[ncl-talk] plotting model output where x/y are not lat/lon
Dennis Shea
shea at ucar.edu
Sun Sep 13 07:04:17 MDT 2015
A bit more ...
Another issue is that if someone writes one or more variables (eg, x,
y, z) containing lat2d/lon2d attributes to a netCDF (or HDF) file,
*each* variable would have the same set of coordinates associated with
it. This results in a bloated file size. The lat2d/lon2d attributes
for each variable should be deleted prior to netCDF creation and
separate variables created to contain the associated coordinate
information.
delete( x at lat2d )
delete( x at lon2d )
delete(y at lat2d)
delete(y at lon2d)
delete(z at lat2d)
delete(z at lon2d)
or,
delete( [/ x at lat2d, x at loned, y at lat2d, y at loned, z at lat2d, z at loned /] )
and, not required, but recommended
x at coordinates = "LAT2D LON2D" ; variable names are arbitrary
y at coordinates = "LAT2D LON2D"
z at coordinates = "LAT2D LON2D"
...
fcn = addfile9"...","c")
X = f->x
Y = f->y
Z = f->z
LAT2D = lat2d
LON2D = lon2d
On Fri, Sep 11, 2015 at 5:56 PM, Dave Allured - NOAA Affiliate
<dave.allured at noaa.gov> wrote:
> Mary and Dennis,
>
> Mary showed several advantages of the use of the lat2d/lon2d special
> attributes for 2-D coordinates. I would like to retract my suggestion for
> changing existing examples.
>
> It seems to me that it is best to use sfXArray and sfYArray attributes only
> in special cases when lat2d and lon2d are not sufficient. Also, lat2d and
> lon2d seem more understandable to me. Perhaps the decision process for
> which method could be enhanced on the "Overlaying data" documentation page:
>
> http://www.ncl.ucar.edu/Document/Graphics/overlays_on_map.shtml
>
> Dennis mentioned a performance problem: "Each variable having an associated
> @lat2d, @lon2d takes up memory." Technically, I agree. However, modern
> workstations have many Gbytes of RAM, so carrying around a few extra medium
> size 2-D arrays is not noticeable unless you are repeating full variable
> assignments within major processing loops. So I think this is not a
> significant problem for retaining lat2d/lon2d.
>
> --Dave
>
>
> On Fri, Sep 11, 2015 at 11:15 AM, Mary Haley <haley at ucar.edu> wrote:
>>
>> Hi Dave,
>>
>> I'm a bit torn about what to do with the examples, because ideally, we
>> (NCL) would come up with a way to represent all types of "coordinate values"
>> (true 1D coordinate arrays, 2D coordinate arrays, 1D arrays for "random"
>> arrays, and something else for unstructured grids, like hexagonal or
>> triangular meshes) through the NCL variable model. We've always tried to
>> model the NetCDF way of handling these variables, and it doesn't yet have a
>> way to recognize all types of coordinates.
>>
>> We have kept the use of lat2d/lon2d attributes in the examples partly
>> because we have advertised them for so long. Because of our strict backwards
>> compatibility rule, we hope to always support this feature unless it becomes
>> unreasonable to do so (which I don't foresee).
>>
>> We also use this method in our ESMF regridding, because it's the only way
>> to "sneak" in these special coordinate arrays to the "ESMF_regrid" routine.
>> ESMF_regrid will look for "lat2d/lon2d" attached to the variable, and it
>> will also return lat2d/lon2d if regridding to a curvilinear grid. The same
>> is true for "lon1d/lat1d", which is a quick-and-dirty way to pass in 1D
>> arrays of lat/lon for a 1D variable that is potentially "random".
>>
>> There's one minor correction to what Dennis said about using one method
>> over the other for plotting: if you have lat2d/lon2d attributes attached to
>> your data when plotting, and you set res at gsnAddCyclic = True, then the
>> gsn_csm_xxxx plotting routines will know how to properly add the cyclic
>> point. However, if you use sfXArray and sfYArray resources, gsnAddCyclic
>> doesn't know anything about these.
>>
>> We have it on our list to modernize many of our aging NCL scripts, and we
>> will add more examples that show the two ways of doing things.
>>
>> --Mary
>>
>>
>> On Fri, Aug 28, 2015 at 4:15 PM, Dave Allured - NOAA Affiliate
>> <dave.allured at noaa.gov> wrote:
>>>
>>> Dennis,
>>>
>>> Thank you for the information about preferred resources sfXArray and
>>> sfYArray for 2-D coordinates, and the reason why this is optimal. I learned
>>> something new here.
