napari 0.4.8

We’re happy to announce the release of napari 0.4.8! napari is a fast, interactive, multi-dimensional image viewer for Python. It’s designed for browsing, annotating, and analyzing large multi-dimensional images. It’s built on top of Qt (for the GUI), vispy (for performant GPU-based rendering), and the scientific Python stack (numpy, scipy).

This release comes with a big change with how you use napari: you should no longer wrap viewer calls in the with napari.gui_qt(): context. Instead, when you want to block and call the viewer, use napari.run(). A minimal example:

import napari
from skimage import data

camera = data.camera()
viewer = napari.view_image(camera)
napari.run()

In interactive workspaces such as IPython and Jupyter Notebook, you should no longer need to use %gui qt, either: napari will enable it for you.

For more information, examples, and documentation, please visit our website: https://napari.org

Highlights

This release adds a new plugin type (i.e. a hook specification) for plugins to provide sample data (#2483). No more demos with np.random! 🎉 We’ve added a built-in sample data plugin for this using the scikit-image data module. Use it with viewer.open_sample(plugin_name, sample_name), for example, viewer.open_sample('scikit-image', 'camera'). Or you can use the File menu at File -> Open Sample. For more on how to provide your own sample datasets to napari, see how to write a plugin and the sample data specification.

The scale bar now has rudimentary support for physical units 📏 (#2617). To use it, set your scale numerically as before, then use viewer.scale_bar.unit = 'um', for example.

We have also added a text overlay, which you can use to display arbitrary text over the viewer (#2595). You can use this to display time series time stamps, for example. Access it at viewer.text_overlay.

Editing segmentations with napari is easier than ever now with varying number of dimensions during painting/filling with labels (#2609). Previously, if you wanted to edit segmentations in a time series, you had to choose between painting 2D planes, or painting in 4D. Now you can edit individual volumes without affecting the others.

If you launch a long running process from napari, you can now display a progress bar on the viewer (#2580). You can find usage examples in the repo here and here.

New Features

  • Add highlight widget to preferences dialog (#2435)

  • Add interface language selection to preferences (#2466)

  • Add Hookspec for providing sample data (#2483)

  • Add ability to run file as plugin (#2503)

  • Add layer.source attribute to track layer provenance (#2518)

  • Add button to drop into debugger in the traceback viewer. (#2534)

  • Add initial welcome screen on canvas (#2542)

  • Text overlay visual (#2595)

  • Add global progress wrapper and ProgressBar widget (#2580)

  • Add FOV to camera model and slider popup (#2636). Right click on the 2D/3D display toggle button to get a perspective projection view in 3D.

Improvements

  • Add stretch to vertical dock widgets (#2154)

  • Use new selection model on existing LayerList (#2441)

  • Add bbox annotator example (#2446)

  • Save last working directory (#2467)

  • add name to dock widget titlebar (#2471)

  • Add QtListModel and ListView for EventedList (#2486)

  • New new qt layerlist (#2493)

  • Move plugin sorter (#2501)

  • Add support for passing shape_type through data attribute for Shapes layers (#2507)

  • Add ColorManager to Vectors (#2512)

  • Enhance translation methods (#2517)

  • Cleanup plugins.init, better test isolation (#2535)

  • Add typing to schema_version (#2536)

  • Add initial restart implementation (#2540)

  • Add data setter for surface layers (#2544)

  • Extract shortcut into their own object. (#2554)

  • Add example tying slider change to point properties change (#2582)

  • Range of label spinbox is more dtype-aware (#2597)

  • Add generic name to unnamed dockwidgets (#2604)

  • Add option to save state separate from geometry (#2606)

  • QtLargeIntSpinbox for label controls (#2608)

  • Support varying number of dimensions during labels painting (#2609)

  • Add units to the ScaleBar visual (#2617)

  • Return widgets created by add_plugin_dock_widget (#2635)

  • Add _QtMainWindow.current (#2638)

  • Relax dask test (#2641)

  • Add table header style (#2645)

  • QLargeIntSpinbox with QAbstractSpinbox and python model (#2648)

  • Add Labels layer get_dtype utility to account for multiscale layers (#2679)

  • Display file format options when saving layers (#2650)

  • Add events to plugin manager (#2663)

  • Add napari module to console namespace (#2687)

  • Change deprecation warnings to future warnings (#2707)

  • Add strict_qt and block_plugin_discovery parameters to make_napari_viewer (#2715)

Bug Fixes

  • Ensure Preferences dialog can only be opened once (#2457)

  • Restore QtNDisplayButton (#2464)

  • Fix label properties setter (issue #2477) (#2478)

  • Fix labels data setter (#2496)

  • Fix localization for colormaps (#2498)

  • Small brackets fix for Perfmon (#2499)

  • Add try except on safe load (#2505)

