INSTRUCTION stringlengths 1 8.43k | RESPONSE stringlengths 75 104k |
|---|---|
This drives the overall parallel period processing for a list of LCs. | def parallel_pf(lclist,
outdir,
timecols=None,
magcols=None,
errcols=None,
lcformat='hat-sql',
lcformatdir=None,
pfmethods=('gls','pdm','mav','win'),
pfkwargs=({},{},{},{}),
si... |
This runs parallel light curve period finding for directory of LCs. | def parallel_pf_lcdir(lcdir,
outdir,
fileglob=None,
recursive=True,
timecols=None,
magcols=None,
errcols=None,
lcformat='hat-sql',
lcformatdir=N... |
This collects variability features into arrays for use with the classifer. | def collect_nonperiodic_features(
featuresdir,
magcol,
outfile,
pklglob='varfeatures-*.pkl',
featurestouse=NONPERIODIC_FEATURES_TO_COLLECT,
maxobjects=None,
labeldict=None,
labeltype='binary',
):
'''This collects variability features into arrays for us... |
This gets the best RF classifier after running cross - validation. | def train_rf_classifier(
collected_features,
test_fraction=0.25,
n_crossval_iterations=20,
n_kfolds=5,
crossval_scoring_metric='f1',
classifier_to_pickle=None,
nworkers=-1,
):
'''This gets the best RF classifier after running cross-validation.
- splits t... |
This applys an RF classifier trained using train_rf_classifier to varfeatures pickles in varfeaturesdir. | def apply_rf_classifier(classifier,
varfeaturesdir,
outpickle,
maxobjects=None):
'''This applys an RF classifier trained using `train_rf_classifier`
to varfeatures pickles in `varfeaturesdir`.
Parameters
----------
classifier ... |
This plots the training results from the classifier run on the training set. | def plot_training_results(classifier,
classlabels,
outfile):
'''This plots the training results from the classifier run on the training
set.
- plots the confusion matrix
- plots the feature importances
- FIXME: plot the learning curves too, see:... |
This returns a summed Fourier cosine series. | def _fourier_func(fourierparams, phase, mags):
'''This returns a summed Fourier cosine series.
Parameters
----------
fourierparams : list
This MUST be a list of the following form like so::
[period,
epoch,
[amplitude_1, amplitude_2, amplitude_3, ..., ampl... |
This is the chisq objective function to be minimized by scipy. minimize. | def _fourier_chisq(fourierparams,
phase,
mags,
errs):
'''This is the chisq objective function to be minimized by `scipy.minimize`.
The parameters are the same as `_fourier_func` above. `errs` is used to
calculate the chisq value.
'''
f = _f... |
This is the residual objective function to be minimized by scipy. leastsq. | def _fourier_residual(fourierparams,
phase,
mags):
'''
This is the residual objective function to be minimized by `scipy.leastsq`.
The parameters are the same as `_fourier_func` above.
'''
f = _fourier_func(fourierparams, phase, mags)
residual = mag... |
This fits a Fourier series to a mag/ flux time series. | def fourier_fit_magseries(times, mags, errs, period,
fourierorder=None,
fourierparams=None,
sigclip=3.0,
magsarefluxes=False,
plotfit=False,
ignoreinitfail=True,
... |
This plots a magnitude/ flux time - series. | def plot_magseries(times,
mags,
magsarefluxes=False,
errs=None,
out=None,
sigclip=30.0,
normto='globalmedian',
normmingap=4.0,
timebin=None,
yrange=N... |
Plots a phased magnitude/ flux time - series using the period provided. | def plot_phased_magseries(times,
mags,
period,
epoch='min',
fitknotfrac=0.01,
errs=None,
magsarefluxes=False,
normto='globalmedian',
... |
This downloads a DSS FITS stamp centered on the coordinates specified. | def skyview_stamp(ra, decl,
survey='DSS2 Red',
scaling='Linear',
flip=True,
convolvewith=None,
forcefetch=False,
cachedir='~/.astrobase/stamp-cache',
timeout=10.0,
retry_failed... |
This makes a finder chart for a given FITS with an optional object position overlay. | def fits_finder_chart(
fitsfile,
outfile,
fitsext=0,
wcsfrom=None,
scale=ZScaleInterval(),
stretch=LinearStretch(),
colormap=plt.cm.gray_r,
findersize=None,
finder_coordlimits=None,
overlay_ra=None,
overlay_decl=None,
overla... |
Makes a plot of periodograms obtained from periodbase functions. | def plot_periodbase_lsp(lspinfo, outfile=None, plotdpi=100):
'''Makes a plot of periodograms obtained from `periodbase` functions.
