[CF-metadata] CF compliant tripolar grid representation

Sebastien Villaume sebastien.villaume at ecmwf.int
Wed Apr 5 07:01:05 MDT 2017


Hi David,

yes the purpose of having index coordinates variables is purely to identify spatial dimensions in this case.

My actual lat and lon are both 2-D, with dimensions (291,360). It could have been described as one long 1-D vector of dimension 291*360=104760. 

But why it has not been done this way?
first of all because you will confuse many software if you have in your files:  

dimensions :
     d = 104760 ;
variables :
    float lat(d);
       ...

    float lon(d);
       ...

    float sea_surface_temp(d);
       ...

secondly, these two dimensions have a meaning! does 360 for the "x" dimension sounds familiar? yep, the grid is a 1deg longitude grid but this is only true for the part of the tripolar grid that follows the regular lat/lon. The "irregular" part will not follow this but it will still have the same number of i points for a given index of the other dimension. This can be seen on this projection:

http://sosie.sourceforge.net/sosie_files/fig_irregular.png

but keep in mind that if I was projecting the same grid but taking the north pole as origin, the previously "irregular" part would look like "regular" and vice versa (actually not exactly regular because the two extra poles and the traditional north pole are not aligned which creates small distortions).

Anyway, I don't see a major issue having index coordinates defined to support the dimensions? Is it because the units for those are in fact "1"? Is it because those are not really what we usually call an "axis"? 

Maybe something else is more appropriate than "axis", maybe the attribute that we use to label a dimension should be extended : not only "axis" but also "angle", "index", etc. The CF requirement would be that you have no more than 3 spatial dimensions to describe a parameter: nr axes + nr angles + nr indices <= 3 

cartesian, curvilinear, etc.: 3 axes (x, y, z)
spherical : 1 axis (r) + 2 angles (theta, phi)
my case : 2 indices (i, j) + 1 axis (z or why not k)

if you think about it, some of the popular z axes are not really z axes and could be classified as "index k" (pressure levels, isotherms, etc...): these are simply a different way (than traditional axis with distance units) to define an origin (0 Pa, 0Kelvin, etc.), some units (Pa, K, et.) and direction (positive/negative) for a specific dimension... Geopotential height is equivalent to height but with a different choice of origin and the same units (meters).

what is making these "z" axis acceptable but not indices?

Regarding sub-regions, you would not extract the sub-regions based on the indices directly but using the lat and lon built on top.


____________________________________ 

Dr. Sébastien Villaume 
Analyst 
ECMWF Shinfield Park, 
Reading RG2 9AX, UK 
+44 7825 521592 
sebastien.villaume at ecmwf.int 
____________________________________

----- Original Message -----
From: "David Hassell" <david.hassell at ncas.ac.uk>
To: "Sebastien Villaume" <sebastien.villaume at ecmwf.int>
Cc: "CF Metadata" <cf-metadata at cgd.ucar.edu>
Sent: Wednesday, 5 April, 2017 11:52:49
Subject: Re: [CF-metadata] CF compliant tripolar grid representation

Hello,

I may not be grasping everything here, but it seems to me that the purpose
of having two index coordinate variables is purely to be able to identify
the *dimensions* as X and Y - is that right?

If so, storing a coordinate variable with integer positions seems
unsatisfactory - what do the contained integer numbers actually mean? What
happens when you extract a sub-region (as Mark pointed out)? I think the
parallel with the magnitude_of_derivative_of_position_wrt_x_coordinate_index
standard name could be a bit misleading, as this is a derivative, so the
absolute values of any x-indices is not important.

Thanks for you patience!

David

On 5 April 2017 at 09:47, Sebastien Villaume <sebastien.villaume at ecmwf.int>
wrote:

