batch identification of eddies over multiple days from a single netCDF file about py-eddy-tracker

[AntSimi]

It's shortly explain here: https://py-eddy-tracker.readthedocs.io/en/latest/grid_identification.html#shell-bash-command

[zhanglan009]

Dear AntSimi,
Thank you very much for your response. However, I am still a bit confused about how to set the indices. The examples it provided seem to set parameters for a single day or layer, like 20190223 with time=0 and date=datetime(2019,2,23), and I have searched through your other examples but couldn't find information on setting indices for multiple days. If my data spans from 20000101 to 20201231, representing a 20-year period, how can I set the indices, identify them, and store them in one NetCDF file? Could you provide an example? Thank you very very much. Additionally, does time=0, 20, 30 correspond to the number of days from the start-1?
Lan

[AntSimi]

Could you share a ncdump of your dataset?

[zhanglan009]

Yes! 20 years data are too large. I upload a 15 days data (I also email it to you cause the file size upload here still limited). The data is downloaded from https://data.marine.copernicus.eu/product/SEALEVEL_GLO_PHY_L4_NRT_008_046/.

[zhanglan009]

Yes! 20 years data are too large. I upload a 15 days data. The data is downloaded from https://data.marine.copernicus.eu/product/SEALEVEL_GLO_PHY_L4_NRT_008_046/. ***@***.***

…

---- Replied Message ---- From Antoine ***@***.***> Date 2/29/2024 16:58 To ***@***.***> Cc ***@***.***> , ***@***.***> Subject Re: [AntSimi/py-eddy-tracker] batch identification of eddies over multiple days from a single netCDF file (Issue #229) Could you share a ncdump of your dataset? —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: ***@***.***> 从 网易邮箱大师 发来的云附件 cmems_obs-sl_glo_phy-ssh_my_allsat-l4-duacs-0.25deg_P1M-m_sla_179.88W-179.88E_89.88S-89.88N_2000-01-01-2023-05-01.nc (1111.4MB,2024年3月15日 17:15 到期) 下载

[AntSimi]

i want juste header of the file with ncdump -h

[zhanglan009]

OK!

netcdf cmems_obs-sl_glo_phy-ssh_nrt_allsat-l4-duacs-0.25deg_P1D_1709197734343 {
dimensions:
        latitude = 720 ;
        longitude = 1440 ;
        time = 16 ;
variables:
        float adt(time, latitude, longitude) ;
                string adt:units = "m" ;
                adt:_FillValue = NaN ;
                string adt:standard_name = "sea_surface_height_above_geoid" ;
                string adt:long_name = "Absolute dynamic topography" ;
        float err_sla(time, latitude, longitude) ;
                string err_sla:units = "m" ;
                err_sla:_FillValue = NaN ;
                string err_sla:standard_name = "sea_surface_height_above_sea_level standard_error" ;
                string err_sla:long_name = "Formal mapping error" ;
        float err_ugosa(time, latitude, longitude) ;
                string err_ugosa:units = "m/s" ;
                err_ugosa:_FillValue = NaN ;
                string err_ugosa:standard_name = "surface_geostrophic_eastward_sea_water_velocity_assuming_sea_level_for_geoid standard_error" ;
                string err_ugosa:long_name = "Formal mapping error on zonal geostrophic velocity anomalies" ;
        float err_vgosa(time, latitude, longitude) ;
                string err_vgosa:units = "m/s" ;
                err_vgosa:_FillValue = NaN ;
                string err_vgosa:standard_name = "surface_geostrophic_northward_sea_water_velocity_assuming_sea_level_for_geoid standard_error" ;
                string err_vgosa:long_name = "Formal mapping error on meridional geostrophic velocity anomalies" ;
        float flag_ice(time, latitude, longitude) ;
                string flag_ice:units = "" ;
                flag_ice:_FillValue = NaN ;
                string flag_ice:standard_name = "status_flag" ;
                string flag_ice:long_name = "Ice Flag for a 15% criterion of ice concentration" ;
        float latitude(latitude) ;
                string latitude:standard_name = "latitude" ;
                string latitude:long_name = "Latitude" ;
                string latitude:units = "degrees_north" ;
                string latitude:unit_long = "Degrees North" ;
                string latitude:axis = "Y" ;
                latitude:valid_min = -89.875f ;
                latitude:valid_max = 89.875f ;
        float longitude(longitude) ;
                string longitude:standard_name = "longitude" ;
                string longitude:long_name = "Longitude" ;
                string longitude:units = "degrees_east" ;
                string longitude:unit_long = "Degrees East" ;
                string longitude:axis = "X" ;
        float sla(time, latitude, longitude) ;
                string sla:units = "m" ;
                sla:_FillValue = NaN ;
                string sla:standard_name = "sea_surface_height_above_sea_level" ;
                string sla:long_name = "Sea level anomaly" ;
        double time(time) ;
                string time:standard_name = "time" ;
                string time:long_name = "Time" ;
                string time:units = "seconds since 1970-01-01 00:00:00" ;
                string time:calendar = "gregorian" ;
                string time:axis = "T" ;
        float ugos(time, latitude, longitude) ;
                string ugos:units = "m/s" ;
                ugos:_FillValue = NaN ;
                string ugos:standard_name = "surface_geostrophic_eastward_sea_water_velocity" ;
                string ugos:long_name = "Absolute geostrophic velocity: zonal component" ;
        float ugosa(time, latitude, longitude) ;
                string ugosa:units = "m/s" ;
                ugosa:_FillValue = NaN ;
                string ugosa:standard_name = "surface_geostrophic_eastward_sea_water_velocity_assuming_sea_level_for_geoid" ;
                string ugosa:long_name = "Geostrophic velocity anomalies: zonal component" ;
        float vgos(time, latitude, longitude) ;
                string vgos:units = "m/s" ;
                vgos:_FillValue = NaN ;
                string vgos:standard_name = "surface_geostrophic_northward_sea_water_velocity" ;
                string vgos:long_name = "Absolute geostrophic velocity: meridian component" ;
        float vgosa(time, latitude, longitude) ;
                string vgosa:units = "m/s" ;
                vgosa:_FillValue = NaN ;
                string vgosa:standard_name = "surface_geostrophic_northward_sea_water_velocity_assuming_sea_level_for_geoid" ;
                string vgosa:long_name = "Geostrophic velocity anomalies: meridian component" ;