  • Be cautious when checking a module’s package attribute (#2516)

  • Trigger label colormap generation on seed change to fix shuffle bug, addresses #2523 (#2524)

  • Modified quaternion2euler function to cap the arcsin’s argument by +-1 (#2530)

  • Single line change to track recoloring function (#2532)

  • Handle Escape on Preferences dialog (#2537)

  • Fix close window handling for non-modals (#2538)

  • Fix trans to use new API (#2539)

  • Fix set_call_order with missing plugin (#2543)

  • Update conditional to use new selection property (#2557)

  • Fix visibility toggle (and other key events) in new qt layerlist (#2561)

  • Delay importing plugins during settings registration (#2575)

  • Don’t create a dask cache if it doesn’t exist (#2590)

  • Update model and actions on menu (#2602)

  • Fix z-index of notifications (hidden by welcome window) (#2611)

  • Make sure Delete is a special key mapping (#2613)

  • Disconnect some events on Canvas destruction (#2615)

  • Add missing QSpinBox import in Labels layer controls (#2619)

  • Use dtype.type when passing to downstream NumPy functions (#2632)

  • Fix notifications when something other than napari or ipython creates QApp (#2633)

  • Update missing translations for 0.4.8 (#2664)

  • Catch dockwidget layout modification error (#2671)

  • Fix warnings in thread_worker, relay messages to gui (#2688)

  • Add missing setters for shape attributes (#2696)

  • Add get_default_shape_type utility introspecting current shape type (#2701)

  • Fix handling of exceptions and notifications of threading threads (#2703)

  • Fix vertical_stretch injection and kwargs passing on DockWidget (#2705)

  • Fix tracks icons, and visibility icons (#2708)

  • Patch horizontalAdvance for older Qt versions (#2711)

  • Fix segfaults in test (#2716)

  • Fix napari_provide_sample_data documentation typo (#2718)

  • Fix mpl colormaps (#2719)

  • Fix active layer keybindings (#2722)

  • Fix labels with large maximum value (#2723)

  • Fix progressbar and notifications segfaults in test (#2726)

API Changes

  • By default, napari used to create a dask cache. This has caused unforeseen bugs, though, so it will no longer be done automatically. (#2590) If you notice a drop in performance for your dask+napari use case, you can restore the previous behaviour with napari.utils.resize_dask_cache(memory_fraction=0.1). You can of course also experiment with other values!

  • The default area for add_dock_widget is now right, and no longer bottom.

  • To avoid oddly spaced sparse widgets, #2154 adds vertical stretch to the bottom of all dock widgets added (via plugins or manually) with an area of left or right, unless:

    1. the widget, or any widget in its primary layout, has a vertical QSizePolicy of Expanding, MinimumExpanding, or Ignored

    2. add_vertical_stretch=False is provided to add_dock_widget, or in the widget options provided with plugin dock widgets.

Deprecations

  • As noted at the top of these notes, napari.gui_qt() is deprecated (#2533). Call napari.run() instead when you want to display the napari UI.

UI changes

  • Toggle theme has been removed from the menubar. (#2462) Instead, change the theme in the preferences panel.

  • The number of 2D interpolation options available from the drop down menu has been reduced. (#2552)

  • The ipy interactive setting has been removed from the preferences panel. (#2605) You can still turn it off from the API with napari.utils.settings.SETTINGS.ipy_interactive = False, but this is not recommended.

  • The n-dimensional tick box in the Labels layer controls has been removed. (#2609) Use “n edit dims” instead.

Documentation

  • Extend release notes: Add breaking API changes in 0.4.7 (#2494)

  • Add about team page (#2508)

  • Update translations guide (#2510)

  • Misc Doc fixes. (#2515)

  • Correct lenght for title underline. (#2541)

  • Minor reformatting. (#2555)

  • Automate doc copy (#2562)

  • Pin docs dependencies (#2568)

  • Example of using magicgui with thread_worker (#2577)

  • Fix typo in docs CI (#2588)

  • Only copy the autosummary templates (#2600)

  • Documentation typos (#2614)

  • Update event loop documentation for gui_qt deprecation (#2639)

  • Example using matplotlib figure (#2668)

Build Tools and Support

  • Add a simple property-based test using Hypothesis (#2469)

  • Add check for strings missing translations (#2521)

  • Check if opengl file exists (#2630)

  • Remove test warnings again, minimize output, hide more async stuff (#2642)

  • Remove raw_stylesheet (#2643)

  • Add link to top level project roadmap page (#2652)

  • Replace pypa/pep517 with pypa/build (#2684)

  • Add provide sample data hook to docs (#2689)

Other Pull Requests

  • Update PULL_REQUEST_TEMPLATE.md (#2497)

  • Non-dynamic base layer classes (#2624)

19 authors added to this release (alphabetical)

20 reviewers added to this release (alphabetical)