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def get_crypto_quote(symbol, info=None):
"""Gets information about a crypto including low price, high price, and open price
:param symbol: The crypto ticker.
:type symbol: str
:param info: Will filter the results to have a list of the values that correspond to key that matches info.
:type info: Optional[str]
:returns: [dict] If info parameter is left as None then the list will contain a dictionary of key/value pairs for each ticker. \
Otherwise, it will be a list of strings where the strings are the values of the key that corresponds to info.
:Dictionary Keys: * asset_currency
* display_only
* id
* max_order_size
* min_order_size
* min_order_price_increment
* min_order_quantity_increment
* name
* quote_currency
* symbol
* tradability
"""
id = get_crypto_info(symbol, info='id')
url = urls.crypto_quote(id)
data = helper.request_get(url)
return(helper.filter(data, info)) | db10e7493ef6e98ad0876d30357c6b5be8269776 | 7,800 |
from .tools.forms import digest as digest_forms
from .multitool import convert
from .protonation import add_missing_hydrogens
from .model_loops import add_loop
def fix(item, missing_atoms=True, missing_residues=True, nonstandard_residues=True,
missing_terminals=True, missing_loops=False, missing_hydrogens=True,
pH=7.4, to_form=None, engine_fix='PDBFixer', engine_hydrogens='PDBFixer',
engine_loops='Modeller', verbose=False):
"""fix_pdb_structure(item, missing_atoms=True, missing_residues=True, nonstandard_residues=True,
missing_terminals=True, missing_loops=False, missing_hydrogens=True,
pH=7.4, to_form=None, engine_fix='PDBFixer', engine_hydrogens='PDBFixer',
engine_loops='Modeller', verbose=False):
Fixing missing atoms, residues, terminals or loops in the molecular model coming from a pdb file.
This method fixes the possible missing atoms, residues, loops or terminals in a molecular
model. The result is a new molecular model, in the desired supported form, with those elements
fixed.
Parameters
----------
item: molecular model
Molecular model in any supported form by MolSysMT.
arg2: type, default='value'
Paragraph with explanation.
Returns
-------
object: type
Paragraph with explanation.
Examples
--------
See Also
--------
:func:`molsysmt.load`
Notes
-----
Todo
----
Warning
-------
The method has being tested with the following input forms: pdbid, pdbfile, pdbfixer.PDBFixer
and openmm.Modeller.
"""
form_in, form_out = digest_forms(item, to_form)
engine_fix = digest_engines(engine_fix)
engine_hydrogens = digest_engines(engine_hydrogens)
engine_loops = digest_engines(engine_loops)
tmp_item = None
if engine_fix=='PDBFixer':
tmp_item = convert(item, to_form='pdbfixer.PDBFixer')
if missing_residues:
tmp_item.findMissingResidues()
if missing_atoms:
tmp_item.findMissingAtoms()
if nonstandard_residues:
tmp_item.findNonstandardResidues()
if verbose:
print('Missing residues:', tmp_item.missingResidues)
print('Non standard residues:', tmp_item.nonstandardResidues)
print('Missing atoms', tmp_item.missingAtoms)
print('Missing terminals:', tmp_item.missingTerminals)
tmp_item.addMissingAtoms()
if verbose:
print('Missing residues or atoms reported fixed.')
if missing_hydrogens:
tmp_item = add_missing_hydrogens(tmp_item, pH=pH, engine=engine_hydrogens, verbose=verbose)
if missing_loops:
tmp_item = add_loop(tmp_item, engine=engine_loops)
tmp_item = convert(tmp_item, to_form=form_out)
return tmp_item | 10bc29a4006e8bc1b18fba126dde7152672b7a24 | 7,801 |
def data_split(*args, **kwargs):
"""A function to split a dataset into train, test, and optionally
validation datasets.
**Arguments**
- ***args** : arbitrary _numpy.ndarray_ datasets
- An arbitrary number of datasets, each required to have
the same number of elements, as numpy arrays.
- **train** : {_int_, _float_}
- If a float, the fraction of elements to include in the training
set. If an integer, the number of elements to include in the
training set. The value `-1` is special and means include the
remaining part of the dataset in the training dataset after
the test and (optionally) val parts have been removed
- **val** : {_int_, _float_}
- If a float, the fraction of elements to include in the validation
set. If an integer, the number of elements to include in the
validation set. The value `0` is special and means do not form
a validation set.
- **test** : {_int_, _float_}
- If a float, the fraction of elements to include in the test
set. If an integer, the number of elements to include in the
test set.
- **shuffle** : _bool_
- A flag to control whether the dataset is shuffled prior to
being split into parts.
**Returns**
- _list_
- A list of the split datasets in train, [val], test order. If
datasets `X`, `Y`, and `Z` were given as `args` (and assuming a
non-zero `val`), then [`X_train`, `X_val`, `X_test`, `Y_train`,
`Y_val`, `Y_test`, `Z_train`, `Z_val`, `Z_test`] will be returned.
"""
# handle valid kwargs
train, val, test = kwargs.pop('train', -1), kwargs.pop('val', 0.0), kwargs.pop('test', 0.1)
shuffle = kwargs.pop('shuffle', True)
if len(kwargs):
raise TypeError('following kwargs are invalid: {}'.format(kwargs))
# validity checks
if len(args) == 0:
raise RuntimeError('Need to pass at least one argument to data_split')
# check for consistent length
n_samples = len(args[0])
for arg in args[1:]:
assert len(arg) == n_samples, 'args to data_split have different length'
# determine numbers
num_val = int(n_samples*val) if val<=1 else val
num_test = int(n_samples*test) if test <=1 else test
num_train = n_samples - num_val - num_test if train==-1 else (int(n_samples*train) if train<=1 else train)
assert num_train >= 0, 'bad parameters: negative num_train'
assert num_train + num_val + num_test <= n_samples, 'too few samples for requested data split'
# calculate masks
perm = np.random.permutation(n_samples) if shuffle else np.arange(n_samples)
train_mask = perm[:num_train]
val_mask = perm[-num_val:]
test_mask = perm[num_train:num_train+num_test]
# apply masks
masks = [train_mask, val_mask, test_mask] if num_val > 0 else [train_mask, test_mask]
# return list of new datasets
return [arg[mask] for arg in args for mask in masks] | e2ad6e52d2868020cc0bcb960533348a1f93ed31 | 7,802 |
def compare(isamAppliance1, isamAppliance2):
"""
Compare Policy Sets between two appliances
"""
ret_obj1 = get_all(isamAppliance1)
ret_obj2 = get_all(isamAppliance2)
for obj in ret_obj1['data']:
del obj['id']
del obj['userlastmodified']
del obj['lastmodified']
del obj['datecreated']
obj['policies'] = _convert_policy_id_to_name(isamAppliance1, obj['policies'])
for obj in ret_obj2['data']:
del obj['id']
del obj['userlastmodified']
del obj['lastmodified']
del obj['datecreated']
obj['policies'] = _convert_policy_id_to_name(isamAppliance2, obj['policies'])
return tools.json_compare(ret_obj1, ret_obj2,
deleted_keys=['id', 'userlastmodified', 'lastmodified', 'datecreated']) | a727eac5efb4e117413d70191e7a74921e3ac284 | 7,803 |
def capacity(quantity, channel, gamma, dim, basis, eps, **kwargs):
"""
Runs the Blahut-Arimoto algorithm to compute the capacity given by
'quantity' (which can be 'h', 'tc', 'coh' or 'qmi' taking the channel,
gamma, dim, basis and tolerance (eps) as inputs).
With the optional keyword arguments 'plot' (Boolean), it outputs a plot
showing how the calculated value changes with the number of iterations.
With the optional keyword arguments 'latexplot' (Boolean), the plot uses
latex in the labels
"""
#to store the calculated values
itern = []
value = []
#initialization
rhoa = DensityMatrix(np.diag((1/dim)*np.ones((1,dim))[0]))
#Blahut-Arimoto algorithm iteration
for iterator in range(int(gamma*np.log2(dim)/eps)):
# for iterator in range(1):
itern.append(iterator)
sigmab = rhoa
rhoa = linalg.expm(np.log(2)*(linalg.logm(sigmab.mat)/np.log(2)
+ (1/gamma)*(F(quantity, sigmab, basis, channel).mat)))
rhoa = DensityMatrix(rhoa/np.trace(rhoa))
value.append(J(quantity, rhoa, rhoa, gamma, basis, channel))
#Plotting
if kwargs['plot'] is True:
# if kwargs['latexplot'] is True:
# plt.rc('text', usetex=True)
# plt.rc('font', family='serif')
fig, ax = plt.subplots()
plt.plot(itern, value,
marker = '.',
markersize='7',
label = r'Capacity value vs iteration'
)
plt.xlabel(r'Number of iterations', fontsize = '14')
plt.ylabel(r'Value of capacity', fontsize = '14')
plt.xticks(fontsize = '8')
plt.yticks(fontsize = '8')
plt.grid(True)
plt.show()
return J(quantity, rhoa, rhoa, gamma, basis, channel) | 6624d045fb953d536b082f183a6c1536dcd9ca50 | 7,804 |
def get_Teq_from_L(L: ArrayLike, d: ArrayLike, A: ArrayLike) -> np.ndarray:
"""Calculates the equilibrium temperature of a planet
given the stellar luminosity L, planetary semi-major axis d
and surface albedo A:
Args:
L (ArrayLike): Stellar luminosity in erg/s.
d (ArrayLike): Planetary semi-major axis in cm.
A (ArrayLike): Planetary albedo.
Returns:
np.ndarray: The planetary equilibrium temperature in K.
"""
return ((L * (1 - A)) / (16 * sigma_b * np.pi * d ** 2)) ** 0.25 | 9f140c554059074d9569e48ae2f971bc430e2fba | 7,805 |
from typing import Type
def lookup_container_plugin_by_type(container: IContainer, plugin_type: Type[ContainerResolutionPlugin]):
"""
Given a container, finds the first plugin that is an instance of the specified type.
:param container: The container to perform the lookup on.
:param plugin_type: The type of the plugin to find.
:return: The first instance of ``plugin_type`` in ``container.plugins``.
