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python | def implied_timescales(sequences, lag_times, n_timescales=10,
msm=None, n_jobs=1, verbose=0):
"""
Calculate the implied timescales for a given MSM.
Parameters
----------
sequences : list of array-like
List of sequences, or a single sequence. Each
sequence should be a 1D iterable of state
labels. Labels can be integers, strings, or
other orderable objects.
lag_times : array-like
Lag times to calculate implied timescales at.
n_timescales : int, optional
Number of timescales to calculate.
msm : msmbuilder.msm.MarkovStateModel, optional
Instance of an MSM to specify parameters other
than the lag time. If None, then the default
parameters (as implemented by msmbuilder.msm.MarkovStateModel)
will be used.
n_jobs : int, optional
Number of jobs to run in parallel
Returns
-------
timescales : np.ndarray, shape = [n_models, n_timescales]
The slowest timescales (in units of lag times) for each
model.
"""
if msm is None:
msm = MarkovStateModel()
param_grid = {'lag_time' : lag_times}
models = param_sweep(msm, sequences, param_grid, n_jobs=n_jobs,
verbose=verbose)
timescales = [m.timescales_ for m in models]
n_timescales = min(n_timescales, min(len(ts) for ts in timescales))
timescales = np.array([ts[:n_timescales] for ts in timescales])
return timescales |
java | @Override
public Long append(final String key, final String value) {
return this.d_append(key, value).getResult();
} |
java | public static ByteBuffer asByteBuffer(String expression, Node node)
throws XPathExpressionException {
return asByteBuffer(expression, node, xpath());
} |
java | @Override
public void generatedFile(final String fileName, final int current, final int total) {
if (log.isDebugEnabled()) {
log.debug("Processing file [" + current + "/" + total + "]: " + fileName);
}
} |
java | @NonNull
private static List<Point> coordAll(@NonNull List<Point> coords, @NonNull Point point) {
coords.add(point);
return coords;
} |
java | @Override
public File findMostRecentSnapshot() throws IOException {
List<File> files = findNValidSnapshots(1);
if (files.size() == 0) {
return null;
}
return files.get(0);
} |
java | @TargetApi(Build.VERSION_CODES.LOLLIPOP)
public static String optString(@Nullable Bundle bundle, @Nullable String key, @Nullable String fallback) {
if (bundle == null) {
return fallback;
}
return bundle.getString(key, fallback);
} |
java | public static void generateCylinder(TFloatList positions, TFloatList normals, TIntList indices, float radius, float height) {
// 0,0,0 will be halfway up the cylinder in the middle
final float halfHeight = height / 2;
// The positions at the rims of the cylinders
final List<Vector3f> rims = new ArrayList<>();
for (int angle = 0; angle < 360; angle += 15) {
final double angleRads = Math.toRadians(angle);
rims.add(new Vector3f(
radius * TrigMath.cos(angleRads),
halfHeight,
radius * -TrigMath.sin(angleRads)));
}
// The normals for the triangles of the top and bottom faces
final Vector3f topNormal = new Vector3f(0, 1, 0);
final Vector3f bottomNormal = new Vector3f(0, -1, 0);
// Add the top and bottom face center vertices
addVector(positions, new Vector3f(0, halfHeight, 0));// 0
addVector(normals, topNormal);
addVector(positions, new Vector3f(0, -halfHeight, 0));// 1
addVector(normals, bottomNormal);
// Add all the faces section by section, turning around the y axis
final int rimsSize = rims.size();
for (int i = 0; i < rimsSize; i++) {
// Get the top and bottom vertex positions and the side normal
final Vector3f t = rims.get(i);
final Vector3f b = new Vector3f(t.getX(), -t.getY(), t.getZ());
final Vector3f n = new Vector3f(t.getX(), 0, t.getZ()).normalize();
// Top face vertex
addVector(positions, t);// index
addVector(normals, topNormal);
// Bottom face vertex
addVector(positions, b);// index + 1
addVector(normals, bottomNormal);
// Side top vertex
addVector(positions, t);// index + 2
addVector(normals, n);
// Side bottom vertex
addVector(positions, b);// index + 3
addVector(normals, n);
// Get the current index for our vertices
final int currentIndex = i * 4 + 2;
// Get the index for the next iteration, wrapping around at the end
final int nextIndex = (i == rimsSize - 1 ? 0 : i + 1) * 4 + 2;
// Add the 4 triangles (1 top, 1 bottom, 2 for the side)
addAll(indices, 0, currentIndex, nextIndex);
addAll(indices, 1, nextIndex + 1, currentIndex + 1);
addAll(indices, currentIndex + 2, currentIndex + 3, nextIndex + 2);
addAll(indices, currentIndex + 3, nextIndex + 3, nextIndex + 2);
}
} |
python | def get_current_shutit_pexpect_session(self, note=None):
"""Returns the currently-set default pexpect child.
@return: default shutit pexpect child object
"""
self.handle_note(note)
res = self.current_shutit_pexpect_session
self.handle_note_after(note)
return res |
java | public Interval withStart(ReadableInstant start) {
long startMillis = DateTimeUtils.getInstantMillis(start);
return withStartMillis(startMillis);
} |
java | public void onDrawFrame(float frameTime)
{
GVRSceneObject owner = getOwnerObject();
if (owner == null)
{
return;
}
if (mSwitchIndex < 0 || mSwitchIndex > owner.rawGetChildren().size())
{
return;
}
int i = 0;
List<GVRSceneObject> children = owner.rawGetChildren();
for (GVRSceneObject child : children)
{
child.setEnable(i++ == mSwitchIndex);
}
} |
python | def _initialize(self, **resource_attributes):
"""
Initialize the collection.
:param resource_attributes: API resource parameters
"""
super(APIResourceCollection, self)._initialize(**resource_attributes)
dict_list = self.data
self.data = []
for resource in dict_list:
self.data.append(self._expected_api_resource(**resource)) |
python | def _find_from_file(full_doc, from_file_keyword):
"""
Finds a line in <full_doc> like
<from_file_keyword> <colon> <path>
and return path
"""
path = None
for line in full_doc.splitlines():
if from_file_keyword in line:
parts = line.strip().split(':')
if len(parts) == 2 and parts[0].strip() == from_file_keyword:
path = parts[1].strip()
break
return path |
java | protected final Stringifier<Long> registerLongStringifier(String name, Stringifier<Long> longStringifier) {
compositeStringifier.add(Long.class, name, longStringifier);
compositeStringifier.add(Long.TYPE, name, longStringifier);
return longStringifier;
} |
python | def backend_fields(self, fields):
'''Return a two elements tuple containing a list
of fields names and a list of field attribute names.'''
dfields = self.dfields
processed = set()
names = []
atts = []
pkname = self.pkname()
for name in fields:
if name == pkname or name in processed:
continue
elif name in dfields:
processed.add(name)
field = dfields[name]
names.append(field.name)
atts.append(field.attname)
else:
bname = name.split(JSPLITTER)[0]
if bname in dfields:
field = dfields[bname]
if field.type in ('json object', 'related object'):
processed.add(name)
names.append(name)
atts.append(name)
return names, atts |
python | def graph(self):
""" Returns MultiDiGraph from kihs. Nodes are helices and edges are kihs. """
g = networkx.MultiDiGraph()
edge_list = [(x.knob_helix, x.hole_helix, x.id, {'kih': x}) for x in self.get_monomers()]
g.add_edges_from(edge_list)
return g |
python | def to_syllables_with_trailing_spaces(line: str, syllables: List[str]) -> List[str]:
"""
Given a line of syllables and spaces, and a list of syllables, produce a list of the
syllables with trailing spaces attached as approriate.
