API reference

API components that most users will interact with.

Attention

In echopype versions prior to 0.5.0, the API in this page focused on the convert and process subpackages. See the 0.4.1 API page if you’re using a previous release. That workflow is being deprecated.

Content

EchoData class

EchoData is an object that handles interfacing raw converted data. It is used for calibration and other processing.

Classes

EchoData(converted_raw_path, …) Echo data model class for handling raw converted data, including multiple files associated with the same data set.

Open raw and converted files

echopype.open_raw(raw_file: Optional[PathHint] = None, sonar_model: Optional[SonarModelsHint] = None, xml_path: Optional[PathHint] = None, convert_params: Optional[Dict[str, str]] = None, storage_options: Optional[Dict[str, str]] = None) → Optional[echopype.echodata.echodata.EchoData]

Create an EchoData object containing parsed data from a single raw data file.

The EchoData object can be used for adding metadata and ancillary data as well as to serialize the parsed data to zarr or netcdf.

Parameters:
raw_file : str

path to raw data file

sonar_model : str

model of the sonar instrument

xml_path : str

path to XML config file used by AZFP

convert_params : dict

parameters (metadata) that may not exist in the raw file and need to be added to the converted file

storage_options : dict

options for cloud storage
Returns:
EchoData object
echopype.open_converted(converted_raw_path: PathHint, storage_options: Dict[str, str] = None)

Create an EchoData object from a single converted netcdf or zarr file.

Parameters:
converted_raw_path : str

path to converted data file

storage_options : dict

options for cloud storage
Returns:
EchoData object

Combine EchoData objects

echopype.combine_echodata(echodatas: List[echopype.echodata.echodata.EchoData], combine_attrs='override') → echopype.echodata.echodata.EchoData

Combines multiple EchoData objects into a single EchoData object.

Parameters:
echodatas: List[EchoData]

The list of EchoData objects to be combined.

combine_attrs: { “override”, “drop”, “identical”, “no_conflicts”, “overwrite_conflicts” }

String indicating how to combine attrs of the EchoData objects being merged. This parameter matches the identically named xarray parameter (see https://xarray.pydata.org/en/latest/generated/xarray.combine_nested.html) with the exception of the “overwrite_conflicts” value.

  • “override”: Default. skip comparing and copy attrs from the first EchoData object to the result.
  • “drop”: empty attrs on returned EchoData object.
  • “identical”: all attrs must be the same on every object.
  • “no_conflicts”: attrs from all objects are combined, any that have the same name must also have the same value.
  • “overwrite_conflicts”: attrs from all EchoData objects are combined, attrs with conflicting keys will be overwritten by later EchoData objects.
Returns:
EchoData

An EchoData object with all of the data from the input EchoData objects combined.
Raises:
ValueError

If echodatas contains EchoData objects with different or None sonar_model values (i.e., all EchoData objects must have the same non-None sonar_model value).

ValueError

If EchoData objects have conflicting source file names.
Warns:
UserWarning

If the sonar_model of the input EchoData objects is “EK60” and any EchoData objects have non-monotonically increasing ping_time, location_time or mru_time values, the corresponding values in the output EchoData object will be increased starting at the timestamp where the reversal occurs such that all values in the output are monotonically increasing. Additionally, the original ping_time, location_time or mru_time values will be stored in the Provenance group, although this behavior may change in future versions.

Warning

Changes in parameters between EchoData objects are not currently checked; however, they may raise an error in future versions.

Notes

  • EchoData objects are combined by combining their groups individually.
  • Attributes from all groups before the combination will be stored in the provenance group, although this behavior may change in future versions.
  • The source_file and converted_raw_path attributes will be copied from the first EchoData object in the given list, but this may change in future versions.

Examples

>>> ed1 = echopype.open_converted("file1.nc")
>>> ed2 = echopype.open_converted("file2.zarr")
>>> combined = echopype.combine_echodata([ed1, ed2])

Data processing subpackages

calibrate

Functions

compute_Sv(echodata, **kwargs) Compute volume backscattering strength (Sv) from raw data.
compute_Sp(echodata, **kwargs) Compute point backscattering strength (Sp) from raw data.

preprocess

Functions

compute_MVBS(ds_Sv[, range_meter_bin, …]) Compute Mean Volume Backscattering Strength (MVBS) based on intervals of range and ping_time specified in physical units.
compute_MVBS_index_binning(ds_Sv[, …]) Compute Mean Volume Backscattering Strength (MVBS) based on intervals of range_bin and ping number specified in index number.
remove_noise(ds_Sv, ping_num, range_bin_num) Remove noise by using estimates of background noise from mean calibrated power of a collection of pings.

qc

Functions

coerce_increasing_time(ds[, time_name, …]) Coerce a time coordinate to always flow forward.
exist_reversed_time(ds, time_name) Test for occurrence of time reversal in specified datetime coordinate variable.

Utilities

Utilities for calculating seawater acoustic properties.

Functions

calc_absorption(frequency[, distance, …]) Calculate sea absorption in dB/m
calc_sound_speed([temperature, salinity, …]) Calculate sound speed in meters per second.