Call external Fiji/ImageJ executable

Source: R/fiji.R

runFijiMacro runs a macro using preferred Fiji executable

fiji returns path to preferred Fiji executable

runFijiMacro(
  macro = "",
  macroArg = "",
  headless = FALSE,
  batch = TRUE,
  MinMem = MaxMem,
  MaxMem = "2500m",
  IncrementalGC = TRUE,
  Threads = NULL,
  fijiArgs = NULL,
  javaArgs = NULL,
  ijArgs = NULL,
  fijiPath = fiji(),
  DryRun = FALSE
)

fiji(fijiPath = NULL)

Arguments

macro

Path to macro to run
macroArg

Arguments for macro
headless

Whether to have ImageJ/Fiji running headless
batch

Use batch mode
MinMem, MaxMem

Memory limits
IncrementalGC

Whether to use incremental garbage collection
Threads

Number of threads
fijiArgs

Arguments for ImageJ/Fiji (as opposed to the macro itself)
javaArgs

Arguments for java
ijArgs

Arguments for ImageJ
fijiPath

Path to fiji executable (can be set by options(jimpipeline.fiji="/some/path"))
DryRun

Whether to return the command to be run rather than actually executing it.

Value

logical indicating if the command completed successfully

Examples

# Path to current Fiji executable
# \donttest{
fiji()

#> Error in fiji(): Unable to find fiji!Set options('jimpipeline.fiji') to point to the fiji command line executable!
# }

if (FALSE) {
# Set path to preferred Fiji executable (this will be remembered)
# you can also set options(jimpipeline.fiji="/some/path")
fiji("/Applications/Fiji.app/Contents/MacOS/ImageJ-macosx")
}