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<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def save_popset(self,filename='popset.h5',**kwargs): """Saves the PopulationSet Calls :func:`PopulationSet.save_hdf`. """
self.popset.save_hdf(os.path.join(self.folder,filename))
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def save_signal(self,filename=None): """ Saves TransitSignal. Calls :func:`TransitSignal.save`; default filename is ``trsig.pkl`` in ``self.folder``. """
if filename is None: filename = os.path.join(self.folder,'trsig.pkl') self.trsig.save(filename)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def modelshift_weaksec(koi): """ Max secondary depth based on model-shift secondary test from Jeff Coughlin secondary metric: mod_depth_sec_dv * (1 + 3*mod_fred_...
num = KOIDATA.ix[ku.koiname(koi), 'koi_tce_plnt_num'] if np.isnan(num): num = 1 kid = KOIDATA.ix[ku.koiname(koi), 'kepid'] tce = '{:09.0f}-{:02.0f}'.format(kid,num) #return largest depth between DV detrending and alternate detrending try: r = ROBOVETDATA.ix[tce] except KeyE...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def use_property(kepid, prop): """Returns true if provenance of property is SPE or AST """
try: prov = kicu.DATA.ix[kepid, '{}_prov'.format(prop)] return any([prov.startswith(s) for s in ['SPE', 'AST']]) except KeyError: raise MissingStellarError('{} not in stellar table?'.format(kepid))
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def star_config(koi, bands=['g','r','i','z','J','H','K'], unc=dict(g=0.05, r=0.05, i=0.05, z=0.05, J=0.02, H=0.02, K=0.02), **kwargs): """returns star config obj...
folder = os.path.join(KOI_FPPDIR, ku.koiname(koi)) if not os.path.exists(folder): os.makedirs(folder) config = ConfigObj(os.path.join(folder,'star.ini')) koi = ku.koiname(koi) maxAV = koi_maxAV(koi) config['maxAV'] = maxAV mags = ku.KICmags(koi) for band in bands: if...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def fpp_config(koi, **kwargs): """returns config object for given KOI """
folder = os.path.join(KOI_FPPDIR, ku.koiname(koi)) if not os.path.exists(folder): os.makedirs(folder) config = ConfigObj(os.path.join(folder,'fpp.ini')) koi = ku.koiname(koi) rowefit = jrowe_fit(koi) config['name'] = koi ra,dec = ku.radec(koi) config['ra'] = ra config['de...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def apply_default_constraints(self): """Applies default secthresh & exclusion radius constraints """
try: self.apply_secthresh(pipeline_weaksec(self.koi)) except NoWeakSecondaryError: logging.warning('No secondary eclipse threshold set for {}'.format(self.koi)) self.set_maxrad(default_r_exclusion(self.koi))
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def get_old_sha(diff_part): """ Returns the SHA for the original file that was changed in a diff part. """
r = re.compile(r'index ([a-fA-F\d]*)') return r.search(diff_part).groups()[0]
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def get_old_filename(diff_part): """ Returns the filename for the original file that was changed in a diff part. """
regexps = ( # e.g. "+++ a/foo/bar" r'^--- a/(.*)', # e.g. "+++ /dev/null" r'^\-\-\- (.*)', ) for regexp in regexps: r = re.compile(regexp, re.MULTILINE) match = r.search(diff_part) if match is not None: return match.groups()[0] raise M...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def get_new_filename(diff_part): """ Returns the filename for the updated file in a diff part. """
regexps = ( # e.g. "+++ b/foo/bar" r'^\+\+\+ b/(.*)', # e.g. "+++ /dev/null" r'^\+\+\+ (.*)', ) for regexp in regexps: r = re.compile(regexp, re.MULTILINE) match = r.search(diff_part) if match is not None: return match.groups()[0] rais...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def get_contents(diff_part): """ Returns a tuple of old content and new content. """
old_sha = get_old_sha(diff_part) old_filename = get_old_filename(diff_part) old_contents = get_old_contents(old_sha, old_filename) new_filename = get_new_filename(diff_part) new_contents = get_new_contents(new_filename) return old_contents, new_contents
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def _loadcache(cachefile): """ Returns a dictionary resulting from reading a likelihood cachefile """
cache = {} if os.path.exists(cachefile): with open(cachefile) as f: for line in f: line = line.split() if len(line) == 2: try: cache[int(line[0])] = float(line[1]) except: ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def fit_trapezoids(self, MAfn=None, msg=None, use_pbar=True, **kwargs): """ Fit trapezoid shape to each eclipse in population For each instance in the population...
