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XRD
darfix
Commits
1855979d
Commit
1855979d
authored
Jun 07, 2021
by
Julia Garriga Ferrer
Browse files
[core][dataset] Add transformation parameter to dataset
parent
630b1bf8
Changes
1
Hide whitespace changes
Inline
Side-by-side
darfix/core/dataset.py
View file @
1855979d
...
...
@@ -26,7 +26,7 @@
__authors__
=
[
"J. Garriga"
]
__license__
=
"MIT"
__date__
=
"0
4
/06/2021"
__date__
=
"0
7
/06/2021"
import
copy
import
glob
...
...
@@ -100,7 +100,7 @@ class Dataset():
"""
def
__init__
(
self
,
_dir
,
data
=
None
,
first_filename
=
None
,
filenames
=
None
,
dims
=
None
,
treated
=
"treated_data"
,
in_memory
=
True
):
dims
=
None
,
treated
=
"treated_data"
,
transformation
=
None
,
in_memory
=
True
):
self
.
_data
=
None
self
.
_frames_intensity
=
[]
...
...
@@ -110,7 +110,7 @@ class Dataset():
self
.
running_data
=
None
self
.
moments_dims
=
{}
self
.
operations_state
=
numpy
.
zeros
(
len
(
Operation
))
self
.
_transformation
=
N
on
e
self
.
_transformation
=
transformati
on
if
not
os
.
path
.
isdir
(
self
.
dir
+
"/"
+
treated
):
try
:
os
.
mkdir
(
self
.
dir
+
"/"
+
treated
)
...
...
@@ -591,7 +591,8 @@ class Dataset():
new_data
=
Data
(
urls
.
reshape
(
self
.
data
.
urls
.
shape
),
self
.
data
.
metadata
,
self
.
_in_memory
)
return
Dataset
(
_dir
=
bs_dir
,
data
=
new_data
,
dims
=
self
.
__dims
,
in_memory
=
self
.
_in_memory
)
return
Dataset
(
_dir
=
bs_dir
,
data
=
new_data
,
dims
=
self
.
__dims
,
transformation
=
self
.
transformation
,
in_memory
=
self
.
_in_memory
)
def
apply_hot_pixel_removal
(
self
,
kernel
=
3
,
indices
=
None
):
"""
...
...
@@ -635,7 +636,8 @@ class Dataset():
new_data
=
Data
(
urls
.
reshape
(
self
.
data
.
urls
.
shape
),
self
.
data
.
metadata
,
self
.
_in_memory
)
return
Dataset
(
_dir
=
_dir
,
data
=
new_data
,
dims
=
self
.
__dims
,
in_memory
=
self
.
_in_memory
)
return
Dataset
(
_dir
=
_dir
,
data
=
new_data
,
dims
=
self
.
__dims
,
transformation
=
self
.
transformation
,
in_memory
=
self
.
_in_memory
)
def
apply_threshold_removal
(
self
,
bottom
=
None
,
top
=
None
,
indices
=
None
):
"""
...
...
@@ -679,7 +681,8 @@ class Dataset():
new_data
=
Data
(
urls
.
reshape
(
self
.
data
.
urls
.
shape
),
self
.
data
.
metadata
,
self
.
_in_memory
)
return
Dataset
(
_dir
=
_dir
,
data
=
new_data
,
dims
=
self
.
__dims
,
in_memory
=
self
.
_in_memory
)
return
Dataset
(
_dir
=
_dir
,
data
=
new_data
,
dims
=
self
.
__dims
,
transformation
=
self
.
transformation
,
in_memory
=
self
.
_in_memory
)
def
apply_roi
(
self
,
origin
=
None
,
size
=
None
,
center
=
None
,
indices
=
None
,
roi_dir
=
None
):
"""
...
...
@@ -722,7 +725,8 @@ class Dataset():
shape
.
append
(
new_data
.
shape
[
-
2
])
shape
.
append
(
new_data
.
shape
[
-
1
])
new_data
=
new_data
.
reshape
(
shape
)
return
Dataset
(
_dir
=
roi_dir
,
data
=
new_data
,
dims
=
self
.
__dims
,
in_memory
=
self
.
_in_memory
)
return
Dataset
(
_dir
=
roi_dir
,
data
=
new_data
,
dims
=
self
.
__dims
,
transformation
=
transformation
,
in_memory
=
self
.
_in_memory
)
def
find_shift
(
self
,
dimension
=
None
,
h_max
=
0.5
,
h_step
=
0.01
,
indices
=
None
):
"""
...
...
@@ -828,7 +832,8 @@ class Dataset():
self
.
_lock
.
release
()
data
=
Data
(
new_urls
.
reshape
(
self
.
data
.
urls
.
shape
),
self
.
data
.
metadata
,
in_memory
=
self
.
_in_memory
)
return
Dataset
(
_dir
=
shift_dir
,
data
=
data
,
dims
=
self
.
__dims
,
in_memory
=
self
.
_in_memory
)
return
Dataset
(
_dir
=
shift_dir
,
data
=
data
,
dims
=
self
.
__dims
,
transformation
=
self
.
transformation
,
in_memory
=
self
.
_in_memory
)
def
find_and_apply_shift
(
self
,
dimension
=
None
,
h_max
=
0.5
,
h_step
=
0.01
,
shift_approach
=
"fft"
,
indices
=
None
,
callback
=
None
):
...
...
@@ -1257,7 +1262,7 @@ class Dataset():
else
:
new_urls
=
numpy
.
array
(
urls
)
data
=
Data
(
new_urls
.
reshape
(
self
.
data
.
urls
.
shape
),
self
.
data
.
metadata
,
in_memory
=
True
)
# to modify
return
Dataset
(
_dir
=
_dir
,
data
=
data
,
dims
=
self
.
__dims
,
in_memory
=
True
)
return
Dataset
(
_dir
=
_dir
,
data
=
data
,
dims
=
self
.
__dims
,
transformation
=
self
.
transformation
,
in_memory
=
True
)
def
compute_transformation
(
self
,
d
,
rotate
=
False
):
...
...
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