[R-sig-Geo] Error in netCDF file: cells are not equally spaced

[Frederico Faleiro]

Dear list,
sorry about the file. The files from the CMIP5 are public, but need a
registration first.
You can access the same file in any of these links:
https://www.sendspace.com/file/famgz3 and
https://drive.google.com/file/d/1L1T03iQ6LU1yYRYeRypxwMB3E7fLjkJI/view?usp=sharing
.

In this meantime I will try the Mike' advices.

Best regards,

Frederico <https://www.sendspace.com/file/famgz3>

On Thu, Aug 22, 2019 at 3:41 PM Frederico Faleiro <fvfaleiro using gmail.com>
wrote:

> Dear list,
>
> sorry about the file. The files from the CMIP5 are public, but need a
> registration first. I am sending the same file attached.
>
> In this meantime I will try the Mike' advices.
>
> Best regards,
>
> Frederico
>
>
>
>
>
> On Thu, Aug 22, 2019 at 5:03 AM Michael Sumner <mdsumner using gmail.com> wrote:
>
>> raster does the wrong thing here in my opinion, the right outcome is to
>> give a grid in index-extent (0, ncol, 0, nrow) and with no projection
>> metadata (crs). There will be coordinate arrays in this file, and they need
>> to be handled as though they are data (with local, x*y dependent values in
>> every cell).
>>
>> With brick() you can proceed to process the data with no problem (using
>> stopIfNotEqualSpaced = FALSE), but you can't rely on the extent being
>> relevant, or any function that works in geographic space to do the right
>> thing. To map a layer of these data you might try
>>
>> grd <- raster(yourfile, stopIfNotEqualSpaced = FALSE)
>> coords <- brick(raster(yourfile, varname = "lon"),
>>                          raster(yourfile, varname = "lat"))   ## but only
>> you will know the names of these variables values "lon", "lat" (might be
>> "TLON", "TLAT" ? )
>>
>> In quadmesh there is a way to plot in geographic space that's not
>> impossibly slow (possibly the coords will need a re-orientation transpose
>> ...):
>>
>> quadmesh::mesh_plot(grd, coords = coords)
>>
>> It's likely that will "map" it properly, but CMIP is likely to wrap
>> around an odd longitude (or something), and so cropping to your area and/or
>> choosing a good project for the crs argument to mesh_plot is probably
>> needed.  You can investigate with plot(coords[[1]]) and plot(coords[[2]])
>> to get a sense of their layout.
>>
>> In the stars package this is all internalized, with
>> stars::read_stars(yourfile) catching all the information required as much
>> as possible, and with plotting methods - but variable choice and actual
>> results vary widely, and depend a lot on very specific details.  (angstroms
>> package has similar helpers for the approach but is unlikely to help here
>> without access to the file to try)
>>
>> To help us guess further you can use the "ncdump" output, raster will
>> print this with
>>
>> print(raster("yourfile"))
>>
>> and from that we could provide better guesses at variable names and
>> subsetting etc.
>>
>> But, as Edzer asked, nothing is as good as having the file - any chance
>> you can share it?  (Personally I think the world rather needs more R
>> attention on climate model output.)
>>
>> Cheers, Mike.
>>
>> On Thu, Aug 22, 2019 at 1:53 PM Frederico Faleiro <fvfaleiro using gmail.com>
>> wrote:
>> >
>> > Dear list,
>> >
>> > I am using some  netCDF files from the CMIP5 climate models in raster
>> > package, but I am having some issues with one model.
>> > The netCDF file from the GFDL-ESM2G model (e.g.
>> >
>> http://aims3.llnl.gov/thredds/fileServer/css03_data/cmip5/output1/NOAA-GFDL/GFDL-ESM2G/rcp45/mon/atmos/Amon/r1i1p1/v20120412/pr/pr_Amon_GFDL-ESM2G_rcp45_r1i1p1_204101-204512.nc
>> > )
>> > have the error message as in bellow example.
>> >
>> > #Example
>> > library(raster)
>> > s1 <- stack("pr_Amon_GFDL-ESM2G_rcp45_r1i1p1_204101-204512.nc")
>> > Error in .rasterObjectFromCDF(x, type = objecttype, band = band, ...) :
>> >   cells are not equally spaced; you should extract values as points
>> >
>> > # I check some solutions that recomend force read the file with the
>> > argument "stopIfNotEqualSpaced = F" as bellow.
>> > sf <- stack("pr_Amon_GFDL-ESM2G_rcp45_r1i1p1_204101-204512.nc",
>> > *stopIfNotEqualSpaced
>> > = F*)
>> > bf <- brick("pr_Amon_GFDL-ESM2G_rcp45_r1i1p1_204101-204512.nc",
>> > *stopIfNotEqualSpaced
>> > = F*)
>> >
>> > I performed some tests and only "works" with brick. However I did not
>> find
>> > any solution to check where is the problem and fix it in the file.
>> >
>> > How can I check if it is really an issue and fix it?
>> >
>> > sessionInfo()
>> > R version 3.5.1 (2018-07-02)
>> > Platform: x86_64-w64-mingw32/x64 (64-bit)
>> > Running under: Windows 10 x64 (build 18362)
>> >
>> > Matrix products: default
>> >
>> > locale:
>> > [1] LC_COLLATE=Portuguese_Brazil.1252  LC_CTYPE=Portuguese_Brazil.1252
>> > [3] LC_MONETARY=Portuguese_Brazil.1252 LC_NUMERIC=C
>> > [5] LC_TIME=Portuguese_Brazil.1252
>> >
>> > attached base packages:
>> > [1] stats     graphics  grDevices utils     datasets  methods   base
>> >
>> > other attached packages:
>> > [1] raster_2.8-19 sp_1.3-1
>> >
>> > loaded via a namespace (and not attached):
>> > [1] compiler_3.5.1   rgdal_1.4-3      Rcpp_1.0.1       codetools_0.2-15
>> > ncdf4_1.16.1
>> > [6] grid_3.5.1       lattice_0.20-35
>> >
>> > Best regards,
>> >
>> > Frederico
>> >
>> >         [[alternative HTML version deleted]]
>> >
>> > _______________________________________________
>> > R-sig-Geo mailing list
>> > R-sig-Geo using r-project.org
>> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>>
>>
>> --
>> Michael Sumner
>> Software and Database Engineer
>> Australian Antarctic Division
>> Hobart, Australia
>> e-mail: mdsumner using gmail.com
>>
>

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