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def compute_cusum_ts(self, ts):
""" Compute the Cumulative Sum at each point 't' of the time series. """ |
mean = np.mean(ts)
cusums = np.zeros(len(ts))
cusum[0] = (ts[0] - mean)
for i in np.arange(1, len(ts)):
cusums[i] = cusums[i - 1] + (ts[i] - mean)
assert(np.isclose(cumsum[-1], 0.0))
return cusums |
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def detect_mean_shift(self, ts, B=1000):
""" Detect mean shift in a time series. B is number of bootstrapped samples to draw. """ |
x = np.arange(0, len(ts))
stat_ts_func = self.compute_balance_mean_ts
null_ts_func = self.shuffle_timeseries
stats_ts, pvals, nums = self.get_ts_stats_significance(x, ts, stat_ts_func, null_ts_func, B=B, permute_fast=True)
return stats_ts, pvals, nums |
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def parallelize_func(iterable, func, chunksz=1, n_jobs=16, *args, **kwargs):
""" Parallelize a function over each element of an iterable. """ |
chunker = func
chunks = more_itertools.chunked(iterable, chunksz)
chunks_results = Parallel(n_jobs=n_jobs, verbose=50)(
delayed(chunker)(chunk, *args, **kwargs) for chunk in chunks)
results = more_itertools.flatten(chunks_results)
return list(results) |
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def ts_stats_significance(ts, ts_stat_func, null_ts_func, B=1000, permute_fast=False):
""" Compute the statistical significance of a test statistic at each point... |
stats_ts = ts_stat_func(ts)
if permute_fast:
# Permute it in 1 shot
null_ts = map(np.random.permutation, np.array([ts, ] * B))
else:
null_ts = np.vstack([null_ts_func(ts) for i in np.arange(0, B)])
stats_null_ts = np.vstack([ts_stat_func(nts) for nts in null_ts])
pvals = []
... |
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def get_ci(theta_star, blockratio=1.0):
""" Get the confidence interval. """ |
# get rid of nans while we sort
b_star = np.sort(theta_star[~np.isnan(theta_star)])
se = np.std(b_star) * np.sqrt(blockratio)
# bootstrap 95% CI based on empirical percentiles
ci = [b_star[int(len(b_star) * .025)], b_star[int(len(b_star) * .975)]]
return ci |
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def get_pvalue(value, ci):
""" Get the p-value from the confidence interval.""" |
from scipy.stats import norm
se = (ci[1] - ci[0]) / (2.0 * 1.96)
z = value / se
pvalue = -2 * norm.cdf(-np.abs(z))
return pvalue |
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def ts_stats_significance_bootstrap(ts, stats_ts, stats_func, B=1000, b=3):
""" Compute the statistical significance of a test statistic at each point of the tim... |
pvals = []
for tp in np.arange(0, len(stats_ts)):
pf = partial(stats_func, t=tp)
bs = bootstrap_ts(ts, pf, B=B, b=b)
ci = get_ci(bs, blockratio=b / len(stats_ts))
pval = abs(get_pvalue(stats_ts[tp], ci))
pvals.append(pval)
return pvals |
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def format_traceback(extracted_tb, exc_type, exc_value, cwd='', term=None, function_color=12, dim_color=8, editor='vi', template=DEFAULT_EDITOR_SHORTCUT_TEMPLATE)... |
def format_shortcut(editor,
path,
line_number,
function=None):
"""Return a pretty-printed editor shortcut."""
return template.format(editor=editor,
line_number=line_number or 0,
... |
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def extract_relevant_tb(tb, exctype, is_test_failure):
"""Return extracted traceback frame 4-tuples that aren't unittest ones. This used to be _exc_info_to_strin... |
# Skip test runner traceback levels:
while tb and _is_unittest_frame(tb):
tb = tb.tb_next
if is_test_failure:
# Skip assert*() traceback levels:
length = _count_relevant_tb_levels(tb)
return extract_tb(tb, length)
return extract_tb(tb) |
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def _unicode_decode_extracted_tb(extracted_tb):
"""Return a traceback with the string elements translated into Unicode.""" |
return [(_decode(file), line_number, _decode(function), _decode(text))
for file, line_number, function, text in extracted_tb] |
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def _count_relevant_tb_levels(tb):
"""Return the number of frames in ``tb`` before all that's left is unittest frames. Unlike its namesake in unittest, this does... |
length = contiguous_unittest_frames = 0
while tb:
length += 1
if _is_unittest_frame(tb):
contiguous_unittest_frames += 1
else:
contiguous_unittest_frames = 0
tb = tb.tb_next
return length - contiguous_unittest_frames |
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def cmdloop(self, *args, **kwargs):
"""Call pdb's cmdloop, making readline work. Patch raw_input so it sees the original stdin and stdout, lest readline refuse t... |
def unwrapping_raw_input(*args, **kwargs):
"""Call raw_input(), making sure it finds an unwrapped stdout."""
wrapped_stdout = sys.stdout
sys.stdout = wrapped_stdout.stream
ret = orig_raw_input(*args, **kwargs)
sys.stdout = wrapped_stdout
return ret
try:
... |
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def set_trace(*args, **kwargs):
"""Call pdb.set_trace, making sure it receives the unwrapped stdout. This is so we don't keep drawing progress bars over debugger... |
# There's no stream attr if capture plugin is enabled:
out = sys.stdout.stream if hasattr(sys.stdout, 'stream') else None
# Python 2.5 can't put an explicit kwarg and **kwargs in the same function
# call.
kwargs['stdout'] = out
debugger = pdb.Pdb(*args, **kwargs)
# Ordinarily (and in a si... |
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def begin(self):
"""Make some monkeypatches to dodge progress bar. Wrap stderr and stdout to keep other users of them from smearing the progress bar. Wrap some p... |
# The calls to begin/finalize end up like this: a call to begin() on
# instance A of the plugin, then a paired begin/finalize for each test
# on instance B, then a final call to finalize() on instance A.
# TODO: Do only if isatty.
self._stderr.append(sys.stderr)
sys.std... |
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def finalize(self, result):
"""Put monkeypatches back as we found them.""" |
sys.stderr = self._stderr.pop()
sys.stdout = self._stdout.pop()
pdb.set_trace = self._set_trace.pop()
pdb.Pdb.cmdloop = self._cmdloop.pop() |
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def configure(self, options, conf):
"""Turn style-forcing on if bar-forcing is on. It'd be messy to position the bar but still have the rest of the terminal capa... |
super(ProgressivePlugin, self).configure(options, conf)
if (getattr(options, 'verbosity', 0) > 1 and
getattr(options, 'enable_plugin_id', False)):
# TODO: Can we forcibly disable the ID plugin?
print ('Using --with-id and --verbosity=2 or higher with '
... |
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def update(self, test_path, number):
"""Draw an updated progress bar. At the moment, the graph takes a fixed width, and the test identifier takes the rest of the... |
# TODO: Play nicely with absurdly narrow terminals. (OS X's won't even
# go small enough to hurt us.)
# Figure out graph:
GRAPH_WIDTH = 14
# min() is in case we somehow get the total test count wrong. It's tricky.
num_filled = int(round(min(1.0, float(number) / self.max... |
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def erase(self):
"""White out the progress bar.""" |
with self._at_last_line():
self.stream.write(self._term.clear_eol)
self.stream.flush() |
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def dodging(bar):
"""Return a context manager which erases the bar, lets you output things, and then redraws the bar. It's reentrant. """ |
class ShyProgressBar(object):
"""Context manager that implements a progress bar that gets out of the way"""
def __enter__(self):
"""Erase the progress bar so bits of disembodied progress bar don't get scrolled up the terminal."""
# My terminal has no sta... |
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def _makeResult(self):
"""Return a Result that doesn't print dots. Nose's ResultProxy will wrap it, and other plugins can still print stuff---but without smashin... |
return ProgressiveResult(self._cwd,
self._totalTests,
self.stream,
config=self.config) |
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| def run(self, test):
"Run the given test case or test suite...quietly."
# These parts of Nose's pluggability are baked into
# nose.core.TextTestRunner. Reproduce them:
wrapper = self.config.plugins.prepareTest(test)
if wrapper is not None:
test = wrapper
wrapp... |
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def _printTraceback(self, test, err):
"""Print a nicely formatted traceback. :arg err: exc_info()-style traceback triple :arg test: the test that precipitated th... |
# Don't bind third item to a local var; that can create
# circular refs which are expensive to collect. See the
# sys.exc_info() docs.
exception_type, exception_value = err[:2]
# TODO: In Python 3, the traceback is attached to the exception
# instance through the __trace... |
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def _printHeadline(self, kind, test, is_failure=True):
"""Output a 1-line error summary to the stream if appropriate. The line contains the kind of error and the... |
if is_failure or self._options.show_advisories:
with self.bar.dodging():
self.stream.writeln(
'\n' +
(self._term.bold if is_failure else '') +
'%s: %s' % (kind, nose_selector(test)) +
(se... |
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def _recordAndPrintHeadline(self, test, error_class, artifact):
"""Record that an error-like thing occurred, and print a summary. Store ``artifact`` with the rec... |
