CropForeground behaviour

[schellenchris]

I am croping my images to match a segmentation when I noticed my x-dimesnion isn't getting cropped somehow. I tested the CropForeground function:

image = np.array(
[[0, 0, 1],
[0, 1, 0],
[0, 0, 0]])
cropper = CropForeground(select_fn=lambda x: x > 0, margin=0)
print(cropper(image))

[[0, 1],
[1, 0],
[0, 0]]

Is this behaviour of CropForeground intended? Shouldn't it get cropped to

[[0, 1],
[1, 0]]

Thanks for your help

[KumoLiu]

Hi @schellenchris, since transforms in MONAI assume that the data is channel-first, so you need to add the channel dimension to the data before passing it into the transforms. Could you please try print(cropper(image[None]))?

Hope it can help you, thanks!

[schellenchris]

Thank you! My x-dimension was in fact the first dimension hence it wasn't getting cropped cause it assumed it was the channel..... My bad