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Wrong initialization H5 writer Grid during validation #55

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EricMarcus-ai opened this issue Jan 25, 2024 · 0 comments · Fixed by #56
Closed

Wrong initialization H5 writer Grid during validation #55

EricMarcus-ai opened this issue Jan 25, 2024 · 0 comments · Fixed by #56
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Describe the bug
During validation H5 writing, the writer is initialized with the first batch, and a grid is made here:

grid = Grid.from_tiling(
However, during validation, we are dealing with ROIs, and the resulting coordinates may be at an arbitrary place in the WSI. This results in a misaligned grid and patches from a subsequent ROI on the same WSI may fall outside the created grid, resulting in errors here
while not np.all(curr_coordinates == self._grid[grid_counter]):
as the correct place is never found.

To Reproduce
A train + validation run with the h5 writing enabled.

Expected behavior
It should write a h5 (slightly) around all ROIs. The correct Grid is already available in the validation dataset.

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