# We duplicate the errorclass handling from super rather than calling
# it and monkeying around with showAll flags to keep it from printing
# anything.
is_error_class = False
for cls, (storage, label, is_failure) in self.errorClasses.items():
if isclass(error_class) ... |
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def addSkip(self, test, reason):
"""Catch skipped tests in Python 2.7 and above. Though ``addSkip()`` is deprecated in the nose plugin API, it is very much not d... |
self._recordAndPrintHeadline(test, SkipTest, reason)
# Python 2.7 users get a little bonus: the reason the test was skipped.
if isinstance(reason, Exception):
reason = getattr(reason, 'message', None) or getattr(
reason, 'args')[0]
if reason and self._options... |
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def printSummary(self, start, stop):
"""As a final summary, print number of tests, broken down by result.""" |
def renderResultType(type, number, is_failure):
"""Return a rendering like '2 failures'.
:arg type: A singular label, like "failure"
:arg number: The number of tests with a result of that type
:arg is_failure: Whether that type counts as a failure
"... |
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def nose_selector(test):
"""Return the string you can pass to nose to run `test`, including argument values if the test was made by a test generator. Return "Unk... |
address = test_address(test)
if address:
file, module, rest = address
if module:
if rest:
try:
return '%s:%s%s' % (module, rest, test.test.arg or '')
except AttributeError:
return '%s:%s' % (module, rest)
... |
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def human_path(path, cwd):
"""Return the most human-readable representation of the given path. If an absolute path is given that's within the current directory, ... |
# TODO: Canonicalize the path to remove /kitsune/../kitsune nonsense.
path = abspath(path)
if cwd and path.startswith(cwd):
path = path[len(cwd) + 1:] # Make path relative. Remove leading slash.
return path |
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def know(self, what, confidence):
"""Know something with the given confidence, and return self for chaining. If confidence is higher than that of what we already... |
if confidence > self.confidence:
self.best = what
self.confidence = confidence
return self |
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def _generate_arg_types(coordlist_length, shape_name):
"""Find coordinate types based on shape name and coordlist length This function returns a list of coordina... |
from .ds9_region_parser import ds9_shape_defs
from .ds9_attr_parser import ds9_shape_in_comment_defs
if shape_name in ds9_shape_defs:
shape_def = ds9_shape_defs[shape_name]
else:
shape_def = ds9_shape_in_comment_defs[shape_name]
initial_arg_types = shape_def.args_list
arg_repe... |
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def convert_to_imagecoord(shape, header):
"""Convert the coordlist of `shape` to image coordinates Parameters shape : `pyregion.parser_helper.Shape` The `Shape` ... |
arg_types = _generate_arg_types(len(shape.coord_list), shape.name)
new_coordlist = []
is_even_distance = True
coord_list_iter = iter(zip(shape.coord_list, arg_types))
new_wcs = WCS(header)
pixel_scales = proj_plane_pixel_scales(new_wcs)
for coordinate, coordinate_type in coord_list_iter:... |
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def get_auth_info():
""" Get authentication details to jottacloud. Will first check environment variables, then the .netrc file. """ |
env_username = os.environ.get('JOTTACLOUD_USERNAME')
env_password = os.environ.get('JOTTACLOUD_PASSWORD')
netrc_auth = None
try:
netrc_file = netrc.netrc()
netrc_auth = netrc_file.authenticators('jottacloud.com')
except IOError:
# .netrc file doesn't exist
pass
n... |
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def calculate_md5(fileobject, size=2**16):
"""Utility function to calculate md5 hashes while being light on memory usage. By reading the fileobject piece by piec... |
fileobject.seek(0)
md5 = hashlib.md5()
for data in iter(lambda: fileobject.read(size), b''):
if not data: break
if isinstance(data, six.text_type):
data = data.encode('utf-8') # md5 needs a byte string
md5.update(data)
fileobject.seek(0) # rewind read head
return... |
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| def deleted(self):
'Return datetime.datetime or None if the file isnt deleted'
_d = self.folder.attrib.get('deleted', None)
if _d is None: return None
return dateutil.parser.parse(str(_d)) |
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| def sync(self):
'Update state of folder from Jottacloud server'
log.info("syncing %r" % self.path)
self.folder = self.jfs.get(self.path)
self.synced = True |
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| def mkdir(self, foldername):
