text
stringlengths
81
112k
Numerical autofocusing of a field using the Helmholtz equation. Parameters ---------- field : 1d or 2d ndarray Electric field is BG-Corrected, i.e. field = EX/BEx nm : float Refractive index of medium. res : float Size of wavelength in pixels. ival : tuple of floats ...
Numerical autofocusing of a stack using the Helmholtz equation. Parameters ---------- fieldstack : 2d or 3d ndarray Electric field is BG-Corrected, i.e. Field = EX/BEx nm : float Refractive index of medium. res : float Size of wavelength in pixels. ival : tuple of float...
Find the focus by minimizing the `metric` of an image Parameters ---------- field : 2d array electric field metric_func : callable some metric to be minimized ival : tuple of floats (minimum, maximum) of interval to search in pixels nm : float RI of medium re...
Generates blacklists / whitelists def prepare_project(project, project_dir, binaries, ips, urls): """ Generates blacklists / whitelists """ # Get Various Lists / Project Waivers lists = get_lists.GetLists() # Get file name black list and project waivers file_audit_list, file_audit_project...
Main scan tasks begin def scan_file(project, project_dir, binaries, ips, urls, file_audit_list, file_audit_project_list, flag_list, ignore_list, hashlist, file_ignore, ignore_directories, url_ignore, ip_ignore, apikey): """ Main scan tasks begin """ logger.info("Commencing s...
If an IP Address is found, scan it def scan_ipaddr(ipaddr, line, project, split_path, apikey): """ If an IP Address is found, scan it """ logger.info('Found what I believe is an IP Address: %s', line.strip()) logger.info('File %s. Parsed IP Address: %s', split_path, ipaddr) with open(reports_di...
If URL is found, scan it def scan_url(url, line, project, split_path, apikey): """ If URL is found, scan it """ logger.info('File %s contains what I believe is a URL: %s', split_path, line.strip()) logger.info('Scanning: %s', url) with open(reports_dir + "urls-" + project + ".log", "a") as gate...
parse the 'Maps' subfolder directory divining criteria for valid maps def getIndex(folderPath=None): """parse the 'Maps' subfolder directory divining criteria for valid maps""" try: return cache.structure except AttributeError: pass # if it doesn't exist, generate and cache the map file data if fold...
Stringify a number, preventing unwanted scientific notations. def _stringify_number(v): ''' Stringify a number, preventing unwanted scientific notations. ''' if isinstance(v, (float, Decimal)): if math.isinf(v) and v > 0: v = 'Infinity' elif math.isinf(v) and v < 0: ...
Resolve the tag using etcd so that the current instance indicates a concrete, latest image. Note that alias resolving does not take the registry component into account. async def resolve_alias(cls, alias_key: str, etcd: etcd.AsyncEtcd): ''' Resolve the tag using etcd so that th...
Accessing web-based ontology service is too long, so we cache the information in a pickle file and query the services only if the info has not already been cached. def getOntoCategory(curie, alwaysFetch=False): """ Accessing web-based ontology service is too long, so we cache the information ...
Setup root logger for package def _init_logging(anteater_log): """ Setup root logger for package """ LOG.setLevel(logging.DEBUG) ch = logging.StreamHandler() formatter = logging.Formatter('%(asctime)s - %(name)s - ' '%(levelname)s - %(message)s') ch.setFormatter(f...
Creates a directory for scan reports def check_dir(): """ Creates a directory for scan reports """ try: os.makedirs(reports_dir) logger.info('Creating reports directory: %s', reports_dir) except OSError as e: if e.errno != errno.EEXIST: raise
Main function, mostly for passing arguments def main(): """ Main function, mostly for passing arguments """ _init_logging(config.get('config', 'anteater_log')) check_dir() arguments = docopt(__doc__, version=__version__) if arguments['<patchset>']: prepare_patchset(arguments['<project>'], ...
Fit a Stan model. Caches the compiled model. *args and **kwargs are passed to the pystan.stan function. Arguments you most likely want to pass: data, init, iter, chains. Unlike pystan.stan, if the n_jobs kwarg is not specified, it defaults to -1. Parameters ------------------- mo...
cross correlate with other, for all pairs closer than rmax, iterate. for r, i, j in A.enumiter(...): ... where r is the distance, i and j are the original input array index of the data. This uses a thread to convert from KDNode.enum. def enu...
cross correlate with other, for all pairs closer than rmax, iterate. >>> def process(r, i, j, **kwargs): >>> ... >>> A.enum(... process, **kwargs): >>> ... where r is the distance, i and j are the original input array index of t...
