lalsuite 7.26.2.dev20251206__cp312-cp312-manylinux_2_28_x86_64.whl

lalpulsar/pulsarpputils.py

@@ -0,0 +1,3638 @@
+# -*- coding: utf-8 -*-
+#
+#       pulsarpputils.py
+#
+#       Copyright 2012
+#       Matthew Pitkin <matthew.pitkin@ligo.org>
+#
+#
+#       This program is free software; you can redistribute it and/or modify
+#       it under the terms of the GNU General Public License as published by
+#       the Free Software Foundation; either version 2 of the License, or
+#       (at your option) any later version.
+#
+#       This program is distributed in the hope that it will be useful,
+#       but WITHOUT ANY WARRANTY; without even the implied warranty of
+#       MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#       GNU General Public License for more details.
+#
+#       You should have received a copy of the GNU General Public License
+#       along with this program; if not, write to the Free Software
+#       Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+#       MA 02110-1301, USA.
+
+# known pulsar analysis post-processing utilities
+
+# Many functions in this a taken from, or derived from equivalents available in
+# the PRESTO pulsar software package http://www.cv.nrao.edu/~sransom/presto/
+
+from __future__ import print_function, division
+
+import sys
+import math
+import cmath
+import os
+import numpy as np
+import struct
+import re
+import h5py
+
+try:
+    from scipy.integrate import trapezoid, cumulative_trapezoid
+except ImportError:
+    # FIXME: Remove this once we require scipy >=1.6.0.
+    from scipy.integrate import trapz as trapezoid, cumtrapz as cumulative_trapezoid
+
+from scipy.interpolate import interp1d
+
+try:
+    from scipy.special import logsumexp
+except ImportError:  # scipy < 0.19.0
+    from scipy.misc import logsumexp
+
+# some common constants taken from psr_constants.py in PRESTO
+ARCSECTORAD = float("4.8481368110953599358991410235794797595635330237270e-6")
+RADTOARCSEC = float("206264.80624709635515647335733077861319665970087963")
+SECTORAD = float("7.2722052166430399038487115353692196393452995355905e-5")
+RADTOSEC = float("13750.987083139757010431557155385240879777313391975")
+RADTODEG = float("57.295779513082320876798154814105170332405472466564")
+DEGTORAD = float("1.7453292519943295769236907684886127134428718885417e-2")
+RADTOHRS = float("3.8197186342054880584532103209403446888270314977710")
+HRSTORAD = float("2.6179938779914943653855361527329190701643078328126e-1")
+PI = float("3.1415926535897932384626433832795028841971693993751")
+TWOPI = float("6.2831853071795864769252867665590057683943387987502")
+PIBYTWO = float("1.5707963267948966192313216916397514420985846996876")
+SECPERDAY = float("86400.0")
+SECPERJULYR = float("31557600.0")
+KMPERPC = float("3.0856776e13")
+KMPERKPC = float("3.0856776e16")
+Tsun = float("4.925490947e-6")  # sec
+Msun = float("1.9891e30")  # kg
+Mjup = float("1.8987e27")  # kg
+Rsun = float("6.9551e8")  # m
+Rearth = float("6.378e6")  # m
+SOL = float("299792458.0")  # m/s
+MSUN = float("1.989e+30")  # kg
+G = float("6.673e-11")  # m^3/s^2/kg
+C = SOL
+KPC = float("3.0856776e19")  # kiloparsec in metres
+I38 = float("1e38")  # moment of inertia kg m^2
+
+
+# some angle conversion functions taken from psr_utils.py in PRESTO
+def rad_to_dms(rad):
+    """
+    rad_to_dms(rad):
+       Convert radians to degrees, minutes, and seconds of arc.
+    """
+    if rad < 0.0:
+        sign = -1
+    else:
+        sign = 1
+    arc = RADTODEG * np.fmod(np.fabs(rad), math.pi)
+    d = int(arc)
+    arc = (arc - d) * 60.0
+    m = int(arc)
+    s = (arc - m) * 60.0
+    if sign == -1 and d == 0:
+        return (sign * d, sign * m, sign * s)
+    else:
+        return (sign * d, m, s)
+
+
+def dms_to_rad(deg, mins, sec):
+    """
+    dms_to_rad(deg, min, sec):
+       Convert degrees, minutes, and seconds of arc to radians.
+    """
+    if deg < 0.0:
+        sign = -1
+    elif deg == 0.0 and (mins < 0.0 or sec < 0.0):
+        sign = -1
+    else:
+        sign = 1
+    return (
+        sign
+        * ARCSECTORAD
+        * (60.0 * (60.0 * np.fabs(deg) + np.fabs(mins)) + np.fabs(sec))
+    )
+
+
+def dms_to_deg(deg, mins, sec):
+    """
+    dms_to_deg(deg, min, sec):
+       Convert degrees, minutes, and seconds of arc to degrees.
+    """
+    return RADTODEG * dms_to_rad(deg, mins, sec)
+
+
+def rad_to_hms(rad):
+    """
+    rad_to_hms(rad):
+       Convert radians to hours, minutes, and seconds of arc.
+    """
+    rad = np.fmod(rad, 2.0 * math.pi)
+    if rad < 0.0:
+        rad = rad + 2.0 * math.pi
+    arc = RADTOHRS * rad
+    h = int(arc)
+    arc = (arc - h) * 60.0
+    m = int(arc)
+    s = (arc - m) * 60.0
+    return (h, m, s)
+
+
+def hms_to_rad(hour, mins, sec):
+    """
+    hms_to_rad(hour, min, sec):
+       Convert hours, minutes, and seconds of arc to radians
+    """
+    if hour < 0.0:
+        sign = -1
+    else:
+        sign = 1
+    return (
+        sign * SECTORAD * (60.0 * (60.0 * np.fabs(hour) + np.fabs(mins)) + np.fabs(sec))
+    )
+
+
+def coord_to_string(h_or_d, m, s):
+    """
+    coord_to_string(h_or_d, m, s):
+       Return a formatted string of RA or DEC values as
+       'hh:mm:ss.ssss' if RA, or 'dd:mm:ss.ssss' if DEC.
+    """
+    retstr = ""
+    if h_or_d < 0:
+        retstr = "-"
+    elif abs(h_or_d) == 0:
+        if (m < 0.0) or (s < 0.0):
+            retstr = "-"
+
+    h_or_d, m, s = abs(h_or_d), abs(m), abs(s)
+    if s >= 9.9995:
+        return retstr + "%.2d:%.2d:%.4f" % (h_or_d, m, s)
+    else:
+        return retstr + "%.2d:%.2d:0%.4f" % (h_or_d, m, s)
+
+
+def rad_to_string(rad, ra_or_dec):
+    """
+    rad_to_string(rad, ra_or_dec):
+       Convert an angle in radians to hours/degrees, minutes seconds and output
+       it as a string in the format 'hh:mm:ss.ssss' if RA, or 'dd:mm:ss.ssss' if DEC.
+       Whether to use hours or degrees is set by whether ra_or_dec is 'RA' or 'DEC'
+    """
+    if ra_or_dec.upper() == "RA":
+        v, m, s = rad_to_hms(rad)
+    elif ra_or_dec.upper() == "DEC":
+        v, m, s = rad_to_dms(rad)
+    else:
+        raise ValueError(
+            "Unrecognised option: Expected 'ra_or_dec' to be 'RA' or 'DEC'"
+        )
+
+    return coord_to_string(v, m, s)
+
+
+def ra_to_rad(ra_string):
+    """
+    ra_to_rad(ar_string):
+       Given a string containing RA information as
+       'hh:mm:ss.ssss', return the equivalent decimal
+       radians. Also deal with cases where input
+       string is just hh:mm, or hh.
+    """
+    hms = ra_string.split(":")
+    if len(hms) == 3:
+        return hms_to_rad(int(hms[0]), int(hms[1]), float(hms[2]))
+    elif len(hms) == 2:
+        return hms_to_rad(int(hms[0]), int(hms[1]), 0.0)
+    elif len(hms) == 1:
+        return hms_to_rad(float(hms[0]), 0.0, 0.0)
+    else:
+        print("Problem parsing RA string %s" % ra_string, file=sys.stderr)
+        sys.exit(1)
+
+
+def dec_to_rad(dec_string):
+    """
+    dec_to_rad(dec_string):
+       Given a string containing DEC information as
+       'dd:mm:ss.ssss', return the equivalent decimal
+       radians. Also deal with cases where input string
+       is just dd:mm or dd
+    """
+    dms = dec_string.split(":")
+    if "-" in dms[0] and float(dms[0]) == 0.0:
+        m = "-"
+    else:
+        m = ""
+
+    if len(dms) == 3:
+        return dms_to_rad(int(dms[0]), int(m + dms[1]), float(m + dms[2]))
+    elif len(dms) == 2:
+        return dms_to_rad(int(dms[0]), int(m + dms[1]), 0.0)
+    elif len(dms) == 1:
+        return dms_to_rad(float(dms[0]), 0.0, 0.0)
+    else:
+        print("Problem parsing DEC string %s" % dec_string, file=sys.stderr)
+        sys.exit(1)
+
+
+def p_to_f(p, pd, pdd=None):
+    """
+    p_to_f(p, pd, pdd=None):
+      Convert period, period derivative and period second
+      derivative to the equivalent frequency counterparts.
+      Will also convert from f to p.
+    """
+    f = 1.0 / p
+    fd = -pd / (p * p)
+    if pdd == None:
+        return [f, fd]
+    else:
+        if pdd == 0.0:
+            fdd = 0.0
+        else:
+            fdd = 2.0 * pd * pd / (p**3.0) - pdd / (p * p)
+
+        return [f, fd, fdd]
+
+
+def pferrs(porf, porferr, pdorfd=None, pdorfderr=None):
+    """
+    pferrs(porf, porferr, pdorfd=None, pdorfderr=None):
+       Calculate the period or frequency errors and
+       the pdot or fdot errors from the opposite one.
+    """
+    if pdorfd == None:
+        return [1.0 / porf, porferr / porf**2.0]
+    else:
+        forperr = porferr / porf**2.0
+        fdorpderr = np.sqrt(
+            (4.0 * pdorfd**2.0 * porferr**2.0) / porf**6.0
+            + pdorfderr**2.0 / porf**4.0
+        )
+        [forp, fdorpd] = p_to_f(porf, pdorfd)
+
+        return [forp, forperr, fdorpd, fdorpderr]
+
+
+# class to read in a pulsar par file - this is heavily based on the function
+# in parfile.py in PRESTO
+float_keys = [
+    "F",
+    "F0",
+    "F1",
+    "F2",
+    "F3",
+    "F4",
+    "F5",
+    "F6",
+    "F7",
+    "F8",
+    "F9",
+    "F10",
+    "F11",
+    "F12",
+    "PEPOCH",
+    "POSEPOCH",
+    "DM",
+    "START",
+    "FINISH",
+    "NTOA",
+    "TRES",
+    "TZRMJD",
+    "TZRFRQ",
+    "TZRSITE",
+    "NITS",
+    "A1",
+    "XDOT",
+    "E",
+    "ECC",
+    "EDOT",
+    "T0",
+    "PB",
+    "PBDOT",
+    "OM",
+    "OMDOT",
+    "EPS1",
+    "EPS2",
+    "EPS1DOT",
+    "EPS2DOT",
+    "TASC",
+    "LAMBDAPIN",
+    "BETA",
+    "RA_RAD",
+    "DEC_RAD",
+    "GAMMA",
+    "SINI",
+    "M2",
+    "MTOT",
+    "FB0",
+    "FB1",
+    "FB2",
+    "ELAT",
+    "ELONG",
+    "PMRA",
+    "PMDEC",
+    "DIST",
+    "PB_2",
+    "PB_3",
+    "T0_2",
+    "T0_3",
+    "A1_2",
+    "A1_3",
+    "OM_2",
+    "OM_3",
+    "ECC_2",
+    "ECC_3",
+    "PX",
+    "KIN",
+    "KOM",
+    "A0",
+    "B0",
+    "D_AOP",
+    # GW PARAMETERS
+    "H0",
+    "COSIOTA",
+    "PSI",
+    "PHI0",
+    "THETA",
+    "I21",
+    "I31",
+    "C22",
+    "HPLUS",
+    "HCROSS",
+    "C21",
+    "PHI22",
+    "PHI21",
+    "SNR",
+    "COSTHETA",
+    "IOTA",
+    "Q22",
+]
+str_keys = [
+    "FILE",
+    "PSR",
+    "PSRJ",
+    "NAME",
+    "RAJ",
+    "DECJ",
+    "RA",
+    "DEC",
+    "EPHEM",
+    "CLK",
+    "BINARY",
+    "UNITS",
+]
+
+
+class psr_par:
+    def __init__(self, parfilenm):
+        """
+        This class parses a TEMPO(2)-style pulsar parameter file. If possible all parameters
+        are converted into SI units and angles are in radians. Epochs will be converted from
+        MJD values into GPS times.
