fix nbody indexing error & add unit test

docs/index.rst

@@ -58,6 +58,7 @@ Changelog:
 
 - discuss MCMC autocorrelation in MCMC tutorial (@michaelkmpoon)
 - add time warning if OFTI doesn't accept an orbit in first 60 s (@michaelkmpoon)
+- bugfix for rebound MCMC fits (issue #357; @sblunt)
 - implementation of Hipparcos-Gaia catalog of accelerations fitting! (@semaphoreP)
 - implementation of residual plotting method for orbit plots (@Saanikachoudhary and @semaphoreP)
 

orbitize/nbody.py

@@ -2,118 +2,142 @@
 import orbitize.basis as basis
 import rebound
 
+
 def calc_orbit(
-    epochs, sma, ecc, inc, aop, pan, tau, plx, mtot, tau_ref_epoch=58849, 
-    m_pl=None, output_star=False
+    epochs,
+    sma,
+    ecc,
+    inc,
+    aop,
+    pan,
+    tau,
+    plx,
+    mtot,
+    tau_ref_epoch=58849,
+    m_pl=None,
+    output_star=False,
+    integrator="ias15",
 ):
     """
     Solves for position for a set of input orbital elements using rebound.
 
     Args:
         epochs (np.array): MJD times for which we want the positions of the planet
-        sma (np.array): semi-major axis of orbit [au]
-        ecc (np.array): eccentricity of the orbit [0,1]
-        inc (np.array): inclination [radians]
-        aop (np.array): argument of periastron [radians]
-        pan (np.array): longitude of the ascending node [radians]
-        tau (np.array): epoch of periastron passage in fraction of orbital period 
-            past MJD=0 [0,1]
-        plx (np.array): parallax [mas]
-        mtot (np.array): total mass of the two-body orbit (M_* + M_planet) 
+        sma (np.array): semi-major axis array of secondary bodies. For three planets,
+            this should look like: np.array([sma1, sma2, sma3]) [au]
+        ecc (np.array): eccentricity of the orbits (same format as sma) [0,1]
+        inc (np.array): inclinations (same format as sma) [radians]
+        aop (np.array): arguments of periastron (same format as sma) [radians]
+        pan (np.array): longitudes of the ascending node (same format as sma) [radians]
+        tau (np.array): epochs of periastron passage in fraction of orbital period
+            past MJD=0 (same format as sma) [0,1]
+        plx (float): parallax [mas]
+        mtot (float): total mass of the two-body orbit (M_* + M_planet)
             [Solar masses]
         tau_ref_epoch (float, optional): reference date that tau is defined with
             respect to
-        m_pl (np.array, optional): mass of the planets[units]
+        m_pl (np.array, optional): masss of the planets (same format as sma) [solar masses]
         output_star (bool): if True, also return the position of the star
             relative to the barycenter.
+        integrator (str): value to set for rebound.sim.integrator. Default "ias15"
 
     Returns:
         3-tuple:
 
-            raoff (np.array): array-like (n_dates x n_orbs) of RA offsets between 
+            raoff (np.array): array-like (n_dates x n_bodies x n_orbs) of RA offsets between
                 the bodies (origin is at the other body) [mas]
 
-            deoff (np.array): array-like (n_dates x n_orbs) of Dec offsets between 
+            deoff (np.array): array-like (n_dates x n_bodies x n_orbs) of Dec offsets between
                 the bodies [mas]
-                
-            vz (np.array): array-like (n_dates x n_orbs) of radial velocity of 
-                one of the bodies (see `mass_for_Kamp` description)  [km/s]
 
-    .. Note:: 
-    
-        return is in format [raoff[planet1, planet2,...,planetn], 
-        deoff[planet1, planet2,...,planetn], vz[planet1, planet2,...,planetn]
+            vz (np.array): array-like (n_dates x n_bodies x n_orbs) of radial velocity of
+                one of the bodies (see `mass_for_Kamp` description)  [km/s]
     """
-
-    sim = rebound.Simulation()      #creating the simulation in Rebound
-    sim.units = ('AU','yr','Msun')  #converting units for uniformity
-    sim.G = 39.476926408897626      #Using a more accurate value in order to minimize differences from prev. Kepler solver
-    ps = sim.particles              #for easier calls
 
-    tx = len(epochs)                #keeping track of how many time steps
-    te = epochs-epochs[0]           #days
+    sim = rebound.Simulation()  # creating the simulation in Rebound
+    sim.units = ("AU", "yr", "Msun")  # converting units for uniformity
+    sim.G = 39.476926408897626  # Using a more accurate value in order to minimize differences from prev. Kepler solver
+    ps = sim.particles  # for easier calls
+
+    tx = len(epochs)  # keeping track of how many time steps
+    te = epochs - epochs[0]  # days
 
