Dolfyn updates + turbulence analysis #232

jmcvey3 · 2023-03-28T19:05:53Z

A slew of bugfixes and inconsistency cleanup, as well as including ADCP turbulence functionality for #227

Changelog:

Bugfixes
- Added check to ensure n_bin is shorter than the total data length when calling dolfyn.TimeBinner.reshape
- Added checks to ensure n_fft and n_fft_coh can't be greater than n_bin
- Fixed bug where dolfyn.adp.nan_beyond_surface overtrimmed TRDI instrument data
- Fixed bug where dolfyn.ADVBinner.cross_spectral_density would fail if n_fft != n_fft_coh
- Improved robustness of Nortek Signature reader for deployments not measuring water velocity
- log file extension changed from ".log" to ".dolfyn.log"
API/Useability
- Calculation of depth from pressure sensor updated to use linear approximation of the equation of state, rather than EOS-80
- Added warnings for ADV motion and turbulence functions
- Updated dataset.velds.U_dir shortcut to automatically convert "degrees CCW from X/East/streamwise" to "degrees CW from X/North/streamwise"
- dolfyn.ADVBinner.cross_spectral_density now returns frequency coordinate coh_freq instead of freq
- Added ADCP turbulence functions
- Added function to calculate Doppler noise to ADV turbulence functions
- Added "beam_angle" attribute to Nortek Signature datasets
- Saved full Nortek Signature "config" dictionary as json string in attributes
- Added warning if "rotate_vars" attribute not found
- Standardized variable metadata based on CF conventions

ssolson · 2023-04-05T16:02:53Z

James pulling the latest develop branch should fix your test failures

* Update calls to grid formatting * run on develop

…#225) In an oversight in merging MHKiT-Software#193 the docstring was updated for the type of return_year in return_year_value but the corresponding assertion was not. Tests for the types of the two input parameters have been added to try to avoid a simular situation occuring the future.

jmcvey3 · 2023-04-21T18:25:05Z

@browniea I've finished my updates for this PR, though I need to update documentation and add an example notebook. Was there something else you wanted to add to it?

jmcvey3 · 2023-06-13T18:50:59Z

Currently working on adding turbulence functions to ADCP example notebook

ssolson · 2023-06-29T13:35:59Z

@jmcvey3 in #236 you said:

@ssolson I just remembered there are some changes in the dolfyn PR (namely to the function/shortcut dolfyn.velocity.U_dir) that will affect this one. I'll try to wrap the dolfyn PR soon here so we can merge these back to back.

So we need to complete this PR first then #236? I am only confused because it seems #236 has passed all tests.

jmcvey3 · 2023-07-18T00:28:57Z

@ssolson Just pushed some updates to the jupyter notebooks to incorporate the ADCP turbulence analysis.

@jmcvey3 in #236 you said:

@ssolson I just remembered there are some changes in the dolfyn PR (namely to the function/shortcut dolfyn.velocity.U_dir) that will affect this one. I'll try to wrap the dolfyn PR soon here so we can merge these back to back.

So we need to complete this PR first then #236? I am only confused because it seems #236 has passed all tests.

Just to have this on paper, it's a change relevant to the tidal performance jupyter notebook

jmcvey3 · 2023-07-18T00:29:31Z

@ssolson Just pushed some updates to the jupyter notebooks to incorporate the ADCP turbulence analysis. This PR should be good to go for final review

into dolfyn_updates

ssolson

James you did a lot of great work here. I have a number of minor suggestions primarily around docstrings. Outside of the new turbulence model this seems to be a great deal of clean up and improvements top the current dolfyn module.

I still need to review the notebooks next week.

ssolson · 2023-07-20T16:01:01Z

mhkit/dolfyn/rotate/base.py

+def calc_tilt(pitch, roll):
+    """
+    Calculate "tilt", the vertical inclination, from pitch and roll.
+
+    Parameters
+    ----------
+    roll : numpy.ndarray or xarray.DataArray
+      Instrument roll
+    pitch : numpy.ndarray or xarray.DataArray
+      Instrument pitch
+
+    Returns
+    -------
+    tilt : numpy.ndarray
+      Vertical inclination of the instrument
+    """
+
+    if 'xarray' in type(pitch).__module__:
+        pitch = pitch.values
+    if 'xarray' in type(roll).__module__:
+        roll = roll.values
+
+    tilt = np.arctan(
+        np.sqrt(np.tan(np.deg2rad(roll)) ** 2 + np.tan(np.deg2rad(pitch)) ** 2)
+    )
+
+    return np.rad2deg(tilt)


We should probably specify in the Parameters & Return that the function expects and returns degrees.

This may be well-known among practitioners. Is vertical inclination always measured from the z-direction?
So my understanding is that if pitch and roll are both 0 then tilt is zero and we have an instrument at perfect level. with 0 degrees being straight down in the water.