>>>
>>> Several NCL examples and at least one documentation page are advocating
>>> the less optimal method using lat2d and lon2d attributes. Perhaps these
>>> examples and pages could eventually be updated to use sfXArray and sfYArray
>>> instead.
>>>
>>> --Dave
>>>
>>>
>>> On Fri, Aug 28, 2015 at 3:54 PM, Dennis Shea <shea at ucar.edu> wrote:
>>>>
>>>> Will's suggestion is correct.
>>>>
>>>> -----
>>>>
>>>> FYI: The ***only*** time you should assign the reserved attributes:
>>>> @lat2d, @lon2d is for plotting.
>>>>
>>>> In fact, the NCL-team would prefer that people use the following
>>>> rather than the reserved attributes.
>>>>
>>>> res at sfXArraya = lon2d
>>>> res at sfYArray = lat2d
>>>> res at trGridType = "TriangularMesh"
>>>>
>>>> ---
>>>>
>>>> Each variable having an associated @lat2d, @lon2d takes up memory.
>>>> If 5 variables a, a at lat2d, a at lon2d, ... b, c, d, e then each will
>>>> require the necessary memory.
>>>> Firther, if you write to netCDF via
>>>>
>>>> fnc->A = a
>>>> fnc->B = b
>>>> fnc->C = c
>>>> fnc->D = d
>>>> fnc->E = e
>>>>
>>>> Then the lat2d/lon2d arrays will be written 5 times (one for each
>>>> variable).
>>>>
>>>> fnc->LAT2D = lat2d
>>>> fnc->LON2D = lon2d
>>>>
>>>> Will write each variable only once!
>>>>
>>>> Cheers
>>>>
>>>>
>>>> On Fri, Aug 28, 2015 at 3:38 PM, Will Hobbs <Will.Hobbs at utas.edu.au>
>>>> wrote:
>>>> > Mira
>>>> >
>>>> > To keep all the attributes from 'sf'....
>>>> >
>>>> >> sf_total = sf(0,:,:) ;sf_total is now a 2-da array with all the
>>>> >>attributes and rightmost dimensions of sf
>>>> >> sf_total = dim_sum_n(sf,0)
>>>> >
>>>> > Will
>>>> >
>>>> >
>>>> > On 29/08/15 5:26 AM, "mberdahl at envsci.rutgers.edu"
>>>> > <mberdahl at envsci.rutgers.edu> wrote:
>>>> >
>>>> >>Excellent, this worked! Thank you!
>>>> >>I just have a quick follow-up question. Once I assign the lat and lon
>>>> >> to
>>>> >>my variables (for example: sf at lon2d = lon2d, sf at lat2d = lat2d), and
>>>> >> then
>>>> >>I would like to do a calculation with sf (eg. sf_total =
>>>> >> dim_sum_n(sf,0)),
>>>> >>it seems I have to assign the the new variable the lat and lon again.
>>>> >> Is
>>>> >>there a way to keep the lat and lon following through the calculations
>>>> >>without always reassigning them?
>>>> >>I hope that makes sense.
>>>> >>Thanks,
>>>> >>Mira
>>>> >>
>>>> >>
>>>> >>> Here is more information about dat with 2-D coordinates. I was
>>>> >>> typing
>>>> >>> this
>>>> >>> up when I saw Will's reply. Some of the other examples indicate
>>>> >>> that trGridTrype may not be needed with some data sets.
>>>> >>>
>>>> >>> Please see section #2 on this documentation page, for a basic
>>>> >>>description.
>>>> >>> Notice the several different working examples:
>>>> >>> https://www.ncl.ucar.edu/Document/Graphics/overlays_on_map.shtml
>>>> >>>
>>>> >>> (Please ignore the link "2D vertical coordinates", that is not about
>>>> >>> geographic surface maps, and can be confusing.)
>>>> >>>
>>>> >>> The simplest example for making map plots with 2-D coordinates is
>>>> >>>example
>>>> >>> 3
>>>> >>> on this page:
>>>> >>> https://www.ncl.ucar.edu/Applications/ice.shtml
>>>> >>>
>>>> >>> I also like NARR example 4 because it shows how the 2-D coordinate
>>>> >>>method
>>>> >>> can be used with different map projections:
>>>> >>> http://www.ncl.ucar.edu/Applications/narr.shtml
>>>> >>>
>>>> >>> --Dave
>>>> >>>
>>>> >>>
>>>> >>> On Thu, Aug 27, 2015 at 9:35 PM, Will Hobbs <Will.Hobbs at utas.edu.au>
>>>> >>> wrote:
>>>> >>>
>>>> >>>> Mira
>>>> >>>>
>>>> >>>> It looks like you have 2-d lat and lon arrays associated with your
>>>> >>>>data,
>>>> >>>> as is often the case with models (especially ocean models).