Gray & Moore based fast dual tree counting. r is the edge of bins: -inf or r[i-1] < count[i] <= r[i] attrs: None or tuple if tuple, attrs = (attr_self, attr_other) Returns: count, count, weight of attrs is not None def count(self, oth...
Friend-of-Friend clustering with linking length. Returns: the label def fof(self, linkinglength, out=None, method='splay'): """ Friend-of-Friend clustering with linking length. Returns: the label """ if out is None: out = numpy.empty(self.size, dtype='intp'...
Calculate the total number of points between [min, max). If attr is given, also calculate the sum of the weight. This is a M log(N) operation, where M is the number of min/max queries and N is number of points. def integrate(self, min, max, attr=None, info={}): """ Calcula...
Divide a tree branch to a forest, each subtree of size at most chunksize def make_forest(self, chunksize): """ Divide a tree branch to a forest, each subtree of size at most chunksize """ heap = [] heappush(heap, (-self.size, self)) while True: w, x...
Install a third party odoo add-on :param string repo_url: url of the repo that contains the patch. :param string branch: name of the branch to checkout. :param string destination: the folder where the add-on should end up at. :param string commit: Optional commit rev to checkout to. If mentioned, that ...
Use the conf file to list all the third party Odoo add-ons that will be installed and the patches that should be applied. :param string destination: the folder where add-ons should end up at. Default: pwd/3rd :param string conf_file: path to a conf file that describe the add-...
Find rightmost value less than x def find_lt(a, x): """Find rightmost value less than x""" i = bisect.bisect_left(a, x) if i: return a[i-1] raise ValueError
Entry point to parse an ISA-Tab directory. isatab_ref can point to a directory of ISA-Tab data, in which case we search for the investigator file, or be a reference to the high level investigation file. def parse(isatab_ref): """Entry point to parse an ISA-Tab directory. isatab_ref can point to a d...
Parse a section of an ISA-Tab, assigning information to a supplied record. def _parse_region(self, rec, line_iter): """Parse a section of an ISA-Tab, assigning information to a supplied record. """ had_info = False keyvals, section = self._parse_keyvals(line_iter) if keyvals: ...
Read tab delimited file, handling ISA-Tab special case headers. def _line_iter(self, in_handle): """Read tab delimited file, handling ISA-Tab special case headers. """ reader = csv.reader(in_handle, dialect="excel-tab") for line in reader: if len(line) > 0 and line[0]: ...
Generate dictionary from key/value pairs. def _parse_keyvals(self, line_iter): """Generate dictionary from key/value pairs. """ out = None line = None for line in line_iter: if len(line) == 1 and line[0].upper() == line[0]: break else: ...
Retrieve row data from files associated with the ISATabRecord. def parse(self, rec): """Retrieve row data from files associated with the ISATabRecord. """ final_studies = [] for study in rec.studies: source_data = self._parse_study(study.metadata["Study File Name"], ...
Parse study or assay row oriented file around the supplied base node. def _parse_study(self, fname, node_types): """Parse study or assay row oriented file around the supplied base node. """ if not os.path.exists(os.path.join(self._dir, fname)): return None nodes = {} ...
Convert node metadata back into a standard dictionary and list. def _finalize_metadata(self, node): """Convert node metadata back into a standard dictionary and list. """ final = {} for key, val in iter(node.metadata.items()): #val = list(val) #if isinstance(val[...
Parse out key value pairs for line information based on a group of values. def _line_by_type(self, line, header, hgroups, htypes, out, want_type, collapse_quals_fn = None): """Parse out key value pairs for line information based on a group of values. """ for index, htype i...
Combine attributes in multiple columns into single named tuple. def _collapse_attributes(self, line, header, indexes): """Combine attributes in multiple columns into single named tuple. """ names = [] vals = [] pat = re.compile("[\W]+") for i in indexes: name...
