HI Daniele,
Thank you for your quick response.
Two remarks though
- I do seem to get from your explanation that it can also be decreasing
rather than increasing, which means it should at least be possible to
work the other way around, which was the case here. There are only two
files, the latest in time is first. So at least the maximum/minimum of
the two extremes should be picked.
- I understand this is a convention for variables in general. But does
this however count also for the order in which aggregated files are
listed in an aggregation with an already pre-existing dimension (which
is the case here)? Perhaps the issue is somewhere else in the code, and
the values should be sorted after reading the list of files.
Kind Regards
Niels
On 23-09-16 15:50, Daniele Romagnoli wrote:
Hi Niels,
On Fri, Sep 23, 2016 at 2:40 PM, Niels Charlier <ni...@scitus.be
<mailto:ni...@scitus.be>> wrote:
Simone, Daniele,
Do you have an opinion on point (3) of this email?
It seems that one of you have written the code that expects a
chronological order of listed aggregation files.
The logic is in
https://github.com/geotools/geotools/blob/master/modules/plugin/coverage-multidim/netcdf/src/main/java/org/geotools/imageio/netcdf/cv/TimeCoordinateVariable.java
<https://github.com/geotools/geotools/blob/master/modules/plugin/coverage-multidim/netcdf/src/main/java/org/geotools/imageio/netcdf/cv/TimeCoordinateVariable.java>
The getMinimum() and getMaximum() methods.
The problem could easily be resolved by searching for the minimum
and maximum rather than expecting a certain order.
I can't find anything in the specs that says they should be in
order, so would you agree if I changed it to that regards?
I think that we developed this based on a best practice for the
NetCDF, assuming that coordinate axis/coordinate variables are monotonic.
https://www.unidata.ucar.edu/software/netcdf/docs/BestPractices.html
Quoting the CoordinateSystems section:
/A ***coordinate variable*** is a one-dimensional variable with the
same name as a dimension, which names the coordinate values of the
dimension. It must not have any missing data (for example, no
|_FillValue| or |missing_value| attributes) *and must be strictly
monotonic (values increasing or decreasing).*
/
/
/
However I'm not against that improvement provided that the time to
index mapping still work and the search isn't too much expensive
(maybe we should cache the min and the max?).
Cheers,
Daniele
Niels
On 08-09-16 14:51, Niels Charlier wrote:
Ben, Sean,
I am also including the geotools list in the discussion, because
it regards both libraries.
I got the aggregation file to work. Apart from some obvious bug
fixes and additions to support the "runtime" dimension in
geotools, I had to make a few changes to the xml file.
What is still unclear to me is whether these changes
- are actually required to work (i.e. the aggregation file is
faulty). in that case we need to work on better error reporting
in geotools (possibly also in netcdf-java)
- should not actually be required, in which case we need to fix
these as bugs in either geotools or netcdf-java
I have included the .ncml file in the attachment to demonstrate.
There are three such changes I made:
1. the Conventions global attribute,as discussed before.
2. removal of the "time" variable in the aggregation (see
commented line in attached .ncml file)
This issue is related to the previous one, it is again about
/makeCoordinateSystemsImplicit/ versus
/makeCoordinateSystemsMaximal/.
* If the "time" variable is included as aggregation variable,
it also gets the "runtime" dimension added to its dimensions.
* As a consequence, netcdf-java does not recognise it as an AXIS.
* As a consequence, /makeCoordinateSystemsImplicit /fails to
include it in the CRS's for the actual variables (water_u,
salinity, etc...).
* As a consequence, /makeCoordinateSystemsMaximal /creates a
CRS for these variables. However, it puts the dimensions in the
order of the /dimension variable/ list
(rather than the variable's own dimensions), which is
completely arbitrary as far as I can see.
* "runtime" ends up as the last axis instead of the first.
This is inconsistent with the order of dimensions in the
variable. Geotools fails on this inconsistency.
I am not sure whether the fault here lies with the .ncml
file, geotools or netcdf-java.
3. changing the order of the list of files in the inner
aggregation tags.
<netcdf location="hycom_glb_regp01_old_t003.nc
<http://hycom_glb_regp01_old_t003.nc>"/> <netcdf location="hycom_glb_regp01_old_t000.nc
<http://hycom_glb_regp01_old_t000.nc>"/>
instead of <netcdf location="hycom_glb_regp01_old_t000.nc
<http://hycom_glb_regp01_old_t000.nc>"/> <netcdf location="hycom_glb_regp01_old_t003.nc
<http://hycom_glb_regp01_old_t003.nc>"/>
Otherwise the one with the earliest time coordinates is last
in the list instead of first... and geotools fails on this. Is
this normal? This issue is definitely unrelated to
netcdf-java, but I am not sure whether this is a bug in geotools
or in the .ncml file. Regards Niels On 07-09-16 13:23, Niels
Charlier wrote:
Ben, Sean, Changing the Convention has resolved this issue.
