# [ncl-talk] Problems converting hdf to netcdf using NCL

BLIUJUS, STEVEN D CTR USAF AFMC AFLCMC/HBAW-OL steven.bliujus.3.ctr at us.af.mil
Wed May 27 12:39:30 MDT 2015

```Found the error Dennis, there was a discrepancy in the dimension size. One of the files has a 205 dimension, so I reformatted the do loop section to look like:

mAcross  = 135
nAlong   = 203
nAlong1  = nAlong + 2

time  = new (   nfili                  , "double", "No_FillValue"   )
data  = new ( (/nfili,nAlong1,mAcross/), "float" , -9999.0)
lat2d = new ( (/nfili,nAlong1,mAcross/), "float" ,  -999.0)
lon2d = new ( (/nfili,nAlong1,mAcross/), "float" ,  -999.0)
print("nfili = ")
print(nfili)
do nf=0,nfili-1                  ; loop over files
time(nf)  = (/ parse_MODIS( fili(nf) ) /)
print("nf="+nf+"  time(nf)="+time(nf))

x        := short2flt(a->\$var\$)
dimx      = dimsizes(x)
print("dimsizex="+dimx)

if (dimx(0).eq.203 .and. dimx(1).eq.135) then
data(nf,0:202,:)  = (/ x /)
lat2d(nf,0:202,:) = (/ a->Latitude  /)
lon2d(nf,0:202,:) = (/ a->Longitude /)
else if(dimx(0).eq.204 .and. dimx(1).eq.135) then
data(nf,0:203:,:)  = (/ x /)
lat2d(nf,0:203,:) = (/ a->Latitude  /)
lon2d(nf,0:203,:) = (/ a->Longitude /)
else
data(nf,:,:)  = (/ x /)
lat2d(nf,:,:) = (/ a->Latitude  /)
lon2d(nf,:,:) = (/ a->Longitude /)
end if
end if
end do

The script runs all the way through but I'm still finding a couple strange things.
#1: The NetCDF file generated only shows ranges for Longitude :  85.1406-172.263 when using ncview, though there are values in there for the entire range...same as latitude, but since I know there are values there I'm not too concerned, just find it odd.
#2: When I do plot there still looks like there is missing data, I've attached both again. Maybe it's removing duplicate values?

-----Original Message-----
From: Dennis Shea [mailto:shea at ucar.edu]
Sent: Wednesday, May 27, 2015 12:43 PM
To: BLIUJUS, STEVEN D CTR USAF AFMC AFLCMC/HBAW-OL
Cc: ncl-talk at ucar.edu
Subject: Re: [ncl-talk] Problems converting hdf to netcdf using NCL

There  is no reason for stopping after 34 iterations.

===
[1]  When I wrote "Each iteration thru the loop .... print the current 'time' value."

I meant ...

do nf=0,nfili-1                  ; loop over files
time(nf)  = (/ parse_MODIS( fili(nf) ) /)
print("nf="+nf+"  time(nf)="+time(nf))     ; print current value
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

[2]  Also ... after the loop is complete ...
^^^^^

end do

time!0 = "time"
time at long_name = "current time as YYYYDDDHHMM"
time&time      = time
printVarSummary(time)

print(time)   ; print all values

On Wed, May 27, 2015 at 10:08 AM, BLIUJUS, STEVEN D CTR USAF AFMC AFLCMC/HBAW-OL <steven.bliujus.3.ctr at us.af.mil> wrote:

Dennis,

Is there a default setting that loops kill after? The loop stops after 34 iterations, thus leaving out the other 226 files, which explains why there is no data anywhere else on the globe. There are so many files because we are doing a global analysis, so these are swaths through the entire day.

As far as the plots.ncl. These values do match the values given by modis.ncl as far as lat/lon/aod. So the real problem is the loop quitting early. I attached the log file I created.

Steve

-----Original Message-----
From: Dennis Shea [mailto:shea at ucar.edu]

Sent: Wednesday, May 27, 2015 10:07 AM
To: BLIUJUS, STEVEN D CTR USAF AFMC AFLCMC/HBAW-OL
Cc: ncl-talk at ucar.edu
Subject: Re: [ncl-talk] Problems converting hdf to netcdf using NCL

I think you have to do some debugging.

===

Look at "time":   time: [20143050010..2.426116152246728e-315]

The last time is obviously wrong! How did this happen?

It did not happen with the 5 sample files ... why with all the files?

