Am 16.01.20 um 11:11 schrieb Davide Cittaro:
Hi again, This is more a python related question, but I'm asking here hoping somebody had a similar issue and worked it out. I need to collect vertex marginals during equilibrate and when I do it in my python console everything works just fine (as in the cookbook):
pv = [None] * len(state.get_levels())
def collect_marginals(s): global pv pv = [sl.collect_vertex_marginals(pv[l]) for l, sl in enumerate(s.get_levels())]
gt.mcmc_equilibrate(state, force_niter=10000, mcmc_args=dict(niter=10), callback=collect_marginals)
as far as understand, every time sl.collect_vertex_marginals is called, it takes as argument the histogram calculated in the previous iterations. My problem is that when I put this code into a function that is imported as a module, scoping is broken and I get an error like
NameError: name 'pv' is not defined
Shortly, I have the function nsbm in file _nsbm.py:
def nsbm(…): […] pv = [None] * len(state.get_levels())
def collect_marginals(s): global pv pv = [sl.collect_vertex_marginals(pv[l]) for l, sl in enumerate(s.get_levels())]
gt.mcmc_equilibrate(state, force_niter=10000, mcmc_args=dict(niter=10), callback=collect_marginals)
which is imported
from ._nsbm import nsbm
by the __init__.py of the package module (named tools), then imported by the main
from . import tools as tl
the directory structure of the package is (among others)
scanpy/tools/_nsbm.py scanpy/tools/__init__.py scanpy/__init__.py
as far as I understand callback function passed to mcmc_equilibrate is not supposed to return anything, collect_vertex_marginals returns the histogram summing the current to the previous. I think I can't pass pv as an argument to the callback as it becomes local to the function. Of course, I'm now reading about variable scoping in python, but if you have any hint it would be greatly appreciated. Thanks
You're looking for the nonlocal keyword, instead of global. See here: https://docs.python.org/3/reference/simple_stmts.html#grammar-token-nonlocal... -- Tiago de Paula Peixoto <tiago@skewed.de>