> Hi all,
>
> I could try to draft an new entry in grid_mapping or a new entry in
> Appendix D (it will not be a dimensionless "vertical" coordinate but a
> dimensionless "horizontal" coordinate)
>
> Could we agree first on what I need to define? I don't want to invest too
> much time in defining something before everyone agree on the way forward.
>
> thanks
>
> ____________________________________
>
> Dr. Sébastien Villaume
> Analyst
> ECMWF Shinfield Park,
> Reading RG2 9AX, UK
> +44 7825 521592
> sebastien.villaume at ecmwf.int
> ____________________________________
>
> ----- Original Message -----
> From: "Jim Biard" <jbiard at cicsnc.org>
> To: cf-metadata at cgd.ucar.edu
> Sent: Tuesday, 4 April, 2017 21:47:36
> Subject: Re: [CF-metadata] CF compliant tripolar grid representation
>
> Hi.
>
> I tend to agree with Jonathan about the use of the grid_mapping variable,
> although it would probably be necessary to provide a clear distinction
> between this sort of information about mapping grid indices to lats and
> lons and providing information about mapping projected coordinate axis
> values to lats and lons. This new use is probably more appropriate for the
> name of the variable ( grid _mapping). Having said that, the potential for
> confusion and complication makes me wonder if a new construct isn't needed.
>
> The problem that I see with x/y_coordinate_index is that the indices are
> very likely indices to lat/lon coordinates, not x/y coordinates. They
> function as a sort of unitless, non-geographic x and y, but I think it
> would better to avoid overloading concepts. It's also possible that these
> indices could be indices to x and y coordinates, so it seems to me that
> lat/lon_coordinate_index would be no better. This is what led me to the
> names in my list that didn't use x, y, lat, or lon. They could be useful in
> other scenarios, such as satellite swath imagery, which have axes of scan
> and sample, so I didn't want to constrain the terms too closely to the mesh
> grid scenario that this discussion started with.
>
> Grace and peace,
>
> Jim
>
> On 4/4/17 4:25 PM, Jonathan Gregory wrote:
>
>
>
> Dear Sébastien et al.
>
> From what you say I understand that the translation of indices to
> coordinate
> values is rather ad-hoc, rather than being done by the same formulae for
> all
> sorts of tripolar grid. You could identify the grid construction, if that
> would
> be useful, in a non-standard way in some attribute such as "comment". To
> provide a standardised description, I still think grid_mapping would be the
> right place, but evidently "tripolar" would not be a sufficient definition.
> Instead you would need different entries in Appendix D for the different
> sorts
> of tripolar grid in use. In these entries you could certainly give URLs to
> documentation, I think, as well as a description. The aim of putting it in
> Appendix D would be to provide a source of information about how the
> indices
> are related to coordinate values.
>
> I suggested [xy]_coordinate_index because these phrases are already used in
> standard names (one of each). If we don't like them now, we ought to
> change the
> existing names, since we should be consistent. I think the phrase
> "coordinate
> index" means "the index to a coordinate value". Just "index" would be less
> informative, I feel.
>
> Best wishes
>
> Jonathan
>
>
> ----- Forwarded message from Sebastien Villaume <
> sebastien.villaume at ecmwf.int> -----
>
>
>
> Date: Mon, 3 Apr 2017 13:56:40 +0000
> From: Sebastien Villaume <sebastien.villaume at ecmwf.int> To:
> cf-metadata at cgd.ucar.edu Subject: Re: [CF-metadata] CF compliant tripolar
> grid representation
> X-Mailer: Zimbra 8.6.0_GA_1200 (ZimbraWebClient - FF50
> (Linux)/8.6.0_GA_1200)
>
>
> Hi Mark,
>
> I agree that we need to find the best way to describe these grids (with
> the appropriate controlled metadata) and not necessarily use an existing
> concept (crs, grid_mapping) if it does not fit the purpose and generates
> confusion.
>
> These tripolar grids are tricky and I guess this is why there is no
> standard systematic way to describe them.
>
> Reading more on it, I realized that some of them are not always "regular
> grids" (by regular I mean monotonic increase of lat and lon when increasing
> i and j indices): it seems that some NEMO configurations reuse some of the
> i and j indices that are over land (large parts of Asia and Africa) and
> relocate them over specific water regions to locally increase the grid
> resolution!
>
> This can be seen here: http://www.nemo-ocean.eu/
> content/download/7538/40914/file/meshmask_grid.pdf Some of these grids do
> not have a simple analytical description since it is a composite of several
> local descriptions. How can I then properly reference/identify them? using