+        """
+        self.FILE = parfilenm
+        pf = open(parfilenm)
+        for line in pf.readlines():
+            # ignore empty lines (i.e. containing only whitespace)
+            if not line.strip():
+                continue
+
+            # Convert any 'D-' or 'D+' to 'E-' or 'E+'
+            line = line.replace("D-", "E-")
+            line = line.replace("D+", "E+")
+            # also check for lower case
+            line = line.replace("d-", "e-")
+            line = line.replace("d+", "e+")
+            splitline = line.split()
+
+            # get all upper case version in case lower case in par file
+            key = splitline[0].upper()
+
+            if key in str_keys:
+                setattr(self, key, splitline[1])
+            elif key in float_keys:
+                try:
+                    setattr(self, key, float(splitline[1]))
+                except:
+                    continue
+
+            if (
+                len(splitline) == 3
+            ):  # Some parfiles don't have flags, but do have errors
+                if splitline[2] not in ["0", "1"]:
+                    setattr(self, key + "_ERR", float(splitline[2]))
+                    setattr(self, key + "_FIT", 0)  # parameter was not fit
+
+            if len(splitline) == 4:
+                if splitline[2] == "1":  # parameter was fit
+                    setattr(self, key + "_FIT", 1)
+                else:
+                    setattr(self, key + "_FIT", 0)
+                setattr(self, key + "_ERR", float(splitline[3]))
+
+        # sky position
+        if hasattr(self, "RAJ"):
+            setattr(self, "RA_RAD", ra_to_rad(self.RAJ))
+
+            # set RA error in rads (rather than secs)
+            if hasattr(self, "RAJ_ERR"):
+                setattr(self, "RA_RAD_ERR", hms_to_rad(0, 0, self.RAJ_ERR))
+
+                if hasattr(self, "RAJ_FIT"):
+                    setattr(self, "RA_RAD_FIT", self["RAJ_FIT"])
+        if hasattr(self, "DECJ"):
+            setattr(self, "DEC_RAD", dec_to_rad(self.DECJ))
+
+            # set DEC error in rads (rather than arcsecs)
+            if hasattr(self, "DECJ_ERR"):
+                setattr(self, "DEC_RAD_ERR", dms_to_rad(0, 0, self.DECJ_ERR))
+
+                if hasattr(self, "DECJ_FIT"):
+                    setattr(self, "DEC_RAD_FIT", self["DECJ_FIT"])
+
+        # convert proper motions to rads/sec from mas/year
+        for pv in ["RA", "DEC"]:
+            if hasattr(self, "PM" + pv):
+                pmv = self["PM" + pv]
+                setattr(self, "PM" + pv + "_ORIGINAL", pmv)  # save original value
+                setattr(
+                    self, "PM" + pv, pmv * np.pi / (180.0 * 3600.0e3 * 365.25 * 86400.0)
+                )
+
+                if hasattr(self, "PM" + pv + "_ERR"):
+                    pmve = self["PM" + pv + "_ERR"]
+                    setattr(
+                        self, "PM" + pv + "_ERR_ORIGINAL", pmv
+                    )  # save original value
+                    setattr(
+                        self,
+                        "PM" + pv + "_ERR",
+                        pmve * np.pi / (180.0 * 3600.0e3 * 365.25 * 86400.0),
+                    )
+
+        # periods and frequencies
+        if hasattr(self, "P"):
+            setattr(self, "P0", self.P)
+        if hasattr(self, "P0"):
+            setattr(self, "F0", 1.0 / self.P0)
+        if hasattr(self, "F0"):
+            setattr(self, "P0", 1.0 / self.F0)
+        if hasattr(self, "FB0"):
+            setattr(self, "PB", (1.0 / self.FB0) / 86400.0)
+        if hasattr(self, "P0_ERR"):
+            if hasattr(self, "P1_ERR"):
+                f, ferr, fd, fderr = pferrs(self.P0, self.P0_ERR, self.P1, self.P1_ERR)
+                setattr(self, "F0_ERR", ferr)
+                setattr(self, "F1", fd)
+                setattr(self, "F1_ERR", fderr)
+            else:
+                if hasattr(self, "P1"):
+                    (
+                        f,
+                        fd,
+                    ) = p_to_f(self.P0, self.P1)
+                    setattr(self, "F0_ERR", self.P0_ERR / (self.P0 * self.P0))
+                    setattr(self, "F1", fd)
+        if hasattr(self, "F0_ERR"):
+            if hasattr(self, "F1_ERR"):
+                p, perr, pd, pderr = pferrs(self.F0, self.F0_ERR, self.F1, self.F1_ERR)
+                setattr(self, "P0_ERR", perr)
+                setattr(self, "P1", pd)
+                setattr(self, "P1_ERR", pderr)
+            else:
+                if hasattr(self, "F1"):
+                    (
+                        p,
+                        pd,
+                    ) = p_to_f(self.F0, self.F1)
+                    setattr(self, "P0_ERR", self.F0_ERR / (self.F0 * self.F0))
+                    setattr(self, "P1", pd)
+
+        # convert epochs (including binary epochs) to GPS if possible
+        try:
+            from lalpulsar import TTMJDtoGPS
+
+            for epoch in [
+                "PEPOCH",
+                "POSEPOCH",
+                "DMEPOCH",
+                "T0",
+                "TASC",
+                "T0_2",
+                "T0_3",
+            ]:
+                if hasattr(self, epoch):
+                    setattr(
+                        self, epoch + "_ORIGINAL", self[epoch]
+                    )  # save original value
+                    setattr(self, epoch, TTMJDtoGPS(self[epoch]))
+
+                    if hasattr(
+                        self, epoch + "_ERR"
+                    ):  # convert errors from days to seconds
+                        setattr(
+                            self, epoch + "_ERR_ORIGINAL", self[epoch + "_ERR"]
+                        )  # save original value
+                        setattr(self, epoch + "_ERR", self[epoch + "_ERR"] * SECPERDAY)
+        except:
+            print(
+                "Could not convert epochs to GPS times. They are all still MJD values.",
+                file=sys.stderr,
+            )
+
+        # distance and parallax (distance: kpc -> metres, parallax: mas -> rads)
+        convfacs = {"DIST": KPC, "PX": 1e-3 * ARCSECTORAD}
+        for item in convfacs:
+            if hasattr(self, item):  # convert kpc to metres
+                setattr(self, item + "_ORIGINAL", self[item])  # save original value
+                setattr(self, item, self[item] * convfacs[item])
+
+                if hasattr(self, item + "_ERR"):
+                    setattr(
+                        self, item + "_ERR_ORIGINAL", self[item + "_ERR"]
+                    )  # save original value
+                    setattr(self, item + "_ERR", self[item + "_ERR"] * convfacs[item])
+
+        # binary parameters
+        # omega (angle of periastron) parameters (or others requiring conversion from degs to rads)
+        for om in ["OM", "OM_2", "OM_3", "KIN", "KOM"]:
+            if hasattr(self, om):  # convert OM from degs to rads
+                setattr(self, om, self[om] / RADTODEG)
+
+                if hasattr(self, om + "_ERR"):
+                    setattr(self, om + "_ERR", self[om + "_ERR"] / RADTODEG)
+
+        # period
+        for pb in ["PB", "PB_2", "PB_3"]:
+            if hasattr(self, pb):  # convert PB from days to seconds
+                setattr(self, pb + "_ORIGINAL", self[pb])  # save original value
+                setattr(self, pb, self[pb] * SECPERDAY)
+
+                if hasattr(self, pb + "_ERR"):
+                    setattr(
+                        self, pb + "_ERR_ORIGINAL", self[pb + "_ERR"]
+                    )  # save original value
+                    setattr(self, pb + "_ERR", self[pb + "_ERR"] * SECPERDAY)
+
+        # OMDOT
+        if hasattr(self, "OMDOT"):  # convert from deg/year to rad/sec
+            setattr(self, "OMDOT_ORIGINAL", self["OMDOT"])  # save original value
+            setattr(self, "OMDOT", self["OMDOT"] / (RADTODEG * 365.25 * SECPERDAY))
+
+            if hasattr(self, "OMDOT_ERR"):
+                setattr(
+                    self, "OMDOT_ERR_ORIGINAL", self["OMDOT_ERR"]
+                )  # save original value
+                setattr(
+                    self,
+                    "OMDOT_ERR",
+                    self["OMDOT_ERR"] / (RADTODEG * 365.25 * SECPERDAY),
+                )
+
+        if hasattr(self, "EPS1") and hasattr(self, "EPS2"):
+            ecc = math.sqrt(self.EPS1 * self.EPS1 + self.EPS2 * self.EPS2)
+            omega = math.atan2(self.EPS1, self.EPS2)
+            setattr(self, "E", ecc)
+            setattr(self, "OM", omega)  # omega in rads
+            setattr(self, "T0", self.TASC + self.PB * omega / TWOPI)
+        if (
+            hasattr(self, "PB")
+            and hasattr(self, "A1")
+            and not (hasattr(self, "E") or hasattr(self, "ECC"))
+        ):
+            setattr(self, "E", 0.0)
+        if (
+            hasattr(self, "T0")
+            and not hasattr(self, "TASC")
+            and hasattr(self, "OM")
+            and hasattr(self, "PB")
+        ):
+            setattr(self, "TASC", self.T0 - self.PB * self.OM / TWOPI)
+
+        # binary unit conversion for small numbers (TEMPO2 checks if these are > 1e-7 and if so then the units are in 1e-12) - errors are not converted
+        for binu in ["XDOT", "PBDOT", "EDOT", "EPS1DOT", "EPS2DOT", "XPBDOT"]:
+            if hasattr(self, binu):
+                setattr(self, binu + "_ORIGINAL", self[binu])  # save original value
+                if np.abs(self[binu]) > 1e-7:
+                    setattr(self, binu, self[binu] * 1.0e-12)
+
+                    # check value is not extremely large due to ATNF catalogue error
+                    if self[binu] > 10000.0:  # set to zero
+                        setattr(self, binu, 0.0)
+
+        # masses
+        for mass in ["M2", "MTOT"]:
+            if hasattr(self, mass):  # convert solar masses to kg
+                setattr(self, mass + "_ORIGINAL", self[mass])  # save original value
+                setattr(self, mass, self[mass] * MSUN)
+
+                if hasattr(self, mass + "_ERR"):
+                    setattr(
+                        self, mass + "_ERR_ORIGINAL", self[mass + "_ERR"]
+                    )  # save original value
+                    setattr(self, mass + "_ERR", self[mass + "_ERR"] * MSUN)
+
+        # D_AOP
+        if hasattr(self, "D_AOP"):  # convert from inverse arcsec to inverse radians
+            setattr(self, "D_AOP_ORIGINAL", self["D_AOP"])  # save original value
+            setattr(self, "D_AOP", self["D_AOP"] * RADTODEG * 3600.0)
+
+        pf.close()
+
+    def __getitem__(self, key):
+        try:
+            par = getattr(self, key)
+        except:
+            par = None
+
+        return par
+
+    def __str__(self):
+        out = ""
+        for k, v in self.__dict__.items():
+            if k[:2] != "__":
+                if isinstance(self.__dict__[k], string_type):
+                    out += "%10s = '%s'\n" % (k, v)
+                else:
+                    out += "%10s = %-20.15g\n" % (k, v)
+
+        return out
+
+
+# class to read in a nested sampling prior file
+class psr_prior:
+    def __init__(self, priorfilenm):
+        self.FILE = priorfilenm
+        pf = open(priorfilenm)
+        for line in pf.readlines():
+            splitline = line.split()
+
+            # get all upper case version in case lower case in par file
+            key = splitline[0].upper()
+
+            if key in str_keys:
+                # everything in a prior files should be numeric
+                setattr(self, key, [float(splitline[2]), float(splitline[3])])
+            elif key in float_keys:
+                setattr(self, key, [float(splitline[2]), float(splitline[3])])
+
+        # get sky positions in rads as strings 'dd/hh:mm:ss.s'
+        if hasattr(self, "RA"):
+            hl, ml, sl = rad_to_hms(self.RA[0])
+            rastrl = coord_to_string(hl, ml, sl)
+            hu, mu, su = rad_to_hms(self.RA[1])
+            rastru = coord_to_string(hu, mu, su)
+            setattr(self, "RA_STR", [rastrl, rastru])
+
+        if hasattr(self, "DEC"):
+            dl, ml, sl = rad_to_dms(self.DEC[0])
+            decstrl = coord_to_string(dl, ml, sl)
+            du, mu, su = rad_to_dms(self.DEC[1])
+            decstru = coord_to_string(du, mu, su)
+            setattr(self, "DEC_STR", [decstrl, decstru])
+
+        pf.close()
+
+    def __getitem__(self, key):
+        try:
+            atr = getattr(self, key)
+        except:
+            atr = None
+
+        return atr
+
+    def __str__(self):
+        out = ""
+        for k, v in self.__dict__.items():
+            if k[:2] != "__":
+                out += "%10s = %-20.15g, %-20.15g\n" % (k, float(v[0]), float(v[1]))
+
+        return out
+
+
+# Function to return a pulsar's strain spin-down limit given its spin frequency
+# (Hz), spin-down (Hz/s) and distance (kpc). The canonical value of moment of
+# inertia of 1e38 kg m^2 is used
+def spin_down_limit(freq, fdot, dist):
+    hsd = np.sqrt((5.0 / 2.0) * (G / C**3) * I38 * np.fabs(fdot) / freq) / (
+        dist * KPC
+    )
+
+    return hsd
+
+
+# Function to convert a pulsar stain into ellipticity assuming the canonical
+# moment of inertia
+def h0_to_ellipticity(h0, freq, dist):
+    ell = h0 * C**4.0 * dist * KPC / (16.0 * np.pi**2 * G * I38 * freq**2)
+
+    return ell
+
+
+# Function to convert a pulsar strain into a mass quadrupole moment
+def h0_to_quadrupole(h0, freq, dist):
+    q22 = (
+        np.sqrt(15.0 / (8.0 * np.pi))
+        * h0
+        * C**4.0
+        * dist
+        * KPC
+        / (16.0 * np.pi**2 * G * freq**2)
+    )
+
+    return q22
+
+
+# Function to conver quadrupole moment to strain
+def quadrupole_to_h0(q22, freq, dist):
+    h0 = (
+        q22
+        * np.sqrt((8.0 * np.pi) / 15.0)
+        * 16.0
+        * np.pi**2
+        * G
+        * freq**2
+        / (C**4.0 * dist * KPC)
+    )
+
+    return h0
+
+
+# function to convert the psi' and phi0' coordinates used in nested sampling
+# into the standard psi and phi0 coordinates (using vectors of those parameters
+def phipsiconvert(phipchain, psipchain):
+    chainlen = len(phipchain)
+
+    phichain = []
+    psichain = []
+
+    theta = math.atan2(1, 2)
+    ct = math.cos(theta)
+    st = math.sin(theta)
+
+    for i in range(0, chainlen):
+        phi0 = (1 / (2 * st)) * phipchain[i] - (1 / (2 * st)) * psipchain[i]
+        psi = (1 / (2 * ct)) * phipchain[i] + (1 / (2 * ct)) * psipchain[i]
+
+        # put psi between +/-pi/4
+        if math.fabs(psi) > math.pi / 4.0:
+            # shift phi0 by pi
+            phi0 = phi0 + math.pi
+
+            # wrap around psi
+            if psi > math.pi / 4.0:
+                psi = -(math.pi / 4.0) + math.fmod(psi + (math.pi / 4.0), math.pi / 2.0)
+            else:
+                psi = (math.pi / 4.0) - math.fmod((math.pi / 4.0) - psi, math.pi / 2.0)
+
+        # get phi0 into 0 -> 2pi range
+        if phi0 > 2.0 * math.pi:
+            phi0 = math.fmod(phi0, 2.0 * math.pi)
+        else:
+            phi0 = 2.0 * math.pi - math.fmod(2.0 * math.pi - phi0, 2.0 * math.pi)
+
+        phichain.append(phi0)
+        psichain.append(psi)
+
+    return phichain, psichain
+
+
+# function to create histogram plot of the 1D posterior (potentially for
+# multiple IFOs) for a parameter (param). If an upper limit is given then
+# that will be output
+def plot_posterior_hist(
+    poslist,
+    param,
+    ifos,
+    parambounds=[float("-inf"), float("inf")],
+    nbins=50,
+    upperlimit=0,
+    overplot=False,
+    parfile=None,
+    mplparams=False,
+):
+    import matplotlib
+    from matplotlib import pyplot as plt
+    from lalpulsar.pulsarhtmlutils import paramlatexdict
+
+    # create list of figures
+    myfigs = []
+
+    # create a list of upper limits
+    ulvals = []
+
+    # set some matplotlib defaults for hist
+    if not mplparams:
+        mplparams = {
+            "backend": "Agg",
+            "text.usetex": True,  # use LaTeX for all text
+            "axes.linewidth": 0.5,  # set axes linewidths to 0.5
+            "axes.grid": True,  # add a grid
+            "grid.linewidth": 0.5,
+            "font.family": "serif",
+            "font.size": 12,
+        }
+
+    matplotlib.rcParams.update(mplparams)
+
+    # ifos line colour specs
+    coldict = {"H1": "r", "H2": "c", "L1": "g", "V1": "b", "G1": "m", "Joint": "k"}
+
+    # param name for axis label
+    try:
+        paraxis = paramlatexdict[param.upper()]
+    except:
+        paraxis = param
+
+    ymax = []
+
+    # if a par file object is given expect that we have an injection file
+    # containing the injected value to overplot on the histgram
+    parval = None
+    if parfile:
+        parval = parfile[param.upper()]
+
+    if ifos == None:
+        # default to just output colour for H1
+        ifos = ["H1"]
+
+    # loop over ifos
+    for idx, ifo in enumerate(ifos):
+        # check whether to plot all figures on top of each other
+        if overplot and idx == 0:
+            myfig = plt.figure(figsize=(4, 4), dpi=200)
+            plt.hold(True)
+        elif not overplot:
+            myfig = plt.figure(figsize=(4, 4), dpi=200)
+
+        pos = poslist[idx]
+
+        pos_samps = pos[param].samples
+
+        # get a normalised histogram for each
+        n, bins = hist_norm_bounds(
+            pos_samps, int(nbins), parambounds[0], parambounds[1]
+        )
+
+        # plot histogram
+        plt.step(bins, n, color=coldict[ifo])
+
+        if "h0" not in param:
+            plt.xlim(parambounds[0], parambounds[1])
+
+        plt.xlabel(r"" + paraxis, fontsize=14, fontweight=100)
+        plt.ylabel(r"Probability Density", fontsize=14, fontweight=100)
+        myfig.subplots_adjust(left=0.18, bottom=0.15)  # adjust size
+
+        if not overplot:
+            plt.ylim(0, n.max() + 0.1 * n.max())
+            # plt.legend(ifo)
+            # set background colour of axes
+            ax = plt.gca()
+            ax.set_axis_bgcolor("#F2F1F0")
+            myfigs.append(myfig)
+        else:
+            ymax.append(n.max() + 0.1 * n.max())
+
+        # if upper limit is needed then integrate posterior using trapezium rule
+        if upperlimit != 0:
+            ct = cumulative_trapezoid(n, bins)
+
+            # prepend a zero to ct
+            ct = np.insert(ct, 0, 0)
+
+            # use linear interpolation to find the value at 'upper limit'
+            ctu, ui = np.unique(ct, return_index=True)
+            intf = interp1d(ctu, bins[ui], kind="linear")
+            ulvals.append(intf(float(upperlimit)))
+
+    # plot parameter values
+    if parval:
+        if not overplot:
+            plt.hold(True)
+            plt.axvline(parval, color="k", ls="--", linewidth=1.5)
+        else:
+            plt.axvline(parval, color="k", ls="--", linewidth=1.5)
+
+    if overplot:
+        plt.ylim(0, max(ymax))
+        # plt.legend(ifos)
+        ax = plt.gca()
+        ax.set_axis_bgcolor("#F2F1F0")
+        plt.hold(False)
+        myfigs.append(myfig)
+
+    return myfigs, ulvals
+
+
+# function to return an upper limit from a posteriors: pos is an array of posteriors samples for a
+# particular parameter
+def upper_limit(
+    pos, upperlimit=0.95, parambounds=[float("-inf"), float("inf")], nbins=50
+):
+    ulval = 0
+
+    # get a normalised histogram of posterior samples
+    n, bins = hist_norm_bounds(pos, int(nbins), parambounds[0], parambounds[1])
+
+    # if upper limit is needed then integrate posterior using trapezium rule
+    if upperlimit != 0:
+        ct = cumulative_trapezoid(n, bins)
+
+        # prepend a zero to ct
+        ct = np.insert(ct, 0, 0)
+
+        # use linear interpolation to find the value at 'upper limit'
+        ctu, ui = np.unique(ct, return_index=True)
+        intf = interp1d(ctu, bins[ui], kind="linear")
+        ulval = intf(float(upperlimit))
+
+    return ulval
+
+
+def upper_limit_greedy(pos, upperlimit=0.95, nbins=100):
+    n, binedges = np.histogram(pos, bins=nbins)
+    dbins = binedges[1] - binedges[0]  # width of a histogram bin
+
+    frac = 0.0
+    j = 0
+    for nv in n:
+        prevfrac = frac
+        frac += float(nv) / len(pos)
+        j += 1
+        if frac > upperlimit:
+            break
+
+    # linearly interpolate to get upper limit
+    ul = binedges[j - 1] + (upperlimit - prevfrac) * (dbins / (frac - prevfrac))
+
+    return ul
+
+
+# function to plot a posterior chain (be it MCMC chains or nested samples)
+# the input should be a list of posteriors for each IFO, and the parameter
+# required, the list of IFO. grr is a list of dictionaries giving
+# the Gelman-Rubins statistics for the given parameter for each IFO.
