raster brick error cells are not equally spaced

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


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--
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