I have a txt file which has data in netcdf format. How to read it?

so i downloaded imerg data for 90 days from GES DISC. the whole file got downloaded in txt but the data in it looks like this

https://data.gesdisc.earthdata.nasa.gov/data/GPM_L3/GPM_3IMERGDF.07/2023/06/3B-DAY.MS.MRG.3IMERG.20230618-S000000-E235959.V07B.nc4. i have 90 of these. how can i open this in matalb. i want to plot a graph like this. how can i do it.

[Ayush Singh]

Hi Shagun,

Is the data in .netcdf format?

Do you want to know how to read and plot from .netcdf data?

[Shagun]

Data is in netcdf format. I have also mentioned the format in the question itself. It’s a link that ends with .nc. It does mean that data is in netcdf right? Correct me if i am wrong. But the whole file is in txt.

[Umar]

Hi Shagun,

You are right. So, before reading NetCDF files in Matlab, ensure that you have the NetCDF library installed on your system. You can download the library from the Unidata website

https://www.unidata.ucar.edu/software/netcdf/

Use the ncread function in Matlab to read NetCDF files like the IMERG data files you downloaded. Since you have 90 files to process, you can create a loop in Matlab to read each file, extract the data, and plot the graph iteratively.Make sure to adjust the file paths and variable names in the loop to handle each file correctly. Here is an example code snippet to read a NetCDF file

% Example code to read a NetCDF file
ncfile = 'path_to_your_file.nc4';
data = ncread(ncfile, 'variable_name');

Replace 'data.nc' with the path to your NetCDF file and 'variable_name' with the name of the variable you want to read from the file. For more information on this function, please refer to

https://www.mathworks.com/help/matlab/ref/ncread.html

By following these steps and utilizing Matlab's NetCDF functions, you can effectively read and work with data stored in NetCDF format, even if the file appears to be in a text format externally.

Afterwards, you need to identify the specific variables you want to plot from the IMERG data files. These could be precipitation values, timestamps, or any other relevant data.Extract and store this data in Matlab variables for plotting.Once you have extracted the necessary data, you can use Matlab's plotting functions like plot, scatter, or imagesc to visualize the data.Depending on the type of graph you want to create (time series, spatial plot, etc.), you can customize the plot accordingly.

I hope this answers your question.

[Star Strider]

When I just now checked, that URL requires you to register and then use a username and password to log in. I have never ttried doing that in MATLAB, however it may be possible. In all likelihood, you wilh need to download the files (or thier URLs) manually, tthen work with them.

After that, MATLAB has an entire set of functions to deal with nettCDF Files. They were introduced in R2011a.

Then, see the documentation on CDF Files.

[Walter Roberson]

Using the MATLAB netcdf libraries does not require downloading anything from Unidata.

[Walter Roberson]

NETCDF files are not text files ??

[Umar]

Hi Shagun,

Cris has answered your question and showed the plot you wanted,please give him a vote to solve your problem for going above and beyond.

@Walter & @Star, thanks for jumping in and helping us to solve this problem as well.

Answer 1

[Cris LaPierre]

The link you shared gives an error, but using the information in the url, I was able to locate the file

• GPM IMERG Final Precipitation L3 1 day 0.1 degree x 0.1 degree V07 (GPM_3IMERGDF)

Use ncdisp to inspect the file contents to obtain the variable names and related info.

ncfile = '3B-DAY.MS.MRG.3IMERG.20230618-S000000-E235959.V07B.nc4';

ncdisp(ncfile)

Source:

GPM_3IMERGDF_07-20240720_125735\3B-DAY.MS.MRG.3IMERG.20230618-S000000-E235959.V07B.nc4

Format:

netcdf4

Global Attributes:

BeginDate = '2023-06-18'

BeginTime = '00:00:00.000Z'

EndDate = '2023-06-18'

EndTime = '23:59:59.999Z'

FileHeader = 'StartGranuleDateTime=2023-06-18T00:00:00.000Z;

StopGranuleDateTime=2023-06-18T23:59:59.999Z'

InputPointer = '3B-HHR.MS.MRG.3IMERG.20230618-S000000-E002959.0000.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S003000-E005959.0030.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S010000-E012959.0060.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S013000-E015959.0090.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S020000-E022959.0120.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S023000-E025959.0150.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S030000-E032959.0180.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S033000-E035959.0210.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S040000-E042959.0240.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S043000-E045959.0270.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S050000-E052959.0300.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S053000-E055959.0330.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S060000-E062959.0360.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S063000-E065959.0390.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S070000-E072959.0420.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S073000-E075959.0450.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S080000-E082959.0480.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S083000-E085959.0510.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S090000-E092959.0540.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S093000-E095959.0570.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S100000-E102959.0600.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S103000-E105959.0630.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S110000-E112959.0660.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S113000-E115959.0690.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S120000-E122959.0720.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S123000-E125959.0750.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S130000-E132959.0780.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S133000-E135959.0810.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S140000-E142959.0840.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S143000-E145959.0870.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S150000-E152959.0900.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S153000-E155959.0930.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S160000-E162959.0960.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S163000-E165959.0990.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S170000-E172959.1020.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S173000-E175959.1050.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S180000-E182959.1080.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S183000-E185959.1110.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S190000-E192959.1140.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S193000-E195959.1170.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S200000-E202959.1200.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S203000-E205959.1230.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S210000-E212959.1260.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S213000-E215959.1290.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S220000-E222959.1320.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S223000-E225959.1350.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S230000-E232959.1380.V07B.HDF5;3B-HHR.MS.MRG.3IMERG.20230618-S233000-E235959.1410.V07B.HDF5'

title = 'GPM IMERG Final Precipitation L3 1 day 0.1 degree x 0.1 degree (GPM_3IMERGDF)'

