merge resolutions

thejoker/__init__.py

@@ -31,6 +31,10 @@
     "phase_coverage_per_period",
 ]
 
+    # SB2:
+    from .thejoker_sb2 import *
+    from .prior_sb2 import JokerSB2Prior
+
 
 __bibtex__ = __citation__ = """@ARTICLE{thejoker,
        author = {{Price-Whelan}, Adrian M. and {Hogg}, David W. and
@@ -55,3 +59,12 @@
       adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
 """
+
+__all__ = [
+    'TheJoker',
+    'RVData',
+    'JokerSamples',
+    'JokerPrior',
+    'plot_rv_curves',
+    'TheJokerSB2'
+]

thejoker/data.py

@@ -33,11 +33,13 @@ class RVData:
         (days). Set to ``False`` to disable subtracting the reference time.
     clean : bool (optional)
         Filter out any NaN or Inf data points.
+    sort : bool (optional)
+        Whether or not to sort on time.
 
     """
 
     @u.quantity_input(rv=u.km / u.s, rv_err=[u.km / u.s, (u.km / u.s) ** 2])
-    def __init__(self, t, rv, rv_err, t_ref=None, clean=True):
+    def __init__(self, t, rv, rv_err, t_ref=None, clean=True, sort=True):
         # For speed, time is saved internally as BMJD:
         if isinstance(t, Time):
             _t_bmjd = t.tcb.mjd
@@ -94,15 +96,16 @@ def __init__(self, t, rv, rv_err, t_ref=None, clean=True):
             else:
                 self.rv_err = self.rv_err[idx]
 
-        # sort on times
-        idx = self._t_bmjd.argsort()
-        self._t_bmjd = self._t_bmjd[idx]
-        self.rv = self.rv[idx]
-        if self._has_cov:
-            self.rv_err = self.rv_err[idx]
-            self.rv_err = self.rv_err[:, idx]
-        else:
-            self.rv_err = self.rv_err[idx]
+        if sort:
+            # sort on times
+            idx = self._t_bmjd.argsort()
+            self._t_bmjd = self._t_bmjd[idx]
+            self.rv = self.rv[idx]
+            if self._has_cov:
+                self.rv_err = self.rv_err[idx]
+                self.rv_err = self.rv_err[:, idx]
+            else:
+                self.rv_err = self.rv_err[idx]
 
         if t_ref is False:
             self.t_ref = None

thejoker/likelihood_helpers.py

@@ -66,8 +66,13 @@ def marginal_ln_likelihood_inmem(joker_helper, prior_samples_batch):
     return np.array(ll)
 
 
-def make_full_samples_inmem(joker_helper, prior_samples_batch, rng, n_linear_samples=1):
-    from .samples import JokerSamples
+def make_full_samples_inmem(
+    joker_helper, prior_samples_batch, rng, n_linear_samples=1, SamplesCls=None
+):
+    if SamplesCls is None:
+        from .samples import JokerSamples
+
+        SamplesCls = JokerSamples
 
     if prior_samples_batch.dtype != np.float64:
         prior_samples_batch = prior_samples_batch.astype(np.float64)
@@ -77,7 +82,7 @@ def make_full_samples_inmem(joker_helper, prior_samples_batch, rng, n_linear_sam
     )
 
     # unpack the raw samples
-    samples = JokerSamples.unpack(
+    samples = SamplesCls.unpack(
         raw_samples,
         joker_helper.internal_units,
         t_ref=joker_helper.data.t_ref,
@@ -96,6 +101,7 @@ def rejection_sample_inmem(
     max_posterior_samples=None,
     n_linear_samples=1,
     return_all_logprobs=False,
+    SamplesCls=None,
 ):
     if max_posterior_samples is None:
         max_posterior_samples = len(prior_samples_batch)
@@ -114,6 +120,7 @@ def rejection_sample_inmem(
         prior_samples_batch[good_samples_idx],
         rng,
         n_linear_samples=n_linear_samples,
+        SamplesCls=SamplesCls,
     )
 
     if ln_prior is not None and ln_prior is not False:
@@ -136,6 +143,7 @@ def iterative_rejection_inmem(
     init_batch_size=None,
     growth_factor=128,
     n_linear_samples=1,
+    SamplesCls=None,
 ):
     n_total_samples = len(prior_samples_batch)
 
