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Cleanup + add strided patches #218

Merged
merged 15 commits into from
Feb 22, 2024
Merged

Cleanup + add strided patches #218

merged 15 commits into from
Feb 22, 2024

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kaczmarj
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The purpose of the PR is to clean up various issues. This PR also adds strided patches (they can be overlapped or spaced apart).

One may use overlapping patches in attempt to smooth out noise. Strided patches with holes may be useful to increase the speed of runtime. If one does not need a dense classification, then strided patches might be useful. An overlap ratio of -1 results results in 4x fewer patches.

Patches spaced apart (overlap=-1)

wsinfer run -m breast-tumor-resnet34.tcga-brca -i slides/ -o outputs-overlap-minus1/ --patch-overlap-ratio -1

image

Patches overlapping by 10% (overlap=0.1)

wsinfer run -m breast-tumor-resnet34.tcga-brca -i slides/ -o outputs-overlap-0.5/ --patch-overlap-ratio 0.5

image

Issues fixed

fixes #216
fixes #214
fixes #205
fixes #203
fixes #202
fixes #195
fixes #185

@kaczmarj kaczmarj merged commit f39f92b into main Feb 22, 2024
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@kaczmarj kaczmarj deleted the enh/cleaning-issues branch February 22, 2024 19:34
@kaczmarj kaczmarj mentioned this pull request Feb 22, 2024
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