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Merge/add transient noise mask (#82)
* 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 * 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 * Changed parser in `parse_azfp.py` to maintain consistency over other parsers. (OSOceanAcoustics#1135) * replaced usage of xml.dom.minidom with xml.etree.ElementTree * modified azfp parser and parsed all parameters * refactored the parse_azfp code and added new tests * small tweak in test, rename conversion function to _camel_to_snake * updated parameter names * Replace camel-to-snake conversion funcitonality (#1) * Create utils camel-to-snake-case function in new misc.py, and use it in ek_raw_parsers * Replace AZFP camel-to-snake function with new utils/misc.py function * fixed minor error in code * minor change in test_convert_azfp.py * fixed failing tests * fixed failing tests related to attribute name * fixed minor bug --------- Co-authored-by: Wu-Jung Lee <leewujung@gmail.com> Co-authored-by: Emilio Mayorga <emiliomayorga@gmail.com> * ci: added support for running individual test files (OSOceanAcoustics#1166) Added a support for testing individual test files also instead of having support for testing only subpackages. * Delinting * refactor(convert): refactor and cleanup parsed2zarr (OSOceanAcoustics#1070) * Bump pypa/gh-action-pypi-publish from 1.6.4 to 1.8.1 (OSOceanAcoustics#999) Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.6.4 to 1.8.1. - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](pypa/gh-action-pypi-publish@v1.6.4...v1.8.1) --- updated-dependencies: - dependency-name: pypa/gh-action-pypi-publish dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/cache from 3.2.5 to 3.3.1 (OSOceanAcoustics#982) Bumps [actions/cache](https://github.com/actions/cache) from 3.2.5 to 3.3.1. - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](actions/cache@v3.2.5...v3.3.1) --- updated-dependencies: - dependency-name: actions/cache dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (OSOceanAcoustics#1022) updates: - [github.com/psf/black: 23.1.0 → 23.3.0](psf/black@23.1.0...23.3.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Bump pypa/gh-action-pypi-publish from 1.8.1 to 1.8.5 (OSOceanAcoustics#1021) Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.1 to 1.8.5. - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](pypa/gh-action-pypi-publish@v1.8.1...v1.8.5) --- updated-dependencies: - dependency-name: pypa/gh-action-pypi-publish 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> * Bump actions/setup-python from 4.5.0 to 4.6.0 (OSOceanAcoustics#1036) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.5.0 to 4.6.0. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v4.5.0...v4.6.0) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump pypa/gh-action-pypi-publish from 1.8.5 to 1.8.6 (OSOceanAcoustics#1041) Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.5 to 1.8.6. - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](pypa/gh-action-pypi-publish@v1.8.5...v1.8.6) --- updated-dependencies: - dependency-name: pypa/gh-action-pypi-publish 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> * Bump mamba-org/provision-with-micromamba from 15 to 16 (OSOceanAcoustics#1048) Bumps [mamba-org/provision-with-micromamba](https://github.com/mamba-org/provision-with-micromamba) from 15 to 16. - [Release notes](https://github.com/mamba-org/provision-with-micromamba/releases) - [Commits](mamba-org/provision-with-micromamba@v15...v16) --- updated-dependencies: - dependency-name: mamba-org/provision-with-micromamba dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/setup-python from 4.6.0 to 4.6.1 (OSOceanAcoustics#1052) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.6.0 to 4.6.1. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v4.6.0...v4.6.1) --- updated-dependencies: - dependency-name: actions/setup-python 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> * Extract out whether_write_to_zarr and remove use_swap arg * Initial add of destination_path * Start using destination path and storage options, modify cleanup * Update docstrings, and add some checks * Add sonar model attribute to parser object * Pass sonar_model to parser and fix bug * Move dataarrays creation to parsed2zarr * Remove atexit registration * Add default DEFAULT_ZARR_TEMP_DIR global var * Initial test for parsed2zarr components * Add explicit no swap for conversion test * fix: add parsed2zarr_obj to self to fix bug * fix: uncomment zarr store close to close the store * fix: remove unneeded typing * fix: no need to close fsmap zarr store anymore, removing