Added p_astro module, modified Makefile.am

gstlal-inspiral/python/Makefile.am

@@ -33,7 +33,8 @@ pkgpython_PYTHON = \
 	streamthinca.py \
 	svd_bank.py \
 	templates.py \
-	webpage.py
+	webpage.py \
+	p_astro_gstlal.py
 
 pkgpyexec_LTLIBRARIES = _rate_estimation.la _snglinspiraltable.la _spawaveform.la
 

gstlal-inspiral/python/p_astro_gstlal.py

+import numpy as np
+from ligo.lw import ligolw
+from ligo.lw.ligolw import LIGOLWContentHandler
+from ligo.lw import array as ligolw_array
+from ligo.lw import param as ligolw_param
+from ligo.lw import utils as ligolw_utils
+from ligo.lw import lsctables
+from ligo.segments import utils as segments_utils
+from lal import rate
+
+def p_astro_update(category, event_bayesfac_dict, mean_values_dict):
+    """
+    Compute `p_astro` for a new event using mean values of Poisson expected
+    counts constructed from all the previous events. Invoked with every new
+    GraceDB entry.
+
+    Parameters
+    ----------
+    category : string
+        source category
+    event_bayesfac_dict : dictionary
+        event Bayes factors
+    mean_values_dict : dictionary
+        mean values of Poisson counts
+
+    Returns
+    -------
+    p_astro : float
+        p_astro by source category
+    """
+    if category == "counts_Terrestrial":
+        numerator = mean_values_dict["counts_Terrestrial"]
+    else:
+        numerator = \
+            event_bayesfac_dict[category] * mean_values_dict[category]
+
+    denominator = mean_values_dict["counts_Terrestrial"] + \
+        np.sum([mean_values_dict[key] * event_bayesfac_dict[key]
+                for key in event_bayesfac_dict.keys()])
+
+    return numerator / denominator
+
+
+def evaluate_p_astro_from_bayesfac(astro_bayesfac,
+                                   mean_values_dict,
+                                   mass1,
+                                   mass2,
+                                   spin1z=None,
+                                   spin2z=None,
+                                   num_bins=None,
+                                   activation_counts=None):
+    """
+    Evaluates `p_astro` for a new event using Bayes factor, masses, and number
+    of astrophysical categories. Invoked with every new GraceDB entry.
+
+    Parameters
+    ----------
+    astro_bayesfac : float
+        astrophysical Bayes factor
+    mean_values_dict: dictionary
+        mean values of Poisson counts
+    mass1 : float
+        event mass1
+    mass2 : float
+        event mass2
+    spin1z : float
+        event spin1z
+    spin2z : float
+        event spin2z
+    url_weights_key: str
+        url config key pointing to weights file
+
+    Returns
+    -------
+    p_astro : dictionary
+        p_astro for all source categories
+    """
+
+    a_hat_bns, a_hat_bbh, a_hat_nsbh, a_hat_mg, num_bins = \
+        make_weights_from_histograms(mass1,
+                                     mass2,
+                                     spin1z,
+                                     spin2z,
+                                     num_bins,
+                                     activation_counts)
+
+    # Compute category-wise Bayes factors
+    # from astrophysical Bayes factor
+    rescaled_fb = num_bins * astro_bayesfac
+    bns_bayesfac = a_hat_bns * rescaled_fb
+    nsbh_bayesfac = a_hat_nsbh * rescaled_fb
+    bbh_bayesfac = a_hat_bbh * rescaled_fb
+    mg_bayesfac = a_hat_mg * rescaled_fb
+
+    # Construct category-wise Bayes factor dictionary
+    event_bayesfac_dict = {"counts_BNS": bns_bayesfac,
+                           "counts_NSBH": nsbh_bayesfac,
+                           "counts_BBH": bbh_bayesfac,
+                           "counts_MassGap": mg_bayesfac}
+
+    # Compute the p-astro values for each source category
+    # using the mean values
+    p_astro_values = {}
+    for category in mean_values_dict:
+        p_astro_values[category.split("_")[1]] = \
+            p_astro_update(category=category,
+                           event_bayesfac_dict=event_bayesfac_dict,
+                           mean_values_dict=mean_values_dict)
+
+    return p_astro_values
+
+
+def make_weights_from_hardcuts(mass1, mass2):
+    """
+    Construct binary weights from component masses based on cuts in component
+    mass space that define astrophysical source categories. To be used for
+    MBTA, PyCBC and SPIIR.
+
+    Parameters
+    ----------
+    mass1 : float
+        heavier component mass of the event
+    mass2 : float
+        lighter component mass of the event
+
+    Returns
+    -------
+    a_bns, a_bbh, a_nshb, a_mg : floats
+        binary weights (i.e, 1 or 0)
+    """
+
+    a_hat_bns = int(mass1 <= 3 and mass2 <= 3)
+    a_hat_bbh = int(mass1 > 5 and mass2 > 5)
