The spectroscopic binary code now works! See Issue Starfish-develop#68.

gully · Jun 11, 2016 · 69884ca · 69884ca
1 parent 9592af8
commit 69884ca
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Showing 2 changed files with 10 additions and 9 deletions.
diff --git a/Starfish/model_bin.py b/Starfish/model_bin.py
@@ -21,7 +21,7 @@ class ThetaParam:
     :param grid: parameters corresponding to the dimensions of the grid.
     :type grid: 1D np.array
     '''
-    def __init__(self, grid, vz=0.0, vsini=0.0, logOmega=0.0, Av=0.0, teff2=6000.0, logOmega2=-0.5, grid2=[3100, 3.8, 0.0], vz2=0.0, vsini2=0.0, logOmega2=0.0):
+    def __init__(self, grid, vz=0.0, vsini=0.0, logOmega=0.0, Av=0.0, grid2=[3100, 3.8, 0.0], vz2=0.0, vsini2=0.0, logOmega2=0.0):
         self.grid = grid
         self.vz = vz
         self.vsini = vsini
@@ -76,7 +76,7 @@ def default(self, o):
                 "vz":o.vz,
                 "vsini":o.vsini,
                 "logOmega":o.logOmega,
-                "Av":o.Av
+                "Av":o.Av,
                 "grid2":o.grid2.tolist(),
                 "vz2":o.vz2,
                 "vsini2":o.vsini2,

diff --git a/scripts/star_binary.py b/scripts/star_binary.py
@@ -2,7 +2,7 @@
 
 # All of the argument parsing is done in the `parallel.py` module.
 
-import multiprocessing
+#import multiprocessing
 import time
 import numpy as np
 import Starfish
@@ -449,25 +449,26 @@ def lnprob_all(p):
 fname = Starfish.specfmt.format(model.spectrum_id, model.order) + "phi.json"
 phi0 = PhiParam.load(fname)
 
-ndim, nwalkers = 12, 40
+ndim, nwalkers = 18, 40
 
-p0 = np.array(start["grid"] + [start["vz"], start["vsini"], start["logOmega"]]
+p0 = np.array(start["grid"] + [start["vz"], start["vsini"], start["logOmega"]] +
               start["grid2"] + [start["vz2"], start["vsini2"], 
               start["logOmega2"]] + 
               phi0.cheb.tolist() + [phi0.sigAmp, phi0.logAmp, phi0.l])
 
-p0_std = [5, 0.02, 0.02, 0.5, 0.5, -0.01,
-          5, 0.02, 0.02, 0.5, 0.5, -0.01, 
-          -0.005, -0.005, -0.005, 0.01, 0.001, 0.5]
+p0_std = [5, 0.02, 0.02, 0.5, 0.5, 0.01,
+          5, 0.02, 0.02, 0.5, 0.5, 0.01, 
+          0.005, 0.005, 0.005, 0.01, 0.001, 0.5]
 
 if args.resume:
     p0_ball = np.load("emcee_chain.npy")[:,-1,:]
 else:
     p0_ball = emcee.utils.sample_ball(p0, p0_std, size=nwalkers)
 
-n_threads = multiprocessing.cpu_count()
+n_threads = 1#multiprocessing.cpu_count()
 sampler = emcee.EnsembleSampler(nwalkers, ndim, lnprob_all, threads=n_threads)
 
+test = lnprob_all(p0)
 
 nsteps = args.samples
 ninc = args.incremental_save