feat(plotting): add plot_surface for displaying meshes in napari#263
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FelipeCybis wants to merge 7 commits into
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feat(plotting): add plot_surface for displaying meshes in napari#263FelipeCybis wants to merge 7 commits into
FelipeCybis wants to merge 7 commits into
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Add plot_surface to display a triangular mesh (vertices, faces) as a napari Surface layer, with an optional per-vertex values array for colormapped shading. Pairs with Atlas.get_mesh to overlay BrainGlobe atlas region surfaces on the reference template or a registered fUSI volume; because both live in the same physical space, the surface aligns without extra scaling. Closes #262
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napari opens in 2D, where a Surface layer is drawn only as its cross-section with the current slice plane, so a 3D mesh is all but invisible. plot_surface now switches the viewer to 3D rendering and resets the view to frame the mesh.
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📖 Doc preview: https://confusius.tools/pr-preview/pr-263/ |
…gion plot_surface now mirrors plot_napari: pass an atlas Dataset and a region, and the layer's mesh, name, default color, and scale-bar unit are all pulled from the atlas (via the .atlas accessor's get_mesh and lookup) instead of a raw (vertices, faces) tuple. Adds side/clip forwarding to get_mesh and draws the surface in the region's Allen color by default. Promotes the atlas test fixtures to tests/unit/conftest.py so the plotting tests reuse the same mock atlas as the atlas tests.
plot_surface goes back to a thin wrapper over napari.add_surface, taking a (vertices, faces) tuple. The atlas-aware behavior moves to a new plot_atlas_mesh(atlas, region, ...) that pulls the mesh, name, Allen color, and units from the atlas and delegates to plot_surface. Also adds an AtlasPlotAccessor exposing ds.atlas.plot.mesh(region, ...). Routes the surface unit through the layer's units param instead of the deprecated ScaleBar.unit setter.
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!Waiting on #274 to continue here!
Closes #262.
What
Adds
confusius.plotting.plot_surface, which displays a triangular mesh as anapari
Surfacelayer —the mesh counterpart to
plot_napari.(vertices, faces)mesh tuple, matchingAtlas.get_mesh's return.valuesfor colormapped shading (flat surface otherwise).viewerto overlay on an existing viewer, and returns(viewer, layer),consistent with the other napari helpers.
"mm", the atlas mesh unit).Because
get_meshreturns vertices already in the atlas physical space and imagelayers sit at their physical origin/spacing, the surface aligns with the image
layers without extra scaling — no
scale/translatejuggling needed.Tests
Added
TestPlotSurfaceintests/unit/test_plotting/test_napari.pycoveringmesh/values round-trip into the layer, the flat-surface default, and
overlay-on-existing-viewer + scale-bar-unit behavior.
Docs
auto-documents it via
__all__.