logging.info('Fitting trapezoid models for {}...'.format(self.model)) if msg is None: msg = '{}: '.format(self.model) n = len(self.stars) deps, durs, slopes = (np.zeros(n), np.zeros(n), np.zeros(n)) secs = np.zeros(n, dtype=bool) dsec = np.zeros(n) ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def eclipseprob(self): """ Array of eclipse probabilities. """
#TODO: incorporate eccentricity/omega for exact calculation? s = self.stars return ((s['radius_1'] + s['radius_2'])*RSUN / (semimajor(s['P'],s['mass_1'] + s['mass_2'])*AU))
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def modelshort(self): """ Short version of model name Dictionary defined in ``populations.py``:: SHORT_MODELNAMES = {'Planets':'pl', 'EBs':'eb', 'HEBs':'heb', 'B...
try: name = SHORT_MODELNAMES[self.model] #add index if specific model is indexed if hasattr(self,'index'): name += '-{}'.format(self.index) return name except KeyError: raise KeyError('No short name for model: %s' % self.mod...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def constrain_secdepth(self, thresh): """ Constrain the observed secondary depth to be less than a given value :param thresh: Maximum allowed fractional depth fo...
self.apply_constraint(UpperLimit(self.secondary_depth, thresh, name='secondary depth'))
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def prior(self): """ Model prior for particular model. Product of eclipse probability (``self.prob``), the fraction of scenario that is allowed by the various co...
prior = self.prob * self.selectfrac for f in self.priorfactors: prior *= self.priorfactors[f] return prior
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def add_priorfactor(self,**kwargs): """Adds given values to priorfactors If given keyword exists already, error will be raised to use :func:`EclipsePopulation.ch...
for kw in kwargs: if kw in self.priorfactors: logging.error('%s already in prior factors for %s. use change_prior function instead.' % (kw,self.model)) continue else: self.priorfactors[kw] = kwargs[kw] logging.info('%s add...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def change_prior(self, **kwargs): """ Changes existing priorfactors. If given keyword isn't already in priorfactors, then will be ignored. """
for kw in kwargs: if kw in self.priorfactors: self.priorfactors[kw] = kwargs[kw] logging.info('{0} changed to {1} for {2} model'.format(kw,kwargs[kw], self.model))
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def _density(self, logd, dur, slope): """ Evaluate KDE at given points. Prepares data according to whether sklearn or scipy KDE in use. :param log, dur, slope: T...
if self.sklearn_kde: #TODO: fix preprocessing pts = np.array([(logd - self.mean_logdepth)/self.std_logdepth, (dur - self.mean_dur)/self.std_dur, (slope - self.mean_slope)/self.std_slope]) return self.kde.score_samples(p...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def lhood(self, trsig, recalc=False, cachefile=None): """Returns likelihood of transit signal Returns sum of ``trsig`` MCMC samples evaluated at ``self.kde``. :p...
if not hasattr(self,'kde'): self._make_kde() if cachefile is None: cachefile = self.lhoodcachefile if cachefile is None: cachefile = 'lhoodcache.dat' lhoodcache = _loadcache(cachefile) key = hashcombine(self, trsig) if key in...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def load_hdf(cls, filename, path=''): #perhaps this doesn't need to be written? """ Loads EclipsePopulation from HDF file Also runs :func:`EclipsePopulation._mak...
