how to use RemoveSmallObjects?

[lg2578]

my codes:

post_pred_val=Compose([
    EnsureType(), 
    FillHoles(),
    RemoveSmallObjects(min_size=64),
    AsDiscrete(argmax=True, to_onehot=2)
])
model.load_state_dict(torch.load(
    os.path.join(root2_dir, "best_metric_model.pth")))
model.eval()

with torch.no_grad():
    for test_data in test_loader:
        test_inputs = test_data["image"].to(device)
        test_labels = test_data["label"].to(device)
#         print(test_inputs.shape,test_labels.shape)
        roi_size = cropsize
        sw_batch_size = 4
        test_outputs = sliding_window_inference(
        test_inputs, roi_size, sw_batch_size, model)
        test_outputs = [post_pred_val(i) for i in decollate_batch(test_outputs)]
        test_labels = [post_label(i) for i in decollate_batch(test_labels)]
        dice_metric(y_pred=test_outputs, y=test_labels)
        hd95_metric(y_pred=test_outputs, y=test_labels)

    # aggregate the final mean dice result
    metric_org = dice_metric.aggregate().item()
    metric_hd = hd95_metric.aggregate().item()
    # reset the status for next validation round
    dice_metric.reset()
    hd95_metric.reset()


print("Metric on test data: ", metric_org,metric_hd)

error messages:

---

ValueError Traceback (most recent call last)
/opt/conda/lib/python3.7/site-packages/skimage/morphology/misc.py in remove_small_objects(ar, min_size, connectivity, in_place)
124 try:
--> 125 component_sizes = np.bincount(ccs.ravel())
126 except ValueError:

<array_function internals> in bincount(*args, **kwargs)

ValueError: 'list' argument must have no negative elements

During handling of the above exception, another exception occurred:

ValueError Traceback (most recent call last)
/opt/conda/lib/python3.7/site-packages/monai/transforms/transform.py in apply_transform(transform, data, map_items, unpack_items, log_stats)
101 return [_apply_transform(transform, item, unpack_items) for item in data]
--> 102 return _apply_transform(transform, data, unpack_items)
103 except Exception as e:

/opt/conda/lib/python3.7/site-packages/monai/transforms/transform.py in _apply_transform(transform, parameters, unpack_parameters)
65
---> 66 return transform(parameters)
67
/opt/conda/lib/python3.7/site-packages/monai/transforms/post/array.py in call(self, img)
388 """
--> 389 return remove_small_objects(img, self.min_size, self.connectivity, self.independent_channels)
390

/opt/conda/lib/python3.7/site-packages/monai/transforms/utils.py in remove_small_objects(img, min_size, connectivity, independent_channels)
1039
-> 1040 out_np = morphology.remove_small_objects(img_np, min_size, connectivity)
1041 out, *_ = convert_to_dst_type(out_np, img)

/opt/conda/lib/python3.7/site-packages/skimage/morphology/misc.py in remove_small_objects(ar, min_size, connectivity, in_place)
126 except ValueError:
--> 127 raise ValueError("Negative value labels are not supported. Try "
128 "relabeling the input with scipy.ndimage.label or "
ValueError: Negative value labels are not supported. Try relabeling the input with scipy.ndimage.label or skimage.morphology.label.

The above exception was the direct cause of the following exception:

RuntimeError Traceback (most recent call last)
/tmp/ipykernel_17/2975415042.py in
18 test_outputs = sliding_window_inference(
19 test_inputs, roi_size, sw_batch_size, model)
---> 20 test_outputs = [post_pred_val(i) for i in decollate_batch(test_outputs)]
21 test_labels = [post_label(i) for i in decollate_batch(test_labels)]
22 #

/tmp/ipykernel_17/2975415042.py in (.0)
18 test_outputs = sliding_window_inference(
19 test_inputs, roi_size, sw_batch_size, model)
---> 20 test_outputs = [post_pred_val(i) for i in decollate_batch(test_outputs)]
21 test_labels = [post_label(i) for i in decollate_batch(test_labels)]
22 #
/opt/conda/lib/python3.7/site-packages/monai/transforms/compose.py in call(self, input_)
172 def call(self, input_):
173 for transform in self.transforms:
--> 174 input = apply_transform(transform, input, self.map_items, self.unpack_items, self.log_stats)
175 return input_
176

/opt/conda/lib/python3.7/site-packages/monai/transforms/transform.py in apply_transform(transform, data, map_items, unpack_items, log_stats)
127 else:
128 _log_stats(data=data)
--> 129 raise RuntimeError(f"applying transform {transform}") from e
130
131

RuntimeError: applying transform <monai.transforms.post.array.RemoveSmallObjects object at 0x7ff51bc439d0>

[KumoLiu]

Hi @lg2578, seems you directly sent output to RemoveSmallObjects which is the reason for the error.
You may need to add an Activation function or use scipy.ndimage.label or skimage.morphology.label before it. Or just move AsDiscrete before it.

post_pred_val=Compose([
    EnsureType(), 
    AsDiscrete(argmax=True, to_onehot=2),
    FillHoles(),
    RemoveSmallObjects(min_size=64),
])

Hope it can help you, thanks!