Thanks both for your tips. I am now dealing with other issues in
the same file... will keep you updated. Kind Regards Niels On
02-09-16 03:00, Ben Caradoc-Davies wrote:
Niels, one thing you could try is to change the Conventions
global attribute of these files to "CF-1.6" to see if this
changes the way they are handled (if these files are close
enough to CF). Sean, do you expect aggregations to behave the
same as single files with the same Conventions? It looks like
Niels has identified a difference. Kind regards, Ben. On
30/08/16 03:29, Sean Arms wrote:
Greetings Niels, The class DefaultConvention is netCDF-Java's
way of trying to handle cases in which a convention is not
specified. It tries to be pretty forgiving in terms of files
where people have tried to be compliant with some convention,
but didn't set a convention attribute, or knew enough about
some conventions in general to sort of get things in the ball
park...for example, setting positive=up on a vertical
coordinate, but not getting the rest of the stuff correct (not
true for your case, but our code tries to handle the more
common case we come across). If a file is actually following
CF, netCDF-Java will use the class CF1Convention. Currently we
handle (or try to) around 30 specific conventions (not sure
all are actually documented conventions), but when all else
fails, we go to the default convention. NcML aggregations in
general can get pretty gnarly, and are very hard to get
correct. Have you looked into using the Forecast Model Run
Collection (FMRC) featureCollection element to serve these
data?
https://www.unidata.ucar.edu/software/thredds/current/tds/tutorial/FmrcFeatureCollectionsTutorial.html
<https://www.unidata.ucar.edu/software/thredds/current/tds/tutorial/FmrcFeatureCollectionsTutorial.html>
Cheers, Sean On Mon, Aug 29, 2016 at 6:11 AM, Niels Charlier
<ni...@scitus.be> <mailto:ni...@scitus.be> wrote:
Hello, I am currently working on the netcdf extensions of
geotools/geoserver, although I should say I am fairly new at
netcdf, so I am still learning. I am currently trying to get
some particular datasets to work with geoserver, and I think
I might have hit against some limitations, perhaps even a
bug, in netcdf-java, so I wanted to ask you for advice. We
have a .ncml have that aggregate datasets based on 'runtime'.
This is an explanation from the client: *"'runtime' is not a
first class coordinate in the data produced by our production
groups, so the initial approach to solve this using unidata
mechanisms is to use NCML to aggregate * *two datasets with
different runtimes together using a 'joinNew' aggregation,
which adds a new coordinate axis 'runtime' to the dataset *
*(this takes place in several of the .ncml files included in
the test data). The runtime axis would then be exposed as a
custom dimension in geoserver so that it can be used for
subsets. This means that a reader would have to be prepared
to handle dimension values that are possibly two
dimensional(a set of values for each available 'runtime'),
which I don't think the current reader can handle? "* My
first question is what it would entail for building support
for this in netcdf-java? In the meantime I have been
extensively debugging what happens when I try to load the
aggregation file, and I can give some detailed information
about what goes wrong in the code. I think I might have found
something else that is going wrong. * as part of the
aggregation, the runtime dimension is being added to every
other variable of each of the .nc files. * During
*CoordSysBuilder.buildCoordinateSystems* some things happen
as a consequence of that that is different from when I read
the .nc files individually: -> In
*makeCoordinateSystemsImplicit*, as a consequence of all
variables having an additional dimension, the CRS with
lacking runtime dimension is not considered sufficient and is
not being set. -> However, in
*makeCoordinateSystemsMaximal* the CRS's are being set,
except for one variable called "surf_el", because it is being
considered an AXIS (see line 873, call to* !vp.isData()*). *
During index building (*NetCDFImageReader.init -> initIndex
-> getCoordinateSystem*), a runtime exception is thrown
because surf_el doesn't have a CRS. The thing is, surf_el is
not an axis. The reason it is considered an axis is because
it has a "positive" attribute. This happens in
*DefaultConvention.findCoordinateAxes -> getAxisType ->
getAxisTypeCoards* (see line 297, *positive != null*). To
quote my colleague Ben who I asked advice about this:
*"surf_el is a time-varying data variable and not any kind
of coordinate. Surface elevation looks to me like an output
of the HYCOM ocean model **<https://hycom.org/>
<https://hycom.org/> <https://hycom.org/>
<https://hycom.org/>**. Any logic that says that a variable
is a coordinate if it has attribute "positive"="up" is
broken. There is this statement in the CF conventions: * *"A
vertical coordinate will be identifiable by: * * units of
pressure; or * * the presence of the positive attribute
with a value of up or down (case insensitive)." *
*http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html
<http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html>
<http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html>
<http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html>*
*There are such things as time-varying multidimensional
coordinate variables (think of the lat and lon grids for a
satellite swathe), but this is not one of these. * *I think
that, to be a coordinate variable, a variable must be
mentioned in the "coordinates" attribute of another variable
in the same file, or have a name that matches its dimension
(i.e. a basic single-dimensional coordinate variable). " * So
have I indeed identified a bug here? please advice. Thank you
for your help. Kind Regards, Niels
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