new = StarPopulation.load_hdf(filename, path=path) #setup lazy loading of starmodel if present try: with pd.HDFStore(filename) as store: if '{}/starmodel'.format(path) in store: new._starmodel = None new._starmodel_file = fil...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def constraints(self): """ Unique list of constraints among all populations in set. """
cs = [] for pop in self.poplist: cs += [c for c in pop.constraints] return list(set(cs))
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def save_hdf(self, filename, path='', overwrite=False): """ Saves PopulationSet to HDF file. """
if os.path.exists(filename) and overwrite: os.remove(filename) for pop in self.poplist: name = pop.modelshort pop.save_hdf(filename, path='{}/{}'.format(path,name), append=True)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def load_hdf(cls, filename, path=''): """ Loads PopulationSet from file """
with pd.HDFStore(filename) as store: models = [] types = [] for k in store.keys(): m = re.search('/(\S+)/stars', k) if m: models.append(m.group(1)) types.append(store.get_storer(m.group(0)).attrs.poptype...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def add_population(self,pop): """Adds population to PopulationSet """
if pop.model in self.modelnames: raise ValueError('%s model already in PopulationSet.' % pop.model) self.modelnames.append(pop.model) self.shortmodelnames.append(pop.modelshort) self.poplist.append(pop)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def remove_population(self,pop): """Removes population from PopulationSet """
iremove=None for i in range(len(self.poplist)): if self.modelnames[i]==self.poplist[i].model: iremove=i if iremove is not None: self.modelnames.pop(i) self.shortmodelnames.pop(i) self.poplist.pop(i)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def colordict(self): """ Dictionary holding colors that correspond to constraints. """
d = {} i=0 n = len(self.constraints) for c in self.constraints: #self.colordict[c] = colors[i % 6] d[c] = cm.jet(1.*i/n) i+=1 return d
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def priorfactors(self): """Combinartion of priorfactors from all populations """
priorfactors = {} for pop in self.poplist: for f in pop.priorfactors: if f in priorfactors: if pop.priorfactors[f] != priorfactors[f]: raise ValueError('prior factor %s is inconsistent!' % f) else: ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def apply_multicolor_transit(self,band,depth): """ Applies constraint corresponding to measuring transit in different band This is not implemented yet. """
if '{} band transit'.format(band) not in self.constraints: self.constraints.append('{} band transit'.format(band)) for pop in self.poplist: pop.apply_multicolor_transit(band,depth)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def set_maxrad(self,newrad): """ Sets max allowed radius in populations. Doesn't operate via the :class:`stars.Constraint` protocol; rather just rescales the sky...
if not isinstance(newrad, Quantity): newrad = newrad * u.arcsec #if 'Rsky' not in self.constraints: # self.constraints.append('Rsky') for pop in self.poplist: if not pop.is_specific: try: pop.maxrad = newrad ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def apply_dmaglim(self,dmaglim=None): """ Applies a constraint that sets the maximum brightness for non-target star :func:`stars.StarPopulation.set_dmaglim` not ...
raise NotImplementedError if 'bright blend limit' not in self.constraints: self.constraints.append('bright blend limit') for pop in self.poplist: if not hasattr(pop,'dmaglim') or pop.is_specific: continue if dmaglim is None: dm...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def apply_trend_constraint(self, limit, dt, **kwargs): """ Applies constraint corresponding to RV trend non-detection to each population See :func:`stars.StarPop...
if 'RV monitoring' not in self.constraints: self.constraints.append('RV monitoring') for pop in self.poplist: if not hasattr(pop,'dRV'): continue pop.apply_trend_constraint(limit, dt, **kwargs) self.trend_limit = limit self.trend_dt = ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def apply_secthresh(self, secthresh, **kwargs): """Applies secondary depth constraint to each population See :func:`EclipsePopulation.apply_secthresh`; all argum...
if 'secondary depth' not in self.constraints: self.constraints.append('secondary depth') for pop in self.poplist: if not isinstance(pop, EclipsePopulation_Px2): pop.apply_secthresh(secthresh, **kwargs) self.secthresh = secthresh
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def constrain_property(self,prop,**kwargs): """ Constrains property for each population See :func:`vespa.stars.StarPopulation.constrain_property`; all arguments ...
if prop not in self.constraints: self.constraints.append(prop) for pop in self.poplist: try: pop.constrain_property(prop,**kwargs) except AttributeError: logging.info('%s model does not have property stars.%s (constraint not applied)' ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def replace_constraint(self,name,**kwargs): """ Replaces removed constraint in each population. See :func:`vespa.stars.StarPopulation.replace_constraint` """
for pop in self.poplist: pop.replace_constraint(name,**kwargs) if name not in self.constraints: self.constraints.append(name)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def remove_constraint(self,*names): """ Removes constraint from each population See :func:`vespa.stars.StarPopulation.remove_constraint """
for name in names: for pop in self.poplist: if name in pop.constraints: pop.remove_constraint(name) else: logging.info('%s model does not have %s constraint' % (pop.model,name)) if name in self.constraints: ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def apply_cc(self, cc, **kwargs): """ Applies contrast curve constraint to each population See :func:`vespa.stars.StarPopulation.apply_cc`; all arguments passed ...
