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medai
software
mednet
Commits
b280ec3a
Commit
b280ec3a
authored
1 year ago
by
André Anjos
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[tests] Make naming more explicit
parent
900f69d4
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!6
Making use of LightningDataModule and simplification of data loading
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tests/test_indian.py
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tests/test_indian.py
tests/test_mc.py
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tests/test_mc.py
tests/test_shenzhen.py
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tests/test_shenzhen.py
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# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
"""
Tests for Montgomery dataset.
"""
import
importlib
import
pytest
@pytest.mark.skip
(
reason
=
"
Test need to be updated
"
)
def
test_protocol_consistency
():
# Default protocol
datamodule
=
importlib
.
import_module
(
"
ptbench.data.montgomery.datamodules.default
"
).
datamodule
subset
=
datamodule
.
splits
assert
len
(
subset
)
==
3
assert
"
train
"
in
subset
assert
len
(
subset
[
"
train
"
])
==
88
for
s
in
subset
[
"
train
"
]:
assert
s
[
0
].
startswith
(
"
CXR_png/MCUCXR_0
"
)
assert
"
validation
"
in
subset
assert
len
(
subset
[
"
validation
"
])
==
22
for
s
in
subset
[
"
validation
"
]:
assert
s
[
0
].
startswith
(
"
CXR_png/MCUCXR_0
"
)
assert
"
test
"
in
subset
assert
len
(
subset
[
"
test
"
])
==
28
for
s
in
subset
[
"
test
"
]:
assert
s
[
0
].
startswith
(
"
CXR_png/MCUCXR_0
"
)
# Check labels
for
s
in
subset
[
"
train
"
]:
assert
s
[
1
]
in
[
0.0
,
1.0
]
for
s
in
subset
[
"
validation
"
]:
assert
s
[
1
]
in
[
0.0
,
1.0
]
for
s
in
subset
[
"
test
"
]:
assert
s
[
1
]
in
[
0.0
,
1.0
]
# Cross-validation fold 0-7
for
f
in
range
(
8
):
datamodule
=
importlib
.
import_module
(
f
"
ptbench.data.montgomery.datamodules.fold_
{
str
(
f
)
}
"
).
datamodule
subset
=
datamodule
.
database_split
assert
len
(
subset
)
==
3
assert
"
train
"
in
subset
assert
len
(
subset
[
"
train
"
])
==
99
for
s
in
subset
[
"
train
"
]:
assert
s
[
0
].
startswith
(
"
CXR_png/MCUCXR_0
"
)
assert
"
validation
"
in
subset
assert
len
(
subset
[
"
validation
"
])
==
25
for
s
in
subset
[
"
validation
"
]:
assert
s
[
0
].
startswith
(
"
CXR_png/MCUCXR_0
"
)
assert
"
test
"
in
subset
assert
len
(
subset
[
"
test
"
])
==
14
for
s
in
subset
[
"
test
"
]:
assert
s
[
0
].
startswith
(
"
CXR_png/MCUCXR_0
"
)
# Check labels
for
s
in
subset
[
"
train
"
]:
assert
s
[
1
]
in
[
0.0
,
1.0
]
for
s
in
subset
[
"
validation
"
]:
assert
s
[
1
]
in
[
0.0
,
1.0
]
for
s
in
subset
[
"
test
"
]:
assert
s
[
1
]
in
[
0.0
,
1.0
]
# Cross-validation fold 8-9
for
f
in
range
(
8
,
10
):
datamodule
=
importlib
.
import_module
(
f
"
ptbench.data.montgomery.datamodules.fold_
{
str
(
f
)
}
"
).
datamodule
subset
=
datamodule
.
database_split
assert
len
(
subset
)
==
3
assert
"
train
"
in
subset
assert
len
(
subset
[
"
train
"
])
==
100
for
s
in
subset
[
"
train
"
]:
assert
s
[
0
].
startswith
(
"
CXR_png/MCUCXR_0
"
)
assert
"
validation
"
in
subset
assert
len
(
subset
[
"
validation
"
])
==
25
for
s
in
subset
[
"
validation
"
]:
assert
s
[
0
].
startswith
(
"
CXR_png/MCUCXR_0
"
)
assert
"
test
"
in
subset
assert
len
(
subset
[
"
test
"
])
==
13
for
s
in
subset
[
"
test
"
]:
assert
s
[
0
].
startswith
(
"
CXR_png/MCUCXR_0
"
)
# Check labels
for
s
in
subset
[
"
train
"
]:
assert
s
[
1
]
in
[
0.0
,
1.0
]
for
s
in
subset
[
"
validation
"
]:
assert
s
[
1
]
in
[
0.0
,
1.0
]
for
s
in
subset
[
"
test
"
]:
assert
s
[
1
]
in
[
0.0
,
1.0
]
@pytest.mark.skip
(
reason
=
"
Test need to be updated
"
)
@pytest.mark.skip_if_rc_var_not_set
(
"
datadir.montgomery
"
)
def
test_loading
():
import
torch
import
torchvision.transforms
from
ptbench.data.datamodule
import
_DelayedLoadingDataset
def
_check_sample
(
s
):
assert
len
(
s
)
==
2
data
=
s
[
0
]
metadata
=
s
[
1
]
assert
isinstance
(
data
,
torch
.
Tensor
)
assert
data
.
size
(
0
)
==
1
# check single channel
assert
data
.
size
(
1
)
==
data
.
size
(
2
)
# check square image
assert
(
torchvision
.
transforms
.
ToPILImage
()(
data
).
mode
==
"
L
"
)
# Check colors
assert
"
label
"
in
metadata
assert
metadata
[
"
label
"
]
in
[
0
,
1
]
# Check labels
limit
=
30
# use this to limit testing to first images only, else None
datamodule
=
importlib
.
import_module
(
"
ptbench.data.montgomery.datamodules.default
"
).
datamodule
subset
=
datamodule
.
database_split
raw_data_loader
=
datamodule
.
raw_data_loader
# Need to use private function so we can limit the number of samples to use
dataset
=
_DelayedLoadingDataset
(
subset
[
"
train
"
][:
limit
],
raw_data_loader
)
for
s
in
dataset
:
_check_sample
(
s
)
@pytest.mark.skip
(
reason
=
"
Test need to be updated
"
)
@pytest.mark.skip_if_rc_var_not_set
(
"
datadir.montgomery
"
)
def
test_check
():
from
ptbench.data.split
import
check_database_split_loading
limit
=
30
# use this to limit testing to first images only, else 0
# Default protocol
datamodule
=
importlib
.
import_module
(
"
ptbench.data.montgomery.datamodules.default
"
).
datamodule
database_split
=
datamodule
.
database_split
raw_data_loader
=
datamodule
.
raw_data_loader
assert
(
check_database_split_loading
(
database_split
,
raw_data_loader
,
limit
=
limit
)
==
0
)
# Folds
for
f
in
range
(
10
):
datamodule
=
importlib
.
import_module
(
f
"
ptbench.data.montgomery.datamodules.fold_
{
f
}
"
).
datamodule
database_split
=
datamodule
.
database_split
raw_data_loader
=
datamodule
.
raw_data_loader
assert
(
check_database_split_loading
(
database_split
,
raw_data_loader
,
limit
=
limit
)
==
0
)
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ch
.py
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tests/test_
shenzhen
.py
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0
−
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