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"""
A collection of utility functions and classes. Many (but not all)
from the Python Cookbook -- hence the name cbook
"""
from __future__ import generators
import re, os, errno, sys, StringIO, traceback, locale, threading, types
import time, datetime
import warnings
import numpy as np
import numpy.ma as ma
from weakref import ref
import cPickle
import os.path
import random
import urllib2
import new
import matplotlib
major, minor1, minor2, s, tmp = sys.version_info
# On some systems, locale.getpreferredencoding returns None,
# which can break unicode; and the sage project reports that
# some systems have incorrect locale specifications, e.g.,
# an encoding instead of a valid locale name. Another
# pathological case that has been reported is an empty string.
# On some systems, getpreferredencoding sets the locale, which has
# side effects. Passing False eliminates those side effects.
try:
preferredencoding = locale.getpreferredencoding(False).strip()
if not preferredencoding:
preferredencoding = None
except (ValueError, ImportError, AttributeError):
preferredencoding = None
def unicode_safe(s):
if preferredencoding is None: return unicode(s)
else: return unicode(s, preferredencoding)
class converter:
"""
Base class for handling string -> python type with support for
missing values
"""
def __init__(self, missing='Null', missingval=None):
self.missing = missing
self.missingval = missingval
def __call__(self, s):
if s==self.missing: return self.missingval
return s
def is_missing(self, s):
return not s.strip() or s==self.missing
class tostr(converter):
'convert to string or None'
def __init__(self, missing='Null', missingval=''):
converter.__init__(self, missing=missing, missingval=missingval)
class todatetime(converter):
'convert to a datetime or None'
def __init__(self, fmt='%Y-%m-%d', missing='Null', missingval=None):
'use a :func:`time.strptime` format string for conversion'
converter.__init__(self, missing, missingval)
self.fmt = fmt
def __call__(self, s):
if self.is_missing(s): return self.missingval
tup = time.strptime(s, self.fmt)
return datetime.datetime(*tup[:6])
class todate(converter):
'convert to a date or None'
def __init__(self, fmt='%Y-%m-%d', missing='Null', missingval=None):
'use a :func:`time.strptime` format string for conversion'
converter.__init__(self, missing, missingval)
self.fmt = fmt
def __call__(self, s):
if self.is_missing(s): return self.missingval
tup = time.strptime(s, self.fmt)
return datetime.date(*tup[:3])
class tofloat(converter):
'convert to a float or None'
def __init__(self, missing='Null', missingval=None):
converter.__init__(self, missing)
self.missingval = missingval
def __call__(self, s):
if self.is_missing(s): return self.missingval
return float(s)
class toint(converter):
'convert to an int or None'
def __init__(self, missing='Null', missingval=None):
converter.__init__(self, missing)
def __call__(self, s):
if self.is_missing(s): return self.missingval
return int(s)
class CallbackRegistry:
"""
Handle registering and disconnecting for a set of signals and
callbacks::
signals = 'eat', 'drink', 'be merry'
def oneat(x):
print 'eat', x
def ondrink(x):
print 'drink', x
callbacks = CallbackRegistry(signals)
ideat = callbacks.connect('eat', oneat)
iddrink = callbacks.connect('drink', ondrink)
#tmp = callbacks.connect('drunk', ondrink) # this will raise a ValueError
callbacks.process('drink', 123) # will call oneat
callbacks.process('eat', 456) # will call ondrink
callbacks.process('be merry', 456) # nothing will be called
callbacks.disconnect(ideat) # disconnect oneat
callbacks.process('eat', 456) # nothing will be called
In practice, one should always disconnect all callbacks when they
are no longer needed to avoid dangling references (and thus memory
leaks). However, real code in matplotlib rarely does so, and due
to its design, it is rather difficult to place this kind of code.
To get around this, and prevent this class of memory leaks, we
instead store weak references to bound methods only, so when the
destination object needs to die, the CallbackRegistry won't keep
it alive. The Python stdlib weakref module can not create weak
references to bound methods directly, so we need to create a proxy
object to handle weak references to bound methods (or regular free
functions). This technique was shared by Peter Parente on his
`"Mindtrove" blog
<http://mindtrove.info/articles/python-weak-references/>`_.
"""
class BoundMethodProxy(object):
'''
Our own proxy object which enables weak references to bound and unbound
methods and arbitrary callables. Pulls information about the function,
class, and instance out of a bound method. Stores a weak reference to the
instance to support garbage collection.
@organization: IBM Corporation
@copyright: Copyright (c) 2005, 2006 IBM Corporation
@license: The BSD License
Minor bugfixes by Michael Droettboom
'''
def __init__(self, cb):
try:
try:
self.inst = ref(cb.im_self)
except TypeError:
self.inst = None
self.func = cb.im_func
self.klass = cb.im_class
except AttributeError:
self.inst = None
self.func = cb
self.klass = None
def __call__(self, *args, **kwargs):
'''
Proxy for a call to the weak referenced object. Take
arbitrary params to pass to the callable.
Raises `ReferenceError`: When the weak reference refers to
a dead object
'''
if self.inst is not None and self.inst() is None:
raise ReferenceError
elif self.inst is not None:
# build a new instance method with a strong reference to the instance
mtd = new.instancemethod(self.func, self.inst(), self.klass)
else:
# not a bound method, just return the func
mtd = self.func
# invoke the callable and return the result
return mtd(*args, **kwargs)
def __eq__(self, other):
'''
Compare the held function and instance with that held by
another proxy.
'''
try:
if self.inst is None:
return self.func == other.func and other.inst is None
else:
return self.func == other.func and self.inst() == other.inst()
except Exception:
return False
def __ne__(self, other):
'''
Inverse of __eq__.