-    indv = len(sma)                 #number of planets orbiting the star
-    num_planets = np.arange(0,indv) #creates an array of indeces for each planet that exists
+    indv = len(sma)  # number of planets orbiting the star
+    num_planets = np.arange(
+        0, indv
+    )  # creates an array of indeces for each planet that exists
 
-    if m_pl is None:                #if no planet masses are input, planet masses set ot zero and mass of star is equal to mtot
-        sim.add(m = mtot)
+    if (
+        m_pl is None
+    ):  # if no planet masses are input, planet masses set ot zero and mass of star is equal to mtot
+        sim.add(m=mtot)
         m_pl = np.zeros(len(sma))
         m_star = mtot
-    else:                           #mass of star is always (mass of system)-(sum of planet masses) 
+    else:  # mass of star is always (mass of system)-(sum of planet masses)
         m_star = mtot - sum(m_pl)
-        sim.add(m = m_star)
+        sim.add(m=m_star)
 
-    #for each planet, create a body in the Rebound sim
+    # for each planet, create a body in the Rebound sim
     for i in num_planets:
-        #calculating mean anomaly
-        m_interior = m_star + sum(m_pl[0:i+1])
-        mnm = basis.tau_to_manom(epochs[0], sma[i], m_interior, tau[i], tau_ref_epoch) 
-        #adding each planet
-        sim.add(m = m_pl[i], a = sma[i], e = ecc[i], inc = inc[i], Omega = pan[i] + np.pi/2, omega =aop[i], M =mnm)
+        # calculating mean anomaly
+        m_interior = m_star + sum(m_pl[0 : i + 1])
+        mnm = basis.tau_to_manom(epochs[0], sma[i], m_interior, tau[i], tau_ref_epoch)
+        # adding each planet
+        sim.add(
+            m=m_pl[i],
+            a=sma[i],
+            e=ecc[i],
+            inc=inc[i],
+            Omega=pan[i] + np.pi / 2,
+            omega=aop[i],
+            M=mnm,
+        )
 
     sim.move_to_com()
-    sim.integrator = "ias15" 
-    sim.dt = ps[1].P/100.       #good rule of thumb: timestep should be at most 10% of the shortest orbital period
+    sim.integrator = integrator
+    sim.dt = (
+        ps[1].P / 100.0
+    )  # good rule of thumb: timestep should be at most 10% of the shortest orbital period
 
     if output_star:
-        ra_reb = np.zeros((tx, indv+1))   #numpy.zeros(number of [arrays], size of each array)
-        dec_reb = np.zeros((tx, indv+1))
-        vz = np.zeros((tx, indv+1))
-        for j,t in enumerate(te):
-            sim.integrate(t/365.25)
-            #for the star and each planet in each epoch denoted by j,t find the RA, Dec, and RV
+        ra_reb = np.zeros(
+            (tx, indv + 1)
+        )  # numpy.zeros(number of [arrays], size of each array)
+        dec_reb = np.zeros((tx, indv + 1))
+        vz = np.zeros((tx, indv + 1))
+        for j, t in enumerate(te):
+            sim.integrate(t / 365.25)
+            # for the star and each planet in each epoch denoted by j,t find the RA, Dec, and RV
             com = sim.com()
-            ra_reb[j,0] = -(ps[0].x-com.x)# ra is negative x
-            dec_reb[j,0] = ps[0].y-com.y
-            vz[j,0] = ps[0].vz
+            ra_reb[j, 0] = -(ps[0].x - com.x)  # ra is negative x
+            dec_reb[j, 0] = ps[0].y - com.y
+            vz[j, 0] = ps[0].vz
             for i in num_planets:
-                ra_reb[j,i+1] = -(ps[int(i+1)].x - ps[0].x) # ra is negative x
-                dec_reb[j,i+1] = ps[int(i+1)].y - ps[0].y
-                vz[j,i+1] = ps[int(i+1)].vz
+                ra_reb[j, i + 1] = -(ps[int(i + 1)].x - ps[0].x)  # ra is negative x
+                dec_reb[j, i + 1] = ps[int(i + 1)].y - ps[0].y
+                vz[j, i + 1] = ps[int(i + 1)].vz
     else:
-        ra_reb = np.zeros((tx, indv))   #numpy.zeros(number of [arrays], size of each array)
+        ra_reb = np.zeros(
+            (tx, indv)
+        )  # numpy.zeros(number of [arrays], size of each array)
         dec_reb = np.zeros((tx, indv))
         vz = np.zeros((tx, indv))
-        #integrate at each epoch
-        for j,t in enumerate(te):
-            sim.integrate(t/365.25)
-            #for each planet in each epoch denoted by j,t find the RA, Dec, and RV
+        # integrate at each epoch
+        for j, t in enumerate(te):
+            sim.integrate(t / 365.25)
+            # for each planet in each epoch denoted by j,t find the RA, Dec, and RV
             for i in num_planets:
-                ra_reb[j,i] = -(ps[int(i+1)].x - ps[0].x) # ra is negative x
-                dec_reb[j,i] = ps[int(i+1)].y - ps[0].y
-                vz[j,i] = ps[int(i+1)].vz
-
-
-    #adjusting for parallax
-    raoff = plx*ra_reb
-    deoff = plx*dec_reb
-
-    #for formatting purposes
-    if len(sma)==1:
-        raoff = raoff.reshape(tx,)
-        deoff = deoff.reshape(tx,)
-        vz = vz.reshape(tx,)
-        return raoff, deoff, vz
-    else: 
-        return raoff, deoff, vz
+                ra_reb[j, i] = -(ps[int(i + 1)].x - ps[0].x)  # ra is negative x
+                dec_reb[j, i] = ps[int(i + 1)].y - ps[0].y
+                vz[j, i] = ps[int(i + 1)].vz
+
+    # adjusting for parallax
+    raoff = plx * ra_reb
+    deoff = plx * dec_reb
+
+    # always assume we're using MCMC (i.e. n_orbits = 1)
+    raoff = raoff.reshape((tx, indv + 1, 1))
+    deoff = deoff.reshape((tx, indv + 1, 1))
+    vz = vz.reshape((tx, indv + 1, 1))
+
+    return raoff, deoff, vz