"""
return next(
plugin
for plugin
in container.plugins
if isinstance(plugin, plugin_type)
) | b41cfc2e1e1328a8f54e938b7944d3f16924d3cf | 7,806 |
from scipy.ndimage import shift
def shift_map_longitude(mapdata, lonshift, spline_order=1):
""" Simple shift of the map by wrapping it around the edges
Internally uses scipy's ndimage.shift with spline interpolation order as
requested for interpolation
Parameters
----------
mapdata : 2D Numpy array
A map with the second dimension the longutide stretched fully along the
map
lonshift : float
A simple float representing the longitude shift of the array
spline_order: int [1, 5]
Returns
-------
A shifted map
"""
# Constant
degrees = 360.0
# Check the map and compute the relative shift
assert len(mapdata.shape) == 2, "Only for 2D maps"
assert mapdata.shape[1] > 1, "Map has only one longitudinal coordinate"
n = (mapdata.shape[1] - 1)
x = degrees * lonshift / n # The number of pixels to shift
# Use scipy for the rest
mapdata_shift = shift(mapdata, [0, x], mode='wrap', order=spline_order)
return mapdata_shift | 72373800f3a53785989cc2e2da4dab08d0976b30 | 7,807 |
def aalogoheights(aahistObj, N=20):
"""For a objhist of AA frequencies, compute the heights
of each AA for a logo plot"""
aahistObj = deepcopy(aahistObj)
keys = list(aahistObj.keys())
for aa in BADAA:
if aa in keys:
dummy = aahistObj.pop(aa)
keys = [aa for aa in aahistObj.sortedKeys(reverse=False)]
freq = aahistObj.freq()
p = np.array([freq[k] for k in keys])
#err = (1/np.log(2))*((N-1) / (2*aahistObj.sum()))
#totEntropy = np.log2(N)-((-p*np.log2(p)).sum() + err)
totEntropy = np.log2(N)-((-p*np.log2(p)).sum())
heights = p * totEntropy
return keys, heights | 8020605d6c2a9a618e5faed57ba7af5e1315dfec | 7,808 |
def cmdline_opts( request ):
"""PyMTL options parsed from pytest commandline options."""
opts = _parse_opts_from_request( request )
# If a fixture is used by a test class, this seems to be the only
# way to retrieve the fixture value.
# https://stackoverflow.com/a/37761165/13190001
if request.cls is not None:
request.cls.cmdline_opts = opts
return opts | 8b3af4ab15a1a5a11a633fa322e4484f2d8257bc | 7,809 |
def replace(index, ndim, axes, rindices):
"""Replace indexing for a specified dimension
Args:
index(index): object used in slicing
ndim(num): number of dimensions
axes(list): dimension to be replaced
rindex(list): new indexing for this dimensions
Returns:
index
"""
index2 = list(expand(index, ndim))
for axis, rindex in zip(axes, rindices):
axis = axisindex(index2, axis, ndim)
index2[axis] = rindex
return tuple(index2) | 3a8c9ac8b9bf12a5d416e422ddfb0f4458cf9417 | 7,810 |
import select
def _closed(sock):
"""Return True if we know socket has been closed, False otherwise.
"""
try:
rd, _, _ = select([sock], [], [], 0)
# Any exception here is equally bad (select.error, ValueError, etc.).
except:
return True
return len(rd) > 0 | 4de2aee7743cac8e660ab01f2920935faf0ee3e9 | 7,811 |
def get_forest_connection(device_name: str, seed=None):
"""Get a connection to a forest backend
Args:
device_name: the device to connect to
Returns:
A connection to either a pyquil simulator or a QPU
"""
if device_name == "wavefunction-simulator":
return WavefunctionSimulator(random_seed=seed)
else:
return get_qc(device_name) | 291c92508b097908fa86fb957b42d73066d65ebd | 7,812 |
def get_slack_colour(level):
"""Return Slack colour value based on log level."""
level = level.upper()
colours = {
"CRITICAL": "ff0000",
"ERROR": "ff9933",
"WARNING": "ffcc00",
"INFO": "33ccff",
"DEBUG": "good"
}
return colours.get(level, "good") | 5a75bc103361b3724921d2b9c03c32f63b9b8115 | 7,813 |
def add_suffix(path, suffix=""):
"""Adds a suffix to a filename *path*"""
return join(dirname(path), basename(path, ext=False) + suffix + extname(path)) | dd95548e06e29c91f0a35c5dd0979889ab945076 | 7,814 |
def MdAE_np(preds, labels):
"""
Median Absolute Error
:param preds:
:param labels:
:return:
"""
preds = np.reshape(preds, [-1])
labels = np.reshape(labels, [-1])
return np.median(np.abs(preds - labels)) | 4a725eb35e5f7bd1f77b8433b7ea7393bbdae92e | 7,815 |
from botocore.exceptions import ClientError, BotoCoreError
async def s3_fetch_object(url, s3, range=None, **kw):
""" returns object with
On success:
.url = url
.data = bytes
.last_modified -- last modified timestamp
.range = None | (in,out)
.error = None
On failure:
.url = url
.data = None
.last_modified = None
.range = None | (in, out)
.error = str| botocore.Exception class
"""
def result(data=None, last_modified=None, error=None):
return SimpleNamespace(url=url, data=data, error=error, last_modified=last_modified, range=range)
bucket, key = s3_url_parse(url)
extra_args = dict(**kw)
if range is not None:
try:
extra_args['Range'] = s3_fmt_range(range)
except Exception:
return result(error='Bad range passed in: ' + str(range))
try:
obj = await s3.get_object(Bucket=bucket, Key=key, **extra_args)
stream = obj.get('Body', None)
if stream is None:
return result(error='Missing Body in response')
async with stream:
data = await stream.read()
except (ClientError, BotoCoreError) as e:
return result(error=e)
except Exception as e:
return result(error="Some Error: " + str(e))
last_modified = obj.get('LastModified', None)
return result(data=data, last_modified=last_modified) | 0da8fadb248abe8c4c23e75367b3ddc884df71d3 | 7,816 |
from . import darwin
from . import linux
from . import windows
import platform
def mss(**kwargs):
# type: (Any) -> MSSMixin
""" Factory returning a proper MSS class instance.
It detects the plateform we are running on
and choose the most adapted mss_class to take
screenshots.
It then proxies its arguments to the class for
instantiation.
"""
# pylint: disable=import-outside-toplevel
os_ = platform.system().lower()
if os_ == "darwin":
return darwin.MSS(**kwargs)
if os_ == "linux":
return linux.MSS(**kwargs)
if os_ == "windows":
return windows.MSS(**kwargs)
raise ScreenShotError("System {!r} not (yet?) implemented.".format(os_)) | 057916bf6b13bd6089ccb6f46b1a2ceb583d5bf8 | 7,817 |
def reshape_fps(X):
"""Reshape 4D fingerprint data to 2D
If X is already 2D, do nothing.
Returns: reshaped X
"""
if len(X.shape) == 4:
num_factors = X.shape[3]
num_fps = np.prod(X.shape[:3])
X.shape = (num_fps,num_factors)
else:
num_factors = X.shape[1]
num_fps = X.shape[0]
return X | ab2cd286194dd6d35fb27a540378a132d25db575 | 7,818 |
def df_fc_overlap_2():
"""Scenario case with 2 fragments overlapping, bound to a common fragment."""
mol = Chem.MolFromSmiles('NC1CC(CCC1O)C1CCC1')
return DataFrame([
['mol_fc_overlap_2', 'XXX', 'O1', 0, 'O1:0', 'O2', 0, 'O2:0', 'ffo', 'fusion', 'false_positive', 'overlap', (7, 6, 5, 4, 3, 2, 1), (0, 1, 2, 3, 4, 5, 6), 12, mol, mol_o1, mol_o2, 'O1:0@1,2,3,4,5,6[ffo]O2:0@1,2,3,4,5,6'],
['mol_fc_overlap_2', 'XXX', 'O1', 0, 'O1:0', 'O3', 0, 'O3:0', 'cm', 'connection', 'monopodal', '', (7, 6, 5, 4, 3, 2, 1), (8, 9, 10, 11), 12, mol, mol_o1, mol_o3, 'O1:0@4[cm]O3:0@0'],
['mol_fc_overlap_2', 'XXX', 'O2', 0, 'O2:0', 'O3', 0, 'O3:0', 'cm', 'connection', 'monopodal', '', (0, 1, 2, 3, 4, 5, 6), (8, 9, 10, 11), 12, mol, mol_o2, mol_o3, 'O2:0@3[cm]O3:0@0'],
], columns=['idm', 'inchikey', 'idf1', 'idxf1', 'fid1', 'idf2', 'idxf2', 'fid2', 'fcc', 'category', 'type', 'subtype', '_aidxf1', '_aidxf2', 'hac', 'mol', 'mol_frag_1', 'mol_frag_2', 'fc']) | 7ee533aa1c7bb821ae6a73a27d39d6a7e796087f | 7,819 |
def show_toolbar(request):
"""Determines whether debug toolbar should be shown for the request.
Requires settings.DEBUG=True, 'debug_toolbar' GET param present,
and request ip in settings.INTERNAL_IPS.
Args:
request: HttpRequest object.
Returns:
Boolean.
"""
if ('debug_toolbar' not in request.GET and
'/__debug__/' not in request.path):
return False
return middleware.show_toolbar(request) | 7a3fec348f5d37adcafd29d5cdd757e5e8de6cad | 7,820 |
from datetime import datetime
def strfnow(fmt=HUMAN_DATETIME):
"""
Returns a string representation of the current timestamp
"""
return datetime.now(tzlocal()).strftime(fmt) | 50fe38d37dfe8581f6cfa07aaaeb588a2e6e72a9 | 7,821 |
def tag_to_dict(node):
"""Assume tag has one layer of children, each of which is text, e.g.
<medalline>
<rank>1</rank>
<organization>USA</organization>
<gold>13</gold>
<silver>10</silver>
<bronze>9</bronze>
<total>32</total>
</medalline>
"""
d = {}
for child in node:
d[child.tag] = child.text
return d | e2131e070dce8620630e994cc25578a9a8438c64 | 7,822 |
from typing import Any
def compute_contact_centroid(molecular_complex: Any,
cutoff: float = 4.5) -> np.ndarray:
"""Computes the (x,y,z) centroid of the contact regions of this molecular complex.
For a molecular complex, it's necessary for various featurizations
that compute voxel grids to find a reasonable center for the
voxelization. This function computes the centroid of all the contact
atoms, defined as an atom that's within `cutoff` Angstroms of an
atom from a different molecule.
Parameters
----------
molecular_complex: Object
A representation of a molecular complex, produced by
`rdkit_util.load_complex`.
cutoff: float, optional
The distance in Angstroms considered for computing contacts.
"""
fragments = reduce_molecular_complex_to_contacts(molecular_complex, cutoff)
coords = [frag[0] for frag in fragments]
contact_coords = merge_molecules_xyz(coords)
centroid = np.mean(contact_coords, axis=0)
return (centroid) | 53b83e6814f6f59645d84c36de458952918123fc | 7,823 |
def general_operator_gamma_norm(matrix, gamma, max_j, max_q):
""" Returns the gamma operator norm of matrix, summing up to max_j and
considering the sup up to max_q. Assumed that matrix is a function
accepting two arguments i,j and not an array () for efficiency.
"""
max_j_sum = -1
q = 1
while(q < max_q):
temp_j_sum = nsum(lambda j: fprod([power(q, gamma), power(j, -gamma),
fabs(matrix(q, j))]), [1, max_j])
max_j_sum = temp_j_sum if temp_j_sum > max_j_sum else max_j_sum
q += 1
return max_j_sum | 56993d0f406af3cead83e662aecb19d9082878fa | 7,824 |
def crop_image_single(img, device):
"""
Implementation of the MTCNN network to crop single image to only show the face as shown in the
facenet_pytorch doc:
https://github.com/timesler/facenet-pytorch/blob/master/examples/infer.ipynb
:param device: pytorch device
:param img: single image to be cropped
:return: cropped image
"""
model = MTCNN(image_size=160, margin=0, min_face_size=20, thresholds=[0.6, 0.7, 0.7],
factor=0.709, post_process=False, device=device)
x_aligned = model(img)
return x_aligned | b2755a1bf464dca74cbfc32a5bf5c61f106758ae | 7,825 |
def tf2zpk(b, a):
"""Return zero, pole, gain (z,p,k) representation from a numerator,
denominator representation of a linear filter.
