Remove mibitiff option in notebooks #772
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ngreenwald
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Oct 13, 2022
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@srivarra has an open PR changing some of these same lines in the notebooks. You guys should coordinate to figure out which branch to merge where/when, resolving merge conflicts in the jupyter notebooks can be annoying sometimes.
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@ngreenwald I'll add the changes to #736. |
srivarra
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Oct 14, 2022
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cool then we can just merge into main |
ngreenwald
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Oct 14, 2022
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Oct 18, 2022
* nb1 dataset download test fixed. Added new tests * dataset tests: nb2 support * dataset works for nb1 * pycodestyle * nb2: notebook tests fix * nb2: notebook tests fix part 2 * docs build fix * removed deprecated dataset test * moved example dataset into it's own respective file and test file * moved example dataset into it's own respective file and test file * added tests for checking if a directory is empty or not * temporary start_docker.sh adjustments * adjusted notebook 2 * dataset auth_token=False * pycodestyle * updated revision, updated dataset config naming scheme * Nuclear mask, CD163 * updated dataset commit hash. * adjust test params * added channel for smoothing in the notebook 2 * tests fix * docstring fix * ValueError String improvements * fiber_segmentation_fix * removed test which runs through all of the Segment Image Data notebook * moving correct merged files over to nb2 * removed excess cell output * removed mibitiff in notebooks 1,2 from #772 * merge main * Added dataset information to the readme * doc build fix
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What is the purpose of this PR?
Closes #686.
How did you implement your changes
Remove mentions of MIBItiff in the notebooks and instead use the underlying default
is_mibitiff=Falsein the functions.