We have found a solution to this problem, which I am posting to the
list for future reference. Thanks very much to John Caron and Don
Murray for helping out with this.
The problem was that the valid_min and valid_max were expressed as
shorts (i.e. packed data) but their numerical range was correct for
unpacked data:
:valid_min = -3; // short
:valid_max = 40; // short
:add_offset = 20.0; // double
:scale_factor = 0.0010; // double
They should have been:
:valid_min = -23000; // short
:valid_max = 20000; // short
i.e. relative to the packed data - this way an app can tell if the
data are out of range without unpacking the data. This would also
have been OK:
:valid_min = -3.0; // double
:valid_max = 40.0; // double
The problem was causing nj22 to read all data as out of range.
Jon
On 19/10/06, Jon Blower <jdb@xxxxxxxxxxxxxxxxxxxx> wrote:
Hi Don,
Thanks for your quick reply. I switched to 2.2.17 and the problem is
still there. The values of temperature from ncdump include (file is
large!):
32767, 32767, 32767, 32767, 32767, 32767, 32767, 32767, 32767, -20974,
-20974, -20979, -20985, 32767, 32767, 32767, 32767, -21054, -21072,
-21083, -21093, -21101, -21108, -21112, -21115, 32767, 32767, 32767,
32767 represents missing data (metadata has :_FillValue = 32767;) and,
for example, -21072 represents (-21072 * 0.001 + 20=) -1.072 degrees
C, which is within the valid range.
According to the file metadata, the convention is COARDS. Also, as I
said in my original post, ncBrowse displays the data without any
problems.
Thanks again,
Jon
On 19/10/06, Don Murray <dmurray@xxxxxxxxxxxxxxxx> wrote:
> Hi Jon-
>
> I suspect the problem is with the valid_max and valid_min
> attributes. The library will return NaN if the
> values are outside the range of the min/max. If the
> type of the attribute is the same as the variable, they
> are compared before scale and offset. If they are different
> they are compared after scaling and offset. I recently
> found a bug with this that was fixed in the 2.2.17 pre-release,
> but I'm not sure if that is why you are seeing what you
> are seeing.
>
> What are the values for temperature in ncdump?
>
> Don
> *************************************************************
> Don Murray UCAR Unidata Program
> dmurray@xxxxxxxxxxxxxxxx P.O. Box 3000
> (303) 497-8628 Boulder, CO 80307
> http://www.unidata.ucar.edu/staff/donm
> *************************************************************
>
>
>
> Jon Blower wrote:
> > Dear all,
> >
> > I'm having some problems reading data from a particular NetCDF file.
> > The code i'm using is:
> >
> > NetcdfDataset nc
> > NetcdfDataset.openDataset("C:\\data\\OA_20060830.nc", true, null);
> > GridDataset gd = new GridDataset(nc);
> > GeoGrid gg = gd.findGridByName("temperature");
> > Array arr = gg.readYXData(0, 0);
> > IndexIterator it = arr.getIndexIteratorFast();
> > while (it.hasNext()) {
> > double val = it.getDoubleNext();
> > System.out.println("" + val);
> > }
> > nc.close();
> >
> > I just get a load of NaNs, even though I know that there are valid
> > data in the file (ncBrowse displays the data perfectly). The only
> > unusual thing about the data is that the data are stored as short
> > integers, with an offset and scale factor:
> >
> > short temperature(time, depth, latitude, longitude);
> > :long_name = "Temperature";
> > :missing_value = 32767; // short
> > :_FillValue = 32767; // short
> > :units = "degree_Celsius";
> > :valid_min = -3; // short
> > :valid_max = 40; // short
> > :add_offset = 20.0; // double
> > :scale_factor = 0.0010; // double
> > :comment = "Temperature estimate (by objective analysis)";
> >
> > I understood that the NetcdfDataset class automatically dealt with
> > offsets and scale factors in "enhanced" mode, which is what I am
> > using (or trying to use). Hence I was expecting to "see" the data as
> > an array of doubles. The same happens if I use getFloatNext() or
> > getShortNext().
> >
> > Can anyone see what I'm doing wrong?
--
--------------------------------------------------------------
Dr Jon Blower Tel: +44 118 378 5213 (direct line)
Technical Director Tel: +44 118 378 8741 (ESSC)
Reading e-Science Centre Fax: +44 118 378 6413
ESSC Email: jdb@xxxxxxxxxxxxxxxxxxxx
University of Reading
3 Earley Gate
Reading RG6 6AL, UK
--------------------------------------------------------------
--
--------------------------------------------------------------
Dr Jon Blower Tel: +44 118 378 5213 (direct line)
Technical Director Tel: +44 118 378 8741 (ESSC)
Reading e-Science Centre Fax: +44 118 378 6413
ESSC Email: jdb@xxxxxxxxxxxxxxxxxxxx
University of Reading
3 Earley Gate
Reading RG6 6AL, UK
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