+    a_hat_nsbh = int(min(mass1, mass2) <= 3 and
+                     max(mass1, mass2) > 5)
+    a_hat_mg = int(3 < mass1 <= 5 or 3 < mass2 <= 5)
+    num_bins = 4
+
+    return a_hat_bns, a_hat_bbh, a_hat_nsbh, a_hat_mg, num_bins
+
+
+def closest_template(params, params_array):
+    """
+    Associate event's template to a template in the template bank. The assumed
+    bank is the one used by Gstlal. Hence, for Gstlal events, the association
+    should be exact, up to rounding errors.
+
+    Parameters
+    ----------
+    params : tuple of floats
+        intrinsic params of event template
+    params_array: array of arrays
+        array of template bank's template params
+
+    Returns
+    -------
+    idx : int
+        index pertaining to params_array
+        for matching template
+    """
+    idx = np.argmin(np.sum((params_array-params)**2,axis=1))
+
+    return idx
+
+
+def make_weights_from_histograms(mass1,
+                                 mass2,
+                                 spin1z,
+                                 spin2z,
+                                 num_bins=None,
+                                 activation_counts=None):
+    """
+    Construct binary weights from bin number provided by GstLAL, and a weights
+    matrix pre-constructed and stored in a file, to be read from a url. The
+    weights are keyed on template parameters of Gstlal's template bank. If that
+    doesn't work, construct binary weights.
+
+    Parameters
+    ----------
+    mass1 : float
+        heavier component mass of the event
+    mass2 : float
+        lighter component mass of the event
+    spin1z : float
+        z component spin of heavier mass
+    spin2z : float
+        z component spin of lighter mass
+    num_bins : int
+        number of bins for template weighting
+    activation_counts : pandas dataframe
+        data frame for template weights
+
+    Returns
+    -------
+    a_hat_bns, a_hat_bbh, a_hat_nsbh, a_hat_mg : floats
+        mass-based template weights
+    """
+
+    if activation_counts is None or num_bins is None:
+        a_hat_bns, a_hat_bbh, a_hat_nsbh, a_hat_mg, num_bins = \
+            make_weights_from_hardcuts(mass1, mass2)
+    else:
+        params = (mass1, mass2, spin1z, spin2z)
+        params_names = ['mass1', 'mass2', 'spin1z', 'spin2z']
+        params_array = \
+            np.array([activation_counts[key][:] for key in params_names]).T
+        idx = closest_template(params, params_array)
+        a_hat_bns = activation_counts['bns'][:][idx]
+        a_hat_mg = activation_counts['mg'][:][idx]
+        a_hat_nsbh = activation_counts['nsbh'][:][idx]
+        a_hat_bbh = activation_counts['bbh'][:][idx]
+
+    return a_hat_bns, a_hat_bbh, a_hat_nsbh, a_hat_mg, num_bins
+
+
+def _get_event_ln_likelihood_ratio_svd_endtime_mass(xmldoc):
+    """
+    Task to acquire event parameters
+
+    Parameters
+    ----------
+    xmldoc : lsctables object
+        Object from which event parameters can be extracted
+
+    Returns
+    -------
+    event parameters : tuple
+        Tuple of event parameters: lnl, component masses, snr, far
+    """
+
+    coinc_event, = lsctables.CoincTable.get_table(xmldoc)
+    sngl_inspiral = lsctables.SnglInspiralTable.get_table(xmldoc)
+    coinc_inspiral = lsctables.CoincInspiralTable.get_table(xmldoc)
+
+    return (coinc_event.likelihood,
+            sngl_inspiral[0].mass1,
+            sngl_inspiral[0].mass2,
+            coinc_inspiral.snr,
+            coinc_inspiral.combined_far)
+
+
+def _get_ln_f_over_b(rankingstatpdf,
+                     ln_likelihood_ratios,
+                     livetime):
+
+    # affect the zeroing of the PDFs below threshold by hacking the
+    # histograms. Do the indexing ourselves to not 0 the bin @ threshold
+    noise_lr_lnpdf = rankingstatpdf.noise_lr_lnpdf
+    signal_lr_lnpdf = rankingstatpdf.signal_lr_lnpdf
+    zero_lag_lr_lnpdf = rankingstatpdf.zero_lag_lr_lnpdf
+    ssorted = zero_lag_lr_lnpdf.array.cumsum()[-1] - 10000
+    idx = zero_lag_lr_lnpdf.array.cumsum().searchsorted(ssorted)
+
+    ln_likelihood_ratio_threshold = \
+        zero_lag_lr_lnpdf.bins[0].lower()[idx]
+
+    # Compute FAR for threshold, and estimate
+    # terrestrial count consistent with threshold
+    fapfar = \
+        FAPFAR(rankingstatpdf.new_with_extinction())
+    far_threshold = fapfar.far_from_rank(ln_likelihood_ratio_threshold)
+    lam_0 = far_threshold*livetime
+    rankingstatpdf.noise_lr_lnpdf.array[
+        :noise_lr_lnpdf.bins[0][ln_likelihood_ratio_threshold]] \
+        = 0.
+    rankingstatpdf.noise_lr_lnpdf.normalize()
+
+    rankingstatpdf.signal_lr_lnpdf.array[
+        :signal_lr_lnpdf.bins[0][ln_likelihood_ratio_threshold]] \
+        = 0.
