72 feature update brats tutorial #73
Merged
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
There was a problem hiding this comment.
Pull Request Overview
This PR updates the BraTS tutorial utility functions to use more type-safe and flexible path handling. The changes improve type annotations and enhance the segmentation visualization by making the background transparent.
- Replace string-only path parameters with Union[str, Path] type annotations throughout utility functions
- Convert DATA_FOLDER from string to Path object for better path handling
- Improve segmentation visualization by masking out background pixels with transparent overlay
Comment on lines
75
to
+78
| ax[0].imshow(modality_np[slice_index, :, :], cmap="gray") | ||
| ax[1].imshow(modality_np[slice_index, :, :], cmap="gray") | ||
| ax[1].imshow(seg_np[slice_index, :, :], cmap="plasma", alpha=0.3) | ||
| ax[1].imshow(seg_slice, cmap="plasma", alpha=np.where(seg_slice > 0, 0.3, 0)) | ||
|
|
There was a problem hiding this comment.
The np.where operation is computed for every pixel on each function call. Consider pre-computing the alpha mask: alpha_mask = np.where(seg_slice > 0, 0.3, 0) then use alpha=alpha_mask for better performance.
Co-authored-by: Copilot <[email protected]>
Co-authored-by: Copilot <[email protected]>
neuronflow
approved these changes
Jul 25, 2025
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.