rename files based on their respective directory name


 
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# 1  
rename files based on their respective directory name

I have a number of files in directories labeled like this:

/Data/tr[8428-9915]_gray/tr[8428-9915]_DTI/dti_FA.nii.gz
(the brackets here represent a range of number that the files are labeled with)

I need to rename each dti_FA.nii.gz file according to the name of the folder it resides in. For example, the file /Data/tr8430_gray/tr8430_DTI/dti_FA.nii.gz should be named 8430_dti_FA.nii.gz

Very basic stuff i know...Thank you.
# 2  
Assuming the file names are all the same as you've indicated, this should work:

Code:
#!/usr/bin/env ksh

# big assumption that this find returns only the files you want to move
# test it first!!!
find /Data -name "*gz" | while read x
do
    n="${x%%_*}"      # dig number after tr and before first _
    n="${n#*tr}"
    fn=${x%/*}/${n}_${x##*/}  # add number to build final pathname
    echo "mv $x $fn"    # remove the echo and quotes to actually rename files
done

Always a good idea to run this kind of script and make sure that the commands generated look good to prevent data loss. Also doesn't hurt to back things up first!
# 3  
this is so great. thank you!

So I copied one entire directory (tr9915_gray) to a separate "test folder" (/Data/DTI_test) to try it out. I ran the script from this test folder and so I thought I should replace the first line:
find /Data -name "*.gz" | while read x
with this:
find ./ -name "*.gz" | while read x
(not sure if I should have done that)

It seemed to work, except the thing is, there are a lot of files that end in .gz in various subdirectories.... and it renamed all the files ending in .gz in the subdirectories of /tr9915_gray and skipped the ones in /tr9915_gray/tr9915_DTI. Here is an example of the last three lines from the output.

mv ./tr9915_gray/MSIT_PPI_MFG_ROI.feat/reg/highres.nii.gz ./tr9915_gray/MSIT_PPI_MFG_ROI.feat/reg/9915_highres.nii.gz
mv ./tr9915_gray/MSIT_PPI_MFG_ROI.feat/reg/highres2standard.nii.gz ./tr9915_gray/MSIT_PPI_MFG_ROI.feat/reg/9915_highres2standard.nii.gz
mv ./8531_dti_FA.nii.gz ././8531_8531_dti_FA.nii.gz


Not really sure what happened with the last line at all!
Since I just want to rename the file called dti_FA.nii.gz which resides in /tr9915_gray/tr9915_DTI

...could I replace the first line you made:
find ./ -name "*.gz" | while read x

with this??
find ./ -name "*_FA.gz" | while read x

thank you again so much!!
# 4  
Quote:
Originally Posted by tk0034
this is so great. thank you!

So I copied one entire directory (tr9915_gray) to a separate "test folder" (/Data/DTI_test) to try it out. I ran the script from this test folder and so I thought I should replace the first line:
find /Data -name "*.gz" | while read x
with this:
find ./ -name "*.gz" | while read x
(not sure if I should have done that)
Good call -- both creating the test environment and the change to ./...

Quote:

It seemed to work, except the thing is, there are a lot of files that end in .gz in various subdirectories.... and it renamed all the files ending in .gz in the subdirectories of /tr9915_gray and skipped the ones in /tr9915_gray/tr9915_DTI. Here is an example of the last three lines from the output.

mv ./tr9915_gray/MSIT_PPI_MFG_ROI.feat/reg/highres.nii.gz ./tr9915_gray/MSIT_PPI_MFG_ROI.feat/reg/9915_highres.nii.gz
mv ./tr9915_gray/MSIT_PPI_MFG_ROI.feat/reg/highres2standard.nii.gz ./tr9915_gray/MSIT_PPI_MFG_ROI.feat/reg/9915_highres2standard.nii.gz
mv ./8531_dti_FA.nii.gz ././8531_8531_dti_FA.nii.gz


Not really sure what happened with the last line at all!
Since I just want to rename the file called dti_FA.nii.gz which resides in /tr9915_gray/tr9915_DTI
Is that file just an oddly named file? The script depends on trNNNN so if the tr is missing odd results will happen.

Quote:
...could I replace the first line you made:
find ./ -name "*.gz" | while read x

with this??
find ./ -name "*_FA.gz" | while read x
Yep, that will work too. You can run the find command by itself to see what files it finds and thus what files will be candidates for renaming. You can tweek your find to get just the right things and then let its output go into the read. Seems like you are on the right track.
 

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