Added bokeh implementation of view_quilt #1365
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On first glance this looks great - I'm currently at a conference and will give it a more careful look when I get back (also hoping @kushalkolar has time to give this a look). Bravo on putting in the time on this. |
pgunn
reviewed
Jul 1, 2024
caiman/utils/visualization.py
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| plot.rect(x='center_x', y='center_y', width='width', height='height', source=source, color=color, alpha=alpha) | ||
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| # Create sliders | ||
| stride_slider = Slider(start=1, end=100, value=rf, step=1, title="Patch half-size (rf)") |
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I'm getting a NameError: name 'Slider' is not defined from this (and the line below), and it's not obvious whether bokeh.models.Slider or matplotlib.widgets.Slider is meant.
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Oh, actually, this is definitely meant to be a bokeh.models.Slider by the arguments.
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This passes tests and looks great. Thanks for the contribution! |
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Thanks, happy to contribute! |
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Description
This PR adds the function
nb_view_quilt()which is a 1:1 implementation of theview_quilt()function in Bokeh. The demo_pipeline notebook referred to an interactive version of the view_quilt function but I was unable to find it. The view_quilt function had a todo for implanting a bokeh version.When this function is evoked, it shows the quilt plot with 2 sliders for changing the
rfandstrideparameters. I opted for modifying the underlaying parameters with the sliders instead of the patch size and overlap, because some width values are impossible to use. For example, the patches can never have a size of 22 because of the formulapatch size = (rf * 2) + 1.The demo_pipeline notebook was also modified to use the Bokeh version.
Has your PR been tested?
caimanmanager demotestran without any issues.caimanmanager testfailed atcaiman.tests.test_sbx...but had no other issues.The
nb_view_quilt()have also been manually tested and it always produced the exact same output asview_quilt(), given identical inputs.