import inspect import signal import random import time import traceback import sys import os import subprocess import math import pickle as pickle from itertools import chain import heapq import hashlib def computeMD5hash(my_string): #https://stackoverflow.com/questions/13259691/convert-string-to-md5 m = hashlib.md5() m.update(my_string.encode('utf-8')) return m.hexdigest() class Thunk(object): # A class for lazy evaluation def __init__(self, thing): self.thing = thing self.evaluated = False def force(self): if self.evaluated: return self.thing else: self.thing = self.thing() self.evaluated = True return self.thing def cindex(i): return lambda a: a[i] class ConstantFunction: def __init__(self,v): self.v = v def __call__(self,*a,**k): return self.v def eprint(*args, **kwargs): print(*args, file=sys.stderr, **kwargs) flushEverything() class Bunch(object): def __init__(self, d): self.__dict__.update(d) def __setitem__(self, key, item): self.__dict__[key] = item def __getitem__(self, key): return self.__dict__[key] def curry(fn): """Curries a function. Hacky way to return a curried version of functions with arbitrary #s of args. """ def make_curry_fn(signature): """Redefines a currying function with the appropriate arguments. Hacky.""" tmp_curry = 'def tmp_curry(f): return ' tmp_curry += " ".join(['lambda %s: ' % argname for argname in signature.parameters]) tmp_curry += 'f' tmp_curry += str(signature) return tmp_curry exec(make_curry_fn(inspect.signature(fn)), globals()) return tmp_curry(fn) class Curried: def __init__(self, f, arguments=None, arity=None): if arity is None: arity = len(inspect.getargspec(f)[0]) self.f = f self.arity = arity if arguments is None: arguments = [] self.arguments = arguments def __call__(self, x): arguments = self.arguments + [x] if len(arguments) == self.arity: return self.f(*arguments) else: return Curried(self.f, arguments=arguments, arity=self.arity) def __str__(self): if len(self.arguments) == 0: return f"Curried({self.f}/{self.arity})" else: return f"Curried({self.f}/{self.arity}, {', '.join(map(str,self.arguments))})" def __repr__(self): return str(self) def hashable(v): """Determine whether `v` can be hashed.""" try: hash(v) except TypeError: return False return True def flatten(x, abort=lambda x: False): """Recursively unroll iterables.""" if abort(x): yield x return try: yield from chain(*(flatten(i, abort) for i in x)) except TypeError: # not iterable yield x def growImage(i, iterations=2): import numpy as np for _ in range(iterations): ip = np.zeros(i.shape) # assume it is monochromatic and get the color c = np.array([i[:,:,j].max() for j in range(4) ]) # assume that the alpha channel indicates where the foreground is foreground = i[:,:,3] > 0 foreground = foreground + \ np.pad(foreground, ((0,1),(0,0)), mode='constant')[1:,:] +\ np.pad(foreground, ((0,0),(0,1)), mode='constant')[:,1:] + \ np.pad(foreground, ((0,0),(1,0)), mode='constant')[:,:-1] + \ np.pad(foreground, ((1,0),(0,0)), mode='constant')[:-1,:] ip[foreground] = c i = ip return ip def summaryStatistics(n, times): if len(times) == 0: eprint(n, "no successful times to report statistics on!") else: eprint(n, "average: ", int(mean(times) + 0.5), "sec.\tmedian:", int(median(times) + 0.5), "\tmax:", int(max(times) + 0.5), "\tstandard deviation", int(standardDeviation(times) + 0.5)) def updateTaskSummaryMetrics(taskSummaryMetrics, newMetricsDict, key): """Updates a taskSummaryMetrics dict from tasks -> metrics with new metrics under the given key.""" for task in newMetricsDict: if task in taskSummaryMetrics: taskSummaryMetrics[task][key] = newMetricsDict[task] else: taskSummaryMetrics[task] = {key : newMetricsDict[task]} NEGATIVEINFINITY = float('-inf') POSITIVEINFINITY = float('inf') PARALLELMAPDATA = None PARALLELBASESEED = None def parallelMap(numberOfCPUs, f, *xs, chunksize=None, maxtasksperchild=None, memorySensitive=False, seedRandom=False): """seedRandom: Should each parallel worker be given a different random seed?""" global PARALLELMAPDATA global PARALLELBASESEED if memorySensitive: memoryUsage = getMemoryUsageFraction()/100. correctedCPUs = max(1, min(int(0.9/memoryUsage),numberOfCPUs)) assert correctedCPUs <= numberOfCPUs assert correctedCPUs >= 1 if correctedCPUs < numberOfCPUs: eprint("In order to not use all of the memory on the machine (%f gb), we are limiting this parallel map to only use %d CPUs"%(howManyGigabytesOfMemory(),correctedCPUs)) numberOfCPUs = correctedCPUs if numberOfCPUs == 1: return list(map(f, *xs)) n = len(xs[0]) for x in xs: assert len(x) == n assert PARALLELMAPDATA is None PARALLELMAPDATA = (f, xs) assert PARALLELBASESEED is None if seedRandom: PARALLELBASESEED = random.random() from multiprocessing import Pool # Randomize the order in case easier ones come earlier or later permutation = list(range(n)) random.shuffle(permutation) inversePermutation = dict(zip(permutation, range(n))) # Batch size of jobs as they are sent to processes if chunksize is None: chunksize = max(1, n // (numberOfCPUs * 2)) pool = Pool(numberOfCPUs, maxtasksperchild=maxtasksperchild) ys = pool.map(parallelMapCallBack, permutation, chunksize=chunksize) pool.terminate() PARALLELMAPDATA = None PARALLELBASESEED = None return [ys[inversePermutation[j]] for j in range(n)] def parallelMapCallBack(j): global PARALLELMAPDATA global PARALLELBASESEED if PARALLELBASESEED is not None: random.seed(PARALLELBASESEED + j) f, xs = PARALLELMAPDATA try: return f(*[x[j] for x in xs]) except Exception as e: eprint( "Exception in worker during lightweight parallel map:\n%s" % (traceback.format_exc())) raise e def log(x): t = type(x) if t == int or t == float: if x == 0: return NEGATIVEINFINITY return math.log(x) return x.log() def exp(x): t = type(x) if t == int or t == float: return math.exp(x) return x.exp() def lse(x, y=None): if y is None: largest = None if len(x) == 0: raise Exception('LSE: Empty sequence') if len(x) == 1: return x[0] # If these are just numbers... t = type(x[0]) if t == int or t == float: largest = max(*x) return largest + math.log(sum(math.exp(z - largest) for z in x)) #added clause to avoid zero -dim tensor problem import torch if t == torch.Tensor and x[0].size() == torch.Size([]): return torchSoftMax([datum.view(1) for datum in x]) # Must be torch return torchSoftMax(x) else: if x is NEGATIVEINFINITY: return y if y is NEGATIVEINFINITY: return x tx = type(x) ty = type(y) if (ty == int or ty == float) and (tx == int or tx == float): if x > y: return x + math.log(1. + math.exp(y - x)) else: return y + math.log(1. + math.exp(x - y)) return torchSoftMax(x, y) def torchSoftMax(x, y=None): from torch.nn.functional import log_softmax import torch if y is None: if isinstance(x, list): x = torch.cat(x) return (x - log_softmax(x, dim=0))[0] x = torch.cat((x, y)) # this is so stupid return (x - log_softmax(x, dim=0))[0] def invalid(x): return math.isinf(x) or math.isnan(x) def valid(x): return not invalid(x) def forkCallBack(x): [f, a, k] = x try: return f(*a, **k) except Exception as e: eprint( "Exception in worker during forking:\n%s" % (traceback.format_exc())) raise e def callFork(f, *arguments, **kw): """Forks a new process to execute the call. Blocks until the call completes.""" global FORKPARAMETERS from multiprocessing import Pool workers = Pool(1) ys = workers.map(forkCallBack, [[f, arguments, kw]]) workers.terminate() assert len(ys) == 1 return ys[0] PARALLELPROCESSDATA = None def launchParallelProcess(f, *a, **k): global PARALLELPROCESSDATA PARALLELPROCESSDATA = [f, a, k] from multiprocessing import Process p = Process(target=_launchParallelProcess, args=tuple([])) p.start() PARALLELPROCESSDATA = None return p def _launchParallelProcess(): global PARALLELPROCESSDATA [f, a, k] = PARALLELPROCESSDATA try: f(*a, **k) except Exception as e: eprint( "Exception in worker