Question about figure plot

[Robert Kern]

On 2015-12-15 02:43, Robert wrote:
> Hi,
>
> When I run the following code, there is no figure shown in the end.
>
>
> //////////
> import pymc
> import numpy as np
>
> n = 5*np.ones(4,dtype=int)
> x = np.array([-.86,-.3,-.05,.73])
>
> alpha = pymc.Normal('alpha',mu=0,tau=.01)
> beta = pymc.Normal('beta',mu=0,tau=.01)
>
> @pymc.deterministic
> def theta(a=alpha, b=beta):
>      """theta = logit^{-1}(a+b)"""
>      return pymc.invlogit(a+b*x)
>
> d = pymc.Binomial('d', n=n, p=theta, value=np.array([0.,1.,3.,5.]),\
>                      observed=True)
> ....
> import pymc
> import mymodel
>
> S = pymc.MCMC(mymodel, db='pickle')
> S.sample(iter=10000, burn=5000, thin=2)
> pymc.Matplot.plot(S)
>
>
>
> I find that the figures are shown after these two lines by myself:
> *************
> import matplotlib.pyplot as plt
> plt.show()
>
> I have searched around and have not found some explanation about it.
> The plot function here is different from Matlab's. Is there better ways than
> my last two lines? (I am not confident whether my last two lines is the
> only choice.

No, that's right. pymc.Matplot.plot() uses matplotlib's pyplot API underneath. 
pyplot can run in two different modes: interactive and non-interactive. When 
used in a standalone script, like I assume here, it defaults to non-interactive. 
That means that it will not raise any plot windows until you call plt.show().

   http://matplotlib.org/faq/usage_faq.html#what-is-interactive-mode

See any of the examples here (note: "pylab" is the essentially the same as 
"pyplot" for these purposes):

   http://matplotlib.org/examples/pylab_examples/index.html

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
  that is made terrible by our own mad attempt to interpret it as though it had
  an underlying truth."
   -- Umberto Eco