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MPBA Radiomics
RADLER
Commits
cfd821c9
Commit
cfd821c9
authored
Mar 19, 2020
by
Alessia Marcolini
Browse files
Fix calculation of InactiveVolume feature
parent
5ebbe3f7
Changes
1
Hide whitespace changes
Inline
Side-by-side
pyradiomics_radler/myfirstorder.py
View file @
cfd821c9
...
...
@@ -234,7 +234,8 @@ class MyRadiomicsFirstOrder(MyRadiomicsFeaturesBase):
a threshold of 0.01 × (SUVmax)^2 followed by closing and opening morphological operations were used
to differentiate active and inactive regions on FDG-PET scans
- input: 3D array representing the PET volume in SUV format
- input: 3D array representing the PET volume in SUV format, with
voxels outside the ROI set to NaNs.
.. note::
Extracted from PET scans and not used in the CT feature set.
...
...
@@ -244,7 +245,8 @@ class MyRadiomicsFirstOrder(MyRadiomicsFeaturesBase):
thresh
=
0.01
*
(
numpy
.
max
(
ROIPet
[
~
numpy
.
isnan
(
ROIPet
)])
**
2
)
mask_inactive
=
ROIPet
>
thresh
mask_thresholded
=
ROIPet
>
thresh
mask_inactive
=
numpy
.
logical_and
(
mask_thresholded
,
mask
)
# MORPHOLOGICAL OPERATIONS
conn
=
numpy
.
zeros
([
5
,
5
,
5
])
...
...
@@ -288,6 +290,7 @@ class MyRadiomicsFirstOrder(MyRadiomicsFeaturesBase):
mask_inactive
=
oc
.
imopen
(
mask_inactive
,
conn
)
new_mask
=
mask_inactive
+
perimeter
new_mask
[
mask
==
0
]
=
10
new_mask
[
new_mask
==
1
]
=
10
new_mask
[
new_mask
==
2
]
=
10
new_mask
[
new_mask
==
0
]
=
1
...
...
@@ -298,21 +301,23 @@ class MyRadiomicsFirstOrder(MyRadiomicsFeaturesBase):
b
=
numpy
.
zeros
((
1
,
int
(
connObjects
.
NumObjects
)))
for
i
in
range
(
int
(
connObjects
.
NumObjects
)):
a
=
numpy
.
where
(
len
(
connObjects
.
PixelIdxList
[
i
])
>=
15
)
# If the number of of pixel forming and object is lower than 15, reject it
if
a
.
size
==
0
:
b
[
i
]
=
0
if
isinstance
(
connObjects
.
PixelIdxList
[
0
][
i
],
numpy
.
ndarray
):
a
=
connObjects
.
PixelIdxList
[
0
][
i
].
shape
[
0
]
# If the number of of pixel forming and object is lower than 15, reject it
if
a
<
15
:
b
[:,
i
]
=
0
else
:
b
[:,
i
]
=
1
else
:
b
[
i
]
=
1
row
,
col
=
numpy
.
where
(
b
>
0
)
sumInactive
=
0
b
[:,
i
]
=
0
for
i
in
range
(
len
(
col
)):
sumInactive
=
sumInactive
+
len
(
connObjects
.
PixelIdxList
[
row
[
i
],
col
[
i
]]
)
rows
,
cols
=
numpy
.
where
(
b
>
0
)
sumInactive
=
sum
(
[
connObjects
.
PixelIdxList
[
rows
,
cols
][
i
].
shape
[
0
]
for
i
in
range
(
len
(
cols
))
]
)
sumVolume
=
numpy
.
sum
(
mask
)
...
...
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