:param line:
:param syllables:
:return:
>>> to_syllables_with_trailing_spaces(' arma virumque cano ',
... ['ar', 'ma', 'vi', 'rum', 'que', 'ca', 'no' ])
[' ar', 'ma ', 'vi', 'rum', 'que ', 'ca', 'no ']
"""
syllabs_spaces = []
idx = 0
linelen = len(line)
for position, syl in enumerate(syllables):
start = line.index(syl, idx)
idx = start + len(syl)
if position == 0 and start > 0: # line starts with punctuation, substituted w/ spaces
syl = (start * " ") + syl
if idx + 1 > len(line):
syllabs_spaces.append(syl)
return syllabs_spaces
nextchar = line[idx]
if nextchar != " ":
syllabs_spaces.append(syl)
continue
else:
tmpidx = idx
while tmpidx < linelen and nextchar == " ":
syl += " "
tmpidx += 1
if tmpidx == linelen:
syllabs_spaces.append(syl)
return syllabs_spaces
nextchar = line[tmpidx]
idx = tmpidx - 1
syllabs_spaces.append(syl)
return syllabs_spaces |
python | def from_dict(cls, d):
"""
Reconstructs the StructureEnvironments object from a dict representation of the StructureEnvironments created
using the as_dict method.
:param d: dict representation of the StructureEnvironments object
:return: StructureEnvironments object
"""
ce_list = [None if (ce_dict == 'None' or ce_dict is None) else {
int(cn): [None if (ced is None or ced == 'None') else
ChemicalEnvironments.from_dict(ced) for ced in ce_dict[cn]]
for cn in ce_dict} for ce_dict in d['ce_list']]
voronoi = DetailedVoronoiContainer.from_dict(d['voronoi'])
structure = Structure.from_dict(d['structure'])
neighbors_sets = [{int(cn): [cls.NeighborsSet.from_dict(dd=nb_set_dict,
structure=structure,
detailed_voronoi=voronoi)
for nb_set_dict in nb_sets]
for cn, nb_sets in site_nbs_sets_dict.items()}
if site_nbs_sets_dict is not None else None
for site_nbs_sets_dict in d['neighbors_sets']]
info = {key: val for key, val in d['info'].items() if key not in ['sites_info']}
if 'sites_info' in d['info']:
info['sites_info'] = [{'nb_sets_info': {int(cn): {int(inb_set): nb_set_info
for inb_set, nb_set_info in cn_sets.items()}
for cn, cn_sets in site_info['nb_sets_info'].items()},
'time': site_info['time']} if 'nb_sets_info' in site_info else {}
for site_info in d['info']['sites_info']]
return cls(voronoi=voronoi, valences=d['valences'],
sites_map=d['sites_map'],
equivalent_sites=[[PeriodicSite.from_dict(psd) for psd in psl] for psl in d['equivalent_sites']],
ce_list=ce_list, structure=structure,
neighbors_sets=neighbors_sets,
info=info) |
java | public void displayDialog() throws Exception {
Map<String, String[]> params = initAdminTool();
// explorer view dialogs
if (CmsExplorerDialog.EXPLORER_TOOLS.contains(getCurrentToolPath())) {
if (getAction() == CmsDialog.ACTION_CANCEL) {
actionCloseDialog();
return;
}
getToolManager().jspForwardPage(this, CmsToolManager.ADMINVIEW_ROOT_LOCATION + "/tool-fs.jsp", params);
return;
}
// real tool
if (!getAdminTool().getHandler().getLink().equals(getCms().getRequestContext().getUri())) {
getToolManager().jspForwardPage(this, getAdminTool().getHandler().getLink(), params);
return;
}
// just grouping
if (getAction() == CmsDialog.ACTION_CANCEL) {
actionCloseDialog();
return;
}
JspWriter out = getJsp().getJspContext().getOut();
out.print(htmlStart());
out.print(bodyStart(null));
out.print(dialogStart());
out.print(dialogContentStart(getParamTitle()));
out.print(dialogContentEnd());
out.print(dialogEnd());
out.print(bodyEnd());
out.print(htmlEnd());
} |
java | public static Observable<? extends AVUser> logIn(String username, String password) {
return logIn(username, password, internalUserClazz());
} |
python | def get_table_name(self, ind):
"""
Return both the table_name (i.e., 'specimens')
and the col_name (i.e., 'specimen')
for a given index in self.ancestry.
"""
if ind >= len(self.ancestry):
return "", ""
if ind > -1:
table_name = self.ancestry[ind]
###name = table_name[:-1] + "_name"
name = table_name[:-1]
return table_name, name
return "", "" |
python | def cal_continue(self, list_data):
""" 計算持續天數
:rtype: int
:returns: 向量數值：正數向上、負數向下。
"""
diff_data = []
for i in range(1, len(list_data)):
if list_data[-i] > list_data[-i - 1]:
diff_data.append(1)
else:
diff_data.append(-1)
cont = 0
for value in diff_data:
if value == diff_data[0]:
cont += 1
else:
break
return cont * diff_data[0] |
python | def flatten(data):
"""Returns a flattened version of a list.
Courtesy of https://stackoverflow.com/a/12472564
Args:
data (`tuple` or `list`): Input data
Returns:
`list`
"""
if not data:
return data
if type(data[0]) in (list, tuple):
return list(flatten(data[0])) + list(flatten(data[1:]))
return list(data[:1]) + list(flatten(data[1:])) |
python | def _get_group_from_state(self, sid):
"""
Args:
sid (int): The state identifier
Return:
int: The group identifier that the state belongs
"""
for index, selectgroup in enumerate(self.groups):
if sid in selectgroup:
return index |
java | public void init(String st, int minsize, int maxsize) {
super.init(buildString(st.trim(), minsize), minsize, maxsize);
} |
java | public VariantMetadata loadPedigree(Pedigree pedigree, String studyId) {
VariantStudyMetadata variantStudyMetadata = getVariantStudyMetadata(studyId);
if (variantStudyMetadata != null) {
boolean found;
org.opencb.biodata.models.metadata.Individual dest = null;
for (Member src: pedigree.getMembers()) {
found = false;
for (int i = 0; i < variantStudyMetadata.getIndividuals().size(); i++) {
dest = variantStudyMetadata.getIndividuals().get(i);
if (dest.getId().equals(src.getName())) {
found = true;
break;
}
}
if (found) {
dest.setFamily(pedigree.getName());
dest.setFather(src.getFather() != null ? src.getFather().getName() : null);
dest.setMother(src.getMother() != null ? src.getMother().getName() : null);
dest.setSex(src.getSex().toString());
dest.setPhenotype(src.getAffectionStatus().toString());
Sample sample = null;
// sanity check
if (dest.getSamples() == null) {
logger.warn("Loading pedigree, individual {} without samples: it will be added.", dest.getId());
dest.setSamples(new ArrayList<>());
}
for (Sample s: dest.getSamples()) {
if (s.getId().equals(dest.getId())) {
sample = s;
break;
}
}
// sample not found, add as a new one
if (sample == null) {
sample = new Sample();
sample.setId(dest.getId());
sample.setAnnotations(new HashMap<>());
dest.getSamples().add(sample);
}
if (sample.getAnnotations() == null) {
sample.setAnnotations(new HashMap<>());
}
// Default annotation (attributes from Individual)
sample.getAnnotations().put(INDIVIDUAL_ID, src.getName());
sample.getAnnotations().put(INDIVIDUAL_FAMILY, pedigree.getName());
if (src.getFather() != null) {
sample.getAnnotations().put(INDIVIDUAL_FATHER, src.getFather().getName());
}
if (src.getMother() != null) {
sample.getAnnotations().put(INDIVIDUAL_MOTHER, src.getMother().getName());
}
if (src.getSex() != null) {
sample.getAnnotations().put(INDIVIDUAL_SEX, src.getSex().toString());
}
if (src.getAffectionStatus() != null) {
sample.getAnnotations().put(INDIVIDUAL_PHENOTYPE, src.getAffectionStatus().toString());
}
if (src.getAttributes() != null && src.getAttributes().size() > 0) {
// Custom annotation
for (String key : src.getAttributes().keySet()) {
if (pedigree.getAttributes().get(key) != null) {
sample.getAnnotations().put(key, src.getAttributes().get(key).toString());
}
}
}
} else {
logger.warn("Loading pedigree, individual {} not found in metadata file, it will not be added.", src.getName());
}
}
} else {
logger.warn("Loading pedigree, nothing to do because study ID '{}' does not exist.", studyId);
}
return variantMetadata;
} |
python | def descendants(self, node):
""" Returns a :class:`QuerySet` with all descendants for a given
:class:`CTENode` `node`.
:param node: the :class:`CTENode` whose descendants are required.
:returns: A :class:`QuerySet` with all descendants of the given
`node`.
