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def read_fakelc(fakelcfile): ''' This just reads a pickled fake LC. Parameters ---------- fakelcfile : str The fake LC file to read. Returns ------- dict This returns an lcdict. ''' try: with open(fakelcfile,'rb') as infd: lcdict = pickle...
def get_varfeatures(simbasedir, mindet=1000, nworkers=None): '''This runs `lcproc.lcvfeatures.parallel_varfeatures` on fake LCs in `simbasedir`. Parameters ---------- simbasedir : str The directory containing the fake LCs to process. mindet : in...
def precision(ntp, nfp): ''' This calculates precision. https://en.wikipedia.org/wiki/Precision_and_recall Parameters ---------- ntp : int The number of true positives. nfp : int The number of false positives. Returns ------- float The precision calc...
def recall(ntp, nfn): ''' This calculates recall. https://en.wikipedia.org/wiki/Precision_and_recall Parameters ---------- ntp : int The number of true positives. nfn : int The number of false negatives. Returns ------- float The precision calculated...
def matthews_correl_coeff(ntp, ntn, nfp, nfn): ''' This calculates the Matthews correlation coefficent. https://en.wikipedia.org/wiki/Matthews_correlation_coefficient Parameters ---------- ntp : int The number of true positives. ntn : int The number of true negatives ...
def get_recovered_variables_for_magbin(simbasedir, magbinmedian, stetson_stdev_min=2.0, inveta_stdev_min=2.0, iqr_stdev_min=2.0, ...
def magbin_varind_gridsearch_worker(task): ''' This is a parallel grid search worker for the function below. ''' simbasedir, gridpoint, magbinmedian = task try: res = get_recovered_variables_for_magbin(simbasedir, magbinmedian, ...
def variable_index_gridsearch_magbin(simbasedir, stetson_stdev_range=(1.0,20.0), inveta_stdev_range=(1.0,20.0), iqr_stdev_range=(1.0,20.0), ngridpoints=32, ...
def plot_varind_gridsearch_magbin_results(gridsearch_results): '''This plots the gridsearch results from `variable_index_gridsearch_magbin`. Parameters ---------- gridsearch_results : dict This is the dict produced by `variable_index_gridsearch_magbin` above. Returns ------- dict...
def run_periodfinding(simbasedir, pfmethods=('gls','pdm','bls'), pfkwargs=({},{},{'startp':1.0,'maxtransitduration':0.3}), getblssnr=False, sigclip=5.0, nperiodworkers=10, ncontrolworkers=...
def check_periodrec_alias(actualperiod, recoveredperiod, tolerance=1.0e-3): '''This determines what kind of aliasing (if any) exists between `recoveredperiod` and `actualperiod`. Parameters ---------- actualperiod : float The actual perio...
def periodicvar_recovery(fakepfpkl, simbasedir, period_tolerance=1.0e-3): '''Recovers the periodic variable status/info for the simulated PF result. - Uses simbasedir and the lcfbasename stored in fakepfpkl to figure out where the LC for this object is. ...
def periodrec_worker(task): '''This is a parallel worker for running period-recovery. Parameters ---------- task : tuple This is used to pass args to the `periodicvar_recovery` function:: task[0] = period-finding result pickle to work on task[1] = simbasedir ...
def parallel_periodicvar_recovery(simbasedir, period_tolerance=1.0e-3, liststartind=None, listmaxobjects=None, nworkers=None): '''This is a parallel driver for `periodicvar_recover...
def plot_periodicvar_recovery_results( precvar_results, aliases_count_as_recovered=None, magbins=None, periodbins=None, amplitudebins=None, ndetbins=None, minbinsize=1, plotfile_ext='png', ): '''This plots the results of periodic var recovery. Thi...
def mast_query(service, params, data=None, apiversion='v0', forcefetch=False, cachedir='~/.astrobase/mast-cache', verbose=True, timeout=10.0, refresh=5.0, maxtimeout=90.0, ...
