pyqt scatter widget

[fjorka]

Description

This PR introduces a complete Scatter Widget based on PyQtGraph, intended to replace the Matplotlib-based Scatter Widget.

Rationale

• Expected improved performance for large datasets.
• Smooth navigation for zooming and panning within the plot.
• Increased flexibility in customization.

Functionality

• It preserves all functionality of the previous widget.
• Documentation notebooks updated with the information and screenshots of the new widget.
• New functionality includes:
  • Separate color controls for continuous and discrete data:
    • Continuous color control offers:
      • Histogram of values chosen for color.
      • Ability to change LUT.
      • Control over contrast.
    • Discrete color control offers:
      • Scrollable legend of colors.
      • Ability to change the color for a selected class.
  • Pseudohistogram plot when only one axis is defined.
  • Highlight of nearby data points under cursor.
  • Dynamic status display of cursor position and highlighted data points.
  • Expanded ROI annotations:
    • Lasso or rectangle tool (useful for thresholding).
    • Ability to use several disjointed ROIs for annotation.
    • Modifiable ROIs.
  • Dialog to choose Annotation name (previously Export).
  • Saving options:
    • When started with AnnData, the Save button opens a path dialog to choose a location for an AnnData file (supports h5ad, zarr, and csv).
    • When opened with the Napari viewer, it mimics the behavior of the Annotation Widget:
      • With backed sdata, Save will modify sdata of the selected layer.
      • Without backed sdata, no saving action.
    • The widget displays the status and saving possibility when started.

Next Steps Beyond This PR

There were some "next steps"/"open points" here. I moved them to this issue #333 to make them more discoverable.

[review-notebook-app]

Check out this pull request on 

See visual diffs & provide feedback on Jupyter Notebooks.

---

Powered by ReviewNB

[fjorka]

The notebooks start with the instruction:

There are two options to install napari-spatialdata:

(1) Run `pip install napari-spatialdata`
or,
(2) Clone this [repo](https://github.com/scverse/napari-spatialdata) and run `pip install -e .`

However, following this instruction and starting napari (or scatter widget) will give an error ImportError: No Qt bindings could be found. What about asking explicitly for napari installation first d40fb7c which will inform a user about Qt?

[fjorka]

To do:

• add explanations in scatterwidget.ipynb and scatterwidget_annotation.ipynb about starting with AnnData and options for saving

There were some "next steps"/"open points" here. I moved them to this issue #333 to make them more discoverable.

[LucaMarconato]

There were some "next steps"/"open points" here. I moved them to this issue #333 to make them more discoverable.

[LucaMarconato]

Thanks @fjorka and @melonora, we finished reviewing and adjusting some last open points, and now we are good to merge!

Really excited to ultimately release this! We will include this PR in a release X.com post that we will make in the near future.

I will consolidate the points open for follow up PRs in a separate issue.

[LucaMarconato]

@fjorka @melonora I forgot about this file https://github.com/fjorka/napari-spatialdata/blob/7d60e030aff750ee08fd874b8c6b6425ec5fff79/tests/test_aaa.py, which if I got it right, was a work-in-progress implementation for an alternative approach to span the test napari viewer, in order to avoid the segfault problem with Python 3.9. I think the problem have disappeared due to having dropped the Python 3.9 support. So please @melonora in the follow up PR can you drop that file? Thanks.

[LucaMarconato]

Actually there is still a problem with tests, I reported it here #335 so we can continue the discussion there. CC @melonora