Remove ISA-Tab specific information from Header[real name] headers. def _clean_header(self, header): """Remove ISA-Tab specific information from Header[real name] headers. """ if header.find("[") >= 0: header = header.replace("]", "").split("[")[-1] # ISATab can start with n...
Characterize header groups into different data types. def _characterize_header(self, header, hgroups): """Characterize header groups into different data types. """ out = [] for h in [header[g[0]] for g in hgroups]: this_ctype = None for ctype, names in self._col_...
Combine header columns into related groups. def _collapse_header(self, header): """Combine header columns into related groups. """ out = [] for i, h in enumerate(header): if h.startswith(self._col_quals): out[-1].append(i) else: ou...
PURPOSE: command-line interface for map information def main(): # mini/unit test """ PURPOSE: command-line interface for map information """ options = optionsParser().parse_args() params = getSelectionParams(options) if options.list or options.details: specifiedMaps = filterMapNames( ...
Parse file extension. - *.pickle: uncompressed, utf-8 encode pickle file - *.gz: compressed, utf-8 encode pickle file def is_pickle_file(abspath): """Parse file extension. - *.pickle: uncompressed, utf-8 encode pickle file - *.gz: compressed, utf-8 encode pickle file """ abspath =...
Load Pickle from file. If file are not exists, returns ``default``. :param abspath: file path. use absolute path as much as you can. extension has to be ``.pickle`` or ``.gz`` (for compressed Pickle). :type abspath: string :param default: default ``dict()``, if ``abspath`` not exists, return the ...
Dump picklable object to file. Provides multiple choice to customize the behavior. :param data: picklable python object. :type data: dict or list :param abspath: ``save as`` path, file extension has to be ``.pickle`` or ``.gz`` (for compressed Pickle) :type abspath: string :param pk_p...
A stable version of :func:`dump`, this method will silently overwrite existing file. There's a issue with :func:`dump`: If your program is interrupted while writing, you got an incomplete file, and you also lose the original file. So this method write pickle to a temporary file first, then rename...
Convert arbitrary pickable Python Object to bytes. **中文文档** 将可Pickle化的Python对象转化为bytestr def obj2bytes(obj, pk_protocol=py23.pk_protocol): """Convert arbitrary pickable Python Object to bytes. **中文文档** 将可Pickle化的Python对象转化为bytestr """ return pickle.dumps(obj, protocol=pk_protocol)
Convert arbitrary object to base64 encoded string. **中文文档** 将可Pickle化的Python对象转化为utf-8编码的 ``纯ASCII字符串`` def obj2str(obj, pk_protocol=py23.pk_protocol): """Convert arbitrary object to base64 encoded string. **中文文档** 将可Pickle化的Python对象转化为utf-8编码的 ``纯ASCII字符串`` """ return base64.urlsafe_b6...
bincount supporting scalar and vector weight def bincount(dig, weight, minlength): """ bincount supporting scalar and vector weight """ if numpy.isscalar(weight): return numpy.bincount(dig, minlength=minlength) * weight else: return numpy.bincount(dig, weight, minlength)
Resets the users network to make changes take effect def reset_network(message): """Resets the users network to make changes take effect""" for command in settings.RESTART_NETWORK: try: subprocess.check_call(command) except: pass print(message)
Disables access to websites that are defined as 'distractors def improve(): """Disables access to websites that are defined as 'distractors'""" with open(settings.HOSTS_FILE, "r+") as hosts_file: contents = hosts_file.read() if not settings.START_TOKEN in contents and not settings.END_TOKEN in ...
Enables access to websites that are defined as 'distractors def lose(): """Enables access to websites that are defined as 'distractors'""" changed = False with open(settings.HOSTS_FILE, "r") as hosts_file: new_file = [] in_block = False for line in hosts_file: if in_bloc...
Enables temporarily breaking concentration def take_break(minutes: hug.types.number=5): """Enables temporarily breaking concentration""" print("") print("######################################### ARE YOU SURE? #####################################") try: for remaining in range(60, -1, -1): ...
Tuple of (low_port, high_port) reflecting the local port range assigned to outbound connections. We use this as part of a heuristic to determine whether a connection is inbound or outbound. def local_port_range(self): """Tuple of (low_port, high_port) reflecting the local port range ass...
