Htykuut

I am trying very simply to plot subplots generated by the PyMC3 traceplot function (see here) to a file.

The function generates a numpy.ndarray (2d) of subplots.

I need to move or copy these subplots into a matplotlib.figure in order to save the image file. Everything I can find shows how to generate the figure's subplots first, then build them out.

As a minimum example, I lifted the sample PyMC3 code from Here, and added to it just a few lines in an attempt to handle the subplots.

from pymc3 import *

import theano.tensor as tt

from theano import as_op

from numpy import arange, array, empty



### Added these three lines relative to source #######################

import matplotlib

matplotlib.use('Agg')

import matplotlib.pyplot as plt



__all__ = ['disasters_data', 'switchpoint', 'early_mean', 'late_mean', 'rate', 'disasters']



# Time series of recorded coal mining disasters in the UK from 1851 to 1962

disasters_data = array([4, 5, 4, 0, 1, 4, 3, 4, 0, 6, 3, 3, 4, 0, 2, 6,

                        3, 3, 5, 4, 5, 3, 1, 4, 4, 1, 5, 5, 3, 4, 2, 5,

                        2, 2, 3, 4, 2, 1, 3, 2, 2, 1, 1, 1, 1, 3, 0, 0,

                        1, 0, 1, 1, 0, 0, 3, 1, 0, 3, 2, 2, 0, 1, 1, 1,

                        0, 1, 0, 1, 0, 0, 0, 2, 1, 0, 0, 0, 1, 1, 0, 2,

                        3, 3, 1, 1, 2, 1, 1, 1, 1, 2, 4, 2, 0, 0, 1, 4,

                        0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 1])

years = len(disasters_data)



@as_op(itypes=[tt.lscalar, tt.dscalar, tt.dscalar], otypes=[tt.dvector])

def rateFunc(switchpoint, early_mean, late_mean):

    out = empty(years)

    out[:switchpoint] = early_mean

    out[switchpoint:] = late_mean

    return out





with Model() as model:



    # Prior for distribution of switchpoint location

    switchpoint = DiscreteUniform('switchpoint', lower=0, upper=years)

    # Priors for pre- and post-switch mean number of disasters

    early_mean = Exponential('early_mean', lam=1.)

    late_mean = Exponential('late_mean', lam=1.)



    # Allocate appropriate Poisson rates to years before and after current switchpoint location

    rate = rateFunc(switchpoint, early_mean, late_mean)



    # Data likelihood

    disasters = Poisson('disasters', rate, observed=disasters_data)



    # Initial values for stochastic nodes

    start = {'early_mean': 2., 'late_mean': 3.}



    # Use slice sampler for means

    step1 = Slice([early_mean, late_mean])

    # Use Metropolis for switchpoint, since it accomodates discrete variables

    step2 = Metropolis([switchpoint])



    # njobs>1 works only with most recent (mid August 2014) Thenao version:

    # https://github.com/Theano/Theano/pull/2021

    tr = sample(1000, tune=500, start=start, step=[step1, step2], njobs=1)



    ### gnashing of teeth starts here ################################

    fig, axarr = plt.subplots(3,2)



    # This gives a KeyError

    # axarr = traceplot(tr, axarr)



    # This finishes without error

    trarr = traceplot(tr)



    # doesn't work

    # axarr[0, 0] = trarr[0, 0]



    fig.savefig("disaster.png")

I've tried a few variations along the subplot() and add_subplot() lines, to no avail -- all errors point toward the fact that empty subplots must first be created for the figure, not assigned to pre-existing subplots.

A different example (see here, about 80% of the way down, beginning with

### Mysterious code to be explained in Chapter 3.

) avoids the utility altogether and builds out the subplots manually, so maybe there's no good answer to this? Is the pymc3.traceplot output indeed an orphaned ndarray of subplots that can't be used?

Can you print type(trarr[0,0]) and post the result?

First of all, matplotlib axes objects are part of a figure and can only live inside a figure. It is therefore not possible to simply take an axes and put it to a different figure. However, in your case it may be, that fig.add_axes(trarr[0,0]) nonetheless works. I doubt it, but you can still try.

Apart from that, traceplot() has a keyword argument called ax.

ax : axes
Matplotlib axes. Defaults to None.

Although it is pretty unclear, how you'd specify several subplots as one axes object, you can still try to play around with it. Try to put a single axes in or your own created subplots axes array axarr or only part of it.

Edit, just that noone oversees the small line in the comments:

According to the answer in the bug report, traceplot(tr, ax = axarr) is indeed reported to work just fine.

I ran into the same problem. I am working with pymc3 3.5 and matplotlib 2.1.2.

I realized it's possible to export the traceplot by:

trarr = traceplot(tr)



fig = plt.gcf() # to get the current figure...

fig.savefig("disaster.png") # and save it directly