This takes the output dict produced by any `astrobase.periodbase`
period-finder function or a pickle filename containing such a dict and makes
a periodogram plot.
Par... |
This reads in a textlc that is complete up to the TFA stage. | def read_hatpi_textlc(lcfile):
'''
This reads in a textlc that is complete up to the TFA stage.
'''
if 'TF1' in lcfile:
thiscoldefs = COLDEFS + [('itf1',float)]
elif 'TF2' in lcfile:
thiscoldefs = COLDEFS + [('itf2',float)]
elif 'TF3' in lcfile:
thiscoldefs = COLDEFS + ... |
This just writes the lcdict to a pickle. | def lcdict_to_pickle(lcdict, outfile=None):
'''This just writes the lcdict to a pickle.
If outfile is None, then will try to get the name from the
lcdict['objectid'] and write to <objectid>-hptxtlc.pkl. If that fails, will
write to a file named hptxtlc.pkl'.
'''
if not outfile and lcdict['obj... |
This just reads a pickle LC. Returns an lcdict. | def read_hatpi_pklc(lcfile):
'''
This just reads a pickle LC. Returns an lcdict.
'''
try:
if lcfile.endswith('.gz'):
infd = gzip.open(lcfile,'rb')
else:
infd = open(lcfile,'rb')
lcdict = pickle.load(infd)
infd.close()
return lcdict
... |
This concatenates a list of light curves. | def concatenate_textlcs(lclist,
sortby='rjd',
normalize=True):
'''This concatenates a list of light curves.
Does not care about overlaps or duplicates. The light curves must all be
from the same aperture.
The intended use is to concatenate light curves a... |
This concatenates all text LCs for an objectid with the given aperture. | def concatenate_textlcs_for_objectid(lcbasedir,
objectid,
aperture='TF1',
postfix='.gz',
sortby='rjd',
normalize=True,
... |
This concatenates all text LCs for the given object and writes to a pklc. | def concat_write_pklc(lcbasedir,
objectid,
aperture='TF1',
postfix='.gz',
sortby='rjd',
normalize=True,
outdir=None,
recursive=True):
'''This concatenates all tex... |
This is a worker for the function below. | def parallel_concat_worker(task):
'''
This is a worker for the function below.
task[0] = lcbasedir
task[1] = objectid
task[2] = {'aperture','postfix','sortby','normalize','outdir','recursive'}
'''
lcbasedir, objectid, kwargs = task
try:
return concat_write_pklc(lcbasedir, obj... |
This concatenates all text LCs for the given objectidlist. | def parallel_concat_lcdir(lcbasedir,
objectidlist,
aperture='TF1',
postfix='.gz',
sortby='rjd',
normalize=True,
outdir=None,
recursive=Tru... |
This merges all TFA text LCs with separate apertures for a single object. | def merge_hatpi_textlc_apertures(lclist):
'''This merges all TFA text LCs with separate apertures for a single object.
The framekey column will be used as the join column across all light curves
in lclist. Missing values will be filled in with nans. This function assumes
all light curves are in the for... |
This reads a binnedlc pickle produced by the HATPI prototype pipeline. | def read_hatpi_binnedlc(binnedpklf, textlcf, timebinsec):
'''This reads a binnedlc pickle produced by the HATPI prototype pipeline.
Converts it into a standard lcdict as produced by the read_hatpi_textlc
function above by using the information in unbinnedtextlc for the same
object.
