From 0a2b31872dcc0399a7d41cfc6c5ce14acaa77063 Mon Sep 17 00:00:00 2001 From: Nic Ma Date: Wed, 15 Dec 2021 17:16:25 +0800 Subject: [PATCH 1/3] [DLMED] add missing images Signed-off-by: Nic Ma --- docs/source/transforms.rst | 12 ++++++++++++ monai/transforms/utils_create_transform_ims.py | 6 ++++++ 2 files changed, 18 insertions(+) diff --git a/docs/source/transforms.rst b/docs/source/transforms.rst index 24167abe75..8b1a77ea4c 100644 --- a/docs/source/transforms.rst +++ b/docs/source/transforms.rst @@ -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__ @@ -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__ @@ -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 diff --git a/monai/transforms/utils_create_transform_ims.py b/monai/transforms/utils_create_transform_ims.py index 59d359639b..c28e4558c2 100644 --- a/monai/transforms/utils_create_transform_ims.py +++ b/monai/transforms/utils_create_transform_ims.py @@ -102,9 +102,11 @@ RandGibbsNoise, RandHistogramShift, RandKSpaceSpikeNoise, + RandRicianNoise, RandScaleIntensity, RandShiftIntensity, RandStdShiftIntensity, + SavitzkyGolaySmooth, ScaleIntensityRange, ScaleIntensityRangePercentiles, ShiftIntensity, @@ -130,6 +132,7 @@ RandGibbsNoised, RandHistogramShiftd, RandKSpaceSpikeNoised, + RandRicianNoised, RandScaleIntensityd, RandShiftIntensityd, RandStdShiftIntensityd, @@ -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) From 1669b865f4e9e9aa993a50f267df85bd0df17487 Mon Sep 17 00:00:00 2001 From: Nic Ma Date: Wed, 15 Dec 2021 17:22:48 +0800 Subject: [PATCH 2/3] [DLMED] fix 3471 Signed-off-by: Nic Ma --- monai/transforms/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/monai/transforms/utils.py b/monai/transforms/utils.py index b0553ff8c7..35f7930df0 100644 --- a/monai/transforms/utils.py +++ b/monai/transforms/utils.py @@ -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: From 8565c654d8388ce23344cf9c96301f926b8e866c Mon Sep 17 00:00:00 2001 From: Nic Ma Date: Wed, 15 Dec 2021 17:54:21 +0800 Subject: [PATCH 3/3] [DLMED] fix AsDiscrete Signed-off-by: Nic Ma --- monai/transforms/utils_create_transform_ims.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/monai/transforms/utils_create_transform_ims.py b/monai/transforms/utils_create_transform_ims.py index c28e4558c2..7dc2fbae6d 100644 --- a/monai/transforms/utils_create_transform_ims.py +++ b/monai/transforms/utils_create_transform_ims.py @@ -646,8 +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