Each iteration thru the loop .... print the current 'time' value.

Also ... after the loop is complete ...

print(time)   ; print all values

This issue must be cleared up!

If 'time' is messed up ... what about other variables?

-------

In the code that reads/plots the netCDF ... did you do any debugging??

diri  = "./"
fili  = "MODIS_L2.Swath.nc"

print(f)

AOT = f->AOT

printVarSummary(AOT)

printMinMax(AOT,0)

lat2d = f->LAT2D

printVarSummary(LAT2D)

printMinMax(lat2d,0)

lon2d = f->LON2D

printVarSummary(lon2d)
printMinMax(lon2d,0)

Do these not match the original created values

--------

Minor: the dimension name "Cell_ACross_Swath"  should be "Cell_Across_Swath"

On Wed, May 27, 2015 at 8:34 AM, BLIUJUS, STEVEN D CTR USAF AFMC AFLCMC/HBAW-OL <steven.bliujus.3.ctr at us.af.mil> wrote:

Dennis the script works however for some reason the data is not getting put into the NetCDF file correctly. I have ~120 files I'm going through, and when the script prints the dimensions, the following are stated:

Variable: time
Type: double
Total Size: 2080 bytes
260 values
Number of Dimensions: 1
Dimensions and sizes:   [time | 260]
Coordinates:
time: [20143050010..2.426116152246728e-315]
Number Of Attributes: 1
long_name :   current time as YYYYDDDHHMM

Variable: data
Type: float
Total Size: 28641600 bytes
7160400 values
Number of Dimensions: 3
Dimensions and sizes:   [time | 260] x [Cell_Along_Swath | 204] x [Cell_ACross_Swath | 135]
Coordinates:
time: [20143050010..2.426116152246728e-315]
Number Of Attributes: 2
long_name :    AOT at 0.55 micron for both ocean and land
_FillValue :  -9999
(0)     data: min=-0.05   max=4.277

Variable: lat2d
Type: float
Total Size: 28641600 bytes
7160400 values
Number of Dimensions: 3
Dimensions and sizes:   [time | 260] x [Cell_Along_Swath | 204] x [Cell_ACross_Swath | 135]
Coordinates:
time: [20143050010..2.426116152246728e-315]
Number Of Attributes: 3
units :       degrees_north
long_name :   Geodetic Latitude
_FillValue :  -999
(0)     lat2d: min=-89.894   max=77.2616

Variable: lon2d
Type: float
Total Size: 28641600 bytes
7160400 values
Number of Dimensions: 3
Dimensions and sizes:   [time | 260] x [Cell_Along_Swath | 204] x [Cell_ACross_Swath | 135]
Coordinates:
time: [20143050010..2.426116152246728e-315]
Number Of Attributes: 3
units :       degrees_east
long_name :   Geodetic Longitude
_FillValue :  -999
(0)     lon2d: min=-179.999   max=179.977
(0)     -----

The thing that stands out is when the NetCDF file is created, the Longitude in the file only goes from 85.1406 - 172.263 and not -179.999 - 179.977 like the varSummary states. There is an error that gets thrown during the run:

fatal:Dimension size mismatch on subscript #1, left-hand and right-hand side dimensions do not match
fatal:["Execute.c":8128]:Execute: Error occurred at or near line 71 in file modis.ncl

I have attached the image created from your script, compared to the image I get from the other script. I also reattached your script as I modified some directory things and added the libraries which shifted some of the lines. It should be noted that the information present from your script does match the data location on the image I created from a different script, it's just missing everything else.

Steve

-----Original Message-----
From: Dennis Shea [mailto:shea at ucar.edu]

Sent: Tuesday, May 26, 2015 5:43 PM
To: BLIUJUS, STEVEN D CTR USAF AFMC AFLCMC/HBAW-OL
Cc: ncl-talk at ucar.edu
Subject: Re: [ncl-talk] Problems converting hdf to netcdf using NCL

I just looked at the 5 sample files you sent ....

The dimension sizes are *not* the same size across all files

The 1st 4files are:

MOD04_L2.A2014305.0000.006.2015077213911.pscs_000500937810.hdf
dimensions:
Cell_Along_Swath = 203       <=====
Cell_Across_Swath = 135

The last file is:

MOD04_L2.A2014305.0500.006.2015077215106.pscs_000500937810
dimensions:
Cell_Along_Swath = 204     <====
Cell_Across_Swath= 135

That can be 'programmed around'.

