Version 1.2.0

Release date: 2022-11-18. Full commit changelog.

Changed

Inference

• The checkpoints have been renamed to a simpler structure: echofilter-v{MAJOR}_{ORIENTATION}_ep{EPOCHS}. For example, the current default checkpoint is now named as "echofilter-v1_bifacing_700ep". This is in keeping with the format used in the manuscript. The previous names for the checkpoints will still work (as an alias to the new names). (#330)
• The ordering of the colour palette listing produced by --show-colors has changed. By default, the colours are now ordered by hue (subsorted by value) instead of sorted alphabetically. The previous default behaviour can be obtained by using the new "alphabetic" argument: --show-colors "alphabetic". (#322)

Fixed

Inference

• Fix a bug with Echoview interaction which was causing the code to fail when overwriting an existing line in the EV file. (#332)
• Fix hiding the Echoview window while echofilter is running and interacting with Echoview. This bug was first seen when using Echoview 13, and was not affecting interactions with Echoview 10 or 11. (#328)

Metadata

• Add missing requests package to requirements. (#320)

Added

Inference

• Add API option --show-cache-dir, which shows the path to the directory in which downloaded checkpoints will be cached. (#321)
• Add "alphabetic" and "full-alphabetic" options to --show-colors which let the colours be sorted by alphabetically, instead of by hue. (#322)

Version 1.1.1

Release date: 2022-11-16. Full commit changelog.

Fixed

Inference

• EVL final value pad was for a timestamp in between the preceding two, not extending forward in time by half a timepoint. (#300)

Metadata

• Declare python_requires<3.11 requirement. (#302)
• Declare torch<1.12.0 requirement. (#302)

Version 1.0.3

Release date: 2022-11-15. Full commit changelog.

This minor patch fix addresses package metadata.

Fixed

Metadata

• Declare python_requires>=3.6,<3.11 requirement. (#264, #302)
• Declare torch<1.12.0 requirement. (#302)

Version 1.1.0

Release date: 2022-11-12. Full commit changelog.

Changed

Inference

• Apply inference on the raw Sv data, disabling any thresholding present in the EV file. (#275)
• Disable logit smoothing by default. The previous behaviour can be restored by setting --logit-smoothing-sigma=1 at the CLI. (#293)

ev2csv

• By default, export raw Sv data, disabling any thresholding present in the EV file. Thresholded data can still be exported, by providing the --keep-thresholds argument to the CLI. (#275)

Fixed

Inference

• Fix bug where joined segments of data would have their first ping dropped. (#272)

Training

• Make the number of channels in the first block respect the initial_channels argument. (#271)

Miscellaneous

• Fix unseen internal bugs, including in generate_shards. (#283)

Added

Inference

• Add support for using a config file to provide arguments to the CLI. (#294)
• Add --continue-on-error argument to inference routine, which will capture an error when processing an individual file and continue running the rest. (#245)
• Break up large files into more manageable chunks of at most 1280 pings, to reduce out-of-memory errors. (#245)
• Reduce GPU memory consumption during inference by moving outputs to CPU memory sooner. (#245)
• Fill in missing values in the input file through 2d linear interpolation. (#246)
• Pad Sv data in timestamp dimension during inference to ensure the data is fully within the network's effective receptive field. (#277)
• Add --prenorm-nan-value and --postnorm-nan-value options to control what value NaN values in the input are mapped to. (#274)
• Add support for providing a single path as a string to the run_inference API. (Note that the CLI already supported this and so is unchanged). (#288)
• Add more verbosity messages. (#276, #278, #292)

ev2csv

• Add --keep-ext argument to ev2csv, which allows the existing extension on the input path to be kept preceding the new file extension. (#242)

Tests

• Add tests which check that inference commands run, whether checking their outputs. (#289)

Internal

• Add EVR reader echofilter.raw.loader.evr_reader. (#280)
• Refactor fixup_dataset_sample, moved into its own function (#279)

Documentation

• Change installation instructions in Usage Guide to point to GitHub releases as the source of exe files. (#265)
• Improve docstrings. (#287)
• Improve README. (#269, #284, #285)

Miscellaneous

• Update black version, blacken notebooks, fix flake8 errors. (#283)

Version 1.0.2

Release date: 2022-11-06. Full commit changelog.

