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ENH: doc of ridge functions #3933

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merged 3 commits into from
Jul 9, 2019
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sciunto
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@sciunto sciunto commented May 25, 2019

Description

This PR aims at improving the doc of #3515 as these functions are designed for processing on vessels, I changed the image for a crop of retina. I added see also sections as well.
Figure_1

Cc @DavidBreuer

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For reviewers

  • Check that the PR title is short, concise, and will make sense 1 year
    later.
  • Check that new functions are imported in corresponding __init__.py.
  • Check that new features, API changes, and deprecations are mentioned in
    doc/release/release_dev.rst.
  • Consider backporting the PR with @meeseeksdev backport to v0.14.x

@sciunto sciunto added the 📄 type: Documentation Updates, fixes and additions to documentation label May 25, 2019
@emmanuelle
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Thanks @sciunto ! The contrast of frangi is flattened because the higher values are at the border of the image, could you please increase the contrast (eg setting vmax) for this filter, since the result is quite good but it doesn't show here.

@emmanuelle
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We could also have more explanations about the differences between the different filters, but this can come in another PR because this PR is already an improvement.

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sciunto commented May 25, 2019

Do you think it is better to set a vmax for a particular case or crop all images of 4 pixels on each edge and add a note saying that Frangi leads to an edge effect removed in this example?

PS: I'm discovering these filters and I'm not familiar at all with these algorithms.

@jni
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jni commented May 26, 2019

I'm confused — doesn't matplotlib automatically stretch the contrast for each image?

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jni commented May 26, 2019

Oh, sorry, misread @emmanuelle's comment. Hmmm. I'm not sure what the best answer is here. @sciunto go with whatever you think is prettiest I reckon. =)

@emmanuelle
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@sciunto I would stretch the contrast for this particular case and explain in the text that Frangi filter does this special thing at the border (which will be visible because these pixels will be saturated). But I also leave it to your personal taste, the important thing is that this subplot is not pitch black and users think frangi is worthless.

@sciunto sciunto added this to the 0.16 milestone Jul 9, 2019
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sciunto commented Jul 9, 2019

I forgot about this PR. I put a crop to improve the rendering.
sphx_glr_plot_ridge_filter_001

@jni
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jni commented Jul 9, 2019

Looks great, thanks @sciunto!!!

@jni jni merged commit 619f5d0 into scikit-image:master Jul 9, 2019
@sciunto sciunto deleted the doc_vessel_filters branch July 9, 2019 15:09
clementkng pushed a commit to clementkng/scikit-image that referenced this pull request Jul 12, 2019
* Replace the page image by vessels from retina

* Add see also section to ridge functions

* Add crop on Meijering and Frangi for rendering purpose
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4 participants