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Remove required dependency on scikit-image and scipy #232

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tvercaut opened this issue Mar 30, 2020 · 2 comments
Closed

Remove required dependency on scikit-image and scipy #232

tvercaut opened this issue Mar 30, 2020 · 2 comments

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@tvercaut
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scikit-image and scipy are currently required dependencies of MONAI. However, it looks like these are used to implement a small number of features that can be implemented with PyTorch.

Limiting the number of required dependencies is good practice and for the particular case at end, replacing these implementations by PyTorch ones may help towards fixing #189

See https://github.com/kornia/kornia/blob/master/kornia/geometry/transform/imgwarp.py#L126 foe examples of replacing skimage.transform.resize and scipy.ndimage.zoom with PyTorch based code based on affine_grid and grid_sample. There is related discussion in #112

@tvercaut tvercaut changed the title Remove dependency on scikit-image and scipy Remove required dependency on scikit-image and scipy Mar 30, 2020
@tvercaut
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This is also linked to #290 where a related issue is highlighted but with cupy

@Bala93 Bala93 mentioned this issue May 1, 2020
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@wyli wyli added this to To-Do in v0.2.0 via automation May 15, 2020
@wyli wyli moved this from To-Do to In progress in v0.2.0 Jun 13, 2020
@wyli wyli removed this from In progress in v0.2.0 Jun 24, 2020
@wyli
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wyli commented Jun 29, 2020

this is mostly done -- scipy removed, scikit-image becomes an optional for the connected component analysis I'm closing this in favour of #554

@wyli wyli closed this as completed Jun 29, 2020
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