[R-sig-Geo] issue when opening raster image in R, the pixel values a rescaled somehow

[Roger Bivand]

On Tue, 24 Mar 2020, Roger Bivand wrote:

> Opening in stars shows that the read data are interpreted as degrees Kelvin:
>
>>  library(stars)
>>  ss <- read_stars("MOD11A2.A2000049.h17v05.006.2015058135048.tif")
>>  print(ss, n=1e8)
> stars object with 2 dimensions and 1 attribute
> attribute(s):
>  MOD11A2.A2000049.h17v05.006.2015058135048.tif [K]
>  Min.   :272.1
>  1st Qu.:293.3
>  Median :296.5
>  Mean   :296.1
>  3rd Qu.:298.8
>  Max.   :309.2
>  NA's   :926190
> dimension(s):
>  from   to   offset    delta  refsys point values
> x    1 1200 -1111951  926.625 unnamed FALSE   NULL [x]
> y    1 1200  4447802 -926.625 unnamed FALSE   NULL [y]
>
> The summary agrees with
>
>>  library(rgdal)
>>  o <- readGDAL("MOD11A2.A2000049.h17v05.006.2015058135048.tif")
>>  summary(o)
> Object of class SpatialGridDataFrame
> Coordinates:
>       min     max
> x -1111951       0
> y  3335852 4447802
> Is projected: TRUE
> proj4string :
> [+proj=sinu +lon_0=0 +x_0=0 +y_0=0 +R=6371007.181 +units=m +no_defs]
> Grid attributes:
>  cellcentre.offset cellsize cells.dim
> x          -1111487 926.6254      1200
> y           3336315 926.6254      1200
> Data attributes:
>      band1
>  Min.   :272.1
>  1st Qu.:293.3
>  Median :296.5
>  Mean   :296.1
>  3rd Qu.:298.8
>  Max.   :309.2
>  NA's   :926190
>
> and
>
>>  library(raster)
>>  r <- raster("MOD11A2.A2000049.h17v05.006.2015058135048.tif")
>>  summary(values(r))
>   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's
>   272.1   293.3   296.5   296.1   298.8   309.2  926190
>
> So my feeling is that the representation is correct in degrees Kelvin.
>
> Others please join in, I'm not familiar with MODIS HDF data. I think 
> something gives the metadata in the GeoTIFF the wrong data bounds - they do 
> seem to be UInt16. The output of gdalinfo (command line) includes:
>
> ...
>   units=K
>   valid_range=7500, 65535
> ...
> Band 1 Block=1200x3 Type=UInt16, ColorInterp=Gray
>   NoData Value=0
>   Unit Type: K
> ...

I missed the next line with the scale in it:

$gdalinfo -stats MOD11A2.A2000049.h17v05.006.2015058135048.tif
...
Band 1 Block=1200x3 Type=UInt16, ColorInterp=Gray
   Minimum=13607.000, Maximum=15461.000, Mean=14804.047, StdDev=191.673
   NoData Value=0
   Unit Type: K
   Offset: 0,   Scale:0.02
   Metadata:
     DESCRIPTION=8-day daytime 1km grid Land-surface Temperature
     STATISTICS_MAXIMUM=15461
     STATISTICS_MEAN=14804.046793562
     STATISTICS_MINIMUM=13607
     STATISTICS_STDDEV=191.67312038983
     STATISTICS_VALID_PERCENT=35.68

and 13607*0.02 = 272.14, 15461*0.02 = 309.22, so GDAL and the R interfaces 
are using the scale factor to read the data as degrees Kelvin. Divide by 
the scale factor if you need the input values.

Roger

>
> Roger
>
>
> On Tue, 24 Mar 2020, Victor F. Rodriguez Galiano wrote:
>
>>  Hi Roger, the link to he image is given below. This image was generated
>>  from a .hdf file using the function gdal_translate.
>>
>>  gdal_translate(sds[1], dst_dataset=paste0(substr(filename, 1,
>>  nchar(filename)-4) ,".tif", ))
>>
>>  https://wetransfer.com/downloads/4569e9a85c02faad5016b83d0b50217820200324084015/f2eafdfafaae74de9ac8e25017fc5cc520200324084015/e46e80
>> 
>>
>>  Thanks
>>
>>  Victor
>>
>>  El lun., 23 mar. 2020 a las 21:07, Roger Bivand (<Roger.Bivand using nhh.no>)
>>  escribió:
>>
>>>  Please make the file in question available for download (url), or the
>>>  url
>>>  you downloaded it from (no login), on this list. It looks as though the
>>>  unsigned 16 bit integer is not right.
>>>
>>>  Roger Bivand
>>>  Norwegian School of Economics
>>>  Bergen, Norway
>>>
>>>  ------------------------------
>>>  *Fra:* R-sig-Geo <r-sig-geo-bounces using r-project.org> på vegne av Victor F.
>>>  Rodriguez Galiano <vrgaliano using gmail.com>
>>>  *Sendt:* mandag 23. mars 2020, 21.02
>>>  *Til:* r-sig-geo using r-project.org
>>>  *Emne:* [R-sig-Geo] issue when opening raster image in R, the pixel
>>>  values a rescaled somehow
>>>
>>>  I opened a Geotiff image in R using the raster function. However, the
>>>  image seems to be rescaled. The minimum and maximum values should be
>>>  13607
>>>  and 15461 but are 275 and 305. The Geotiff image when opened in a GIS is
>>>  correct but not in R. This is my code: Script: library(raster)
>>>  trial<-raster("MOD11A2.A2000049.h17v05.006.2015058135048.tif", datatype
>>>  =
>>>  "INT2U") trial plot(trial) [[alternative HTML version deleted]]
>>>  _______________________________________________ R-sig-Geo mailing list
>>>  R-sig-Geo using r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>> 
>> 
>
>

-- 
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: Roger.Bivand using nhh.no
https://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en