DOLfYN: Add dimensional averaging, current speed/direction calculations, and enhance ADCP example

[simmsa]

Overview

• Added surface interference cleaning, averaging, speed and direction calculations to ADCP example
• Added current speed and direction calculation functions
• Added averaging by dimension calculations for flexible data analysis
• Improved DOLFYN tests for better reliability
• Added standardization features to dolfyn_plot for consistent visualizations
• Improved performance of read_signature function
• Enhanced NetCDF support: Now reading all data attributes, not just "units"

Details

• Added .m file for acdp_example.m
  • Fixed typos, added clarity where MATLAB deviates from Python
  • Added additional visualizations for all velocity directions
• Added averaging by dimension calculation
• Added horizontal speed and velocity calculations
• dolfyn_plot
  • Use dataset attributes for labels, if they exist
  • Add argument to set color bar range
  • Add argument to plot histograms, kind
  • Allow plotting multiple directions using subplots
  • Added colormaps that use matplotlib colors
• Added caching to py_struct_2_bytes_format for better performance
• Updated write_netcdf for MATLAB 2022+ compatibility

Function Renaming to Match MHKiT-Python Conventions

• find_surface_from_P → water_depth_from_pressure
• nan_beyond_surface → remove_surface_interference

These renames align our function names with MHKiT-Python conventions for better consistency across the ecosystem.

Testing

• Added averaging, speed, and velocity calculation tests
• Added tests for NetCDF data attribute reading
• Added simple tests for read_netcdf
• Verified surface masking calculations

[rpauly18]

@simmsa I have a few tests failing - screenshots below. I am looking into it, but let me know if you have seen these before.

[simmsa]

@rpauly18 thank you. Those failing tests look familiar, can you try the code from here: https://github.com/simmsa/MHKiT-MATLAB/tree/dolfyn-parity?

git clone [email protected]:simmsa/MHKiT-MATLAB.git dolfyn-parity

cd dolfyn-parity

git checkout -b dolfyn-parity

Those tests are fixed in develop and I merged them into this pr here: simmsa@486f817 to avoid any merge conflicts and can see changes the dolfyn-parity branch above, but I do not see the changes in this PR. LMK if this doesn't work.