[Rspatial-devel] new("SpatialGridDataFrame") time issue

[Roger Bivand]

With revision 1200, the same test is:

    user  system elapsed
   7.763   0.346   8.119

but no validity checks are done. As may be sensible, something may be done 
about validity checking, but an order of magnitude speedup is worth 
having, I think.

Roger

On Sun, 22 Jan 2012, Roger Bivand wrote:

> Hi,
>
> Working with Rainer Krug on making readRAST6() in spgrass6 faster, we've 
> identified an issue with time wasting in creating SGDF. For 2.14.1, sp 
> 0.9-93, rgdal 0.7-8:
>
>> Rprof("readGDAL.out")
>> system.time(for (i in 1:50) SP27GTIF <- 
> readGDAL(system.file("pictures/SP27GTIF.TIF", package = "rgdal")[1]))
>   user  system elapsed
> 122.961   4.678 131.383
>> Rprof("")
>> summaryRprof("readGDAL.out")
> $by.self
>                        self.time self.pct total.time total.pct
> "getGridIndex"              32.32    25.31      45.44     35.59
> "asMethod"                  10.60     8.30     119.04     93.23
> "slot<-"                     8.50     6.66       8.64      6.77
> "apply"                      7.52     5.89      15.12     11.84
> "validityMethod"             7.24     5.67     120.30     94.22
> ".local"                     6.40     5.01      22.92     17.95
> "structure"                  5.56     4.35       5.58      4.37
> "expand.grid"                5.14     4.03      12.72      9.96
> "FUN"                        4.86     3.81       4.86      3.81
> "initialize"                 4.34     3.40     123.08     96.40
> "SpatialPixels"              3.06     2.40      96.18     75.33
> "aperm.default"              2.70     2.11       2.70      2.11
> "SpatialPoints"              2.54     1.99      49.16     38.50
> "gc"                         2.52     1.97       2.52      1.97
> ....
> $by.total
>                        total.time total.pct self.time self.pct
> "system.time"               127.68    100.00      0.00     0.00
> "readGDAL"                  127.64     99.97      0.00     0.00
> "new"                       123.10     96.41      0.02     0.02
> "initialize"                123.08     96.40      4.34     3.40
> "SpatialGridDataFrame"      123.04     96.37      0.00     0.00
> "validObject"               120.42     94.31      0.00     0.00
> "validityMethod"            120.30     94.22      7.24     5.67
> "anyStrings"                120.30     94.22      0.00     0.00
> "as"                        119.08     93.26      0.00     0.00
> "asMethod"                  119.04     93.23     10.60     8.30
> "SpatialPixels"              96.18     75.33      3.06     2.40
> "nrow"                       96.18     75.33      0.00     0.00
> "SpatialGrid"                59.22     46.38      0.00     0.00
> "SpatialPoints"              49.16     38.50      2.54     1.99
> "getGridIndex"               45.44     35.59     32.32    25.31
> "standardGeneric"            27.94     21.88      0.00     0.00
> "is"                         26.28     20.58      0.02     0.02
> ".local"                     22.92     17.95      6.40     5.01
> "coordinates"                22.92     17.95      0.00     0.00
> "do.call"                    16.48     12.91      0.00     0.00
> ".bboxCoords"                15.16     11.87      0.02     0.02
> "t"                          15.14     11.86      0.02     0.02
> "apply"                      15.12     11.84      7.52     5.89
> "expand.grid"                12.72      9.96      5.14     4.03
> "slot<-"                      8.64      6.77      8.50     6.66
> "structure"                   5.58      4.37      5.56     4.35
>
>
> The getGridIndex() call is particularly odd, taking 25% of execution time. 
> I've put the Rprof file on rspatial/misc. This looks like an S4 oddity to me. 
> I can't see where the validity checks might recurse to trip calls to other 
> classes. The validity check ought to be a no-brainer, really. I don't know 
> when this happened, it may be caused by recent methods.
>
> Any ideas?
>
> Roger
>
>

-- 
Roger Bivand
Department of Economics, NHH Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: Roger.Bivand at nhh.no