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David Keitel
PyFstat
Commits
f7aab64d
Commit
f7aab64d
authored
Apr 15, 2018
by
Gregory Ashton
Browse files
Minor polishing to MCMC searches
- Adds chains to saved data - Add catch for when corner plots error
parent
37041071
Changes
1
Hide whitespace changes
Inline
Side-by-side
pyfstat/mcmc_based_searches.py
View file @
f7aab64d
...
@@ -492,6 +492,7 @@ class MCMCSearch(core.BaseSearchClass):
...
@@ -492,6 +492,7 @@ class MCMCSearch(core.BaseSearchClass):
self
.
lnprobs
=
d
[
'lnprobs'
]
self
.
lnprobs
=
d
[
'lnprobs'
]
self
.
lnlikes
=
d
[
'lnlikes'
]
self
.
lnlikes
=
d
[
'lnlikes'
]
self
.
all_lnlikelihood
=
d
[
'all_lnlikelihood'
]
self
.
all_lnlikelihood
=
d
[
'all_lnlikelihood'
]
self
.
chain
=
d
[
'chain'
]
return
return
self
.
_initiate_search_object
()
self
.
_initiate_search_object
()
...
@@ -533,21 +534,27 @@ class MCMCSearch(core.BaseSearchClass):
...
@@ -533,21 +534,27 @@ class MCMCSearch(core.BaseSearchClass):
logging
.
info
(
'Running final burn and prod with {} steps'
.
format
(
logging
.
info
(
'Running final burn and prod with {} steps'
.
format
(
nburn
+
nprod
))
nburn
+
nprod
))
sampler
=
self
.
_run_sampler
(
sampler
,
p0
,
nburn
=
nburn
,
nprod
=
nprod
)
sampler
=
self
.
_run_sampler
(
sampler
,
p0
,
nburn
=
nburn
,
nprod
=
nprod
)
if
create_plots
:
if
create_plots
:
fig
,
axes
=
self
.
_plot_walkers
(
sampler
,
nprod
=
nprod
,
**
kwargs
)
try
:
fig
.
tight_layout
()
fig
,
axes
=
self
.
_plot_walkers
(
sampler
,
nprod
=
nprod
,
**
kwargs
)
fig
.
savefig
(
'{}/{}_walkers.png'
.
format
(
self
.
outdir
,
self
.
label
),
fig
.
tight_layout
()
)
fig
.
savefig
(
'{}/{}_walkers.png'
.
format
(
self
.
outdir
,
self
.
label
))
except
RuntimeError
as
e
:
logging
.
warning
(
"Failed to save walker plots due to Erro {}"
.
format
(
e
))
samples
=
sampler
.
chain
[
0
,
:,
nburn
:,
:].
reshape
((
-
1
,
self
.
ndim
))
samples
=
sampler
.
chain
[
0
,
:,
nburn
:,
:].
reshape
((
-
1
,
self
.
ndim
))
lnprobs
=
sampler
.
logprobability
[
0
,
:,
nburn
:].
reshape
((
-
1
))
lnprobs
=
sampler
.
logprobability
[
0
,
:,
nburn
:].
reshape
((
-
1
))
lnlikes
=
sampler
.
loglikelihood
[
0
,
:,
nburn
:].
reshape
((
-
1
))
lnlikes
=
sampler
.
loglikelihood
[
0
,
:,
nburn
:].
reshape
((
-
1
))
all_lnlikelihood
=
sampler
.
loglikelihood
[:,
:,
nburn
:]
all_lnlikelihood
=
sampler
.
loglikelihood
[:,
:,
nburn
:]
self
.
samples
=
samples
self
.
samples
=
samples
self
.
chain
=
sampler
.
chain
self
.
lnprobs
=
lnprobs
self
.
lnprobs
=
lnprobs
self
.
lnlikes
=
lnlikes
self
.
lnlikes
=
lnlikes
self
.
all_lnlikelihood
=
all_lnlikelihood
self
.
all_lnlikelihood
=
all_lnlikelihood
self
.
_save_data
(
sampler
,
samples
,
lnprobs
,
lnlikes
,
all_lnlikelihood
)
self
.