Parameters
----------
b : ndarray
Numerator polynomial.
a : ndarray
Denominator polynomial.
Returns
-------
z : ndarray
Zeros of the transfer function.
p : ndarray
Poles of the transfer function.
k : float
System gain.
Notes
-----
If some values of ``b`` are too close to 0, they are removed. In that case,
a BadCoefficients warning is emitted.
"""
b, a = normalize(b, a)
b = (b + 0.0) / a[0]
a = (a + 0.0) / a[0]
k = b[0]
b /= b[0]
z = roots(b)
p = roots(a)
return z, p, k | 3d83d4053a89be19c3738650a11216d38845d6a6 | 7,826 |
def gpiod_line_is_free(line: gpiod_line) -> bool:
"""
@brief Check if the calling user has neither requested ownership of this
line nor configured any event notifications.
@param line: GPIO line object.
@return True if given line is free, false otherwise.
"""
return line.state == _LINE_FREE | 939320d0737406789bbb81bc9c73023dff71fb51 | 7,827 |
import random
def train_step(optimizer, inputs, learning_rate_fn, dropout_rng=None):
"""Perform a single training step."""
weights = jnp.where(inputs > 0, 1, 0)
# We handle PRNG splitting inside the top pmap, rather
# than handling it outside in the training loop - doing the
# latter can add some stalls to the devices.
dropout_rng, new_dropout_rng = random.split(dropout_rng)
def loss_fn(model):
"""Loss function used for training."""
with nn.stochastic(dropout_rng):
logits = model(inputs, train=True)
loss, weight_sum = compute_weighted_cross_entropy(logits, inputs, weights)
mean_loss = loss / weight_sum
return mean_loss, logits
step = optimizer.state.step
lr = learning_rate_fn(step)
grad_fn = jax.value_and_grad(loss_fn, has_aux=True)
(_, logits), grad = grad_fn(optimizer.target)
grad = jax.lax.pmean(grad, 'batch')
new_optimizer = optimizer.apply_gradient(grad, learning_rate=lr)
metrics = compute_metrics(logits, inputs, weights)
metrics['learning_rate'] = lr
return new_optimizer, metrics, new_dropout_rng | 2dae63fcfb9fc5bc059b084bf748886d3d257c4c | 7,828 |
def doublet_line_polar_u(rcp,zcp,dmz_dz, bSelfInd=False):
"""
Velocity field induced by a semi-infinite doublet line (on the z axis) of intensity `dmz_dz`
Control points defined by polar coordinates `rcp` and `zcp`.
\int 1/(r^2 + (z-x)^2 )^(3/2) dx
\int 1/(r^2 + (z-x)^2 )^(5/2) dx
"""
if np.any(rcp<0):
raise Exception('Script meant for positive r')
r=np.asarray(rcp)
z=np.asarray(zcp)
# Vectorial "if" statements to isolate singular regions of the domain
bZ0 = np.abs(z)<1e-8
bR0 = np.abs(r)<1e-8
bZ0R0 = np.logical_and(bZ0,bR0)
bZ0Rp = np.logical_and(bZ0, np.abs(r)>1e-8)
bR0Zp = np.logical_and(bR0, z>1e-8)
bR0Zm = np.logical_and(bR0, z<-1e-8)
bOK = np.logical_and(~bZ0,~bR0)
uz=np.zeros(r.shape)
ur=np.zeros(r.shape)
norm2 = r**2+z**2
uz[bOK] = dmz_dz/(4*np.pi) * 1/r[bOK]**2 * ( z[bOK]**3/(norm2[bOK])**(3/2) - z[bOK]/(norm2[bOK])**(1/2) )
uz[bZ0Rp] = 0
uz[bR0Zm] = dmz_dz/(4*np.pi) * 1/norm2[bR0Zm]
#uz[bR0Zp] = dmz_dz/(4*np.pi) * 1/norm2[bR0Zp] #<<< No singularity there, but we force it to 0
ur[bOK] =-dmz_dz/(4*np.pi) * r[bOK] * 1/(norm2[bOK] )**(3/2)
ur[bZ0Rp] =-dmz_dz/(4*np.pi) * r[bZ0Rp] * 1/(norm2[bZ0Rp])**(3/2)
ur[bR0Zm] = 0
ur[bR0Zp] = 0
ur[bZ0R0] = 0
uz[bZ0R0] = 0
return ur, uz | 9dcee49192273a6482b269120af01683a11916b6 | 7,829 |
def paginate(text: str):
"""Simple generator that paginates text."""
last = 0
pages = []
for curr in range(0, len(text)):
if curr % 1980 == 0:
pages.append(text[last:curr])
last = curr
appd_index = curr
if appd_index != len(text) - 1:
pages.append(text[last:curr])
return list(filter(lambda a: a != '', pages)) | f40b97e0f221b4c6afffcc4dd707daf48685d04a | 7,830 |
def get_batch_copy(vocab_size, batch_size, seq_len):
"""Generates random data for copying."""
batch = np.random.choice(
vocab_size - 1, size=[batch_size, seq_len // 2 - 1]) + 1
batch = np.concatenate([np.zeros([batch_size, 1], dtype=int), batch], axis=1)
batch = np.concatenate([batch] * 2, axis=1)
batch_mask = np.concatenate([
np.zeros([batch_size, seq_len // 2], dtype=bool),
np.ones([batch_size, seq_len // 2], dtype=bool)
],
axis=1)
return batch, batch_mask | f1b6092393a0b8e7cb6c2a2ae191c29d28d2d89f | 7,831 |
import pandas
def buildCompareDFs(strTodayFileName):
"""read in and return today's CSV as DF, determine appropriate old CSV as DF, and the old file name for use later"""
# get today's file
dfTodaysCards = pandas.read_csv(
DATA_DIR_NAME + strTodayFileName, dtype={'Card Number': object})
dfTodaysCards = cleanCardDataFrame(dfTodaysCards)
# getting older file is a bit trickier, check the run log, find the most recent run, find the old file used, get the next recent old file to compare with
dictRunLog = readRunLog()
strOldFileName = determineCompareFile(dictRunLog)
print("ToCompareAgainst: " + strOldFileName)
dfOldCards = pandas.read_csv(
DATA_DIR_NAME + strOldFileName, dtype={'Card Number': object})
dfOldCards = cleanCardDataFrame(dfOldCards)
dfOldCards = dfOldCards.rename(
index=str, columns={"Count": "OldCount", "Price": "OldPrice"})
return dfTodaysCards, dfOldCards, strOldFileName | 488afcd0704b9c73a83cab3bd898703d290ac557 | 7,832 |
def _vj_stat(v = None, j = None, freq_type = 'vj_occur_freq', ts = None):
"""
Return estimate of a single v-gene, j-gene, or vj-gene-pairings frequency
specified < v > and <j> argumens , given a tcrsamper instance < ts >
Parameters
----------
v : str
j : str
e.g.,
freq_type : str
'vj_occur_freq', 'vj_freq', 'v_occur_freq', 'v_freq', 'j_occur_freq', 'j_freq'
df : pd.DataFrame
DataFrame containing v and j gene names
ts : tcrsampler.sampler.TCRsampler
sampler instance
Example
-------
>>> import pandas as pd
>>> import os
>>> from tcrsampler.sampler import TCRsampler
>>> from tcrregex.vj_diff import *
>>> t = TCRsampler()
>>> fn = os.path.join("tcrregex", "test_files", 'britanova_chord_blood_sample_5000.csv' )
>>> t.ref_df = pd.read_csv(fn)
>>> t.build_background()
>>> _vj_stat(v = 'TRBV20-1*01' , j ='TRBJ2-1*01', ts = t, freq_type = 'vj_occur_freq')
0.014802960592118424
>>> _vj_stat(v = 'TRBV20-1*01' , ts = t, freq_type = 'v_occur_freq')
0.060012002400480095
>>> _vj_stat(j = 'TRBJ2-1*01', ts = t, freq_type = 'j_occur_freq')
0.272254450890178
"""
if ts is None:
raise ValueError("._vj_stat requires < ts > be a TCRsampler instance")
if v is None and j is None:
raise ValueError("Niether a v- nor j-gene was supplied to ._vj_stat ; atleast one must be provided")
if v is None:
tp = j
assert freq_type in ['j_freq', 'j_occur_freq']
elif j is None:
tp = v
assert freq_type in ['v_freq', 'v_occur_freq']
else:
tp = (v,j)
assert freq_type in ['vj_freq', 'vj_occur_freq']
return ts.__dict__[freq_type][tp] | 99228d17714c5ba403071ad0251f8642bc3148e6 | 7,833 |
def __cvx_eda(y, delta, tau0=2., tau1=0.7, delta_knot=10., alpha=8e-4, gamma=1e-2, solver=None,
options={'reltol': 1e-9, 'show_progress': False}):
"""
CVXEDA Convex optimization approach to electrodermal activity processing
This function implements the cvxEDA algorithm described in "cvxEDA: a
Convex Optimization Approach to Electrodermal Activity Processing"
(http://dx.doi.org/10.1109/TBME.2015.2474131, also available from the
authors' homepages).
Arguments:
y: observed EDA signal (we recommend normalizing it: y = zscore(y))
delta: sampling interval (in seconds) of y
tau0: slow time constant of the Bateman function
tau1: fast time constant of the Bateman function
delta_knot: time between knots of the tonic spline function
alpha: penalization for the sparse SMNA driver
gamma: penalization for the tonic spline coefficients
solver: sparse QP solver to be used, see cvxopt.solvers.qp
options: solver options, see: http://cvxopt.org/userguide/coneprog.html#algorithm-parameters
Returns (see paper for details):
r: phasic component
p: sparse SMNA driver of phasic component
t: tonic component
l: coefficients of tonic spline
d: offset and slope of the linear drift term
e: model residuals
obj: value of objective function being minimized (eq 15 of paper)
"""
n = len(y)
y = cvx.matrix(y)
# bateman ARMA model
a1 = 1. / min(tau1, tau0) # a1 > a0
a0 = 1. / max(tau1, tau0)
ar = np.array([(a1 * delta + 2.) * (a0 * delta + 2.), 2. * a1 * a0 * delta ** 2 - 8.,
(a1 * delta - 2.) * (a0 * delta - 2.)]) / ((a1 - a0) * delta ** 2)
ma = np.array([1., 2., 1.])