Adds a 'binned'... |
This reads the binned LC and writes it out to a pickle. | def generate_hatpi_binnedlc_pkl(binnedpklf, textlcf, timebinsec,
outfile=None):
'''
This reads the binned LC and writes it out to a pickle.
'''
binlcdict = read_hatpi_binnedlc(binnedpklf, textlcf, timebinsec)
if binlcdict:
if outfile is None:
ou... |
This generates the binnedlc pkls for a directory of such files. | def parallel_gen_binnedlc_pkls(binnedpkldir,
textlcdir,
timebinsec,
binnedpklglob='*binned*sec*.pkl',
textlcglob='*.tfalc.TF1*'):
'''
This generates the binnedlc pkls for a directory of su... |
Adds catalog info to objectinfo key of all pklcs in lcdir. | def pklc_fovcatalog_objectinfo(
pklcdir,
fovcatalog,
fovcatalog_columns=[0,1,2,
6,7,
8,9,
10,11,
13,14,15,16,
17,18,19,
20,21],
... |
This converts the base64 encoded string to a file. | def _base64_to_file(b64str, outfpath, writetostrio=False):
'''This converts the base64 encoded string to a file.
Parameters
----------
b64str : str
A base64 encoded strin that is the output of `base64.b64encode`.
outfpath : str
The path to where the file will be written. This shou... |
This reads a checkplot gzipped pickle file back into a dict. | def _read_checkplot_picklefile(checkplotpickle):
'''This reads a checkplot gzipped pickle file back into a dict.
NOTE: the try-except is for Python 2 pickles that have numpy arrays in
them. Apparently, these aren't compatible with Python 3. See here:
http://stackoverflow.com/q/11305790
The workar... |
This writes the checkplotdict to a ( gzipped ) pickle file. | def _write_checkplot_picklefile(checkplotdict,
outfile=None,
protocol=None,
outgzip=False):
'''This writes the checkplotdict to a (gzipped) pickle file.
Parameters
----------
checkplotdict : dict
T... |
Does phase - folding for the mag/ flux time - series given a period. | def get_phased_quantities(stimes, smags, serrs, period):
'''Does phase-folding for the mag/flux time-series given a period.
Given finite and sigma-clipped times, magnitudes, and errors, along with the
period at which to phase-fold the data, perform the phase-folding and
return the phase-folded values.
... |
This makes a plot of the LC model fit. | def make_fit_plot(phase, pmags, perrs, fitmags,
period, mintime, magseriesepoch,
plotfit,
magsarefluxes=False,
wrap=False,
model_over_lc=False):
'''This makes a plot of the LC model fit.
Parameters
----------
pha... |
This queries the GAIA TAP service for a list of objects near the coords. | def objectlist_conesearch(racenter,
declcenter,
searchradiusarcsec,
gaia_mirror=None,
columns=('source_id',
'ra','dec',
'phot_g_mean_mag',
... |
This queries the GAIA TAP service for a list of objects in an equatorial coordinate box. | def objectlist_radeclbox(radeclbox,
gaia_mirror=None,
columns=('source_id',
'ra','dec',
'phot_g_mean_mag',
'l','b',
'parallax, paralla... |
This queries the GAIA TAP service for a single GAIA source ID. | def objectid_search(gaiaid,
gaia_mirror=None,
columns=('source_id',
'ra','dec',
'phot_g_mean_mag',
'phot_bp_mean_mag',
'phot_rp_mean_mag',
... |
Generalized LSP value for a single omega. | def generalized_lsp_value(times, mags, errs, omega):
'''Generalized LSP value for a single omega.
The relations used are::
P(w) = (1/YY) * (YC*YC/CC + YS*YS/SS)
where: YC, YS, CC, and SS are all calculated at T
and where: tan 2omegaT = 2*CS/(CC - SS)
and where:
Y = ... |
Generalized LSP value for a single omega. | def generalized_lsp_value_withtau(times, mags, errs, omega):
'''Generalized LSP value for a single omega.
This uses tau to provide an arbitrary time-reference point.
