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Convert between BANC cell ids and root ids

Source: R/ids.R
banc_cellid_from_segid.Rd

Converts between BANC cell ids (should survive most edits) and root ids (guaranteed to match just one edit state). See details.

Usage

banc_cellid_from_segid(
  rootids = NULL,
  timestamp = NULL,
  version = NULL,
  cellid_table = NULL,
  rval = c("ids", "data.frame")
)

banc_segid_from_cellid(
  cellids = NULL,
  timestamp = NULL,
  version = NULL,
  rval = c("ids", "data.frame"),
  integer64 = FALSE,
  cellid_table = NULL
)

Arguments

rootids

banc root ids in any form understood by banc_ids. The default value of NULL will return all cell ids.

timestamp

An optional time stamp. You should give only one of version or timestamp. When both are missing, ids should match the live materialisation version including up to the second edits.

version

An optional integer CAVE materialisation version. You should give only one of version or timestamp. When both are missing, ids should match the live materialisation version including up to the second edits.

cellid_table

Optional name of cell id table (the default value of NULL should find the correct table).

rval

Whether to return the cell ids or the whole of the CAVE table with additional columns.

cellids

Integer cell ids between between 1 and around 20000 that should uniquely identify each cell in the dataset.

integer64

Whether to return ids as bit64::integer64 or character vectors. Default value of NA leaves the ids unmodified.

Value

Either a vector of ids or a data.frame depending on rval. For cell ids the vector will be an integer for root ids (segment ids), a character vector or an bit64::integer64 vector depending on the integer64 argument.

Details

CAVE/PyChunkedGraph assigns a 64 bit integer root id to all bodies in the segmentation. These root ids are persistent in a computer science sense, which is often the exact opposite of what neuroscientists might imagine. Specifically, a given root id is matched to a single edit state of a neuron. If the neuron is edited, then root id changes. In contrast, cell ids do not change even in the face of edits. However, it is important to understand that they correspond to a specific point on a neuron, commonly the nucleus. If the nucleus is edited away from a the rest of a neuron to which it previously belonged, then the cell id and any associated edits will effectively with move it.

For further details see banc slack and banc wiki.

See also

Other banc-ids: banc_ids(), banc_islatest(), banc_latestid(), banc_leaves(), banc_rootid(), banc_xyz2id()

Examples

# \donttest{
banc_cellid_from_segid(banc_latestid("720575941626035769"))
#> Error in py_call_impl(callable, call_args$unnamed, call_args$named) : 
#>   requests.exceptions.SSLError: HTTPSConnectionPool(host='global.daf-apis.com', port=443): Max retries exceeded with url: /info/api/v2/datastack/full/brain_and_nerve_cord (Caused by SSLError("Can't connect to HTTPS URL because the SSL module is not available."))
#> Run `reticulate::py_last_error()` for details.
#> • Please run dr_fafbseg() to help diagnose.
#> Error in (function (datastack_name = getOption("fafbseg.cave.datastack_name",     "flywire_fafb_production")) {    cavec = check_cave()    client = try(cavec$CAVEclient(datastack_name))    if (inherits(client, "try-error")) {        ui_todo("\nPlease run dr_fafbseg() to help diagnose.")        stop("There seems to be a problem connecting to datastack: ",             datastack_name)    }    client})(): There seems to be a problem connecting to datastack: brain_and_nerve_cord
# }
# \donttest{
banc_cellid_from_segid(banc_latestid("720575941480769421"))
#> Error in py_call_impl(callable, call_args$unnamed, call_args$named) : 
#>   requests.exceptions.SSLError: HTTPSConnectionPool(host='global.daf-apis.com', port=443): Max retries exceeded with url: /info/api/v2/datastack/full/brain_and_nerve_cord (Caused by SSLError("Can't connect to HTTPS URL because the SSL module is not available."))
#> Run `reticulate::py_last_error()` for details.
#> • Please run dr_fafbseg() to help diagnose.
#> Error in (function (datastack_name = getOption("fafbseg.cave.datastack_name",     "flywire_fafb_production")) {    cavec = check_cave()    client = try(cavec$CAVEclient(datastack_name))    if (inherits(client, "try-error")) {        ui_todo("\nPlease run dr_fafbseg() to help diagnose.")        stop("There seems to be a problem connecting to datastack: ",             datastack_name)    }    client})(): There seems to be a problem connecting to datastack: brain_and_nerve_cord
# }