Merge branch 'nanograv:master' into ne_sw1

nanograv · Nov 22, 2024 · 0e5f3a4 · 0e5f3a4
2 parents 12ef298 + 96adf4b
commit 0e5f3a4
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diff --git a/CHANGELOG-unreleased.md b/CHANGELOG-unreleased.md
@@ -9,6 +9,7 @@ the released changes.
 
 ## Unreleased
 ### Changed
+- Command line scripts now automatically do `allow_tcb` and `allow_T2` while reading par files.
 - Updated the `plot_chains` function in `event_optimize` so that the subplots are a fixed size to prevent the subplots from being condensed in the case of many fit parameters.
 ### Added
 - Time derivatives of NE_SW in `SolarWindDispersion`

diff --git a/src/pint/__init__.py b/src/pint/__init__.py
@@ -105,6 +105,9 @@
     "hourangle_second": hourangle_second,
 }
 
+# define a units equivalency for gauss in cgs
+gauss_equiv = [u.Gauss, u.Hz * (u.g / u.cm) ** (1 / 2), lambda x: x, lambda x: x]
+
 import astropy.version
 
 if astropy.version.major < 4:

diff --git a/src/pint/derived_quantities.py b/src/pint/derived_quantities.py
@@ -136,6 +136,14 @@ def pferrs(
     return (forp, forperr, fdorpd, fdorpderr)
 
 
+def _to_gauss(B: u.Quantity) -> u.G:
+    """Convert quantity with mass, length, and time units to Gauss.
+
+    In cgs units, magnetic field is has units (mass/length)^(1/2) / time.
+    """
+    return B.to(u.Gauss, equivalencies=[pint.gauss_equiv])
+
+
 @u.quantity_input(f=u.Hz, fdot=u.Hz / u.s, fo=u.Hz)
 def pulsar_age(
     f: u.Quantity, fdot: u.Quantity, n: int = 3, fo: u.Quantity = 1e99 * u.Hz
@@ -219,19 +227,27 @@ def pulsar_edot(
     return (-4.0 * np.pi**2 * I * f * fdot).to(u.erg / u.s)
 
 
-@u.quantity_input(f=u.Hz, fdot=u.Hz / u.s)
-def pulsar_B(f: u.Quantity, fdot: u.Quantity) -> u.G:
+@u.quantity_input(f=u.Hz, fdot=u.Hz / u.s, I=u.g * u.cm**2, R=u.km)
+def pulsar_B(
+    f: u.Quantity,
+    fdot: u.Quantity,
+    I: u.Quantity = 1.0e45 * u.g * u.cm**2,
+    R: u.Quantity = 10 * u.km,
+) -> u.G:
     r"""Compute pulsar surface magnetic field
 
-    Return the estimated pulsar surface magnetic field strength
-    given the spin frequency and frequency derivative.
+    Return the pulsar surface magnetic field strength given the spin frequency `f` and frequency derivative `fdot`.
 
     Parameters
     ----------
     f : astropy.units.Quantity
         pulsar frequency
     fdot : astropy.units.Quantity
         frequency derivative :math:`\dot f`
+    I : astropy.units.Quantity, optional
+        pulsar moment of inertia, default of 1e45 g*cm**2
+    R : astropy.units.Quantity, optional
+        pulsar radius, default of 10 km
 
     Returns
     -------
@@ -247,15 +263,19 @@ def pulsar_B(f: u.Quantity, fdot: u.Quantity) -> u.G:
 
     Notes
     -----
-    Calculates :math:`B=3.2\times 10^{19}\,{\rm  G}\sqrt{ f \dot f^{-3}}`
+    Calculates :math:`B=\sqrt{\frac{3\,I\,c^3}{8\pi^2\,R^6}\times\frac{-\dot{f}}{f^3}}`
     """
-    # This is a hack to use the traditional formula by stripping the units.
-    # It would be nice to improve this to a  proper formula with units
-    return 3.2e19 * u.G * np.sqrt(-fdot.to_value(u.Hz / u.s) / f.to_value(u.Hz) ** 3.0)
+    factor = (3.0 * I * const.c**3) / (8.0 * np.pi**2 * R**6)
+    return _to_gauss((factor * (-fdot) / f**3) ** 0.5)
 
