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

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

…hat I have the correct one though since the test isn't passing

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

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

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

…cation data

…cation data

… 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.

…n maps

Update outdated information in comments about empty masks

* 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

* added support for AZFP multiple phase attributes parsing (OSOceanAcoustics#1182)

* added support for multiple phase attributes parsing

* minor changes to code

* Update echopype/convert/set_groups_azfp.py

Co-authored-by: Emilio Mayorga <emiliomayorga@gmail.com>

* Update set_groups_azfp.py

* Update test_convert_azfp.py

---------

Co-authored-by: Emilio Mayorga <emiliomayorga@gmail.com>

* ci: Update CI to barebone python [all tests ci] (OSOceanAcoustics#1192)

* ci: Add installed packages listing

* ci: Add pip listing

* ci: Remove conda from PR action

* ci: Update worklows and add P2Z skip

* ci: More cleanup to workflow

* ci: Bump actions/setup-python from 4.7.0 to 4.7.1

* fix: Fix encoding in 'to_zarr' to remove 'preferred_chunks' before saving (OSOceanAcoustics#1128)

* Encoding and Chunk matching only if DaskArray

* Removing preffered chunks from encoding dict

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* `parse_azfp` now parses AZFP pressure data according to given matlab code (OSOceanAcoustics#1189)

* added support for parsing azfp pressure data

* fixed failing ci tests

* Revert "fixed failing ci tests"

This reverts commit c378dc0.

* minor changes to tests

* Update test_convert_azfp.py

* Update echopype/tests/convert/test_convert_azfp.py

---------

Co-authored-by: Emilio Mayorga <emiliomayorga@gmail.com>

* Enhanced `update_platform` to Auto-assign first `ping_time` as `Platform` timestamp for fixed-location update case without timestamp. [all tests ci] (OSOceanAcoustics#1196)

* first  is auto assigned as  timestamp for lon and lat update without timestamp

* fix small typo

---------

Co-authored-by: Wu-Jung Lee <leewujung@gmail.com>

* Added `depth_from_pressure` method required for the calculation of `vertical_offset` value (OSOceanAcoustics#1207)

* added depth_from_pressure method

* Function arguments can be scalars or sequences; and add more tests (#2)

* Reverse order of equation terms to match UNESCO 1983 source

* For depth_from_pressure, accept scalars, lists and arrays for all 3 arguments. Include consistency checks.

* Add a greater variety of depth_from_pressure tests.

* Update echopype/utils/misc.py

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---------

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

* fix(commongrid): fix bugs and improve `compute_NASC` using flox (OSOceanAcoustics#1167)

* 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.

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* 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>

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* 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.

* revive the function to make changes easier to see

* add TODOs

* add computation steps

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* remove unused _lin2log

* 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

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* 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'.

* refactor: Initial unification of MVBS and NASC

Added setup and validate function for shared checks
between compute MVBS and NASC so only unique
checks are in its individual function.

* fix typo when porting from notebook

* correct attribute units from m to nmi

* refactor: Add typehints and use method

* feat: Add get_x_along_channels

Added 'get_x_along_channels' function that generalizes
the reduction routines from 'get_MVBS_along_channels'.
This now removes the old function in mvbs.py module.

Additionally, uses of 'get_MVBS_along_channels' has
been removed from the test and code for 'compute_MVBS'.

* feat: Implement new 'compute_NASC'

Use 'get_x_along_channels' for 'compute_NASC'
and turn on old 'test_nasc.py' for initial nasc testing

* test: Renamed and moved get_x_along_channels test

* fix: Use 'ffill' and 'bfill'

Fixes the 'FutureWarning' coming from pandas
since as of pandas version 2.1.0 the 'method'
argument for 'fillna' is deprecated.

Ref: OSOceanAcoustics#1167 (comment)

* feat: Allow import 'compute_NASC' from 'commongrid' module

* fix: Fix bug on setup and validate and test

Fixes bug on 'setup_and_validate' during variable checks.

Also added simple testing for values from flox vs echoview.

* test: Update simple NASC integration test

* test: Add brute force values test for NASC

* chore: Apply suggestions from code review

Co-authored-by: Wu-Jung Lee <leewujung@gmail.com>

* refactor: Extract position reduction

* refactor: Separate sv mean and raw computations

* test: Remove empty test_nasc.py

* docs: Update docs for functions

* refactor: Move helper funcs to utils.py

* add L4 processing level to compute_NASC

---------

Co-authored-by: Landung 'Don' Setiawan <landungs@uw.edu>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Emilio Mayorga <emiliomayorga@gmail.com>

---------

Co-authored-by: Don Setiawan <landungs@uw.edu>
Co-authored-by: Praneeth Ratna <63547155+praneethratna@users.noreply.github.com>
Co-authored-by: Emilio Mayorga <emiliomayorga@gmail.com>
Co-authored-by: Soham Butala <38330817+Sohambutala@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Wu-Jung Lee <leewujung@gmail.com>

* Ariza conversion and initial version of ariza_interactive

* Added xarray mask transformations

* Added experimental secondary thressholding support

* Added shoal demasking option for ariza (they show up as "spikes" in the mask)

* Stash

* Functional blackwell

* Functional blackwell

* For merge reasons

* Blackwell can now take custom percentile values

* Implemented modified Blackwell

* Fixed requirements.txt