[R-sig-Geo] reading .hdf files

[dododave]

Yes, I checked the projection info from the newly converted tiff file, and it
is blank. I even tried to set the projection with the command below to match
my poly file; 

projection(rast) <- "+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0"

but this isn't right. I tried to use the GDALinfo command to extract the
metadata, but that doesn't work either. The ftp site I downloaded the .hdf
files from is run by the NOAA, and I found some info;
	
Table 2 Description of File attributes (Meta data)
Meta data tag	Content
GRID_ROWS	Number of rows for data grid
GRID_COLUMNS	Number of columns for data grid
START_LATITUDE_RANGE	The latitude of the grid’s northern edge 
END_LATITUDE_RANGE	The latitude of the  grid’s southern edge
START_LONGITUDE_RANGE	The longitude of the grid’s western edge
END_LONGITUDE_RANGE	The longitude of the  grid’s eastern edge
PROJECTION	Projection type

But how do I view the metadata?



Jonathan Greenberg-3 wrote
> I want to follow up with this -- I confirmed Barry's suspicion that
> that file you sent above ("GVIX_NL_G16_C07_NVI_Y2005_P26.hdf") has no
> projection information (or bounding box or pixel resolution), so there
> is no way to do the extract unless that is fixed.  Run a:
> 
> gdalinfo("GVIX_NL_G16_C07_NVI_Y2005_P26.hdf")
> 
> and you'll see there is not a properly set projection -- the .tif,
> thus, also doesn't have any projection info.  This is an issue with
> the input file, not with any of our functions.  You will need to set
> your own projection, bounding box, and pixel sizes on the raster via
> e.g. ?projection, ?res, ?extent
> 
> What are these files?  Are they satellite data?  Do you know if there
> is another source for them that may have the information set
> "properly"?
> 
> --j
> 
> On Fri, Mar 28, 2014 at 11:38 AM, Barry Rowlingson
> <

> b.rowlingson at .ac

> > wrote:
>> On Fri, Mar 28, 2014 at 4:11 PM, dododave <

> dododave@

> > wrote:
>>
>>> I am now able to convert the hdf files into GeoTiffs. I have a follow-up
>>> question though.
>>>
>>> I now need to extract the mean ndvi value from within a polygon overlaid
>>> on
>>> that GeoTiff. The issue I am having is that the code is returning NULL
>>> when
>>> I do.
>>>
>>> >       rast <- raster("2011_P01.tif")
>>> >       mean.ndvi <- extract(rast, poly, fun=mean)
>>> > mean.ndvi
>>> [[1]]
>>> NULL
>>>
>>>
>>> Here is the output when I call rast;
>>> > rast
>>> class       : RasterLayer
>>> dimensions  : 904, 2500, 2260000  (nrow, ncol, ncell)
>>> resolution  : 1, 1  (x, y)
>>> extent      : 0, 2500, 0, 904  (xmin, xmax, ymin, ymax)
>>> coord. ref. : NA
>>> data source : /Volumes/GOLONDRINA/tiff/2011_P01.tif
>>> names       : X2011_P01
>>> values      : -32768, 32767  (min, max)
>>>
>>> Help appreciated!
>>>
>>
>> Are you sure your polygon is in the right place?
>>
>> r=raster()
>> r[]=runif(180*360)
>> pts=data.frame(x=c(-50,50,50,-50,-50),y=c(-50,-50,50,50,-50))
>> poly = SpatialPolygons(list(Polygons(list(Polygon(pts)),ID=1)))
>> extract(r,poly,fun=mean)
>> [1] 0.4997085
>>
>>  - so that;s all good, but if I move the polygon way off the raster:
>>
>> poly2 = SpatialPolygons(list(Polygons(list(Polygon(pts+200)),ID=1)))
>> extract(r,poly2,fun=mean)
>> [[1]]
>> NULL
>>
>>  I get what you're getting.  Check your polygon coordinates and CRS
>> string
>> is correct...
>>
>> Barry
>>
>>         [[alternative HTML version deleted]]
>>
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> 
> 
> 
> -- 
> Jonathan A. Greenberg, PhD
> Assistant Professor
> Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
> Department of Geography and Geographic Information Science
> University of Illinois at Urbana-Champaign
> 259 Computing Applications Building, MC-150
> 605 East Springfield Avenue
> Champaign, IL  61820-6371
> Phone: 217-300-1924
> http://www.geog.illinois.edu/~jgrn/
> AIM: jgrn307, MSN: 

> jgrn307@

> , Gchat: jgrn307, Skype: jgrn3007
> 
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