>>>> >>>>
>>>> >>>> This can be plotted by NCL without regridding, see the examples
>>>> >>>> here:
>>>> >>>> http://www.ncl.ucar.edu/Applications/ease.shtml
>>>> >>>> Although you are not using the EASE grid, the principal is exactly
>>>> >>>> the
>>>> >>>> same:
>>>> >>>>
>>>> >>>> 1. Set your map plot grid type resource
>>>> >>>> >res at trGridTrype = "TriangularMesh"
>>>> >>>>
>>>> >>>> 2. Set the lat and lon arrays as attributes of the array you are
>>>> >>>> plotting,
>>>> >>>> so if your array is 'x'
>>>> >>>> > x at lat2d = LAT
>>>> >>>> > x at lon2d = LON
>>>> >>>>
>>>> >>>> The just use one of the gsn_csm contour map plotting functions as
>>>> >>>> normal.
>>>> >>>>
>>>> >>>> I hope that's clear.
>>>> >>>>
>>>> >>>> Will
>>>> >>>>
>>>> >>>>
>>>> >>>> On 28/08/15 1:27 PM, "Yuqiang Zhang" <yuqiangzhang.thu at gmail.com>
>>>> >>>>wrote:
>>>> >>>>
>>>> >>>> >Hi Mira,
>>>> >>>> >
>>>> >>>> >Check the link here
>>>> >>>> >http://www.ncl.ucar.edu/FAQ/
>>>> >>>> >For Q 27:
>>>> >>>> >
>>>> >>>> >When I call one of the gsn_csm_xxxx_map plotting scripts, I get an
>>>> >>>> error
>>>> >>>> >message about a units attribute not being correct.
>>>> >>>> >If you are using one of the gsn_csm_xxx_map functions to overlay
>>>> >>>> > data
>>>> >>>> on a
>>>> >>>> >map, and seeing one or both of the following error messages:
>>>> >>>> >
>>>> >>>> > (0) is_valid_lat_ycoord: Warning: The units attribute of
>>>> >>>> > the Y coordinate array is not set to one of the allowable
>>>> >>>> > units values (i.e. 'degrees_north'). Your latitude labels
>>>> >>>> > may not be correct.
>>>> >>>> >
>>>> >>>> > (0) is_valid_lat_xcoord: Warning: The units attribute of
>>>> >>>> > the X coordinate array is not set to one of the allowable
>>>> >>>> > units values (i.e. 'degrees_east'). Your longitude labels
>>>> >>>> > may not be correct.
>>>> >>>> >then this means that your data contains coordinate arrays, but the
>>>> >>>> >coordinate arrays either don't have the necessary "units"
>>>> >>>> > attribute,
>>>> >>>>or
>>>> >>>> >it's
>>>> >>>> >not set to one of the allowable values ("degrees_east" for
>>>> >>>> > longitude
>>>> >>>> >values
>>>> >>>> >and "degrees_north" for latitude values).
>>>> >>>> >If your coordinate arrays are indeed degrees east and degrees
>>>> >>>> > north,
>>>> >>>> then
>>>> >>>> >you can set the units attribute as follows (this code snippet
>>>> >>>> > assumes
>>>> >>>> your
>>>> >>>> >data array is called "data" and that the coordinate arrays are
>>>> >>>> > called
>>>> >>>> >"lat"
>>>> >>>> >and "lon"):
>>>> >>>> >
>>>> >>>> > data&lat at units = "degrees_north"
>>>> >>>> > data&lon at units = "degrees_east"
>>>> >>>> >
>>>> >>>> >Regards,
>>>> >>>> >Yuqiang
>>>> >>>> >
>>>> >>>> >-----Original Message-----
>>>> >>>> >From: ncl-talk-bounces at ucar.edu [mailto:ncl-talk-bounces at ucar.edu]
>>>> >>>> > On
>>>> >>>> >Behalf
>>>> >>>> >Of mberdahl at envsci.rutgers.edu
>>>> >>>> >Sent: Thursday, August 27, 2015 10:21 PM
>>>> >>>> >To: ncl-talk at ucar.edu
>>>> >>>> >Subject: [ncl-talk] plotting model output where x/y are not
>>>> >>>> > lat/lon
>>>> >>>> >
>>>> >>>> >Hi all,
>>>> >>>> >
>>>> >>>> >I'm trying to make a simple plot of cumulative snowfall with data
>>>> >>>> > from
>>>> >>>> a
>>>> >>>> >model I did not run. When I try to make a simple plot, I receive
>>>> >>>> > the
>>>> >>>> >following error:
>>>> >>>> >
>>>> >>>> >(0) check_for_y_lat_coord: Warning: Data either does not
>>>> >>>> > contain a
>>>> >>>> >valid latitude coordinate array or doesn't contain one at all.
