[ncl-talk] How to resolve SVD warning: column contains constant
Bithi De
bde at purdue.edu
Thu Dec 17 07:00:34 MST 2015
Hi All,
Thanks for the reply Will!
But is there any way to suppress the warning and let the code run? I'm having too many warning.
I'm copying the 1st part of the code (before doing SVD) here, if anybody could help to clean it up! There is no error message but probably I did something wrong .
Thanks in advance!
Bithi
;********************************************************
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"
;*********************************************************
begin
;********************************
;read binary files
;********************************
data_path = "/scratch/lustreD/b/bde/seaice_bin/"
;data_filename= "bt_197812_n07_v02_n.bin"
nrows = 448
ncols = 304
;************* read sic data *************************************************************************
; documentation of the data at http://nsidc.org/data/docs/daac/nsidc0079_bootstrap_seaice.gd.html
; 2-byte integer is NCL type "short"
; divide stored value by 10 to get the percent (SIC values stored as 0-1000)
; land is registered as 1200 andnorth pole as 1100
;***************************************************************************************************
nrec=0
Idims1 = (/448,304/)
fils = systemfunc("ls /scratch/lustreD/b/bde/seaice_bin/*.bin")
SIC = new((/dimsizes(fils),nrows,ncols/),”short") ; predefine array for data files
do gg =0,dimsizes(fils)-1
setfileoption("bin","ReadByteOrder","LittleEndian")
SIC(gg,:,:) = fbindirread(fils(gg),nrec,dims1,"short")
end do
printVarSummary(SIC)
printMinMax(SIC,True)
SIC_f= short2flt(SIC)
SIC_f at _FillValue = -999
SIC_f = SIC_f/10
printVarSummary(SIC_f)
printMinMax(SIC_f,True)
SIC_f = where(SIC_f .gt. 100,SIC_f at _FillValue,SIC_f)
SIC_f at _FillValue = -999
printVarSummary(SIC_f)
printMinMax(SIC_f,True)
;*********************** read lat-lon for 25x25 km grid points in polar stereographic projection *
; documentation for the grid ;http://nsidc.org/data/polar_stereo/tools_geo_pixel.html#psn25_pss25_lats
; Grids that determine the latitude of a given pixel for the 25 km grids for either hemisphere
; 4-byte integer(little endian), scaled by 100,000
; Each array location (i, j) contains the latitude/longitude value at the center of the ;corresponding data grid cells
; 304 columns x 448 rows, range = [31.102, 89.836] for lats ; 304 columns x 448 rows, range = ;[-180.000, 179.814] for lons
;****************************************************************************************************
setfileoption("bin","ReadByteOrder","LittleEndian")
lat = fbindirread("/scratch/lustreD/b/bde/seaice_bin/psn25lats_v3.dat",0,(/nrows,ncols/), "integer") /100000.
lon = fbindirread("/scratch/lustreD/b/bde/seaice_bin/psn25lons_v3.dat",0,(/nrows,ncols/), "integer") /100000.
lat at units = "degrees_north"
lon at units = "degrees_east"
printVarSummary(lon)
printVarSummary(lat)
print(max(lon)+" " +min(lon))
print(max(lat)+" " +min(lat))
SIC_f at lat2d = lat
SIC_f at lon2d = lon
printVarSummary(SIC_f)
printMinMax(SIC_f,True)
;************* remove mean ****************8
ice_ano= dim_rmvmean_n_Wrap(SIC_f,0) ;timexlatxlon
printVarSummary(ice_ano)
printMinMax(ice_ano,True)
if(any(ismissing(ice_ano))) then
print("Your data contains some missing values. Beware.")
