Improve flexibility and robustness of Acoustics Module by jmcvey3 · Pull Request #433 · MHKiT-Software/MHKiT-Python

jmcvey3 · 2026-01-21T22:22:43Z

There are three main changes in this pull request:

Added the option to determine the number of datapoints in each FFT when creating the sound pressure PSDs. This was currently hardcoded to the maximum FFT length, i.e. the total number of datapoints in each window, which might be more resolution and require more storage space than desired
Changed names of bin and windowing related attributes on the PSDs to make them easier to understand
Gain was improperly added - the sign has been corrected

Minor changes are refactoring some of the argument type checks to clean them up.

…utes

…PSDs are calculated

jmcvey3 · 2026-01-21T22:52:36Z

Looks like some remaining dependency issues related to timestamps

akeeste

Thanks @jmcvey3! Just two small suggestions on the use of _check_numeric

simmsa · 2026-02-18T23:54:46Z

@jmcvey3, from my perspective you are not obligated to have all of the tests passing here to merge this into develop. Do you have any thoughts/preferences here? I'm guessing all of the tests pass locally for you, so let us know what makes sense.

This is likely going to continue to be an issue moving forward with MHKiT, so I wonder if there is better way for the tests to only check "things that matter", and maybe only run pytest on the modules where the code has changed.

It is def appreciated to get the tests working here, but I think this is more of the tests are broken in general vs this PR's tests are not passing...

Happy to take any feedback here also. The actions have a lot of false positives IMO. I like the CI/CD idea in general, but there are also a lot of ways that this impedes actual development, so it seems like we need to find a balance...

jmcvey3 · 2026-02-18T23:58:07Z

Well.... I tracked down the not-pretty bug in the cdip.py file and fixed that since it was a recurring issue.

In the process, I cleaned up the dependencies in the conda environment file, so now hopefully these tests will run faster now that they don't have to install dependencies twice each time. I most likely broke the pip installation because of the h5-related libraries, but we'll see whenever those tests finish.

jmcvey3 · 2026-02-19T00:02:43Z

@jmcvey3, from my perspective you are not obligated to have all of the tests passing here to merge this into develop. Do you have any thoughts/preferences here? I'm guessing all of the tests pass locally for you, so let us know what makes sense.

This is likely going to continue to be an issue moving forward with MHKiT, so I wonder if there is better way for the tests to only check "things that matter", and maybe only run pytest on the modules where the code has changed.

It is def appreciated to get the tests working here, but I think this is more of the tests are broken in general vs this PR's tests are not passing...

Happy to take any feedback here also. The actions have a lot of false positives IMO. I like the CI/CD idea in general, but there are also a lot of ways that this impedes actual development, so it seems like we need to find a balance...

Perhaps, but these have been frustrating for a while now, and I need this PR merged. I'm realizing what I'm running through now may have been why the packaging was difficult for the 1.0 release

simmsa · 2026-02-19T00:21:46Z

Perhaps, but these have been frustrating for a while now, and I need this PR merged. I'm realizing what I'm running through now may have been why the packaging was difficult for the 1.0 release.

Do you just need this merged into develop? I think if you are happy with Adam's review and your tests are passing locally it is fine to merge this?

I pulled your branch and all of the tests in the acoustics module pass locally for me in a fresh virtual environment:

 pytest -v mhkit/tests/acoustics
=============================================================================================== test session starts ================================================================================================
platform darwin -- Python 3.11.12, pytest-8.4.2, pluggy-1.6.0 -- /opt/homebrew/opt/python@3.11/bin/python3.11
cachedir: .pytest_cache
benchmark: 5.2.3 (defaults: timer=time.perf_counter disable_gc=False min_rounds=5 min_time=0.000005 max_time=1.0 calibration_precision=10 warmup=False warmup_iterations=100000)
rootdir: /Users/asimms/Desktop/Programming/mcvey_mhkit/MHKiT-Python
configfile: pyproject.toml
plugins: benchmark-5.2.3, cov-6.0.0, anyio-4.11.0, asyncio-0.25.3, nbval-0.11.0, typeguard-4.4.2
asyncio: mode=Mode.STRICT, asyncio_default_fixture_loop_scope=function
collected 18 items

