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Convert between filenames and neuroglancer ids

Source: R/ids.R
fafbseg-ids.Rd

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).

Value

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

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.

Examples

swc2segmentid("10001654273.1.swc")
#> [1] 10001654273
swc2segmentid(sprintf("10001654273.%d.swc", 0:2), include.fragment=TRUE)
#>          segment fragment
#> [1,] 10001654273        0
#> [2,] 10001654273        1
#> [3,] 10001654273        2
if (FALSE) {
# 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")))
}