# matrices for ARMA model
i = np.arange(2, n)
A = cvx.spmatrix(np.tile(ar, (n - 2, 1)), np.c_[i, i, i], np.c_[i, i - 1, i - 2], (n, n))
M = cvx.spmatrix(np.tile(ma, (n - 2, 1)), np.c_[i, i, i], np.c_[i, i - 1, i - 2], (n, n))
# spline
delta_knot_s = int(round(delta_knot / delta))
spl = np.r_[np.arange(1., delta_knot_s), np.arange(delta_knot_s, 0., -1.)] # order 1
spl = np.convolve(spl, spl, 'full')
spl /= max(spl)
# matrix of spline regressors
i = np.c_[np.arange(-(len(spl) // 2), (len(spl) + 1) // 2)] + np.r_[np.arange(0, n, delta_knot_s)]
nB = i.shape[1]
j = np.tile(np.arange(nB), (len(spl), 1))
p = np.tile(spl, (nB, 1)).T
valid = (i >= 0) & (i < n)
B = cvx.spmatrix(p[valid], i[valid], j[valid])
# trend
C = cvx.matrix(np.c_[np.ones(n), np.arange(1., n + 1.) / n])
nC = C.size[1]
# Solve the problem:
# .5*(M*q + B*l + C*d - y)^2 + alpha*sum(A,1)*p + .5*gamma*l'*l
# s.t. A*q >= 0
# old_options = cvx.solvers.options.copy()
cvx.solvers.options.clear()
cvx.solvers.options.update(options)
if solver == 'conelp':
# Use conelp
z = lambda m, n: cvx.spmatrix([], [], [], (m, n))
G = cvx.sparse([[-A, z(2, n), M, z(nB + 2, n)], [z(n + 2, nC), C, z(nB + 2, nC)],
[z(n, 1), -1, 1, z(n + nB + 2, 1)], [z(2 * n + 2, 1), -1, 1, z(nB, 1)],
[z(n + 2, nB), B, z(2, nB), cvx.spmatrix(1.0, range(nB), range(nB))]])
h = cvx.matrix([z(n, 1), .5, .5, y, .5, .5, z(nB, 1)])
c = cvx.matrix([(cvx.matrix(alpha, (1, n)) * A).T, z(nC, 1), 1, gamma, z(nB, 1)])
res = cvx.solvers.conelp(c, G, h, dims={'l': n, 'q': [n + 2, nB + 2], 's': []})
obj = res['primal objective']
else:
# Use qp
Mt, Ct, Bt = M.T, C.T, B.T
H = cvx.sparse([[Mt * M, Ct * M, Bt * M], [Mt * C, Ct * C, Bt * C],
[Mt * B, Ct * B, Bt * B + gamma * cvx.spmatrix(1.0, range(nB), range(nB))]])
f = cvx.matrix([(cvx.matrix(alpha, (1, n)) * A).T - Mt * y, -(Ct * y), -(Bt * y)])
res = cvx.solvers.qp(H, f, cvx.spmatrix(-A.V, A.I, A.J, (n, len(f))),
cvx.matrix(0., (n, 1)), solver=solver)
obj = res['primal objective'] + .5 * (y.T * y)
# cvx.solvers.options.clear()
# cvx.solvers.options.update(old_options)
l = res['x'][-nB:]
d = res['x'][n:n + nC]
t = B * l + C * d
q = res['x'][:n]
p = A * q
r = M * q
e = y - r - t
return r, t
# return r, p, t, l, d, e, obj | 5d4b333c7ab99a339d20adc379ea48792e2b43aa | 7,834 |
import torch
def pulsar_from_opencv_projection(
R: torch.Tensor,
tvec: torch.Tensor,
camera_matrix: torch.Tensor,
image_size: torch.Tensor,
znear: float = 0.1,
) -> torch.Tensor:
"""
Convert OpenCV style camera parameters to Pulsar style camera parameters.
Note:
* Pulsar does NOT support different focal lengths for x and y.
For conversion, we use the average of fx and fy.
* The Pulsar renderer MUST use a left-handed coordinate system for this
mapping to work.
* The resulting image will be vertically flipped - which has to be
addressed AFTER rendering by the user.
* The parameters `R, tvec, camera_matrix` correspond to the outputs
of `cv2.decomposeProjectionMatrix`.
Args:
R: A batch of rotation matrices of shape `(N, 3, 3)`.
tvec: A batch of translation vectors of shape `(N, 3)`.
camera_matrix: A batch of camera calibration matrices of shape `(N, 3, 3)`.
image_size: A tensor of shape `(N, 2)` containing the sizes of the images
(height, width) attached to each camera.
znear (float): The near clipping value to use for Pulsar.
Returns:
cameras_pulsar: A batch of `N` Pulsar camera vectors in the Pulsar
convention `(N, 13)` (3 translation, 6 rotation, focal_length, sensor_width,
c_x, c_y).
"""
return _pulsar_from_opencv_projection(R, tvec, camera_matrix, image_size, znear) | 854349a4442e5e57554995439e62de74000c9b3d | 7,835 |
def identity(gender:str = None) -> dict:
""" Generates a pseudo-random identity.
Optional args
gender: 'm' for traditionally male, 'f' for traditionally female.
Returns a dict with the following keys:
name -> full name
given -> given name / first name
family -> family name / last name
address -> well formed address (fake of course)
city -> city of residence
state -> state of residence
zip_code -> zip code of residence (matches the city and state)
phone - > a phone number with an area code from the state of residence.
email -> a valid email address (fake of course)
"""
if gender and gender.lower() not in ["m", "f"]:
raise ValueError("'gender' must be 'm' or 'f'")
if gender and gender.lower() == "m":
given = _pluck(MGIVEN)
elif gender and gender.lower() == "f":
given = _pluck(FGIVEN)
else:
given = _pluck(MGIVEN + FGIVEN)
family = _pluck(FAMILY)
email = _make_email(given, family)
zip_code, city, state_code = _pluck(AREA)
phone = _make_phone(state_code)
address = _make_address()
return dict(name=f"{given} {family}".title(),
given=given.title(),
family=family.title(),
address=address,
city=city.title(),
state=state_code.upper(),
zip_code=zip_code,
phone=phone,
email=email) | 1917b6723a5bfe2c0b7477dca18f450c8a0e07c3 | 7,836 |
def matthews_corrcoef(y_true, y_pred):
"""Returns matthew's correlation coefficient for binary classes
The Matthews correlation coefficient is used in machine learning as a
measure of the quality of binary (two-class) classifications. It takes
into account true and false positives and negatives and is generally
regarded as a balanced measure which can be used even if the classes are
of very different sizes. The MCC is in essence a correlation coefficient
value between -1 and +1. A coefficient of +1 represents a perfect
prediction, 0 an average random prediction and -1 an inverse prediction.
The statistic is also known as the phi coefficient. [source: Wikipedia]
Only in the binary case does this relate to information about true and
false positives and negatives. See references below.
Parameters
----------
y_true : array, shape = [n_samples]
true targets
y_pred : array, shape = [n_samples]
estimated targets
Returns
-------
mcc : float
matthew's correlation coefficient (+1 represents a perfect prediction,
0 an average random prediction and -1 and inverse prediction).
References
----------
http://en.wikipedia.org/wiki/Matthews_correlation_coefficient
http://dx.doi.org/10.1093/bioinformatics/16.5.412
"""
mcc = np.corrcoef(y_true, y_pred)[0, 1]
if np.isnan(mcc):
return 0.
else:
return mcc | b4af31bac942a99fabb6f20c29ed59aa7b55e32d | 7,837 |
import os
def convert_image_link(image):
"""Convert an image link specification into a Markdown image link
Args:
image (Match): A Match object corresponding to an image link
Returns:
str: Markdown formatted link to the image
"""
image_name = str(image.group(1))
file_ext = 'jpg'
if '|' in image_name:
image_name, file_ext = image_name.split('|')
image_link = f")}.{file_ext})"
return image_link | 7ef746cc9d062107b4d8f6fa79d544e75ee00e9b | 7,838 |
from typing import Dict
from typing import Any
import yaml
def yaml_dump(dict_to_dump: Dict[str, Any]) -> str:
"""Dump the dictionary as a YAML document."""
return yaml.safe_dump(dict_to_dump, default_flow_style=False) | 4635514ba8ff901656b8a4b5869a6ae101528fa8 | 7,839 |
def completeness(importance_matrix):
""""Compute completeness of the representation."""
per_factor = completeness_per_code(importance_matrix)
if importance_matrix.sum() == 0.:
importance_matrix = np.ones_like(importance_matrix)
factor_importance = importance_matrix.sum(axis=0) / importance_matrix.sum()
return np.sum(per_factor*factor_importance) | 39407833b501e974f2ddb421ecad59055153260e | 7,840 |
def image_stat(image_id):
"""
Return the statistics ofd an image as a pd dataframe
:param image_id:
:return:
"""
counts, total_area, mean_area, std_area = {}, {}, {}, {}
img_area = get_image_area(image_id)
for cl in CLASSES:
polygon_list = get_polygon_list(image_id, cl)
counts[cl] = len(polygon_list)
if len(polygon_list) > 0:
total_area[cl] = np.sum([poly.area for poly in polygon_list])\
/ img_area * 100.
mean_area[cl] = np.mean([poly.area for poly in polygon_list])\
/ img_area * 100.
std_area[cl] = np.std([poly.area for poly in polygon_list])\
/ img_area * 100.
return pd.DataFrame({'Class': CLASSES, 'Counts': counts,
'TotalArea': total_area, 'MeanArea': mean_area,
'STDArea': std_area}) | a20c1d702f983c576ab506061ab19181b90c8684 | 7,841 |
def delete_original():
"""
Decorator that deletes the original
Discord message upon command execution.
:return: boolean
"""
async def predicate(ctx):
if ctx.invoked_with != "help": # Don't try to delete if help command
if isinstance(ctx.message.channel, discord.TextChannel):
try:
await ctx.message.delete()
except discord.errors.NotFound as e:
log.fatal(f"Unable to delete message.\n\t{e}")
return True
return commands.check(predicate) | 08f71c271b679fb6389754c21a896e11ae6f05c0 | 7,842 |
import os
def list_template_dirs():
"""List names of directories containnig parallel programming templates."""
dirs = []
for templates_dir in settings.TEMPLATE_DIRS:
for template_dir in os.listdir(templates_dir):
path = os.path.join(templates_dir,template_dir)
if os.path.isdir(path):
dirs.append(template_dir)
return dirs | 2af89460be234e3c649b1a0c67db150062299f14 | 7,843 |
def get_H_OS():
"""屋根又は天井の温度差係数 (-)
Args:
Returns:
float: 屋根又は天井の温度差係数 (-)
"""
adjacent_type = '外気'
return get_H(adjacent_type) | cb3b68063d2c734b03d96b261e5cba23b79c3bc7 | 7,844 |
def forward_softmax(x):
"""
Compute softmax function for a single example.
The shape of the input is of size # num classes.
Important Note: You must be careful to avoid overflow for this function. Functions
like softmax have a tendency to overflow when very large numbers like e^10000 are computed.
You will know that your function is overflow resistent when it can handle input like:
np.array([[10000, 10010, 10]]) without issues.
x: A 1d numpy float array of shape number_of_classes
Returns:
A 1d numpy float array containing the softmax results of shape number_of_classes
"""
x = x - np.max(x,axis=0)
exp = np.exp(x)
s = exp / np.sum(exp,axis=0)
return s | 8c0f54294c2dc5b385466398726b67a3acd674b0 | 7,845 |
import numpy
def applySpectralClusters(kmeansObj, img, imgNullVal):
"""
Use the given KMeans object to predict spectral clusters on
a whole image array.
The kmeansObj is an instance of sklearn.cluster.KMeans,
as returned by fitSpectralClusters().
The img array is a numpy array of the image to predict on,
of shape (nBands, nRows, nCols).
Any pixels in img which have value imgNullVal will be set to
SEGNULLVAL (i.e. zero) in the output cluster image.
