Upload Mesh to Google Cloud Storage for BANC Neuroglancer

This function uploads a mesh.obj file to a Google Cloud Storage bucket that can be accessed by BANC neuroglancer. It uses reticulate to call Python code and manages a conda environment.

The underlying Python code is based on the bikinibottom package: https://github.com/jasper-tms/bikini-bottom/tree/main

Usage

banc_upload_mesh(
  mesh,
  mesh_id,
  vol = "precomputed://gs://lee-lab_brain-and-nerve-cord-fly-connectome/volume_meshes/",
  compress = TRUE,
  overwrite = FALSE
)

Arguments

mesh: Character or mesh3d object. Either a path to the .obj file or an R mesh object.
mesh_id: Integer. ID for the mesh.
vol: Character. URL for the precomputed volume.
compress: Logical. Whether to compress the mesh. Default is TRUE.
overwrite: Logical. Whether or not to overwrite an extant file of the same name and path at the location specified by vol+mesh_id. Default is FALSE.

Value

Invisible NULL. The function is called for it upload effect.

Details

For this function to work the global environment variable GOOGLE_APPLICATION_CREDENTIALS to something like "$HOME/.config/gcloud/legacy_credentials/firstname.secondname@gmail.com/adc.json". This file can be obtains by installing gsutil and running gsutil init in the terminal.

References

bikinibottom package: https://github.com/jasper-tms/bikini-bottom/tree/main

Examples

if (FALSE) { # \dontrun{
banc_upload_mesh(
mesh = "/Users/abates/projects/flyconnectome/bancpipeline/deformetrica/obj/banc_brain_neuropil.obj",
mesh_id = 3,
vol = "precomputed://gs://lee-lab_brain-and-nerve-cord-fly-connectome/volume_meshes/meshes"
)
} # }