code * feat: write tx datagram to zarr in during p2z * feat: add property for ek80 p2z * feat: set from swap array * fix: missing transmit data when no swap * fix: only delete col when it exists in p2z_ek80 * test(echodata): add simple P2Z object to utils mock * fix: Import 'List' typehint Added import for 'List' that is currently in use but missing. * fix: Remove elif for column removal Changed the if elif to a for if so it removes both 'power' and 'angle' columns for RAW4 'tx_datagram_df' data. * fix: Removed dependency to 'more-itertools' Removed dependency to 'more-itertools' by using similar method that uses 'numpy.array_split' instead to evenly split data into desired chunks * test: Set 'no_swap' for 'test_combine_echodata_combined_append' Assign 'no_swap' to 'destination_path' during 'open_raw' to ensure that everything is in memory since the new parsed to zarr functionality is 'auto' by default. * feat: Add 'auto' keyword to enable auto 'use_swap' Changed the way that 'auto' determination of 'use_swap' by specifying an 'auto' keyword, rather than by default. Now defaulting back to 'no_swap' for empty 'destination_path'. * revert: Removed 'no_swap' in 'test_combine_echodata_combined_append' On OSOceanAcoustics@b6b79fa 'no_swap' was set, however because now the default is 'no_swap' this shouldn't be needed! * fix: Use convention yaml for 'backscatter_x' Sets 'long_name' attributes for 'backscatter_r' and 'backscatter_i' from the convention yaml for p2z outputs. Additionally, units changed from 'V' to 'dB' to sync up with the "no_swap" counterpart. Old tests for 'test_direct_to_zarr_integration' has been activated again to ensure equivalency b/w the two methods. * test: Added P2Z Arrays tests Added testing for underlying methods that gets called during a 'datagram_to_zarr' call to ensure that zarr arrays actually gets created. Ref: OSOceanAcoustics#777 --------- 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> * fix(commongrid): improve 'compute_MVBS' using flox [all tests ci] (OSOceanAcoustics#1124) * chore(deps): add flox dependency >=0.7.2 * fix(commongrid): fixes 'compute_MVBS' so it can work better and scale Under the hood, binning along ping time and echo range now uses flox. This allows for scalability and more community-maintained. * docs: add small code comment * refactor: change how ping_time index is retrieved * refactor: remove for loop for channel * test(mvbs): add mock Sv datasets and tests for dims (#2) Note that @leewujung also changed mean to nanmean for skipping NaNs in each bin. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix: change dask to numpy Changed the use of dask for log10 to numpy instead since numpy can also handle dask array inputs properly. * feat: Add method argument Added 'method' argument to 'get_MVBS_along_channels' and also expose additional keyword arguments control for flox. * fix(commongrid): Fixed to include lat lon Fixed 'compute_MVBS' function to now include latitude and longitude if the variables exists in the Sv dataset. Additionally, the flox method and keyword arguments are now exposed within the 'compute_MVBS' function. Ref: Issue OSOceanAcoustics#1002 * refactor: Set defaults to recommended After some investigation, @lsetiawan concluded that at this time the method 'map-reduce', engine 'numpy', and reindex True works the best, so this is now set as default. Also, getting echo range maximum is through direct data slicing rather than computation. * feat(commongrid): Add 'range_var' argument to 'compute_MVBS' Added a new argument 'range_var' so that user can set the range variable to perform binning with. There are 2 options of 'echo_range' and 'depth': - 'echo_range': When this is set, variable 'water_level' is now included in the resulting MVBS dataset - 'depth': A check is in place to ensure that this variable exists before moving forward and use this to perform range binning. Ref: Issue OSOceanAcoustics#1002 * fix: Add missing attributes for lat lon * test: Update test to use random generator * fix: Add case for no 'water_level' Added a case for dataset that doesn't have water level variable. * test(nasc): Remove 'compute_NASC' import to avoid failure * fix: Removed assumption on echo range max Reverted back the echo range max computation to computing on the fly since there may be some NaN values. * test: Extract api test and add markings Extracted fixtures to conftest.py for commongrid. Additionally, clean up unused functions and mark tests b/w unit and integration. Added a new test module called 'test_api.py' for 'commongrid.api'. * test: Add latlon test for 'compute_MVBS' Added a test for Sv