Denoise nl_means script #972
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Hello @EmmaRenauld, Thank you for updating ! There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻 Comment last updated at 2024-10-18 15:46:59 UTC |
EmmaRenauld
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #972 +/- ##
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+ Coverage 68.73% 68.79% +0.06%
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Files 429 432 +3
Lines 22262 22498 +236
Branches 3322 3049 -273
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+ Hits 15301 15478 +177
- Misses 5674 5716 +42
- Partials 1287 1304 +17
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I tested all options and it works.
Since, all calls Dipy stuff, I feel ok with this. And we go back to what we had in the past with proper support of Rician noise and Piesno. Not perfect but can be quite useful in advance context.
Would love to make this PR go to the master quickly as it would be extremely useful for my IMN530 group.
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Thanks! I'll check your comments soon. I was also wondering: I only used the parameters that were used in the bitbucket for piesno, but there are other parameters:
(See https://github.com/dipy/dipy/blob/master/dipy/denoise/noise_estimate.py) Should I add those parameters too? |
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Good question @EmmaRenauld... not sure we should give access to these advanced parameters. I would not know how to tweak them myself... I guess an expert that would wish to play with this would probably write his own python script and call dipy directly, no? @arnaudbore thoughts? Ping me if you want to chat about it. |
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| def estimate_piesno_sigma(data, number_coils=0): |
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Are you sure this should goes into stats ?
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In scilpy.image we have:
volume_math: that's strictly the stuff from the script volume_mathvolume_operations: it could go here, but it's not really an operation?
Or I create a scilpy.image.volume_metrics?
Co-authored-by: Arnaud Bore <[email protected]>
Putting this here so that I don't forget this work in progress. See issue #939