def tic_conesearch( ra, decl, radius_arcmin=5.0, apiversion='v0', forcefetch=False, cachedir='~/.astrobase/mast-cache', verbose=True, timeout=10.0, refresh=5.0, maxtimeout=90.0, maxtries=3, jitter=5.0, raiseonfail=Fa...
def tic_xmatch( ra, decl, radius_arcsec=5.0, apiversion='v0', forcefetch=False, cachedir='~/.astrobase/mast-cache', verbose=True, timeout=90.0, refresh=5.0, maxtimeout=180.0, maxtries=3, jitter=5.0, raiseonfail=False...
def tic_objectsearch( objectid, idcol_to_use="ID", apiversion='v0', forcefetch=False, cachedir='~/.astrobase/mast-cache', verbose=True, timeout=90.0, refresh=5.0, maxtimeout=180.0, maxtries=3, jitter=5.0, raiseonfail=False )...
def send_email(sender, subject, content, email_recipient_list, email_address_list, email_user=None, email_pass=None, email_server=None): '''This sends an email to addresses, informing them about events. The...
def fourier_sinusoidal_func(fourierparams, times, mags, errs): '''This generates a sinusoidal light curve using a Fourier cosine series. Parameters ---------- fourierparams : list This MUST be a list of the following form like so:: [period, epoch, [amplit...
def fourier_sinusoidal_residual(fourierparams, times, mags, errs): ''' This returns the residual between the model mags and the actual mags. Parameters ---------- fourierparams : list This MUST be a list of the following form like so:: [period, epoch, ...
def _make_periodogram(axes, lspinfo, objectinfo, findercmap, finderconvolve, verbose=True, findercachedir='~/.astrobase/stamp-cache'): '''Makes periodogram, objectinfo, and finder tile...
def _make_magseries_plot(axes, stimes, smags, serrs, magsarefluxes=False, ms=2.0): '''Makes the mag-series plot tile for `checkplot_png` and `twolsp_checkplot_png`. axes : matplotlib...
def _make_phased_magseries_plot(axes, periodind, stimes, smags, serrs, varperiod, varepoch, phasewrap, phasesort, phasebin, minbinelems, ...
def checkplot_png(lspinfo, times, mags, errs, varepoch='min', magsarefluxes=False, objectinfo=None, findercmap='gray_r', finderconvolve=None, findercachedir='...
def twolsp_checkplot_png(lspinfo1, lspinfo2, times, mags, errs, varepoch='min', magsarefluxes=False, objectinfo=None, fi...
def precess_coordinates(ra, dec, epoch_one, epoch_two, jd=None, mu_ra=0.0, mu_dec=0.0, outscalar=False): '''Precesses target coordinates `ra`, `dec` from `epoch_one` to `epoch_two`. This take...
def _single_true(iterable): '''This returns True if only one True-ish element exists in `iterable`. Parameters ---------- iterable : iterable Returns ------- bool True if only one True-ish element exists in `iterable`. False otherwise. ''' # return True if exactly one t...
def get_epochs_given_midtimes_and_period( t_mid, period, err_t_mid=None, t0_fixed=None, t0_percentile=None, verbose=False ): '''This calculates the future epochs for a transit, given a period and a starting epoch The equation used is:: t_mid = period...
def unixtime_to_jd(unix_time): '''This converts UNIX time in seconds to a Julian date in UTC (JD_UTC). Parameters ---------- unix_time : float A UNIX time in decimal seconds since the 1970 UNIX epoch. Returns ------- jd : float The Julian date corresponding to the provide...
def datetime_to_jd(dt): '''This converts a Python datetime object (naive, time in UT) to JD_UTC. Parameters ---------- dt : datetime A naive Python `datetime` object (e.g. with no tz attribute) measured at UTC. Returns ------- jd : float The Julian date correspond...
def jd_to_datetime(jd, returniso=False): '''This converts a UTC JD to a Python `datetime` object or ISO date string. Parameters ---------- jd : float The Julian date measured at UTC. returniso : bool If False, returns a naive Python `datetime` object corresponding to `jd`....
