[R-sig-Geo] reading .hdf files

Jonathan Greenberg jgrn at illinois.edu
Fri Mar 28 19:58:38 CET 2014 

It's not just the projection -- you need to know the upper left
coordinates (or the full bounding box) and the pixel resolution, and
set those as well.  When you said you downloaded this from NOAA --
what is the main site describing the dataset?  What are you trying to
do with this data?

gdalUtils:::gdalinfo() will give you a "fuller" set of metadata of the
input data than rgdal:::GDALinfo does, just as a note.

--j

On Fri, Mar 28, 2014 at 1:51 PM, dododave <dododave at gmail.com> wrote:
> 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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>
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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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-- 
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 at hotmail.com, Gchat: jgrn307, Skype: jgrn3007

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