[ncl-talk] Data conversion

Adam Phillips asphilli at ucar.edu
Fri Feb 5 09:54:46 MST 2016


That error message is indicating that your workstation (=output graphic) is
going over your current limit of 100MB in size. In your .hluresfile
(usually located in your default home directory), try increasing your
wsMaximumSize to 500000000:

*wsMaximumSize : 500000000

For more information:
https://www.ncl.ucar.edu/Document/Graphics/hlures.shtml


On Fri, Feb 5, 2016 at 9:16 AM, HAVENER, KEVIN F GS-12 USAF ACC 14 WS/WXED <
kevin.havener at us.af.mil> wrote:

> I had trouble here, too.  If the end goal is to get a netcdf, just comment
> out the plotting part.
>
> Kevin Havener, DAFC, 14WS/WXED
> Comm 828-271-4323; DSN 673-9044
> NIPRNet kevin.havener at us.af.mil
> SIPRNet kevin.f.havener.civ at mail.smil.mil
>
> -----Original Message-----
> From: Benjamin Alabi [mailto:alabibenjamin2 at gmail.com]
> Sent: Friday, February 05, 2016 11:08 AM
> To: Adam Phillips
> Cc: HAVENER, KEVIN F GS-12 USAF ACC 14 WS/WXED; ncl-talk at ucar.edu
> Subject: Re: [ncl-talk] Data conversion
>
> Thanks Sir,
>
> After arranging it like this
> load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_code.ncl"
> load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_csm.ncl"
> load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/contributed.ncl"
> load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl"
>
>
> I get this error:
>
>
> fatal:ContourPlotDraw: Workspace reallocation would exceed maximum size
> 100000000
> fatal:ContourPlotDraw: draw error
> warning:WorkstationDeactivate: workstation not active or not opened
>
>
>
> On Fri, Feb 5, 2016 at 4:57 PM, Adam Phillips <asphilli at ucar.edu> wrote:
>
>
>         I'll second the call that you should upgrade to the newest version
> of ncl (v6.3.0). I think your current error is occurring due to you loading
> shea_util before contributed. Try loading the files in this order:
>         load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_code.ncl"
>         load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_csm.ncl"
>         load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/contributed.ncl"
>         load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl"
>
>
>
>         If that doesn't work let ncl-talk know..
>         Adam
>
>         On Fri, Feb 5, 2016 at 8:21 AM, HAVENER, KEVIN F GS-12 USAF ACC 14
> WS/WXED <kevin.havener at us.af.mil> wrote:
>
>
>                 Which version of ncl are you running?
>
>                 Kevin Havener
>
>                 -----Original Message-----
>                 From: Benjamin Alabi [mailto:alabibenjamin2 at gmail.com]
>                 Sent: Friday, February 05, 2016 10:09 AM
>                 To: HAVENER, KEVIN F GS-12 USAF ACC 14 WS/WXED
>                 Cc: alesall; ncl-talk at ucar.edu
>                 Subject: Re: [ncl-talk] Data conversion
>
>                 Thanks alot for your assistance.
>
>
>                 I added the following before ' Begin' as you have
> instructed me load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_code.ncl"
>                 load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_csm.ncl"
>                 load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl"
>                 load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/contributed.ncl"
>
>
>                 After running it, it's generated the following error:
>
>
>                 fatal:syntax error: line 3232 in file
> $NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl before or near \n
>                   copy_VarCoords(x, advect)
>                 ---------------------------^
>
>                 fatal:syntax error: possibly an undefined procedure
> fatal:Syntax Error in block, block not executed fatal:error at line 3255 in
> file $NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl
>
>                 fatal:syntax error: line 3364 in file
> $NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl before or near \n
>                   copy_VarCoords(X, Xdp)
>                 ------------------------^
>
>                 fatal:syntax error: possibly an undefined procedure
> fatal:Syntax Error in block, block not executed fatal:error at line 3400 in
> file $NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl
>
>                 fatal:syntax error: line 3478 in file
> $NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl before or near \n
>                   copy_VarCoords(t, theta)
>                 --------------------------^
>
>                 fatal:syntax error: possibly an undefined procedure
> fatal:Syntax Error in block, block not executed fatal:error at line 3482 in
> file $NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl
>
>                 fatal:syntax error: line 3573 in file
> $NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl before or near \n
>                   copy_VarCoords(t,s)
>                 ---------------------^
>
>                 fatal:syntax error: possibly an undefined procedure
> fatal:Syntax Error in block, block not executed fatal:error at line 3576 in
