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Updated ADCP examples - #448

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akeeste merged 14 commits into
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browniea:updated_examples
Jun 29, 2026
Merged

Updated ADCP examples #448
akeeste merged 14 commits into
MHKiT-Software:developfrom
browniea:updated_examples

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@browniea

@browniea browniea commented Jun 16, 2026 •
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Adding visualizations to match the MHKiT_MATLAB ADCP example and addressing several issues:

Qhull Error #444

D3D coordinate systems #442

@browniea browniea mentioned this pull request Jun 16, 2026
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@browniea

browniea commented Jun 16, 2026 •
edited by akeeste
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#432 (comment) "Aiming to have this PR done by 6/22 so that we have time to review/merge before getting the develop branch into main before 7/1"

@browniea

browniea commented Jun 18, 2026

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MHKiT matlab had a function dolfyn_plot. For now I'm opting to add the plots without rewriting a plotting script. I find this to be more transparent and easier to troubleshoot for the user but, I'm open to feedback.

@browniea
browniea requested a review from akeeste June 18, 2026 18:12
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browniea commented Jun 19, 2026 •
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I need to updo the changes to ‎examples/ADCP_Delft3D_TRTS_example.ipynb. I was just testing the USGS code and accidentally pushed it.

@browniea

browniea commented Jun 23, 2026

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@akeeste this is ready for review.

There might be a more robust solution to the issue #442 but I'll need to fun more D3D cases. I'll keep an eye out for it in the future.

I believe I undid the changes to ADCP_Delft3D_TRTS_example.ipynb‎ but it's still showing up as a "Files changed"

@simmsa simmsa mentioned this pull request Jun 29, 2026
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This was linked to issues Jun 29, 2026
3D interpolation Qhull error #444
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D3d switch between coordinate systems #442
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Thanks @browniea! The notebooks and fix for #442 look good. One requested change around the fix for #444. Let's see if this can be simplified and double check the range on the valiues

Comment thread mhkit/river/io/d3d.py Outdated
Comment thread mhkit/river/io/d3d.py Outdated
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browniea requested a review from akeeste June 29, 2026 17:49
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Thanks for the quick update @browniea! Approved and merging.

@akeeste
akeeste merged commit 89c44a5 into MHKiT-Software:develop Jun 29, 2026
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@browniea

browniea commented Jun 29, 2026

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Thanks @akeeste closing Issues:
Qhull Error #444

D3D coordinate systems #442

@akeeste akeeste mentioned this pull request Jul 2, 2026
Merged
simmsa added a commit that referenced this pull request Jul 8, 2026
@simmsa
Release: Prepare MHKiT-Python v1.1.0 (#449)
31f3c78 
# 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
@simmsa simmsa mentioned this pull request Jul 8, 2026
Merged
simmsa pushed a commit to simmsa/MHKiT-Python that referenced this pull request Jul 10, 2026
@browniea
Updated ADCP examples (MHKiT-Software#448)
17ba78d 
Adding visualizations to match the [MHKiT_MATLAB ADCP
example](https://github.com/MHKiT-Software/MHKiT-MATLAB/blob/master/examples/acoustics_example.mlx)
and addressing several issues:

Qhull Error MHKiT-Software#444

D3D coordinate systems
MHKiT-Software#442
simmsa added a commit to simmsa/MHKiT-Python that referenced this pull request Jul 10, 2026
@simmsa
Release: Prepare MHKiT-Python v1.1.0 (MHKiT-Software#449)
80671f0 
# 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
simmsa pushed a commit that referenced this pull request Jul 10, 2026
@browniea @simmsa
Updated ADCP examples (#448)
b3ea75f 
Adding visualizations to match the [MHKiT_MATLAB ADCP
example](https://github.com/MHKiT-Software/MHKiT-MATLAB/blob/master/examples/acoustics_example.mlx)
and addressing several issues:

Qhull Error #444

D3D coordinate systems
#442
simmsa added a commit that referenced this pull request Jul 10, 2026
@simmsa
Release: Prepare MHKiT-Python v1.1.0 (#449)
8aa27ee 
# 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
simmsa added a commit that referenced this pull request Jul 10, 2026
@simmsa
Release: MHKiT v1.1.0
9fa9f9c 
# 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
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3D interpolation Qhull error D3d switch between coordinate systems

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