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MPBA Radiomics
RADLER
Commits
5ebbe3f7
Commit
5ebbe3f7
authored
Mar 19, 2020
by
Alessia Marcolini
Browse files
Fix dtype NumObjects
parent
d3f1d17b
Changes
1
Show whitespace changes
Inline
Side-by-side
pyradiomics_radler/myfirstorder.py
View file @
5ebbe3f7
...
@@ -226,7 +226,6 @@ class MyRadiomicsFirstOrder(MyRadiomicsFeaturesBase):
...
@@ -226,7 +226,6 @@ class MyRadiomicsFirstOrder(MyRadiomicsFeaturesBase):
return
numpy
.
mean
(
neighborsMax
[
~
numpy
.
isnan
(
neighborsMax
)])
return
numpy
.
mean
(
neighborsMax
[
~
numpy
.
isnan
(
neighborsMax
)])
def
getInactiveVolumeFeatureValue
(
self
):
def
getInactiveVolumeFeatureValue
(
self
):
r
"""
r
"""
**26. Inactive volume **
**26. Inactive volume **
...
@@ -243,8 +242,6 @@ class MyRadiomicsFirstOrder(MyRadiomicsFeaturesBase):
...
@@ -243,8 +242,6 @@ class MyRadiomicsFirstOrder(MyRadiomicsFeaturesBase):
ROIPet
=
self
.
imageArray
ROIPet
=
self
.
imageArray
mask
=
self
.
maskArray
mask
=
self
.
maskArray
ROIPet
[
~
mask
]
=
0
thresh
=
0.01
*
(
numpy
.
max
(
ROIPet
[
~
numpy
.
isnan
(
ROIPet
)])
**
2
)
thresh
=
0.01
*
(
numpy
.
max
(
ROIPet
[
~
numpy
.
isnan
(
ROIPet
)])
**
2
)
mask_inactive
=
ROIPet
>
thresh
mask_inactive
=
ROIPet
>
thresh
...
@@ -290,17 +287,18 @@ class MyRadiomicsFirstOrder(MyRadiomicsFeaturesBase):
...
@@ -290,17 +287,18 @@ class MyRadiomicsFirstOrder(MyRadiomicsFeaturesBase):
mask_inactive
=
oc
.
imclose
(
mask_inactive
,
conn
)
mask_inactive
=
oc
.
imclose
(
mask_inactive
,
conn
)
mask_inactive
=
oc
.
imopen
(
mask_inactive
,
conn
)
mask_inactive
=
oc
.
imopen
(
mask_inactive
,
conn
)
new_mask
=
mask_inactive
+
perimeter
new_mask
=
mask_inactive
+
perimeter
new_mask
[
mask
==
0
]
=
10
new_mask
[
new_mask
==
1
]
=
10
new_mask
[
new_mask
==
1
]
=
10
new_mask
[
new_mask
==
2
]
=
10
new_mask
[
new_mask
==
2
]
=
10
new_mask
[
new_mask
==
0
]
=
1
new_mask
[
new_mask
==
0
]
=
1
new_mask
[
new_mask
==
10
]
=
0
new_mask
[
new_mask
==
10
]
=
0
connObjects
=
oc
.
bwconncomp
(
new_mask
,
26
)
connObjects
=
oc
.
bwconncomp
(
new_mask
,
26
)
b
=
numpy
.
zeros
((
1
,
connObjects
.
NumObjects
))
for
i
in
range
(
connObjects
.
NumObjects
):
b
=
numpy
.
zeros
((
1
,
int
(
connObjects
.
NumObjects
)))
a
=
oc
.
find
(
for
i
in
range
(
int
(
connObjects
.
NumObjects
)):
a
=
numpy
.
where
(
len
(
connObjects
.
PixelIdxList
[
i
])
>=
15
len
(
connObjects
.
PixelIdxList
[
i
])
>=
15
)
# If the number of of pixel forming and object is lower than 15, reject it
)
# If the number of of pixel forming and object is lower than 15, reject it
if
a
.
size
==
0
:
if
a
.
size
==
0
:
...
@@ -308,8 +306,7 @@ class MyRadiomicsFirstOrder(MyRadiomicsFeaturesBase):
...
@@ -308,8 +306,7 @@ class MyRadiomicsFirstOrder(MyRadiomicsFeaturesBase):
else
:
else
:
b
[
i
]
=
1
b
[
i
]
=
1
[
row
,
col
]
=
oc
.
find
(
b
>
0
)
row
,
col
=
numpy
.
where
(
b
>
0
)
sumInactive
=
0
sumInactive
=
0
for
i
in
range
(
len
(
col
)):
for
i
in
range
(
len
(
col
)):
...
@@ -318,9 +315,6 @@ class MyRadiomicsFirstOrder(MyRadiomicsFeaturesBase):
...
@@ -318,9 +315,6 @@ class MyRadiomicsFirstOrder(MyRadiomicsFeaturesBase):
)
)
sumVolume
=
numpy
.
sum
(
mask
)
sumVolume
=
numpy
.
sum
(
mask
)
import
ipdb
ipdb
.
set_trace
()
except
Oct2PyError
as
e
:
except
Oct2PyError
as
e
:
print
(
e
)
print
(
e
)
...
...
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