Working with converted files
Contents
Working with converted files¶
Open a converted netCDF or Zarr dataset¶
Converted netCDF files can be opened with the open_converted function that returns a lazy-loaded EchoData object (only metadata are read during opening):
import echopype as ep
file_path = "./converted_files/file.nc" # path to a converted nc file
ed = ep.open_converted(file_path) # create an EchoData object
Likewise, specify the path to open a Zarr dataset. To open such a dataset from cloud storage, use the same storage_options parameter as with open_raw. For example:
s3_path = "s3://s3bucketname/directory_path/dataset.zarr" # S3 dataset path
ed = ep.open_converted(s3_path, storage_options={"anon": True})
Combine EchoData objects¶
Converted data found in multiple files corresponding to the same instrument deployment can be combined into a single EchoData object. First assemble a list of EchoData objects from the converted files (netCDF or Zarr). Then apply combine_echodata on this list to combine all the data into a single EchoData object in memory:
ed_list = []
for converted_file in ["convertedfile1.nc", "convertedfile2.nc"]:
ed_list.append(ep.open_converted(converted_file))
combined_ed = ep.combine_echodata(ed_list)
Warning
We are aware that the combine_echodata method may result in memory problems when the EchoData objects hold large amount of data. This is an issue we are actively working on.