[MINC-development] Welcome

[Peter NEELIN]

On Tue, 12 Nov 2002, Andrew Janke wrote:

> To this end, netCDF can also read many other formats like
> HDF so there is also no reason as to why we need limit outselves to the netCDF
> version of network transparency.

Another clarification: Unless things have changed, NetCDF does not read
HDF. You can, however, compile against the HDF library since it has a
NetCDF-compatible API that will read NetCDF files, but will
only write HDF files. (My information may be out of date - I haven't
checked recently.)

> As such perhaps we need to make MINC more 'netCDF'ish' :). In order that many of
> the other freeware netCDF viewers out there can read MINC files without to much
> munging of the header.

The one big issue is the rescaling of data. I intentionally departed from
the standard since I felt that it was more important to be able to scale
slices separately (and so not have to store the whole volume in memory). I
had thought about writing a MINC to NetCDF "converter" (really a
fixer-upper), but I never found any NetCDF applications that really
justified the effort.

> ncview come to mind:
>    http://meteora.ucsd.edu/~pierce/ncview_home_page.html

This looks neat. Have you tried it out? It should work, although the slice
scaling would be off with some files. Try "mincreshape -normalize" to get
all slices onto the same scale, and then use "minc_modify_header -dinsert"
to stuff in scale and offset for the image variable and you should have a
NetCDF-compliant file.

> re: Compression: I seem to remember reading somewhere about netCDF and
> compression, the consensus was that netCDF probably shouldn't do this as HDF
> already does it.  (remember, netCDF can read HDF tranparently).

I don't believe that the NetCDF folks are planning on giving up on it yet!
HDF just provides a NetCDF-like API and can read NetCDF files. But once
gone over to HDF, there is no going back. Someone has made modifications
to 3.3 (I think) that makes use of zlib for compression. The NetCDF folks
are not big fans of on-the-fly compression since it interferes with random
access and fast IO (I think that that is the gist of the argument - have a
look at the NetCDF FAQ).

            Peter
----
            Peter Neelin (neelin@bic.mni.mcgill.ca)