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def _jit(function):
""" Compile a function using a jit compiler. The function is always compiled to check errors, but is only used outside tests, so that code co... |
import sys
compiled = numba.jit(function)
if hasattr(sys, '_called_from_test'):
return function
else: # pragma: no cover
return compiled |
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def _sqrt(x):
""" Return square root of an ndarray. This sqrt function for ndarrays tries to use the exponentiation operator if the objects stored do not supply ... |
x = np.clip(x, a_min=0, a_max=None)
try:
return np.sqrt(x)
except AttributeError:
exponent = 0.5
try:
exponent = np.take(x, 0).from_float(exponent)
except AttributeError:
pass
return x ** exponent |
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def _transform_to_2d(t):
"""Convert vectors to column matrices, to always have a 2d shape.""" |
t = np.asarray(t)
dim = len(t.shape)
assert dim <= 2
if dim < 2:
t = np.atleast_2d(t).T
return t |
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def _can_be_double(x):
""" Return if the array can be safely converted to double. That happens when the dtype is a float with the same size of a double or narrow... |
return ((np.issubdtype(x.dtype, np.floating) and
x.dtype.itemsize <= np.dtype(float).itemsize) or
(np.issubdtype(x.dtype, np.signedinteger) and
np.can_cast(x, float))) |
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def _cdist_naive(x, y, exponent=1):
"""Pairwise distance, custom implementation.""" |
squared_norms = ((x[_np.newaxis, :, :] - y[:, _np.newaxis, :]) ** 2).sum(2)
exponent = exponent / 2
try:
exponent = squared_norms.take(0).from_float(exponent)
except AttributeError:
pass
return squared_norms ** exponent |
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def _cdist_scipy(x, y, exponent=1):
"""Pairwise distance between the points in two sets.""" |
metric = 'euclidean'
if exponent != 1:
metric = 'sqeuclidean'
distances = _spatial.distance.cdist(x, y, metric=metric)
if exponent != 1:
distances **= exponent / 2
return distances |
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def _cdist(x, y, exponent=1):
""" Pairwise distance between points in two sets. As Scipy converts every value to double, this wrapper uses a less efficient imple... |
if _can_be_double(x) and _can_be_double(y):
return _cdist_scipy(x, y, exponent)
else:
return _cdist_naive(x, y, exponent) |
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def respond(self, content=EmptyValue, content_type=EmptyValue, always_hash_content=True, ext=None):
""" Respond to the request. This generates the :attr:`mohawk.... |
log.debug('generating response header')
resource = Resource(url=self.resource.url,
credentials=self.resource.credentials,
ext=ext,
app=self.parsed_header.get('app', None),
dlg=self.parsed_h... |
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def calculate_payload_hash(payload, algorithm, content_type):
"""Calculates a hash for a given payload.""" |
p_hash = hashlib.new(algorithm)
parts = []
parts.append('hawk.' + str(HAWK_VER) + '.payload\n')
parts.append(parse_content_type(content_type) + '\n')
parts.append(payload or '')
parts.append('\n')
for i, p in enumerate(parts):
# Make sure we are about to hash binary strings.
... |
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def normalize_string(mac_type, resource, content_hash):
"""Serializes mac_type and resource into a HAWK string.""" |
normalized = [
'hawk.' + str(HAWK_VER) + '.' + mac_type,
normalize_header_attr(resource.timestamp),
normalize_header_attr(resource.nonce),
normalize_header_attr(resource.method or ''),
normalize_header_attr(resource.name or ''),
normalize_header_attr(resource.host),... |
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def get_bewit(resource):
""" Returns a bewit identifier for the resource as a string. :param resource: Resource to generate a bewit for :type resource: `mohawk.b... |
if resource.method != 'GET':
raise ValueError('bewits can only be generated for GET requests')
if resource.nonce != '':
raise ValueError('bewits must use an empty nonce')
mac = calculate_mac(
'bewit',
resource,
None,
)
if isinstance(mac, six.binary_type):
... |
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def strip_bewit(url):
""" Strips the bewit parameter out of a url. Returns (encoded_bewit, stripped_url) Raises InvalidBewit if no bewit found. :param url: The u... |
m = re.search('[?&]bewit=([^&]+)', url)
if not m:
raise InvalidBewit('no bewit data found')
bewit = m.group(1)
stripped_url = url[:m.start()] + url[m.end():]
return bewit, stripped_url |
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def check_bewit(url, credential_lookup, now=None):
""" Validates the given bewit. Returns True if the resource has a valid bewit parameter attached, or raises a ... |
raw_bewit, stripped_url = strip_bewit(url)
bewit = parse_bewit(raw_bewit)
try:
credentials = credential_lookup(bewit.id)
except LookupError:
raise CredentialsLookupError('Could not find credentials for ID {0}'
.format(bewit.id))
res = Resource(u... |
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def accept_response(self, response_header, content=EmptyValue, content_type=EmptyValue, accept_untrusted_content=False, localtime_offset_in_seconds=0, timestamp_s... |
log.debug('accepting response {header}'
.format(header=response_header))
parsed_header = parse_authorization_header(response_header)
resource = Resource(ext=parsed_header.get('ext', None),
content=content,
content_type=... |
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def current_state(self):
""" Returns a ``field -> value`` dict of the current state of the instance. """ |
field_names = set()
[field_names.add(f.name) for f in self._meta.local_fields]
[field_names.add(f.attname) for f in self._meta.local_fields]
return dict([(field_name, getattr(self, field_name)) for field_name in field_names]) |
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def _trim(cls, s):
""" Remove trailing colons from the URI back to the first non-colon. :param string s: input URI string :returns: URI string with trailing colo... |
reverse = s[::-1]
idx = 0
for i in range(0, len(reverse)):
if reverse[i] == ":":
idx += 1
else:
