Re: [netcdfgroup] [Hdf-forum] Detecting netCDF versus HDF5

This is a super interesting conversation for me! ;-)

I must admit that when putting netCDF-4 together I never considered that
someone might want to tell the difference between a "native" HDF5 file and
a netCDF-4/HDF5 file. Well, you can't think of everything.

I agree that it is not possible to canonically tell the difference. The
netCDF-4 API does use some special attributes to track named dimensions,
and to tell whether classic mode should be enforced. But it can easily
produce files without any named dimensions, etc. So I don't think there is
any easy way to tell.

However, you can attempt to open a HDF5 file with nc_create, and, if it
fails, use HDF5. (It should very rarely fail.)

Ed



On Wed, Mar 2, 2016 at 7:07 PM, Miller, Mark C. <miller86@xxxxxxxx> wrote:

> I like John's suggestion here.
>
> But, any code you add to any applications now will work *only* for files
> that were produced post-adoption of this convention.
>
> There are probably a bazillion files out there at this point that don't
> follow that convention and you probably still want your applications to be
> able to read them.
>
> In VisIt, we support >140 format readers. Over 20 of those are different
> variants of HDF5 files (H5part, Xdmf, Pixie, Silo, Samrai, netCDF, Flash,
> Enzo, Chombo, etc., etc.) When opening a file, how does VisIt figure out
> which plugin to use? In particular, how do we avoid one poorly written
> reader plugin (which may be the wrong one for a given file) from preventing
> the correct one from being found. Its kinda a hard problem.
>
> Some of our discussion is captured here. . .
>
> http://www.visitusers.org/index.php?title=Database_Format_Detection
>
> Mark
>
>
> From: Hdf-forum <hdf-forum-bounces@xxxxxxxxxxxxxxxxxx> on behalf of John
> Shalf <jshalf@xxxxxxx>
> Reply-To: HDF Users Discussion List <hdf-forum@xxxxxxxxxxxxxxxxxx>
> Date: Wednesday, March 2, 2016 1:02 PM
> To: HDF Users Discussion List <hdf-forum@xxxxxxxxxxxxxxxxxx>
> Cc: "netcdfgroup@xxxxxxxxxxxxxxxx" <netcdfgroup@xxxxxxxxxxxxxxxx>, Ward
> Fisher <wfisher@xxxxxxxx>
> Subject: Re: [Hdf-forum] Detecting netCDF versus HDF5
>
> Perhaps NetCDF (and other higher-level APIs that are built on top of HDF5)
> should include an attribute attached to the root group that identifies the
> name and version of the API that created the file?  (adopt this as a
> convention)
>
> -john
>
> On Mar 2, 2016, at 12:55 PM, Pedro Vicente <
> pedro.vicente@xxxxxxxxxxxxxxxxxx> wrote:
> Hi Ward
> As you know, Data Explorer is going to be a general purpose data reader
> for many formats, including HDF5 and netCDF.
> Here
> http://www.space-research.org/
> Regarding the handling of both HDF5 and netCDF, it seems there is a
> potential issue, which is, how to tell if any HDF5 file was saved by the
> HDF5 API or by the netCDF API?
> It seems to me that this is not possible. Is this correct?
> netCDF uses an internal function NC_check_file_type to examine the first
> few bytes of a file, and for example for any HDF5 file the test is
> /* Look at the magic number */
>    /* Ignore the first byte for HDF */
>    if(magic[1] == 'H' && magic[2] == 'D' && magic[3] == 'F') {
>      *filetype = FT_HDF;
>      *version = 5;
> The problem is that this test works for any HDF5 file and for any netCDF
> file, which makes it impossible to tell which is which.
> Which makes it impossible for any general purpose data reader to decide to
> use the netCDF API or the HDF5 API.
> I have a possible solution for this , but before going any further, I
> would just like to confirm that
> 1)      Is indeed not possible
> 2)      See if you have a solid workaround for this, excluding the dumb
> ones, for example deciding on a extension .nc or .h5, or traversing the
> HDF5 file to see if it's non netCDF conforming one. Yes, to further
> complicate things, it is possible that the above test says OK for a HDF5
> file, but then the read by the netCDF API fails because the file is a HDF5
> non netCDF conformant
> Thanks
> ----------------------
> Pedro Vicente
> pedro.vicente@xxxxxxxxxxxxxxxxxx
> http://www.space-research.org/
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