[MINC-users] Tempdir handling by some MINC tools

[Gabriel A. Devenyi]

Can you please open an issue listing all the scripts you caught this in and
I'll look into swapping in some more robust code. Maybe we can do this
before we push 1.9.18

Thanks!

--------------------------------------------------------
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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 16:46, Gabriel A. Devenyi <gabriel.devenyi at mcgill.ca>
wrote:

> We can fix this up with "mktemp -d" in shell scripts.
> --------------------------------------------------------
> Asking for technical help? Get help fast:
> https://www.chiark.greenend.org.uk/~sgtatham/bugs.html
> http://www.catb.org/~esr/faqs/smart-questions.html#beprecise
> https://en.wikipedia.org/wiki/XY_problem
> https://stackoverflow.com/help/minimal-reproducible-example
>
>
> --
> 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
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>