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def niftilist_mask_to_array(img_filelist, mask_file=None, outdtype=None):
"""From the list of absolute paths to nifti files, creates a Numpy array
with the masked data.
Parameters
----------
img_filelist: list of str
List of absolute file paths to nifti files. All nifti files must have
... |
def create(_):
"""Create a client for Service Fabric APIs."""
endpoint = client_endpoint()
if not endpoint:
raise CLIError("Connection endpoint not found. "
"Before running sfctl commands, connect to a cluster using "
"the 'sfctl cluster select' comman... |
def aggregate(self, clazz, new_col, *args):
"""
Aggregate the rows of the DataFrame into a single value.
:param clazz: name of a class that extends class Callable
:type clazz: class
:param new_col: name of the new column
:type new_col: str
:param args: list of co... |
def subset(self, *args):
"""
Subset only some of the columns of the DataFrame.
:param args: list of column names of the object that should be subsetted
:type args: tuple
:return: returns dataframe with only the columns you selected
:rtype: DataFrame
"""
c... |
def modify(self, clazz, new_col, *args):
"""
Modify some columns (i.e. apply a function) and add the
result to the table.
:param clazz: name of a class that extends class Callable
:type clazz: class
:param new_col: name of the new column
:type new_col: str
... |
def group(*args):
"""
Pipeable grouping method.
Takes either
- a dataframe and a tuple of strings for grouping,
- a tuple of strings if a dataframe has already been piped into.
:Example:
group(dataframe, "column")
:Example:
dataframe >> group("column")
... |
def aggregate(*args):
"""
Pipeable aggregation method.
Takes either
- a dataframe and a tuple of arguments required for aggregation,
- a tuple of arguments if a dataframe has already been piped into.
In any case one argument has to be a class that extends callable.
:Example:
ag... |
def subset(*args):
"""
Pipeable subsetting method.
Takes either
- a dataframe and a tuple of arguments required for subsetting,
- a tuple of arguments if a dataframe has already been piped into.
:Example:
subset(dataframe, "column")
:Example:
dataframe >> subse... |
def modify(*args):
"""
Pipeable modification method
Takes either
- a dataframe and a tuple of arguments required for modification,
- a tuple of arguments if a dataframe has already been piped into.
In any case one argument has to be a class that extends callable.
:Example:
mod... |
def _escape_char(c, escape_char=ESCAPE_CHAR):
"""Escape a single character"""
buf = []
for byte in c.encode('utf8'):
buf.append(escape_char)
buf.append('%X' % _ord(byte))
return ''.join(buf) |
def escape(to_escape, safe=SAFE, escape_char=ESCAPE_CHAR, allow_collisions=False):
"""Escape a string so that it only contains characters in a safe set.
Characters outside the safe list will be escaped with _%x_,
where %x is the hex value of the character.
If `allow_collisions` is True, occurrences of... |
def unescape(escaped, escape_char=ESCAPE_CHAR):
"""Unescape a string escaped with `escape`
escape_char must be the same as that used in the call to escape.
"""
if isinstance(escaped, bytes):
# always work on text
escaped = escaped.decode('utf8')
escape_pat = re.compile(re.e... |
def can_send(self, user, notice_type):
"""
Determines whether this backend is allowed to send a notification to
the given user and notice_type.
"""
from notification.models import NoticeSetting
return NoticeSetting.for_user(user, notice_type, self.medium_id).send |
def get_formatted_messages(self, formats, label, context):
"""
Returns a dictionary with the format identifier as the key. The values are
are fully rendered templates with the given context.
"""
format_templates = {}
for fmt in formats:
# conditionally turn of... |
def copy_attributes(source, destination, ignore_patterns=[]):
"""
Copy the attributes from a source object to a destination object.
"""
for attr in _wildcard_filter(dir(source), *ignore_patterns):
setattr(destination, attr, getattr(source, attr)) |
def row(self, idx):
"""
Returns DataFrameRow of the DataFrame given its index.
:param idx: the index of the row in the DataFrame.
:return: returns a DataFrameRow
"""
return DataFrameRow(idx, [x[idx] for x in self], self.colnames) |
def notice_settings(request):
"""
The notice settings view.
