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ift
tutorial_nifty_resolve
Commits
873e5a29
Commit
873e5a29
authored
2 years ago
by
Philipp Frank
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Merge branch 'iid2022' into 'main'
make evidences an array See merge request
!5
parents
86057d21
c720aeae
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1 merge request
!5
make evidences an array
Pipeline
#148616
passed
2 years ago
Stage: test
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demo_poisson.ipynb
+4
-4
4 additions, 4 deletions
demo_poisson.ipynb
demo_poisson_solution.ipynb
+5
-5
5 additions, 5 deletions
demo_poisson_solution.ipynb
with
9 additions
and
9 deletions
demo_poisson.ipynb
+
4
−
4
View file @
873e5a29
...
...
@@ -28,7 +28,7 @@
"from utils import plot_2D, load_psf, geovi_sampling, plot_posterior\n",
"\n",
"ift.random.push_sseq_from_seed(42)\n",
"evidences =
[]
"
"evidences =
np.zeros(3)
"
]
},
{
...
...
@@ -74,7 +74,7 @@
"\n",
"\n",
"print(evidence)\n",
"evidences
+
=
[
evidence
, ]
"
"evidences
[0]
= evidence"
]
},
{
...
...
@@ -88,7 +88,7 @@
"# Inference model 2\n",
"\n",
"\n",
"evidences
+
=
[
evidence
, ]
"
"evidences
[1]
= evidence"
]
},
{
...
...
@@ -149,7 +149,7 @@
"source": [
"# Inference model 3\n",
"\n",
"evidences
+
=
[
evidence
, ]
"
"evidences
[2]
= evidence"
]
},
{
...
...
%% Cell type:markdown id: tags:
Nifty tutorial for Poisson count data
=====================================
%% Cell type:markdown id: tags:
Setup
-----
%% Cell type:code id: tags:
```
python
import
numpy
as
np
import
matplotlib.pyplot
as
plt
import
nifty8
as
ift
from
utils
import
plot_2D
,
load_psf
,
geovi_sampling
,
plot_posterior
ift
.
random
.
push_sseq_from_seed
(
42
)
evidences
=
[]
evidences
=
np
.
zeros
(
3
)
```
%% Cell type:code id: tags:
```
python
# Load data and visualize
data
=
np
.
load
(
'
data/poisson.npz
'
)
```
%% Cell type:code id: tags:
```
python
position_space
=
ift
.
RGSpace
([
128
,
128
])
# Homogeneous poisson process
print
(
model1
)
```
%% Cell type:code id: tags:
```
python
# Set up likelihood & PSF
```
%% Cell type:code id: tags:
```
python
# Inference model 1
print
(
evidence
)
evidences
+
=
[
evidence
,
]
evidences
[
0
]
=
evidence
```
%% Cell type:code id: tags:
```
python
# Independent poisson process
# Inference model 2
evidences
+
=
[
evidence
,
]
evidences
[
1
]
=
evidence
```
%% Cell type:code id: tags:
```
python
# Compare evidence
print
(
evidences
)
```
%% Cell type:code id: tags:
```
python
# Diffuse poisson process
args
=
{
'
offset_mean
'
:
.
5
,
'
offset_std
'
:
(
1.
,
1E-5
),
# Amplitude of field fluctuations
'
fluctuations
'
:
(
1.5
,
0.5
),
# 1.0, 1e-2
# Exponent of power law power spectrum component
'
loglogavgslope
'
:
(
-
4.
,
1
),
# -6.0, 1
# Amplitude of integrated Wiener process power spectrum component
'
flexibility
'
:
(
1.
,
0.2
),
# 2.0, 1.0
# How ragged the integrated Wiener process component is
'
asperity
'
:
(
0.1
,
0.01
),
# 0.1, 0.5
# Name of the input keys
'
prefix
'
:
'
diffuse
'
}
correlated_field
=
ift
.
SimpleCorrelatedField
(
position_space
,
**
args
)
pspec
=
correlated_field
.
power_spectrum
```
%% Cell type:code id: tags:
```
python
# Prior samples
```
%% Cell type:code id: tags:
```
python
# Inference model 3
evidences
+
=
[
evidence
,
]
evidences
[
2
]
=
evidence
```
%% Cell type:code id: tags:
```
python
# Compare evidence
print
(
evidences
)
print
(
evidences
-
evidences
[
-
1
])
```
%% Cell type:markdown id: tags:
Posterior visualization
-----------------------
%% Cell type:code id: tags:
```
python
plot_posterior
(
samples
,
data
,
model3
,
diffuse
,
model2
,
pspec
)
```
...
...
This diff is collapsed.
Click to expand it.
demo_poisson_solution.ipynb
+
5
−
5
View file @
873e5a29
...
...
@@ -28,7 +28,7 @@
"from utils import plot_2D, load_psf, geovi_sampling, plot_posterior\n",
"\n",
"ift.random.push_sseq_from_seed(42)\n",
"evidences =
[]
"
"evidences =
np.zeros(3)
"
]
},
{
...
...
@@ -84,7 +84,7 @@
"samples, evidence = geovi_sampling(likelihood @ model1)\n",
"plot_2D(samples.average(model1).val, 'model1 posterior mean')\n",
"print(evidence)\n",
"evidences
+
=
[
evidence
, ]
"
"evidences
[0]
= evidence"
]
},
{
...
...