def jd_corr(jd, ra, dec, obslon=None, obslat=None, obsalt=None, jd_type='bjd'): '''Returns BJD_TDB or HJD_TDB for input JD_UTC. The equation used is:: BJD_TDB = JD_UTC + JD_to_TDB_corr + romer_delay where: - JD_to_TDB_corr is the di...
def _lclist_parallel_worker(task): '''This is a parallel worker for makelclist. Parameters ---------- task : tuple This is a tuple containing the following items: task[0] = lcf task[1] = columns task[2] = lcformat task[3] = lcformatdir task[4] = lcndetk...
def make_lclist(basedir, outfile, use_list_of_filenames=None, lcformat='hat-sql', lcformatdir=None, fileglob=None, recursive=True, columns=['objectid', 'objectinfo.ra', ...
def filter_lclist(lc_catalog, objectidcol='objectid', racol='ra', declcol='decl', xmatchexternal=None, xmatchdistarcsec=3.0, externalcolnums=(0,1,2), externalcolnames=['objectid','ra','decl'], ...
def _cpinfo_key_worker(task): '''This wraps `checkplotlist.checkplot_infokey_worker`. This is used to get the correct dtype for each element in retrieved results. Parameters ---------- task : tuple task[0] = cpfile task[1] = keyspeclist (infokeys kwarg from `add_cpinfo_to_lclist`)...
def add_cpinfo_to_lclist( checkplots, # list or a directory path initial_lc_catalog, magcol, # to indicate checkplot magcol outfile, checkplotglob='checkplot*.pkl*', infokeys=CPINFO_DEFAULTKEYS, nworkers=NCPUS ): '''This adds checkplot info to the initial li...
def variability_threshold(featuresdir, outfile, magbins=DEFAULT_MAGBINS, maxobjects=None, timecols=None, magcols=None, errcols=None, lcfor...
def plot_variability_thresholds(varthreshpkl, xmin_lcmad_stdev=5.0, xmin_stetj_stdev=2.0, xmin_iqr_stdev=2.0, xmin_inveta_stdev=2.0, lcformat='hat-sql', ...
def get_stamp(ra, decl, survey='DSS2 Red', scaling='Linear', sizepix=300, forcefetch=False, cachedir='~/.astrobase/stamp-cache', timeout=10.0, retry_failed=True, verbose=True, jitter=5.0): '...
def _update_proxy(self, change): """ An observer which sends the state change to the proxy. """ if change['type'] == 'container': #: Only update what's needed self.proxy.update_points(change) else: super(MapPolyline, self)._update_proxy(change)
def _update_proxy(self, change): """ An observer which sends the state change to the proxy. """ if change['type'] == 'container': #: Only update what's needed self.proxy.update_points(change) else: super(MapPolygon, self)._update_proxy(change)
def handle_change(self, change): """ Handle changes from atom ContainerLists """ op = change['operation'] if op in 'append': self.add(len(change['value']), LatLng(*change['item'])) elif op == 'insert': self.add(change['index'], LatLng(*change['item'])) eli...
def create_widget(self): """ Create the underlying widget. """ self.init_options() #: Retrieve the actual map MapFragment.newInstance(self.options).then( self.on_map_fragment_created) # Holder for the fragment self.widget = FrameLayout(self.get_cont...
def init_options(self): """ Initialize the underlying map options. """ self.options = GoogleMapOptions() d = self.declaration self.set_map_type(d.map_type) if d.ambient_mode: self.set_ambient_mode(d.ambient_mode) if (d.camera_position or d.camera_zoom...
def init_map(self): """ Add markers, polys, callouts, etc..""" d = self.declaration if d.show_location: self.set_show_location(d.show_location) if d.show_traffic: self.set_show_traffic(d.show_traffic) if d.show_indoors: self.set_show_indoors(d....
def init_info_window_adapter(self): """ Initialize the info window adapter. Should only be done if one of the markers defines a custom view. """ adapter = self.adapter if adapter: return #: Already initialized adapter = GoogleMap.InfoWindowAdapter() ...
