[ncl-talk] Advice on extracting point locations from array

[Dennis Shea]

'Brain Trust' ... "great idea"  ===> Nope ... Sorry
---
IMHO:
I don't think the loop can be replaced by array operations. I'm not sure
how the underlying netCDF software would implement something like

Tprof = fi->T(pInd(*:*,0),*:*,pInd(*:*,1),pInd(*:*,2))
---

  nprofile   = ...
  nlev        = ...
  Tprof      = *new*((/*nprofile,nlev*/),float)   ; reorder from your code
  begTime = *get_cpu_time*()
  do i = 0, nprofile-1
     Tprof(i,:) = fi->T(pInd(i,0),:,pInd(i,1),pInd(i,2))    ;pInd is an
array with coord triplets
  end do

  printVarSummary(Tprof)
  printMinMax(Tprof,0)
  print("Tprof generation time: " + (*get_cpu_time*() - begTime)+" seconds;
nprofile="+nprofile)
  print("---")
---

If it takes a long time, I'd suggest saving the created variable(s) in a
netCDF file. Untested:

;------------------
;  netCDF
;-----------------
  netCDF = True
  if (netCDF) then
      profile   = *ispan*(0,nprofile-1,1)   ; or, ispan(1,nprofile,1)
      profile at long_name = "Profile Number"
      profile!0 = "profile"
      profile&profile = profile

      TIME   = fi->time(pInd(:,0))
      LAT     = fi->lat(pInd(:,1))
      LON    = fi->lon(pInd(:,2))

      Tprof!0= "profile"
      TIME!0 = "profile"
      LAT!0   = "profile"
      LON!0  = "profile"
      Tprof&profile  = profile
      TIME&profile  = profile
      LAT&profile    = profile
      LON&profile   = profile

      dir_nc  = "./"
      fil_nc   = "FOO.nc"
      pth_nc = dir_nc + fil_nc
      print(pth_nc)

      *system*("/bin/rm -f "+pth_nc)           ; remove any pre-existing
file
      ncdf = *addfile*(pth_nc ,*"c"*)            ; open output netCDF file

;===================================================================
; Create global attributes of the file (optional)
;===================================================================
       fAtt               = True            ; assign file attributes
       fAtt at title         = "Selected Profiles"
      ;fAtt at source_info   =  "..."
       fAtt at Conventions   = "None"
       fAtt at creation_date = *systemfunc *("date")
       *fileattdef(* ncdf, fAtt )            ; copy file attributes

;===================================================================
; Make profile an UNLIMITED dimension; recommended  for most applications
; Allows for future profiles to be appended
;===================================================================
       *filedimdef*f(ncdf,"profile",-1,True)

;===================================================================
; output variable(s) directly; NCL will call appropriate functions
;===================================================================
       ncdf->TIME  = TIME
       ncdf->LAT   = LAT
       ncdf->LON   = LON
       ncdf->TPROF = Tprof
  end if   ; netCDF



On Mon, Oct 15, 2018 at 11:53 PM Will Hobbs <will.hobbs at utas.edu.au> wrote:

> Hi all
>
>
>
> This one is for the NCL ‘Brains Trust’. I’m extracting a large number of
> ocean profiles from a 4-d array (dimensioned time,depth,lat,lon), using
> coordinate triplets based on time,lat and lon, (i.e. a 2-d array of indices
> dimensioned nprofile, 3),  but it’s a slow process and I wonder if anyone
> has any smart ideas on speeding it up.
>
>
>
> At the moment (partly to manage memory), I’m reading each profile in a
> loop, viz:
>
>
>
>
>
> Tprof = new((/nlev,nprofile/),float)
>
> do i = 0, nprofile-1
>
>      Tprof(:,i) = fi->T(pInd(i,0),:,pInd(i,1),pInd(i,2))    ;pInd is an
> array with coord triplets
>
> end do
>
>
>
> Obviously one obvious way of speeding things up would be to read the
> entire array of input data and extract the locations, to avoid multiple i/o
> calls. What I really want to do though is somehow get rid of the loop
> entirely. Is there any way of extracting coordinate pairs (or in this case
> triplets) without looping through each profile?
>
>
>
> The only way I can think of is to turn the input array (T in my example
> above) into a 1-d array, and somehow convert ‘pInd’ into the elements of
> that 1-d array – this seems fraught with opportunity for error though.
> Catastrophic error I can deal with – it’s the sneaky, inobvious error that
> scares me….
>
>
>
> Hoping someone has a great idea….
>
>
>
> Will
>
>
>
> University of Tasmania Electronic Communications Policy (December, 2014).
> This email is confidential, and is for the intended recipient only.
> Access, disclosure, copying, distribution, or reliance on any of it by
> anyone outside the intended recipient organisation is prohibited and may be
> a criminal offence. Please delete if obtained in error and email
> confirmation to the sender. The views expressed in this email are not
> necessarily the views of the University of Tasmania, unless clearly
> intended otherwise.
> _______________________________________________
> ncl-talk mailing list
> ncl-talk at ucar.edu
> List instructions, subscriber options, unsubscribe:
> http://mailman.ucar.edu/mailman/listinfo/ncl-talk
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.ucar.edu/pipermail/ncl-talk/attachments/20181016/ef75c92b/attachment.html>