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Implementation of intensity clipping transform: bot hard and soft approaches #7535
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… soft clipping approaches Signed-off-by: Lucas Robinet <[email protected]>
Signed-off-by: Lucas Robinet <[email protected]>
KumoLiu
requested review from
atbenmurray,
ericspod,
Nic-Ma,
KumoLiu and
dongyang0122
March 18, 2024 03:17
KumoLiu
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Thanks for the PR, overall looks good to me.
Signed-off-by: Lucas Robinet <[email protected]>
… percentile-clipper
Signed-off-by: Lucas Robinet <[email protected]>
Signed-off-by: Lucas Robinet <[email protected]>
for more information, see https://pre-commit.ci
Signed-off-by: Lucas Robinet <[email protected]>
… percentile-clipper
dongyang0122
reviewed
Apr 4, 2024
Signed-off-by: Lucas Robinet <[email protected]>
Signed-off-by: Lucas Robinet <[email protected]>
dongyang0122
approved these changes
Apr 4, 2024
dongyang0122
reviewed
Apr 4, 2024
…ames for ClipIntensityPercentiles class Signed-off-by: Lucas Robinet <[email protected]>
for more information, see https://pre-commit.ci
…lues Signed-off-by: Lucas Robinet <[email protected]>
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Fixes Issue #7512.
Description
Addition of a transformation allowing values above or below a certain percentile to be clipped.
Clipping can be hard or soft.
With soft clipping, the function remains derivable and the order of the values is respected, with smoother corners.
The soft clipping function is based on this medium article https://medium.com/life-at-hopper/clip-it-clip-it-good-1f1bf711b291
It's important to note that I've chosen to switch from Nones values to percentiles to take account of the fact that soft clipping can be one-sided or two-sided.
In fact, providing percentiles of 100 or 0 doesn't change anything in the case of hard clipping, but it does in the case of soft clipping because the function is smoothed. Hence the interest in introducing the possibility of putting None to avoid smoothing the function on one side or the other.
To implement this we had to define a
softplus
function inmonai.transforms.utils_pytorch_numpy_unification.py
. One of the problems is thatnp.logaddexp
do not exactly yields same outputs astorch.logaddexp
. I've left it as is and lowered the tolerance of the tests slightly, but it's possible to force the conversion to numpy and then switch back to torch to ensure better unification between the frameworks.I've also added the
soft_clip
function inmonai.transforms.utils.py
with the associated unit tests to ensure that the transformation works properly.Types of changes
./runtests.sh -f -u --net --coverage
../runtests.sh --quick --unittests --disttests
.make html
command in thedocs/
folder.