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David Keitel
PyFstat
Commits
9c2a9c57
Commit
9c2a9c57
authored
7 years ago
by
Gregory Ashton
Browse files
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Add transform_dict methods to plot_walkers
parent
ecf6c1c2
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1 changed file
pyfstat/mcmc_based_searches.py
+25
-23
25 additions, 23 deletions
pyfstat/mcmc_based_searches.py
with
25 additions
and
23 deletions
pyfstat/mcmc_based_searches.py
+
25
−
23
View file @
9c2a9c57
...
@@ -502,7 +502,6 @@ class MCMCSearch(core.BaseSearchClass):
...
@@ -502,7 +502,6 @@ class MCMCSearch(core.BaseSearchClass):
sampler
=
self
.
_run_sampler
(
sampler
,
p0
,
nburn
=
n
,
window
=
window
)
sampler
=
self
.
_run_sampler
(
sampler
,
p0
,
nburn
=
n
,
window
=
window
)
if
create_plots
:
if
create_plots
:
fig
,
axes
=
self
.
_plot_walkers
(
sampler
,
fig
,
axes
=
self
.
_plot_walkers
(
sampler
,
symbols
=
self
.
theta_symbols
,
**
kwargs
)
**
kwargs
)
fig
.
tight_layout
()
fig
.
tight_layout
()
fig
.
savefig
(
'
{}/{}_init_{}_walkers.png
'
.
format
(
fig
.
savefig
(
'
{}/{}_init_{}_walkers.png
'
.
format
(
...
@@ -522,8 +521,7 @@ class MCMCSearch(core.BaseSearchClass):
...
@@ -522,8 +521,7 @@ class MCMCSearch(core.BaseSearchClass):
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
,
symbols
=
self
.
theta_symbols
,
fig
,
axes
=
self
.
_plot_walkers
(
sampler
,
nprod
=
nprod
,
**
kwargs
)
nprod
=
nprod
,
**
kwargs
)
fig
.
tight_layout
()
fig
.
tight_layout
()
fig
.
savefig
(
'
{}/{}_walkers.png
'
.
format
(
self
.
outdir
,
self
.
label
),
fig
.
savefig
(
'
{}/{}_walkers.png
'
.
format
(
self
.
outdir
,
self
.
label
),
)
)
...
@@ -603,7 +601,7 @@ class MCMCSearch(core.BaseSearchClass):
...
@@ -603,7 +601,7 @@ class MCMCSearch(core.BaseSearchClass):
return
samples
return
samples
def
_get_labels
(
self
):
def
_get_labels
(
self
,
newline_units
=
False
):
"""
Combine the units, symbols and rescaling to give labels
"""
"""
Combine the units, symbols and rescaling to give labels
"""
labels
=
[]
labels
=
[]
...
@@ -620,7 +618,10 @@ class MCMCSearch(core.BaseSearchClass):
...
@@ -620,7 +618,10 @@ class MCMCSearch(core.BaseSearchClass):
if
'
unit
'
in
self
.
transform_dictionary
[
key
]:
if
'
unit
'
in
self
.
transform_dictionary
[
key
]:
u
=
self
.
transform_dictionary
[
key
][
'
unit
'
]
u
=
self
.
transform_dictionary
[
key
][
'
unit
'
]
if
label
is
None
:
if
label
is
None
:
if
newline_units
:
label
=
'
{}
\n
[{}]
'
.
format
(
s
,
u
)
label
=
'
{}
\n
[{}]
'
.
format
(
s
,
u
)
else
:
label
=
'
{} [{}]
'
.
format
(
s
,
u
)
labels
.
append
(
label
)
labels
.
append
(
label
)
return
labels
return
labels
...
@@ -694,7 +695,7 @@ class MCMCSearch(core.BaseSearchClass):
...
@@ -694,7 +695,7 @@ class MCMCSearch(core.BaseSearchClass):
fig
,
axes
=
fig_and_axes
fig
,
axes
=
fig_and_axes
samples_plt
=
copy
.
copy
(
self
.
samples
)
samples_plt
=
copy
.
copy
(
self
.
samples
)
labels
=
self
.
_get_labels
()
labels
=
self
.
_get_labels
(
newline_units
=
True
)
samples_plt
=
self
.
_scale_samples
(
samples_plt
,
self
.
theta_keys
)
samples_plt
=
self
.
_scale_samples
(
samples_plt
,
self
.
theta_keys
)
...
@@ -963,9 +964,11 @@ class MCMCSearch(core.BaseSearchClass):
...
@@ -963,9 +964,11 @@ class MCMCSearch(core.BaseSearchClass):
def
_plot_walkers
(
self
,
sampler
,
symbols
=
None
,
alpha
=
0.8
,
color
=
"
k
"
,
def
_plot_walkers
(
self
,
sampler
,
symbols
=
None
,
alpha
=
0.8
,
color
=
"
k
"
,
temp
=
0
,
lw
=
0.1
,
nprod
=
0
,
add_det_stat_burnin
=
False
,
temp
=
0
,
lw
=
0.1
,
nprod
=
0
,
add_det_stat_burnin
=
False
,
fig
=
None
,
axes
=
None
,
xoffset
=
0
,
plot_det_stat
=
False
,
fig
=
None
,
axes
=
None
,
xoffset
=
0
,
plot_det_stat
=
False
,
context
=
'
ggplot
'
,
subtractions
=
None
,
labelpad
=
0.0
5
):
context
=
'
ggplot
'
,
labelpad
=
5
):
"""
Plot all the chains from a sampler
"""
"""
Plot all the chains from a sampler
"""
if
symbols
is
None
:
symbols
=
self
.
_get_labels
()
if
context
not
in
plt
.
style
.
available
:
if
context
not
in
plt
.
style
.
available
:
raise
ValueError
((
raise
ValueError
((
'
The requested context {} is not available; please select a
'
'
The requested context {} is not available; please select a
'
...
@@ -977,7 +980,7 @@ class MCMCSearch(core.BaseSearchClass):
...
@@ -977,7 +980,7 @@ class MCMCSearch(core.BaseSearchClass):
shape
=
sampler
.
chain
.
shape
shape
=
sampler
.
chain
.
shape
if
len
(
shape
)
==
3
:
if
len
(
shape
)
==
3
:
nwalkers
,
nsteps
,
ndim
=
shape
nwalkers
,
nsteps
,
ndim
=
shape
chain
=
sampler
.
chain
[:,
:,
:]
chain
=
sampler
.
chain
[:,
:,
:]
.
copy
()
if
len
(
shape
)
==
4
:
if
len
(
shape
)
==
4
:
ntemps
,
nwalkers
,
nsteps
,
ndim
=
shape
ntemps
,
nwalkers
,
nsteps
,
ndim
=
shape
if
temp
<
ntemps
:
if
temp
<
ntemps
:
...
@@ -985,13 +988,11 @@ class MCMCSearch(core.BaseSearchClass):
...
@@ -985,13 +988,11 @@ class MCMCSearch(core.BaseSearchClass):
else
:
else
:
raise
ValueError
((
"
Requested temperature {} outside of
"
raise
ValueError
((
"
Requested temperature {} outside of
"
"
available range
"
).
format
(
temp
))
"
available range
"
).
format
(
temp
))
chain
=
sampler
.
chain
[
temp
,
:,
:,
:]
chain
=
sampler
.
chain
[
temp
,
:,
:,
:]
.
copy
()
if
subtractions
is
None
:
samples
=
chain
.
reshape
((
nwalkers
*
nsteps
,
ndim
))
subtractions
=
[
0
for
i
in
range
(
ndim
)]
samples
=
self
.
_scale_samples
(
samples
,
self
.
theta_keys
)
else
:
chain
=
chain
.
reshape
((
nwalkers
,
nsteps
,
ndim
))
if
len
(
subtractions
)
!=
self
.
ndim
:
raise
ValueError
(
'
subtractions must be of length ndim
'
)
if
plot_det_stat
:
if
plot_det_stat
:
extra_subplots
=
1
extra_subplots
=
1
...