The relations used are::
P(w) = (1/YY) * (YC*YC/CC + YS*YS/SS)
where: YC, YS, CC, and SS are all calculated at T
... |
This is the simplified version not using tau. | def generalized_lsp_value_notau(times, mags, errs, omega):
'''
This is the simplified version not using tau.
The relations used are::
W = sum (1.0/(errs*errs) )
w_i = (1/W)*(1/(errs*errs))
Y = sum( w_i*y_i )
C = sum( w_i*cos(wt_i) )
S = sum( w_i*sin(wt_i) )
... |
This calculates the peak associated with the spectral window function for times and at the specified omega. | def specwindow_lsp_value(times, mags, errs, omega):
'''This calculates the peak associated with the spectral window function
for times and at the specified omega.
NOTE: this is classical Lomb-Scargle, not the Generalized
Lomb-Scargle. `mags` and `errs` are silently ignored since we're calculating
t... |
This calculates the generalized Lomb - Scargle periodogram. | def pgen_lsp(
times,
mags,
errs,
magsarefluxes=False,
startp=None,
endp=None,
stepsize=1.0e-4,
autofreq=True,
nbestpeaks=5,
periodepsilon=0.1,
sigclip=10.0,
nworkers=None,
workchunksize=None,
glspfunc=_glsp_w... |
This calculates the spectral window function. | def specwindow_lsp(
times,
mags,
errs,
magsarefluxes=False,
startp=None,
endp=None,
stepsize=1.0e-4,
autofreq=True,
nbestpeaks=5,
periodepsilon=0.1,
sigclip=10.0,
nworkers=None,
glspfunc=_glsp_worker_specwindow,
... |
This returns the analytic false alarm probabilities for periodogram peak values. | def analytic_false_alarm_probability(lspinfo,
times,
conservative_nfreq_eff=True,
peakvals=None,
inplace=True):
'''This returns the analytic false alarm probabilities ... |
This validates if an API key for the specified LCC - Server is available. | def check_existing_apikey(lcc_server):
'''This validates if an API key for the specified LCC-Server is available.
API keys are stored using the following file scheme::
~/.astrobase/lccs/apikey-domain.of.lccserver.org
e.g. for the HAT LCC-Server at https://data.hatsurveys.org::
~/.astroba... |
This gets a new API key from the specified LCC - Server. | def get_new_apikey(lcc_server):
'''This gets a new API key from the specified LCC-Server.
NOTE: this only gets an anonymous API key. To get an API key tied to a user
account (and associated privilege level), see the `import_apikey` function
below.
Parameters
----------
lcc_server : str
... |
This imports an API key from text and writes it to the cache dir. | def import_apikey(lcc_server, apikey_text_json):
'''This imports an API key from text and writes it to the cache dir.
Use this with the JSON text copied from the API key text box on your
LCC-Server user home page. The API key will thus be tied to the privileges
of that user account and can then access ... |
This submits a POST query to an LCC - Server search API endpoint. | def submit_post_searchquery(url, data, apikey):
'''This submits a POST query to an LCC-Server search API endpoint.
Handles streaming of the results, and returns the final JSON stream. Also
handles results that time out.
Parameters
----------
url : str
The URL of the search API endpoin... |
This retrieves a search result dataset s CSV and any LC zip files. | def retrieve_dataset_files(searchresult,
getpickle=False,
outdir=None,
apikey=None):
'''This retrieves a search result dataset's CSV and any LC zip files.
Takes the output from the `submit_post_searchquery` function above or a
... |
This runs a cone - search query. | def cone_search(lcc_server,
center_ra,
center_decl,
radiusarcmin=5.0,
result_visibility='unlisted',
email_when_done=False,
collections=None,
columns=None,
filters=None,
sortspe... |
This runs a cross - match search query. | def xmatch_search(lcc_server,
file_to_upload,
xmatch_dist_arcsec=3.0,
result_visibility='unlisted',
email_when_done=False,
collections=None,
columns=None,
filters=None,
sortspe... |
This downloads a JSON form of a dataset from the specified lcc_server. | def get_dataset(lcc_server,
dataset_id,
strformat=False,
page=1):
'''This downloads a JSON form of a dataset from the specified lcc_server.
