astrobase/fakelcs/recovery.py
def run_periodfinding(simbasedir,
                      pfmethods=('gls','pdm','bls'),
                      pfkwargs=({},{},{'startp':1.0,'maxtransitduration':0.3}),
                      getblssnr=False,
                      sigclip=5.0,
                      nperiodworkers=10,
                      ncontrolworkers=4,
                      liststartindex=None,
                      listmaxobjects=None):
    '''This runs periodfinding using several period-finders on a collection of
    fake LCs.

    As a rough benchmark, 25000 fake LCs with 10000--50000 points per LC take
    about 26 days in total to run on an invocation of this function using
    GLS+PDM+BLS and 10 periodworkers and 4 controlworkers (so all 40 'cores') on
    a 2 x Xeon E5-2660v3 machine.

    Parameters
    ----------

    pfmethods : sequence of str
        This is used to specify which periodfinders to run. These must be in the
        `lcproc.periodsearch.PFMETHODS` dict.

    pfkwargs : sequence of dict
        This is used to provide optional kwargs to the period-finders.

    getblssnr : bool
        If this is True, will run BLS SNR calculations for each object and
        magcol. This takes a while to run, so it's disabled (False) by default.

    sigclip : float or int or sequence of two floats/ints or None
        If a single float or int, a symmetric sigma-clip will be performed using
        the number provided as the sigma-multiplier to cut out from the input
        time-series.

        If a list of two ints/floats is provided, the function will perform an
        'asymmetric' sigma-clip. The first element in this list is the sigma
        value to use for fainter flux/mag values; the second element in this
        list is the sigma value to use for brighter flux/mag values. For
        example, `sigclip=[10., 3.]`, will sigclip out greater than 10-sigma
        dimmings and greater than 3-sigma brightenings. Here the meaning of
        "dimming" and "brightening" is set by *physics* (not the magnitude
        system), which is why the `magsarefluxes` kwarg must be correctly set.

        If `sigclip` is None, no sigma-clipping will be performed, and the
        time-series (with non-finite elems removed) will be passed through to
        the output.

    nperiodworkers : int
        This is the number of parallel period-finding worker processes to use.

    ncontrolworkers : int
        This is the number of parallel period-finding control workers to
        use. Each control worker will launch `nperiodworkers` worker processes.

    liststartindex : int
        The starting index of processing. This refers to the filename list
        generated by running `glob.glob` on the fake LCs in `simbasedir`.

    maxobjects : int
        The maximum number of objects to process in this run. Use this with
        `liststartindex` to effectively distribute working on a large list of
        input light curves over several sessions or machines.

    Returns
    -------

    str
        The path to the output summary pickle produced by
        `lcproc.periodsearch.parallel_pf`

    '''

    # get the info from the simbasedir
    with open(os.path.join(simbasedir, 'fakelcs-info.pkl'),'rb') as infd:
        siminfo = pickle.load(infd)

    lcfpaths = siminfo['lcfpath']
    pfdir = os.path.join(simbasedir,'periodfinding')

    # get the column defs for the fakelcs
    timecols = siminfo['timecols']
    magcols = siminfo['magcols']
    errcols = siminfo['errcols']

    # register the fakelc pklc as a custom lcproc format
    # now we should be able to use all lcproc functions correctly
    fakelc_formatkey = 'fake-%s' % siminfo['lcformat']
    lcproc.register_lcformat(
        fakelc_formatkey,
        '*-fakelc.pkl',
        timecols,
        magcols,
        errcols,
        'astrobase.lcproc',
        '_read_pklc',
        magsarefluxes=siminfo['magsarefluxes']
    )

    if liststartindex:
        lcfpaths = lcfpaths[liststartindex:]

    if listmaxobjects:
        lcfpaths = lcfpaths[:listmaxobjects]

    pfinfo = periodsearch.parallel_pf(lcfpaths,
                                      pfdir,
                                      lcformat=fakelc_formatkey,
                                      pfmethods=pfmethods,
                                      pfkwargs=pfkwargs,
                                      getblssnr=getblssnr,
                                      sigclip=sigclip,
                                      nperiodworkers=nperiodworkers,
                                       ncontrolworkers=ncontrolworkers)

    with open(os.path.join(simbasedir,
                           'fakelc-periodsearch.pkl'),'wb') as outfd:
        pickle.dump(pfinfo, outfd, pickle.HIGHEST_PROTOCOL)

    return os.path.join(simbasedir,'fakelc-periodsearch.pkl')
def run_periodfinding(simbasedir,
                      pfmethods=('gls','pdm','bls'),
                      pfkwargs=({},{},{'startp':1.0,'maxtransitduration':0.3}),
                      getblssnr=False,
                      sigclip=5.0,
                      nperiodworkers=10,
                      ncontrolworkers=4,
                      liststartindex=None,
                      listmaxobjects=None):
    '''This runs periodfinding using several period-finders on a collection of
    fake LCs.

    As a rough benchmark, 25000 fake LCs with 10000--50000 points per LC take
    about 26 days in total to run on an invocation of this function using
    GLS+PDM+BLS and 10 periodworkers and 4 controlworkers (so all 40 'cores') on
    a 2 x Xeon E5-2660v3 machine.

    Parameters
    ----------

    pfmethods : sequence of str
        This is used to specify which periodfinders to run. These must be in the
        `lcproc.periodsearch.PFMETHODS` dict.

    pfkwargs : sequence of dict
        This is used to provide optional kwargs to the period-finders.

    getblssnr : bool
        If this is True, will run BLS SNR calculations for each object and
        magcol. This takes a while to run, so it's disabled (False) by default.

    sigclip : float or int or sequence of two floats/ints or None
        If a single float or int, a symmetric sigma-clip will be performed using
        the number provided as the sigma-multiplier to cut out from the input
        time-series.

