Echofilter

------------------------------------------------------------------------

Release date: 2022-11-18.
`Full commit changelog <https://github.com/DeepSenseCA/echofilter/compare/1.1.1...1.2.0>`__.


.. _v1.2.0 Changed:

Changed
~~~~~~~

.. _v1.2.0 Changed Inference:

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 <https://github.com/DeepSenseCA/echofilter/pull/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 <https://github.com/DeepSenseCA/echofilter/pull/322>`__)


.. _v1.2.0 Fixed:

Fixed
~~~~~

.. _v1.2.0 Fixed Inference:

Inference
^^^^^^^^^

- Fix a bug with Echoview interaction which was causing the code to fail when overwriting an existing line in the EV file.
(`332 <https://github.com/DeepSenseCA/echofilter/pull/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 <https://github.com/DeepSenseCA/echofilter/pull/328>`__)

.. _v1.2.0 Fixed Metadata:

Metadata
^^^^^^^^

- Add missing ``requests`` package to requirements.
(`320 <https://github.com/DeepSenseCA/echofilter/pull/320>`__)


.. _v1.2.0 Added:

Added
~~~~~

.. _v1.2.0 Added Inference:

Inference
^^^^^^^^^

- Add API option ``--show-cache-dir``, which shows the path to the directory in which downloaded checkpoints will be cached.
(`321 <https://github.com/DeepSenseCA/echofilter/pull/321>`__)
- Add ``"alphabetic"`` and ``"full-alphabetic"`` options to ``--show-colors`` which let the colours be sorted by alphabetically, instead of by hue.
(`322 <https://github.com/DeepSenseCA/echofilter/pull/322>`__)

------------------------------------------------------------------------

Release date: 2022-11-16.
`Full commit changelog <https://github.com/DeepSenseCA/echofilter/compare/1.1.0...1.1.1>`__.


.. _v1.1.1 Fixed:

Fixed
~~~~~

.. _v1.1.1 Fixed Inference:

Inference
^^^^^^^^^

- EVL final value pad was for a timestamp in between the preceding two, not extending forward in time by half a timepoint.
(`300 <https://github.com/DeepSenseCA/echofilter/pull/300>`__)

.. _v1.1.1 Fixed Metadata:

Metadata
^^^^^^^^

- Declare ``python_requires<3.11`` requirement.
(`302 <https://github.com/DeepSenseCA/echofilter/pull/302>`__)
- Declare ``torch<1.12.0`` requirement.
(`302 <https://github.com/DeepSenseCA/echofilter/pull/302>`__)

------------------------------------------------------------------------

Release date: 2022-11-12.
`Full commit changelog <https://github.com/DeepSenseCA/echofilter/compare/1.0.2...1.1.0>`__.


.. _v1.1.0 Changed:

Changed
~~~~~~~

.. _v1.1.0 Changed Inference:

Inference
^^^^^^^^^

- Disable logit smoothing by default. The previous behaviour can be restored
by setting ``--logit-smoothing-sigma=1`` at the CLI.
(`293 <https://github.com/DeepSenseCA/echofilter/pull/293>`__)


.. _v1.1.0 Fixed:

Fixed
~~~~~

.. _v1.1.0 Fixed Inference:

Inference
^^^^^^^^^

- Fix bug where joined segments of data would have their first ping dropped.
(`272 <https://github.com/DeepSenseCA/echofilter/pull/272>`__)

.. _v1.1.0 Fixed Training:

Training
^^^^^^^^

- Make the number of channels in the first block respect the ``initial_channels`` argument.
(`271 <https://github.com/DeepSenseCA/echofilter/pull/271>`__)

.. _v1.1.0 Fixed Miscellaneous:

Miscellaneous
^^^^^^^^^^^^^

- Fix unseen internal bugs, including in ``generate_shards``.
(`283 <https://github.com/DeepSenseCA/echofilter/pull/283>`__)


.. _v1.1.0 Added:

Added
~~~~~

.. _v1.1.0 Added Inference:

Inference
^^^^^^^^^

- Add support for using a config file to provide arguments to the CLI.
(`294 <https://github.com/DeepSenseCA/echofilter/pull/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 <https://github.com/DeepSenseCA/echofilter/pull/245>`__)
- Break up large files into more manageable chunks of at most 1280 pings,
to reduce out-of-memory errors.
(`245 <https://github.com/DeepSenseCA/echofilter/pull/245>`__)
- Reduce GPU memory consumption during inference by moving outputs to CPU
memory sooner.
(`245 <https://github.com/DeepSenseCA/echofilter/pull/245>`__)
- Fill in missing values in the input file through 2d linear interpolation.
(`246 <https://github.com/DeepSenseCA/echofilter/pull/246>`__)
- Pad Sv data in timestamp dimension during inference to ensure the data is fully within the network's effective receptive field.
(`277 <https://github.com/DeepSenseCA/echofilter/pull/277>`__)
- Add ``--prenorm-nan-value`` and ``--postnorm-nan-value`` options to control what value NaN values in the input are mapped to.
(`274 <https://github.com/DeepSenseCA/echofilter/pull/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 <https://github.com/DeepSenseCA/echofilter/pull/288>`__)
- Add more verbosity messages.
(`276 <https://github.com/DeepSenseCA/echofilter/pull/276>`__,
`278 <https://github.com/DeepSenseCA/echofilter/pull/278>`__,
`292 <https://github.com/DeepSenseCA/echofilter/pull/292>`__)

.. _v1.1.0 Added ev2csv:

ev2csv
^^^^^^

- Add ``--keep-thresholds`` option which allow for exporting Sv data with thresholds and exclusions enabled (set as they currently are in the EV file).
The default behaviour is still to export raw Sv data (disabling all thresholds).
The default file name for the CSV file depends on whether the export is of raw or thresholded data.
(`275 <https://github.com/DeepSenseCA/echofilter/pull/275>`__)
- Add ``--keep-ext`` argument to ev2csv, which allows the existing
extension on the input path to be kept preceding the new file extension.
(`242 <https://github.com/DeepSenseCA/echofilter/pull/242>`__)

.. _v1.1.0 Added Tests:

Tests
^^^^^

- Add tests which check that inference commands run, whether checking their outputs.
(`289 <https://github.com/DeepSenseCA/echofilter/pull/289>`__)


.. _v1.1.0 Added Internal:

Internal
^^^^^^^^

- Add EVR reader ``echofilter.raw.loader.evr_reader``.
(`280 <https://github.com/DeepSenseCA/echofilter/pull/280>`__)

------------------------------------------------------------------------

Release date: 2022-11-15.
`Full commit changelog <https://github.com/DeepSenseCA/echofilter/compare/1.0.2...1.0.3>`__.

This minor patch fix addresses package metadata.

.. _v1.0.3 Fixed:

Fixed
~~~~~

.. _v1.0.3 Fixed Metadata:

Metadata
^^^^^^^^

- Declare ``python_requires>=3.6,<3.11`` requirement.
(`264 <https://github.com/DeepSenseCA/echofilter/pull/264>`__,
`302 <https://github.com/DeepSenseCA/echofilter/pull/302>`__)
- Declare ``torch<1.12.0`` requirement.
(`302 <https://github.com/DeepSenseCA/echofilter/pull/302>`__)

------------------------------------------------------------------------

Release date: 2022-11-06.
`Full commit changelog <https://github.com/DeepSenseCA/echofilter/compare/1.0.1...1.0.2>`__.

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

.. _v1.0.2 Changed:

Changed
~~~~~~~

.. _v1.0.2 Changed Requirements:

Requirements
^^^^^^^^^^^^

- Change ``torch_lr_finder`` train requirement from a specific github commit ref to >=0.2.0.
(`260 <https://github.com/DeepSenseCA/echofilter/pull/260>`__)
- Remove `ranger <https://github.com/lessw2020/Ranger-Deep-Learning-Optimizer>`__ from train requirements.
(`261 <https://github.com/DeepSenseCA/echofilter/pull/261>`__)

.. _v1.0.2 Changed Training:

Training
^^^^^^^^

- Default optimizer changed from ``"rangerva"`` to ``"adam"``.
If you have manually installed `ranger <https://github.com/lessw2020/Ranger-Deep-Learning-Optimizer>`__ you can still use the ``"rangerva"`` optimizer if you specify it.
(`261 <https://github.com/DeepSenseCA/echofilter/pull/261>`__)

------------------------------------------------------------------------

Release date: 2022-11-06.
`Full commit changelog <https://github.com/DeepSenseCA/echofilter/compare/1.0.0...1.0.1>`__.

This patch fix addresses requirement inconsistencies and documentation building.
This release is provided under the `AGPLv3 <https://www.gnu.org/licenses/agpl-3.0.en.html>`__ license.

.. _v1.0.1 Changed:

Changed
~~~~~~~

.. _v1.0.1 Changed Requirements:

Requirements
^^^^^^^^^^^^

- Add a vendorized copy of functions from
`torchutils <https://github.com/scottclowe/pytorch-utils>`__
and remove it from the requirements.
(`249 <https://github.com/DeepSenseCA/echofilter/pull/249>`__)

.. _v1.0.1 Fixed:

Fixed
~~~~~

.. _v1.0.1 Fixed Release:

Release
^^^^^^^

- Added checkpoints.yaml file to package_data.
(`255 <https://github.com/DeepSenseCA/echofilter/pull/255>`__)
- Added appdirs package, required for caching model checkpoints.
(`240 <https://github.com/DeepSenseCA/echofilter/pull/240>`__)
- Support for pytorch>=1.11 by dropping import of ``torch._six.container_abcs``.
(`250 <https://github.com/DeepSenseCA/echofilter/pull/250>`__)