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Updates stitcher to trim all edges evenly rather than right/bottom only. #24

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Merged
k-rl merged 2 commits into from
Jun 2, 2025
Merged

Updates stitcher to trim all edges evenly rather than right/bottom only. #24

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f29fe3d
Updates stitcher to trim all edges evenly rather than right/bottom only.
palmhjell Jun 2, 2025
97b583e
Fixes stitcher update syntax and formatting
palmhjell Jun 2, 2025
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19 changes: 14 additions & 5 deletions src/magnify/stitch.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,11 +8,20 @@ def __init__(self, overlap: int = 102):
self.overlap = overlap

def __call__(self, assay: xr.Dataset) -> xr.Dataset:
tiles = assay.tile[
...,
: assay.tile.shape[-2] - self.overlap,
: assay.tile.shape[-1] - self.overlap,
]
# Only clip if overlap is non-zero
if self.overlap > 0:
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@k-rl k-rl Jun 2, 2025

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Rather than checking for this condition could you do the same thing I did in the previous version of the code which is to just have:

tiles = assay.tile[
    ...,
    clip : assay.tile.shape[-2] - clip + remainder,
    clip : assay.tile.shape[-1] - clip + remainder,
]

That way you're minimizing how much branching happens in the code which makes it easier to reason about. If you're concerned about a bug being introduced later on when the code gets changed because of the tricky indexing you can leave a comment explaining that we're intentionally not using the negative endpoint indexing here because of when self. overlap is 0.

clip = self.overlap//2
# Account for odd overlaps
remainder = self.overlap%2

# Adjust tiles
tiles = assay.tile[
...,
clip:-clip+remainder,
clip:-clip+remainder,
]
else:
tiles = assay.tile

# Move the time and channel axes last so we can focus on joining images.
tiles = tiles.transpose("tile_row", "tile_col", "tile_y", "tile_x", "channel", "time")
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