Bug for changing `channel_dim` in Whole slide image reader

[Dylan-H-Wang]

I tried to change the default value for channel_dim in CuCIMWSIReader and found that the outputs were not correct. Therefore, I checked the source code and identified the buggy part:

MONAI/monai/data/wsi_reader.py

Lines 821 to 827 in e5cf74a

	if mode in "RGB":
	if patch.shape[self.channel_dim] not in [3, 4]:
	raise ValueError(
	f"The image is expected to have three or four color channels in '{mode}' mode but has "
	f"{patch.shape[self.channel_dim]}. "
	)
	patch = patch[:3]

Suppose I set channel_dim=-1, and then patch = patch[:3] is not modifying the channel part at all, instead, it changes the image dimension!

Same problem for TiffFileWSIReader:

MONAI/monai/data/wsi_reader.py

Lines 1179 to 1186 in e5cf74a

	# Check if the color channel is 3 (RGB) or 4 (RGBA)
	if mode in "RGB":
	if patch.shape[self.channel_dim] not in [3, 4]:
	raise ValueError(
	f"The image is expected to have three or four color channels in '{mode}' mode but has "
	f"{patch.shape[self.channel_dim]}. "
	)
	patch = patch[:3]

[KumoLiu]

Hi @Dylan-H-Wang, it seems the channel dim changes in L818. Could you please give me a small piece of code that can reproduce the bug, so then I could take a look at it?

MONAI/monai/data/wsi_reader.py

Lines 817 to 818 in e5cf74a

	# Make the channel to desired dimensions
	patch = np.moveaxis(patch, -1, self.channel_dim)

Thanks!

[Dylan-H-Wang]

Hi @Dylan-H-Wang, it seems the channel dim changes in L818. Could you please give me a small piece of code that can reproduce the bug, so then I could take a look at it?

MONAI/monai/data/wsi_reader.py

Lines 817 to 818 in e5cf74a

	# Make the channel to desired dimensions
	patch = np.moveaxis(patch, -1, self.channel_dim)

Thanks!

Yes, that is what causes this bug. Since the channel_dim is moved to desired position self.channel_dim, this line

MONAI/monai/data/wsi_reader.py

Line 1186 in e5cf74a

patch = patch[:3]

should also based on the self.channel_dim instead of assuming its default value at self.channel_dim=0

Here is the code to reproduce the bug

from monai.data import CuCIMWSIReader, TiffFileWSIReader

img_path = "./data/CAMELYON16/images/normal_150.tif"

reader = CuCIMWSIReader(channel_dim=0)
slide = reader.read(img_path)
slide_data= reader.get_data(slide, level=0)[0]
print(slide_data.shape) # (3, 60928, 65536)
      
reader = CuCIMWSIReader(channel_dim=-1)
slide = reader.read(img_path)
slide_data= reader.get_data(slide, level=0)[0]
print(slide_data.shape) # 3, 65536, 3)

reader = TiffFileWSIReader(channel_dim=-1)
slide = reader.read(img_path)
slide_data= reader.get_data(slide, level=0)[0]
print(slide_data.shape) # (3, 65426, 3)

[KumoLiu]

Thanks, now I can reproduce it, I will create a PR to fix it.

[KumoLiu]

Hi @Dylan-H-Wang, I just create a PR to fix it. It would be great if you could test it on your side to see if it works.
Thanks!

[Dylan-H-Wang]

Hi @Dylan-H-Wang, I just create a PR to fix it. It would be great if you could test it on your side to see if it works.
Thanks!

Seems perfect on my side. Thank you for the helps!