'''
return not self.__eq__(other)
def __init__(self, signals):
'*signals* is a sequence of valid signals'
self.signals = set(signals)
self.callbacks = dict([(s, dict()) for s in signals])
self._cid = 0
def _check_signal(self, s):
'make sure *s* is a valid signal or raise a ValueError'
if s not in self.signals:
signals = list(self.signals)
signals.sort()
raise ValueError('Unknown signal "%s"; valid signals are %s'%(s, signals))
def connect(self, s, func):
"""
register *func* to be called when a signal *s* is generated
func will be called
"""
self._check_signal(s)
proxy = self.BoundMethodProxy(func)
for cid, callback in self.callbacks[s].items():
# Clean out dead references
if callback.inst is not None and callback.inst() is None:
del self.callbacks[s][cid]
elif callback == proxy:
return cid
self._cid += 1
self.callbacks[s][self._cid] = proxy
return self._cid
def disconnect(self, cid):
"""
disconnect the callback registered with callback id *cid*
"""
for eventname, callbackd in self.callbacks.items():
try:
del callbackd[cid]
except KeyError:
continue
else:
return
def process(self, s, *args, **kwargs):
"""
process signal *s*. All of the functions registered to receive
callbacks on *s* will be called with *\*args* and *\*\*kwargs*
"""
self._check_signal(s)
for cid, proxy in self.callbacks[s].items():
# Clean out dead references
if proxy.inst is not None and proxy.inst() is None:
del self.callbacks[s][cid]
else:
proxy(*args, **kwargs)
class Scheduler(threading.Thread):
"""
Base class for timeout and idle scheduling
"""
idlelock = threading.Lock()
id = 0
def __init__(self):
threading.Thread.__init__(self)
self.id = Scheduler.id
self._stopped = False
Scheduler.id += 1
self._stopevent = threading.Event()
def stop(self):
if self._stopped: return
self._stopevent.set()
self.join()
self._stopped = True
class Timeout(Scheduler):
"""
Schedule recurring events with a wait time in seconds
"""
def __init__(self, wait, func):
Scheduler.__init__(self)
self.wait = wait
self.func = func
def run(self):
while not self._stopevent.isSet():
self._stopevent.wait(self.wait)
Scheduler.idlelock.acquire()
b = self.func(self)
Scheduler.idlelock.release()
if not b: break
class Idle(Scheduler):
"""
Schedule callbacks when scheduler is idle
"""
# the prototype impl is a bit of a poor man's idle handler. It
# just implements a short wait time. But it will provide a
# placeholder for a proper impl ater
waittime = 0.05
def __init__(self, func):
Scheduler.__init__(self)
self.func = func
def run(self):
while not self._stopevent.isSet():
self._stopevent.wait(Idle.waittime)
Scheduler.idlelock.acquire()
b = self.func(self)
Scheduler.idlelock.release()
if not b: break
class silent_list(list):
"""
override repr when returning a list of matplotlib artists to
prevent long, meaningless output. This is meant to be used for a
homogeneous list of a give type
"""
def __init__(self, type, seq=None):
self.type = type
if seq is not None: self.extend(seq)
def __repr__(self):
return '<a list of %d %s objects>' % (len(self), self.type)
def __str__(self):
return '<a list of %d %s objects>' % (len(self), self.type)
def strip_math(s):
'remove latex formatting from mathtext'
remove = (r'\mathdefault', r'\rm', r'\cal', r'\tt', r'\it', '\\', '{', '}')
s = s[1:-1]
for r in remove: s = s.replace(r,'')
return s
class Bunch:
"""
Often we want to just collect a bunch of stuff together, naming each
item of the bunch; a dictionary's OK for that, but a small do- nothing
class is even handier, and prettier to use. Whenever you want to
group a few variables:
>>> point = Bunch(datum=2, squared=4, coord=12)
>>> point.datum
By: Alex Martelli
From: http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/52308
"""
def __init__(self, **kwds):
self.__dict__.update(kwds)
def __repr__(self):
keys = self.__dict__.keys()
return 'Bunch(%s)'%', '.join(['%s=%s'%(k,self.__dict__[k]) for k in keys])
def unique(x):
'Return a list of unique elements of *x*'
return dict([ (val, 1) for val in x]).keys()
def iterable(obj):
'return true if *obj* is iterable'
try: len(obj)
except: return False
return True
def is_string_like(obj):
'Return True if *obj* looks like a string'
if isinstance(obj, (str, unicode)): return True
# numpy strings are subclass of str, ma strings are not
if ma.isMaskedArray(obj):
if obj.ndim == 0 and obj.dtype.kind in 'SU':
return True
else:
return False
try: obj + ''
except: return False
return True
def is_sequence_of_strings(obj):
"""
Returns true if *obj* is iterable and contains strings
"""
if not iterable(obj): return False
if is_string_like(obj): return False
for o in obj:
if not is_string_like(o): return False
return True
def is_writable_file_like(obj):
'return true if *obj* looks like a file object with a *write* method'
return hasattr(obj, 'write') and callable(obj.write)
def is_scalar(obj):
'return true if *obj* is not string like and is not iterable'
return not is_string_like(obj) and not iterable(obj)
def is_numlike(obj):
'return true if *obj* looks like a number'
try: obj+1
except: return False
else: return True
def to_filehandle(fname, flag='rU', return_opened=False):
"""
*fname* can be a filename or a file handle. Support for gzipped
files is automatic, if the filename ends in .gz. *flag* is a
read/write flag for :func:`file`
"""
if is_string_like(fname):
if fname.endswith('.gz'):
import gzip
# get rid of 'U' in flag for gzipped files.
flag = flag.replace('U','')
fh = gzip.open(fname, flag)
elif fname.endswith('.bz2'):
# get rid of 'U' in flag for bz2 files
flag = flag.replace('U','')
import bz2
fh = bz2.BZ2File(fname, flag)
else:
fh = file(fname, flag)
opened = True
elif hasattr(fname, 'seek'):
fh = fname
opened = False
else:
raise ValueError('fname must be a string or file handle')
if return_opened:
return fh, opened
return fh
def is_scalar_or_string(val):
return is_string_like(val) or not iterable(val)
class ViewVCCachedServer(urllib2.BaseHandler):
"""
Urllib2 handler that takes care of caching files.
The file cache.pck holds the directory of files that have been cached.