mhkit/tests/acoustics/test_analysis.py::TestAnalysis::test_apply_calibration PASSED                                                                                                                          [  5%]
mhkit/tests/acoustics/test_analysis.py::TestAnalysis::test_averaging PASSED                                                                                                                                  [ 11%]
mhkit/tests/acoustics/test_analysis.py::TestAnalysis::test_fmax_warning PASSED                                                                                                                               [ 16%]
mhkit/tests/acoustics/test_analysis.py::TestAnalysis::test_freq_loss PASSED                                                                                                                                  [ 22%]
mhkit/tests/acoustics/test_analysis.py::TestAnalysis::test_sound_pressure_spectral_density PASSED                                                                                                            [ 27%]
mhkit/tests/acoustics/test_analysis.py::TestAnalysis::test_spsdl PASSED                                                                                                                                      [ 33%]
mhkit/tests/acoustics/test_analysis.py::TestAnalysis::test_validate_method PASSED                                                                                                                            [ 38%]
mhkit/tests/acoustics/test_io.py::TestIO::test_audio_export PASSED                                                                                                                                           [ 44%]
mhkit/tests/acoustics/test_io.py::TestIO::test_calculate_voltage_and_time PASSED                                                                                                                             [ 50%]
mhkit/tests/acoustics/test_io.py::TestIO::test_calibration PASSED                                                                                                                                            [ 55%]
mhkit/tests/acoustics/test_io.py::TestIO::test_read_iclisten PASSED                                                                                                                                          [ 61%]
mhkit/tests/acoustics/test_io.py::TestIO::test_read_iclisten_metadata PASSED                                                                                                                                 [ 66%]
mhkit/tests/acoustics/test_io.py::TestIO::test_read_soundtrap PASSED                                                                                                                                         [ 72%]
mhkit/tests/acoustics/test_io.py::TestIO::test_read_wav_metadata PASSED                                                                                                                                      [ 77%]
mhkit/tests/acoustics/test_metrics.py::TestMetrics::test_nmfs_weighting PASSED                                                                                                                               [ 83%]
mhkit/tests/acoustics/test_metrics.py::TestMetrics::test_sel PASSED                                                                                                                                          [ 88%]
mhkit/tests/acoustics/test_metrics.py::TestMetrics::test_spl PASSED                                                                                                                                          [ 94%]
mhkit/tests/acoustics/test_metrics.py::TestMetrics::test_spl_vs_sel PASSED                                                                                                                                   [100%]

================================================================================================= warnings summary =================================================================================================
mhkit/tests/acoustics/test_analysis.py::TestAnalysis::test_averaging
  /Users/asimms/Desktop/Programming/mcvey_mhkit/MHKiT-Python/mhkit/acoustics/analysis.py:84: UserWarning: `fmax` = 100000 is greater than the Nyquist frequency. Settingfmax = 48000.0
    warnings.warn(

mhkit/tests/acoustics/test_analysis.py::TestAnalysis::test_fmax_warning
  /Users/asimms/Desktop/Programming/mcvey_mhkit/MHKiT-Python/mhkit/acoustics/analysis.py:84: UserWarning: `fmax` = 1500 is greater than the Nyquist frequency. Settingfmax = 1000
    warnings.warn(

mhkit/tests/acoustics/test_io.py::TestIO::test_audio_export
mhkit/tests/acoustics/test_io.py::TestIO::test_read_iclisten
  /Users/asimms/Desktop/Programming/mcvey_mhkit/MHKiT-Python/mhkit/acoustics/io.py:457: UserWarning: no explicit representation of timezones available for np.datetime64
    start_time = np.datetime64(metadata["icrd"])

mhkit/tests/acoustics/test_metrics.py::TestMetrics::test_sel
mhkit/tests/acoustics/test_metrics.py::TestMetrics::test_spl
mhkit/tests/acoustics/test_metrics.py::TestMetrics::test_spl_vs_sel
  /Users/asimms/Desktop/Programming/mcvey_mhkit/MHKiT-Python/mhkit/acoustics/analysis.py:84: UserWarning: `fmax` = 100000 is greater than the Nyquist frequency. Settingfmax = 48000
    warnings.warn(

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
========================================================================================= 18 passed, 7 warnings in 14.28s ==========================================================================================

What do you think? I don't want to set a bad precedent, but you are not merging this into main, you are merging into develop, and that seems like what the develop branch is for.

My own opinion is that some of the changes you are making in this PR are out of scope. That is fine and I get it, but I think we need to be careful about doing too many things to "appease the tests".

jmcvey3 · 2026-02-19T00:40:05Z

What do you think? I don't want to set a bad precedent, but you are not merging this into main, you are merging into develop, and that seems like what the develop branch is for.

My own opinion is that some of the changes you are making in this PR are out of scope. That is fine and I get it, but I think we need to be careful about doing too many things to "appease the tests".

Sure sure. I can create a new branch and a new PR for these changes and then rebase this PR back to just the acoustics code. I'll redo the "black" commit too so it's just editing the acoustics files as well.

akeeste · 2026-02-19T17:01:19Z

I agree with your first comment @simmsa , if the relevant tests are passing I think we should merge PRs as is to get that feature taken care of and then move to fixing the tests. Ideally, we'd do the test fixes first into develop and pull the updates into the feature PR (such as this one)--but none of us have the bandwidth to do so very quickly.

@jmcvey3 For this particular PR, I will support whatever will be most efficient, whether that's merging as is, putting another fix here for the last test, or rebasing the test fixes into a new PR

jmcvey3 · 2026-02-19T17:29:38Z

I agree with your first comment @simmsa , if the relevant tests are passing I think we should merge PRs as is to get that feature taken care of and then move to fixing the tests. Ideally, we'd do the test fixes first into develop and pull the updates into the feature PR (such as this one)--but none of us have the bandwidth to do so very quickly.

@jmcvey3 For this particular PR, I will support whatever will be most efficient, whether that's merging as is, putting another fix here for the last test, or rebasing the test fixes into a new PR

