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MPBA Radiomics
RADLER
Commits
433f429e
Commit
433f429e
authored
Mar 17, 2020
by
Alessia Marcolini
Browse files
Dataset augmentation script
parent
603710b7
Changes
2
Show whitespace changes
Inline
Side-by-side
01_preprocessing/augment_dataset.ipynb
deleted
100644 → 0
View file @
603710b7
%% Cell type:markdown id: tags:
## Augment dataset class-wise
%% Cell type:code id: tags:
```
python
%
HN_env
```
%%%% Output: execute_result
<IPython.core.display.HTML object>
%% Cell type:code id: tags:
```
python
import
os
PATH
=
os
.
path
.
join
(
os
.
path
.
abspath
(
os
.
path
.
curdir
),
'..'
)
import
sys
import
numpy
as
np
from
dataset
import
NumpyCSVDataset
,
augment_3D_HN
import
SimpleITK
as
sitk
```
%% Cell type:code id: tags:
```
python
#%%
DATASETDIR
=
'/thunderdisk/HN/processed/bbox_fixed2_64/'
AUGMENT_DIR
=
'/thunderdisk/HN/processed/bbox_64_augmented_LR'
os
.
makedirs
(
AUGMENT_DIR
,
exist_ok
=
False
)
SIZE
=
64
dataset
=
NumpyCSVDataset
(
DATASETDIR
,
f
'
{
PATH
}
/data/clinical_data.csv'
,
'Locoregional'
,
SIZE
,
mode
=
'test'
)
labels
=
dataset
.
get_labels
()
idx_positive
=
np
.
where
(
labels
==
'1'
)[
0
]
augment_K
=
5
ratio_NP
=
int
((
len
(
labels
)
-
len
(
idx_positive
))
/
len
(
idx_positive
))
```
%% Cell type:code id: tags:
```
python
len
(
labels
),
len
(
idx_positive
)
```
%%%% Output: execute_result
(294, 42)
%% Cell type:code id: tags:
```
python
#%%
for
i
in
range
(
len
(
dataset
)):
sample
=
dataset
[
i
]
SUB
=
sample
[
'filename'
]
print
(
SUB
)
image_orig
=
sample
[
'data'
]
label
=
sample
[
'target'
]
ratio
=
1
if
label
==
'0'
else
ratio_NP
# print(ratio)
id_image
=
0
for
j
in
range
(
ratio
):
for
k
in
range
(
augment_K
):
image_aug
=
augment_3D_HN
(
image_orig
,
'train'
,
SIZE
)
np
.
save
(
f
'
{
AUGMENT_DIR
}
/
{
SUB
}
_
{
id_image
}
.npy'
,
image_aug
)
id_image
+=
1
```
%%%% Output: stream
HN-CHUM-001.npy
<class 'numpy.str_'>
HN-CHUM-002.npy
<class 'numpy.str_'>
HN-CHUM-003.npy
<class 'numpy.str_'>
HN-CHUM-004.npy
<class 'numpy.str_'>
HN-CHUM-005.npy
<class 'numpy.str_'>
HN-CHUM-006.npy
<class 'numpy.str_'>
HN-CHUM-007.npy
<class 'numpy.str_'>
HN-CHUM-008.npy
<class 'numpy.str_'>
HN-CHUM-009.npy
<class 'numpy.str_'>
HN-CHUM-010.npy
<class 'numpy.str_'>
HN-CHUM-011.npy
<class 'numpy.str_'>
HN-CHUM-012.npy
<class 'numpy.str_'>
HN-CHUM-013.npy
<class 'numpy.str_'>
HN-CHUM-014.npy
<class 'numpy.str_'>