during forking:\n%s" % (traceback.format_exc())) raise e def jsonBinaryInvoke(binary, message): import json import subprocess import os message = json.dumps(message) try: process = subprocess.Popen(binary, stdin=subprocess.PIPE, stdout=subprocess.PIPE) response, error = process.communicate(bytes(message, encoding="utf-8")) except OSError as exc: raise exc try: response = json.loads(response.decode("utf-8")) except Exception as e: eprint("Could not parse json.") with open("/tmp/_message","w") as handle: handle.write(message) with open("/tmp/_response","w") as handle: handle.write(response.decode("utf-8")) raise e return response class CompiledTimeout(Exception): pass def get_root_dir(): """ Returns the absolute path to the root directory of the repository as a string. This method is primarily used in order to locate the binaries at the root of the repository. """ return os.path.join(os.path.dirname(__file__), os.pardir) def get_data_dir(): """ Returns the absolute path to the data directory of the repository as a string. """ return os.path.join(get_root_dir(), 'data') def callCompiled(f, *arguments, **keywordArguments): import dill pypyArgs = [] profile = keywordArguments.pop('profile', None) if profile: pypyArgs = ['-m', 'vmprof', '-o', profile] PIDCallBack = keywordArguments.pop("PIDCallBack", None) timeout = keywordArguments.pop('compiledTimeout', None) # Use absolute paths. compiled_driver_file = os.path.join(get_root_dir(), 'bin', 'compiledDriver.py') p = subprocess.Popen(['pypy3'] + pypyArgs + [compiled_driver_file], stdin=subprocess.PIPE, stdout=subprocess.PIPE) if PIDCallBack is not None: PIDCallBack(p.pid) request = { "function": f, "arguments": arguments, "keywordArguments": keywordArguments, } start = time.time() dill.dump(request, p.stdin) #p.stdin.write(request) p.stdin.flush() #p.stdin.close() dt = time.time() - start if dt > 1: eprint("(Python side of compiled driver: SLOW) Wrote serialized message for {} in time {}".format( f.__name__, dt)) if timeout is None: success, result = dill.load(p.stdout) else: eprint("Running with timeout", timeout) def timeoutCallBack(_1, _2): raise CompiledTimeout() signal.signal(signal.SIGALRM, timeoutCallBack) signal.alarm(int(math.ceil(timeout))) try: success, result = dill.load(p.stdout) signal.alarm(0) except CompiledTimeout: # Kill the process p.kill() raise CompiledTimeout() if not success: sys.exit(1) return result class timing(object): def __init__(self, message): self.message = message def __enter__(self): self.start = time.time() return self def __exit__(self, type, value, traceback): dt = time.time() - self.start if isinstance(self.message, str): message = self.message elif callable(self.message): message = self.message(dt) else: assert False, "Timing message should be string function" eprint("%s in %.1f seconds" % (message, dt)) class random_seed(object): def __init__(self, seed): self.seed = seed def __enter__(self): self._oldSeed = random.getstate() random.seed(self.seed) return self def __exit__(self, type, value, traceback): random.setstate(self._oldSeed) def randomPermutation(l): import random l = list(l) random.shuffle(l) return l def batches(data, size=1): import random # Randomly permute the data data = list(data) random.shuffle(data) start = 0 while start < len(data): yield data[start:size + start] start += size def sampleDistribution(d): """ Expects d to be a list of tuples The first element should be the probability If the tuples are of length 2 then it returns the second element Otherwise it returns the suffix tuple """ import random z = float(sum(t[0] for t in d)) if z == 0.: eprint("sampleDistribution: z = 0") eprint(d) r = random.random() u = 0. for index, t in enumerate(d): p = t[0] / z # This extra condition is needed for floating-point bullshit if r <= u + p or index == len(d) - 1: if len(t) <= 2: return t[1] else: return t[1:] u += p assert False def