'Create a new subfolder and return the new JFSFolder'
#url = '%s?mkDir=true' % posixpath.join(self.path, foldername)
url = posixpath.join(self.path, foldername)
params = {'mkDir':'true'}
r = self.jfs.post(url, params)
self.sync()
retur... |
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| def delete(self):
'Delete this folder and return a deleted JFSFolder'
#url = '%s?dlDir=true' % self.path
params = {'dlDir':'true'}
r = self.jfs.post(self.path, params)
self.sync()
return r |
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| def hard_delete(self):
'Deletes without possibility to restore'
url = 'https://www.jottacloud.com/rest/webrest/%s/action/delete' % self.jfs.username
data = {'paths[]': self.path.replace(JFS_ROOT, ''),
'web': 'true',
'ts': int(time.time()),
'authTok... |
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| def rename(self, newpath):
"Move folder to a new name, possibly a whole new path"
# POST https://www.jottacloud.com/jfs/**USERNAME**/Jotta/Sync/Ny%20mappe?mvDir=/**USERNAME**/Jotta/Sync/testFolder
#url = '%s?mvDir=/%s%s' % (self.path, self.jfs.username, newpath)
params = {'mvDir':'/%s%s'... |
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| def up(self, fileobj_or_path, filename=None, upload_callback=None):
'Upload a file to current folder and return the new JFSFile'
close_on_done = False
if isinstance(fileobj_or_path, six.string_types):
filename = filename or os.path.basename(fileobj_or_path)
fileobj_or_pa... |
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| def factory(fileobject, jfs, parentpath): # fileobject from lxml.objectify
'Class method to get the correct file class instatiated'
if hasattr(fileobject, 'currentRevision'): # a normal file
return JFSFile(fileobject, jfs, parentpath)
elif str(fileobject.latestRevision.state) == Prot... |
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| def resume(self, data):
'Resume uploading an incomplete file, after a previous upload was interrupted. Returns new file object'
if not hasattr(data, 'read'):
data = six.BytesIO(data)#StringIO(data)
#Check that we actually know from what byte to resume.
#If self.size === -1, ... |
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def size(self):
"""Bytes uploaded of the file so far. Note that we only have the file size if the file was requested directly, not if it's part of a folder listi... |
if hasattr(self.f.latestRevision, 'size'):
return int(self.f.latestRevision.size)
return None |
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| def stream(self, chunk_size=64*1024):
'Returns a generator to iterate over the file contents'
#return self.jfs.stream(url='%s?mode=bin' % self.path, chunk_size=chunk_size)
return self.jfs.stream(url=self.path, params={'mode':'bin'}, chunk_size=chunk_size) |
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| def restore(self):
'Restore the file'
#
#
# As of 2016-06-15, Jottacloud.com has changed their restore api
# To restore, this is what's done
#
# HTTP POST to https://www.jottacloud.com/web/restore/trash/list
# Data:
# hash:undefined
# ... |
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| def delete(self):
'Delete this file and return the new, deleted JFSFile'
#url = '%s?dl=true' % self.path
r = self.jfs.post(url=self.path, params={'dl':'true'})
return r |
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| def thumb(self, size=BIGTHUMB):
'''Get a thumbnail as string or None if the file isnt an image
size would be one of JFSFile.BIGTHUMB, .MEDIUMTHUMB, .SMALLTHUMB or .XLTHUMB'''
if not self.is_image():
return None
if not size in (self.BIGTHUMB, self.MEDIUMTHUMB, self.SMALLTHUMB... |
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def new_mountpoint(self, name):
"""Create a new mountpoint""" |
url = posixpath.join(self.path, name)
r = self._jfs.post(url, extra_headers={'content-type': 'application/x-www-form-urlencoded'})
return r |
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| def sharedFiles(self):
'iterate over shared files and get their public URI'
for f in self.sharing.files.iterchildren():
yield (f.attrib['name'], f.attrib['uuid'],
'https://www.jottacloud.com/p/%s/%s' % (self.jfs.username, f.publicURI.text)) |
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| def files(self):
'iterate over found files'
for _f in self.searchresult.files.iterchildren():
yield ProtoFile.factory(_f, jfs=self.jfs, parentpath=unicode(_f.abspath)) |
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| def request(self, url, extra_headers=None, params=None):
'Make a GET request for url, with or without caching'
if not url.startswith('http'):
# relative url
url = self.rootpath + url
log.debug("getting url: %r, extra_headers=%r, params=%r", url, extra_headers, params)
... |
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| def raw(self, url, extra_headers=None, params=None):