"""
def __init__(self, cache_dir, baseurl):
self.cache_dir = cache_dir
self.baseurl = baseurl
self.read_cache()
self.remove_stale_files()
self.opener = urllib2.build_opener(self)
def in_cache_dir(self, fn):
# make sure the datadir exists
reldir, filename = os.path.split(fn)
datadir = os.path.join(self.cache_dir, reldir)
if not os.path.exists(datadir):
os.makedirs(datadir)
return os.path.join(datadir, filename)
def read_cache(self):
"""
Read the cache file from the cache directory.
"""
fn = self.in_cache_dir('cache.pck')
if not os.path.exists(fn):
self.cache = {}
return
f = open(fn, 'rb')
cache = cPickle.load(f)
f.close()
# Earlier versions did not have the full paths in cache.pck
for url, (fn, x, y) in cache.items():
if not os.path.isabs(fn):
cache[url] = (self.in_cache_dir(fn), x, y)
# If any files are deleted, drop them from the cache
for url, (fn, _, _) in cache.items():
if not os.path.exists(fn):
del cache[url]
self.cache = cache
def remove_stale_files(self):
"""
Remove files from the cache directory that are not listed in
cache.pck.
"""
# TODO: remove empty subdirectories
listed = set(fn for (_, (fn, _, _)) in self.cache.items())
existing = reduce(set.union,
(set(os.path.join(dirpath, fn) for fn in filenames)
for (dirpath, _, filenames) in os.walk(self.cache_dir)))
matplotlib.verbose.report(
'ViewVCCachedServer: files listed in cache.pck: %s' % listed, 'debug')
matplotlib.verbose.report(
'ViewVCCachedServer: files in cache directory: %s' % existing, 'debug')
for path in existing - listed - set([self.in_cache_dir('cache.pck')]):
matplotlib.verbose.report('ViewVCCachedServer:remove_stale_files: removing %s'%path,
level='debug')
os.remove(path)
def write_cache(self):
"""
Write the cache data structure into the cache directory.
"""
fn = self.in_cache_dir('cache.pck')
f = open(fn, 'wb')
cPickle.dump(self.cache, f, -1)
f.close()
def cache_file(self, url, data, headers):
"""
Store a received file in the cache directory.
"""
# Pick a filename
fn = url[len(self.baseurl):]
fullpath = self.in_cache_dir(fn)
f = open(fullpath, 'wb')
f.write(data)
f.close()
# Update the cache
self.cache[url] = (fullpath, headers.get('ETag'), headers.get('Last-Modified'))
self.write_cache()
# These urllib2 entry points are used:
# http_request for preprocessing requests
# http_error_304 for handling 304 Not Modified responses
# http_response for postprocessing requests
def http_request(self, req):
"""
Make the request conditional if we have a cached file.
"""
url = req.get_full_url()
if url in self.cache:
_, etag, lastmod = self.cache[url]
req.add_header("If-None-Match", etag)
req.add_header("If-Modified-Since", lastmod)
return req
def http_error_304(self, req, fp, code, msg, hdrs):
"""
Read the file from the cache since the server has no newer version.
"""
url = req.get_full_url()
fn, _, _ = self.cache[url]
matplotlib.verbose.report('ViewVCCachedServer: reading data file from cache file "%s"'
%fn, 'debug')
file = open(fn, 'rb')
handle = urllib2.addinfourl(file, hdrs, url)
handle.code = 304
return handle
def http_response(self, req, response):
"""
Update the cache with the returned file.
"""
matplotlib.verbose.report('ViewVCCachedServer: received response %d: %s'
% (response.code, response.msg), 'debug')
if response.code != 200:
return response
else:
data = response.read()
self.cache_file(req.get_full_url(), data, response.headers)
result = urllib2.addinfourl(StringIO.StringIO(data),
response.headers,
req.get_full_url())
result.code = response.code
result.msg = response.msg
return result
def get_sample_data(self, fname, asfileobj=True):
"""
Check the cachedirectory for a sample_data file. If it does
not exist, fetch it with urllib from the svn repo and
store it in the cachedir.
If asfileobj is True, a file object will be returned. Else the
path to the file as a string will be returned.
"""
# TODO: time out if the connection takes forever
# (may not be possible with urllib2 only - spawn a helper process?)
# quote is not in python2.4, so check for it and get it from
# urllib if it is not available
quote = getattr(urllib2, 'quote', None)
if quote is None:
import urllib
quote = urllib.quote
# retrieve the URL for the side effect of refreshing the cache
url = self.baseurl + quote(fname)
error = 'unknown error'
matplotlib.verbose.report('ViewVCCachedServer: retrieving %s'
% url, 'debug')
try:
response = self.opener.open(url)
except urllib2.URLError, e:
# could be a missing network connection
error = str(e)
cached = self.cache.get(url)
if cached is None:
msg = 'file %s not in cache; received %s when trying to retrieve' \
% (fname, error)
raise KeyError(msg)
fname = cached[0]
if asfileobj:
if os.path.splitext(fname)[-1].lower() in ('.csv', '.xrc', '.txt'):
mode = 'r'
else:
mode = 'rb'
return open(fname, mode)
else:
return fname
def get_sample_data(fname, asfileobj=True):
"""
Check the cachedirectory ~/.matplotlib/sample_data for a sample_data
file. If it does not exist, fetch it with urllib from the mpl svn repo
http://matplotlib.svn.sourceforge.net/svnroot/matplotlib/trunk/sample_data/
and store it in the cachedir.
If asfileobj is True, a file object will be returned. Else the
path to the file as a string will be returned
To add a datafile to this directory, you need to check out
sample_data from matplotlib svn::
svn co https://matplotlib.svn.sourceforge.net/svnroot/matplotlib/trunk/sample_data
and svn add the data file you want to support. This is primarily
intended for use in mpl examples that need custom data.
To bypass all downloading, set the rc parameter examples.download to False
and examples.directory to the directory where we should look.