if type(cc)==type(''): pass if cc.name not in self.constraints: self.constraints.append(cc.name) for pop in self.poplist: if not pop.is_specific: try: pop.apply_cc(cc, **kwargs) except AttributeError: ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def apply_vcc(self,vcc): """ Applies velocity contrast curve constraint to each population See :func:`vespa.stars.StarPopulation.apply_vcc`; all arguments passed...
if 'secondary spectrum' not in self.constraints: self.constraints.append('secondary spectrum') for pop in self.poplist: if not pop.is_specific: try: pop.apply_vcc(vcc) except: logging.info('VCC constraint no...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def get_trilegal(filename,ra,dec,folder='.', galactic=False, filterset='kepler_2mass',area=1,maglim=27,binaries=False, trilegal_version='1.6',sigma_AV=0.1,convert...
if galactic: l, b = ra, dec else: try: c = SkyCoord(ra,dec) except UnitsError: c = SkyCoord(ra,dec,unit='deg') l,b = (c.galactic.l.value,c.galactic.b.value) if os.path.isabs(filename): folder = '' if not re.search('\.dat$',filename): ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def log_wrapper(self): """ Wrapper to set logging parameters for output """
log = logging.getLogger('client.py') # Set the log format and log level try: debug = self.params["debug"] log.setLevel(logging.DEBUG) except KeyError: log.setLevel(logging.INFO) # Set the log format. stream = logging.StreamHandler() ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def decode_setid(encoded): """Decode setid as uint128"""
try: lo, hi = struct.unpack('<QQ', b32decode(encoded.upper() + '======')) except struct.error: raise ValueError('Cannot decode {!r}'.format(encoded)) return (hi << 64) + lo
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def encode_setid(uint128): """Encode uint128 setid as stripped b32encoded string"""
hi, lo = divmod(uint128, 2**64) return b32encode(struct.pack('<QQ', lo, hi))[:-6].lower()
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def _reduce_opacity(self, watermark, opacity): """ Returns an image with reduced opacity. Converts image to RGBA if needs. Simple watermark.opacity(65535 - int(6...
if watermark.type() != ImageType.TrueColorMatteType: watermark.type(ImageType.TrueColorMatteType) depth = 255 - int(255 * opacity) watermark.quantumOperator(ChannelType.OpacityChannel, QuOp.MaxQuantumOp, depth)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def cleanup_relations(self): """Cleanup listing relations"""
collections = self.collections for relation in [x for col in collections.values() for x in col.model.relations.values()]: db.session.query(relation)\ .filter(~relation.listing.any())\ .delete(synchronize_session=False) ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def marvcli_cleanup(ctx, discarded, unused_tags): """Cleanup unused tags and discarded datasets."""
if not any([discarded, unused_tags]): click.echo(ctx.get_help()) ctx.exit(1) site = create_app().site if discarded: site.cleanup_discarded() if unused_tags: site.cleanup_tags() site.cleanup_relations()
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def marvcli_develop_server(port, public): """Run development webserver. ATTENTION: By default it is only served on localhost. To run it within a container and ac...
from flask_cors import CORS app = create_app(push=False) app.site.load_for_web() CORS(app) class IPDBMiddleware(object): def __init__(self, app): self.app = app def __call__(self, environ, start_response): from ipdb import launch_ipdb_on_exception ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def marvcli_discard(datasets, all_nodes, nodes, tags, comments, confirm): """Mark DATASETS to be discarded or discard associated data. Without any options the sp...
mark_discarded = not any([all_nodes, nodes, tags, comments]) site = create_app().site setids = parse_setids(datasets) if tags or comments: if confirm: msg = ' and '.join(filter(None, ['tags' if tags else None, 'comments' if comments els...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def marvcli_undiscard(datasets): """Undiscard DATASETS previously discarded."""