See attached

On Tue, May 26, 2015 at 6:34 AM, BLIUJUS, STEVEN D CTR USAF AFMC AFLCMC/HBAW-OL <steven.bliujus.3.ctr at us.af.mil> wrote:

Dennis,

#2 and #3: Cell_Along_Swath, and Cell_Across_Swath are exactly the same for every file as far as actual dimension size, the variables are not though.
#4: I am trying to create a mosaic of all the files and that is why I am wanting to generate one NetCDF file. So when I run my script the image above is what comes out. This image is what I want to create in a NetCDF file (Globe.PNG).
#5: I did this because I was following a script online that I found where I needed to give the main variable(Optical Depth) the latitude/longitude dimensions. It used (::5) which what I just followed. When I try plotting using just (:,:), the plot take an extremely long time to plot(though there is much more data prevalent)...If it is one file it doesn’t take long, but when you add them all in the mosaic form, it takes a much more substantial amount of time to generate the image.
#6: I'm not sure exactly what you mean by this as there is not time field in the file.
#7: See 5 attached MODIS files
#8: I am trying to create a NetCDF file for a coworker to use for his verification software. He only reads in NetCDF files or text files (though he would prefer NetCDF files)

I also attached the script (with all previous commented lines removed) that plots the files and also creates a text table of the data.

Any help would be appreciated.

Steve

-----Original Message-----
From: Dennis Shea [mailto:shea at ucar.edu]

Sent: Saturday, May 23, 2015 2:30 PM
To: BLIUJUS, STEVEN D CTR USAF AFMC AFLCMC/HBAW-OL
Cc: ncl-talk at ucar.edu
Subject: Re: [ncl-talk] Problems converting hdf to netcdf using NCL

I have looked at this and there are *lots* of issues.

"... taking several hdf files (200-400) and trying to generate one NetCDF file."

So ...  **Conceptually**, you want

AOT(time, Cell_Along_Swath, Cell_Across_Swath)

Thing  is your geographic coordinates are 2-dimensional. see below

[1]

The files contain swath data. From your dump:

path:   MOD04_L2.A2014306.2330.006.2015077230656.pscs_000500937810.hdf
file global attributes:
HDFEOSVersion : HDFEOS_V2.17
GROUP=SWATH_1
SwathName="mod04"

[2] Are the dimension sizes

(Cell_Along_Swath,Cell_Across_Swath) => (203,135)

exactly the same for *all* files?

[3] If [2] is satisfied  .... Are the *values* contained within the following variables

Latitude ( Cell_Along_Swath, Cell_Across_Swath)

Longitude ( Cell_Along_Swath, Cell_Across_Swath )

*exactly* the same for *all* files?  ie: homogeneous space!

My (limited) experience with satellite swath data is that the answer is "no"

[4] If [2] *and* [3] are not satisfied, I see no advantage of creating a single netCDF file.

You would end up with 200-400 sets of dimension sizes *and* 200-400 variables

associated 200-400two-dimensional spatial variables.

[5]  I have no idea why you are sub-sampling [decimating] the array by 5:
(::5,::5) the resolution from (203,135) to  ??(41,27)??. This seems drastic!

Sub-sampling (array decimation) is commonly used used when the resolution is (say) (2500,4000) and the data are reasonably smooth.

[6] In any case you should be using

ListSetType(a,"join")

to add a record dimension ... which you should fill in with 'time'

(parse file name) or some sequential number.

Example 3 illustrates what "join" will do.

[7] I do not have your ?MODIS? data file. Based upon your dump, I created a script that creates a netCDF file for each HDF file and (I hope) a sample graphic.

[8] I am not sure of ultimate use of the data but from an NCL perspective, there is no reason to convert to netCDF.

===========================

============================

On Fri, May 22, 2015 at 9:59 AM, BLIUJUS, STEVEN D CTR USAF AFMC AFLCMC/HBAW-OL <steven.bliujus.3.ctr at us.af.mil> wrote:

I wanted to provide an example of what is in the hdf file. See attached.