 
-@u.quantity_input(f=u.Hz, fdot=u.Hz / u.s)
-def pulsar_B_lightcyl(f: u.Quantity, fdot: u.Quantity) -> u.G:
+@u.quantity_input(f=u.Hz, fdot=u.Hz / u.s, I=u.g * u.cm**2, R=u.km)
+def pulsar_B_lightcyl(
+    f: u.Quantity,
+    fdot: u.Quantity,
+    I: u.Quantity = 1.0e45 * u.g * u.cm**2,
+    R=10 * u.km,
+) -> u.G:
     r"""Compute pulsar magnetic field at the light cylinder
 
     Return the estimated pulsar magnetic field strength at the
@@ -268,6 +288,10 @@ def pulsar_B_lightcyl(f: u.Quantity, fdot: u.Quantity) -> u.G:
         pulsar frequency
     fdot : astropy.units.Quantity
         frequency derivative :math:`\dot f`
+    I : astropy.units.Quantity, optional
+        pulsar moment of inertia, default of 1e45 g*cm**2
+    R : astropy.units.Quantity, optional
+        pulsar radius, default of 10 km
 
     Returns
     -------
@@ -283,17 +307,10 @@ def pulsar_B_lightcyl(f: u.Quantity, fdot: u.Quantity) -> u.G:
 
     Notes
     -----
-    Calculates :math:`B_{LC} = 2.9\times 10^8\,{\rm G} P^{-5/2} \dot P^{1/2}`
+    Calculates :math:`B_{LC} = \sqrt{\frac{-24\pi^4\,I}{c^3}\dot{f}f^3}`
     """
-    p, pd = p_to_f(f, fdot)
-    # This is a hack to use the traditional formula by stripping the units.
-    # It would be nice to improve this to a  proper formula with units
-    return (
-        2.9e8
-        * u.G
-        * p.to_value(u.s) ** (-5.0 / 2.0)
-        * np.sqrt(pd.to(u.dimensionless_unscaled).value)
-    )
+    factor = 24.0 * np.pi**4.0 * I / const.c**3.0
+    return _to_gauss((factor * (-fdot) * f**3.0) ** 0.5)
 
 
 @u.quantity_input(pb=u.d, x=u.cm)

diff --git a/src/pint/pintk/pulsar.py b/src/pint/pintk/pulsar.py
@@ -151,7 +151,9 @@ def __contains__(self, key):
         return key in self.prefit_model.params
 
     def reset_model(self):
-        self.prefit_model = pint.models.get_model(self.parfile)
+        self.prefit_model = pint.models.get_model(
+            self.parfile, allow_T2=True, allow_tcb=True
+        )
         self.add_model_params()
         self.postfit_model = None
         self.postfit_resids = None
@@ -172,7 +174,9 @@ def reset_TOAs(self):
         self.update_resids()
 
     def resetAll(self):
-        self.prefit_model = pint.models.get_model(self.parfile)
+        self.prefit_model = pint.models.get_model(
+            self.parfile, allow_T2=True, allow_tcb=True
+        )
         self.postfit_model = None
         self.postfit_resids = None
         self.fitted = False

diff --git a/src/pint/scripts/compare_parfiles.py b/src/pint/scripts/compare_parfiles.py
@@ -83,14 +83,25 @@ def main(argv=None):
     parser.add_argument(
         "-q", "--quiet", default=0, action="count", help="Decrease output verbosity"
     )
+    parser.add_argument(
+        "--allow_tcb",
+        action="store_true",
+        help="Convert TCB par files to TDB automatically",
+    )
+    parser.add_argument(
+        "--allow_T2",
+        action="store_true",
+        help="Guess the underlying binary model when T2 is given",
+    )
 
     args = parser.parse_args(argv)
     pint.logging.setup(
         level=pint.logging.get_level(args.loglevel, args.verbosity, args.quiet)
     )
 
