[ncl-talk] NDVI_mask problem
Md. Jalal Uddin
dmjalal90 at gmail.com
Sat May 12 00:45:24 MDT 2018
Thanks a lot. It works now.
On Fri, May 11, 2018 at 9:59 PM, Dennis Shea <shea at ucar.edu> wrote:
> [1] *setfileoption* is placed *BEFORE *opening the nc file
> [2] the *missing_value* attribute is associated with 'ndvi' not 'NDVI'
> ===================================================
> ;---Read NDVI data to contour and mask
> dir = "./"
> filename = "ndvi3g_geo_v1_1985_0106.nc4"
>
> setfileoption("nc","MissingToFillValue", False) ; eliminate *warning*
> message
> f = addfile(dir+filename,"r")
> ndvi = f->ndvi(0,:,:)
>
> ndvi&lat at units = "degrees_north" ; Add units
> attribute
> ndvi&lon at units = "degrees_east"
> ndvi at _FillValue = toshort(ndvi at missing_value) ; match typeof 'ndvi'
> (netCDF rule)
> printVarSummary(ndvi)
> printMinMax(ndvi,0)
>
> NDVI = floor(ndvi/10)/1000 ; no
> meta data
> copy_VarCoords(ndvi, NDVI) ; add
> coordinate meta data
> NDVI at long_name = "Normalized Difference Vegetation Index" ; add a
> long_name
> printVarSummary(NDVI)
> printMinMax(NDVI,0)
>
>
> On Fri, May 11, 2018 at 7:02 AM, Md. Jalal Uddin <dmjalal90 at gmail.com>
> wrote:
>
>> I am still getting following warnings though I put
>> setfileoption("nc","MissingToFillValue", False)
>> NDVI at _FillValue = toshort(NDVI at missing_value) ; match typeof
>> 'ndvi' (netCDF rule).
>>
>>
>> warning:NetOpenFile: MissingToFillValue option set True, but
>> missing_value attribute and data variable (ndvi) types differ: not adding
>> virtual _FillValue attribute
>> warning:Attempt to reference attribute (missing_value) which is undefined
>> warning:toshort: there are 1 int less than SHRT_MIN, which has been
>> flagged missing.
>>
>> Please find the script herewith. Please help me to fix these problems.
>>
>>
>>
>> On Thu, May 10, 2018 at 10:02 PM, Dennis Shea <shea at ucar.edu> wrote:
>>
>>> 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
>>>>
>>>
>>>
>>
>>
>> --
>> *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
>>
>
>
--
*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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