[ncl-talk] hdf confusion

Tue Jun 13 15:48:07 MDT 2017

In particular the example from that page, hdf4eos_5.ncl
<https://www.ncl.ucar.edu/Applications/Scripts/hdf4eos_5.ncl>, shows how to
use the function dim_gbits to get the values of particular bits from byte,
ubyte, short, ushort, or integer data. It does not really matter in this
case whether the data is unsigned or signed because when decoded as bits
the results are the same either way.

The default hdfeos5 reader still treats the data as signed because it does
not use the advanced file system and therefore is limited to the types
allowed for NetCDF3. There is an advanced version of the the reader but it
is not yet recommended for general use because not all the kinks have been
worked out.
 -dave

On Tue, Jun 13, 2017 at 3:14 PM, Marston Johnston <shejo284 at gmail.com>
wrote:

> Here’s a NCL page dedicated to the handling of HDF files used by
> satellites such as MODIS.
>
>
>
> https://www.ncl.ucar.edu/Applications/HDF.shtml
>
>
>
> /M
>
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> Marston S. Johnston, PhD
>
> Department of Earth Sciences
>
> University of Gothenburg, Sweden
>
> Email: marston.johnston at gu.se
>
> SkypeID: marston.johnston
>
> Phone: +46-31-7864901 <+46%2031%20786%2049%2001>
>
> Only the fruitful thing is true!
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>
>
>
>
> *From: *Michael Notaro <mnotaro at wisc.edu>
> *Date: *Tuesday, 13 June 2017 at 22:46
> *To: *Marston Johnston <shejo284 at gmail.com>, "ncl-talk at ucar.edu" <
> ncl-talk at ucar.edu>
>
> *Subject: *Re: [ncl-talk] hdf confusion
>
>
>
> Thanks.  I tried the following and only end up with a 2d grid of values
> like 2066, 18709, etc.
>
> How can I retrieve slot [11-13] land/water flag with values like 000, 001,
> 010, etc?
>
> Michael
>
>
>
> aa=addfile("h10v04_yellowstone/MOD13Q1.A2012001.
> h10v04.006.2015236172021.hdf.hdfeos","r")
>
> lat2d=doubletofloat(aa->GridLat_MODIS_Grid_16DAY_250m_500m_VI(::-1,:))
>
> lon2d=doubletofloat(aa->GridLon_MODIS_Grid_16DAY_250m_500m_VI(::-1,:))
>
> lat2d!0="nlat"
>
> lat2d!1="nlon"
>
> lon2d!0="nlat"
>
> lon2d!1="nlon"
>
> land=short2flt_hdf(aa->250m_16_days_VI_Quality_MODIS_Grid_
> 16DAY_250m_500m_VI)
>
> print(land)
>
>
>
>
>
> Michael Notaro
>
> Associate Director
>
> Nelson Institute Center for Climatic Research
>
> University of Wisconsin-Madison
>
> Phone: (608) 261-1503
>
> Email: mnotaro at wisc.edu
>
>
> ------------------------------
>
> *From:* Marston Johnston <shejo284 at gmail.com>
> *Sent:* Tuesday, June 13, 2017 3:37 PM
> *To:* Michael Notaro; ncl-talk at ucar.edu
> *Subject:* Re: [ncl-talk] hdf confusion
>
>
>
> Hi,
>
>
>
> Try this function: http://www.ncl.ucar.edu/Document/Functions/
> Contributed/short2flt_hdf.shtml
>
> short2flt_hdf - ncl.ucar.edu
> <http://www.ncl.ucar.edu/Document/Functions/Contributed/short2flt_hdf.shtml>
>
> www.ncl.ucar.edu
>
> NCL Home > Documentation > Functions > Type converters short2flt_hdf.
> Converts values of type short to values of type float using the "scale" and
> "offset" attributes ...
>
>
>
>
>
> /M
>
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> Marston S. Johnston, PhD
>
> Department of Earth Sciences
>
> University of Gothenburg, Sweden
>
> Email: marston.johnston at gu.se
>
> SkypeID: marston.johnston
>
> Phone: +46-31-7864901 <+46%2031%20786%2049%2001>
>
> Only the fruitful thing is true!
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>
>
>
>
> *From: *<ncl-talk-bounces at ucar.edu> on behalf of Michael Notaro <
> mnotaro at wisc.edu>
> *Date: *Tuesday, 13 June 2017 at 22:33
> *To: *"ncl-talk at ucar.edu" <ncl-talk at ucar.edu>
> *Subject: *[ncl-talk] hdf confusion
>
>
>
> Sorry for the ignorant question but I am having trouble figuring out
>
> how to properly retrieve the land-lake-ocean mask off this MODIS hdf file.
>
> If I ncl_filedump *hdf, it shows the variable as ushort.  If I
> ncl_filedump *hdf.hdfeos,
>
> it shows the variable as short.  Which should I use in addfile and how do