create_app() setids = parse_setids(datasets, discarded=True) dataset = Dataset.__table__ stmt = dataset.update()\ .where(dataset.c.setid.in_(setids))\ .values(discarded=False) db.session.execute(stmt) db.session.commit()
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def marvcli_restore(file): """Restore previously dumped database"""
data = json.load(file) site = create_app().site site.restore_database(**data)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def marvcli_query(ctx, list_tags, collections, discarded, outdated, path, tags, null): """Query datasets. Use --collection=* to list all datasets across all coll...
if not any([collections, discarded, list_tags, outdated, path, tags]): click.echo(ctx.get_help()) ctx.exit(1) sep = '\x00' if null else '\n' site = create_app().site if '*' in collections: collections = None else: for col in collections: if col not in ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def marvcli_tag(ctx, add, remove, datasets): """Add or remove tags to datasets"""
if not any([add, remove]) or not datasets: click.echo(ctx.get_help()) ctx.exit(1) app = create_app() setids = parse_setids(datasets) app.site.tag(setids, add, remove)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def marvcli_comment_add(user, message, datasets): """Add comment as user for one or more datasets"""
app = create_app() try: db.session.query(User).filter(User.name==user).one() except NoResultFound: click.echo("ERROR: No such user '{}'".format(user), err=True) sys.exit(1) ids = parse_setids(datasets, dbids=True) app.site.comment(user, message, ids)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def marvcli_comment_list(datasets): """Lists comments for datasets. Output: setid comment_id date time author message """
app = create_app() ids = parse_setids(datasets, dbids=True) comments = db.session.query(Comment)\ .options(db.joinedload(Comment.dataset))\ .filter(Comment.dataset_id.in_(ids)) for comment in sorted(comments, key=lambda x: (x.dataset._setid, x.id)): ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def marvcli_comment_rm(ids): """Remove comments. Remove comments by id as given in second column of: marv comment list """
app = create_app() db.session.query(Comment)\ .filter(Comment.id.in_(ids))\ .delete(synchronize_session=False) db.session.commit()
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def marvcli_user_list(): """List existing users"""
app = create_app() for name in db.session.query(User.name).order_by(User.name): click.echo(name[0])
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def marvcli_user_rm(ctx, username): """Remove a user"""
app = create_app() try: app.um.user_rm(username) except ValueError as e: ctx.fail(e.args[0])
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def watermark(self, image, options): """ Wrapper for ``_watermark`` Takes care of all the options handling. """
watermark_img = options.get("watermark", settings.THUMBNAIL_WATERMARK) if not watermark_img: raise AttributeError("No THUMBNAIL_WATERMARK defined or set on tag.") watermark_path = find(watermark_img) if not watermark_path: raise RuntimeError("Could not find the c...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def make_funcs(dataset, setdir, store): """Functions available for listing columns and filters."""
return { 'cat': lambda *lists: [x for lst in lists for x in lst], 'comments': lambda: None, 'detail_route': detail_route, 'format': lambda fmt, *args: fmt.format(*args), 'get': partial(getnode, dataset, setdir, store), 'join': lambda sep, *args: sep.join([x for x in ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def make_summary_funcs(rows, ids): """Functions available for listing summary fields."""
return { 'len': len, 'list': lambda *x: filter(None, list(x)), 'max': max, 'min': min, 'rows': partial(summary_rows, rows, ids), 'sum': sum, 'trace': print_trace }
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def cached_property(func): """Create read-only property that caches its function's value"""
@functools.wraps(func) def cached_func(self): cacheattr = '_{}'.format(func.func_name) try: return getattr(self, cacheattr) except AttributeError: value = func(self) setattr(self, cacheattr, value) return value return property(cached_f...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def create_stream(name, **header): """Create a stream for publishing messages. All keyword arguments will be used to form the header. """
assert isinstance(name, basestring), name return CreateStream(parent=None, name=name, group=False, header=header)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def pull(handle, enumerate=False): """Pulls next message for handle. Args: handle: A :class:`.stream.Handle` or GroupHandle. enumerate (bool): boolean to indica...
assert isinstance(handle, Handle), handle return Pull(handle, enumerate)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def parse_geometry(geometry, ratio=None): """ Enhanced parse_geometry parser with percentage support. """
if "%" not in geometry: # fall back to old parser return xy_geometry_parser(geometry, ratio) # parse with float so geometry strings like "42.11%" are possible return float(geometry.strip("%")) / 100.0
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def image(cam): """Extract first image of input stream to jpg file. Args: cam: Input stream of raw rosbag messages. Returns: File instance for first image of inp...
# Set output stream title and pull first message yield marv.set_header(title=cam.topic) msg = yield marv.pull(cam) if msg is None: return # Deserialize raw ros message pytype = get_message_type(cam) rosmsg = pytype() rosmsg.deserialize(msg.data) # Write image to jpeg and p...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def image_section(image, title): """Create detail section with one image. Args: title (str): Title to be displayed for detail section. image: marv image file. R...
# pull first image img = yield marv.pull(image) if img is None: return # create image widget and section containing it widget = {'title': image.title, 'image': {'src': img.relpath}} section = {'title': title, 'widgets': [widget]} yield marv.push(section)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def images(cam): """Extract images from input stream to jpg files. Args: cam: Input stream of raw rosbag messages. Returns: File instances for images of input st...
# Set output stream title and pull first message yield marv.set_header(title=cam.topic) # Fetch and process first 20 image messages name_template = '%s-{}.jpg' % cam.topic.replace('/', ':')[1:] while True: idx, msg = yield marv.pull(cam, enumerate=True) if msg is None or idx >= 20:...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def gallery_section(images, title): """Create detail section with gallery. Args: title (str): Title to be displayed for detail section. images: stream of marv i...
# pull all images imgs = [] while True: img = yield marv.pull(images) if img is None: break imgs.append({'src': img.relpath}) if not imgs: return # create gallery widget and section containing it widget = {'title': images.title, 'gallery': {'images':...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def filesizes(images): """Stat filesize of files. Args: images: stream of marv image files Returns: Stream of filesizes """
# Pull each image and push its filesize while True: img = yield marv.pull(images) if img is None: break yield marv.push(img.size)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def name(name, validator=None): """ Set a name on a validator callable. Useful for user-friendly reporting when using lambdas to populate the [`Invalid.expected`...
# Decorator mode if validator is None: def decorator(f): f.name = name return f return decorator # Direct mode validator.name = name return validator
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def stringmethod(func): """ Validator factory which call a single method on the string. """
method_name = func() @wraps(func) def factory(): def validator(v): if not isinstance(v, six.string_types): raise Invalid(_(u'Not a string'), get_type_name(six.text_type), get_type_name(type(v))) return getattr(v, method_name)() return validator r...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def parse_z(cls, offset): """ Parse %z offset into `timedelta` """
assert len(offset) == 5, 'Invalid offset string format, must be "+HHMM"' return timedelta(hours=int(offset[:3]), minutes=int(offset[0] + offset[3:]))
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def format_z(cls, offset): """ Format `timedelta` into %z """
sec = offset.total_seconds() return '{s}{h:02d}{m:02d}'.format(s='-' if sec<0 else '+', h=abs(int(sec/3600)), m=int((sec%3600)/60))
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def strptime(cls, value, format): """ Parse a datetime string using the provided format. This also emulates `%z` support on Python 2. :param value: Datetime stri...
# Simplest case: direct parsing if cls.python_supports_z or '%z' not in format: return datetime.strptime(value, format) else: # %z emulation case assert format[-2:] == '%z', 'For performance, %z is only supported at the end of the string' # Parse...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def generate_random_type(valid): """ Generate a random type and samples for it. :param valid: Generate valid samples? :type valid: bool :return: type, sample-gen...
type = choice(['int', 'str']) r = lambda: randrange(-1000000000, 1000000000) if type == 'int': return int, (r() if valid else str(r()) for i in itertools.count()) elif type == 'str': return str, (str(r()) if valid else r() for i in itertools.count()) else: raise Assertion...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def generate_random_schema(valid): """ Generate a random plain schema, and a sample generation function. :param valid: Generate valid samples? :type valid: bool ...
schema_type = choice(['literal', 'type']) if schema_type == 'literal': type, gen = generate_random_type(valid) value = next(gen) return value, (value if valid else None for i in itertools.count()) elif schema_type == 'type': return generate_random_type(valid) else: ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def generate_dict_schema(size, valid): """ Generate a schema dict of size `size` using library `lib`. In addition, it returns samples generator :param size: Sche...