"""
if not matplotlib.rcParams['examples.download']:
directory = matplotlib.rcParams['examples.directory']
f = os.path.join(directory, fname)
if asfileobj:
return open(f, 'rb')
else:
return f
myserver = get_sample_data.myserver
if myserver is None:
configdir = matplotlib.get_configdir()
cachedir = os.path.join(configdir, 'sample_data')
baseurl = 'http://matplotlib.svn.sourceforge.net/svnroot/matplotlib/trunk/sample_data/'
myserver = get_sample_data.myserver = ViewVCCachedServer(cachedir, baseurl)
return myserver.get_sample_data(fname, asfileobj=asfileobj)
get_sample_data.myserver = None
def flatten(seq, scalarp=is_scalar_or_string):
"""
this generator flattens nested containers such as
>>> l=( ('John', 'Hunter'), (1,23), [[[[42,(5,23)]]]])
so that
>>> for i in flatten(l): print i,
John Hunter 1 23 42 5 23
By: Composite of Holger Krekel and Luther Blissett
From: http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/121294
and Recipe 1.12 in cookbook
"""
for item in seq:
if scalarp(item): yield item
else:
for subitem in flatten(item, scalarp):
yield subitem
class Sorter:
"""
Sort by attribute or item
Example usage::
sort = Sorter()
list = [(1, 2), (4, 8), (0, 3)]
dict = [{'a': 3, 'b': 4}, {'a': 5, 'b': 2}, {'a': 0, 'b': 0},
{'a': 9, 'b': 9}]
sort(list) # default sort
sort(list, 1) # sort by index 1
sort(dict, 'a') # sort a list of dicts by key 'a'
"""
def _helper(self, data, aux, inplace):
aux.sort()
result = [data[i] for junk, i in aux]
if inplace: data[:] = result
return result
def byItem(self, data, itemindex=None, inplace=1):
if itemindex is None:
if inplace:
data.sort()
result = data
else:
result = data[:]
result.sort()
return result
else:
aux = [(data[i][itemindex], i) for i in range(len(data))]
return self._helper(data, aux, inplace)
def byAttribute(self, data, attributename, inplace=1):
aux = [(getattr(data[i],attributename),i) for i in range(len(data))]
return self._helper(data, aux, inplace)
# a couple of handy synonyms
sort = byItem
__call__ = byItem
class Xlator(dict):
"""
All-in-one multiple-string-substitution class
Example usage::
text = "Larry Wall is the creator of Perl"
adict = {
"Larry Wall" : "Guido van Rossum",
"creator" : "Benevolent Dictator for Life",
"Perl" : "Python",
}
print multiple_replace(adict, text)
xlat = Xlator(adict)
print xlat.xlat(text)
"""
def _make_regex(self):
""" Build re object based on the keys of the current dictionary """
return re.compile("|".join(map(re.escape, self.keys())))
def __call__(self, match):
""" Handler invoked for each regex *match* """
return self[match.group(0)]
def xlat(self, text):
""" Translate *text*, returns the modified text. """
return self._make_regex().sub(self, text)
def soundex(name, len=4):
""" soundex module conforming to Odell-Russell algorithm """
# digits holds the soundex values for the alphabet
soundex_digits = '01230120022455012623010202'
sndx = ''
fc = ''
# Translate letters in name to soundex digits
for c in name.upper():
if c.isalpha():
if not fc: fc = c # Remember first letter
d = soundex_digits[ord(c)-ord('A')]
# Duplicate consecutive soundex digits are skipped
if not sndx or (d != sndx[-1]):
sndx += d
# Replace first digit with first letter
sndx = fc + sndx[1:]
# Remove all 0s from the soundex code
sndx = sndx.replace('0', '')
# Return soundex code truncated or 0-padded to len characters
return (sndx + (len * '0'))[:len]
class Null:
""" Null objects always and reliably "do nothing." """
def __init__(self, *args, **kwargs): pass
def __call__(self, *args, **kwargs): return self
def __str__(self): return "Null()"
def __repr__(self): return "Null()"
def __nonzero__(self): return 0
def __getattr__(self, name): return self
def __setattr__(self, name, value): return self
def __delattr__(self, name): return self
def mkdirs(newdir, mode=0777):
"""
make directory *newdir* recursively, and set *mode*. Equivalent to ::
> mkdir -p NEWDIR
> chmod MODE NEWDIR
"""
try:
if not os.path.exists(newdir):
parts = os.path.split(newdir)
for i in range(1, len(parts)+1):
thispart = os.path.join(*parts[:i])
if not os.path.exists(thispart):
os.makedirs(thispart, mode)
except OSError, err:
# Reraise the error unless it's about an already existing directory
if err.errno != errno.EEXIST or not os.path.isdir(newdir):
raise
class GetRealpathAndStat:
def __init__(self):
self._cache = {}
def __call__(self, path):
result = self._cache.get(path)
if result is None:
realpath = os.path.realpath(path)
if sys.platform == 'win32':
stat_key = realpath
else:
stat = os.stat(realpath)
stat_key = (stat.st_ino, stat.st_dev)
result = realpath, stat_key
self._cache[path] = result
return result
get_realpath_and_stat = GetRealpathAndStat()
def dict_delall(d, keys):
'delete all of the *keys* from the :class:`dict` *d*'
for key in keys:
try: del d[key]
except KeyError: pass
class RingBuffer:
""" class that implements a not-yet-full buffer """
def __init__(self,size_max):
self.max = size_max
self.data = []
class __Full:
""" class that implements a full buffer """
def append(self, x):
""" Append an element overwriting the oldest one. """
self.data[self.cur] = x
self.cur = (self.cur+1) % self.max
def get(self):
""" return list of elements in correct order """
return self.data[self.cur:]+self.data[:self.cur]
def append(self,x):
"""append an element at the end of the buffer"""
self.data.append(x)
if len(self.data) == self.max:
self.cur = 0
# Permanently change self's class from non-full to full
self.__class__ = __Full
def get(self):
""" Return a list of elements from the oldest to the newest. """
return self.data
def __get_item__(self, i):
return self.data[i % len(self.data)]
def get_split_ind(seq, N):
"""
*seq* is a list of words. Return the index into seq such that::
len(' '.join(seq[:ind])<=N
"""
sLen = 0
# todo: use Alex's xrange pattern from the cbook for efficiency
for (word, ind) in zip(seq, range(len(seq))):
sLen += len(word) + 1 # +1 to account for the len(' ')
if sLen>=N: return ind
return len(seq)
def wrap(prefix, text, cols):
'wrap *text* with *prefix* at length *cols*'
pad = ' '*len(prefix.expandtabs())
available = cols - len(pad)
seq = text.split(' ')
Nseq = len(seq)
ind = 0
lines = []
while ind<Nseq:
lastInd = ind
ind += get_split_ind(seq[ind:], available)
lines.append(seq[lastInd:ind])
# add the prefix to the first line, pad with spaces otherwise
ret = prefix + ' '.join(lines[0]) + '\n'
for line in lines[1:]:
ret += pad + ' '.join(line) + '\n'