break
# Return the substring after all trailing colons,
# reversed back to its original character order.
new_s = rever... |
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def _get_attribute_components(self, att):
""" Returns the component list of input attribute. :param string att: Attribute name to get :returns: List of Component... |
lc = []
if not CPEComponent.is_valid_attribute(att):
errmsg = "Invalid attribute name '{0}' is not exist".format(att)
raise ValueError(errmsg)
for pk in CPE.CPE_PART_KEYS:
elements = self.get(pk)
for elem in elements:
lc.append(... |
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def _pack_edition(self):
""" Pack the values of the five arguments into the simple edition component. If all the values are blank, just return a blank. :returns:... |
COMP_KEYS = (CPEComponent.ATT_EDITION,
CPEComponent.ATT_SW_EDITION,
CPEComponent.ATT_TARGET_SW,
CPEComponent.ATT_TARGET_HW,
CPEComponent.ATT_OTHER)
separator = CPEComponent2_3_URI_edpacked.SEPARATOR_COMP
pack... |
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def as_uri_2_3(self):
""" Returns the CPE Name as URI string of version 2.3. :returns: CPE Name as URI string of version 2.3 :rtype: string :exception: TypeError... |
uri = []
uri.append("cpe:/")
ordered_comp_parts = {
0: CPEComponent.ATT_PART,
1: CPEComponent.ATT_VENDOR,
2: CPEComponent.ATT_PRODUCT,
3: CPEComponent.ATT_VERSION,
4: CPEComponent.ATT_UPDATE,
5: CPEComponent.ATT_EDITION,
... |
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def as_wfn(self):
""" Returns the CPE Name as Well-Formed Name string of version 2.3. :return: CPE Name as WFN string :rtype: string :exception: TypeError - inco... |
from .cpe2_3_wfn import CPE2_3_WFN
wfn = []
wfn.append(CPE2_3_WFN.CPE_PREFIX)
for i in range(0, len(CPEComponent.ordered_comp_parts)):
ck = CPEComponent.ordered_comp_parts[i]
lc = self._get_attribute_components(ck)
if len(lc) > 1:
... |
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def as_fs(self):
""" Returns the CPE Name as formatted string of version 2.3. :returns: CPE Name as formatted string :rtype: string :exception: TypeError - incom... |
fs = []
fs.append("cpe:2.3:")
for i in range(0, len(CPEComponent.ordered_comp_parts)):
ck = CPEComponent.ordered_comp_parts[i]
lc = self._get_attribute_components(ck)
if len(lc) > 1:
# Incompatible version 1.1, there are two or more element... |
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def _is_alphanum(cls, c):
""" Returns True if c is an uppercase letter, a lowercase letter, a digit or an underscore, otherwise False. :param string c: Character... |
alphanum_rxc = re.compile(CPEComponentSimple._ALPHANUM_PATTERN)
return (alphanum_rxc.match(c) is not None) |
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def _parse(self, comp_att):
""" Check if the value of component is correct in the attribute "comp_att". :param string comp_att: attribute associated with value o... |
errmsg = "Invalid attribute '{0}'".format(comp_att)
if not CPEComponent.is_valid_attribute(comp_att):
raise ValueError(errmsg)
comp_str = self._encoded_value
errmsg = "Invalid value of attribute '{0}': {1}".format(
comp_att, comp_str)
# Check part (s... |
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def as_fs(self):
""" Returns the value of component encoded as formatted string. Inspect each character in value of component. Certain nonalpha characters pass t... |
s = self._standard_value
result = []
idx = 0
while (idx < len(s)):
c = s[idx] # get the idx'th character of s
if c != "\\":
# unquoted characters pass thru unharmed
result.append(c)
else:
# Escaped ch... |
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def as_uri_2_3(self):
""" Returns the value of component encoded as URI string. Scans an input string s and applies the following transformations: - Pass alphanu... |
s = self._standard_value
result = []
idx = 0
while (idx < len(s)):
thischar = s[idx] # get the idx'th character of s
# alphanumerics (incl. underscore) pass untouched
if (CPEComponentSimple._is_alphanum(thischar)):
result.append(thi... |