Template: :template:`notification/notice_settings.html`
Context:
notice_types
A list of all :model:`notification.NoticeType` objects.
notice_settings
A dictionary containing ``column_headers`` for eac... |
def query(self, input = '', params = {}):
"""Query Wolfram Alpha and return a Result object"""
# Get and construct query parameters
# Default parameters
payload = {'input': input,
'appid': self.appid}
# Additional parameters (from params), formatted for url
... |
def pods(self):
"""Return list of all Pod objects in result"""
# Return empty list if xml_tree is not defined (error Result object)
if not self.xml_tree:
return []
# Create a Pod object for every pod group in xml
return [Pod(elem) for elem in self.xml_tree.findall('p... |
def format(self):
"""
Dictionary of available formats, corresponding to a list of the values
Example: pod.format['plaintext'] will return a list of every plaintext
content in the pod's subpods
"""
formats = {}
# Iterate through all the tags (formats) in ... |
def find(self, *args):
"""
Find a node in the tree. If the node is not found it is added first and then returned.
:param args: a tuple
:return: returns the node
"""
curr_node = self.__root
return self.__traverse(curr_node, 0, *args) |
def get_notification_language(user):
"""
Returns site-specific notification language for this user. Raises
LanguageStoreNotAvailable if this site does not use translated
notifications.
"""
if getattr(settings, "NOTIFICATION_LANGUAGE_MODULE", False):
try:
app_label, model_name... |
def send_now(users, label, extra_context=None, sender=None):
"""
Creates a new notice.
This is intended to be how other apps create new notices.
notification.send(user, "friends_invite_sent", {
"spam": "eggs",
"foo": "bar",
)
"""
sent = False
if extra_context is None:
... |
def send(*args, **kwargs):
"""
A basic interface around both queue and send_now. This honors a global
flag NOTIFICATION_QUEUE_ALL that helps determine whether all calls should
be queued or not. A per call ``queue`` or ``now`` keyword argument can be
used to always override the default global behavio... |
def queue(users, label, extra_context=None, sender=None):
"""
Queue the notification in NoticeQueueBatch. This allows for large amounts
of user notifications to be deferred to a seperate process running outside
the webserver.
"""
if extra_context is None:
extra_context = {}
if isinst... |
def write_table_pair_potential(func, dfunc=None, bounds=(1.0, 10.0), samples=1000, tollerance=1e-6, keyword='PAIR'):
"""A helper function to write lammps pair potentials to string. Assumes that
functions are vectorized.
Parameters
----------
func: function
A function that will be evaluated f... |
def write_tersoff_potential(parameters):
"""Write tersoff potential file from parameters to string
Parameters
----------
parameters: dict
keys are tuple of elements with the values being the parameters length 14
"""
lines = []
for (e1, e2, e3), params in parameters.items():
i... |
def subset(self, *args):
"""
Subset only some of the columns of the DataFrame.
:param args: list of column names of the object that should be subsetted
:type args: tuple
:return: returns DataFrame with only the columns you selected
:rtype: DataFrame
"""
a... |
def modify(self, clazz, new_col, *args):
"""
Modify some columns (i.e. apply a function)
and add the result to the table.
:param clazz: name of a class that extends class Callable
:type clazz: class
:param new_col: name of the new column
:type new_col: str
... |
def aggregate(self, clazz, new_col, *args):
"""
Aggregate the rows of each group into a single value.
:param clazz: name of a class that extends class Callable
:type clazz: class
:param new_col: name of the new column
:type new_col: str
:param args: list of colum... |
def reader(ltsvfile, labels=None):
"""Make LTSV Reader for reading selected labels.
:param ltsvfile: iterable of lines.
:param labels: sequence of labels. (optional)
:return: generator of record in [[label, value], ...] form.
"""
label_pattern = re.compile(r"^[0-9A-Za-z_.-]+:")
if labels... |
def DictReader(ltsvfile, labels=None, dict_type=dict):
"""Make LTSV Reader for reading selected labels.
:param ltsvfile: iterable of lines.
:param labels: sequence of labels.
:return: generator of record in {label: value, ...} form.
"""
for rec in reader(ltsvfile, labels):
yield dict_... |
def is_disjoint(set1, set2, warn):
"""
Checks if elements of set2 are in set1.