return ret
# A regular expression used to determine the amount of space to
# remove. It looks for the first sequence of spaces immediately
# following the first newline, or at the beginning of the string.
_find_dedent_regex = re.compile("(?:(?:\n\r?)|^)( *)\S")
# A cache to hold the regexs that actually remove the indent.
_dedent_regex = {}
def dedent(s):
"""
Remove excess indentation from docstring *s*.
Discards any leading blank lines, then removes up to n whitespace
characters from each line, where n is the number of leading
whitespace characters in the first line. It differs from
textwrap.dedent in its deletion of leading blank lines and its use
of the first non-blank line to determine the indentation.
It is also faster in most cases.
"""
# This implementation has a somewhat obtuse use of regular
# expressions. However, this function accounted for almost 30% of
# matplotlib startup time, so it is worthy of optimization at all
# costs.
if not s: # includes case of s is None
return ''
match = _find_dedent_regex.match(s)
if match is None:
return s
# This is the number of spaces to remove from the left-hand side.
nshift = match.end(1) - match.start(1)
if nshift == 0:
return s
# Get a regex that will remove *up to* nshift spaces from the
# beginning of each line. If it isn't in the cache, generate it.
unindent = _dedent_regex.get(nshift, None)
if unindent is None:
unindent = re.compile("\n\r? {0,%d}" % nshift)
_dedent_regex[nshift] = unindent
result = unindent.sub("\n", s).strip()
return result
def listFiles(root, patterns='*', recurse=1, return_folders=0):
"""
Recursively list files
from Parmar and Martelli in the Python Cookbook
"""
import os.path, fnmatch
# Expand patterns from semicolon-separated string to list
pattern_list = patterns.split(';')
# Collect input and output arguments into one bunch
class Bunch:
def __init__(self, **kwds): self.__dict__.update(kwds)
arg = Bunch(recurse=recurse, pattern_list=pattern_list,
return_folders=return_folders, results=[])
def visit(arg, dirname, files):
# Append to arg.results all relevant files (and perhaps folders)
for name in files:
fullname = os.path.normpath(os.path.join(dirname, name))
if arg.return_folders or os.path.isfile(fullname):
for pattern in arg.pattern_list:
if fnmatch.fnmatch(name, pattern):
arg.results.append(fullname)
break
# Block recursion if recursion was disallowed
if not arg.recurse: files[:]=[]
os.path.walk(root, visit, arg)
return arg.results
def get_recursive_filelist(args):
"""
Recurse all the files and dirs in *args* ignoring symbolic links
and return the files as a list of strings
"""
files = []
for arg in args:
if os.path.isfile(arg):
files.append(arg)
continue
if os.path.isdir(arg):
newfiles = listFiles(arg, recurse=1, return_folders=1)
files.extend(newfiles)
return [f for f in files if not os.path.islink(f)]
def pieces(seq, num=2):
"Break up the *seq* into *num* tuples"
start = 0
while 1:
item = seq[start:start+num]
if not len(item): break
yield item
start += num
def exception_to_str(s = None):
sh = StringIO.StringIO()
if s is not None: print >>sh, s
traceback.print_exc(file=sh)
return sh.getvalue()
def allequal(seq):
"""
Return *True* if all elements of *seq* compare equal. If *seq* is
0 or 1 length, return *True*
"""
if len(seq)<2: return True
val = seq[0]
for i in xrange(1, len(seq)):
thisval = seq[i]
if thisval != val: return False
return True
def alltrue(seq):
"""
Return *True* if all elements of *seq* evaluate to *True*. If
*seq* is empty, return *False*.
"""
if not len(seq): return False
for val in seq:
if not val: return False
return True
def onetrue(seq):
"""
Return *True* if one element of *seq* is *True*. It *seq* is
empty, return *False*.
"""
if not len(seq): return False
for val in seq:
if val: return True
return False
def allpairs(x):
"""
return all possible pairs in sequence *x*
Condensed by Alex Martelli from this thread_ on c.l.python
.. _thread: http://groups.google.com/groups?q=all+pairs+group:*python*&hl=en&lr=&ie=UTF-8&selm=mailman.4028.1096403649.5135.python-list%40python.org&rnum=1
"""
return [ (s, f) for i, f in enumerate(x) for s in x[i+1:] ]
class maxdict(dict):
"""
A dictionary with a maximum size; this doesn't override all the
relevant methods to contrain size, just setitem, so use with
caution
"""
def __init__(self, maxsize):
dict.__init__(self)
self.maxsize = maxsize
self._killkeys = []
def __setitem__(self, k, v):
if k not in self:
if len(self)>=self.maxsize:
del self[self._killkeys[0]]
del self._killkeys[0]
self._killkeys.append(k)
dict.__setitem__(self, k, v)
class Stack(object):
"""
Implement a stack where elements can be pushed on and you can move
back and forth. But no pop. Should mimic home / back / forward
in a browser
"""
def __init__(self, default=None):
self.clear()
self._default = default
def __call__(self):
'return the current element, or None'
if not len(self._elements): return self._default
else: return self._elements[self._pos]
def __len__(self):
return self._elements.__len__()
def __getitem__(self, ind):
return self._elements.__getitem__(ind)
def forward(self):
'move the position forward and return the current element'
N = len(self._elements)
if self._pos<N-1: self._pos += 1
return self()
def back(self):
'move the position back and return the current element'
if self._pos>0: self._pos -= 1
return self()
def push(self, o):
"""
push object onto stack at current position - all elements
occurring later than the current position are discarded
"""
self._elements = self._elements[:self._pos+1]
self._elements.append(o)
self._pos = len(self._elements)-1
return self()
def home(self):
'push the first element onto the top of the stack'
if not len(self._elements): return
self.push(self._elements[0])
return self()
def empty(self):
return len(self._elements)==0
def clear(self):
'empty the stack'
self._pos = -1
self._elements = []
def bubble(self, o):
"""
raise *o* to the top of the stack and return *o*. *o* must be
in the stack
"""
if o not in self._elements:
raise ValueError('Unknown element o')
old = self._elements[:]
self.clear()
bubbles = []
for thiso in old:
if thiso==o: bubbles.append(thiso)
else: self.push(thiso)
for thiso in bubbles:
self.push(o)
return o
def remove(self, o):
'remove element *o* from the stack'
if o not in self._elements:
raise ValueError('Unknown element o')
old = self._elements[:]
self.clear()
for thiso in old:
if thiso==o: continue
else: self.push(thiso)
def popall(seq):
'empty a list'
for i in xrange(len(seq)): seq.pop()
def finddir(o, match, case=False):
"""
return all attributes of *o* which match string in match. if case
is True require an exact case match.
