[ncl-talk] Problems converting hdf to netcdf using NCL

BLIUJUS, STEVEN D CTR USAF AFMC AFLCMC/HBAW-OL steven.bliujus.3.ctr at us.af.mil
Wed May 27 08:34:28 MDT 2015


Dennis the script works however for some reason the data is not getting put into the NetCDF file correctly. I have ~120 files I'm going through, and when the script prints the dimensions, the following are stated:

Variable: time
Type: double
Total Size: 2080 bytes
            260 values
Number of Dimensions: 1
Dimensions and sizes:   [time | 260]
Coordinates:
            time: [20143050010..2.426116152246728e-315]
Number Of Attributes: 1
  long_name :   current time as YYYYDDDHHMM

Variable: data
Type: float
Total Size: 28641600 bytes
            7160400 values
Number of Dimensions: 3
Dimensions and sizes:   [time | 260] x [Cell_Along_Swath | 204] x [Cell_ACross_Swath | 135]
Coordinates:
            time: [20143050010..2.426116152246728e-315]
Number Of Attributes: 2
  long_name :    AOT at 0.55 micron for both ocean and land
  _FillValue :  -9999
(0)     data: min=-0.05   max=4.277

Variable: lat2d
Type: float
Total Size: 28641600 bytes
            7160400 values
Number of Dimensions: 3
Dimensions and sizes:   [time | 260] x [Cell_Along_Swath | 204] x [Cell_ACross_Swath | 135]
Coordinates:
            time: [20143050010..2.426116152246728e-315]
Number Of Attributes: 3
  units :       degrees_north
  long_name :   Geodetic Latitude
  _FillValue :  -999
(0)     lat2d: min=-89.894   max=77.2616

Variable: lon2d
Type: float
Total Size: 28641600 bytes
            7160400 values
Number of Dimensions: 3
Dimensions and sizes:   [time | 260] x [Cell_Along_Swath | 204] x [Cell_ACross_Swath | 135]
Coordinates:
            time: [20143050010..2.426116152246728e-315]
Number Of Attributes: 3
  units :       degrees_east
  long_name :   Geodetic Longitude
  _FillValue :  -999
(0)     lon2d: min=-179.999   max=179.977
(0)     -----


The thing that stands out is when the NetCDF file is created, the Longitude in the file only goes from 85.1406 - 172.263 and not -179.999 - 179.977 like the varSummary states. There is an error that gets thrown during the run:

fatal:Dimension size mismatch on subscript #1, left-hand and right-hand side dimensions do not match
fatal:["Execute.c":8128]:Execute: Error occurred at or near line 71 in file modis.ncl

I have attached the image created from your script, compared to the image I get from the other script. I also reattached your script as I modified some directory things and added the libraries which shifted some of the lines. It should be noted that the information present from your script does match the data location on the image I created from a different script, it's just missing everything else.


Steve

-----Original Message-----
From: Dennis Shea [mailto:shea at ucar.edu] 
Sent: Tuesday, May 26, 2015 5:43 PM
To: BLIUJUS, STEVEN D CTR USAF AFMC AFLCMC/HBAW-OL
Cc: ncl-talk at ucar.edu
Subject: Re: [ncl-talk] Problems converting hdf to netcdf using NCL

I just looked at the 5 sample files you sent ....  

The dimension sizes are *not* the same size across all files


The 1st 4files are:


MOD04_L2.A2014305.0000.006.2015077213911.pscs_000500937810.hdf
  dimensions:
      Cell_Along_Swath = 203       <=====
      Cell_Across_Swath = 135

The last file is:

MOD04_L2.A2014305.0500.006.2015077215106.pscs_000500937810
   dimensions:
      Cell_Along_Swath = 204     <====
      Cell_Across_Swath= 135


That can be 'programmed around'.


See attached




On Tue, May 26, 2015 at 6:34 AM, BLIUJUS, STEVEN D CTR USAF AFMC AFLCMC/HBAW-OL <steven.bliujus.3.ctr at us.af.mil> wrote:


	Dennis,
	
	#2 and #3: Cell_Along_Swath, and Cell_Across_Swath are exactly the same for every file as far as actual dimension size, the variables are not though.
	#4: I am trying to create a mosaic of all the files and that is why I am wanting to generate one NetCDF file. So when I run my script the image above is what comes out. This image is what I want to create in a NetCDF file (Globe.PNG).
	#5: I did this because I was following a script online that I found where I needed to give the main variable(Optical Depth) the latitude/longitude dimensions. It used (::5) which what I just followed. When I try plotting using just (:,:), the plot take an extremely long time to plot(though there is much more data prevalent)...If it is one file it doesn’t take long, but when you add them all in the mosaic form, it takes a much more substantial amount of time to generate the image.
	#6: I'm not sure exactly what you mean by this as there is not time field in the file.
	#7: See 5 attached MODIS files
	#8: I am trying to create a NetCDF file for a coworker to use for his verification software. He only reads in NetCDF files or text files (though he would prefer NetCDF files)
	
	I also attached the script (with all previous commented lines removed) that plots the files and also creates a text table of the data.
	