> I
>
> retrieve the values of 001=land, 000=ocean, etc?
>
> Michael
>
>
>
>
>
> ncl_filedump h10v04_yellowstone/MOD13Q1.A2012001.h10v04.006.
> 2015236172021.hdf.hdfeos
>
>
>
>     short 250m_16_days_VI_Quality_MODIS_Grid_16DAY_250m_500m_VI (
> YDim_MODIS_Grid_16DAY_250m_500m_VI, XDim_MODIS_Grid_16DAY_250m_500m_VI )
>
>          coordinates :
>
> GridLat_MODIS_Grid_16DAY_250m_500m_VI, GridLon_MODIS_Grid_16DAY_250m_
> 500m_VI
>
>          hdfeos_name :
>
> 250m 16 days VI Quality
>
>          projection :
>
> Sinusoidal
>
>          unsigned :
>
> True
>
>          Legend :
>
> Bit Fields Description (Right to Left):
>
> [0-1] : MODLAND_QA [2 bit range]
>
> 00: VI produced, good quality
>
> 01: VI produced, but check other QA
>
> 10: Pixel produced, but most probably cloudy
>
> 11: Pixel not produced due to other reasons than clouds
>
> [2-5] : VI usefulness [4 bit range]
>
> 0000: Highest quality
>
> 0001: Lower quality
>
> 0010..1010: Decreasing quality
>
> 1100: Lowest quality
>
> 1101: Quality so low that it is not useful
>
> 1110: L1B data faulty
>
> 1111: Not useful for any other reason/not processed
>
> [6-7] : Aerosol quantity [2 bit range]
>
> 00: Climatology
>
> 01: Low
>
> 10: Average
>
> 11: High (11)
>
> [8] : Adjacent cloud detected; [1 bit range]
>
> 1: Yes
>
> 0: No
>
> [9] : Atmosphere BRDF correction performed [1 bit range]
>
> 1: Yes
>
> 0: No
>
> [10] : Mixed clouds  [1 bit range]
>
> 1: Yes
>
> 0: No
>
> [11-13] : Land/Water Flag [3 bit range]
>
> 000: Shallow ocean
>
> 001: Land (Nothing else but land)
>
> 010: Ocean coastlines and lake shorelines
>
> 011: Shallow inland water
>
> 100: Ephemeral water
>
> 101: Deep inland water
>
> 110: Moderate or continental ocean
>
> 111: Deep ocean
>
> [14] : Possible snow/ice [1 bit range]
>
> 1: Yes
>
> 0: No
>
> [15] : Possible shadow [1 bit range]
>
> 1: Yes
>
> 0: No
>
>          _FillValue :
>
> -1
>
>          valid_range :
>
> ( 0, -2 )
>
>          units :
>
> bit field
>
>          long_name :
>
> 250m 16 days VI Quality
>
>
>
> ncl_filedump h10v04_yellowstone/MOD13Q1.A2012001.h10v04.006.
> 2015236172021.hdf
>
>
>
>       ushort 250m_16_days_VI_Quality ( YDim_MODIS_Grid_16DAY_250m_500m_VI,
> XDim_MODIS_Grid_16DAY_250m_500m_VI )
>
>          long_name :
>
> 250m 16 days VI Quality
>
>          units :
>
> bit field
>
>          valid_range :
>
> ( 0, 65534 )
>
>          _FillValue :
>
> 65535
>
>          Legend :
>
> Bit Fields Description (Right to Left):
>
> [0-1] : MODLAND_QA [2 bit range]
>
> 00: VI produced, good quality
>
> 01: VI produced, but check other QA
>
> 10: Pixel produced, but most probably cloudy
>
> 11: Pixel not produced due to other reasons than clouds
>
> [2-5] : VI usefulness [4 bit range]
>
> 0000: Highest quality
>
> 0001: Lower quality
>
> 0010..1010: Decreasing quality
>
> 1100: Lowest quality
>
> 1101: Quality so low that it is not useful
>
> 1110: L1B data faulty
>
> 1111: Not useful for any other reason/not processed
>
> [6-7] : Aerosol quantity [2 bit range]
>
> 00: Climatology
>
> 01: Low
>
> 10: Average
>
> 11: High (11)
>
> [8] : Adjacent cloud detected; [1 bit range]
>
> 1: Yes
>
> 0: No
>
> [9] : Atmosphere BRDF correction performed [1 bit range]
>
> 1: Yes
>
> 0: No
>
> [10] : Mixed clouds  [1 bit range]
>
> 1: Yes
>
> 0: No
>
> [11-13] : Land/Water Flag [3 bit range]
>
> 000: Shallow ocean
>
> 001: Land (Nothing else but land)
>
> 010: Ocean coastlines and lake shorelines
>
> 011: Shallow inland water
>
> 100: Ephemeral water
>
> 101: Deep inland water
>
> 110: Moderate or continental ocean
>
> 111: Deep ocean
>
> [14] : Possible snow/ice [1 bit range]
>
> 1: Yes
>
> 0: No
>
> [15] : Possible shadow [1 bit range]
>
> 1: Yes
>
> 0: No
>
>          hdf_name :
>
> 250m 16 days VI Quality
>
>
>
>
>
> Michael Notaro
>
> Associate Director
>
> Nelson Institute Center for Climatic Research
>
> University of Wisconsin-Madison
>
> Phone: (608) 261-1503
>
> Email: mnotaro at wisc.edu
>
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