"""
if case:
names = [(name,name) for name in dir(o) if is_string_like(name)]
else:
names = [(name.lower(), name) for name in dir(o) if is_string_like(name)]
match = match.lower()
return [orig for name, orig in names if name.find(match)>=0]
def reverse_dict(d):
'reverse the dictionary -- may lose data if values are not unique!'
return dict([(v,k) for k,v in d.items()])
def report_memory(i=0): # argument may go away
'return the memory consumed by process'
from subprocess import Popen, PIPE
pid = os.getpid()
if sys.platform=='sunos5':
a2 = Popen('ps -p %d -o osz' % pid, shell=True,
stdout=PIPE).stdout.readlines()
mem = int(a2[-1].strip())
elif sys.platform.startswith('linux'):
a2 = Popen('ps -p %d -o rss,sz' % pid, shell=True,
stdout=PIPE).stdout.readlines()
mem = int(a2[1].split()[1])
elif sys.platform.startswith('darwin'):
a2 = Popen('ps -p %d -o rss,vsz' % pid, shell=True,
stdout=PIPE).stdout.readlines()
mem = int(a2[1].split()[0])
return mem
_safezip_msg = 'In safezip, len(args[0])=%d but len(args[%d])=%d'
def safezip(*args):
'make sure *args* are equal len before zipping'
Nx = len(args[0])
for i, arg in enumerate(args[1:]):
if len(arg) != Nx:
raise ValueError(_safezip_msg % (Nx, i+1, len(arg)))
return zip(*args)
def issubclass_safe(x, klass):
'return issubclass(x, klass) and return False on a TypeError'
try:
return issubclass(x, klass)
except TypeError:
return False
def safe_masked_invalid(x):
x = np.asanyarray(x)
try:
xm = np.ma.masked_invalid(x, copy=False)
xm.shrink_mask()
except TypeError:
return x
return xm
class MemoryMonitor:
def __init__(self, nmax=20000):
self._nmax = nmax
self._mem = np.zeros((self._nmax,), np.int32)
self.clear()
def clear(self):
self._n = 0
self._overflow = False
def __call__(self):
mem = report_memory()
if self._n < self._nmax:
self._mem[self._n] = mem
self._n += 1
else:
self._overflow = True
return mem
def report(self, segments=4):
n = self._n
segments = min(n, segments)
dn = int(n/segments)
ii = range(0, n, dn)
ii[-1] = n-1
print
print 'memory report: i, mem, dmem, dmem/nloops'
print 0, self._mem[0]
for i in range(1, len(ii)):
di = ii[i] - ii[i-1]
if di == 0:
continue
dm = self._mem[ii[i]] - self._mem[ii[i-1]]
print '%5d %5d %3d %8.3f' % (ii[i], self._mem[ii[i]],
dm, dm / float(di))
if self._overflow:
print "Warning: array size was too small for the number of calls."
def xy(self, i0=0, isub=1):
x = np.arange(i0, self._n, isub)
return x, self._mem[i0:self._n:isub]
def plot(self, i0=0, isub=1, fig=None):
if fig is None:
from pylab import figure, show
fig = figure()
ax = fig.add_subplot(111)
ax.plot(*self.xy(i0, isub))
fig.canvas.draw()
def print_cycles(objects, outstream=sys.stdout, show_progress=False):
"""
*objects*
A list of objects to find cycles in. It is often useful to
pass in gc.garbage to find the cycles that are preventing some
objects from being garbage collected.
*outstream*
The stream for output.
*show_progress*
If True, print the number of objects reached as they are found.
"""
import gc
from types import FrameType
def print_path(path):
for i, step in enumerate(path):
# next "wraps around"
next = path[(i + 1) % len(path)]
outstream.write(" %s -- " % str(type(step)))
if isinstance(step, dict):
for key, val in step.items():
if val is next:
outstream.write("[%s]" % repr(key))
break
if key is next:
outstream.write("[key] = %s" % repr(val))
break
elif isinstance(step, list):
outstream.write("[%d]" % step.index(next))
elif isinstance(step, tuple):
outstream.write("( tuple )")
else:
outstream.write(repr(step))
outstream.write(" ->\n")
outstream.write("\n")
def recurse(obj, start, all, current_path):
if show_progress:
outstream.write("%d\r" % len(all))
all[id(obj)] = None
referents = gc.get_referents(obj)
for referent in referents:
# If we've found our way back to the start, this is
# a cycle, so print it out
if referent is start:
print_path(current_path)
# Don't go back through the original list of objects, or
# through temporary references to the object, since those
# are just an artifact of the cycle detector itself.
elif referent is objects or isinstance(referent, FrameType):
continue
# We haven't seen this object before, so recurse
elif id(referent) not in all:
recurse(referent, start, all, current_path + [obj])
for obj in objects:
outstream.write("Examining: %r\n" % (obj,))
recurse(obj, obj, { }, [])
class Grouper(object):
"""
This class provides a lightweight way to group arbitrary objects
together into disjoint sets when a full-blown graph data structure
would be overkill.
