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AFM-SPM / TopoStats

An AFM image analysis program to batch process data and obtain statistics from images
https://afm-spm.github.io/TopoStats/
GNU Lesser General Public License v3.0
60 stars 11 forks source link

Optimized Area thresholding #983

Open AuroVarat opened 1 month ago

AuroVarat commented 1 month ago

This modification enhances the area thresholding function, significantly improving processing speed, especially for large images.

ns-rse commented 1 month ago

Thanks for the Pull Request @AuroVarat I'll take a look through this on Monday.

In the mean time would you be able to address the failing tests please?

If you're not familiar with tests the software development section of our docs has some advice. You'll want to pip install -e .[dev,tests.docs] and ideally install the pre-commit hooks with pre-commit install. We use the pytest-testmon extension and so you'd have to run the tests once to check everything is working with pytest --testmon and then when you make commits only the tests that are affected will run.

Note also that pre-commit.ci has modified this branch by fixing some minor linting errors so you may want to git pull to get those changes (although if you install pre-commit locally it will make them before you can make your next commit again).

AuroVarat commented 1 week ago

Hi, I am not familiar with tests but I managed to go through the steps and do the "pytest --testmon". It fails 8 tests, but it fails 8 tests regardless of my changes ( I did the same test by running it on the current main branch). Maybe I am doing something wrong, I will look at it when I have more time.

But if you see my changes, they are minimal and should not result in this failure. The code seems to be working fine when I am doing my analysis.

Thanks.