[ncl-talk] segfault error with wavelet function.

Rick Brownrigg brownrig at ucar.edu
Tue Apr 18 10:04:38 MDT 2017 

Hi,

It appears to work for me; if I uncomment the printVarSummary(w), I get the
output below. Do the values look reasonable?   Which version of NCL are you
using? Perhaps an upgrade to v6.4.0 would solve the issue

Rick

$ ncl foo.ncl
 Copyright (C) 1995-2017 - All Rights Reserved
 University Corporation for Atmospheric Research
 NCAR Command Language Version 6.4.1
 The use of this software is governed by a License Agreement.
 See http://www.ncl.ucar.edu/ for more details.


Variable: ntime
Type: integer
Total Size: 4 bytes
            1 values
Number of Dimensions: 1
Dimensions and sizes:    [1]
Coordinates:
(0)    504

Variable: w
Type: float
Total Size: 145152 bytes
            36288 values
Number of Dimensions: 3
Dimensions and sizes:    [2] x [36] x [504]
Coordinates:
Number Of Attributes: 15
  psi0 :    0.7511256
  cdelta :    0.776
  lag1 :    0.7689273
  stdev :    0.7335985
  mean :    -4.20585e-09
  r1 :    0.7689273
  phase :    <ARRAY of 18144 elements>
  power :    <ARRAY of 18144 elements>
  gws :    <ARRAY of 36 elements>
  signif :    <ARRAY of 36 elements>
  fft_theor :    <ARRAY of 36 elements>
  dof :    <ARRAY of 36 elements>
  coi :    <ARRAY of 504 elements>
  period :    <ARRAY of 36 elements>
  scale :    <ARRAY of 36 elements>


On Tue, Apr 18, 2017 at 9:39 AM, Dipti Sharma <sdipti596 at gmail.com> wrote:

