import sys import datetime import os import subprocess import shlex import re import fractions from functools import reduce from optparse import Option import numpy as np from . import version # limit visibility __all__=[ 'srepr', 'croak', 'report', 'emph','deemph','warn','strikeout', 'execute', 'show_progress', 'scale_to_coprime', 'project_stereographic', 'hybrid_IA', 'return_message', 'extendableOption', 'execution_stamp', 'shapeshifter', 'shapeblender', 'extend_docstring', 'extended_docstring' ] #################################################################################################### # Functions #################################################################################################### def srepr(arg,glue = '\n'): r""" Join arguments with glue string. Parameters ---------- arg : iterable Items to join. glue : str, optional Glue used for joining operation. Defaults to \n. """ if (not hasattr(arg, "strip") and (hasattr(arg, "__getitem__") or hasattr(arg, "__iter__"))): return glue.join(str(x) for x in arg) return arg if isinstance(arg,str) else repr(arg) def croak(what, newline = True): """ Write formated to stderr. DEPRECATED Parameters ---------- what : str or iterable Content to be displayed. newline : bool, optional Separate items of what by newline. Defaults to True. """ if what is not None: sys.stderr.write(srepr(what,glue = '\n') + ('\n' if newline else '')) sys.stderr.flush() def report(who = None, what = None): """ Report script and file name. DEPRECATED """ croak( (emph(who)+': ' if who is not None else '') + (what if what is not None else '') + '\n' ) def emph(what): """Formats string with emphasis.""" return bcolors.BOLD+srepr(what)+bcolors.ENDC def deemph(what): """Formats string with deemphasis.""" return bcolors.DIM+srepr(what)+bcolors.ENDC def warn(what): """Formats string for warning.""" return bcolors.WARNING+emph(what)+bcolors.ENDC def strikeout(what): """Formats string as strikeout.""" return bcolors.CROSSOUT+srepr(what)+bcolors.ENDC def execute(cmd, stream_in = None, wd = './', env = None): """ Execute command. Parameters ---------- cmd : str Command to be executed. stream_in : file object, optional Input (via pipe) for executed process. wd : str, optional Working directory of process. Defaults to ./ . env : dict, optional Environment for execution. """ initialPath = os.getcwd() myEnv = os.environ if env is None else env os.chdir(wd) print(f"executing '{cmd}' in '{wd}'") process = subprocess.Popen(shlex.split(cmd), stdout = subprocess.PIPE, stderr = subprocess.PIPE, stdin = subprocess.PIPE, env = myEnv) stdout, stderr = [i for i in (process.communicate() if stream_in is None else process.communicate(stream_in.read().encode('utf-8')))] os.chdir(initialPath) stdout = stdout.decode('utf-8').replace('\x08','') stderr = stderr.decode('utf-8').replace('\x08','') if process.returncode != 0: raise RuntimeError(f"'{cmd}' failed with returncode {process.returncode}") return stdout, stderr def show_progress(iterable,N_iter=None,prefix='',bar_length=50): """ Decorate a loop with a status bar. Use similar like enumerate. Parameters ---------- iterable : iterable/function with yield statement Iterable (or function with yield statement) to be decorated. N_iter : int Total # of iterations. Needed if number of iterations can not be obtained as len(iterable). prefix : str, optional. Prefix string. bar_length : int, optional Character length of bar. Defaults to 50. """ status = _ProgressBar(N_iter if N_iter else len(iterable),prefix,bar_length) for i,item in enumerate(iterable): yield item status.update(i) def scale_to_coprime(v): """ Scale vector to co-prime (relatively prime) integers. Parameters ---------- v : numpy.ndarray of shape (:) Vector to scale. """ MAX_DENOMINATOR = 1000000 def get_square_denominator(x): """Denominator of the square of a number.""" return fractions.Fraction(x ** 2).limit_denominator(MAX_DENOMINATOR).denominator def lcm(a, b): """Least common multiple.""" # Python 3.9 provides math.lcm, see