WEBKNOSSOS: mito-segEM mesh rendering

mito-segem-meshes.js

// Adds a keyboard shortcut "S", which collects all segments as marked by a skeleton node of the active tree.
// This allows users to collect segments using the skeleton feature and then render all meshes of these segments.
// The meshes can also be conveniently downloaded.
webknossos.apiReady(3).then((api) => {
  api.utils.registerKeyHandler("s", async () => {
    const layerName = api.data.getVolumeTracingLayerName();

    // Is there a precomputed mesh availble?
    let meshFile = api.data.getActiveMeshFile();
    if (meshFile == null) {
      const availableMeshFileNames = api.data.getAvailableMeshFiles();
      if (availableMeshFileNames.length > 0) {
        api.data.setActiveMeshFile(availableMeshFileNames[0]);
        meshFile = availableMeshFileNames[0];
      }
    }

    // Resolve segment ids for nodes
    const activeTree = api.tracing.getAllTrees()[api.tracing.getActiveTreeId()]
    const nodes = activeTree.nodes;
    const nodeSegmentIds = [];
    for (const node of nodes.map(n => n)) {
      const position = node.untransformedPosition;
      const segmentId = await api.data.getDataValue(layerName, position);
      if (segmentId !== 0) {
        nodeSegmentIds.push({ position, segmentId });
      }
    }

    // Is there a segment group already?
    let groupId = nodeSegmentIds.find(({ segmentId }) => {
      try {
        return api.tracing.getSegment(segmentId, layerName);
      } catch {
        return null;
      }
    });
    if (groupId == null) {
      groupId = api.tracing.createSegmentGroup(activeTree.name, -1, layerName);
    }

    // Register all segments with this segment group and render meshes
    for (const { position, segmentId } of nodeSegmentIds) {
      api.tracing.registerSegment(segmentId, position, null, layerName);
      api.tracing.updateSegment(segmentId, { groupId }, layerName);
      if (meshFile == null) {
        api.data.computeMeshOnDemand(segmentId, position);
      } else {
        api.data.loadPrecomputedMesh(segmentId, position);
      }
    }
  });
});