From 1558bf8e365a3dc110fbde4e5a9b2c40568de831 Mon Sep 17 00:00:00 2001 From: KumoLiu Date: Mon, 4 Sep 2023 10:40:20 +0800 Subject: [PATCH 1/3] fix #6685 Signed-off-by: KumoLiu --- monai/auto3dseg/utils.py | 2 +- monai/transforms/utils_create_transform_ims.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/monai/auto3dseg/utils.py b/monai/auto3dseg/utils.py index 61ca58b6fe..8e6e6a9573 100644 --- a/monai/auto3dseg/utils.py +++ b/monai/auto3dseg/utils.py @@ -62,7 +62,7 @@ def get_foreground_image(image: MetaTensor) -> np.ndarray: the size of the output is smaller than the input. """ - copper = CropForeground(select_fn=lambda x: x > 0) + copper = CropForeground(select_fn=lambda x: x > 0, allow_smaller=False) image_foreground = copper(image) return cast(np.ndarray, image_foreground) diff --git a/monai/transforms/utils_create_transform_ims.py b/monai/transforms/utils_create_transform_ims.py index a98cdfe936..4b5990abd3 100644 --- a/monai/transforms/utils_create_transform_ims.py +++ b/monai/transforms/utils_create_transform_ims.py @@ -538,8 +538,8 @@ def create_transform_im( ) create_transform_im(DivisiblePad, dict(k=64), data) create_transform_im(DivisiblePadd, dict(keys=keys, k=64), data) - create_transform_im(CropForeground, dict(), data) - create_transform_im(CropForegroundd, dict(keys=keys, source_key=CommonKeys.IMAGE), data) + create_transform_im(CropForeground, dict(allow_smaller=False), data) + create_transform_im(CropForegroundd, dict(keys=keys, source_key=CommonKeys.IMAGE, allow_smaller=False), data) create_transform_im(RandGaussianNoise, dict(prob=1, mean=0, std=0.1), data) create_transform_im(RandGaussianNoised, dict(keys=CommonKeys.IMAGE, prob=1, mean=0, std=0.1), data) create_transform_im(KSpaceSpikeNoise, dict(loc=(100, 100, 100), k_intensity=13), data) From 8b9f2aae40b8e35363832ebfa595804b0d66f8e6 Mon Sep 17 00:00:00 2001 From: KumoLiu Date: Mon, 4 Sep 2023 11:27:14 +0800 Subject: [PATCH 2/3] minor fix Signed-off-by: KumoLiu --- monai/auto3dseg/utils.py | 2 +- monai/metrics/utils.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/monai/auto3dseg/utils.py b/monai/auto3dseg/utils.py index 8e6e6a9573..7aee846225 100644 --- a/monai/auto3dseg/utils.py +++ b/monai/auto3dseg/utils.py @@ -62,7 +62,7 @@ def get_foreground_image(image: MetaTensor) -> np.ndarray: the size of the output is smaller than the input. """ - copper = CropForeground(select_fn=lambda x: x > 0, allow_smaller=False) + copper = CropForeground(select_fn=lambda x: x > 0, allow_smaller=True) image_foreground = copper(image) return cast(np.ndarray, image_foreground) diff --git a/monai/metrics/utils.py b/monai/metrics/utils.py index 3213689b33..62b2f1b6ec 100644 --- a/monai/metrics/utils.py +++ b/monai/metrics/utils.py @@ -176,7 +176,7 @@ def get_mask_edges( else: # pytorch subvoxel, maybe on gpu, but croppad boolean values on GPU is not supported seg_pred, seg_gt, or_vol = convert_to_tensor(channel_first, dtype=torch.float16) cropper = CropForegroundD( - ["pred", "gt"], source_key="src", margin=1, allow_smaller=False, start_coord_key=None, end_coord_key=None + ["pred", "gt"], source_key="src", margin=1, allow_smaller=True, start_coord_key=None, end_coord_key=None ) cropped = cropper({"pred": seg_pred, "gt": seg_gt, "src": or_vol}) # type: ignore seg_pred, seg_gt = cropped["pred"][0], cropped["gt"][0] From fbc8290d23ff1d3a7c17f32f37a5ceabf73f5631 Mon Sep 17 00:00:00 2001 From: KumoLiu Date: Mon, 4 Sep 2023 12:58:27 +0800 Subject: [PATCH 3/3] minor fix Signed-off-by: KumoLiu --- monai/metrics/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/monai/metrics/utils.py b/monai/metrics/utils.py index 62b2f1b6ec..3213689b33 100644 --- a/monai/metrics/utils.py +++ b/monai/metrics/utils.py @@ -176,7 +176,7 @@ def get_mask_edges( else: # pytorch subvoxel, maybe on gpu, but croppad boolean values on GPU is not supported seg_pred, seg_gt, or_vol = convert_to_tensor(channel_first, dtype=torch.float16) cropper = CropForegroundD( - ["pred", "gt"], source_key="src", margin=1, allow_smaller=True, start_coord_key=None, end_coord_key=None + ["pred", "gt"], source_key="src", margin=1, allow_smaller=False, start_coord_key=None, end_coord_key=None ) cropped = cropper({"pred": seg_pred, "gt": seg_gt, "src": or_vol}) # type: ignore seg_pred, seg_gt = cropped["pred"][0], cropped["gt"][0]