Objects can be joined using :meth:`join`, tested for connectedness
using :meth:`joined`, and all disjoint sets can be retreived by
using the object as an iterator.
The objects being joined must be hashable and weak-referenceable.
For example:
>>> class Foo:
... def __init__(self, s):
... self.s = s
... def __repr__(self):
... return self.s
...
>>> a, b, c, d, e, f = [Foo(x) for x in 'abcdef']
>>> g = Grouper()
>>> g.join(a, b)
>>> g.join(b, c)
>>> g.join(d, e)
>>> list(g)
[[d, e], [a, b, c]]
>>> g.joined(a, b)
True
>>> g.joined(a, c)
True
>>> g.joined(a, d)
False
"""
def __init__(self, init=[]):
mapping = self._mapping = {}
for x in init:
mapping[ref(x)] = [ref(x)]
def __contains__(self, item):
return ref(item) in self._mapping
def clean(self):
"""
Clean dead weak references from the dictionary
"""
mapping = self._mapping
for key, val in mapping.items():
if key() is None:
del mapping[key]
val.remove(key)
def join(self, a, *args):
"""
Join given arguments into the same set. Accepts one or more
arguments.
"""
mapping = self._mapping
set_a = mapping.setdefault(ref(a), [ref(a)])
for arg in args:
set_b = mapping.get(ref(arg))
if set_b is None:
set_a.append(ref(arg))
mapping[ref(arg)] = set_a
elif set_b is not set_a:
if len(set_b) > len(set_a):
set_a, set_b = set_b, set_a
set_a.extend(set_b)
for elem in set_b:
mapping[elem] = set_a
self.clean()
def joined(self, a, b):
"""
Returns True if *a* and *b* are members of the same set.
"""
self.clean()
mapping = self._mapping
try:
return mapping[ref(a)] is mapping[ref(b)]
except KeyError:
return False
def __iter__(self):
"""
Iterate over each of the disjoint sets as a list.
The iterator is invalid if interleaved with calls to join().
"""
self.clean()
class Token: pass
token = Token()
# Mark each group as we come across if by appending a token,
# and don't yield it twice
for group in self._mapping.itervalues():
if not group[-1] is token:
yield [x() for x in group]
group.append(token)
# Cleanup the tokens
for group in self._mapping.itervalues():
if group[-1] is token:
del group[-1]
def get_siblings(self, a):
"""
Returns all of the items joined with *a*, including itself.
"""
self.clean()
siblings = self._mapping.get(ref(a), [ref(a)])
return [x() for x in siblings]
def simple_linear_interpolation(a, steps):
if steps == 1:
return a
steps = np.floor(steps)
new_length = ((len(a) - 1) * steps) + 1
new_shape = list(a.shape)
new_shape[0] = new_length
result = np.zeros(new_shape, a.dtype)
result[0] = a[0]
a0 = a[0:-1]
a1 = a[1: ]
delta = ((a1 - a0) / steps)
for i in range(1, int(steps)):
result[i::steps] = delta * i + a0
result[steps::steps] = a1
return result
def recursive_remove(path):
if os.path.isdir(path):
for fname in glob.glob(os.path.join(path, '*')) + glob.glob(os.path.join(path, '.*')):
if os.path.isdir(fname):
recursive_remove(fname)
os.removedirs(fname)
else:
os.remove(fname)
#os.removedirs(path)
else:
os.remove(path)
def delete_masked_points(*args):
"""
Find all masked and/or non-finite points in a set of arguments,
and return the arguments with only the unmasked points remaining.
Arguments can be in any of 5 categories:
1) 1-D masked arrays
2) 1-D ndarrays
3) ndarrays with more than one dimension
4) other non-string iterables
5) anything else
The first argument must be in one of the first four categories;
any argument with a length differing from that of the first
argument (and hence anything in category 5) then will be
passed through unchanged.
Masks are obtained from all arguments of the correct length
in categories 1, 2, and 4; a point is bad if masked in a masked
array or if it is a nan or inf. No attempt is made to
extract a mask from categories 2, 3, and 4 if :meth:`np.isfinite`
does not yield a Boolean array.
All input arguments that are not passed unchanged are returned
as ndarrays after removing the points or rows corresponding to
masks in any of the arguments.
A vastly simpler version of this function was originally
written as a helper for Axes.scatter().
"""
if not len(args):
return ()
if (is_string_like(args[0]) or not iterable(args[0])):
raise ValueError("First argument must be a sequence")
nrecs = len(args[0])
margs = []
seqlist = [False] * len(args)
for i, x in enumerate(args):
if (not is_string_like(x)) and iterable(x) and len(x) == nrecs:
seqlist[i] = True
if ma.isMA(x):
if x.ndim > 1:
raise ValueError("Masked arrays must be 1-D")
else:
x = np.asarray(x)
margs.append(x)
masks = [] # list of masks that are True where good
for i, x in enumerate(margs):
if seqlist[i]:
if x.ndim > 1:
continue # Don't try to get nan locations unless 1-D.
if ma.isMA(x):
masks.append(~ma.getmaskarray(x)) # invert the mask
xd = x.data
else:
xd = x
try:
mask = np.isfinite(xd)
if isinstance(mask, np.ndarray):
masks.append(mask)
except: #Fixme: put in tuple of possible exceptions?
pass
if len(masks):
mask = reduce(np.logical_and, masks)
igood = mask.nonzero()[0]
if len(igood) < nrecs:
for i, x in enumerate(margs):
if seqlist[i]:
margs[i] = x.take(igood, axis=0)
for i, x in enumerate(margs):
if seqlist[i] and ma.isMA(x):
margs[i] = x.filled()
return margs
def unmasked_index_ranges(mask, compressed = True):
'''
Find index ranges where *mask* is *False*.
*mask* will be flattened if it is not already 1-D.
