[R-sig-Geo] [R] Unexpected parameter problem using rsaga.geoprocessor() {RSAGA}

[Amelie LESCROEL]

Dear Alex,
Thanks again for your help. I'll seriously think about using setwd(), I 
promise! I also succeeded circumventing the problem by using the 
following code:

library(RSAGA)
library(rgdal)
rsaga.geoprocessor("io_grid", 4, list(GRID="grid1.sgrd", 
FILE_DATA='"C:/.../nt_200602_f13_v01_s.bin"', NX=316, NY=332, DXY=25, 
XMIN=-3950, YMIN=-3950, DATA_OFFSET=300, TOPDOWN=1))
rsaga.geoprocessor("grid_calculus", 1, list(INPUT="grid1.sgrd", 
RESULT="grid2.sgrd", FORMUL="a*0.4"))
rsaga.geoprocessor("grid_tools", 15, list(INPUT="grid2.sgrd", 
RESULT="grid3.sgrd", METHOD=1, MIN=101, MAX=101.6, RNEW=-99999, 
ROPERATOR=0))
rsaga.geoprocessor("grid_calculus", 1, 
list(INPUT="grid3.sgrd;Crozier_lat.sgrd;Crozier_lon.sgrd", 
RESULT="grid4.sgrd", FORMUL="a*b*c"))
rsaga.sgrd.to.esri(in.sgrds="grid4.sgrd", out.grids="grid4.asc")
x1 <- new("GDALReadOnlyDataset", "grid4.asc")
x2 <- getRasterTable(x1)
data <- x2$band1[!is.na(x2$band1)]
mean(data)