end if
;; SVD will not contain any data with missingvalue so change fillvalue to 0.0
;; http://www.ncl.ucar.edu/Support/talk_archives/2013/3756.html
ice_ano at _FillValue=0.0
delete(ice_ano at _FillValue)
printVarSummary(ice_ano)
;**************************************************
; split into month and year
;********************************************************
ice_ym = new((/12,35,448,304/),"float")
m = 0
y = 0
do ii = 2,421
; print(ii)
; print(m)
; print(y)
ice_ym(m,y,:,:) = ice_ano(ii,:,:)
m = m+1
if (m .eq. 12)
y = y+1
m = 0
end if
end do
printVarSummary(ice_ym)
ice_Jan=ice_ym(0,:,:,:)
copy_VarCoords(ice_ym(0,0,:,:),ice_Jan)
printVarSummary(ice_Jan)
ice_Feb=ice_ym(1,:,:,:)
copy_VarCoords(ice_ym(0,0,:,:),ice_Feb)
printVarSummary(ice_Feb)
ice_Dec=ice_ym(11,:,:,:)
copy_VarCoords(ice_ym(0,0,:,:),ice_Dec)
printVarSummary(ice_Dec)
ice_Wint = new((/3,35,448,304/),"float")
ice_Wint(0,:,:,:)=ice_Dec
ice_Wint(1,:,:,:)=ice_Jan
ice_Wint(2,:,:,:)=ice_Feb
printVarSummary(ice_Wint)
printMinMax(ice_Wint,True)
ice_djf=dim_avg_n_Wrap(ice_Wint,0)
printVarSummary(ice_djf)
printMinMax(ice_djf,True)
if(any(ismissing(ice_djf))) then
print("Your data contains some missing values. Beware.")
end if
;***********************************************************************************************************
; read Z500 data and remove climatology for each winter month
;***********************************************************************************************************
in = addfile("/scratch/lustreD/b/bde/reanalysis/ERA_data/ERA_z500_lowreso.nc","r")
lat1 = in->latitude
lon1 = in->longitude
printVarSummary(lat1)
printVarSummary(lon1)
latz=lat1({90:20})
l1 = dimsizes(latz)
z500 = (short2flt(in->z)) ;m2/s2 geopotential
printVarSummary(z500)
printMinMax(z500,True)
z5 = (z500(0,0,:)/9.8) ;geopotential height
copy_VarCoords(z500,z5)
printVarSummary(z5)
printMinMax(z5,True)
z_35 =z5(2:421,:,:); ;timesteps for 1979-2013, 35 years
printVarSummary(z_35)
printMinMax(z_35,True)
zClm = clmMonTLL( z_35 ) ; monthly climatology (12xlatxlon)
printVarSummary(zClm)
printMinMax(zClm,True)
;************* remove monthly climatology and calculate anomaly for each month *************
zAno= calcMonAnomTLL (z_35,zClm)
printVarSummary(zAno)
printMinMax(zAno,True) ;time(420=35*12)xlatxlon for zanomaly
if(any(ismissing(zAno))) then
print("Your data contains some missing values. Beware.")
end if
;; SVD will not contain any data with missingvalue so change fillvalue to 0.0
zAno at _FillValue=0.0
delete(zAno at _FillValue)
printVarSummary(zAno)
printMinMax(zAno,True)
if(any(ismissing(zAno))) then
print("Your data contains some missing values. Beware.")
end if
;********************* split in monthsxyear of the z-anomaly ***********************************
z_ym = new((/12,35,dimsizes(lat1),dimsizes(lon1)/),"float")
m = 0
y = 0
do ii = 0,419
z_ym(m,y,:,:) = zAno(ii,:,:)
m = m+1
if (m .eq. 12)
y = y+1
m = 0
end if
end do
printVarSummary(z_ym)
printMinMax(z_ym,True)
z_Jan=z_ym(0,:,:,:)
printVarSummary(z_Jan)
z_Feb=z_ym(1,:,:,:)
printVarSummary(z_Feb)
z_Dec=z_ym(11,:,:,:)
printVarSummary(z_Dec)
z_Wint = new((/3,35,dimsizes(latz),dimsizes(lon1)/),"float")
z_Wint(0,:,:,:)=z_Dec(:,{90:20},:)
z_Wint(1,:,:,:)=z_Jan(:,{90:20},:)
z_Wint(2,:,:,:)=z_Feb(:,{90:20},:)
printVarSummary(z_Wint)
printMinMax(z_Wint,True)
z_djf=dim_avg_n_Wrap(z_Wint,0)
z_djf!0="time"
printVarSummary(z_djf)
printMinMax(z_djf,True)
if(any(ismissing(z_djf))) then
print("Your data contains some missing values. Beware.")
