Evaluate an expression after temporarily setting malevnc options

yakuba is a thin wrapper around malevnc. This function temporarily changes the server/dataset options for malevnc while running your expression.

choose_dyak() swaps out the default malevnc dataset for the yakuba dataset. This means that all functions from the malevnc package should target yakuba instead. It is recommended that you use with_dyak() to do this temporarily unless you have no intention of using other FlyEM datasets. To switch the default yakuba dataset please see choose_dyak_dataset().

When Clio dataset lookup is unavailable, choose_dyak() falls back to a built-in neuprint-only configuration for the main yakuba dataset aliases. DVID/Clio-backed functionality may be unavailable in that session.

Usage

with_dyak(expr, dataset = dyak_default_dataset())

choose_dyak(dataset = dyak_default_dataset(), set = TRUE)

Arguments

expr: An expression involving malevnc/yakuba functions to evaluate with the specified autosegmentation.
dataset: The name of the dataset as reported in Clio or neuprint.
set: Whether to set the relevant package options or just to return a list of the required options.

Value

with_dyak() returns the result of expr. choose_dyak_dataset() and choose_dyak() return named lists of previous option values, matching options().

Details

Note that it can also temporarily switch out the active dataset for the yakuba package if you specify the dataset argument and this is different from the current active dataset. This allows you to easily run the same expression for different yakuba dataset variants.

Examples

# \donttest{
with_dyak(dyak_ids("DNa02"))
#> Error in (function (path, body = NULL, server = NULL, conf = NULL, parse.json = TRUE,     include_headers = TRUE, simplifyVector = FALSE, app = NULL,     ...) {    if (is.null(app))         app = paste0("neuprintr/", utils::packageVersion("neuprintr"))    req <- if (is.null(body)) {        httr::GET(url = file.path(server, path, fsep = "/"),             config = conf, httr::user_agent(app), ...)    }    else {        httr::POST(url = file.path(server, path, fsep = "/"),             body = body, config = conf, httr::user_agent(app),             ...)    }    neuprint_error_check(req)    if (parse.json) {        parsed = neuprint_parse_json(req, simplifyVector = simplifyVector)        if (length(parsed) == 2 && isTRUE(names(parsed)[2] ==             "error")) {            stop("neuPrint error: ", parsed$error)        }        if (include_headers) {            fields_to_include = c("url", "headers")            attributes(parsed) = c(attributes(parsed), req[fields_to_include])        }        parsed    }    else req})(path = path, body = body, server = server, conf = conf, parse.json = parse.json,     include_headers = include_headers, simplifyVector = simplifyVector,     app = app): Unauthorized (HTTP 401). Failed to process url: https://neuprint-yakuba.janelia.org/api/dbmeta/datasets with neuPrint error: invalid or expired jwt.

old <- choose_dyak("yakuba", set = FALSE)
str(old)
#> List of 5
#>  $ malevnc.server          : chr "https://emdata7-yakuba.janelia.org"
#>  $ malevnc.rootnode        : chr "04d73f090f864fe3ba17e57410b8c7ce"
#>  $ malevnc.dataset         : chr "yakuba"
#>  $ malevnc.neuprint        : chr "https://neuprint-yakuba.janelia.org"
#>  $ malevnc.neuprint_dataset: chr "yakuba-vnc"
# }