540 lines
16 KiB
Python
540 lines
16 KiB
Python
import sys
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import datetime
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import os
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import subprocess
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import shlex
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import re
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import fractions
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from functools import reduce
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from optparse import Option
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import numpy as np
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import h5py
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from . import version
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# limit visibility
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__all__=[
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'srepr',
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'croak',
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'report',
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'emph','deemph','warn','strikeout',
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'execute',
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'show_progress',
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'scale_to_coprime',
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'project_stereographic',
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'hybrid_IA',
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'return_message',
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'extendableOption',
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'execution_stamp',
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'shapeshifter', 'shapeblender',
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'extend_docstring', 'extended_docstring',
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'DREAM3D_base_group', 'DREAM3D_cell_data_group'
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]
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####################################################################################################
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# Functions
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####################################################################################################
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def srepr(arg,glue = '\n'):
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r"""
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Join arguments with glue string.
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Parameters
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----------
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arg : iterable
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Items to join.
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glue : str, optional
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Glue used for joining operation. Defaults to \n.
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"""
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if (not hasattr(arg, "strip") and
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(hasattr(arg, "__getitem__") or
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hasattr(arg, "__iter__"))):
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return glue.join(str(x) for x in arg)
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return arg if isinstance(arg,str) else repr(arg)
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def croak(what, newline = True):
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"""
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Write formated to stderr.
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DEPRECATED
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Parameters
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----------
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what : str or iterable
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Content to be displayed.
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newline : bool, optional
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Separate items of what by newline. Defaults to True.
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"""
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if what is not None:
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sys.stderr.write(srepr(what,glue = '\n') + ('\n' if newline else ''))
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sys.stderr.flush()
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def report(who = None,
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what = None):
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"""
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Report script and file name.
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DEPRECATED
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"""
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croak( (emph(who)+': ' if who is not None else '') + (what if what is not None else '') + '\n' )
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def emph(what):
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"""Formats string with emphasis."""
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return bcolors.BOLD+srepr(what)+bcolors.ENDC
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def deemph(what):
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"""Formats string with deemphasis."""
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return bcolors.DIM+srepr(what)+bcolors.ENDC
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def warn(what):
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"""Formats string for warning."""
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return bcolors.WARNING+emph(what)+bcolors.ENDC
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def strikeout(what):
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"""Formats string as strikeout."""
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return bcolors.CROSSOUT+srepr(what)+bcolors.ENDC
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def execute(cmd,
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stream_in = None,
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wd = './',
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env = None):
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"""
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Execute command.
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Parameters
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----------
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cmd : str
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Command to be executed.
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stream_in : file object, optional
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Input (via pipe) for executed process.
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wd : str, optional
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Working directory of process. Defaults to ./ .
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env : dict, optional
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Environment for execution.
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"""
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initialPath = os.getcwd()
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myEnv = os.environ if env is None else env
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os.chdir(wd)
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print(f"executing '{cmd}' in '{wd}'")
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process = subprocess.Popen(shlex.split(cmd),
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stdout = subprocess.PIPE,
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stderr = subprocess.PIPE,
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stdin = subprocess.PIPE,
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env = myEnv)
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stdout, stderr = [i for i in (process.communicate() if stream_in is None
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else process.communicate(stream_in.read().encode('utf-8')))]
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os.chdir(initialPath)
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stdout = stdout.decode('utf-8').replace('\x08','')
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stderr = stderr.decode('utf-8').replace('\x08','')
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if process.returncode != 0:
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print(stdout)
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print(stderr)
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raise RuntimeError(f"'{cmd}' failed with returncode {process.returncode}")
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return stdout, stderr
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def show_progress(iterable,N_iter=None,prefix='',bar_length=50):
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"""
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Decorate a loop with a status bar.
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Use similar like enumerate.
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Parameters
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----------
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iterable : iterable/function with yield statement
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Iterable (or function with yield statement) to be decorated.
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N_iter : int
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Total # of iterations. Needed if number of iterations can not be obtained as len(iterable).