dataset that contains latitude and longitude going through 'compute_MVBS' to ensure that those variables gets propagated through. Ref: OSOceanAcoustics#1002 * test: Add small get_MVBS_along_channels test Added test for 'get_MVBS_along_channels' with either 'depth' as the 'range_var' or checking for 'has_positions' is True or False. * refactor: Integrate suggested changes Integrated suggested changes from review such as additional comments in code, fixing some variable names, and extracting out the lin2log and log2lin functions. Additionally, now echopype imports pint library to start having unit checks in the input for compute_MVBS. * test: Added check for position values * test: Update range_meter_bin to strings * test: Added 'compute_MVBS' values test * Update echopype/tests/utils/test_processinglevels_integration.py compute_MVBS now should preserve the processing level attributes. So, test for presence rather than absence * test: Add 'nan' sprinkles Sprinkled 'nan' values all over 'echo_range' to ensure that computed values from 'compute_MVBS' doesn't take into account the 'nan'. Added check for the expected distribution of 'nan' in the resulting array. Ref: OSOceanAcoustics#1124 (comment) * revert: Revert the use of 'pint' Removed dependency to 'pint' and use simple regex to ensure that 'range_bin' input is unit 'm'. Renamed 'range_meter_bin' argument to 'range_bin'. Ref: OSOceanAcoustics#1124 (comment) * feat: Allow 'range_bin' to have space * fix: Apply suggestions from code review Applied fix for regex not capturing decimal values by @emiliom Ref: https://github.com/OSOceanAcoustics/echopype/pull/1124/files#r1320422121 Co-authored-by: Emilio Mayorga <emiliomayorga@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * test: Fix test text for wrong unit * test: Remove the 'e.g.' part on pytest Removed the part with '(e.g., '10m')' since it's messing up pytests regex matching. * test: Remove remnant for test_ek.py * refactor: Extract range_bin parsing and add close arg Extracts out the 'range_bin' string to float into a private function. Additionally now there's a fine tune argument for bin close edges so user can specify either close is 'left' or 'right'. Bins are converted to pandas interval index before passing into 'get_MVBS_along_channels'. * refactor: Update arg types to include interval index Added argument type options for 'range_interval' and 'ping_interval' to also be interval index. * test: Update tests to have brute force creation Changed mock mvbs to be created by doing brute force rather than hard coding. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * test: Fix brute force mvbs gen Fixes the generation of expected mvbs with brute force as well as tweaks to mvbs_along_channel test. * chore: Clean up old code for doing compute MVBS Removes old code that perfoms compute_MVBS since now we've switched over to flox * chore(pytest): Added custom markers 'unit' and 'integration' * docs: Update docstring for `compute_MVBS` Added options for literal arguments * refactor: Change 'parse_range_bin' to 'parse_x_bin' Make bin parsing to be more general by making it to 'parse_x_bin'. * chore: Update suggested changes Update some texts from suggested review as discussed. Ref: OSOceanAcoustics#1124 (review) --------- Co-authored-by: Wu-Jung Lee <leewujung@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Emilio Mayorga <emiliomayorga@gmail.com> * ci: Fix run-test.py for module runs (OSOceanAcoustics#1180) Fixes the 'run-test.py' script so it can run module based testing rather than only specific test files. Ref: OSOceanAcoustics#1166 * Impulse noise: modified ryan_iterable to use ryan directly * Impulse noise: renamed medianf * Consolidating functions * Impulse noise refactoring: using a parameter dictionary and a function map * Frequency filtering * Frequency filtering (temp add to transient noise and signal attenuation, will refactor) * Signal attenuation refactor * Transmission noise refactor * Impulse noise default params * Multichannel noise masks * Made the noise masks able to handle taking a file path as an input * Fixed import * Fix * Update conftest.py extra parenthesis on pytest fixture decorator * Update test_noise.py Fixed the missing parenthesis for the tests. --------- 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: Praneeth Ratna <63547155+praneethratna@users.noreply.github.com> Co-authored-by: Wu-Jung Lee <leewujung@gmail.com> Co-authored-by: Emilio Mayorga <emiliomayorga@gmail.com> Co-authored-by: Don Setiawan <landungs@uw.edu> 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>
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