napari-vedo-bridge 0.2.0

Transfer mesh data between napari and vedo for interactive processing

napari-vedo-bridge

To be able to use interactive processing of meshes in napari, this plugin provides a bridge to the vedo library. It allows to transfer meshes between napari and vedo and to use the interactive processing capabilities of vedo in napari.

I/O

The plugin allows to export and import meshes and point layers. The following are supported:

napari layer type	File Format	Import	Export	Features
Surface	.vtp	✓	✓	✓
Surface	.vtk	✓	✓	✗
Surface	.obj	✓	✓	✗
Surface	.stl	✓	✓	✗
Surface	.ply	✓	✓	✗
Points	.vtp	✓	✓	✓
Points	.vtk	✓	✓	✗
Points	.ply	✓	✓	✗
Points	.obj	✓	✓	✗

Interactive mesh cutting

To interactively cut meshes in the napari-vedo MeshCutter, install the plugin (see below) and open the plugin it from the napari plugins menu (Plugins > Mesh Cutter (napari-vedo-bridge)).

To cut meshes you can use the following cutters:

• PlaneCutter: cuts a mesh with a plane
• SphereCutter: cuts a mesh with a sphere
• BoxCutter: cuts a mesh with a box

To send and get data into and from the plugin, you can:

• Retrieve the current mesh from napari (click Retrieve mesh from napari) - this imports the currently selected mesh layer from napari
• Load a mesh from file (click Load mesh)
• Send a mesh to napari (click Send back to napari) - this creates a new mesh layer in napari

Mesh Processing Functions

The plugin also provides a set of mesh processing functions that can be used in napari. These functions are wrapped from the vedo library and provide various mesh processing capabilities. The following functions are available:

• compute_normals: Compute normals for the given mesh.
• shrink: Shrink the given mesh.
• join: Join the given meshes.
• subdivide: Subdivide the given mesh.
• decimate: Decimate the given mesh.
• decimate_pro: Decimate the given mesh using the Pro algorithm.
• decimate_binned: Decimate the given mesh using the Binned algorithm.
• smooth: Smooth the given mesh.
• fill_holes: Fill holes in the given mesh.
• inside_points: Get the points inside the given mesh.
• extrude: Extrude the given mesh.
• split: Split the given mesh into connected components.
• extract_largest_region: Extract the largest region from the given mesh.
• binarize: Binarize the given mesh.

Pointcloud Processing Functions

The plugin also provides a set of pointcloud processing functions that can be used in napari. These functions are wrapped from the vedo library and provide various pointcloud processing capabilities. The following functions are available:

• smooth_points: Smooth the given points.
• decimate_points: Decimate the given points.
• cluster_points: Cluster the given points.
• remove_outliers: Remove outliers from the given points.
• compute_normals_points: Compute normals for the given points.
• extract_largest_cluster: Extract the largest cluster from the given points.

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This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.

Installation

You can install napari-vedo-bridge via pip:

pip install napari-vedo-bridge

Contributing

Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

License

Distributed under the terms of the BSD-3 license, "napari-vedo-bridge" is free and open source software

Issues

If you encounter any problems, please [file an issue] along with a detailed description.