> Dear All,
>
> I am trying to understand how to do the wavelet analysis and started using
> an example code and the data available online. But I got an error message
> as "segmentation fault (core dumped)" when I ran the program. I have given
> the code that I used as below for you to review. Also I have attached the
> data I used in the email.
>
> So, could you please suggest me how I solve this problem?
>
> Thanks in advance.
>
> THE CODE is here and the data is attached in the email,
>
>  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"
>  load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl"
>
> ;--------------------------------------------------------------------
> ; CREATE SAME WAVELET FIGURE AS TORRENCE & COMPO using seasonal Nino3
> ; from 1871-1997
> begin
> ninoseas = asciiread("C:\diptic\sst\sst_nino3.dat",-1,"float")
>   ninoseas!0 = "time"
>   ntime = dimsizes(ninoseas)
>   timeo = fspan(1871.25,1996.,ntime)
>   print(ntime)
>   ninoseas&time = timeo
>   ninomam = dim_avg_Wrap(ninoseas(0::4))
>   ninojja = dim_avg_Wrap(ninoseas(1::4))
>   ninoson = dim_avg_Wrap(ninoseas(2::4))
>   ninodjf = dim_avg_Wrap(ninoseas(3::4))
>   ninoseas(0::4) = ninoseas(0::4) - ninomam
>   ninoseas(1::4) = ninoseas(1::4) - ninojja
>   ninoseas(2::4) = ninoseas(2::4) - ninoson
>   ninoseas(3::4) = ninoseas(3::4) - ninodjf
>   time  = timeo
>   N     = dimsizes(time)
> ;_FillValue=1e+36
> ;printMinMax(ninoseas,False)
> ;return
> ;************************************
> ; compute wavelet
> ;************************************
>   mother  = 0
>   param   = 6.0
>   dt      = 0.25    ;timesteps in units of years
>   s0      = dt
>   dj      = 0.25
>   jtot    = 1+floattointeger(((log10(N*dt/s0))/dj)/log10(2.))
>   npad    = N
>   nadof   = 0.0
>   noise   = 1
>   siglvl  = 0.05
>   isigtest= 0
> ;print(nadof)
> w =wavelet(ninoseas,mother,dt,param,s0,dj,jtot,npad,noise,
> isigtest,siglvl,nadof)
> ;printVarSummary(w)
> return
> end
> segmentation fault (core dumped)
>
> On Tue, Apr 18, 2017 at 3:29 AM, <ncl-talk-request at ucar.edu> wrote:
>
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>> Today's Topics:
>>
>>    1. Re: Problem with gsn_add_text (Stavros Dafis)
>>    2. Problem with contour plot (Guilherme Martins)
>>    3. Re: Problem with gsn_add_text (Rick Brownrigg)
>>    4. Re: Problem with contour plot (Mary Haley)
>>    5. how to draw this kind of plot (wen)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Mon, 17 Apr 2017 21:48:31 +0300
>> From: Stavros Dafis <sdafis at cc.uoi.gr>
>> Subject: Re: [ncl-talk] Problem with gsn_add_text
>> To: Rick Brownrigg <brownrig at ucar.edu>
>> Cc: "ncl-talk at ucar.edu" <ncl-talk at ucar.edu>
>> Message-ID: <1492454911.58f50dffc9203 at webmail.uoi.gr>
>> Content-Type: text/plain; charset=ISO-8859-7
>>
>> Dear Rick, thank you for your suggestion, I have tried to assign both the
>> FillValue and the missing value (@missing_value) but nothing seems to
>> work.
>>
>> I forgot to mention that I am using NCL 6.2.0, 6.3.0 and 6.4.0, on
>> different
>> machines.
>>
>>
>> --
>> Stavros NTAFIS (DAFIS)
>> -----------------------------------------------
>> Physicist - Meteorologist, M.Sc.
>> Research Associate, National Observatory of Athens
>> (+33)9 81 94 22 12 <+33%209%2081%2094%2022%2012>, Mobile: +30 697 04 20
>> 242
>> ---------------
>> Weather charts:
>> http://www.meteo.gr
>> http://www.meteo.gr/meteomaps/
>>
>>
>> Quoting Rick Brownrigg <brownrig at ucar.edu>:
>>
>> > Hi Stavros,
>> >
>> > I don't know for certain, but I suspect you need to assign the
>> _FillValue
>> > to the string array "points" that you constructed from "t2" (I don't see
>> > how the attributes from t2 would carry to points via the sprintf() ).
>> >
>> > Hope that helps...
>> > Rick
>> >
>> > On Sun, Apr 16, 2017 at 12:56 PM, Stavros Dafis <sdafis at cc.uoi.gr>
>> wrote:
>> >
>> > > Hello everyone, I am facing a problem with the function gsn_add_text.
>> In
>> > > the
>> > > description of the function, it is mentioned that no missing values
>> will be
>> > > plotted:
>> > >
>> > > &#8220;This function attaches a list of text strings to the given
>> plot.
>> > > The text
>> > > strings will be drawn only when the plot is drawn. If a missing value
>> is