Best regards,

Amélie

Alexander Brenning a écrit :
> Hi Amelie,
>
> 1) Problem with spaces in file/folder names: Same problem as before, 
> use '"my file"' style double quotes for file names with spaces. I will 
> fix this in the next version for the wrapper functions, but not for 
> the low-level rsaga.geoprocessor (which doesn't know if an argument is 
> a filename or some other character string).
>
> So for example...
>
> my.grid.matrix = read.sgrd('"my file"', return.header = FALSE)
>
> ...will return the grid matrix (without the header).
> Again, in your case using the setwd() function to go to the working 
> directory from the beginning also helps and makes the code more readable.
>
> 2) read.Rd.grid
>
>> read.Rd.grid("C:/Documents and 
>> Settings/lescroel/Bureau/FORAGING_AREA_OCT97.sdat") Erreur : mauvais
>
> A .sdat file is not a .Rd file, so I would be surprised if it worked.
>
> I hope this helps...
>  Alex
>
>
>
> Amelie LESCROEL wrote:
>> Dear Alex, Thanks a lot for your quick and efficient answer. I did
>> not think about "double double-quoting" the path '""', as "simple" 
>> double-quoting "" usually works in R for paths containing spaces.
>> Now, it works perfectly well and I was able to process my grids from
>> within R in the same way as I processed them in SAGA: > 
>> rsaga.geoprocessor("io_grid", 4, list(GRID="199710.sgrd", 
>> FILE_DATA='"C:/Documents and Settings/lescroel/Mes 
>> documents/pub/DATASETS/seaice/polar-stereo/nasateam/final-gsfc/south/monthly/nt_199710_f13_v01_s.bin"', 
>>
>>  NX=316, NY=332, DXY=25, XMIN=-3950, YMIN=-3950, DATA_OFFSET=300, 
>> TOPDOWN=1)) > rsaga.geoprocessor("grid_calculus", 1, 
>> list(INPUT="199710.sgrd", RESULT="SIC_DATA_OCT_97.sgrd", 
>> FORMUL="a*0.4")) > rsaga.geoprocessor("grid_tools", 15, 
>> list(INPUT="SIC_DATA_OCT_97.sgrd", RESULT="SIC_OCT97_wo_Land.sgrd", 
>> METHOD=1, MIN=101, MAX=101.6, RNEW=-99999, ROPERATOR=0)) > 
>> rsaga.geoprocessor("grid_calculus", 1, 
>> list(INPUT="SIC_OCT98_wo_Land.sgrd;Crozier_lat.sgrd;Crozier_lon.sgrd",
>>  RESULT="FORAGING_AREA_OCT97.sgrd", FORMUL="a*b*c")) I'm encountering
>> a new problem though: now, I would like to work with the last
>> obtained grid "FORAGING_AREA_OCT97.sgrd" in R for performing basic
>> statistics (like obtaining the mean value of all cells). I was not
>> able to find a way to transform or read the .sgrd file into a R
>> object (matrix or data frame) that I could easily manipulate. I tried
>> the following: > oct97 <- read.sgrd("C:/Documents and 
>> Settings/lescroel/Bureau/FORAGING_AREA_OCT97.sgrd") Erreur dans 
>> read.sgrd("C:/Documents and 
>> Settings/lescroel/Bureau/FORAGING_AREA_OCT97.sgrd") : error
>> converting the SAGA sgrd file to a temporary ASCII grid file > oct97
>> <- read.Rd.grid("C:/Documents and 
>> Settings/lescroel/Bureau/FORAGING_AREA_OCT97.sdat") Erreur : mauvais
>>  numéro magique de restauration de fichier (le fichier est peut être
>>  corrompu) -- aucune donnée chargée ## Translation of the error
>> message "Error: wrong file restoring magic number (the file may be
>> corrupted) - no data loaded" De plus : Warning message: file 
>> 'FORAGING_AREA_OCT97.sdat' has magic number '€OÃÇ€' Use of save
>> versions prior to 2 is deprecated Could you or someone else help me
>> again? Many thanks, Amélie PS: I'm posting this message to the
>> R-sig-geo list this time! Message: 140 Date: Tue, 12 Aug 2008
>> 03:02:03 -0400 From: Alexander Brenning
>> <brenning at fesmail.uwaterloo.ca> Subject: Re: [R] Unexpected parameter
>> problem using rsaga.geoprocessor() {RSAGA} To: Am?lie Lescro?l 
>> <lescroel_cebc at no-log.org> Cc: r-help at R-project.org Message-ID: 
>> <48A1356B.10404 at fes.uwaterloo.ca> Content-Type: text/plain; 
>> charset=windows-1252; format=flowed Dear Amelie, > Le service Beep
>> n'est pas lanc?. this can be fixed by passing an additional argument
>> beep.off = FALSE to the rsaga.geoprocessor function; the most recent
>> RSAGA release on CRAN does not cause this problem any more, I
>> recommend you to update the package in your installation. The
>> beep.off thing was an attempt to stop SAGA from beeping each time a
>> module has been executed.
>>> Unexpected parameter 'and' If a file path or file name contains
>> spaces as in "Documents and Settings", you would have to double quote
>>  it, e.g., '"My Folder"' rather than "My Folder" This will make sure
>> that SAGA knows that the space does not separate different arguments.
>> After all, RSAGA uses the SAGA command line interface. However, it is
>> always a good idea to use the setwd() function to change the working
>> directory. This will keep the path short. I hope this helps. Alex
>> P.S.: You might wish to consider the R-sig-geo list for questions
>> regarding spatial/GIS support in R. Am?lie Lescro?l wrote:
>>
>>>> Hello, I discovered SAGA, an interesting free GIS, a few days ago
>>>> and now,
>>> I > would like to use it from within R 2.6.2 using the RSAGA