schema = {} generator_items = [] # Generate schema for i in range(0, size): while True: key_schema, key_generator = generate_random_schema(valid) if key_schema not in schema: break value_schema, value_generator = generate_random_schema(valid...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def _calc_q_statistic(x, h, nt): """Calculate Portmanteau statistics up to a lag of h. """
t, m, n = x.shape # covariance matrix of x c0 = acm(x, 0) # LU factorization of covariance matrix c0f = sp.linalg.lu_factor(c0, overwrite_a=False, check_finite=True) q = np.zeros((3, h + 1)) for l in range(1, h + 1): cl = acm(x, l) # calculate tr(cl' * c0^-1 * cl * c0^-1...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def _calc_q_h0(n, x, h, nt, n_jobs=1, verbose=0, random_state=None): """Calculate q under the null hypothesis of whiteness. """
rng = check_random_state(random_state) par, func = parallel_loop(_calc_q_statistic, n_jobs, verbose) q = par(func(rng.permutation(x.T).T, h, nt) for _ in range(n)) return np.array(q)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def copy(self): """Create a copy of the VAR model."""
other = self.__class__(self.p) other.coef = self.coef.copy() other.residuals = self.residuals.copy() other.rescov = self.rescov.copy() return other
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def from_yw(self, acms): """Determine VAR model from autocorrelation matrices by solving the Yule-Walker equations. Parameters acms : array, shape (n_lags, n_cha...
if len(acms) != self.p + 1: raise ValueError("Number of autocorrelation matrices ({}) does not" " match model order ({}) + 1.".format(len(acms), self.p)) n_channels = acms[0].shape[0] a...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def predict(self, data): """Predict samples on actual data. The result of this function is used for calculating the residuals. Parameters data : array, shape (tr...
data = atleast_3d(data) t, m, l = data.shape p = int(np.shape(self.coef)[1] / m) y = np.zeros(data.shape) if t > l - p: # which takes less loop iterations for k in range(1, p + 1): bp = self.coef[:, (k - 1)::p] for n in range(p, l):...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def is_stable(self): """Test if VAR model is stable. This function tests stability of the VAR model as described in [1]_. Returns ------- out : bool True if the ...
m, mp = self.coef.shape p = mp // m assert(mp == m * p) # TODO: replace with raise? top_block = [] for i in range(p): top_block.append(self.coef[:, i::p]) top_block = np.hstack(top_block) im = np.eye(m) eye_block = im for i in range...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def fetch(dataset="mi", datadir=datadir): """Fetch example dataset. If the requested dataset is not found in the location specified by `datadir`, the function at...
if dataset not in datasets: raise ValueError("Example data '{}' not available.".format(dataset)) else: files = datasets[dataset]["files"] url = datasets[dataset]["url"] md5 = datasets[dataset]["md5"] if not isdir(datadir): makedirs(datadir) data = [] for n,...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def supports_undefined(self): """ Test whether this schema supports Undefined. A Schema that supports `Undefined`, when given `Undefined`, should return some val...
# Test try: yes = self(const.UNDEFINED) is not const.UNDEFINED except (Invalid, SchemaError): yes = False # Remember (lame @cached_property) self.__dict__['supports_undefined'] = yes return yes
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def get_schema_type(cls, schema): """ Get schema type for the argument :param schema: Schema to analyze :return: COMPILED_TYPE constant :rtype: str|None """
schema_type = type(schema) # Marker if issubclass(schema_type, markers.Marker): return const.COMPILED_TYPE.MARKER # Marker Type elif issubclass(schema_type, six.class_types) and issubclass(schema, markers.Marker): return const.COMPILED_TYPE.MARKER ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def priority(self): """ Get priority for this Schema. Used to sort mapping keys :rtype: int """
# Markers have priority set on the class if self.compiled_type == const.COMPILED_TYPE.MARKER: return self.compiled.priority # Other types have static priority return const.compiled_type_priorities[self.compiled_type]
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def sort_schemas(cls, schemas_list): """ Sort the provided list of schemas according to their priority. This also supports markers, and markers of a single type ...
return sorted(schemas_list, key=lambda x: ( # Top-level priority: # priority of the schema itself x.priority, # Second-level priority (for markers of the common type) ...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def sub_compile(self, schema, path=None, matcher=False): """ Compile a sub-schema :param schema: Validation schema :type schema: * :param path: Path to this sche...
return type(self)( schema, self.path + (path or []), None, None, matcher )
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def Invalid(self, message, expected): """ Helper for Invalid errors. Typical use: err_type = self.Invalid(_(u'Message'), self.name) raise err_type(<provided-valu...
def InvalidPartial(provided, path=None, **info): """ Create an Invalid exception :type provided: unicode :type path: list|None :rtype: Invalid """ return Invalid( message, expected, #six.text_type(expected)...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def get_schema_compiler(self, schema): """ Get compiler method for the provided schema :param schema: Schema to analyze :return: Callable compiled :rtype: callab...
