72 feature update brats tutorial #73
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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
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| 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)) | ||
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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.
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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
neuronflow
approved these changes
Jul 25, 2025
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