Shift out-of-FOV crops and preserve background pixels#16
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MattsonCam merged 4 commits intomainfrom May 7, 2026
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April 30, 2026 14:41
Fail fast in `_compute_shifted_window` when `axis_limit <= 0` by raising a `ValueError` instead of returning `(0, 0)`. This makes invalid image-dimension inputs explicit, prevents silent creation of empty windows, and surfaces upstream data issues earlier during cache building. Also update the function docstring to document the new exception.
Make `_compute_shifted_window` fail fast on invalid inputs by raising `ValueError` when `axis_limit <= 0` or `target_size <= 0`, instead of silently returning an empty window for invalid axis limits. Refactor window placement to clamp `window_start` once within valid bounds and derive `window_end` from it. This guarantees fixed `target_size` window length whenever `target_size < axis_limit`, while preserving full-axis fallback behavior when the requested crop size exceeds the image axis.
wli51
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May 7, 2026
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LGTM! Good change minimizing the introduction artifacts into training data.
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Thanks @wli51 ! Merging now |
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This pr shifts nuclei crops if they extend outside of the FOV so additional black pixels are not needed. Likewise, the pixels between the nuclei bounding box and the crop are preserved.