	Any help would be appreciated.
	
	Steve
	
	
	
	-----Original Message-----
	From: Dennis Shea [mailto:shea at ucar.edu]
	
	Sent: Saturday, May 23, 2015 2:30 PM
	To: BLIUJUS, STEVEN D CTR USAF AFMC AFLCMC/HBAW-OL
	Cc: ncl-talk at ucar.edu
	Subject: Re: [ncl-talk] Problems converting hdf to netcdf using NCL
	
	I have looked at this and there are *lots* of issues.
	
	"... taking several hdf files (200-400) and trying to generate one NetCDF file."
	
	
	So ...  **Conceptually**, you want
	
	
	    AOT(time, Cell_Along_Swath, Cell_Across_Swath)
	
	
	Thing  is your geographic coordinates are 2-dimensional. see below
	
	
	
	
	[1]
	
	The files contain swath data. From your dump:
	
	path:   MOD04_L2.A2014306.2330.006.2015077230656.pscs_000500937810.hdf
	   file global attributes:
	      HDFEOSVersion : HDFEOS_V2.17
	      StructMetadata_0 : GROUP=SwathStructure
	        GROUP=SWATH_1
	                SwathName="mod04"
	
	
	[2] Are the dimension sizes
	
	       (Cell_Along_Swath,Cell_Across_Swath) => (203,135)
	
	
	     exactly the same for *all* files?
	
	
	[3] If [2] is satisfied  .... Are the *values* contained within the following variables
	
	       Latitude ( Cell_Along_Swath, Cell_Across_Swath)
	
	       Longitude ( Cell_Along_Swath, Cell_Across_Swath )
	
	
	      *exactly* the same for *all* files?  ie: homogeneous space!
	
	
	     My (limited) experience with satellite swath data is that the answer is "no"
	
	
	[4] If [2] *and* [3] are not satisfied, I see no advantage of creating a single netCDF file.
	
	     You would end up with 200-400 sets of dimension sizes *and* 200-400 variables
	
	     associated 200-400two-dimensional spatial variables.
	
	
	[5]  I have no idea why you are sub-sampling [decimating] the array by 5:
	       (::5,::5) the resolution from (203,135) to  ??(41,27)??. This seems drastic!
	
	      Sub-sampling (array decimation) is commonly used used when the resolution is (say) (2500,4000) and the data are reasonably smooth.
	
	
	
	[6] In any case you should be using
	
	      ListSetType(a,"join")
	
	
	     to add a record dimension ... which you should fill in with 'time'
	
	     (parse file name) or some sequential number.
	
	
	     Please read
	        https://www.ncl.ucar.edu/Document/Functions/Built-in/addfiles.shtml
	
	     Example 3 illustrates what "join" will do.
	
	
	
	[7] I do not have your ?MODIS? data file. Based upon your dump, I created a script that creates a netCDF file for each HDF file and (I hope) a sample graphic.
	
	
	[8] I am not sure of ultimate use of the data but from an NCL perspective, there is no reason to convert to netCDF.
	
	
	===========================
	
	
	Please upgrade to 6.3.0
	
	http://www.ncl.ucar.edu/Download/
	
	============================
	
	
	
	
	
	On Fri, May 22, 2015 at 9:59 AM, BLIUJUS, STEVEN D CTR USAF AFMC AFLCMC/HBAW-OL <steven.bliujus.3.ctr at us.af.mil> wrote:
	
	
	        I wanted to provide an example of what is in the hdf file. See attached.
	
	        Steve
	
	
	        -----Original Message-----
	        From: ncl-talk-bounces at ucar.edu [mailto:ncl-talk-bounces at ucar.edu] On Behalf Of BLIUJUS, STEVEN D CTR USAF AFMC AFLCMC/HBAW-OL
	        Sent: Friday, May 22, 2015 10:36 AM
	        To: ncl-talk at ucar.edu
	        Subject: [ncl-talk] Problems converting hdf to netcdf using NCL
	
	        I am taking several hdf files (200-400) and trying to generate one NetCDF file. I am able to plot it on a grid, but when I try to write to a NetCDF file, I get the following error:
	
	        fatal:Number of dimensions in parameter (2) of (filedimdef) is (2), (1) dimensions were expected
	        fatal:["Execute.c":8128]:Execute: Error occurred at or near line 82 in file File.ncl
	
