Any idea why the following macro MWE
setBatchMode(true); run("AuPbSn 40"); run("Frangi Vesselness", "dogauss=true spacingstring=[1, 1] scalestring=[2, 5]"); imageCalculator("Add create", "AuPbSn40.jpg","result"); setBatchMode(false);
fails with the following error message:
Image not found in line 4
? The debug window shows the following additional information:
Memory * 122MB of 3931MB (3%)
nImages() * 1
getTitle() * “AuPbSn40.jpg”
The same macro executes flawlessly when the first line
setBatchMode(true) is deleted/commented. Expected behaviour: with
setBatchMode(true) the macro does all the calculation and shows the images only in the end.
In other words, in batch mode (as opposed to non-batch-mode) the window created by the Frangi Vesselness plugin is not added to the window list, and is therefore unselectable. This of course makes the batch mode unusable.
I feel this must be more or less a FAQ, but I searched the forum for quite a bit without finding an answer. One of the most closely related posts are:
but the `solution’ appears to involve some on-and-off-switching of the batch mode, which defeats the purpose of the batch mode itself.
I first thought this was an issue in headless mode only (where the same issue arises without even setting
setBatchMode(true)), prompting the topic