Merge/add shoal mask #55
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ruxandra-valcu
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beatfactor,
mihaiboldeanu and
simedroniraluca
ruxandra-valcu
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Sep 21, 2023
* 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] <[email protected]> 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 <[email protected]> * Update echopype/utils/mask_transformation.py Co-authored-by: Raluca Simedroni <[email protected]> * Update echopype/utils/mask_transformation.py Co-authored-by: Raluca Simedroni <[email protected]> * Update echopype/utils/mask_transformation.py Co-authored-by: Raluca Simedroni <[email protected]> * Update echopype/utils/mask_transformation.py Co-authored-by: Raluca Simedroni <[email protected]> * Update echopype/utils/mask_transformation.py Co-authored-by: Raluca Simedroni <[email protected]> * Update echopype/utils/mask_transformation.py Co-authored-by: Raluca Simedroni <[email protected]> * Cleaned up mask_transformation * moved files and rerouted importing paths accordingly (#36) Co-authored-by: alejandro-ariza <[email protected]> * Feature/add transient noise mask (#35) * Completed feature #3 transient noise mask --------- Co-authored-by: Mihai Boldeanu <[email protected]> Co-authored-by: Raluca Simedroni <[email protected]> Co-authored-by: ruxandra valcu <[email protected]> * 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] <[email protected]> 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 <[email protected]> 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] <[email protected]> Co-authored-by: Mihai Boldeanu <[email protected]> Co-authored-by: Mihai Boldeanu <[email protected]> Co-authored-by: Andrei Rusu <[email protected]> Co-authored-by: Raluca Simedroni <[email protected]> Co-authored-by: Andrei Rusu <[email protected]> Co-authored-by: alejandro-ariza <[email protected]> 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 <[email protected]> * Update echopype/utils/mask_transformation.py Co-authored-by: Raluca Simedroni <[email protected]> * Update echopype/utils/mask_transformation.py Co-authored-by: Raluca Simedroni <[email protected]> * Update echopype/utils/mask_transformation.py Co-authored-by: Raluca Simedroni <[email protected]> * Update echopype/utils/mask_transformation.py Co-authored-by: Raluca Simedroni <[email protected]> * Update echopype/utils/mask_transformation.py Co-authored-by: Raluca Simedroni <[email protected]> * Update echopype/utils/mask_transformation.py Co-authored-by: Raluca Simedroni <[email protected]> * Cleaned up mask_transformation * Update echopype/mask/mask_attenuated_signal.py Co-authored-by: Raluca Simedroni <[email protected]> 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 <[email protected]> Co-authored-by: Mihai Boldeanu <[email protected]> Co-authored-by: Andrei Rusu <[email protected]> Co-authored-by: Raluca Simedroni <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * Update echopype/tests/mask/test_mask_seabed.py Co-authored-by: Raluca Simedroni <[email protected]> * 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 <[email protected]> * Update echopype/mask/mask_seabed.py Co-authored-by: Raluca Simedroni <[email protected]> * Update echopype/mask/mask_seabed.py Co-authored-by: Raluca Simedroni <[email protected]> * 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 <[email protected]> Co-authored-by: Andrei Rusu <[email protected]> Co-authored-by: Andrei Rusu <[email protected]> Co-authored-by: Raluca Simedroni <[email protected]> * 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] <[email protected]> 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 <[email protected]> Co-authored-by: Mihai Boldeanu <[email protected]> Co-authored-by: Andrei Rusu <[email protected]> Co-authored-by: Raluca Simedroni <[email protected]> Co-authored-by: Andrei Rusu <[email protected]> Co-authored-by: alejandro-ariza <[email protected]>
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