[MINC-users] minccomplete's completeness

[Claude LEPAGE]

Alex,

Here is what I've been doing to check for completeness of minc2 files
(for BigBrain 7404 slices):

sub minc_valid {

  my $input = shift;

  my $ret = `h5ls -r $input`;
  return( 0 ) if( !( $ret =~ m/\/minc-2.0\/info/ ) );
  return( 0 ) if( !( $ret =~ m/\/minc-2.0\/image\/0\/image/ ) );
  return( 0 ) if( !( $ret =~ m/\/minc-2.0\/image\/0\/image-min/ ) );
  return( 0 ) if( !( $ret =~ m/\/minc-2.0\/image\/0\/image-max/ ) );

  return( 1 );
}

h5ls is a HDF5 tool.

Claude

>
> 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
>