Masking NetCDF data with a shapefile in that has more than one variable Python

Question

I'm using NetCDF (TROPOSIF data) which i have been able plot and I now want to mask out my AOI with a shapefile.

I imported

import rioxarray
import geopandas as gpd

I opened the dataset using

ds = rioxarray.open_rasterio('TROPOSIF_L2B_2020-01-01.nc')
ds

Then I used ds[0] to view the xarray.Dataset

shapefile = "C:\Shapefiles\wv2modin\MODIN BY WV2.shp"
countries =gpd.read_file(shapefile)
countries

fig,ax = plt.subplots(figsize=(16,10))
countries.plot(ax=ax,column="FolderPath")

Now I can view the polygon with the above code but I don't know how to create mask because am new to Python.

link for the netcdf data shapefile

Answer 1

https://corteva.github.io/rioxarray/stable/examples/clip_geom.html#Clip-using-a-GeoDataFrame

clipped = ds[0].rio.clip(countries.geometry.values, countries.crs, drop=False)

UPDATE:

The NetCDF file does not appear to be a raster grid:

ncdump -h TROPOSIF_L2B_2020-01-01.nc 
netcdf TROPOSIF_L2B_2020-01-01 {
dimensions:
    n_elem = 3092691 ;
    num_bd_rfl = 7 ;
    ncorner = 4 ;
    time = 1 ;

// global attributes:
        :title = "TROPOSIF_L2B" ;
        :date_created = "2021-09-14 21:26:44.262511" ;

group: METADATA {

  group: ALGORITHM_SETTINGS {

    // group attributes:
            :Polynomial\ degree\ win-743\ nm = 3LL ;
            :Number\ SVs\ win-743\ nm = 4LL ;
            :Fitting\ window\ win-743\ nm\ \(nm\) = 743., 758. ;
            :Polynomial\ degree\ win-735\ nm = 3LL ;
            :Number\ SVs\ win-735\ nm = 7LL ;
            :Fitting\ window\ win-735\ nm\ \(nm\) = 735., 758. ;
            :Cloud\ fraction\ threshold = 0.8 ;
            :SZA\ threshold = 70. ;
            :VZA\ threshold = 60. ;
            :Quality\ level\ threshold = 80LL ;
            :SIF\ reference\ wavelength\ \(nm\) = 740. ;
            :Masked-out\ spectral\ channels\ for\ SIF\ retrieval\ \(\#\) = 179LL ;
            :FWHM\ of\ macro-channels\ for\ TOA\ reflectance = 3., 3., 3. ;
    } // group ALGORITHM_SETTINGS
  } // group METADATA

group: PRODUCT {
  variables:
    float time(time) ;
        time:units = "seconds since 2010-01-01 00:00:00" ;
        time:standard_name = "time" ;
        time:comment = "Reference time of the measurements. The reference time is set to yyyy-mm-ddT00:00:00 UTC, where yyyy-mm-dd is the day on which the measurements of a particular data granule start." ;
        time:long_name = "reference start time of measurement" ;
    int delta_time(n_elem) ;
        delta_time:units = "milliseconds since 2020-01-01T00:00:00 UTC" ;
        delta_time:standard_name = "delta time" ;
        delta_time:comment = "Time difference with time for each measurement" ;
        delta_time:long_name = "offset from the reference start time of measurement" ;
    float SIF_743(n_elem) ;
        SIF_743:units = "mW/m2/sr/nm" ;
        SIF_743:standard_name = "retrieved SIF@740 743-758 nm fitting window" ;
        SIF_743:long_name = "retrieved SIF@740 (743-758nm)" ;
    float SIF_Corr_743(n_elem) ;
        SIF_Corr_743:units = "mW/m2/sr/nm" ;
        SIF_Corr_743:standard_name = "daylength-corr SIF@740 743-758 nm fitting window" ;
        SIF_Corr_743:long_name = "daylength-corr SIF@740 (743-758nm)" ;
    float SIF_ERROR_743(n_elem) ;
        SIF_ERROR_743:units = "mW/m2/sr/nm" ;
        SIF_ERROR_743:standard_name = "1-sigma error 743-758 nm fitting window" ;
        SIF_ERROR_743:long_name = "1-sigma SIF retrieval error (743-758nm)" ;
    float SIF_735(n_elem) ;
        SIF_735:units = "mW/m2/sr/nm" ;
        SIF_735:standard_name = "retrieved SIF@740 735-758 nm fitting window" ;
        SIF_735:long_name = "retrieved SIF@740 (735-758nm)" ;
    float SIF_Corr_735(n_elem) ;
        SIF_Corr_735:units = "mW/m2/sr/nm" ;
        SIF_Corr_735:standard_name = "daylength-corr SIF@740 735-758 nm fitting window" ;
        SIF_Corr_735:long_name = "daylength-corr SIF@740 (735-758nm)" ;
    float SIF_ERROR_735(n_elem) ;
        SIF_ERROR_735:units = "mW/m2/sr/nm" ;
        SIF_ERROR_735:standard_name = "1-sigma error 735-758 nm fitting window" ;
        SIF_ERROR_735:long_name = "1-sigma SIF retrieval error (735-758nm)" ;
    float latitude(n_elem) ;
        latitude:standard_name = "latitude" ;
    float longitude(n_elem) ;
        longitude:standard_name = "longitude" ;

