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Test bug/next dev #63

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merged 10 commits into from
Sep 21, 2023
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dependabot bot and others added 10 commits September 12, 2023 08:42
Bumps [actions/cache](https://github.com/actions/cache) from 3.3.1 to 3.3.2.
- [Release notes](https://github.com/actions/cache/releases)
- [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md)
- [Commits](actions/cache@v3.3.1...v3.3.2)

---
updated-dependencies:
- dependency-name: actions/cache
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…1162)

updates:
- [github.com/psf/black: 23.7.0 → 23.9.1](psf/black@23.7.0...23.9.1)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* added the feature described in issue 1

* Moved code for the signal attenuation mask to new file

* Resolved merge conflicts by accepting remote versions of files

* Update mask_attenuated_signal.py

* renamed utils

* Added unit test

* Test can now automatically download its data

* Update echopype/utils/mask_transformation.py

Co-authored-by: Raluca Simedroni <92971445+simedroniraluca@users.noreply.github.com>

* Update echopype/utils/mask_transformation.py

Co-authored-by: Raluca Simedroni <92971445+simedroniraluca@users.noreply.github.com>

* Update echopype/utils/mask_transformation.py

Co-authored-by: Raluca Simedroni <92971445+simedroniraluca@users.noreply.github.com>

* Update echopype/utils/mask_transformation.py

Co-authored-by: Raluca Simedroni <92971445+simedroniraluca@users.noreply.github.com>

* Update echopype/utils/mask_transformation.py

Co-authored-by: Raluca Simedroni <92971445+simedroniraluca@users.noreply.github.com>

* Update echopype/utils/mask_transformation.py

Co-authored-by: Raluca Simedroni <92971445+simedroniraluca@users.noreply.github.com>

* Update echopype/utils/mask_transformation.py

Co-authored-by: Raluca Simedroni <92971445+simedroniraluca@users.noreply.github.com>

* Cleaned up mask_transformation

* moved files and rerouted importing paths accordingly (#36)

Co-authored-by: alejandro-ariza <alejandro.ariza@ird.fr>

* Feature/add transient noise mask (#35)

* Completed feature #3 transient noise mask
---------

Co-authored-by: Mihai Boldeanu <35964395+mihaiboldeanu@users.noreply.github.com>
Co-authored-by: Raluca Simedroni <92971445+simedroniraluca@users.noreply.github.com>
Co-authored-by: ruxandra valcu <ruxandra.valcu@gmail.com>

* Added extra tests for the utils/mask_transformation module to increase coverage

* Reverted test_mask.py reformating

* Moved impulse and transient noise functions to echopype/clean

* Fixed import order

* Fixed missing import in clean/conftest.py

* Moved content of tests/clean/conftest.py to tests/conftest.py

* Refactoring

* Running some linters on the code

* ci(deps): Bump actions/cache from 3.3.1 to 3.3.2 (OSOceanAcoustics#1161)

Bumps [actions/cache](https://github.com/actions/cache) from 3.3.1 to 3.3.2.
- [Release notes](https://github.com/actions/cache/releases)
- [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md)
- [Commits](actions/cache@v3.3.1...v3.3.2)

---
updated-dependencies:
- dependency-name: actions/cache
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* chore(deps): [pre-commit.ci] pre-commit autoupdate (OSOceanAcoustics#1162)

updates:
- [github.com/psf/black: 23.7.0 → 23.9.1](psf/black@23.7.0...23.9.1)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Fix unused imports in conftest

* Update echopype/mask/mask_attenuated_signal.py

Co-authored-by: Raluca Simedroni <92971445+simedroniraluca@users.noreply.github.com>

Update mask_transformation.py

Cleaned up mask_transformation

Delinted

Removing pytest req

Refactoring

Refactoring and cleaning imports

Fixed twod test

Fixing some future merge conflicts

Fix unused import

Added attenuation mask to init

* Added channel selection to signal attenuation mask

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Mihai Boldeanu <mishu_boldy@yahoo.com>
Co-authored-by: Mihai Boldeanu <35964395+mihaiboldeanu@users.noreply.github.com>
Co-authored-by: Andrei Rusu <andrei.rusu@beatfactor.net>
Co-authored-by: Raluca Simedroni <92971445+simedroniraluca@users.noreply.github.com>
Co-authored-by: Andrei Rusu <beatfactor@users.noreply.github.com>
Co-authored-by: alejandro-ariza <alejandro.ariza@ird.fr>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* added the feature described in issue 1

* Moved code for the signal attenuation mask to new file

* Resolved merge conflicts by accepting remote versions of files

* Update mask_attenuated_signal.py

* renamed utils

* Added unit test

* Test can now automatically download its data

* Update echopype/utils/mask_transformation.py

Co-authored-by: Raluca Simedroni <92971445+simedroniraluca@users.noreply.github.com>

* Update echopype/utils/mask_transformation.py

Co-authored-by: Raluca Simedroni <92971445+simedroniraluca@users.noreply.github.com>

* Update echopype/utils/mask_transformation.py

Co-authored-by: Raluca Simedroni <92971445+simedroniraluca@users.noreply.github.com>

* Update echopype/utils/mask_transformation.py

Co-authored-by: Raluca Simedroni <92971445+simedroniraluca@users.noreply.github.com>

* Update echopype/utils/mask_transformation.py

Co-authored-by: Raluca Simedroni <92971445+simedroniraluca@users.noreply.github.com>

* Update echopype/utils/mask_transformation.py

Co-authored-by: Raluca Simedroni <92971445+simedroniraluca@users.noreply.github.com>

* Update echopype/utils/mask_transformation.py

Co-authored-by: Raluca Simedroni <92971445+simedroniraluca@users.noreply.github.com>

* Cleaned up mask_transformation

* Update echopype/mask/mask_attenuated_signal.py

Co-authored-by: Raluca Simedroni <92971445+simedroniraluca@users.noreply.github.com>

Update mask_transformation.py

Cleaned up mask_transformation

Delinted

Removing pytest req

Refactoring

Refactoring and cleaning imports

Fixed twod test

Fixing some future merge conflicts

Fix unused import

Added attenuation mask to init

* Added channel selection to signal attenuation mask

---------

Co-authored-by: Mihai Boldeanu <mishu_boldy@yahoo.com>
Co-authored-by: Mihai Boldeanu <35964395+mihaiboldeanu@users.noreply.github.com>
Co-authored-by: Andrei Rusu <andrei.rusu@beatfactor.net>
Co-authored-by: Raluca Simedroni <92971445+simedroniraluca@users.noreply.github.com>
* Add conversion factors for NASC computation

- Convert backscattering cross-section to scattering cross-section.

- Convert meters to nmi.

* Fix nasc test

---------

Co-authored-by: Raluca Simedroni <92971445+simedroniraluca@users.noreply.github.com>
* Mask utils

* rename

* Mask utils

* Weill shoal mask

* Decided against implementing the echoview method

* Turned out not to need these

* Add wrapper function

* Refactoring and adding channel selection capability
* Initial implementation of the seabed masking.

* Code for seabed masking

* Changed dilation source package from cv2 to skimage.

* some refactoring and add unit test

* Update echopype/mask/mask_seabed.py

Co-authored-by: Raluca Simedroni <92971445+simedroniraluca@users.noreply.github.com>

* Update echopype/tests/mask/test_mask_seabed.py

Co-authored-by: Raluca Simedroni <92971445+simedroniraluca@users.noreply.github.com>

* Re-added mask_transformation, with only the necessary functions kept

* Changed the tests to be able to autodownload its files - must check that I have the correct one though since the test isn't passing

* Cleaned up mask_transformation

* Copyright notices

Co-authored-by: Raluca Simedroni <92971445+simedroniraluca@users.noreply.github.com>

* Update echopype/mask/mask_seabed.py

Co-authored-by: Raluca Simedroni <92971445+simedroniraluca@users.noreply.github.com>

* Update echopype/mask/mask_seabed.py

Co-authored-by: Raluca Simedroni <92971445+simedroniraluca@users.noreply.github.com>

* Update incorrect file name

* Mask transformation consistency

* Mask transformation consistency

* Removing pytest req

* Refactoring

* Fix twod test

* Refactoring

* Test fixes

* Fixing merge compatibility

* Added dataset generation for datasets enriched with beam angle and location data

* Added dataset generation for datasets enriched with beam angle and location data

* Added channel selection.

* Modified Blackwell methods to use the physical beam angle rather than the raw EK60 beam angle - doing this using a correction on the angle itself (rather than modifying the constants) since the changes are nonlinear so if I want a linear transformation, I need to apply it on the angle data itself - angle * 22 * 128 / 180, which gets it close to how a decently calibrated EK60 instrument as used by Blackwell et al stores its raw angle data.

* Indent fix

* Merge fixes

---------

Co-authored-by: Mihai Boldeanu <mishu_boldy@yahoo.com>
Co-authored-by: Andrei Rusu <andrei.rusu@beatfactor.net>
Co-authored-by: Andrei Rusu <beatfactor@users.noreply.github.com>
Co-authored-by: Raluca Simedroni <92971445+simedroniraluca@users.noreply.github.com>
* Initial multichannel mask

* Fixed a has-channels check in apply_mask, added tests

* Documentation
@ruxandra-valcu ruxandra-valcu merged commit 8433cd7 into feature/add_multichannel_masks Sep 21, 2023
11 of 14 checks passed
@ruxandra-valcu ruxandra-valcu deleted the test_bug/next-dev branch September 21, 2023 09:51
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