"""
# We need to read the _cte_node_* attributes, so ensure they exist.
self._ensure_parameters()
# This is implemented in the CTE WHERE logic, so we pass a reference to
# the offset CTENode to the custom QuerySet, which will process it.
# Because the compiler will include the node in question in the offset,
# we must exclude it here.
return CTEQuerySet(self.model, using=self._db, offset=node).exclude(pk=node.pk) |
java | protected void createLibraryHandlingGroup(Composite parent) {
fLibraryHandlingGroup= new Composite(parent, SWT.NONE);
GridLayout layout= new GridLayout();
fLibraryHandlingGroup.setLayout(layout);
fLibraryHandlingGroup.setLayoutData(new GridData(GridData.HORIZONTAL_ALIGN_FILL | GridData.VERTICAL_ALIGN_FILL | GridData.GRAB_HORIZONTAL));
createLabel(fLibraryHandlingGroup, FatJarPackagerMessages.FatJarPackageWizardPage_libraryHandlingGroupTitle, false);
fExtractJarsRadioButton= new Button(fLibraryHandlingGroup, SWT.RADIO | SWT.LEFT);
fExtractJarsRadioButton.setText(FatJarPackagerMessages.FatJarPackageWizardPage_extractJars_text);
fExtractJarsRadioButton.setLayoutData(new GridData(GridData.FILL_HORIZONTAL));
fExtractJarsRadioButton.addListener(SWT.Selection, new Listener() {
@Override
public void handleEvent(Event event) {
if (((Button)event.widget).getSelection())
fLibraryHandler= new ExtractLibraryHandler();
}
});
fPackageJarsRadioButton= new Button(fLibraryHandlingGroup, SWT.RADIO | SWT.LEFT);
fPackageJarsRadioButton.setText(FatJarPackagerMessages.FatJarPackageWizardPage_packageJars_text);
fPackageJarsRadioButton.setLayoutData(new GridData(GridData.FILL_HORIZONTAL));
fPackageJarsRadioButton.addListener(SWT.Selection, new Listener() {
@Override
public void handleEvent(Event event) {
if (((Button)event.widget).getSelection())
fLibraryHandler= new PackageLibraryHandler();
}
});
fCopyJarFilesRadioButton= new Button(fLibraryHandlingGroup, SWT.RADIO | SWT.LEFT);
fCopyJarFilesRadioButton.setText(FatJarPackagerMessages.FatJarPackageWizardPage_copyJarFiles_text);
fCopyJarFilesRadioButton.setLayoutData(new GridData(GridData.FILL_HORIZONTAL));
fCopyJarFilesRadioButton.addListener(SWT.Selection, new Listener() {
@Override
public void handleEvent(Event event) {
if (((Button)event.widget).getSelection())
fLibraryHandler= new CopyLibraryHandler();
}
});
// set default for first selection (no previous widget settings to restore)
setLibraryHandler(new ExtractLibraryHandler());
} |
python | def conditional_jit(function=None, **kwargs): # noqa: D202
"""Use numba's jit decorator if numba is installed.
Notes
-----
If called without arguments then return wrapped function.
@conditional_jit
def my_func():
return
else called with arguments
@conditional_jit(nopython=True)
def my_func():
return
"""
def wrapper(function):
try:
numba = importlib.import_module("numba")
return numba.jit(**kwargs)(function)
except ImportError:
return function
if function:
return wrapper(function)
else:
return wrapper |
python | def postActivate_(self):
"""Whatever you need to do after creating the shmem client
"""
if (self.requiredGPU_MB(self.required_mb)):
self.analyzer = YoloV3TinyAnalyzer(verbose = self.verbose)
else:
self.warning_message = "WARNING: not enough GPU memory!"
self.analyzer = None |
python | def _to_dict(objects):
'''
Potentially interprets a string as JSON for usage with mongo
'''
try:
if isinstance(objects, six.string_types):
objects = salt.utils.json.loads(objects)
except ValueError as err:
log.error("Could not parse objects: %s", err)
raise err
return objects |
python | def private_config_file(self):
"""
Returns the private-config file for this IOU VM.
:returns: path to config file. None if the file doesn't exist
"""
path = os.path.join(self.working_dir, 'private-config.cfg')
if os.path.exists(path):
return path
else:
return None |
java | public Observable<ManagementPolicyInner> createOrUpdateAsync(String resourceGroupName, String accountName, ManagementPolicySchema policy) {
return createOrUpdateWithServiceResponseAsync(resourceGroupName, accountName, policy).map(new Func1<ServiceResponse<ManagementPolicyInner>, ManagementPolicyInner>() {
@Override
public ManagementPolicyInner call(ServiceResponse<ManagementPolicyInner> response) {
return response.body();
}
});
} |
python | def explained_variance(returns, values):
""" Calculate how much variance in returns do the values explain """
exp_var = 1 - torch.var(returns - values) / torch.var(returns)
return exp_var.item() |
python | def query(self,sql):
"""
Execute an SQL query on the server and fetch the resulting XML file
back.
@return: message received (may be empty) from LDBD Server as a string
"""
msg = "QUERY\0" + sql + "\0"
self.sfile.write(msg)
ret, output = self.__response__()
reply = str(output[0])
if ret:
msg = "Error executing query on server %d:%s" % (ret, reply)
raise LDBDClientException, msg
return reply |
python | def user_data(self, access_token, *args, **kwargs):
"""Loads user data from service"""
try:
user_data = super().user_data(access_token, *args, **kwargs)
if not user_data.get('email'):
raise AuthFailed(self, _('You must have a public email configured in GitHub. '
'Goto Settings/Profile and choose your public email'))
except AuthFailed:
raise AuthFailed(self, _('Sorry, you do not seem to be a public member of %s') % self.setting('NAME'))
return user_data |
java | public String buildJson() throws ODataRenderException {
LOG.debug("Start building Json service root document");
try (ByteArrayOutputStream stream = new ByteArrayOutputStream()) {
JsonGenerator jsonGenerator = JSON_FACTORY.createGenerator(stream, JsonEncoding.UTF8);
jsonGenerator.writeStartObject();
jsonGenerator.writeStringField(CONTEXT, getContextURL(uri, entityDataModel));
jsonGenerator.writeArrayFieldStart(VALUE);
List<EntitySet> entities = entityDataModel.getEntityContainer().getEntitySets();
for (EntitySet entity : entities) {
if (entity.isIncludedInServiceDocument()) {
writeObject(jsonGenerator, entity);
}
}
List<Singleton> singletons = entityDataModel.getEntityContainer().getSingletons();
for (Singleton singleton : singletons) {
writeObject(jsonGenerator, singleton);
}
jsonGenerator.writeEndArray();
jsonGenerator.writeEndObject();
jsonGenerator.close();
return stream.toString(StandardCharsets.UTF_8.name());
} catch (IOException e) {
throw new ODataRenderException("It is unable to render service document", e);
}
} |
java | public GetDatabaseOperation buildGetDatabaseOperation(String databasePath, String key, String name) {
return new GetDatabaseOperation(getOperationFactory(), databasePath, key, name);
} |
java | protected static String makeComponentPrefix(String tokenName, String className) {
String simpleClassName = className;
if (null != className) {
int lastDotIdx = className.lastIndexOf(".");
if (lastDotIdx > -1) {
simpleClassName = className.substring(lastDotIdx + 1, className.length());
}
}
return tokenName + "." + simpleClassName + ".";
} |
python | def compute_correlation(matrix1, matrix2, return_nans=False):
"""compute correlation between two sets of variables
Correlate the rows of matrix1 with the rows of matrix2.
If matrix1 == matrix2, it is auto-correlation computation
resulting in a symmetric correlation matrix.
The number of columns MUST agree between set1 and set2.