Return value is a numpy array of shape (nRows, nCols),
with each element being the segment ID value for that pixel.
"""
# Predict on the whole image. In principle we could omit the nulls,
# but it makes little difference to run time, and just adds complexity.
(nBands, nRows, nCols) = img.shape
# Re-organise the image data so it matches what sklearn
# expects.
xFull = numpy.transpose(img, axes=(1, 2, 0))
xFull = xFull.reshape((nRows*nCols, nBands))
clustersFull = kmeansObj.predict(xFull)
del xFull
clustersImg = clustersFull.reshape((nRows, nCols))
# Make the cluster ID numbers start from 1, and use SEGNULLVAL
# (i.e. zero) in null pixels
clustersImg += 1
if imgNullVal is not None:
nullmask = (img == imgNullVal).any(axis=0)
clustersImg[nullmask] = SEGNULLVAL
return clustersImg | 2b2fb5616c20c4e5d9278bf8555c888bfab80cb8 | 7,846 |
from sys import path
def get_config_and_project_dir(config_file: str):
"""Guess config file name and project dir"""
if config_file is not None:
config_file = path.abspath(config_file)
project_dir = path.dirname(config_file)
else:
project_dir = find_project_dir()
config_file = '{}/stakkr.yml'.format(project_dir)
return config_file, project_dir | 2b3e7e219c97ef504e76468512a90926c351b949 | 7,847 |
def get_config() -> ConfigParser:
"""
Parse the config file.
:return: config
"""
cfg = ConfigParser()
cfg.read(CONFIG_PATH)
return cfg | 14f9ce4719bf665d62f1a2d06c980f4e85d2b8a5 | 7,848 |
from calendra.registry import registry
def iso_register(iso_code):
"""
Registers Calendar class as country or region in IsoRegistry.
Registered country must set class variables ``iso`` using this decorator.
>>> from calendra.core import Calendar
>>> from calendra.registry import registry
>>> from calendra.registry_tools import iso_register
>>> @iso_register('MC-MR')
... class MyRegion(Calendar):
... 'My Region'
Region calendar is then retrievable from registry:
>>> calendar = registry.get('MC-MR')
"""
def wrapper(cls):
registry.register(iso_code, cls)
return cls
return wrapper | 7fcb55a37f5af948ff6be8baf797d00328f241a8 | 7,849 |
def dict_check_defaults(dd, **defaults):
"""Check that a dictionary has some default values
Parameters
----------
dd: dict
Dictionary to check
**defs: dict
Dictionary of default values
Example
-------
.. ipython:: python
@suppress
from xoa.misc import dict_check_defaults
dd = dict(color='blue')
dict_check_defaults(dd, color='red', size=10)
"""
if defaults is None:
defaults = {}
for item in defaults.items():
dd.setdefault(*item)
return dd | 8edc3fdb351f7ec2d4ec3b1e788e6aa5cc0f8787 | 7,850 |
import os
def construct_search_params():
"""Iterates through user-defined Entrez Search settings to assemble the search parameters.
Envars hold the most recent user-defined Entrez settings, such as rettype, retmax, database,
etc. These settings are iterated through, and their values are returned and appended to the
query.
"""
params = {}
for setting in ev.settings_eSearch:
if os.environ.get(setting[1]) != 'None':
params.update({setting[0].lower(): os.environ.get(setting[1])})
return params | 0c6c2fd566246d86cf9225ca2ba2404451b79d2c | 7,851 |
def get_invested_and_worth(account):
"""Gets the money invested and the actual worth of an account"""
data = query_indexa(f"accounts/{account}/performance")
invested = data["return"]["investment"]
worth = data["return"]["total_amount"]
return {"invested": round(invested, 2), "worth": round(worth, 2)} | fc1542f54c8954622aff86d59d7d6fb82e63832b | 7,852 |
def make_album(singer, name, number = ''):
"""Return singers' names and album"""
album = {'singer': singer, 'name': name}
if number:
album['number'] = number
return album | 1f1bfaaeb501be0aa6fefd358177922246488b31 | 7,853 |
from typing import Dict
from typing import List
from typing import Generator
def fit_ctmp_meas_mitigator(cal_data: Dict[int, Dict[int, int]],
num_qubits: int,
generators: List[Generator] = None) -> CTMPExpvalMeasMitigator:
"""Return FullMeasureErrorMitigator from result data.
Args:
cal_data: calibration dataset.
num_qubits: the number of qubits for the calibation dataset.
generators: Optional, input generator set.
Returns:
Measurement error mitigator object.
Raises:
QiskitError: if input arguments are invalid.
"""
if not isinstance(num_qubits, int):
raise QiskitError('Number of qubits must be an int')
if generators is None:
generators = standard_generator_set(num_qubits)
gen_mat_dict = {}
for gen in generators + _supplementary_generators(generators):
if len(gen[2]) > 1:
mat = _local_g_matrix(gen, cal_data, num_qubits)
gen_mat_dict[gen] = mat
# Compute rates for generators
rates = [_get_ctmp_error_rate(gen, gen_mat_dict, num_qubits) for gen in generators]
return CTMPExpvalMeasMitigator(generators, rates) | 2dab6ca0da19acb174b6d0e8b96c7833d5de74e8 | 7,854 |
def discounted_item(data):
"""
DOCSTRING: Classifies item purchases as 'Promoted' or 'Not Promoted' based on 'Item Discount' column. Also 'COD Collectibles' column gets restructured by eliminating undesired default values, like 'Online'.
INPUT:
> data : Only accepts Pandas DataFrame or TextParser, that has been pre-processed earlier.
OUTPUT: Pandas DataFrame or TextParser with 1 additional column, i.e. 'On Promotion'.
"""
data["On Promotion"] = np.nan
data["Phone num"] = np.nan
data["COD Collectible"] = np.nan # Later again gets renamed within this func.
for i,v in data["Item Discount"].iteritems():
if v != 0:
data.loc[i, "On Promotion"] = "Promoted"
else:
data.loc[i, "On Promotion"] = "Not Promoted"
# Also taking care of COD Collectible:
for i,v in data["COD Collectibles"].iteritems():
if v == "Online":
data.loc[i, "COD Collectible"] = 0
else:
data.loc[i, "COD Collectible"] = v
# Also taking care of 'Phone No.' column:
for i,v in data["Phone No."].iteritems():
if v == "Online":
data.loc[i, "Phone num"] = "Unavailable"
else:
data.loc[i, "Phone num"] = v
data.drop(["COD Collectibles"], axis=1, inplace=True)
data.drop(["Phone No."], axis=1, inplace=True)
data.rename(columns={"COD Collectible": "COD Collectibles"}, inplace=True)
data.rename(columns={"Phone num": "Phone No."}, inplace=True)
return data | 178c5e7d8e9c2e3bdd91d4606ea52c34c7cf099c | 7,855 |
def NamespacedKubernetesSyncer(namespace, use_rsync=False):
"""Wrapper to return a ``KubernetesSyncer`` for a Kubernetes namespace.
Args:
namespace (str): Kubernetes namespace.
use_rsync (bool): Use ``rsync`` if True or ``kubectl cp``
if False. If True, ``rsync`` will need to be
installed in the Kubernetes pods for this to work.
If False, ``tar`` will need to be installed instead.
Returns: A ``KubernetesSyncer`` class to be passed to ``tune.run()``.
Example:
.. code-block:: python
from ray.tune.integration.kubernetes import NamespacedKubernetesSyncer
tune.run(train,
sync_to_driver=NamespacedKubernetesSyncer("ray"))
"""
class _NamespacedKubernetesSyncer(KubernetesSyncer):
_namespace = namespace
_use_rsync = use_rsync
return _NamespacedKubernetesSyncer | 9da5a049a12a248623040c1ace79c2ebedd3400c | 7,856 |
def _cons8_88(m8, L88, d_gap, k, Cp, h_gap):
"""dz constrant for edge gap sc touching 2 edge gap sc"""
term1 = 2 * h_gap * L88 / m8 / Cp # conv to inner/outer ducts
term2 = 2 * k * d_gap / m8 / Cp / L88 # cond to adj bypass edge
return 1 / (term1 + term2) | 7c48c4999ce2dd3dbdec799edd7ad441a6f66e7b | 7,857 |
import hashlib
def cache_key(path):
"""Return cache key for `path`."""
return 'folder-{}'.format(hashlib.md5(path.encode('utf-8')).hexdigest()) | 6b9afe1267e0cc0c7168bf3b0d5c7536e2b3c768 | 7,858 |
def ref_731(n):
"""Reference number calculator. Returns reference number
calculated using 7-3-1 algorithm used in Estonian banks.
:param string n: base number (client id, etc)
:rtype: string
"""
return "%s%d" % (n,((10 - (sum(map(\
lambda l: int(n[-l])*(7,3,1)[(l-1) % 3], \
xrange(1, len(n)+1))))) % 10)) | b1958511947d9f369db2547cde15222603dc0773 | 7,859 |
import traceback
async def exception_as_response(e: Exception):
"""
Wraps an exception into a JSON Response.
"""
data = {
"message": str(e),
"traceback": "".join(traceback.TracebackException.from_exception(e).format())
}
return web.json_response(data, status=500) | 60f226cb7cd4c3aba3026d44d28e774928e6bbf7 | 7,860 |
def canvas_merge_union(layers, full=True, blend=canvas_compose_over):
"""Blend multiple `layers` into single large enough image"""
if not layers:
raise ValueError("can not blend zero layers")
elif len(layers) == 1:
return layers[0]
min_x, min_y, max_x, max_y = None, None, None, None
for image, offset in layers:
x, y = offset
w, h = image.shape[:2]
if min_x is None:
min_x, min_y = x, y
max_x, max_y = x + w, y + h
else:
min_x, min_y = min(min_x, x), min(min_y, y)
max_x, max_y = max(max_x, x + w), max(max_y, y + h)
width, height = max_x - min_x, max_y - min_y
if full:
output = None
for image, offset in layers:
x, y = offset
w, h = image.shape[:2]
ox, oy = x - min_x, y - min_y
image_full = np.zeros((width, height, 4), dtype=FLOAT)
image_full[ox : ox + w, oy : oy + h] = image
if output is None:
output = image_full
else:
output = blend(output, image_full)
else:
# this is optimization for method `over` blending
output = np.zeros((max_x - min_x, max_y - min_y, 4), dtype=FLOAT)
for index, (image, offset) in enumerate(layers):
x, y = offset
w, h = image.shape[:2]
ox, oy = x - min_x, y - min_y
effected = output[ox : ox + w, oy : oy + h]
if index == 0:
effected[...] = image
else:
effected[...] = blend(effected, image)
return output, (min_x, min_y) | ffbb3b78e908ed1e131a1f0827f2d3097415edc9 | 7,861 |
import json
def exception_response(request, code=400, exception=None):
"""
Create a response for an exception
:param request: request instance
:param code: exception code
:param exception: exception instance
:return: exception formatted response
"""
code = code if code in [400, 403, 404, 500] else 400
exception_repr = get_error_msg(exception)
log.error(usr=request.user, msg=f'{code} - {exception_repr}')
context = dict(
message=f"Error {code}",
request_path=request.path,
exception=exception_repr
)
if is_browser(request):
template = loader.get_template(f'error/{code}.html')
rtn = dict(
content=template.render(context, request),
content_type='text/html'
)
else:
rtn = dict(
content=json.dumps(context),
content_type='application/json'
)
return rtn | 1ef145ea4b07557fbc31a9d5c52621e79c2b99ff | 7,862 |
import os
def get_jira_issues(jira, exclude_stories, epics_only, all_status, filename,
user):
"""
Query Jira and then creates a status update file (either temporary or named)
containing all information found from the JQL query.
