3D viewers in Glue

A plugin with 3D viewers for glue, powered by VisPy, is available. Provided that you installed glue with conda or with pip, you should already have the 3D viewers available. You can check this by going to the Canvas menu in glue and selecting New Data Viewer, or alternatively by dragging a dataset onto the canvas area. If the 3D viewers plugin is installed, you should see the 3D viewers in the list:

../_images/3d_viewers_select.png

If you don’t see these in the list, then if you are using Anaconda to manage your Python distribution, you can install the 3D viewers plugin using:

pip install glue-vispy-viewers

With the plugin installed, you will now have access to two new data viewers in Glue:

  • 3D scatter viewer
  • 3D volume rendering viewer

Please read on to understand the current functionality and limitations of each viewer. If you are interested in getting involved in implementing some of the missing functionality or fixing known issues, please join the glue-viz-dev mailing list and let us know!

Common options for all viewers

All 3D viewers share a similar panel in the bottom left:

../_images/common_options.png

In addition, all viewers will show a rectangular 3D box, which by default is a cube. The edges of the cube correspond to the min/max values in the options panel above. If these values are changed, the data is renormalized inside the cube, but the white cube stays the same. It is also possible to instead stretch the cube into a rectangular box with a different size in each dimension, using the sliders. This can be useful in the case of a volume rendering, if the number of pixels is very different along different axes.

3D Scatter Plot Viewer

The 3D scatter plot viewer is the most feature-complete of the viewers at the moment. It is currently able to:

  • Display markers based on any 3 data components
  • Highlight subsets made in other viewers
  • Control the visual appearance of both data and subsets
  • Color code markers using any component
  • Set the size of markers to depend on any component
  • Scale the absolute size and the transparency of markers in each layer using sliders

The following visualization shows a 3D scatter plot with the location of earthquakes around the globe, color coded by depth and with the size set by the magnitude of the earthquake:

../_images/3d_scatter.jpg

At the moment this viewer is not able to show multiple datasets (just one dataset with subsets), but this will be added shortly.

3D Volume Rendering Viewer

The 3D volume rendering is currently able to show only 3D datasets (not e.g. 4D cubes sliced along one dimension). The viewer is able to also highlight subsets made in other viewers:

../_images/3d_volume.jpg

At the moment, the 3D viewer is only able to show multiple datasets if they are on the same grid. Note that for this viewer, the limits in the options panel in the bottom left are in pixel coordinates, not world coordinates.

3D Isosurface Viewer

A 3D isosurface viewer is in development. This viewer is still highly experimental and currently very slow for displaying isosurfaces. In addition, it is only able to show a single isosurface level. We do not recommend using it at this time, and have disabled it by default. If you are interested in trying it out, see the README.md file in the glue-vispy-viewers repository.

Reporting issues

Please report any issues with the 3D viewers in the following issue tracker. Please first check that there is not already a similar issue open – if there is, please feel free to comment on that issue to let us know you ran into that problem too!