axiomcura commented 1 month ago

Description

Thank you for your contribution to pycytominer! Please succinctly summarize your proposed change. What motivated you to make this change?

This PR updates the README with instructions on how to handle morphological features extracted from software other than CellProfiler. These changes were conducted due to a reviewer’s comment/suggestion.

"When I used the function pycytominer.normalize() on a dataset originating from my own work, I encountered an error message saying “No CP features found. Are you sure this dataframe is from CellProfiler?”. I could easily fix the problem because I know the properties of a CellProfiler dataset, and the error message was hinting at some “Metadata” missing. The fix was very easy, I just needed to add the prefix “Metadata” to my metadata columns. My dataset comes from another commonly used proprietary software called Harmony. I understand that the authors are in favor of using open-source resources, but I think that the pycytominer tool could be useful in a much larger context, and take as input different types of datasets. In the readme file, that I followed to perform the normalization, I couldn’t find anywhere that the dataset has to come from CellProfiler. The author should state clearly, that only cellprofiler datasets can be used. Instead, currently, the sentence in the readme files of the pycytominer github repository says “Image data flow from a microscope to cell segmentation and feature extraction tools (e.g. CellProfiler or DeepProfiler)”. And in the code chunck the sentence says “Each function takes as input a pandas DataFrame or file path”, but in reality, it has to be a specifically formatted pandas dataframe (at least regarding the column names). I think the authors should fix this misunderstanding in the documentation. Alternatively, the better option would be to support the use of different datasets, and explain how the column names should be formatted to be easily processed by the different functions. I can’t exclude that this is described somewhere in the tutorials, but I didn’t encounter it when following the instructions on the readmefile. I would also make the error message more self-explanatory because for now, it implies that I know what CellProfiler is and how its output is formatted. If I don’t have this knowledge, as a user, I might give up on using this tool. This would be unfortunate, as I believe that this tool is a fundamental step in image-based profiling. Considering how easy was to fix this issue for my own dataset, which allowed me to immediately see the outputs of your tool, I recommend reconsidering how to best document the formatting steps necessary to be able to use the different functions of the pycytominer too"

Please also link to any relevant issues that your code is associated with.

What is the nature of your change?

[ ] Bug fix (fixes an issue).
[ ] Enhancement (adds functionality).
[ ] Breaking change (fix or feature that would cause existing functionality to not work as expected).
[X] This change requires a documentation update.

Checklist

Please ensure that all boxes are checked before indicating that a pull request is ready for review.

[X] I have read the CONTRIBUTING.md guidelines.
[X] My code follows the style guidelines of this project.
[X] I have performed a self-review of my own code.
[X] I have commented my code, particularly in hard-to-understand areas.
[X] I have made corresponding changes to the documentation.
[X] My changes generate no new warnings.
[X] New and existing unit tests pass locally with my changes.
[ ] I have added tests that prove my fix is effective or that my feature works.
[ ] I have deleted all non-relevant text in this pull request template.

codecov-commenter commented 1 month ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 94.72%. Comparing base (409d2aa) to head (6caab11). Report is 8 commits behind head on main.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #430 +/- ## ========================================= + Coverage 0 94.72% +94.72% ========================================= Files 0 57 +57 Lines 0 3145 +3145 ========================================= + Hits 0 2979 +2979 - Misses 0 166 +166 ``` | [Flag](https://app.codecov.io/gh/cytomining/pycytominer/pull/430/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=cytomining) | Coverage Δ | | |---|---|---| | [unittests](https://app.codecov.io/gh/cytomining/pycytominer/pull/430/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=cytomining) | `94.72% <ø> (?)` | | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=cytomining#carryforward-flags-in-the-pull-request-comment) to find out more.

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