"""
issue_types = ["Epic"]
if not epics_only:
issue_types.append("Initiative")
if not exclude_stories:
issue_types.append("Story")
issue_type = "issuetype in (%s)" % ", ".join(issue_types)
status = "status in (\"In Progress\")"
if all_status:
status = "status not in (Resolved, Closed)"
if user is None:
user = "currentUser()"
else:
user = "\"%s\"" % add_domain(user)
jql = "%s AND assignee = %s AND %s" % (issue_type, user, status)
vprint(jql)
my_issues = jira.search_issues(jql)
msg = message_header + email_to_name(os.environ['JIRA_USERNAME']) + "\n\n"
f = open_file(filename)
filename = f.name
f.write(msg)
vprint("Found issue:")
for issue in my_issues:
vprint("%s : %s" % (issue, issue.fields.summary))
f.write("[%s]\n" % issue)
f.write("# Header: %s\n" % issue.fields.summary)
f.write("# Type: %s\n" % issue.fields.issuetype)
f.write("# Status: %s\n" % issue.fields.status)
f.write("No updates since last week.\n\n")
f.close()
return filename | c495326f0790f3bec8c95a2fae1c645409100d27 | 7,863 |
def entropy(series):
"""Normalized Shannon Index"""
# a series in which all the entries are equal should result in normalized entropy of 1.0
# eliminate 0s
series1 = series[series!=0]
# if len(series) < 2 (i.e., 0 or 1) then return 0
if len(series1) > 1:
# calculate the maximum possible entropy for given length of input series
max_s = -np.log(1.0/len(series))
total = float(sum(series1))
p = series1.astype('float')/float(total)
return sum(-p*np.log(p))/max_s
else:
return 0.0 | 30f8f3cc6fed73d8cfa0b3705008891a60af028a | 7,864 |
def spatially_whiten(X:np.ndarray, *args, **kwargs):
"""spatially whiten the nd-array X
Args:
X (np.ndarray): the data to be whitened, with channels/space in the *last* axis
Returns:
X (np.ndarray): the whitened X
W (np.ndarray): the whitening matrix used to whiten X
"""
Cxx = updateCxx(None,X,None)
W,_ = robust_whitener(Cxx, *args, **kwargs)
X = X @ W #np.einsum("...d,dw->...w",X,W)
return (X,W) | a0c9ae88e8f451378503754e4768ee554e50ed3e | 7,865 |
from pathlib import Path
import yaml
def get_settings(basename: str="settings.yml", path: Path=PROJECT_ROOT / "conf") -> dict:
"""
Loads settings file
Args:
basename (str, optional): Basename of settings file. Defaults to "settings.yml".
path (Path, optional): Path of seetings file. Defaults to PROJECT_ROOT/"conf".
Raises:
exc: Yaml load exception
Returns:
dict: settings
"""
with open(str(path / basename), 'r') as stream:
try:
settings = yaml.safe_load(stream)
except yaml.YAMLError as exc:
raise exc
return settings | 2317f9fbd125a16a7c34086d35b02973f1be5d8f | 7,866 |
import torch
def quaternion2rotationPT( q ):
""" Convert unit quaternion to rotation matrix
Args:
q(torch.tensor): unit quaternion (N,4)
Returns:
torch.tensor: rotation matrix (N,3,3)
"""
r11 = (q[:,0]**2+q[:,1]**2-q[:,2]**2-q[:,3]**2).unsqueeze(0).T
r12 = (2.0*(q[:,1]*q[:,2]-q[:,0]*q[:,3])).unsqueeze(0).T
r13 = (2.0*(q[:,1]*q[:,3]+q[:,0]*q[:,2])).unsqueeze(0).T
r21 = (2.0*(q[:,1]*q[:,2]+q[:,0]*q[:,3])).unsqueeze(0).T
r22 = (q[:,0]**2+q[:,2]**2-q[:,1]**2-q[:,3]**2).unsqueeze(0).T
r23 = (2.0*(q[:,2]*q[:,3]-q[:,0]*q[:,1])).unsqueeze(0).T
r31 = (2.0*(q[:,1]*q[:,3]-q[:,0]*q[:,2])).unsqueeze(0).T
r32 = (2.0*(q[:,2]*q[:,3]+q[:,0]*q[:,1])).unsqueeze(0).T
r33 = (q[:,0]**2+q[:,3]**2-q[:,1]**2-q[:,2]**2).unsqueeze(0).T
r = torch.cat( (r11,r12,r13,
r21,r22,r23,
r31,r32,r33), 1 )
r = torch.reshape( r, (q.shape[0],3,3))
return r | feeed764ee179b31674790f9d2afc7b606a02aef | 7,867 |
def _expand_and_tile(tensor, multiple, dim=0, name=None):
"""Slice `tensor` shape in 2, then tile along the sliced dimension.
A new dimension is inserted in shape of `tensor` before `dim`, then values are
tiled `multiple` times along the new dimension.
Args:
tensor: Input `Tensor` or `SparseTensor`.
multiple: Integer, number of times to tile.
dim: Integer, dimension along which to tile.
name: Name of operation.
Returns:
`Tensor` result of expanding and tiling `tensor`.
Raises:
ValueError: if `multiple` is less than 1, or `dim` is not in
`[-rank(tensor), rank(tensor)]`.
"""
if multiple < 1:
raise ValueError(f'Invalid argument multiple={multiple} for '
'expand_and_tile call. `multiple` must be an integer > 0')
with ops.name_scope(name, 'expand_and_tile',
(tensor, multiple, dim)) as scope:
# Sparse.
tensor = sparse_tensor.convert_to_tensor_or_sparse_tensor(tensor)
if isinstance(tensor, sparse_tensor.SparseTensor):
if dim < 0:
expand_dims = array_ops.reshape(
array_ops.size(tensor.dense_shape) + dim, [1])
else:
expand_dims = [dim]
expanded_shape = array_ops.concat(
(array_ops.slice(tensor.dense_shape, [0], expand_dims), [1],
array_ops.slice(tensor.dense_shape, expand_dims, [-1])),
0,
name='expanded_shape')
expanded = sparse_ops.sparse_reshape(
tensor, shape=expanded_shape, name='expand')
if multiple == 1:
return expanded
return sparse_ops.sparse_concat(
dim - 1 if dim < 0 else dim, [expanded] * multiple, name=scope)
# Dense.
expanded = array_ops.expand_dims(
tensor, dim if (dim >= 0) else (dim - 1), name='expand')
if multiple == 1:
return expanded
ones = array_ops.ones_like(array_ops.shape(tensor))
tile_multiples = array_ops.concat(
(ones[:dim], (multiple,), ones[dim:]), 0, name='multiples')
return array_ops.tile(expanded, tile_multiples, name=scope) | aa9840fdaee56fee19937c8f632c72628fbd3995 | 7,868 |
import random
def eval_model(opt, print_parser=None):
"""Evaluates a model.
:param opt: tells the evaluation function how to run
:param bool print_parser: if provided, prints the options that are set within the
model after loading the model
:return: the final result of calling report()
"""
random.seed(42)
# load model and possibly print opt
agent = create_agent(opt, requireModelExists=True)
if print_parser:
# show args after loading model
print_parser.opt = agent.opt
print_parser.print_args()
tasks = opt['task'].split(',')
reports = []
for task in tasks:
task_report = _eval_single_world(opt, agent, task)
reports.append(task_report)
report = aggregate_task_reports(
reports, tasks, micro=opt.get('aggregate_micro', True)
)
# print announcements and report
print_announcements(opt)
print(
'[ Finished evaluating tasks {} using datatype {} ]'.format(
tasks, opt.get('datatype', 'N/A')
)
)
print(report)
return report | 153dbead7ebd37ba2f61d745bc499f9eddfa0d03 | 7,869 |
def login(request):
"""
Login with Dummy Test Account.
"""
if 'user' in request.environ['beaker.session']:
return app.redirect('index')
users.store_to_session(request, users.create())
return app.redirect('index') | 0f2d06e7a6ac2fed0daee73e4c2e216012452e08 | 7,870 |
def safe_plus(x,y):
"""
Handle "x + y" where x and y could be some combination of ints and strs.
"""
# Handle Excel Cell objects. Grrr.
if excel.is_cell_dict(x):
x = x["value"]
if excel.is_cell_dict(y):
y = y["value"]
# Handle NULLs.
if (x == "NULL"):
x = 0
if (y == "NULL"):
y = 0
# Easy case first.
if ((isinstance(x, int) or isinstance(x, float)) and
(isinstance(y, int) or isinstance(y, float))):
return x + y
# Fix data types.
if (isinstance(y, str)):
# NULL string in VB.
if (x == 0):
x = ""
# String concat.
return str(x) + y
if (isinstance(x, str)):
# NULL string in VB.
if (y == 0):
y = ""
# String concat.
return x + str(y)
# Punt. We are not doing pure numeric addition and
# we have already handled string concatentaion. Just
# convert things to strings and hope for the best.
return str(x) + str(y) | e3f5e43ee3e083669d0b744c7fb46a4ae62b4eec | 7,871 |
import types
def full_like(a, fill_value, dtype=types.float32, split=None, device=None, comm=None, order="C"):
"""
Return a full array with the same shape and type as a given array.
Parameters
----------
a : object
The shape and data-type of 'a' define these same attributes of the returned array.
fill_value : scalar
Fill value.
dtype : ht.dtype, optional
Overrides the data type of the result.
split: int, optional
The axis along which the array is split and distributed, defaults to None (no distribution).
device : str, ht.Device or None, optional
Specifies the device the tensor shall be allocated on, defaults to None (i.e. globally set default device).
comm: Communication, optional
Handle to the nodes holding distributed parts or copies of this tensor.
Returns
-------
out : ht.DNDarray
Array of fill_value with the same shape and type as a.
Examples
--------
>>> x = ht.zeros((2, 3,))
>>> x
tensor([[0., 0., 0.],
[0., 0., 0.]])
>>> ht.full_like(a, 1.0)
tensor([[1., 1., 1.],
[1., 1., 1.]])
"""
return __factory_like(a, dtype, split, full, device, comm, fill_value=fill_value, order=order) | 4a615e493ae20d925eeda7c0bd6ca9508c338bc2 | 7,872 |
import glob
def gather_pulled_downloads(input_dir, output_dir):
"""
Gather MPEG stream files from input_dir into a single MP4 file in output_dir
"""
dash_globstr = f"{input_dir.absolute() / '*.dash'}"
dash_glob = glob(dash_globstr)
if len(dash_glob) < 1:
raise ValueError(f"No dash file found in {input_dir}")
elif len(dash_glob) > 1:
raise ValueError(f"Multiple dash files found in {input_dir}")
else:
dash_file = dash_glob[0]
m4s_globstr = f"{input_dir.absolute() / '*.m4s'}"
m4s_files = sorted(glob(m4s_globstr))
output_mp4 = output_dir.absolute() / "output.mp4"
gather_m4s_to_mp4(dash_file, m4s_files, output_mp4)
return output_mp4 | a1b9c334ab717292db006666bdcdd0749b2620d7 | 7,873 |
import functools
def Parallelize(ListIn, f, procs = -1, **kwargs):
"""This function packages the "starmap" function in multiprocessing, to allow multiple iterable inputs for the parallelized function.