>> > > encountered in the text strings or x/y values, then no text string
>> will be
>> > > drawn at this pair.&#8221;
>> > >
>> > > My script reads a netCDF file with 3 variables t2(lat,lon), lat(lat),
>> > > lon(lon),
>> > > so in order to attach values on the plot using this function, I have
>> to
>> > > make
>> > > new 2-D variables for lat/lon and define the string to be plotted on
>> the
>> > > map.
>> > > Values are assigned just fine on the plot, over the land, but missing
>> > > values
>> > > are also printed over the sea. I tried to use landsea masking but my
>> data
>> > > have
>> > > high horizontal resolution (5km). Any suggestions?
>> > >
>> > > I have the same problem with WRF data, with already 2-D lat/lon
>> arrays.
>> > >
>> > >  This is the part of the code which prints the values:
>> > > .
>> > > .
>> > > .
>> > > contour = gsn_csm_contour_map(wks,t2,res)
>> > >
>> > > t2 at missing_value = -1
>> > > t2 at _FillValue = -1
>> > > (default missing values = -999)
>> > >
>> > > lat2 = new(dimsizes(t2),typeof(lat),-1)
>> > > lon2 = new(dimsizes(t2),typeof(lon),-1)
>> > >
>> > > nb = dimsizes(t2)
>> > >
>> > > do nl=0,nb(0)-1,1
>> > > do ml=0,nb(1)-1,1
>> > >
>> > > lat2(nl,ml) = lat(nl)
>> > > lon2(nl,ml) = lon(ml)
>> > >
>> > > end do
>> > > end do
>> > >
>> > > points = sprintf("%3.0f", t2)
>> > > ;points = ""+t2(:,:)+""
>> > >
>> > > values = gsn_add_text(wks,contour,points,lon2(:,:),lat2(:,:),True)
>> > >
>> > >
>> > >
>> > > --
>> > > Stavros NTAFIS (DAFIS)
>> > > -----------------------------------------------
>> > > Physicist - Meteorologist, M.Sc.
>> > > Research Associate, National Observatory of Athens
>> > > (+33)9 81 94 22 12 <+33%209%2081%2094%2022%2012>, Mobile: +30 697 04
>> 20 242
>> > > ---------------
>> > > Weather charts:
>> > > http://www.meteo.gr
>> > > http://www.meteo.gr/meteomaps/
>> > >
>> > >
>> > >
>> > > _______________________________________________
>> > > ncl-talk mailing list
>> > > ncl-talk at ucar.edu
>> > > List instructions, subscriber options, unsubscribe:
>> > > http://mailman.ucar.edu/mailman/listinfo/ncl-talk
>> > >
>> >
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Mon, 17 Apr 2017 19:00:02 +0000
>> From: Guilherme Martins <jgmsantos at gmail.com>
>> Subject: [ncl-talk] Problem with contour plot
>> To: NCL <ncl-talk at ucar.edu>
>> Message-ID:
>>         <CAH+t_hMaRUDHM0wMkLC9cz2pFmMYGXgGC+X+bcxDLo=+8fgWQg at mail.
>> gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Dear users,
>>
>> After searching extensively on the NCL website I was not able to find a
>> solution to my problem. I only want values within the contour of the
>> continent, but some edges appear in the figure that are stemming from the
>> mask that I applied and I do not know how to remove this. The figure is
>> attached for a better view of my problem.
>>
>> Best regards,
>>
>> Guilherme.
>> --
>> ------------------------------------------------------------
>> ------------------------------------
>> Instituto Nacional de Pesquisas Espaciais (INPE)
>> Centro de Previs?o de Tempo e Estudos Clim?ticos (CPTEC)
>> Divis?o de Sat?lites e Sistemas Ambientais (DSA)
>> Programa de Monitoramento de Queimadas
>> Telefone (INPE/CP): +55 12 3186-9205 || Celular (TIM): +55 12 98111-4292
>> E-mail: guilherme.martins at inpe.br || jgmsantos at gmail.com
>> Skype: guilherme.martins.
>> Homepage: https://sites.google.com/site/jgmsantos
>> Curr?culo Lattes: http://lattes.cnpq.br/5997657584785803
>> ------------------------------------------------------------
>> ------------------------------------
>> -------------- next part --------------
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>> ------------------------------
>>
>> Message: 3
>> Date: Mon, 17 Apr 2017 14:32:43 -0600
>> From: Rick Brownrigg <brownrig at ucar.edu>
>> Subject: Re: [ncl-talk] Problem with gsn_add_text
>> To: Stavros Dafis <sdafis at cc.uoi.gr>
>> Cc: "ncl-talk at ucar.edu" <ncl-talk at ucar.edu>
>> Message-ID:
>>         <CAGKRhbHX1v-1sJ3G=QrXGA+0wSJ2KKsBB_7GqbCnp9krh9fkkQ at mail.
>> gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Hi,
>>
>> You used -1 as _FillValue for variable "t2". Note it is an integer value
>> --
>> what type is the array t2 -- float or int?  In any case, you created the