Sounds good. I've rebased here and created a new PR for the other changes

@jmcvey3

# MHKiT-Python v1.1.0 ## Additions * Acoustics: Add millicdecade and WISPR instrument support * Added millidecade spectral conversion * Added a WISPR hydrophone reader * Added a voltage-based `export_audio` resampling option * Refactored band-averaging to avoid losing information at frequency-band boundaries * #447 * Author: @jmcvey3 * Reviewer: @simmsa * DOLfYN: Add [Nortek Aquadopp](https://www.nortekgroup.com/oceanography/aquadopp-series) ADCP support * Added DOLfYN support for reading Aquadopp instruments * Cleaned Nortek parsing code * Simplified handling of the non-cabled ADV orientation flag * #434 * Author: @jmcvey3 * Reviewer: @akeeste * Examples: Add ADCP waves example: `example/adcp_waves_example.ipynb` * Added an example notebook showing how to ingest and analyze wave measurements from a dual-profile Nortek Signature 250 deployment at PacWave. * #430 * Author: @jmcvey3 * Reviewer: @akeeste ## Improvements ### Acoustics - Improved flexibility and robustness of the Acoustics module - Added a configurable FFT length for sound pressure PSDs - Renamed bin/windowing attributes for clarity - Fixed an incorrectly signed gain correction - #433 - Author: @jmcvey3 - Reviewer: @akeeste ### DOLfYN - Refactored PSD calculations to use `scipy.signal.welch` - Replaced DOLfYN's custom Welch-like PSD implementation (built each segment from bin slices, could not overlap FFT segments) with `scipy.signal.welch` - Removed the bin-based segment structure and added a `step` argument to control overlap - Dropped float32 casts in some functions in favor of float64 - Removed `fft.py` and renamed `tools/misc.py` to `tools.py` - Breaking Changes: - NaNs are no longer tolerated in PSD calculations - DOLfYN defaults to 0% overlap to preserve existing array shapes - Acoustics defaults to 50% overlap - PSD output time dimension renamed to `time_psd` - #452 - Author: @jmcvey3 - Reviewer: @akeeste, @simmsa - Improved handling of "averaged" profiles - Fixed handling of Nortek Signature dual-profile ADCP data by defaulting to "_avg" velocity variables when untagged ones are absent. - #430 - Author: @jmcvey3 - Reviewer: @akeeste - Critical PSD bugfix - Fixed a bug where individual FFTs received a 50% overlap twice, which corrupted the first and last spectrum of a timeseries. - #430 - Author: @jmcvey3 - Reviewer: @akeeste ### Examples - Added histograms to ADCP example - #448 - Author: @browniea - Reviewer: @akeeste ### River/IO - Fixed Qhull interpolation and D3D coordinate-system errors - #448 - Author: @browniea - Reviewer: @akeeste - Fixes: #442, #444 - Delft3D module updates - Added new Delft3D coordinate names - Added a new grid-convergence-index calculation function - Added support for xarray/netCDF4 input in the D3D module - #428 - Author: @browniea - Reviewer: @akeeste ### Wave - NDBC Directional Wave Units - Fixed NDBC directional wave spectrum output to return degrees instead of radians - Updated polar plots so 0 deg is at the top and increases clockwise - #437 - Author: @jmcvey3 - Reviewer: @akeeste - Fixes: #427 ### Wave/Hindcast - Added a `hindcast_guard` exception-handling decorator (`hindcast_exceptions.py`) that surfaces a clear error on HSDS request failures, distinguishing the known NLR HSDS outage (#450) from other failures - #449 - Author: @simmsa - Reviewer: @akeeste ## Maintenance - Added Python 3.13 support - #445 - Author: @simmsa - Reviewer: @akeeste - Fixes: #441 - Added [pandas 3](https://pandas.pydata.org/community/blog/pandas-3.0.html) Support - Updated the pandas dependency to allow pandas 3.x - Added a compatibility shim for NDBC missing-value handling related to pandas 3 object to String dtype api changes - Fixed a deprecated period alias in tests - #443 - Author: @simmsa - Reviewer: @akeeste - Fixes: #440 - Updated GitHub Actions CI, expanded installation/developer documentation, refreshed dev environment, and trimmed dependencies - Refactored optional dependencies - Standardized conda/conda-forge environment builds - Scoped black linting to changed files - #436 - Author: @simmsa - Reviewer: @akeeste - Update `rex` dependency to target pypi package to [`NLR-rex[hsds]>=0.5.0`](https://pypi.org/project/NLR-rex/) - #449 - Author: @simmsa - Reviewer: @akeeste

