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FSL
fslpy
Commits
1d8aba54
Commit
1d8aba54
authored
Apr 17, 2017
by
Paul McCarthy
Browse files
Unit tests for 'advanced' image features (indexed, calcrange)
parent
e3ab8905
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tests/test_image_advanced.py
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1d8aba54
#!/usr/bin/env python
#
# test_image_advanced.py -
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
import
os.path
as
op
import
time
import
numpy
as
np
import
nibabel
as
nib
import
tests
import
fsl.data.image
as
fslimage
def
test_image_indexed_threaded
(
):
_test_image_indexed
(
True
)
def
test_image_indexed_unthreaded
():
_test_image_indexed
(
False
)
def
_test_image_indexed
(
threaded
):
with
tests
.
testdir
()
as
testdir
:
filename
=
op
.
join
(
testdir
,
'image.nii.gz'
)
# Data range grows with volume
data
=
np
.
zeros
((
100
,
100
,
100
,
50
))
for
vol
in
range
(
data
.
shape
[
-
1
]):
data
[...,
vol
]
=
vol
fslimage
.
Image
(
data
).
save
(
filename
)
img
=
fslimage
.
Image
(
filename
,
loadData
=
False
,
calcRange
=
False
,
indexed
=
True
,
threaded
=
threaded
)
# First iteration through the image
start1
=
time
.
time
()
for
vol
in
range
(
data
.
shape
[
-
1
]):
img
[...,
vol
]
if
threaded
:
img
.
getImageWrapper
().
getTaskThread
().
waitUntilIdle
()
assert
img
.
dataRange
==
(
0
,
vol
)
end1
=
time
.
time
()
# Second iteration through
start2
=
time
.
time
()
for
vol
in
range
(
data
.
shape
[
-
1
]):
img
[...,
vol
]
end2
=
time
.
time
()
# Second iteration should be much faster!
assert
(
end1
-
start1
)
>
(
end2
-
start2
)
def
test_image_indexed_read4D_threaded
(
seed
):
_test_image_indexed_read4D
(
True
)
def
test_image_indexed_read4D_unthreaded
(
seed
):
_test_image_indexed_read4D
(
False
)
def
_test_image_indexed_read4D
(
threaded
):
with
tests
.
testdir
()
as
testdir
:
filename
=
op
.
join
(
testdir
,
'image.nii.gz'
)
# Data range grows with volume
nvols
=
50
data
=
np
.
zeros
((
100
,
100
,
100
,
nvols
))
for
vol
in
range
(
nvols
):
data
[...,
vol
]
=
vol
fslimage
.
Image
(
data
).
save
(
filename
)
img
=
fslimage
.
Image
(
filename
,
loadData
=
False
,
calcRange
=
False
,
indexed
=
True
,
threaded
=
threaded
)
# Test reading slice through
# 4D (e.g. voxel time course)
#
# n.b. This is SUPER SLOW!!
voxels
=
tests
.
random_voxels
((
100
,
100
,
100
),
5
)
for
i
,
xyz
in
enumerate
(
voxels
):
x
,
y
,
z
=
[
int
(
v
)
for
v
in
xyz
]
data
=
img
[
x
,
y
,
z
,
:]
if
threaded
:
img
.
getImageWrapper
().
getTaskThread
().
waitUntilIdle
()
assert
np
.
all
(
data
==
np
.
arange
(
nvols
))
def
test_image_indexed_save_threaded
(
):
_test_image_indexed_save
(
True
)
def
test_image_indexed_save_unthreaded
():
_test_image_indexed_save
(
False
)
def
_test_image_indexed_save
(
threaded
):
with
tests
.
testdir
()
as
testdir
:
filename
=
op
.
join
(
testdir
,
'image.nii.gz'
)
# Data range grows with volume
data
=
np
.
zeros
((
100
,
100
,
100
,
50
))
for
vol
in
range
(
data
.
shape
[
-
1
]):
data
[...,
vol
]
=
vol
fslimage
.
Image
(
data
).
save
(
filename
)
img
=
fslimage
.
Image
(
filename
,
loadData
=
False
,
calcRange
=
False
,
indexed
=
True
,
threaded
=
threaded
)
# access some data
img
[...,
0
]
img
[...,
40
]
if
threaded
:
img
.
getImageWrapper
().
getTaskThread
().
waitUntilIdle
()
# make sure the data range is correct
assert
img
.
dataRange
==
(
0
,
40
)
# change some data
data
=
np
.
zeros
((
100
,
100
,
100
))
data
[:]
=
45
img
[...,
40
]
=
data
if
threaded
:
img
.
getImageWrapper
().
getTaskThread
().
waitUntilIdle
()
# save the image
img
.
save
()
assert
img
.
dataRange
==
(
0
,
45
)
# access the data - index should
# get rebuilt to this point
img
[...,
0
]
img
[...,
40
]
if
threaded
:
img
.
getImageWrapper
().
getTaskThread
().
waitUntilIdle
()
# make sure we got the modified data
assert
img
.
dataRange
==
(
0
,
45
)
img
[...,
49
]
if
threaded
:
img
.
getImageWrapper
().
getTaskThread
().
waitUntilIdle
()
# make sure we got the modified data
assert
img
.
dataRange
==
(
0
,
49
)
# Finally, reload, and verify the change
img
=
fslimage
.
Image
(
filename
)
assert
np
.
all
(
img
[...,
40
]
==
45
)
def
test_image_no_calcRange_threaded
():
_test_image_no_calcRange
(
True
)
def
test_image_no_calcRange_unthreaded
():
_test_image_no_calcRange
(
False
)
def
_test_image_no_calcRange
(
threaded
):
# Data range grows with volume
data
=
np
.
zeros
((
100
,
100
,
100
,
50
))
for
vol
in
range
(
data
.
shape
[
-
1
]):
data
[...,
vol
]
=
vol
img
=
nib
.
nifti1
.
Nifti1Image
(
data
,
np
.
eye
(
4
))
img
.
header
[
'cal_min'
]
=
95
img
.
header
[
'cal_max'
]
=
643
img
=
fslimage
.
Image
(
img
,
loadData
=
False
,
calcRange
=
False
,
threaded
=
threaded
)
# dataRange should fallback to
# cal_min/max if it is unknown
assert
img
.
dataRange
==
(
95
,
643
)
for
i
in
[
0
,
7
,
40
]:
img
[...,
i
]
if
threaded
:
img
.
getImageWrapper
().
getTaskThread
().
waitUntilIdle
()
assert
img
.
dataRange
==
(
0
,
i
)
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