-    m1 = get_model(args.input1)
-    m2 = get_model(args.input2)
+    m1 = get_model(args.input1, allow_T2=args.allow_T2, allow_tcb=args.allow_tcb)
+    m2 = get_model(args.input2, allow_T2=args.allow_T2, allow_tcb=args.allow_tcb)
+
     print(
         m1.compare(
             m2,

diff --git a/src/pint/scripts/convert_parfile.py b/src/pint/scripts/convert_parfile.py
@@ -73,6 +73,16 @@ def main(argv=None):
     parser.add_argument(
         "-q", "--quiet", default=0, action="count", help="Decrease output verbosity"
     )
+    parser.add_argument(
+        "--allow_tcb",
+        action="store_true",
+        help="Convert TCB par files to TDB automatically",
+    )
+    parser.add_argument(
+        "--allow_T2",
+        action="store_true",
+        help="Guess the underlying binary model when T2 is given",
+    )
 
     args = parser.parse_args(argv)
     pint.logging.setup(
@@ -83,7 +93,9 @@ def main(argv=None):
         return
 
     log.info(f"Reading '{args.input}'")
-    model = get_model(args.input)
+
+    model = get_model(args.input, allow_T2=args.allow_T2, allow_tcb=args.allow_tcb)
+
     if hasattr(model, "BINARY") and args.binary is not None:
         log.info(f"Converting from {model.BINARY.value} to {args.binary}")
         if args.binary == "ELL1H":

diff --git a/src/pint/scripts/event_optimize.py b/src/pint/scripts/event_optimize.py
@@ -706,6 +706,16 @@ def main(argv=None):
         action="store_true",
         dest="linearize_model",
     )
+    parser.add_argument(
+        "--allow_tcb",
+        action="store_true",
+        help="Convert TCB par files to TDB automatically",
+    )
+    parser.add_argument(
+        "--allow_T2",
+        action="store_true",
+        help="Guess the underlying binary model when T2 is given",
+    )
 
     args = parser.parse_args(argv)
     pint.logging.setup(
@@ -739,7 +749,9 @@ def main(argv=None):
     ncores = args.ncores
 
     # Read in initial model
-    modelin = pint.models.get_model(parfile)
+    modelin = pint.models.get_model(
+        parfile, allow_T2=args.allow_T2, allow_tcb=args.allow_tcb
+    )
 
     # File name setup and clobber file check
     filepath = args.filepath or os.getcwd()

diff --git a/src/pint/scripts/event_optimize_MCMCFitter.py b/src/pint/scripts/event_optimize_MCMCFitter.py
@@ -128,6 +128,17 @@ def main(argv=None):
         help="Logging level",
         dest="loglevel",
     )
+    parser.add_argument(
+        "--allow_tcb",
+        action="store_true",
+        help="Convert TCB par files to TDB automatically",
+    )
+    parser.add_argument(
+        "--allow_T2",
+        action="store_true",
+        help="Guess the underlying binary model when T2 is given",
+    )
+
     global nwalkers, nsteps, ftr
 
     args = parser.parse_args(argv)
@@ -164,7 +175,9 @@ def main(argv=None):
     wgtexp = args.wgtexp
 
     # Read in initial model
-    modelin = pint.models.get_model(parfile)
+    modelin = pint.models.get_model(
+        parfile, allow_T2=args.allow_T2, allow_tcb=args.allow_tcb
+    )
 
     # The custom_timing version below is to manually construct the TimingModel
     # class, which allows it to be pickled. This is needed for parallelizing

diff --git a/src/pint/scripts/event_optimize_multiple.py b/src/pint/scripts/event_optimize_multiple.py
@@ -228,6 +228,16 @@ def main(argv=None):
         help="Logging level",
         dest="loglevel",
     )
+    parser.add_argument(
+        "--allow_tcb",
+        action="store_true",
+        help="Convert TCB par files to TDB automatically",
+    )
+    parser.add_argument(
+        "--allow_T2",
+        action="store_true",
+        help="Guess the underlying binary model when T2 is given",
+    )
 
     global nwalkers, nsteps, ftr
 
@@ -261,7 +271,9 @@ def main(argv=None):
     wgtexp = args.wgtexp
 
     # Read in initial model
-    modelin = pint.models.get_model(parfile)
+    modelin = pint.models.get_model(
+        parfile, allow_T2=args.allow_T2, allow_tcb=args.allow_tcb
+    )
 