Format a number using base-2 SI prefixes def _si(number): """Format a number using base-2 SI prefixes""" prefixes = ['', 'K', 'M', 'G', 'T', 'P', 'E', 'Z', 'Y'] while number > 1024: number /= 1024.0 prefixes.pop(0) return '%0.2f%s' % (number, prefixes.pop(0))
Retrieve requested URL def _get_url(url): """Retrieve requested URL""" try: data = HTTP_SESSION.get(url, stream=True) data.raise_for_status() except requests.exceptions.RequestException as exc: raise FetcherException(exc) return data
Extract files while explicitly setting the proper permissions def _extract_file(zip_fp, info, path): """Extract files while explicitly setting the proper permissions""" zip_fp.extract(info.filename, path=path) out_path = os.path.join(path, info.filename) perm = info.external_attr >> 16 perm |= sta...
Taskcluster denotes builds in one of two formats - i.e. linux64-asan or linux64-asan-opt The latter is generated. If it fails, the caller should try the former. def build_string(self): """ Taskcluster denotes builds in one of two formats - i.e. linux64-asan or linux64-asan-opt The latte...
Generate platform prefix for cross-platform downloads. def auto_name_prefix(self): """ Generate platform prefix for cross-platform downloads. """ # if the platform is not native, auto_name would clobber native downloads. # make a prefix to avoid this native_system = std_...
Generator for all possible BuildTasks with these parameters def iterall(cls, build, branch, flags, platform=None): """Generator for all possible BuildTasks with these parameters""" # Prepare build type if platform is None: platform = Platform() target_platform = platform.gec...
Multiple entries exist per push date. Iterate over all until a working entry is found def _pushdate_urls(cls, pushdate, branch, target_platform): """Multiple entries exist per push date. Iterate over all until a working entry is found""" url_base = cls.URL_BASE + '/namespaces/gecko.v2.mozilla-' + branc...
Retrieve the URL for revision based builds def _revision_url(cls, rev, branch, target_platform): """Retrieve the URL for revision based builds""" namespace = 'gecko.v2.mozilla-' + branch + '.revision.' + rev product = 'mobile' if 'android' in target_platform else 'firefox' return cls.UR...
Return an iterable for all available builds matching a particular build type def iterall(cls, target, branch, build, flags, platform=None): """Return an iterable for all available builds matching a particular build type""" flags = BuildFlags(*flags) for task in BuildTask.iterall(build, branch, ...
Retrieve the artifacts json object def _artifacts(self): """Retrieve the artifacts json object""" if '_artifacts' not in self._memo: json = _get_url(self._artifacts_url).json() self._memo['_artifacts'] = json['artifacts'] return self._memo['_artifacts']
Build the artifact basename Builds are base.tar.bz2, info is base.json, shell is base.jsshell.zip... def _artifact_base(self): """ Build the artifact basename Builds are base.tar.bz2, info is base.json, shell is base.jsshell.zip... """ if '_artifact_base' not in self._me...
Return the build's info def build_info(self): """Return the build's info""" if 'build_info' not in self._memo: self._memo['build_info'] = _get_url(self.artifact_url('json')).json() return self._memo['build_info']
Return the build's mozinfo def moz_info(self): """Return the build's mozinfo""" if 'moz_info' not in self._memo: self._memo['moz_info'] = _get_url(self.artifact_url('mozinfo.json')).json() return self._memo['moz_info']
Download and extract the build and requested extra artifacts @type path: @param path: @type tests: @param tests: @type full_symbols: @param full_symbols: def extract_build(self, path='.', tests=None, full_symbols=False): """ Download and extract the bu...
Update directory to work with DOMFuzz @type path: str @param path: A string representation of the fuzzmanager config path def _layout_for_domfuzz(self, path): """ Update directory to work with DOMFuzz @type path: str @param path: A string representation of the fuzzmana...
Write fuzzmanager config file for selected build @type path: basestring @param path: A string representation of the fuzzmanager config path def _write_fuzzmanagerconf(self, path): """ Write fuzzmanager config file for selected build @type path: basestring @param path: ...
Download and extract a zip artifact @type suffix: @param suffix: @type path: @param path: def extract_zip(self, suffix, path='.'): """ Download and extract a zip artifact @type suffix: @param suffix: @type path: @param path: ""...