sampleLogDistribution(d): """ Expects d to be a list of tuples The first element should be the log probability If the tuples are of length 2 then it returns the second element Otherwise it returns the suffix tuple """ import random z = lse([t[0] for t in d]) r = random.random() u = 0. for t in d: p = math.exp(t[0] - z) if r < u + p: if len(t) <= 2: return t[1] else: return t[1:] u += p assert False def testTrainSplit(x, trainingFraction, seed=0): if trainingFraction > 1.1: # Assume that the training fraction is actually the number of tasks # that we want to train on trainingFraction = float(trainingFraction) / len(x) needToTrain = { j for j, d in enumerate(x) if hasattr(d, 'mustTrain') and d.mustTrain } mightTrain = [j for j in range(len(x)) if j not in needToTrain] trainingSize = max(0, int(len(x) * trainingFraction - len(needToTrain))) import random random.seed(seed) random.shuffle(mightTrain) training = set(mightTrain[:trainingSize]) | needToTrain train = [t for j, t in enumerate(x) if j in training] test = [t for j, t in enumerate(x) if j not in training] return test, train def numberOfCPUs(): import multiprocessing return multiprocessing.cpu_count() def loadPickle(f): with open(f, 'rb') as handle: d = pickle.load(handle) return d def dumpPickle(o,f): with open(f, 'wb') as handle: pickle.dump(o,handle) def fst(l): for v in l: return v def mean(l): n = 0 t = None for x in l: if t is None: t = x else: t = t + x n += 1 if n == 0: eprint("warning: asked to calculate the mean of an empty list. returning zero.") return 0 return t / float(n) def variance(l): m = mean(l) return sum((x - m)**2 for x in l) / len(l) def standardDeviation(l): return variance(l)**0.5 def median(l): if len(l) <= 0: return None l = sorted(l) if len(l) % 2 == 1: return l[len(l) // 2] return 0.5 * (l[len(l) // 2] + l[len(l) // 2 - 1]) def percentile(l, p): l = sorted(l) j = int(len(l)*p) if j < len(l): return l[j] return 0 def makeTemporaryFile(directory="/tmp"): import tempfile fd,p = tempfile.mkstemp(dir=directory) os.close(fd) return p class Stopwatch(): def __init__(self): self._elapsed = 0. self.running = False self._latestStart = None def start(self): if self.running: eprint( "(stopwatch: attempted to start an already running stopwatch. Silently ignoring.)") return self.running = True self._latestStart = time.time() def stop(self): if not self.running: eprint( "(stopwatch: attempted to stop a stopwatch that is not running. Silently ignoring.)") return self.running = False self._elapsed += time.time() - self._latestStart self._latestStart = None @property def elapsed(self): e = self._elapsed if self.running: e = e + time.time() - self._latestStart return e def userName(): import getpass return getpass.getuser() def hostname(): import socket return socket.gethostname() def getPID(): return os.getpid() def CPULoad(): try: import psutil except BaseException: return "unknown - install psutil" return psutil.cpu_percent() def flushEverything(): sys.stdout.flush() sys.stderr.flush() class RunWithTimeout(Exception): pass def runWithTimeout(k, timeout): if timeout is None: return k() def timeoutCallBack(_1,_2): raise RunWithTimeout() signal.signal(signal.SIGPROF, timeoutCallBack) signal.setitimer(signal.ITIMER_PROF, timeout) try: result = k() signal.signal(signal.SIGPROF, lambda *_:None) signal.setitimer(signal.ITIMER_PROF, 0) return result except RunWithTimeout: signal.signal(signal.SIGPROF, lambda *_:None) signal.setitimer(signal.ITIMER_PROF, 0) raise RunWithTimeout() except: signal.signal(signal.SIGPROF, lambda *_:None) signal.setitimer(signal.ITIMER_PROF, 0) raise def crossProduct(a, b): b = list(b) for x in a: for y in b: yield x, y class PQ(object): """why the fuck does Python not wrap this in a class""" def __init__(self): self.h = [] self.index2value = {} self.nextIndex = 0 def push(self, priority, v): self.index2value[self.nextIndex] = v