_save_data
(
sampler
,
samples
,
lnprobs
,
lnlikes
,
all_lnlikelihood
,
sampler
.
chain
)
return
sampler
return
sampler
def
_get_rescale_multiplier_for_key
(
self
,
key
):
def
_get_rescale_multiplier_for_key
(
self
,
key
):
...
@@ -1215,11 +1222,13 @@ class MCMCSearch(core.BaseSearchClass):
...
@@ -1215,11 +1222,13 @@ class MCMCSearch(core.BaseSearchClass):
maxStartTime
=
self
.
maxStartTime
)
maxStartTime
=
self
.
maxStartTime
)
return
d
return
d
def
_save_data
(
self
,
sampler
,
samples
,
lnprobs
,
lnlikes
,
all_lnlikelihood
):
def
_save_data
(
self
,
sampler
,
samples
,
lnprobs
,
lnlikes
,
all_lnlikelihood
,
chain
):
d
=
self
.
_get_data_dictionary_to_save
()
d
=
self
.
_get_data_dictionary_to_save
()
d
[
'samples'
]
=
samples
d
[
'samples'
]
=
samples
d
[
'lnprobs'
]
=
lnprobs
d
[
'lnprobs'
]
=
lnprobs
d
[
'lnlikes'
]
=
lnlikes
d
[
'lnlikes'
]
=
lnlikes
d
[
'chain'
]
=
chain
d
[
'all_lnlikelihood'
]
=
all_lnlikelihood
d
[
'all_lnlikelihood'
]
=
all_lnlikelihood
if
os
.
path
.
isfile
(
self
.
pickle_path
):
if
os
.
path
.
isfile
(
self
.
pickle_path
):
...
@@ -1254,6 +1263,7 @@ class MCMCSearch(core.BaseSearchClass):
...
@@ -1254,6 +1263,7 @@ class MCMCSearch(core.BaseSearchClass):
old_d
.
pop
(
'lnprobs'
)
old_d
.
pop
(
'lnprobs'
)
old_d
.
pop
(
'lnlikes'
)
old_d
.
pop
(
'lnlikes'
)
old_d
.
pop
(
'all_lnlikelihood'
)
old_d
.
pop
(
'all_lnlikelihood'
)
old_d
.
pop
(
'chain'
)
for
key
in
'minStartTime'
,
'maxStartTime'
:
for
key
in
'minStartTime'
,
'maxStartTime'
:
if
new_d
[
key
]
is
None
:
if
new_d
[
key
]
is
None
:
...
@@ -1616,7 +1626,7 @@ class MCMCGlitchSearch(MCMCSearch):
...
@@ -1616,7 +1626,7 @@ class MCMCGlitchSearch(MCMCSearch):
'multiplier'
:
1
/
86400.
,
'multiplier'
:
1
/
86400.
,
'subtractor'
:
'minStartTime'
,
'subtractor'
:
'minStartTime'
,
'unit'
:
'day'
,
'unit'
:
'day'
,
'label'
:
'$t^{g}_0$
\n
[d
ays
]'
}
'label'
:
'$t^{g}_0$
\n
[d]'
}
)
)
@
helper_functions
.
initializer
@
helper_functions
.
initializer
...
@@ -2108,6 +2118,7 @@ class MCMCFollowUpSearch(MCMCSemiCoherentSearch):
...
@@ -2108,6 +2118,7 @@ class MCMCFollowUpSearch(MCMCSemiCoherentSearch):
self
.
lnprobs
=
d
[
'lnprobs'
]
self
.
lnprobs
=
d
[
'lnprobs'
]
self
.
lnlikes
=
d
[
'lnlikes'
]
self
.
lnlikes
=
d
[
'lnlikes'
]
self
.
all_lnlikelihood
=
d
[
'all_lnlikelihood'
]
self
.
all_lnlikelihood
=
d
[
'all_lnlikelihood'
]
self
.
chain
=
d
[
'chain'
]
self
.
nsegs
=
run_setup
[
-
1
][
1
]
self
.
nsegs
=
run_setup
[
-
1
][
1
]
return
return
...
...
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