Extract builds with .tar.(*) extension When unpacking a build archive, only extract the firefox directory @type suffix: @param suffix: @type path: @param path: def extract_tar(self, suffix, path='.'): """ Extract builds with .tar.(*) extension When unpa...
Download Android .apk @type path: @param path: def download_apk(self, path='.'): """ Download Android .apk @type path: @param path: """ apk_fd, apk_fn = tempfile.mkstemp(prefix='fuzzfetch-', suffix='.apk') os.close(apk_fd) try: ...
Extract builds with .dmg extension Will only work if `hdiutil` is available. @type path: @param path: def extract_dmg(self, path='.'): """ Extract builds with .dmg extension Will only work if `hdiutil` is available. @type path: @param path: ""...
Construct a Fetcher from given command line arguments. @type args: list(str) @param args: Command line arguments (optional). Default is to use args from sys.argv @type skip_dir_check: bool @param skip_dir_check: Boolean identifying whether to check for existing build directory ...
fuzzfetch main entry point Run with --help for usage def main(cls): """ fuzzfetch main entry point Run with --help for usage """ log_level = logging.INFO log_fmt = '[%(asctime)s] %(message)s' if bool(os.getenv('DEBUG')): log_level = logging....
Get the original response for comparing, confirm ``is_cookie_necessary`` def init_original_response(self): """Get the original response for comparing, confirm ``is_cookie_necessary``""" if 'json' in self.request: self.request['data'] = json.dumps(self.request.pop('json')).encode( ...
Get the original response for comparing, confirm is_cookie_necessary def init_original_response(self): """Get the original response for comparing, confirm is_cookie_necessary""" no_cookie_resp = None self.is_cookie_necessary = True if 'json' in self.request: self.request['da...
Do nothing but sort the params of url. raw_url: the raw url to be sorted; kwargs: (optional) same kwargs for ``sorted``. def sort_url_qsl(cls, raw_url, **kwargs): """Do nothing but sort the params of url. raw_url: the raw url to be sorted; kwargs: (optional) ...
Only clean the url params and return self. def clean_url(self): """Only clean the url params and return self.""" raw_url = self.request['url'] parsed_url = urlparse(raw_url) qsl = parse_qsl(parsed_url.query) for qs in qsl: new_url = self._join_url(parsed_url, ...
Only clean the post-data and return self. Including form-data / bytes-data / json-data. def clean_post_data(self): """Only clean the post-data and return self. Including form-data / bytes-data / json-data.""" data = self.request.get('data') if not (data and s...
Only clean the cookie from headers and return self. def clean_cookie(self): """Only clean the cookie from headers and return self.""" if not self.is_cookie_necessary: return self headers = self.request.get('headers', {}) cookies = SimpleCookie(headers['Cookie']) for ...
Only clean the headers (cookie include) and return self. def clean_headers(self): """Only clean the headers (cookie include) and return self.""" if not isinstance(self.request.get('headers'), dict): return self headers = self.request['headers'] if 'Cookie' in headers: ...
Remove the non-sense args from the self.ignore, return self.new_request def reset_new_request(self): """Remove the non-sense args from the self.ignore, return self.new_request""" raw_url = self.new_request['url'] parsed_url = urlparse(raw_url) qsl = parse_qsl(parsed_url.query) n...
Whole task, clean_all + reset_new_request, return self.new_request. def result(self): """Whole task, clean_all + reset_new_request, return self.new_request.""" if not self.tasks: self.clean_all() tasks_length = len(self.tasks) self.logger_function( '%s tasks of r...
Property return key-value json-string from __slots__. def as_json(self, ensure_ascii=False): """Property return key-value json-string from __slots__.""" return json.dumps(self.as_dict, ensure_ascii=ensure_ascii)
the main entry point for the HelpMe Command line application. Currently, the user can request help or set config values for a particular helper. def main(): '''the main entry point for the HelpMe Command line application. Currently, the user can request help or set config values for a particular help...
Get value stored in cache file or store there default value. :param key: :param default_value: :return: def get_or_save_default(self, key, default_value): """ Get value stored in cache file or store there default value. :param key: :param default_value: :...