heapq.heappush(self.h, (-priority, self.nextIndex)) self.nextIndex += 1 def popMaximum(self): i = heapq.heappop(self.h)[1] v = self.index2value[i] del self.index2value[i] return v def __iter__(self): for _, v in self.h: yield self.index2value[v] def __len__(self): return len(self.h) class UnionFind: class Class: def __init__(self, x): self.members = {x} self.leader = None def chase(self): k = self while k.leader is not None: k = k.leader self.leader = k return k def __init__(self): # Map from keys to classes self.classes = {} def unify(self,x,y): k1 = self.classes[x].chase() k2 = self.classes[y].chase() # k2 will be the new leader k1.leader = k2 k2.members |= k1.members k1.members = None self.classes[x] = k2 self.classes[y] = k2 return k2 def newClass(self,x): if x not in self.classes: n = Class(x) self.classes[x] = n def otherMembers(self,x): k = self.classes[x].chase() self.classes[x] = k return k.members def substringOccurrences(ss, s): return sum(s[i:].startswith(ss) for i in range(len(s))) def normal(s=1., m=0.): u = random.random() v = random.random() n = math.sqrt(-2.0 * log(u)) * math.cos(2.0 * math.pi * v) return s * n + m def powerOfTen(n): if n <= 0: return False while True: if n == 1: return True if n % 10 != 0: return False n = n / 10 def powerOf(p, n): if n <= 0: return False while True: if n == 1: return True if n % p != 0: return False n = n / p def getThisMemoryUsage(): import os import psutil process = psutil.Process(os.getpid()) return process.memory_info().rss def getMemoryUsageFraction(): import psutil return psutil.virtual_memory().percent def howManyGigabytesOfMemory(): import psutil return psutil.virtual_memory().total/10**9 def tuplify(x): if isinstance(x,(list,tuple)): return tuple(tuplify(z) for z in x) return x # image montage! def makeNiceArray(l, columns=None): n = columns or int(len(l)**0.5) a = [] while l: a.append(l[:n]) l = l[n:] return a def montageMatrix(matrix): import numpy as np arrays = matrix m = max(len(t) for t in arrays) size = arrays[0][0].shape tp = arrays[0][0].dtype arrays = [np.concatenate(ts + [np.zeros(size, dtype=tp)] * (m - len(ts)), axis=1) for ts in arrays] arrays = np.concatenate(arrays, axis=0) return arrays def montage(arrays, columns=None): return montageMatrix(makeNiceArray(arrays, columns=columns)) def showArrayAsImage(a): from pylab import imshow,show imshow(a) show() class ParseFailure(Exception): pass def parseSExpression(s): s = s.strip() def p(n): while n <= len(s) and s[n].isspace(): n += 1 if n == len(s): raise ParseFailure(s) if s[n] == '#': e,n = p(n + 1) return ['#', e],n if s[n] == '(': l = [] n += 1 while True: x,n = p(n) l.append(x) while n <= len(s) and s[n].isspace(): n += 1 if n == len(s): raise ParseFailure(s) if s[n] == ')': n += 1 break return l,n name = [] while n < len(s) and not s[n].isspace() and s[n] not in '()': name.append(s[n]) n += 1 name = "".join(name) return name,n e,n = p(0) if n == len(s): return e raise ParseFailure(s) def diffuseImagesOutward(imageCoordinates, labelCoordinates, d, maximumRadius = 2.5, minimumRadius = 1.5): import numpy as np n = imageCoordinates.shape[0] #d = (np.random.rand(n,2)*2 - 1)*(maximumRadius/2 + minimumRadius/2) def _constrainRadii(p): r = (p*p).sum() if r > maximumRadius: return maximumRadius*p/(r**0.5) if r < minimumRadius: return minimumRadius*p/(r**0.5) return p def constrainRadii(): for j in range(n): d[j,:] = _constrainRadii(d[j,:]) for _ in range(10): for i in range(n): force = np.array([0.,0.]) for j in range(n): if i == j: continue p1 = imageCoordinates[i] + d[i] p2 = imageCoordinates[j] + d[j] l = ((p1 - p2)**2).sum()**0.5 if l > 1.5: continue force += (p1 - p2)/l/max(l,0.2) if force.sum() > 0: force = force/( (force*force).sum()**0.5) d[i] += force constrainRadii() return d if __name__ == "__main__": def f(n): if n == 0: return None return [f(n - 1),f(n - 1)] z = f(22) eprint(getMemoryUsageFraction().percent) eprint(getThisMemoryUsage())