[ncl-talk] NDVI_mask problem
Dennis Shea
shea at ucar.edu
Thu May 10 08:02:49 MDT 2018
ncl 1> ndvi = f->ndvi
ncl 2> print("typeof(ndvi)="+typeof(ndvi)) ; *"short"*
ncl 3> print("typeof(ndvi at missing_value)="+typeof(ndvi at missing_value)) ;
*"double"*
The variable (ndvi) does not have an *_FillValue* attribute associated with
it. By default, NCL tries to be 'smart' and set the variable's (ndvi)
*missing_value* to* _FillValue*. However, by netCDF (hence, NCL) rule the
type of the variable (ndvi) and the type of _FillValue attribute should
match. They do not. Again, one variable is type "short" the other is type
"double".
The issue is explicitly mentioned in the error message.
MissingToFillValue option set True, but missing_value attribute and data
variable (ndvi) types differ: not adding virtual _FillValue attribute
Please read the text associated with:
https://www.ncl.ucar.edu/Document/Functions/Built-in/setfileoption.shtml
* MissingToFillValue*
You can explicitly set this option to False"
* setfileoption*("nc","*MissingToFillValue*", False)
This will eliminate the warning message.
Still, you are left with no way to identify _FillValue. This is the
attribute NCL recognizes.
The following script on the NDVI page explicitly converts the type double
missing_value (=5000.0d)
to type short.
ndvi_2.ncl
NDVI = f->ndvi ; original unpacked values
NDVI at _FillValue = toshort(NDVI at missing_value) ; match typeof
'ndvi' (netCDF rule)
You need to do this for masking.
Good Luck
On Thu, May 10, 2018 at 6:00 AM, Md. Jalal Uddin <dmjalal90 at gmail.com>
wrote:
> Thank you for your help. Mary's suggestions are working now. However, I am
> getting following errors.
>
> MissingToFillValue option set True, but missing_value attribute and data
> variable (ndvi) types differ: not adding virtual _FillValue attribute
>
> I also went to the NCL NDVI examples page (https://www.ncl.ucar.edu/
> Applications/ndvi.shtml) and tried to follow Example 2 that suggested by Dennis
> Shea. I got output but received the same problem.
>
> How could I solve the problem?
>
>
> On Wed, May 9, 2018 at 11:54 PM, Dennis Shea <shea at ucar.edu> wrote:
>
>> If you go to NCL's Examples page:
>>
>> https://www.ncl.ucar.edu/Applications/
>>
>> Under 'Datasets', click 'NDVI'
>>
>> There are three examples of differently sourced NDVI data sets.
>>
>> The 'GIMMS' version is Example 2.
>>
>> Please read the associated text description and the actual script.
>> As noted, the netCDF file is poorly written.
>>
>>
>>
>> On Wed, May 9, 2018 at 8:14 AM, Mary Haley <haley at ucar.edu> wrote:
>>
>>> Hi Jalal,
>>>
>>> I took a look at one of these NDVI data files, and noticed that the
>>> lat/lon coordinate arrays on the file have no attributes, which is not good.
>>>
>>> These arrays should at least have "units" and "long_name" attributes and
>>> units should be something like "degrees_north" and "degrees_east". For
>>> rectilinear data (data with lat/lon coordinate arrays), NCL needs these
>>> units to be something that indicates they are in degrees, or otherwise it
>>> can't be sure it is plotting the data correctly.
>>>
>>> It's always important to look at your data when you get errors like
>>> this. You do have:
>>>
>>> printVarSummary(ndvi)
>>>
>>> but I also added:
>>>
>>> printVarSummary(ndvi&lat)
>>> printVarSummary(ndvi&lon)
>>>
>>> in order to look at the lat/lon arrays to see what the units were and
>>> you can see there are none:
>>>
>>> Variable: lat (coordinate)
>>> Type: double
>>> Total Size: 17280 bytes
>>> 2160 values
>>> Number of Dimensions: 1
>>> Dimensions and sizes: [lat | 2160]
>>> Coordinates:
>>> Number Of Attributes: 0
>>>
>>>
>>> To fix this, I did this after reading in ndvi:
>>>
>>> ndvi = f->ndvi(0,:,:)
>>> ndvi&lat at units = "degrees_north" ; Fix the units
>>> ndvi&lon at units = "degrees_east"
>>> printVarSummary(ndvi)
>>>
>>> I also had to remove the reference to "ndvi at long_name" in a later title
>>> string, because ndvi doesn't have a long_name attribute.
