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FeaturesLineWidget#200

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zoccoler wants to merge 10 commits intomatplotlib:mainfrom
zoccoler:line_and_featuresline_widgets
Open

FeaturesLineWidget#200
zoccoler wants to merge 10 commits intomatplotlib:mainfrom
zoccoler:line_and_featuresline_widgets

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@zoccoler zoccoler commented Jul 29, 2023

Hi @dstansby ,

As suggested in #184 , I am transferring the code here without the LineWidget.

This PR brings a BaseLineWidget and a FeaturesLineWidget to napari-matplotlib, where the FeaturesLineWidget has an object-id field capable of grouping objects before plotting, thus displaying individual line plots for each object.

Best,
Marcelo

zoccoler and others added 9 commits October 28, 2022 17:06
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Create line.py
35e5808
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Update line.py
bfb655a
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remove minimum size
e2eb48f 
Co-authored-by: David Stansby <dstansby@gmail.com>
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Merge branch 'main' into line_plot_widget
22f7ce6
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WIP: re-factor line widgets
86ac6d2 
- make LineBaseWidget
- make LineWidget for plotting intensities under shapes layer
- make FeaturesLineWidget for plotting features from labels layer (grouped by a label column matching labels in layer)
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remove unused packages
5891f7f
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add examples
c2a0586
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revert changes in base
4607213
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remove line widget
7fff195
@zoccoler zoccoler mentioned this pull request Jul 29, 2023
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dstansby
dstansby reviewed Jul 30, 2023
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Just having a play around with this, and I'm confused by what the "object-id" selector is for? Why are there not just two selectors that select what is being plotted on the x/y axes?

And following on from that, how is this different from the FeaturesScatterWidget? Could we add the functionality desired by just doing exactly the same as FeaturesScatterWidget, but joining the scatter points with a line?

src/napari_matplotlib/base.py
@@ -210,6 +210,9 @@ def current_z(self) -> int:
Current z-step of the napari viewer.
"""
return self.viewer.dims.current_step[0]
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Suggested change
return self.viewer.dims.current_step[0]

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I assume the line self.viewer.dims.current_step[-3] is a bug fix below for datasets that have >= 4 dimensions?

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We can drop it for now since it does no affect this PR anymore. It had to do with other dimensions, yes

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zoccoler commented Aug 1, 2023

Just having a play around with this, and I'm confused by what the "object-id" selector is for? Why are there not just two selectors that select what is being plotted on the x/y axes?

Good question. So the object_id is the factor that groups elements from the table using the .groupby from pandas. This allows individual lines for each label with different colors. Typically this is just a column named 'label' in the table containing the label numbers, but as this can vary from different people and I cannot anticipate what it will be, so I chose to add it in the interface and let the user decide.

By the way, I noticed I was still calling 'label' in other places, so I renamed them to object_id now to make it more general.

And following on from that, how is this different from the FeaturesScatterWidget? Could we add the functionality desired by just doing exactly the same as FeaturesScatterWidget, but joining the scatter points with a line?

Hmm I am not sure. Over there, the .scatter is being used, which returns a PathCollection right? I am interested in having access to Line2D objects. That also why I was adding a _lines list as a property of the class before, to store current Line2D artists in the plot, because I thought it would be faster to update existing lines data with .set_xdata and .set_ydata than redraw all the lines.

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zoccoler commented Sep 16, 2023

Hi @dstansby ,

Did you have some time to consider this feature?

Thanks for your time on reviewing this!

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zoccoler commented Oct 25, 2023

This would close #60

@dstansby dstansby added the New feature New feature or request label Jan 7, 2024
@dstansby dstansby mentioned this pull request Jan 11, 2024
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