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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