[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 10:08:23 MDT 2015


Dennis,

Is there a default setting that loops kill after? The loop stops after 34 iterations, thus leaving out the other 226 files, which explains why there is no data anywhere else on the globe. There are so many files because we are doing a global analysis, so these are swaths through the entire day.

As far as the plots.ncl. These values do match the values given by modis.ncl as far as lat/lon/aod. So the real problem is the loop quitting early. I attached the log file I created.

Steve

-----Original Message-----
From: Dennis Shea [mailto:shea at ucar.edu] 
Sent: Wednesday, May 27, 2015 10:07 AM
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 think you have to do some debugging.

===


Look at "time":   time: [20143050010..2.426116152246728e-315]

The last time is obviously wrong! How did this happen? 

It did not happen with the 5 sample files ... why with all the files?


Each iteration thru the loop .... print the current 'time' value. 


Also ... after the loop is complete ... 


print(time)   ; print all values


This issue must be cleared up!


If 'time' is messed up ... what about other variables?


-------


In the code that reads/plots the netCDF ... did you do any debugging?? 

    diri  = "./"
    fili  = "MODIS_L2.Swath.nc"
    f     = addfile(diri+fili, "r")


    print(f)


    AOT = f->AOT

    printVarSummary(AOT)

    printMinMax(AOT,0)


   lat2d = f->LAT2D

   printVarSummary(LAT2D)

   printMinMax(lat2d,0)


   lon2d = f->LON2D

   printVarSummary(lon2d)
   printMinMax(lon2d,0)


Do these not match the original created values


--------

Minor: the dimension name "Cell_ACross_Swath"  should be "Cell_Across_Swath" 


On Wed, May 27, 2015 at 8:34 AM, BLIUJUS, STEVEN D CTR USAF AFMC AFLCMC/HBAW-OL <steven.bliujus.3.ctr at us.af.mil> wrote:


	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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