Fix how the joint MultivariateGaussian prior is set when reading it from a file

Currently, if trying to read in and use a MultivariateGaussian prior from a file it fails. For example, a regular file and JSON file of such a distribution could be created with:

import bilby

names = ["m", "c"]
mus = [[-5.0, -5.0], [5.0, 5.0]]  # means of the two modes
corrcoefs = [
    [[1.0, -0.7], [-0.7, 1.0]],
    [[1.0, 0.7], [0.7, 1.0]],
]  # correlation coefficients of the two modes
sigmas = [[1.5, 1.5], [2.1, 2.1]]  # standard deviations of the two modes
weights = [1.0, 3.0]  # relative weights of each mode
nmodes = 2
mvg = bilby.core.prior.MultivariateGaussianDist(
    names, nmodes=2, mus=mus, corrcoefs=corrcoefs, sigmas=sigmas, weights=weights
)
priors = bilby.core.prior.PriorDict()
priors["m"] = bilby.core.prior.MultivariateGaussian(mvg, "m")
priors["c"] = bilby.core.prior.MultivariateGaussian(mvg, "c")

# write out to file
priors.to_file(".", "mvgprior")

# write out to JSON file
priors.to_json(".", "mvgprior")

Now, if we try and read in the regular file:

from bilby.core.prior import PriorDict
p = PriorDict()
p.from_file("mvgprior.prior")

it gives a NameError: name 'MultivariateGaussianDist' is not defined. If we try and read in from the JSON file, it works, but if we draw samples form the prior we see that they are incorrect:

from matplotlib import pyplot as plt

p = PriorDict.from_json("mvgprior_prior.json")

samps = priors.sample(10000)  # original prior dict
plt.scatter(samps["m"], samps["c"], label="Original")

nsamps = p.sample(10000)  # read-in prior
plt.scatter(nsamps["m"], nsamps["c"], alpha=0.1, label="read-in")
plt.legend()

The reason for this problem is that within the MultivariateGaussian priors the dist attribute for each should point to the same object, but when read in from the JSON file it points to two different objects.

The MR fixes both the issue with not reading the regular file and the above one when reading from the JSON file.

added Bug Priors labels

Just to note, I ran black on dict.py and joint.py, so most changes are formatting changes from that. Within dict.py the actual relevant changes are lines 193 to 206 and 248 to 276.

added 1 commit

• dcc97f08 - dict_test.py: attempt to fix the test of writing and reading a JSON prior

Compare with previous version

changed milestone to %1.2.0

added 1 commit

• f0e6629c - dict_test.py: another attempt to fix the test

Compare with previous version

added 1 commit

• 1de40d47 - dict_test.py: fix test

Compare with previous version

added 1 commit

• 099e03cd - dict_test.py: add test to check that MultivariateGaussian point to same dist

Compare with previous version

@bruce.edelman you may want to check this as the other main person who has developed the JointPrior stuff.

changed the description

Thanks @matthew-pitkin just a few comments.

added 1 commit

• 03591c16 - dict.py: deepcopy dictionary

Compare with previous version

added 1 commit

• 123125ae - joint_test.py: add unit test for from_repr of a MultivariateGaussianDist

Compare with previous version

added 1 commit

• 300e0091 - dict.py: remove superfluous if statement

Compare with previous version

resolved all threads

approved this merge request

added 1 commit

• d98d6262 - dict.py: fix test failure due to deepcopy

Compare with previous version

approved this merge request

resolved all threads

approved this merge request

merged

mentioned in commit 7e832e0b

mentioned in epic cwinpy&1 (closed)

mentioned in issue cwinpy/cwinpy#86 (closed)