Evaluate an expression after temporarily setting malevnc options

with_fish temporarily changes the server/dataset options for the malevnc package so that they target the fish2 dataset while running your expression.

choose_fish_dataset sets the default dataset used by all fish_* functions. It is the recommended way to access fish2 dataset variants. Unlike choose_fish it does not permanently change the default dataset used when callers use functions from the malevnc package directly.

choose_fish swaps out the default malevnc dataset for the fish2 dataset. This means that all functions from the malevnc package should target fish2 instead. It is recommended that you use with_fish to do this temporarily unless you have no intention of using other FlyEM datasets. To switch the default fishr dataset please see choose_fish_dataset.

When Clio dataset lookup is unavailable, choose_fish falls back to a built-in neuprint-only configuration for the main fish2 dataset. Clio-backed functionality may be unavailable in that session.

Usage

with_fish(expr, dataset = fish_default_dataset())

choose_fish_dataset(dataset = "fish2")

choose_fish(dataset = fish_default_dataset(), set = TRUE, use_clio = NA)

Arguments

expr: An expression involving malevnc/fishr functions to evaluate with the specified dataset.
dataset: The name of the dataset as reported in Clio (default "fish2").
set: Whether to set the relevant package options or just to return a list of the required options.
use_clio: Whether to use a live Clio lookup for fish dataset settings. The default NA first reuses any cached live lookup for the dataset, otherwise it tries Clio and falls back to baked-in fish2 neuprint settings when available. Use FALSE to avoid Clio and rely only on cached or built-in settings. Use TRUE to require a live Clio lookup.

Value

with_fish returns the result of expr. choose_fish and choose_fish_dataset return a named list of previous option values, matching options.

Details

choose_fish first tries a live Clio lookup via malevnc::choose_flyem_dataset. If that fails (e.g. no network / no Clio token), it falls back to baked-in neuprint settings. Clio-backed functions will be unavailable in that fallback session.

Examples

if (FALSE) { # \dontrun{
# temporarily target fish2 for one call
with_fish(read_fish_meshes(12345))

# or set fish2 as the active dataset for the rest of the session
choose_fish()
read_fish_meshes(12345)
} # }