> an attribute like "model_grid_mapping" or "model_mesh_mapping" or simply
> "mesh_mapping" instead of "grid_mapping" and points to an URN/URI?
>
> AMy main issue is that I can not derive directly from the metadata the
> type of grid used. I have to plot it to know what it is and this is not
> satisfactory.
>
> Regardless of the preferred solution (if one exists), I would still like
> to have a proper standard name for my 1-D mesh indices i and j.
>
> thanks
> ____________________________________
>
> Dr. Sébastien Villaume
> Analyst
> ECMWF Shinfield Park,
> Reading RG2 9AX, UK
> +44 7825 521592 sebastien.villaume at ecmwf.int
> ____________________________________
>
> ----- Original Message -----
> From: "Hedley, Mark" <mark.hedley at metoffice.gov.uk> To: "Jim Biard" <
> jbiard at cicsnc.org> , cf-metadata at cgd.ucar.edu Sent: Monday, 3 April, 2017
> 10:28:05
> Subject: Re: [CF-metadata] CF compliant tripolar grid representation
>
> Hello All,
>
> I'd like to pick up on an earlier comment from Jim:
> If I'm not mistaken, we would need to propose a new grid_mapping to be
> added to the Conventions that would define a Tripolar Coordinate Reference
> System, along with any attributes that don't currently exist that are
> needed to complete the definition. I did a search for a standard tripolar
> CRS in proj4 or epsg, and was unable to find one. Is it possible to make
> such a definition?
> I don't think this is the correct approach
>
> In my opinion, the tri-polar grid is described with respect to a
> Geographic Coordinate Reference System: typically the one used to co-locate
> the observations for assimilation, by spatial coordinates.
> The 'Grid' is not a projection and it is not a coordinate reference
> system: it is the description of a model grid.
> In data files I have seen, each spatial location is defined by a location
> in latitude, longitude and depth, with respect to a suitable geodetic datum.
>
>
> I agree with your more recent comment Jim:
>
> I'm wondering if x and y have too strong an association to projected
> coordinate
> systems. I also like u/v, but that may be too strongly associated for some
> people
> with vector components (wind, for example).
>
> I think that describing grid indices should be carefully distinguished
> from spatial coordinates. Put a different way, I don't think a grid index
> can be georeferenceable.
>
> I think that a good deal of care not to confuse the grid indices with any
> interpretation of 'grid_mapping' relations is required here.
> I don't think that a CF grid mapping should be used to connect any
> description of model index space with geographic space in these cases.
>
> Sebastien states:
>
> I would like to propose for addition standard names to support the mesh
> indices/coordinates:
>
> "mesh_grid_i/j_index" suggested by Jim
> or
> "x/y_coordinate_index" suggested by Jonathan
>
> The mixing of the terms coordinate and index gives me pause for thought.
> What information is being encoded here?
>
> A key question I have is about the expectation for values of these
> indices, under operations such as sub-setting. I have seen many files which
> do not have coordinate variables for the x-like and y-like dimensions, the
> only horizontal spatial metadata is contained in auxiliary coordinates.
> Clearly I can perform index operations on these arrays, but I don't
> consider the index values important and I don't preserve them.
>
> Sebastien:
> Is it the case that you would like to ensure that model index space values
> are preserved, for example when removing a regional subset from a tri-polar
> ocean model?
> Would you like to be able to encode a result where it is clear that a
> regional subset of 50 <= x < 150, 70 <= x < 120 has been taken from a
> larger extent model?
>
> If standard names are provided to encode such information, I would
> advocate clear descriptive text stating that there is no mathematical
> relationship between such index coordinates (i still don't like mixing
> these terms) and projection coordinates or geographic coordinates
>
> Sebastien states:
> I have checked both IPSL and CNRM CMIP5 datasets. It is indeed NEMO
> datasets and it is probably a
> ORCA tripolar grid in both cases. I write "probably" because it is not
> clear and conclusive
> without plotting the datasets: lat and lon are 2D fields, the datasets
> define 2 extra 1D coordinates "i" and "j"
> to be used as mesh indices (but without a proper standard name).
> The datasets also have bounds for lat and lon, defined as "lat_vertices"
> and "lon_vertices" which I think
> is one solution to describe the tripolar grid. I would prefer something
> more standardized and documented so
> that one can quickly identify from the metadata that it is a tripolar grid