:param set1: a set of values
:param set2: a set of values
:param warn: the error message that should be thrown
when the sets are NOT disjoint
:return: returns true no elements of set2 are in set1
"""
for... |
def contains_all(set1, set2, warn):
"""
Checks if all elements from set2 are in set1.
:param set1: a set of values
:param set2: a set of values
:param warn: the error message that should be thrown
when the sets are not containd
:return: returns true if all values of set2 are in set1
... |
def to_XML(self):
"""
Serialize object back to XML string.
Returns:
str: String which should be same as original input, if everything\
works as expected.
"""
marcxml_template = """<record xmlns="http://www.loc.gov/MARC21/slim/"
xmlns:xsi="http://www.... |
def _parse_string(self, xml):
"""
Parse MARC XML document to dicts, which are contained in
self.controlfields and self.datafields.
Args:
xml (str or HTMLElement): input data
Also detect if this is oai marc format or not (see elf.oai_marc).
"""
if not... |
def _parse_control_fields(self, fields, tag_id="tag"):
"""
Parse control fields.
Args:
fields (list): list of HTMLElements
tag_id (str): parameter name, which holds the information, about
field name this is normally "tag", but in case of
... |
def _parse_data_fields(self, fields, tag_id="tag", sub_id="code"):
"""
Parse data fields.
Args:
fields (list): of HTMLElements
tag_id (str): parameter name, which holds the information, about
field name this is normally "tag", but in case of
... |
def add_ctl_field(self, name, value):
"""
Add new control field `value` with under `name` into control field
dictionary :attr:`controlfields`.
"""
if len(name) != 3:
raise ValueError("name parameter have to be exactly 3 chars long!")
self.controlfields[name] ... |
def add_data_field(self, name, i1, i2, subfields_dict):
"""
Add new datafield into :attr:`datafields` and take care of OAI MARC
differencies.
Args:
name (str): Name of datafield.
i1 (char): Value of i1/ind1 parameter.
i2 (char): Value of i2/ind2 param... |
def get_i_name(self, num, is_oai=None):
"""
This method is used mainly internally, but it can be handy if you work
with with raw MARC XML object and not using getters.
Args:
num (int): Which indicator you need (1/2).
is_oai (bool/None): If None, :attr:`.oai_marc`... |
def get_ctl_field(self, controlfield, alt=None):
"""
Method wrapper over :attr:`.controlfields` dictionary.
Args:
controlfield (str): Name of the controlfield.
alt (object, default None): Alternative value of the `controlfield`
when `controlfield` couldn'... |
def getDataRecords(self, datafield, subfield, throw_exceptions=True):
"""
.. deprecated::
Use :func:`get_subfields` instead.
"""
return self.get_subfields(
datafield=datafield,
subfield=subfield,
exception=throw_exceptions
) |
def get_subfields(self, datafield, subfield, i1=None, i2=None,
exception=False):
"""
Return content of given `subfield` in `datafield`.
Args:
datafield (str): Section name (for example "001", "100", "700").
subfield (str): Subfield name (for exampl... |
def timeit_block(unit='s', label=""):
"""
测试代码块耗时
:param unit: 时间单位，有 's','m','h' 可选（seconds，minutes，hours）
:param label: 代码块标签
"""
start = time.time()
try:
yield
finally:
_format(unit, time.time() - start, label) |
def timeit(unit='s'):
"""
测试函数耗时
:param unit: 时间单位，有 's','m','h' 可选（seconds，minutes，hours）
"""
def wrapper(func):
@wraps(func)
def inner(*args, **kwargs):
start = time.time()
_result = func(*args, **kwargs)
_format(unit, time.time() - start, func.... |
def _print(stats, limit, label):
"""
控制输出量
"""
print("TraceMalloc for {}".format(label))
for index, stat in enumerate(stats):
if index < limit:
print(stat)
else:
break |
def memoryit(group_by='lineno', limit=10):
"""
追踪函数内存消耗情况
:param group_by: 统计分组，有 'filename', 'lineno', 'traceback' 可选
:param limit: 限制输出行数
"""
def wrapper(func):
@wraps(func)
def inner(*args, **kwargs):
tracemalloc.start()
_start = tracemalloc.take_snaps... |
def memoryit_block(group_by='lineno', limit=10, label='code block'):
"""
追踪代码块内存消耗情况
:param group_by: 统计分组，有 'filename', 'lineno', 'traceback' 可选
:param limit: 限制输出行数
:param label: 代码块标签
"""
tracemalloc.start()
_start = tracemalloc.take_snapshot()
try:
yield
finally:
... |
def _get_params(target, param, dof):
'''Get the given param from each of the DOFs for a joint.'''