>> formatted string array "points" from t2 as "%3.0f", so that any data
>> values
>> in t2 that were -1 are now " -1", and thus it seems your _FillValue should
>> be " -1". Did you do this, and do the types between data and _FillValue
>> agree everywhere?
>>
>> If that's not the issue, I think we may need to see script and dataset to
>> figure out what the issue is.
>>
>> HTH...
>> Rick
>>
>> On Mon, Apr 17, 2017 at 12:48 PM, Stavros Dafis <sdafis at cc.uoi.gr> wrote:
>>
>> > Dear Rick, thank you for your suggestion, I have tried to assign both
>> the
>> > FillValue and the missing value (@missing_value) but nothing seems to
>> work.
>> >
>> > I forgot to mention that I am using NCL 6.2.0, 6.3.0 and 6.4.0, on
>> > different
>> > machines.
>> >
>> >
>> > --
>> > Stavros NTAFIS (DAFIS)
>> > -----------------------------------------------
>> > Physicist - Meteorologist, M.Sc.
>> > Research Associate, National Observatory of Athens
>> > (+33)9 81 94 22 12 <+33%209%2081%2094%2022%2012>, Mobile: +30 697 04
>> 20 242
>> > ---------------
>> > Weather charts:
>> > http://www.meteo.gr
>> > http://www.meteo.gr/meteomaps/
>> >
>> >
>> > Quoting Rick Brownrigg <brownrig at ucar.edu>:
>> >
>> > > Hi Stavros,
>> > >
>> > > I don't know for certain, but I suspect you need to assign the
>> _FillValue
>> > > to the string array "points" that you constructed from "t2" (I don't
>> see
>> > > how the attributes from t2 would carry to points via the sprintf() ).
>> > >
>> > > Hope that helps...
>> > > Rick
>> > >
>> > > On Sun, Apr 16, 2017 at 12:56 PM, Stavros Dafis <sdafis at cc.uoi.gr>
>> > wrote:
>> > >
>> > > > Hello everyone, I am facing a problem with the function
>> gsn_add_text.
>> > In
>> > > > the
>> > > > description of the function, it is mentioned that no missing values
>> > will be
>> > > > plotted:
>> > > >
>> > > > &#8220;This function attaches a list of text strings to the given
>> plot.
>> > > > The text
>> > > > strings will be drawn only when the plot is drawn. If a missing
>> value
>> > is
>> > > > encountered in the text strings or x/y values, then no text string
>> > will be
>> > > > drawn at this pair.&#8221;
>> > > >
>> > > > My script reads a netCDF file with 3 variables t2(lat,lon),
>> lat(lat),
>> > > > lon(lon),
>> > > > so in order to attach values on the plot using this function, I
>> have to
>> > > > make
>> > > > new 2-D variables for lat/lon and define the string to be plotted on
>> > the
>> > > > map.
>> > > > Values are assigned just fine on the plot, over the land, but
>> missing
>> > > > values
>> > > > are also printed over the sea. I tried to use landsea masking but my
>> > data
>> > > > have
>> > > > high horizontal resolution (5km). Any suggestions?
>> > > >
>> > > > I have the same problem with WRF data, with already 2-D lat/lon
>> arrays.
>> > > >
>> > > >  This is the part of the code which prints the values:
>> > > > .
>> > > > .
>> > > > .
>> > > > contour = gsn_csm_contour_map(wks,t2,res)
>> > > >
>> > > > t2 at missing_value = -1
>> > > > t2 at _FillValue = -1
>> > > > (default missing values = -999)
>> > > >
>> > > > lat2 = new(dimsizes(t2),typeof(lat),-1)
>> > > > lon2 = new(dimsizes(t2),typeof(lon),-1)
>> > > >
>> > > > nb = dimsizes(t2)
>> > > >
>> > > > do nl=0,nb(0)-1,1
>> > > > do ml=0,nb(1)-1,1
>> > > >
>> > > > lat2(nl,ml) = lat(nl)
>> > > > lon2(nl,ml) = lon(ml)
>> > > >
>> > > > end do
>> > > > end do
>> > > >
>> > > > points = sprintf("%3.0f", t2)
>> > > > ;points = ""+t2(:,:)+""
>> > > >
>> > > > values = gsn_add_text(wks,contour,points,lon2(:,:),lat2(:,:),True)
>> > > >
>> > > >
>> > > >
>> > > > --
>> > > > Stavros NTAFIS (DAFIS)
>> > > > -----------------------------------------------
>> > > > Physicist - Meteorologist, M.Sc.
>> > > > Research Associate, National Observatory of Athens
>> > > > (+33)9 81 94 22 12 <+33%209%2081%2094%2022%2012>, Mobile: +30 697
>> 04 20 242
>> > > > ---------------
>> > > > Weather charts:
>> > > > http://www.meteo.gr
>> > > > http://www.meteo.gr/meteomaps/
>> > > >
>> > > >
>> > > >
>> > > > _______________________________________________
>> > > > ncl-talk mailing list
>> > > > ncl-talk at ucar.edu
>> > > > List instructions, subscriber options, unsubscribe:
>> > > > http://mailman.ucar.edu/mailman/listinfo/ncl-talk
>> > > >
>> > >
>> >