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def _is_valid_value(self):
""" Return True if the value of component in generic attribute is valid, and otherwise False. :returns: True if value is valid, False ... |
comp_str = self._encoded_value
value_pattern = []
value_pattern.append("^((")
value_pattern.append("~[")
value_pattern.append(CPEComponent1_1._STRING)
value_pattern.append("]+")
value_pattern.append(")|(")
value_pattern.append("[")
value_pattern... |
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def _create_component(cls, att, value):
""" Returns a component with value "value". :param string att: Attribute name :param string value: Attribute value :retur... |
if value == CPEComponent2_3_URI.VALUE_UNDEFINED:
comp = CPEComponentUndefined()
elif (value == CPEComponent2_3_URI.VALUE_ANY or
value == CPEComponent2_3_URI.VALUE_EMPTY):
comp = CPEComponentAnyValue()
elif (value == CPEComponent2_3_URI.VALUE_NA):
... |
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def as_wfn(self):
""" Returns the CPE Name as Well-Formed Name string of version 2.3. If edition component is not packed, only shows the first seven components, ... |
if self._str.find(CPEComponent2_3_URI.SEPARATOR_PACKED_EDITION) == -1:
# Edition unpacked, only show the first seven components
wfn = []
wfn.append(CPE2_3_WFN.CPE_PREFIX)
for ck in CPEComponent.CPE_COMP_KEYS:
lc = self._get_attribute_components... |
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def _is_valid_edition(self):
""" Return True if the input value of attribute "edition" is valid, and otherwise False. :returns: True if value is valid, False oth... |
comp_str = self._standard_value[0]
packed = []
packed.append("(")
packed.append(CPEComponent2_3_URI.SEPARATOR_PACKED_EDITION)
packed.append(CPEComponent2_3_URI._string)
packed.append("){5}")
value_pattern = []
value_pattern.append("^(")
value_p... |
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def _compare_strings(cls, source, target):
""" Compares a source string to a target string, and addresses the condition in which the source string includes unquo... |
start = 0
end = len(source)
begins = 0
ends = 0
# Reading of initial wildcard in source
if source.startswith(CPEComponent2_3_WFN.WILDCARD_MULTI):
# Source starts with "*"
start = 1
begins = -1
else:
while ((start ... |
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def compare_wfns(cls, source, target):
""" Compares two WFNs and returns a generator of pairwise attribute-value comparison results. It provides full access to t... |
# Compare results using the get() function in WFN
for att in CPEComponent.CPE_COMP_KEYS_EXTENDED:
value_src = source.get_attribute_values(att)[0]
if value_src.find('"') > -1:
# Not a logical value: del double quotes
value_src = value_src[1:-1]
... |
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def cpe_disjoint(cls, source, target):
""" Compares two WFNs and returns True if the set-theoretic relation between the names is DISJOINT. :param CPE2_3_WFN sour... |
# If any pairwise comparison returned DISJOINT then
# the overall name relationship is DISJOINT
for att, result in CPESet2_3.compare_wfns(source, target):
isDisjoint = result == CPESet2_3.LOGICAL_VALUE_DISJOINT
if isDisjoint:
return True
return ... |
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def cpe_equal(cls, source, target):
""" Compares two WFNs and returns True if the set-theoretic relation between the names is EQUAL. :param CPE2_3_WFN source: fi... |
# If any pairwise comparison returned EQUAL then
# the overall name relationship is EQUAL
for att, result in CPESet2_3.compare_wfns(source, target):
isEqual = result == CPESet2_3.LOGICAL_VALUE_EQUAL
if not isEqual:
return False
return True |
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def append(self, cpe):
""" Adds a CPE element to the set if not already. Only WFN CPE Names are valid, so this function converts the input CPE object of version ... |
if cpe.VERSION != CPE2_3.VERSION:
errmsg = "CPE Name version {0} not valid, version 2.3 expected".format(