If the dataset contains more than 1000 rows, it will be paginated, so you
must use the `page` kwarg to get the page you... |
This gets information on a single object from the LCC - Server. | def object_info(lcc_server, objectid, db_collection_id):
'''This gets information on a single object from the LCC-Server.
Returns a dict with all of the available information on an object, including
finding charts, comments, object type and variability tags, and
period-search results (if available).
... |
This lists recent publicly visible datasets available on the LCC - Server. | def list_recent_datasets(lcc_server, nrecent=25):
'''This lists recent publicly visible datasets available on the LCC-Server.
If you have an LCC-Server API key present in `~/.astrobase/lccs/` that is
associated with an LCC-Server user account, datasets that belong to this
user will be returned as well,... |
This lists all light curve collections made available on the LCC - Server. | def list_lc_collections(lcc_server):
'''This lists all light curve collections made available on the LCC-Server.
If you have an LCC-Server API key present in `~/.astrobase/lccs/` that is
associated with an LCC-Server user account, light curve collections visible
to this user will be returned as well, e... |
This calculates the Stetson index for the magseries based on consecutive pairs of observations. | def stetson_jindex(ftimes, fmags, ferrs, weightbytimediff=False):
'''This calculates the Stetson index for the magseries, based on consecutive
pairs of observations.
Based on Nicole Loncke's work for her Planets and Life certificate at
Princeton in 2014.
Parameters
----------
ftimes,fmags... |
This calculates the Stetson K index ( a robust measure of the kurtosis ). | def stetson_kindex(fmags, ferrs):
'''This calculates the Stetson K index (a robust measure of the kurtosis).
Parameters
----------
fmags,ferrs : np.array
The input mag/flux time-series to process. Must have no non-finite
elems.
Returns
-------
float
The Stetson K ... |
This calculates the weighted mean stdev median MAD percentiles skew kurtosis fraction of LC beyond 1 - stdev and IQR. | def lightcurve_moments(ftimes, fmags, ferrs):
'''This calculates the weighted mean, stdev, median, MAD, percentiles, skew,
kurtosis, fraction of LC beyond 1-stdev, and IQR.
Parameters
----------
ftimes,fmags,ferrs : np.array
The input mag/flux time-series with all non-finite elements remov... |
This calculates percentiles and percentile ratios of the flux. | def lightcurve_flux_measures(ftimes, fmags, ferrs, magsarefluxes=False):
'''This calculates percentiles and percentile ratios of the flux.
Parameters
----------
ftimes,fmags,ferrs : np.array
The input mag/flux time-series with all non-finite elements removed.
magsarefluxes : bool
... |
This calculates various point - to - point measures ( eta in Kim + 2014 ). | def lightcurve_ptp_measures(ftimes, fmags, ferrs):
'''This calculates various point-to-point measures (`eta` in Kim+ 2014).
Parameters
----------
ftimes,fmags,ferrs : np.array
The input mag/flux time-series with all non-finite elements removed.
Returns
-------
dict
A dict... |
This calculates the following nonperiodic features of the light curve listed in Richards et al. 2011 ): | def nonperiodic_lightcurve_features(times, mags, errs, magsarefluxes=False):
'''This calculates the following nonperiodic features of the light curve,
listed in Richards, et al. 2011):
- amplitude
- beyond1std
- flux_percentile_ratio_mid20
- flux_percentile_ratio_mid35
- flux_percentile_rat... |
This calculates the CDPP of a timeseries using the method in the paper: | def gilliland_cdpp(times, mags, errs,
windowlength=97,
polyorder=2,
binsize=23400, # in seconds: 6.5 hours for classic CDPP
sigclip=5.0,
magsarefluxes=False,
**kwargs):
'''This calculates the CDPP of a... |
This rolls up the feature functions above and returns a single dict. | def all_nonperiodic_features(times, mags, errs,
magsarefluxes=False,
stetson_weightbytimediff=True):
'''This rolls up the feature functions above and returns a single dict.
