DC-analysis / dclab

Python library for the post-measurement analysis of real-time deformability cytometry (RT-DC) data sets
https://dclab.readthedocs.io
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Implement viscosity calculation buyukurganci_22 #205

Closed felix-r closed 1 year ago

felix-r commented 1 year ago

PR to implement new viscosity functions as introduced by Büyükurganci et al.

To do before puling:

codecov-commenter commented 1 year ago

Codecov Report

Base: 91.02% // Head: 90.78% // Decreases project coverage by -0.24% :warning:

Coverage data is based on head (620fb24) compared to base (1a092a8). Patch coverage: 5.00% of modified lines in pull request are covered.

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Additional details and impacted files ```diff @@ Coverage Diff @@ ## viscosity_model_buyukurganci_22 #205 +/- ## =================================================================== - Coverage 91.02% 90.78% -0.24% =================================================================== Files 96 96 Lines 6849 6868 +19 =================================================================== + Hits 6234 6235 +1 - Misses 615 633 +18 ``` | [Impacted Files](https://codecov.io/gh/DC-analysis/dclab/pull/205?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=DC-analysis) | Coverage Δ | | |---|---|---| | [dclab/features/emodulus/viscosity.py](https://codecov.io/gh/DC-analysis/dclab/pull/205?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=DC-analysis#diff-ZGNsYWIvZmVhdHVyZXMvZW1vZHVsdXMvdmlzY29zaXR5LnB5) | `64.38% <5.00%> (-20.81%)` | :arrow_down: | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=DC-analysis). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=DC-analysis)

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felix-r commented 1 year ago

Now that the equations are available on arxiv, I would not write an extensive documentation and rather leave it to you, how to edit the documentation for the new model. Some comments from my side to the notes you have in the docs:

Under the section Viscosity:

This paragraph is imcomplete:

    - Which of the models should one choose? https://github.com/DC-analysis/dclab/issues/197
    - How does CellCarrier correspond to which concentration of MC in PBS?

Under the section Büyükurgancı 2022: I don't think you need to get into all the things you commented there. If you show the Carreau-Yasuda plot, it should become clear how the viscosity behaves. You can also use Figure 3 from the arxiv paper (2023) to illustrate how the viscosity changes depending on temperature, flow rate and channel size.

Do you still want me to add something to the code?

paulmueller commented 1 year ago

Thanks for the comments. I am currently looking into the arxiv paper and will get back to you if I encounter any issues.