Then for non zero roll, pitch those degrees will vary between -90 and 90 which seems maybe slightly more problematic than having an always positive degree like 0 to 180. This is all mostly me just thinking out loud and making sure I understand. My guess is that it can be handled either way and the way you have done it here makes the most sense in this application

Yes, tilt for ADCPs is the vertical inclination and ranges from +/- 90 degrees for pitch and roll

mhkit/dolfyn/adv/motion.py

mhkit/dolfyn/rotate/vector.py

mhkit/dolfyn/adp/turbulence.py

ssolson · 2023-08-03T15:42:27Z

@jmcvey3 please ping me when you are ready for me to take a look. On this PR I have jmcvey3#4 open agains your branch for my suggestions for the ipython notebook.

Example Notebooks

jmcvey3 · 2023-08-03T17:08:26Z

@ssolson Ready to go! I cleaned up the rest of the docstrings (I think I got everything) and added more checks for function inputs.

ssolson · 2023-08-04T14:43:00Z

James thank you making all those changes.

Currently the CI/CD has passed all but the hindcast which this PR does not modify. As such I am going to proceed with the merge.

@mbruggs

**MHKiT 0.7.0 Release Notes** This release introduces exciting new features and improvements to the MHKiT package: - **Mooring Module**: We are pleased to introduce the new mooring module. This addition primarily supports outputs from MoorDyn. Within this module, users can: - Import data - Calculate lay length - Visualize mooring line movements in 2D and 3D with graphical animations. Accompanying this module is an example notebook to guide users on its functionalities. - **Dolfyn Module Revamp**: The Dolfyn module has been overhauled. Enhancements include: - Turbulence calculation capability - Performance measures for tidal power as outlined in IEC/TS 6200-200. - **New Contributions**: A big shoutout to our community member, @mbruggs, for adding the ability to compute surface elevation using IFFT. - **NDBC Buoy Metadata**: Users can now fetch NDBC buoy metadata directly through MHKiT. - **Delft3D Module Update**: Stay up to date with support for the latest Delft3D NetCDF format. **Additions** - #235 - #232 - #236 - #250 - #239 - #248 **Bug Fixes** - #226 - #238 **Meta/Minor Changes** - #220 - #243 - #225 - #231 - #224 Thank you to all of the contributers who helpped with this release: @mbruggs @Graham-EGI @castillocesar @jmcvey3 @hivanov-nrel @browniea @cmichelenstrofer @akeeste @maxwelllevin @rpauly18 @ssolson

jmcvey3 added 5 commits March 10, 2023 12:24

General updates

268b43b

Update notebooks

e687e60

Fix n_fft_coh related errors

50edffc

Bugfixes and cleanup

ed012d5

ADCP turbulence functions

e2112af

jmcvey3 changed the title ~~Dolfyn updates~~ Dolfyn updates + turbulence analysis Mar 28, 2023

jmcvey3 added 2 commits March 28, 2023 12:15

n_bin fix

a3ae441

Silent assumption fix

17a5521

jmcvey3 added 2 commits April 10, 2023 12:49

More cleanup and bugfixes

946e96b

More cleanup and bugfixes

5713f9e

jmcvey3 added the dolfyn module label Apr 14, 2023

ssolson and others added 3 commits April 14, 2023 11:16

Update grid calls & run tests on develop (MHKiT-Software#226)

16aed26

* Update calls to grid formatting * run on develop

Catch up

f79439e

ssolson assigned jmcvey3 May 2, 2023

'standard_name' corrections

d1c42b8

ssolson changed the base branch from master to develop July 12, 2023 16:17

jmcvey3 added 3 commits July 13, 2023 10:14

Remove dependency on 'vel' variable, formatting fixes

96c969b

Update notebooks for turbulence estimations

e6e8dfe

Merge remote-tracking branch 'upstream/develop' into dolfyn_updates

fde62d6

Merge branch 'dolfyn_updates' of https://github.com/jmcvey3/MHKiT-Python

48ff99d

into dolfyn_updates

ssolson reviewed Jul 21, 2023

View reviewed changes

ssolson added 2 commits July 24, 2023 10:56

suggested improvements to example explinations

68a27aa

suggested improvements

7fffa18

jmcvey3 added 2 commits August 2, 2023 18:36

Docstring updates

21aacf4

Docstring cleanup

2544396

jmcvey3 added 2 commits August 3, 2023 09:20

Merge pull request #4 from ssolson/dolfyn_updates

7a362c9

Example Notebooks

Add warnings for functions

60c012a

ssolson approved these changes Aug 4, 2023

View reviewed changes

ssolson merged commit 7845dd2 into MHKiT-Software:develop Aug 4, 2023
16 of 18 checks passed

This was referenced Aug 4, 2023

Tidal prf jmcvey3/MHKiT-Python#5

Merged

Tidal power performance #236

Merged

MHKiT 0.7.0 #256

Merged

jmcvey3 deleted the dolfyn_updates branch October 3, 2023 16:21

rpauly18 mentioned this pull request Jan 26, 2024

Matlab Parity with Python MHKiT-Software/MHKiT-MATLAB#110

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Dolfyn updates + turbulence analysis #232

Dolfyn updates + turbulence analysis #232

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Dolfyn updates + turbulence analysis #232

Dolfyn updates + turbulence analysis #232

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