@@ -1017,23 +1018,24 @@ class MCMCSearch(core.BaseSearchClass):
...
@@ -1017,23 +1018,24 @@ class MCMCSearch(core.BaseSearchClass):
cs
=
chain
[:,
:,
i
].
T
cs
=
chain
[:,
:,
i
].
T
if
burnin_idx
>
0
:
if
burnin_idx
>
0
:
axes
[
i
].
plot
(
xoffset
+
idxs
[:
last_idx
+
1
],
axes
[
i
].
plot
(
xoffset
+
idxs
[:
last_idx
+
1
],
cs
[:
last_idx
+
1
]
-
subtractions
[
i
]
,
cs
[:
last_idx
+
1
],
color
=
"
C3
"
,
alpha
=
alpha
,
color
=
"
C3
"
,
alpha
=
alpha
,
lw
=
lw
)
lw
=
lw
)
axes
[
i
].
axvline
(
xoffset
+
last_idx
,
axes
[
i
].
axvline
(
xoffset
+
last_idx
,
color
=
'
k
'
,
ls
=
'
--
'
,
lw
=
0.5
)
color
=
'
k
'
,
ls
=
'
--
'
,
lw
=
0.5
)
axes
[
i
].
plot
(
xoffset
+
idxs
[
burnin_idx
:],
axes
[
i
].
plot
(
xoffset
+
idxs
[
burnin_idx
:],
cs
[
burnin_idx
:]
-
subtractions
[
i
]
,
cs
[
burnin_idx
:],
color
=
"
k
"
,
alpha
=
alpha
,
lw
=
lw
)
color
=
"
k
"
,
alpha
=
alpha
,
lw
=
lw
)
axes
[
i
].
set_xlim
(
0
,
xoffset
+
idxs
[
-
1
])
axes
[
i
].
set_xlim
(
0
,
xoffset
+
idxs
[
-
1
])
if
symbols
:
if
symbols
:
if
subtractions
[
i
]
==
0
:
axes
[
i
].
set_ylabel
(
symbols
[
i
],
labelpad
=
labelpad
)
axes
[
i
].
set_ylabel
(
symbols
[
i
],
labelpad
=
labelpad
)
else
:
#if subtractions[i] == 0:
axes
[
i
].
set_ylabel
(
# axes[i].set_ylabel(symbols[i], labelpad=labelpad)
symbols
[
i
]
+
'
$-$
'
+
symbols
[
i
]
+
'
$^\mathrm{s}$
'
,
#else:
labelpad
=
labelpad
)
# axes[i].set_ylabel(
# symbols[i]+'$-$'+symbols[i]+'$^\mathrm{s}$',
# labelpad=labelpad)
# if hasattr(self, 'convergence_diagnostic'):
# if hasattr(self, 'convergence_diagnostic'):
# ax = axes[i].twinx()
# ax = axes[i].twinx()
...
@@ -2120,7 +2122,7 @@ class MCMCFollowUpSearch(MCMCSemiCoherentSearch):
...
@@ -2120,7 +2122,7 @@ class MCMCFollowUpSearch(MCMCSemiCoherentSearch):
if
create_plots
:
if
create_plots
:
fig
,
axes
=
self
.
_plot_walkers
(
fig
,
axes
=
self
.
_plot_walkers
(
sampler
,
symbols
=
self
.
theta_symbols
,
fig
=
fig
,
axes
=
axes
,
sampler
,
fig
=
fig
,
axes
=
axes
,
nprod
=
nprod
,
xoffset
=
nsteps_total
,
**
kwargs
)
nprod
=
nprod
,
xoffset
=
nsteps_total
,
**
kwargs
)
for
ax
in
axes
[:
self
.
ndim
]:
for
ax
in
axes
[:
self
.
ndim
]:
ax
.
axvline
(
nsteps_total
,
color
=
'
k
'
,
ls
=
'
--
'
,
lw
=
0.25
)
ax
.
axvline
(
nsteps_total
,
color
=
'
k
'
,
ls
=
'
--
'
,
lw
=
0.25
)
...
...
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