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Support single z-stack tif file for input #67
Support single z-stack tif file for input #67
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Could you use
with TiffFile(file_path) as tiff:
for this section? This will ensure the connection is closed correctly, as they require in their docsThere was a problem hiding this comment.
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Applied the change.
Check warning on line 691 in brainglobe_utils/image_io/load.py
Codecov / codecov/patch
brainglobe_utils/image_io/load.py#L689-L691
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Ideally these would use
ImageIOLoadException
rather thanValueError
. This would need some restructuring ofImageIOLoadException
though - so happy to leave as-is for now, and I'll look into this once it's all merged.There was a problem hiding this comment.
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Sounds good. I left it as is then.
Check warning on line 695 in brainglobe_utils/image_io/load.py
Codecov / codecov/patch
brainglobe_utils/image_io/load.py#L694-L695
Check warning on line 700 in brainglobe_utils/image_io/load.py
Codecov / codecov/patch
brainglobe_utils/image_io/load.py#L699-L700
Check warning on line 704 in brainglobe_utils/image_io/load.py
Codecov / codecov/patch
brainglobe_utils/image_io/load.py#L702-L704
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I think you could remove the
indices = {ax: i for i, ax in enumerate(axes)}
line above, and do this in one line with something like:image_shape = {ax: sh for ax, sh in zip(axes, shape)}
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Good catch! I applied the change.
Check warning on line 710 in brainglobe_utils/image_io/load.py
Codecov / codecov/patch
brainglobe_utils/image_io/load.py#L709-L710