> file $NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl
>
>                 fatal:syntax error: line 3666 in file
> $NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl before or near \n
>                   copy_VarCoords(t, theta)
>                 --------------------------^
>
>                 fatal:syntax error: possibly an undefined procedure
> fatal:syntax error: line 3706 in file
> $NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl before or near \n
>                   copy_VarCoords(t,pv)
>                 ----------------------^
>
>                 fatal:syntax error: possibly an undefined procedure
> fatal:Syntax Error in block, block not executed fatal:error at line 3709 in
> file $NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl
>
>                 fatal:syntax error: line 3802 in file
> $NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl before or near \n
>                   copy_VarCoords(t, theta)
>                 --------------------------^
>
>                 fatal:syntax error: possibly an undefined procedure
> fatal:syntax error: line 3813 in file
> $NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl before or near \n
>                   copy_VarCoords(t,s)
>                 ---------------------^
>
>                 fatal:syntax error: possibly an undefined procedure
> fatal:syntax error: line 3852 in file
> $NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl before or near \n
>                   copy_VarCoords(t,pv)
>                 ----------------------^
>
>                 fatal:syntax error: possibly an undefined procedure
> fatal:Syntax Error in block, block not executed fatal:error at line 3855 in
> file $NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl
>
>                 fatal:syntax error: line 4205 in file
> $NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl before or near \n
>                       copy_VarCoords(runs(0,:,:), maxrun)
> -----------------------------------------^
>
>                 fatal:syntax error: possibly an undefined procedure
> fatal:Syntax Error in block, block not executed fatal:error at line 4210 in
> file $NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl
>
>                 fatal:syntax error: line 4254 in file
> $NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl before or near \n
>                   copy_VarCoords(t, dthdz)
>                 --------------------------^
>
>                 fatal:syntax error: possibly an undefined procedure
> fatal:syntax error: line 4261 in file
> $NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl before or near \n
>                   copy_VarCoords(u, brunt)
>                 --------------------------^
>
>                 fatal:syntax error: possibly an undefined procedure
> fatal:syntax error: line 4267 in file
> $NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl before or near \n
>                   copy_VarCoords(u, dudz)
>                 -------------------------^
>
>                 fatal:syntax error: possibly an undefined procedure
> fatal:syntax error: line 4273 in file
> $NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl before or near \n
>                   copy_VarCoords(v, dvdz)
>                 -------------------------^
>
>                 fatal:syntax error: possibly an undefined procedure
> fatal:syntax error: line 4279 in file
> $NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl before or near \n
>                   copy_VarCoords(u, Ri)
>                 -----------------------^
>
>                 fatal:syntax error: possibly an undefined procedure
> fatal:Syntax Error in block, block not executed fatal:error at line 4284 in
> file $NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl
>
>                 fatal:ContourPlotDraw: Workspace reallocation would exceed
> maximum size 100000000
>                 fatal:ContourPlotDraw: draw error
>                 warning:WorkstationDeactivate: workstation not active or
> not opened
>
>
>                 On Fri, Feb 5, 2016 at 3:15 PM, HAVENER, KEVIN F GS-12
> USAF ACC 14 WS/WXED <kevin.havener at us.af.mil> wrote:
>
>
>                         And you don't want to try to add 75.0 to the fill
> value in the script.
>
>                         Kevin Havener
>
>                         -----Original Message-----
>                         From: ncl-talk-bounces at ucar.edu [mailto:
> ncl-talk-bounces at ucar.edu] On Behalf Of alesall
>                         Sent: Friday, February 05, 2016 9:03 AM
>                         To: Benjamin Alabi
>                         Cc: ncl-talk at ucar.edu
>                         Subject: Re: [ncl-talk] Data conversion
>
>
>                         the error message is:
>
>                         fatal:Undefined identifier: (byte2flt) is
> undefined, can't continue
>
>                         it is not finding the function “byte2flt"
>                         on the documentation page, this one: <
> http://ncl.ucar.edu/Document/Functions/Contributed/byte2flt.shtml>
>                         it says that such function is in the “contributed”
> file.