https://stackoverflow.com/questions/51716916. return a * b // np.gcd(a, b) m = (np.array(v) * reduce(lcm, map(lambda x: int(get_square_denominator(x)),v)) ** 0.5).astype(int) m = m//reduce(np.gcd,m) with np.errstate(invalid='ignore'): if not np.allclose(np.ma.masked_invalid(v/m),v[np.argmax(abs(v))]/m[np.argmax(abs(v))]): raise ValueError(f'Invalid result {m} for input {v}. Insufficient precision?') return m def project_stereographic(vector,direction='z',normalize=True,keepdims=False): """ Apply stereographic projection to vector. Parameters ---------- vector : numpy.ndarray of shape (...,3) Vector coordinates to be projected. direction : str or int Projection direction 'x' | 0, 'y' | 1, or 'z' | 2. Defaults to 'z'. normalize : bool Ensure unit length of input vector. Defaults to True. keepdims : bool Maintain three-dimensional output coordinates. Default two-dimensional output uses right-handed frame spanned by the next and next-next axis relative to the projection direction, e.g. x-y when projecting along z and z-x when projecting along y. Returns ------- coordinates : numpy.ndarray of shape (...,2 | 3) Projected coordinates. Examples -------- >>> project_stereographic(np.ones(3)) [0.3660254, 0.3660254] >>> project_stereographic(np.ones(3),direction='x',normalize=False,keepdims=True) [0, 0.5, 0.5] >>> project_stereographic([0,1,1],direction='y',normalize=True,keepdims=False) [0.41421356, 0] """ shift = 2-('xyzXYZ'.index(direction)%3 if isinstance(direction,str) else int(direction)) v_ = np.roll(vector/np.linalg.norm(vector,axis=-1,keepdims=True) if normalize else vector, shift,axis=-1) return np.roll(np.block([v_[...,:2]/(1+np.abs(v_[...,2:3])),np.zeros_like(v_[...,2:3])]), -shift if keepdims else 0,axis=-1)[...,:3 if keepdims else 2] def execution_stamp(class_name,function_name=None): """Timestamp the execution of a (function within a) class.""" now = datetime.datetime.now().astimezone().strftime('%Y-%m-%d %H:%M:%S%z') _function_name = '' if function_name is None else f'.{function_name}' return f'damask.{class_name}{_function_name} v{version} ({now})' def hybrid_IA(dist,N,rng_seed=None): """ Hybrid integer approximation. Parameters ---------- dist : numpy.ndarray Distribution to be approximated N : int Number of samples to draw. rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional A seed to initialize the BitGenerator. Defaults to None. If None, then fresh, unpredictable entropy will be pulled from the OS. """ N_opt_samples,N_inv_samples = (max(np.count_nonzero(dist),N),0) # random subsampling if too little samples requested scale_,scale,inc_factor = (0.0,float(N_opt_samples),1.0) while (not np.isclose(scale, scale_)) and (N_inv_samples != N_opt_samples): repeats = np.rint(scale*dist).astype(int) N_inv_samples = np.sum(repeats) scale_,scale,inc_factor = (scale,scale+inc_factor*0.5*(scale - scale_), inc_factor*2.0) \ if N_inv_samples < N_opt_samples else \ (scale_,0.5*(scale_ + scale), 1.0) return np.repeat(np.arange(len(dist)),repeats)[np.random.default_rng(rng_seed).permutation(N_inv_samples)[:N]] def shapeshifter(fro,to,mode='left',keep_ones=False): """ Return a tuple that reshapes 'fro' to become broadcastable to 'to'. Parameters ---------- fro : tuple Original shape of array. to : tuple Target shape of array after broadcasting. len(to) cannot be less than len(fro). mode : str, optional Indicates whether new axes are preferably added to either 'left' or 'right' of the original shape. Defaults to 'left'. keep_ones : bool, optional Treat '1' in fro as literal value instead of dimensional placeholder. Defaults to False. """ beg = dict(left ='(^.*\\b)', right='(^.*?\\b)') sep = dict(left ='(.*\\b)', right='(.*?\\b)') end = dict(left ='(.*?$)', right='(.*$)') fro = (1,) if not len(fro) else fro to = (1,) if not len(to) else to try: grp = re.match(beg[mode] +f',{sep[mode]}'.join(map(lambda x: f'{x}' if x>1 or (keep_ones and len(fro)>1) else '\\d+',fro)) +f',{end[mode]}', ','.join(map(str,to))+',').groups() except AttributeError: raise ValueError(f'Shapes can not be shifted {fro} --> {to}') fill = () for g,d in zip(grp,fro+(None,)): fill += (1,)*g.count(',')+(d,) return fill[:-1] def shapeblender(a,b): """ Return a shape that overlaps the rightmost entries of 'a' with the leftmost of 'b'. Parameters ---------- a : tuple Shape of first array. b : tuple Shape of second array. Examples -------- >>> shapeblender((4,4,3),(3,2,1)) (4,4,3,2,1) >>> shapeblender((1,2),(1,2,3)) (1,2,3) >>> shapeblender((1,),(2,2,1)) (1,2,2,1) >>> shapeblender((3,2),(3,2)) (3,2) """ i = min(len(a),len(b)) while i > 0 and a[-i:] != b[:i]: i -= 1 return a + b[i:] def extend_docstring(extra_docstring): """ Decorator: Append to function's docstring. Parameters ---------- extra_docstring : str Docstring to append. """ def _decorator(func): func.__doc__ += extra_docstring return func return _decorator def extended_docstring(f,extra_docstring): """ Decorator: Combine another function's docstring with a given docstring. Parameters ---------- f : function Function of which the docstring is taken. extra_docstring : str Docstring to append. """ def _decorator(func): func.__doc__ = f.__doc__ + extra_docstring return func return _decorator #################################################################################################### # Classes #################################################################################################### class extendableOption(Option): """ Used for definition of new option parser action 'extend', which enables to take multiple option arguments. Adopted from online tutorial http://docs.python.org/library/optparse.html DEPRECATED """ ACTIONS = Option.ACTIONS + ("extend",) STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",) TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",) ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",) def take_action(self, action, dest, opt, value, values, parser): if action == "extend": lvalue = value.split(",") values.ensure_value(dest, []).extend(lvalue) else: Option.take_action(self, action, dest, opt, value, values, parser) class _ProgressBar: """ Report progress of an interation as a status bar. Works for 0-based loops, ETA is estimated by linear extrapolation. """ def __init__(self,total,prefix,bar_length): """ Inititalize a progress bar to current time as basis for ETA estimation. Parameters ---------- total : int Total # of iterations. prefix : str Prefix string. bar_length : int Character length of bar. """ self.total = total self.prefix = prefix self.bar_length = bar_length self.start_time = datetime.datetime.now() self.last_fraction = 0.0 sys.stderr.write(f"{self.prefix} {'░'*self.bar_length} 0% ETA n/a") sys.stderr.flush() def update(self,iteration): fraction = (iteration+1) / self.total filled_length = int(self.bar_length * fraction) if filled_length > int(self.bar_length * self.last_fraction): bar = '█' * filled_length + '░' * (self.bar_length - filled_length) delta_time = datetime.datetime.now() - self.start_time remaining_time = (self.total - (iteration+1)) * delta_time / (iteration+1) remaining_time -= datetime.timedelta(microseconds=remaining_time.microseconds) # remove μs sys.stderr.write(f'\r{self.prefix} {bar} {fraction:>4.0%} ETA {remaining_time}') sys.stderr.flush() self.last_fraction = fraction if iteration == self.total - 1: sys.stderr.write('\n') sys.stderr.flush() class bcolors: """ ASCII colors. https://svn.blender.org/svnroot/bf-blender/trunk/blender/build_files/scons/tools/bcolors.py https://stackoverflow.com/questions/287871 """ HEADER = '\033[95m' OKBLUE = '\033[94m' OKGREEN = '\033[92m' WARNING = '\033[93m' FAIL = '\033[91m' ENDC = '\033[0m' BOLD = '\033[1m' DIM = '\033[2m' UNDERLINE = '\033[4m' CROSSOUT = '\033[9m' class return_message: """Object with formatted return message.""" def __init__(self,message): """ Sets return message. Parameters ---------- message : str or list of str message for output to screen """ self.message = message def __repr__(self): """Return message suitable for interactive shells.""" return srepr(self.message)