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Tamino Huxohl
mu-map
Commits
b816d3ac
Commit
b816d3ac
authored
2 years ago
by
Tamino Huxohl
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replace prepare script
parent
68b1f0dd
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1 changed file
mu_map/polar_map/prepare.py
+55
-68
55 additions, 68 deletions
mu_map/polar_map/prepare.py
with
55 additions
and
68 deletions
mu_map/polar_map/prepare.py
+
55
−
68
View file @
b816d3ac
...
...
@@ -2,7 +2,7 @@ import argparse
import
os
from
typing
import
List
from
mu_map.file.dicom
import
DICOM
from
mu_map.file.dicom
import
DICOM
,
DICOMTime
def
get_files_recursive
(
_dir
:
str
)
->
List
[
str
]:
...
...
@@ -25,7 +25,7 @@ def get_files_recursive(_dir: str) -> List[str]:
def
is_scatter_corrected
(
dcm
:
DICOM
)
->
bool
:
return
not
(
"
No
SC
"
in
dcm
.
SeriesDescription
)
return
"
SC
"
in
dcm
.
SeriesDescription
def
is_attenuation_corrected
(
dcm
:
DICOM
)
->
bool
:
...
...
@@ -33,14 +33,14 @@ def is_attenuation_corrected(dcm: DICOM) -> bool:
def
shows_segments
(
dcm
:
DICOM
)
->
bool
:
return
"
PolarMapSeg
"
in
dcm
.
SeriesDescription
return
"
segment
"
in
dcm
.
SeriesDescription
.
lower
()
def
get_type
(
dcm
:
DICOM
)
->
str
:
description
=
dcm
.
SeriesDescription
.
lower
()
if
"
syn
"
in
description
:
return
"
synthetic
"
elif
"
ct
"
in
description
:
if
"
DLAC
"
in
description
:
return
"
dl
"
elif
"
CTAC
"
in
description
:
return
"
ct
"
else
:
return
"
symbia
"
...
...
@@ -100,10 +100,17 @@ if __name__ == "__main__":
help
=
"
the csv file containing meta information of the dataset of which the generated polar maps are
"
,
)
parser
.
add_argument
(
"
--rect
"
,
"
--rect
_upper
"
,
type
=
int
,
nargs
=
4
,
default
=
[
19
,
938
,
649
,
1568
],
default
=
[
22
,
1499
,
22
+
588
,
1500
+
588
],
help
=
"
rectangle as [top, left, bottom, right] coordinates where the polar map is found in the DICOM images
"
,
)
parser
.
add_argument
(
"
--rect_lower
"
,
type
=
int
,
nargs
=
4
,
default
=
[
634
,
1499
,
634
+
588
,
1500
+
588
],
help
=
"
rectangle as [top, left, bottom, right] coordinates where the polar map is found in the DICOM images
"
,
)
parser
.
add_argument
(
...
...
@@ -143,6 +150,8 @@ if __name__ == "__main__":
os
.
mkdir
(
args
.
images_dir
)
meta
=
pd
.
read_csv
(
args
.
meta_csv
)
meta
[
meta_headers
.
datetime_acquisition
]
=
pd
.
to_datetime
(
meta
[
meta_headers
.
datetime_acquisition
])
dcm_files
=
sorted
(
get_files_recursive
(
args
.
polar_map_dir
))
data
=
pd
.
DataFrame
(
...
...
@@ -168,78 +177,56 @@ if __name__ == "__main__":
protocol
=
get_protocol
(
dcm
)
patient_id
=
int
(
dcm
.
PatientID
)
meta_row
=
meta
[
meta_row
s
=
meta
[
(
meta
[
meta_headers
.
patient_id
]
==
patient_id
)
&
(
meta
[
meta_headers
.
protocol
]
==
protocol
)
].
iloc
[
0
]
&
(
meta
[
meta_headers
.
datetime_acquisition
]
==
DICOMTime
.
Acquisition
.
to_datetime
(
dcm
))
]
assert
len
(
meta_rows
)
==
1
meta_row
=
meta_rows
.
iloc
[
0
]
row
=
{
headers
.
id
:
meta_row
[
meta_headers
.
id
],
headers
.
sc
:
is_scatter_corrected
(
dcm
),
headers
.
ac
:
is_attenuation_corrected
(
dcm
),
headers
.
segments
:
shows_segments
(
dcm
),
headers
.
type
:
get_type
(
dcm
),
}
top
,
left
,
bottom
,
right
=
args
.
rect
polar_map
=
img
[
top
:
bottom
,
left
:
right
]
polar_map
=
cv
.
cvtColor
(
polar_map
,
cv
.