>>> package. I read > the documentation for this package and thought
>>> that I understood it > correctly for trying to call some of the
>>> SAGA modules. For getting the > information on the usage of and
>>> arguments required by the SAGA command > line "Import Binary Raw
>>> Data" module, I used:
>>>>>> rsaga.get.usage("io_grid", 4)
>>>> SAGA CMD 2.0.3 library path: C:/Progra~1/saga_vc/modules library
>>>> name: io_grid module name : Import Binary Raw Data Usage: 4
>>>> [-GRID <str>] [-FILE_DATA <str>] [-NX <num>] [-NY <num>]
>>> [-DXY > <str>] [-XMIN <str>] [-YMIN <str>] [-UNIT <str>] [-ZFACTOR
>>>  <str>] > [-NODATA <str>] [-DATA_OFFSET <num>] [-LINE_OFFSET <num>]
>>>  [-LINE_ENDSET > <num>] [-DATA_TYPE <num>] [-BYTEORDER_BIG <num>] 
>>> [-TOPDOWN <num>]
>>>> -GRID:<str> Grid Data Object (optional output) -FILE_DATA:<str>
>>>> Raw Data File File path -NX:<num> Cell Count (X) Integer -NY:<num> 
>>>> Cell Count (Y) Integer -DXY:<str> Cell Size Floating
>>>> point -XMIN:<str> Left Border (X) Floating point -YMIN:<str>
>>>> Lower Border (Y) Floating point -UNIT:<str> Unit Name Text 
>>>> -ZFACTOR:<str> Z Multiplier Floating point -NODATA:<str> No Data
>>>> Value Floating point -DATA_OFFSET:<num> Data Offset (Bytes) Integer 
>>>> -LINE_OFFSET:<num> Line Offset (Bytes) Integer -LINE_ENDSET:<num> 
>>>> Line Endset (Bytes) Integer -DATA_TYPE:<num>
>>>> Data Type Choice Available Choices: [0] 1 Byte Integer (unsigned)
>>>>  [1] 1 Byte Integer (signed) [2] 2 Byte Integer (unsigned) [3] 2
>>>> Byte Integer (signed) [4] 4 Byte Integer (unsigned) [5] 4 Byte
>>>> Integer (signed) [6] 4 Byte Floating Point [7] 8 Byte Floating
>>>> Point -BYTEORDER_BIG:<num> Byte Order Choice Available Choices: [0] 
>>>> Little Endian (Intel) [1] Big Endian (Motorola) -TOPDOWN:<num> Line 
>>>> Order Choice Available Choices: [0] Bottom to
>>>> Top [1] Top to Bottom
>>>>> Then, I wrote the following command for importing a grid of
>>>>> binary
>>> raw > data while specifying the parameters I usually enter under
>>> SAGA:
>>>>>> rsaga.geoprocessor("io_grid", 4, list(GRID="199710.sgrd", >
>>> FILE_DATA="C:/Documents and Settings/lescroel/Mes > 
>>> documents/pub/DATASETS/seaice/polar-stereo/nasateam/final-gsfc/south/monthly/nt_199710_f13_v01_s.bin", 
>>>
>>>
>>>> NX=316, NY=332, DXY=25, XMIN=-3950, DATA_OFFSET=300, TOPDOWN=1))
>>>>> and I got: Le service Beep n'est pas lanc?. Vous obtiendrez une
>>>>> aide suppl?mentaire en entrant NET HELPMSG 3521.
>>>>>> C:\Documents and >
>>> Settings\lescroel\Bureau>C:\Progra~1\saga_vc\saga_cmd.exe io_grid 4
>>> > -silent -GRID 199710.sgrd -FILE_DATA C:\Documents and > 
>>> Settings\lescroel\Mes > 
>>> documents\pub\DATASETS\seaice\polar-stereo\nasateam\final-gsfc\south\monthly\nt_199710_f13_v01_s.bin 
>>>
>>>
>>>> -NX 316 -NY 332 -DXY 25 -XMIN -3950 -DATA_OFFSET 300 -TOPDOWN 1
>>>>> SAGA CMD 2.0.3
>>>> library path: C:/Progra~1/saga_vc/modules library name: io_grid 
>>>> module name : Import Binary Raw Data author : (c) 2003 by
>>>> O.Conrad
>>>>> error: executing module [Import Binary Raw Data]
>>>> Usage: -silent [-GRID <str>] [-FILE_DATA <str>] [-NX <num>] [-NY
>>>>
>>> <num>] > [-DXY <str>] [-XMIN <str>] [-YMIN <str>] [-UNIT <str>] 
>>> [-ZFACTOR <str>] > [-NODATA <str>] [-DATA_OFFSET <num>]
>>> [-LINE_OFFSET <num>] [-LINE_ENDSET > <num>] [-DATA_TYPE <num>]
>>> [-BYTEORDER_BIG <num>] [-TOPDOWN <num>]
>>>> -GRID:<str> Grid Data Object (optional output) -FILE_DATA:<str>
>>>> Raw Data File File path -NX:<num> Cell Count (X) Integer -NY:<num> 
>>>> Cell Count (Y) Integer -DXY:<str> Cell Size Floating
>>>> point -XMIN:<str> Left Border (X) Floating point -YMIN:<str>
>>>> Lower Border (Y) Floating point -UNIT:<str> Unit Name Text 
>>>> -ZFACTOR:<str> Z Multiplier Floating point -NODATA:<str> No Data
>>>> Value Floating point -DATA_OFFSET:<num> Data Offset (Bytes) Integer 
>>>> -LINE_OFFSET:<num> Line Offset (Bytes) Integer -LINE_ENDSET:<num> 
>>>> Line Endset (Bytes) Integer -DATA_TYPE:<num>
>>>> Data Type Choice Available Choices: [0] 1 Byte Integer (unsigned)
>>>>  [1] 1 Byte Integer (signed) [2] 2 Byte Integer (unsigned) [3] 2
>>>> Byte Integer (signed) [4] 4 Byte Integer (unsigned) [5] 4 Byte
>>>> Integer (signed) [6] 4 Byte Floating Point [7] 8 Byte Floating
>>>> Point -BYTEORDER_BIG:<num> Byte Order Choice Available Choices: [0] 
>>>> Little Endian (Intel) [1] Big Endian (Motorola) -TOPDOWN:<num> Line 
>>>> Order Choice Available Choices: [0] Bottom to
>>>> Top [1] Top to Bottom Unexpected parameter 'and'
>>>>> Could someone already using the RSAGA package provide some help
>>>>> in
>>>> telling me what I did wrong? Thanks for your help,
>>>>> Am?lie
>>>
>>
>> -- Alexander Brenning
>> Department of Geography and Environmental Management University
>> of Waterloo 200 University Ave. W - Waterloo, ON - Canada N2L 3G1 
>> http://www.fes.uwaterloo.ca/geography/faculty/brenning/
>>
>



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