Cross-platform in-memory serialization of netcdf4 (like the current scipy-based dumps)

[ebrevdo]

It would be nice to create in-memory netCDF4 objects. This is difficult with the netCDF4 library, which requires a filename (possibly one that it can mmap, but probably not, based on its opendap documentation).

One solution is to call os.mkfifo (in *nix) or its windows equivalent (if the library is available) using tempfile.mktemp as the path. Pass this to the netCDF4 object. dumps() is equivalent to calling sync, close, reading from the pipe, then deleting the result.

We may actually be able to use the same functionality in reverse for creating a netCDF4 object from a StringIO.

[shoyer]

Another option is to add an HDF5 backend with pytables. @ToddSmall has a demo script somewhere that shows how you can pass around in-memory HDF5 objects between processes.

[akleeman]

Another similar option would be to use in-memory HDF5 objects for which Todd Small found an option:

Writing to a string:

h5_file = tables.open_file("in-memory", title=my_title, mode="w",   12
                               driver="H5FD_CORE", driver_core_backing_store=0)
... [add variables] ...
image = h5_file.get_file_image()

Reading from a string

h5_file = tables.open_file("in-memory", mode="r", driver="H5FD_CORE",
                               driver_core_image=image,
                               driver_core_backing_store=0)

[ebrevdo]

Looks like this may be the only option. Based on my tests, netCDF4 is strongly antithetical to any kind of streams/piped buffers. If we go the hdf5 route, we'd have to reimplement the CDM/netcdf4 on top of hdf5, no?

[shoyer]

HDF5 supports homogeneous n-dimensional arrays and metadata, which in
principle should be all we need. Actually, under the covers netCDF4 is
HDF5. But yes, we would have to do some work to reinvent this.

On Wed, Feb 26, 2014 at 2:32 PM, ebrevdo notifications@github.com wrote:

Looks like this may be the only option. Based on my tests, netCDF4 is
strongly antithetical to any kind of streams/piped buffers. If we go the
hdf5 route, we'd have to reimplement the CDM/netcdf4 on top of hdf5, no?

Reply to this email directly or view it on GitHubhttps://github.com/akleeman/xray/issues/23#issuecomment-36186205
.

[shoyer]

Just wrote a little library to do netCDF4 via h5py: https://github.com/shoyer/h5netcdf

Unfortunately h5py still can't do in-memory file images (h5py/h5py#552). But it does give an alternative way to read/write netCDF4 without going via the Unidata libraries. There is experimental support for engine='h5netcdf' in my dask PR: #381

pytables was not a viable option because it can't read or write HDF5 dimension scales, which are necessary for dimensions in netCDF4 files.

[max-sixty]

In an effort to reduce the issue backlog, I'll close this, but please reopen if you disagree

[shoyer]

This is actually finally possible to support now with h5py, which as of the latest release supports reading/writing to file-like objects in Python.

[stale]

In order to maintain a list of currently relevant issues, we mark issues as stale after a period of inactivity

If this issue remains relevant, please comment here or remove the stale label; otherwise it will be marked as closed automatically

[pikulmar]

Still an issue, as far as I can tell. Possibly duplicated in #3372.