COLOR_RGB2BGR
)
# Note: the images created by Syngo.Via show polar maps of rest studies
# further down per default. This little bit of code selects this area
# further down if correcting this was forgotten
if
polar_map
.
mean
()
<
10
:
offset
=
649
top
=
top
+
offset
bottom
=
bottom
+
offset
types
=
dcm
.
SeriesDescription
.
split
(
"
-
"
)[
-
1
]
types
=
types
[:
-
1
].
strip
()
types
=
types
.
split
(
"
/
"
)
for
_type
,
rect
in
zip
(
types
,
[
args
.
rect_upper
,
args
.
rect_lower
]):
top
,
left
,
bottom
,
right
=
rect
polar_map
=
img
[
top
:
bottom
,
left
:
right
]
polar_map
=
cv
.
cvtColor
(
polar_map
,
cv
.
COLOR_RGB2BGR
)
_ac
=
"
ac
"
if
row
[
headers
.
ac
]
else
"
nac
"
_sc
=
"
sc
"
if
row
[
headers
.
sc
]
else
"
nsc
"
_seg
=
"
segments
"
if
row
[
headers
.
segments
]
else
"
gray
"
_file
=
f
"
{
row
[
headers
.
id
]
:
04
d
}
-
{
_seg
}
_
{
_ac
}
_
{
_sc
}
_
{
row
[
headers
.
type
]
}
.png
"
row
[
headers
.
file
]
=
_file
_file
=
os
.
path
.
join
(
args
.
images_dir
,
_file
)
if
(
len
(
data
[
(
data
[
headers
.
id
]
==
row
[
headers
.
id
])
&
(
data
[
headers
.
sc
]
==
row
[
headers
.
sc
])
&
(
data
[
headers
.
ac
]
==
row
[
headers
.
ac
])
&
(
data
[
headers
.
segments
]
==
row
[
headers
.
segments
])
&
(
data
[
headers
.
type
]
==
row
[
headers
.
type
])
]
)
>
0
):
logger
.
warning
(
f
"
Skip
{
dcm_file
}
as it is a duplicate for row:
{
row
}
"
)
continue
logger
.
debug
(
f
"
For series
{
dcm
.
SeriesDescription
}
store row
{
row
}
"
)
store
=
not
args
.
interactive
if
args
.
interactive
:
while
True
:
cv
.
imshow
(
"
Polar Map
"
,
cv
.
resize
(
polar_map
,
(
512
,
512
)))
key
=
cv
.
waitKey
(
0
)
if
key
==
ord
(
"
q
"
):
exit
(
0
)
elif
key
==
ord
(
"
n
"
):
break
elif
key
==
ord
(
"
s
"
):
store
=
True
break
if
store
:
cv
.
imwrite
(
_file
,
polar_map
)
row
=
pd
.
DataFrame
(
row
,
index
=
[
0
])
data
=
pd
.
concat
((
data
,
row
),
ignore_index
=
True
)
data
=
data
.
sort_values
(
by
=
[
headers
.
id
,
headers
.
file
])
data
.
to_csv
(
args
.
csv
,
index
=
False
)
row
[
headers
.
type
]
=
_type
[:
2
].
lower
()
_seg
=
"
segments
"
if
row
[
headers
.
segments
]
else
"
gray
"
_file
=
f
"
{
row
[
headers
.
id
]
:
04
d
}
-
{
_seg
}
_ac_nsc_
{
row
[
headers
.
type
]
}
.png
"
row
[
headers
.
file
]
=
_file
_file
=
os
.
path
.
join
(
args
.
images_dir
,
_file
)
logger
.
debug
(
f
"
For series
{
dcm
.
SeriesDescription
}
store row
{
row
}
"
)
store
=
not
args
.
interactive
if
args
.
interactive
:
while
True
:
cv
.
imshow
(
"
Polar Map
"
,
cv
.
resize
(
polar_map
,
(
1024
,
1024
)))
key
=
cv
.
waitKey
(
0
)
if
key
==
ord
(
"
q
"
):
exit
(
0
)
elif
key
==
ord
(
"
n
"
):
break
elif
key
==
ord
(
"
s
"
):
store
=
True
break
if
store
:
cv
.
imwrite
(
_file
,
polar_map
)
data
=
pd
.
concat
((
data
,
pd
.
DataFrame
(
row
,
index
=
[
0
])),
ignore_index
=
True
)
data
=
data
.
sort_values
(
by
=
[
headers
.
id
,
headers
.
file
])
data
.
to_csv
(
args
.
csv
,
index
=
False
)
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