How to prevent file overwriting in bash script?

Question

I am trying to automate a process which take a file type NIFTI, preprocess it, and places the new processed file in an output folder.

deepbrain-extractor -i <input-dir> -o <output-dir>

I wrote this bash script to automate this process for all files in a directory:

for file in path/*.nii
do
    deepbrain-extractor -i $file -o path/newfiles
done

The problem is every time the code runs, it overwrites the old files (since all automatically get the same name). Is there a way to prevent that?

In this case, the shell has no control, as it is deepbrain-extractor that defines what happens to path/newfiles. — chepner
– chepner, Commented Nov 13, 2020 at 20:46
Copy the files into a backup directory, run deepbrain-extractor, then move them back (with changed names, maybe <file>-old.nii — Michael Bianconi
– Michael Bianconi, Commented Nov 13, 2020 at 20:48
Do you want path/newfiles to be different for each input file? What behavior do you want to happen, instead of the behavior you actually get? — Charles Duffy
– Charles Duffy, Commented Nov 13, 2020 at 20:52
If what you want is to create an output file name based on the input name, then it might be something like deepbrain-extractor -i "$file" -o "${file%.nii}.out" (and this question would be a duplicate of ones already in our knowledge base). — Charles Duffy
– Charles Duffy, Commented Nov 13, 2020 at 20:57
How to create one output file for each file passed to a loop in bash is one such duplicate. — Charles Duffy
– Charles Duffy, Commented Nov 13, 2020 at 20:59

Feras Altwal · Accepted Answer · 2020-11-13 21:39:25Z

2

Thanks for the suggestions and comments! seems like using this code gives me what I want.

deepbrain-extractor -i "$file" -o "${file%.nii}.out"

Thanks a lot!!

answered Nov 13, 2020 at 21:39

Feras Altwal

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Comments

convex · Accepted Answer · 2020-11-13 21:19:23Z

0

A common way to get a unique file name is to use the current date and time. You can combine this with the input file name to ensure that output files are never overwritten.

if [ ! -f "$FILE" ]; then
    echo "$FILE does not exist."
    for file in path/*.nii
    do
    deepbrain-extractor -i $file -o path/newfiles_${file##*/}_$(date +"%Y-%m-%d_%H-%M-%S")
    done
fi

so the output directory has a name like newfiles_input_2020-11-13_12-34-56

Also see How to create one output file for each file passed to a loop in bash?

edited Nov 13, 2020 at 21:19

answered Nov 13, 2020 at 21:13

convex

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1 Comment

Charles Duffy Over a year ago

Duplicative questions should be closed, not answered. See the Answer Well-Asked Questions section of How to Answer.

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