The correlation being computed here is
the Pearson's correlation coefficient, which can be expressed as
.. math:: corr(X, Y) = \\frac{cov(X, Y)}{\\sigma_X\\sigma_Y}
where cov(X, Y) is the covariance of variable X and Y, and
.. math:: \\sigma_X
is the standard deviation of variable X
Reducing the correlation computation to matrix multiplication
and using BLAS GEMM API wrapped by Scipy can speedup the numpy built-in
correlation computation (numpy.corrcoef) by one order of magnitude
.. math::
corr(X, Y)
&= \\frac{\\sum\\limits_{i=1}^n (x_i-\\bar{x})(y_i-\\bar{y})}{(n-1)
\\sqrt{\\frac{\\sum\\limits_{j=1}^n x_j^2-n\\bar{x}}{n-1}}
\\sqrt{\\frac{\\sum\\limits_{j=1}^{n} y_j^2-n\\bar{y}}{n-1}}}\\\\
&= \\sum\\limits_{i=1}^n(\\frac{(x_i-\\bar{x})}
{\\sqrt{\\sum\\limits_{j=1}^n x_j^2-n\\bar{x}}}
\\frac{(y_i-\\bar{y})}{\\sqrt{\\sum\\limits_{j=1}^n y_j^2-n\\bar{y}}})
By default (return_nans=False), returns zeros for vectors with NaNs.
If return_nans=True, convert zeros to NaNs (np.nan) in output.
Parameters
----------
matrix1: 2D array in shape [r1, c]
MUST be continuous and row-major
matrix2: 2D array in shape [r2, c]
MUST be continuous and row-major
return_nans: bool, default:False
If False, return zeros for NaNs; if True, return NaNs
Returns
-------
corr_data: 2D array in shape [r1, r2]
continuous and row-major in np.float32
"""
matrix1 = matrix1.astype(np.float32)
matrix2 = matrix2.astype(np.float32)
[r1, d1] = matrix1.shape
[r2, d2] = matrix2.shape
if d1 != d2:
raise ValueError('Dimension discrepancy')
# preprocess two components
matrix1 = _normalize_for_correlation(matrix1, 1,
return_nans=return_nans)
matrix2 = _normalize_for_correlation(matrix2, 1,
return_nans=return_nans)
corr_data = np.empty((r1, r2), dtype=np.float32, order='C')
# blas routine is column-major
blas.compute_single_matrix_multiplication('T', 'N',
r2, r1, d1,
1.0,
matrix2, d2,
matrix1, d1,
0.0,
corr_data,
r2)
return corr_data |
java | public void configConstant(Constants me) {
//load properties
this.loadPropertyFile();
me.setViewType(ViewType.JSP);
me.setDevMode(this.getAppDevMode());
me.setEncoding(Const.DEFAULT_ENCODING);
me.setError404View(PageViewKit.get404PageView());
me.setError500View(PageViewKit.get500PageView());
me.setError403View(PageViewKit.get403PageView());
JFinalConfigExt.APP_NAME = this.getAppName();
// config others
configMoreConstants(me);
} |
java | public void addExcludedlaceId(final String placeId) {
if (null == this.countryCodes) {
this.excludePlaceIds = new ArrayList<String>();
}
this.excludePlaceIds.add(placeId);
} |
java | @Override
public Document parseXML(String string) {
try {
return loadXML(new ByteArrayInputStream(string.getBytes("UTF-8")));
} catch (UnsupportedEncodingException e) {
throw new BugError("JVM with missing support for UTF-8.");
}
} |
python | def parse_numeric(self):
"""Tokenize a Fortran numerical value."""
word = ''
frac = False
if self.char == '-':
word += self.char
self.update_chars()
while self.char.isdigit() or (self.char == '.' and not frac):
# Only allow one decimal point
if self.char == '.':
frac = True
word += self.char
self.update_chars()
# Check for float exponent
if self.char in 'eEdD':
word += self.char
self.update_chars()
if self.char in '+-':
word += self.char
self.update_chars()
while self.char.isdigit():
word += self.char
self.update_chars()
return word |
java | @Override
public UpdateGatewayGroupResult updateGatewayGroup(UpdateGatewayGroupRequest request) {
request = beforeClientExecution(request);
return executeUpdateGatewayGroup(request);
} |
java | private String getUserDn(String callerName, String filter, SearchControls controls) {
String userDn = null;
String searchBase = idStoreDefinition.getCallerSearchBase();
if (searchBase == null || searchBase.isEmpty()) {
userDn = idStoreDefinition.getCallerNameAttribute() + "=" + callerName + "," + idStoreDefinition.getCallerBaseDn();
} else {
DirContext ctx = null;
try {
ctx = bind();
} catch (NamingException e) {
Tr.error(tc, "JAVAEESEC_ERROR_EXCEPTION_ON_BIND", new Object[] { this.idStoreDefinition.getBindDn(), e });
throw new IllegalStateException(e);
}
try {
if (tc.isDebugEnabled()) {
Tr.debug(tc, "JNDI_CALL search", new Object[] { searchBase, filter, printControls(controls) });
}
NamingEnumeration<SearchResult> ne = ctx.search(new LdapName(searchBase), filter, controls);
if (ne.hasMoreElements()) {
userDn = ne.nextElement().getNameInNamespace();
if (ne.hasMoreElements()) {
Tr.warning(tc, "JAVAEESEC_WARNING_MULTI_CALLER_LDAP", new Object[] { callerName, filter, searchBase });
return null;
}
}
} catch (NamingException e) {
Tr.error(tc, "JAVAEESEC_ERROR_EXCEPTION_ON_SEARCH", new Object[] { callerName, filter, searchBase, e });
throw new IllegalStateException(e);
}
}
return userDn;
} |
java | public static TimerJobEntity createTimerEntityForTimerEventDefinition(TimerEventDefinition timerEventDefinition, boolean isInterruptingTimer,
ExecutionEntity executionEntity, String jobHandlerType, String jobHandlerConfig) {
ProcessEngineConfigurationImpl processEngineConfiguration = Context.getProcessEngineConfiguration();
String businessCalendarRef = null;
Expression expression = null;
ExpressionManager expressionManager = processEngineConfiguration.getExpressionManager();
// ACT-1415: timer-declaration on start-event may contain expressions NOT
// evaluating variables but other context, evaluating should happen nevertheless
VariableScope scopeForExpression = executionEntity;
if (scopeForExpression == null) {
scopeForExpression = NoExecutionVariableScope.getSharedInstance();
}
if (StringUtils.isNotEmpty(timerEventDefinition.getTimeDate())) {
businessCalendarRef = DueDateBusinessCalendar.NAME;
expression = expressionManager.createExpression(timerEventDefinition.getTimeDate());
} else if (StringUtils.isNotEmpty(timerEventDefinition.getTimeCycle())) {
businessCalendarRef = CycleBusinessCalendar.NAME;
expression = expressionManager.createExpression(timerEventDefinition.getTimeCycle());
} else if (StringUtils.isNotEmpty(timerEventDefinition.getTimeDuration())) {
businessCalendarRef = DurationBusinessCalendar.NAME;
expression = expressionManager.createExpression(timerEventDefinition.getTimeDuration());
}
if (StringUtils.isNotEmpty(timerEventDefinition.getCalendarName())) {
businessCalendarRef = timerEventDefinition.getCalendarName();
Expression businessCalendarExpression = expressionManager.createExpression(businessCalendarRef);
businessCalendarRef = businessCalendarExpression.getValue(scopeForExpression).toString();
}
if (expression == null) {
throw new ActivitiException("Timer needs configuration (either timeDate, timeCycle or timeDuration is needed) (" + timerEventDefinition.getId() + ")");
}
BusinessCalendar businessCalendar = processEngineConfiguration.getBusinessCalendarManager().getBusinessCalendar(businessCalendarRef);
String dueDateString = null;
Date duedate = null;
Object dueDateValue = expression.getValue(scopeForExpression);
if (dueDateValue instanceof String) {
dueDateString = (String) dueDateValue;
} else if (dueDateValue instanceof Date) {
duedate = (Date) dueDateValue;
} else if (dueDateValue instanceof DateTime) {
//JodaTime support
duedate = ((DateTime) dueDateValue).toDate();
} else if (dueDateValue != null) {
