[MINC-users] minccomplete's completeness

[Andrew Janke]

And that sounds even better.  Never realised it was part of HDF5.


a

On 14 May 2016 at 18:53, Vladimir S. FONOV <vladimir.fonov at gmail.com> wrote:
> Hello,
>
> the only thing minccomplete does is read the contents of the image:complete
> attribute. Which is not even respected by all minc tools.
> One real way to check the consistency of the minc file would be to enable
> checksum , integrated into HDF5 file format.
>
> Currently it can be enabled by setting the environment variable
> MINC_CHECKSUM to 1 , at the time when file is created. Obviously, this
> works only with MINC2 file format and it was not tested very well yet.
>
> On Fri, May 13, 2016 at 3:35 PM, Alex Zijdenbos <zijdenbos at gmail.com> wrote:
>
>> Hi all,
>>
>> I managed to generate a large number of broken MINC files; possibly/likely
>> due to a filesystem problem. The processes that created them (e.g.,
>> mincaverage) did not produce any warnings and completed successfully; in
>> addition, minccomplete tells me that the files are complete.
>>
>> Unfortunately, trying to read these files throws HDF5 and miicv errors (see
>> below) and they are obviously corrupt.
>>
>> I am thinking that it would be useful to complete minccomplete by having it
>> actually test-read the data, such that it would report on file integrity?
>> This would make it easy to find these kinds of corruptions - and could even
>> tack that end the end of scripts to make sure outputs are intact. I'm
>> currently using 'mincstats -quiet -min' to locate them, but it seems the
>> natural place for this test would actually be minccomplete.
>>
>> -- A
>>
>> HDF5-DIAG: Error detected in HDF5 (1.8.9) thread 0:
>>   #000: H5Dio.c line 174 in H5Dread(): can't read data
>>     major: Dataset
>>     minor: Read failed
>>   #001: H5Dio.c line 449 in H5D_read(): can't read data
>>     major: Dataset
>>     minor: Read failed
>>   #002: H5Dchunk.c line 1729 in H5D_chunk_read(): unable to read raw data
>> chunk
>>     major: Low-level I/O
>>     minor: Read failed
>>   #003: H5Dchunk.c line 2760 in H5D_chunk_lock(): data pipeline read failed
>>     major: Data filters
>>     minor: Filter operation failed
>>   #004: H5Z.c line 1120 in H5Z_pipeline(): filter returned failure during
>> read
>>     major: Data filters
>>     minor: Read failed
>>   #005: H5Zdeflate.c line 125 in H5Z_filter_deflate(): inflate() failed
>>     major: Data filters
>>     minor: Unable to initialize object
>> mincstats (from miicv_get): Can't read dataset /minc-2.0/image/0/image
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>
>
>
> --
> Best regards,
>
>  Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users