def on_map_fragment_created(self, obj_id): """ Create the fragment and pull the map reference when it's loaded. """ self.fragment = MapFragment(__id__=obj_id) #: Setup callback so we know when the map is ready self.map.onMapReady.connect(self.on_map_ready) self.fragment...
def on_map_clicked(self, pos): """ Called when the map is clicked """ d = self.declaration d.clicked({ 'click': 'short', 'position': tuple(pos) })
def on_map_long_clicked(self, pos): """ Called when the map is clicked """ d = self.declaration d.clicked({ 'click': 'long', 'position': tuple(pos) })
def destroy(self): """ Remove the marker if it was added to the map when destroying""" marker = self.marker parent = self.parent() if marker: if parent: del parent.markers[marker.__id__] marker.remove() super(AndroidMapItemBase, self).destr...
def child_added(self, child): """ If a child is added we have to make sure the map adapter exists """ if child.widget: # TODO: Should we keep count and remove the adapter if not all # markers request it? self.parent().init_info_window_adapter() super(AndroidMa...
def on_marker(self, marker): """ Convert our options into the actual marker object""" mid, pos = marker self.marker = Marker(__id__=mid) mapview = self.parent() # Save ref mapview.markers[mid] = self # Required so the packer can pass the id self.marker.se...
def on_marker(self, mid): """ Convert our options into the actual circle object""" self.marker = Circle(__id__=mid) self.parent().markers[mid] = self #: Required so the packer can pass the id self.marker.setTag(mid) d = self.declaration if d.clickable: ...
def fit_transform(self, raw_documents, y=None): """ Learn the vocabulary dictionary and return term-document matrix. This is equivalent to fit followed by transform, but more efficiently implemented. Parameters ---------- raw_documents : iterable An iterable ...
def data(self, X=None, y=None, sentences=None): """ Add data to flow """ self.X = X self.y = y self.sentences = sentences
def transform(self, transformer): """ Add transformer to flow and apply transformer to data in flow Parameters ---------- transformer : Transformer a transformer to transform data """ self.transformers.append(transformer) from languageflow.tra...
def train(self): """ Train model with transformed data """ for i, model in enumerate(self.models): N = [int(i * len(self.y)) for i in self.lc_range] for n in N: X = self.X[:n] y = self.y[:n] e = Experiment(X, y, mode...
def export(self, model_name, export_folder): """ Export model and transformers to export_folder Parameters ---------- model_name: string name of model to export export_folder: string folder to store exported model and transformers """ ...
def fit_transform(self, raw_documents, y=None): """Learn vocabulary and idf, return term-document matrix. This is equivalent to fit followed by transform, but more efficiently implemented. Parameters ---------- raw_documents : iterable an iterable which yields...
def fit(self, X, y, coef_init=None, intercept_init=None, sample_weight=None): """Fit linear model with Stochastic Gradient Descent. Parameters ---------- X : {array-like, sparse matrix}, shape (n_samples, n_features) Training data y : numpy array, shape ...
def print_cm(cm, labels, hide_zeroes=False, hide_diagonal=False, hide_threshold=None): """pretty print for confusion matrixes""" columnwidth = max([len(x) for x in labels] + [5]) # 5 is value length empty_cell = " " * columnwidth # Print header print(" " + empty_cell, end=" ") for label in l...
def load_big_file(f): """ Workaround for loading a big pickle file. Files over 2GB cause pickle errors on certin Mac and Windows distributions. :param f: :return: """ logger.info(f'loading file {f}') with open(f, 'r+b') as f_in: # mmap seems to be much more memory efficient b...
def url_to_filename(url: str, etag: str = None) -> str: """ Converts a url into a filename in a reversible way. If `etag` is specified, add it on the end, separated by a period (which necessarily won't appear in the base64-encoded filename). Get rid of the quotes in the etag, since Windows doesn't l...
def filename_to_url(filename: str) -> Tuple[str, str]: """ Recovers the the url from the encoded filename. Returns it and the ETag (which may be ``None``) """ try: # If there is an etag, it's everything after the first period decoded, etag = filename.split(".", 1) except ValueErr...