+# If withhist is set then it will also output a histgram, with withhist number
+# of bins
+def plot_posterior_chain(poslist, param, ifos, grr=None, withhist=0, mplparams=False):
+    import matplotlib
+    from matplotlib import pyplot as plt
+    from lalpulsar.pulsarhtmlutils import paramlatexdict
+
+    try:
+        from matplotlib import gridspec
+    except:
+        return None
+
+    if not mplparams:
+        mplparams = {
+            "backend": "Agg",
+            "text.usetex": True,  # use LaTeX for all text
+            "axes.linewidth": 0.5,  # set axes linewidths to 0.5
+            "axes.grid": True,  # add a grid
+            "grid.linewidth": 0.5,
+            "font.family": "sans-serif",
+            "font.sans-serif": "Avant Garde, Helvetica, Computer Modern Sans serif",
+            "font.size": 15,
+        }
+
+    matplotlib.rcParams.update(mplparams)
+
+    coldict = {"H1": "r", "H2": "c", "L1": "g", "V1": "b", "G1": "m", "Joint": "k"}
+
+    # param name for axis label
+    try:
+        if param == "iota":
+            p = "cosiota"
+        else:
+            p = param
+
+        paryaxis = paramlatexdict[p.upper()]
+    except:
+        paryaxis = param
+
+    if grr:
+        legendvals = []
+
+    maxiter = 0
+    maxn = 0
+    minsamp = float("inf")
+    maxsamp = -float("inf")
+
+    for idx, ifo in enumerate(ifos):
+        if idx == 0:
+            myfig = plt.figure(figsize=(12, 4), dpi=200)
+            myfig.subplots_adjust(bottom=0.15)
+
+            if withhist:
+                gs = gridspec.GridSpec(1, 4, wspace=0)
+                ax1 = plt.subplot(gs[:-1])
+                ax2 = plt.subplot(gs[-1])
+
+        pos = list(poslist)[idx]
+
+        # check for cosiota
+        if "iota" == param:
+            pos_samps = np.cos(pos["iota"].samples)
+        else:
+            pos_samps = pos[param].samples
+
+        if np.min(pos_samps) < minsamp:
+            minsamp = np.min(pos_samps)
+        if np.max(pos_samps) > maxsamp:
+            maxsamp = np.max(pos_samps)
+
+        if withhist:
+            ax1.plot(pos_samps, ".", color=coldict[ifo], markersize=1)
+
+            n, binedges = np.histogram(pos_samps, withhist, density=True)
+            n = np.append(n, 0)
+            ax2.step(n, binedges, color=coldict[ifo])
+
+            if np.max(n) > maxn:
+                maxn = np.max(n)
+        else:
+            plt.plot(pos_samps, ".", color=coldict[ifo], markersize=1)
+
+        if grr:
+            try:
+                legendvals.append(r"$R = %.2f$" % grr[idx][param])
+            except:
+                legendvals = []
+        else:
+            legendvals = None
+
+        if len(pos_samps) > maxiter:
+            maxiter = len(pos_samps)
+
+    if not withhist:
+        ax1 = plt.gca()
+
+    bounds = [minsamp, maxsamp]
+
+    ax1.set_ylabel(r"" + paryaxis, fontsize=16, fontweight=100)
+    ax1.set_xlabel(r"Iterations", fontsize=16, fontweight=100)
+
+    ax1.set_xlim(0, maxiter)
+    ax1.set_ylim(bounds[0], bounds[1])
+
+    if withhist:
+        ax2.set_ylim(bounds[0], bounds[1])
+        ax2.set_xlim(0, maxn + 0.1 * maxn)
+        ax2.set_yticklabels([])
+        ax2.set_axis_bgcolor("#F2F1F0")
+
+    # add gelman-rubins stat data
+    if legendvals:
+        ax1.legend(legendvals, title="Gelman-Rubins test")
+
+    return myfig
+
+
+# function to read in and plot a 2D histogram from a binary file, where the files
+# structure is of the form:
+#   a header of six doubles with:
+#     - minimum of N-dim
+#     - the step size in N-dim
+#     - N - number of N-dim values
+#     - minimum of M-dim
+#     - the step size in M-dim
+#     - M - number of M-dim values
+#   followed by an NxM double array of values.
+# The information returned are two lists of the x and y-axis bin centres, along
+# with a numpy array containing the histogram values.
+def read_hist_from_file(histfile):
+    # read in 2D binary file
+    try:
+        fp = open(histfile, "rb")
+    except:
+        print("Could not open prior file %s" % histfile, file=sys.stderr)
+        return None, None, None
+
+    try:
+        pd = fp.read()  # read in all the data
+    except:
+        print("Could not read in data from prior file %s" % histfile, file=sys.stderr)
+        return None, None, None
+
+    fp.close()
+
+    # read in the header (6 doubles)
+    # try:
+    header = struct.unpack("d" * 6, pd[: 6 * 8])
+    # except:
+    #  print >> sys.stderr, "Could not read in header data from prior file %s" % histfile
+    #  return None, None, None
+
+    # read in histogram grid (NxM doubles)
+    # try:
+    grid = struct.unpack("d" * int(header[2]) * int(header[5]), pd[6 * 8 :])
+    # except:
+    #  print >> sys.stderr, "Could not read in header data from prior file %s" % histfile
+    #  return None, None, None
+
+    header = list(header)
+
+    # convert grid into numpy array
+    g = list(grid)  # convert to list
+    histarr = np.array([g[: int(header[5])]], ndmin=2)
+    for i in range(int(header[2]) - 1):
+        histarr = np.append(
+            histarr, [g[(i + 1) * int(header[5]) : (i + 2) * int(header[5])]], axis=0
+        )
+
+    xbins = np.linspace(
+        header[0], header[0] + header[1] * (header[2] - 1), int(header[2])
+    )
+    ybins = np.linspace(
+        header[3], header[3] + header[4] * (header[5] - 1), int(header[5])
+    )
+
+    return xbins, ybins, histarr
+
+
+# Function to plot a 2D histogram of from a binary file containing it.
+# Also supply the label names for the n-dimension (x-axis) and m-dimension
+# (y-axis). If margpars is true marginalised plots of both dimensions will
+# also be returned.
+def plot_2Dhist_from_file(
+    histfile, ndimlabel, mdimlabel, margpars=True, mplparams=False
+):
+    import matplotlib
+    from matplotlib import pyplot as plt
+    from lalpulsar.pulsarhtmlutils import paramlatexdict
+
+    # read in 2D h0 vs cos(iota) binary prior file
+    xbins, ybins, histarr = read_hist_from_file(histfile)
+
+    if not xbins.any():
+        print("Could not read binary histogram file", file=sys.stderr)
+        return None
+
+    figs = []
+
+    # set some matplotlib defaults for amplitude spectral density
+    if not mplparams:
+        mplparams = {
+            "backend": "Agg",
+            "text.usetex": True,  # use LaTeX for all text
+            "axes.linewidth": 0.5,  # set axes linewidths to 0.5
+            "axes.grid": True,  # add a grid
+            "grid.linewidth": 0.5,
+            "font.family": "serif",
+            "font.size": 12,
+        }
+
+    matplotlib.rcParams.update(mplparams)
+
+    fig = plt.figure(figsize=(4, 4), dpi=200)
+
+    # param name for axis label
+    try:
+        parxaxis = paramlatexdict[ndimlabel.upper()]
+    except:
+        parxaxis = ndimlabel
+
+    try:
+        paryaxis = paramlatexdict[mdimlabel.upper()]
+    except:
+        paryaxis = mdimlabel
+
+    plt.xlabel(r"" + parxaxis, fontsize=14, fontweight=100)
+    plt.ylabel(r"" + paryaxis, fontsize=14, fontweight=100, rotation=270)
+
+    dx = xbins[1] - xbins[0]
+    dy = ybins[1] - ybins[0]
+
+    extent = [
+        xbins[0] - dx / 2.0,
+        xbins[-1] + dx / 2.0,
+        ybins[-1] + dy / 2.0,
+        ybins[0] - dy / 2.0,
+    ]
+
+    plt.imshow(
+        np.transpose(histarr),
+        aspect="auto",
+        extent=extent,
+        interpolation="bicubic",
+        cmap="gray_r",
+    )
+
+    fig.subplots_adjust(left=0.18, bottom=0.15)  # adjust size
+    fax = (fig.get_axes())[0].axis()
+
+    figs.append(fig)
+
+    if margpars:
+        # marginalise over y-axes and produce plots
+        xmarg = []
+        for i in range(len(xbins)):
+            xmarg.append(trapezoid(histarr[:][i], x=ybins))
+
+        # normalise
+        xarea = trapezoid(xmarg, x=xbins)
+        xmarg = map(lambda x: x / xarea, xmarg)
+
+        ymarg = []
+        for i in range(len(ybins)):
+            ymarg.append(trapezoid(np.transpose(histarr)[:][i], x=xbins))
+
+        # normalise
+        yarea = trapezoid(ymarg, x=ybins)
+        ymarg = map(lambda x: x / yarea, ymarg)
+
+        # plot x histogram
+        figx = plt.figure(figsize=(4, 4), dpi=200)
+        plt.step(xbins, xmarg, color="k")
+        plt.ylim(0, max(xmarg) + 0.1 * max(xmarg))
+        plt.xlim(fax[0], fax[1])
+        plt.xlabel(r"" + parxaxis, fontsize=14, fontweight=100)
+        plt.ylabel(r"Probability Density", fontsize=14, fontweight=100)
+        figx.subplots_adjust(left=0.18, bottom=0.15)  # adjust size
+        ax = plt.gca()
+        ax.set_axis_bgcolor("#F2F1F0")
+
+        # plot y histogram
+        figy = plt.figure(figsize=(4, 4), dpi=200)
+        plt.step(ybins, ymarg, color="k")
+        plt.ylim(0, max(ymarg) + 0.1 * max(ymarg))
+        plt.xlim(fax[3], fax[2])
+        plt.xlabel(r"" + paryaxis, fontsize=14, fontweight=100)
+        plt.ylabel(r"Probability Density", fontsize=14, fontweight=100)
+        figy.subplots_adjust(left=0.18, bottom=0.15)  # adjust size
+        ax = plt.gca()
+        ax.set_axis_bgcolor("#F2F1F0")
+
+        figs.append(figx)
+        figs.append(figy)
+
+    return figs
+
+
+# using a binary file containing a histogram oh h0 vs cos(iota) calculate the
+# upper limit on h0
+def h0ul_from_prior_file(priorfile, ulval=0.95):
+    # read in 2D h0 vs cos(iota) binary prior file
+    h0bins, cibins, histarr = read_hist_from_file(priorfile)
+
+    if not h0bins.any():
+        print("Could not read binary histogram file", file=sys.stderr)
+        return None
+
+    # marginalise over cos(iota)
+    h0marg = []
+    for i in range(len(h0bins)):
+        h0marg.append(trapezoid(histarr[:][i], x=cibins))
+
+    # normalise h0 posterior
+    h0bins = h0bins - (h0bins[1] - h0bins[0]) / 2
+    h0area = trapezoid(h0marg, x=h0bins)
+    h0margnorm = map(lambda x: x / h0area, h0marg)
+
+    # get cumulative probability
+    ct = cumulative_trapezoid(h0margnorm, h0bins)
+
+    # prepend a zero to ct
+    ct = np.insert(ct, 0, 0)
+
+    # use spline interpolation to find the value at 'upper limit'
+    ctu, ui = np.unique(ct, return_index=True)
+    intf = interp1d(ctu, h0bins[ui], kind="linear")
+    return intf(float(ulval))
+
+
+# function to create a histogram plot of the 2D posterior
+def plot_posterior_hist2D(
+    poslist,
+    params,
+    ifos,
+    bounds=None,
+    nbins=[50, 50],
+    parfile=None,
+    overplot=False,
+    mplparams=False,
+):
+    import matplotlib
+    from matplotlib import pyplot as plt
+    from lalpulsar.pulsarhtmlutils import paramlatexdict
+
+    if len(params) != 2:
+        print("Require 2 parameters", file=sys.stderr)
+        sys.exit(1)
+
+    # set some matplotlib defaults for amplitude spectral density
+    if not mplparams:
+        mplparams = {
+            "backend": "Agg",
+            "text.usetex": True,  # use LaTeX for all text
+            "axes.linewidth": 0.5,  # set axes linewidths to 0.5
+            "axes.grid": True,  # add a grid
+            "grid.linewidth": 0.5,
+            "font.family": "serif",
+            "font.size": 12,
+        }
+
+    matplotlib.rcParams.update(mplparams)
+
+    if overplot:
+        coldict = {
+            "H1": "Reds",
+            "H2": "GnBu",
+            "L1": "Greens",
+            "V1": "Blues",
+            "G1": "BuPu",
+            "Joint": "Greys",
+        }
+
+    myfigs = []
+
+    # param name for axis label
+    try:
+        parxaxis = paramlatexdict[params[0].upper()]
+    except:
+        parxaxis = params[0]
+
+    try:
+        paryaxis = paramlatexdict[params[1].upper()]
+    except:
+        paryaxis = params[1]
+
+    parval1 = None
+    parval2 = None
+
+    if parfile:
+        parval1 = parfile[params[0].upper()]
+        parval2 = parfile[params[1].upper()]
+
+    if ifos == None:
+        ifos = ["H1"]
+
+    for idx, ifo in enumerate(ifos):
+        if overplot:
+            if idx == 0:
+                # if overplotting just have one figure
+                myfig = plt.figure(figsize=(4, 4), dpi=200)
+
+            if len(ifos) == 1:
+                alpha = 1.0
+                cmap = plt.cm.get_cmap("Greys")
+            else:
+                alpha = 0.5  # set transparency
+                cmap = plt.cm.get_cmap(coldict[ifo])  # set colormap
+                # cmap.set_bad(alpha=0.) # set 'bad' masked values to be transparent
+        else:
+            myfig = plt.figure(figsize=(4, 4), dpi=200)
+            alpha = 1.0  # no transparency
+            cmap = plt.cm.get_cmap("Greys")
+
+        posterior = poslist[idx]
+
+        a = np.squeeze(posterior[params[0]].samples)
+        b = np.squeeze(posterior[params[1]].samples)
+
+        # Create 2D bin array
+        par1pos_min = a.min()
+        par2pos_min = b.min()
+
+        par1pos_max = a.max()
+        par2pos_max = b.max()
+
+        plt.xlabel(r"" + parxaxis, fontsize=14, fontweight=100)
+        plt.ylabel(r"" + paryaxis, fontsize=14, fontweight=100, rotation=270)
+
+        H, xedges, yedges = np.histogram2d(a, b, nbins, normed=True)
+
+        # if overplot and len(ifos) > 1:
+        #  # mask values that are zero, so that they are
+        #  Hm = np.ma.masked_where(np.transpose(H) == 0, np.transpose(H))
+        # else:
+        #  Hm = np.transpose(H)
+        Hm = np.transpose(H)
+
+        extent = [xedges[0], xedges[-1], yedges[-1], yedges[0]]
+        plt.imshow(
+            Hm,
+            aspect="auto",
+            extent=extent,
+            interpolation="bilinear",
+            cmap=cmap,
+            alpha=alpha,
+        )
+        # plt.colorbar()
+
+        if bounds:
+            plt.xlim(bounds[0][0], bounds[0][1])
+            plt.ylim(bounds[1][0], bounds[1][1])
+
+        # plot injection values if given
+        if parval1 and parval2:
+            if overplot and idx == len(ifos) - 1:
+                # only plot after final posterior has been plotted
+                plt.hold(True)
+                plt.plot(parval1, parval2, "rx", markersize=8, mew=2)
+            else:
+                plt.hold(True)
+                plt.plot(parval1, parval2, "rx", markersize=8, mew=2)
+
+        if overplot:
+            plt.hold(True)
+        if not overplot:
+            myfig.subplots_adjust(left=0.18, bottom=0.15)  # adjust size
+            myfigs.append(myfig)
+
+    if overplot:
+        myfig.subplots_adjust(left=0.18, bottom=0.15)  # adjust size
+        myfigs.append(myfig)
+
+    return myfigs
+
+
+# a function that creates and normalises a histograms of samples, with nbins
+# between an upper and lower bound a upper and lower bound. The values at the
+# bin points (with length nbins+2) will be returned as numpy arrays
+def hist_norm_bounds(samples, nbins, low=float("-inf"), high=float("inf")):
+    # get histogram
+    n, binedges = np.histogram(samples, nbins)
+
+    # get bin width
+    binwidth = binedges[1] - binedges[0]
+
+    # create bin centres
+    bincentres = np.array([])
+    for i in range(0, len(binedges) - 1):
+        bincentres = np.append(bincentres, binedges[i] + binwidth / 2)
+
+    # if histogram points are not close to boundaries (i.e. within a bin of the
+    # boundaries) then add zeros to histrogram edges
+    if bincentres[0] - binwidth > low:
+        # prepend a zero to n
+        n = np.insert(n, 0, 0)
+
+        # prepend a new bin centre at bincentres[0] - binwidth
+        bincentres = np.insert(bincentres, 0, bincentres[0] - binwidth)
+    else:
+        # we're  closer to the boundary edge than the bin width then, so set a new
+        # bin on the boundary with a value linearly extrapolated from the
+        # gradiant of the adjacent points
+        dx = bincentres[0] - low
+
+        # prepend low value to bins
+        bincentres = np.insert(bincentres, 0, low)
+
+        dn = n[1] - n[0]
+
+        nbound = n[0] - (dn / binwidth) * dx
+
+        n = n.astype(float)  # convert to floats
+
+        # prepend to n
+        n = np.insert(n, 0, nbound)
+
+    # now the other end!
