[R-sig-Geo] raster brick error cells are not equally spaced
Robert J. Hijmans
r.hijmans at gmail.com
Sun Aug 31 00:47:43 CEST 2014
Dave,
The "code now works on both machines". Perhaps it works, but the
results are probably incorrect.
There always a check for non-regularly spaced values, but some cases
slipped through. This has now been fixed.
Robert
On Tue, Aug 19, 2014 at 12:42 PM, Chagaris, Dave
<Dave.Chagaris at myfwc.com> wrote:
> Thanks Mike. That appears to be the problem. I was able to install all the libraries from my laptop onto the workstation and the code now works on both machines (with older version of raster).
>
> Dave
>
> -----Original Message-----
> From: Michael Sumner [mailto:mdsumner at gmail.com]
> Sent: Thursday, August 14, 2014 10:19 AM
> To: Chagaris, Dave
> Subject: Re: [R-sig-Geo] raster brick error cells are not equally spaced
>
> On Thu, Aug 14, 2014 at 11:58 PM, Chagaris, Dave <Dave.Chagaris at myfwc.com> wrote:
>> [deleted]. Any reason why it would work on one computer and not on the other? Is it possible I don't have all the required packages (or wrong versions) on the workstation?
>>
>
> Only if you had a more recent version of raster on one computer that predated checks for these irregular axes.
>
> (Please use the list in public).
>
> Cheers, Mike.
>
>>
>>
>> -----Original Message-----
>> From: Michael Sumner [mailto:mdsumner at gmail.com]
>> Sent: Wednesday, August 13, 2014 8:59 PM
>> To: Chagaris, Dave
>> Cc: r-sig-geo at r-project.org
>> Subject: Re: [R-sig-Geo] raster brick error cells are not equally
>> spaced
>>
>> Hello, can you point to or share one of the files? Sometimes these things are just a regular grid under the hood but that has been forgotten in favour of longitude/latitude arrays.
>>
>> If that's the case you can reconstruct the original grid and all is well, there's not really any precedent for this but I have a lot of examples that work well. (Also sometimes there's only a small amount of numeric fuzz that you can ignore).
>>
>> The raster types cannot take grids that have irregular (rectilinear or
>> curvilinear) coordinates. There's no way around this except some combination of these:
>>
>> - read the data in the raw using ncdf/ncdf4 or RNetCDF and use base
>> graphics with image() (which can deal with rectilinear grids), or
>> points() or maybe polygons (which with care can deal with curvilinear grids).
>> - use the hidden argument "stopIfNotEqualSpaced=FALSE" to raster() to
>> get the data out and deal with the arrays as "index-only" grids
>>
>>
>> Cheers, Mike.
>>
>>
>>
>> On Thu, Aug 14, 2014 at 2:26 AM, Chagaris, Dave <Dave.Chagaris at myfwc.com> wrote:
>>> I am trying to read netcdf files into R using the brick function. I have many netcdf files and want to process them on a 64bit workstation instead my 32bit laptop. The code I'm using works fine on my 32 bit laptop, but on the workstation I get an error "Error in .rasterObjectFromCDF(x, type = objecttype, band = band, ...) :
>>> cells are not equally spaced; you should extract values as points".
>>>
>>> Any help is appreciated.
>>>
>>> On Laptop...
>>>> library(raster)
>>>
>>>> library(ncdf)
>>>
>>>> windows(record=T)
>>>
>>>> sessionInfo()
>>> R version 2.15.0 (2012-03-30)
>>> Platform: i386-pc-mingw32/i386 (32-bit)
>>>
>>> locale:
>>> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C
>>> [5] LC_TIME=English_United States.1252
>>>
>>> attached base packages:
>>> [1] grDevices datasets splines graphics stats tcltk utils methods base
>>>
>>> other attached packages:
>>> [1] ncdf_1.6.6 raster_2.0-41 sp_1.0-11 svSocket_0.9-53 TinnR_1.0-5 R2HTML_2.2 Hmisc_3.9-3 survival_2.36-12
>>>
>>> loaded via a namespace (and not attached):
>>> [1] cluster_1.14.2 grid_2.15.0 lattice_0.20-6 svMisc_0.9-65 tools_2.15.0
>>>
>>>> i = "expt_31.0_20130226.nc"
>>>
>>>> open.ncdf(paste(getwd(),i,sep='/'))
>>> [1] "file C:/dave.chagaris/HYCOM/expt_31.0_20130226.nc has 4 dimensions:"
>>> [1] "MT Size: 1"
>>> [1] "Depth Size: 40"
>>> [1] "Latitude Size: 213"
>>> [1] "Longitude Size: 290"
>>> [1] "------------------------"
>>> [1] "file C:/dave.chagaris/HYCOM/expt_31.0_20130226.nc has 8 variables:"
>>> [1] "float ssh[Longitude,Latitude,MT] Longname: sea surf. height [31.0H] Missval:1.26765060022823e+30"
>>> [1] "float u[Longitude,Latitude,Depth,MT] Longname: u-veloc. [31.0H] Missval:1.26765060022823e+30"
>>> [1] "float v[Longitude,Latitude,Depth,MT] Longname: v-veloc. [31.0H] Missval:1.26765060022823e+30"
>>> [1] "float w_velocity[Longitude,Latitude,Depth,MT] Longname: w-veloc. [31.0H] Missval:1.26765060022823e+30"
>>> [1] "float temperature[Longitude,Latitude,Depth,MT] Longname: temp [31.0H] Missval:1.26765060022823e+30"
>>> [1] "float salinity[Longitude,Latitude,Depth,MT] Longname: salinity [31.0H] Missval:1.26765060022823e+30"
>>> [1] "float mld[Longitude,Latitude,MT] Longname: MLT (0.20 degC) [31.0H] Missval:1.26765060022823e+30"
>>> [1] "float mlp[Longitude,Latitude,MT] Longname: MLT (0.03 kg/m3) [31.0H] Missval:1.26765060022823e+30"
>>>
>>>> salt =
>>>> brick(paste(getwd(),i,sep='/'),varname='salinity',lvar=4,level=2)
>>> Warning messages:
>>> 1: In rm(.SavedPlots) : object '.SavedPlots' not found
>>> 2: In .rasterObjectFromCDF(x, type = objecttype, band = band, ...) :
>>> level set to: 1
>>>
>>> on workstation...
