Batch processing

What is the best way to run a module on many images? Ideally I’d like some sort of batch upload / batch process feature.


I’ll second this. My existing macros were written as batch processors…I’ve had to re-adapt them to a single file.

Is this a docker implementation where we could copy our files in, or is using the JSON param files a better approach? Perhaps there could be a module for handling an entire folder of images?

Dear both
currently (until we have a more elegant solution) I am doing it this way
package your files into a zip file and use the “Single File Upload” Module to upload the ZIP file. Then use the “Unzip” Module to Unzip said ZIP file. As an output the “Unzip” Module gives you a list of files that you can use as input for your module.

Sidenote: If you use an ImageJ Macro an essentially use the “Import --> File Sequence” command you need to extract the folder path from the input json that the Unzip module generate.
Just look for the value “input_files[0]” when reading the json file this should give you the full path to the first file extracted from the zip file

then use the ImageJ macro functions

path_substring = lastIndexOf(, “/”);
DIR = substring(, 0, path_substring+1);

DIR will then contain the path to the directory that contains all your unzipped files
and then you can run

run(“Image Sequence…”, “open=” + DIR + " file="" sort");