+    if bincentres[-1] + binwidth < high:
+        # append a zero to n
+        n = np.append(n, 0)
+
+        # append a new bin centre at bincentres[end] + binwidth
+        bincentres = np.append(bincentres, bincentres[-1] + binwidth)
+    else:
+        dx = high - bincentres[-1]
+
+        # prepend low value to bins
+        bincentres = np.append(bincentres, high)
+
+        dn = n[-1] - n[-2]
+
+        nbound = n[-1] + (dn / binwidth) * dx
+
+        n = n.astype(float)  # convert to floats
+
+        # prepend to n
+        n = np.append(n, nbound)
+
+    # now calculate area and normalise
+    area = trapezoid(n, x=bincentres)
+
+    ns = np.array([])
+    for i in range(0, len(bincentres)):
+        ns = np.append(ns, float(n[i]) / area)
+
+    return ns, bincentres
+
+
+# create a Tukey window of length N
+def tukey_window(N, alpha=0.5):
+    # if alpha >= 1 just return a Hanning window
+    if alpha >= 1:
+        return np.hanning(N)
+
+    # get x values at which to calculate window
+    x = np.linspace(0, 1, N)
+
+    # initial square window
+    win = np.ones(x.shape)
+
+    # get the left-hand side of the window  0 <= x < alpha/2
+    lhs = x < alpha / 2
+    win[lhs] = 0.5 * (1 + np.cos(2 * np.pi / alpha * (x[lhs] - alpha / 2)))
+
+    # get right hand side condition 1 - alpha / 2 <= x <= 1
+    rhs = x >= (1 - alpha / 2)
+    win[rhs] = 0.5 * (1 + np.cos(2 * np.pi / alpha * (x[rhs] - 1 + alpha / 2)))
+
+    return win
+
+
+# create a function for plotting the absolute value of Bk data (read in from
+# data files) and an averaged 1 day "two-sided" amplitude spectral density
+# spectrogram for each IFO. Bkdata should be a dictionary contains the files
+# keyed to the IFO
+def plot_Bks_ASDs(
+    Bkdata,
+    delt=86400,
+    plotpsds=True,
+    plotfscan=False,
+    removeoutlier=None,
+    mplparams=False,
+):
+    import matplotlib
+    from matplotlib.mlab import specgram
+    from matplotlib import colors
+    from matplotlib import pyplot as plt
+
+    # create list of figures
+    Bkfigs = []
+    psdfigs = []
+    fscanfigs = []
+    asdlist = []
+    sampledt = []
+
+    # set some matplotlib defaults for amplitude spectral density
+    if not mplparams:
+        mplparams = {
+            "backend": "Agg",
+            "text.usetex": True,  # use LaTeX for all text
+            "axes.linewidth": 0.5,  # set axes linewidths to 0.5
+            "axes.grid": True,  # add a grid
+            "grid.linewidth": 0.5,
+            "font.family": "sans-serif",
+            "font.sans-serif": "Avant Garde, Helvetica, Computer Modern Sans serif",
+            "font.size": 15,
+        }
+
+    matplotlib.rcParams.update(mplparams)
+    matplotlib.rcParams["text.latex.preamble"] = r"\usepackage{xfrac}"
+
+    # ifos line colour specs
+    coldict = {"H1": "r", "H2": "c", "L1": "g", "V1": "b", "G1": "m"}
+    colmapdic = {
+        "H1": "Reds",
+        "H2": "PuBu",
+        "L1": "Greens",
+        "V1": "Blues",
+        "G1": "PuRd",
+    }
+
+    # there should be data for each ifo
+    for ifo in Bkdata:
+        # get data for given ifo
+        try:
+            Bk = np.loadtxt(Bkdata[ifo], comments=["#", "%"])
+        except:
+            print("Could not open file %s" % Bkdata[ifo], file=sys.stderr)
+            sys.exit(-1)
+
+        # sort the array in time
+        Bk = Bk[Bk[:, 0].argsort()]
+
+        # make sure times are unique
+        uargs = np.unique(Bk[:, 0], return_index=True)[1]
+        Bk = Bk[uargs, :]
+
+        # should be three lines in file
+        gpstime = []
+
+        # remove outliers at Xsigma by working out sigma from the peak of the
+        # distribution of the log absolute value
+        if removeoutlier:
+            n, binedges = np.histogram(
+                np.log(np.fabs(np.concatenate((Bk[:, 1], Bk[:, 2])))), 50
+            )
+            j = n.argmax(0)
+
+            # standard devaition estimate
+            stdest = math.exp((binedges[j] + binedges[j + 1]) / 2)
+
+            # get values within +/-8 sigma
+            # test real parts
+            vals = np.where(np.fabs(Bk[:, 1]) < removeoutlier * stdest)
+            Bknew = Bk[vals, :][-1]
+            # test imag parts
+            vals = np.where(np.fabs(Bknew[:, 2]) < removeoutlier * stdest)
+            Bk = Bknew[vals, :][-1]
+
+        gpstime = Bk[:, 0]
+
+        # minimum time step between points (should generally be 60 seconds)
+        mindt = min(np.diff(gpstime))
+        sampledt.append(mindt)
+
+        Bkabs = np.sqrt(Bk[:, 1] ** 2 + Bk[:, 2] ** 2)
+
+        # plot the time series of the data
+        Bkfig = plt.figure(figsize=(11, 3.5), dpi=200)
+        Bkfig.subplots_adjust(bottom=0.15, left=0.09, right=0.94)
+
+        tms = list(map(lambda x: x - gpstime[0], gpstime))
+
+        plt.plot(tms, Bkabs, ".", color=coldict[ifo], markersize=1)
+        plt.xlabel(r"GPS - %d" % int(gpstime[0]), fontsize=14, fontweight=100)
+        plt.ylabel(r"$|B_k|$", fontsize=14, fontweight=100)
+        # plt.title(r'$B_k$s for ' + ifo.upper(), fontsize=14)
+        plt.xlim(tms[0], tms[-1])
+
+        Bkfigs.append(Bkfig)
+
+        if plotpsds or plotfscan:
+            # create PSD by splitting data into days, padding with zeros to give a
+            # sample a second, getting the PSD for each day and combining them
+            totlen = gpstime[-1] - gpstime[0]  # total data length
+
+            # check mindt is an integer and greater than 1
+            if math.fmod(mindt, 1) != 0.0 or mindt < 1:
+                print(
+                    "Error... time steps between data points must be integers",
+                    file=sys.stderr,
+                )
+                sys.exit(-1)
+
+            count = 0
+
+            # zero pad the data and bin each point in the nearest bin
+            datazeropad = np.zeros(int(math.ceil(totlen / mindt)) + 1, dtype=complex)
+
+            idx = list(map(lambda x: int(math.floor((x / mindt) + 0.5)), tms))
+            for i in range(0, len(idx)):
+                datazeropad[idx[i]] = complex(Bk[i, 1], Bk[i, 2])
+
+            win = tukey_window(math.floor(delt / mindt), alpha=0.1)
+
+            Fs = 1.0 / mindt  # sample rate in Hz
+
+            fscan, freqs, t = specgram(
+                datazeropad,
+                NFFT=int(math.floor(delt / mindt)),
+                Fs=Fs,
+                window=win,
+                noverlap=int(math.floor(delt / (2.0 * mindt))),
+            )
+
+            if plotpsds:
+                fshape = fscan.shape
+
+                totalasd = np.zeros(fshape[0])
+
+                for i in range(0, fshape[0]):
+                    scanasd = np.sqrt(fscan[i, :])
+                    nonzasd = np.nonzero(scanasd)
+                    scanasd = scanasd[nonzasd]
+
+                    # median amplitude spectral density
+                    # totalasd[i] = hmean(scanasd)
+                    totalasd[i] = np.median(scanasd)
+
+                # average amplitude spectral density
+                asdlist.append(totalasd)
+
+                # plot PSD
+                psdfig = plt.figure(figsize=(4, 3.5), dpi=200)
+                psdfig.subplots_adjust(left=0.18, bottom=0.15)
+
+                plt.plot(freqs, totalasd, color=coldict[ifo])
+                plt.xlim(freqs[0], freqs[-1])
+                plt.xlabel(r"Frequency (Hz)", fontsize=14, fontweight=100)
+                plt.ylabel(r"$h/\sqrt{\rm Hz}$", fontsize=14, fontweight=100)
+
+                # convert frequency labels to fractions
+                ax = plt.gca()
+                xt = [-Fs / 2.0, -Fs / 4.0, 0.0, Fs / 2.0, Fs / 4.0]
+                ax.set_xticks(xt)
+                xl = []
+                for item in xt:
+                    if item == 0:
+                        xl.append("0")
+                    else:
+                        if item < 0:
+                            xl.append(r"$-\sfrac{1}{%d}$" % (-1.0 / item))
+                        else:
+                            xl.append(r"$\sfrac{1}{%d}$" % (1.0 / item))
+                ax.set_xticklabels(xl)
+                # plt.setp(ax.get_xticklabels(), fontsize=16)  # increase font size
+                plt.tick_params(axis="x", which="major", labelsize=14)
+
+                psdfigs.append(psdfig)
+
+            if plotfscan:
+                fscanfig = plt.figure(figsize=(11, 3.5), dpi=200)
+                fscanfig.subplots_adjust(bottom=0.15, left=0.09, right=0.94)
+
+                extent = [tms[0], tms[-1], freqs[0], freqs[-1]]
+                plt.imshow(
+                    np.sqrt(np.flipud(fscan)),
+                    aspect="auto",
+                    extent=extent,
+                    interpolation=None,
+                    cmap=colmapdic[ifo],
+                    norm=colors.Normalize(),
+                )
+                plt.ylabel(r"Frequency (Hz)", fontsize=14, fontweight=100)
+                plt.xlabel(r"GPS - %d" % int(gpstime[0]), fontsize=14, fontweight=100)
+
+                # convert frequency labels to fractions
+                ax = plt.gca()
+                yt = [-Fs / 2.0, -Fs / 4.0, 0.0, Fs / 2.0, Fs / 4.0]
+                ax.set_yticks(yt)
+                yl = []
+                for item in yt:
+                    if item == 0:
+                        yl.append("0")
+                    else:
+                        if item < 0:
+                            yl.append(r"$-\sfrac{1}{%d}$" % (-1.0 / item))
+                        else:
+                            yl.append(r"$\sfrac{1}{%d}$" % (1.0 / item))
+                ax.set_yticklabels(yl)
+                plt.tick_params(axis="y", which="major", labelsize=14)
+
+                fscanfigs.append(fscanfig)
+
+    return Bkfigs, psdfigs, fscanfigs, asdlist, sampledt
+
+
+# a function to create a histogram of log10(results) for a list of a given parameter
+# (if a list with previous value is given they will be plotted as well)
+#  - lims is a dictionary of lists for each IFO
+def plot_limits_hist(
+    lims, param, ifos, prevlims=None, bins=20, overplot=False, mplparams=False
+):
+    import matplotlib
+    from matplotlib import pyplot as plt
+    from lalpulsar.pulsarhtmlutils import paramlatexdict
+
+    if not mplparams:
+        mplparams = {
+            "backend": "Agg",
+            "text.usetex": True,  # use LaTeX for all text
+            "axes.linewidth": 0.5,  # set axes linewidths to 0.5
+            "axes.grid": True,  # add a grid
+            "grid.linewidth": 0.5,
+            "font.family": "serif",
+            "font.size": 12,
+        }
+
+    matplotlib.rcParams.update(mplparams)
+
+    myfigs = []
+
+    # ifos line colour specs
+    coldict = {"H1": "r", "H2": "c", "L1": "g", "V1": "b", "G1": "m", "Joint": "k"}
+
+    try:
+        parxaxis = paramlatexdict[param.upper()]
+    except:
+        parxaxis = param
+
+    paryaxis = "Number of Pulsars"
+
+    # get log10 of previous results
+    logprevlims = None
+    if prevlims is not None:
+        logprevlims = np.log10(prevlims)
+
+    # get the limits of the histogram range
+    hrange = None
+    stacked = False
+    if overplot:
+        highbins = []
+        lowbins = []
+
+        # combine dataset to plot as stacked
+        stackdata = []
+        stacked = True
+
+        for j, ifo in enumerate(ifos):
+            theselims = lims[ifo]
+
+            # remove any None's
+            for i, val in enumerate(theselims):
+                if val == None:
+                    del theselims[i]
+
+            loglims = np.log10(theselims)
+
+            stackdata.append(loglims)
+
+            highbins.append(np.max(loglims))
+            lowbins.append(np.min(loglims))
+
+        if logprevlims is not None:
+            highbins.append(max(logprevlims))
+            lowbins.append(min(logprevlims))
+
+        hrange = (min(lowbins), max(highbins))
+
+    for j, ifo in enumerate(ifos):
+        # get log10 of results
+        theselims = lims[ifo]
+
+        # remove any None's
+        for i, val in enumerate(theselims):
+            if val == None:
+                del theselims[i]
+
+        loglims = np.log10(theselims)
+
+        if not overplot:
+            stackdata = loglims
+
+        # if not overplot or (overplot and j == 0):
+        myfig = plt.figure(figsize=(4, 4), dpi=200)
+        maxlims = []
+        minlims = []
+
+        if overplot:
+            edgecolor = []
+            facecolor = []
+            for ifoname in ifos:
+                edgecolor.append(coldict[ifoname])
+                facecolor.append(coldict[ifoname])
+        else:
+            edgecolor = [coldict[ifo]]
+            facecolor = [coldict[ifo]]
+
+        # plt.hist(loglims, bins, range=hrange, histtype='step', fill=True, edgecolor=coldict[ifo], facecolor=coldict[ifo], alpha=0.6)
+        n, bins, patches = plt.hist(
+            stackdata,
+            bins,
+            range=hrange,
+            histtype="step",
+            stacked=stacked,
+            fill=True,
+            color=edgecolor,
+            alpha=0.6,
+        )
+        for i, patch in enumerate(patches):
+            plt.setp(patch, "facecolor", facecolor[i])
+
+        if not overplot:
+            maxlims.append(np.max(loglims))
+            minlims.append(np.min(loglims))
+
+        if logprevlims is not None:
+            if not overplot:
+                maxlims.append(max(logprevlims))
+                minlims.append(min(logprevlims))
+
+                maxlim = max(maxlims)
+                minlim = min(minlims)
+            else:
+                maxlim = hrange[1]
+                minlim = hrange[0]
+
+            plt.hold(True)
+            plt.hist(
+                logprevlims,
+                bins,
+                range=hrange,
+                edgecolor="k",
+                lw=2,
+                histtype="step",
+                fill=False,
+            )
+            plt.hold(False)
+        else:
+            if not overplot:
+                maxlim = max(maxlims)
+                minlim = min(minlims)
+            else:
+                maxlim = hrange[1]
+                minlim = hrange[0]
+
+        # set xlabels to 10^x
+        ax = plt.gca()
+
+        # work out how many ticks to set
+        tickvals = range(int(math.ceil(maxlim) - math.floor(minlim)))
+        tickvals = map(lambda x: x + int(math.floor(minlim)), tickvals)
+        ax.set_xticks(tickvals)
+        tls = map(lambda x: "$10^{%d}$" % x, tickvals)
+        ax.set_xticklabels(tls)
+
+        plt.ylabel(r"" + paryaxis, fontsize=14, fontweight=100)
+        plt.xlabel(r"" + parxaxis, fontsize=14, fontweight=100)
+
+        myfig.subplots_adjust(left=0.18, bottom=0.15)  # adjust size
+
+        myfigs.append(myfig)
+
+        if overplot:
+            break
+
+    return myfigs
+
+
+# a function plot upper limits verses GW frequency in log-log space. If upper and
+# lower estimates for the upper limit are supplied these will also be plotted as a
+# band. If previous limits are supplied these will be plotted as well.