>>>> >>>> >(0) A valid latitude coordinate array should have a 'units'
>>>> >>>> attribute
>>>> >>>> >equal to one of the following values:
>>>> >>>> >(0) 'degrees_north' 'degrees-north' 'degree_north'
>>>> >>>> > 'degrees
>>>> >>>> north'
>>>> >>>> >'degrees_N' 'Degrees_north' 'degree_N' 'degreeN' 'degreesN' 'deg
>>>> >>>>north'
>>>> >>>> >(0) check_for_lon_coord: Warning: Data either does not contain
>>>> >>>> > a
>>>> >>>> valid
>>>> >>>> >longitude coordinate array or doesn't contain one at all.
>>>> >>>> >(0) A valid longitude coordinate array should have a 'units'
>>>> >>>> attribute
>>>> >>>> >equal to one of the following values:
>>>> >>>> >(0) 'degrees_east' 'degrees-east' 'degree_east' 'degrees
>>>> >>>> > east'
>>>> >>>> >'degrees_E' 'Degrees_east' 'degree_E' 'degreeE' 'degreesE' 'deg
>>>> >>>> > east'
>>>> >>>> >
>>>> >>>> >
>>>> >>>>
>>>>
>>>> >>>>> >>>>>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>>> >>>> >
>>>> >>>> >When I dump the file it looks like this:
>>>> >>>> >
>>>> >>>> >netcdf ICE.1983.01-12.f77 {
>>>> >>>> >dimensions:
>>>> >>>> > TIME = UNLIMITED ; // (365 currently)
>>>> >>>> > X10_69 = 60 ;
>>>> >>>> > Y18_127 = 110 ;
>>>> >>>> > SECTOR = 2 ;
>>>> >>>> > SECTOR1_1 = 1 ;
>>>> >>>> > ATMLAY14_23 = 10 ;
>>>> >>>> > bnds = 2 ;
>>>> >>>> > ATMLAY23_23 = 1 ;
>>>> >>>> > ATM6H3_3 = 1 ;
>>>> >>>> > OUTLAY = 20 ;
>>>> >>>> > OUTLAY1_1 = 1 ;
>>>> >>>> >
>>>> >>>> >variables:
>>>> >>>> > double TIME(TIME) ;
>>>> >>>> > TIME:units = "HOURS since 1901-01-15 00:00:00" ;
>>>> >>>> > TIME:long_name = "time" ;
>>>> >>>> > TIME:time_origin = "15-JAN-1901 00:00:00" ;
>>>> >>>> > TIME:axis = "T" ;
>>>> >>>> > float DATE(TIME) ;
>>>> >>>> > DATE:units = "YYYYMMDDHH" ;
>>>> >>>> > DATE:long_name = "Date(YYYY MM DD HH)" ;
>>>> >>>> > DATE:history = "From ICE.f77.1983.01.01-15" ;
>>>> >>>> > double X10_69(X10_69) ;
>>>> >>>> > X10_69:units = "km" ;
>>>> >>>> > X10_69:long_name = "x" ;
>>>> >>>> > X10_69:point_spacing = "even" ;
>>>> >>>> > X10_69:axis = "X" ;
>>>> >>>> >
>>>> >>>> > double Y18_127(Y18_127) ;
>>>> >>>> > Y18_127:units = "km" ;
>>>> >>>> > Y18_127:long_name = "y" ;
>>>> >>>> > Y18_127:point_spacing = "even" ;
>>>> >>>> > Y18_127:axis = "Y" ;
>>>> >>>> > float LON(Y18_127, X10_69) ;
>>>> >>>> > LON:units = "degrees" ;
>>>> >>>> > LON:long_name = "Longitude" ;
>>>> >>>> > LON:history = "From ICE.f77.1983.01.01-15" ;
>>>> >>>> > float LAT(Y18_127, X10_69) ;
>>>> >>>> > LAT:units = "degrees" ;
>>>> >>>> > LAT:long_name = "Latitude" ;
>>>> >>>> > LAT:history = "From ICE.f77.1983.01.01-15" ;
>>>> >>>> >
>>>> >>>> >Clearly there are lats and lons associated with the x and y
>>>> >>>> > spacing,
>>>> >>>> but
>>>> >>>> >I'm
>>>> >>>> >not sure how to tell NCL how to use those. Does anyone have
>>>> >>>> > advice on
>>>> >>>> >this?
>>>> >>>> >
>>>> >>>> >Thanks in advance,
>>>> >>>> >Mira
>
>
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