HN-CHUM-015.npy
<class 'numpy.str_'>
HN-CHUM-016.npy
<class 'numpy.str_'>
HN-CHUM-017.npy
<class 'numpy.str_'>
HN-CHUM-018.npy
<class 'numpy.str_'>
HN-CHUM-019.npy
<class 'numpy.str_'>
HN-CHUM-021.npy
<class 'numpy.str_'>
HN-CHUM-022.npy
<class 'numpy.str_'>
HN-CHUM-023.npy
<class 'numpy.str_'>
HN-CHUM-024.npy
<class 'numpy.str_'>
HN-CHUM-025.npy
<class 'numpy.str_'>
HN-CHUM-026.npy
<class 'numpy.str_'>
HN-CHUM-027.npy
<class 'numpy.str_'>
HN-CHUM-028.npy
<class 'numpy.str_'>
HN-CHUM-029.npy
<class 'numpy.str_'>
HN-CHUM-030.npy
<class 'numpy.str_'>
HN-CHUM-031.npy
<class 'numpy.str_'>
HN-CHUM-032.npy
<class 'numpy.str_'>
HN-CHUM-033.npy
<class 'numpy.str_'>
HN-CHUM-034.npy
<class 'numpy.str_'>
HN-CHUM-035.npy
<class 'numpy.str_'>
HN-CHUM-036.npy
<class 'numpy.str_'>
HN-CHUM-037.npy
<class 'numpy.str_'>
HN-CHUM-038.npy
<class 'numpy.str_'>
HN-CHUM-039.npy
<class 'numpy.str_'>
HN-CHUM-040.npy
<class 'numpy.str_'>
HN-CHUM-041.npy
<class 'numpy.str_'>
HN-CHUM-042.npy
<class 'numpy.str_'>
HN-CHUM-043.npy
<class 'numpy.str_'>
HN-CHUM-044.npy
<class 'numpy.str_'>
HN-CHUM-045.npy
<class 'numpy.str_'>
HN-CHUM-046.npy
<class 'numpy.str_'>
HN-CHUM-047.npy
<class 'numpy.str_'>
HN-CHUM-048.npy
<class 'numpy.str_'>
HN-CHUM-049.npy
<class 'numpy.str_'>
HN-CHUM-050.npy
<class 'numpy.str_'>
HN-CHUM-051.npy
<class 'numpy.str_'>
HN-CHUM-052.npy
<class 'numpy.str_'>
HN-CHUM-053.npy
<class 'numpy.str_'>
HN-CHUM-054.npy
<class 'numpy.str_'>
HN-CHUM-055.npy
<class 'numpy.str_'>
HN-CHUM-056.npy
<class 'numpy.str_'>
HN-CHUM-057.npy
<class 'numpy.str_'>
HN-CHUM-058.npy
<class 'numpy.str_'>
HN-CHUM-059.npy
<class 'numpy.str_'>
HN-CHUM-060.npy
<class 'numpy.str_'>
HN-CHUM-061.npy
<class 'numpy.str_'>
HN-CHUM-062.npy
<class 'numpy.str_'>
HN-CHUM-063.npy
<class 'numpy.str_'>
HN-CHUM-064.npy
<class 'numpy.str_'>
HN-CHUM-065.npy
<class 'numpy.str_'>
HN-CHUS-001.npy
<class 'numpy.str_'>
HN-CHUS-002.npy
<class 'numpy.str_'>
HN-CHUS-003.npy
<class 'numpy.str_'>
HN-CHUS-004.npy
<class 'numpy.str_'>
HN-CHUS-005.npy
<class 'numpy.str_'>
HN-CHUS-006.npy
<class 'numpy.str_'>
HN-CHUS-007.npy
<class 'numpy.str_'>
HN-CHUS-008.npy
<class 'numpy.str_'>
HN-CHUS-009.npy
<class 'numpy.str_'>
HN-CHUS-010.npy
<class 'numpy.str_'>
HN-CHUS-011.npy
<class 'numpy.str_'>
HN-CHUS-012.npy
<class 'numpy.str_'>
HN-CHUS-013.npy
<class 'numpy.str_'>
HN-CHUS-014.npy
<class 'numpy.str_'>
HN-CHUS-015.npy
<class 'numpy.str_'>