+# h0lims is a dictionary of lists of h0 upper limits for each of the IFOs given in
+# the list of ifos
+# ulesttop and ulestbot are the upper and lower ranges of the estimates limit given
+# as a dictionary if list for each ifo.
+# prevlim is a list of previous upper limits at the frequencies prevlimf0gw
+# xlims is the frequency range for the plot
+# overplot - set to true to plot different IFOs on same plot
+def plot_h0_lims(
+    h0lims,
+    f0gw,
+    ifos,
+    xlims=[10, 1500],
+    ulesttop=None,
+    ulestbot=None,
+    prevlim=None,
+    prevlimf0gw=None,
+    overplot=False,
+    mplparams=False,
+):
+    import matplotlib
+    from matplotlib import pyplot as plt
+
+    if not mplparams:
+        mplparams = {
+            "backend": "Agg",
+            "text.usetex": True,  # use LaTeX for all text
+            "axes.linewidth": 0.5,  # set axes linewidths to 0.5
+            "axes.grid": True,  # add a grid
+            "grid.linewidth": 0.5,
+            "font.family": "serif",
+            "font.size": 12,
+        }
+
+    matplotlib.rcParams.update(mplparams)
+
+    myfigs = []
+
+    # ifos line colour specs
+    coldict = {"H1": "r", "H2": "c", "L1": "g", "V1": "b", "G1": "m", "Joint": "k"}
+
+    parxaxis = "Frequency (Hz)"
+    paryaxis = "$h_0$"
+
+    for j, ifo in enumerate(ifos):
+        h0lim = h0lims[ifo]
+
+        if len(ifos) > 1:
+            f0s = f0gw[ifo]
+        else:
+            f0s = f0gw
+
+        if len(h0lim) != len(f0s):
+            return None  # exit if lengths aren't correct
+
+        if not overplot or (overplot and j == 0):
+            myfig = plt.figure(figsize=(7, 5.5), dpi=200)
+
+        plt.hold(True)
+        if ulesttop is not None and ulestbot is not None:
+            ult = ulesttop[ifo]
+            ulb = ulestbot[ifo]
+
+            if len(ult) == len(ulb) and len(ult) == len(f0s):
+                for i in range(len(ult)):
+                    plt.loglog(
+                        [f0s[i], f0s[i]], [ulb[i], ult[i]], ls="-", lw=3, c="lightgrey"
+                    )
+
+        if (
+            prevlim is not None
+            and prevlimf0gw is not None
+            and len(prevlim) == len(prevlimf0gw)
+        ):
+            if not overplot or (overplot and j == len(ifos) - 1):
+                plt.loglog(
+                    prevlimf0gw,
+                    prevlim,
+                    marker="*",
+                    ms=10,
+                    alpha=0.7,
+                    mfc="None",
+                    mec="k",
+                    ls="None",
+                )
+
+        # plot current limits
+        plt.loglog(
+            f0s, h0lim, marker="*", ms=10, mfc=coldict[ifo], mec=coldict[ifo], ls="None"
+        )
+
+        plt.ylabel(r"" + paryaxis, fontsize=14, fontweight=100)
+        plt.xlabel(r"" + parxaxis, fontsize=14, fontweight=100)
+
+        plt.xlim(xlims[0], xlims[1])
+
+        if not overplot or (overplot and j == len(ifos) - 1):
+            plt.hold(False)
+            myfig.subplots_adjust(left=0.12, bottom=0.10)  # adjust size
+            myfigs.append(myfig)
+
+    return myfigs
+
+
+# a function to create the signal model for a heterodyned triaxial pulsar given
+# a signal GPS start time, signal duration (in seconds), sample interval
+# (seconds), detector, and the parameters h0, cos(iota), psi (rads), initial
+# phase phi0 (rads), right ascension (rads) and declination (rads) in a
+# dictionary. The list of time stamps, and the real and imaginary parts of the
+# signal are returned
+def heterodyned_triaxial_pulsar(starttime, duration, dt, detector, pardict):
+    # create a list of times stamps
+    ts = []
+    tmpts = starttime
+
+    # create real and imaginary parts of the signal
+    s = np.array([], dtype=complex)
+
+    sphi = np.sin(pardict["phi0"])
+    cphi = np.cos(pardict["phi0"])
+
+    Xplus = 0.25 * (1.0 + pardict["cosiota"] * pardict["cosiota"]) * pardict["h0"]
+    Xcross = 0.5 * pardict["cosiota"] * pardict["h0"]
+    Xpsinphi = Xplus * sphi
+    Xcsinphi = Xcross * sphi
+    Xpcosphi = Xplus * cphi
+    Xccosphi = Xcross * cphi
+
+    i = 0
+    while tmpts < starttime + duration:
+        ts.append(starttime + (dt * i))
+
+        # get the antenna response
+        fp, fc = antenna_response(
+            ts[i], pardict["ra"], pardict["dec"], pardict["psi"], detector
+        )
+
+        # create real part of signal
+        s = np.append(
+            s, (fp * Xpcosphi + fc * Xcsinphi) + 1j * (fp * Xpsinphi - fc * Xccosphi)
+        )
+
+        tmpts = ts[i] + dt
+
+        i = i + 1
+
+    return ts, s
+
+
+# a function to create a heterodyned signal model for a neutron star using the complex
+# amplitude parameters C22, phi22, C21 and phi21 and the orientation parameters cos(iota)
+# and psi. If both C22 and C21 are non-zero then a signal at both the rotation frequency
+# and twice the rotation frequency will be generated.
+#
+# Note that for the purely triaxial signal the waveform, as defined in Jones (2015)
+# http://arxiv.org/abs/1501.05832 (and subsequently Pitkin et al (2015) http://arxiv.org/abs/1508.00416),
+# has the opposite sign to the convention in e.g. JKS (which is used for signal generation in hardware
+# injections). Hence, when converting h0, from the conventional model, to C22 a minus sign needs to be
+# introduced. Also, phi0 here is defined as the rotational phase of the source, so when converting to phi22
+# a factor of 2 is needed.
+def heterodyned_pulsar_signal(
+    pardict, detector, starttime=900000000.0, duration=86400.0, dt=60.0, datatimes=None
+):
+    if "cosiota" in pardict:
+        cosiota = pardict["cosiota"]
+        iota = math.acos(cosiota)
+        siniota = math.sin(iota)
+    else:
+        raise KeyError("cos(iota) not defined!")
+
+    if "psi" in pardict:
+        psi = pardict["psi"]
+    else:
+        raise KeyError("psi not defined!")
+
+    if "C22" in pardict:
+        C22 = pardict["C22"]
+    else:
+        if "h0" in pardict:
+            C22 = -pardict["h0"] / 2.0
+        else:
+            C22 = 0.0
+
+    if "phi22" in pardict:
+        phi22 = pardict["phi22"]
+    else:
+        if "phi0" in pardict:
+            phi22 = 2.0 * pardict["phi0"]
+        else:
+            phi22 = 0.0
+
+    ePhi22 = cmath.exp(phi22 * 1j)
+
+    if "C21" in pardict:
+        C21 = pardict["C21"]
+    else:
+        C21 = 0.0
+
+    if "phi21" in pardict:
+        phi21 = pardict["phi21"]
+    else:
+        phi21 = 0.0
+
+    ePhi21 = cmath.exp(phi21 * 1j)
+
+    s = []  # signal
+    ts = []  # times
+
+    if "C21" in pardict and "C22" in pardict and "h0" not in pardict:
+        freqs = [1.0, 2.0]
+    else:
+        freqs = [2.0]
+
+    for f in freqs:
+        i = 0
+        if datatimes is None:
+            datatimes = np.arange(starttime, starttime + duration, dt)
+
+        # get the antenna response
+        fp, fc = antenna_response(
+            datatimes, pardict["ra"], pardict["dec"], pardict["psi"], detector
+        )
+
+        if f == 1.0:
+            sf = (
+                -(C21 / 4.0) * ePhi21 * siniota * cosiota * fp
+                + 1j * (C21 / 4.0) * ePhi21 * siniota * fc
+            )
+        elif f == 2.0:
+            sf = (
+                -(C22 / 2.0) * ePhi22 * (1.0 + cosiota**2.0) * fp
+                + 1j * (C22) * ePhi22 * cosiota * fc
+            )
+
+        ts.append(datatimes)
+        s.append(sf)
+
+    return ts, s
+
+
+# a function to convert the pinned superfluid model parameters to the complex
+# amplitude parameters using the Eqns 76-79 defined in Jones 2012 LIGO DCC T1200265-v3
+def convert_model_parameters(pardict):
+    costheta = pardict["costheta"]
+    theta = np.arccos(costheta)
+    sintheta = math.sin(theta)
+    sin2theta = math.sin(2.0 * theta)
+    sinlambda = math.sin(pardict["lambdapin"])
+    coslambda = math.cos(pardict["lambdapin"])
+    sin2lambda = math.sin(2.0 * pardict["lambdapin"])
+
+    phi0 = pardict["phi0"]
+
+    I21 = pardict["I21"]
+    I31 = pardict["I31"]
+
+    A22 = I21 * (sinlambda**2 - (coslambda * costheta) ** 2) - I31 * sintheta**2
+    B22 = I21 * sin2lambda * costheta
+
+    C22 = 2.0 * math.sqrt(A22**2 + B22**2)
+
+    A21 = I21 * sin2lambda * sintheta
+    B21 = (I21 * coslambda**2 - I31) * sin2theta
+
+    C21 = 2.0 * math.sqrt(A21**2 + B21**2)
+
+    phi22 = np.fmod(2.0 * phi0 - math.atan2(B22, A22), 2.0 * np.pi)
+    phi21 = np.fmod(phi0 - math.atan2(B21, A21), 2.0 * np.pi)
+
+    outvals = {"C22": C22, "C21": C21, "phi22": phi22, "phi21": phi21}
+
+    return outvals
+
+
+# a function to create the signal model for a heterodyned pinned superfluid
+# model pulsar a signal GPS start time, signal duration (in seconds),
+# sample interval (seconds), detector, and the parameters I21, I31,
+# cos(theta), lambda, cos(iota), psi (rads), initial phase phi0 (for l=m=2 mode in rads), right
+# ascension (rads), declination (rads), distance (kpc) and frequency (f0) in a
+# dictionary. The list of time stamps, and the real and imaginary parts of the
+# 1f and 2f signals are returned in an array
+def heterodyned_pinsf_pulsar(starttime, duration, dt, detector, pardict):
+    iota = np.arccos(pardict["cosiota"])
+    theta = np.arccos(pardict["costheta"])
+    siniota = math.sin(iota)
+    sintheta = math.sin(theta)
+    sin2theta = math.sin(2.0 * theta)
+    sinlambda = math.sin(pardict["lambdapin"])
+    coslambda = math.cos(pardict["lambdapin"])
+    sin2lambda = math.sin(2.0 * pardict["lambdapin"])
+
+    ePhi = cmath.exp(0.5 * pardict["phi0"] * 1j)
+    e2Phi = cmath.exp(pardict["phi0"] * 1j)
+
+    f2_r = pardict["f0"] ** 2 / pardict["dist"]
+
+    """
+      This model is a complex heterodyned time series for a pinned superfluid
+      neutron star emitting at its roation frequency and twice its rotation
+      frequency (as defined in Eqns 35-38 of Jones 2012 LIGO DCC T1200265-v3)
+    """
+
+    Xplusf = -(f2_r / 2.0) * siniota * pardict["cosiota"]
+    Xcrossf = (f2_r / 2.0) * siniota
+
+    Xplus2f = -f2_r * (1.0 + pardict["cosiota"] ** 2)
+    Xcross2f = 2.0 * f2_r * pardict["cosiota"]
+
+    A21 = pardict["I21"] * sin2lambda * sintheta
+    B21 = (pardict["I21"] * coslambda**2 - pardict["I31"]) * sin2theta
+
+    A22 = (
+        pardict["I21"] * (sinlambda**2 - coslambda**2 * pardict["costheta"] ** 2)
+        - pardict["I31"] * sintheta**2
+    )
+    B22 = pardict["I21"] * sin2lambda * pardict["costheta"]
+
+    # create a list of times stamps
+    ts1 = []
+    ts2 = []
+    tmpts = starttime
+
+    # create real and imaginary parts of the 1f signal
+    s1 = np.array([], dtype=complex)
+    s2 = np.array([], dtype=complex)
+
+    i = 0
+    while tmpts < starttime + duration:
+        ts1.append(starttime + (dt * i))
+        ts2.append(starttime + (dt * i))
+
+        # get the antenna response
+        fp, fc = antenna_response(
+            ts1[i], pardict["ra"], pardict["dec"], pardict["psi"], detector
+        )
+
+        # create the complex signal amplitude model at 1f
+        s1 = np.append(
+            s1,
+            (fp * Xplusf * ePhi * (A21 - 1j * B21))
+            + (fc * Xcrossf * ePhi * (B21 + 1j * A21)),
+        )
+
+        # create the complex signal amplitude model at 2f
+        s2 = np.append(
+            s2,
+            (fp * Xplus2f * e2Phi * (A22 - 1j * B22))
+            + (fc * Xcross2f * e2Phi * (B22 + 1j * A22)),
+        )
+
+        tmpts = ts1[i] + dt
+
+        i = i + 1
+
+    # combine data into 1 array
+    ts = np.vstack([ts1, ts2])
+    s = np.vstack([s1, s2])
+
+    return ts, s
+
+
+# function to get the antenna response for a given detector. It takes in a GPS time or list (or numpy array)
+# of GPS times, right  ascension (rads), declination (rads), polarisation angle (rads) and a detector name
+# e.g. H1, L1, V1. The plus and cross polarisations are returned.
