R and ImageJ sync issues

Asked Dec 31 '15 at 10:36

Active Jan 02 '16 at 12:31

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I have a script in R (written by someone else) which calls ImageJ for image analysis using shell() with '-batch' switch:

shell("C:\\ImageJ\\imagej.exe -batch [args]")

The analysis indeed begins, but it seems that R continues to perform the next lines before the analysis is done, and therefore tries to access some files before they are created.

If I run it with a debugger break point,and wait until it's done before I continue, everything works fine. But if I try to run it as a whole, I get an error resulting from reading an empty folder.

The shell() command has an optional argument 'wait' with a default value "TRUE", but I guess that launching ImageJ, and not its completion, is considered as "finish" for shell and that's why R continues. So what can I do to force R to wait until ImageJ is done? I know I can check the number of created files in a while loop, so it will practically hold until all the files are created. But I rather have a more elegant and less dangerous solution. Thanks!

edited Jan 02 '16 at 12:31

Jan Eglinger

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asked Dec 31 '15 at 10:36

Inbal H

It would be a good idea to post the code you have – Mark Chorley Dec 31 '15 at 10:44
This is a great question, but you might want to include some code as well. – Tim Biegeleisen Dec 31 '15 at 10:44
The code is long and complicated... I added the line of shell() command in the question. The problem is (in mu opinion) more generic: IJ works in background so R doesn't wait. How can I change this? – Inbal H Dec 31 '15 at 13:12
You could use the `readline()` function and continue after the batch analysis is finished. – mrub Dec 31 '15 at 15:54
But that will involve the user... and it shouldn't – Inbal H Dec 31 '15 at 16:27
There is a `Sys.sleep()` function if you need to suspend R execution while waiting for an external process to complete. – IRTFM Dec 31 '15 at 16:54

R and ImageJ sync issues

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