'Make a GET request for url and return whatever content we get'
r = self.request(url, extra_headers=extra_headers, params=params)
# uncomment to dump raw xml
# with open('/tmp/%s.xml' % time.time(), 'wb') as f:
# f.write(r.... |
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| def get(self, url, params=None):
'Make a GET request for url and return the response content as a generic lxml.objectify object'
url = self.escapeUrl(url)
content = six.BytesIO(self.raw(url, params=params))
# We need to make sure that the xml fits in available memory before we parse
... |
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| def devices(self):
'return generator of configured devices'
return self.fs is not None and [JFSDevice(d, self, parentpath=self.rootpath) for d in self.fs.devices.iterchildren()] or [x for x in []] |
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def parse(region_string):
"""Parse DS9 region string into a ShapeList. Parameters region_string : str Region string Returns ------- shapes : `ShapeList` List of ... |
rp = RegionParser()
ss = rp.parse(region_string)
sss1 = rp.convert_attr(ss)
sss2 = _check_wcs(sss1)
shape_list, comment_list = rp.filter_shape2(sss2)
return ShapeList(shape_list, comment_list=comment_list) |
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def open(fname):
"""Open, read and parse DS9 region file. Parameters fname : str Filename Returns ------- shapes : `ShapeList` List of `~pyregion.Shape` """ |
with _builtin_open(fname) as fh:
region_string = fh.read()
return parse(region_string) |
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def read_region(s):
"""Read region. Parameters s : str Region string Returns ------- shapes : `ShapeList` List of `~pyregion.Shape` """ |
rp = RegionParser()
ss = rp.parse(s)
sss1 = rp.convert_attr(ss)
sss2 = _check_wcs(sss1)
shape_list = rp.filter_shape(sss2)
return ShapeList(shape_list) |
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def read_region_as_imagecoord(s, header):
"""Read region as image coordinates. Parameters s : str Region string header : `~astropy.io.fits.Header` FITS header Re... |
rp = RegionParser()
ss = rp.parse(s)
sss1 = rp.convert_attr(ss)
sss2 = _check_wcs(sss1)
sss3 = rp.sky_to_image(sss2, header)
shape_list = rp.filter_shape(sss3)
return ShapeList(shape_list) |
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def get_mask(region, hdu, origin=1):
"""Get mask. Parameters region : `~pyregion.ShapeList` List of `~pyregion.Shape` hdu : `~astropy.io.fits.ImageHDU` FITS imag... |
from pyregion.region_to_filter import as_region_filter
data = hdu.data
region_filter = as_region_filter(region, origin=origin)
mask = region_filter.mask(data)
return mask |
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def as_imagecoord(self, header):
"""New shape list in image coordinates. Parameters header : `~astropy.io.fits.Header` FITS header Returns ------- shape_list : `... |
comment_list = self._comment_list
if comment_list is None:
comment_list = cycle([None])
r = RegionParser.sky_to_image(zip(self, comment_list),
header)
shape_list, comment_list = zip(*list(r))
return ShapeList(shape_list, commen... |
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def get_mask(self, hdu=None, header=None, shape=None):
"""Create a 2-d mask. Parameters hdu : `astropy.io.fits.ImageHDU` FITS image HDU header : `~astropy.io.fit... |
if hdu and header is None:
header = hdu.header
if hdu and shape is None:
shape = hdu.data.shape
region_filter = self.get_filter(header=header)
mask = region_filter.mask(shape)
return mask |
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def write(self, outfile):
"""Write this shape list to a region file. Parameters outfile : str File name """ |
if len(self) < 1:
print("WARNING: The region list is empty. The region file "
"'{:s}' will be empty.".format(outfile))
try:
outf = _builtin_open(outfile, 'w')
outf.close()
return
except IOError as e:
... |
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def AppConfigFlagHandler(feature=None):
""" This is the default handler. It checks for feature flags in the current app's configuration. For example, to have 'un... |
if not current_app:
log.warn(u"Got a request to check for {feature} but we're outside the request context. Returning False".format(feature=feature))
return False
try:
return current_app.config[FEATURE_FLAGS_CONFIG][feature]
except (AttributeError, KeyError):
raise NoFeatureFlagFound() |
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def is_active(feature):
""" Check if a feature is active """ |
if current_app:
feature_flagger = current_app.extensions.get(EXTENSION_NAME)
if feature_flagger:
return feature_flagger.check(feature)
else:
raise AssertionError("Oops. This application doesn't have the Flask-FeatureFlag extention installed.")
