flywire_cloudvolume: Low level access to FlyWire data via Python cloudvolume...

In natverse/fafbseg: Support Functions for Analysis of FAFB EM Segmentation

Low level access to FlyWire data via Python cloudvolume module

Description

Low level access to FlyWire data via Python cloudvolume module

Usage

flywire_cloudvolume(
  cloudvolume.url = NULL,
  cached = TRUE,
  min_version = NULL,
  ...
)

Arguments

cloudvolume.url	URL for CloudVolume to fetch segmentation image data. The default value of NULL chooses the flywire production segmentation dataset.
cached	When TRUE (the default) reuses a cached CloudVolume object from the current Python session. See details.
min_version	A minimum version for the cloudvolume Python module e.g. "3.12". The default NULL implies any version is acceptable.
...	Additional arguments passed to the CloudVolume constructor

Details

this is the equivalent of doing (in Python):

⁠from cloudvolume import CloudVolume vol = CloudVolume('graphene://https://prodv1.flywire-daf.com/segmentation/table/fly_v31', use_https=True)⁠

The cache tries to be intelligent by

• 1. generating a new object for every input parameter combination (which of course you would need to do in Python)

• 2. avoiding stale references by checking that Python is currently running and that the returned CloudVolume object is non-null. It also regenerates the object every hour.

Note that reticulate the package which allows R/Python interaction binds to one Python session. Furthermore Python cannot be restarted without also restarting R.

See Also

simple_python for installation of the necessary Python packages.

Examples

## Not run: 
cv=flywire_cloudvolume()

# detailed info about the image volume
cv$info
# bounding box (Python format in raw voxels)
cv$bounds
# in nm
boundingbox(cv)

# get help for a function
reticulate::py_help(cv$get_roots)

## End(Not run)

natverse/fafbseg documentation built on Nov. 11, 2024, 9:50 p.m.