EchoData#
- class echopype.echodata.EchoData(converted_raw_path: Optional[PathHint] = None, storage_options: Optional[Dict[str, Any]] = None, source_file: Optional[PathHint] = None, xml_path: Optional[PathHint] = None, sonar_model: Optional[SonarModelsHint] = None, open_kwargs: Optional[Dict[str, Any]] = None, parsed2zarr_obj=None)#
Bases:
object
Echo data model class for handling raw converted data, including multiple files associated with the same data set.
- Attributes
- group_paths
- nbytes
- nc_path
- version_info
- zarr_path
Methods
to_netcdf
([save_path, compress, overwrite, ...])Save content of EchoData to netCDF.
to_zarr
([save_path, compress, overwrite, ...])Save content of EchoData to zarr.
update_platform
(extra_platform_data[, ...])Updates the EchoData["Platform"] group with additional external platform data.
from_file
Attributes Summary
Methods Summary
from_file
(converted_raw_path[, ...])to_netcdf
([save_path, compress, overwrite, ...])Save content of EchoData to netCDF.
to_zarr
([save_path, compress, overwrite, ...])Save content of EchoData to zarr.
update_platform
(extra_platform_data[, ...])Updates the EchoData["Platform"] group with additional external platform data.
Attributes Documentation
- group_map: Dict[str, Any] = {'beam': {'description': 'contains backscatter data (either complex samples or uncalibrated power samples) and other beam or channel-specific data, including split-beam angle data when they exist.', 'ep_group': 'Sonar/Beam_group1', 'name': 'Beam_group1'}, 'beam_group3': {'description': '', 'ep_group': 'Sonar/Beam_group3', 'name': 'Beam_group3'}, 'beam_group4': {'description': '', 'ep_group': 'Sonar/Beam_group4', 'name': 'Beam_group4'}, 'beam_power': {'description': 'contains backscatter power (uncalibrated) and other beam or channel-specific data, including split-beam angle data when they exist. Only exists if complex backscatter data are already in Sonar/Beam_group1', 'ep_group': 'Sonar/Beam_group2', 'name': 'Beam_group2'}, 'environment': {'description': 'contains information relevant to acoustic propagation through water.', 'ep_group': 'Environment', 'name': 'Environment'}, 'nmea': {'description': 'contains information specific to the NMEA protocol.', 'ep_group': 'Platform/NMEA', 'name': 'NMEA'}, 'platform': {'description': 'contains information about the platform on which the sonar is installed.', 'ep_group': 'Platform', 'name': 'Platform'}, 'provenance': {'description': 'contains metadata about how the SONAR-netCDF4 version of the data were obtained.', 'ep_group': 'Provenance', 'name': 'Provenance'}, 'sonar': {'description': 'contains sonar system metadata and sonar beam groups.', 'ep_group': 'Sonar', 'name': 'Sonar'}, 'top': {'description': 'contains metadata about the SONAR-netCDF4 file format.', 'ep_group': None, 'name': 'Top-level'}, 'vendor': {'description': 'contains vendor-specific information about the sonar and the data.', 'ep_group': 'Vendor_specific', 'name': 'Vendor_specific'}}#
- group_paths#
- nbytes#
- nc_path#
- version_info#
- zarr_path#
Methods Documentation
- classmethod from_file(converted_raw_path: str, storage_options: Optional[Dict[str, Any]] = None, open_kwargs: Dict[str, Any] = {}) echopype.echodata.echodata.EchoData #
- to_netcdf(save_path: Optional[PathHint] = None, compress: bool = True, overwrite: bool = False, parallel: bool = False, output_storage_options: Dict[str, str] = {}, **kwargs)#
Save content of EchoData to netCDF.
- Parameters
- save_pathstr
path that converted .nc file will be saved
- compressbool
whether or not to perform compression on data variables Defaults to
True
- overwritebool
whether or not to overwrite existing files Defaults to
False
- parallelbool
whether or not to use parallel processing. (Not yet implemented)
- output_storage_optionsdict
Additional keywords to pass to the filesystem class.
- **kwargsdict, optional
Extra arguments to xr.Dataset.to_netcdf: refer to xarray’s documentation for a list of all possible arguments.
- to_zarr(save_path: Optional[PathHint] = None, compress: bool = True, overwrite: bool = False, parallel: bool = False, output_storage_options: Dict[str, str] = {}, consolidated: bool = True, **kwargs)#
Save content of EchoData to zarr.
- Parameters
- save_pathstr
path that converted .nc file will be saved
- compressbool
whether or not to perform compression on data variables Defaults to
True
- overwritebool
whether or not to overwrite existing files Defaults to
False
- parallelbool
whether or not to use parallel processing. (Not yet implemented)
- output_storage_optionsdict
Additional keywords to pass to the filesystem class.
- consolidatedbool
Flag to consolidate zarr metadata. Defaults to
True
- **kwargsdict, optional
Extra arguments to xr.Dataset.to_zarr: refer to xarray’s documentation for a list of all possible arguments.
- update_platform(extra_platform_data: xarray.core.dataset.Dataset, time_dim='time', extra_platform_data_file_name=None)#
Updates the EchoData[“Platform”] group with additional external platform data.
extra_platform_data must be an xarray Dataset. The name of the time dimension in extra_platform_data is specified by the time_dim parameter. Data is extracted from extra_platform_data by variable name; only the data in extra_platform_data with the following variable names will be used:
“pitch”
“roll”
“vertical_offset”
“latitude”
“longitude”
“water_level”
The data inserted into the Platform group will be indexed by a dimension named “time1”.
- Parameters
- extra_platform_dataxr.Dataset
An xr.Dataset containing the additional platform data to be added to the EchoData[“Platform”] group.
- time_dim: str, default=”time”
The name of the time dimension in extra_platform_data; used for extracting data from extra_platform_data.
- extra_platform_data_file_name: str, default=None
File name for source of extra platform data, if read from a file
Examples
>>> ed = echopype.open_raw(raw_file, "EK60") >>> extra_platform_data = xr.open_dataset(extra_platform_data_file) >>> ed.update_platform(extra_platform_data, >>> extra_platform_data_file_name=extra_platform_data_file)