return [target.getParam(getattr(ode, 'Param{}{}'.format(param, s)))
for s in ['', '2', '3'][:dof]] |
def _set_params(target, param, values, dof):
'''Set the given param for each of the DOFs for a joint.'''
if not isinstance(values, (list, tuple, np.ndarray)):
values = [values] * dof
assert dof == len(values)
for s, value in zip(['', '2', '3'][:dof], values):
target.setParam(getattr(ode,... |
def make_quaternion(theta, *axis):
'''Given an angle and an axis, create a quaternion.'''
x, y, z = axis
r = np.sqrt(x * x + y * y + z * z)
st = np.sin(theta / 2.)
ct = np.cos(theta / 2.)
return [x * st / r, y * st / r, z * st / r, ct] |
def center_of_mass(bodies):
'''Given a set of bodies, compute their center of mass in world coordinates.
'''
x = np.zeros(3.)
t = 0.
for b in bodies:
m = b.mass
x += b.body_to_world(m.c) * m.mass
t += m.mass
return x / t |
def state(self):
'''The state of this body includes:
- name of the body (str)
- position (3-tuple)
- quaternion (4-tuple)
- linear velocity (3-tuple)
- angular velocity (3-tuple)
'''
return BodyState(self.name,
... |
def state(self, state):
'''Set the state of this body.
Parameters
----------
state : BodyState tuple
The desired state of the body.
'''
assert self.name == state.name, \
'state name "{}" != body name "{}"'.format(state.name, self.name)
sel... |
def rotation(self, rotation):
'''Set the rotation of this body using a rotation matrix.
Parameters
----------
rotation : sequence of 9 floats
The desired rotation matrix for this body.
'''
if isinstance(rotation, np.ndarray):
rotation = rotation.r... |
def is_kinematic(self, is_kinematic):
'''Set the kinematic/dynamic attribute for this body.
In pagoda, kinematic bodies have infinite mass and do interact with
other bodies via collisions.
Parameters
----------
is_kinematic : bool
If True, this body will be ... |
def body_to_world(self, position):
'''Convert a body-relative offset to world coordinates.
Parameters
----------
position : 3-tuple of float
A tuple giving body-relative offsets.
Returns
-------
position : 3-tuple of float
A tuple giving ... |
def world_to_body(self, position):
'''Convert a point in world coordinates to a body-relative offset.
Parameters
----------
position : 3-tuple of float
A world coordinates position.
Returns
-------
offset : 3-tuple of float
A tuple giving... |
def relative_offset_to_world(self, offset):
'''Convert a relative body offset to world coordinates.
Parameters
----------
offset : 3-tuple of float
The offset of the desired point, given as a relative fraction of the
size of this body. For example, offset (0, 0, ... |
def add_force(self, force, relative=False, position=None, relative_position=None):
'''Add a force to this body.
Parameters
----------
force : 3-tuple of float
A vector giving the forces along each world or body coordinate axis.
relative : bool, optional
I... |
def add_torque(self, torque, relative=False):
'''Add a torque to this body.
Parameters
----------
force : 3-tuple of float
A vector giving the torque along each world or body coordinate axis.
relative : bool, optional
If False, the torque values are assum... |
def join_to(self, joint, other_body=None, **kwargs):
'''Connect this body to another one using a joint.
This method creates a joint to fasten this body to the other one. See
:func:`World.join`.
Parameters
----------
joint : str
The type of joint to use when ... |
def connect_to(self, joint, other_body, offset=(0, 0, 0), other_offset=(0, 0, 0),
**kwargs):
'''Move another body next to this one and join them together.
