> I'm trying to adapt a series of scripts for use with the -batch
> command line
> option for GUI-less operation. I'm struggling however to understand the
> basics of how execution differs.
>
> Example: I'm currently trying to run the "measure" command on a
> directory of
> images in command line batch mode and generate a single output file.
>
> I've written a macro file "measuretest.txt"
>
> macro "measuretest" {
> dir = getDirectory("Choose a Directory ");
> list = getFileList(dir);
> setBatchMode(true);
> for (i=0; i<list.length; i++) {
> path = dir+list[i];
> showProgress(i, list.length);
> if (!endsWith(path,"/")) open(path);
> if (nImages>=1) {
> run("Measure");
> close();
> }
> }
> saveAs("Measurements", "Results.xls");
> }
>
> When I run this from the ImageJ GUI (Fiji > Plugins > Macros > Run
> "measuretest.txt") or from the command line in macro mode ("java -jar
> ij.jar
> -macro measuretest.txt") and choose a directory of 10 images, the
> result is
> a "Results.xls" file containing the full results.
>
> 1 circle-01.png 50.82 46.00
> 2 circle-02.png 3.13 23.54
> 3 circle-03.png 150.46 32.76
> ...
> 10 circle-10.png 16384 206.34
>
> However, when I run the same macro in batch mode ("java -jar ij.jar
> -batch
> measuretest.txt") the terminal output shows line 1 of the results table
> being written to over and over again, and the output "Results.xls" is a
> 1-result file containing the last output.
>
> 1 circle-10.png 16384 206.34
>
> A further unexpected difference was that while -macro wrote the
> "Results.xls" file to the root directory, -batch writes the file to the
> working directory from which ij.jar was invoked.
>
> How do I fix this example to generate a single output file in -batch
> mode?
> Thanks for your time.
>
> -- Jeremy
>
> NOTE: There was a similar old thread
> (
http://n2.nabble.com/batch-measurements-to-single-data-file-
> td635183.html#a635183)
> about accidentally clearing the results table with each measure, but
> the
> solution didn't seem to pertain.
>
> --
> View this message in context:
>
http://n2.nabble.com/Multiple-results-output-from-batch-mode-command-
> line-tp2373942p2373942.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
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