def cached_path(url_or_filename: str, cache_dir: Path) -> Path: """ Given something that might be a URL (or might be a local path), determine which. If it's a URL, download the file and cache it, and return the path to the cached file. If it's already a local path, make sure the file exists and then...
def get_from_cache(url: str, cache_dir: Path = None) -> Path: """ Given a URL, look for the corresponding dataset in the local cache. If it's not there, download it. Then return the path to the cached file. """ cache_dir.mkdir(parents=True, exist_ok=True) filename = re.sub(r'.+/', '', url) ...
def fit(self, X, y): """Fit CRF according to X, y Parameters ---------- X : list of text each item is a text y: list each item is either a label (in multi class problem) or list of labels (in multi label problem) """ trainer = py...
def predict(self, X): """Predict class labels for samples in X. Parameters ---------- X : {array-like, sparse matrix}, shape = [n_samples, n_features] Samples. """ if isinstance(X[0], list): return [self.estimator.tag(x) for x in X] return...
def serve(self, port=62000): """ Start LanguageBoard web application Parameters ---------- port: int port to serve web application """ from http.server import HTTPServer, CGIHTTPRequestHandler os.chdir(self.log_folder) httpd = HTTPServer((''...
def analyze(self, output_folder=".", auto_remove=False): """ :type auto_remove: boolean :param boolean auto_remove: auto remove previous files in analyze folder """ if auto_remove: try: shutil.rmtree(output_folder) except: p...
def predict(self, X): """ In order to obtain the most likely label for a list of text Parameters ---------- X : list of string Raw texts Returns ------- C : list of string List labels """ x = X if not isinstance(X,...
def log(model_folder, binary_file="count.transformer.bin", log_folder="analyze"): """ Parameters ---------- model_folder : string folder contains binaries file of model binary_file : string file path to count transformer binary file log...
def fit(self, X, y): """Fit KimCNNClassifier according to X, y Parameters ---------- X : list of string each item is a raw text y : list of string each item is a label """ #################### # Data Loader ################...
def config_sources(app, environment, cluster, configs_dirs, app_dir, local=False, build=False): """Return the config files for an environment & cluster specific app.""" sources = [ # Machine-specific (configs_dirs, 'hostname'), (configs_dirs, 'hostname-local'), ...
def available_sources(sources): """Yield the sources that are present.""" for dirs, name in sources: for directory in dirs: fn = os.path.join(directory, name) + '.py' if os.path.isfile(fn): yield fn
def smush_config(sources, initial=None): """Merge the configuration sources and return the resulting DotDict.""" if initial is None: initial = {} config = DotDict(initial) for fn in sources: log.debug('Merging %s', fn) mod = get_config_module(fn) config = mod.update(conf...
def merge_dicts(d1, d2, _path=None): """ Merge dictionary d2 into d1, overriding entries in d1 with values from d2. d1 is mutated. _path is for internal, recursive use. """ if _path is None: _path = () if isinstance(d1, dict) and isinstance(d2, dict): for k, v in d2.items()...
def filter_dict(unfiltered, filter_keys): """Return a subset of a dictionary using the specified keys.""" filtered = DotDict() for k in filter_keys: filtered[k] = unfiltered[k] return filtered
def _convert_item(self, obj): """ Convert obj into a DotDict, or list of DotDict. Directly nested lists aren't supported. Returns the result """ if isinstance(obj, dict) and not isinstance(obj, DotDict): obj = DotDict(obj) elif isinstance(obj, list): ...
def filter_config(config, deploy_config): """Return a config subset using the filter defined in the deploy config.""" if not os.path.isfile(deploy_config): return DotDict() config_module = get_config_module(deploy_config) return config_module.filter(config)
def seeded_auth_token(client, service, seed): """Return an auth token based on the client+service+seed tuple.""" hash_func = hashlib.md5() token = ','.join((client, service, seed)).encode('utf-8') hash_func.update(token) return hash_func.hexdigest()
def write_config(config, app_dir, filename='configuration.json'): """Write configuration to the applicaiton directory.""" path = os.path.join(app_dir, filename) with open(path, 'w') as f: json.dump( config, f, indent=4, cls=DetectMissingEncoder, separators=(',', ': '))
def get_config_module(config_pathname): """Imports the config file to yoconfigurator.configs.<config_basename>.""" configs_mod = 'yoconfigurator.configs' if configs_mod not in sys.modules: sys.modules[configs_mod] = types.ModuleType(configs_mod) module_name = os.path.basename(config_pathname).rs...