NOTE: this doesn't calculate the CDPP to save time since binning and
smoothi... |
This runs the pyeebls. eebls function using the given inputs. | def _bls_runner(times,
mags,
nfreq,
freqmin,
stepsize,
nbins,
minduration,
maxduration):
'''This runs the pyeebls.eebls function using the given inputs.
Parameters
----------
times,mags : np... |
This wraps the BLS function for the parallel driver below. | def _parallel_bls_worker(task):
'''
This wraps the BLS function for the parallel driver below.
Parameters
----------
tasks : tuple
This is of the form::
task[0] = times
task[1] = mags
task[2] = nfreq
task[3] = freqmin
task[4] = s... |
Runs the Box Least Squares Fitting Search for transit - shaped signals. | def bls_serial_pfind(
times, mags, errs,
magsarefluxes=False,
startp=0.1, # search from 0.1 d to...
endp=100.0, # ... 100.0 d -- don't search full timebase
stepsize=5.0e-4,
mintransitduration=0.01, # minimum transit length in phase
maxtransitduration=0.4, # m... |
Runs the Box Least Squares Fitting Search for transit - shaped signals. | def bls_parallel_pfind(
times, mags, errs,
magsarefluxes=False,
startp=0.1, # by default, search from 0.1 d to...
endp=100.0, # ... 100.0 d -- don't search full timebase
stepsize=1.0e-4,
mintransitduration=0.01, # minimum transit length in phase
maxtransitdurat... |
Actually calculates the stats. | def _get_bls_stats(stimes,
smags,
serrs,
thistransdepth,
thistransduration,
ingressdurationfraction,
nphasebins,
thistransingressbin,
thistransegressbin,
... |
This calculates the SNR depth duration a refit period and time of center - transit for a single period. | def bls_stats_singleperiod(times, mags, errs, period,
magsarefluxes=False,
sigclip=10.0,
perioddeltapercent=10,
nphasebins=200,
mintransitduration=0.01,
maxtr... |
Calculates the signal to noise ratio for each best peak in the BLS periodogram along with transit depth duration and refit period and epoch. | def bls_snr(blsdict,
times,
mags,
errs,
assumeserialbls=False,
magsarefluxes=False,
sigclip=10.0,
npeaks=None,
perioddeltapercent=10,
ingressdurationfraction=0.1,
verbose=True):
'''Calculates the ... |
This function gets the Fortney mass - radius relation for planets. | def massradius(age, planetdist, coremass,
mass='massjupiter',
radius='radiusjupiter'):
'''This function gets the Fortney mass-radius relation for planets.
Parameters
----------
age : float
This should be one of: 0.3, 1.0, 4.5 [in Gyr].
planetdist : float
... |
This is a parallel worker to gather LC stats. | def _collect_tfa_stats(task):
'''
This is a parallel worker to gather LC stats.
task[0] = lcfile
task[1] = lcformat
task[2] = lcformatdir
task[3] = timecols
task[4] = magcols
task[5] = errcols
task[6] = custom_bandpasses
'''
try:
(lcfile, lcformat, lcformatdir,
... |
This is a parallel worker that reforms light curves for TFA. | def _reform_templatelc_for_tfa(task):
'''
This is a parallel worker that reforms light curves for TFA.
task[0] = lcfile
task[1] = lcformat
task[2] = lcformatdir
task[3] = timecol
task[4] = magcol
task[5] = errcol
task[6] = timebase
task[7] = interpolate_type
task[8] = sigcli... |
This selects template objects for TFA. | def tfa_templates_lclist(
lclist,
lcinfo_pkl=None,
outfile=None,
target_template_frac=0.1,
max_target_frac_obs=0.25,
min_template_number=10,
max_template_number=1000,
max_rms=0.15,
max_mult_above_magmad=1.5,
max_mult_above_mageta=1.5,
... |
This applies the TFA correction to an LC given TFA template information. | def apply_tfa_magseries(lcfile,
timecol,
magcol,
errcol,
templateinfo,
mintemplatedist_arcmin=10.0,
lcformat='hat-sql',
lcformatdir=None,
... |
This is a parallel worker for the function below. | def _parallel_tfa_worker(task):
'''
This is a parallel worker for the function below.