+def antenna_response(gpsTime, ra, dec, psi, det):
+    import lal
+
+    # create detector-name map
+    detMap = {
+        "H1": lal.LALDetectorIndexLHODIFF,
+        "H2": lal.LALDetectorIndexLHODIFF,
+        "L1": lal.LALDetectorIndexLLODIFF,
+        "G1": lal.LALDetectorIndexGEO600DIFF,
+        "V1": lal.LALDetectorIndexVIRGODIFF,
+        "T1": lal.LALDetectorIndexTAMA300DIFF,
+        "AL1": lal.LALDetectorIndexLLODIFF,
+        "AH1": lal.LALDetectorIndexLHODIFF,
+        "AV1": lal.LALDetectorIndexVIRGODIFF,
+        "E1": lal.LALDetectorIndexE1DIFF,
+        "E2": lal.LALDetectorIndexE2DIFF,
+        "E3": lal.LALDetectorIndexE3DIFF,
+    }
+
+    try:
+        detector = detMap[det]
+    except KeyError:
+        raise KeyError("ERROR. Key {} is not a valid detector name.".format(det))
+
+    # get detector
+    detval = lal.CachedDetectors[detector]
+    response = detval.response
+
+    # check if ra and dec are floats or strings (if strings in hh/dd:mm:ss.s format then convert to rads)
+    if not isinstance(ra, float):
+        if isinstance(ra, str):
+            try:
+                ra = ra_to_rad(ra)
+            except:
+                raise ValueError(
+                    "Right ascension string '{}' not formatted properly".format(ra)
+                )
+        else:
+            raise ValueError(
+                "Right ascension must be a 'float' in radians or a string of the format 'hh:mm:ss.s'"
+            )
+
+    if not isinstance(dec, float):
+        if isinstance(dec, str):
+            try:
+                dec = dec_to_rad(dec)
+            except:
+                raise ValueError(
+                    "Declination string '{}' not formatted properly".format(ra)
+                )
+        else:
+            raise ValueError(
+                "Declination must be a 'float' in radians or a string of the format 'dd:mm:ss.s'"
+            )
+
+    # check if gpsTime is just a float or int, and if so convert into an array
+    if isinstance(gpsTime, float) or isinstance(gpsTime, int):
+        gpsTime = np.array([gpsTime])
+    else:  # make sure it's a numpy array
+        gpsTime = np.copy(gpsTime)
+
+    # make sure times are floats
+    gpsTime = gpsTime.astype("float64")
+
+    # if gpsTime is a list of regularly spaced values then use ComputeDetAMResponseSeries
+    if len(gpsTime) == 1 or np.unique(np.diff(gpsTime)).size == 1:
+        gpsStart = lal.LIGOTimeGPS(gpsTime[0])
+        dt = 0.0
+        if len(gpsTime) > 1:
+            dt = gpsTime[1] - gpsTime[0]
+        fp, fc = lal.ComputeDetAMResponseSeries(
+            response, ra, dec, psi, gpsStart, dt, len(gpsTime)
+        )
+
+        # return elements from Time Series
+        return fp.data.data, fc.data.data
+    else:  # we'll have to work out the value at each point in the time series
+        fp = np.zeros(len(gpsTime))
+        fc = np.zeros(len(gpsTime))
+
+        for i in range(len(gpsTime)):
+            gps = lal.LIGOTimeGPS(gpsTime[i])
+            gmst_rad = lal.GreenwichMeanSiderealTime(gps)
+
+            # actual computation of antenna factors
+            fp[i], fc[i] = lal.ComputeDetAMResponse(response, ra, dec, psi, gmst_rad)
+
+        return fp, fc
+
+
+# a function to inject a heterodyned pulsar signal into noise of a
+# given level for detectors. it will return the signal + noise and the optimal
+# SNR. If an snrscale value is passed to the function the signal will be scaled
+# to that SNR. nsigs
+def inject_pulsar_signal(
+    starttime,
+    duration,
+    dt,
+    detectors,
+    pardict,
+    freqfac=[2.0],
+    npsds=None,
+    snrscale=None,
+):
+    # if detectors is just a string (i.e. one detector) then make it a list
+    if isinstance(detectors, str):
+        detectors = [detectors]
+
+    # if not noise sigma's are given then generate a noise level from the given
+    # detector noise curves
+    if npsds is None:
+        npsds = []
+
+        for det in detectors:
+            for frf in freqfac:
+                psd = detector_noise(det, frf * pardict["f0"])
+
+                # convert to time domain standard devaition shared between real and
+                # imaginary signal
+                ns = np.sqrt((psd / 2.0) / (2.0 * dt))
+
+                npsds.append(ns)
+    else:
+        # convert input psds into time domain noise standard deviation
+        tmpnpsds = []
+
+        count = 0
+        for j, det in enumerate(detectors):
+            for frf in freqfac:
+                if len(npsds) == 1:
+                    tmpnpsds.append(np.sqrt((npsds[0] / 2.0) / (2.0 * dt)))
+                else:
+                    tmpnpsds.append(np.sqrt((npsds[count] / 2.0) / (2.0 * dt)))
+
+                count = count + 1
+
+        npsds = tmpnpsds
+
+    if len(freqfac) == 1 and len(detectors) != len(npsds):
+        raise ValueError(
+            "Number of detectors {} not the same as number of noises {}".format(
+                len(detectors), len(npsds)
+            )
+        )
+
+    if len(freqfac) == 2 and 2 * len(detectors) != len(npsds):
+        raise ValueError(
+            "Number of detectors {} not half the number of noises {}".format(
+                len(detectors), len(npsds)
+            )
+        )
+
+    tss = np.array([])
+    ss = np.array([])
+
+    snrtot = 0
+    for j, det in enumerate(detectors):
+        # create the pulsar signal
+        if len(freqfac) == 1 and freqfac[0] == 2.0:
+            ts, s = heterodyned_pulsar_signal(pardict, det, starttime, duration, dt)
+
+            if j == 0:
+                tss = np.append(tss, ts)
+                ss = np.append(ss, s)
+            else:
+                tss = np.vstack([tss, ts])
+                ss = np.vstack([ss, s])
+
+            # get SNR
+            snrtmp = get_optimal_snr(s[0], npsds[j])
+        elif len(freqfac) == 2:
+            ts, s = heterodyned_pulsar_signal(pardict, det, starttime, duration, dt)
+
+            snrtmp = 0
+            for k, frf in enumerate(freqfac):
+                if j == 0 and k == 0:
+                    tss = np.append(tss, ts[k][:])
+                    ss = np.append(ss, s[k][:])
+                else:
+                    tss = np.vstack([tss, ts[k][:]])
+                    ss = np.vstack([ss, s[k][:]])
+
+                snrtmp2 = get_optimal_snr(s[k][:], npsds[2 * j + k])
+                snrtmp = snrtmp + snrtmp2 * snrtmp2
+
+            snrtmp = np.sqrt(snrtmp)
+
+        snrtot = snrtot + snrtmp * snrtmp
+
+    # total multidetector/data stream snr
+    snrtot = np.sqrt(snrtot)
+
+    # add noise and rescale signals if necessary
+    if snrscale is not None:
+        if snrscale != 0:
+            snrscale = snrscale / snrtot
+        # print snrscale
+    else:
+        snrscale = 1
+
+    signalonly = ss.copy()
+
+    i = 0
+    for det in detectors:
+        # for triaxial model
+        if len(freqfac) == 1:
+            # generate random numbers
+            rs = np.random.randn(len(ts[0]), 2)
+
+            for j, t in enumerate(ts[0]):
+                if len(tss.shape) == 1:
+                    signalonly[j] = (snrscale * ss[j].real) + 1j * (
+                        snrscale * ss[j].imag
+                    )
+                    ss[j] = (snrscale * ss[j].real + npsds[i] * rs[j][0]) + 1j * (
+                        snrscale * ss[j].imag + npsds[i] * rs[j][1]
+                    )
+                else:
+                    signalonly[i][j] = (snrscale * ss[i][j].real) + 1j * (
+                        snrscale * ss[i][j].imag
+                    )
+                    ss[i][j] = (snrscale * ss[i][j].real + npsds[i] * rs[j][0]) + 1j * (
+                        snrscale * ss[i][j].imag + npsds[i] * rs[j][1]
+                    )
+
+            i = i + 1
+        elif len(freqfac) == 2:
+            # generate random numbers
+            rs = np.random.randn(len(ts[0][:]), 4)
+
+            for j, t in enumerate(ts[0][:]):
+                signalonly[i][j] = (snrscale * ss[i][j].real) + 1j * (
+                    snrscale * ss[i][j].imag
+                )
+                ss[i][j] = (snrscale * ss[i][j].real + npsds[i] * rs[j][0]) + 1j * (
+                    snrscale * ss[i][j].imag + npsds[i] * rs[j][1]
+                )
+                signalonly[i + 1][j] = (snrscale * ss[i + 1][j].real) + 1j * (
+                    snrscale * ss[i + 1][j].imag
+                )
+                ss[i + 1][j] = (
+                    snrscale * ss[i + 1][j].real + npsds[i + 1] * rs[j][2]
+                ) + 1j * (snrscale * ss[i + 1][j].imag + npsds[i + 1] * rs[j][3])
+
+            i = i + 2
+        else:
+            print("Something wrong with injection", file=sys.stderr)
+            sys.exit(1)
+
+    snrtot = snrtot * snrscale
+
+    return tss, ss, signalonly, snrtot, snrscale, npsds
+
+
+# function to create a time domain PSD from theoretical
+# detector noise curves. It takes in the detector name and the frequency at
+# which to generate the noise.
+#
+# The noise models are taken from those in lalsimulation/lib/LALSimNoisePSD.c
+def detector_noise(det, f):
+    import lalsimulation
+
+    if det == "AV1":  # Advanced Virgo
+        return lalsimulation.SimNoisePSDAdvVirgo(f)
+    elif det == "H1" or det == "L1":  # iLIGO SRD
+        return lalsimulation.SimNoisePSDiLIGOSRD(f)
+    elif det == "H2":
+        return lalsimulation.SimNoisePSDiLIGOSRD(f) * 2.0
+    elif det == "G1":  # GEO_600
+        return lalsimulation.SimNoisePSDGEO(f)
+    elif det == "V1":  # initial Virgo
+        return lalsimulation.SimNoisePSDVirgo(f)
+    elif det == "T1":  # TAMA
+        return lalsimulation.SimNoisePSDTAMA(f)
+    elif det == "K1":  # KAGRA
+        return lalsimulation.SimNoisePSDKAGRA(f)
+    elif det == "AL1" or det == "AH1":
+        return lalsimulation.SimNoisePSDaLIGOZeroDetHighPower(f)
+    else:
+        raise ValueError("{} is not a recognised detector".format(det))
+
+
+# function to calculate the optimal SNR of a heterodyned pulsar signal - it
+# takes in a complex signal model and noise standard deviation
+def get_optimal_snr(s, sig):
+    ss = 0
+    # sum square of signal
+    for val in s:
+        ss = ss + val.real**2 + val.imag**2
+
+    return np.sqrt(ss / sig**2)
+
+
+# use the Gelman-Rubins convergence test for MCMC chains, where chains is a list
+# of MCMC numpy chain arrays - this copies the gelman_rubins function in
+# bayespputils
+def gelman_rubins(chains):
+    chainMeans = [np.mean(data) for data in chains]
+    chainVars = [np.var(data) for data in chains]
+
+    BoverN = np.var(chainMeans)
+    W = np.mean(chainVars)
+
+    sigmaHat2 = W + BoverN
+
+    m = len(chains)
+
+    VHat = sigmaHat2 + BoverN / m
+
+    R = VHat / W
+
+    return R
+
+
+# function to convert MCMC files output from pulsar_parameter_estimation into
+# a posterior class object - also outputting:
+#  - the mean effective sample size of each parameter chain
+#  - the Gelman-Rubins statistic for each parameter (a dictionary)
+#  - the original length of each chain
+# Th input is a list of MCMC chain files
+def pulsar_mcmc_to_posterior(chainfiles):
+    from lalinference import bayespputils as bppu
+
+    cl = []
+    neffs = []
+    grr = {}
+
+    mcmc = []
+
+    for cfile in chainfiles:
+        if os.path.isfile(cfile):
+            # load MCMC chain
+            mcmcChain = read_pulsar_mcmc_file(cfile)
+
+            # if no chain found then exit with None's
+            if mcmcChain is None:
+                return None, None, None, None
+
+            # find number of effective samples for the chain
+            neffstmp = []
+            for j in range(1, mcmcChain.shape[1]):
+                neff, acl, acf = bppu.effectiveSampleSize(mcmcChain[:, j])
+                neffstmp.append(neff)
+
+            # get the minimum effective sample size
+            # neffs.append(min(neffstmp))
+            # get the mean effective sample size
+            neffs.append(math.floor(np.mean(neffstmp)))
+
+            # nskip = math.ceil(mcmcChain.shape[0]/min(neffstmp))
+            nskip = int(math.ceil(mcmcChain.shape[0] / np.mean(neffstmp)))
+
+            # output every nskip (independent) value
+            mcmc.append(mcmcChain[::nskip, :])
+            cl.append(mcmcChain.shape[0])
+        else:
+            print("File %s does not exist!" % cfile, file=sys.stderr)
+            return None, None, None, None
+
+    # output data to common results format
+    # get first line of MCMC chain file for header names
+    cf = open(chainfiles[0], "r")
+    headers = cf.readline()
+    headers = cf.readline()  # column names are on the second line
+    # remove % from start
+    headers = re.sub("%", "", headers)
+    # remove rads
+    headers = re.sub("rads", "", headers)
+    # remove other brackets e.g. around (iota)
+    headers = re.sub("[()]", "", headers)
+    cf.close()
+
+    # get Gelman-Rubins stat for each parameter
+    for idx, parv in enumerate(headers.split()):
+        lgr = []
+        if parv != "logL":
+            for j in range(0, len(mcmc)):
+                achain = mcmc[j]
+                singlechain = achain[:, idx]
+                lgr.append(singlechain)
+            grr[parv.lower()] = gelman_rubins(lgr)
+
+    # logL in chain is actually log posterior, so also output the posterior
+    # values (can be used to estimate the evidence)
+    headers = headers.replace("\n", "\tpost\n")
+
+    # output full data to common format
+    comfile = chainfiles[0] + "_common_tmp.dat"
+    try:
+        cf = open(comfile, "w")
+    except:
+        print("Can't open common posterior file!", file=sys.stderr)
+        sys.exit(0)
+
+    cf.write(headers)
+    for narr in mcmc:
+        for j in range(0, narr.shape[0]):
+            mline = narr[j, :]
+            # add on posterior
+            mline = np.append(mline, np.exp(mline[0]))
+
+            strmline = " ".join(str(x) for x in mline) + "\n"
+            cf.write(strmline)
+    cf.close()
+
+    # read in as common object
+    peparser = bppu.PEOutputParser("common")
+    cf = open(comfile, "r")
+    commonResultsObj = peparser.parse(cf)
+    cf.close()
+
+    # remove temporary file
+    os.remove(comfile)
+
+    # create posterior class
+    pos = bppu.Posterior(commonResultsObj, SimInspiralTableEntry=None, votfile=None)
+
+    # convert iota back to cos(iota)
+    # create 1D posterior class of cos(iota) values
+    cipos = None
+    cipos = bppu.PosteriorOneDPDF("cosiota", np.cos(pos["iota"].samples))
+
+    # add it back to posterior
+    pos.append(cipos)
+
+    # remove iota samples
+    pos.pop("iota")
+
+    return pos, neffs, grr, cl
+
+
+# a function that attempt to load an pulsar MCMC chain file: first it tries using
+# numpy.loadtxt; if it fails it tries reading line by line and checking
+# for consistent line numbers, skipping lines that are inconsistent; if this
+# fails it returns None
+def read_pulsar_mcmc_file(cf):
+    cfdata = None
+
+    # first try reading in with loadtxt (skipping lines starting with %)
+    try:
+        cfdata = np.loadtxt(cf, comments="%")
+    except:
+        try:
+            fc = open(cf, "r")
+
+            # read in header lines and count how many values each line should have
+            headers = fc.readline()
+            headers = fc.readline()  # column names are on the second line
+            fc.close()
+            # remove % from start
+            headers = re.sub("%", "", headers)
+            # remove rads
+            headers = re.sub("rads", "", headers)
+            # remove other brackets e.g. around (iota)
+            headers = re.sub("[()]", "", headers)
+
+            lh = len(headers.split())
+
+            cfdata = np.array([])
+
+            lines = cf.readlines()
+
+            for i, line in enumerate(lines):
+                if "%" in line:  # skip lines containing %
+                    continue
+
+                lvals = line.split()
+
+                # skip line if number of values isn't consistent with header
+                if len(lvals) != lh:
+                    continue
+
+                # convert values to floats
+                try:
+                    lvalsf = map(float, lvals)
+                except:
+                    continue
+
+                # add values to array
+                if i == 0:
+                    cfdata = np.array(lvalsf)
+                else:
+                    cfdata = np.vstack((cfdata, lvalsf))
+
+            if cfdata.size == 0:
+                cfdata = None
+        except:
+            cfdata = None
+
+    return cfdata
+
+
+def pulsar_nest_to_posterior(postfile, nestedsamples=False, removeuntrig=True):
+    """
+    This function will import a posterior sample file created by `lalapps_nest2pos` (or a nested
+    sample file). It will be returned as a Posterior class object from `bayespputils`. The
+    signal evidence and noise evidence are also returned.
