[gdal-dev] NetCDF driver improvements (including groups support)

[Etienne Tourigny]

Hi Julien

These improvements look really great!

Unfortunately I am on a long-term vacation and semi-retired from my GIS
work. So I am sorry but I cannot really help on testing and committing the
work...
That is why I did not respond sooner.

As the last "official" netcdf maintainer I should at least give some
comments.

Perhaps Even can test the patches and commit them, or someone could step in
as a new netcdf maintainer.

If it is possible, It would be best to separate these improvements into a
number of patches. In any case you should add your patch(es) to a number of
new gdal trac ticket(s) (or existing ticket if it fixes a bug).  I did
significant improvements some time ago and I understand that it is hard to
separate these improvements in several patches, so I don't think it is
absolutely necessary to split them up - but it helps debugging any
regressions. Especially the groups support, I/O improvements and NASA
products should have independent patches and tickets.

Regarding 10) it would be best to maintain backwards compatibility, but if
the issue is only with 1D dataset I don't think it matters that much.

Cheers,
Etienne

On Thu, Feb 5, 2015 at 11:10 PM, Julien Demaria <Julien.Demaria at acri-st.fr>
wrote:

> Hi GDAL team,
>
> I've implemented several improvements to the NetCDF driver and I would
> like to provide them to the community.
> Main goal of the changes is to add full support of NetCDF-4 including
> groups.
> NetCDF-4 is the future format of ESA Sentinel-3 products (no groups) and
> NASA Ocean Color team is switching their L2/L3 products to NetCDF-4 with
> groups (VIIRS has already switched to the new format in December).
> With the changes NASA L2 products geolocation is automatically handled as
> geolocation arrays and can be reprojected using gdalwarp.
>
> I validated with autotests that nothing is broken in tests netcdf.py
> (excepting test 13 but see my point 5), netcdf_cf.py and hdf5.py, using
> NetCDF-3 and 4 libraries.
> I've also tested the new functionalities on various NetCDF-4 files.
> I think the only possible regression could be for marginal cases where a
> file was seen directly as a dataset and is now seen as multiple subdatasets
> (for example if a file has only one var in the top group and has nested
> groups containing variables), but I think this is not very common.
>
> For the moment I have all these changes in local GIT separated commits on
> the latest gdal-1.11 branch, let me know what changes you want and how can
> I provide them.
>
> Changes :
>
> 1) Implement full support for NetCDF-4 groups on reading:
>     - explore recursively all nested groups to create the subdatasets list
>     - subdatasets in nested groups use the /group1/group2/.../groupn/var
> standard
>       NetCDF-4 convention, excepting for variables in the root group which
> do not
>       have a leading slash for backward compatibility
>     - when accessing a subdataset using NETCDF:$file:$path, the leading
> slash is optional
>     - global attributes of each nested group are also collected in the
> GDAL dataset
>       metadata, using the same convention
> /group1/group2/.../groupn/NC_GLOBAL#attr_name,
>       excepting for the root group which do not have a leading slash for
> backward compatibility
>     - when searching for a variable containing auxiliary information on
> the selected subdataset,
>       like coordinate variables or grid_mapping, we now also search in
> parent groups (using NCDFResolveVar).
>       I now this is something not specified at this time in the CF
> convention because CF does not know groups,
>       but it seems logical to me to support this: NetCDF-4 specifies that
> dimensions of a group are
>       shared to its nested groups, so associated coordinate variables
> could be defined as the same level of its
>       corresponding dimension.
>     - reference to coordinate variables using the "coordinates" attribute
> support now also absolute paths,
>       this allow for example to specify coordinate variables located
> outside the group of the selected variable
>       or its parents. Relative paths could be implemented if needed.
>       This feature is used to add support for new NASA Ocean Color L2
> products.
>
> 2) Implement full read/write support for new NetCDF4 types NC_UBYTE,
> NC_USHORT, NC_UINT and NC_STRING, only if NETCDF_HAS_NC4 is defined (and
> only if format=NC4 for writing).
>     Support implemented for variables and attributes.
>     NC_STRING type is supported for reading (scalar and arrays) attributes
> and is used for writing only for array attributes (scalar are still written
> as NC_CHAR).
>     If NETCDF_HAS_NC4 is not defined or format!=NC4, NC_STRING array
> attributes are written as a single NC_CHAR string using the GDAL
> {v1,v2,...} convention.
>     Add missing support for NC_BYTE in CreateBandMetadata() and
> NC_BYTE/SHORT in NCDFPut1DVar().
>
> 3) Add support for new NASA Ocean Color L2 products and ESA Sentinel-3 L1
> or
>     L2 products which use the NetCDF-4 format (with groups for NASA, see
>     http://oceancolor.gsfc.nasa.gov/DOCS/FormatChange.html):
>     - NASA products: simulate a "coordinates" variable attribute to detect
> CF
>       geolocation arrays, and set bBottomUp to FALSE
>     - ESA products: set bBottomUp to FALSE and disable warning on missing
>       Conventions attribute
>
> 4) Fix bug #4554 with a more generic solution by disabling the
> installation of the HDF5 atexit() cleanup routine using H5dont_atexit().
>     Previous fix was to call GDALExit() (for the moment only defined
> gdalwarp.cpp) at the end of every program, which is more painful.
>
> 5) Fix implementation of GetScale/Offset to not always return
> pbSuccess=TRUE.
>     Fix CopyMetadata to handle bands with only scale or offset.
>     ==> WARNING this commit breaks the autotest netcdf_13 (check for
> scale/offset = 1.0/0.0 if no scale or offset is available), but for me it
> is not logical to return always pbSuccess=TRUE
>
> 6) Optimize IReadBlock() and CheckData() handling of partial blocks in the
> x axis by re-using the GDAL block buffer instead of allocating a new
> temporary buffer for each block.
>
> 7) Force block size to 1 scanline for bottom-up datasets if nBlockYSize !=
> 1 instead of raising a fatal error
>     ==> Solve a recent problem raised on the mailing list
>
> 8) Implement Get/SetUnitType using the standard "units" NetCDF attribute
>
> 9) Change default block size to 256x256 instead of scanline (only affect
> file without NetCDF chunking)
>     ==> because I think this is better for a random access to the data,
> but I'm not sure if the community want this change which could impact
> performances
>
> 10) I've also implemented for my needs support for 1D variables by
> simulating 2D datasets with only one row (dimensionless variables are not
> supported for the moment),
>        but this breaks backward compatibility because files containing
> only one variable and associated 1D coordinate variables are now seen as
> multiple sub datasets...
>        and maybe this is not the goal of GDAL to give access to
> not-2D-raster variables (but sometimes it's useful ;-) )
>
> Thanks for GDAL!
>
> Julien
>
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