cpe.VERSION)
raise ValueError(errmsg)
for k in self.K:
if cpe._str == k._str:
return None
if isinstance(cpe, CPE2_3_WF... |
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def name_match(self, wfn):
""" Accepts a set of CPE Names K and a candidate CPE Name X. It returns 'True' if X matches any member of K, and 'False' otherwise. :p... |
for N in self.K:
if CPESet2_3.cpe_superset(wfn, N):
return True
return False |
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def _parse(self):
""" Checks if CPE Name is valid. :returns: None :exception: ValueError - bad-formed CPE Name """ |
# CPE Name must not have whitespaces
if (self._str.find(" ") != -1):
msg = "Bad-formed CPE Name: it must not have whitespaces"
raise ValueError(msg)
# Partitioning of CPE Name
parts_match = CPE2_2._parts_rxc.match(self._str)
# Validation of CPE Name pa... |
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def as_wfn(self):
""" Returns the CPE Name as WFN string of version 2.3. Only shows the first seven components. :return: CPE Name as WFN string :rtype: string :e... |
wfn = []
wfn.append(CPE2_3_WFN.CPE_PREFIX)
for ck in CPEComponent.CPE_COMP_KEYS:
lc = self._get_attribute_components(ck)
comp = lc[0]
if (isinstance(comp, CPEComponentUndefined) or
isinstance(comp, CPEComponentEmpty)):
# Do... |
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def _unbind(cls, boundname):
""" Unbinds a bound form to a WFN. :param string boundname: CPE name :returns: WFN object associated with boundname. :rtype: CPE2_3_... |
try:
fs = CPE2_3_FS(boundname)
except:
# CPE name is not formatted string
try:
uri = CPE2_3_URI(boundname)
except:
# CPE name is not URI but WFN
return CPE2_3_WFN(boundname)
else:
... |
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def is_component(w, ids):
"""Check if the set of ids form a single connected component Parameters w : spatial weights boject ids : list identifiers of units that... |
components = 0
marks = dict([(node, 0) for node in ids])
q = []
for node in ids:
if marks[node] == 0:
components += 1
q.append(node)
if components > 1:
return False
while q:
node = q.pop()
marks[node] = compone... |
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def check_contiguity(w, neighbors, leaver):
"""Check if contiguity is maintained if leaver is removed from neighbors Parameters w : spatial weights object simple... |
ids = neighbors[:]
ids.remove(leaver)
return is_component(w, ids) |
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def jsonapi(f):
""" Declare the view as a JSON API method This converts view return value into a :cls:JsonResponse. The following return types are supported: - t... |
@wraps(f)
def wrapper(*args, **kwargs):
rv = f(*args, **kwargs)
return make_json_response(rv)
return wrapper |
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def _unpack(c, tmp, package, version, git_url=None):
""" Download + unpack given package into temp dir ``tmp``. Return ``(real_version, source)`` where ``real_ve... |
real_version = version[:]
source = None
if git_url:
pass
# git clone into tempdir
# git checkout <version>
# set target to checkout
# if version does not look SHA-ish:
# in the checkout, obtain SHA from that branch
# set real_version to that value
els... |
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def make_sudouser(c):
""" Create a passworded sudo-capable user. Used by other tasks to execute the test suite so sudo tests work. """ |
user = c.travis.sudo.user
password = c.travis.sudo.password
# --create-home because we need a place to put conf files, keys etc
# --groups travis because we must be in the Travis group to access the
# (created by Travis for us) virtualenv and other contents within
# /home/travis.
c.sudo("us... |
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def make_sshable(c):
""" Set up passwordless SSH keypair & authorized_hosts access to localhost. """ |
user = c.travis.sudo.user
home = "~{0}".format(user)
# Run sudo() as the new sudo user; means less chown'ing, etc.
c.config.sudo.user = user
ssh_dir = "{0}/.ssh".format(home)