@jmcvey3

# MHKiT-Python v1.1.0 ## Additions * Acoustics: Add millicdecade and WISPR instrument support * Added millidecade spectral conversion * Added a WISPR hydrophone reader * Added a voltage-based `export_audio` resampling option * Refactored band-averaging to avoid losing information at frequency-band boundaries * MHKiT-Software#447 * Author: @jmcvey3 * Reviewer: @simmsa * DOLfYN: Add [Nortek Aquadopp](https://www.nortekgroup.com/oceanography/aquadopp-series) ADCP support * Added DOLfYN support for reading Aquadopp instruments * Cleaned Nortek parsing code * Simplified handling of the non-cabled ADV orientation flag * MHKiT-Software#434 * Author: @jmcvey3 * Reviewer: @akeeste * Examples: Add ADCP waves example: `example/adcp_waves_example.ipynb` * Added an example notebook showing how to ingest and analyze wave measurements from a dual-profile Nortek Signature 250 deployment at PacWave. * MHKiT-Software#430 * Author: @jmcvey3 * Reviewer: @akeeste ## Improvements ### Acoustics - Improved flexibility and robustness of the Acoustics module - Added a configurable FFT length for sound pressure PSDs - Renamed bin/windowing attributes for clarity - Fixed an incorrectly signed gain correction - MHKiT-Software#433 - Author: @jmcvey3 - Reviewer: @akeeste ### DOLfYN - Refactored PSD calculations to use `scipy.signal.welch` - Replaced DOLfYN's custom Welch-like PSD implementation (built each segment from bin slices, could not overlap FFT segments) with `scipy.signal.welch` - Removed the bin-based segment structure and added a `step` argument to control overlap - Dropped float32 casts in some functions in favor of float64 - Removed `fft.py` and renamed `tools/misc.py` to `tools.py` - Breaking Changes: - NaNs are no longer tolerated in PSD calculations - DOLfYN defaults to 0% overlap to preserve existing array shapes - Acoustics defaults to 50% overlap - PSD output time dimension renamed to `time_psd` - MHKiT-Software#452 - Author: @jmcvey3 - Reviewer: @akeeste, @simmsa - Improved handling of "averaged" profiles - Fixed handling of Nortek Signature dual-profile ADCP data by defaulting to "_avg" velocity variables when untagged ones are absent. - MHKiT-Software#430 - Author: @jmcvey3 - Reviewer: @akeeste - Critical PSD bugfix - Fixed a bug where individual FFTs received a 50% overlap twice, which corrupted the first and last spectrum of a timeseries. - MHKiT-Software#430 - Author: @jmcvey3 - Reviewer: @akeeste ### Examples - Added histograms to ADCP example - MHKiT-Software#448 - Author: @browniea - Reviewer: @akeeste ### River/IO - Fixed Qhull interpolation and D3D coordinate-system errors - MHKiT-Software#448 - Author: @browniea - Reviewer: @akeeste - Fixes: MHKiT-Software#442, MHKiT-Software#444 - Delft3D module updates - Added new Delft3D coordinate names - Added a new grid-convergence-index calculation function - Added support for xarray/netCDF4 input in the D3D module - MHKiT-Software#428 - Author: @browniea - Reviewer: @akeeste ### Wave - NDBC Directional Wave Units - Fixed NDBC directional wave spectrum output to return degrees instead of radians - Updated polar plots so 0 deg is at the top and increases clockwise - MHKiT-Software#437 - Author: @jmcvey3 - Reviewer: @akeeste - Fixes: MHKiT-Software#427 ### Wave/Hindcast - Added a `hindcast_guard` exception-handling decorator (`hindcast_exceptions.py`) that surfaces a clear error on HSDS request failures, distinguishing the known NLR HSDS outage (MHKiT-Software#450) from other failures - MHKiT-Software#449 - Author: @simmsa - Reviewer: @akeeste ## Maintenance - Added Python 3.13 support - MHKiT-Software#445 - Author: @simmsa - Reviewer: @akeeste - Fixes: MHKiT-Software#441 - Added [pandas 3](https://pandas.pydata.org/community/blog/pandas-3.0.html) Support - Updated the pandas dependency to allow pandas 3.x - Added a compatibility shim for NDBC missing-value handling related to pandas 3 object to String dtype api changes - Fixed a deprecated period alias in tests - MHKiT-Software#443 - Author: @simmsa - Reviewer: @akeeste - Fixes: MHKiT-Software#440 - Updated GitHub Actions CI, expanded installation/developer documentation, refreshed dev environment, and trimmed dependencies - Refactored optional dependencies - Standardized conda/conda-forge environment builds - Scoped black linting to changed files - MHKiT-Software#436 - Author: @simmsa - Reviewer: @akeeste - Update `rex` dependency to target pypi package to [`NLR-rex[hsds]>=0.5.0`](https://pypi.org/project/NLR-rex/) - MHKiT-Software#449 - Author: @simmsa - Reviewer: @akeeste