This method will move the ``other_body`` so that the anchor points for
the joint coincide. It then creates a joint to fas... |
def positions(self):
'''List of positions for linear degrees of freedom.'''
return [self.ode_obj.getPosition(i) for i in range(self.LDOF)] |
def position_rates(self):
'''List of position rates for linear degrees of freedom.'''
return [self.ode_obj.getPositionRate(i) for i in range(self.LDOF)] |
def angles(self):
'''List of angles for rotational degrees of freedom.'''
return [self.ode_obj.getAngle(i) for i in range(self.ADOF)] |
def angle_rates(self):
'''List of angle rates for rotational degrees of freedom.'''
return [self.ode_obj.getAngleRate(i) for i in range(self.ADOF)] |
def axes(self):
'''List of axes for this object's degrees of freedom.'''
return [np.array(self.ode_obj.getAxis(i))
for i in range(self.ADOF or self.LDOF)] |
def axes(self, axes):
'''Set the axes for this object's degrees of freedom.
Parameters
----------
axes : list of axes specifications
A list of axis values to set. This list must have the same number of
elements as the degrees of freedom of the underlying ODE obje... |
def lo_stops(self, lo_stops):
'''Set the lo stop values for this object's degrees of freedom.
Parameters
----------
lo_stops : float or sequence of float
A lo stop value to set on all degrees of freedom, or a list
containing one such value for each degree of free... |
def hi_stops(self, hi_stops):
'''Set the hi stop values for this object's degrees of freedom.
Parameters
----------
hi_stops : float or sequence of float
A hi stop value to set on all degrees of freedom, or a list
containing one such value for each degree of free... |
def velocities(self, velocities):
'''Set the target velocities for this object's degrees of freedom.
Parameters
----------
velocities : float or sequence of float
A target velocity value to set on all degrees of freedom, or a list
containing one such value for ea... |
def max_forces(self, max_forces):
'''Set the maximum forces for this object's degrees of freedom.
Parameters
----------
max_forces : float or sequence of float
A maximum force value to set on all degrees of freedom, or a list
containing one such value for each de... |
def erps(self, erps):
'''Set the ERP values for this object's degrees of freedom.
Parameters
----------
erps : float or sequence of float
An ERP value to set on all degrees of freedom, or a list
containing one such value for each degree of freedom.
'''
... |
def cfms(self, cfms):
'''Set the CFM values for this object's degrees of freedom.
Parameters
----------
cfms : float or sequence of float
A CFM value to set on all degrees of freedom, or a list
containing one such value for each degree of freedom.
'''
... |
def stop_cfms(self, stop_cfms):
'''Set the CFM values for this object's DOF limits.
Parameters
----------
stop_cfms : float or sequence of float
A CFM value to set on all degrees of freedom limits, or a list
containing one such value for each degree of freedom li... |
def stop_erps(self, stop_erps):
'''Set the ERP values for this object's DOF limits.
Parameters
----------
stop_erps : float or sequence of float
An ERP value to set on all degrees of freedom limits, or a list
containing one such value for each degree of freedom l... |
def axes(self, axes):
'''Set the axes for this object's degrees of freedom.
Parameters
----------
axes : list of axis parameters
A list of axis values to set. This list must have the same number of
elements as the degrees of freedom of the underlying ODE object.
... |
def axes(self, axes):
'''Set the linear axis of displacement for this joint.
Parameters
----------
axes : list containing one 3-tuple of floats
A list of the axes for this joint. For a slider joint, which has one
degree of freedom, this must contain one 3-tuple s... |
def axes(self, axes):
'''Set the angular axis of rotation for this joint.
Parameters
----------
axes : list containing one 3-tuple of floats
A list of the axes for this joint. For a hinge joint, which has one
degree of freedom, this must contain one 3-tuple speci... |
def axes(self):
'''A list of axes of rotation for this joint.'''
return [np.array(self.ode_obj.getAxis1()),
np.array(self.ode_obj.getAxis2())] |
def create_body(self, shape, name=None, **kwargs):
'''Create a new body.
Parameters
----------
shape : str
The "shape" of the body to be created. This should name a type of
body object, e.g., "box" or "cap".
name : str, optional
The name to us... |
def join(self, shape, body_a, body_b=None, name=None, **kwargs):
'''Create a new joint that connects two bodies together.
Parameters
----------
shape : str
The "shape" of the joint to use for joining together two bodies.