else:
log.warn(u"Got a request to check f... |
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def is_active_feature(feature, redirect_to=None, redirect=None):
""" Decorator for Flask views. If a feature is off, it can either return a 404 or redirect to a ... |
def _is_active_feature(func):
@wraps(func)
def wrapped(*args, **kwargs):
if not is_active(feature):
url = redirect_to
if redirect:
url = url_for(redirect)
if url:
log.debug(u'Feature {feature} is off, redirecting to {url}'.format(feature=feature, url=url))
... |
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def init_app(self, app):
""" Add ourselves into the app config and setup, and add a jinja function test """ |
app.config.setdefault(FEATURE_FLAGS_CONFIG, {})
app.config.setdefault(RAISE_ERROR_ON_MISSING_FEATURES, False)
if hasattr(app, "add_template_test"):
# flask 0.10 and higher has a proper hook
app.add_template_test(self.check, name=self.JINJA_TEST_NAME)
else:
app.jinja_env.tests[self.J... |
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def check(self, feature):
""" Loop through all our feature flag checkers and return true if any of them are true. The order of handlers matters - we will immedia... |
found = False
for handler in self.handlers:
try:
if handler(feature):
return True
except StopCheckingFeatureFlags:
return False
except NoFeatureFlagFound:
pass
else:
found = True
if not found:
message = u"No feature flag defined for ... |
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def yank_path(self, path):
"""Clear cache of results from a specific path""" |
for func in self._caches:
cache = {}
for key in self._caches[func].keys():
log.debug("cache key %s for func %s", key, func)
if path in key[0]:
log.debug("del cache key %s", key)
del self._caches[func][key] |
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| def release(self, path, fh):
"Run after a read or write operation has finished. This is where we upload on writes"
#print "release! inpath:", path in self.__newfiles.keys()
# if the path exists in self.__newfiles.keys(), we have a new version to upload
try:
f = self.__newfile... |
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| def truncate(self, path, length, fh=None):
"Download existing path, truncate and reupload"
try:
f = self._getpath(path)
except JFS.JFSError:
raise OSError(errno.ENOENT, '')
if isinstance(f, (JFS.JFSFile, JFS.JFSFolder)) and f.is_deleted():
raise OSErro... |
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| def commandline_text(bytestring):
'Convert bytestring from command line to unicode, using default file system encoding'
if six.PY3:
return bytestring
unicode_string = bytestring.decode(sys.getfilesystemencoding())
return unicode_string |
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def sky_to_image(shape_list, header):
"""Converts a `ShapeList` into shapes with coordinates in image coordinates Parameters shape_list : `pyregion.ShapeList` Th... |
for shape, comment in shape_list:
if isinstance(shape, Shape) and \
(shape.coord_format not in image_like_coordformats):
new_coords = convert_to_imagecoord(shape, header)
l1n = copy.copy(shape)
l1n.coord_list = new_coords
... |
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| def _new(self, src_path, dry_run=False, remove_uploaded=False):
'Code to upload'
# are we getting a symbolic link?
if os.path.islink(src_path):
sourcefile = os.path.normpath(os.path.join(self.topdir, os.readlink(src_path)))
if not os.path.exists(source... |
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def _estimate_angle(angle, reg_coordinate_frame, header):
"""Transform an angle into a different frame Parameters angle : float, int The number of degrees, measu... |
y_axis_rot = _calculate_rotation_angle(reg_coordinate_frame, header)
return angle - y_axis_rot |
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def _calculate_rotation_angle(reg_coordinate_frame, header):
"""Calculates the rotation angle from the region to the header's frame This attempts to be compatibl... |
new_wcs = WCS(header)
region_frame = SkyCoord(
'0d 0d',
frame=reg_coordinate_frame,
obstime='J2000')
region_frame = SkyCoord(
'0d 0d',
frame=reg_coordinate_frame,
obstime='J2000',
equinox=region_frame.equinox)
origin = SkyCoord.from_pixel(
... |
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def sf(f, dirpath, jottapath):
"""Create and return a SyncFile tuple from filename. localpath will be a byte string with utf8 code points jottapath will be a uni... |
log.debug('Create SyncFile from %s', repr(f))
log.debug('Got encoded filename %r, joining with dirpath %r', _encode_filename_to_filesystem(f), dirpath)
return SyncFile(localpath=os.path.join(dirpath, _encode_filename_to_filesystem(f)),
jottapath=posixpath.join(_decode_filename_to_unicode(... |
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def get_jottapath(localtopdir, dirpath, jottamountpoint):
"""Translate localtopdir to jottapath. Returns unicode string""" |
log.debug("get_jottapath %r %r %r", localtopdir, dirpath, jottamountpoint)
normpath = posixpath.normpath(posixpath.join(jottamountpoint, posixpath.basename(localtopdir),
posixpath.relpath(dirpath, localtopdir)))
return _decode_filename_to_unicode(normpath) |
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def is_file(jottapath, JFS):
"""Check if a file exists on jottacloud""" |
log.debug("is_file %r", jottapath)
try:
jf = JFS.getObject(jottapath)
except JFSNotFoundError:
return False
return isinstance(jf, JFSFile) |
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def compare(localtopdir, jottamountpoint, JFS, followlinks=False, exclude_patterns=None):
"""Make a tree of local files and folders and compare it with what's cu... |
def excluded(unicodepath, fname):
fpath = os.path.join(unicodepath, _decode_filename_to_unicode(fname))
# skip FIFOs, block devices, character devices and the like, see bug#129
mode = os.stat(fpath).st_mode
if not (stat.S_ISREG(mode) or
stat.S_ISLNK(mode) or
... |
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| def _decode_filename_to_unicode(f):
'''Get bytestring filename and return unicode.