     # Set the target coords for automatic weighting if necessary
     if "ELONG" in modelin.params:

diff --git a/src/pint/scripts/fermiphase.py b/src/pint/scripts/fermiphase.py
@@ -77,6 +77,16 @@ def main(argv=None):
     parser.add_argument(
         "-q", "--quiet", default=0, action="count", help="Decrease output verbosity"
     )
+    parser.add_argument(
+        "--allow_tcb",
+        action="store_true",
+        help="Convert TCB par files to TDB automatically",
+    )
+    parser.add_argument(
+        "--allow_T2",
+        action="store_true",
+        help="Guess the underlying binary model when T2 is given",
+    )
 
     args = parser.parse_args(argv)
     pint.logging.setup(
@@ -88,7 +98,10 @@ def main(argv=None):
         args.addphase = True
 
     # Read in model
-    modelin = pint.models.get_model(args.parfile)
+    modelin = pint.models.get_model(
+        args.parfile, allow_T2=args.allow_T2, allow_tcb=args.allow_tcb
+    )
+
     if "ELONG" in modelin.params:
         tc = SkyCoord(
             modelin.ELONG.quantity,

diff --git a/src/pint/scripts/photonphase.py b/src/pint/scripts/photonphase.py
@@ -112,6 +112,16 @@ def main(argv=None):
     parser.add_argument(
         "-q", "--quiet", default=0, action="count", help="Decrease output verbosity"
     )
+    parser.add_argument(
+        "--allow_tcb",
+        action="store_true",
+        help="Convert TCB par files to TDB automatically",
+    )
+    parser.add_argument(
+        "--allow_T2",
+        action="store_true",
+        help="Guess the underlying binary model when T2 is given",
+    )
 
     args = parser.parse_args(argv)
     pint.logging.setup(
@@ -153,7 +163,10 @@ def main(argv=None):
                 "Please barycenter the event file using the official mission tools before processing with PINT"
             )
     # Read in model
-    modelin = pint.models.get_model(args.parfile)
+    modelin = pint.models.get_model(
+        args.parfile, allow_T2=args.allow_T2, allow_tcb=args.allow_tcb
+    )
+
     use_planets = False
     if "PLANET_SHAPIRO" in modelin.params:
         if modelin.PLANET_SHAPIRO.value:

diff --git a/src/pint/scripts/pintbary.py b/src/pint/scripts/pintbary.py
@@ -74,6 +74,16 @@ def main(argv=None):
     parser.add_argument(
         "-q", "--quiet", default=0, action="count", help="Decrease output verbosity"
     )
+    parser.add_argument(
+        "--allow_tcb",
+        action="store_true",
+        help="Convert TCB par files to TDB automatically",
+    )
+    parser.add_argument(
+        "--allow_T2",
+        action="store_true",
+        help="Guess the underlying binary model when T2 is given",
+    )
 
     args = parser.parse_args(argv)
     pint.logging.setup(
@@ -105,7 +115,9 @@ def main(argv=None):
     )
 
     if args.parfile is not None:
-        m = pint.models.get_model(args.parfile)
+        m = pint.models.get_model(
+            args.parfile, allow_T2=args.allow_T2, allow_tcb=args.allow_tcb
+        )
     else:
         # Construct model by hand
         m = pint.models.StandardTimingModel

diff --git a/src/pint/scripts/pintempo.py b/src/pint/scripts/pintempo.py
@@ -62,14 +62,26 @@ def main(argv=None):
     parser.add_argument(
         "-q", "--quiet", default=0, action="count", help="Decrease output verbosity"
     )
+    parser.add_argument(
+        "--allow_tcb",
+        action="store_true",
+        help="Convert TCB par files to TDB automatically",
+    )
+    parser.add_argument(
+        "--allow_T2",
+        action="store_true",
+        help="Guess the underlying binary model when T2 is given",
+    )
 
     args = parser.parse_args(argv)
     pint.logging.setup(
         level=pint.logging.get_level(args.loglevel, args.verbosity, args.quiet)
     )
 
     log.info("Reading model from {0}".format(args.parfile))
-    m = pint.models.get_model(args.parfile)
+    m = pint.models.get_model(
+        args.parfile, allow_T2=args.allow_T2, allow_tcb=args.allow_tcb
+    )
 
     log.warning(m.params)