This should name a type of joint, such as ... |
def move_next_to(self, body_a, body_b, offset_a, offset_b):
'''Move one body to be near another one.
After moving, the location described by ``offset_a`` on ``body_a`` will
be coincident with the location described by ``offset_b`` on ``body_b``.
Parameters
----------
bo... |
def set_body_states(self, states):
'''Set the states of some bodies in the world.
Parameters
----------
states : sequence of states
A complete state tuple for one or more bodies in the world. See
:func:`get_body_states`.
'''
for state in states:
... |
def step(self, substeps=2):
'''Step the world forward by one frame.
Parameters
----------
substeps : int, optional
Split the step into this many sub-steps. This helps to prevent the
time delta for an update from being too large.
'''
self.frame_no ... |
def on_key_press(self, key, modifiers, keymap):
'''Handle an otherwise unhandled keypress event (from a GUI).'''
if key == keymap.ENTER:
self.reset()
return True |
def are_connected(self, body_a, body_b):
'''Determine whether the given bodies are currently connected.
Parameters
----------
body_a : str or :class:`Body`
One body to test for connectedness. If this is a string, it is
treated as the name of a body to look up.
... |
def on_collision(self, args, geom_a, geom_b):
'''Callback function for the collide() method.
Parameters
----------
args : None
Arguments passed when the callback was registered. Not used.
geom_a : ODE geometry
The geometry object of one of the bodies that... |
def record_iterator(xml):
"""
Iterate over all ``<record>`` tags in `xml`.
Args:
xml (str/file): Input string with XML. UTF-8 is prefered encoding,
unicode should be ok.
Yields:
MARCXMLRecord: For each corresponding ``<record>``.
"""
# handle file-like o... |
def profileit(field='cumulative'):
"""
测试函数运行消耗情况
:param field: 输出内容排序方式。
可选参数为 "stdname", "calls", "time", "cumulative"
"""
def wrapper(func):
@wraps(func)
def inner(*args, **kwargs):
pro = Profile()
pro.runcall(func, *args, **kwargs)
sta... |
def parse(source, world, jointgroup=None, density=1000, color=None):
'''Load and parse a source file.
Parameters
----------
source : file
A file-like object that contains text information describing bodies and
joints to add to the world.
world : :class:`pagoda.physics.World`
... |
def parse_asf(source, world, jointgroup=None, density=1000, color=None):
'''Load and parse a source file.
Parameters
----------
source : file
A file-like object that contains text information describing bodies and
joints to add to the world.
world : :class:`pagoda.physics.World`
... |
def parse_amc(source):
'''Parse an AMC motion capture data file.
Parameters
----------
source : file
A file-like object that contains AMC motion capture text.
Yields
------
frame : dict
Yields a series of motion capture frames. Each frame is a dictionary
that maps a... |
def create_bodies(self, translate=(0, 1, 0), size=0.1):
'''Traverse the bone hierarchy and create physics bodies.'''
stack = [('root', 0, self.root['position'] + translate)]
while stack:
name, depth, end = stack.pop()
for child in self.hierarchy.get(name, ()):
... |
def create_joints(self):
'''Traverse the bone hierarchy and create physics joints.'''
stack = ['root']
while stack:
parent = stack.pop()
for child in self.hierarchy.get(parent, ()):
stack.append(child)
if parent not in self.bones:
... |
def format_cookies(path):
"""
将 cookie 字符串转化为字典
:param path: cookies 文件路径
:return: cookies 字典
"""
with open(path, 'r') as f:
_cookies = {}
for row in f.read().split(';'):
k, v = row.strip().split('=', 1)
_cookies[k] = v
return _cookies |
def delete_empty_dir(directory):
"""
删除空目录
:param directory: 目录路径
"""
if os.path.exists(directory):
if os.path.isdir(directory):
for d in os.listdir(directory):
path = os.path.join(directory, d)
if os.path.isdir(path):
delete_e... |
def _parse_corporations(self, datafield, subfield, roles=["any"]):
"""
Parse informations about corporations from given field identified
by `datafield` parameter.
Args:
datafield (str): MARC field ID ("``110``", "``610``", etc..)
subfield (str): MARC subfield ID... |
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