# TODO: worth wrapping in 'sh -c' and using '&&' instead of doing this?
for cmd in ("mkdir {0}", "chmod 0700 {0}"):
... |
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def blacken(c):
""" Install and execute ``black`` under appropriate circumstances, with diffs. Installs and runs ``black`` under Python 3.6 (the first version it... |
if not PYTHON.startswith("3.6"):
msg = "Not blackening, since Python {} != Python 3.6".format(PYTHON)
print(msg, file=sys.stderr)
return
# Install, allowing config override of hardcoded default version
config = c.config.get("travis", {}).get("black", {})
version = config.get("ve... |
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def decorator(self, func):
""" Wrapper function to decorate a function """ |
if inspect.isfunction(func):
func._methodview = self
elif inspect.ismethod(func):
func.__func__._methodview = self
else:
raise AssertionError('Can only decorate function and methods, {} given'.format(func))
return func |
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def matches(self, verb, params):
""" Test if the method matches the provided set of arguments :param verb: HTTP verb. Uppercase :type verb: str :param params: Ex... |
return (self.ifset is None or self.ifset <= params) and \
(self.ifnset is None or self.ifnset.isdisjoint(params)) and \
(self.methods is None or verb in self.methods) |
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def _match_view(self, method, route_params):
""" Detect a view matching the query :param method: HTTP method :param route_params: Route parameters dict :return: ... |
method = method.upper()
route_params = frozenset(k for k, v in route_params.items() if v is not None)
for view_name, info in self.methods_map[method].items():
if info.matches(method, route_params):
return getattr(self, view_name)
else:
return Non... |
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def steady_state(P):
""" Calculates the steady state probability vector for a regular Markov transition matrix P. Parameters P : array (k, k), an ergodic Markov ... |
v, d = la.eig(np.transpose(P))
d = np.array(d)
# for a regular P maximum eigenvalue will be 1
mv = max(v)
# find its position
i = v.tolist().index(mv)
row = abs(d[:, i])
# normalize eigenvector corresponding to the eigenvalue 1
return row / sum(row) |
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def fmpt(P):
""" Calculates the matrix of first mean passage times for an ergodic transition probability matrix. Parameters P : array (k, k), an ergodic Markov t... |
P = np.matrix(P)
k = P.shape[0]
A = np.zeros_like(P)
ss = steady_state(P).reshape(k, 1)
for i in range(k):
A[:, i] = ss
A = A.transpose()
I = np.identity(k)
Z = la.inv(I - P + A)
E = np.ones_like(Z)
A_diag = np.diag(A)
A_diag = A_diag + (A_diag == 0)
D = np.diag... |
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def var_fmpt(P):
""" Variances of first mean passage times for an ergodic transition probability matrix. Parameters P : array (k, k), an ergodic Markov transitio... |
P = np.matrix(P)
A = P ** 1000
n, k = A.shape
I = np.identity(k)
Z = la.inv(I - P + A)
E = np.ones_like(Z)
D = np.diag(1. / np.diag(A))
Zdg = np.diag(np.diag(Z))
M = (I - Z + E * Zdg) * D
ZM = Z * M
ZMdg = np.diag(np.diag(ZM))
W = M * (2 * Zdg * D - I) + 2 * (ZM - E * Z... |
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def _converge(c):
""" Examine world state, returning data on what needs updating for release. :param c: Invoke ``Context`` object or subclass. :returns: Two dict... |
#
# Data/state gathering
#
# Get data about current repo context: what branch are we on & what kind of
# release does it appear to represent?
branch, release_type = _release_line(c)
# Short-circuit if type is undefined; we can't do useful work for that.
if release_type is Release.UNDEF... |
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def prepare(c):
""" Edit changelog & version, git commit, and git tag, to set up for release. """ |
# Print dry-run/status/actions-to-take data & grab programmatic result
# TODO: maybe expand the enum-based stuff to have values that split up
# textual description, command string, etc. See the TODO up by their
# definition too, re: just making them non-enum classes period.
# TODO: otherwise, we at... |
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def _release_line(c):
""" Examine current repo state to determine what type of release to prep. :returns: A two-tuple of ``(branch-name, line-type)`` where: - ``... |
# TODO: I don't _think_ this technically overlaps with Releases (because
# that only ever deals with changelog contents, and therefore full release
# version numbers) but in case it does, move it there sometime.
# TODO: this and similar calls in this module may want to be given an
# explicit pointe... |
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def _versions_from_changelog(changelog):
""" Return all released versions from given ``changelog``, sorted. :param dict changelog: A changelog dict as returned b... |
versions = [Version(x) for x in changelog if BUGFIX_RELEASE_RE.match(x)]
return sorted(versions) |
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def _release_and_issues(changelog, branch, release_type):
""" Return most recent branch-appropriate release, if any, and its contents. :param dict changelog: Cha... |
# Bugfix lines just use the branch to find issues
bucket = branch
# Features need a bit more logic
if release_type is Release.FEATURE:
bucket = _latest_feature_bucket(changelog)
# Issues is simply what's in the bucket
issues = changelog[bucket]
# Latest release is undefined for feat... |
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def _get_tags(c):
""" Return sorted list of release-style tags as semver objects. """ |
tags_ = []
for tagstr in c.run("git tag", hide=True).stdout.strip().split("\n"):
try:
tags_.append(Version(tagstr))
# Ignore anything non-semver; most of the time they'll be non-release
# tags, and even if they are, we can't reason about anything
# non-semver anyways... |
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def _find_package(c):
""" Try to find 'the' One True Package for this project. Mostly for obtaining the ``_version`` file within it. Uses the ``packaging.package... |
# TODO: is there a way to get this from the same place setup.py does w/o
# setup.py barfing (since setup() runs at import time and assumes CLI use)?
configured_value = c.get("packaging", {}).get("package", None)
if configured_value:
return configured_value
# TODO: tests covering this stuff ... |
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def publish( c, sdist=True, wheel=False, index=None, sign=False, dry_run=False, directory=None, dual_wheels=False, alt_python=None, check_desc=False, ):