>>>
>>> --Mary
>>>
>>> On Wed, May 9, 2018 at 3:44 AM, Md. Jalal Uddin <dmjalal90 at gmail.com>
>>> wrote:
>>>
>>>> Hi all,
>>>>
>>>> I tried to plot gimms ndvi (https://ecocast.ar
>>>> c.nasa.gov/data/pub/gimms/3g.v1/) data by masking. I am getting
>>>> following errors. I used copy_VarCoords(ndvi,ndvi_mask) command to
>>>> fix it but failed. Please help to solve this problem. Please find my script
>>>> in the attachment.
>>>>
>>>> (0) check_for_y_lat_coord: Warning: Data either does not contain a
>>>> valid latitude coordinate array or doesn't contain one at all.
>>>> (0) A valid latitude coordinate array should have a 'units' attribute
>>>> equal to one of the following values:
>>>> (0) 'degrees_north' 'degrees-north' 'degree_north' 'degrees north'
>>>> 'degrees_N' 'Degrees_north' 'degree_N' 'degreeN' 'degreesN' 'deg north'
>>>> (0) check_for_lon_coord: Warning: Data either does not contain a valid
>>>> longitude coordinate array or doesn't contain one at all.
>>>> (0) A valid longitude coordinate array should have a 'units' attribute
>>>> equal to one of the following values:
>>>> (0) 'degrees_east' 'degrees-east' 'degree_east' 'degrees east'
>>>> 'degrees_E' 'Degrees_east' 'degree_E' 'degreeE' 'degreesE' 'deg east'
>>>> (0) check_for_y_lat_coord: Warning: Data either does not contain a
>>>> valid latitude coordinate array or doesn't contain one at all.
>>>> (0) A valid latitude coordinate array should have a 'units' attribute
>>>> equal to one of the following values:
>>>> (0) 'degrees_north' 'degrees-north' 'degree_north' 'degrees north'
>>>> 'degrees_N' 'Degrees_north' 'degree_N' 'degreeN' 'degreesN' 'deg north'
>>>> (0) check_for_lon_coord: Warning: Data either does not contain a valid
>>>> longitude coordinate array or doesn't contain one at all.
>>>> (0) A valid longitude coordinate array should have a 'units' attribute
>>>> equal to one of the following values:
>>>> (0) 'degrees_east' 'degrees-east' 'degree_east' 'degrees east'
>>>> 'degrees_E' 'Degrees_east' 'degree_E' 'degreeE' 'degreesE' 'deg east'
>>>> warning:Attempt to reference attribute (long_name) which is undefined
>>>>
>>>> Cheers,
>>>> Jalal
>>>> --
>>>> *Md. Jalal Uddin*
>>>> MSc in Applied Meteorology (English Language)
>>>> Nanjing University of Information, Science and Technology, China
>>>> Jasmine Jiangsu Government Scholar
>>>> Cell: +8613260859092
>>>> Office: Beichen Building, School of Geography and Remote Sensing, Room
>>>> No. 406
>>>>
>>>> *AND *
>>>> B.Sc. in Disaster Management (Hons.)
>>>> Patuakhali Science and Technology University, Bangladesh.
>>>> Cell: +8801792052662, +8801838613203
>>>> Email: dmjalal90 at gmail.com
>>>> Web: www.dmjalal90.weebly.com
>>>> Facebook: jalal.hossen.39
>>>> LinkedIn: https://bd.linkedin.com/in/md-jalal-uddin-80a026b0
>>>> Twitter: dmjalal90
>>>> Skype: dmjalal90
>>>>
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>>>
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>>
>
>
> --
> *Md. Jalal Uddin*
> MSc in Applied Meteorology (English Language)
> Nanjing University of Information, Science and Technology, China
> Jasmine Jiangsu Government Scholar
> Cell: +8613260859092
> Office: Beichen Building, School of Geography and Remote Sensing, Room No.
> 406
>
> *AND *
> B.Sc. in Disaster Management (Hons.)
> Patuakhali Science and Technology University, Bangladesh.
> Cell: +8801792052662, +8801838613203
> Email: dmjalal90 at gmail.com
> Web: www.dmjalal90.weebly.com
> Facebook: jalal.hossen.39
> LinkedIn: https://bd.linkedin.com/in/md-jalal-uddin-80a026b0
> Twitter: dmjalal90
> Skype: dmjalal90
>
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