First, try to decode from default file system encoding
If that fails, use ``chardet`` module to guess encoding.
As a last resort, try to decode as utf-8.
If the argument already is unicode, return as is'''
log.d... |
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| def _encode_filename_to_filesystem(f):
'''Get a unicode filename and return bytestring, encoded to file system default.
If the argument already is a bytestring, return as is'''
log.debug('_encode_filename_to_filesystem(%s)', repr(f))
if isinstance(f, str):
return f
try:
return f.enc... |
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def resume(localfile, jottafile, JFS):
"""Continue uploading a new file from local file (already exists on JottaCloud""" |
with open(localfile) as lf:
_complete = jottafile.resume(lf)
return _complete |
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def replace_if_changed(localfile, jottapath, JFS):
"""Compare md5 hash to determine if contents have changed. Upload a file from local disk and replace file on J... |
jf = JFS.getObject(jottapath)
lf_hash = getxattrhash(localfile) # try to read previous hash, stored in xattr
if lf_hash is None: # no valid hash found in xattr,
with open(localfile) as lf:
lf_hash = calculate_md5(lf) # (re)calculate it
if type(jf) == JFSIncompleteFile:... |
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def iter_tree(jottapath, JFS):
"""Get a tree of of files and folders. use as an iterator, you get something like os.walk""" |
filedirlist = JFS.getObject('%s?mode=list' % jottapath)
log.debug("got tree: %s", filedirlist)
if not isinstance(filedirlist, JFSFileDirList):
yield ( '', tuple(), tuple() )
for path in filedirlist.tree:
yield path |
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def _query(self, filename):
"""Get size of filename""" |
# - Query metadata of one file
# - Return a dict with a 'size' key, and a file size value (-1 for not found)
# - Retried if an exception is thrown
log.Info('Querying size of %s' % filename)
from jottalib.JFS import JFSNotFoundError, JFSIncompleteFile
remote_path = pos... |
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def parse_drawing(document, container, elem):
"""Parse drawing element. We don't do much with drawing element. We can find embeded image but we don't do more tha... |
_blip = elem.xpath('.//a:blip', namespaces=NAMESPACES)
if len(_blip) > 0:
blip = _blip[0]
_rid = blip.attrib[_name('{{{r}}}embed')]
img = doc.Image(_rid)
container.elements.append(img) |
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| def parse_footnote(document, container, elem):
"Parse the footnote element."
_rid = elem.attrib[_name('{{{w}}}id')]
foot = doc.Footnote(_rid)
container.elements.append(foot) |
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| def parse_text(document, container, element):
"Parse text element."
txt = None
alternate = element.find(_name('{{{mc}}}AlternateContent'))
if alternate is not None:
parse_alternate(document, container, alternate)
br = element.find(_name('{{{w}}}br'))
if br is not None:
if _n... |
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def parse_paragraph(document, par):
"""Parse paragraph element. Some other elements could be found inside of paragraph element (math, links). """ |
paragraph = doc.Paragraph()
paragraph.document = document
for elem in par:
if elem.tag == _name('{{{w}}}pPr'):
parse_paragraph_properties(document, paragraph, elem)
if elem.tag == _name('{{{w}}}r'):
parse_text(document, paragraph, elem)
if elem.tag == _na... |
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| def parse_table_properties(doc, table, prop):
"Parse table properties."