Parameters
----------
ListIn: list
each item in the list is a tuple of non-keyworded arguments for f.
f : func
function to be parallelized. Signature must not contain any other non-keyworded arguments other than those passed as iterables.
Example:
.. highlight:: python
.. code-block:: python
def multiply(x, y, factor = 1.0):
return factor*x*y
X = np.linspace(0,1,1000)
Y = np.linspace(1,2,1000)
XY = [ (x, Y[i]) for i, x in enumerate(X)] # List of tuples
Z = Parallelize_MultiIn(XY, multiply, factor = 3.0, procs = 8)
Create as many positional arguments as required, but all must be packed into a list of tuples.
"""
if type(ListIn[0]) != tuple:
ListIn = [(ListIn[i],) for i in range(len(ListIn))]
reduced_argfunc = functools.partial(f, **kwargs)
if procs == -1:
opt_procs = int(np.interp(len(ListIn), [1,100,500,1000,3000,5000,10000] ,[1,2,4,8,12,36,48]))
procs = min(opt_procs, cpu_count())
if procs == 1:
OutList = [reduced_argfunc(*ListIn[iS]) for iS in range(len(ListIn))]
else:
p = Pool(processes = procs)
OutList = p.starmap(reduced_argfunc, ListIn)
p.close()
p.join()
return OutList | 84fc1509c96c7bf765246e46983f2fa01745f4b2 | 7,874 |
def method_not_found(e):
""" Custom response for methods not allowed for the requested URLs :param e: Exception :return: """
return response('failed', 'The method is not allowed for the requested URL', 405) | 18a48d53d602c1a90017e3f00adc75c4c33479b5 | 7,875 |
def get_total_trainsets(df_anual_data, segments):
"""
# Fill the training_sets dict
:param df_anual_data:
:return:
"""
rows_per_day = int(((60 / 15) * 24))
training_sets = {'ID_SEGMENT': [], 'MES': [], 'COD_LABORALIDAD': [], 'TRAINING_SET': []}
for seg_id in segments: # 1) Particionar anual_data por segmento
df_seg = df_anual_data.loc[df_anual_data.ID_SEGMENT == seg_id]
for month_i in df_seg.FECHA.dt.month.unique(): # 2) Dividir mensual_data en 12 datasets
df_month_seg = df_seg.loc[df_seg.FECHA.dt.month == month_i]
for code_i in df_month_seg.COD_LABORALIDAD.unique(): # 3) Particionar por dias con mismo código de lab
df_month_seg_code = df_month_seg.loc[df_month_seg.COD_LABORALIDAD == code_i]
# Fill training_sets dictionary
training_sets['ID_SEGMENT'].append(seg_id)
training_sets['MES'].append(month_i)
training_sets['COD_LABORALIDAD'].append(code_i)
training_sets['TRAINING_SET'].append(df_month_seg_code)
return training_sets | 968c3af1fdba5eb759eb93618ed48e3ca3ce5223 | 7,876 |
def uni2diff(u):
"""Convert speed and angular rate to wheel speeds."""
v = u[0]
omega = u[1]
v_L = v - ELL / 2 * omega
v_R = v + ELL / 2 * omega
return np.array([v_L, v_R]) | 83b743758aa7a549eda9067843a03eb57efde523 | 7,877 |
import re
def extract_service_and_module(repo_url):
"""Extract service and module from repository url.
:param str repo_url: repository url
:return (service, module)
:rtype (str, str)
"""
m = re.match(r'.+[/@]([^\.]+\.[^\.]+)[:/]([^/]+/[^/]+)\.git/?$', repo_url)
if not m:
m = re.match(r'.+[/@]([^\.]+\.[^\.]+)[:/]([^/]+/[^/]+)/?$', repo_url)
if not m:
raise Exception(
'cannot detect service and module from {}'.format(repo_url))
service = m.group(1)
module = m.group(2)
if service not in _pull_request_url.keys():
raise Exception(
'service not supported: {}'.format(service))
return (service, module) | eafe6cf39fc2fe4153830c491147633fb07f95dd | 7,878 |
import numpy
def triangular(left, mode, right, size=None):
"""Triangular distribution.
Draw samples from the triangular distribution over the interval
[left, right].
For full documentation refer to :obj:`numpy.random.triangular`.
Limitations
-----------
Parameter ``left``, ``mode`` and ``right`` are supported as scalar.
Otherwise, :obj:`numpy.random.triangular(left, mode, right, size)`
samples are drawn.
Output array data type is :obj:`dpnp.float64`.
Examples
--------
Draw samples from the distribution:
>>> df = 2.
>>> s = dpnp.random.triangular(-3, 0, 8, 1000000)
"""
if not use_origin_backend(left):
# TODO:
# array_like of floats for `left`, `mode`, `right`.
if not dpnp.isscalar(left):
pass
elif not dpnp.isscalar(mode):
pass
elif not dpnp.isscalar(right):
pass
elif left > mode:
pass
elif mode > right:
pass
elif left == right:
pass
else:
return dpnp_rng_triangular(left, mode, right, size).get_pyobj()
return call_origin(numpy.random.triangular, left, mode, right, size) | c92d1461fe9052648e0b141e8b962f350e1d23b4 | 7,879 |
def format_hexa(value: str) -> ColorBytes:
"""
Examples:
"bda" => (187, 221, 170, 255)
"4fcd" => (68, 255, 204, 221)
"60B0C4" => (96, 176, 196, 255)
"2BEA40D0" => (43, 234, 64, 208)
"""
if len(value) in {3, 4}:
expanded_color = ''.join(s * 2 for s in value)
else:
expanded_color = value
length = len(expanded_color)
if length in {6, 8}:
hex_parts = [expanded_color[i:(i + 2)] for i in range(0, length, 2)]
return format_color_bytes([int(v, 16) for v in hex_parts])
else:
raise ValueError(value) | 4865e1498ed87c933160e5666adcc41b45162fdd | 7,880 |
def normalize_community_features(features):
"""
This performs TF-IDF-like normalization of community embedding features.
Introduced in: Tang, L., Wang, X., Liu, H., & Wang, L. (2010, July).
A multi-resolution approach to learning with overlapping communities.
In Proceedings of the First Workshop on Social Media Analytics (pp. 14-22). ACM.
Input: - X in R^(nxC_n): The community indicator matrix.
Output: - X_norm in R^(nxC_n): The tf-idf + row normalized community indicator matrix.
"""
# Calculate inverse document frequency.
features = normalize_columns(features)
# Normalize each row of term frequencies to 1
features = normalize_rows(features)
return features | 9f5018ad3e20810d2bb66443bac4c2f7f6359d0f | 7,881 |
def __extend_prefixed(pu):
"""
:param pu:
:return:
"""
parts = pu.split(':')
if len(parts) == 1:
parts = ('', parts[0])
try:
return URIRef(_prefixes[parts[0]] + parts[1])
except KeyError:
return BNode(pu) | d6e5c25c94e8b3252d8b0925e8d37747caceebdd | 7,882 |
def angle(u: Vec, v: Vec) -> float:
"""
Returns the cosine (angle) between two vectors u and v
:param u: (Vec) vector u
:param v: (Vec) vector v
:return: The scaled dot product, cosine of u and v's angle
"""
if u.is_zero or v.is_zero:
raise ValueError("Angle with lower dimensional 0 vector cannot be determined")
l_u = u.length
l_v = v.length
return u.dot(v) / (l_u * l_v) | 6c79390af1ed38fc1a99006165684234dabb0b4a | 7,883 |
def find_most_similar(top_k, probs, cache_dict, num=10):
"""返回最相似的num张照片的文件名，如果找到相似的，
则返回一个包括匹配元组的列表，否则返回一个空列表
top_k : 包含最佳分类的索引的列表
probs : 包含最佳分类索引对应的概率
cache_dict: 缓存中的索引和概率
num : 返回最近匹配的数目
"""
similar = []
for filename in cache_dict:
score = 0
count = 0
other_top_k, other_probs = cache_dict[filename]
for i, t in enumerate(top_k):
if t in other_top_k:
prob = probs[i]
other_prob = other_probs[other_top_k.tolist().index(t)]
score += abs(prob-other_prob)
count += 1
if count > 0:
score = score / count
similar.append((filename, score))
if similar:
similar.sort(key=lambda item: item[1]) # 根据score升序排序
return similar[:num]
return similar | 471083e1ed2b0fadb98cafad64d314ba779aa9e6 | 7,884 |
def load(url_or_handle, allow_unsafe_formats=False, cache=None, **kwargs):
"""Load a file.
File format is inferred from url. File retrieval strategy is inferred from
URL. Returned object type is inferred from url extension.
Args:
url_or_handle: a (reachable) URL, or an already open file handle
allow_unsafe_formats: set to True to allow saving unsafe formats (eg. pickles)
cache: whether to attempt caching the resource. Defaults to True only if
the given URL specifies a remote resource.
Raises:
RuntimeError: If file extension or URL is not supported.
"""
# handle lists of URLs in a performant manner
if isinstance(url_or_handle, (list, tuple)):
return _load_urls(url_or_handle, cache=cache, **kwargs)
ext, decompressor_ext = _get_extension(url_or_handle)
try:
ext = ext.lower()
if ext in loaders:
loader = loaders[ext]
elif ext in unsafe_loaders:
if not allow_unsafe_formats:
raise ValueError(f"{ext} is considered unsafe, you must explicitly allow its use by passing allow_unsafe_formats=True")
loader = unsafe_loaders[ext]
else:
raise KeyError(f'no loader found for {ext}')
decompressor = decompressors[decompressor_ext] if decompressor_ext is not None else nullcontext
message = "Using inferred loader '%s' due to passed file extension '%s'."
log.debug(message, loader.__name__[6:], ext)
return load_using_loader(url_or_handle, decompressor, loader, cache, **kwargs)
except KeyError:
log.warning("Unknown extension '%s', attempting to load as image.", ext)
try:
with read_handle(url_or_handle, cache=cache) as handle:
result = _load_img(handle)
except Exception as e:
message = "Could not load resource %s as image. Supported extensions: %s"
log.error(message, url_or_handle, list(loaders))
raise RuntimeError(message.format(url_or_handle, list(loaders)))
else:
log.info("Unknown extension '%s' successfully loaded as image.", ext)
return result | 89fec9684dda24b6b16b63e6b478bc4f67d00f07 | 7,885 |
import time
import torch
def evaluate_full_batch(model, minibatch, mode='val'):
"""
Full batch evaluation: for validation and test sets only.
When calculating the F1 score, we will mask the relevant root nodes.