DOI = '10.5067/GPM/IMERGDF/DAY/07'

ProductionTime = '2024-01-12T16:20:48.000Z'

Dimensions:

lon = 3600

lat = 1800

time = 1

nv = 2

Variables:

precipitation

Size: 1800x3600x1

Dimensions: lat,lon,time

Datatype: single

Attributes:

units = "mm/day"

long_name = "Daily mean precipitation rate (combined microwave-IR) estimate. Formerly precipitationCal."

coordinates = "time lon lat"

_FillValue = -9999.9004

precipitation_cnt

Size: 1800x3600x1

Dimensions: lat,lon,time

Datatype: int8

Attributes:

units = "count"

long_name = "Count of all valid half-hourly precipitation retrievals for the day"

coordinates = "time lon lat"

precipitation_cnt_cond

Size: 1800x3600x1

Dimensions: lat,lon,time

Datatype: int8

Attributes:

units = "count"

long_name = "Count of half-hourly precipitation retrievals for the day where precipitation is at least 0.01 mm/hr"

coordinates = "time lon lat"

MWprecipitation

Size: 1800x3600x1

Dimensions: lat,lon,time

Datatype: single

Attributes:

units = "mm/day"

long_name = "Daily mean High Quality precipitation rate from all available microwave sources. Formerly HQprecipitation."

coordinates = "time lon lat"

_FillValue = -9999.9004

MWprecipitation_cnt

Size: 1800x3600x1

Dimensions: lat,lon,time

Datatype: int8

Attributes:

units = "count"

long_name = "Count of all valid half-hourly MWprecipitation retrievals for the day"

coordinates = "time lon lat"

MWprecipitation_cnt_cond

Size: 1800x3600x1

Dimensions: lat,lon,time

Datatype: int8

Attributes:

units = "count"

long_name = "Count of half-hourly MWprecipitation retrievals for the day where precipitation is at least 0.01 mm/hr"

coordinates = "time lon lat"

randomError

Size: 1800x3600x1

Dimensions: lat,lon,time

Datatype: single

Attributes:

units = "mm/day"

long_name = "Root-mean-square error estimate for combined microwave-IR daily precipitation rate"

coordinates = "time lon lat"

_FillValue = -9999.9004

randomError_cnt

Size: 1800x3600x1

Dimensions: lat,lon,time

Datatype: int8

Attributes:

units = "count"

long_name = "Count of valid half-hourly randomError retrievals for the day"

coordinates = "time lon lat"

probabilityLiquidPrecipitation

Size: 1800x3600x1

Dimensions: lat,lon,time

Datatype: int8

Attributes:

units = "percent"

long_name = "Probability of liquid precipitation"

description = "Probability of liquid precipitation estimated with a diagnostic parameterization using ancillary data. 0=missing values; 1=likely solid; 100=likely liquid or no precipitation. Screen by positive precipitation or precipitation_cnt_cond to locate meaningful probabilities."

coordinates = "time lon lat"

lon

Size: 3600x1

Dimensions: lon

Datatype: single

Attributes:

units = "degrees_east"

long_name = "Longitude"

lat

Size: 1800x1

Dimensions: lat

Datatype: double

Attributes:

units = "degrees_north"

long_name = "Latitude"

time

Size: 1x1

Dimensions: time

Datatype: double

Attributes:

units = "days since 1980-01-06 00:00:00Z"

standard_name = "time"

long_name = "time"

bounds = "time_bnds"

time_bnds

Size: 2x1

Dimensions: nv,time

Datatype: double

Attributes:

units = "days since 1980-01-06 00:00:00Z"

coordinates = "time nv"

Loading the data from the file is straightforward enough once you know the variable names

lat = ncread(ncfile,'lat');

lon = ncread(ncfile,'lon');

precip = ncread(ncfile,'precipitation');

The real challenge is only plotting the data that overlaps the United Kingdom. There are many viable approaches. I'll share what worked for me. I used the following functions

• inpolygon - determine which points fall inside the borders of the United Kingdom
• axesm - create a map axes with the projection of the data (WGS84 or mercator)
• pcolorm - create a geolocated grid of the precipitation data.
• reducem - reduce density of border data (speeds up plotting)

You will also need to find boundaries for the United Kingdom. Based on your example, the coastlines data in MATLAB is too coarse. You might consider using either of these File Exchange submissions:

• borders
• Climate Data Toolbox for MATLAB

Otherwise, you can find the data yourself. For example, see this answer: How to plot boundaries region contours of countries in worldmap?

The shapefile I used was very detailed, so I used reducem to reduce the number of points.

gb = shaperead('UKshapefile.shp')

[X, Y] = reducem(gb.X',gb.Y',0.005);

The data files are too big to upload here, so I am loading a mat file of the results of the above code (variables lat, lon, precip, X, Y)

load ncData.mat

% create matrices of lat and lon data so they are the same size as precip
[LN,LT] = meshgrid(double(lon),double(lat));

% identify points that lie inside boundaries of UK
IN = inpolygon(LN(:),LT(:),X,Y);

% plot borders of UK
figure
axesm('mercator','Frame','off')
geoshow(Y,X)

% Set all points outside the UK to nan so they are not colored
LN(~IN) = nan;
LT(~IN) = nan;
precip(~IN) = nan;

% plot precipitation data
pcolorm(LT,LN,precip)
colormap('jet')
c = colorbar;
c.Label.String = "Daily mean precipitation rate (mm/day)";
title("Daily mean precipitation rate (mm/day)")