+
+    If there are samples in 'Q22' and not 'H0', and also a distance, or distance samples, then
+    the Q22 samples will be converted into equivalent H0 values.
+
+    Parameters
+    ----------
+    postfile : str, required
+        The file name of the posterior or nested sample file. In general this should be a HDF5 file with the extension
+        '.hdf' or '.h5', although older format ascii files are still supported at the moment.
+    nestedsamples : bool, default: False
+        If the file being input contains nested samples, rather than posterior samples, then this flag must be set to
+        True
+    removeuntrig : bool, default: True
+        If this is True then any parameters that are sines or cosines of a value will have the value removed if present
+        e.g. if cosiota and iota exist then iota will be removed.
+    """
+
+    from lalinference import bayespputils as bppu
+    from lalinference.bayespputils import replace_column
+
+    fe = os.path.splitext(postfile)[-1].lower()  # file extension
+
+    # combine multiple nested sample files for an IFO into a single posterior (copied from lalapps_nest2pos)
+    if fe == ".h5" or fe == ".hdf":  # HDF5 file
+        if nestedsamples:
+            # use functions from lalapps_nest2pos to read values from nested sample files i.e. not a posterior file created by lalapps_nest2pos
+            try:
+                from lalinference.io import read_samples
+                from lalinference import LALInferenceHDF5NestedSamplesDatasetName
+
+                samples = read_samples(
+                    postfile, tablename=LALInferenceHDF5NestedSamplesDatasetName
+                )
+                params = samples.colnames
+
+                # make everything a float, since that's what's excected of a CommonResultsObj
+                for param in params:
+                    replace_column(samples, param, samples[param].astype(float))
+
+                nsResultsObject = (
+                    samples.colnames,
+                    samples.as_array().view(float).reshape(-1, len(params)),
+                )
+            except:
+                raise IOError("Could not import nested samples")
+        else:  # assume posterior file has been created with lalapps_nest2pos
+            peparser = bppu.PEOutputParser("hdf5")
+            nsResultsObject = peparser.parse(postfile)
+    elif fe == ".gz":  # gzipped file
+        import gzip
+
+        peparser = bppu.PEOutputParser("common")
+        nsResultsObject = peparser.parse(gzip.open(postfile, "r"))
+    else:  # assume an ascii text file
+        peparser = bppu.PEOutputParser("common")
+        nsResultsObject = peparser.parse(open(postfile, "r"))
+
+    pos = bppu.Posterior(nsResultsObject, SimInspiralTableEntry=None)
+
+    # remove any unchanging variables and randomly shuffle the rest
+    pnames = pos.names
+    nsamps = len(pos[pnames[0]].samples)
+    permarr = np.arange(nsamps)
+    np.random.shuffle(permarr)
+    posdist = None
+    posfreqs = None
+    for pname in pnames:
+        # check if all samples are the same
+        if pos[pname].samples.tolist().count(pos[pname].samples[0]) == len(
+            pos[pname].samples
+        ):
+            if pname == "f0_fixed":
+                # try getting a fixed f0 value (for calculating h0 from Q22)
+                posfreqs = pos[pname].samples[0]
+            elif pname == "dist":
+                # try getting a fixed distance value (for calculating h0 from Q22 if required)
+                posdist = pos[pname].samples[0] / KPC
+
+            pos.pop(pname)
+        else:
+            # shuffle
+            shufpos = None
+            shufpos = bppu.PosteriorOneDPDF(pname, pos[pname].samples[permarr])
+            pos.pop(pname)
+            pos.append(shufpos)
+
+    # check whether iota has been used
+    posIota = None
+    if "iota" in pos.names:
+        posIota = pos["iota"].samples
+
+    if posIota is not None:
+        cipos = None
+        cipos = bppu.PosteriorOneDPDF("cosiota", np.cos(posIota))
+        pos.append(cipos)
+        if removeuntrig:
+            pos.pop("iota")
+
+    # check whether sin(i) binary parameter has been used
+    posI = None
+    if "i" in pos.names:
+        posI = pos["i"].samples
+
+    if posI is not None:
+        sinipos = None
+        sinipos = bppu.PosteriorOneDPDF("sini", np.sin(posI))
+        pos.append(sinipos)
+        if removeuntrig:
+            pos.pop("i")
+
+    # convert C22 back into h0, and phi22 back into phi0 if required
+    posC21 = None
+    if "c21" in pos.names:
+        posC21 = pos["c21"].samples
+
+    posC22 = None
+    if "c22" in pos.names:
+        posC22 = pos["c22"].samples
+
+    posphi22 = None
+    if "phi22" in pos.names:
+        posphi22 = pos["phi22"].samples
+
+    # convert C22 back into h0, and phi22 back into phi0 if required
+    if posC22 is not None and posC21 is None:
+        h0pos = None
+        h0pos = bppu.PosteriorOneDPDF("h0", 2.0 * pos["c22"].samples)
+
+        pos.append(h0pos)
+        pos.pop("c22")
+
+        if posphi22 is not None:
+            phi0pos = None
+            phi0pos = bppu.PosteriorOneDPDF(
+                "phi0", np.fmod(pos["phi22"].samples + math.pi, 2.0 * math.pi)
+            )
+
+            pos.append(phi0pos)
+            pos.pop("phi22")
+
+    # convert Q22 to h0 is required
+    posQ22 = None
+    if "q22" in pos.names:
+        posQ22 = pos["q22"].samples
+
+    if "dist" in pos.names:
+        posdist = (
+            pos["dist"].samples / KPC
+        )  # distance in kpc (for use in converting Q22 to h0)
+
+        # convert distance samples to kpc
+        pos.pop("dist")
+        distpos = bppu.PosteriorOneDPDF("dist", posdist)
+        pos.append(distpos)
+
+    if "f0" in pos.names:
+        posfreqs = pos["f0"].samples
+        # if not found this will have been set from the f0_fixed value above
+
+    if posQ22 is not None and posdist is not None and "h0" not in pos.names:
+        h0pos = None
+        h0pos = bppu.PosteriorOneDPDF("h0", quadrupole_to_h0(posQ22, posfreqs, posdist))
+
+        pos.append(h0pos)
+
+    # get evidence (as in lalapps_nest2pos)
+    if fe == ".h5" or fe == ".hdf":
+        # read evidence from HDF5 file
+        hdf = h5py.File(postfile, "r")
+        a = hdf["lalinference"]["lalinference_nest"]
+        sigev = a.attrs["log_evidence"]
+        noiseev = a.attrs["log_noise_evidence"]
+        hdf.close()
+    else:
+        B = np.loadtxt(postfile.replace(".gz", "") + "_B.txt")
+        sigev = B[1]
+        noiseev = B[2]
+
+    # return posterior samples, signal evidence (B[1]) and noise evidence (B[2])
+    return pos, sigev, noiseev
+
+
+# function to add two exponentiated log values and return the log of the result
+def logplus(x, y):
+    return np.logaddexp(x, y)
+
+
+def logtrapz(lnf, dx):
+    """
+    Perform trapezium rule integration for the logarithm of a function on a regular grid.
+
+    Inputs
+    ------
+    lnf - a numpy array of values that are the natural logarithm of a function
+    dx  - a float giving the step size between values in the function
+
+    Returns
+    -------
+    The natural logarithm of the area under the function.
+    """
+
+    return np.log(dx / 2.0) + logsumexp([logsumexp(lnf[:-1]), logsumexp(lnf[1:])])
+
+
+# function to marginalise over a parameter
+def marginalise(like, pname, pnames, ranges):
+    # like - a copy of the loglikelihood array
+    # pname - the parameter to marginalise over
+    # pnames - a copy of the list of parameters that haven't been marginalised over
+    # ranges - a copy of the dictionary of ranges that haven't been marginalised over
+
+    places = ranges[pname]
+    axis = pnames.index(pname)
+
+    # perform marginalisation
+    if len(places) > 1:
+        x = np.apply_along_axis(logtrapz, axis, like, places[1] - places[0])
+    elif len(places) == 1:
+        # no marginalisation required just remove the specific singleton dimension via reshaping
+        z = like.shape
+        q = np.arange(0, len(z)).astype(int) != axis
+        newshape = tuple((np.array(list(z)))[q])
+        x = np.reshape(like, newshape)
+
+    # remove name from pnames and ranges
+    del ranges[pname]
+    pnames.remove(pname)
+
+    return x
+
+
+# return the log marginal posterior on a given parameter (if 'all' marginalise over all parameters)
+def marginal(lnlike, pname, pnames, ranges, multflatprior=False):
+    from copy import deepcopy
+
+    # make copies of everything
+    lnliketmp = deepcopy(lnlike)
+    pnamestmp = deepcopy(pnames)
+    rangestmp = deepcopy(ranges)
+
+    for name in pnames:
+        if name != pname:
+            if multflatprior:  # multiply by flat prior range
+                lnliketmp = marginalise(
+                    lnliketmp
+                    + np.log(1.0 / (rangestmp[name][-1] - rangestmp[name][0])),
+                    name,
+                    pnamestmp,
+                    rangestmp,
+                )
+            else:
+                lnliketmp = marginalise(lnliketmp, name, pnamestmp, rangestmp)
+
+    return lnliketmp
+
+
+# a function to chop the data time series, ts, up into contigous segments with a maximum length, chunkMax
+def get_chunk_lengths(ts, chunkMax):
+    i = j = count = 0
+
+    length = len(ts)
+
+    chunkLengths = []
+
+    dt = np.min(np.diff(ts))  # the time steps in the data
+
+    # create vector of data segment length
+    while True:
+        count += 1  # counter
+
+        # break clause
+        if i > length - 2:
+            # set final value of chunkLength
+            chunkLengths.append(count)
+            break
+
+        i += 1
+
+        t1 = ts[i - 1]
+        t2 = ts[i]
+
+        # if consecutive points are within two sample times of each other count as in the same chunk
+        if t2 - t1 > 2.0 * dt or count == chunkMax:
+            chunkLengths.append(count)
+            count = 0  # reset counter
+
+            j += 1
+
+    return chunkLengths
+
+
+def pulsar_estimate_snr(source, det, tstart, duration, Sn, dt=1800):
+    """
+    A function to estimate the signal-to-noise ratio of a pulsar signal (for a triaxial neutron
+    star emitting at twice the rotation frequency from the l=m=2 quadrupole mode) in a given
+    detector over a given time range, for a given one-sided power spectral density.
+
+    Inputs
+    ------
+        source - a dictionary containing 'h0', 'cosiota', 'psi', 'ra' (rads or string), 'dec' (rads or string)
+           det - the detector, e.g. 'H1'
+        tstart - a GPS start time
+      duration - a signal duration (seconds)
+            Sn - a one-sided power spectral density
+            dt - timestep for antenna response calculation [default: 1800s]
+
+    Returns
+    -------
+    rho        - an estimate of the optimal matched filter SNR
+    """
+
+    # if duration is greater than a sidereal day then just calculate the antenna pattern for 1 sidereal day plus the remainder
+    sidday = 86164.0905  # one sidereal day in seconds
+    Ndays = duration / sidday
+    Nsamps = np.floor(sidday / dt)  # number of time samples in 1 sidereal day
+    tend = tstart + duration
+
+    sFp = 0
+    sFc = 0
+
+    # get antenna pattern and sum over the square of it
+    if Ndays > 1:
+        tts = np.arange(tstart, tstart + sidday, dt)
+
+        # get antenna pattern over one sidereal day
+        Fp, Fc = antenna_response(tts, source["ra"], source["dec"], source["psi"], det)
+
+        sFp = np.floor(Ndays) * np.sum(Fp**2)
+        sFc = np.floor(Ndays) * np.sum(Fc**2)
+
+    # add on extra fractional part of a day
+    if np.floor(Ndays) * sidday > dt:
+        tts = np.arange(tstart + sidday * np.floor(Ndays), tend, dt)
+
+        Fp, Fc = antenna_response(tts, source["ra"], source["dec"], source["psi"], det)
+
+        sFp += np.sum(Fp**2)
+        sFc += np.sum(Fc**2)
+
+    # get snr squared
+    snr2 = (
+        (source["h0"] ** 2 / Sn)
+        * dt
+        * (
+            sFp * (0.5 * (1 + source["cosiota"] ** 2)) ** 2
+            + sFc * source["cosiota"] ** 2
+        )
+    )
+
+    return np.sqrt(snr2)
+
+
+def pulsar_estimate_h0_from_snr(snr, source, det, tstart, duration, Sn, dt=600):
+    """
+    A function to estimate the signal amplitude of a pulsar signal (for a triaxial neutron star emitting at twice
+    the rotation frequency from the l=m=2 quadrupole mode) for a given SNR in a particular detector over
+    a given time range, for a given one-sided power spectral density.
+
+    Inputs
+    ------
+           snr - the optimal matched filter signal-to-noise ratio
+        source - a dictionary containing 'cosiota', 'psi', 'ra' (rads or string), 'dec' (rads or string)
+           det - the detector, e.g. 'H1'
+        tstart - a GPS start time for the signal
+      duration - a signal duration (seconds)
+            Sn - a one-sided power spectral density
+            dt - timestep for antenna response calculation [default: 600s]
+
+    Returns
+    -------
+    h0         - an estimate of signal amplitude required to give the input SNR
+    """
+
+    # if duration is greater than a sidereal day then just calculate the antenna pattern for 1 sidereal day plus the remainder
+    sidday = 86164.0905  # one sidereal day in seconds
+    Ndays = duration / sidday
+    Nsamps = np.floor(sidday / dt)  # number of time samples in 1 sidereal day
+    tend = tstart + duration
+
+    sFp = 0
+    sFc = 0
+
+    # get antenna pattern and sum over the square of it
+    if Ndays > 1:
+        tts = np.arange(tstart, tstart + sidday, dt)
+
+        # get antenna pattern over one sidereal day
+        Fp, Fc = antenna_response(tts, source["ra"], source["dec"], source["psi"], det)
+
+        sFp = np.floor(Ndays) * np.sum(Fp**2)
+        sFc = np.floor(Ndays) * np.sum(Fc**2)
+
+    # add on extra fractional part of a day
+    if np.floor(Ndays) * sidday > dt:
+        tts = np.arange(tstart + sidday * np.floor(Ndays), tend, dt)
+
+        Fp, Fc = antenna_response(tts, source["ra"], source["dec"], source["psi"], det)
+
+        sFp += np.sum(Fp**2)
+        sFc += np.sum(Fc**2)
+
+    # get h0 squared
+    h02 = (snr**2 * Sn) / (
+        dt
+        * (
+            sFp * (0.5 * (1 + source["cosiota"] ** 2)) ** 2
+            + sFc * source["cosiota"] ** 2
+        )
+    )
+
+    return np.sqrt(h02)
+
+
+def pulsar_posterior_grid(
+    dets,
+    ts,
+    data,
+    ra,
+    dec,
+    sigmas=None,
+    paramranges={},
+    datachunks=30,
+    chunkmin=5,
+    ngrid=50,
+    outputlike=False,
+):
+    """
+    A function to calculate the 4-parameter posterior probability density for a continuous wave signal
+    given a set of processed data from a set of detectors.