        If a list of two ints/floats is provided, the function will perform an
        'asymmetric' sigma-clip. The first element in this list is the sigma
        value to use for fainter flux/mag values; the second element in this
        list is the sigma value to use for brighter flux/mag values. For
        example, `sigclip=[10., 3.]`, will sigclip out greater than 10-sigma
        dimmings and greater than 3-sigma brightenings. Here the meaning of
        "dimming" and "brightening" is set by *physics* (not the magnitude
        system), which is why the `magsarefluxes` kwarg must be correctly set.

        If `sigclip` is None, no sigma-clipping will be performed, and the
        time-series (with non-finite elems removed) will be passed through to
        the output.

    nperiodworkers : int
        This is the number of parallel period-finding worker processes to use.

    ncontrolworkers : int
        This is the number of parallel period-finding control workers to
        use. Each control worker will launch `nperiodworkers` worker processes.

    liststartindex : int
        The starting index of processing. This refers to the filename list
        generated by running `glob.glob` on the fake LCs in `simbasedir`.

    maxobjects : int
        The maximum number of objects to process in this run. Use this with
        `liststartindex` to effectively distribute working on a large list of
        input light curves over several sessions or machines.

    Returns
    -------

    str
        The path to the output summary pickle produced by
        `lcproc.periodsearch.parallel_pf`

    '''

    # get the info from the simbasedir
    with open(os.path.join(simbasedir, 'fakelcs-info.pkl'),'rb') as infd:
        siminfo = pickle.load(infd)

    lcfpaths = siminfo['lcfpath']
    pfdir = os.path.join(simbasedir,'periodfinding')

    # get the column defs for the fakelcs
    timecols = siminfo['timecols']
    magcols = siminfo['magcols']
    errcols = siminfo['errcols']

    # register the fakelc pklc as a custom lcproc format
    # now we should be able to use all lcproc functions correctly
    fakelc_formatkey = 'fake-%s' % siminfo['lcformat']
    lcproc.register_lcformat(
        fakelc_formatkey,
        '*-fakelc.pkl',
        timecols,
        magcols,
        errcols,
        'astrobase.lcproc',
        '_read_pklc',
        magsarefluxes=siminfo['magsarefluxes']
    )

    if liststartindex:
        lcfpaths = lcfpaths[liststartindex:]

    if listmaxobjects:
        lcfpaths = lcfpaths[:listmaxobjects]

    pfinfo = periodsearch.parallel_pf(lcfpaths,
                                      pfdir,
                                      lcformat=fakelc_formatkey,
                                      pfmethods=pfmethods,
                                      pfkwargs=pfkwargs,
                                      getblssnr=getblssnr,
                                      sigclip=sigclip,
                                      nperiodworkers=nperiodworkers,
                                       ncontrolworkers=ncontrolworkers)

    with open(os.path.join(simbasedir,
                           'fakelc-periodsearch.pkl'),'wb') as outfd:
        pickle.dump(pfinfo, outfd, pickle.HIGHEST_PROTOCOL)

    return os.path.join(simbasedir,'fakelc-periodsearch.pkl')
This runs periodfinding using several period-finders on a collection of
    fake LCs.

    As a rough benchmark, 25000 fake LCs with 10000--50000 points per LC take
    about 26 days in total to run on an invocation of this function using
    GLS+PDM+BLS and 10 periodworkers and 4 controlworkers (so all 40 'cores') on
    a 2 x Xeon E5-2660v3 machine.

    Parameters
    ----------

    pfmethods : sequence of str
        This is used to specify which periodfinders to run. These must be in the
        `lcproc.periodsearch.PFMETHODS` dict.

    pfkwargs : sequence of dict
        This is used to provide optional kwargs to the period-finders.

    getblssnr : bool
        If this is True, will run BLS SNR calculations for each object and
        magcol. This takes a while to run, so it's disabled (False) by default.

    sigclip : float or int or sequence of two floats/ints or None
        If a single float or int, a symmetric sigma-clip will be performed using
        the number provided as the sigma-multiplier to cut out from the input
        time-series.

        If a list of two ints/floats is provided, the function will perform an
        'asymmetric' sigma-clip. The first element in this list is the sigma
        value to use for fainter flux/mag values; the second element in this
        list is the sigma value to use for brighter flux/mag values. For
        example, `sigclip=[10., 3.]`, will sigclip out greater than 10-sigma
        dimmings and greater than 3-sigma brightenings. Here the meaning of
        "dimming" and "brightening" is set by *physics* (not the magnitude
        system), which is why the `magsarefluxes` kwarg must be correctly set.

        If `sigclip` is None, no sigma-clipping will be performed, and the
        time-series (with non-finite elems removed) will be passed through to
        the output.

    nperiodworkers : int
        This is the number of parallel period-finding worker processes to use.

    ncontrolworkers : int
        This is the number of parallel period-finding control workers to
        use. Each control worker will launch `nperiodworkers` worker processes.

    liststartindex : int
        The starting index of processing. This refers to the filename list
        generated by running `glob.glob` on the fake LCs in `simbasedir`.

    maxobjects : int
        The maximum number of objects to process in this run. Use this with
        `liststartindex` to effectively distribute working on a large list of
        input light curves over several sessions or machines.

    Returns
    -------

    str
        The path to the output summary pickle produced by
        `lcproc.periodsearch.parallel_pf`