Save overlay to dicom. def saveOverlayToDicomCopy(input_dcmfilelist, output_dicom_dir, overlays, crinfo, orig_shape): """ Save overlay to dicom. """ from . import datawriter as dwriter # import qmisc if not os.path.exists(output_dicom_dir): os.makedirs(output_dicom_d...
Create path with "_segmentation" suffix and keep extension. :param path: :return: def __get_segmentation_path(self, path): """ Create path with "_segmentation" suffix and keep extension. :param path: :return: """ startpath, ext = os.path.splitext(path) ...
:param data3d: input ndarray data :param path: output path, to specify slice number advanced formatting options (like {:06d}) can be used Check function filename_format() for more details. :param metadata: {'voxelsize_mm': [1, 1, 1]} :param filetype: dcm, vtk, rawiv, image_stack ...
There is a bug in simple ITK for Z axis in 3D images. This is a fix :param path: :param metadata: :return: def _fix_sitk_bug(self, path, metadata): """ There is a bug in simple ITK for Z axis in 3D images. This is a fix :param path: :param metadata: :retu...
Function make 3D data from dicom file slices :dcmfilelist list of sorted .dcm files :overlays dictionary of binary overlays. {1:np.array([...]), 3:...} :out_dir output directory def DataCopyWithOverlay(self, dcmfilelist, out_dir, overlays): """ Function make 3D data from dicom ...
Function adds overlay to existing file. def add_overlay_to_slice_file( self, filename, overlay, i_overlay, filename_out=None ): """ Function adds overlay to existing file. """ if filename_out is None: filename_out = filename filena...
Flags a method as deprecated. :param instructions: A human-friendly string of instructions, such as: 'Please migrate to add_proxy() ASAP.' :return: DeprecatedWarning def deprecated(instructions): """ Flags a method as deprecated. :param instructions: A human-friendly string of instructions, such ...
Logs a message only when logging level is verbose. :param str|list[str] message: The message. def log_verbose(self, message): """ Logs a message only when logging level is verbose. :param str|list[str] message: The message. """ if self.get_verbosity() >= Output.VERBOSI...
Logs a message only when logging level is very verbose. :param str|list[str] message: The message. def log_very_verbose(self, message): """ Logs a message only when logging level is very verbose. :param str|list[str] message: The message. """ if self.get_verbosity() >=...
Get a feed Arguments: config -- the configuration url -- The URL of the feed retval -- a tuple of feed,previous_version,changed async def get_feed(config, url): """ Get a feed Arguments: config -- the configuration url -- The URL of the feed retval -- a tuple of feed,previous_...
Returns the known namespace of the RFC5005 extension, if any def archive_namespace(self): """ Returns the known namespace of the RFC5005 extension, if any """ try: for ns_prefix, url in self.feed.namespaces.items(): if url == 'http://purl.org/syndication/history/1.0': ...
Given a parsed feed, return the links to its entries, including ones which disappeared (as a quick-and-dirty way to support deletions) def entry_links(self): """ Given a parsed feed, return the links to its entries, including ones which disappeared (as a quick-and-dirty way to support deletions...
Given a parsed feed, returns True if this is an archive feed def is_archive(self): """ Given a parsed feed, returns True if this is an archive feed """ ns_prefix = self.archive_namespace if ns_prefix: if ns_prefix + '_archive' in self.feed.feed: # This is declared t...
Update WebSub hub to know about this feed async def update_websub(self, config, hub): """ Update WebSub hub to know about this feed """ try: LOGGER.debug("WebSub: Notifying %s of %s", hub, self.url) request = await utils.retry_post( config, hub, ...
Returns a list of tags. @param str name: The name of the tag. :rtype: list[str] def get_tags(self, name): """ Returns a list of tags. @param str name: The name of the tag. :rtype: list[str] """ tags = list() for tag in self._tags: ...
Removes leading empty lines from a list of lines. :param list[str] lines: The lines. def __remove_leading_empty_lines(lines): """ Removes leading empty lines from a list of lines. :param list[str] lines: The lines. """ tmp = list() empty = True for i in...
Removes leading empty lines from a list of lines. :param list[str] lines: The lines. def __remove_trailing_empty_lines(lines): """ Removes leading empty lines from a list of lines. :param list[str] lines: The lines. """ lines.reverse() tmp = DocBlockReflection....