throw new ActivitiException("Timer '" + executionEntity.getActivityId()
+ "' was not configured with a valid duration/time, either hand in a java.util.Date or a String in format 'yyyy-MM-dd'T'hh:mm:ss'");
}
if (duedate == null && dueDateString != null) {
duedate = businessCalendar.resolveDuedate(dueDateString);
}
TimerJobEntity timer = null;
if (duedate != null) {
timer = Context.getCommandContext().getTimerJobEntityManager().create();
timer.setJobType(JobEntity.JOB_TYPE_TIMER);
timer.setRevision(1);
timer.setJobHandlerType(jobHandlerType);
timer.setJobHandlerConfiguration(jobHandlerConfig);
timer.setExclusive(true);
timer.setRetries(processEngineConfiguration.getAsyncExecutorNumberOfRetries());
timer.setDuedate(duedate);
if (executionEntity != null) {
timer.setExecution(executionEntity);
timer.setProcessDefinitionId(executionEntity.getProcessDefinitionId());
timer.setProcessInstanceId(executionEntity.getProcessInstanceId());
// Inherit tenant identifier (if applicable)
if (executionEntity.getTenantId() != null) {
timer.setTenantId(executionEntity.getTenantId());
}
}
}
if (StringUtils.isNotEmpty(timerEventDefinition.getTimeCycle())) {
// See ACT-1427: A boundary timer with a cancelActivity='true', doesn't need to repeat itself
boolean repeat = !isInterruptingTimer;
// ACT-1951: intermediate catching timer events shouldn't repeat according to spec
if (executionEntity != null) {
FlowElement currentElement = executionEntity.getCurrentFlowElement();
if (currentElement instanceof IntermediateCatchEvent) {
repeat = false;
}
}
if (repeat) {
String prepared = prepareRepeat(dueDateString);
timer.setRepeat(prepared);
}
}
if (timer != null && executionEntity != null) {
timer.setExecution(executionEntity);
timer.setProcessDefinitionId(executionEntity.getProcessDefinitionId());
// Inherit tenant identifier (if applicable)
if (executionEntity.getTenantId() != null) {
timer.setTenantId(executionEntity.getTenantId());
}
}
return timer;
} |
java | public String getTypeGeneric(boolean includeBrackets) {
if (isTypeGeneric() == false) {
return "";
}
String result = typeGenericName[0] + typeGenericExtends[0];
if (typeGenericExtends.length > 1) {
result += ", " + typeGenericName[1] + typeGenericExtends[1];
if (typeGenericExtends.length > 2) {
result += ", " + typeGenericName[2] + typeGenericExtends[2];
}
}
return includeBrackets && result.length() > 0 ? '<' + result + '>' : result;
} |
java | public void registerType(ModelElementType modelElementType, Class<? extends ModelElementInstance> instanceType) {
QName qName = ModelUtil.getQName(modelElementType.getTypeNamespace(), modelElementType.getTypeName());
typesByName.put(qName, modelElementType);
typesByClass.put(instanceType, modelElementType);
} |
python | def unflatten(flat_dict, separator='_'):
"""
Creates a hierarchical dictionary from a flattened dictionary
Assumes no lists are present
:param flat_dict: a dictionary with no hierarchy
:param separator: a string that separates keys
:return: a dictionary with hierarchy
"""
_unflatten_asserts(flat_dict, separator)
# This global dictionary is mutated and returned
unflattened_dict = dict()
def _unflatten(dic, keys, value):
for key in keys[:-1]:
dic = dic.setdefault(key, {})
dic[keys[-1]] = value
for item in flat_dict:
_unflatten(unflattened_dict, item.split(separator), flat_dict[item])
return unflattened_dict |
java | public GetSecurityPolicyResponse getSecurityPolicy(GetSecurityPolicyRequest request) {
checkNotNull(request, "The parameter request should NOT be null.");
checkStringNotEmpty(request.getName(),
"The parameter name should NOT be null or empty string.");
InternalRequest internalRequest = createRequest(HttpMethodName.GET, request, LIVE_SECURITY_POLICY,
request.getName());
return invokeHttpClient(internalRequest, GetSecurityPolicyResponse.class);
} |
java | static void setTheme(Context context, AttributeSet attrs) {
boolean nightModeEnabled = isNightModeEnabled(context);
if (shouldSetThemeFromPreferences(context)) {
int prefLightTheme = retrieveThemeResIdFromPreferences(context, NavigationConstants.NAVIGATION_VIEW_LIGHT_THEME);
int prefDarkTheme = retrieveThemeResIdFromPreferences(context, NavigationConstants.NAVIGATION_VIEW_DARK_THEME);
prefLightTheme = prefLightTheme == 0 ? R.style.NavigationViewLight : prefLightTheme;
prefDarkTheme = prefLightTheme == 0 ? R.style.NavigationViewDark : prefDarkTheme;
context.setTheme(nightModeEnabled ? prefDarkTheme : prefLightTheme);
return;
}
TypedArray styledAttributes = context.obtainStyledAttributes(attrs, R.styleable.NavigationView);
int lightTheme = styledAttributes.getResourceId(R.styleable.NavigationView_navigationLightTheme,
R.style.NavigationViewLight);
int darkTheme = styledAttributes.getResourceId(R.styleable.NavigationView_navigationDarkTheme,
R.style.NavigationViewDark);
styledAttributes.recycle();
context.setTheme(nightModeEnabled ? darkTheme : lightTheme);
} |
java | private void handleResidueAnnotation(String seqName, String featureName, String value) {
if (featureName.equals(GR_SURFACE_ACCESSIBILITY)) {
stockholmStructure.addSurfaceAccessibility(seqName, value);
} else if (featureName.equals(GR_TRANS_MEMBRANE)) {
stockholmStructure.addTransMembrane(seqName, value);
} else if (featureName.equals(GR_POSTERIOR_PROBABILITY)) {
stockholmStructure.addPosteriorProbability(seqName, value);
} else if (featureName.equals(GR_LIGAND_BINDING)) {
stockholmStructure.addLigandBinding(seqName, value);
} else if (featureName.equals(GR_ACTIVE_SITE)) {
stockholmStructure.addActiveSite(seqName, value);
} else if (featureName.equals(GR_AS_PFAM_PREDICTED)) {
stockholmStructure.addASPFamPredicted(seqName, value);
} else if (featureName.equals(GR_AS_SWISSPROT)) {
stockholmStructure.addASSwissProt(seqName, value);
} else if (featureName.equals(GR_INTRON)) {
stockholmStructure.addIntron(seqName, value);
} else if (featureName.equals(GR_SECONDARY_STRUCTURE)) {
stockholmStructure.addSecondaryStructure(seqName, value);
} else {
// unknown feature
logger.warn("Unknown Residue Feature [{}].\nPlease contact the Biojava team.", featureName);
}
} |
python | def read(self, filename):
'''
Read a file content.
:param string filename: The storage root-relative filename
:raises FileNotFound: If the file does not exists
'''
if not self.backend.exists(filename):
raise FileNotFound(filename)
return self.backend.read(filename) |
python | def _table_arg_to_table_ref(value, default_project=None):
"""Helper to convert a string or Table to TableReference.
This function keeps TableReference and other kinds of objects unchanged.
"""
if isinstance(value, six.string_types):
value = TableReference.from_string(value, default_project=default_project)
if isinstance(value, (Table, TableListItem)):
value = value.reference
return value |
python | def hash(self):
"""(property) Returns a unique hash value for the result."""
data_str = ';'.join(
[str(repr(var)) for var in
[self.N, self.K, self.X, self.L,
self.stat, self.cutoff, self.pval,
self.pval_thresh, self.escore_pval_thresh]])
data_str += ';'
data = data_str.encode('UTF-8') + self.indices.tobytes()
return str(hashlib.md5(data).hexdigest()) |
python | def post(self, ddata, url=SETUP_ENDPOINT, referer=SETUP_ENDPOINT):
"""Method to update some attributes on namespace."""
