This PR brings aBaseLineWidget and aFeaturesLineWidget to napari-matplotlib, where theFeaturesLineWidget has anobject-id field capable of grouping objects before plotting, thus displaying individual line plots for each object.

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Marcelo

zoccolerand others added9 commits

October 28, 2022 17:06

Create line.py

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Update line.py

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remove minimum size

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Co-authored-by: David Stansby <dstansby@gmail.com>

Merge branch 'main' into line_plot_widget

22f7ce6

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)

remove unused packages

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add examples

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revert changes in base

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remove line widget

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zoccoler mentioned this pull request

Jul 29, 2023

Line plot widget with features#184

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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 theFeaturesScatterWidget? Could we add the functionality desired by just doing exactly the same asFeaturesScatterWidget, 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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dstansbyJul 30, 2023

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Suggested change

return self.viewer.dims.current_step[0]

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dstansbyJul 30, 2023

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

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zoccolerAug 1, 2023

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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 commentedAug 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 theobject_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 toobject_id now to make it more general.

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

Hmm I am not sure. Over there, the.scatter is being used, which returns aPathCollection right? I am interested in having access toLine2D objects. That also why I was adding a_lines list as a property of the class before, to store currentLine2D 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.