@@ -100,7 +100,7 @@
"samples, evidence = geovi_sampling(likelihood @ model2)\n",
"plot_2D(samples.average(model2).val, 'model2 posterior mean')\n",
"print(evidence)\n",
"evidences
+
=
[
evidence
, ]
"
"evidences
[1]
= evidence"
]
},
{
...
...
@@ -110,7 +110,7 @@
"outputs": [],
"source": [
"# Compare evidence\n",
"print(evidences)"
"print(evidences
[:2]
)"
]
},
{
...
...
@@ -169,7 +169,7 @@
"samples, evidence = geovi_sampling(likelihood @ model3)\n",
"plot_2D(samples.average(model3).val, 'model3 posterior mean')\n",
"print(evidence)\n",
"evidences
+
=
[
evidence
, ]
"
"evidences
[2]
= evidence"
]
},
{
...
...
%% Cell type:markdown id: tags:
Nifty tutorial for Poisson count data
=====================================
%% Cell type:markdown id: tags:
Setup
-----
%% Cell type:code id: tags:
```
python
import
numpy
as
np
import
matplotlib.pyplot
as
plt
import
nifty8
as
ift
from
utils
import
plot_2D
,
load_psf
,
geovi_sampling
,
plot_posterior
ift
.
random
.
push_sseq_from_seed
(
42
)
evidences
=
[]
evidences
=
np
.
zeros
(
3
)
```
%% Cell type:code id: tags:
```
python
# Load data and visualize
data
=
np
.
load
(
'
data/poisson.npz
'
)
print
(
data
[
'
data
'
].
shape
)
plot_2D
(
data
[
'
data
'
],
'
Data
'
)
```
%% Cell type:code id: tags:
```
python
position_space
=
ift
.
RGSpace
([
128
,
128
])
# Homogeneous poisson process
projection
=
ift
.
VdotOperator
(
ift
.
full
(
position_space
,
1.
)).
adjoint
model1
=
ift
.
FieldAdapter
(
projection
.
domain
,
'
hom
'
)
model1
=
ift
.
exp
(
5.
*
model1
)
model1
=
projection
@
model1
print
(
model1
)
```
%% Cell type:code id: tags:
```
python
# Set up likelihood & PSF
d
=
ift
.
makeField
(
position_space
,
data
[
'
data
'
])
likelihood
=
ift
.
PoissonianEnergy
(
d
)
PSF_op
,
psf
=
load_psf
(
position_space
)
plot_2D
(
psf
,
'
PSF
'
)
likelihood
=
likelihood
@
PSF_op
```
%% Cell type:code id: tags:
```
python
# Inference model 1
samples
,
evidence
=
geovi_sampling
(
likelihood
@
model1
)
plot_2D
(
samples
.
average
(
model1
).
val
,
'
model1 posterior mean
'
)
print
(
evidence
)
evidences
+
=
[
evidence
,
]
evidences
[
0
]
=
evidence
```
%% Cell type:code id: tags:
```
python
# Independent poisson process
model2
=
ift
.
InverseGammaOperator
(
position_space
,
2.
,
3.
).
ducktape
(
'
independent
'
)
# Inference model 2
samples
,
evidence
=
geovi_sampling
(
likelihood
@
model2
)
plot_2D
(
samples
.
average
(
model2
).
val
,
'
model2 posterior mean
'
)
print
(
evidence
)
evidences
+
=
[
evidence
,
]
evidences
[
1
]
=
evidence
```
%% Cell type:code id: tags:
```
python
# Compare evidence
print
(
evidences
)
print
(
evidences
[:
2
]
)
```
%% Cell type:code id: tags:
```
python
# Diffuse poisson process
args
=
{
'
offset_mean
'
:
.
5
,
'
offset_std
'
:
(
1.
,
1E-5
),
# Amplitude of field fluctuations
'
fluctuations
'
:
(
1.5
,
0.5
),
# 1.0, 1e-2
# Exponent of power law power spectrum component
'
loglogavgslope
'
:
(
-
4.
,
1
),
# -6.0, 1
# Amplitude of integrated Wiener process power spectrum component
'
flexibility
'
:
(
1.
,
0.2
),
# 2.0, 1.0
# How ragged the integrated Wiener process component is
'
asperity
'
:
(
0.1
,
0.01
),
# 0.1, 0.5
# Name of the input keys
'
prefix
'
:
'
diffuse
'
}
correlated_field
=
ift
.
SimpleCorrelatedField
(
position_space
,
**
args
)
pspec
=
correlated_field
.
power_spectrum
diffuse
=
correlated_field
.
exp
()
model3
=
diffuse
+
model2
```
%% Cell type:code id: tags:
```
python
# Prior samples
pl
=
ift
.
Plot
()
for
_
in
range
(
9
):
pl
.
add
(
model3
(
ift
.
from_random
(
model3
.
domain
)))
pl
.
output
()
```
%% Cell type:code id: tags:
```
python
# Inference model 3
samples
,
evidence
=
geovi_sampling
(
likelihood
@
model3
)
plot_2D
(
samples
.
average
(
model3
).
val
,
'
model3 posterior mean
'
)
print
(
evidence
)
evidences
+
=
[
evidence
,
]
evidences
[
2
]
=
evidence
```
%% Cell type:code id: tags:
```
python
# Compare evidence
print
(
evidences
)
print
(
evidences
-
evidences
[
-
1
])
```
%% Cell type:markdown id: tags:
Posterior visualization
-----------------------
%% Cell type:code id: tags:
```
python
plot_posterior
(
samples
,
data
,
model3
,
diffuse
,
model2
,
pspec
)
```
...
...
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