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prefix : str, optional.
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Prefix string.
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bar_length : int, optional
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Character length of bar. Defaults to 50.
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"""
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status = _ProgressBar(N_iter if N_iter else len(iterable),prefix,bar_length)
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for i,item in enumerate(iterable):
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yield item
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status.update(i)
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def scale_to_coprime(v):
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"""
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Scale vector to co-prime (relatively prime) integers.
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Parameters
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----------
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v : numpy.ndarray of shape (:)
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Vector to scale.
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"""
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MAX_DENOMINATOR = 1000000
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def get_square_denominator(x):
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"""Denominator of the square of a number."""
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return fractions.Fraction(x ** 2).limit_denominator(MAX_DENOMINATOR).denominator
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def lcm(a, b):
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"""Least common multiple."""
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# Python 3.9 provides math.lcm, see https://stackoverflow.com/questions/51716916.
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return a * b // np.gcd(a, b)
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m = (np.array(v) * reduce(lcm, map(lambda x: int(get_square_denominator(x)),v)) ** 0.5).astype(int)
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m = m//reduce(np.gcd,m)
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with np.errstate(invalid='ignore'):
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if not np.allclose(np.ma.masked_invalid(v/m),v[np.argmax(abs(v))]/m[np.argmax(abs(v))]):
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raise ValueError(f'Invalid result {m} for input {v}. Insufficient precision?')
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return m
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def project_stereographic(vector,direction='z',normalize=True,keepdims=False):
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"""
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Apply stereographic projection to vector.
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Parameters
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----------
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vector : numpy.ndarray of shape (...,3)
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Vector coordinates to be projected.
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direction : str
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Projection direction 'x', 'y', or 'z'.
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Defaults to 'z'.
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normalize : bool
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Ensure unit length of input vector. Defaults to True.
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keepdims : bool
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Maintain three-dimensional output coordinates.
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Default two-dimensional output uses right-handed frame spanned by
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the next and next-next axis relative to the projection direction,
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e.g. x-y when projecting along z and z-x when projecting along y.
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Returns
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-------
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coordinates : numpy.ndarray of shape (...,2 | 3)
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Projected coordinates.
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Examples
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--------
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>>> project_stereographic(np.ones(3))
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[0.3660254, 0.3660254]
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>>> project_stereographic(np.ones(3),direction='x',normalize=False,keepdims=True)
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[0, 0.5, 0.5]
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>>> project_stereographic([0,1,1],direction='y',normalize=True,keepdims=False)
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[0.41421356, 0]
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"""
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shift = 'zyx'.index(direction)
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v_ = np.roll(vector/np.linalg.norm(vector,axis=-1,keepdims=True) if normalize else vector,
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shift,axis=-1)
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return np.roll(np.block([v_[...,:2]/(1+np.abs(v_[...,2:3])),np.zeros_like(v_[...,2:3])]),
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-shift if keepdims else 0,axis=-1)[...,:3 if keepdims else 2]
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def execution_stamp(class_name,function_name=None):
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"""Timestamp the execution of a (function within a) class."""
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now = datetime.datetime.now().astimezone().strftime('%Y-%m-%d %H:%M:%S%z')
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_function_name = '' if function_name is None else f'.{function_name}'
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return f'damask.{class_name}{_function_name} v{version} ({now})'
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def hybrid_IA(dist,N,rng_seed=None):
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"""
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Hybrid integer approximation.
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Parameters
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----------
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dist : numpy.ndarray
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Distribution to be approximated
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N : int
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Number of samples to draw.
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rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
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A seed to initialize the BitGenerator. Defaults to None.
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If None, then fresh, unpredictable entropy will be pulled from the OS.
