Skip to content

[WIP] Make more diagnostics accessible via the PyFBU class #5

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
Revile77 wants to merge 3 commits into
base: master
Choose a base branch
from
Open

[WIP] Make more diagnostics accessible via the PyFBU class #5

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
031683b
Add configurable option for sampler initialization
Revile77 Jul 22, 2019
6ab66fd
Print MAP minimization steps in verbose mode.
Revile77 Aug 15, 2019
35219c9
Accesible PyMC summary of trace and actual trace object.
Revile77 Oct 3, 2019
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
11 changes: 6 additions & 5 deletions fbu/PyFBU.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@ def __init__(self,data=[],response=[],background={},
self.nCores = 1 # number of CPU threads to utilize
self.nChains = 2 # number of Markov chains to sample
self.nuts_kwargs = None
self.init_method = 'jitter+adapt_diag'
self.discard_tuned_samples = True # whether to discard tuning steps from posterior
self.lower = lower # lower sampling bounds
self.upper = upper # upper sampling bounds
Expand Down Expand Up @@ -156,11 +157,9 @@ def unfold():
from datetime import timedelta
init_time = time.time()

print(self.nuts_kwargs)


if self.mode:
map_estimate = mc.find_MAP(model=model, method=self.MAP_method)
map_estimate = mc.find_MAP(model=model, method=self.MAP_method,
options={'disp':self.verbose})
print (map_estimate)
self.MAP = map_estimate
self.trace = []
Expand All @@ -169,6 +168,7 @@ def unfold():

trace = mc.sample(self.nMCMC,tune=self.nTune,cores=self.nCores,
chains=self.nChains, nuts_kwargs=self.nuts_kwargs,
init=self.init_method, n_init=200000,
discard_tuned_samples=self.discard_tuned_samples,
progressbar=self.sampling_progressbar)
finish_time = time.time()
Expand All @@ -178,7 +178,8 @@ def unfold():
))

self.trace = [trace['truth%d'%bin][:] for bin in range(truthdim)]
#self.trace = [copy.deepcopy(trace['truth%d'%bin][:]) for bin in range(truthdim)]
self.__trace__ = trace # for full access
self.trace_summary = mc.summary(trace)
self.nuisancestrace = {}
if nbckg>0:
for name,err in zip(backgroundkeys,backgroundnormsysts):
Expand Down