HN-CHUS-016.npy
<class 'numpy.str_'>
HN-CHUS-017.npy
<class 'numpy.str_'>
HN-CHUS-018.npy
<class 'numpy.str_'>
HN-CHUS-019.npy
<class 'numpy.str_'>
HN-CHUS-020.npy
<class 'numpy.str_'>
HN-CHUS-021.npy
<class 'numpy.str_'>
HN-CHUS-022.npy
<class 'numpy.str_'>
HN-CHUS-023.npy
<class 'numpy.str_'>
HN-CHUS-024.npy
<class 'numpy.str_'>
HN-CHUS-025.npy
<class 'numpy.str_'>
HN-CHUS-026.npy
<class 'numpy.str_'>
HN-CHUS-027.npy
<class 'numpy.str_'>
HN-CHUS-028.npy
<class 'numpy.str_'>
HN-CHUS-029.npy
<class 'numpy.str_'>
HN-CHUS-030.npy
<class 'numpy.str_'>
HN-CHUS-031.npy
<class 'numpy.str_'>
HN-CHUS-032.npy
<class 'numpy.str_'>
HN-CHUS-033.npy
<class 'numpy.str_'>
HN-CHUS-034.npy
<class 'numpy.str_'>
HN-CHUS-035.npy
<class 'numpy.str_'>
HN-CHUS-036.npy
<class 'numpy.str_'>
HN-CHUS-037.npy
<class 'numpy.str_'>
HN-CHUS-038.npy
<class 'numpy.str_'>
HN-CHUS-039.npy
<class 'numpy.str_'>
HN-CHUS-040.npy
<class 'numpy.str_'>
HN-CHUS-041.npy
<class 'numpy.str_'>
HN-CHUS-042.npy
<class 'numpy.str_'>
HN-CHUS-043.npy
<class 'numpy.str_'>
HN-CHUS-044.npy
<class 'numpy.str_'>
HN-CHUS-045.npy
<class 'numpy.str_'>
HN-CHUS-046.npy
<class 'numpy.str_'>
HN-CHUS-047.npy
<class 'numpy.str_'>
HN-CHUS-048.npy
<class 'numpy.str_'>
HN-CHUS-049.npy
<class 'numpy.str_'>
HN-CHUS-050.npy
<class 'numpy.str_'>
HN-CHUS-051.npy
<class 'numpy.str_'>
HN-CHUS-052.npy
<class 'numpy.str_'>
HN-CHUS-053.npy
<class 'numpy.str_'>
HN-CHUS-054.npy
<class 'numpy.str_'>
HN-CHUS-055.npy
<class 'numpy.str_'>
HN-CHUS-056.npy
<class 'numpy.str_'>
HN-CHUS-057.npy
<class 'numpy.str_'>
HN-CHUS-058.npy
<class 'numpy.str_'>
HN-CHUS-059.npy
<class 'numpy.str_'>
HN-CHUS-060.npy
<class 'numpy.str_'>
HN-CHUS-061.npy
<class 'numpy.str_'>
HN-CHUS-062.npy
<class 'numpy.str_'>
HN-CHUS-063.npy
<class 'numpy.str_'>
HN-CHUS-064.npy
<class 'numpy.str_'>
HN-CHUS-065.npy
<class 'numpy.str_'>
HN-CHUS-066.npy
<class 'numpy.str_'>
HN-CHUS-067.npy
<class 'numpy.str_'>
HN-CHUS-068.npy
<class 'numpy.str_'>
HN-CHUS-069.npy
<class 'numpy.str_'>
HN-CHUS-070.npy
<class 'numpy.str_'>
HN-CHUS-071.npy
<class 'numpy.str_'>
HN-CHUS-072.npy
<class 'numpy.str_'>
HN-CHUS-073.npy
<class 'numpy.str_'>
HN-CHUS-074.npy
<class 'numpy.str_'>
HN-CHUS-075.npy
<class 'numpy.str_'>
HN-CHUS-076.npy
<class 'numpy.str_'>
HN-CHUS-077.npy
<class 'numpy.str_'>
HN-CHUS-078.npy
<class 'numpy.str_'>
HN-CHUS-080.npy
<class 'numpy.str_'>
HN-CHUS-081.npy
<class 'numpy.str_'>