	
	        The data I am creating is AOD with two dimensions (lat/lon). I am uncertain as to why it is expecting one dimension. Below is my script. FYI, the original files had to be manipulated in order to make AOD have the lat/lon dimensions. Any help would be greatly appreciated.
	
	
	        load "/home/bliujuss/ncl/lib/ncarg/nclscripts/csm/gsn_code.ncl"
	        load "/home/bliujuss/ncl/lib/ncarg/nclscripts/wrf/WRFUserARW.ncl"
	        load "/home/bliujuss/ncl/lib/ncarg/nclscripts/csm/gsn_csm.ncl"
	        load "/home/bliujuss/ncl/lib/ncarg/nclscripts/csm/shea_util.ncl"
	        begin
	
	        diri = "/home/bliujuss/Verification_data/Test/"
	        fili = systemfunc("ls "+diri+"*.hdf")
	        a = addfiles(fili,"r")
	
	        ;ListSetType(a,"cat")
	
	        var1=a[:]->Optical_Depth_Land_And_Ocean(:,:)
	        Optical_Depth_Land_And_Ocean = short2flt(var1)
	
	        var2=a[:]->Longitude(:,:)
	        Longitude=var2
	
	
	        var3 = a[:]->Latitude(:,:)
	        Latitude=var3
	
	        dims = dimsizes(Optical_Depth_Land_And_Ocean)
	        nrows = dims(0) ;203
	        npixels = dims(1) ;135
	
	        lat2d = new((/nrows,npixels/),float)
	        lon2d = new((/nrows,npixels/),float)
	
	        do i=0,npixels-1
	          lat2d(:,i) = Latitude(:,i)
	        end do
	
	        do i=0,nrows-1
	          lon2d(i,:) = Longitude(i,:)
	        end do
	
	        Optical_Depth_Land_And_Ocean at lat2d = lat2d(::5,::5) Optical_Depth_Land_And_Ocean at lon2d = lon2d(::5,::5)
	
	
	        wks = gsn_open_wks("x11","plot_aod")
	        gsn_define_colormap(wks,"NCV_banded")
	        setvalues NhlGetWorkspaceObjectId()
	          "wsMaximumSize": 300000000
	        end setvalues
	
	        res                   = True               ; plot mods desired
	        res at cnLinesOn         = False              ; turn off contour lines
	        res at cnFillOn          = True               ; color plot desired
	        res at cnLineLabelsOn    = False              ; turn off contour lines
	        res at gsnAddCyclic      = False             ; non-global data
	        res at gsnSpreadColors   = True               ; use full range of colormap
	        ;res at cnFillMode        = "RasterFill"       ; turn on raster mode
	        res at lbLabelAutoStride = True               ; nice spacing of lables
	        res at gsnMaximize       = True               ; blow up plot as much as poss
	        ;print(min(lat2d))
	        ;print(max(lat2d))
	        ;print(min(lon2d))
	        ;print(max(lon2d))
	
	        plot = gsn_csm_contour_map_ce(wks,Optical_Depth_Land_And_Ocean(::5,::5),res)
	        print(max(Optical_Depth_Land_And_Ocean(::5,::5)))
	
	        nlat = dimsizes(lat2d(::5,::5))
	        nlon = dimsizes(lon2d(::5,::5))
	
	        diro = "/home/bliujuss/Plots/"
	        filo = "example.nc"
	        system("rm -f" + diro + filo)
	        fout = addfile (diro + filo, "c")
	
	        setfileoption(fout,"DefineMode",True)
	
	        dim_names = (/"lat", "lon"/)
	        dim_sizes = (/nlat, nlon/)
	        dimUnlim = (/False, False/)
	        filedimdef(fout,dim_names,dim_sizes,dimUnlim)
	
	        filevardef(fout, "lat", typeof(lat2d(::5,::5)),getvardims(lat2d(::5,::5)))
	        filevardef(fout, "lon", typeof(lon2d(::5,::5)),getvardims(lon2d(::5,::5)))
	        filevardef(fout, "AOT", typeof(Optical_Depth_Land_And_Ocean(::5,::5)),getvardims(Optical_Depth_Land_And_Ocean(::5,::5)))
	
	        filevarattdef(fout,"AOT", Optical_Depth_Land_And_Ocean(::5,::5))
	        filevarattdef(fout,"lat", lat2d(::5,::5)) filevarattdef(fout,"lon", lon2d(::5,::5))
	
	        setfileoption(fout,"DefineMode",False)
	
	        fout->Optical_Depth_Land_And_Ocean(::5,::5) =
	
	        fout->(/Optical_Depth_Land_And_Ocean(::5,::5)/)
	
	        fout->lat2d(::5,::5) = (/lat2d(::5,::5)/)
	        fout->lon2d(::5,::5) = (/lon2d(::5,::5)/)
	
	        end
	
	
	        Steven Bliujus
	
	
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