headers = HEADERS.copy()
if referer is None:
headers.pop('Referer')
else:
headers['Referer'] = referer
# append csrftoken
if 'csrfmiddlewaretoken' not in ddata.keys():
ddata['csrfmiddlewaretoken'] = self._parent.csrftoken
req = self._parent.client.post(url, headers=headers, data=ddata)
if req.status_code == 200:
self.update() |
java | @GuardedBy("evictionLock")
void drainWriteBuffer() {
for (int i = 0; i < WRITE_BUFFER_DRAIN_THRESHOLD; i++) {
final Runnable task = writeBuffer.poll();
if (task == null) {
break;
}
task.run();
}
} |
java | @Generated(value = "com.ibm.jtc.jax.tools.xjc.Driver", date = "2014-06-11T05:49:00-04:00", comments = "JAXB RI v2.2.3-11/28/2011 06:21 AM(foreman)-")
public List<ExceptionClassFilter.Include> getIncludeList() {
if (includeList == null) {
includeList = new ArrayList<ExceptionClassFilter.Include>();
}
return this.includeList;
} |
java | public static void putScript(String name, KotlinCompiledScript script) {
getInstance().scripts.put(name, script);
} |
python | def ra(self,*args,**kwargs):
"""
NAME:
ra
PURPOSE:
return the right ascension
INPUT:
t - (optional) time at which to get ra
obs=[X,Y,Z] - (optional) position of observer (in kpc)
(default=Object-wide default)
OR Orbit object that corresponds to the orbit
of the observer
Y is ignored and always assumed to be zero
ro= distance in kpc corresponding to R=1. (default=Object-wide default)
OUTPUT:
ra(t)
HISTORY:
2011-02-23 - Written - Bovy (NYU)
"""
_check_roSet(self,kwargs,'ra')
radec= self._radec(*args,**kwargs)
return radec[:,0] |
java | public void skipHttpHeader() throws IOException {
if (this.httpHeaderStream != null) {
// Empty the httpHeaderStream
for (int available = this.httpHeaderStream.available();
this.httpHeaderStream != null &&
(available = this.httpHeaderStream.available()) > 0;) {
// We should be in this loop once only we should only do this
// buffer allocation once.
byte [] buffer = new byte[available];
// The read nulls out httpHeaderStream when done with it so
// need check for null in the loop control line.
read(buffer, 0, available);
}
}
} |
java | @Override
public void removeByCommercePriceListId(long commercePriceListId) {
for (CommercePriceListUserSegmentEntryRel commercePriceListUserSegmentEntryRel : findByCommercePriceListId(
commercePriceListId, QueryUtil.ALL_POS, QueryUtil.ALL_POS, null)) {
remove(commercePriceListUserSegmentEntryRel);
}
} |
python | def sort_versions(self):
"""Sort entries by version.
The order is typically descending, but package order functions can
change this.
"""
if self.sorted:
return
for orderer in (self.solver.package_orderers or []):
entries = orderer.reorder(self.entries, key=lambda x: x.package)
if entries is not None:
self.entries = entries
self.sorted = True
if self.pr:
self.pr("sorted: %s packages: %s", self.package_name, repr(orderer))
return
# default ordering is version descending
self.entries = sorted(self.entries, key=lambda x: x.version, reverse=True)
self.sorted = True
if self.pr:
self.pr("sorted: %s packages: version descending", self.package_name) |
java | public EClass getRMI() {
if (rmiEClass == null) {
rmiEClass = (EClass)EPackage.Registry.INSTANCE.getEPackage(AfplibPackage.eNS_URI).getEClassifiers().get(332);
}
return rmiEClass;
} |
java | public static String getURL(URI uri) {
final StringBuilder buffer = new StringBuilder();
buffer.append(uri.getPath());
String query = uri.getQuery();
String fragment = uri.getFragment();
if (StringUtils.isNotBlank(query)) {
buffer.append('?').append(query);
}
if (StringUtils.isNotBlank(fragment)) {
buffer.append('#').append(fragment);
}
return buffer.toString();
} |
java | public int getNbWritten() throws DevFailed {
manageExceptions("getNbWritten");
return attrval.w_dim.dim_x * DIM_MINI(attrval.w_dim.dim_y);
} |
python | def otsu(fpath):
"""
Returns value of otsu threshold for an image
"""
img = imread(fpath, as_grey=True)
thresh = skimage.filter.threshold_otsu(img)
return thresh |
java | @Override
public void endElement(String uri, String l, String q) {
/*
* 1. If current element is a String, update its value from the string buffer.
* 2. Add the element to parent.
*/
XDB.Element element = Enum.valueOf(XDB.Element.class, l.toUpperCase());
switch (element) {
case M:
break;
case P:
_binder.put(_name, _text.toString());
break;
case T:
break;
case H:
_heading = _data.toArray(new String[_data.size()]);
break;
case R:
++_rindex;
break;
case C:
if (_heading == null) {
_data.add(_text.toString());
} else {
_binder.put(_name + '[' + _rindex + "]." + _heading[_cindex], _text.toString());
++_cindex;
}
break;
}
_text.setLength(0);
} |
java | public QueueReference build(Map<String, String> params) throws IOException {
return build(params, null,false);
} |
java | public Observable<ExpressRouteGatewayInner> createOrUpdateAsync(String resourceGroupName, String expressRouteGatewayName, ExpressRouteGatewayInner putExpressRouteGatewayParameters) {
return createOrUpdateWithServiceResponseAsync(resourceGroupName, expressRouteGatewayName, putExpressRouteGatewayParameters).map(new Func1<ServiceResponse<ExpressRouteGatewayInner>, ExpressRouteGatewayInner>() {
@Override
public ExpressRouteGatewayInner call(ServiceResponse<ExpressRouteGatewayInner> response) {
return response.body();
}
});
} |
python | def time_stops(self):
""" Valid time steps for this service as a list of datetime objects. """
if not self.supports_time:
return []
if self.service.calendar == 'standard':
units = self.service.time_interval_units
interval = self.service.time_interval
steps = [self.time_start]
if units in ('years', 'decades', 'centuries'):
if units == 'years':
years = interval
elif units == 'decades':
years = 10 * interval
else:
years = 100 * interval
next_value = lambda x: x.replace(year=x.year + years)
elif units == 'months':
def _fn(x):
year = x.year + (x.month+interval-1) // 12
month = (x.month+interval) % 12 or 12
day = min(x.day, calendar.monthrange(year, month)[1])
return x.replace(year=year, month=month, day=day)
next_value = _fn
else:
if units == 'milliseconds':
delta = timedelta(milliseconds=interval)
elif units == 'seconds':
delta = timedelta(seconds=interval)
elif units == 'minutes':
delta = timedelta(minutes=interval)
elif units == 'hours':
delta = timedelta(hours=interval)
elif units == 'days':
delta = timedelta(days=interval)
elif units == 'weeks':
delta = timedelta(weeks=interval)
else:
raise ValidationError(
"Service has an invalid time_interval_units: {}".format(self.service.time_interval_units)
)
next_value = lambda x: x + delta
while steps[-1] < self.time_end:
value = next_value(steps[-1])
if value > self.time_end:
break
steps.append(value)
return steps
else:
# TODO
raise NotImplementedError |
java | public Observable<Void> deleteAsync(String locationName, String longTermRetentionServerName, String longTermRetentionDatabaseName, String backupName) {
return deleteWithServiceResponseAsync(locationName, longTermRetentionServerName, longTermRetentionDatabaseName, backupName).map(new Func1<ServiceResponse<Void>, Void>() {
@Override
public Void call(ServiceResponse<Void> response) {
return response.body();
}
});
} |
python | def _set_group_best(self, v, load=False):
"""
Setter method for group_best, mapped from YANG variable /routing_system/route_map/content/match/additional_paths/advertise_set/group_best (empty)
If this variable is read-only (config: false) in the
source YANG file, then _set_group_best is considered as a private
method. Backends looking to populate this variable should
do so via calling thisObj._set_group_best() directly.