There are three main changes in this pull request: 1. Added the option to determine the number of datapoints in each FFT when creating the sound pressure PSDs. This was currently hardcoded to the maximum FFT length, i.e. the total number of datapoints in each window, which might be more resolution and require more storage space than desired 2. Changed names of bin and windowing related attributes on the PSDs to make them easier to understand 3. Gain was improperly added - the sign has been corrected Minor changes are refactoring some of the argument type checks to clean them up.

@jmcvey3

# MHKiT-Python v1.1.0 ## Additions * Acoustics: Add millicdecade and WISPR instrument support * Added millidecade spectral conversion * Added a WISPR hydrophone reader * Added a voltage-based `export_audio` resampling option * Refactored band-averaging to avoid losing information at frequency-band boundaries * #447 * Author: @jmcvey3 * Reviewer: @simmsa * DOLfYN: Add [Nortek Aquadopp](https://www.nortekgroup.com/oceanography/aquadopp-series) ADCP support * Added DOLfYN support for reading Aquadopp instruments * Cleaned Nortek parsing code * Simplified handling of the non-cabled ADV orientation flag * #434 * Author: @jmcvey3 * Reviewer: @akeeste * Examples: Add ADCP waves example: `example/adcp_waves_example.ipynb` * Added an example notebook showing how to ingest and analyze wave measurements from a dual-profile Nortek Signature 250 deployment at PacWave. * #430 * Author: @jmcvey3 * Reviewer: @akeeste ## Improvements ### Acoustics - Improved flexibility and robustness of the Acoustics module - Added a configurable FFT length for sound pressure PSDs - Renamed bin/windowing attributes for clarity - Fixed an incorrectly signed gain correction - #433 - Author: @jmcvey3 - Reviewer: @akeeste ### DOLfYN - Refactored PSD calculations to use `scipy.signal.welch` - Replaced DOLfYN's custom Welch-like PSD implementation (built each segment from bin slices, could not overlap FFT segments) with `scipy.signal.welch` - Removed the bin-based segment structure and added a `step` argument to control overlap - Dropped float32 casts in some functions in favor of float64 - Removed `fft.py` and renamed `tools/misc.py` to `tools.py` - Breaking Changes: - NaNs are no longer tolerated in PSD calculations - DOLfYN defaults to 0% overlap to preserve existing array shapes - Acoustics defaults to 50% overlap - PSD output time dimension renamed to `time_psd` - #452 - Author: @jmcvey3 - Reviewer: @akeeste, @simmsa - Improved handling of "averaged" profiles - Fixed handling of Nortek Signature dual-profile ADCP data by defaulting to "_avg" velocity variables when untagged ones are absent. - #430 - Author: @jmcvey3 - Reviewer: @akeeste - Critical PSD bugfix - Fixed a bug where individual FFTs received a 50% overlap twice, which corrupted the first and last spectrum of a timeseries. - #430 - Author: @jmcvey3 - Reviewer: @akeeste ### Examples - Added histograms to ADCP example - #448 - Author: @browniea - Reviewer: @akeeste ### River/IO - Fixed Qhull interpolation and D3D coordinate-system errors - #448 - Author: @browniea - Reviewer: @akeeste - Fixes: #442, #444 - Delft3D module updates - Added new Delft3D coordinate names - Added a new grid-convergence-index calculation function - Added support for xarray/netCDF4 input in the D3D module - #428 - Author: @browniea - Reviewer: @akeeste ### Wave - NDBC Directional Wave Units - Fixed NDBC directional wave spectrum output to return degrees instead of radians - Updated polar plots so 0 deg is at the top and increases clockwise - #437 - Author: @jmcvey3 - Reviewer: @akeeste - Fixes: #427 ### Wave/Hindcast - Added a `hindcast_guard` exception-handling decorator (`hindcast_exceptions.py`) that surfaces a clear error on HSDS request failures, distinguishing the known NLR HSDS outage (#450) from other failures - #449 - Author: @simmsa - Reviewer: @akeeste ## Maintenance - Added Python 3.13 support - #445 - Author: @simmsa - Reviewer: @akeeste - Fixes: #441 - Added [pandas 3](https://pandas.pydata.org/community/blog/pandas-3.0.html) Support - Updated the pandas dependency to allow pandas 3.x - Added a compatibility shim for NDBC missing-value handling related to pandas 3 object to String dtype api changes - Fixed a deprecated period alias in tests - #443 - Author: @simmsa - Reviewer: @akeeste - Fixes: #440 - Updated GitHub Actions CI, expanded installation/developer documentation, refreshed dev environment, and trimmed dependencies - Refactored optional dependencies - Standardized conda/conda-forge environment builds - Scoped black linting to changed files - #436 - Author: @simmsa - Reviewer: @akeeste - Update `rex` dependency to target pypi package to [`NLR-rex[hsds]>=0.5.0`](https://pypi.org/project/NLR-rex/) - #449 - Author: @simmsa - Reviewer: @akeeste

