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ignore low_contrast warning #292

Merged
merged 2 commits into from
Oct 24, 2020
Merged

ignore low_contrast warning #292

merged 2 commits into from
Oct 24, 2020

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omerbt
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@omerbt omerbt commented Oct 23, 2020 •
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What is the purpose of this PR?

To avoid the repeating warning: 'X.tif is a low contrast image'. closes #260
This warning is raised when saving the preprocessed .tif images to the deepcell_input dir.

How did you implement your changes

Setting the optional parameter check_contrast of skimage.io.imsave to false.

ngreenwald
ngreenwald requested changes Oct 23, 2020
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Great! Not sure if you did this already, but can you do a search through the repository to see if there are any other spots where we save images that this same warning might come up?

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omerbt commented Oct 24, 2020

We save images also in plot_overlay. The images that are saved in this function are not supposed to be with low contrast. I'm not sure if we should turn off this flag there, because in case we do get this warning when saving images in this function, it might be because of a real unexpected problem.

ngreenwald
ngreenwald approved these changes Oct 24, 2020
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Okay great, thanks

@omerbt omerbt merged commit 68c5589 into master Oct 24, 2020
@omerbt omerbt deleted the low_contrast_warning branch October 24, 2020 17:47
alex-l-kong pushed a commit that referenced this pull request Jan 14, 2021
@omerbt
Merge pull request #292 from angelolab/low_contrast_warning
69f2dcd 
ignore low_contrast warning
y2kbugger pushed a commit that referenced this pull request Jul 29, 2021
@omerbt
Merge pull request #292 from angelolab/low_contrast_warning
345273f 
ignore low_contrast warning
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low contrast image warning
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@omerbt @ngreenwald