ValueError: operands could not be broadcast together with shapes (1,2) (20,100)

Question

I'm using emcee mcmc hammer in order to reconstruct a 1D Gaussian from 20 samples with random standard deviations. Here is the relevant part of my code:

def loglike(alpha,datapoints):
mu, sig = alpha
return nbabies*(np.log(1/(nsamples*np.sqrt(2*np.pi)*sig)))+np.sum(scipy.misc.logsumexp(-(datapoints-mu)**2/(2*sig**2),axis=1),axis=0)

import scipy.optimize as op
nll = lambda *args: -loglike(*args)
result = op.minimize(nll, [mupop, sigpop], args=(datapoints))
muml,sigml = result["x"]

def logprior(alpha):
   mu, sig = alpha
    if 0 < sig < 1 and 0.0 < mu < 1:
      return 0.0
return -np.inf

def logprob(alpha,datapoints):
   lp = logprior(alpha)
    if not np.isfinite(lp):
      return -np.inf
return lp + loglike(alpha,datapoints)

rendim = 2
renwalkers = 100
rensamples = 10000

p0 = [result["x"]+np.random.rand(rendim) for i in range(renwalkers)]

#now we run emcee!
momma2 = emcee.EnsembleSampler(renwalkers, rendim, logprob, args=(datapoints))
momma2.run_mcmc(p0, rensamples)
momma2samps = momma2.flatchain[0.2*renwalkers*rensamples:,]

But I keep getting the error message "ValueError: operands could not be broadcast together with shapes (1,2) (20,100)." What's the deal?

Answer 1

Your problem is that the line

result = op.minimize(nll, [mupop, sigpop], args=(datapoints))

should be

result = op.minimize(nll, [mupop, sigpop], args=(datapoints,))

minimize takes a tuple as args, and if you don't include the comma, it does not interpret the arguments correctly.