+
+    Inputs
+    ------
+           dets - a list of strings containing the detectors being used in the likelihood calculation
+             ts - a dictionary of 1d numpy arrays containing the GPS times of the data for each detector
+           data - a dictionary of 1d numpy arrays containing the complex data values for each detector
+             ra - the right ascension (in rads) of the source
+            dec - the declination (in rads) of the source
+         sigmas - a dictionary of 1d numpy arrays containing the times series of standard deviation
+                  values for each detector. If this is not given a Student's t likelihood will be used,
+                  but if it is given a Gaussian likelihood will be used (default: None)
+    paramranges - a dictionary of tuples for each parameter ('h0', 'phi0', 'psi' and 'cosiota') giving
+                  the lower and upper ranges of the parameter grid and the number of grid points. If not
+                  given then defaults will be used.
+     datachunks - in the calculation split the data into stationary chunks with a maximum length given
+                  by this value. If set to 0 or inf then the data will not be split. (default: 30)
+       chunkmin - this is the shortest chunk length allowed to be included in the likelihood calculation
+                  (default: 5)
+          ngrid - the number of grid points to use for each dimension of the likelihood calculation. This
+                  is used if the values are not specified in the paramranges argument (default: 50)
+     outputlike - output the log likelihoods rather than posteriors (default: False)
+
+    Returns
+    -------
+    L           - The 4d posterior (or likelihood) over all parameters
+    h0pdf       - The 1d marginal posterior for h0
+    phi0pdf     - The 1d marginal posterior for phi0 (the rotation frequency, not GW frequency)
+    psipdf      - The 1d marginal posterior for psi
+    cosiotapdf  - The 1d marginal posterior for cosiota
+    lingrids    - A dictionary of the grid points for each parameter
+    sigev       - The log evidence for the signal model
+    noiseev     - The log evidence for the noise model
+
+    An example would be:
+    # set the detectors
+    dets = ['H1', 'L1']
+
+    # set the time series and data
+    ts = {}
+    data = {}
+    for det in dets:
+      ts[det] = np.arange(900000000., 921000843., 60.)
+      data[det] = np.random.randn(len(ts[det])) + 1j*np.random.randn(len(ts[det]))
+
+    # set the parameter ranges
+    ra = 0.2
+    dec = -0.8
+    paramranges = {}
+    paramranges['h0'] = (0., 2., 50)
+    paramranges['psi'] = (0., np.pi/2., 50)
+    paramranges['phi0'] = (0., np.pi, 50)
+    paramranges['cosiota'] = (-1., 1., 50)
+
+    L, h0pdf, phi0pdf, psipdf, cosiotapdf, grid, sigev, noiseev = pulsar_posterior_grid(dets, ts, data, ra, dec,
+                                                                                        paramranges=paramranges)
+    """
+
+    # import numpy
+    import numpy as np
+    import sys
+    from scipy.special import gammaln
+
+    # set the likelihood to either Student's or Gaussian
+    if sigmas == None:
+        liketype = "studentst"
+    else:
+        liketype = "gaussian"
+
+    # if dets is just a single string
+    if not isinstance(dets, list):
+        if isinstance(dets, str):
+            dets = [dets]  # make into list
+        else:
+            print("Detector not, or incorrectly, set", file=sys.stderr)
+            return
+
+    # allowed list of detectors
+    alloweddets = ["H1", "L1", "V1", "G1", "T1", "H2"]
+
+    # check consistency of arguments
+    for det in dets:
+        if det not in alloweddets:
+            print(
+                "Detector not in list of allowed detectors ("
+                + ",".join(alloweddets)
+                + ")",
+                file=sys.stderr,
+            )
+            return
+
+        # checks on time stamps
+        if det not in ts:
+            print("No time stamps given for detector %s" % det, file=sys.stderr)
+            return
+
+        # checks on data
+        if det not in data:
+            print("No data time series given for detector %s" % det, file=sys.stderr)
+            return
+
+        # checks on sigmas
+        if sigmas != None:
+            if det not in sigmas:
+                print(
+                    "No sigma time series given for detector %s" % det, file=sys.stderr
+                )
+                return
+
+        # check length consistency
+        if len(ts[det]) != len(data[det]):
+            print(
+                "Length of times stamps array and data array are inconsistent for %s"
+                % det,
+                file=sys.stderr,
+            )
+
+        if sigmas != None:
+            if len(ts[det]) != len(sigmas[det]):
+                print(
+                    "Length of times stamps array and sigma array are inconsistent for %s"
+                    % det,
+                    file=sys.stderr,
+                )
+
+    # setup grid on parameter space
+    params = ["h0", "phi0", "psi", "cosiota"]
+    defaultranges = {}  # default ranges for use if not specified
+    defaultranges["phi0"] = (0.0, np.pi, ngrid)  # 0 to pi for phi0
+    defaultranges["psi"] = (0.0, np.pi / 2.0, ngrid)  # 0 to pi/2 for psi
+    defaultranges["cosiota"] = (-1.0, 1.0, ngrid)  # -1 to 1 for cos(iota)
+    # 0 to 2 times the max standard deviation of the data (scaled to the data length)
+    defaultranges["h0"] = (
+        0.0,
+        2.0
+        * np.max([np.std(data[dv]) for dv in data])
+        * np.sqrt(1440.0 / np.max([len(ts[dtx]) for dtx in ts])),
+        ngrid,
+    )
+    lingrids = {}
+    shapetuple = ()
+    for param in params:
+        if param in paramranges:
+            if len(paramranges[param]) != 3:
+                paramranges[param] = defaultranges[param]  # set to default range
+            else:
+                if (
+                    paramranges[param][1] < paramranges[param][0]
+                    or paramranges[param][2] < 1
+                ):
+                    print(
+                        "Parameter ranges wrong for %s, reverting to defaults" % param,
+                        file=sys.stderr,
+                    )
+                    paramranges[param] = defaultranges[param]
+        else:  # use defaults
+            paramranges[param] = defaultranges[param]
+
+        lingrids[param] = np.linspace(
+            paramranges[param][0], paramranges[param][1], paramranges[param][2]
+        )
+        shapetuple += (paramranges[param][2],)
+
+    # set up meshgrid on parameter space
+    [H0S, PHI0S, PSIS, COSIS] = np.meshgrid(
+        lingrids["h0"],
+        lingrids["phi0"],
+        lingrids["psi"],
+        lingrids["cosiota"],
+        indexing="ij",
+    )
+
+    APLUS = 0.5 * (1.0 + COSIS**2)
+    ACROSS = COSIS
+    SINPHI = np.sin(2.0 * PHI0S)  # multiply phi0 by two to get GW frequency
+    COSPHI = np.cos(2.0 * PHI0S)
+    SIN2PSI = np.sin(2.0 * PSIS)
+    COS2PSI = np.cos(2.0 * PSIS)
+
+    Apsinphi_2 = 0.5 * APLUS * SINPHI
+    Acsinphi_2 = 0.5 * ACROSS * SINPHI
+    Apcosphi_2 = 0.5 * APLUS * COSPHI
+    Accosphi_2 = 0.5 * ACROSS * COSPHI
+    Acpsphicphi_2 = 0.5 * APLUS * ACROSS * COSPHI * SINPHI
+
+    AP2 = APLUS**2
+    AC2 = ACROSS**2
+    TWOAPACSPCP = 2.0 * APLUS * ACROSS * SINPHI * COSPHI
+    SP2 = SINPHI**2
+    CP2 = COSPHI**2
+
+    C2PS2P = COS2PSI * SIN2PSI
+    C2P2 = COS2PSI**2
+    S2P2 = SIN2PSI**2
+
+    H02 = H0S**2
+
+    # initialise loglikelihood
+    like = np.zeros(shapetuple)
+    noiselike = 0.0
+
+    # get flat prior
+    logprior = 0.0
+    for p in params:
+        logprior -= np.log(paramranges[p][1] - paramranges[p][0])
+
+    # loop over detectors and calculate the log likelihood
+    for det in dets:
+        if liketype == "gaussian":
+            nstd = sigmas[det]
+        else:
+            nstd = np.ones(len(ts[det]))
+
+        # get the antenna pattern
+        [As, Bs] = antenna_response(ts[det], ra, dec, 0.0, det)
+
+        # split the data into chunks if required
+        if np.isfinite(datachunks) and datachunks > 0:
+            chunklengths = get_chunk_lengths(ts[det], datachunks)
+        else:
+            chunklengths = [len(ts[det])]
+
+        startidx = 0
+        for cl in chunklengths:
+            endidx = startidx + cl
+
+            # check for shortest allowed chunks
+            if cl < chunkmin:
+                continue
+
+            thisdata = data[det][startidx:endidx] / nstd[startidx:endidx]
+            ast = As[startidx:endidx] / nstd[startidx:endidx]
+            bst = Bs[startidx:endidx] / nstd[startidx:endidx]
+
+            A = np.sum(ast**2)
+            B = np.sum(bst**2)
+            AB = np.dot(ast, bst)
+
+            dA1real = np.dot(thisdata.real, ast)
+            dA1imag = np.dot(thisdata.imag, ast)
+
+            dB1real = np.dot(thisdata.real, bst)
+            dB1imag = np.dot(thisdata.imag, bst)
+
+            dd1real = np.sum(thisdata.real**2)
+            dd1imag = np.sum(thisdata.imag**2)
+
+            P1 = A * C2P2 + B * S2P2 + 2.0 * AB * C2PS2P
+            P2 = B * C2P2 + A * S2P2 - 2.0 * AB * C2PS2P
+            P3 = AB * (C2P2 - S2P2) - A * C2PS2P + B * C2PS2P
+
+            hr2 = (Apcosphi_2**2) * P1 + (Acsinphi_2**2) * P2 + Acpsphicphi_2 * P3
+            hi2 = (Apsinphi_2**2) * P1 + (Accosphi_2**2) * P2 - Acpsphicphi_2 * P3
+
+            d1hr = Apcosphi_2 * (dA1real * COS2PSI + dB1real * SIN2PSI) + Acsinphi_2 * (
+                dB1real * COS2PSI - dA1real * SIN2PSI
+            )
+            d1hi = Apsinphi_2 * (dA1imag * COS2PSI + dB1imag * SIN2PSI) - Accosphi_2 * (
+                dB1imag * COS2PSI - dA1imag * SIN2PSI
+            )
+
+            chiSq = dd1real + dd1imag + H02 * (hr2 + hi2) - 2.0 * H0S * (d1hr + d1hi)
+
+            if liketype == "gaussian":
+                like -= 0.5 * (chiSq)
+                like -= (cl * np.log(2.0 * np.pi)) + 2.0 * np.sum(
+                    np.log(nstd[startidx:endidx])
+                )
+                noiselike -= 0.5 * (dd1real + dd1imag)
+                noiselike -= (cl * np.log(2.0 * np.pi)) + 2.0 * np.sum(
+                    np.log(nstd[startidx:endidx])
+                )
+            else:
+                like -= float(cl) * np.log(chiSq)
+                like += gammaln(cl) - np.log(2.0) - cl * np.log(np.pi)
+                noiselike -= float(cl) * np.log(dd1real + dd1imag)
+                noiselike += gammaln(cl) - np.log(2.0) - cl * np.log(np.pi)
+
+            startidx += cl  # updated start index
+
+    # convert to posterior
+    like += logprior
+
+    # get signal evidence
+    sigev = marginal(like, "all", params, lingrids)
+
+    # normalise posterior
+    if not outputlike:
+        like -= sigev
+    else:
+        like -= logprior  # remove prior if outputting likelihood
+
+    # get marginal posteriors for each parameter
+    posts = {}
+    for p in params:
+        if not outputlike:
+            posts[p] = np.exp(marginal(like, p, params, lingrids))
+        else:
+            posts[p] = marginal(
+                like, p, params, lingrids, multflatprior=True
+            )  # output individual log likelihoods
+
+    # odds ratio for signal versus noise
+    evrat = sigev - noiselike
+
+    return (
+        like,
+        posts["h0"],
+        posts["phi0"],
+        posts["psi"],
+        posts["cosiota"],
+        lingrids,
+        sigev,
+        noiselike,
+    )
+
+
+# current version of the ATNF pulsar catalogue
+ATNF_VERSION = "1.58"
+
+
+def get_atnf_info(psr):
+    """
+    Get the pulsar (psr) distance (DIST in kpc), proper motion corrected period derivative (P1_I) and any association
+    (ASSOC e.g. GC) from the ATNF catalogue.
+    """
+
+    import requests
+
+    psrname = re.sub(r"\+", "%2B", psr)  # switch '+' for unicode character
+
+    atnfurl = (
+        "http://www.atnf.csiro.au/people/pulsar/psrcat/proc_form.php?version="
+        + ATNF_VERSION
+    )
+    atnfurl += "&Dist=Dist&Assoc=Assoc&P1_i=P1_i"  # set parameters to get
+    atnfurl += (
+        "&startUserDefined=true&c1_val=&c2_val=&c3_val=&c4_val=&sort_attr=jname&sort_order=asc&condition=&pulsar_names="
+        + psrname
+    )
+    atnfurl += "&ephemeris=selected&submit_ephemeris=Get+Ephemeris&coords_unit=raj%2Fdecj&radius=&coords_1=&coords_2="
+    atnfurl += "&style=Long+with+last+digit+error&no_value=*&fsize=3&x_axis=&x_scale=linear&y_axis=&y_scale=linear&state=query"
+
+    try:
+        urldat = requests.get(atnfurl)  # read ATNF url
+        predat = re.search(
+            r"<pre[^>]*>([^<]+)</pre>", str(urldat.content)
+        )  # to extract data within pre environment (without using BeautifulSoup) see e.g. http://stackoverflow.com/a/3369000/1862861 and http://stackoverflow.com/a/20046030/1862861
+        pdat = (
+            predat.group(1).strip().split(r"\n")
+        )  # remove preceeding and trailing new lines and split lines
+    except:
+        print(
+            "Warning... could not get information from ATNF pulsar catalogue.",
+            file=sys.stderr,
+        )
+        return None
+
+    # check whether information could be found and get distance, age and association from data
+    dist = None
+    p1_I = None
+    assoc = None
+    for line in [p for p in pdat if len(p) != 0]:
+        if "WARNING" in line or "not in catalogue" in line:
+            return None
+        vals = line.split()
+        if "DIST" in vals[0]:
+            dist = float(vals[1])
+        if "P1_I" in vals[0]:
+            age = float(vals[1])
+        if "ASSOC" in vals[0]:
+            assoc = vals[1]
+
+    return (dist, p1_I, assoc, atnfurl)
+
+
+def cov_to_cor(cov):
+    """
+    Convert a covariance matrix to a correlation coefficient matrix.
+    Return the correlation coefficient matrix and the standard deviations
+    from the covariance matrix.
+    """
+
+    # get the standard deviations from the covariance matrix
+    sigmas = np.sqrt(np.diag(cov))
+
+    # convert these into a diagonal matrix
+    D = sigmas * np.identity(cov.shape[0])
+
+    # invert D
+    Dinv = np.linalg.inv(D)
+
+    # get correlation coefficient matrix
+    Ccor = np.dot(np.dot(Dinv, cov), Dinv)
+
+    return Ccor, sigmas