Merge branch 'development' into HDF5-results
This commit is contained in:
Martin Diehl
commit
c43af6aac3
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@ -18,7 +18,7 @@ from . import Orientation
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from . import Environment
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from . import grid_filters
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class Result():
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class Result:
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"""
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Read and write to DADF5 files.
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@ -1002,10 +1002,9 @@ class Result():
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groups = self.groups_with_datasets(datasets.values())
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default_arg = partial(self._job,func=func,datasets=datasets,args=args,lock=lock)
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util.progressBar(iteration=0,total=len(groups))
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for i,result in enumerate(pool.imap_unordered(default_arg,groups)):
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util.progressBar(iteration=i+1,total=len(groups))
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if not result: continue
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for result in util.show_progress(pool.imap_unordered(default_arg,groups),len(groups)):
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if not result:
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continue
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lock.acquire()
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with h5py.File(self.fname, 'a') as f:
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try:
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@ -1,9 +1,9 @@
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import sys
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import time
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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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from fractions import Fraction
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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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@ -11,10 +11,10 @@ import numpy as np
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class bcolors:
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"""
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ASCII Colors (Blender code).
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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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http://stackoverflow.com/questions/287871/print-in-terminal-with-colors-using-python
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https://stackoverflow.com/questions/287871
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"""
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HEADER = '\033[95m'
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@ -38,18 +38,18 @@ class bcolors:
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self.BOLD = ''
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self.UNDERLINE = ''
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self.CROSSOUT = ''
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def srepr(arg,glue = '\n'):
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r"""
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Join arguments as individual lines.
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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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Defaults to \n.
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Defaults to \n.
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"""
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if (not hasattr(arg, "strip") and
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@ -62,13 +62,13 @@ def srepr(arg,glue = '\n'):
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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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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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Separate items of what by newline. Defaults to True.
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"""
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if not what:
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@ -165,63 +165,93 @@ class extendableOption(Option):
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Option.take_action(self, action, dest, opt, value, values, parser)
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def progressBar(iteration, total, prefix='', bar_length=50):
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class _ProgressBar:
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"""
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Call in a loop to create terminal progress bar.
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From https://gist.github.com/aubricus/f91fb55dc6ba5557fbab06119420dd6a
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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('{} {} 0% ETA n/a'.format(self.prefix, '░'*self.bar_length))
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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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if int(self.bar_length * fraction) > int(self.bar_length * self.last_fraction):
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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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filled_length = int(self.bar_length * fraction)
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bar = '█' * filled_length + '░' * (self.bar_length - filled_length)
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sys.stderr.write('\r{} {} {:>4.0%} ETA {}'.format(self.prefix, bar, fraction, 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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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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iteration : int
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Current iteration.
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total : int
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Total iterations.
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prefix : str, optional
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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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fraction = iteration / float(total)
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if not hasattr(progressBar, "last_fraction"): # first call to function
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progressBar.start_time = time.time()
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progressBar.last_fraction = -1.0
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remaining_time = ' n/a'
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else:
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if fraction <= progressBar.last_fraction or iteration == 0: # reset: called within a new loop
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progressBar.start_time = time.time()
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progressBar.last_fraction = -1.0
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remaining_time = ' n/a'
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else:
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progressBar.last_fraction = fraction
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remainder = (total - iteration) * (time.time()-progressBar.start_time)/iteration
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remaining_time = '{: 3d}:'.format(int( remainder//3600)) + \
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'{:02d}:'.format(int((remainder//60)%60)) + \
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'{:02d}' .format(int( remainder %60))
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status = _ProgressBar(N_iter if N_iter else len(iterable),prefix,bar_length)
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filled_length = int(round(bar_length * fraction))
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bar = '█' * filled_length + '░' * (bar_length - filled_length)
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sys.stderr.write('\r{} {} {}'.format(prefix, bar, remaining_time)),
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if iteration == total:
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sys.stderr.write('\n')
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sys.stderr.flush()
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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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"""Scale vector to co-prime (relatively prime) integers."""
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MAX_DENOMINATOR = 1000
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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 Fraction(x ** 2).limit_denominator(MAX_DENOMINATOR).denominator
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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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return a * b // np.gcd(a, b)
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denominators = [int(get_square_denominator(i)) for i in v]
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s = reduce(lcm, denominators) ** 0.5
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m = (np.array(v)*s).astype(np.int)
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@ -230,7 +260,7 @@ def scale_to_coprime(v):
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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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@ -242,7 +272,7 @@ class return_message():
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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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