"""
time_s = time.time()
loss, preds, labels = model.eval_step(*minibatch.one_batch(mode=mode))
torch.cuda.synchronize()
time_e = time.time()
node_val_test = minibatch.node_val if mode == 'val' else minibatch.node_test
f1_scores = calc_f1(to_numpy(labels[node_val_test]),
to_numpy(preds[node_val_test]), model.sigmoid_loss)
# node_test=minibatch.node_test
# f1_test=calc_f1(to_numpy(labels[node_test]),to_numpy(preds[node_test]),model.sigmoid_loss)
# printf(' ******TEST: loss = {:.4f}\tmic = {:.4f}\tmac = {:.4f}'.format(loss,f1_test[0],f1_test[1]),style='yellow')
del labels
del preds
return loss, f1_scores[0], f1_scores[1], time_e - time_s | b1d183118b304edf6f076caefa2b1160316ad92c | 7,886 |
from operator import mul
from operator import inv
def berlekamp_massey(s):
"""Given a sequence of LFSR outputs, find the coefficients of the LFSR."""
C, B, L, m, b = [1], [1], 0, 1, 1
for n in range(len(s)):
d = s[n]
for i in range(1, L + 1):
d ^= mul(C[i], s[n - i])
if d == 0:
m += 1
else:
T = list(C)
while len(C) <= len(B) + m:
C += [0]
t = mul(d, inv(b))
for i in range(len(B)):
C[i + m] ^= mul(t, B[i])
if 2 * L <= n:
L, B, b, m = n + 1 - L, T, d, 1
else:
m += 1
return C[0:L + 1] | 351f52dce7e4a95b986cc169f380347f317f851a | 7,887 |
import json
import sys
def vocab_from_file(vocabfile):
"""
Generates vocabulary from a vocabulary file in JSON
Outputs vocabulary and inverted vocabulary
"""
with smart_open(vocabfile, 'r') as f:
inv_vocab = json.loads(f.read())
vocabulary = {}
for no, word in enumerate(inv_vocab):
vocabulary[word] = no
print('Vocabulary size = %d' % len(vocabulary), file=sys.stderr)
return vocabulary, inv_vocab | a75fab1e94f5091aa691ad2ab188f0ada406f6ea | 7,888 |
from typing import Optional
def sample(image: type_alias.TensorLike,
warp: type_alias.TensorLike,
resampling_type: ResamplingType = ResamplingType.BILINEAR,
border_type: BorderType = BorderType.ZERO,
pixel_type: PixelType = PixelType.HALF_INTEGER,
name: Optional[str] = None) -> tf.Tensor:
"""Samples an image at user defined coordinates.
Note:
The warp maps target to source. In the following, A1 to An are optional
batch dimensions.
Args:
image: A tensor of shape `[B, H_i, W_i, C]`, where `B` is the batch size,
`H_i` the height of the image, `W_i` the width of the image, and `C` the
number of channels of the image.
warp: A tensor of shape `[B, A_1, ..., A_n, 2]` containing the x and y
coordinates at which sampling will be performed. The last dimension must
be 2, representing the (x, y) coordinate where x is the index for width
and y is the index for height.
resampling_type: Resampling mode. Supported values are
`ResamplingType.NEAREST` and `ResamplingType.BILINEAR`.
border_type: Border mode. Supported values are `BorderType.ZERO` and
`BorderType.DUPLICATE`.
pixel_type: Pixel mode. Supported values are `PixelType.INTEGER` and
`PixelType.HALF_INTEGER`.
name: A name for this op. Defaults to "sample".
Returns:
Tensor of sampled values from `image`. The output tensor shape
is `[B, A_1, ..., A_n, C]`.
Raises:
ValueError: If `image` has rank != 4. If `warp` has rank < 2 or its last
dimension is not 2. If `image` and `warp` batch dimension does not match.
"""
with tf.name_scope(name or "sample"):
image = tf.convert_to_tensor(image, name="image")
warp = tf.convert_to_tensor(warp, name="warp")
shape.check_static(image, tensor_name="image", has_rank=4)
shape.check_static(
warp,
tensor_name="warp",
has_rank_greater_than=1,
has_dim_equals=(-1, 2))
shape.compare_batch_dimensions(
tensors=(image, warp), last_axes=0, broadcast_compatible=False)
if pixel_type == PixelType.HALF_INTEGER:
warp -= 0.5
if resampling_type == ResamplingType.NEAREST:
warp = tf.math.round(warp)
if border_type == BorderType.DUPLICATE:
image_size = tf.cast(tf.shape(image)[1:3], dtype=warp.dtype)
height, width = tf.unstack(image_size, axis=-1)
warp_x, warp_y = tf.unstack(warp, axis=-1)
warp_x = tf.clip_by_value(warp_x, 0.0, width - 1.0)
warp_y = tf.clip_by_value(warp_y, 0.0, height - 1.0)
warp = tf.stack((warp_x, warp_y), axis=-1)
return tfa_image.resampler(image, warp) | c9a202a6415d13bddac38cfa75e280ad45f1bda6 | 7,889 |
def normalize_parameter(kv):
"""
Translate a parameter into standard form.
"""
(k, v) = kv
if k[0] == 'requiressl' and v in ('1', True):
k[0] = 'sslmode'
v = 'require'
elif k[0] == 'dbname':
k[0] = 'database'
elif k[0] == 'sslmode':
v = v.lower()
return (tuple(k),v) | 933ea71f452a16c1d4ae2630d6b58a92da1cbec0 | 7,890 |
def pulse_broadening(DM, f_ctr):
"""
pulse_broadening(DM, f_ctr):
Return the approximate pulse broadening (tau) in ms due to scattering
based on the rough relation in Cordes' 'Pulsar Observations I' paper.
'f_ctr' should be in MHz. The approximate error is 0.65 in log(tau).
"""
logDM = Num.log10(DM)
return 10.0**(-3.59 + 0.129*logDM + 1.02*logDM**2.0 -
4.4*Num.log10(f_ctr/1000.0))/1000.0 | 48830e02774247e551605e5e8ad693ece68634ad | 7,891 |
from amset.tools.wavefunction import wave
from pathlib import Path
from click.testing import CliRunner
def generate_wavefunction_coefficients(dir_name: str):
"""
Generate wavefunction.h5 file using amset.
Parameters
----------
dir_name : str
Directory containing WAVECAR and vasprun.xml files (can be gzipped).
Returns
-------
dict
A dictionary with the keys:
- "dir_name" (str): containing the directory where the wavefunction.h5 file was
generated.
- "log" (str): The output log from ``amset wave``.
- "ibands" (Tuple[List[int], ...]): The bands included in the wavefunction.h5
file. Given as a tuple of one or two lists (one for each spin channel).
The bands indices are zero indexed.
"""
dir_name = strip_hostname(dir_name) # TODO: Handle hostnames properly.
fc = FileClient()
files = fc.listdir(dir_name)
vasprun_file = Path(dir_name) / get_zfile(files, "vasprun.xml")
wavecar_file = Path(dir_name) / get_zfile(files, "WAVECAR")
# wavecar can't be gzipped, so copy it to current directory and unzip it
fc.copy(wavecar_file, wavecar_file.name)
fc.gunzip(wavecar_file.name)
args = ["--wavecar=WAVECAR", f"--vasprun={vasprun_file}"]
runner = CliRunner()
result = runner.invoke(wave, args, catch_exceptions=False)
ibands = _extract_ibands(result.output)
# remove WAVECAR from current directory
fc.remove("WAVECAR")
return {"dir_name": str(Path.cwd()), "log": result.output, "ibands": ibands} | 0119d18436373753d9e2a1202f185c983fa83963 | 7,892 |
def logged_in_student(browser, override_allowed_hosts, base_test_data):
"""
Fixture for a logged-in student user
Returns:
User: User object
"""
return LoginPage(browser).log_in_via_admin(base_test_data.student_user, DEFAULT_PASSWORD) | 4513e8c8356cd8fbd643e9018e1019c5ec403bcd | 7,893 |
import numpy as np
import tqdm
def test_model(data_set=None, langider=None, lang_to_idx=None, ) -> np.ndarray:
"""
Tests a given langid.py model on the given data set.
:param data_set: data set to test on
:param langider: model to test
:param lang_to_idx: mapping of languages to ids
"""
langs = data_set.get_tag_set()
pred_prob = np.zeros((len(data_set), len(langs) + 1))
dataloader = DataLoader(data_set)
for i, elem in enumerate(tqdm(dataloader)):
text = elem['text'][0]
label = elem['label'][0]
ranking = langider.rank(text)
for lang, prob in ranking:
pred_prob[i, lang_to_idx[lang]] = prob
pred_prob[i, len(langs)] = lang_to_idx[label]
return pred_prob | 2b955b637a289d0596c0584ac0761d8014e27e86 | 7,894 |
from bs4 import BeautifulSoup
def search(querry, lim=5):
"""Search the querry in youtube and return lim number of results.
Querry is the keyword, i:e name of the song
lim is the number of songs that will be added to video array and returned
"""
# Replace all the spaces with +
querry = querry.replace(' ', '+')
url = "https://www.youtube.com/results?search_query={}".format(querry)
response = urlopen(url)
html = response.read()
soup = BeautifulSoup(html, "html.parser")
count = 0
for vid in soup.findAll(attrs={'class': 'yt-uix-tile-link'}):
if lim == count:
break
url = vid['href']
data = scan_video(url)
if not data:
break
video.append(data)
urls.append(url)
count += 1
return (video, urls) | 92771e6aaa88ea65034981ff0c0c3b203addacec | 7,895 |
def calculate_center_of_mass(symbols, coordinates):
"""Calculate the center of mass of a molecule.
The center of mass is weighted by each atom's weight.
Parameters
----------
symbols : list
A list of elements for the molecule
coordinates : np.ndarray
The coordinates of the molecule.
Returns
-------
center_of_mass: np.ndarray
The center of mass of the molecule.
Notes
-----
The center of mass is calculated with the formula
.. math:: \\vec{R}=\\frac{1}{M} \\sum_{i=1}^{n} m_{i}\\vec{r_{}i}
"""
total_mass = calculate_molecular_mass(symbols)
center_of_mass = np.array([0.0, 0.0, 0.0])
for atom_number in range(len(symbols)):
atom_type = symbols[atom_number]
mass_of_atom = atomic_weights[atom_type]
atom_position = coordinates[atom_number]
center_of_mass += mass_of_atom * atom_position
center_of_mass = center_of_mass / total_mass
return center_of_mass | 34a32e86c42875db59ad9d1bd1a6801d6fd51eb1 | 7,896 |
def __iadd__(self, other):
"""Pythonic use of concat
Example:
xs += ys
Returns self.concat(self, other)"""
return self.concat(self, other) | 713980aed9713c2882a19ae9837315a431611bbc | 7,897 |
def remove_stopwords(texts, stop_words):
"""
Define functions for stopwords
:param texts: Processed texts from main module
:return: Texts that already removed a stopwords
"""
return [[word for word in simple_preprocess(str(doc)) if word not in stop_words] for doc in texts] | 9e2f4bcf87886a35c3877de34d6746942af19065 | 7,898 |
import json
def dumps(obj):
"""Output json with formatting edits + object handling."""
return json.dumps(obj, indent=4, sort_keys=True,
cls=CustomEncoder) | a9ad97c589a8f610d3186723566420604d99f4de | 7,899 |
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