> (defining the resolution,
> where are the poles, how it is derived, etc.)
>
> I appreciate the desire to have a standardised approach to defining such a
> model grid. I would not advocate trying to use grid mapping variables
> and relationships for this, I think this could do more harm than good.
> I don't have a better suggestion to hand, I'm sad to say.
>
> I am not raising principled objections to this conversation or the
> direction of travel; I am raising waryness and caution about introducing
> further confusion or implying stronger relationships than can be provided.
>
> all the best
> mark
>
>
> From: CF-metadata [ cf-metadata-bounces at cgd.ucar.edu ] on behalf of Jim
> Biard [ jbiard at cicsnc.org ]
> Sent: 31 March 2017 23:26
> To: cf-metadata at cgd.ucar.edu Subject: Re: [CF-metadata] CF compliant
> tripolar grid representation
>
>
>
> Hi.
>
> I like the more generic x/y_coordinate_index name, but I'm wondering if x
> and y have too strong an association to projected coordinate systems. I
> also like u/v, but that may be too strongly associated for some people with
> vector components (wind, for example). What do the rest of you think? Here
> are some names that come to mind. Feel free to suggest something better!
>
>
>     * mesh_grid_i_index, mesh_grid_j_index
>     * grid_i_index, grid_j_index
>     * grid_i_coordinate, grid_j_coordinate
>     * x_coordinate_index, y_coordinate_index
>     * index_x_coordinate, index_y_coordinate (this ordering matches the
> projection_x/y_coordinate naming)
>     * u_coordinate, v_coordinate
>     * i_coordinate, j_coordinate
>     * grid_row_coordinate, grid_column_coordinate
>     * row_coordinate, column_coordinate
>
>
> The more I look at these, the more I like the last two.
>
>
> As for a definitions, how about something like this variation on the ones
> for the projection_x/y_coordinate?
>
>
>
>
> column_coordinate: "column" indicates the fastest-changing dimension of a
> two-dimensional grid, when this is not associated with a spatial coordinate
> dimension such as longitude or projected X, positive with increasing
> column. The column coordinate, possibly in conjunction with the row
> coordinate, serves as a parametric driver mapping abstract grid positions
> to spatial coordinates such as latitude and longitude.
>
>
> row_coordinate: "row" indicates the the slowest-changing dimension of a
> 2-dimensional grid, when this is not associated with a spatial coordinate
> dimension such as latitude or projected Y, positive with increasing row.
> The row and column coordinates serve as a parametric driver mapping
> abstract grid positions to spatial coordinates such as latitude and
> longitude. Grace and peace,
>
> Jim
>
> On 3/31/17 5:37 PM, Sebastien Villaume wrote:
>
>
>
> Hi all,
>
> I have checked both IPSL and CNRM CMIP5 datasets. It is indeed NEMO
> datasets and it is probably a ORCA tripolar grid in both cases. I write
> "probably" because it is not clear and conclusive without plotting the
> datasets: lat and lon are 2D fields, the datasets define 2 extra 1D
> coordinates "i" and "j" to be used as mesh indices (but without a proper
> standard name). The datasets also have bounds for lat and lon, defined as
> "lat_vertices" and "lon_vertices" which I think is one solution to describe
> the tripolar grid. I would prefer something more standardized and
> documented so that one can quickly identify from the metadata that it is a
> tripolar grid (defining the resolution, where are the poles, how it is
> derived, etc.)
>
> I would like to propose for addition standard names to support the mesh
> indices/coordinates:
>
> "mesh_grid_i/j_index" suggested by Jim
> or
> "x/y_coordinate_index" suggested by Jonathan
>
> I let the experts in standard names decide which pair suits best the
> present case.
>
> Regarding tripolar grids characteristics, I did some research and came to
> the conclusion that "Murray tripolar grids" are not identical to "ORCA/NEMO
> tripolar grids". This is true even without considering characteristics like
> the grid resolution, the location of the poles or where the latitude
> boundary is placed between the modified and unmodified parts.
>
> The Murray tripolar grid (used by GFDL) has its "north" poles on the
> boundary as shown here: https://www.gfdl.noaa.gov/wp-
> content/uploads/pix/user_images/mw/bipolar.gif The ORCA/NEMO tripolar
> grids have the "north" poles within the modified regions but not on the
> boundary as shown in my original post: http://www.geomar.de/
> typo3temp/pics/globe_grid2_14_b8edb639ae.png This complicates things...
>
>
> ____________________________________
>
> Dr. Sébastien Villaume
> Analyst
> ECMWF Shinfield Park,
> Reading RG2 9AX, UK
> +44 7825 521592 sebastien.villaume at ecmwf.int