HN-CHUS-082.npy
<class 'numpy.str_'>
HN-CHUS-083.npy
<class 'numpy.str_'>
HN-CHUS-084.npy
<class 'numpy.str_'>
HN-CHUS-085.npy
<class 'numpy.str_'>
HN-CHUS-086.npy
<class 'numpy.str_'>
HN-CHUS-087.npy
<class 'numpy.str_'>
HN-CHUS-088.npy
<class 'numpy.str_'>
HN-CHUS-089.npy
<class 'numpy.str_'>
HN-CHUS-090.npy
<class 'numpy.str_'>
HN-CHUS-091.npy
<class 'numpy.str_'>
HN-CHUS-092.npy
<class 'numpy.str_'>
HN-CHUS-094.npy
<class 'numpy.str_'>
HN-CHUS-095.npy
<class 'numpy.str_'>
HN-CHUS-096.npy
<class 'numpy.str_'>
HN-CHUS-097.npy
<class 'numpy.str_'>
HN-CHUS-098.npy
<class 'numpy.str_'>
HN-CHUS-099.npy
<class 'numpy.str_'>
HN-CHUS-100.npy
<class 'numpy.str_'>
HN-CHUS-101.npy
<class 'numpy.str_'>
HN-CHUS-102.npy
<class 'numpy.str_'>
HN-HGJ-001.npy
<class 'numpy.str_'>
HN-HGJ-002.npy
<class 'numpy.str_'>
HN-HGJ-003.npy
<class 'numpy.str_'>
HN-HGJ-004.npy
<class 'numpy.str_'>
HN-HGJ-005.npy
<class 'numpy.str_'>
HN-HGJ-006.npy
<class 'numpy.str_'>
HN-HGJ-007.npy
<class 'numpy.str_'>
HN-HGJ-008.npy
<class 'numpy.str_'>
HN-HGJ-009.npy
<class 'numpy.str_'>
HN-HGJ-010.npy
<class 'numpy.str_'>
HN-HGJ-011.npy
<class 'numpy.str_'>
HN-HGJ-012.npy
<class 'numpy.str_'>
HN-HGJ-013.npy
<class 'numpy.str_'>
HN-HGJ-014.npy
<class 'numpy.str_'>
HN-HGJ-015.npy
<class 'numpy.str_'>
HN-HGJ-016.npy
<class 'numpy.str_'>
HN-HGJ-017.npy
<class 'numpy.str_'>
HN-HGJ-018.npy
<class 'numpy.str_'>
HN-HGJ-019.npy
<class 'numpy.str_'>
HN-HGJ-020.npy
<class 'numpy.str_'>
HN-HGJ-021.npy
<class 'numpy.str_'>
HN-HGJ-022.npy
<class 'numpy.str_'>
HN-HGJ-023.npy
<class 'numpy.str_'>
HN-HGJ-024.npy
<class 'numpy.str_'>
HN-HGJ-025.npy
<class 'numpy.str_'>
HN-HGJ-026.npy
<class 'numpy.str_'>
HN-HGJ-027.npy
<class 'numpy.str_'>
HN-HGJ-028.npy
<class 'numpy.str_'>
HN-HGJ-029.npy
<class 'numpy.str_'>
HN-HGJ-030.npy
<class 'numpy.str_'>
HN-HGJ-031.npy
<class 'numpy.str_'>
HN-HGJ-032.npy
<class 'numpy.str_'>
HN-HGJ-033.npy
<class 'numpy.str_'>
HN-HGJ-034.npy
<class 'numpy.str_'>
HN-HGJ-035.npy
<class 'numpy.str_'>
HN-HGJ-036.npy
<class 'numpy.str_'>
HN-HGJ-037.npy
<class 'numpy.str_'>
HN-HGJ-038.npy
<class 'numpy.str_'>
HN-HGJ-039.npy
<class 'numpy.str_'>
HN-HGJ-040.npy
<class 'numpy.str_'>
HN-HGJ-041.npy
<class 'numpy.str_'>
HN-HGJ-042.npy
<class 'numpy.str_'>
HN-HGJ-043.npy
<class 'numpy.str_'>
HN-HGJ-044.npy
<class 'numpy.str_'>
HN-HGJ-045.npy
<class 'numpy.str_'>
HN-HGJ-046.npy
<class 'numpy.str_'>
