Introduce upcrossing analysis module #252
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The loads_extreme.global_peaks function was previously missing a test. The test uses a simple function which can be independently analysed. The results of global_peaks and the independent analysis are then compared.
Previously there was no general means of performing an upcrossing analysis. The load.extreme.global_peaks function could only calculate peaks. The module provides some common methods but also the ability for the user to define their own function over the zero crossing points.
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Hello! Thanks as always for all the work on MHKit! I wasn't sure exactly where to put this new functionality as it doesn't nicely sit within any of the existing modules. I opted for the |
With the recent addition of the upcrossing module, we can implement the loads.extreme.global_peaks function using it.
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It looks like the check below hasn't passed it dosen't seem to be related to my change: Py 3.7 3.8, 3.9 | Windows Mac Linux / pip-windows-latest/3.9 (pull_request) |
Mark No worries and thank you. There are API issues that are being addressed in #241 . |
akeeste
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Oct 11, 2023
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Hi @mbruggs
Sorry for the delay. Thanks for your contribution here. I reviewed your PR and made some minor linting/docstring suggestions in mbruggs#2
The last piece before merging is to find an appropriate spot for this. Right now the QC module is made up entirely of pecos functions and more focused on the clean-up of timeseries data than its analysis.
Right now I'm leaning towards within mhkit.loads as a submodule mhkit.loads.upcrossing or within the general submodule mhkit.loads.general. I'm open to discussion on location though
akeeste
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Oct 30, 2023
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Apologies about all the sporadic final commits. I missed a few things when moving the upcrossing module. Tests are now passing. Merging this PR. Thanks @mbruggs! |
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@akeeste Thanks very much for all your work on this! |
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# MHKiT v0.8.0 We're excited to announce the release of MHKiT v0.8.0, which brings a host of new features, enhancements, and bug fixes across various modules, ensuring compatibility with Python 3.10 and 3.11, and introducing full xarray support for more flexible data handling. Significant updates in the Wave and DOLfYN modules improve functionality and extend capabilities. ## Python 3.10 & 3.11 Support MHKiT now supports python 3.10 and 3.11. Support for 3.12 will follow in the next minor update. - #240 ## Wave Module ### Enhancements: **Automatic Threshold Calculation for Peaks-Over-Threshold**: We've introduced a new feature that automatically calculates the "best" threshold for identifying significant wave events. This method, originally developed by Neary, V. S., et al. in their 2020 study, has now been translated from Matlab to Python, enhancing our existing peaks-over-threshold functionality. **Wave Heights Analysis**: A new function, `wave_heights`, has been added to extract the heights of individual waves from a time series. This function uses zero up-crossing analysis to accurately measure wave heights, improving upon our previous methods which only provided the maximum value between up-crossings. **Enhanced Zero Crossing Analysis**: Building on the above, the zero crossing code previously embedded in `global_peaks` has been isolated into a helper function. This modular approach not only refines the codebase but also supports new functionalities such as calculating wave heights, zero crossing periods, and identifying crests. ### Bug Fixes: **Contour Sampling Error in Wave Contours**: A bug identified in `mhkit.wave.contours.samples_contour` has been resolved. The issue occurred when period samples defined using the maximum period resulted in values outside the interpolation range of the contour data. This was corrected by ensuring that all sampling points are within the interpolation range and adjusting the contour data selection process accordingly. - #268 - #252 - #278 ## Xarray Support MHKiT functions now fully support the use of xarray for passing and returning data. - #279 - #282 - #285 - #302 - #310 ## DOLfYN Thanks to the many user contributions and users of MHKiT the DOLFYN module include a significant number of enhancements and bug fixes. ### Enhancements: **Altimeter Support**: Enhanced the Nortek Signature Reader to add capability for reading ADCP dual profile configurations. **Data Handling Improvements**: Introduced logic to skip messy header data that can accumulate during measurements collected via Nortek software on PCs and Macs. **Instrument Noise Subtraction**: Added a function to subtract instrument noise from turbulence intensity estimation using RMS calculations, providing results that differ by approximately 1% from the existing standard deviation-based "I" property. **Improved File Handling**: Updates for RDI files to handle changing "number of cells" and variable "cell sizes," which are now bin-averaged into the largest cell size. ### Bug Fixes: **Power Spectra Calculation**: Fixed a bug where a given noise value was not being subtracted from the power spectra, and noise was inadvertently added as an input to dissipation rate calculations. **Improved Header Handling**: Allowed RDI reader to skip junk headers effectively. **Nortek Reader C Types Update**: Adjusted C types in the Nortek reader to handle below-zero water temperatures and to allow pitch and roll values to go negative. - #280 - #289 - #290 - #292 - #293 - #294 - #299 ## River & Tidal: D3D Added limits to `variable_interpolation` and added 3 array input capability to `create_points` - #271 ## Developer Experience ### Black formatting Black formatting is now enforced on all MHKiT files. This ensures consistent formatting across the MHKiT package. - #281 ### Linting & Type Hints MHKiT is in the process of enforcing pylint and adding type hints to all functions. Currently this has been achieved and is enforced in the Loads and Power modules. - #288 - #296 ### CI/CD This release introduces significant reduction in testing time for development. This is achieved by reducing the number of tests for pulls against the develop branch and only running hindcast test when changes are made to it. A bug in the hindcast CI was fixed which only ran on changes to the hindcast tests instead of the hindcast module. Additionally the wave and wind hindcast needed to be separated in 2 jobs due to the excessive time taken to run a wind cache. This created a number of follow on PRs around solidifying the logic of these job. A special case for Python 3.8, pip, and Mac OS was added to use homebrew to install NetCDF and HDF5 to get tests to pass. - #241 - #270 - #306 - #311 - #317 - #318 - #319 - #320 - #324 ### Clean Up MHKiT fixed an implementation error where functions used assert instead of built in errors for type and value checking. Additionally these PRs removed unused files, fixed typos, and created an argument which allows users to run CDIP API calls silently. - #276 - #272 - #273
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As disussed in #230, there were no general methods for performing an upcrossing analysis. This series of commits introduces such a module and uses it to implement the existing functionality within the loads.extreme.global_peaks function.