if not table:
return
style = prop.find(_name('{{{w}}}tblStyle'))
if style is not None:
table.style_id = style.attrib[_name('{{{w}}}val')]
doc.add_style_as_used(table.style_id) |
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| def parse_table_column_properties(doc, cell, prop):
"Parse table column properties."
if not cell:
return
grid = prop.find(_name('{{{w}}}gridSpan'))
if grid is not None:
cell.grid_span = int(grid.attrib[_name('{{{w}}}val')])
vmerge = prop.find(_name('{{{w}}}vMerge'))
if vmerg... |
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| def parse_table(document, tbl):
"Parse table element."
def _change(rows, pos_x):
if len(rows) == 1:
return rows
count_x = 1
for x in rows[-1]:
if count_x == pos_x:
x.row_span += 1
count_x += x.grid_span
return rows
tab... |
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def parse_document(xmlcontent):
"""Parse document with content. Content is placed in file 'document.xml'. """ |
document = etree.fromstring(xmlcontent)
body = document.xpath('.//w:body', namespaces=NAMESPACES)[0]
document = doc.Document()
for elem in body:
if elem.tag == _name('{{{w}}}p'):
document.elements.append(parse_paragraph(document, elem))
if elem.tag == _name('{{{w}}}tbl'... |
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def parse_relationship(document, xmlcontent, rel_type):
"""Parse relationship document. Relationships hold information like external or internal references for l... |
doc = etree.fromstring(xmlcontent)
for elem in doc:
if elem.tag == _name('{{{pr}}}Relationship'):
rel = {'target': elem.attrib['Target'],
'type': elem.attrib['Type'],
'target_mode': elem.attrib.get('TargetMode', 'Internal')}
document.rela... |
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def parse_style(document, xmlcontent):
"""Parse styles document. Styles are defined in file 'styles.xml'. """ |
styles = etree.fromstring(xmlcontent)
_r = styles.xpath('.//w:rPrDefault', namespaces=NAMESPACES)
if len(_r) > 0:
rpr = _r[0].find(_name('{{{w}}}rPr'))
if rpr is not None:
st = doc.Style()
parse_previous_properties(document, st, rpr)
document.default_... |
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def parse_comments(document, xmlcontent):
"""Parse comments document. Comments are defined in file 'comments.xml' """ |
comments = etree.fromstring(xmlcontent)
document.comments = {}
for comment in comments.xpath('.//w:comment', namespaces=NAMESPACES):
# w:author
# w:id
# w: date
comment_id = comment.attrib[_name('{{{w}}}id')]
comm = doc.CommentContent(comment_id)
comm.auth... |
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def parse_footnotes(document, xmlcontent):
"""Parse footnotes document. Footnotes are defined in file 'footnotes.xml' """ |
footnotes = etree.fromstring(xmlcontent)
document.footnotes = {}
for footnote in footnotes.xpath('.//w:footnote', namespaces=NAMESPACES):
_type = footnote.attrib.get(_name('{{{w}}}type'), None)
# don't know what to do with these now
if _type in ['separator', 'continuationSeparato... |
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def parse_endnotes(document, xmlcontent):
"""Parse endnotes document. Endnotes are defined in file 'endnotes.xml' """ |
endnotes = etree.fromstring(xmlcontent)
document.endnotes = {}
for note in endnotes.xpath('.//w:endnote', namespaces=NAMESPACES):
paragraphs = [parse_paragraph(document, para) for para in note.xpath('.//w:p', namespaces=NAMESPACES)]
document.endnotes[note.attrib[_name('{{{w}}}id')]] = pa... |
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def parse_numbering(document, xmlcontent):
"""Parse numbering document. Numbering is defined in file 'numbering.xml'. """ |
numbering = etree.fromstring(xmlcontent)
document.abstruct_numbering = {}
document.numbering = {}
for abstruct_num in numbering.xpath('.//w:abstractNum', namespaces=NAMESPACES):
numb = {}
for lvl in abstruct_num.xpath('./w:lvl', namespaces=NAMESPACES):
ilvl = int(lvl.attr... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def parse_from_file(file_object):
"""Parses existing OOXML file. :Args: - file_object (:class:`ooxml.docx.DOCXFile`):
OOXML file object :Returns: Returns parsed... |
logger.info('Parsing %s file.', file_object.file_name)
# Read the files
doc_content = file_object.read_file('document.xml')
# Parse the document
document = parse_document(doc_content)
try:
style_content = file_object.read_file('styles.xml')
parse_style(document, style_conten... |
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