fafbseg-ids: Convert between filenames and neuroglancer ids

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

Convert between filenames and neuroglancer ids

Description

swc2segmentid converts an swc filename to a segment id

segmentid2zip converts a segment id to the zip file that contains it

zip2segmentstem converts a zip file to the initial part of the segment id i.e. the segment stem (see details).

Usage

swc2segmentid(x, include.fragment = FALSE)

segmentid2zip(x)

zip2segmentstem(x)

Arguments

x	Input file or id
include.fragment	Whether to include the sub identifier of the skeleton fragment (see details).

Details

Segment ids are unique integers. There are about 8E8 in the current skeletonisation but it seems that the ids can still be > 2^31 (usually .Machine$integer.max). Therefore they will be stored in R as numeric values or the bit64::integer64 values.

Each segmentation has keen skeletonised however this usually results in multiple skeleton fragments which have been written out as separate SWC files: "named <segment id>.<fragment>.swc"

Each segment id is mapped onto a zip file by dividing by a divisor and discarding the remainder. Peter Li's data release of 2018-10-02 switched from 1E5 to 1E6.

Value

for swc2segmentid a numeric vector or matrix depending on the value of include.fragment

Examples

swc2segmentid("10001654273.1.swc")
swc2segmentid(sprintf("10001654273.%d.swc", 0:2), include.fragment=TRUE)
## Not run: 
# NB the default segmentation for fafbseg (flywire) no longer implies a local
# collection of skeletons, wrap calls in with_segmentation
with_segmentation("20190805", segmentid2zip(10001654273))
with_segmentation("20190805",
  segmentid2zip(swc2segmentid("10001654273.1.swc")))

## End(Not run)

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