>
>                         you need to add statements such as:
>                         load
> "$NCARG_ROOT/lib/ncarg/nclscripts/csm/contributed.ncl <
> http://ncl.ucar.edu/Document/Functions/Contributed/contrib.shtml> "
>
>                         at the beginning of your script, actually before
> the “begin”
>
>                         I have all of these in my scripts:
>
>                         load
> "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_code.ncl"
>                         load
> "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_csm.ncl"
>                         load
> "$NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl"
>                         load
> "$NCARG_ROOT/lib/ncarg/nclscripts/csm/contributed.ncl"
>
>                         hope this helps!
>
>
>
>                         --
>                         Alessandra Giannini
>                         IRI for Climate and Society - The Earth Institute
> at Columbia University P.O. Box 1000, Palisades NY 10964-8000
>                         phone/fax: +1 845 680-4473
> <tel:%2B1%20845%20680-4473> /4864 - email: alesall at iri.columbia.edu
>
>
>                                 On Feb 5, 2016, at 8:57 AM, Benjamin Alabi
> <alabibenjamin2 at gmail.com> wrote:
>
>                                 Goodday sir,
>
>                                 I appreciate your effort in guiding me.
> I'm new in this platform, please dont be offended by sending the message
> three times, I'm just learning to get help from here.
>
>                                 I used the script,
>                                 begin
>                                 file_name_read = "merg_2012090101
> _4km-pixel"
>
>                                 ir_u = byte2flt( fbindirread
> (file_name_read ,0, (/2,3298,9896/),"ubyte")) +75.0
>
>
>                                 lon_g = fspan(0.0182,360,9896)
>                                 lat_g =
> fspan(59.982,59.982-0.036383683*3298,3298)
>
>                                 lon_g at units      = "degrees_east"
>                                 lon_g at long_name  = "longitude"
>                                 lon_g at short_name = "longitude"
>                                 lon_g!0 = "lon"
>                                 lon_g&lon = lon_g
>
>                                 lat_g at units      = "degrees_north"
>                                 lat_g at long_name  = "latitude"
>                                 lat_g at short_name = "latitude"
>                                 lat_g!0 = "lat"
>                                 lat_g&lat = lat_g
>
>
>                                 ir_u!0      = "time"
>                                 ir_u!1      = "lat"
>                                 ir_u!2      = "lon"
>
>                                 ir_u&lat    = lat_g
>                                 ir_u&lon    = lon_g
>
>                                 ir_u at _FillValue= 255+75.0
>
>
>                                 wks = gsn_open_wks("X11","")
>                                 res = True
>                                 res at cnFillOn = True
>                                 res at cnFillMode = "RasterFill"
>                                 res at cnLinesOn = False
>                                 plot = gsn_csm_contour_map(wks,
> ir_u(0,:,:), res)
>
>                                 ncout = addfile(file_name_read+".nc","c")
>                                 ncout->ir_data = ir_u
>
>                                 end
>
>
>                                 But it was generating this error:
>                                 fatal:Undefined identifier: (byte2flt) is
> undefined, can't continue
>                                 fatal:["Execute.c":7741]:Execute: Error
> occurred at or near line 41
>
>
>                                 Waiting for guide, Thanks.
>
>
>
>                                 On Thu, Feb 4, 2016 at 8:07 PM, Alan
> Brammer <abrammer at albany.edu> wrote:
>
>
>                                         Forgot the offset, which is
> mentioned in the link Kevin sent.
>
>
>                                         ir_u = byte2flt( fbindirread
> (file_name_read ,0, (/2,3298,9896/),"ubyte")) +75.
>                                         ir_u at _FillValue= 255+75.
>
>                                         "Each record is a 9896 x 3298
> Fortran array of IR brightness temperatures that have been scaled to fit
> into 1-byte by subtracting "75" from each datum. Therefore it is necessary
> for the user to add a value of "75" to each data value when using the data."
>
>
>
>                                                 On 4 Feb 2016, at 13:30,
> Alan Brammer <abrammer at albany.edu> wrote:
>
>                                                 ok, wow. Don’t send the
> same message 3 times, if the first answers weren’t complete at least expand
> and attempt something not just copy paste the same lines again.
>
>                                                 as said before .Z means
> it’s compressed.  gunzip merg_2016020123_4km-pixel.Z  will uncompress it.
> Then you have a binary file as a small amount of googling would have told
