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imaging update: overlay_images #77

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merged 5 commits into from
Nov 8, 2023

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thawn
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@thawn thawn commented Nov 8, 2023

changed default output for the method option "Segmentation mask over image" to png so that it can be directly viewed in the browser.

closes issue #75

FOR CONTRIBUTOR:

  • - I have read the CONTRIBUTING.md document and this tool is appropriate for the galaxy-image-analysis repo.
  • - License permits unrestricted use (educational + commercial)
  • - This PR adds a new tool or tool collection
  • - This PR updates an existing tool or tool collection
  • - This PR does something else (explain below)

@thawn
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thawn commented Nov 8, 2023

please note github does not show that we removed test3.tif, but we checked and it is gone in the feature branch.

@kostrykin kostrykin requested a review from bgruening November 8, 2023 10:08
</data>
<data format="png" name="out" from_work_dir="output.png">
<filter>method_option['method'] == 'seg_contour'</filter>
</data>
</outputs>
<tests>
<test>
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It would be nice if you could add expect_num_outputs https://docs.galaxyproject.org/en/latest/dev/schema.html#id94 to the tests. This is mainly to check that the filters are working on the outputs.

@bgruening
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Thanks @thawn

tools/overlay_images/test-data/test3.tif → tools/overlay_images/test-data/test3.png

The remove is shown as a renaming here.

thawn added 2 commits November 8, 2023 11:41
also fixed lint errors for the output name and label
somehow, the github CI produces a smaller png file.
opened the PNG in GIMP and saved it with compression 9 and without exif data.
@bgruening
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Thanks @thawn!

@bgruening bgruening merged commit 8cd85b1 into BMCV:master Nov 8, 2023
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@thawn
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thawn commented Nov 9, 2023

@bgruening you are welcome
Thanks for merging so quickly

@kostrykin kostrykin deleted the overlay_images_update branch November 14, 2023 12:59
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2 participants