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Run macro

Description

Run a specific ImageJ macro once (as opposed to the "Run macro on objects" module, which runs once per object). This module can optionally open an image into ImageJ for the macro to run on. It can also intercept the output image and store it in the MIA workspace. Variables assigned during the macro can be extracted and stored as measurements associated with the input image.

Note: ImageJ can only run one macro at a time, so by using this module the "Simultaneous jobs" parameter of the "Input control" module must be set to 1.

Note: When this module runs, all windows currently open in ImageJ will be automatically hidden, then re-opened upon macro completion. This is to prevent accidental interference while the macro is running. It also allows the macro to run much faster (batch mode). To keep images open while the macro is running (for example, during debugging) start the macro with the command "setBatchMode(false)".

Parameters