task[0] = lcfile
task[1] = timecol
task[2] = magcol
task[3] = errcol
task[4] = templateinfo
task[5] = lcformat
task[6] = lcformatdir
task[6] = interp
task[7] = sigclip
'''
(lcfile... |
This applies TFA in parallel to all LCs in the given list of file names. | def parallel_tfa_lclist(lclist,
templateinfo,
timecols=None,
magcols=None,
errcols=None,
lcformat='hat-sql',
lcformatdir=None,
interp='nearest',
... |
This applies TFA in parallel to all LCs in a directory. | def parallel_tfa_lcdir(lcdir,
templateinfo,
lcfileglob=None,
timecols=None,
magcols=None,
errcols=None,
lcformat='hat-sql',
lcformatdir=None,
... |
This updates a checkplot objectinfo dict. | def update_checkplot_objectinfo(cpf,
fast_mode=False,
findercmap='gray_r',
finderconvolve=None,
deredden_object=True,
custom_bandpasses=None,
... |
This just reads a light curve pickle file. | def _read_pklc(lcfile):
'''
This just reads a light curve pickle file.
Parameters
----------
lcfile : str
The file name of the pickle to open.
Returns
-------
dict
This returns an lcdict.
'''
if lcfile.endswith('.gz'):
try:
with gzip.ope... |
This imports the module specified. | def _check_extmodule(module, formatkey):
'''This imports the module specified.
Used to dynamically import Python modules that are needed to support LC
formats not natively supported by astrobase.
Parameters
----------
module : str
This is either:
- a Python module import path... |
This adds a new LC format to the astrobase LC format registry. | def register_lcformat(formatkey,
fileglob,
timecols,
magcols,
errcols,
readerfunc_module,
readerfunc,
readerfunc_kwargs=None,
normfunc_module=No... |
This loads an LC format description from a previously - saved JSON file. | def get_lcformat(formatkey, use_lcformat_dir=None):
'''This loads an LC format description from a previously-saved JSON file.
Parameters
----------
formatkey : str
The key used to refer to the LC format. This is part of the JSON file's
name, e.g. the format key 'hat-csv' maps to the fo... |
This opens an SSH connection to the EC2 instance at ip_address. | def ec2_ssh(ip_address,
keypem_file,
username='ec2-user',
raiseonfail=False):
"""This opens an SSH connection to the EC2 instance at `ip_address`.
Parameters
----------
ip_address : str
IP address of the AWS EC2 instance to connect to.
keypem_file : str... |
This gets a file from an S3 bucket. | def s3_get_file(bucket,
filename,
local_file,
altexts=None,
client=None,
raiseonfail=False):
"""This gets a file from an S3 bucket.
Parameters
----------
bucket : str
The AWS S3 bucket name.
filename : str
... |
This gets a file from an S3 bucket based on its s3:// URL. | def s3_get_url(url,
altexts=None,
client=None,
raiseonfail=False):
"""This gets a file from an S3 bucket based on its s3:// URL.
Parameters
----------
url : str
S3 URL to download. This should begin with 's3://'.
altexts : None or list of str
... |
This uploads a file to S3. | def s3_put_file(local_file, bucket, client=None, raiseonfail=False):
"""This uploads a file to S3.
Parameters
----------
local_file : str
Path to the file to upload to S3.
bucket : str
The AWS S3 bucket to upload the file to.
client : boto3.Client or None
If None, thi... |
This deletes a file from S3. | def s3_delete_file(bucket, filename, client=None, raiseonfail=False):
"""This deletes a file from S3.
Parameters
----------
bucket : str
The AWS S3 bucket to delete the file from.
filename : str
The full file name of the file to delete, including any prefixes.
client : boto3.... |
This creates an SQS queue. | def sqs_create_queue(queue_name, options=None, client=None):
"""
This creates an SQS queue.
