Have you considered using Matlab for extracting netcdf files? Recently, I came across a helpful video that demonstrates using lon and lat to extract temperature values from a netcdf file. Not sure if it would help. 

https://www.youtube.com/watch?v=PJurb-IPKM8&index=3&list=LLAECjp5cXJoIyHl69MCcOBQ

Hello Jayanti,

if you are familiar with "R", i can give you a straightforward and simple solution.

Let me know

Rgds

Malcolm

Thanks for your reply. but I have to extract data from netcdf on lat lon provided in csv file which means first I have to read lat lon from csv file then read lat lon from netcdf file, then data will be extracted from netcdf over those lat lon which is in CSV file.

Will it possible in NCL?

You can do all that in R very easily. Read csv/excel file in R and save your coordinates as dataframe/matrix. Read netcdf (full file) in R and save it as raster stack or brick object. Then simply extract temperature from the raster stack/brick using the coordinates from the dataframe/matrix and save that as another dataframe (say temperature_df). You can write this temperature_df to a .csv/excel file; all operations in R, few lines of code. 

NCL should also be possible, but i used it a while back. May be someone more familiar with NCL can advise better. Both R and NCL can also write the desired output as netcdf file. It all depends on what you want to do further with the output (if some statistical analysis, stick to R).

By the way, R and NCL are free, Matlab is not. 

I use a Python script to do the same. I might share the script if you are familiar with Python and interested to get it.

Hi AFM, I'm interested by your Python script...

The script is available in my github here: https://github.com/kamal0013/Climate-Data-Assessment/blob/master/Extract_netCDF.py

May be this link is helpful for you.

https://www.researchgate.net/post/How_can_I_extract_data_from_NetCDF_file_by_python2

It is very easy in ArcGIS 10,

1. Open NetCDF file in ArcBox

2. Open Multidimation tool

3. Make NetCDF table view

4. In this box

just fill the information

variable- temp

Row Dimension (Time)

Dimension values - Mention lat and long

table will generate

just export in excel file.

If you have large number of station then first make shape file all location and then do same process.

try it , otherwise I can also help you, send me lat and long of station I will extract data.

If you can please provide the NetCDF file I can make a python scripts for you to extract data from NetCDF on given lat lon

you can use Python script. With KDTree spatial function of Scipy, it will help you to find the nearest point of given coordinate. Alternatively, you can use CDO function like remapnn to find values from a single grid which corresponds to your given lat lon coordinate

I found a link with good description and easy solution!

https://gis.stackexchange.com/questions/290138/extracting-values-at-specific-latitude-longitude-from-modis-swath-data

You need to use only 1 line in python:

coordinates = np.unravel_index((np.abs(Latitude - lat_obs) + np.abs(Longitude - long_obs)).argmin(), Latitude.shape)

Hi everyone,

I have the same question.

I need the data of temperature from this area: Longitude 117.05 - 123.95, Latitude 18.05 - 26.05 from 2005 - 2018. I have nc files downloaded from NASA. These nc files are daily seawater temperatures.

How to extract the data of temperature from these nc files and convert it to excel data?

Thank you in advance.

Hi

As you when you want to extract nc or nc4 files you should write codes in different languages and software tools. Actually, it is not an easy process since the nc4 files have different format in temporal and spatial scales.

There are various software tools and programming languages, namely NCL, ArcGIS, Matlab, GRADS, R, and etc., but you should enough information about coding in the mentioned tools and programming languages.

For example the output of CMIP5 data are in nc4 ( https://agrimetsoft.com/Netcdf-Extractor.aspx), and CMIP5 has around 60 models that they are different in time and distance. So, if you want to write a unique code for extract every of CMIP5 models it would not be easy.

However, I wanna inform you a useful and powerful tool which can easily extract every data file in any spatial and temporal scales. Such as CORDEX data, CMIP5, and etc. Just see the "Open nc file" link for further clarifications.

https://agrimetsoft.com/open_nc_file_for_coordinates.aspx

Kind Regards

The easiest one in which you can get the answer with the use of ferret.

Ex.

list/x=long_valur/y=lat_value variable

If 4 dimension that includes depth/height you can write the command as

list/x=long_valur/y=lat_value/z=depth_value variable

Hi all,

CDO works very good with netCDF

This command can be used for specific locations (long, lat)

cdo -outputtab,date,value -remapnn,lon=X_lat=Y infile.nc > output.txt

here X = longitude and Y = latitude

Dear all,

Check the beta version of ncextract matlab function (https://se.mathworks.com/matlabcentral/fileexchange/73055-automated-nctools) for an automated extraction of netcdf data at specified coordinates (see example).

If you have any questions or problems, contact: [email protected]

It is possible using ArcGIS 10,

1. Open NetCDF file in ArcBox

2. Open Multidimation tool

The netCDF4 package in python could be helpful for this kind of analysis. You can import it and use Dataset for further manipulation of your data:

from netCDF4 import Dataset

nc = Dataset("met.nc") nc dates = nc.variables['Time'][:] lats = nc.variables['XLAT'][:] lons = nc.variables['XLONG'][:]

lats = 40 lons = 50

You can do it using python with netcdf4 and numpy libraries.

The extraction also depends on the dimensions of your variable.

For example, the T2 from WRF output is function of (Time, south_north, west_east)

so you need to import the Dataset from netcdf4 and read the netcdf file

df = Dataset('path_to_your_file', mode='r')

after this, you need to specify the time range, the row number and the column number, like this:

T2 = df.variables['T2'][0, 30,30]

in the command above I am extracting the T2 from the netcdf file at the first hour of the data (0), at row 30 and column 30.

if you want to extract from a specific location I would recommend to use the pyproj libraries to set the coordinates system and convert the lat/lon into row/col information, and with this row and col you can extract the correct location.

you also can extract the entire matrix for one hour using this:

T2 = df.variables['T2'][0, :,:]

in this case you will the 2D array with the data at time 0 of the netcdf file.

Thus, it depends on the dimensions of you variables. There variables which are in function of Times, vertical level, row, col... in this case, you also need to specify which vertical level you want to get the information.

you can adapt this example to extract your data.

Regards