""" Publ... |
# Don't hide by default, this step likes to be verbose most of the time.
c.config.run.hide = False
# Config hooks
config = c.config.get("packaging", {})
index = config.get("index", index)
sign = config.get("sign", sign)
dual_wheels = config.get("dual_wheels", dual_wheels)
check_desc = c... |
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def tmpdir(skip_cleanup=False, explicit=None):
""" Context-manage a temporary directory. Can be given ``skip_cleanup`` to skip cleanup, and ``explicit`` to choos... |
tmp = explicit if explicit is not None else mkdtemp()
try:
yield tmp
finally:
if not skip_cleanup:
rmtree(tmp) |
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def permute(self, permutations=99, alternative='two.sided'):
""" Generate ransom spatial permutations for inference on LISA vectors. Parameters permutations : in... |
rY = self.Y.copy()
idxs = np.arange(len(rY))
counts = np.zeros((permutations, len(self.counts)))
for m in range(permutations):
np.random.shuffle(idxs)
res = self._calc(rY[idxs, :], self.w, self.k)
counts[m] = res['counts']
self.counts_perm = c... |
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def plot(self, attribute=None, ax=None, **kwargs):
""" Plot the rose diagram. Parameters attribute : (n,) ndarray, optional Variable to specify colors of the col... |
from splot.giddy import dynamic_lisa_rose
fig, ax = dynamic_lisa_rose(self, attribute=attribute,
ax=ax, **kwargs)
return fig, ax |
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def plot_origin(self):
# TODO add attribute option to color vectors """ Plot vectors of positional transition of LISA values starting from the same origin. """ |
import matplotlib.cm as cm
import matplotlib.pyplot as plt
ax = plt.subplot(111)
xlim = [self._dx.min(), self._dx.max()]
ylim = [self._dy.min(), self._dy.max()]
for x, y in zip(self._dx, self._dy):
xs = [0, x]
ys = [0, y]
plt.plot(xs, ... |
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def plot_vectors(self, arrows=True):
""" Plot vectors of positional transition of LISA values within quadrant in scatterplot in a polar plot. Parameters ax : Mat... |
from splot.giddy import dynamic_lisa_vectors
fig, ax = dynamic_lisa_vectors(self, arrows=arrows)
return fig, ax |
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def _clean(c):
""" Nuke docs build target directory so next build is clean. """ |
if isdir(c.sphinx.target):
rmtree(c.sphinx.target) |
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def build( c, clean=False, browse=False, nitpick=False, opts=None, source=None, target=None, ):
""" Build the project's Sphinx docs. """ |
if clean:
_clean(c)
if opts is None:
opts = ""
if nitpick:
opts += " -n -W -T"
cmd = "sphinx-build{0} {1} {2}".format(
(" " + opts) if opts else "",
source or c.sphinx.source,
target or c.sphinx.target,
)
c.run(cmd, pty=True)
if browse:
... |
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def tree(c):
""" Display documentation contents with the 'tree' program. """ |
ignore = ".git|*.pyc|*.swp|dist|*.egg-info|_static|_build|_templates"
c.run('tree -Ca -I "{0}" {1}'.format(ignore, c.sphinx.source)) |
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def watch_docs(c):
""" Watch both doc trees & rebuild them if files change. This includes e.g. rebuilding the API docs if the source code changes; rebuilding the... |