YANG Description: BGP Add-Path advertise group-best path
"""
if hasattr(v, "_utype"):
v = v._utype(v)
try:
t = YANGDynClass(v,base=YANGBool, is_leaf=True, yang_name="group-best", rest_name="group-best", parent=self, path_helper=self._path_helper, extmethods=self._extmethods, register_paths=True, extensions={u'tailf-common': {u'info': u'BGP Add-Path advertise group-best path', u'code-name': u'additional-paths-advertise-set-group-best', u'cli-full-command': None}}, namespace='urn:brocade.com:mgmt:brocade-ip-policy', defining_module='brocade-ip-policy', yang_type='empty', is_config=True)
except (TypeError, ValueError):
raise ValueError({
'error-string': """group_best must be of a type compatible with empty""",
'defined-type': "empty",
'generated-type': """YANGDynClass(base=YANGBool, is_leaf=True, yang_name="group-best", rest_name="group-best", parent=self, path_helper=self._path_helper, extmethods=self._extmethods, register_paths=True, extensions={u'tailf-common': {u'info': u'BGP Add-Path advertise group-best path', u'code-name': u'additional-paths-advertise-set-group-best', u'cli-full-command': None}}, namespace='urn:brocade.com:mgmt:brocade-ip-policy', defining_module='brocade-ip-policy', yang_type='empty', is_config=True)""",
})
self.__group_best = t
if hasattr(self, '_set'):
self._set() |
java | public void setupKeys()
{
KeyAreaInfo keyArea = null;
keyArea = new KeyAreaInfo(this, Constants.UNIQUE, ID_KEY);
keyArea.addKeyField(ID, Constants.ASCENDING);
keyArea = new KeyAreaInfo(this, Constants.UNIQUE, KEY_FILENAME_KEY);
keyArea.addKeyField(KEY_FILENAME, Constants.ASCENDING);
keyArea.addKeyField(KEY_NUMBER, Constants.ASCENDING);
} |
python | def change_time(filename, newtime):
"""Change the time of a process or group of processes by writing a new time to the time file."""
with open(filename, "w") as faketimetxt_handle:
faketimetxt_handle.write("@" + newtime.strftime("%Y-%m-%d %H:%M:%S")) |
python | def tail(self, rows: int=5):
"""
Returns the main dataframe's tail
:param rows: number of rows to print, defaults to 5
:param rows: int, optional
:return: a pandas dataframe
:rtype: pd.DataFrame
:example: ``ds.tail()``
"""
if self.df is None:
self.warning("Dataframe is empty: no tail available")
return self.df.tail(rows) |
python | def time_series_rdd_from_observations(dt_index, df, ts_col, key_col, val_col):
"""
Instantiates a TimeSeriesRDD from a DataFrame of observations.
An observation is a row containing a timestamp, a string key, and float value.
Parameters
----------
dt_index : DateTimeIndex
The index of the RDD to create. Observations not contained in this index will be ignored.
df : DataFrame
ts_col : string
The name of the column in the DataFrame containing the timestamps.
key_col : string
The name of the column in the DataFrame containing the keys.
val_col : string
The name of the column in the DataFrame containing the values.
"""
jvm = df._sc._jvm
jtsrdd = jvm.com.cloudera.sparkts.api.java.JavaTimeSeriesRDDFactory.timeSeriesRDDFromObservations( \
dt_index._jdt_index, df._jdf, ts_col, key_col, val_col)
return TimeSeriesRDD(None, None, jtsrdd, df._sc) |
java | protected CellFormatter createDefaultFormatter(final String name, final Locale... locales) {
final String key = String.format("format.%s", name);
final String defaultFormat = messageResolver.getMessage(key);
if(defaultFormat == null) {
return null;
}
CellFormatter formatter = createFormatter(defaultFormat);
// ロケールのフォーマットの取得
for(Locale locale : locales) {
final String localeFormat = messageResolver.getMessage(locale, key, null);
if(localeFormat == null) {
continue;
}
final LocaleSwitchFormatter switchFormatter;
if(formatter instanceof LocaleSwitchFormatter) {
switchFormatter = (LocaleSwitchFormatter) formatter;
} else {
// LocaleSwitchFormatterに入れ替える。
switchFormatter = new LocaleSwitchFormatter(formatter);
formatter = switchFormatter;
}
// ロケールごとのフォーマットの登録
if(locale.equals(Locale.JAPANESE)) {
switchFormatter.register(createFormatter(localeFormat), JAPANESE_LOCALES);
} else {
switchFormatter.register(createFormatter(localeFormat), locale);
}
}
return formatter;
} |
java | @Override
public int read() throws IOException {
try {
int value = super.read();
eofReached = value == -1;
if (!eofReached) {
bytesRead++;
}
return value;
} catch (Exception e) {
return onException(e);
}
} |
python | def controller(self):
"""
Check if multiple controllers are connected.
:returns: Return the controller_id of the active controller.
:rtype: string
"""
if hasattr(self, 'controller_id'):
if len(self.controller_info['controllers']) > 1:
raise TypeError(
'Only one controller per account is supported.'
)
return self.controller_id
raise AttributeError('No controllers assigned to this account.') |
java | public void setMailTimeout(Integer timeout) throws SecurityException {
checkWriteAccess();
boolean hasAccess = ConfigWebUtil.hasAccess(config, SecurityManager.TYPE_MAIL);
if (!hasAccess) throw new SecurityException("no access to update mail server settings");
Element mail = _getRootElement("mail");
mail.setAttribute("timeout", Caster.toString(timeout, ""));
// config.setMailTimeout(timeout);
} |
python | def start(self):
"""Overrides default start behaviour by raising ConnectionError instead
of custom requests_mock.exceptions.NoMockAddress.
"""
if self._http_last_send is not None:
raise RuntimeError('HttpMock has already been started')
# 1) save request.Session.send in self._last_send
# 2) replace request.Session.send with MockerCore send function
super(HttpMock, self).start()
# 3) save MockerCore send function in self._http_last_send
# 4) replace request.Session.send with HttpMock send function
self._patch_last_send() |
python | def create(backbone: ModelFactory, input_block: typing.Optional[ModelFactory]=None):
""" Vel factory function """
if input_block is None:
input_block = IdentityFactory()
return QModelFactory(input_block=input_block, backbone=backbone) |
python | def write(self, script):
# type: (str) -> None
"""Send a script to FORM.
Write the given script to the communication channel to FORM. It could
be buffered and so FORM may not execute the sent script until
:meth:`flush` or :meth:`read` is called.
"""
if self._closed:
raise IOError('tried to write to closed connection')
script = script.strip()
if script:
assert self._parentout is not None
self._parentout.write(script)
self._parentout.write('\n') |
python | def version_add(package, version, pkghash, force=False):
"""
Add a new version for a given package hash.
Version format needs to follow PEP 440.
Versions are permanent - once created, they cannot be modified or deleted.
"""
team, owner, pkg = parse_package(package)
session = _get_session(team)
try:
Version(version)
except ValueError:
url = "https://www.python.org/dev/peps/pep-0440/#examples-of-compliant-version-schemes"
raise CommandException(
"Invalid version format; see %s" % url
)
if not force:
answer = input("Versions cannot be modified or deleted; are you sure? (y/n) ")
if answer.lower() != 'y':
return
session.put(
"{url}/api/version/{owner}/{pkg}/{version}".format(
url=get_registry_url(team),
owner=owner,
pkg=pkg,
version=version
),
data=json.dumps(dict(
hash=_match_hash(package, pkghash)
))
) |
python | def from_api_response(cls, reddit_session, json_dict):
"""Return an instance of the appropriate class from the json dict."""
# The Multireddit response contains the Subreddits attribute as a list
# of dicts of the form {'name': 'subredditname'}.
# We must convert each of these into a Subreddit object.
json_dict['subreddits'] = [Subreddit(reddit_session, item['name'])
for item in json_dict['subreddits']]
return cls(reddit_session, None, None, json_dict) |
python | def create_detector(self, detector):
"""Creates a new detector.
Args:
detector (object): the detector model object. Will be serialized as
JSON.
Returns:
dictionary of the response (created detector model).
"""
resp = self._post(self._u(self._DETECTOR_ENDPOINT_SUFFIX),
data=detector)
resp.raise_for_status()
return resp.json() |
java | public void setBinding(String binding) throws JspException
{
if (!isValueReference(binding))
{
throw new IllegalArgumentException("not a valid binding: " + binding);
}
_binding = binding;
} |
python | def parseFullScan(self, i, modifications=True):
"""
parses scan info for giving a Spectrum Obj for plotting. takes significantly longer since it has to unzip/parse xml
"""
scanObj = PeptideObject()
peptide = str(i[1])
pid=i[2]
if modifications:
sql = 'select aam.ModificationName,pam.Position,aam.DeltaMass from peptidesaminoacidmodifications pam left join aminoacidmodifications aam on (aam.AminoAcidModificationID=pam.AminoAcidModificationID) where pam.PeptideID=%s'%pid
for row in self.conn.execute(sql):
scanObj.addModification(peptide[row[1]], str(row[1]), str(row[2]), row[0])
scanObj.peptide = peptide
if self.decompressScanInfo(scanObj, i[0]):
return scanObj
return None |
python | def ParseRecord(self, parser_mediator, key, structure):
"""Parse each record structure and return an EventObject if applicable.
