Struggling with write_file() function

[rba27]

Hello! Thank you so much for this lovely Python package. It has been very useful in my biological oceanography research.

I am having a problem saving my Eddies Observations object to a usable file. When I try to save the object to a NetCDF file, I get the following error:

Traceback (most recent call last):
[...]
TypeError: illegal data type for attribute b'rotation_type', must be one of dict_keys(['S1', 'i1', 'u1', 'i2', 'u2', 'i4', 'u4', 'i8', 'u8', 'f4', 'f8']), got O

I am able to save the file to zarr format, but when I then attempt to open it again in a different script using load_from_zarr(), I get this error:

"/Users/miniconda3/envs/eddy_tracker/lib/python3.10/site-packages/py_eddy_tracker/observations/observation.py", line 819, in load_from_zarr
   track_array_variables = h_zarr.attrs["track_array_variables"]
 File "/Users/miniconda3/envs/eddy_tracker/lib/python3.10/site-packages/zarr/attrs.py", line 72, in __getitem__
   return self.asdict()[item]
KeyError: 'track_array_variables' 

Here is the code I am using to produce the Eddy Observations:

from datetime import datetime
import numpy as np
import pandas as pd
from py_eddy_tracker import data
from py_eddy_tracker.dataset.grid import RegularGridDataset
from py_eddy_tracker.observations.observation import EddiesObservations
from netCDF4 import Dataset
from py_eddy_tracker.eddy_feature import Contours
from matplotlib import pyplot as plt

def start_axes(title):
   fig = plt.figure(figsize=(13, 8))
   ax = fig.add_axes([0.03, 0.03, 0.90, 0.94])
   ax.set_xlim(279, 304), ax.set_ylim(29, 44)
   ax.set_aspect("equal")
   ax.set_title(title, weight="bold")
   return ax


def update_axes(ax, mappable=None):
   ax.grid()
   if mappable:
       plt.colorbar(mappable, cax=ax.figure.add_axes([0.94, 0.05, 0.01, 0.9]))

file_path = "/Users/Desktop/EddyTracking/new_adt_22_23_360.nc"

output_path = "./Eddies_GS/"
output_file = "gs_eddies_observations.nc"
nc_file = Dataset(file_path, 'r')
time_var = nc_file.variables['time']
time_values = time_var[:] 
nc_file.close()

base_date = datetime(2022, 1, 11)

a_eddy_observations = EddiesObservations()
c_eddy_observations = EddiesObservations()

for t, time in enumerate(time_values):
   print(f"starting analysis for time {t}")
   grid = RegularGridDataset(
       file_path,
       "longitude",
       "latitude",
       indexs=dict(
           time = t
       ),
   )

   grid.bessel_high_filter("adt", 700)

   date = base_date + pd.Timedelta(days=t) 
   a, c = grid.eddy_identification(
       "adt",  
       "ugos", "vgos",  
       date,
       0.002,
       shape_error=55
   )

   a_eddy_observations = a_eddy_observations.merge(a)
   c_eddy_observations = c_eddy_observations.merge(c)

a_eddy_observations.write_file(
   output_path,
   "a_test_eddies_observations.nc",
   zarr_flag=False

)

c_eddy_observations.write_file(
   output_path,
   "c_test_eddies_observations.nc",
   zarr_flag=False

)

print("All eddy observations have been processed and saved.")

Do you know what may be causing this issue? Thank you so much for your help!

[AntSimi]

Which version of netCDF4/numba and numpy did you use? with which python?

[rba27]

So sorry for the very delayed response. I am using NetCDF4=1.5.8, numba=0.55.2, and numpy=1.22.4 with python=3.10.14