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Merge/add multichannel masks #57

Merged
merged 4 commits into from
Sep 20, 2023
Merged

Merge/add multichannel masks #57

merged 4 commits into from
Sep 20, 2023

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ruxandra-valcu
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Added multichannel mask support to apply_mask - if a channelless or single-channel mask is provided it'll apply it to all channels of the dataset, whereas if a mask with multiple channels is provided, it'll apply each channel of the mask to the corresponding channel individually.

@ruxandra-valcu ruxandra-valcu added enhancement New feature or request echopype labels Sep 20, 2023
@simedroniraluca
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Is it safe to apply a single-channel mask across all channels if no specific mask is designed for each individual channel?

@simedroniraluca
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If you enhanced the functionality of apply_mask, shouldn't you also update the modified function's documentation?

@ruxandra-valcu
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Is it safe to apply a single-channel mask across all channels if no specific mask is designed for each individual channel?

This is the previous behaviour of the function - if you give it a mask with channels, it just applies channel 0 to everything

@ruxandra-valcu
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If you enhanced the functionality of apply_mask, shouldn't you also update the modified function's documentation?

Updated

mihaiboldeanu
mihaiboldeanu approved these changes Sep 20, 2023
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Looks good! It should be fine to add at this time, but we will have to investigate how to solve the test failing.

@ruxandra-valcu ruxandra-valcu merged commit 674091b into next-dev Sep 20, 2023
3 of 6 checks passed
@ruxandra-valcu ruxandra-valcu deleted the merge/add_multichannel_masks branch September 20, 2023 11:32
ruxandra-valcu added a commit that referenced this pull request Sep 21, 2023
@ruxandra-valcu @dependabot
@pre-commit-ci @mihaiboldeanu @beatfactor @simedroniraluca @alejandro-ariza
Test bug/next dev (#63)
8433cd7 
* 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>

* Feature/add transient noise mask (#49)

* 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>

* Feature/add attenuation mask (#50)

* 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>

* Patch/nasc (#51)

* 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>

* Merge/add shoal mask (#55)

* 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

* Merge/add seabed mask (#56)

* 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>

* Merge/add multichannel masks (#57)

* Initial multichannel mask

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

* Documentation

* Made changes to conftest

---------

Signed-off-by: dependabot[bot] <support@github.com>
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>
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>
beatfactor pushed a commit that referenced this pull request May 24, 2024
@ruxandra-valcu @beatfactor
Merge/add multichannel masks (#57)
2e14e83 
* Initial multichannel mask

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

* Documentation
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@mihaiboldeanu mihaiboldeanu mihaiboldeanu approved these changes

@simedroniraluca simedroniraluca simedroniraluca approved these changes

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