This minor patch fix addresses github dependencies so the package can be pushed to PyPI.

Changed

Requirements

• Change torch_lr_finder train requirement from a specific github commit ref to >=0.2.0. (#260)
• Remove ranger from train requirements. (#261)

Training

• Default optimizer changed from "rangerva" to "adam". (#261)

Version 1.0.1

Release date: 2022-11-06. Full commit changelog.

This patch fix addresses requirement inconsistencies and documentation building. This release is provided under the AGPLv3 license.

Added

Documentation

• Deploy documentation on github pages. (#251)
• Include link to built documentation in README. (#253)

Changed

Requirements

• Add a vendorized copy of functions from torchutils and remove it from the requirements. (#249)

Checkpoints

• Look for checkpoints.yaml in repo/executable dir as well as package dir. (#256)

Fixed

Release

• Added checkpoints.yaml file to package_data. (#255)
• Added appdirs package, required for caching model checkpoints. (#240)
• Support for pytorch>=1.11 by dropping import of torch._six.container_abcs. (#250)

Documentation

• Fix some API docstrings and CLI help text (#241, #243, #251)

Version 1.0.0

Release date: 2020-10-18. Full commit changelog.

This is the first major release of echofilter.

Added

Inference

• Add support for loading checkpoints shipped as part of the package. (#228)
• More detailed error messages when unable to downlaod or load a model i.e. due to a problem with the Internet connection, a 404 error, or because the hard disk is out of space. (#228)

Documentation

• Add Usage Guide source and sphinx documentation PDF generation routines (#232, #233, #234, #235)

Fixed

Documentation

• Fix formatting of some CHANGELOG and docstrings (#230, #231, #235)

Version 1.0.0rc3

Release date: 2020-09-23. Full commit changelog.

This is the third release candidate for the forthcoming v1.0.0 major release.

Fixed

Inference

• Include extension in temporary EVL file, fixing issue importing it into Echoview. (#224)

Version 1.0.0rc2

Release date: 2020-09-23. Full commit changelog.

This is the second release candidate for the forthcoming v1.0.0 major release.

Fixed

Inference

• Fix reference to echofilter.raw.loader.evl_loader when loading EVL files into Echoview. (#222)

Version 1.0.0rc1

Release date: 2020-09-23. Full commit changelog.

This is a release candidate for the forthcoming v1.0.0 major release.

Changed

Inference

• Import lines into Echoview twice, once with and once without offset. (#218)
• EVL outputs now indicate raw depths, before any offset or clipping is applied. (#218)
• Change default --lines-during-passive value from "predict" to "interpolate-time". (#216)
• Disable all bad data region outputs by default. (#217)
• Change default nearfield cut-off behaviour to only clip the bottom line (upfacing data) and not the turbulence line (downfacing data). (#219)

Training

• Reduce minimum distance by which surface line must be above turbulence line from 0.25m to 0m. (#212)
• Reduce minimum distance by which bottom line must be above surface line from 0.5m to 0.02m. (#212)

Fixed

Inference

• Change nearfield line for downfacing recordings to be nearfield distance below the shallowest recording depth, not at a depth equal to the nearfield distance. (#214)

Added

Inference

• Add new checkpoints: v2.0, v2.1 for stationary model; v2.0, v2.1, v2.2 for conditional hybrid model. (#213)
• Add notes to lines imported into Echoview. (#215)
• Add arguments controlling color and thickness of offset lines (--color-surface-offset, etc). (#218)
• Add argument --cutoff-at-nearfield which re-enables clipping of the turbulence line at nearfield depth with downfacing data. (#219)