I don't know how the others get a dump on this. I tried every which way to
download this and my ncdump still does not like it. For people who did
download it can you mail it to me or see if netcdf4 or xarray can read it.
IMO opinion, the real question is why is this file corrupt. Is it something
to do with whatever software created it in the "minc format"
(https://en.wikibooks.org/wiki/MINC/SoftwareDevelopment/MINC2.0_File_Format_Reference),
something to do with the format itself, or something to do with the original
file transfer. But I do not think you should be distributing a corrupt file,
period.
I looked at your code to read netcdf files and you are using code based on
pupynere from our old buddy Roberto. pupynere operates at a low level on the
file, not using the standard library calls, and therefore can probably pass
over some problems in the file. But the fact that you can write code that can
pass over problems in a file doesn't mean you should. If standard netcdf
libraries/packages can't read the file, you should get a new file that isn't
corrupt and that standard libraries can read.
HTH,
-Roy
> On Jun 23, 2018, at 10:27 AM, Ankur Sinha <sanjay.ankur@xxxxxxxxx> wrote:
>
> Hi Roy, Wei-keng,
>
>
> On Fri, Jun 22, 2018 19:18:42 -0500, Wei-keng Liao wrote:
>> The file is corrupted. I ran it against ncvalidator and got the following
>> errors.
>
> Thanks for looking into this. Someone had commented on the scipy issue[1]
> about the offsets but I hadn't understood completely what they'd meant.
> Thanks for clarifying it up.
>
> Would the suggested way of handling such files be to simply flag them as
> corrupt and not process them at all then?
>
> While the scipy implementation crashes with this file, the netcdf
> implementation that nibabel uses does not. I'm still trying to figure
> out what they do differently.
>
> [1] https://github.com/scipy/scipy/issues/8153#issuecomment-364757198
>
> --
> Thanks,
> Regards,
>
> Ankur Sinha "FranciscoD"
>
> https://fedoraproject.org/wiki/User:Ankursinha
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**********************
"The contents of this message do not reflect any position of the U.S.
Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: Roy.Mendelssohn@xxxxxxxx www: http://www.pfeg.noaa.gov/
"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected"
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
