Re: reading raw (packed) data from NetCDF files and avoiding missing-value check

Jon and John-

Why is it so much slower using the GeoGrid directly?  Perhaps
there can be some performance tuning on the GeoGrid side to
avoid people having to jump through the hoops that Jon is?
Is it because the GeoGrid scales and offsets the entire grid
before subsetting instead of subsetting and then scale and
offset (which seems to be what Jon ends up doing).  Jon,
when you say you are scaling and offsetting only the individual
values, is this all the values in the subset or if not, what
percentage of the subset are you doing this on?

We've been doing some profiling of the netcdf-java reading
in the IDV and if this is an area where we could get some
performance enhancements, I'd like to implement something
in the IDV.


Jon Blower wrote:
Hi John (cc list),

Thanks for you help - I found a solution that works well in my app.
As you suggested, I open the dataset without enhancement, then added
the coordinate systems:

           nc = NetcdfDataset.openDataset(location, false, null);
           // Add the coordinate systems
           CoordSysBuilder.addCoordinateSystems(nc, null);
           GridDataset gd = new GridDataset(nc);
           GeoGrid geogrid = gd.findGridByName(varID);

I then create an EnhanceScaleMissingImpl:

           EnhanceScaleMissingImpl enhanced = new

(Unfortunately this class is package-private so I made a copy from the
source code in my local directory.  Could this class be made public

This means that when I read data using geogrid.subset() it does not
check for missing values or unpack the data and is therefore quicker.
I then do enhanced.convertScaleOffsetMissing() only on the individual
values I need to work with.  Seems to work well and is pretty quick.
Is there anything dangerous in the above?

Thanks again,

On 26/10/06, John Caron <caron@xxxxxxxxxxxxxxxx> wrote:
Hi Jon:

Jon Blower wrote:
> Hi John,
> I need some of the functionality of a GridDataset to allow me to read
> coordinate system information.  Also, I might be opening an NcML
> aggregation.  Is it sensible to use NetcdfDataset.getReferencedFile()?
> In the case of an NcML aggregation, is it possible to get a handle to
> a specific NetcdfFile (given relevant information such as the
> timestep)?

You are getting into the internals, so its a bit dangerous.

I think this will work:

NetcdfDataset ncd = openDataset(String location, false, null); // dont enhance ucar.nc2.dataset.CoordSysBuilder.addCoordinateSystems(ncd, null); // add coord info
 GridDataset gds = new GridDataset( ncd); // make into a grid

BTW, you will want to switch to the new GridDataset in ucar.nc2.dt.grid when you start using 2.2.17. It should be compatible, let me know.

> On a related note, is it efficient to read data from a NetcdfFile (or
> NetcdfDataset) point-by-point?  I have been assuming that reading
> contiguous chunks of data is more efficient than reading individual
> points, even if it means reading more data than I actually need, but
> perhaps this is not the case?  Unfortunately I'm not at my usual
> computer so I can't do a quick check myself.  If reading data
> point-by-point is efficient (enough) my problem goes away.

It depends on data locality. If the points are close together on disk, then they will likely to be already in the random access file buffer. The bigger the buffer the more likely, you can try different buffer sizes with:

NetcdfDataset openDataset(String location, boolean enhance, int buffer_size, ucar.nc2.util.CancelTask cancelTask, Object spiObject);

> Thanks, Jon
> On 26/10/06, John Caron <caron@xxxxxxxxxxxxxxxx> wrote:
>> Hi Jon:
>> One obvious thing would be to open it as a NetcdfFile, not a
>> GridDataset. Is that a possibility?
>> Jon Blower wrote:
>> > Hi,
>> >
>> > I'm writing an application that reads data from NetCDF files and
>> > produces images.  I've noticed (through profiling) that a slow point
>> > in the data reading process is the unpacking of packed data (i.e.
>> > applying scale and offset) and checking for missing values.  I would
>> > like to minimize the use of these calls.
>> >
>> > To cut a long post short, I would like to find a low-level function
>> > that allows me to read the packed data, exactly as they appear in the
>> > file.  I can then "manually" apply the unpacking and missing-value
>> > checks only to those data points that I need to display.
>> >
>> > I'm using nj22, version 2.2.16.  I've tried reading data from
>> > GeoGrid.subset() but this (of course) performs the unpacking. I then
>> > tried getting the "unenhanced" variable object through
>> > GeoGrid.getVariable().getOriginalVariable(), but (unexpectedly) this
>> > also seems to perform unpacking and missing-value checks - I expected
>> > it to give raw data.
>> >
>> > Can anyone help me to find a function for reading raw (packed) data
>> > without performing missing-value checks?
>> >
>> > Thanks in advance,
>> > Jon
>> >
>> ===============================================================================
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Don Murray                               UCAR Unidata Program
dmurray@xxxxxxxxxxxxxxxx                        P.O. Box 3000
(303) 497-8628                              Boulder, CO 80307

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