[MINC-users] minccomplete's completeness

[Robert D. Vincent]

Hi all,

In any case, Alex is entirely correct HDF5 errors should be better handled
in a few key places - outright read errors should cause obvious things like
"exit(-1)" or something. The format is so full of redundancy that it's
quite unlikely you would successfully read a broken file, with or without
checksumming the data (there are already checksums built into most HDF5
data structures, e.g.).

I'll make these changes asap.

    -bert

On Sat, May 14, 2016 at 6:53 AM, 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
>