Parameters
----------
queue_name : str
The name of the queue to create.
options : dict or None
A dict of options indicate extra attributes the queue should have.
See the SQS doc... |
This deletes an SQS queue given its URL | def sqs_delete_queue(queue_url, client=None):
"""This deletes an SQS queue given its URL
Parameters
----------
queue_url : str
The SQS URL of the queue to delete.
client : boto3.Client or None
If None, this function will instantiate a new `boto3.Client` object to
use in it... |
This pushes a dict serialized to JSON to the specified SQS queue. | def sqs_put_item(queue_url,
item,
delay_seconds=0,
client=None,
raiseonfail=False):
"""This pushes a dict serialized to JSON to the specified SQS queue.
Parameters
----------
queue_url : str
The SQS URL of the queue to push th... |
This gets a single item from the SQS queue. | def sqs_get_item(queue_url,
max_items=1,
wait_time_seconds=5,
client=None,
raiseonfail=False):
"""This gets a single item from the SQS queue.
The `queue_url` is composed of some internal SQS junk plus a
`queue_name`. For our purposes (`lcp... |
This deletes a message from the queue effectively acknowledging its receipt. | def sqs_delete_item(queue_url,
receipt_handle,
client=None,
raiseonfail=False):
"""This deletes a message from the queue, effectively acknowledging its
receipt.
Call this only when all messages retrieved from the queue have been
processed, sin... |
This makes new EC2 worker nodes. | def make_ec2_nodes(
security_groupid,
subnet_id,
keypair_name,
iam_instance_profile_arn,
launch_instances=1,
ami='ami-04681a1dbd79675a5',
instance='t3.micro',
ebs_optimized=True,
user_data=None,
wait_until_up=True,
client=None,
... |
This deletes EC2 nodes and terminates the instances. | def delete_ec2_nodes(
instance_id_list,
client=None
):
"""This deletes EC2 nodes and terminates the instances.
Parameters
----------
instance_id_list : list of str
A list of EC2 instance IDs to terminate.
client : boto3.Client or None
If None, this function will in... |
This makes an EC2 spot - fleet cluster. | def make_spot_fleet_cluster(
security_groupid,
subnet_id,
keypair_name,
iam_instance_profile_arn,
spot_fleet_iam_role,
target_capacity=20,
spot_price=0.4,
expires_days=7,
allocation_strategy='lowestPrice',
instance_types=SPOT_INSTANCE_TYPES... |
This deletes a spot - fleet cluster. | def delete_spot_fleet_cluster(
spot_fleet_reqid,
client=None,
):
"""
This deletes a spot-fleet cluster.
Parameters
----------
spot_fleet_reqid : str
The fleet request ID returned by `make_spot_fleet_cluster`.
client : boto3.Client or None
If None, this function... |
This gets a single file from a Google Cloud Storage bucket. | def gcs_get_file(bucketname,
filename,
local_file,
altexts=None,
client=None,
service_account_json=None,
raiseonfail=False):
"""This gets a single file from a Google Cloud Storage bucket.
Parameters
------... |
This gets a single file from a Google Cloud Storage bucket. | def gcs_get_url(url,
altexts=None,
client=None,
service_account_json=None,
raiseonfail=False):
"""This gets a single file from a Google Cloud Storage bucket.
This uses the gs:// URL instead of a bucket name and key.
Parameters
----------
... |
This puts a single file into a Google Cloud Storage bucket. | def gcs_put_file(local_file,
bucketname,
service_account_json=None,
client=None,
raiseonfail=False):
"""This puts a single file into a Google Cloud Storage bucket.
Parameters
----------
local_file : str
Path to the file to upl... |
This reads a consolidated HAT LC written by the functions above. | def read_hatlc(hatlc):
'''
This reads a consolidated HAT LC written by the functions above.
Returns a dict.
'''
lcfname = os.path.basename(hatlc)
# unzip the files first
if '.gz' in lcfname:
lcf = gzip.open(hatlc,'rb')
elif '.bz2' in lcfname:
lcf = bz2.BZ2File(hatlc, ... |
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