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Merged
wyli merged 8 commits into from
Dec 15, 2021
Merged

3471 3491 Add example images for intensity transforms #3494

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42a45e0
Merge pull request #19 from Project-MONAI/master
Nic-Ma Feb 1, 2021
cd16a13
Merge pull request #32 from Project-MONAI/master
Nic-Ma Feb 24, 2021
6f87afd
Merge pull request #180 from Project-MONAI/dev
Nic-Ma Jul 22, 2021
f398298
Merge pull request #214 from Project-MONAI/dev
Nic-Ma Sep 8, 2021
d7b86b5
Merge pull request #323 from Project-MONAI/dev
Nic-Ma Dec 15, 2021
0a2b318
[DLMED] add missing images
Nic-Ma Dec 15, 2021
1669b86
[DLMED] fix 3471
Nic-Ma Dec 15, 2021
8565c65
[DLMED] fix AsDiscrete
Nic-Ma Dec 15, 2021
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12 changes: 12 additions & 0 deletions docs/source/transforms.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -324,6 +324,8 @@ Intensity

`SavitzkyGolaySmooth`
"""""""""""""""""""""
.. image:: https://github.com/Project-MONAI/DocImages/raw/main/transforms/SavitzkyGolaySmooth.png
:alt: example of SavitzkyGolaySmooth
.. autoclass:: SavitzkyGolaySmooth
:members:
:special-members: __call__
Expand Down Expand Up @@ -408,6 +410,8 @@ Intensity

`RandRicianNoise`
"""""""""""""""""
.. image:: https://github.com/Project-MONAI/DocImages/raw/main/transforms/RandRicianNoise.png
:alt: example of RandRicianNoise
.. autoclass:: RandRicianNoise
:members:
:special-members: __call__
Expand Down Expand Up @@ -1173,6 +1177,14 @@ Intensity (Dict)
:members:
:special-members: __call__

`RandRicianNoised`
""""""""""""""""""
.. image:: https://github.com/Project-MONAI/DocImages/raw/main/transforms/RandRicianNoised.png
:alt: example of RandRicianNoised
.. autoclass:: RandRicianNoised
:members:
:special-members: __call__

`ScaleIntensityRangePercentilesd`
"""""""""""""""""""""""""""""""""
.. image:: https://github.com/Project-MONAI/DocImages/raw/main/transforms/ScaleIntensityRangePercentilesd.png
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2 changes: 1 addition & 1 deletion monai/transforms/utils.py
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Expand Up @@ -873,7 +873,7 @@ def generate_spatial_bounding_box(
margin: Union[Sequence[int], int] = 0,
) -> Tuple[List[int], List[int]]:
"""
generate the spatial bounding box of foreground in the image with start-end positions.
generate the spatial bounding box of foreground in the image with start-end positions (inclusive).
Users can define arbitrary function to select expected foreground from the whole image or specified channels.
And it can also add margin to every dim of the bounding box.
The output format of the coordinates is:
Expand Down
10 changes: 8 additions & 2 deletions monai/transforms/utils_create_transform_ims.py
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Expand Up @@ -102,9 +102,11 @@
RandGibbsNoise,
RandHistogramShift,
RandKSpaceSpikeNoise,
RandRicianNoise,
RandScaleIntensity,
RandShiftIntensity,
RandStdShiftIntensity,
SavitzkyGolaySmooth,
ScaleIntensityRange,
ScaleIntensityRangePercentiles,
ShiftIntensity,
Expand All @@ -130,6 +132,7 @@
RandGibbsNoised,
RandHistogramShiftd,
RandKSpaceSpikeNoised,
RandRicianNoised,
RandScaleIntensityd,
RandShiftIntensityd,
RandStdShiftIntensityd,
Expand Down Expand Up @@ -520,6 +523,9 @@ def create_transform_im(
dict(keys=CommonKeys.IMAGE, global_prob=1, prob=1, common_sampling=True, intensity_range=(13, 15)),
data,
)
create_transform_im(RandRicianNoise, dict(prob=1.0, mean=1, std=0.5), data)
create_transform_im(RandRicianNoised, dict(keys=CommonKeys.IMAGE, prob=1.0, mean=1, std=0.5), data)
create_transform_im(SavitzkyGolaySmooth, dict(window_length=5, order=1), data)
create_transform_im(GibbsNoise, dict(alpha=0.8), data)
create_transform_im(GibbsNoised, dict(keys=CommonKeys.IMAGE, alpha=0.8), data)
create_transform_im(RandGibbsNoise, dict(prob=1.0, alpha=(0.6, 0.8)), data)
Expand Down Expand Up @@ -640,8 +646,8 @@ def create_transform_im(
create_transform_im(RandScaleCropd, dict(keys=keys, roi_scale=0.4), data)
create_transform_im(CenterScaleCrop, dict(roi_scale=0.4), data)
create_transform_im(CenterScaleCropd, dict(keys=keys, roi_scale=0.4), data)
create_transform_im(AsDiscrete, dict(to_onehot=2, threshold=10), data, is_post=True, colorbar=True)
create_transform_im(AsDiscreted, dict(keys=CommonKeys.LABEL, to_onehot=2, threshold=10), data, is_post=True)
create_transform_im(AsDiscrete, dict(to_onehot=None, threshold=10), data, is_post=True, colorbar=True)
create_transform_im(AsDiscreted, dict(keys=CommonKeys.LABEL, to_onehot=None, threshold=10), data, is_post=True)
create_transform_im(LabelFilter, dict(applied_labels=(1, 2, 3, 4, 5, 6)), data, is_post=True)
create_transform_im(
LabelFilterd, dict(keys=CommonKeys.LABEL, applied_labels=(1, 2, 3, 4, 5, 6)), data, is_post=True
Expand Down