> ____________________________________
>
> ----- Original Message -----
> From: "James Orr" <James.Orr at lsce.ipsl.fr> To: "Karl Taylor" <
> taylor13 at llnl.gov> Cc: cf-metadata at cgd.ucar.edu Sent: Thursday, 30 March,
> 2017 23:01:54
> Subject: Re: [CF-metadata] CF compliant tripolar grid representation
>
> The IPSL and CNRM cimate models that participated in CMIP5 both used the
> NEMO
> model (ORCA2 and ORCA1 configurations) with tripolar grids.  Both provided
> output the was CF compliant.
>
> James
>
> On Thu, 30 Mar 2017, Karl Taylor wrote:
>
>
>
> Hi Sebastien,
>
> More than one group stored output on a tripolar grid in CMIP5.  I'm pretty
> sure they did it in a CF-conforming way.  I know at least some of the GFDL
> model output was reported on a tripolar grid, as described at
> http://nomads.gfdl.noaa.gov/CM2.X/oceangrid.html (or search on "tripolar
> grid" for additional links).  You could look to their example, and see if
> you
> think it is done correctly.
>
> I don't think extensions or modifications to CF are needed for tripolar
> grids.
>
> best regards,
> Karl
>
> On 3/30/17 9:42 AM, Jim Biard wrote:
>
>
>
> Sébastien,
>
> If I'm not mistaken, we would need to propose a new grid_mapping to be
> added to the Conventions that would define a Tripolar Coordinate Reference
> System, along with any attributes that don't currently exist that are
> needed to complete the definition. I did a search for a standard tripolar
> CRS in proj4 or epsg, and was unable to find one. Is it possible to make
> such a definition?
>
> Regarding the standard names for your X and Y coordinate variables, I think
> you could use "projection_x/y_coordinate" once a grid_mapping has been
> defined. Of course you could always leave the attribute off, since a
> standard_name attribute is not a requirement.
>
> If making a new grid_mapping is not feasible, you could request standard
> names along the lines of mesh_grid_i_index and mesh_grid_j_index. These
> standard names would (on reading their definitions) make it clear that the
> measurements are on a mesh grid for which there is no CRS. At least that's
> what comes to mind at the moment.
>
> Grace and peace,
>
> Jim
>
> On 3/30/17 11:52 AM, Sebastien Villaume wrote:
>
>
>
> Hello all,
>
> I am looking for the best approach to describe in a CF compliant way the
> tripolar grids usually used in NEMO configurations.
>
> Basically, the difference with a usual bipolar grid (north pole-south
> pole) is that the north pole is split into 2 poles moved over Canada and
> Russia (to have distortions/singularities not over the ocean). A good
> visual representation can be found here: http://www.geomar.de/
> typo3temp/pics/globe_grid2_14_b8edb639ae.png everything south of the
> green line (40degN) is identical to a regular
> grid, but everything north of it is computed using a technique described
> here:
>
> Madec, G. and M. Imbard, 1996 : A global ocean mesh to overcome the north
> pole singularity. Clim. Dyn., 12, 381–388.
>
>
> The usual NEMO output of the grid looks like this:
>
>      float longitude(y, x) ;
>          longitude:standard_name = "longitude" ;
>          longitude:units = "degrees_east" ;
>          longitude:long_name = "longitude" ;
>      float latitude(y, x) ;
>          latitude:standard_name = "latitude" ;
>          latitude:units = "degrees_north" ;
>          latitude:long_name = "latitude" ;
>
>
> Basically both latitudes and longitudes need to be specified for each grid
> point, hence lat and lon are 2D arrays. This is not a problem itself but I
> would like to give more information through maybe grid_mapping or crs so
> it is clear that the grid is tripolar. This is useful information if one
> want to project/interpolate this back to a more regular representation.
>
> Looking at the CF conventions, I can see that grids can be fairly nicely
> documented but nothing for tripolar grids.
>
> Is there some documentation/guidelines on how to derive a proper
> grid_mapping/crs with valid attributes for tripolar grids?
>
> I would also like to add to my netcdf file a way to better describe axes:
>
>      double y(y) ;
>          y:units = "1" ;
>          y:long_name = "j-index of mesh grid" ;
>          y:standard_name = ??? ;
>      double x(x) ;
>          x:units = "1" ;
>          x:long_name = "i-index of mesh grid" ;
>          x:standard_name = ??? ;
>
> what would be the standard name of these?
>
> Thanks,
>
> ____________________________________
>
> Dr. Sébastien Villaume
> Analyst
> ECMWF Shinfield Park,
> Reading RG2 9AX, UK
> +44 7825 521592 sebastien.villaume at ecmwf.int
> ____________________________________
> _______________________________________________
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