Args:
parser_mediator (ParserMediator): mediates interactions between parsers
and other components, such as storage and dfvfs.
key (str): identifier of the structure of tokens.
structure (pyparsing.ParseResults): structure of tokens derived from
a line of a text file.
Raises:
ParseError: when the structure type is unknown.
"""
if key not in ('header', 'logline'):
raise errors.ParseError(
'Unable to parse record, unknown structure: {0:s}'.format(key))
if key == 'logline':
self._ParseLine(parser_mediator, structure)
elif key == 'header':
self._ParseHeader(parser_mediator, structure) |
java | public void setLocaterInfo(SourceLocator locator)
{
m_publicId = locator.getPublicId();
m_systemId = locator.getSystemId();
super.setLocaterInfo(locator);
} |
python | def QA_save_tdx_to_mongo(file_dir, client=DATABASE):
"""save file
Arguments:
file_dir {str:direction} -- 文件的地址
Keyword Arguments:
client {Mongodb:Connection} -- Mongo Connection (default: {DATABASE})
"""
reader = TdxMinBarReader()
__coll = client.stock_min_five
for a, v, files in os.walk(file_dir):
for file in files:
if (str(file)[0:2] == 'sh' and int(str(file)[2]) == 6) or \
(str(file)[0:2] == 'sz' and int(str(file)[2]) == 0) or \
(str(file)[0:2] == 'sz' and int(str(file)[2]) == 3):
QA_util_log_info('Now_saving ' + str(file)
[2:8] + '\'s 5 min tick')
fname = file_dir + os.sep + file
df = reader.get_df(fname)
df['code'] = str(file)[2:8]
df['market'] = str(file)[0:2]
df['datetime'] = [str(x) for x in list(df.index)]
df['date'] = [str(x)[0:10] for x in list(df.index)]
df['time_stamp'] = df['datetime'].apply(
lambda x: QA_util_time_stamp(x))
df['date_stamp'] = df['date'].apply(
lambda x: QA_util_date_stamp(x))
data_json = json.loads(df.to_json(orient='records'))
__coll.insert_many(data_json) |
python | def cross_entropy_loss(logits, one_hot_labels, label_smoothing=0,
weight=1.0, scope=None):
"""Define a Cross Entropy loss using softmax_cross_entropy_with_logits.
It can scale the loss by weight factor, and smooth the labels.
Args:
logits: [batch_size, num_classes] logits outputs of the network .
one_hot_labels: [batch_size, num_classes] target one_hot_encoded labels.
label_smoothing: if greater than 0 then smooth the labels.
weight: scale the loss by this factor.
scope: Optional scope for name_scope.
Returns:
A tensor with the softmax_cross_entropy loss.
"""
logits.get_shape().assert_is_compatible_with(one_hot_labels.get_shape())
with tf.name_scope(scope, 'CrossEntropyLoss', [logits, one_hot_labels]):
num_classes = one_hot_labels.get_shape()[-1].value
one_hot_labels = tf.cast(one_hot_labels, logits.dtype)
if label_smoothing > 0:
smooth_positives = 1.0 - label_smoothing
smooth_negatives = label_smoothing / num_classes
one_hot_labels = one_hot_labels * smooth_positives + smooth_negatives
cross_entropy = tf.contrib.nn.deprecated_flipped_softmax_cross_entropy_with_logits(
logits, one_hot_labels, name='xentropy')
weight = tf.convert_to_tensor(weight,
dtype=logits.dtype.base_dtype,
name='loss_weight')
loss = tf.multiply(weight, tf.reduce_mean(cross_entropy), name='value')
tf.add_to_collection(LOSSES_COLLECTION, loss)
return loss |
python | def position_result_list(change_list):
"""
Returns a template which iters through the models and appends a new
position column.
"""
result = result_list(change_list)
# Remove sortable attributes
for x in range(0, len(result['result_headers'])):
result['result_headers'][x]['sorted'] = False
if result['result_headers'][x]['sortable']:
result['result_headers'][x]['class_attrib'] = mark_safe(
' class="sortable"')
# Append position <th> element
result['result_headers'].append({
'url_remove': '?o=',
'sort_priority': 1,
'sortable': True,
'class_attrib': mark_safe(' class="sortable sorted ascending"'),
'sorted': True,
'text': 'position',
'ascending': True,
'url_primary': '?o=-1',
'url_toggle': '?o=-1',
})
# Append the editable field to every result item
for x in range(0, len(result['results'])):
obj = change_list.result_list[x]
# Get position object
c_type = ContentType.objects.get_for_model(obj)
try:
object_position = ObjectPosition.objects.get(
content_type__pk=c_type.id, object_id=obj.id)
except ObjectPosition.DoesNotExist:
object_position = ObjectPosition.objects.create(content_object=obj)
# Add the <td>
html = ('<td><input class="vTextField" id="id_position-{0}"'
' maxlength="10" name="position-{0}" type="text"'
' value="{1}" /></td>').format(object_position.id,
object_position.position)
result['results'][x].append(mark_safe(html))
return result |
python | async def check_passwd(self,
identity: str,
passwd: str
) -> SessionIdentity :
""" 通过密码检查身份 """
assert identity
value, _ = await self._client.get(f"{self._prefix_identity}/{identity}")
if value is None:
logger.debug(f'Not found identity: {identity}')
raise Unauthorized(f"无此登录身份'{identity}'")
profile = json.loads(value.decode('utf-8'))
user_id = profile['user_id']
identity = profile['identity']
hashed = profile['hashed']
if sha256_crypt.verify(passwd, hashed):
return SessionIdentity(user_id=user_id, identity=identity)
else:
raise Unauthorized(f"登录身份'{identity}'认证失败") |
python | def watermark(url, args=''):
"""
Returns the URL to a watermarked copy of the image specified.
"""
# initialize some variables
args = args.split(',')
params = dict(
name=args.pop(0),
opacity=0.5,
tile=False,
scale=1.0,
greyscale=False,
rotation=0,
position=None,
quality=QUALITY,
obscure=OBSCURE_ORIGINAL,
random_position_once=RANDOM_POSITION_ONCE,
)
params['url'] = unquote(url)
# iterate over all parameters to see what we need to do
for arg in args:
key, value = arg.split('=')
key, value = key.strip(), value.strip()
if key == 'position':
params['position'] = value
elif key == 'opacity':
params['opacity'] = utils._percent(value)
elif key == 'tile':
params['tile'] = bool(int(value))
elif key == 'scale':
params['scale'] = value
elif key == 'greyscale':
params['greyscale'] = bool(int(value))
elif key == 'rotation':
params['rotation'] = value
elif key == 'quality':
params['quality'] = int(value)
elif key == 'obscure':
params['obscure'] = bool(int(value))
elif key == 'random_position_once':
params['random_position_once'] = bool(int(value))
return Watermarker()(**params) |
java | public void clear() {
//release a static buffer if possible
if (_buffersToReuse != null && !_buffersToReuse.isEmpty()) {
StaticBuffers.getInstance().releaseByteBuffer(BUFFER_KEY, _buffersToReuse.peek());
} else if (!_buffers.isEmpty()) {
StaticBuffers.getInstance().releaseByteBuffer(BUFFER_KEY, _buffers.get(0));
}
if (_buffersToReuse != null) {
_buffersToReuse.clear();
}
_buffers.clear();
_position = 0;
_flushPosition = 0;
_size = 0;
} |
java | public static Object jsoupParse(final ChainedHttpConfig config, final FromServer fromServer) {
try {
return Jsoup.parse(fromServer.getInputStream(), fromServer.getCharset().name(), fromServer.getUri().toString());
} catch (IOException e) {
throw new TransportingException(e);
}
} |
java | public static ExpressionTree stripParentheses(ExpressionTree tree) {
while (tree instanceof ParenthesizedTree) {
tree = ((ParenthesizedTree) tree).getExpression();
}
return tree;
} |
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