# Schema type schema_type = self.get_schema_type(schema) if schema_type is None: return None # Compiler compilers = { const.COMPILED_TYPE.LITERAL: self._compile_literal, const.COMPILED_TYPE.TYPE: self._compile_type, const.COMPILED...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def compile_schema(self, schema): """ Compile the current schema into a callable validator :return: Callable validator :rtype: callable :raises SchemaError: Sche...
compiler = self.get_schema_compiler(schema) if compiler is None: raise SchemaError(_(u'Unsupported schema data type {!r}').format(type(schema).__name__)) return compiler(schema)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def _compile_schema(self, schema): """ Compile another schema """
assert self.matcher == schema.matcher self.name = schema.name self.compiled_type = schema.compiled_type return schema.compiled
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def loadmat(filename): """This function should be called instead of direct spio.loadmat as it cures the problem of not properly recovering python dictionaries fr...
data = sploadmat(filename, struct_as_record=False, squeeze_me=True) return _check_keys(data)
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def _check_keys(dictionary): """ checks if entries in dictionary are mat-objects. If yes todict is called to change them to nested dictionaries """
for key in dictionary: if isinstance(dictionary[key], matlab.mio5_params.mat_struct): dictionary[key] = _todict(dictionary[key]) return dictionary
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def _todict(matobj): """ a recursive function which constructs from matobjects nested dictionaries """
dictionary = {} #noinspection PyProtectedMember for strg in matobj._fieldnames: elem = matobj.__dict__[strg] if isinstance(elem, matlab.mio5_params.mat_struct): dictionary[strg] = _todict(elem) else: dictionary[strg] = elem return dictionary
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def plainica(x, reducedim=0.99, backend=None, random_state=None): """ Source decomposition with ICA. Apply ICA to the data x, with optional PCA dimensionality re...
x = atleast_3d(x) t, m, l = np.shape(x) if backend is None: backend = scotbackend # pre-transform the data with PCA if reducedim == 'no pca': c = np.eye(m) d = np.eye(m) xpca = x else: c, d, xpca = backend['pca'](x, reducedim) # run on residuals I...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def _msge_with_gradient_underdetermined(data, delta, xvschema, skipstep, p): """Calculate mean squared generalization error and its gradient for underdetermined ...
t, m, l = data.shape d = None j, k = 0, 0 nt = np.ceil(t / skipstep) for trainset, testset in xvschema(t, skipstep): a, b = _construct_var_eqns(atleast_3d(data[trainset, :, :]), p) c, d = _construct_var_eqns(atleast_3d(data[testset, :, :]), p) e = sp.linalg.inv(np.eye(a.sh...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def _msge_with_gradient_overdetermined(data, delta, xvschema, skipstep, p): """Calculate mean squared generalization error and its gradient for overdetermined eq...
t, m, l = data.shape d = None l, k = 0, 0 nt = np.ceil(t / skipstep) for trainset, testset in xvschema(t, skipstep): a, b = _construct_var_eqns(atleast_3d(data[trainset, :, :]), p) c, d = _construct_var_eqns(atleast_3d(data[testset, :, :]), p) e = sp.linalg.inv(np.eye(a.sh...
<SYSTEM_TASK:> Solve the following problem using Python, implementing the functions described below, one line at a time <END_TASK> <USER_TASK:> Description: def _get_msge_with_gradient(data, delta, xvschema, skipstep, p): """Calculate mean squared generalization error and its gradient, automatically selecting the bes...
t, m, l = data.shape n = (l - p) * t underdetermined = n < m * p if underdetermined: return _msge_with_gradient_underdetermined(data, delta, xvschema, skipstep, p) else: return _msge_with_gradient_overdetermined(data, delta, xvsch...