tests/test_rebound.py

@@ -1,5 +1,6 @@
 from matplotlib import pyplot as plt
 from astropy.time import Time
+from orbitize import sampler
 from orbitize.system import System
 from orbitize import DATADIR
 from orbitize.read_input import read_file
@@ -125,8 +126,8 @@ def test_8799_rebound_vs_kepler(plotname=None):
         params_arr, epochs=epochs, comp_rebound=False
     )
 
-    delta_ra = abs(rra - kra[:, :, 0])
-    delta_de = abs(rde - kde[:, :, 0])
+    delta_ra = abs(rra - kra)
+    delta_de = abs(rde - kde)
     yepochs = Time(epochs, format="mjd").decimalyear
 
     # check that the difference between these two solvers is smaller than
@@ -179,8 +180,8 @@ def test_8799_rebound_vs_kepler(plotname=None):
         plt.plot(kra[:, 1:5, 0], kde[:, 1:5, 0], "indigo", label="Orbitize approx.")
         plt.plot(kra[-1, 1:5, 0], kde[-1, 1:5, 0], "o")
 
-        plt.plot(rra, rde, "r", label="Rebound", alpha=0.25)
-        plt.plot(rra[-1], rde[-1], "o", alpha=0.25)
+        plt.plot(rra[:, 1:5, 0], rde[:, 1:5, 0], "r", label="Rebound", alpha=0.25)
+        plt.plot(rra[-1, 1:5, 0], rde[-1, 1:5, 0], "o", alpha=0.25)
 
         plt.plot(0, 0, "*")
         plt.legend()
@@ -199,5 +200,29 @@ def test_8799_rebound_vs_kepler(plotname=None):
         plt.savefig("{}_primaryorbittrack.png".format(plotname), dpi=250)
 
 
+def test_rebound_mcmc():
+    """
+    Test that a rebound fit runs through one MCMC iteration successfully.
+    """
+
+    input_file = "{}/GJ504.csv".format(DATADIR)
+    data_table = read_file(input_file)
+
+    my_sys = System(
+        num_secondary_bodies=1,
+        use_rebound=True,
+        fit_secondary_mass=True,
+        data_table=data_table,
+        stellar_or_system_mass=1.22,
+        mass_err=0,
+        plx=56.95,
+        plx_err=0.0,
+    )
+
+    my_mcmc_samp = sampler.MCMC(my_sys, num_temps=1, num_walkers=14, num_threads=1)
+    my_mcmc_samp.run_sampler(1, burn_steps=0)
+
+
 if __name__ == "__main__":
-    test_8799_rebound_vs_kepler(plotname="hr8799_diffs")
+    # test_8799_rebound_vs_kepler(plotname="hr8799_diffs")
+    test_rebound_mcmc()