# TODO: break back down into generic single-site version, then create split
# tasks as with docs/www above. Probably wants invoke#63.
# NOTE: 'www'/'docs' refer to the module level sub-collections. meh.
# Readme & WWW triggers WWW
www_c = Context(config=c.config.clone())
www_c.update(**www.co... |
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def shuffle_matrix(X, ids):
""" Random permutation of rows and columns of a matrix Parameters X : array (k, k), array to be permutated. ids : array range (k, ). ... |
np.random.shuffle(ids)
return X[ids, :][:, ids] |
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def markov_mobility(p, measure="P", ini=None):
""" Markov-based mobility index. Parameters p : array (k, k), Markov transition probability matrix. measure : stri... |
p = np.array(p)
k = p.shape[1]
if measure == "P":
t = np.trace(p)
mobi = (k - t) / (k - 1)
elif measure == "D":
mobi = 1 - abs(la.det(p))
elif measure == "L2":
w, v = la.eig(p)
eigen_value_abs = abs(w)
mobi = 1 - np.sort(eigen_value_abs)[-2]
elif... |
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def chi2(T1, T2):
""" chi-squared test of difference between two transition matrices. Parameters T1 : array (k, k), matrix of transitions (counts). T2 : array (k... |
rs2 = T2.sum(axis=1)
rs1 = T1.sum(axis=1)
rs2nz = rs2 > 0
rs1nz = rs1 > 0
dof1 = sum(rs1nz)
dof2 = sum(rs2nz)
rs2 = rs2 + (rs2 == 0)
dof = (dof1 - 1) * (dof2 - 1)
p = np.diag(1 / rs2) * np.matrix(T2)
E = np.diag(rs1) * np.matrix(p)
num = T1 - E
num = np.multiply(num, num... |
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def kullback(F):
""" Kullback information based test of Markov Homogeneity. Parameters F : array (s, r, r), values are transitions (not probabilities) for s stra... |
F1 = F == 0
F1 = F + F1
FLF = F * np.log(F1)
T1 = 2 * FLF.sum()
FdJK = F.sum(axis=0)
FdJK1 = FdJK + (FdJK == 0)
FdJKLFdJK = FdJK * np.log(FdJK1)
T2 = 2 * FdJKLFdJK.sum()
FdJd = F.sum(axis=0).sum(axis=1)
FdJd1 = FdJd + (FdJd == 0)
T3 = 2 * (FdJd * np.log(FdJd1)).sum()
... |
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def prais(pmat):
""" Prais conditional mobility measure. Parameters pmat : matrix (k, k), Markov probability transition matrix. Returns ------- pr : matrix (1, k... |
pmat = np.array(pmat)
pr = 1 - np.diag(pmat)
return pr |
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def homogeneity(transition_matrices, regime_names=[], class_names=[], title="Markov Homogeneity Test"):
""" Test for homogeneity of Markov transition probabiliti... |
return Homogeneity_Results(transition_matrices, regime_names=regime_names,
class_names=class_names, title=title) |
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def sojourn_time(p):
""" Calculate sojourn time based on a given transition probability matrix. Parameters p : array (k, k), a Markov transition probability matr... |
p = np.asarray(p)
pii = p.diagonal()
if not (1 - pii).all():
print("Sojourn times are infinite for absorbing states!")
return 1 / (1 - pii) |
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| def _calc(self, y, w):
'''Helper to estimate spatial lag conditioned Markov transition
probability matrices based on maximum likelihood techniques.
'''
if self.discrete:
self.lclass_ids = weights.lag_categorical(w, self.class_ids,
... |
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def summary(self, file_name=None):
""" A summary method to call the Markov homogeneity test to test for temporally lagged spatial dependence. To learn more about... |
class_names = ["C%d" % i for i in range(self.k)]
regime_names = ["LAG%d" % i for i in range(self.k)]
ht = homogeneity(self.T, class_names=class_names,
regime_names=regime_names)
title = "Spatial Markov Test"
if self.variable_name:
title = ti... |
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| def _maybe_classify(self, y, k, cutoffs):
'''Helper method for classifying continuous data.
'''
rows, cols = y.shape
if cutoffs is None:
if self.fixed:
mcyb = mc.Quantiles(y.flatten(), k=k)
yb = mcyb.yb.reshape(y.shape)
cutoff... |
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def spillover(self, quadrant=1, neighbors_on=False):
""" Detect spillover locations for diffusion in LISA Markov. Parameters quadrant : int which quadrant in the... |
n, k = self.q.shape
if self.permutations:
spill_over = np.zeros((n, k - 1))
components = np.zeros((n, k))
i2id = {} # handle string keys
for key in list(self.w.neighbors.keys()):
idx = self.w.id2i[key]
i2id[idx] = key
... |
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def get_entity_propnames(entity):
""" Get entity property names :param entity: Entity :type entity: sqlalchemy.ext.declarative.api.DeclarativeMeta :returns: Set ... |
ins = entity if isinstance(entity, InstanceState) else inspect(entity)
return set(
ins.mapper.column_attrs.keys() + # Columns
ins.mapper.relationships.keys() # Relationships
) |
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def next_minor(self):
""" Return a Version whose minor number is one greater than self's. .. note:: The new Version will always have a zeroed-out bugfix/tertiary... |
clone = self.clone()
clone.minor += 1
clone.patch = 0
return clone |
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def encoding_for(source_path, encoding='automatic', fallback_encoding=None):
""" The encoding used by the text file stored in ``source_path``. The algorithm used... |
assert encoding is not None
if encoding == 'automatic':
with open(source_path, 'rb') as source_file:
heading = source_file.read(128)
result = None
if len(heading) == 0:
# File is empty, assume a dummy encoding.
result = 'utf-8'
if result is N... |
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| def polynomial(img, mask, inplace=False, replace_all=False,
max_dev=1e-5, max_iter=20, order=2):
'''
replace all masked values
calculate flatField from 2d-polynomal fit filling
all high gradient areas within averaged fit-image
returns flatField, average background level, fitte... |
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| def SNR_IEC(i1, i2, ibg=0, allow_color_images=False):
'''
Calculate the averaged signal-to-noise ratio SNR50
as defined by IEC NP 60904-13
needs 2 reference EL images and one background image
'''
# ensure images are type float64 (double precision):
i1 = np.asfarray(i1)
i2 = np.... |
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| def _evaluate(x, y, weights):
'''
get the parameters of the, needed by 'function'
through curve fitting
'''
i = _validI(x, y, weights)
xx = x[i]
y = y[i]
try:
fitParams = _fit(xx, y)
# bound noise fn to min defined y value:
minY = function(xx[0], *fit... |
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| def function(x, ax, ay):
'''
general square root function
'''
with np.errstate(invalid='ignore'):
return ay * (x - ax)**0.5 |
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| def _validI(x, y, weights):
'''
return indices that have enough data points and are not erroneous
'''
# density filter:
i = np.logical_and(np.isfinite(y), weights > np.median(weights))
# filter outliers:
try:
grad = np.abs(np.gradient(y[i]))
max_gradient = 4 * np.me... |
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| def smooth(x, y, weights):
'''
in case the NLF cannot be described by
a square root function
commit bounded polynomial interpolation
'''
# Spline hard to smooth properly, therefore solfed with
# bounded polynomal interpolation
# ext=3: no extrapolation, but boundary value
# ... |
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| def oneImageNLF(img, img2=None, signal=None):
'''
Estimate the NLF from one or two images of the same kind
'''
x, y, weights, signal = calcNLF(img, img2, signal)
_, fn, _ = _evaluate(x, y, weights)
return fn, signal |
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| def _getMinMax(img):
'''
Get the a range of image intensities
that most pixels are in with
'''
av = np.mean(img)
std = np.std(img)
# define range for segmentation:
mn = av - 3 * std
mx = av + 3 * std
return max(img.min(), mn, 0), min(img.max(), mx) |
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| def polyfit2d(x, y, z, order=3 #bounds=None
):
'''
fit unstructured data
'''
ncols = (order + 1)**2
G = np.zeros((x.size, ncols))
ij = itertools.product(list(range(order+1)), list(range(order+1)))
for k, (i,j) in enumerate(ij):
G[:,k] = x**i * y**j
m = np... |
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| def polyfit2dGrid(arr, mask=None, order=3, replace_all=False,
copy=True, outgrid=None):
'''
replace all masked values with polynomial fitted ones
'''
s0,s1 = arr.shape
if mask is None:
if outgrid is None:
y,x = np.mgrid[:float(s0),:float(s1)]
... |
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| def reconstructImage(self):
'''
do inverse Fourier transform and return result
'''
f_ishift = np.fft.ifftshift(self.fshift)
return np.real(np.fft.ifft2(f_ishift)) |
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Description:
| def relativeAreaSTE(self):
'''
return STE area - relative to image area
'''
s = self.noSTE.shape
return np.sum(self.mask_STE) / (s[0] * s[1]) |
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Description:
| def intensityDistributionSTE(self, bins=10, range=None):
'''
return distribution of STE intensity
'''
v = np.abs(self._last_diff[self.mask_STE])
return np.histogram(v, bins, range) |
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Solve the following problem using Python, implementing the functions described below, one line at a time
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Description:
| def toFloatArray(img):
'''
transform an unsigned integer array into a
float array of the right size
'''
_D = {1: np.float32, # uint8
2: np.float32, # uint16
4: np.float64, # uint32
8: np.float64} # uint64
return img.astype(_D[img.itemsize]) |
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Description:
| def toNoUintArray(arr):
'''
cast array to the next higher integer array
if dtype=unsigned integer
'''
d = arr.dtype
if d.kind == 'u':
arr = arr.astype({1: np.int16,
2: np.int32,
4: np.int64}[d.itemsize])
return arr |
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Solve the following problem using Python, implementing the functions described below, one line at a time
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Description:
| def rot90(img):
'''
rotate one or multiple grayscale or color images 90 degrees
'''
s = img.shape
if len(s) == 3:
if s[2] in (3, 4): # color image
out = np.empty((s[1], s[0], s[2]), dtype=img.dtype)
for i in range(s[2]):
out[:, :, i] = np.rot... |
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Description:
| def _insertDateIndex(date, l):
'''
returns the index to insert the given date in a list
where each items first value is a date
'''
return next((i for i, n in enumerate(l) if n[0] < date), len(l)) |
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Description:
| def _getFromDate(l, date):
'''
returns the index of given or best fitting date
'''
try:
date = _toDate(date)
i = _insertDateIndex(date, l) - 1
if i == -1:
return l[0]
return l[i]
except (ValueError, TypeError):
# ValueError: date invalid... |
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