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"""
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N_opt_samples,N_inv_samples = (max(np.count_nonzero(dist),N),0) # random subsampling if too little samples requested
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scale_,scale,inc_factor = (0.0,float(N_opt_samples),1.0)
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while (not np.isclose(scale, scale_)) and (N_inv_samples != N_opt_samples):
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repeats = np.rint(scale*dist).astype(int)
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N_inv_samples = np.sum(repeats)
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scale_,scale,inc_factor = (scale,scale+inc_factor*0.5*(scale - scale_), inc_factor*2.0) \
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if N_inv_samples < N_opt_samples else \
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(scale_,0.5*(scale_ + scale), 1.0)
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return np.repeat(np.arange(len(dist)),repeats)[np.random.default_rng(rng_seed).permutation(N_inv_samples)[:N]]
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def shapeshifter(fro,to,mode='left',keep_ones=False):
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"""
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Return a tuple that reshapes 'fro' to become broadcastable to 'to'.
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Parameters
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----------
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fro : tuple
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Original shape of array.
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to : tuple
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Target shape of array after broadcasting.
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len(to) cannot be less than len(fro).
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mode : str, optional
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Indicates whether new axes are preferably added to
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either 'left' or 'right' of the original shape.
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Defaults to 'left'.
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keep_ones : bool, optional
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Treat '1' in fro as literal value instead of dimensional placeholder.
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Defaults to False.
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"""
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beg = dict(left ='(^.*\\b)',
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right='(^.*?\\b)')
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sep = dict(left ='(.*\\b)',
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right='(.*?\\b)')
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end = dict(left ='(.*?$)',
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right='(.*$)')
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fro = (1,) if not len(fro) else fro
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to = (1,) if not len(to) else to
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try:
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grp = re.match(beg[mode]
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+f',{sep[mode]}'.join(map(lambda x: f'{x}'
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if x>1 or (keep_ones and len(fro)>1) else
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'\\d+',fro))
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+f',{end[mode]}',
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','.join(map(str,to))+',').groups()
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except AttributeError:
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raise ValueError(f'Shapes can not be shifted {fro} --> {to}')
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fill = ()
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for g,d in zip(grp,fro+(None,)):
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fill += (1,)*g.count(',')+(d,)
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return fill[:-1]
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def shapeblender(a,b):
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"""
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Return a shape that overlaps the rightmost entries of 'a' with the leftmost of 'b'.
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Parameters
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----------
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a : tuple
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Shape of first array.
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b : tuple
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Shape of second array.
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Examples
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--------
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>>> shapeblender((4,4,3),(3,2,1))
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(4,4,3,2,1)
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>>> shapeblender((1,2),(1,2,3))
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(1,2,3)
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>>> shapeblender((1,),(2,2,1))
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(1,2,2,1)
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>>> shapeblender((3,2),(3,2))
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(3,2)
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"""
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i = min(len(a),len(b))
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while i > 0 and a[-i:] != b[:i]: i -= 1
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return a + b[i:]
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def extend_docstring(extra_docstring):
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"""
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Decorator: Append to function's docstring.
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Parameters
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----------
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extra_docstring : str
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Docstring to append.
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"""
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def _decorator(func):
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func.__doc__ += extra_docstring
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return func
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return _decorator
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def extended_docstring(f,extra_docstring):
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"""
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Decorator: Combine another function's docstring with a given docstring.
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Parameters
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----------
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f : function
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Function of which the docstring is taken.
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extra_docstring : str
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Docstring to append.
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"""
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def _decorator(func):
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func.__doc__ = f.__doc__ + extra_docstring
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return func
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return _decorator
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def DREAM3D_base_group(fname):
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"""
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Determine the base group of a DREAM.3D file.
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The base group is defined as the group (folder) that contains
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a 'SPACING' dataset in a '_SIMPL_GEOMETRY' group.
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Parameters
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----------
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fname : str
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Filename of the DREAM.3D (HDF5) file.
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"""
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with h5py.File(fname,'r') as f:
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base_group = f.visit(lambda path: path.rsplit('/',2)[0] if '_SIMPL_GEOMETRY/SPACING' in path else None)
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if base_group is None:
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raise ValueError('Could not determine base group in file {fname}.')
