[ncl-talk] NDVI from Advanced Very High-Resolution Radiometer (AVHRR)
Setareh Rahimi
setareh.rahimi at gmail.com
Sun Jun 26 10:12:34 MDT 2022
Dear Dennis,
I put all NDVI files in one folder(like the attached image), and tried to
run the attached script to plot the NDVI anomaly from 1986 to 2021.
However, I faced another issue(attached). May I ask you, please to advise
me why this message appeared? How can I remove this issue, please?
Many thanks for considering my request.
Best wishes,
On Tue, Jun 21, 2022 at 10:09 PM Dennis Shea <shea at ucar.edu> wrote:
> I downloaded 5 files for a test.
>
> %> ncl NDVI_anomaly.ncl
>
> Copyright (C) 1995-2017 - All Rights Reserved
> University Corporation for Atmospheric Research
> NCAR Command Language Version 6.5.0
> The use of this software is governed by a License Agreement.
> See http://www.ncl.ucar.edu/ for more details.
>
>
> Variable: fils
> Type: string
> Total Size: 40 bytes
> 5 values
> Number of Dimensions: 1
> Dimensions and sizes: [5]
> Coordinates:
> (0) AVHRR-Land_v005_AVH13C1_NOAA-09_19860101_c20170612092103.nc
> (1) AVHRR-Land_v005_AVH13C1_NOAA-09_19860102_c20170612093403.nc
> (2) AVHRR-Land_v005_AVH13C1_NOAA-09_19861229_c20170612212717.nc
> (3) AVHRR-Land_v005_AVH13C1_NOAA-09_19861230_c20170612214313.nc
> (4) AVHRR-Land_v005_AVH13C1_NOAA-09_19861231_c20170612215936.nc
>
> Variable: prc
> Type: float
> Total Size: 518400000 bytes
> 129600000 values
> Number of Dimensions: 3
> Dimensions and sizes: [time | 5] x [latitude | 3600] x [longitude | 7200]
> Coordinates:
> time: [1826..2190]
> latitude: [89.975..-89.97499]
> longitude: [-179.975..179.975]
> Number Of Attributes: 7
> long_name : NOAA Climate Data Record of Normalized Difference
> Vegetation Index
> units : 1
> grid_mapping : crs
> standard_name : normalized_difference_vegetation_index
> _FillValue_original : -9999
> _FillValue : -9999
> ========================================================================
> ========================================================================
> ========================================================================
> It seems to me that you have path or file problems.
> I am not sure what else I can do.
>
> Others?
>
>
>
> On Tue, Jun 21, 2022 at 5:49 AM Setareh Rahimi <setareh.rahimi at gmail.com>
> wrote:
>
>> Dear Dennis,
>> So many thanks for your advice. I run the script on a remote server with
>> at least *1 terabyte* of memory. I think this is not the case.
>> I used the below commands to check the files:
>> ===========================================
>> fils = systemfunc("ls [1-2][8-9-0-1]*/*nc")
>> print(fils)
>>
>> f = addfiles (fils, "r")
>>
>> x = short2flt(f[:]->NDVI)
>>
>> printVarSummary(x)
>> ===========================================
>> , and attached the result. Please look at the image, and kindly help me
>> sort the issue out. I do not know what is wrong with the files I downloaded.
>> best regards,
>>
>> On Sat, Jun 18, 2022 at 10:52 PM Dennis Shea <shea at ucar.edu> wrote:
>>
>>> Based on the provided information, I have no idea why you would get
>>> "returned nothing to me"
>>>
>>> I know that NDVI files are 0.1 degree resolution (3600,7200). You have
>>> 36 years (1986-2021) of daily data.
>>> So, 36*365=13140 [+ a few Leap Year days)
>>>
>>> prc(13140,3600,7200) => daily data
>>>
>>> A lot of memory is needed. Maybe your computer can not handle this?
>>>
>>> After the
>>> xM = calculate_monthly_values (prc, "avg", 0,opt)
>>> printVarSummary(xM)
>>>
>>> xM(432,3600,7200)
>>>
>>>
>>>
>>> On Sat, Jun 18, 2022 at 5:01 AM Setareh Rahimi via ncl-talk <
>>> ncl-talk at mailman.ucar.edu> wrote:
>>>
>>>> Dear all,
>>>>
>>>> I need to calculate the monthly anomaly of the Normalized Difference
>>>> Vegetation Index (NDVI), from Advanced Very High-Resolution Radiometer
>>>> (AVHRR) sensor. I have downloaded AVHRR data (1986-2021) from the link
>>>> below:
>>>>
>>>> https://www.ncei.noaa.gov/metadata/geoportal/rest/metadata/item/gov.noaa.ncdc:C01558/html
>>>> I first tried to prepare a script to combine all the data, and then
>>>> calculate the monthly average from daily data ( the link provides daily
>>>> data). After having monthly data I tried to figure out anomalies (the
>>>> script has been attached). But NCL stopped and returned nothing to me. I
>>>> just wonder what is wrong. Please kindly advise me on this issue.
