I've come across this problem again useing a smaller macro.
I'm not clear on what / how / why Bioformat is opening
I have a folder with 2 .tiff images (3 channels), the small macro I'm running is to make new folders named for the images using the batch mode. When I run the macro below on the directory in the 'Test' option of batch mode, it works fine.
When I run "process" in batch mode, the macro is executed (folders are made) but I think the image files are edited or saved in a different format. The windows icon changes and when I try to open the file in Fiji, the BioFormat importer window appears.
Here is the macro I'm trying to run through batch processing.
mainTitle_path = substring(mainTitle, 0, lengthOf(mainTitle)-4);//remove tiff
input = "C:\Users\alpeterson7\Desktop\macro material\test\";
dirCropOutput = input+mainTitle_path;
Why are the tiff files changed this way when they are run through batch processing? Is there a way to turn off BioFormat?
I don't really understand how BioFormat in working under the hood of Fiji with the Batch processing, I may be missing a major point of why BioFormat can't be turned off. I am still learning how to feed macros into the batch processing.