+    rankingstatpdf.signal_lr_lnpdf.normalize()
+
+    rankingstatpdf.zero_lag_lr_lnpdf.array[
+        :zero_lag_lr_lnpdf.bins[0][ln_likelihood_ratio_threshold]] \
+        = 0.
+    rankingstatpdf.zero_lag_lr_lnpdf.normalize()
+
+    f = rankingstatpdf.signal_lr_lnpdf
+    b = rankingstatpdf.noise_lr_lnpdf
+    ln_f_over_b = \
+        np.array([f[ln_lr, ] - b[ln_lr, ] for ln_lr in ln_likelihood_ratios])
+    if np.isnan(ln_f_over_b).any():
+        raise ValueError("NaN encountered in ranking statistic PDF ratios")
+    if np.isinf(np.exp(ln_f_over_b)).any():
+        raise ValueError(
+            "infinity encountered in ranking statistic PDF ratios")
+    return ln_f_over_b, lam_0
+
+
+def compute_p_astro(event_ln_likelihood_ratio,
+                    event_mass1,
+                    event_mass2,
+                    snr,
+                    far,
+                    livetime,
+                    mean_values_dict):
+    """
+    Task to compute `p_astro` by source category.
+
+    Parameters
+    ----------
+    event_ln_likelihood_ratio : float
+        Event's log likelihood ratio value
+    event_mass1 : float
+        Event's heavier component mass value
+    event_mass2 : float
+        Event's lighter component mass value
+    snr: float
+        Event's snr value
+    far: float
+        Event's far value
+    livetime: float
+        Livetime consistent with estimate of Poisson counts. 
+        Eg. If counts are from O1 and O2, livetime is O1-O2
+        livetime in seconds.
+    mean_values_dict : dictionary
+        dictionary of source specific FGMC Poisson counts
+
+    Returns
+    -------
+    p_astros : str
+        JSON dump of the p_astro by source category
+
+    Example
+    -------
+    >>> p_astros = json.loads(compute_p_astro(files))
+    >>> p_astros
+    {'BNS': 0.999, 'BBH': 0.0, 'NSBH': 0.0, 'Terrestrial': 0.001}
+    """
+
+    # Using the zerolag log likelihood ratio value event,
+    # and the foreground/background model information provided
+    # in ranking_data.xml.gz, compute the ln(f/b) value for this event
+    zerolag_ln_likelihood_ratios = np.array([event_ln_likelihood_ratio])
+    try:
+        ln_f_over_b, lam_0 = \
+            _get_ln_f_over_b(rankingstatpdf,
+                             zerolag_ln_likelihood_ratios,
+                             livetime)
+    except ValueError:
+        return compute_p_astro_approx(snr,
+                                      far,
+                                      event_mass1,
+                                      event_mass2,
+                                      mean_values_dict)
+
+    # Read mean values from url file
+    mean_values_dict["counts_Terrestrial"] = lam_0
+
+    # Compute categorical p_astro values
+    p_astro_values = \
+        evaluate_p_astro_from_bayesfac(np.exp(ln_f_over_b[0]),
+                                       mean_values_dict,
+                                       event_mass1,
+                                       event_mass2)
+
+    # Dump values in json file
+    return json.dumps(p_astro_values)
+
+def compute_p_astro_approx(snr, far, mass1, mass2, livetime, mean_values_dict):
+    """
+    Task to compute `p_astro` by source category.
+
+    Parameters
+    ----------
+    snr : float
+        event's SNR
+    far : float
+        event's cfar
+    mass1 : float
+        event's mass1
+    mass2 : float
+        event's mass2
+    livetime: float
+        Livetime consistent with estimate of Poisson counts. 
+        Eg. If counts are from O1 and O2, livetime is O1-O2
+        livetime in seconds. 
+    mean_values_dict : dictionary
+        dictionary of source specific FGMC Poisson counts
+
+    Returns
+    -------
+    p_astros : str
+        JSON dump of the p_astro by source category
+
+    Example
+    -------
+    >>> p_astros = json.loads(compute_p_astro(files))
+    >>> p_astros
+    {'BNS': 0.999, 'BBH': 0.0, 'NSBH': 0.0, 'Terrestrial': 0.001}
+    """
+
+    # Define constants to compute bayesfactors
+    snr_star = 8.5
+    far_star = 1 / (30 * 86400)
+
+    # Compute astrophysical bayesfactor for
+    # GraceDB event
+    fground = 3 * snr_star**3 / (snr_choice**4)
+    bground = far / far_star
+    astro_bayesfac = fground / bground
+
+    # Update terrestrial count based on far threshold
+    lam_0 = far_star * livetime
+    mean_values_dict["counts_Terrestrial"] = lam_0
+
+    # Compute categorical p_astro values
+    p_astro_values = \
+        evaluate_p_astro_from_bayesfac(astro_bayesfac,
+                                       mean_values_dict,
+                                       mass1,
+                                       mass2)
+    # Dump mean values in json file
+    return json.dumps(p_astro_values)