[MINC-users] Tempdir handling by some MINC tools

[Gabriel A. Devenyi]

We can fix this up with "mktemp -d" in shell scripts.
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--
Gabriel A. Devenyi Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
Affiliate, Department of Psychiatry
McGill University
t: 514.761.6131x4781
e: gabriel.devenyi at mcgill.ca


On Thu, 25 Jun 2020 at 16:26, Alex Zijdenbos <zijdenbos at gmail.com> wrote:

> Hello all,
>
> I recently figured out why I am now and again running into some annoying
> mincdiff failures, where mincdiff does not report "Images are identical"
> even though they actually are. This comes back to the way mincheader
> creates and uses a temporary directory, here:
>
>
> https://github.com/BIC-MNI/minc-tools/blob/master/progs/mincheader/mincheader#L68-L76
>
>
> There are two problems with this bit of code:
>
>    1. it will generate a tempdir solely based on the pid. The pid is of
>    course unique at that moment, but the generated directory may not be -
> for
>    example, in case previous invocations with a (past) identical pid were
> not
>    cleaned up. So something like mincdiff (that calls mincheader) might
> fail,
>    solely because of a tempdir name clash
>    2. in the case of mincheader, the only use case for this appears to be
>    in case of externally compressed .mnc.gz files. I am not sure who still
>    uses those (I don't), but this means that working with internally
>    compressed MINC2 files, each mincheader call will create a dir in /tmp
> that
>    is subsequently not used for anything.
>
> Similar bits of tempdir/file code exist in mincinfo, mincdiff, and likely
> others.
>
> I was wondering if anybody might have fixed this already. In perl this is
> easy, using File::Temp that will guarantee unique temporary files - but
> these tools are all shell scripts. If somebody has some .sh code lying
> around that does this better, perhaps that can be slotted into these tools
> pretty easily?
>
> Thanks,
>
> -- A
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