HN-HGJ-047.npy
<class 'numpy.str_'>
HN-HGJ-048.npy
<class 'numpy.str_'>
HN-HGJ-049.npy
<class 'numpy.str_'>
HN-HGJ-050.npy
<class 'numpy.str_'>
HN-HGJ-051.npy
<class 'numpy.str_'>
HN-HGJ-052.npy
<class 'numpy.str_'>
HN-HGJ-053.npy
<class 'numpy.str_'>
HN-HGJ-054.npy
<class 'numpy.str_'>
HN-HGJ-055.npy
<class 'numpy.str_'>
HN-HGJ-056.npy
<class 'numpy.str_'>
HN-HGJ-057.npy
<class 'numpy.str_'>
HN-HGJ-058.npy
<class 'numpy.str_'>
HN-HGJ-059.npy
<class 'numpy.str_'>
HN-HGJ-060.npy
<class 'numpy.str_'>
HN-HGJ-061.npy
<class 'numpy.str_'>
HN-HGJ-062.npy
<class 'numpy.str_'>
HN-HGJ-063.npy
<class 'numpy.str_'>
HN-HGJ-064.npy
<class 'numpy.str_'>
HN-HGJ-065.npy
<class 'numpy.str_'>
HN-HGJ-066.npy
<class 'numpy.str_'>
HN-HGJ-067.npy
<class 'numpy.str_'>
HN-HGJ-069.npy
<class 'numpy.str_'>
HN-HGJ-070.npy
<class 'numpy.str_'>
HN-HGJ-071.npy
<class 'numpy.str_'>
HN-HGJ-072.npy
<class 'numpy.str_'>
HN-HGJ-073.npy
<class 'numpy.str_'>
HN-HGJ-074.npy
<class 'numpy.str_'>
HN-HGJ-075.npy
<class 'numpy.str_'>
HN-HGJ-076.npy
<class 'numpy.str_'>
HN-HGJ-077.npy
<class 'numpy.str_'>
HN-HGJ-078.npy
<class 'numpy.str_'>
HN-HGJ-079.npy
<class 'numpy.str_'>
HN-HGJ-080.npy
<class 'numpy.str_'>
HN-HGJ-081.npy
<class 'numpy.str_'>
HN-HGJ-082.npy
<class 'numpy.str_'>
HN-HGJ-083.npy
<class 'numpy.str_'>
HN-HGJ-084.npy
<class 'numpy.str_'>
HN-HGJ-085.npy
<class 'numpy.str_'>
HN-HGJ-086.npy
<class 'numpy.str_'>
HN-HGJ-087.npy
<class 'numpy.str_'>
HN-HGJ-088.npy
<class 'numpy.str_'>
HN-HGJ-089.npy
<class 'numpy.str_'>
HN-HGJ-090.npy
<class 'numpy.str_'>
HN-HGJ-091.npy
<class 'numpy.str_'>
HN-HGJ-092.npy
<class 'numpy.str_'>
HN-HMR-001.npy
<class 'numpy.str_'>
HN-HMR-002.npy
<class 'numpy.str_'>
HN-HMR-003.npy
<class 'numpy.str_'>
HN-HMR-004.npy
<class 'numpy.str_'>
HN-HMR-005.npy
<class 'numpy.str_'>
HN-HMR-006.npy
<class 'numpy.str_'>
HN-HMR-008.npy
<class 'numpy.str_'>
HN-HMR-009.npy
<class 'numpy.str_'>
HN-HMR-010.npy
<class 'numpy.str_'>
HN-HMR-011.npy
<class 'numpy.str_'>
HN-HMR-012.npy
<class 'numpy.str_'>
HN-HMR-013.npy
<class 'numpy.str_'>
HN-HMR-014.npy
<class 'numpy.str_'>
HN-HMR-015.npy
<class 'numpy.str_'>
HN-HMR-016.npy
<class 'numpy.str_'>
HN-HMR-018.npy
<class 'numpy.str_'>
HN-HMR-019.npy
<class 'numpy.str_'>
HN-HMR-020.npy
<class 'numpy.str_'>
HN-HMR-021.npy
<class 'numpy.str_'>
HN-HMR-022.npy
<class 'numpy.str_'>
HN-HMR-023.npy
<class 'numpy.str_'>
HN-HMR-024.npy
<class 'numpy.str_'>