@@ -219,6 +227,7 @@ def iterative_rejection_inmem(
         prior_samples_batch[full_samples_idx],
         rng,
         n_linear_samples=n_linear_samples,
+        SamplesCls=SamplesCls,
     )
 
     # FIXME: copy-pasted from function above

thejoker/multiproc_helpers.py

@@ -155,6 +155,7 @@ def make_full_samples(
     samples_idx,
     n_linear_samples=1,
     n_batches=None,
+    SamplesCls=JokerSamples,
 ):
     task_args = (prior_samples_file, joker_helper, n_linear_samples)
     results = run_worker(
@@ -164,14 +165,14 @@ def make_full_samples(
         task_args=task_args,
         n_batches=n_batches,
         samples_idx=samples_idx,
-        rng=rng,
+        random_state=rng,
     )
 
     # Concatenate all of the raw samples arrays
     raw_samples = np.concatenate(results)
 
     # unpack the raw samples
-    samples = JokerSamples.unpack(
+    samples = SamplesCls.unpack(
         raw_samples,
         joker_helper.internal_units,
         t_ref=joker_helper.data.t_ref,
@@ -195,6 +196,7 @@ def rejection_sample_helper(
     n_batches=None,
     randomize_prior_order=False,
     return_all_logprobs=False,
+    SamplesCls=None,
 ):
     # Total number of samples in the cache:
     with tb.open_file(prior_samples_file, mode="r") as f:
@@ -271,6 +273,7 @@ def rejection_sample_helper(
         full_samples_idx,
         n_linear_samples=n_linear_samples,
         n_batches=n_batches,
+        SamplesCls=SamplesCls,
     )
 
     if return_logprobs:
@@ -300,6 +303,7 @@ def iterative_rejection_helper(
     return_logprobs=False,
     n_batches=None,
     randomize_prior_order=False,
+    SamplesCls=None,
 ):
     # Total number of samples in the cache:
     with tb.open_file(prior_samples_file, mode="r") as f:
@@ -412,6 +416,7 @@ def iterative_rejection_helper(
         full_samples_idx,
         n_linear_samples=n_linear_samples,
         n_batches=n_batches,
+        SamplesCls=SamplesCls,
     )
 
     # FIXME: copy-pasted from function above

thejoker/prior.py

@@ -38,6 +38,8 @@ def _validate_model(model):
 
 
 class JokerPrior:
+    _sb2 = False
+
     def __init__(self, pars=None, poly_trend=1, v0_offsets=None, model=None):
         """
         This class controls the prior probability distributions for the
@@ -121,7 +123,9 @@ def __init__(self, pars=None, poly_trend=1, v0_offsets=None, model=None):
         # are only used to validate that the units for each parameter are
         # equivalent to these
         self._nonlinear_equiv_units = get_nonlinear_equiv_units()
-        self._linear_equiv_units = get_linear_equiv_units(self.poly_trend)
+        self._linear_equiv_units = get_linear_equiv_units(
+            self.poly_trend, sb2=self._sb2
+        )
         self._v0_offsets_equiv_units = get_v0_offsets_equiv_units(self.n_offsets)
         self._all_par_unit_equiv = {
             **self._nonlinear_equiv_units,
@@ -291,10 +295,7 @@ def __repr__(self):
     def __str__(self):
         return ", ".join(self.par_names)
 
-    @deprecated_renamed_argument(
-        "random_state", "rng", since="v1.3", warning_type=DeprecationWarning
-    )
-    def sample(
+    def _get_raw_samples(
         self,
         size=1,
         generate_linear=False,
@@ -303,29 +304,6 @@ def sample(
         dtype=None,
         **kwargs,
     ):
-        """
-        Generate random samples from the prior.
-
-        Parameters
-        ----------
-        size : int (optional)
-            The number of samples to generate.
-        generate_linear : bool (optional)
-            Also generate samples in the linear parameters.
-        return_logprobs : bool (optional)
-            Generate the log-prior probability at the position of each sample.
-        **kwargs
-            Additional keyword arguments are passed to the
-            `~thejoker.JokerSamples` initializer.
-
-        Returns
-        -------
-        samples : `thejoker.Jokersamples`
-            The random samples.
-
-        """
-        from .samples import JokerSamples
-
         if dtype is None:
             dtype = np.float64
 