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return base_group
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def DREAM3D_cell_data_group(fname):
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"""
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Determine the cell data group of a DREAM.3D file.
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The cell data group is defined as the group (folder) that contains
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a dataset in the base group whose length matches the total number
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of points as specified in '_SIMPL_GEOMETRY/DIMENSIONS'.
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Parameters
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----------
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fname : str
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Filename of the DREAM.3D (HDF5) file.
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"""
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base_group = DREAM3D_base_group(fname)
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with h5py.File(fname,'r') as f:
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N_points = np.prod(f[os.path.join(base_group,'_SIMPL_GEOMETRY','DIMENSIONS')])
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cell_data_group = f[base_group].visititems(lambda path,obj: path.split('/')[0] \
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if isinstance(obj,h5py._hl.dataset.Dataset) and np.prod(np.shape(obj)) == N_points \
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else None)
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if cell_data_group is None:
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raise ValueError('Could not determine cell data group in file {fname}.')
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return cell_data_group
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####################################################################################################
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# Classes
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####################################################################################################
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class extendableOption(Option):
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"""
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Used for definition of new option parser action 'extend', which enables to take multiple option arguments.
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Adopted from online tutorial http://docs.python.org/library/optparse.html
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DEPRECATED
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"""
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ACTIONS = Option.ACTIONS + ("extend",)
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STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
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TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
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ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
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def take_action(self, action, dest, opt, value, values, parser):
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if action == "extend":
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lvalue = value.split(",")
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values.ensure_value(dest, []).extend(lvalue)
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else:
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Option.take_action(self, action, dest, opt, value, values, parser)
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class _ProgressBar:
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"""
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Report progress of an interation as a status bar.
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Works for 0-based loops, ETA is estimated by linear extrapolation.
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"""
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def __init__(self,total,prefix,bar_length):
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"""
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Inititalize a progress bar to current time as basis for ETA estimation.
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Parameters
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----------
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total : int
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Total # of iterations.
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prefix : str
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Prefix string.
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bar_length : int
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Character length of bar.
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"""
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self.total = total
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self.prefix = prefix
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self.bar_length = bar_length
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self.start_time = datetime.datetime.now()
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self.last_fraction = 0.0
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sys.stderr.write(f"{self.prefix} {'░'*self.bar_length} 0% ETA n/a")
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sys.stderr.flush()
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def update(self,iteration):
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fraction = (iteration+1) / self.total
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filled_length = int(self.bar_length * fraction)
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if filled_length > int(self.bar_length * self.last_fraction):
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bar = '█' * filled_length + '░' * (self.bar_length - filled_length)
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delta_time = datetime.datetime.now() - self.start_time
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remaining_time = (self.total - (iteration+1)) * delta_time / (iteration+1)
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remaining_time -= datetime.timedelta(microseconds=remaining_time.microseconds) # remove μs
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sys.stderr.write(f'\r{self.prefix} {bar} {fraction:>4.0%} ETA {remaining_time}')
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sys.stderr.flush()
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self.last_fraction = fraction
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if iteration == self.total - 1:
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sys.stderr.write('\n')
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sys.stderr.flush()
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class bcolors:
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"""
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ASCII colors.
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https://svn.blender.org/svnroot/bf-blender/trunk/blender/build_files/scons/tools/bcolors.py
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https://stackoverflow.com/questions/287871
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"""
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HEADER = '\033[95m'
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OKBLUE = '\033[94m'
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OKGREEN = '\033[92m'
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WARNING = '\033[93m'
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FAIL = '\033[91m'
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ENDC = '\033[0m'
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BOLD = '\033[1m'
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DIM = '\033[2m'
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UNDERLINE = '\033[4m'
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CROSSOUT = '\033[9m'
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class return_message:
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"""Object with formatted return message."""
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def __init__(self,message):
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"""
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Sets return message.
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Parameters
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----------
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message : str or list of str
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message for output to screen
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"""
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self.message = message
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def __repr__(self):
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"""Return message suitable for interactive shells."""
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return srepr(self.message)
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