  group: SUPPORT_DATA {

    group: DETAILED_RESULTS {
      variables:
        float TOA_RFL(n_elem, num_bd_rfl) ;
            TOA_RFL:units = "-" ;
            TOA_RFL:standard_name = "TOA Reflectance (cloud frac<0.2)" ;
            TOA_RFL:long_name = "TOA Reflectance at atmospheric windows within 665-785 nm" ;
        float WVL_RFL(num_bd_rfl) ;
            WVL_RFL:units = "nm" ;
            WVL_RFL:standard_name = "WVL_RFL" ;
            WVL_RFL:long_name = "Spectral points at which TOA_RFL is calculated" ;
        float Mean_TOA_RAD_743(n_elem) ;
            Mean_TOA_RAD_743:units = "mW/m2/sr/nm" ;
            Mean_TOA_RAD_743:standard_name = "TOA Radiance" ;
            Mean_TOA_RAD_743:long_name = "Mean TOA Radiance in 743-758 nm fitting window" ;
        float Mean_TOA_RAD_735(n_elem) ;
            Mean_TOA_RAD_735:units = "mW/m2/sr/nm" ;
            Mean_TOA_RAD_735:standard_name = "TOA Radiance" ;
            Mean_TOA_RAD_735:long_name = "Mean TOA Radiance in 735-758 nm fitting window" ;
      } // group DETAILED_RESULTS

    group: GEOLOCATIONS {
      variables:
        float viewing_zenith_angle(n_elem) ;
            viewing_zenith_angle:standard_name = "viewing zenith angle" ;
        float solar_zenith_angle(n_elem) ;
            solar_zenith_angle:standard_name = "solar zenith angle" ;
        float relative_azimuth_angle(n_elem) ;
            relative_azimuth_angle:standard_name = "relative azimuth angle" ;
        float latitude_bounds(n_elem, ncorner) ;
            latitude_bounds:standard_name = "latitude_bounds" ;
            latitude_bounds:units = "degrees_north" ;
            latitude_bounds:comment = "The four latitude boundaries of each ground pixel" ;
        float longitude_bounds(n_elem, ncorner) ;
            longitude_bounds:standard_name = "longitude_bounds" ;
            longitude_bounds:units = "degrees_east" ;
            longitude_bounds:comment = "The four longitude boundaries of each ground pixel" ;
      } // group GEOLOCATIONS

    group: INPUT_DATA {
      variables:
        float cloud_fraction_L2(n_elem) ;
            cloud_fraction_L2:standard_name = "cloud_fraction" ;
        ubyte LC_MASK(n_elem) ;
            LC_MASK:units = "([ENF=1, EBF=2, DNF=3, DBF=4, MF=5, CS=6, OS=7, WS=8, S=9, G=10, PW=11, C=12, U=13, CNV=14, SI=15, B=16])" ;
            LC_MASK:standard_name = "Land Cover Map (MODIS MCD12C1 2018)" ;
            LC_MASK:long_name = "Land Cover Map" ;
      } // group INPUT_DATA
    } // group SUPPORT_DATA
  } // group PRODUCT
}

You will need to convert this data to a grid before you can clip the data.