end if
;***********************************************************
; calculate SVD
;***************************************** *******
;posted before
end
________________________________
From: Will Hobbs <will.hobbs at utas.edu.au>
Sent: Wednesday, December 16, 2015 6:29 PM
To: Bithi De; ncl-talk at ucar.edu
Subject: Re: [ncl-talk] How to resolve SVD warning: column contains constant
Bithi
You will have constant values in the SIC array anywhere that is a) land, b) perenially ice covered or c) never ice covered. Any of these conditions are physically plausible for some data points in either the Arctic or Southern Ocean, and you would get the same warning with a regular cross-correlation using escort()
In short, it's not (necessarily) a problem and is encountered in almost all gridded ocean data.
Will
From: Bithi De <bde at purdue.edu<mailto:bde at purdue.edu>>
Date: Thursday, 17 December 2015 10:19 AM
To: "ncl-talk at ucar.edu<mailto:ncl-talk at ucar.edu>" <ncl-talk at ucar.edu<mailto:ncl-talk at ucar.edu>>
Subject: [ncl-talk] How to resolve SVD warning: column contains constant
Hi All,
I am calculating SVD between seaice concentration anomaly (documentation of the data at http://nsidc.org/data/docs/daac/nsidc0079_bootstrap_seaice.gd.html ) and geopotential height anomaly from ERA-interim data, for winter(35years). I am not getting any error until the step for calculating SVD.
The part of my code is as follows:
;***********************************************************
; calculate SVD
;**************************************************
; Z-anomaly (timexlatxlon)
nxy = dimsizes(lon1)*dimsizes(latz) ;size(space)
ntim = 35 ;size(time)
; reorder so time varying fast
; create spacextime matrix for Z_ano
Z = z_djf(longitude|:,latitude|:,time|:)
printVarSummary(Z)
Z2 = onedtond(ndtooned(Z),(/nxy,ntim/)) ;convert into spacextime matrix
printVarSummary(Z2)
printMinMax(Z2,True)
Z2!0="space"
Z2!1="time"
Z2 at _FillValue=0.0<mailto:Z2 at _FillValue=0.0>
delete(Z2 at _FillValue)
printVarSummary(Z2)
printMinMax(Z2,True)
if(any(ismissing(Z2))) then
print("Your data contains some missing values. Beware.")
end if ; did not get any error
;********* SIC anomaly *********************
; create spacextime matrix for sic_ano(timex448x304) ; 448rows x304columns in 25kmx25km grid
xy=448*304
si = ice_djf(::-1,::-1,::-1) ;dimension reordering -->448x304xtime
printVarSummary(si)
Si2 = onedtond(ndtooned(si),(/xy,ntim/)) ;convert into (spacextime)
printVarSummary(Si2)
printMinMax(Si2,True)
Si2!0="space"
Si2!1="time"
Si2 at _FillValue=0.0<mailto:Si2 at _FillValue=0.0>
delete(Si2 at _FillValue)
printVarSummary(Si2)
printMinMax(Si2,True)
if(any(ismissing(Si2))) then
print("Your data contains some missing values. Beware.")
end if ; did not get any error
; check if some columns has constant value
p2d=Si2(time|:,space|:)
printVarSummary(p2d)
p2d_dims = dimsizes(p2d) ; I assume this is time x p1d
ntim = p2d_dims(0)
np1d = p2d_dims(1)
;do i=0,np1d-1
;pmin = min(p2d(:,i))
; pmax = max(p2d(:,i))
;if(pmin.eq.pmax) then
; print("p2d contains all constant values at np1d = " + i)
;end if
;end do
exit
; delete([/Z,Zano,SIC,si/])
;***************************************************
;spatial plot of 1st mode of left and right singular vector
;*************************************************************
nsvd = nxy
svLeft = new((/nsvd,nxy/),float) ; pre-allocate space
svRight = new((/nsvd,xy/),float)
pc = svdcov_sv(Z2,Si2,nsvd,svLeft,svRight)
printVarSummary(pc)
end
;; giving warning ==> all Y values in columns are missing or constant
*********
I checked for Si2 following the http://www.ncl.ucar.edu/Support/talk_archives/2011/2803.html and it is shows it has constant value.
Could you suggest how I can solve it?
Thanks in advance!
Bithi De
Purdue University
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