I'm trying to loop a python script through a bunch of files. The python script looks at two types of files each run: a XX.nii.gz file and an associated XX_aparc aseg.nii.gz file. The XX is a number identifier of the file.

The python script has the following format: ./pythonscript.sh -s XX -t XX.nii.gz -a XX_aparc aseg.nii.gz -o output_dir. The -s flag creates a folder in the output_dir with the specified name (I would like the name to be the number identifier of the file XX). The -t flag looks at the specified XX.nii.gz file. The -a flag looks at the specified XX_aparc aseg.nii.gz file.

I've tried for f in *.nii.gz; do ./pythonscript.sh -s XX -t XX.nii.gz -a XX_aparc aseg.nii.gz -o output_dir; done. I know that wouldn't work because of how the files are named, but I can't quite figure out how to specify the values that I would like for each of the flags whilst only iterating through the relevant files. I would like the python script to run on only the XX.nii.gz files whilst specifying the associated XX_aparc aseg.nii.gz file. There are also other types of files and subfolders in the directory related to the execution of the python script that I would not like the python script to look at.

CodePudding user response：

Notice that this has very little to to with either Python or Terminal, and everything to do with the shell you are using, which is probably zsh if you're on a reasonably modern Mac.

In that case, you could do something like

for f in *.nii.gz(:s/.nii.gz//); do
    ./pythonscript.sh -s $f -t ${f}.nii.gz -a ${f}_aparc aseg.nii.gz -o output_dir
done

This magic uses the : glob qualifier to invoke the s/// history modifier to delete part of the matched filename. (This is also described in the zshexpn(1) manpage that you can read by running man zshexpn.)