Returns Nx2 :class:`numpy.ndarray` with each row the start and stop
indices for slices of the compressed :class:`numpy.ndarray`
corresponding to each of *N* uninterrupted runs of unmasked
values. If optional argument *compressed* is *False*, it returns
the start and stop indices into the original :class:`numpy.ndarray`,
not the compressed :class:`numpy.ndarray`. Returns *None* if there
are no unmasked values.
Example::
y = ma.array(np.arange(5), mask = [0,0,1,0,0])
ii = unmasked_index_ranges(ma.getmaskarray(y))
# returns array [[0,2,] [2,4,]]
y.compressed()[ii[1,0]:ii[1,1]]
# returns array [3,4,]
ii = unmasked_index_ranges(ma.getmaskarray(y), compressed=False)
# returns array [[0, 2], [3, 5]]
y.filled()[ii[1,0]:ii[1,1]]
# returns array [3,4,]
Prior to the transforms refactoring, this was used to support
masked arrays in Line2D.
'''
mask = mask.reshape(mask.size)
m = np.concatenate(((1,), mask, (1,)))
indices = np.arange(len(mask) + 1)
mdif = m[1:] - m[:-1]
i0 = np.compress(mdif == -1, indices)
i1 = np.compress(mdif == 1, indices)
assert len(i0) == len(i1)
if len(i1) == 0:
return None # Maybe this should be np.zeros((0,2), dtype=int)
if not compressed:
return np.concatenate((i0[:, np.newaxis], i1[:, np.newaxis]), axis=1)
seglengths = i1 - i0
breakpoints = np.cumsum(seglengths)
ic0 = np.concatenate(((0,), breakpoints[:-1]))
ic1 = breakpoints
return np.concatenate((ic0[:, np.newaxis], ic1[:, np.newaxis]), axis=1)
# a dict to cross-map linestyle arguments
_linestyles = [('-', 'solid'),
('--', 'dashed'),
('-.', 'dashdot'),
(':', 'dotted')]
ls_mapper = dict(_linestyles)
ls_mapper.update([(ls[1], ls[0]) for ls in _linestyles])
def less_simple_linear_interpolation( x, y, xi, extrap=False ):
"""
This function has been moved to matplotlib.mlab -- please import
it from there
"""
# deprecated from cbook in 0.98.4
warnings.warn('less_simple_linear_interpolation has been moved to matplotlib.mlab -- please import it from there', DeprecationWarning)
import matplotlib.mlab as mlab
return mlab.less_simple_linear_interpolation( x, y, xi, extrap=extrap )
def isvector(X):
"""
This function has been moved to matplotlib.mlab -- please import
it from there
"""
# deprecated from cbook in 0.98.4
warnings.warn('isvector has been moved to matplotlib.mlab -- please import it from there', DeprecationWarning)
import matplotlib.mlab as mlab
return mlab.isvector( x, y, xi, extrap=extrap )
def vector_lengths( X, P=2., axis=None ):
"""
This function has been moved to matplotlib.mlab -- please import
it from there
"""
# deprecated from cbook in 0.98.4
warnings.warn('vector_lengths has been moved to matplotlib.mlab -- please import it from there', DeprecationWarning)
import matplotlib.mlab as mlab
return mlab.vector_lengths( X, P=2., axis=axis )
def distances_along_curve( X ):
"""
This function has been moved to matplotlib.mlab -- please import
it from there
"""
# deprecated from cbook in 0.98.4
warnings.warn('distances_along_curve has been moved to matplotlib.mlab -- please import it from there', DeprecationWarning)
import matplotlib.mlab as mlab
return mlab.distances_along_curve( X )
def path_length(X):
"""
This function has been moved to matplotlib.mlab -- please import
it from there
"""
# deprecated from cbook in 0.98.4
warnings.warn('path_length has been moved to matplotlib.mlab -- please import it from there', DeprecationWarning)
import matplotlib.mlab as mlab
return mlab.path_length(X)
def is_closed_polygon(X):
"""
This function has been moved to matplotlib.mlab -- please import
it from there
"""
# deprecated from cbook in 0.98.4
warnings.warn('is_closed_polygon has been moved to matplotlib.mlab -- please import it from there', DeprecationWarning)
import matplotlib.mlab as mlab
return mlab.is_closed_polygon(X)
def quad2cubic(q0x, q0y, q1x, q1y, q2x, q2y):
"""
This function has been moved to matplotlib.mlab -- please import
it from there
"""
# deprecated from cbook in 0.98.4
warnings.warn('quad2cubic has been moved to matplotlib.mlab -- please import it from there', DeprecationWarning)
import matplotlib.mlab as mlab
return mlab.quad2cubic(q0x, q0y, q1x, q1y, q2x, q2y)
def align_iterators(func, *iterables):
"""
This generator takes a bunch of iterables that are ordered by func
It sends out ordered tuples:
(func(row), [rows from all iterators matching func(row)])
It is used by :func:`matplotlib.mlab.recs_join` to join record arrays
"""
class myiter:
def __init__(self, it):
self.it = it
self.key = self.value = None
self.iternext()
def iternext(self):
try:
self.value = self.it.next()
self.key = func(self.value)
except StopIteration:
self.value = self.key = None
def __call__(self, key):
retval = None
if key == self.key:
retval = self.value
self.iternext()
elif self.key and key > self.key:
raise ValueError, "Iterator has been left behind"
return retval
# This can be made more efficient by not computing the minimum key for each iteration
iters = [myiter(it) for it in iterables]
minvals = minkey = True
while 1:
minvals = (filter(None, [it.key for it in iters]))
if minvals:
minkey = min(minvals)
yield (minkey, [it(minkey) for it in iters])
else:
break
def is_math_text(s):
# Did we find an even number of non-escaped dollar signs?
# If so, treat is as math text.
s = unicode(s)
dollar_count = s.count(r'$') - s.count(r'\$')
even_dollars = (dollar_count > 0 and dollar_count % 2 == 0)
return even_dollars
if __name__=='__main__':
assert( allequal([1,1,1]) )
assert(not allequal([1,1,0]) )
assert( allequal([]) )
assert( allequal(('a', 'a')))
assert( not allequal(('a', 'b')))