@jmcvey3

# MHKiT-Python v1.1.0 ## Additions * Acoustics: Add millicdecade and WISPR instrument support * Added millidecade spectral conversion * Added a WISPR hydrophone reader * Added a voltage-based `export_audio` resampling option * Refactored band-averaging to avoid losing information at frequency-band boundaries * #447 * Author: @jmcvey3 * Reviewer: @simmsa * DOLfYN: Add [Nortek Aquadopp](https://www.nortekgroup.com/oceanography/aquadopp-series) ADCP support * Added DOLfYN support for reading Aquadopp instruments * Cleaned Nortek parsing code * Simplified handling of the non-cabled ADV orientation flag * #434 * Author: @jmcvey3 * Reviewer: @akeeste * Examples: Add ADCP waves example: `example/adcp_waves_example.ipynb` * Added an example notebook showing how to ingest and analyze wave measurements from a dual-profile Nortek Signature 250 deployment at PacWave. * #430 * Author: @jmcvey3 * Reviewer: @akeeste ## Improvements ### Acoustics - Improved flexibility and robustness of the Acoustics module - Added a configurable FFT length for sound pressure PSDs - Renamed bin/windowing attributes for clarity - Fixed an incorrectly signed gain correction - #433 - Author: @jmcvey3 - Reviewer: @akeeste ### DOLfYN - Refactored PSD calculations to use `scipy.signal.welch` - Replaced DOLfYN's custom Welch-like PSD implementation (built each segment from bin slices, could not overlap FFT segments) with `scipy.signal.welch` - Removed the bin-based segment structure and added a `step` argument to control overlap - Dropped float32 casts in some functions in favor of float64 - Removed `fft.py` and renamed `tools/misc.py` to `tools.py` - Breaking Changes: - NaNs are no longer tolerated in PSD calculations - DOLfYN defaults to 0% overlap to preserve existing array shapes - Acoustics defaults to 50% overlap - PSD output time dimension renamed to `time_psd` - #452 - Author: @jmcvey3 - Reviewer: @akeeste, @simmsa - Improved handling of "averaged" profiles - Fixed handling of Nortek Signature dual-profile ADCP data by defaulting to "_avg" velocity variables when untagged ones are absent. - #430 - Author: @jmcvey3 - Reviewer: @akeeste - Critical PSD bugfix - Fixed a bug where individual FFTs received a 50% overlap twice, which corrupted the first and last spectrum of a timeseries. - #430 - Author: @jmcvey3 - Reviewer: @akeeste ### Examples - Added histograms to ADCP example - #448 - Author: @browniea - Reviewer: @akeeste ### River/IO - Fixed Qhull interpolation and D3D coordinate-system errors - #448 - Author: @browniea - Reviewer: @akeeste - Fixes: #442, #444 - Delft3D module updates - Added new Delft3D coordinate names - Added a new grid-convergence-index calculation function - Added support for xarray/netCDF4 input in the D3D module - #428 - Author: @browniea - Reviewer: @akeeste ### Wave - NDBC Directional Wave Units - Fixed NDBC directional wave spectrum output to return degrees instead of radians - Updated polar plots so 0 deg is at the top and increases clockwise - #437 - Author: @jmcvey3 - Reviewer: @akeeste - Fixes: #427 ### Wave/Hindcast - Added a `hindcast_guard` exception-handling decorator (`hindcast_exceptions.py`) that surfaces a clear error on HSDS request failures, distinguishing the known NLR HSDS outage (#450) from other failures - #449 - Author: @simmsa - Reviewer: @akeeste ## Maintenance - Added Python 3.13 support - #445 - Author: @simmsa - Reviewer: @akeeste - Fixes: #441 - Added [pandas 3](https://pandas.pydata.org/community/blog/pandas-3.0.html) Support - Updated the pandas dependency to allow pandas 3.x - Added a compatibility shim for NDBC missing-value handling related to pandas 3 object to String dtype api changes - Fixed a deprecated period alias in tests - #443 - Author: @simmsa - Reviewer: @akeeste - Fixes: #440 - Updated GitHub Actions CI, expanded installation/developer documentation, refreshed dev environment, and trimmed dependencies - Refactored optional dependencies - Standardized conda/conda-forge environment builds - Scoped black linting to changed files - #436 - Author: @simmsa - Reviewer: @akeeste - Update `rex` dependency to target pypi package to [`NLR-rex[hsds]>=0.5.0`](https://pypi.org/project/NLR-rex/) - #449 - Author: @simmsa - Reviewer: @akeeste