Steve

-----Original Message-----
From: ncl-talk-bounces at ucar.edu [mailto:ncl-talk-bounces at ucar.edu] On Behalf Of BLIUJUS, STEVEN D CTR USAF AFMC AFLCMC/HBAW-OL
Sent: Friday, May 22, 2015 10:36 AM
To: ncl-talk at ucar.edu
Subject: [ncl-talk] Problems converting hdf to netcdf using NCL

I am taking several hdf files (200-400) and trying to generate one NetCDF file. I am able to plot it on a grid, but when I try to write to a NetCDF file, I get the following error:

fatal:Number of dimensions in parameter (2) of (filedimdef) is (2), (1) dimensions were expected
fatal:["Execute.c":8128]:Execute: Error occurred at or near line 82 in file File.ncl

The data I am creating is AOD with two dimensions (lat/lon). I am uncertain as to why it is expecting one dimension. Below is my script. FYI, the original files had to be manipulated in order to make AOD have the lat/lon dimensions. Any help would be greatly appreciated.

begin

diri = "/home/bliujuss/Verification_data/Test/"
fili = systemfunc("ls "+diri+"*.hdf")

;ListSetType(a,"cat")

var1=a[:]->Optical_Depth_Land_And_Ocean(:,:)
Optical_Depth_Land_And_Ocean = short2flt(var1)

var2=a[:]->Longitude(:,:)
Longitude=var2

var3 = a[:]->Latitude(:,:)
Latitude=var3

dims = dimsizes(Optical_Depth_Land_And_Ocean)
nrows = dims(0) ;203
npixels = dims(1) ;135

lat2d = new((/nrows,npixels/),float)
lon2d = new((/nrows,npixels/),float)

do i=0,npixels-1
lat2d(:,i) = Latitude(:,i)
end do

do i=0,nrows-1
lon2d(i,:) = Longitude(i,:)
end do

Optical_Depth_Land_And_Ocean at lat2d = lat2d(::5,::5) Optical_Depth_Land_And_Ocean at lon2d = lon2d(::5,::5)

wks = gsn_open_wks("x11","plot_aod")
gsn_define_colormap(wks,"NCV_banded")
setvalues NhlGetWorkspaceObjectId()
"wsMaximumSize": 300000000
end setvalues

res                   = True               ; plot mods desired
res at cnLinesOn         = False              ; turn off contour lines
res at cnFillOn          = True               ; color plot desired
res at cnLineLabelsOn    = False              ; turn off contour lines
res at gsnAddCyclic      = False             ; non-global data
res at gsnSpreadColors   = True               ; use full range of colormap
;res at cnFillMode        = "RasterFill"       ; turn on raster mode
res at lbLabelAutoStride = True               ; nice spacing of lables
res at gsnMaximize       = True               ; blow up plot as much as poss
;print(min(lat2d))
;print(max(lat2d))
;print(min(lon2d))
;print(max(lon2d))

plot = gsn_csm_contour_map_ce(wks,Optical_Depth_Land_And_Ocean(::5,::5),res)
print(max(Optical_Depth_Land_And_Ocean(::5,::5)))

nlat = dimsizes(lat2d(::5,::5))
nlon = dimsizes(lon2d(::5,::5))

diro = "/home/bliujuss/Plots/"
filo = "example.nc"
system("rm -f" + diro + filo)
fout = addfile (diro + filo, "c")

setfileoption(fout,"DefineMode",True)

dim_names = (/"lat", "lon"/)
dim_sizes = (/nlat, nlon/)
dimUnlim = (/False, False/)
filedimdef(fout,dim_names,dim_sizes,dimUnlim)

filevardef(fout, "lat", typeof(lat2d(::5,::5)),getvardims(lat2d(::5,::5)))
filevardef(fout, "lon", typeof(lon2d(::5,::5)),getvardims(lon2d(::5,::5)))
filevardef(fout, "AOT", typeof(Optical_Depth_Land_And_Ocean(::5,::5)),getvardims(Optical_Depth_Land_And_Ocean(::5,::5)))

filevarattdef(fout,"AOT", Optical_Depth_Land_And_Ocean(::5,::5))
filevarattdef(fout,"lat", lat2d(::5,::5)) filevarattdef(fout,"lon", lon2d(::5,::5))

setfileoption(fout,"DefineMode",False)

fout->Optical_Depth_Land_And_Ocean(::5,::5) =

fout->(/Optical_Depth_Land_And_Ocean(::5,::5)/)

fout->lat2d(::5,::5) = (/lat2d(::5,::5)/)
fout->lon2d(::5,::5) = (/lon2d(::5,::5)/)

end

Steven Bliujus

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