Skip to content

Update WSIReader #4171

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 2 commits into from
Apr 26, 2022
Merged

Update WSIReader #4171

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
e1e5545
Move RGB/RGBA checks to base class
bhashemian Apr 25, 2022
de859e9
Merge branch 'dev' into update-wsireader
Nic-Ma Apr 26, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
27 changes: 10 additions & 17 deletions monai/data/wsi_reader.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -180,7 +180,16 @@ def get_data(
f"The image dimension should be 3 but has {patch.ndim}. "
"`WSIReader` is designed to work only with 2D images with color channel."
)

# Check if there are four color channels for RGBA
if mode == "RGBA" and patch.shape[0] != 4:
raise ValueError(
f"The image is expected to have four color channels in '{mode}' mode but has {patch.shape[0]}."
)
# Check if there are three color channels for RGB
elif mode in "RGB" and patch.shape[0] != 3:
raise ValueError(
f"The image is expected to have three color channels in '{mode}' mode but has {patch.shape[0]}. "
)
# Create a list of patches
patch_list.append(patch)

Expand Down Expand Up @@ -408,11 +417,6 @@ def get_patch(
patch = AsChannelFirst()(patch) # type: ignore

# Check if the color channel is 3 (RGB) or 4 (RGBA)
if mode == "RGBA" and patch.shape[0] != 4:
raise ValueError(
f"The image is expected to have four color channels in '{mode}' mode but has {patch.shape[0]}."
)

if mode in "RGB":
if patch.shape[0] not in [3, 4]:
raise ValueError(
Expand Down Expand Up @@ -537,15 +541,4 @@ def get_patch(
# Make it channel first
patch = AsChannelFirst()(patch) # type: ignore

# Check if the color channel is 3 (RGB) or 4 (RGBA)
if mode == "RGBA" and patch.shape[0] != 4:
raise ValueError(
f"The image is expected to have four color channels in '{mode}' mode but has {patch.shape[0]}."
)

elif mode in "RGB" and patch.shape[0] != 3:
raise ValueError(
f"The image is expected to have three color channels in '{mode}' mode but has {patch.shape[0]}. "
)

return patch