Make a feature histogram exploration widget

[jo-mueller]

Feature proposal

Hi @dstansby ,

I created a feature exploration widget in a different repository together with @zoccoler which shows a Layer.features in a histogram along with the cumulative density function. I think it would make sense to move it upstream (e.g., here) - what do you think of it?

Here's a small demo of how it looks/works:

The plugin is currently inheriting from HistogramWidget.

[dstansby]

Oooh this looks interesting! Could you post or link to a higher resolution movie of the gif above? I can't make out the text in the plugin.

Do you have a short summary of what extra features the widget would add on top of HistogramWidget too? Perhaps we could consider just adding some of that functionality directly to HistogramWidget?

[jo-mueller]

Thanks for the reply, will make a higher resolution gif as soon as possible 😃

As for adding the functionality to the Histogram Widget - not sure. The Histogram widget shows actual pixel intensities of an image layer whereas the example above shows features associated with any layer that supports features. Conceptionally I think it's actually closer to the ScatterBaseWidget🤔

Edit: Maybe we could merge the two functionalities ScatterBaseWidget and this histogram widget into some sort of feature exploration widget?

In the Scatter widget, this could mean:

• only one feature is selected in the axis dropdowns --> draw histogram
• two features are selected --> draw scatter plot

[jo-mueller]

@dstansby here's a more high-res screenshot

The CDF button shows the cumulative density function:

[dstansby]

Thanks for those images - I think this would be a really nice feature to add. It looks like there might be lots of smaller bits here (the image selection, changing the number of bins, adding a CDF, changing the percentiles, exporting as csv) that could be built incrementally on top of the existing histogram widget. I would strongly prefer for these features to be added in as small as possible chunks in individual PRs, which will make it much easier to review. How does that sound?

I don't have time to work or review this now, but in the new year have CZI funding to work on napari-matplotlib and I will definitely add this to our todo list 😄

[jo-mueller]

Hi @dstansby ,

thanks for the feedback! I agree, it does make sense to build this on top of the existing histogram rather than building several widgets for specific layers. I guess the key thing would be to build the current histogram widget to feed the data from

• image intensity if an Image layer is selected
• layer.features if any other layer is selected?

[dstansby]

👍 sounds good - PRs very welcome! I think the Historgram widget should do Image intensity for a grayscale image, are you looking for intensity for an RGB image?

[jo-mueller]

Nah, I don't do RGB much, so as long as nobody complains I would leave it at that (material for another PR, I guess)

[jo-mueller]

Hi @dstansby ,

with #148 merged, would you be interested in bringing the second half of this (e.g., coloring the bars of the histogram according to colormap/face_colormap/edge_colormap of the layer) to the features histogram? I think it could be done with a relatively small change here after drawing the histogram.

[dstansby]

Thanks for the reminder for this issue! Mirroring the colourmap of the histgoram with the layer colourmap would definitely be a welcome feature 👍

[jo-mueller]

Thanks for merging!