def validate_date(date_text): """Return True if valid, raise ValueError if not""" try: if int(date_text) < 0: return True except ValueError: pass try: datetime.strptime(date_text, '%Y-%m-%d') return True except ValueError: pass raise ValueErr...
def get_download_total(rows): """Return the total downloads, and the downloads column""" headers = rows.pop(0) index = headers.index('download_count') total_downloads = sum(int(row[index]) for row in rows) rows.insert(0, headers) return total_downloads, index
def add_download_total(rows): """Add a final row to rows showing the total downloads""" total_row = [""] * len(rows[0]) total_row[0] = "Total" total_downloads, downloads_column = get_download_total(rows) total_row[downloads_column] = str(total_downloads) rows.append(total_row) return rows
def pypinfo( ctx, project, fields, auth, run, json, indent, timeout, limit, days, start_date, end_date, where, order, all_installers, percent, markdown, ): """Valid fields are:\n project | version | file | pyversion | percent3 | percent2 | impl...
def find_and_patch_entry(soup, entry): """ Modify soup so Dash.app can generate TOCs on the fly. """ link = soup.find("a", {"class": "headerlink"}, href="#" + entry.anchor) tag = soup.new_tag("a") tag["name"] = APPLE_REF_TEMPLATE.format(entry.type, entry.name) if link: link.parent.in...
def inv_entry_to_path(data): """ Determine the path from the intersphinx inventory entry Discard the anchors between head and tail to make it compatible with situations where extra meta information is encoded. """ path_tuple = data[2].split("#") if len(path_tuple) > 1: path_str = "#...
def main( source, force, name, quiet, verbose, destination, add_to_dash, add_to_global, icon, index_page, enable_js, online_redirect_url, parser, ): """ Convert docs from SOURCE to Dash.app's docset format. """ try: logging.config.dictConfig( ...
def create_log_config(verbose, quiet): """ We use logging's levels as an easy-to-use verbosity controller. """ if verbose and quiet: raise ValueError( "Supplying both --quiet and --verbose makes no sense." ) elif verbose: level = logging.DEBUG elif quiet: ...
def setup_paths(source, destination, name, add_to_global, force): """ Determine source and destination using the options. """ if source[-1] == "/": source = source[:-1] if not name: name = os.path.split(source)[-1] elif name.endswith(".docset"): name = name.replace(".docs...
def prepare_docset( source, dest, name, index_page, enable_js, online_redirect_url ): """ Create boilerplate files & directories and copy vanilla docs inside. Return a tuple of path to resources and connection to sqlite db. """ resources = os.path.join(dest, "Contents", "Resources") docs = ...
def add_icon(icon_data, dest): """ Add icon to docset """ with open(os.path.join(dest, "icon.png"), "wb") as f: f.write(icon_data)
def patch_anchors(parser, show_progressbar): """ Consume ``ParseEntry``s then patch docs for TOCs by calling *parser*'s ``find_and_patch_entry``. """ files = defaultdict(list) try: while True: pentry = (yield) try: fname, anchor = pentry.path.split...
def has_file_with(path, filename, content): """ Check whether *filename* in *path* contains the string *content*. """ try: with open(os.path.join(path, filename), "rb") as f: return content in f.read() except IOError as e: if e.errno == errno.ENOENT: return Fa...
def run_cell(self, cell): """Run the Cell code using the IPython globals and locals Args: cell (str): Python code to be executed """ globals = self.ipy_shell.user_global_ns locals = self.ipy_shell.user_ns globals.update({ "__ipy_scope__": None, ...