What’s new¶

See GitHub releases page for the complete history.

v0.5.2 (2021 Jul 18)¶

Overview¶

This is a minor release that addresses issues related to time encoding for data variables related to platform locations and data conversion/encoding for AD2CP data files.

Bug fixes and improvements¶

Fixed the location_time encoding in the Platform group for latitude and longitude data variables (#393)
Fixed the location_time encoding in the Platform/NMEA group (#395)
Updated EchoData repr to show Platform/NMEA (#395, #396)
Improved AD2CP data parsing and conversion (#388)
- Cleaned up organization of data from different sampling modes and their corresponding time coordinates
- Fixed parsing issues that generated spikes in parsed echosounder mode amplitude data
- Removed the Beam_complex group and put raw IQ samples in the Vendor group per convention requirements
- Populated the Sonar group with AD2CP information

v0.5.1 (2021 Jun 16)¶

Overview¶

This is a minor release that addresses a couple of issues from the last major version (0.5.0) and improves code maintenance and testing procedures.

New features¶

Added experimental functions to detect and correct ping_time reversals. See qc subpackage (#297)

Updates and bug fixes¶

Fixed ADCP encoding issues (#361)
Updated SetGroupsBase to use ABC (Abstract Base Classes) Interface (#366)
Whole code-base linted for pep8 (#317)
Removed old test data from the repository (#369)
Updated package dependencies (#365)
Simplified requirements for setting up local test environment (#375)

CI improvements¶

Added code coverage checking (#317)
Added version check for echopype install (#367, #370)

v0.5.0 (2021 May 17)¶

Overview¶

This major release includes:

major API updates to provide a more coherent data access pattern
restructuring of subpackages and classes to allow better maintenance and future expansion
reorganization of documentation, which also documents the API changes
overhaul and improvements of CI, including removing the use of Git LFS to store test data
new features
bug fixes

API updates¶

The existing API for converting files from raw instrument formats to a standardized format, and for calibrating data and performing operations such as binned averages and noise removal has been updated.

The new API uses a new EchoData object to encapsulate all data and metadata related to/parsed from a raw instrument data file. Beyond the calibration of backscatter quantities, other processing functions follow a consistent form to take an xarray Dataset as input argument and returns another xarray Dataset as output.

The major changes include:

change from an object-oriented method calls to functional calls for file conversion (using the new convert subpackage), and deprecate the previous Convert class for handling file parsing and conversion
deprecate the previous Process class, which use object-oriented method calls for performing both calibration and data processing
separate out calibration functions to a new calibrate subpackage
separate out noise removal and data reduction functions to a new preprocess subpackage
create a new EchoData object class that encapsulates all raw data and metadata from instrument data files, regardless of whether the data is being parsed directly from the raw binary instrument files (returned by the new function open_raw) or being read from an already converted file (returned by the new function open_converted)

Subpackage and class restructuring¶

The subpackages and classes were restructured to improve modularity that will help will future expansion and maintenance. The major restructuring includes: (“SONAR” below is used to indicate the sonar model, such as EK60, EK80 or AZFP)

consolidate overlapping EK60/EK80 components, deprecate the previous Convert classes that handled file parsing and serialization, and revise new ParseSONAR and SetGroupsSONAR classes for file parsing and serialization
consolidate all calibration-related components to a new calibrate submodule, which uses CalibrateSONAR classes under the hood
consolidate all preprocessing functions into a a new preprocess submodule, which will be later expanded to include other functions with similar use in a workflow

CI overhaul and improvements¶

Added github workflows for testing, building test docker images, and publishing directly to PyPI
Deprecated usage of Travis CI
Test run is now selective on Github, to run tests only on changed/added files. Or run all locally with run-test.py script. (#280, #302)

Documentation reorganization and updates¶

Re-organization of pages with better grouping
Added “What’s New” page
Added “Contributing to echopype” page
Overhaul “API reference” page

New features¶

Add interfacing capability to read from and write to cloud object storage directly. (#216, #240)
Allow environmental and calibration parameters to be optionally used in calibration in place of the values stored in data file
Mean volume backscattering strength (MVBS) can now be computed based on actual time interval (specified in seconds) and range (specified in meters) (#54)
Add NMEA message type as a data variable in the Platform group (#232), which allows users to freely select the suitable ones depending on use
Add support to convert .ad2cp files generated by Nortek’s Signature series ADCP (#326)

Bug fixes¶

Fix EK80 config XML parsing problem for files containing either PulseDuration or PulseLength (#305)
Fix time encoding discrepancy in AZFP conversion (#328)
Fix problematic automatic encoding of AZFP frequency (previously as int) to float64 (#309)
Overhaul EK80 pulse compressed calibration (current implementation remaining in beta, see #308)

v0.4.1 (2020 Oct 20)¶

Patches and enhancements to file conversion

This minor release includes the following changes:

Bug fixes¶

Fix bug in top level .nc output when combining multiple AZPF .01A files
Correct time stamp for .raw MRU data to be from the MRU datagram, instead of those from the RAW3 datagrams (although they are identical from the test files we have).
Remove unused parameter sa_correction from broadband .raw files
Make sure import statement works on Google colab

Enhancements¶

Parse Simrad EK80 config XML correctly for data generated by WBAT and WBT Mini, and those involving the 2-in-1 “combi” transducer
Parse Simrad .raw files with NME1 datagram, such as files generated by the Simrad EA640 echosounder
Handle missing or partially valid GPS data in .raw files by padding with NaN
Handle missing MRU data in .raw files by padding with NaN
Parse .raw filename with postfix beyond HHMMSS
Allow export EK80 XML configuration datagram as a separate XML file

Notes¶

To increase maintenance efficiency and code readability we are refactoring the convert and process modules. Some usage of these modules will change in the next major release.

v0.4.0 (2020 Jun 24)¶

Add EK80 conversion, rename subpackage model to process

New features¶

Add EK80 support:
- File conversion from EK80 .raw files to netCDF and zarr formats
- “Simple” calibration to frequency-average Sv based on pulse compression output is implemented but needs to be thoroughly tested.
Rename subpackage echopype.model to echopype.process
- The new name better describes the subpackage’s function to process data for further analysis
- Also rename class EchoData to Process to mirror the structure in Convert better.
- Importing using the old names will be deprecated in the next release.
Overhaul converting multiple files with combine_opt=True
- If target format is netCDF, temporary files will be created and finally combined to a single netCDF. This is due to current restriction that xarray does not allow simply appending new data to an existing file.
- If target format is zarr, data in each file are unpacked and appended to the same output file.
Allow reading Zarr into Process in addition to netCDF: thanks @lsetiawan!
Add a logo!

Bug fixes¶

Fix bugs in slicing NMEA group data based on the same time base when range_bin is changed