>> -------------- next part --------------
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>>
>> ------------------------------
>>
>> Message: 4
>> Date: Mon, 17 Apr 2017 15:02:08 -0600
>> From: Mary Haley <haley at ucar.edu>
>> Subject: Re: [ncl-talk] Problem with contour plot
>> To: Guilherme Martins <jgmsantos at gmail.com>
>> Cc: NCL <ncl-talk at ucar.edu>
>> Message-ID:
>>         <CACNN_CJz1yvpMXMABZ8FhSEov1T0qN63rzsNBBVXBhLos3UKjg at mail.
>> gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Guilherme,
>>
>> Please see examples shapefiles_21.ncl at:
>>
>> http://www.ncl.ucar.edu/Applications/shapefiles.shtml#ex21
>>
>> It explains why you see these "blocky" contours in NCL.
>>
>> Simply put, if you have four points that represent a box at the edge of a
>> domain, and three of them have data one them and one is missing, then NCL
>> will only draw contours in half of the box, because it won't extrapolate
>> to
>> that missing point.
>>
>> The real question is: do you simply want the graphics not to have gaps, or
>> do you actually want there to be data in locations that fall just outside
>> the geographical boundary?  You can do things to force values just outside
>> the geographical boundary, but this depends on how you are masking in the
>> first place.
>>
>> If you are masking based on a shapefile, then see example
>> shapefiles_18.ncl
>> on the same page:
>>
>> http://www.ncl.ucar.edu/Applications/shapefiles.shtml#ex18
>>
>> Note, however, that this mask is now returning values outside the range of
>> interest.
>>
>> If you are simply trying to mask your data *graphically* by some
>> geographical area, then instead of trying to use a mask function, you can
>> draw the full data, and then draw polygons filled in with white in the
>> areas you don't want to see graphically.  That's what example 21 is
>> showing.
>>
>> --Mary
>>
>>
>> On Mon, Apr 17, 2017 at 1:00 PM, Guilherme Martins <jgmsantos at gmail.com>
>> wrote:
>>
>> > Dear users,
>> >
>> > After searching extensively on the NCL website I was not able to find a
>> > solution to my problem. I only want values within the contour of the
>> > continent, but some edges appear in the figure that are stemming from
>> the
>> > mask that I applied and I do not know how to remove this. The figure is
>> > attached for a better view of my problem.
>> >
>> > Best regards,
>> >
>> > Guilherme.
>> > --
>> > ------------------------------------------------------------
>> > ------------------------------------
>> > Instituto Nacional de Pesquisas Espaciais (INPE)
>> > Centro de Previs?o de Tempo e Estudos Clim?ticos (CPTEC)
>> > Divis?o de Sat?lites e Sistemas Ambientais (DSA)
>> > Programa de Monitoramento de Queimadas
>> > Telefone (INPE/CP): +55 12 3186-9205 <+55%2012%203186-9205> || Celular
>> > (TIM): +55 12 98111-4292 <+55%2012%2098111-4292>
>> > E-mail: guilherme.martins at inpe.br || jgmsantos at gmail.com
>> > Skype: guilherme.martins.
>> > Homepage: https://sites.google.com/site/jgmsantos
>> > Curr?culo Lattes: http://lattes.cnpq.br/5997657584785803
>> > ------------------------------------------------------------
>> > ------------------------------------
>> >
>> > _______________________________________________
>> > ncl-talk mailing list
>> > ncl-talk at ucar.edu
>> > List instructions, subscriber options, unsubscribe:
>> > http://mailman.ucar.edu/mailman/listinfo/ncl-talk
>> >
>> >
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>> ------------------------------
>>
>> Message: 5
>> Date: Tue, 18 Apr 2017 15:29:04 +0800 (CST)
>> From: wen <wenguanhuan at 163.com>
>> Subject: [ncl-talk] how to draw this kind of plot
>> To: ncl-list <ncl-talk at ucar.edu>
>> Message-ID: <5de3ed86.9f7f.15b7ff6fb6f.Coremail.wenguanhuan at 163.com>
>> Content-Type: text/plain; charset="gbk"
>>
>> Hi all,
>>   I am trying to use TRMM 3B42 data  to draw this kind of plot. I haven't
>> found a example on the website to draw it.  Do anyone know  how to make it.
>> Which function should I
>> use. Thank you!
>>
>>
>>
>>
>>
>>
>>
>>
>> --
>>
>> ??
>> ???
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>> ------------------------------
>>
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>> ncl-talk at ucar.edu
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