Tom,
Before we go into this in detail can you double check that your second data
image
is OK.
Just try something like image( z)
where z is the matrix of values for the second image. ( the $z component of
an image list)
My quick guess is that the second image is all NAs due to a few missing in the
first image.
Doug
-----------------------------------------------------------------------------
Doug Nychka,
Institute for Mathematics Applied to Geosciences
National Center for Atmospheric Research
Boulder, CO
Email: nychka "AT" ucar "DOT" edu Web: www.image.ucar.edu/~nychka
Voice: 303-497-1711 FAX: 303-497-1298 Business Cell: 303-725-3199
On Feb 3, 2012, at 9:16 AM, Tom Roche wrote:
>
> summary: image.plot-ing two sets of netCDF data, with the second
> derived from the first. First plots to PDF as expected (title, data,
> legend). Second plots the data and title, but abends before drawing
> the legend, with
>
>> Error in if (del == 0 && to == 0) return(to) :
>> missing value where TRUE/FALSE needed
>> Calls: plot.layers.for.timestep -> image.plot -> seq -> seq.default
>
> Debugging shows image.plot.info(...) is returning
>
>> Browse[2]> info
>> $xlim
>> [1] NA
>
>> $ylim
>> [1] NA
>
>> $zlim
>> [1] NA
>
>> $poly.grid
>> [1] FALSE
>
> details:
>
> (Hopefully the following is not too long-winded; I'm just trying to be
> complete.) I'm running on a cluster (where I don't have root) with
>
> me@it4:~ $ lsb_release -a
> LSB Version:
> :core-3.1-amd64:core-3.1-ia32:core-3.1-noarch:graphics-3.1-amd64:graphics-3.1-ia32:graphics-3.1-noarch
> Distributor ID: RedHatEnterpriseServer
> Description: Red Hat Enterprise Linux Server release 5.4 (Tikanga)
> Release: 5.4
> Codename: Tikanga
> me@it4:~ $ uname -a
> Linux it4 2.6.18-164.el5 #1 SMP Tue Aug 18 15:51:48 EDT 2009 x86_64 x86_64
> x86_64 GNU/Linux
> me@it4:~ $ R
> R version 2.14.0 (2011-10-31)
> ...
>> library(help = fields)
> ...
> Package: fields
> Version: 6.6.2
> Date: November 16, 2011
> ...
> Maintainer: Doug Nychka <nyc...@ucar.edu>
>
> I have an IOAPI (netCDF classic plus spatial metadata) dataset with
> structure {cols, rows, layers, timestep=1}, where {cols,rows}
> represent a land-cover grid. The layers are sparse, in that all have
> some NAs; some have all NAs--call those "trivial"). The non-trivial
> layers have a problem: data was logged so that values sum. (I.e.,
> instead of logging value=a in gridcell [i,j] and value=b in the "next"
> non-NA gridcell[i+m,j+n], value(gridcell[i+m,j+n]) = a+b.) I wrote an
> R routine that "demonotonicizes" (since all data >= 0) the source
> data, writing to a new "fixed" or "target" file with the same
> structure as the source. As part of the routine I check that each
> target layer contains values s.t.
>
> * â target values v: (v > 0) || is.na(v)
> * âi,j: is.na(value(source[i,j])) â is.na(value(target[i,j]))
>
> I also want, for each layer, to plot both the source and the target.
> My plot code is like
>
> plot.layers.for.timestep <- function(source.file, source.datavar,
> target.datavar, datavar.name, datavar.n.layers, colors, map) {
> # Get the grid origin, cell sizes, cell centers, etc
> # ...
>
> pdf("compare.source.target.pdf", height=3.5, width=5, pointsize=1)
> for (i.layer in 1:datavar.n.layers) {
> # plot the source data
> # debugging
> print(paste('Non-null image.plot for source layer=', i.layer))
> # for non-trivial layers
> if (sum(!is.na(source.datavar[,,i.layer]))) {
> image.plot(x.cell.centers.km, y.cell.centers.km,
> source.datavar[,,i.layer],
> xlab="", ylab="", axes=F, col=colors(100),
> main=paste("Source: ", datavar.name, ",
> Layer: ", i.layer, sep="")
> )
> lines(map)
> } else { # trivial layers
> ...
> }
> # plot the fixed data
> # debugging
> print(paste('Non-null image.plot for target layer=', i.layer))
> debug(image.plot)
> # for non-trivial layers
> if (sum(!is.na(target.datavar[,,i.layer]))) {
> image.plot(x.cell.centers.km, y.cell.centers.km, xlab="", ylab="",
> target.datavar[,,i.layer], axes=F, col=colors(100),
> main=paste("Target: ", datavar.name,", Layer: ", i.layer,
> sep=""))
> lines(map)
> } else { # trivial layers
> ...
> }
> }
> dev.off()
> } # end function plot.layers.for.timestep.fun
>
> The first layer is non-trivial, and the source layer plots to
> ./compare.source.target.pdf as expected: data, title, legend.
> Then the target title and data plot, but abends before drawing
> the legend, with
>
>> Error in if (del == 0 && to == 0) return(to) :
>> missing value where TRUE/FALSE needed
>> Calls: plot.layers.for.timestep -> image.plot -> seq -> seq.default
>
> Being a relatively new R user, I read Peng's "Introduction to the
> Interactive Debugging Tools in R" (though 10 years old, everything
> worked as advertised) and instrumented as above. During the debug
> session, I did
>
>> debug(image.plot.info)
>
> and stepped in. image.plot.info(...) tried/failed several ways to set
> values, before exiting with
>
>> Browse[2]> info
>> $xlim
>> [1] NA
>
>> $ylim
>> [1] NA
>
>> $zlim
>> [1] NA
>
>> $poly.grid
>> [1] FALSE
>
> which then causes the exception above.
>
> How to proceed? If there's a better way to report the bug, please let
> me know (and feel free to forward). I can debug further if
> instructions are provided. I can provide the offending dataset, but
> it's fairly large (638 MB).
>
> TIA, Tom Roche <tom_ro...@pobox.com>
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