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Version 1.8.0
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@schlegelp schlegelp released this 22 Sep 16:56
· 115 commits to master since this release
v1.8.0
1c98298

This version contains a major internal rework of both navis.plot2d and navis.plot3d to make them more consistent and easier to use.

Breaking

  • Plotting: the synapse_layout parameter was renamed to cn_layout (matching e.g. other parameters such as cn_colors)
  • Negative views in navis.plot2d (e.g. view=("x", "-z")) will now invert axes rather than changing the underlying data
  • Minimum version of matplotlib is now 3.9 (was 3.6)
  • The plotly backend is not part of a minimal install anymore (still installed via navis[all])
  • The Vispy backend is now deprecated and will be removed in a future release
  • Removed navis.screenshot - please use the Octarine/Vispy viewer's .screenshot() method instead
  • navis.tortuosity now calculates tortuosity as-is (i.e. without resampling) by default

Additions

  • Added Octarine as the default backend for plotting from terminal
  • New Function: navis.ivscc_features() computes some basic ICSCC features
  • New function: navis.graph.skeleton_adjacency_matrix() computes the node adjacency for skeletons
  • New function: navis.graph.simplify_graph() simplifies skeleton graphs to only root, branch and leaf nodes while preserving branch length (i.e. weights)
  • New NeuronList method: get_neuron_attributes is analagous to dict.get
  • NeuronLists now implement the | (__or__) operator which can be used to get the union of two [NeuronLists]navis.NeuronList]
  • Tree/MeshNeurons, Volumes and Dotprops now support addition/subtraction (similar to the already existing multiplication and division) to allow offsetting neurons
  • navis.Volume now have an (optional) .units property similar to neurons

Improvements

  • Plotting:
    • navis.plot3d:
      • legendgroup parameter (plotly backend) now also sets the legend group's title
      • new parameters for the plotly backend:
        • legend (default True): determines whether legends is shown
        • legend_orientation (default v): determines whether legend is aranged vertically (v) or horizontally (h)
        • linestyle (default -): determines line style for skeletons
      • default for radius is now "auto"
    • navis.plot2d:
      • the view parameter now also works with methods 3d and 3d_complex
      • the color_by and shade_by parameters now also work when plotting skeletons with radius=True
      • new defaults: radius="auto", alpha=1, figsize=None (use matplotlib defaults)
      • new parameters for methods 3d and 3d_complex: mesh_shade=False and non_view_axes3d
      • the scalebar and soma parameters can now also be dictionaries to style (color, width, etc) the scalebar/soma
    • the connectors parameter can now be used to show specific connector types (e.g. connectors="pre")
  • I/O:
    • read_* functions are now able to read from FTP servers (ftp://...)
    • the limit parameter used in many read_* functions can now also be a regex pattern or a slice
  • New parameter in navis.resample_skeleton() use map_column to include arbitrary columns in the resampling
  • navis.prune_twigs() and navis.cable_length() now accept a mask parameter
  • General improvements to docs and tutorials

Fixes

  • Memory usage of Neuron/Lists is now correctly re-calculated when the neuron is modified
  • Various fixes and improvements for the MICrONS interface (navis.interfaces.microns)
  • navis.graph.node_label_sorting() now correctly prioritizes total branch length
  • navis.TreeNeuron.simple now correctly drops soma nodes if they aren't root, branch or leaf points themselves

Full Changelog: v1.7.0...v1.8.0

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