i in range(var_count): key = pickler.load() out[key] = pickler.load() return out def save_pickle(path, obj): """ simple method to save a picklable object :param path: path to save :param obj: a picklable object :return: None """ with open(path, 'wb') as f: pickle.dump(obj, f, pickle.HIGHEST_PROTOCOL) def load_pickle(path): """ load a pickled object :param path: .pkl path :return: the pickled object """ with open(path, 'rb') as f: return pickle.load(f) def make_new_dir(dir_path, remove_existing=False, mode=511): """note: default mode in ubuntu is 511""" if not os.path.exists(dir_path): try: if mode == 777: oldmask = os.umask(000) os.makedirs(dir_path, 0o777) os.umask(oldmask) else: os.makedirs(dir_path, mode) except OSError as exc: # Python >2.5 if exc.errno == errno.EEXIST and os.path.isdir(dir_path): pass else: raise if remove_existing: for file_obj in os.listdir(dir_path): file_path = os.path.join(dir_path, file_obj) if os.path.isfile(file_path): os.unlink(file_path) def get_latest_file(root, pattern): """ get the latest file in a directory that match the provided pattern useful for getting the last checkpoint :param root: search directory :param pattern: search pattern containing 1 wild card representing a number e.g. 'ckpt_*.tar' :return: full path of the file with largest number in wild card, None if not found """ out = None parts = pattern.split('*') max_id = - np.inf for path in glob.glob(os.path.join(root, pattern)): id_ = os.path.basename(path) for part in parts: id_ = id_.replace(part, '') try: id_ = int(id_) if id_ > max_id: max_id = id_ out = path except: continue return out class Locker(object): """place a lock file in specified location useful for distributed computing""" def __init__(self, name='lock.txt', mode=511): """INPUT: name default file name to be created as a lock mode if a directory has to be created, set its permission to mode""" self.name = name self.mode = mode def lock(self, path): make_new_dir(path, False, self.mode) with open(os.path.join(path, self.name), 'w') as f: f.write('progress') def finish(self, path): make_new_dir(path, False, self.mode) with open(os.path.join(path, self.name), 'w') as f: f.write('finish') def customise(self, path, text): make_new_dir(path, False, self.mode) with open(os.path.join(path, self.name), 'w') as f: f.write(text) def is_locked(self, path): out = False check_path = os.path.join(path, self.name) if os.path.exists(check_path): text = open(check_path, 'r').readline().strip() out = True if text == 'progress' else False return out def is_finished(self, path): out = False check_path = os.path.join(path, self.name) if os.path.exists(check_path): text = open(check_path, 'r').readline().strip() out = True if text == 'finish' else False return out def is_locked_or_finished(self, path): return self.is_locked(path) | self.is_finished(path) def clean(self, path): check_path = os.path.join(path, self.name) if os.path.exists(check_path): try: os.remove(check_path) except Exception as e: print('Unable to remove %s: %s.' % (check_path, e)) class ProgressBar(object): """show progress""" def __init__(self, total, increment=5): self.total = total self.point = self.total / 100.0 self.increment = increment self.interval = int(self.total * self.increment / 100) self.milestones = list(range(0, total, self.interval)) + [self.total, ] self.id = 0 def show_progress(self, i): if i >= self.milestones[self.id]: while i >= self.milestones[self.id]: self.id += 1 sys.stdout.write("\r[" + "=" * int(i / self.interval) + " " * int((self.total - i) / self.interval) + "]" + str(int((i + 1) / self.point)) + "%") sys.stdout.flush() class Timer(object): def __init__(self): self.start_t = time.time() self.last_t = self.start_t def time(self, lap=False): end_t = time.time() if lap: out = timedelta(seconds=int(end_t - self.last_t)) # count from last stop point else: out = timedelta(seconds=int(end_t - self.start_t)) # count from beginning self.last_t = end_t return out class ExThread(Thread): def run(self): self.exc = None try: if hasattr(self, '_Thread__target'): # Thread uses name mangling prior to Python 3. self.ret = self._Thread__target(*self._Thread__args, **self._Thread__kwargs) else: self.ret = self._target(*self._args, **self._kwargs) except BaseException as e: self.exc = e def join(self): super(ExThread, self).join() if self.exc: raise RuntimeError('Exception in thread.') from self.exc return self.ret def get_gpu_free_mem(): """return a list of free GPU memory""" sp = subprocess.Popen(['nvidia-smi', '-q'], stdout=subprocess.PIPE, stderr=subprocess.PIPE) out_str = sp.communicate() out_list = out_str[0].decode("utf-8") .split('\n') out = [] for i in range(len(out_list)): item = out_list[i] if item.strip() == 'FB Memory Usage': free_mem = int(out_list[i + 3].split(':')[1].strip().split(' ')[0]) out.append(free_mem) return out def float2hex(x): """ x: a vector return: x in hex """ f = np.float32(x) out = '' if f.size == 1: # just a single number f = [f, ] for e in f: h = hex(struct.unpack('