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Dear Friends,

5 messages · Rodrigo W. Soria Auza, Agustin Lobo, Virgilio Gomez-Rubio +2 more

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Rodrigo W. Soria Auza
# 
Hi all,
I have a file (MOD06_auza_gridded_cldstats.bin) created by a college 
(Richard Frey). It is a binary written with FORTRAN in a little-endian 
(Linux) machine that contains a 400x300x84-bite integer array. The 400 
represents 1/20 degree cells in a N-S direction (7S-27S), 300 is 1/20 
degree cells in the E-W direction (55-70W). The 8 products in order for 
each of the 120000 cells:
1) Number retrievals
2) Yearly mean cloud fraction
3) Frequency of high, thick clouds
4) Frequency of thick clouds top temperatures <-65C
5) Same as # 4 but <-38C
6) Same as # 4 but <-12C
7) Center of cell latitude
8) Center of cell longitude
So as you can see is a multi layer file
Now neither Richard (the guy who made this file) nor I know how to 
import this kind of file into other GIS software, and I would like to 
know if somebody here could give us detailed instructions or advise to 
convert layer by layer into a common format (separate from each other. 
so we could manage every layer independently from the others), so we 
will be able to import them into other GIS software (Arcview or DIVA 
GIS) as raster (or grid) layers. (maybe ascii?).
I have a limited experience using R, but every day I learn a bit more 
and I think (actually hope) there is a package that is able to do this.
Sincerely,
Rodrigo


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Agustin Lobo
# 
Hola Rodrigo,

Hice algo parecido para los quality flags de imagenes
Modis usando Matlab. Seguramente se puede hacer en R
(no se si tiene enteros de 4 bits; por cierto,
bite no puede ser, es bit o byte, yo entiendo
que son 4 bits; tambien deberias saber
si son signed o unsigned)
pero si nadie te da una buena respuesta escribeme
y nos miramos como lo hice en Matlab. Luego
escribimos en tif o lo que quieras.

Saludos,

Agus
Rodrigo W. Soria Auza wrote:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Virgilio Gomez-Rubio
    

    

      
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?Dear Rodrigo,

I believe that you can use 'readBin' to read from binary files in R. So
you should be able to read your data with R. Given that you have the
full information about the grid points at which your data was taken, it
should be possible to make a SpatialGrid with this information and put
all the data (grid + covariates) together in a SpatialGridDataFrame.

I am afraid that this may require a bit of programming (not much though)
and that there is probably no specific function to read your data as it
is.

Hope this helps,

Virgilio

        
On Fri, 2008-05-23 at 15:54 +0200, Rodrigo W. Soria Auza wrote:

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Roger Bivand
    

    

      
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On Fri, 23 May 2008, Rodrigo W. Soria Auza wrote:

        

            

      
      
      
    

        
If you have access to the Fortran source code, use readBin() to read the 
chunks. I'm puzzled by the 84 bytes, because that suggests that each cell 
record contains more than 8 8-byte double precision numbers (which would 
be 64 bytes). So you need a more detailed description than you have now.

If you read the data into pre-allocated vectors (perhaps grouped in a 
list), thes can readily be converted to a data frame. This can be 
converted into a SpatialPointsDataFrame (class defiled in the sp package) 
and further to a SpatialGridDataFrame. This can then be exported using 
writeGDAL() in the rgdal package, to a range of different formats, defined 
by the drivers in your installed GDAL, see gdalDrivers() for the ones you 
have.

Roger

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    
1 day later

    

      
      

        


  

        

      Michael Sumner
    

    

      
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Apparently it's common for extra bytes to be added by Fortran "raw 
binary" writers. I don't know exactly, but I had to figure this out by 
trial and error for some binary versions of the Reynolds SST products - 
that had precise descriptions of the file arrangement that doesn't 
include the extra bytes. Some colleagues with more experience confirmed 
that there were some strange additional bytes to be expected from Fortran.

ftp://podaac.jpl.nasa.gov/pub/sea_surface_temperature/reynolds/oisst/software/v2/README.v2
When reading from these files you can see the bytes that I ignore as 
"junk", the rest of the data in there is tidy and predictable:

    if (length(grep(".gz", fl)) == 1)
      con <- gzfile(file.path(dir, fl), "rb") else    con <- 
file(file.path(dir, fl), "rb")
   
    head <- readBin(con, "integer", size = 4, n = 11, endian = "big",  
signed = FALSE)
    temps <- readBin(con, "numeric", size = 4, n = 180 * 360,endian = "big")
    junk <- readBin(con, "integer", size = 4, endian = "big", n = 2)

    err <- readBin(con, "numeric", size = 4, n = 180 * 360, endian = "big")
    junk <- readBin(con, "integer", size = 4, endian = "big", n = 2)
    ice <- readBin(con, "integer", size = 1, n = 180 * 360, endian = 
"big",signed = FALSE)

    close(con)

HTH
Cheers, Mike.

        
Roger Bivand wrote: