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whuie2
experiment-control
Commits
0e6dc676
Commit
0e6dc676
authored
Dec 09, 2021
by
Yb Tweezer
Browse files
don't compress saved arrays for speed; add better option for rendering debugging arrays
parent
82ea1796
Changes
1
Hide whitespace changes
Inline
Side-by-side
lib/imaging.py
View file @
0e6dc676
...
...
@@ -38,7 +38,8 @@ class ImagingData:
arrays_file
=
io
.
fresh_filename
(
T
.
joinpath
(
"arrays.npz"
),
overwrite
)
if
printflag
:
print
(
"[imaging] save arrays"
)
np
.
savez_compressed
(
arrays_file
,
**
self
.
arrays
)
#np.savez_compressed(arrays_file, **self.arrays)
np
.
savez
(
arrays_file
,
**
self
.
arrays
)
config_file
=
io
.
fresh_filename
(
T
.
joinpath
(
"config.toml"
),
overwrite
)
if
printflag
:
print
(
"[imaging] save camera config"
)
...
...
@@ -190,9 +191,9 @@ class FluorescenceData(ImagingData):
N_bkgd
=
compute_mot_number
(
self
.
arrays
[
"background"
].
astype
(
np
.
float64
),
**
compute_mot_number_params
,
k
=
0
k
=
None
)
if
subtract_bkgd
and
"background"
in
self
.
arrays
.
keys
()
else
0.0
for
label
,
array
in
self
.
arrays
.
items
():
for
k
,
(
label
,
array
)
in
enumerate
(
self
.
arrays
.
items
()
)
:
dtype_info
=
np
.
iinfo
(
array
.
dtype
)
if
array
.
max
()
>=
(
dtype_info
.
max
-
dtype_info
.
bits
):
print
(
...
...
@@ -200,7 +201,7 @@ class FluorescenceData(ImagingData):
N
=
compute_mot_number
(
array
.
astype
(
np
.
float64
),
**
compute_mot_number_params
,
k
=
1
k
=
None
)
sx
,
sy
=
lls_fit_gaussian
(
array
,
_dA
)
self
.
results
=
dict
()
if
self
.
results
is
None
else
self
.
results
...
...
@@ -215,15 +216,16 @@ class FluorescenceData(ImagingData):
return
self
def
compute_mot_number
(
image
,
QE
,
gain
,
exposure_time
,
solid_angle
,
detuning
,
intensity_parameter
,
k
=
0
):
detuning
,
intensity_parameter
,
k
=
None
):
H
,
W
=
image
.
shape
K_h
=
3.0
slice_h
=
pd
.
S
[
int
(
H
/
K_h
)
:
int
((
K_h
-
1
)
*
H
/
K_h
)]
K_w
=
3.0
slice_w
=
pd
.
S
[
int
(
W
/
K_w
)
:
int
((
K_w
-
1
)
*
W
/
K_w
)]
im
=
image
[
slice_h
,
slice_w
]
#pd.Plotter().imshow(image).savefig(f"image_{k}.png").close()
#pd.Plotter().imshow(im).savefig(f"img_{k}.png").close()
if
k
is
not
None
:
pd
.
Plotter
().
imshow
(
image
).
savefig
(
f
"image_
{
k
}
.png"
).
close
()
pd
.
Plotter
().
imshow
(
im
).
savefig
(
f
"img_
{
k
}
.png"
).
close
()
electron_rate
=
im
.
astype
(
np
.
float64
).
sum
()
photon_rate
=
(
electron_rate
...
...
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