> you.
>                                                 The same search would have
> linked you to various messages on here and various scripts where other
> people have included simple examples of this file type (myself included).
> Here is an example of reading and making a simple plot.  There are plenty
> of examples on how to write netcdf on the NCL website so you should develop
> code from there.  Most simple example at bottom of script below.
>
> https://www.ncl.ucar.edu/Applications/o-netcdf.shtml
>
>                                                 Read the documentation on
> the below functions and understand what is occurring .
>
>
>                                                 begin
>                                                 file_name_read = "merg_
> 2016020123_4km-pixel"
>
>                                                 ir_u = byte2flt(
> fbindirread (file_name_read ,0, (/2,3298,9896/),"ubyte"))
>
>
>                                                 lon_g =
> fspan(0.0182,360,9896)
>                                                 lat_g =
> fspan(59.982,59.982-0.036383683*3298,3298)
>
>                                                 lon_g at units      =
> "degrees_east"
>                                                 lon_g at long_name  =
> "longitude"
>                                                 lon_g at short_name =
> "longitude"
>                                                 lon_g!0 = "lon"
>                                                 lon_g&lon = lon_g
>
>                                                 lat_g at units      =
> "degrees_north"
>                                                 lat_g at long_name  =
> "latitude"
>                                                 lat_g at short_name =
> "latitude"
>                                                 lat_g!0 = "lat"
>                                                 lat_g&lat = lat_g
>
>
>                                                 ir_u!0      = "time"
>                                                 ir_u!1      = "lat"
>                                                 ir_u!2      = "lon"
>
>                                                 ir_u&lat    = lat_g
>                                                 ir_u&lon    = lon_g
>
>                                                 ir_u at _FillValue= 255
>
>
>                                                 wks =
> gsn_open_wks("X11","")
>                                                 res = True
>                                                 res at cnFillOn = True
>                                                 res at cnFillMode =
> "RasterFill"
>                                                 res at cnLinesOn = False
>                                                 plot =
> gsn_csm_contour_map(wks, ir_u(0,:,:), res)
>
>                                                 ncout =
> addfile(file_name_read+”.nc”,”c”)
>                                                 ncout->ir_data = ir_u
>
>                                                 end
>
>
>
>
>
>
>                                                         On 4 Feb 2016, at
> 13:04, Benjamin Alabi <alabibenjamin2 at gmail.com> wrote:
>
>                                                         Thanks for your
> assistance sir. I've tried the cdo to get general information on the data,
> but it didn't work
>                                                         I need help from
> someone that can guide me to convert this data format - 'merg_2012091000_4km-pixel.Z'
> to netcdf format.
>                                                         I download
> Gobally-merged (60N-60S) pixel-resolution IR brightness temperature data
> (equivalent blackbody temps), merged from all available geostationary
> satellites (GOES-8/10, METEOSAT-7/5)
>                                                         This is the link:
>
> http://mirador.gsfc.nasa.gov/cgi-bin/mirador/presentNavigation.pl?tree=project&dataset=Global-merged%20IR%20Brightness%20Temperature%20Data&project=TRMM&dataGroup=Ancillary&version=001&CGISESSID=25c6337b80163b3743e8bea85d015558
> .
>
>                                                         I really want it
> to be in netcdf format.
>
>
>                                                         Regard
>
>
>
>
>
> _______________________________________________
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>
>
>
>
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>
>
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>
>
>
>
>         --
>
>         Adam Phillips
>
>         Associate Scientist,  Climate and Global Dynamics Laboratory, NCAR
>
>         www.cgd.ucar.edu/staff/asphilli/   303-497-1726
>
>
>
>         <http://www.cgd.ucar.edu/staff/asphilli>
>
>
> _______________________________________________
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-- 
Adam Phillips
Associate Scientist,  Climate and Global Dynamics Laboratory, NCAR
www.cgd.ucar.edu/staff/asphilli/   303-497-1726

<http://www.cgd.ucar.edu/staff/asphilli>
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