>>>
>>>> setwd('E:\\work\\data\\HYCOM')
>>>
>>>> .libPaths('C:\\Users\\dave.chagaris\\Documents\\R\\win-library\\3.1'
>>>> )
>>>
>>>> library(raster)
>>>
>>>> library(ncdf)
>>>
>>>> sessionInfo()
>>>
>>> R version 2.15.1 (2012-06-22)
>>>
>>> Platform: x86_64-pc-mingw32/x64 (64-bit)
>>>
>>>
>>>
>>> locale:
>>>
>>> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
>>> States.1252
>>>
>>> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
>>>
>>> [5] LC_TIME=English_United States.1252
>>>
>>>
>>>
>>> attached base packages:
>>>
>>> [1] stats graphics grDevices utils datasets methods base
>>>
>>>
>>>
>>> other attached packages:
>>>
>>> [1] ncdf_1.6.6 raster_2.2-31 sp_1.0-15
>>>
>>>
>>>
>>> loaded via a namespace (and not attached):
>>>
>>> [1] grid_2.15.1 lattice_0.20-6 tools_2.15.1
>>>
>>>> i = "expt_31.0_20130226.nc"
>>>
>>>> open.ncdf(paste(getwd(),i,sep='/'))
>>>
>>> [1] "file E:/work/data/HYCOM/expt_31.0_20130226.nc has 4 dimensions:"
>>>
>>> [1] "MT Size: 1"
>>>
>>> [1] "Depth Size: 40"
>>>
>>> [1] "Latitude Size: 213"
>>>
>>> [1] "Longitude Size: 290"
>>>
>>> [1] "------------------------"
>>>
>>> [1] "file E:/work/data/HYCOM/expt_31.0_20130226.nc has 8 variables:"
>>>
>>> [1] "float ssh[Longitude,Latitude,MT] Longname: sea surf. height [31.0H] Missval:1.26765060022823e+30"
>>>
>>> [1] "float u[Longitude,Latitude,Depth,MT] Longname: u-veloc. [31.0H] Missval:1.26765060022823e+30"
>>>
>>> [1] "float v[Longitude,Latitude,Depth,MT] Longname: v-veloc. [31.0H] Missval:1.26765060022823e+30"
>>>
>>> [1] "float w_velocity[Longitude,Latitude,Depth,MT] Longname: w-veloc. [31.0H] Missval:1.26765060022823e+30"
>>>
>>> [1] "float temperature[Longitude,Latitude,Depth,MT] Longname: temp [31.0H] Missval:1.26765060022823e+30"
>>>
>>> [1] "float salinity[Longitude,Latitude,Depth,MT] Longname: salinity [31.0H] Missval:1.26765060022823e+30"
>>>
>>> [1] "float mld[Longitude,Latitude,MT] Longname: MLT (0.20 degC) [31.0H] Missval:1.26765060022823e+30"
>>>
>>> [1] "float mlp[Longitude,Latitude,MT] Longname: MLT (0.03 kg/m3) [31.0H] Missval:1.26765060022823e+30"
>>>
>>>> salt =
>>>> brick(paste(getwd(),i,sep='/'),varname='salinity',lvar=4,level=2)
>>>
>>> Error in .rasterObjectFromCDF(x, type = objecttype, band = band, ...) :
>>>
>>> cells are not equally spaced; you should extract values as points
>>>
>>> In addition: Warning message:
>>>
>>> In .rasterObjectFromCDF(x, type = objecttype, band = band, ...) :
>>>
>>> level set to: 1
>>>
>>>
>>>
>>> David Chagaris, PhD
>>> Associate Research Scientist
>>> Florida Fish and Wildlife Conservation Commission Fish and Wildlife
>>> Research Institute
>>> 100 8th Ave SE
>>> St. Petersburg, FL 33701
>>> 727-502-4959
>>> fax: 727-893-1374
>>>
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> R-sig-Geo mailing list
>>> R-sig-Geo at 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 at gmail.com
>
>
>
> --
> Michael Sumner
> Software and Database Engineer
> Australian Antarctic Division
> Hobart, Australia
> e-mail: mdsumner at gmail.com
> _______________________________________________
> R-sig-Geo mailing list
> R-sig-Geo at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
More information about the R-sig-Geo
mailing list