jmcvey3 added 5 commits January 12, 2026 10:00

Change hardwired variables to function inputs, improve fmin/fmax checks

7f3405b

Use n_bin to define time now that n_fft can be adjusted

085f56a

Change 'nbin' to 'bin_length' and specify time interval in SPL attrib…

593e198

…utes

Use 'time_resolution' instead of 'time_interval' for time over which …

c222670

…PSDs are calculated

Make sure test gets updated

c514cda

jmcvey3 added enhancement New feature or request Clean Up Improve code consistency and readability acoustics Acoustics Module labels Jan 21, 2026

akeeste self-assigned this Feb 3, 2026

akeeste self-requested a review February 3, 2026 17:11

Fix one instance of check_numeric call input

9cd0857

akeeste reviewed Feb 3, 2026

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Comment thread mhkit/acoustics/analysis.py

Comment thread mhkit/acoustics/io.py Outdated

Fix error checking mistake

469d469

Set time coordinates to nanoseconds to not break pandas 3.0

ffc3f65

jmcvey3 force-pushed the acoustics-options branch from d965fc0 to ffc3f65 Compare February 19, 2026 17:28

simmsa mentioned this pull request Feb 19, 2026

Acoustics Module: Need to review MHKiT-Python PR #433 MHKiT-Software/MHKiT-MATLAB#195

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jmcvey3 merged commit 6f806c8 into MHKiT-Software:develop Feb 20, 2026
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jmcvey3 deleted the acoustics-options branch February 20, 2026 22:43

simmsa mentioned this pull request Jun 29, 2026

Release: Prepare MHKiT-Python v1.1.0 #449

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hivanov-nrel mentioned this pull request Jun 30, 2026

Acoustics Module Updates MHKiT-Software/MHKiT-MATLAB#198

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simmsa mentioned this pull request Jul 8, 2026

Release: MHKiT v1.1.0 #453

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Improve flexibility and robustness of Acoustics Module - #433

Improve flexibility and robustness of Acoustics Module#433
jmcvey3 merged 8 commits into
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jmcvey3:acoustics-options

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