@@ -339,11 +317,6 @@ def sample(
             )
         }
 
-        if generate_linear:
-            par_names = self.par_names
-        else:
-            par_names = list(self._nonlinear_equiv_units.keys())
-
         # MAJOR HACK RELATED TO UPSTREAM ISSUES WITH pymc3:
         # init_shapes = {}
         # for name, par in sub_pars.items():
@@ -374,12 +347,68 @@ def sample(
 
                 logp.append(_logp)
             log_prior = np.sum(logp, axis=0)
+        else:
+            log_prior = None
 
         # CONTINUED MAJOR HACK RELATED TO UPSTREAM ISSUES WITH pymc3:
         # for name, par in sub_pars.items():
         #     if hasattr(par, "distribution"):
         #         par.distribution.shape = init_shapes[name]
 
+        return raw_samples, sub_pars, log_prior
+
+    @deprecated_renamed_argument(
+        "random_state", "rng", since="v1.3", warning_type=DeprecationWarning
+    )
+    def sample(
+        self,
+        size=1,
+        generate_linear=False,
+        return_logprobs=False,
+        rng=None,
+        dtype=None,
+        **kwargs,
+    ):
+        """
+        Generate random samples from the prior.
+
+        .. note::
+
+            Right now, generating samples with the prior values is slow (i.e.
+            with ``return_logprobs=True``) because of pymc3 issues (see
+            discussion here:
+            https://discourse.pymc.io/t/draw-values-speed-scaling-with-transformed-variables/4076).
+            This will hopefully be resolved in the future...
+
+        Parameters
+        ----------
+        size : int (optional)
+            The number of samples to generate.
+        generate_linear : bool (optional)
+            Also generate samples in the linear parameters.
+        return_logprobs : bool (optional)
+            Generate the log-prior probability at the position of each sample.
+        **kwargs
+            Additional keyword arguments are passed to the
+            `~thejoker.JokerSamples` initializer.
+
+        Returns
+        -------
+        samples : `thejoker.Jokersamples`
+            The random samples.
+
+        """
+        from thejoker.samples import JokerSamples
+
+        raw_samples, sub_pars, log_prior = self._get_raw_samples(
+            size, generate_linear, return_logprobs, rng, dtype, **kwargs
+        )
+
+        if generate_linear:
+            par_names = self.par_names
+        else:
+            par_names = list(self._nonlinear_equiv_units.keys())
+
         # Apply units if they are specified:
         prior_samples = JokerSamples(
             poly_trend=self.poly_trend, n_offsets=self.n_offsets, **kwargs
@@ -448,9 +477,8 @@ def default_nonlinear_prior(P_min=None, P_max=None, s=None, model=None, pars=Non
 
     if isinstance(s, pt.TensorVariable):
         pars["s"] = pars.get("s", s)
-    else:
-        if not hasattr(s, "unit") or not s.unit.is_equivalent(u.km / u.s):
-            raise u.UnitsError("Invalid unit for s: must be equivalent to km/s")
+    elif not hasattr(s, "unit") or not s.unit.is_equivalent(u.km / u.s):
+        raise u.UnitsError("Invalid unit for s: must be equivalent to km/s")
 
     # dictionary of parameters to return
     out_pars = {}

thejoker/prior_helpers.py

@@ -31,12 +31,19 @@ def validate_poly_trend(poly_trend):
     return poly_trend, vtrend_names
 
 
-def get_linear_equiv_units(poly_trend):
+def get_linear_equiv_units(poly_trend, sb2=False):
     poly_trend, v_names = validate_poly_trend(poly_trend)
-    return {
-        'K': u.m/u.s,
-        **{name: u.m/u.s/u.day**i for i, name in enumerate(v_names)}
-    }
+    if sb2:
+        return {
+            'K1': u.m/u.s,
+            'K2': u.m/u.s,
+            **{name: u.m/u.s/u.day**i for i, name in enumerate(v_names)}
+        }
+    else:
+        return {
+            'K': u.m/u.s,
+            **{name: u.m/u.s/u.day**i for i, name in enumerate(v_names)}
+        }
 
 
 def validate_sigma_v(sigma_v, poly_trend, v_names):