>>>> Best wishes,
>>>>
>>>>
>>>> --
>>>> S.Rahimi
>>>>
>>>> _______________________________________________
>>>> ncl-talk mailing list
>>>> ncl-talk at mailman.ucar.edu
>>>> List instructions, subscriber options, unsubscribe:
>>>> https://mailman.ucar.edu/mailman/listinfo/ncl-talk
>>>>
>>>
>>
>> --
>> S.Rahimi
>>
>>
--
S.Rahimi
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begin
;************************************************
; Read the file
;************************************************
ymStrt = 198601 ; climatology start year/month
ymLast = 202112 ; " last year/month a = addfile("air.mon.mean.nc","r")
;--------------------------------------
fils = systemfunc("ls *.nc")
print(fils)
a = addfiles (fils, "r")
;-----------------------------------------
time = a[:]->time
yyyymm = cd_calendar(time, -1)
ntStrt = ind(yyyymm.eq.ymStrt) ; start time index
ntLast = ind(yyyymm.eq.ymLast) ; last time index
ndvi =short2flt(a[:]->NDVI(ntStrt:ntLast,:,:)) ; (time,lat,lon)
ntim = dimsizes(time)
printMinMax(ndvi,0)
months = (/"January", "February", "March", "April" \
,"May", "June", "July", "August" \
,"September", "October", "November" \
,"December" /)
;************************************************
; Compute the climatology using a function in contributed.ncl
;************************************************
;prcClm = clmMonTLL(tmp)
;printVarSummary(prcClm)
xM = calculate_monthly_values (ndvi, "avg", 0,opt)
printVarSummary(xM)
anom = calcMonAnomTLL(ndvi,xM)
;************************************************
; create colors
;*************************************************
wks = gsn_open_wks("png","NDVI-anomaly_ghcn") ; send graphics to PNG file
;************************************************
; create panel plots
;*************************************************
plot = new (12, graphic) ; create graphical array
res = True ; plot options desired
res at gsnDraw = False
res at gsnFrame = False
res at cnFillOn = True ; turn on color fill
res at cnFillPalette = "amwg256" ; set color map
res at cnInfoLabelOn = False ; turn off contour info label
res at cnLinesOn = False ; turn off contour lines
res at cnLineLabelsOn = False ; turn off line labels
res at cnLevelSelectionMode = "ManualLevels" ; set manual contour levels
res at cnMinLevelValF = -1 ; set min contour level
res at cnMaxLevelValF = 1 ; set max contour level
res at cnLevelSpacingF = 0.2 ; set contour spacing
;res at mpFillOn = False ; turn off gray continents
res at mpCenterLonF = 0 ; Centers the plot at 0
;res at lbLabelBarOn = False ; No single label bar
res at mpMaxLatF = 60 ; choose subregion
res at mpMinLatF = 0
res at mpMaxLonF = 70
res at mpMinLonF = -50
res at mpDataBaseVersion = "MediumRes" ; better map outlines
res at gsnRightString = " mm"
resP = True ; panel options
resP at gsnPanelMainString = " NDVI anomaly : "+(ymStrt/100)+"-"+(ymLast/100)
resP at gsnMaximize = True ; maximize image
resP at gsnPanelLabelBar = True ; Add common label bar
do nmo=0,2 ; loop over the months
res at gsnLeftString = months(nmo)
plot(nmo) = gsn_csm_contour_map(wks,anom(nmo,:,:), res) ; create plot
end do
do nmo=9,11 ; loop over the months
res at gsnLeftString = months(nmo)
plot(nmo) = gsn_csm_contour_map(wks,anom(nmo,:,:), res) ; create plot
end do
;shapefile_name1 = "clip.basin3.shp"
shapefile_name2 = "IRN_adm0.shp"
lnres = True
lnres at gsLineThicknessF = 5
lnres at gsLineColor = "Black"
;shape1 = gsn_add_shapefile_polylines(wks,plot,shapefile_name1,lnres)
shape2 = gsn_add_shapefile_polylines(wks,plot,shapefile_name2,lnres)
;gsn_panel(wks,plot,(/2,3/),resP)
gsn_panel(wks,(/plot(0),plot(1),plot(2),plot(9),plot(10),plot(11)/),(/2,3/),resP)
end
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