runFijiMacro: Call external Fiji/ImageJ executable

In jefferislab/jimpipeline: Package to wrap Jefferis lab image processing / registration pipeline

Description

runFijiMacro runs a macro using preferred Fiji executable

fiji returns path to preferred Fiji executable

Usage

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

fiji()


## Not run: 
# 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")

## End(Not run)

jefferislab/jimpipeline documentation built on Sept. 14, 2020, 3:41 p.m.