[MINC-development] weird minc 2 bug

[Robert VINCENT]

Hi Jonathan,

I agree that the behavior of 'mincinfo -dimnames' isn't especially
intuitive for people who don't know all of the inner workings of MINC.
But I think Peter implemented it intentionally as a method for listing all
of the dimensions defined in a file. He also created the "-vardims" option
to actually print the dimensions associated with a variable in the correct
order. So:

mincinfo -vardims image <filename.mnc>

should always give the right result for either netCDF or HDF5. So it is
probably the more useful option, and people have understandably failed to
appreciate the difference.

	-bert

On Wed, 7 Jun 2006, Jonathan HARLAP wrote:

> Hi Bert,
>
> This argument seems internally consistent, although probably
> counterintuitive to any user who doesn't feel a need to understand in
> great detail the inner workings of MINC - and, by extension, the subtle
> difference between the order of dimensions in the file and the order of
> variables.
>
> Fixing the perl library does seem an easy and quick solution, although
> there are probably many other scripts out there that do the same thing
> and will thus break similarly...
>
> That said, what would you suggest is the right way for someone at the
> command line to find out the dimension order of a MINC file?  (IE, what
> could I use instead of mincinfo -dimnames)
>
> Cheers,
> J
>
>
> Robert VINCENT wrote:
> > Hi Jonathan,
> >
> > Interesting point. Because the 'mincinfo -dimnames' option does not query
> > the image variable dimensions, it looks as though the dimension order was
> > never intended to be correct. The reported dimensions simply reflect the
> > _file_ order, which as you know, is independent of the variable ordering.
> > It just happens to be the case that most netCDF files created with our
> > tools will coincidentally have the same dimension ordering in the file as
> > in the image variable. But nothing prevents someone from creating a valid
> > netCDF MINC file with fewer image dimensions than file dimensions, or with
> > a different ordering in the image variable, and the 'mincinfo -dimnames'
> > option will not reflect these facts.
> >
> > So I'd argue it was mistaken to use the -dimnames option assuming
> > that it will return only the image variables dimensions, in the proper
> > order. This contradicts both the code and the documented function of the
> > option.
> >
> > However, we may have to find a way to preserve this behavior to prevent
> > breaking the existing perl libraries. But we should probably fix the perl
> > library was well, as it has probably caused some subtle bugs from time to
> > time.
> >
> > 	-bert
> >
> > On Wed, 7 Jun 2006, Jonathan HARLAP wrote:
> >
> >> Here's a neat one:
> >>
> >> Take a CDF file, run it through mincconvert -2 to get the corresponding
> >> HDF file.  Now open both file in register (or just use
> >> mincinfo/mincheader).  You'll see that the dimension order is, as it
> >> should be, identical.
> >>
> >> Now, the fun part.  Run mincinfo -dimnames on the two files, and observe
> >> the different dimension order.
> >>
> >> This fun bug is great in that it's a subtle little glitch in mincinfo,
> >> but affects many little programs, such as mni-perllib's
> >> MNI::MincUtilities::get_dimension_order()
> >>
> >> Example output below.
> >>
> >> Cheers,
> >> J
> >>
> >>
> >> % mincinfo  m?.mnc
> >> file: m1.mnc
> >> image: signed__ short 0 to 4095
> >> image dimensions: xspace zspace yspace
> >>      dimension name         length         step        start
> >>      --------------         ------         ----        -----
> >>      xspace                    124          1.4        -86.8
> >>      zspace                    256     -1.01562      118.492
> >>      yspace                    256     -1.01562      130.992
> >>
> >>
> >> file: m2.mnc
> >> image: signed__ short 0 to 4095
> >> image dimensions: xspace zspace yspace
> >>      dimension name         length         step        start
> >>      --------------         ------         ----        -----
> >>      xspace                    124          1.4        -86.8
> >>      zspace                    256     -1.01562      118.492
> >>      yspace                    256     -1.01562      130.992
> >>
> >>
> >> % mincinfo -dimnames m?.mnc
> >> xspace zspace yspace
> >>
> >>
> >> xspace yspace zspace
> >>
> >>
> >>
> >> _______________________________________________
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> >> MINC-development at bic.mni.mcgill.ca
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> >>
> >
> >
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