[R-sig-Geo] get data from nc file

[Antonio Silva]

Thanks for you nice idea and code Ben. I will use them for sure.

Have a wonderful 2019. All the best

Antonio Olinto
Fisheries Institute
Brazil


Em qua, 26 de dez de 2018 às 22:01, Ben Tupper <btupper using bigelow.org>
escreveu:

> Hi,
>
> .  I don't think there is any other way as the attributes are sort of
> buried in the string; that's unfortunate.  I guess you could at least make
> a reusable function assuming you'll be doing this again or looking to pull
> other attributes.  Something like this...
>
>
> #' Extract one of the GLobal Attributes of a TRMM NetCDF as a named vector
> #'
> #' @param nc the ncdf4 object
> #' @param name the name of the global attribute
> #' @param sep the separator used to delimit fields in the attribute
> #' @return named character vector of attributes
> nc_att_split <- function(nc, name = "FileHeader", sep = ";\n"){
>
>         a1 <- ncdf4::ncatt_get(nc, 0)[[name[1]]]
>         if (is.null(a1)) return(a1)
>
>         a2 <- strsplit(a1,";\n", fixed = TRUE)[[1]]
>         aa <- strsplit(a2, "=", fixed = TRUE)
>
>         x <- sapply(aa,
>                 function(s) x = if(length(s) <= 1) "" else s[2]
>                 )
>         names(x) <- sapply(aa,
>                 function(s) x = if(length(s) <= 1) "unknown" else s[1]
>                 )
>
>         x
> }
>
>
> nc <- ncdf4::nc_open("3B43.20080101.7A.HDF.nc")
> x <- nc_att_split(nc)
> as.Date(x[['StartGranuleDateTime']], format = "%Y-%m-%dT%H:%M:%OSZ")
> [1] "2008-01-01"
>
>
> Cheers,
> Ben
>
> > On Dec 26, 2018, at 3:42 PM, Antonio Silva <aolinto.lst using gmail.com>
> wrote:
> >
> > Dear list members
> >
> > I downloaded some nc files with precipitation data from
> > https://pmm.nasa.gov/data-access/downloads/trmm (Level 3 3B43:
> > Multisatellite Precipitation). For the image link see the global
> attribute
> > "history" (below).
> >
> > With ncdf4::nc_open I cloud open the file (nc.data <- nc_open("
> > 3B43.20080101.7A.HDF.nc")
> >
> > I want to extract the "StartGranuleDateTime" but it is inside the global
> > attribute FileHeader (see below).
> >
> > With ncatt_get(nc.data,0,"FileHeader")$value I got
> > [1]
> >
> "AlgorithmID=3B43;\nAlgorithmVersion=3B43_7.0;\nFileName=3B43.20080101.7A.HDF;\nGenerationDateTime=2012-11-29T19:12:01.000Z;\nStartGranuleDateTime=2008-01-01T00:00:00.000Z;\nStopGranuleDateTime=2008-01-31T23:59:59.999Z;\nGranuleNumber=;\nNumberOfSwaths=0;\nNumberOfGrids=1;\nGranuleStart=;\nTimeInterval=MONTH;\nProcessingSystem=PPS;\nProductVersion=7A;\nMissingData=;\n"
> >
> > Is there any way to extract only the string "2008-01-01T00:00:00.000Z"?
> >
> > The best I could do was
> >
> as.Date(substr(strsplit(ncatt_get(nc.data,0,"FileHeader")$value,";\n")[[1]][5],22,45),"%Y-%m-%dT%H:%M:%OSZ")
> >
> > but probably, I suppose, there must be a more direct way of getting the
> > data. I appreciate any suggestions.
> >
> > Best regards,
> >
> > Antonio Olinto
> > Fisheries Institute
> > Brazil
> >
> > nc.data
> > File 3B43.20080101.7A.HDF.nc (NC_FORMAT_CLASSIC):
> >
> >     1 variables (excluding dimension variables):
> >        float precipitation[nlat,nlon]
> >            units: mm/hr
> >            coordinates: nlon nlat
> >            _FillValue: -9999.900390625
> >
> >     2 dimensions:
> >        nlon  Size:33
> >            long_name: longitude
> >            standard_name: longitude
> >            units: degrees_east
> >        nlat  Size:41
> >            long_name: latitude
> >            standard_name: latitude
> >            units: degrees_north
> >
> >    5 global attributes:
> >        Grid.GridHeader: BinMethod=ARITHMETIC_MEAN;
> > Registration=CENTER;
> > LatitudeResolution=0.25;
> > LongitudeResolution=0.25;
> > NorthBoundingCoordinate=50;
> > SouthBoundingCoordinate=-50;
> > EastBoundingCoordinate=180;
> > WestBoundingCoordinate=-180;
> > Origin=SOUTHWEST;
> >
> >        FileHeader: AlgorithmID=3B43;
> > AlgorithmVersion=3B43_7.0;
> > FileName=3B43.20080101.7A.HDF;
> > GenerationDateTime=2012-11-29T19:12:01.000Z;
> > StartGranuleDateTime=2008-01-01T00:00:00.000Z;
> > StopGranuleDateTime=2008-01-31T23:59:59.999Z;
> > GranuleNumber=;
> > NumberOfSwaths=0;
> > NumberOfGrids=1;
> > GranuleStart=;
> > TimeInterval=MONTH;
> > ProcessingSystem=PPS;
> > ProductVersion=7A;
> > MissingData=;
> >
> >        FileInfo: DataFormatVersion=m;
> > TKCodeBuildVersion=1;
> > MetadataVersion=m;
> > FormatPackage=HDF Version 4.2 Release 4, January 25, 2009;
> > BlueprintFilename=TRMM.V7.3B43.blueprint.xml;
> > BlueprintVersion=BV_13;
> > TKIOVersion=1.6;
> > MetadataStyle=PVL;
> > EndianType=LITTLE_ENDIAN;
> >
> >        GridHeader: BinMethod=ARITHMETIC_MEAN;
> > Registration=CENTER;
> > LatitudeResolution=0.25;
> > LongitudeResolution=0.25;
> > NorthBoundingCoordinate=50;
> > SouthBoundingCoordinate=-50;
> > EastBoundingCoordinate=180;
> > WestBoundingCoordinate=-180;
> > Origin=SOUTHWEST;
> >
> >        history: 2018-12-26 17:57:56 GMT Hyrax-1.13.4
> >
> https://disc2.gesdisc.eosdis.nasa.gov:443/opendap/TRMM_L3/TRMM_3B43.7/2008/3B43.20080101.7A.HDF.nc?precipitation[604:636][3:43],nlat[3:43],nlon[604:636]
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
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> > R-sig-Geo using r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>
> Ben Tupper
> Bigelow Laboratory for Ocean Sciences
> 60 Bigelow Drive, P.O. Box 380
> East Boothbay, Maine 04544
> http://www.bigelow.org
>
> Ecological Forecasting: https://eco.bigelow.org

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