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(np.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,normalize=False):
"""
Apply stereographic projection to vector.
Parameters
----------
vector : numpy.ndarray of shape (...,3)
Vector coordinates to be projected.
normalize : bool
Ensure unit length for vector. Defaults to False.
Returns
-------
coordinates : numpy.ndarray of shape (...,2)
Projected coordinates.
"""
v_ = vector/np.linalg.norm(vector,axis=-1,keepdims=True) if normalize else vector
return np.block([v_[...,:2]/(1+np.abs(v_[...,2:3])),
np.zeros_like(v_[...,2:3])])
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)