// global attributes:
                string :Conventions = "CF-1.11" ;
                string :title = "NRT merged all satellites Global Ocean Gridded SSALTO/DUACS Sea Surface Height L4 product and derived variables" ;
                string :institution = "CLS, CNES" ;
                string :source = "Altimetry measurements" ;
                string :history = "2023-11-24 00:53:07Z: Creation" ;
                string :contact = "[email protected]" ;
                string :references = "http://marine.copernicus.eu" ;
                string :comment = "Sea Surface Height measured by Altimetry and derived variables" ;
                string :subset\:source = "ARCO data downloaded from the Marine Data Store using the MyOcean Data Portal" ;
                string :subset\:productId = "SEALEVEL_GLO_PHY_L4_NRT_008_046" ;
                string :subset\:datasetId = "cmems_obs-sl_glo_phy-ssh_nrt_allsat-l4-duacs-0.25deg_P1D_202311" ;
                string :subset\:date = "2024-02-29T09:08:54.343Z" ;
}

[AntSimi]

You must do an identification for each day of interest, so you could use --indexs time=i to do identification on each time step of your netcdf, where i is an int.

[zhanglan009]

Thank you very much!! I'll be back when I try it.

[zhanglan009]

Thank you very much for your response. After adding the parameter index time=i, it seems that the three-dimensional data, including time, is being read. However, when executing functions like g.display, g.bessel_high_filter, etc., I encountered an IndexError: index exceeds dimension bounds error. How can I further implement these functions?

# %%
# Load Input grid, ADT is used to detect eddies
grid_name= ("cmems_obs-sl_glo_phy-ssh_nrt_allsat-l4-duacs-0.25deg_P1D_1709197734343.nc")
g = RegularGridDataset(grid_name, "longitude","latitude", nan_masking=True,
#manual area subset
indexs=dict(longitude=slice(1141,1264),
            latitude=slice(337,504),
            time=360
),)

ax = start_axes("SLA (m)")
m = g.display(ax, "sla", vmin=-0.15, vmax=0.15, cmap="RdBu_r")
update_axes(ax, m)
plt.show()

---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
Cell In[7], line 12
      4 g = RegularGridDataset(grid_name, "longitude","latitude", nan_masking=True,
      5 #manual area subset
      6 indexs=dict(longitude=slice(1141,1264),
      7             latitude=slice(337,504),
      8             time=360
      9 ),)
     11 ax = start_axes("SLA (m)")
---> 12 m = g.display(ax, "sla", vmin=-0.15, vmax=0.15, cmap="RdBu_r")
     13 update_axes(ax, m)
     14 plt.show()

File ~/miniconda3/envs/pyed/lib/python3.10/site-packages/py_eddy_tracker/dataset/grid.py:1912, in RegularGridDataset.display(self, ax, name, factor, ref, **kwargs)
   1910 if "cmap" not in kwargs:
   1911     kwargs["cmap"] = "coolwarm"
-> 1912 data = self.grid(name) if isinstance(name, str) else name
   1913 if ref is None:
   1914     x = self.x_bounds

File ~/miniconda3/envs/pyed/lib/python3.10/site-packages/py_eddy_tracker/dataset/grid.py:547, in GridDataset.grid(self, varname, indexs)
    537 dims = h.variables[varname].dimensions
    538 sl = [
    539     indexs.get(
    540         dim,
   (...)
    545     for dim in dims
    546 ]
--> 547 self.vars[varname] = h.variables[varname][sl]
    548 if len(self.x_dim) == 1:
    549     i_x = where(array(dims) == self.x_dim)[0][0]

File src/netCDF4/_netCDF4.pyx:4406, in netCDF4._netCDF4.Variable.__getitem__()

File src/netCDF4/_netCDF4.pyx:5348, in netCDF4._netCDF4.Variable._get()

IndexError: index exceeds dimension bounds

[zhanglan009]

I have another problem: when I use the ORCAGrid function from your issue #6 (#6), and import an irregular gird data with a longitude range of [157, 324], after executing a, c = h.eddy_identification(*args, **kwargs), attempting to plot with a.display(ax, label='Anticyclonic', color='green', **kwargs_display) does not work. I can only get a blank map between [-180, 180], and anything beyond >180 cannot be plotted. if I set ax.set_xlim(220, 260), could plot the eddies, but the coastline cannot show. How could I set the index or modified the a.display function or other part? Thank you very much for your help!!!

[AntSimi]

which matplotlib version did you use?

[zhanglan009]

matplotlib version is 3.7.1